Multiple sequence alignment - TraesCS4D01G336600

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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 TraesCS4D01G336600 chr4D 100.000 2786 0 0 1 2786 494266060 494268845 0.000000e+00 5145.0
1 TraesCS4D01G336600 chr4D 77.303 445 68 22 3 426 506708103 506707671 6.000000e-57 231.0
2 TraesCS4D01G336600 chr5A 92.991 1969 86 11 836 2786 673772773 673774707 0.000000e+00 2824.0
3 TraesCS4D01G336600 chr4B 89.275 2275 118 51 585 2784 633759487 633761710 0.000000e+00 2734.0
4 TraesCS4D01G336600 chr4B 91.304 138 12 0 1810 1947 151437391 151437528 3.660000e-44 189.0
5 TraesCS4D01G336600 chr4A 94.434 539 15 2 1039 1562 494074157 494073619 0.000000e+00 815.0
6 TraesCS4D01G336600 chr4A 87.589 282 26 6 1812 2092 604531250 604531523 4.480000e-83 318.0
7 TraesCS4D01G336600 chr4A 84.416 154 13 9 1158 1308 246254891 246255036 1.040000e-29 141.0
8 TraesCS4D01G336600 chr4A 95.238 42 2 0 1511 1552 494073637 494073596 1.790000e-07 67.6
9 TraesCS4D01G336600 chr2B 96.439 337 9 1 1229 1562 109134267 109133931 1.130000e-153 553.0
10 TraesCS4D01G336600 chr2B 96.133 181 7 0 1039 1219 109134946 109134766 2.100000e-76 296.0
11 TraesCS4D01G336600 chr2B 95.238 42 2 0 1511 1552 109133949 109133908 1.790000e-07 67.6
12 TraesCS4D01G336600 chr5D 90.426 282 18 7 1812 2092 189932374 189932647 2.040000e-96 363.0
13 TraesCS4D01G336600 chr5D 81.897 348 50 12 3 342 42912115 42912457 5.880000e-72 281.0
14 TraesCS4D01G336600 chr5D 89.773 176 13 2 1810 1984 123154121 123154292 1.300000e-53 220.0
15 TraesCS4D01G336600 chr5D 79.522 293 40 12 116 390 540614031 540613741 1.020000e-44 191.0
16 TraesCS4D01G336600 chr5D 76.364 275 48 10 109 369 478211311 478211582 6.260000e-27 132.0
17 TraesCS4D01G336600 chr5B 94.142 239 8 2 1327 1559 248767143 248767381 2.640000e-95 359.0
18 TraesCS4D01G336600 chr5B 96.350 137 5 0 1039 1175 248766996 248767132 2.790000e-55 226.0
19 TraesCS4D01G336600 chr5B 95.238 42 2 0 1511 1552 248767366 248767407 1.790000e-07 67.6
20 TraesCS4D01G336600 chr6B 89.437 284 21 4 1810 2092 148519708 148519433 1.590000e-92 350.0
21 TraesCS4D01G336600 chr6B 88.732 284 21 6 1810 2092 148438167 148437894 1.240000e-88 337.0
22 TraesCS4D01G336600 chr7D 89.085 284 22 7 1810 2092 184648341 184648066 7.390000e-91 344.0
23 TraesCS4D01G336600 chr2D 88.380 284 23 8 1810 2092 477223519 477223793 1.600000e-87 333.0
24 TraesCS4D01G336600 chr2D 78.819 288 47 13 2 283 312059898 312059619 6.130000e-42 182.0
25 TraesCS4D01G336600 chr3A 81.499 427 58 19 11 427 111078029 111078444 5.750000e-87 331.0
26 TraesCS4D01G336600 chr3A 87.676 284 26 6 1810 2092 51678716 51678991 3.460000e-84 322.0
27 TraesCS4D01G336600 chr3A 79.870 308 40 18 10 310 677841645 677841937 3.640000e-49 206.0
28 TraesCS4D01G336600 chr6A 87.986 283 23 8 1812 2092 75254327 75254054 9.620000e-85 324.0
29 TraesCS4D01G336600 chr7B 79.467 375 53 17 63 422 740058578 740058943 7.710000e-61 244.0
30 TraesCS4D01G336600 chr3D 87.565 193 14 8 4 194 22360068 22360252 6.040000e-52 215.0
31 TraesCS4D01G336600 chr3D 79.787 282 37 16 6 281 587317509 587317242 1.320000e-43 187.0
32 TraesCS4D01G336600 chr1B 85.714 210 22 7 5 211 469171764 469171560 6.040000e-52 215.0
33 TraesCS4D01G336600 chr1B 97.297 37 1 0 1039 1075 375808059 375808095 2.320000e-06 63.9
34 TraesCS4D01G336600 chr7A 75.050 497 78 33 2 481 156871147 156871614 3.660000e-44 189.0


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 TraesCS4D01G336600 chr4D 494266060 494268845 2785 False 5145.000000 5145 100.000000 1 2786 1 chr4D.!!$F1 2785
