Multiple sequence alignment - TraesCS7A01G510500

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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 TraesCS7A01G510500 chr7A 100.000 2429 0 0 1 2429 697986589 697984161 0.000000e+00 4486.0
1 TraesCS7A01G510500 chr7A 98.872 798 9 0 1 798 697886861 697886064 0.000000e+00 1424.0
2 TraesCS7A01G510500 chr7A 91.050 838 36 18 1613 2429 697830639 697829820 0.000000e+00 1096.0
3 TraesCS7A01G510500 chr7A 96.422 531 19 0 1 531 697831873 697831343 0.000000e+00 876.0
4 TraesCS7A01G510500 chr7A 96.739 276 9 0 523 798 697830923 697830648 6.120000e-126 460.0
5 TraesCS7A01G510500 chr1B 97.236 796 22 0 817 1612 374333850 374334645 0.000000e+00 1349.0
6 TraesCS7A01G510500 chr6B 97.111 796 23 0 817 1612 437148121 437147326 0.000000e+00 1343.0
7 TraesCS7A01G510500 chrUn 96.863 797 24 1 817 1612 62695135 62694339 0.000000e+00 1332.0
8 TraesCS7A01G510500 chr6A 96.859 796 24 1 817 1612 457604912 457604118 0.000000e+00 1330.0
9 TraesCS7A01G510500 chr6A 96.357 796 29 0 817 1612 457587510 457586715 0.000000e+00 1310.0
10 TraesCS7A01G510500 chr3B 96.389 803 28 1 817 1619 725371831 725372632 0.000000e+00 1321.0
11 TraesCS7A01G510500 chr5A 95.980 796 32 0 817 1612 704586226 704585431 0.000000e+00 1293.0
12 TraesCS7A01G510500 chr2D 95.107 797 38 1 817 1612 532133561 532134357 0.000000e+00 1254.0
13 TraesCS7A01G510500 chr2D 94.849 796 39 1 817 1612 122037377 122036584 0.000000e+00 1242.0
14 TraesCS7A01G510500 chr2D 93.023 43 1 2 1872 1913 583588252 583588293 7.250000e-06 62.1
15 TraesCS7A01G510500 chr2D 92.683 41 1 2 1902 1942 607998676 607998638 9.380000e-05 58.4
16 TraesCS7A01G510500 chr7D 94.773 727 27 3 71 794 605961882 605961164 0.000000e+00 1122.0
17 TraesCS7A01G510500 chr7D 94.530 585 31 1 214 798 606112324 606111741 0.000000e+00 902.0
18 TraesCS7A01G510500 chr7D 92.650 585 42 1 214 798 606016233 606015650 0.000000e+00 841.0
19 TraesCS7A01G510500 chr7D 86.547 446 48 8 42 485 13930203 13930638 4.700000e-132 481.0
20 TraesCS7A01G510500 chr7D 92.905 296 18 3 1613 1906 606015641 606015347 6.210000e-116 427.0
21 TraesCS7A01G510500 chr7D 92.542 295 21 1 1613 1906 605961151 605960857 2.890000e-114 422.0
22 TraesCS7A01G510500 chr7D 87.838 296 12 3 1613 1906 606111732 606111459 2.330000e-85 326.0
23 TraesCS7A01G510500 chr7D 96.296 54 2 0 1 54 605961928 605961875 3.330000e-14 89.8
24 TraesCS7A01G510500 chr7D 97.368 38 0 1 1902 1939 207968889 207968853 2.020000e-06 63.9
25 TraesCS7A01G510500 chr1A 84.428 533 59 13 42 571 55650344 55649833 1.000000e-138 503.0
26 TraesCS7A01G510500 chr5D 86.466 266 23 7 42 305 565205423 565205169 1.840000e-71 279.0
27 TraesCS7A01G510500 chr5D 92.683 41 1 2 1902 1942 553870729 553870767 9.380000e-05 58.4
28 TraesCS7A01G510500 chr4B 93.182 44 1 2 1892 1935 193523459 193523418 2.020000e-06 63.9
29 TraesCS7A01G510500 chr3D 95.122 41 1 1 1899 1939 31895700 31895661 2.020000e-06 63.9
30 TraesCS7A01G510500 chr7B 92.857 42 3 0 1894 1935 4820465 4820506 7.250000e-06 62.1
31 TraesCS7A01G510500 chr2B 92.683 41 1 2 1902 1942 782850865 782850903 9.380000e-05 58.4
32 TraesCS7A01G510500 chr2B 92.683 41 1 2 1902 1942 782975352 782975390 9.380000e-05 58.4


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 TraesCS7A01G510500 chr7A 697984161 697986589 2428 True 4486.000000 4486 100.0000 1 2429 1 chr7A.!!$R2 2428
1 TraesCS7A01G510500 chr7A 697886064 697886861 797 True 1424.000000 1424 98.8720 1 798 1 chr7A.!!$R1 797
