Multiple sequence alignment - TraesCS2D01G473100

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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 TraesCS2D01G473100 chr2D 100.000 4432 0 0 1 4432 576849385 576853816 0.000000e+00 8185.0
1 TraesCS2D01G473100 chr2D 95.556 180 7 1 2881 3059 632423579 632423758 2.020000e-73 287.0
2 TraesCS2D01G473100 chr2D 95.000 180 8 1 2881 3059 632685870 632686049 9.390000e-72 281.0
3 TraesCS2D01G473100 chr2B 96.103 2900 93 11 1 2887 692710625 692713517 0.000000e+00 4711.0
4 TraesCS2D01G473100 chr2B 93.537 851 38 8 3048 3896 692713515 692714350 0.000000e+00 1251.0
5 TraesCS2D01G473100 chr2B 88.387 310 25 6 4018 4320 692714508 692714813 3.260000e-96 363.0
6 TraesCS2D01G473100 chr2B 89.806 206 15 6 2867 3069 456021157 456021359 4.400000e-65 259.0
7 TraesCS2D01G473100 chr2B 88.462 52 4 2 4332 4383 694052546 694052595 1.330000e-05 62.1
8 TraesCS2D01G473100 chr2A 95.243 2670 90 18 75 2737 714622041 714624680 0.000000e+00 4193.0
9 TraesCS2D01G473100 chr2A 96.169 783 23 4 3048 3830 714624784 714625559 0.000000e+00 1273.0
10 TraesCS2D01G473100 chr2A 95.953 593 22 2 3841 4432 714625648 714626239 0.000000e+00 961.0
11 TraesCS2D01G473100 chr2A 97.959 98 2 0 2784 2881 714624678 714624775 2.120000e-38 171.0
12 TraesCS2D01G473100 chr5D 84.339 613 66 15 2295 2903 298133964 298134550 1.380000e-159 573.0
13 TraesCS2D01G473100 chr5D 88.651 467 38 5 1757 2221 298133470 298133923 5.010000e-154 555.0
14 TraesCS2D01G473100 chr5D 83.135 504 74 10 3188 3690 298134677 298135170 2.430000e-122 449.0
15 TraesCS2D01G473100 chr5D 95.977 174 7 0 2884 3057 274578177 274578004 2.610000e-72 283.0
16 TraesCS2D01G473100 chr1D 87.190 484 47 8 1822 2300 408737939 408737466 1.810000e-148 536.0
17 TraesCS2D01G473100 chr1D 91.803 61 5 0 4276 4336 479770869 479770929 7.900000e-13 86.1
18 TraesCS2D01G473100 chr3B 84.813 428 51 10 3268 3690 259375304 259375722 6.860000e-113 418.0
19 TraesCS2D01G473100 chr3B 95.429 175 8 0 2880 3054 571752520 571752694 3.380000e-71 279.0
20 TraesCS2D01G473100 chr4D 96.512 172 6 0 2880 3051 93079373 93079202 7.260000e-73 285.0
21 TraesCS2D01G473100 chr4D 86.538 52 5 2 4332 4383 482704162 482704211 6.190000e-04 56.5
22 TraesCS2D01G473100 chr7B 95.455 176 7 1 2884 3059 186866520 186866694 3.380000e-71 279.0
23 TraesCS2D01G473100 chr3A 94.505 182 7 2 2877 3057 582946253 582946432 1.210000e-70 278.0
24 TraesCS2D01G473100 chr3A 89.474 209 17 5 2843 3049 217823163 217823368 4.400000e-65 259.0
25 TraesCS2D01G473100 chr1A 91.667 60 5 0 4277 4336 576217309 576217368 2.840000e-12 84.2
26 TraesCS2D01G473100 chr1A 86.885 61 8 0 4276 4336 576212494 576212554 7.950000e-08 69.4
27 TraesCS2D01G473100 chr7D 97.619 42 1 0 4341 4382 230465039 230465080 6.150000e-09 73.1
28 TraesCS2D01G473100 chr5B 93.182 44 3 0 4340 4383 603885796 603885839 1.030000e-06 65.8
29 TraesCS2D01G473100 chr3D 90.196 51 3 2 4332 4382 543010791 543010743 1.030000e-06 65.8
30 TraesCS2D01G473100 chr7A 95.000 40 2 0 4343 4382 623776178 623776139 3.700000e-06 63.9
31 TraesCS2D01G473100 chr4B 86.538 52 5 2 4332 4383 612274879 612274928 6.190000e-04 56.5
