Multiple sequence alignment - TraesCS3A01G216000

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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 TraesCS3A01G216000 chr3A 100.000 3211 0 0 1 3211 393367477 393370687 0.000000e+00 5930
1 TraesCS3A01G216000 chr3A 85.779 443 55 5 2692 3126 460759134 460758692 2.260000e-126 462
2 TraesCS3A01G216000 chr3A 97.802 91 2 0 3121 3211 606449774 606449684 1.190000e-34 158
3 TraesCS3A01G216000 chr3D 90.947 1215 79 6 1 1201 295288659 295289856 0.000000e+00 1605
4 TraesCS3A01G216000 chr3D 89.926 943 76 7 1728 2652 295289852 295290793 0.000000e+00 1197
5 TraesCS3A01G216000 chr3D 86.767 529 64 6 1202 1727 332808908 332808383 4.620000e-163 584
6 TraesCS3A01G216000 chr3D 85.551 263 29 5 2430 2683 594953137 594953399 1.900000e-67 267
7 TraesCS3A01G216000 chr3D 85.019 267 31 5 943 1201 52845164 52844899 2.460000e-66 263
8 TraesCS3A01G216000 chr3D 100.000 88 0 0 3121 3208 295291176 295291263 2.560000e-36 163
9 TraesCS3A01G216000 chr3D 97.802 91 2 0 3121 3211 342120729 342120819 1.190000e-34 158
10 TraesCS3A01G216000 chr3B 87.094 1046 90 13 1728 2738 389493934 389494969 0.000000e+00 1142
11 TraesCS3A01G216000 chr3B 91.224 433 37 1 770 1201 389493506 389493938 3.570000e-164 588
12 TraesCS3A01G216000 chr3B 88.400 500 29 10 303 774 389485536 389486034 2.780000e-160 575
13 TraesCS3A01G216000 chr3B 93.624 298 16 2 1 296 389485068 389485364 2.940000e-120 442
14 TraesCS3A01G216000 chr3B 87.347 245 29 2 958 1201 521411093 521411336 2.440000e-71 279
15 TraesCS3A01G216000 chr4D 79.435 992 141 37 1728 2689 428643232 428642274 0.000000e+00 643
16 TraesCS3A01G216000 chr4D 88.631 431 47 2 2692 3122 436383353 436383781 1.020000e-144 523
17 TraesCS3A01G216000 chr4D 88.426 432 48 2 2692 3122 80917964 80917534 1.320000e-143 520
18 TraesCS3A01G216000 chr4D 83.060 549 64 6 2692 3211 401957061 401956513 3.750000e-129 472
19 TraesCS3A01G216000 chr4D 81.414 495 46 19 699 1176 428643706 428643241 2.350000e-96 363
20 TraesCS3A01G216000 chr4D 86.415 265 29 3 2430 2689 108844005 108843743 1.890000e-72 283
21 TraesCS3A01G216000 chr4D 85.214 257 29 5 952 1201 392722119 392722373 4.110000e-64 255
22 TraesCS3A01G216000 chr4D 83.265 245 39 2 958 1201 108844872 108844629 1.160000e-54 224
23 TraesCS3A01G216000 chr4D 85.455 220 25 3 2430 2642 488850356 488850137 4.170000e-54 222
24 TraesCS3A01G216000 chr4D 83.265 245 37 4 958 1201 488851200 488850959 4.170000e-54 222
25 TraesCS3A01G216000 chr4D 98.901 91 1 0 3121 3211 80917508 80917418 2.560000e-36 163
26 TraesCS3A01G216000 chr6D 88.324 531 56 6 1202 1728 75742393 75742921 1.630000e-177 632
27 TraesCS3A01G216000 chr6D 86.939 245 30 2 958 1201 45729615 45729372 1.130000e-69 274
28 TraesCS3A01G216000 chr6D 84.791 263 32 3 2433 2689 45728726 45728466 1.140000e-64 257
29 TraesCS3A01G216000 chr6D 97.802 91 2 0 3121 3211 388094318 388094228 1.190000e-34 158
30 TraesCS3A01G216000 chr7D 88.136 531 56 7 1202 1727 276518368 276517840 2.720000e-175 625
31 TraesCS3A01G216000 chr7D 85.955 534 66 9 1200 1728 334895975 334896504 2.160000e-156 562
32 TraesCS3A01G216000 chr7D 84.146 328 42 10 882 1201 630175605 630175280 3.110000e-80 309
