Multiple sequence alignment - TraesCS6A01G213500

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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 TraesCS6A01G213500 chr6A 100.000 4580 0 0 1 4580 388210058 388214637 0.000000e+00 8458
1 TraesCS6A01G213500 chr6B 96.414 2482 63 6 1394 3862 433273359 433275827 0.000000e+00 4067
2 TraesCS6A01G213500 chr6B 95.221 1423 58 4 1 1416 433271904 433273323 0.000000e+00 2242
3 TraesCS6A01G213500 chr6B 90.244 328 30 1 4204 4529 433281546 433281873 1.180000e-115 427
4 TraesCS6A01G213500 chr7B 96.728 2353 52 8 1394 3731 438421870 438424212 0.000000e+00 3895
5 TraesCS6A01G213500 chr7B 94.815 1138 49 6 284 1416 438420703 438421835 0.000000e+00 1766
6 TraesCS6A01G213500 chr7B 91.131 327 29 0 4204 4530 438436834 438437160 1.170000e-120 444
7 TraesCS6A01G213500 chr7B 92.642 299 12 2 1 293 438399470 438399764 5.480000e-114 422
8 TraesCS6A01G213500 chr7B 89.552 134 14 0 3729 3862 438424270 438424403 2.190000e-38 171
9 TraesCS6A01G213500 chr6D 95.531 1432 46 8 1 1416 272108675 272110104 0.000000e+00 2274
10 TraesCS6A01G213500 chr6D 96.365 1293 35 2 1394 2681 272110141 272111426 0.000000e+00 2117
11 TraesCS6A01G213500 chr6D 95.640 1101 34 5 2675 3770 272111459 272112550 0.000000e+00 1755
12 TraesCS6A01G213500 chr6D 86.637 449 50 4 4134 4580 272112976 272113416 5.330000e-134 488


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 TraesCS6A01G213500 chr6A 388210058 388214637 4579 False 8458.0 8458 100.000000 1 4580 1 chr6A.!!$F1 4579
1 TraesCS6A01G213500 chr6B 433271904 433275827 3923 False 3154.5 4067 95.817500 1 3862 2 chr6B.!!$F2 3861
2 TraesCS6A01G213500 chr7B 438420703 438424403 3700 False 1944.0 3895 93.698333 284 3862 3 chr7B.!!$F3 3578
3 TraesCS6A01G213500 chr6D 272108675 272113416 4741 False 1658.5 2274 93.543250 1 4580 4 chr6D.!!$F1 4579

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
253 260 0.682852 TCAGTACCACCTCCAAACCG 59.317 55.000 0.0 0.0 0.00 4.44 F
1017 1038 1.004560 CATGTCCACTGCGGTCTGT 60.005 57.895 0.0 0.0 35.57 3.41 F
1614 1694 0.460811 GCATGACCGTGAGAGCATCA 60.461 55.000 0.0 0.0 37.82 3.07 F
1940 2020 0.733909 CGAAGAGCGTCTGCATGTCA 60.734 55.000 0.0 0.0 46.23 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 1105 0.471617 CTGGCTGGTGGGAGATAAGG 59.528 60.000 0.00 0.0 0.00 2.69 R
1940 2020 1.003928 TGGCAGATGCACTCATTCACT 59.996 47.619 7.19 0.0 44.36 3.41 R
3043 3169 2.355108 GCTGTTTATGAGGACCAGAGCA 60.355 50.000 0.00 0.0 0.00 4.26 R
3876 4177 0.034767 TGCATCTTTGAGAGGGCCTG 60.035 55.000 12.95 0.0 30.27 4.85 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
61 62 2.472488 CGCATGCTTGTTTTTGAACCTC 59.528 45.455 17.13 0.00 0.00 3.85
107 108 9.945904 AAAAAGGTTATCCAACAAACAAAGTAA 57.054 25.926 0.00 0.00 36.29 2.24
122 123 6.509418 ACAAAGTAAACAGCAACAGAGAAA 57.491 33.333 0.00 0.00 0.00 2.52
134 135 4.560108 GCAACAGAGAAATGTCAAATGGCT 60.560 41.667 0.00 0.00 31.50 4.75
253 260 0.682852 TCAGTACCACCTCCAAACCG 59.317 55.000 0.00 0.00 0.00 4.44
293 300 2.702478 AGGAGCATCTGCAGCAGTAATA 59.298 45.455 22.10 2.89 45.16 0.98
345 355 9.927668 ATACAAAAATCCACTTATTTCACTTGG 57.072 29.630 0.00 0.00 0.00 3.61
470 480 5.446143 ACGCCAAAACAAGAATCATGTAA 57.554 34.783 0.00 0.00 0.00 2.41
