Multiple sequence alignment - TraesCS7B01G024600

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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 TraesCS7B01G024600 chr7B 100.000 3854 0 0 1 3854 23515172 23519025 0.000000e+00 7118.0
1 TraesCS7B01G024600 chr7B 85.414 3044 384 43 839 3854 23524431 23527442 0.000000e+00 3107.0
2 TraesCS7B01G024600 chr7B 83.847 2953 388 37 906 3854 23933304 23936171 0.000000e+00 2728.0
3 TraesCS7B01G024600 chr7B 85.431 2066 271 13 1814 3854 23583141 23585201 0.000000e+00 2121.0
4 TraesCS7B01G024600 chr7B 85.227 2051 273 19 1810 3854 23958838 23960864 0.000000e+00 2082.0
5 TraesCS7B01G024600 chr7B 87.692 1235 119 18 522 1736 23596304 23597525 0.000000e+00 1408.0
6 TraesCS7B01G024600 chr7B 85.905 901 117 7 844 1743 23582227 23583118 0.000000e+00 952.0
7 TraesCS7B01G024600 chr7B 88.971 272 17 4 1 272 23595854 23596112 1.340000e-84 324.0
8 TraesCS7B01G024600 chr7B 88.406 69 8 0 3785 3853 23941365 23941433 2.470000e-12 84.2
9 TraesCS7B01G024600 chr7D 86.387 2975 346 33 789 3741 76929714 76932651 0.000000e+00 3195.0
10 TraesCS7B01G024600 chr7D 83.882 2916 416 32 839 3747 76635978 76633110 0.000000e+00 2732.0
11 TraesCS7B01G024600 chr7D 83.760 2888 415 31 877 3752 76625287 76622442 0.000000e+00 2686.0
12 TraesCS7B01G024600 chr7D 85.652 2063 253 22 1810 3854 76920132 76922169 0.000000e+00 2130.0
13 TraesCS7B01G024600 chr7D 85.234 2052 256 26 1812 3854 76744405 76746418 0.000000e+00 2067.0
14 TraesCS7B01G024600 chr7D 85.483 1915 261 7 1948 3854 76973468 76975373 0.000000e+00 1980.0
15 TraesCS7B01G024600 chr7D 84.051 2044 289 22 1821 3854 76785030 76787046 0.000000e+00 1934.0
16 TraesCS7B01G024600 chr7D 85.796 1577 193 18 2286 3854 77045885 77047438 0.000000e+00 1642.0
17 TraesCS7B01G024600 chr7D 83.974 1691 219 23 2179 3854 76955728 76957381 0.000000e+00 1574.0
18 TraesCS7B01G024600 chr7D 85.823 1319 140 26 450 1742 76743086 76744383 0.000000e+00 1356.0
19 TraesCS7B01G024600 chr7D 86.878 945 105 11 813 1742 76784059 76784999 0.000000e+00 1040.0
20 TraesCS7B01G024600 chr7D 87.556 900 97 10 839 1736 76919223 76920109 0.000000e+00 1027.0
21 TraesCS7B01G024600 chr7D 84.194 930 143 2 1800 2728 7561896 7562822 0.000000e+00 900.0
22 TraesCS7B01G024600 chr7D 85.253 868 126 2 1811 2677 7549220 7550086 0.000000e+00 893.0
23 TraesCS7B01G024600 chr7D 92.018 451 22 8 1 450 76742481 76742918 4.230000e-174 621.0
24 TraesCS7B01G024600 chr7D 86.842 76 10 0 3779 3854 76633036 76632961 6.860000e-13 86.1
25 TraesCS7B01G024600 chr7A 85.707 2050 259 19 1812 3854 80862826 80864848 0.000000e+00 2132.0
26 TraesCS7B01G024600 chr7A 86.140 1241 133 19 522 1742 80861583 80862804 0.000000e+00 1303.0
27 TraesCS7B01G024600 chr7A 77.893 1737 336 29 1829 3548 56175053 56176758 0.000000e+00 1037.0
28 TraesCS7B01G024600 chr7A 91.718 326 23 4 1 324 80860984 80861307 2.110000e-122 449.0
29 TraesCS7B01G024600 chr4A 85.606 924 129 4 1813 2734 731616013 731615092 0.000000e+00 966.0
30 TraesCS7B01G024600 chr3B 85.239 901 131 2 1829 2728 741464018 741464917 0.000000e+00 926.0


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 TraesCS7B01G024600 chr7B 23515172 23519025 3853 False 7118.000000 7118 100.000000 1 3854 1 chr7B.!!$F1 3853
