Multiple sequence alignment - TraesCS6A01G249700

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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 TraesCS6A01G249700 chr6A 100.000 3530 0 0 1 3530 463167017 463163488 0.000000e+00 6519.0
1 TraesCS6A01G249700 chr6A 94.388 1782 63 11 951 2712 462255290 462253526 0.000000e+00 2702.0
2 TraesCS6A01G249700 chr6A 85.507 207 20 7 2707 2908 462252832 462252631 1.280000e-49 207.0
3 TraesCS6A01G249700 chr6A 85.811 148 15 4 2965 3112 462252538 462252397 6.100000e-33 152.0
4 TraesCS6A01G249700 chr6B 92.206 2412 88 26 253 2622 498277436 498279789 0.000000e+00 3321.0
5 TraesCS6A01G249700 chr6B 90.099 202 14 3 2963 3159 498280035 498280235 1.260000e-64 257.0
6 TraesCS6A01G249700 chr6B 93.333 60 3 1 3172 3231 498281168 498281226 1.750000e-13 87.9
7 TraesCS6A01G249700 chr6D 90.639 1581 86 32 1 1536 324827426 324825863 0.000000e+00 2043.0
8 TraesCS6A01G249700 chr6D 92.777 1163 39 16 1572 2711 324825857 324824717 0.000000e+00 1640.0
9 TraesCS6A01G249700 chr3B 89.971 339 18 3 1956 2294 23382136 23381814 1.170000e-114 424.0
10 TraesCS6A01G249700 chr7A 92.982 114 5 3 1728 1840 219026924 219027035 2.820000e-36 163.0
11 TraesCS6A01G249700 chr7A 89.916 119 8 4 1724 1840 260926364 260926480 2.200000e-32 150.0
12 TraesCS6A01G249700 chr7A 92.473 93 7 0 3437 3529 102268440 102268348 2.210000e-27 134.0
13 TraesCS6A01G249700 chr2A 81.553 206 30 6 1573 1777 670685486 670685288 2.820000e-36 163.0
14 TraesCS6A01G249700 chr2D 81.281 203 30 6 1573 1774 526112122 526112317 1.310000e-34 158.0
15 TraesCS6A01G249700 chr2B 81.068 206 31 6 1573 1777 621313483 621313285 1.310000e-34 158.0
16 TraesCS6A01G249700 chr2B 91.489 94 7 1 3437 3530 142750567 142750475 1.030000e-25 128.0
17 TraesCS6A01G249700 chrUn 89.231 130 6 7 1719 1844 34347893 34348018 4.720000e-34 156.0
18 TraesCS6A01G249700 chr1A 93.617 94 6 0 3437 3530 33303844 33303751 1.320000e-29 141.0
19 TraesCS6A01G249700 chr5A 88.298 94 10 1 3437 3530 590613830 590613738 1.040000e-20 111.0
20 TraesCS6A01G249700 chr5A 100.000 32 0 0 3499 3530 616146538 616146507 3.810000e-05 60.2
21 TraesCS6A01G249700 chr3A 85.849 106 12 2 3427 3530 303162637 303162741 3.730000e-20 110.0
22 TraesCS6A01G249700 chr4A 93.151 73 4 1 3458 3530 547759215 547759286 4.820000e-19 106.0


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 TraesCS6A01G249700 chr6A 463163488 463167017 3529 True 6519.000000 6519 100.000000 1 3530 1 chr6A.!!$R1 3529
1 TraesCS6A01G249700 chr6A 462252397 462255290 2893 True 1020.333333 2702 88.568667 951 3112 3 chr6A.!!$R2 2161
2 TraesCS6A01G249700 chr6B 498277436 498281226 3790 False 1221.966667 3321 91.879333 253 3231 3 chr6B.!!$F1 2978
3 TraesCS6A01G249700 chr6D 324824717 324827426 2709 True 1841.500000 2043 91.708000 1 2711 2 chr6D.!!$R1 2710

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
750 767 0.248134 CGCCGAGCACTGTAGTACTC 60.248 60.0 0.00 2.75 35.59 2.59 F
1349 1396 1.065031 GTAACGCTTTGCATGCACGG 61.065 55.0 26.52 20.04 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1623 0.169009 GCACTTCACCTGCGGAATTC 59.831 55.0 0.0 0.0 0.00 2.17 R
3247 5054 0.252197 AACAATAGAGGTCACGCCCC 59.748 55.0 0.0 0.0 38.26 5.80 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
124 125 5.928264 AGTTTGCATCTTTTATTGGAGTTGC 59.072 36.000 0.00 0.00 38.47 4.17
126 127 5.314923 TGCATCTTTTATTGGAGTTGCTC 57.685 39.130 7.62 0.00 38.67 4.26
130 131 6.870439 GCATCTTTTATTGGAGTTGCTCTTTT 59.130 34.615 0.00 0.00 36.28 2.27
131 132 8.028938 GCATCTTTTATTGGAGTTGCTCTTTTA 58.971 33.333 0.00 0.00 36.28 1.52