471 481 5.837437 ACGCCAAAACAAGAATCATGTAAA 58.163 33.333 0.00 0.00 0.00 2.01
571 591 4.092771 CAAACAGATTGCTGAGACATGG 57.907 45.455 0.00 0.00 45.17 3.66
585 605 1.607178 CATGGGAACTTGGGCAGCA 60.607 57.895 0.00 0.00 32.13 4.41
839 859 4.868116 AAACACCACGCCACCGCT 62.868 61.111 0.00 0.00 38.22 5.52
1017 1038 1.004560 CATGTCCACTGCGGTCTGT 60.005 57.895 0.00 0.00 35.57 3.41
1051 1072 1.996292 CGAGATTTCAAGGCGAGTCA 58.004 50.000 0.00 0.00 0.00 3.41
1084 1105 2.181021 CCCTCCACGTGTACTCGC 59.819 66.667 15.65 0.00 0.00 5.03
1131 1152 1.671742 CCAACTCCGCCTGTGTACT 59.328 57.895 0.00 0.00 0.00 2.73
1173 1194 1.112916 TGAAGCTCCTCGTGTCACCA 61.113 55.000 0.00 0.00 0.00 4.17
1176 1197 2.574955 GCTCCTCGTGTCACCACCT 61.575 63.158 0.00 0.00 38.41 4.00
1221 1242 2.355363 CGCCGTTCAGGTTCGTGA 60.355 61.111 0.00 0.00 43.70 4.35
1223 1244 1.300697 GCCGTTCAGGTTCGTGAGT 60.301 57.895 0.00 0.00 43.70 3.41
1229 1250 0.598562 TCAGGTTCGTGAGTGCTCTC 59.401 55.000 8.86 8.86 40.79 3.20
1245 1266 2.609244 GCTCTCGCTGGGAATCTCATAC 60.609 54.545 0.00 0.00 0.00 2.39
1282 1303 6.709846 CCCTAATCTGATCACAAGAATCTTCC 59.290 42.308 0.00 0.00 0.00 3.46
1287 1308 2.496899 TCACAAGAATCTTCCCAGGC 57.503 50.000 0.00 0.00 0.00 4.85
1297 1318 2.487775 TCTTCCCAGGCAAGGCTATTA 58.512 47.619 0.00 0.00 0.00 0.98
1341 1362 2.816087 AGCAACACGAGAATCTTGCAAT 59.184 40.909 0.00 0.00 43.67 3.56
1344 1365 3.837213 ACACGAGAATCTTGCAATTGG 57.163 42.857 7.72 0.00 38.00 3.16
1394 1415 5.627503 GCAGGTAAAATCCAATCCAATGCTT 60.628 40.000 0.00 0.00 0.00 3.91
1420 1500 2.756760 GGTGCCATGAATCATGAACACT 59.243 45.455 30.01 0.00 43.81 3.55
1423 1503 3.193903 TGCCATGAATCATGAACACTTGG 59.806 43.478 23.55 18.60 43.81 3.61
1426 1506 5.449588 GCCATGAATCATGAACACTTGGTAG 60.450 44.000 23.55 4.36 43.81 3.18
1562 1642 3.263053 GCCTTACGATGGTACCGAC 57.737 57.895 7.57 2.66 0.00 4.79
1583 1663 2.700897 CCGTCTCCCAGATGTAAATCCT 59.299 50.000 0.00 0.00 29.27 3.24
1614 1694 0.460811 GCATGACCGTGAGAGCATCA 60.461 55.000 0.00 0.00 37.82 3.07
1936 2016 1.888436 TTCCCGAAGAGCGTCTGCAT 61.888 55.000 0.00 0.00 46.23 3.96
1940 2020 0.733909 CGAAGAGCGTCTGCATGTCA 60.734 55.000 0.00 0.00 46.23 3.58
1978 2058 2.618816 GCCATGGAATTCCTGACTCACA 60.619 50.000 24.73 2.61 36.82 3.58
1981 2061 1.691976 TGGAATTCCTGACTCACACGT 59.308 47.619 24.73 0.00 36.82 4.49
2153 2233 8.500667 TGTAGTAGGCCCTATTGTATTTGTAT 57.499 34.615 0.00 0.00 0.00 2.29
2608 2693 8.464404 CAGATGAGAAGAAAGCCAAATTATCAA 58.536 33.333 0.00 0.00 0.00 2.57
2773 2897 4.498241 CATCCTCAGAAAATGTCTCGACA 58.502 43.478 1.79 1.79 46.44 4.35
3043 3169 3.754323 CCACATGAGCAATTTTTGGCAAT 59.246 39.130 0.00 0.00 0.00 3.56
3161 3290 0.393537 CGCTTCCATGGCCTTCTTCT 60.394 55.000 6.96 0.00 0.00 2.85
3162 3291 1.844687 GCTTCCATGGCCTTCTTCTT 58.155 50.000 6.96 0.00 0.00 2.52
3163 3292 1.747924 GCTTCCATGGCCTTCTTCTTC 59.252 52.381 6.96 0.00 0.00 2.87
3164 3293 2.620108 GCTTCCATGGCCTTCTTCTTCT 60.620 50.000 6.96 0.00 0.00 2.85
3165 3294 3.694926 CTTCCATGGCCTTCTTCTTCTT 58.305 45.455 6.96 0.00 0.00 2.52
3166 3295 3.356529 TCCATGGCCTTCTTCTTCTTC 57.643 47.619 6.96 0.00 0.00 2.87
3167 3296 2.915604 TCCATGGCCTTCTTCTTCTTCT 59.084 45.455 6.96 0.00 0.00 2.85
3168 3297 3.331889 TCCATGGCCTTCTTCTTCTTCTT 59.668 43.478 6.96 0.00 0.00 2.52
