Multiple sequence alignment - TraesCS7A01G188100

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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 TraesCS7A01G188100 chr7A 100.000 3666 0 0 1 3666 144127052 144130717 0.000000e+00 6770
1 TraesCS7A01G188100 chr7B 94.168 2469 108 12 396 2847 106773815 106776264 0.000000e+00 3729
2 TraesCS7A01G188100 chr7B 81.649 485 56 22 2921 3399 106776261 106776718 4.470000e-99 372
3 TraesCS7A01G188100 chr7B 88.934 244 20 6 2 243 106773576 106773814 9.960000e-76 294
4 TraesCS7A01G188100 chr7D 95.032 1711 69 10 1143 2847 141634147 141632447 0.000000e+00 2675
5 TraesCS7A01G188100 chr7D 96.077 1198 34 8 1 1189 141635337 141634144 0.000000e+00 1940
6 TraesCS7A01G188100 chr7D 87.966 349 27 7 3314 3657 141631961 141631623 7.380000e-107 398
7 TraesCS7A01G188100 chr7D 83.171 410 20 28 2923 3313 141632445 141632066 2.730000e-86 329
8 TraesCS7A01G188100 chr7D 86.452 155 17 4 241 394 507424552 507424703 2.260000e-37 167
9 TraesCS7A01G188100 chr7D 97.059 68 0 2 2857 2922 623848548 623848615 2.990000e-21 113
10 TraesCS7A01G188100 chr2B 86.765 204 22 5 3426 3626 540439007 540438806 4.760000e-54 222
11 TraesCS7A01G188100 chr2B 97.059 68 0 2 2857 2923 36604112 36604178 2.990000e-21 113
12 TraesCS7A01G188100 chr2D 90.323 155 11 3 241 394 467062614 467062463 2.230000e-47 200
13 TraesCS7A01G188100 chr6A 93.333 135 8 1 261 394 99403047 99403181 8.030000e-47 198
14 TraesCS7A01G188100 chr6A 88.961 154 13 3 242 394 570942745 570942895 1.740000e-43 187
15 TraesCS7A01G188100 chr6B 89.610 154 13 2 242 394 641305433 641305584 3.740000e-45 193
16 TraesCS7A01G188100 chr2A 89.189 148 13 3 247 393 694587351 694587206 8.090000e-42 182
17 TraesCS7A01G188100 chr2A 92.105 76 6 0 2857 2932 562095123 562095048 1.390000e-19 108
18 TraesCS7A01G188100 chr2A 90.361 83 4 3 2844 2922 461399492 461399574 5.010000e-19 106
19 TraesCS7A01G188100 chr5D 88.591 149 14 2 252 399 61714062 61713916 1.050000e-40 178
20 TraesCS7A01G188100 chr5D 88.506 87 4 3 2844 2924 501203833 501203747 2.330000e-17 100
21 TraesCS7A01G188100 chr5B 90.769 130 11 1 248 377 230883390 230883518 4.870000e-39 172
22 TraesCS7A01G188100 chr5A 78.082 219 37 11 3416 3626 676971220 676971005 1.070000e-25 128
23 TraesCS7A01G188100 chr6D 95.775 71 2 1 2857 2926 387886008 387886078 2.990000e-21 113
24 TraesCS7A01G188100 chr4D 94.366 71 3 1 2857 2926 236940145 236940215 1.390000e-19 108
25 TraesCS7A01G188100 chr3D 94.366 71 3 1 2853 2922 107462705 107462635 1.390000e-19 108
26 TraesCS7A01G188100 chr3B 87.368 95 6 3 2836 2924 828795271 828795177 1.800000e-18 104


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 TraesCS7A01G188100 chr7A 144127052 144130717 3665 False 6770.0 6770 100.000000 1 3666 1 chr7A.!!$F1 3665
1 TraesCS7A01G188100 chr7B 106773576 106776718 3142 False 1465.0 3729 88.250333 2 3399 3 chr7B.!!$F1 3397
2 TraesCS7A01G188100 chr7D 141631623 141635337 3714 True 1335.5 2675 90.561500 1 3657 4 chr7D.!!$R1 3656

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
676 681 1.41271 AGAAGACGGAGCAACTTCACA 59.587 47.619 0.0 0.0 41.37 3.58 F
1269 1325 0.03601 AAGGAGGATGGTTGAGCGTG 60.036 55.000 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 1984 0.046397 AGTTGGGGGAGGCTAGGATT 59.954 55.0 0.0 0.0 0.0 3.01 R
3188 3263 0.035630 GAGCACTGCCTCATTCCACT 60.036 55.0 0.0 0.0 0.0 4.00 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
140 143 9.716507 CGTTGATTTATAATTTACTGTTCTGGG 57.283 33.333 0.00 0.00 0.00 4.45
