Multiple sequence alignment - TraesCS1D01G389800

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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 TraesCS1D01G389800 chr1D 100.000 3200 0 0 1 3200 461423928 461420729 0.000000e+00 5910.0
1 TraesCS1D01G389800 chr1D 87.003 377 42 5 1000 1371 461539107 461538733 4.940000e-113 418.0
2 TraesCS1D01G389800 chr1D 85.294 374 45 7 1000 1371 461752702 461752337 8.380000e-101 377.0
3 TraesCS1D01G389800 chr1A 92.087 2262 125 23 542 2770 552909067 552906827 0.000000e+00 3136.0
4 TraesCS1D01G389800 chr1A 87.200 375 35 9 1000 1366 552976530 552976161 6.390000e-112 414.0
5 TraesCS1D01G389800 chr1A 84.881 377 41 13 1000 1371 553047248 553046883 1.810000e-97 366.0
6 TraesCS1D01G389800 chr1A 83.088 408 44 10 1 403 552909597 552909210 6.570000e-92 348.0
7 TraesCS1D01G389800 chr1A 93.137 204 13 1 2794 2996 552906551 552906348 6.710000e-77 298.0
8 TraesCS1D01G389800 chr1A 77.342 459 72 20 1139 1570 553133960 553133507 3.190000e-60 243.0
9 TraesCS1D01G389800 chr1B 93.734 1915 82 15 836 2736 634313853 634311963 0.000000e+00 2837.0
10 TraesCS1D01G389800 chr1B 91.791 670 35 2 2090 2759 634251802 634251153 0.000000e+00 915.0
11 TraesCS1D01G389800 chr1B 85.942 377 48 3 1000 1372 634564798 634565173 6.430000e-107 398.0
12 TraesCS1D01G389800 chr1B 87.407 270 25 5 136 404 634314371 634314110 5.190000e-78 302.0
13 TraesCS1D01G389800 chr1B 90.265 226 14 2 2983 3200 634250361 634250136 4.040000e-74 289.0
14 TraesCS1D01G389800 chr1B 93.007 143 9 1 2370 2512 634288207 634288066 1.160000e-49 207.0
15 TraesCS1D01G389800 chr1B 93.478 138 7 1 2861 2996 634250564 634250427 1.500000e-48 204.0
16 TraesCS1D01G389800 chr1B 91.262 103 9 0 1556 1658 634251900 634251798 1.200000e-29 141.0
17 TraesCS1D01G389800 chr1B 97.101 69 2 0 2794 2862 634250726 634250658 2.020000e-22 117.0
18 TraesCS1D01G389800 chr1B 98.113 53 1 0 769 821 634313953 634313901 3.400000e-15 93.5
19 TraesCS1D01G389800 chr1B 97.727 44 1 0 2756 2799 634251031 634250988 3.420000e-10 76.8
20 TraesCS1D01G389800 chrUn 87.766 376 39 5 1001 1371 1068260 1067887 1.760000e-117 433.0
21 TraesCS1D01G389800 chr6D 94.444 162 9 0 2477 2638 467802432 467802271 1.910000e-62 250.0
22 TraesCS1D01G389800 chr6D 92.899 169 11 1 2477 2645 128093068 128092901 8.870000e-61 244.0
23 TraesCS1D01G389800 chr5A 92.857 168 12 0 2477 2644 320214405 320214238 8.870000e-61 244.0
24 TraesCS1D01G389800 chr3D 93.827 162 10 0 2477 2638 375693829 375693990 8.870000e-61 244.0
25 TraesCS1D01G389800 chr3D 86.256 211 25 3 1042 1252 31868168 31868374 3.210000e-55 226.0
26 TraesCS1D01G389800 chr7B 92.814 167 12 0 2473 2639 176002996 176002830 3.190000e-60 243.0
27 TraesCS1D01G389800 chr7A 93.293 164 11 0 2476 2639 494786828 494786991 3.190000e-60 243.0
28 TraesCS1D01G389800 chr3A 90.683 161 13 2 1042 1201 44442065 44441906 2.500000e-51 213.0


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 TraesCS1D01G389800 chr1D 461420729 461423928 3199 True 5910.000000 5910 100.000000 1 3200 1 chr1D.!!$R1 3199