1 TraesCS4D01G336600 chr5A 673772773 673774707 1934 False 2824.000000 2824 92.991000 836 2786 1 chr5A.!!$F1 1950
2 TraesCS4D01G336600 chr4B 633759487 633761710 2223 False 2734.000000 2734 89.275000 585 2784 1 chr4B.!!$F2 2199
3 TraesCS4D01G336600 chr4A 494073596 494074157 561 True 441.300000 815 94.836000 1039 1562 2 chr4A.!!$R1 523
4 TraesCS4D01G336600 chr2B 109133908 109134946 1038 True 305.533333 553 95.936667 1039 1562 3 chr2B.!!$R1 523

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
533 534 0.032952 TCAAGTAGGACGTGCCACAC 59.967 55.0 8.47 2.32 40.02 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2489 0.931662 GCACAAACAAGCAGTCGCAG 60.932 55.0 0.0 0.0 42.27 5.18 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
110 111 9.199982 AGCATTTGAGAAAATATTGAACAAGTG 57.800 29.630 0.00 0.00 0.00 3.16
111 112 8.981647 GCATTTGAGAAAATATTGAACAAGTGT 58.018 29.630 14.82 0.00 0.00 3.55
133 134 9.651913 AGTGTTTGAAAAATGTTAATCAAGTGT 57.348 25.926 0.00 0.00 33.71 3.55
138 139 9.658799 TTGAAAAATGTTAATCAAGTGTTTGGA 57.341 25.926 0.00 0.00 34.97 3.53
139 140 9.658799 TGAAAAATGTTAATCAAGTGTTTGGAA 57.341 25.926 0.00 0.00 34.97 3.53
143 144 9.612066 AAATGTTAATCAAGTGTTTGGAAATGT 57.388 25.926 0.00 0.00 34.97 2.71
144 145 9.612066 AATGTTAATCAAGTGTTTGGAAATGTT 57.388 25.926 0.00 0.00 34.97 2.71
150 151 9.612066 AATCAAGTGTTTGGAAATGTTAAATGT 57.388 25.926 0.00 0.00 34.97 2.71
151 152 8.417780 TCAAGTGTTTGGAAATGTTAAATGTG 57.582 30.769 0.00 0.00 34.97 3.21
152 153 6.843069 AGTGTTTGGAAATGTTAAATGTGC 57.157 33.333 0.00 0.00 0.00 4.57
153 154 6.344500 AGTGTTTGGAAATGTTAAATGTGCA 58.656 32.000 0.00 0.00 0.00 4.57
154 155 6.991531 AGTGTTTGGAAATGTTAAATGTGCAT 59.008 30.769 0.00 0.00 0.00 3.96
155 156 7.498570 AGTGTTTGGAAATGTTAAATGTGCATT 59.501 29.630 0.00 0.00 34.69 3.56
156 157 7.587028 GTGTTTGGAAATGTTAAATGTGCATTG 59.413 33.333 0.00 0.00 33.68 2.82
157 158 7.496920 TGTTTGGAAATGTTAAATGTGCATTGA 59.503 29.630 0.00 0.00 33.68 2.57
158 159 8.341173 GTTTGGAAATGTTAAATGTGCATTGAA 58.659 29.630 0.00 0.00 33.68 2.69
159 160 8.442632 TTGGAAATGTTAAATGTGCATTGAAA 57.557 26.923 0.00 0.00 33.68 2.69
160 161 8.442632 TGGAAATGTTAAATGTGCATTGAAAA 57.557 26.923 0.00 0.00 33.68 2.29
161 162 8.896744 TGGAAATGTTAAATGTGCATTGAAAAA 58.103 25.926 0.00 0.00 33.68 1.94
264 265 9.528018 AATGTTAATCTTGTGTTCGAAAAATGT 57.472 25.926 0.00 0.00 0.00 2.71
265 266 8.918961 TGTTAATCTTGTGTTCGAAAAATGTT 57.081 26.923 0.00 0.00 0.00 2.71
270 271 9.743057 AATCTTGTGTTCGAAAAATGTTAATGA 57.257 25.926 0.00 0.00 0.00 2.57
271 272 9.743057 ATCTTGTGTTCGAAAAATGTTAATGAA 57.257 25.926 0.00 0.00 0.00 2.57
272 273 9.015577 TCTTGTGTTCGAAAAATGTTAATGAAC 57.984 29.630 0.00 0.00 35.88 3.18
273 274 7.687005 TGTGTTCGAAAAATGTTAATGAACC 57.313 32.000 0.00 0.00 34.78 3.62
274 275 7.258441 TGTGTTCGAAAAATGTTAATGAACCA 58.742 30.769 0.00 0.00 34.78 3.67
275 276 7.923344 TGTGTTCGAAAAATGTTAATGAACCAT 59.077 29.630 0.00 0.00 34.78 3.55
276 277 8.760569 GTGTTCGAAAAATGTTAATGAACCATT 58.239 29.630 0.00 0.00 37.80 3.16
277 278 9.319143 TGTTCGAAAAATGTTAATGAACCATTT 57.681 25.926 0.00 0.00 35.54 2.32
278 279 9.579610 GTTCGAAAAATGTTAATGAACCATTTG 57.420 29.630 0.00 0.00 35.54 2.32
279 280 9.534565 TTCGAAAAATGTTAATGAACCATTTGA 57.465 25.926 0.00 0.00 35.54 2.69
280 281 9.534565 TCGAAAAATGTTAATGAACCATTTGAA 57.465 25.926 0.00 0.00 35.54 2.69
329 330 9.672086 AATGTTGCGCGTATATTAATAAAATGT 57.328 25.926 8.43 0.00 0.00 2.71
330 331 9.672086 ATGTTGCGCGTATATTAATAAAATGTT 57.328 25.926 8.43 0.00 0.00 2.71
467 468 7.414814 AAAAACTGAAGAAACAAGCGAAAAA 57.585 28.000 0.00 0.00 0.00 1.94
