Multiple sequence alignment - TraesCS3D01G402700

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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 TraesCS3D01G402700 chr3D 100.000 5170 0 0 1 5170 516883434 516878265 0.000000e+00 9548
1 TraesCS3D01G402700 chr3D 90.610 426 17 9 1 426 7403976 7403574 1.270000e-150 544
2 TraesCS3D01G402700 chr3D 91.489 94 8 0 487 580 7403482 7403389 4.200000e-26 130
3 TraesCS3D01G402700 chr3A 94.060 2761 130 16 586 3331 652029914 652027173 0.000000e+00 4159
4 TraesCS3D01G402700 chr3A 93.176 1861 77 18 3333 5170 652027116 652025283 0.000000e+00 2687
5 TraesCS3D01G402700 chr3A 92.723 426 28 1 1 426 101963410 101962988 3.420000e-171 612
6 TraesCS3D01G402700 chr3A 95.181 83 4 0 2887 2969 203994036 203993954 1.170000e-26 132
7 TraesCS3D01G402700 chr3B 91.964 1879 97 20 3333 5167 680423804 680425672 0.000000e+00 2584
8 TraesCS3D01G402700 chr3B 95.606 1593 63 7 1741 3327 680422151 680423742 0.000000e+00 2547
9 TraesCS3D01G402700 chr3B 94.917 1082 52 3 607 1687 680419728 680420807 0.000000e+00 1690
10 TraesCS3D01G402700 chr3B 95.402 87 4 0 2887 2973 126580147 126580061 6.980000e-29 139
11 TraesCS3D01G402700 chr2D 96.714 426 14 0 1 426 76989678 76990103 0.000000e+00 710
12 TraesCS3D01G402700 chr2D 96.000 425 16 1 2 426 32458621 32459044 0.000000e+00 689
13 TraesCS3D01G402700 chr2D 94.681 94 5 0 487 580 32459136 32459229 4.170000e-31 147
14 TraesCS3D01G402700 chr2D 91.304 92 8 0 2878 2969 299891012 299891103 5.430000e-25 126
15 TraesCS3D01G402700 chr2D 91.304 92 8 0 2878 2969 557267175 557267266 5.430000e-25 126
16 TraesCS3D01G402700 chr5A 95.305 426 20 0 1 426 616556548 616556973 0.000000e+00 676
17 TraesCS3D01G402700 chr5A 94.845 97 4 1 487 582 616557065 616557161 3.220000e-32 150
18 TraesCS3D01G402700 chr1D 94.836 426 22 0 1 426 152726704 152727129 0.000000e+00 665
19 TraesCS3D01G402700 chr1D 87.162 148 19 0 2652 2799 360479489 360479342 8.900000e-38 169
20 TraesCS3D01G402700 chr1D 93.617 94 6 0 487 580 152727221 152727314 1.940000e-29 141
21 TraesCS3D01G402700 chr6B 94.787 422 20 1 1 422 669559483 669559902 0.000000e+00 656
22 TraesCS3D01G402700 chr2B 93.525 139 9 0 158 296 90578227 90578089 1.890000e-49 207
23 TraesCS3D01G402700 chr2B 92.941 85 5 1 2887 2970 529265428 529265344 7.030000e-24 122
24 TraesCS3D01G402700 chr1A 87.162 148 19 0 2652 2799 460332529 460332382 8.900000e-38 169
25 TraesCS3D01G402700 chr2A 95.294 85 3 1 2887 2970 593655992 593655908 3.250000e-27 134
26 TraesCS3D01G402700 chr1B 95.062 81 4 0 2887 2967 120657845 120657925 1.510000e-25 128
27 TraesCS3D01G402700 chr4D 85.345 116 17 0 3848 3963 74370435 74370320 2.530000e-23 121
28 TraesCS3D01G402700 chr4B 85.345 116 17 0 3848 3963 106855604 106855489 2.530000e-23 121
29 TraesCS3D01G402700 chr4A 87.500 104 13 0 3848 3951 513292616 513292719 2.530000e-23 121


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 TraesCS3D01G402700 chr3D 516878265 516883434 5169 True 9548.000000 9548 100.000000 1 5170 1 chr3D.!!$R1 5169
1 TraesCS3D01G402700 chr3D 7403389 7403976 587 True 337.000000 544 91.049500 1 580 2 chr3D.!!$R2 579
2 TraesCS3D01G402700 chr3A 652025283 652029914 4631 True 3423.000000 4159 93.618000 586 5170 2 chr3A.!!$R3 4584
3 TraesCS3D01G402700 chr3B 680419728 680425672 5944 False 2273.666667 2584 94.162333 607 5167 3 chr3B.!!$F1 4560