32 TraesCS2D01G473100 chr4A 86.538 52 5 2 4338 4388 255306986 255307036 6.190000e-04 56.5


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 TraesCS2D01G473100 chr2D 576849385 576853816 4431 False 8185.000000 8185 100.000000 1 4432 1 chr2D.!!$F1 4431
1 TraesCS2D01G473100 chr2B 692710625 692714813 4188 False 2108.333333 4711 92.675667 1 4320 3 chr2B.!!$F3 4319
2 TraesCS2D01G473100 chr2A 714622041 714626239 4198 False 1649.500000 4193 96.331000 75 4432 4 chr2A.!!$F1 4357
3 TraesCS2D01G473100 chr5D 298133470 298135170 1700 False 525.666667 573 85.375000 1757 3690 3 chr5D.!!$F1 1933

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
439 446 0.032813 TCGGTAGGGTCGGGAGATTT 60.033 55.000 0.00 0.0 43.27 2.17 F
440 447 0.828677 CGGTAGGGTCGGGAGATTTT 59.171 55.000 0.00 0.0 43.27 1.82 F
1060 1070 1.001764 CTGCCCATTGAGCCACTCA 60.002 57.895 0.00 0.0 38.87 3.41 F
2389 2401 0.462789 GATTTTCCAGCTGCCATGGG 59.537 55.000 15.13 0.0 38.44 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 2383 0.252375 ACCCATGGCAGCTGGAAAAT 60.252 50.000 17.12 0.0 35.70 1.82 R
2389 2401 5.590530 ACCTGATGTTATCTCAGTCTCAC 57.409 43.478 0.00 0.0 38.77 3.51 R
2926 2946 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.0 0.00 3.16 R
3832 3856 0.173935 CACCTGTCCGTTGCCGTATA 59.826 55.000 0.00 0.0 0.00 1.47 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
274 277 4.036734 GCTCATGTCTGGTTTGTTTCTTGA 59.963 41.667 0.00 0.00 0.00 3.02
353 360 5.163754 GGTTCCTCTGTTTTGATCCGTATTG 60.164 44.000 0.00 0.00 0.00 1.90
355 362 3.941483 CCTCTGTTTTGATCCGTATTGCT 59.059 43.478 0.00 0.00 0.00 3.91
396 403 1.451387 GTGCCCCATTGTAGGACGG 60.451 63.158 0.00 0.00 0.00 4.79
408 415 2.111077 TGTAGGACGGGATGGGATGATA 59.889 50.000 0.00 0.00 0.00 2.15
419 426 6.060788 GGGATGGGATGATATTCTAGATTGC 58.939 44.000 0.00 0.00 0.00 3.56
420 427 6.126536 GGGATGGGATGATATTCTAGATTGCT 60.127 42.308 0.00 0.00 0.00 3.91
424 431 5.105146 GGGATGATATTCTAGATTGCTCGGT 60.105 44.000 0.00 0.00 0.00 4.69
429 436 2.750141 TCTAGATTGCTCGGTAGGGT 57.250 50.000 0.00 0.00 0.00 4.34
430 437 2.584236 TCTAGATTGCTCGGTAGGGTC 58.416 52.381 0.00 0.00 0.00 4.46
432 439 1.067582 GATTGCTCGGTAGGGTCGG 59.932 63.158 0.00 0.00 0.00 4.79
433 440 2.365095 GATTGCTCGGTAGGGTCGGG 62.365 65.000 0.00 0.00 0.00 5.14
434 441 2.866523 ATTGCTCGGTAGGGTCGGGA 62.867 60.000 0.00 0.00 0.00 5.14
435 442 3.217743 GCTCGGTAGGGTCGGGAG 61.218 72.222 0.00 0.00 0.00 4.30
436 443 2.593978 CTCGGTAGGGTCGGGAGA 59.406 66.667 0.00 0.00 0.00 3.71
437 444 1.150992 CTCGGTAGGGTCGGGAGAT 59.849 63.158 0.00 0.00 43.27 2.75
438 445 0.467659 CTCGGTAGGGTCGGGAGATT 60.468 60.000 0.00 0.00 43.27 2.40
439 446 0.032813 TCGGTAGGGTCGGGAGATTT 60.033 55.000 0.00 0.00 43.27 2.17
440 447 0.828677 CGGTAGGGTCGGGAGATTTT 59.171 55.000 0.00 0.00 43.27 1.82
441 448 1.202498 CGGTAGGGTCGGGAGATTTTC 60.202 57.143 0.00 0.00 43.27 2.29
442 449 1.835531 GGTAGGGTCGGGAGATTTTCA 59.164 52.381 0.00 0.00 43.27 2.69
443 450 2.419713 GGTAGGGTCGGGAGATTTTCAC 60.420 54.545 0.00 0.00 43.27 3.18
454 461 1.985895 AGATTTTCACCCCCTCTCGTT 59.014 47.619 0.00 0.00 0.00 3.85
