Multiple sequence alignment - TraesCS1A01G299200

Loading Multiple Alignment...

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 TraesCS1A01G299200 chr1A 100.000 3804 0 0 1 3804 494023227 494027030 0.000000e+00 7025
1 TraesCS1A01G299200 chr1A 98.097 578 11 0 3199 3776 566089521 566088944 0.000000e+00 1007
2 TraesCS1A01G299200 chr1B 93.307 2495 104 21 740 3206 531535018 531537477 0.000000e+00 3624
3 TraesCS1A01G299200 chr1B 90.828 894 46 13 2335 3201 531650019 531650903 0.000000e+00 1164
4 TraesCS1A01G299200 chr1B 86.491 644 42 13 98 732 531534372 531534979 0.000000e+00 665
5 TraesCS1A01G299200 chr1D 96.047 1872 52 6 404 2272 391278482 391276630 0.000000e+00 3027
6 TraesCS1A01G299200 chr1D 93.603 891 41 11 2271 3151 391276547 391275663 0.000000e+00 1315
7 TraesCS1A01G299200 chr1D 95.993 599 23 1 3207 3804 15320530 15319932 0.000000e+00 972
8 TraesCS1A01G299200 chr1D 95.690 232 8 1 125 356 391278788 391278559 4.640000e-99 372
9 TraesCS1A01G299200 chr7B 98.515 606 9 0 3199 3804 534547994 534547389 0.000000e+00 1070
10 TraesCS1A01G299200 chr7B 97.851 605 12 1 3200 3804 686847563 686846960 0.000000e+00 1044
11 TraesCS1A01G299200 chr7B 97.521 605 15 0 3200 3804 12959118 12958514 0.000000e+00 1035
12 TraesCS1A01G299200 chr6A 97.529 607 15 0 3198 3804 534655896 534656502 0.000000e+00 1038
13 TraesCS1A01G299200 chr6B 96.700 606 12 1 3199 3804 255980542 255979945 0.000000e+00 1002
14 TraesCS1A01G299200 chr2D 95.731 609 25 1 3197 3804 619364900 619364292 0.000000e+00 979
15 TraesCS1A01G299200 chr2D 84.857 350 42 4 1062 1409 636085963 636085623 3.640000e-90 342
16 TraesCS1A01G299200 chr5B 95.207 605 28 1 3201 3804 705115794 705116398 0.000000e+00 955
17 TraesCS1A01G299200 chr5B 82.671 277 41 7 2451 2721 610348525 610348800 4.910000e-59 239
18 TraesCS1A01G299200 chr3A 80.170 1175 184 37 1050 2210 595934497 595933358 0.000000e+00 833
19 TraesCS1A01G299200 chr3A 83.202 381 54 7 2337 2709 595933103 595932725 1.310000e-89 340
20 TraesCS1A01G299200 chr3D 83.271 801 124 9 1050 1842 453985591 453984793 0.000000e+00 728
21 TraesCS1A01G299200 chr3D 80.524 801 145 10 1045 1837 1993207 1992410 4.200000e-169 604
22 TraesCS1A01G299200 chr3D 83.123 397 59 8 2320 2709 453984197 453983802 4.670000e-94 355
23 TraesCS1A01G299200 chr3D 81.203 399 61 10 2321 2709 1991857 1991463 3.690000e-80 309
24 TraesCS1A01G299200 chr3B 83.313 803 120 11 1050 1842 596412711 596411913 0.000000e+00 728
25 TraesCS1A01G299200 chr3B 83.375 397 58 7 2320 2709 596411314 596410919 1.000000e-95 361
26 TraesCS1A01G299200 chr7A 81.477 772 127 13 1045 1805 465591 464825 1.500000e-173 619
27 TraesCS1A01G299200 chrUn 84.167 360 48 4 1050 1409 354266475 354266825 1.310000e-89 340
28 TraesCS1A01G299200 chrUn 87.600 250 31 0 1160 1409 247902080 247902329 1.340000e-74 291
29 TraesCS1A01G299200 chr2A 80.833 240 23 6 1062 1301 761070864 761071080 2.350000e-37 167


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 TraesCS1A01G299200 chr1A 494023227 494027030 3803 False 7025.000000 7025 100.000000 1 3804 1 chr1A.!!$F1 3803
1 TraesCS1A01G299200 chr1A 566088944 566089521 577 True 1007.000000 1007 98.097000 3199 3776 1 chr1A.!!$R1 577
