Multiple sequence alignment - TraesCS4D01G287100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G287100 chr4D 100.000 2374 0 0 1 2374 459059225 459061598 0.000000e+00 4385
1 TraesCS4D01G287100 chr4D 85.897 624 38 15 1064 1681 459066134 459066713 9.320000e-174 619
2 TraesCS4D01G287100 chr4D 84.468 470 69 3 1908 2373 459066759 459067228 5.980000e-126 460
3 TraesCS4D01G287100 chr4D 78.931 318 30 14 1047 1357 459068444 459068731 5.210000e-42 182
4 TraesCS4D01G287100 chr4B 91.931 979 42 14 602 1562 573295869 573296828 0.000000e+00 1336
5 TraesCS4D01G287100 chr4B 88.235 340 21 9 277 612 573295528 573295852 2.860000e-104 388
6 TraesCS4D01G287100 chr4B 90.189 265 16 6 4 259 573294656 573294919 1.050000e-88 337
7 TraesCS4D01G287100 chr4A 91.847 969 44 11 707 1675 9908358 9907425 0.000000e+00 1319
8 TraesCS4D01G287100 chr4A 86.882 526 36 16 194 706 9908916 9908411 2.060000e-155 558
9 TraesCS4D01G287100 chr4A 85.219 433 29 15 1249 1681 9629193 9628796 1.700000e-111 412
10 TraesCS4D01G287100 chr4A 82.366 448 33 11 1064 1505 9626518 9626111 4.860000e-92 348
11 TraesCS4D01G287100 chr4A 78.767 292 29 9 1076 1364 9623470 9623209 5.250000e-37 165
12 TraesCS4D01G287100 chr1A 76.453 327 58 15 2009 2323 59959159 59959478 2.440000e-35 159
13 TraesCS4D01G287100 chr7D 75.078 321 69 8 2011 2323 263526553 263526236 3.180000e-29 139
14 TraesCS4D01G287100 chr7D 75.261 287 61 6 2045 2324 443524128 443523845 6.890000e-26 128


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 TraesCS4D01G287100 chr4D 459059225 459061598 2373 False 4385.000000 4385 100.000000 1 2374 1 chr4D.!!$F1 2373
1 TraesCS4D01G287100 chr4D 459066134 459068731 2597 False 420.333333 619 83.098667 1047 2373 3 chr4D.!!$F2 1326
2 TraesCS4D01G287100 chr4B 573294656 573296828 2172 False 687.000000 1336 90.118333 4 1562 3 chr4B.!!$F1 1558
3 TraesCS4D01G287100 chr4A 9907425 9908916 1491 True 938.500000 1319 89.364500 194 1675 2 chr4A.!!$R2 1481
4 TraesCS4D01G287100 chr4A 9623209 9629193 5984 True 308.333333 412 82.117333 1064 1681 3 chr4A.!!$R1 617

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
935 1632 0.459585 GCTTATCCGAACCGAGCACA 60.46 55.0 0.0 0.0 33.68 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 4345 0.310854 CAAAGAGAAACACCACCGCC 59.689 55.0 0.0 0.0 0.0 6.13 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
66 67 1.620819 ACGAAGAACAGCCTCTCATGT 59.379 47.619 0.00 0.00 0.00 3.21
71 72 1.834263 GAACAGCCTCTCATGTAGGGT 59.166 52.381 13.54 13.54 45.62 4.34
73 74 1.556911 ACAGCCTCTCATGTAGGGTTG 59.443 52.381 15.81 14.09 42.10 3.77
75 76 1.204146 GCCTCTCATGTAGGGTTGGA 58.796 55.000 15.65 0.00 34.46 3.53
79 80 2.840651 CTCTCATGTAGGGTTGGAAGGT 59.159 50.000 0.00 0.00 0.00 3.50
80 81 2.571653 TCTCATGTAGGGTTGGAAGGTG 59.428 50.000 0.00 0.00 0.00 4.00
81 82 2.305927 CTCATGTAGGGTTGGAAGGTGT 59.694 50.000 0.00 0.00 0.00 4.16
82 83 3.517901 CTCATGTAGGGTTGGAAGGTGTA 59.482 47.826 0.00 0.00 0.00 2.90
84 85 3.992943 TGTAGGGTTGGAAGGTGTATG 57.007 47.619 0.00 0.00 0.00 2.39
87 88 2.344592 AGGGTTGGAAGGTGTATGTCA 58.655 47.619 0.00 0.00 0.00 3.58
127 134 7.028926 TCGAAGAGTTGTTGTAGATCTATCC 57.971 40.000 5.57 0.00 0.00 2.59
128 135 6.039493 TCGAAGAGTTGTTGTAGATCTATCCC 59.961 42.308 5.57 0.00 0.00 3.85
