Multiple sequence alignment - TraesCS3A01G156000

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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 TraesCS3A01G156000 chr3A 100.000 3521 0 0 1 3521 149988369 149984849 0.000000e+00 6503.0
1 TraesCS3A01G156000 chr3A 76.531 196 40 6 2795 2986 474969653 474969460 6.220000e-18 102.0
2 TraesCS3A01G156000 chr3D 95.337 2852 96 18 162 3000 135045991 135043164 0.000000e+00 4495.0
3 TraesCS3A01G156000 chr3D 89.507 467 36 5 3066 3521 135043166 135042702 2.360000e-161 579.0
4 TraesCS3A01G156000 chr3D 80.645 124 23 1 2827 2949 516183214 516183337 1.040000e-15 95.3
5 TraesCS3A01G156000 chr3D 75.568 176 41 2 2795 2968 62916383 62916558 6.260000e-13 86.1
6 TraesCS3A01G156000 chr3B 93.863 2770 114 28 1 2734 191191313 191188564 0.000000e+00 4122.0
7 TraesCS3A01G156000 chr3B 84.545 110 17 0 2864 2973 679508822 679508931 3.720000e-20 110.0
8 TraesCS3A01G156000 chr3B 76.961 204 36 9 2769 2967 141734809 141734612 4.810000e-19 106.0
9 TraesCS3A01G156000 chr3B 89.855 69 5 2 3437 3504 258746368 258746435 1.740000e-13 87.9
10 TraesCS3A01G156000 chr7D 81.281 203 28 6 3299 3498 167080652 167080457 4.710000e-34 156.0
11 TraesCS3A01G156000 chr7D 77.202 193 39 4 2795 2984 554414385 554414195 1.340000e-19 108.0
12 TraesCS3A01G156000 chr2D 78.448 232 41 6 3292 3521 561326557 561326781 3.660000e-30 143.0
13 TraesCS3A01G156000 chr2D 77.698 139 22 7 3288 3423 49905866 49905998 3.770000e-10 76.8
14 TraesCS3A01G156000 chr5A 78.673 211 35 8 3292 3499 510075965 510075762 7.930000e-27 132.0
15 TraesCS3A01G156000 chr5A 76.170 235 45 6 3288 3521 353156348 353156124 2.870000e-21 113.0
16 TraesCS3A01G156000 chr5A 80.137 146 23 2 3339 3484 649403744 649403883 1.730000e-18 104.0
17 TraesCS3A01G156000 chr1B 78.404 213 37 7 3292 3501 668721319 668721113 2.850000e-26 130.0
18 TraesCS3A01G156000 chr5D 78.788 198 33 6 3288 3484 265661290 265661101 1.330000e-24 124.0
19 TraesCS3A01G156000 chr5D 83.486 109 17 1 3288 3395 501083857 501083749 2.240000e-17 100.0
20 TraesCS3A01G156000 chr7A 81.250 160 23 3 3329 3487 727720813 727720660 4.770000e-24 122.0
21 TraesCS3A01G156000 chr5B 79.042 167 33 2 2795 2959 399775259 399775425 2.870000e-21 113.0
22 TraesCS3A01G156000 chr5B 78.571 196 21 8 3312 3504 319814610 319814433 3.720000e-20 110.0
23 TraesCS3A01G156000 chr5B 76.720 189 40 4 2795 2980 579367520 579367333 6.220000e-18 102.0


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 TraesCS3A01G156000 chr3A 149984849 149988369 3520 True 6503 6503 100.000 1 3521 1 chr3A.!!$R1 3520
1 TraesCS3A01G156000 chr3D 135042702 135045991 3289 True 2537 4495 92.422 162 3521 2 chr3D.!!$R1 3359
2 TraesCS3A01G156000 chr3B 191188564 191191313 2749 True 4122 4122 93.863 1 2734 1 chr3B.!!$R2 2733

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
206 212 0.174162 CAAATAACCAGCCAGCCAGC 59.826 55.0 0.0 0.0 0.0 4.85 F
827 847 0.179056 GCATAAAGGTGGCGAGGCTA 60.179 55.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1799 1.006086 CGTTGACGAGCATGGCATTA 58.994 50.0 0.00 0.0 43.02 1.9 R
2542 2568 0.101399 ACGCGCACTCTCCTAATCAG 59.899 55.0 5.73 0.0 0.00 2.9 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
27 28 9.606631 ACATGTGGTTATGTGTTAAAAACATTT 57.393 25.926 0.00 0.00 44.35 2.32
29 30 8.649973 TGTGGTTATGTGTTAAAAACATTTCC 57.350 30.769 9.61 11.70 44.35 3.13