1 TraesCS7B01G024600 chr7B 23524431 23527442 3011 False 3107.000000 3107 85.414000 839 3854 1 chr7B.!!$F2 3015
2 TraesCS7B01G024600 chr7B 23933304 23936171 2867 False 2728.000000 2728 83.847000 906 3854 1 chr7B.!!$F3 2948
3 TraesCS7B01G024600 chr7B 23958838 23960864 2026 False 2082.000000 2082 85.227000 1810 3854 1 chr7B.!!$F5 2044
4 TraesCS7B01G024600 chr7B 23582227 23585201 2974 False 1536.500000 2121 85.668000 844 3854 2 chr7B.!!$F6 3010
5 TraesCS7B01G024600 chr7B 23595854 23597525 1671 False 866.000000 1408 88.331500 1 1736 2 chr7B.!!$F7 1735
6 TraesCS7B01G024600 chr7D 76929714 76932651 2937 False 3195.000000 3195 86.387000 789 3741 1 chr7D.!!$F3 2952
7 TraesCS7B01G024600 chr7D 76622442 76625287 2845 True 2686.000000 2686 83.760000 877 3752 1 chr7D.!!$R1 2875
8 TraesCS7B01G024600 chr7D 76973468 76975373 1905 False 1980.000000 1980 85.483000 1948 3854 1 chr7D.!!$F5 1906
9 TraesCS7B01G024600 chr7D 77045885 77047438 1553 False 1642.000000 1642 85.796000 2286 3854 1 chr7D.!!$F6 1568
10 TraesCS7B01G024600 chr7D 76919223 76922169 2946 False 1578.500000 2130 86.604000 839 3854 2 chr7D.!!$F9 3015
11 TraesCS7B01G024600 chr7D 76955728 76957381 1653 False 1574.000000 1574 83.974000 2179 3854 1 chr7D.!!$F4 1675
12 TraesCS7B01G024600 chr7D 76784059 76787046 2987 False 1487.000000 1934 85.464500 813 3854 2 chr7D.!!$F8 3041
13 TraesCS7B01G024600 chr7D 76632961 76635978 3017 True 1409.050000 2732 85.362000 839 3854 2 chr7D.!!$R2 3015
14 TraesCS7B01G024600 chr7D 76742481 76746418 3937 False 1348.000000 2067 87.691667 1 3854 3 chr7D.!!$F7 3853
15 TraesCS7B01G024600 chr7D 7561896 7562822 926 False 900.000000 900 84.194000 1800 2728 1 chr7D.!!$F2 928
16 TraesCS7B01G024600 chr7D 7549220 7550086 866 False 893.000000 893 85.253000 1811 2677 1 chr7D.!!$F1 866
17 TraesCS7B01G024600 chr7A 80860984 80864848 3864 False 1294.666667 2132 87.855000 1 3854 3 chr7A.!!$F2 3853
18 TraesCS7B01G024600 chr7A 56175053 56176758 1705 False 1037.000000 1037 77.893000 1829 3548 1 chr7A.!!$F1 1719
19 TraesCS7B01G024600 chr4A 731615092 731616013 921 True 966.000000 966 85.606000 1813 2734 1 chr4A.!!$R1 921
20 TraesCS7B01G024600 chr3B 741464018 741464917 899 False 926.000000 926 85.239000 1829 2728 1 chr3B.!!$F1 899

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
513 688 0.037975 CAAAACATCCTGCTGCCACC 60.038 55.0 0.00 0.0 0.00 4.61 F
761 1008 0.108615 CCTCTTCGTCGGTTGCATCT 60.109 55.0 0.00 0.0 0.00 2.90 F
940 1227 0.108945 CATCTCGCAGTGCTCACTCA 60.109 55.0 14.33 0.0 40.20 3.41 F
1803 2118 0.173935 CACATGAAACATGGCGCCAT 59.826 50.0 36.10 36.1 37.08 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2099 0.173935 ATGGCGCCATGTTTCATGTG 59.826 50.000 40.10 2.96 35.03 3.21 R
2749 3116 0.381801 GGATGTGGCAGCCGTTTATG 59.618 55.000 7.03 0.00 27.64 1.90 R
2750 3117 0.751643 GGGATGTGGCAGCCGTTTAT 60.752 55.000 7.03 0.00 41.37 1.40 R
3031 3419 1.072331 AGCTGACCAATGTTTCGAGGT 59.928 47.619 0.00 0.00 37.00 3.85 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
68 70 1.271163 CCTGGGTGACGTATGTTGGTT 60.271 52.381 0.00 0.00 0.00 3.67
105 107 0.888285 GCTGTCCTTGCACAGAAGCT 60.888 55.000 6.25 0.00 45.92 3.74
106 108 1.155042 CTGTCCTTGCACAGAAGCTC 58.845 55.000 0.00 0.00 45.92 4.09
131 133 0.540923 AGCTCAAGCATCCTGGAGAC 59.459 55.000 1.52 0.00 40.98 3.36