153 156 9.575868 TTTACTGTTCTGGGTTTATTCACATTA 57.424 29.630 0.00 0.00 0.00 1.90
208 211 5.928976 TGCTTGGCTGTTGAGTATGTATAT 58.071 37.500 0.00 0.00 0.00 0.86
209 212 5.759763 TGCTTGGCTGTTGAGTATGTATATG 59.240 40.000 0.00 0.00 0.00 1.78
251 254 7.626390 TGAATAATTTGTATATACCCCCTCCG 58.374 38.462 10.38 0.00 0.00 4.63
390 393 8.525290 AAACATCTTATATTTGTGAAGGAGGG 57.475 34.615 0.00 0.00 0.00 4.30
392 395 7.512992 ACATCTTATATTTGTGAAGGAGGGAG 58.487 38.462 0.00 0.00 0.00 4.30
394 397 6.889198 TCTTATATTTGTGAAGGAGGGAGTG 58.111 40.000 0.00 0.00 0.00 3.51
676 681 1.412710 AGAAGACGGAGCAACTTCACA 59.587 47.619 0.00 0.00 41.37 3.58
757 770 2.239907 GGGGCATGTATCCTTAGATCCC 59.760 54.545 0.00 0.00 33.67 3.85
781 794 6.219473 CCAGCCTCTTGTACATATCTGTTAG 58.781 44.000 0.00 0.00 36.79 2.34
847 860 2.099756 GCAACTCCAGTCAGTGCTTTTT 59.900 45.455 0.00 0.00 0.00 1.94
970 983 6.716934 TTAAAAGGCAAGGTAATGAACACA 57.283 33.333 0.00 0.00 0.00 3.72
1019 1032 1.405821 GATGGACACCAGTACTCCTCG 59.594 57.143 0.00 0.00 36.75 4.63
1103 1116 7.645058 TCTTCCATTCTTTCTCTGTTTTTGT 57.355 32.000 0.00 0.00 0.00 2.83
1116 1129 5.581605 TCTGTTTTTGTTCAAGCATGAGAC 58.418 37.500 0.00 0.00 36.78 3.36
1124 1137 3.606595 TCAAGCATGAGACTGGAGAAG 57.393 47.619 0.00 0.00 0.00 2.85
1186 1242 8.494433 TCATATGTCCTCTTTAACCTTGCTAAT 58.506 33.333 1.90 0.00 0.00 1.73
1269 1325 0.036010 AAGGAGGATGGTTGAGCGTG 60.036 55.000 0.00 0.00 0.00 5.34
1284 1340 1.535462 AGCGTGCTTATGTTCACAACC 59.465 47.619 0.00 0.00 33.03 3.77
1291 1347 4.764308 TGCTTATGTTCACAACCATAGCAA 59.236 37.500 0.00 0.00 0.00 3.91
1293 1349 6.601217 TGCTTATGTTCACAACCATAGCAATA 59.399 34.615 0.00 0.00 0.00 1.90
1320 1376 3.431486 GCTTCTACACTGGGATTCTCCTG 60.431 52.174 0.00 0.00 36.57 3.86
1515 1571 0.321564 TCGACTTCCATGTTGCTGGG 60.322 55.000 0.00 0.00 36.89 4.45
1567 1623 3.569701 TCTGATTTTCAGCCTGTTGGTTC 59.430 43.478 0.00 0.00 43.95 3.62
1651 1707 0.248661 CTCCGTCATTCTCATCGCGT 60.249 55.000 5.77 0.00 0.00 6.01
1741 1797 1.678101 GTATTCCAACTGCCATGAGCC 59.322 52.381 0.00 0.00 42.71 4.70
1770 1826 2.596923 TGTTTCAGCGGCCATGCA 60.597 55.556 2.24 0.00 37.31 3.96
1809 1865 3.567164 ACACTGGAATGAGCAACAGAAAG 59.433 43.478 0.00 0.00 35.08 2.62
1897 1953 6.158598 AGCAAATATAACTTTTGTGTGGCAG 58.841 36.000 0.00 0.00 36.63 4.85
1939 1995 0.105039 CCACGACCAATCCTAGCCTC 59.895 60.000 0.00 0.00 0.00 4.70
2044 2100 0.723414 CATGTTGTAGCAGCACTCCG 59.277 55.000 0.00 0.00 0.00 4.63
2099 2156 4.275936 CCCATTACATAAAGCTGCAGTACC 59.724 45.833 16.64 0.00 0.00 3.34
2188 2245 3.896272 TCATCATCTGCACTCTCAGCTAT 59.104 43.478 0.00 0.00 34.19 2.97
2191 2248 1.117994 TCTGCACTCTCAGCTATGGG 58.882 55.000 0.00 0.00 34.19 4.00
2308 2365 3.461061 CATCTACACCACGCTGATCAAT 58.539 45.455 0.00 0.00 0.00 2.57
2338 2395 4.299547 TTCGCGCTGCTGGTCACT 62.300 61.111 5.56 0.00 0.00 3.41
2392 2449 2.644992 GGCAAGAACAAGGCCGTG 59.355 61.111 17.83 17.83 38.04 4.94
2521 2578 1.450848 CACGATGCTGCTCCCATGT 60.451 57.895 0.00 0.00 0.00 3.21
2623 2680 1.373812 GGTAGGGCTTGTGGTCGTT 59.626 57.895 0.00 0.00 0.00 3.85
2725 2782 4.483950 TGCAGTGGAGCCTATTCTAGTAT 58.516 43.478 0.00 0.00 0.00 2.12
2776 2833 5.897250 TCTGTACCTATGTTCTGGCAAGATA 59.103 40.000 0.00 0.00 30.72 1.98
2806 2868 7.676683 AGGAATTTAGCTTACATAGGACTGA 57.323 36.000 0.00 0.00 0.00 3.41
2848 2913 8.228035 AGATGTGTAGTATTGAGACTTACTCC 57.772 38.462 0.00 0.00 44.34 3.85
2849 2914 6.770746 TGTGTAGTATTGAGACTTACTCCC 57.229 41.667 0.00 0.00 44.34 4.30
