Multiple sequence alignment - TraesCS1A01G211300

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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 TraesCS1A01G211300 chr1A 100.000 3662 0 0 1 3662 374170194 374166533 0.000000e+00 6763
1 TraesCS1A01G211300 chr1D 92.498 3226 162 33 396 3595 299812025 299808854 0.000000e+00 4543
2 TraesCS1A01G211300 chr1D 89.924 397 27 7 1 390 299813669 299813279 1.960000e-137 499
3 TraesCS1A01G211300 chr1D 91.209 91 5 2 3572 3662 355374380 355374467 1.790000e-23 121
4 TraesCS1A01G211300 chr1B 90.363 2480 144 43 646 3094 404302538 404300123 0.000000e+00 3168
5 TraesCS1A01G211300 chr1B 88.756 667 52 9 1 658 404309549 404308897 0.000000e+00 795
6 TraesCS1A01G211300 chr1B 87.433 374 39 6 3193 3566 404174116 404173751 1.220000e-114 424
7 TraesCS1A01G211300 chr6B 96.250 80 0 3 3584 3662 211634354 211634277 1.070000e-25 128
8 TraesCS1A01G211300 chr2A 95.122 82 2 2 3583 3662 508067217 508067136 1.070000e-25 128
9 TraesCS1A01G211300 chr6D 93.023 86 4 2 3579 3662 78207653 78207568 1.380000e-24 124
10 TraesCS1A01G211300 chr6D 98.507 67 1 0 3596 3662 363381472 363381406 6.420000e-23 119
11 TraesCS1A01G211300 chr6D 87.619 105 7 6 3559 3662 429629808 429629907 2.310000e-22 117
12 TraesCS1A01G211300 chr4B 92.941 85 4 2 3579 3662 127204023 127204106 4.970000e-24 122
13 TraesCS1A01G211300 chr7D 91.304 92 3 3 3576 3662 187020125 187020034 1.790000e-23 121
14 TraesCS1A01G211300 chr6A 91.111 90 4 3 3573 3662 18477188 18477273 6.420000e-23 119


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 TraesCS1A01G211300 chr1A 374166533 374170194 3661 True 6763 6763 100.000 1 3662 1 chr1A.!!$R1 3661
1 TraesCS1A01G211300 chr1D 299808854 299813669 4815 True 2521 4543 91.211 1 3595 2 chr1D.!!$R1 3594
2 TraesCS1A01G211300 chr1B 404300123 404302538 2415 True 3168 3168 90.363 646 3094 1 chr1B.!!$R2 2448
3 TraesCS1A01G211300 chr1B 404308897 404309549 652 True 795 795 88.756 1 658 1 chr1B.!!$R3 657

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
517 1773 0.109723 TCCCTTTCTCCCACCAAACG 59.890 55.0 0.0 0.0 0.0 3.60 F
518 1774 0.179001 CCCTTTCTCCCACCAAACGT 60.179 55.0 0.0 0.0 0.0 3.99 F
2155 3437 0.234884 CGGTTCCTGCACGTTTTCTC 59.765 55.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 3237 0.761802 GCTGTTAGATGGAGGGAGGG 59.238 60.000 0.00 0.0 0.0 4.30 R
2167 3477 1.001974 CAGTCACACCGGAATCAAGGA 59.998 52.381 9.46 0.0 0.0 3.36 R
3631 4970 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.0 43.2 4.57 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
31 32 1.719780 GTTCGTTAGTTGGTCTCTGCG 59.280 52.381 0.00 0.00 0.00 5.18
55 56 1.302752 GAGTGGCCACATGTGCAGA 60.303 57.895 36.39 2.58 0.00 4.26
83 84 6.569179 TTGAAGAAATAAAAAGAGGGGTCG 57.431 37.500 0.00 0.00 0.00 4.79
137 145 0.179124 GAGAGCTGACACCCGATCAC 60.179 60.000 0.00 0.00 0.00 3.06
261 269 1.878953 ATGGTTCGCAACGTCTTTCT 58.121 45.000 0.00 0.00 0.00 2.52
285 293 2.892425 CCGAATCAGAGGCCACGC 60.892 66.667 5.01 0.00 0.00 5.34
326 334 6.306987 ACACACCATTTCTCTCACCTAAAAT 58.693 36.000 0.00 0.00 0.00 1.82
336 344 6.349300 TCTCTCACCTAAAATATGCCAGTTC 58.651 40.000 0.00 0.00 0.00 3.01
337 345 5.437060 TCTCACCTAAAATATGCCAGTTCC 58.563 41.667 0.00 0.00 0.00 3.62
342 350 5.829924 ACCTAAAATATGCCAGTTCCATCTG 59.170 40.000 0.00 0.00 35.45 2.90
359 367 1.005867 TGTCCTAACGTTGACGCCC 60.006 57.895 11.99 0.00 44.43 6.13
365 373 0.320073 TAACGTTGACGCCCCTCTTG 60.320 55.000 11.99 0.00 44.43 3.02
416 1672 2.222819 GGTACGAGAAGAAATTGCAGCG 60.223 50.000 0.00 0.00 0.00 5.18
