Multiple sequence alignment - TraesCS6A01G367700

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 TraesCS6A01G367700 chr6A 100.000 2246 0 0 1 2246 594516541 594514296 0.000000e+00 4148.0
1 TraesCS6A01G367700 chr6A 81.519 698 116 9 541 1233 594529933 594529244 1.510000e-156 562.0
2 TraesCS6A01G367700 chr6A 77.216 1049 177 28 205 1231 594498908 594497900 7.010000e-155 556.0
3 TraesCS6A01G367700 chr6A 78.093 493 64 17 1772 2246 594528929 594528463 2.840000e-69 272.0
4 TraesCS6A01G367700 chr6A 80.357 168 31 2 1772 1939 594497313 594497148 2.340000e-25 126.0
5 TraesCS6A01G367700 chr6D 88.446 1480 129 24 1 1448 448428886 448430355 0.000000e+00 1748.0
6 TraesCS6A01G367700 chr6D 85.714 1106 135 12 132 1231 448485497 448486585 0.000000e+00 1146.0
7 TraesCS6A01G367700 chr6D 84.914 1107 142 14 132 1231 448059474 448058386 0.000000e+00 1096.0
8 TraesCS6A01G367700 chr6D 78.957 1112 199 21 131 1233 448365341 448366426 0.000000e+00 725.0
9 TraesCS6A01G367700 chr6D 90.260 308 27 3 1941 2246 448432873 448433179 1.250000e-107 399.0
10 TraesCS6A01G367700 chr6D 80.242 496 63 19 1761 2246 448366809 448367279 7.680000e-90 340.0
11 TraesCS6A01G367700 chr6D 76.122 624 132 16 225 841 448034339 448033726 6.020000e-81 311.0
12 TraesCS6A01G367700 chr6D 85.000 140 18 1 1312 1448 448159042 448158903 3.010000e-29 139.0
13 TraesCS6A01G367700 chr6B 87.984 1473 143 28 1 1448 679330533 679329070 0.000000e+00 1709.0
14 TraesCS6A01G367700 chr6B 87.449 1482 143 28 1 1448 679284860 679286332 0.000000e+00 1666.0
15 TraesCS6A01G367700 chr6B 82.466 1095 171 17 152 1231 679244098 679245186 0.000000e+00 939.0
16 TraesCS6A01G367700 chr6B 89.535 516 38 7 1745 2246 679288733 679289246 6.760000e-180 640.0
17 TraesCS6A01G367700 chr6B 89.535 516 38 7 1745 2246 679326670 679326157 6.760000e-180 640.0
18 TraesCS6A01G367700 chr6B 82.784 546 86 4 693 1231 678930963 678930419 4.340000e-132 481.0
19 TraesCS6A01G367700 chr6B 79.110 584 106 8 659 1229 679360488 679361068 2.700000e-104 388.0
20 TraesCS6A01G367700 chr6B 80.597 536 66 16 132 637 678931515 678930988 1.630000e-101 379.0
21 TraesCS6A01G367700 chr3A 91.632 239 20 0 1001 1239 377683314 377683076 4.620000e-87 331.0
22 TraesCS6A01G367700 chr3A 96.000 50 2 0 1237 1286 377683031 377682982 5.140000e-12 82.4
23 TraesCS6A01G367700 chr7A 96.000 50 2 0 1237 1286 512894145 512894096 5.140000e-12 82.4


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 TraesCS6A01G367700 chr6A 594514296 594516541 2245 True 4148.0 4148 100.0000 1 2246 1 chr6A.!!$R1 2245
1 TraesCS6A01G367700 chr6A 594528463 594529933 1470 True 417.0 562 79.8060 541 2246 2 chr6A.!!$R3 1705
2 TraesCS6A01G367700 chr6A 594497148 594498908 1760 True 341.0 556 78.7865 205 1939 2 chr6A.!!$R2 1734
3 TraesCS6A01G367700 chr6D 448485497 448486585 1088 False 1146.0 1146 85.7140 132 1231 1 chr6D.!!$F1 1099
4 TraesCS6A01G367700 chr6D 448058386 448059474 1088 True 1096.0 1096 84.9140 132 1231 1 chr6D.!!$R2 1099
5 TraesCS6A01G367700 chr6D 448428886 448433179 4293 False 1073.5 1748 89.3530 1 2246 2 chr6D.!!$F3 2245
