Multiple sequence alignment - TraesCS6D01G174000

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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 TraesCS6D01G174000 chr6D 100.000 5515 0 0 1 5515 163127250 163132764 0.000000e+00 10185.0
1 TraesCS6D01G174000 chr6D 89.781 274 27 1 195 467 119992719 119992992 3.160000e-92 350.0
2 TraesCS6D01G174000 chr6D 94.000 100 4 2 2997 3095 316232293 316232391 3.440000e-32 150.0
3 TraesCS6D01G174000 chr6A 96.441 2585 67 17 2948 5515 223410776 223413352 0.000000e+00 4241.0
4 TraesCS6D01G174000 chr6A 93.220 1180 32 13 1770 2947 223409556 223410689 0.000000e+00 1692.0
5 TraesCS6D01G174000 chr6A 96.387 858 28 3 852 1706 223408541 223409398 0.000000e+00 1410.0
6 TraesCS6D01G174000 chr6A 88.953 860 61 13 1 845 223405591 223406431 0.000000e+00 1031.0
7 TraesCS6D01G174000 chr6A 89.377 273 29 0 195 467 457075316 457075044 1.470000e-90 344.0
8 TraesCS6D01G174000 chr6B 95.219 2447 67 22 3083 5515 299051416 299049006 0.000000e+00 3825.0
9 TraesCS6D01G174000 chr6B 95.966 818 32 1 898 1715 299054933 299054117 0.000000e+00 1327.0
10 TraesCS6D01G174000 chr6B 90.978 920 46 16 1770 2678 299053984 299053091 0.000000e+00 1205.0
11 TraesCS6D01G174000 chr6B 94.286 245 13 1 2700 2944 299051797 299051554 1.880000e-99 374.0
12 TraesCS6D01G174000 chr2D 86.455 347 33 1 195 541 645666038 645666370 8.730000e-98 368.0
13 TraesCS6D01G174000 chr2D 90.000 280 26 2 195 473 258812539 258812261 1.460000e-95 361.0
14 TraesCS6D01G174000 chr1B 90.110 273 27 0 195 467 453522294 453522022 6.790000e-94 355.0
15 TraesCS6D01G174000 chr1B 93.939 99 5 1 2992 3090 456268077 456268174 1.240000e-31 148.0
16 TraesCS6D01G174000 chr5B 89.744 273 28 0 195 467 638783530 638783258 3.160000e-92 350.0
17 TraesCS6D01G174000 chr5B 85.547 256 34 3 196 450 582837305 582837558 1.180000e-66 265.0
18 TraesCS6D01G174000 chr2A 89.744 273 28 0 195 467 138922710 138922438 3.160000e-92 350.0
19 TraesCS6D01G174000 chr4D 89.377 273 29 0 195 467 397696909 397697181 1.470000e-90 344.0
20 TraesCS6D01G174000 chr4D 96.512 86 3 0 3001 3086 333063357 333063272 5.760000e-30 143.0
21 TraesCS6D01G174000 chr4B 85.217 345 37 4 195 539 39046849 39047179 5.290000e-90 342.0
22 TraesCS6D01G174000 chr7D 89.412 255 26 1 213 467 4154382 4154129 2.480000e-83 320.0
23 TraesCS6D01G174000 chr7D 94.737 95 5 0 2991 3085 41837669 41837763 1.240000e-31 148.0
24 TraesCS6D01G174000 chr7D 93.000 100 7 0 2986 3085 606659457 606659358 4.450000e-31 147.0
25 TraesCS6D01G174000 chr3A 81.503 346 43 4 195 540 68806856 68807180 1.180000e-66 265.0
26 TraesCS6D01G174000 chr5D 86.735 196 24 2 273 467 475504817 475505011 3.350000e-52 217.0
27 TraesCS6D01G174000 chr5D 96.629 89 3 0 2997 3085 240428130 240428042 1.240000e-31 148.0
28 TraesCS6D01G174000 chr1D 93.204 103 5 2 2984 3085 139162818 139162919 3.440000e-32 150.0
29 TraesCS6D01G174000 chr1D 90.278 72 4 3 467 537 375984052 375983983 2.120000e-14 91.6
30 TraesCS6D01G174000 chr4A 92.308 104 5 3 2984 3085 556768057 556767955 1.600000e-30 145.0


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 TraesCS6D01G174000 chr6D 163127250 163132764 5514 False 10185.00 10185 100.00000 1 5515 1 chr6D.!!$F2 5514
1 TraesCS6D01G174000 chr6A 223405591 223413352 7761 False 2093.50 4241 93.75025 1 5515 4 chr6A.!!$F1 5514
2 TraesCS6D01G174000 chr6B 299049006 299054933 5927 True 1682.75 3825 94.11225 898 5515 4 chr6B.!!$R1 4617

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
