Multiple sequence alignment - TraesCS7B01G295100

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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 TraesCS7B01G295100 chr7B 100.000 3239 0 0 1 3239 531815649 531818887 0.000000e+00 5982.0
1 TraesCS7B01G295100 chr7B 92.043 1219 63 11 609 1817 531890789 531891983 0.000000e+00 1683.0
2 TraesCS7B01G295100 chr7B 85.756 688 80 7 1735 2404 531891988 531892675 0.000000e+00 712.0
3 TraesCS7B01G295100 chr7B 89.595 173 15 3 248 418 531844580 531844751 1.960000e-52 217.0
4 TraesCS7B01G295100 chr7D 89.204 2149 135 47 248 2352 503290514 503292609 0.000000e+00 2593.0
5 TraesCS7B01G295100 chr7D 88.189 1922 131 38 505 2408 503738410 503740253 0.000000e+00 2204.0
6 TraesCS7B01G295100 chr7D 90.206 1358 83 12 609 1958 503337661 503338976 0.000000e+00 1725.0
7 TraesCS7B01G295100 chr7D 85.789 767 82 14 1654 2408 503338731 503339482 0.000000e+00 787.0
8 TraesCS7B01G295100 chr7D 78.834 926 133 33 613 1519 459427420 459426539 1.690000e-157 566.0
9 TraesCS7B01G295100 chr7D 91.139 237 14 4 1 236 616529529 616529299 6.750000e-82 315.0
10 TraesCS7B01G295100 chr7D 82.215 298 18 22 278 544 503337348 503337641 1.170000e-54 224.0
11 TraesCS7B01G295100 chr7D 96.512 86 3 0 324 409 503738258 503738343 3.370000e-30 143.0
12 TraesCS7B01G295100 chr7A 90.809 1458 85 20 503 1958 570174132 570175542 0.000000e+00 1905.0
13 TraesCS7B01G295100 chr7A 91.375 1229 71 14 532 1756 571363377 571364574 0.000000e+00 1650.0
14 TraesCS7B01G295100 chr7A 91.129 744 61 4 1669 2408 570175367 570176109 0.000000e+00 1003.0
15 TraesCS7B01G295100 chr7A 81.047 1203 171 28 994 2143 540798188 540799386 0.000000e+00 905.0
16 TraesCS7B01G295100 chr7A 86.937 666 67 12 1753 2408 571370694 571371349 0.000000e+00 730.0
17 TraesCS7B01G295100 chr7A 85.595 479 63 5 987 1460 491260495 491260018 6.240000e-137 497.0
18 TraesCS7B01G295100 chr7A 89.212 241 14 5 1 236 687904462 687904695 1.140000e-74 291.0
19 TraesCS7B01G295100 chr7A 87.124 233 30 0 1726 1958 570175253 570175485 6.890000e-67 265.0
20 TraesCS7B01G295100 chr7A 89.202 213 8 7 255 466 570173846 570174044 5.360000e-63 252.0
21 TraesCS7B01G295100 chr7A 90.286 175 12 4 248 418 571360664 571360837 1.170000e-54 224.0
22 TraesCS7B01G295100 chr7A 90.506 158 10 4 2253 2405 571324197 571324354 1.520000e-48 204.0
23 TraesCS7B01G295100 chr4A 90.856 853 40 13 2421 3239 722193227 722192379 0.000000e+00 1109.0
24 TraesCS7B01G295100 chr4A 81.818 88 11 3 2408 2495 75881285 75881367 5.800000e-08 69.4
25 TraesCS7B01G295100 chr5D 87.730 326 29 7 2396 2716 2108532 2108851 1.420000e-98 370.0
26 TraesCS7B01G295100 chr5D 87.023 262 24 6 1 254 13171192 13170933 1.470000e-73 287.0
27 TraesCS7B01G295100 chr5D 81.148 244 19 11 2832 3050 2109043 2109284 1.550000e-38 171.0
28 TraesCS7B01G295100 chr5D 84.884 172 19 5 3073 3238 2109273 2109443 2.000000e-37 167.0
29 TraesCS7B01G295100 chr2D 86.859 312 31 9 2408 2716 625667585 625667889 1.110000e-89 340.0
30 TraesCS7B01G295100 chr2A 91.393 244 11 5 1 236 174751713 174751472 3.120000e-85 326.0
31 TraesCS7B01G295100 chr2A 93.519 108 7 0 2553 2660 28447367 28447260 9.300000e-36 161.0
32 TraesCS7B01G295100 chr2A 79.144 187 16 9 2835 2999 28447214 28447029 1.230000e-19 108.0
33 TraesCS7B01G295100 chr5B 90.323 248 10 7 1 236 705985185 705984940 2.430000e-81 313.0
