Multiple sequence alignment - TraesCS3D01G444600

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 TraesCS3D01G444600 chr3D 100.000 3610 0 0 1 3610 553742843 553739234 0.000000e+00 6667.0
1 TraesCS3D01G444600 chr3D 94.220 173 9 1 3102 3274 254827010 254826839 2.760000e-66 263.0
2 TraesCS3D01G444600 chr3A 92.971 3130 129 29 14 3104 690196162 690193085 0.000000e+00 4477.0
3 TraesCS3D01G444600 chr3A 88.272 162 15 3 3452 3610 690192816 690192656 1.320000e-44 191.0
4 TraesCS3D01G444600 chr3B 93.682 2770 103 32 3 2728 734735351 734732610 0.000000e+00 4080.0
5 TraesCS3D01G444600 chr2D 98.182 165 3 0 3103 3267 509744305 509744469 4.560000e-74 289.0
6 TraesCS3D01G444600 chr2D 94.536 183 7 3 3087 3266 428669580 428669398 2.740000e-71 279.0
7 TraesCS3D01G444600 chr7D 95.833 168 6 1 3100 3266 577917838 577917671 1.650000e-68 270.0
8 TraesCS3D01G444600 chr7D 100.000 28 0 0 2705 2732 90810946 90810973 7.000000e-03 52.8
9 TraesCS3D01G444600 chr5B 94.798 173 7 2 3097 3267 157026196 157026368 5.940000e-68 268.0
10 TraesCS3D01G444600 chr5B 100.000 28 0 0 1320 1347 611802452 611802479 7.000000e-03 52.8
11 TraesCS3D01G444600 chr7B 94.318 176 7 3 3092 3266 34678221 34678048 2.140000e-67 267.0
12 TraesCS3D01G444600 chr1D 93.407 182 9 3 3086 3266 178466485 178466306 2.140000e-67 267.0
13 TraesCS3D01G444600 chr4A 92.818 181 13 0 3087 3267 216394766 216394946 2.760000e-66 263.0
14 TraesCS3D01G444600 chr5D 91.146 192 13 4 3079 3267 560508165 560508355 1.290000e-64 257.0
15 TraesCS3D01G444600 chr5D 100.000 28 0 0 2704 2731 5804103 5804130 7.000000e-03 52.8
16 TraesCS3D01G444600 chr7A 100.000 29 0 0 2704 2732 167261641 167261669 2.000000e-03 54.7
17 TraesCS3D01G444600 chr5A 100.000 29 0 0 2704 2732 30215437 30215465 2.000000e-03 54.7
18 TraesCS3D01G444600 chr2A 100.000 29 0 0 2704 2732 32146260 32146232 2.000000e-03 54.7
19 TraesCS3D01G444600 chr2A 100.000 28 0 0 2704 2731 83819800 83819773 7.000000e-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 TraesCS3D01G444600 chr3D 553739234 553742843 3609 True 6667 6667 100.0000 1 3610 1 chr3D.!!$R2 3609
1 TraesCS3D01G444600 chr3A 690192656 690196162 3506 True 2334 4477 90.6215 14 3610 2 chr3A.!!$R1 3596
2 TraesCS3D01G444600 chr3B 734732610 734735351 2741 True 4080 4080 93.6820 3 2728 1 chr3B.!!$R1 2725

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
367 374 0.109723 TGAAACTTTGCTACCCGCCT 59.890 50.000 0.0 0.0 38.05 5.52 F
596 604 0.515564 CACAACGATTTGACCGTCCC 59.484 55.000 0.0 0.0 39.57 4.46 F
1015 1030 1.229984 CTCCCCCACTTTCCCCTCT 60.230 63.158 0.0 0.0 0.00 3.69 F
1265 1280 1.241165 TTGCATGGAAGTGTGCTGAG 58.759 50.000 0.0 0.0 41.78 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1511 0.668535 GGTTCTTGCGCCTTCTTTGT 59.331 50.0 4.18 0.00 0.00 2.83 R
2404 2444 0.365523 CGTTGAACATGTCGCCGTAG 59.634 55.0 0.00 0.00 0.00 3.51 R
2601 2652 0.179137 CATGCATGCACCAAGCTCAG 60.179 55.0 25.37 0.69 45.94 3.35 R
3254 3309 0.545171 TCGTCTCATACTCCCTCCGT 59.455 55.0 0.00 0.00 0.00 4.69 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
104 107 1.068588 GAAAGCGGTGGCCTTTCTTTT 59.931 47.619 3.32 0.00 41.24 2.27
148 151 2.483013 GGCCACTATGCACGACTAATCA 60.483 50.000 0.00 0.00 0.00 2.57
