Multiple sequence alignment - TraesCS1B01G398500

Loading Multiple Alignment...

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 TraesCS1B01G398500 chr1B 100.000 4283 0 0 1 4283 629651723 629656005 0.000000e+00 7910
1 TraesCS1B01G398500 chr1B 89.367 4157 372 23 122 4273 6059627 6063718 0.000000e+00 5164
2 TraesCS1B01G398500 chr1B 87.565 3289 386 15 992 4273 5694913 5698185 0.000000e+00 3786
3 TraesCS1B01G398500 chr1B 87.575 3171 356 24 927 4077 6281065 6284217 0.000000e+00 3639
4 TraesCS1B01G398500 chr1B 84.442 3291 462 28 995 4273 7256967 7253715 0.000000e+00 3195
5 TraesCS1B01G398500 chr1B 83.102 3249 479 44 1000 4235 22714496 22711305 0.000000e+00 2894
6 TraesCS1B01G398500 chr1B 82.615 3319 493 40 999 4273 5851588 5854866 0.000000e+00 2856
7 TraesCS1B01G398500 chr1B 83.690 2802 401 31 989 3781 6194308 6197062 0.000000e+00 2591
8 TraesCS1B01G398500 chr1B 83.356 2205 323 25 995 3189 5985933 5988103 0.000000e+00 1999
9 TraesCS1B01G398500 chr1B 83.435 1968 288 21 992 2955 7290055 7291988 0.000000e+00 1794
10 TraesCS1B01G398500 chr1D 89.670 2875 272 9 1410 4271 77380 74518 0.000000e+00 3640
11 TraesCS1B01G398500 chr1D 85.241 3293 438 25 995 4279 5135216 5131964 0.000000e+00 3345
12 TraesCS1B01G398500 chr1D 89.108 1166 123 3 3115 4279 3972948 3971786 0.000000e+00 1447
13 TraesCS1B01G398500 chr1D 84.934 458 63 4 3825 4279 4196196 4195742 3.900000e-125 459
14 TraesCS1B01G398500 chr1D 86.765 408 50 3 3874 4278 4237045 4236639 6.530000e-123 451
15 TraesCS1B01G398500 chr1A 85.364 3300 423 35 995 4271 6341259 6337997 0.000000e+00 3363
16 TraesCS1B01G398500 chr1A 84.653 3297 452 28 992 4271 5505990 5502731 0.000000e+00 3236
17 TraesCS1B01G398500 chr1A 83.846 1659 239 14 960 2608 6012565 6010926 0.000000e+00 1552
18 TraesCS1B01G398500 chr1A 83.462 520 72 8 3759 4268 4500504 4501019 5.010000e-129 472
19 TraesCS1B01G398500 chrUn 82.609 966 135 19 999 1957 9744196 9743257 0.000000e+00 822


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 TraesCS1B01G398500 chr1B 629651723 629656005 4282 False 7910 7910 100.000 1 4283 1 chr1B.!!$F8 4282
1 TraesCS1B01G398500 chr1B 6059627 6063718 4091 False 5164 5164 89.367 122 4273 1 chr1B.!!$F4 4151
2 TraesCS1B01G398500 chr1B 5694913 5698185 3272 False 3786 3786 87.565 992 4273 1 chr1B.!!$F1 3281
3 TraesCS1B01G398500 chr1B 6281065 6284217 3152 False 3639 3639 87.575 927 4077 1 chr1B.!!$F6 3150
4 TraesCS1B01G398500 chr1B 7253715 7256967 3252 True 3195 3195 84.442 995 4273 1 chr1B.!!$R1 3278
5 TraesCS1B01G398500 chr1B 22711305 22714496 3191 True 2894 2894 83.102 1000 4235 1 chr1B.!!$R2 3235
6 TraesCS1B01G398500 chr1B 5851588 5854866 3278 False 2856 2856 82.615 999 4273 1 chr1B.!!$F2 3274
7 TraesCS1B01G398500 chr1B 6194308 6197062 2754 False 2591 2591 83.690 989 3781 1 chr1B.!!$F5 2792
8 TraesCS1B01G398500 chr1B 5985933 5988103 2170 False 1999 1999 83.356 995 3189 1 chr1B.!!$F3 2194
9 TraesCS1B01G398500 chr1B 7290055 7291988 1933 False 1794 1794 83.435 992 2955 1 chr1B.!!$F7 1963
10 TraesCS1B01G398500 chr1D 74518 77380 2862 True 3640 3640 89.670 1410 4271 1 chr1D.!!$R1 2861
11 TraesCS1B01G398500 chr1D 5131964 5135216 3252 True 3345 3345 85.241 995 4279 1 chr1D.!!$R5 3284
12 TraesCS1B01G398500 chr1D 3971786 3972948 1162 True 1447 1447 89.108 3115 4279 1 chr1D.!!$R2 1164