2 TraesCS7A01G510500 chr7A 697829820 697831873 2053 True 810.666667 1096 94.7370 1 2429 3 chr7A.!!$R3 2428
3 TraesCS7A01G510500 chr1B 374333850 374334645 795 False 1349.000000 1349 97.2360 817 1612 1 chr1B.!!$F1 795
4 TraesCS7A01G510500 chr6B 437147326 437148121 795 True 1343.000000 1343 97.1110 817 1612 1 chr6B.!!$R1 795
5 TraesCS7A01G510500 chrUn 62694339 62695135 796 True 1332.000000 1332 96.8630 817 1612 1 chrUn.!!$R1 795
6 TraesCS7A01G510500 chr6A 457604118 457604912 794 True 1330.000000 1330 96.8590 817 1612 1 chr6A.!!$R2 795
7 TraesCS7A01G510500 chr6A 457586715 457587510 795 True 1310.000000 1310 96.3570 817 1612 1 chr6A.!!$R1 795
8 TraesCS7A01G510500 chr3B 725371831 725372632 801 False 1321.000000 1321 96.3890 817 1619 1 chr3B.!!$F1 802
9 TraesCS7A01G510500 chr5A 704585431 704586226 795 True 1293.000000 1293 95.9800 817 1612 1 chr5A.!!$R1 795
10 TraesCS7A01G510500 chr2D 532133561 532134357 796 False 1254.000000 1254 95.1070 817 1612 1 chr2D.!!$F1 795
11 TraesCS7A01G510500 chr2D 122036584 122037377 793 True 1242.000000 1242 94.8490 817 1612 1 chr2D.!!$R1 795
12 TraesCS7A01G510500 chr7D 606015347 606016233 886 True 634.000000 841 92.7775 214 1906 2 chr7D.!!$R3 1692
13 TraesCS7A01G510500 chr7D 606111459 606112324 865 True 614.000000 902 91.1840 214 1906 2 chr7D.!!$R4 1692
14 TraesCS7A01G510500 chr7D 605960857 605961928 1071 True 544.600000 1122 94.5370 1 1906 3 chr7D.!!$R2 1905
15 TraesCS7A01G510500 chr1A 55649833 55650344 511 True 503.000000 503 84.4280 42 571 1 chr1A.!!$R1 529

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
549 1005 0.040157 CAACCAACAGCCGTCATGTG 60.04 55.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 2159 0.465705 CTTCCAATCTAGCTGCGGGA 59.534 55.0 0.0 0.0 0.0 5.14 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
119 144 4.080356 TGGGACATGAGGATTGAAGTTAGG 60.080 45.833 0.00 0.00 0.00 2.69
549 1005 0.040157 CAACCAACAGCCGTCATGTG 60.040 55.000 0.00 0.00 0.00 3.21
798 1257 1.202687 TGATCGGTCAAGCATCATCCC 60.203 52.381 0.00 0.00 0.00 3.85
799 1258 0.839277 ATCGGTCAAGCATCATCCCA 59.161 50.000 0.00 0.00 0.00 4.37
800 1259 0.178767 TCGGTCAAGCATCATCCCAG 59.821 55.000 0.00 0.00 0.00 4.45
801 1260 0.816825 CGGTCAAGCATCATCCCAGG 60.817 60.000 0.00 0.00 0.00 4.45
802 1261 0.257039 GGTCAAGCATCATCCCAGGT 59.743 55.000 0.00 0.00 0.00 4.00
803 1262 1.490490 GGTCAAGCATCATCCCAGGTA 59.510 52.381 0.00 0.00 0.00 3.08
804 1263 2.107204 GGTCAAGCATCATCCCAGGTAT 59.893 50.000 0.00 0.00 0.00 2.73
805 1264 3.435601 GGTCAAGCATCATCCCAGGTATT 60.436 47.826 0.00 0.00 0.00 1.89
806 1265 4.210331 GTCAAGCATCATCCCAGGTATTT 58.790 43.478 0.00 0.00 0.00 1.40
807 1266 4.276926 GTCAAGCATCATCCCAGGTATTTC 59.723 45.833 0.00 0.00 0.00 2.17
808 1267 3.515602 AGCATCATCCCAGGTATTTCC 57.484 47.619 0.00 0.00 0.00 3.13
809 1268 2.154462 GCATCATCCCAGGTATTTCCG 58.846 52.381 0.00 0.00 41.99 4.30
810 1269 2.487265 GCATCATCCCAGGTATTTCCGT 60.487 50.000 0.00 0.00 41.99 4.69
811 1270 3.141398 CATCATCCCAGGTATTTCCGTG 58.859 50.000 0.00 0.00 41.99 4.94
812 1271 1.134220 TCATCCCAGGTATTTCCGTGC 60.134 52.381 0.00 0.00 41.99 5.34
813 1272 1.134098 CATCCCAGGTATTTCCGTGCT 60.134 52.381 0.00 0.00 41.99 4.40
814 1273 0.988832 TCCCAGGTATTTCCGTGCTT 59.011 50.000 0.00 0.00 41.99 3.91
815 1274 1.353022 TCCCAGGTATTTCCGTGCTTT 59.647 47.619 0.00 0.00 41.99 3.51
882 1341 2.912956 TGCAGAGGAGTCATTTAGGGTT 59.087 45.455 0.00 0.00 0.00 4.11