197 200 0.961019 CCAACACAACACTCCATGGG 59.039 55.000 13.02 5.22 0.00 4.00
367 374 0.109723 TGAAACTTTGCTACCCGCCT 59.890 50.000 0.00 0.00 38.05 5.52
448 455 9.734984 TCTTAAAGCAATAATAATAGGGCCTAC 57.265 33.333 17.19 0.00 0.00 3.18
535 542 8.515414 GTTTGTGAGCTTCCTAACTAAAATGAT 58.485 33.333 0.00 0.00 0.00 2.45
542 549 6.900299 GCTTCCTAACTAAAATGATCGTTTCG 59.100 38.462 13.21 9.99 0.00 3.46
560 567 5.392585 CGTTTCGACACTTTGAGAAATTCAC 59.607 40.000 0.00 0.00 34.94 3.18
571 579 9.014297 ACTTTGAGAAATTCACAAATACCCTAG 57.986 33.333 16.49 7.76 36.61 3.02
593 601 5.232463 AGTATTACACAACGATTTGACCGT 58.768 37.500 0.00 0.00 42.61 4.83
596 604 0.515564 CACAACGATTTGACCGTCCC 59.484 55.000 0.00 0.00 39.57 4.46
632 642 6.096705 TGAAAAAGATTCAGCACCAGAAAGAA 59.903 34.615 0.00 0.00 0.00 2.52
642 652 3.737774 GCACCAGAAAGAAACATTCAAGC 59.262 43.478 0.00 0.00 0.00 4.01
657 667 1.448540 AAGCGCCATTCGTCCTCTG 60.449 57.895 2.29 0.00 41.07 3.35
725 735 5.704515 TGATGAGCTCAAAAAGAAGAGGAAG 59.295 40.000 22.50 0.00 32.54 3.46
755 767 1.344087 CCAGTACCACCCTCCATAGGT 60.344 57.143 0.00 0.00 41.89 3.08
843 857 1.806247 GCCTCAAAGGGTGTGTTTTGC 60.806 52.381 0.00 0.00 35.37 3.68
903 918 6.540083 ACTAGTTTATACATATGCCCAACCC 58.460 40.000 1.58 0.00 0.00 4.11
1015 1030 1.229984 CTCCCCCACTTTCCCCTCT 60.230 63.158 0.00 0.00 0.00 3.69
1082 1097 3.320673 CCTGTAGAGTTTCAGGTGGTC 57.679 52.381 3.38 0.00 44.19 4.02
1137 1152 4.882842 TTGTGGTCTTGCACTAGTGATA 57.117 40.909 27.08 11.44 0.00 2.15
1173 1188 4.395231 AGCATGTTCATGTGTCTGATCAAG 59.605 41.667 13.24 0.00 30.81 3.02
1181 1196 5.128335 TCATGTGTCTGATCAAGCACTAGAT 59.872 40.000 22.06 10.69 35.33 1.98
1222 1237 9.772973 TTACTATTTAAGTCATGTGTGAGTTGT 57.227 29.630 8.37 1.57 45.31 3.32
1223 1238 8.677148 ACTATTTAAGTCATGTGTGAGTTGTT 57.323 30.769 8.37 0.00 45.31 2.83
1224 1239 8.559536 ACTATTTAAGTCATGTGTGAGTTGTTG 58.440 33.333 8.37 0.82 45.31 3.33
1225 1240 6.751514 TTTAAGTCATGTGTGAGTTGTTGT 57.248 33.333 8.37 0.00 45.31 3.32
1265 1280 1.241165 TTGCATGGAAGTGTGCTGAG 58.759 50.000 0.00 0.00 41.78 3.35
1387 1402 2.880890 GGTATGCCTCGCTGATTTGATT 59.119 45.455 0.00 0.00 0.00 2.57
1392 1407 2.349249 GCCTCGCTGATTTGATTGATCG 60.349 50.000 0.00 0.00 0.00 3.69
1408 1423 2.743664 TGATCGCCATCTGTTGTTTCAG 59.256 45.455 0.00 0.00 36.85 3.02
1495 1511 5.123186 GCAAACACTGCCATACTAACATGTA 59.877 40.000 0.00 0.00 46.13 2.29
1504 1520 6.597672 TGCCATACTAACATGTACAAAGAAGG 59.402 38.462 0.00 0.00 0.00 3.46
1508 1524 1.890876 ACATGTACAAAGAAGGCGCA 58.109 45.000 10.83 0.00 0.00 6.09
1551 1567 7.230510 TGGTTATGCTGAGTTACTGAACAAAAT 59.769 33.333 0.00 0.00 38.10 1.82
1757 1773 1.811359 CAGAGAGCCAAAGCCAAGAAG 59.189 52.381 0.00 0.00 41.25 2.85
2000 2031 5.410355 TGATCATCATGATAAGCCGATGA 57.590 39.130 8.15 0.49 45.98 2.92
2022 2053 1.983224 CCAGGGTGACGATGGAGTT 59.017 57.895 0.00 0.00 39.56 3.01
2083 2114 1.750399 CCACCAGTACATGCCAGCC 60.750 63.158 0.00 0.00 0.00 4.85
2260 2297 1.895238 GAACTACTACAGCCGGCCA 59.105 57.895 26.15 7.96 0.00 5.36
2546 2594 5.009210 AGAGCCGAGATTTTAGTAGTAGCAG 59.991 44.000 0.00 0.00 0.00 4.24
2601 2652 7.115095 CCATGCTAGTACTAGAATAAAACGAGC 59.885 40.741 30.09 15.06 35.80 5.03
2644 2695 0.340208 AGAGGAAGAACGGGAGGGAT 59.660 55.000 0.00 0.00 0.00 3.85