13 TraesCS1B01G398500 chr1A 6337997 6341259 3262 True 3363 3363 85.364 995 4271 1 chr1A.!!$R3 3276
14 TraesCS1B01G398500 chr1A 5502731 5505990 3259 True 3236 3236 84.653 992 4271 1 chr1A.!!$R1 3279
15 TraesCS1B01G398500 chr1A 6010926 6012565 1639 True 1552 1552 83.846 960 2608 1 chr1A.!!$R2 1648
16 TraesCS1B01G398500 chr1A 4500504 4501019 515 False 472 472 83.462 3759 4268 1 chr1A.!!$F1 509
17 TraesCS1B01G398500 chrUn 9743257 9744196 939 True 822 822 82.609 999 1957 1 chrUn.!!$R1 958

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
337 338 1.002921 ACCCCATCCATCCGTCTCA 59.997 57.895 0.00 0.00 0.00 3.27 F
1718 1733 0.664166 AAGCATTTTCCGTTGCAGCG 60.664 50.000 16.72 16.72 41.35 5.18 F
2147 2179 1.090728 GCCTCTCCTTTAGCTGCAAC 58.909 55.000 1.02 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2216 0.107703 CCTTCCATTCTGCCACGCTA 60.108 55.0 0.00 0.00 0.00 4.26 R
3061 3117 0.453390 GGTCCAATAACTGCTGCTGC 59.547 55.0 8.89 8.89 40.20 5.25 R
3863 3925 0.249784 CGACTGCATCCCATCTCTGG 60.250 60.0 0.00 0.00 42.73 3.86 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
49 50 9.995957 ATTTCAAAACGGAAAACAAATAAAAGG 57.004 25.926 0.00 0.00 39.94 3.11
51 52 8.773404 TCAAAACGGAAAACAAATAAAAGGAA 57.227 26.923 0.00 0.00 0.00 3.36
52 53 9.216117 TCAAAACGGAAAACAAATAAAAGGAAA 57.784 25.926 0.00 0.00 0.00 3.13
55 56 8.725405 AACGGAAAACAAATAAAAGGAAACAT 57.275 26.923 0.00 0.00 0.00 2.71
56 57 9.819267 AACGGAAAACAAATAAAAGGAAACATA 57.181 25.926 0.00 0.00 0.00 2.29
72 73 9.905713 AAGGAAACATAAGTATGATAGAAGCAA 57.094 29.630 5.33 0.00 37.15 3.91
73 74 9.905713 AGGAAACATAAGTATGATAGAAGCAAA 57.094 29.630 5.33 0.00 37.15 3.68
93 94 9.959749 AAGCAAAATAAGACAAGAAAATTACGA 57.040 25.926 0.00 0.00 0.00 3.43
94 95 9.959749 AGCAAAATAAGACAAGAAAATTACGAA 57.040 25.926 0.00 0.00 0.00 3.85
102 103 9.726232 AAGACAAGAAAATTACGAAAAAGTACC 57.274 29.630 0.00 0.00 0.00 3.34
103 104 9.117183 AGACAAGAAAATTACGAAAAAGTACCT 57.883 29.630 0.00 0.00 0.00 3.08
110 111 9.968870 AAAATTACGAAAAAGTACCTAAATGCA 57.031 25.926 0.00 0.00 0.00 3.96
111 112 8.959734 AATTACGAAAAAGTACCTAAATGCAC 57.040 30.769 0.00 0.00 0.00 4.57
112 113 5.366829 ACGAAAAAGTACCTAAATGCACC 57.633 39.130 0.00 0.00 0.00 5.01
113 114 5.067954 ACGAAAAAGTACCTAAATGCACCT 58.932 37.500 0.00 0.00 0.00 4.00
114 115 6.232692 ACGAAAAAGTACCTAAATGCACCTA 58.767 36.000 0.00 0.00 0.00 3.08
116 117 6.592607 CGAAAAAGTACCTAAATGCACCTAGA 59.407 38.462 5.63 0.00 0.00 2.43
117 118 7.118680 CGAAAAAGTACCTAAATGCACCTAGAA 59.881 37.037 5.63 0.00 0.00 2.10
203 204 5.012354 ACGGGAATGTTTTCAGGTCTAGTTA 59.988 40.000 0.00 0.00 33.23 2.24
220 221 3.214328 AGTTAGCAACCTGACAAACCTG 58.786 45.455 0.00 0.00 30.46 4.00
237 238 2.131776 CTGGAAGGAGAGAGTACGGT 57.868 55.000 0.00 0.00 0.00 4.83
246 247 6.497624 AGGAGAGAGTACGGTCTAGAAATA 57.502 41.667 0.00 0.00 0.00 1.40
332 333 1.601759 GCATGACCCCATCCATCCG 60.602 63.158 0.00 0.00 0.00 4.18
337 338 1.002921 ACCCCATCCATCCGTCTCA 59.997 57.895 0.00 0.00 0.00 3.27
379 380 2.717639 ATCGAATTCCTTCCCCACAG 57.282 50.000 0.00 0.00 0.00 3.66
420 421 6.155136 CCTGAATTCTTTTCCAAAGAAGAGC 58.845 40.000 15.06 8.72 39.36 4.09
421 422 6.015603 CCTGAATTCTTTTCCAAAGAAGAGCT 60.016 38.462 15.06 0.00 39.36 4.09
422 423 7.352079 TGAATTCTTTTCCAAAGAAGAGCTT 57.648 32.000 15.06 6.55 39.36 3.74
