Multiple sequence alignment - TraesCS2D01G248100

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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 TraesCS2D01G248100 chr2D 100.000 1712 0 0 679 2390 291910659 291912370 0.000000e+00 3162.0
1 TraesCS2D01G248100 chr2D 100.000 405 0 0 1 405 291909981 291910385 0.000000e+00 749.0
2 TraesCS2D01G248100 chr2D 94.178 292 12 4 118 405 637337315 637337605 7.840000e-120 440.0
3 TraesCS2D01G248100 chr7A 91.475 1173 87 7 806 1974 327311643 327312806 0.000000e+00 1600.0
4 TraesCS2D01G248100 chr7A 89.373 734 64 7 1176 1899 526528600 526529329 0.000000e+00 911.0
5 TraesCS2D01G248100 chr7A 91.505 412 31 4 1424 1833 238551337 238550928 4.460000e-157 564.0
6 TraesCS2D01G248100 chr7A 92.778 360 23 3 2028 2386 238550928 238550571 3.520000e-143 518.0
7 TraesCS2D01G248100 chr7A 91.967 361 22 5 2028 2386 64006349 64005994 1.280000e-137 499.0
8 TraesCS2D01G248100 chr7A 91.255 263 16 6 2129 2390 526546161 526546417 3.780000e-93 351.0
9 TraesCS2D01G248100 chr1A 94.653 879 43 3 806 1683 235353007 235353882 0.000000e+00 1360.0
10 TraesCS2D01G248100 chr1A 96.046 607 22 2 1785 2390 235359941 235360546 0.000000e+00 987.0
11 TraesCS2D01G248100 chr1A 91.667 132 11 0 679 810 235352656 235352787 1.460000e-42 183.0
12 TraesCS2D01G248100 chr1A 95.192 104 5 0 1682 1785 235358727 235358830 5.290000e-37 165.0
13 TraesCS2D01G248100 chr6B 91.363 961 70 13 1435 2388 233232105 233231151 0.000000e+00 1303.0
14 TraesCS2D01G248100 chr6B 85.748 856 83 13 1204 2049 716082119 716081293 0.000000e+00 869.0
15 TraesCS2D01G248100 chr6B 89.982 559 47 6 1424 1975 471136051 471136607 0.000000e+00 713.0
16 TraesCS2D01G248100 chr6B 85.938 256 26 5 806 1058 716082402 716082154 5.070000e-67 265.0
17 TraesCS2D01G248100 chr6B 90.323 186 16 2 1 184 267929133 267928948 2.370000e-60 243.0
18 TraesCS2D01G248100 chr6B 95.536 112 5 0 1293 1404 233233373 233233262 1.890000e-41 180.0
19 TraesCS2D01G248100 chr6B 93.750 112 7 0 1293 1404 471127123 471127234 4.090000e-38 169.0
20 TraesCS2D01G248100 chr5B 90.550 963 77 14 1435 2390 592100321 592101276 0.000000e+00 1262.0
21 TraesCS2D01G248100 chr5B 94.776 268 14 0 128 395 516534339 516534606 3.670000e-113 418.0
22 TraesCS2D01G248100 chr5B 94.643 112 6 0 1293 1404 592098947 592099058 8.780000e-40 174.0
23 TraesCS2D01G248100 chr3D 87.204 719 63 12 1141 1849 212868654 212869353 0.000000e+00 791.0
24 TraesCS2D01G248100 chr3D 92.961 412 25 4 1424 1833 286532727 286532318 4.400000e-167 597.0
25 TraesCS2D01G248100 chr3D 93.333 360 21 3 2028 2386 286532318 286531961 1.630000e-146 529.0
26 TraesCS2D01G248100 chr3D 93.594 281 14 4 128 405 217655681 217655402 1.320000e-112 416.0
27 TraesCS2D01G248100 chr3D 90.909 297 20 3 109 405 612665331 612665620 2.230000e-105 392.0
28 TraesCS2D01G248100 chr3D 89.623 212 21 1 1836 2046 212869368 212869579 3.920000e-68 268.0
29 TraesCS2D01G248100 chr3D 89.032 155 15 2 2047 2201 212869614 212869766 8.720000e-45 191.0
30 TraesCS2D01G248100 chr3D 89.262 149 14 2 2243 2390 12939646 12939499 4.060000e-43 185.0
31 TraesCS2D01G248100 chr3D 95.536 112 5 0 1293 1404 286534052 286533941 1.890000e-41 180.0
32 TraesCS2D01G248100 chr3D 84.810 79 4 1 1417 1487 170930813 170930891 3.300000e-09 73.1