250 254 4.852962 GGAGATGCTCCTGCTCAC 57.147 61.111 6.23 0.00 46.41 3.51
335 347 3.137637 AAAGCCCAGTGCACGTTGC 62.138 57.895 12.01 14.70 44.83 4.17
337 349 4.030452 GCCCAGTGCACGTTGCTC 62.030 66.667 12.01 7.49 45.31 4.26
350 365 1.817941 TTGCTCGGGCGCTTAATCC 60.818 57.895 7.64 0.00 42.25 3.01
396 411 3.426117 CTACGTACTGGCTGCGGGG 62.426 68.421 0.00 0.00 31.13 5.73
545 561 4.570663 GGAGGGATCGACGGTGCG 62.571 72.222 0.00 0.00 0.00 5.34
602 618 2.027745 ACAGCAGTTGACCGATCTGAAT 60.028 45.455 0.00 0.00 0.00 2.57
749 766 0.959372 ACGCCGAGCACTGTAGTACT 60.959 55.000 0.00 0.00 0.00 2.73
750 767 0.248134 CGCCGAGCACTGTAGTACTC 60.248 60.000 0.00 2.75 35.59 2.59
754 771 2.181426 GAGCACTGTAGTACTCGCTG 57.819 55.000 13.92 0.66 29.77 5.18
757 774 1.467713 GCACTGTAGTACTCGCTGGTC 60.468 57.143 0.00 0.00 0.00 4.02
772 789 2.151202 CTGGTCGCTGGTGTACAAATT 58.849 47.619 0.00 0.00 0.00 1.82
840 857 8.632679 AGTGTTCAGATTGCTTTTTAAAGATCA 58.367 29.630 6.41 0.00 38.28 2.92
844 861 7.950512 TCAGATTGCTTTTTAAAGATCACCAA 58.049 30.769 6.41 1.55 38.28 3.67
965 985 5.264395 ACCAAGGGAGAATTTAATCACTGG 58.736 41.667 0.00 0.00 0.00 4.00
1285 1319 3.893813 AGGGAGCGACGGTAATTAATACT 59.106 43.478 0.00 0.00 34.74 2.12
1286 1320 5.048504 CAGGGAGCGACGGTAATTAATACTA 60.049 44.000 0.00 0.00 34.74 1.82
1287 1321 5.048434 AGGGAGCGACGGTAATTAATACTAC 60.048 44.000 0.00 0.00 34.74 2.73
1291 1325 6.973843 AGCGACGGTAATTAATACTACATGA 58.026 36.000 0.00 0.00 34.74 3.07
1349 1396 1.065031 GTAACGCTTTGCATGCACGG 61.065 55.000 26.52 20.04 0.00 4.94
1403 1450 2.747686 GACCAACCGCCCTTCTCA 59.252 61.111 0.00 0.00 0.00 3.27
1475 1522 1.605058 GCTCTTGCTACCAGGTCCGA 61.605 60.000 0.00 0.00 36.03 4.55
1563 1623 1.204228 GCGCGCATTCCATTGATGTG 61.204 55.000 29.10 0.00 0.00 3.21
1569 1629 4.046462 CGCATTCCATTGATGTGAATTCC 58.954 43.478 2.27 0.00 30.54 3.01
1840 1909 0.668401 AACGGCACACGGTAAGCTAC 60.668 55.000 0.00 0.00 43.57 3.58
1937 2006 4.430765 CCGACTAACCGCCGTGCT 62.431 66.667 0.00 0.00 0.00 4.40
2026 2113 2.173569 GGACATAGCCTTCAAGGTGGAT 59.826 50.000 5.03 0.00 37.80 3.41
2054 2141 0.381089 CAACTCCTACTACCTCGCCG 59.619 60.000 0.00 0.00 0.00 6.46
2505 2601 4.752101 GTGTGAAGCTTGTGTTATCTGTCT 59.248 41.667 2.10 0.00 0.00 3.41
2576 2672 3.306849 GCCGGGAAGAGTTTCTACTTCTT 60.307 47.826 2.18 0.00 41.25 2.52
2590 2686 1.003355 TTCTTGCCCCTCGCTCTTG 60.003 57.895 0.00 0.00 38.78 3.02
2602 2698 0.940126 CGCTCTTGTTGTTGCAGTCT 59.060 50.000 0.00 0.00 0.00 3.24
2603 2699 1.070309 CGCTCTTGTTGTTGCAGTCTC 60.070 52.381 0.00 0.00 0.00 3.36
2616 2712 4.430137 TGCAGTCTCATTTCATTTGCTC 57.570 40.909 0.00 0.00 0.00 4.26
2622 2718 7.242079 CAGTCTCATTTCATTTGCTCTACAAG 58.758 38.462 0.00 0.00 40.06 3.16
2624 2720 6.150140 GTCTCATTTCATTTGCTCTACAAGGT 59.850 38.462 0.00 0.00 40.06 3.50
2625 2721 7.334421 GTCTCATTTCATTTGCTCTACAAGGTA 59.666 37.037 0.00 0.00 40.06 3.08
2626 2722 7.334421 TCTCATTTCATTTGCTCTACAAGGTAC 59.666 37.037 0.00 0.00 40.06 3.34
2645 2741 2.157738 ACTACTGGAGTGTGACGGTAC 58.842 52.381 0.00 0.00 36.87 3.34
2657 2753 4.055360 TGTGACGGTACTTCATTCACTTG 58.945 43.478 0.00 0.00 39.27 3.16
2667 2763 2.688477 TCATTCACTTGGGCCCTTTTT 58.312 42.857 25.70 0.92 0.00 1.94
2705 3500 0.172352 CGCCAGCCTAGCTAGCTATC 59.828 60.000 24.36 18.07 40.85 2.08
2752 3549 9.166126 GCTAGAAAAACAAATGTGTACAAGTAC 57.834 33.333 0.00 3.47 36.80 2.73
2761 3558 9.944376 ACAAATGTGTACAAGTACAAGAGATAT 57.056 29.630 14.08 1.62 46.33 1.63
2764 3561 9.731819 AATGTGTACAAGTACAAGAGATATACG 57.268 33.333 14.08 0.00 46.33 3.06
2790 3587 6.500775 CAAATCTTTGTCACATTCACACAC 57.499 37.500 0.00 0.00 33.59 3.82