273 275 1.201965 GCATCGTTTCGAGCTTTCCAG 60.202 52.381 0.00 0.00 39.91 3.86
277 279 3.770666 TCGTTTCGAGCTTTCCAGATAG 58.229 45.455 0.00 0.00 0.00 2.08
278 280 2.860735 CGTTTCGAGCTTTCCAGATAGG 59.139 50.000 0.00 0.00 39.47 2.57
289 291 1.207089 TCCAGATAGGCCACAAGAACG 59.793 52.381 5.01 0.00 37.29 3.95
301 303 4.443034 GCCACAAGAACGTATAGAGGGAAT 60.443 45.833 0.00 0.00 0.00 3.01
308 310 7.062749 AGAACGTATAGAGGGAATTTATGCA 57.937 36.000 0.00 0.00 0.00 3.96
327 329 2.222027 CATATTTCGGTTGGAGGCTCC 58.778 52.381 26.95 26.95 36.96 4.70
343 345 7.023120 TGGAGGCTCCCTAAAATATACTGTAT 58.977 38.462 30.03 5.53 35.03 2.29
382 385 5.346522 CCCATACGTCTGGTTTAGAGTAAC 58.653 45.833 17.74 0.00 35.70 2.50
409 412 7.173218 TGTGAAAACAAAACATACCAAGCAAAA 59.827 29.630 0.00 0.00 0.00 2.44
471 642 1.808945 GGACATGGAGTTTGTGCAGAG 59.191 52.381 0.00 0.00 35.71 3.35
507 682 2.431782 ACTGCAAACAAAACATCCTGCT 59.568 40.909 0.00 0.00 0.00 4.24
512 687 0.675633 ACAAAACATCCTGCTGCCAC 59.324 50.000 0.00 0.00 0.00 5.01
513 688 0.037975 CAAAACATCCTGCTGCCACC 60.038 55.000 0.00 0.00 0.00 4.61
527 744 3.005791 GCTGCCACCAGTTTTCTGTTATT 59.994 43.478 0.00 0.00 45.68 1.40
693 925 6.246420 TGCAAGTTTAGCATCTCTTCTTTC 57.754 37.500 0.00 0.00 37.02 2.62
694 926 5.182001 TGCAAGTTTAGCATCTCTTCTTTCC 59.818 40.000 0.00 0.00 37.02 3.13
695 927 5.392487 GCAAGTTTAGCATCTCTTCTTTCCC 60.392 44.000 0.00 0.00 0.00 3.97
696 928 4.849518 AGTTTAGCATCTCTTCTTTCCCC 58.150 43.478 0.00 0.00 0.00 4.81
697 929 3.933861 TTAGCATCTCTTCTTTCCCCC 57.066 47.619 0.00 0.00 0.00 5.40
752 999 1.463831 TCTTCGTCTTCCTCTTCGTCG 59.536 52.381 0.00 0.00 0.00 5.12
754 1001 0.604780 TCGTCTTCCTCTTCGTCGGT 60.605 55.000 0.00 0.00 0.00 4.69
760 1007 0.108804 TCCTCTTCGTCGGTTGCATC 60.109 55.000 0.00 0.00 0.00 3.91
761 1008 0.108615 CCTCTTCGTCGGTTGCATCT 60.109 55.000 0.00 0.00 0.00 2.90
774 1037 4.082787 CGGTTGCATCTATTTTCACCAACT 60.083 41.667 0.00 0.00 33.55 3.16
775 1038 5.402398 GGTTGCATCTATTTTCACCAACTC 58.598 41.667 0.00 0.00 33.55 3.01
807 1074 0.249911 CCCATAGTAGCCTTGGCGAC 60.250 60.000 15.45 15.45 0.00 5.19
819 1086 1.597854 TGGCGACAAAGCTCCACAG 60.598 57.895 0.00 0.00 37.44 3.66
918 1200 6.970043 TGTGTTTTATTCTTCTTCGGTTGTTG 59.030 34.615 0.00 0.00 0.00 3.33
926 1211 2.688507 TCTTCGGTTGTTGCTCATCTC 58.311 47.619 0.00 0.00 0.00 2.75
927 1212 1.391485 CTTCGGTTGTTGCTCATCTCG 59.609 52.381 0.00 0.00 0.00 4.04
935 1220 0.738762 TTGCTCATCTCGCAGTGCTC 60.739 55.000 14.33 0.00 38.80 4.26
937 1222 1.419874 GCTCATCTCGCAGTGCTCAC 61.420 60.000 14.33 0.00 0.00 3.51
940 1227 0.108945 CATCTCGCAGTGCTCACTCA 60.109 55.000 14.33 0.00 40.20 3.41
1015 1315 1.202734 AGATCATGGCCGAATCACTGG 60.203 52.381 12.69 0.00 0.00 4.00
1021 1321 0.250513 GGCCGAATCACTGGTTCTCT 59.749 55.000 0.58 0.00 0.00 3.10
1029 1329 1.964223 TCACTGGTTCTCTCTGTGGTC 59.036 52.381 0.00 0.00 35.63 4.02
1035 1335 1.002544 GTTCTCTCTGTGGTCCAAGGG 59.997 57.143 0.00 0.00 0.00 3.95
1177 1480 1.283321 AGGAAAGGAGCCAGACCAATC 59.717 52.381 0.00 0.00 0.00 2.67
1203 1512 2.048601 CTCAGGAGCTGGATGGAGAAT 58.951 52.381 0.00 0.00 31.51 2.40
1211 1520 2.486907 GCTGGATGGAGAATCTCAAGGG 60.487 54.545 12.79 0.00 35.43 3.95
1377 1686 0.251634 GGAAGCTCAAGGGAGTCCTG 59.748 60.000 9.58 0.00 44.07 3.86
1434 1743 4.985538 AGTTTGGCCTTGAGAATTCTGTA 58.014 39.130 14.00 0.00 0.00 2.74
