Multiple sequence alignment - TraesCS5D01G108900

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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 TraesCS5D01G108900 chr5D 100.000 2414 0 0 1 2414 122628431 122626018 0.000000e+00 4458.0
1 TraesCS5D01G108900 chr5D 90.336 1221 79 10 553 1746 399295778 399296986 0.000000e+00 1565.0
2 TraesCS5D01G108900 chr5D 89.655 1218 84 18 545 1750 424819155 424820342 0.000000e+00 1513.0
3 TraesCS5D01G108900 chr5D 95.047 949 45 2 801 1748 408295039 408295986 0.000000e+00 1491.0
4 TraesCS5D01G108900 chr5D 90.395 885 73 10 871 1748 538241575 538240696 0.000000e+00 1153.0
5 TraesCS5D01G108900 chr5D 81.935 620 63 26 1815 2414 402727732 402727142 1.680000e-131 479.0
6 TraesCS5D01G108900 chr5D 90.544 349 13 3 545 874 538253583 538253236 6.120000e-121 444.0
7 TraesCS5D01G108900 chr5D 83.085 201 22 7 2184 2384 559608837 559609025 3.190000e-39 172.0
8 TraesCS5D01G108900 chr6D 90.325 1230 84 17 545 1746 120664845 120666067 0.000000e+00 1580.0
9 TraesCS5D01G108900 chr7D 91.880 1133 68 6 634 1746 557359129 557360257 0.000000e+00 1561.0
10 TraesCS5D01G108900 chr6A 89.283 1185 84 16 555 1718 397974401 397973239 0.000000e+00 1445.0
11 TraesCS5D01G108900 chr1D 92.661 1022 46 6 745 1746 12411553 12412565 0.000000e+00 1445.0
12 TraesCS5D01G108900 chr3A 87.911 1216 120 8 553 1746 534368963 534367753 0.000000e+00 1406.0
13 TraesCS5D01G108900 chr3A 87.142 1221 98 20 539 1748 743517373 743518545 0.000000e+00 1330.0
14 TraesCS5D01G108900 chr3A 87.565 1158 101 15 552 1697 23344584 23343458 0.000000e+00 1301.0
15 TraesCS5D01G108900 chr3A 85.021 948 108 22 537 1470 140954245 140953318 0.000000e+00 933.0
16 TraesCS5D01G108900 chr1B 92.260 969 62 6 784 1746 659569126 659568165 0.000000e+00 1362.0
17 TraesCS5D01G108900 chr4D 87.052 1228 81 30 545 1748 477156199 477157372 0.000000e+00 1315.0
18 TraesCS5D01G108900 chr4D 91.129 496 24 12 552 1028 375563615 375563121 0.000000e+00 654.0
19 TraesCS5D01G108900 chr4D 92.701 274 15 3 537 807 401538239 401538510 8.090000e-105 390.0
20 TraesCS5D01G108900 chr4D 89.286 56 2 3 2189 2240 384952713 384952768 1.550000e-07 67.6
21 TraesCS5D01G108900 chr4D 96.970 33 0 1 2173 2205 384952810 384952779 1.000000e-03 54.7
22 TraesCS5D01G108900 chr5A 92.897 535 27 5 1 528 135154342 135153812 0.000000e+00 767.0
23 TraesCS5D01G108900 chr5B 91.485 458 20 5 1 457 136018416 136017977 1.590000e-171 612.0
24 TraesCS5D01G108900 chr2A 90.385 416 29 8 537 946 739657388 739656978 9.820000e-149 536.0
25 TraesCS5D01G108900 chr7A 77.143 210 28 15 2185 2388 521563679 521563874 1.180000e-18 104.0
26 TraesCS5D01G108900 chr3B 84.848 99 12 3 1802 1898 325875931 325875834 1.980000e-16 97.1
27 TraesCS5D01G108900 chr3D 91.667 48 4 0 2191 2238 418752565 418752612 1.550000e-07 67.6
28 TraesCS5D01G108900 chr3D 100.000 28 0 0 1815 1842 545698453 545698480 4.000000e-03 52.8


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 TraesCS5D01G108900 chr5D 122626018 122628431 2413 True 4458 4458 100.000 1 2414 1 chr5D.!!$R1 2413
1 TraesCS5D01G108900 chr5D 399295778 399296986 1208 False 1565 1565 90.336 553 1746 1 chr5D.!!$F1 1193
2 TraesCS5D01G108900 chr5D 424819155 424820342 1187 False 1513 1513 89.655 545 1750 1 chr5D.!!$F3 1205
3 TraesCS5D01G108900 chr5D 408295039 408295986 947 False 1491 1491 95.047 801 1748 1 chr5D.!!$F2 947
4 TraesCS5D01G108900 chr5D 538240696 538241575 879 True 1153 1153 90.395 871 1748 1 chr5D.!!$R3 877
5 TraesCS5D01G108900 chr5D 402727142 402727732 590 True 479 479 81.935 1815 2414 1 chr5D.!!$R2 599
