Multiple sequence alignment - TraesCS2D01G410900

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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 TraesCS2D01G410900 chr2D 100.000 3917 0 0 1 3917 525938631 525934715 0.000000e+00 7234
1 TraesCS2D01G410900 chr2D 94.329 864 41 6 1 857 69145984 69145122 0.000000e+00 1317
2 TraesCS2D01G410900 chr2D 92.500 880 49 11 1 872 567651811 567650941 0.000000e+00 1243
3 TraesCS2D01G410900 chr2B 93.061 2277 107 25 869 3110 621664610 621666870 0.000000e+00 3282
4 TraesCS2D01G410900 chr2B 94.199 362 17 4 3214 3573 621666865 621667224 2.060000e-152 549
5 TraesCS2D01G410900 chr2B 93.214 280 13 1 3644 3917 621667258 621667537 1.310000e-109 407
6 TraesCS2D01G410900 chr2B 94.828 116 5 1 3109 3223 770902447 770902332 3.110000e-41 180
7 TraesCS2D01G410900 chr2A 91.960 2189 90 23 959 3111 670791891 670794029 0.000000e+00 2988
8 TraesCS2D01G410900 chr2A 92.213 732 28 14 3214 3917 670794027 670794757 0.000000e+00 1009
9 TraesCS2D01G410900 chr2A 88.971 136 11 3 3101 3235 10581245 10581377 8.710000e-37 165
10 TraesCS2D01G410900 chr6A 95.260 865 32 7 1 857 286336299 286335436 0.000000e+00 1362
11 TraesCS2D01G410900 chr6A 92.221 887 49 13 1 871 170016532 170015650 0.000000e+00 1238
12 TraesCS2D01G410900 chr6D 94.792 864 36 7 1 857 455520567 455521428 0.000000e+00 1338
13 TraesCS2D01G410900 chr6D 93.503 862 48 7 1 857 223933580 223932722 0.000000e+00 1275
14 TraesCS2D01G410900 chr6D 93.410 865 45 8 1 857 420557668 420556808 0.000000e+00 1271
15 TraesCS2D01G410900 chr6D 98.131 107 2 0 3109 3215 249445908 249445802 1.860000e-43 187
16 TraesCS2D01G410900 chr1D 94.682 865 35 8 1 857 432633785 432632924 0.000000e+00 1332
17 TraesCS2D01G410900 chr4B 93.496 861 50 4 1 855 538694519 538695379 0.000000e+00 1275
18 TraesCS2D01G410900 chr7B 96.552 116 3 1 3109 3224 420072796 420072682 1.440000e-44 191
19 TraesCS2D01G410900 chr7B 96.396 111 4 0 3105 3215 58656008 58655898 2.400000e-42 183
20 TraesCS2D01G410900 chr4D 95.726 117 5 0 3109 3225 441486814 441486698 5.170000e-44 189
21 TraesCS2D01G410900 chr7D 96.396 111 4 0 3105 3215 478908880 478908770 2.400000e-42 183
22 TraesCS2D01G410900 chr3B 94.118 119 7 0 3108 3226 449155950 449155832 8.650000e-42 182
23 TraesCS2D01G410900 chr5B 94.783 115 6 0 3102 3216 679351531 679351645 3.110000e-41 180


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 TraesCS2D01G410900 chr2D 525934715 525938631 3916 True 7234.000000 7234 100.000000 1 3917 1 chr2D.!!$R2 3916
1 TraesCS2D01G410900 chr2D 69145122 69145984 862 True 1317.000000 1317 94.329000 1 857 1 chr2D.!!$R1 856
2 TraesCS2D01G410900 chr2D 567650941 567651811 870 True 1243.000000 1243 92.500000 1 872 1 chr2D.!!$R3 871
3 TraesCS2D01G410900 chr2B 621664610 621667537 2927 False 1412.666667 3282 93.491333 869 3917 3 chr2B.!!$F1 3048
4 TraesCS2D01G410900 chr2A 670791891 670794757 2866 False 1998.500000 2988 92.086500 959 3917 2 chr2A.!!$F2 2958
5 TraesCS2D01G410900 chr6A 286335436 286336299 863 True 1362.000000 1362 95.260000 1 857 1 chr6A.!!$R2 856
6 TraesCS2D01G410900 chr6A 170015650 170016532 882 True 1238.000000 1238 92.221000 1 871 1 chr6A.!!$R1 870
7 TraesCS2D01G410900 chr6D 455520567 455521428 861 False 1338.000000 1338 94.792000 1 857 1 chr6D.!!$F1 856