435 436 0.390124 TAGTCGTCGCTTGGTGGTTT 59.610 50.000 0.00 0.00 0.00 3.27 F
841 855 0.394192 TTCAGAGTGCAGTGACCAGG 59.606 55.000 0.00 0.00 0.00 4.45 F
1639 3762 0.532196 GACGTCCCCATTTCGGATCC 60.532 60.000 3.51 0.00 36.56 3.36 F
2967 6589 0.385473 ATGAGTTTTCGCGCGGTTTG 60.385 50.000 31.69 0.24 0.00 2.93 F
3300 6926 2.228822 AGGTTCTTGCTGTTATTTGGCG 59.771 45.455 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 4131 0.461961 AGCACGGTGAGCCTAGATTC 59.538 55.000 13.29 0.0 0.00 2.52 R
1906 4132 0.461961 GAGCACGGTGAGCCTAGATT 59.538 55.000 13.29 0.0 0.00 2.40 R
3108 6730 0.953727 TCCATGCAGCTGTTTGACAC 59.046 50.000 16.64 0.0 0.00 3.67 R
3928 7555 1.670811 CGATTTTCTAGCCGGTGCATT 59.329 47.619 1.90 0.0 41.13 3.56 R
5045 8681 0.779997 AGGGTTCAGGAATGCCAGTT 59.220 50.000 0.00 0.0 36.29 3.16 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
48 49 1.775385 AGTTGTTGGTGAAGTTGGGG 58.225 50.000 0.00 0.00 0.00 4.96
54 55 3.423154 GTGAAGTTGGGGCGCTCG 61.423 66.667 7.64 0.00 0.00 5.03
115 116 0.589708 AAAGTTTGAAGCCCGTACGC 59.410 50.000 10.49 0.00 0.00 4.42
127 128 2.092291 CGTACGCAGCGATTGGTGT 61.092 57.895 24.65 0.00 45.36 4.16
131 132 2.324330 CGCAGCGATTGGTGTTGGA 61.324 57.895 9.98 0.00 45.36 3.53
147 148 2.945668 GTTGGAGTGTTTTCAGACTGCT 59.054 45.455 0.00 0.00 0.00 4.24
150 151 3.206150 GGAGTGTTTTCAGACTGCTCAA 58.794 45.455 0.00 0.00 0.00 3.02
158 159 2.838736 TCAGACTGCTCAACAACCTTC 58.161 47.619 0.00 0.00 0.00 3.46
169 170 5.004922 TCAACAACCTTCCAACATTGTTC 57.995 39.130 0.00 0.00 41.98 3.18
186 187 6.534793 ACATTGTTCGAAGAATGCAAGTTTTT 59.465 30.769 35.02 18.36 45.90 1.94
215 216 8.641541 ACTGTTCTATTTGGATCATGTTTTTGT 58.358 29.630 0.00 0.00 0.00 2.83
246 247 3.562557 GTCCGTGTGGTTACAAGTTTGAT 59.437 43.478 0.00 0.00 38.82 2.57
253 254 6.020201 GTGTGGTTACAAGTTTGATTTTTCCG 60.020 38.462 0.00 0.00 38.82 4.30
269 270 7.545965 TGATTTTTCCGATCTACAACTCTCTTC 59.454 37.037 0.00 0.00 0.00 2.87
275 276 3.784701 TCTACAACTCTCTTCATCGGC 57.215 47.619 0.00 0.00 0.00 5.54
287 288 2.108514 CATCGGCGATGGTTGCTGT 61.109 57.895 35.72 4.93 39.73 4.40
303 304 2.031163 GTTCTGGTGCGCTGGTCT 59.969 61.111 9.73 0.00 0.00 3.85
307 308 1.165907 TCTGGTGCGCTGGTCTTTTG 61.166 55.000 9.73 0.00 0.00 2.44
319 320 3.408634 TGGTCTTTTGTAGCCTTAGCAC 58.591 45.455 0.00 0.00 43.56 4.40
324 325 0.883153 TTGTAGCCTTAGCACGACGA 59.117 50.000 0.00 0.00 43.56 4.20
355 356 6.229936 ACTGTCTACTACAACAAGGTTTGA 57.770 37.500 0.00 0.00 37.74 2.69
359 360 5.465724 GTCTACTACAACAAGGTTTGACCAG 59.534 44.000 0.00 0.00 41.95 4.00
362 363 2.024414 ACAACAAGGTTTGACCAGCTC 58.976 47.619 0.00 0.00 41.95 4.09
369 370 0.534203 GTTTGACCAGCTCCGGTGAA 60.534 55.000 7.92 0.00 40.22 3.18
381 382 2.190578 GGTGAAGGAGGGGCGATG 59.809 66.667 0.00 0.00 0.00 3.84
383 384 1.700042 GGTGAAGGAGGGGCGATGAT 61.700 60.000 0.00 0.00 0.00 2.45
423 424 1.661112 GCTCCAATGCTTGTAGTCGTC 59.339 52.381 0.00 0.00 0.00 4.20
427 428 1.726791 CAATGCTTGTAGTCGTCGCTT 59.273 47.619 0.00 0.00 0.00 4.68
435 436 0.390124 TAGTCGTCGCTTGGTGGTTT 59.610 50.000 0.00 0.00 0.00 3.27
466 467 9.596308 ACCTGGTTGTAATTTTTATTACCTCTT 57.404 29.630 0.00 0.00 36.46 2.85
565 566 4.166144 ACCATACCCATAGAAAGAAGGTGG 59.834 45.833 0.00 0.00 31.89 4.61
566 567 2.808906 ACCCATAGAAAGAAGGTGGC 57.191 50.000 0.00 0.00 0.00 5.01
571 572 4.528206 CCCATAGAAAGAAGGTGGCTTTTT 59.472 41.667 0.00 0.00 35.83 1.94
632 640 5.883503 TTTATAAGAACGCAAACGGGATT 57.116 34.783 0.00 0.00 46.04 3.01
634 642 1.600023 AAGAACGCAAACGGGATTCA 58.400 45.000 0.00 0.00 46.04 2.57
