Multiple sequence alignment - TraesCS7D01G075600

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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 TraesCS7D01G075600 chr7D 100.000 3262 0 0 1 3262 44719618 44716357 0.000000e+00 6024.0
1 TraesCS7D01G075600 chr7D 89.535 86 7 1 1988 2071 240991889 240991974 1.240000e-19 108.0
2 TraesCS7D01G075600 chr5D 93.376 2008 79 23 21 1992 441572023 441570034 0.000000e+00 2922.0
3 TraesCS7D01G075600 chr5D 93.211 1738 67 25 292 1995 490439530 490437810 0.000000e+00 2508.0
4 TraesCS7D01G075600 chr5D 94.588 1164 50 8 2085 3242 441570007 441568851 0.000000e+00 1788.0
5 TraesCS7D01G075600 chr5D 93.782 1158 54 9 2085 3229 490437786 490436634 0.000000e+00 1724.0
6 TraesCS7D01G075600 chr5D 92.405 79 4 1 1992 2068 195768965 195769043 9.570000e-21 111.0
7 TraesCS7D01G075600 chr5D 100.000 48 0 0 3215 3262 441568850 441568803 4.480000e-14 89.8
8 TraesCS7D01G075600 chr6D 92.628 1994 101 15 21 1982 420230961 420228982 0.000000e+00 2826.0
9 TraesCS7D01G075600 chr6D 93.800 1000 43 12 2270 3262 28310772 28309785 0.000000e+00 1485.0
10 TraesCS7D01G075600 chr6D 94.340 583 26 5 2084 2663 420228947 420228369 0.000000e+00 887.0
11 TraesCS7D01G075600 chr6D 96.680 241 8 0 3022 3262 420225684 420225444 5.070000e-108 401.0
12 TraesCS7D01G075600 chr6D 87.356 348 21 12 1665 1999 28311336 28310999 8.540000e-101 377.0
13 TraesCS7D01G075600 chr6D 94.828 174 9 0 2141 2314 28310945 28310772 4.150000e-69 272.0
14 TraesCS7D01G075600 chr4A 92.528 1994 101 19 22 1982 581495557 581493579 0.000000e+00 2813.0
15 TraesCS7D01G075600 chr4A 92.593 945 65 3 22 962 15920448 15919505 0.000000e+00 1352.0
16 TraesCS7D01G075600 chr4A 91.952 584 40 5 2084 2663 581493544 581492964 0.000000e+00 811.0
17 TraesCS7D01G075600 chr4A 91.219 558 22 10 1004 1549 682752144 682752686 0.000000e+00 734.0
18 TraesCS7D01G075600 chr4A 90.305 557 28 8 1004 1549 15919495 15918954 0.000000e+00 706.0
19 TraesCS7D01G075600 chr4A 90.698 86 6 1 1988 2071 134781086 134781171 2.660000e-21 113.0
20 TraesCS7D01G075600 chr4A 91.358 81 5 1 1992 2070 542393533 542393453 3.440000e-20 110.0
21 TraesCS7D01G075600 chr5A 91.441 1998 99 24 21 1982 611980856 611978895 0.000000e+00 2676.0
22 TraesCS7D01G075600 chr5A 92.788 1456 67 15 76 1505 124618276 124619719 0.000000e+00 2073.0
23 TraesCS7D01G075600 chr5A 93.467 597 32 5 2667 3262 611977603 611977013 0.000000e+00 880.0
24 TraesCS7D01G075600 chr5A 94.085 541 25 5 2125 2662 611978838 611978302 0.000000e+00 815.0
25 TraesCS7D01G075600 chr5A 91.610 584 42 5 2084 2663 124621893 124622473 0.000000e+00 800.0
26 TraesCS7D01G075600 chr5A 93.729 303 19 0 1503 1805 124620563 124620865 3.840000e-124 455.0
27 TraesCS7D01G075600 chr5A 97.419 155 4 0 1828 1982 124621704 124621858 6.940000e-67 265.0
28 TraesCS7D01G075600 chr5B 92.561 1519 69 14 43 1537 604870051 604871549 0.000000e+00 2139.0
29 TraesCS7D01G075600 chr5B 93.911 542 27 4 2723 3262 604858078 604857541 0.000000e+00 813.0
30 TraesCS7D01G075600 chr5B 93.913 460 21 5 2290 2745 604871911 604872367 0.000000e+00 688.0
31 TraesCS7D01G075600 chr5B 97.093 172 5 0 2085 2256 604871739 604871910 1.140000e-74 291.0
32 TraesCS7D01G075600 chr5B 95.758 165 7 0 1828 1992 604871548 604871712 1.930000e-67 267.0