1435 1744 5.574188 AGTTTGGCCTTGAGAATTCTGTAT 58.426 37.500 14.00 0.00 0.00 2.29
1441 1750 6.100279 TGGCCTTGAGAATTCTGTATATCAGT 59.900 38.462 14.00 0.00 43.97 3.41
1442 1751 6.995091 GGCCTTGAGAATTCTGTATATCAGTT 59.005 38.462 14.00 0.00 43.97 3.16
1530 1839 1.566231 GATGATGACAAGGAGGGGGTT 59.434 52.381 0.00 0.00 0.00 4.11
1663 1972 1.202758 ACGTCCAGCAACATTTCCAGA 60.203 47.619 0.00 0.00 0.00 3.86
1784 2099 9.770097 AAAAGAAAGAGAAAAAGAATTGGATCC 57.230 29.630 4.20 4.20 0.00 3.36
1785 2100 8.482852 AAGAAAGAGAAAAAGAATTGGATCCA 57.517 30.769 11.44 11.44 0.00 3.41
1786 2101 7.890515 AGAAAGAGAAAAAGAATTGGATCCAC 58.109 34.615 15.91 2.84 0.00 4.02
1789 2104 7.166691 AGAGAAAAAGAATTGGATCCACATG 57.833 36.000 15.91 0.00 0.00 3.21
1792 2107 7.965718 AGAAAAAGAATTGGATCCACATGAAA 58.034 30.769 15.91 0.00 0.00 2.69
1793 2108 7.874528 AGAAAAAGAATTGGATCCACATGAAAC 59.125 33.333 15.91 2.23 0.00 2.78
1794 2109 6.669125 AAAGAATTGGATCCACATGAAACA 57.331 33.333 15.91 0.00 0.00 2.83
1795 2110 6.862469 AAGAATTGGATCCACATGAAACAT 57.138 33.333 15.91 0.00 0.00 2.71
1796 2111 6.216801 AGAATTGGATCCACATGAAACATG 57.783 37.500 15.91 9.72 0.00 3.21
1797 2112 5.128171 AGAATTGGATCCACATGAAACATGG 59.872 40.000 15.91 0.00 34.58 3.66
1798 2113 2.101783 TGGATCCACATGAAACATGGC 58.898 47.619 11.44 0.00 33.20 4.40
1799 2114 1.066002 GGATCCACATGAAACATGGCG 59.934 52.381 6.95 6.58 33.20 5.69
1800 2115 0.457035 ATCCACATGAAACATGGCGC 59.543 50.000 14.70 0.00 33.20 6.53
1801 2116 1.153784 CCACATGAAACATGGCGCC 60.154 57.895 22.73 22.73 0.00 6.53
1802 2117 1.585517 CACATGAAACATGGCGCCA 59.414 52.632 34.80 34.80 0.00 5.69
1803 2118 0.173935 CACATGAAACATGGCGCCAT 59.826 50.000 36.10 36.10 37.08 4.40
1807 2122 2.121291 TGAAACATGGCGCCATTCTA 57.879 45.000 38.86 20.72 33.90 2.10
1819 2134 2.286831 CGCCATTCTAGCAGCATTGAAG 60.287 50.000 0.00 0.00 0.00 3.02
1825 2140 6.261603 CCATTCTAGCAGCATTGAAGTATTGA 59.738 38.462 0.00 0.00 0.00 2.57
1841 2156 8.712363 TGAAGTATTGAAGAAGAAACTTGATCG 58.288 33.333 0.00 0.00 0.00 3.69
1852 2167 3.340814 AACTTGATCGAGTCATTGGCT 57.659 42.857 16.17 0.00 36.54 4.75
1923 2241 5.521696 AGGATGTGGGATGATGAATTGAAA 58.478 37.500 0.00 0.00 0.00 2.69
2010 2328 2.036733 GGCCTCTATAATGTGCACCGTA 59.963 50.000 15.69 6.72 0.00 4.02
2123 2442 3.162666 AGTTAGTCACCATCGGAAGACA 58.837 45.455 11.08 0.00 46.97 3.41
2212 2531 5.072741 AGCAACAAGTACATGAATGGAAGT 58.927 37.500 4.87 0.00 0.00 3.01
2274 2593 5.589367 AATATGAGGTCATGCCCATACTT 57.411 39.130 0.00 2.81 37.15 2.24
2296 2615 7.277396 ACTTAAGTTAAGCTACAAACACCTGA 58.723 34.615 20.31 0.00 39.39 3.86
2351 2670 3.769300 GCACTTTTCCCCAAGGATTATGT 59.231 43.478 0.00 0.00 43.54 2.29
2353 2672 4.160252 CACTTTTCCCCAAGGATTATGTGG 59.840 45.833 0.00 0.00 43.54 4.17
2428 2747 6.660949 AGAAGAGGGAACAATGGATTTAACAG 59.339 38.462 0.00 0.00 0.00 3.16
2495 2817 3.881688 CTGCAAGATATGGAAGTGGAAGG 59.118 47.826 0.00 0.00 34.07 3.46
2516 2850 3.865745 GGCATATATGGTGTCTATCGTGC 59.134 47.826 14.51 0.00 0.00 5.34
2600 2934 4.463539 AGATGTTAGCAATGAATGTGCCAA 59.536 37.500 0.00 0.00 43.27 4.52
2620 2954 7.487189 GTGCCAACATAGAAGAATTGATTGAAG 59.513 37.037 0.00 0.00 0.00 3.02
2630 2964 8.460428 AGAAGAATTGATTGAAGAGAAAGCATC 58.540 33.333 0.00 0.00 0.00 3.91
2729 3078 3.119459 TCTCTCCGCACTTTGTTAGCTAG 60.119 47.826 0.00 0.00 0.00 3.42