2 TraesCS1A01G299200 chr1B 531534372 531537477 3105 False 2144.500000 3624 89.899000 98 3206 2 chr1B.!!$F2 3108
3 TraesCS1A01G299200 chr1B 531650019 531650903 884 False 1164.000000 1164 90.828000 2335 3201 1 chr1B.!!$F1 866
4 TraesCS1A01G299200 chr1D 391275663 391278788 3125 True 1571.333333 3027 95.113333 125 3151 3 chr1D.!!$R2 3026
5 TraesCS1A01G299200 chr1D 15319932 15320530 598 True 972.000000 972 95.993000 3207 3804 1 chr1D.!!$R1 597
6 TraesCS1A01G299200 chr7B 534547389 534547994 605 True 1070.000000 1070 98.515000 3199 3804 1 chr7B.!!$R2 605
7 TraesCS1A01G299200 chr7B 686846960 686847563 603 True 1044.000000 1044 97.851000 3200 3804 1 chr7B.!!$R3 604
8 TraesCS1A01G299200 chr7B 12958514 12959118 604 True 1035.000000 1035 97.521000 3200 3804 1 chr7B.!!$R1 604
9 TraesCS1A01G299200 chr6A 534655896 534656502 606 False 1038.000000 1038 97.529000 3198 3804 1 chr6A.!!$F1 606
10 TraesCS1A01G299200 chr6B 255979945 255980542 597 True 1002.000000 1002 96.700000 3199 3804 1 chr6B.!!$R1 605
11 TraesCS1A01G299200 chr2D 619364292 619364900 608 True 979.000000 979 95.731000 3197 3804 1 chr2D.!!$R1 607
12 TraesCS1A01G299200 chr5B 705115794 705116398 604 False 955.000000 955 95.207000 3201 3804 1 chr5B.!!$F2 603
13 TraesCS1A01G299200 chr3A 595932725 595934497 1772 True 586.500000 833 81.686000 1050 2709 2 chr3A.!!$R1 1659
14 TraesCS1A01G299200 chr3D 453983802 453985591 1789 True 541.500000 728 83.197000 1050 2709 2 chr3D.!!$R2 1659
15 TraesCS1A01G299200 chr3D 1991463 1993207 1744 True 456.500000 604 80.863500 1045 2709 2 chr3D.!!$R1 1664
16 TraesCS1A01G299200 chr3B 596410919 596412711 1792 True 544.500000 728 83.344000 1050 2709 2 chr3B.!!$R1 1659
17 TraesCS1A01G299200 chr7A 464825 465591 766 True 619.000000 619 81.477000 1045 1805 1 chr7A.!!$R1 760

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 93 0.030369 CGCCATCTGGGTACGTAGAC 59.970 60.0 0.0 0.0 39.65 2.59 F
666 721 0.109272 TGCTAAAGCGTCTGGTCTCG 60.109 55.0 0.0 0.0 45.83 4.04 F
695 750 0.616111 CCACTCACTCCTACCAGGCT 60.616 60.0 0.0 0.0 34.61 4.58 F
1948 2043 0.858139 AAGGAGGAGGAGGAGGAGGT 60.858 60.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2068 1.000993 GAGCTCCTCCTGACCTCCA 59.999 63.158 0.87 0.00 0.00 3.86 R
2310 2495 1.447489 CCGCTCCTGCTCAAGTCAG 60.447 63.158 0.00 0.00 36.97 3.51 R
2656 2957 4.767255 CACGTGAGGCCCCAGAGC 62.767 72.222 10.90 0.00 0.00 4.09 R
3075 3407 1.273886 TGGTTGGATCGACGATTCACA 59.726 47.619 18.46 11.38 25.65 3.58 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
17 18 2.046411 TGGGTATGTGTGGCAGCG 60.046 61.111 0.00 0.00 0.00 5.18
18 19 2.046314 GGGTATGTGTGGCAGCGT 60.046 61.111 0.00 0.00 0.00 5.07
19 20 2.398554 GGGTATGTGTGGCAGCGTG 61.399 63.158 0.00 0.00 0.00 5.34
20 21 1.671054 GGTATGTGTGGCAGCGTGT 60.671 57.895 0.00 0.00 0.00 4.49
21 22 1.234615 GGTATGTGTGGCAGCGTGTT 61.235 55.000 0.00 0.00 0.00 3.32
22 23 1.434555 GTATGTGTGGCAGCGTGTTA 58.565 50.000 0.00 0.00 0.00 2.41
23 24 1.801771 GTATGTGTGGCAGCGTGTTAA 59.198 47.619 0.00 0.00 0.00 2.01
24 25 1.313772 ATGTGTGGCAGCGTGTTAAA 58.686 45.000 0.00 0.00 0.00 1.52
