Multiple sequence alignment - TraesCS1B01G050900

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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 TraesCS1B01G050900 chr1B 100.000 2141 0 0 1 2141 30848158 30846018 0.000000e+00 3954
1 TraesCS1B01G050900 chr1B 100.000 388 0 0 2465 2852 30845694 30845307 0.000000e+00 717
2 TraesCS1B01G050900 chr1B 91.176 102 7 1 2588 2689 24772902 24773001 1.380000e-28 137
3 TraesCS1B01G050900 chr1A 93.490 891 58 0 996 1886 18085259 18084369 0.000000e+00 1325
4 TraesCS1B01G050900 chr1A 90.048 623 53 4 384 997 18086114 18085492 0.000000e+00 798
5 TraesCS1B01G050900 chr1A 83.750 160 14 5 1915 2073 18084306 18084158 1.070000e-29 141
6 TraesCS1B01G050900 chr1A 88.764 89 8 2 1906 1993 18102351 18102264 1.080000e-19 108
7 TraesCS1B01G050900 chr1D 91.461 890 62 9 998 1887 16897709 16896834 0.000000e+00 1210
8 TraesCS1B01G050900 chr1D 93.120 814 48 6 186 997 16898747 16897940 0.000000e+00 1186
9 TraesCS1B01G050900 chr1D 94.561 239 6 5 1906 2141 16896780 16896546 2.090000e-96 363
10 TraesCS1B01G050900 chr1D 80.756 291 29 13 2566 2850 16895879 16895610 4.820000e-48 202
11 TraesCS1B01G050900 chr1D 93.548 93 6 0 98 190 16899108 16899016 3.830000e-29 139
12 TraesCS1B01G050900 chr1D 91.011 89 8 0 2479 2567 16896163 16896075 1.390000e-23 121
13 TraesCS1B01G050900 chr2D 91.234 867 73 1 996 1859 174457646 174456780 0.000000e+00 1177
14 TraesCS1B01G050900 chr2D 88.926 894 84 7 996 1874 30328067 30327174 0.000000e+00 1088
15 TraesCS1B01G050900 chr2D 84.722 504 77 0 469 972 174458363 174457860 3.280000e-139 505
16 TraesCS1B01G050900 chr2B 90.487 862 79 1 996 1854 222235343 222234482 0.000000e+00 1134
17 TraesCS1B01G050900 chr3A 90.369 841 73 4 996 1835 13536169 13535336 0.000000e+00 1098
18 TraesCS1B01G050900 chr3B 89.405 840 83 6 996 1835 8074065 8074898 0.000000e+00 1053
19 TraesCS1B01G050900 chr2A 87.912 910 78 7 996 1887 3539141 3540036 0.000000e+00 1042
20 TraesCS1B01G050900 chr2A 91.495 729 59 1 996 1721 174445657 174444929 0.000000e+00 1000
21 TraesCS1B01G050900 chr3D 88.333 840 92 6 996 1835 6677245 6678078 0.000000e+00 1003


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 TraesCS1B01G050900 chr1B 30845307 30848158 2851 True 2335.500000 3954 100.000000 1 2852 2 chr1B.!!$R1 2851
1 TraesCS1B01G050900 chr1A 18084158 18086114 1956 True 754.666667 1325 89.096000 384 2073 3 chr1A.!!$R2 1689
2 TraesCS1B01G050900 chr1D 16895610 16899108 3498 True 536.833333 1210 90.742833 98 2850 6 chr1D.!!$R1 2752
3 TraesCS1B01G050900 chr2D 30327174 30328067 893 True 1088.000000 1088 88.926000 996 1874 1 chr2D.!!$R1 878
4 TraesCS1B01G050900 chr2D 174456780 174458363 1583 True 841.000000 1177 87.978000 469 1859 2 chr2D.!!$R2 1390
5 TraesCS1B01G050900 chr2B 222234482 222235343 861 True 1134.000000 1134 90.487000 996 1854 1 chr2B.!!$R1 858
6 TraesCS1B01G050900 chr3A 13535336 13536169 833 True 1098.000000 1098 90.369000 996 1835 1 chr3A.!!$R1 839
7 TraesCS1B01G050900 chr3B 8074065 8074898 833 False 1053.000000 1053 89.405000 996 1835 1 chr3B.!!$F1 839
