Multiple sequence alignment - TraesCS7B01G043100

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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 TraesCS7B01G043100 chr7B 100.000 4089 0 0 1 4089 42779885 42775797 0.000000e+00 7552.0
1 TraesCS7B01G043100 chr7B 81.350 563 91 9 2262 2811 643339900 643340461 2.900000e-121 446.0
2 TraesCS7B01G043100 chr7B 77.953 254 38 10 1642 1883 643339349 643339596 4.260000e-30 143.0
3 TraesCS7B01G043100 chr7B 98.113 53 1 0 1 53 747447103 747447155 4.350000e-15 93.5
4 TraesCS7B01G043100 chr7B 95.000 40 2 0 51 90 713282783 713282822 3.410000e-06 63.9
5 TraesCS7B01G043100 chr7B 91.304 46 3 1 41 86 30202066 30202110 1.230000e-05 62.1
6 TraesCS7B01G043100 chr7D 95.479 3340 120 12 214 3534 91809276 91812603 0.000000e+00 5302.0
7 TraesCS7B01G043100 chr7D 85.603 514 41 10 3595 4089 91812909 91813408 3.650000e-140 508.0
8 TraesCS7B01G043100 chr7D 82.771 563 83 9 2262 2811 579142646 579143207 1.320000e-134 490.0
9 TraesCS7B01G043100 chr7D 91.111 135 7 3 89 222 91808456 91808586 1.170000e-40 178.0
10 TraesCS7B01G043100 chr7D 77.606 259 40 10 1642 1888 579142086 579142338 1.530000e-29 141.0
11 TraesCS7B01G043100 chr7A 96.348 2574 74 5 650 3211 93487834 93490399 0.000000e+00 4215.0
12 TraesCS7B01G043100 chr7A 91.958 858 59 5 3240 4089 93490683 93491538 0.000000e+00 1194.0
13 TraesCS7B01G043100 chr7A 90.446 314 22 2 519 828 93475191 93475500 1.370000e-109 407.0
14 TraesCS7B01G043100 chr7A 85.417 336 21 13 214 536 93487195 93487515 1.420000e-84 324.0
15 TraesCS7B01G043100 chr7A 89.671 213 13 5 214 424 93460834 93461039 3.130000e-66 263.0
16 TraesCS7B01G043100 chr5A 81.541 558 98 3 2260 2813 567782269 567782825 4.820000e-124 455.0
17 TraesCS7B01G043100 chr5A 76.240 766 126 33 1175 1903 567781223 567781969 5.030000e-94 355.0
18 TraesCS7B01G043100 chr5A 72.658 1046 200 55 1167 2156 567896526 567897541 6.740000e-68 268.0
19 TraesCS7B01G043100 chr5A 91.304 46 3 1 41 86 272142870 272142914 1.230000e-05 62.1
20 TraesCS7B01G043100 chr5D 74.113 1043 190 50 1167 2156 449014967 449015982 1.400000e-94 357.0
21 TraesCS7B01G043100 chr3D 79.371 509 91 9 2333 2829 598465199 598464693 3.030000e-91 346.0
22 TraesCS7B01G043100 chr3D 79.958 474 90 3 2333 2802 571706793 571707265 1.090000e-90 344.0
23 TraesCS7B01G043100 chr6D 79.290 507 94 7 2333 2829 63716787 63716282 1.090000e-90 344.0
24 TraesCS7B01G043100 chr5B 74.711 779 134 37 1167 1903 549082876 549082119 5.170000e-74 289.0
25 TraesCS7B01G043100 chr6B 81.065 169 24 8 2340 2504 213398917 213399081 1.190000e-25 128.0
26 TraesCS7B01G043100 chr6B 98.077 52 1 0 1 52 72316923 72316974 1.570000e-14 91.6
27 TraesCS7B01G043100 chr6B 98.077 52 1 0 1 52 72319716 72319767 1.570000e-14 91.6
28 TraesCS7B01G043100 chr6B 98.077 52 1 0 1 52 72322516 72322567 1.570000e-14 91.6
29 TraesCS7B01G043100 chr6B 94.915 59 2 1 1 58 72328109 72328167 1.570000e-14 91.6
30 TraesCS7B01G043100 chr2B 98.113 53 1 0 1 53 184668468 184668416 4.350000e-15 93.5
31 TraesCS7B01G043100 chr2B 93.182 44 2 1 50 93 504240761 504240719 3.410000e-06 63.9
32 TraesCS7B01G043100 chr2B 90.000 50 3 2 41 90 723130516 723130563 3.410000e-06 63.9
33 TraesCS7B01G043100 chr2B 92.857 42 3 0 51 92 44110043 44110002 1.230000e-05 62.1