34 TraesCS7B01G295100 chr1D 90.756 238 16 5 1 236 462135220 462135453 2.430000e-81 313.0
35 TraesCS7B01G295100 chrUn 88.797 241 19 5 1 236 134232646 134232409 4.090000e-74 289.0
36 TraesCS7B01G295100 chr5A 88.750 240 16 6 1 232 494869223 494868987 1.900000e-72 283.0
37 TraesCS7B01G295100 chr4D 88.983 236 14 7 1 232 464045761 464045534 6.840000e-72 281.0
38 TraesCS7B01G295100 chr4D 100.000 28 0 0 2855 2882 111594440 111594467 6.000000e-03 52.8
39 TraesCS7B01G295100 chr2B 84.016 244 22 10 2515 2750 743848197 743847963 5.440000e-53 219.0
40 TraesCS7B01G295100 chr3A 82.156 269 29 8 2396 2660 362665760 362666013 2.530000e-51 213.0
41 TraesCS7B01G295100 chr3A 86.047 172 17 5 3073 3238 362666286 362666456 9.230000e-41 178.0
42 TraesCS7B01G295100 chr3A 79.184 245 23 12 2832 3050 362666055 362666297 9.370000e-31 145.0
43 TraesCS7B01G295100 chr1A 85.507 207 22 6 2408 2611 101769644 101769443 3.270000e-50 209.0
44 TraesCS7B01G295100 chr1A 84.884 172 19 5 3073 3238 101769131 101768961 2.000000e-37 167.0
45 TraesCS7B01G295100 chr1A 79.752 242 21 12 2835 3050 101769359 101769120 2.010000e-32 150.0
46 TraesCS7B01G295100 chr3B 84.302 172 20 5 3073 3238 739253807 739253977 9.300000e-36 161.0
47 TraesCS7B01G295100 chr3B 100.000 28 0 0 2552 2579 188442255 188442228 6.000000e-03 52.8
48 TraesCS7B01G295100 chr6B 90.141 71 5 1 2406 2476 377938984 377939052 1.240000e-14 91.6
49 TraesCS7B01G295100 chr6B 83.158 95 12 2 2408 2498 646022850 646022756 2.070000e-12 84.2
50 TraesCS7B01G295100 chr4B 89.855 69 5 1 2408 2476 605930779 605930713 1.600000e-13 87.9


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 TraesCS7B01G295100 chr7B 531815649 531818887 3238 False 5982.00 5982 100.000000 1 3239 1 chr7B.!!$F1 3238
1 TraesCS7B01G295100 chr7B 531890789 531892675 1886 False 1197.50 1683 88.899500 609 2404 2 chr7B.!!$F3 1795
2 TraesCS7B01G295100 chr7D 503290514 503292609 2095 False 2593.00 2593 89.204000 248 2352 1 chr7D.!!$F1 2104
3 TraesCS7B01G295100 chr7D 503738258 503740253 1995 False 1173.50 2204 92.350500 324 2408 2 chr7D.!!$F3 2084
4 TraesCS7B01G295100 chr7D 503337348 503339482 2134 False 912.00 1725 86.070000 278 2408 3 chr7D.!!$F2 2130
5 TraesCS7B01G295100 chr7D 459426539 459427420 881 True 566.00 566 78.834000 613 1519 1 chr7D.!!$R1 906
6 TraesCS7B01G295100 chr7A 571360664 571364574 3910 False 937.00 1650 90.830500 248 1756 2 chr7A.!!$F6 1508
7 TraesCS7B01G295100 chr7A 540798188 540799386 1198 False 905.00 905 81.047000 994 2143 1 chr7A.!!$F1 1149
8 TraesCS7B01G295100 chr7A 570173846 570176109 2263 False 856.25 1905 89.566000 255 2408 4 chr7A.!!$F5 2153
9 TraesCS7B01G295100 chr7A 571370694 571371349 655 False 730.00 730 86.937000 1753 2408 1 chr7A.!!$F3 655
10 TraesCS7B01G295100 chr4A 722192379 722193227 848 True 1109.00 1109 90.856000 2421 3239 1 chr4A.!!$R1 818
11 TraesCS7B01G295100 chr5D 2108532 2109443 911 False 236.00 370 84.587333 2396 3238 3 chr5D.!!$F1 842

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
235 236 0.035056 CCGGGAGCTGAAAATCCAGT 60.035 55.0 0.00 0.00 37.33 4.00 F
590 3095 0.037017 TTTCCCACCACCATACCGTG 59.963 55.0 0.00 0.00 0.00 4.94 F
1567 4159 0.179026 CCAGCAGCTGCAGATGGTAT 60.179 55.0 38.24 14.33 40.43 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 4814 0.372679 GTCATGACTGCATCGCACAG 59.627 55.000 18.83 0.0 41.08 3.66 R