2792 3589 3.526534 TCTTTGTCACATTCACACACGA 58.473 40.909 0.00 0.00 0.00 4.35
2793 3590 3.935828 TCTTTGTCACATTCACACACGAA 59.064 39.130 0.00 0.00 0.00 3.85
2794 3591 3.666883 TTGTCACATTCACACACGAAC 57.333 42.857 0.00 0.00 0.00 3.95
2798 3595 0.303493 ACATTCACACACGAACGCAC 59.697 50.000 0.00 0.00 0.00 5.34
2826 3623 7.463913 CGCACAAAAATGCTTGAGAGTTTTAAA 60.464 33.333 0.00 0.00 43.80 1.52
2829 3626 7.010091 ACAAAAATGCTTGAGAGTTTTAAACCG 59.990 33.333 4.01 0.00 0.00 4.44
2832 3637 3.314080 TGCTTGAGAGTTTTAAACCGGTG 59.686 43.478 8.52 0.00 0.00 4.94
2836 3641 4.124238 TGAGAGTTTTAAACCGGTGACAG 58.876 43.478 8.52 0.00 0.00 3.51
2843 3648 6.991531 AGTTTTAAACCGGTGACAGTATACAA 59.008 34.615 8.52 0.00 0.00 2.41
2908 3716 8.359642 TCTTGTTGCATTAATTTGAGTTAGCTT 58.640 29.630 0.00 0.00 0.00 3.74
2936 3817 7.202016 TGTCTGTTGAAAAAGACATATCCAC 57.798 36.000 11.28 0.00 45.97 4.02
2937 3818 6.206634 TGTCTGTTGAAAAAGACATATCCACC 59.793 38.462 11.28 0.00 45.97 4.61
2938 3819 6.206634 GTCTGTTGAAAAAGACATATCCACCA 59.793 38.462 8.25 0.00 42.01 4.17
2939 3820 6.775142 TCTGTTGAAAAAGACATATCCACCAA 59.225 34.615 0.00 0.00 0.00 3.67
2940 3821 6.980593 TGTTGAAAAAGACATATCCACCAAG 58.019 36.000 0.00 0.00 0.00 3.61
2941 3822 6.549364 TGTTGAAAAAGACATATCCACCAAGT 59.451 34.615 0.00 0.00 0.00 3.16
2942 3823 7.069331 TGTTGAAAAAGACATATCCACCAAGTT 59.931 33.333 0.00 0.00 0.00 2.66
2943 3824 6.980593 TGAAAAAGACATATCCACCAAGTTG 58.019 36.000 0.00 0.00 0.00 3.16
2944 3825 6.775142 TGAAAAAGACATATCCACCAAGTTGA 59.225 34.615 3.87 0.00 0.00 3.18
2945 3826 7.286546 TGAAAAAGACATATCCACCAAGTTGAA 59.713 33.333 3.87 0.00 0.00 2.69
2946 3827 7.595819 AAAAGACATATCCACCAAGTTGAAA 57.404 32.000 3.87 0.00 0.00 2.69
2947 3828 7.595819 AAAGACATATCCACCAAGTTGAAAA 57.404 32.000 3.87 0.00 0.00 2.29
2948 3829 7.595819 AAGACATATCCACCAAGTTGAAAAA 57.404 32.000 3.87 0.00 0.00 1.94
2988 3869 3.703001 ATCATTTCCCTCTTGTGACGT 57.297 42.857 0.00 0.00 0.00 4.34
2989 3870 4.819105 ATCATTTCCCTCTTGTGACGTA 57.181 40.909 0.00 0.00 0.00 3.57
2996 3878 5.223449 TCCCTCTTGTGACGTAGAAAATT 57.777 39.130 0.00 0.00 0.00 1.82
3038 3920 1.757118 CCAGAGGCAGGATCGAGTTTA 59.243 52.381 0.00 0.00 0.00 2.01
3087 3970 5.163673 GCAAAAGGAAGAAAATTTTGGCACA 60.164 36.000 8.47 0.00 41.82 4.57
3105 3988 6.668645 TGGCACACCTAAGGATTTATATGTT 58.331 36.000 0.00 0.00 36.63 2.71
3145 4032 6.039382 GTGTTTGGAAAGGACTTGTGATACTT 59.961 38.462 0.00 0.00 0.00 2.24
3151 4038 8.598916 TGGAAAGGACTTGTGATACTTAATACA 58.401 33.333 0.00 0.00 0.00 2.29
3159 4046 9.733556 ACTTGTGATACTTAATACATTTCCACA 57.266 29.630 0.00 0.00 0.00 4.17
3168 4055 8.100164 ACTTAATACATTTCCACATTTTTGGGG 58.900 33.333 0.00 0.00 37.24 4.96
3169 4056 6.446909 AATACATTTCCACATTTTTGGGGT 57.553 33.333 0.00 0.00 37.24 4.95
3170 4057 4.350368 ACATTTCCACATTTTTGGGGTC 57.650 40.909 0.00 0.00 37.24 4.46
3179 4986 4.401202 CACATTTTTGGGGTCCATACCTAC 59.599 45.833 0.00 0.00 45.95 3.18
3187 4994 1.141053 GGTCCATACCTACTGGCAAGG 59.859 57.143 3.63 3.63 43.08 3.61
3189 4996 2.238898 GTCCATACCTACTGGCAAGGTT 59.761 50.000 15.68 2.41 45.26 3.50
3194 5001 3.629142 ACCTACTGGCAAGGTTGATAC 57.371 47.619 5.01 0.00 45.26 2.24
3201 5008 0.719465 GCAAGGTTGATACGTGGACG 59.281 55.000 0.00 0.00 46.33 4.79
3231 5038 0.037447 TTCCGGTTGATGCATGACCA 59.963 50.000 22.20 6.13 32.95 4.02
3232 5039 0.676466 TCCGGTTGATGCATGACCAC 60.676 55.000 22.20 4.84 32.95 4.16
3233 5040 0.959867 CCGGTTGATGCATGACCACA 60.960 55.000 22.20 5.47 32.95 4.17
3234 5041 1.097232 CGGTTGATGCATGACCACAT 58.903 50.000 22.20 0.00 37.19 3.21
3235 5042 1.473677 CGGTTGATGCATGACCACATT 59.526 47.619 22.20 0.00 34.15 2.71
