Multiple sequence alignment - TraesCS3A01G219900

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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 TraesCS3A01G219900 chr3A 100.000 3695 0 0 1 3695 405627884 405624190 0.000000e+00 6824.0
1 TraesCS3A01G219900 chr3A 93.103 58 3 1 2900 2956 720175936 720175879 2.360000e-12 84.2
2 TraesCS3A01G219900 chr3A 91.379 58 4 1 2900 2956 720146929 720146872 1.100000e-10 78.7
3 TraesCS3A01G219900 chr3D 94.533 2890 109 26 1 2861 320504218 320507087 0.000000e+00 4416.0
4 TraesCS3A01G219900 chr3D 88.626 211 24 0 3261 3471 320507477 320507687 1.320000e-64 257.0
5 TraesCS3A01G219900 chr3B 93.143 2902 128 34 1 2867 399903003 399900138 0.000000e+00 4191.0
6 TraesCS3A01G219900 chr3B 91.111 180 16 0 3292 3471 399899495 399899316 1.030000e-60 244.0
7 TraesCS3A01G219900 chr3B 91.275 149 10 2 3149 3294 399900006 399899858 2.250000e-47 200.0
8 TraesCS3A01G219900 chr2A 84.510 510 68 9 3191 3691 755440570 755441077 9.220000e-136 494.0
9 TraesCS3A01G219900 chr1A 98.582 141 2 0 3005 3145 278527918 278528058 2.200000e-62 250.0
10 TraesCS3A01G219900 chr1A 97.872 141 3 0 3005 3145 278530660 278530800 1.030000e-60 244.0
11 TraesCS3A01G219900 chr1A 92.958 71 2 3 2939 3008 4011090 4011158 2.350000e-17 100.0
12 TraesCS3A01G219900 chrUn 98.551 138 2 0 3008 3145 354077250 354077113 1.030000e-60 244.0
13 TraesCS3A01G219900 chrUn 92.958 71 2 3 2939 3008 442413966 442414034 2.350000e-17 100.0
14 TraesCS3A01G219900 chr6D 97.872 141 3 0 3005 3145 108491912 108492052 1.030000e-60 244.0
15 TraesCS3A01G219900 chr6D 98.551 138 2 0 3008 3145 168263979 168263842 1.030000e-60 244.0
16 TraesCS3A01G219900 chr6D 98.551 138 2 0 3008 3145 458921633 458921496 1.030000e-60 244.0
17 TraesCS3A01G219900 chr4D 98.551 138 2 0 3008 3145 365079038 365078901 1.030000e-60 244.0
18 TraesCS3A01G219900 chr1D 97.872 141 3 0 3005 3145 254390973 254391113 1.030000e-60 244.0
19 TraesCS3A01G219900 chr1D 97.872 141 3 0 3005 3145 254391491 254391631 1.030000e-60 244.0
20 TraesCS3A01G219900 chr5A 91.071 168 15 0 2263 2430 573988380 573988213 1.030000e-55 228.0
21 TraesCS3A01G219900 chr6B 96.721 61 1 1 2949 3008 183446349 183446289 2.350000e-17 100.0
22 TraesCS3A01G219900 chr6B 92.958 71 2 3 2939 3008 625949504 625949572 2.350000e-17 100.0
23 TraesCS3A01G219900 chr4A 92.958 71 2 3 2939 3008 73808396 73808464 2.350000e-17 100.0
24 TraesCS3A01G219900 chr4A 91.549 71 3 3 2939 3008 687977296 687977364 1.090000e-15 95.3
25 TraesCS3A01G219900 chr4A 95.238 42 1 1 2912 2952 2150280 2150321 8.570000e-07 65.8
26 TraesCS3A01G219900 chr5D 94.030 67 1 3 2945 3008 357560173 357560239 8.450000e-17 99.0
27 TraesCS3A01G219900 chr4B 91.549 71 3 3 2939 3008 308691030 308691098 1.090000e-15 95.3
28 TraesCS3A01G219900 chr2B 95.082 61 2 1 2949 3008 782436125 782436065 1.090000e-15 95.3
29 TraesCS3A01G219900 chr7D 91.228 57 2 2 2896 2949 584302453 584302509 1.420000e-09 75.0
