Multiple sequence alignment - TraesCS6B01G085900

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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 TraesCS6B01G085900 chr6B 100.000 3155 0 0 1 3155 62388799 62391953 0.000000e+00 5827
1 TraesCS6B01G085900 chr6B 90.806 1501 129 7 1025 2524 62709296 62707804 0.000000e+00 1999
2 TraesCS6B01G085900 chr6B 94.967 755 24 7 174 926 715710405 715709663 0.000000e+00 1171
3 TraesCS6B01G085900 chr6B 84.588 850 110 16 1685 2524 62650861 62650023 0.000000e+00 824
4 TraesCS6B01G085900 chr6B 77.982 1090 231 7 1075 2159 14330532 14331617 0.000000e+00 675
5 TraesCS6B01G085900 chr6B 80.202 495 95 3 1303 1796 77745752 77746244 4.970000e-98 368
6 TraesCS6B01G085900 chrUn 95.675 2243 73 10 927 3155 101944333 101942101 0.000000e+00 3583
7 TraesCS6B01G085900 chrUn 90.978 1574 130 10 955 2524 102006667 102005102 0.000000e+00 2109
8 TraesCS6B01G085900 chr6A 91.057 1599 134 7 927 2524 34303964 34302374 0.000000e+00 2152
9 TraesCS6B01G085900 chr6A 90.869 1599 137 7 927 2524 34414668 34413078 0.000000e+00 2135
10 TraesCS6B01G085900 chr6A 92.518 1390 89 4 1777 3155 34212425 34211040 0.000000e+00 1977
11 TraesCS6B01G085900 chr6A 86.501 763 71 14 173 926 567344551 567345290 0.000000e+00 809
12 TraesCS6B01G085900 chr6A 77.318 1402 273 34 997 2378 8261972 8260596 0.000000e+00 785
13 TraesCS6B01G085900 chr6A 77.374 1211 249 21 963 2157 7977695 7978896 0.000000e+00 695
14 TraesCS6B01G085900 chr6A 89.184 527 52 4 927 1452 34239279 34238757 0.000000e+00 652
15 TraesCS6B01G085900 chr6A 85.503 338 48 1 1448 1784 34221416 34221079 5.010000e-93 351
16 TraesCS6B01G085900 chr6A 94.706 170 8 1 753 921 203220054 203220223 2.410000e-66 263
17 TraesCS6B01G085900 chr5B 94.709 756 28 5 173 926 447267870 447268615 0.000000e+00 1164
18 TraesCS6B01G085900 chr5B 76.744 1204 255 19 997 2186 421499441 421500633 0.000000e+00 649
19 TraesCS6B01G085900 chr7B 92.867 757 37 8 169 922 687546460 687545718 0.000000e+00 1083
20 TraesCS6B01G085900 chr2B 91.557 758 47 8 174 927 136957947 136957203 0.000000e+00 1029
21 TraesCS6B01G085900 chr2B 95.402 174 8 0 753 926 415337447 415337620 8.620000e-71 278
22 TraesCS6B01G085900 chr7A 90.464 776 48 8 174 930 735110341 735109573 0.000000e+00 1000
23 TraesCS6B01G085900 chr3A 86.905 756 74 12 174 926 746320025 746320758 0.000000e+00 824
24 TraesCS6B01G085900 chr6D 77.973 1312 237 43 967 2250 7477196 7475909 0.000000e+00 774
25 TraesCS6B01G085900 chr7D 86.145 664 45 17 174 824 530907054 530906425 0.000000e+00 673
26 TraesCS6B01G085900 chr5D 76.783 1206 251 23 997 2186 356636805 356637997 0.000000e+00 649
27 TraesCS6B01G085900 chr1D 90.138 436 26 11 220 645 369912553 369912125 4.600000e-153 551
28 TraesCS6B01G085900 chr1D 94.611 167 9 0 755 921 472424340 472424506 3.120000e-65 259
29 TraesCS6B01G085900 chr4B 91.155 407 19 7 524 926 570738936 570738543 1.290000e-148 536