3236 5043 2.094597 CGGTTGATGCATGACCACATTT 60.095 45.455 22.20 0.00 34.15 2.32
3237 5044 3.614630 CGGTTGATGCATGACCACATTTT 60.615 43.478 22.20 0.00 34.15 1.82
3238 5045 4.317488 GGTTGATGCATGACCACATTTTT 58.683 39.130 19.21 0.00 34.15 1.94
3255 5062 3.192799 TTTTTGTTGAGGGGCGTGA 57.807 47.368 0.00 0.00 0.00 4.35
3256 5063 0.741915 TTTTTGTTGAGGGGCGTGAC 59.258 50.000 0.00 0.00 0.00 3.67
3257 5064 1.104577 TTTTGTTGAGGGGCGTGACC 61.105 55.000 0.00 0.00 37.93 4.02
3258 5065 1.990160 TTTGTTGAGGGGCGTGACCT 61.990 55.000 0.00 0.00 42.18 3.85
3264 5071 4.857251 GGGGCGTGACCTCTATTG 57.143 61.111 0.00 0.00 35.16 1.90
3265 5072 1.905512 GGGGCGTGACCTCTATTGT 59.094 57.895 0.00 0.00 35.16 2.71
3266 5073 0.252197 GGGGCGTGACCTCTATTGTT 59.748 55.000 0.00 0.00 35.16 2.83
3267 5074 1.369625 GGGCGTGACCTCTATTGTTG 58.630 55.000 0.00 0.00 39.10 3.33
3268 5075 1.338769 GGGCGTGACCTCTATTGTTGT 60.339 52.381 0.00 0.00 39.10 3.32
3269 5076 2.093869 GGGCGTGACCTCTATTGTTGTA 60.094 50.000 0.00 0.00 39.10 2.41
3270 5077 3.592059 GGCGTGACCTCTATTGTTGTAA 58.408 45.455 0.00 0.00 34.51 2.41
3271 5078 3.370061 GGCGTGACCTCTATTGTTGTAAC 59.630 47.826 0.00 0.00 34.51 2.50
3272 5079 3.991773 GCGTGACCTCTATTGTTGTAACA 59.008 43.478 0.00 0.00 37.08 2.41
3273 5080 4.630069 GCGTGACCTCTATTGTTGTAACAT 59.370 41.667 0.00 0.00 38.95 2.71
3274 5081 5.220416 GCGTGACCTCTATTGTTGTAACATC 60.220 44.000 0.00 0.00 38.95 3.06
3275 5082 6.100004 CGTGACCTCTATTGTTGTAACATCT 58.900 40.000 0.00 0.00 38.95 2.90
3276 5083 7.255569 CGTGACCTCTATTGTTGTAACATCTA 58.744 38.462 0.00 0.00 38.95 1.98
3277 5084 7.921214 CGTGACCTCTATTGTTGTAACATCTAT 59.079 37.037 0.00 0.00 38.95 1.98
3278 5085 9.601217 GTGACCTCTATTGTTGTAACATCTATT 57.399 33.333 0.00 0.00 38.95 1.73
3322 5129 9.973661 TTCCTCCATTTCAAAATAAGTATCTCA 57.026 29.630 0.00 0.00 0.00 3.27
3323 5130 9.973661 TCCTCCATTTCAAAATAAGTATCTCAA 57.026 29.630 0.00 0.00 0.00 3.02
3356 5163 9.959721 TCCTAAAATAAGCATCTCAACTTTAGT 57.040 29.630 0.00 0.00 0.00 2.24
3362 5169 9.726438 AATAAGCATCTCAACTTTAGTACAACT 57.274 29.630 0.00 0.00 0.00 3.16
3363 5170 9.726438 ATAAGCATCTCAACTTTAGTACAACTT 57.274 29.630 0.00 0.00 0.00 2.66
3364 5171 8.451908 AAGCATCTCAACTTTAGTACAACTTT 57.548 30.769 0.00 0.00 0.00 2.66
3365 5172 9.555727 AAGCATCTCAACTTTAGTACAACTTTA 57.444 29.630 0.00 0.00 0.00 1.85
3366 5173 9.726438 AGCATCTCAACTTTAGTACAACTTTAT 57.274 29.630 0.00 0.00 0.00 1.40
3367 5174 9.760660 GCATCTCAACTTTAGTACAACTTTATG 57.239 33.333 0.00 0.00 0.00 1.90
3407 5214 5.995055 GTGAAGACACTTCTTTTGAGATGG 58.005 41.667 11.79 0.00 42.53 3.51
3408 5215 5.760253 GTGAAGACACTTCTTTTGAGATGGA 59.240 40.000 11.79 0.00 42.53 3.41
3409 5216 5.994054 TGAAGACACTTCTTTTGAGATGGAG 59.006 40.000 11.79 0.00 42.53 3.86
3410 5217 4.904241 AGACACTTCTTTTGAGATGGAGG 58.096 43.478 0.00 0.00 0.00 4.30
3411 5218 4.006319 GACACTTCTTTTGAGATGGAGGG 58.994 47.826 0.00 0.00 0.00 4.30
3412 5219 3.652869 ACACTTCTTTTGAGATGGAGGGA 59.347 43.478 0.00 0.00 0.00 4.20
3413 5220 4.260170 CACTTCTTTTGAGATGGAGGGAG 58.740 47.826 0.00 0.00 0.00 4.30
3414 5221 3.913163 ACTTCTTTTGAGATGGAGGGAGT 59.087 43.478 0.00 0.00 0.00 3.85
3415 5222 5.046304 CACTTCTTTTGAGATGGAGGGAGTA 60.046 44.000 0.00 0.00 0.00 2.59
3416 5223 5.728741 ACTTCTTTTGAGATGGAGGGAGTAT 59.271 40.000 0.00 0.00 0.00 2.12
3417 5224 6.903534 ACTTCTTTTGAGATGGAGGGAGTATA 59.096 38.462 0.00 0.00 0.00 1.47
3418 5225 7.570607 ACTTCTTTTGAGATGGAGGGAGTATAT 59.429 37.037 0.00 0.00 0.00 0.86
3419 5226 7.546250 TCTTTTGAGATGGAGGGAGTATATC 57.454 40.000 0.00 0.00 0.00 1.63
3420 5227 7.075797 TCTTTTGAGATGGAGGGAGTATATCA 58.924 38.462 0.00 0.00 0.00 2.15