30 TraesCS3A01G219900 chr7D 95.238 42 2 0 2907 2948 36048887 36048846 2.380000e-07 67.6
31 TraesCS3A01G219900 chr7D 97.059 34 1 0 2916 2949 105651368 105651335 1.430000e-04 58.4


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 TraesCS3A01G219900 chr3A 405624190 405627884 3694 True 6824.0 6824 100.0000 1 3695 1 chr3A.!!$R1 3694
1 TraesCS3A01G219900 chr3D 320504218 320507687 3469 False 2336.5 4416 91.5795 1 3471 2 chr3D.!!$F1 3470
2 TraesCS3A01G219900 chr3B 399899316 399903003 3687 True 1545.0 4191 91.8430 1 3471 3 chr3B.!!$R1 3470
3 TraesCS3A01G219900 chr2A 755440570 755441077 507 False 494.0 494 84.5100 3191 3691 1 chr2A.!!$F1 500
4 TraesCS3A01G219900 chr1A 278527918 278530800 2882 False 247.0 250 98.2270 3005 3145 2 chr1A.!!$F2 140
5 TraesCS3A01G219900 chr1D 254390973 254391631 658 False 244.0 244 97.8720 3005 3145 2 chr1D.!!$F1 140

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
546 574 0.918983 ATTCGAGATCCAAAGGCCCA 59.081 50.0 0.00 0.0 0.0 5.36 F
1443 1477 0.395173 ACCAAGGCTTGTTCACCGTT 60.395 50.0 24.57 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1702 0.178970 GGGACTGGAGGATAGCCGTA 60.179 60.0 0.00 0.0 39.96 4.02 R
2955 3101 0.385974 GCGCGCTTCTGTCAAAACAT 60.386 50.0 26.67 0.0 34.13 2.71 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
23 24 6.604735 AGTAGAAACGCCAATTATGTGATC 57.395 37.500 0.00 0.00 0.00 2.92
25 26 6.823689 AGTAGAAACGCCAATTATGTGATCTT 59.176 34.615 0.00 0.00 0.00 2.40
27 28 6.324819 AGAAACGCCAATTATGTGATCTTTG 58.675 36.000 0.00 0.00 0.00 2.77
95 103 9.244799 CATTTCAATGAAGTTGATATGGACATG 57.755 33.333 11.10 0.00 45.11 3.21
99 107 8.245491 TCAATGAAGTTGATATGGACATGTTTG 58.755 33.333 0.00 0.00 41.79 2.93
128 136 4.915704 TCTTTGAAAGCGTCGAAACAAAT 58.084 34.783 0.00 0.00 0.00 2.32
158 166 5.862845 ACATATACAAAGGAGCCTGATGAG 58.137 41.667 8.95 0.00 0.00 2.90
159 167 5.604231 ACATATACAAAGGAGCCTGATGAGA 59.396 40.000 8.95 0.00 0.00 3.27
329 353 6.560253 AGCGAGTTTCACATAAATCTTGTT 57.440 33.333 0.00 0.00 0.00 2.83
370 396 2.263077 CATGTACTCACCAGAACGCTC 58.737 52.381 0.00 0.00 0.00 5.03
520 548 2.104111 ACAGGTTGTTGGACGATCTGAA 59.896 45.455 13.99 0.00 42.16 3.02
546 574 0.918983 ATTCGAGATCCAAAGGCCCA 59.081 50.000 0.00 0.00 0.00 5.36
566 594 5.163612 GCCCATGTTAGAGATTCCAAGTTTC 60.164 44.000 0.00 0.00 0.00 2.78
587 615 8.116026 AGTTTCCATTGGATACTACCTCATTTT 58.884 33.333 22.61 0.55 41.03 1.82
610 638 2.362889 CCCATGGCCACAAGGTCC 60.363 66.667 8.16 0.00 39.40 4.46
628 656 3.105283 GTCCTGGGGTTGACATAGTAGT 58.895 50.000 0.00 0.00 0.00 2.73
629 657 4.284178 GTCCTGGGGTTGACATAGTAGTA 58.716 47.826 0.00 0.00 0.00 1.82
631 659 4.231195 TCCTGGGGTTGACATAGTAGTAGA 59.769 45.833 0.00 0.00 0.00 2.59
705 733 1.452833 GAGGGCTTCATCCAGCACC 60.453 63.158 0.00 0.00 45.23 5.01
706 734 2.440980 GGGCTTCATCCAGCACCC 60.441 66.667 0.00 0.00 42.10 4.61
800 828 2.813179 CGCCGGAATTTGCCTCGAG 61.813 63.158 5.05 5.13 0.00 4.04