6 TraesCS5D01G108900 chr6D 120664845 120666067 1222 False 1580 1580 90.325 545 1746 1 chr6D.!!$F1 1201
7 TraesCS5D01G108900 chr7D 557359129 557360257 1128 False 1561 1561 91.880 634 1746 1 chr7D.!!$F1 1112
8 TraesCS5D01G108900 chr6A 397973239 397974401 1162 True 1445 1445 89.283 555 1718 1 chr6A.!!$R1 1163
9 TraesCS5D01G108900 chr1D 12411553 12412565 1012 False 1445 1445 92.661 745 1746 1 chr1D.!!$F1 1001
10 TraesCS5D01G108900 chr3A 534367753 534368963 1210 True 1406 1406 87.911 553 1746 1 chr3A.!!$R3 1193
11 TraesCS5D01G108900 chr3A 743517373 743518545 1172 False 1330 1330 87.142 539 1748 1 chr3A.!!$F1 1209
12 TraesCS5D01G108900 chr3A 23343458 23344584 1126 True 1301 1301 87.565 552 1697 1 chr3A.!!$R1 1145
13 TraesCS5D01G108900 chr3A 140953318 140954245 927 True 933 933 85.021 537 1470 1 chr3A.!!$R2 933
14 TraesCS5D01G108900 chr1B 659568165 659569126 961 True 1362 1362 92.260 784 1746 1 chr1B.!!$R1 962
15 TraesCS5D01G108900 chr4D 477156199 477157372 1173 False 1315 1315 87.052 545 1748 1 chr4D.!!$F3 1203
16 TraesCS5D01G108900 chr5A 135153812 135154342 530 True 767 767 92.897 1 528 1 chr5A.!!$R1 527

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
332 338 0.026674 CACGTTGCCGCATCTATGTG 59.973 55.0 0.0 0.0 37.7 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1876 0.036483 TGCCACACATGTATGCGAGT 60.036 50.0 0.0 0.0 0.0 4.18 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
55 56 1.207085 CGATCGCTCCTACGGTAGC 59.793 63.158 9.70 0.35 35.33 3.58
63 64 5.618236 TCGCTCCTACGGTAGCATATATAT 58.382 41.667 9.70 0.00 38.70 0.86
64 65 6.762333 TCGCTCCTACGGTAGCATATATATA 58.238 40.000 9.70 0.00 38.70 0.86
65 66 6.648310 TCGCTCCTACGGTAGCATATATATAC 59.352 42.308 9.70 0.00 38.70 1.47
66 67 6.426025 CGCTCCTACGGTAGCATATATATACA 59.574 42.308 9.70 0.00 38.70 2.29
67 68 7.119407 CGCTCCTACGGTAGCATATATATACAT 59.881 40.741 9.70 0.00 38.70 2.29
70 71 7.668469 TCCTACGGTAGCATATATATACATGGG 59.332 40.741 9.70 7.61 0.00 4.00
88 89 2.450243 GAGAGAGGTGGGGTGGGA 59.550 66.667 0.00 0.00 0.00 4.37
91 92 1.134438 AGAGAGGTGGGGTGGGAAAC 61.134 60.000 0.00 0.00 0.00 2.78
152 158 6.313905 CAGTTATACTAACTCAAACCAGGCAG 59.686 42.308 0.00 0.00 0.00 4.85
179 185 0.256752 CCATGGCAGGACATCTCCAA 59.743 55.000 0.00 0.00 39.39 3.53
188 194 4.518970 GCAGGACATCTCCAACAGTTTTAA 59.481 41.667 0.00 0.00 39.39 1.52
209 215 1.737236 GATAGTGTTGCGTTCATGGCA 59.263 47.619 0.00 0.00 38.93 4.92
259 265 3.433598 GGTGGAATAGATTACTGGCAGCA 60.434 47.826 15.89 0.00 0.00 4.41
278 284 7.176340 TGGCAGCAATAATTTTTAAATTGGCTT 59.824 29.630 14.97 4.72 38.41 4.35
323 329 2.725815 GCTTGTTCACGTTGCCGC 60.726 61.111 0.00 0.00 37.70 6.53
328 334 0.319986 TGTTCACGTTGCCGCATCTA 60.320 50.000 0.00 0.00 37.70 1.98
330 336 1.006086 TTCACGTTGCCGCATCTATG 58.994 50.000 0.00 0.00 37.70 2.23
331 337 0.108377 TCACGTTGCCGCATCTATGT 60.108 50.000 0.00 0.00 37.70 2.29
332 338 0.026674 CACGTTGCCGCATCTATGTG 59.973 55.000 0.00 0.00 37.70 3.21
338 344 1.413812 TGCCGCATCTATGTGAGTCAT 59.586 47.619 5.09 0.00 40.61 3.06
341 347 3.573598 CCGCATCTATGTGAGTCATCTC 58.426 50.000 5.09 0.00 40.61 2.75
373 379 2.098934 TGCACTTCTCGCACAAAACAAT 59.901 40.909 0.00 0.00 33.55 2.71
397 403 0.518636 CTTGCACATCACAAGGTCGG 59.481 55.000 0.00 0.00 40.68 4.79
400 406 1.076332 GCACATCACAAGGTCGGTAC 58.924 55.000 0.00 0.00 0.00 3.34
436 442 3.097614 AGTTCAGCGTTAGGGTATGAGT 58.902 45.455 0.00 0.00 0.00 3.41
482 489 4.383052 GCGTGCATATATATGGATAGCGTC 59.617 45.833 21.50 12.07 36.43 5.19
483 490 5.519722 CGTGCATATATATGGATAGCGTCA 58.480 41.667 21.50 7.79 36.43 4.35