1 TraesCS1D01G389800 chr1A 552906348 552909597 3249 True 1260.666667 3136 89.437333 1 2996 3 chr1A.!!$R4 2995
2 TraesCS1D01G389800 chr1B 634311963 634314371 2408 True 1077.500000 2837 93.084667 136 2736 3 chr1B.!!$R3 2600
3 TraesCS1D01G389800 chr1B 634250136 634251900 1764 True 290.466667 915 93.604000 1556 3200 6 chr1B.!!$R2 1644

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
92 94 0.032515 TGGAGGAATCCGACCAGCTA 60.033 55.0 14.91 0.00 33.10 3.32 F
531 583 0.181350 AAGCCGGCCAGAGGAATAAG 59.819 55.0 26.15 0.00 0.00 1.73 F
898 992 0.325296 ATAAGCGGACTCAGGTGGGA 60.325 55.0 0.00 0.00 0.00 4.37 F
1878 1994 0.528470 ACTCTCAGGAGCGCTTGTAC 59.472 55.0 13.26 2.41 42.98 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1928 0.108186 CCTCAACACTGAGCGGCATA 60.108 55.000 1.45 0.0 46.76 3.14 R
1905 2021 0.109086 AGACCGTGAGCTGACAATCG 60.109 55.000 3.68 0.0 0.00 3.34 R
1988 2104 0.752658 CACCTCATCATCGCCTACCA 59.247 55.000 0.00 0.0 0.00 3.25 R
3020 3707 1.203013 GGAACTGTAGGCCCAAAACCT 60.203 52.381 0.00 0.0 41.57 3.50 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
37 38 7.616528 TTGATTATGTGACTAGATGGATGGA 57.383 36.000 0.00 0.00 0.00 3.41
50 51 4.101448 ATGGAGCTGCGTGGGGAC 62.101 66.667 0.00 0.00 0.00 4.46
58 59 3.351416 GCGTGGGGACGTCAAACC 61.351 66.667 18.91 16.15 35.26 3.27
59 60 2.424302 CGTGGGGACGTCAAACCT 59.576 61.111 18.91 0.00 0.00 3.50
62 63 0.464916 GTGGGGACGTCAAACCTTGT 60.465 55.000 18.91 0.00 0.00 3.16
63 64 0.256464 TGGGGACGTCAAACCTTGTT 59.744 50.000 18.91 0.00 0.00 2.83
65 66 2.092538 TGGGGACGTCAAACCTTGTTTA 60.093 45.455 18.91 0.00 0.00 2.01
72 73 7.308710 GGGACGTCAAACCTTGTTTATTCAATA 60.309 37.037 18.91 0.00 0.00 1.90
91 93 0.692419 ATGGAGGAATCCGACCAGCT 60.692 55.000 20.99 7.74 37.95 4.24
92 94 0.032515 TGGAGGAATCCGACCAGCTA 60.033 55.000 14.91 0.00 33.10 3.32
100 102 2.291043 CCGACCAGCTACCAAGGGT 61.291 63.158 0.00 0.00 40.16 4.34
101 103 1.079127 CGACCAGCTACCAAGGGTG 60.079 63.158 0.00 0.00 36.19 4.61
125 127 2.231380 GGGGGAGGGCAGAGAAACA 61.231 63.158 0.00 0.00 0.00 2.83
126 128 1.767692 GGGGAGGGCAGAGAAACAA 59.232 57.895 0.00 0.00 0.00 2.83
127 129 0.609406 GGGGAGGGCAGAGAAACAAC 60.609 60.000 0.00 0.00 0.00 3.32
128 130 0.402121 GGGAGGGCAGAGAAACAACT 59.598 55.000 0.00 0.00 0.00 3.16
129 131 1.528129 GGAGGGCAGAGAAACAACTG 58.472 55.000 0.00 0.00 37.22 3.16
130 132 1.072331 GGAGGGCAGAGAAACAACTGA 59.928 52.381 0.00 0.00 36.38 3.41
131 133 2.421619 GAGGGCAGAGAAACAACTGAG 58.578 52.381 0.00 0.00 36.38 3.35
132 134 1.072965 AGGGCAGAGAAACAACTGAGG 59.927 52.381 0.00 0.00 36.38 3.86
227 229 2.748209 TACCACCTCTCATCCGATCA 57.252 50.000 0.00 0.00 0.00 2.92
230 232 3.576861 ACCACCTCTCATCCGATCAATA 58.423 45.455 0.00 0.00 0.00 1.90
232 234 4.594920 ACCACCTCTCATCCGATCAATATT 59.405 41.667 0.00 0.00 0.00 1.28
259 263 4.310769 CCATCCGATGTTCTTGGTAGATC 58.689 47.826 7.60 0.00 0.00 2.75
317 321 5.512788 CGATCAATGCATCACCTTGTAAAAC 59.487 40.000 0.00 0.00 0.00 2.43
378 385 9.573133 AATCTTACATCAAATTTTCACGGATTC 57.427 29.630 0.00 0.00 0.00 2.52
404 411 2.425143 AATGCCCTCATTCATGTCGT 57.575 45.000 0.00 0.00 38.47 4.34
412 463 2.083774 TCATTCATGTCGTTCCAAGCC 58.916 47.619 0.00 0.00 0.00 4.35
