Multiple sequence alignment - TraesCS3A01G353300

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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 TraesCS3A01G353300 chr3A 100.000 4691 0 0 1 4691 601343381 601338691 0.000000e+00 8663.0
1 TraesCS3A01G353300 chr3A 83.425 543 42 24 488 987 601368630 601368093 1.190000e-125 460.0
2 TraesCS3A01G353300 chr3A 83.824 136 22 0 762 897 601380663 601380528 3.810000e-26 130.0
3 TraesCS3A01G353300 chr3A 76.515 264 41 15 633 888 601374683 601374433 1.770000e-24 124.0
4 TraesCS3A01G353300 chr2A 97.304 3672 79 4 1020 4691 718926344 718922693 0.000000e+00 6215.0
5 TraesCS3A01G353300 chr2A 95.088 2769 135 1 1892 4660 207350187 207347420 0.000000e+00 4359.0
6 TraesCS3A01G353300 chr2A 97.601 1459 34 1 3233 4691 678126321 678127778 0.000000e+00 2499.0
7 TraesCS3A01G353300 chr2A 96.870 1214 35 1 1983 3193 678124780 678125993 0.000000e+00 2028.0
8 TraesCS3A01G353300 chr5B 94.476 3657 198 4 1036 4691 392100224 392103877 0.000000e+00 5631.0
9 TraesCS3A01G353300 chr5B 93.959 2152 130 0 1036 3187 392056384 392058535 0.000000e+00 3254.0
10 TraesCS3A01G353300 chr5B 93.888 2127 130 0 1036 3162 392041363 392043489 0.000000e+00 3208.0
11 TraesCS3A01G353300 chr5B 94.769 1472 74 3 3221 4691 392058897 392060366 0.000000e+00 2289.0
12 TraesCS3A01G353300 chr1B 94.459 2310 122 4 2384 4691 42065699 42063394 0.000000e+00 3552.0
13 TraesCS3A01G353300 chr3B 94.051 2034 118 3 2659 4691 28334024 28331993 0.000000e+00 3083.0
14 TraesCS3A01G353300 chr3B 94.810 1657 74 4 3045 4691 373619621 373617967 0.000000e+00 2573.0
15 TraesCS3A01G353300 chr3B 84.717 530 51 20 488 989 606380447 606379920 1.950000e-138 503.0
16 TraesCS3A01G353300 chr3B 89.818 275 24 4 2 274 606274514 606274242 2.690000e-92 350.0
17 TraesCS3A01G353300 chr3B 88.973 263 19 4 558 810 606224236 606223974 2.720000e-82 316.0
18 TraesCS3A01G353300 chr3B 87.047 193 22 3 322 513 606274235 606274045 1.020000e-51 215.0
19 TraesCS3A01G353300 chr3B 90.598 117 11 0 880 996 606223742 606223626 6.280000e-34 156.0
20 TraesCS3A01G353300 chr3B 82.803 157 25 2 751 907 606558829 606558675 6.330000e-29 139.0
21 TraesCS3A01G353300 chr3B 72.780 518 80 33 504 972 606421222 606420717 8.250000e-23 119.0
22 TraesCS3A01G353300 chr3B 96.491 57 1 1 274 329 773166010 773165954 5.000000e-15 93.5
23 TraesCS3A01G353300 chr3B 97.727 44 1 0 505 548 606274011 606273968 5.030000e-10 76.8
24 TraesCS3A01G353300 chr7A 96.444 1434 50 1 3258 4691 35448447 35447015 0.000000e+00 2364.0
25 TraesCS3A01G353300 chr7A 80.526 2737 470 33 1036 3766 500180634 500183313 0.000000e+00 2043.0
26 TraesCS3A01G353300 chrUn 95.420 1201 55 0 1416 2616 426443589 426444789 0.000000e+00 1914.0
27 TraesCS3A01G353300 chrUn 95.420 1201 55 0 1416 2616 426444890 426446090 0.000000e+00 1914.0
28 TraesCS3A01G353300 chrUn 93.791 918 57 0 1036 1953 429314774 429313857 0.000000e+00 1380.0
29 TraesCS3A01G353300 chrUn 91.850 319 26 0 1036 1354 435173092 435173410 3.330000e-121 446.0
30 TraesCS3A01G353300 chr6A 82.779 1835 306 9 1934 3766 49100968 49099142 0.000000e+00 1629.0
31 TraesCS3A01G353300 chr6B 93.619 1050 44 6 2317 3364 663186274 663187302 0.000000e+00 1546.0
