Multiple sequence alignment - TraesCS2A01G407500

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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 TraesCS2A01G407500 chr2A 100.000 3590 0 0 1 3590 663147775 663144186 0.000000e+00 6630
1 TraesCS2A01G407500 chr2A 85.000 360 41 10 1226 1579 10979572 10979924 1.590000e-93 353
2 TraesCS2A01G407500 chr2D 93.541 2926 78 41 1 2873 518968249 518971116 0.000000e+00 4253
3 TraesCS2A01G407500 chr2D 81.301 492 42 12 2992 3436 518971110 518971598 1.590000e-93 353
4 TraesCS2A01G407500 chr2B 93.793 2497 67 26 432 2867 611191620 611194089 0.000000e+00 3672
5 TraesCS2A01G407500 chr2B 89.474 627 24 6 2998 3588 611194090 611194710 0.000000e+00 754
6 TraesCS2A01G407500 chr2B 84.840 343 22 10 1 341 611191219 611191533 5.780000e-83 318
7 TraesCS2A01G407500 chr2B 93.525 139 9 0 2866 3004 118833793 118833931 1.310000e-49 207
8 TraesCS2A01G407500 chr2B 91.275 149 11 2 2871 3019 590923786 590923640 6.080000e-48 202
9 TraesCS2A01G407500 chr6A 88.960 1567 158 8 998 2552 456011563 456013126 0.000000e+00 1921
10 TraesCS2A01G407500 chr6A 95.385 130 6 0 2871 3000 116901392 116901263 1.310000e-49 207
11 TraesCS2A01G407500 chr6B 88.471 1570 162 13 997 2552 505683196 505681632 0.000000e+00 1879
12 TraesCS2A01G407500 chr6D 88.322 1567 168 8 998 2552 318453704 318455267 0.000000e+00 1866
13 TraesCS2A01G407500 chr3D 79.487 624 114 12 1892 2508 474655592 474656208 7.120000e-117 431
14 TraesCS2A01G407500 chr3D 76.868 696 115 34 1043 1718 474654761 474655430 5.700000e-93 351
15 TraesCS2A01G407500 chr3D 82.418 182 23 7 2226 2404 69906482 69906307 2.230000e-32 150
16 TraesCS2A01G407500 chr3B 79.327 624 115 12 1892 2508 631049171 631049787 3.310000e-115 425
17 TraesCS2A01G407500 chr3B 77.299 696 124 28 1043 1718 631048328 631049009 2.620000e-101 379
18 TraesCS2A01G407500 chr3B 91.034 145 11 2 2871 3014 421238968 421238825 1.020000e-45 195
19 TraesCS2A01G407500 chr3A 79.167 624 116 14 1892 2508 617074295 617074911 1.540000e-113 420
20 TraesCS2A01G407500 chr3A 77.122 695 127 26 1043 1718 617073452 617074133 1.220000e-99 374
21 TraesCS2A01G407500 chr4B 82.851 449 46 10 1558 1992 86080378 86079947 1.220000e-99 374
22 TraesCS2A01G407500 chrUn 94.203 138 5 3 2868 3004 259016 258881 1.310000e-49 207
23 TraesCS2A01G407500 chr1A 94.030 134 8 0 2864 2997 12159678 12159811 1.690000e-48 204
24 TraesCS2A01G407500 chr7A 92.754 138 10 0 2860 2997 77440530 77440667 2.190000e-47 200
25 TraesCS2A01G407500 chr7A 92.754 138 10 0 2871 3008 501074675 501074812 2.190000e-47 200
26 TraesCS2A01G407500 chr4A 92.754 138 10 0 2860 2997 112769335 112769472 2.190000e-47 200


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 TraesCS2A01G407500 chr2A 663144186 663147775 3589 True 6630.000000 6630 100.0000 1 3590 1 chr2A.!!$R1 3589
1 TraesCS2A01G407500 chr2D 518968249 518971598 3349 False 2303.000000 4253 87.4210 1 3436 2 chr2D.!!$F1 3435
2 TraesCS2A01G407500 chr2B 611191219 611194710 3491 False 1581.333333 3672 89.3690 1 3588 3 chr2B.!!$F2 3587