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 TraesCS6B01G085900 chr6B 62388799 62391953 3154 False 5827 5827 100.000 1 3155 1 chr6B.!!$F2 3154
1 TraesCS6B01G085900 chr6B 62707804 62709296 1492 True 1999 1999 90.806 1025 2524 1 chr6B.!!$R2 1499
2 TraesCS6B01G085900 chr6B 715709663 715710405 742 True 1171 1171 94.967 174 926 1 chr6B.!!$R3 752
3 TraesCS6B01G085900 chr6B 62650023 62650861 838 True 824 824 84.588 1685 2524 1 chr6B.!!$R1 839
4 TraesCS6B01G085900 chr6B 14330532 14331617 1085 False 675 675 77.982 1075 2159 1 chr6B.!!$F1 1084
5 TraesCS6B01G085900 chrUn 101942101 101944333 2232 True 3583 3583 95.675 927 3155 1 chrUn.!!$R1 2228
6 TraesCS6B01G085900 chrUn 102005102 102006667 1565 True 2109 2109 90.978 955 2524 1 chrUn.!!$R2 1569
7 TraesCS6B01G085900 chr6A 34302374 34303964 1590 True 2152 2152 91.057 927 2524 1 chr6A.!!$R5 1597
8 TraesCS6B01G085900 chr6A 34413078 34414668 1590 True 2135 2135 90.869 927 2524 1 chr6A.!!$R6 1597
9 TraesCS6B01G085900 chr6A 34211040 34212425 1385 True 1977 1977 92.518 1777 3155 1 chr6A.!!$R2 1378
10 TraesCS6B01G085900 chr6A 567344551 567345290 739 False 809 809 86.501 173 926 1 chr6A.!!$F3 753
11 TraesCS6B01G085900 chr6A 8260596 8261972 1376 True 785 785 77.318 997 2378 1 chr6A.!!$R1 1381
12 TraesCS6B01G085900 chr6A 7977695 7978896 1201 False 695 695 77.374 963 2157 1 chr6A.!!$F1 1194
13 TraesCS6B01G085900 chr6A 34238757 34239279 522 True 652 652 89.184 927 1452 1 chr6A.!!$R4 525
14 TraesCS6B01G085900 chr5B 447267870 447268615 745 False 1164 1164 94.709 173 926 1 chr5B.!!$F2 753
15 TraesCS6B01G085900 chr5B 421499441 421500633 1192 False 649 649 76.744 997 2186 1 chr5B.!!$F1 1189
16 TraesCS6B01G085900 chr7B 687545718 687546460 742 True 1083 1083 92.867 169 922 1 chr7B.!!$R1 753
17 TraesCS6B01G085900 chr2B 136957203 136957947 744 True 1029 1029 91.557 174 927 1 chr2B.!!$R1 753
18 TraesCS6B01G085900 chr7A 735109573 735110341 768 True 1000 1000 90.464 174 930 1 chr7A.!!$R1 756
19 TraesCS6B01G085900 chr3A 746320025 746320758 733 False 824 824 86.905 174 926 1 chr3A.!!$F1 752
20 TraesCS6B01G085900 chr6D 7475909 7477196 1287 True 774 774 77.973 967 2250 1 chr6D.!!$R1 1283
21 TraesCS6B01G085900 chr7D 530906425 530907054 629 True 673 673 86.145 174 824 1 chr7D.!!$R1 650
22 TraesCS6B01G085900 chr5D 356636805 356637997 1192 False 649 649 76.783 997 2186 1 chr5D.!!$F1 1189

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
60 61 0.027716 CAAGATGATGCGTGCTGCTC 59.972 55.0 0.0 0.0 46.63 4.26 F
61 62 0.107800 AAGATGATGCGTGCTGCTCT 60.108 50.0 0.0 0.0 46.63 4.09 F
362 378 0.180171 TGGTGATCGGCCCATAACTG 59.820 55.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1580 1.478916 GCTTGACCACCCTCTCTAGAC 59.521 57.143 0.00 0.00 0.00 2.59 R
1844 1905 2.148687 GACTTGCTCTGCAGTGTCG 58.851 57.895 14.67 6.58 40.61 4.35 R
2233 2295 0.671251 GGCAATGAACACGGAACCAA 59.329 50.000 0.00 0.00 0.00 3.67 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