3169 3298 3.693578 CCATGGCCTTCTTCTTCTTCTTC 59.306 47.826 3.32 0.00 0.00 2.87
3316 3453 2.576191 ACATGGGTGGTGTAGCTGTAAT 59.424 45.455 0.00 0.00 0.00 1.89
3329 3466 7.383572 GGTGTAGCTGTAATTGAGATATGTCAG 59.616 40.741 2.46 0.00 0.00 3.51
3357 3494 3.937706 CTGATGATCTCCGTCTGCTTTTT 59.062 43.478 0.00 0.00 0.00 1.94
3606 3752 1.598130 GAAAGGTGGTGCGTCAGCT 60.598 57.895 5.19 5.19 46.02 4.24
3633 3779 2.162319 TGAGCGTATGTTCACAAGCA 57.838 45.000 0.00 0.00 29.60 3.91
3652 3801 0.976641 AGAGTTCAGCCCATTGACGA 59.023 50.000 0.00 0.00 0.00 4.20
3717 3866 7.712797 TGAAGAAAAAGTTATGTTTGAGGTCC 58.287 34.615 0.00 0.00 0.00 4.46
3793 4091 6.963083 ATAGTTAGTGACGGAGCTAAATCT 57.037 37.500 0.00 0.00 29.93 2.40
3800 4098 1.134670 ACGGAGCTAAATCTGGCAGAC 60.135 52.381 21.37 6.65 0.00 3.51
3802 4100 2.362397 CGGAGCTAAATCTGGCAGACTA 59.638 50.000 21.37 13.15 0.00 2.59
3841 4139 5.026121 AGTCTGATAGTCTTGTTGGATGGA 58.974 41.667 0.00 0.00 0.00 3.41
3849 4147 5.397360 AGTCTTGTTGGATGGAAAAAGGAT 58.603 37.500 0.00 0.00 0.00 3.24
3864 4162 0.539901 AGGATACGAGGGGACATCGG 60.540 60.000 8.19 0.00 44.36 4.18
3866 4164 0.314302 GATACGAGGGGACATCGGTG 59.686 60.000 8.19 0.00 44.36 4.94
3877 4178 1.933021 ACATCGGTGTCCTAGGTTCA 58.067 50.000 9.08 6.98 31.41 3.18
3890 4191 0.695347 AGGTTCAGGCCCTCTCAAAG 59.305 55.000 0.00 0.00 0.00 2.77
3892 4193 1.283321 GGTTCAGGCCCTCTCAAAGAT 59.717 52.381 0.00 0.00 0.00 2.40
3894 4195 0.254178 TCAGGCCCTCTCAAAGATGC 59.746 55.000 0.00 0.00 0.00 3.91
3900 4201 3.429960 GGCCCTCTCAAAGATGCAAAATC 60.430 47.826 0.00 0.00 0.00 2.17
3901 4202 3.429960 GCCCTCTCAAAGATGCAAAATCC 60.430 47.826 0.00 0.00 0.00 3.01
3903 4204 5.195940 CCCTCTCAAAGATGCAAAATCCTA 58.804 41.667 0.00 0.00 0.00 2.94
3908 4209 5.245531 TCAAAGATGCAAAATCCTACGTCT 58.754 37.500 0.00 0.00 0.00 4.18
3910 4211 5.551760 AAGATGCAAAATCCTACGTCTTG 57.448 39.130 0.00 0.00 37.09 3.02
3911 4212 4.579869 AGATGCAAAATCCTACGTCTTGT 58.420 39.130 0.00 0.00 0.00 3.16
3924 4225 8.659925 TCCTACGTCTTGTTTTTGTTGTATTA 57.340 30.769 0.00 0.00 0.00 0.98
3961 4262 9.884465 GGATTTAGAATACATGTGAACTATTGC 57.116 33.333 9.11 2.55 0.00 3.56
3967 4268 7.712639 AGAATACATGTGAACTATTGCGAGATT 59.287 33.333 9.11 0.00 0.00 2.40
3968 4269 5.475273 ACATGTGAACTATTGCGAGATTG 57.525 39.130 0.00 0.00 0.00 2.67
3973 4274 5.347635 TGTGAACTATTGCGAGATTGTGTAC 59.652 40.000 0.00 0.00 0.00 2.90
3974 4275 5.347635 GTGAACTATTGCGAGATTGTGTACA 59.652 40.000 0.00 0.00 0.00 2.90
3983 4284 5.643348 TGCGAGATTGTGTACAAATGAATCT 59.357 36.000 15.40 15.40 39.55 2.40
4000 4301 0.034380 TCTGTCCTCTACGGTCCTGG 60.034 60.000 0.00 0.00 35.78 4.45
4007 4308 3.064987 CTACGGTCCTGGCACCTCG 62.065 68.421 11.75 3.97 33.77 4.63
4012 4313 1.675219 GTCCTGGCACCTCGGTTTA 59.325 57.895 0.00 0.00 0.00 2.01
4021 4322 4.281688 TGGCACCTCGGTTTATATAGGTAC 59.718 45.833 0.00 0.00 40.39 3.34
4022 4323 4.525874 GGCACCTCGGTTTATATAGGTACT 59.474 45.833 0.00 0.00 40.39 2.73
4026 4327 4.465305 CCTCGGTTTATATAGGTACTGGGG 59.535 50.000 5.53 5.53 41.52 4.96
4049 4350 4.080751 GTGCCTAGGGTTACAAATAGGTCA 60.081 45.833 11.72 0.00 37.66 4.02
4054 4355 5.578157 AGGGTTACAAATAGGTCAGTTGT 57.422 39.130 0.00 0.00 46.54 3.32
4074 4375 0.981183 ATCTAGGGTCAAACGTGCCA 59.019 50.000 0.00 0.00 0.00 4.92
4078 4379 2.617274 GGGTCAAACGTGCCAGAGC 61.617 63.158 0.00 0.00 40.48 4.09