810 838 1.629043 TTGCCTCGAGTAACTGGACT 58.371 50.000 12.31 0.00 0.00 3.85
846 874 3.120991 GGTTGAAACTGAATCGTCACTCG 60.121 47.826 0.00 0.00 41.41 4.18
1008 1039 1.226859 GATCGACGCCATGGACGAA 60.227 57.895 27.68 16.07 38.22 3.85
1034 1068 4.137872 CGCAGCAAAGCCCATGGG 62.138 66.667 27.87 27.87 38.57 4.00
1119 1153 1.677217 CCCTTTGCTCTAGACACTGCC 60.677 57.143 0.00 0.00 0.00 4.85
1122 1156 1.536073 TTGCTCTAGACACTGCCGCT 61.536 55.000 0.00 0.00 0.00 5.52
1314 1348 1.158484 TCGCTACGGACGAGGAGATG 61.158 60.000 0.00 0.00 33.96 2.90
1315 1349 1.437772 CGCTACGGACGAGGAGATGT 61.438 60.000 0.00 0.00 0.00 3.06
1356 1390 4.426112 CGCGTGCAGAGCAGGAGA 62.426 66.667 14.96 0.00 45.68 3.71
1359 1393 1.227205 CGTGCAGAGCAGGAGATCC 60.227 63.158 5.84 0.00 45.68 3.36
1443 1477 0.395173 ACCAAGGCTTGTTCACCGTT 60.395 50.000 24.57 0.00 0.00 4.44
1452 1486 1.937278 TGTTCACCGTTTACAAGCGA 58.063 45.000 0.00 0.00 34.38 4.93
1468 1502 0.738762 GCGACTCTTCATGCTCTGCA 60.739 55.000 0.00 0.00 44.86 4.41
1479 1513 2.532256 GCTCTGCATCGCGCTGAAT 61.532 57.895 15.14 0.00 46.55 2.57
1792 1826 3.822192 CGCCACCCGAGATCGTGA 61.822 66.667 1.09 0.00 40.02 4.35
2352 2386 1.827969 AGCATGTACCAGAGAGTCACC 59.172 52.381 0.00 0.00 0.00 4.02
2397 2431 0.878961 GCGTGTTCCTGTCGTTCCTT 60.879 55.000 0.00 0.00 0.00 3.36
2406 2440 2.422597 CTGTCGTTCCTTATGCAACCA 58.577 47.619 0.00 0.00 0.00 3.67
2507 2541 1.000955 GAGCAACGAGAACCTTGGAGA 59.999 52.381 0.00 0.00 0.00 3.71
2637 2671 3.462678 GAGGGGAGCAGGGACGTC 61.463 72.222 7.13 7.13 0.00 4.34
2646 2680 1.674651 CAGGGACGTCGTGAGGAGA 60.675 63.158 9.92 0.00 33.39 3.71
2699 2733 6.642733 TCCTATCTGGGACTCTTGATTTTT 57.357 37.500 0.00 0.00 36.20 1.94
2700 2734 7.749377 TCCTATCTGGGACTCTTGATTTTTA 57.251 36.000 0.00 0.00 36.20 1.52
2750 2786 7.816513 ACTTTTATGTTAAGTACTCCTCCGTTC 59.183 37.037 0.00 0.00 34.22 3.95
2756 2792 4.635699 AAGTACTCCTCCGTTCCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
2759 2795 5.485620 AGTACTCCTCCGTTCCAAAATAAC 58.514 41.667 0.00 0.00 0.00 1.89
2760 2796 4.635699 ACTCCTCCGTTCCAAAATAACT 57.364 40.909 0.00 0.00 0.00 2.24
2766 2802 6.943718 TCCTCCGTTCCAAAATAACTTTGTAT 59.056 34.615 0.00 0.00 42.57 2.29
2797 2834 5.873164 AGGTACACTTATTTTAGCACGGAAG 59.127 40.000 0.00 0.00 0.00 3.46
2810 2847 2.930682 GCACGGAAGGAGTATGAAGAAC 59.069 50.000 0.00 0.00 0.00 3.01
2816 2853 5.480205 GGAAGGAGTATGAAGAACGAACTT 58.520 41.667 0.00 0.00 0.00 2.66
2817 2854 5.577554 GGAAGGAGTATGAAGAACGAACTTC 59.422 44.000 15.32 15.32 44.31 3.01
2891 3035 9.495572 CTAGGTCAACTTCTTTAGATTTCACTT 57.504 33.333 0.00 0.00 0.00 3.16
2913 3059 9.575783 CACTTAGTCTACAAAAATACTCTCTCC 57.424 37.037 0.00 0.00 0.00 3.71
2914 3060 8.460428 ACTTAGTCTACAAAAATACTCTCTCCG 58.540 37.037 0.00 0.00 0.00 4.63
2915 3061 6.837471 AGTCTACAAAAATACTCTCTCCGT 57.163 37.500 0.00 0.00 0.00 4.69
2916 3062 7.229581 AGTCTACAAAAATACTCTCTCCGTT 57.770 36.000 0.00 0.00 0.00 4.44