25 26 1.095600 TGTGTGGCAGCGTGTTAAAA 58.904 45.000 0.00 0.00 0.00 1.52
26 27 1.064803 TGTGTGGCAGCGTGTTAAAAG 59.935 47.619 0.00 0.00 0.00 2.27
27 28 1.332375 GTGTGGCAGCGTGTTAAAAGA 59.668 47.619 0.00 0.00 0.00 2.52
28 29 1.601903 TGTGGCAGCGTGTTAAAAGAG 59.398 47.619 0.00 0.00 0.00 2.85
29 30 1.871039 GTGGCAGCGTGTTAAAAGAGA 59.129 47.619 0.00 0.00 0.00 3.10
30 31 2.289547 GTGGCAGCGTGTTAAAAGAGAA 59.710 45.455 0.00 0.00 0.00 2.87
31 32 2.946329 TGGCAGCGTGTTAAAAGAGAAA 59.054 40.909 0.00 0.00 0.00 2.52
32 33 3.003275 TGGCAGCGTGTTAAAAGAGAAAG 59.997 43.478 0.00 0.00 0.00 2.62
33 34 3.250040 GGCAGCGTGTTAAAAGAGAAAGA 59.750 43.478 0.00 0.00 0.00 2.52
34 35 4.458708 GCAGCGTGTTAAAAGAGAAAGAG 58.541 43.478 0.00 0.00 0.00 2.85
35 36 4.211374 GCAGCGTGTTAAAAGAGAAAGAGA 59.789 41.667 0.00 0.00 0.00 3.10
36 37 5.613577 GCAGCGTGTTAAAAGAGAAAGAGAG 60.614 44.000 0.00 0.00 0.00 3.20
37 38 5.692204 CAGCGTGTTAAAAGAGAAAGAGAGA 59.308 40.000 0.00 0.00 0.00 3.10
38 39 5.923684 AGCGTGTTAAAAGAGAAAGAGAGAG 59.076 40.000 0.00 0.00 0.00 3.20
39 40 5.921408 GCGTGTTAAAAGAGAAAGAGAGAGA 59.079 40.000 0.00 0.00 0.00 3.10
40 41 6.088883 GCGTGTTAAAAGAGAAAGAGAGAGAG 59.911 42.308 0.00 0.00 0.00 3.20
41 42 7.364200 CGTGTTAAAAGAGAAAGAGAGAGAGA 58.636 38.462 0.00 0.00 0.00 3.10
42 43 7.537306 CGTGTTAAAAGAGAAAGAGAGAGAGAG 59.463 40.741 0.00 0.00 0.00 3.20
43 44 8.573035 GTGTTAAAAGAGAAAGAGAGAGAGAGA 58.427 37.037 0.00 0.00 0.00 3.10
44 45 9.137459 TGTTAAAAGAGAAAGAGAGAGAGAGAA 57.863 33.333 0.00 0.00 0.00 2.87
48 49 7.573968 AAGAGAAAGAGAGAGAGAGAATAGC 57.426 40.000 0.00 0.00 0.00 2.97
49 50 6.904626 AGAGAAAGAGAGAGAGAGAATAGCT 58.095 40.000 0.00 0.00 0.00 3.32
50 51 6.769822 AGAGAAAGAGAGAGAGAGAATAGCTG 59.230 42.308 0.00 0.00 0.00 4.24
51 52 5.300286 AGAAAGAGAGAGAGAGAATAGCTGC 59.700 44.000 0.00 0.00 0.00 5.25
52 53 3.141398 AGAGAGAGAGAGAATAGCTGCG 58.859 50.000 0.00 0.00 0.00 5.18
53 54 2.878406 GAGAGAGAGAGAATAGCTGCGT 59.122 50.000 0.00 0.00 0.00 5.24
54 55 4.062293 GAGAGAGAGAGAATAGCTGCGTA 58.938 47.826 0.00 0.00 0.00 4.42
55 56 4.456535 AGAGAGAGAGAATAGCTGCGTAA 58.543 43.478 0.00 0.00 0.00 3.18
56 57 5.070001 AGAGAGAGAGAATAGCTGCGTAAT 58.930 41.667 0.00 0.00 0.00 1.89
57 58 5.534654 AGAGAGAGAGAATAGCTGCGTAATT 59.465 40.000 0.00 0.00 0.00 1.40
58 59 5.527951 AGAGAGAGAATAGCTGCGTAATTG 58.472 41.667 0.00 0.00 0.00 2.32
59 60 4.626042 AGAGAGAATAGCTGCGTAATTGG 58.374 43.478 0.00 0.00 0.00 3.16
60 61 3.134458 AGAGAATAGCTGCGTAATTGGC 58.866 45.455 0.00 0.00 0.00 4.52
61 62 2.872245 GAGAATAGCTGCGTAATTGGCA 59.128 45.455 0.00 5.96 38.92 4.92
62 63 2.614057 AGAATAGCTGCGTAATTGGCAC 59.386 45.455 0.00 1.44 36.24 5.01
63 64 0.937304 ATAGCTGCGTAATTGGCACG 59.063 50.000 0.00 0.00 42.24 5.34
64 65 0.390603 TAGCTGCGTAATTGGCACGT 60.391 50.000 0.00 0.00 41.41 4.49
65 66 1.511887 GCTGCGTAATTGGCACGTG 60.512 57.895 12.28 12.28 41.41 4.49
66 67 1.866237 CTGCGTAATTGGCACGTGT 59.134 52.632 18.38 0.00 41.41 4.49
67 68 0.452618 CTGCGTAATTGGCACGTGTG 60.453 55.000 18.38 0.00 41.41 3.82
68 69 1.154301 GCGTAATTGGCACGTGTGG 60.154 57.895 18.38 0.00 41.41 4.17
85 86 4.175337 GCAGCCGCCATCTGGGTA 62.175 66.667 0.00 0.00 39.65 3.69