32 TraesCS3A01G353300 chr3D 85.124 363 40 7 322 673 459088639 459088280 4.460000e-95 359.0
33 TraesCS3A01G353300 chr3D 80.503 477 47 18 558 989 459105145 459104670 1.630000e-84 324.0
34 TraesCS3A01G353300 chr3D 87.160 257 20 8 20 274 459088891 459088646 3.570000e-71 279.0
35 TraesCS3A01G353300 chr3D 94.574 129 7 0 868 996 459088280 459088152 2.860000e-47 200.0
36 TraesCS3A01G353300 chr3D 77.258 299 43 14 633 907 459195037 459194740 8.130000e-33 152.0
37 TraesCS3A01G353300 chr3D 96.429 56 2 0 274 329 134554612 134554557 5.000000e-15 93.5
38 TraesCS3A01G353300 chr3D 94.915 59 2 1 274 331 555317352 555317410 1.800000e-14 91.6
39 TraesCS3A01G353300 chr5D 96.429 56 2 0 274 329 34047538 34047483 5.000000e-15 93.5
40 TraesCS3A01G353300 chr5D 94.828 58 2 1 273 329 398523158 398523101 6.470000e-14 89.8
41 TraesCS3A01G353300 chr1D 96.429 56 2 0 274 329 432549943 432549888 5.000000e-15 93.5
42 TraesCS3A01G353300 chr5A 96.429 56 1 1 275 329 622536829 622536884 1.800000e-14 91.6
43 TraesCS3A01G353300 chr5A 93.443 61 2 2 271 329 680718575 680718515 6.470000e-14 89.8
44 TraesCS3A01G353300 chr4D 92.063 63 3 2 274 334 53754803 53754741 2.330000e-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 TraesCS3A01G353300 chr3A 601338691 601343381 4690 True 8663.000000 8663 100.000000 1 4691 1 chr3A.!!$R1 4690
1 TraesCS3A01G353300 chr3A 601368093 601368630 537 True 460.000000 460 83.425000 488 987 1 chr3A.!!$R2 499
2 TraesCS3A01G353300 chr2A 718922693 718926344 3651 True 6215.000000 6215 97.304000 1020 4691 1 chr2A.!!$R2 3671
3 TraesCS3A01G353300 chr2A 207347420 207350187 2767 True 4359.000000 4359 95.088000 1892 4660 1 chr2A.!!$R1 2768
4 TraesCS3A01G353300 chr2A 678124780 678127778 2998 False 2263.500000 2499 97.235500 1983 4691 2 chr2A.!!$F1 2708
5 TraesCS3A01G353300 chr5B 392100224 392103877 3653 False 5631.000000 5631 94.476000 1036 4691 1 chr5B.!!$F2 3655
6 TraesCS3A01G353300 chr5B 392041363 392043489 2126 False 3208.000000 3208 93.888000 1036 3162 1 chr5B.!!$F1 2126
7 TraesCS3A01G353300 chr5B 392056384 392060366 3982 False 2771.500000 3254 94.364000 1036 4691 2 chr5B.!!$F3 3655
8 TraesCS3A01G353300 chr1B 42063394 42065699 2305 True 3552.000000 3552 94.459000 2384 4691 1 chr1B.!!$R1 2307
9 TraesCS3A01G353300 chr3B 28331993 28334024 2031 True 3083.000000 3083 94.051000 2659 4691 1 chr3B.!!$R1 2032
10 TraesCS3A01G353300 chr3B 373617967 373619621 1654 True 2573.000000 2573 94.810000 3045 4691 1 chr3B.!!$R2 1646
11 TraesCS3A01G353300 chr3B 606379920 606380447 527 True 503.000000 503 84.717000 488 989 1 chr3B.!!$R3 501
12 TraesCS3A01G353300 chr3B 606223626 606224236 610 True 236.000000 316 89.785500 558 996 2 chr3B.!!$R7 438
13 TraesCS3A01G353300 chr3B 606273968 606274514 546 True 213.933333 350 91.530667 2 548 3 chr3B.!!$R8 546
14 TraesCS3A01G353300 chr7A 35447015 35448447 1432 True 2364.000000 2364 96.444000 3258 4691 1 chr7A.!!$R1 1433
15 TraesCS3A01G353300 chr7A 500180634 500183313 2679 False 2043.000000 2043 80.526000 1036 3766 1 chr7A.!!$F1 2730
16 TraesCS3A01G353300 chrUn 426443589 426446090 2501 False 1914.000000 1914 95.420000 1416 2616 2 chrUn.!!$F2 1200