6 TraesCS6A01G367700 chr6D 448365341 448367279 1938 False 532.5 725 79.5995 131 2246 2 chr6D.!!$F2 2115
7 TraesCS6A01G367700 chr6D 448033726 448034339 613 True 311.0 311 76.1220 225 841 1 chr6D.!!$R1 616
8 TraesCS6A01G367700 chr6B 679326157 679330533 4376 True 1174.5 1709 88.7595 1 2246 2 chr6B.!!$R2 2245
9 TraesCS6A01G367700 chr6B 679284860 679289246 4386 False 1153.0 1666 88.4920 1 2246 2 chr6B.!!$F3 2245
10 TraesCS6A01G367700 chr6B 679244098 679245186 1088 False 939.0 939 82.4660 152 1231 1 chr6B.!!$F1 1079
11 TraesCS6A01G367700 chr6B 678930419 678931515 1096 True 430.0 481 81.6905 132 1231 2 chr6B.!!$R1 1099
12 TraesCS6A01G367700 chr6B 679360488 679361068 580 False 388.0 388 79.1100 659 1229 1 chr6B.!!$F2 570

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
480 524 0.179163 CGGAGAAAATTCAAGCGGCC 60.179 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 2009 0.25589 CCCGGTGGAGGTTCAATCAT 59.744 55.0 0.0 0.0 0.0 2.45 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
328 351 3.469863 TTCAAAGTCGGCGGCCACT 62.470 57.895 20.71 17.62 0.00 4.00
362 385 1.208535 CTACTACCCCAACGGCATGAA 59.791 52.381 0.00 0.00 33.26 2.57
459 497 1.557269 GCTTCTGCCTCTCTGGGGAA 61.557 60.000 0.00 0.00 36.00 3.97
480 524 0.179163 CGGAGAAAATTCAAGCGGCC 60.179 55.000 0.00 0.00 0.00 6.13
855 948 2.586792 GAGGGCAAGGCTGACGAT 59.413 61.111 0.00 0.00 0.00 3.73
901 997 1.070786 GTGGAGGTGTTCAAGGCGA 59.929 57.895 0.00 0.00 0.00 5.54
908 1004 0.955428 GTGTTCAAGGCGATGCTCCA 60.955 55.000 0.00 0.00 0.00 3.86
942 1041 1.099879 GCTCATTGCCCGAGATGCTT 61.100 55.000 0.00 0.00 35.15 3.91
945 1044 2.945008 CTCATTGCCCGAGATGCTTAAA 59.055 45.455 0.00 0.00 31.84 1.52
1009 1108 4.404098 GGTTCGACATGGGGCGGT 62.404 66.667 0.00 0.00 0.00 5.68
1020 1119 1.678970 GGGGCGGTTGAAGCTGATT 60.679 57.895 0.00 0.00 34.52 2.57
1053 1152 2.416547 GCTGTGCGAGTACATTGACATT 59.583 45.455 0.00 0.00 0.00 2.71
1093 1199 2.281070 CACTGGCCGAGCAACACT 60.281 61.111 0.00 0.00 0.00 3.55
1104 1210 2.912624 GCAACACTGCTGTGAGGGC 61.913 63.158 27.99 21.79 46.55 5.19
1134 1240 2.416431 GGCATGCTTTGATTTTCTCGCT 60.416 45.455 18.92 0.00 0.00 4.93
1142 1248 1.276138 TGATTTTCTCGCTGCTCCAGA 59.724 47.619 0.00 0.00 32.44 3.86
1160 1266 1.706287 GAAAATCTGAGGGCCGTCGC 61.706 60.000 19.99 0.00 0.00 5.19
1185 1291 0.809241 CTGACGGCTTCCAGCATCTC 60.809 60.000 0.00 0.00 44.75 2.75
1219 1325 2.287308 CCTTCTCTTATGGTCGAGCTCG 60.287 54.545 30.03 30.03 41.45 5.03
1233 1339 3.716195 CTCGTGGCCATGTCCCCA 61.716 66.667 24.24 3.92 0.00 4.96
1235 1341 4.033776 CGTGGCCATGTCCCCAGT 62.034 66.667 17.42 0.00 0.00 4.00
1240 1388 2.639327 GCCATGTCCCCAGTGCAAC 61.639 63.158 0.00 0.00 0.00 4.17
1249 1397 1.497278 CCAGTGCAACGGTGAATCG 59.503 57.895 3.55 0.00 45.86 3.34
1298 1477 1.373497 GCCGTCCTGCATCTATCCG 60.373 63.158 0.00 0.00 0.00 4.18
1333 1516 6.038356 CGAGATGCAAAATTAGCCTCATTTT 58.962 36.000 0.00 0.00 34.75 1.82
1347 1530 3.052036 CTCATTTTGCCCTGTTTTGTCG 58.948 45.455 0.00 0.00 0.00 4.35
1387 1570 3.723325 ACCATGCCAATTAACCAGGAAT 58.277 40.909 0.00 0.00 0.00 3.01