33 TraesCS3A01G216000 chr2D 87.828 534 62 3 1199 1729 315281226 315280693 9.780000e-175 623
34 TraesCS3A01G216000 chr2D 85.294 544 70 9 1202 1738 288393345 288392805 1.300000e-153 553
35 TraesCS3A01G216000 chr2D 84.195 329 41 11 882 1201 573448160 573447834 3.110000e-80 309
36 TraesCS3A01G216000 chr2D 85.393 267 32 3 2430 2689 380679891 380679625 1.470000e-68 270
37 TraesCS3A01G216000 chr4A 90.909 429 39 0 2694 3122 345852455 345852883 7.720000e-161 577
38 TraesCS3A01G216000 chr4A 82.286 350 55 7 1728 2072 628884485 628884138 2.420000e-76 296
39 TraesCS3A01G216000 chr5A 85.526 532 70 6 1205 1731 167366019 167365490 1.680000e-152 549
40 TraesCS3A01G216000 chr5A 87.850 214 23 3 2322 2533 78441966 78442178 6.880000e-62 248
41 TraesCS3A01G216000 chr6A 85.171 526 72 5 1207 1728 260132838 260133361 4.710000e-148 534
42 TraesCS3A01G216000 chr6A 82.815 547 66 11 2692 3211 506635367 506634822 6.270000e-127 464
43 TraesCS3A01G216000 chr6A 85.985 264 30 3 2433 2689 117535213 117534950 3.160000e-70 276
44 TraesCS3A01G216000 chr6A 85.393 267 32 3 2430 2689 116691826 116691560 1.470000e-68 270
45 TraesCS3A01G216000 chr6A 84.127 252 35 4 956 1203 117536159 117535909 4.140000e-59 239
46 TraesCS3A01G216000 chr6A 78.947 342 54 14 1728 2069 71099644 71099967 1.940000e-52 217
47 TraesCS3A01G216000 chr5D 85.122 531 70 8 1202 1727 183543382 183543908 4.710000e-148 534
48 TraesCS3A01G216000 chr5D 83.161 386 47 10 2322 2689 391327852 391328237 1.430000e-88 337
49 TraesCS3A01G216000 chr5D 78.393 560 85 26 1728 2263 282368727 282368180 6.640000e-87 331
50 TraesCS3A01G216000 chr5D 81.313 396 51 15 821 1201 305759357 305759744 1.870000e-77 300
51 TraesCS3A01G216000 chr5D 81.186 388 55 14 821 1201 391326926 391327302 2.420000e-76 296
52 TraesCS3A01G216000 chr5D 86.508 252 28 2 2438 2683 406909970 406909719 4.080000e-69 272
53 TraesCS3A01G216000 chr5D 85.603 257 28 5 952 1201 356116802 356117056 8.840000e-66 261
54 TraesCS3A01G216000 chr5D 86.000 250 28 3 959 1201 422773080 422772831 8.840000e-66 261
55 TraesCS3A01G216000 chr5D 97.802 91 2 0 3121 3211 259449671 259449581 1.190000e-34 158
56 TraesCS3A01G216000 chr1B 88.684 433 47 2 2693 3123 165161571 165161139 7.890000e-146 527
57 TraesCS3A01G216000 chr1B 87.755 245 28 2 958 1201 539847265 539847508 5.240000e-73 285
58 TraesCS3A01G216000 chr1B 78.405 301 58 4 1728 2024 438690500 438690797 4.230000e-44 189
59 TraesCS3A01G216000 chr1D 88.167 431 51 0 2692 3122 160958390 160957960 6.140000e-142 514
60 TraesCS3A01G216000 chr1D 88.259 247 27 2 958 1203 392707296 392707541 8.710000e-76 294
61 TraesCS3A01G216000 chr1D 85.824 261 30 3 2430 2683 42895445 42895705 1.470000e-68 270
62 TraesCS3A01G216000 chr1D 85.425 247 34 2 958 1203 42894561 42894806 4.110000e-64 255
63 TraesCS3A01G216000 chr1D 84.490 245 36 2 958 1201 4306176 4306419 1.150000e-59 241
64 TraesCS3A01G216000 chr1D 84.490 245 36 2 958 1201 7183156 7182913 1.150000e-59 241
65 TraesCS3A01G216000 chr1D 97.802 91 2 0 3121 3211 160957934 160957844 1.190000e-34 158
66 TraesCS3A01G216000 chr4B 87.327 434 51 4 2692 3122 538275364 538275796 8.000000e-136 494
