Multiple sequence alignment - TraesCS3A01G396000

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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 TraesCS3A01G396000 chr3A 100.000 3359 0 0 1 3359 643211800 643208442 0.000000e+00 6204.0
1 TraesCS3A01G396000 chr3D 93.889 2111 75 15 804 2866 505066634 505064530 0.000000e+00 3134.0
2 TraesCS3A01G396000 chr3D 84.762 420 25 11 2879 3287 505064203 505063812 5.260000e-103 385.0
3 TraesCS3A01G396000 chr3D 91.250 80 5 1 3282 3359 505056563 505056484 1.270000e-19 108.0
4 TraesCS3A01G396000 chr3B 92.316 1822 90 23 801 2583 666792115 666790305 0.000000e+00 2543.0
5 TraesCS3A01G396000 chr3B 85.360 444 44 14 2865 3304 666789762 666789336 1.110000e-119 440.0
6 TraesCS3A01G396000 chr3B 91.701 241 14 1 2626 2866 666790310 666790076 2.500000e-86 329.0
7 TraesCS3A01G396000 chr5B 86.391 823 92 9 1 804 628674228 628675049 0.000000e+00 881.0
8 TraesCS3A01G396000 chr5B 84.000 800 120 6 1 797 423735120 423735914 0.000000e+00 761.0
9 TraesCS3A01G396000 chr5B 89.474 57 2 2 3072 3128 703505801 703505853 6.010000e-08 69.4
10 TraesCS3A01G396000 chrUn 86.228 806 107 2 1 802 41351117 41350312 0.000000e+00 870.0
11 TraesCS3A01G396000 chrUn 84.881 840 91 23 1120 1941 74559370 74558549 0.000000e+00 815.0
12 TraesCS3A01G396000 chrUn 76.037 217 35 10 2147 2362 74558361 74558161 2.760000e-16 97.1
13 TraesCS3A01G396000 chrUn 81.250 96 5 7 3103 3197 132079199 132079116 7.780000e-07 65.8
14 TraesCS3A01G396000 chr1B 86.279 809 102 7 2 806 642154461 642155264 0.000000e+00 870.0
15 TraesCS3A01G396000 chr2B 86.139 808 102 7 1 804 534701910 534701109 0.000000e+00 863.0
16 TraesCS3A01G396000 chr2B 85.411 802 110 5 1 802 16788849 16788055 0.000000e+00 826.0
17 TraesCS3A01G396000 chr2B 80.139 861 154 16 1103 1954 485751279 485750427 7.910000e-176 627.0
18 TraesCS3A01G396000 chr6D 85.782 844 76 22 1120 1941 431470629 431469808 0.000000e+00 854.0
19 TraesCS3A01G396000 chr5A 85.926 810 99 10 5 805 634065744 634064941 0.000000e+00 850.0
20 TraesCS3A01G396000 chr5A 79.787 94 9 5 3066 3158 477539649 477539565 3.620000e-05 60.2
21 TraesCS3A01G396000 chr2D 85.608 806 112 3 1 806 606123173 606123974 0.000000e+00 843.0
22 TraesCS3A01G396000 chr2D 79.490 863 159 18 1095 1948 412254627 412255480 6.200000e-167 597.0
23 TraesCS3A01G396000 chr2D 100.000 28 0 0 3130 3157 13837866 13837893 6.000000e-03 52.8
24 TraesCS3A01G396000 chr2D 100.000 28 0 0 3130 3157 528993054 528993081 6.000000e-03 52.8
25 TraesCS3A01G396000 chr6B 85.181 830 90 18 1121 1935 651423116 651423927 0.000000e+00 821.0
26 TraesCS3A01G396000 chr1D 84.178 809 109 15 1 802 362519343 362518547 0.000000e+00 767.0
27 TraesCS3A01G396000 chr2A 80.257 856 151 16 1095 1941 579583340 579584186 2.200000e-176 628.0
28 TraesCS3A01G396000 chr5D 87.500 64 4 2 3065 3128 357610036 357610095 1.670000e-08 71.3