2850 2915 6.491383 TGTGTAGTATTGAGACTTACTCCCT 58.509 40.000 0.00 0.00 44.34 4.20
2851 2916 6.952358 TGTGTAGTATTGAGACTTACTCCCTT 59.048 38.462 0.00 0.00 44.34 3.95
2852 2917 7.122353 TGTGTAGTATTGAGACTTACTCCCTTC 59.878 40.741 0.00 0.00 44.34 3.46
2853 2918 5.838531 AGTATTGAGACTTACTCCCTTCG 57.161 43.478 0.00 0.00 44.34 3.79
2854 2919 5.262804 AGTATTGAGACTTACTCCCTTCGT 58.737 41.667 0.00 0.00 44.34 3.85
2855 2920 5.715753 AGTATTGAGACTTACTCCCTTCGTT 59.284 40.000 0.00 0.00 44.34 3.85
2856 2921 6.888632 AGTATTGAGACTTACTCCCTTCGTTA 59.111 38.462 0.00 0.00 44.34 3.18
2857 2922 6.793505 ATTGAGACTTACTCCCTTCGTTAT 57.206 37.500 0.00 0.00 44.34 1.89
2858 2923 7.893124 ATTGAGACTTACTCCCTTCGTTATA 57.107 36.000 0.00 0.00 44.34 0.98
2859 2924 7.893124 TTGAGACTTACTCCCTTCGTTATAT 57.107 36.000 0.00 0.00 44.34 0.86
2860 2925 8.985315 TTGAGACTTACTCCCTTCGTTATATA 57.015 34.615 0.00 0.00 44.34 0.86
2861 2926 8.985315 TGAGACTTACTCCCTTCGTTATATAA 57.015 34.615 0.00 0.00 44.34 0.98
2862 2927 9.064706 TGAGACTTACTCCCTTCGTTATATAAG 57.935 37.037 0.00 0.00 44.34 1.73
2863 2928 9.282569 GAGACTTACTCCCTTCGTTATATAAGA 57.717 37.037 0.00 0.00 39.53 2.10
2864 2929 9.287373 AGACTTACTCCCTTCGTTATATAAGAG 57.713 37.037 0.00 1.03 0.00 2.85
2865 2930 8.993404 ACTTACTCCCTTCGTTATATAAGAGT 57.007 34.615 13.96 13.96 37.18 3.24
2866 2931 8.848182 ACTTACTCCCTTCGTTATATAAGAGTG 58.152 37.037 16.99 8.46 35.18 3.51
2867 2932 8.757982 TTACTCCCTTCGTTATATAAGAGTGT 57.242 34.615 16.99 2.05 35.18 3.55
2868 2933 7.657023 ACTCCCTTCGTTATATAAGAGTGTT 57.343 36.000 10.42 0.00 32.37 3.32
2869 2934 8.075761 ACTCCCTTCGTTATATAAGAGTGTTT 57.924 34.615 10.42 0.00 32.37 2.83
2870 2935 8.537858 ACTCCCTTCGTTATATAAGAGTGTTTT 58.462 33.333 10.42 0.00 32.37 2.43
2871 2936 9.379791 CTCCCTTCGTTATATAAGAGTGTTTTT 57.620 33.333 0.00 0.00 0.00 1.94
2872 2937 9.158233 TCCCTTCGTTATATAAGAGTGTTTTTG 57.842 33.333 0.00 0.00 0.00 2.44
2873 2938 9.158233 CCCTTCGTTATATAAGAGTGTTTTTGA 57.842 33.333 0.00 0.00 0.00 2.69
2874 2939 9.968743 CCTTCGTTATATAAGAGTGTTTTTGAC 57.031 33.333 0.00 0.00 0.00 3.18
2887 2952 7.859325 AGTGTTTTTGACATTACACTAGTGT 57.141 32.000 30.13 30.13 46.72 3.55
2888 2953 8.951787 AGTGTTTTTGACATTACACTAGTGTA 57.048 30.769 27.99 27.99 46.72 2.90
2904 2969 9.649167 ACACTAGTGTAAAAACGCTCTTATATT 57.351 29.630 26.91 0.00 42.90 1.28
2909 2974 9.052759 AGTGTAAAAACGCTCTTATATTATGGG 57.947 33.333 0.00 0.00 0.00 4.00
2910 2975 9.048446 GTGTAAAAACGCTCTTATATTATGGGA 57.952 33.333 0.00 0.00 0.00 4.37
2911 2976 9.048446 TGTAAAAACGCTCTTATATTATGGGAC 57.952 33.333 0.00 0.00 0.00 4.46
3000 3065 1.270041 GCCTGATGTCTAGCTAGTGGC 60.270 57.143 20.10 18.33 42.19 5.01
3012 3077 1.198637 GCTAGTGGCTGTTTCTTGCTG 59.801 52.381 0.00 0.00 38.06 4.41
3013 3078 1.198637 CTAGTGGCTGTTTCTTGCTGC 59.801 52.381 0.00 0.00 0.00 5.25
3016 3081 1.372623 GGCTGTTTCTTGCTGCTGC 60.373 57.895 8.89 8.89 40.20 5.25
3018 3083 0.386985 GCTGTTTCTTGCTGCTGCTC 60.387 55.000 17.00 0.00 40.48 4.26
3022 3087 0.885879 TTTCTTGCTGCTGCTCATGG 59.114 50.000 17.00 2.92 40.48 3.66
3044 3109 3.067320 GTCAGCAGAGTTTCAGCCTTTTT 59.933 43.478 0.00 0.00 28.14 1.94
3045 3110 3.316308 TCAGCAGAGTTTCAGCCTTTTTC 59.684 43.478 0.00 0.00 28.14 2.29
3047 3112 3.956848 AGCAGAGTTTCAGCCTTTTTCTT 59.043 39.130 0.00 0.00 28.14 2.52
3048 3113 4.047142 GCAGAGTTTCAGCCTTTTTCTTG 58.953 43.478 0.00 0.00 0.00 3.02
3049 3114 4.047142 CAGAGTTTCAGCCTTTTTCTTGC 58.953 43.478 0.00 0.00 0.00 4.01
3050 3115 3.701040 AGAGTTTCAGCCTTTTTCTTGCA 59.299 39.130 0.00 0.00 0.00 4.08