17 TraesCS3A01G353300 chrUn 429313857 429314774 917 True 1380.000000 1380 93.791000 1036 1953 1 chrUn.!!$R1 917
18 TraesCS3A01G353300 chr6A 49099142 49100968 1826 True 1629.000000 1629 82.779000 1934 3766 1 chr6A.!!$R1 1832
19 TraesCS3A01G353300 chr6B 663186274 663187302 1028 False 1546.000000 1546 93.619000 2317 3364 1 chr6B.!!$F1 1047
20 TraesCS3A01G353300 chr3D 459088152 459088891 739 True 279.333333 359 88.952667 20 996 3 chr3D.!!$R4 976

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
865 973 0.034089 AGGTGCAAATAGCCCAGACC 60.034 55.0 0.00 0.0 44.83 3.85 F
985 1093 0.740737 GGTGTGGGTGCTTGATATGC 59.259 55.0 0.00 0.0 0.00 3.14 F
1706 1814 0.247695 GCTCGCGGTTGCAAGAATAC 60.248 55.0 6.13 0.0 42.97 1.89 F
3538 4898 0.033503 TGCTCGTAGTCTGGGGATCA 60.034 55.0 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1814 1.429148 GGAGCTTAATGGACGCCACG 61.429 60.000 0.5 0.0 35.80 4.94 R
2393 2502 2.046700 GAATGGCGTTGGGGTCGA 60.047 61.111 0.0 0.0 0.00 4.20 R
3583 4943 0.106708 TGCTCCTTGAAACGCTCAGT 59.893 50.000 0.0 0.0 34.81 3.41 R
4469 5840 2.164422 GTGAACCTCCTATTTTGCAGGC 59.836 50.000 0.0 0.0 32.82 4.85 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
156 158 6.484977 TGAAACAAAGGCAAAAGTTTTGTCTT 59.515 30.769 32.51 32.51 45.21 3.01
205 207 9.869757 AGTTGCAAATTAATACATAGAAAACCC 57.130 29.630 0.00 0.00 0.00 4.11
223 225 1.133025 CCCGATGAAAACTGTGATGGC 59.867 52.381 0.00 0.00 0.00 4.40
240 242 7.622713 TGTGATGGCCTTTAAATTTGATCAAT 58.377 30.769 9.40 0.00 0.00 2.57
241 243 7.765360 TGTGATGGCCTTTAAATTTGATCAATC 59.235 33.333 9.40 0.00 0.00 2.67
249 251 8.863049 CCTTTAAATTTGATCAATCCTCAAACG 58.137 33.333 9.40 0.00 43.31 3.60
262 264 5.523438 TCCTCAAACGGCTAATTGTTTTT 57.477 34.783 0.00 0.00 36.22 1.94
274 276 6.280643 GCTAATTGTTTTTGGAGTGAACCTT 58.719 36.000 0.00 0.00 0.00 3.50
275 277 6.761242 GCTAATTGTTTTTGGAGTGAACCTTT 59.239 34.615 0.00 0.00 0.00 3.11
277 279 7.994425 AATTGTTTTTGGAGTGAACCTTTTT 57.006 28.000 0.00 0.00 0.00 1.94
278 280 7.609760 ATTGTTTTTGGAGTGAACCTTTTTC 57.390 32.000 0.00 0.00 0.00 2.29
280 282 5.047943 TGTTTTTGGAGTGAACCTTTTTCGA 60.048 36.000 0.00 0.00 0.00 3.71
281 283 4.625972 TTTGGAGTGAACCTTTTTCGAC 57.374 40.909 0.00 0.00 0.00 4.20
282 284 3.269538 TGGAGTGAACCTTTTTCGACA 57.730 42.857 0.00 0.00 0.00 4.35
283 285 3.611970 TGGAGTGAACCTTTTTCGACAA 58.388 40.909 0.00 0.00 0.00 3.18
284 286 4.011023 TGGAGTGAACCTTTTTCGACAAA 58.989 39.130 0.00 0.00 0.00 2.83
285 287 4.095782 TGGAGTGAACCTTTTTCGACAAAG 59.904 41.667 15.59 15.59 34.06 2.77
290 292 2.793278 CCTTTTTCGACAAAGGGTGG 57.207 50.000 28.14 9.78 46.49 4.61
291 293 2.303175 CCTTTTTCGACAAAGGGTGGA 58.697 47.619 28.14 0.00 46.49 4.02
292 294 2.890945 CCTTTTTCGACAAAGGGTGGAT 59.109 45.455 28.14 0.00 46.49 3.41
293 295 3.320826 CCTTTTTCGACAAAGGGTGGATT 59.679 43.478 28.14 0.00 46.49 3.01
294 296 4.202212 CCTTTTTCGACAAAGGGTGGATTT 60.202 41.667 28.14 0.00 46.49 2.17
295 297 5.346181 TTTTTCGACAAAGGGTGGATTTT 57.654 34.783 0.00 0.00 34.00 1.82
296 298 6.461788 CCTTTTTCGACAAAGGGTGGATTTTA 60.462 38.462 28.14 0.00 46.49 1.52
297 299 6.658188 TTTTCGACAAAGGGTGGATTTTAT 57.342 33.333 0.00 0.00 34.00 1.40
298 300 6.658188 TTTCGACAAAGGGTGGATTTTATT 57.342 33.333 0.00 0.00 34.00 1.40