2732 2785 7.968956 TGAACTGCAAAAACGTCTTACATTTAA 59.031 29.630 0.00 0.00 0.00 1.52
2735 2788 9.953697 ACTGCAAAAACGTCTTACATTTAAATA 57.046 25.926 0.00 0.00 0.00 1.40
2751 2804 5.786264 TTAAATAGGAGCCTCTTCTACGG 57.214 43.478 0.00 0.00 0.00 4.02
2856 2909 1.781786 TCCTCAGAGTATGGTGCTCC 58.218 55.000 0.00 0.00 33.69 4.70
2857 2910 0.387202 CCTCAGAGTATGGTGCTCCG 59.613 60.000 0.00 0.00 36.30 4.63
2869 2922 2.334946 TGCTCCGATGGCTGTTTGC 61.335 57.895 0.00 0.00 41.94 3.68
2886 2939 1.081242 GCCATGCGGTGTTCTTGTG 60.081 57.895 0.00 0.00 33.28 3.33
2893 2946 0.951040 CGGTGTTCTTGTGCTCCTCC 60.951 60.000 0.00 0.00 0.00 4.30
2931 2984 1.610522 GTAATGCTGATGGTGGATGGC 59.389 52.381 0.00 0.00 0.00 4.40
2935 2988 1.453235 CTGATGGTGGATGGCGGAT 59.547 57.895 0.00 0.00 0.00 4.18
2955 3008 3.829886 TGACGATTTGGTTCAGCAATC 57.170 42.857 0.00 0.00 0.00 2.67
2960 3013 1.243902 TTTGGTTCAGCAATCGACCC 58.756 50.000 0.00 0.00 0.00 4.46
2983 3036 6.938030 CCCCCTTAGCGACATGTTTATAATTA 59.062 38.462 0.00 0.00 0.00 1.40
3016 3071 2.160813 GGTGTGTTTTCTGTTGTGTCGT 59.839 45.455 0.00 0.00 0.00 4.34
3031 3086 2.616842 GTGTCGTGATGGTTGTCCTTTT 59.383 45.455 0.00 0.00 34.23 2.27
3053 3108 2.028839 TGGTGTTGTATAGTGTGGACCG 60.029 50.000 0.00 0.00 0.00 4.79
3064 3119 0.321741 TGTGGACCGTGTGTGTTGTT 60.322 50.000 0.00 0.00 0.00 2.83
3065 3120 0.806241 GTGGACCGTGTGTGTTGTTT 59.194 50.000 0.00 0.00 0.00 2.83
3066 3121 0.805614 TGGACCGTGTGTGTTGTTTG 59.194 50.000 0.00 0.00 0.00 2.93
3067 3122 0.806241 GGACCGTGTGTGTTGTTTGT 59.194 50.000 0.00 0.00 0.00 2.83
3110 3165 9.778741 TGATGAACACATAATAAATACTCCCTC 57.221 33.333 0.00 0.00 0.00 4.30
3111 3166 9.220767 GATGAACACATAATAAATACTCCCTCC 57.779 37.037 0.00 0.00 0.00 4.30
3112 3167 7.214381 TGAACACATAATAAATACTCCCTCCG 58.786 38.462 0.00 0.00 0.00 4.63
3113 3168 6.742559 ACACATAATAAATACTCCCTCCGT 57.257 37.500 0.00 0.00 0.00 4.69
3114 3169 7.133133 ACACATAATAAATACTCCCTCCGTT 57.867 36.000 0.00 0.00 0.00 4.44
3115 3170 7.215085 ACACATAATAAATACTCCCTCCGTTC 58.785 38.462 0.00 0.00 0.00 3.95
3116 3171 6.649557 CACATAATAAATACTCCCTCCGTTCC 59.350 42.308 0.00 0.00 0.00 3.62
3117 3172 6.557633 ACATAATAAATACTCCCTCCGTTCCT 59.442 38.462 0.00 0.00 0.00 3.36
3118 3173 7.731688 ACATAATAAATACTCCCTCCGTTCCTA 59.268 37.037 0.00 0.00 0.00 2.94
3119 3174 8.591072 CATAATAAATACTCCCTCCGTTCCTAA 58.409 37.037 0.00 0.00 0.00 2.69
3120 3175 7.441903 AATAAATACTCCCTCCGTTCCTAAA 57.558 36.000 0.00 0.00 0.00 1.85
3121 3176 5.970501 AAATACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
3122 3177 8.731591 ATAAATACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
3123 3178 7.628501 AAATACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
3124 3179 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
3125 3180 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3126 3181 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3127 3182 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3128 3183 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3129 3184 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3130 3185 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3131 3186 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3132 3187 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3133 