86 87 2.203070 CAGCCGCCATCTGGGTAC 60.203 66.667 0.00 0.00 39.65 3.34
87 88 3.849951 AGCCGCCATCTGGGTACG 61.850 66.667 0.00 0.00 39.65 3.67
88 89 4.157120 GCCGCCATCTGGGTACGT 62.157 66.667 0.00 0.00 39.65 3.57
89 90 2.788640 GCCGCCATCTGGGTACGTA 61.789 63.158 0.00 0.00 39.65 3.57
90 91 1.362717 CCGCCATCTGGGTACGTAG 59.637 63.158 0.00 0.00 39.65 3.51
91 92 1.105167 CCGCCATCTGGGTACGTAGA 61.105 60.000 0.00 0.00 39.65 2.59
92 93 0.030369 CGCCATCTGGGTACGTAGAC 59.970 60.000 0.00 0.00 39.65 2.59
93 94 0.030369 GCCATCTGGGTACGTAGACG 59.970 60.000 0.00 0.00 41.74 4.18
94 95 2.620996 GCCATCTGGGTACGTAGACGT 61.621 57.143 12.90 12.90 46.24 4.34
95 96 3.323258 GCCATCTGGGTACGTAGACGTA 61.323 54.545 10.73 10.73 45.07 3.57
162 163 1.122849 GCGAGTGAAACGACACGTAA 58.877 50.000 0.00 0.00 45.86 3.18
322 324 4.088762 CATGCACACGTGTCCCGC 62.089 66.667 20.49 19.84 41.42 6.13
396 406 2.498941 CCCCGATTCTCGCTAGCCA 61.499 63.158 9.66 0.00 38.82 4.75
407 453 1.554891 CGCTAGCCATGATGCAGTCG 61.555 60.000 9.66 0.00 0.00 4.18
460 506 2.446435 TCCCCTGCTTAATTTGACAGC 58.554 47.619 0.00 0.00 0.00 4.40
461 507 2.041620 TCCCCTGCTTAATTTGACAGCT 59.958 45.455 0.00 0.00 34.42 4.24
462 508 2.165030 CCCCTGCTTAATTTGACAGCTG 59.835 50.000 13.48 13.48 34.42 4.24
463 509 3.084039 CCCTGCTTAATTTGACAGCTGA 58.916 45.455 23.35 0.00 35.18 4.26
464 510 3.698040 CCCTGCTTAATTTGACAGCTGAT 59.302 43.478 23.35 4.35 35.18 2.90
465 511 4.439700 CCCTGCTTAATTTGACAGCTGATG 60.440 45.833 23.35 0.00 35.18 3.07
466 512 4.100707 TGCTTAATTTGACAGCTGATGC 57.899 40.909 23.35 10.27 40.05 3.91
623 669 1.208052 GCATGTGAGCCAGAACCTAGA 59.792 52.381 0.00 0.00 0.00 2.43
624 670 2.355108 GCATGTGAGCCAGAACCTAGAA 60.355 50.000 0.00 0.00 0.00 2.10
629 675 3.748568 GTGAGCCAGAACCTAGAAAGTTG 59.251 47.826 0.00 0.00 0.00 3.16
649 695 1.392510 GGAATCCTTCACGTACGTTGC 59.607 52.381 20.23 3.74 0.00 4.17
665 720 1.727335 GTTGCTAAAGCGTCTGGTCTC 59.273 52.381 0.00 0.00 45.83 3.36
666 721 0.109272 TGCTAAAGCGTCTGGTCTCG 60.109 55.000 0.00 0.00 45.83 4.04
677 732 4.525949 GGTCTCGCCCGGCTTACC 62.526 72.222 8.05 8.29 0.00 2.85
688 743 1.471119 CGGCTTACCACTCACTCCTA 58.529 55.000 0.00 0.00 34.57 2.94
689 744 1.134560 CGGCTTACCACTCACTCCTAC 59.865 57.143 0.00 0.00 34.57 3.18
690 745 1.481363 GGCTTACCACTCACTCCTACC 59.519 57.143 0.00 0.00 35.26 3.18
691 746 2.176889 GCTTACCACTCACTCCTACCA 58.823 52.381 0.00 0.00 0.00 3.25
692 747 2.166664 GCTTACCACTCACTCCTACCAG 59.833 54.545 0.00 0.00 0.00 4.00
693 748 2.526888 TACCACTCACTCCTACCAGG 57.473 55.000 0.00 0.00 36.46 4.45
694 749 0.905337 ACCACTCACTCCTACCAGGC 60.905 60.000 0.00 0.00 34.61 4.85
695 750 0.616111 CCACTCACTCCTACCAGGCT 60.616 60.000 0.00 0.00 34.61 4.58
845 931 2.840651 ACTAGGAAAGCACATAGGCAGT 59.159 45.455 0.00 0.00 35.83 4.40
859 945 1.969923 AGGCAGTGCTGATCTATCCTC 59.030 52.381 16.11 0.00 0.00 3.71
1042 1128 2.163509 GGGAGAGAGGGAAGCAAAAAC 58.836 52.381 0.00 0.00 0.00 2.43
1047 1133 1.620323 AGAGGGAAGCAAAAACCATGC 59.380 47.619 0.00 0.00 44.15 4.06
1514 1600 3.497763 CCAAGTTCTACACCACCATGGAA 60.498 47.826 21.47 0.00 40.96 3.53
1910 2002 1.074405 TGCTGGCTCAACAAGGAGATT 59.926 47.619 0.00 0.00 37.05 2.40
1948 2043 0.858139 AAGGAGGAGGAGGAGGAGGT 60.858 60.000 0.00 0.00 0.00 3.85