299 301 7.762588 TTTCGACAAAGGGTGGATTTTATTA 57.237 32.000 0.00 0.00 34.00 0.98
300 302 7.762588 TTCGACAAAGGGTGGATTTTATTAA 57.237 32.000 0.00 0.00 34.00 1.40
301 303 7.148355 TCGACAAAGGGTGGATTTTATTAAC 57.852 36.000 0.00 0.00 28.37 2.01
302 304 6.943718 TCGACAAAGGGTGGATTTTATTAACT 59.056 34.615 0.00 0.00 28.37 2.24
303 305 7.120138 TCGACAAAGGGTGGATTTTATTAACTC 59.880 37.037 0.00 0.00 28.37 3.01
304 306 7.094549 CGACAAAGGGTGGATTTTATTAACTCA 60.095 37.037 0.00 0.00 0.00 3.41
305 307 8.485578 ACAAAGGGTGGATTTTATTAACTCAA 57.514 30.769 0.00 0.00 0.00 3.02
306 308 8.929487 ACAAAGGGTGGATTTTATTAACTCAAA 58.071 29.630 0.00 0.00 0.00 2.69
307 309 9.771534 CAAAGGGTGGATTTTATTAACTCAAAA 57.228 29.630 0.00 0.00 0.00 2.44
309 311 9.942850 AAGGGTGGATTTTATTAACTCAAAATG 57.057 29.630 8.29 0.00 35.14 2.32
310 312 9.320295 AGGGTGGATTTTATTAACTCAAAATGA 57.680 29.630 8.29 0.00 35.14 2.57
311 313 9.936759 GGGTGGATTTTATTAACTCAAAATGAA 57.063 29.630 8.29 0.00 35.14 2.57
321 323 8.752766 ATTAACTCAAAATGAAGCATCAAGTG 57.247 30.769 0.00 0.00 39.49 3.16
322 324 6.395426 AACTCAAAATGAAGCATCAAGTGA 57.605 33.333 0.00 0.00 39.49 3.41
323 325 6.585695 ACTCAAAATGAAGCATCAAGTGAT 57.414 33.333 0.00 0.00 39.49 3.06
324 326 7.692460 ACTCAAAATGAAGCATCAAGTGATA 57.308 32.000 0.00 0.00 39.49 2.15
346 348 9.691362 TGATAAAAAGAAATCCACTTAGCAAAC 57.309 29.630 0.00 0.00 0.00 2.93
348 350 9.696917 ATAAAAAGAAATCCACTTAGCAAACTG 57.303 29.630 0.00 0.00 0.00 3.16
350 352 3.507622 AGAAATCCACTTAGCAAACTGGC 59.492 43.478 0.00 0.00 0.00 4.85
354 356 1.895131 CCACTTAGCAAACTGGCCATT 59.105 47.619 5.51 0.00 0.00 3.16
356 358 3.509575 CCACTTAGCAAACTGGCCATTAA 59.490 43.478 5.51 0.00 0.00 1.40
364 366 4.680172 GCAAACTGGCCATTAATGTGCATA 60.680 41.667 22.31 13.72 0.00 3.14
374 376 7.548780 GGCCATTAATGTGCATAAGAAAAGAAA 59.451 33.333 22.31 0.00 0.00 2.52
387 389 1.055849 AAAGAAAATGGTGGGGTGGC 58.944 50.000 0.00 0.00 0.00 5.01
388 390 0.190815 AAGAAAATGGTGGGGTGGCT 59.809 50.000 0.00 0.00 0.00 4.75
407 414 1.682344 GGGTGGGTGCTTCCAATCC 60.682 63.158 0.27 0.00 38.72 3.01
428 435 2.096496 CGCAGGATCTGAATGTTTGTCC 59.904 50.000 0.00 0.00 32.44 4.02
433 440 6.409704 CAGGATCTGAATGTTTGTCCTCTAA 58.590 40.000 0.00 0.00 34.00 2.10
473 480 4.365514 TCACTTCATTAGGGTTGCTTCA 57.634 40.909 0.00 0.00 0.00 3.02
476 483 5.774690 TCACTTCATTAGGGTTGCTTCAAAT 59.225 36.000 0.00 0.00 0.00 2.32
490 500 4.231890 TGCTTCAAATATACCCCTTCCCTT 59.768 41.667 0.00 0.00 0.00 3.95
570 634 3.746940 AGCAAATACTAACCCACGTGTT 58.253 40.909 15.65 5.69 0.00 3.32
574 638 5.179929 GCAAATACTAACCCACGTGTTACTT 59.820 40.000 15.65 2.38 0.00 2.24
601 665 0.468226 AGCGAGTCAACTTGTTCCCA 59.532 50.000 0.00 0.00 0.00 4.37
606 670 1.202651 AGTCAACTTGTTCCCAGACCG 60.203 52.381 0.00 0.00 0.00 4.79
609 673 0.106918 AACTTGTTCCCAGACCGCAA 60.107 50.000 0.00 0.00 0.00 4.85
653 735 0.882474 AGAAGAACGCGCAGTCTAGT 59.118 50.000 5.73 0.00 0.00 2.57
730 815 1.484444 AAACCAGCTCTCGCCTTCCT 61.484 55.000 0.00 0.00 36.60 3.36
731 816 1.484444 AACCAGCTCTCGCCTTCCTT 61.484 55.000 0.00 0.00 36.60 3.36
747 850 2.175202 TCCTTGCAACACAAACCAAGT 58.825 42.857 0.00 0.00 37.96 3.16
748 851 2.564947 TCCTTGCAACACAAACCAAGTT 59.435 40.909 0.00 0.00 37.96 2.66
