Multiple sequence alignment - TraesCS7D01G443900

Loading Multiple Alignment...

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 TraesCS7D01G443900 chr7D 100.000 3530 0 0 1 3530 564532400 564535929 0.000000e+00 6519.0
1 TraesCS7D01G443900 chr7D 100.000 850 0 0 2641 3490 564563410 564564259 0.000000e+00 1570.0
2 TraesCS7D01G443900 chr7D 86.486 592 54 14 1264 1848 242336807 242336235 8.320000e-176 627.0
3 TraesCS7D01G443900 chr7D 96.899 258 8 0 3273 3530 339113613 339113356 1.950000e-117 433.0
4 TraesCS7D01G443900 chr7D 98.374 246 3 1 3264 3508 564563168 564563413 7.000000e-117 431.0
5 TraesCS7D01G443900 chr7B 88.874 1528 117 24 1 1496 614296612 614295106 0.000000e+00 1831.0
6 TraesCS7D01G443900 chr7B 89.892 1395 70 35 1502 2864 614294986 614293631 0.000000e+00 1729.0
7 TraesCS7D01G443900 chr7B 83.908 870 98 21 1474 2308 404520615 404521477 0.000000e+00 793.0
8 TraesCS7D01G443900 chr7B 87.937 315 25 7 2959 3270 614293562 614293258 3.350000e-95 359.0
9 TraesCS7D01G443900 chr5A 85.735 1367 141 33 980 2308 614168871 614167521 0.000000e+00 1395.0
10 TraesCS7D01G443900 chr5A 82.988 482 63 14 2268 2733 533281449 533281927 5.450000e-113 418.0
11 TraesCS7D01G443900 chr5A 78.112 233 34 14 2300 2529 606050071 606049853 7.950000e-27 132.0
12 TraesCS7D01G443900 chr4B 84.953 1369 150 33 980 2308 359900543 359899191 0.000000e+00 1336.0
13 TraesCS7D01G443900 chr4B 83.784 74 7 5 3461 3530 86708931 86709003 8.180000e-07 65.8
14 TraesCS7D01G443900 chr6A 84.931 1367 149 34 980 2308 304901084 304899737 0.000000e+00 1330.0
15 TraesCS7D01G443900 chr6A 86.978 407 46 4 1489 1891 606002394 606001991 5.370000e-123 451.0
16 TraesCS7D01G443900 chr6A 86.019 422 51 5 1474 1891 575002337 575001920 2.500000e-121 446.0
17 TraesCS7D01G443900 chr6A 85.579 423 52 6 1474 1891 583750710 583751128 5.410000e-118 435.0
18 TraesCS7D01G443900 chr6A 87.382 317 21 13 291 588 207162072 207162388 2.610000e-91 346.0
19 TraesCS7D01G443900 chr6A 86.154 65 5 4 917 978 571020091 571020154 2.270000e-07 67.6
20 TraesCS7D01G443900 chr7A 90.178 957 82 10 1892 2842 649478112 649477162 0.000000e+00 1236.0
21 TraesCS7D01G443900 chr7A 85.122 1230 137 33 1621 2834 649800103 649798904 0.000000e+00 1216.0
22 TraesCS7D01G443900 chr7A 82.933 1248 156 38 668 1892 649479352 649478139 0.000000e+00 1072.0
23 TraesCS7D01G443900 chr7A 81.948 1119 121 39 1 1072 649801874 649800790 0.000000e+00 872.0
24 TraesCS7D01G443900 chr7A 85.545 422 54 4 1474 1891 17541341 17541759 5.410000e-118 435.0
25 TraesCS7D01G443900 chr7A 84.532 278 32 10 841 1112 649426691 649426419 7.510000e-67 265.0
26 TraesCS7D01G443900 chr7A 77.157 197 21 14 2961 3150 649476952 649476773 3.750000e-15 93.5
27 TraesCS7D01G443900 chr1A 84.597 844 84 28 1498 2308 562697574 562698404 0.000000e+00 797.0
28 TraesCS7D01G443900 chr1A 85.915 355 43 5 980 1333 562697227 562697575 4.300000e-99 372.0
29 TraesCS7D01G443900 chr1A 86.885 61 4 4 3473 3530 13750049 13749990 8.180000e-07 65.8