2167 5013 2.874780 CGAGTGCGCCGTGTAGTC 60.875 66.667 4.18 0.0 0.00 2.59 R
3065 6047 0.539986 GAACACTAGGATTCCCCGCA 59.460 55.000 0.00 0.0 40.87 5.69 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
48 49 9.893305 AAATTACTGCTCAAAAGTACACATAAC 57.107 29.630 0.00 0.00 29.93 1.89
49 50 8.848474 ATTACTGCTCAAAAGTACACATAACT 57.152 30.769 0.00 0.00 29.93 2.24
50 51 8.671384 TTACTGCTCAAAAGTACACATAACTT 57.329 30.769 0.00 0.00 38.82 2.66
51 52 7.568199 ACTGCTCAAAAGTACACATAACTTT 57.432 32.000 0.00 0.00 46.45 2.66
52 53 7.417612 ACTGCTCAAAAGTACACATAACTTTG 58.582 34.615 2.26 0.00 44.35 2.77
53 54 7.282224 ACTGCTCAAAAGTACACATAACTTTGA 59.718 33.333 2.26 0.00 44.35 2.69
54 55 7.990917 TGCTCAAAAGTACACATAACTTTGAA 58.009 30.769 2.26 0.00 44.35 2.69
55 56 7.913297 TGCTCAAAAGTACACATAACTTTGAAC 59.087 33.333 2.26 0.00 44.35 3.18
56 57 7.913297 GCTCAAAAGTACACATAACTTTGAACA 59.087 33.333 2.26 0.00 44.35 3.18
57 58 9.221775 CTCAAAAGTACACATAACTTTGAACAC 57.778 33.333 2.26 0.00 44.35 3.32
58 59 8.952278 TCAAAAGTACACATAACTTTGAACACT 58.048 29.630 2.26 0.00 44.35 3.55
59 60 9.009327 CAAAAGTACACATAACTTTGAACACTG 57.991 33.333 2.26 0.00 44.35 3.66
60 61 8.500753 AAAGTACACATAACTTTGAACACTGA 57.499 30.769 0.00 0.00 43.66 3.41
61 62 8.677148 AAGTACACATAACTTTGAACACTGAT 57.323 30.769 0.00 0.00 33.39 2.90
62 63 8.677148 AGTACACATAACTTTGAACACTGATT 57.323 30.769 0.00 0.00 0.00 2.57
63 64 9.120538 AGTACACATAACTTTGAACACTGATTT 57.879 29.630 0.00 0.00 0.00 2.17
64 65 9.730420 GTACACATAACTTTGAACACTGATTTT 57.270 29.630 0.00 0.00 0.00 1.82
84 85 2.421751 TTTTTGTGAGGGTTCCACGA 57.578 45.000 0.00 0.00 37.34 4.35
85 86 2.421751 TTTTGTGAGGGTTCCACGAA 57.578 45.000 0.00 0.00 37.34 3.85
86 87 2.649531 TTTGTGAGGGTTCCACGAAT 57.350 45.000 0.00 0.00 37.34 3.34
87 88 1.890876 TTGTGAGGGTTCCACGAATG 58.109 50.000 0.00 0.00 37.34 2.67
88 89 0.762418 TGTGAGGGTTCCACGAATGT 59.238 50.000 0.00 0.00 37.34 2.71
89 90 1.142060 TGTGAGGGTTCCACGAATGTT 59.858 47.619 0.00 0.00 37.34 2.71
90 91 2.227194 GTGAGGGTTCCACGAATGTTT 58.773 47.619 0.00 0.00 0.00 2.83
91 92 2.621526 GTGAGGGTTCCACGAATGTTTT 59.378 45.455 0.00 0.00 0.00 2.43
92 93 3.067601 GTGAGGGTTCCACGAATGTTTTT 59.932 43.478 0.00 0.00 0.00 1.94
118 119 4.558178 TGCTAAAACTTGCATGAACATGG 58.442 39.130 15.15 3.20 39.16 3.66
119 120 4.280425 TGCTAAAACTTGCATGAACATGGA 59.720 37.500 15.15 10.43 39.16 3.41
120 121 5.221402 TGCTAAAACTTGCATGAACATGGAA 60.221 36.000 17.69 17.69 44.92 3.53
121 122 5.870978 GCTAAAACTTGCATGAACATGGAAT 59.129 36.000 18.67 9.25 45.71 3.01
122 123 8.478224 TGCTAAAACTTGCATGAACATGGAATG 61.478 37.037 18.67 15.17 45.71 2.67
140 141 9.419297 CATGGAATGTTTGATCATATTTGATCC 57.581 33.333 19.55 7.27 46.70 3.36
149 150 5.937492 ATCATATTTGATCCCCCAGAGTT 57.063 39.130 0.00 0.00 38.18 3.01
150 151 5.732331 TCATATTTGATCCCCCAGAGTTT 57.268 39.130 0.00 0.00 0.00 2.66
151 152 5.694995 TCATATTTGATCCCCCAGAGTTTC 58.305 41.667 0.00 0.00 0.00 2.78
152 153 5.193527 TCATATTTGATCCCCCAGAGTTTCA 59.806 40.000 0.00 0.00 0.00 2.69
153 154 3.439857 TTTGATCCCCCAGAGTTTCAG 57.560 47.619 0.00 0.00 0.00 3.02
154 155 2.342406 TGATCCCCCAGAGTTTCAGA 57.658 50.000 0.00 0.00 0.00 3.27
155 156 2.850833 TGATCCCCCAGAGTTTCAGAT 58.149 47.619 0.00 0.00 0.00 2.90
156 157 3.192944 TGATCCCCCAGAGTTTCAGATT 58.807 45.455 0.00 0.00 0.00 2.40