8 TraesCS1B01G050900 chr2A 3539141 3540036 895 False 1042.000000 1042 87.912000 996 1887 1 chr2A.!!$F1 891
9 TraesCS1B01G050900 chr2A 174444929 174445657 728 True 1000.000000 1000 91.495000 996 1721 1 chr2A.!!$R1 725
10 TraesCS1B01G050900 chr3D 6677245 6678078 833 False 1003.000000 1003 88.333000 996 1835 1 chr3D.!!$F1 839

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
463 741 0.181824 TTACAGAATTAGCCCCGGCC 59.818 55.0 1.02 0.0 43.17 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2616 1.748879 ACACACACACACACAGGGC 60.749 57.895 0.0 0.0 0.0 5.19 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
22 23 4.757799 TGTCGACAAAACATTACCATGG 57.242 40.909 17.62 11.19 34.27 3.66
23 24 4.390264 TGTCGACAAAACATTACCATGGA 58.610 39.130 21.47 0.00 34.27 3.41
24 25 4.822350 TGTCGACAAAACATTACCATGGAA 59.178 37.500 21.47 8.96 34.27 3.53
25 26 5.049060 TGTCGACAAAACATTACCATGGAAG 60.049 40.000 21.47 7.34 34.27 3.46
26 27 4.083003 TCGACAAAACATTACCATGGAAGC 60.083 41.667 21.47 0.00 34.27 3.86
27 28 4.494484 GACAAAACATTACCATGGAAGCC 58.506 43.478 21.47 0.00 34.27 4.35
28 29 4.159557 ACAAAACATTACCATGGAAGCCT 58.840 39.130 21.47 0.00 34.27 4.58
29 30 5.329399 ACAAAACATTACCATGGAAGCCTA 58.671 37.500 21.47 0.00 34.27 3.93
30 31 5.957774 ACAAAACATTACCATGGAAGCCTAT 59.042 36.000 21.47 0.00 34.27 2.57
31 32 6.127366 ACAAAACATTACCATGGAAGCCTATG 60.127 38.462 21.47 13.44 34.27 2.23
32 33 4.796110 ACATTACCATGGAAGCCTATGT 57.204 40.909 21.47 14.03 34.27 2.29
33 34 4.464008 ACATTACCATGGAAGCCTATGTG 58.536 43.478 21.47 4.93 34.27 3.21
34 35 4.079787 ACATTACCATGGAAGCCTATGTGT 60.080 41.667 21.47 5.53 34.27 3.72
35 36 5.131977 ACATTACCATGGAAGCCTATGTGTA 59.868 40.000 21.47 0.00 34.27 2.90
36 37 5.702065 TTACCATGGAAGCCTATGTGTAA 57.298 39.130 21.47 0.00 0.00 2.41
37 38 4.156455 ACCATGGAAGCCTATGTGTAAG 57.844 45.455 21.47 0.00 0.00 2.34
38 39 3.780294 ACCATGGAAGCCTATGTGTAAGA 59.220 43.478 21.47 0.00 0.00 2.10
39 40 4.130118 CCATGGAAGCCTATGTGTAAGAC 58.870 47.826 5.56 0.00 0.00 3.01
40 41 3.906720 TGGAAGCCTATGTGTAAGACC 57.093 47.619 0.00 0.00 0.00 3.85
41 42 2.504175 TGGAAGCCTATGTGTAAGACCC 59.496 50.000 0.00 0.00 0.00 4.46
42 43 2.483188 GGAAGCCTATGTGTAAGACCCG 60.483 54.545 0.00 0.00 0.00 5.28
43 44 2.154567 AGCCTATGTGTAAGACCCGA 57.845 50.000 0.00 0.00 0.00 5.14
44 45 1.755380 AGCCTATGTGTAAGACCCGAC 59.245 52.381 0.00 0.00 0.00 4.79
45 46 1.479323 GCCTATGTGTAAGACCCGACA 59.521 52.381 0.00 0.00 0.00 4.35
46 47 2.093869 GCCTATGTGTAAGACCCGACAA 60.094 50.000 0.00 0.00 0.00 3.18
47 48 3.618019 GCCTATGTGTAAGACCCGACAAA 60.618 47.826 0.00 0.00 0.00 2.83
48 49 4.766375 CCTATGTGTAAGACCCGACAAAT 58.234 43.478 0.00 0.00 0.00 2.32
49 50 5.183228 CCTATGTGTAAGACCCGACAAATT 58.817 41.667 0.00 0.00 0.00 1.82
50 51 5.064707 CCTATGTGTAAGACCCGACAAATTG 59.935 44.000 0.00 0.00 0.00 2.32
51 52 2.550606 TGTGTAAGACCCGACAAATTGC 59.449 45.455 0.00 0.00 0.00 3.56
52 53 2.550606 GTGTAAGACCCGACAAATTGCA 59.449 45.455 0.00 0.00 0.00 4.08
53 54 3.003897 GTGTAAGACCCGACAAATTGCAA 59.996 43.478 0.00 0.00 0.00 4.08
54 55 3.823873 TGTAAGACCCGACAAATTGCAAT 59.176 39.130 5.99 5.99 0.00 3.56
