Multiple sequence alignment - TraesCS1D01G399400

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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 TraesCS1D01G399400 chr1D 100.000 3053 0 0 1 3053 465977985 465981037 0.000000e+00 5638.0
1 TraesCS1D01G399400 chr1D 80.120 669 103 25 2304 2964 493735158 493734512 3.560000e-129 472.0
2 TraesCS1D01G399400 chr1D 100.000 31 0 0 8 38 411585442 411585472 1.180000e-04 58.4
3 TraesCS1D01G399400 chr1D 100.000 31 0 0 8 38 411706785 411706815 1.180000e-04 58.4
4 TraesCS1D01G399400 chr1D 100.000 31 0 0 8 38 411751915 411751945 1.180000e-04 58.4
5 TraesCS1D01G399400 chr1A 90.989 2497 163 25 123 2604 558320727 558323176 0.000000e+00 3308.0
6 TraesCS1D01G399400 chr1A 79.117 589 79 23 2327 2908 531021748 531022299 1.730000e-97 366.0
7 TraesCS1D01G399400 chr1A 78.777 556 82 23 2304 2840 592066556 592066018 1.050000e-89 340.0
8 TraesCS1D01G399400 chr1B 89.362 2115 126 43 117 2192 642791257 642793311 0.000000e+00 2567.0
9 TraesCS1D01G399400 chr1B 90.937 651 46 6 1620 2267 642990583 642991223 0.000000e+00 863.0
10 TraesCS1D01G399400 chr1B 86.253 742 52 18 966 1695 642802672 642803375 0.000000e+00 760.0
11 TraesCS1D01G399400 chr1B 84.733 655 72 15 117 750 642989929 642990576 5.560000e-177 630.0
12 TraesCS1D01G399400 chr1B 89.604 202 20 1 1687 1888 642809112 642809312 3.910000e-64 255.0
13 TraesCS1D01G399400 chr1B 94.253 87 2 3 15 100 642989858 642989942 2.470000e-26 130.0
14 TraesCS1D01G399400 chr1B 94.048 84 2 3 15 97 642791186 642791267 1.150000e-24 124.0
15 TraesCS1D01G399400 chr1B 87.255 102 8 3 2199 2299 642795561 642795658 8.950000e-21 111.0
16 TraesCS1D01G399400 chr1B 100.000 31 0 0 8 38 555124710 555124740 1.180000e-04 58.4
17 TraesCS1D01G399400 chr7D 80.981 673 92 25 2304 2962 138504931 138505581 4.540000e-138 501.0
18 TraesCS1D01G399400 chr7D 80.120 669 105 20 2304 2960 548906859 548906207 9.910000e-130 473.0
19 TraesCS1D01G399400 chr7D 81.435 237 28 7 1342 1578 37427962 37427742 2.420000e-41 180.0
20 TraesCS1D01G399400 chr7A 79.911 677 97 25 2304 2964 138733985 138734638 7.710000e-126 460.0
21 TraesCS1D01G399400 chr7A 78.929 560 86 22 2336 2886 679822924 679822388 4.840000e-93 351.0
22 TraesCS1D01G399400 chr5A 84.149 511 31 21 815 1317 546208422 546207954 1.670000e-122 449.0
23 TraesCS1D01G399400 chr5A 85.938 64 9 0 1 64 455480859 455480796 5.460000e-08 69.4
24 TraesCS1D01G399400 chr5B 78.806 670 110 24 2308 2963 13503151 13502500 3.640000e-114 422.0
25 TraesCS1D01G399400 chr6D 78.326 669 114 21 2306 2961 308924132 308923482 1.320000e-108 403.0
26 TraesCS1D01G399400 chr6D 77.578 611 74 28 2305 2900 83227004 83227566 8.220000e-81 311.0
27 TraesCS1D01G399400 chr4A 77.810 685 112 29 2305 2970 604028032 604027369 1.330000e-103 387.0
28 TraesCS1D01G399400 chr3D 74.672 533 87 26 2304 2825 599501565 599502060 3.110000e-45 193.0
29 TraesCS1D01G399400 chr3B 83.333 96 14 2 2870 2964 819821863 819821957 1.510000e-13 87.9
30 TraesCS1D01G399400 chr5D 78.082 146 20 7 2309 2453 487286246 487286112 7.020000e-12 82.4
31 TraesCS1D01G399400 chr7B 85.507 69 8 2 2305 2371 672410408 672410476 1.520000e-08 71.3
32 TraesCS1D01G399400 chrUn 100.000 30 0 0 9 38 319710533 319710504 4.250000e-04 56.5
33 TraesCS1D01G399400 chrUn 100.000 30 0 0 9 38 325765969 325765940 4.250000e-04 56.5
34 TraesCS1D01G399400 chr2A 100.000 30 0 0 2935 2964 673545135 673545106 4.250000e-04 56.5