88 89 5.365021 TCCAAAATTTCCAAACATGTGGT 57.635 34.783 0.00 0.00 39.88 4.16
89 90 5.749462 TCCAAAATTTCCAAACATGTGGTT 58.251 33.333 0.00 0.00 42.98 3.67
90 91 6.889198 TCCAAAATTTCCAAACATGTGGTTA 58.111 32.000 0.00 0.00 39.29 2.85
114 115 0.389757 TTTAAAACAGGTTGCGCCCC 59.610 50.000 4.18 4.73 38.26 5.80
159 160 7.594758 GCAGTTGCACTAAAATAGATGTCAAAA 59.405 33.333 0.00 0.00 41.59 2.44
160 161 9.121517 CAGTTGCACTAAAATAGATGTCAAAAG 57.878 33.333 0.00 0.00 0.00 2.27
172 173 5.245531 AGATGTCAAAAGAAATAGCGGTGA 58.754 37.500 0.00 0.00 0.00 4.02
205 211 1.549203 ACAAATAACCAGCCAGCCAG 58.451 50.000 0.00 0.00 0.00 4.85
206 212 0.174162 CAAATAACCAGCCAGCCAGC 59.826 55.000 0.00 0.00 0.00 4.85
207 213 0.972471 AAATAACCAGCCAGCCAGCC 60.972 55.000 0.00 0.00 0.00 4.85
208 214 2.153898 AATAACCAGCCAGCCAGCCA 62.154 55.000 0.00 0.00 0.00 4.75
209 215 2.563013 ATAACCAGCCAGCCAGCCAG 62.563 60.000 0.00 0.00 0.00 4.85
254 260 5.399013 GGTTGCAGTAAATGAACATGTACC 58.601 41.667 0.00 0.00 33.03 3.34
277 290 1.629013 TGTCTTGCATGACGACGATC 58.371 50.000 23.17 3.33 39.64 3.69
388 401 0.692756 TCCACCCAATCCATCGCCTA 60.693 55.000 0.00 0.00 0.00 3.93
393 406 2.031163 AATCCATCGCCTAGCCGC 59.969 61.111 0.00 0.00 0.00 6.53
394 407 3.537206 AATCCATCGCCTAGCCGCC 62.537 63.158 0.00 0.00 0.00 6.13
411 424 1.379044 CCCCTTGCATCACCTCACC 60.379 63.158 0.00 0.00 0.00 4.02
412 425 1.687612 CCCTTGCATCACCTCACCT 59.312 57.895 0.00 0.00 0.00 4.00
413 426 0.911769 CCCTTGCATCACCTCACCTA 59.088 55.000 0.00 0.00 0.00 3.08
414 427 1.134280 CCCTTGCATCACCTCACCTAG 60.134 57.143 0.00 0.00 0.00 3.02
458 475 2.202932 CCGTTGGATGCCGAGGAG 60.203 66.667 0.00 0.00 0.00 3.69
759 779 0.740737 GCCTCCATCCACCGATTTTG 59.259 55.000 0.00 0.00 0.00 2.44
803 823 1.570813 GGGTTTATACGTACGTGCCC 58.429 55.000 30.25 24.98 0.00 5.36
827 847 0.179056 GCATAAAGGTGGCGAGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
991 1017 1.484240 GAGTGGCTTGCTGGAGATAGT 59.516 52.381 0.00 0.00 0.00 2.12
995 1021 0.543749 GCTTGCTGGAGATAGTGGGT 59.456 55.000 0.00 0.00 0.00 4.51
1467 1493 3.075005 GGCCGTGTCCCTGCTCTA 61.075 66.667 0.00 0.00 0.00 2.43
1725 1751 2.383527 CGTCAAGGCGTGGAAGCTC 61.384 63.158 0.00 0.00 37.29 4.09
2052 2078 2.580601 CGTCGGGTTCCTCAAGGGT 61.581 63.158 0.00 0.00 36.25 4.34
2061 2087 2.750350 CTCAAGGGTCACCGGCTT 59.250 61.111 0.00 0.00 43.47 4.35
2346 2372 1.950909 GAGGAGGACGACGAAGATGAT 59.049 52.381 0.00 0.00 0.00 2.45
2349 2375 2.099263 GGAGGACGACGAAGATGATGAA 59.901 50.000 0.00 0.00 0.00 2.57
2647 2701 5.725110 AATCAGTCGATTTTCCATCTTCG 57.275 39.130 0.00 0.00 38.80 3.79
2713 2770 0.318441 CGGGCTCAGAGTGTCTTTCA 59.682 55.000 0.00 0.00 0.00 2.69
2735 2793 4.671880 TTTTTACGCAGTACAATCGCAT 57.328 36.364 0.00 0.00 45.76 4.73
2743 2801 3.245284 GCAGTACAATCGCATACGTTCAT 59.755 43.478 0.00 0.00 41.18 2.57
2746 2804 6.307077 GCAGTACAATCGCATACGTTCATATA 59.693 38.462 0.00 0.00 41.18 0.86
2749 2807 8.027189 AGTACAATCGCATACGTTCATATACAT 58.973 33.333 0.00 0.00 41.18 2.29
2757 2815 9.887189 CGCATACGTTCATATACATTTATCTTC 57.113 33.333 0.00 0.00 33.53 2.87
2775 2833 3.431912 TCTTCATGAACACACACATACGC 59.568 43.478 3.38 0.00 0.00 4.42
2780 2838 5.584251 TCATGAACACACACATACGCATTAT 59.416 36.000 0.00 0.00 0.00 1.28
2781 2839 5.463499 TGAACACACACATACGCATTATC 57.537 39.130 0.00 0.00 0.00 1.75
2789 2847 6.863645 ACACACATACGCATTATCTCTATGAC 59.136 38.462 0.00 0.00 0.00 3.06