423 424 8.463930 TGAATTCTTTTCCAAAGAAGAGCTTA 57.536 30.769 15.06 0.00 39.36 3.09
424 425 8.571336 TGAATTCTTTTCCAAAGAAGAGCTTAG 58.429 33.333 15.06 0.00 39.36 2.18
425 426 5.948992 TCTTTTCCAAAGAAGAGCTTAGC 57.051 39.130 0.00 0.00 34.86 3.09
441 442 3.502572 GCCTTAGCTGCTTTCCCG 58.497 61.111 7.79 0.00 35.50 5.14
455 456 3.687264 GCTTTCCCGAATCCTATTCCCAA 60.687 47.826 0.00 0.00 0.00 4.12
490 491 1.649664 CTGCTCCCAGAAATCTCACG 58.350 55.000 0.00 0.00 41.77 4.35
508 509 4.910585 CCCACGTATCCCCGCTGC 62.911 72.222 0.00 0.00 0.00 5.25
509 510 3.849951 CCACGTATCCCCGCTGCT 61.850 66.667 0.00 0.00 0.00 4.24
510 511 2.279517 CACGTATCCCCGCTGCTC 60.280 66.667 0.00 0.00 0.00 4.26
523 524 1.520342 CTGCTCTAGCTTCACCGGC 60.520 63.158 0.00 0.00 42.66 6.13
526 527 3.356639 CTCTAGCTTCACCGGCGCA 62.357 63.158 10.83 0.00 34.52 6.09
527 528 2.434185 CTAGCTTCACCGGCGCAA 60.434 61.111 10.83 0.00 34.52 4.85
585 586 1.483595 TTCTGGGTACTGCTGCTGCT 61.484 55.000 17.00 0.00 40.48 4.24
586 587 1.744368 CTGGGTACTGCTGCTGCTG 60.744 63.158 18.66 18.66 42.70 4.41
587 588 3.130160 GGGTACTGCTGCTGCTGC 61.130 66.667 22.51 22.51 41.07 5.25
588 589 2.046507 GGTACTGCTGCTGCTGCT 60.047 61.111 27.67 14.24 41.07 4.24
589 590 2.396955 GGTACTGCTGCTGCTGCTG 61.397 63.158 27.75 27.75 41.07 4.41
687 688 1.143684 TGGTTTCTCAGGAGCAAGCTT 59.856 47.619 11.09 0.00 34.14 3.74
864 866 7.638444 TCACCCCTGTAGATTCATAAATTTCA 58.362 34.615 0.00 0.00 0.00 2.69
915 917 6.299141 AGGTTCAGCAAAGTTCAGATTTAGA 58.701 36.000 0.00 0.00 0.00 2.10
916 918 6.205658 AGGTTCAGCAAAGTTCAGATTTAGAC 59.794 38.462 0.00 0.00 0.00 2.59
917 919 6.017109 GGTTCAGCAAAGTTCAGATTTAGACA 60.017 38.462 0.00 0.00 0.00 3.41
918 920 7.417612 GTTCAGCAAAGTTCAGATTTAGACAA 58.582 34.615 0.00 0.00 0.00 3.18
919 921 6.959361 TCAGCAAAGTTCAGATTTAGACAAC 58.041 36.000 0.00 0.00 0.00 3.32
920 922 6.542005 TCAGCAAAGTTCAGATTTAGACAACA 59.458 34.615 0.00 0.00 0.00 3.33
921 923 6.634436 CAGCAAAGTTCAGATTTAGACAACAC 59.366 38.462 0.00 0.00 0.00 3.32
922 924 6.318648 AGCAAAGTTCAGATTTAGACAACACA 59.681 34.615 0.00 0.00 0.00 3.72
923 925 6.972328 GCAAAGTTCAGATTTAGACAACACAA 59.028 34.615 0.00 0.00 0.00 3.33
924 926 7.487829 GCAAAGTTCAGATTTAGACAACACAAA 59.512 33.333 0.00 0.00 0.00 2.83
925 927 9.520204 CAAAGTTCAGATTTAGACAACACAAAT 57.480 29.630 0.00 0.00 0.00 2.32
1007 1019 1.395608 CGTAAGTGTTACAATGGCGGG 59.604 52.381 0.00 0.00 35.89 6.13
1113 1125 1.371467 TGGAGGGAATGGAGAAGCAA 58.629 50.000 0.00 0.00 0.00 3.91
1116 1128 2.357569 GGAGGGAATGGAGAAGCAACAT 60.358 50.000 0.00 0.00 0.00 2.71
1359 1371 1.004200 CCCTACCCACAACCGTGTC 60.004 63.158 0.00 0.00 41.93 3.67
1685 1700 5.922739 TTAGCGCAACTCATATACAATGG 57.077 39.130 11.47 0.00 0.00 3.16
1718 1733 0.664166 AAGCATTTTCCGTTGCAGCG 60.664 50.000 16.72 16.72 41.35 5.18
1754 1769 6.758886 GTCTCTGATACCTTCGATGTGAATTT 59.241 38.462 0.00 0.00 35.63 1.82
1780 1795 5.520649 GTGGCTAAGAGTATAGTTGAAGCAC 59.479 44.000 9.72 0.00 0.00 4.40
1980 2007 3.120199 CCCGTGATAAACAAGTTGCTGAG 60.120 47.826 1.81 0.00 0.00 3.35
2072 2103 9.360901 TGATACTAGAGCATTCAGTTTAGAGAT 57.639 33.333 0.00 0.00 0.00 2.75
2129 2161 3.257393 AGATTGTGAAGAGATGTCGTGC 58.743 45.455 0.00 0.00 0.00 5.34
2147 2179 1.090728 GCCTCTCCTTTAGCTGCAAC 58.909 55.000 1.02 0.00 0.00 4.17
2148 2180 1.339535 GCCTCTCCTTTAGCTGCAACT 60.340 52.381 1.02 0.00 0.00 3.16
2149 2181 2.354259 CCTCTCCTTTAGCTGCAACTG 58.646 52.381 1.02 0.00 0.00 3.16