1403 1586 3.191162 CAGGAATTGCGTTGGAATCAGAA 59.809 43.478 0.00 0.00 0.00 3.02
1453 1674 5.762825 ATGATAGCTTGTGGTTTAGCATG 57.237 39.130 0.00 0.00 39.85 4.06
1457 1678 0.532115 CTTGTGGTTTAGCATGGGGC 59.468 55.000 0.00 0.00 45.30 5.80
1476 1707 1.198637 GCGCTTCATGCTTTCTGAACT 59.801 47.619 0.00 0.00 40.11 3.01
1482 1713 6.583806 CGCTTCATGCTTTCTGAACTTTATTT 59.416 34.615 0.00 0.00 40.11 1.40
1484 1715 9.410556 GCTTCATGCTTTCTGAACTTTATTTAA 57.589 29.630 0.00 0.00 38.95 1.52
1532 1916 2.351726 GTGGTACATGATTTCAGCGACC 59.648 50.000 0.00 0.00 44.52 4.79
1534 1918 3.206150 GGTACATGATTTCAGCGACCAT 58.794 45.455 0.00 0.00 0.00 3.55
1535 1919 4.141824 TGGTACATGATTTCAGCGACCATA 60.142 41.667 0.00 0.00 30.90 2.74
1536 1920 4.997395 GGTACATGATTTCAGCGACCATAT 59.003 41.667 0.00 0.00 0.00 1.78
1537 1921 5.120830 GGTACATGATTTCAGCGACCATATC 59.879 44.000 0.00 0.00 0.00 1.63
1538 1922 4.965814 ACATGATTTCAGCGACCATATCT 58.034 39.130 0.00 0.00 0.00 1.98
1539 1923 5.371526 ACATGATTTCAGCGACCATATCTT 58.628 37.500 0.00 0.00 0.00 2.40
1540 1924 5.824624 ACATGATTTCAGCGACCATATCTTT 59.175 36.000 0.00 0.00 0.00 2.52
1541 1925 5.991328 TGATTTCAGCGACCATATCTTTC 57.009 39.130 0.00 0.00 0.00 2.62
1542 1926 5.674525 TGATTTCAGCGACCATATCTTTCT 58.325 37.500 0.00 0.00 0.00 2.52
1543 1927 6.816136 TGATTTCAGCGACCATATCTTTCTA 58.184 36.000 0.00 0.00 0.00 2.10
1544 1928 7.272244 TGATTTCAGCGACCATATCTTTCTAA 58.728 34.615 0.00 0.00 0.00 2.10
1545 1929 7.439356 TGATTTCAGCGACCATATCTTTCTAAG 59.561 37.037 0.00 0.00 0.00 2.18
1546 1930 5.201713 TCAGCGACCATATCTTTCTAAGG 57.798 43.478 0.00 0.00 0.00 2.69
1547 1931 4.893524 TCAGCGACCATATCTTTCTAAGGA 59.106 41.667 0.00 0.00 0.00 3.36
1548 1932 5.010112 TCAGCGACCATATCTTTCTAAGGAG 59.990 44.000 0.00 0.00 0.00 3.69
1549 1933 5.010112 CAGCGACCATATCTTTCTAAGGAGA 59.990 44.000 0.00 0.00 0.00 3.71
1550 1934 5.777732 AGCGACCATATCTTTCTAAGGAGAT 59.222 40.000 0.00 0.00 36.61 2.75
1551 1935 5.866633 GCGACCATATCTTTCTAAGGAGATG 59.133 44.000 3.26 3.26 34.60 2.90
1552 1936 6.294787 GCGACCATATCTTTCTAAGGAGATGA 60.295 42.308 10.07 0.00 34.33 2.92
1553 1937 7.312154 CGACCATATCTTTCTAAGGAGATGAG 58.688 42.308 10.07 4.55 34.33 2.90
1554 1938 7.003402 ACCATATCTTTCTAAGGAGATGAGC 57.997 40.000 10.07 0.00 34.33 4.26
1555 1939 6.556495 ACCATATCTTTCTAAGGAGATGAGCA 59.444 38.462 10.07 0.00 34.33 4.26
1556 1940 7.098477 CCATATCTTTCTAAGGAGATGAGCAG 58.902 42.308 10.07 0.00 34.33 4.24
1557 1941 7.256261 CCATATCTTTCTAAGGAGATGAGCAGT 60.256 40.741 10.07 0.00 34.33 4.40
1558 1942 8.801299 CATATCTTTCTAAGGAGATGAGCAGTA 58.199 37.037 4.03 0.00 34.33 2.74
1559 1943 7.854166 ATCTTTCTAAGGAGATGAGCAGTAT 57.146 36.000 0.00 0.00 31.65 2.12
1560 1944 7.283625 TCTTTCTAAGGAGATGAGCAGTATC 57.716 40.000 0.00 0.00 0.00 2.24
1561 1945 6.836007 TCTTTCTAAGGAGATGAGCAGTATCA 59.164 38.462 0.00 0.00 0.00 2.15
1562 1946 6.647334 TTCTAAGGAGATGAGCAGTATCAG 57.353 41.667 0.00 0.00 31.44 2.90
1563 1947 5.946486 TCTAAGGAGATGAGCAGTATCAGA 58.054 41.667 0.00 0.00 31.44 3.27
1564 1948 4.935352 AAGGAGATGAGCAGTATCAGAC 57.065 45.455 0.00 0.00 31.44 3.51