30 TraesCS7D01G443900 chr1A 83.784 74 7 5 3461 3530 516384451 516384523 8.180000e-07 65.8
31 TraesCS7D01G443900 chr5D 83.026 760 87 24 1988 2738 418430206 418430932 0.000000e+00 651.0
32 TraesCS7D01G443900 chr5D 75.620 242 44 11 2292 2529 484413555 484413325 4.820000e-19 106.0
33 TraesCS7D01G443900 chr5B 83.196 726 75 30 1988 2695 505770382 505771078 3.870000e-174 621.0
34 TraesCS7D01G443900 chr5B 77.778 234 34 13 2300 2529 595622522 595622303 1.030000e-25 128.0
35 TraesCS7D01G443900 chr6D 84.122 592 68 13 1264 1848 76997857 76997285 1.850000e-152 549.0
36 TraesCS7D01G443900 chr3B 89.696 427 36 7 1886 2308 615276560 615276982 4.010000e-149 538.0
37 TraesCS7D01G443900 chr2A 86.019 422 52 4 1474 1891 197933873 197934291 2.500000e-121 446.0
38 TraesCS7D01G443900 chr2A 86.458 384 31 11 293 665 532362622 532362995 5.490000e-108 401.0
39 TraesCS7D01G443900 chr2A 83.784 74 7 5 3461 3530 43663355 43663427 8.180000e-07 65.8
40 TraesCS7D01G443900 chr3D 85.782 422 53 4 1474 1891 482118683 482119101 1.160000e-119 440.0
41 TraesCS7D01G443900 chr3D 87.597 387 29 9 291 667 318682524 318682147 7.000000e-117 431.0
42 TraesCS7D01G443900 chr3D 85.294 238 30 5 3295 3530 347611983 347612217 1.270000e-59 241.0
43 TraesCS7D01G443900 chr3D 85.204 196 26 3 3295 3490 347624908 347625100 7.730000e-47 198.0
44 TraesCS7D01G443900 chr3A 88.068 352 23 8 326 667 725550032 725550374 1.970000e-107 399.0
45 TraesCS7D01G443900 chr3A 87.500 352 25 6 326 667 725592564 725592906 4.270000e-104 388.0
46 TraesCS7D01G443900 chr3A 87.500 352 25 8 326 667 725633557 725633899 4.270000e-104 388.0
47 TraesCS7D01G443900 chrUn 88.525 61 3 3 3473 3530 325526604 325526663 1.760000e-08 71.3
48 TraesCS7D01G443900 chr2B 88.525 61 3 3 3473 3530 359503936 359503877 1.760000e-08 71.3


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 TraesCS7D01G443900 chr7D 564532400 564535929 3529 False 6519.000000 6519 100.000000 1 3530 1 chr7D.!!$F1 3529
1 TraesCS7D01G443900 chr7D 564563168 564564259 1091 False 1000.500000 1570 99.187000 2641 3508 2 chr7D.!!$F2 867
2 TraesCS7D01G443900 chr7D 242336235 242336807 572 True 627.000000 627 86.486000 1264 1848 1 chr7D.!!$R1 584
3 TraesCS7D01G443900 chr7B 614293258 614296612 3354 True 1306.333333 1831 88.901000 1 3270 3 chr7B.!!$R1 3269
4 TraesCS7D01G443900 chr7B 404520615 404521477 862 False 793.000000 793 83.908000 1474 2308 1 chr7B.!!$F1 834
5 TraesCS7D01G443900 chr5A 614167521 614168871 1350 True 1395.000000 1395 85.735000 980 2308 1 chr5A.!!$R2 1328
6 TraesCS7D01G443900 chr4B 359899191 359900543 1352 True 1336.000000 1336 84.953000 980 2308 1 chr4B.!!$R1 1328
7 TraesCS7D01G443900 chr6A 304899737 304901084 1347 True 1330.000000 1330 84.931000 980 2308 1 chr6A.!!$R1 1328
8 TraesCS7D01G443900 chr7A 649798904 649801874 2970 True 1044.000000 1216 83.535000 1 2834 2 chr7A.!!$R3 2833
9 TraesCS7D01G443900 chr7A 649476773 649479352 2579 True 800.500000 1236 83.422667 668 3150 3 chr7A.!!$R2 2482