465 472 2.438021 CCCCTCTCGTTTGGATATTGGA 59.562 50.000 0.00 0.00 0.00 3.53
467 474 4.446311 CCCCTCTCGTTTGGATATTGGATT 60.446 45.833 0.00 0.00 0.00 3.01
504 511 6.103205 AGGTCTTAATGTGTTGGATGGGATAT 59.897 38.462 0.00 0.00 0.00 1.63
716 724 7.173390 GGATCTATTAAGTTGCTGTTATGGACC 59.827 40.741 0.00 0.00 0.00 4.46
723 731 4.832266 AGTTGCTGTTATGGACCAAAATGA 59.168 37.500 0.00 0.00 0.00 2.57
746 755 3.731652 TGCAAGTTTGTAGCAGCATTT 57.268 38.095 0.00 0.00 33.75 2.32
753 762 2.437200 TGTAGCAGCATTTGGTTTGC 57.563 45.000 0.00 0.00 38.70 3.68
757 766 1.571215 GCAGCATTTGGTTTGCCTGC 61.571 55.000 0.00 0.00 41.06 4.85
774 783 3.074412 CCTGCCTTGTGTACCTTTGTAG 58.926 50.000 0.00 0.00 0.00 2.74
928 937 8.695456 ACTGTTGTTCTCATTGAAGGTAAATTT 58.305 29.630 0.00 0.00 35.01 1.82
960 970 2.171840 GTAGACTCAGCACTCTTGGGA 58.828 52.381 0.00 0.00 0.00 4.37
1060 1070 1.001764 CTGCCCATTGAGCCACTCA 60.002 57.895 0.00 0.00 38.87 3.41
1324 1334 5.251764 GACCTGTAGAGTCTGGTAGTACAA 58.748 45.833 1.86 0.00 39.21 2.41
1787 1797 7.969004 TCGGTTATATCTGGGAATGTATCAAA 58.031 34.615 0.00 0.00 0.00 2.69
2292 2304 9.798994 AGCATGCAATTAAAAATTTGAACAAAA 57.201 22.222 21.98 0.00 33.56 2.44
2371 2383 3.936203 AGGCCAAACTCCGCGTGA 61.936 61.111 5.01 0.59 0.00 4.35
2389 2401 0.462789 GATTTTCCAGCTGCCATGGG 59.537 55.000 15.13 0.00 38.44 4.00
2867 2882 2.361757 TGATTGGACTTGTTTGGCTGTG 59.638 45.455 0.00 0.00 0.00 3.66
2887 2907 8.414778 GGCTGTGTGAGACTAAAGTATAATACT 58.585 37.037 0.00 0.00 41.73 2.12
2890 2910 8.910944 TGTGTGAGACTAAAGTATAATACTCCC 58.089 37.037 0.00 0.00 38.26 4.30
2891 2911 9.134055 GTGTGAGACTAAAGTATAATACTCCCT 57.866 37.037 0.00 0.00 38.26 4.20
2892 2912 9.352191 TGTGAGACTAAAGTATAATACTCCCTC 57.648 37.037 0.00 0.00 38.26 4.30
2893 2913 8.795513 GTGAGACTAAAGTATAATACTCCCTCC 58.204 40.741 0.00 0.00 38.26 4.30
2894 2914 7.664731 TGAGACTAAAGTATAATACTCCCTCCG 59.335 40.741 0.00 0.00 38.26 4.63
2896 2916 8.003629 AGACTAAAGTATAATACTCCCTCCGTT 58.996 37.037 0.00 0.00 38.26 4.44
2898 2918 6.416631 AAAGTATAATACTCCCTCCGTTCC 57.583 41.667 0.00 0.00 38.26 3.62
2899 2919 5.336491 AGTATAATACTCCCTCCGTTCCT 57.664 43.478 0.00 0.00 32.47 3.36
2903 2923 7.954620 AGTATAATACTCCCTCCGTTCCTAAAT 59.045 37.037 0.00 0.00 32.47 1.40
2905 2925 8.912614 ATAATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
2907 2927 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2908 2928 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2909 2929 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2910 2930 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2911 2931 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2912 2932 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2913 2933 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2916 2936 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2917 2937 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2918 2938 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2933 2953 9.996554 TGTCTTTCTAGATATTTCAACAAGTGA 57.003 29.630 0.00 0.00 31.86 3.41
2942 2962 9.302345 AGATATTTCAACAAGTGACTACATACG 57.698 33.333 0.00 0.00 35.39 3.06