33 TraesCS7D01G075600 chr7A 93.797 1322 46 9 699 1995 47296922 47295612 0.000000e+00 1954.0
34 TraesCS7D01G075600 chr7A 94.920 1181 44 8 2085 3262 47295588 47294421 0.000000e+00 1834.0
35 TraesCS7D01G075600 chr4D 91.590 975 70 8 38 1005 472682749 472681780 0.000000e+00 1336.0
36 TraesCS7D01G075600 chr4D 90.844 557 28 8 1004 1549 451038884 451039428 0.000000e+00 725.0
37 TraesCS7D01G075600 chr4D 90.833 480 23 5 1009 1477 472680725 472680256 9.940000e-175 623.0
38 TraesCS7D01G075600 chr6A 91.309 1001 44 11 2270 3262 29577274 29578239 0.000000e+00 1327.0
39 TraesCS7D01G075600 chr6A 89.368 348 20 5 1665 1999 29576716 29577059 3.890000e-114 422.0
40 TraesCS7D01G075600 chr1A 90.969 764 38 9 710 1454 538399895 538400646 0.000000e+00 1000.0
41 TraesCS7D01G075600 chr3A 84.880 873 95 19 835 1691 282154337 282155188 0.000000e+00 846.0
42 TraesCS7D01G075600 chr2D 88.966 580 39 8 1131 1697 376351357 376351924 0.000000e+00 693.0
43 TraesCS7D01G075600 chr2D 91.765 85 5 1 1988 2070 254337462 254337546 2.060000e-22 117.0
44 TraesCS7D01G075600 chr2D 90.588 85 6 1 1988 2070 493213309 493213393 9.570000e-21 111.0
45 TraesCS7D01G075600 chr4B 91.632 478 16 8 1080 1546 564152535 564152999 9.870000e-180 640.0
46 TraesCS7D01G075600 chr2A 91.941 273 22 0 1425 1697 509548167 509548439 1.840000e-102 383.0
47 TraesCS7D01G075600 chr6B 90.588 85 6 1 1988 2070 549253333 549253249 9.570000e-21 111.0
48 TraesCS7D01G075600 chr3D 90.588 85 6 2 1988 2070 157146728 157146644 9.570000e-21 111.0
49 TraesCS7D01G075600 chr3B 88.764 89 8 1 1988 2074 614123717 614123805 1.240000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G075600 chr7D 44716357 44719618 3261 True 6024.000000 6024 100.000000 1 3262 1 chr7D.!!$R1 3261
1 TraesCS7D01G075600 chr5D 490436634 490439530 2896 True 2116.000000 2508 93.496500 292 3229 2 chr5D.!!$R2 2937
2 TraesCS7D01G075600 chr5D 441568803 441572023 3220 True 1599.933333 2922 95.988000 21 3262 3 chr5D.!!$R1 3241
3 TraesCS7D01G075600 chr6D 420225444 420230961 5517 True 1371.333333 2826 94.549333 21 3262 3 chr6D.!!$R2 3241
4 TraesCS7D01G075600 chr6D 28309785 28311336 1551 True 711.333333 1485 91.994667 1665 3262 3 chr6D.!!$R1 1597
5 TraesCS7D01G075600 chr4A 581492964 581495557 2593 True 1812.000000 2813 92.240000 22 2663 2 chr4A.!!$R3 2641
6 TraesCS7D01G075600 chr4A 15918954 15920448 1494 True 1029.000000 1352 91.449000 22 1549 2 chr4A.!!$R2 1527
7 TraesCS7D01G075600 chr4A 682752144 682752686 542 False 734.000000 734 91.219000 1004 1549 1 chr4A.!!$F2 545
8 TraesCS7D01G075600 chr5A 611977013 611980856 3843 True 1457.000000 2676 92.997667 21 3262 3 chr5A.!!$R1 3241
9 TraesCS7D01G075600 chr5A 124618276 124622473 4197 False 898.250000 2073 93.886500 76 2663 4 chr5A.!!$F1 2587
10 TraesCS7D01G075600 chr5B 604870051 604872367 2316 False 846.250000 2139 94.831250 43 2745 4 chr5B.!!$F1 2702
11 TraesCS7D01G075600 chr5B 604857541 604858078 537 True 813.000000 813 93.911000 2723 3262 1 chr5B.!!$R1 539
12 TraesCS7D01G075600 chr7A 47294421 47296922 2501 True 1894.000000 1954 94.358500 699 3262 2 chr7A.!!$R1 2563
13 TraesCS7D01G075600 chr4D 472680256 472682749 2493 True 979.500000 1336 91.211500 38 1477 2 chr4D.!!$R1 1439
14 TraesCS7D01G075600 chr4D 451038884 451039428 544 False 725.000000 725 90.844000 1004 1549 1 chr4D.!!$F1 545