1227 1686 7.039293 AGGATTTTGTTAACCATTCCTGTAACC 60.039 37.037 13.66 0.00 30.36 2.85
1257 1716 2.501723 TGCGGAAAGGAGCTTCTCTAAT 59.498 45.455 0.00 0.00 0.00 1.73
1585 2046 2.287909 CCATTTTTCTTTTCGCACCGGA 60.288 45.455 9.46 0.00 0.00 5.14
1603 2064 1.984288 GACCCCCGAATTCCTGGAGG 61.984 65.000 9.69 10.74 0.00 4.30
1614 2075 3.164269 CTGGAGGCGGCCCTGTAT 61.164 66.667 17.02 0.00 43.12 2.29
1615 2076 1.837051 CTGGAGGCGGCCCTGTATA 60.837 63.158 17.02 0.00 43.12 1.47
1617 2078 0.766674 TGGAGGCGGCCCTGTATATT 60.767 55.000 17.02 0.00 43.12 1.28
1618 2079 0.321653 GGAGGCGGCCCTGTATATTG 60.322 60.000 17.02 0.00 43.12 1.90
1619 2080 0.321653 GAGGCGGCCCTGTATATTGG 60.322 60.000 17.02 0.00 43.12 3.16
1620 2081 0.766674 AGGCGGCCCTGTATATTGGA 60.767 55.000 17.02 0.00 40.94 3.53
1621 2082 0.109723 GGCGGCCCTGTATATTGGAA 59.890 55.000 8.12 0.00 0.00 3.53
1622 2083 1.523758 GCGGCCCTGTATATTGGAAG 58.476 55.000 0.00 0.00 0.00 3.46
1623 2084 1.882352 GCGGCCCTGTATATTGGAAGG 60.882 57.143 0.00 0.00 0.00 3.46
1624 2085 1.697432 CGGCCCTGTATATTGGAAGGA 59.303 52.381 0.00 0.00 30.92 3.36
1625 2086 2.289694 CGGCCCTGTATATTGGAAGGAG 60.290 54.545 0.00 0.00 30.92 3.69
1626 2087 2.979678 GGCCCTGTATATTGGAAGGAGA 59.020 50.000 0.00 0.00 30.92 3.71
1627 2088 3.394606 GGCCCTGTATATTGGAAGGAGAA 59.605 47.826 0.00 0.00 30.92 2.87
1628 2089 4.505742 GGCCCTGTATATTGGAAGGAGAAG 60.506 50.000 0.00 0.00 30.92 2.85
1629 2090 4.348168 GCCCTGTATATTGGAAGGAGAAGA 59.652 45.833 0.00 0.00 30.92 2.87
1630 2091 5.163195 GCCCTGTATATTGGAAGGAGAAGAA 60.163 44.000 0.00 0.00 30.92 2.52
1631 2092 6.634955 GCCCTGTATATTGGAAGGAGAAGAAA 60.635 42.308 0.00 0.00 30.92 2.52
1632 2093 7.521669 CCCTGTATATTGGAAGGAGAAGAAAT 58.478 38.462 0.00 0.00 30.92 2.17
1633 2094 8.660435 CCCTGTATATTGGAAGGAGAAGAAATA 58.340 37.037 0.00 0.00 30.92 1.40
1634 2095 9.717942 CCTGTATATTGGAAGGAGAAGAAATAG 57.282 37.037 0.00 0.00 30.92 1.73
1640 2101 7.928307 TTGGAAGGAGAAGAAATAGTTGATG 57.072 36.000 0.00 0.00 0.00 3.07
1641 2102 6.418101 TGGAAGGAGAAGAAATAGTTGATGG 58.582 40.000 0.00 0.00 0.00 3.51
1642 2103 5.298026 GGAAGGAGAAGAAATAGTTGATGGC 59.702 44.000 0.00 0.00 0.00 4.40
1643 2104 5.441718 AGGAGAAGAAATAGTTGATGGCA 57.558 39.130 0.00 0.00 0.00 4.92
1644 2105 5.189180 AGGAGAAGAAATAGTTGATGGCAC 58.811 41.667 0.00 0.00 0.00 5.01
1645 2106 4.034510 GGAGAAGAAATAGTTGATGGCACG 59.965 45.833 0.00 0.00 0.00 5.34
1646 2107 4.832248 AGAAGAAATAGTTGATGGCACGA 58.168 39.130 0.00 0.00 0.00 4.35
1647 2108 5.245531 AGAAGAAATAGTTGATGGCACGAA 58.754 37.500 0.00 0.00 0.00 3.85
1648 2109 5.705441 AGAAGAAATAGTTGATGGCACGAAA 59.295 36.000 0.00 0.00 0.00 3.46
1649 2110 5.551760 AGAAATAGTTGATGGCACGAAAG 57.448 39.130 0.00 0.00 0.00 2.62
1650 2111 5.245531 AGAAATAGTTGATGGCACGAAAGA 58.754 37.500 0.00 0.00 0.00 2.52
1651 2112 5.705441 AGAAATAGTTGATGGCACGAAAGAA 59.295 36.000 0.00 0.00 0.00 2.52
1652 2113 5.957842 AATAGTTGATGGCACGAAAGAAA 57.042 34.783 0.00 0.00 0.00 2.52
1653 2114 5.957842 ATAGTTGATGGCACGAAAGAAAA 57.042 34.783 0.00 0.00 0.00 2.29
1654 2115 4.853924 AGTTGATGGCACGAAAGAAAAT 57.146 36.364 0.00 0.00 0.00 1.82
1655 2116 4.798574 AGTTGATGGCACGAAAGAAAATC 58.201 39.130 0.00 0.00 0.00 2.17
1656 2117 3.469899 TGATGGCACGAAAGAAAATCG 57.530 42.857 0.00 0.00 45.47 3.34
1657 2118 3.070748 TGATGGCACGAAAGAAAATCGA 58.929 40.909 2.65 0.00 42.76 3.59
1658 2119 3.689161 TGATGGCACGAAAGAAAATCGAT 59.311 39.130 2.65 0.00 42.76 3.59