55 56 5.004448 TGTAAGACCCGACAAATTGCAATA 58.996 37.500 13.39 0.00 0.00 1.90
56 57 5.650266 TGTAAGACCCGACAAATTGCAATAT 59.350 36.000 13.39 1.04 0.00 1.28
57 58 5.659440 AAGACCCGACAAATTGCAATATT 57.341 34.783 13.39 6.69 0.00 1.28
58 59 6.767524 AAGACCCGACAAATTGCAATATTA 57.232 33.333 13.39 0.00 0.00 0.98
59 60 6.131544 AGACCCGACAAATTGCAATATTAC 57.868 37.500 13.39 4.63 0.00 1.89
60 61 5.650266 AGACCCGACAAATTGCAATATTACA 59.350 36.000 13.39 0.00 0.00 2.41
61 62 6.151985 AGACCCGACAAATTGCAATATTACAA 59.848 34.615 13.39 3.60 0.00 2.41
62 63 6.692486 ACCCGACAAATTGCAATATTACAAA 58.308 32.000 13.39 0.00 0.00 2.83
63 64 7.155328 ACCCGACAAATTGCAATATTACAAAA 58.845 30.769 13.39 0.00 0.00 2.44
64 65 7.657761 ACCCGACAAATTGCAATATTACAAAAA 59.342 29.630 13.39 0.00 0.00 1.94
65 66 8.663911 CCCGACAAATTGCAATATTACAAAAAT 58.336 29.630 13.39 0.00 0.00 1.82
89 90 8.911918 ATAGTATTCTTGAGACATCTCTACGT 57.088 34.615 10.18 0.00 43.25 3.57
90 91 9.999660 ATAGTATTCTTGAGACATCTCTACGTA 57.000 33.333 10.18 0.00 43.25 3.57
91 92 8.911918 AGTATTCTTGAGACATCTCTACGTAT 57.088 34.615 10.18 1.78 43.25 3.06
92 93 9.999660 AGTATTCTTGAGACATCTCTACGTATA 57.000 33.333 10.18 0.00 43.25 1.47
96 97 8.481974 TCTTGAGACATCTCTACGTATATAGC 57.518 38.462 10.18 0.00 43.25 2.97
97 98 8.095169 TCTTGAGACATCTCTACGTATATAGCA 58.905 37.037 10.18 0.00 43.25 3.49
98 99 7.835634 TGAGACATCTCTACGTATATAGCAG 57.164 40.000 10.18 0.00 43.25 4.24
99 100 7.612677 TGAGACATCTCTACGTATATAGCAGA 58.387 38.462 10.18 0.00 43.25 4.26
100 101 7.546316 TGAGACATCTCTACGTATATAGCAGAC 59.454 40.741 10.18 0.00 43.25 3.51
101 102 7.387643 AGACATCTCTACGTATATAGCAGACA 58.612 38.462 0.00 0.00 0.00 3.41
102 103 7.878644 AGACATCTCTACGTATATAGCAGACAA 59.121 37.037 0.00 0.00 0.00 3.18
103 104 8.392372 ACATCTCTACGTATATAGCAGACAAA 57.608 34.615 0.00 0.00 0.00 2.83
166 167 2.166254 CTGGATGGTGCCCAAAACATAC 59.834 50.000 0.00 0.00 36.95 2.39
190 464 5.928264 CCTTAGCAATTTTTGGGTCAAGAAG 59.072 40.000 0.00 0.00 0.00 2.85
202 476 6.353404 TGGGTCAAGAAGAAAACTTTGTTT 57.647 33.333 0.00 0.00 0.00 2.83
259 534 5.335191 CCAATGTCTCTTTGGCAACTAGTTC 60.335 44.000 4.77 0.93 37.42 3.01
312 587 4.520111 GGGCAAGGAAAATTTGAGCAAAAT 59.480 37.500 0.00 0.00 40.32 1.82
350 625 6.578163 TTTTTACCCTATTTGTGTGGTAGC 57.422 37.500 0.00 0.00 34.96 3.58
382 657 8.978874 TTTAGGAGCACATGTGATTACATTAT 57.021 30.769 29.80 7.15 45.01 1.28
439 714 8.429493 ACTCAGTTACTAACTTGTTTTACCAC 57.571 34.615 0.00 0.00 40.46 4.16
450 725 6.108015 ACTTGTTTTACCACGTTCTTACAGA 58.892 36.000 0.00 0.00 0.00 3.41
455 730 8.767085 TGTTTTACCACGTTCTTACAGAATTAG 58.233 33.333 0.00 0.00 36.50 1.73
463 741 0.181824 TTACAGAATTAGCCCCGGCC 59.818 55.000 1.02 0.00 43.17 6.13
464 742 2.035237 TACAGAATTAGCCCCGGCCG 62.035 60.000 21.04 21.04 43.17 6.13
483 761 1.689959 GTCGCATTTGGAGTGCAAAG 58.310 50.000 15.33 8.63 42.62 2.77
560 844 1.752498 GTTGATCAGAATGGCATGGCA 59.248 47.619 25.52 25.52 36.16 4.92
656 940 3.854669 CCTCCCGGCGCTTCTCAT 61.855 66.667 7.64 0.00 0.00 2.90
657 941 2.187946 CTCCCGGCGCTTCTCATT 59.812 61.111 7.64 0.00 0.00 2.57
675 959 1.843462 TTAAGGGCCCGCTGCAAGTA 61.843 55.000 18.44 0.00 43.89 2.24