19 20 2.691409 TTCGACTATTGGGCCTCAAG 57.309 50.000 4.53 1.22 38.95 3.02
20 21 1.568504 TCGACTATTGGGCCTCAAGT 58.431 50.000 4.53 4.91 38.95 3.16
21 22 1.906574 TCGACTATTGGGCCTCAAGTT 59.093 47.619 4.53 0.00 38.95 2.66
22 23 2.009774 CGACTATTGGGCCTCAAGTTG 58.990 52.381 4.53 5.38 38.95 3.16
23 24 2.369394 GACTATTGGGCCTCAAGTTGG 58.631 52.381 4.53 0.00 38.95 3.77
24 25 1.005924 ACTATTGGGCCTCAAGTTGGG 59.994 52.381 4.53 0.00 38.95 4.12
28 29 2.436109 GGCCTCAAGTTGGGCTCA 59.564 61.111 25.23 0.00 46.80 4.26
29 30 1.000396 GGCCTCAAGTTGGGCTCAT 60.000 57.895 25.23 0.00 46.80 2.90
30 31 0.613012 GGCCTCAAGTTGGGCTCATT 60.613 55.000 25.23 0.00 46.80 2.57
31 32 0.813821 GCCTCAAGTTGGGCTCATTC 59.186 55.000 21.45 0.00 44.48 2.67
32 33 1.467920 CCTCAAGTTGGGCTCATTCC 58.532 55.000 2.34 0.00 0.00 3.01
33 34 1.467920 CTCAAGTTGGGCTCATTCCC 58.532 55.000 2.34 0.00 46.73 3.97
39 40 4.129148 GGGCTCATTCCCGGGCTT 62.129 66.667 18.49 1.40 36.38 4.35
40 41 2.043953 GGCTCATTCCCGGGCTTT 60.044 61.111 18.49 0.00 0.00 3.51
41 42 2.121538 GGCTCATTCCCGGGCTTTC 61.122 63.158 18.49 1.90 0.00 2.62
42 43 1.378514 GCTCATTCCCGGGCTTTCA 60.379 57.895 18.49 0.00 0.00 2.69
43 44 0.965363 GCTCATTCCCGGGCTTTCAA 60.965 55.000 18.49 4.42 0.00 2.69
44 45 1.098050 CTCATTCCCGGGCTTTCAAG 58.902 55.000 18.49 4.23 0.00 3.02
45 46 0.695924 TCATTCCCGGGCTTTCAAGA 59.304 50.000 18.49 3.42 0.00 3.02
46 47 1.284785 TCATTCCCGGGCTTTCAAGAT 59.715 47.619 18.49 0.00 0.00 2.40
47 48 1.406539 CATTCCCGGGCTTTCAAGATG 59.593 52.381 18.49 5.66 0.00 2.90
48 49 0.695924 TTCCCGGGCTTTCAAGATGA 59.304 50.000 18.49 0.00 0.00 2.92
49 50 0.918983 TCCCGGGCTTTCAAGATGAT 59.081 50.000 18.49 0.00 0.00 2.45
50 51 1.027357 CCCGGGCTTTCAAGATGATG 58.973 55.000 8.08 0.00 0.00 3.07
51 52 0.383231 CCGGGCTTTCAAGATGATGC 59.617 55.000 0.00 0.00 0.00 3.91
52 53 0.028505 CGGGCTTTCAAGATGATGCG 59.971 55.000 0.00 0.00 30.53 4.73
53 54 1.098050 GGGCTTTCAAGATGATGCGT 58.902 50.000 0.00 0.00 30.53 5.24
54 55 1.202222 GGGCTTTCAAGATGATGCGTG 60.202 52.381 0.00 0.00 30.53 5.34
55 56 1.542544 GCTTTCAAGATGATGCGTGC 58.457 50.000 0.00 0.00 0.00 5.34
56 57 1.131883 GCTTTCAAGATGATGCGTGCT 59.868 47.619 0.00 0.00 0.00 4.40
57 58 2.782163 CTTTCAAGATGATGCGTGCTG 58.218 47.619 0.00 0.00 0.00 4.41
58 59 0.448990 TTCAAGATGATGCGTGCTGC 59.551 50.000 0.00 0.00 46.70 5.25
59 60 0.392060 TCAAGATGATGCGTGCTGCT 60.392 50.000 0.00 0.00 46.63 4.24
60 61 0.027716 CAAGATGATGCGTGCTGCTC 59.972 55.000 0.00 0.00 46.63 4.26
61 62 0.107800 AAGATGATGCGTGCTGCTCT 60.108 50.000 0.00 0.00 46.63 4.09
62 63 0.810426 AGATGATGCGTGCTGCTCTG 60.810 55.000 0.00 0.00 46.63 3.35
63 64 1.078637 ATGATGCGTGCTGCTCTGT 60.079 52.632 0.00 0.00 46.63 3.41
64 65 0.675837 ATGATGCGTGCTGCTCTGTT 60.676 50.000 0.00 0.00 46.63 3.16
65 66 1.134075 GATGCGTGCTGCTCTGTTG 59.866 57.895 0.00 0.00 46.63 3.33
66 67 2.249557 GATGCGTGCTGCTCTGTTGG 62.250 60.000 0.00 0.00 46.63 3.77
67 68 2.666190 GCGTGCTGCTCTGTTGGA 60.666 61.111 0.00 0.00 41.73 3.53