1659 2120 3.469899 TGGCACGAAAGAAAATCGATG 57.530 42.857 0.00 0.00 42.76 3.84
1660 2121 2.161410 TGGCACGAAAGAAAATCGATGG 59.839 45.455 0.00 0.00 42.76 3.51
1661 2122 2.177173 GCACGAAAGAAAATCGATGGC 58.823 47.619 0.00 0.00 42.76 4.40
1662 2123 2.785679 CACGAAAGAAAATCGATGGCC 58.214 47.619 0.00 0.00 42.76 5.36
1663 2124 2.161410 CACGAAAGAAAATCGATGGCCA 59.839 45.455 8.56 8.56 42.76 5.36
1664 2125 2.161609 ACGAAAGAAAATCGATGGCCAC 59.838 45.455 8.16 0.47 42.76 5.01
1665 2126 2.161410 CGAAAGAAAATCGATGGCCACA 59.839 45.455 8.16 0.00 42.76 4.17
1666 2127 3.501950 GAAAGAAAATCGATGGCCACAC 58.498 45.455 8.16 4.31 0.00 3.82
1667 2128 2.198827 AGAAAATCGATGGCCACACA 57.801 45.000 8.16 0.00 0.00 3.72
1668 2129 2.513753 AGAAAATCGATGGCCACACAA 58.486 42.857 8.16 0.00 0.00 3.33
1669 2130 2.228822 AGAAAATCGATGGCCACACAAC 59.771 45.455 8.16 0.00 0.00 3.32
1670 2131 0.521291 AAATCGATGGCCACACAACG 59.479 50.000 8.16 9.69 0.00 4.10
1671 2132 1.305219 AATCGATGGCCACACAACGG 61.305 55.000 8.16 0.00 0.00 4.44
1672 2133 3.430862 CGATGGCCACACAACGGG 61.431 66.667 8.16 0.00 0.00 5.28
1673 2134 2.033448 GATGGCCACACAACGGGA 59.967 61.111 8.16 0.00 0.00 5.14
1674 2135 1.378514 GATGGCCACACAACGGGAT 60.379 57.895 8.16 0.00 0.00 3.85
1675 2136 1.656818 GATGGCCACACAACGGGATG 61.657 60.000 8.16 0.00 0.00 3.51
1676 2137 2.033448 GGCCACACAACGGGATGA 59.967 61.111 0.00 0.00 0.00 2.92
1677 2138 2.332654 GGCCACACAACGGGATGAC 61.333 63.158 0.00 0.00 0.00 3.06
1678 2139 2.677003 GCCACACAACGGGATGACG 61.677 63.158 0.00 0.00 40.31 4.35
1679 2140 2.032634 CCACACAACGGGATGACGG 61.033 63.158 0.00 0.00 38.39 4.79
1680 2141 1.005512 CACACAACGGGATGACGGA 60.006 57.895 0.00 0.00 38.39 4.69
1681 2142 1.014044 CACACAACGGGATGACGGAG 61.014 60.000 0.00 0.00 38.39 4.63
1714 2175 1.750193 TTTTCCCGCAGCTAGATTGG 58.250 50.000 0.00 0.00 0.00 3.16
1715 2176 0.908910 TTTCCCGCAGCTAGATTGGA 59.091 50.000 0.00 0.00 0.00 3.53
1716 2177 0.908910 TTCCCGCAGCTAGATTGGAA 59.091 50.000 0.00 0.00 0.00 3.53
1717 2178 0.465705 TCCCGCAGCTAGATTGGAAG 59.534 55.000 0.00 0.00 0.00 3.46
1718 2179 0.533755 CCCGCAGCTAGATTGGAAGG 60.534 60.000 0.00 0.00 0.00 3.46
1719 2180 0.465705 CCGCAGCTAGATTGGAAGGA 59.534 55.000 0.00 0.00 0.00 3.36
1720 2181 1.539929 CCGCAGCTAGATTGGAAGGAG 60.540 57.143 0.00 0.00 0.00 3.69
1721 2182 1.410517 CGCAGCTAGATTGGAAGGAGA 59.589 52.381 0.00 0.00 0.00 3.71
1722 2183 2.036992 CGCAGCTAGATTGGAAGGAGAT 59.963 50.000 0.00 0.00 0.00 2.75
1723 2184 3.401182 GCAGCTAGATTGGAAGGAGATG 58.599 50.000 0.00 0.00 0.00 2.90
1724 2185 3.806507 GCAGCTAGATTGGAAGGAGATGG 60.807 52.174 0.00 0.00 0.00 3.51
1725 2186 3.645212 CAGCTAGATTGGAAGGAGATGGA 59.355 47.826 0.00 0.00 0.00 3.41
1726 2187 4.102210 CAGCTAGATTGGAAGGAGATGGAA 59.898 45.833 0.00 0.00 0.00 3.53
1727 2188 4.102367 AGCTAGATTGGAAGGAGATGGAAC 59.898 45.833 0.00 0.00 0.00 3.62
1742 2203 2.314246 TGGAACAATTGATGTGTGGCA 58.686 42.857 13.59 0.00 42.99 4.92
1743 2204 2.697229 TGGAACAATTGATGTGTGGCAA 59.303 40.909 13.59 0.00 42.99 4.52
1744 2205 3.133542 TGGAACAATTGATGTGTGGCAAA 59.866 39.130 13.59 0.00 42.99 3.68
1745 2206 4.125703 GGAACAATTGATGTGTGGCAAAA 58.874 39.130 13.59 0.00 42.99 2.44
1746 2207 4.574013 GGAACAATTGATGTGTGGCAAAAA 59.426 37.500 13.59 0.00 42.99 1.94
1770 2231 2.879462 GATCGTGTCCGACGGTGC 60.879 66.667 14.79 8.93 43.17 5.01
1948 2411 2.625282 ATAATAGGGGAGGGGAGACG 57.375 55.000 0.00 0.00 0.00 4.18
1968 2431 2.750948 GACGTTTGGACTCTACTGCAA 58.249 47.619 0.00 0.00 0.00 4.08