715 999 0.605319 GATGGGGAGCGTGTTCACAA 60.605 55.000 3.87 0.00 0.00 3.33
729 1013 3.693578 TGTTCACAATGAGACTGTTGCAA 59.306 39.130 0.00 0.00 0.00 4.08
765 1049 1.074775 GGTTGGGCCAGATGTGTCA 59.925 57.895 6.23 0.00 37.17 3.58
1185 1735 1.005394 CAGGTACAAAGACGGCCGT 60.005 57.895 34.89 34.89 0.00 5.68
1216 1766 3.900892 CGGAGGTCGTCGGGATGG 61.901 72.222 0.00 0.00 0.00 3.51
1268 1821 3.129502 CTCCAGCACGGGCACATG 61.130 66.667 14.57 0.00 44.61 3.21
1269 1822 4.720902 TCCAGCACGGGCACATGG 62.721 66.667 14.57 11.97 44.61 3.66
1270 1823 4.720902 CCAGCACGGGCACATGGA 62.721 66.667 14.57 0.00 44.61 3.41
1271 1824 3.434319 CAGCACGGGCACATGGAC 61.434 66.667 14.57 0.00 44.61 4.02
1272 1825 4.722700 AGCACGGGCACATGGACC 62.723 66.667 14.57 0.00 44.61 4.46
1428 1995 1.302832 CAAGGAGGTTCTGCGGCTT 60.303 57.895 0.00 0.00 0.00 4.35
1487 2054 1.743995 GCTTTACCGTGCGGACCAT 60.744 57.895 18.16 0.00 38.96 3.55
1588 2155 0.613853 CAAGGACCCGGAGAGGTACA 60.614 60.000 0.73 0.00 44.05 2.90
1653 2220 0.179134 GAGCATTCTCGTACACGGCT 60.179 55.000 1.39 2.17 40.29 5.52
1859 2435 4.034048 GTCAACGACCGCTTAAATCATGAT 59.966 41.667 1.18 1.18 0.00 2.45
1889 2465 9.563593 TCAGAGACCCTACATATATCTACTACT 57.436 37.037 0.00 0.00 0.00 2.57
1998 2616 4.112634 CGTGAGTGACATAATAGTGGTGG 58.887 47.826 0.00 0.00 0.00 4.61
2014 2632 2.124320 GGCCCTGTGTGTGTGTGT 60.124 61.111 0.00 0.00 0.00 3.72
2015 2633 2.480610 GGCCCTGTGTGTGTGTGTG 61.481 63.158 0.00 0.00 0.00 3.82
2016 2634 1.748879 GCCCTGTGTGTGTGTGTGT 60.749 57.895 0.00 0.00 0.00 3.72
2091 2710 7.903145 TGTGAATGTATTATACCGCCTCTTAT 58.097 34.615 0.00 0.00 0.00 1.73
2092 2711 9.027202 TGTGAATGTATTATACCGCCTCTTATA 57.973 33.333 0.00 0.00 0.00 0.98
2511 3175 4.163458 AGAGATAATAAACGTGCCCCTTCA 59.837 41.667 0.00 0.00 0.00 3.02
2517 3181 2.351706 AACGTGCCCCTTCAGTTTAA 57.648 45.000 0.00 0.00 0.00 1.52
2519 3183 2.227194 ACGTGCCCCTTCAGTTTAAAG 58.773 47.619 0.00 0.00 0.00 1.85
2564 3228 8.150945 ACAACTAATCTGTTCACTAGTTCATGT 58.849 33.333 0.00 0.00 33.39 3.21
2620 3481 9.959721 ACAAACTTGAAACCATATCTAGTACAT 57.040 29.630 0.00 0.00 32.88 2.29
2653 3514 5.923733 ACAACAAAACACAGTAAATCCCA 57.076 34.783 0.00 0.00 0.00 4.37
2654 3515 5.901552 ACAACAAAACACAGTAAATCCCAG 58.098 37.500 0.00 0.00 0.00 4.45
2667 3528 6.659242 CAGTAAATCCCAGTTGATACACCTTT 59.341 38.462 0.00 0.00 0.00 3.11
2668 3529 7.176690 CAGTAAATCCCAGTTGATACACCTTTT 59.823 37.037 0.00 0.00 0.00 2.27
2669 3530 5.982890 AATCCCAGTTGATACACCTTTTG 57.017 39.130 0.00 0.00 0.00 2.44
2670 3531 4.447138 TCCCAGTTGATACACCTTTTGT 57.553 40.909 0.00 0.00 42.84 2.83
2673 3534 6.001460 TCCCAGTTGATACACCTTTTGTAAG 58.999 40.000 0.00 0.00 44.11 2.34
2675 3536 6.488683 CCCAGTTGATACACCTTTTGTAAGAA 59.511 38.462 0.00 0.00 44.11 2.52
2676 3537 7.013846 CCCAGTTGATACACCTTTTGTAAGAAA 59.986 37.037 0.00 0.00 44.11 2.52
2677 3538 8.410141 CCAGTTGATACACCTTTTGTAAGAAAA 58.590 33.333 0.00 0.00 44.11 2.29
2678 3539 9.796120 CAGTTGATACACCTTTTGTAAGAAAAA 57.204 29.630 0.00 0.00 44.11 1.94
2769 3639 5.734855 ACAAATAGTGAATATGCACCGAC 57.265 39.130 10.44 0.00 39.59 4.79
2770 3640 4.574828 ACAAATAGTGAATATGCACCGACC 59.425 41.667 10.44 0.00 39.59 4.79