3421 5228 7.568738 TCTTTTGAGATGGAGGGAGTATATCAA 59.431 37.037 0.00 0.00 32.21 2.57
3422 5229 7.690454 TTTGAGATGGAGGGAGTATATCAAA 57.310 36.000 0.00 0.00 38.77 2.69
3423 5230 7.690454 TTGAGATGGAGGGAGTATATCAAAA 57.310 36.000 0.00 0.00 31.43 2.44
3424 5231 7.067496 TGAGATGGAGGGAGTATATCAAAAC 57.933 40.000 0.00 0.00 0.00 2.43
3425 5232 6.846505 TGAGATGGAGGGAGTATATCAAAACT 59.153 38.462 0.00 0.00 0.00 2.66
3426 5233 7.348274 TGAGATGGAGGGAGTATATCAAAACTT 59.652 37.037 0.00 0.00 0.00 2.66
3427 5234 8.107196 AGATGGAGGGAGTATATCAAAACTTT 57.893 34.615 0.00 0.00 0.00 2.66
3428 5235 8.560903 AGATGGAGGGAGTATATCAAAACTTTT 58.439 33.333 0.00 0.00 0.00 2.27
3429 5236 9.847224 GATGGAGGGAGTATATCAAAACTTTTA 57.153 33.333 0.00 0.00 0.00 1.52
3449 5256 8.173130 ACTTTTATTACACACTAGTAAATGCGC 58.827 33.333 0.00 0.00 37.50 6.09
3450 5257 7.598189 TTTATTACACACTAGTAAATGCGCA 57.402 32.000 14.96 14.96 37.50 6.09
3451 5258 4.914312 TTACACACTAGTAAATGCGCAC 57.086 40.909 14.90 0.00 31.45 5.34
3452 5259 1.724623 ACACACTAGTAAATGCGCACG 59.275 47.619 14.90 0.00 0.00 5.34
3453 5260 1.724623 CACACTAGTAAATGCGCACGT 59.275 47.619 14.90 5.96 0.00 4.49
3454 5261 1.724623 ACACTAGTAAATGCGCACGTG 59.275 47.619 14.90 12.28 0.00 4.49
3455 5262 0.719465 ACTAGTAAATGCGCACGTGC 59.281 50.000 30.42 30.42 37.78 5.34
3476 5283 5.743467 TGCGATGCACGTTAATATTTTAGG 58.257 37.500 9.76 0.00 44.60 2.69
3477 5284 4.611366 GCGATGCACGTTAATATTTTAGGC 59.389 41.667 9.76 0.00 44.60 3.93
3478 5285 5.743467 CGATGCACGTTAATATTTTAGGCA 58.257 37.500 0.00 0.00 37.22 4.75
3479 5286 6.195868 CGATGCACGTTAATATTTTAGGCAA 58.804 36.000 0.00 0.00 37.22 4.52
3480 5287 6.855914 CGATGCACGTTAATATTTTAGGCAAT 59.144 34.615 0.00 0.00 37.22 3.56
3481 5288 8.012809 CGATGCACGTTAATATTTTAGGCAATA 58.987 33.333 0.00 0.00 37.22 1.90
3482 5289 9.840427 GATGCACGTTAATATTTTAGGCAATAT 57.160 29.630 0.00 0.00 31.72 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.819259 GTTCAGCTGCTGGTCAACCA 60.819 55.000 27.79 5.33 45.30 3.67
80 81 0.524414 AGAAATGTAAAACCGGCCGC 59.476 50.000 22.85 5.24 0.00 6.53
86 87 9.476202 AAAGATGCAAACTAGAAATGTAAAACC 57.524 29.630 0.00 0.00 0.00 3.27
335 347 2.661866 CCGGATTAAGCGCCCGAG 60.662 66.667 21.34 9.27 45.58 4.63
350 365 1.805945 GTAGTCAGCGTCCTTGCCG 60.806 63.158 0.00 0.00 34.65 5.69
354 369 3.003113 GCCGGTAGTCAGCGTCCTT 62.003 63.158 1.90 0.00 44.06 3.36
396 411 2.668280 GCTCACGCGTTCACTTCCC 61.668 63.158 10.22 0.00 0.00 3.97
399 414 2.108157 TGGCTCACGCGTTCACTT 59.892 55.556 10.22 0.00 36.88 3.16
421 436 1.302511 CCTCCCGGTTGACTTGTGG 60.303 63.158 0.00 0.00 0.00 4.17
545 561 0.457851 CAGGATCTCACACCGTCTCC 59.542 60.000 0.00 0.00 0.00 3.71
556 572 0.741915 GGTCCAGTCGTCAGGATCTC 59.258 60.000 0.00 0.00 36.11 2.75
557 573 0.333312 AGGTCCAGTCGTCAGGATCT 59.667 55.000 1.06 1.06 40.52 2.75
602 618 1.356059 TCCATTTCACCATCCCCGAAA 59.644 47.619 0.00 0.00 33.48 3.46
611 628 2.034999 GCCCCGTCCATTTCACCA 59.965 61.111 0.00 0.00 0.00 4.17
752 769 1.808411 ATTTGTACACCAGCGACCAG 58.192 50.000 0.00 0.00 0.00 4.00
753 770 2.264005 AATTTGTACACCAGCGACCA 57.736 45.000 0.00 0.00 0.00 4.02
754 771 2.351350 CCAAATTTGTACACCAGCGACC 60.351 50.000 16.73 0.00 0.00 4.79
757 774 3.252215 TCTTCCAAATTTGTACACCAGCG 59.748 43.478 16.73 0.00 0.00 5.18
840 857 5.963176 AATAAATAAACCCGTTCGTTGGT 57.037 34.783 0.00 0.00 36.06 3.67
936 956 8.367911 GTGATTAAATTCTCCCTTGGTTTCTTT 58.632 33.333 0.00 0.00 0.00 2.52
1140 1174 1.361668 CCATGAACACGGCGAAGGAG 61.362 60.000 16.62 0.00 0.00 3.69
1304 1338 7.167924 TGCATAATGCTGGAGAAATTAAACA 57.832 32.000 0.00 0.00 45.31 2.83