157 158 3.593328 TGATCCCCCAGAGTTTCAGATTT 59.407 43.478 0.00 0.00 0.00 2.17
158 159 4.044571 TGATCCCCCAGAGTTTCAGATTTT 59.955 41.667 0.00 0.00 0.00 1.82
159 160 4.469469 TCCCCCAGAGTTTCAGATTTTT 57.531 40.909 0.00 0.00 0.00 1.94
203 204 8.870160 TTGTTTTGAATTTAGTGTTCATGAGG 57.130 30.769 0.00 0.00 35.68 3.86
204 205 7.432869 TGTTTTGAATTTAGTGTTCATGAGGG 58.567 34.615 0.00 0.00 35.68 4.30
205 206 7.069331 TGTTTTGAATTTAGTGTTCATGAGGGT 59.931 33.333 0.00 0.00 35.68 4.34
206 207 6.573664 TTGAATTTAGTGTTCATGAGGGTG 57.426 37.500 0.00 0.00 35.68 4.61
207 208 4.458989 TGAATTTAGTGTTCATGAGGGTGC 59.541 41.667 0.00 0.00 31.07 5.01
208 209 2.489938 TTAGTGTTCATGAGGGTGCC 57.510 50.000 0.00 0.00 0.00 5.01
209 210 0.618458 TAGTGTTCATGAGGGTGCCC 59.382 55.000 0.00 0.00 0.00 5.36
210 211 1.678970 GTGTTCATGAGGGTGCCCC 60.679 63.158 3.17 2.16 45.90 5.80
227 228 4.020617 CTGCACCCGGGAGCTGAA 62.021 66.667 37.52 20.81 33.96 3.02
228 229 3.551496 CTGCACCCGGGAGCTGAAA 62.551 63.158 37.52 20.46 33.96 2.69
229 230 2.282180 GCACCCGGGAGCTGAAAA 60.282 61.111 32.83 0.00 0.00 2.29
230 231 1.678970 GCACCCGGGAGCTGAAAAT 60.679 57.895 32.83 1.51 0.00 1.82
231 232 1.657751 GCACCCGGGAGCTGAAAATC 61.658 60.000 32.83 3.89 0.00 2.17
232 233 1.032114 CACCCGGGAGCTGAAAATCC 61.032 60.000 32.02 0.00 34.64 3.01
233 234 1.302949 CCCGGGAGCTGAAAATCCA 59.697 57.895 18.48 0.00 37.33 3.41
234 235 0.749454 CCCGGGAGCTGAAAATCCAG 60.749 60.000 18.48 0.00 37.33 3.86
235 236 0.035056 CCGGGAGCTGAAAATCCAGT 60.035 55.000 0.00 0.00 37.33 4.00
236 237 1.089920 CGGGAGCTGAAAATCCAGTG 58.910 55.000 0.00 0.00 37.33 3.66
237 238 1.611673 CGGGAGCTGAAAATCCAGTGT 60.612 52.381 0.00 0.00 37.33 3.55
238 239 2.354704 CGGGAGCTGAAAATCCAGTGTA 60.355 50.000 0.00 0.00 37.33 2.90
239 240 3.682718 CGGGAGCTGAAAATCCAGTGTAT 60.683 47.826 0.00 0.00 37.33 2.29
240 241 4.273318 GGGAGCTGAAAATCCAGTGTATT 58.727 43.478 0.00 0.00 37.33 1.89
241 242 4.706962 GGGAGCTGAAAATCCAGTGTATTT 59.293 41.667 0.00 0.00 37.33 1.40
242 243 5.885912 GGGAGCTGAAAATCCAGTGTATTTA 59.114 40.000 0.00 0.00 37.33 1.40
243 244 6.038714 GGGAGCTGAAAATCCAGTGTATTTAG 59.961 42.308 0.00 0.00 37.33 1.85
244 245 6.599638 GGAGCTGAAAATCCAGTGTATTTAGT 59.400 38.462 0.00 0.00 36.57 2.24
245 246 7.769044 GGAGCTGAAAATCCAGTGTATTTAGTA 59.231 37.037 0.00 0.00 36.57 1.82
246 247 8.494016 AGCTGAAAATCCAGTGTATTTAGTAC 57.506 34.615 0.00 0.00 36.57 2.73
561 3047 2.435693 CCAAGCCTCTCTACCGGGG 61.436 68.421 6.32 0.00 0.00 5.73
587 3092 3.276281 GGTTTCCCACCACCATACC 57.724 57.895 0.00 0.00 46.42 2.73
588 3093 0.678684 GGTTTCCCACCACCATACCG 60.679 60.000 0.00 0.00 46.42 4.02
589 3094 0.037160 GTTTCCCACCACCATACCGT 59.963 55.000 0.00 0.00 0.00 4.83
590 3095 0.037017 TTTCCCACCACCATACCGTG 59.963 55.000 0.00 0.00 0.00 4.94
592 3097 0.252148 TCCCACCACCATACCGTGTA 60.252 55.000 0.00 0.00 31.47 2.90
595 3100 0.244450 CACCACCATACCGTGTACGT 59.756 55.000 3.57 0.00 37.74 3.57
597 3102 2.099592 CACCACCATACCGTGTACGTAT 59.900 50.000 0.00 0.00 37.74 3.06
598 3103 2.358898 ACCACCATACCGTGTACGTATC 59.641 50.000 0.00 0.00 37.74 2.24
599 3104 2.620115 CCACCATACCGTGTACGTATCT 59.380 50.000 0.00 0.00 37.74 1.98
600 3105 3.304257 CCACCATACCGTGTACGTATCTC 60.304 52.174 0.00 0.00 37.74 2.75
601 3106 2.880890 ACCATACCGTGTACGTATCTCC 59.119 50.000 0.00 0.00 37.74 3.71
602 3107 2.880268 CCATACCGTGTACGTATCTCCA 59.120 50.000 0.00 0.00 37.74 3.86