2738 3090 5.106908 GCACTTTGTTAGCTAGTTCAAGGAG 60.107 44.000 17.38 13.06 0.00 3.69
2746 3113 4.348486 AGCTAGTTCAAGGAGACATCAGA 58.652 43.478 0.00 0.00 0.00 3.27
2749 3116 5.752955 GCTAGTTCAAGGAGACATCAGAATC 59.247 44.000 0.00 0.00 0.00 2.52
2750 3117 5.752036 AGTTCAAGGAGACATCAGAATCA 57.248 39.130 0.00 0.00 0.00 2.57
2761 3140 3.313526 ACATCAGAATCATAAACGGCTGC 59.686 43.478 0.00 0.00 0.00 5.25
2762 3141 2.288666 TCAGAATCATAAACGGCTGCC 58.711 47.619 9.11 9.11 0.00 4.85
2763 3142 2.016318 CAGAATCATAAACGGCTGCCA 58.984 47.619 20.29 0.00 0.00 4.92
2764 3143 2.017049 AGAATCATAAACGGCTGCCAC 58.983 47.619 20.29 0.00 0.00 5.01
2765 3144 1.742831 GAATCATAAACGGCTGCCACA 59.257 47.619 20.29 0.00 0.00 4.17
2766 3145 2.057137 ATCATAAACGGCTGCCACAT 57.943 45.000 20.29 5.91 0.00 3.21
2767 3146 1.378531 TCATAAACGGCTGCCACATC 58.621 50.000 20.29 0.00 0.00 3.06
2829 3217 2.545742 GCACAAGTTTCAAGGCCGAAAT 60.546 45.455 8.78 0.00 37.24 2.17
2876 3264 2.612672 CTCTCCACTTGTAGCGTCGATA 59.387 50.000 0.00 0.00 0.00 2.92
3064 3452 4.098914 TGGTCAGCTAAACAACCTTCAT 57.901 40.909 0.00 0.00 32.82 2.57
3116 3504 3.846588 AGATGGTTGTGGTATTGAGGAGT 59.153 43.478 0.00 0.00 0.00 3.85
3118 3506 3.750371 TGGTTGTGGTATTGAGGAGTTG 58.250 45.455 0.00 0.00 0.00 3.16
3142 3531 2.500098 AGACCTGCGGTATCTTAGCAAA 59.500 45.455 0.09 0.00 40.63 3.68
3202 3591 2.159327 AGCATGCAAAAGAAGCCAAC 57.841 45.000 21.98 0.00 0.00 3.77
3319 3717 3.055819 TGTTCCAGCATCTAGAACCTCAC 60.056 47.826 0.00 0.00 39.30 3.51
3362 3760 8.934697 TGGAGTTATATGGATATAATGGCCTAC 58.065 37.037 3.32 0.00 37.50 3.18
3493 3891 6.351033 CCTCACTGGAGTACTTATGCTTACAA 60.351 42.308 0.00 0.00 39.64 2.41
3604 4002 2.103941 GGAGATAGTCTTGGAAGGGCTG 59.896 54.545 0.00 0.00 0.00 4.85
3607 4005 0.902984 TAGTCTTGGAAGGGCTGCGA 60.903 55.000 0.00 0.00 0.00 5.10
3611 4009 0.890996 CTTGGAAGGGCTGCGAAGTT 60.891 55.000 0.00 0.00 0.00 2.66
3631 4029 4.017130 AGTTTAGAGGGATGGGCAGAAAAT 60.017 41.667 0.00 0.00 0.00 1.82
3721 4119 2.614057 CCCTAAGCTTGCAAGTATTCCG 59.386 50.000 26.55 15.20 0.00 4.30
3736 4137 4.394712 CCGCTGAGCCCCGTTCTT 62.395 66.667 0.00 0.00 0.00 2.52
3743 4144 1.695242 TGAGCCCCGTTCTTAAAGTCA 59.305 47.619 0.00 0.00 0.00 3.41
3762 4163 7.698163 AAGTCATGAGGTTAGGAGGATATTT 57.302 36.000 0.00 0.00 0.00 1.40
3763 4164 7.698163 AGTCATGAGGTTAGGAGGATATTTT 57.302 36.000 0.00 0.00 0.00 1.82
3766 4173 8.871125 GTCATGAGGTTAGGAGGATATTTTCTA 58.129 37.037 0.00 0.00 0.00 2.10
3777 4228 6.014925 GGAGGATATTTTCTAGACCTGGAGTC 60.015 46.154 0.00 0.00 46.71 3.36
3797 4248 6.442513 AGTCTTTACTGCATATTCCAAAGC 57.557 37.500 0.00 0.00 33.57 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.607225 TATCCACCATTTCAGGCCCT 58.393 50.000 0.00 0.00 0.00 5.19
105 107 1.562942 AGGATGCTTGAGCTTGATGGA 59.437 47.619 4.44 0.00 42.66 3.41
106 108 1.676529 CAGGATGCTTGAGCTTGATGG 59.323 52.381 4.44 0.00 42.66 3.51
131 133 1.064803 ACGATACAGCTCGCTCTTCAG 59.935 52.381 0.00 0.00 42.35 3.02
222 224 3.701664 CAGGAAATTAAGTGCCCCTTCT 58.298 45.455 0.00 0.00 34.46 2.85
273 275 5.449107 TCTATACGTTCTTGTGGCCTATC 57.551 43.478 3.32 0.00 0.00 2.08
277 279 2.483188 CCCTCTATACGTTCTTGTGGCC 60.483 54.545 0.00 0.00 0.00 5.36
278 280 2.429610 TCCCTCTATACGTTCTTGTGGC 59.570 50.000 0.00 0.00 0.00 5.01
301 303 4.037446 GCCTCCAACCGAAATATGCATAAA 59.963 41.667 11.13 0.00 0.00 1.40
