Multiple sequence alignment - TraesCS7A01G428300

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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 TraesCS7A01G428300 chr7A 100.000 4309 0 0 1 4309 621586435 621582127 0.000000e+00 7958
1 TraesCS7A01G428300 chr7A 87.255 102 13 0 3321 3422 112786251 112786352 2.720000e-22 117
2 TraesCS7A01G428300 chr7A 86.275 102 14 0 3321 3422 112799856 112799755 1.270000e-20 111
3 TraesCS7A01G428300 chr7B 95.289 4182 150 18 1 4169 583478895 583474748 0.000000e+00 6588
4 TraesCS7A01G428300 chr7D 90.196 3774 241 63 1 3738 540234396 540238076 0.000000e+00 4800
5 TraesCS7A01G428300 chr6D 86.897 145 16 3 4164 4308 473291568 473291427 4.460000e-35 159
6 TraesCS7A01G428300 chr6D 84.071 113 17 1 3310 3422 155253497 155253608 1.640000e-19 108
7 TraesCS7A01G428300 chr3D 86.806 144 16 1 4169 4309 419996029 419996172 1.600000e-34 158
8 TraesCS7A01G428300 chr2A 87.143 140 17 1 4171 4309 398502873 398502734 1.600000e-34 158
9 TraesCS7A01G428300 chr2A 84.173 139 19 2 4172 4307 14569429 14569567 9.720000e-27 132
10 TraesCS7A01G428300 chr3A 87.681 138 12 4 4173 4308 705591734 705591600 5.770000e-34 156
11 TraesCS7A01G428300 chr2B 86.713 143 16 1 4170 4309 168522861 168523003 5.770000e-34 156
12 TraesCS7A01G428300 chr2D 85.612 139 18 1 4173 4309 565159406 565159268 1.250000e-30 145
13 TraesCS7A01G428300 chr2D 84.507 142 14 2 4171 4309 606195583 606195447 2.700000e-27 134
14 TraesCS7A01G428300 chr2D 87.255 102 12 1 3318 3419 636776251 636776351 9.790000e-22 115
15 TraesCS7A01G428300 chr6B 84.173 139 18 3 4175 4309 72434455 72434593 9.720000e-27 132
16 TraesCS7A01G428300 chr4D 87.129 101 13 0 3321 3421 375135019 375134919 9.790000e-22 115
17 TraesCS7A01G428300 chr1B 87.755 98 12 0 3321 3418 572529358 572529455 9.790000e-22 115
18 TraesCS7A01G428300 chr1B 87.500 104 7 6 3318 3418 572529459 572529359 9.790000e-22 115
19 TraesCS7A01G428300 chr5D 84.483 116 10 8 3307 3418 34876217 34876328 1.640000e-19 108


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 TraesCS7A01G428300 chr7A 621582127 621586435 4308 True 7958 7958 100.000 1 4309 1 chr7A.!!$R2 4308
1 TraesCS7A01G428300 chr7B 583474748 583478895 4147 True 6588 6588 95.289 1 4169 1 chr7B.!!$R1 4168
2 TraesCS7A01G428300 chr7D 540234396 540238076 3680 False 4800 4800 90.196 1 3738 1 chr7D.!!$F1 3737

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
218 227 0.109319 ATTTTGTGGGCGCACGATTC 60.109 50.0 26.42 5.43 0.00 2.52 F
471 487 0.521291 TTGAAGCAGGAAATTCGCCG 59.479 50.0 0.00 0.00 0.00 6.46 F
2043 2073 0.958822 TTGCTCTGCGTGAGACTGTA 59.041 50.0 10.24 0.00 45.39 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1356 0.874175 TCTGCAGACGGTTGACAACG 60.874 55.000 13.74 9.83 0.00 4.10 R
2239 2269 1.138036 CCATGTTCATGCGCCTGTG 59.862 57.895 12.54 5.43 0.00 3.66 R
3760 3811 0.324285 AGAGCAGAGACAAAGCTGGG 59.676 55.000 0.00 0.00 39.02 4.45 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
65 66 2.981400 TCCTGCGGATTTCGTTTTTC 57.019 45.000 0.00 0.00 41.72 2.29
66 67 2.500229 TCCTGCGGATTTCGTTTTTCT 58.500 42.857 0.00 0.00 41.72 2.52