2150 2182 1.736681 CTCTCCTTTAGCTGCAACTGC 59.263 52.381 1.02 0.00 42.50 4.40
2151 2183 1.349026 TCTCCTTTAGCTGCAACTGCT 59.651 47.619 1.02 1.59 42.66 4.24
2152 2184 2.567169 TCTCCTTTAGCTGCAACTGCTA 59.433 45.455 1.02 0.48 42.66 3.49
2184 2216 4.398673 GGATCTGTACTTCGTACCAAGACT 59.601 45.833 7.27 0.00 38.14 3.24
2278 2310 8.494347 CAATACTCAAGCTTAGCTACAATGATC 58.506 37.037 7.32 0.00 38.25 2.92
2345 2377 6.959639 TCCCAAGGATTACAAGATTAATGC 57.040 37.500 0.00 0.00 31.66 3.56
2446 2478 8.922058 AAAACATATTTTCAATGAGCTAGCAG 57.078 30.769 18.83 1.12 32.29 4.24
2463 2495 4.292186 AGCAGCAAGGTCATTCTTTCTA 57.708 40.909 0.00 0.00 0.00 2.10
2472 2504 7.766278 GCAAGGTCATTCTTTCTAGACATAGAA 59.234 37.037 11.48 11.48 44.51 2.10
2625 2678 2.186076 CTTTCGGATACTGCTCGACAC 58.814 52.381 0.00 0.00 32.39 3.67
2644 2697 4.269183 ACACTTGTCCTTGTCATGTGAAA 58.731 39.130 15.21 0.00 40.77 2.69
2766 2819 2.838386 AATACAGCTCTTTGCATGCG 57.162 45.000 14.09 0.00 45.94 4.73
2808 2864 5.926894 CAAAATCATTTGCACTGAGATCG 57.073 39.130 4.62 0.00 39.50 3.69
2820 2876 5.209240 GCACTGAGATCGAAGTATCTACAC 58.791 45.833 3.39 0.00 36.33 2.90
2858 2914 3.978718 TCTCTCGTGCAGTGATATCAG 57.021 47.619 5.42 0.00 0.00 2.90
2960 3016 5.541845 TCCGAGGCAAATGAAGTATATGAG 58.458 41.667 0.00 0.00 0.00 2.90
2976 3032 1.684734 GAGTTCCCTCCGCCACCTA 60.685 63.158 0.00 0.00 0.00 3.08
2998 3054 2.890808 TACTCATGGATGTCCGAAGC 57.109 50.000 0.00 0.00 39.43 3.86
3029 3085 2.108168 GCCCCCAGAATTAGGAAAACC 58.892 52.381 0.00 0.00 0.00 3.27
3042 3098 3.238597 AGGAAAACCCAATAAGCTGCAA 58.761 40.909 1.02 0.00 37.41 4.08
3057 3113 2.405025 GCTGCAAACGCTTACATGTTTC 59.595 45.455 2.30 0.00 36.22 2.78
3060 3116 3.247886 TGCAAACGCTTACATGTTTCGTA 59.752 39.130 2.30 0.00 36.22 3.43
3061 3117 3.838550 GCAAACGCTTACATGTTTCGTAG 59.161 43.478 2.30 8.92 36.22 3.51
3062 3118 3.717350 AACGCTTACATGTTTCGTAGC 57.283 42.857 2.30 5.20 32.71 3.58
3081 3137 1.825090 CAGCAGCAGTTATTGGACCA 58.175 50.000 0.00 0.00 0.00 4.02
3125 3181 2.697751 TGCAGCATTTAAACCTTGGTGT 59.302 40.909 16.58 0.00 40.16 4.16
3126 3182 3.243704 TGCAGCATTTAAACCTTGGTGTC 60.244 43.478 16.58 11.38 40.16 3.67
3150 3206 4.057432 AGTTAGAGCTACGTCGGATAGAC 58.943 47.826 0.00 0.00 46.16 2.59
3166 3225 5.580691 CGGATAGACAATGTTACAGAAGCAA 59.419 40.000 0.00 0.00 0.00 3.91
3223 3282 6.978080 GGATCTCAGAGAACTGACATTAAGAC 59.022 42.308 3.63 0.00 46.55 3.01
3244 3303 3.754323 ACGGACTTTTCTGTTTGTGACAA 59.246 39.130 0.00 0.00 38.26 3.18
3288 3347 4.096190 CCACATGATGGGCTAGAGATTT 57.904 45.455 0.00 0.00 45.95 2.17
3353 3412 5.357878 GCAAAACATGGTTGAGATCCATCTA 59.642 40.000 13.82 0.00 42.92 1.98
3363 3422 6.263842 GGTTGAGATCCATCTATTTCATTGCA 59.736 38.462 0.00 0.00 37.25 4.08
3393 3452 4.114794 GCAAGTTTTGTTCTGATGCAGTT 58.885 39.130 0.00 0.00 32.61 3.16
3406 3465 5.180680 TCTGATGCAGTTCAATCTTCACTTG 59.819 40.000 0.00 0.00 32.61 3.16
3466 3525 3.895041 GGTTTTGAGAGATGGTGGGAAAA 59.105 43.478 0.00 0.00 0.00 2.29
3475 3534 5.014544 AGAGATGGTGGGAAAAAGATGAGAA 59.985 40.000 0.00 0.00 0.00 2.87
3604 3666 6.412214 GTGAAGGTGGTTATACATTGGTACT 58.588 40.000 0.00 0.00 30.94 2.73
3643 3705 6.866770 GCCCTAAAGGTACTCAAAATGAAAAC 59.133 38.462 0.00 0.00 38.49 2.43
3653 3715 6.129179 ACTCAAAATGAAAACCTTGGAGAGA 58.871 36.000 0.00 0.00 0.00 3.10