2792 2850 8.961634 ACACATACGCATTATCTCTATGACTAT 58.038 33.333 0.00 0.00 0.00 2.12
2793 2851 9.444534 CACATACGCATTATCTCTATGACTATC 57.555 37.037 0.00 0.00 0.00 2.08
2794 2852 9.178758 ACATACGCATTATCTCTATGACTATCA 57.821 33.333 0.00 0.00 0.00 2.15
2797 2855 8.286191 ACGCATTATCTCTATGACTATCATGA 57.714 34.615 0.00 0.00 37.70 3.07
2798 2856 8.404765 ACGCATTATCTCTATGACTATCATGAG 58.595 37.037 0.09 6.72 37.70 2.90
2799 2857 7.379262 CGCATTATCTCTATGACTATCATGAGC 59.621 40.741 0.09 0.00 37.70 4.26
2800 2858 8.196103 GCATTATCTCTATGACTATCATGAGCA 58.804 37.037 0.09 0.00 37.70 4.26
2804 2862 7.628769 TCTCTATGACTATCATGAGCATCTC 57.371 40.000 0.09 0.00 37.70 2.75
2808 2866 3.505293 TGACTATCATGAGCATCTCCGAG 59.495 47.826 0.09 0.00 34.92 4.63
2812 2870 4.717233 ATCATGAGCATCTCCGAGATAC 57.283 45.455 10.65 5.56 32.12 2.24
2818 2876 1.611006 GCATCTCCGAGATACTGAGCA 59.389 52.381 10.65 0.00 32.12 4.26
2820 2878 3.145286 CATCTCCGAGATACTGAGCAGA 58.855 50.000 10.65 0.00 32.12 4.26
2821 2879 2.566913 TCTCCGAGATACTGAGCAGAC 58.433 52.381 4.21 0.00 31.43 3.51
2822 2880 1.262950 CTCCGAGATACTGAGCAGACG 59.737 57.143 4.21 2.60 0.00 4.18
2823 2881 0.317436 CCGAGATACTGAGCAGACGC 60.317 60.000 4.21 0.00 38.99 5.19
2828 2886 4.614764 CGAGATACTGAGCAGACGCATATT 60.615 45.833 4.21 0.00 42.27 1.28
2833 2891 4.194640 ACTGAGCAGACGCATATTTTGAT 58.805 39.130 4.21 0.00 42.27 2.57
2843 2901 5.694816 ACGCATATTTTGATGTTGACGAAA 58.305 33.333 0.00 0.00 0.00 3.46
2847 2905 7.008176 CGCATATTTTGATGTTGACGAAATCAA 59.992 33.333 4.37 4.37 45.39 2.57
2882 2940 7.713073 CCTTATAGTTGATGGGAAAGTCTTCTC 59.287 40.741 0.00 0.00 32.05 2.87
2883 2941 4.982241 AGTTGATGGGAAAGTCTTCTCA 57.018 40.909 0.00 0.00 46.17 3.27
2884 2942 4.646572 AGTTGATGGGAAAGTCTTCTCAC 58.353 43.478 0.00 0.00 44.92 3.51
2888 2946 3.753294 TGGGAAAGTCTTCTCACACTC 57.247 47.619 0.00 0.00 37.11 3.51
2891 2949 4.103153 TGGGAAAGTCTTCTCACACTCAAT 59.897 41.667 0.00 0.00 37.11 2.57
2903 2961 2.986479 CACACTCAATGAACATCGTCGA 59.014 45.455 0.00 0.00 0.00 4.20
2938 2996 4.965119 AATCCAGAAAAATGCGAGTACC 57.035 40.909 0.00 0.00 0.00 3.34
2942 3000 4.155826 TCCAGAAAAATGCGAGTACCAATG 59.844 41.667 0.00 0.00 0.00 2.82
2958 3016 7.228590 AGTACCAATGCCAAGTCTAAAACTTA 58.771 34.615 0.00 0.00 46.69 2.24
2977 3035 8.966069 AAACTTAAATCCTGATAGGCTAGTTC 57.034 34.615 0.00 0.00 34.61 3.01
2980 3038 7.293535 ACTTAAATCCTGATAGGCTAGTTCCAT 59.706 37.037 0.00 0.00 34.61 3.41
2983 3042 3.898123 TCCTGATAGGCTAGTTCCATCAC 59.102 47.826 0.00 0.00 34.61 3.06
2988 3047 5.880332 TGATAGGCTAGTTCCATCACAAAAC 59.120 40.000 0.00 0.00 0.00 2.43
2990 3049 4.666512 AGGCTAGTTCCATCACAAAACAT 58.333 39.130 0.00 0.00 0.00 2.71
3000 3059 4.931002 CCATCACAAAACATCAAACCATCC 59.069 41.667 0.00 0.00 0.00 3.51
3001 3060 4.599047 TCACAAAACATCAAACCATCCC 57.401 40.909 0.00 0.00 0.00 3.85
3002 3061 3.323403 TCACAAAACATCAAACCATCCCC 59.677 43.478 0.00 0.00 0.00 4.81
3003 3062 3.324556 CACAAAACATCAAACCATCCCCT 59.675 43.478 0.00 0.00 0.00 4.79
3004 3063 3.973305 ACAAAACATCAAACCATCCCCTT 59.027 39.130 0.00 0.00 0.00 3.95
3005 3064 4.202346 ACAAAACATCAAACCATCCCCTTG 60.202 41.667 0.00 0.00 0.00 3.61
3006 3065 2.236489 ACATCAAACCATCCCCTTGG 57.764 50.000 0.00 0.00 42.82 3.61
3012 3071 2.677228 CCATCCCCTTGGTTCGCT 59.323 61.111 0.00 0.00 31.74 4.93
3013 3072 1.452108 CCATCCCCTTGGTTCGCTC 60.452 63.158 0.00 0.00 31.74 5.03
3014 3073 1.815421 CATCCCCTTGGTTCGCTCG 60.815 63.158 0.00 0.00 0.00 5.03
