Multiple sequence alignment - TraesCS2B01G090300

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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 TraesCS2B01G090300 chr2B 100.000 2639 0 0 1 2639 51227758 51230396 0.000000e+00 4874
1 TraesCS2B01G090300 chr2A 92.424 1254 69 16 785 2018 33271238 33269991 0.000000e+00 1766
2 TraesCS2B01G090300 chr2A 91.793 792 34 12 12 801 33272671 33271909 0.000000e+00 1074
3 TraesCS2B01G090300 chr2D 93.889 900 46 6 879 1771 30980188 30979291 0.000000e+00 1349
4 TraesCS2B01G090300 chr2D 90.852 962 51 13 879 1829 30935692 30934757 0.000000e+00 1254
5 TraesCS2B01G090300 chr2D 92.201 577 27 10 12 585 30981111 30980550 0.000000e+00 800
6 TraesCS2B01G090300 chr2D 90.149 335 25 6 1768 2095 30979137 30978804 1.880000e-116 429
7 TraesCS2B01G090300 chr2D 91.500 200 7 4 687 881 30980506 30980312 1.560000e-67 267
8 TraesCS2B01G090300 chr7D 90.960 708 55 7 936 1639 133327725 133327023 0.000000e+00 944
9 TraesCS2B01G090300 chr7A 90.254 708 60 7 936 1639 131937295 131936593 0.000000e+00 917
10 TraesCS2B01G090300 chr7B 89.407 708 66 7 936 1639 94630775 94630073 0.000000e+00 883
11 TraesCS2B01G090300 chr4D 78.506 549 75 30 2096 2630 497873860 497874379 1.180000e-83 320
12 TraesCS2B01G090300 chr4D 80.802 349 34 12 2291 2639 119286500 119286185 2.620000e-60 243
13 TraesCS2B01G090300 chr5B 80.425 424 64 15 2222 2639 704904796 704905206 3.300000e-79 305
14 TraesCS2B01G090300 chr5A 81.963 377 51 11 2267 2639 268586643 268586280 1.190000e-78 303
15 TraesCS2B01G090300 chr5A 89.048 210 21 2 2431 2639 168241184 168241392 2.610000e-65 259
16 TraesCS2B01G090300 chr5D 83.117 308 35 17 2267 2570 207991990 207991696 5.600000e-67 265
17 TraesCS2B01G090300 chr1D 88.725 204 23 0 2436 2639 63604916 63604713 1.570000e-62 250
18 TraesCS2B01G090300 chr3B 88.152 211 22 3 2431 2639 11012677 11012886 5.640000e-62 248
19 TraesCS2B01G090300 chr3B 80.255 314 48 9 2092 2394 791266489 791266799 9.510000e-55 224
20 TraesCS2B01G090300 chr4B 87.619 210 25 1 2431 2639 182183229 182183438 2.620000e-60 243
21 TraesCS2B01G090300 chr4A 86.222 225 24 6 2416 2638 666369762 666369981 1.220000e-58 237
22 TraesCS2B01G090300 chr6D 89.674 184 16 2 2221 2403 136464190 136464009 5.680000e-57 231
23 TraesCS2B01G090300 chr3A 80.696 316 44 12 2221 2532 45605610 45605912 2.040000e-56 230
24 TraesCS2B01G090300 chr3A 79.412 306 35 23 2128 2417 726299664 726299957 9.640000e-45 191
25 TraesCS2B01G090300 chr6B 88.757 169 16 2 2236 2403 234675326 234675160 1.240000e-48 204
26 TraesCS2B01G090300 chr3D 78.387 310 44 19 2121 2418 22685984 22686282 2.090000e-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 TraesCS2B01G090300 chr2B 51227758 51230396 2638 False 4874.00 4874 100.00000 1 2639 1 chr2B.!!$F1 2638
1 TraesCS2B01G090300 chr2A 33269991 33272671 2680 True 1420.00 1766 92.10850 12 2018 2 chr2A.!!$R1 2006
2 TraesCS2B01G090300 chr2D 30934757 30935692 935 True 1254.00 1254 90.85200 879 1829 1 chr2D.!!$R1 950
3 TraesCS2B01G090300 chr2D 30978804 30981111 2307 True 711.25 1349 91.93475 12 2095 4 chr2D.!!$R2 2083
4 TraesCS2B01G090300 chr7D 133327023 133327725 702 True 944.00 944 90.96000 936 1639 1 chr7D.!!$R1 703
5 TraesCS2B01G090300 chr7A 131936593 131937295 702 True 917.00 917 90.25400 936 1639 1 chr7A.!!$R1 703