8 TraesCS2D01G410900 chr6D 223932722 223933580 858 True 1275.000000 1275 93.503000 1 857 1 chr6D.!!$R1 856
9 TraesCS2D01G410900 chr6D 420556808 420557668 860 True 1271.000000 1271 93.410000 1 857 1 chr6D.!!$R3 856
10 TraesCS2D01G410900 chr1D 432632924 432633785 861 True 1332.000000 1332 94.682000 1 857 1 chr1D.!!$R1 856
11 TraesCS2D01G410900 chr4B 538694519 538695379 860 False 1275.000000 1275 93.496000 1 855 1 chr4B.!!$F1 854

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
159 161 0.252197 GGTGCTCATCCTAAACCGGT 59.748 55.0 0.0 0.0 0.00 5.28 F
1406 1437 1.078759 CAGGTCATCGACGTTCCAGC 61.079 60.0 0.0 0.0 32.65 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 1999 0.777446 AGGCTTGGCAAGGAGGTTTA 59.223 50.0 27.25 0.00 0.00 2.01 R
3199 3300 0.744414 TACGTACTCCCTCCGTTCGG 60.744 60.0 4.74 4.74 36.12 4.30 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
94 96 3.742882 GCATTCCTCCTTTGCTGAAAAAC 59.257 43.478 0.00 0.00 33.61 2.43
159 161 0.252197 GGTGCTCATCCTAAACCGGT 59.748 55.000 0.00 0.00 0.00 5.28
283 285 2.660552 CGAACCACCGTGCTTCGT 60.661 61.111 17.23 0.00 37.94 3.85
348 354 9.406113 CTCCTCTTCCATATCAAATTCTTCTTT 57.594 33.333 0.00 0.00 0.00 2.52
480 486 4.243008 TCGAACACCTTGCGGGCA 62.243 61.111 0.00 0.00 39.10 5.36
778 809 4.622456 CTGTTTTTGCGCGCCCGT 62.622 61.111 30.77 0.00 36.67 5.28
781 812 3.889044 TTTTTGCGCGCCCGTTGA 61.889 55.556 30.77 5.30 36.67 3.18
919 950 6.487299 AGGCTCTAAAGTAATTACTCCAGG 57.513 41.667 18.28 12.19 34.99 4.45
1406 1437 1.078759 CAGGTCATCGACGTTCCAGC 61.079 60.000 0.00 0.00 32.65 4.85
1520 1551 3.104519 TCGGTAGGACCTGATAACCAA 57.895 47.619 3.53 0.00 35.66 3.67
1528 1559 7.396339 GGTAGGACCTGATAACCAATTCTTTTT 59.604 37.037 3.53 0.00 34.73 1.94
1566 1597 5.759506 TTCTTGTTATTTGAAGGCGTGAA 57.240 34.783 0.00 0.00 0.00 3.18
1567 1598 5.103290 TCTTGTTATTTGAAGGCGTGAAC 57.897 39.130 0.00 0.00 0.00 3.18
1587 1618 3.111098 ACGGTGCTATATCGACGTTTTC 58.889 45.455 0.00 0.00 36.11 2.29
1692 1723 6.144724 GTGCACAAGAGTTTGTTTGTTTGTTA 59.855 34.615 13.17 0.00 45.01 2.41
1700 1735 9.915629 AGAGTTTGTTTGTTTGTTACACATTAA 57.084 25.926 0.00 0.00 36.21 1.40
1729 1764 5.865013 ACAAAACCACGTAAAAAGAACAAGG 59.135 36.000 0.00 0.00 0.00 3.61
1769 1804 5.245531 TGGCGATTCAGTTTAATCACTCTT 58.754 37.500 0.00 0.00 35.93 2.85
1824 1859 8.375465 CACTGAAACAAACTGTGAGAAAATTTC 58.625 33.333 0.00 0.00 38.73 2.17
1905 1940 7.121315 GTGCCTAATGAATAACTTCCAAGTCTT 59.879 37.037 0.00 0.00 38.57 3.01
1921 1956 8.251750 TCCAAGTCTTAACATTGTTTATCTCG 57.748 34.615 7.45 0.00 0.00 4.04
1942 1977 2.367567 GTCCTCACACCAACCTCTTGTA 59.632 50.000 0.00 0.00 0.00 2.41
1943 1978 3.042682 TCCTCACACCAACCTCTTGTAA 58.957 45.455 0.00 0.00 0.00 2.41
1944 1979 3.456644 TCCTCACACCAACCTCTTGTAAA 59.543 43.478 0.00 0.00 0.00 2.01
1945 1980 3.564225 CCTCACACCAACCTCTTGTAAAC 59.436 47.826 0.00 0.00 0.00 2.01
1946 1981 4.451900 CTCACACCAACCTCTTGTAAACT 58.548 43.478 0.00 0.00 0.00 2.66
1947 1982 4.850680 TCACACCAACCTCTTGTAAACTT 58.149 39.130 0.00 0.00 0.00 2.66
1948 1983 5.258051 TCACACCAACCTCTTGTAAACTTT 58.742 37.500 0.00 0.00 0.00 2.66
1949 1984 5.712917 TCACACCAACCTCTTGTAAACTTTT 59.287 36.000 0.00 0.00 0.00 2.27
1950 1985 6.209788 TCACACCAACCTCTTGTAAACTTTTT 59.790 34.615 0.00 0.00 0.00 1.94