647 655 2.017049 GGGATTCAAACATCTCGGTGG 58.983 52.381 0.00 0.00 0.00 4.61
648 656 2.618045 GGGATTCAAACATCTCGGTGGT 60.618 50.000 0.00 0.00 0.00 4.16
678 692 5.339200 CCATAGTCAAAGACCAACACCCTAT 60.339 44.000 0.00 0.00 32.18 2.57
679 693 6.126883 CCATAGTCAAAGACCAACACCCTATA 60.127 42.308 0.00 0.00 32.18 1.31
708 722 8.480853 CAAACTAGTTTACTCTCTCAGAAAACG 58.519 37.037 20.15 0.00 32.82 3.60
730 744 2.408565 TCTAATCCACCATCACCTCCC 58.591 52.381 0.00 0.00 0.00 4.30
759 773 2.483889 CCTTCCTCCAGACGGCTATTTC 60.484 54.545 0.00 0.00 0.00 2.17
772 786 4.693566 ACGGCTATTTCGTCAAGAATTTGA 59.306 37.500 0.00 0.00 40.92 2.69
773 787 5.180492 ACGGCTATTTCGTCAAGAATTTGAA 59.820 36.000 0.00 0.00 44.49 2.69
774 788 6.083630 CGGCTATTTCGTCAAGAATTTGAAA 58.916 36.000 0.00 0.00 44.49 2.69
797 811 3.874392 AAAAAGATCCCGGATTTGCAG 57.126 42.857 0.73 0.00 0.00 4.41
800 814 2.338577 AGATCCCGGATTTGCAGAAG 57.661 50.000 0.73 0.00 0.00 2.85
805 819 0.609131 CCGGATTTGCAGAAGGGTGT 60.609 55.000 0.00 0.00 0.00 4.16
837 851 4.060900 TGAGATTTTCAGAGTGCAGTGAC 58.939 43.478 0.00 0.00 0.00 3.67
841 855 0.394192 TTCAGAGTGCAGTGACCAGG 59.606 55.000 0.00 0.00 0.00 4.45
845 859 1.620819 AGAGTGCAGTGACCAGGTTAG 59.379 52.381 0.00 0.00 0.00 2.34
855 2977 3.249320 GTGACCAGGTTAGGAAACGAAAC 59.751 47.826 0.00 0.00 36.39 2.78
858 2980 4.271661 ACCAGGTTAGGAAACGAAACAAA 58.728 39.130 0.00 0.00 34.76 2.83
938 3060 1.139058 ACAGTCGCCACTTCTCAAAGT 59.861 47.619 0.00 0.00 46.80 2.66
974 3096 3.982058 TCGAGAAAAGAAAGCGAGAGAAC 59.018 43.478 0.00 0.00 0.00 3.01
1110 3232 2.661718 CTCTTCCTCCTAGTCCACCTC 58.338 57.143 0.00 0.00 0.00 3.85
1314 3436 3.402681 ATGGAGTCTGCCCCCGTG 61.403 66.667 0.00 0.00 0.00 4.94
1326 3448 3.322466 CCCGTGCCAGAGGACCTT 61.322 66.667 0.00 0.00 0.00 3.50
1329 3451 2.360475 GTGCCAGAGGACCTTGCC 60.360 66.667 0.00 0.00 32.93 4.52
1633 3756 1.017387 GCTCATGACGTCCCCATTTC 58.983 55.000 14.12 0.00 0.00 2.17
1639 3762 0.532196 GACGTCCCCATTTCGGATCC 60.532 60.000 3.51 0.00 36.56 3.36
1687 3810 3.995048 CCTAGTCAGGAAAAAGTTCGTCC 59.005 47.826 0.00 0.00 45.91 4.79
1706 3829 7.792364 TCGTCCATTGGGAGATAATTATACT 57.208 36.000 2.09 0.00 46.12 2.12
1712 3835 9.170734 CCATTGGGAGATAATTATACTCATGTG 57.829 37.037 18.49 13.51 35.59 3.21
1724 3847 2.847327 CTCATGTGAGTTGTGAGGGT 57.153 50.000 1.84 0.00 36.57 4.34
1725 3848 3.961480 CTCATGTGAGTTGTGAGGGTA 57.039 47.619 1.84 0.00 36.57 3.69
1726 3849 3.854666 CTCATGTGAGTTGTGAGGGTAG 58.145 50.000 1.84 0.00 36.57 3.18
1727 3850 3.239449 TCATGTGAGTTGTGAGGGTAGT 58.761 45.455 0.00 0.00 0.00 2.73
1729 3852 2.673258 TGTGAGTTGTGAGGGTAGTGA 58.327 47.619 0.00 0.00 0.00 3.41
1731 3854 3.006859 TGTGAGTTGTGAGGGTAGTGATG 59.993 47.826 0.00 0.00 0.00 3.07
1732 3855 2.028112 TGAGTTGTGAGGGTAGTGATGC 60.028 50.000 0.00 0.00 0.00 3.91
1746 3972 5.587844 GGTAGTGATGCATTTGATTCAGAGT 59.412 40.000 0.00 0.00 0.00 3.24
1753 3979 6.882610 TGCATTTGATTCAGAGTTGTAGTT 57.117 33.333 0.00 0.00 0.00 2.24
1756 3982 7.020010 GCATTTGATTCAGAGTTGTAGTTCAG 58.980 38.462 0.00 0.00 0.00 3.02
1760 3986 5.304357 TGATTCAGAGTTGTAGTTCAGTCCA 59.696 40.000 0.00 0.00 0.00 4.02
1761 3987 4.585955 TCAGAGTTGTAGTTCAGTCCAC 57.414 45.455 0.00 0.00 0.00 4.02
1762 3988 4.215908 TCAGAGTTGTAGTTCAGTCCACT 58.784 43.478 0.00 0.00 0.00 4.00
1763 3989 4.649674 TCAGAGTTGTAGTTCAGTCCACTT 59.350 41.667 0.00 0.00 0.00 3.16
1764 3990 5.831525 TCAGAGTTGTAGTTCAGTCCACTTA 59.168 40.000 0.00 0.00 0.00 2.24
1765 3991 6.016192 TCAGAGTTGTAGTTCAGTCCACTTAG 60.016 42.308 0.00 0.00 0.00 2.18
1766 3992 5.834204 AGAGTTGTAGTTCAGTCCACTTAGT 59.166 40.000 0.00 0.00 0.00 2.24