4 TraesCS3D01G402700 chr2D 32458621 32459229 608 False 418.000000 689 95.340500 2 580 2 chr2D.!!$F4 578
5 TraesCS3D01G402700 chr5A 616556548 616557161 613 False 413.000000 676 95.075000 1 582 2 chr5A.!!$F1 581
6 TraesCS3D01G402700 chr1D 152726704 152727314 610 False 403.000000 665 94.226500 1 580 2 chr1D.!!$F1 579

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
605 675 0.901827 TTGGCGAGCAGATCTTGGTA 59.098 50.000 0.00 0.0 37.72 3.25 F
973 1044 1.620739 GGTACGGAGGGAGGGTTTCC 61.621 65.000 0.00 0.0 46.00 3.13 F
1731 3022 0.112995 TTGGCCTGAGCAATGGTTCT 59.887 50.000 3.32 0.0 42.56 3.01 F
2044 3409 2.280628 GCGTTTGCTCCTGCTATACTT 58.719 47.619 0.00 0.0 40.48 2.24 F
3592 5028 1.089920 GCTGTTGTCCATGTGGCTAG 58.910 55.000 0.00 0.0 34.44 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1740 0.250901 TGAAGCCAAGAACAGCCTCC 60.251 55.000 0.00 0.0 0.00 4.30 R
2044 3409 1.488812 AGTGCACCAAGTGGAGTAACA 59.511 47.619 14.63 0.0 35.85 2.41 R
2815 4188 2.270352 AAGCAACGGAAGAACCATCA 57.730 45.000 0.00 0.0 38.90 3.07 R
4037 5498 2.856039 TAGGCAGAGTCGGTGGGAGG 62.856 65.000 0.00 0.0 0.00 4.30 R
4506 5981 0.586319 ACACGCAAAGAACATCACCG 59.414 50.000 0.00 0.0 0.00 4.94 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
123 124 1.463674 CGGGTTTAAAGCAGCTGGAT 58.536 50.000 17.12 0.00 0.00 3.41
348 349 2.649034 GGTCGAACGTCTCTGGCA 59.351 61.111 0.00 0.00 0.00 4.92
395 396 0.937441 AGGAGATGGACTAGGCAGGA 59.063 55.000 0.00 0.00 0.00 3.86
426 427 6.824958 TTTAGGTATGGAAAGGCTAGTCAT 57.175 37.500 0.00 0.00 0.00 3.06
427 428 4.965200 AGGTATGGAAAGGCTAGTCATC 57.035 45.455 0.00 0.00 0.00 2.92
428 429 4.561752 AGGTATGGAAAGGCTAGTCATCT 58.438 43.478 0.00 0.00 0.00 2.90
431 432 4.592485 ATGGAAAGGCTAGTCATCTACG 57.408 45.455 0.00 0.00 0.00 3.51
433 434 3.380637 TGGAAAGGCTAGTCATCTACGTC 59.619 47.826 0.00 0.00 0.00 4.34
435 436 2.616634 AGGCTAGTCATCTACGTCGA 57.383 50.000 0.00 0.00 0.00 4.20
436 437 2.485903 AGGCTAGTCATCTACGTCGAG 58.514 52.381 0.00 0.00 0.00 4.04
437 438 1.532007 GGCTAGTCATCTACGTCGAGG 59.468 57.143 3.03 3.03 0.00 4.63
438 439 2.211806 GCTAGTCATCTACGTCGAGGT 58.788 52.381 15.89 15.89 0.00 3.85
439 440 2.613133 GCTAGTCATCTACGTCGAGGTT 59.387 50.000 16.86 0.00 0.00 3.50
440 441 3.303263 GCTAGTCATCTACGTCGAGGTTC 60.303 52.174 16.86 1.47 0.00 3.62
443 444 3.312973 AGTCATCTACGTCGAGGTTCATC 59.687 47.826 16.86 3.42 0.00 2.92
444 445 3.312973 GTCATCTACGTCGAGGTTCATCT 59.687 47.826 16.86 0.00 0.00 2.90
445 446 4.510711 GTCATCTACGTCGAGGTTCATCTA 59.489 45.833 16.86 0.00 0.00 1.98
446 447 4.510711 TCATCTACGTCGAGGTTCATCTAC 59.489 45.833 16.86 0.00 0.00 2.59
447 448 2.862536 TCTACGTCGAGGTTCATCTACG 59.137 50.000 16.86 9.26 42.26 3.51
465 535 5.057149 TCTACGTCGATAAGGTTAGGGTAC 58.943 45.833 0.00 0.00 0.00 3.34
485 555 6.314784 GGTACCAATTTCAGAGATTCAAACG 58.685 40.000 7.15 0.00 0.00 3.60
486 556 6.072673 GGTACCAATTTCAGAGATTCAAACGT 60.073 38.462 7.15 0.00 0.00 3.99
487 557 6.002062 ACCAATTTCAGAGATTCAAACGTC 57.998 37.500 0.00 0.00 0.00 4.34
488 558 5.082059 CCAATTTCAGAGATTCAAACGTCG 58.918 41.667 0.00 0.00 0.00 5.12
489 559 5.107104 CCAATTTCAGAGATTCAAACGTCGA 60.107 40.000 0.00 0.00 0.00 4.20
490 560 6.402550 CCAATTTCAGAGATTCAAACGTCGAT 60.403 38.462 0.00 0.00 0.00 3.59
491 561 7.201522 CCAATTTCAGAGATTCAAACGTCGATA 60.202 37.037 0.00 0.00 0.00 2.92