3015 3074 3.682292 ATCCCCTTGGTTCGCTCGC 62.682 63.158 0.00 0.00 0.00 5.03
3016 3075 4.394712 CCCCTTGGTTCGCTCGCT 62.395 66.667 0.00 0.00 0.00 4.93
3017 3076 2.358737 CCCTTGGTTCGCTCGCTT 60.359 61.111 0.00 0.00 0.00 4.68
3018 3077 1.079405 CCCTTGGTTCGCTCGCTTA 60.079 57.895 0.00 0.00 0.00 3.09
3019 3078 1.084370 CCCTTGGTTCGCTCGCTTAG 61.084 60.000 0.00 0.00 0.00 2.18
3020 3079 0.108804 CCTTGGTTCGCTCGCTTAGA 60.109 55.000 0.00 0.00 0.00 2.10
3034 3093 6.382821 CTCGCTTAGAGTGTCTTACTTTTG 57.617 41.667 0.00 0.00 40.53 2.44
3035 3094 4.684703 TCGCTTAGAGTGTCTTACTTTTGC 59.315 41.667 0.00 0.00 40.53 3.68
3036 3095 4.447724 CGCTTAGAGTGTCTTACTTTTGCA 59.552 41.667 0.00 0.00 40.53 4.08
3037 3096 5.612709 CGCTTAGAGTGTCTTACTTTTGCAC 60.613 44.000 0.00 0.00 40.53 4.57
3038 3097 5.236478 GCTTAGAGTGTCTTACTTTTGCACA 59.764 40.000 0.00 0.00 40.53 4.57
3039 3098 6.598753 TTAGAGTGTCTTACTTTTGCACAC 57.401 37.500 0.00 0.00 40.53 3.82
3040 3099 4.513442 AGAGTGTCTTACTTTTGCACACA 58.487 39.130 3.54 0.00 40.53 3.72
3041 3100 4.941263 AGAGTGTCTTACTTTTGCACACAA 59.059 37.500 3.54 0.00 40.53 3.33
3042 3101 4.981794 AGTGTCTTACTTTTGCACACAAC 58.018 39.130 3.54 0.00 39.91 3.32
3043 3102 4.102649 GTGTCTTACTTTTGCACACAACC 58.897 43.478 0.00 0.00 37.81 3.77
3044 3103 3.129638 TGTCTTACTTTTGCACACAACCC 59.870 43.478 0.00 0.00 34.87 4.11
3045 3104 3.129638 GTCTTACTTTTGCACACAACCCA 59.870 43.478 0.00 0.00 34.87 4.51
3046 3105 3.764434 TCTTACTTTTGCACACAACCCAA 59.236 39.130 0.00 0.00 34.87 4.12
3047 3106 2.378445 ACTTTTGCACACAACCCAAC 57.622 45.000 0.00 0.00 34.87 3.77
3048 3107 1.899142 ACTTTTGCACACAACCCAACT 59.101 42.857 0.00 0.00 34.87 3.16
3049 3108 3.093057 ACTTTTGCACACAACCCAACTA 58.907 40.909 0.00 0.00 34.87 2.24
3050 3109 3.119280 ACTTTTGCACACAACCCAACTAC 60.119 43.478 0.00 0.00 34.87 2.73
3051 3110 2.428544 TTGCACACAACCCAACTACT 57.571 45.000 0.00 0.00 0.00 2.57
3052 3111 1.961793 TGCACACAACCCAACTACTC 58.038 50.000 0.00 0.00 0.00 2.59
3053 3112 0.865769 GCACACAACCCAACTACTCG 59.134 55.000 0.00 0.00 0.00 4.18
3054 3113 0.865769 CACACAACCCAACTACTCGC 59.134 55.000 0.00 0.00 0.00 5.03
3055 3114 0.756903 ACACAACCCAACTACTCGCT 59.243 50.000 0.00 0.00 0.00 4.93
3056 3115 1.140252 ACACAACCCAACTACTCGCTT 59.860 47.619 0.00 0.00 0.00 4.68
3057 3116 1.798813 CACAACCCAACTACTCGCTTC 59.201 52.381 0.00 0.00 0.00 3.86
3058 3117 1.692519 ACAACCCAACTACTCGCTTCT 59.307 47.619 0.00 0.00 0.00 2.85
3059 3118 2.288886 ACAACCCAACTACTCGCTTCTC 60.289 50.000 0.00 0.00 0.00 2.87
3060 3119 1.629043 ACCCAACTACTCGCTTCTCA 58.371 50.000 0.00 0.00 0.00 3.27
3061 3120 1.968493 ACCCAACTACTCGCTTCTCAA 59.032 47.619 0.00 0.00 0.00 3.02
3062 3121 2.288886 ACCCAACTACTCGCTTCTCAAC 60.289 50.000 0.00 0.00 0.00 3.18
3063 3122 2.028930 CCCAACTACTCGCTTCTCAACT 60.029 50.000 0.00 0.00 0.00 3.16
3064 3123 3.192844 CCCAACTACTCGCTTCTCAACTA 59.807 47.826 0.00 0.00 0.00 2.24
3065 3124 4.321750 CCCAACTACTCGCTTCTCAACTAA 60.322 45.833 0.00 0.00 0.00 2.24
3066 3125 5.411781 CCAACTACTCGCTTCTCAACTAAT 58.588 41.667 0.00 0.00 0.00 1.73
3067 3126 5.517054 CCAACTACTCGCTTCTCAACTAATC 59.483 44.000 0.00 0.00 0.00 1.75
3076 3135 5.119588 CGCTTCTCAACTAATCAAAACGGTA 59.880 40.000 0.00 0.00 0.00 4.02
3113 3172 9.594936 TTCCTAAGAAAAATAAAGGTCATTCCA 57.405 29.630 0.00 0.00 39.02 3.53
3114 3173 9.594936 TCCTAAGAAAAATAAAGGTCATTCCAA 57.405 29.630 0.00 0.00 39.02 3.53