3 TraesCS2A01G407500 chr6A 456011563 456013126 1563 False 1921.000000 1921 88.9600 998 2552 1 chr6A.!!$F1 1554
4 TraesCS2A01G407500 chr6B 505681632 505683196 1564 True 1879.000000 1879 88.4710 997 2552 1 chr6B.!!$R1 1555
5 TraesCS2A01G407500 chr6D 318453704 318455267 1563 False 1866.000000 1866 88.3220 998 2552 1 chr6D.!!$F1 1554
6 TraesCS2A01G407500 chr3D 474654761 474656208 1447 False 391.000000 431 78.1775 1043 2508 2 chr3D.!!$F1 1465
7 TraesCS2A01G407500 chr3B 631048328 631049787 1459 False 402.000000 425 78.3130 1043 2508 2 chr3B.!!$F1 1465
8 TraesCS2A01G407500 chr3A 617073452 617074911 1459 False 397.000000 420 78.1445 1043 2508 2 chr3A.!!$F1 1465

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
397 421 0.105778 GCATGGCTCACCTAGACCTC 59.894 60.0 0.0 0.0 36.63 3.85 F
871 990 0.106569 TTCATTGCCATCCATCGCCT 60.107 50.0 0.0 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2369 2.033917 CGAGTAGATGGAGTACGTGACG 60.034 54.545 2.24 2.24 0.00 4.35 R
2641 2808 0.105224 CCCATATGGCACGAACCGTA 59.895 55.000 16.97 0.00 38.32 4.02 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
66 82 2.282040 GTGCAGGCTGCTTGACCT 60.282 61.111 36.50 0.00 45.31 3.85
70 86 2.753029 AGGCTGCTTGACCTGACC 59.247 61.111 0.00 0.00 34.07 4.02
134 150 1.133790 CTGCATTAGCTTTGCCTGACC 59.866 52.381 16.13 0.00 42.74 4.02
135 151 1.272092 TGCATTAGCTTTGCCTGACCT 60.272 47.619 16.13 0.00 42.74 3.85
136 152 1.133790 GCATTAGCTTTGCCTGACCTG 59.866 52.381 9.56 0.00 37.91 4.00
137 153 2.715046 CATTAGCTTTGCCTGACCTGA 58.285 47.619 0.00 0.00 0.00 3.86
138 154 3.285484 CATTAGCTTTGCCTGACCTGAT 58.715 45.455 0.00 0.00 0.00 2.90
139 155 4.454678 CATTAGCTTTGCCTGACCTGATA 58.545 43.478 0.00 0.00 0.00 2.15
140 156 2.706339 AGCTTTGCCTGACCTGATAG 57.294 50.000 0.00 0.00 0.00 2.08
141 157 1.211457 AGCTTTGCCTGACCTGATAGG 59.789 52.381 0.00 0.00 42.49 2.57
155 171 4.840680 ACCTGATAGGCTGATAGTAATGCA 59.159 41.667 0.00 0.00 39.63 3.96
178 194 1.779061 TTGGCACCAACCTCTCCTCC 61.779 60.000 0.00 0.00 0.00 4.30
179 195 2.671682 GCACCAACCTCTCCTCCC 59.328 66.667 0.00 0.00 0.00 4.30
180 196 2.972819 GCACCAACCTCTCCTCCCC 61.973 68.421 0.00 0.00 0.00 4.81
181 197 1.229658 CACCAACCTCTCCTCCCCT 60.230 63.158 0.00 0.00 0.00 4.79
182 198 1.081277 ACCAACCTCTCCTCCCCTC 59.919 63.158 0.00 0.00 0.00 4.30
185 201 0.689412 CAACCTCTCCTCCCCTCTCC 60.689 65.000 0.00 0.00 0.00 3.71
240 258 1.659098 CAAATCAAGGCTACGTCCGTC 59.341 52.381 0.00 0.00 0.00 4.79
244 262 2.694760 AAGGCTACGTCCGTCCGTC 61.695 63.158 0.00 0.00 42.00 4.79
246 264 3.130160 GCTACGTCCGTCCGTCCT 61.130 66.667 0.00 0.00 42.00 3.85
247 265 3.096791 CTACGTCCGTCCGTCCTC 58.903 66.667 0.00 0.00 42.00 3.71
249 267 2.866085 CTACGTCCGTCCGTCCTCCT 62.866 65.000 0.00 0.00 42.00 3.69
251 269 2.572284 GTCCGTCCGTCCTCCTTG 59.428 66.667 0.00 0.00 0.00 3.61
277 300 3.356267 ATGCACGCACACGCATGT 61.356 55.556 0.00 0.00 46.78 3.21
279 302 2.353376 GCACGCACACGCATGTTT 60.353 55.556 0.00 0.00 45.53 2.83
296 319 3.620488 TGTTTCACTGTTTCCTCAAGCT 58.380 40.909 0.00 0.00 0.00 3.74