1565 1949 4.183223 AGGAGATGAGCAGTATCAGACT 57.817 45.455 0.00 0.00 39.82 3.24
1578 1962 5.798132 AGTATCAGACTGTTTCAGCAATGA 58.202 37.500 1.59 0.33 36.87 2.57
1579 1963 5.641209 AGTATCAGACTGTTTCAGCAATGAC 59.359 40.000 1.59 0.00 36.87 3.06
1580 1964 3.807553 TCAGACTGTTTCAGCAATGACA 58.192 40.909 1.59 0.00 34.37 3.58
1581 1965 3.561310 TCAGACTGTTTCAGCAATGACAC 59.439 43.478 1.59 0.00 34.37 3.67
1582 1966 2.880890 AGACTGTTTCAGCAATGACACC 59.119 45.455 0.00 0.00 34.37 4.16
1583 1967 1.956477 ACTGTTTCAGCAATGACACCC 59.044 47.619 0.00 0.00 34.37 4.61
1584 1968 2.233271 CTGTTTCAGCAATGACACCCT 58.767 47.619 0.00 0.00 0.00 4.34
1585 1969 2.624838 CTGTTTCAGCAATGACACCCTT 59.375 45.455 0.00 0.00 0.00 3.95
1586 1970 2.361757 TGTTTCAGCAATGACACCCTTG 59.638 45.455 0.00 0.00 0.00 3.61
1587 1971 0.961019 TTCAGCAATGACACCCTTGC 59.039 50.000 4.41 4.41 46.32 4.01
1588 1972 0.895100 TCAGCAATGACACCCTTGCC 60.895 55.000 8.31 0.00 46.99 4.52
1589 1973 1.607467 AGCAATGACACCCTTGCCC 60.607 57.895 8.31 0.00 46.99 5.36
1590 1974 1.907807 GCAATGACACCCTTGCCCA 60.908 57.895 1.50 0.00 41.45 5.36
1591 1975 1.259840 GCAATGACACCCTTGCCCAT 61.260 55.000 1.50 0.00 41.45 4.00
1592 1976 1.269012 CAATGACACCCTTGCCCATT 58.731 50.000 0.00 0.00 32.53 3.16
1593 1977 1.624813 CAATGACACCCTTGCCCATTT 59.375 47.619 0.00 0.00 30.92 2.32
1594 1978 2.830923 CAATGACACCCTTGCCCATTTA 59.169 45.455 0.00 0.00 30.92 1.40
1595 1979 2.917713 TGACACCCTTGCCCATTTAT 57.082 45.000 0.00 0.00 0.00 1.40
1596 1980 4.534647 ATGACACCCTTGCCCATTTATA 57.465 40.909 0.00 0.00 0.00 0.98
1597 1981 4.323569 TGACACCCTTGCCCATTTATAA 57.676 40.909 0.00 0.00 0.00 0.98
1598 1982 4.877773 TGACACCCTTGCCCATTTATAAT 58.122 39.130 0.00 0.00 0.00 1.28
1599 1983 4.648762 TGACACCCTTGCCCATTTATAATG 59.351 41.667 0.00 0.00 0.00 1.90
1600 1984 3.966665 ACACCCTTGCCCATTTATAATGG 59.033 43.478 10.77 10.77 38.88 3.16
1601 1985 4.222336 CACCCTTGCCCATTTATAATGGA 58.778 43.478 17.78 0.00 41.64 3.41
1602 1986 4.840115 CACCCTTGCCCATTTATAATGGAT 59.160 41.667 17.78 0.00 41.64 3.41
1603 1987 4.840115 ACCCTTGCCCATTTATAATGGATG 59.160 41.667 17.78 5.44 41.64 3.51
1604 1988 4.223477 CCCTTGCCCATTTATAATGGATGG 59.777 45.833 17.78 12.99 41.64 3.51
1605 1989 4.322953 CCTTGCCCATTTATAATGGATGGC 60.323 45.833 17.78 13.33 41.64 4.40
1606 1990 4.130719 TGCCCATTTATAATGGATGGCT 57.869 40.909 17.78 0.00 41.64 4.75
1607 1991 5.268131 TGCCCATTTATAATGGATGGCTA 57.732 39.130 17.78 4.12 41.64 3.93
1608 1992 5.841209 TGCCCATTTATAATGGATGGCTAT 58.159 37.500 17.78 0.00 41.64 2.97
1620 2004 5.708736 TGGATGGCTATTTTTCAGGTAGA 57.291 39.130 0.00 0.00 0.00 2.59
1625 2009 6.061022 TGGCTATTTTTCAGGTAGATGTGA 57.939 37.500 0.00 0.00 0.00 3.58
1641 2025 3.071874 TGTGATGATTGAACCTCCACC 57.928 47.619 0.00 0.00 0.00 4.61
1647 2031 2.075355 ATTGAACCTCCACCGGGCAA 62.075 55.000 6.32 0.00 0.00 4.52
1648 2032 2.671963 GAACCTCCACCGGGCAAC 60.672 66.667 6.32 0.00 0.00 4.17
1650 2034 1.833787 GAACCTCCACCGGGCAACTA 61.834 60.000 6.32 0.00 0.00 2.24
1651 2035 1.205460 AACCTCCACCGGGCAACTAT 61.205 55.000 6.32 0.00 0.00 2.12
1652 2036 1.205460 ACCTCCACCGGGCAACTATT 61.205 55.000 6.32 0.00 0.00 1.73