484 491 6.152379 CGTGCATATATATGGATAGCGTCAT 58.848 40.000 21.50 0.00 36.43 3.06
499 507 2.883730 CATTGCGTGCATGGCAGC 60.884 61.111 13.96 5.11 42.12 5.25
507 515 0.665369 GTGCATGGCAGCAGTCAAAC 60.665 55.000 11.09 0.00 46.69 2.93
530 538 3.616956 TGGCATCTCCAACAGTTAGAG 57.383 47.619 2.47 2.47 43.21 2.43
531 539 2.284190 GGCATCTCCAACAGTTAGAGC 58.716 52.381 3.97 2.59 34.01 4.09
532 540 2.355108 GGCATCTCCAACAGTTAGAGCA 60.355 50.000 3.97 0.00 34.01 4.26
533 541 3.539604 GCATCTCCAACAGTTAGAGCAT 58.460 45.455 3.97 0.00 0.00 3.79
534 542 3.559242 GCATCTCCAACAGTTAGAGCATC 59.441 47.826 3.97 0.00 0.00 3.91
535 543 7.654770 GGCATCTCCAACAGTTAGAGCATCT 62.655 48.000 3.97 0.00 41.74 2.90
546 554 2.378028 GAGCATCTCCAACAGTCGC 58.622 57.895 0.00 0.00 0.00 5.19
547 555 1.416813 GAGCATCTCCAACAGTCGCG 61.417 60.000 0.00 0.00 0.00 5.87
548 556 3.084579 CATCTCCAACAGTCGCGC 58.915 61.111 0.00 0.00 0.00 6.86
549 557 1.737735 CATCTCCAACAGTCGCGCA 60.738 57.895 8.75 0.00 0.00 6.09
550 558 1.086067 CATCTCCAACAGTCGCGCAT 61.086 55.000 8.75 0.00 0.00 4.73
713 746 0.859232 CTATAAATTGCGGCGCTCGT 59.141 50.000 33.26 17.24 41.72 4.18
728 761 3.320078 CGTCACGCGCCTATTCCG 61.320 66.667 5.73 0.00 0.00 4.30
942 1006 3.936203 ACCTTCCAGACGGCGCAA 61.936 61.111 10.83 0.00 0.00 4.85
1077 1141 1.664649 TCTTCGCACGGCACAAGAG 60.665 57.895 0.00 0.00 0.00 2.85
1307 1372 1.679944 CGTTGAGAATGGTGGGCAGAT 60.680 52.381 0.00 0.00 0.00 2.90
1317 1382 2.846206 TGGTGGGCAGATGATCTTTACT 59.154 45.455 0.00 0.00 0.00 2.24
1350 1415 0.036765 GTTGGGACGACATGTGGCTA 60.037 55.000 1.15 0.00 0.00 3.93
1399 1467 0.247537 CGACGATGACGATGACGACA 60.248 55.000 0.00 0.00 45.90 4.35
1409 1477 1.352156 GATGACGACAACGACTGGGC 61.352 60.000 0.00 0.00 42.66 5.36
1641 1722 1.440188 CGCGCGCTCAATTTTGACA 60.440 52.632 30.48 0.00 32.90 3.58
1654 1735 0.249868 TTTGACACGTCTGCTGGAGG 60.250 55.000 0.00 0.00 36.08 4.30
1748 1833 2.484417 CGGCTGTTGGAGATGCTCTAAT 60.484 50.000 0.00 0.00 33.81 1.73
1749 1834 3.243873 CGGCTGTTGGAGATGCTCTAATA 60.244 47.826 0.00 0.00 33.81 0.98
1751 1836 4.754114 GGCTGTTGGAGATGCTCTAATAAG 59.246 45.833 0.00 0.00 33.81 1.73
1752 1837 4.213059 GCTGTTGGAGATGCTCTAATAAGC 59.787 45.833 12.05 12.05 42.82 3.09
1753 1838 5.609423 CTGTTGGAGATGCTCTAATAAGCT 58.391 41.667 0.00 0.00 42.94 3.74
1754 1839 6.731292 TGTTGGAGATGCTCTAATAAGCTA 57.269 37.500 0.00 0.00 42.94 3.32
1755 1840 6.516718 TGTTGGAGATGCTCTAATAAGCTAC 58.483 40.000 0.00 0.00 42.94 3.58
1756 1841 6.325028 TGTTGGAGATGCTCTAATAAGCTACT 59.675 38.462 0.00 0.00 42.94 2.57
1757 1842 7.505923 TGTTGGAGATGCTCTAATAAGCTACTA 59.494 37.037 0.00 0.00 42.94 1.82
1758 1843 8.527810 GTTGGAGATGCTCTAATAAGCTACTAT 58.472 37.037 0.00 0.00 42.94 2.12
1759 1844 9.755122 TTGGAGATGCTCTAATAAGCTACTATA 57.245 33.333 0.00 0.00 42.94 1.31
1760 1845 9.402320 TGGAGATGCTCTAATAAGCTACTATAG 57.598 37.037 0.00 0.00 42.94 1.31
1783 1868 4.623814 ATGACGTGCATGGAGGTG 57.376 55.556 17.61 0.00 35.42 4.00
1784 1869 1.078214 ATGACGTGCATGGAGGTGG 60.078 57.895 17.61 0.00 35.42 4.61
1785 1870 1.552799 ATGACGTGCATGGAGGTGGA 61.553 55.000 17.61 4.19 35.42 4.02
1786 1871 1.003839 GACGTGCATGGAGGTGGAA 60.004 57.895 17.61 0.00 0.00 3.53
1787 1872 1.298859 GACGTGCATGGAGGTGGAAC 61.299 60.000 17.61 0.00 0.00 3.62
1788 1873 1.003355 CGTGCATGGAGGTGGAACT 60.003 57.895 0.00 0.00 36.74 3.01
1789 1874 0.249120 CGTGCATGGAGGTGGAACTA 59.751 55.000 0.00 0.00 36.74 2.24
1790 1875 1.740380 CGTGCATGGAGGTGGAACTAG 60.740 57.143 0.00 0.00 36.74 2.57
1791 1876 1.555075 GTGCATGGAGGTGGAACTAGA 59.445 52.381 0.00 0.00 36.74 2.43
1792 1877 1.555075 TGCATGGAGGTGGAACTAGAC 59.445 52.381 0.00 0.00 36.74 2.59