297 320 3.378112 TGTTTCACTGTTTCCTCAAGCTG 59.622 43.478 0.00 0.00 0.00 4.24
298 321 1.597742 TCACTGTTTCCTCAAGCTGC 58.402 50.000 0.00 0.00 0.00 5.25
300 323 0.538287 ACTGTTTCCTCAAGCTGCCC 60.538 55.000 0.00 0.00 0.00 5.36
301 324 1.228552 TGTTTCCTCAAGCTGCCCC 60.229 57.895 0.00 0.00 0.00 5.80
303 326 3.567579 TTTCCTCAAGCTGCCCCGG 62.568 63.158 0.00 0.00 0.00 5.73
331 355 3.129502 CCTGCATGCACACTCCGG 61.130 66.667 18.46 11.89 0.00 5.14
341 365 0.243907 CACACTCCGGTCCTGTGTAG 59.756 60.000 18.75 12.47 42.19 2.74
343 367 0.811915 CACTCCGGTCCTGTGTAGAG 59.188 60.000 0.00 0.00 0.00 2.43
344 368 0.404812 ACTCCGGTCCTGTGTAGAGT 59.595 55.000 0.00 0.00 0.00 3.24
345 369 1.632409 ACTCCGGTCCTGTGTAGAGTA 59.368 52.381 0.00 0.00 33.01 2.59
346 370 2.241685 ACTCCGGTCCTGTGTAGAGTAT 59.758 50.000 0.00 0.00 33.01 2.12
347 371 2.619177 CTCCGGTCCTGTGTAGAGTATG 59.381 54.545 0.00 0.00 0.00 2.39
348 372 2.025605 TCCGGTCCTGTGTAGAGTATGT 60.026 50.000 0.00 0.00 0.00 2.29
349 373 3.200605 TCCGGTCCTGTGTAGAGTATGTA 59.799 47.826 0.00 0.00 0.00 2.29
350 374 4.141321 TCCGGTCCTGTGTAGAGTATGTAT 60.141 45.833 0.00 0.00 0.00 2.29
351 375 4.023107 CCGGTCCTGTGTAGAGTATGTATG 60.023 50.000 0.00 0.00 0.00 2.39
352 376 4.579340 CGGTCCTGTGTAGAGTATGTATGT 59.421 45.833 0.00 0.00 0.00 2.29
353 377 5.505819 CGGTCCTGTGTAGAGTATGTATGTG 60.506 48.000 0.00 0.00 0.00 3.21
354 378 5.360144 GGTCCTGTGTAGAGTATGTATGTGT 59.640 44.000 0.00 0.00 0.00 3.72
355 379 6.544931 GGTCCTGTGTAGAGTATGTATGTGTA 59.455 42.308 0.00 0.00 0.00 2.90
356 380 7.067859 GGTCCTGTGTAGAGTATGTATGTGTAA 59.932 40.741 0.00 0.00 0.00 2.41
357 381 8.464404 GTCCTGTGTAGAGTATGTATGTGTAAA 58.536 37.037 0.00 0.00 0.00 2.01
358 382 9.197306 TCCTGTGTAGAGTATGTATGTGTAAAT 57.803 33.333 0.00 0.00 0.00 1.40
393 417 0.543277 CCAAGCATGGCTCACCTAGA 59.457 55.000 0.00 0.00 40.58 2.43
394 418 1.661341 CAAGCATGGCTCACCTAGAC 58.339 55.000 0.00 0.00 38.25 2.59
395 419 0.543749 AAGCATGGCTCACCTAGACC 59.456 55.000 0.00 0.00 38.25 3.85
396 420 0.326048 AGCATGGCTCACCTAGACCT 60.326 55.000 0.00 0.00 30.62 3.85
397 421 0.105778 GCATGGCTCACCTAGACCTC 59.894 60.000 0.00 0.00 36.63 3.85
398 422 0.387202 CATGGCTCACCTAGACCTCG 59.613 60.000 0.00 0.00 36.63 4.63
497 554 2.653130 GCGCGCATTGAATGGCTC 60.653 61.111 29.10 0.57 0.00 4.70
799 918 0.180642 CCTCCAGCTGCAGTGATCAT 59.819 55.000 16.64 0.00 0.00 2.45
800 919 1.584175 CTCCAGCTGCAGTGATCATC 58.416 55.000 16.64 0.00 0.00 2.92
801 920 0.906775 TCCAGCTGCAGTGATCATCA 59.093 50.000 16.64 0.00 0.00 3.07
871 990 0.106569 TTCATTGCCATCCATCGCCT 60.107 50.000 0.00 0.00 0.00 5.52
879 998 2.123428 ATCCATCGCCTTGCTTGCC 61.123 57.895 0.00 0.00 0.00 4.52
883 1002 2.976490 ATCGCCTTGCTTGCCCTCT 61.976 57.895 0.00 0.00 0.00 3.69
964 1083 0.609406 CGTCCTCACCTCACCTCTCA 60.609 60.000 0.00 0.00 0.00 3.27
966 1085 0.251832 TCCTCACCTCACCTCTCACC 60.252 60.000 0.00 0.00 0.00 4.02
2641 2808 1.083806 CATGCATGCTCCACGTACGT 61.084 55.000 16.72 16.72 0.00 3.57
2642 2809 0.458260 ATGCATGCTCCACGTACGTA 59.542 50.000 22.34 5.28 0.00 3.57
2643 2810 0.457166 TGCATGCTCCACGTACGTAC 60.457 55.000 22.34 15.90 0.00 3.67