1960 2055 3.787001 GGAGGTGAAGGAGGCCGG 61.787 72.222 0.00 0.00 0.00 6.13
1989 2084 1.828768 CATGGAGGTCAGGAGGAGC 59.171 63.158 0.00 0.00 44.43 4.70
2227 2322 2.279069 CCCACCTCACTCGCTCTGT 61.279 63.158 0.00 0.00 0.00 3.41
2251 2346 7.819415 TGTTCTCTTCATCGTCACTTTGAATAT 59.181 33.333 0.00 0.00 0.00 1.28
2253 2348 8.189709 TCTCTTCATCGTCACTTTGAATATTG 57.810 34.615 0.00 0.00 0.00 1.90
2255 2350 7.742151 TCTTCATCGTCACTTTGAATATTGTG 58.258 34.615 0.00 0.00 0.00 3.33
2298 2480 7.393841 ACTGTACTTGGTAGTAGATTCTGAC 57.606 40.000 0.00 0.00 37.53 3.51
2299 2481 7.176490 ACTGTACTTGGTAGTAGATTCTGACT 58.824 38.462 0.00 0.00 37.53 3.41
2301 2483 8.734218 TGTACTTGGTAGTAGATTCTGACTAG 57.266 38.462 0.00 0.00 37.53 2.57
2302 2484 8.546322 TGTACTTGGTAGTAGATTCTGACTAGA 58.454 37.037 0.00 0.00 37.53 2.43
2303 2485 9.563748 GTACTTGGTAGTAGATTCTGACTAGAT 57.436 37.037 0.00 0.00 37.53 1.98
2740 3041 1.740296 GAGGAGCGGCGCTAACAAA 60.740 57.895 36.55 0.00 39.88 2.83
2805 3114 5.505286 GCCACATGATCGAGTGAATAAAAG 58.495 41.667 16.34 2.34 37.97 2.27
2840 3150 6.273825 CGTAGCTAGGTGATGTAACATCTTT 58.726 40.000 4.27 0.00 33.08 2.52
2850 3160 8.352942 GGTGATGTAACATCTTTCTTGTTTCTT 58.647 33.333 0.00 0.00 38.26 2.52
2851 3161 9.387123 GTGATGTAACATCTTTCTTGTTTCTTC 57.613 33.333 0.00 0.00 38.26 2.87
2852 3162 8.567948 TGATGTAACATCTTTCTTGTTTCTTCC 58.432 33.333 0.00 0.00 38.26 3.46
2853 3163 7.272037 TGTAACATCTTTCTTGTTTCTTCCC 57.728 36.000 0.00 0.00 38.26 3.97
2854 3164 5.791336 AACATCTTTCTTGTTTCTTCCCC 57.209 39.130 0.00 0.00 33.64 4.81
2969 3299 5.888691 TGTAAAAGAACAACAGAGCACAA 57.111 34.783 0.00 0.00 0.00 3.33
3002 3332 3.760684 AGAACTGGATGCTGAAATTCACC 59.239 43.478 0.00 0.00 0.00 4.02
3004 3334 2.086869 CTGGATGCTGAAATTCACCGT 58.913 47.619 0.00 0.00 0.00 4.83
3074 3406 9.437045 CTTTGGATGCAAATTTTACAAGTTTTC 57.563 29.630 13.13 0.00 0.00 2.29
3075 3407 8.729805 TTGGATGCAAATTTTACAAGTTTTCT 57.270 26.923 0.00 0.00 0.00 2.52
3102 3436 1.588404 CGTCGATCCAACCAGATTTCG 59.412 52.381 0.00 0.00 0.00 3.46
3124 3458 1.097547 ACGTCGGGGTACATCTACCG 61.098 60.000 0.00 0.00 43.39 4.02
3181 3515 1.742761 CCTGTCTCGACATGCCAAAT 58.257 50.000 0.00 0.00 41.01 2.32
3263 3597 9.520515 TTGATTAAGAAGAAGTAAGAATTGCCT 57.479 29.630 0.00 0.00 0.00 4.75
3382 3716 3.882888 TGCAAAGAAGAAAAGACATCCGT 59.117 39.130 0.00 0.00 0.00 4.69
3403 3737 1.741770 GGGAGTCGCAAGCGTCATT 60.742 57.895 14.57 0.00 40.74 2.57
3689 4024 1.031571 ACGCCATCATCGTTGCCAAT 61.032 50.000 0.00 0.00 36.72 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.234615 AACACGCTGCCACACATACC 61.235 55.000 0.00 0.00 0.00 2.73
3 4 1.434555 TAACACGCTGCCACACATAC 58.565 50.000 0.00 0.00 0.00 2.39
5 6 1.313772 TTTAACACGCTGCCACACAT 58.686 45.000 0.00 0.00 0.00 3.21
6 7 1.064803 CTTTTAACACGCTGCCACACA 59.935 47.619 0.00 0.00 0.00 3.72
7 8 1.332375 TCTTTTAACACGCTGCCACAC 59.668 47.619 0.00 0.00 0.00 3.82
8 9 1.601903 CTCTTTTAACACGCTGCCACA 59.398 47.619 0.00 0.00 0.00 4.17
9 10 1.871039 TCTCTTTTAACACGCTGCCAC 59.129 47.619 0.00 0.00 0.00 5.01
10 11 2.248280 TCTCTTTTAACACGCTGCCA 57.752 45.000 0.00 0.00 0.00 4.92