2013 2071 4.016444 TCTTTGGCAATAAAAGATCCGCT 58.984 39.130 0.00 0.00 38.43 5.52
2025 2083 0.815615 GATCCGCTGTGGTTGATCCC 60.816 60.000 7.20 0.00 39.52 3.85
2027 2085 0.616395 TCCGCTGTGGTTGATCCCTA 60.616 55.000 7.20 0.00 39.52 3.53
2033 2091 3.193479 GCTGTGGTTGATCCCTAAAAAGG 59.807 47.826 0.00 0.00 34.77 3.11
2034 2092 4.662278 CTGTGGTTGATCCCTAAAAAGGA 58.338 43.478 0.00 0.00 37.93 3.36
2067 2125 6.476378 TCTTTTCTTCTTGGAAGATAGGGTG 58.524 40.000 10.23 1.03 34.49 4.61
2068 2126 6.272324 TCTTTTCTTCTTGGAAGATAGGGTGA 59.728 38.462 10.23 2.86 34.49 4.02
2069 2127 5.683876 TTCTTCTTGGAAGATAGGGTGAG 57.316 43.478 10.23 0.00 34.49 3.51
2070 2128 4.689062 TCTTCTTGGAAGATAGGGTGAGT 58.311 43.478 5.96 0.00 34.49 3.41
2096 2154 4.024809 GTGACACAGTTTCTAACTTCCAGC 60.025 45.833 0.00 0.00 40.46 4.85
2111 2169 2.180276 TCCAGCTTCAGTTAGGTCCTC 58.820 52.381 0.00 0.00 0.00 3.71
2146 2204 5.942961 AGAGGAGATTGAGCAAATGATCAT 58.057 37.500 1.18 1.18 40.42 2.45
2153 2211 7.210174 AGATTGAGCAAATGATCATGGATTTG 58.790 34.615 9.46 11.64 40.42 2.32
2241 2300 2.200955 AGAACAGGAGGGGAAGAATCC 58.799 52.381 0.00 0.00 45.77 3.01
2297 2356 2.953466 TTAGCGGTCTCACATGGTAC 57.047 50.000 0.00 0.00 0.00 3.34
2311 2370 4.864916 CATGGTACTGTCATGTTGCTAC 57.135 45.455 0.00 0.00 37.72 3.58
2374 2433 1.182385 TGGATTTGGTTGGCCCGAAC 61.182 55.000 0.00 0.00 39.53 3.95
2376 2435 0.898326 GATTTGGTTGGCCCGAACCT 60.898 55.000 22.04 5.86 45.07 3.50
2460 2535 8.162878 TCTAAATAACACGGGTATCTGAGTAG 57.837 38.462 0.00 0.00 0.00 2.57
2503 2578 8.325046 AGGTGATAATTTTCAGACTAGAAGCTT 58.675 33.333 0.00 0.00 0.00 3.74
2587 2663 3.344515 ACACGGGAGAAAAGCTTAATCC 58.655 45.455 13.55 13.55 0.00 3.01
2611 2710 6.369005 CAAGTGAGCTAGAAAATGACAAGTG 58.631 40.000 0.00 0.00 0.00 3.16
2618 2717 8.396272 AGCTAGAAAATGACAAGTGTAATGTT 57.604 30.769 0.00 0.00 0.00 2.71
2795 2894 5.357878 TCTTTCGCTTTCCTGCAATGATATT 59.642 36.000 0.00 0.00 0.00 1.28
3052 3153 8.790718 CCCTTCATTTTACTATACGACTAGCTA 58.209 37.037 0.00 0.00 0.00 3.32
3089 3190 5.943416 AGGTATGCAGCTAGATACTCTACAG 59.057 44.000 11.98 0.00 0.00 2.74
3098 3199 8.941977 CAGCTAGATACTCTACAGTAGGTAATG 58.058 40.741 7.79 3.59 38.56 1.90
3114 3215 5.417754 GGTAATGCCTATTAGGTACTCCC 57.582 47.826 11.38 4.14 41.75 4.30
3116 3217 5.187381 GGTAATGCCTATTAGGTACTCCCTC 59.813 48.000 11.38 0.00 44.81 4.30
3117 3218 3.255634 TGCCTATTAGGTACTCCCTCC 57.744 52.381 11.38 0.00 44.81 4.30
3118 3219 2.169330 GCCTATTAGGTACTCCCTCCG 58.831 57.143 11.38 0.00 44.81 4.63
3119 3220 2.490535 GCCTATTAGGTACTCCCTCCGT 60.491 54.545 11.38 0.00 44.81 4.69
3120 3221 3.419943 CCTATTAGGTACTCCCTCCGTC 58.580 54.545 1.17 0.00 44.81 4.79
3121 3222 2.378378 ATTAGGTACTCCCTCCGTCC 57.622 55.000 0.00 0.00 44.81 4.79
3122 3223 1.302907 TTAGGTACTCCCTCCGTCCT 58.697 55.000 0.00 0.00 44.81 3.85
3123 3224 0.549950 TAGGTACTCCCTCCGTCCTG 59.450 60.000 0.00 0.00 44.81 3.86
3124 3225 1.212934 AGGTACTCCCTCCGTCCTGA 61.213 60.000 0.00 0.00 40.71 3.86
3125 3226 0.324091 GGTACTCCCTCCGTCCTGAA 60.324 60.000 0.00 0.00 0.00 3.02
3126 3227 1.688627 GGTACTCCCTCCGTCCTGAAT 60.689 57.143 0.00 0.00 0.00 2.57
3127 3228 2.108970 GTACTCCCTCCGTCCTGAATT 58.891 52.381 0.00 0.00 0.00 2.17
3128 3229 2.544844 ACTCCCTCCGTCCTGAATTA 57.455 50.000 0.00 0.00 0.00 1.40