487 1743 1.188871 TCCACAGATGGCGTACACCA 61.189 55.000 4.80 4.80 46.80 4.17
511 1767 0.912006 AGCCTCTCCCTTTCTCCCAC 60.912 60.000 0.00 0.00 0.00 4.61
512 1768 1.916206 GCCTCTCCCTTTCTCCCACC 61.916 65.000 0.00 0.00 0.00 4.61
513 1769 0.547712 CCTCTCCCTTTCTCCCACCA 60.548 60.000 0.00 0.00 0.00 4.17
514 1770 1.362224 CTCTCCCTTTCTCCCACCAA 58.638 55.000 0.00 0.00 0.00 3.67
515 1771 1.705186 CTCTCCCTTTCTCCCACCAAA 59.295 52.381 0.00 0.00 0.00 3.28
516 1772 1.423921 TCTCCCTTTCTCCCACCAAAC 59.576 52.381 0.00 0.00 0.00 2.93
517 1773 0.109723 TCCCTTTCTCCCACCAAACG 59.890 55.000 0.00 0.00 0.00 3.60
518 1774 0.179001 CCCTTTCTCCCACCAAACGT 60.179 55.000 0.00 0.00 0.00 3.99
537 1793 1.901464 CCAAACCCCACCACTTCCG 60.901 63.158 0.00 0.00 0.00 4.30
564 1820 2.747396 TGCATCTGGAAAAACATGCC 57.253 45.000 0.00 0.00 40.86 4.40
611 1871 3.792956 GTGCACACAATCAAAAGTCACAG 59.207 43.478 13.17 0.00 0.00 3.66
658 1918 7.226757 TGAGTACGAGTAACTATTAGACGTG 57.773 40.000 0.00 0.00 32.97 4.49
673 1933 0.670546 ACGTGCGACCAGGAAAGATG 60.671 55.000 0.00 0.00 0.00 2.90
693 1953 1.323271 TGAGGAGATGGTCGACAGGC 61.323 60.000 18.91 5.27 0.00 4.85
785 2045 3.493767 AAGAACCACTTCTTCTCCACC 57.506 47.619 0.00 0.00 42.14 4.61
786 2046 2.695585 AGAACCACTTCTTCTCCACCT 58.304 47.619 0.00 0.00 32.29 4.00
787 2047 3.858135 AGAACCACTTCTTCTCCACCTA 58.142 45.455 0.00 0.00 32.29 3.08
788 2048 3.579151 AGAACCACTTCTTCTCCACCTAC 59.421 47.826 0.00 0.00 32.29 3.18
789 2049 2.972348 ACCACTTCTTCTCCACCTACA 58.028 47.619 0.00 0.00 0.00 2.74
790 2050 3.521727 ACCACTTCTTCTCCACCTACAT 58.478 45.455 0.00 0.00 0.00 2.29
791 2051 3.261897 ACCACTTCTTCTCCACCTACATG 59.738 47.826 0.00 0.00 0.00 3.21
792 2052 3.369892 CCACTTCTTCTCCACCTACATGG 60.370 52.174 0.00 0.00 41.57 3.66
843 2103 3.079578 AGTGTCCTTGTGATGCATCTTG 58.920 45.455 26.32 13.39 0.00 3.02
878 2140 2.224402 CCCTAGTCTTTAGGATGCTGCC 60.224 54.545 0.00 0.00 36.85 4.85
899 2161 1.519234 CACCGCGCTTGCTCTGATA 60.519 57.895 5.56 0.00 36.08 2.15
1257 2522 4.315588 GCACTGAGCAGCAAGGAT 57.684 55.556 0.00 0.00 44.79 3.24
1266 2531 0.807496 GCAGCAAGGATCAGAACACC 59.193 55.000 0.00 0.00 0.00 4.16
1447 2712 1.144716 GCGCTGAGGGACATGATGA 59.855 57.895 0.00 0.00 0.00 2.92
1448 2713 0.250209 GCGCTGAGGGACATGATGAT 60.250 55.000 0.00 0.00 0.00 2.45
1556 2821 3.798954 CTCGGATGGAGAAGGCCGC 62.799 68.421 0.00 0.00 46.23 6.53
1638 2903 5.414360 CGAGTATATTGATGAGGTGATGGG 58.586 45.833 0.00 0.00 0.00 4.00
1649 2914 1.304282 GTGATGGGTGGTCATGGCT 59.696 57.895 0.00 0.00 0.00 4.75
1650 2915 0.323725 GTGATGGGTGGTCATGGCTT 60.324 55.000 0.00 0.00 0.00 4.35
1652 2917 1.000739 ATGGGTGGTCATGGCTTGG 59.999 57.895 0.00 0.00 0.00 3.61
1653 2918 3.070576 GGGTGGTCATGGCTTGGC 61.071 66.667 0.00 0.00 0.00 4.52
1654 2919 2.283101 GGTGGTCATGGCTTGGCA 60.283 61.111 7.32 0.00 0.00 4.92
1655 2920 2.639327 GGTGGTCATGGCTTGGCAC 61.639 63.158 7.32 0.00 0.00 5.01
1656 2921 2.672651 TGGTCATGGCTTGGCACG 60.673 61.111 7.32 0.00 0.00 5.34
1657 2922 4.120331 GGTCATGGCTTGGCACGC 62.120 66.667 7.54 7.54 0.00 5.34
1658 2923 4.465512 GTCATGGCTTGGCACGCG 62.466 66.667 3.53 3.53 0.00 6.01
1660 2925 4.764336 CATGGCTTGGCACGCGTG 62.764 66.667 34.01 34.01 0.00 5.34
1821 3086 2.994995 TCGCACCATGGGAGTCGT 60.995 61.111 18.09 0.00 34.23 4.34
1823 3088 2.390599 CGCACCATGGGAGTCGTTG 61.391 63.158 18.09 4.15 31.21 4.10
1826 3091 0.391661 CACCATGGGAGTCGTTGGAG 60.392 60.000 18.09 0.98 0.00 3.86
1827 3092 1.221840 CCATGGGAGTCGTTGGAGG 59.778 63.158 2.85 0.00 0.00 4.30