492 562 7.827819 ATTTCAGAGATTCAAACGTCGATAA 57.172 32.000 0.00 0.00 0.00 1.75
493 563 7.646446 TTTCAGAGATTCAAACGTCGATAAA 57.354 32.000 0.00 0.00 0.00 1.40
494 564 6.871044 TCAGAGATTCAAACGTCGATAAAG 57.129 37.500 0.00 0.00 0.00 1.85
495 565 6.387465 TCAGAGATTCAAACGTCGATAAAGT 58.613 36.000 0.00 0.00 0.00 2.66
496 566 6.866770 TCAGAGATTCAAACGTCGATAAAGTT 59.133 34.615 0.00 0.00 0.00 2.66
497 567 8.024865 TCAGAGATTCAAACGTCGATAAAGTTA 58.975 33.333 0.00 0.00 0.00 2.24
498 568 8.314635 CAGAGATTCAAACGTCGATAAAGTTAG 58.685 37.037 0.00 0.00 0.00 2.34
499 569 7.488471 AGAGATTCAAACGTCGATAAAGTTAGG 59.512 37.037 0.00 0.00 0.00 2.69
500 570 6.534079 AGATTCAAACGTCGATAAAGTTAGGG 59.466 38.462 0.00 0.00 0.00 3.53
501 571 5.138125 TCAAACGTCGATAAAGTTAGGGT 57.862 39.130 0.00 0.00 0.00 4.34
502 572 6.266168 TCAAACGTCGATAAAGTTAGGGTA 57.734 37.500 0.00 0.00 0.00 3.69
550 620 3.003482 GGTTCATCTACGTCGTGCTCTAT 59.997 47.826 8.47 0.00 0.00 1.98
580 650 5.986004 AGGTTTAAAACAGACTTCACTCG 57.014 39.130 5.94 0.00 0.00 4.18
581 651 5.667466 AGGTTTAAAACAGACTTCACTCGA 58.333 37.500 5.94 0.00 0.00 4.04
582 652 5.753921 AGGTTTAAAACAGACTTCACTCGAG 59.246 40.000 11.84 11.84 0.00 4.04
583 653 5.050295 GGTTTAAAACAGACTTCACTCGAGG 60.050 44.000 18.41 5.96 0.00 4.63
584 654 5.524971 TTAAAACAGACTTCACTCGAGGA 57.475 39.130 18.41 8.44 0.00 3.71
591 661 1.002366 CTTCACTCGAGGAATTGGCG 58.998 55.000 18.41 2.08 0.00 5.69
596 666 1.150567 CTCGAGGAATTGGCGAGCAG 61.151 60.000 3.91 0.00 43.88 4.24
605 675 0.901827 TTGGCGAGCAGATCTTGGTA 59.098 50.000 0.00 0.00 37.72 3.25
786 856 2.203365 TCCGATCCGCTCTCCTCC 60.203 66.667 0.00 0.00 0.00 4.30
787 857 3.665226 CCGATCCGCTCTCCTCCG 61.665 72.222 0.00 0.00 0.00 4.63
973 1044 1.620739 GGTACGGAGGGAGGGTTTCC 61.621 65.000 0.00 0.00 46.00 3.13
1207 1278 2.854522 GCAGGTGACCTAATTGCGT 58.145 52.632 2.59 0.00 29.64 5.24
1230 1301 3.070878 TGCTTACCATCGAGGCATCATTA 59.929 43.478 0.00 0.00 43.14 1.90
1320 1391 3.165058 GACGCTGGTGTCTGATTATGA 57.835 47.619 6.99 0.00 35.95 2.15
1419 1491 7.497249 GTCAGAGTTTAGGCTGATAATGTTGAT 59.503 37.037 0.00 0.00 42.51 2.57
1467 1539 2.584835 TGCTGGAGTTTGTAGCCAAT 57.415 45.000 0.00 0.00 36.64 3.16
1471 1543 3.157087 CTGGAGTTTGTAGCCAATGGTT 58.843 45.455 0.00 0.00 0.00 3.67
1504 1576 4.095782 TGTCGGTATTGCTTTTATTCTGCC 59.904 41.667 0.00 0.00 0.00 4.85
1513 1585 4.757657 TGCTTTTATTCTGCCTTGTTCGTA 59.242 37.500 0.00 0.00 0.00 3.43
1516 1588 4.914312 TTATTCTGCCTTGTTCGTAACG 57.086 40.909 0.00 0.00 0.00 3.18
1542 1614 2.297315 TGCACTGTAGTCTGGTTCTCAG 59.703 50.000 0.00 0.00 44.68 3.35
1576 1648 7.471721 TCAGCCAATCGAGTACATTAATTTTG 58.528 34.615 0.00 0.00 0.00 2.44
1647 1720 6.548441 TCCAAACACGGTAAAAGTTATCAG 57.452 37.500 0.00 0.00 0.00 2.90
1658 1731 7.508134 GGTAAAAGTTATCAGTCTGTCGTTTC 58.492 38.462 0.00 0.00 0.00 2.78
1667 1740 4.025229 TCAGTCTGTCGTTTCGATTTTTGG 60.025 41.667 0.00 0.00 38.42 3.28
1671 1744 2.550606 TGTCGTTTCGATTTTTGGGAGG 59.449 45.455 0.00 0.00 38.42 4.30
1672 1745 1.538075 TCGTTTCGATTTTTGGGAGGC 59.462 47.619 0.00 0.00 0.00 4.70
1673 1746 1.539827 CGTTTCGATTTTTGGGAGGCT 59.460 47.619 0.00 0.00 0.00 4.58
1674 1747 2.668279 CGTTTCGATTTTTGGGAGGCTG 60.668 50.000 0.00 0.00 0.00 4.85
1676 1749 2.286365 TCGATTTTTGGGAGGCTGTT 57.714 45.000 0.00 0.00 0.00 3.16
1682 2973 0.827507 TTTGGGAGGCTGTTCTTGGC 60.828 55.000 0.00 0.00 0.00 4.52