70 71 3.135225 TGCGGATTTCGTTTTTCTCTCA 58.865 40.909 0.00 0.00 41.72 3.27
83 84 0.832135 TCTCTCACTCGGTTTGGGCT 60.832 55.000 0.00 0.00 0.00 5.19
133 142 7.761038 TCGATTCCAGATACATACATACACT 57.239 36.000 0.00 0.00 0.00 3.55
178 187 2.160417 GTGTGTGTTTATGAGCTGAGGC 59.840 50.000 0.00 0.00 39.06 4.70
218 227 0.109319 ATTTTGTGGGCGCACGATTC 60.109 50.000 26.42 5.43 0.00 2.52
219 228 1.169661 TTTTGTGGGCGCACGATTCT 61.170 50.000 26.42 0.00 0.00 2.40
299 308 8.875803 TGTTATTCTTTACGCGATTGAGTATTT 58.124 29.630 15.93 0.00 30.20 1.40
314 323 9.638239 GATTGAGTATTTTGCCAACATTTCTTA 57.362 29.630 0.00 0.00 0.00 2.10
425 441 6.534793 CCATGACCCAAGTGTTTTTATATTGC 59.465 38.462 0.00 0.00 0.00 3.56
432 448 5.305139 AGTGTTTTTATATTGCGTGGGTC 57.695 39.130 0.00 0.00 0.00 4.46
469 485 3.011949 TGTTTGAAGCAGGAAATTCGC 57.988 42.857 0.00 0.00 0.00 4.70
471 487 0.521291 TTGAAGCAGGAAATTCGCCG 59.479 50.000 0.00 0.00 0.00 6.46
572 599 6.395426 TTTGGGATAATGAACAGATGATGC 57.605 37.500 0.00 0.00 0.00 3.91
574 601 3.438087 GGGATAATGAACAGATGATGCCG 59.562 47.826 0.00 0.00 0.00 5.69
740 770 1.787155 CGCCGCTACAACATAGTGATC 59.213 52.381 0.00 0.00 0.00 2.92
823 853 7.440255 TCTTAACTAACAGTAGGTGCAAAGTTC 59.560 37.037 0.00 0.00 31.56 3.01
849 879 3.193267 TGTTTGGTGCTATTGGAGATTGC 59.807 43.478 0.00 0.00 0.00 3.56
1024 1054 1.108132 GGAGAACGCCGGTAGATCCT 61.108 60.000 1.90 0.00 0.00 3.24
1049 1079 6.041409 TCCACAACAATTGGCATTCTAAGAAA 59.959 34.615 10.83 0.00 33.71 2.52
1212 1242 7.493971 CGTGACTCTTTTAATTCATCAGGATCT 59.506 37.037 0.00 0.00 0.00 2.75
1326 1356 5.989777 TGCTGAAAGTAGTAACAGAAGAACC 59.010 40.000 0.00 0.00 35.30 3.62
2043 2073 0.958822 TTGCTCTGCGTGAGACTGTA 59.041 50.000 10.24 0.00 45.39 2.74
2239 2269 4.399303 CCCCACAAATGTTTAGAGATGTCC 59.601 45.833 0.00 0.00 0.00 4.02
2473 2503 4.082026 GTGTTGCTAGCATTGGAAAGGATT 60.082 41.667 20.13 0.00 0.00 3.01
2532 2562 6.035975 CCTTTTGTCCTTGTTTGCAACTTTAG 59.964 38.462 0.00 0.00 0.00 1.85
2578 2608 3.579709 CTCTGAAGCGTGTTCTGTACAT 58.420 45.455 0.00 0.00 39.39 2.29
2721 2751 7.288810 ACCATGATATTGATTTTGCCGTAAT 57.711 32.000 0.00 0.00 0.00 1.89
2784 2814 4.460263 ACTCTGTAACCATTCAGTTTGCA 58.540 39.130 0.00 0.00 33.89 4.08
2795 2826 6.488006 ACCATTCAGTTTGCATGTATAGATCC 59.512 38.462 0.00 0.00 0.00 3.36
2910 2941 2.328099 CGTGAGCACTGCCCTTTCC 61.328 63.158 0.00 0.00 0.00 3.13
3057 3088 5.022787 TGGGCCATTATTACTGCTTCTTTT 58.977 37.500 0.00 0.00 0.00 2.27
3067 3098 4.725790 ACTGCTTCTTTTGCAAGAAACT 57.274 36.364 0.00 0.00 46.35 2.66
3138 3174 6.690530 ACATATGTTTTTGACATTGACTGGG 58.309 36.000 1.41 0.00 46.80 4.45
3276 3312 0.390472 AGCTTCAGCAGTACCTTCGC 60.390 55.000 0.75 0.00 45.16 4.70
3279 3315 1.812686 TTCAGCAGTACCTTCGCCGT 61.813 55.000 0.00 0.00 0.00 5.68
3280 3316 1.805945 CAGCAGTACCTTCGCCGTC 60.806 63.158 0.00 0.00 0.00 4.79
3281 3317 2.879462 GCAGTACCTTCGCCGTCG 60.879 66.667 0.00 0.00 0.00 5.12
3282 3318 2.202570 CAGTACCTTCGCCGTCGG 60.203 66.667 6.99 6.99 36.13 4.79
3283 3319 2.360350 AGTACCTTCGCCGTCGGA 60.360 61.111 17.49 0.00 36.13 4.55
3284 3320 2.202531 GTACCTTCGCCGTCGGAC 60.203 66.667 17.49 5.49 36.13 4.79
3285 3321 3.803082 TACCTTCGCCGTCGGACG 61.803 66.667 22.88 22.88 42.11 4.79