6 TraesCS2B01G090300 chr7B 94630073 94630775 702 True 883.00 883 89.40700 936 1639 1 chr7B.!!$R1 703
7 TraesCS2B01G090300 chr4D 497873860 497874379 519 False 320.00 320 78.50600 2096 2630 1 chr4D.!!$F1 534

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
394 396 0.038892 ATTGCAAAAGCAGCTCACCG 60.039 50.0 1.71 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 3220 0.249031 GCACCATATTTTCCAGCGCC 60.249 55.0 2.29 0.0 0.0 6.53 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
62 63 9.239551 CATCACATAATATCCTGTCCATGAATT 57.760 33.333 0.00 0.00 0.00 2.17
63 64 8.625786 TCACATAATATCCTGTCCATGAATTG 57.374 34.615 0.00 0.00 0.00 2.32
111 112 7.500892 TCTTAGACCAGCAGTTAAAATTTCACA 59.499 33.333 0.00 0.00 0.00 3.58
112 113 6.655078 AGACCAGCAGTTAAAATTTCACAT 57.345 33.333 0.00 0.00 0.00 3.21
113 114 6.449698 AGACCAGCAGTTAAAATTTCACATG 58.550 36.000 0.00 0.00 0.00 3.21
114 115 4.990426 ACCAGCAGTTAAAATTTCACATGC 59.010 37.500 9.25 9.25 0.00 4.06
130 131 6.316440 TCACATGCATGATTAATTACGCAT 57.684 33.333 32.75 7.84 40.55 4.73
135 136 4.821260 TGCATGATTAATTACGCATCAGGT 59.179 37.500 0.00 0.00 32.51 4.00
136 137 5.049474 TGCATGATTAATTACGCATCAGGTC 60.049 40.000 0.00 5.56 32.51 3.85
137 138 5.180117 GCATGATTAATTACGCATCAGGTCT 59.820 40.000 0.00 0.00 32.51 3.85
138 139 6.368791 GCATGATTAATTACGCATCAGGTCTA 59.631 38.462 0.00 0.00 32.51 2.59
139 140 7.095229 GCATGATTAATTACGCATCAGGTCTAA 60.095 37.037 0.00 0.00 32.51 2.10
140 141 7.946655 TGATTAATTACGCATCAGGTCTAAG 57.053 36.000 0.00 0.00 0.00 2.18
141 142 7.722363 TGATTAATTACGCATCAGGTCTAAGA 58.278 34.615 0.00 0.00 0.00 2.10
142 143 8.367911 TGATTAATTACGCATCAGGTCTAAGAT 58.632 33.333 0.00 0.00 0.00 2.40
143 144 8.764524 ATTAATTACGCATCAGGTCTAAGATC 57.235 34.615 0.00 0.00 0.00 2.75
144 145 5.791336 ATTACGCATCAGGTCTAAGATCA 57.209 39.130 0.00 0.00 0.00 2.92
181 182 7.608308 TTGTTTAGCAAAGCAACAAAAGAAT 57.392 28.000 5.50 0.00 31.72 2.40
184 185 2.874086 AGCAAAGCAACAAAAGAATGCC 59.126 40.909 0.00 0.00 40.93 4.40
225 226 0.833287 TTGCTAGGCCAGAGATGACC 59.167 55.000 5.01 0.00 0.00 4.02
306 308 2.674852 TCTCACACTAAGCTACGTACCG 59.325 50.000 0.00 0.00 0.00 4.02
325 327 5.258456 ACCGTACGTGATAATTGAGACAT 57.742 39.130 15.21 0.00 0.00 3.06
351 353 9.869757 TTGAGTTCATATAAACTTCTGATTCGA 57.130 29.630 0.00 0.00 39.55 3.71
394 396 0.038892 ATTGCAAAAGCAGCTCACCG 60.039 50.000 1.71 0.00 0.00 4.94
506 508 2.434884 CACTGGCTGCCCTACGTG 60.435 66.667 17.53 13.71 0.00 4.49
619 621 7.329962 TCGTCAAATATCACTCACGTTACATTT 59.670 33.333 0.00 0.00 0.00 2.32
627 629 5.693104 TCACTCACGTTACATTTGTTCTACC 59.307 40.000 0.00 0.00 0.00 3.18
653 656 6.710744 TGTGAACTCCCTTTATTTCAAGAGAC 59.289 38.462 0.00 0.00 30.00 3.36
656 659 5.561679 ACTCCCTTTATTTCAAGAGACACC 58.438 41.667 0.00 0.00 0.00 4.16
672 675 5.011227 AGAGACACCTGAAGTTCTAGGTTTC 59.989 44.000 21.14 21.14 44.72 2.78
674 677 4.962155 ACACCTGAAGTTCTAGGTTTCTG 58.038 43.478 18.70 12.70 44.72 3.02
744 766 8.184192 ACATCAAATCGGTTTCATTAGATTCAC 58.816 33.333 0.00 0.00 32.79 3.18
872 1585 4.287766 AGTATTTTGGAGCGAAGGAAGT 57.712 40.909 0.00 0.00 0.00 3.01
873 1586 5.416271 AGTATTTTGGAGCGAAGGAAGTA 57.584 39.130 0.00 0.00 0.00 2.24
874 1587 5.176592 AGTATTTTGGAGCGAAGGAAGTAC 58.823 41.667 0.00 0.00 0.00 2.73