418 469 1.371558 GTCGTTCCAAGCCACCTCT 59.628 57.895 0.00 0.00 0.00 3.69
421 472 0.593128 CGTTCCAAGCCACCTCTTTG 59.407 55.000 0.00 0.00 0.00 2.77
425 476 1.181098 CCAAGCCACCTCTTTGGGTG 61.181 60.000 6.67 6.67 46.96 4.61
467 519 4.058124 CGAGAATGAGGAAGAAACACACA 58.942 43.478 0.00 0.00 0.00 3.72
470 522 4.576463 AGAATGAGGAAGAAACACACACAC 59.424 41.667 0.00 0.00 0.00 3.82
471 523 3.342377 TGAGGAAGAAACACACACACA 57.658 42.857 0.00 0.00 0.00 3.72
472 524 3.006940 TGAGGAAGAAACACACACACAC 58.993 45.455 0.00 0.00 0.00 3.82
473 525 3.006940 GAGGAAGAAACACACACACACA 58.993 45.455 0.00 0.00 0.00 3.72
475 527 2.486203 GGAAGAAACACACACACACACA 59.514 45.455 0.00 0.00 0.00 3.72
476 528 3.488489 GAAGAAACACACACACACACAC 58.512 45.455 0.00 0.00 0.00 3.82
478 530 2.483877 AGAAACACACACACACACACAG 59.516 45.455 0.00 0.00 0.00 3.66
480 532 1.725641 ACACACACACACACACAGAG 58.274 50.000 0.00 0.00 0.00 3.35
481 533 1.275010 ACACACACACACACACAGAGA 59.725 47.619 0.00 0.00 0.00 3.10
482 534 1.929169 CACACACACACACACAGAGAG 59.071 52.381 0.00 0.00 0.00 3.20
483 535 1.824852 ACACACACACACACAGAGAGA 59.175 47.619 0.00 0.00 0.00 3.10
484 536 2.159184 ACACACACACACACAGAGAGAG 60.159 50.000 0.00 0.00 0.00 3.20
485 537 2.099756 CACACACACACACAGAGAGAGA 59.900 50.000 0.00 0.00 0.00 3.10
486 538 2.360483 ACACACACACACAGAGAGAGAG 59.640 50.000 0.00 0.00 0.00 3.20
487 539 2.620585 CACACACACACAGAGAGAGAGA 59.379 50.000 0.00 0.00 0.00 3.10
488 540 2.884012 ACACACACACAGAGAGAGAGAG 59.116 50.000 0.00 0.00 0.00 3.20
489 541 3.145286 CACACACACAGAGAGAGAGAGA 58.855 50.000 0.00 0.00 0.00 3.10
490 542 3.189080 CACACACACAGAGAGAGAGAGAG 59.811 52.174 0.00 0.00 0.00 3.20
491 543 3.072330 ACACACACAGAGAGAGAGAGAGA 59.928 47.826 0.00 0.00 0.00 3.10
492 544 3.686241 CACACACAGAGAGAGAGAGAGAG 59.314 52.174 0.00 0.00 0.00 3.20
493 545 3.582647 ACACACAGAGAGAGAGAGAGAGA 59.417 47.826 0.00 0.00 0.00 3.10
494 546 4.186926 CACACAGAGAGAGAGAGAGAGAG 58.813 52.174 0.00 0.00 0.00 3.20
495 547 4.081476 CACACAGAGAGAGAGAGAGAGAGA 60.081 50.000 0.00 0.00 0.00 3.10
496 548 4.161189 ACACAGAGAGAGAGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
497 549 4.403752 CACAGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
498 550 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
499 551 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
500 552 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
512 564 3.706594 GAGAGAGAGAGAGAGAGAGGACA 59.293 52.174 0.00 0.00 0.00 4.02
516 568 2.024414 GAGAGAGAGAGAGGACAAGCC 58.976 57.143 0.00 0.00 0.00 4.35
520 572 3.378399 GAGAGAGGACAAGCCGGCC 62.378 68.421 26.15 7.48 43.43 6.13
531 583 0.181350 AAGCCGGCCAGAGGAATAAG 59.819 55.000 26.15 0.00 0.00 1.73
532 584 0.691078 AGCCGGCCAGAGGAATAAGA 60.691 55.000 26.15 0.00 0.00 2.10
533 585 0.398318 GCCGGCCAGAGGAATAAGAT 59.602 55.000 18.11 0.00 0.00 2.40
534 586 1.879796 GCCGGCCAGAGGAATAAGATG 60.880 57.143 18.11 0.00 0.00 2.90
535 587 1.271054 CCGGCCAGAGGAATAAGATGG 60.271 57.143 2.24 0.00 0.00 3.51
536 588 1.271054 CGGCCAGAGGAATAAGATGGG 60.271 57.143 2.24 0.00 0.00 4.00