1731 3022 0.112995 TTGGCCTGAGCAATGGTTCT 59.887 50.000 3.32 0.00 42.56 3.01
1747 3109 7.752686 GCAATGGTTCTGAAGATTTTAGTTCTC 59.247 37.037 0.00 0.00 0.00 2.87
1764 3126 9.436957 TTTAGTTCTCAAGCTATTTAGTTCTGG 57.563 33.333 0.00 0.00 0.00 3.86
1766 3128 6.876257 AGTTCTCAAGCTATTTAGTTCTGGTG 59.124 38.462 0.00 0.00 0.00 4.17
1837 3200 3.181575 GGTTACGCACAAATTTGCTGTTC 59.818 43.478 18.12 9.97 40.62 3.18
1912 3275 6.372659 CAGGAATGATTACAAGTAAGTGCACT 59.627 38.462 15.25 15.25 0.00 4.40
1958 3323 9.366216 CATGTACTGCTTCTACTTAACAATGTA 57.634 33.333 0.00 0.00 0.00 2.29
2044 3409 2.280628 GCGTTTGCTCCTGCTATACTT 58.719 47.619 0.00 0.00 40.48 2.24
2047 3412 3.684788 CGTTTGCTCCTGCTATACTTGTT 59.315 43.478 0.00 0.00 40.48 2.83
2352 3724 3.901844 TGCTACAGAACCAGGTACTTTCT 59.098 43.478 0.00 0.00 36.09 2.52
2360 3732 7.396339 ACAGAACCAGGTACTTTCTTTTCTTTT 59.604 33.333 0.00 0.00 33.71 2.27
2433 3805 9.102757 TGTTTTTGTATTTTCTTGCAGCATTTA 57.897 25.926 0.00 0.00 0.00 1.40
2446 3818 8.298854 TCTTGCAGCATTTATATTTTATGCGAT 58.701 29.630 0.00 0.00 46.97 4.58
2495 3867 6.170506 GCTCATATTCCGTTATATCCCACAA 58.829 40.000 0.00 0.00 0.00 3.33
2564 3936 6.304624 TGTAGGATCTCTATCGGTATGTGTT 58.695 40.000 0.00 0.00 32.44 3.32
2566 3938 5.386060 AGGATCTCTATCGGTATGTGTTCA 58.614 41.667 0.00 0.00 32.44 3.18
2815 4188 9.476202 GAACAAGGTAACAATAATTTCTTTGCT 57.524 29.630 0.00 0.00 41.41 3.91
2841 4214 3.751698 GGTTCTTCCGTTGCTTAGTGATT 59.248 43.478 0.00 0.00 0.00 2.57
2910 4283 9.381038 TGCTCCCTCTGTAACTTAATATAAGAT 57.619 33.333 4.24 0.00 0.00 2.40
2944 4318 4.750098 ACTGTCATGGACTCTAAAAACGTG 59.250 41.667 0.00 0.00 33.15 4.49
2980 4354 7.733773 TTCAGAGGGAGTACATCTTTAATCA 57.266 36.000 0.00 0.00 0.00 2.57
3039 4413 5.016051 TCTGAGTACATGATTCTCCTTGC 57.984 43.478 0.00 0.00 0.00 4.01
3041 4415 5.188555 TCTGAGTACATGATTCTCCTTGCTT 59.811 40.000 0.00 0.00 0.00 3.91
3056 4430 4.826733 TCCTTGCTTCAAACTTATGCTTGA 59.173 37.500 0.00 0.00 0.00 3.02
3145 4519 8.273557 GCAGTTGTTTCACCAATATACTATACG 58.726 37.037 0.00 0.00 0.00 3.06
3208 4582 6.071616 TGTTCAAGGTAACATATTTGGGCTTC 60.072 38.462 0.00 0.00 34.50 3.86
3212 4587 5.377478 AGGTAACATATTTGGGCTTCTAGC 58.623 41.667 0.00 0.00 39.25 3.42
3237 4612 5.692115 TTTTATGGTGCTCTAGATGGTCA 57.308 39.130 0.00 0.00 0.00 4.02
3252 4628 6.155475 AGATGGTCATCTTAGTCTACTTGC 57.845 41.667 7.59 0.00 45.31 4.01
3286 4662 8.993121 CAAGTTTAACATGAGATCAAGTAGTGT 58.007 33.333 0.00 0.00 0.00 3.55
3293 4669 5.929697 TGAGATCAAGTAGTGTTTGCTTG 57.070 39.130 0.00 0.00 46.99 4.01
3299 4675 7.815068 AGATCAAGTAGTGTTTGCTTGTACTAG 59.185 37.037 0.00 0.00 46.10 2.57
3328 4704 4.795278 CAGTGAATTGCTTTTAGAATCGCC 59.205 41.667 0.00 0.00 0.00 5.54
3331 4707 4.217334 TGAATTGCTTTTAGAATCGCCACA 59.783 37.500 0.00 0.00 0.00 4.17
3353 4785 3.777522 AGAATGAGGTCTGAGTAAAGGGG 59.222 47.826 0.00 0.00 0.00 4.79
3355 4787 3.269592 TGAGGTCTGAGTAAAGGGGAA 57.730 47.619 0.00 0.00 0.00 3.97
3370 4802 3.236047 AGGGGAACAATGTTACCCAAAC 58.764 45.455 39.40 18.91 43.96 2.93
3396 4828 5.069648 TGTCATTGCCAACCAATTTTCTGTA 59.930 36.000 0.00 0.00 42.15 2.74
3397 4829 5.405269 GTCATTGCCAACCAATTTTCTGTAC 59.595 40.000 0.00 0.00 42.15 2.90
3409 4841 9.280174 ACCAATTTTCTGTACGAGAGAATTTTA 57.720 29.630 15.07 0.00 40.81 1.52
3417 4849 9.144298 TCTGTACGAGAGAATTTTAGGGATTAT 57.856 33.333 0.00 0.00 0.00 1.28