3188 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3134 3189 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3135 3190 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3136 3191 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3149 3204 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3150 3205 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3151 3206 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3152 3207 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3153 3208 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3154 3209 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3155 3210 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3156 3211 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3157 3212 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
3159 3214 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3160 3215 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3161 3216 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
3162 3217 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3163 3218 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
3164 3219 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3165 3220 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3166 3221 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3167 3222 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3168 3223 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3169 3224 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3170 3225 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3171 3226 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3172 3227 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3173 3228 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3174 3229 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3175 3230 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3176 3231 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3177 3232 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3178 3233 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3179 3234 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3180 3235 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3181 3236 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3182 3237 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3183 3238 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3258 3313 9.947433 TTAGAAAGACAAATATTTAGGAACGGA 57.053 29.630 0.00 0.00 0.00 4.69
3259 3314 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3260 3315 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3261 3316 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3262 3317 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3263 3318 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3264 3319 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3265 3320 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3270 3325 1.569548 AGGAACGGAGGGAGTATGAGA 59.430 52.381 0.00 0.00 0.00 3.27
3271 3326 1.682323 GGAACGGAGGGAGTATGAGAC 59.318 57.143 0.00 0.00 0.00 3.36
3280 3335 1.877443 GGAGTATGAGACGAGCCTCTC 59.123 57.143 0.00 0.00 37.75 3.20