1919 3184 2.438434 GGCGCCCAAGTATGCAGT 60.438 61.111 18.11 0.00 0.00 4.40
1934 3199 1.144057 CAGTCGCACTCCCCCATAC 59.856 63.158 0.00 0.00 0.00 2.39
1935 3200 1.305802 AGTCGCACTCCCCCATACA 60.306 57.895 0.00 0.00 0.00 2.29
1936 3201 1.153429 GTCGCACTCCCCCATACAC 60.153 63.158 0.00 0.00 0.00 2.90
1937 3202 1.610967 TCGCACTCCCCCATACACA 60.611 57.895 0.00 0.00 0.00 3.72
1938 3203 1.153369 CGCACTCCCCCATACACAG 60.153 63.158 0.00 0.00 0.00 3.66
1939 3204 1.613317 CGCACTCCCCCATACACAGA 61.613 60.000 0.00 0.00 0.00 3.41
1946 3216 3.264897 CCATACACAGAGCGCGCC 61.265 66.667 30.33 19.60 0.00 6.53
1966 3236 2.616842 CCCACACGCTTGTTTACTTCTT 59.383 45.455 0.00 0.00 31.66 2.52
1967 3237 3.303791 CCCACACGCTTGTTTACTTCTTC 60.304 47.826 0.00 0.00 31.66 2.87
1969 3239 2.876550 ACACGCTTGTTTACTTCTTCCC 59.123 45.455 0.00 0.00 28.43 3.97
1970 3240 3.139077 CACGCTTGTTTACTTCTTCCCT 58.861 45.455 0.00 0.00 0.00 4.20
1981 3251 2.592512 ACTTCTTCCCTCCCTCCATCTA 59.407 50.000 0.00 0.00 0.00 1.98
2119 3399 1.301009 TACGCACGCCACAATCACA 60.301 52.632 0.00 0.00 0.00 3.58
2123 3403 1.208358 CACGCCACAATCACAGCAG 59.792 57.895 0.00 0.00 0.00 4.24
2151 3433 2.593436 CCCGGTTCCTGCACGTTT 60.593 61.111 0.00 0.00 0.00 3.60
2155 3437 0.234884 CGGTTCCTGCACGTTTTCTC 59.765 55.000 0.00 0.00 0.00 2.87
2156 3466 1.594331 GGTTCCTGCACGTTTTCTCT 58.406 50.000 0.00 0.00 0.00 3.10
2168 3478 4.521892 CGTTTTCTCTACGTACGTTGTC 57.478 45.455 27.92 10.78 34.47 3.18
2174 3484 4.005650 TCTCTACGTACGTTGTCCTTGAT 58.994 43.478 27.92 0.00 0.00 2.57
2192 3502 1.308069 ATTCCGGTGTGACTGCATGC 61.308 55.000 11.82 11.82 0.00 4.06
2503 3817 7.070798 GTCGACTAGTTGCACTATATCTACAC 58.929 42.308 8.70 0.00 29.08 2.90
2658 3972 2.436115 GCTTCCGGGTGGTGCTAC 60.436 66.667 0.00 0.00 36.30 3.58
2717 4031 3.402628 TTAAGATAAGATGCCGGGCTC 57.597 47.619 21.46 14.63 0.00 4.70
2873 4191 4.023536 CGTGTGCTGTAAATAGTGGGTTTT 60.024 41.667 0.00 0.00 0.00 2.43
2891 4209 4.449131 GTTTTCTGGGTAGGTAGGCATAC 58.551 47.826 0.00 0.00 0.00 2.39
2900 4218 6.171213 GGGTAGGTAGGCATACATTTACATC 58.829 44.000 11.12 3.39 33.92 3.06
2902 4220 4.894784 AGGTAGGCATACATTTACATCCG 58.105 43.478 11.12 0.00 33.21 4.18
2915 4233 8.974060 ACATTTACATCCGGATACTGTAATTT 57.026 30.769 23.21 14.46 35.82 1.82
2916 4234 8.836413 ACATTTACATCCGGATACTGTAATTTG 58.164 33.333 23.21 22.95 35.82 2.32
2917 4235 9.051679 CATTTACATCCGGATACTGTAATTTGA 57.948 33.333 23.21 12.95 35.82 2.69
2918 4236 9.621629 ATTTACATCCGGATACTGTAATTTGAA 57.378 29.630 23.21 12.67 35.82 2.69
2919 4237 6.920569 ACATCCGGATACTGTAATTTGAAC 57.079 37.500 18.63 0.00 0.00 3.18
2920 4238 5.820947 ACATCCGGATACTGTAATTTGAACC 59.179 40.000 18.63 0.00 0.00 3.62
2921 4239 5.423704 TCCGGATACTGTAATTTGAACCA 57.576 39.130 0.00 0.00 0.00 3.67
2922 4240 5.996644 TCCGGATACTGTAATTTGAACCAT 58.003 37.500 0.00 0.00 0.00 3.55
2923 4241 6.419791 TCCGGATACTGTAATTTGAACCATT 58.580 36.000 0.00 0.00 0.00 3.16
2924 4242 6.540914 TCCGGATACTGTAATTTGAACCATTC 59.459 38.462 0.00 0.00 0.00 2.67
2925 4243 6.317642 CCGGATACTGTAATTTGAACCATTCA 59.682 38.462 0.00 0.00 38.04 2.57
2990 4324 1.559368 CTGGGGCATGGAAAACATCA 58.441 50.000 0.00 0.00 37.84 3.07
2994 4328 3.272581 GGGGCATGGAAAACATCAAATG 58.727 45.455 0.00 0.00 37.84 2.32
3010 4344 3.689161 TCAAATGCTATCCCTCAAACGTG 59.311 43.478 0.00 0.00 0.00 4.49
3014 4348 0.739462 CTATCCCTCAAACGTGCGCA 60.739 55.000 5.66 5.66 0.00 6.09
3019 4353 1.011684 CTCAAACGTGCGCAAACGA 60.012 52.632 24.76 11.00 46.49 3.85
3020 4354 0.986874 CTCAAACGTGCGCAAACGAG 60.987 55.000 24.76 16.07 46.49 4.18