1305 1341 7.761249 ACTTGCATAATGCTGGAGAAATTAAAC 59.239 33.333 0.00 0.00 45.31 2.01
1349 1396 1.361668 CGCATGCACCACCTACAGAC 61.362 60.000 19.57 0.00 0.00 3.51
1391 1438 0.982852 TCATGGATGAGAAGGGCGGT 60.983 55.000 0.00 0.00 32.11 5.68
1403 1450 4.687215 CCGGCGGCGATCATGGAT 62.687 66.667 34.49 0.00 0.00 3.41
1475 1522 3.895232 AAGAGCTGGTTGTATGATCGT 57.105 42.857 0.00 0.00 0.00 3.73
1555 1615 2.424601 CACCTGCGGAATTCACATCAAT 59.575 45.455 7.93 0.00 0.00 2.57
1556 1616 1.811965 CACCTGCGGAATTCACATCAA 59.188 47.619 7.93 0.00 0.00 2.57
1563 1623 0.169009 GCACTTCACCTGCGGAATTC 59.831 55.000 0.00 0.00 0.00 2.17
1663 1723 2.599281 TCGAAGTGGACGGGCTCA 60.599 61.111 0.00 0.00 0.00 4.26
1840 1909 3.449227 TCCGGACACGCAGCTAGG 61.449 66.667 0.00 0.00 39.22 3.02
1861 1930 1.512098 GCTTGCCGCTCTTTTACGC 60.512 57.895 0.00 0.00 35.14 4.42
1937 2006 0.899717 GATGCCAGGGCCAAGACAAA 60.900 55.000 6.18 0.00 41.09 2.83
2026 2113 2.284331 TAGGAGTTGGAGCCGGCA 60.284 61.111 31.54 4.59 0.00 5.69
2054 2141 1.015109 TCCTCGTACTCGATGAGCAC 58.985 55.000 0.00 0.00 45.21 4.40
2200 2287 2.722201 GGTGAGGCGGACCGAGAAT 61.722 63.158 20.50 0.00 42.76 2.40
2523 2619 4.578928 GCCCCGATACAGTTTATTTCACAT 59.421 41.667 0.00 0.00 0.00 3.21
2590 2686 5.332808 GCAAATGAAATGAGACTGCAACAAC 60.333 40.000 0.00 0.00 0.00 3.32
2602 2698 7.168219 AGTACCTTGTAGAGCAAATGAAATGA 58.832 34.615 0.00 0.00 36.53 2.57
2603 2699 7.383102 AGTACCTTGTAGAGCAAATGAAATG 57.617 36.000 0.00 0.00 36.53 2.32
2616 2712 5.008331 TCACACTCCAGTAGTACCTTGTAG 58.992 45.833 0.00 0.00 35.76 2.74
2622 2718 1.471684 CCGTCACACTCCAGTAGTACC 59.528 57.143 0.00 0.00 35.76 3.34
2624 2720 2.574006 ACCGTCACACTCCAGTAGTA 57.426 50.000 0.00 0.00 35.76 1.82
2625 2721 2.157738 GTACCGTCACACTCCAGTAGT 58.842 52.381 0.00 0.00 39.81 2.73
2626 2722 2.434428 AGTACCGTCACACTCCAGTAG 58.566 52.381 0.00 0.00 0.00 2.57
2645 2741 1.928868 AAGGGCCCAAGTGAATGAAG 58.071 50.000 27.56 0.00 0.00 3.02
2657 2753 2.039879 TGAGACTAGACAAAAAGGGCCC 59.960 50.000 16.46 16.46 0.00 5.80
2667 2763 1.813178 CGCCTTCAGTGAGACTAGACA 59.187 52.381 0.00 0.00 0.00 3.41
2729 3524 9.567848 CTTGTACTTGTACACATTTGTTTTTCT 57.432 29.630 12.51 0.00 37.15 2.52
2779 3576 0.303493 GTGCGTTCGTGTGTGAATGT 59.697 50.000 0.00 0.00 37.23 2.71
2780 3577 0.717896 CGTGCGTTCGTGTGTGAATG 60.718 55.000 0.00 0.00 37.81 2.67
2945 3826 5.659440 ACATATTCCACGGAGCAATTTTT 57.341 34.783 0.00 0.00 0.00 1.94
2946 3827 6.545666 TGATACATATTCCACGGAGCAATTTT 59.454 34.615 0.00 0.00 0.00 1.82
2947 3828 6.061441 TGATACATATTCCACGGAGCAATTT 58.939 36.000 0.00 0.00 0.00 1.82
2948 3829 5.620206 TGATACATATTCCACGGAGCAATT 58.380 37.500 0.00 0.00 0.00 2.32
2949 3830 5.227569 TGATACATATTCCACGGAGCAAT 57.772 39.130 0.00 0.00 0.00 3.56
2950 3831 4.681074 TGATACATATTCCACGGAGCAA 57.319 40.909 0.00 0.00 0.00 3.91
2951 3832 4.890158 ATGATACATATTCCACGGAGCA 57.110 40.909 0.00 0.00 0.00 4.26
2952 3833 5.122396 GGAAATGATACATATTCCACGGAGC 59.878 44.000 14.45 0.00 40.81 4.70
2953 3834 5.643777 GGGAAATGATACATATTCCACGGAG 59.356 44.000 17.86 0.00 42.50 4.63
2954 3835 5.309543 AGGGAAATGATACATATTCCACGGA 59.690 40.000 17.86 0.00 42.50 4.69
2955 3836 5.560724 AGGGAAATGATACATATTCCACGG 58.439 41.667 17.86 0.00 42.50 4.94
2956 3837 6.467677 AGAGGGAAATGATACATATTCCACG 58.532 40.000 17.86 0.00 42.50 4.94
2957 3838 7.721399 ACAAGAGGGAAATGATACATATTCCAC 59.279 37.037 17.86 13.75 42.50 4.02
2958 3839 7.720957 CACAAGAGGGAAATGATACATATTCCA 59.279 37.037 17.86 0.00 42.50 3.53
2959 3840 7.939039 TCACAAGAGGGAAATGATACATATTCC 59.061 37.037 0.00 0.00 40.48 3.01