1653 2037 0.834612 CCTCCACCGGGCAACTATTA 59.165 55.000 6.32 0.00 0.00 0.98
1658 2042 3.712733 TCCACCGGGCAACTATTAGTTAT 59.287 43.478 6.32 0.00 36.03 1.89
1659 2043 4.062991 CCACCGGGCAACTATTAGTTATC 58.937 47.826 6.32 4.53 36.03 1.75
1661 2045 4.750098 CACCGGGCAACTATTAGTTATCTG 59.250 45.833 6.32 8.79 36.03 2.90
1662 2046 4.202326 ACCGGGCAACTATTAGTTATCTGG 60.202 45.833 22.09 22.09 36.03 3.86
1663 2047 4.202326 CCGGGCAACTATTAGTTATCTGGT 60.202 45.833 18.66 0.00 36.03 4.00
1664 2048 5.365619 CGGGCAACTATTAGTTATCTGGTT 58.634 41.667 8.71 0.00 36.03 3.67
1665 2049 6.463331 CCGGGCAACTATTAGTTATCTGGTTA 60.463 42.308 18.66 0.00 36.03 2.85
1666 2050 6.645415 CGGGCAACTATTAGTTATCTGGTTAG 59.355 42.308 8.71 0.00 36.03 2.34
1704 2094 6.564709 TTTCCTATGCATACAGATGAATGC 57.435 37.500 1.16 0.44 46.92 3.56
1705 2095 5.494390 TCCTATGCATACAGATGAATGCT 57.506 39.130 1.16 0.00 46.87 3.79
1716 2112 3.012518 AGATGAATGCTACACTTGTGCC 58.987 45.455 0.10 0.00 0.00 5.01
1717 2113 1.155889 TGAATGCTACACTTGTGCCG 58.844 50.000 0.10 0.00 0.00 5.69
1718 2114 1.270571 TGAATGCTACACTTGTGCCGA 60.271 47.619 0.10 0.00 0.00 5.54
1719 2115 1.394917 GAATGCTACACTTGTGCCGAG 59.605 52.381 0.10 0.00 0.00 4.63
1722 2118 0.319555 GCTACACTTGTGCCGAGTGA 60.320 55.000 22.22 10.10 45.84 3.41
1723 2119 1.872237 GCTACACTTGTGCCGAGTGAA 60.872 52.381 22.22 0.00 45.84 3.18
1727 2123 2.146342 CACTTGTGCCGAGTGAATCTT 58.854 47.619 14.24 0.00 45.84 2.40
1728 2124 2.158449 CACTTGTGCCGAGTGAATCTTC 59.842 50.000 14.24 0.00 45.84 2.87
1741 2137 3.544684 TGAATCTTCACTGCACAACTGT 58.455 40.909 0.00 0.00 31.01 3.55
1742 2138 3.947196 TGAATCTTCACTGCACAACTGTT 59.053 39.130 0.00 0.00 31.01 3.16
1743 2139 5.122519 TGAATCTTCACTGCACAACTGTTA 58.877 37.500 0.00 0.00 31.01 2.41
1816 4342 6.711277 TCTACTCTGCCTGTTAATCAAACAT 58.289 36.000 0.00 0.00 46.81 2.71
1878 4405 4.263771 TGGTCCTGTTATTTTCTCCCCTTC 60.264 45.833 0.00 0.00 0.00 3.46
1879 4406 4.018324 GGTCCTGTTATTTTCTCCCCTTCT 60.018 45.833 0.00 0.00 0.00 2.85
1892 4420 4.737611 TCTCCCCTTCTCCTTCTCCTTATA 59.262 45.833 0.00 0.00 0.00 0.98
1895 4423 4.471548 CCCTTCTCCTTCTCCTTATACGA 58.528 47.826 0.00 0.00 0.00 3.43
1897 4425 5.134661 CCTTCTCCTTCTCCTTATACGACT 58.865 45.833 0.00 0.00 0.00 4.18
1960 5424 2.009774 CCAGGAATTCTGCAGGTAACG 58.990 52.381 15.13 0.00 42.05 3.18
2024 5497 3.009723 GGGCGTCATGAAAATTCTCTGA 58.990 45.455 0.00 0.00 0.00 3.27
2051 5524 3.569701 TCATGAAAACCAGTTTGCCTCTC 59.430 43.478 0.00 0.00 32.36 3.20
2054 5527 0.537371 AAACCAGTTTGCCTCTCGGG 60.537 55.000 0.00 0.00 38.36 5.14
2058 5531 1.600916 AGTTTGCCTCTCGGGTTGC 60.601 57.895 0.00 0.00 37.43 4.17
2059 5532 1.600916 GTTTGCCTCTCGGGTTGCT 60.601 57.895 0.86 0.00 37.43 3.91
2095 5568 9.685828 ATGTTTTAAGTACATGTTAAACGCAAT 57.314 25.926 2.30 0.00 35.03 3.56
2169 5643 4.550076 TTACAAGAAATTTGCATGGGGG 57.450 40.909 0.00 0.00 0.00 5.40
2188 5662 4.168101 GGGGTCATGGGATACTATCTCAA 58.832 47.826 2.61 0.00 44.21 3.02
2194 5668 6.266558 GTCATGGGATACTATCTCAACTCAGT 59.733 42.308 2.61 0.00 44.21 3.41