2030 2493 7.148407 GGTTGTGAGTTCTCCTTTATATGTGTG 60.148 40.741 0.00 0.00 0.00 3.82
2042 2505 0.673333 TATGTGTGGCGTGCCTGAAG 60.673 55.000 12.84 0.00 36.94 3.02
2062 2525 8.233190 CCTGAAGCAAAATACTAGACAGAAAAG 58.767 37.037 0.00 0.00 0.00 2.27
2131 2600 2.963320 GGCGTCGTTGTCGTTGGT 60.963 61.111 0.00 0.00 38.33 3.67
2144 2613 3.930229 TGTCGTTGGTGATGTTGCTATAC 59.070 43.478 0.00 0.00 0.00 1.47
2148 2617 2.276201 TGGTGATGTTGCTATACACGC 58.724 47.619 0.00 0.00 33.08 5.34
2149 2618 1.257936 GGTGATGTTGCTATACACGCG 59.742 52.381 3.53 3.53 33.08 6.01
2151 2620 1.134936 TGATGTTGCTATACACGCGGT 60.135 47.619 12.47 8.38 0.00 5.68
2152 2621 1.257936 GATGTTGCTATACACGCGGTG 59.742 52.381 12.47 9.20 39.75 4.94
2165 2634 4.735132 CGGTGTGTCATCGCGGGT 62.735 66.667 6.13 0.00 29.25 5.28
2166 2635 2.813908 GGTGTGTCATCGCGGGTC 60.814 66.667 6.13 0.00 0.00 4.46
2167 2636 2.813908 GTGTGTCATCGCGGGTCC 60.814 66.667 6.13 0.00 0.00 4.46
2168 2637 4.429212 TGTGTCATCGCGGGTCCG 62.429 66.667 6.13 4.85 43.09 4.79
2171 2640 4.570663 GTCATCGCGGGTCCGGAG 62.571 72.222 3.06 0.00 40.19 4.63
2185 2654 2.511600 GGAGGATGTTCCGCGTGG 60.512 66.667 9.28 9.28 42.75 4.94
2240 2709 1.343821 GCTACGTGGCGTTTCATCG 59.656 57.895 8.55 0.00 41.54 3.84
2248 2717 0.742990 GGCGTTTCATCGTGGATCCA 60.743 55.000 11.44 11.44 0.00 3.41
2258 2727 1.376812 GTGGATCCACGGGGTGTTC 60.377 63.158 28.52 3.15 37.19 3.18
2325 2794 2.554032 CAAGTTGTCCCAGACCATGTTC 59.446 50.000 0.00 0.00 0.00 3.18
2339 2822 1.852157 ATGTTCACGTCCCCTGGCAT 61.852 55.000 0.00 0.00 0.00 4.40
2362 2845 0.886563 CCTTCCTGCTTCTTGCCAAG 59.113 55.000 0.00 0.00 42.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 114 1.135960 TCCTCATGTCCCACACACAA 58.864 50.000 0.00 0.00 38.04 3.33
119 144 1.201780 GCTAAGCGCACGTACAGAAAC 60.202 52.381 11.47 0.00 38.92 2.78
549 1005 3.246687 TGGTGGTTCCAGTGACCC 58.753 61.111 0.00 0.00 41.93 4.46
798 1257 5.560966 ATTGTAAAGCACGGAAATACCTG 57.439 39.130 0.00 0.00 36.31 4.00
799 1258 5.163794 CGAATTGTAAAGCACGGAAATACCT 60.164 40.000 0.00 0.00 36.31 3.08
800 1259 5.025826 CGAATTGTAAAGCACGGAAATACC 58.974 41.667 0.00 0.00 0.00 2.73
801 1260 5.860641 TCGAATTGTAAAGCACGGAAATAC 58.139 37.500 0.00 0.00 0.00 1.89
802 1261 6.314152 TCATCGAATTGTAAAGCACGGAAATA 59.686 34.615 0.00 0.00 0.00 1.40
803 1262 5.123186 TCATCGAATTGTAAAGCACGGAAAT 59.877 36.000 0.00 0.00 0.00 2.17
804 1263 4.452795 TCATCGAATTGTAAAGCACGGAAA 59.547 37.500 0.00 0.00 0.00 3.13
805 1264 3.997681 TCATCGAATTGTAAAGCACGGAA 59.002 39.130 0.00 0.00 0.00 4.30
806 1265 3.591023 TCATCGAATTGTAAAGCACGGA 58.409 40.909 0.00 0.00 0.00 4.69
807 1266 3.242413 CCTCATCGAATTGTAAAGCACGG 60.242 47.826 0.00 0.00 0.00 4.94
808 1267 3.242413 CCCTCATCGAATTGTAAAGCACG 60.242 47.826 0.00 0.00 0.00 5.34
809 1268 3.689649 ACCCTCATCGAATTGTAAAGCAC 59.310 43.478 0.00 0.00 0.00 4.40
810 1269 3.689161 CACCCTCATCGAATTGTAAAGCA 59.311 43.478 0.00 0.00 0.00 3.91
811 1270 3.487544 GCACCCTCATCGAATTGTAAAGC 60.488 47.826 0.00 0.00 0.00 3.51
812 1271 3.689161 TGCACCCTCATCGAATTGTAAAG 59.311 43.478 0.00 0.00 0.00 1.85
813 1272 3.680490 TGCACCCTCATCGAATTGTAAA 58.320 40.909 0.00 0.00 0.00 2.01
814 1273 3.055458 TCTGCACCCTCATCGAATTGTAA 60.055 43.478 0.00 0.00 0.00 2.41
815 1274 2.499693 TCTGCACCCTCATCGAATTGTA 59.500 45.455 0.00 0.00 0.00 2.41
882 1341 7.335673 TGATCGACCACTTGCAGAAAATAATTA 59.664 33.333 0.00 0.00 0.00 1.40
978 1437 2.035704 AGATCGCAGCCTATCTGAAGTG 59.964 50.000 4.45 0.00 45.72 3.16