29 TraesCS3A01G396000 chr5D 89.474 57 1 3 3101 3157 24128936 24128885 2.160000e-07 67.6
30 TraesCS3A01G396000 chr4B 86.364 66 3 5 3065 3130 521723330 521723271 2.160000e-07 67.6
31 TraesCS3A01G396000 chr7B 80.208 96 8 5 3064 3157 595688603 595688517 1.010000e-05 62.1
32 TraesCS3A01G396000 chr7B 89.130 46 1 3 3130 3175 451153209 451153168 2.000000e-03 54.7
33 TraesCS3A01G396000 chr6A 100.000 28 0 0 3130 3157 448154741 448154714 6.000000e-03 52.8
34 TraesCS3A01G396000 chr4A 100.000 28 0 0 3130 3157 614170441 614170414 6.000000e-03 52.8


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 TraesCS3A01G396000 chr3A 643208442 643211800 3358 True 6204.00 6204 100.000000 1 3359 1 chr3A.!!$R1 3358
1 TraesCS3A01G396000 chr3D 505063812 505066634 2822 True 1759.50 3134 89.325500 804 3287 2 chr3D.!!$R2 2483
2 TraesCS3A01G396000 chr3B 666789336 666792115 2779 True 1104.00 2543 89.792333 801 3304 3 chr3B.!!$R1 2503
3 TraesCS3A01G396000 chr5B 628674228 628675049 821 False 881.00 881 86.391000 1 804 1 chr5B.!!$F2 803
4 TraesCS3A01G396000 chr5B 423735120 423735914 794 False 761.00 761 84.000000 1 797 1 chr5B.!!$F1 796
5 TraesCS3A01G396000 chrUn 41350312 41351117 805 True 870.00 870 86.228000 1 802 1 chrUn.!!$R1 801
6 TraesCS3A01G396000 chrUn 74558161 74559370 1209 True 456.05 815 80.459000 1120 2362 2 chrUn.!!$R3 1242
7 TraesCS3A01G396000 chr1B 642154461 642155264 803 False 870.00 870 86.279000 2 806 1 chr1B.!!$F1 804
8 TraesCS3A01G396000 chr2B 534701109 534701910 801 True 863.00 863 86.139000 1 804 1 chr2B.!!$R3 803
9 TraesCS3A01G396000 chr2B 16788055 16788849 794 True 826.00 826 85.411000 1 802 1 chr2B.!!$R1 801
10 TraesCS3A01G396000 chr2B 485750427 485751279 852 True 627.00 627 80.139000 1103 1954 1 chr2B.!!$R2 851
11 TraesCS3A01G396000 chr6D 431469808 431470629 821 True 854.00 854 85.782000 1120 1941 1 chr6D.!!$R1 821
12 TraesCS3A01G396000 chr5A 634064941 634065744 803 True 850.00 850 85.926000 5 805 1 chr5A.!!$R2 800
13 TraesCS3A01G396000 chr2D 606123173 606123974 801 False 843.00 843 85.608000 1 806 1 chr2D.!!$F4 805
14 TraesCS3A01G396000 chr2D 412254627 412255480 853 False 597.00 597 79.490000 1095 1948 1 chr2D.!!$F2 853
15 TraesCS3A01G396000 chr6B 651423116 651423927 811 False 821.00 821 85.181000 1121 1935 1 chr6B.!!$F1 814
16 TraesCS3A01G396000 chr1D 362518547 362519343 796 True 767.00 767 84.178000 1 802 1 chr1D.!!$R1 801
17 TraesCS3A01G396000 chr2A 579583340 579584186 846 False 628.00 628 80.257000 1095 1941 1 chr2A.!!$F1 846

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
472 497 0.325203 AGAAGGAGGACTGAGCTCCC 60.325 60.0 12.15 5.22 37.98 4.30 F
1971 2104 0.248134 CGGATGAGGAAGACGACGAC 60.248 60.0 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2248 0.464373 CCGGCAGCATTATGGTCAGT 60.464 55.0 0.0 0.0 0.0 3.41 R