3358 3394 8.626526 TCCCAAAATAAGTGTCTCAACTTTAAC 58.373 33.333 0.00 0.00 40.77 2.01
3425 3461 3.288964 AGACGGTGGGAGTAGTATGAAG 58.711 50.000 0.00 0.00 0.00 3.02
3496 3532 5.705905 GGCCCTCCAACTTGTGAATATATAC 59.294 44.000 0.00 0.00 0.00 1.47
3497 3533 6.296026 GCCCTCCAACTTGTGAATATATACA 58.704 40.000 0.00 0.00 0.00 2.29
3525 3561 2.289002 ACTGTTTCTCTCTTGCAAAGCG 59.711 45.455 0.00 0.00 45.70 4.68
3589 3637 1.602165 CCACTCACAGTACACGTCACC 60.602 57.143 0.00 0.00 0.00 4.02
3627 3675 2.024414 GGAAAACGATCATCCTTGGGG 58.976 52.381 0.00 0.00 0.00 4.96
3632 3680 1.152368 GATCATCCTTGGGGCTGGG 59.848 63.158 0.00 0.00 30.32 4.45
3641 3689 2.029892 TTGGGGCTGGGAAATGGTGT 62.030 55.000 0.00 0.00 0.00 4.16
3642 3690 1.143329 TGGGGCTGGGAAATGGTGTA 61.143 55.000 0.00 0.00 0.00 2.90
3643 3691 0.683179 GGGGCTGGGAAATGGTGTAC 60.683 60.000 0.00 0.00 0.00 2.90
3740 3791 8.800370 AGAAGCTCCTAGGAAAAGAATAAAAG 57.200 34.615 13.77 0.00 0.00 2.27
3746 3797 5.594725 CCTAGGAAAAGAATAAAAGGAGGGC 59.405 44.000 1.05 0.00 0.00 5.19
3750 3801 2.044123 AGAATAAAAGGAGGGCGCAG 57.956 50.000 10.83 0.00 0.00 5.18
3756 3807 0.179034 AAAGGAGGGCGCAGATGATC 60.179 55.000 10.83 0.00 0.00 2.92
3769 3820 1.450531 GATGATCGGCCCCAGCTTTG 61.451 60.000 0.00 0.00 39.73 2.77
3770 3821 2.044946 GATCGGCCCCAGCTTTGT 60.045 61.111 0.00 0.00 39.73 2.83
3771 3822 2.044946 ATCGGCCCCAGCTTTGTC 60.045 61.111 0.00 0.00 39.73 3.18
3803 3855 3.028130 TCCCATCATTACTCGTGCTGTA 58.972 45.455 0.00 0.00 0.00 2.74
3812 3864 1.613925 ACTCGTGCTGTACTGTGTCAT 59.386 47.619 1.46 0.00 0.00 3.06
3813 3865 2.817844 ACTCGTGCTGTACTGTGTCATA 59.182 45.455 1.46 0.00 0.00 2.15
3814 3866 3.172050 CTCGTGCTGTACTGTGTCATAC 58.828 50.000 1.46 0.00 0.00 2.39
3815 3867 2.817844 TCGTGCTGTACTGTGTCATACT 59.182 45.455 1.46 0.00 0.00 2.12
3816 3868 2.917343 CGTGCTGTACTGTGTCATACTG 59.083 50.000 1.46 0.00 0.00 2.74
3823 3875 6.569801 GCTGTACTGTGTCATACTGTAACTCA 60.570 42.308 1.46 0.00 42.81 3.41
3875 3927 1.098050 GTGATCATGGTGGCCAACTC 58.902 55.000 24.13 11.85 36.95 3.01
3887 3939 6.486056 TGGTGGCCAACTCTTTTATTATACA 58.514 36.000 24.13 0.00 0.00 2.29
3918 3970 2.905075 CATAGTTGGTCAAGATCCGCA 58.095 47.619 0.00 0.00 0.00 5.69
3924 3976 0.169009 GGTCAAGATCCGCACTTTGC 59.831 55.000 0.00 0.00 40.69 3.68
3933 3985 4.987419 GCACTTTGCGTTCAACGA 57.013 50.000 15.79 0.00 46.05 3.85
3939 3991 2.285756 ACTTTGCGTTCAACGATCGAAA 59.714 40.909 24.34 10.05 46.05 3.46
3948 4000 3.499048 TCAACGATCGAAACAGCTACTC 58.501 45.455 24.34 0.00 0.00 2.59
3985 4037 7.279090 GCTTGTTCTTCTCCTAATTAACCTCTC 59.721 40.741 0.00 0.00 0.00 3.20
4004 4056 0.376152 CAAAGTCATGGCAGCGCTAG 59.624 55.000 10.99 5.98 0.00 3.42
4006 4058 0.742281 AAGTCATGGCAGCGCTAGTG 60.742 55.000 10.99 6.89 0.00 2.74
4042 4094 5.237048 TGTTTGCCAAAAATATTCTGAGGC 58.763 37.500 11.91 11.91 40.93 4.70
4089 4141 0.608035 TGATTCGTTGTTGGGCCTCC 60.608 55.000 4.53 0.00 0.00 4.30
4120 4172 3.115390 TGGGCTTCCTACTTCTAATGCT 58.885 45.455 0.00 0.00 0.00 3.79
4169 4221 1.146930 GGAATGATGAGGGAGCGCA 59.853 57.895 11.47 0.00 0.00 6.09
4170 4222 0.883814 GGAATGATGAGGGAGCGCAG 60.884 60.000 11.47 0.00 0.00 5.18