33 TraesCS2D01G248100 chr2A 85.634 710 87 8 1346 2046 442137730 442138433 0.000000e+00 732.0
34 TraesCS2D01G248100 chr3B 93.611 360 20 2 2028 2386 358639211 358638854 3.500000e-148 534.0
35 TraesCS2D01G248100 chr3B 92.521 361 22 4 2028 2386 259701666 259701309 1.640000e-141 512.0
36 TraesCS2D01G248100 chr5A 92.758 359 23 2 2028 2386 116893977 116893622 1.270000e-142 516.0
37 TraesCS2D01G248100 chr5A 87.429 175 20 2 1 173 316897951 316897777 1.450000e-47 200.0
38 TraesCS2D01G248100 chr6A 89.320 412 40 4 1424 1833 155935654 155936063 4.560000e-142 514.0
39 TraesCS2D01G248100 chr6A 90.808 359 28 3 2028 2386 155936063 155936416 2.150000e-130 475.0
40 TraesCS2D01G248100 chr6A 92.388 289 20 2 118 405 540468490 540468203 6.150000e-111 411.0
41 TraesCS2D01G248100 chr6A 90.847 295 24 3 112 405 327885597 327885305 2.230000e-105 392.0
42 TraesCS2D01G248100 chr6A 86.572 283 37 1 1920 2201 296770476 296770758 6.420000e-81 311.0
43 TraesCS2D01G248100 chr6A 95.413 109 5 0 1293 1401 155933983 155934091 8.780000e-40 174.0
44 TraesCS2D01G248100 chr7B 92.617 298 20 2 109 405 175192593 175192297 6.110000e-116 427.0
45 TraesCS2D01G248100 chr7B 89.542 153 13 3 2240 2390 543915905 543916056 8.720000e-45 191.0
46 TraesCS2D01G248100 chr7B 95.536 112 5 0 1293 1404 315071755 315071644 1.890000e-41 180.0
47 TraesCS2D01G248100 chr7B 90.909 66 6 0 2136 2201 296239349 296239284 3.270000e-14 89.8
48 TraesCS2D01G248100 chr7B 90.909 66 6 0 2136 2201 331036376 331036311 3.270000e-14 89.8
49 TraesCS2D01G248100 chr5D 93.357 286 17 2 120 405 4177549 4177832 2.840000e-114 422.0
50 TraesCS2D01G248100 chr5D 87.975 158 17 2 1 156 157673219 157673376 4.060000e-43 185.0
51 TraesCS2D01G248100 chr4A 91.186 295 23 3 113 405 462074373 462074666 4.790000e-107 398.0
52 TraesCS2D01G248100 chr4A 86.391 169 22 1 1 168 489691675 489691507 1.460000e-42 183.0
53 TraesCS2D01G248100 chr1B 85.375 253 19 7 1417 1668 314605031 314604796 1.830000e-61 246.0
54 TraesCS2D01G248100 chrUn 88.889 162 14 4 5 162 102466937 102466776 1.870000e-46 196.0
55 TraesCS2D01G248100 chr6D 88.158 152 17 1 2 152 210000013 210000164 1.890000e-41 180.0
56 TraesCS2D01G248100 chr6D 85.135 148 17 5 5 148 192226195 192226341 1.910000e-31 147.0
57 TraesCS2D01G248100 chr4D 85.629 167 22 2 1 165 169977183 169977349 8.780000e-40 174.0
58 TraesCS2D01G248100 chr7D 86.842 152 14 5 1 146 422116375 422116526 5.290000e-37 165.0
59 TraesCS2D01G248100 chr4B 92.727 55 4 0 2336 2390 216834537 216834483 1.970000e-11 80.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G248100 chr2D 291909981 291912370 2389 False 1955.500000 3162 100.000000 1 2390 2 chr2D.!!$F2 2389
1 TraesCS2D01G248100 chr7A 327311643 327312806 1163 False 1600.000000 1600 91.475000 806 1974 1 chr7A.!!$F1 1168
2 TraesCS2D01G248100 chr7A 526528600 526529329 729 False 911.000000 911 89.373000 1176 1899 1 chr7A.!!$F2 723
3 TraesCS2D01G248100 chr7A 238550571 238551337 766 True 541.000000 564 92.141500 1424 2386 2 chr7A.!!$R2 962
4 TraesCS2D01G248100 chr1A 235352656 235353882 1226 False 771.500000 1360 93.160000 679 1683 2 chr1A.!!$F1 1004
5 TraesCS2D01G248100 chr1A 235358727 235360546 1819 False 576.000000 987 95.619000 1682 2390 2 chr1A.!!$F2 708