3051 3116 4.047142 GAGTTTCAGCCTTTTTCTTGCAG 58.953 43.478 0.00 0.00 0.00 4.41
3052 3117 3.701040 AGTTTCAGCCTTTTTCTTGCAGA 59.299 39.130 0.00 0.00 0.00 4.26
3053 3118 4.343239 AGTTTCAGCCTTTTTCTTGCAGAT 59.657 37.500 0.00 0.00 0.00 2.90
3057 3122 5.316167 TCAGCCTTTTTCTTGCAGATAAGA 58.684 37.500 0.00 0.00 35.02 2.10
3134 3208 4.129737 CACCCAGACCGCGACGAT 62.130 66.667 8.23 0.00 0.00 3.73
3140 3215 0.311165 CAGACCGCGACGATAAGGAT 59.689 55.000 8.23 0.00 0.00 3.24
3141 3216 1.534163 CAGACCGCGACGATAAGGATA 59.466 52.381 8.23 0.00 0.00 2.59
3142 3217 2.161808 CAGACCGCGACGATAAGGATAT 59.838 50.000 8.23 0.00 0.00 1.63
3143 3218 2.818432 AGACCGCGACGATAAGGATATT 59.182 45.455 8.23 0.00 0.00 1.28
3144 3219 2.915463 GACCGCGACGATAAGGATATTG 59.085 50.000 8.23 0.00 0.00 1.90
3145 3220 2.259618 CCGCGACGATAAGGATATTGG 58.740 52.381 8.23 0.00 0.00 3.16
3146 3221 2.094906 CCGCGACGATAAGGATATTGGA 60.095 50.000 8.23 0.00 0.00 3.53
3147 3222 3.428999 CCGCGACGATAAGGATATTGGAT 60.429 47.826 8.23 0.00 0.00 3.41
3179 3254 3.584834 CATTCAGGTATGTCGACACACA 58.415 45.455 26.79 8.20 34.48 3.72
3181 3256 1.957877 TCAGGTATGTCGACACACACA 59.042 47.619 26.79 8.32 30.82 3.72
3186 3261 1.215014 ATGTCGACACACACACGCTG 61.215 55.000 22.71 0.00 34.48 5.18
3187 3262 1.587876 GTCGACACACACACGCTGA 60.588 57.895 11.55 0.00 0.00 4.26
3188 3263 1.139947 TCGACACACACACGCTGAA 59.860 52.632 0.00 0.00 0.00 3.02
3192 3284 1.089481 ACACACACACGCTGAAGTGG 61.089 55.000 8.22 1.52 45.80 4.00
3199 3291 1.081892 CACGCTGAAGTGGAATGAGG 58.918 55.000 0.00 0.00 38.40 3.86
3201 3293 0.674581 CGCTGAAGTGGAATGAGGCA 60.675 55.000 0.00 0.00 0.00 4.75
3215 3307 2.980233 GGCAGTGCTCGTGGCTTT 60.980 61.111 16.11 0.00 42.39 3.51
3216 3308 2.558313 GCAGTGCTCGTGGCTTTC 59.442 61.111 8.18 0.00 42.39 2.62
3217 3309 2.970974 GCAGTGCTCGTGGCTTTCC 61.971 63.158 8.18 0.00 42.39 3.13
3218 3310 1.302033 CAGTGCTCGTGGCTTTCCT 60.302 57.895 5.00 0.00 42.39 3.36
3219 3311 1.302033 AGTGCTCGTGGCTTTCCTG 60.302 57.895 5.00 0.00 42.39 3.86
3220 3312 1.301716 GTGCTCGTGGCTTTCCTGA 60.302 57.895 5.00 0.00 42.39 3.86
3221 3313 0.884704 GTGCTCGTGGCTTTCCTGAA 60.885 55.000 5.00 0.00 42.39 3.02
3222 3314 0.603707 TGCTCGTGGCTTTCCTGAAG 60.604 55.000 5.00 0.00 42.39 3.02
3223 3315 0.603975 GCTCGTGGCTTTCCTGAAGT 60.604 55.000 0.00 0.00 37.69 3.01
3224 3316 1.884235 CTCGTGGCTTTCCTGAAGTT 58.116 50.000 0.00 0.00 37.69 2.66
3225 3317 2.870435 GCTCGTGGCTTTCCTGAAGTTA 60.870 50.000 0.00 0.00 37.69 2.24
3226 3318 3.600388 CTCGTGGCTTTCCTGAAGTTAT 58.400 45.455 0.00 0.00 37.69 1.89
3227 3319 3.596214 TCGTGGCTTTCCTGAAGTTATC 58.404 45.455 0.00 0.00 37.69 1.75
3228 3320 3.260884 TCGTGGCTTTCCTGAAGTTATCT 59.739 43.478 0.00 0.00 37.69 1.98
3229 3321 3.372206 CGTGGCTTTCCTGAAGTTATCTG 59.628 47.826 0.00 0.00 37.69 2.90
3230 3322 3.127721 GTGGCTTTCCTGAAGTTATCTGC 59.872 47.826 0.00 0.00 37.69 4.26
3231 3323 3.009473 TGGCTTTCCTGAAGTTATCTGCT 59.991 43.478 0.00 0.00 37.69 4.24
3232 3324 3.625313 GGCTTTCCTGAAGTTATCTGCTC 59.375 47.826 0.00 0.00 37.69 4.26
3268 3360 1.610522 GGTCTGCCCATATGTTGATGC 59.389 52.381 1.24 0.00 0.00 3.91
3275 3367 5.078256 TGCCCATATGTTGATGCATTGATA 58.922 37.500 0.00 0.00 30.88 2.15
3327 3523 9.146984 CCAAAGAAGTACACAATATTAACGAGA 57.853 33.333 0.00 0.00 0.00 4.04
3356 3555 1.396653 ACAATCTGCAGGCATAAGGC 58.603 50.000 15.13 0.00 43.74 4.35
3425 3625 6.879458 GGGTCTTGAGATGTTTGTATGTTAGT 59.121 38.462 0.00 0.00 0.00 2.24
3428 3628 9.088512 GTCTTGAGATGTTTGTATGTTAGTAGG 57.911 37.037 0.00 0.00 0.00 3.18