911 1756 0.750546 ACGCCTCTACCGTCTATGCA 60.751 55.000 0.00 0.00 32.83 3.96
918 1767 1.609555 CTACCGTCTATGCACCTCCTC 59.390 57.143 0.00 0.00 0.00 3.71
976 1827 2.129607 CACACAGTACGTACCCAACAC 58.870 52.381 21.80 0.00 0.00 3.32
1056 1914 0.341258 TCCTCATCCTGCCCTTCTCT 59.659 55.000 0.00 0.00 0.00 3.10
1057 1915 1.211456 CCTCATCCTGCCCTTCTCTT 58.789 55.000 0.00 0.00 0.00 2.85
1095 1953 2.992689 TTCTGCGTGGCCGACCTA 60.993 61.111 0.00 0.00 36.63 3.08
1215 2073 4.015406 ATCAAGGCGGCCGTCACA 62.015 61.111 34.17 15.65 0.00 3.58
1536 2394 1.589196 GCAGATCACCGACTACGCC 60.589 63.158 0.00 0.00 38.29 5.68
1658 2516 3.795623 AGCATTAATCAAGCAAGCAGG 57.204 42.857 0.00 0.00 0.00 4.85
1677 2535 1.476891 GGTCTCTATGCAAGGTCGTCA 59.523 52.381 0.00 0.00 0.00 4.35
1681 2539 5.348986 GTCTCTATGCAAGGTCGTCATTTA 58.651 41.667 0.00 0.00 0.00 1.40
1684 2542 5.297547 TCTATGCAAGGTCGTCATTTATCC 58.702 41.667 0.00 0.00 0.00 2.59
1686 2544 3.270027 TGCAAGGTCGTCATTTATCCTG 58.730 45.455 0.00 0.00 0.00 3.86
1695 2555 2.936498 GTCATTTATCCTGGTGTCACCG 59.064 50.000 17.27 11.48 42.58 4.94
1713 2573 1.818850 CGTGTCGGATTACGTACCTG 58.181 55.000 0.00 0.00 44.69 4.00
1728 2588 1.520787 CCTGGACGATAACACCGCC 60.521 63.158 0.00 0.00 0.00 6.13
1732 2592 0.527817 GGACGATAACACCGCCAGAG 60.528 60.000 0.00 0.00 0.00 3.35
1735 2595 1.274167 ACGATAACACCGCCAGAGAAA 59.726 47.619 0.00 0.00 0.00 2.52
1736 2596 2.093658 ACGATAACACCGCCAGAGAAAT 60.094 45.455 0.00 0.00 0.00 2.17
1738 2598 2.107950 TAACACCGCCAGAGAAATGG 57.892 50.000 0.00 0.00 43.72 3.16
1763 2625 4.083565 TCTACCTATACCGTGCATGCATA 58.916 43.478 25.64 13.01 0.00 3.14
1873 2896 9.787435 TGTCCTAAATTGTTGTATAGTGTTTCT 57.213 29.630 0.00 0.00 0.00 2.52
1899 2924 8.877808 ATGAGATTGTTTTCTTCCTTCAAAAC 57.122 30.769 0.00 0.00 41.13 2.43
1904 2929 8.797266 ATTGTTTTCTTCCTTCAAAACGTATC 57.203 30.769 0.00 0.00 42.85 2.24
1914 2939 9.834628 TTCCTTCAAAACGTATCATAATGTTTC 57.165 29.630 0.00 0.00 37.55 2.78
1925 2950 6.903883 ATCATAATGTTTCACCGTGTACTC 57.096 37.500 0.00 0.00 0.00 2.59
2032 3059 8.811017 TGAATGAAGCAAAAGTTTTATGGGATA 58.189 29.630 0.00 0.00 0.00 2.59
2049 3076 3.384789 GGGATACTCATGCCATATCGCTA 59.615 47.826 14.84 0.00 42.13 4.26
2050 3077 4.141937 GGGATACTCATGCCATATCGCTAA 60.142 45.833 14.84 0.00 42.13 3.09
2051 3078 5.046529 GGATACTCATGCCATATCGCTAAG 58.953 45.833 0.00 0.00 0.00 2.18
2054 3081 3.257393 CTCATGCCATATCGCTAAGGAC 58.743 50.000 0.00 0.00 0.00 3.85
2059 3086 2.417719 CCATATCGCTAAGGACAAGGC 58.582 52.381 0.00 0.00 0.00 4.35
2100 3127 3.480470 ACAACTCTGCACTAACAGCATT 58.520 40.909 0.00 0.00 41.82 3.56
2104 3131 2.421424 CTCTGCACTAACAGCATTTCCC 59.579 50.000 0.00 0.00 41.82 3.97
2109 3136 2.095059 CACTAACAGCATTTCCCACAGC 60.095 50.000 0.00 0.00 0.00 4.40
2132 3159 4.770874 AACCCCGCGCGTGCTAAT 62.771 61.111 29.95 6.65 39.65 1.73
2133 3160 4.770874 ACCCCGCGCGTGCTAATT 62.771 61.111 29.95 2.03 39.65 1.40
2135 3162 2.483288 CCCGCGCGTGCTAATTTT 59.517 55.556 29.95 0.00 39.65 1.82
2156 3185 2.817538 TTTACAGCGCCGAAATAAGC 57.182 45.000 2.29 0.00 0.00 3.09
2158 3187 1.948104 TACAGCGCCGAAATAAGCAT 58.052 45.000 2.29 0.00 0.00 3.79
2159 3188 1.094785 ACAGCGCCGAAATAAGCATT 58.905 45.000 2.29 0.00 0.00 3.56
2190 3219 3.315142 CTGGGCGCTAACTCCAGCA 62.315 63.158 15.31 0.00 41.88 4.41