3454 4887 5.067674 TGAAACTGAACTCATCAAACCAAGG 59.932 40.000 0.00 0.00 37.67 3.61
3457 4890 2.238521 GAACTCATCAAACCAAGGGCA 58.761 47.619 0.00 0.00 0.00 5.36
3458 4891 2.610438 ACTCATCAAACCAAGGGCAT 57.390 45.000 0.00 0.00 0.00 4.40
3476 4909 6.491714 GGGCATACCTATCATGATCTATGT 57.508 41.667 12.53 7.87 35.72 2.29
3479 4912 7.208777 GGCATACCTATCATGATCTATGTCAG 58.791 42.308 12.53 1.79 38.01 3.51
3586 5022 2.596346 TGATTTGGCTGTTGTCCATGT 58.404 42.857 0.00 0.00 32.92 3.21
3592 5028 1.089920 GCTGTTGTCCATGTGGCTAG 58.910 55.000 0.00 0.00 34.44 3.42
3599 5035 2.076863 GTCCATGTGGCTAGACAACAC 58.923 52.381 0.00 0.00 35.75 3.32
3610 5046 6.260271 GTGGCTAGACAACACTTCTAAAGTTT 59.740 38.462 0.00 0.00 40.46 2.66
3660 5113 2.481289 AGCCTTTTAGTCAGCACTCC 57.519 50.000 0.00 0.00 33.62 3.85
3661 5114 1.699634 AGCCTTTTAGTCAGCACTCCA 59.300 47.619 0.00 0.00 33.62 3.86
3675 5128 8.270744 AGTCAGCACTCCATAATCTAATTTCTT 58.729 33.333 0.00 0.00 0.00 2.52
3678 5131 8.341173 CAGCACTCCATAATCTAATTTCTTGTC 58.659 37.037 0.00 0.00 0.00 3.18
3688 5141 5.886609 TCTAATTTCTTGTCCCATGGTCAA 58.113 37.500 11.73 14.14 30.88 3.18
3711 5164 7.994911 TCAATATTATGCCATCTTGAGTTCAGT 59.005 33.333 0.00 0.00 0.00 3.41
3783 5237 7.575414 TCTGTTAAACTTGATAAAACTGCCA 57.425 32.000 0.00 0.00 0.00 4.92
3831 5285 9.352784 GACAATGCTCACAGATATTATAGACTC 57.647 37.037 0.00 0.00 0.00 3.36
3834 5288 7.459795 TGCTCACAGATATTATAGACTCCTG 57.540 40.000 0.00 0.00 0.00 3.86
3908 5362 3.003689 CAGAGATGTGTGGTTTTGTGACC 59.996 47.826 0.00 0.00 40.23 4.02
4037 5498 6.768381 ACTTCTAACTTTCTGGCATTATAGGC 59.232 38.462 0.00 0.00 0.00 3.93
4091 5552 2.747446 ACATGGTGATGAAAACGGCTAC 59.253 45.455 0.00 0.00 33.36 3.58
4148 5609 3.609703 CTCCCTCTGAGGTCACCG 58.390 66.667 21.70 6.76 37.45 4.94
4506 5981 2.159393 TGCGCACTATTTTCTCATTGGC 60.159 45.455 5.66 0.00 0.00 4.52
4522 5997 1.154225 GGCGGTGATGTTCTTTGCG 60.154 57.895 0.00 0.00 0.00 4.85
4658 6137 0.319405 AACCCCGTAACCTTCTCGTG 59.681 55.000 0.00 0.00 0.00 4.35
4683 6162 3.625853 TCAAACCCAACAATCTCACACA 58.374 40.909 0.00 0.00 0.00 3.72
4684 6163 3.380004 TCAAACCCAACAATCTCACACAC 59.620 43.478 0.00 0.00 0.00 3.82
4689 6168 0.889186 AACAATCTCACACACCCGCC 60.889 55.000 0.00 0.00 0.00 6.13
4703 6182 3.777925 CGCCTGCACACGCACTAC 61.778 66.667 0.00 0.00 45.36 2.73
4719 6198 1.340405 ACTACCAATGGCTGAGCAAGG 60.340 52.381 6.82 4.42 0.00 3.61
4754 6233 0.596083 GGTGCTCATCGATCAGACCG 60.596 60.000 0.00 0.00 0.00 4.79
5167 6646 3.716006 CTGTTCCACACCGCGCTG 61.716 66.667 5.56 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
361 362 4.468689 CCTTCCTCCCGTTCCCGC 62.469 72.222 0.00 0.00 0.00 6.13
415 416 2.873472 CTCGACGTAGATGACTAGCCTT 59.127 50.000 0.00 0.00 0.00 4.35
426 427 2.862536 CGTAGATGAACCTCGACGTAGA 59.137 50.000 0.00 0.00 38.79 2.59
427 428 3.236030 CGTAGATGAACCTCGACGTAG 57.764 52.381 0.00 0.00 38.79 3.51
431 432 1.662629 TCGACGTAGATGAACCTCGAC 59.337 52.381 0.00 0.00 33.82 4.20
433 434 4.456019 CTTATCGACGTAGATGAACCTCG 58.544 47.826 19.88 0.52 32.39 4.63
435 436 4.205587 ACCTTATCGACGTAGATGAACCT 58.794 43.478 19.88 0.00 32.39 3.50
436 437 4.564940 ACCTTATCGACGTAGATGAACC 57.435 45.455 19.88 0.00 32.39 3.62
437 438 6.141462 CCTAACCTTATCGACGTAGATGAAC 58.859 44.000 19.88 0.00 32.39 3.18
438 439 5.240183 CCCTAACCTTATCGACGTAGATGAA 59.760 44.000 19.88 9.87 32.39 2.57
439 440 4.758674 CCCTAACCTTATCGACGTAGATGA 59.241 45.833 19.88 11.67 32.39 2.92