3133 3192 1.142474 AACGCCGACTCTTAAAACGG 58.858 50.000 0.00 0.00 46.74 4.44
3152 3211 8.658499 AAAACGGACACTACATTTATCTATCC 57.342 34.615 0.00 0.00 0.00 2.59
3194 3253 3.259876 GGGGCACATATATGGAAGTCGTA 59.740 47.826 16.96 0.00 0.00 3.43
3207 3266 2.024176 AGTCGTACATCCAACCATGC 57.976 50.000 0.00 0.00 0.00 4.06
3220 3279 0.891904 ACCATGCCCGCTAAACGTTT 60.892 50.000 18.90 18.90 41.42 3.60
3372 3442 6.883756 TGAATTCAACTAGCACATATGTTCCA 59.116 34.615 5.37 0.00 0.00 3.53
3396 3466 1.001633 GTCCTCTTTAAGTGCCCACGA 59.998 52.381 0.00 0.00 36.20 4.35
3402 3472 0.250124 TTAAGTGCCCACGACCACAG 60.250 55.000 0.00 0.00 34.48 3.66
3412 3482 1.195448 CACGACCACAGTTGCTCAATC 59.805 52.381 0.00 0.00 0.00 2.67
3429 3499 7.889469 TGCTCAATCAAATCTTCTTTAAGCTT 58.111 30.769 3.48 3.48 32.36 3.74
3448 3518 3.120060 GCTTTTCATGAGTTGCTCGATGT 60.120 43.478 0.00 0.00 32.35 3.06
3450 3520 3.317603 TTCATGAGTTGCTCGATGTCA 57.682 42.857 0.00 0.00 32.35 3.58
3464 3534 5.572511 GCTCGATGTCAAATTTGTTAATGCA 59.427 36.000 17.47 8.77 0.00 3.96
3466 3536 7.201461 GCTCGATGTCAAATTTGTTAATGCATT 60.201 33.333 17.56 17.56 0.00 3.56
3467 3537 8.531622 TCGATGTCAAATTTGTTAATGCATTT 57.468 26.923 18.75 1.81 0.00 2.32
3480 3550 6.867816 TGTTAATGCATTTGGACAAACTCATC 59.132 34.615 18.75 0.00 32.51 2.92
3485 3555 5.049167 GCATTTGGACAAACTCATCAAACA 58.951 37.500 0.00 0.00 32.51 2.83
3487 3557 6.867816 GCATTTGGACAAACTCATCAAACATA 59.132 34.615 0.00 0.00 32.51 2.29
3516 3586 7.805071 CGGATTCTAATTTGACAATTGGATAGC 59.195 37.037 10.83 0.00 39.05 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.576873 TCTTGTACAATCGCAAACTTTGGA 59.423 37.500 9.13 0.00 0.00 3.53
28 29 4.854399 TCTTGTACAATCGCAAACTTTGG 58.146 39.130 9.13 0.00 0.00 3.28
29 30 4.911610 CCTCTTGTACAATCGCAAACTTTG 59.088 41.667 9.13 0.00 0.00 2.77
33 34 3.746492 ACTCCTCTTGTACAATCGCAAAC 59.254 43.478 9.13 0.00 0.00 2.93
88 89 4.740695 GCGCAACCTGTTTTAAACACATAA 59.259 37.500 6.41 0.00 36.25 1.90
89 90 4.291783 GCGCAACCTGTTTTAAACACATA 58.708 39.130 6.41 0.00 36.25 2.29
90 91 3.120041 GCGCAACCTGTTTTAAACACAT 58.880 40.909 6.41 0.00 36.25 3.21
114 115 1.258982 GCTATTTCGACATGGAGTGCG 59.741 52.381 0.00 0.00 0.00 5.34
205 211 1.566018 GCGTATATTGGACGGCTGGC 61.566 60.000 0.00 0.00 40.66 4.85
206 212 0.249699 TGCGTATATTGGACGGCTGG 60.250 55.000 0.00 0.00 40.66 4.85
207 213 1.139989 CTGCGTATATTGGACGGCTG 58.860 55.000 0.00 0.00 40.66 4.85
208 214 1.037493 TCTGCGTATATTGGACGGCT 58.963 50.000 0.00 0.00 40.66 5.52
209 215 1.726791 CATCTGCGTATATTGGACGGC 59.273 52.381 0.00 0.00 40.66 5.68
210 216 1.726791 GCATCTGCGTATATTGGACGG 59.273 52.381 0.00 0.00 40.66 4.79
254 260 0.647410 GTCGTCATGCAAGACATCGG 59.353 55.000 20.91 5.72 36.64 4.18
393 406 1.379044 GGTGAGGTGATGCAAGGGG 60.379 63.158 0.00 0.00 0.00 4.79
394 407 0.911769 TAGGTGAGGTGATGCAAGGG 59.088 55.000 0.00 0.00 0.00 3.95
395 408 1.745141 GCTAGGTGAGGTGATGCAAGG 60.745 57.143 0.00 0.00 0.00 3.61
742 759 1.462616 TGCAAAATCGGTGGATGGAG 58.537 50.000 0.00 0.00 31.83 3.86
772 792 0.037605 ATAAACCCGATCGCGATCCC 60.038 55.000 36.16 18.96 40.82 3.85
841 866 4.096003 CTGCCCTACCCACCACCG 62.096 72.222 0.00 0.00 0.00 4.94
991 1017 1.552023 CCCAAAATCCATCACCACCCA 60.552 52.381 0.00 0.00 0.00 4.51
995 1021 0.969917 CCGCCCAAAATCCATCACCA 60.970 55.000 0.00 0.00 0.00 4.17
1107 1133 3.039526 CCCCCTCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1455 1481 3.461773 GCCGCTAGAGCAGGGACA 61.462 66.667 12.28 0.00 42.21 4.02