2960 3841 8.778358 GTCACAAGAGGGAAATGATACATATTC 58.222 37.037 0.00 0.00 0.00 1.75
2961 3842 7.442364 CGTCACAAGAGGGAAATGATACATATT 59.558 37.037 0.00 0.00 0.00 1.28
2962 3843 6.931281 CGTCACAAGAGGGAAATGATACATAT 59.069 38.462 0.00 0.00 0.00 1.78
2963 3844 6.127168 ACGTCACAAGAGGGAAATGATACATA 60.127 38.462 0.00 0.00 34.03 2.29
2964 3845 5.118990 CGTCACAAGAGGGAAATGATACAT 58.881 41.667 0.00 0.00 0.00 2.29
2965 3846 4.020573 ACGTCACAAGAGGGAAATGATACA 60.021 41.667 0.00 0.00 34.03 2.29
2988 3869 6.097554 TCAACTTGGTGGAGCAAAATTTTCTA 59.902 34.615 0.00 0.00 0.00 2.10
2989 3870 5.104982 TCAACTTGGTGGAGCAAAATTTTCT 60.105 36.000 0.00 1.74 0.00 2.52
2996 3878 2.031120 CCTTCAACTTGGTGGAGCAAA 58.969 47.619 0.00 0.00 0.00 3.68
3054 3937 1.146774 TCTTCCTTTTGCATCCACCCA 59.853 47.619 0.00 0.00 0.00 4.51
3055 3938 1.923356 TCTTCCTTTTGCATCCACCC 58.077 50.000 0.00 0.00 0.00 4.61
3111 3994 7.448748 AGTCCTTTCCAAACACATGTTATAC 57.551 36.000 0.00 0.00 37.25 1.47
3113 3996 6.323739 ACAAGTCCTTTCCAAACACATGTTAT 59.676 34.615 0.00 0.00 37.25 1.89
3115 3998 4.466015 ACAAGTCCTTTCCAAACACATGTT 59.534 37.500 0.00 0.00 40.50 2.71
3116 3999 4.023291 ACAAGTCCTTTCCAAACACATGT 58.977 39.130 0.00 0.00 0.00 3.21
3117 4000 4.097741 TCACAAGTCCTTTCCAAACACATG 59.902 41.667 0.00 0.00 0.00 3.21
3118 4001 4.277476 TCACAAGTCCTTTCCAAACACAT 58.723 39.130 0.00 0.00 0.00 3.21
3119 4002 3.691575 TCACAAGTCCTTTCCAAACACA 58.308 40.909 0.00 0.00 0.00 3.72
3120 4003 4.918810 ATCACAAGTCCTTTCCAAACAC 57.081 40.909 0.00 0.00 0.00 3.32
3145 4032 7.310734 GGACCCCAAAAATGTGGAAATGTATTA 60.311 37.037 0.00 0.00 41.65 0.98
3151 4038 3.321950 TGGACCCCAAAAATGTGGAAAT 58.678 40.909 0.00 0.00 41.65 2.17
3167 4054 1.141053 CCTTGCCAGTAGGTATGGACC 59.859 57.143 0.00 0.00 44.45 4.46
3168 4055 1.838077 ACCTTGCCAGTAGGTATGGAC 59.162 52.381 10.65 0.00 44.45 4.02
3169 4056 2.238646 CAACCTTGCCAGTAGGTATGGA 59.761 50.000 10.65 0.00 45.17 3.41
3170 4057 2.238646 TCAACCTTGCCAGTAGGTATGG 59.761 50.000 0.00 3.55 45.17 2.74
3179 4986 1.086696 CCACGTATCAACCTTGCCAG 58.913 55.000 0.00 0.00 0.00 4.85
3194 5001 2.049433 GTGTCCTCCACGTCCACG 60.049 66.667 0.00 0.00 46.33 4.94
3201 5008 0.602905 CAACCGGAAGTGTCCTCCAC 60.603 60.000 9.46 0.00 42.44 4.02
3237 5044 0.741915 GTCACGCCCCTCAACAAAAA 59.258 50.000 0.00 0.00 0.00 1.94
3238 5045 1.104577 GGTCACGCCCCTCAACAAAA 61.105 55.000 0.00 0.00 0.00 2.44
3239 5046 1.527380 GGTCACGCCCCTCAACAAA 60.527 57.895 0.00 0.00 0.00 2.83
3240 5047 2.112297 GGTCACGCCCCTCAACAA 59.888 61.111 0.00 0.00 0.00 2.83
3241 5048 2.847234 AGGTCACGCCCCTCAACA 60.847 61.111 0.00 0.00 38.26 3.33
3242 5049 2.047179 GAGGTCACGCCCCTCAAC 60.047 66.667 9.95 0.00 46.46 3.18
3246 5053 0.617820 ACAATAGAGGTCACGCCCCT 60.618 55.000 0.00 0.00 38.26 4.79
3247 5054 0.252197 AACAATAGAGGTCACGCCCC 59.748 55.000 0.00 0.00 38.26 5.80
3248 5055 1.338769 ACAACAATAGAGGTCACGCCC 60.339 52.381 0.00 0.00 38.26 6.13
3249 5056 2.094762 ACAACAATAGAGGTCACGCC 57.905 50.000 0.00 0.00 37.58 5.68
3250 5057 3.991773 TGTTACAACAATAGAGGTCACGC 59.008 43.478 0.00 0.00 35.67 5.34
3251 5058 6.100004 AGATGTTACAACAATAGAGGTCACG 58.900 40.000 0.00 0.00 43.03 4.35
3252 5059 9.601217 AATAGATGTTACAACAATAGAGGTCAC 57.399 33.333 0.00 0.00 43.03 3.67
3296 5103 9.973661 TGAGATACTTATTTTGAAATGGAGGAA 57.026 29.630 0.00 0.00 0.00 3.36
3297 5104 9.973661 TTGAGATACTTATTTTGAAATGGAGGA 57.026 29.630 0.00 0.00 0.00 3.71
3330 5137 9.959721 ACTAAAGTTGAGATGCTTATTTTAGGA 57.040 29.630 0.00 0.00 33.44 2.94
3336 5143 9.726438 AGTTGTACTAAAGTTGAGATGCTTATT 57.274 29.630 0.00 0.00 0.00 1.40
3337 5144 9.726438 AAGTTGTACTAAAGTTGAGATGCTTAT 57.274 29.630 0.00 0.00 0.00 1.73