2191 3220 2.512515 GGGCGCTAACTCCAGCAG 60.513 66.667 7.64 0.00 41.88 4.24
2192 3221 2.512515 GGCGCTAACTCCAGCAGG 60.513 66.667 7.64 0.00 41.88 4.85
2206 3235 3.557207 GCAGGCGCTGGAAAATATG 57.443 52.632 7.64 0.00 34.30 1.78
2208 3237 1.392589 CAGGCGCTGGAAAATATGGT 58.607 50.000 7.64 0.00 0.00 3.55
2210 3239 0.249031 GGCGCTGGAAAATATGGTGC 60.249 55.000 7.64 0.00 0.00 5.01
2212 3241 0.029300 CGCTGGAAAATATGGTGCGG 59.971 55.000 0.00 0.00 38.54 5.69
2213 3242 0.249031 GCTGGAAAATATGGTGCGGC 60.249 55.000 0.00 0.00 0.00 6.53
2214 3243 0.029300 CTGGAAAATATGGTGCGGCG 59.971 55.000 0.51 0.51 0.00 6.46
2215 3244 0.393132 TGGAAAATATGGTGCGGCGA 60.393 50.000 12.98 0.00 0.00 5.54
2216 3245 0.951558 GGAAAATATGGTGCGGCGAT 59.048 50.000 12.98 0.00 0.00 4.58
2217 3246 2.147958 GGAAAATATGGTGCGGCGATA 58.852 47.619 12.98 0.00 0.00 2.92
2218 3247 2.747446 GGAAAATATGGTGCGGCGATAT 59.253 45.455 12.98 1.45 31.12 1.63
2220 3249 4.034048 GGAAAATATGGTGCGGCGATATAG 59.966 45.833 12.98 0.00 29.96 1.31
2223 3252 0.321671 ATGGTGCGGCGATATAGCTT 59.678 50.000 12.98 0.00 37.29 3.74
2224 3253 0.319555 TGGTGCGGCGATATAGCTTC 60.320 55.000 12.98 1.06 37.29 3.86
2227 3256 0.958822 TGCGGCGATATAGCTTCAGA 59.041 50.000 12.98 0.00 37.29 3.27
2230 3259 2.351835 GCGGCGATATAGCTTCAGAAGA 60.352 50.000 12.98 0.00 37.29 2.87
2235 3264 2.121116 TATAGCTTCAGAAGACGCGC 57.879 50.000 14.86 0.00 43.23 6.86
2241 3270 2.094417 GCTTCAGAAGACGCGCTAAATT 59.906 45.455 14.86 0.00 28.90 1.82
2244 3273 4.835199 TCAGAAGACGCGCTAAATTTAC 57.165 40.909 5.73 0.00 0.00 2.01
2265 3296 4.011654 GCACGCGCATCACACACA 62.012 61.111 5.73 0.00 38.36 3.72
2272 3303 1.715519 GCGCATCACACACAACATTTC 59.284 47.619 0.30 0.00 0.00 2.17
2273 3304 2.605338 GCGCATCACACACAACATTTCT 60.605 45.455 0.30 0.00 0.00 2.52
2278 3309 5.734220 GCATCACACACAACATTTCTCACTT 60.734 40.000 0.00 0.00 0.00 3.16
2279 3310 5.895636 TCACACACAACATTTCTCACTTT 57.104 34.783 0.00 0.00 0.00 2.66
2280 3311 6.993786 TCACACACAACATTTCTCACTTTA 57.006 33.333 0.00 0.00 0.00 1.85
2285 3316 9.086336 ACACACAACATTTCTCACTTTAAAATG 57.914 29.630 5.71 5.71 43.02 2.32
2307 3338 6.957920 TGGAATCAAGAAGATCAAACACAA 57.042 33.333 0.00 0.00 35.39 3.33
2434 3469 9.956720 AAAATCAAACAAAACAACATCAAACAA 57.043 22.222 0.00 0.00 0.00 2.83
2439 3474 8.467574 CAAACAAAACAACATCAAACAAACAAC 58.532 29.630 0.00 0.00 0.00 3.32
2440 3475 7.251704 ACAAAACAACATCAAACAAACAACA 57.748 28.000 0.00 0.00 0.00 3.33
2441 3476 7.869800 ACAAAACAACATCAAACAAACAACAT 58.130 26.923 0.00 0.00 0.00 2.71
2442 3477 8.014517 ACAAAACAACATCAAACAAACAACATC 58.985 29.630 0.00 0.00 0.00 3.06
2443 3478 7.664082 AAACAACATCAAACAAACAACATCA 57.336 28.000 0.00 0.00 0.00 3.07
2444 3479 7.664082 AACAACATCAAACAAACAACATCAA 57.336 28.000 0.00 0.00 0.00 2.57
2453 3488 9.134734 TCAAACAAACAACATCAAACTAGTTTC 57.865 29.630 18.00 0.00 0.00 2.78
2458 3493 4.807304 ACAACATCAAACTAGTTTCGTCGT 59.193 37.500 18.00 8.53 0.00 4.34
2464 3499 5.051816 TCAAACTAGTTTCGTCGTCCATTT 58.948 37.500 18.00 0.00 0.00 2.32
2465 3500 5.176223 TCAAACTAGTTTCGTCGTCCATTTC 59.824 40.000 18.00 0.00 0.00 2.17
2470 3505 1.083489 TTCGTCGTCCATTTCATGCC 58.917 50.000 0.00 0.00 0.00 4.40
2481 3516 0.482446 TTTCATGCCCACCACTCCTT 59.518 50.000 0.00 0.00 0.00 3.36
2499 3534 7.066766 CCACTCCTTGATTAGATCCTTTTGAAG 59.933 40.741 0.00 0.00 0.00 3.02