4171 4223 0.883814 GAATGATGAGGGAGCGCAGG 60.884 60.000 11.47 0.00 0.00 4.85
4172 4224 2.335092 AATGATGAGGGAGCGCAGGG 62.335 60.000 11.47 0.00 0.00 4.45
4173 4225 3.157252 GATGAGGGAGCGCAGGGA 61.157 66.667 11.47 0.00 0.00 4.20
4174 4226 3.160047 ATGAGGGAGCGCAGGGAG 61.160 66.667 11.47 0.00 0.00 4.30
4179 4231 4.400961 GGAGCGCAGGGAGCAACT 62.401 66.667 11.47 0.00 46.13 3.16
4180 4232 2.579201 GAGCGCAGGGAGCAACTA 59.421 61.111 11.47 0.00 46.13 2.24
4181 4233 1.520342 GAGCGCAGGGAGCAACTAG 60.520 63.158 11.47 0.00 46.13 2.57
4182 4234 2.232298 GAGCGCAGGGAGCAACTAGT 62.232 60.000 11.47 0.00 46.13 2.57
4183 4235 1.376037 GCGCAGGGAGCAACTAGTT 60.376 57.895 0.30 1.12 46.13 2.24
4184 4236 1.362406 GCGCAGGGAGCAACTAGTTC 61.362 60.000 4.77 1.12 46.13 3.01
4185 4237 0.037326 CGCAGGGAGCAACTAGTTCA 60.037 55.000 4.77 0.00 46.13 3.18
4186 4238 1.443802 GCAGGGAGCAACTAGTTCAC 58.556 55.000 4.77 0.80 44.79 3.18
4187 4239 1.714794 CAGGGAGCAACTAGTTCACG 58.285 55.000 4.77 0.00 35.78 4.35
4188 4240 1.272490 CAGGGAGCAACTAGTTCACGA 59.728 52.381 4.77 0.00 35.78 4.35
4189 4241 1.546476 AGGGAGCAACTAGTTCACGAG 59.454 52.381 4.77 0.00 35.78 4.18
4190 4242 1.351153 GGAGCAACTAGTTCACGAGC 58.649 55.000 4.77 5.95 0.00 5.03
4191 4243 0.985549 GAGCAACTAGTTCACGAGCG 59.014 55.000 4.77 0.00 0.00 5.03
4192 4244 1.009389 AGCAACTAGTTCACGAGCGC 61.009 55.000 4.77 0.00 0.00 5.92
4193 4245 1.009389 GCAACTAGTTCACGAGCGCT 61.009 55.000 11.27 11.27 0.00 5.92
4194 4246 0.985549 CAACTAGTTCACGAGCGCTC 59.014 55.000 27.64 27.64 0.00 5.03
4195 4247 0.109226 AACTAGTTCACGAGCGCTCC 60.109 55.000 30.66 16.60 0.00 4.70
4196 4248 0.961358 ACTAGTTCACGAGCGCTCCT 60.961 55.000 30.66 22.52 0.00 3.69
4197 4249 0.171455 CTAGTTCACGAGCGCTCCTT 59.829 55.000 30.66 15.94 0.00 3.36
4198 4250 0.170561 TAGTTCACGAGCGCTCCTTC 59.829 55.000 30.66 16.31 0.00 3.46
4199 4251 2.126463 TTCACGAGCGCTCCTTCG 60.126 61.111 30.66 22.24 0.00 3.79
4200 4252 3.626680 TTCACGAGCGCTCCTTCGG 62.627 63.158 30.66 18.71 0.00 4.30
4211 4263 3.450282 TCCTTCGGGAGTCTCACAA 57.550 52.632 2.35 0.00 39.58 3.33
4212 4264 0.966920 TCCTTCGGGAGTCTCACAAC 59.033 55.000 2.35 0.00 39.58 3.32
4213 4265 0.388649 CCTTCGGGAGTCTCACAACG 60.389 60.000 2.35 1.40 37.25 4.10
4214 4266 0.596577 CTTCGGGAGTCTCACAACGA 59.403 55.000 2.35 3.76 0.00 3.85
4215 4267 1.202582 CTTCGGGAGTCTCACAACGAT 59.797 52.381 2.35 0.00 0.00 3.73
4216 4268 0.809385 TCGGGAGTCTCACAACGATC 59.191 55.000 2.35 0.00 0.00 3.69
4217 4269 0.526211 CGGGAGTCTCACAACGATCA 59.474 55.000 2.35 0.00 0.00 2.92
4218 4270 1.468224 CGGGAGTCTCACAACGATCAG 60.468 57.143 2.35 0.00 0.00 2.90
4219 4271 1.634702 GGAGTCTCACAACGATCAGC 58.365 55.000 1.47 0.00 0.00 4.26
4230 4282 3.329114 CGATCAGCGTCACTTAGCA 57.671 52.632 0.00 0.00 35.48 3.49
4231 4283 0.917259 CGATCAGCGTCACTTAGCAC 59.083 55.000 0.00 0.00 35.48 4.40
4232 4284 0.917259 GATCAGCGTCACTTAGCACG 59.083 55.000 0.55 0.55 39.09 5.34
4236 4288 4.870305 CGTCACTTAGCACGCTCT 57.130 55.556 0.00 0.00 0.00 4.09
4237 4289 2.643044 CGTCACTTAGCACGCTCTC 58.357 57.895 0.00 0.00 0.00 3.20
4238 4290 0.109735 CGTCACTTAGCACGCTCTCA 60.110 55.000 0.00 0.00 0.00 3.27
4239 4291 1.623359 GTCACTTAGCACGCTCTCAG 58.377 55.000 0.00 0.00 0.00 3.35