6 TraesCS2D01G248100 chr6B 233231151 233233373 2222 True 741.500000 1303 93.449500 1293 2388 2 chr6B.!!$R2 1095
7 TraesCS2D01G248100 chr6B 471136051 471136607 556 False 713.000000 713 89.982000 1424 1975 1 chr6B.!!$F2 551
8 TraesCS2D01G248100 chr6B 716081293 716082402 1109 True 567.000000 869 85.843000 806 2049 2 chr6B.!!$R3 1243
9 TraesCS2D01G248100 chr5B 592098947 592101276 2329 False 718.000000 1262 92.596500 1293 2390 2 chr5B.!!$F2 1097
10 TraesCS2D01G248100 chr3D 286531961 286534052 2091 True 435.333333 597 93.943333 1293 2386 3 chr3D.!!$R3 1093
11 TraesCS2D01G248100 chr3D 212868654 212869766 1112 False 416.666667 791 88.619667 1141 2201 3 chr3D.!!$F3 1060
12 TraesCS2D01G248100 chr2A 442137730 442138433 703 False 732.000000 732 85.634000 1346 2046 1 chr2A.!!$F1 700
13 TraesCS2D01G248100 chr6A 155933983 155936416 2433 False 387.666667 514 91.847000 1293 2386 3 chr6A.!!$F2 1093

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
21 22 0.031043 CACAACCGCATGCATATGGG 59.969 55.0 19.57 12.73 44.38 4.00 F
1051 1282 0.035820 GTCCATGAACGGGGTTGCTA 60.036 55.0 0.00 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 1325 0.315869 CAAAGACGAACCGTGTGCAC 60.316 55.000 10.75 10.75 41.37 4.57 R
1986 4970 2.102357 AGATCGTAGGCACACGCG 59.898 61.111 3.53 3.53 41.67 6.01 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
17 18 3.195683 GGCACAACCGCATGCATA 58.804 55.556 19.57 0.00 43.93 3.14
18 19 1.735360 GGCACAACCGCATGCATAT 59.265 52.632 19.57 0.00 43.93 1.78
19 20 0.595567 GGCACAACCGCATGCATATG 60.596 55.000 19.57 14.56 43.93 1.78
20 21 0.595567 GCACAACCGCATGCATATGG 60.596 55.000 19.57 13.13 41.65 2.74
21 22 0.031043 CACAACCGCATGCATATGGG 59.969 55.000 19.57 12.73 44.38 4.00
22 23 1.007038 CAACCGCATGCATATGGGC 60.007 57.895 19.57 8.68 43.68 5.36
23 24 2.202395 AACCGCATGCATATGGGCC 61.202 57.895 19.57 0.00 43.68 5.80
24 25 3.376078 CCGCATGCATATGGGCCC 61.376 66.667 17.59 17.59 43.68 5.80
25 26 3.376078 CGCATGCATATGGGCCCC 61.376 66.667 22.27 3.07 39.87 5.80
26 27 2.999063 GCATGCATATGGGCCCCC 60.999 66.667 22.27 2.69 34.79 5.40
27 28 2.677524 CATGCATATGGGCCCCCG 60.678 66.667 22.27 5.83 39.42 5.73
28 29 2.858476 ATGCATATGGGCCCCCGA 60.858 61.111 22.27 4.19 39.42 5.14
29 30 3.210012 ATGCATATGGGCCCCCGAC 62.210 63.158 22.27 5.56 39.42 4.79
31 32 3.556306 CATATGGGCCCCCGACGT 61.556 66.667 22.27 0.00 39.42 4.34
32 33 3.556306 ATATGGGCCCCCGACGTG 61.556 66.667 22.27 0.00 39.42 4.49
33 34 4.781616 TATGGGCCCCCGACGTGA 62.782 66.667 22.27 0.00 39.42 4.35
53 54 4.759096 GTGCGCACGCCCAATCAC 62.759 66.667 26.77 0.00 41.09 3.06
55 56 4.465512 GCGCACGCCCAATCACTG 62.466 66.667 0.30 0.00 34.56 3.66
56 57 2.741985 CGCACGCCCAATCACTGA 60.742 61.111 0.00 0.00 0.00 3.41
57 58 2.870372 GCACGCCCAATCACTGAC 59.130 61.111 0.00 0.00 0.00 3.51
58 59 1.965930 GCACGCCCAATCACTGACA 60.966 57.895 0.00 0.00 0.00 3.58
59 60 1.915614 GCACGCCCAATCACTGACAG 61.916 60.000 0.00 0.00 0.00 3.51
60 61 0.320683 CACGCCCAATCACTGACAGA 60.321 55.000 10.08 0.00 0.00 3.41
61 62 0.036952 ACGCCCAATCACTGACAGAG 60.037 55.000 10.08 0.55 0.00 3.35
62 63 1.364626 CGCCCAATCACTGACAGAGC 61.365 60.000 10.08 0.00 0.00 4.09