10 TraesCS7D01G443900 chr1A 562697227 562698404 1177 False 584.500000 797 85.256000 980 2308 2 chr1A.!!$F2 1328
11 TraesCS7D01G443900 chr5D 418430206 418430932 726 False 651.000000 651 83.026000 1988 2738 1 chr5D.!!$F1 750
12 TraesCS7D01G443900 chr5B 505770382 505771078 696 False 621.000000 621 83.196000 1988 2695 1 chr5B.!!$F1 707
13 TraesCS7D01G443900 chr6D 76997285 76997857 572 True 549.000000 549 84.122000 1264 1848 1 chr6D.!!$R1 584

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
315 361 0.117340 AGGGAGGGCAAGTGTCTAGT 59.883 55.0 0.00 0.0 0.00 2.57 F
1022 1101 0.246910 GTGAGTTTCCTCTCCCCGAC 59.753 60.0 0.00 0.0 38.61 4.79 F
1675 2139 1.517238 TGGATTAGGGCTGGCATACA 58.483 50.0 2.88 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2326 0.172578 GGGGCGTGGAAAATTGCTAC 59.827 55.000 0.00 0.00 0.00 3.58 R
1870 2340 0.243636 GTGTTTGATTCCAAGGGGCG 59.756 55.000 0.00 0.00 33.23 6.13 R
2555 3100 1.541588 GGGAAGTTCTGGCACAACATC 59.458 52.381 8.35 5.45 38.70 3.06 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
147 161 9.816354 AAATTAAGTACTGAAACAATTTGCTGT 57.184 25.926 0.00 0.00 0.00 4.40
160 174 0.836606 TTGCTGTCAGACCCTCACAA 59.163 50.000 3.32 0.00 0.00 3.33
211 225 4.843220 AAAAATCAAGTGCCTGTCAGAG 57.157 40.909 0.00 0.00 0.00 3.35
214 228 0.972134 TCAAGTGCCTGTCAGAGAGG 59.028 55.000 9.41 9.41 0.00 3.69
216 230 0.178921 AAGTGCCTGTCAGAGAGGGA 60.179 55.000 15.42 9.88 0.00 4.20
217 231 0.614415 AGTGCCTGTCAGAGAGGGAG 60.614 60.000 15.42 0.00 30.44 4.30
218 232 1.305633 TGCCTGTCAGAGAGGGAGG 60.306 63.158 15.42 0.00 0.00 4.30
219 233 2.063378 GCCTGTCAGAGAGGGAGGG 61.063 68.421 15.42 0.00 0.00 4.30
220 234 1.390125 CCTGTCAGAGAGGGAGGGT 59.610 63.158 5.64 0.00 0.00 4.34
221 235 0.631753 CCTGTCAGAGAGGGAGGGTA 59.368 60.000 5.64 0.00 0.00 3.69
224 238 1.717077 TGTCAGAGAGGGAGGGTAAGT 59.283 52.381 0.00 0.00 0.00 2.24
226 240 1.717077 TCAGAGAGGGAGGGTAAGTGT 59.283 52.381 0.00 0.00 0.00 3.55
227 241 2.104170 CAGAGAGGGAGGGTAAGTGTC 58.896 57.143 0.00 0.00 0.00 3.67
228 242 2.004589 AGAGAGGGAGGGTAAGTGTCT 58.995 52.381 0.00 0.00 0.00 3.41
229 243 2.384029 AGAGAGGGAGGGTAAGTGTCTT 59.616 50.000 0.00 0.00 0.00 3.01
230 244 2.761767 GAGAGGGAGGGTAAGTGTCTTC 59.238 54.545 0.00 0.00 0.00 2.87
231 245 2.384029 AGAGGGAGGGTAAGTGTCTTCT 59.616 50.000 0.00 0.00 0.00 2.85
232 246 2.498078 GAGGGAGGGTAAGTGTCTTCTG 59.502 54.545 0.00 0.00 0.00 3.02
233 247 2.111972 AGGGAGGGTAAGTGTCTTCTGA 59.888 50.000 0.00 0.00 0.00 3.27
234 248 2.904434 GGGAGGGTAAGTGTCTTCTGAA 59.096 50.000 0.00 0.00 0.00 3.02
235 249 3.519913 GGGAGGGTAAGTGTCTTCTGAAT 59.480 47.826 0.00 0.00 0.00 2.57
283 297 9.905171 TCGATCTTCTGAATATCATCTACAAAG 57.095 33.333 13.91 0.00 0.00 2.77
304 350 0.980231 ACATGTCAGAGAGGGAGGGC 60.980 60.000 0.00 0.00 0.00 5.19
306 352 0.252881 ATGTCAGAGAGGGAGGGCAA 60.253 55.000 0.00 0.00 0.00 4.52
315 361 0.117340 AGGGAGGGCAAGTGTCTAGT 59.883 55.000 0.00 0.00 0.00 2.57