4240 4292 0.109086 TCACTTAGCACGCTCTCAGC 60.109 55.000 0.00 0.00 38.02 4.26
4241 4293 1.080995 CACTTAGCACGCTCTCAGCC 61.081 60.000 0.00 0.00 38.18 4.85
4242 4294 1.875813 CTTAGCACGCTCTCAGCCG 60.876 63.158 0.00 0.00 38.18 5.52
4243 4295 3.989698 TTAGCACGCTCTCAGCCGC 62.990 63.158 0.00 0.00 38.18 6.53
4262 4314 4.813526 CGCTACGTGTCGCGCTCT 62.814 66.667 5.56 0.00 46.11 4.09
4263 4315 3.241059 GCTACGTGTCGCGCTCTG 61.241 66.667 5.56 0.00 46.11 3.35
4264 4316 2.577112 CTACGTGTCGCGCTCTGG 60.577 66.667 5.56 0.00 46.11 3.86
4265 4317 4.111016 TACGTGTCGCGCTCTGGG 62.111 66.667 5.56 0.00 46.11 4.45
4285 4337 4.917906 GGTGCTCCCTCCAGATTATATT 57.082 45.455 0.00 0.00 0.00 1.28
4286 4338 5.248380 GGTGCTCCCTCCAGATTATATTT 57.752 43.478 0.00 0.00 0.00 1.40
4287 4339 5.635120 GGTGCTCCCTCCAGATTATATTTT 58.365 41.667 0.00 0.00 0.00 1.82
4288 4340 6.779860 GGTGCTCCCTCCAGATTATATTTTA 58.220 40.000 0.00 0.00 0.00 1.52
4289 4341 7.406104 GGTGCTCCCTCCAGATTATATTTTAT 58.594 38.462 0.00 0.00 0.00 1.40
4290 4342 7.890655 GGTGCTCCCTCCAGATTATATTTTATT 59.109 37.037 0.00 0.00 0.00 1.40
4291 4343 9.301897 GTGCTCCCTCCAGATTATATTTTATTT 57.698 33.333 0.00 0.00 0.00 1.40
4292 4344 9.881773 TGCTCCCTCCAGATTATATTTTATTTT 57.118 29.630 0.00 0.00 0.00 1.82
4297 4349 9.626045 CCTCCAGATTATATTTTATTTTTCCGC 57.374 33.333 0.00 0.00 0.00 5.54
4302 4354 9.128107 AGATTATATTTTATTTTTCCGCATGCG 57.872 29.630 32.60 32.60 39.44 4.73
4303 4355 8.810652 ATTATATTTTATTTTTCCGCATGCGT 57.189 26.923 35.55 20.26 37.81 5.24
4304 4356 8.635877 TTATATTTTATTTTTCCGCATGCGTT 57.364 26.923 35.55 16.52 37.81 4.84
4305 4357 5.854431 ATTTTATTTTTCCGCATGCGTTT 57.146 30.435 35.55 16.84 37.81 3.60
4306 4358 5.659048 TTTTATTTTTCCGCATGCGTTTT 57.341 30.435 35.55 17.50 37.81 2.43
4307 4359 4.894798 TTATTTTTCCGCATGCGTTTTC 57.105 36.364 35.55 0.00 37.81 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 0.671781 CAGCCCAAACCGAGTGAGAG 60.672 60.000 0.00 0.00 0.00 3.20
66 67 1.371183 CAGCCCAAACCGAGTGAGA 59.629 57.895 0.00 0.00 0.00 3.27
70 71 1.003718 GTAGCAGCCCAAACCGAGT 60.004 57.895 0.00 0.00 0.00 4.18
83 84 2.039974 CAGGCGCAACCATGTAGCA 61.040 57.895 10.83 0.00 43.14 3.49
133 142 9.203421 CACGGATTACAGATTACTGCATAATAA 57.797 33.333 0.00 0.00 46.95 1.40
156 165 2.413112 CCTCAGCTCATAAACACACACG 59.587 50.000 0.00 0.00 0.00 4.49
178 187 2.496679 TAAGAATCCCTCCCCTCAGG 57.503 55.000 0.00 0.00 0.00 3.86
218 227 4.981674 GCCTTCTGAATCATTACGAGAGAG 59.018 45.833 0.00 0.00 0.00 3.20
219 228 4.402474 TGCCTTCTGAATCATTACGAGAGA 59.598 41.667 0.00 0.00 0.00 3.10
299 308 9.255304 GATTTACAAACTAAGAAATGTTGGCAA 57.745 29.630 0.00 0.00 0.00 4.52
373 389 6.127810 ACTATGTCATGTGCAAACATCATC 57.872 37.500 8.13 0.00 35.38 2.92
432 448 0.535102 ACAAAAGACTGTCTGGGGCG 60.535 55.000 11.71 1.65 0.00 6.13
434 450 3.287222 TCAAACAAAAGACTGTCTGGGG 58.713 45.455 11.71 6.23 0.00 4.96
469 485 6.035005 CAGTTTAGATTGTGATACAGTGACGG 59.965 42.308 0.00 0.00 0.00 4.79
471 487 7.891183 ACAGTTTAGATTGTGATACAGTGAC 57.109 36.000 0.00 0.00 0.00 3.67
519 538 7.945033 TTGGAATTAGCAGTTGAATGAAAAC 57.055 32.000 0.00 0.00 0.00 2.43