3129 3230 2.108970 ACTCCCTCCGTCCTGAATTAC 58.891 52.381 0.00 0.00 0.00 1.89
3130 3231 2.292323 ACTCCCTCCGTCCTGAATTACT 60.292 50.000 0.00 0.00 0.00 2.24
3131 3232 2.766828 CTCCCTCCGTCCTGAATTACTT 59.233 50.000 0.00 0.00 0.00 2.24
3132 3233 2.500098 TCCCTCCGTCCTGAATTACTTG 59.500 50.000 0.00 0.00 0.00 3.16
3133 3234 2.236395 CCCTCCGTCCTGAATTACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
3134 3235 3.522553 CCTCCGTCCTGAATTACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
3135 3236 3.179830 CTCCGTCCTGAATTACTTGTCG 58.820 50.000 0.00 0.00 0.00 4.35
3136 3237 1.659098 CCGTCCTGAATTACTTGTCGC 59.341 52.381 0.00 0.00 0.00 5.19
3137 3238 2.333926 CGTCCTGAATTACTTGTCGCA 58.666 47.619 0.00 0.00 0.00 5.10
3138 3239 2.345641 CGTCCTGAATTACTTGTCGCAG 59.654 50.000 0.00 0.00 0.00 5.18
3139 3240 3.585862 GTCCTGAATTACTTGTCGCAGA 58.414 45.455 0.00 0.00 0.00 4.26
3140 3241 3.994392 GTCCTGAATTACTTGTCGCAGAA 59.006 43.478 0.00 0.00 39.69 3.02
3141 3242 4.451096 GTCCTGAATTACTTGTCGCAGAAA 59.549 41.667 0.00 0.00 39.69 2.52
3142 3243 5.122396 GTCCTGAATTACTTGTCGCAGAAAT 59.878 40.000 0.00 0.00 39.69 2.17
3143 3244 5.122239 TCCTGAATTACTTGTCGCAGAAATG 59.878 40.000 0.00 0.00 39.69 2.32
3144 3245 5.295431 TGAATTACTTGTCGCAGAAATGG 57.705 39.130 0.00 0.00 39.69 3.16
3145 3246 5.000591 TGAATTACTTGTCGCAGAAATGGA 58.999 37.500 0.00 0.00 39.69 3.41
3146 3247 5.647658 TGAATTACTTGTCGCAGAAATGGAT 59.352 36.000 0.00 0.00 39.69 3.41
3147 3248 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
3148 3249 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
3149 3250 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
3150 3251 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
3151 3252 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
3152 3253 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
3153 3254 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
3154 3255 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
3155 3256 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
3156 3257 6.183360 TGTCGCAGAAATGGATGTATCTAGAA 60.183 38.462 0.00 0.00 39.69 2.10
3157 3258 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3158 3259 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3159 3260 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3160 3261 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3161 3262 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3188 3289 8.818141 AATGTCTACATACATCCATTTCTACG 57.182 34.615 0.00 0.00 39.16 3.51
3189 3290 7.576861 TGTCTACATACATCCATTTCTACGA 57.423 36.000 0.00 0.00 0.00 3.43
3190 3291 7.423199 TGTCTACATACATCCATTTCTACGAC 58.577 38.462 0.00 0.00 0.00 4.34
3191 3292 7.067737 TGTCTACATACATCCATTTCTACGACA 59.932 37.037 0.00 0.00 0.00 4.35
3192 3293 7.919091 GTCTACATACATCCATTTCTACGACAA 59.081 37.037 0.00 0.00 0.00 3.18
3193 3294 8.135529 TCTACATACATCCATTTCTACGACAAG 58.864 37.037 0.00 0.00 0.00 3.16
3194 3295 6.640518 ACATACATCCATTTCTACGACAAGT 58.359 36.000 0.00 0.00 0.00 3.16
3195 3296 7.778083 ACATACATCCATTTCTACGACAAGTA 58.222 34.615 0.00 0.00 0.00 2.24
3196 3297 8.255206 ACATACATCCATTTCTACGACAAGTAA 58.745 33.333 0.00 0.00 34.45 2.24
3197 3298 9.261180 CATACATCCATTTCTACGACAAGTAAT 57.739 33.333 0.00 0.00 34.45 1.89
3198 3299 9.832445 ATACATCCATTTCTACGACAAGTAATT 57.168 29.630 0.00 0.00 34.45 1.40