1227 1686 1.370414 CCTTTCCGCAGTTGCAACG 60.370 57.895 23.21 18.29 42.21 4.10
1257 1716 7.538334 CGCAAATATGATTTCAACAACTTGAGA 59.462 33.333 0.00 0.00 37.70 3.27
1329 1788 4.012374 TCTCCAAGACATCATTTTCCAGC 58.988 43.478 0.00 0.00 0.00 4.85
1332 1791 7.401955 AATCTTCTCCAAGACATCATTTTCC 57.598 36.000 0.00 0.00 41.64 3.13
1376 1835 7.174946 GTCTTGTGTTCCTGGAAATGAAATCTA 59.825 37.037 11.40 0.00 0.00 1.98
1389 1848 1.442769 CCATCCGTCTTGTGTTCCTG 58.557 55.000 0.00 0.00 0.00 3.86
1555 2016 5.624509 GCGAAAAGAAAAATGGAGCCCTAAT 60.625 40.000 0.00 0.00 0.00 1.73
1563 2024 2.287909 CCGGTGCGAAAAGAAAAATGGA 60.288 45.455 0.00 0.00 0.00 3.41
1585 2046 2.001269 CCTCCAGGAATTCGGGGGT 61.001 63.158 9.58 0.00 37.39 4.95
1603 2064 1.523758 CTTCCAATATACAGGGCCGC 58.476 55.000 0.00 0.00 0.00 6.53
1614 2075 9.618890 CATCAACTATTTCTTCTCCTTCCAATA 57.381 33.333 0.00 0.00 0.00 1.90
1615 2076 7.559170 CCATCAACTATTTCTTCTCCTTCCAAT 59.441 37.037 0.00 0.00 0.00 3.16
1617 2078 6.418101 CCATCAACTATTTCTTCTCCTTCCA 58.582 40.000 0.00 0.00 0.00 3.53
1618 2079 5.298026 GCCATCAACTATTTCTTCTCCTTCC 59.702 44.000 0.00 0.00 0.00 3.46
1619 2080 5.882557 TGCCATCAACTATTTCTTCTCCTTC 59.117 40.000 0.00 0.00 0.00 3.46
1620 2081 5.649831 GTGCCATCAACTATTTCTTCTCCTT 59.350 40.000 0.00 0.00 0.00 3.36
1621 2082 5.189180 GTGCCATCAACTATTTCTTCTCCT 58.811 41.667 0.00 0.00 0.00 3.69
1622 2083 4.034510 CGTGCCATCAACTATTTCTTCTCC 59.965 45.833 0.00 0.00 0.00 3.71
1623 2084 4.870426 TCGTGCCATCAACTATTTCTTCTC 59.130 41.667 0.00 0.00 0.00 2.87
1624 2085 4.832248 TCGTGCCATCAACTATTTCTTCT 58.168 39.130 0.00 0.00 0.00 2.85
1625 2086 5.545658 TTCGTGCCATCAACTATTTCTTC 57.454 39.130 0.00 0.00 0.00 2.87
1626 2087 5.705441 TCTTTCGTGCCATCAACTATTTCTT 59.295 36.000 0.00 0.00 0.00 2.52
1627 2088 5.245531 TCTTTCGTGCCATCAACTATTTCT 58.754 37.500 0.00 0.00 0.00 2.52
1628 2089 5.545658 TCTTTCGTGCCATCAACTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
1629 2090 5.957842 TTCTTTCGTGCCATCAACTATTT 57.042 34.783 0.00 0.00 0.00 1.40
1630 2091 5.957842 TTTCTTTCGTGCCATCAACTATT 57.042 34.783 0.00 0.00 0.00 1.73
1631 2092 5.957842 TTTTCTTTCGTGCCATCAACTAT 57.042 34.783 0.00 0.00 0.00 2.12
1632 2093 5.390461 CGATTTTCTTTCGTGCCATCAACTA 60.390 40.000 0.00 0.00 32.08 2.24
1633 2094 4.613622 CGATTTTCTTTCGTGCCATCAACT 60.614 41.667 0.00 0.00 32.08 3.16
1634 2095 3.603770 CGATTTTCTTTCGTGCCATCAAC 59.396 43.478 0.00 0.00 32.08 3.18
1635 2096 3.500299 TCGATTTTCTTTCGTGCCATCAA 59.500 39.130 0.00 0.00 37.82 2.57
1636 2097 3.070748 TCGATTTTCTTTCGTGCCATCA 58.929 40.909 0.00 0.00 37.82 3.07
1637 2098 3.740044 TCGATTTTCTTTCGTGCCATC 57.260 42.857 0.00 0.00 37.82 3.51
1638 2099 3.181497 CCATCGATTTTCTTTCGTGCCAT 60.181 43.478 0.00 0.00 37.82 4.40
1639 2100 2.161410 CCATCGATTTTCTTTCGTGCCA 59.839 45.455 0.00 0.00 37.82 4.92
1640 2101 2.785679 CCATCGATTTTCTTTCGTGCC 58.214 47.619 0.00 0.00 37.82 5.01
1641 2102 2.177173 GCCATCGATTTTCTTTCGTGC 58.823 47.619 0.00 0.00 37.82 5.34
1642 2103 2.161410 TGGCCATCGATTTTCTTTCGTG 59.839 45.455 0.00 0.00 37.82 4.35
1643 2104 2.161609 GTGGCCATCGATTTTCTTTCGT 59.838 45.455 9.72 0.00 37.82 3.85
1644 2105 2.161410 TGTGGCCATCGATTTTCTTTCG 59.839 45.455 9.72 0.00 37.94 3.46
1645 2106 3.057596 TGTGTGGCCATCGATTTTCTTTC 60.058 43.478 9.72 0.00 0.00 2.62
1646 2107 2.890311 TGTGTGGCCATCGATTTTCTTT 59.110 40.909 9.72 0.00 0.00 2.52
1647 2108 2.513753 TGTGTGGCCATCGATTTTCTT 58.486 42.857 9.72 0.00 0.00 2.52
1648 2109 2.198827 TGTGTGGCCATCGATTTTCT 57.801 45.000 9.72 0.00 0.00 2.52