1793 1878 1.834263 GCATGGAGGTGGAACTAGACT 59.166 52.381 0.00 0.00 36.74 3.24
1794 1879 2.159028 GCATGGAGGTGGAACTAGACTC 60.159 54.545 0.00 0.00 36.74 3.36
1795 1880 1.835494 TGGAGGTGGAACTAGACTCG 58.165 55.000 0.00 0.00 36.74 4.18
1796 1881 0.456628 GGAGGTGGAACTAGACTCGC 59.543 60.000 0.00 0.00 36.74 5.03
1797 1882 1.174783 GAGGTGGAACTAGACTCGCA 58.825 55.000 0.00 0.00 36.74 5.10
1798 1883 1.751924 GAGGTGGAACTAGACTCGCAT 59.248 52.381 0.00 0.00 36.74 4.73
1799 1884 2.950309 GAGGTGGAACTAGACTCGCATA 59.050 50.000 0.00 0.00 36.74 3.14
1800 1885 2.688958 AGGTGGAACTAGACTCGCATAC 59.311 50.000 0.00 0.00 36.74 2.39
1801 1886 2.426024 GGTGGAACTAGACTCGCATACA 59.574 50.000 0.00 0.00 36.74 2.29
1802 1887 3.068307 GGTGGAACTAGACTCGCATACAT 59.932 47.826 0.00 0.00 36.74 2.29
1803 1888 4.045104 GTGGAACTAGACTCGCATACATG 58.955 47.826 0.00 0.00 0.00 3.21
1804 1889 3.699538 TGGAACTAGACTCGCATACATGT 59.300 43.478 2.69 2.69 0.00 3.21
1805 1890 4.045104 GGAACTAGACTCGCATACATGTG 58.955 47.826 9.11 0.00 39.55 3.21
1806 1891 4.440250 GGAACTAGACTCGCATACATGTGT 60.440 45.833 9.11 0.00 39.25 3.72
1807 1892 4.033990 ACTAGACTCGCATACATGTGTG 57.966 45.455 17.50 17.50 39.25 3.82
1808 1893 2.299993 AGACTCGCATACATGTGTGG 57.700 50.000 22.20 13.14 39.25 4.17
1809 1894 0.652592 GACTCGCATACATGTGTGGC 59.347 55.000 22.20 14.70 39.25 5.01
1810 1895 0.036483 ACTCGCATACATGTGTGGCA 60.036 50.000 22.20 0.00 39.25 4.92
1811 1896 0.374758 CTCGCATACATGTGTGGCAC 59.625 55.000 22.20 11.55 39.25 5.01
1812 1897 0.036483 TCGCATACATGTGTGGCACT 60.036 50.000 22.20 0.00 39.25 4.40
1813 1898 0.804364 CGCATACATGTGTGGCACTT 59.196 50.000 22.20 0.59 35.11 3.16
1824 1909 1.694150 TGTGGCACTTAGAGCAACTCT 59.306 47.619 19.83 2.23 43.83 3.24
1851 1936 2.885894 GGTGACCCATTTTGTCCGTTTA 59.114 45.455 0.00 0.00 31.60 2.01
1853 1938 3.057806 GTGACCCATTTTGTCCGTTTAGG 60.058 47.826 0.00 0.00 42.97 2.69
1861 1946 1.548081 TGTCCGTTTAGGTCATCCGA 58.452 50.000 0.00 0.00 41.99 4.55
1862 1947 1.203052 TGTCCGTTTAGGTCATCCGAC 59.797 52.381 0.00 0.00 41.99 4.79
1895 1982 1.730451 AACAAGGCGACCAAAACGGG 61.730 55.000 0.00 0.00 40.22 5.28
1904 1991 0.891904 ACCAAAACGGGCATAGCGTT 60.892 50.000 0.00 0.00 40.22 4.84
1907 1994 0.952010 AAAACGGGCATAGCGTTCGT 60.952 50.000 0.00 0.00 33.66 3.85
1911 1998 2.526120 GGGCATAGCGTTCGTCTGC 61.526 63.158 0.00 7.04 0.00 4.26
1913 2000 0.248907 GGCATAGCGTTCGTCTGCTA 60.249 55.000 7.48 7.48 46.75 3.49
1921 2008 2.159881 GCGTTCGTCTGCTATTCGTTTT 60.160 45.455 0.00 0.00 0.00 2.43
1923 2010 3.121126 CGTTCGTCTGCTATTCGTTTTGT 60.121 43.478 0.00 0.00 0.00 2.83
1926 2013 3.805422 TCGTCTGCTATTCGTTTTGTGTT 59.195 39.130 0.00 0.00 0.00 3.32
1936 2023 1.063469 CGTTTTGTGTTCGCTTGGACT 59.937 47.619 0.00 0.00 0.00 3.85
1943 2030 3.195610 TGTGTTCGCTTGGACTCATATCT 59.804 43.478 0.00 0.00 0.00 1.98
1944 2031 4.401202 TGTGTTCGCTTGGACTCATATCTA 59.599 41.667 0.00 0.00 0.00 1.98
1948 2035 3.891977 TCGCTTGGACTCATATCTAGCTT 59.108 43.478 0.00 0.00 0.00 3.74
1966 2053 7.601856 TCTAGCTTAAATTTGGGTCACATTTG 58.398 34.615 0.00 0.00 28.67 2.32
1967 2054 6.418057 AGCTTAAATTTGGGTCACATTTGA 57.582 33.333 0.00 0.00 28.67 2.69
1968 2055 7.008021 AGCTTAAATTTGGGTCACATTTGAT 57.992 32.000 0.00 0.00 33.11 2.57
1969 2056 7.099120 AGCTTAAATTTGGGTCACATTTGATC 58.901 34.615 0.00 0.00 33.11 2.92
1973 2060 1.721487 GGGTCACATTTGATCCGCG 59.279 57.895 0.00 0.00 43.41 6.46
1987 2086 2.806198 CGCGGCGGACGTTTTCTA 60.806 61.111 15.84 0.00 46.52 2.10
1991 2090 0.738412 CGGCGGACGTTTTCTATGGT 60.738 55.000 0.00 0.00 37.93 3.55