137 144 5.019657 TGTAGATCTATCCCCGGGTAAAT 57.980 43.478 21.85 12.50 0.00 1.40
149 156 1.597663 CGGGTAAATCGTTGGCTGATC 59.402 52.381 0.00 0.00 0.00 2.92
155 162 5.353123 GGTAAATCGTTGGCTGATCTTTGTA 59.647 40.000 0.00 0.00 0.00 2.41
157 164 2.346803 TCGTTGGCTGATCTTTGTAGC 58.653 47.619 0.00 0.00 36.74 3.58
159 166 2.076863 GTTGGCTGATCTTTGTAGCGT 58.923 47.619 0.00 0.00 38.31 5.07
162 169 1.202076 GGCTGATCTTTGTAGCGTTGC 60.202 52.381 0.00 0.00 38.31 4.17
178 185 2.222999 CGTTGCGCACATGATGTTATCA 60.223 45.455 11.12 0.00 44.55 2.15
241 250 1.000993 TGTGGTTTGTGCAAGGGGT 59.999 52.632 0.00 0.00 0.00 4.95
251 263 4.296265 CAAGGGGTGCCTCGTAAC 57.704 61.111 0.00 0.00 0.00 2.50
278 881 2.472059 CGGTGGGCGACATGAATGG 61.472 63.158 0.00 0.00 0.00 3.16
320 930 1.963515 ACATGCGGGCTTTTCTTTCTT 59.036 42.857 0.00 0.00 0.00 2.52
326 936 3.621268 GCGGGCTTTTCTTTCTTGTTTTT 59.379 39.130 0.00 0.00 0.00 1.94
373 984 7.330946 CCAGTTTCTGTATCGTGTTATTTCTCA 59.669 37.037 0.00 0.00 0.00 3.27
381 992 2.864343 CGTGTTATTTCTCATCGGTCCC 59.136 50.000 0.00 0.00 0.00 4.46
382 993 3.430374 CGTGTTATTTCTCATCGGTCCCT 60.430 47.826 0.00 0.00 0.00 4.20
383 994 4.120589 GTGTTATTTCTCATCGGTCCCTC 58.879 47.826 0.00 0.00 0.00 4.30
385 996 2.182516 ATTTCTCATCGGTCCCTCCT 57.817 50.000 0.00 0.00 0.00 3.69
522 1134 3.999769 TGACTCGAGAATTCGTCGTTAG 58.000 45.455 21.68 15.20 46.72 2.34
528 1140 4.091365 TCGAGAATTCGTCGTTAGTCGTTA 59.909 41.667 19.64 3.04 46.72 3.18
529 1141 4.429485 CGAGAATTCGTCGTTAGTCGTTAG 59.571 45.833 15.03 0.00 41.84 2.34
530 1142 5.288543 AGAATTCGTCGTTAGTCGTTAGT 57.711 39.130 0.00 0.00 40.80 2.24
531 1143 5.319931 AGAATTCGTCGTTAGTCGTTAGTC 58.680 41.667 0.00 0.00 40.80 2.59
533 1145 2.058798 TCGTCGTTAGTCGTTAGTCGT 58.941 47.619 0.00 0.00 40.80 4.34
534 1146 2.090658 TCGTCGTTAGTCGTTAGTCGTC 59.909 50.000 0.00 0.00 40.80 4.20
535 1147 2.091277 CGTCGTTAGTCGTTAGTCGTCT 59.909 50.000 0.00 0.00 40.50 4.18
536 1148 3.300853 CGTCGTTAGTCGTTAGTCGTCTA 59.699 47.826 0.00 0.00 38.63 2.59
551 1163 9.415544 GTTAGTCGTCTAATCTAAAACAAAGGA 57.584 33.333 5.44 0.00 38.25 3.36
553 1165 8.897872 AGTCGTCTAATCTAAAACAAAGGAAA 57.102 30.769 0.00 0.00 0.00 3.13
616 1259 7.914537 CAACAACTGGAAGATAAACAAGTTC 57.085 36.000 0.00 0.00 37.43 3.01
660 1303 4.349048 AGCCTGGAAGATACATATCTGCAA 59.651 41.667 8.81 0.00 41.96 4.08
673 1316 2.034843 TGCAACGCCAATAGCCCA 59.965 55.556 0.00 0.00 38.78 5.36
935 1632 0.459585 GCTTATCCGAACCGAGCACA 60.460 55.000 0.00 0.00 33.68 4.57
942 1639 1.007038 GAACCGAGCACACCGTGTA 60.007 57.895 3.25 0.00 35.75 2.90
1205 2824 2.741211 GTGAACTTCGGGGCCGTC 60.741 66.667 0.00 0.00 40.74 4.79
1544 3824 6.237384 GCAACTATGCGAGATTTTGACATTTG 60.237 38.462 0.00 0.00 43.83 2.32
1571 3851 1.660560 AATTTGGGCGCTGCTGCTAG 61.661 55.000 14.03 0.00 36.97 3.42
1614 3894 0.609131 AAGCCCAAACCGATGACCTG 60.609 55.000 0.00 0.00 0.00 4.00
1661 3942 1.134936 TCCCATGTACGGTCACGATTG 60.135 52.381 0.00 0.00 44.60 2.67
1666 3947 2.161855 TGTACGGTCACGATTGGTACT 58.838 47.619 0.00 0.00 44.60 2.73
1680 3961 5.924254 CGATTGGTACTGACTCAGTTGTTTA 59.076 40.000 16.89 0.00 42.59 2.01
1681 3962 6.590292 CGATTGGTACTGACTCAGTTGTTTAT 59.410 38.462 16.89 5.37 42.59 1.40
1682 3963 7.411912 CGATTGGTACTGACTCAGTTGTTTATG 60.412 40.741 16.89 0.52 42.59 1.90