2943 2963 6.721571 ATTTCAACAAGTGACTACATACGG 57.278 37.500 0.00 0.00 35.39 4.02
2944 2964 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2945 2965 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2946 2966 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2947 2967 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2948 2968 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2949 2969 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2950 2970 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2951 2971 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2952 2972 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2953 2973 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2954 2974 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2955 2975 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2956 2976 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2957 2977 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2958 2978 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2959 2979 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2960 2980 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2961 2981 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2962 2982 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2963 2983 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2964 2984 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2965 2985 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3003 3023 4.806330 CATACATCCGTATGTGGTAGTCC 58.194 47.826 3.56 0.00 46.70 3.85
3004 3024 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
3005 3025 3.101437 ACATCCGTATGTGGTAGTCCAA 58.899 45.455 0.00 0.00 44.79 3.53
3006 3026 3.709653 ACATCCGTATGTGGTAGTCCAAT 59.290 43.478 0.00 0.00 44.79 3.16
3007 3027 4.163458 ACATCCGTATGTGGTAGTCCAATT 59.837 41.667 0.00 0.00 44.79 2.32
3008 3028 4.131649 TCCGTATGTGGTAGTCCAATTG 57.868 45.455 0.00 0.00 46.15 2.32
3009 3029 3.770388 TCCGTATGTGGTAGTCCAATTGA 59.230 43.478 7.12 0.00 46.15 2.57
3010 3030 4.223255 TCCGTATGTGGTAGTCCAATTGAA 59.777 41.667 7.12 0.00 46.15 2.69
3011 3031 4.938832 CCGTATGTGGTAGTCCAATTGAAA 59.061 41.667 7.12 0.00 46.15 2.69
3012 3032 5.588648 CCGTATGTGGTAGTCCAATTGAAAT 59.411 40.000 7.12 0.00 46.15 2.17
3013 3033 6.458206 CCGTATGTGGTAGTCCAATTGAAATG 60.458 42.308 7.12 0.00 46.15 2.32
3014 3034 6.093495 CGTATGTGGTAGTCCAATTGAAATGT 59.907 38.462 7.12 0.00 46.15 2.71
3015 3035 5.957842 TGTGGTAGTCCAATTGAAATGTC 57.042 39.130 7.12 0.00 46.15 3.06
3016 3036 5.630121 TGTGGTAGTCCAATTGAAATGTCT 58.370 37.500 7.12 0.00 46.15 3.41
3017 3037 6.774673 TGTGGTAGTCCAATTGAAATGTCTA 58.225 36.000 7.12 0.00 46.15 2.59
3018 3038 6.653320 TGTGGTAGTCCAATTGAAATGTCTAC 59.347 38.462 7.12 7.50 46.15 2.59
3019 3039 6.653320 GTGGTAGTCCAATTGAAATGTCTACA 59.347 38.462 7.12 0.00 46.15 2.74
3020 3040 7.174253 GTGGTAGTCCAATTGAAATGTCTACAA 59.826 37.037 7.12 0.00 46.15 2.41
3021 3041 7.721842 TGGTAGTCCAATTGAAATGTCTACAAA 59.278 33.333 7.12 0.00 41.25 2.83
3022 3042 8.237267 GGTAGTCCAATTGAAATGTCTACAAAG 58.763 37.037 7.12 0.00 31.27 2.77