2917 3063 7.668492 AGTCTACAAAAATACTCTCTCCGTTT 58.332 34.615 0.00 0.00 0.00 3.60
2918 3064 7.813627 AGTCTACAAAAATACTCTCTCCGTTTC 59.186 37.037 0.00 0.00 0.00 2.78
2919 3065 7.597743 GTCTACAAAAATACTCTCTCCGTTTCA 59.402 37.037 0.00 0.00 0.00 2.69
2920 3066 8.145767 TCTACAAAAATACTCTCTCCGTTTCAA 58.854 33.333 0.00 0.00 0.00 2.69
2921 3067 7.562454 ACAAAAATACTCTCTCCGTTTCAAA 57.438 32.000 0.00 0.00 0.00 2.69
2922 3068 7.992008 ACAAAAATACTCTCTCCGTTTCAAAA 58.008 30.769 0.00 0.00 0.00 2.44
2923 3069 8.630037 ACAAAAATACTCTCTCCGTTTCAAAAT 58.370 29.630 0.00 0.00 0.00 1.82
2926 3072 9.720769 AAAATACTCTCTCCGTTTCAAAATAGA 57.279 29.630 0.00 0.00 0.00 1.98
2927 3073 9.892130 AAATACTCTCTCCGTTTCAAAATAGAT 57.108 29.630 0.00 0.00 0.00 1.98
2931 3077 9.892130 ACTCTCTCCGTTTCAAAATAGATAATT 57.108 29.630 0.00 0.00 0.00 1.40
2933 3079 9.884636 TCTCTCCGTTTCAAAATAGATAATTCA 57.115 29.630 0.00 0.00 0.00 2.57
2967 3113 9.391006 ACTAACTTAGTTCAATGTTTTGACAGA 57.609 29.630 0.00 0.00 41.50 3.41
2970 3116 7.196331 ACTTAGTTCAATGTTTTGACAGAAGC 58.804 34.615 0.00 0.00 41.50 3.86
2971 3117 4.601019 AGTTCAATGTTTTGACAGAAGCG 58.399 39.130 0.00 0.00 41.50 4.68
2972 3118 2.998772 TCAATGTTTTGACAGAAGCGC 58.001 42.857 0.00 0.00 36.94 5.92
2973 3119 1.710249 CAATGTTTTGACAGAAGCGCG 59.290 47.619 0.00 0.00 34.60 6.86
2974 3120 0.385974 ATGTTTTGACAGAAGCGCGC 60.386 50.000 26.66 26.66 0.00 6.86
2975 3121 2.069277 GTTTTGACAGAAGCGCGCG 61.069 57.895 28.44 28.44 0.00 6.86
2976 3122 3.235292 TTTTGACAGAAGCGCGCGG 62.235 57.895 33.06 16.99 0.00 6.46
2977 3123 4.961511 TTGACAGAAGCGCGCGGT 62.962 61.111 30.98 30.98 0.00 5.68
2980 3126 4.351938 ACAGAAGCGCGCGGTGTA 62.352 61.111 36.63 0.00 0.00 2.90
2981 3127 3.109547 CAGAAGCGCGCGGTGTAA 61.110 61.111 36.63 0.00 0.00 2.41
2982 3128 2.125673 AGAAGCGCGCGGTGTAAT 60.126 55.556 36.63 20.49 0.00 1.89
2983 3129 1.740296 AGAAGCGCGCGGTGTAATT 60.740 52.632 36.63 20.04 0.00 1.40
2984 3130 1.296649 GAAGCGCGCGGTGTAATTC 60.297 57.895 36.63 24.27 0.00 2.17
2985 3131 2.627201 GAAGCGCGCGGTGTAATTCC 62.627 60.000 36.63 13.03 0.00 3.01
2986 3132 3.492545 GCGCGCGGTGTAATTCCA 61.493 61.111 33.06 0.00 0.00 3.53
2987 3133 2.819552 GCGCGCGGTGTAATTCCAT 61.820 57.895 33.06 0.00 0.00 3.41
2988 3134 1.719117 CGCGCGGTGTAATTCCATT 59.281 52.632 24.84 0.00 0.00 3.16
2989 3135 0.588730 CGCGCGGTGTAATTCCATTG 60.589 55.000 24.84 0.00 0.00 2.82
2990 3136 0.730265 GCGCGGTGTAATTCCATTGA 59.270 50.000 8.83 0.00 0.00 2.57
2991 3137 1.333619 GCGCGGTGTAATTCCATTGAT 59.666 47.619 8.83 0.00 0.00 2.57
2992 3138 2.223479 GCGCGGTGTAATTCCATTGATT 60.223 45.455 8.83 0.00 0.00 2.57
2993 3139 3.733684 GCGCGGTGTAATTCCATTGATTT 60.734 43.478 8.83 0.00 0.00 2.17
2994 3140 4.420168 CGCGGTGTAATTCCATTGATTTT 58.580 39.130 0.00 0.00 0.00 1.82
2995 3141 4.862018 CGCGGTGTAATTCCATTGATTTTT 59.138 37.500 0.00 0.00 0.00 1.94
3145 3291 9.463443 CCTATAATTAGCTTTTCGGGAAATTTG 57.537 33.333 0.00 0.00 0.00 2.32