1683 3964 6.169557 TGGTACTGACTCAGTTGTTTATGT 57.830 37.500 16.89 0.00 42.59 2.29
1684 3965 7.292713 TGGTACTGACTCAGTTGTTTATGTA 57.707 36.000 16.89 0.00 42.59 2.29
1685 3966 7.375834 TGGTACTGACTCAGTTGTTTATGTAG 58.624 38.462 16.89 0.00 42.59 2.74
1686 3967 6.310711 GGTACTGACTCAGTTGTTTATGTAGC 59.689 42.308 16.89 2.12 42.59 3.58
1687 3968 4.923871 ACTGACTCAGTTGTTTATGTAGCG 59.076 41.667 5.82 0.00 42.59 4.26
1688 3969 3.678072 TGACTCAGTTGTTTATGTAGCGC 59.322 43.478 0.00 0.00 0.00 5.92
1689 3970 3.000727 ACTCAGTTGTTTATGTAGCGCC 58.999 45.455 2.29 0.00 0.00 6.53
1690 3971 3.000041 CTCAGTTGTTTATGTAGCGCCA 59.000 45.455 2.29 0.00 0.00 5.69
1691 3972 2.739913 TCAGTTGTTTATGTAGCGCCAC 59.260 45.455 2.29 0.00 0.00 5.01
1692 3973 2.742053 CAGTTGTTTATGTAGCGCCACT 59.258 45.455 7.64 0.00 0.00 4.00
1693 3974 3.930229 CAGTTGTTTATGTAGCGCCACTA 59.070 43.478 7.64 0.00 0.00 2.74
1694 3975 4.570772 CAGTTGTTTATGTAGCGCCACTAT 59.429 41.667 7.64 2.13 32.15 2.12
1695 3976 4.570772 AGTTGTTTATGTAGCGCCACTATG 59.429 41.667 7.64 0.00 32.15 2.23
1696 3977 3.462982 TGTTTATGTAGCGCCACTATGG 58.537 45.455 7.64 0.00 41.55 2.74
1697 3978 3.133183 TGTTTATGTAGCGCCACTATGGA 59.867 43.478 7.64 0.00 40.96 3.41
1698 3979 3.660501 TTATGTAGCGCCACTATGGAG 57.339 47.619 7.64 0.00 40.96 3.86
1705 3986 3.760693 GCCACTATGGAGCGAGAAA 57.239 52.632 0.00 0.00 40.96 2.52
1706 3987 2.024176 GCCACTATGGAGCGAGAAAA 57.976 50.000 0.00 0.00 40.96 2.29
1707 3988 2.356135 GCCACTATGGAGCGAGAAAAA 58.644 47.619 0.00 0.00 40.96 1.94
1728 4009 3.684103 AAAACACACACACACATACCG 57.316 42.857 0.00 0.00 0.00 4.02
1729 4010 0.941542 AACACACACACACATACCGC 59.058 50.000 0.00 0.00 0.00 5.68
1730 4011 0.882927 ACACACACACACATACCGCC 60.883 55.000 0.00 0.00 0.00 6.13
1731 4012 1.302192 ACACACACACATACCGCCC 60.302 57.895 0.00 0.00 0.00 6.13
1732 4013 2.038269 CACACACACATACCGCCCC 61.038 63.158 0.00 0.00 0.00 5.80
1733 4014 2.221299 ACACACACATACCGCCCCT 61.221 57.895 0.00 0.00 0.00 4.79
1734 4015 1.745115 CACACACATACCGCCCCTG 60.745 63.158 0.00 0.00 0.00 4.45
1735 4016 2.221299 ACACACATACCGCCCCTGT 61.221 57.895 0.00 0.00 0.00 4.00
1736 4017 1.745115 CACACATACCGCCCCTGTG 60.745 63.158 0.00 0.00 44.51 3.66
1737 4018 2.824041 CACATACCGCCCCTGTGC 60.824 66.667 0.00 0.00 34.47 4.57
1745 4026 4.660938 GCCCCTGTGCGTTCCCTT 62.661 66.667 0.00 0.00 0.00 3.95
1746 4027 2.115266 CCCCTGTGCGTTCCCTTT 59.885 61.111 0.00 0.00 0.00 3.11
1747 4028 2.268076 CCCCTGTGCGTTCCCTTTG 61.268 63.158 0.00 0.00 0.00 2.77
1748 4029 2.644992 CCTGTGCGTTCCCTTTGC 59.355 61.111 0.00 0.00 0.00 3.68
1749 4030 2.192861 CCTGTGCGTTCCCTTTGCA 61.193 57.895 0.00 0.00 36.02 4.08
1750 4031 1.526575 CCTGTGCGTTCCCTTTGCAT 61.527 55.000 0.00 0.00 41.23 3.96
1751 4032 0.387622 CTGTGCGTTCCCTTTGCATG 60.388 55.000 0.00 0.00 41.23 4.06
1752 4033 1.080569 GTGCGTTCCCTTTGCATGG 60.081 57.895 0.00 0.00 41.23 3.66
1753 4034 1.228398 TGCGTTCCCTTTGCATGGA 60.228 52.632 7.73 2.22 32.86 3.41
1754 4035 0.611618 TGCGTTCCCTTTGCATGGAT 60.612 50.000 7.73 0.00 32.86 3.41
1755 4036 0.532115 GCGTTCCCTTTGCATGGATT 59.468 50.000 7.73 0.00 0.00 3.01
1756 4037 1.736696 GCGTTCCCTTTGCATGGATTG 60.737 52.381 7.73 2.55 0.00 2.67
1786 4067 0.246910 TTGCTAACCGTCGGTATGCA 59.753 50.000 28.83 28.83 40.34 3.96