3023 3043 8.999431 GTAGTCCAATTGAAATGTCTACAAAGA 58.001 33.333 7.12 0.00 0.00 2.52
3040 3060 9.158233 TCTACAAAGACAAATATTTAGGAACGG 57.842 33.333 0.00 0.00 0.00 4.44
3041 3061 7.153217 ACAAAGACAAATATTTAGGAACGGG 57.847 36.000 0.00 0.00 0.00 5.28
3042 3062 6.152154 ACAAAGACAAATATTTAGGAACGGGG 59.848 38.462 0.00 0.00 0.00 5.73
3043 3063 4.788679 AGACAAATATTTAGGAACGGGGG 58.211 43.478 0.00 0.00 0.00 5.40
3125 3147 1.670811 CCCGTGAATAGTGCAATGTCC 59.329 52.381 0.00 0.00 0.00 4.02
3182 3206 6.311935 CCAAAATATTTCTTGTCTGCCATGTG 59.688 38.462 0.10 0.00 0.00 3.21
3333 3357 2.821969 CAAGGGCTAACAAACTGATGCT 59.178 45.455 0.00 0.00 0.00 3.79
3421 3445 2.288640 GCAAAGAAAGCAGGCTGACAAT 60.289 45.455 20.86 0.00 0.00 2.71
3509 3533 0.991920 GGGGTCTTTCTGTGGATGGA 59.008 55.000 0.00 0.00 0.00 3.41
3648 3672 1.942657 CATGGCAATGAGTAGAACGGG 59.057 52.381 0.00 0.00 35.67 5.28
3818 3842 1.272781 TTTGCCAAACGTTTGCTTCG 58.727 45.000 31.02 19.93 36.86 3.79
3830 3854 3.245754 CGTTTGCTTCGGTGTAAACTACA 59.754 43.478 15.35 0.00 39.32 2.74
3831 3855 4.607557 CGTTTGCTTCGGTGTAAACTACAG 60.608 45.833 15.35 2.72 39.32 2.74
3832 3856 3.738830 TGCTTCGGTGTAAACTACAGT 57.261 42.857 0.00 0.00 39.77 3.55
3833 3857 4.852134 TGCTTCGGTGTAAACTACAGTA 57.148 40.909 0.00 0.00 39.77 2.74
3835 3859 6.513806 TGCTTCGGTGTAAACTACAGTATA 57.486 37.500 0.00 0.00 39.77 1.47
3940 4042 0.106015 AAAAGGCTGGCAGACCTGTT 60.106 50.000 24.65 22.67 36.07 3.16
3977 4084 2.681778 ACTCGGCCTCAGAGGGTG 60.682 66.667 18.83 5.98 39.90 4.61
4002 4109 2.076100 GTTGTGTCATCCTCGATTGCA 58.924 47.619 0.00 0.00 0.00 4.08
4230 4413 9.889128 CAAACTATCCCATTGTTATTGGAATTT 57.111 29.630 0.00 0.00 36.26 1.82
4264 4447 5.894298 ACAAGGGAATCTATGCACTATCA 57.106 39.130 0.00 0.00 0.00 2.15
4343 4526 6.388619 AACACCCATCCACTAAGATTTAGT 57.611 37.500 0.00 0.00 0.00 2.24
4344 4527 7.365295 GGAACACCCATCCACTAAGATTTAGTA 60.365 40.741 1.50 0.00 36.92 1.82
4373 4556 4.155826 TCAGCGACACTTATTTTGGAATGG 59.844 41.667 0.00 0.00 0.00 3.16
4399 4582 4.685165 GGAGTAACTTCTTCAAGGTCGAAC 59.315 45.833 0.00 0.00 33.37 3.95
4424 4607 4.261801 GCCAAGCAACTTGTAGAAGGATA 58.738 43.478 4.45 0.00 39.58 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.324736 GACGATGTGGCTCGATTGAAC 59.675 52.381 1.39 0.00 41.12 3.18
327 334 1.468914 GGATCAAAACAGAGGAACCGC 59.531 52.381 0.00 0.00 0.00 5.68
328 335 1.732259 CGGATCAAAACAGAGGAACCG 59.268 52.381 0.00 0.00 0.00 4.44
353 360 2.096496 CCAAAACATCATCGGACAGAGC 59.904 50.000 0.00 0.00 0.00 4.09
355 362 2.710377 CCCAAAACATCATCGGACAGA 58.290 47.619 0.00 0.00 0.00 3.41
383 390 0.108585 CCCATCCCGTCCTACAATGG 59.891 60.000 0.00 0.00 37.27 3.16
387 394 0.263468 TCATCCCATCCCGTCCTACA 59.737 55.000 0.00 0.00 0.00 2.74
396 403 6.897986 AGCAATCTAGAATATCATCCCATCC 58.102 40.000 0.00 0.00 0.00 3.51
408 415 3.574826 GACCCTACCGAGCAATCTAGAAT 59.425 47.826 0.00 0.00 0.00 2.40
419 426 0.467659 AATCTCCCGACCCTACCGAG 60.468 60.000 0.00 0.00 0.00 4.63
420 427 0.032813 AAATCTCCCGACCCTACCGA 60.033 55.000 0.00 0.00 0.00 4.69
424 431 1.835531 GGTGAAAATCTCCCGACCCTA 59.164 52.381 0.00 0.00 0.00 3.53