2237 5712 2.697431 TTTCTTGTTTTCGATGCGGG 57.303 45.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 0.809241 GAGACTGATGGCGGCTTCTG 60.809 60.000 23.32 23.32 0.00 3.02
459 497 0.804989 CCGCTTGAATTTTCTCCGCT 59.195 50.000 0.00 0.00 0.00 5.52
502 546 1.550524 CCTCCTGGACGAGAATGTGAA 59.449 52.381 0.00 0.00 34.57 3.18
695 773 3.984732 GCTTGCCAAGGTCCCCCT 61.985 66.667 6.57 0.00 45.63 4.79
855 948 3.816367 TTCCACACGCACGATGCCA 62.816 57.895 0.00 0.00 41.12 4.92
908 1004 1.832883 TGAGCCGGTGTATGCAAAAT 58.167 45.000 1.90 0.00 0.00 1.82
933 1029 5.518487 GTCTTCCTCTTCTTTAAGCATCTCG 59.482 44.000 0.00 0.00 32.36 4.04
942 1041 4.022242 CAGGTGACGTCTTCCTCTTCTTTA 60.022 45.833 23.02 0.00 0.00 1.85
945 1044 1.889829 CAGGTGACGTCTTCCTCTTCT 59.110 52.381 23.02 6.58 0.00 2.85
978 1077 1.300931 GAACCTGTCTGCAGCGACA 60.301 57.895 9.47 16.02 41.26 4.35
1009 1108 2.079158 CTCCTCGCAAATCAGCTTCAA 58.921 47.619 0.00 0.00 0.00 2.69
1020 1119 1.669115 GCACAGCTTCTCCTCGCAA 60.669 57.895 0.00 0.00 0.00 4.85
1093 1199 1.418097 TTCTTCAGGCCCTCACAGCA 61.418 55.000 0.00 0.00 0.00 4.41
1134 1240 1.340405 GCCCTCAGATTTTCTGGAGCA 60.340 52.381 4.78 0.00 44.39 4.26
1142 1248 1.745489 GCGACGGCCCTCAGATTTT 60.745 57.895 0.00 0.00 0.00 1.82
1219 1325 2.361610 CACTGGGGACATGGCCAC 60.362 66.667 22.13 18.87 41.51 5.01
1233 1339 1.227999 CCACGATTCACCGTTGCACT 61.228 55.000 0.00 0.00 41.29 4.40
1235 1341 0.816018 AACCACGATTCACCGTTGCA 60.816 50.000 0.00 0.00 41.29 4.08
1240 1388 2.921754 GTCTAGAAACCACGATTCACCG 59.078 50.000 0.00 0.00 0.00 4.94
1288 1467 3.489785 CGGTTGTTAACTCGGATAGATGC 59.510 47.826 7.22 0.00 0.00 3.91
1298 1477 4.742438 TTTGCATCTCGGTTGTTAACTC 57.258 40.909 7.22 0.24 0.00 3.01
1333 1516 0.394488 TGAACCGACAAAACAGGGCA 60.394 50.000 0.00 0.00 0.00 5.36
1334 1517 0.958822 ATGAACCGACAAAACAGGGC 59.041 50.000 0.00 0.00 0.00 5.19
1368 1551 3.872771 GCAATTCCTGGTTAATTGGCATG 59.127 43.478 17.58 0.00 42.17 4.06
1369 1552 3.430651 CGCAATTCCTGGTTAATTGGCAT 60.431 43.478 17.58 0.00 42.17 4.40
1387 1570 0.881118 GCCTTCTGATTCCAACGCAA 59.119 50.000 0.00 0.00 0.00 4.85
1419 1602 7.448469 ACCACAAGCTATCATTGTCTAAAAACT 59.552 33.333 0.00 0.00 38.80 2.66
1428 1611 5.009631 TGCTAAACCACAAGCTATCATTGT 58.990 37.500 0.00 0.00 41.47 2.71
1504 1810 5.365403 TGAAATCATGTACCACGAAAACC 57.635 39.130 0.00 0.00 0.00 3.27
1527 1833 5.455056 TCTCCTTAGAAAGATATGGTCGC 57.545 43.478 0.00 0.00 0.00 5.19
1529 1835 7.096551 GCTCATCTCCTTAGAAAGATATGGTC 58.903 42.308 0.00 0.00 34.73 4.02
1532 1916 7.669427 ACTGCTCATCTCCTTAGAAAGATATG 58.331 38.462 0.00 0.00 34.73 1.78
1534 1918 8.948401 ATACTGCTCATCTCCTTAGAAAGATA 57.052 34.615 0.00 0.00 34.73 1.98
1535 1919 7.508636 TGATACTGCTCATCTCCTTAGAAAGAT 59.491 37.037 0.00 0.00 34.73 2.40
1536 1920 6.836007 TGATACTGCTCATCTCCTTAGAAAGA 59.164 38.462 0.00 0.00 34.73 2.52
1537 1921 7.014134 TCTGATACTGCTCATCTCCTTAGAAAG 59.986 40.741 0.00 0.00 34.73 2.62
1538 1922 6.836007 TCTGATACTGCTCATCTCCTTAGAAA 59.164 38.462 0.00 0.00 34.73 2.52
1539 1923 6.264292 GTCTGATACTGCTCATCTCCTTAGAA 59.736 42.308 0.00 0.00 34.73 2.10
1540 1924 5.767665 GTCTGATACTGCTCATCTCCTTAGA 59.232 44.000 0.00 0.00 35.80 2.10