501 502 1.037493 AAAACCGGGAGAAAACTGGC 58.963 50.000 6.32 0.00 37.93 4.85
502 503 0.185175 AAACCGGGAGAAAACTGGCT 59.815 50.000 6.32 0.00 37.93 4.75
503 504 0.250770 AACCGGGAGAAAACTGGCTC 60.251 55.000 6.32 0.00 37.93 4.70
504 505 1.128188 ACCGGGAGAAAACTGGCTCT 61.128 55.000 6.32 0.00 37.93 4.09
505 506 0.391793 CCGGGAGAAAACTGGCTCTC 60.392 60.000 0.00 0.00 37.87 3.20
506 507 0.610687 CGGGAGAAAACTGGCTCTCT 59.389 55.000 1.40 0.00 38.52 3.10
507 508 1.002544 CGGGAGAAAACTGGCTCTCTT 59.997 52.381 1.40 0.00 38.52 2.85
508 509 2.705730 GGGAGAAAACTGGCTCTCTTC 58.294 52.381 1.40 0.00 38.52 2.87
509 510 2.039084 GGGAGAAAACTGGCTCTCTTCA 59.961 50.000 1.40 0.00 38.52 3.02
510 511 3.070748 GGAGAAAACTGGCTCTCTTCAC 58.929 50.000 1.40 0.00 38.52 3.18
511 512 3.244387 GGAGAAAACTGGCTCTCTTCACT 60.244 47.826 1.40 0.00 38.52 3.41
512 513 3.993736 GAGAAAACTGGCTCTCTTCACTC 59.006 47.826 0.00 0.00 36.06 3.51
513 514 3.645687 AGAAAACTGGCTCTCTTCACTCT 59.354 43.478 0.00 0.00 0.00 3.24
514 515 4.102367 AGAAAACTGGCTCTCTTCACTCTT 59.898 41.667 0.00 0.00 0.00 2.85
515 516 3.676291 AACTGGCTCTCTTCACTCTTC 57.324 47.619 0.00 0.00 0.00 2.87
516 517 2.603021 ACTGGCTCTCTTCACTCTTCA 58.397 47.619 0.00 0.00 0.00 3.02
517 518 2.968574 ACTGGCTCTCTTCACTCTTCAA 59.031 45.455 0.00 0.00 0.00 2.69
518 519 3.006752 ACTGGCTCTCTTCACTCTTCAAG 59.993 47.826 0.00 0.00 0.00 3.02
519 520 2.968574 TGGCTCTCTTCACTCTTCAAGT 59.031 45.455 0.00 0.00 39.44 3.16
520 521 4.152647 TGGCTCTCTTCACTCTTCAAGTA 58.847 43.478 0.00 0.00 36.07 2.24
521 522 4.219507 TGGCTCTCTTCACTCTTCAAGTAG 59.780 45.833 0.00 0.00 36.07 2.57
522 523 4.381505 GGCTCTCTTCACTCTTCAAGTAGG 60.382 50.000 0.00 0.00 36.07 3.18
523 524 4.461081 GCTCTCTTCACTCTTCAAGTAGGA 59.539 45.833 0.00 0.00 36.07 2.94
524 525 5.621329 GCTCTCTTCACTCTTCAAGTAGGAC 60.621 48.000 0.00 0.00 36.07 3.85
525 526 4.456222 TCTCTTCACTCTTCAAGTAGGACG 59.544 45.833 0.00 0.00 36.07 4.79
526 527 4.142790 TCTTCACTCTTCAAGTAGGACGT 58.857 43.478 0.00 0.00 36.07 4.34
527 528 3.917329 TCACTCTTCAAGTAGGACGTG 57.083 47.619 0.00 0.00 36.07 4.49
528 529 2.030185 TCACTCTTCAAGTAGGACGTGC 60.030 50.000 0.00 0.00 36.07 5.34
529 530 1.272769 ACTCTTCAAGTAGGACGTGCC 59.727 52.381 2.38 0.00 36.07 5.01
530 531 1.272490 CTCTTCAAGTAGGACGTGCCA 59.728 52.381 2.38 0.00 40.02 4.92
531 532 1.000506 TCTTCAAGTAGGACGTGCCAC 59.999 52.381 2.38 0.00 40.02 5.01
532 533 0.753867 TTCAAGTAGGACGTGCCACA 59.246 50.000 8.47 0.00 40.02 4.17
533 534 0.032952 TCAAGTAGGACGTGCCACAC 59.967 55.000 8.47 2.32 40.02 3.82
534 535 0.949105 CAAGTAGGACGTGCCACACC 60.949 60.000 8.47 0.00 40.02 4.16
535 536 2.430382 AAGTAGGACGTGCCACACCG 62.430 60.000 8.47 0.00 40.02 4.94
536 537 2.598099 TAGGACGTGCCACACCGA 60.598 61.111 2.38 0.00 40.02 4.69
537 538 1.980232 TAGGACGTGCCACACCGAT 60.980 57.895 2.38 0.00 40.02 4.18
538 539 0.680601 TAGGACGTGCCACACCGATA 60.681 55.000 2.38 0.00 40.02 2.92
539 540 1.518572 GGACGTGCCACACCGATAG 60.519 63.158 0.00 0.00 36.34 2.08
540 541 2.125673 ACGTGCCACACCGATAGC 60.126 61.111 0.00 0.00 0.00 2.97
541 542 2.125713 CGTGCCACACCGATAGCA 60.126 61.111 0.00 0.00 0.00 3.49
542 543 2.167219 CGTGCCACACCGATAGCAG 61.167 63.158 0.00 0.00 35.56 4.24
543 544 2.125147 TGCCACACCGATAGCAGC 60.125 61.111 0.00 0.00 0.00 5.25
544 545 3.264897 GCCACACCGATAGCAGCG 61.265 66.667 0.00 0.00 0.00 5.18
545 546 3.264897 CCACACCGATAGCAGCGC 61.265 66.667 0.00 0.00 0.00 5.92
546 547 2.509111 CACACCGATAGCAGCGCA 60.509 61.111 11.47 0.00 0.00 6.09
547 548 2.202797 ACACCGATAGCAGCGCAG 60.203 61.111 11.47 1.31 0.00 5.18