34 TraesCS7B01G043100 chrUn 98.077 52 1 0 1 52 357719647 357719596 1.570000e-14 91.6
35 TraesCS7B01G043100 chrUn 98.077 52 1 0 1 52 358531401 358531350 1.570000e-14 91.6
36 TraesCS7B01G043100 chrUn 95.000 40 1 1 51 90 41388877 41388839 1.230000e-05 62.1
37 TraesCS7B01G043100 chr1B 96.429 56 1 1 1 56 374015923 374015977 1.570000e-14 91.6
38 TraesCS7B01G043100 chr1D 97.436 39 1 0 1266 1304 487351026 487351064 2.640000e-07 67.6
39 TraesCS7B01G043100 chr1D 100.000 28 0 0 1673 1700 345375572 345375599 7.000000e-03 52.8
40 TraesCS7B01G043100 chr2D 90.000 50 3 2 41 90 636480569 636480616 3.410000e-06 63.9
41 TraesCS7B01G043100 chr3B 94.872 39 2 0 1266 1304 59464143 59464181 1.230000e-05 62.1
42 TraesCS7B01G043100 chr1A 91.304 46 3 1 41 86 590350106 590350150 1.230000e-05 62.1
43 TraesCS7B01G043100 chr1A 100.000 28 0 0 1673 1700 445503080 445503107 7.000000e-03 52.8


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 TraesCS7B01G043100 chr7B 42775797 42779885 4088 True 7552.0 7552 100.0000 1 4089 1 chr7B.!!$R1 4088
1 TraesCS7B01G043100 chr7B 643339349 643340461 1112 False 294.5 446 79.6515 1642 2811 2 chr7B.!!$F4 1169
2 TraesCS7B01G043100 chr7D 91808456 91813408 4952 False 1996.0 5302 90.7310 89 4089 3 chr7D.!!$F1 4000
3 TraesCS7B01G043100 chr7D 579142086 579143207 1121 False 315.5 490 80.1885 1642 2811 2 chr7D.!!$F2 1169
4 TraesCS7B01G043100 chr7A 93487195 93491538 4343 False 1911.0 4215 91.2410 214 4089 3 chr7A.!!$F3 3875
5 TraesCS7B01G043100 chr5A 567781223 567782825 1602 False 405.0 455 78.8905 1175 2813 2 chr5A.!!$F3 1638
6 TraesCS7B01G043100 chr5A 567896526 567897541 1015 False 268.0 268 72.6580 1167 2156 1 chr5A.!!$F2 989
7 TraesCS7B01G043100 chr5D 449014967 449015982 1015 False 357.0 357 74.1130 1167 2156 1 chr5D.!!$F1 989
8 TraesCS7B01G043100 chr3D 598464693 598465199 506 True 346.0 346 79.3710 2333 2829 1 chr3D.!!$R1 496
9 TraesCS7B01G043100 chr6D 63716282 63716787 505 True 344.0 344 79.2900 2333 2829 1 chr6D.!!$R1 496
10 TraesCS7B01G043100 chr5B 549082119 549082876 757 True 289.0 289 74.7110 1167 1903 1 chr5B.!!$R1 736

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
23 24 0.316841 CTAATCGCTGAGGAGCCTCC 59.683 60.0 13.69 1.26 42.91 4.30 F
1127 2063 0.179089 CTCCGATCAAGAGGGCAGTG 60.179 60.0 2.42 0.00 0.00 3.66 F
1723 2686 0.321671 CACTCTTCCTCCTCCGCAAA 59.678 55.0 0.00 0.00 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 2458 0.179148 CGTCGACGACCATCATCCAA 60.179 55.000 33.35 0.0 43.02 3.53 R
2257 3292 0.689080 ACGGCACCATGATCTCCTCT 60.689 55.000 0.00 0.0 0.00 3.69 R
3476 4791 1.555533 CTCCCTAACTCGGCCTTTTCT 59.444 52.381 0.00 0.0 0.00 2.52 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 0.673437 AGCTCTAATCGCTGAGGAGC 59.327 55.000 15.50 15.50 46.54 4.70
20 21 0.319469 GCTCTAATCGCTGAGGAGCC 60.319 60.000 0.00 0.00 42.91 4.70
21 22 1.327303 CTCTAATCGCTGAGGAGCCT 58.673 55.000 0.00 0.00 42.91 4.58
22 23 1.269448 CTCTAATCGCTGAGGAGCCTC 59.731 57.143 9.61 9.61 42.91 4.70
23 24 0.316841 CTAATCGCTGAGGAGCCTCC 59.683 60.000 13.69 1.26 42.91 4.30
32 33 2.191641 GGAGCCTCCTGCATCCAC 59.808 66.667 2.64 0.00 44.83 4.02
33 34 2.373707 GGAGCCTCCTGCATCCACT 61.374 63.158 2.64 0.00 44.83 4.00
34 35 1.145819 GAGCCTCCTGCATCCACTC 59.854 63.158 0.00 0.00 44.83 3.51