15 TraesCS7D01G075600 chr6A 29576716 29578239 1523 False 874.500000 1327 90.338500 1665 3262 2 chr6A.!!$F1 1597
16 TraesCS7D01G075600 chr1A 538399895 538400646 751 False 1000.000000 1000 90.969000 710 1454 1 chr1A.!!$F1 744
17 TraesCS7D01G075600 chr3A 282154337 282155188 851 False 846.000000 846 84.880000 835 1691 1 chr3A.!!$F1 856
18 TraesCS7D01G075600 chr2D 376351357 376351924 567 False 693.000000 693 88.966000 1131 1697 1 chr2D.!!$F2 566

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
193 195 1.059584 TCAGGTTTGCCTCCACCTCA 61.060 55.0 0.0 0.0 44.97 3.86 F
1246 2333 0.516877 CGCTGAGATTCACCGCAAAA 59.483 50.0 0.0 0.0 0.00 2.44 F
2052 4842 0.530870 GCTTCGGTGGTAGGAGCATC 60.531 60.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 4835 0.104671 GCAGACTCTGAGGATGCTCC 59.895 60.0 21.82 0.0 32.44 4.70 R
2061 4851 0.371301 CGTCGTGTCCAATGATGCAG 59.629 55.0 0.00 0.0 0.00 4.41 R
3105 8338 1.299541 ACTGAACTTGACACTTGGCG 58.700 50.0 0.00 0.0 0.00 5.69 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
70 72 1.900351 CCTCAGAAGATGGGCGTCA 59.100 57.895 0.00 0.00 0.00 4.35
74 76 1.278985 TCAGAAGATGGGCGTCAACAT 59.721 47.619 0.00 0.00 0.00 2.71
113 115 1.103803 GTGACTCCACGCATCTCCTA 58.896 55.000 0.00 0.00 33.10 2.94
193 195 1.059584 TCAGGTTTGCCTCCACCTCA 61.060 55.000 0.00 0.00 44.97 3.86
204 206 3.465403 CACCTCAGCTCTCCCCCG 61.465 72.222 0.00 0.00 0.00 5.73
463 469 7.121315 ACTTGGTATGGAGAAGTTTTCTTATGC 59.879 37.037 0.00 0.00 40.87 3.14
503 510 1.635487 TGCAGAACTATTTGGGCTCCT 59.365 47.619 0.00 0.00 0.00 3.69
642 654 1.093159 TCGCGAGGAAGAGTAGGAAC 58.907 55.000 3.71 0.00 0.00 3.62
680 692 6.154021 GGGTTTCACATACCTCTTCTACACTA 59.846 42.308 0.00 0.00 35.92 2.74
706 718 3.893813 AGTCTTTGCTTTTCAGGATTGCT 59.106 39.130 0.00 0.00 0.00 3.91
845 863 9.856162 AGTCTCCTTTATTTTGTTTACCTACAA 57.144 29.630 0.00 0.00 36.30 2.41
1021 2090 5.065914 TGATGGAAGTATGCCTAATCTTGC 58.934 41.667 0.00 0.00 31.46 4.01
1022 2091 3.466836 TGGAAGTATGCCTAATCTTGCG 58.533 45.455 0.00 0.00 31.46 4.85
1100 2175 8.613060 TCTAAGCTATTGAATTAGGAAGCATG 57.387 34.615 0.00 0.00 32.42 4.06
1106 2181 4.970662 TGAATTAGGAAGCATGCAGTTC 57.029 40.909 21.98 15.42 0.00 3.01
1239 2326 2.467826 GCTGGGCGCTGAGATTCAC 61.468 63.158 7.64 0.00 35.14 3.18
1240 2327 1.817099 CTGGGCGCTGAGATTCACC 60.817 63.158 7.64 0.00 0.00 4.02
1241 2328 2.892425 GGGCGCTGAGATTCACCG 60.892 66.667 7.64 0.00 0.00 4.94
1244 2331 3.874873 CGCTGAGATTCACCGCAA 58.125 55.556 0.00 0.00 0.00 4.85
1245 2332 2.161831 CGCTGAGATTCACCGCAAA 58.838 52.632 0.00 0.00 0.00 3.68
1246 2333 0.516877 CGCTGAGATTCACCGCAAAA 59.483 50.000 0.00 0.00 0.00 2.44
1247 2334 1.131126 CGCTGAGATTCACCGCAAAAT 59.869 47.619 0.00 0.00 0.00 1.82
1308 2395 2.814805 AGGTGAGTTGGATCCATTGG 57.185 50.000 17.06 0.00 0.00 3.16
1420 2527 7.826252 CCAGATTCACCCATATAAAGTATCCTG 59.174 40.741 0.00 0.00 0.00 3.86
1648 3613 1.850345 ACCAAGGAACCTCCAAAGACA 59.150 47.619 0.00 0.00 39.61 3.41
1996 4786 4.012895 GGCGACGTGCTGTTGGTG 62.013 66.667 0.00 0.00 45.43 4.17
1997 4787 4.666532 GCGACGTGCTGTTGGTGC 62.667 66.667 0.00 0.00 41.73 5.01
1998 4788 3.268603 CGACGTGCTGTTGGTGCA 61.269 61.111 0.00 0.00 38.19 4.57
1999 4789 2.633657 GACGTGCTGTTGGTGCAG 59.366 61.111 0.00 0.00 41.41 4.41