2000 2099 3.257624 ACGTTTTCTATGGTCTCCTCGTT 59.742 43.478 0.00 0.00 0.00 3.85
2003 2102 1.022735 TCTATGGTCTCCTCGTTCGC 58.977 55.000 0.00 0.00 0.00 4.70
2061 2160 1.338136 CGAGAGGCCACCTACCCATT 61.338 60.000 5.01 0.00 31.76 3.16
2069 2168 1.621514 ACCTACCCATTCCACCCCC 60.622 63.158 0.00 0.00 0.00 5.40
2070 2169 2.752807 CCTACCCATTCCACCCCCG 61.753 68.421 0.00 0.00 0.00 5.73
2071 2170 1.999002 CTACCCATTCCACCCCCGT 60.999 63.158 0.00 0.00 0.00 5.28
2072 2171 1.979619 CTACCCATTCCACCCCCGTC 61.980 65.000 0.00 0.00 0.00 4.79
2073 2172 2.480255 TACCCATTCCACCCCCGTCT 62.480 60.000 0.00 0.00 0.00 4.18
2074 2173 2.590092 CCATTCCACCCCCGTCTC 59.410 66.667 0.00 0.00 0.00 3.36
2075 2174 1.995626 CCATTCCACCCCCGTCTCT 60.996 63.158 0.00 0.00 0.00 3.10
2085 2188 1.903183 CCCCCGTCTCTCTCTTTTTCT 59.097 52.381 0.00 0.00 0.00 2.52
2100 2203 6.717084 TCTCTTTTTCTTTCTTTCTCCCATCC 59.283 38.462 0.00 0.00 0.00 3.51
2222 2325 4.530857 GCCGGCCGAGCTGTATGT 62.531 66.667 30.73 0.00 32.22 2.29
2286 2397 3.660111 GCCGCAACCACACAGGAC 61.660 66.667 0.00 0.00 41.22 3.85
2287 2398 3.345808 CCGCAACCACACAGGACG 61.346 66.667 0.00 0.00 41.22 4.79
2288 2399 2.279851 CGCAACCACACAGGACGA 60.280 61.111 0.00 0.00 41.22 4.20
2289 2400 2.594962 CGCAACCACACAGGACGAC 61.595 63.158 0.00 0.00 41.22 4.34
2290 2401 2.594962 GCAACCACACAGGACGACG 61.595 63.158 0.00 0.00 41.22 5.12
2291 2402 2.279918 AACCACACAGGACGACGC 60.280 61.111 0.00 0.00 41.22 5.19
2292 2403 3.802418 AACCACACAGGACGACGCC 62.802 63.158 0.00 0.00 41.22 5.68
2315 2426 3.558099 CTGCACAGAGACGACGCCA 62.558 63.158 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 7.234371 CCACCTCTCTCCCCATGTATATATATG 59.766 44.444 11.48 11.48 0.00 1.78
63 64 0.031111 CCCACCTCTCTCCCCATGTA 60.031 60.000 0.00 0.00 0.00 2.29
64 65 1.307343 CCCACCTCTCTCCCCATGT 60.307 63.158 0.00 0.00 0.00 3.21
65 66 2.074948 CCCCACCTCTCTCCCCATG 61.075 68.421 0.00 0.00 0.00 3.66
66 67 2.374342 CCCCACCTCTCTCCCCAT 59.626 66.667 0.00 0.00 0.00 4.00
67 68 3.208592 ACCCCACCTCTCTCCCCA 61.209 66.667 0.00 0.00 0.00 4.96
70 71 2.689034 CCCACCCCACCTCTCTCC 60.689 72.222 0.00 0.00 0.00 3.71
88 89 0.031994 GCGTTGCATGTTGAGGGTTT 59.968 50.000 0.00 0.00 0.00 3.27
91 92 1.295357 TACGCGTTGCATGTTGAGGG 61.295 55.000 20.78 0.00 0.00 4.30
152 158 1.303561 TCCTGCCATGGTTGACAGC 60.304 57.895 14.67 0.00 0.00 4.40
179 185 6.259167 TGAACGCAACACTATCTTAAAACTGT 59.741 34.615 0.00 0.00 0.00 3.55
188 194 2.009774 GCCATGAACGCAACACTATCT 58.990 47.619 0.00 0.00 0.00 1.98
209 215 1.133976 GCTAGTTCCACCTCCATGCAT 60.134 52.381 0.00 0.00 0.00 3.96
259 265 8.546597 AGTCGCAAGCCAATTTAAAAATTATT 57.453 26.923 0.56 0.00 35.34 1.40
278 284 0.036105 TACGGAGGTACAGAGTCGCA 60.036 55.000 0.00 0.00 0.00 5.10
323 329 6.880942 TCTCAGAGATGACTCACATAGATG 57.119 41.667 0.00 0.00 44.79 2.90
328 334 3.004629 GCGATCTCAGAGATGACTCACAT 59.995 47.826 18.22 0.00 44.79 3.21
330 336 2.357323 TGCGATCTCAGAGATGACTCAC 59.643 50.000 18.22 1.22 44.79 3.51
331 337 2.648059 TGCGATCTCAGAGATGACTCA 58.352 47.619 18.22 2.85 44.79 3.41
332 338 3.567530 CATGCGATCTCAGAGATGACTC 58.432 50.000 18.22 3.19 42.90 3.36
338 344 1.109609 AGTGCATGCGATCTCAGAGA 58.890 50.000 14.09 1.54 0.00 3.10
341 347 1.859703 GAGAAGTGCATGCGATCTCAG 59.140 52.381 28.21 0.00 37.17 3.35
373 379 1.955778 CCTTGTGATGTGCAAGTTCCA 59.044 47.619 0.00 0.00 41.08 3.53
397 403 0.531200 CTGTCCTTGACCTCCCGTAC 59.469 60.000 0.00 0.00 0.00 3.67
400 406 0.037232 GAACTGTCCTTGACCTCCCG 60.037 60.000 0.00 0.00 0.00 5.14
401 407 1.002544 CTGAACTGTCCTTGACCTCCC 59.997 57.143 0.00 0.00 0.00 4.30
408 414 2.069273 CCTAACGCTGAACTGTCCTTG 58.931 52.381 0.00 0.00 0.00 3.61