537 589 1.902938 GCCAGAGGAATAAGATGGGC 58.097 55.000 0.00 0.00 0.00 5.36
538 590 1.423161 GCCAGAGGAATAAGATGGGCT 59.577 52.381 0.00 0.00 37.22 5.19
539 591 2.813354 GCCAGAGGAATAAGATGGGCTG 60.813 54.545 0.00 0.00 37.22 4.85
540 592 2.224719 CCAGAGGAATAAGATGGGCTGG 60.225 54.545 0.00 0.00 36.14 4.85
541 593 2.707791 CAGAGGAATAAGATGGGCTGGA 59.292 50.000 0.00 0.00 0.00 3.86
547 599 2.396590 TAAGATGGGCTGGAACGTTC 57.603 50.000 20.14 20.14 0.00 3.95
551 603 0.693049 ATGGGCTGGAACGTTCTCTT 59.307 50.000 26.32 8.05 0.00 2.85
554 606 1.542547 GGGCTGGAACGTTCTCTTGAA 60.543 52.381 26.32 6.28 0.00 2.69
559 611 4.510340 GCTGGAACGTTCTCTTGAAACTTA 59.490 41.667 26.32 0.00 33.52 2.24
568 620 4.637276 TCTCTTGAAACTTATCGTTGCCA 58.363 39.130 0.00 0.00 35.61 4.92
602 654 3.572584 AGCGGTCTTCGTTAAGTGTTAG 58.427 45.455 0.00 0.00 41.72 2.34
627 681 8.303876 AGTTCTTCGGTGCAATATTGTTTAATT 58.696 29.630 16.61 0.00 0.00 1.40
744 804 1.222567 AAATATCTCAAGGGCGGGGT 58.777 50.000 0.00 0.00 0.00 4.95
750 810 2.203422 CAAGGGCGGGGTTGTTGA 60.203 61.111 0.00 0.00 0.00 3.18
751 811 1.830408 CAAGGGCGGGGTTGTTGAA 60.830 57.895 0.00 0.00 0.00 2.69
752 812 1.530655 AAGGGCGGGGTTGTTGAAG 60.531 57.895 0.00 0.00 0.00 3.02
753 813 2.002018 AAGGGCGGGGTTGTTGAAGA 62.002 55.000 0.00 0.00 0.00 2.87
754 814 1.529713 GGGCGGGGTTGTTGAAGAA 60.530 57.895 0.00 0.00 0.00 2.52
755 815 1.110518 GGGCGGGGTTGTTGAAGAAA 61.111 55.000 0.00 0.00 0.00 2.52
756 816 0.747852 GGCGGGGTTGTTGAAGAAAA 59.252 50.000 0.00 0.00 0.00 2.29
757 817 1.343142 GGCGGGGTTGTTGAAGAAAAT 59.657 47.619 0.00 0.00 0.00 1.82
758 818 2.559231 GGCGGGGTTGTTGAAGAAAATA 59.441 45.455 0.00 0.00 0.00 1.40
761 821 5.051153 GCGGGGTTGTTGAAGAAAATAAAA 58.949 37.500 0.00 0.00 0.00 1.52
818 878 0.530744 CACCGTACAGAGCCTAAGCA 59.469 55.000 0.00 0.00 43.56 3.91
821 881 1.469940 CCGTACAGAGCCTAAGCACAG 60.470 57.143 0.00 0.00 43.56 3.66
822 882 1.469940 CGTACAGAGCCTAAGCACAGG 60.470 57.143 0.00 0.00 43.56 4.00
823 883 1.825474 GTACAGAGCCTAAGCACAGGA 59.175 52.381 7.76 0.00 43.56 3.86
854 947 1.407989 CCAGAGCCTAAAAGCCCAGAG 60.408 57.143 0.00 0.00 0.00 3.35
888 982 2.414161 GGAGCACAAACAATAAGCGGAC 60.414 50.000 0.00 0.00 0.00 4.79
890 984 2.484264 AGCACAAACAATAAGCGGACTC 59.516 45.455 0.00 0.00 0.00 3.36
891 985 2.225491 GCACAAACAATAAGCGGACTCA 59.775 45.455 0.00 0.00 0.00 3.41
898 992 0.325296 ATAAGCGGACTCAGGTGGGA 60.325 55.000 0.00 0.00 0.00 4.37
923 1027 1.517913 GCTACGAACCACCCTACGC 60.518 63.158 0.00 0.00 0.00 4.42
927 1031 3.324108 GAACCACCCTACGCCCCA 61.324 66.667 0.00 0.00 0.00 4.96
1604 1717 3.731716 TGCTCTTGCAGGATGTTGT 57.268 47.368 0.00 0.00 45.31 3.32
1608 1724 2.082231 CTCTTGCAGGATGTTGTGGAG 58.918 52.381 0.00 0.00 39.31 3.86
1758 1874 1.376609 CCCTGCATTTGACTACCCGC 61.377 60.000 0.00 0.00 0.00 6.13
1850 1966 6.012337 TGAGGAAATGTTGGATATTGGCTA 57.988 37.500 0.00 0.00 0.00 3.93
1878 1994 0.528470 ACTCTCAGGAGCGCTTGTAC 59.472 55.000 13.26 2.41 42.98 2.90
1905 2021 9.125906 GCTTTGCATATGAATTATTCTGATGAC 57.874 33.333 17.55 11.77 0.00 3.06
1988 2104 1.189752 ACAGCTGACATGTCGGAGAT 58.810 50.000 33.99 17.33 40.67 2.75