3199 3300 8.197988 ACATCCATTTCTACGACAAGTAATTC 57.802 34.615 0.00 0.00 34.45 2.17
3200 3301 7.280205 ACATCCATTTCTACGACAAGTAATTCC 59.720 37.037 0.00 0.00 34.45 3.01
3201 3302 5.808540 TCCATTTCTACGACAAGTAATTCCG 59.191 40.000 0.00 0.00 34.45 4.30
3202 3303 5.808540 CCATTTCTACGACAAGTAATTCCGA 59.191 40.000 0.00 0.00 34.45 4.55
3203 3304 6.311935 CCATTTCTACGACAAGTAATTCCGAA 59.688 38.462 0.00 0.00 34.45 4.30
3204 3305 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
3205 3306 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
3206 3307 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
3207 3308 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
3208 3309 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3209 3310 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3210 3311 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3211 3312 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3212 3313 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3258 3359 8.863872 AATAGCACTGTAGTTTCTTATGGTTT 57.136 30.769 0.00 0.00 0.00 3.27
3283 3384 9.638239 TTGAAATCAAGTTGTAAATCTTATGCC 57.362 29.630 2.11 0.00 0.00 4.40
3296 3397 3.076621 TCTTATGCCACTTCAGCACTTG 58.923 45.455 0.00 0.00 44.40 3.16
3372 3500 6.111382 CAGTGCAGATCTTCCTCTTTTATGA 58.889 40.000 0.00 0.00 0.00 2.15
3376 3504 7.498570 GTGCAGATCTTCCTCTTTTATGAGATT 59.501 37.037 0.00 0.00 36.23 2.40
3540 3668 7.931015 AATATACAAAGATCTAGTGGTGGGA 57.069 36.000 10.19 0.00 0.00 4.37
3573 3701 9.723601 AAAATGCATGGTAAGTTCAATTTATGT 57.276 25.926 0.00 0.00 0.00 2.29
3574 3702 8.706492 AATGCATGGTAAGTTCAATTTATGTG 57.294 30.769 0.00 0.00 0.00 3.21
3596 3724 6.037062 TGTGGTACATGCAATATTCTTCTTCG 59.963 38.462 0.00 0.00 44.52 3.79
3618 3746 8.850454 TTCGAAAAATTGGTTAAGACTTCAAG 57.150 30.769 0.00 0.00 0.00 3.02
3705 3834 3.006659 TGTAAAACGCCTCAATTGCAC 57.993 42.857 0.00 0.00 0.00 4.57
3788 3923 8.918658 CATGATAGTATAATTGCCAAATTGCAC 58.081 33.333 0.00 0.00 41.88 4.57
3800 3935 6.291377 TGCCAAATTGCACCTATTTTGTTAA 58.709 32.000 0.00 0.00 36.04 2.01
3847 3982 4.273969 TGTTTTGTAGAACTGGGTAAAGCG 59.726 41.667 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 3.506059 CTAGCGAGCCATGACCGGG 62.506 68.421 6.32 0.00 0.00 5.73
159 161 2.037511 ACCCGGAGTTGTATTTTCGTCA 59.962 45.455 0.73 0.00 0.00 4.35
348 354 8.200120 AGATGAGTTCGTCATATGATTCTTTCA 58.800 33.333 9.02 10.84 46.64 2.69
698 725 2.484662 CGCCGCTTATTTGCTGCA 59.515 55.556 0.00 0.00 42.03 4.41
881 912 4.035278 AGAGCCTTTCTTCTTCGTATCG 57.965 45.455 0.00 0.00 29.61 2.92
919 950 1.002366 CTCACGTACTGATGCTTGGC 58.998 55.000 0.00 0.00 0.00 4.52
1007 1038 3.400255 GTGTGGGTTTGGAAGAGTAGTC 58.600 50.000 0.00 0.00 0.00 2.59
1101 1132 3.724914 GAAGAGGGCGCGGAGGAAG 62.725 68.421 8.83 0.00 0.00 3.46
1406 1437 0.951040 GACGTTGTTGAGGCTCCCAG 60.951 60.000 12.86 0.98 0.00 4.45
1528 1559 5.070770 ACAAGAATGCAGTTGTCAAACAA 57.929 34.783 6.15 0.00 38.88 2.83
1534 1565 7.115378 CCTTCAAATAACAAGAATGCAGTTGTC 59.885 37.037 11.17 0.00 35.83 3.18
1566 1597 2.857592 AAACGTCGATATAGCACCGT 57.142 45.000 0.00 0.00 0.00 4.83
1567 1598 3.179795 CAGAAAACGTCGATATAGCACCG 59.820 47.826 0.00 0.00 0.00 4.94
1587 1618 2.715268 CACGTGTAAACCTGCAAACAG 58.285 47.619 7.58 0.00 44.05 3.16