63 64 1.364626 GCCCAATCACTGACAGAGCG 61.365 60.000 10.08 0.00 0.00 5.03
64 65 1.364626 CCCAATCACTGACAGAGCGC 61.365 60.000 10.08 0.00 0.00 5.92
65 66 1.690283 CCAATCACTGACAGAGCGCG 61.690 60.000 10.08 0.00 0.00 6.86
66 67 2.097038 AATCACTGACAGAGCGCGC 61.097 57.895 26.66 26.66 0.00 6.86
88 89 1.139095 GAGGGACGCCAGTAGAACG 59.861 63.158 0.00 0.00 0.00 3.95
89 90 2.508663 GGGACGCCAGTAGAACGC 60.509 66.667 0.00 0.00 0.00 4.84
90 91 2.572284 GGACGCCAGTAGAACGCT 59.428 61.111 0.00 0.00 0.00 5.07
91 92 1.516603 GGACGCCAGTAGAACGCTC 60.517 63.158 0.00 0.00 0.00 5.03
92 93 1.516603 GACGCCAGTAGAACGCTCC 60.517 63.158 0.00 0.00 0.00 4.70
93 94 2.579787 CGCCAGTAGAACGCTCCG 60.580 66.667 0.00 0.00 0.00 4.63
94 95 2.886124 GCCAGTAGAACGCTCCGC 60.886 66.667 0.00 0.00 0.00 5.54
109 110 4.764336 CGCGGTCGCCTCAACGTA 62.764 66.667 9.85 0.00 37.98 3.57
110 111 2.202703 GCGGTCGCCTCAACGTAT 60.203 61.111 3.73 0.00 34.56 3.06
111 112 1.064621 GCGGTCGCCTCAACGTATA 59.935 57.895 3.73 0.00 34.56 1.47
112 113 0.318445 GCGGTCGCCTCAACGTATAT 60.318 55.000 3.73 0.00 34.56 0.86
113 114 1.069022 GCGGTCGCCTCAACGTATATA 60.069 52.381 3.73 0.00 34.56 0.86
114 115 2.415090 GCGGTCGCCTCAACGTATATAT 60.415 50.000 3.73 0.00 34.56 0.86
115 116 3.181507 GCGGTCGCCTCAACGTATATATA 60.182 47.826 3.73 0.00 34.56 0.86
116 117 4.497006 GCGGTCGCCTCAACGTATATATAT 60.497 45.833 3.73 0.00 34.56 0.86
117 118 5.277490 GCGGTCGCCTCAACGTATATATATA 60.277 44.000 3.73 0.00 34.56 0.86
118 119 6.567321 GCGGTCGCCTCAACGTATATATATAT 60.567 42.308 10.10 10.10 34.56 0.86
119 120 7.360353 GCGGTCGCCTCAACGTATATATATATA 60.360 40.741 8.16 8.16 34.56 0.86
120 121 8.663025 CGGTCGCCTCAACGTATATATATATAT 58.337 37.037 17.37 17.37 33.68 0.86
209 210 1.192428 GACTATTCGTCACCCTGGGT 58.808 55.000 14.05 14.05 42.37 4.51
224 225 4.100279 CCTGGGTGGGGAATAGTTATTC 57.900 50.000 3.75 3.75 40.96 1.75
225 226 3.722101 CCTGGGTGGGGAATAGTTATTCT 59.278 47.826 10.71 0.00 41.33 2.40
226 227 4.168088 CCTGGGTGGGGAATAGTTATTCTT 59.832 45.833 10.71 0.00 41.33 2.52
227 228 5.377478 CTGGGTGGGGAATAGTTATTCTTC 58.623 45.833 10.71 5.44 41.33 2.87
228 229 4.791334 TGGGTGGGGAATAGTTATTCTTCA 59.209 41.667 10.71 7.38 41.33 3.02
229 230 5.131067 GGGTGGGGAATAGTTATTCTTCAC 58.869 45.833 18.47 18.47 41.33 3.18
230 231 5.131067 GGTGGGGAATAGTTATTCTTCACC 58.869 45.833 23.84 23.84 45.63 4.02
231 232 5.131067 GTGGGGAATAGTTATTCTTCACCC 58.869 45.833 17.23 15.31 41.33 4.61
232 233 4.167307 TGGGGAATAGTTATTCTTCACCCC 59.833 45.833 0.00 0.00 43.61 4.95
233 234 4.447325 GGGGAATAGTTATTCTTCACCCCC 60.447 50.000 0.00 0.00 41.33 5.40
258 259 2.428544 TTTTACCACCAGTGCACTGT 57.571 45.000 37.55 25.59 42.27 3.55
259 260 3.562343 TTTTACCACCAGTGCACTGTA 57.438 42.857 37.55 24.11 42.27 2.74
260 261 3.562343 TTTACCACCAGTGCACTGTAA 57.438 42.857 37.55 27.58 42.27 2.41
261 262 3.780804 TTACCACCAGTGCACTGTAAT 57.219 42.857 37.55 23.67 42.27 1.89
262 263 2.656947 ACCACCAGTGCACTGTAATT 57.343 45.000 37.55 20.78 42.27 1.40
263 264 2.944129 ACCACCAGTGCACTGTAATTT 58.056 42.857 37.55 19.50 42.27 1.82
264 265 3.295973 ACCACCAGTGCACTGTAATTTT 58.704 40.909 37.55 18.54 42.27 1.82
265 266 4.465886 ACCACCAGTGCACTGTAATTTTA 58.534 39.130 37.55 0.00 42.27 1.52
266 267 4.277423 ACCACCAGTGCACTGTAATTTTAC 59.723 41.667 37.55 0.00 42.27 2.01