320 366 0.250513 GGGCAAGTGTCTAGTGAGGG 59.749 60.000 0.00 0.00 0.00 4.30
321 367 1.267121 GGCAAGTGTCTAGTGAGGGA 58.733 55.000 0.00 0.00 0.00 4.20
456 502 1.073125 CTCTCGCTCATCCTCCTCCTA 59.927 57.143 0.00 0.00 0.00 2.94
457 503 1.707989 TCTCGCTCATCCTCCTCCTAT 59.292 52.381 0.00 0.00 0.00 2.57
458 504 2.091541 CTCGCTCATCCTCCTCCTATC 58.908 57.143 0.00 0.00 0.00 2.08
471 525 2.625883 CCTCCTATCACCACCACCACTA 60.626 54.545 0.00 0.00 0.00 2.74
519 577 1.488390 ATGGCGGCTCAAATCCAATT 58.512 45.000 11.43 0.00 31.66 2.32
527 585 4.178540 GGCTCAAATCCAATTCACACATG 58.821 43.478 0.00 0.00 0.00 3.21
566 626 0.253610 GACGGAGAGACCAGAGGAGA 59.746 60.000 0.00 0.00 38.90 3.71
569 629 0.333312 GGAGAGACCAGAGGAGACCA 59.667 60.000 0.00 0.00 38.79 4.02
748 819 5.416083 CATTTAGACCTTCGGTGTCACATA 58.584 41.667 5.12 0.00 35.25 2.29
779 851 0.333312 ACCATTTCACCGGCCCAATA 59.667 50.000 0.00 0.00 0.00 1.90
871 945 0.801067 GCCGCGCCCTCGTATATAAG 60.801 60.000 0.00 0.00 38.14 1.73
900 974 2.970639 TCGCTCTCCGACCCTTTG 59.029 61.111 0.00 0.00 41.89 2.77
1009 1088 2.360350 CCGCAGCCATGGTGAGTT 60.360 61.111 14.67 0.00 32.22 3.01
1015 1094 1.004044 CAGCCATGGTGAGTTTCCTCT 59.996 52.381 14.67 0.00 38.61 3.69
1019 1098 1.065126 CATGGTGAGTTTCCTCTCCCC 60.065 57.143 8.00 0.00 46.39 4.81
1020 1099 1.192146 TGGTGAGTTTCCTCTCCCCG 61.192 60.000 8.00 0.00 46.39 5.73
1021 1100 0.903454 GGTGAGTTTCCTCTCCCCGA 60.903 60.000 0.00 0.00 42.89 5.14
1022 1101 0.246910 GTGAGTTTCCTCTCCCCGAC 59.753 60.000 0.00 0.00 38.61 4.79
1072 1152 2.779506 GATTGTCCTGGTTTCCGAACT 58.220 47.619 0.00 0.00 36.03 3.01
1092 1172 3.967987 ACTAGCCCAGATTCGGTAGATTT 59.032 43.478 0.00 0.00 34.80 2.17
1102 1182 6.313905 CAGATTCGGTAGATTTACAACAGCTT 59.686 38.462 0.00 0.00 0.00 3.74
1120 1200 1.940883 TTCGGCGCTCGGTAGAATGT 61.941 55.000 7.64 0.00 39.77 2.71
1191 1273 4.439974 GCTGTTAATCGGATGAAATTGCCA 60.440 41.667 0.00 0.00 0.00 4.92
1199 1281 2.560105 GGATGAAATTGCCATAGGAGCC 59.440 50.000 0.00 0.00 0.00 4.70
1215 1297 5.012328 AGGAGCCGTGTATTTCTCTTAAG 57.988 43.478 0.00 0.00 0.00 1.85
1219 1301 3.000022 GCCGTGTATTTCTCTTAAGTCGC 60.000 47.826 1.63 0.00 0.00 5.19
1386 1475 2.969262 ACGGATGGGTTGGTTTGAATTT 59.031 40.909 0.00 0.00 0.00 1.82
1394 1483 6.054295 TGGGTTGGTTTGAATTTTCATCTTG 58.946 36.000 0.00 0.00 37.00 3.02
1464 1559 4.546570 TGTTAGTCGAGTTGTCATCACTG 58.453 43.478 0.00 0.00 0.00 3.66
1613 2074 5.825593 TCCTGAAACCTATGGCTATAAGG 57.174 43.478 0.00 0.00 0.00 2.69
1632 2096 9.416794 CTATAAGGAATGAGTGACATGATGTAC 57.583 37.037 0.00 0.00 39.39 2.90
1660 2124 5.494341 TCCTACAGCCTATCTCTCTATGGAT 59.506 44.000 0.00 0.00 0.00 3.41
1675 2139 1.517238 TGGATTAGGGCTGGCATACA 58.483 50.000 2.88 0.00 0.00 2.29
1709 2173 5.061179 GCTAACTCAACCTGTCCTGTTTAA 58.939 41.667 0.00 0.00 0.00 1.52
1779 2248 4.081406 AGTTCAGCATAACATCTTTGGCA 58.919 39.130 4.30 0.00 0.00 4.92
1791 2260 4.699257 ACATCTTTGGCATGAGTTCTCTTC 59.301 41.667 0.00 0.00 0.00 2.87