68 69 2.253758 GCGTGCTGCTCTGTTGGAA 61.254 57.895 0.00 0.00 41.73 3.53
69 70 1.571460 CGTGCTGCTCTGTTGGAAC 59.429 57.895 0.00 0.00 0.00 3.62
70 71 1.159713 CGTGCTGCTCTGTTGGAACA 61.160 55.000 0.00 0.00 37.37 3.18
75 76 3.873805 GCTCTGTTGGAACAAAGCC 57.126 52.632 6.57 0.00 45.01 4.35
76 77 1.032014 GCTCTGTTGGAACAAAGCCA 58.968 50.000 6.57 0.00 45.01 4.75
77 78 1.000938 GCTCTGTTGGAACAAAGCCAG 60.001 52.381 6.57 0.00 45.01 4.85
78 79 3.329932 GCTCTGTTGGAACAAAGCCAGA 61.330 50.000 6.57 1.45 45.01 3.86
79 80 5.393880 GCTCTGTTGGAACAAAGCCAGAC 62.394 52.174 6.57 0.00 45.01 3.51
82 83 3.109847 TGGAACAAAGCCAGACCAC 57.890 52.632 0.00 0.00 31.92 4.16
83 84 0.817634 TGGAACAAAGCCAGACCACG 60.818 55.000 0.00 0.00 31.92 4.94
84 85 0.534203 GGAACAAAGCCAGACCACGA 60.534 55.000 0.00 0.00 0.00 4.35
85 86 0.868406 GAACAAAGCCAGACCACGAG 59.132 55.000 0.00 0.00 0.00 4.18
86 87 0.180406 AACAAAGCCAGACCACGAGT 59.820 50.000 0.00 0.00 0.00 4.18
87 88 0.180406 ACAAAGCCAGACCACGAGTT 59.820 50.000 0.00 0.00 0.00 3.01
88 89 0.588252 CAAAGCCAGACCACGAGTTG 59.412 55.000 0.00 0.00 0.00 3.16
89 90 1.166531 AAAGCCAGACCACGAGTTGC 61.167 55.000 0.00 0.00 0.00 4.17
90 91 2.031163 GCCAGACCACGAGTTGCT 59.969 61.111 0.00 0.00 0.00 3.91
91 92 1.185618 AGCCAGACCACGAGTTGCTA 61.186 55.000 0.00 0.00 0.00 3.49
92 93 0.320421 GCCAGACCACGAGTTGCTAA 60.320 55.000 0.00 0.00 0.00 3.09
93 94 1.876416 GCCAGACCACGAGTTGCTAAA 60.876 52.381 0.00 0.00 0.00 1.85
94 95 2.489971 CCAGACCACGAGTTGCTAAAA 58.510 47.619 0.00 0.00 0.00 1.52
95 96 2.875933 CCAGACCACGAGTTGCTAAAAA 59.124 45.455 0.00 0.00 0.00 1.94
116 117 2.821991 ATATAAGCCAGACCACGAGC 57.178 50.000 0.00 0.00 0.00 5.03
117 118 1.776662 TATAAGCCAGACCACGAGCT 58.223 50.000 0.00 0.00 37.10 4.09
118 119 0.905357 ATAAGCCAGACCACGAGCTT 59.095 50.000 1.39 1.39 46.70 3.74
119 120 0.246635 TAAGCCAGACCACGAGCTTC 59.753 55.000 0.00 0.00 44.13 3.86
120 121 2.771763 AAGCCAGACCACGAGCTTCG 62.772 60.000 0.00 0.00 41.60 3.79
121 122 2.811317 CCAGACCACGAGCTTCGC 60.811 66.667 5.63 0.00 45.12 4.70
122 123 2.049156 CAGACCACGAGCTTCGCA 60.049 61.111 5.63 0.00 45.12 5.10
123 124 2.091112 CAGACCACGAGCTTCGCAG 61.091 63.158 5.63 1.11 45.12 5.18
124 125 2.049063 GACCACGAGCTTCGCAGT 60.049 61.111 5.63 3.85 45.12 4.40
125 126 2.049063 ACCACGAGCTTCGCAGTC 60.049 61.111 5.63 0.00 45.12 3.51
126 127 2.811317 CCACGAGCTTCGCAGTCC 60.811 66.667 5.63 0.00 45.12 3.85
127 128 3.175240 CACGAGCTTCGCAGTCCG 61.175 66.667 5.63 0.00 45.12 4.79
130 131 3.482783 GAGCTTCGCAGTCCGCAC 61.483 66.667 0.00 0.00 42.60 5.34
133 134 2.434884 CTTCGCAGTCCGCACCAT 60.435 61.111 0.00 0.00 42.60 3.55
134 135 2.031919 TTCGCAGTCCGCACCATT 59.968 55.556 0.00 0.00 42.60 3.16
135 136 2.244436 CTTCGCAGTCCGCACCATTG 62.244 60.000 0.00 0.00 42.60 2.82
136 137 4.465512 CGCAGTCCGCACCATTGC 62.466 66.667 0.00 0.00 46.21 3.56
146 147 2.818130 GCACCATTGCCTCAAGAAAA 57.182 45.000 0.00 0.00 43.66 2.29
147 148 3.110447 GCACCATTGCCTCAAGAAAAA 57.890 42.857 0.00 0.00 43.66 1.94