4095 4396 1.227380 GCCTGTCTCTATGCCGTGG 60.227 63.158 0.00 0.00 0.00 4.94
4097 4398 0.387202 CCTGTCTCTATGCCGTGGAG 59.613 60.000 0.00 0.00 36.81 3.86
4099 4400 1.066303 CTGTCTCTATGCCGTGGAGTC 59.934 57.143 0.00 0.00 36.82 3.36
4102 4403 0.249238 CTCTATGCCGTGGAGTCTGC 60.249 60.000 0.00 0.00 31.27 4.26
4104 4405 3.716539 TATGCCGTGGAGTCTGCGC 62.717 63.158 0.00 0.00 0.00 6.09
4107 4408 3.449227 CCGTGGAGTCTGCGCCTA 61.449 66.667 4.18 0.00 35.46 3.93
4108 4409 2.103143 CGTGGAGTCTGCGCCTAG 59.897 66.667 4.18 0.00 35.46 3.02
4109 4410 2.701780 CGTGGAGTCTGCGCCTAGT 61.702 63.158 4.18 0.00 35.46 2.57
4110 4411 1.139947 GTGGAGTCTGCGCCTAGTC 59.860 63.158 4.18 5.06 35.46 2.59
4111 4412 1.000771 TGGAGTCTGCGCCTAGTCT 60.001 57.895 4.18 0.00 35.46 3.24
4112 4413 0.612174 TGGAGTCTGCGCCTAGTCTT 60.612 55.000 4.18 0.00 35.46 3.01
4113 4414 0.533032 GGAGTCTGCGCCTAGTCTTT 59.467 55.000 4.18 0.00 0.00 2.52
4114 4415 1.634702 GAGTCTGCGCCTAGTCTTTG 58.365 55.000 4.18 0.00 0.00 2.77
4115 4416 0.247736 AGTCTGCGCCTAGTCTTTGG 59.752 55.000 4.18 0.00 0.00 3.28
4116 4417 0.246635 GTCTGCGCCTAGTCTTTGGA 59.753 55.000 4.18 0.00 0.00 3.53
4117 4418 1.134670 GTCTGCGCCTAGTCTTTGGAT 60.135 52.381 4.18 0.00 0.00 3.41
4118 4419 1.137086 TCTGCGCCTAGTCTTTGGATC 59.863 52.381 4.18 0.00 0.00 3.36
4119 4420 1.137872 CTGCGCCTAGTCTTTGGATCT 59.862 52.381 4.18 0.00 0.00 2.75
4120 4421 1.555075 TGCGCCTAGTCTTTGGATCTT 59.445 47.619 4.18 0.00 0.00 2.40
4121 4422 2.027192 TGCGCCTAGTCTTTGGATCTTT 60.027 45.455 4.18 0.00 0.00 2.52
4122 4423 3.010420 GCGCCTAGTCTTTGGATCTTTT 58.990 45.455 0.00 0.00 0.00 2.27
4123 4424 3.440522 GCGCCTAGTCTTTGGATCTTTTT 59.559 43.478 0.00 0.00 0.00 1.94
4158 4459 4.916183 AGTCTTTGGATCTTTCCTTCCTG 58.084 43.478 0.00 0.00 43.07 3.86
4166 4467 5.907662 TGGATCTTTCCTTCCTGATGTAGAT 59.092 40.000 0.00 0.00 43.07 1.98
4176 4477 6.239829 CCTTCCTGATGTAGATGAATTAGGCT 60.240 42.308 0.00 0.00 31.30 4.58
4177 4478 7.038729 CCTTCCTGATGTAGATGAATTAGGCTA 60.039 40.741 0.00 0.00 31.30 3.93
4196 4497 1.507140 AATCGGTGATGGGCTTAGGA 58.493 50.000 0.00 0.00 0.00 2.94
4199 4500 1.839894 GGTGATGGGCTTAGGAGGG 59.160 63.158 0.00 0.00 0.00 4.30
4200 4501 1.149401 GTGATGGGCTTAGGAGGGC 59.851 63.158 0.00 0.00 0.00 5.19
4226 4527 1.139853 GCCCATCCAAGAGACTGGTAG 59.860 57.143 0.00 0.00 37.74 3.18
4233 4534 2.613977 CCAAGAGACTGGTAGCCAACAG 60.614 54.545 0.00 0.00 40.48 3.16
4252 4553 1.527370 GCCGAGCACCCCTTAATCT 59.473 57.895 0.00 0.00 0.00 2.40
4261 4562 3.654273 CACCCCTTAATCTAGGACTCCA 58.346 50.000 0.00 0.00 37.50 3.86
4276 4577 2.465813 ACTCCATCAGTCTCCCTTGAG 58.534 52.381 0.00 0.00 40.17 3.02
4277 4578 1.138661 CTCCATCAGTCTCCCTTGAGC 59.861 57.143 0.00 0.00 38.58 4.26
4278 4579 0.179936 CCATCAGTCTCCCTTGAGCC 59.820 60.000 0.00 0.00 38.58 4.70
4280 4581 1.333636 ATCAGTCTCCCTTGAGCCGG 61.334 60.000 0.00 0.00 38.58 6.13
4281 4582 2.120718 AGTCTCCCTTGAGCCGGT 59.879 61.111 1.90 0.00 38.58 5.28
4282 4583 1.985116 AGTCTCCCTTGAGCCGGTC 60.985 63.158 1.90 0.00 38.58 4.79
4284 4585 1.229209 TCTCCCTTGAGCCGGTCTT 60.229 57.895 1.90 0.00 38.58 3.01
4285 4586 1.219393 CTCCCTTGAGCCGGTCTTC 59.781 63.158 1.90 0.00 0.00 2.87
4286 4587 1.535444 TCCCTTGAGCCGGTCTTCA 60.535 57.895 1.90 1.94 0.00 3.02
4288 4589 1.078848 CCTTGAGCCGGTCTTCAGG 60.079 63.158 1.90 5.64 0.00 3.86