3338 5145 9.555727 AAAGTTGTACTAAAGTTGAGATGCTTA 57.444 29.630 0.00 0.00 0.00 3.09
3339 5146 8.451908 AAAGTTGTACTAAAGTTGAGATGCTT 57.548 30.769 0.00 0.00 0.00 3.91
3340 5147 9.726438 ATAAAGTTGTACTAAAGTTGAGATGCT 57.274 29.630 0.00 0.00 0.00 3.79
3341 5148 9.760660 CATAAAGTTGTACTAAAGTTGAGATGC 57.239 33.333 0.00 0.00 0.00 3.91
3384 5191 5.760253 TCCATCTCAAAAGAAGTGTCTTCAC 59.240 40.000 11.27 0.00 43.59 3.18
3385 5192 5.928976 TCCATCTCAAAAGAAGTGTCTTCA 58.071 37.500 11.27 0.00 43.59 3.02
3386 5193 5.411053 CCTCCATCTCAAAAGAAGTGTCTTC 59.589 44.000 1.76 1.76 43.59 2.87
3387 5194 5.312079 CCTCCATCTCAAAAGAAGTGTCTT 58.688 41.667 0.00 0.00 46.47 3.01
3388 5195 4.263243 CCCTCCATCTCAAAAGAAGTGTCT 60.263 45.833 0.00 0.00 34.49 3.41
3389 5196 4.006319 CCCTCCATCTCAAAAGAAGTGTC 58.994 47.826 0.00 0.00 34.49 3.67
3390 5197 3.652869 TCCCTCCATCTCAAAAGAAGTGT 59.347 43.478 0.00 0.00 34.49 3.55
3391 5198 4.260170 CTCCCTCCATCTCAAAAGAAGTG 58.740 47.826 0.00 0.00 34.49 3.16
3392 5199 3.913163 ACTCCCTCCATCTCAAAAGAAGT 59.087 43.478 0.00 0.00 34.49 3.01
3393 5200 4.566426 ACTCCCTCCATCTCAAAAGAAG 57.434 45.455 0.00 0.00 34.49 2.85
3394 5201 7.568738 TGATATACTCCCTCCATCTCAAAAGAA 59.431 37.037 0.00 0.00 34.49 2.52
3395 5202 7.075797 TGATATACTCCCTCCATCTCAAAAGA 58.924 38.462 0.00 0.00 35.54 2.52
3396 5203 7.308450 TGATATACTCCCTCCATCTCAAAAG 57.692 40.000 0.00 0.00 0.00 2.27
3397 5204 7.690454 TTGATATACTCCCTCCATCTCAAAA 57.310 36.000 0.00 0.00 0.00 2.44
3398 5205 7.690454 TTTGATATACTCCCTCCATCTCAAA 57.310 36.000 0.00 0.00 0.00 2.69
3399 5206 7.348274 AGTTTTGATATACTCCCTCCATCTCAA 59.652 37.037 0.00 0.00 0.00 3.02
3400 5207 6.846505 AGTTTTGATATACTCCCTCCATCTCA 59.153 38.462 0.00 0.00 0.00 3.27
3401 5208 7.309770 AGTTTTGATATACTCCCTCCATCTC 57.690 40.000 0.00 0.00 0.00 2.75
3402 5209 7.698163 AAGTTTTGATATACTCCCTCCATCT 57.302 36.000 0.00 0.00 0.00 2.90
3403 5210 8.753497 AAAAGTTTTGATATACTCCCTCCATC 57.247 34.615 0.00 0.00 0.00 3.51
3423 5230 8.173130 GCGCATTTACTAGTGTGTAATAAAAGT 58.827 33.333 5.39 0.00 33.16 2.66
3424 5231 8.172484 TGCGCATTTACTAGTGTGTAATAAAAG 58.828 33.333 5.66 0.00 33.16 2.27
3425 5232 7.958567 GTGCGCATTTACTAGTGTGTAATAAAA 59.041 33.333 15.91 0.00 33.16 1.52
3426 5233 7.457868 GTGCGCATTTACTAGTGTGTAATAAA 58.542 34.615 15.91 0.00 33.16 1.40
3427 5234 6.237622 CGTGCGCATTTACTAGTGTGTAATAA 60.238 38.462 15.91 0.00 33.16 1.40
3428 5235 5.230516 CGTGCGCATTTACTAGTGTGTAATA 59.769 40.000 15.91 0.00 33.16 0.98
3429 5236 4.032445 CGTGCGCATTTACTAGTGTGTAAT 59.968 41.667 15.91 0.00 33.16 1.89
3430 5237 3.365520 CGTGCGCATTTACTAGTGTGTAA 59.634 43.478 15.91 0.00 0.00 2.41
3431 5238 2.918600 CGTGCGCATTTACTAGTGTGTA 59.081 45.455 15.91 0.00 0.00 2.90
3432 5239 1.724623 CGTGCGCATTTACTAGTGTGT 59.275 47.619 15.91 0.00 0.00 3.72
3433 5240 1.724623 ACGTGCGCATTTACTAGTGTG 59.275 47.619 15.91 3.09 0.00 3.82
3434 5241 1.724623 CACGTGCGCATTTACTAGTGT 59.275 47.619 15.91 0.00 0.00 3.55
3435 5242 1.526986 GCACGTGCGCATTTACTAGTG 60.527 52.381 26.77 15.60 0.00 2.74
3436 5243 0.719465 GCACGTGCGCATTTACTAGT 59.281 50.000 26.77 0.00 0.00 2.57
3437 5244 3.491934 GCACGTGCGCATTTACTAG 57.508 52.632 26.77 0.66 0.00 2.57
3453 5260 5.743467 CCTAAAATATTAACGTGCATCGCA 58.257 37.500 8.31 0.00 44.19 5.10
3454 5261 4.611366 GCCTAAAATATTAACGTGCATCGC 59.389 41.667 8.31 0.00 44.19 4.58
3455 5262 5.743467 TGCCTAAAATATTAACGTGCATCG 58.257 37.500 7.07 7.07 46.00 3.84
3456 5263 9.840427 ATATTGCCTAAAATATTAACGTGCATC 57.160 29.630 0.00 0.00 30.18 3.91


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

AutoCloner maintained by Alex Coulton.