2773 3643 6.360370 AATAGTGAATATGCACCGACCTAT 57.640 37.500 10.44 0.00 39.59 2.57
2774 3644 3.995199 AGTGAATATGCACCGACCTATG 58.005 45.455 10.44 0.00 39.59 2.23
2775 3645 3.388024 AGTGAATATGCACCGACCTATGT 59.612 43.478 10.44 0.00 39.59 2.29
2782 3652 7.900782 ATATGCACCGACCTATGTAAAATAC 57.099 36.000 0.00 0.00 0.00 1.89
2790 3660 7.508296 ACCGACCTATGTAAAATACTCCAGTAT 59.492 37.037 0.00 0.00 42.60 2.12
2804 3674 5.784177 ACTCCAGTATATTATGTTCCAGCG 58.216 41.667 0.00 0.00 0.00 5.18
2811 3681 3.550437 ATTATGTTCCAGCGCTCTCTT 57.450 42.857 7.13 0.00 0.00 2.85
2812 3682 3.334583 TTATGTTCCAGCGCTCTCTTT 57.665 42.857 7.13 0.00 0.00 2.52
2813 3683 4.465632 TTATGTTCCAGCGCTCTCTTTA 57.534 40.909 7.13 0.00 0.00 1.85
2814 3684 2.831685 TGTTCCAGCGCTCTCTTTAA 57.168 45.000 7.13 0.00 0.00 1.52
2815 3685 3.334583 TGTTCCAGCGCTCTCTTTAAT 57.665 42.857 7.13 0.00 0.00 1.40
2816 3686 3.002791 TGTTCCAGCGCTCTCTTTAATG 58.997 45.455 7.13 0.00 0.00 1.90
2817 3687 3.003480 GTTCCAGCGCTCTCTTTAATGT 58.997 45.455 7.13 0.00 0.00 2.71
2818 3688 2.893637 TCCAGCGCTCTCTTTAATGTC 58.106 47.619 7.13 0.00 0.00 3.06
2819 3689 2.497675 TCCAGCGCTCTCTTTAATGTCT 59.502 45.455 7.13 0.00 0.00 3.41
2820 3690 3.699538 TCCAGCGCTCTCTTTAATGTCTA 59.300 43.478 7.13 0.00 0.00 2.59
2821 3691 4.159693 TCCAGCGCTCTCTTTAATGTCTAA 59.840 41.667 7.13 0.00 0.00 2.10
2824 3694 5.578727 CAGCGCTCTCTTTAATGTCTAAACT 59.421 40.000 7.13 0.00 0.00 2.66
2825 3695 5.808030 AGCGCTCTCTTTAATGTCTAAACTC 59.192 40.000 2.64 0.00 0.00 3.01
2826 3696 5.275974 GCGCTCTCTTTAATGTCTAAACTCG 60.276 44.000 0.00 0.00 0.00 4.18
2829 3699 6.032956 TCTCTTTAATGTCTAAACTCGCCA 57.967 37.500 0.00 0.00 0.00 5.69
2830 3700 6.460781 TCTCTTTAATGTCTAAACTCGCCAA 58.539 36.000 0.00 0.00 0.00 4.52
2831 3701 6.367969 TCTCTTTAATGTCTAAACTCGCCAAC 59.632 38.462 0.00 0.00 0.00 3.77
2832 3702 6.228258 TCTTTAATGTCTAAACTCGCCAACT 58.772 36.000 0.00 0.00 0.00 3.16
2833 3703 7.380536 TCTTTAATGTCTAAACTCGCCAACTA 58.619 34.615 0.00 0.00 0.00 2.24
2834 3704 8.038944 TCTTTAATGTCTAAACTCGCCAACTAT 58.961 33.333 0.00 0.00 0.00 2.12
2835 3705 9.309516 CTTTAATGTCTAAACTCGCCAACTATA 57.690 33.333 0.00 0.00 0.00 1.31
2850 3720 7.936847 TCGCCAACTATAATAATCCATGAAGTT 59.063 33.333 0.00 0.00 0.00 2.66
2851 3721 8.567948 CGCCAACTATAATAATCCATGAAGTTT 58.432 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.390264 TCCATGGTAATGTTTTGTCGACA 58.610 39.130 15.76 15.76 31.27 4.35
2 3 5.365403 TTCCATGGTAATGTTTTGTCGAC 57.635 39.130 12.58 9.11 31.27 4.20
3 4 4.083003 GCTTCCATGGTAATGTTTTGTCGA 60.083 41.667 12.58 0.00 31.27 4.20
4 5 4.165779 GCTTCCATGGTAATGTTTTGTCG 58.834 43.478 12.58 0.00 31.27 4.35
5 6 4.220602 AGGCTTCCATGGTAATGTTTTGTC 59.779 41.667 12.58 0.00 31.27 3.18
6 7 4.159557 AGGCTTCCATGGTAATGTTTTGT 58.840 39.130 12.58 0.00 31.27 2.83
7 8 4.806640 AGGCTTCCATGGTAATGTTTTG 57.193 40.909 12.58 0.00 31.27 2.44
8 9 5.957774 ACATAGGCTTCCATGGTAATGTTTT 59.042 36.000 12.58 0.00 31.27 2.43
9 10 5.360714 CACATAGGCTTCCATGGTAATGTTT 59.639 40.000 12.58 0.00 31.27 2.83
10 11 4.889409 CACATAGGCTTCCATGGTAATGTT 59.111 41.667 12.58 0.00 31.27 2.71