1773 1799 1.006086 CGTTGACGAGCATGGCATTA 58.994 50.000 0.00 0.00 43.02 1.90
2346 2372 3.304764 CTCGCCGTCGTCGTCTTCA 62.305 63.158 0.71 0.00 36.96 3.02
2361 2387 0.106469 TGTCCTCCATCTCCTCCTCG 60.106 60.000 0.00 0.00 0.00 4.63
2391 2417 1.694169 ATCCACATCGCCCTTCCCT 60.694 57.895 0.00 0.00 0.00 4.20
2403 2429 1.591703 GTCTCTCACGGCATCCACA 59.408 57.895 0.00 0.00 0.00 4.17
2542 2568 0.101399 ACGCGCACTCTCCTAATCAG 59.899 55.000 5.73 0.00 0.00 2.90
2634 2687 2.514458 AGTGGGCGAAGATGGAAAAT 57.486 45.000 0.00 0.00 0.00 1.82
2641 2695 2.243810 GAGAGGATAGTGGGCGAAGAT 58.756 52.381 0.00 0.00 0.00 2.40
2647 2701 1.349357 GGATTGGAGAGGATAGTGGGC 59.651 57.143 0.00 0.00 0.00 5.36
2713 2770 4.671880 TGCGATTGTACTGCGTAAAAAT 57.328 36.364 0.00 0.00 0.00 1.82
2746 2804 7.509141 TGTGTGTGTTCATGAAGATAAATGT 57.491 32.000 8.80 0.00 0.00 2.71
2749 2807 7.623297 GCGTATGTGTGTGTTCATGAAGATAAA 60.623 37.037 8.80 0.00 0.00 1.40
2757 2815 3.745332 ATGCGTATGTGTGTGTTCATG 57.255 42.857 0.00 0.00 0.00 3.07
2780 2838 6.602803 GGAGATGCTCATGATAGTCATAGAGA 59.397 42.308 16.44 2.68 34.28 3.10
2781 2839 6.458615 CGGAGATGCTCATGATAGTCATAGAG 60.459 46.154 0.00 11.58 34.28 2.43
2789 2847 4.987408 ATCTCGGAGATGCTCATGATAG 57.013 45.455 19.31 0.00 32.80 2.08
2792 2850 3.505293 CAGTATCTCGGAGATGCTCATGA 59.495 47.826 28.60 7.78 42.80 3.07
2793 2851 3.505293 TCAGTATCTCGGAGATGCTCATG 59.495 47.826 28.60 20.73 42.80 3.07
2794 2852 3.758023 CTCAGTATCTCGGAGATGCTCAT 59.242 47.826 28.60 11.83 42.80 2.90
2795 2853 3.145286 CTCAGTATCTCGGAGATGCTCA 58.855 50.000 28.60 19.55 42.80 4.26
2796 2854 2.095263 GCTCAGTATCTCGGAGATGCTC 60.095 54.545 28.60 17.62 42.80 4.26
2797 2855 1.885887 GCTCAGTATCTCGGAGATGCT 59.114 52.381 26.61 26.61 46.41 3.79
2798 2856 1.611006 TGCTCAGTATCTCGGAGATGC 59.389 52.381 26.72 25.05 40.01 3.91
2799 2857 3.058293 GTCTGCTCAGTATCTCGGAGATG 60.058 52.174 26.72 14.41 40.01 2.90
2800 2858 3.146066 GTCTGCTCAGTATCTCGGAGAT 58.854 50.000 22.96 22.96 40.01 2.75
2801 2859 2.566913 GTCTGCTCAGTATCTCGGAGA 58.433 52.381 10.62 10.62 40.01 3.71
2804 2862 0.317436 GCGTCTGCTCAGTATCTCGG 60.317 60.000 0.00 0.00 38.39 4.63
2808 2866 5.463392 TCAAAATATGCGTCTGCTCAGTATC 59.537 40.000 0.00 0.00 43.34 2.24
2812 2870 4.034858 ACATCAAAATATGCGTCTGCTCAG 59.965 41.667 0.00 0.00 43.34 3.35
2818 2876 4.629634 TCGTCAACATCAAAATATGCGTCT 59.370 37.500 0.00 0.00 0.00 4.18
2820 2878 4.937696 TCGTCAACATCAAAATATGCGT 57.062 36.364 0.00 0.00 0.00 5.24
2821 2879 6.468637 TGATTTCGTCAACATCAAAATATGCG 59.531 34.615 0.00 0.00 32.78 4.73
2822 2880 7.739022 TGATTTCGTCAACATCAAAATATGC 57.261 32.000 0.00 0.00 32.78 3.14
2847 2905 6.385759 TCCCATCAACTATAAGGTGTATGTGT 59.614 38.462 0.00 0.00 33.77 3.72
2882 2940 2.986479 TCGACGATGTTCATTGAGTGTG 59.014 45.455 6.99 0.00 0.00 3.82
2883 2941 3.297830 TCGACGATGTTCATTGAGTGT 57.702 42.857 6.99 0.00 0.00 3.55
2884 2942 4.645667 TTTCGACGATGTTCATTGAGTG 57.354 40.909 0.00 0.00 0.00 3.51
2888 2946 5.075448 CAGACTTTTCGACGATGTTCATTG 58.925 41.667 0.00 0.00 0.00 2.82
2891 2949 3.972403 TCAGACTTTTCGACGATGTTCA 58.028 40.909 0.00 0.00 0.00 3.18
2958 3016 5.608437 TGATGGAACTAGCCTATCAGGATTT 59.392 40.000 7.41 0.00 37.67 2.17
2977 3035 4.931002 GGATGGTTTGATGTTTTGTGATGG 59.069 41.667 0.00 0.00 0.00 3.51
2980 3038 3.323403 GGGGATGGTTTGATGTTTTGTGA 59.677 43.478 0.00 0.00 0.00 3.58