440 441 4.518211 ACCCTAACCTTATCGACGTAGATG 59.482 45.833 19.88 7.11 32.39 2.90
443 444 4.214332 GGTACCCTAACCTTATCGACGTAG 59.786 50.000 0.00 0.00 36.53 3.51
444 445 4.134563 GGTACCCTAACCTTATCGACGTA 58.865 47.826 0.00 0.00 36.53 3.57
445 446 2.952310 GGTACCCTAACCTTATCGACGT 59.048 50.000 0.00 0.00 36.53 4.34
446 447 2.951642 TGGTACCCTAACCTTATCGACG 59.048 50.000 10.07 0.00 40.44 5.12
447 448 5.541953 ATTGGTACCCTAACCTTATCGAC 57.458 43.478 10.07 0.00 40.44 4.20
465 535 5.082059 CGACGTTTGAATCTCTGAAATTGG 58.918 41.667 0.00 0.00 0.00 3.16
466 536 5.915857 TCGACGTTTGAATCTCTGAAATTG 58.084 37.500 0.00 0.00 0.00 2.32
467 537 6.727824 ATCGACGTTTGAATCTCTGAAATT 57.272 33.333 0.00 0.00 0.00 1.82
468 538 7.827819 TTATCGACGTTTGAATCTCTGAAAT 57.172 32.000 0.00 0.00 0.00 2.17
469 539 7.384115 ACTTTATCGACGTTTGAATCTCTGAAA 59.616 33.333 0.00 0.00 0.00 2.69
470 540 6.866770 ACTTTATCGACGTTTGAATCTCTGAA 59.133 34.615 0.00 0.00 0.00 3.02
471 541 6.387465 ACTTTATCGACGTTTGAATCTCTGA 58.613 36.000 0.00 0.00 0.00 3.27
472 542 6.633668 ACTTTATCGACGTTTGAATCTCTG 57.366 37.500 0.00 0.00 0.00 3.35
473 543 7.488471 CCTAACTTTATCGACGTTTGAATCTCT 59.512 37.037 0.00 0.00 0.00 3.10
474 544 7.254017 CCCTAACTTTATCGACGTTTGAATCTC 60.254 40.741 0.00 0.00 0.00 2.75
475 545 6.534079 CCCTAACTTTATCGACGTTTGAATCT 59.466 38.462 0.00 0.00 0.00 2.40
476 546 6.312180 ACCCTAACTTTATCGACGTTTGAATC 59.688 38.462 0.00 0.00 0.00 2.52
477 547 6.168389 ACCCTAACTTTATCGACGTTTGAAT 58.832 36.000 0.00 0.00 0.00 2.57
478 548 5.540911 ACCCTAACTTTATCGACGTTTGAA 58.459 37.500 0.00 0.00 0.00 2.69
479 549 5.138125 ACCCTAACTTTATCGACGTTTGA 57.862 39.130 0.00 0.00 0.00 2.69
480 550 6.753279 TGATACCCTAACTTTATCGACGTTTG 59.247 38.462 0.00 0.00 0.00 2.93
481 551 6.866480 TGATACCCTAACTTTATCGACGTTT 58.134 36.000 0.00 0.00 0.00 3.60
482 552 6.455360 TGATACCCTAACTTTATCGACGTT 57.545 37.500 0.00 0.00 0.00 3.99
483 553 6.455360 TTGATACCCTAACTTTATCGACGT 57.545 37.500 0.00 0.00 0.00 4.34
484 554 7.941795 AATTGATACCCTAACTTTATCGACG 57.058 36.000 0.00 0.00 0.00 5.12
492 562 9.642343 GAATCCCTAAAATTGATACCCTAACTT 57.358 33.333 0.00 0.00 0.00 2.66
493 563 8.787818 TGAATCCCTAAAATTGATACCCTAACT 58.212 33.333 0.00 0.00 0.00 2.24
494 564 8.990163 TGAATCCCTAAAATTGATACCCTAAC 57.010 34.615 0.00 0.00 0.00 2.34
495 565 9.998752 TTTGAATCCCTAAAATTGATACCCTAA 57.001 29.630 0.00 0.00 0.00 2.69
496 566 9.416284 GTTTGAATCCCTAAAATTGATACCCTA 57.584 33.333 0.00 0.00 0.00 3.53
497 567 7.068226 CGTTTGAATCCCTAAAATTGATACCCT 59.932 37.037 0.00 0.00 0.00 4.34
498 568 7.147966 ACGTTTGAATCCCTAAAATTGATACCC 60.148 37.037 0.00 0.00 0.00 3.69
499 569 7.768240 ACGTTTGAATCCCTAAAATTGATACC 58.232 34.615 0.00 0.00 0.00 2.73
500 570 8.455682 TGACGTTTGAATCCCTAAAATTGATAC 58.544 33.333 0.00 0.00 0.00 2.24
501 571 8.568676 TGACGTTTGAATCCCTAAAATTGATA 57.431 30.769 0.00 0.00 0.00 2.15
502 572 7.461182 TGACGTTTGAATCCCTAAAATTGAT 57.539 32.000 0.00 0.00 0.00 2.57
580 650 1.202627 AGATCTGCTCGCCAATTCCTC 60.203 52.381 0.00 0.00 0.00 3.71
581 651 0.835941 AGATCTGCTCGCCAATTCCT 59.164 50.000 0.00 0.00 0.00 3.36
582 652 1.332997 CAAGATCTGCTCGCCAATTCC 59.667 52.381 0.00 0.00 0.00 3.01
583 653 1.332997 CCAAGATCTGCTCGCCAATTC 59.667 52.381 0.00 0.00 0.00 2.17
584 654 1.340405 ACCAAGATCTGCTCGCCAATT 60.340 47.619 0.00 0.00 0.00 2.32