561 562 4.767255 GCAGCGTGGTGGCTAGCT 62.767 66.667 15.72 0.00 42.53 3.32
563 564 3.314331 AGCGTGGTGGCTAGCTGT 61.314 61.111 15.72 0.00 42.62 4.40
564 565 3.121030 GCGTGGTGGCTAGCTGTG 61.121 66.667 15.72 0.34 0.00 3.66
565 566 3.121030 CGTGGTGGCTAGCTGTGC 61.121 66.667 15.72 0.00 0.00 4.57
566 567 2.348998 GTGGTGGCTAGCTGTGCT 59.651 61.111 15.72 0.00 43.41 4.40
567 568 1.743252 GTGGTGGCTAGCTGTGCTC 60.743 63.158 15.72 0.00 40.44 4.26
568 569 2.510238 GGTGGCTAGCTGTGCTCG 60.510 66.667 15.72 0.00 40.44 5.03
569 570 3.191539 GTGGCTAGCTGTGCTCGC 61.192 66.667 15.72 7.41 44.83 5.03
570 571 3.385384 TGGCTAGCTGTGCTCGCT 61.385 61.111 15.72 9.39 44.91 4.93
571 572 2.125350 GGCTAGCTGTGCTCGCTT 60.125 61.111 15.72 0.00 44.91 4.68
572 573 2.170434 GGCTAGCTGTGCTCGCTTC 61.170 63.158 15.72 0.00 44.91 3.86
573 574 1.153667 GCTAGCTGTGCTCGCTTCT 60.154 57.895 7.70 0.00 42.76 2.85
574 575 0.739112 GCTAGCTGTGCTCGCTTCTT 60.739 55.000 7.70 0.00 42.76 2.52
575 576 1.276415 CTAGCTGTGCTCGCTTCTTC 58.724 55.000 0.00 0.00 40.44 2.87
576 577 0.891373 TAGCTGTGCTCGCTTCTTCT 59.109 50.000 0.00 0.00 40.44 2.85
577 578 0.034616 AGCTGTGCTCGCTTCTTCTT 59.965 50.000 0.00 0.00 30.62 2.52
578 579 0.165511 GCTGTGCTCGCTTCTTCTTG 59.834 55.000 0.00 0.00 0.00 3.02
579 580 0.795085 CTGTGCTCGCTTCTTCTTGG 59.205 55.000 0.00 0.00 0.00 3.61
580 581 0.392706 TGTGCTCGCTTCTTCTTGGA 59.607 50.000 0.00 0.00 0.00 3.53
581 582 1.074752 GTGCTCGCTTCTTCTTGGAG 58.925 55.000 0.00 0.00 0.00 3.86
582 583 0.969149 TGCTCGCTTCTTCTTGGAGA 59.031 50.000 0.00 0.00 0.00 3.71
583 584 1.067283 TGCTCGCTTCTTCTTGGAGAG 60.067 52.381 0.00 0.00 0.00 3.20
591 592 0.539051 CTTCTTGGAGAGCCACCGAT 59.461 55.000 0.00 0.00 45.94 4.18
632 633 4.805231 CCGTCACGGCCGCATACA 62.805 66.667 28.58 0.63 41.17 2.29
635 636 4.830765 TCACGGCCGCATACAGCC 62.831 66.667 28.58 0.00 46.17 4.85
667 668 0.541296 AGCCAAGGAGTGCAAGCAAT 60.541 50.000 0.00 0.00 0.00 3.56
688 708 0.833834 CTCCCACTCCGGCATATCCT 60.834 60.000 0.00 0.00 0.00 3.24
689 709 0.832135 TCCCACTCCGGCATATCCTC 60.832 60.000 0.00 0.00 0.00 3.71
691 711 1.674057 CACTCCGGCATATCCTCCC 59.326 63.158 0.00 0.00 0.00 4.30
692 712 1.908793 ACTCCGGCATATCCTCCCG 60.909 63.158 0.00 0.00 41.60 5.14
696 716 4.394712 GGCATATCCTCCCGGCCG 62.395 72.222 21.04 21.04 34.56 6.13
778 800 3.838271 GGCATCTCGTCTCGGCCA 61.838 66.667 2.24 0.00 44.01 5.36
779 801 2.583593 GCATCTCGTCTCGGCCAC 60.584 66.667 2.24 0.00 0.00 5.01
783 805 3.680786 CTCGTCTCGGCCACACCA 61.681 66.667 2.24 0.00 39.03 4.17
785 807 3.680786 CGTCTCGGCCACACCAGA 61.681 66.667 2.24 0.00 39.03 3.86
786 808 2.048127 GTCTCGGCCACACCAGAC 60.048 66.667 2.24 1.67 38.53 3.51
787 809 2.523168 TCTCGGCCACACCAGACA 60.523 61.111 2.24 0.00 39.03 3.41
788 810 2.357517 CTCGGCCACACCAGACAC 60.358 66.667 2.24 0.00 39.03 3.67
789 811 3.157949 TCGGCCACACCAGACACA 61.158 61.111 2.24 0.00 39.03 3.72
790 812 2.972505 CGGCCACACCAGACACAC 60.973 66.667 2.24 0.00 39.03 3.82
791 813 2.510906 GGCCACACCAGACACACT 59.489 61.111 0.00 0.00 38.86 3.55
792 814 1.598130 GGCCACACCAGACACACTC 60.598 63.158 0.00 0.00 38.86 3.51
799 821 0.179111 ACCAGACACACTCACACACG 60.179 55.000 0.00 0.00 0.00 4.49
1416 1965 4.742201 GCGCTGCTCAAGTCCGGA 62.742 66.667 0.00 0.00 0.00 5.14
1740 2289 2.606519 TGGTTGGAGGAGGACCCG 60.607 66.667 0.00 0.00 40.87 5.28
1920 2474 2.704572 GCTTCCTAGCTCATGTGTGTT 58.295 47.619 0.00 0.00 44.27 3.32
1921 2475 2.417933 GCTTCCTAGCTCATGTGTGTTG 59.582 50.000 0.00 0.00 44.27 3.33
1935 2489 4.739195 TGTGTGTTGGTTTTTCAGTTAGC 58.261 39.130 0.00 0.00 0.00 3.09