1767 3993 7.002879 AGAGTTGTAGTTCAGTCCACTTAGTA 58.997 38.462 0.00 0.00 0.00 1.82
1768 3994 7.670559 AGAGTTGTAGTTCAGTCCACTTAGTAT 59.329 37.037 0.00 0.00 0.00 2.12
1888 4114 2.490115 CAGTCCTCAGTCCTGACTACAC 59.510 54.545 0.00 0.00 40.20 2.90
1895 4121 5.336055 CCTCAGTCCTGACTACACTTAACTG 60.336 48.000 0.00 0.00 40.20 3.16
1899 4125 5.241949 AGTCCTGACTACACTTAACTGACTG 59.758 44.000 0.00 0.00 40.43 3.51
1900 4126 5.009811 GTCCTGACTACACTTAACTGACTGT 59.990 44.000 0.00 0.00 0.00 3.55
1901 4127 5.009710 TCCTGACTACACTTAACTGACTGTG 59.990 44.000 0.00 0.00 36.59 3.66
1902 4128 5.009710 CCTGACTACACTTAACTGACTGTGA 59.990 44.000 0.00 0.00 34.81 3.58
1903 4129 6.294787 CCTGACTACACTTAACTGACTGTGAT 60.295 42.308 0.00 0.00 34.81 3.06
1904 4130 6.447162 TGACTACACTTAACTGACTGTGATG 58.553 40.000 0.00 0.00 34.81 3.07
1905 4131 5.784177 ACTACACTTAACTGACTGTGATGG 58.216 41.667 0.00 0.00 34.81 3.51
1906 4132 4.955811 ACACTTAACTGACTGTGATGGA 57.044 40.909 0.00 0.00 34.81 3.41
1907 4133 5.290493 ACACTTAACTGACTGTGATGGAA 57.710 39.130 0.00 0.00 34.81 3.53
1908 4134 5.869579 ACACTTAACTGACTGTGATGGAAT 58.130 37.500 0.00 0.00 34.81 3.01
1909 4135 5.934625 ACACTTAACTGACTGTGATGGAATC 59.065 40.000 0.00 0.00 45.83 2.52
1910 4136 6.169094 CACTTAACTGACTGTGATGGAATCT 58.831 40.000 0.00 0.00 45.81 2.40
1911 4137 7.039011 ACACTTAACTGACTGTGATGGAATCTA 60.039 37.037 0.00 0.00 45.81 1.98
1912 4138 7.490725 CACTTAACTGACTGTGATGGAATCTAG 59.509 40.741 0.00 0.00 45.81 2.43
1913 4139 5.350504 AACTGACTGTGATGGAATCTAGG 57.649 43.478 0.00 0.00 45.81 3.02
1914 4140 3.133721 ACTGACTGTGATGGAATCTAGGC 59.866 47.826 0.00 0.00 45.81 3.93
1915 4141 3.378512 TGACTGTGATGGAATCTAGGCT 58.621 45.455 0.00 0.00 45.81 4.58
1916 4142 3.386078 TGACTGTGATGGAATCTAGGCTC 59.614 47.826 0.00 0.00 45.81 4.70
1917 4143 3.378512 ACTGTGATGGAATCTAGGCTCA 58.621 45.455 0.00 0.00 45.81 4.26
1918 4144 3.133721 ACTGTGATGGAATCTAGGCTCAC 59.866 47.826 0.00 0.00 45.81 3.51
1919 4145 2.435805 TGTGATGGAATCTAGGCTCACC 59.564 50.000 0.00 0.00 45.81 4.02
1926 4152 1.395826 ATCTAGGCTCACCGTGCTCC 61.396 60.000 0.00 0.00 42.76 4.70
1990 4216 5.482175 TCAAATTGACCGTATTTGGGGAAAT 59.518 36.000 0.00 0.00 41.24 2.17
2129 4358 5.524646 TGTTTCCTGGTTCAACTAGTAAACG 59.475 40.000 14.61 0.00 37.99 3.60
2261 4496 2.216046 ACTCATTCATGTGCGCCTATG 58.784 47.619 4.18 9.92 0.00 2.23
2304 4539 3.686016 AGCATCCTTTGATAAACCGTGT 58.314 40.909 0.00 0.00 0.00 4.49
2467 4702 4.192317 GGTGACGGCTTTCTAAATCTGAT 58.808 43.478 0.00 0.00 0.00 2.90
2698 6207 3.221771 TCAACAGCTACTTTTGCATGGT 58.778 40.909 0.00 0.00 0.00 3.55
2830 6340 6.095377 AGGCAGATCATTTTGAAATTCGAAC 58.905 36.000 0.00 0.00 0.00 3.95
2959 6581 7.095649 TGCATGATACTACATATGAGTTTTCGC 60.096 37.037 10.38 8.77 0.00 4.70
2967 6589 0.385473 ATGAGTTTTCGCGCGGTTTG 60.385 50.000 31.69 0.24 0.00 2.93
3024 6646 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3108 6730 9.088512 GTATCTTGGTACTTGATTAGTCAACTG 57.911 37.037 0.00 0.00 39.36 3.16
3152 6774 2.790433 GTTGGTACTTGAATCCAGCCA 58.210 47.619 0.00 0.00 32.63 4.75
3300 6926 2.228822 AGGTTCTTGCTGTTATTTGGCG 59.771 45.455 0.00 0.00 0.00 5.69
3315 6941 3.343941 TTGGCGCCTATAGTTGAACTT 57.656 42.857 29.70 0.00 0.00 2.66
3412 7038 4.600692 ATGGTTTTGGTTAGGCACTTTC 57.399 40.909 0.00 0.00 41.75 2.62
3532 7158 8.029782 TGTGCAGGTAAACAGGATAGTATAAT 57.970 34.615 0.00 0.00 0.00 1.28
3618 7244 8.206189 CCAATTAAAACCAGCTATTTCATCCAT 58.794 33.333 0.00 0.00 0.00 3.41