1541 1925 5.769662 AGTCTGATACTGCTCATCTCCTTAG 59.230 44.000 0.00 0.00 36.93 2.18
1542 1926 5.700183 AGTCTGATACTGCTCATCTCCTTA 58.300 41.667 0.00 0.00 36.93 2.69
1543 1927 4.545678 AGTCTGATACTGCTCATCTCCTT 58.454 43.478 0.00 0.00 36.93 3.36
1544 1928 4.183223 AGTCTGATACTGCTCATCTCCT 57.817 45.455 0.00 0.00 36.93 3.69
1553 1937 9.667930 GTCATTGCTGAAACAGTCTGATACTGC 62.668 44.444 6.91 11.88 45.45 4.40
1554 1938 6.401903 GTCATTGCTGAAACAGTCTGATACTG 60.402 42.308 6.91 3.67 46.22 2.74
1555 1939 5.641209 GTCATTGCTGAAACAGTCTGATACT 59.359 40.000 6.91 0.00 33.63 2.12
1556 1940 5.409520 TGTCATTGCTGAAACAGTCTGATAC 59.590 40.000 6.91 0.00 33.43 2.24
1557 1941 5.409520 GTGTCATTGCTGAAACAGTCTGATA 59.590 40.000 6.91 0.00 39.15 2.15
1558 1942 4.214971 GTGTCATTGCTGAAACAGTCTGAT 59.785 41.667 6.91 0.00 39.15 2.90
1559 1943 3.561310 GTGTCATTGCTGAAACAGTCTGA 59.439 43.478 6.91 0.00 39.15 3.27
1560 1944 3.304257 GGTGTCATTGCTGAAACAGTCTG 60.304 47.826 0.00 0.00 40.83 3.51
1561 1945 2.880890 GGTGTCATTGCTGAAACAGTCT 59.119 45.455 0.00 0.00 40.83 3.24
1562 1946 2.030805 GGGTGTCATTGCTGAAACAGTC 60.031 50.000 0.00 0.00 40.83 3.51
1563 1947 1.956477 GGGTGTCATTGCTGAAACAGT 59.044 47.619 0.00 0.00 40.83 3.55
1564 1948 2.233271 AGGGTGTCATTGCTGAAACAG 58.767 47.619 0.00 0.00 40.83 3.16
1565 1949 2.361757 CAAGGGTGTCATTGCTGAAACA 59.638 45.455 0.00 0.00 40.83 2.83
1566 1950 3.017265 CAAGGGTGTCATTGCTGAAAC 57.983 47.619 0.00 0.00 38.69 2.78
1573 1957 1.269012 AATGGGCAAGGGTGTCATTG 58.731 50.000 0.00 0.00 37.68 2.82
1574 1958 2.028561 AAATGGGCAAGGGTGTCATT 57.971 45.000 0.00 0.00 34.50 2.57
1575 1959 2.917713 TAAATGGGCAAGGGTGTCAT 57.082 45.000 0.00 0.00 0.00 3.06
1576 1960 2.917713 ATAAATGGGCAAGGGTGTCA 57.082 45.000 0.00 0.00 0.00 3.58
1577 1961 4.039124 CCATTATAAATGGGCAAGGGTGTC 59.961 45.833 10.29 0.00 35.58 3.67
1578 1962 3.966665 CCATTATAAATGGGCAAGGGTGT 59.033 43.478 10.29 0.00 35.58 4.16
1579 1963 4.222336 TCCATTATAAATGGGCAAGGGTG 58.778 43.478 16.58 0.00 39.60 4.61
1580 1964 4.551215 TCCATTATAAATGGGCAAGGGT 57.449 40.909 16.58 0.00 39.60 4.34
1581 1965 4.223477 CCATCCATTATAAATGGGCAAGGG 59.777 45.833 16.58 6.91 39.60 3.95
1582 1966 4.322953 GCCATCCATTATAAATGGGCAAGG 60.323 45.833 16.58 13.74 40.29 3.61
1583 1967 4.529377 AGCCATCCATTATAAATGGGCAAG 59.471 41.667 16.58 6.67 40.29 4.01
1584 1968 4.491675 AGCCATCCATTATAAATGGGCAA 58.508 39.130 16.58 0.79 40.29 4.52
1585 1969 4.130719 AGCCATCCATTATAAATGGGCA 57.869 40.909 16.58 1.44 40.29 5.36
1586 1970 6.796785 AATAGCCATCCATTATAAATGGGC 57.203 37.500 16.58 12.61 40.29 5.36
1587 1971 9.657419 GAAAAATAGCCATCCATTATAAATGGG 57.343 33.333 16.58 6.00 40.29 4.00
1591 1975 9.432982 ACCTGAAAAATAGCCATCCATTATAAA 57.567 29.630 0.00 0.00 0.00 1.40
1593 1977 9.739276 CTACCTGAAAAATAGCCATCCATTATA 57.261 33.333 0.00 0.00 0.00 0.98
1594 1978 8.448008 TCTACCTGAAAAATAGCCATCCATTAT 58.552 33.333 0.00 0.00 0.00 1.28
1595 1979 7.811282 TCTACCTGAAAAATAGCCATCCATTA 58.189 34.615 0.00 0.00 0.00 1.90
1596 1980 6.672593 TCTACCTGAAAAATAGCCATCCATT 58.327 36.000 0.00 0.00 0.00 3.16