2005 4795 3.664495 CTGTTGGTGCAGCAGAGG 58.336 61.111 19.25 8.94 43.65 3.69
2006 4796 1.970114 CTGTTGGTGCAGCAGAGGG 60.970 63.158 19.25 7.20 43.65 4.30
2007 4797 3.368571 GTTGGTGCAGCAGAGGGC 61.369 66.667 19.25 4.91 45.30 5.19
2017 4807 3.584947 GCAGAGGGCTTTGATCCTT 57.415 52.632 0.00 0.00 40.25 3.36
2018 4808 1.844687 GCAGAGGGCTTTGATCCTTT 58.155 50.000 0.00 0.00 40.25 3.11
2019 4809 2.174360 GCAGAGGGCTTTGATCCTTTT 58.826 47.619 0.00 0.00 40.25 2.27
2020 4810 2.094338 GCAGAGGGCTTTGATCCTTTTG 60.094 50.000 0.00 0.00 40.25 2.44
2021 4811 3.424703 CAGAGGGCTTTGATCCTTTTGA 58.575 45.455 0.00 0.00 32.74 2.69
2022 4812 3.192212 CAGAGGGCTTTGATCCTTTTGAC 59.808 47.826 0.00 0.00 32.74 3.18
2023 4813 3.075134 AGAGGGCTTTGATCCTTTTGACT 59.925 43.478 0.00 0.00 32.74 3.41
2024 4814 3.829026 GAGGGCTTTGATCCTTTTGACTT 59.171 43.478 0.00 0.00 32.74 3.01
2025 4815 3.829026 AGGGCTTTGATCCTTTTGACTTC 59.171 43.478 0.00 0.00 0.00 3.01
2026 4816 3.829026 GGGCTTTGATCCTTTTGACTTCT 59.171 43.478 0.00 0.00 0.00 2.85
2027 4817 4.281941 GGGCTTTGATCCTTTTGACTTCTT 59.718 41.667 0.00 0.00 0.00 2.52
2028 4818 5.465051 GGCTTTGATCCTTTTGACTTCTTC 58.535 41.667 0.00 0.00 0.00 2.87
2029 4819 5.242615 GGCTTTGATCCTTTTGACTTCTTCT 59.757 40.000 0.00 0.00 0.00 2.85
2030 4820 6.239148 GGCTTTGATCCTTTTGACTTCTTCTT 60.239 38.462 0.00 0.00 0.00 2.52
2031 4821 6.860539 GCTTTGATCCTTTTGACTTCTTCTTC 59.139 38.462 0.00 0.00 0.00 2.87
2032 4822 7.255416 GCTTTGATCCTTTTGACTTCTTCTTCT 60.255 37.037 0.00 0.00 0.00 2.85
2033 4823 7.502120 TTGATCCTTTTGACTTCTTCTTCTG 57.498 36.000 0.00 0.00 0.00 3.02
2034 4824 5.471456 TGATCCTTTTGACTTCTTCTTCTGC 59.529 40.000 0.00 0.00 0.00 4.26
2035 4825 5.041191 TCCTTTTGACTTCTTCTTCTGCT 57.959 39.130 0.00 0.00 0.00 4.24
2036 4826 5.440610 TCCTTTTGACTTCTTCTTCTGCTT 58.559 37.500 0.00 0.00 0.00 3.91
2037 4827 5.529060 TCCTTTTGACTTCTTCTTCTGCTTC 59.471 40.000 0.00 0.00 0.00 3.86
2038 4828 5.409643 TTTTGACTTCTTCTTCTGCTTCG 57.590 39.130 0.00 0.00 0.00 3.79
2039 4829 3.032017 TGACTTCTTCTTCTGCTTCGG 57.968 47.619 0.00 0.00 0.00 4.30
2040 4830 2.365617 TGACTTCTTCTTCTGCTTCGGT 59.634 45.455 0.00 0.00 0.00 4.69
2041 4831 2.734079 GACTTCTTCTTCTGCTTCGGTG 59.266 50.000 0.00 0.00 0.00 4.94
2042 4832 2.072298 CTTCTTCTTCTGCTTCGGTGG 58.928 52.381 0.00 0.00 0.00 4.61
2043 4833 1.048601 TCTTCTTCTGCTTCGGTGGT 58.951 50.000 0.00 0.00 0.00 4.16
2044 4834 2.244695 TCTTCTTCTGCTTCGGTGGTA 58.755 47.619 0.00 0.00 0.00 3.25
2045 4835 2.231478 TCTTCTTCTGCTTCGGTGGTAG 59.769 50.000 0.00 0.00 0.00 3.18
2046 4836 0.895530 TCTTCTGCTTCGGTGGTAGG 59.104 55.000 0.00 0.00 0.00 3.18
2047 4837 0.895530 CTTCTGCTTCGGTGGTAGGA 59.104 55.000 0.00 0.00 0.00 2.94
2048 4838 0.895530 TTCTGCTTCGGTGGTAGGAG 59.104 55.000 0.00 0.00 31.63 3.69
2049 4839 1.153549 CTGCTTCGGTGGTAGGAGC 60.154 63.158 0.00 0.00 0.00 4.70
2050 4840 1.888436 CTGCTTCGGTGGTAGGAGCA 61.888 60.000 0.00 0.00 0.00 4.26
2051 4841 1.264749 TGCTTCGGTGGTAGGAGCAT 61.265 55.000 0.00 0.00 0.00 3.79
2052 4842 0.530870 GCTTCGGTGGTAGGAGCATC 60.531 60.000 0.00 0.00 0.00 3.91
2064 4854 3.665544 GAGCATCCTCAGAGTCTGC 57.334 57.895 15.72 11.75 38.03 4.26
2065 4855 0.822811 GAGCATCCTCAGAGTCTGCA 59.177 55.000 15.72 3.88 38.03 4.41
2066 4856 1.413445 GAGCATCCTCAGAGTCTGCAT 59.587 52.381 15.72 4.42 38.03 3.96