3297 3352 2.689658 TCTCTGTTGAGAACCTTGGGA 58.310 47.619 0.00 0.00 45.42 4.37
3313 3368 4.156008 CCTTGGGAGAAATCGTCGAAAAAT 59.844 41.667 0.00 0.00 0.00 1.82
3333 3388 1.003233 GGAGTGTCAGAAGGGTGCC 60.003 63.158 0.00 0.00 0.00 5.01
3343 3398 5.132648 TGTCAGAAGGGTGCCTGATTATTAT 59.867 40.000 0.00 0.00 40.95 1.28
3392 3447 9.715119 AATATATTATTTCCTCAATTAGGGGCC 57.285 33.333 0.00 0.00 46.55 5.80
3423 3478 4.724279 AAGGACCCAAATAGTTCACACT 57.276 40.909 0.00 0.00 36.99 3.55
3427 3482 2.108250 ACCCAAATAGTTCACACTGCCT 59.892 45.455 0.00 0.00 34.06 4.75
3432 3487 1.272807 TAGTTCACACTGCCTACCCC 58.727 55.000 0.00 0.00 34.06 4.95
3449 3504 1.064685 CCCCCAGGTGTCATTTACCTC 60.065 57.143 0.00 0.00 45.19 3.85
3451 3506 1.916181 CCCAGGTGTCATTTACCTCCT 59.084 52.381 0.00 0.00 45.19 3.69
3452 3507 3.112263 CCCAGGTGTCATTTACCTCCTA 58.888 50.000 0.00 0.00 45.19 2.94
3453 3508 3.134804 CCCAGGTGTCATTTACCTCCTAG 59.865 52.174 0.00 0.00 45.19 3.02
3488 3630 5.684704 TCCACAATCCACATCTTCTATTCC 58.315 41.667 0.00 0.00 0.00 3.01
3491 3633 6.604795 CCACAATCCACATCTTCTATTCCTTT 59.395 38.462 0.00 0.00 0.00 3.11
3511 3653 6.873076 TCCTTTGTAATTTGTTTGATGATGCC 59.127 34.615 0.00 0.00 0.00 4.40
3516 3658 8.674263 TGTAATTTGTTTGATGATGCCTTTTT 57.326 26.923 0.00 0.00 0.00 1.94
3553 3696 1.839994 GATGTCTCCCTCATGGTTCCA 59.160 52.381 0.00 0.00 34.77 3.53
3554 3697 0.984230 TGTCTCCCTCATGGTTCCAC 59.016 55.000 0.00 0.00 34.77 4.02
3556 3699 1.450312 CTCCCTCATGGTTCCACGC 60.450 63.158 0.00 0.00 34.77 5.34
3577 3720 1.898574 ACCAGCGTTTGCAGAAGGG 60.899 57.895 0.00 0.00 46.23 3.95
3578 3721 2.256461 CAGCGTTTGCAGAAGGGC 59.744 61.111 0.00 0.00 46.23 5.19
3579 3722 2.203337 AGCGTTTGCAGAAGGGCA 60.203 55.556 0.00 0.00 46.23 5.36
3582 3725 2.653115 GTTTGCAGAAGGGCAGGC 59.347 61.111 0.00 0.00 45.88 4.85
3602 3745 2.677524 GGGACAATGGCAGCAGCA 60.678 61.111 2.65 0.00 44.61 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.106908 TGCGAGAGAGAGATGTTATGATACG 60.107 44.000 0.00 0.00 0.00 3.06
1 2 6.083630 GTGCGAGAGAGAGATGTTATGATAC 58.916 44.000 0.00 0.00 0.00 2.24
41 44 6.156519 AGAGTTTTGTTTTGTCACAAAGTCC 58.843 36.000 2.58 0.00 45.21 3.85
197 200 3.004752 TGCTAAGATTCTTTGCCCCTC 57.995 47.619 23.75 3.77 0.00 4.30
360 367 3.426615 TCATTTTCATTTACAGGCGGGT 58.573 40.909 0.00 0.00 0.00 5.28
399 406 9.574516 AAGATTTATAACACCAATATGTCTCCC 57.425 33.333 0.00 0.00 30.55 4.30
466 473 4.094887 ACGGCATTCTGTTAGCTTAACATG 59.905 41.667 0.00 0.00 46.51 3.21
535 542 5.292345 TGAATTTCTCAAAGTGTCGAAACGA 59.708 36.000 0.00 0.00 0.00 3.85
542 549 7.595130 GGGTATTTGTGAATTTCTCAAAGTGTC 59.405 37.037 23.25 15.43 41.30 3.67
560 567 8.882415 ATCGTTGTGTAATACTAGGGTATTTG 57.118 34.615 6.70 0.00 43.65 2.32
571 579 5.445010 GGACGGTCAAATCGTTGTGTAATAC 60.445 44.000 10.76 0.00 41.22 1.89
575 583 2.406130 GGACGGTCAAATCGTTGTGTA 58.594 47.619 10.76 0.00 41.22 2.90
580 588 1.271163 ACATGGGACGGTCAAATCGTT 60.271 47.619 10.76 0.00 41.22 3.85
593 601 4.531854 TCTTTTTCAGTTCACACATGGGA 58.468 39.130 0.00 0.00 0.00 4.37
596 604 6.143438 GCTGAATCTTTTTCAGTTCACACATG 59.857 38.462 14.76 0.00 45.66 3.21
632 642 0.881118 ACGAATGGCGCTTGAATGTT 59.119 45.000 7.64 0.00 46.04 2.71
657 667 1.815840 GTAGGCCGGAGCTGCTTTC 60.816 63.158 5.05 0.00 39.73 2.62
725 735 0.107654 GTGGTACTGGTGATGGCTCC 60.108 60.000 0.00 0.00 0.00 4.70