2503 3538 7.712639 TCCTTGATTAGATCCTTTTGAAGATCG 59.287 37.037 0.00 0.00 0.00 3.69
2532 3567 4.118480 GGCACGTCGAATGGCATA 57.882 55.556 16.84 0.00 42.03 3.14
2540 3575 3.254060 CGTCGAATGGCATAATAGGAGG 58.746 50.000 0.00 0.00 0.00 4.30
2542 3577 2.906389 TCGAATGGCATAATAGGAGGCT 59.094 45.455 0.00 0.00 0.00 4.58
2544 3579 4.716784 TCGAATGGCATAATAGGAGGCTAT 59.283 41.667 0.00 0.00 0.00 2.97
2562 3597 2.676163 ATAAATCGGGCCACCCTCGC 62.676 60.000 4.39 0.00 42.67 5.03
2571 3606 4.457496 CACCCTCGCAGCCGTCAT 62.457 66.667 0.00 0.00 35.54 3.06
2574 3609 4.147449 CCTCGCAGCCGTCATCCA 62.147 66.667 0.00 0.00 35.54 3.41
2580 3615 1.807165 CAGCCGTCATCCACACTCG 60.807 63.158 0.00 0.00 0.00 4.18
2594 3629 2.885644 CTCGCATGGAACGTCCCG 60.886 66.667 0.00 0.00 35.03 5.14
2596 3631 3.186047 CGCATGGAACGTCCCGAC 61.186 66.667 0.00 0.00 35.03 4.79
2598 3633 1.669760 GCATGGAACGTCCCGACAA 60.670 57.895 0.00 0.00 35.03 3.18
2599 3634 1.024579 GCATGGAACGTCCCGACAAT 61.025 55.000 0.00 0.00 35.03 2.71
2601 3636 1.396996 CATGGAACGTCCCGACAATTC 59.603 52.381 0.00 0.00 35.03 2.17
2630 3665 7.121315 ACTGAGAATAGTCTAAATTTTGCCCAC 59.879 37.037 0.00 0.00 32.80 4.61
2631 3666 6.093495 TGAGAATAGTCTAAATTTTGCCCACG 59.907 38.462 0.00 0.00 32.80 4.94
2632 3667 4.632538 ATAGTCTAAATTTTGCCCACGC 57.367 40.909 0.00 0.00 0.00 5.34
2633 3668 1.544246 AGTCTAAATTTTGCCCACGCC 59.456 47.619 0.00 0.00 0.00 5.68
2634 3669 0.892063 TCTAAATTTTGCCCACGCCC 59.108 50.000 0.00 0.00 0.00 6.13
2635 3670 0.605589 CTAAATTTTGCCCACGCCCA 59.394 50.000 0.00 0.00 0.00 5.36
2636 3671 1.206849 CTAAATTTTGCCCACGCCCAT 59.793 47.619 0.00 0.00 0.00 4.00
2637 3672 0.399833 AAATTTTGCCCACGCCCATT 59.600 45.000 0.00 0.00 0.00 3.16
2638 3673 0.036483 AATTTTGCCCACGCCCATTC 60.036 50.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.712425 CCAGCAGGCAAGCGCAAC 62.712 66.667 11.47 0.00 41.24 4.17
5 6 4.666253 TGGGACCAGCAGGCAAGC 62.666 66.667 0.00 0.00 39.06 4.01
6 7 1.114722 TTTTGGGACCAGCAGGCAAG 61.115 55.000 0.00 0.00 39.06 4.01
7 8 1.075674 TTTTGGGACCAGCAGGCAA 60.076 52.632 0.00 0.00 39.06 4.52
8 9 1.531365 CTTTTGGGACCAGCAGGCA 60.531 57.895 0.00 0.00 39.06 4.75
9 10 0.251165 TACTTTTGGGACCAGCAGGC 60.251 55.000 0.00 0.00 39.06 4.85
10 11 2.514458 ATACTTTTGGGACCAGCAGG 57.486 50.000 0.00 0.00 42.21 4.85
62 63 2.150390 TGCACGCTTCTAGATTTTGCA 58.850 42.857 12.38 12.38 36.20 4.08
63 64 2.476854 CCTGCACGCTTCTAGATTTTGC 60.477 50.000 0.00 1.30 0.00 3.68
112 113 4.821260 ACCTGATGCGTAATTAATCATGCA 59.179 37.500 7.95 7.95 40.72 3.96
113 114 5.180117 AGACCTGATGCGTAATTAATCATGC 59.820 40.000 0.00 0.00 30.31 4.06
114 115 6.791887 AGACCTGATGCGTAATTAATCATG 57.208 37.500 5.68 3.49 30.31 3.07
130 131 8.169393 AGATATCAGTGATGATCTTAGACCTGA 58.831 37.037 16.15 0.00 32.80 3.86
139 140 9.270640 GCTAAACAAAGATATCAGTGATGATCT 57.729 33.333 16.15 15.06 0.00 2.75
140 141 9.049523 TGCTAAACAAAGATATCAGTGATGATC 57.950 33.333 16.15 13.31 0.00 2.92
141 142 8.969260 TGCTAAACAAAGATATCAGTGATGAT 57.031 30.769 16.15 5.47 0.00 2.45
142 143 8.791327 TTGCTAAACAAAGATATCAGTGATGA 57.209 30.769 16.15 0.63 34.56 2.92
181 182 0.749818 TGGAGACAAAAACTGCGGCA 60.750 50.000 1.29 1.29 37.44 5.69
184 185 2.842208 TTGTGGAGACAAAAACTGCG 57.158 45.000 0.00 0.00 46.06 5.18