3051 4386 1.199097 CAAATTCGGCAAAGCGGTAGT 59.801 47.619 0.00 0.00 0.00 2.73
3081 4416 1.078143 GCTTTCCCGACATCTGCCT 60.078 57.895 0.00 0.00 0.00 4.75
3088 4423 0.107456 CCGACATCTGCCTAGCCAAT 59.893 55.000 0.00 0.00 0.00 3.16
3094 4429 4.088634 ACATCTGCCTAGCCAATCAAAAA 58.911 39.130 0.00 0.00 0.00 1.94
3098 4433 3.172339 TGCCTAGCCAATCAAAAACCAT 58.828 40.909 0.00 0.00 0.00 3.55
3101 4436 4.747810 CCTAGCCAATCAAAAACCATCAC 58.252 43.478 0.00 0.00 0.00 3.06
3112 4447 4.540153 CCATCACGTGGGACATCC 57.460 61.111 17.00 0.00 44.79 3.51
3114 4449 1.521457 CATCACGTGGGACATCCGG 60.521 63.158 17.00 0.00 44.52 5.14
3122 4457 3.793888 GGACATCCGGACACCCCC 61.794 72.222 6.12 0.00 0.00 5.40
3138 4473 3.771160 CCCGTCCCTCCTCAACCG 61.771 72.222 0.00 0.00 0.00 4.44
3142 4477 2.363795 TCCCTCCTCAACCGCGAT 60.364 61.111 8.23 0.00 0.00 4.58
3146 4481 0.673985 CCTCCTCAACCGCGATATGA 59.326 55.000 8.23 8.03 0.00 2.15
3152 4487 2.866156 CTCAACCGCGATATGAACATGT 59.134 45.455 8.23 0.00 0.00 3.21
3168 4503 6.475504 TGAACATGTGTAGATGGATGAAACT 58.524 36.000 0.00 0.00 0.00 2.66
3196 4531 9.584008 GATAAATATGGGATAGCATTGGATGAT 57.416 33.333 0.00 0.00 0.00 2.45
3213 4548 1.988107 TGATTCCATCCCCTATCCTGC 59.012 52.381 0.00 0.00 0.00 4.85
3219 4558 1.130054 ATCCCCTATCCTGCGCACAT 61.130 55.000 5.66 3.83 0.00 3.21
3245 4584 1.933115 GACATGCCCGCGGACATTTT 61.933 55.000 30.73 16.34 0.00 1.82
3252 4591 2.804931 GCGGACATTTTGCGGTGC 60.805 61.111 0.00 0.00 39.95 5.01
3253 4592 2.953821 CGGACATTTTGCGGTGCT 59.046 55.556 0.00 0.00 34.92 4.40
3259 4598 2.726241 GACATTTTGCGGTGCTCTTTTC 59.274 45.455 0.00 0.00 0.00 2.29
3260 4599 2.100584 ACATTTTGCGGTGCTCTTTTCA 59.899 40.909 0.00 0.00 0.00 2.69
3269 4608 3.219281 GGTGCTCTTTTCAGGGTTTGTA 58.781 45.455 0.00 0.00 0.00 2.41
3273 4612 4.280677 TGCTCTTTTCAGGGTTTGTATTGG 59.719 41.667 0.00 0.00 0.00 3.16
3274 4613 4.522789 GCTCTTTTCAGGGTTTGTATTGGA 59.477 41.667 0.00 0.00 0.00 3.53
3286 4625 5.437060 GTTTGTATTGGAGATGCCCTTAGA 58.563 41.667 0.00 0.00 34.97 2.10
3292 4631 2.103094 TGGAGATGCCCTTAGATCGTTG 59.897 50.000 0.00 0.00 34.97 4.10
3318 4657 4.179579 GGCCTGCCGCGTGAAATC 62.180 66.667 4.92 0.00 38.94 2.17
3323 4662 4.160635 GCCGCGTGAAATCCACCG 62.161 66.667 4.92 0.00 42.76 4.94
3366 4705 5.848036 GCATAACTAGCTTTGCATATGTTCG 59.152 40.000 4.29 0.00 35.22 3.95
3386 4725 8.547967 TGTTCGAACTTCAATTTAGATAGCTT 57.452 30.769 27.32 0.00 0.00 3.74
3395 4734 6.179756 TCAATTTAGATAGCTTCAAGCACCA 58.820 36.000 13.10 0.00 45.56 4.17
3398 4737 3.423539 AGATAGCTTCAAGCACCACAA 57.576 42.857 13.10 0.00 45.56 3.33
3416 4755 7.523052 GCACCACAACTAAATTAAATCACCTCA 60.523 37.037 0.00 0.00 0.00 3.86
3454 4793 6.211184 TCCTCAACAAATGCACTTCCAATATT 59.789 34.615 0.00 0.00 0.00 1.28
3465 4804 5.335897 GCACTTCCAATATTCAGTGAAAGCA 60.336 40.000 10.14 0.00 39.25 3.91
3539 4878 5.403897 AATTAAATCATCACGGTAGCACG 57.596 39.130 0.00 0.00 40.31 5.34
3587 4926 2.672996 ATTCACACGTGCAGGGGC 60.673 61.111 17.22 0.00 41.68 5.80
3597 4936 2.034687 GCAGGGGCAGACACATGT 59.965 61.111 0.00 0.00 40.72 3.21
3598 4937 1.604593 GCAGGGGCAGACACATGTT 60.605 57.895 0.00 0.00 40.72 2.71
3599 4938 1.870055 GCAGGGGCAGACACATGTTG 61.870 60.000 0.00 0.00 40.72 3.33
3600 4939 1.075482 AGGGGCAGACACATGTTGG 59.925 57.895 0.00 0.00 0.00 3.77
3601 4940 1.978617 GGGGCAGACACATGTTGGG 60.979 63.158 0.00 0.00 0.00 4.12
3602 4941 1.074775 GGGCAGACACATGTTGGGA 59.925 57.895 0.00 0.00 0.00 4.37
3603 4942 0.539438 GGGCAGACACATGTTGGGAA 60.539 55.000 0.00 0.00 0.00 3.97
