Multiple sequence alignment - TraesCS7A01G191900

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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 TraesCS7A01G191900 chr7A 100.000 3809 0 0 1 3809 149863723 149859915 0.000000e+00 7035.0
1 TraesCS7A01G191900 chr7A 94.706 1889 81 8 735 2608 150021606 150023490 0.000000e+00 2916.0
2 TraesCS7A01G191900 chr7A 89.007 282 25 4 2620 2901 150023537 150023812 1.010000e-90 344.0
3 TraesCS7A01G191900 chr7D 93.626 2369 120 16 557 2901 149086223 149083862 0.000000e+00 3509.0
4 TraesCS7A01G191900 chr7D 89.050 2621 171 48 301 2898 149180634 149183161 0.000000e+00 3144.0
5 TraesCS7A01G191900 chr7D 94.406 143 6 1 8 148 149090986 149090844 6.410000e-53 219.0
6 TraesCS7A01G191900 chr7D 92.568 148 7 2 2896 3042 149083838 149083694 3.860000e-50 209.0
7 TraesCS7A01G191900 chr7D 84.541 207 10 13 147 339 149086676 149086478 6.500000e-43 185.0
8 TraesCS7A01G191900 chr7D 91.406 128 6 3 2896 3022 149183700 149183823 1.820000e-38 171.0
9 TraesCS7A01G191900 chr7D 93.478 92 6 0 2810 2901 149183585 149183676 1.850000e-28 137.0
10 TraesCS7A01G191900 chr7B 93.176 1656 87 14 965 2608 111942407 111944048 0.000000e+00 2409.0
11 TraesCS7A01G191900 chr7B 86.326 841 58 29 98 903 111941377 111942195 0.000000e+00 863.0
12 TraesCS7A01G191900 chr7B 87.943 282 28 3 2620 2901 111944097 111944372 1.020000e-85 327.0
13 TraesCS7A01G191900 chr2B 84.248 1841 265 18 1002 2824 232291327 232289494 0.000000e+00 1770.0
14 TraesCS7A01G191900 chr2B 84.988 1612 223 14 1002 2600 232261507 232263112 0.000000e+00 1618.0
15 TraesCS7A01G191900 chr2D 81.742 2158 316 59 771 2880 165485590 165483463 0.000000e+00 1731.0
16 TraesCS7A01G191900 chr3A 96.741 767 23 1 3045 3809 697759975 697760741 0.000000e+00 1277.0
17 TraesCS7A01G191900 chr3A 96.466 764 27 0 3046 3809 40944376 40943613 0.000000e+00 1262.0
18 TraesCS7A01G191900 chr3A 83.696 1196 182 9 1623 2807 608195755 608194562 0.000000e+00 1116.0
19 TraesCS7A01G191900 chr6A 96.623 770 23 3 3043 3809 2932390 2931621 0.000000e+00 1275.0
20 TraesCS7A01G191900 chr6A 96.615 768 24 2 3043 3809 555424080 555424846 0.000000e+00 1273.0
21 TraesCS7A01G191900 chr6A 96.340 765 28 0 3045 3809 596336588 596337352 0.000000e+00 1258.0
22 TraesCS7A01G191900 chr6A 95.958 767 27 3 3045 3809 401680803 401681567 0.000000e+00 1242.0
23 TraesCS7A01G191900 chr4B 96.359 769 24 2 3045 3809 364664587 364663819 0.000000e+00 1262.0
24 TraesCS7A01G191900 chr4A 96.471 765 25 1 3047 3809 584463979 584464743 0.000000e+00 1262.0
25 TraesCS7A01G191900 chr4A 79.775 89 8 3 631 711 631621073 631620987 5.320000e-04 56.5
26 TraesCS7A01G191900 chr5A 96.349 767 27 1 3044 3809 548656607 548655841 0.000000e+00 1260.0
27 TraesCS7A01G191900 chr2A 84.375 1216 172 11 1623 2824 185364107 185362896 0.000000e+00 1177.0
28 TraesCS7A01G191900 chr2A 82.160 1222 180 20 1623 2835 185269423 185270615 0.000000e+00 1014.0
29 TraesCS7A01G191900 chr2A 90.280 535 52 0 1002 1536 185364736 185364202 0.000000e+00 701.0
30 TraesCS7A01G191900 chr3D 84.341 1207 165 12 1623 2807 464808957 464807753 0.000000e+00 1160.0
31 TraesCS7A01G191900 chr3B 83.609 1208 173 20 1623 2807 618155763 618154558 0.000000e+00 1110.0
32 TraesCS7A01G191900 chr5B 85.237 779 89 17 766 1536 679310910 679311670 0.000000e+00 778.0
33 TraesCS7A01G191900 chr5B 94.872 39 2 0 670 708 679310785 679310823 1.140000e-05 62.1