1948 2502 0.034059 AGTTAGCTGCGACTGCTTGT 59.966 50.000 14.20 0.00 43.34 3.16
1957 2511 1.865248 GCGACTGCTTGTTTGTGCATT 60.865 47.619 0.00 0.00 38.59 3.56
2008 2563 4.481368 AATCGGTGGTTTATGCTCACTA 57.519 40.909 0.00 0.00 0.00 2.74
2026 2584 6.294286 GCTCACTACTTGTCTCCATATACCTC 60.294 46.154 0.00 0.00 0.00 3.85
2079 2637 9.762381 TTATATTGAGTTTGGGAATTTGGTACT 57.238 29.630 0.00 0.00 0.00 2.73
2157 2715 1.700186 AGTTTCACTTCTGGAGGGGAC 59.300 52.381 0.00 0.00 0.00 4.46
2228 2789 4.767409 GGAACTTTTGCTGGAACCTTAGAT 59.233 41.667 0.00 0.00 0.00 1.98
2233 2794 1.630369 TGCTGGAACCTTAGATGCAGT 59.370 47.619 0.00 0.00 37.33 4.40
2247 2808 4.202441 AGATGCAGTGTTTCAGTTTCAGT 58.798 39.130 0.00 0.00 0.00 3.41
2319 2880 4.819630 TGCGGATTTTCTATATTGTGGGTC 59.180 41.667 0.00 0.00 0.00 4.46
2342 2903 6.529125 GTCATTGTTGGATAACTTGAATGCAG 59.471 38.462 0.00 0.00 37.68 4.41
2439 3000 9.490663 GCATTACTGAGTACATGATGTAAAAAC 57.509 33.333 6.89 0.00 34.21 2.43
2458 3020 0.598158 CAGTGCCCATTGTTGTGTGC 60.598 55.000 0.00 0.00 0.00 4.57
2480 3042 4.212214 GCACTTCACCTTTGAGTTCTACTG 59.788 45.833 0.00 0.00 31.71 2.74
2482 3044 4.141711 ACTTCACCTTTGAGTTCTACTGCA 60.142 41.667 0.00 0.00 31.71 4.41
2486 3048 4.576463 CACCTTTGAGTTCTACTGCAAACT 59.424 41.667 1.14 1.14 38.40 2.66
2491 3053 7.220875 CCTTTGAGTTCTACTGCAAACTTTTTC 59.779 37.037 3.15 0.00 35.90 2.29
2607 3176 4.227864 AGATAGGCTTTTGGGTTCTCTG 57.772 45.455 0.00 0.00 0.00 3.35
2615 3184 4.338400 GCTTTTGGGTTCTCTGTTGTAACT 59.662 41.667 0.00 0.00 0.00 2.24
2639 3208 0.174845 CGATCTACAAGGGTTCGGCA 59.825 55.000 0.00 0.00 0.00 5.69
2722 3293 0.257039 GGTGCTCTTGATGGATGGGT 59.743 55.000 0.00 0.00 0.00 4.51
2762 3333 3.817647 AGTTGCTCTCTTTTTGCCACTAG 59.182 43.478 0.00 0.00 32.19 2.57
2763 3334 3.492102 TGCTCTCTTTTTGCCACTAGT 57.508 42.857 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 9.199982 CACTTGTTCAATATTTTCTCAAATGCT 57.800 29.630 0.00 0.00 34.29 3.79
85 86 8.981647 ACACTTGTTCAATATTTTCTCAAATGC 58.018 29.630 0.00 0.00 34.29 3.56
107 108 9.651913 ACACTTGATTAACATTTTTCAAACACT 57.348 25.926 0.00 0.00 0.00 3.55
112 113 9.658799 TCCAAACACTTGATTAACATTTTTCAA 57.341 25.926 0.00 0.00 34.14 2.69
113 114 9.658799 TTCCAAACACTTGATTAACATTTTTCA 57.341 25.926 0.00 0.00 34.14 2.69
117 118 9.612066 ACATTTCCAAACACTTGATTAACATTT 57.388 25.926 0.00 0.00 34.14 2.32
118 119 9.612066 AACATTTCCAAACACTTGATTAACATT 57.388 25.926 0.00 0.00 34.14 2.71
124 125 9.612066 ACATTTAACATTTCCAAACACTTGATT 57.388 25.926 0.00 0.00 34.14 2.57
125 126 9.044150 CACATTTAACATTTCCAAACACTTGAT 57.956 29.630 0.00 0.00 34.14 2.57
126 127 7.010923 GCACATTTAACATTTCCAAACACTTGA 59.989 33.333 0.00 0.00 34.14 3.02
127 128 7.125113 GCACATTTAACATTTCCAAACACTTG 58.875 34.615 0.00 0.00 0.00 3.16
128 129 6.820656 TGCACATTTAACATTTCCAAACACTT 59.179 30.769 0.00 0.00 0.00 3.16
129 130 6.344500 TGCACATTTAACATTTCCAAACACT 58.656 32.000 0.00 0.00 0.00 3.55
130 131 6.595772 TGCACATTTAACATTTCCAAACAC 57.404 33.333 0.00 0.00 0.00 3.32
131 132 7.496920 TCAATGCACATTTAACATTTCCAAACA 59.503 29.630 0.00 0.00 31.82 2.83
132 133 7.859598 TCAATGCACATTTAACATTTCCAAAC 58.140 30.769 0.00 0.00 31.82 2.93
133 134 8.442632 TTCAATGCACATTTAACATTTCCAAA 57.557 26.923 0.00 0.00 31.82 3.28
134 135 8.442632 TTTCAATGCACATTTAACATTTCCAA 57.557 26.923 0.00 0.00 31.82 3.53
135 136 8.442632 TTTTCAATGCACATTTAACATTTCCA 57.557 26.923 0.00 0.00 31.82 3.53
238 239 9.528018 ACATTTTTCGAACACAAGATTAACATT 57.472 25.926 0.00 0.00 0.00 2.71
239 240 9.528018 AACATTTTTCGAACACAAGATTAACAT 57.472 25.926 0.00 0.00 0.00 2.71
240 241 8.918961 AACATTTTTCGAACACAAGATTAACA 57.081 26.923 0.00 0.00 0.00 2.41