751 854 0.920664 GCAACACAAACCAAGTTCGC 59.079 50.000 0.00 0.00 0.00 4.70
753 856 2.808244 CAACACAAACCAAGTTCGCAT 58.192 42.857 0.00 0.00 0.00 4.73
768 876 0.897863 CGCATAGGAGGAGGAGGAGG 60.898 65.000 0.00 0.00 0.00 4.30
781 889 1.411216 GGAGGAGGAATGGAGTACGGA 60.411 57.143 0.00 0.00 0.00 4.69
794 902 2.141448 TACGGACACCCCTGCAACA 61.141 57.895 0.00 0.00 0.00 3.33
795 903 1.697082 TACGGACACCCCTGCAACAA 61.697 55.000 0.00 0.00 0.00 2.83
796 904 2.551912 CGGACACCCCTGCAACAAC 61.552 63.158 0.00 0.00 0.00 3.32
803 911 2.620112 CCCTGCAACAACAGCTCCG 61.620 63.158 0.00 0.00 36.29 4.63
860 968 0.457443 GCTCAAGGTGCAAATAGCCC 59.543 55.000 0.00 0.00 44.83 5.19
865 973 0.034089 AGGTGCAAATAGCCCAGACC 60.034 55.000 0.00 0.00 44.83 3.85
877 985 3.655211 CAGACCCTGGGCAGCCTT 61.655 66.667 14.08 0.00 0.00 4.35
880 988 3.511610 ACCCTGGGCAGCCTTGTT 61.512 61.111 14.08 0.00 0.00 2.83
890 998 2.904866 GCCTTGTTGTGCCGGTCA 60.905 61.111 1.90 0.00 0.00 4.02
900 1008 2.112297 GCCGGTCACCAGGAACAA 59.888 61.111 1.90 0.00 30.31 2.83
959 1067 4.505922 CAGCTTCTCGACCAATTTAGCTAG 59.494 45.833 0.00 0.00 35.87 3.42
984 1092 1.745087 GTGGTGTGGGTGCTTGATATG 59.255 52.381 0.00 0.00 0.00 1.78
985 1093 0.740737 GGTGTGGGTGCTTGATATGC 59.259 55.000 0.00 0.00 0.00 3.14
996 1104 4.637534 GTGCTTGATATGCATACATAGGGG 59.362 45.833 8.99 0.00 41.97 4.79
997 1105 4.289410 TGCTTGATATGCATACATAGGGGT 59.711 41.667 8.99 0.00 41.97 4.95
998 1106 4.637534 GCTTGATATGCATACATAGGGGTG 59.362 45.833 8.99 0.00 41.97 4.61
999 1107 4.842531 TGATATGCATACATAGGGGTGG 57.157 45.455 8.99 0.00 41.97 4.61
1000 1108 4.434195 TGATATGCATACATAGGGGTGGA 58.566 43.478 8.99 0.00 41.97 4.02
1001 1109 5.038962 TGATATGCATACATAGGGGTGGAT 58.961 41.667 8.99 0.00 41.97 3.41
1002 1110 3.726557 ATGCATACATAGGGGTGGATG 57.273 47.619 0.00 0.00 42.26 3.51
1003 1111 2.700354 TGCATACATAGGGGTGGATGA 58.300 47.619 3.38 0.00 41.99 2.92
1004 1112 3.052329 TGCATACATAGGGGTGGATGAA 58.948 45.455 3.38 0.00 41.99 2.57
1005 1113 3.072915 TGCATACATAGGGGTGGATGAAG 59.927 47.826 3.38 0.00 41.99 3.02
1006 1114 3.327757 GCATACATAGGGGTGGATGAAGA 59.672 47.826 3.38 0.00 41.99 2.87
1007 1115 4.018960 GCATACATAGGGGTGGATGAAGAT 60.019 45.833 3.38 0.00 41.99 2.40
1008 1116 5.738909 CATACATAGGGGTGGATGAAGATC 58.261 45.833 0.00 0.00 41.99 2.75
1015 1123 4.055654 GGATGAAGATCCTGCGGC 57.944 61.111 0.00 0.00 44.58 6.53
1016 1124 1.146930 GGATGAAGATCCTGCGGCA 59.853 57.895 1.29 1.29 44.58 5.69
1017 1125 1.162800 GGATGAAGATCCTGCGGCAC 61.163 60.000 0.00 0.00 44.58 5.01
1280 1388 1.935327 GACTCGGAGTTCGTCCCTGG 61.935 65.000 12.67 0.00 43.47 4.45
1706 1814 0.247695 GCTCGCGGTTGCAAGAATAC 60.248 55.000 6.13 0.00 42.97 1.89
2277 2386 3.171388 GGGATCCCGGTCCATGCT 61.171 66.667 17.02 0.00 40.17 3.79
2393 2502 4.681978 GCTCTGGGCGTGGACGTT 62.682 66.667 0.52 0.00 42.22 3.99
2628 2840 0.107312 GAGACAGGCATGCTGGTCAT 60.107 55.000 30.13 20.51 35.31 3.06
2746 2969 3.838271 GCATCCGTCGCTCCCTGA 61.838 66.667 0.00 0.00 0.00 3.86
3538 4898 0.033503 TGCTCGTAGTCTGGGGATCA 60.034 55.000 0.00 0.00 0.00 2.92
3546 4906 4.528596 CGTAGTCTGGGGATCATTAAGGAT 59.471 45.833 1.48 1.48 0.00 3.24