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 TraesCS7A01G191900 chr7A 149859915 149863723 3808 True 7035.000000 7035 100.000000 1 3809 1 chr7A.!!$R1 3808
1 TraesCS7A01G191900 chr7A 150021606 150023812 2206 False 1630.000000 2916 91.856500 735 2901 2 chr7A.!!$F1 2166
2 TraesCS7A01G191900 chr7D 149083694 149086676 2982 True 1301.000000 3509 90.245000 147 3042 3 chr7D.!!$R2 2895
3 TraesCS7A01G191900 chr7D 149180634 149183823 3189 False 1150.666667 3144 91.311333 301 3022 3 chr7D.!!$F1 2721
4 TraesCS7A01G191900 chr7B 111941377 111944372 2995 False 1199.666667 2409 89.148333 98 2901 3 chr7B.!!$F1 2803
5 TraesCS7A01G191900 chr2B 232289494 232291327 1833 True 1770.000000 1770 84.248000 1002 2824 1 chr2B.!!$R1 1822
6 TraesCS7A01G191900 chr2B 232261507 232263112 1605 False 1618.000000 1618 84.988000 1002 2600 1 chr2B.!!$F1 1598
7 TraesCS7A01G191900 chr2D 165483463 165485590 2127 True 1731.000000 1731 81.742000 771 2880 1 chr2D.!!$R1 2109
8 TraesCS7A01G191900 chr3A 697759975 697760741 766 False 1277.000000 1277 96.741000 3045 3809 1 chr3A.!!$F1 764
9 TraesCS7A01G191900 chr3A 40943613 40944376 763 True 1262.000000 1262 96.466000 3046 3809 1 chr3A.!!$R1 763
10 TraesCS7A01G191900 chr3A 608194562 608195755 1193 True 1116.000000 1116 83.696000 1623 2807 1 chr3A.!!$R2 1184
11 TraesCS7A01G191900 chr6A 2931621 2932390 769 True 1275.000000 1275 96.623000 3043 3809 1 chr6A.!!$R1 766
12 TraesCS7A01G191900 chr6A 555424080 555424846 766 False 1273.000000 1273 96.615000 3043 3809 1 chr6A.!!$F2 766
13 TraesCS7A01G191900 chr6A 596336588 596337352 764 False 1258.000000 1258 96.340000 3045 3809 1 chr6A.!!$F3 764
14 TraesCS7A01G191900 chr6A 401680803 401681567 764 False 1242.000000 1242 95.958000 3045 3809 1 chr6A.!!$F1 764
15 TraesCS7A01G191900 chr4B 364663819 364664587 768 True 1262.000000 1262 96.359000 3045 3809 1 chr4B.!!$R1 764
16 TraesCS7A01G191900 chr4A 584463979 584464743 764 False 1262.000000 1262 96.471000 3047 3809 1 chr4A.!!$F1 762
17 TraesCS7A01G191900 chr5A 548655841 548656607 766 True 1260.000000 1260 96.349000 3044 3809 1 chr5A.!!$R1 765
18 TraesCS7A01G191900 chr2A 185269423 185270615 1192 False 1014.000000 1014 82.160000 1623 2835 1 chr2A.!!$F1 1212
19 TraesCS7A01G191900 chr2A 185362896 185364736 1840 True 939.000000 1177 87.327500 1002 2824 2 chr2A.!!$R1 1822
20 TraesCS7A01G191900 chr3D 464807753 464808957 1204 True 1160.000000 1160 84.341000 1623 2807 1 chr3D.!!$R1 1184
21 TraesCS7A01G191900 chr3B 618154558 618155763 1205 True 1110.000000 1110 83.609000 1623 2807 1 chr3B.!!$R1 1184
22 TraesCS7A01G191900 chr5B 679310785 679311670 885 False 420.050000 778 90.054500 670 1536 2 chr5B.!!$F1 866

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
130 131 0.030908 GGAGCGTAGGAGGACGAATG 59.969 60.0 0.00 0.0 45.82 2.67 F
920 1065 0.108992 CTTCTGCATGCATTTGCGGT 60.109 50.0 22.97 0.0 46.81 5.68 F
1908 2254 0.814010 GCACCTTCGACAACACCACT 60.814 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2434 0.468226 AGAAGAACGGCTTGTCCACA 59.532 50.0 0.0 0.0 36.83 4.17 R
2222 2572 0.539669 TGAAGTGCGACTGGAGGAGA 60.540 55.0 0.0 0.0 0.00 3.71 R
3068 4023 0.107993 CTTTCTGATGCAGAGGCCGA 60.108 55.0 0.0 0.0 41.75 5.54 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
28 29 9.923143 ATATGAGATATCCATGCAAAAATTGTG 57.077 29.630 13.77 0.00 0.00 3.33
29 30 7.407393 TGAGATATCCATGCAAAAATTGTGA 57.593 32.000 0.00 0.00 0.00 3.58