35 36 2.191641 GCCTCCTGCATCCACTCC 59.808 66.667 0.00 0.00 40.77 3.85
36 37 2.373707 GCCTCCTGCATCCACTCCT 61.374 63.158 0.00 0.00 40.77 3.69
37 38 1.828768 CCTCCTGCATCCACTCCTC 59.171 63.158 0.00 0.00 0.00 3.71
38 39 0.690411 CCTCCTGCATCCACTCCTCT 60.690 60.000 0.00 0.00 0.00 3.69
39 40 0.752054 CTCCTGCATCCACTCCTCTC 59.248 60.000 0.00 0.00 0.00 3.20
40 41 0.337773 TCCTGCATCCACTCCTCTCT 59.662 55.000 0.00 0.00 0.00 3.10
41 42 1.202330 CCTGCATCCACTCCTCTCTT 58.798 55.000 0.00 0.00 0.00 2.85
42 43 2.023984 TCCTGCATCCACTCCTCTCTTA 60.024 50.000 0.00 0.00 0.00 2.10
43 44 2.971330 CCTGCATCCACTCCTCTCTTAT 59.029 50.000 0.00 0.00 0.00 1.73
44 45 3.390639 CCTGCATCCACTCCTCTCTTATT 59.609 47.826 0.00 0.00 0.00 1.40
45 46 4.141528 CCTGCATCCACTCCTCTCTTATTT 60.142 45.833 0.00 0.00 0.00 1.40
46 47 5.435291 CTGCATCCACTCCTCTCTTATTTT 58.565 41.667 0.00 0.00 0.00 1.82
47 48 5.819991 TGCATCCACTCCTCTCTTATTTTT 58.180 37.500 0.00 0.00 0.00 1.94
48 49 5.649395 TGCATCCACTCCTCTCTTATTTTTG 59.351 40.000 0.00 0.00 0.00 2.44
49 50 5.067023 GCATCCACTCCTCTCTTATTTTTGG 59.933 44.000 0.00 0.00 0.00 3.28
50 51 6.418101 CATCCACTCCTCTCTTATTTTTGGA 58.582 40.000 0.00 0.00 35.17 3.53
51 52 6.642733 TCCACTCCTCTCTTATTTTTGGAT 57.357 37.500 0.00 0.00 0.00 3.41
52 53 6.418101 TCCACTCCTCTCTTATTTTTGGATG 58.582 40.000 0.00 0.00 0.00 3.51
53 54 6.215431 TCCACTCCTCTCTTATTTTTGGATGA 59.785 38.462 0.00 0.00 0.00 2.92
54 55 7.059156 CCACTCCTCTCTTATTTTTGGATGAT 58.941 38.462 0.00 0.00 0.00 2.45
55 56 8.213679 CCACTCCTCTCTTATTTTTGGATGATA 58.786 37.037 0.00 0.00 0.00 2.15
56 57 9.050601 CACTCCTCTCTTATTTTTGGATGATAC 57.949 37.037 0.00 0.00 0.00 2.24
57 58 7.928706 ACTCCTCTCTTATTTTTGGATGATACG 59.071 37.037 0.00 0.00 0.00 3.06
58 59 8.018537 TCCTCTCTTATTTTTGGATGATACGA 57.981 34.615 0.00 0.00 0.00 3.43
59 60 8.482943 TCCTCTCTTATTTTTGGATGATACGAA 58.517 33.333 0.00 0.00 0.00 3.85
60 61 9.277783 CCTCTCTTATTTTTGGATGATACGAAT 57.722 33.333 0.00 0.00 0.00 3.34
62 63 9.830975 TCTCTTATTTTTGGATGATACGAATGA 57.169 29.630 0.00 0.00 0.00 2.57
64 65 9.830975 TCTTATTTTTGGATGATACGAATGAGA 57.169 29.630 0.00 0.00 0.00 3.27
65 66 9.869844 CTTATTTTTGGATGATACGAATGAGAC 57.130 33.333 0.00 0.00 0.00 3.36
66 67 7.864108 ATTTTTGGATGATACGAATGAGACA 57.136 32.000 0.00 0.00 0.00 3.41
67 68 6.662414 TTTTGGATGATACGAATGAGACAC 57.338 37.500 0.00 0.00 0.00 3.67
68 69 5.337578 TTGGATGATACGAATGAGACACA 57.662 39.130 0.00 0.00 0.00 3.72
69 70 5.535753 TGGATGATACGAATGAGACACAT 57.464 39.130 0.00 0.00 41.45 3.21
70 71 6.648879 TGGATGATACGAATGAGACACATA 57.351 37.500 0.00 0.00 38.38 2.29
71 72 7.232118 TGGATGATACGAATGAGACACATAT 57.768 36.000 0.00 0.00 38.38 1.78
72 73 7.670364 TGGATGATACGAATGAGACACATATT 58.330 34.615 0.00 0.00 38.38 1.28
73 74 8.802267 TGGATGATACGAATGAGACACATATTA 58.198 33.333 0.00 0.00 38.38 0.98
74 75 9.077674 GGATGATACGAATGAGACACATATTAC 57.922 37.037 0.00 0.00 38.38 1.89
75 76 8.988064 ATGATACGAATGAGACACATATTACC 57.012 34.615 0.00 0.00 38.38 2.85
76 77 7.947282 TGATACGAATGAGACACATATTACCA 58.053 34.615 0.00 0.00 38.38 3.25
77 78 8.585018 TGATACGAATGAGACACATATTACCAT 58.415 33.333 0.00 0.00 38.38 3.55
78 79 8.763049 ATACGAATGAGACACATATTACCATG 57.237 34.615 0.00 0.00 38.38 3.66