2082 2198 0.798776 GGGATGAACAGCTTGTGTCG 59.201 55.000 0.00 0.00 39.03 4.35
2307 2423 7.212976 TGTGGCTTTGAGCAATGTTATTTTAA 58.787 30.769 2.04 0.00 44.75 1.52
2308 2424 7.712639 TGTGGCTTTGAGCAATGTTATTTTAAA 59.287 29.630 2.04 0.00 44.75 1.52
2309 2425 8.555361 GTGGCTTTGAGCAATGTTATTTTAAAA 58.445 29.630 2.51 2.51 44.75 1.52
2310 2426 9.282569 TGGCTTTGAGCAATGTTATTTTAAAAT 57.717 25.926 17.18 17.18 44.75 1.82
2311 2427 9.545611 GGCTTTGAGCAATGTTATTTTAAAATG 57.454 29.630 21.19 7.93 44.75 2.32
2312 2428 9.054191 GCTTTGAGCAATGTTATTTTAAAATGC 57.946 29.630 21.19 16.32 41.89 3.56
2372 2488 8.390354 CACTTCGATCTATTTGCTTTCATGTAA 58.610 33.333 0.00 0.00 0.00 2.41
2401 2517 3.118408 TGCTGTGGTCACTTGTTAGTCTT 60.118 43.478 2.66 0.00 30.26 3.01
2448 2564 6.946340 TGAGAACAAGTTATCTATGCTTGGA 58.054 36.000 8.77 0.00 42.60 3.53
2470 2586 6.016276 TGGAACTATCTGCCTTTTCACTTTTC 60.016 38.462 0.00 0.00 0.00 2.29
2485 2601 3.055021 CACTTTTCCCTTCTACTCCCTCC 60.055 52.174 0.00 0.00 0.00 4.30
2486 2602 2.265526 TTTCCCTTCTACTCCCTCCC 57.734 55.000 0.00 0.00 0.00 4.30
2592 2710 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
2599 2717 4.692625 GCTCCGTATGTAGTCCGTATTAGA 59.307 45.833 0.00 0.00 0.00 2.10
2606 2724 9.363763 CGTATGTAGTCCGTATTAGAATCTCTA 57.636 37.037 0.00 0.00 0.00 2.43
2675 2793 1.549203 ATGCATGTTCTCCACAACCC 58.451 50.000 0.00 0.00 39.50 4.11
2821 3331 5.877012 ACTACCTAGCATTCTGAATTGTGTG 59.123 40.000 0.00 0.00 0.00 3.82
2900 3505 0.895530 TGGTTCTAGACTTCCAGCCG 59.104 55.000 0.00 0.00 0.00 5.52
2908 3515 5.844004 TCTAGACTTCCAGCCGATTATTTC 58.156 41.667 0.00 0.00 0.00 2.17
2928 3535 9.832445 TTATTTCTATGGAACCTGTAAAGCTAG 57.168 33.333 0.00 0.00 0.00 3.42
2931 3538 3.587797 TGGAACCTGTAAAGCTAGACG 57.412 47.619 0.00 0.00 0.00 4.18
2941 3548 6.132791 TGTAAAGCTAGACGAGAATAGTGG 57.867 41.667 0.00 0.00 0.00 4.00
2946 3553 6.963083 AGCTAGACGAGAATAGTGGTTAAT 57.037 37.500 0.00 0.00 0.00 1.40
3020 3707 5.345741 GTCGAAATTTTACCGCTGTACACTA 59.654 40.000 0.00 0.00 0.00 2.74
3021 3708 5.574055 TCGAAATTTTACCGCTGTACACTAG 59.426 40.000 0.00 0.00 0.00 2.57
3030 3717 1.810755 GCTGTACACTAGGTTTTGGGC 59.189 52.381 0.00 0.00 0.00 5.36
3051 3738 2.557056 CCTACAGTTCCGACACTGAGAA 59.443 50.000 17.80 5.17 46.29 2.87
3077 3764 4.763073 TCTGTAGATCATGCAAGTCCTTG 58.237 43.478 2.63 2.63 43.14 3.61
3093 3780 8.674263 CAAGTCCTTGCTATGAATAAGATTCT 57.326 34.615 1.24 0.00 33.45 2.40
3112 3799 8.659925 AGATTCTGATCTTATTGCTGTAGTTG 57.340 34.615 0.00 0.00 39.63 3.16
3148 3835 0.322456 CTCGGTTTCTGCCAATGGGA 60.322 55.000 0.00 0.00 35.59 4.37
3154 3841 0.899717 TTCTGCCAATGGGACTTGCC 60.900 55.000 0.00 0.00 35.59 4.52
3174 3868 3.507233 GCCCATCTTGATTTCACTTGTGA 59.493 43.478 0.00 0.00 0.00 3.58
3185 3879 3.319137 TCACTTGTGATCAGCTGTACC 57.681 47.619 14.67 4.77 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.033178 TCCATCCATCTAGTCACATAATCAAA 57.967 34.615 0.00 0.00 0.00 2.69
18 19 4.525874 CAGCTCCATCCATCTAGTCACATA 59.474 45.833 0.00 0.00 0.00 2.29
29 30 2.191375 CCACGCAGCTCCATCCAT 59.809 61.111 0.00 0.00 0.00 3.41
50 51 8.240682 TCCATATTGAATAAACAAGGTTTGACG 58.759 33.333 4.69 0.00 33.22 4.35