2767 2934 7.209340 AGGTGAGTATATCTACATCGGGATA 57.791 40.000 0.00 0.00 0.00 2.59
2854 3022 1.112950 GCCCCTCTCCTGTACTGTAC 58.887 60.000 10.98 10.98 0.00 2.90
2873 3041 7.222872 ACTGTACTGTACTGTACTGAACTACT 58.777 38.462 35.08 20.49 41.65 2.57
2874 3042 7.387397 ACTGTACTGTACTGTACTGAACTACTC 59.613 40.741 35.08 15.28 41.65 2.59
2875 3043 6.652481 TGTACTGTACTGTACTGAACTACTCC 59.348 42.308 30.96 11.21 42.22 3.85
2876 3044 5.878627 ACTGTACTGTACTGAACTACTCCT 58.121 41.667 25.41 3.27 0.00 3.69
2877 3045 6.305411 ACTGTACTGTACTGAACTACTCCTT 58.695 40.000 25.41 2.66 0.00 3.36
2878 3046 6.776603 ACTGTACTGTACTGAACTACTCCTTT 59.223 38.462 25.41 2.23 0.00 3.11
2879 3047 7.040548 ACTGTACTGTACTGAACTACTCCTTTC 60.041 40.741 25.41 0.00 0.00 2.62
2880 3048 6.774170 TGTACTGTACTGAACTACTCCTTTCA 59.226 38.462 17.98 0.00 0.00 2.69
2881 3049 6.919775 ACTGTACTGAACTACTCCTTTCAT 57.080 37.500 6.77 0.00 31.41 2.57
2882 3050 7.304497 ACTGTACTGAACTACTCCTTTCATT 57.696 36.000 6.77 0.00 31.41 2.57
2883 3051 7.379750 ACTGTACTGAACTACTCCTTTCATTC 58.620 38.462 6.77 0.00 31.41 2.67
2884 3052 6.698380 TGTACTGAACTACTCCTTTCATTCC 58.302 40.000 0.00 0.00 31.41 3.01
2885 3053 6.497259 TGTACTGAACTACTCCTTTCATTCCT 59.503 38.462 0.00 0.00 31.41 3.36
2886 3054 7.672660 TGTACTGAACTACTCCTTTCATTCCTA 59.327 37.037 0.00 0.00 31.41 2.94
2887 3055 7.554959 ACTGAACTACTCCTTTCATTCCTAA 57.445 36.000 0.00 0.00 31.41 2.69
2888 3056 8.152023 ACTGAACTACTCCTTTCATTCCTAAT 57.848 34.615 0.00 0.00 31.41 1.73
2889 3057 8.606830 ACTGAACTACTCCTTTCATTCCTAATT 58.393 33.333 0.00 0.00 31.41 1.40
2891 3059 9.886132 TGAACTACTCCTTTCATTCCTAATTAC 57.114 33.333 0.00 0.00 0.00 1.89
2894 3062 9.892130 ACTACTCCTTTCATTCCTAATTACTTG 57.108 33.333 0.00 0.00 0.00 3.16
2895 3063 9.892130 CTACTCCTTTCATTCCTAATTACTTGT 57.108 33.333 0.00 0.00 0.00 3.16
2896 3064 8.794335 ACTCCTTTCATTCCTAATTACTTGTC 57.206 34.615 0.00 0.00 0.00 3.18
2897 3065 8.606830 ACTCCTTTCATTCCTAATTACTTGTCT 58.393 33.333 0.00 0.00 0.00 3.41
2898 3066 9.454859 CTCCTTTCATTCCTAATTACTTGTCTT 57.545 33.333 0.00 0.00 0.00 3.01
2899 3067 9.231297 TCCTTTCATTCCTAATTACTTGTCTTG 57.769 33.333 0.00 0.00 0.00 3.02
2900 3068 8.462016 CCTTTCATTCCTAATTACTTGTCTTGG 58.538 37.037 0.00 0.00 0.00 3.61
2901 3069 9.231297 CTTTCATTCCTAATTACTTGTCTTGGA 57.769 33.333 0.00 0.00 0.00 3.53
2902 3070 9.753674 TTTCATTCCTAATTACTTGTCTTGGAT 57.246 29.630 0.00 0.00 0.00 3.41
2903 3071 9.753674 TTCATTCCTAATTACTTGTCTTGGATT 57.246 29.630 0.00 0.00 0.00 3.01
2904 3072 9.753674 TCATTCCTAATTACTTGTCTTGGATTT 57.246 29.630 0.00 0.00 0.00 2.17
2905 3073 9.793252 CATTCCTAATTACTTGTCTTGGATTTG 57.207 33.333 0.00 0.00 0.00 2.32
2906 3074 8.934023 TTCCTAATTACTTGTCTTGGATTTGT 57.066 30.769 0.00 0.00 0.00 2.83
2907 3075 8.561738 TCCTAATTACTTGTCTTGGATTTGTC 57.438 34.615 0.00 0.00 0.00 3.18
2908 3076 8.383175 TCCTAATTACTTGTCTTGGATTTGTCT 58.617 33.333 0.00 0.00 0.00 3.41
2909 3077 9.667107 CCTAATTACTTGTCTTGGATTTGTCTA 57.333 33.333 0.00 0.00 0.00 2.59