3668 7294 3.849563 TTGTGTTAGCCAGTACCAAGT 57.150 42.857 0.00 0.00 0.00 3.16
3687 7313 2.237392 AGTAGGTGATCCAGGCTGAAAC 59.763 50.000 17.94 8.08 35.89 2.78
3701 7327 5.180492 CAGGCTGAAACGTTTATCCAAACTA 59.820 40.000 14.65 0.00 41.62 2.24
3835 7462 6.881065 CAGGGAAAGAGACAAAGATAATGACA 59.119 38.462 0.00 0.00 0.00 3.58
3863 7490 9.780413 GAAGCTCAATTTCCAAGAGTTTTATAG 57.220 33.333 0.00 0.00 33.81 1.31
3867 7494 8.934023 TCAATTTCCAAGAGTTTTATAGTGGT 57.066 30.769 0.00 0.00 0.00 4.16
3928 7555 3.378512 ACAGATGACTCCAATGGCTCTA 58.621 45.455 0.00 0.00 0.00 2.43
4362 7989 7.094377 TGCAGTATGTTTCTCAAGAAATTACCC 60.094 37.037 8.34 8.26 44.69 3.69
4371 7998 5.710099 TCTCAAGAAATTACCCGCTGATTTT 59.290 36.000 0.00 0.00 0.00 1.82
4493 8121 9.060347 GCTTTATTCACAGAAGATGATTATGGA 57.940 33.333 0.00 0.00 0.00 3.41
4729 8358 6.762702 TCACGGTATATCAGTTGAAGTACA 57.237 37.500 0.00 0.00 0.00 2.90
4735 8364 9.908152 CGGTATATCAGTTGAAGTACATTATCA 57.092 33.333 0.00 0.00 0.00 2.15
5042 8678 5.544176 AGCTGTAGGGCTTGTATGTATGTAT 59.456 40.000 0.00 0.00 39.86 2.29
5043 8679 5.639506 GCTGTAGGGCTTGTATGTATGTATG 59.360 44.000 0.00 0.00 0.00 2.39
5044 8680 6.740944 TGTAGGGCTTGTATGTATGTATGT 57.259 37.500 0.00 0.00 0.00 2.29
5045 8681 7.524863 GCTGTAGGGCTTGTATGTATGTATGTA 60.525 40.741 0.00 0.00 0.00 2.29
5280 8923 4.235360 CCCAAGCCTACTCGTAAATATCG 58.765 47.826 0.00 0.00 0.00 2.92
5299 8942 1.673033 CGTCTGTCCAGCCAAGGTTAG 60.673 57.143 0.00 0.00 0.00 2.34
5362 9005 4.501071 TCCGAAATGTAAGTGGTTCTAGC 58.499 43.478 0.00 0.00 0.00 3.42
5370 9013 5.676552 TGTAAGTGGTTCTAGCTTTGTCAA 58.323 37.500 0.00 0.00 0.00 3.18
5372 9015 5.948992 AAGTGGTTCTAGCTTTGTCAATC 57.051 39.130 0.00 0.00 0.00 2.67
5388 9031 9.219603 CTTTGTCAATCTGACCAAGTTTATAGA 57.780 33.333 10.82 0.00 46.40 1.98
5389 9032 8.777865 TTGTCAATCTGACCAAGTTTATAGAG 57.222 34.615 4.42 0.00 46.40 2.43
5390 9033 8.134202 TGTCAATCTGACCAAGTTTATAGAGA 57.866 34.615 4.42 0.00 46.40 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.396166 ACCAACAACTAGAAGCATATGCAC 59.604 41.667 28.62 20.74 45.16 4.57
19 20 6.476378 ACTTCACCAACAACTAGAAGCATAT 58.524 36.000 0.00 0.00 39.33 1.78
48 49 1.588861 GTCTAAAGAATCCACGAGCGC 59.411 52.381 0.00 0.00 0.00 5.92
54 55 4.072131 TGCACAAGGTCTAAAGAATCCAC 58.928 43.478 0.00 0.00 0.00 4.02
115 116 0.518636 CACTCCAACACCAATCGCTG 59.481 55.000 0.00 0.00 0.00 5.18
127 128 3.206150 GAGCAGTCTGAAAACACTCCAA 58.794 45.455 3.32 0.00 0.00 3.53
131 132 3.609853 TGTTGAGCAGTCTGAAAACACT 58.390 40.909 3.32 0.00 0.00 3.55
147 148 4.439426 CGAACAATGTTGGAAGGTTGTTGA 60.439 41.667 2.20 0.00 42.80 3.18
150 151 3.283751 TCGAACAATGTTGGAAGGTTGT 58.716 40.909 8.36 0.00 36.43 3.32
158 159 3.899734 TGCATTCTTCGAACAATGTTGG 58.100 40.909 22.04 1.83 33.27 3.77
169 170 6.430451 ACAGTCTAAAAACTTGCATTCTTCG 58.570 36.000 0.00 0.00 0.00 3.79
186 187 9.739276 AAAACATGATCCAAATAGAACAGTCTA 57.261 29.630 0.00 0.00 40.68 2.59
215 216 1.451067 ACCACACGGACAAAAACGAA 58.549 45.000 0.00 0.00 35.59 3.85
246 247 6.755206 TGAAGAGAGTTGTAGATCGGAAAAA 58.245 36.000 0.00 0.00 0.00 1.94
253 254 4.295051 GCCGATGAAGAGAGTTGTAGATC 58.705 47.826 0.00 0.00 0.00 2.75
269 270 1.647545 AACAGCAACCATCGCCGATG 61.648 55.000 19.87 19.87 39.52 3.84
275 276 0.518636 CACCAGAACAGCAACCATCG 59.481 55.000 0.00 0.00 0.00 3.84
287 288 0.465460 AAAAGACCAGCGCACCAGAA 60.465 50.000 11.47 0.00 0.00 3.02
303 304 2.063266 CGTCGTGCTAAGGCTACAAAA 58.937 47.619 0.00 0.00 39.59 2.44
307 308 0.450983 AGTCGTCGTGCTAAGGCTAC 59.549 55.000 0.00 0.00 39.59 3.58
319 320 1.154263 GACAGTCGGGAAGTCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