1856 2326 2.472695 TTTGGACCCTCGTGATTCAG 57.527 50.000 0.00 0.00 0.00 3.02
1870 2340 5.088739 CGTGATTCAGTAGCAATTTTCCAC 58.911 41.667 0.00 0.00 0.00 4.02
1934 2466 9.034544 GCTATGAAGTTCTTTTTGTTTGTCATT 57.965 29.630 4.17 0.00 0.00 2.57
1941 2473 8.835439 AGTTCTTTTTGTTTGTCATTTGTTGTT 58.165 25.926 0.00 0.00 0.00 2.83
1942 2474 9.444534 GTTCTTTTTGTTTGTCATTTGTTGTTT 57.555 25.926 0.00 0.00 0.00 2.83
1967 2500 4.798882 TCCTGGTTGTTTATTCCTGTTGT 58.201 39.130 0.00 0.00 0.00 3.32
2216 2757 8.217111 TGTGGGCATATATCTTCTTTGATGTAA 58.783 33.333 0.00 0.00 0.00 2.41
2248 2789 2.169561 ACTTTGGAAATGTTGGCCGTTT 59.830 40.909 0.00 0.00 34.95 3.60
2249 2790 3.385111 ACTTTGGAAATGTTGGCCGTTTA 59.615 39.130 0.00 0.00 32.37 2.01
2251 2792 4.608948 TTGGAAATGTTGGCCGTTTATT 57.391 36.364 0.00 0.00 32.37 1.40
2253 2794 5.723672 TGGAAATGTTGGCCGTTTATTTA 57.276 34.783 0.00 0.00 32.37 1.40
2256 2797 6.160684 GGAAATGTTGGCCGTTTATTTACTT 58.839 36.000 0.00 0.00 32.37 2.24
2257 2798 6.090223 GGAAATGTTGGCCGTTTATTTACTTG 59.910 38.462 0.00 0.00 32.37 3.16
2258 2799 5.715434 ATGTTGGCCGTTTATTTACTTGT 57.285 34.783 0.00 0.00 0.00 3.16
2259 2800 5.517322 TGTTGGCCGTTTATTTACTTGTT 57.483 34.783 0.00 0.00 0.00 2.83
2260 2801 5.903810 TGTTGGCCGTTTATTTACTTGTTT 58.096 33.333 0.00 0.00 0.00 2.83
2261 2802 5.978322 TGTTGGCCGTTTATTTACTTGTTTC 59.022 36.000 0.00 0.00 0.00 2.78
2264 2805 5.299782 TGGCCGTTTATTTACTTGTTTCTGT 59.700 36.000 0.00 0.00 0.00 3.41
2266 2807 6.143278 GGCCGTTTATTTACTTGTTTCTGTTG 59.857 38.462 0.00 0.00 0.00 3.33
2293 2836 7.707624 TTGCATCTGGATGTTTATTCTTCTT 57.292 32.000 11.52 0.00 40.80 2.52
2403 2947 2.106166 CCTGCATCCCTCTTATCTGCTT 59.894 50.000 0.00 0.00 34.02 3.91
2405 2949 3.548770 TGCATCCCTCTTATCTGCTTTG 58.451 45.455 0.00 0.00 34.02 2.77
2433 2977 9.888878 CATTTCCTTGCTATATTCTGTTATGTG 57.111 33.333 0.00 0.00 0.00 3.21
2451 2995 7.710475 TGTTATGTGTATGTATCTGACACCATG 59.290 37.037 2.22 0.00 42.17 3.66
2537 3081 5.534207 ACATCTCTCTTCTAAGCTGATGG 57.466 43.478 16.21 0.00 34.38 3.51
2555 3100 6.428159 GCTGATGGTATCCTGTTATGTTTAGG 59.572 42.308 0.00 0.00 0.00 2.69
3496 4175 8.405418 GATTAAATAAATCCTAACACTCCCCC 57.595 38.462 0.00 0.00 38.47 5.40
3497 4176 7.533923 TTAAATAAATCCTAACACTCCCCCT 57.466 36.000 0.00 0.00 0.00 4.79
3498 4177 8.641498 TTAAATAAATCCTAACACTCCCCCTA 57.359 34.615 0.00 0.00 0.00 3.53
3499 4178 7.533923 AAATAAATCCTAACACTCCCCCTAA 57.466 36.000 0.00 0.00 0.00 2.69
3500 4179 7.723109 AATAAATCCTAACACTCCCCCTAAT 57.277 36.000 0.00 0.00 0.00 1.73
3501 4180 5.648330 AAATCCTAACACTCCCCCTAATC 57.352 43.478 0.00 0.00 0.00 1.75
3502 4181 3.788116 TCCTAACACTCCCCCTAATCA 57.212 47.619 0.00 0.00 0.00 2.57
3503 4182 4.083080 TCCTAACACTCCCCCTAATCAA 57.917 45.455 0.00 0.00 0.00 2.57
3504 4183 4.641868 TCCTAACACTCCCCCTAATCAAT 58.358 43.478 0.00 0.00 0.00 2.57
3505 4184 4.412199 TCCTAACACTCCCCCTAATCAATG 59.588 45.833 0.00 0.00 0.00 2.82
3506 4185 2.736670 ACACTCCCCCTAATCAATGC 57.263 50.000 0.00 0.00 0.00 3.56