2912 3080 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2914 3082 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2915 3083 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
2916 3084 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
2917 3085 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
2918 3086 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
2919 3087 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
2920 3088 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
2921 3089 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
2922 3090 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
2940 3108 9.130312 CGGATGTATCTAGACTTATTTTAGTGC 57.870 37.037 0.00 0.00 0.00 4.40
2952 3120 9.562583 GACTTATTTTAGTGCTAGATATCTCCG 57.437 37.037 8.95 3.05 0.00 4.63
2953 3121 9.080097 ACTTATTTTAGTGCTAGATATCTCCGT 57.920 33.333 8.95 0.00 0.00 4.69
2957 3125 8.865420 TTTTAGTGCTAGATATCTCCGTATCT 57.135 34.615 8.95 4.71 42.50 1.98
2958 3126 9.955102 TTTTAGTGCTAGATATCTCCGTATCTA 57.045 33.333 8.95 3.82 40.79 1.98
2972 3140 8.380743 TCTCCGTATCTAGACAAATCTAAGAC 57.619 38.462 0.00 0.00 36.98 3.01
2973 3141 7.991460 TCTCCGTATCTAGACAAATCTAAGACA 59.009 37.037 0.00 0.00 36.98 3.41
2974 3142 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2975 3143 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2976 3144 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
2983 3151 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
2984 3152 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
2985 3153 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
2986 3154 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
3006 3174 2.421424 ACGGAGGAAGTACGTATGACAC 59.579 50.000 0.00 0.00 39.30 3.67
3008 3176 3.730061 CGGAGGAAGTACGTATGACACAC 60.730 52.174 0.00 0.00 0.00 3.82
3154 3350 1.077716 GTTGGTCCGGGCTGCTTAT 60.078 57.895 5.77 0.00 0.00 1.73
3156 3352 0.913205 TTGGTCCGGGCTGCTTATTA 59.087 50.000 5.77 0.00 0.00 0.98
3157 3353 0.913205 TGGTCCGGGCTGCTTATTAA 59.087 50.000 5.77 0.00 0.00 1.40
3322 3556 3.384668 CTTTGTCGAGGCGATACATCAT 58.615 45.455 0.00 0.00 38.42 2.45
3370 3604 3.285484 AGGAGGCAATGCAAACTGATAG 58.715 45.455 7.79 0.00 0.00 2.08
3507 3749 6.255887 GTCACTTTATTTCTGAATCGTCCGAT 59.744 38.462 0.00 0.00 36.23 4.18
3519 3761 1.332686 TCGTCCGATCAGTATCCAACG 59.667 52.381 0.00 0.00 37.64 4.10
3558 3800 5.048434 CAGAAGGAAAGAGGGAAAATGTGAC 60.048 44.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 82 2.669569 GGCTGCGAGCTTTGGTCA 60.670 61.111 7.85 0.00 41.99 4.02
67 83 3.793144 CGGCTGCGAGCTTTGGTC 61.793 66.667 7.85 0.00 41.99 4.02
132 148 4.840680 TGCATTACTATCAGCCTATCAGGT 59.159 41.667 0.00 0.00 37.80 4.00
134 150 6.035368 ACTGCATTACTATCAGCCTATCAG 57.965 41.667 0.00 0.00 0.00 2.90
135 151 6.425210 AACTGCATTACTATCAGCCTATCA 57.575 37.500 0.00 0.00 0.00 2.15
136 152 7.308229 CCAAAACTGCATTACTATCAGCCTATC 60.308 40.741 0.00 0.00 0.00 2.08
137 153 6.488006 CCAAAACTGCATTACTATCAGCCTAT 59.512 38.462 0.00 0.00 0.00 2.57
138 154 5.822519 CCAAAACTGCATTACTATCAGCCTA 59.177 40.000 0.00 0.00 0.00 3.93
139 155 4.641989 CCAAAACTGCATTACTATCAGCCT 59.358 41.667 0.00 0.00 0.00 4.58