2983 3042 4.317488 CAAGGGGATGGTTTGATGTTTTG 58.683 43.478 0.00 0.00 0.00 2.44
3000 3059 1.079405 TAAGCGAGCGAACCAAGGG 60.079 57.895 0.00 0.00 0.00 3.95
3001 3060 0.108804 TCTAAGCGAGCGAACCAAGG 60.109 55.000 0.00 0.00 0.00 3.61
3002 3061 1.272781 CTCTAAGCGAGCGAACCAAG 58.727 55.000 0.00 0.00 31.99 3.61
3003 3062 0.601558 ACTCTAAGCGAGCGAACCAA 59.398 50.000 0.00 0.00 43.85 3.67
3004 3063 0.109272 CACTCTAAGCGAGCGAACCA 60.109 55.000 0.00 0.00 43.85 3.67
3005 3064 0.109226 ACACTCTAAGCGAGCGAACC 60.109 55.000 0.00 0.00 43.85 3.62
3006 3065 1.135632 AGACACTCTAAGCGAGCGAAC 60.136 52.381 0.00 0.00 43.85 3.95
3007 3066 1.166129 AGACACTCTAAGCGAGCGAA 58.834 50.000 0.00 0.00 43.85 4.70
3008 3067 1.166129 AAGACACTCTAAGCGAGCGA 58.834 50.000 0.00 0.00 43.85 4.93
3009 3068 2.096174 AGTAAGACACTCTAAGCGAGCG 59.904 50.000 0.00 0.00 43.85 5.03
3010 3069 3.768468 AGTAAGACACTCTAAGCGAGC 57.232 47.619 0.00 0.00 43.85 5.03
3011 3070 5.164041 GCAAAAGTAAGACACTCTAAGCGAG 60.164 44.000 0.00 0.00 45.56 5.03
3012 3071 4.684703 GCAAAAGTAAGACACTCTAAGCGA 59.315 41.667 0.00 0.00 36.04 4.93
3013 3072 4.447724 TGCAAAAGTAAGACACTCTAAGCG 59.552 41.667 0.00 0.00 36.04 4.68
3014 3073 5.236478 TGTGCAAAAGTAAGACACTCTAAGC 59.764 40.000 0.00 0.00 36.04 3.09
3015 3074 6.257849 TGTGTGCAAAAGTAAGACACTCTAAG 59.742 38.462 0.00 0.00 38.19 2.18
3016 3075 6.110033 TGTGTGCAAAAGTAAGACACTCTAA 58.890 36.000 0.00 0.00 38.19 2.10
3017 3076 5.666462 TGTGTGCAAAAGTAAGACACTCTA 58.334 37.500 0.00 0.00 38.19 2.43
3018 3077 4.513442 TGTGTGCAAAAGTAAGACACTCT 58.487 39.130 0.00 0.00 38.19 3.24
3019 3078 4.875544 TGTGTGCAAAAGTAAGACACTC 57.124 40.909 0.00 0.00 38.19 3.51
3020 3079 4.142469 GGTTGTGTGCAAAAGTAAGACACT 60.142 41.667 0.00 0.00 38.19 3.55
3021 3080 4.102649 GGTTGTGTGCAAAAGTAAGACAC 58.897 43.478 0.00 0.00 36.22 3.67
3022 3081 3.129638 GGGTTGTGTGCAAAAGTAAGACA 59.870 43.478 0.00 0.00 36.22 3.41
3023 3082 3.129638 TGGGTTGTGTGCAAAAGTAAGAC 59.870 43.478 0.00 0.00 36.22 3.01
3024 3083 3.357203 TGGGTTGTGTGCAAAAGTAAGA 58.643 40.909 0.00 0.00 36.22 2.10
3025 3084 3.791973 TGGGTTGTGTGCAAAAGTAAG 57.208 42.857 0.00 0.00 36.22 2.34
3026 3085 3.511934 AGTTGGGTTGTGTGCAAAAGTAA 59.488 39.130 0.00 0.00 36.22 2.24
3027 3086 3.093057 AGTTGGGTTGTGTGCAAAAGTA 58.907 40.909 0.00 0.00 36.22 2.24
3028 3087 1.899142 AGTTGGGTTGTGTGCAAAAGT 59.101 42.857 0.00 0.00 36.22 2.66
3029 3088 2.671130 AGTTGGGTTGTGTGCAAAAG 57.329 45.000 0.00 0.00 36.22 2.27
3030 3089 3.093057 AGTAGTTGGGTTGTGTGCAAAA 58.907 40.909 0.00 0.00 36.22 2.44
3031 3090 2.685897 GAGTAGTTGGGTTGTGTGCAAA 59.314 45.455 0.00 0.00 36.22 3.68
3032 3091 2.294074 GAGTAGTTGGGTTGTGTGCAA 58.706 47.619 0.00 0.00 0.00 4.08
3033 3092 1.808512 CGAGTAGTTGGGTTGTGTGCA 60.809 52.381 0.00 0.00 0.00 4.57
3034 3093 0.865769 CGAGTAGTTGGGTTGTGTGC 59.134 55.000 0.00 0.00 0.00 4.57
3035 3094 0.865769 GCGAGTAGTTGGGTTGTGTG 59.134 55.000 0.00 0.00 0.00 3.82
3036 3095 0.756903 AGCGAGTAGTTGGGTTGTGT 59.243 50.000 0.00 0.00 0.00 3.72
3037 3096 1.798813 GAAGCGAGTAGTTGGGTTGTG 59.201 52.381 0.00 0.00 0.00 3.33
3038 3097 1.692519 AGAAGCGAGTAGTTGGGTTGT 59.307 47.619 0.00 0.00 0.00 3.32
3039 3098 2.288825 TGAGAAGCGAGTAGTTGGGTTG 60.289 50.000 0.00 0.00 0.00 3.77
3040 3099 1.968493 TGAGAAGCGAGTAGTTGGGTT 59.032 47.619 0.00 0.00 0.00 4.11
3041 3100 1.629043 TGAGAAGCGAGTAGTTGGGT 58.371 50.000 0.00 0.00 0.00 4.51
3042 3101 2.028930 AGTTGAGAAGCGAGTAGTTGGG 60.029 50.000 0.00 0.00 0.00 4.12