3583 4943 1.688942 CCAAGGCCCTGGATGCATTTA 60.689 52.381 16.11 0.00 38.96 1.40
3843 5214 1.121378 TTGGTCCGTGTAAGTGTGGA 58.879 50.000 0.00 0.00 0.00 4.02
3873 5244 3.364460 TGGCACAAGCATAACCATAGT 57.636 42.857 0.00 0.00 44.61 2.12
4166 5537 0.884704 TTTTGCTGCTCTGGGACGAC 60.885 55.000 0.00 0.00 0.00 4.34
4458 5829 3.278574 ACACTGCAAAGTTGTGAGCTTA 58.721 40.909 9.75 0.00 35.83 3.09
4469 5840 6.952935 AGTTGTGAGCTTAAAAGAGATACG 57.047 37.500 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.157645 AGTCTAGACAAGATTTGATGGTCCAT 59.842 38.462 24.44 3.26 36.36 3.41
44 45 5.814705 CAGTCTAGACAAGATTTGATGGTCC 59.185 44.000 24.44 0.00 36.36 4.46
126 128 9.617975 CAAAACTTTTGCCTTTGTTTCAAAATA 57.382 25.926 1.30 0.00 38.51 1.40
127 129 8.140628 ACAAAACTTTTGCCTTTGTTTCAAAAT 58.859 25.926 13.22 0.00 39.61 1.82
131 133 5.994668 AGACAAAACTTTTGCCTTTGTTTCA 59.005 32.000 13.22 0.00 41.95 2.69
132 134 6.480524 AGACAAAACTTTTGCCTTTGTTTC 57.519 33.333 13.22 2.59 41.95 2.78
191 193 7.610305 ACAGTTTTCATCGGGTTTTCTATGTAT 59.390 33.333 0.00 0.00 0.00 2.29
196 198 5.369833 TCACAGTTTTCATCGGGTTTTCTA 58.630 37.500 0.00 0.00 0.00 2.10
205 207 2.086869 AGGCCATCACAGTTTTCATCG 58.913 47.619 5.01 0.00 0.00 3.84
223 225 8.863049 CGTTTGAGGATTGATCAAATTTAAAGG 58.137 33.333 13.09 11.51 45.54 3.11
240 242 5.285651 CAAAAACAATTAGCCGTTTGAGGA 58.714 37.500 0.00 0.00 35.57 3.71
241 243 4.447389 CCAAAAACAATTAGCCGTTTGAGG 59.553 41.667 0.00 0.00 35.57 3.86
249 251 4.988540 GGTTCACTCCAAAAACAATTAGCC 59.011 41.667 0.00 0.00 0.00 3.93
262 264 3.269538 TGTCGAAAAAGGTTCACTCCA 57.730 42.857 0.00 0.00 0.00 3.86
274 276 6.658188 ATAAAATCCACCCTTTGTCGAAAA 57.342 33.333 0.00 0.00 0.00 2.29
275 277 6.658188 AATAAAATCCACCCTTTGTCGAAA 57.342 33.333 0.00 0.00 0.00 3.46
277 279 6.943718 AGTTAATAAAATCCACCCTTTGTCGA 59.056 34.615 0.00 0.00 0.00 4.20
278 280 7.094549 TGAGTTAATAAAATCCACCCTTTGTCG 60.095 37.037 0.00 0.00 0.00 4.35
280 282 8.485578 TTGAGTTAATAAAATCCACCCTTTGT 57.514 30.769 0.00 0.00 0.00 2.83
281 283 9.771534 TTTTGAGTTAATAAAATCCACCCTTTG 57.228 29.630 0.00 0.00 0.00 2.77
283 285 9.942850 CATTTTGAGTTAATAAAATCCACCCTT 57.057 29.630 0.00 0.00 35.07 3.95
284 286 9.320295 TCATTTTGAGTTAATAAAATCCACCCT 57.680 29.630 0.00 0.00 35.07 4.34
285 287 9.936759 TTCATTTTGAGTTAATAAAATCCACCC 57.063 29.630 0.00 0.00 35.07 4.61
295 297 9.844790 CACTTGATGCTTCATTTTGAGTTAATA 57.155 29.630 2.75 0.00 0.00 0.98
296 298 8.579006 TCACTTGATGCTTCATTTTGAGTTAAT 58.421 29.630 2.75 0.00 0.00 1.40
297 299 7.939782 TCACTTGATGCTTCATTTTGAGTTAA 58.060 30.769 2.75 0.00 0.00 2.01
298 300 7.509141 TCACTTGATGCTTCATTTTGAGTTA 57.491 32.000 2.75 0.00 0.00 2.24
299 301 6.395426 TCACTTGATGCTTCATTTTGAGTT 57.605 33.333 2.75 0.00 0.00 3.01
300 302 6.585695 ATCACTTGATGCTTCATTTTGAGT 57.414 33.333 2.75 0.90 32.68 3.41
301 303 8.975410 TTTATCACTTGATGCTTCATTTTGAG 57.025 30.769 2.75 0.28 36.05 3.02
302 304 9.761504 TTTTTATCACTTGATGCTTCATTTTGA 57.238 25.926 2.75 6.89 36.05 2.69
304 306 9.985730 TCTTTTTATCACTTGATGCTTCATTTT 57.014 25.926 2.75 0.00 36.05 1.82
305 307 9.985730 TTCTTTTTATCACTTGATGCTTCATTT 57.014 25.926 2.75 0.00 36.05 2.32
306 308 9.985730 TTTCTTTTTATCACTTGATGCTTCATT 57.014 25.926 2.75 0.00 36.05 2.57