79 80 5.466728 ACGAATGAGACACATATTACCATGC 59.533 40.000 0.00 0.00 38.38 4.06
80 81 5.466393 CGAATGAGACACATATTACCATGCA 59.534 40.000 0.00 0.00 38.38 3.96
81 82 6.018016 CGAATGAGACACATATTACCATGCAA 60.018 38.462 0.00 0.00 38.38 4.08
82 83 7.467131 CGAATGAGACACATATTACCATGCAAA 60.467 37.037 0.00 0.00 38.38 3.68
83 84 7.643569 ATGAGACACATATTACCATGCAAAA 57.356 32.000 0.00 0.00 37.46 2.44
84 85 7.459795 TGAGACACATATTACCATGCAAAAA 57.540 32.000 0.00 0.00 0.00 1.94
130 132 3.879295 CACTCTGTGACTTTCCATGTGTT 59.121 43.478 0.00 0.00 35.23 3.32
142 144 7.136119 ACTTTCCATGTGTTTGTATTTGTACG 58.864 34.615 0.00 0.00 0.00 3.67
144 146 5.064558 TCCATGTGTTTGTATTTGTACGGT 58.935 37.500 0.00 0.00 0.00 4.83
145 147 5.049336 TCCATGTGTTTGTATTTGTACGGTG 60.049 40.000 0.00 0.00 0.00 4.94
146 148 5.278071 CCATGTGTTTGTATTTGTACGGTGT 60.278 40.000 0.00 0.00 0.00 4.16
147 149 5.814764 TGTGTTTGTATTTGTACGGTGTT 57.185 34.783 0.00 0.00 0.00 3.32
269 970 6.875948 TCGGATGAAGAAAGTTCATTGAAA 57.124 33.333 0.00 0.00 39.08 2.69
327 1028 7.040823 GGATCATAGAATTTTGGTCACCAGATC 60.041 40.741 0.00 2.48 33.81 2.75
329 1030 3.701664 AGAATTTTGGTCACCAGATCCC 58.298 45.455 0.00 0.00 33.81 3.85
330 1031 3.334881 AGAATTTTGGTCACCAGATCCCT 59.665 43.478 0.00 0.00 33.81 4.20
331 1032 4.540099 AGAATTTTGGTCACCAGATCCCTA 59.460 41.667 0.00 0.00 33.81 3.53
332 1033 4.510167 ATTTTGGTCACCAGATCCCTAG 57.490 45.455 0.00 0.00 33.81 3.02
344 1045 4.582656 CCAGATCCCTAGCTATAGAATCCG 59.417 50.000 3.21 0.00 0.00 4.18
346 1047 5.067153 CAGATCCCTAGCTATAGAATCCGTG 59.933 48.000 3.21 0.00 0.00 4.94
454 1166 7.659799 GCACTACTCTCTACTCTCTCATCAATA 59.340 40.741 0.00 0.00 0.00 1.90
557 1337 5.749596 TGACATCTCAATCGTGTGTTTTT 57.250 34.783 0.00 0.00 0.00 1.94
578 1358 5.452078 TTCCTGTTCCTATGTTTTGCAAG 57.548 39.130 0.00 0.00 0.00 4.01
585 1365 3.826157 TCCTATGTTTTGCAAGTTCCTGG 59.174 43.478 0.00 0.35 0.00 4.45
607 1387 0.636101 TGCAATCCAAATAGGCCCCT 59.364 50.000 0.00 0.00 37.29 4.79
608 1388 1.856259 TGCAATCCAAATAGGCCCCTA 59.144 47.619 0.00 0.00 37.29 3.53
609 1389 2.246067 TGCAATCCAAATAGGCCCCTAA 59.754 45.455 0.00 0.00 37.29 2.69
610 1390 3.116784 TGCAATCCAAATAGGCCCCTAAT 60.117 43.478 0.00 0.00 37.29 1.73
659 1581 7.384660 TGTGACTTTTATGCCATCATTGTTTTC 59.615 33.333 0.00 0.00 34.22 2.29
818 1740 4.586001 AGCAAGAGACAAAACATGAATGGT 59.414 37.500 0.00 0.00 0.00 3.55
849 1771 7.595130 AGAAGAGCGTATTCCAAATTTTCAAAC 59.405 33.333 0.00 0.00 0.00 2.93
862 1787 4.803098 TTTTCAAACGAAAAGAACCCCA 57.197 36.364 0.00 0.00 37.44 4.96
863 1788 4.803098 TTTCAAACGAAAAGAACCCCAA 57.197 36.364 0.00 0.00 29.44 4.12
900 1825 1.585261 TCGATCGCGACATCAACCG 60.585 57.895 12.93 6.82 42.51 4.44
939 1864 0.609151 TCCCACGTTCTTATCGCCAA 59.391 50.000 0.00 0.00 0.00 4.52
1045 1981 1.218047 GCATGGTCGTGGCTAGTGA 59.782 57.895 0.00 0.00 0.00 3.41
1126 2062 1.965754 GCTCCGATCAAGAGGGCAGT 61.966 60.000 10.82 0.00 0.00 4.40
1127 2063 0.179089 CTCCGATCAAGAGGGCAGTG 60.179 60.000 2.42 0.00 0.00 3.66
1128 2064 1.153289 CCGATCAAGAGGGCAGTGG 60.153 63.158 0.00 0.00 0.00 4.00
1129 2065 1.817099 CGATCAAGAGGGCAGTGGC 60.817 63.158 8.47 8.47 40.13 5.01
1130 2066 1.300963 GATCAAGAGGGCAGTGGCA 59.699 57.895 19.48 0.00 43.71 4.92
1131 2067 0.747283 GATCAAGAGGGCAGTGGCAG 60.747 60.000 19.48 2.73 43.71 4.85