2067 4857 1.413445 AGCATCCTCAGAGTCTGCATC 59.587 52.381 15.72 1.57 35.32 3.91
2068 4858 1.138464 GCATCCTCAGAGTCTGCATCA 59.862 52.381 15.72 0.00 33.13 3.07
2069 4859 2.224329 GCATCCTCAGAGTCTGCATCAT 60.224 50.000 15.72 1.97 33.13 2.45
2070 4860 3.744846 GCATCCTCAGAGTCTGCATCATT 60.745 47.826 15.72 0.00 33.13 2.57
2071 4861 3.538634 TCCTCAGAGTCTGCATCATTG 57.461 47.619 15.72 0.00 0.00 2.82
2072 4862 2.169978 TCCTCAGAGTCTGCATCATTGG 59.830 50.000 15.72 8.22 0.00 3.16
2241 5050 4.002037 GCTGCAAATGTATGCCGC 57.998 55.556 0.00 0.16 46.55 6.53
2482 5337 2.203480 GCTGTGTGGGAAGGGCAA 60.203 61.111 0.00 0.00 0.00 4.52
2483 5338 1.832167 GCTGTGTGGGAAGGGCAAA 60.832 57.895 0.00 0.00 0.00 3.68
2546 5405 4.533815 TCAGGTCTTTTATCGCTCTCCTA 58.466 43.478 0.00 0.00 0.00 2.94
2547 5406 4.954202 TCAGGTCTTTTATCGCTCTCCTAA 59.046 41.667 0.00 0.00 0.00 2.69
2678 6234 5.253330 TCCAACGCCAGAGAGAAAATTTAT 58.747 37.500 0.00 0.00 0.00 1.40
2679 6235 6.411376 TCCAACGCCAGAGAGAAAATTTATA 58.589 36.000 0.00 0.00 0.00 0.98
2680 6236 6.315393 TCCAACGCCAGAGAGAAAATTTATAC 59.685 38.462 0.00 0.00 0.00 1.47
2682 6238 7.148239 CCAACGCCAGAGAGAAAATTTATACTT 60.148 37.037 0.00 0.00 0.00 2.24
2684 6240 7.103641 ACGCCAGAGAGAAAATTTATACTTCA 58.896 34.615 0.00 0.00 0.00 3.02
2685 6241 7.064728 ACGCCAGAGAGAAAATTTATACTTCAC 59.935 37.037 0.00 0.00 0.00 3.18
2686 6242 7.278868 CGCCAGAGAGAAAATTTATACTTCACT 59.721 37.037 0.00 0.00 0.00 3.41
2739 6295 5.296780 TGTGTTCTGCCTTTCTCAAAGTAAG 59.703 40.000 0.00 0.00 36.77 2.34
2752 6310 9.705290 TTTCTCAAAGTAAGAAAAGCAAAAGTT 57.295 25.926 0.00 0.00 39.22 2.66
2769 6327 8.157476 AGCAAAAGTTGGAGAGAGAAATTACTA 58.843 33.333 0.00 0.00 0.00 1.82
2844 6795 5.860182 TGTCAGTGTTAGCGTGTACTTATTC 59.140 40.000 0.00 0.00 0.00 1.75
2894 6845 3.891366 GGTTCAGCAGCCACCATATAATT 59.109 43.478 1.72 0.00 0.00 1.40
2982 7079 8.803397 ACTATACGTATGGTATGAGCTATTCA 57.197 34.615 21.49 0.00 41.87 2.57
3010 7789 0.655733 CGAACTTGTTGAACACGGCT 59.344 50.000 6.76 0.00 0.00 5.52
3015 7794 4.267349 ACTTGTTGAACACGGCTATACT 57.733 40.909 6.76 0.00 0.00 2.12
3016 7795 3.994392 ACTTGTTGAACACGGCTATACTG 59.006 43.478 6.76 0.00 0.00 2.74
3017 7796 2.967362 TGTTGAACACGGCTATACTGG 58.033 47.619 0.00 0.00 0.00 4.00
3038 8271 3.584834 GTGGTGAACAAAAGCACAAGTT 58.415 40.909 0.00 0.00 43.75 2.66
3101 8334 6.075762 GCATTATGCATGGTATTCAGTCAA 57.924 37.500 12.80 0.00 44.26 3.18
3103 8336 6.238842 GCATTATGCATGGTATTCAGTCAAGT 60.239 38.462 12.80 0.00 44.26 3.16
3105 8338 5.824904 ATGCATGGTATTCAGTCAAGTTC 57.175 39.130 0.00 0.00 0.00 3.01
3167 8407 6.752285 AGTGTTAAGTTTAGGTAACAGGGA 57.248 37.500 0.00 0.00 40.06 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.150348 CACCACCATAAAATTTGGTTAAAGATC 57.850 33.333 0.00 0.00 45.19 2.75
1 2 7.606073 GCACCACCATAAAATTTGGTTAAAGAT 59.394 33.333 0.00 0.00 45.19 2.40
2 3 6.931840 GCACCACCATAAAATTTGGTTAAAGA 59.068 34.615 0.00 0.00 45.19 2.52
3 4 6.128688 CGCACCACCATAAAATTTGGTTAAAG 60.129 38.462 0.00 0.00 45.19 1.85
4 5 5.696724 CGCACCACCATAAAATTTGGTTAAA 59.303 36.000 0.00 0.00 45.19 1.52
6 7 4.322049 CCGCACCACCATAAAATTTGGTTA 60.322 41.667 0.00 0.00 45.19 2.85
7 8 3.556004 CCGCACCACCATAAAATTTGGTT 60.556 43.478 0.00 0.00 45.19 3.67