3657 3719 8.485392 TCAAAATGAAAACCTTGGAGAGATTTT 58.515 29.630 0.00 0.00 0.00 1.82
3675 3737 4.842531 TTTTAGAGATGGGATGCAGTCA 57.157 40.909 0.00 0.00 0.00 3.41
3731 3793 4.628333 CGGCTTGAGAAACTATCGGTTAAA 59.372 41.667 0.00 0.00 37.12 1.52
3740 3802 2.169978 ACTATCGGTTAAAGACTGCCCC 59.830 50.000 0.00 0.00 34.46 5.80
3923 3994 4.458295 CAGCTTGAGAAATTGTCAGTCCAT 59.542 41.667 0.00 0.00 0.00 3.41
3977 4048 5.283060 CACCAAAACTCAGTGCACTATAC 57.717 43.478 21.20 0.00 0.00 1.47
3988 4059 5.525012 TCAGTGCACTATACATTGAAGATGC 59.475 40.000 21.20 0.00 31.71 3.91
4041 4112 9.479549 ACAGGTATTTATCTTCATTGACCAATT 57.520 29.630 0.00 0.00 0.00 2.32
4049 4120 9.513906 TTATCTTCATTGACCAATTTGACACTA 57.486 29.630 0.00 0.00 0.00 2.74
4050 4121 8.585471 ATCTTCATTGACCAATTTGACACTAT 57.415 30.769 0.00 0.00 0.00 2.12
4077 4149 6.293626 GCTAGAACACACAGAAACAACATCAT 60.294 38.462 0.00 0.00 0.00 2.45
4109 4181 0.523072 CTTCAATTGTGCCGGTGGAG 59.477 55.000 1.90 0.00 0.00 3.86
4143 4215 2.721906 TGGAACCAGAAATCCCCTCTTT 59.278 45.455 0.00 0.00 34.68 2.52
4146 4218 3.441500 ACCAGAAATCCCCTCTTTCAC 57.558 47.619 0.00 0.00 35.51 3.18
4153 4225 6.541641 CAGAAATCCCCTCTTTCACTTATGAG 59.458 42.308 0.00 0.00 35.83 2.90
4183 4255 4.206375 TGTTGCAACTCATTCTTTGGAGA 58.794 39.130 28.61 1.76 35.17 3.71
4184 4256 4.828939 TGTTGCAACTCATTCTTTGGAGAT 59.171 37.500 28.61 0.00 35.17 2.75
4236 4308 5.184892 ACATCTTGGAGAGCTGGTAATTT 57.815 39.130 0.00 0.00 0.00 1.82
4246 4318 5.431765 AGAGCTGGTAATTTACAGATGTGG 58.568 41.667 11.85 0.00 36.86 4.17
4268 4340 3.023949 GCTCGTCCACTGGCCAGAT 62.024 63.158 39.19 20.19 0.00 2.90
4273 4345 1.383523 GTCCACTGGCCAGATAAAGC 58.616 55.000 39.19 18.40 0.00 3.51
4274 4346 0.991146 TCCACTGGCCAGATAAAGCA 59.009 50.000 39.19 12.01 0.00 3.91
4279 4351 1.959282 CTGGCCAGATAAAGCATTCCC 59.041 52.381 29.88 0.00 0.00 3.97
4280 4352 0.954452 GGCCAGATAAAGCATTCCCG 59.046 55.000 0.00 0.00 0.00 5.14
4281 4353 0.954452 GCCAGATAAAGCATTCCCGG 59.046 55.000 0.00 0.00 0.00 5.73
4282 4354 0.954452 CCAGATAAAGCATTCCCGGC 59.046 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.995957 CCTTTTATTTGTTTTCCGTTTTGAAAT 57.004 25.926 0.00 0.00 34.41 2.17
26 27 8.773404 TTCCTTTTATTTGTTTTCCGTTTTGA 57.227 26.923 0.00 0.00 0.00 2.69
27 28 9.268255 GTTTCCTTTTATTTGTTTTCCGTTTTG 57.732 29.630 0.00 0.00 0.00 2.44
29 30 8.549338 TGTTTCCTTTTATTTGTTTTCCGTTT 57.451 26.923 0.00 0.00 0.00 3.60
30 31 8.725405 ATGTTTCCTTTTATTTGTTTTCCGTT 57.275 26.923 0.00 0.00 0.00 4.44
31 32 9.819267 TTATGTTTCCTTTTATTTGTTTTCCGT 57.181 25.926 0.00 0.00 0.00 4.69
45 46 9.905713 TGCTTCTATCATACTTATGTTTCCTTT 57.094 29.630 0.00 0.00 35.26 3.11
46 47 9.905713 TTGCTTCTATCATACTTATGTTTCCTT 57.094 29.630 0.00 0.00 35.26 3.36
47 48 9.905713 TTTGCTTCTATCATACTTATGTTTCCT 57.094 29.630 0.00 0.00 35.26 3.36
67 68 9.959749 TCGTAATTTTCTTGTCTTATTTTGCTT 57.040 25.926 0.00 0.00 0.00 3.91
68 69 9.959749 TTCGTAATTTTCTTGTCTTATTTTGCT 57.040 25.926 0.00 0.00 0.00 3.91
76 77 9.726232 GGTACTTTTTCGTAATTTTCTTGTCTT 57.274 29.630 0.00 0.00 0.00 3.01
77 78 9.117183 AGGTACTTTTTCGTAATTTTCTTGTCT 57.883 29.630 0.00 0.00 27.25 3.41
84 85 9.968870 TGCATTTAGGTACTTTTTCGTAATTTT 57.031 25.926 0.00 0.00 41.75 1.82
85 86 9.401873 GTGCATTTAGGTACTTTTTCGTAATTT 57.598 29.630 0.00 0.00 41.75 1.82
88 89 6.711645 AGGTGCATTTAGGTACTTTTTCGTAA 59.288 34.615 0.00 0.00 41.75 3.18