244 245 9.743057 TCATTAACATTTTTCGAACACAAGATT 57.257 25.926 0.00 0.00 0.00 2.40
245 246 9.743057 TTCATTAACATTTTTCGAACACAAGAT 57.257 25.926 0.00 0.00 0.00 2.40
246 247 9.015577 GTTCATTAACATTTTTCGAACACAAGA 57.984 29.630 0.00 0.00 35.56 3.02
247 248 8.265998 GGTTCATTAACATTTTTCGAACACAAG 58.734 33.333 0.00 0.00 37.34 3.16
248 249 7.759886 TGGTTCATTAACATTTTTCGAACACAA 59.240 29.630 0.00 0.00 37.34 3.33
249 250 7.258441 TGGTTCATTAACATTTTTCGAACACA 58.742 30.769 0.00 0.00 37.34 3.72
250 251 7.687005 TGGTTCATTAACATTTTTCGAACAC 57.313 32.000 0.00 0.00 37.34 3.32
251 252 8.879342 AATGGTTCATTAACATTTTTCGAACA 57.121 26.923 0.00 0.00 37.34 3.18
252 253 9.579610 CAAATGGTTCATTAACATTTTTCGAAC 57.420 29.630 0.00 0.00 37.34 3.95
253 254 9.534565 TCAAATGGTTCATTAACATTTTTCGAA 57.465 25.926 0.00 0.00 37.34 3.71
254 255 9.534565 TTCAAATGGTTCATTAACATTTTTCGA 57.465 25.926 0.00 0.00 37.34 3.71
303 304 9.672086 ACATTTTATTAATATACGCGCAACATT 57.328 25.926 5.73 3.41 0.00 2.71
304 305 9.672086 AACATTTTATTAATATACGCGCAACAT 57.328 25.926 5.73 0.00 0.00 2.71
443 444 7.414814 TTTTTCGCTTGTTTCTTCAGTTTTT 57.585 28.000 0.00 0.00 0.00 1.94
481 482 1.411246 GCCAGTTTTCTCCCGGTTTTT 59.589 47.619 0.00 0.00 0.00 1.94
482 483 1.037493 GCCAGTTTTCTCCCGGTTTT 58.963 50.000 0.00 0.00 0.00 2.43
483 484 0.185175 AGCCAGTTTTCTCCCGGTTT 59.815 50.000 0.00 0.00 0.00 3.27
484 485 0.250770 GAGCCAGTTTTCTCCCGGTT 60.251 55.000 0.00 0.00 0.00 4.44
485 486 1.128188 AGAGCCAGTTTTCTCCCGGT 61.128 55.000 0.00 0.00 0.00 5.28
486 487 0.391793 GAGAGCCAGTTTTCTCCCGG 60.392 60.000 0.00 0.00 34.99 5.73
487 488 0.610687 AGAGAGCCAGTTTTCTCCCG 59.389 55.000 0.00 0.00 40.53 5.14
488 489 2.039084 TGAAGAGAGCCAGTTTTCTCCC 59.961 50.000 0.00 0.00 40.53 4.30
489 490 3.070748 GTGAAGAGAGCCAGTTTTCTCC 58.929 50.000 0.00 0.00 40.53 3.71
490 491 3.993736 GAGTGAAGAGAGCCAGTTTTCTC 59.006 47.826 0.00 0.00 40.07 2.87
491 492 3.645687 AGAGTGAAGAGAGCCAGTTTTCT 59.354 43.478 0.00 0.00 0.00 2.52
492 493 4.001618 AGAGTGAAGAGAGCCAGTTTTC 57.998 45.455 0.00 0.00 0.00 2.29
493 494 4.141620 TGAAGAGTGAAGAGAGCCAGTTTT 60.142 41.667 0.00 0.00 0.00 2.43
494 495 3.389329 TGAAGAGTGAAGAGAGCCAGTTT 59.611 43.478 0.00 0.00 0.00 2.66
495 496 2.968574 TGAAGAGTGAAGAGAGCCAGTT 59.031 45.455 0.00 0.00 0.00 3.16
496 497 2.603021 TGAAGAGTGAAGAGAGCCAGT 58.397 47.619 0.00 0.00 0.00 4.00
497 498 3.006752 ACTTGAAGAGTGAAGAGAGCCAG 59.993 47.826 0.00 0.00 37.17 4.85
498 499 2.968574 ACTTGAAGAGTGAAGAGAGCCA 59.031 45.455 0.00 0.00 37.17 4.75
499 500 3.676291 ACTTGAAGAGTGAAGAGAGCC 57.324 47.619 0.00 0.00 37.17 4.70
500 501 4.461081 TCCTACTTGAAGAGTGAAGAGAGC 59.539 45.833 0.00 0.00 39.48 4.09
501 502 5.391523 CGTCCTACTTGAAGAGTGAAGAGAG 60.392 48.000 0.00 0.00 39.48 3.20
502 503 4.456222 CGTCCTACTTGAAGAGTGAAGAGA 59.544 45.833 0.00 0.00 39.48 3.10
503 504 4.216687 ACGTCCTACTTGAAGAGTGAAGAG 59.783 45.833 0.00 0.00 39.48 2.85
504 505 4.023107 CACGTCCTACTTGAAGAGTGAAGA 60.023 45.833 0.00 0.00 39.48 2.87
505 506 4.230657 CACGTCCTACTTGAAGAGTGAAG 58.769 47.826 0.00 0.00 39.48 3.02
506 507 3.552273 GCACGTCCTACTTGAAGAGTGAA 60.552 47.826 0.00 0.00 39.48 3.18
507 508 2.030185 GCACGTCCTACTTGAAGAGTGA 60.030 50.000 0.00 0.00 39.48 3.41
508 509 2.329379 GCACGTCCTACTTGAAGAGTG 58.671 52.381 0.00 0.93 39.48 3.51
509 510 1.272769 GGCACGTCCTACTTGAAGAGT 59.727 52.381 0.00 0.00 42.55 3.24
510 511 1.272490 TGGCACGTCCTACTTGAAGAG 59.728 52.381 0.00 0.00 35.26 2.85
511 512 1.000506 GTGGCACGTCCTACTTGAAGA 59.999 52.381 0.00 0.00 35.26 2.87
512 513 1.270094 TGTGGCACGTCCTACTTGAAG 60.270 52.381 13.77 0.00 35.26 3.02