3604 4943 1.327303 GGCAGACACATGTTGGGAAA 58.673 50.000 0.00 0.00 0.00 3.13
3605 4944 1.000274 GGCAGACACATGTTGGGAAAC 60.000 52.381 0.00 0.00 0.00 2.78
3606 4945 1.334960 GCAGACACATGTTGGGAAACG 60.335 52.381 0.00 0.00 0.00 3.60
3607 4946 1.946768 CAGACACATGTTGGGAAACGT 59.053 47.619 0.00 0.00 0.00 3.99
3608 4947 3.135225 CAGACACATGTTGGGAAACGTA 58.865 45.455 0.00 0.00 0.00 3.57
3609 4948 3.186409 CAGACACATGTTGGGAAACGTAG 59.814 47.826 0.00 0.00 0.00 3.51
3611 4950 4.039488 AGACACATGTTGGGAAACGTAGTA 59.961 41.667 0.00 0.00 45.00 1.82
3612 4951 4.706035 ACACATGTTGGGAAACGTAGTAA 58.294 39.130 0.00 0.00 45.00 2.24
3613 4952 5.310451 ACACATGTTGGGAAACGTAGTAAT 58.690 37.500 0.00 0.00 45.00 1.89
3614 4953 5.766174 ACACATGTTGGGAAACGTAGTAATT 59.234 36.000 0.00 0.00 45.00 1.40
3615 4954 6.263617 ACACATGTTGGGAAACGTAGTAATTT 59.736 34.615 0.00 0.00 45.00 1.82
3616 4955 6.799925 CACATGTTGGGAAACGTAGTAATTTC 59.200 38.462 0.00 0.00 45.00 2.17
3617 4956 6.487331 ACATGTTGGGAAACGTAGTAATTTCA 59.513 34.615 0.00 0.00 45.00 2.69
3618 4957 6.939132 TGTTGGGAAACGTAGTAATTTCAA 57.061 33.333 9.32 0.00 45.00 2.69
3619 4958 7.330900 TGTTGGGAAACGTAGTAATTTCAAA 57.669 32.000 9.32 2.83 45.00 2.69
3620 4959 7.769220 TGTTGGGAAACGTAGTAATTTCAAAA 58.231 30.769 9.32 2.58 45.00 2.44
3621 4960 8.248945 TGTTGGGAAACGTAGTAATTTCAAAAA 58.751 29.630 9.32 0.83 45.00 1.94
3638 4977 2.325509 AAAATTTCCTACGCACACGC 57.674 45.000 0.00 0.00 45.53 5.34
3639 4978 1.231221 AAATTTCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
3640 4979 1.231221 AATTTCCTACGCACACGCAA 58.769 45.000 0.00 0.00 45.53 4.85
3641 4980 0.796312 ATTTCCTACGCACACGCAAG 59.204 50.000 0.00 0.00 45.53 4.01
3642 4981 0.249531 TTTCCTACGCACACGCAAGA 60.250 50.000 0.00 0.00 45.53 3.02
3643 4982 0.037697 TTCCTACGCACACGCAAGAT 60.038 50.000 0.00 0.00 45.53 2.40
3644 4983 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
3645 4984 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
3646 4985 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
3647 4986 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
3648 4987 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
3649 4988 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
3650 4989 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
3651 4990 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
3652 4991 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
3653 4992 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
3654 4993 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
3655 4994 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
3656 4995 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
3657 4996 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
3658 4997 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
3659 4998 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
3660 4999 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
3661 5000 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 4.452733 CCTGGCGAACGACCCCTC 62.453 72.222 0.00 0.00 0.00 4.30
81 82 3.949885 TAGCTCCCCTGGCGAACGA 62.950 63.158 0.00 0.00 34.52 3.85
82 83 3.432051 CTAGCTCCCCTGGCGAACG 62.432 68.421 0.00 0.00 34.52 3.95
83 84 1.614241 TTCTAGCTCCCCTGGCGAAC 61.614 60.000 0.00 0.00 34.52 3.95
93 96 4.553156 CGACTCGTTCACTATTCTAGCTCC 60.553 50.000 0.00 0.00 0.00 4.70
137 145 1.340658 CGTCTGATTCTGGTGACACG 58.659 55.000 0.00 0.00 35.60 4.49
261 269 1.735376 GCCTCTGATTCGGCCGTAGA 61.735 60.000 27.15 21.36 40.43 2.59
326 334 2.481441 AGGACAGATGGAACTGGCATA 58.519 47.619 0.00 0.00 46.67 3.14