1787 4068 0.179121 TGCTAACCGTCGGTATGCAG 60.179 55.000 28.83 19.60 38.43 4.41
1788 4069 0.179119 GCTAACCGTCGGTATGCAGT 60.179 55.000 26.53 11.78 33.12 4.40
1789 4070 1.066002 GCTAACCGTCGGTATGCAGTA 59.934 52.381 26.53 12.22 33.12 2.74
1790 4071 2.288030 GCTAACCGTCGGTATGCAGTAT 60.288 50.000 26.53 10.52 33.12 2.12
1791 4072 2.218953 AACCGTCGGTATGCAGTATG 57.781 50.000 19.21 0.00 33.12 2.39
1811 4092 2.044053 CCCCATTGACGGCCATGT 60.044 61.111 2.24 0.00 0.00 3.21
1829 4110 3.385384 CAGCCTCAGCCCGTCTCA 61.385 66.667 0.00 0.00 41.25 3.27
1836 4117 4.385405 AGCCCGTCTCAGCAGCAC 62.385 66.667 0.00 0.00 0.00 4.40
1840 4121 2.341543 CGTCTCAGCAGCACCACT 59.658 61.111 0.00 0.00 0.00 4.00
1841 4122 1.735920 CGTCTCAGCAGCACCACTC 60.736 63.158 0.00 0.00 0.00 3.51
1843 4124 1.838396 TCTCAGCAGCACCACTCCA 60.838 57.895 0.00 0.00 0.00 3.86
1844 4125 1.071987 CTCAGCAGCACCACTCCAA 59.928 57.895 0.00 0.00 0.00 3.53
1845 4126 0.954449 CTCAGCAGCACCACTCCAAG 60.954 60.000 0.00 0.00 0.00 3.61
1846 4127 1.970114 CAGCAGCACCACTCCAAGG 60.970 63.158 0.00 0.00 0.00 3.61
1847 4128 2.113986 GCAGCACCACTCCAAGGT 59.886 61.111 0.00 0.00 40.85 3.50
1848 4129 1.968540 GCAGCACCACTCCAAGGTC 60.969 63.158 0.00 0.00 37.23 3.85
1849 4130 1.669115 CAGCACCACTCCAAGGTCG 60.669 63.158 0.00 0.00 37.23 4.79
1850 4131 3.050275 GCACCACTCCAAGGTCGC 61.050 66.667 0.00 0.00 37.23 5.19
1851 4132 2.425592 CACCACTCCAAGGTCGCA 59.574 61.111 0.00 0.00 37.23 5.10
1852 4133 1.227823 CACCACTCCAAGGTCGCAA 60.228 57.895 0.00 0.00 37.23 4.85
1853 4134 1.227853 ACCACTCCAAGGTCGCAAC 60.228 57.895 0.00 0.00 32.90 4.17
1854 4135 1.227823 CCACTCCAAGGTCGCAACA 60.228 57.895 0.00 0.00 0.00 3.33
1855 4136 1.507141 CCACTCCAAGGTCGCAACAC 61.507 60.000 0.00 0.00 0.00 3.32
1856 4137 1.227853 ACTCCAAGGTCGCAACACC 60.228 57.895 0.00 0.00 36.58 4.16
1857 4138 1.227823 CTCCAAGGTCGCAACACCA 60.228 57.895 0.00 0.00 39.16 4.17
1858 4139 1.507141 CTCCAAGGTCGCAACACCAC 61.507 60.000 0.00 0.00 39.16 4.16
1859 4140 2.551912 CCAAGGTCGCAACACCACC 61.552 63.158 0.00 0.00 39.16 4.61
1860 4141 1.525995 CAAGGTCGCAACACCACCT 60.526 57.895 0.00 0.00 42.72 4.00
1916 4220 1.509703 GGTTTGTGGTCGTTCTCCTC 58.490 55.000 0.00 0.00 0.00 3.71
1977 4281 0.039180 GGGTTTGGGGTTCTCGGATT 59.961 55.000 0.00 0.00 0.00 3.01
1980 4284 1.068948 TTTGGGGTTCTCGGATTCCA 58.931 50.000 3.09 0.00 0.00 3.53
1984 4288 1.486211 GGGTTCTCGGATTCCAGAGA 58.514 55.000 17.66 17.66 41.26 3.10
1992 4296 1.529309 GATTCCAGAGAGGTGGCCC 59.471 63.158 0.00 0.00 37.53 5.80
1993 4297 1.229951 ATTCCAGAGAGGTGGCCCA 60.230 57.895 0.00 0.00 37.53 5.36
1997 4301 2.284995 AGAGAGGTGGCCCAGGAC 60.285 66.667 0.00 0.00 0.00 3.85
2024 4328 1.736645 CACACGGTTGGCTCTACGG 60.737 63.158 0.00 0.00 0.00 4.02
2030 4334 1.214589 GTTGGCTCTACGGCGAGAA 59.785 57.895 16.62 0.00 42.02 2.87
2041 4345 4.520846 GCGAGAAATGTGGCGGCG 62.521 66.667 0.51 0.51 0.00 6.46
2043 4347 4.179579 GAGAAATGTGGCGGCGGC 62.180 66.667 27.76 27.76 38.90 6.53
2057 4361 2.030562 CGGCGGTGGTGTTTCTCT 59.969 61.111 0.00 0.00 0.00 3.10
2096 4406 1.075525 CGAGGTGGTGGGGATCCTA 60.076 63.158 12.58 0.00 0.00 2.94
2134 4444 3.618594 CGGCAATTGTATCTCCCATATCG 59.381 47.826 7.40 0.00 0.00 2.92
2159 4469 0.032615 TGGAGGCTTGTTTTGGTGGT 60.033 50.000 0.00 0.00 0.00 4.16