308 310 9.630098 GATTTCTTTTTATCACTTGATGCTTCA 57.370 29.630 1.77 0.00 36.05 3.02
309 311 9.080915 GGATTTCTTTTTATCACTTGATGCTTC 57.919 33.333 1.77 0.00 36.05 3.86
310 312 8.587608 TGGATTTCTTTTTATCACTTGATGCTT 58.412 29.630 1.77 0.00 36.05 3.91
311 313 8.031277 GTGGATTTCTTTTTATCACTTGATGCT 58.969 33.333 1.77 0.00 36.05 3.79
312 314 8.031277 AGTGGATTTCTTTTTATCACTTGATGC 58.969 33.333 1.77 0.00 36.05 3.91
313 315 9.918630 AAGTGGATTTCTTTTTATCACTTGATG 57.081 29.630 1.77 0.00 36.05 3.07
316 318 9.346725 GCTAAGTGGATTTCTTTTTATCACTTG 57.653 33.333 13.81 7.03 33.28 3.16
317 319 9.077885 TGCTAAGTGGATTTCTTTTTATCACTT 57.922 29.630 0.00 0.00 35.08 3.16
318 320 8.635765 TGCTAAGTGGATTTCTTTTTATCACT 57.364 30.769 0.00 0.00 0.00 3.41
319 321 9.691362 TTTGCTAAGTGGATTTCTTTTTATCAC 57.309 29.630 0.00 0.00 0.00 3.06
320 322 9.691362 GTTTGCTAAGTGGATTTCTTTTTATCA 57.309 29.630 0.00 0.00 0.00 2.15
321 323 9.914131 AGTTTGCTAAGTGGATTTCTTTTTATC 57.086 29.630 0.00 0.00 0.00 1.75
322 324 9.696917 CAGTTTGCTAAGTGGATTTCTTTTTAT 57.303 29.630 7.73 0.00 32.16 1.40
340 342 2.354003 GCACATTAATGGCCAGTTTGCT 60.354 45.455 12.70 0.00 0.00 3.91
346 348 5.518848 TTCTTATGCACATTAATGGCCAG 57.481 39.130 19.37 13.77 0.00 4.85
348 350 6.572519 TCTTTTCTTATGCACATTAATGGCC 58.427 36.000 19.37 9.98 0.00 5.36
354 356 9.421806 CACCATTTTCTTTTCTTATGCACATTA 57.578 29.630 0.00 0.00 0.00 1.90
356 358 6.875195 CCACCATTTTCTTTTCTTATGCACAT 59.125 34.615 0.00 0.00 0.00 3.21
364 366 3.390967 CCACCCCACCATTTTCTTTTCTT 59.609 43.478 0.00 0.00 0.00 2.52
374 376 3.996621 CCCAGCCACCCCACCATT 61.997 66.667 0.00 0.00 0.00 3.16
387 389 0.967380 GATTGGAAGCACCCACCCAG 60.967 60.000 0.00 0.00 35.62 4.45
388 390 1.076549 GATTGGAAGCACCCACCCA 59.923 57.895 0.00 0.00 35.62 4.51
407 414 2.096496 GGACAAACATTCAGATCCTGCG 59.904 50.000 0.00 0.00 0.00 5.18
428 435 9.231297 TGAACCTTTTTATCCATGAACTTAGAG 57.769 33.333 0.00 0.00 0.00 2.43
433 440 7.505585 TGAAGTGAACCTTTTTATCCATGAACT 59.494 33.333 0.00 0.00 32.03 3.01
473 480 9.021747 ACACTAATTAAGGGAAGGGGTATATTT 57.978 33.333 0.00 0.00 30.77 1.40
476 483 7.140990 TCACACTAATTAAGGGAAGGGGTATA 58.859 38.462 0.00 0.00 30.77 1.47
490 500 6.040955 CCTGGCTCTCACTATCACACTAATTA 59.959 42.308 0.00 0.00 0.00 1.40
570 634 7.225931 ACAAGTTGACTCGCTTTATTTGAAGTA 59.774 33.333 10.54 0.00 0.00 2.24
574 638 6.371809 AACAAGTTGACTCGCTTTATTTGA 57.628 33.333 10.54 0.00 0.00 2.69
601 665 1.599047 CCCATCTCTGTTGCGGTCT 59.401 57.895 0.00 0.00 0.00 3.85
606 670 3.350219 TTAACTCCCCATCTCTGTTGC 57.650 47.619 0.00 0.00 0.00 4.17
609 673 7.989947 TTACTAATTAACTCCCCATCTCTGT 57.010 36.000 0.00 0.00 0.00 3.41
653 735 2.243602 AAGTTTTCGGGCACGTTCTA 57.756 45.000 8.89 0.00 41.85 2.10
705 787 3.129792 CGAGAGCTGGTTTGAGGAC 57.870 57.895 0.00 0.00 0.00 3.85
730 815 2.600731 CGAACTTGGTTTGTGTTGCAA 58.399 42.857 0.00 0.00 34.87 4.08
731 816 1.734047 GCGAACTTGGTTTGTGTTGCA 60.734 47.619 0.00 0.00 30.22 4.08
747 850 0.556258 TCCTCCTCCTCCTATGCGAA 59.444 55.000 0.00 0.00 0.00 4.70
748 851 0.111446 CTCCTCCTCCTCCTATGCGA 59.889 60.000 0.00 0.00 0.00 5.10
751 854 3.172339 CATTCCTCCTCCTCCTCCTATG 58.828 54.545 0.00 0.00 0.00 2.23
753 856 1.505538 CCATTCCTCCTCCTCCTCCTA 59.494 57.143 0.00 0.00 0.00 2.94