58 59 8.292448 CGGATTCCTCCATATTGAATAAACAAG 58.708 37.037 0.30 0.00 42.19 3.16
59 60 7.996066 TCGGATTCCTCCATATTGAATAAACAA 59.004 33.333 0.30 0.00 42.19 2.83
62 63 6.940298 GGTCGGATTCCTCCATATTGAATAAA 59.060 38.462 0.30 0.00 42.19 1.40
63 64 6.043822 TGGTCGGATTCCTCCATATTGAATAA 59.956 38.462 10.97 0.00 42.19 1.40
65 66 4.350816 TGGTCGGATTCCTCCATATTGAAT 59.649 41.667 10.97 0.00 42.19 2.57
72 73 0.692419 AGCTGGTCGGATTCCTCCAT 60.692 55.000 14.11 2.04 42.19 3.41
91 93 2.126372 CCTCCCCCACCCTTGGTA 59.874 66.667 0.00 0.00 42.10 3.25
107 109 1.789576 TTGTTTCTCTGCCCTCCCCC 61.790 60.000 0.00 0.00 0.00 5.40
125 127 4.536090 TCCAAGGTTCATCATACCTCAGTT 59.464 41.667 0.00 0.00 45.17 3.16
126 128 4.104086 TCCAAGGTTCATCATACCTCAGT 58.896 43.478 0.00 0.00 45.17 3.41
127 129 4.760530 TCCAAGGTTCATCATACCTCAG 57.239 45.455 0.00 0.00 45.17 3.35
128 130 4.971282 AGATCCAAGGTTCATCATACCTCA 59.029 41.667 0.00 0.00 45.17 3.86
129 131 5.070981 TCAGATCCAAGGTTCATCATACCTC 59.929 44.000 0.00 0.00 45.17 3.85
131 133 5.296151 TCAGATCCAAGGTTCATCATACC 57.704 43.478 0.00 0.00 35.85 2.73
132 134 6.769822 ACAATCAGATCCAAGGTTCATCATAC 59.230 38.462 0.00 0.00 0.00 2.39
167 169 3.950397 AGATCGTCTTGCATAAAACCCA 58.050 40.909 0.00 0.00 0.00 4.51
218 220 6.457392 CGGATGGCTAAAATATTGATCGGATG 60.457 42.308 0.00 0.00 0.00 3.51
227 229 7.255590 CCAAGAACATCGGATGGCTAAAATATT 60.256 37.037 21.19 3.94 33.60 1.28
230 232 4.339247 CCAAGAACATCGGATGGCTAAAAT 59.661 41.667 21.19 1.99 33.60 1.82
232 234 3.278574 CCAAGAACATCGGATGGCTAAA 58.721 45.455 21.19 0.00 33.60 1.85
357 364 5.874831 CGGAATCCGTGAAAATTTGATGTA 58.125 37.500 14.46 0.00 42.73 2.29
404 411 0.178964 CCCAAAGAGGTGGCTTGGAA 60.179 55.000 2.75 0.00 37.34 3.53
418 469 1.003812 CCAGGTCGTATTCCACCCAAA 59.996 52.381 0.00 0.00 32.45 3.28
421 472 1.070289 GATCCAGGTCGTATTCCACCC 59.930 57.143 0.00 0.00 32.45 4.61
424 475 1.954382 CTCGATCCAGGTCGTATTCCA 59.046 52.381 0.00 0.00 42.07 3.53
425 476 1.336056 GCTCGATCCAGGTCGTATTCC 60.336 57.143 0.00 0.00 42.07 3.01
467 519 2.884012 CTCTCTCTCTCTGTGTGTGTGT 59.116 50.000 0.00 0.00 0.00 3.72
470 522 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
471 523 3.582647 TCTCTCTCTCTCTCTCTGTGTGT 59.417 47.826 0.00 0.00 0.00 3.72
472 524 4.081476 TCTCTCTCTCTCTCTCTCTGTGTG 60.081 50.000 0.00 0.00 0.00 3.82
473 525 4.096681 TCTCTCTCTCTCTCTCTCTGTGT 58.903 47.826 0.00 0.00 0.00 3.72
475 527 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
476 528 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
478 530 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
480 532 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
481 533 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
482 534 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
483 535 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
484 536 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
485 537 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
486 538 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
487 539 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