30 31 7.838884 TGAGATATCCATGCAAAAATTGTGAA 58.161 30.769 0.00 0.00 0.00 3.18
31 32 7.977293 TGAGATATCCATGCAAAAATTGTGAAG 59.023 33.333 0.00 0.00 0.00 3.02
32 33 7.844009 AGATATCCATGCAAAAATTGTGAAGT 58.156 30.769 0.00 0.00 0.00 3.01
33 34 7.762615 AGATATCCATGCAAAAATTGTGAAGTG 59.237 33.333 0.00 0.00 0.00 3.16
34 35 5.273674 TCCATGCAAAAATTGTGAAGTGA 57.726 34.783 0.00 0.00 0.00 3.41
35 36 5.856156 TCCATGCAAAAATTGTGAAGTGAT 58.144 33.333 0.00 0.00 0.00 3.06
36 37 5.697178 TCCATGCAAAAATTGTGAAGTGATG 59.303 36.000 0.00 0.00 0.00 3.07
37 38 5.697178 CCATGCAAAAATTGTGAAGTGATGA 59.303 36.000 0.00 0.00 0.00 2.92
38 39 6.370442 CCATGCAAAAATTGTGAAGTGATGAT 59.630 34.615 0.00 0.00 0.00 2.45
39 40 6.772770 TGCAAAAATTGTGAAGTGATGATG 57.227 33.333 0.00 0.00 0.00 3.07
40 41 5.177881 TGCAAAAATTGTGAAGTGATGATGC 59.822 36.000 0.00 0.00 0.00 3.91
41 42 5.177881 GCAAAAATTGTGAAGTGATGATGCA 59.822 36.000 0.00 0.00 0.00 3.96
42 43 6.292973 GCAAAAATTGTGAAGTGATGATGCAA 60.293 34.615 0.00 0.00 0.00 4.08
43 44 7.631822 CAAAAATTGTGAAGTGATGATGCAAA 58.368 30.769 0.00 0.00 0.00 3.68
44 45 6.774354 AAATTGTGAAGTGATGATGCAAAC 57.226 33.333 0.00 0.00 0.00 2.93
45 46 3.541071 TGTGAAGTGATGATGCAAACG 57.459 42.857 0.00 0.00 0.00 3.60
46 47 2.877786 TGTGAAGTGATGATGCAAACGT 59.122 40.909 0.00 0.00 0.00 3.99
47 48 3.314913 TGTGAAGTGATGATGCAAACGTT 59.685 39.130 0.00 0.00 0.00 3.99
48 49 3.665409 GTGAAGTGATGATGCAAACGTTG 59.335 43.478 0.00 0.00 0.00 4.10
49 50 2.995466 AGTGATGATGCAAACGTTGG 57.005 45.000 0.00 0.00 0.00 3.77
50 51 2.229792 AGTGATGATGCAAACGTTGGT 58.770 42.857 0.00 0.00 0.00 3.67
51 52 2.030893 AGTGATGATGCAAACGTTGGTG 60.031 45.455 0.00 0.00 0.00 4.17
52 53 1.952990 TGATGATGCAAACGTTGGTGT 59.047 42.857 0.00 0.00 0.00 4.16
53 54 3.058570 GTGATGATGCAAACGTTGGTGTA 60.059 43.478 0.00 0.00 0.00 2.90
54 55 3.058570 TGATGATGCAAACGTTGGTGTAC 60.059 43.478 0.00 0.00 0.00 2.90
55 56 2.566913 TGATGCAAACGTTGGTGTACT 58.433 42.857 0.00 0.00 0.00 2.73
56 57 2.289274 TGATGCAAACGTTGGTGTACTG 59.711 45.455 0.00 0.00 0.00 2.74
57 58 2.025589 TGCAAACGTTGGTGTACTGA 57.974 45.000 0.00 0.00 0.00 3.41
58 59 2.357075 TGCAAACGTTGGTGTACTGAA 58.643 42.857 0.00 0.00 0.00 3.02
59 60 2.096174 TGCAAACGTTGGTGTACTGAAC 59.904 45.455 0.00 0.00 0.00 3.18
60 61 2.096174 GCAAACGTTGGTGTACTGAACA 59.904 45.455 0.00 0.00 35.06 3.18
61 62 3.242936 GCAAACGTTGGTGTACTGAACAT 60.243 43.478 0.00 0.00 41.10 2.71
62 63 4.278858 CAAACGTTGGTGTACTGAACATG 58.721 43.478 0.00 0.00 41.10 3.21
63 64 3.462483 ACGTTGGTGTACTGAACATGA 57.538 42.857 0.00 0.00 41.10 3.07
64 65 3.799366 ACGTTGGTGTACTGAACATGAA 58.201 40.909 0.00 0.00 41.10 2.57
65 66 3.558418 ACGTTGGTGTACTGAACATGAAC 59.442 43.478 0.00 0.00 41.10 3.18
66 67 3.558006 CGTTGGTGTACTGAACATGAACA 59.442 43.478 0.00 0.00 41.10 3.18
67 68 4.213270 CGTTGGTGTACTGAACATGAACAT 59.787 41.667 0.00 0.00 41.10 2.71
68 69 5.407084 CGTTGGTGTACTGAACATGAACATA 59.593 40.000 0.00 0.00 41.10 2.29
69 70 6.401047 CGTTGGTGTACTGAACATGAACATAG 60.401 42.308 0.00 0.00 41.10 2.23
70 71 6.109156 TGGTGTACTGAACATGAACATAGT 57.891 37.500 0.00 0.00 41.10 2.12
71 72 5.931724 TGGTGTACTGAACATGAACATAGTG 59.068 40.000 0.00 0.00 41.10 2.74
72 73 5.932303 GGTGTACTGAACATGAACATAGTGT 59.068 40.000 0.00 0.00 41.10 3.55
73 74 7.094631 GGTGTACTGAACATGAACATAGTGTA 58.905 38.462 0.00 0.00 41.10 2.90
74 75 7.764443 GGTGTACTGAACATGAACATAGTGTAT 59.236 37.037 0.00 0.00 41.10 2.29
75 76 9.151471 GTGTACTGAACATGAACATAGTGTATT 57.849 33.333 0.00 0.00 41.10 1.89