3206 3707 0.037512 TGCCCGGTTTTATCGAACGA 60.038 50.0 0.0 0.0 0.0 3.85 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
199 224 0.602638 AACTCATCGCCGTCAAGCAA 60.603 50.000 0.00 0.00 0.00 3.91
353 378 2.232452 CTCGAACACCTCATCCTCAAGT 59.768 50.000 0.00 0.00 0.00 3.16
362 387 2.762887 CTCATCCTCAAGTAGGCAGTCA 59.237 50.000 0.00 0.00 46.10 3.41
365 390 0.888619 CCTCAAGTAGGCAGTCACGA 59.111 55.000 0.00 0.00 38.97 4.35
394 419 1.067776 GTCGTGAAGGACAAGGACGAT 60.068 52.381 0.00 0.00 36.91 3.73
436 461 2.110901 AGCAGAGGCAGAAGTTCATG 57.889 50.000 5.50 2.10 44.61 3.07
446 471 3.111838 CAGAAGTTCATGGATCTCGTCG 58.888 50.000 5.50 0.00 0.00 5.12
451 476 0.466372 TCATGGATCTCGTCGGCTCT 60.466 55.000 0.00 0.00 0.00 4.09
454 479 1.098129 TGGATCTCGTCGGCTCTGAG 61.098 60.000 0.00 0.00 0.00 3.35
455 480 0.816018 GGATCTCGTCGGCTCTGAGA 60.816 60.000 9.28 0.00 42.47 3.27
472 497 0.325203 AGAAGGAGGACTGAGCTCCC 60.325 60.000 12.15 5.22 37.98 4.30
668 699 3.745799 TGCAATTTCTCCCGTGAAAGTA 58.254 40.909 0.00 0.00 39.01 2.24
674 705 7.810759 GCAATTTCTCCCGTGAAAGTATTTTTA 59.189 33.333 0.00 0.00 39.27 1.52
713 748 1.128200 ACAGGGTATATTCTGCCGCA 58.872 50.000 0.00 0.00 34.57 5.69
717 752 2.076863 GGGTATATTCTGCCGCACATC 58.923 52.381 0.00 0.00 0.00 3.06
726 761 1.200716 CTGCCGCACATCATTTCAACT 59.799 47.619 0.00 0.00 0.00 3.16
728 763 1.199789 GCCGCACATCATTTCAACTCA 59.800 47.619 0.00 0.00 0.00 3.41
729 764 2.159338 GCCGCACATCATTTCAACTCAT 60.159 45.455 0.00 0.00 0.00 2.90
734 769 6.753279 CCGCACATCATTTCAACTCATAAAAT 59.247 34.615 0.00 0.00 0.00 1.82
736 771 9.288124 CGCACATCATTTCAACTCATAAAATAA 57.712 29.630 0.00 0.00 0.00 1.40
812 847 6.039616 GCTAGAGATGGTCTTACACAGAAAG 58.960 44.000 0.00 0.00 36.64 2.62
823 858 6.972328 GTCTTACACAGAAAGATAGAGCTCAG 59.028 42.308 17.77 0.00 35.53 3.35
861 903 2.550101 GCCAGATTCATGGGCTCGC 61.550 63.158 2.95 0.00 44.32 5.03
884 926 4.429212 CGCCACGACATCACCCGA 62.429 66.667 0.00 0.00 0.00 5.14
914 965 2.493675 CACTGAATTCTCCTCGACTGGA 59.506 50.000 7.05 0.00 34.52 3.86
978 1036 2.245942 CCATTCGCTCGTCATAGATCG 58.754 52.381 0.00 0.00 0.00 3.69
980 1038 2.665056 TTCGCTCGTCATAGATCGTC 57.335 50.000 0.00 0.00 32.39 4.20
983 1041 1.261885 CGCTCGTCATAGATCGTCTGT 59.738 52.381 0.00 0.00 0.00 3.41
1339 1445 4.783621 TGCTCCGGCACATGCTCC 62.784 66.667 0.00 0.00 44.28 4.70
1950 2080 1.880340 GCCGTTCGATCAGGAGCAG 60.880 63.158 5.64 0.00 0.00 4.24
1971 2104 0.248134 CGGATGAGGAAGACGACGAC 60.248 60.000 0.00 0.00 0.00 4.34
2004 2137 3.073209 AGAAGAAGAAGGTTGGGAAGGAC 59.927 47.826 0.00 0.00 0.00 3.85
2103 2248 2.367202 GGGTGGGAGCGGATCAGAA 61.367 63.158 0.00 0.00 0.00 3.02
2242 2411 1.090052 CCGGGAAAAGGACGATCTGC 61.090 60.000 0.00 0.00 0.00 4.26
2260 2429 2.594962 CCGCCGATGCATTCCGTAC 61.595 63.158 0.00 0.00 37.32 3.67