140 156 4.734695 GCCAAAACTGCATTACTATCAGCC 60.735 45.833 0.00 0.00 0.00 4.85
141 157 4.142403 TGCCAAAACTGCATTACTATCAGC 60.142 41.667 0.00 0.00 32.85 4.26
155 171 1.692411 GAGAGGTTGGTGCCAAAACT 58.308 50.000 5.09 7.12 37.70 2.66
178 194 3.391382 GGGACGTGTGGGAGAGGG 61.391 72.222 0.00 0.00 0.00 4.30
240 258 1.672356 CAACAGGCAAGGAGGACGG 60.672 63.158 0.00 0.00 0.00 4.79
251 269 4.345962 TGCGTGCATGCAACAGGC 62.346 61.111 30.70 22.19 46.34 4.85
277 300 2.358898 GCAGCTTGAGGAAACAGTGAAA 59.641 45.455 0.00 0.00 0.00 2.69
279 302 1.597742 GCAGCTTGAGGAAACAGTGA 58.402 50.000 0.00 0.00 0.00 3.41
303 326 4.853050 ATGCAGGCTCGCAGCTCC 62.853 66.667 14.99 0.00 46.99 4.70
304 327 3.574445 CATGCAGGCTCGCAGCTC 61.574 66.667 14.99 0.13 46.99 4.09
313 337 3.807538 CGGAGTGTGCATGCAGGC 61.808 66.667 23.41 18.05 0.00 4.85
331 355 6.452494 ACACATACATACTCTACACAGGAC 57.548 41.667 0.00 0.00 0.00 3.85
357 381 9.912634 CCATGCTTGGTCGATTTTATATTTTAT 57.087 29.630 10.48 0.00 38.30 1.40
358 382 7.865385 GCCATGCTTGGTCGATTTTATATTTTA 59.135 33.333 19.05 0.00 45.57 1.52
359 383 6.701400 GCCATGCTTGGTCGATTTTATATTTT 59.299 34.615 19.05 0.00 45.57 1.82
360 384 6.040842 AGCCATGCTTGGTCGATTTTATATTT 59.959 34.615 19.05 0.00 45.57 1.40
361 385 5.536161 AGCCATGCTTGGTCGATTTTATATT 59.464 36.000 19.05 0.00 45.57 1.28
362 386 5.072741 AGCCATGCTTGGTCGATTTTATAT 58.927 37.500 19.05 0.00 45.57 0.86
363 387 4.460263 AGCCATGCTTGGTCGATTTTATA 58.540 39.130 19.05 0.00 45.57 0.98
374 398 0.543277 TCTAGGTGAGCCATGCTTGG 59.457 55.000 14.22 14.22 46.66 3.61
422 451 4.096003 CCCTGCACCACCCTACCG 62.096 72.222 0.00 0.00 0.00 4.02
642 731 3.670377 GGCCATTAATCGCCGCCC 61.670 66.667 8.41 0.00 34.94 6.13
692 800 0.934496 TGAAGAAGGTTTGACGTGCG 59.066 50.000 0.00 0.00 0.00 5.34
871 990 4.033776 CGGGGAGAGGGCAAGCAA 62.034 66.667 0.00 0.00 0.00 3.91
883 1002 0.040058 TATATAGAAGCGGCCGGGGA 59.960 55.000 29.38 0.00 0.00 4.81
990 1109 0.879400 CTGCCTCCATCGCTAAGCTG 60.879 60.000 0.00 0.00 0.00 4.24
1801 1926 4.070552 GGACCCGTCGCTCTTGCT 62.071 66.667 0.00 0.00 36.97 3.91
2208 2366 2.054232 AGATGGAGTACGTGACGGAT 57.946 50.000 10.66 0.00 0.00 4.18
2211 2369 2.033917 CGAGTAGATGGAGTACGTGACG 60.034 54.545 2.24 2.24 0.00 4.35
2641 2808 0.105224 CCCATATGGCACGAACCGTA 59.895 55.000 16.97 0.00 38.32 4.02
2642 2809 1.153249 CCCATATGGCACGAACCGT 60.153 57.895 16.97 0.00 42.36 4.83
2643 2810 1.891919 CCCCATATGGCACGAACCG 60.892 63.158 16.97 0.00 0.00 4.44
2644 2811 0.106918 TTCCCCATATGGCACGAACC 60.107 55.000 16.97 0.00 0.00 3.62
2767 2934 9.768215 TTGGATATTTTTAGACAGATCCCTTTT 57.232 29.630 0.00 0.00 33.33 2.27
2837 3005 3.088789 ACAGTACAGTACAGGAGAGGG 57.911 52.381 13.37 0.00 0.00 4.30
2854 3022 6.821031 AAGGAGTAGTTCAGTACAGTACAG 57.179 41.667 13.37 5.12 0.00 2.74
2873 3041 9.231297 CAAGACAAGTAATTAGGAATGAAAGGA 57.769 33.333 0.00 0.00 0.00 3.36
2874 3042 8.462016 CCAAGACAAGTAATTAGGAATGAAAGG 58.538 37.037 0.00 0.00 0.00 3.11
2875 3043 9.231297 TCCAAGACAAGTAATTAGGAATGAAAG 57.769 33.333 0.00 0.00 0.00 2.62