436 442 7.549842 ACGCCATATAAGTATTGTTGTTGTACA 59.450 33.333 0.00 0.00 0.00 2.90
473 480 1.276844 GCACGCAATGACGCTATCC 59.723 57.895 0.00 0.00 36.19 2.59
482 489 2.883730 GCTGCCATGCACGCAATG 60.884 61.111 11.16 2.78 35.40 2.82
483 490 3.350909 CTGCTGCCATGCACGCAAT 62.351 57.895 11.16 0.00 40.16 3.56
484 491 4.045771 CTGCTGCCATGCACGCAA 62.046 61.111 11.16 0.00 40.16 4.85
499 507 1.747355 GGAGATGCCATGGTTTGACTG 59.253 52.381 14.67 0.00 36.34 3.51
528 536 1.416813 CGCGACTGTTGGAGATGCTC 61.417 60.000 0.00 0.00 0.00 4.26
529 537 1.446792 CGCGACTGTTGGAGATGCT 60.447 57.895 0.00 0.00 0.00 3.79
530 538 3.084579 CGCGACTGTTGGAGATGC 58.915 61.111 0.00 0.00 0.00 3.91
531 539 1.086067 ATGCGCGACTGTTGGAGATG 61.086 55.000 12.10 0.00 0.00 2.90
532 540 0.807667 GATGCGCGACTGTTGGAGAT 60.808 55.000 12.10 0.00 0.00 2.75
533 541 1.446099 GATGCGCGACTGTTGGAGA 60.446 57.895 12.10 0.00 0.00 3.71
534 542 2.792290 CGATGCGCGACTGTTGGAG 61.792 63.158 12.10 0.00 44.57 3.86
535 543 2.809174 CGATGCGCGACTGTTGGA 60.809 61.111 12.10 0.00 44.57 3.53
536 544 3.853330 CCGATGCGCGACTGTTGG 61.853 66.667 12.10 0.83 44.57 3.77
537 545 1.348538 TTACCGATGCGCGACTGTTG 61.349 55.000 12.10 0.00 44.57 3.33
538 546 0.668096 TTTACCGATGCGCGACTGTT 60.668 50.000 12.10 0.00 44.57 3.16
539 547 1.080366 TTTACCGATGCGCGACTGT 60.080 52.632 12.10 5.49 44.57 3.55
540 548 1.343821 GTTTACCGATGCGCGACTG 59.656 57.895 12.10 0.00 44.57 3.51
541 549 1.808390 GGTTTACCGATGCGCGACT 60.808 57.895 12.10 0.00 44.57 4.18
542 550 2.699212 GGTTTACCGATGCGCGAC 59.301 61.111 12.10 0.88 44.57 5.19
596 604 1.143183 GACTTTCCCGCCATCGCTA 59.857 57.895 0.00 0.00 0.00 4.26
713 746 4.136511 TGCGGAATAGGCGCGTGA 62.137 61.111 13.84 0.00 0.00 4.35
728 761 2.694213 GGAAGAGGAAGAGAAGTGTGC 58.306 52.381 0.00 0.00 0.00 4.57
994 1058 0.317160 TCGTGGAAGTTCATCTGCGT 59.683 50.000 5.01 0.00 0.00 5.24
1107 1171 2.044352 TCATGGGCGACGAGGAGA 60.044 61.111 0.00 0.00 0.00 3.71
1159 1224 0.928505 TAGGTGACATCCTCCGGGTA 59.071 55.000 0.00 0.00 38.86 3.69
1207 1272 1.003233 GCCTTTGCGTCTCCTCCTT 60.003 57.895 0.00 0.00 0.00 3.36
1307 1372 7.720442 ACGATCATCATCAGAAGTAAAGATCA 58.280 34.615 0.00 0.00 32.00 2.92
1317 1382 3.797039 GTCCCAACGATCATCATCAGAA 58.203 45.455 0.00 0.00 0.00 3.02
1350 1415 0.629596 TGGTCTGGTCCGAGGTATCT 59.370 55.000 0.00 0.00 0.00 1.98
1399 1467 2.995574 AGCCTACGCCCAGTCGTT 60.996 61.111 0.00 0.00 43.15 3.85
1409 1477 2.117137 CATACGCAACTACAGCCTACG 58.883 52.381 0.00 0.00 0.00 3.51
1766 1851 1.078214 CCACCTCCATGCACGTCAT 60.078 57.895 0.00 0.00 35.31 3.06
1767 1852 1.763546 TTCCACCTCCATGCACGTCA 61.764 55.000 0.00 0.00 0.00 4.35
1768 1853 1.003839 TTCCACCTCCATGCACGTC 60.004 57.895 0.00 0.00 0.00 4.34
1769 1854 1.302511 GTTCCACCTCCATGCACGT 60.303 57.895 0.00 0.00 0.00 4.49
1770 1855 0.249120 TAGTTCCACCTCCATGCACG 59.751 55.000 0.00 0.00 0.00 5.34
1771 1856 1.555075 TCTAGTTCCACCTCCATGCAC 59.445 52.381 0.00 0.00 0.00 4.57
1772 1857 1.555075 GTCTAGTTCCACCTCCATGCA 59.445 52.381 0.00 0.00 0.00 3.96
1773 1858 1.834263 AGTCTAGTTCCACCTCCATGC 59.166 52.381 0.00 0.00 0.00 4.06
1774 1859 2.099921 CGAGTCTAGTTCCACCTCCATG 59.900 54.545 0.00 0.00 0.00 3.66
1775 1860 2.379972 CGAGTCTAGTTCCACCTCCAT 58.620 52.381 0.00 0.00 0.00 3.41
1776 1861 1.835494 CGAGTCTAGTTCCACCTCCA 58.165 55.000 0.00 0.00 0.00 3.86
1777 1862 0.456628 GCGAGTCTAGTTCCACCTCC 59.543 60.000 0.00 0.00 0.00 4.30
1778 1863 1.174783 TGCGAGTCTAGTTCCACCTC 58.825 55.000 0.00 0.00 0.00 3.85
1779 1864 1.853963 ATGCGAGTCTAGTTCCACCT 58.146 50.000 0.00 0.00 0.00 4.00