67 TraesCS3A01G216000 chr4B 84.098 327 44 8 882 1201 187441095 187440770 3.110000e-80 309
68 TraesCS3A01G216000 chr2A 83.729 547 61 8 2692 3211 229652641 229652096 2.880000e-135 492
69 TraesCS3A01G216000 chr2A 86.517 267 29 3 2430 2689 38505554 38505820 1.460000e-73 287
70 TraesCS3A01G216000 chr5B 90.374 374 30 4 2317 2689 647903389 647903757 1.340000e-133 486
71 TraesCS3A01G216000 chr5B 81.542 428 54 13 2285 2689 39754933 39754508 2.390000e-86 329
72 TraesCS3A01G216000 chr5B 82.908 392 42 13 2322 2689 461486844 461487234 2.390000e-86 329
73 TraesCS3A01G216000 chr5B 80.660 424 60 14 2285 2687 39786547 39786125 3.110000e-80 309
74 TraesCS3A01G216000 chr5B 77.020 557 101 20 1728 2263 461486297 461486847 8.710000e-76 294
75 TraesCS3A01G216000 chr5B 86.142 267 30 3 2430 2689 418360719 418360985 6.780000e-72 281
76 TraesCS3A01G216000 chr5B 78.161 435 67 17 1840 2263 39755828 39755411 5.320000e-63 252
77 TraesCS3A01G216000 chr5B 81.169 308 50 5 882 1186 39812621 39812319 1.150000e-59 241
78 TraesCS3A01G216000 chr7B 81.671 371 61 5 1728 2092 527024003 527024372 5.210000e-78 302
79 TraesCS3A01G216000 chr7B 86.939 245 30 2 958 1201 9311653 9311896 1.130000e-69 274
80 TraesCS3A01G216000 chr7A 82.421 347 54 6 1728 2069 658703738 658704082 2.420000e-76 296
81 TraesCS3A01G216000 chr7A 82.000 350 56 7 1728 2072 576406326 576405979 1.130000e-74 291
82 TraesCS3A01G216000 chr1A 80.779 385 45 18 830 1201 13811093 13811461 1.130000e-69 274
83 TraesCS3A01G216000 chr1A 80.729 384 47 15 830 1201 20823628 20823996 1.130000e-69 274
84 TraesCS3A01G216000 chr1A 80.779 385 45 17 830 1201 34340288 34339920 1.130000e-69 274
85 TraesCS3A01G216000 chr1A 86.166 253 29 2 2437 2683 571999618 571999870 5.280000e-68 268
86 TraesCS3A01G216000 chr1A 77.620 353 48 12 2359 2682 542354414 542354764 5.470000e-43 185
87 TraesCS3A01G216000 chr1A 74.203 345 75 10 1732 2076 518146933 518146603 7.230000e-27 132
88 TraesCS3A01G216000 chr2B 82.450 302 46 5 1728 2024 629731233 629731532 1.140000e-64 257
89 TraesCS3A01G216000 chr2B 97.802 91 2 0 3121 3211 291566048 291565958 1.190000e-34 158


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 TraesCS3A01G216000 chr3A 393367477 393370687 3210 False 5930.000000 5930 100.000000 1 3211 1 chr3A.!!$F1 3210
1 TraesCS3A01G216000 chr3D 295288659 295291263 2604 False 988.333333 1605 93.624333 1 3208 3 chr3D.!!$F3 3207
2 TraesCS3A01G216000 chr3D 332808383 332808908 525 True 584.000000 584 86.767000 1202 1727 1 chr3D.!!$R2 525
3 TraesCS3A01G216000 chr3B 389493506 389494969 1463 False 865.000000 1142 89.159000 770 2738 2 chr3B.!!$F3 1968
4 TraesCS3A01G216000 chr3B 389485068 389486034 966 False 508.500000 575 91.012000 1 774 2 chr3B.!!$F2 773
5 TraesCS3A01G216000 chr4D 428642274 428643706 1432 True 503.000000 643 80.424500 699 2689 2 chr4D.!!$R4 1990
6 TraesCS3A01G216000 chr4D 401956513 401957061 548 True 472.000000 472 83.060000 2692 3211 1 chr4D.!!$R1 519
7 TraesCS3A01G216000 chr4D 80917418 80917964 546 True 341.500000 520 93.663500 2692 3211 2 chr4D.!!$R2 519
8 TraesCS3A01G216000 chr4D 108843743 108844872 1129 True 253.500000 283 84.840000 958 2689 2 chr4D.!!$R3 1731