755 767 8.700439 AAAGTTGCTTGGAACTAAACCTATTA 57.300 30.769 7.89 0.00 35.01 0.98
843 857 1.463674 GAGGTGGCTTTACATGTGGG 58.536 55.000 9.11 0.00 0.00 4.61
903 918 0.537188 ATGGAGAGTAGTGGGCGTTG 59.463 55.000 0.00 0.00 0.00 4.10
1015 1030 0.179084 GAATGATTCGCAGTCGGGGA 60.179 55.000 0.00 0.00 31.34 4.81
1080 1095 5.869344 TCACAGCTAGTATGTTGAATGTGAC 59.131 40.000 0.00 0.00 40.44 3.67
1082 1097 6.018425 GGATCACAGCTAGTATGTTGAATGTG 60.018 42.308 0.00 0.00 38.46 3.21
1137 1152 3.244665 TGAACATGCTCATGACCAGAAGT 60.245 43.478 15.96 0.00 41.20 3.01
1241 1256 4.096833 TCAGCACACTTCCATGCAAATATC 59.903 41.667 0.00 0.00 44.59 1.63
1265 1280 2.238521 TCAGAGCAAACCAAACCATCC 58.761 47.619 0.00 0.00 0.00 3.51
1387 1402 2.743664 CTGAAACAACAGATGGCGATCA 59.256 45.455 11.55 0.00 39.94 2.92
1408 1423 5.521372 GCATGGAAATTTCTACAAAGGCATC 59.479 40.000 17.42 0.00 0.00 3.91
1495 1511 0.668535 GGTTCTTGCGCCTTCTTTGT 59.331 50.000 4.18 0.00 0.00 2.83
1504 1520 4.268405 CCATGATTATTTTGGTTCTTGCGC 59.732 41.667 0.00 0.00 0.00 6.09
1551 1567 3.634448 TGCAAGATCAAAGGAAACGGAAA 59.366 39.130 0.00 0.00 0.00 3.13
1757 1773 1.538047 TCATCTGCTTGGTTCTTGGC 58.462 50.000 0.00 0.00 0.00 4.52
2000 2031 2.047274 CATCGTCACCCTGGCGTT 60.047 61.111 0.00 0.00 46.84 4.84
2404 2444 0.365523 CGTTGAACATGTCGCCGTAG 59.634 55.000 0.00 0.00 0.00 3.51
2546 2594 4.327854 GCAATACTGCTAATACATCGGC 57.672 45.455 0.00 0.00 45.74 5.54
2571 2619 9.043079 GTTTTATTCTAGTACTAGCATGGAACC 57.957 37.037 22.87 8.16 33.32 3.62
2601 2652 0.179137 CATGCATGCACCAAGCTCAG 60.179 55.000 25.37 0.69 45.94 3.35
2644 2695 2.497273 TCGATCAGAGCTGTTCCATGAA 59.503 45.455 0.00 0.00 0.00 2.57
2732 2785 3.596940 TCCGTAGAAGAGGCTCCTATT 57.403 47.619 11.71 0.00 0.00 1.73
2869 2922 1.081242 GCACAAGAACACCGCATGG 60.081 57.895 0.00 0.00 42.84 3.66
2931 2984 1.062587 GCTGAACCAAATCGTCATCCG 59.937 52.381 0.00 0.00 38.13 4.18
2935 2988 2.159430 CGATTGCTGAACCAAATCGTCA 59.841 45.455 8.45 0.00 0.00 4.35
2955 3008 1.227263 CATGTCGCTAAGGGGGTCG 60.227 63.158 0.00 0.00 0.00 4.79
3016 3071 3.370104 ACACCAAAAAGGACAACCATCA 58.630 40.909 0.00 0.00 41.22 3.07
3031 3086 3.555377 CGGTCCACACTATACAACACCAA 60.555 47.826 0.00 0.00 0.00 3.67
3091 3146 6.649557 GGAACGGAGGGAGTATTTATTATGTG 59.350 42.308 0.00 0.00 0.00 3.21
3104 3159 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3105 3160 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3106 3161 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3107 3162 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3108 3163 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3109 3164 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3110 3165 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3123 3178 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3124 3179 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3125 3180 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3126 3181 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3127 3182 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3128 3183 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3129 3184 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3130 3185 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3131 3186 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3132 3187 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3133 3188 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3134 3189 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3135 3190 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