267 268 4.277174 CCACCAGTGCACTGTAATTTTACA 59.723 41.667 37.55 3.34 42.27 2.41
268 269 5.048083 CCACCAGTGCACTGTAATTTTACAT 60.048 40.000 37.55 12.58 42.26 2.29
269 270 6.446318 CACCAGTGCACTGTAATTTTACATT 58.554 36.000 37.55 10.22 42.26 2.71
270 271 6.582295 CACCAGTGCACTGTAATTTTACATTC 59.418 38.462 37.55 0.00 42.26 2.67
271 272 6.092748 CCAGTGCACTGTAATTTTACATTCC 58.907 40.000 37.55 0.00 42.26 3.01
272 273 5.794945 CAGTGCACTGTAATTTTACATTCCG 59.205 40.000 34.04 6.59 42.26 4.30
273 274 5.472137 AGTGCACTGTAATTTTACATTCCGT 59.528 36.000 20.97 0.00 42.26 4.69
274 275 6.651643 AGTGCACTGTAATTTTACATTCCGTA 59.348 34.615 20.97 0.00 42.26 4.02
275 276 7.173562 AGTGCACTGTAATTTTACATTCCGTAA 59.826 33.333 20.97 0.00 42.26 3.18
276 277 7.480542 GTGCACTGTAATTTTACATTCCGTAAG 59.519 37.037 10.32 0.00 42.26 2.34
277 278 7.173562 TGCACTGTAATTTTACATTCCGTAAGT 59.826 33.333 3.76 0.00 42.26 2.24
278 279 8.019094 GCACTGTAATTTTACATTCCGTAAGTT 58.981 33.333 3.76 0.00 42.26 2.66
279 280 9.887406 CACTGTAATTTTACATTCCGTAAGTTT 57.113 29.630 3.76 0.00 42.26 2.66
305 306 7.941795 TTCTTACTTCTGACGTAAAAAGAGG 57.058 36.000 7.94 4.55 0.00 3.69
306 307 5.924825 TCTTACTTCTGACGTAAAAAGAGGC 59.075 40.000 7.94 0.00 0.00 4.70
307 308 3.400255 ACTTCTGACGTAAAAAGAGGCC 58.600 45.455 0.00 0.00 0.00 5.19
308 309 2.074547 TCTGACGTAAAAAGAGGCCG 57.925 50.000 0.00 0.00 0.00 6.13
309 310 1.342174 TCTGACGTAAAAAGAGGCCGT 59.658 47.619 0.00 0.00 0.00 5.68
310 311 2.557924 TCTGACGTAAAAAGAGGCCGTA 59.442 45.455 0.00 0.00 0.00 4.02
311 312 3.005684 TCTGACGTAAAAAGAGGCCGTAA 59.994 43.478 0.00 0.00 0.00 3.18
312 313 3.319755 TGACGTAAAAAGAGGCCGTAAG 58.680 45.455 0.00 0.00 0.00 2.34
313 314 3.005684 TGACGTAAAAAGAGGCCGTAAGA 59.994 43.478 0.00 0.00 43.02 2.10
314 315 3.989817 GACGTAAAAAGAGGCCGTAAGAA 59.010 43.478 0.00 0.00 43.02 2.52
315 316 4.379652 ACGTAAAAAGAGGCCGTAAGAAA 58.620 39.130 0.00 0.00 43.02 2.52
316 317 4.815846 ACGTAAAAAGAGGCCGTAAGAAAA 59.184 37.500 0.00 0.00 43.02 2.29
317 318 5.471116 ACGTAAAAAGAGGCCGTAAGAAAAT 59.529 36.000 0.00 0.00 43.02 1.82
318 319 6.650390 ACGTAAAAAGAGGCCGTAAGAAAATA 59.350 34.615 0.00 0.00 43.02 1.40
319 320 7.335171 ACGTAAAAAGAGGCCGTAAGAAAATAT 59.665 33.333 0.00 0.00 43.02 1.28
320 321 8.819974 CGTAAAAAGAGGCCGTAAGAAAATATA 58.180 33.333 0.00 0.00 43.02 0.86
327 328 9.654663 AGAGGCCGTAAGAAAATATATAATCAC 57.345 33.333 0.00 0.00 43.02 3.06
328 329 8.788325 AGGCCGTAAGAAAATATATAATCACC 57.212 34.615 0.00 0.00 43.02 4.02
329 330 7.548075 AGGCCGTAAGAAAATATATAATCACCG 59.452 37.037 0.00 0.00 43.02 4.94
330 331 7.332678 GGCCGTAAGAAAATATATAATCACCGT 59.667 37.037 0.00 0.00 43.02 4.83
331 332 9.357652 GCCGTAAGAAAATATATAATCACCGTA 57.642 33.333 0.00 0.00 43.02 4.02
379 380 9.517609 AAATTACAAACGTAAAAACATAGTGCA 57.482 25.926 0.00 0.00 32.75 4.57
380 381 9.517609 AATTACAAACGTAAAAACATAGTGCAA 57.482 25.926 0.00 0.00 32.75 4.08
381 382 8.906636 TTACAAACGTAAAAACATAGTGCAAA 57.093 26.923 0.00 0.00 0.00 3.68
382 383 7.813852 ACAAACGTAAAAACATAGTGCAAAA 57.186 28.000 0.00 0.00 0.00 2.44
383 384 8.413899 ACAAACGTAAAAACATAGTGCAAAAT 57.586 26.923 0.00 0.00 0.00 1.82
384 385 9.517609 ACAAACGTAAAAACATAGTGCAAAATA 57.482 25.926 0.00 0.00 0.00 1.40