76 77 9.366216 TGTACTGAACATGAACATAGTGTATTC 57.634 33.333 0.00 0.00 31.43 1.75
77 78 7.525688 ACTGAACATGAACATAGTGTATTCG 57.474 36.000 0.00 0.00 0.00 3.34
78 79 7.097192 ACTGAACATGAACATAGTGTATTCGT 58.903 34.615 0.00 0.00 0.00 3.85
79 80 7.063426 ACTGAACATGAACATAGTGTATTCGTG 59.937 37.037 0.00 0.00 42.52 4.35
83 84 8.766000 ACATGAACATAGTGTATTCGTGTTAA 57.234 30.769 0.00 0.00 45.75 2.01
84 85 9.210329 ACATGAACATAGTGTATTCGTGTTAAA 57.790 29.630 0.00 0.00 45.75 1.52
85 86 9.472995 CATGAACATAGTGTATTCGTGTTAAAC 57.527 33.333 0.00 0.00 35.53 2.01
86 87 8.590719 TGAACATAGTGTATTCGTGTTAAACA 57.409 30.769 0.00 0.00 33.55 2.83
87 88 9.043079 TGAACATAGTGTATTCGTGTTAAACAA 57.957 29.630 0.00 0.00 33.55 2.83
88 89 9.866936 GAACATAGTGTATTCGTGTTAAACAAA 57.133 29.630 0.00 0.00 33.55 2.83
125 126 0.966370 ACACTGGAGCGTAGGAGGAC 60.966 60.000 0.00 0.00 0.00 3.85
130 131 0.030908 GGAGCGTAGGAGGACGAATG 59.969 60.000 0.00 0.00 45.82 2.67
132 133 1.141019 GCGTAGGAGGACGAATGCA 59.859 57.895 0.00 0.00 45.82 3.96
135 136 1.135083 CGTAGGAGGACGAATGCAAGT 60.135 52.381 0.00 0.00 45.82 3.16
136 137 2.098607 CGTAGGAGGACGAATGCAAGTA 59.901 50.000 0.00 0.00 45.82 2.24
137 138 2.969628 AGGAGGACGAATGCAAGTAG 57.030 50.000 0.00 0.00 0.00 2.57
138 139 2.180276 AGGAGGACGAATGCAAGTAGT 58.820 47.619 0.00 0.00 0.00 2.73
139 140 3.362706 AGGAGGACGAATGCAAGTAGTA 58.637 45.455 0.00 0.00 0.00 1.82
141 142 3.130693 GGAGGACGAATGCAAGTAGTAGT 59.869 47.826 0.00 0.00 0.00 2.73
142 143 4.337555 GGAGGACGAATGCAAGTAGTAGTA 59.662 45.833 0.00 0.00 0.00 1.82
145 146 7.094291 GGAGGACGAATGCAAGTAGTAGTATAT 60.094 40.741 0.00 0.00 0.00 0.86
225 232 5.687166 AGATAGGAGTACTAGCTAGCGAT 57.313 43.478 20.91 6.28 46.09 4.58
226 233 5.424757 AGATAGGAGTACTAGCTAGCGATG 58.575 45.833 20.91 6.11 46.09 3.84
261 277 3.802685 GTGGTGACAGTGACTAACAGAAC 59.197 47.826 0.00 0.00 44.46 3.01
279 295 6.951971 ACAGAACTAACTATCCATCTTGCTT 58.048 36.000 0.00 0.00 0.00 3.91
281 297 7.550906 ACAGAACTAACTATCCATCTTGCTTTC 59.449 37.037 0.00 0.00 0.00 2.62
282 298 7.768120 CAGAACTAACTATCCATCTTGCTTTCT 59.232 37.037 0.00 0.00 0.00 2.52
294 310 7.884877 TCCATCTTGCTTTCTTTTATCTCTTCA 59.115 33.333 0.00 0.00 0.00 3.02
313 333 8.325787 TCTCTTCATGGGCTAACTAATTAAACA 58.674 33.333 0.00 0.00 0.00 2.83
314 334 8.276252 TCTTCATGGGCTAACTAATTAAACAC 57.724 34.615 0.00 0.00 0.00 3.32
340 360 6.465439 TGGAGTATCATACAAGTGATCGTT 57.535 37.500 0.00 0.00 39.45 3.85
341 361 6.273071 TGGAGTATCATACAAGTGATCGTTG 58.727 40.000 0.00 6.16 39.45 4.10
342 362 6.096282 TGGAGTATCATACAAGTGATCGTTGA 59.904 38.462 13.15 1.83 39.45 3.18
423 484 8.249327 CAGGCATGCAATCTATACTAAACTAG 57.751 38.462 21.36 0.00 0.00 2.57
425 486 8.310382 AGGCATGCAATCTATACTAAACTAGAG 58.690 37.037 21.36 0.00 0.00 2.43
426 487 7.547370 GGCATGCAATCTATACTAAACTAGAGG 59.453 40.741 21.36 0.00 0.00 3.69
427 488 8.091449 GCATGCAATCTATACTAAACTAGAGGT 58.909 37.037 14.21 0.00 0.00 3.85
447 518 0.817654 AATCGATCGAGTGCACTGGA 59.182 50.000 30.14 30.14 35.23 3.86
455 526 0.807667 GAGTGCACTGGATGTAGCCG 60.808 60.000 27.27 0.00 0.00 5.52
561 655 2.893682 ATTGCCGCCTAAGCCTGTCC 62.894 60.000 0.00 0.00 34.57 4.02
586 680 0.599558 GCGGCCATTCATGCATGTAT 59.400 50.000 25.43 18.99 0.00 2.29
652 746 0.110486 TTTGGGACCTCCTGTTCAGC 59.890 55.000 0.00 0.00 36.20 4.26
653 747 1.059584 TTGGGACCTCCTGTTCAGCA 61.060 55.000 0.00 0.00 36.20 4.41
671 765 6.136541 TCAGCACATATATATACTCAGCCG 57.863 41.667 0.00 0.00 0.00 5.52