2183 4493 0.686769 GACCTGGGACCGTGGTATCT 60.687 60.000 6.98 0.00 33.74 1.98
2192 4502 2.717044 CGTGGTATCTCGGGTGGCA 61.717 63.158 0.00 0.00 0.00 4.92
2193 4503 1.830145 GTGGTATCTCGGGTGGCAT 59.170 57.895 0.00 0.00 0.00 4.40
2203 4513 3.127533 GGTGGCATGCGTGAGACC 61.128 66.667 12.44 10.46 0.00 3.85
2251 4561 0.578683 GACGACGATGATGCATGTGG 59.421 55.000 2.46 0.00 0.00 4.17
2256 4566 1.097232 CGATGATGCATGTGGGTGTT 58.903 50.000 2.46 0.00 0.00 3.32
2258 4568 0.533491 ATGATGCATGTGGGTGTTGC 59.467 50.000 2.46 0.00 36.91 4.17
2267 4577 2.047179 GGGTGTTGCGTCCCTCTC 60.047 66.667 0.00 0.00 40.48 3.20
2282 4593 3.353836 CTCGGGGCGTTGTTGTGG 61.354 66.667 0.00 0.00 0.00 4.17
2305 4616 1.662438 CCCTCTCCGTGTCAGAGCTC 61.662 65.000 5.27 5.27 36.77 4.09
2306 4617 1.662438 CCTCTCCGTGTCAGAGCTCC 61.662 65.000 10.93 0.00 36.77 4.70
2330 4641 3.005791 GGTGAAAACCCTTGATTGTCCTG 59.994 47.826 0.00 0.00 0.00 3.86
2332 4643 1.247567 AAACCCTTGATTGTCCTGCG 58.752 50.000 0.00 0.00 0.00 5.18
2336 4647 0.321564 CCTTGATTGTCCTGCGGTCA 60.322 55.000 0.00 0.00 0.00 4.02
2337 4648 1.679944 CCTTGATTGTCCTGCGGTCAT 60.680 52.381 0.00 0.00 0.00 3.06
2350 4661 3.490759 GTCATGGCAGTGACGGCG 61.491 66.667 4.80 4.80 39.12 6.46
2373 4684 0.608640 AGCTCAGGTACCTTTCGGTG 59.391 55.000 13.15 0.15 45.18 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 3.517901 CTGACATACACCTTCCAACCCTA 59.482 47.826 0.00 0.00 0.00 3.53
71 72 3.495983 CCACACTGACATACACCTTCCAA 60.496 47.826 0.00 0.00 0.00 3.53
73 74 2.301870 TCCACACTGACATACACCTTCC 59.698 50.000 0.00 0.00 0.00 3.46
75 76 4.041567 TCAATCCACACTGACATACACCTT 59.958 41.667 0.00 0.00 0.00 3.50
79 80 5.863965 TCTTTCAATCCACACTGACATACA 58.136 37.500 0.00 0.00 0.00 2.29
80 81 6.237942 CGATCTTTCAATCCACACTGACATAC 60.238 42.308 0.00 0.00 0.00 2.39
81 82 5.812127 CGATCTTTCAATCCACACTGACATA 59.188 40.000 0.00 0.00 0.00 2.29
82 83 4.633126 CGATCTTTCAATCCACACTGACAT 59.367 41.667 0.00 0.00 0.00 3.06
84 85 4.245660 TCGATCTTTCAATCCACACTGAC 58.754 43.478 0.00 0.00 0.00 3.51
87 88 5.152623 TCTTCGATCTTTCAATCCACACT 57.847 39.130 0.00 0.00 0.00 3.55
127 134 1.078001 AGCCAACGATTTACCCGGG 60.078 57.895 22.25 22.25 0.00 5.73
128 135 0.391927 TCAGCCAACGATTTACCCGG 60.392 55.000 0.00 0.00 0.00 5.73
137 144 2.346803 GCTACAAAGATCAGCCAACGA 58.653 47.619 0.00 0.00 0.00 3.85
157 164 2.222999 TGATAACATCATGTGCGCAACG 60.223 45.455 14.00 3.11 33.59 4.10
178 185 1.795170 AAGCGCGGTTTCTGCAACAT 61.795 50.000 19.31 0.00 37.07 2.71
212 219 0.317269 CAAACCACAGCAGCTTCACG 60.317 55.000 0.00 0.00 0.00 4.35
241 250 3.697747 CCCCGGTGTTACGAGGCA 61.698 66.667 0.00 0.00 35.47 4.75
259 271 2.824041 ATTCATGTCGCCCACCGC 60.824 61.111 0.00 0.00 36.73 5.68
278 881 3.374988 TGAGCCGTGTTGATTGATTCATC 59.625 43.478 0.00 0.00 33.34 2.92
309 919 7.049140 AGCGAACAAAAACAAGAAAGAAAAG 57.951 32.000 0.00 0.00 0.00 2.27
310 920 6.183359 CGAGCGAACAAAAACAAGAAAGAAAA 60.183 34.615 0.00 0.00 0.00 2.29
320 930 1.529438 CCTAGCGAGCGAACAAAAACA 59.471 47.619 0.00 0.00 0.00 2.83
326 936 4.143333 GGGCCTAGCGAGCGAACA 62.143 66.667 0.84 0.00 0.00 3.18
344 954 7.772332 AATAACACGATACAGAAACTGGATC 57.228 36.000 12.41 12.41 45.58 3.36
373 984 0.479378 GTAGGAGAGGAGGGACCGAT 59.521 60.000 0.00 0.00 44.74 4.18