336 344 2.259618 CGTCAACGTTAGGACAGATGG 58.740 52.381 16.28 0.00 33.66 3.51
337 345 1.654105 GCGTCAACGTTAGGACAGATG 59.346 52.381 16.28 8.67 42.22 2.90
342 350 1.739196 GGGGCGTCAACGTTAGGAC 60.739 63.158 0.00 4.46 42.22 3.85
416 1672 3.105157 CAATTTGGCCGTGCGCAC 61.105 61.111 30.42 30.42 40.31 5.34
470 1726 1.361668 GCTGGTGTACGCCATCTGTG 61.362 60.000 27.72 16.71 37.96 3.66
487 1743 0.341609 AGAAAGGGAGAGGCTAGGCT 59.658 55.000 20.36 20.36 0.00 4.58
511 1767 1.737201 GTGGGGTTTGGACGTTTGG 59.263 57.895 0.00 0.00 0.00 3.28
512 1768 1.038130 TGGTGGGGTTTGGACGTTTG 61.038 55.000 0.00 0.00 0.00 2.93
513 1769 1.038681 GTGGTGGGGTTTGGACGTTT 61.039 55.000 0.00 0.00 0.00 3.60
514 1770 1.454295 GTGGTGGGGTTTGGACGTT 60.454 57.895 0.00 0.00 0.00 3.99
515 1771 1.928714 AAGTGGTGGGGTTTGGACGT 61.929 55.000 0.00 0.00 0.00 4.34
516 1772 1.152839 AAGTGGTGGGGTTTGGACG 60.153 57.895 0.00 0.00 0.00 4.79
517 1773 0.826256 GGAAGTGGTGGGGTTTGGAC 60.826 60.000 0.00 0.00 0.00 4.02
518 1774 1.539665 GGAAGTGGTGGGGTTTGGA 59.460 57.895 0.00 0.00 0.00 3.53
564 1820 4.726416 CATCACCATGGAAAGTTCTTTCG 58.274 43.478 21.47 7.46 0.00 3.46
611 1871 4.264253 TCACACCATCAGATCATTTCACC 58.736 43.478 0.00 0.00 0.00 4.02
658 1918 1.363744 CTCACATCTTTCCTGGTCGC 58.636 55.000 0.00 0.00 0.00 5.19
673 1933 0.457851 CCTGTCGACCATCTCCTCAC 59.542 60.000 14.12 0.00 0.00 3.51
693 1953 4.478206 ACCAGATGCCATATATTCTCGG 57.522 45.455 0.00 0.00 0.00 4.63
776 2036 5.719085 AGATATAGCCATGTAGGTGGAGAAG 59.281 44.000 0.00 0.00 42.02 2.85
785 2045 4.399618 ACGCCACTAGATATAGCCATGTAG 59.600 45.833 0.00 0.00 0.00 2.74
786 2046 4.341487 ACGCCACTAGATATAGCCATGTA 58.659 43.478 0.00 0.00 0.00 2.29
787 2047 3.165875 ACGCCACTAGATATAGCCATGT 58.834 45.455 0.00 0.00 0.00 3.21
788 2048 3.876274 ACGCCACTAGATATAGCCATG 57.124 47.619 0.00 0.00 0.00 3.66
789 2049 4.891992 AAACGCCACTAGATATAGCCAT 57.108 40.909 0.00 0.00 0.00 4.40
790 2050 4.377021 CAAAACGCCACTAGATATAGCCA 58.623 43.478 0.00 0.00 0.00 4.75
791 2051 3.746492 CCAAAACGCCACTAGATATAGCC 59.254 47.826 0.00 0.00 0.00 3.93
792 2052 4.628074 TCCAAAACGCCACTAGATATAGC 58.372 43.478 0.00 0.00 0.00 2.97
843 2103 1.826096 ACTAGGGGAGAAGAAGAACGC 59.174 52.381 0.00 0.00 0.00 4.84
845 2105 5.748670 AAAGACTAGGGGAGAAGAAGAAC 57.251 43.478 0.00 0.00 0.00 3.01
853 2113 3.207777 AGCATCCTAAAGACTAGGGGAGA 59.792 47.826 0.00 0.00 35.45 3.71
855 2115 3.309296 CAGCATCCTAAAGACTAGGGGA 58.691 50.000 0.00 0.00 35.45 4.81
878 2140 3.349006 AGAGCAAGCGCGGTGTTG 61.349 61.111 13.41 8.88 45.49 3.33
899 2161 6.699575 AATAAAATTAAGCTGCTCCGATGT 57.300 33.333 1.00 0.00 0.00 3.06
995 2260 2.728817 CGGCGGACTCCATAGACC 59.271 66.667 0.00 0.00 34.59 3.85
1447 2712 2.770048 CCCCTCCCTCTTCCGCAT 60.770 66.667 0.00 0.00 0.00 4.73
1448 2713 4.332543 ACCCCTCCCTCTTCCGCA 62.333 66.667 0.00 0.00 0.00 5.69
1638 2903 2.964978 GTGCCAAGCCATGACCAC 59.035 61.111 0.00 0.00 0.00 4.16
1796 3061 4.864334 CATGGTGCGAGGAGGGGC 62.864 72.222 0.00 0.00 0.00 5.80
1919 3184 1.610967 TGTGTATGGGGGAGTGCGA 60.611 57.895 0.00 0.00 0.00 5.10
1946 3216 3.303791 GGAAGAAGTAAACAAGCGTGTGG 60.304 47.826 5.91 0.00 38.27 4.17
1952 3222 3.082548 GGGAGGGAAGAAGTAAACAAGC 58.917 50.000 0.00 0.00 0.00 4.01
1966 3236 1.692762 GCTGTTAGATGGAGGGAGGGA 60.693 57.143 0.00 0.00 0.00 4.20
1967 3237 0.761802 GCTGTTAGATGGAGGGAGGG 59.238 60.000 0.00 0.00 0.00 4.30
1969 3239 2.896685 CCTAGCTGTTAGATGGAGGGAG 59.103 54.545 0.00 0.00 0.00 4.30
1970 3240 2.426414 CCCTAGCTGTTAGATGGAGGGA 60.426 54.545 6.58 0.00 44.27 4.20