3507 4186 2.208872 ACACTCCCCCTAATCAATGCT 58.791 47.619 0.00 0.00 0.00 3.79
3508 4187 2.582636 ACACTCCCCCTAATCAATGCTT 59.417 45.455 0.00 0.00 0.00 3.91
3509 4188 2.954318 CACTCCCCCTAATCAATGCTTG 59.046 50.000 0.00 0.00 0.00 4.01
3510 4189 2.582636 ACTCCCCCTAATCAATGCTTGT 59.417 45.455 0.00 0.00 0.00 3.16
3511 4190 3.011708 ACTCCCCCTAATCAATGCTTGTT 59.988 43.478 0.00 0.00 0.00 2.83
3512 4191 4.026052 CTCCCCCTAATCAATGCTTGTTT 58.974 43.478 0.00 0.00 0.00 2.83
3513 4192 3.768757 TCCCCCTAATCAATGCTTGTTTG 59.231 43.478 0.00 0.00 0.00 2.93
3514 4193 3.515104 CCCCCTAATCAATGCTTGTTTGT 59.485 43.478 0.00 0.00 0.00 2.83
3515 4194 4.497300 CCCCTAATCAATGCTTGTTTGTG 58.503 43.478 0.00 0.00 0.00 3.33
3516 4195 3.928375 CCCTAATCAATGCTTGTTTGTGC 59.072 43.478 0.00 0.00 0.00 4.57
3517 4196 4.558178 CCTAATCAATGCTTGTTTGTGCA 58.442 39.130 0.00 0.00 43.67 4.57
3518 4197 4.624024 CCTAATCAATGCTTGTTTGTGCAG 59.376 41.667 0.00 0.00 42.74 4.41
3519 4198 3.738830 ATCAATGCTTGTTTGTGCAGT 57.261 38.095 0.00 0.00 42.74 4.40
3520 4199 4.852134 ATCAATGCTTGTTTGTGCAGTA 57.148 36.364 0.00 0.00 42.74 2.74
3521 4200 4.852134 TCAATGCTTGTTTGTGCAGTAT 57.148 36.364 0.00 0.00 42.74 2.12
3522 4201 5.199024 TCAATGCTTGTTTGTGCAGTATT 57.801 34.783 0.00 0.00 42.74 1.89
3523 4202 6.324561 TCAATGCTTGTTTGTGCAGTATTA 57.675 33.333 0.00 0.00 42.74 0.98
3524 4203 6.923012 TCAATGCTTGTTTGTGCAGTATTAT 58.077 32.000 0.00 0.00 42.74 1.28
3525 4204 7.028962 TCAATGCTTGTTTGTGCAGTATTATC 58.971 34.615 0.00 0.00 42.74 1.75
3526 4205 5.956068 TGCTTGTTTGTGCAGTATTATCA 57.044 34.783 0.00 0.00 34.84 2.15
3527 4206 6.513806 TGCTTGTTTGTGCAGTATTATCAT 57.486 33.333 0.00 0.00 34.84 2.45
3528 4207 6.554419 TGCTTGTTTGTGCAGTATTATCATC 58.446 36.000 0.00 0.00 34.84 2.92
3529 4208 6.375174 TGCTTGTTTGTGCAGTATTATCATCT 59.625 34.615 0.00 0.00 34.84 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.730296 ACCAGAATGATTCCTATCCTACG 57.270 43.478 0.75 0.00 39.69 3.51
147 161 4.673968 ACTGTACTATTGTGAGGGTCTGA 58.326 43.478 0.00 0.00 0.00 3.27
160 174 7.549488 GCTGGTTTAGTTCATCAACTGTACTAT 59.451 37.037 0.00 0.00 43.17 2.12
205 219 2.104170 CACTTACCCTCCCTCTCTGAC 58.896 57.143 0.00 0.00 0.00 3.51
206 220 1.717077 ACACTTACCCTCCCTCTCTGA 59.283 52.381 0.00 0.00 0.00 3.27
207 221 2.104170 GACACTTACCCTCCCTCTCTG 58.896 57.143 0.00 0.00 0.00 3.35
208 222 2.004589 AGACACTTACCCTCCCTCTCT 58.995 52.381 0.00 0.00 0.00 3.10
209 223 2.535836 AGACACTTACCCTCCCTCTC 57.464 55.000 0.00 0.00 0.00 3.20
210 224 2.384029 AGAAGACACTTACCCTCCCTCT 59.616 50.000 0.00 0.00 0.00 3.69
211 225 2.498078 CAGAAGACACTTACCCTCCCTC 59.502 54.545 0.00 0.00 0.00 4.30
214 228 4.828072 ATTCAGAAGACACTTACCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
216 230 7.682787 ATGATATTCAGAAGACACTTACCCT 57.317 36.000 0.00 0.00 0.00 4.34
217 231 8.738645 AAATGATATTCAGAAGACACTTACCC 57.261 34.615 0.00 0.00 0.00 3.69
221 235 9.678260 AGCTAAAATGATATTCAGAAGACACTT 57.322 29.630 0.00 0.00 0.00 3.16