324 325 3.430042 TGTAGTAGACAGTCGGGAAGT 57.570 47.619 0.00 0.00 32.86 3.01
355 356 2.203788 TCCTTCACCGGAGCTGGT 60.204 61.111 9.46 0.00 45.21 4.00
369 370 3.564218 GCCATCATCGCCCCTCCT 61.564 66.667 0.00 0.00 0.00 3.69
423 424 2.936498 CAGGTCTATAAACCACCAAGCG 59.064 50.000 0.00 0.00 42.12 4.68
427 428 3.653836 ACAACCAGGTCTATAAACCACCA 59.346 43.478 0.00 0.00 42.12 4.17
469 470 8.627403 CGGTATAGAGAACACAAGAGGTAATAA 58.373 37.037 0.00 0.00 0.00 1.40
470 471 7.776969 ACGGTATAGAGAACACAAGAGGTAATA 59.223 37.037 0.00 0.00 0.00 0.98
471 472 6.606395 ACGGTATAGAGAACACAAGAGGTAAT 59.394 38.462 0.00 0.00 0.00 1.89
472 473 5.948162 ACGGTATAGAGAACACAAGAGGTAA 59.052 40.000 0.00 0.00 0.00 2.85
473 474 5.503927 ACGGTATAGAGAACACAAGAGGTA 58.496 41.667 0.00 0.00 0.00 3.08
474 475 4.342359 ACGGTATAGAGAACACAAGAGGT 58.658 43.478 0.00 0.00 0.00 3.85
475 476 4.398358 TGACGGTATAGAGAACACAAGAGG 59.602 45.833 0.00 0.00 0.00 3.69
476 477 5.562506 TGACGGTATAGAGAACACAAGAG 57.437 43.478 0.00 0.00 0.00 2.85
477 478 5.650703 TCATGACGGTATAGAGAACACAAGA 59.349 40.000 0.00 0.00 0.00 3.02
478 479 5.744345 GTCATGACGGTATAGAGAACACAAG 59.256 44.000 10.69 0.00 0.00 3.16
479 480 5.417894 AGTCATGACGGTATAGAGAACACAA 59.582 40.000 19.85 0.00 36.20 3.33
480 481 4.948004 AGTCATGACGGTATAGAGAACACA 59.052 41.667 19.85 0.00 36.20 3.72
614 622 2.768698 TGAATCCCGTTTGCGTTCTTA 58.231 42.857 0.00 0.00 36.15 2.10
620 628 2.095263 AGATGTTTGAATCCCGTTTGCG 60.095 45.455 0.00 0.00 37.95 4.85
623 631 2.747446 CCGAGATGTTTGAATCCCGTTT 59.253 45.455 0.00 0.00 0.00 3.60
627 635 2.017049 CCACCGAGATGTTTGAATCCC 58.983 52.381 0.00 0.00 0.00 3.85
632 640 1.542328 CCACACCACCGAGATGTTTGA 60.542 52.381 0.00 0.00 0.00 2.69
634 642 0.762418 TCCACACCACCGAGATGTTT 59.238 50.000 0.00 0.00 0.00 2.83
647 655 3.244422 TGGTCTTTGACTATGGTCCACAC 60.244 47.826 6.77 0.00 41.47 3.82
648 656 2.976185 TGGTCTTTGACTATGGTCCACA 59.024 45.455 6.77 0.00 41.47 4.17
658 666 5.836024 TTATAGGGTGTTGGTCTTTGACT 57.164 39.130 0.00 0.00 32.47 3.41
665 673 6.938596 ACTAGTTTGTTTATAGGGTGTTGGTC 59.061 38.462 0.00 0.00 0.00 4.02
679 693 9.886132 TTTCTGAGAGAGTAAACTAGTTTGTTT 57.114 29.630 27.40 14.21 42.10 2.83
702 716 5.007724 GGTGATGGTGGATTAGATCGTTTTC 59.992 44.000 0.00 0.00 0.00 2.29
708 722 3.008485 GGGAGGTGATGGTGGATTAGATC 59.992 52.174 0.00 0.00 0.00 2.75
779 793 2.806945 TCTGCAAATCCGGGATCTTT 57.193 45.000 10.56 0.00 0.00 2.52
784 798 1.302949 CCCTTCTGCAAATCCGGGA 59.697 57.895 0.00 0.00 33.46 5.14
797 811 9.764363 AAAATCTCAATTTAAAAGACACCCTTC 57.236 29.630 0.00 0.00 33.93 3.46
800 814 9.196552 CTGAAAATCTCAATTTAAAAGACACCC 57.803 33.333 0.00 0.00 33.93 4.61
805 819 9.683069 GCACTCTGAAAATCTCAATTTAAAAGA 57.317 29.630 0.00 0.00 33.93 2.52
837 851 4.904253 TTTGTTTCGTTTCCTAACCTGG 57.096 40.909 0.00 0.00 0.00 4.45
868 2990 4.525487 TCGTGGGTGAACTCACTATACTTT 59.475 41.667 11.50 0.00 45.73 2.66
874 2996 1.884579 GAGTCGTGGGTGAACTCACTA 59.115 52.381 11.50 0.00 45.73 2.74
938 3060 7.786178 TCTTTTCTCGATGTTTCTTTCTTCA 57.214 32.000 0.00 0.00 0.00 3.02
974 3096 3.384014 GAGTCACGACTCGGAGCGG 62.384 68.421 20.20 9.70 46.93 5.52
1110 3232 2.107141 GATGGCGACGAAGGGGAG 59.893 66.667 0.00 0.00 0.00 4.30
1314 3436 3.706373 TCGGCAAGGTCCTCTGGC 61.706 66.667 13.98 13.98 41.76 4.85
1326 3448 2.046988 TCGTCCTCGTAGTCGGCA 60.047 61.111 0.00 0.00 38.33 5.69
1329 3451 1.633561 TGTACTCGTCCTCGTAGTCG 58.366 55.000 0.00 0.00 38.33 4.18
1601 3723 3.573598 GTCATGAGCTCGGATCATACAG 58.426 50.000 9.64 0.00 35.64 2.74