4334 4635 2.417107 CGAGCTGCTCTCAATCTTCAGT 60.417 50.000 25.59 0.00 41.98 3.41
4335 4636 3.189285 GAGCTGCTCTCAATCTTCAGTC 58.811 50.000 21.93 0.00 41.51 3.51
4336 4637 2.833338 AGCTGCTCTCAATCTTCAGTCT 59.167 45.455 0.00 0.00 0.00 3.24
4337 4638 3.261390 AGCTGCTCTCAATCTTCAGTCTT 59.739 43.478 0.00 0.00 0.00 3.01
4338 4639 3.618150 GCTGCTCTCAATCTTCAGTCTTC 59.382 47.826 0.00 0.00 0.00 2.87
4339 4640 4.818642 CTGCTCTCAATCTTCAGTCTTCA 58.181 43.478 0.00 0.00 0.00 3.02
4340 4641 5.219343 TGCTCTCAATCTTCAGTCTTCAA 57.781 39.130 0.00 0.00 0.00 2.69
4350 4651 3.281727 TCAGTCTTCAACCTTGCAAGT 57.718 42.857 24.35 10.37 0.00 3.16
4370 4671 0.895100 TGGTTCAACTCCCATGCAGC 60.895 55.000 0.00 0.00 0.00 5.25
4375 4676 0.323178 CAACTCCCATGCAGCCTTCT 60.323 55.000 0.00 0.00 0.00 2.85
4402 4703 4.737054 CAATTTCATTTTGGGTCGAGGAG 58.263 43.478 0.00 0.00 0.00 3.69
4410 4711 1.101635 TGGGTCGAGGAGTCGCATAG 61.102 60.000 0.00 0.00 46.39 2.23
4411 4712 1.008309 GGTCGAGGAGTCGCATAGC 60.008 63.158 0.00 0.00 46.39 2.97
4423 4724 3.517100 AGTCGCATAGCTTGGATATCCAT 59.483 43.478 25.07 13.07 46.97 3.41
4450 4753 9.431887 GGTATTCCAGCGTCATCTATATTTAAA 57.568 33.333 0.00 0.00 0.00 1.52
4479 4782 0.875474 CTTGCAACACCCAAAAGCGG 60.875 55.000 0.00 0.00 0.00 5.52
4486 4789 0.821711 CACCCAAAAGCGGTCTTGGA 60.822 55.000 21.04 0.00 44.16 3.53
4491 4794 1.135689 CAAAAGCGGTCTTGGATTCGG 60.136 52.381 0.00 0.00 31.78 4.30
4510 4813 1.262640 GGGACCAACTCCTTAGGCGA 61.263 60.000 0.00 0.00 39.39 5.54
4513 4816 1.153349 CCAACTCCTTAGGCGAGCC 60.153 63.158 5.89 5.89 0.00 4.70
4549 4852 1.613925 CGTTCTCAGGTCAGGACAAGA 59.386 52.381 1.41 0.00 0.00 3.02
4553 4856 4.114015 TCTCAGGTCAGGACAAGAACTA 57.886 45.455 1.41 0.00 30.39 2.24
4572 4875 2.286935 ATGGTCAGGTCCAACCCTAT 57.713 50.000 10.19 0.00 39.75 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 8.652463 CCTTTTTAGGTTTTGTTGTACACTTTG 58.348 33.333 0.00 0.00 0.00 2.77
93 94 6.364706 TCTGTTGCTGTTTACTTTGTTTGTTG 59.635 34.615 0.00 0.00 0.00 3.33
107 108 5.581126 TTTGACATTTCTCTGTTGCTGTT 57.419 34.783 0.00 0.00 0.00 3.16
134 135 6.826231 TCTTGGCTAAAATCGTATGATCCAAA 59.174 34.615 13.28 5.46 34.74 3.28
166 173 7.785033 TCATTCTGTATGACATCTTGCTTCTA 58.215 34.615 0.00 0.00 38.35 2.10
269 276 2.253403 CTGCTGCAGATGCTCCTGGA 62.253 60.000 24.88 0.00 42.66 3.86
345 355 2.541556 GCAAGGTACTACTAGTGCTGC 58.458 52.381 5.39 4.11 38.49 5.25
470 480 1.067635 GTGCAATTGCTTCCACGGATT 60.068 47.619 29.37 0.00 42.66 3.01
471 481 0.527565 GTGCAATTGCTTCCACGGAT 59.472 50.000 29.37 0.00 42.66 4.18
571 591 3.365265 CGGTGCTGCCCAAGTTCC 61.365 66.667 0.00 0.00 0.00 3.62
1051 1072 4.029809 GGGGCGTACTGGCTGGTT 62.030 66.667 10.15 0.00 44.11 3.67
1084 1105 0.471617 CTGGCTGGTGGGAGATAAGG 59.528 60.000 0.00 0.00 0.00 2.69
1114 1135 1.531149 CAAAGTACACAGGCGGAGTTG 59.469 52.381 0.00 0.00 0.00 3.16
1145 1166 2.125106 GGAGCTTCATCGCCGGTT 60.125 61.111 1.90 0.00 0.00 4.44
1173 1194 4.324991 GGGAACAACGGCGGAGGT 62.325 66.667 13.24 0.13 0.00 3.85
1176 1197 4.011517 GAGGGGAACAACGGCGGA 62.012 66.667 13.24 0.00 0.00 5.54
1183 1204 2.204244 GGGGGAGGAGGGGAACAA 60.204 66.667 0.00 0.00 0.00 2.83
1229 1250 2.760374 GGAAGTATGAGATTCCCAGCG 58.240 52.381 0.00 0.00 39.29 5.18