711 806 3.125656 TCATTCCACCCTCCATCATCTT 58.874 45.455 0.00 0.00 0.00 2.40
760 878 6.169094 TCAAGATACAGAAGCTCAAAAGGAG 58.831 40.000 0.00 0.00 46.93 3.69
788 912 2.349167 ATGGCCATGGCTATCTCCTA 57.651 50.000 34.70 12.26 37.83 2.94
916 1061 3.793797 TCCATCTTCTGCATGCATTTG 57.206 42.857 22.97 10.20 0.00 2.32
920 1065 0.108992 CTTCTGCATGCATTTGCGGT 60.109 50.000 22.97 0.00 46.81 5.68
990 1287 5.740569 TCGTCTTGATCGAAACCTTAATACG 59.259 40.000 0.00 0.00 34.36 3.06
1050 1351 1.745115 GTGCGGCACCAAGAGCATA 60.745 57.895 22.19 0.00 41.88 3.14
1395 1696 1.966451 GCACAAAGAGGTCCCGGTG 60.966 63.158 0.00 0.00 0.00 4.94
1518 1819 2.746375 CCCTGGGCCGCTCTACAAT 61.746 63.158 0.00 0.00 0.00 2.71
1680 2026 0.955428 ACATGTTGCGCCTCGTCAAT 60.955 50.000 4.18 0.00 0.00 2.57
1722 2068 0.824109 TCTTCTCCGTCGCCAATCAT 59.176 50.000 0.00 0.00 0.00 2.45
1737 2083 3.250744 CAATCATACACTCACCGTCGTT 58.749 45.455 0.00 0.00 0.00 3.85
1908 2254 0.814010 GCACCTTCGACAACACCACT 60.814 55.000 0.00 0.00 0.00 4.00
1914 2260 4.438346 GACAACACCACTGTCGCT 57.562 55.556 0.00 0.00 34.32 4.93
1982 2328 1.569479 GACAAGGACTTGCCGCTGTC 61.569 60.000 11.73 8.07 44.03 3.51
2099 2445 1.961277 CACGGTCTGTGGACAAGCC 60.961 63.158 3.65 0.00 45.21 4.35
2201 2551 1.787847 GGCCATGAACAACGTCTCG 59.212 57.895 0.00 0.00 0.00 4.04
2222 2572 4.021925 GTGCTCCCTTCCACGGCT 62.022 66.667 0.00 0.00 0.00 5.52
2432 2782 1.381327 CTTCGAGAGCCACCCCCTA 60.381 63.158 0.00 0.00 0.00 3.53
2883 3806 1.134699 TGCGATTGATGTCTCCTGTCC 60.135 52.381 0.00 0.00 0.00 4.02
2942 3895 8.898761 TCTTTCACTTGATTAGCAGTTTGTAAA 58.101 29.630 0.00 0.00 0.00 2.01
2943 3896 9.515020 CTTTCACTTGATTAGCAGTTTGTAAAA 57.485 29.630 0.00 0.00 0.00 1.52
2944 3897 9.862371 TTTCACTTGATTAGCAGTTTGTAAAAA 57.138 25.926 0.00 0.00 0.00 1.94
2945 3898 8.850454 TCACTTGATTAGCAGTTTGTAAAAAC 57.150 30.769 0.00 0.00 0.00 2.43
2975 3928 4.839668 TTTGAGGGGTGTTGAATAAACG 57.160 40.909 0.00 0.00 42.10 3.60
3031 3984 1.205460 TGGAAGGGACCCTGGTAAGC 61.205 60.000 15.76 0.00 32.13 3.09
3039 3992 1.227853 CCCTGGTAAGCGCCATACC 60.228 63.158 25.51 25.51 42.62 2.73
3042 3995 0.178068 CTGGTAAGCGCCATACCTGT 59.822 55.000 29.51 0.00 42.73 4.00
3043 3996 0.616371 TGGTAAGCGCCATACCTGTT 59.384 50.000 29.51 9.88 42.73 3.16
3136 4091 7.309499 CCAAATAAAGTAGTGCCAACATGGTTA 60.309 37.037 0.00 0.00 40.46 2.85
3234 4191 1.441732 GAAAAGACGCCACAACCGGT 61.442 55.000 0.00 0.00 0.00 5.28
3364 4321 4.804420 ATGCTCCCTGGCCTCCGA 62.804 66.667 3.32 0.00 0.00 4.55
3380 4337 1.384989 CCGACTGGGTGAGTAGCGAT 61.385 60.000 0.00 0.00 33.83 4.58
3474 4431 4.491676 CAAATCATTTCTGCAAGTCCAGG 58.508 43.478 0.00 0.00 33.64 4.45
3590 4547 8.840321 ACAGAATTCGGTGGATTGATATTAAAG 58.160 33.333 10.60 0.00 0.00 1.85
3607 4564 0.981183 AAGGCAATGTGGACCGTCTA 59.019 50.000 0.00 0.00 0.00 2.59
3628 4585 1.600023 CAAAGTACCTTGGCCAACGA 58.400 50.000 16.05 0.00 0.00 3.85
3664 4621 4.104086 AGGTGTTTGATAGTCTCATCCCA 58.896 43.478 0.00 0.00 32.72 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.014070 TCACAATTTTTGCATGGATATCTCAT 57.986 30.769 2.05 2.02 0.00 2.90
6 7 7.977853 ACTTCACAATTTTTGCATGGATATCTC 59.022 33.333 2.05 0.00 0.00 2.75
7 8 7.762615 CACTTCACAATTTTTGCATGGATATCT 59.237 33.333 2.05 0.00 0.00 1.98
8 9 7.760794 TCACTTCACAATTTTTGCATGGATATC 59.239 33.333 0.00 0.00 0.00 1.63
10 11 6.990798 TCACTTCACAATTTTTGCATGGATA 58.009 32.000 0.00 0.00 0.00 2.59
11 12 5.856156 TCACTTCACAATTTTTGCATGGAT 58.144 33.333 0.00 0.00 0.00 3.41