572 599 5.970592 TCATTATCATATCTGCCTCTTCGG 58.029 41.667 0.00 0.00 0.00 4.30
574 601 8.093307 TCTGTTCATTATCATATCTGCCTCTTC 58.907 37.037 0.00 0.00 0.00 2.87
587 614 9.177608 CAAAATAAGACCCTCTGTTCATTATCA 57.822 33.333 0.00 0.00 0.00 2.15
705 735 1.010419 CGGCGCTACAAGTTAACCGT 61.010 55.000 7.64 2.70 34.61 4.83
823 853 3.689161 TCTCCAATAGCACCAAACAATCG 59.311 43.478 0.00 0.00 0.00 3.34
849 879 8.986929 AGAAAATGGGAAGAAGGTAATGATAG 57.013 34.615 0.00 0.00 0.00 2.08
1024 1054 5.076182 TCTTAGAATGCCAATTGTTGTGGA 58.924 37.500 4.43 0.00 38.54 4.02
1049 1079 1.059913 CAAGGAGACACCAGAACCCT 58.940 55.000 0.00 0.00 42.04 4.34
1212 1242 5.185828 TGAAGAGCTTGCAGATACAGACTTA 59.814 40.000 0.00 0.00 0.00 2.24
1326 1356 0.874175 TCTGCAGACGGTTGACAACG 60.874 55.000 13.74 9.83 0.00 4.10
1973 2003 2.961741 CTCATCCTAGCCTGCTGAGTAA 59.038 50.000 0.97 0.00 30.98 2.24
2043 2073 3.782443 GGTTGACGAGCCCCCGAT 61.782 66.667 0.00 0.00 0.00 4.18
2109 2139 3.282885 CAACTCCATAGGAAAAGGCCTC 58.717 50.000 5.23 0.00 39.50 4.70
2239 2269 1.138036 CCATGTTCATGCGCCTGTG 59.862 57.895 12.54 5.43 0.00 3.66
2473 2503 9.012161 TCATAAGACAATTCATCATGTTGTTCA 57.988 29.630 3.76 0.00 36.30 3.18
2532 2562 6.199154 GCTAAGTTGGCAAGAAAAGAGAAAAC 59.801 38.462 6.31 0.00 0.00 2.43
2602 2632 6.125029 CACTGAGGAATAGATTGGTTTCCAT 58.875 40.000 3.96 0.00 41.15 3.41
2735 2765 8.751302 ACAATTGTTAACAAAGAAAAGAACGT 57.249 26.923 23.97 1.17 39.55 3.99
2754 2784 8.099364 ACTGAATGGTTACAGAGTAACAATTG 57.901 34.615 21.22 13.25 32.78 2.32
2784 2814 8.686739 AGGGCTACATTTTAGGATCTATACAT 57.313 34.615 0.00 0.00 0.00 2.29
2910 2941 3.070018 ACACTTCTCCAATTGCTCTTCG 58.930 45.455 0.00 0.00 0.00 3.79
3138 3174 6.550108 TCCTCAATGTACTCCTCCTGTAATAC 59.450 42.308 0.00 0.00 0.00 1.89
3286 3322 3.158648 TATCCCCCTTGTCCGCGG 61.159 66.667 22.12 22.12 0.00 6.46
3382 3418 8.666573 CGTCTCAGAATAACTGTCTCTACTTTA 58.333 37.037 0.00 0.00 45.86 1.85
3401 3437 2.414994 TACTACTCCCACCGTCTCAG 57.585 55.000 0.00 0.00 0.00 3.35
3404 3440 3.053842 TCTTCATACTACTCCCACCGTCT 60.054 47.826 0.00 0.00 0.00 4.18
3463 3499 1.147817 AGTTGGAGGGCCTTGATTTGT 59.852 47.619 7.89 0.00 34.31 2.83
3496 3532 5.180680 TGCAAGAGAGAAACAGTTCATCATG 59.819 40.000 0.00 0.00 36.09 3.07
3497 3533 5.311265 TGCAAGAGAGAAACAGTTCATCAT 58.689 37.500 0.00 0.00 36.09 2.45
3502 3538 4.286101 GCTTTGCAAGAGAGAAACAGTTC 58.714 43.478 0.00 0.00 0.00 3.01
3560 3600 5.564063 CGTGTACTGTGAGTGGAACAAGATA 60.564 44.000 0.00 0.00 44.16 1.98
3561 3601 4.632153 GTGTACTGTGAGTGGAACAAGAT 58.368 43.478 0.00 0.00 44.16 2.40
3562 3602 3.490249 CGTGTACTGTGAGTGGAACAAGA 60.490 47.826 0.00 0.00 44.16 3.02
3570 3610 1.767289 GGTGACGTGTACTGTGAGTG 58.233 55.000 0.00 0.00 0.00 3.51
3609 3657 1.005924 AGCCCCAAGGATGATCGTTTT 59.994 47.619 0.00 0.00 33.47 2.43
3627 3675 3.343941 TGTAGTACACCATTTCCCAGC 57.656 47.619 0.00 0.00 0.00 4.85
3632 3680 6.567050 TCCGTAGATTGTAGTACACCATTTC 58.433 40.000 1.43 0.00 0.00 2.17
3641 3689 9.399797 TCTTTCAGTAATCCGTAGATTGTAGTA 57.600 33.333 0.00 0.00 42.78 1.82
3642 3690 8.289939 TCTTTCAGTAATCCGTAGATTGTAGT 57.710 34.615 0.00 0.00 42.78 2.73
3643 3691 7.863375 CCTCTTTCAGTAATCCGTAGATTGTAG 59.137 40.741 0.00 0.00 42.78 2.74