3437 3637 4.175516 TGTATGTTAGTAGGTTTTCGCCG 58.824 43.478 0.00 0.00 0.00 6.46
3470 3670 0.108472 TCGAGCTTGAGCATCCACAG 60.108 55.000 0.00 0.00 45.16 3.66
3473 3673 2.758089 GCTTGAGCATCCACAGCGG 61.758 63.158 0.00 0.00 41.59 5.52
3490 3690 1.017387 CGGGTTTCCTGCTAATGCTC 58.983 55.000 0.00 0.00 40.48 4.26
3496 3696 4.261801 GTTTCCTGCTAATGCTCCAACTA 58.738 43.478 0.00 0.00 40.48 2.24
3501 3701 2.131183 GCTAATGCTCCAACTAGCTCG 58.869 52.381 0.00 0.00 43.19 5.03
3504 3704 0.461961 ATGCTCCAACTAGCTCGTCC 59.538 55.000 0.00 0.00 43.19 4.79
3514 3714 4.083862 GCTCGTCCCTTTCCCGCT 62.084 66.667 0.00 0.00 0.00 5.52
3534 3734 5.420409 CGCTCCCTTATCTCTGTTAGTTTT 58.580 41.667 0.00 0.00 0.00 2.43
3539 3739 9.589111 CTCCCTTATCTCTGTTAGTTTTAGTTC 57.411 37.037 0.00 0.00 0.00 3.01
3563 3763 5.127194 CCCTTGCTGTGTCTGAACTACTATA 59.873 44.000 0.00 0.00 0.00 1.31
3564 3764 6.183360 CCCTTGCTGTGTCTGAACTACTATAT 60.183 42.308 0.00 0.00 0.00 0.86
3565 3765 7.014326 CCCTTGCTGTGTCTGAACTACTATATA 59.986 40.741 0.00 0.00 0.00 0.86
3566 3766 8.580720 CCTTGCTGTGTCTGAACTACTATATAT 58.419 37.037 0.00 0.00 0.00 0.86
3622 3825 0.753479 TTGTGAGCCCGGCTGAAAAA 60.753 50.000 19.21 3.73 39.88 1.94
3653 3856 0.982673 CGAAGCTTCGTTCTACCACG 59.017 55.000 34.97 11.21 45.09 4.94
3654 3857 1.665161 CGAAGCTTCGTTCTACCACGT 60.665 52.381 34.97 0.00 45.09 4.49
3656 3859 3.568538 GAAGCTTCGTTCTACCACGTTA 58.431 45.455 11.40 0.00 41.16 3.18
3657 3860 3.213249 AGCTTCGTTCTACCACGTTAG 57.787 47.619 0.00 0.00 41.16 2.34
3658 3861 1.652619 GCTTCGTTCTACCACGTTAGC 59.347 52.381 0.00 7.12 41.16 3.09
3659 3862 2.670509 GCTTCGTTCTACCACGTTAGCT 60.671 50.000 12.49 0.00 41.43 3.32
3660 3863 3.426695 GCTTCGTTCTACCACGTTAGCTA 60.427 47.826 12.49 0.00 41.43 3.32
3661 3864 4.726416 CTTCGTTCTACCACGTTAGCTAA 58.274 43.478 0.86 0.86 41.16 3.09
3662 3865 4.083581 TCGTTCTACCACGTTAGCTAAC 57.916 45.455 24.05 24.05 41.16 2.34
3663 3866 3.501828 TCGTTCTACCACGTTAGCTAACA 59.498 43.478 30.63 13.91 41.16 2.41
3664 3867 4.023279 TCGTTCTACCACGTTAGCTAACAA 60.023 41.667 30.63 15.94 41.16 2.83
3665 3868 4.681025 CGTTCTACCACGTTAGCTAACAAA 59.319 41.667 30.63 13.21 35.99 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.530419 GGTGGGAACATGGTGTGCA 60.530 57.895 0.00 0.00 46.14 4.57
114 116 9.716507 CCCAGAACAGTAAATTATAAATCAACG 57.283 33.333 0.00 0.00 0.00 4.10
164 167 4.762251 GCAATGTTCTAGAGGGAAACTGTT 59.238 41.667 0.00 0.00 0.00 3.16
390 393 2.418334 CCCGGTTAGCTAGAAACCACTC 60.418 54.545 20.97 2.07 45.59 3.51
392 395 1.277273 ACCCGGTTAGCTAGAAACCAC 59.723 52.381 20.97 0.58 45.59 4.16
394 397 2.775911 AACCCGGTTAGCTAGAAACC 57.224 50.000 14.48 14.48 42.52 3.27
757 770 4.679373 ACAGATATGTACAAGAGGCTGG 57.321 45.455 0.00 0.00 0.00 4.85
781 794 7.959733 TGTACAATGTATGTTCGATTTCTCAC 58.040 34.615 0.00 0.00 43.63 3.51
856 869 7.014615 CCATCTCTCAAAAAGAAGGGAGAAAAA 59.985 37.037 0.00 0.00 36.09 1.94
970 983 3.768878 AGTAGTGCTGTTGGACTAGACT 58.231 45.455 0.00 0.00 45.47 3.24
1019 1032 1.673329 GGAAGCTCGTCCCAGACTTTC 60.673 57.143 0.00 0.00 0.00 2.62
1103 1116 3.326006 ACTTCTCCAGTCTCATGCTTGAA 59.674 43.478 3.65 0.00 0.00 2.69
1186 1242 9.008965 TGCAAGATAGAAAGTTAATACTGCAAA 57.991 29.630 0.00 0.00 34.01 3.68
1207 1263 4.216257 CGATAATATTCCAACCCCTGCAAG 59.784 45.833 0.00 0.00 0.00 4.01
1269 1325 4.963276 TGCTATGGTTGTGAACATAAGC 57.037 40.909 6.55 6.55 0.00 3.09
1291 1347 6.328672 AGAATCCCAGTGTAGAAGCAGATTAT 59.671 38.462 0.00 0.00 0.00 1.28