432 439 1.134371 CGAGAGGGGGTGAAAATCTCC 60.134 57.143 0.00 0.00 34.26 3.71
433 440 1.555533 ACGAGAGGGGGTGAAAATCTC 59.444 52.381 0.00 0.00 34.40 2.75
434 441 1.657804 ACGAGAGGGGGTGAAAATCT 58.342 50.000 0.00 0.00 0.00 2.40
435 442 2.488153 CAAACGAGAGGGGGTGAAAATC 59.512 50.000 0.00 0.00 0.00 2.17
436 443 2.514803 CAAACGAGAGGGGGTGAAAAT 58.485 47.619 0.00 0.00 0.00 1.82
437 444 1.477923 CCAAACGAGAGGGGGTGAAAA 60.478 52.381 0.00 0.00 0.00 2.29
438 445 0.109723 CCAAACGAGAGGGGGTGAAA 59.890 55.000 0.00 0.00 0.00 2.69
439 446 0.765135 TCCAAACGAGAGGGGGTGAA 60.765 55.000 0.00 0.00 0.00 3.18
440 447 0.546747 ATCCAAACGAGAGGGGGTGA 60.547 55.000 0.00 0.00 0.00 4.02
441 448 1.200519 TATCCAAACGAGAGGGGGTG 58.799 55.000 0.00 0.00 0.00 4.61
442 449 2.172717 CAATATCCAAACGAGAGGGGGT 59.827 50.000 0.00 0.00 0.00 4.95
443 450 2.487265 CCAATATCCAAACGAGAGGGGG 60.487 54.545 0.00 0.00 0.00 5.40
480 487 3.963129 TCCCATCCAACACATTAAGACC 58.037 45.455 0.00 0.00 0.00 3.85
481 488 7.502226 TCAATATCCCATCCAACACATTAAGAC 59.498 37.037 0.00 0.00 0.00 3.01
483 490 7.822161 TCAATATCCCATCCAACACATTAAG 57.178 36.000 0.00 0.00 0.00 1.85
490 497 9.659135 AAATTCTTATCAATATCCCATCCAACA 57.341 29.630 0.00 0.00 0.00 3.33
504 511 8.070034 ACATCTGAATGGCAAATTCTTATCAA 57.930 30.769 11.37 0.00 37.19 2.57
629 636 8.597662 AATGTTATGCAATAATCAATCCAAGC 57.402 30.769 0.00 0.00 41.51 4.01
689 697 7.715249 GTCCATAACAGCAACTTAATAGATCCA 59.285 37.037 0.00 0.00 0.00 3.41
701 709 4.923281 GTCATTTTGGTCCATAACAGCAAC 59.077 41.667 0.00 0.00 31.11 4.17
716 724 5.519566 TGCTACAAACTTGCAAGTCATTTTG 59.480 36.000 31.20 29.31 38.57 2.44
723 731 2.023673 TGCTGCTACAAACTTGCAAGT 58.976 42.857 26.36 26.36 42.04 3.16
746 755 0.106469 TACACAAGGCAGGCAAACCA 60.106 50.000 0.00 0.00 39.06 3.67
753 762 1.981256 ACAAAGGTACACAAGGCAGG 58.019 50.000 0.00 0.00 0.00 4.85
757 766 6.094325 TGTTGAAACTACAAAGGTACACAAGG 59.906 38.462 0.00 0.00 0.00 3.61
774 783 7.381948 TCAATGATGTAAACTGCATGTTGAAAC 59.618 33.333 0.00 3.66 39.13 2.78
913 922 8.987890 CCTGTTGGTTTAAATTTACCTTCAATG 58.012 33.333 10.72 5.74 35.41 2.82
944 954 1.622811 CTTCTCCCAAGAGTGCTGAGT 59.377 52.381 0.00 0.00 41.26 3.41
980 990 3.325293 TCTCTACTGGCTTGCTTCAAG 57.675 47.619 2.40 2.40 43.57 3.02
1060 1070 1.789078 CGCTTTGCACCAGAGCTTGT 61.789 55.000 6.25 0.00 39.08 3.16
1324 1334 7.264373 AGACTTGATTTTCACGAAACTTGAT 57.736 32.000 0.00 0.00 0.00 2.57
1828 1838 1.372087 GGCACCACAGTAGCTGATGC 61.372 60.000 0.00 9.04 37.51 3.91
2071 2083 3.947834 CTGACAGGGTTGACAAGTTTCTT 59.052 43.478 0.00 0.00 0.00 2.52
2292 2304 7.922699 ACTCTTTTCCATATTAGAGGTAGCT 57.077 36.000 0.00 0.00 38.71 3.32
2371 2383 0.252375 ACCCATGGCAGCTGGAAAAT 60.252 50.000 17.12 0.00 35.70 1.82
2389 2401 5.590530 ACCTGATGTTATCTCAGTCTCAC 57.409 43.478 0.00 0.00 38.77 3.51
2565 2579 8.812329 GCGCATCAACCAAATAACAATAAAATA 58.188 29.630 0.30 0.00 0.00 1.40
2867 2882 8.795513 GGAGGGAGTATTATACTTTAGTCTCAC 58.204 40.741 6.33 0.00 39.59 3.51
2887 2907 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2890 2910 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2891 2911 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2892 2912 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2907 2927 9.996554 TCACTTGTTGAAATATCTAGAAAGACA 57.003 29.630 0.00 0.00 33.57 3.41