12 13 5.273674 TCACTTCACAATTTTTGCATGGA 57.726 34.783 0.00 0.00 0.00 3.41
13 14 5.697178 TCATCACTTCACAATTTTTGCATGG 59.303 36.000 0.00 0.00 0.00 3.66
14 15 6.772770 TCATCACTTCACAATTTTTGCATG 57.227 33.333 0.00 0.00 0.00 4.06
15 16 6.128391 GCATCATCACTTCACAATTTTTGCAT 60.128 34.615 0.00 0.00 0.00 3.96
16 17 5.177881 GCATCATCACTTCACAATTTTTGCA 59.822 36.000 0.00 0.00 0.00 4.08
17 18 5.177881 TGCATCATCACTTCACAATTTTTGC 59.822 36.000 0.00 0.00 0.00 3.68
18 19 6.772770 TGCATCATCACTTCACAATTTTTG 57.227 33.333 0.00 0.00 0.00 2.44
19 20 7.517101 CGTTTGCATCATCACTTCACAATTTTT 60.517 33.333 0.00 0.00 0.00 1.94
20 21 6.074195 CGTTTGCATCATCACTTCACAATTTT 60.074 34.615 0.00 0.00 0.00 1.82
21 22 5.403166 CGTTTGCATCATCACTTCACAATTT 59.597 36.000 0.00 0.00 0.00 1.82
22 23 4.919168 CGTTTGCATCATCACTTCACAATT 59.081 37.500 0.00 0.00 0.00 2.32
23 24 4.022935 ACGTTTGCATCATCACTTCACAAT 60.023 37.500 0.00 0.00 0.00 2.71
24 25 3.314913 ACGTTTGCATCATCACTTCACAA 59.685 39.130 0.00 0.00 0.00 3.33
25 26 2.877786 ACGTTTGCATCATCACTTCACA 59.122 40.909 0.00 0.00 0.00 3.58
26 27 3.542712 ACGTTTGCATCATCACTTCAC 57.457 42.857 0.00 0.00 0.00 3.18
27 28 3.304592 CCAACGTTTGCATCATCACTTCA 60.305 43.478 0.00 0.00 0.00 3.02
28 29 3.236816 CCAACGTTTGCATCATCACTTC 58.763 45.455 0.00 0.00 0.00 3.01
29 30 2.622942 ACCAACGTTTGCATCATCACTT 59.377 40.909 0.00 0.00 0.00 3.16
30 31 2.030893 CACCAACGTTTGCATCATCACT 60.031 45.455 0.00 0.00 0.00 3.41
31 32 2.287547 ACACCAACGTTTGCATCATCAC 60.288 45.455 0.00 0.00 0.00 3.06
32 33 1.952990 ACACCAACGTTTGCATCATCA 59.047 42.857 0.00 0.00 0.00 3.07
33 34 2.704725 ACACCAACGTTTGCATCATC 57.295 45.000 0.00 0.00 0.00 2.92
34 35 3.058293 CAGTACACCAACGTTTGCATCAT 60.058 43.478 0.00 0.00 0.00 2.45
35 36 2.289274 CAGTACACCAACGTTTGCATCA 59.711 45.455 0.00 0.00 0.00 3.07
36 37 2.546368 TCAGTACACCAACGTTTGCATC 59.454 45.455 0.00 0.00 0.00 3.91
37 38 2.566913 TCAGTACACCAACGTTTGCAT 58.433 42.857 0.00 0.00 0.00 3.96
38 39 2.025589 TCAGTACACCAACGTTTGCA 57.974 45.000 0.00 0.00 0.00 4.08
39 40 2.096174 TGTTCAGTACACCAACGTTTGC 59.904 45.455 0.00 0.00 0.00 3.68
40 41 4.034626 TCATGTTCAGTACACCAACGTTTG 59.965 41.667 0.00 0.00 40.19 2.93
41 42 4.193090 TCATGTTCAGTACACCAACGTTT 58.807 39.130 0.00 0.00 40.19 3.60
42 43 3.799366 TCATGTTCAGTACACCAACGTT 58.201 40.909 0.00 0.00 40.19 3.99
43 44 3.462483 TCATGTTCAGTACACCAACGT 57.538 42.857 0.00 0.00 40.19 3.99
44 45 3.558006 TGTTCATGTTCAGTACACCAACG 59.442 43.478 0.00 0.00 40.19 4.10
45 46 5.689383 ATGTTCATGTTCAGTACACCAAC 57.311 39.130 0.00 0.00 40.19 3.77
46 47 6.426633 CACTATGTTCATGTTCAGTACACCAA 59.573 38.462 0.00 0.00 40.19 3.67
47 48 5.931724 CACTATGTTCATGTTCAGTACACCA 59.068 40.000 0.00 0.00 40.19 4.17
48 49 5.932303 ACACTATGTTCATGTTCAGTACACC 59.068 40.000 0.00 0.00 40.19 4.16
49 50 8.703604 ATACACTATGTTCATGTTCAGTACAC 57.296 34.615 0.00 0.00 40.19 2.90
50 51 9.366216 GAATACACTATGTTCATGTTCAGTACA 57.634 33.333 0.00 0.00 41.97 2.90
51 52 8.532341 CGAATACACTATGTTCATGTTCAGTAC 58.468 37.037 0.00 0.00 0.00 2.73
52 53 8.248253 ACGAATACACTATGTTCATGTTCAGTA 58.752 33.333 0.00 0.00 0.00 2.74
53 54 7.063426 CACGAATACACTATGTTCATGTTCAGT 59.937 37.037 0.00 0.00 0.00 3.41
54 55 7.063426 ACACGAATACACTATGTTCATGTTCAG 59.937 37.037 0.00 0.00 31.71 3.02
55 56 6.871492 ACACGAATACACTATGTTCATGTTCA 59.129 34.615 0.00 0.00 31.71 3.18
56 57 7.290857 ACACGAATACACTATGTTCATGTTC 57.709 36.000 0.00 0.00 31.71 3.18