3146 3292 9.463443 CTATAATTAGCTTTTCGGGAAATTTGG 57.537 33.333 0.00 0.00 0.00 3.28
3147 3293 4.529109 TTAGCTTTTCGGGAAATTTGGG 57.471 40.909 0.00 0.00 0.00 4.12
3149 3295 2.562738 AGCTTTTCGGGAAATTTGGGAG 59.437 45.455 0.00 0.00 0.00 4.30
3150 3296 2.299013 GCTTTTCGGGAAATTTGGGAGT 59.701 45.455 0.00 0.00 0.00 3.85
3151 3297 3.508402 GCTTTTCGGGAAATTTGGGAGTA 59.492 43.478 0.00 0.00 0.00 2.59
3156 3302 9.297037 CTTTTCGGGAAATTTGGGAGTATATAT 57.703 33.333 0.00 0.00 0.00 0.86
3160 3306 7.881232 TCGGGAAATTTGGGAGTATATATCAAC 59.119 37.037 0.00 0.00 0.00 3.18
3184 3330 4.153673 AGATTCTCTGATTTCCCTGCTG 57.846 45.455 0.00 0.00 0.00 4.41
3207 3353 8.907885 GCTGGAAATCTATTCTAAAGGTGAAAT 58.092 33.333 0.00 0.00 0.00 2.17
3297 3948 4.804597 TCATAGGCAAGCTCCTCTTAGTA 58.195 43.478 0.00 0.00 37.66 1.82
3302 3953 3.432890 GGCAAGCTCCTCTTAGTAAGCAT 60.433 47.826 4.93 0.00 37.22 3.79
3312 3963 3.850173 TCTTAGTAAGCATTTCCCCCAGT 59.150 43.478 4.93 0.00 0.00 4.00
3351 4002 3.391296 TGAGCCTGAAAGTACTGTTTCCT 59.609 43.478 0.00 0.00 35.85 3.36
3365 4016 5.892348 ACTGTTTCCTAATTCCACCAGATT 58.108 37.500 0.00 0.00 0.00 2.40
3369 4020 9.627123 CTGTTTCCTAATTCCACCAGATTAATA 57.373 33.333 0.00 0.00 0.00 0.98
3380 4031 8.877864 TCCACCAGATTAATATGAACAACTTT 57.122 30.769 11.65 0.00 0.00 2.66
3424 4075 5.009631 TGAGTTGCTTAATTAGTGGCATGT 58.990 37.500 9.50 0.00 34.59 3.21
3443 4096 1.092921 TGGTGCGTGTCTGTGGAAAC 61.093 55.000 0.00 0.00 0.00 2.78
3455 4108 3.953612 TCTGTGGAAACTTTGCAACTCAT 59.046 39.130 0.00 0.00 30.97 2.90
3478 4131 9.330063 TCATTAATGAATCTGATACTGTTCACC 57.670 33.333 15.82 0.00 33.85 4.02
3485 4138 0.252197 GATACTGTTCACCGGGGCTT 59.748 55.000 6.32 0.00 0.00 4.35
3487 4140 0.609662 TACTGTTCACCGGGGCTTAC 59.390 55.000 6.32 0.87 0.00 2.34
3498 4151 3.028130 CCGGGGCTTACATAAAAATGGT 58.972 45.455 0.00 0.00 0.00 3.55
3499 4152 3.181480 CCGGGGCTTACATAAAAATGGTG 60.181 47.826 0.00 0.00 0.00 4.17
3501 4154 4.641094 CGGGGCTTACATAAAAATGGTGTA 59.359 41.667 0.00 0.00 0.00 2.90
3539 4193 7.816995 TCCATGTATAAATGGCTTGAAAAACAC 59.183 33.333 16.28 0.00 45.82 3.32
3543 4197 7.655328 TGTATAAATGGCTTGAAAAACACCTTG 59.345 33.333 0.00 0.00 0.00 3.61
3545 4199 1.134551 TGGCTTGAAAAACACCTTGCC 60.135 47.619 0.00 0.00 39.53 4.52
3560 4214 1.686052 CTTGCCAGGTGCCACTTTAAA 59.314 47.619 0.00 0.00 40.16 1.52
3561 4215 2.008242 TGCCAGGTGCCACTTTAAAT 57.992 45.000 0.00 0.00 40.16 1.40
3602 4270 8.962884 AGTTGCCTTTGAAAATACAAATCTTT 57.037 26.923 0.00 0.00 38.73 2.52
3605 4273 8.816640 TGCCTTTGAAAATACAAATCTTTCTC 57.183 30.769 0.00 0.00 38.73 2.87
3609 4277 9.971922 CTTTGAAAATACAAATCTTTCTCTGGT 57.028 29.630 0.00 0.00 38.73 4.00
3622 4290 6.055588 TCTTTCTCTGGTAGTTGTTCCAAAG 58.944 40.000 0.00 0.00 33.06 2.77
3630 4298 1.404035 AGTTGTTCCAAAGTGCGGTTC 59.596 47.619 0.00 0.00 0.00 3.62
3632 4300 1.305201 TGTTCCAAAGTGCGGTTCTC 58.695 50.000 0.00 0.00 0.00 2.87
3637 5252 2.103432 TCCAAAGTGCGGTTCTCACTAA 59.897 45.455 0.00 0.00 43.36 2.24