11 12 4.079787 ACACATAGGCTTCCATGGTAATGT 60.080 41.667 12.58 6.13 31.27 2.71
12 13 4.464008 ACACATAGGCTTCCATGGTAATG 58.536 43.478 12.58 5.47 0.00 1.90
13 14 4.796110 ACACATAGGCTTCCATGGTAAT 57.204 40.909 12.58 0.00 0.00 1.89
14 15 5.427157 TCTTACACATAGGCTTCCATGGTAA 59.573 40.000 12.58 4.08 0.00 2.85
15 16 4.966168 TCTTACACATAGGCTTCCATGGTA 59.034 41.667 12.58 0.02 0.00 3.25
16 17 3.780294 TCTTACACATAGGCTTCCATGGT 59.220 43.478 12.58 0.00 0.00 3.55
17 18 4.130118 GTCTTACACATAGGCTTCCATGG 58.870 47.826 4.97 4.97 0.00 3.66
18 19 4.130118 GGTCTTACACATAGGCTTCCATG 58.870 47.826 0.00 0.00 0.00 3.66
19 20 3.136626 GGGTCTTACACATAGGCTTCCAT 59.863 47.826 0.00 0.00 0.00 3.41
20 21 2.504175 GGGTCTTACACATAGGCTTCCA 59.496 50.000 0.00 0.00 0.00 3.53
21 22 2.483188 CGGGTCTTACACATAGGCTTCC 60.483 54.545 0.00 0.00 0.00 3.46
22 23 2.429610 TCGGGTCTTACACATAGGCTTC 59.570 50.000 0.00 0.00 0.00 3.86
23 24 2.167900 GTCGGGTCTTACACATAGGCTT 59.832 50.000 0.00 0.00 0.00 4.35
24 25 1.755380 GTCGGGTCTTACACATAGGCT 59.245 52.381 0.00 0.00 0.00 4.58
25 26 1.479323 TGTCGGGTCTTACACATAGGC 59.521 52.381 0.00 0.00 0.00 3.93
26 27 3.880047 TTGTCGGGTCTTACACATAGG 57.120 47.619 0.00 0.00 0.00 2.57
27 28 5.447279 GCAATTTGTCGGGTCTTACACATAG 60.447 44.000 0.00 0.00 0.00 2.23
28 29 4.393680 GCAATTTGTCGGGTCTTACACATA 59.606 41.667 0.00 0.00 0.00 2.29
29 30 3.190535 GCAATTTGTCGGGTCTTACACAT 59.809 43.478 0.00 0.00 0.00 3.21
30 31 2.550606 GCAATTTGTCGGGTCTTACACA 59.449 45.455 0.00 0.00 0.00 3.72
31 32 2.550606 TGCAATTTGTCGGGTCTTACAC 59.449 45.455 0.00 0.00 0.00 2.90
32 33 2.852449 TGCAATTTGTCGGGTCTTACA 58.148 42.857 0.00 0.00 0.00 2.41
33 34 3.907894 TTGCAATTTGTCGGGTCTTAC 57.092 42.857 0.00 0.00 0.00 2.34
34 35 6.767524 AATATTGCAATTTGTCGGGTCTTA 57.232 33.333 18.75 0.00 0.00 2.10
35 36 5.659440 AATATTGCAATTTGTCGGGTCTT 57.341 34.783 18.75 0.00 0.00 3.01
36 37 5.650266 TGTAATATTGCAATTTGTCGGGTCT 59.350 36.000 18.75 0.00 0.00 3.85
37 38 5.885881 TGTAATATTGCAATTTGTCGGGTC 58.114 37.500 18.75 0.51 0.00 4.46
38 39 5.906113 TGTAATATTGCAATTTGTCGGGT 57.094 34.783 18.75 0.00 0.00 5.28
39 40 7.588143 TTTTGTAATATTGCAATTTGTCGGG 57.412 32.000 18.75 0.00 32.91 5.14
63 64 9.344772 ACGTAGAGATGTCTCAAGAATACTATT 57.655 33.333 12.21 0.00 45.21 1.73
64 65 8.911918 ACGTAGAGATGTCTCAAGAATACTAT 57.088 34.615 12.21 0.00 45.21 2.12
65 66 9.999660 ATACGTAGAGATGTCTCAAGAATACTA 57.000 33.333 12.21 2.31 45.21 1.82
66 67 8.911918 ATACGTAGAGATGTCTCAAGAATACT 57.088 34.615 12.21 0.00 45.21 2.12
70 71 8.937884 GCTATATACGTAGAGATGTCTCAAGAA 58.062 37.037 12.21 0.00 45.21 2.52
71 72 8.095169 TGCTATATACGTAGAGATGTCTCAAGA 58.905 37.037 12.21 0.00 45.21 3.02
72 73 8.257830 TGCTATATACGTAGAGATGTCTCAAG 57.742 38.462 12.21 5.57 45.21 3.02
73 74 8.095169 TCTGCTATATACGTAGAGATGTCTCAA 58.905 37.037 12.21 0.00 45.21 3.02
74 75 7.546316 GTCTGCTATATACGTAGAGATGTCTCA 59.454 40.741 12.21 0.00 45.21 3.27
75 76 7.546316 TGTCTGCTATATACGTAGAGATGTCTC 59.454 40.741 0.08 1.75 43.17 3.36
76 77 7.387643 TGTCTGCTATATACGTAGAGATGTCT 58.612 38.462 0.08 0.00 36.75 3.41
77 78 7.598189 TGTCTGCTATATACGTAGAGATGTC 57.402 40.000 0.08 0.00 0.00 3.06