2916 2936 9.302345 CGTATGTAGTCACTTGTTGAAATATCT 57.698 33.333 0.00 0.00 35.39 1.98
2917 2937 8.540492 CCGTATGTAGTCACTTGTTGAAATATC 58.460 37.037 0.00 0.00 35.39 1.63
2918 2938 8.255206 TCCGTATGTAGTCACTTGTTGAAATAT 58.745 33.333 0.00 0.00 35.39 1.28
2919 2939 7.604549 TCCGTATGTAGTCACTTGTTGAAATA 58.395 34.615 0.00 0.00 35.39 1.40
2921 2941 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2923 2943 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2924 2944 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2925 2945 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2926 2946 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2927 2947 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2928 2948 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2929 2949 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2930 2950 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2931 2951 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2932 2952 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2933 2953 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2934 2954 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2935 2955 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2936 2956 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2937 2957 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2938 2958 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2939 2959 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2940 2960 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2941 2961 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2942 2962 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2943 2963 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2982 3002 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2983 3003 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2985 3005 3.812156 TTGGACTACCACATACGGATG 57.188 47.619 5.94 5.94 46.80 3.51
2986 3006 4.407621 TCAATTGGACTACCACATACGGAT 59.592 41.667 5.42 0.00 46.80 4.18
2987 3007 3.770388 TCAATTGGACTACCACATACGGA 59.230 43.478 5.42 0.00 46.80 4.69
2988 3008 4.131649 TCAATTGGACTACCACATACGG 57.868 45.455 5.42 0.00 46.80 4.02
2989 3009 6.093495 ACATTTCAATTGGACTACCACATACG 59.907 38.462 5.42 0.00 46.80 3.06
2990 3010 7.336931 AGACATTTCAATTGGACTACCACATAC 59.663 37.037 5.42 0.00 46.80 2.39
2991 3011 7.402054 AGACATTTCAATTGGACTACCACATA 58.598 34.615 5.42 0.00 46.80 2.29
2992 3012 6.248433 AGACATTTCAATTGGACTACCACAT 58.752 36.000 5.42 0.00 46.80 3.21
2993 3013 5.630121 AGACATTTCAATTGGACTACCACA 58.370 37.500 5.42 0.00 46.80 4.17
2994 3014 6.653320 TGTAGACATTTCAATTGGACTACCAC 59.347 38.462 5.42 0.00 46.80 4.16
2995 3015 6.774673 TGTAGACATTTCAATTGGACTACCA 58.225 36.000 5.42 0.00 45.34 3.25
2996 3016 7.681939 TTGTAGACATTTCAATTGGACTACC 57.318 36.000 5.42 0.00 0.00 3.18
2997 3017 8.999431 TCTTTGTAGACATTTCAATTGGACTAC 58.001 33.333 5.42 9.67 0.00 2.73