2383 2552 1.224069 CCACGCAGTCAGTTGTCCTG 61.224 60.000 0.00 0.00 41.61 3.86
2419 2594 7.324616 CGCACGGTTATTAGTTAGGAGTATTAC 59.675 40.741 0.00 0.00 0.00 1.89
2479 2654 4.209080 GCTTTTTCGTTTTGAGATGTTGGG 59.791 41.667 0.00 0.00 0.00 4.12
2492 2667 7.016153 TGAGATGTTGGGATTGTTAGTTAGT 57.984 36.000 0.00 0.00 0.00 2.24
2498 2673 6.183361 TGTTGGGATTGTTAGTTAGTGAAGGA 60.183 38.462 0.00 0.00 0.00 3.36
2541 2716 4.051922 ACGGCGTATGATCATTTCTCTTC 58.948 43.478 12.58 0.00 0.00 2.87
2560 2735 7.201145 TCTCTTCTGTGACAACTTTGTACTAC 58.799 38.462 0.00 0.00 42.43 2.73
2561 2736 7.068348 TCTCTTCTGTGACAACTTTGTACTACT 59.932 37.037 0.00 0.00 42.43 2.57
2562 2737 8.229253 TCTTCTGTGACAACTTTGTACTACTA 57.771 34.615 0.00 0.00 42.43 1.82
2585 2760 7.474222 ACTAAATCAGTGACACTTATTGTGGGA 60.474 37.037 14.27 3.56 42.80 4.37
2600 2775 6.617782 ATTGTGGGATGGAGAGAGTATATG 57.382 41.667 0.00 0.00 0.00 1.78
2606 2781 6.666980 TGGGATGGAGAGAGTATATGATTCAG 59.333 42.308 0.00 0.00 0.00 3.02
2653 2828 1.910772 TGGCCCGGGAATTTTGTGG 60.911 57.895 29.31 0.00 0.00 4.17
2722 2897 2.154854 TTGAGTGGTTTCGAGCAGAG 57.845 50.000 0.00 0.00 0.00 3.35
2727 2902 2.067013 GTGGTTTCGAGCAGAGGTTAC 58.933 52.381 0.00 0.00 0.00 2.50
2752 2927 1.461127 GCAAGTGGTTGACGATCAGAC 59.539 52.381 0.00 0.00 35.46 3.51
2753 2928 2.754472 CAAGTGGTTGACGATCAGACA 58.246 47.619 0.00 0.00 35.46 3.41
2759 2934 2.673368 GGTTGACGATCAGACATTGTCC 59.327 50.000 13.14 0.00 32.71 4.02
2931 3421 5.411669 GTGTTGGGACGATTAGAACTTGATT 59.588 40.000 0.00 0.00 0.00 2.57
2946 3436 1.432514 TGATTGCGAGACAACAGCTC 58.567 50.000 0.00 0.00 42.27 4.09
2958 3448 1.471684 CAACAGCTCAAGGGCATCTTC 59.528 52.381 0.00 0.00 32.41 2.87
2965 3455 1.071542 TCAAGGGCATCTTCAACACGA 59.928 47.619 0.00 0.00 32.41 4.35
2978 3468 4.086199 TCAACACGAACCTTCAAAACAC 57.914 40.909 0.00 0.00 0.00 3.32
2986 3476 2.028876 ACCTTCAAAACACCCGGAAAG 58.971 47.619 0.73 0.00 0.00 2.62
2991 3481 1.751924 CAAAACACCCGGAAAGGTTCA 59.248 47.619 0.73 0.00 38.39 3.18
3013 3503 1.367471 TGAGGTGTTCAGACGCTGG 59.633 57.895 6.95 0.00 36.52 4.85
3016 3506 0.468226 AGGTGTTCAGACGCTGGAAA 59.532 50.000 6.95 0.00 36.52 3.13
3044 3542 2.579201 CGGCACCTCATCGGTTCT 59.421 61.111 0.00 0.00 46.37 3.01
3050 3548 1.954382 CACCTCATCGGTTCTCGGATA 59.046 52.381 0.00 0.00 46.37 2.59
3095 3595 8.231837 GCTCACCGTATATTACAAAAAGTTCAA 58.768 33.333 0.00 0.00 0.00 2.69
3118 3618 9.163899 TCAACATGCATGCATTATAAAAATGTT 57.836 25.926 30.32 24.01 36.45 2.71
3251 3752 0.108756 GGAACCGGTCTCTACAGTGC 60.109 60.000 8.04 0.00 0.00 4.40
3287 3789 3.562557 ACCAGTTCATTACGTTGTTGGTC 59.437 43.478 0.00 0.00 32.52 4.02
3293 3795 3.324268 TCATTACGTTGTTGGTCCCTACA 59.676 43.478 0.00 0.00 0.00 2.74
3295 3797 2.943036 ACGTTGTTGGTCCCTACAAT 57.057 45.000 14.74 0.00 41.78 2.71
3296 3798 2.500229 ACGTTGTTGGTCCCTACAATG 58.500 47.619 22.76 22.76 46.32 2.82