308 310 1.143073 GGGAGCCTCCAACCGAAATAT 59.857 52.381 13.90 0.00 38.64 1.28
343 345 2.824689 TGGGGATTTCTATTGCTGCA 57.175 45.000 0.00 0.00 0.00 4.41
354 356 3.732048 AAACCAGACGTATGGGGATTT 57.268 42.857 31.17 19.89 45.25 2.17
382 385 5.809562 TGCTTGGTATGTTTTGTTTTCACAG 59.190 36.000 0.00 0.00 33.22 3.66
409 412 7.231467 ACATCTACCAACAGAAACACCTTAAT 58.769 34.615 0.00 0.00 0.00 1.40
497 672 1.303888 CTGGTGGCAGCAGGATGTT 60.304 57.895 33.24 0.00 39.87 2.71
507 682 3.957497 ACAATAACAGAAAACTGGTGGCA 59.043 39.130 0.00 0.00 0.00 4.92
512 687 8.844441 TTTTACGAACAATAACAGAAAACTGG 57.156 30.769 0.00 0.00 0.00 4.00
527 744 4.972201 ACGTTTGCTTCTTTTTACGAACA 58.028 34.783 0.00 0.00 33.60 3.18
568 785 7.804712 TGCTTTTACCGTTCGTTGAATTAATA 58.195 30.769 0.00 0.00 0.00 0.98
575 792 2.285756 CACTGCTTTTACCGTTCGTTGA 59.714 45.455 0.00 0.00 0.00 3.18
702 934 9.494271 GCAAAGGGAAAAGAAGAGAAAAATAAT 57.506 29.630 0.00 0.00 0.00 1.28
703 935 7.931407 GGCAAAGGGAAAAGAAGAGAAAAATAA 59.069 33.333 0.00 0.00 0.00 1.40
704 936 7.290014 AGGCAAAGGGAAAAGAAGAGAAAAATA 59.710 33.333 0.00 0.00 0.00 1.40
705 937 6.100279 AGGCAAAGGGAAAAGAAGAGAAAAAT 59.900 34.615 0.00 0.00 0.00 1.82
706 938 5.425217 AGGCAAAGGGAAAAGAAGAGAAAAA 59.575 36.000 0.00 0.00 0.00 1.94
707 939 4.962362 AGGCAAAGGGAAAAGAAGAGAAAA 59.038 37.500 0.00 0.00 0.00 2.29
708 940 4.546674 AGGCAAAGGGAAAAGAAGAGAAA 58.453 39.130 0.00 0.00 0.00 2.52
709 941 4.141158 AGAGGCAAAGGGAAAAGAAGAGAA 60.141 41.667 0.00 0.00 0.00 2.87
710 942 3.395941 AGAGGCAAAGGGAAAAGAAGAGA 59.604 43.478 0.00 0.00 0.00 3.10
711 943 3.755905 GAGAGGCAAAGGGAAAAGAAGAG 59.244 47.826 0.00 0.00 0.00 2.85
712 944 3.395941 AGAGAGGCAAAGGGAAAAGAAGA 59.604 43.478 0.00 0.00 0.00 2.87
713 945 3.760738 AGAGAGGCAAAGGGAAAAGAAG 58.239 45.455 0.00 0.00 0.00 2.85
714 946 3.884037 AGAGAGGCAAAGGGAAAAGAA 57.116 42.857 0.00 0.00 0.00 2.52
715 947 3.756117 GAAGAGAGGCAAAGGGAAAAGA 58.244 45.455 0.00 0.00 0.00 2.52
716 948 2.485814 CGAAGAGAGGCAAAGGGAAAAG 59.514 50.000 0.00 0.00 0.00 2.27
717 949 2.158667 ACGAAGAGAGGCAAAGGGAAAA 60.159 45.455 0.00 0.00 0.00 2.29
718 950 1.420138 ACGAAGAGAGGCAAAGGGAAA 59.580 47.619 0.00 0.00 0.00 3.13
719 951 1.002087 GACGAAGAGAGGCAAAGGGAA 59.998 52.381 0.00 0.00 0.00 3.97
752 999 5.391312 AGTTGGTGAAAATAGATGCAACC 57.609 39.130 0.00 0.00 0.00 3.77
754 1001 5.076182 TGGAGTTGGTGAAAATAGATGCAA 58.924 37.500 0.00 0.00 0.00 4.08
760 1007 4.096984 GGATGCTGGAGTTGGTGAAAATAG 59.903 45.833 0.00 0.00 0.00 1.73
761 1008 4.016444 GGATGCTGGAGTTGGTGAAAATA 58.984 43.478 0.00 0.00 0.00 1.40
774 1037 1.706866 CTATGGGAATGGGATGCTGGA 59.293 52.381 0.00 0.00 0.00 3.86
775 1038 1.426598 ACTATGGGAATGGGATGCTGG 59.573 52.381 0.00 0.00 0.00 4.85
807 1074 0.035630 CTCCCCTCTGTGGAGCTTTG 60.036 60.000 0.00 0.00 42.75 2.77
834 1101 1.871080 AATCGATCAGATCCAACGCC 58.129 50.000 0.00 0.00 38.98 5.68
918 1200 1.153686 TGAGCACTGCGAGATGAGC 60.154 57.895 0.00 0.00 0.00 4.26
935 1220 4.342862 TGAAAGAAGGGAAGAGTGAGTG 57.657 45.455 0.00 0.00 0.00 3.51
937 1222 5.526846 GCATATGAAAGAAGGGAAGAGTGAG 59.473 44.000 6.97 0.00 0.00 3.51
940 1227 5.441718 TGCATATGAAAGAAGGGAAGAGT 57.558 39.130 6.97 0.00 0.00 3.24
1015 1315 1.002544 CCCTTGGACCACAGAGAGAAC 59.997 57.143 0.00 0.00 0.00 3.01