603 3108 3.058432 CCATACCGTGTACGTATCTCCAG 60.058 52.174 0.00 0.00 37.74 3.86
604 3109 2.408271 ACCGTGTACGTATCTCCAGA 57.592 50.000 0.00 0.00 37.74 3.86
605 3110 2.286872 ACCGTGTACGTATCTCCAGAG 58.713 52.381 0.00 0.00 37.74 3.35
606 3111 2.286872 CCGTGTACGTATCTCCAGAGT 58.713 52.381 0.00 0.00 37.74 3.24
607 3112 3.118629 ACCGTGTACGTATCTCCAGAGTA 60.119 47.826 0.00 0.00 37.74 2.59
624 3130 6.939163 TCCAGAGTAGGAGTACGTTATAATCC 59.061 42.308 0.00 0.00 33.97 3.01
657 3163 1.009829 GCTAATCACGGCCTCAAGTG 58.990 55.000 0.00 0.88 39.55 3.16
732 3238 3.553511 CAGACTGATGCAAGATTACGGAC 59.446 47.826 0.00 0.00 0.00 4.79
741 3247 7.441157 TGATGCAAGATTACGGACCTTAATAAG 59.559 37.037 3.32 0.00 0.00 1.73
742 3248 5.526111 TGCAAGATTACGGACCTTAATAAGC 59.474 40.000 3.32 8.32 0.00 3.09
743 3249 5.049612 GCAAGATTACGGACCTTAATAAGCC 60.050 44.000 3.32 0.00 0.00 4.35
744 3250 6.289064 CAAGATTACGGACCTTAATAAGCCT 58.711 40.000 3.32 0.00 0.00 4.58
745 3251 7.439381 CAAGATTACGGACCTTAATAAGCCTA 58.561 38.462 3.32 0.00 0.00 3.93
746 3252 7.229581 AGATTACGGACCTTAATAAGCCTAG 57.770 40.000 3.32 0.00 0.00 3.02
747 3253 6.781507 AGATTACGGACCTTAATAAGCCTAGT 59.218 38.462 3.32 0.00 0.00 2.57
816 3329 0.679002 TTCGGGAGAGACGGACGAAT 60.679 55.000 0.00 0.00 41.75 3.34
817 3330 1.094073 TCGGGAGAGACGGACGAATC 61.094 60.000 0.00 0.00 0.00 2.52
818 3331 1.734748 GGGAGAGACGGACGAATCC 59.265 63.158 0.00 0.18 42.28 3.01
1043 3596 2.105930 GCTCATCGAGAAGGCGCT 59.894 61.111 7.64 0.00 0.00 5.92
1197 3753 1.682684 GGAGGAGGGAGTGCTCGAA 60.683 63.158 0.00 0.00 44.54 3.71
1566 4158 1.222661 CCAGCAGCTGCAGATGGTA 59.777 57.895 38.24 0.00 40.43 3.25
1567 4159 0.179026 CCAGCAGCTGCAGATGGTAT 60.179 55.000 38.24 14.33 40.43 2.73
1965 4789 1.135632 GCTGACTACGACTGGACTGAC 60.136 57.143 0.00 0.00 0.00 3.51
1982 4806 2.424842 GACCTGACCATGTGGGCCAA 62.425 60.000 8.40 0.00 44.80 4.52
1990 4814 4.980805 TGTGGGCCAACGACGAGC 62.981 66.667 8.40 0.84 0.00 5.03
2008 4832 1.363885 GCTGTGCGATGCAGTCATGA 61.364 55.000 0.00 0.00 40.08 3.07
2012 4836 0.320596 TGCGATGCAGTCATGACACA 60.321 50.000 27.02 23.13 33.32 3.72
2104 4950 1.214367 CTACGTCAACACACCACCAC 58.786 55.000 0.00 0.00 0.00 4.16
2164 5010 3.852536 CGACAACTTCACTAATCTCGACC 59.147 47.826 0.00 0.00 0.00 4.79
2167 5013 1.202154 ACTTCACTAATCTCGACCGCG 60.202 52.381 0.00 0.00 39.35 6.46
2183 5029 2.874780 CGACTACACGGCGCACTC 60.875 66.667 10.83 0.00 0.00 3.51
2225 5071 1.746991 GCAGTCTGTTGCTAGGGGC 60.747 63.158 0.93 0.00 40.89 5.80
2272 5130 5.814783 AGAATATTCTCACGCATTTGAAGC 58.185 37.500 12.37 0.00 29.94 3.86
2376 5243 6.554334 TTATGGAACTTTCACGAAAAGAGG 57.446 37.500 17.68 0.00 46.18 3.69
2451 5323 4.821260 TGCAACGGAACATATGCATATTCT 59.179 37.500 16.71 6.73 43.32 2.40
2652 5527 6.385649 TTCTAAGTTTCTCAATTTGCCGTT 57.614 33.333 0.00 0.00 0.00 4.44
2653 5528 6.385649 TCTAAGTTTCTCAATTTGCCGTTT 57.614 33.333 0.00 0.00 0.00 3.60
2696 5571 4.946160 TCCCCTCAAACACAAGGATTAT 57.054 40.909 0.00 0.00 34.35 1.28
2725 5600 2.071778 ATGCCTTGTGTTTGTGGAGT 57.928 45.000 0.00 0.00 0.00 3.85
2906 5863 7.829725 CAATCATGGATACCAAGTTTCTTCAA 58.170 34.615 0.00 0.00 36.95 2.69
2952 5926 3.306502 CCTTCTGCAACCAAATCAGCATT 60.307 43.478 0.00 0.00 36.28 3.56
2982 5959 6.947733 TGATTCTACAACAATGATCCCTTTGT 59.052 34.615 0.00 0.00 40.87 2.83
2998 5980 3.126858 CCTTTGTAACGTGCTGCACATAT 59.873 43.478 29.86 17.95 33.40 1.78