78 79 7.981102 TTGTCTGCTATATACGTAGAGATGT 57.019 36.000 0.08 0.00 0.00 3.06
79 80 8.722394 TCTTTGTCTGCTATATACGTAGAGATG 58.278 37.037 0.08 0.00 0.00 2.90
80 81 8.850007 TCTTTGTCTGCTATATACGTAGAGAT 57.150 34.615 0.08 0.00 0.00 2.75
81 82 8.850007 ATCTTTGTCTGCTATATACGTAGAGA 57.150 34.615 0.08 0.00 0.00 3.10
115 116 8.217111 TGTCCATATCATTGCTGGTATTTAGAA 58.783 33.333 0.00 0.00 0.00 2.10
122 123 5.072193 AGACATGTCCATATCATTGCTGGTA 59.928 40.000 22.21 0.00 0.00 3.25
131 132 3.975982 ACCATCCAGACATGTCCATATCA 59.024 43.478 22.21 1.34 0.00 2.15
166 167 5.467035 TCTTGACCCAAAAATTGCTAAGG 57.533 39.130 0.00 0.00 0.00 2.69
202 476 1.189752 TGGCAGCCACTCAAACAAAA 58.810 45.000 11.22 0.00 0.00 2.44
205 479 2.284754 TATTGGCAGCCACTCAAACA 57.715 45.000 15.89 0.00 30.78 2.83
206 480 3.874392 AATATTGGCAGCCACTCAAAC 57.126 42.857 15.89 0.00 30.78 2.93
259 534 1.868498 CCAACATTGGCAAGCAAACTG 59.132 47.619 5.96 0.00 42.21 3.16
288 563 2.045524 TGCTCAAATTTTCCTTGCCCA 58.954 42.857 0.00 0.00 0.00 5.36
360 635 7.056006 TCAATAATGTAATCACATGTGCTCCT 58.944 34.615 21.38 7.41 44.83 3.69
382 657 0.108992 GTACGCGAGACACCCATCAA 60.109 55.000 15.93 0.00 0.00 2.57
450 725 4.540735 CGACGGCCGGGGCTAATT 62.541 66.667 31.76 4.91 41.60 1.40
463 741 0.040514 TTTGCACTCCAAATGCGACG 60.041 50.000 0.00 0.00 46.49 5.12
464 742 1.266718 TCTTTGCACTCCAAATGCGAC 59.733 47.619 0.00 0.00 46.49 5.19
483 761 5.105997 CCAAAGGACTCTTGTCAATTCCATC 60.106 44.000 9.54 0.00 44.61 3.51
578 862 2.225727 GGAGGTGATCGTTTGGTTGTTC 59.774 50.000 0.00 0.00 0.00 3.18
656 940 1.843462 TACTTGCAGCGGGCCCTTAA 61.843 55.000 22.43 6.54 43.89 1.85
657 941 1.843462 TTACTTGCAGCGGGCCCTTA 61.843 55.000 22.43 0.00 43.89 2.69
715 999 1.265095 CTTGCGTTGCAACAGTCTCAT 59.735 47.619 28.01 0.00 43.99 2.90
765 1049 1.203225 AGCCCTTGGAAGAAATGGCTT 60.203 47.619 0.00 0.00 45.55 4.35
789 1073 1.101635 CGTCCTGGCTGATCTCCGTA 61.102 60.000 0.00 0.00 0.00 4.02
849 1133 1.904144 CGAAATCTACGTCGAAGGCA 58.096 50.000 0.00 0.00 39.64 4.75
928 1212 2.125326 CCATGAGTCGGGCGTAGGA 61.125 63.158 0.00 0.00 0.00 2.94
1078 1616 0.969149 ATGCCGGAGAATATCTCGCA 59.031 50.000 5.05 10.81 44.28 5.10
1216 1766 3.112709 GAACAGCGCCGAGACCAC 61.113 66.667 2.29 0.00 0.00 4.16
1236 1789 2.282040 GAGCTTGTGTGCTGCCCT 60.282 61.111 0.00 0.00 44.17 5.19
1293 1860 4.892965 AGGTGCTTGGCGTTGGCA 62.893 61.111 0.00 0.00 42.47 4.92
1473 2040 2.680707 TCCATGGTCCGCACGGTA 60.681 61.111 12.58 0.00 36.47 4.02
1487 2054 2.753043 GGTACTCGTCGCCCTCCA 60.753 66.667 0.00 0.00 0.00 3.86
1728 2295 4.163427 TCTCCATCTCAAAGTTCCTCAGT 58.837 43.478 0.00 0.00 0.00 3.41
1859 2435 7.350044 AGATATATGTAGGGTCTCTGAAGGA 57.650 40.000 0.00 0.00 0.00 3.36
1894 2470 7.648142 CGCAACTGTAATTTATTGGTCCATAT 58.352 34.615 0.00 0.00 0.00 1.78
1895 2471 6.459024 GCGCAACTGTAATTTATTGGTCCATA 60.459 38.462 0.30 0.00 0.00 2.74
1898 2474 4.102649 GCGCAACTGTAATTTATTGGTCC 58.897 43.478 0.30 0.00 0.00 4.46
1899 2475 4.102649 GGCGCAACTGTAATTTATTGGTC 58.897 43.478 10.83 0.00 0.00 4.02
1998 2616 1.748879 ACACACACACACACAGGGC 60.749 57.895 0.00 0.00 0.00 5.19