11 12 3.250040 TCTTTCTCTTTTAACACGCTGCC 59.750 43.478 0.00 0.00 0.00 4.85
12 13 4.211374 TCTCTTTCTCTTTTAACACGCTGC 59.789 41.667 0.00 0.00 0.00 5.25
13 14 5.692204 TCTCTCTTTCTCTTTTAACACGCTG 59.308 40.000 0.00 0.00 0.00 5.18
14 15 5.844004 TCTCTCTTTCTCTTTTAACACGCT 58.156 37.500 0.00 0.00 0.00 5.07
15 16 5.921408 TCTCTCTCTTTCTCTTTTAACACGC 59.079 40.000 0.00 0.00 0.00 5.34
16 17 7.364200 TCTCTCTCTCTTTCTCTTTTAACACG 58.636 38.462 0.00 0.00 0.00 4.49
17 18 8.573035 TCTCTCTCTCTCTTTCTCTTTTAACAC 58.427 37.037 0.00 0.00 0.00 3.32
18 19 8.698973 TCTCTCTCTCTCTTTCTCTTTTAACA 57.301 34.615 0.00 0.00 0.00 2.41
22 23 8.470002 GCTATTCTCTCTCTCTCTTTCTCTTTT 58.530 37.037 0.00 0.00 0.00 2.27
23 24 7.836183 AGCTATTCTCTCTCTCTCTTTCTCTTT 59.164 37.037 0.00 0.00 0.00 2.52
24 25 7.284034 CAGCTATTCTCTCTCTCTCTTTCTCTT 59.716 40.741 0.00 0.00 0.00 2.85
25 26 6.769822 CAGCTATTCTCTCTCTCTCTTTCTCT 59.230 42.308 0.00 0.00 0.00 3.10
26 27 6.514048 GCAGCTATTCTCTCTCTCTCTTTCTC 60.514 46.154 0.00 0.00 0.00 2.87
27 28 5.300286 GCAGCTATTCTCTCTCTCTCTTTCT 59.700 44.000 0.00 0.00 0.00 2.52
28 29 5.523369 GCAGCTATTCTCTCTCTCTCTTTC 58.477 45.833 0.00 0.00 0.00 2.62
29 30 4.036734 CGCAGCTATTCTCTCTCTCTCTTT 59.963 45.833 0.00 0.00 0.00 2.52
30 31 3.565482 CGCAGCTATTCTCTCTCTCTCTT 59.435 47.826 0.00 0.00 0.00 2.85
31 32 3.141398 CGCAGCTATTCTCTCTCTCTCT 58.859 50.000 0.00 0.00 0.00 3.10
32 33 2.878406 ACGCAGCTATTCTCTCTCTCTC 59.122 50.000 0.00 0.00 0.00 3.20
33 34 2.930950 ACGCAGCTATTCTCTCTCTCT 58.069 47.619 0.00 0.00 0.00 3.10
34 35 4.822036 TTACGCAGCTATTCTCTCTCTC 57.178 45.455 0.00 0.00 0.00 3.20
35 36 5.508825 CCAATTACGCAGCTATTCTCTCTCT 60.509 44.000 0.00 0.00 0.00 3.10
36 37 4.683781 CCAATTACGCAGCTATTCTCTCTC 59.316 45.833 0.00 0.00 0.00 3.20
37 38 4.626042 CCAATTACGCAGCTATTCTCTCT 58.374 43.478 0.00 0.00 0.00 3.10
38 39 3.185391 GCCAATTACGCAGCTATTCTCTC 59.815 47.826 0.00 0.00 0.00 3.20
39 40 3.134458 GCCAATTACGCAGCTATTCTCT 58.866 45.455 0.00 0.00 0.00 3.10
40 41 2.872245 TGCCAATTACGCAGCTATTCTC 59.128 45.455 0.00 0.00 0.00 2.87
41 42 2.614057 GTGCCAATTACGCAGCTATTCT 59.386 45.455 0.00 0.00 36.78 2.40
42 43 2.599848 CGTGCCAATTACGCAGCTATTC 60.600 50.000 0.00 0.00 36.78 1.75
43 44 1.330521 CGTGCCAATTACGCAGCTATT 59.669 47.619 0.00 0.00 36.78 1.73
44 45 0.937304 CGTGCCAATTACGCAGCTAT 59.063 50.000 0.00 0.00 36.78 2.97
45 46 0.390603 ACGTGCCAATTACGCAGCTA 60.391 50.000 0.00 0.00 44.87 3.32
46 47 1.671054 ACGTGCCAATTACGCAGCT 60.671 52.632 0.00 0.00 44.87 4.24
47 48 1.511887 CACGTGCCAATTACGCAGC 60.512 57.895 0.82 0.00 44.87 5.25
48 49 0.452618 CACACGTGCCAATTACGCAG 60.453 55.000 17.22 0.00 44.87 5.18
49 50 1.571953 CACACGTGCCAATTACGCA 59.428 52.632 17.22 0.00 44.87 5.24
50 51 1.154301 CCACACGTGCCAATTACGC 60.154 57.895 17.22 0.00 44.87 4.42
51 52 1.154301 GCCACACGTGCCAATTACG 60.154 57.895 17.22 0.00 46.31 3.18
52 53 0.109781 CTGCCACACGTGCCAATTAC 60.110 55.000 17.22 0.00 0.00 1.89
53 54 1.861542 GCTGCCACACGTGCCAATTA 61.862 55.000 17.22 0.00 0.00 1.40
54 55 3.041701 CTGCCACACGTGCCAATT 58.958 55.556 17.22 0.00 0.00 2.32
55 56 3.673484 GCTGCCACACGTGCCAAT 61.673 61.111 17.22 0.00 0.00 3.16
68 69 4.175337 TACCCAGATGGCGGCTGC 62.175 66.667 9.72 9.72 37.83 5.25