1597 1981 6.266131 TCTACCTGAAAAATAGCCATCCAT 57.734 37.500 0.00 0.00 0.00 3.41
1598 1982 5.708736 TCTACCTGAAAAATAGCCATCCA 57.291 39.130 0.00 0.00 0.00 3.41
1599 1983 6.016777 CACATCTACCTGAAAAATAGCCATCC 60.017 42.308 0.00 0.00 0.00 3.51
1600 1984 6.767902 TCACATCTACCTGAAAAATAGCCATC 59.232 38.462 0.00 0.00 0.00 3.51
1601 1985 6.662755 TCACATCTACCTGAAAAATAGCCAT 58.337 36.000 0.00 0.00 0.00 4.40
1602 1986 6.061022 TCACATCTACCTGAAAAATAGCCA 57.939 37.500 0.00 0.00 0.00 4.75
1603 1987 6.767902 TCATCACATCTACCTGAAAAATAGCC 59.232 38.462 0.00 0.00 0.00 3.93
1604 1988 7.792374 TCATCACATCTACCTGAAAAATAGC 57.208 36.000 0.00 0.00 0.00 2.97
1606 1990 9.904198 TCAATCATCACATCTACCTGAAAAATA 57.096 29.630 0.00 0.00 0.00 1.40
1607 1991 8.812513 TCAATCATCACATCTACCTGAAAAAT 57.187 30.769 0.00 0.00 0.00 1.82
1608 1992 8.514594 GTTCAATCATCACATCTACCTGAAAAA 58.485 33.333 0.00 0.00 0.00 1.94
1620 2004 3.624777 GGTGGAGGTTCAATCATCACAT 58.375 45.455 0.00 0.00 0.00 3.21
1625 2009 0.255890 CCCGGTGGAGGTTCAATCAT 59.744 55.000 0.00 0.00 0.00 2.45
1641 2025 4.957296 ACCAGATAACTAATAGTTGCCCG 58.043 43.478 15.34 2.48 39.11 6.13
1647 2031 9.884814 ACCAGATCTAACCAGATAACTAATAGT 57.115 33.333 0.00 0.00 41.78 2.12
1686 2070 6.762333 AGTGTAGCATTCATCTGTATGCATA 58.238 36.000 19.58 1.16 46.80 3.14
1697 2087 1.739466 CGGCACAAGTGTAGCATTCAT 59.261 47.619 1.79 0.00 0.00 2.57
1699 2089 1.394917 CTCGGCACAAGTGTAGCATTC 59.605 52.381 1.79 0.00 0.00 2.67
1700 2090 1.270839 ACTCGGCACAAGTGTAGCATT 60.271 47.619 1.79 0.00 0.00 3.56
1704 2094 2.148916 TTCACTCGGCACAAGTGTAG 57.851 50.000 10.86 0.80 35.31 2.74
1705 2095 2.299013 AGATTCACTCGGCACAAGTGTA 59.701 45.455 10.86 3.93 35.31 2.90
1721 2117 4.558538 AACAGTTGTGCAGTGAAGATTC 57.441 40.909 0.00 0.00 0.00 2.52
1722 2118 5.126067 ACTAACAGTTGTGCAGTGAAGATT 58.874 37.500 0.00 0.00 0.00 2.40
1723 2119 4.708177 ACTAACAGTTGTGCAGTGAAGAT 58.292 39.130 0.00 0.00 0.00 2.40
1727 2123 5.696270 CAGATAACTAACAGTTGTGCAGTGA 59.304 40.000 0.00 0.00 39.11 3.41
1728 2124 5.106948 CCAGATAACTAACAGTTGTGCAGTG 60.107 44.000 0.00 0.00 39.11 3.66
1730 2126 4.997395 ACCAGATAACTAACAGTTGTGCAG 59.003 41.667 0.00 0.00 39.11 4.41
1731 2127 4.968259 ACCAGATAACTAACAGTTGTGCA 58.032 39.130 0.00 0.00 39.11 4.57
1732 2128 5.941948 AACCAGATAACTAACAGTTGTGC 57.058 39.130 0.00 0.00 39.11 4.57
1921 4455 6.555711 TCCTGGATCTTTTTCTTCATTTCCT 58.444 36.000 0.00 0.00 0.00 3.36
1939 4473 2.354704 CGTTACCTGCAGAATTCCTGGA 60.355 50.000 17.39 0.00 43.13 3.86
1960 5424 5.825593 TCTCAAGGGTATGGGTATTGATC 57.174 43.478 0.00 0.00 30.13 2.92
2007 5480 9.073368 CATGATTTGTCAGAGAATTTTCATGAC 57.927 33.333 16.04 15.95 42.07 3.06
2024 5497 4.815846 GGCAAACTGGTTTTCATGATTTGT 59.184 37.500 14.09 0.05 31.11 2.83
2051 5524 3.013921 ACATACCAACAATAGCAACCCG 58.986 45.455 0.00 0.00 0.00 5.28
2089 5562 9.454585 CTGATGAACATAATCAAATTATTGCGT 57.545 29.630 0.00 0.00 36.45 5.24
2090 5563 9.667989 TCTGATGAACATAATCAAATTATTGCG 57.332 29.630 0.00 0.00 36.45 4.85
2169 5643 6.266558 ACTGAGTTGAGATAGTATCCCATGAC 59.733 42.308 6.53 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.