707 708 3.979497 CCCCACCACCAACCTCCC 61.979 72.222 0.00 0.00 0.00 4.30
734 735 3.655810 GAGTGCCTCCTCCAGTGCG 62.656 68.421 0.00 0.00 0.00 5.34
776 777 1.671379 GACGCACTTCTTCCCCCAC 60.671 63.158 0.00 0.00 0.00 4.61
964 1189 0.719015 TGAGATCCCTCCACCTCCTT 59.281 55.000 0.00 0.00 38.66 3.36
1007 1238 4.568380 CCTTGGATCTTCAAGAATGGGACA 60.568 45.833 11.91 0.00 44.98 4.02
1051 1282 0.035820 GTCCATGAACGGGGTTGCTA 60.036 55.000 0.00 0.00 0.00 3.49
1084 1325 2.793946 CTTCAATTCAGCGGGGCG 59.206 61.111 0.00 0.00 0.00 6.13
1342 1589 0.843309 TGGTGTGAGGAGAAGCCAAA 59.157 50.000 0.00 0.00 40.02 3.28
1478 3309 0.617249 CTGGTGCTCCTCTCCCTCTT 60.617 60.000 6.34 0.00 34.23 2.85
1487 3318 0.540923 CTCTCCCTCTTCTGCCTTGG 59.459 60.000 0.00 0.00 0.00 3.61
1504 3335 0.549469 TGGATGCTGTGATGCCATCT 59.451 50.000 6.21 0.00 0.00 2.90
1526 3360 6.317312 TCTCCTCCTACTGTACAAAAGGTTA 58.683 40.000 18.22 8.09 0.00 2.85
1772 3616 2.161012 CGCATCTTGTTTCAGACTGCAT 59.839 45.455 0.00 0.00 31.80 3.96
1997 4981 4.293648 AGTGTGCGCGTGTGCCTA 62.294 61.111 8.43 0.00 38.08 3.93
2020 5005 3.376234 CGATCTGAAACAATGCCTGATGT 59.624 43.478 0.00 0.00 0.00 3.06
2042 5027 3.750652 TGAGCGATGACTTTAATTGTGCA 59.249 39.130 0.00 0.00 0.00 4.57
2191 5210 8.887036 ATCACGAAAATGAGTGCATATAGTTA 57.113 30.769 0.00 0.00 38.19 2.24
2224 5243 8.893563 AACCTCCAGGAAATTCAAACATTATA 57.106 30.769 0.00 0.00 38.94 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.595567 CATATGCATGCGGTTGTGCC 60.596 55.000 14.09 0.00 40.56 5.01
1 2 0.595567 CCATATGCATGCGGTTGTGC 60.596 55.000 14.09 0.00 41.61 4.57
3 4 1.737355 GCCCATATGCATGCGGTTGT 61.737 55.000 14.09 0.00 0.00 3.32
6 7 2.598394 GGCCCATATGCATGCGGT 60.598 61.111 14.09 6.93 0.00 5.68
8 9 3.376078 GGGGCCCATATGCATGCG 61.376 66.667 26.86 0.00 0.00 4.73
9 10 2.999063 GGGGGCCCATATGCATGC 60.999 66.667 26.86 11.82 35.81 4.06
10 11 2.677524 CGGGGGCCCATATGCATG 60.678 66.667 26.86 0.00 35.37 4.06
11 12 2.858476 TCGGGGGCCCATATGCAT 60.858 61.111 26.86 3.79 35.37 3.96
12 13 3.884774 GTCGGGGGCCCATATGCA 61.885 66.667 26.86 0.00 35.37 3.96
14 15 3.556306 ACGTCGGGGGCCCATATG 61.556 66.667 26.86 18.77 35.37 1.78
15 16 3.556306 CACGTCGGGGGCCCATAT 61.556 66.667 26.86 0.89 35.37 1.78
16 17 4.781616 TCACGTCGGGGGCCCATA 62.782 66.667 26.86 8.72 35.37 2.74
36 37 4.759096 GTGATTGGGCGTGCGCAC 62.759 66.667 30.42 30.42 46.35 5.34
38 39 4.465512 CAGTGATTGGGCGTGCGC 62.466 66.667 8.17 8.17 41.06 6.09
39 40 2.741985 TCAGTGATTGGGCGTGCG 60.742 61.111 0.00 0.00 0.00 5.34
40 41 1.915614 CTGTCAGTGATTGGGCGTGC 61.916 60.000 0.00 0.00 0.00 5.34
41 42 0.320683 TCTGTCAGTGATTGGGCGTG 60.321 55.000 0.00 0.00 0.00 5.34
42 43 0.036952 CTCTGTCAGTGATTGGGCGT 60.037 55.000 0.00 0.00 0.00 5.68
43 44 1.364626 GCTCTGTCAGTGATTGGGCG 61.365 60.000 6.09 0.00 0.00 6.13
44 45 1.364626 CGCTCTGTCAGTGATTGGGC 61.365 60.000 6.09 9.36 34.07 5.36
45 46 1.364626 GCGCTCTGTCAGTGATTGGG 61.365 60.000 0.00 0.00 34.07 4.12
46 47 1.690283 CGCGCTCTGTCAGTGATTGG 61.690 60.000 5.56 0.00 34.07 3.16
47 48 1.706301 CGCGCTCTGTCAGTGATTG 59.294 57.895 5.56 0.00 34.07 2.67
48 49 2.097038 GCGCGCTCTGTCAGTGATT 61.097 57.895 26.67 0.00 34.07 2.57
49 50 2.507992 GCGCGCTCTGTCAGTGAT 60.508 61.111 26.67 0.00 34.07 3.06
68 69 2.050350 TTCTACTGGCGTCCCTCCG 61.050 63.158 0.00 0.00 0.00 4.63