9 TraesCS3A01G216000 chr4D 488850137 488851200 1063 True 222.000000 222 84.360000 958 2642 2 chr4D.!!$R5 1684
10 TraesCS3A01G216000 chr6D 75742393 75742921 528 False 632.000000 632 88.324000 1202 1728 1 chr6D.!!$F1 526
11 TraesCS3A01G216000 chr6D 45728466 45729615 1149 True 265.500000 274 85.865000 958 2689 2 chr6D.!!$R2 1731
12 TraesCS3A01G216000 chr7D 276517840 276518368 528 True 625.000000 625 88.136000 1202 1727 1 chr7D.!!$R1 525
13 TraesCS3A01G216000 chr7D 334895975 334896504 529 False 562.000000 562 85.955000 1200 1728 1 chr7D.!!$F1 528
14 TraesCS3A01G216000 chr2D 315280693 315281226 533 True 623.000000 623 87.828000 1199 1729 1 chr2D.!!$R2 530
15 TraesCS3A01G216000 chr2D 288392805 288393345 540 True 553.000000 553 85.294000 1202 1738 1 chr2D.!!$R1 536
16 TraesCS3A01G216000 chr5A 167365490 167366019 529 True 549.000000 549 85.526000 1205 1731 1 chr5A.!!$R1 526
17 TraesCS3A01G216000 chr6A 260132838 260133361 523 False 534.000000 534 85.171000 1207 1728 1 chr6A.!!$F2 521
18 TraesCS3A01G216000 chr6A 506634822 506635367 545 True 464.000000 464 82.815000 2692 3211 1 chr6A.!!$R2 519
19 TraesCS3A01G216000 chr6A 117534950 117536159 1209 True 257.500000 276 85.056000 956 2689 2 chr6A.!!$R3 1733
20 TraesCS3A01G216000 chr5D 183543382 183543908 526 False 534.000000 534 85.122000 1202 1727 1 chr5D.!!$F1 525
21 TraesCS3A01G216000 chr5D 282368180 282368727 547 True 331.000000 331 78.393000 1728 2263 1 chr5D.!!$R2 535
22 TraesCS3A01G216000 chr5D 391326926 391328237 1311 False 316.500000 337 82.173500 821 2689 2 chr5D.!!$F4 1868
23 TraesCS3A01G216000 chr1D 160957844 160958390 546 True 336.000000 514 92.984500 2692 3211 2 chr1D.!!$R2 519
24 TraesCS3A01G216000 chr1D 42894561 42895705 1144 False 262.500000 270 85.624500 958 2683 2 chr1D.!!$F3 1725
25 TraesCS3A01G216000 chr2A 229652096 229652641 545 True 492.000000 492 83.729000 2692 3211 1 chr2A.!!$R1 519
26 TraesCS3A01G216000 chr5B 461486297 461487234 937 False 311.500000 329 79.964000 1728 2689 2 chr5B.!!$F3 961
27 TraesCS3A01G216000 chr5B 39754508 39755828 1320 True 290.500000 329 79.851500 1840 2689 2 chr5B.!!$R3 849

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
500 681 0.178973 TTCACCACTCCCTCTCGACA 60.179 55.0 0.0 0.0 0.0 4.35 F
1762 2032 0.107456 GATCCTGCCCATCGACATGT 59.893 55.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2145 0.667487 CGTCATCGTCTTGGTGCACT 60.667 55.0 17.98 0.0 0.0 4.40 R
2965 3978 0.107831 CCACGGGTTGAAGTCTCCAA 59.892 55.0 0.00 0.0 0.0 3.53 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
59 60 0.884704 CTGGTCGACACCCAACCTTG 60.885 60.000 18.91 0.00 42.99 3.61
85 86 7.729431 GGGAGAAGAAGGTAGTACTTATATGGT 59.271 40.741 0.00 0.00 0.00 3.55
193 196 2.077413 TTGGCATTTGAAATCCACGC 57.923 45.000 8.07 0.27 0.00 5.34
195 198 0.801836 GGCATTTGAAATCCACGCCG 60.802 55.000 1.88 0.00 0.00 6.46
233 236 1.604604 ACGCCGGCTATATTGCATTT 58.395 45.000 26.68 0.00 34.04 2.32
236 239 1.669795 GCCGGCTATATTGCATTTGCC 60.670 52.381 22.15 7.05 41.18 4.52
288 291 1.128692 GCCTGCAATGTCGAACACTAC 59.871 52.381 0.00 0.00 0.00 2.73
500 681 0.178973 TTCACCACTCCCTCTCGACA 60.179 55.000 0.00 0.00 0.00 4.35
505 686 1.228894 ACTCCCTCTCGACAAGCCA 60.229 57.895 0.00 0.00 0.00 4.75