1780 1865 2.426024 TGTATGCGAGTCTAGTTCCACC 59.574 50.000 0.00 0.00 0.00 4.61
1781 1866 3.777465 TGTATGCGAGTCTAGTTCCAC 57.223 47.619 0.00 0.00 0.00 4.02
1782 1867 3.699538 ACATGTATGCGAGTCTAGTTCCA 59.300 43.478 0.00 0.00 0.00 3.53
1783 1868 4.045104 CACATGTATGCGAGTCTAGTTCC 58.955 47.826 0.00 0.00 0.00 3.62
1784 1869 4.500837 CACACATGTATGCGAGTCTAGTTC 59.499 45.833 0.00 0.00 0.00 3.01
1785 1870 4.424626 CACACATGTATGCGAGTCTAGTT 58.575 43.478 0.00 0.00 0.00 2.24
1786 1871 3.181486 CCACACATGTATGCGAGTCTAGT 60.181 47.826 0.00 0.00 0.00 2.57
1787 1872 3.375642 CCACACATGTATGCGAGTCTAG 58.624 50.000 0.00 0.00 0.00 2.43
1788 1873 2.481276 GCCACACATGTATGCGAGTCTA 60.481 50.000 0.00 0.00 0.00 2.59
1789 1874 1.740380 GCCACACATGTATGCGAGTCT 60.740 52.381 0.00 0.00 0.00 3.24
1790 1875 0.652592 GCCACACATGTATGCGAGTC 59.347 55.000 0.00 0.00 0.00 3.36
1791 1876 0.036483 TGCCACACATGTATGCGAGT 60.036 50.000 0.00 0.00 0.00 4.18
1792 1877 0.374758 GTGCCACACATGTATGCGAG 59.625 55.000 0.00 0.00 34.08 5.03
1793 1878 0.036483 AGTGCCACACATGTATGCGA 60.036 50.000 0.00 0.00 36.74 5.10
1794 1879 0.804364 AAGTGCCACACATGTATGCG 59.196 50.000 0.00 0.00 36.74 4.73
1795 1880 3.270027 TCTAAGTGCCACACATGTATGC 58.730 45.455 0.00 2.55 36.74 3.14
1796 1881 3.310774 GCTCTAAGTGCCACACATGTATG 59.689 47.826 0.00 0.00 36.74 2.39
1797 1882 3.055167 TGCTCTAAGTGCCACACATGTAT 60.055 43.478 0.00 0.00 36.74 2.29
1798 1883 2.301583 TGCTCTAAGTGCCACACATGTA 59.698 45.455 0.00 0.00 36.74 2.29
1799 1884 1.072173 TGCTCTAAGTGCCACACATGT 59.928 47.619 0.00 0.00 36.74 3.21
1800 1885 1.812235 TGCTCTAAGTGCCACACATG 58.188 50.000 0.00 0.00 36.74 3.21
1801 1886 2.154462 GTTGCTCTAAGTGCCACACAT 58.846 47.619 0.00 0.00 36.74 3.21
1802 1887 1.140852 AGTTGCTCTAAGTGCCACACA 59.859 47.619 0.00 0.00 36.74 3.72
1803 1888 1.801178 GAGTTGCTCTAAGTGCCACAC 59.199 52.381 0.00 0.00 34.10 3.82
1804 1889 1.694150 AGAGTTGCTCTAAGTGCCACA 59.306 47.619 0.00 0.00 39.28 4.17
1805 1890 2.464157 AGAGTTGCTCTAAGTGCCAC 57.536 50.000 0.00 0.00 39.28 5.01
1813 1898 4.402793 GGTCACCTCATTAGAGTTGCTCTA 59.597 45.833 2.07 2.07 41.50 2.43
1824 1909 4.340617 GGACAAAATGGGTCACCTCATTA 58.659 43.478 10.07 0.00 37.00 1.90
1829 1914 0.476771 ACGGACAAAATGGGTCACCT 59.523 50.000 0.00 0.00 37.00 4.00
1853 1938 2.989422 CCAAGTTTTGGTCGGATGAC 57.011 50.000 0.00 0.00 45.93 3.06
1873 1960 0.249280 GTTTTGGTCGCCTTGTTGGG 60.249 55.000 0.00 0.00 36.00 4.12
1879 1966 3.292159 GCCCGTTTTGGTCGCCTT 61.292 61.111 0.00 0.00 35.15 4.35
1880 1967 2.472414 TATGCCCGTTTTGGTCGCCT 62.472 55.000 0.00 0.00 35.15 5.52
1895 1982 1.772182 ATAGCAGACGAACGCTATGC 58.228 50.000 13.65 9.62 46.93 3.14
1898 1985 1.399440 ACGAATAGCAGACGAACGCTA 59.601 47.619 6.84 6.84 44.40 4.26
1904 1991 3.386486 ACACAAAACGAATAGCAGACGA 58.614 40.909 0.00 0.00 0.00 4.20
1907 1994 3.363575 GCGAACACAAAACGAATAGCAGA 60.364 43.478 0.00 0.00 0.00 4.26
1911 1998 3.906008 CCAAGCGAACACAAAACGAATAG 59.094 43.478 0.00 0.00 0.00 1.73
1913 2000 2.356382 TCCAAGCGAACACAAAACGAAT 59.644 40.909 0.00 0.00 0.00 3.34
1915 2002 1.062880 GTCCAAGCGAACACAAAACGA 59.937 47.619 0.00 0.00 0.00 3.85
1921 2008 3.195610 AGATATGAGTCCAAGCGAACACA 59.804 43.478 0.00 0.00 0.00 3.72
1923 2010 4.499865 GCTAGATATGAGTCCAAGCGAACA 60.500 45.833 0.00 0.00 0.00 3.18
1926 2013 3.491342 AGCTAGATATGAGTCCAAGCGA 58.509 45.455 0.00 0.00 34.53 4.93
1936 2023 8.271458 TGTGACCCAAATTTAAGCTAGATATGA 58.729 33.333 0.00 0.00 0.00 2.15
1943 2030 7.531857 TCAAATGTGACCCAAATTTAAGCTA 57.468 32.000 0.00 0.00 30.45 3.32
1944 2031 6.418057 TCAAATGTGACCCAAATTTAAGCT 57.582 33.333 0.00 0.00 30.45 3.74