786 856 3.230245 TTTTTGGCTGTGGGGGCG 61.230 61.111 0.00 0.00 34.31 6.13
787 857 2.425592 GTTTTTGGCTGTGGGGGC 59.574 61.111 0.00 0.00 0.00 5.80
956 1027 4.466898 GGAAACCCTCCCTCCGTA 57.533 61.111 0.00 0.00 38.44 4.02
1207 1278 1.209261 TGATGCCTCGATGGTAAGCAA 59.791 47.619 0.00 0.00 36.95 3.91
1230 1301 0.616111 AGGAGATCGACAGGCAAGGT 60.616 55.000 0.00 0.00 0.00 3.50
1298 1369 3.195610 TCATAATCAGACACCAGCGTCTT 59.804 43.478 0.00 0.00 43.84 3.01
1320 1391 5.393068 TTTCAGCTGGAATGGGATCTAAT 57.607 39.130 15.13 0.00 34.91 1.73
1419 1491 2.238646 ACTCCCAACATCTAAATCGGCA 59.761 45.455 0.00 0.00 0.00 5.69
1467 1539 3.404978 CGACATCGTTACGGAACCA 57.595 52.632 4.57 0.00 31.28 3.67
1513 1585 1.219522 GACTACAGTGCAACCGCGTT 61.220 55.000 4.92 0.00 42.97 4.84
1516 1588 1.291877 CCAGACTACAGTGCAACCGC 61.292 60.000 0.00 0.00 37.80 5.68
1542 1614 1.739466 TCGATTGGCTGAACAATGAGC 59.261 47.619 0.00 0.00 40.92 4.26
1576 1648 9.832445 TCTCCACTAAATTGAACTAATACATCC 57.168 33.333 0.00 0.00 0.00 3.51
1583 1656 8.383175 AGGTCATTCTCCACTAAATTGAACTAA 58.617 33.333 0.00 0.00 0.00 2.24
1647 1720 3.249080 TCCCAAAAATCGAAACGACAGAC 59.751 43.478 0.00 0.00 39.18 3.51
1658 1731 2.162681 AGAACAGCCTCCCAAAAATCG 58.837 47.619 0.00 0.00 0.00 3.34
1667 1740 0.250901 TGAAGCCAAGAACAGCCTCC 60.251 55.000 0.00 0.00 0.00 4.30
1682 2973 3.997021 AGTTTCTCCGCACATACTTGAAG 59.003 43.478 0.00 0.00 0.00 3.02
1837 3200 2.681064 CCACCAACCCCTGCCATG 60.681 66.667 0.00 0.00 0.00 3.66
1912 3275 6.950842 ACATGAAGATCCACTTGTATCAGAA 58.049 36.000 0.00 0.00 39.13 3.02
1958 3323 3.935203 CAGCACTGAATACCGTCAAGATT 59.065 43.478 0.00 0.00 0.00 2.40
1962 3327 2.831685 ACAGCACTGAATACCGTCAA 57.168 45.000 4.31 0.00 0.00 3.18
2044 3409 1.488812 AGTGCACCAAGTGGAGTAACA 59.511 47.619 14.63 0.00 35.85 2.41
2047 3412 2.289444 GCTAAGTGCACCAAGTGGAGTA 60.289 50.000 14.63 0.00 36.56 2.59
2087 3452 2.565391 TCATTAAGGACCGCACTTCTGA 59.435 45.455 0.00 0.00 0.00 3.27
2352 3724 6.723298 TGGTTGCTAATCAGGAAAAGAAAA 57.277 33.333 0.00 0.00 33.47 2.29
2433 3805 6.742718 GCAAGCACGATTATCGCATAAAATAT 59.257 34.615 14.97 0.00 45.12 1.28
2468 3840 4.804139 GGGATATAACGGAATATGAGCACG 59.196 45.833 0.00 0.00 0.00 5.34
2495 3867 6.692849 ACCATGATATGTGTCTGACCATAT 57.307 37.500 21.39 21.39 37.06 1.78
2564 3936 8.644216 TGGGCTAATTATTCGTAAGTAGAATGA 58.356 33.333 6.80 0.00 38.61 2.57
2815 4188 2.270352 AAGCAACGGAAGAACCATCA 57.730 45.000 0.00 0.00 38.90 3.07
2875 4248 6.485171 AGTTACAGAGGGAGCAATAATTTGT 58.515 36.000 0.00 0.00 35.17 2.83
2885 4258 9.646427 CATCTTATATTAAGTTACAGAGGGAGC 57.354 37.037 0.00 0.00 0.00 4.70
2944 4318 9.498176 TGTACTCCCTCTGAAACTTTTTATAAC 57.502 33.333 0.00 0.00 0.00 1.89
2957 4331 6.183360 GCTGATTAAAGATGTACTCCCTCTGA 60.183 42.308 0.00 0.00 0.00 3.27
3034 4408 5.125100 TCAAGCATAAGTTTGAAGCAAGG 57.875 39.130 0.00 0.00 41.20 3.61
3039 4413 8.356533 ACAAAACATCAAGCATAAGTTTGAAG 57.643 30.769 1.33 0.27 45.95 3.02
3041 4415 8.409371 TGTACAAAACATCAAGCATAAGTTTGA 58.591 29.630 0.00 0.00 46.69 2.69
3145 4519 7.201617 GCCAGTATTGTTAGTGAGGTAAACATC 60.202 40.741 0.00 0.00 33.44 3.06
3154 4528 4.045104 CGCTAGCCAGTATTGTTAGTGAG 58.955 47.826 9.66 0.00 31.43 3.51
3236 4611 8.201554 TGCAATTAAGCAAGTAGACTAAGATG 57.798 34.615 0.00 0.00 42.46 2.90
3252 4628 9.844790 TGATCTCATGTTAAACTTGCAATTAAG 57.155 29.630 0.00 0.00 0.00 1.85
3286 4662 4.935205 CACTGCATACCTAGTACAAGCAAA 59.065 41.667 0.00 0.00 0.00 3.68