224 238 9.453572 AACAGCTAAAATGATATTCAGAAGACA 57.546 29.630 0.00 0.00 0.00 3.41
226 240 8.400947 GCAACAGCTAAAATGATATTCAGAAGA 58.599 33.333 0.00 0.00 0.00 2.87
227 241 8.186163 TGCAACAGCTAAAATGATATTCAGAAG 58.814 33.333 0.00 0.00 0.00 2.85
228 242 8.054152 TGCAACAGCTAAAATGATATTCAGAA 57.946 30.769 0.00 0.00 0.00 3.02
229 243 7.628769 TGCAACAGCTAAAATGATATTCAGA 57.371 32.000 0.00 0.00 0.00 3.27
230 244 8.132995 TGATGCAACAGCTAAAATGATATTCAG 58.867 33.333 0.00 0.00 0.00 3.02
231 245 7.998580 TGATGCAACAGCTAAAATGATATTCA 58.001 30.769 0.00 0.00 0.00 2.57
232 246 9.125906 GATGATGCAACAGCTAAAATGATATTC 57.874 33.333 4.82 0.00 0.00 1.75
233 247 7.806487 CGATGATGCAACAGCTAAAATGATATT 59.194 33.333 10.59 0.00 0.00 1.28
234 248 7.173735 TCGATGATGCAACAGCTAAAATGATAT 59.826 33.333 10.59 0.00 0.00 1.63
235 249 6.482973 TCGATGATGCAACAGCTAAAATGATA 59.517 34.615 10.59 0.00 0.00 2.15
283 297 2.035632 CCCTCCCTCTCTGACATGTAC 58.964 57.143 0.00 0.00 0.00 2.90
304 350 1.827969 CCCTCCCTCACTAGACACTTG 59.172 57.143 0.00 0.00 0.00 3.16
306 352 1.006162 GTCCCTCCCTCACTAGACACT 59.994 57.143 0.00 0.00 0.00 3.55
315 361 2.450243 GTCCAGGTCCCTCCCTCA 59.550 66.667 0.00 0.00 36.75 3.86
320 366 1.677637 GGATGTCGTCCAGGTCCCTC 61.678 65.000 6.19 0.00 46.96 4.30
321 367 1.686110 GGATGTCGTCCAGGTCCCT 60.686 63.158 6.19 0.00 46.96 4.20
456 502 2.239654 CAGGAATAGTGGTGGTGGTGAT 59.760 50.000 0.00 0.00 0.00 3.06
457 503 1.628340 CAGGAATAGTGGTGGTGGTGA 59.372 52.381 0.00 0.00 0.00 4.02
458 504 1.351017 ACAGGAATAGTGGTGGTGGTG 59.649 52.381 0.00 0.00 0.00 4.17
471 525 4.104738 TCCTTTTCTTGGAGTGACAGGAAT 59.895 41.667 0.00 0.00 36.52 3.01
519 577 4.030216 TGCCTAGTAGGATTCATGTGTGA 58.970 43.478 21.02 0.00 37.67 3.58
527 585 2.891580 TCGATGGTGCCTAGTAGGATTC 59.108 50.000 21.02 8.54 37.67 2.52
537 595 2.362503 TCTCCGTCGATGGTGCCT 60.363 61.111 22.88 0.00 0.00 4.75
566 626 1.227853 GGTTGCGAGGTGAGTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
569 629 1.227853 GGTGGTTGCGAGGTGAGTT 60.228 57.895 0.00 0.00 0.00 3.01
887 961 1.002087 GAAAGCTCAAAGGGTCGGAGA 59.998 52.381 0.00 0.00 0.00 3.71
1009 1088 0.631753 AGATCAGTCGGGGAGAGGAA 59.368 55.000 0.00 0.00 0.00 3.36
1015 1094 1.144503 GGTACCTAGATCAGTCGGGGA 59.855 57.143 4.06 0.00 0.00 4.81
1019 1098 1.264557 CGCAGGTACCTAGATCAGTCG 59.735 57.143 15.80 5.71 0.00 4.18
1072 1152 4.897076 TGTAAATCTACCGAATCTGGGCTA 59.103 41.667 0.00 0.00 0.00 3.93
1102 1182 1.940883 AACATTCTACCGAGCGCCGA 61.941 55.000 17.96 0.22 41.76 5.54
1191 1273 6.324254 ACTTAAGAGAAATACACGGCTCCTAT 59.676 38.462 10.09 0.00 0.00 2.57
1199 1281 4.031426 GGTGCGACTTAAGAGAAATACACG 59.969 45.833 10.09 0.00 0.00 4.49
1215 1297 2.173382 GCATCAACACGGTGCGAC 59.827 61.111 8.30 0.00 0.00 5.19
1219 1301 1.208358 CAGCAGCATCAACACGGTG 59.792 57.895 6.58 6.58 0.00 4.94
1386 1475 2.806434 CCAATGGGGTCACAAGATGAA 58.194 47.619 0.00 0.00 39.72 2.57
1421 1510 9.522804 CTAACAAGACTGGAGACTAATGTATTC 57.477 37.037 0.00 0.00 0.00 1.75