3136 3191 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
3137 3192 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
3138 3193 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3139 3194 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3140 3195 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
3141 3196 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
3142 3197 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3143 3198 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3144 3199 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3145 3200 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3146 3201 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3147 3202 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3148 3203 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3149 3204 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3150 3205 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3151 3206 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3152 3207 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3153 3208 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3154 3209 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3155 3210 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3156 3211 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3157 3212 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3158 3213 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3159 3214 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3160 3215 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3161 3216 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3232 3287 9.947433 TCCGTTCCTAAATATTTGTCTTTCTAA 57.053 29.630 11.05 0.00 0.00 2.10
3233 3288 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3234 3289 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3235 3290 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3236 3291 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3237 3292 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3238 3293 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3239 3294 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3240 3295 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3241 3296 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3242 3297 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3243 3298 6.785963 TCATACTCCCTCCGTTCCTAAATATT 59.214 38.462 0.00 0.00 0.00 1.28
3244 3299 6.320518 TCATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
3245 3300 5.708544 TCATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
3246 3301 4.553678 TCATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
3247 3302 3.958798 CTCATACTCCCTCCGTTCCTAAA 59.041 47.826 0.00 0.00 0.00 1.85
3248 3303 3.203710 TCTCATACTCCCTCCGTTCCTAA 59.796 47.826 0.00 0.00 0.00 2.69