3668 5283 3.073798 TGAGATAAACAAAGTGGCCTGGA 59.926 43.478 3.32 0.00 0.00 3.86
3670 5285 3.826729 AGATAAACAAAGTGGCCTGGAAC 59.173 43.478 3.32 0.00 0.00 3.62
3672 5287 1.106944 AACAAAGTGGCCTGGAACCG 61.107 55.000 3.32 0.00 0.00 4.44
3673 5288 1.528309 CAAAGTGGCCTGGAACCGT 60.528 57.895 3.32 0.00 0.00 4.83
3674 5289 1.528309 AAAGTGGCCTGGAACCGTG 60.528 57.895 3.32 0.00 0.00 4.94
3692 5781 2.996621 CGTGTTGGTCCTTTTGCAAAAA 59.003 40.909 23.92 9.02 0.00 1.94
3694 5783 4.806247 CGTGTTGGTCCTTTTGCAAAAATA 59.194 37.500 23.92 12.91 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.394971 ACATATCAGTTCAATTGTCACAAAGA 57.605 30.769 5.13 0.00 0.00 2.52
23 24 9.121517 GAACATATCAGTTCAATTGTCACAAAG 57.878 33.333 5.13 0.00 45.53 2.77
90 98 7.148689 GCTTTCAAAGATTCCATCAAACATGTC 60.149 37.037 0.00 0.00 0.00 3.06
95 103 5.222631 ACGCTTTCAAAGATTCCATCAAAC 58.777 37.500 0.00 0.00 0.00 2.93
99 107 3.370978 TCGACGCTTTCAAAGATTCCATC 59.629 43.478 0.00 0.00 0.00 3.51
128 136 8.764558 TCAGGCTCCTTTGTATATGTAGTTTTA 58.235 33.333 0.00 0.00 0.00 1.52
158 166 7.817962 TGTGGCTTTTGACTATTTCTACTACTC 59.182 37.037 0.00 0.00 0.00 2.59
159 167 7.676947 TGTGGCTTTTGACTATTTCTACTACT 58.323 34.615 0.00 0.00 0.00 2.57
347 371 3.257375 AGCGTTCTGGTGAGTACATGTAA 59.743 43.478 7.25 0.00 0.00 2.41
349 373 1.618837 AGCGTTCTGGTGAGTACATGT 59.381 47.619 2.69 2.69 0.00 3.21
391 417 7.496346 ACTTCTGGGTTATATCTGTTCTTCA 57.504 36.000 0.00 0.00 0.00 3.02
520 548 3.430374 CCTTTGGATCTCGAATGTACGGT 60.430 47.826 0.00 0.00 0.00 4.83
546 574 7.123247 CCAATGGAAACTTGGAATCTCTAACAT 59.877 37.037 0.00 0.00 44.95 2.71
566 594 7.339212 TGTTCAAAATGAGGTAGTATCCAATGG 59.661 37.037 0.00 0.00 0.00 3.16
578 606 2.899256 CCATGGGTGTTCAAAATGAGGT 59.101 45.455 2.85 0.00 0.00 3.85
579 607 2.354003 GCCATGGGTGTTCAAAATGAGG 60.354 50.000 15.13 0.00 0.00 3.86
587 615 0.827089 CTTGTGGCCATGGGTGTTCA 60.827 55.000 9.72 0.00 0.00 3.18
610 638 5.509840 GCATCTACTACTATGTCAACCCCAG 60.510 48.000 0.00 0.00 0.00 4.45
795 823 6.787085 AAATTTGAAGTCCAGTTACTCGAG 57.213 37.500 11.84 11.84 0.00 4.04
824 852 3.120991 CGAGTGACGATTCAGTTTCAACC 60.121 47.826 0.00 0.00 45.77 3.77
890 918 5.718246 CAGATGCGCATACGTATTTATAGC 58.282 41.667 25.40 5.78 45.07 2.97
980 1008 1.629504 GCGTCGATCGGCAAGTAAC 59.370 57.895 21.12 5.65 40.26 2.50
1008 1039 4.912395 TTTGCTGCGGGGCCTTGT 62.912 61.111 0.84 0.00 0.00 3.16
1034 1068 1.760192 AGAGAACTTGATGGCCATGC 58.240 50.000 26.56 15.28 0.00 4.06
1104 1138 0.679960 TAGCGGCAGTGTCTAGAGCA 60.680 55.000 1.45 0.00 0.00 4.26
1356 1390 4.460683 TTAGCCGGCGCGTTGGAT 62.461 61.111 23.20 17.17 41.18 3.41
1443 1477 3.056536 AGAGCATGAAGAGTCGCTTGTAA 60.057 43.478 0.00 0.00 36.83 2.41
1503 1537 3.324108 TAAGGGAAGCGGCCGGTT 61.324 61.111 40.18 40.18 38.65 4.44
1668 1702 0.178970 GGGACTGGAGGATAGCCGTA 60.179 60.000 0.00 0.00 39.96 4.02
1962 1996 3.776969 TCAGCCTGTGGTAAGATCTGATT 59.223 43.478 0.00 0.00 0.00 2.57
2295 2329 1.288127 GGCGAAGTGGACTGTACGT 59.712 57.895 0.00 0.00 0.00 3.57