1948 2035 5.623368 GCGGATCAAATGTGACCCAAATTTA 60.623 40.000 0.00 0.00 37.26 1.40
1971 2058 1.347221 CATAGAAAACGTCCGCCGC 59.653 57.895 0.00 0.00 41.42 6.53
1972 2059 0.738412 ACCATAGAAAACGTCCGCCG 60.738 55.000 0.00 0.00 44.03 6.46
1973 2060 1.004595 GACCATAGAAAACGTCCGCC 58.995 55.000 0.00 0.00 0.00 6.13
1987 2086 1.668101 GAGGCGAACGAGGAGACCAT 61.668 60.000 0.00 0.00 0.00 3.55
1991 2090 3.132139 CGGAGGCGAACGAGGAGA 61.132 66.667 0.00 0.00 0.00 3.71
2029 2128 1.227205 CTCTCGCTGACAGATGGGC 60.227 63.158 6.65 0.00 0.00 5.36
2061 2160 1.801302 AAGAGAGAGACGGGGGTGGA 61.801 60.000 0.00 0.00 0.00 4.02
2069 2168 7.095816 GGAGAAAGAAAGAAAAAGAGAGAGACG 60.096 40.741 0.00 0.00 0.00 4.18
2070 2169 7.172532 GGGAGAAAGAAAGAAAAAGAGAGAGAC 59.827 40.741 0.00 0.00 0.00 3.36
2071 2170 7.147479 TGGGAGAAAGAAAGAAAAAGAGAGAGA 60.147 37.037 0.00 0.00 0.00 3.10
2072 2171 6.995091 TGGGAGAAAGAAAGAAAAAGAGAGAG 59.005 38.462 0.00 0.00 0.00 3.20
2073 2172 6.900194 TGGGAGAAAGAAAGAAAAAGAGAGA 58.100 36.000 0.00 0.00 0.00 3.10
2074 2173 7.094420 GGATGGGAGAAAGAAAGAAAAAGAGAG 60.094 40.741 0.00 0.00 0.00 3.20
2075 2174 6.717084 GGATGGGAGAAAGAAAGAAAAAGAGA 59.283 38.462 0.00 0.00 0.00 3.10
2085 2188 1.357761 GGGGTGGATGGGAGAAAGAAA 59.642 52.381 0.00 0.00 0.00 2.52
2124 2227 3.737172 CAACGGAGGCCAAAGCGG 61.737 66.667 5.01 0.00 41.24 5.52
2140 2243 4.827087 GCTGCCTGCTAGCTCGCA 62.827 66.667 22.47 22.47 38.14 5.10
2159 2262 3.741476 GCTCCAACAAGCAGCCCG 61.741 66.667 0.00 0.00 42.05 6.13
2211 2314 2.655364 CCCGCGACATACAGCTCG 60.655 66.667 8.23 0.00 0.00 5.03
2212 2315 1.878522 CACCCGCGACATACAGCTC 60.879 63.158 8.23 0.00 0.00 4.09
2213 2316 2.184322 CACCCGCGACATACAGCT 59.816 61.111 8.23 0.00 0.00 4.24
2214 2317 2.622903 TAGCACCCGCGACATACAGC 62.623 60.000 8.23 1.22 45.49 4.40
2215 2318 0.595053 CTAGCACCCGCGACATACAG 60.595 60.000 8.23 0.00 45.49 2.74
2216 2319 1.435925 CTAGCACCCGCGACATACA 59.564 57.895 8.23 0.00 45.49 2.29
2217 2320 1.949631 GCTAGCACCCGCGACATAC 60.950 63.158 8.23 0.00 45.49 2.39
2218 2321 0.820482 TAGCTAGCACCCGCGACATA 60.820 55.000 18.83 0.00 45.49 2.29
2219 2322 2.076622 CTAGCTAGCACCCGCGACAT 62.077 60.000 18.83 0.00 45.49 3.06
2220 2323 2.752640 TAGCTAGCACCCGCGACA 60.753 61.111 18.83 0.00 45.49 4.35
2221 2324 2.026301 CTAGCTAGCACCCGCGAC 59.974 66.667 18.83 0.00 45.49 5.19
2269 2380 3.660111 GTCCTGTGTGGTTGCGGC 61.660 66.667 0.00 0.00 37.07 6.53
2270 2381 3.345808 CGTCCTGTGTGGTTGCGG 61.346 66.667 0.00 0.00 37.07 5.69
2272 2383 2.594962 CGTCGTCCTGTGTGGTTGC 61.595 63.158 0.00 0.00 37.07 4.17
2273 2384 2.594962 GCGTCGTCCTGTGTGGTTG 61.595 63.158 0.00 0.00 37.07 3.77
2274 2385 2.279918 GCGTCGTCCTGTGTGGTT 60.280 61.111 0.00 0.00 37.07 3.67
2275 2386 4.295119 GGCGTCGTCCTGTGTGGT 62.295 66.667 0.00 0.00 37.07 4.16
2290 2401 4.724602 TCTCTGTGCAGTCGCGGC 62.725 66.667 0.21 0.21 42.97 6.53
2291 2402 2.807045 GTCTCTGTGCAGTCGCGG 60.807 66.667 6.13 0.00 42.97 6.46
2292 2403 3.168604 CGTCTCTGTGCAGTCGCG 61.169 66.667 0.00 0.00 42.97 5.87
2293 2404 2.083522 GTCGTCTCTGTGCAGTCGC 61.084 63.158 0.00 0.00 39.24 5.19
2294 2405 1.794003 CGTCGTCTCTGTGCAGTCG 60.794 63.158 0.00 4.11 0.00 4.18
2295 2406 2.083522 GCGTCGTCTCTGTGCAGTC 61.084 63.158 0.00 0.00 0.00 3.51
2296 2407 2.049985 GCGTCGTCTCTGTGCAGT 60.050 61.111 0.00 0.00 0.00 4.40
2302 2413 3.691744 GAGGCTGGCGTCGTCTCTG 62.692 68.421 0.00 0.00 0.00 3.35
2303 2414 3.444805 GAGGCTGGCGTCGTCTCT 61.445 66.667 0.00 0.00 0.00 3.10
2304 2415 4.838486 CGAGGCTGGCGTCGTCTC 62.838 72.222 23.49 3.85 45.51 3.36


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

AutoCloner maintained by Alex Coulton.