1245 1266 2.379030 GATTAGGGGTCGGCGGGAAG 62.379 65.000 7.21 0.00 0.00 3.46
1282 1303 2.373169 TCTGGATAATAGCCTTGCCTGG 59.627 50.000 0.00 0.00 0.00 4.45
1287 1308 6.294397 GGAAATGCTTCTGGATAATAGCCTTG 60.294 42.308 0.00 0.00 32.73 3.61
1297 1318 1.679680 CGCATGGAAATGCTTCTGGAT 59.320 47.619 8.87 0.00 44.90 3.41
1344 1365 1.971695 CGTTCTGTTGGCTTCCCCC 60.972 63.158 0.00 0.00 0.00 5.40
1377 1398 5.093849 CAAGGAAGCATTGGATTGGATTT 57.906 39.130 0.00 0.00 0.00 2.17
1394 1415 2.025131 TCATGATTCATGGCACCAAGGA 60.025 45.455 23.07 1.48 41.66 3.36
1420 1500 3.882888 CCTTCAGTTTCAACAGCTACCAA 59.117 43.478 0.00 0.00 0.00 3.67
1423 1503 3.477530 ACCCTTCAGTTTCAACAGCTAC 58.522 45.455 0.00 0.00 0.00 3.58
1426 1506 2.799562 GCAACCCTTCAGTTTCAACAGC 60.800 50.000 0.00 0.00 0.00 4.40
1562 1642 2.700897 AGGATTTACATCTGGGAGACGG 59.299 50.000 0.00 0.00 0.00 4.79
1568 1648 3.668447 CCGATCAGGATTTACATCTGGG 58.332 50.000 0.00 0.00 45.00 4.45
1583 1663 0.740149 GGTCATGCATTTGCCGATCA 59.260 50.000 0.00 0.00 41.18 2.92
1614 1694 2.082231 GCATGCGGCTCTCATATGAAT 58.918 47.619 0.00 0.00 40.25 2.57
1760 1840 6.587206 TGAACAATCCATTGCAGAATACAA 57.413 33.333 0.00 0.00 41.38 2.41
1936 2016 3.332034 CAGATGCACTCATTCACTGACA 58.668 45.455 0.00 0.00 31.96 3.58
1940 2020 1.003928 TGGCAGATGCACTCATTCACT 59.996 47.619 7.19 0.00 44.36 3.41
1978 2058 1.234821 TGTTTCGACCCGTAGTACGT 58.765 50.000 20.60 3.67 40.58 3.57
1981 2061 3.067180 GGATCATGTTTCGACCCGTAGTA 59.933 47.826 0.00 0.00 0.00 1.82
2013 2093 6.178607 TGCTAGCAATTGGAGAATCAGATA 57.821 37.500 16.84 0.00 36.25 1.98
2153 2233 8.584157 ACACCTCAAAATGTGCTTAATTTATCA 58.416 29.630 0.00 0.00 35.90 2.15
2282 2362 8.383175 TGGAACTTGGAAGTAATCAGTAGAAAT 58.617 33.333 0.00 0.00 38.57 2.17
2697 2821 3.960571 ACTGATAAACTGCATCAAGGCT 58.039 40.909 0.00 0.00 32.20 4.58
2773 2897 9.778741 TGTTTAGATTCTCAAGTGATAAACAGT 57.221 29.630 10.80 0.00 36.97 3.55
3043 3169 2.355108 GCTGTTTATGAGGACCAGAGCA 60.355 50.000 0.00 0.00 0.00 4.26
3161 3290 9.230122 TGCACATATTGTTATCTTGAAGAAGAA 57.770 29.630 0.00 0.00 41.64 2.52
3162 3291 8.791327 TGCACATATTGTTATCTTGAAGAAGA 57.209 30.769 0.00 0.00 42.53 2.87
3163 3292 8.886719 TCTGCACATATTGTTATCTTGAAGAAG 58.113 33.333 0.00 0.00 0.00 2.85
3164 3293 8.668353 GTCTGCACATATTGTTATCTTGAAGAA 58.332 33.333 0.00 0.00 0.00 2.52
3165 3294 8.043113 AGTCTGCACATATTGTTATCTTGAAGA 58.957 33.333 0.00 0.00 0.00 2.87
3166 3295 8.206325 AGTCTGCACATATTGTTATCTTGAAG 57.794 34.615 0.00 0.00 0.00 3.02
3167 3296 8.453320 CAAGTCTGCACATATTGTTATCTTGAA 58.547 33.333 0.00 0.00 32.17 2.69
3168 3297 7.607607 ACAAGTCTGCACATATTGTTATCTTGA 59.392 33.333 0.00 0.00 33.88 3.02
3169 3298 7.755591 ACAAGTCTGCACATATTGTTATCTTG 58.244 34.615 0.00 0.00 30.18 3.02
3299 3428 3.055385 TCTCAATTACAGCTACACCACCC 60.055 47.826 0.00 0.00 0.00 4.61
3357 3494 7.772292 AGTCCTACGTTACTTACATCTATCACA 59.228 37.037 0.00 0.00 0.00 3.58
3606 3752 3.429543 GTGAACATACGCTCAAACGGTAA 59.570 43.478 0.00 0.00 37.37 2.85
3633 3779 0.976641 TCGTCAATGGGCTGAACTCT 59.023 50.000 0.00 0.00 0.00 3.24
3652 3801 4.086706 ACTTTTCTTCAATGAGACGGGT 57.913 40.909 0.00 0.00 0.00 5.28
3717 3866 8.675705 AATTTTTGATTTGTAAGTTCCAAGGG 57.324 30.769 0.00 0.00 0.00 3.95
3793 4091 0.399949 CCCCTACCCATAGTCTGCCA 60.400 60.000 0.00 0.00 0.00 4.92