3740 3791 2.356793 CGATCATCTGCGCCCTCC 60.357 66.667 4.18 0.00 0.00 4.30
3746 3797 4.240103 TGGGGCCGATCATCTGCG 62.240 66.667 0.00 0.00 0.00 5.18
3750 3801 1.152881 AAAGCTGGGGCCGATCATC 60.153 57.895 0.00 0.00 39.73 2.92
3756 3807 2.747855 GAGACAAAGCTGGGGCCG 60.748 66.667 0.00 0.00 39.73 6.13
3760 3811 0.324285 AGAGCAGAGACAAAGCTGGG 59.676 55.000 0.00 0.00 39.02 4.45
3769 3820 2.106566 TGATGGGAGAAGAGCAGAGAC 58.893 52.381 0.00 0.00 0.00 3.36
3770 3821 2.539432 TGATGGGAGAAGAGCAGAGA 57.461 50.000 0.00 0.00 0.00 3.10
3771 3822 3.842007 AATGATGGGAGAAGAGCAGAG 57.158 47.619 0.00 0.00 0.00 3.35
3803 3855 7.116376 CGAATTTGAGTTACAGTATGACACAGT 59.884 37.037 0.00 0.00 39.69 3.55
3812 3864 4.633175 TGGCACGAATTTGAGTTACAGTA 58.367 39.130 0.00 0.00 0.00 2.74
3813 3865 3.472652 TGGCACGAATTTGAGTTACAGT 58.527 40.909 0.00 0.00 0.00 3.55
3814 3866 3.498397 ACTGGCACGAATTTGAGTTACAG 59.502 43.478 0.00 5.17 0.00 2.74
3815 3867 3.472652 ACTGGCACGAATTTGAGTTACA 58.527 40.909 0.00 0.00 0.00 2.41
3816 3868 4.024387 TGAACTGGCACGAATTTGAGTTAC 60.024 41.667 0.00 0.00 0.00 2.50
3823 3875 0.598065 GGCTGAACTGGCACGAATTT 59.402 50.000 0.00 0.00 0.00 1.82
3918 3970 1.493772 TCGATCGTTGAACGCAAAGT 58.506 45.000 15.94 0.00 42.21 2.66
3924 3976 1.455786 AGCTGTTTCGATCGTTGAACG 59.544 47.619 15.94 12.12 44.19 3.95
3933 3985 4.645136 TGACATAGGAGTAGCTGTTTCGAT 59.355 41.667 0.00 0.00 0.00 3.59
3939 3991 2.428890 GCACTGACATAGGAGTAGCTGT 59.571 50.000 0.00 0.00 0.00 4.40
3948 4000 4.573900 AGAAGAACAAGCACTGACATAGG 58.426 43.478 0.00 0.00 0.00 2.57
3985 4037 0.376152 CTAGCGCTGCCATGACTTTG 59.624 55.000 22.90 0.00 0.00 2.77
4089 4141 2.845363 AGGAAGCCCAAATTTTGCAG 57.155 45.000 11.03 0.00 33.88 4.41
4120 4172 2.221169 GCAAATGATCTATGTCGGGCA 58.779 47.619 0.00 0.00 0.00 5.36
4169 4221 1.546476 CTCGTGAACTAGTTGCTCCCT 59.454 52.381 14.14 0.00 0.00 4.20
4170 4222 1.997669 CTCGTGAACTAGTTGCTCCC 58.002 55.000 14.14 0.00 0.00 4.30
4171 4223 1.351153 GCTCGTGAACTAGTTGCTCC 58.649 55.000 14.14 0.00 0.00 4.70
4172 4224 0.985549 CGCTCGTGAACTAGTTGCTC 59.014 55.000 14.14 0.00 0.00 4.26
4173 4225 1.009389 GCGCTCGTGAACTAGTTGCT 61.009 55.000 14.14 0.00 0.00 3.91
4174 4226 1.009389 AGCGCTCGTGAACTAGTTGC 61.009 55.000 14.14 8.80 0.00 4.17
4175 4227 0.985549 GAGCGCTCGTGAACTAGTTG 59.014 55.000 23.61 0.00 0.00 3.16
4176 4228 0.109226 GGAGCGCTCGTGAACTAGTT 60.109 55.000 29.81 8.13 0.00 2.24
4177 4229 0.961358 AGGAGCGCTCGTGAACTAGT 60.961 55.000 30.10 4.18 0.00 2.57
4178 4230 0.171455 AAGGAGCGCTCGTGAACTAG 59.829 55.000 31.14 0.00 0.00 2.57
4179 4231 0.170561 GAAGGAGCGCTCGTGAACTA 59.829 55.000 31.14 0.00 0.00 2.24
4180 4232 1.080434 GAAGGAGCGCTCGTGAACT 60.080 57.895 31.14 19.11 0.00 3.01
4181 4233 2.437343 CGAAGGAGCGCTCGTGAAC 61.437 63.158 31.14 22.55 0.00 3.18
4182 4234 2.126463 CGAAGGAGCGCTCGTGAA 60.126 61.111 31.14 0.00 0.00 3.18
4195 4247 0.596577 TCGTTGTGAGACTCCCGAAG 59.403 55.000 0.00 0.00 0.00 3.79
4196 4248 1.201647 GATCGTTGTGAGACTCCCGAA 59.798 52.381 0.00 0.00 0.00 4.30
4197 4249 0.809385 GATCGTTGTGAGACTCCCGA 59.191 55.000 0.00 3.33 0.00 5.14
4198 4250 0.526211 TGATCGTTGTGAGACTCCCG 59.474 55.000 0.00 0.00 0.00 5.14