641 837 9.125026 ACTTTTCTGAATCTATGTGAACTTTGT 57.875 29.630 0.00 0.00 0.00 2.83
653 849 3.088532 TGAACTTTGTTGCACCTCACTT 58.911 40.909 0.00 0.00 0.00 3.16
754 956 7.004555 TCAACACACTCTGACCATTAACTAT 57.995 36.000 0.00 0.00 0.00 2.12
756 958 8.251026 TCAACACACTCTGACCATTAACTATAG 58.749 37.037 0.00 0.00 0.00 1.31
790 1001 3.383185 CCCTTCCAGAGTAGTCTCATGAC 59.617 52.174 0.00 0.00 42.66 3.06
859 1070 3.290948 ACTTTTCCACTGCCACACTAA 57.709 42.857 0.00 0.00 0.00 2.24
880 1093 2.530701 ACCTCCACTTACACTCCTCTG 58.469 52.381 0.00 0.00 0.00 3.35
918 1132 3.100671 GACCTATCCACCTCACTTCTGT 58.899 50.000 0.00 0.00 0.00 3.41
932 1163 4.160439 TCACTTCTGTCACACTCCATATCC 59.840 45.833 0.00 0.00 0.00 2.59
939 1170 6.841229 TCTGTCACACTCCATATCCTTAGAAT 59.159 38.462 0.00 0.00 0.00 2.40
940 1171 7.345653 TCTGTCACACTCCATATCCTTAGAATT 59.654 37.037 0.00 0.00 0.00 2.17
946 1177 9.213777 ACACTCCATATCCTTAGAATTTCACTA 57.786 33.333 0.00 0.00 0.00 2.74
1058 1318 0.314935 CATGCTTCTTGGTTTGGCGT 59.685 50.000 0.00 0.00 0.00 5.68
1060 1320 1.034838 TGCTTCTTGGTTTGGCGTGT 61.035 50.000 0.00 0.00 0.00 4.49
1061 1321 0.594796 GCTTCTTGGTTTGGCGTGTG 60.595 55.000 0.00 0.00 0.00 3.82
1063 1323 2.010582 TTCTTGGTTTGGCGTGTGGC 62.011 55.000 0.00 0.00 42.51 5.01
1064 1324 3.822403 CTTGGTTTGGCGTGTGGCG 62.822 63.158 0.00 0.00 44.92 5.69
1065 1325 4.858680 TGGTTTGGCGTGTGGCGA 62.859 61.111 0.00 0.00 44.92 5.54
1083 1343 1.746220 CGACAAGACCTCTTCCTCGAT 59.254 52.381 6.03 0.00 36.22 3.59
1107 1367 9.494271 GATTACATGAAGGTTGCTATGAGATAA 57.506 33.333 0.00 0.00 0.00 1.75
1148 1408 4.586841 GGTAGATGCAGTAGAGGAAGTGAT 59.413 45.833 0.00 0.00 0.00 3.06
1156 1416 5.105554 GCAGTAGAGGAAGTGATGAAGAAGA 60.106 44.000 0.00 0.00 0.00 2.87
1162 1422 4.221703 AGGAAGTGATGAAGAAGATGACGT 59.778 41.667 0.00 0.00 0.00 4.34
1177 1437 0.315568 GACGTGTGAGGAGAAGCAGT 59.684 55.000 0.00 0.00 0.00 4.40
1196 1456 2.435805 AGTACATGGACCAGCACTATGG 59.564 50.000 3.84 0.00 46.47 2.74
1197 1457 1.583556 ACATGGACCAGCACTATGGA 58.416 50.000 0.00 0.00 43.57 3.41
1276 1540 4.402155 TGTTGGCAACTCAAGAATGAAAGT 59.598 37.500 28.71 0.00 34.49 2.66
1353 1619 3.378399 GAGGCCCAAGACTCGGAGC 62.378 68.421 4.58 0.00 0.00 4.70
1450 1717 1.726853 CTTGGACTCTTGTAAGCCCG 58.273 55.000 0.00 0.00 0.00 6.13
1476 1743 6.388435 GTCTCGACCTGTGTATATAAAGGT 57.612 41.667 10.99 10.99 45.75 3.50
1483 1750 5.962031 ACCTGTGTATATAAAGGTGAGACCA 59.038 40.000 10.43 0.00 41.52 4.02
1492 1759 2.662596 GTGAGACCATGTGGCGGA 59.337 61.111 0.00 0.00 39.32 5.54
1503 1770 2.851263 TGTGGCGGATTAACTCAAGT 57.149 45.000 0.00 0.00 0.00 3.16
1514 1781 8.609176 GCGGATTAACTCAAGTTACAATCAATA 58.391 33.333 15.28 0.00 39.92 1.90
1543 1810 1.078708 TCAAACGATTCCGCTCCCC 60.079 57.895 0.00 0.00 39.95 4.81
1544 1811 2.112815 CAAACGATTCCGCTCCCCC 61.113 63.158 0.00 0.00 39.95 5.40
1585 1854 2.634600 ACAACACAAAGCAGGACGTAA 58.365 42.857 0.00 0.00 0.00 3.18
1600 1869 6.324819 CAGGACGTAAGATTTTACCTCGTTA 58.675 40.000 0.84 0.00 43.62 3.18
1628 1897 1.343142 CCAAACCTGGGTAAACCTTGC 59.657 52.381 0.00 0.00 39.30 4.01
1681 1951 0.249120 TAGGTTGTGATGGCTCCACG 59.751 55.000 0.00 0.00 37.34 4.94
1694 1964 1.398390 GCTCCACGCCTAAGTCATTTG 59.602 52.381 0.00 0.00 0.00 2.32