168 169 1.443802 AAAGAGCTCCGCACTAAAGC 58.556 50.000 10.93 0.00 36.27 3.51
169 170 0.391793 AAGAGCTCCGCACTAAAGCC 60.392 55.000 10.93 0.00 36.69 4.35
170 171 1.079127 GAGCTCCGCACTAAAGCCA 60.079 57.895 0.87 0.00 36.69 4.75
171 172 1.362406 GAGCTCCGCACTAAAGCCAC 61.362 60.000 0.87 0.00 36.69 5.01
362 378 0.180171 TGGTGATCGGCCCATAACTG 59.820 55.000 0.00 0.00 0.00 3.16
440 469 2.279073 CCTCCTCGACCCTAGGCA 59.721 66.667 2.05 0.00 33.84 4.75
534 566 1.109920 ACATCCGACTAGCCGCTCAT 61.110 55.000 0.00 0.00 0.00 2.90
727 768 9.917887 ATAATTTTTCTCTCTCATGGAGTGATT 57.082 29.630 13.28 9.20 42.02 2.57
733 774 5.839606 TCTCTCTCATGGAGTGATTGATCAT 59.160 40.000 0.00 0.00 42.40 2.45
745 786 7.664731 GGAGTGATTGATCATTATCTGTTCCAT 59.335 37.037 8.49 0.00 39.30 3.41
746 787 8.392372 AGTGATTGATCATTATCTGTTCCATG 57.608 34.615 8.49 0.00 39.30 3.66
747 788 7.997223 AGTGATTGATCATTATCTGTTCCATGT 59.003 33.333 8.49 0.00 39.30 3.21
748 789 8.074370 GTGATTGATCATTATCTGTTCCATGTG 58.926 37.037 8.49 0.00 39.30 3.21
749 790 7.776500 TGATTGATCATTATCTGTTCCATGTGT 59.224 33.333 8.49 0.00 32.93 3.72
750 791 9.276590 GATTGATCATTATCTGTTCCATGTGTA 57.723 33.333 0.00 0.00 32.93 2.90
751 792 8.437360 TTGATCATTATCTGTTCCATGTGTAC 57.563 34.615 0.00 0.00 32.93 2.90
932 973 1.094785 AATCAATTTCCTCGCCACCG 58.905 50.000 0.00 0.00 0.00 4.94
965 1007 2.874664 CGAACGTCCCCACTTCCCA 61.875 63.158 0.00 0.00 0.00 4.37
1381 1441 0.877743 CCTATCGCGCTCTGAGATCA 59.122 55.000 9.28 0.00 38.20 2.92
1520 1580 2.561419 TCAAGTACTTTCTCAGGTCCGG 59.439 50.000 5.07 0.00 0.00 5.14
1560 1620 2.943033 GCCCAATATTGAGTTACTGCGT 59.057 45.455 17.23 0.00 0.00 5.24
1844 1905 3.025978 TGATGCTGACCAAATCCAATCC 58.974 45.455 0.00 0.00 0.00 3.01
2007 2068 3.430042 AATGGATTGCTAGATCGCCAT 57.570 42.857 0.00 0.00 37.71 4.40
2233 2295 5.484715 TCTGCGTAGTAAGCTGGTAAATTT 58.515 37.500 13.38 0.00 34.85 1.82
2240 2302 6.340962 AGTAAGCTGGTAAATTTTGGTTCC 57.659 37.500 0.00 0.00 0.00 3.62
2304 2371 2.196749 CCCTGACGAATTGATGACTCG 58.803 52.381 0.00 0.00 38.53 4.18
2639 2716 4.553756 TCTCGTCTGTTCCGAATGATAG 57.446 45.455 0.00 0.00 33.34 2.08
2653 2730 5.932303 CCGAATGATAGGACGTTTTGGATAT 59.068 40.000 0.00 0.00 0.00 1.63
2657 2734 9.450807 GAATGATAGGACGTTTTGGATATTTTG 57.549 33.333 0.00 0.00 0.00 2.44
2683 2761 5.018539 TGGACTAATACGGACTGAAATGG 57.981 43.478 0.00 0.00 0.00 3.16
2693 2771 3.255642 CGGACTGAAATGGGTGAACAAAT 59.744 43.478 0.00 0.00 0.00 2.32
2695 2773 5.048364 CGGACTGAAATGGGTGAACAAATAA 60.048 40.000 0.00 0.00 0.00 1.40
2706 2784 8.879342 TGGGTGAACAAATAAACTAAAACATG 57.121 30.769 0.00 0.00 0.00 3.21
2826 2911 4.960332 TCTTCCCCTCTATTCTCCAAAGA 58.040 43.478 0.00 0.00 0.00 2.52
2871 2959 3.634910 ACAATACTTTTGCTGGGAAACGT 59.365 39.130 2.87 2.87 0.00 3.99
3000 3088 4.188462 TGGCATGATTTAGTCTTACCACG 58.812 43.478 0.00 0.00 0.00 4.94
3006 3094 7.456253 CATGATTTAGTCTTACCACGTTTCTG 58.544 38.462 0.00 0.00 0.00 3.02
3012 3100 6.251655 AGTCTTACCACGTTTCTGTACTAG 57.748 41.667 0.00 0.00 0.00 2.57