488 540 4.038642 GTCCTCTCTCTCTCTCTCTCTCTC 59.961 54.167 0.00 0.00 0.00 3.20
489 541 3.964031 GTCCTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
490 542 3.706594 TGTCCTCTCTCTCTCTCTCTCTC 59.293 52.174 0.00 0.00 0.00 3.20
491 543 3.724478 TGTCCTCTCTCTCTCTCTCTCT 58.276 50.000 0.00 0.00 0.00 3.10
492 544 4.446371 CTTGTCCTCTCTCTCTCTCTCTC 58.554 52.174 0.00 0.00 0.00 3.20
493 545 3.370953 GCTTGTCCTCTCTCTCTCTCTCT 60.371 52.174 0.00 0.00 0.00 3.10
494 546 2.945668 GCTTGTCCTCTCTCTCTCTCTC 59.054 54.545 0.00 0.00 0.00 3.20
495 547 2.357154 GGCTTGTCCTCTCTCTCTCTCT 60.357 54.545 0.00 0.00 0.00 3.10
496 548 2.024414 GGCTTGTCCTCTCTCTCTCTC 58.976 57.143 0.00 0.00 0.00 3.20
497 549 1.681780 CGGCTTGTCCTCTCTCTCTCT 60.682 57.143 0.00 0.00 0.00 3.10
498 550 0.738389 CGGCTTGTCCTCTCTCTCTC 59.262 60.000 0.00 0.00 0.00 3.20
499 551 0.682855 CCGGCTTGTCCTCTCTCTCT 60.683 60.000 0.00 0.00 0.00 3.10
500 552 1.813192 CCGGCTTGTCCTCTCTCTC 59.187 63.158 0.00 0.00 0.00 3.20
512 564 0.181350 CTTATTCCTCTGGCCGGCTT 59.819 55.000 28.56 3.80 0.00 4.35
516 568 1.271054 CCCATCTTATTCCTCTGGCCG 60.271 57.143 0.00 0.00 0.00 6.13
520 572 2.707791 TCCAGCCCATCTTATTCCTCTG 59.292 50.000 0.00 0.00 0.00 3.35
531 583 0.250513 AGAGAACGTTCCAGCCCATC 59.749 55.000 24.22 13.24 0.00 3.51
532 584 0.693049 AAGAGAACGTTCCAGCCCAT 59.307 50.000 24.22 4.05 0.00 4.00
533 585 0.250295 CAAGAGAACGTTCCAGCCCA 60.250 55.000 24.22 0.00 0.00 5.36
534 586 0.034896 TCAAGAGAACGTTCCAGCCC 59.965 55.000 24.22 9.02 0.00 5.19
535 587 1.878953 TTCAAGAGAACGTTCCAGCC 58.121 50.000 24.22 11.37 0.00 4.85
536 588 2.872858 AGTTTCAAGAGAACGTTCCAGC 59.127 45.455 24.22 14.04 32.39 4.85
537 589 6.400091 CGATAAGTTTCAAGAGAACGTTCCAG 60.400 42.308 24.22 11.87 32.39 3.86
538 590 5.404366 CGATAAGTTTCAAGAGAACGTTCCA 59.596 40.000 24.22 1.21 32.39 3.53
539 591 5.404667 ACGATAAGTTTCAAGAGAACGTTCC 59.595 40.000 24.22 15.46 32.39 3.62
540 592 6.449448 ACGATAAGTTTCAAGAGAACGTTC 57.551 37.500 20.71 20.71 32.39 3.95
541 593 6.646636 CAACGATAAGTTTCAAGAGAACGTT 58.353 36.000 0.00 0.00 42.02 3.99
547 599 5.356882 TTGGCAACGATAAGTTTCAAGAG 57.643 39.130 0.00 0.00 42.02 2.85
551 603 2.817258 CCCTTGGCAACGATAAGTTTCA 59.183 45.455 0.00 0.00 42.02 2.69
568 620 2.273449 CCGCTCTTCATGGCCCTT 59.727 61.111 0.00 0.00 0.00 3.95
593 645 4.325028 TGCACCGAAGAACTAACACTTA 57.675 40.909 0.00 0.00 0.00 2.24
602 654 8.460831 AATTAAACAATATTGCACCGAAGAAC 57.539 30.769 15.48 0.00 0.00 3.01
668 727 6.998258 ATTTCTTGCAAATTCTCGAAACTG 57.002 33.333 10.40 0.00 0.00 3.16
738 798 2.812358 ATTTTCTTCAACAACCCCGC 57.188 45.000 0.00 0.00 0.00 6.13
822 882 3.627690 CTCTGGAGCCTGGGACTC 58.372 66.667 0.00 0.00 0.00 3.36
898 992 1.670083 GTGGTTCGTAGCGGGCTTT 60.670 57.895 0.00 0.00 0.00 3.51
918 1022 1.740296 CGGAAGTTGTGGGGCGTAG 60.740 63.158 0.00 0.00 0.00 3.51
923 1027 1.795170 CTTGTGCGGAAGTTGTGGGG 61.795 60.000 0.00 0.00 0.00 4.96
927 1031 1.404035 GAAACCTTGTGCGGAAGTTGT 59.596 47.619 0.00 0.00 0.00 3.32
1364 1477 1.269569 TGGCGTCGTGTATGGATGATC 60.270 52.381 0.00 0.00 0.00 2.92
1602 1715 2.571757 GCGTCGTGATCCTCCACA 59.428 61.111 0.00 0.00 36.89 4.17