3036 6018 6.490040 TGTGGGAAATTTCTTGAGGAAAGTAG 59.510 38.462 17.42 0.00 45.61 2.57
3093 6075 5.598830 GGGAATCCTAGTGTTCACTCTGATA 59.401 44.000 8.80 0.00 0.00 2.15
3094 6076 6.098409 GGGAATCCTAGTGTTCACTCTGATAA 59.902 42.308 8.80 0.00 0.00 1.75
3138 6120 9.243637 GTGCAAAATTTCTTGTACAAATGTCTA 57.756 29.630 10.03 0.00 40.43 2.59
3228 6216 6.071463 GCAAACACACTAAACTAACATCGAG 58.929 40.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.893305 GTTATGTGTACTTTTGAGCAGTAATTT 57.107 29.630 0.00 0.00 0.00 1.82
23 24 9.284968 AGTTATGTGTACTTTTGAGCAGTAATT 57.715 29.630 0.00 0.00 0.00 1.40
24 25 8.848474 AGTTATGTGTACTTTTGAGCAGTAAT 57.152 30.769 0.00 0.00 0.00 1.89
25 26 8.671384 AAGTTATGTGTACTTTTGAGCAGTAA 57.329 30.769 0.00 0.00 32.06 2.24
26 27 8.556194 CAAAGTTATGTGTACTTTTGAGCAGTA 58.444 33.333 0.00 0.00 42.32 2.74
27 28 7.282224 TCAAAGTTATGTGTACTTTTGAGCAGT 59.718 33.333 0.00 0.00 42.32 4.40
28 29 7.639039 TCAAAGTTATGTGTACTTTTGAGCAG 58.361 34.615 0.00 0.00 42.32 4.24
29 30 7.561021 TCAAAGTTATGTGTACTTTTGAGCA 57.439 32.000 0.00 0.00 42.32 4.26
30 31 7.913297 TGTTCAAAGTTATGTGTACTTTTGAGC 59.087 33.333 0.00 5.15 42.32 4.26
31 32 9.221775 GTGTTCAAAGTTATGTGTACTTTTGAG 57.778 33.333 0.00 0.00 42.32 3.02
32 33 8.952278 AGTGTTCAAAGTTATGTGTACTTTTGA 58.048 29.630 0.00 0.00 42.32 2.69
33 34 9.009327 CAGTGTTCAAAGTTATGTGTACTTTTG 57.991 33.333 0.00 0.00 42.32 2.44
34 35 8.952278 TCAGTGTTCAAAGTTATGTGTACTTTT 58.048 29.630 0.00 0.00 42.32 2.27
35 36 8.500753 TCAGTGTTCAAAGTTATGTGTACTTT 57.499 30.769 0.00 0.00 44.38 2.66
36 37 8.677148 ATCAGTGTTCAAAGTTATGTGTACTT 57.323 30.769 0.00 0.00 37.43 2.24
37 38 8.677148 AATCAGTGTTCAAAGTTATGTGTACT 57.323 30.769 0.00 0.00 0.00 2.73
38 39 9.730420 AAAATCAGTGTTCAAAGTTATGTGTAC 57.270 29.630 0.00 0.00 0.00 2.90
65 66 2.421751 TCGTGGAACCCTCACAAAAA 57.578 45.000 0.00 0.00 35.03 1.94
66 67 2.421751 TTCGTGGAACCCTCACAAAA 57.578 45.000 0.00 0.00 35.03 2.44
67 68 2.226330 CATTCGTGGAACCCTCACAAA 58.774 47.619 0.00 0.00 35.03 2.83
68 69 1.142060 ACATTCGTGGAACCCTCACAA 59.858 47.619 0.00 0.00 35.03 3.33
69 70 0.762418 ACATTCGTGGAACCCTCACA 59.238 50.000 0.00 0.00 35.03 3.58
70 71 1.892209 AACATTCGTGGAACCCTCAC 58.108 50.000 0.00 0.00 0.00 3.51
71 72 2.649531 AAACATTCGTGGAACCCTCA 57.350 45.000 0.00 0.00 0.00 3.86
96 97 4.280425 TCCATGTTCATGCAAGTTTTAGCA 59.720 37.500 7.21 0.00 45.92 3.49
97 98 4.808558 TCCATGTTCATGCAAGTTTTAGC 58.191 39.130 7.21 0.00 0.00 3.09
98 99 6.869913 ACATTCCATGTTCATGCAAGTTTTAG 59.130 34.615 7.21 0.00 41.63 1.85
99 100 6.757237 ACATTCCATGTTCATGCAAGTTTTA 58.243 32.000 7.21 0.00 41.63 1.52
100 101 5.613329 ACATTCCATGTTCATGCAAGTTTT 58.387 33.333 7.21 0.00 41.63 2.43
101 102 5.217978 ACATTCCATGTTCATGCAAGTTT 57.782 34.783 7.21 0.00 41.63 2.66
102 103 4.877378 ACATTCCATGTTCATGCAAGTT 57.123 36.364 7.21 0.00 41.63 2.66
128 129 5.193527 TGAAACTCTGGGGGATCAAATATGA 59.806 40.000 0.00 0.00 40.57 2.15
129 130 5.448654 TGAAACTCTGGGGGATCAAATATG 58.551 41.667 0.00 0.00 0.00 1.78
130 131 5.433051 TCTGAAACTCTGGGGGATCAAATAT 59.567 40.000 0.00 0.00 0.00 1.28
131 132 4.788075 TCTGAAACTCTGGGGGATCAAATA 59.212 41.667 0.00 0.00 0.00 1.40
132 133 3.593328 TCTGAAACTCTGGGGGATCAAAT 59.407 43.478 0.00 0.00 0.00 2.32
133 134 2.986019 TCTGAAACTCTGGGGGATCAAA 59.014 45.455 0.00 0.00 0.00 2.69
134 135 2.631384 TCTGAAACTCTGGGGGATCAA 58.369 47.619 0.00 0.00 0.00 2.57