225 226 6.347402 CCAGAACTTGTATGGTAACTTCGTTG 60.347 42.308 0.00 0.00 33.56 4.10
238 239 5.548406 ACGTAAAAGAGCCAGAACTTGTAT 58.452 37.500 0.00 0.00 0.00 2.29
306 308 7.757097 ACTCAATGTCTCAATTATCACGTAC 57.243 36.000 0.00 0.00 0.00 3.67
325 327 9.869757 TCGAATCAGAAGTTTATATGAACTCAA 57.130 29.630 12.80 1.09 38.86 3.02
394 396 2.736670 ATTAGGGAATGGCAGGACAC 57.263 50.000 0.00 0.00 0.00 3.67
506 508 1.004745 TCAGGATTTGTGGGGAGAAGC 59.995 52.381 0.00 0.00 0.00 3.86
590 592 3.192844 ACGTGAGTGATATTTGACGAGGT 59.807 43.478 0.00 0.00 46.97 3.85
619 621 2.972348 AGGGAGTTCACAGGTAGAACA 58.028 47.619 8.54 0.00 45.93 3.18
627 629 6.936900 TCTCTTGAAATAAAGGGAGTTCACAG 59.063 38.462 0.00 0.00 33.47 3.66
653 656 3.748568 GCAGAAACCTAGAACTTCAGGTG 59.251 47.826 11.46 3.91 44.55 4.00
656 659 4.083590 GCTTGCAGAAACCTAGAACTTCAG 60.084 45.833 0.00 0.00 0.00 3.02
672 675 5.869344 TGTATACACTCAACTTAGCTTGCAG 59.131 40.000 0.08 0.00 0.00 4.41
674 677 6.147164 TGTTGTATACACTCAACTTAGCTTGC 59.853 38.462 4.68 0.00 42.71 4.01
849 1558 4.695928 ACTTCCTTCGCTCCAAAATACTTC 59.304 41.667 0.00 0.00 0.00 3.01
911 1756 2.972153 AAGGTGATAAGGGAGGAGGT 57.028 50.000 0.00 0.00 0.00 3.85
918 1767 6.831664 ATATAGGCCATAAGGTGATAAGGG 57.168 41.667 5.01 0.00 37.19 3.95
976 1827 0.605083 TGCTAGTGTGCTCTGGTGAG 59.395 55.000 0.00 0.00 42.96 3.51
1056 1914 4.608514 TGGGTCAGGGCCAGGGAA 62.609 66.667 6.18 0.00 0.00 3.97
1182 2040 4.141287 CCTTGATGAGGTTGTTGGTGTTA 58.859 43.478 0.00 0.00 40.95 2.41
1536 2394 1.856265 GCAGGTTGTTGGCGAAGAGG 61.856 60.000 0.00 0.00 0.00 3.69
1639 2497 3.129988 AGACCTGCTTGCTTGATTAATGC 59.870 43.478 0.00 0.00 0.00 3.56
1658 2516 2.941453 TGACGACCTTGCATAGAGAC 57.059 50.000 0.00 0.00 0.00 3.36
1677 2535 2.304761 ACACGGTGACACCAGGATAAAT 59.695 45.455 24.18 0.00 38.47 1.40
1681 2539 1.671742 GACACGGTGACACCAGGAT 59.328 57.895 24.18 6.41 38.47 3.24
1684 2542 2.355837 CCGACACGGTGACACCAG 60.356 66.667 24.18 17.41 42.73 4.00
1695 2555 1.745087 TCCAGGTACGTAATCCGACAC 59.255 52.381 0.00 0.00 40.70 3.67
1709 2569 1.217244 GCGGTGTTATCGTCCAGGT 59.783 57.895 0.00 0.00 0.00 4.00
1713 2573 0.527817 CTCTGGCGGTGTTATCGTCC 60.528 60.000 0.00 0.00 0.00 4.79
1728 2588 6.924060 CGGTATAGGTAGAAACCATTTCTCTG 59.076 42.308 7.08 0.00 46.62 3.35
1738 2598 3.493503 GCATGCACGGTATAGGTAGAAAC 59.506 47.826 14.21 0.00 0.00 2.78
1748 2608 9.914131 CTACTATATAATATGCATGCACGGTAT 57.086 33.333 25.37 20.55 0.00 2.73
1753 2613 8.331022 GCACACTACTATATAATATGCATGCAC 58.669 37.037 25.37 0.00 0.00 4.57
1763 2625 7.623630 TGGATGCATGCACACTACTATATAAT 58.376 34.615 25.37 0.52 0.00 1.28
1843 2866 9.787435 ACACTATACAACAATTTAGGACAAGAA 57.213 29.630 0.00 0.00 0.00 2.52
1873 2896 9.965824 GTTTTGAAGGAAGAAAACAATCTCATA 57.034 29.630 0.00 0.00 40.35 2.15
1874 2897 7.649306 CGTTTTGAAGGAAGAAAACAATCTCAT 59.351 33.333 0.00 0.00 40.55 2.90
1882 2907 9.887406 TTATGATACGTTTTGAAGGAAGAAAAC 57.113 29.630 0.00 0.00 38.26 2.43
1899 2924 5.712217 ACACGGTGAAACATTATGATACG 57.288 39.130 16.29 0.00 39.98 3.06
1904 2929 5.637810 ACTGAGTACACGGTGAAACATTATG 59.362 40.000 16.29 0.00 39.98 1.90
1914 2939 3.426426 GCTCTCTTACTGAGTACACGGTG 60.426 52.174 14.27 6.58 43.13 4.94
2020 3047 7.201644 CGATATGGCATGAGTATCCCATAAAAC 60.202 40.741 10.98 6.06 39.34 2.43
2021 3048 6.823182 CGATATGGCATGAGTATCCCATAAAA 59.177 38.462 10.98 0.00 39.34 1.52