1762 2032 0.107456 GATCCTGCCCATCGACATGT 59.893 55.000 0.00 0.00 0.00 3.21
1772 2042 2.485302 CCATCGACATGTTGCTATGGGA 60.485 50.000 19.63 0.00 32.07 4.37
1822 2092 2.203625 AAAGGCAACGGTGGGCAT 60.204 55.556 12.04 0.00 46.39 4.40
1824 2094 0.324275 AAAGGCAACGGTGGGCATAT 60.324 50.000 12.04 0.00 46.39 1.78
1828 2098 0.748005 GCAACGGTGGGCATATCACT 60.748 55.000 0.90 0.00 35.61 3.41
1837 2107 2.705127 TGGGCATATCACTGCTATGTCA 59.295 45.455 6.78 2.09 41.95 3.58
1872 2145 1.330521 GCGACTCAAGCAAACACAGAA 59.669 47.619 0.00 0.00 34.19 3.02
1893 2166 0.246360 TGCACCAAGACGATGACGAT 59.754 50.000 0.00 0.00 42.66 3.73
1920 2193 2.579657 CGTCCCACCACCAGCACTA 61.580 63.158 0.00 0.00 0.00 2.74
1926 2199 2.045926 CCACCAGCACTACAGGCC 60.046 66.667 0.00 0.00 0.00 5.19
1965 2244 4.451435 CCCATCATCGTCATCAATGAAGAG 59.549 45.833 12.86 6.82 45.70 2.85
1984 2263 3.012274 AGAGGAAGATGAAGAGGAGGTGA 59.988 47.826 0.00 0.00 0.00 4.02
1991 2270 0.035915 GAAGAGGAGGTGAAGGTGCC 60.036 60.000 0.00 0.00 0.00 5.01
2012 2300 2.741878 CGCCAAATCCTACCGAAGTCAT 60.742 50.000 0.00 0.00 0.00 3.06
2025 2314 2.926200 CGAAGTCATGCAAGAGGTACAG 59.074 50.000 0.00 0.00 0.00 2.74
2032 2321 1.416030 TGCAAGAGGTACAGTGCTCAA 59.584 47.619 9.69 0.00 37.87 3.02
2035 2324 3.618507 GCAAGAGGTACAGTGCTCAAGAT 60.619 47.826 0.00 0.00 34.13 2.40
2079 2369 6.814506 AAGTGATTCTGAATCTGAAACAGG 57.185 37.500 25.83 0.00 38.72 4.00
2104 2410 9.490379 GGAAGTTTCAGATTTAGTTGTCTCTAA 57.510 33.333 0.00 0.00 0.00 2.10
2124 2493 7.656137 TCTCTAATGTTGTTCAGTCTTACCAAC 59.344 37.037 0.00 0.00 36.74 3.77
2204 2631 3.710209 ATGCTATCTATTGTGCCTCCC 57.290 47.619 0.00 0.00 0.00 4.30
2295 3265 5.554822 TGGTTTCAGTGTTGTTTAGTGTC 57.445 39.130 0.00 0.00 0.00 3.67
2630 3636 5.311385 ACTTACCAACCATAGGTACCACTTT 59.689 40.000 15.94 0.00 41.13 2.66
2632 3638 5.846528 ACCAACCATAGGTACCACTTTAA 57.153 39.130 15.94 0.00 37.67 1.52
2654 3660 3.754965 TCCTCCATGACAACTTCTTTGG 58.245 45.455 0.00 0.00 39.84 3.28
2669 3675 4.781775 TCTTTGGTCTTGTCCACCTTTA 57.218 40.909 0.00 0.00 37.20 1.85
2677 3683 2.969821 TGTCCACCTTTACCTTGCAT 57.030 45.000 0.00 0.00 0.00 3.96
2683 3689 2.428171 CACCTTTACCTTGCATCCATGG 59.572 50.000 4.97 4.97 40.97 3.66
2690 3696 0.466739 CTTGCATCCATGGCCAGCTA 60.467 55.000 13.05 4.62 0.00 3.32
2705 3711 2.757868 CCAGCTATAGGATCGGAGAAGG 59.242 54.545 1.04 0.00 43.58 3.46
2711 3717 2.850695 AGGATCGGAGAAGGTAGGTT 57.149 50.000 0.00 0.00 43.58 3.50
2740 3750 5.429130 GGGGTGAATAGACTCTTAACCAAG 58.571 45.833 8.91 0.00 0.00 3.61
2798 3810 5.873732 GCAGATTTTGGCACTAGTTAAGAG 58.126 41.667 0.00 0.00 0.00 2.85
2815 3827 4.550076 AAGAGATCACCAAGACTTCCTG 57.450 45.455 0.00 0.00 0.00 3.86
2840 3852 4.934001 ACATGCATCTCTAAAGATATGGCG 59.066 41.667 0.00 0.00 40.38 5.69
2895 3908 7.549842 GGAAAGTAAAGGGTAGAGATGAAAGAC 59.450 40.741 0.00 0.00 0.00 3.01
2957 3970 6.661805 TCCGATAAGTGGTGCTATCATACATA 59.338 38.462 0.00 0.00 0.00 2.29
2965 3978 5.047847 GGTGCTATCATACATACACGTTGT 58.952 41.667 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 7.729431 ACCATATAAGTACTACCTTCTTCTCCC 59.271 40.741 0.00 0.00 0.00 4.30
85 86 6.150307 GTGTGAGAGAGTAGATTTGAGTGAGA 59.850 42.308 0.00 0.00 0.00 3.27