135 136 2.342406 TCTGAAACTCTGGGGGATCA 57.658 50.000 0.00 0.00 0.00 2.92
136 137 3.941704 AATCTGAAACTCTGGGGGATC 57.058 47.619 0.00 0.00 0.00 3.36
137 138 4.682021 AAAATCTGAAACTCTGGGGGAT 57.318 40.909 0.00 0.00 0.00 3.85
138 139 4.469469 AAAAATCTGAAACTCTGGGGGA 57.531 40.909 0.00 0.00 0.00 4.81
177 178 9.480053 CCTCATGAACACTAAATTCAAAACAAT 57.520 29.630 0.00 0.00 39.43 2.71
178 179 7.925483 CCCTCATGAACACTAAATTCAAAACAA 59.075 33.333 0.00 0.00 39.43 2.83
179 180 7.069331 ACCCTCATGAACACTAAATTCAAAACA 59.931 33.333 0.00 0.00 39.43 2.83
180 181 7.382218 CACCCTCATGAACACTAAATTCAAAAC 59.618 37.037 0.00 0.00 39.43 2.43
181 182 7.432869 CACCCTCATGAACACTAAATTCAAAA 58.567 34.615 0.00 0.00 39.43 2.44
182 183 6.516527 GCACCCTCATGAACACTAAATTCAAA 60.517 38.462 0.00 0.00 39.43 2.69
183 184 5.048083 GCACCCTCATGAACACTAAATTCAA 60.048 40.000 0.00 0.00 39.43 2.69
184 185 4.458989 GCACCCTCATGAACACTAAATTCA 59.541 41.667 0.00 0.00 40.25 2.57
185 186 4.142381 GGCACCCTCATGAACACTAAATTC 60.142 45.833 0.00 0.00 0.00 2.17
186 187 3.763897 GGCACCCTCATGAACACTAAATT 59.236 43.478 0.00 0.00 0.00 1.82
187 188 3.356290 GGCACCCTCATGAACACTAAAT 58.644 45.455 0.00 0.00 0.00 1.40
188 189 2.790433 GGCACCCTCATGAACACTAAA 58.210 47.619 0.00 0.00 0.00 1.85
189 190 2.489938 GGCACCCTCATGAACACTAA 57.510 50.000 0.00 0.00 0.00 2.24
210 211 3.551496 TTTCAGCTCCCGGGTGCAG 62.551 63.158 40.44 34.57 42.57 4.41
211 212 2.424842 ATTTTCAGCTCCCGGGTGCA 62.425 55.000 40.44 24.95 42.57 4.57
212 213 1.657751 GATTTTCAGCTCCCGGGTGC 61.658 60.000 35.10 35.10 42.57 5.01
213 214 1.032114 GGATTTTCAGCTCCCGGGTG 61.032 60.000 22.86 20.53 44.04 4.61
214 215 1.303282 GGATTTTCAGCTCCCGGGT 59.697 57.895 22.86 0.00 0.00 5.28
215 216 0.749454 CTGGATTTTCAGCTCCCGGG 60.749 60.000 16.85 16.85 0.00 5.73
216 217 0.035056 ACTGGATTTTCAGCTCCCGG 60.035 55.000 0.00 0.00 38.26 5.73
217 218 1.089920 CACTGGATTTTCAGCTCCCG 58.910 55.000 0.00 0.00 38.26 5.14
218 219 2.206576 ACACTGGATTTTCAGCTCCC 57.793 50.000 0.00 0.00 38.26 4.30
219 220 5.904362 AAATACACTGGATTTTCAGCTCC 57.096 39.130 0.00 0.00 38.26 4.70
220 221 7.617041 ACTAAATACACTGGATTTTCAGCTC 57.383 36.000 4.49 0.00 38.26 4.09
221 222 8.322091 AGTACTAAATACACTGGATTTTCAGCT 58.678 33.333 4.49 0.00 38.26 4.24
222 223 8.494016 AGTACTAAATACACTGGATTTTCAGC 57.506 34.615 4.49 0.00 38.26 4.26
238 239 9.804758 GCACTGATCAAACTAGTAGTACTAAAT 57.195 33.333 11.15 0.00 29.00 1.40
239 240 7.966753 CGCACTGATCAAACTAGTAGTACTAAA 59.033 37.037 11.15 0.00 29.00 1.85
240 241 7.335171 TCGCACTGATCAAACTAGTAGTACTAA 59.665 37.037 11.15 0.00 29.00 2.24
241 242 6.820152 TCGCACTGATCAAACTAGTAGTACTA 59.180 38.462 9.66 9.66 0.00 1.82
242 243 5.646793 TCGCACTGATCAAACTAGTAGTACT 59.353 40.000 8.14 8.14 0.00 2.73
243 244 5.877031 TCGCACTGATCAAACTAGTAGTAC 58.123 41.667 2.50 0.00 0.00 2.73
244 245 5.646793 ACTCGCACTGATCAAACTAGTAGTA 59.353 40.000 2.50 0.00 0.00 1.82
245 246 4.459685 ACTCGCACTGATCAAACTAGTAGT 59.540 41.667 0.00 0.00 0.00 2.73
246 247 4.987832 ACTCGCACTGATCAAACTAGTAG 58.012 43.478 0.00 0.00 0.00 2.57
487 546 0.813610 TCATTAATCCCTGCACGGCG 60.814 55.000 4.80 4.80 0.00 6.46
495 554 2.592102 ATGCGGCATCATTAATCCCT 57.408 45.000 10.23 0.00 0.00 4.20
583 3088 4.063689 CTCTGGAGATACGTACACGGTAT 58.936 47.826 6.72 2.26 44.95 2.73
584 3089 3.118629 ACTCTGGAGATACGTACACGGTA 60.119 47.826 6.72 0.00 44.95 4.02