3013 3101 4.855937 GTCTTACCACGTTTCTGTACTAGC 59.144 45.833 0.00 0.00 0.00 3.42
3059 3149 4.976116 GTGTCCAATCACAAAACTACTTGC 59.024 41.667 0.00 0.00 38.12 4.01
3069 3159 7.946207 TCACAAAACTACTTGCATAATTTGGA 58.054 30.769 0.00 0.00 32.20 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.906574 ACTTGAGGCCCAATAGTCGAA 59.093 47.619 0.00 0.00 33.68 3.71
1 2 1.568504 ACTTGAGGCCCAATAGTCGA 58.431 50.000 0.00 0.00 33.68 4.20
3 4 2.369394 CCAACTTGAGGCCCAATAGTC 58.631 52.381 0.00 0.00 33.68 2.59
6 7 0.324275 GCCCAACTTGAGGCCCAATA 60.324 55.000 0.00 0.00 43.76 1.90
7 8 1.610379 GCCCAACTTGAGGCCCAAT 60.610 57.895 0.00 0.00 43.76 3.16
8 9 2.203625 GCCCAACTTGAGGCCCAA 60.204 61.111 0.00 2.36 43.76 4.12
13 14 1.467920 GGAATGAGCCCAACTTGAGG 58.532 55.000 0.00 0.00 0.00 3.86
22 23 3.662117 AAAGCCCGGGAATGAGCCC 62.662 63.158 29.31 2.84 45.10 5.19
23 24 2.043953 AAAGCCCGGGAATGAGCC 60.044 61.111 29.31 3.77 0.00 4.70
24 25 0.965363 TTGAAAGCCCGGGAATGAGC 60.965 55.000 29.31 7.49 0.00 4.26
25 26 1.098050 CTTGAAAGCCCGGGAATGAG 58.902 55.000 29.31 9.72 0.00 2.90
26 27 0.695924 TCTTGAAAGCCCGGGAATGA 59.304 50.000 29.31 8.68 0.00 2.57
27 28 1.406539 CATCTTGAAAGCCCGGGAATG 59.593 52.381 29.31 9.66 0.00 2.67
28 29 1.284785 TCATCTTGAAAGCCCGGGAAT 59.715 47.619 29.31 9.24 0.00 3.01
29 30 0.695924 TCATCTTGAAAGCCCGGGAA 59.304 50.000 29.31 8.26 0.00 3.97
30 31 0.918983 ATCATCTTGAAAGCCCGGGA 59.081 50.000 29.31 0.00 0.00 5.14
31 32 1.027357 CATCATCTTGAAAGCCCGGG 58.973 55.000 19.09 19.09 0.00 5.73
32 33 0.383231 GCATCATCTTGAAAGCCCGG 59.617 55.000 0.00 0.00 0.00 5.73
33 34 0.028505 CGCATCATCTTGAAAGCCCG 59.971 55.000 0.00 0.00 30.75 6.13
34 35 1.098050 ACGCATCATCTTGAAAGCCC 58.902 50.000 0.00 0.00 30.75 5.19
35 36 1.796617 GCACGCATCATCTTGAAAGCC 60.797 52.381 0.00 0.00 30.75 4.35
36 37 1.131883 AGCACGCATCATCTTGAAAGC 59.868 47.619 0.00 0.00 0.00 3.51
37 38 2.782163 CAGCACGCATCATCTTGAAAG 58.218 47.619 0.00 0.00 0.00 2.62
38 39 1.135603 GCAGCACGCATCATCTTGAAA 60.136 47.619 0.00 0.00 41.79 2.69
39 40 0.448990 GCAGCACGCATCATCTTGAA 59.551 50.000 0.00 0.00 41.79 2.69
40 41 0.392060 AGCAGCACGCATCATCTTGA 60.392 50.000 0.00 0.00 46.13 3.02
41 42 0.027716 GAGCAGCACGCATCATCTTG 59.972 55.000 0.00 0.00 46.13 3.02
42 43 0.107800 AGAGCAGCACGCATCATCTT 60.108 50.000 0.00 0.00 46.13 2.40
43 44 0.810426 CAGAGCAGCACGCATCATCT 60.810 55.000 0.00 0.00 46.13 2.90
44 45 1.088340 ACAGAGCAGCACGCATCATC 61.088 55.000 0.00 0.00 46.13 2.92
45 46 0.675837 AACAGAGCAGCACGCATCAT 60.676 50.000 0.00 0.00 46.13 2.45
46 47 1.301953 AACAGAGCAGCACGCATCA 60.302 52.632 0.00 0.00 46.13 3.07
47 48 1.134075 CAACAGAGCAGCACGCATC 59.866 57.895 0.00 0.00 46.13 3.91
48 49 2.330372 CCAACAGAGCAGCACGCAT 61.330 57.895 0.00 0.00 46.13 4.73
49 50 2.939133 TTCCAACAGAGCAGCACGCA 62.939 55.000 0.00 0.00 46.13 5.24
50 51 2.253758 TTCCAACAGAGCAGCACGC 61.254 57.895 0.00 0.00 42.91 5.34
51 52 1.159713 TGTTCCAACAGAGCAGCACG 61.160 55.000 0.00 0.00 34.30 5.34