4199 4251 1.737363 GCTGATCGTTGTGAGACTCCC 60.737 57.143 0.00 0.00 0.00 4.30
4200 4252 1.634702 GCTGATCGTTGTGAGACTCC 58.365 55.000 0.00 0.00 0.00 3.85
4201 4253 1.263776 CGCTGATCGTTGTGAGACTC 58.736 55.000 0.00 0.00 0.00 3.36
4202 4254 3.408389 CGCTGATCGTTGTGAGACT 57.592 52.632 0.00 0.00 0.00 3.24
4212 4264 0.917259 GTGCTAAGTGACGCTGATCG 59.083 55.000 0.00 0.00 45.38 3.69
4213 4265 0.917259 CGTGCTAAGTGACGCTGATC 59.083 55.000 0.00 0.00 0.00 2.92
4214 4266 3.036026 CGTGCTAAGTGACGCTGAT 57.964 52.632 0.00 0.00 0.00 2.90
4215 4267 4.552278 CGTGCTAAGTGACGCTGA 57.448 55.556 0.00 0.00 0.00 4.26
4219 4271 0.109735 TGAGAGCGTGCTAAGTGACG 60.110 55.000 0.00 0.00 38.63 4.35
4220 4272 1.623359 CTGAGAGCGTGCTAAGTGAC 58.377 55.000 0.00 0.00 0.00 3.67
4221 4273 0.109086 GCTGAGAGCGTGCTAAGTGA 60.109 55.000 0.00 0.00 0.00 3.41
4222 4274 1.080995 GGCTGAGAGCGTGCTAAGTG 61.081 60.000 0.00 0.00 43.62 3.16
4223 4275 1.216710 GGCTGAGAGCGTGCTAAGT 59.783 57.895 0.00 0.00 43.62 2.24
4224 4276 1.875813 CGGCTGAGAGCGTGCTAAG 60.876 63.158 0.00 0.00 43.62 2.18
4225 4277 2.181777 CGGCTGAGAGCGTGCTAA 59.818 61.111 0.00 0.00 43.62 3.09
4226 4278 4.498520 GCGGCTGAGAGCGTGCTA 62.499 66.667 0.00 0.00 43.62 3.49
4246 4298 3.241059 CAGAGCGCGACACGTAGC 61.241 66.667 12.10 0.00 46.11 3.58
4247 4299 2.577112 CCAGAGCGCGACACGTAG 60.577 66.667 12.10 0.00 46.11 3.51
4248 4300 4.111016 CCCAGAGCGCGACACGTA 62.111 66.667 12.10 0.00 46.11 3.57
4264 4316 4.917906 AATATAATCTGGAGGGAGCACC 57.082 45.455 0.00 0.00 40.67 5.01
4265 4317 8.870075 AATAAAATATAATCTGGAGGGAGCAC 57.130 34.615 0.00 0.00 0.00 4.40
4266 4318 9.881773 AAAATAAAATATAATCTGGAGGGAGCA 57.118 29.630 0.00 0.00 0.00 4.26
4271 4323 9.626045 GCGGAAAAATAAAATATAATCTGGAGG 57.374 33.333 0.00 0.00 0.00 4.30
4276 4328 9.128107 CGCATGCGGAAAAATAAAATATAATCT 57.872 29.630 31.99 0.00 35.56 2.40
4277 4329 8.911662 ACGCATGCGGAAAAATAAAATATAATC 58.088 29.630 39.95 0.00 44.69 1.75
4278 4330 8.810652 ACGCATGCGGAAAAATAAAATATAAT 57.189 26.923 39.95 12.90 44.69 1.28
4279 4331 8.635877 AACGCATGCGGAAAAATAAAATATAA 57.364 26.923 39.95 0.00 44.69 0.98
4280 4332 8.635877 AAACGCATGCGGAAAAATAAAATATA 57.364 26.923 39.95 0.00 44.69 0.86
4281 4333 7.532682 AAACGCATGCGGAAAAATAAAATAT 57.467 28.000 39.95 14.34 44.69 1.28
4282 4334 6.952935 AAACGCATGCGGAAAAATAAAATA 57.047 29.167 39.95 0.00 44.69 1.40
4283 4335 5.854431 AAACGCATGCGGAAAAATAAAAT 57.146 30.435 39.95 15.00 44.69 1.82
4284 4336 5.610552 CGAAAACGCATGCGGAAAAATAAAA 60.611 36.000 39.95 0.00 44.69 1.52
4285 4337 4.143514 CGAAAACGCATGCGGAAAAATAAA 60.144 37.500 39.95 0.00 44.69 1.40
4286 4338 3.362237 CGAAAACGCATGCGGAAAAATAA 59.638 39.130 39.95 0.00 44.69 1.40
4287 4339 2.911723 CGAAAACGCATGCGGAAAAATA 59.088 40.909 39.95 0.00 44.69 1.40
4288 4340 1.718711 CGAAAACGCATGCGGAAAAAT 59.281 42.857 39.95 21.35 44.69 1.82
4289 4341 1.124462 CGAAAACGCATGCGGAAAAA 58.876 45.000 39.95 0.00 44.69 1.94
4290 4342 2.789813 CGAAAACGCATGCGGAAAA 58.210 47.368 39.95 0.00 44.69 2.29
4291 4343 4.524305 CGAAAACGCATGCGGAAA 57.476 50.000 39.95 0.00 44.69 3.13


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

AutoCloner maintained by Alex Coulton.