69 70 1.516423 GTTCTACTGGCGTCCCTCC 59.484 63.158 0.00 0.00 0.00 4.30
70 71 1.139095 CGTTCTACTGGCGTCCCTC 59.861 63.158 0.00 0.00 0.00 4.30
71 72 3.003113 GCGTTCTACTGGCGTCCCT 62.003 63.158 0.00 0.00 0.00 4.20
72 73 2.508663 GCGTTCTACTGGCGTCCC 60.509 66.667 0.00 0.00 0.00 4.46
73 74 1.516603 GAGCGTTCTACTGGCGTCC 60.517 63.158 0.00 0.00 0.00 4.79
74 75 1.516603 GGAGCGTTCTACTGGCGTC 60.517 63.158 0.00 0.00 0.00 5.19
75 76 2.572284 GGAGCGTTCTACTGGCGT 59.428 61.111 0.00 0.00 0.00 5.68
76 77 2.579787 CGGAGCGTTCTACTGGCG 60.580 66.667 0.00 0.00 0.00 5.69
92 93 2.651367 TATACGTTGAGGCGACCGCG 62.651 60.000 8.36 0.00 43.06 6.46
93 94 0.318445 ATATACGTTGAGGCGACCGC 60.318 55.000 5.75 5.75 41.06 5.68
94 95 2.975410 TATATACGTTGAGGCGACCG 57.025 50.000 0.00 0.00 35.59 4.79
191 192 3.393854 ACCCAGGGTGACGAATAGT 57.606 52.632 11.70 0.00 32.98 2.12
203 204 3.722101 AGAATAACTATTCCCCACCCAGG 59.278 47.826 5.95 0.00 42.29 4.45
204 205 5.104109 TGAAGAATAACTATTCCCCACCCAG 60.104 44.000 5.95 0.00 42.29 4.45
205 206 4.791334 TGAAGAATAACTATTCCCCACCCA 59.209 41.667 5.95 0.00 42.29 4.51
206 207 5.131067 GTGAAGAATAACTATTCCCCACCC 58.869 45.833 14.61 0.74 42.29 4.61
207 208 5.131067 GGTGAAGAATAACTATTCCCCACC 58.869 45.833 21.98 21.98 46.24 4.61
208 209 5.131067 GGGTGAAGAATAACTATTCCCCAC 58.869 45.833 16.01 16.01 42.29 4.61
209 210 4.167307 GGGGTGAAGAATAACTATTCCCCA 59.833 45.833 16.82 9.15 43.93 4.96
210 211 4.447325 GGGGGTGAAGAATAACTATTCCCC 60.447 50.000 11.39 11.39 43.85 4.81
211 212 4.726583 GGGGGTGAAGAATAACTATTCCC 58.273 47.826 5.95 0.00 42.29 3.97
245 246 8.259618 GGAATGTAAAATTACAGTGCACTGGTG 61.260 40.741 41.42 24.32 45.30 4.17
246 247 6.294508 GGAATGTAAAATTACAGTGCACTGGT 60.295 38.462 41.42 30.33 45.30 4.00
247 248 6.092748 GGAATGTAAAATTACAGTGCACTGG 58.907 40.000 41.42 27.04 45.30 4.00
248 249 5.794945 CGGAATGTAAAATTACAGTGCACTG 59.205 40.000 38.76 38.76 45.94 3.66
249 250 5.472137 ACGGAATGTAAAATTACAGTGCACT 59.528 36.000 15.25 15.25 45.94 4.40
250 251 5.695818 ACGGAATGTAAAATTACAGTGCAC 58.304 37.500 19.92 9.40 45.94 4.57
251 252 5.950758 ACGGAATGTAAAATTACAGTGCA 57.049 34.783 19.92 0.00 45.94 4.57
252 253 7.524065 ACTTACGGAATGTAAAATTACAGTGC 58.476 34.615 10.60 11.96 45.80 4.40
253 254 9.887406 AAACTTACGGAATGTAAAATTACAGTG 57.113 29.630 10.60 1.29 45.80 3.66
279 280 8.823818 CCTCTTTTTACGTCAGAAGTAAGAAAA 58.176 33.333 11.59 8.78 35.75 2.29
280 281 7.042254 GCCTCTTTTTACGTCAGAAGTAAGAAA 60.042 37.037 11.59 11.75 35.75 2.52
281 282 6.423001 GCCTCTTTTTACGTCAGAAGTAAGAA 59.577 38.462 8.68 9.65 35.75 2.52
282 283 5.924825 GCCTCTTTTTACGTCAGAAGTAAGA 59.075 40.000 8.68 2.76 35.75 2.10
283 284 5.120363 GGCCTCTTTTTACGTCAGAAGTAAG 59.880 44.000 8.68 1.10 35.75 2.34
284 285 4.992951 GGCCTCTTTTTACGTCAGAAGTAA 59.007 41.667 4.95 4.95 32.84 2.24
285 286 4.563061 GGCCTCTTTTTACGTCAGAAGTA 58.437 43.478 0.00 0.00 0.00 2.24
286 287 3.400255 GGCCTCTTTTTACGTCAGAAGT 58.600 45.455 0.00 0.00 0.00 3.01
287 288 2.412089 CGGCCTCTTTTTACGTCAGAAG 59.588 50.000 0.00 0.00 0.00 2.85
288 289 2.224113 ACGGCCTCTTTTTACGTCAGAA 60.224 45.455 0.00 0.00 31.39 3.02
289 290 1.342174 ACGGCCTCTTTTTACGTCAGA 59.658 47.619 0.00 0.00 31.39 3.27
290 291 1.792006 ACGGCCTCTTTTTACGTCAG 58.208 50.000 0.00 0.00 31.39 3.51