52 53 1.024271 TTGTTCCAACAGAGCAGCAC 58.976 50.000 0.00 0.00 40.50 4.40
53 54 1.677576 CTTTGTTCCAACAGAGCAGCA 59.322 47.619 0.00 0.00 40.50 4.41
54 55 2.412421 CTTTGTTCCAACAGAGCAGC 57.588 50.000 0.00 0.00 40.50 5.25
58 59 2.291741 GTCTGGCTTTGTTCCAACAGAG 59.708 50.000 5.77 5.77 42.28 3.35
59 60 2.297701 GTCTGGCTTTGTTCCAACAGA 58.702 47.619 0.00 0.00 40.50 3.41
60 61 1.338020 GGTCTGGCTTTGTTCCAACAG 59.662 52.381 0.00 0.00 40.50 3.16
61 62 1.341482 TGGTCTGGCTTTGTTCCAACA 60.341 47.619 0.00 0.00 37.08 3.33
62 63 1.067060 GTGGTCTGGCTTTGTTCCAAC 59.933 52.381 0.00 0.00 32.41 3.77
63 64 1.398692 GTGGTCTGGCTTTGTTCCAA 58.601 50.000 0.00 0.00 32.41 3.53
64 65 0.817634 CGTGGTCTGGCTTTGTTCCA 60.818 55.000 0.00 0.00 0.00 3.53
65 66 0.534203 TCGTGGTCTGGCTTTGTTCC 60.534 55.000 0.00 0.00 0.00 3.62
66 67 0.868406 CTCGTGGTCTGGCTTTGTTC 59.132 55.000 0.00 0.00 0.00 3.18
67 68 0.180406 ACTCGTGGTCTGGCTTTGTT 59.820 50.000 0.00 0.00 0.00 2.83
68 69 0.180406 AACTCGTGGTCTGGCTTTGT 59.820 50.000 0.00 0.00 0.00 2.83
69 70 0.588252 CAACTCGTGGTCTGGCTTTG 59.412 55.000 0.00 0.00 0.00 2.77
70 71 1.166531 GCAACTCGTGGTCTGGCTTT 61.167 55.000 0.00 0.00 0.00 3.51
71 72 1.598130 GCAACTCGTGGTCTGGCTT 60.598 57.895 0.00 0.00 0.00 4.35
72 73 1.185618 TAGCAACTCGTGGTCTGGCT 61.186 55.000 0.00 0.00 39.22 4.75
73 74 0.320421 TTAGCAACTCGTGGTCTGGC 60.320 55.000 0.00 0.00 39.22 4.85
74 75 2.163818 TTTAGCAACTCGTGGTCTGG 57.836 50.000 0.00 0.00 39.22 3.86
93 94 4.335594 GCTCGTGGTCTGGCTTATATTTTT 59.664 41.667 0.00 0.00 0.00 1.94
94 95 3.877508 GCTCGTGGTCTGGCTTATATTTT 59.122 43.478 0.00 0.00 0.00 1.82
95 96 3.134804 AGCTCGTGGTCTGGCTTATATTT 59.865 43.478 0.00 0.00 0.00 1.40
96 97 2.700897 AGCTCGTGGTCTGGCTTATATT 59.299 45.455 0.00 0.00 0.00 1.28
97 98 2.320781 AGCTCGTGGTCTGGCTTATAT 58.679 47.619 0.00 0.00 0.00 0.86
98 99 1.776662 AGCTCGTGGTCTGGCTTATA 58.223 50.000 0.00 0.00 0.00 0.98
99 100 0.905357 AAGCTCGTGGTCTGGCTTAT 59.095 50.000 0.00 0.00 42.23 1.73
100 101 0.246635 GAAGCTCGTGGTCTGGCTTA 59.753 55.000 0.00 0.00 43.74 3.09
101 102 1.004440 GAAGCTCGTGGTCTGGCTT 60.004 57.895 0.00 0.00 45.91 4.35
102 103 2.659610 GAAGCTCGTGGTCTGGCT 59.340 61.111 0.00 0.00 36.53 4.75
103 104 2.811317 CGAAGCTCGTGGTCTGGC 60.811 66.667 0.00 0.00 34.72 4.85
155 156 2.100631 CGGTGGCTTTAGTGCGGAG 61.101 63.158 0.00 0.00 0.00 4.63
156 157 2.047655 CGGTGGCTTTAGTGCGGA 60.048 61.111 0.00 0.00 0.00 5.54
157 158 2.047655 TCGGTGGCTTTAGTGCGG 60.048 61.111 0.00 0.00 0.00 5.69
158 159 2.100631 CCTCGGTGGCTTTAGTGCG 61.101 63.158 0.00 0.00 0.00 5.34
159 160 0.321298 TTCCTCGGTGGCTTTAGTGC 60.321 55.000 0.00 0.00 35.26 4.40
160 161 2.178912 TTTCCTCGGTGGCTTTAGTG 57.821 50.000 0.00 0.00 35.26 2.74
161 162 3.081804 CAATTTCCTCGGTGGCTTTAGT 58.918 45.455 0.00 0.00 35.26 2.24
162 163 3.127030 GTCAATTTCCTCGGTGGCTTTAG 59.873 47.826 0.00 0.00 35.26 1.85
163 164 3.078837 GTCAATTTCCTCGGTGGCTTTA 58.921 45.455 0.00 0.00 35.26 1.85
164 165 1.886542 GTCAATTTCCTCGGTGGCTTT 59.113 47.619 0.00 0.00 35.26 3.51