513 514 0.753867 TGTGGCACGTCCTACTTGAA 59.246 50.000 13.77 0.00 35.26 2.69
514 515 0.032952 GTGTGGCACGTCCTACTTGA 59.967 55.000 13.77 0.00 35.26 3.02
515 516 0.949105 GGTGTGGCACGTCCTACTTG 60.949 60.000 19.65 0.00 34.83 3.16
516 517 1.370064 GGTGTGGCACGTCCTACTT 59.630 57.895 19.65 0.00 34.83 2.24
517 518 2.927580 CGGTGTGGCACGTCCTACT 61.928 63.158 22.63 0.00 34.83 2.57
518 519 2.221906 ATCGGTGTGGCACGTCCTAC 62.222 60.000 22.63 11.96 34.83 3.18
519 520 0.680601 TATCGGTGTGGCACGTCCTA 60.681 55.000 22.63 15.74 34.83 2.94
520 521 1.945354 CTATCGGTGTGGCACGTCCT 61.945 60.000 22.63 12.08 34.83 3.85
521 522 1.518572 CTATCGGTGTGGCACGTCC 60.519 63.158 13.77 16.17 34.83 4.79
522 523 2.165301 GCTATCGGTGTGGCACGTC 61.165 63.158 13.77 8.55 34.83 4.34
523 524 2.125673 GCTATCGGTGTGGCACGT 60.126 61.111 13.77 0.00 34.83 4.49
524 525 2.125713 TGCTATCGGTGTGGCACG 60.126 61.111 13.77 0.77 34.83 5.34
525 526 2.464459 GCTGCTATCGGTGTGGCAC 61.464 63.158 11.55 11.55 0.00 5.01
526 527 2.125147 GCTGCTATCGGTGTGGCA 60.125 61.111 0.00 0.00 0.00 4.92
527 528 3.264897 CGCTGCTATCGGTGTGGC 61.265 66.667 0.00 0.00 0.00 5.01
528 529 3.264897 GCGCTGCTATCGGTGTGG 61.265 66.667 0.00 0.00 0.00 4.17
529 530 2.509111 TGCGCTGCTATCGGTGTG 60.509 61.111 9.73 0.00 0.00 3.82
530 531 2.202797 CTGCGCTGCTATCGGTGT 60.203 61.111 9.73 0.00 0.00 4.16
531 532 3.634072 GCTGCGCTGCTATCGGTG 61.634 66.667 29.28 0.00 0.00 4.94
534 535 3.981159 CACGCTGCGCTGCTATCG 61.981 66.667 32.06 20.81 0.00 2.92
535 536 3.634072 CCACGCTGCGCTGCTATC 61.634 66.667 32.06 8.45 0.00 2.08
536 537 4.457496 ACCACGCTGCGCTGCTAT 62.457 61.111 32.06 19.87 0.00 2.97
544 545 4.767255 AGCTAGCCACCACGCTGC 62.767 66.667 12.13 0.00 40.08 5.25
545 546 2.816958 CAGCTAGCCACCACGCTG 60.817 66.667 12.13 0.00 43.10 5.18
546 547 3.314331 ACAGCTAGCCACCACGCT 61.314 61.111 12.13 0.00 43.09 5.07
547 548 3.121030 CACAGCTAGCCACCACGC 61.121 66.667 12.13 0.00 0.00 5.34
548 549 3.121030 GCACAGCTAGCCACCACG 61.121 66.667 12.13 0.00 0.00 4.94
549 550 1.743252 GAGCACAGCTAGCCACCAC 60.743 63.158 12.13 0.00 39.88 4.16
550 551 2.665000 GAGCACAGCTAGCCACCA 59.335 61.111 12.13 0.00 39.88 4.17
551 552 2.510238 CGAGCACAGCTAGCCACC 60.510 66.667 12.13 0.00 39.88 4.61
556 557 1.135141 AGAAGAAGCGAGCACAGCTAG 60.135 52.381 0.00 0.00 45.31 3.42
557 558 0.891373 AGAAGAAGCGAGCACAGCTA 59.109 50.000 0.00 0.00 45.31 3.32
559 560 0.165511 CAAGAAGAAGCGAGCACAGC 59.834 55.000 0.00 0.00 0.00 4.40
560 561 0.795085 CCAAGAAGAAGCGAGCACAG 59.205 55.000 0.00 0.00 0.00 3.66
561 562 0.392706 TCCAAGAAGAAGCGAGCACA 59.607 50.000 0.00 0.00 0.00 4.57
562 563 1.074752 CTCCAAGAAGAAGCGAGCAC 58.925 55.000 0.00 0.00 0.00 4.40
563 564 0.969149 TCTCCAAGAAGAAGCGAGCA 59.031 50.000 0.00 0.00 0.00 4.26
564 565 1.639280 CTCTCCAAGAAGAAGCGAGC 58.361 55.000 0.00 0.00 0.00 5.03
565 566 1.639280 GCTCTCCAAGAAGAAGCGAG 58.361 55.000 0.00 0.00 0.00 5.03
566 567 0.247736 GGCTCTCCAAGAAGAAGCGA 59.752 55.000 0.00 0.00 0.00 4.93
567 568 0.036952 TGGCTCTCCAAGAAGAAGCG 60.037 55.000 0.00 0.00 39.99 4.68
568 569 1.447945 GTGGCTCTCCAAGAAGAAGC 58.552 55.000 0.00 0.00 45.53 3.86
569 570 1.674221 CGGTGGCTCTCCAAGAAGAAG 60.674 57.143 0.00 0.00 45.53 2.85
570 571 0.321671 CGGTGGCTCTCCAAGAAGAA 59.678 55.000 0.00 0.00 45.53 2.52
571 572 0.541998 TCGGTGGCTCTCCAAGAAGA 60.542 55.000 0.00 0.00 45.53 2.87
572 573 0.539051 ATCGGTGGCTCTCCAAGAAG 59.461 55.000 0.00 0.00 45.53 2.85
573 574 0.537188 GATCGGTGGCTCTCCAAGAA 59.463 55.000 0.00 0.00 45.53 2.52
574 575 1.667154 CGATCGGTGGCTCTCCAAGA 61.667 60.000 7.38 0.00 45.53 3.02