3043 3102 3.305398 AGTTGAGAAGCGAGTAGTTGG 57.695 47.619 0.00 0.00 0.00 3.77
3044 3103 6.093404 TGATTAGTTGAGAAGCGAGTAGTTG 58.907 40.000 0.00 0.00 0.00 3.16
3045 3104 6.268825 TGATTAGTTGAGAAGCGAGTAGTT 57.731 37.500 0.00 0.00 0.00 2.24
3046 3105 5.899120 TGATTAGTTGAGAAGCGAGTAGT 57.101 39.130 0.00 0.00 0.00 2.73
3047 3106 7.449027 GTTTTGATTAGTTGAGAAGCGAGTAG 58.551 38.462 0.00 0.00 0.00 2.57
3048 3107 6.089016 CGTTTTGATTAGTTGAGAAGCGAGTA 59.911 38.462 0.00 0.00 0.00 2.59
3049 3108 5.107453 CGTTTTGATTAGTTGAGAAGCGAGT 60.107 40.000 0.00 0.00 0.00 4.18
3050 3109 5.308927 CGTTTTGATTAGTTGAGAAGCGAG 58.691 41.667 0.00 0.00 0.00 5.03
3051 3110 4.151689 CCGTTTTGATTAGTTGAGAAGCGA 59.848 41.667 0.00 0.00 0.00 4.93
3052 3111 4.084013 ACCGTTTTGATTAGTTGAGAAGCG 60.084 41.667 0.00 0.00 0.00 4.68
3053 3112 5.358298 ACCGTTTTGATTAGTTGAGAAGC 57.642 39.130 0.00 0.00 0.00 3.86
3054 3113 9.968743 GTTATACCGTTTTGATTAGTTGAGAAG 57.031 33.333 0.00 0.00 0.00 2.85
3055 3114 9.491675 TGTTATACCGTTTTGATTAGTTGAGAA 57.508 29.630 0.00 0.00 0.00 2.87
3056 3115 9.146984 CTGTTATACCGTTTTGATTAGTTGAGA 57.853 33.333 0.00 0.00 0.00 3.27
3057 3116 8.932791 ACTGTTATACCGTTTTGATTAGTTGAG 58.067 33.333 0.00 0.00 0.00 3.02
3058 3117 8.836268 ACTGTTATACCGTTTTGATTAGTTGA 57.164 30.769 0.00 0.00 0.00 3.18
3065 3124 9.457436 AGGAATTAACTGTTATACCGTTTTGAT 57.543 29.630 0.37 0.00 28.66 2.57
3066 3125 8.851541 AGGAATTAACTGTTATACCGTTTTGA 57.148 30.769 0.37 0.00 28.66 2.69
3100 3159 1.807742 CGGCGTTTGGAATGACCTTTA 59.192 47.619 0.00 0.00 39.86 1.85
3111 3170 2.660900 CGTTTTAAGAGTCGGCGTTTGG 60.661 50.000 6.85 0.00 0.00 3.28
3113 3172 1.528161 CCGTTTTAAGAGTCGGCGTTT 59.472 47.619 6.85 0.00 36.68 3.60
3114 3173 1.142474 CCGTTTTAAGAGTCGGCGTT 58.858 50.000 6.85 0.00 36.68 4.84
3151 3210 2.475864 CGGACGATTCTCGACTAGTAGG 59.524 54.545 0.00 0.00 43.74 3.18
3152 3211 2.475864 CCGGACGATTCTCGACTAGTAG 59.524 54.545 0.00 0.00 43.74 2.57
3161 3220 2.202892 GTGCCCCGGACGATTCTC 60.203 66.667 0.73 0.00 0.00 2.87
3165 3224 1.207089 CATATATGTGCCCCGGACGAT 59.793 52.381 0.73 0.00 0.00 3.73
3168 3227 0.981183 TCCATATATGTGCCCCGGAC 59.019 55.000 0.73 0.00 0.00 4.79
3194 3253 1.920734 TAGCGGGCATGGTTGGATGT 61.921 55.000 0.00 0.00 0.00 3.06
3207 3266 2.549329 ACAAAGGTAAACGTTTAGCGGG 59.451 45.455 32.68 27.92 46.52 6.13
3372 3442 1.351350 GGGCACTTAAAGAGGACACCT 59.649 52.381 0.00 0.00 36.03 4.00
3396 3466 4.147321 AGATTTGATTGAGCAACTGTGGT 58.853 39.130 0.00 0.00 38.47 4.16
3402 3472 7.811713 AGCTTAAAGAAGATTTGATTGAGCAAC 59.188 33.333 0.00 0.00 35.71 4.17
3429 3499 3.663025 TGACATCGAGCAACTCATGAAA 58.337 40.909 0.00 0.00 0.00 2.69
3448 3518 8.442632 TTGTCCAAATGCATTAACAAATTTGA 57.557 26.923 24.64 2.69 40.73 2.69
3450 3520 8.901793 AGTTTGTCCAAATGCATTAACAAATTT 58.098 25.926 30.09 23.53 37.77 1.82
3464 3534 7.092716 GCTATGTTTGATGAGTTTGTCCAAAT 58.907 34.615 0.00 0.00 32.36 2.32
3466 3536 5.048083 GGCTATGTTTGATGAGTTTGTCCAA 60.048 40.000 0.00 0.00 0.00 3.53
3467 3537 4.458989 GGCTATGTTTGATGAGTTTGTCCA 59.541 41.667 0.00 0.00 0.00 4.02
3480 3550 6.912591 GTCAAATTAGAATCCGGCTATGTTTG 59.087 38.462 0.00 7.84 31.79 2.93
3485 3555 7.255590 CCAATTGTCAAATTAGAATCCGGCTAT 60.256 37.037 4.43 0.00 34.14 2.97
3487 3557 5.163519 CCAATTGTCAAATTAGAATCCGGCT 60.164 40.000 4.43 0.00 34.14 5.52


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

AutoCloner maintained by Alex Coulton.