585 3090 2.286872 CTCTGGAGATACGTACACGGT 58.713 52.381 6.72 0.00 44.95 4.83
586 3091 2.286872 ACTCTGGAGATACGTACACGG 58.713 52.381 6.72 0.00 44.95 4.94
587 3092 3.493877 CCTACTCTGGAGATACGTACACG 59.506 52.174 0.00 0.00 46.33 4.49
588 3093 4.701765 TCCTACTCTGGAGATACGTACAC 58.298 47.826 0.00 0.00 0.00 2.90
599 3104 6.939163 GGATTATAACGTACTCCTACTCTGGA 59.061 42.308 0.00 0.00 34.52 3.86
600 3105 6.150809 GGGATTATAACGTACTCCTACTCTGG 59.849 46.154 0.00 0.00 0.00 3.86
601 3106 6.150809 GGGGATTATAACGTACTCCTACTCTG 59.849 46.154 0.00 0.00 0.00 3.35
602 3107 6.045341 AGGGGATTATAACGTACTCCTACTCT 59.955 42.308 0.00 0.00 0.00 3.24
603 3108 6.150809 CAGGGGATTATAACGTACTCCTACTC 59.849 46.154 0.00 0.00 0.00 2.59
604 3109 6.008960 CAGGGGATTATAACGTACTCCTACT 58.991 44.000 0.00 0.20 0.00 2.57
605 3110 5.336293 GCAGGGGATTATAACGTACTCCTAC 60.336 48.000 0.00 0.00 0.00 3.18
606 3111 4.768968 GCAGGGGATTATAACGTACTCCTA 59.231 45.833 0.00 0.00 0.00 2.94
607 3112 3.577415 GCAGGGGATTATAACGTACTCCT 59.423 47.826 0.00 0.00 0.00 3.69
741 3247 0.389757 GTAGGCAGTAGGCACTAGGC 59.610 60.000 0.00 0.00 44.14 3.93
742 3248 1.683917 CAGTAGGCAGTAGGCACTAGG 59.316 57.143 0.00 0.00 44.14 3.02
743 3249 4.170136 GGCAGTAGGCAGTAGGCACTAG 62.170 59.091 0.00 0.00 43.84 2.57
996 3549 3.672255 CTTGCGGCAAGGCATCGTG 62.672 63.158 30.28 7.33 43.52 4.35
1756 4538 1.141881 CATTGGCGAGGTCTAGCGT 59.858 57.895 0.00 0.00 31.73 5.07
1883 4701 4.065088 GGAGTTGTTGTAGTCAGCATTGA 58.935 43.478 0.00 0.00 34.96 2.57
1982 4806 2.504899 CATCGCACAGCTCGTCGT 60.505 61.111 0.00 0.00 0.00 4.34
1990 4814 0.372679 GTCATGACTGCATCGCACAG 59.627 55.000 18.83 0.00 41.08 3.66
2104 4950 3.841758 GTACCCGTACCCGCCAGG 61.842 72.222 0.00 0.00 43.78 4.45
2167 5013 2.874780 CGAGTGCGCCGTGTAGTC 60.875 66.667 4.18 0.00 0.00 2.59
2225 5071 5.657474 AGCTCCAAAATTATGACTGCATTG 58.343 37.500 0.00 0.00 35.94 2.82
2361 5228 3.999663 AGCTCATCCTCTTTTCGTGAAAG 59.000 43.478 7.43 7.43 44.99 2.62
2376 5243 5.876612 AAAGACATTGTGAAGAGCTCATC 57.123 39.130 17.77 14.72 36.14 2.92
2436 5308 8.355169 GTTGAATCACCAGAATATGCATATGTT 58.645 33.333 19.77 6.12 0.00 2.71
2652 5527 6.348950 GGAATGTTGGAATGACATAACACGAA 60.349 38.462 4.73 0.00 36.76 3.85
2653 5528 5.123186 GGAATGTTGGAATGACATAACACGA 59.877 40.000 4.73 0.00 36.76 4.35
2696 5571 0.950836 CACAAGGCATTGTCCGTCAA 59.049 50.000 14.86 0.00 46.90 3.18
2891 5848 4.411256 ACGAGGTTGAAGAAACTTGGTA 57.589 40.909 0.00 0.00 35.49 3.25
2906 5863 5.869888 GTGTTATCATCAGAGAAAACGAGGT 59.130 40.000 0.00 0.00 0.00 3.85
2952 5926 4.545208 TCATTGTTGTAGAATCACCCGA 57.455 40.909 0.00 0.00 0.00 5.14
2982 5959 3.245518 AGACATATGTGCAGCACGTTA 57.754 42.857 25.20 16.68 37.14 3.18
3036 6018 4.464069 AGAGAGTGAACACTAGGATTGC 57.536 45.455 7.46 0.00 42.66 3.56
3063 6045 0.988832 ACACTAGGATTCCCCGCAAA 59.011 50.000 0.00 0.00 40.87 3.68
3064 6046 0.988832 AACACTAGGATTCCCCGCAA 59.011 50.000 0.00 0.00 40.87 4.85
3065 6047 0.539986 GAACACTAGGATTCCCCGCA 59.460 55.000 0.00 0.00 40.87 5.69
3066 6048 0.539986 TGAACACTAGGATTCCCCGC 59.460 55.000 0.00 0.00 40.87 6.13
3067 6049 1.831736 AGTGAACACTAGGATTCCCCG 59.168 52.381 5.62 0.00 40.43 5.73
3093 6075 1.657804 CCTCCTGGGTCCAACTACTT 58.342 55.000 0.00 0.00 0.00 2.24
3094 6076 3.401032 CCTCCTGGGTCCAACTACT 57.599 57.895 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.