99 100 0.034059 CCCGCAAAGTGTGAGAGAGT 59.966 55.000 0.00 0.00 0.00 3.24
173 176 2.411904 GCGTGGATTTCAAATGCCAAA 58.588 42.857 0.00 0.00 31.18 3.28
195 198 3.732721 GCGTACGAATTATGGTCACTACC 59.267 47.826 21.65 0.00 46.98 3.18
233 236 1.214325 CTATGACCACACGACGGCA 59.786 57.895 0.00 0.00 0.00 5.69
236 239 2.185262 CACATCTATGACCACACGACG 58.815 52.381 0.00 0.00 0.00 5.12
288 291 1.792006 ACCTTTTTCGACGCCACTAG 58.208 50.000 0.00 0.00 0.00 2.57
300 303 6.380095 TTTATGTTGCGTGTCTACCTTTTT 57.620 33.333 0.00 0.00 0.00 1.94
641 837 3.202906 GTGTAGACAAAGTGAGGTGCAA 58.797 45.455 0.00 0.00 0.00 4.08
687 883 6.372937 TGCCATTGTTCATTGTCGAAGTTATA 59.627 34.615 0.00 0.00 0.00 0.98
695 891 2.995466 ACTGCCATTGTTCATTGTCG 57.005 45.000 0.00 0.00 0.00 4.35
754 956 2.116238 GGAAGGGTGGTAGATGTGCTA 58.884 52.381 0.00 0.00 0.00 3.49
756 958 0.618458 TGGAAGGGTGGTAGATGTGC 59.382 55.000 0.00 0.00 0.00 4.57
790 1001 4.319766 GGTGTAGTGTTTCAGTGCTTGATG 60.320 45.833 0.00 0.00 35.27 3.07
859 1070 2.900546 CAGAGGAGTGTAAGTGGAGGTT 59.099 50.000 0.00 0.00 0.00 3.50
880 1093 6.239092 GGATAGGTCTTGAGTAGGAGTTAAGC 60.239 46.154 0.00 0.00 0.00 3.09
918 1132 7.987458 GTGAAATTCTAAGGATATGGAGTGTGA 59.013 37.037 0.00 0.00 0.00 3.58
932 1163 9.145865 GAGGAGAGTTGTTAGTGAAATTCTAAG 57.854 37.037 0.00 0.00 0.00 2.18
939 1170 5.047235 GCTAGGAGGAGAGTTGTTAGTGAAA 60.047 44.000 0.00 0.00 0.00 2.69
940 1171 4.463186 GCTAGGAGGAGAGTTGTTAGTGAA 59.537 45.833 0.00 0.00 0.00 3.18
946 1177 2.225394 TGGAGCTAGGAGGAGAGTTGTT 60.225 50.000 0.00 0.00 0.00 2.83
947 1178 1.359474 TGGAGCTAGGAGGAGAGTTGT 59.641 52.381 0.00 0.00 0.00 3.32
1058 1318 0.033504 GAAGAGGTCTTGTCGCCACA 59.966 55.000 0.00 0.00 36.11 4.17
1060 1320 0.832135 AGGAAGAGGTCTTGTCGCCA 60.832 55.000 0.00 0.00 36.11 5.69
1061 1321 0.108567 GAGGAAGAGGTCTTGTCGCC 60.109 60.000 0.00 0.00 36.11 5.54
1063 1323 1.166129 TCGAGGAAGAGGTCTTGTCG 58.834 55.000 12.10 12.10 38.97 4.35
1064 1324 3.878160 AATCGAGGAAGAGGTCTTGTC 57.122 47.619 0.00 0.00 36.11 3.18
1065 1325 4.087182 TGTAATCGAGGAAGAGGTCTTGT 58.913 43.478 0.00 0.00 36.11 3.16
1083 1343 9.109393 GTTTATCTCATAGCAACCTTCATGTAA 57.891 33.333 0.00 0.00 0.00 2.41
1107 1367 0.468029 CCAGCCCTTGAACACTGGTT 60.468 55.000 0.00 0.00 43.86 3.67
1148 1408 2.890945 TCCTCACACGTCATCTTCTTCA 59.109 45.455 0.00 0.00 0.00 3.02
1156 1416 0.969149 TGCTTCTCCTCACACGTCAT 59.031 50.000 0.00 0.00 0.00 3.06
1162 1422 2.234661 CCATGTACTGCTTCTCCTCACA 59.765 50.000 0.00 0.00 0.00 3.58
1177 1437 2.758130 TCCATAGTGCTGGTCCATGTA 58.242 47.619 0.00 0.00 37.57 2.29
1196 1456 5.163269 ACGGGGTTATATCCCTAACAGTTTC 60.163 44.000 16.89 0.00 46.27 2.78
1197 1457 4.723285 ACGGGGTTATATCCCTAACAGTTT 59.277 41.667 16.89 0.00 46.27 2.66
1232 1492 4.014075 TAACCCGCCCCTCCTGGA 62.014 66.667 0.00 0.00 35.39 3.86
1276 1540 1.575788 TCTCCTCAGGCCCATCTAAGA 59.424 52.381 0.00 0.00 0.00 2.10
1476 1743 1.199615 TAATCCGCCACATGGTCTCA 58.800 50.000 0.00 0.00 37.57 3.27
1483 1750 3.350219 ACTTGAGTTAATCCGCCACAT 57.650 42.857 0.00 0.00 0.00 3.21
1514 1781 4.261656 CGGAATCGTTTGACCTAGCTATCT 60.262 45.833 0.00 0.00 0.00 1.98
1544 1811 5.765176 TGTATTGATGGAGTACCGATTACG 58.235 41.667 0.00 0.00 39.42 3.18