2027 3054 2.169352 AGCGATATGGCATGAGTATCCC 59.831 50.000 10.98 0.00 34.64 3.85
2032 3059 2.899900 TCCTTAGCGATATGGCATGAGT 59.100 45.455 10.98 0.00 34.64 3.41
2049 3076 0.251033 GTAAACCCCGCCTTGTCCTT 60.251 55.000 0.00 0.00 0.00 3.36
2050 3077 1.131928 AGTAAACCCCGCCTTGTCCT 61.132 55.000 0.00 0.00 0.00 3.85
2051 3078 0.675837 GAGTAAACCCCGCCTTGTCC 60.676 60.000 0.00 0.00 0.00 4.02
2054 3081 0.879090 GTTGAGTAAACCCCGCCTTG 59.121 55.000 0.00 0.00 32.13 3.61
2059 3086 2.194201 ATGGTGTTGAGTAAACCCCG 57.806 50.000 0.00 0.00 39.04 5.73
2060 3087 4.023726 TGTATGGTGTTGAGTAAACCCC 57.976 45.455 0.00 0.00 36.87 4.95
2118 3145 1.154112 AAAAATTAGCACGCGCGGG 60.154 52.632 35.22 33.30 45.49 6.13
2135 3162 3.058155 TGCTTATTTCGGCGCTGTAAAAA 60.058 39.130 17.37 10.10 0.00 1.94
2159 3188 2.718731 CCCAGTCACGCGCAAAAA 59.281 55.556 5.73 0.00 0.00 1.94
2167 3196 1.805945 GAGTTAGCGCCCAGTCACG 60.806 63.158 2.29 0.00 0.00 4.35
2169 3198 1.888436 CTGGAGTTAGCGCCCAGTCA 61.888 60.000 18.32 4.51 41.81 3.41
2170 3199 1.153549 CTGGAGTTAGCGCCCAGTC 60.154 63.158 18.32 11.19 41.81 3.51
2171 3200 2.982130 CTGGAGTTAGCGCCCAGT 59.018 61.111 18.32 2.61 41.81 4.00
2173 3202 3.315142 CTGCTGGAGTTAGCGCCCA 62.315 63.158 2.29 2.28 46.61 5.36
2175 3204 2.512515 CCTGCTGGAGTTAGCGCC 60.513 66.667 2.29 0.00 46.61 6.53
2178 3207 3.198489 GCGCCTGCTGGAGTTAGC 61.198 66.667 14.77 6.30 43.95 3.09
2190 3219 1.392589 CACCATATTTTCCAGCGCCT 58.607 50.000 2.29 0.00 0.00 5.52
2191 3220 0.249031 GCACCATATTTTCCAGCGCC 60.249 55.000 2.29 0.00 0.00 6.53
2192 3221 0.592247 CGCACCATATTTTCCAGCGC 60.592 55.000 0.00 0.00 37.20 5.92
2198 3227 4.494199 GCTATATCGCCGCACCATATTTTC 60.494 45.833 0.00 0.00 0.00 2.29
2206 3235 0.319555 TGAAGCTATATCGCCGCACC 60.320 55.000 0.00 0.00 0.00 5.01
2208 3237 0.958822 TCTGAAGCTATATCGCCGCA 59.041 50.000 0.00 0.00 0.00 5.69
2210 3239 3.238441 GTCTTCTGAAGCTATATCGCCG 58.762 50.000 12.54 0.00 0.00 6.46
2212 3241 2.659279 GCGTCTTCTGAAGCTATATCGC 59.341 50.000 12.54 15.00 42.85 4.58
2213 3242 2.905546 CGCGTCTTCTGAAGCTATATCG 59.094 50.000 12.54 10.27 43.73 2.92
2214 3243 2.659279 GCGCGTCTTCTGAAGCTATATC 59.341 50.000 12.54 0.00 43.73 1.63
2215 3244 2.294791 AGCGCGTCTTCTGAAGCTATAT 59.705 45.455 12.54 0.00 43.73 0.86
2216 3245 1.676529 AGCGCGTCTTCTGAAGCTATA 59.323 47.619 12.54 0.00 43.73 1.31
2217 3246 0.457851 AGCGCGTCTTCTGAAGCTAT 59.542 50.000 12.54 0.00 43.73 2.97
2218 3247 1.092348 TAGCGCGTCTTCTGAAGCTA 58.908 50.000 12.54 8.17 43.73 3.32
2220 3249 1.068474 TTTAGCGCGTCTTCTGAAGC 58.932 50.000 12.54 7.08 42.76 3.86
2223 3252 4.239304 TGTAAATTTAGCGCGTCTTCTGA 58.761 39.130 8.43 0.00 0.00 3.27
2224 3253 4.569029 CTGTAAATTTAGCGCGTCTTCTG 58.431 43.478 8.43 0.00 0.00 3.02
2227 3256 3.385079 GCTGTAAATTTAGCGCGTCTT 57.615 42.857 8.43 0.00 0.00 3.01
2235 3264 1.442765 CGCGTGCGCTGTAAATTTAG 58.557 50.000 9.73 0.00 39.32 1.85
2250 3279 1.506309 ATGTTGTGTGTGATGCGCGT 61.506 50.000 8.43 0.00 0.00 6.01
2254 3285 3.976942 GTGAGAAATGTTGTGTGTGATGC 59.023 43.478 0.00 0.00 0.00 3.91
2257 3288 5.895636 AAAGTGAGAAATGTTGTGTGTGA 57.104 34.783 0.00 0.00 0.00 3.58
2262 3293 8.870160 TCCATTTTAAAGTGAGAAATGTTGTG 57.130 30.769 11.94 0.00 38.47 3.33
2279 3310 9.912634 GTGTTTGATCTTCTTGATTCCATTTTA 57.087 29.630 0.00 0.00 35.14 1.52