381 992 5.365025 TCCAATGATTTCAGTAGGAGAGGAG 59.635 44.000 0.00 0.00 0.00 3.69
382 993 5.280499 TCCAATGATTTCAGTAGGAGAGGA 58.720 41.667 0.00 0.00 0.00 3.71
383 994 5.454471 CCTCCAATGATTTCAGTAGGAGAGG 60.454 48.000 19.29 11.46 39.38 3.69
385 996 5.280499 TCCTCCAATGATTTCAGTAGGAGA 58.720 41.667 19.29 8.94 39.38 3.71
522 1134 8.440021 TTGTTTTAGATTAGACGACTAACGAC 57.560 34.615 9.49 5.19 45.77 4.34
528 1140 8.897872 TTTCCTTTGTTTTAGATTAGACGACT 57.102 30.769 0.00 0.00 0.00 4.18
531 1143 9.262472 CGAATTTCCTTTGTTTTAGATTAGACG 57.738 33.333 0.00 0.00 0.00 4.18
534 1146 9.262472 CGACGAATTTCCTTTGTTTTAGATTAG 57.738 33.333 0.00 0.00 31.22 1.73
535 1147 8.776470 ACGACGAATTTCCTTTGTTTTAGATTA 58.224 29.630 0.00 0.00 31.22 1.75
536 1148 7.645402 ACGACGAATTTCCTTTGTTTTAGATT 58.355 30.769 0.00 0.00 31.22 2.40
551 1163 0.511221 CAAGCACCGACGACGAATTT 59.489 50.000 9.28 0.00 42.66 1.82
553 1165 2.380410 GCAAGCACCGACGACGAAT 61.380 57.895 9.28 0.00 42.66 3.34
614 1257 1.272212 TGCACAGTCACGCATAGAGAA 59.728 47.619 0.00 0.00 31.95 2.87
616 1259 1.275505 CTGCACAGTCACGCATAGAG 58.724 55.000 0.00 0.00 37.54 2.43
660 1303 2.438434 GCACTGGGCTATTGGCGT 60.438 61.111 0.00 0.00 42.94 5.68
833 1530 5.289917 TCGCCTGTTTGTTTGTATGTATG 57.710 39.130 0.00 0.00 0.00 2.39
907 1604 2.954020 TTCGGATAAGCCTCTGCGCG 62.954 60.000 0.00 0.00 44.33 6.86
935 1632 1.229400 ATGGGTCTGGGTACACGGT 60.229 57.895 3.31 0.00 0.00 4.83
942 1639 3.017581 GCTGGGATGGGTCTGGGT 61.018 66.667 0.00 0.00 0.00 4.51
1180 2799 2.669240 CGAAGTTCACCCTCCCCC 59.331 66.667 3.32 0.00 0.00 5.40
1205 2824 2.282462 GAGCCCCACACCTTGGTG 60.282 66.667 17.34 17.34 45.25 4.17
1544 3824 0.603065 AGCGCCCAAATTCAAAGACC 59.397 50.000 2.29 0.00 0.00 3.85
1597 3877 2.700773 GCAGGTCATCGGTTTGGGC 61.701 63.158 0.00 0.00 0.00 5.36
1622 3902 1.373497 CTGCGACTGGACACTGGAC 60.373 63.158 0.00 0.00 0.00 4.02
1623 3903 1.806461 GACTGCGACTGGACACTGGA 61.806 60.000 0.00 0.00 0.00 3.86
1624 3904 1.373497 GACTGCGACTGGACACTGG 60.373 63.158 0.00 0.00 0.00 4.00
1625 3905 1.373497 GGACTGCGACTGGACACTG 60.373 63.158 0.00 0.00 0.00 3.66
1626 3906 2.574955 GGGACTGCGACTGGACACT 61.575 63.158 0.00 0.00 0.00 3.55
1627 3907 2.048127 GGGACTGCGACTGGACAC 60.048 66.667 0.00 0.00 0.00 3.67
1628 3908 1.913262 ATGGGACTGCGACTGGACA 60.913 57.895 0.00 0.00 0.00 4.02
1661 3942 6.310711 GCTACATAAACAACTGAGTCAGTACC 59.689 42.308 25.71 0.00 44.62 3.34
1666 3947 3.678072 GCGCTACATAAACAACTGAGTCA 59.322 43.478 0.00 0.00 0.00 3.41
1680 3961 0.034059 GCTCCATAGTGGCGCTACAT 59.966 55.000 26.36 13.98 44.42 2.29
1681 3962 1.441729 GCTCCATAGTGGCGCTACA 59.558 57.895 26.36 12.25 44.42 2.74
1682 3963 1.661821 CGCTCCATAGTGGCGCTAC 60.662 63.158 17.10 17.10 45.57 3.58
1683 3964 1.796190 CTCGCTCCATAGTGGCGCTA 61.796 60.000 10.65 10.65 45.57 4.26
1684 3965 3.144120 CTCGCTCCATAGTGGCGCT 62.144 63.158 7.64 5.62 45.57 5.92
1685 3966 2.629050 TTCTCGCTCCATAGTGGCGC 62.629 60.000 0.00 0.00 44.38 6.53
1687 3968 2.024176 TTTTCTCGCTCCATAGTGGC 57.976 50.000 0.00 0.00 37.47 5.01
1707 3988 3.732471 GCGGTATGTGTGTGTGTGTTTTT 60.732 43.478 0.00 0.00 0.00 1.94
1708 3989 2.223386 GCGGTATGTGTGTGTGTGTTTT 60.223 45.455 0.00 0.00 0.00 2.43
1709 3990 1.332375 GCGGTATGTGTGTGTGTGTTT 59.668 47.619 0.00 0.00 0.00 2.83