1552 1819 6.072728 TGCTTTGTGTTGTATTGATGGAGTAC 60.073 38.462 0.00 0.00 0.00 2.73
1558 1825 5.156355 GTCCTGCTTTGTGTTGTATTGATG 58.844 41.667 0.00 0.00 0.00 3.07
1600 1869 2.772924 CCAGGTTTGGCCCCTCAT 59.227 61.111 0.00 0.00 37.73 2.90
1681 1951 2.164422 GCCCTTGTCAAATGACTTAGGC 59.836 50.000 20.50 19.53 44.99 3.93
1762 2032 3.902218 CCTCCTTCATTTCCCATAGCAA 58.098 45.455 0.00 0.00 0.00 3.91
1772 2042 3.863407 GAGTCCGCCTCCTTCATTT 57.137 52.632 0.00 0.00 33.79 2.32
1806 2076 0.751643 GATATGCCCACCGTTGCCTT 60.752 55.000 0.00 0.00 0.00 4.35
1822 2092 4.101430 TGCTGGATTGACATAGCAGTGATA 59.899 41.667 0.00 0.00 40.88 2.15
1824 2094 2.236893 TGCTGGATTGACATAGCAGTGA 59.763 45.455 0.00 0.00 40.88 3.41
1828 2098 2.785540 TGTGCTGGATTGACATAGCA 57.214 45.000 0.00 0.00 43.26 3.49
1852 2122 0.937304 TCTGTGTTTGCTTGAGTCGC 59.063 50.000 0.00 0.00 0.00 5.19
1872 2145 0.667487 CGTCATCGTCTTGGTGCACT 60.667 55.000 17.98 0.00 0.00 4.40
1893 2166 1.276989 GGTGGTGGGACGATCTGTAAA 59.723 52.381 0.00 0.00 0.00 2.01
1906 2179 1.003355 CCTGTAGTGCTGGTGGTGG 60.003 63.158 0.00 0.00 0.00 4.61
1965 2244 3.118445 CCTTCACCTCCTCTTCATCTTCC 60.118 52.174 0.00 0.00 0.00 3.46
1984 2263 0.679960 GTAGGATTTGGCGGCACCTT 60.680 55.000 22.15 9.46 40.22 3.50
1991 2270 1.287425 GACTTCGGTAGGATTTGGCG 58.713 55.000 0.00 0.00 0.00 5.69
2012 2300 1.047801 TGAGCACTGTACCTCTTGCA 58.952 50.000 7.56 0.00 37.44 4.08
2025 2314 1.669779 CCTGCTAAGCATCTTGAGCAC 59.330 52.381 0.00 0.00 39.93 4.40
2032 2321 0.822532 GCATGCCCTGCTAAGCATCT 60.823 55.000 6.36 0.00 46.58 2.90
2104 2410 7.450074 TGATAGTTGGTAAGACTGAACAACAT 58.550 34.615 20.76 12.62 42.73 2.71
2195 2622 1.278985 CTAGTTCACATGGGAGGCACA 59.721 52.381 0.00 0.00 0.00 4.57
2259 3211 6.155827 CACTGAAACCAAAACTGAAACTTGA 58.844 36.000 0.00 0.00 0.00 3.02
2295 3265 4.701956 ACACTGAAACTGAAACTTGGTG 57.298 40.909 0.00 0.00 0.00 4.17
2630 3636 5.945784 CCAAAGAAGTTGTCATGGAGGATTA 59.054 40.000 0.00 0.00 37.57 1.75
2632 3638 4.202609 ACCAAAGAAGTTGTCATGGAGGAT 60.203 41.667 10.65 0.00 38.34 3.24
2654 3660 2.552743 GCAAGGTAAAGGTGGACAAGAC 59.447 50.000 0.00 0.00 0.00 3.01
2669 3675 1.380785 CTGGCCATGGATGCAAGGT 60.381 57.895 18.40 0.00 0.00 3.50
2677 3683 2.191400 GATCCTATAGCTGGCCATGGA 58.809 52.381 18.40 8.01 0.00 3.41
2683 3689 1.840737 TCTCCGATCCTATAGCTGGC 58.159 55.000 0.00 0.00 0.00 4.85
2690 3696 4.472690 AACCTACCTTCTCCGATCCTAT 57.527 45.455 0.00 0.00 0.00 2.57
2755 3765 8.729805 ATCTGCCTAATTTTCAAGAGAACTAG 57.270 34.615 0.00 0.00 32.39 2.57
2798 3810 2.079925 GTGCAGGAAGTCTTGGTGATC 58.920 52.381 0.00 0.00 0.00 2.92
2815 3827 5.391736 GCCATATCTTTAGAGATGCATGTGC 60.392 44.000 2.46 0.00 42.55 4.57
2836 3848 1.658994 CTTTACTATTTCCGCCGCCA 58.341 50.000 0.00 0.00 0.00 5.69
2840 3852 2.357637 TGCATGCTTTACTATTTCCGCC 59.642 45.455 20.33 0.00 0.00 6.13
2895 3908 1.662876 CCGTGTCTTCATTGCGTTTGG 60.663 52.381 0.00 0.00 0.00 3.28
2957 3970 2.676342 GTTGAAGTCTCCAACAACGTGT 59.324 45.455 0.00 0.00 42.40 4.49
2965 3978 0.107831 CCACGGGTTGAAGTCTCCAA 59.892 55.000 0.00 0.00 0.00 3.53
3094 4107 4.820716 GCCTACTTCGTGAAGATCTACCTA 59.179 45.833 16.10 0.00 40.79 3.08


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

AutoCloner maintained by Alex Coulton.