2876 3044 9.753674 ATCCAAGACAAGTAATTAGGAATGAAA 57.246 29.630 0.00 0.00 0.00 2.69
2877 3045 9.753674 AATCCAAGACAAGTAATTAGGAATGAA 57.246 29.630 0.00 0.00 0.00 2.57
2878 3046 9.753674 AAATCCAAGACAAGTAATTAGGAATGA 57.246 29.630 0.00 0.00 0.00 2.57
2879 3047 9.793252 CAAATCCAAGACAAGTAATTAGGAATG 57.207 33.333 0.00 0.00 0.00 2.67
2880 3048 9.533831 ACAAATCCAAGACAAGTAATTAGGAAT 57.466 29.630 0.00 0.00 0.00 3.01
2881 3049 8.934023 ACAAATCCAAGACAAGTAATTAGGAA 57.066 30.769 0.00 0.00 0.00 3.36
2882 3050 8.383175 AGACAAATCCAAGACAAGTAATTAGGA 58.617 33.333 0.00 0.00 0.00 2.94
2883 3051 8.567285 AGACAAATCCAAGACAAGTAATTAGG 57.433 34.615 0.00 0.00 0.00 2.69
2886 3054 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2888 3056 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2889 3057 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
2890 3058 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
2891 3059 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
2892 3060 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
2893 3061 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
2894 3062 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
2895 3063 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
2896 3064 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
2897 3065 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
2898 3066 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
2914 3082 9.130312 GCACTAAAATAAGTCTAGATACATCCG 57.870 37.037 0.00 0.00 0.00 4.18
2926 3094 9.562583 CGGAGATATCTAGCACTAAAATAAGTC 57.437 37.037 4.89 0.00 0.00 3.01
2927 3095 9.080097 ACGGAGATATCTAGCACTAAAATAAGT 57.920 33.333 4.89 0.00 0.00 2.24
2931 3099 9.469097 AGATACGGAGATATCTAGCACTAAAAT 57.531 33.333 4.89 0.00 39.63 1.82
2932 3100 8.865420 AGATACGGAGATATCTAGCACTAAAA 57.135 34.615 4.89 0.00 39.63 1.52
2946 3114 9.005777 GTCTTAGATTTGTCTAGATACGGAGAT 57.994 37.037 0.00 0.00 0.00 2.75
2947 3115 7.991460 TGTCTTAGATTTGTCTAGATACGGAGA 59.009 37.037 0.00 0.00 0.00 3.71
2948 3116 8.155821 TGTCTTAGATTTGTCTAGATACGGAG 57.844 38.462 0.00 0.00 0.00 4.63
2949 3117 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2950 3118 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
2957 3125 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
2958 3126 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
2959 3127 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
2960 3128 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
2961 3129 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
2962 3130 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
2963 3131 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
2964 3132 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
2965 3133 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
2966 3134 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
2967 3135 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