1692 1723 6.854778 ACGTGGTTTTGTAAAGTTAATGTGT 58.145 32.000 0.00 0.00 0.00 3.72
1700 1735 8.081025 TGTTCTTTTTACGTGGTTTTGTAAAGT 58.919 29.630 0.00 0.00 40.48 2.66
1824 1859 8.093659 TCGACTCATCTGATTCTTACTCATAG 57.906 38.462 0.00 0.00 0.00 2.23
1905 1940 6.588756 GTGTGAGGACGAGATAAACAATGTTA 59.411 38.462 0.00 0.00 0.00 2.41
1921 1956 1.141053 ACAAGAGGTTGGTGTGAGGAC 59.859 52.381 0.00 0.00 38.07 3.85
1960 1995 1.886542 CTTGGCAAGGAGGTTTACACC 59.113 52.381 19.55 0.00 44.67 4.16
1961 1996 1.269723 GCTTGGCAAGGAGGTTTACAC 59.730 52.381 27.25 4.04 0.00 2.90
1962 1997 1.616159 GCTTGGCAAGGAGGTTTACA 58.384 50.000 27.25 0.00 0.00 2.41
1963 1998 0.888619 GGCTTGGCAAGGAGGTTTAC 59.111 55.000 27.25 8.81 0.00 2.01
1964 1999 0.777446 AGGCTTGGCAAGGAGGTTTA 59.223 50.000 27.25 0.00 0.00 2.01
2013 2071 4.508405 CCTCCTTTTTAGGGATCAACCACA 60.508 45.833 0.00 0.00 41.20 4.17
2027 2085 8.762645 AGAAGAAAAGAAACAATCCTCCTTTTT 58.237 29.630 0.00 0.00 37.23 1.94
2033 2091 7.277174 TCCAAGAAGAAAAGAAACAATCCTC 57.723 36.000 0.00 0.00 0.00 3.71
2034 2092 7.561356 TCTTCCAAGAAGAAAAGAAACAATCCT 59.439 33.333 4.59 0.00 30.73 3.24
2062 2120 1.383943 TGTGTCACCCACTCACCCT 60.384 57.895 0.00 0.00 44.81 4.34
2067 2125 2.622064 AGAAACTGTGTCACCCACTC 57.378 50.000 0.00 0.00 44.81 3.51
2068 2126 3.454812 AGTTAGAAACTGTGTCACCCACT 59.545 43.478 0.00 0.00 44.81 4.00
2069 2127 3.805207 AGTTAGAAACTGTGTCACCCAC 58.195 45.455 0.00 0.00 41.01 4.61
2070 2128 4.448210 GAAGTTAGAAACTGTGTCACCCA 58.552 43.478 0.00 0.00 41.91 4.51
2087 2145 3.244596 GGACCTAACTGAAGCTGGAAGTT 60.245 47.826 12.12 12.12 37.82 2.66
2096 2154 4.008330 TCTACGTGAGGACCTAACTGAAG 58.992 47.826 7.44 2.21 0.00 3.02
2111 2169 6.419413 GCTCAATCTCCTCTTATTTCTACGTG 59.581 42.308 0.00 0.00 0.00 4.49
2146 2204 1.710244 TGAGAAAGGCTCCCAAATCCA 59.290 47.619 0.00 0.00 43.26 3.41
2153 2211 1.002011 GGTGGTGAGAAAGGCTCCC 60.002 63.158 0.00 0.00 43.26 4.30
2241 2300 1.952296 GCATTCTACCTTCCATGCCAG 59.048 52.381 0.00 0.00 36.77 4.85
2297 2356 6.919662 AGTTGATTTTTGTAGCAACATGACAG 59.080 34.615 0.00 0.00 42.16 3.51
2311 2370 9.748708 TCCATTTCTCAAGTTAGTTGATTTTTG 57.251 29.630 2.71 0.73 44.44 2.44
2442 2517 3.377253 TCCTACTCAGATACCCGTGTT 57.623 47.619 0.00 0.00 0.00 3.32
2460 2535 3.652869 TCACCTTGAATCCTCCCATATCC 59.347 47.826 0.00 0.00 0.00 2.59
2503 2578 5.760743 TGAAAACCGTTGATCTTACACATCA 59.239 36.000 0.00 0.00 0.00 3.07
2569 2645 4.010349 ACTTGGATTAAGCTTTTCTCCCG 58.990 43.478 3.20 5.57 40.16 5.14
2587 2663 6.017605 ACACTTGTCATTTTCTAGCTCACTTG 60.018 38.462 0.00 0.00 0.00 3.16
2795 2894 9.709495 CAAACCTGAAAATGAAGATAATGGAAA 57.291 29.630 0.00 0.00 0.00 3.13
2886 2985 2.554142 CAAGAATATGGAGCACGCTCA 58.446 47.619 20.02 7.39 44.40 4.26
2948 3047 7.708998 TGTCTACGCACATAATATGAAGTGTA 58.291 34.615 7.33 13.28 35.48 2.90
3089 3190 6.154192 GGGAGTACCTAATAGGCATTACCTAC 59.846 46.154 6.17 0.00 44.85 3.18
3107 3208 1.777941 ATTCAGGACGGAGGGAGTAC 58.222 55.000 0.00 0.00 0.00 2.73
3108 3209 2.544844 AATTCAGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
3109 3210 2.108970 GTAATTCAGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
3110 3211 2.389715 AGTAATTCAGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
3111 3212 2.500098 CAAGTAATTCAGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