3297 3799 1.199097 CGTTGTTGGTCCCTACAATGC 59.801 52.381 16.22 5.83 41.78 3.56
3300 3802 1.423541 TGTTGGTCCCTACAATGCTGT 59.576 47.619 0.00 0.00 39.75 4.40
3304 3806 4.374689 TGGTCCCTACAATGCTGTTTTA 57.625 40.909 0.00 0.00 36.96 1.52
3305 3807 4.730966 TGGTCCCTACAATGCTGTTTTAA 58.269 39.130 0.00 0.00 36.96 1.52
3307 3809 5.777732 TGGTCCCTACAATGCTGTTTTAATT 59.222 36.000 0.00 0.00 36.96 1.40
3308 3810 6.268847 TGGTCCCTACAATGCTGTTTTAATTT 59.731 34.615 0.00 0.00 36.96 1.82
3309 3811 6.811665 GGTCCCTACAATGCTGTTTTAATTTC 59.188 38.462 0.00 0.00 36.96 2.17
3310 3812 7.309805 GGTCCCTACAATGCTGTTTTAATTTCT 60.310 37.037 0.00 0.00 36.96 2.52
3311 3813 7.755373 GTCCCTACAATGCTGTTTTAATTTCTC 59.245 37.037 0.00 0.00 36.96 2.87
3312 3814 7.669722 TCCCTACAATGCTGTTTTAATTTCTCT 59.330 33.333 0.00 0.00 36.96 3.10
3313 3815 8.306761 CCCTACAATGCTGTTTTAATTTCTCTT 58.693 33.333 0.00 0.00 36.96 2.85
3314 3816 9.346725 CCTACAATGCTGTTTTAATTTCTCTTC 57.653 33.333 0.00 0.00 36.96 2.87
3315 3817 9.346725 CTACAATGCTGTTTTAATTTCTCTTCC 57.653 33.333 0.00 0.00 36.96 3.46
3316 3818 7.154656 ACAATGCTGTTTTAATTTCTCTTCCC 58.845 34.615 0.00 0.00 28.57 3.97
3317 3819 6.916360 ATGCTGTTTTAATTTCTCTTCCCA 57.084 33.333 0.00 0.00 0.00 4.37
3318 3820 6.331369 TGCTGTTTTAATTTCTCTTCCCAG 57.669 37.500 0.00 0.00 0.00 4.45
3319 3821 5.164233 GCTGTTTTAATTTCTCTTCCCAGC 58.836 41.667 0.00 0.00 35.40 4.85
3320 3822 5.371115 TGTTTTAATTTCTCTTCCCAGCG 57.629 39.130 0.00 0.00 0.00 5.18
3321 3823 4.825085 TGTTTTAATTTCTCTTCCCAGCGT 59.175 37.500 0.00 0.00 0.00 5.07
3322 3824 5.048991 TGTTTTAATTTCTCTTCCCAGCGTC 60.049 40.000 0.00 0.00 0.00 5.19
3323 3825 2.115343 AATTTCTCTTCCCAGCGTCC 57.885 50.000 0.00 0.00 0.00 4.79
3324 3826 0.984230 ATTTCTCTTCCCAGCGTCCA 59.016 50.000 0.00 0.00 0.00 4.02
3325 3827 0.762418 TTTCTCTTCCCAGCGTCCAA 59.238 50.000 0.00 0.00 0.00 3.53
3326 3828 0.762418 TTCTCTTCCCAGCGTCCAAA 59.238 50.000 0.00 0.00 0.00 3.28
3327 3829 0.762418 TCTCTTCCCAGCGTCCAAAA 59.238 50.000 0.00 0.00 0.00 2.44
3328 3830 1.351017 TCTCTTCCCAGCGTCCAAAAT 59.649 47.619 0.00 0.00 0.00 1.82
3329 3831 1.470098 CTCTTCCCAGCGTCCAAAATG 59.530 52.381 0.00 0.00 0.00 2.32
3330 3832 0.527565 CTTCCCAGCGTCCAAAATGG 59.472 55.000 0.00 0.00 39.43 3.16
3331 3833 3.287445 CCCAGCGTCCAAAATGGG 58.713 61.111 0.00 0.00 46.14 4.00
3332 3834 2.573340 CCAGCGTCCAAAATGGGC 59.427 61.111 0.00 0.00 39.19 5.36
3333 3835 1.978617 CCAGCGTCCAAAATGGGCT 60.979 57.895 0.00 0.00 40.79 5.19
3334 3836 1.213537 CAGCGTCCAAAATGGGCTG 59.786 57.895 11.50 11.50 43.07 4.85
3335 3837 1.978617 AGCGTCCAAAATGGGCTGG 60.979 57.895 0.00 0.00 40.79 4.85
3336 3838 2.573340 CGTCCAAAATGGGCTGGC 59.427 61.111 0.00 0.00 40.79 4.85
3337 3839 2.981302 GTCCAAAATGGGCTGGCC 59.019 61.111 14.23 14.23 39.55 5.36
3338 3840 1.610379 GTCCAAAATGGGCTGGCCT 60.610 57.895 21.72 4.10 39.55 5.19