57 58 7.667043 AACACGAATACACTATGTTCATGTT 57.333 32.000 0.00 0.00 39.20 2.71
58 59 8.766000 TTAACACGAATACACTATGTTCATGT 57.234 30.769 0.00 0.00 36.54 3.21
59 60 9.472995 GTTTAACACGAATACACTATGTTCATG 57.527 33.333 0.00 0.00 35.26 3.07
60 61 9.210329 TGTTTAACACGAATACACTATGTTCAT 57.790 29.630 0.00 0.00 35.26 2.57
61 62 8.590719 TGTTTAACACGAATACACTATGTTCA 57.409 30.769 0.00 0.00 35.26 3.18
62 63 9.866936 TTTGTTTAACACGAATACACTATGTTC 57.133 29.630 0.00 0.00 35.26 3.18
112 113 0.595310 GCATTCGTCCTCCTACGCTC 60.595 60.000 0.00 0.00 42.56 5.03
114 115 0.459585 TTGCATTCGTCCTCCTACGC 60.460 55.000 0.00 0.00 42.56 4.42
125 126 7.295930 TCGTCATATACTACTACTTGCATTCG 58.704 38.462 0.00 0.00 0.00 3.34
130 131 7.587028 GTCAGTTCGTCATATACTACTACTTGC 59.413 40.741 0.00 0.00 0.00 4.01
132 133 7.493971 ACGTCAGTTCGTCATATACTACTACTT 59.506 37.037 0.00 0.00 40.04 2.24
135 136 7.776933 AACGTCAGTTCGTCATATACTACTA 57.223 36.000 0.00 0.00 43.38 1.82
136 137 6.674694 AACGTCAGTTCGTCATATACTACT 57.325 37.500 0.00 0.00 43.38 2.57
137 138 8.119226 AGTAAACGTCAGTTCGTCATATACTAC 58.881 37.037 0.00 0.00 43.38 2.73
138 139 8.118607 CAGTAAACGTCAGTTCGTCATATACTA 58.881 37.037 0.00 0.00 43.38 1.82
139 140 6.965500 CAGTAAACGTCAGTTCGTCATATACT 59.035 38.462 0.00 0.00 43.38 2.12
141 142 5.740569 GCAGTAAACGTCAGTTCGTCATATA 59.259 40.000 0.00 0.00 43.38 0.86
142 143 4.561606 GCAGTAAACGTCAGTTCGTCATAT 59.438 41.667 0.00 0.00 43.38 1.78
145 146 2.121786 GCAGTAAACGTCAGTTCGTCA 58.878 47.619 0.00 0.00 43.38 4.35
196 203 7.988599 GCTAGCTAGTACTCCTATCTTGCTATA 59.011 40.741 21.62 0.00 39.90 1.31
197 204 6.826741 GCTAGCTAGTACTCCTATCTTGCTAT 59.173 42.308 21.62 0.00 39.90 2.97
198 205 6.174760 GCTAGCTAGTACTCCTATCTTGCTA 58.825 44.000 21.62 0.00 37.53 3.49
199 206 5.007682 GCTAGCTAGTACTCCTATCTTGCT 58.992 45.833 21.62 0.00 37.53 3.91
200 207 4.142773 CGCTAGCTAGTACTCCTATCTTGC 60.143 50.000 21.62 2.42 37.31 4.01
201 208 5.239351 TCGCTAGCTAGTACTCCTATCTTG 58.761 45.833 21.62 0.00 0.00 3.02
223 230 3.259876 TCACCACACCAACCTACTACATC 59.740 47.826 0.00 0.00 0.00 3.06
225 232 2.366266 GTCACCACACCAACCTACTACA 59.634 50.000 0.00 0.00 0.00 2.74
226 233 2.366266 TGTCACCACACCAACCTACTAC 59.634 50.000 0.00 0.00 0.00 2.73
279 295 7.633789 AGTTAGCCCATGAAGAGATAAAAGAA 58.366 34.615 0.00 0.00 0.00 2.52
281 297 8.964476 TTAGTTAGCCCATGAAGAGATAAAAG 57.036 34.615 0.00 0.00 0.00 2.27
282 298 9.920946 AATTAGTTAGCCCATGAAGAGATAAAA 57.079 29.630 0.00 0.00 0.00 1.52
287 303 8.325787 TGTTTAATTAGTTAGCCCATGAAGAGA 58.674 33.333 0.00 0.00 0.00 3.10
288 304 8.398665 GTGTTTAATTAGTTAGCCCATGAAGAG 58.601 37.037 0.00 0.00 0.00 2.85
294 310 5.065988 CAGCGTGTTTAATTAGTTAGCCCAT 59.934 40.000 0.00 0.00 0.00 4.00
313 333 3.699538 TCACTTGTATGATACTCCAGCGT 59.300 43.478 4.03 0.00 0.00 5.07
314 334 4.307443 TCACTTGTATGATACTCCAGCG 57.693 45.455 4.03 0.00 0.00 5.18
413 474 8.147058 ACTCGATCGATTACCTCTAGTTTAGTA 58.853 37.037 19.78 0.00 0.00 1.82
418 479 4.023878 GCACTCGATCGATTACCTCTAGTT 60.024 45.833 19.78 0.00 0.00 2.24
420 481 3.498777 TGCACTCGATCGATTACCTCTAG 59.501 47.826 19.78 5.96 0.00 2.43
421 482 3.250280 GTGCACTCGATCGATTACCTCTA 59.750 47.826 19.78 0.00 0.00 2.43
422 483 2.033550 GTGCACTCGATCGATTACCTCT 59.966 50.000 19.78 0.00 0.00 3.69
423 484 2.033550 AGTGCACTCGATCGATTACCTC 59.966 50.000 19.78 8.43 0.00 3.85
425 486 2.120232 CAGTGCACTCGATCGATTACC 58.880 52.381 18.64 8.16 0.00 2.85