3112 3213 2.236395 ACAAGTAATTCAGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
3113 3214 3.522553 GACAAGTAATTCAGGACGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
3114 3215 3.179830 CGACAAGTAATTCAGGACGGAG 58.820 50.000 0.00 0.00 0.00 4.63
3115 3216 2.673043 GCGACAAGTAATTCAGGACGGA 60.673 50.000 0.00 0.00 0.00 4.69
3116 3217 1.659098 GCGACAAGTAATTCAGGACGG 59.341 52.381 0.00 0.00 0.00 4.79
3117 3218 2.333926 TGCGACAAGTAATTCAGGACG 58.666 47.619 0.00 0.00 0.00 4.79
3118 3219 3.585862 TCTGCGACAAGTAATTCAGGAC 58.414 45.455 0.00 0.00 0.00 3.85
3119 3220 3.953712 TCTGCGACAAGTAATTCAGGA 57.046 42.857 0.00 0.00 0.00 3.86
3120 3221 5.327091 CATTTCTGCGACAAGTAATTCAGG 58.673 41.667 0.00 0.00 0.00 3.86
3121 3222 5.122239 TCCATTTCTGCGACAAGTAATTCAG 59.878 40.000 0.00 0.00 0.00 3.02
3122 3223 5.000591 TCCATTTCTGCGACAAGTAATTCA 58.999 37.500 0.00 0.00 0.00 2.57
3123 3224 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
3124 3225 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
3125 3226 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
3126 3227 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
3127 3228 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
3128 3229 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
3129 3230 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
3130 3231 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
3131 3232 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
3132 3233 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3133 3234 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3134 3235 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3135 3236 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3162 3263 9.261180 CGTAGAAATGGATGTATGTAGACATTT 57.739 33.333 0.00 0.00 40.18 2.32
3163 3264 8.638873 TCGTAGAAATGGATGTATGTAGACATT 58.361 33.333 0.00 0.00 40.18 2.71
3164 3265 8.082852 GTCGTAGAAATGGATGTATGTAGACAT 58.917 37.037 0.08 0.08 40.04 3.06
3165 3266 7.067737 TGTCGTAGAAATGGATGTATGTAGACA 59.932 37.037 0.00 0.00 39.69 3.41
3166 3267 7.423199 TGTCGTAGAAATGGATGTATGTAGAC 58.577 38.462 0.00 0.00 39.69 2.59
3167 3268 7.576861 TGTCGTAGAAATGGATGTATGTAGA 57.423 36.000 0.00 0.00 39.69 2.59
3168 3269 7.921214 ACTTGTCGTAGAAATGGATGTATGTAG 59.079 37.037 0.00 0.00 39.69 2.74
3169 3270 7.778083 ACTTGTCGTAGAAATGGATGTATGTA 58.222 34.615 0.00 0.00 39.69 2.29
3170 3271 6.640518 ACTTGTCGTAGAAATGGATGTATGT 58.359 36.000 0.00 0.00 39.69 2.29
3171 3272 8.642908 TTACTTGTCGTAGAAATGGATGTATG 57.357 34.615 0.00 0.00 39.69 2.39
3172 3273 9.832445 AATTACTTGTCGTAGAAATGGATGTAT 57.168 29.630 0.00 0.00 39.69 2.29
3173 3274 9.309516 GAATTACTTGTCGTAGAAATGGATGTA 57.690 33.333 0.00 0.00 39.69 2.29
3174 3275 7.280205 GGAATTACTTGTCGTAGAAATGGATGT 59.720 37.037 0.00 0.00 39.69 3.06
3175 3276 7.516785 CGGAATTACTTGTCGTAGAAATGGATG 60.517 40.741 0.00 0.00 39.69 3.51
3176 3277 6.479001 CGGAATTACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
3177 3278 5.808540 CGGAATTACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
3178 3279 5.808540 TCGGAATTACTTGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
3179 3280 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
3180 3281 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