1369 2311 0.892755 ACGAGATGGAGCGGTACAAA 59.107 50.000 2.34 0.00 0.00 2.83
1705 2668 0.614697 TGCTCGAGAACCAGATCCCA 60.615 55.000 18.75 0.00 0.00 4.37
1723 2686 0.321671 CACTCTTCCTCCTCCGCAAA 59.678 55.000 0.00 0.00 0.00 3.68
2942 3998 2.798283 GACATAATTGGCATGCATGTGC 59.202 45.455 26.79 15.96 44.31 4.57
3070 4126 7.540745 GCCATTGGTTTGTAAACATACTAACTG 59.459 37.037 4.26 5.53 40.63 3.16
3168 4224 5.391312 AAAGATTTGAAATCTCGGTTGGG 57.609 39.130 19.66 0.00 0.00 4.12
3211 4267 1.216710 GCTCCGTGCTCTAGTTGCT 59.783 57.895 10.68 0.00 38.95 3.91
3254 4565 4.219944 GGGGACAATTAGGGTTTCAAACTC 59.780 45.833 0.00 0.00 0.00 3.01
3258 4573 6.373495 GGACAATTAGGGTTTCAAACTCGTAT 59.627 38.462 0.00 0.00 36.83 3.06
3262 4577 7.754851 ATTAGGGTTTCAAACTCGTATTGTT 57.245 32.000 0.00 0.00 36.83 2.83
3289 4604 6.259387 CGGTTATAAGATAGTGTTGGGGTTTC 59.741 42.308 0.00 0.00 0.00 2.78
3294 4609 3.263425 AGATAGTGTTGGGGTTTCGACAT 59.737 43.478 0.00 0.00 34.02 3.06
3356 4671 0.105760 AGAGGGATGGTCGATGCTCT 60.106 55.000 0.00 0.00 0.00 4.09
3379 4694 3.194005 CCGTAGAGGCAACATGGTAAT 57.806 47.619 0.00 0.00 41.41 1.89
3453 4768 4.285775 TGTAGGTTGTGATGAGGTCATTGA 59.714 41.667 0.00 0.00 39.48 2.57
3457 4772 4.946157 GGTTGTGATGAGGTCATTGAGAAT 59.054 41.667 0.00 0.00 39.48 2.40
3476 4791 7.632861 TGAGAATGAGGATGATTGGAAGTAAA 58.367 34.615 0.00 0.00 0.00 2.01
3485 4800 5.722021 TGATTGGAAGTAAAGAAAAGGCC 57.278 39.130 0.00 0.00 0.00 5.19
3498 4813 1.880941 AAAGGCCGAGTTAGGGAGAT 58.119 50.000 0.00 0.00 0.00 2.75
3504 4819 1.688772 CGAGTTAGGGAGATTCGGGA 58.311 55.000 0.00 0.00 0.00 5.14
3519 4834 3.173668 TCGGGATTATGGTTGTCGAAG 57.826 47.619 0.00 0.00 0.00 3.79
3536 4851 4.335594 GTCGAAGGGAAGGAAATATTGTGG 59.664 45.833 0.00 0.00 0.00 4.17
3564 4879 7.708322 GCATTCGATATAGATTCATTGGCTAGA 59.292 37.037 0.00 0.00 0.00 2.43
3572 4887 1.860641 TCATTGGCTAGACGGGAAGA 58.139 50.000 0.00 0.00 0.00 2.87
3592 4907 2.154074 GGAGGGGAGGTGTGGTTGT 61.154 63.158 0.00 0.00 0.00 3.32
3602 5162 2.301296 AGGTGTGGTTGTGAGATCTCAG 59.699 50.000 25.76 0.00 40.75 3.35
3603 5163 2.037772 GGTGTGGTTGTGAGATCTCAGT 59.962 50.000 25.76 0.00 40.75 3.41
3605 5165 2.029918 TGTGGTTGTGAGATCTCAGTCG 60.030 50.000 25.76 0.00 40.75 4.18
3610 5170 4.424626 GTTGTGAGATCTCAGTCGCAATA 58.575 43.478 25.76 3.75 43.19 1.90
3611 5171 4.718940 TGTGAGATCTCAGTCGCAATAA 57.281 40.909 25.76 0.00 40.75 1.40
3743 5313 2.582636 ACTGGAGAAATGGGCCATACTT 59.417 45.455 21.54 11.71 0.00 2.24
3744 5314 3.785887 ACTGGAGAAATGGGCCATACTTA 59.214 43.478 21.54 13.43 0.00 2.24
3753 5323 2.632996 TGGGCCATACTTAAGATCTCCG 59.367 50.000 10.09 0.00 0.00 4.63
3799 5369 6.012658 TCAACATTAACATGAGAACCAAGC 57.987 37.500 0.00 0.00 34.11 4.01
3817 5387 7.775053 ACCAAGCATCCTTTATGTAGAAAAA 57.225 32.000 0.00 0.00 37.93 1.94
3927 5501 8.750515 TGATCCACATTGCATAATTTAGAGAA 57.249 30.769 0.00 0.00 0.00 2.87
3959 5533 2.510800 TCACCATCATCACCACCATCAT 59.489 45.455 0.00 0.00 0.00 2.45
4067 5651 7.936584 TGTTCTGGATTTTCGTACAAAAGAAT 58.063 30.769 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.419586 AGGAGGCTCCTCAGCGATTAGA 62.420 54.545 30.46 0.00 45.66 2.10
4 5 2.095769 AGGAGGCTCCTCAGCGATTAG 61.096 57.143 30.46 0.00 45.66 1.73
5 6 0.105964 AGGAGGCTCCTCAGCGATTA 60.106 55.000 30.46 0.00 45.66 1.75