1981 3251 1.073199 GTGTGGTGCCCTAGCTGTT 59.927 57.895 0.00 0.00 40.80 3.16
1995 3265 1.208358 CGACCTGCATGCAAGTGTG 59.792 57.895 26.13 14.24 0.00 3.82
2059 3339 2.771639 TTGGCCTCGATCTCGGTCG 61.772 63.158 3.32 0.00 42.74 4.79
2086 3366 1.514873 CGTACCGTGGCGTAGAACC 60.515 63.158 0.00 0.00 0.00 3.62
2110 3390 6.088824 GGAAACTTAATCTGCTGTGATTGTG 58.911 40.000 9.34 5.78 37.27 3.33
2119 3399 1.633945 ACCGGGGAAACTTAATCTGCT 59.366 47.619 6.32 0.00 0.00 4.24
2123 3403 3.014623 CAGGAACCGGGGAAACTTAATC 58.985 50.000 6.32 0.00 0.00 1.75
2151 3433 3.814842 TCAAGGACAACGTACGTAGAGAA 59.185 43.478 23.12 0.00 0.00 2.87
2155 3437 3.855950 GGAATCAAGGACAACGTACGTAG 59.144 47.826 23.12 6.10 0.00 3.51
2156 3466 3.670359 CGGAATCAAGGACAACGTACGTA 60.670 47.826 23.12 3.16 0.00 3.57
2165 3475 1.052617 TCACACCGGAATCAAGGACA 58.947 50.000 9.46 0.00 0.00 4.02
2166 3476 1.002087 AGTCACACCGGAATCAAGGAC 59.998 52.381 9.46 5.77 0.00 3.85
2167 3477 1.001974 CAGTCACACCGGAATCAAGGA 59.998 52.381 9.46 0.00 0.00 3.36
2168 3478 1.442769 CAGTCACACCGGAATCAAGG 58.557 55.000 9.46 0.00 0.00 3.61
2174 3484 1.965930 GCATGCAGTCACACCGGAA 60.966 57.895 14.21 0.00 0.00 4.30
2235 3545 3.435186 GTCCTTGCAAGCTCGCCC 61.435 66.667 21.43 0.66 0.00 6.13
2327 3637 1.725066 AAAAACGACGTGCCACCAG 59.275 52.632 0.00 0.00 0.00 4.00
2446 3756 7.522236 GCACTTAGAAAAGCAAAGGAGTATTGT 60.522 37.037 0.00 0.00 36.05 2.71
2520 3834 2.878406 CACCGGACTCACACAAGAATTT 59.122 45.455 9.46 0.00 0.00 1.82
2568 3882 2.342910 TCGCCTGAACTAAGTTCGTC 57.657 50.000 0.00 0.00 44.55 4.20
2658 3972 4.149571 CGTGTGAGACTGATCAAAACTCAG 59.850 45.833 19.45 9.77 44.60 3.35
2833 4151 0.737019 ACGGTCGTTCAACACACGTT 60.737 50.000 0.00 0.00 38.81 3.99
2834 4152 1.153784 ACGGTCGTTCAACACACGT 60.154 52.632 0.00 0.00 38.81 4.49
2835 4153 1.271549 CACGGTCGTTCAACACACG 59.728 57.895 0.00 0.00 39.08 4.49
2873 4191 3.630625 ATGTATGCCTACCTACCCAGA 57.369 47.619 0.00 0.00 0.00 3.86
2891 4209 9.051679 TCAAATTACAGTATCCGGATGTAAATG 57.948 33.333 27.55 24.86 41.34 2.32
2900 4218 6.317642 TGAATGGTTCAAATTACAGTATCCGG 59.682 38.462 0.00 0.00 36.59 5.14
2923 4241 6.094881 GGTCTCCGAATGGTTCAAATAATTGA 59.905 38.462 0.00 0.00 43.70 2.57
2924 4242 6.127758 TGGTCTCCGAATGGTTCAAATAATTG 60.128 38.462 0.00 0.00 35.70 2.32
2925 4243 5.949354 TGGTCTCCGAATGGTTCAAATAATT 59.051 36.000 0.00 0.00 36.30 1.40
2926 4244 5.505780 TGGTCTCCGAATGGTTCAAATAAT 58.494 37.500 0.00 0.00 36.30 1.28
2927 4245 4.912586 TGGTCTCCGAATGGTTCAAATAA 58.087 39.130 0.00 0.00 36.30 1.40
2928 4246 4.561500 TGGTCTCCGAATGGTTCAAATA 57.438 40.909 0.00 0.00 36.30 1.40
2929 4247 3.433306 TGGTCTCCGAATGGTTCAAAT 57.567 42.857 0.00 0.00 36.30 2.32
2930 4248 2.940994 TGGTCTCCGAATGGTTCAAA 57.059 45.000 0.00 0.00 36.30 2.69
2954 4288 0.747283 CAGGCCATGGCAGAGTCTTC 60.747 60.000 36.56 17.44 44.11 2.87
2990 4324 2.423538 GCACGTTTGAGGGATAGCATTT 59.576 45.455 0.00 0.00 0.00 2.32
2994 4328 2.006772 CGCACGTTTGAGGGATAGC 58.993 57.895 0.00 0.00 0.00 2.97
3019 4353 1.296056 CGAATTTGAACGCCCGGACT 61.296 55.000 0.73 0.00 0.00 3.85
3020 4354 1.133869 CGAATTTGAACGCCCGGAC 59.866 57.895 0.73 0.00 0.00 4.79
3026 4360 0.434628 GCTTTGCCGAATTTGAACGC 59.565 50.000 0.00 0.00 0.00 4.84
3030 4364 1.466950 CTACCGCTTTGCCGAATTTGA 59.533 47.619 0.00 0.00 0.00 2.69
3081 4416 3.823873 ACGTGATGGTTTTTGATTGGCTA 59.176 39.130 0.00 0.00 0.00 3.93
3098 4433 2.283316 TCCGGATGTCCCACGTGA 60.283 61.111 19.30 0.00 34.14 4.35
3101 4436 2.125673 GTGTCCGGATGTCCCACG 60.126 66.667 7.81 0.00 34.14 4.94