9 10 2.615869 CCGCACCACCATAAAATTTGG 58.384 47.619 0.00 0.00 40.26 3.28
10 11 1.999024 GCCGCACCACCATAAAATTTG 59.001 47.619 0.00 0.00 0.00 2.32
11 12 1.403514 CGCCGCACCACCATAAAATTT 60.404 47.619 0.00 0.00 0.00 1.82
12 13 0.172352 CGCCGCACCACCATAAAATT 59.828 50.000 0.00 0.00 0.00 1.82
13 14 1.662438 CCGCCGCACCACCATAAAAT 61.662 55.000 0.00 0.00 0.00 1.82
14 15 2.336478 CCGCCGCACCACCATAAAA 61.336 57.895 0.00 0.00 0.00 1.52
15 16 2.748251 CCGCCGCACCACCATAAA 60.748 61.111 0.00 0.00 0.00 1.40
193 195 4.390556 AGAGCACGGGGGAGAGCT 62.391 66.667 0.00 0.00 40.61 4.09
204 206 1.067213 GGGAGACAAGAGTGAGAGCAC 60.067 57.143 0.00 0.00 45.49 4.40
282 285 9.299465 GTAGTCCATAGATAAGCTAACTACCTT 57.701 37.037 0.00 0.00 36.15 3.50
354 357 1.385368 AGCACCATTCACCCATGCT 59.615 52.632 0.00 0.00 41.72 3.79
359 362 1.839424 AGCTAAAGCACCATTCACCC 58.161 50.000 4.54 0.00 45.16 4.61
463 469 7.919690 TCTGCATACAAGAATCTTTATTTCCG 58.080 34.615 0.00 0.00 0.00 4.30
503 510 6.001460 ACTAAAACCAACTAATACAGCTGCA 58.999 36.000 15.27 0.00 0.00 4.41
642 654 3.007290 TGTGAAACCCTCTCTGACTGATG 59.993 47.826 0.00 0.00 34.36 3.07
680 692 5.859205 ATCCTGAAAAGCAAAGACTTGTT 57.141 34.783 0.00 0.00 34.79 2.83
851 869 6.036300 CCAGCAAAATTATCAATCGTGCATTT 59.964 34.615 0.00 0.00 34.66 2.32
1021 2090 3.398954 ACAACGGCAATAAATGTAGCG 57.601 42.857 0.00 0.00 0.00 4.26
1022 2091 3.857093 CCAACAACGGCAATAAATGTAGC 59.143 43.478 0.00 0.00 0.00 3.58
1100 2175 3.935828 GGGTCTCAAACAGATAGAACTGC 59.064 47.826 0.00 0.00 41.06 4.40
1106 2181 2.969628 AGCGGGTCTCAAACAGATAG 57.030 50.000 0.00 0.00 32.08 2.08
1239 2326 2.270275 TGTATTTGCGGATTTTGCGG 57.730 45.000 0.00 0.00 34.24 5.69
1240 2327 3.694734 AGATGTATTTGCGGATTTTGCG 58.305 40.909 0.00 0.00 34.24 4.85
1241 2328 6.437928 TCATAGATGTATTTGCGGATTTTGC 58.562 36.000 0.00 0.00 0.00 3.68
1242 2329 7.592533 CCTTCATAGATGTATTTGCGGATTTTG 59.407 37.037 0.00 0.00 0.00 2.44
1243 2330 7.285401 ACCTTCATAGATGTATTTGCGGATTTT 59.715 33.333 0.00 0.00 0.00 1.82
1244 2331 6.772716 ACCTTCATAGATGTATTTGCGGATTT 59.227 34.615 0.00 0.00 0.00 2.17
1245 2332 6.299141 ACCTTCATAGATGTATTTGCGGATT 58.701 36.000 0.00 0.00 0.00 3.01
1246 2333 5.869579 ACCTTCATAGATGTATTTGCGGAT 58.130 37.500 0.00 0.00 0.00 4.18
1247 2334 5.163353 TGACCTTCATAGATGTATTTGCGGA 60.163 40.000 0.00 0.00 0.00 5.54
1308 2395 3.670625 TGGCATTATAATACCACGAGGC 58.329 45.455 12.66 5.09 39.06 4.70
1342 2442 6.659745 TGTATACAACAACGATAGCCCTAT 57.340 37.500 2.20 0.00 34.29 2.57
1420 2527 5.344396 GCTGCTTCAGAAATAAGAACAAAGC 59.656 40.000 0.00 0.00 38.61 3.51
1455 2573 2.161012 GGTAGGGCAGAAGTTAAAACGC 59.839 50.000 0.00 0.00 0.00 4.84
1982 4772 2.633657 CTGCACCAACAGCACGTC 59.366 61.111 0.00 0.00 37.02 4.34
1999 4789 1.844687 AAAGGATCAAAGCCCTCTGC 58.155 50.000 0.00 0.00 41.71 4.26
2000 4790 3.192212 GTCAAAAGGATCAAAGCCCTCTG 59.808 47.826 0.00 0.00 31.17 3.35
2001 4791 3.075134 AGTCAAAAGGATCAAAGCCCTCT 59.925 43.478 0.00 0.00 31.17 3.69
2002 4792 3.425659 AGTCAAAAGGATCAAAGCCCTC 58.574 45.455 0.00 0.00 31.17 4.30
2003 4793 3.532641 AGTCAAAAGGATCAAAGCCCT 57.467 42.857 0.00 0.00 0.00 5.19
2004 4794 3.829026 AGAAGTCAAAAGGATCAAAGCCC 59.171 43.478 0.00 0.00 0.00 5.19
2005 4795 5.242615 AGAAGAAGTCAAAAGGATCAAAGCC 59.757 40.000 0.00 0.00 0.00 4.35
2006 4796 6.324561 AGAAGAAGTCAAAAGGATCAAAGC 57.675 37.500 0.00 0.00 0.00 3.51