2968 3136 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2969 3137 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2970 3138 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2971 3139 2.564062 TCCTCCGTTCCGAATTACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
2972 3140 3.241067 TCCTCCGTTCCGAATTACTTG 57.759 47.619 0.00 0.00 0.00 3.16
2973 3141 3.260128 ACTTCCTCCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
2974 3142 2.830321 ACTTCCTCCGTTCCGAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
2975 3143 3.242549 ACTTCCTCCGTTCCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
2976 3144 3.181497 CGTACTTCCTCCGTTCCGAATTA 60.181 47.826 0.00 0.00 0.00 1.40
2977 3145 2.416431 CGTACTTCCTCCGTTCCGAATT 60.416 50.000 0.00 0.00 0.00 2.17
2978 3146 1.133790 CGTACTTCCTCCGTTCCGAAT 59.866 52.381 0.00 0.00 0.00 3.34
2979 3147 0.523072 CGTACTTCCTCCGTTCCGAA 59.477 55.000 0.00 0.00 0.00 4.30
2980 3148 0.606401 ACGTACTTCCTCCGTTCCGA 60.606 55.000 0.00 0.00 0.00 4.55
2981 3149 1.086696 TACGTACTTCCTCCGTTCCG 58.913 55.000 0.00 0.00 36.12 4.30
2982 3150 2.684881 TCATACGTACTTCCTCCGTTCC 59.315 50.000 0.00 0.00 36.12 3.62
2983 3151 3.127548 TGTCATACGTACTTCCTCCGTTC 59.872 47.826 0.00 0.00 36.12 3.95
2984 3152 3.084039 TGTCATACGTACTTCCTCCGTT 58.916 45.455 0.00 0.00 36.12 4.44
2985 3153 2.421424 GTGTCATACGTACTTCCTCCGT 59.579 50.000 0.00 0.00 38.53 4.69
2986 3154 2.421073 TGTGTCATACGTACTTCCTCCG 59.579 50.000 0.00 0.00 0.00 4.63
2987 3155 3.442977 AGTGTGTCATACGTACTTCCTCC 59.557 47.826 0.00 0.00 0.00 4.30
2988 3156 4.698583 AGTGTGTCATACGTACTTCCTC 57.301 45.455 0.00 0.00 0.00 3.71
2989 3157 5.494724 TCTAGTGTGTCATACGTACTTCCT 58.505 41.667 0.00 0.00 0.00 3.36
2990 3158 5.808042 TCTAGTGTGTCATACGTACTTCC 57.192 43.478 0.00 0.00 0.00 3.46
2991 3159 6.741811 CACTTCTAGTGTGTCATACGTACTTC 59.258 42.308 0.00 0.00 41.19 3.01
2992 3160 6.609533 CACTTCTAGTGTGTCATACGTACTT 58.390 40.000 0.00 0.00 41.19 2.24
2993 3161 6.179504 CACTTCTAGTGTGTCATACGTACT 57.820 41.667 0.00 0.00 41.19 2.73
3008 3176 7.707035 ACGAATTTGGAGCTTATACACTTCTAG 59.293 37.037 0.00 0.00 0.00 2.43
3096 3267 5.428496 AATCATATGTTTCACCTCGCATG 57.572 39.130 1.90 0.00 0.00 4.06
3154 3350 5.592688 CGCCAGAAATAGAAAGGGGAATTAA 59.407 40.000 0.00 0.00 34.56 1.40
3156 3352 3.954258 CGCCAGAAATAGAAAGGGGAATT 59.046 43.478 0.00 0.00 34.56 2.17
3157 3353 3.053619 ACGCCAGAAATAGAAAGGGGAAT 60.054 43.478 0.00 0.00 36.31 3.01
3288 3493 1.149148 GACAAAGGAAGAGTGTCGCC 58.851 55.000 0.00 0.00 32.98 5.54
3370 3604 3.628280 AAGGCGCGTCGGAACTCTC 62.628 63.158 8.43 0.00 0.00 3.20
3465 3707 5.841957 AGTGACTGAAACAGCTGAAAAAT 57.158 34.783 23.35 0.27 34.37 1.82
3472 3714 6.767902 TCAGAAATAAAGTGACTGAAACAGCT 59.232 34.615 0.00 0.00 35.20 4.24
3473 3715 6.959361 TCAGAAATAAAGTGACTGAAACAGC 58.041 36.000 0.00 0.00 35.20 4.40
3474 3716 9.604626 GATTCAGAAATAAAGTGACTGAAACAG 57.395 33.333 0.00 0.00 45.89 3.16
3480 3722 6.454318 CGGACGATTCAGAAATAAAGTGACTG 60.454 42.308 0.00 0.00 0.00 3.51
3507 3749 5.785243 TGTATGTTGTTCGTTGGATACTGA 58.215 37.500 0.00 0.00 37.61 3.41
3519 3761 6.371809 TTCCTTCTGTGTTGTATGTTGTTC 57.628 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.