6 7 1.382420 AGGAGGCTCCTCAGCGATT 60.382 57.895 30.46 6.00 45.66 3.34
7 8 2.132996 CAGGAGGCTCCTCAGCGAT 61.133 63.158 33.04 8.36 45.66 4.58
8 9 2.757508 CAGGAGGCTCCTCAGCGA 60.758 66.667 33.04 0.00 45.66 4.93
9 10 4.527583 GCAGGAGGCTCCTCAGCG 62.528 72.222 33.04 22.09 45.66 5.18
10 11 2.663423 GATGCAGGAGGCTCCTCAGC 62.663 65.000 33.04 31.04 45.66 4.26
11 12 1.446791 GATGCAGGAGGCTCCTCAG 59.553 63.158 33.04 23.18 45.66 3.35
12 13 2.068821 GGATGCAGGAGGCTCCTCA 61.069 63.158 33.04 29.29 45.66 3.86
13 14 2.068821 TGGATGCAGGAGGCTCCTC 61.069 63.158 33.04 25.19 45.66 3.71
15 16 2.191641 GTGGATGCAGGAGGCTCC 59.808 66.667 26.42 26.42 45.15 4.70
16 17 1.145819 GAGTGGATGCAGGAGGCTC 59.854 63.158 5.78 5.78 45.15 4.70
17 18 2.373707 GGAGTGGATGCAGGAGGCT 61.374 63.158 0.00 0.00 45.15 4.58
18 19 2.191641 GGAGTGGATGCAGGAGGC 59.808 66.667 0.00 0.00 45.13 4.70
19 20 0.690411 AGAGGAGTGGATGCAGGAGG 60.690 60.000 0.00 0.00 0.00 4.30
20 21 0.752054 GAGAGGAGTGGATGCAGGAG 59.248 60.000 0.00 0.00 0.00 3.69
21 22 0.337773 AGAGAGGAGTGGATGCAGGA 59.662 55.000 0.00 0.00 0.00 3.86
22 23 1.202330 AAGAGAGGAGTGGATGCAGG 58.798 55.000 0.00 0.00 0.00 4.85
23 24 4.686191 AATAAGAGAGGAGTGGATGCAG 57.314 45.455 0.00 0.00 0.00 4.41
24 25 5.441718 AAAATAAGAGAGGAGTGGATGCA 57.558 39.130 0.00 0.00 0.00 3.96
25 26 5.067023 CCAAAAATAAGAGAGGAGTGGATGC 59.933 44.000 0.00 0.00 0.00 3.91
26 27 6.418101 TCCAAAAATAAGAGAGGAGTGGATG 58.582 40.000 0.00 0.00 0.00 3.51
27 28 6.642733 TCCAAAAATAAGAGAGGAGTGGAT 57.357 37.500 0.00 0.00 0.00 3.41
28 29 6.215431 TCATCCAAAAATAAGAGAGGAGTGGA 59.785 38.462 0.00 0.00 37.07 4.02
29 30 6.418101 TCATCCAAAAATAAGAGAGGAGTGG 58.582 40.000 0.00 0.00 0.00 4.00
30 31 9.050601 GTATCATCCAAAAATAAGAGAGGAGTG 57.949 37.037 0.00 0.00 0.00 3.51
31 32 7.928706 CGTATCATCCAAAAATAAGAGAGGAGT 59.071 37.037 0.00 0.00 0.00 3.85
32 33 8.144478 TCGTATCATCCAAAAATAAGAGAGGAG 58.856 37.037 0.00 0.00 0.00 3.69
33 34 8.018537 TCGTATCATCCAAAAATAAGAGAGGA 57.981 34.615 0.00 0.00 0.00 3.71
34 35 8.662781 TTCGTATCATCCAAAAATAAGAGAGG 57.337 34.615 0.00 0.00 0.00 3.69
36 37 9.830975 TCATTCGTATCATCCAAAAATAAGAGA 57.169 29.630 0.00 0.00 0.00 3.10
38 39 9.830975 TCTCATTCGTATCATCCAAAAATAAGA 57.169 29.630 0.00 0.00 0.00 2.10
39 40 9.869844 GTCTCATTCGTATCATCCAAAAATAAG 57.130 33.333 0.00 0.00 0.00 1.73
40 41 9.389755 TGTCTCATTCGTATCATCCAAAAATAA 57.610 29.630 0.00 0.00 0.00 1.40
41 42 8.826710 GTGTCTCATTCGTATCATCCAAAAATA 58.173 33.333 0.00 0.00 0.00 1.40
42 43 7.336679 TGTGTCTCATTCGTATCATCCAAAAAT 59.663 33.333 0.00 0.00 0.00 1.82
43 44 6.652900 TGTGTCTCATTCGTATCATCCAAAAA 59.347 34.615 0.00 0.00 0.00 1.94
44 45 6.169800 TGTGTCTCATTCGTATCATCCAAAA 58.830 36.000 0.00 0.00 0.00 2.44
45 46 5.729510 TGTGTCTCATTCGTATCATCCAAA 58.270 37.500 0.00 0.00 0.00 3.28
46 47 5.337578 TGTGTCTCATTCGTATCATCCAA 57.662 39.130 0.00 0.00 0.00 3.53
47 48 5.535753 ATGTGTCTCATTCGTATCATCCA 57.464 39.130 0.00 0.00 32.08 3.41
48 49 9.077674 GTAATATGTGTCTCATTCGTATCATCC 57.922 37.037 0.00 0.00 37.91 3.51
49 50 9.077674 GGTAATATGTGTCTCATTCGTATCATC 57.922 37.037 0.00 0.00 37.91 2.92
50 51 8.585018 TGGTAATATGTGTCTCATTCGTATCAT 58.415 33.333 0.00 0.00 37.91 2.45
51 52 7.947282 TGGTAATATGTGTCTCATTCGTATCA 58.053 34.615 0.00 0.00 37.91 2.15