3800 4098 4.662617 GGGACCCCCTACCCATAG 57.337 66.667 0.00 0.00 44.96 2.23
3819 4117 5.344743 TCCATCCAACAAGACTATCAGAC 57.655 43.478 0.00 0.00 0.00 3.51
3824 4122 6.552008 TCCTTTTTCCATCCAACAAGACTAT 58.448 36.000 0.00 0.00 0.00 2.12
3841 4139 3.431766 CGATGTCCCCTCGTATCCTTTTT 60.432 47.826 0.00 0.00 0.00 1.94
3849 4147 1.000521 ACACCGATGTCCCCTCGTA 60.001 57.895 0.00 0.00 31.55 3.43
3866 4164 0.325765 AGAGGGCCTGAACCTAGGAC 60.326 60.000 17.98 9.73 45.74 3.85
3870 4171 1.909302 CTTTGAGAGGGCCTGAACCTA 59.091 52.381 12.95 0.00 38.79 3.08
3876 4177 0.034767 TGCATCTTTGAGAGGGCCTG 60.035 55.000 12.95 0.00 30.27 4.85
3877 4178 0.700564 TTGCATCTTTGAGAGGGCCT 59.299 50.000 5.25 5.25 30.27 5.19
3890 4191 4.946784 ACAAGACGTAGGATTTTGCATC 57.053 40.909 0.00 0.00 0.00 3.91
3892 4193 5.508200 AAAACAAGACGTAGGATTTTGCA 57.492 34.783 0.00 0.00 0.00 4.08
3894 4195 7.274686 ACAACAAAAACAAGACGTAGGATTTTG 59.725 33.333 18.67 18.67 40.35 2.44
3900 4201 9.887406 ATTAATACAACAAAAACAAGACGTAGG 57.113 29.630 0.00 0.00 0.00 3.18
3903 4204 9.575783 ACAATTAATACAACAAAAACAAGACGT 57.424 25.926 0.00 0.00 0.00 4.34
3930 4231 8.497745 AGTTCACATGTATTCTAAATCCCATCT 58.502 33.333 0.00 0.00 0.00 2.90
3931 4232 8.682936 AGTTCACATGTATTCTAAATCCCATC 57.317 34.615 0.00 0.00 0.00 3.51
3937 4238 9.325198 TCGCAATAGTTCACATGTATTCTAAAT 57.675 29.630 0.00 0.00 0.00 1.40
3939 4240 8.194769 TCTCGCAATAGTTCACATGTATTCTAA 58.805 33.333 0.00 0.00 0.00 2.10
3940 4241 7.712797 TCTCGCAATAGTTCACATGTATTCTA 58.287 34.615 0.00 1.88 0.00 2.10
3942 4243 6.828502 TCTCGCAATAGTTCACATGTATTC 57.171 37.500 0.00 0.00 0.00 1.75
3958 4259 5.681337 TTCATTTGTACACAATCTCGCAA 57.319 34.783 0.00 0.00 35.55 4.85
3959 4260 5.643348 AGATTCATTTGTACACAATCTCGCA 59.357 36.000 0.00 0.00 35.55 5.10
3961 4262 7.065216 ACAGATTCATTTGTACACAATCTCG 57.935 36.000 12.46 11.18 32.59 4.04
3967 4268 6.114187 AGAGGACAGATTCATTTGTACACA 57.886 37.500 0.00 0.00 30.29 3.72
3968 4269 6.253727 CGTAGAGGACAGATTCATTTGTACAC 59.746 42.308 0.00 0.00 30.29 2.90
3973 4274 4.759782 ACCGTAGAGGACAGATTCATTTG 58.240 43.478 0.00 0.00 45.00 2.32
3974 4275 4.141914 GGACCGTAGAGGACAGATTCATTT 60.142 45.833 0.00 0.00 45.00 2.32
3983 4284 1.681327 GCCAGGACCGTAGAGGACA 60.681 63.158 0.00 0.00 45.00 4.02
4000 4301 5.467705 CAGTACCTATATAAACCGAGGTGC 58.532 45.833 2.66 1.44 42.36 5.01
4007 4308 4.263199 GGCACCCCAGTACCTATATAAACC 60.263 50.000 0.00 0.00 0.00 3.27
4012 4313 3.246021 CCTAGGCACCCCAGTACCTATAT 60.246 52.174 0.00 0.00 40.57 0.86
4021 4322 0.912487 TGTAACCCTAGGCACCCCAG 60.912 60.000 2.05 0.00 0.00 4.45
4022 4323 0.476023 TTGTAACCCTAGGCACCCCA 60.476 55.000 2.05 0.00 0.00 4.96
4026 4327 4.080751 TGACCTATTTGTAACCCTAGGCAC 60.081 45.833 2.05 1.18 35.20 5.01
4049 4350 4.817517 CACGTTTGACCCTAGATACAACT 58.182 43.478 0.00 0.00 0.00 3.16
4054 4355 2.167693 CTGGCACGTTTGACCCTAGATA 59.832 50.000 0.00 0.00 0.00 1.98
4078 4379 0.387202 CTCCACGGCATAGAGACAGG 59.613 60.000 0.00 0.00 0.00 4.00
4097 4398 0.246635 TCCAAAGACTAGGCGCAGAC 59.753 55.000 10.83 0.00 0.00 3.51
4099 4400 1.137872 AGATCCAAAGACTAGGCGCAG 59.862 52.381 10.83 0.19 0.00 5.18
4123 4424 5.163457 GATCCAAAGACTTGGGTGTCAAAAA 60.163 40.000 8.55 0.00 46.72 1.94
4124 4425 4.340950 GATCCAAAGACTTGGGTGTCAAAA 59.659 41.667 8.55 0.00 46.72 2.44