3339 3841 0.324275 GTCCAAAATGGGCTGGCCTA 60.324 55.000 21.72 7.88 39.55 3.93
3340 3842 0.636101 TCCAAAATGGGCTGGCCTAT 59.364 50.000 21.72 10.02 38.32 2.57
3342 3844 1.413812 CCAAAATGGGCTGGCCTATTC 59.586 52.381 20.42 1.70 44.80 1.75
3343 3845 1.067516 CAAAATGGGCTGGCCTATTCG 59.932 52.381 20.42 12.63 44.80 3.34
3344 3846 0.550914 AAATGGGCTGGCCTATTCGA 59.449 50.000 20.42 0.00 44.80 3.71
3345 3847 0.550914 AATGGGCTGGCCTATTCGAA 59.449 50.000 21.72 0.00 42.48 3.71
3346 3848 0.109342 ATGGGCTGGCCTATTCGAAG 59.891 55.000 21.72 0.00 33.24 3.79
3347 3849 1.227973 GGGCTGGCCTATTCGAAGG 60.228 63.158 13.80 0.59 39.87 3.46
3354 3856 3.733236 CCTATTCGAAGGCACGTCA 57.267 52.632 3.35 0.00 36.40 4.35
3355 3857 2.004583 CCTATTCGAAGGCACGTCAA 57.995 50.000 3.35 0.00 36.40 3.18
3356 3858 2.343101 CCTATTCGAAGGCACGTCAAA 58.657 47.619 3.35 0.00 36.40 2.69
3357 3859 2.936498 CCTATTCGAAGGCACGTCAAAT 59.064 45.455 3.35 1.01 36.40 2.32
3358 3860 3.374058 CCTATTCGAAGGCACGTCAAATT 59.626 43.478 3.35 0.00 36.40 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 112 1.658686 GGAAGAGGAAGAGCTCGCGA 61.659 60.000 9.26 9.26 0.00 5.87
199 224 1.228124 CTCGATCTCCTCCGGCTCT 60.228 63.158 0.00 0.00 0.00 4.09
236 261 1.376683 CGGCCACCAAATCTTCGGA 60.377 57.895 2.24 0.00 0.00 4.55
276 301 0.179215 CAAGCTCCGTTCGACAATGC 60.179 55.000 0.00 0.00 0.00 3.56
353 378 0.830444 AGGTTGGTCGTGACTGCCTA 60.830 55.000 0.00 0.00 0.00 3.93
365 390 0.834612 TCCTTCACGACAAGGTTGGT 59.165 50.000 14.30 0.00 43.31 3.67
378 403 2.029020 CACTCATCGTCCTTGTCCTTCA 60.029 50.000 0.00 0.00 0.00 3.02
416 441 2.434428 CATGAACTTCTGCCTCTGCTT 58.566 47.619 0.00 0.00 38.71 3.91
436 461 0.816018 TCTCAGAGCCGACGAGATCC 60.816 60.000 0.00 0.00 30.94 3.36
446 471 0.823460 CAGTCCTCCTTCTCAGAGCC 59.177 60.000 0.00 0.00 0.00 4.70
451 476 1.618345 GGAGCTCAGTCCTCCTTCTCA 60.618 57.143 17.19 0.00 44.40 3.27
454 479 1.334384 GGGGAGCTCAGTCCTCCTTC 61.334 65.000 17.19 0.00 46.48 3.46
455 480 1.306568 GGGGAGCTCAGTCCTCCTT 60.307 63.158 17.19 0.00 46.48 3.36
491 516 1.428448 CAAAATGGACGAGCTCACGA 58.572 50.000 15.40 4.82 37.03 4.35
622 653 9.371136 CAACAACACTAGTTCATCACATACTAT 57.629 33.333 0.00 0.00 35.28 2.12
644 675 1.974265 TCACGGGAGAAATTGCAACA 58.026 45.000 0.00 0.00 0.00 3.33
685 718 7.987458 CGGCAGAATATACCCTGTATATGAAAT 59.013 37.037 7.36 0.00 33.19 2.17
696 729 1.128200 TGTGCGGCAGAATATACCCT 58.872 50.000 1.18 0.00 0.00 4.34
701 734 3.884693 TGAAATGATGTGCGGCAGAATAT 59.115 39.130 1.18 0.00 0.00 1.28
734 769 7.326789 AGACGTTTACAATTCGACGAAGAATTA 59.673 33.333 16.40 2.16 45.80 1.40
736 771 5.632347 AGACGTTTACAATTCGACGAAGAAT 59.368 36.000 16.40 6.03 42.13 2.40
749 784 3.548668 CGATCCGCATAAGACGTTTACAA 59.451 43.478 0.00 0.00 0.00 2.41
812 847 3.190535 GTCTCGGGAATCTGAGCTCTATC 59.809 52.174 16.19 7.58 44.15 2.08
823 858 1.641577 CAAAGGACGTCTCGGGAATC 58.358 55.000 16.46 0.00 0.00 2.52