89 90 6.232692 AGGTGCATTTAGGTACTTTTTCGTA 58.767 36.000 0.00 0.00 41.75 3.43
90 91 5.067954 AGGTGCATTTAGGTACTTTTTCGT 58.932 37.500 0.00 0.00 41.75 3.85
91 92 5.622770 AGGTGCATTTAGGTACTTTTTCG 57.377 39.130 0.00 0.00 41.75 3.46
92 93 7.916914 TCTAGGTGCATTTAGGTACTTTTTC 57.083 36.000 0.00 0.00 41.75 2.29
93 94 7.094334 GCTTCTAGGTGCATTTAGGTACTTTTT 60.094 37.037 0.00 0.00 41.75 1.94
94 95 6.374613 GCTTCTAGGTGCATTTAGGTACTTTT 59.625 38.462 0.00 0.00 41.75 2.27
95 96 5.880887 GCTTCTAGGTGCATTTAGGTACTTT 59.119 40.000 0.00 0.00 41.75 2.66
96 97 5.189934 AGCTTCTAGGTGCATTTAGGTACTT 59.810 40.000 9.79 0.00 41.75 2.24
100 101 3.370953 CCAGCTTCTAGGTGCATTTAGGT 60.371 47.826 9.79 0.00 42.05 3.08
101 102 3.118261 TCCAGCTTCTAGGTGCATTTAGG 60.118 47.826 9.79 4.71 42.05 2.69
102 103 4.142609 TCCAGCTTCTAGGTGCATTTAG 57.857 45.455 9.79 0.00 42.05 1.85
103 104 4.019321 AGTTCCAGCTTCTAGGTGCATTTA 60.019 41.667 9.79 0.00 42.05 1.40
105 106 2.307098 AGTTCCAGCTTCTAGGTGCATT 59.693 45.455 9.79 0.00 42.05 3.56
107 108 1.002430 CAGTTCCAGCTTCTAGGTGCA 59.998 52.381 9.79 0.00 42.05 4.57
108 109 1.002544 ACAGTTCCAGCTTCTAGGTGC 59.997 52.381 0.51 0.00 42.05 5.01
109 110 2.300152 TGACAGTTCCAGCTTCTAGGTG 59.700 50.000 0.00 0.00 42.96 4.00
110 111 2.609747 TGACAGTTCCAGCTTCTAGGT 58.390 47.619 0.00 0.00 0.00 3.08
111 112 3.902881 ATGACAGTTCCAGCTTCTAGG 57.097 47.619 0.00 0.00 0.00 3.02
112 113 3.373439 GCAATGACAGTTCCAGCTTCTAG 59.627 47.826 0.00 0.00 0.00 2.43
113 114 3.008375 AGCAATGACAGTTCCAGCTTCTA 59.992 43.478 0.00 0.00 0.00 2.10
114 115 2.157738 GCAATGACAGTTCCAGCTTCT 58.842 47.619 0.00 0.00 0.00 2.85
116 117 2.283145 AGCAATGACAGTTCCAGCTT 57.717 45.000 0.00 0.00 0.00 3.74
117 118 3.423539 TTAGCAATGACAGTTCCAGCT 57.576 42.857 0.00 0.00 34.84 4.24
203 204 0.550914 TCCAGGTTTGTCAGGTTGCT 59.449 50.000 0.00 0.00 0.00 3.91
220 221 2.423446 AGACCGTACTCTCTCCTTCC 57.577 55.000 0.00 0.00 0.00 3.46
265 266 4.286808 AGCCAAATTTTAGTGCCAATCCTT 59.713 37.500 0.00 0.00 0.00 3.36
332 333 4.520492 TCTTTGGCAAAGAGGAAATGAGAC 59.480 41.667 32.85 0.00 42.31 3.36
379 380 0.254178 AGGGAGACATGCATGTGGTC 59.746 55.000 35.92 28.07 41.95 4.02
424 425 0.676782 TTCGGGAAAGCAGCTAAGGC 60.677 55.000 0.00 0.00 39.06 4.35
425 426 1.943340 GATTCGGGAAAGCAGCTAAGG 59.057 52.381 0.00 0.00 0.00 2.69
441 442 6.628175 GCTTTTGGAAGTTGGGAATAGGATTC 60.628 42.308 0.00 0.00 35.25 2.52
455 456 1.758862 AGCAGCAAAGCTTTTGGAAGT 59.241 42.857 9.53 0.00 43.70 3.01
490 491 4.910585 CAGCGGGGATACGTGGGC 62.911 72.222 0.00 0.00 35.98 5.36
496 497 1.290639 GCTAGAGCAGCGGGGATAC 59.709 63.158 0.00 0.00 41.37 2.24
508 509 2.583593 GCGCCGGTGAAGCTAGAG 60.584 66.667 21.76 0.00 0.00 2.43
509 510 2.938086 TTGCGCCGGTGAAGCTAGA 61.938 57.895 21.76 0.00 0.00 2.43
510 511 2.434185 TTGCGCCGGTGAAGCTAG 60.434 61.111 21.76 0.00 0.00 3.42
606 607 2.825836 GGCATGTGGAAGCCGAGG 60.826 66.667 0.00 0.00 41.70 4.63
636 637 1.905922 GCAGCAACAGCGAGGAAGAC 61.906 60.000 0.00 0.00 0.00 3.01
679 680 3.214696 AGTTACCTTCACAAGCTTGCT 57.785 42.857 26.27 10.81 0.00 3.91
687 688 2.304470 TGCAGCCATAGTTACCTTCACA 59.696 45.455 0.00 0.00 0.00 3.58
702 703 6.369615 ACAACTCAAAATCAAATATTGCAGCC 59.630 34.615 0.00 0.00 0.00 4.85
730 731 5.239306 TGCTTGACATCTGTTCTTTAACCAG 59.761 40.000 0.00 0.00 34.49 4.00
736 737 4.454678 TGAGTGCTTGACATCTGTTCTTT 58.545 39.130 0.00 0.00 0.00 2.52