69 70 2.203070 GTACCCAGATGGCGGCTG 60.203 66.667 11.43 0.00 37.83 4.85
70 71 3.849951 CGTACCCAGATGGCGGCT 61.850 66.667 11.43 0.00 37.83 5.52
71 72 2.694829 CTACGTACCCAGATGGCGGC 62.695 65.000 0.00 0.00 37.83 6.53
72 73 1.105167 TCTACGTACCCAGATGGCGG 61.105 60.000 0.00 0.00 37.83 6.13
73 74 0.030369 GTCTACGTACCCAGATGGCG 59.970 60.000 0.00 0.00 37.83 5.69
74 75 0.030369 CGTCTACGTACCCAGATGGC 59.970 60.000 0.00 0.00 33.83 4.40
93 94 5.476752 ACTTGGATTCTCGTAGTACGTAC 57.523 43.478 21.38 18.10 43.14 3.67
94 95 4.268644 CGACTTGGATTCTCGTAGTACGTA 59.731 45.833 21.38 9.19 43.14 3.57
95 96 3.063180 CGACTTGGATTCTCGTAGTACGT 59.937 47.826 21.38 2.82 43.14 3.57
96 97 3.308053 TCGACTTGGATTCTCGTAGTACG 59.692 47.826 16.65 16.65 44.19 3.67
97 98 4.871993 TCGACTTGGATTCTCGTAGTAC 57.128 45.455 0.00 0.00 0.00 2.73
98 99 5.413833 ACTTTCGACTTGGATTCTCGTAGTA 59.586 40.000 0.00 0.00 0.00 1.82
99 100 4.217983 ACTTTCGACTTGGATTCTCGTAGT 59.782 41.667 0.00 0.00 0.00 2.73
100 101 4.734917 ACTTTCGACTTGGATTCTCGTAG 58.265 43.478 0.00 0.00 0.00 3.51
105 106 4.625607 AAGGACTTTCGACTTGGATTCT 57.374 40.909 0.00 0.00 0.00 2.40
162 163 4.469657 TGGGTTAAACTTGTCAGCAATCT 58.530 39.130 0.00 0.00 33.65 2.40
322 324 1.003545 GCATCCGATCATGGTTTCGTG 60.004 52.381 11.01 6.45 33.60 4.35
386 396 0.249784 ACTGCATCATGGCTAGCGAG 60.250 55.000 9.00 0.70 34.04 5.03
396 406 1.452651 CTTGGGGCGACTGCATCAT 60.453 57.895 0.00 0.00 45.35 2.45
407 453 1.300620 GACGGCAAAAACTTGGGGC 60.301 57.895 0.00 0.00 0.00 5.80
460 506 2.159327 TGCATCGTATCAGGCATCAG 57.841 50.000 0.00 0.00 0.00 2.90
461 507 2.809696 CAATGCATCGTATCAGGCATCA 59.190 45.455 0.00 0.00 45.52 3.07
462 508 2.413765 GCAATGCATCGTATCAGGCATC 60.414 50.000 0.00 0.00 45.52 3.91
464 510 0.946528 GCAATGCATCGTATCAGGCA 59.053 50.000 0.00 0.00 41.00 4.75
465 511 1.233019 AGCAATGCATCGTATCAGGC 58.767 50.000 8.35 0.00 0.00 4.85
466 512 3.657634 AGTAGCAATGCATCGTATCAGG 58.342 45.455 8.35 0.00 0.00 3.86
623 669 3.744426 CGTACGTGAAGGATTCCAACTTT 59.256 43.478 7.22 0.00 46.93 2.66
624 670 3.243975 ACGTACGTGAAGGATTCCAACTT 60.244 43.478 22.14 0.00 46.93 2.66
629 675 1.392510 GCAACGTACGTGAAGGATTCC 59.607 52.381 23.57 0.00 46.93 3.01
665 720 4.077184 TGAGTGGTAAGCCGGGCG 62.077 66.667 14.39 0.00 37.67 6.13
666 721 2.436115 GTGAGTGGTAAGCCGGGC 60.436 66.667 12.11 12.11 37.67 6.13
667 722 1.218316 GAGTGAGTGGTAAGCCGGG 59.782 63.158 2.18 0.00 37.67 5.73
668 723 1.218316 GGAGTGAGTGGTAAGCCGG 59.782 63.158 0.00 0.00 37.67 6.13
669 724 1.134560 GTAGGAGTGAGTGGTAAGCCG 59.865 57.143 0.00 0.00 37.67 5.52
670 725 1.481363 GGTAGGAGTGAGTGGTAAGCC 59.519 57.143 0.00 0.00 0.00 4.35
671 726 2.166664 CTGGTAGGAGTGAGTGGTAAGC 59.833 54.545 0.00 0.00 0.00 3.09
672 727 2.761208 CCTGGTAGGAGTGAGTGGTAAG 59.239 54.545 0.00 0.00 37.67 2.34
673 728 2.816411 CCTGGTAGGAGTGAGTGGTAA 58.184 52.381 0.00 0.00 37.67 2.85
677 732 1.751924 GTAGCCTGGTAGGAGTGAGTG 59.248 57.143 0.00 0.00 37.67 3.51
688 743 1.372501 AAGATTGGTGGTAGCCTGGT 58.627 50.000 0.00 0.00 0.00 4.00
689 744 2.514458 AAAGATTGGTGGTAGCCTGG 57.486 50.000 0.00 0.00 0.00 4.45
690 745 3.420893 TGAAAAGATTGGTGGTAGCCTG 58.579 45.455 0.00 0.00 0.00 4.85