52 53 8.864024 CATGGTAATATGTGTCTCATTCGTATC 58.136 37.037 0.00 0.00 37.91 2.24
53 54 7.331934 GCATGGTAATATGTGTCTCATTCGTAT 59.668 37.037 0.00 0.00 37.91 3.06
54 55 6.645003 GCATGGTAATATGTGTCTCATTCGTA 59.355 38.462 0.00 0.00 37.91 3.43
55 56 5.466728 GCATGGTAATATGTGTCTCATTCGT 59.533 40.000 0.00 0.00 37.91 3.85
56 57 5.466393 TGCATGGTAATATGTGTCTCATTCG 59.534 40.000 0.00 0.00 37.91 3.34
57 58 6.866010 TGCATGGTAATATGTGTCTCATTC 57.134 37.500 0.00 0.00 37.91 2.67
58 59 7.643569 TTTGCATGGTAATATGTGTCTCATT 57.356 32.000 0.00 0.00 37.91 2.57
59 60 7.643569 TTTTGCATGGTAATATGTGTCTCAT 57.356 32.000 0.00 0.00 40.25 2.90
60 61 7.459795 TTTTTGCATGGTAATATGTGTCTCA 57.540 32.000 0.00 0.00 0.00 3.27
81 82 4.822896 TGGGAAGTACACACGCTTATTTTT 59.177 37.500 0.00 0.00 0.00 1.94
82 83 4.391155 TGGGAAGTACACACGCTTATTTT 58.609 39.130 0.00 0.00 0.00 1.82
83 84 4.010667 TGGGAAGTACACACGCTTATTT 57.989 40.909 0.00 0.00 0.00 1.40
84 85 3.688694 TGGGAAGTACACACGCTTATT 57.311 42.857 0.00 0.00 0.00 1.40
85 86 3.688694 TTGGGAAGTACACACGCTTAT 57.311 42.857 0.00 0.00 0.00 1.73
86 87 3.472283 TTTGGGAAGTACACACGCTTA 57.528 42.857 0.00 0.00 0.00 3.09
87 88 2.335316 TTTGGGAAGTACACACGCTT 57.665 45.000 0.00 0.00 0.00 4.68
88 89 2.224426 TGATTTGGGAAGTACACACGCT 60.224 45.455 0.00 0.00 0.00 5.07
89 90 2.095919 GTGATTTGGGAAGTACACACGC 60.096 50.000 0.00 0.00 0.00 5.34
90 91 3.399330 AGTGATTTGGGAAGTACACACG 58.601 45.455 0.00 0.00 33.18 4.49
130 132 6.432607 TGAACAAACACCGTACAAATACAA 57.567 33.333 0.00 0.00 0.00 2.41
142 144 9.349145 GGTAATACACATTAATGAACAAACACC 57.651 33.333 22.16 14.70 0.00 4.16
327 1028 4.337145 AGACACGGATTCTATAGCTAGGG 58.663 47.826 0.00 0.00 0.00 3.53
329 1030 6.459024 GGCATAGACACGGATTCTATAGCTAG 60.459 46.154 0.00 0.00 35.01 3.42
330 1031 5.357314 GGCATAGACACGGATTCTATAGCTA 59.643 44.000 0.00 0.00 35.01 3.32
331 1032 4.158764 GGCATAGACACGGATTCTATAGCT 59.841 45.833 15.55 0.00 35.01 3.32
332 1033 4.425520 GGCATAGACACGGATTCTATAGC 58.574 47.826 0.00 8.28 35.01 2.97
344 1045 7.817418 TTATGGAATAAAAGGGCATAGACAC 57.183 36.000 0.00 0.00 35.49 3.67
371 1072 9.632807 GCTTAGAGATCATGTTAAGATTCGTAT 57.367 33.333 0.00 0.00 0.00 3.06
372 1073 8.851145 AGCTTAGAGATCATGTTAAGATTCGTA 58.149 33.333 0.00 0.00 0.00 3.43
373 1074 7.721402 AGCTTAGAGATCATGTTAAGATTCGT 58.279 34.615 0.00 0.00 0.00 3.85
557 1337 4.469657 ACTTGCAAAACATAGGAACAGGA 58.530 39.130 0.00 0.00 0.00 3.86
578 1358 3.959535 TTTGGATTGCATTCCAGGAAC 57.040 42.857 25.03 0.00 46.22 3.62
585 1365 2.037641 GGGGCCTATTTGGATTGCATTC 59.962 50.000 0.84 0.00 38.35 2.67
607 1387 4.654262 GTGACACTCCCTCCATCCTTATTA 59.346 45.833 0.00 0.00 0.00 0.98
608 1388 3.456277 GTGACACTCCCTCCATCCTTATT 59.544 47.826 0.00 0.00 0.00 1.40
609 1389 3.041946 GTGACACTCCCTCCATCCTTAT 58.958 50.000 0.00 0.00 0.00 1.73
610 1390 2.044492 AGTGACACTCCCTCCATCCTTA 59.956 50.000 1.07 0.00 0.00 2.69
659 1581 4.766375 ACAAGTTAATCATGGGTCGGTAG 58.234 43.478 0.00 0.00 0.00 3.18
720 1642 2.046217 GAGGGGACAGCCGGAAAC 60.046 66.667 5.05 0.00 33.83 2.78
725 1647 3.234630 TTTCGTGAGGGGACAGCCG 62.235 63.158 0.00 0.00 33.83 5.52
818 1740 6.817765 ATTTGGAATACGCTCTTCTTTTGA 57.182 33.333 0.00 0.00 0.00 2.69
870 1795 1.621107 GCGATCGAACGTACTCCAAA 58.379 50.000 21.57 0.00 35.59 3.28
911 1836 6.475207 CGATAAGAACGTGGGAATTAACAAG 58.525 40.000 0.00 0.00 0.00 3.16