426 487 2.120232 CCAGTGCACTCGATCGATTAC 58.880 52.381 18.64 14.36 0.00 1.89
427 488 2.021457 TCCAGTGCACTCGATCGATTA 58.979 47.619 18.64 2.46 0.00 1.75
447 518 1.026718 GCTTTGGAGTGCGGCTACAT 61.027 55.000 0.00 0.00 37.99 2.29
455 526 2.109126 CGCCCTAGCTTTGGAGTGC 61.109 63.158 5.44 1.32 36.60 4.40
561 655 3.195002 ATGAATGGCCGCACGACG 61.195 61.111 0.00 0.00 43.15 5.12
570 664 4.795268 CTTGAGATACATGCATGAATGGC 58.205 43.478 32.75 17.76 31.46 4.40
586 680 1.678635 CCGGGCCATTTGCTTGAGA 60.679 57.895 4.39 0.00 40.92 3.27
652 746 6.473778 GCACTTCGGCTGAGTATATATATGTG 59.526 42.308 5.44 2.06 0.00 3.21
653 747 6.378564 AGCACTTCGGCTGAGTATATATATGT 59.621 38.462 5.44 0.00 43.89 2.29
671 765 4.818534 TGAATGTTGAGACAAGCACTTC 57.181 40.909 0.00 0.00 39.66 3.01
711 806 1.554836 CTCTTGAGGAGCAGAGGACA 58.445 55.000 0.00 0.00 35.08 4.02
760 878 0.954452 GCCATGGCCATAGCTTGTAC 59.046 55.000 26.56 3.61 39.73 2.90
788 912 3.011517 ACGGAGCTGGAAGGCCAT 61.012 61.111 5.01 0.00 44.91 4.40
916 1061 3.103447 TCAGATCAAGATGATGACCGC 57.897 47.619 0.00 0.00 37.20 5.68
1050 1351 2.522436 TCCCCGTTCACCGTCACT 60.522 61.111 0.00 0.00 33.66 3.41
1383 1684 1.609794 GAAGACCACCGGGACCTCT 60.610 63.158 6.32 0.00 38.05 3.69
1395 1696 2.432628 CACCACTCGCCGAAGACC 60.433 66.667 0.00 0.00 0.00 3.85
1518 1819 2.611971 CGTAGTACCTTTGGCAGAGCAA 60.612 50.000 0.00 0.00 0.00 3.91
1617 1963 6.261826 CCTTCAGTTTGAAAGTGTCTGAGATT 59.738 38.462 12.07 0.00 35.73 2.40
1621 1967 4.635765 CACCTTCAGTTTGAAAGTGTCTGA 59.364 41.667 12.07 2.64 41.49 3.27
1680 2026 4.733371 TCATCGTTGAGCGCGGCA 62.733 61.111 8.83 0.83 41.07 5.69
1701 2047 1.001520 TGATTGGCGACGGAGAAGAAA 59.998 47.619 0.00 0.00 0.00 2.52
1722 2068 0.594602 CCTCAACGACGGTGAGTGTA 59.405 55.000 34.15 6.60 0.00 2.90
1737 2083 2.046988 TAGACGGCGTCGACCTCA 60.047 61.111 31.59 12.82 37.67 3.86
1908 2254 3.068064 TCGAGGATGCCAGCGACA 61.068 61.111 0.00 0.00 30.27 4.35
1914 2260 1.271856 TTTGGTACTCGAGGATGCCA 58.728 50.000 18.41 12.91 0.00 4.92
2088 2434 0.468226 AGAAGAACGGCTTGTCCACA 59.532 50.000 0.00 0.00 36.83 4.17
2099 2445 1.007336 CCCGACCGTGAAGAAGAACG 61.007 60.000 0.00 0.00 39.48 3.95
2201 2551 2.360475 GTGGAAGGGAGCACCAGC 60.360 66.667 1.58 0.00 43.89 4.85
2222 2572 0.539669 TGAAGTGCGACTGGAGGAGA 60.540 55.000 0.00 0.00 0.00 3.71
2432 2782 2.186826 GTTGAAGCCGTGCAGGTGT 61.187 57.895 5.57 0.00 43.70 4.16
2914 3867 7.196331 ACAAACTGCTAATCAAGTGAAAGAAC 58.804 34.615 0.00 0.00 0.00 3.01
2942 3895 3.317993 CACCCCTCAAAACATTCTCGTTT 59.682 43.478 0.00 0.00 40.79 3.60
2943 3896 2.884639 CACCCCTCAAAACATTCTCGTT 59.115 45.455 0.00 0.00 0.00 3.85
2944 3897 2.158667 ACACCCCTCAAAACATTCTCGT 60.159 45.455 0.00 0.00 0.00 4.18
2945 3898 2.504367 ACACCCCTCAAAACATTCTCG 58.496 47.619 0.00 0.00 0.00 4.04
3068 4023 0.107993 CTTTCTGATGCAGAGGCCGA 60.108 55.000 0.00 0.00 41.75 5.54
3234 4191 7.266905 AGTTTCCCTATCTAGTTTTAGCCAA 57.733 36.000 0.00 0.00 0.00 4.52
3272 4229 1.745232 TTGGATGGCGGTCATGTAAC 58.255 50.000 0.00 0.00 35.97 2.50
3364 4321 0.818296 GTGATCGCTACTCACCCAGT 59.182 55.000 0.00 0.00 37.61 4.00
3380 4337 1.511305 GGCTCTGATCCGTTCGTGA 59.489 57.895 0.00 0.00 0.00 4.35
3474 4431 1.593196 TGTGCTTTGCTGTGGACTAC 58.407 50.000 0.00 0.00 0.00 2.73
3590 4547 0.743345 GGTAGACGGTCCACATTGCC 60.743 60.000 8.88 0.00 0.00 4.52
3664 4621 4.803098 ACTAGGTGTAGTTTCTGCGATT 57.197 40.909 0.00 0.00 35.88 3.34


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

AutoCloner maintained by Alex Coulton.