2007 4797 8.074972 CAGAAGAAGAAGTCAAAAGGATCAAAG 58.925 37.037 0.00 0.00 0.00 2.77
2008 4798 7.469181 GCAGAAGAAGAAGTCAAAAGGATCAAA 60.469 37.037 0.00 0.00 0.00 2.69
2009 4799 6.016777 GCAGAAGAAGAAGTCAAAAGGATCAA 60.017 38.462 0.00 0.00 0.00 2.57
2010 4800 5.471456 GCAGAAGAAGAAGTCAAAAGGATCA 59.529 40.000 0.00 0.00 0.00 2.92
2011 4801 5.704978 AGCAGAAGAAGAAGTCAAAAGGATC 59.295 40.000 0.00 0.00 0.00 3.36
2012 4802 5.629125 AGCAGAAGAAGAAGTCAAAAGGAT 58.371 37.500 0.00 0.00 0.00 3.24
2013 4803 5.041191 AGCAGAAGAAGAAGTCAAAAGGA 57.959 39.130 0.00 0.00 0.00 3.36
2014 4804 5.559799 CGAAGCAGAAGAAGAAGTCAAAAGG 60.560 44.000 0.00 0.00 0.00 3.11
2015 4805 5.438972 CGAAGCAGAAGAAGAAGTCAAAAG 58.561 41.667 0.00 0.00 0.00 2.27
2016 4806 4.273480 CCGAAGCAGAAGAAGAAGTCAAAA 59.727 41.667 0.00 0.00 0.00 2.44
2017 4807 3.809832 CCGAAGCAGAAGAAGAAGTCAAA 59.190 43.478 0.00 0.00 0.00 2.69
2018 4808 3.181465 ACCGAAGCAGAAGAAGAAGTCAA 60.181 43.478 0.00 0.00 0.00 3.18
2019 4809 2.365617 ACCGAAGCAGAAGAAGAAGTCA 59.634 45.455 0.00 0.00 0.00 3.41
2020 4810 2.734079 CACCGAAGCAGAAGAAGAAGTC 59.266 50.000 0.00 0.00 0.00 3.01
2021 4811 2.548920 CCACCGAAGCAGAAGAAGAAGT 60.549 50.000 0.00 0.00 0.00 3.01
2022 4812 2.072298 CCACCGAAGCAGAAGAAGAAG 58.928 52.381 0.00 0.00 0.00 2.85
2023 4813 1.416401 ACCACCGAAGCAGAAGAAGAA 59.584 47.619 0.00 0.00 0.00 2.52
2024 4814 1.048601 ACCACCGAAGCAGAAGAAGA 58.951 50.000 0.00 0.00 0.00 2.87
2025 4815 2.611518 CTACCACCGAAGCAGAAGAAG 58.388 52.381 0.00 0.00 0.00 2.85
2026 4816 1.275291 CCTACCACCGAAGCAGAAGAA 59.725 52.381 0.00 0.00 0.00 2.52
2027 4817 0.895530 CCTACCACCGAAGCAGAAGA 59.104 55.000 0.00 0.00 0.00 2.87
2028 4818 0.895530 TCCTACCACCGAAGCAGAAG 59.104 55.000 0.00 0.00 0.00 2.85
2029 4819 0.895530 CTCCTACCACCGAAGCAGAA 59.104 55.000 0.00 0.00 0.00 3.02
2030 4820 1.605058 GCTCCTACCACCGAAGCAGA 61.605 60.000 0.00 0.00 33.21 4.26
2031 4821 1.153549 GCTCCTACCACCGAAGCAG 60.154 63.158 0.00 0.00 33.21 4.24
2032 4822 1.264749 ATGCTCCTACCACCGAAGCA 61.265 55.000 0.00 0.00 46.04 3.91
2033 4823 0.530870 GATGCTCCTACCACCGAAGC 60.531 60.000 0.00 0.00 0.00 3.86
2034 4824 0.105039 GGATGCTCCTACCACCGAAG 59.895 60.000 0.00 0.00 32.53 3.79
2035 4825 2.208527 GGATGCTCCTACCACCGAA 58.791 57.895 0.00 0.00 32.53 4.30
2036 4826 3.950232 GGATGCTCCTACCACCGA 58.050 61.111 0.00 0.00 32.53 4.69
2045 4835 0.104671 GCAGACTCTGAGGATGCTCC 59.895 60.000 21.82 0.00 32.44 4.70
2046 4836 0.822811 TGCAGACTCTGAGGATGCTC 59.177 55.000 26.23 7.39 37.76 4.26
2047 4837 1.413445 GATGCAGACTCTGAGGATGCT 59.587 52.381 26.23 16.85 37.76 3.79
2048 4838 1.138464 TGATGCAGACTCTGAGGATGC 59.862 52.381 22.13 22.13 37.40 3.91
2049 4839 3.755112 ATGATGCAGACTCTGAGGATG 57.245 47.619 10.45 8.17 32.44 3.51
2050 4840 3.181453 CCAATGATGCAGACTCTGAGGAT 60.181 47.826 10.45 0.00 32.44 3.24
2051 4841 2.169978 CCAATGATGCAGACTCTGAGGA 59.830 50.000 10.45 0.00 32.44 3.71
2052 4842 2.169978 TCCAATGATGCAGACTCTGAGG 59.830 50.000 10.45 0.27 32.44 3.86
2053 4843 3.196463 GTCCAATGATGCAGACTCTGAG 58.804 50.000 10.45 2.45 32.44 3.35
2054 4844 2.568509 TGTCCAATGATGCAGACTCTGA 59.431 45.455 10.45 0.00 32.44 3.27
2055 4845 2.676839 GTGTCCAATGATGCAGACTCTG 59.323 50.000 1.21 1.21 34.12 3.35
2056 4846 2.676176 CGTGTCCAATGATGCAGACTCT 60.676 50.000 0.00 0.00 0.00 3.24