791 792 5.127491 CCCTGAACCAGTTACAACTTACAA 58.873 41.667 0.00 0.00 37.08 2.41
792 793 4.164604 ACCCTGAACCAGTTACAACTTACA 59.835 41.667 0.00 0.00 37.08 2.41
793 794 4.514066 CACCCTGAACCAGTTACAACTTAC 59.486 45.833 0.00 0.00 37.08 2.34
794 795 4.164604 ACACCCTGAACCAGTTACAACTTA 59.835 41.667 0.00 0.00 37.08 2.24
795 796 3.053917 ACACCCTGAACCAGTTACAACTT 60.054 43.478 0.00 0.00 37.08 2.66
796 797 2.508300 ACACCCTGAACCAGTTACAACT 59.492 45.455 0.00 0.00 40.60 3.16
797 798 2.927028 ACACCCTGAACCAGTTACAAC 58.073 47.619 0.00 0.00 0.00 3.32
841 843 8.893563 TTTGAAATTTATGAATCTACAGGGGT 57.106 30.769 0.00 0.00 0.00 4.95
874 876 6.516527 GCTGAACCTATTTGTGAAATGTTCCA 60.517 38.462 0.00 0.00 34.99 3.53
915 917 6.035843 CAGCAAGACTTGTAATTTGTGTTGT 58.964 36.000 16.39 0.00 37.32 3.32
916 918 6.197096 GTCAGCAAGACTTGTAATTTGTGTTG 59.803 38.462 16.39 0.00 44.09 3.33
917 919 6.265577 GTCAGCAAGACTTGTAATTTGTGTT 58.734 36.000 16.39 0.00 44.09 3.32
918 920 5.821204 GTCAGCAAGACTTGTAATTTGTGT 58.179 37.500 16.39 0.00 44.09 3.72
1072 1084 5.510349 CCATCACATTGTACTCATCGAGGAT 60.510 44.000 0.00 0.00 33.35 3.24
1113 1125 3.535561 CCTGCGTTTCAGAATCCTATGT 58.464 45.455 0.00 0.00 45.72 2.29
1116 1128 1.555075 AGCCTGCGTTTCAGAATCCTA 59.445 47.619 0.00 0.00 45.72 2.94
1531 1546 2.309613 TCTGCTGGCAATTTCTTGTGT 58.690 42.857 0.00 0.00 34.69 3.72
1595 1610 3.468770 AGATCTGCATTGCTAGCTTCAG 58.531 45.455 17.23 15.92 0.00 3.02
1685 1700 6.528072 CGGAAAATGCTTCTGAATTTTAGGTC 59.472 38.462 1.42 0.00 40.50 3.85
1718 1733 1.954362 ATCAGAGACGCAGACCCAGC 61.954 60.000 0.00 0.00 0.00 4.85
1754 1769 5.395324 GCTTCAACTATACTCTTAGCCACCA 60.395 44.000 0.00 0.00 0.00 4.17
1980 2007 5.234466 AGGTTCTATCTGCACCCATAATC 57.766 43.478 0.00 0.00 32.13 1.75
2049 2079 9.190317 TCAATCTCTAAACTGAATGCTCTAGTA 57.810 33.333 0.00 0.00 0.00 1.82
2050 2080 8.072321 TCAATCTCTAAACTGAATGCTCTAGT 57.928 34.615 0.00 0.00 0.00 2.57
2129 2161 2.354259 CAGTTGCAGCTAAAGGAGAGG 58.646 52.381 1.52 0.00 0.00 3.69
2149 2181 0.539051 ACAGATCCCAGTGCAGTAGC 59.461 55.000 0.00 0.00 42.57 3.58
2150 2182 3.027412 AGTACAGATCCCAGTGCAGTAG 58.973 50.000 0.00 0.00 0.00 2.57
2151 2183 3.101643 AGTACAGATCCCAGTGCAGTA 57.898 47.619 0.00 0.00 0.00 2.74
2152 2184 1.944177 AGTACAGATCCCAGTGCAGT 58.056 50.000 0.00 0.00 0.00 4.40
2184 2216 0.107703 CCTTCCATTCTGCCACGCTA 60.108 55.000 0.00 0.00 0.00 4.26
2192 2224 8.303780 TCTAGATGATATAGCCTTCCATTCTG 57.696 38.462 0.00 0.00 0.00 3.02
2241 2273 4.774200 AGCTTGAGTATTGGCAAAATTCCT 59.226 37.500 3.01 0.00 0.00 3.36
2278 2310 1.211969 GCTTCATGTGTGCTGGCAG 59.788 57.895 10.94 10.94 0.00 4.85
2345 2377 4.310769 CCATAGTTGGATAAGCTTCTCCG 58.689 47.826 21.99 9.48 46.92 4.63
2446 2478 7.268586 TCTATGTCTAGAAAGAATGACCTTGC 58.731 38.462 0.00 0.00 32.16 4.01
2463 2495 6.049790 GTCGCCCTTAAATTCTTCTATGTCT 58.950 40.000 0.00 0.00 0.00 3.41
2472 2504 0.107361 CCCCGTCGCCCTTAAATTCT 60.107 55.000 0.00 0.00 0.00 2.40
2691 2744 7.359598 GGACTATCGCATATCAGTGTTTGAATC 60.360 40.741 0.00 0.00 39.77 2.52
2766 2819 2.000447 GTCCACATACGGAGCTTCAAC 59.000 52.381 0.00 0.00 35.10 3.18
2804 2860 4.579340 TCAGGTGGTGTAGATACTTCGATC 59.421 45.833 0.00 0.00 0.00 3.69
2808 2864 4.024670 ACCTCAGGTGGTGTAGATACTTC 58.975 47.826 0.00 0.00 39.17 3.01
2820 2876 4.222336 AGAGATCAAGATACCTCAGGTGG 58.778 47.826 6.61 0.00 36.19 4.61