1649 2110 2.595386 GTTGTGTGGCCATCGATTTTC 58.405 47.619 9.72 0.00 0.00 2.29
1650 2111 1.068610 CGTTGTGTGGCCATCGATTTT 60.069 47.619 9.72 0.00 30.97 1.82
1651 2112 0.521291 CGTTGTGTGGCCATCGATTT 59.479 50.000 9.72 0.00 30.97 2.17
1652 2113 1.305219 CCGTTGTGTGGCCATCGATT 61.305 55.000 9.72 0.00 30.97 3.34
1653 2114 1.745115 CCGTTGTGTGGCCATCGAT 60.745 57.895 9.72 0.00 30.97 3.59
1654 2115 2.358125 CCGTTGTGTGGCCATCGA 60.358 61.111 9.72 2.25 30.97 3.59
1655 2116 3.430862 CCCGTTGTGTGGCCATCG 61.431 66.667 9.72 9.36 0.00 3.84
1656 2117 1.378514 ATCCCGTTGTGTGGCCATC 60.379 57.895 9.72 6.30 0.00 3.51
1657 2118 1.678635 CATCCCGTTGTGTGGCCAT 60.679 57.895 9.72 0.00 0.00 4.40
1658 2119 2.282110 CATCCCGTTGTGTGGCCA 60.282 61.111 0.00 0.00 0.00 5.36
1659 2120 2.033448 TCATCCCGTTGTGTGGCC 59.967 61.111 0.00 0.00 0.00 5.36
1660 2121 2.677003 CGTCATCCCGTTGTGTGGC 61.677 63.158 0.00 0.00 0.00 5.01
1661 2122 2.032634 CCGTCATCCCGTTGTGTGG 61.033 63.158 0.00 0.00 0.00 4.17
1662 2123 1.005512 TCCGTCATCCCGTTGTGTG 60.006 57.895 0.00 0.00 0.00 3.82
1663 2124 1.292223 CTCCGTCATCCCGTTGTGT 59.708 57.895 0.00 0.00 0.00 3.72
1664 2125 0.528924 TACTCCGTCATCCCGTTGTG 59.471 55.000 0.00 0.00 0.00 3.33
1665 2126 1.407979 GATACTCCGTCATCCCGTTGT 59.592 52.381 0.00 0.00 0.00 3.32
1666 2127 1.681793 AGATACTCCGTCATCCCGTTG 59.318 52.381 0.00 0.00 0.00 4.10
1667 2128 1.955080 GAGATACTCCGTCATCCCGTT 59.045 52.381 0.00 0.00 0.00 4.44
1668 2129 1.133884 TGAGATACTCCGTCATCCCGT 60.134 52.381 0.00 0.00 0.00 5.28
1669 2130 1.605753 TGAGATACTCCGTCATCCCG 58.394 55.000 0.00 0.00 0.00 5.14
1670 2131 3.426615 AGATGAGATACTCCGTCATCCC 58.573 50.000 7.72 0.00 45.22 3.85
1671 2132 4.331968 AGAGATGAGATACTCCGTCATCC 58.668 47.826 7.72 1.47 45.22 3.51
1672 2133 5.957842 AAGAGATGAGATACTCCGTCATC 57.042 43.478 3.80 3.80 44.69 2.92
1673 2134 6.723298 AAAAGAGATGAGATACTCCGTCAT 57.277 37.500 0.00 0.00 34.13 3.06
1674 2135 6.531503 AAAAAGAGATGAGATACTCCGTCA 57.468 37.500 0.00 0.00 34.13 4.35
1694 2155 2.091541 CCAATCTAGCTGCGGGAAAAA 58.908 47.619 0.00 0.00 0.00 1.94
1695 2156 1.280710 TCCAATCTAGCTGCGGGAAAA 59.719 47.619 0.00 0.00 0.00 2.29
1696 2157 0.908910 TCCAATCTAGCTGCGGGAAA 59.091 50.000 0.00 0.00 0.00 3.13
1697 2158 0.908910 TTCCAATCTAGCTGCGGGAA 59.091 50.000 0.00 0.00 32.35 3.97
1698 2159 0.465705 CTTCCAATCTAGCTGCGGGA 59.534 55.000 0.00 0.00 0.00 5.14
1699 2160 0.533755 CCTTCCAATCTAGCTGCGGG 60.534 60.000 0.00 0.00 0.00 6.13
1700 2161 0.465705 TCCTTCCAATCTAGCTGCGG 59.534 55.000 0.00 0.00 0.00 5.69
1701 2162 1.410517 TCTCCTTCCAATCTAGCTGCG 59.589 52.381 0.00 0.00 0.00 5.18
1702 2163 3.401182 CATCTCCTTCCAATCTAGCTGC 58.599 50.000 0.00 0.00 0.00 5.25
1703 2164 3.645212 TCCATCTCCTTCCAATCTAGCTG 59.355 47.826 0.00 0.00 0.00 4.24
1704 2165 3.933886 TCCATCTCCTTCCAATCTAGCT 58.066 45.455 0.00 0.00 0.00 3.32
1705 2166 4.141620 TGTTCCATCTCCTTCCAATCTAGC 60.142 45.833 0.00 0.00 0.00 3.42
1706 2167 5.620738 TGTTCCATCTCCTTCCAATCTAG 57.379 43.478 0.00 0.00 0.00 2.43
1707 2168 6.581388 ATTGTTCCATCTCCTTCCAATCTA 57.419 37.500 0.00 0.00 0.00 1.98
1708 2169 4.934797 TTGTTCCATCTCCTTCCAATCT 57.065 40.909 0.00 0.00 0.00 2.40
1709 2170 5.653769 TCAATTGTTCCATCTCCTTCCAATC 59.346 40.000 5.13 0.00 0.00 2.67
1710 2171 5.582953 TCAATTGTTCCATCTCCTTCCAAT 58.417 37.500 5.13 0.00 0.00 3.16
1711 2172 4.996793 TCAATTGTTCCATCTCCTTCCAA 58.003 39.130 5.13 0.00 0.00 3.53
1712 2173 4.656100 TCAATTGTTCCATCTCCTTCCA 57.344 40.909 5.13 0.00 0.00 3.53