3293 4669 5.360591 AGCAATTCACTGCATACCTAGTAC 58.639 41.667 0.00 0.00 45.18 2.73
3299 4675 6.194796 TCTAAAAGCAATTCACTGCATACC 57.805 37.500 0.00 0.00 45.18 2.73
3328 4704 5.174395 CCTTTACTCAGACCTCATTCTGTG 58.826 45.833 0.30 1.01 43.19 3.66
3331 4707 3.777522 CCCCTTTACTCAGACCTCATTCT 59.222 47.826 0.00 0.00 0.00 2.40
3370 4802 4.998672 AGAAAATTGGTTGGCAATGACATG 59.001 37.500 1.92 0.00 0.00 3.21
3375 4807 4.385447 CGTACAGAAAATTGGTTGGCAATG 59.615 41.667 1.92 0.00 0.00 2.82
3396 4828 9.853177 AAATGATAATCCCTAAAATTCTCTCGT 57.147 29.630 0.00 0.00 0.00 4.18
3424 4857 8.233190 GGTTTGATGAGTTCAGTTTCAGATAAG 58.767 37.037 0.00 0.00 35.27 1.73
3454 4887 7.069208 TCTGACATAGATCATGATAGGTATGCC 59.931 40.741 21.40 15.74 38.10 4.40
3476 4909 8.521176 GTCCTAGACTTGTAAACACTAATCTGA 58.479 37.037 0.00 0.00 0.00 3.27
3479 4912 9.654663 ATTGTCCTAGACTTGTAAACACTAATC 57.345 33.333 0.00 0.00 33.15 1.75
3490 4923 6.986817 CGATAATTGGATTGTCCTAGACTTGT 59.013 38.462 0.00 0.00 37.46 3.16
3491 4924 7.210174 TCGATAATTGGATTGTCCTAGACTTG 58.790 38.462 0.00 0.00 37.46 3.16
3586 5022 5.546621 ACTTTAGAAGTGTTGTCTAGCCA 57.453 39.130 0.00 0.00 41.01 4.75
3678 5131 5.266788 AGATGGCATAATATTGACCATGGG 58.733 41.667 18.09 0.00 41.15 4.00
3688 5141 7.285566 ACACTGAACTCAAGATGGCATAATAT 58.714 34.615 0.00 0.00 0.00 1.28
3745 5199 7.164230 AGTTTAACAGAACCATTTGTTGACA 57.836 32.000 0.00 0.00 37.98 3.58
3757 5211 7.918562 TGGCAGTTTTATCAAGTTTAACAGAAC 59.081 33.333 0.00 0.00 0.00 3.01
3777 5231 5.621193 ACTCTATACAACAAAACTGGCAGT 58.379 37.500 15.88 15.88 0.00 4.40
3783 5237 9.826574 TTGTCACTAACTCTATACAACAAAACT 57.173 29.630 0.00 0.00 0.00 2.66
3791 5245 7.093945 TGTGAGCATTGTCACTAACTCTATACA 60.094 37.037 15.53 0.00 46.06 2.29
3831 5285 3.118629 TCCTGCAAGCAAGTACTATCAGG 60.119 47.826 0.00 7.16 39.11 3.86
3834 5288 3.868077 CAGTCCTGCAAGCAAGTACTATC 59.132 47.826 0.00 0.00 0.00 2.08
3908 5362 5.259632 AGAAGAAATGTCCCAGAAAGGATG 58.740 41.667 0.00 0.00 41.22 3.51
4037 5498 2.856039 TAGGCAGAGTCGGTGGGAGG 62.856 65.000 0.00 0.00 0.00 4.30
4091 5552 3.442996 AGGAATTCCTTCAGACGCG 57.557 52.632 21.89 3.53 46.09 6.01
4148 5609 4.440663 GGTCAAAATTATTCTGCTGCCCTC 60.441 45.833 0.00 0.00 0.00 4.30
4342 5804 9.672673 TCCTCAAAAACAAAAATACATGGAAAA 57.327 25.926 0.00 0.00 0.00 2.29
4343 5805 9.672673 TTCCTCAAAAACAAAAATACATGGAAA 57.327 25.926 0.00 0.00 0.00 3.13
4344 5806 9.103861 GTTCCTCAAAAACAAAAATACATGGAA 57.896 29.630 0.00 0.00 0.00 3.53
4345 5807 7.713073 GGTTCCTCAAAAACAAAAATACATGGA 59.287 33.333 0.00 0.00 0.00 3.41
4420 5894 7.557875 TCAGATTCTTTCCCCATTTTCAAAT 57.442 32.000 0.00 0.00 0.00 2.32
4430 5904 7.761038 TTTTAGTTCTTCAGATTCTTTCCCC 57.239 36.000 0.00 0.00 0.00 4.81
4506 5981 0.586319 ACACGCAAAGAACATCACCG 59.414 50.000 0.00 0.00 0.00 4.94
4522 5997 1.202177 CGGAGCATTGCCATTACACAC 60.202 52.381 4.70 0.00 0.00 3.82
4658 6137 4.278170 TGTGAGATTGTTGGGTTTGATGAC 59.722 41.667 0.00 0.00 0.00 3.06
4701 6180 0.991146 TCCTTGCTCAGCCATTGGTA 59.009 50.000 4.26 0.00 0.00 3.25
4703 6182 1.035932 CCTCCTTGCTCAGCCATTGG 61.036 60.000 0.00 0.00 0.00 3.16
4719 6198 4.081420 TGAGCACCTTGTATTCTTCTCCTC 60.081 45.833 0.00 0.00 0.00 3.71
4801 6280 1.512310 GAAGCTCGAGGTGTCGTCG 60.512 63.158 19.39 5.66 46.85 5.12


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

AutoCloner maintained by Alex Coulton.