1293 1349 4.472833 AGAATCCCAGTGTAGAAGCAGATT 59.527 41.667 0.00 0.00 0.00 2.40
1515 1571 0.455005 GCTTGCCTCCAATCTTGAGC 59.545 55.000 0.00 0.00 0.00 4.26
1567 1623 0.110238 CGAAACCATGTCGTTGGCAG 60.110 55.000 0.00 0.00 40.68 4.85
1651 1707 3.398318 TGCTCCTACCCAGATAACAGA 57.602 47.619 0.00 0.00 0.00 3.41
1741 1797 4.210120 GCCGCTGAAACAGAATGAGTATAG 59.790 45.833 2.81 0.00 39.69 1.31
1770 1826 5.431731 TCCAGTGTATATCATGGGGAAAACT 59.568 40.000 0.00 0.00 33.45 2.66
1809 1865 5.472137 TGCTTTACTTACTGTTGGGAACATC 59.528 40.000 0.00 0.00 41.26 3.06
1886 1942 3.849563 AGTACTAACCTGCCACACAAA 57.150 42.857 0.00 0.00 0.00 2.83
1887 1943 3.118186 ACAAGTACTAACCTGCCACACAA 60.118 43.478 0.00 0.00 0.00 3.33
1897 1953 6.127675 TGGTTTCCAACAAACAAGTACTAACC 60.128 38.462 0.00 2.29 32.04 2.85
1924 1980 1.419720 GGGGGAGGCTAGGATTGGTC 61.420 65.000 0.00 0.00 0.00 4.02
1928 1984 0.046397 AGTTGGGGGAGGCTAGGATT 59.954 55.000 0.00 0.00 0.00 3.01
1939 1995 7.471399 GCAAGATTTAACCATAATAGTTGGGGG 60.471 40.741 0.00 0.00 38.64 5.40
2044 2100 4.593956 ACAGGATTCCAGTTTCCAGAATC 58.406 43.478 5.29 3.87 43.30 2.52
2099 2156 3.354089 AAGCACAAACGTGATTCCTTG 57.646 42.857 0.00 0.00 38.61 3.61
2308 2365 1.952133 CGCGAACTTGGTGAACGGA 60.952 57.895 0.00 0.00 0.00 4.69
2515 2572 1.452651 CAGGTAGCAGGCACATGGG 60.453 63.158 0.00 0.00 0.00 4.00
2521 2578 1.483827 CTGATCTTCAGGTAGCAGGCA 59.516 52.381 0.00 0.00 40.71 4.75
2623 2680 3.241530 AGCGAACTGGAGGTGCCA 61.242 61.111 0.00 0.00 46.96 4.92
2635 2692 1.207811 TGGATGATCTGCTTCAGCGAA 59.792 47.619 0.00 0.00 45.83 4.70
2638 2695 2.485903 CTCTGGATGATCTGCTTCAGC 58.514 52.381 0.00 0.00 42.50 4.26
2800 2862 8.437274 TCTTAGGGATTATTCCTATTCAGTCC 57.563 38.462 0.00 0.00 42.20 3.85
2847 2912 9.158233 TCAAAAACACTCTTATATAACGAAGGG 57.842 33.333 0.00 0.00 0.00 3.95
2848 2913 9.968743 GTCAAAAACACTCTTATATAACGAAGG 57.031 33.333 0.00 0.00 0.00 3.46
2878 2943 9.649167 AATATAAGAGCGTTTTTACACTAGTGT 57.351 29.630 30.13 30.13 46.87 3.55
2883 2948 9.052759 CCCATAATATAAGAGCGTTTTTACACT 57.947 33.333 0.00 0.00 0.00 3.55
2884 2949 9.048446 TCCCATAATATAAGAGCGTTTTTACAC 57.952 33.333 0.00 0.00 0.00 2.90
2885 2950 9.048446 GTCCCATAATATAAGAGCGTTTTTACA 57.952 33.333 0.00 0.00 0.00 2.41
2886 2951 9.048446 TGTCCCATAATATAAGAGCGTTTTTAC 57.952 33.333 0.00 0.00 0.00 2.01
2887 2952 9.268268 CTGTCCCATAATATAAGAGCGTTTTTA 57.732 33.333 0.00 0.00 0.00 1.52
2888 2953 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
2889 2954 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
2890 2955 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
2891 2956 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
2892 2957 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
2893 2958 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
2894 2959 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
2895 2960 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
2896 2961 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
2897 2962 7.896496 AGTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
2898 2963 7.776745 AGTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
2899 2964 7.358255 AGTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
2900 2965 6.234404 AGTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
2901 2966 5.681494 AGTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
2902 2967 4.561254 AGTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
2903 2968 4.264668 TGAAGTACTCCCTCTGTCCCATAA 60.265 45.833 0.00 0.00 0.00 1.90