1021 1321 3.574952 CACCCCTTGGACCACAGA 58.425 61.111 0.00 0.00 34.81 3.41
1050 1350 3.995219 CTGGATGAGCGCGTCTGCA 62.995 63.158 8.43 6.57 42.97 4.41
1155 1458 0.178891 TGGTCTGGCTCCTTTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
1233 1542 2.254471 CTGGAAGTCGTCGAGGACA 58.746 57.895 32.71 16.12 39.42 4.02
1377 1686 8.871125 TCCTCCACTAACTTATTGATCTTATCC 58.129 37.037 0.00 0.00 0.00 2.59
1434 1743 1.065491 TGTTGCCGCTCCAACTGATAT 60.065 47.619 14.68 0.00 44.12 1.63
1435 1744 0.323302 TGTTGCCGCTCCAACTGATA 59.677 50.000 14.68 0.00 44.12 2.15
1441 1750 1.074775 AAGGATGTTGCCGCTCCAA 59.925 52.632 0.00 0.00 0.00 3.53
1442 1751 1.675310 CAAGGATGTTGCCGCTCCA 60.675 57.895 0.00 0.00 0.00 3.86
1530 1839 1.416030 TGGTCTAGCAGCAACTTCACA 59.584 47.619 0.00 0.00 0.00 3.58
1555 1864 1.264749 ACCTGCACCTTCCGCTGATA 61.265 55.000 0.00 0.00 0.00 2.15
1584 1893 2.358195 GCCAAGACCTCCCATACCAAAT 60.358 50.000 0.00 0.00 0.00 2.32
1614 1923 4.635765 TCATTGTACACCATCTTAGCAAGC 59.364 41.667 0.00 0.00 0.00 4.01
1663 1972 2.156917 CACACAGTGCCACATCTTCAT 58.843 47.619 0.00 0.00 0.00 2.57
1687 1996 8.644619 CAGAAGAGCAATAACATCAAAATTGTG 58.355 33.333 0.00 0.00 33.96 3.33
1766 2081 7.161773 TCATGTGGATCCAATTCTTTTTCTC 57.838 36.000 18.20 0.00 0.00 2.87
1769 2084 7.507829 TGTTTCATGTGGATCCAATTCTTTTT 58.492 30.769 18.20 0.00 0.00 1.94
1770 2085 7.065120 TGTTTCATGTGGATCCAATTCTTTT 57.935 32.000 18.20 0.00 0.00 2.27
1772 2087 6.351541 CCATGTTTCATGTGGATCCAATTCTT 60.352 38.462 18.20 0.00 34.94 2.52
1774 2089 5.353938 CCATGTTTCATGTGGATCCAATTC 58.646 41.667 18.20 4.76 34.94 2.17
1777 2092 2.496871 GCCATGTTTCATGTGGATCCAA 59.503 45.455 18.20 7.57 34.94 3.53
1778 2093 2.101783 GCCATGTTTCATGTGGATCCA 58.898 47.619 11.44 11.44 34.94 3.41
1783 2098 1.153784 GGCGCCATGTTTCATGTGG 60.154 57.895 24.80 0.00 36.09 4.17
1784 2099 0.173935 ATGGCGCCATGTTTCATGTG 59.826 50.000 40.10 2.96 35.03 3.21
1785 2100 0.896923 AATGGCGCCATGTTTCATGT 59.103 45.000 41.00 21.10 36.68 3.21
1786 2101 1.135527 AGAATGGCGCCATGTTTCATG 59.864 47.619 41.00 3.11 36.68 3.07
1789 2104 1.268743 GCTAGAATGGCGCCATGTTTC 60.269 52.381 41.00 32.98 36.68 2.78
1792 2107 4.147701 GCTAGAATGGCGCCATGT 57.852 55.556 41.00 31.43 36.68 3.21
1799 2114 2.686915 ACTTCAATGCTGCTAGAATGGC 59.313 45.455 0.00 0.00 46.05 4.40
1800 2115 6.261603 TCAATACTTCAATGCTGCTAGAATGG 59.738 38.462 0.00 0.00 0.00 3.16
1801 2116 7.255491 TCAATACTTCAATGCTGCTAGAATG 57.745 36.000 0.00 0.00 0.00 2.67
1802 2117 7.772292 TCTTCAATACTTCAATGCTGCTAGAAT 59.228 33.333 0.00 0.00 0.00 2.40
1803 2118 7.105588 TCTTCAATACTTCAATGCTGCTAGAA 58.894 34.615 0.00 1.73 0.00 2.10
1807 2122 5.942236 TCTTCTTCAATACTTCAATGCTGCT 59.058 36.000 0.00 0.00 0.00 4.24
1819 2134 8.245701 ACTCGATCAAGTTTCTTCTTCAATAC 57.754 34.615 0.00 0.00 0.00 1.89
1825 2140 6.148480 CCAATGACTCGATCAAGTTTCTTCTT 59.852 38.462 0.00 0.00 41.93 2.52
1840 2155 2.426522 TCTTTTCCAGCCAATGACTCG 58.573 47.619 0.00 0.00 0.00 4.18
1841 2156 5.397142 AAATCTTTTCCAGCCAATGACTC 57.603 39.130 0.00 0.00 0.00 3.36
1881 2199 5.521906 TCCTCTTCTCTTCATTCCATACG 57.478 43.478 0.00 0.00 0.00 3.06
2010 2328 2.834638 ATGTTAGCTCATGGGGCTTT 57.165 45.000 16.63 0.48 40.74 3.51
2089 2408 4.212214 GGTGACTAACTCTGTTTGCTCTTG 59.788 45.833 0.00 0.00 0.00 3.02
2157 2476 2.134789 ATCCACCCATTGTCTTCAGC 57.865 50.000 0.00 0.00 0.00 4.26