1603 1716 2.202756 GGCGTCGTGATCCTCCAC 60.203 66.667 0.00 0.00 0.00 4.02
1604 1717 3.822192 CGGCGTCGTGATCCTCCA 61.822 66.667 0.00 0.00 0.00 3.86
1608 1724 3.823330 ACTCCGGCGTCGTGATCC 61.823 66.667 9.28 0.00 33.95 3.36
1695 1811 5.588648 AGGTGAACCATTGTAATAATCCACG 59.411 40.000 1.62 0.00 38.89 4.94
1758 1874 5.233050 GTCCACTGTGATCACTGAATTATCG 59.767 44.000 31.99 14.30 34.80 2.92
1812 1928 0.108186 CCTCAACACTGAGCGGCATA 60.108 55.000 1.45 0.00 46.76 3.14
1833 1949 4.761739 CCGATGTAGCCAATATCCAACATT 59.238 41.667 0.00 0.00 0.00 2.71
1835 1951 3.495983 CCCGATGTAGCCAATATCCAACA 60.496 47.826 0.00 0.00 0.00 3.33
1838 1954 1.003118 GCCCGATGTAGCCAATATCCA 59.997 52.381 0.00 0.00 0.00 3.41
1850 1966 1.305297 TCCTGAGAGTGCCCGATGT 60.305 57.895 0.00 0.00 0.00 3.06
1878 1994 8.019094 TCATCAGAATAATTCATATGCAAAGCG 58.981 33.333 0.00 0.00 0.00 4.68
1905 2021 0.109086 AGACCGTGAGCTGACAATCG 60.109 55.000 3.68 0.00 0.00 3.34
1988 2104 0.752658 CACCTCATCATCGCCTACCA 59.247 55.000 0.00 0.00 0.00 3.25
2082 2198 8.889717 TGAAATTTCCTCTTTTCCATATCGTAC 58.110 33.333 15.48 0.00 32.14 3.67
2372 2488 5.165961 ACAAGTGACCACAGCATAACTAT 57.834 39.130 2.78 0.00 0.00 2.12
2401 2517 1.266178 TCACAGATTCGCTCCAGGAA 58.734 50.000 0.00 0.00 0.00 3.36
2448 2564 5.243954 GGGAAAAGTGAAAAGGCAGATAGTT 59.756 40.000 0.00 0.00 0.00 2.24
2470 2586 1.693083 GGAAGGGAGGGAGTAGAAGGG 60.693 61.905 0.00 0.00 0.00 3.95
2562 2680 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2628 2746 6.954102 AGTTGCAGGAAATAAATACTCCCTTT 59.046 34.615 0.00 0.00 0.00 3.11
2666 2784 5.708736 ATACATATGAACAGGGTTGTGGA 57.291 39.130 10.38 0.00 37.67 4.02
2675 2793 7.915397 GCCCAGTTTACAAATACATATGAACAG 59.085 37.037 10.38 0.00 0.00 3.16
2821 3331 5.869753 TTCAAGAACTAGAAGATTGCAGC 57.130 39.130 0.00 0.00 0.00 5.25
2900 3505 9.343539 AGCTTTACAGGTTCCATAGAAATAATC 57.656 33.333 0.00 0.00 32.58 1.75
2908 3515 5.067413 TCGTCTAGCTTTACAGGTTCCATAG 59.933 44.000 0.00 0.00 31.45 2.23
2928 3535 7.787725 ATTGGAATTAACCACTATTCTCGTC 57.212 36.000 0.00 0.00 39.85 4.20
2946 3553 7.175990 GTCACAAATAGGTGGTCTAAATTGGAA 59.824 37.037 0.00 0.00 39.27 3.53
2998 3684 4.657075 AGTGTACAGCGGTAAAATTTCG 57.343 40.909 0.00 0.00 0.00 3.46
3020 3707 1.203013 GGAACTGTAGGCCCAAAACCT 60.203 52.381 0.00 0.00 41.57 3.50
3021 3708 1.254026 GGAACTGTAGGCCCAAAACC 58.746 55.000 0.00 0.00 0.00 3.27
3030 3717 2.160205 TCTCAGTGTCGGAACTGTAGG 58.840 52.381 15.18 9.06 46.33 3.18
3071 3758 8.845413 ATCAGAATCTTATTCATAGCAAGGAC 57.155 34.615 2.74 0.00 0.00 3.85
3093 3780 5.874810 GTGGTCAACTACAGCAATAAGATCA 59.125 40.000 0.00 0.00 0.00 2.92
3105 3792 2.228582 GCATGCATTGTGGTCAACTACA 59.771 45.455 14.21 0.00 36.33 2.74
3112 3799 1.268386 CGAGATGCATGCATTGTGGTC 60.268 52.381 32.60 20.16 36.70 4.02
3148 3835 3.771216 AGTGAAATCAAGATGGGCAAGT 58.229 40.909 0.00 0.00 0.00 3.16
3154 3841 6.505044 TGATCACAAGTGAAATCAAGATGG 57.495 37.500 7.02 0.00 43.58 3.51
3174 3868 3.906720 ATGGTTAACGGTACAGCTGAT 57.093 42.857 23.35 7.41 0.00 2.90


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

AutoCloner maintained by Alex Coulton.