575 576 1.227089 CGATCGGTGGCTCTCCAAG 60.227 63.158 7.38 0.00 45.53 3.61
576 577 1.043116 ATCGATCGGTGGCTCTCCAA 61.043 55.000 16.41 0.00 45.53 3.53
577 578 1.455773 ATCGATCGGTGGCTCTCCA 60.456 57.895 16.41 0.00 40.85 3.86
578 579 1.287503 GATCGATCGGTGGCTCTCC 59.712 63.158 16.41 0.00 0.00 3.71
579 580 1.081774 CGATCGATCGGTGGCTCTC 60.082 63.158 34.54 2.55 45.93 3.20
580 581 3.034878 CGATCGATCGGTGGCTCT 58.965 61.111 34.54 0.00 45.93 4.09
628 629 4.386951 TGCACGCGGTGGCTGTAT 62.387 61.111 12.47 0.00 36.88 2.29
648 649 0.541296 ATTGCTTGCACTCCTTGGCT 60.541 50.000 0.00 0.00 0.00 4.75
667 668 1.629043 GATATGCCGGAGTGGGAGTA 58.371 55.000 5.05 0.00 43.72 2.59
741 763 0.784778 GATTCCGAAGAATAGCCGCG 59.215 55.000 0.00 0.00 42.93 6.46
778 800 0.901827 TGTGTGAGTGTGTCTGGTGT 59.098 50.000 0.00 0.00 0.00 4.16
779 801 1.290203 GTGTGTGAGTGTGTCTGGTG 58.710 55.000 0.00 0.00 0.00 4.17
783 805 1.327690 ACCCGTGTGTGAGTGTGTCT 61.328 55.000 0.00 0.00 0.00 3.41
785 807 1.143183 GACCCGTGTGTGAGTGTGT 59.857 57.895 0.00 0.00 0.00 3.72
786 808 0.461163 TTGACCCGTGTGTGAGTGTG 60.461 55.000 0.00 0.00 0.00 3.82
787 809 0.461339 GTTGACCCGTGTGTGAGTGT 60.461 55.000 0.00 0.00 0.00 3.55
788 810 1.157870 GGTTGACCCGTGTGTGAGTG 61.158 60.000 0.00 0.00 0.00 3.51
789 811 1.145377 GGTTGACCCGTGTGTGAGT 59.855 57.895 0.00 0.00 0.00 3.41
790 812 0.677288 TAGGTTGACCCGTGTGTGAG 59.323 55.000 0.00 0.00 38.74 3.51
791 813 0.677288 CTAGGTTGACCCGTGTGTGA 59.323 55.000 0.00 0.00 38.74 3.58
792 814 0.677288 TCTAGGTTGACCCGTGTGTG 59.323 55.000 0.00 0.00 38.74 3.82
799 821 3.017442 GCCAGATTTTCTAGGTTGACCC 58.983 50.000 0.00 0.00 36.42 4.46
958 996 3.631046 GCCATAGGAGAGGGGGCG 61.631 72.222 0.00 0.00 34.56 6.13
963 1020 0.755686 GTCACAGGCCATAGGAGAGG 59.244 60.000 5.01 0.00 0.00 3.69
1416 1965 3.118956 CGGAGTTCTTGGAGAGCTTGTAT 60.119 47.826 0.00 0.00 35.86 2.29
1509 2058 3.164011 GCGACCTTGACGACGACG 61.164 66.667 5.58 5.58 45.75 5.12
1605 2154 2.747855 GTGAGGCCAAGGAAGCGG 60.748 66.667 5.01 0.00 0.00 5.52
1740 2289 2.936032 AGCAACAGGGAGGGGTCC 60.936 66.667 0.00 0.00 0.00 4.46
1828 2377 7.435192 TCTGATGATATAAGCAACTGTACAACG 59.565 37.037 0.00 0.00 0.00 4.10
1935 2489 0.931662 GCACAAACAAGCAGTCGCAG 60.932 55.000 0.00 0.00 42.27 5.18
1948 2502 3.772387 TGATTGAGGGGTAATGCACAAA 58.228 40.909 0.00 0.00 0.00 2.83
1957 2511 6.195600 ACTTTACTTGTTGATTGAGGGGTA 57.804 37.500 0.00 0.00 0.00 3.69
2080 2638 8.969260 TCTACATCAGCAAAACTATCATCAAT 57.031 30.769 0.00 0.00 0.00 2.57
2228 2789 5.182487 TCTTACTGAAACTGAAACACTGCA 58.818 37.500 0.00 0.00 0.00 4.41
2271 2832 6.492429 AGTTGGTTAACAGGGAAAATCCTAAC 59.508 38.462 8.10 0.00 39.30 2.34
2319 2880 5.808540 CCTGCATTCAAGTTATCCAACAATG 59.191 40.000 0.00 0.00 37.10 2.82
2342 2903 3.959535 TTCAATTGATGGGTTTCAGCC 57.040 42.857 9.40 0.00 36.00 4.85
2439 3000 3.573569 CACACAACAATGGGCACTG 57.426 52.632 0.00 0.00 31.04 3.66
2458 3020 4.212214 GCAGTAGAACTCAAAGGTGAAGTG 59.788 45.833 0.00 0.00 31.88 3.16
2480 3042 9.900264 CATGTTGTACTTAAAGAAAAAGTTTGC 57.100 29.630 0.00 0.00 38.18 3.68
2541 3108 9.883142 CAGGCCCAAGATAAATAAATAACAAAA 57.117 29.630 0.00 0.00 0.00 2.44
2552 3119 4.895297 CCATTGTACAGGCCCAAGATAAAT 59.105 41.667 0.00 0.00 0.00 1.40
2607 3176 4.445452 TGTAGATCGGGTCAGTTACAAC 57.555 45.455 0.00 0.00 0.00 3.32
2639 3208 9.753674 CTCCTAGAGGATTCTGAACTATTCTAT 57.246 37.037 0.00 0.00 44.46 1.98
2680 3251 5.276820 CCGCAGAAAATGAGAAAAACAAACC 60.277 40.000 0.00 0.00 0.00 3.27
2762 3333 6.775594 AGGCCAAGAACTCCATATTTTAAC 57.224 37.500 5.01 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.