2904 2969 3.271225 TGAAGTACTCCCTCTGTCCCATA 59.729 47.826 0.00 0.00 0.00 2.74
2905 2970 2.044492 TGAAGTACTCCCTCTGTCCCAT 59.956 50.000 0.00 0.00 0.00 4.00
2906 2971 1.431633 TGAAGTACTCCCTCTGTCCCA 59.568 52.381 0.00 0.00 0.00 4.37
2907 2972 2.104170 CTGAAGTACTCCCTCTGTCCC 58.896 57.143 0.00 0.00 0.00 4.46
2908 2973 3.088789 TCTGAAGTACTCCCTCTGTCC 57.911 52.381 0.00 0.00 0.00 4.02
2909 2974 4.337145 TCTTCTGAAGTACTCCCTCTGTC 58.663 47.826 16.43 0.00 0.00 3.51
2910 2975 4.390129 TCTTCTGAAGTACTCCCTCTGT 57.610 45.455 16.43 0.00 0.00 3.41
2911 2976 5.245075 AGTTTCTTCTGAAGTACTCCCTCTG 59.755 44.000 16.43 0.00 33.28 3.35
2912 2977 5.245075 CAGTTTCTTCTGAAGTACTCCCTCT 59.755 44.000 16.43 3.91 37.61 3.69
2913 2978 5.474825 CAGTTTCTTCTGAAGTACTCCCTC 58.525 45.833 16.43 0.00 37.61 4.30
2914 2979 4.262678 GCAGTTTCTTCTGAAGTACTCCCT 60.263 45.833 16.43 3.84 37.61 4.20
2915 2980 3.997681 GCAGTTTCTTCTGAAGTACTCCC 59.002 47.826 16.43 10.37 37.61 4.30
2916 2981 4.888917 AGCAGTTTCTTCTGAAGTACTCC 58.111 43.478 16.43 11.38 37.61 3.85
2917 2982 5.755861 ACAAGCAGTTTCTTCTGAAGTACTC 59.244 40.000 16.43 13.34 37.61 2.59
2918 2983 5.675538 ACAAGCAGTTTCTTCTGAAGTACT 58.324 37.500 16.43 16.50 37.61 2.73
2919 2984 5.993106 ACAAGCAGTTTCTTCTGAAGTAC 57.007 39.130 16.43 14.81 37.61 2.73
2920 2985 5.989777 GGTACAAGCAGTTTCTTCTGAAGTA 59.010 40.000 16.43 4.97 37.61 2.24
3000 3065 0.949397 TGAGCAGCAGCAAGAAACAG 59.051 50.000 3.17 0.00 45.49 3.16
3016 3081 3.001414 CTGAAACTCTGCTGACCATGAG 58.999 50.000 0.00 0.00 0.00 2.90
3018 3083 1.467734 GCTGAAACTCTGCTGACCATG 59.532 52.381 0.00 0.00 38.17 3.66
3022 3087 1.889545 AAGGCTGAAACTCTGCTGAC 58.110 50.000 5.65 0.00 40.57 3.51
3049 3114 5.702670 TGGAACAGCAGACTTTTCTTATCTG 59.297 40.000 0.00 0.00 42.33 2.90
3050 3115 5.869579 TGGAACAGCAGACTTTTCTTATCT 58.130 37.500 0.00 0.00 33.83 1.98
3051 3116 6.017109 TGTTGGAACAGCAGACTTTTCTTATC 60.017 38.462 0.00 0.00 46.59 1.75
3052 3117 5.827797 TGTTGGAACAGCAGACTTTTCTTAT 59.172 36.000 0.00 0.00 46.59 1.73
3053 3118 5.189928 TGTTGGAACAGCAGACTTTTCTTA 58.810 37.500 0.00 0.00 46.59 2.10
3134 3208 5.414454 GCGCACCAATAATCCAATATCCTTA 59.586 40.000 0.30 0.00 0.00 2.69
3140 3215 4.582240 TGAATGCGCACCAATAATCCAATA 59.418 37.500 14.90 0.00 0.00 1.90
3141 3216 3.384146 TGAATGCGCACCAATAATCCAAT 59.616 39.130 14.90 0.00 0.00 3.16
3142 3217 2.757314 TGAATGCGCACCAATAATCCAA 59.243 40.909 14.90 0.00 0.00 3.53
3143 3218 2.358582 CTGAATGCGCACCAATAATCCA 59.641 45.455 14.90 0.00 0.00 3.41
3144 3219 2.287788 CCTGAATGCGCACCAATAATCC 60.288 50.000 14.90 0.00 0.00 3.01
3145 3220 2.358898 ACCTGAATGCGCACCAATAATC 59.641 45.455 14.90 3.28 0.00 1.75
3146 3221 2.378038 ACCTGAATGCGCACCAATAAT 58.622 42.857 14.90 0.00 0.00 1.28
3147 3222 1.832883 ACCTGAATGCGCACCAATAA 58.167 45.000 14.90 0.00 0.00 1.40
3179 3254 1.609061 CCTCATTCCACTTCAGCGTGT 60.609 52.381 0.00 0.00 33.07 4.49
3181 3256 0.674895 GCCTCATTCCACTTCAGCGT 60.675 55.000 0.00 0.00 0.00 5.07
3186 3261 0.807496 GCACTGCCTCATTCCACTTC 59.193 55.000 0.00 0.00 0.00 3.01
3187 3262 0.403271 AGCACTGCCTCATTCCACTT 59.597 50.000 0.00 0.00 0.00 3.16
3188 3263 0.035630 GAGCACTGCCTCATTCCACT 60.036 55.000 0.00 0.00 0.00 4.00
3192 3284 1.364626 CCACGAGCACTGCCTCATTC 61.365 60.000 0.00 0.00 0.00 2.67
3214 3306 4.780021 AGGAAGAGCAGATAACTTCAGGAA 59.220 41.667 0.00 0.00 40.89 3.36
3215 3307 4.161189 CAGGAAGAGCAGATAACTTCAGGA 59.839 45.833 0.00 0.00 40.89 3.86
3216 3308 4.161189 TCAGGAAGAGCAGATAACTTCAGG 59.839 45.833 0.00 0.00 40.89 3.86