691 746 3.806949 TGAAAAGATTGGTGGTAGCCT 57.193 42.857 0.00 0.00 0.00 4.58
692 747 3.365969 CGTTGAAAAGATTGGTGGTAGCC 60.366 47.826 0.00 0.00 0.00 3.93
693 748 3.252458 ACGTTGAAAAGATTGGTGGTAGC 59.748 43.478 0.00 0.00 0.00 3.58
694 749 5.212194 CAACGTTGAAAAGATTGGTGGTAG 58.788 41.667 23.90 0.00 0.00 3.18
695 750 4.498345 GCAACGTTGAAAAGATTGGTGGTA 60.498 41.667 31.62 0.00 0.00 3.25
798 884 4.036498 GCTCTCCAATTGATGTCTCCATTG 59.964 45.833 7.12 0.00 35.37 2.82
845 931 3.376546 CGATCGATGAGGATAGATCAGCA 59.623 47.826 10.26 0.00 39.48 4.41
1514 1600 2.925170 AGCCCCTTGAGCGTGTCT 60.925 61.111 0.00 0.00 34.64 3.41
1960 2055 3.200593 CTCCATGCTCCACGCTGC 61.201 66.667 0.00 0.00 40.11 5.25
1962 2057 3.005539 ACCTCCATGCTCCACGCT 61.006 61.111 0.00 0.00 40.11 5.07
1973 2068 1.000993 GAGCTCCTCCTGACCTCCA 59.999 63.158 0.87 0.00 0.00 3.86
2227 2322 8.659491 CAATATTCAAAGTGACGATGAAGAGAA 58.341 33.333 10.78 0.00 36.59 2.87
2290 2472 7.715657 AGTCAGAACATCATCTAGTCAGAATC 58.284 38.462 0.00 0.00 33.50 2.52
2291 2473 7.658525 AGTCAGAACATCATCTAGTCAGAAT 57.341 36.000 0.00 0.00 33.50 2.40
2292 2474 7.177392 TCAAGTCAGAACATCATCTAGTCAGAA 59.823 37.037 0.00 0.00 33.50 3.02
2294 2476 6.861144 TCAAGTCAGAACATCATCTAGTCAG 58.139 40.000 0.00 0.00 0.00 3.51
2296 2478 5.748152 GCTCAAGTCAGAACATCATCTAGTC 59.252 44.000 0.00 0.00 0.00 2.59
2298 2480 5.658468 TGCTCAAGTCAGAACATCATCTAG 58.342 41.667 0.00 0.00 0.00 2.43
2299 2481 5.394993 CCTGCTCAAGTCAGAACATCATCTA 60.395 44.000 0.00 0.00 33.54 1.98
2301 2483 3.622163 CCTGCTCAAGTCAGAACATCATC 59.378 47.826 0.00 0.00 33.54 2.92
2302 2484 3.262660 TCCTGCTCAAGTCAGAACATCAT 59.737 43.478 0.00 0.00 33.54 2.45
2303 2485 2.634453 TCCTGCTCAAGTCAGAACATCA 59.366 45.455 0.00 0.00 33.54 3.07
2310 2495 1.447489 CCGCTCCTGCTCAAGTCAG 60.447 63.158 0.00 0.00 36.97 3.51
2656 2957 4.767255 CACGTGAGGCCCCAGAGC 62.767 72.222 10.90 0.00 0.00 4.09
2733 3034 4.213482 CAGAAACTTCCGGTCCTTTGTTAG 59.787 45.833 0.00 0.00 0.00 2.34
2740 3041 1.900486 CTACCAGAAACTTCCGGTCCT 59.100 52.381 0.00 0.00 38.79 3.85
2805 3114 4.338682 TCACCTAGCTACGGAGATCTTTTC 59.661 45.833 0.00 0.00 0.00 2.29
2895 3208 8.766151 CAGAGAAGTTTAGTCAAGAAACTAACC 58.234 37.037 1.48 0.00 44.43 2.85
3002 3332 6.141053 CACCGGTAACTTTATTCAAACAAACG 59.859 38.462 6.87 0.00 0.00 3.60
3004 3334 7.330900 TCACCGGTAACTTTATTCAAACAAA 57.669 32.000 6.87 0.00 0.00 2.83
3074 3406 1.927174 GGTTGGATCGACGATTCACAG 59.073 52.381 18.46 0.00 25.65 3.66
3075 3407 1.273886 TGGTTGGATCGACGATTCACA 59.726 47.619 18.46 11.38 25.65 3.58
3102 3436 2.480244 GGTAGATGTACCCCGACGTTTC 60.480 54.545 7.86 0.00 42.91 2.78
3112 3446 2.277084 CAACTTGCCGGTAGATGTACC 58.723 52.381 9.04 9.04 44.99 3.34
3124 3458 4.981806 TTATGCCTGATAACAACTTGCC 57.018 40.909 0.00 0.00 0.00 4.52
3167 3501 1.742761 ACTCCATTTGGCATGTCGAG 58.257 50.000 0.00 0.00 34.44 4.04
3489 3824 2.577644 GCATGTGCCGTCATTGCG 60.578 61.111 0.00 0.00 34.31 4.85
3689 4024 3.399181 AGGGGCGCCGATTTCTGA 61.399 61.111 22.54 0.00 0.00 3.27
3782 4117 2.125106 GAAGGGCGGCATCTTCGT 60.125 61.111 12.47 0.00 31.51 3.85


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

AutoCloner maintained by Alex Coulton.