2212 2531 5.480073 CCCCAATGTTACTTTCTTCAATGGA 59.520 40.000 0.00 0.00 34.05 3.41
2274 2593 6.584488 TGTCAGGTGTTTGTAGCTTAACTTA 58.416 36.000 0.00 0.00 0.00 2.24
2296 2615 6.073440 GCAAAACATTGCTTCATTTCAGATGT 60.073 34.615 6.31 0.00 44.15 3.06
2351 2670 3.998913 TCAACATATCCTTCTGCACCA 57.001 42.857 0.00 0.00 0.00 4.17
2353 2672 4.454678 TGGATCAACATATCCTTCTGCAC 58.545 43.478 4.63 0.00 44.98 4.57
2428 2747 8.059798 TCATGGAAAATGAATTCTCCTTTCTC 57.940 34.615 18.48 12.90 0.00 2.87
2495 2817 4.748892 AGCACGATAGACACCATATATGC 58.251 43.478 7.24 0.00 41.38 3.14
2540 2874 5.799435 TGCATTAAGTCGTGCATTTTACATG 59.201 36.000 0.00 0.00 45.60 3.21
2553 2887 2.223340 GGCCAAGTCATGCATTAAGTCG 60.223 50.000 0.00 0.00 0.00 4.18
2729 3078 8.394121 GTTTATGATTCTGATGTCTCCTTGAAC 58.606 37.037 0.00 0.00 0.00 3.18
2738 3090 4.553547 GCAGCCGTTTATGATTCTGATGTC 60.554 45.833 0.00 0.00 0.00 3.06
2746 3113 1.832883 TGTGGCAGCCGTTTATGATT 58.167 45.000 7.03 0.00 0.00 2.57
2749 3116 0.381801 GGATGTGGCAGCCGTTTATG 59.618 55.000 7.03 0.00 27.64 1.90
2750 3117 0.751643 GGGATGTGGCAGCCGTTTAT 60.752 55.000 7.03 0.00 41.37 1.40
2761 3140 4.452114 CGTAATGATACATGTGGGATGTGG 59.548 45.833 9.11 0.00 33.76 4.17
2762 3141 5.296748 TCGTAATGATACATGTGGGATGTG 58.703 41.667 9.11 0.00 33.76 3.21
2763 3142 5.541845 CTCGTAATGATACATGTGGGATGT 58.458 41.667 9.11 0.00 36.13 3.06
2764 3143 4.389992 GCTCGTAATGATACATGTGGGATG 59.610 45.833 9.11 0.00 32.02 3.51
2765 3144 4.040339 TGCTCGTAATGATACATGTGGGAT 59.960 41.667 9.11 0.00 32.02 3.85
2766 3145 3.386402 TGCTCGTAATGATACATGTGGGA 59.614 43.478 9.11 0.00 32.02 4.37
2767 3146 3.727726 TGCTCGTAATGATACATGTGGG 58.272 45.455 9.11 0.00 32.02 4.61
2829 3217 6.858993 GTCAAGATACCGTAAATGTTTTGCAA 59.141 34.615 0.00 0.00 0.00 4.08
3031 3419 1.072331 AGCTGACCAATGTTTCGAGGT 59.928 47.619 0.00 0.00 37.00 3.85
3142 3531 3.118038 TCAAGTTGTACAGTTCCAGCCTT 60.118 43.478 2.11 0.00 0.00 4.35
3202 3591 3.949754 TCAGATTTTGCTTATGCTGGAGG 59.050 43.478 1.96 0.00 40.48 4.30
3353 3751 4.405358 CCATTGTGGTATTTGTAGGCCATT 59.595 41.667 5.01 0.00 33.20 3.16
3354 3752 3.960102 CCATTGTGGTATTTGTAGGCCAT 59.040 43.478 5.01 0.00 33.20 4.40
3362 3760 6.206243 GGATCTCTCATCCATTGTGGTATTTG 59.794 42.308 0.00 0.00 39.03 2.32
3399 3797 6.531594 GGCAATTATGAGTTTTCTTAAGCACC 59.468 38.462 0.00 0.00 0.00 5.01
3493 3891 6.976934 AATGTCTTCAGTTTACCCATGTTT 57.023 33.333 0.00 0.00 0.00 2.83
3604 4002 1.954927 CCCATCCCTCTAAACTTCGC 58.045 55.000 0.00 0.00 0.00 4.70
3607 4005 2.562296 TCTGCCCATCCCTCTAAACTT 58.438 47.619 0.00 0.00 0.00 2.66
3611 4009 4.726825 ACTATTTTCTGCCCATCCCTCTAA 59.273 41.667 0.00 0.00 0.00 2.10
3631 4029 1.691337 AATAGCCACCCCCGCACTA 60.691 57.895 0.00 0.00 0.00 2.74
3689 4087 1.195115 AGCTTAGGGCATCTGTCGAA 58.805 50.000 0.00 0.00 44.79 3.71
3721 4119 1.087501 CTTTAAGAACGGGGCTCAGC 58.912 55.000 0.00 0.00 0.00 4.26
3736 4137 8.798975 AATATCCTCCTAACCTCATGACTTTA 57.201 34.615 0.00 0.00 0.00 1.85
3743 4144 9.095700 GTCTAGAAAATATCCTCCTAACCTCAT 57.904 37.037 0.00 0.00 0.00 2.90
3777 4228 5.039333 GCAGCTTTGGAATATGCAGTAAAG 58.961 41.667 0.00 0.00 36.88 1.85
3785 4236 4.217118 GGATGTAGGCAGCTTTGGAATATG 59.783 45.833 0.00 0.00 0.00 1.78
3797 4248 5.047092 ACAAAATTTCAAGGGATGTAGGCAG 60.047 40.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.