768 876 0.177373 GGGGTGTCCGTACTCCATTC 59.823 60.000 1.53 0.00 41.08 2.67
781 889 2.127232 GCTGTTGTTGCAGGGGTGT 61.127 57.895 0.00 0.00 37.00 4.16
794 902 1.898574 CCTTGTTGCCGGAGCTGTT 60.899 57.895 5.05 0.00 40.80 3.16
795 903 2.281761 CCTTGTTGCCGGAGCTGT 60.282 61.111 5.05 0.00 40.80 4.40
796 904 2.032528 TCCTTGTTGCCGGAGCTG 59.967 61.111 5.05 0.00 40.80 4.24
803 911 0.962855 GGCCTCTTCTCCTTGTTGCC 60.963 60.000 0.00 0.00 0.00 4.52
860 968 3.655211 AAGGCTGCCCAGGGTCTG 61.655 66.667 16.57 4.96 0.00 3.51
865 973 2.203538 ACAACAAGGCTGCCCAGG 60.204 61.111 16.57 7.70 0.00 4.45
890 998 2.408565 TCTCCTGAAGTTGTTCCTGGT 58.591 47.619 0.00 0.00 31.09 4.00
900 1008 1.767681 GGCCATCTCATCTCCTGAAGT 59.232 52.381 0.00 0.00 32.14 3.01
959 1067 0.751643 AAGCACCCACACCACACTTC 60.752 55.000 0.00 0.00 0.00 3.01
984 1092 3.327757 TCTTCATCCACCCCTATGTATGC 59.672 47.826 0.00 0.00 0.00 3.14
985 1093 5.738909 GATCTTCATCCACCCCTATGTATG 58.261 45.833 0.00 0.00 0.00 2.39
1013 1121 2.491022 ATAGGTCTCGCTCCGTGCC 61.491 63.158 0.00 0.00 38.78 5.01
1014 1122 1.299468 CATAGGTCTCGCTCCGTGC 60.299 63.158 0.00 0.00 38.57 5.34
1015 1123 0.309302 CTCATAGGTCTCGCTCCGTG 59.691 60.000 0.00 0.00 0.00 4.94
1016 1124 1.448922 GCTCATAGGTCTCGCTCCGT 61.449 60.000 0.00 0.00 0.00 4.69
1017 1125 1.284408 GCTCATAGGTCTCGCTCCG 59.716 63.158 0.00 0.00 0.00 4.63
1018 1126 1.663173 GGCTCATAGGTCTCGCTCC 59.337 63.158 0.00 0.00 0.00 4.70
1019 1127 1.109920 TGGGCTCATAGGTCTCGCTC 61.110 60.000 0.00 0.00 0.00 5.03
1020 1128 1.075970 TGGGCTCATAGGTCTCGCT 60.076 57.895 0.00 0.00 0.00 4.93
1021 1129 1.068250 GTGGGCTCATAGGTCTCGC 59.932 63.158 0.00 0.00 0.00 5.03
1022 1130 1.742768 GGTGGGCTCATAGGTCTCG 59.257 63.158 0.00 0.00 0.00 4.04
1091 1199 4.738998 CAGGTTGGCCGGCATGGA 62.739 66.667 30.85 7.55 42.00 3.41
1706 1814 1.429148 GGAGCTTAATGGACGCCACG 61.429 60.000 0.50 0.00 35.80 4.94
1816 1924 4.814041 GAGGAGAGGCCAGCCCCT 62.814 72.222 5.01 5.50 40.02 4.79
2002 2110 2.365635 AGGGACATCCTCACGGGG 60.366 66.667 0.00 0.00 44.06 5.73
2206 2315 2.669569 ATTGTCAGCGTGCGCCTT 60.670 55.556 13.21 0.00 43.17 4.35
2277 2386 2.279741 GCAGCGATGTACTCATTCCAA 58.720 47.619 1.22 0.00 34.06 3.53
2367 2476 3.695606 GCCCAGAGCGACAGGTCA 61.696 66.667 0.00 0.00 46.62 4.02
2393 2502 2.046700 GAATGGCGTTGGGGTCGA 60.047 61.111 0.00 0.00 0.00 4.20
2466 2575 2.842462 ACACGGTGTCTCAGGCCA 60.842 61.111 8.21 0.00 0.00 5.36
2535 2644 2.920912 GGAGGTGGTGGGTCGTCA 60.921 66.667 0.00 0.00 0.00 4.35
3041 3617 4.357947 GAGGCAGCACCGACGTGA 62.358 66.667 0.00 0.00 46.52 4.35
3538 4898 5.453903 CCGTGATGTCTTCTCCATCCTTAAT 60.454 44.000 0.00 0.00 38.32 1.40
3546 4906 1.191489 TGGCCGTGATGTCTTCTCCA 61.191 55.000 0.00 0.00 0.00 3.86
3583 4943 0.106708 TGCTCCTTGAAACGCTCAGT 59.893 50.000 0.00 0.00 34.81 3.41
3843 5214 1.976898 CTTGTGCCATGCAACCCAT 59.023 52.632 0.00 0.00 41.47 4.00
3873 5244 0.685785 ACATGCCACACACAACCCAA 60.686 50.000 0.00 0.00 0.00 4.12
4458 5829 5.066505 CCTATTTTGCAGGCGTATCTCTTTT 59.933 40.000 0.00 0.00 0.00 2.27
4469 5840 2.164422 GTGAACCTCCTATTTTGCAGGC 59.836 50.000 0.00 0.00 32.82 4.85


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

AutoCloner maintained by Alex Coulton.