2014 2632 3.856521 CGAGAAAAACAACAATGTGCACA 59.143 39.130 24.08 24.08 40.46 4.57
2015 2633 4.101942 TCGAGAAAAACAACAATGTGCAC 58.898 39.130 10.75 10.75 40.46 4.57
2016 2634 4.362932 TCGAGAAAAACAACAATGTGCA 57.637 36.364 0.00 0.00 40.46 4.57
2486 3150 6.042781 TGAAGGGGCACGTTTATTATCTCTAT 59.957 38.462 0.00 0.00 0.00 1.98
2511 3175 1.834188 CCCATCGTGCCCTTTAAACT 58.166 50.000 0.00 0.00 0.00 2.66
2517 3181 0.904394 AATTTGCCCATCGTGCCCTT 60.904 50.000 0.00 0.00 0.00 3.95
2519 3183 0.820871 TTAATTTGCCCATCGTGCCC 59.179 50.000 0.00 0.00 0.00 5.36
2524 3188 6.692681 CAGATTAGTTGTTAATTTGCCCATCG 59.307 38.462 0.00 0.00 32.09 3.84
2584 3445 7.654022 TGGTTTCAAGTTTGTTAGAGGATTT 57.346 32.000 0.00 0.00 0.00 2.17
2594 3455 9.959721 ATGTACTAGATATGGTTTCAAGTTTGT 57.040 29.630 0.00 0.00 0.00 2.83
2620 3481 8.764524 ACTGTGTTTTGTTGTTGCTAAATTTA 57.235 26.923 0.00 0.00 0.00 1.40
2698 3559 7.450124 TTGTGTTTAACAAGTACCTTCACAA 57.550 32.000 0.00 0.00 43.96 3.33
2720 3581 8.925700 GCTTTGACAATAATTAGGGTTTTCTTG 58.074 33.333 0.00 0.00 0.00 3.02
2721 3582 8.646900 TGCTTTGACAATAATTAGGGTTTTCTT 58.353 29.630 0.00 0.00 0.00 2.52
2722 3583 8.088365 GTGCTTTGACAATAATTAGGGTTTTCT 58.912 33.333 0.00 0.00 0.00 2.52
2723 3584 7.870445 TGTGCTTTGACAATAATTAGGGTTTTC 59.130 33.333 0.00 0.00 0.00 2.29
2724 3585 7.731054 TGTGCTTTGACAATAATTAGGGTTTT 58.269 30.769 0.00 0.00 0.00 2.43
2725 3586 7.296628 TGTGCTTTGACAATAATTAGGGTTT 57.703 32.000 0.00 0.00 0.00 3.27
2736 3597 9.577110 CATATTCACTATTTGTGCTTTGACAAT 57.423 29.630 0.00 0.00 45.81 2.71
2739 3600 7.008628 GTGCATATTCACTATTTGTGCTTTGAC 59.991 37.037 0.00 0.00 45.81 3.18
2757 3627 8.154856 AGTATTTTACATAGGTCGGTGCATATT 58.845 33.333 0.00 0.00 0.00 1.28
2782 3652 4.627467 GCGCTGGAACATAATATACTGGAG 59.373 45.833 0.00 0.00 38.20 3.86
2790 3660 4.672587 AAGAGAGCGCTGGAACATAATA 57.327 40.909 18.48 0.00 38.20 0.98
2796 3666 3.003480 ACATTAAAGAGAGCGCTGGAAC 58.997 45.455 18.48 0.00 0.00 3.62
2800 3670 5.578727 AGTTTAGACATTAAAGAGAGCGCTG 59.421 40.000 18.48 0.00 0.00 5.18
2804 3674 5.005875 GGCGAGTTTAGACATTAAAGAGAGC 59.994 44.000 0.00 0.00 0.00 4.09
2811 3681 9.826574 ATTATAGTTGGCGAGTTTAGACATTAA 57.173 29.630 0.00 0.00 0.00 1.40
2813 3683 9.826574 TTATTATAGTTGGCGAGTTTAGACATT 57.173 29.630 0.00 0.00 0.00 2.71
2814 3684 9.998106 ATTATTATAGTTGGCGAGTTTAGACAT 57.002 29.630 0.00 0.00 0.00 3.06
2815 3685 9.472361 GATTATTATAGTTGGCGAGTTTAGACA 57.528 33.333 0.00 0.00 0.00 3.41
2816 3686 8.923683 GGATTATTATAGTTGGCGAGTTTAGAC 58.076 37.037 0.00 0.00 0.00 2.59
2817 3687 8.644216 TGGATTATTATAGTTGGCGAGTTTAGA 58.356 33.333 0.00 0.00 0.00 2.10
2818 3688 8.827177 TGGATTATTATAGTTGGCGAGTTTAG 57.173 34.615 0.00 0.00 0.00 1.85
2819 3689 9.214957 CATGGATTATTATAGTTGGCGAGTTTA 57.785 33.333 0.00 0.00 0.00 2.01
2820 3690 7.936847 TCATGGATTATTATAGTTGGCGAGTTT 59.063 33.333 0.00 0.00 0.00 2.66
2821 3691 7.450074 TCATGGATTATTATAGTTGGCGAGTT 58.550 34.615 0.00 0.00 0.00 3.01
2824 3694 7.450074 ACTTCATGGATTATTATAGTTGGCGA 58.550 34.615 0.00 0.00 0.00 5.54
2825 3695 7.672983 ACTTCATGGATTATTATAGTTGGCG 57.327 36.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.