3217 3309 5.336150 TCAGGAAGAGCAGATAACTTCAG 57.664 43.478 0.00 0.00 40.89 3.02
3218 3310 5.247110 ACTTCAGGAAGAGCAGATAACTTCA 59.753 40.000 15.51 0.00 40.89 3.02
3219 3311 5.729510 ACTTCAGGAAGAGCAGATAACTTC 58.270 41.667 15.51 0.00 40.79 3.01
3220 3312 5.753721 ACTTCAGGAAGAGCAGATAACTT 57.246 39.130 15.51 0.00 40.79 2.66
3221 3313 5.753721 AACTTCAGGAAGAGCAGATAACT 57.246 39.130 15.51 0.00 40.79 2.24
3222 3314 7.437862 CAGATAACTTCAGGAAGAGCAGATAAC 59.562 40.741 15.51 0.00 40.79 1.89
3223 3315 7.418368 CCAGATAACTTCAGGAAGAGCAGATAA 60.418 40.741 15.51 0.00 40.79 1.75
3224 3316 6.041409 CCAGATAACTTCAGGAAGAGCAGATA 59.959 42.308 15.51 0.64 40.79 1.98
3225 3317 5.163322 CCAGATAACTTCAGGAAGAGCAGAT 60.163 44.000 15.51 1.91 40.79 2.90
3226 3318 4.161189 CCAGATAACTTCAGGAAGAGCAGA 59.839 45.833 15.51 0.00 40.79 4.26
3227 3319 4.081198 ACCAGATAACTTCAGGAAGAGCAG 60.081 45.833 15.51 0.00 40.79 4.24
3228 3320 3.840666 ACCAGATAACTTCAGGAAGAGCA 59.159 43.478 15.51 1.10 40.79 4.26
3229 3321 4.161377 AGACCAGATAACTTCAGGAAGAGC 59.839 45.833 15.51 0.00 40.79 4.09
3230 3322 5.659463 CAGACCAGATAACTTCAGGAAGAG 58.341 45.833 15.51 0.00 40.79 2.85
3231 3323 4.081420 GCAGACCAGATAACTTCAGGAAGA 60.081 45.833 15.51 0.00 40.79 2.87
3232 3324 4.187694 GCAGACCAGATAACTTCAGGAAG 58.812 47.826 7.47 7.47 43.79 3.46
3268 3360 8.886719 CATGTATTGGTAGGCAGTATATCAATG 58.113 37.037 2.50 0.00 0.00 2.82
3275 3367 5.887214 TGTCATGTATTGGTAGGCAGTAT 57.113 39.130 0.00 0.00 0.00 2.12
3327 3523 3.503748 GCCTGCAGATTGTAACTCTGTTT 59.496 43.478 17.39 0.00 41.77 2.83
3356 3555 1.129209 CGCTGTCGCATATCGCATG 59.871 57.895 0.00 0.00 42.60 4.06
3357 3556 1.278172 GACGCTGTCGCATATCGCAT 61.278 55.000 0.00 0.00 42.60 4.73
3358 3557 1.944184 GACGCTGTCGCATATCGCA 60.944 57.895 0.00 0.00 42.60 5.10
3359 3558 1.870268 CTGACGCTGTCGCATATCGC 61.870 60.000 4.65 0.00 39.84 4.58
3360 3559 1.271446 CCTGACGCTGTCGCATATCG 61.271 60.000 4.65 0.00 39.84 2.92
3361 3560 0.030773 TCCTGACGCTGTCGCATATC 59.969 55.000 4.65 0.00 39.84 1.63
3362 3561 0.031314 CTCCTGACGCTGTCGCATAT 59.969 55.000 4.65 0.00 39.84 1.78
3425 3625 2.739287 CCACGCGGCGAAAACCTA 60.739 61.111 30.94 0.00 0.00 3.08
3428 3628 4.676586 CCACCACGCGGCGAAAAC 62.677 66.667 30.94 0.00 34.57 2.43
3470 3670 1.032114 AGCATTAGCAGGAAACCCGC 61.032 55.000 0.00 0.00 45.49 6.13
3473 3673 2.128771 TGGAGCATTAGCAGGAAACC 57.871 50.000 0.00 0.00 45.49 3.27
3490 3690 1.405661 GGAAAGGGACGAGCTAGTTGG 60.406 57.143 0.00 0.00 0.00 3.77
3496 3696 4.083862 GCGGGAAAGGGACGAGCT 62.084 66.667 0.00 0.00 0.00 4.09
3501 3701 1.269703 TAAGGGAGCGGGAAAGGGAC 61.270 60.000 0.00 0.00 0.00 4.46
3504 3704 1.070914 GAGATAAGGGAGCGGGAAAGG 59.929 57.143 0.00 0.00 0.00 3.11
3514 3714 8.537858 GGAACTAAAACTAACAGAGATAAGGGA 58.462 37.037 0.00 0.00 0.00 4.20
3534 3734 2.325484 TCAGACACAGCAAGGGAACTA 58.675 47.619 0.00 0.00 42.68 2.24
3539 3739 2.037772 AGTAGTTCAGACACAGCAAGGG 59.962 50.000 0.00 0.00 0.00 3.95
3581 3781 8.531146 CACAACCCTTTCCATTAATCACTTAAT 58.469 33.333 0.00 0.00 37.92 1.40
3603 3803 0.753479 TTTTTCAGCCGGGCTCACAA 60.753 50.000 20.97 2.00 36.40 3.33
3622 3825 0.818040 AAGCTTCGCACGGACCTTTT 60.818 50.000 0.00 0.00 0.00 2.27
3625 3828 2.048127 GAAGCTTCGCACGGACCT 60.048 61.111 11.40 0.00 0.00 3.85
3636 3839 2.521105 AACGTGGTAGAACGAAGCTT 57.479 45.000 0.00 0.00 46.49 3.74
3641 3844 3.501828 TGTTAGCTAACGTGGTAGAACGA 59.498 43.478 27.07 6.47 46.49 3.85


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

AutoCloner maintained by Alex Coulton.