939 1864 2.488545 GTGGATAGCGATCGATGGTAGT 59.511 50.000 21.57 0.00 32.28 2.73
1059 1995 2.684843 GCTAGGTGTGCAGTGCAGC 61.685 63.158 20.42 13.70 40.08 5.25
1516 2458 0.179148 CGTCGACGACCATCATCCAA 60.179 55.000 33.35 0.00 43.02 3.53
1705 2668 1.056660 TTTTGCGGAGGAGGAAGAGT 58.943 50.000 0.00 0.00 0.00 3.24
1723 2686 2.042831 GCACTGCGGCTCAAGGATT 61.043 57.895 0.00 0.00 0.00 3.01
1771 2746 2.047274 CCGGTGACCATGCTCGTT 60.047 61.111 1.11 0.00 0.00 3.85
2248 3283 1.252175 TGATCTCCTCTATCAGCGGC 58.748 55.000 0.00 0.00 0.00 6.53
2257 3292 0.689080 ACGGCACCATGATCTCCTCT 60.689 55.000 0.00 0.00 0.00 3.69
2305 3340 1.073199 GGTTGTGGCTGCTACCTGT 59.927 57.895 13.76 0.00 32.76 4.00
2508 3552 4.373116 GCAGAAGGGCCACGTCGA 62.373 66.667 6.18 0.00 32.45 4.20
2542 3588 3.217242 GCTCTTCAAGCGGTTCAGA 57.783 52.632 0.00 1.02 42.21 3.27
2942 3998 4.388469 CGAAAATACCAATGCCAAACCAAG 59.612 41.667 0.00 0.00 0.00 3.61
3168 4224 5.591877 ACCAAGAAATTGCATGGTCTAGATC 59.408 40.000 7.56 0.00 42.36 2.75
3211 4267 1.939974 GCAGGTGCGTCATCTATCAA 58.060 50.000 0.00 0.00 0.00 2.57
3238 4549 7.590279 CAACAATACGAGTTTGAAACCCTAAT 58.410 34.615 4.14 0.00 0.00 1.73
3254 4565 7.168637 ACACTATCTTATAACCGCAACAATACG 59.831 37.037 0.00 0.00 0.00 3.06
3258 4573 6.092944 CCAACACTATCTTATAACCGCAACAA 59.907 38.462 0.00 0.00 0.00 2.83
3262 4577 4.443739 CCCCAACACTATCTTATAACCGCA 60.444 45.833 0.00 0.00 0.00 5.69
3420 4735 2.637382 TCACAACCTACAATGCTCTCCA 59.363 45.455 0.00 0.00 0.00 3.86
3453 4768 7.865820 TCTTTACTTCCAATCATCCTCATTCT 58.134 34.615 0.00 0.00 0.00 2.40
3457 4772 7.394359 CCTTTTCTTTACTTCCAATCATCCTCA 59.606 37.037 0.00 0.00 0.00 3.86
3476 4791 1.555533 CTCCCTAACTCGGCCTTTTCT 59.444 52.381 0.00 0.00 0.00 2.52
3485 4800 1.688772 TCCCGAATCTCCCTAACTCG 58.311 55.000 0.00 0.00 0.00 4.18
3498 4813 3.527533 CTTCGACAACCATAATCCCGAA 58.472 45.455 0.00 0.00 34.17 4.30
3504 4819 3.521937 TCCTTCCCTTCGACAACCATAAT 59.478 43.478 0.00 0.00 0.00 1.28
3519 4834 2.039418 GCCCCACAATATTTCCTTCCC 58.961 52.381 0.00 0.00 0.00 3.97
3536 4851 5.220931 GCCAATGAATCTATATCGAATGCCC 60.221 44.000 0.00 0.00 0.00 5.36
3564 4879 3.281787 TCCCCTCCCTCTTCCCGT 61.282 66.667 0.00 0.00 0.00 5.28
3572 4887 3.128767 AACCACACCTCCCCTCCCT 62.129 63.158 0.00 0.00 0.00 4.20
3592 4907 7.550551 AGAAATTTTATTGCGACTGAGATCTCA 59.449 33.333 23.75 23.75 38.06 3.27
3715 5285 2.751806 GCCCATTTCTCCAGTTCTCTTG 59.248 50.000 0.00 0.00 0.00 3.02
3743 5313 0.669077 GCGCCTTCTCGGAGATCTTA 59.331 55.000 8.81 0.00 33.93 2.10
3744 5314 1.439644 GCGCCTTCTCGGAGATCTT 59.560 57.895 8.81 0.00 33.93 2.40
3753 5323 1.227002 CCGACTAAGGCGCCTTCTC 60.227 63.158 43.34 33.38 37.47 2.87
3874 5444 2.291209 TCTCATGTGGGCACAAATGT 57.709 45.000 18.74 0.00 45.41 2.71
3875 5445 3.446161 AGAATCTCATGTGGGCACAAATG 59.554 43.478 13.38 13.38 45.41 2.32
3876 5446 3.705051 AGAATCTCATGTGGGCACAAAT 58.295 40.909 0.00 0.00 45.41 2.32
3877 5447 3.159213 AGAATCTCATGTGGGCACAAA 57.841 42.857 0.00 0.00 45.41 2.83
3878 5448 2.885135 AGAATCTCATGTGGGCACAA 57.115 45.000 0.00 0.00 45.41 3.33
3951 5525 5.107337 CGATTTAAGGATGACGATGATGGTG 60.107 44.000 0.00 0.00 0.00 4.17
3959 5533 3.130516 AGTGAGCGATTTAAGGATGACGA 59.869 43.478 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.