1710 3991 0.941542 GCGGTATGTGTGTGTGTGTT 59.058 50.000 0.00 0.00 0.00 3.32
1711 3992 0.882927 GGCGGTATGTGTGTGTGTGT 60.883 55.000 0.00 0.00 0.00 3.72
1712 3993 1.573829 GGGCGGTATGTGTGTGTGTG 61.574 60.000 0.00 0.00 0.00 3.82
1713 3994 1.302192 GGGCGGTATGTGTGTGTGT 60.302 57.895 0.00 0.00 0.00 3.72
1714 3995 2.038269 GGGGCGGTATGTGTGTGTG 61.038 63.158 0.00 0.00 0.00 3.82
1715 3996 2.221299 AGGGGCGGTATGTGTGTGT 61.221 57.895 0.00 0.00 0.00 3.72
1716 3997 1.745115 CAGGGGCGGTATGTGTGTG 60.745 63.158 0.00 0.00 0.00 3.82
1717 3998 2.221299 ACAGGGGCGGTATGTGTGT 61.221 57.895 0.00 0.00 0.00 3.72
1718 3999 1.745115 CACAGGGGCGGTATGTGTG 60.745 63.158 0.00 0.00 39.54 3.82
1719 4000 2.668632 CACAGGGGCGGTATGTGT 59.331 61.111 0.00 0.00 39.54 3.72
1720 4001 2.824041 GCACAGGGGCGGTATGTG 60.824 66.667 0.31 0.31 45.59 3.21
1728 4009 4.660938 AAGGGAACGCACAGGGGC 62.661 66.667 0.00 0.00 0.00 5.80
1729 4010 2.115266 AAAGGGAACGCACAGGGG 59.885 61.111 0.00 0.00 0.00 4.79
1730 4011 2.919494 GCAAAGGGAACGCACAGGG 61.919 63.158 0.00 0.00 0.00 4.45
1731 4012 1.526575 ATGCAAAGGGAACGCACAGG 61.527 55.000 0.00 0.00 38.73 4.00
1732 4013 0.387622 CATGCAAAGGGAACGCACAG 60.388 55.000 0.00 0.00 38.73 3.66
1733 4014 1.659233 CATGCAAAGGGAACGCACA 59.341 52.632 0.00 0.00 38.73 4.57
1734 4015 1.080569 CCATGCAAAGGGAACGCAC 60.081 57.895 0.00 0.00 38.73 5.34
1735 4016 0.611618 ATCCATGCAAAGGGAACGCA 60.612 50.000 8.91 0.00 40.50 5.24
1736 4017 0.532115 AATCCATGCAAAGGGAACGC 59.468 50.000 8.91 0.00 36.62 4.84
1737 4018 2.282701 CAATCCATGCAAAGGGAACG 57.717 50.000 8.91 0.96 36.62 3.95
1748 4029 2.924926 CAATTTCCACGTGCAATCCATG 59.075 45.455 10.91 2.70 36.50 3.66
1749 4030 2.674747 GCAATTTCCACGTGCAATCCAT 60.675 45.455 10.91 0.00 38.19 3.41
1750 4031 1.336702 GCAATTTCCACGTGCAATCCA 60.337 47.619 10.91 0.00 38.19 3.41
1751 4032 1.067635 AGCAATTTCCACGTGCAATCC 60.068 47.619 10.91 5.78 40.83 3.01
1752 4033 2.352503 AGCAATTTCCACGTGCAATC 57.647 45.000 10.91 0.20 40.83 2.67
1753 4034 3.574614 GTTAGCAATTTCCACGTGCAAT 58.425 40.909 10.91 7.71 40.83 3.56
1754 4035 2.287909 GGTTAGCAATTTCCACGTGCAA 60.288 45.455 10.91 0.00 40.83 4.08
1755 4036 1.268352 GGTTAGCAATTTCCACGTGCA 59.732 47.619 10.91 0.00 40.83 4.57
1756 4037 1.727857 CGGTTAGCAATTTCCACGTGC 60.728 52.381 10.91 0.00 38.59 5.34
1757 4038 1.533731 ACGGTTAGCAATTTCCACGTG 59.466 47.619 9.08 9.08 31.60 4.49
1758 4039 1.802365 GACGGTTAGCAATTTCCACGT 59.198 47.619 0.00 0.00 35.89 4.49
1759 4040 1.201877 CGACGGTTAGCAATTTCCACG 60.202 52.381 0.00 0.00 0.00 4.94
1760 4041 1.129811 CCGACGGTTAGCAATTTCCAC 59.870 52.381 5.48 0.00 0.00 4.02
1761 4042 1.270947 ACCGACGGTTAGCAATTTCCA 60.271 47.619 15.37 0.00 27.29 3.53
1762 4043 1.445871 ACCGACGGTTAGCAATTTCC 58.554 50.000 15.37 0.00 27.29 3.13
1763 4044 3.545426 GCATACCGACGGTTAGCAATTTC 60.545 47.826 27.06 2.70 37.09 2.17
1764 4045 2.353579 GCATACCGACGGTTAGCAATTT 59.646 45.455 27.06 0.00 37.09 1.82
1786 4067 0.469917 CCGTCAATGGGGAGCATACT 59.530 55.000 0.00 0.00 0.00 2.12
1787 4068 1.166531 GCCGTCAATGGGGAGCATAC 61.167 60.000 0.00 0.00 0.00 2.39
1788 4069 1.148273 GCCGTCAATGGGGAGCATA 59.852 57.895 0.00 0.00 0.00 3.14
1789 4070 2.124151 GCCGTCAATGGGGAGCAT 60.124 61.111 0.00 0.00 0.00 3.79
1790 4071 4.424711 GGCCGTCAATGGGGAGCA 62.425 66.667 0.00 0.00 0.00 4.26