1633 3756 0.589708 TGTATCGCTACACGGATCCG 59.410 55.000 32.20 32.20 43.89 4.18
1687 3810 9.948964 TCACATGAGTATAATTATCTCCCAATG 57.051 33.333 0.00 10.16 0.00 2.82
1706 3829 3.006859 CACTACCCTCACAACTCACATGA 59.993 47.826 0.00 0.00 0.00 3.07
1712 3835 2.028112 TGCATCACTACCCTCACAACTC 60.028 50.000 0.00 0.00 0.00 3.01
1715 3838 3.719268 AATGCATCACTACCCTCACAA 57.281 42.857 0.00 0.00 0.00 3.33
1716 3839 3.008923 TCAAATGCATCACTACCCTCACA 59.991 43.478 0.00 0.00 0.00 3.58
1717 3840 3.609853 TCAAATGCATCACTACCCTCAC 58.390 45.455 0.00 0.00 0.00 3.51
1718 3841 3.998913 TCAAATGCATCACTACCCTCA 57.001 42.857 0.00 0.00 0.00 3.86
1720 3843 4.858850 TGAATCAAATGCATCACTACCCT 58.141 39.130 0.00 0.00 0.00 4.34
1721 3844 4.883585 TCTGAATCAAATGCATCACTACCC 59.116 41.667 0.00 0.00 0.00 3.69
1723 3846 6.674694 ACTCTGAATCAAATGCATCACTAC 57.325 37.500 0.00 0.00 0.00 2.73
1724 3847 6.656270 ACAACTCTGAATCAAATGCATCACTA 59.344 34.615 0.00 0.00 0.00 2.74
1725 3848 5.475909 ACAACTCTGAATCAAATGCATCACT 59.524 36.000 0.00 0.00 0.00 3.41
1726 3849 5.706916 ACAACTCTGAATCAAATGCATCAC 58.293 37.500 0.00 0.00 0.00 3.06
1727 3850 5.970317 ACAACTCTGAATCAAATGCATCA 57.030 34.783 0.00 0.00 0.00 3.07
1729 3852 7.175467 TGAACTACAACTCTGAATCAAATGCAT 59.825 33.333 0.00 0.00 0.00 3.96
1731 3854 6.902341 TGAACTACAACTCTGAATCAAATGC 58.098 36.000 0.00 0.00 0.00 3.56
1732 3855 8.092521 ACTGAACTACAACTCTGAATCAAATG 57.907 34.615 0.00 0.00 0.00 2.32
1746 3972 8.874744 AGTATACTAAGTGGACTGAACTACAA 57.125 34.615 2.75 0.00 0.00 2.41
1764 3990 7.980099 GGCCGCATTCATTATACTAAGTATACT 59.020 37.037 0.00 0.00 31.71 2.12
1765 3991 7.980099 AGGCCGCATTCATTATACTAAGTATAC 59.020 37.037 0.00 0.00 31.71 1.47
1766 3992 8.074613 AGGCCGCATTCATTATACTAAGTATA 57.925 34.615 0.00 0.00 30.79 1.47
1767 3993 6.947464 AGGCCGCATTCATTATACTAAGTAT 58.053 36.000 0.00 0.00 33.05 2.12
1768 3994 6.354794 AGGCCGCATTCATTATACTAAGTA 57.645 37.500 0.00 0.00 0.00 2.24
1787 4013 2.876581 TCCTCTTCCTTTTTGAAGGCC 58.123 47.619 0.00 0.00 41.67 5.19
1888 4114 6.983307 CCTAGATTCCATCACAGTCAGTTAAG 59.017 42.308 0.00 0.00 0.00 1.85
1895 4121 3.386078 TGAGCCTAGATTCCATCACAGTC 59.614 47.826 0.00 0.00 0.00 3.51
1899 4125 2.546795 CGGTGAGCCTAGATTCCATCAC 60.547 54.545 0.00 0.00 37.04 3.06
1900 4126 1.688735 CGGTGAGCCTAGATTCCATCA 59.311 52.381 0.00 0.00 0.00 3.07
1901 4127 1.689273 ACGGTGAGCCTAGATTCCATC 59.311 52.381 0.00 0.00 0.00 3.51
1902 4128 1.414181 CACGGTGAGCCTAGATTCCAT 59.586 52.381 0.74 0.00 0.00 3.41
1903 4129 0.824109 CACGGTGAGCCTAGATTCCA 59.176 55.000 0.74 0.00 0.00 3.53
1904 4130 0.530870 GCACGGTGAGCCTAGATTCC 60.531 60.000 13.29 0.00 0.00 3.01
1905 4131 0.461961 AGCACGGTGAGCCTAGATTC 59.538 55.000 13.29 0.00 0.00 2.52
1906 4132 0.461961 GAGCACGGTGAGCCTAGATT 59.538 55.000 13.29 0.00 0.00 2.40
1907 4133 1.395826 GGAGCACGGTGAGCCTAGAT 61.396 60.000 13.29 0.00 0.00 1.98
1908 4134 2.052690 GGAGCACGGTGAGCCTAGA 61.053 63.158 13.29 0.00 0.00 2.43
1909 4135 1.608717 AAGGAGCACGGTGAGCCTAG 61.609 60.000 18.50 0.00 0.00 3.02
1910 4136 1.192146 AAAGGAGCACGGTGAGCCTA 61.192 55.000 18.50 0.00 0.00 3.93
1911 4137 2.520536 AAAGGAGCACGGTGAGCCT 61.521 57.895 13.29 13.82 0.00 4.58
1912 4138 2.032681 AAAGGAGCACGGTGAGCC 59.967 61.111 13.29 11.68 0.00 4.70
1913 4139 1.294659 CTCAAAGGAGCACGGTGAGC 61.295 60.000 13.29 2.09 33.67 4.26
1914 4140 2.832931 CTCAAAGGAGCACGGTGAG 58.167 57.895 13.29 0.00 33.67 3.51
1926 4152 5.422666 TGGCATTATATGAACGCTCAAAG 57.577 39.130 0.00 0.00 34.49 2.77