2397 2431 1.247419 CCGCCCAACTTGGTTGCATA 61.247 55.000 7.06 0.00 41.62 3.14
2406 2440 0.831307 GAGATACCTCCGCCCAACTT 59.169 55.000 0.00 0.00 33.30 2.66
2637 2671 1.649664 CCTTCTTGCATCTCCTCACG 58.350 55.000 0.00 0.00 0.00 4.35
2646 2680 2.043652 ATGCCGGCCTTCTTGCAT 60.044 55.556 26.77 4.61 39.49 3.96
2727 2761 6.211184 TGGAACGGAGGAGTACTTAACATAAA 59.789 38.462 0.00 0.00 0.00 1.40
2740 2775 5.699839 CAAAGTTATTTTGGAACGGAGGAG 58.300 41.667 0.00 0.00 41.99 3.69
2775 2811 5.870978 TCCTTCCGTGCTAAAATAAGTGTAC 59.129 40.000 0.00 0.00 0.00 2.90
2788 2825 2.457598 TCTTCATACTCCTTCCGTGCT 58.542 47.619 0.00 0.00 0.00 4.40
2790 2827 3.119602 TCGTTCTTCATACTCCTTCCGTG 60.120 47.826 0.00 0.00 0.00 4.94
2849 2894 8.334734 AGTTGACCTAGGACATACTTAGAACTA 58.665 37.037 17.98 0.00 28.61 2.24
2868 3012 9.274206 ACTAAGTGAAATCTAAAGAAGTTGACC 57.726 33.333 0.00 0.00 0.00 4.02
2891 3035 7.934855 ACGGAGAGAGTATTTTTGTAGACTA 57.065 36.000 0.00 0.00 0.00 2.59
2907 3053 9.884636 TGAATTATCTATTTTGAAACGGAGAGA 57.115 29.630 0.00 0.00 0.00 3.10
2941 3087 9.391006 TCTGTCAAAACATTGAACTAAGTTAGT 57.609 29.630 9.85 9.85 36.13 2.24
2944 3090 7.702348 GCTTCTGTCAAAACATTGAACTAAGTT 59.298 33.333 0.00 0.00 34.13 2.66
2945 3091 7.196331 GCTTCTGTCAAAACATTGAACTAAGT 58.804 34.615 0.00 0.00 34.13 2.24
2946 3092 6.358030 CGCTTCTGTCAAAACATTGAACTAAG 59.642 38.462 0.00 0.00 34.13 2.18
2947 3093 6.198687 CGCTTCTGTCAAAACATTGAACTAA 58.801 36.000 0.00 0.00 34.13 2.24
2948 3094 5.747565 CGCTTCTGTCAAAACATTGAACTA 58.252 37.500 0.00 0.00 34.13 2.24
2949 3095 4.601019 CGCTTCTGTCAAAACATTGAACT 58.399 39.130 0.00 0.00 34.13 3.01
2950 3096 3.180387 GCGCTTCTGTCAAAACATTGAAC 59.820 43.478 0.00 0.00 34.13 3.18
2951 3097 3.371168 GCGCTTCTGTCAAAACATTGAA 58.629 40.909 0.00 0.00 34.13 2.69
2952 3098 2.601979 CGCGCTTCTGTCAAAACATTGA 60.602 45.455 5.56 0.00 34.13 2.57
2953 3099 1.710249 CGCGCTTCTGTCAAAACATTG 59.290 47.619 5.56 0.00 34.13 2.82
2954 3100 1.925946 GCGCGCTTCTGTCAAAACATT 60.926 47.619 26.67 0.00 34.13 2.71
2955 3101 0.385974 GCGCGCTTCTGTCAAAACAT 60.386 50.000 26.67 0.00 34.13 2.71
2956 3102 1.010125 GCGCGCTTCTGTCAAAACA 60.010 52.632 26.67 0.00 0.00 2.83
2957 3103 2.069277 CGCGCGCTTCTGTCAAAAC 61.069 57.895 30.48 0.00 0.00 2.43
2958 3104 2.248140 CGCGCGCTTCTGTCAAAA 59.752 55.556 30.48 0.00 0.00 2.44
2959 3105 3.711842 CCGCGCGCTTCTGTCAAA 61.712 61.111 30.48 0.00 0.00 2.69
2960 3106 4.961511 ACCGCGCGCTTCTGTCAA 62.962 61.111 30.48 0.00 0.00 3.18
2963 3109 3.851845 TTACACCGCGCGCTTCTGT 62.852 57.895 30.48 25.96 0.00 3.41
2964 3110 1.966493 AATTACACCGCGCGCTTCTG 61.966 55.000 30.48 21.83 0.00 3.02
2965 3111 1.693083 GAATTACACCGCGCGCTTCT 61.693 55.000 30.48 11.01 0.00 2.85
2966 3112 1.296649 GAATTACACCGCGCGCTTC 60.297 57.895 30.48 19.55 0.00 3.86
2967 3113 2.746803 GGAATTACACCGCGCGCTT 61.747 57.895 30.48 14.82 0.00 4.68
2968 3114 3.192922 GGAATTACACCGCGCGCT 61.193 61.111 30.48 8.51 0.00 5.92