2280 3311 8.423349 TGTGTTTGATCTTCTTGATTCCATTTT 58.577 29.630 0.00 0.00 35.14 1.82
2285 3316 8.647143 TTTTTGTGTTTGATCTTCTTGATTCC 57.353 30.769 0.00 0.00 35.14 3.01
2406 3441 9.392021 GTTTGATGTTGTTTTGTTTGATTTTGT 57.608 25.926 0.00 0.00 0.00 2.83
2407 3442 9.390795 TGTTTGATGTTGTTTTGTTTGATTTTG 57.609 25.926 0.00 0.00 0.00 2.44
2408 3443 9.956720 TTGTTTGATGTTGTTTTGTTTGATTTT 57.043 22.222 0.00 0.00 0.00 1.82
2409 3444 9.956720 TTTGTTTGATGTTGTTTTGTTTGATTT 57.043 22.222 0.00 0.00 0.00 2.17
2410 3445 9.392021 GTTTGTTTGATGTTGTTTTGTTTGATT 57.608 25.926 0.00 0.00 0.00 2.57
2411 3446 8.562892 TGTTTGTTTGATGTTGTTTTGTTTGAT 58.437 25.926 0.00 0.00 0.00 2.57
2412 3447 7.919690 TGTTTGTTTGATGTTGTTTTGTTTGA 58.080 26.923 0.00 0.00 0.00 2.69
2413 3448 8.467574 GTTGTTTGTTTGATGTTGTTTTGTTTG 58.532 29.630 0.00 0.00 0.00 2.93
2414 3449 8.184192 TGTTGTTTGTTTGATGTTGTTTTGTTT 58.816 25.926 0.00 0.00 0.00 2.83
2415 3450 7.697691 TGTTGTTTGTTTGATGTTGTTTTGTT 58.302 26.923 0.00 0.00 0.00 2.83
2416 3451 7.251704 TGTTGTTTGTTTGATGTTGTTTTGT 57.748 28.000 0.00 0.00 0.00 2.83
2417 3452 8.013947 TGATGTTGTTTGTTTGATGTTGTTTTG 58.986 29.630 0.00 0.00 0.00 2.44
2418 3453 8.092521 TGATGTTGTTTGTTTGATGTTGTTTT 57.907 26.923 0.00 0.00 0.00 2.43
2419 3454 7.664082 TGATGTTGTTTGTTTGATGTTGTTT 57.336 28.000 0.00 0.00 0.00 2.83
2420 3455 7.664082 TTGATGTTGTTTGTTTGATGTTGTT 57.336 28.000 0.00 0.00 0.00 2.83
2434 3469 5.292589 ACGACGAAACTAGTTTGATGTTGTT 59.707 36.000 25.17 11.43 32.11 2.83
2439 3474 3.985279 TGGACGACGAAACTAGTTTGATG 59.015 43.478 25.17 15.96 32.11 3.07
2440 3475 4.247267 TGGACGACGAAACTAGTTTGAT 57.753 40.909 25.17 12.60 32.11 2.57
2441 3476 3.713858 TGGACGACGAAACTAGTTTGA 57.286 42.857 25.17 0.00 32.11 2.69
2442 3477 4.985044 AATGGACGACGAAACTAGTTTG 57.015 40.909 25.17 18.00 32.11 2.93
2443 3478 5.051816 TGAAATGGACGACGAAACTAGTTT 58.948 37.500 20.67 20.67 35.14 2.66
2444 3479 4.624015 TGAAATGGACGACGAAACTAGTT 58.376 39.130 1.12 1.12 0.00 2.24
2453 3488 1.024046 TGGGCATGAAATGGACGACG 61.024 55.000 0.00 0.00 46.86 5.12
2458 3493 0.409092 AGTGGTGGGCATGAAATGGA 59.591 50.000 0.00 0.00 46.86 3.41
2464 3499 1.133181 TCAAGGAGTGGTGGGCATGA 61.133 55.000 0.00 0.00 0.00 3.07
2465 3500 0.033796 ATCAAGGAGTGGTGGGCATG 60.034 55.000 0.00 0.00 0.00 4.06
2470 3505 3.713764 AGGATCTAATCAAGGAGTGGTGG 59.286 47.826 0.00 0.00 0.00 4.61
2481 3516 7.555965 TGACGATCTTCAAAAGGATCTAATCA 58.444 34.615 0.00 0.00 36.97 2.57
2499 3534 0.657312 TGCCGAAATGCATGACGATC 59.343 50.000 21.64 14.82 36.04 3.69
2532 3567 3.200165 GGCCCGATTTATAGCCTCCTATT 59.800 47.826 0.00 0.00 42.34 1.73
2540 3575 2.942641 GGGTGGCCCGATTTATAGC 58.057 57.895 0.00 0.00 32.13 2.97
2562 3597 1.807165 CGAGTGTGGATGACGGCTG 60.807 63.158 0.00 0.00 0.00 4.85
2564 3599 3.188786 GCGAGTGTGGATGACGGC 61.189 66.667 0.00 0.00 0.00 5.68
2567 3602 0.108186 TCCATGCGAGTGTGGATGAC 60.108 55.000 0.00 0.00 39.78 3.06
2569 3604 0.729116 GTTCCATGCGAGTGTGGATG 59.271 55.000 0.00 0.00 43.61 3.51
2570 3605 0.740868 CGTTCCATGCGAGTGTGGAT 60.741 55.000 0.00 0.00 43.61 3.41
2571 3606 1.374125 CGTTCCATGCGAGTGTGGA 60.374 57.895 0.00 0.00 42.55 4.02
2574 3609 1.374252 GGACGTTCCATGCGAGTGT 60.374 57.895 0.00 0.00 36.28 3.55


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

AutoCloner maintained by Alex Coulton.