861 903 3.490759 GATGTCGTGGCGTGGCTG 61.491 66.667 0.00 0.00 0.00 4.85
884 926 4.344865 AATTCAGTGGCCGGCGGT 62.345 61.111 28.82 3.91 0.00 5.68
965 1023 8.068380 TGTAATTAACAGACGATCTATGACGAG 58.932 37.037 0.00 0.00 33.01 4.18
1035 1094 4.498520 ATGTCGGCCGACTCTGCG 62.499 66.667 46.72 13.93 44.80 5.18
1049 1116 4.082523 CGTCCCCGTGCTCCATGT 62.083 66.667 0.00 0.00 0.00 3.21
1078 1160 3.080121 CTCCTCCTCCCGCTGCTT 61.080 66.667 0.00 0.00 0.00 3.91
1339 1445 2.281345 GCAGGCCTCCATCATCCG 60.281 66.667 0.00 0.00 0.00 4.18
1950 2080 1.227002 GTCGTCTTCCTCATCCGCC 60.227 63.158 0.00 0.00 0.00 6.13
1971 2104 3.367910 CCTTCTTCTTCTTCACCTCCTCG 60.368 52.174 0.00 0.00 0.00 4.63
2004 2137 3.461773 AGGCCATCGTCGTCCCTG 61.462 66.667 5.01 0.00 0.00 4.45
2103 2248 0.464373 CCGGCAGCATTATGGTCAGT 60.464 55.000 0.00 0.00 0.00 3.41
2136 2281 0.809241 GGCTCTCCTCTGTGATTGCG 60.809 60.000 0.00 0.00 0.00 4.85
2242 2411 2.279851 TACGGAATGCATCGGCGG 60.280 61.111 7.21 6.49 45.35 6.13
2322 2491 1.520174 CGCAGCACATGATCTACTTCG 59.480 52.381 0.00 0.00 0.00 3.79
2383 2552 1.925229 TAACCGTGCGTAACATAGGC 58.075 50.000 0.00 0.00 39.82 3.93
2437 2612 3.723325 AGCAACCCCAACATGGAAATAT 58.277 40.909 0.00 0.00 40.96 1.28
2541 2716 9.256477 TGATTTAGTAGTACAAAGTTGTCACAG 57.744 33.333 2.52 0.00 42.35 3.66
2585 2760 8.489676 ACAACTGAATCATATACTCTCTCCAT 57.510 34.615 0.00 0.00 0.00 3.41
2600 2775 9.736023 AATGAAGTTTTGTTCTACAACTGAATC 57.264 29.630 0.00 0.00 37.90 2.52
2606 2781 7.275560 AGCACAAATGAAGTTTTGTTCTACAAC 59.724 33.333 1.34 0.00 45.14 3.32
2722 2897 3.068560 TCAACCACTTGCATACGTAACC 58.931 45.455 0.00 0.00 0.00 2.85
2727 2902 1.424403 TCGTCAACCACTTGCATACG 58.576 50.000 0.00 0.00 0.00 3.06
2789 2964 2.990479 GACAGCCTCGTCCCCATT 59.010 61.111 0.00 0.00 0.00 3.16
2874 3364 3.482156 AGATTTGACATGGGATCGAGG 57.518 47.619 0.00 0.00 0.00 4.63
2931 3421 0.601046 CCTTGAGCTGTTGTCTCGCA 60.601 55.000 0.00 0.00 33.41 5.10
2946 3436 1.522668 TCGTGTTGAAGATGCCCTTG 58.477 50.000 0.00 0.00 34.68 3.61
2958 3448 3.175929 GGTGTTTTGAAGGTTCGTGTTG 58.824 45.455 0.00 0.00 0.00 3.33
2965 3455 2.146920 TTCCGGGTGTTTTGAAGGTT 57.853 45.000 0.00 0.00 0.00 3.50
2978 3468 0.685097 TCAGTCTGAACCTTTCCGGG 59.315 55.000 0.00 0.00 36.97 5.73
2986 3476 2.760374 CTGAACACCTCAGTCTGAACC 58.240 52.381 3.67 0.00 45.76 3.62
3013 3503 2.178273 GCCGCGTTGGATGGTTTC 59.822 61.111 4.92 0.00 42.00 2.78
3042 3540 0.241749 ACAAACGCACGTATCCGAGA 59.758 50.000 9.04 0.00 37.88 4.04
3044 3542 0.241749 AGACAAACGCACGTATCCGA 59.758 50.000 9.04 0.00 37.88 4.55
3050 3548 1.596954 GCATTTCAGACAAACGCACGT 60.597 47.619 0.00 0.00 0.00 4.49
3052 3550 2.286950 TGAGCATTTCAGACAAACGCAC 60.287 45.455 0.00 0.00 0.00 5.34
3095 3595 8.719560 TGAACATTTTTATAATGCATGCATGT 57.280 26.923 32.79 24.98 36.68 3.21