2969 3115 2.317685 AATGGAATTACACCGCGCGC 62.318 55.000 27.36 23.91 32.46 6.86
2970 3116 0.588730 CAATGGAATTACACCGCGCG 60.589 55.000 25.67 25.67 32.46 6.86
2971 3117 0.730265 TCAATGGAATTACACCGCGC 59.270 50.000 0.00 0.00 32.46 6.86
2972 3118 3.691049 AATCAATGGAATTACACCGCG 57.309 42.857 0.00 0.00 32.46 6.46
2992 3138 9.744468 TCTATCATCAGACGATCGAAATAAAAA 57.256 29.630 24.34 0.94 0.00 1.94
2993 3139 9.914131 ATCTATCATCAGACGATCGAAATAAAA 57.086 29.630 24.34 2.46 0.00 1.52
2994 3140 9.914131 AATCTATCATCAGACGATCGAAATAAA 57.086 29.630 24.34 2.09 0.00 1.40
2995 3141 9.561270 GAATCTATCATCAGACGATCGAAATAA 57.439 33.333 24.34 3.23 0.00 1.40
2996 3142 8.730680 TGAATCTATCATCAGACGATCGAAATA 58.269 33.333 24.34 4.74 31.50 1.40
2997 3143 7.597386 TGAATCTATCATCAGACGATCGAAAT 58.403 34.615 24.34 0.00 31.50 2.17
2998 3144 6.970484 TGAATCTATCATCAGACGATCGAAA 58.030 36.000 24.34 3.99 31.50 3.46
2999 3145 6.560253 TGAATCTATCATCAGACGATCGAA 57.440 37.500 24.34 4.38 31.50 3.71
3000 3146 6.374578 GTTGAATCTATCATCAGACGATCGA 58.625 40.000 24.34 0.00 38.03 3.59
3001 3147 5.570973 GGTTGAATCTATCATCAGACGATCG 59.429 44.000 14.88 14.88 38.03 3.69
3002 3148 6.686630 AGGTTGAATCTATCATCAGACGATC 58.313 40.000 0.00 0.00 38.03 3.69
3003 3149 6.493115 AGAGGTTGAATCTATCATCAGACGAT 59.507 38.462 0.00 0.00 38.03 3.73
3006 3152 7.048629 TCAGAGGTTGAATCTATCATCAGAC 57.951 40.000 0.00 0.00 38.03 3.51
3160 3306 8.643385 CCAGCAGGGAAATCAGAGAATCTAGG 62.643 50.000 0.00 0.00 42.02 3.02
3176 3322 6.409695 CCTTTAGAATAGATTTCCAGCAGGGA 60.410 42.308 0.00 0.00 46.61 4.20
3178 3324 6.261826 CACCTTTAGAATAGATTTCCAGCAGG 59.738 42.308 0.00 0.00 0.00 4.85
3233 3385 4.581309 AGCAATATCATCCATCCCGATT 57.419 40.909 0.00 0.00 0.00 3.34
3297 3948 2.101640 AACAACTGGGGGAAATGCTT 57.898 45.000 0.00 0.00 0.00 3.91
3302 3953 2.757894 TAGCAAACAACTGGGGGAAA 57.242 45.000 0.00 0.00 0.00 3.13
3369 4020 7.352079 ACCTTCTCATGAAAAAGTTGTTCAT 57.648 32.000 14.49 14.49 44.63 2.57
3380 4031 5.879763 TCAGGATTCAACCTTCTCATGAAA 58.120 37.500 0.00 0.00 38.32 2.69
3424 4075 1.092921 GTTTCCACAGACACGCACCA 61.093 55.000 0.00 0.00 0.00 4.17
3455 4108 6.761242 CCGGTGAACAGTATCAGATTCATTAA 59.239 38.462 0.00 0.00 33.85 1.40
3478 4131 3.445805 ACACCATTTTTATGTAAGCCCCG 59.554 43.478 0.00 0.00 0.00 5.73
3543 4197 3.352648 TCTATTTAAAGTGGCACCTGGC 58.647 45.455 15.27 0.00 43.74 4.85
3545 4199 6.332630 CCAAATCTATTTAAAGTGGCACCTG 58.667 40.000 15.27 0.00 0.00 4.00
3590 4258 9.574516 AACAACTACCAGAGAAAGATTTGTATT 57.425 29.630 0.00 0.00 0.00 1.89
3622 4290 1.461127 CTTGCTTAGTGAGAACCGCAC 59.539 52.381 0.00 0.00 34.50 5.34
3637 5252 6.072286 CCACTTTGTTTATCTCATCACTTGCT 60.072 38.462 0.00 0.00 0.00 3.91
3655 5270 1.528309 ACGGTTCCAGGCCACTTTG 60.528 57.895 5.01 0.00 0.00 2.77
3670 5285 0.457851 TTGCAAAAGGACCAACACGG 59.542 50.000 0.00 0.00 42.50 4.94


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

AutoCloner maintained by Alex Coulton.