2057 4847 1.662629 CGTGTCCAATGATGCAGACTC 59.337 52.381 0.00 0.00 0.00 3.36
2058 4848 1.276138 TCGTGTCCAATGATGCAGACT 59.724 47.619 0.00 0.00 0.00 3.24
2059 4849 1.394917 GTCGTGTCCAATGATGCAGAC 59.605 52.381 0.00 0.00 0.00 3.51
2060 4850 1.725641 GTCGTGTCCAATGATGCAGA 58.274 50.000 0.00 0.00 0.00 4.26
2061 4851 0.371301 CGTCGTGTCCAATGATGCAG 59.629 55.000 0.00 0.00 0.00 4.41
2062 4852 1.018752 CCGTCGTGTCCAATGATGCA 61.019 55.000 0.00 0.00 30.45 3.96
2063 4853 0.739462 TCCGTCGTGTCCAATGATGC 60.739 55.000 0.00 0.00 30.45 3.91
2064 4854 0.999406 GTCCGTCGTGTCCAATGATG 59.001 55.000 0.00 0.00 0.00 3.07
2065 4855 0.457853 CGTCCGTCGTGTCCAATGAT 60.458 55.000 0.00 0.00 34.52 2.45
2066 4856 1.081041 CGTCCGTCGTGTCCAATGA 60.081 57.895 0.00 0.00 34.52 2.57
2067 4857 2.726691 GCGTCCGTCGTGTCCAATG 61.727 63.158 0.00 0.00 42.13 2.82
2068 4858 2.431942 GCGTCCGTCGTGTCCAAT 60.432 61.111 0.00 0.00 42.13 3.16
2069 4859 4.986587 CGCGTCCGTCGTGTCCAA 62.987 66.667 0.00 0.00 43.87 3.53
2118 4926 2.880268 CTGCAAGATGGAGAACACAACA 59.120 45.455 0.00 0.00 38.14 3.33
2241 5050 3.742882 CACTATCCGTATGGTGATGCAAG 59.257 47.826 0.00 0.00 44.94 4.01
2440 5294 1.669779 CAGTAGCCAAGCAAGCTCATC 59.330 52.381 0.00 0.00 41.83 2.92
2482 5337 9.528489 TTAAAATCCATAGCTCTGGTAAAAGTT 57.472 29.630 17.04 1.72 37.57 2.66
2483 5338 8.957466 GTTAAAATCCATAGCTCTGGTAAAAGT 58.043 33.333 17.04 0.00 37.57 2.66
2546 5405 4.292306 ACCCCACTGGACTCAGATAAATTT 59.708 41.667 0.00 0.00 43.49 1.82
2547 5406 3.852578 ACCCCACTGGACTCAGATAAATT 59.147 43.478 0.00 0.00 43.49 1.82
2678 6234 7.402071 AGGTGGATTCCTATTAACAGTGAAGTA 59.598 37.037 3.95 0.00 35.87 2.24
2679 6235 6.215636 AGGTGGATTCCTATTAACAGTGAAGT 59.784 38.462 3.95 0.00 35.87 3.01
2680 6236 6.653989 AGGTGGATTCCTATTAACAGTGAAG 58.346 40.000 3.95 0.00 35.87 3.02
2682 6238 5.724370 TGAGGTGGATTCCTATTAACAGTGA 59.276 40.000 3.95 0.00 38.02 3.41
2684 6240 5.395324 CGTGAGGTGGATTCCTATTAACAGT 60.395 44.000 3.95 0.00 38.02 3.55
2685 6241 5.050490 CGTGAGGTGGATTCCTATTAACAG 58.950 45.833 3.95 0.00 38.02 3.16
2686 6242 4.468510 ACGTGAGGTGGATTCCTATTAACA 59.531 41.667 3.95 0.00 38.02 2.41
2739 6295 5.757850 TCTCTCTCCAACTTTTGCTTTTC 57.242 39.130 0.00 0.00 0.00 2.29
2844 6795 3.133003 ACGGTTACTCCAATCATCTCTGG 59.867 47.826 0.00 0.00 35.57 3.86
2894 6845 9.982651 GCCTACTAGTCTATTAATTGTGATTCA 57.017 33.333 0.00 0.00 0.00 2.57
2982 7079 2.080693 TCAACAAGTTCGCGGCAATAT 58.919 42.857 6.13 0.00 0.00 1.28
3010 7789 4.517453 GTGCTTTTGTTCACCACCAGTATA 59.483 41.667 0.00 0.00 0.00 1.47
3015 7794 1.550327 TGTGCTTTTGTTCACCACCA 58.450 45.000 0.00 0.00 32.51 4.17
3016 7795 2.094234 ACTTGTGCTTTTGTTCACCACC 60.094 45.455 0.00 0.00 32.51 4.61
3017 7796 3.230743 ACTTGTGCTTTTGTTCACCAC 57.769 42.857 0.00 0.00 32.51 4.16
3038 8271 2.158971 TCTTAGCTCACACTGCACACAA 60.159 45.455 0.00 0.00 0.00 3.33
3101 8334 1.940613 GAACTTGACACTTGGCGAACT 59.059 47.619 0.00 0.00 0.00 3.01
3103 8336 1.939934 CTGAACTTGACACTTGGCGAA 59.060 47.619 0.00 0.00 0.00 4.70
3105 8338 1.299541 ACTGAACTTGACACTTGGCG 58.700 50.000 0.00 0.00 0.00 5.69
3167 8407 2.563179 CCAGCTACAGTTACTCCACAGT 59.437 50.000 0.00 0.00 36.55 3.55


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

AutoCloner maintained by Alex Coulton.