1464 1559 4.025040 TGCATATCTGGGATCAATCACC 57.975 45.455 0.00 0.00 0.00 4.02
1613 2074 4.130118 GGGGTACATCATGTCACTCATTC 58.870 47.826 0.00 0.00 34.09 2.67
1632 2096 1.431243 AGAGATAGGCTGTAGGAGGGG 59.569 57.143 0.00 0.00 0.00 4.79
1660 2124 2.889170 TGTTTGTATGCCAGCCCTAA 57.111 45.000 0.00 0.00 0.00 2.69
1675 2139 5.182001 CAGGTTGAGTTAGCTAGCAATGTTT 59.818 40.000 18.83 0.00 0.00 2.83
1709 2173 8.147244 ACAAAAGGGAGTACATTACATACTCT 57.853 34.615 10.97 0.00 45.31 3.24
1856 2326 0.172578 GGGGCGTGGAAAATTGCTAC 59.827 55.000 0.00 0.00 0.00 3.58
1870 2340 0.243636 GTGTTTGATTCCAAGGGGCG 59.756 55.000 0.00 0.00 33.23 6.13
1934 2466 9.535878 GAATAAACAACCAGGAATAAACAACAA 57.464 29.630 0.00 0.00 0.00 2.83
1941 2473 7.507616 ACAACAGGAATAAACAACCAGGAATAA 59.492 33.333 0.00 0.00 0.00 1.40
1942 2474 7.007723 ACAACAGGAATAAACAACCAGGAATA 58.992 34.615 0.00 0.00 0.00 1.75
1976 2512 5.335269 CGTTCACCTACAAAAATGCCATACA 60.335 40.000 0.00 0.00 0.00 2.29
2216 2757 7.763985 CCAACATTTCCAAAGTAACTTGAGTTT 59.236 33.333 1.20 0.00 39.31 2.66
2248 2789 7.261325 TGCAAAGCAACAGAAACAAGTAAATA 58.739 30.769 0.00 0.00 34.76 1.40
2249 2790 6.105333 TGCAAAGCAACAGAAACAAGTAAAT 58.895 32.000 0.00 0.00 34.76 1.40
2251 2792 5.065704 TGCAAAGCAACAGAAACAAGTAA 57.934 34.783 0.00 0.00 34.76 2.24
2253 2794 3.591196 TGCAAAGCAACAGAAACAAGT 57.409 38.095 0.00 0.00 34.76 3.16
2256 2797 3.491276 CCAGATGCAAAGCAACAGAAACA 60.491 43.478 0.00 0.00 43.62 2.83
2257 2798 3.054878 CCAGATGCAAAGCAACAGAAAC 58.945 45.455 0.00 0.00 43.62 2.78
2258 2799 2.957680 TCCAGATGCAAAGCAACAGAAA 59.042 40.909 0.00 0.00 43.62 2.52
2259 2800 2.585330 TCCAGATGCAAAGCAACAGAA 58.415 42.857 0.00 0.00 43.62 3.02
2260 2801 2.275134 TCCAGATGCAAAGCAACAGA 57.725 45.000 0.00 0.00 43.62 3.41
2261 2802 2.230508 ACATCCAGATGCAAAGCAACAG 59.769 45.455 7.56 0.00 43.62 3.16
2264 2805 5.664294 ATAAACATCCAGATGCAAAGCAA 57.336 34.783 7.56 0.00 43.62 3.91
2266 2807 5.899299 AGAATAAACATCCAGATGCAAAGC 58.101 37.500 7.56 0.00 42.39 3.51
2293 2836 3.259374 TGTTGTCTTGGCCTGAAACAAAA 59.741 39.130 3.32 1.95 32.17 2.44
2403 2947 5.893255 ACAGAATATAGCAAGGAAATGGCAA 59.107 36.000 0.00 0.00 0.00 4.52
2405 2949 6.396829 AACAGAATATAGCAAGGAAATGGC 57.603 37.500 0.00 0.00 0.00 4.40
2433 2977 8.668510 AAGAAATCATGGTGTCAGATACATAC 57.331 34.615 0.00 0.00 41.10 2.39
2436 2980 6.942005 ACAAAGAAATCATGGTGTCAGATACA 59.058 34.615 0.00 0.00 35.06 2.29
2451 2995 6.426937 TGCACCTCTGTAGTAACAAAGAAATC 59.573 38.462 0.00 0.00 34.49 2.17
2537 3081 8.612619 CACAACATCCTAAACATAACAGGATAC 58.387 37.037 2.17 0.00 45.44 2.24
2555 3100 1.541588 GGGAAGTTCTGGCACAACATC 59.458 52.381 8.35 5.45 38.70 3.06
3502 4181 6.923012 TGATAATACTGCACAAACAAGCATT 58.077 32.000 0.00 0.00 40.42 3.56
3503 4182 6.513806 TGATAATACTGCACAAACAAGCAT 57.486 33.333 0.00 0.00 40.42 3.79
3504 4183 5.956068 TGATAATACTGCACAAACAAGCA 57.044 34.783 0.00 0.00 39.25 3.91
3505 4184 6.789262 AGATGATAATACTGCACAAACAAGC 58.211 36.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.