165 166 1.073923 AGTCAATTTCCTCGGTGGCTT 59.926 47.619 0.00 0.00 35.26 4.35
166 167 0.693049 AGTCAATTTCCTCGGTGGCT 59.307 50.000 0.00 0.00 35.26 4.75
167 168 2.396590 TAGTCAATTTCCTCGGTGGC 57.603 50.000 0.00 0.00 35.26 5.01
168 169 7.568199 AATAAATAGTCAATTTCCTCGGTGG 57.432 36.000 0.00 0.00 38.71 4.61
362 378 1.226888 GGCGTGGACCGATGTAGAC 60.227 63.158 0.00 0.00 39.56 2.59
440 469 2.684881 GGCACCAGATGATGAATTCGTT 59.315 45.455 0.77 0.00 0.00 3.85
534 566 7.033791 AGATTAGAAACAGCGTCGAAGAATTA 58.966 34.615 1.37 0.00 39.69 1.40
583 615 5.401550 AGGTGCAACGATTTTCATTATGTG 58.598 37.500 0.00 0.00 38.12 3.21
587 623 7.441890 TTCTTAGGTGCAACGATTTTCATTA 57.558 32.000 0.00 0.00 38.12 1.90
745 786 3.926821 TCGATTGCTACACAGTACACA 57.073 42.857 0.00 0.00 0.00 3.72
746 787 4.500837 CAGATCGATTGCTACACAGTACAC 59.499 45.833 0.00 0.00 0.00 2.90
747 788 4.157840 ACAGATCGATTGCTACACAGTACA 59.842 41.667 0.00 0.00 0.00 2.90
748 789 4.673441 ACAGATCGATTGCTACACAGTAC 58.327 43.478 0.00 0.00 0.00 2.73
749 790 4.983671 ACAGATCGATTGCTACACAGTA 57.016 40.909 0.00 0.00 0.00 2.74
750 791 3.876274 ACAGATCGATTGCTACACAGT 57.124 42.857 0.00 0.00 0.00 3.55
751 792 5.565638 CGTATACAGATCGATTGCTACACAG 59.434 44.000 0.00 0.00 0.00 3.66
1520 1580 1.478916 GCTTGACCACCCTCTCTAGAC 59.521 57.143 0.00 0.00 0.00 2.59
1844 1905 2.148687 GACTTGCTCTGCAGTGTCG 58.851 57.895 14.67 6.58 40.61 4.35
2233 2295 0.671251 GGCAATGAACACGGAACCAA 59.329 50.000 0.00 0.00 0.00 3.67
2240 2302 6.363577 ACATCTAATTAGGCAATGAACACG 57.636 37.500 15.82 0.00 0.00 4.49
2304 2371 4.436183 GCAATGCTTTCTTCTCTACCGAAC 60.436 45.833 0.00 0.00 0.00 3.95
2621 2698 3.372954 GTCCTATCATTCGGAACAGACG 58.627 50.000 0.00 0.00 0.00 4.18
2639 2716 7.860872 GTCCATATCAAAATATCCAAAACGTCC 59.139 37.037 0.00 0.00 0.00 4.79
2653 2730 8.014070 TCAGTCCGTATTAGTCCATATCAAAA 57.986 34.615 0.00 0.00 0.00 2.44
2657 2734 7.545965 CCATTTCAGTCCGTATTAGTCCATATC 59.454 40.741 0.00 0.00 0.00 1.63
2675 2753 9.757227 TTTAGTTTATTTGTTCACCCATTTCAG 57.243 29.630 0.00 0.00 0.00 3.02
2683 2761 9.744468 AGACATGTTTTAGTTTATTTGTTCACC 57.256 29.630 0.00 0.00 0.00 4.02
2695 2773 9.383519 CAGTCCATATGTAGACATGTTTTAGTT 57.616 33.333 12.76 0.00 37.15 2.24
2737 2815 6.372931 TGGTCCCTCCATTCCAAAATATAAG 58.627 40.000 0.00 0.00 41.93 1.73
2761 2839 9.920946 AATGAACATACACAAATATACTCCCTT 57.079 29.630 0.00 0.00 0.00 3.95
2791 2876 4.296044 AGAGGGGAAGAAATCAAAAGGGAT 59.704 41.667 0.00 0.00 0.00 3.85
2793 2878 4.053009 AGAGGGGAAGAAATCAAAAGGG 57.947 45.455 0.00 0.00 0.00 3.95
2808 2893 5.636903 TCAATCTTTGGAGAATAGAGGGG 57.363 43.478 0.00 0.00 35.07 4.79
3012 3100 3.781079 TTTACATATGCAAGCACTGGC 57.219 42.857 1.58 0.00 41.61 4.85
3013 3101 5.097529 CAGTTTTACATATGCAAGCACTGG 58.902 41.667 15.95 0.00 0.00 4.00
3059 3149 7.712264 TCAACAGTTTTGCTTCCAAATTATG 57.288 32.000 0.00 0.00 40.40 1.90


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

AutoCloner maintained by Alex Coulton.