291 292 3.005684 TCTTACGGCCTCTTTTTACGTCA 59.994 43.478 0.00 0.00 38.79 4.35
292 293 3.578688 TCTTACGGCCTCTTTTTACGTC 58.421 45.455 0.00 0.00 38.79 4.34
293 294 3.665745 TCTTACGGCCTCTTTTTACGT 57.334 42.857 0.00 0.00 41.10 3.57
294 295 4.996062 TTTCTTACGGCCTCTTTTTACG 57.004 40.909 0.00 0.00 0.00 3.18
301 302 9.654663 GTGATTATATATTTTCTTACGGCCTCT 57.345 33.333 0.00 0.00 0.00 3.69
302 303 8.880750 GGTGATTATATATTTTCTTACGGCCTC 58.119 37.037 0.00 0.00 0.00 4.70
303 304 7.548075 CGGTGATTATATATTTTCTTACGGCCT 59.452 37.037 0.00 0.00 0.00 5.19
304 305 7.332678 ACGGTGATTATATATTTTCTTACGGCC 59.667 37.037 0.00 0.00 0.00 6.13
305 306 8.248117 ACGGTGATTATATATTTTCTTACGGC 57.752 34.615 0.00 0.00 0.00 5.68
353 354 9.517609 TGCACTATGTTTTTACGTTTGTAATTT 57.482 25.926 0.00 0.00 40.14 1.82
354 355 9.517609 TTGCACTATGTTTTTACGTTTGTAATT 57.482 25.926 0.00 0.00 40.14 1.40
355 356 9.517609 TTTGCACTATGTTTTTACGTTTGTAAT 57.482 25.926 0.00 0.00 40.14 1.89
356 357 8.906636 TTTGCACTATGTTTTTACGTTTGTAA 57.093 26.923 0.00 0.00 38.77 2.41
357 358 8.906636 TTTTGCACTATGTTTTTACGTTTGTA 57.093 26.923 0.00 0.00 0.00 2.41
358 359 7.813852 TTTTGCACTATGTTTTTACGTTTGT 57.186 28.000 0.00 0.00 0.00 2.83
681 682 4.660938 GTGGTGGGGGACAGGTGC 62.661 72.222 0.00 0.00 0.00 5.01
682 683 3.966543 GGTGGTGGGGGACAGGTG 61.967 72.222 0.00 0.00 0.00 4.00
683 684 4.525028 TGGTGGTGGGGGACAGGT 62.525 66.667 0.00 0.00 0.00 4.00
684 685 3.182263 TTGGTGGTGGGGGACAGG 61.182 66.667 0.00 0.00 0.00 4.00
685 686 2.115266 GTTGGTGGTGGGGGACAG 59.885 66.667 0.00 0.00 0.00 3.51
686 687 3.503839 GGTTGGTGGTGGGGGACA 61.504 66.667 0.00 0.00 0.00 4.02
687 688 3.182996 AGGTTGGTGGTGGGGGAC 61.183 66.667 0.00 0.00 0.00 4.46
688 689 2.856988 GAGGTTGGTGGTGGGGGA 60.857 66.667 0.00 0.00 0.00 4.81
689 690 3.979497 GGAGGTTGGTGGTGGGGG 61.979 72.222 0.00 0.00 0.00 5.40
690 691 3.979497 GGGAGGTTGGTGGTGGGG 61.979 72.222 0.00 0.00 0.00 4.96
964 1189 3.053544 AGGAGAATCGAGGAGGAGTACAA 60.054 47.826 0.00 0.00 34.37 2.41
1007 1238 0.912486 AGAAGCCACCGGAGCTATTT 59.088 50.000 21.21 8.57 40.49 1.40
1084 1325 0.315869 CAAAGACGAACCGTGTGCAC 60.316 55.000 10.75 10.75 41.37 4.57
1262 1504 4.431035 CGTGAACCGGACACAAGT 57.569 55.556 25.99 0.00 38.04 3.16
1478 3309 0.622136 ATCACAGCATCCAAGGCAGA 59.378 50.000 0.00 0.00 0.00 4.26
1487 3318 1.202782 AGGAGATGGCATCACAGCATC 60.203 52.381 27.93 15.50 35.83 3.91
1504 3335 6.317312 TCTAACCTTTTGTACAGTAGGAGGA 58.683 40.000 24.33 17.01 0.00 3.71
1688 3532 9.980780 GAGTTGATTAAAACAAGAATAGAGAGC 57.019 33.333 0.00 0.00 32.21 4.09
1772 3616 4.277515 CTGAAGAATCTCAGTGTTGGGA 57.722 45.455 0.00 0.00 38.42 4.37
1986 4970 2.102357 AGATCGTAGGCACACGCG 59.898 61.111 3.53 3.53 41.67 6.01
1997 4981 3.057969 TCAGGCATTGTTTCAGATCGT 57.942 42.857 0.00 0.00 0.00 3.73
2020 5005 3.750652 TGCACAATTAAAGTCATCGCTCA 59.249 39.130 0.00 0.00 0.00 4.26
2042 5027 3.070446 TCCTCTCCAACAACATTACGTGT 59.930 43.478 0.00 0.00 44.84 4.49
2096 5115 6.207417 CACAAAGTAGATGAACCTTGTCCAAT 59.793 38.462 0.00 0.00 32.92 3.16
2191 5210 3.570912 TTTCCTGGAGGTTTTCTCGTT 57.429 42.857 0.00 0.00 43.34 3.85
2354 5374 2.407562 AGGCTTTTGGGGTTTTGTGAT 58.592 42.857 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.