3181 3282 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
3182 3283 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
3183 3284 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
3184 3285 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
3185 3286 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
3186 3287 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
3187 3288 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3188 3289 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3189 3290 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3190 3291 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3191 3292 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3192 3293 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3193 3294 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3194 3295 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3195 3296 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
3196 3297 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
3197 3298 1.308069 CGTACTCCCTCCGTTCGGAA 61.308 60.000 14.79 0.04 33.41 4.30
3198 3299 1.746615 CGTACTCCCTCCGTTCGGA 60.747 63.158 13.34 13.34 0.00 4.55
3199 3300 0.744414 TACGTACTCCCTCCGTTCGG 60.744 60.000 4.74 4.74 36.12 4.30
3200 3301 1.003116 CATACGTACTCCCTCCGTTCG 60.003 57.143 0.00 0.00 36.12 3.95
3201 3302 2.019984 ACATACGTACTCCCTCCGTTC 58.980 52.381 0.00 0.00 36.12 3.95
3202 3303 2.134789 ACATACGTACTCCCTCCGTT 57.865 50.000 0.00 0.00 36.12 4.44
3203 3304 3.498774 ATACATACGTACTCCCTCCGT 57.501 47.619 0.00 0.00 38.53 4.69
3204 3305 4.940046 ACATATACATACGTACTCCCTCCG 59.060 45.833 0.00 0.00 0.00 4.63
3205 3306 6.830873 AACATATACATACGTACTCCCTCC 57.169 41.667 0.00 0.00 0.00 4.30
3206 3307 7.879070 TCAAACATATACATACGTACTCCCTC 58.121 38.462 0.00 0.00 0.00 4.30
3207 3308 7.828508 TCAAACATATACATACGTACTCCCT 57.171 36.000 0.00 0.00 0.00 4.20
3208 3309 8.876275 TTTCAAACATATACATACGTACTCCC 57.124 34.615 0.00 0.00 0.00 4.30
3258 3359 8.801299 TGGCATAAGATTTACAACTTGATTTCA 58.199 29.630 0.00 0.00 0.00 2.69
3334 3436 4.956085 TCTGCACTGCTTACTTTAGTGAA 58.044 39.130 7.71 0.00 43.35 3.18
3335 3437 4.600692 TCTGCACTGCTTACTTTAGTGA 57.399 40.909 7.71 0.00 43.35 3.41
3540 3668 5.806654 ACTTACCATGCATTTTCCAAACT 57.193 34.783 0.00 0.00 0.00 2.66
3573 3701 6.345298 TCGAAGAAGAATATTGCATGTACCA 58.655 36.000 0.00 0.00 0.00 3.25
3574 3702 6.844696 TCGAAGAAGAATATTGCATGTACC 57.155 37.500 0.00 0.00 0.00 3.34
3596 3724 8.194769 TGACCTTGAAGTCTTAACCAATTTTTC 58.805 33.333 0.00 0.00 37.66 2.29
3633 3762 7.817418 TGGAGCCTGGTGTTAAATATATTTC 57.183 36.000 13.95 2.31 0.00 2.17
3648 3777 2.338381 GCATATGCTTGGAGCCTGG 58.662 57.895 20.64 0.00 41.51 4.45
3705 3834 4.935205 TGACAGTTCCCGAACATTTCATAG 59.065 41.667 10.07 0.00 43.47 2.23
3800 3935 9.565090 ACATAAATCTGACATGCACACTTATAT 57.435 29.630 0.00 0.00 0.00 0.86
3806 3941 6.642131 ACAAAACATAAATCTGACATGCACAC 59.358 34.615 0.00 0.00 0.00 3.82
3824 3959 4.273969 CGCTTTACCCAGTTCTACAAAACA 59.726 41.667 0.00 0.00 0.00 2.83
3847 3982 3.748568 CACAAACCTCTTCCTCAAGCTAC 59.251 47.826 0.00 0.00 0.00 3.58
3882 4017 4.916041 TTGACCTGACTCAAATGAGGAT 57.084 40.909 14.50 0.00 46.13 3.24


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

AutoCloner maintained by Alex Coulton.