2960 3016 1.349067 ATATAGGTGGCGGAGGGAAC 58.651 55.000 0.00 0.00 0.00 3.62
2976 3032 4.774726 AGCTTCGGACATCCATGAGTATAT 59.225 41.667 0.00 0.00 35.14 0.86
2998 3054 2.036098 TGGGGGCATGCACTTCAG 59.964 61.111 21.47 0.00 0.00 3.02
3042 3098 3.061322 TGCTACGAAACATGTAAGCGTT 58.939 40.909 20.52 2.96 36.51 4.84
3057 3113 1.328680 CCAATAACTGCTGCTGCTACG 59.671 52.381 17.00 7.69 40.48 3.51
3060 3116 1.457346 GTCCAATAACTGCTGCTGCT 58.543 50.000 17.00 0.00 40.48 4.24
3061 3117 0.453390 GGTCCAATAACTGCTGCTGC 59.547 55.000 8.89 8.89 40.20 5.25
3062 3118 1.825090 TGGTCCAATAACTGCTGCTG 58.175 50.000 4.89 4.89 0.00 4.41
3125 3181 1.065926 TCCGACGTAGCTCTAACTGGA 60.066 52.381 0.00 0.00 0.00 3.86
3126 3182 1.376543 TCCGACGTAGCTCTAACTGG 58.623 55.000 0.00 0.00 0.00 4.00
3166 3225 3.009026 CAAGGTTTGCCACTTTTGCTTT 58.991 40.909 0.00 0.00 37.19 3.51
3223 3282 4.095610 GTTGTCACAAACAGAAAAGTCCG 58.904 43.478 0.00 0.00 39.58 4.79
3244 3303 2.948979 TCAAAATTGTCGAGCACCTTGT 59.051 40.909 0.00 0.00 0.00 3.16
3363 3422 7.466320 GCATCAGAACAAAACTTGCAATCTTTT 60.466 33.333 0.00 4.41 0.00 2.27
3384 3443 4.823442 ACAAGTGAAGATTGAACTGCATCA 59.177 37.500 0.00 0.00 0.00 3.07
3393 3452 5.885352 TCAGTTTTGGACAAGTGAAGATTGA 59.115 36.000 0.00 0.00 33.90 2.57
3406 3465 3.303791 CGTAAGCACCTTCAGTTTTGGAC 60.304 47.826 0.00 0.00 0.00 4.02
3466 3525 5.700373 GTCTGTTCTTCTTGCTTCTCATCTT 59.300 40.000 0.00 0.00 0.00 2.40
3475 3534 6.944862 AGGAAATATTGTCTGTTCTTCTTGCT 59.055 34.615 0.00 0.00 0.00 3.91
3643 3705 5.367937 TCCCATCTCTAAAATCTCTCCAAGG 59.632 44.000 0.00 0.00 0.00 3.61
3653 3715 5.378230 TGACTGCATCCCATCTCTAAAAT 57.622 39.130 0.00 0.00 0.00 1.82
3657 3719 4.033009 TCTTTGACTGCATCCCATCTCTA 58.967 43.478 0.00 0.00 0.00 2.43
3675 3737 9.829507 CAATATATGTTCTCCTTGAGTCTCTTT 57.170 33.333 0.65 0.00 0.00 2.52
3731 3793 1.003442 TATCAGCTGGGGGCAGTCT 59.997 57.895 15.13 0.00 44.79 3.24
3740 3802 4.754114 GCTTCAGGTAAATCTATCAGCTGG 59.246 45.833 15.13 0.00 38.14 4.85
3863 3925 0.249784 CGACTGCATCCCATCTCTGG 60.250 60.000 0.00 0.00 42.73 3.86
3970 4041 5.297527 TGCTTGGCATCTTCAATGTATAGTG 59.702 40.000 0.00 0.00 31.71 2.74
3975 4046 4.334552 TCTTGCTTGGCATCTTCAATGTA 58.665 39.130 0.00 0.00 38.76 2.29
3977 4048 3.442625 TCTCTTGCTTGGCATCTTCAATG 59.557 43.478 0.00 0.00 38.76 2.82
3988 4059 3.008330 CAGTGGAAGATCTCTTGCTTGG 58.992 50.000 11.91 0.00 43.54 3.61
4041 4112 4.039852 TGTGTGTTCTAGCCATAGTGTCAA 59.960 41.667 0.00 0.00 0.00 3.18
4049 4120 4.085357 TGTTTCTGTGTGTTCTAGCCAT 57.915 40.909 0.00 0.00 0.00 4.40
4050 4121 3.552132 TGTTTCTGTGTGTTCTAGCCA 57.448 42.857 0.00 0.00 0.00 4.75
4109 4181 2.751806 CTGGTTCCATTTCTCCTTGCTC 59.248 50.000 0.00 0.00 0.00 4.26
4143 4215 5.118990 GCAACATCTTAGCCTCATAAGTGA 58.881 41.667 0.00 0.00 34.87 3.41
4146 4218 5.587844 AGTTGCAACATCTTAGCCTCATAAG 59.412 40.000 30.11 0.00 34.63 1.73
4153 4225 4.397417 AGAATGAGTTGCAACATCTTAGCC 59.603 41.667 30.11 11.63 0.00 3.93
4183 4255 0.182061 CCATGGCTCTAGTGCACCAT 59.818 55.000 14.63 5.77 43.70 3.55
4184 4256 1.603842 CCATGGCTCTAGTGCACCA 59.396 57.895 14.63 3.10 36.43 4.17
4236 4308 0.966179 ACGAGCACACCACATCTGTA 59.034 50.000 0.00 0.00 0.00 2.74
4246 4318 3.044305 GCCAGTGGACGAGCACAC 61.044 66.667 15.20 0.00 37.86 3.82


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

AutoCloner maintained by Alex Coulton.