3206 3707 0.037512 TGCCCGGTTTTATCGAACGA 60.038 50.000 0.00 0.00 0.00 3.85
3242 3743 1.877576 CTGCGGTCCAGCACTGTAGA 61.878 60.000 4.55 0.00 44.83 2.59
3287 3789 7.830739 AGAGAAATTAAAACAGCATTGTAGGG 58.169 34.615 0.00 0.00 36.23 3.53
3293 3795 7.301868 TGGGAAGAGAAATTAAAACAGCATT 57.698 32.000 0.00 0.00 0.00 3.56
3295 3797 5.278957 GCTGGGAAGAGAAATTAAAACAGCA 60.279 40.000 0.00 0.00 44.90 4.41
3296 3798 5.164233 GCTGGGAAGAGAAATTAAAACAGC 58.836 41.667 0.00 0.00 40.40 4.40
3297 3799 5.048713 ACGCTGGGAAGAGAAATTAAAACAG 60.049 40.000 0.00 0.00 0.00 3.16
3300 3802 4.457949 GGACGCTGGGAAGAGAAATTAAAA 59.542 41.667 0.00 0.00 0.00 1.52
3304 3806 1.351017 TGGACGCTGGGAAGAGAAATT 59.649 47.619 0.00 0.00 0.00 1.82
3305 3807 0.984230 TGGACGCTGGGAAGAGAAAT 59.016 50.000 0.00 0.00 0.00 2.17
3307 3809 0.762418 TTTGGACGCTGGGAAGAGAA 59.238 50.000 0.00 0.00 0.00 2.87
3308 3810 0.762418 TTTTGGACGCTGGGAAGAGA 59.238 50.000 0.00 0.00 0.00 3.10
3309 3811 1.470098 CATTTTGGACGCTGGGAAGAG 59.530 52.381 0.00 0.00 0.00 2.85
3310 3812 1.533625 CATTTTGGACGCTGGGAAGA 58.466 50.000 0.00 0.00 0.00 2.87
3311 3813 0.527565 CCATTTTGGACGCTGGGAAG 59.472 55.000 0.00 0.00 40.96 3.46
3312 3814 2.652313 CCATTTTGGACGCTGGGAA 58.348 52.632 0.00 0.00 40.96 3.97
3313 3815 4.413928 CCATTTTGGACGCTGGGA 57.586 55.556 0.00 0.00 40.96 4.37
3314 3816 3.287445 CCCATTTTGGACGCTGGG 58.713 61.111 0.00 0.00 40.96 4.45
3315 3817 1.978617 AGCCCATTTTGGACGCTGG 60.979 57.895 0.00 0.00 40.96 4.85
3316 3818 1.213537 CAGCCCATTTTGGACGCTG 59.786 57.895 9.42 9.42 43.07 5.18
3317 3819 1.978617 CCAGCCCATTTTGGACGCT 60.979 57.895 0.00 0.00 40.96 5.07
3318 3820 2.573340 CCAGCCCATTTTGGACGC 59.427 61.111 0.00 0.00 40.96 5.19
3319 3821 2.573340 GCCAGCCCATTTTGGACG 59.427 61.111 0.00 0.00 40.96 4.79
3320 3822 0.324275 TAGGCCAGCCCATTTTGGAC 60.324 55.000 5.01 0.00 40.96 4.02
3321 3823 0.636101 ATAGGCCAGCCCATTTTGGA 59.364 50.000 5.01 0.00 40.96 3.53
3322 3824 1.413812 GAATAGGCCAGCCCATTTTGG 59.586 52.381 5.01 0.00 37.25 3.28
3323 3825 1.067516 CGAATAGGCCAGCCCATTTTG 59.932 52.381 5.01 0.00 36.58 2.44
3324 3826 1.064017 TCGAATAGGCCAGCCCATTTT 60.064 47.619 5.01 0.00 36.58 1.82
3325 3827 0.550914 TCGAATAGGCCAGCCCATTT 59.449 50.000 5.01 0.00 36.58 2.32
3326 3828 0.550914 TTCGAATAGGCCAGCCCATT 59.449 50.000 5.01 3.11 36.58 3.16
3327 3829 0.109342 CTTCGAATAGGCCAGCCCAT 59.891 55.000 5.01 0.00 36.58 4.00
3328 3830 1.526887 CTTCGAATAGGCCAGCCCA 59.473 57.895 5.01 0.00 36.58 5.36
3329 3831 1.227973 CCTTCGAATAGGCCAGCCC 60.228 63.158 5.01 0.00 36.58 5.19
3330 3832 4.464262 CCTTCGAATAGGCCAGCC 57.536 61.111 5.01 0.00 0.00 4.85
3336 3838 2.004583 TTGACGTGCCTTCGAATAGG 57.995 50.000 0.00 0.00 38.40 2.57
3337 3839 4.600012 AATTTGACGTGCCTTCGAATAG 57.400 40.909 0.00 0.00 34.70 1.73


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

AutoCloner maintained by Alex Coulton.