1791 4072 3.721370 ATGGCCGTCAATGGGGAGC 62.721 63.158 0.00 0.00 0.00 4.70
1792 4073 1.825191 CATGGCCGTCAATGGGGAG 60.825 63.158 0.00 0.00 0.00 4.30
1793 4074 2.275089 CATGGCCGTCAATGGGGA 59.725 61.111 0.00 0.00 0.00 4.81
1794 4075 2.044053 ACATGGCCGTCAATGGGG 60.044 61.111 0.00 0.00 0.00 4.96
1795 4076 1.378382 TGACATGGCCGTCAATGGG 60.378 57.895 10.68 0.00 42.82 4.00
1811 4092 3.071206 GAGACGGGCTGAGGCTGA 61.071 66.667 22.53 0.00 37.92 4.26
1829 4110 2.403132 GACCTTGGAGTGGTGCTGCT 62.403 60.000 0.00 0.00 38.03 4.24
1836 4117 1.227823 TGTTGCGACCTTGGAGTGG 60.228 57.895 0.45 0.00 0.00 4.00
1840 4121 1.525077 GTGGTGTTGCGACCTTGGA 60.525 57.895 0.45 0.00 36.88 3.53
1841 4122 2.551912 GGTGGTGTTGCGACCTTGG 61.552 63.158 0.45 0.00 41.98 3.61
1845 4126 2.668550 GGAGGTGGTGTTGCGACC 60.669 66.667 0.45 0.00 45.08 4.79
1846 4127 2.668550 GGGAGGTGGTGTTGCGAC 60.669 66.667 0.00 0.00 0.00 5.19
1847 4128 3.948719 GGGGAGGTGGTGTTGCGA 61.949 66.667 0.00 0.00 0.00 5.10
1850 4131 4.344865 CCGGGGGAGGTGGTGTTG 62.345 72.222 0.00 0.00 0.00 3.33
1889 4170 4.941309 ACCACAAACCCCGTCGGC 62.941 66.667 5.50 0.00 33.26 5.54
1893 4174 1.524393 GAACGACCACAAACCCCGT 60.524 57.895 0.00 0.00 34.74 5.28
1903 4207 0.601558 CTTTCGGAGGAGAACGACCA 59.398 55.000 0.00 0.00 39.04 4.02
1916 4220 7.219535 CAGCATAGATTTGATTTTGTCTTTCGG 59.780 37.037 0.00 0.00 0.00 4.30
1959 4263 1.460504 GAATCCGAGAACCCCAAACC 58.539 55.000 0.00 0.00 0.00 3.27
1977 4281 2.284921 CTGGGCCACCTCTCTGGA 60.285 66.667 0.00 0.00 39.71 3.86
1980 4284 2.284995 GTCCTGGGCCACCTCTCT 60.285 66.667 0.00 0.00 37.76 3.10
2019 4323 1.752501 CGCCACATTTCTCGCCGTAG 61.753 60.000 0.00 0.00 0.00 3.51
2024 4328 4.520846 CGCCGCCACATTTCTCGC 62.521 66.667 0.00 0.00 0.00 5.03
2041 4345 0.310854 CAAAGAGAAACACCACCGCC 59.689 55.000 0.00 0.00 0.00 6.13
2043 4347 0.310854 GCCAAAGAGAAACACCACCG 59.689 55.000 0.00 0.00 0.00 4.94
2057 4361 2.904866 GTCGCCCACACAGCCAAA 60.905 61.111 0.00 0.00 0.00 3.28
2075 4382 3.391665 GATCCCCACCACCTCGCTG 62.392 68.421 0.00 0.00 0.00 5.18
2086 4396 2.445845 CCACCGCTAGGATCCCCA 60.446 66.667 8.55 0.00 41.02 4.96
2088 4398 4.301027 CGCCACCGCTAGGATCCC 62.301 72.222 8.55 0.00 41.02 3.85
2110 4420 3.576078 ATGGGAGATACAATTGCCGAA 57.424 42.857 5.05 0.00 0.00 4.30
2134 4444 1.111277 AAAACAAGCCTCCACACCAC 58.889 50.000 0.00 0.00 0.00 4.16
2159 4469 4.567597 ACGGTCCCAGGTCCACCA 62.568 66.667 0.00 0.00 38.89 4.17
2183 4493 4.758251 CTCACGCATGCCACCCGA 62.758 66.667 13.15 0.59 0.00 5.14
2192 4502 4.101448 GCCTGGGGTCTCACGCAT 62.101 66.667 0.00 0.00 32.03 4.73
2211 4521 2.383527 CGCTGAACCACGGAGCTTC 61.384 63.158 0.00 0.00 0.00 3.86
2218 4528 3.767230 CGTCTGCGCTGAACCACG 61.767 66.667 19.14 14.42 0.00 4.94
2231 4541 1.564207 CACATGCATCATCGTCGTCT 58.436 50.000 0.00 0.00 0.00 4.18
2251 4561 2.432628 CGAGAGGGACGCAACACC 60.433 66.667 0.00 0.00 0.00 4.16
2330 4641 3.490759 CGTCACTGCCATGACCGC 61.491 66.667 10.85 0.00 45.23 5.68
2332 4643 3.127533 GCCGTCACTGCCATGACC 61.128 66.667 10.85 0.00 45.23 4.02
2343 4654 4.056125 CTGAGCTCCACGCCGTCA 62.056 66.667 12.15 0.00 40.39 4.35
2350 4661 1.404315 CGAAAGGTACCTGAGCTCCAC 60.404 57.143 17.14 3.85 33.71 4.02


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

AutoCloner maintained by Alex Coulton.