3014 3034 9.158233 CCGTTCCTAAATATTTGTCTTTGTAGA 57.842 33.333 11.05 0.00 0.00 2.59
3015 3035 8.395633 CCCGTTCCTAAATATTTGTCTTTGTAG 58.604 37.037 11.05 0.00 0.00 2.74
3016 3036 7.337436 CCCCGTTCCTAAATATTTGTCTTTGTA 59.663 37.037 11.05 0.00 0.00 2.41
3017 3037 6.152154 CCCCGTTCCTAAATATTTGTCTTTGT 59.848 38.462 11.05 0.00 0.00 2.83
3018 3038 6.405397 CCCCCGTTCCTAAATATTTGTCTTTG 60.405 42.308 11.05 0.00 0.00 2.77
3019 3039 5.655090 CCCCCGTTCCTAAATATTTGTCTTT 59.345 40.000 11.05 0.00 0.00 2.52
3020 3040 5.198207 CCCCCGTTCCTAAATATTTGTCTT 58.802 41.667 11.05 0.00 0.00 3.01
3021 3041 4.788679 CCCCCGTTCCTAAATATTTGTCT 58.211 43.478 11.05 0.00 0.00 3.41
3040 3060 4.856509 AGCTTCTTATTTTGTACTCCCCC 58.143 43.478 0.00 0.00 0.00 5.40
3041 3061 5.944007 TGAAGCTTCTTATTTTGTACTCCCC 59.056 40.000 26.09 0.00 0.00 4.81
3042 3062 7.631717 ATGAAGCTTCTTATTTTGTACTCCC 57.368 36.000 26.09 0.00 0.00 4.30
3043 3063 9.914131 AAAATGAAGCTTCTTATTTTGTACTCC 57.086 29.630 25.26 1.41 33.05 3.85
3125 3147 8.017373 GCATATAACTGTAGTAATTGTGGCATG 58.983 37.037 0.00 0.00 0.00 4.06
3333 3357 5.645056 TCTGGGATGCAAATATCAAGGTA 57.355 39.130 0.00 0.00 0.00 3.08
3421 3445 5.049060 CCAAACAACAGGATTTATGTCGTCA 60.049 40.000 0.00 0.00 0.00 4.35
3509 3533 2.026075 ACTAGTCTGCTCTAGGGTTCGT 60.026 50.000 12.87 0.00 40.97 3.85
3551 3575 8.043710 ACCTTTGACCATATAAAGTCAGAGAAG 58.956 37.037 19.52 14.34 44.08 2.85
3628 3652 1.942657 CCCGTTCTACTCATTGCCATG 59.057 52.381 0.00 0.00 0.00 3.66
3678 3702 8.182227 CGCTTGTATATATTCGTCATCTTCCTA 58.818 37.037 0.00 0.00 0.00 2.94
3679 3703 7.030165 CGCTTGTATATATTCGTCATCTTCCT 58.970 38.462 0.00 0.00 0.00 3.36
3818 3842 4.997565 TGCCGTATACTGTAGTTTACACC 58.002 43.478 11.39 4.19 33.82 4.16
3830 3854 0.458669 CCTGTCCGTTGCCGTATACT 59.541 55.000 0.56 0.00 0.00 2.12
3831 3855 0.174162 ACCTGTCCGTTGCCGTATAC 59.826 55.000 0.00 0.00 0.00 1.47
3832 3856 0.173935 CACCTGTCCGTTGCCGTATA 59.826 55.000 0.00 0.00 0.00 1.47
3833 3857 1.079405 CACCTGTCCGTTGCCGTAT 60.079 57.895 0.00 0.00 0.00 3.06
3859 3961 6.576442 GCAAGTATAGGGGAAACAGAAGAAGA 60.576 42.308 0.00 0.00 0.00 2.87
3905 4007 4.835056 AGCCTTTTATTTTCCTGTTGCTCT 59.165 37.500 0.00 0.00 0.00 4.09
3940 4042 1.570024 TCCATCAATCAATCCAGGCCA 59.430 47.619 5.01 0.00 0.00 5.36
3977 4084 1.272490 TCGAGGATGACACAACAGACC 59.728 52.381 0.00 0.00 0.00 3.85
4020 4127 2.151502 TTTCCAAACCACCTGCAGAA 57.848 45.000 17.39 0.00 0.00 3.02
4022 4129 1.538849 GCTTTTCCAAACCACCTGCAG 60.539 52.381 6.78 6.78 0.00 4.41
4230 4413 8.689061 CATAGATTCCCTTGTTTGATCAATCAA 58.311 33.333 23.80 23.80 44.42 2.57
4264 4447 9.838339 GATAGCTATGTATGGCCAAAGTATAAT 57.162 33.333 10.96 0.00 34.49 1.28
4343 4526 7.820386 TCCAAAATAAGTGTCGCTGATTTAGTA 59.180 33.333 8.84 0.00 37.29 1.82
4344 4527 6.653320 TCCAAAATAAGTGTCGCTGATTTAGT 59.347 34.615 8.84 0.00 37.29 2.24
4353 4536 4.438744 CCTCCATTCCAAAATAAGTGTCGC 60.439 45.833 0.00 0.00 0.00 5.19
4373 4556 4.618693 CGACCTTGAAGAAGTTACTCCCTC 60.619 50.000 0.00 0.00 0.00 4.30
4399 4582 3.366679 CCTTCTACAAGTTGCTTGGCATG 60.367 47.826 12.66 0.00 44.81 4.06


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

AutoCloner maintained by Alex Coulton.