3122 4457 4.452733 GCGGTTGAGGAGGGACGG 62.453 72.222 0.00 0.00 0.00 4.79
3138 4473 5.230182 TCCATCTACACATGTTCATATCGC 58.770 41.667 0.00 0.00 0.00 4.58
3142 4477 8.267183 AGTTTCATCCATCTACACATGTTCATA 58.733 33.333 0.00 0.00 0.00 2.15
3146 4481 5.649395 CCAGTTTCATCCATCTACACATGTT 59.351 40.000 0.00 0.00 0.00 2.71
3168 4503 7.282689 TCCAATGCTATCCCATATTTATCCA 57.717 36.000 0.00 0.00 0.00 3.41
3196 4531 1.768684 GCGCAGGATAGGGGATGGAA 61.769 60.000 0.30 0.00 0.00 3.53
3201 4536 1.766059 ATGTGCGCAGGATAGGGGA 60.766 57.895 12.22 0.00 0.00 4.81
3230 4569 4.049640 GCAAAATGTCCGCGGGCA 62.050 61.111 37.37 37.37 0.00 5.36
3237 4576 0.598065 AAGAGCACCGCAAAATGTCC 59.402 50.000 0.00 0.00 0.00 4.02
3245 4584 1.600636 CCCTGAAAAGAGCACCGCA 60.601 57.895 0.00 0.00 0.00 5.69
3249 4588 5.222631 CAATACAAACCCTGAAAAGAGCAC 58.777 41.667 0.00 0.00 0.00 4.40
3252 4591 6.003950 TCTCCAATACAAACCCTGAAAAGAG 58.996 40.000 0.00 0.00 0.00 2.85
3253 4592 5.947663 TCTCCAATACAAACCCTGAAAAGA 58.052 37.500 0.00 0.00 0.00 2.52
3259 4598 2.689983 GGCATCTCCAATACAAACCCTG 59.310 50.000 0.00 0.00 34.01 4.45
3260 4599 2.358195 GGGCATCTCCAATACAAACCCT 60.358 50.000 0.00 0.00 36.21 4.34
3269 4608 2.975489 ACGATCTAAGGGCATCTCCAAT 59.025 45.455 0.00 0.00 36.21 3.16
3273 4612 3.735237 TCAACGATCTAAGGGCATCTC 57.265 47.619 0.00 0.00 0.00 2.75
3274 4613 3.244353 CCATCAACGATCTAAGGGCATCT 60.244 47.826 0.00 0.00 0.00 2.90
3318 4657 1.949525 CATTGAATAGGAAGCCGGTGG 59.050 52.381 1.90 0.00 0.00 4.61
3366 4705 8.454106 TGCTTGAAGCTATCTAAATTGAAGTTC 58.546 33.333 18.94 0.00 42.97 3.01
3386 4725 7.865385 GTGATTTAATTTAGTTGTGGTGCTTGA 59.135 33.333 0.00 0.00 0.00 3.02
3395 4734 8.947115 GCTACTGAGGTGATTTAATTTAGTTGT 58.053 33.333 0.00 0.00 0.00 3.32
3398 4737 8.100791 TGTGCTACTGAGGTGATTTAATTTAGT 58.899 33.333 0.00 0.00 0.00 2.24
3416 4755 5.483685 TTGTTGAGGAGTTATGTGCTACT 57.516 39.130 0.00 0.00 0.00 2.57
3465 4804 3.555956 CGAACGGATGCAAAGCTAGTTAT 59.444 43.478 0.00 0.00 0.00 1.89
3539 4878 1.807142 GTGCCTTTGCTGAGGAGTTAC 59.193 52.381 9.74 0.57 39.25 2.50
3570 4909 2.672996 GCCCCTGCACGTGTGAAT 60.673 61.111 18.38 0.00 37.47 2.57
3587 4926 1.946768 ACGTTTCCCAACATGTGTCTG 59.053 47.619 0.00 0.00 32.54 3.51
3592 4931 6.487331 TGAAATTACTACGTTTCCCAACATGT 59.513 34.615 0.00 0.00 34.29 3.21
3593 4932 6.904498 TGAAATTACTACGTTTCCCAACATG 58.096 36.000 0.00 0.00 34.29 3.21
3594 4933 7.513371 TTGAAATTACTACGTTTCCCAACAT 57.487 32.000 0.00 0.00 34.29 2.71
3595 4934 6.939132 TTGAAATTACTACGTTTCCCAACA 57.061 33.333 0.00 0.00 34.29 3.33
3596 4935 8.631676 TTTTTGAAATTACTACGTTTCCCAAC 57.368 30.769 0.00 0.00 34.29 3.77
3618 4957 2.657184 GCGTGTGCGTAGGAAATTTTT 58.343 42.857 0.00 0.00 40.81 1.94
3619 4958 2.325509 GCGTGTGCGTAGGAAATTTT 57.674 45.000 0.00 0.00 40.81 1.82
3631 4970 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
3632 4971 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
3633 4972 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
3634 4973 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
3635 4974 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
3636 4975 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
3637 4976 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
3638 4977 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
3639 4978 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
3640 4979 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75


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

AutoCloner maintained by Alex Coulton.