4125 4426 3.888930 GATCCAAAGACTTGGGTGTCAAA 59.111 43.478 8.55 0.00 46.72 2.69
4126 4427 3.138283 AGATCCAAAGACTTGGGTGTCAA 59.862 43.478 8.55 0.00 46.72 3.18
4127 4428 2.711009 AGATCCAAAGACTTGGGTGTCA 59.289 45.455 8.55 0.00 46.72 3.58
4128 4429 3.425162 AGATCCAAAGACTTGGGTGTC 57.575 47.619 8.55 8.26 46.72 3.67
4129 4430 3.884037 AAGATCCAAAGACTTGGGTGT 57.116 42.857 8.55 0.00 46.72 4.16
4130 4431 3.507622 GGAAAGATCCAAAGACTTGGGTG 59.492 47.826 8.55 0.00 46.72 4.61
4144 4445 7.060383 TCATCTACATCAGGAAGGAAAGATC 57.940 40.000 0.00 0.00 0.00 2.75
4158 4459 7.276658 CACCGATTAGCCTAATTCATCTACATC 59.723 40.741 0.00 0.00 0.00 3.06
4166 4467 4.504864 CCCATCACCGATTAGCCTAATTCA 60.505 45.833 0.00 0.00 0.00 2.57
4176 4477 2.632996 CTCCTAAGCCCATCACCGATTA 59.367 50.000 0.00 0.00 0.00 1.75
4177 4478 1.417890 CTCCTAAGCCCATCACCGATT 59.582 52.381 0.00 0.00 0.00 3.34
4200 4501 1.228063 CTCTTGGATGGGCCGATGG 60.228 63.158 4.37 0.00 40.66 3.51
4202 4503 0.692419 AGTCTCTTGGATGGGCCGAT 60.692 55.000 0.00 0.00 40.66 4.18
4233 4534 1.526225 GATTAAGGGGTGCTCGGCC 60.526 63.158 0.00 0.00 0.00 6.13
4236 4537 2.036089 GTCCTAGATTAAGGGGTGCTCG 59.964 54.545 0.00 0.00 37.24 5.03
4242 4543 4.493618 TGATGGAGTCCTAGATTAAGGGG 58.506 47.826 11.33 0.00 37.24 4.79
4267 4568 1.219393 GAAGACCGGCTCAAGGGAG 59.781 63.158 0.00 0.00 44.33 4.30
4268 4569 1.535444 TGAAGACCGGCTCAAGGGA 60.535 57.895 0.00 0.00 0.00 4.20
4272 4573 2.347490 GCCTGAAGACCGGCTCAA 59.653 61.111 0.00 0.00 42.98 3.02
4280 4581 2.432628 CGTCCACGGCCTGAAGAC 60.433 66.667 0.00 1.36 35.37 3.01
4281 4582 4.373116 GCGTCCACGGCCTGAAGA 62.373 66.667 0.00 0.00 40.23 2.87
4282 4583 4.680237 TGCGTCCACGGCCTGAAG 62.680 66.667 0.00 0.00 40.23 3.02
4334 4635 2.733956 ACCAACTTGCAAGGTTGAAGA 58.266 42.857 29.18 0.00 44.58 2.87
4335 4636 3.119173 TGAACCAACTTGCAAGGTTGAAG 60.119 43.478 29.18 18.63 45.15 3.02
4336 4637 2.828520 TGAACCAACTTGCAAGGTTGAA 59.171 40.909 29.18 12.71 45.15 2.69
4337 4638 2.451490 TGAACCAACTTGCAAGGTTGA 58.549 42.857 29.18 16.51 45.15 3.18
4338 4639 2.929398 GTTGAACCAACTTGCAAGGTTG 59.071 45.455 29.18 25.80 45.15 3.77
4340 4641 2.959507 GTTGAACCAACTTGCAAGGT 57.040 45.000 29.18 22.09 40.73 3.50
4350 4651 1.619654 CTGCATGGGAGTTGAACCAA 58.380 50.000 0.00 0.00 40.73 3.67
4402 4703 3.319137 TGGATATCCAAGCTATGCGAC 57.681 47.619 22.52 0.00 44.35 5.19
4423 4724 6.605471 AATATAGATGACGCTGGAATACCA 57.395 37.500 0.00 0.00 44.76 3.25
4450 4753 3.450457 TGGGTGTTGCAAGAATCTTTTGT 59.550 39.130 0.00 0.00 0.00 2.83
4461 4764 1.142748 CCGCTTTTGGGTGTTGCAA 59.857 52.632 0.00 0.00 0.00 4.08
4468 4771 0.112412 ATCCAAGACCGCTTTTGGGT 59.888 50.000 0.55 0.00 43.22 4.51
4479 4782 0.326927 TTGGTCCCCGAATCCAAGAC 59.673 55.000 0.00 0.00 36.48 3.01
4515 4818 1.390463 GAGAACGCTTCGCCACTTAAG 59.610 52.381 0.00 0.00 34.02 1.85
4522 4825 2.048127 ACCTGAGAACGCTTCGCC 60.048 61.111 0.00 0.00 34.02 5.54
4525 4828 0.603569 TCCTGACCTGAGAACGCTTC 59.396 55.000 0.00 0.00 0.00 3.86
4537 4840 3.260884 TGACCATAGTTCTTGTCCTGACC 59.739 47.826 0.00 0.00 0.00 4.02
4549 4852 1.633945 GGGTTGGACCTGACCATAGTT 59.366 52.381 16.37 0.00 39.82 2.24
4553 4856 2.127708 GATAGGGTTGGACCTGACCAT 58.872 52.381 16.37 12.91 42.02 3.55


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

AutoCloner maintained by Alex Coulton.