1713 2174 4.952335 ACATCAATTGTTCCATCTCCTTCC 59.048 41.667 5.13 0.00 33.74 3.46
1714 2175 5.416952 ACACATCAATTGTTCCATCTCCTTC 59.583 40.000 5.13 0.00 36.00 3.46
1715 2176 5.184479 CACACATCAATTGTTCCATCTCCTT 59.816 40.000 5.13 0.00 36.00 3.36
1716 2177 4.703575 CACACATCAATTGTTCCATCTCCT 59.296 41.667 5.13 0.00 36.00 3.69
1717 2178 4.142315 CCACACATCAATTGTTCCATCTCC 60.142 45.833 5.13 0.00 36.00 3.71
1718 2179 4.676196 GCCACACATCAATTGTTCCATCTC 60.676 45.833 5.13 0.00 36.00 2.75
1719 2180 3.194116 GCCACACATCAATTGTTCCATCT 59.806 43.478 5.13 0.00 36.00 2.90
1720 2181 3.056678 TGCCACACATCAATTGTTCCATC 60.057 43.478 5.13 0.00 36.00 3.51
1721 2182 2.898612 TGCCACACATCAATTGTTCCAT 59.101 40.909 5.13 0.00 36.00 3.41
1722 2183 2.314246 TGCCACACATCAATTGTTCCA 58.686 42.857 5.13 0.00 36.00 3.53
1723 2184 3.383620 TTGCCACACATCAATTGTTCC 57.616 42.857 5.13 0.00 36.00 3.62
1724 2185 5.731599 TTTTTGCCACACATCAATTGTTC 57.268 34.783 5.13 0.00 36.00 3.18
1744 2205 3.328382 TCGGACACGATCATCCTTTTT 57.672 42.857 0.00 0.00 45.59 1.94
1757 2218 3.986006 TCCTGCACCGTCGGACAC 61.986 66.667 20.51 7.14 0.00 3.67
1758 2219 3.986006 GTCCTGCACCGTCGGACA 61.986 66.667 20.51 14.52 45.08 4.02
1761 2222 2.071844 ATATCGTCCTGCACCGTCGG 62.072 60.000 10.48 10.48 0.00 4.79
1948 2411 2.433868 TGCAGTAGAGTCCAAACGTC 57.566 50.000 0.00 0.00 0.00 4.34
2042 2505 8.178313 GGATCACTTTTCTGTCTAGTATTTTGC 58.822 37.037 0.00 0.00 0.00 3.68
2044 2507 8.095169 ACGGATCACTTTTCTGTCTAGTATTTT 58.905 33.333 0.00 0.00 0.00 1.82
2050 2513 6.400091 CGAAAACGGATCACTTTTCTGTCTAG 60.400 42.308 18.05 0.00 35.21 2.43
2131 2600 1.134936 ACCGCGTGTATAGCAACATCA 60.135 47.619 4.92 0.00 34.19 3.07
2148 2617 4.735132 ACCCGCGATGACACACCG 62.735 66.667 8.23 0.00 0.00 4.94
2149 2618 2.813908 GACCCGCGATGACACACC 60.814 66.667 8.23 0.00 0.00 4.16
2151 2620 4.429212 CGGACCCGCGATGACACA 62.429 66.667 8.23 0.00 0.00 3.72
2154 2623 4.570663 CTCCGGACCCGCGATGAC 62.571 72.222 8.23 0.00 38.24 3.06
2157 2626 4.916314 ATCCTCCGGACCCGCGAT 62.916 66.667 8.23 0.00 38.24 4.58
2160 2629 3.735037 GAACATCCTCCGGACCCGC 62.735 68.421 0.00 0.00 38.24 6.13
2161 2630 2.499685 GAACATCCTCCGGACCCG 59.500 66.667 0.00 0.66 32.98 5.28
2162 2631 2.908796 GGAACATCCTCCGGACCC 59.091 66.667 0.00 0.00 32.98 4.46
2168 2637 2.511600 CCACGCGGAACATCCTCC 60.512 66.667 12.47 0.00 33.30 4.30
2169 2638 2.100631 CACCACGCGGAACATCCTC 61.101 63.158 12.47 0.00 33.30 3.71
2170 2639 2.047274 CACCACGCGGAACATCCT 60.047 61.111 12.47 0.00 33.30 3.24
2171 2640 3.124921 CCACCACGCGGAACATCC 61.125 66.667 12.47 0.00 35.59 3.51
2172 2641 3.124921 CCCACCACGCGGAACATC 61.125 66.667 12.47 0.00 35.59 3.06
2173 2642 4.715523 CCCCACCACGCGGAACAT 62.716 66.667 12.47 0.00 35.59 2.71
2175 2644 4.941309 AACCCCACCACGCGGAAC 62.941 66.667 12.47 0.00 35.59 3.62
2176 2645 4.629523 GAACCCCACCACGCGGAA 62.630 66.667 12.47 0.00 35.59 4.30
2240 2709 1.376812 GAACACCCCGTGGATCCAC 60.377 63.158 31.59 31.59 43.01 4.02
2248 2717 2.590575 CAGCGTTGAACACCCCGT 60.591 61.111 0.00 0.00 0.00 5.28
2250 2719 3.670377 GCCAGCGTTGAACACCCC 61.670 66.667 0.00 0.00 0.00 4.95
2314 2783 0.673644 GGGGACGTGAACATGGTCTG 60.674 60.000 12.94 7.16 0.00 3.51
2325 2794 2.040544 GTGAATGCCAGGGGACGTG 61.041 63.158 0.00 0.00 44.70 4.49
2339 2822 1.609208 GCAAGAAGCAGGAAGGTGAA 58.391 50.000 0.00 0.00 44.79 3.18


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

AutoCloner maintained by Alex Coulton.