3249 3304 2.781757 TCTCATACTCCCTCCGTTCCTA 59.218 50.000 0.00 0.00 0.00 2.94
3250 3305 1.569548 TCTCATACTCCCTCCGTTCCT 59.430 52.381 0.00 0.00 0.00 3.36
3251 3306 1.682323 GTCTCATACTCCCTCCGTTCC 59.318 57.143 0.00 0.00 0.00 3.62
3252 3307 1.334243 CGTCTCATACTCCCTCCGTTC 59.666 57.143 0.00 0.00 0.00 3.95
3253 3308 1.064906 TCGTCTCATACTCCCTCCGTT 60.065 52.381 0.00 0.00 0.00 4.44
3254 3309 0.545171 TCGTCTCATACTCCCTCCGT 59.455 55.000 0.00 0.00 0.00 4.69
3255 3310 1.231221 CTCGTCTCATACTCCCTCCG 58.769 60.000 0.00 0.00 0.00 4.63
3256 3311 0.955905 GCTCGTCTCATACTCCCTCC 59.044 60.000 0.00 0.00 0.00 4.30
3257 3312 0.955905 GGCTCGTCTCATACTCCCTC 59.044 60.000 0.00 0.00 0.00 4.30
3258 3313 0.553819 AGGCTCGTCTCATACTCCCT 59.446 55.000 0.00 0.00 0.00 4.20
3259 3314 0.955905 GAGGCTCGTCTCATACTCCC 59.044 60.000 0.00 0.00 34.13 4.30
3260 3315 1.877443 GAGAGGCTCGTCTCATACTCC 59.123 57.143 9.22 0.00 42.36 3.85
3261 3316 2.548057 CAGAGAGGCTCGTCTCATACTC 59.452 54.545 18.23 0.00 44.83 2.59
3262 3317 2.092646 ACAGAGAGGCTCGTCTCATACT 60.093 50.000 18.23 3.42 44.83 2.12
3263 3318 2.294074 ACAGAGAGGCTCGTCTCATAC 58.706 52.381 18.23 1.50 44.83 2.39
3264 3319 2.685388 CAACAGAGAGGCTCGTCTCATA 59.315 50.000 18.23 0.00 44.83 2.15
3265 3320 1.476085 CAACAGAGAGGCTCGTCTCAT 59.524 52.381 18.23 6.50 44.83 2.90
3270 3325 1.271102 GTTCTCAACAGAGAGGCTCGT 59.729 52.381 9.22 0.00 39.43 4.18
3271 3326 1.403514 GGTTCTCAACAGAGAGGCTCG 60.404 57.143 9.22 0.00 39.43 5.03
3280 3335 3.492102 TTCTCCCAAGGTTCTCAACAG 57.508 47.619 0.00 0.00 0.00 3.16
3297 3352 5.238650 ACACTCCAATTTTTCGACGATTTCT 59.761 36.000 0.00 0.00 0.00 2.52
3313 3368 0.108585 GCACCCTTCTGACACTCCAA 59.891 55.000 0.00 0.00 0.00 3.53
3392 3447 1.501582 TTGGGTCCTTTTTGGGTTGG 58.498 50.000 0.00 0.00 36.20 3.77
3403 3458 3.810743 GCAGTGTGAACTATTTGGGTCCT 60.811 47.826 0.00 0.00 0.00 3.85
3423 3478 2.609610 GACACCTGGGGGTAGGCA 60.610 66.667 0.00 0.00 45.41 4.75
3427 3482 1.917568 GGTAAATGACACCTGGGGGTA 59.082 52.381 0.00 0.00 45.41 3.69
3432 3487 3.432326 GCTAGGAGGTAAATGACACCTGG 60.432 52.174 0.00 0.00 46.60 4.45
3445 3500 0.850784 GAGAGAGGGAGCTAGGAGGT 59.149 60.000 0.00 0.00 0.00 3.85
3446 3501 1.073923 GAGAGAGAGGGAGCTAGGAGG 59.926 61.905 0.00 0.00 0.00 4.30
3448 3503 1.145571 GGAGAGAGAGGGAGCTAGGA 58.854 60.000 0.00 0.00 0.00 2.94
3449 3504 0.850100 TGGAGAGAGAGGGAGCTAGG 59.150 60.000 0.00 0.00 0.00 3.02
3451 3506 1.299939 TGTGGAGAGAGAGGGAGCTA 58.700 55.000 0.00 0.00 0.00 3.32
3452 3507 0.411452 TTGTGGAGAGAGAGGGAGCT 59.589 55.000 0.00 0.00 0.00 4.09
3453 3508 1.412343 GATTGTGGAGAGAGAGGGAGC 59.588 57.143 0.00 0.00 0.00 4.70
3488 3630 7.894376 AGGCATCATCAAACAAATTACAAAG 57.106 32.000 0.00 0.00 0.00 2.77
3491 3633 8.674263 AAAAAGGCATCATCAAACAAATTACA 57.326 26.923 0.00 0.00 0.00 2.41
3516 3658 4.837860 AGACATCTTGGTGCCCAAATAAAA 59.162 37.500 7.87 0.00 43.44 1.52
3556 3699 2.133742 CTTCTGCAAACGCTGGTGGG 62.134 60.000 0.00 0.00 0.00 4.61
3565 3708 2.653115 GCCTGCCCTTCTGCAAAC 59.347 61.111 0.00 0.00 41.51 2.93
3582 3725 4.738998 TGCTGCCATTGTCCCCGG 62.739 66.667 0.00 0.00 0.00 5.73
3585 3728 2.677524 TGCTGCTGCCATTGTCCC 60.678 61.111 13.47 0.00 38.71 4.46


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

AutoCloner maintained by Alex Coulton.