1964 4190 4.013728 CCCCAAATACGGTCAATTTGAGA 58.986 43.478 14.84 0.00 43.79 3.27
2007 4236 8.455682 AGAAAATTGTTCAGAACACGAACTTAA 58.544 29.630 15.93 0.00 42.63 1.85
2243 4478 2.618442 TCATAGGCGCACATGAATGA 57.382 45.000 17.75 10.06 0.00 2.57
2244 4479 2.603892 GCTTCATAGGCGCACATGAATG 60.604 50.000 26.41 21.64 39.69 2.67
2261 4496 5.459434 GCTTGACCTACTTATTACGAGCTTC 59.541 44.000 0.00 0.00 33.59 3.86
2304 4539 7.448161 ACATGTGATCATTTGGTAGTTGAAGAA 59.552 33.333 0.00 0.00 31.15 2.52
2507 4742 7.009179 AGAACAATCATGGTACTTCAGAAGA 57.991 36.000 17.56 0.00 0.00 2.87
2698 6207 8.445275 TTTTGCAGAACTGAACACTAATAAGA 57.555 30.769 5.97 0.00 0.00 2.10
2857 6367 3.640029 TCGACCCCTTTACTATGATCCAC 59.360 47.826 0.00 0.00 0.00 4.02
2967 6589 4.501071 TGCTTCAGAGTTCGGTTATAACC 58.499 43.478 22.69 22.69 45.76 2.85
3072 6694 1.777941 ACCAAGATACTCCCTCCGTC 58.222 55.000 0.00 0.00 0.00 4.79
3108 6730 0.953727 TCCATGCAGCTGTTTGACAC 59.046 50.000 16.64 0.00 0.00 3.67
3300 6926 4.123506 GGCTCTCAAGTTCAACTATAGGC 58.876 47.826 4.43 0.00 0.00 3.93
3315 6941 2.622942 GTGATGTTTTTGGTGGCTCTCA 59.377 45.455 0.00 0.00 0.00 3.27
3390 7016 4.500716 CGAAAGTGCCTAACCAAAACCATT 60.501 41.667 0.00 0.00 0.00 3.16
3412 7038 4.563337 TTCATACGACTCCTTGATACCG 57.437 45.455 0.00 0.00 0.00 4.02
3668 7294 1.207089 CGTTTCAGCCTGGATCACCTA 59.793 52.381 0.00 0.00 37.04 3.08
3701 7327 8.485578 TGTGTCAGGGTTCCTAAAATAAATTT 57.514 30.769 0.00 0.00 34.92 1.82
3835 7462 4.379302 ACTCTTGGAAATTGAGCTTCCT 57.621 40.909 3.15 0.00 42.52 3.36
3863 7490 5.163834 TGTCGAACTGAGTAAAACAAACCAC 60.164 40.000 0.00 0.00 0.00 4.16
3867 7494 7.222417 TCGTAATGTCGAACTGAGTAAAACAAA 59.778 33.333 0.00 0.00 36.89 2.83
3876 7503 5.273944 TCATCATCGTAATGTCGAACTGAG 58.726 41.667 0.00 0.00 42.99 3.35
3928 7555 1.670811 CGATTTTCTAGCCGGTGCATT 59.329 47.619 1.90 0.00 41.13 3.56
4176 7803 4.936411 AGAAACAGAATGAGATGCTGTCAG 59.064 41.667 0.00 0.00 41.65 3.51
4735 8364 5.928264 GGTGCAAAAGCAATGAATAAGAACT 59.072 36.000 0.00 0.00 0.00 3.01
4868 8498 9.590451 AAGCATCTTAATGTAACAAATGAATGG 57.410 29.630 0.00 0.00 35.18 3.16
5042 8678 2.554344 GGGTTCAGGAATGCCAGTTACA 60.554 50.000 0.00 0.00 36.29 2.41
5043 8679 2.092323 GGGTTCAGGAATGCCAGTTAC 58.908 52.381 0.00 0.00 36.29 2.50
5044 8680 1.992557 AGGGTTCAGGAATGCCAGTTA 59.007 47.619 0.00 0.00 36.29 2.24
5045 8681 0.779997 AGGGTTCAGGAATGCCAGTT 59.220 50.000 0.00 0.00 36.29 3.16
5099 8735 5.009110 TCGCACGAGAAGAGAATAGAATCAT 59.991 40.000 0.00 0.00 0.00 2.45
5183 8824 1.902918 ATTTTGACTGCGCCTGCCA 60.903 52.632 4.18 0.00 41.78 4.92
5280 8923 1.623811 TCTAACCTTGGCTGGACAGAC 59.376 52.381 3.00 0.00 36.85 3.51
5447 9090 8.754991 TCTAGTAGTTTTGTCCCAAAATCAAA 57.245 30.769 5.53 0.00 0.00 2.69
5448 9091 8.754991 TTCTAGTAGTTTTGTCCCAAAATCAA 57.245 30.769 5.53 0.00 0.00 2.57
5449 9092 8.934023 ATTCTAGTAGTTTTGTCCCAAAATCA 57.066 30.769 5.53 0.00 0.00 2.57
5450 9093 9.626045 CAATTCTAGTAGTTTTGTCCCAAAATC 57.374 33.333 5.53 1.23 0.00 2.17
5451 9094 8.088365 GCAATTCTAGTAGTTTTGTCCCAAAAT 58.912 33.333 5.53 0.00 0.00 1.82
5452 9095 7.286775 AGCAATTCTAGTAGTTTTGTCCCAAAA 59.713 33.333 12.96 0.00 0.00 2.44
5453 9096 6.775629 AGCAATTCTAGTAGTTTTGTCCCAAA 59.224 34.615 12.96 0.00 0.00 3.28
5454 9097 6.303839 AGCAATTCTAGTAGTTTTGTCCCAA 58.696 36.000 12.96 0.00 0.00 4.12
5455 9098 5.876357 AGCAATTCTAGTAGTTTTGTCCCA 58.124 37.500 12.96 0.00 0.00 4.37
5456 9099 6.612306 CAAGCAATTCTAGTAGTTTTGTCCC 58.388 40.000 12.96 2.23 0.00 4.46


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

AutoCloner maintained by Alex Coulton.