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 TraesCS1D01G399400 chr1D 465977985 465981037 3052 False 5638 5638 100.000000 1 3053 1 chr1D.!!$F4 3052
1 TraesCS1D01G399400 chr1D 493734512 493735158 646 True 472 472 80.120000 2304 2964 1 chr1D.!!$R1 660
2 TraesCS1D01G399400 chr1A 558320727 558323176 2449 False 3308 3308 90.989000 123 2604 1 chr1A.!!$F2 2481
3 TraesCS1D01G399400 chr1A 531021748 531022299 551 False 366 366 79.117000 2327 2908 1 chr1A.!!$F1 581
4 TraesCS1D01G399400 chr1A 592066018 592066556 538 True 340 340 78.777000 2304 2840 1 chr1A.!!$R1 536
5 TraesCS1D01G399400 chr1B 642791186 642795658 4472 False 934 2567 90.221667 15 2299 3 chr1B.!!$F4 2284
6 TraesCS1D01G399400 chr1B 642802672 642803375 703 False 760 760 86.253000 966 1695 1 chr1B.!!$F2 729
7 TraesCS1D01G399400 chr1B 642989858 642991223 1365 False 541 863 89.974333 15 2267 3 chr1B.!!$F5 2252
8 TraesCS1D01G399400 chr7D 138504931 138505581 650 False 501 501 80.981000 2304 2962 1 chr7D.!!$F1 658
9 TraesCS1D01G399400 chr7D 548906207 548906859 652 True 473 473 80.120000 2304 2960 1 chr7D.!!$R2 656
10 TraesCS1D01G399400 chr7A 138733985 138734638 653 False 460 460 79.911000 2304 2964 1 chr7A.!!$F1 660
11 TraesCS1D01G399400 chr7A 679822388 679822924 536 True 351 351 78.929000 2336 2886 1 chr7A.!!$R1 550
12 TraesCS1D01G399400 chr5B 13502500 13503151 651 True 422 422 78.806000 2308 2963 1 chr5B.!!$R1 655
13 TraesCS1D01G399400 chr6D 308923482 308924132 650 True 403 403 78.326000 2306 2961 1 chr6D.!!$R1 655
14 TraesCS1D01G399400 chr6D 83227004 83227566 562 False 311 311 77.578000 2305 2900 1 chr6D.!!$F1 595
15 TraesCS1D01G399400 chr4A 604027369 604028032 663 True 387 387 77.810000 2305 2970 1 chr4A.!!$R1 665

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
356 365 0.595588 CGAGCCAGATAGAGCACGAT 59.404 55.0 0.0 0.0 44.29 3.73 F
1142 1203 0.031616 GAGGAGGAGGAGGATGGTGT 60.032 60.0 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 1617 1.375908 GGCTTGATGTCGAGGTGCA 60.376 57.895 0.0 0.0 0.0 4.57 R
3024 5402 0.928505 TCCGACACTATCTACCCCCA 59.071 55.000 0.0 0.0 0.0 4.96 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
48 50 3.804036 TGTTAAGATGGGCCTTATCACG 58.196 45.455 18.51 0.00 0.00 4.35
86 88 3.581265 TGCCCATGAGCAATAGATCAA 57.419 42.857 0.00 0.00 44.32 2.57
87 89 3.900971 TGCCCATGAGCAATAGATCAAA 58.099 40.909 0.00 0.00 44.32 2.69
88 90 4.279982 TGCCCATGAGCAATAGATCAAAA 58.720 39.130 0.00 0.00 44.32 2.44
89 91 4.710865 TGCCCATGAGCAATAGATCAAAAA 59.289 37.500 0.00 0.00 44.32 1.94
90 92 5.045872 GCCCATGAGCAATAGATCAAAAAC 58.954 41.667 0.00 0.00 44.32 2.43
91 93 5.163478 GCCCATGAGCAATAGATCAAAAACT 60.163 40.000 0.00 0.00 44.32 2.66
92 94 6.039717 GCCCATGAGCAATAGATCAAAAACTA 59.960 38.462 0.00 0.00 44.32 2.24
93 95 7.646314 CCCATGAGCAATAGATCAAAAACTAG 58.354 38.462 0.00 0.00 44.32 2.57
94 96 7.500227 CCCATGAGCAATAGATCAAAAACTAGA 59.500 37.037 0.00 0.00 44.32 2.43
95 97 9.064706 CCATGAGCAATAGATCAAAAACTAGAT 57.935 33.333 0.00 0.00 44.32 1.98
96 98 9.880064 CATGAGCAATAGATCAAAAACTAGATG 57.120 33.333 0.00 0.00 44.32 2.90
97 99 9.624373 ATGAGCAATAGATCAAAAACTAGATGT 57.376 29.630 0.00 0.00 44.32 3.06
98 100 9.102757 TGAGCAATAGATCAAAAACTAGATGTC 57.897 33.333 0.00 0.00 37.20 3.06
99 101 9.102757 GAGCAATAGATCAAAAACTAGATGTCA 57.897 33.333 0.00 0.00 0.00 3.58
100 102 9.107177 AGCAATAGATCAAAAACTAGATGTCAG 57.893 33.333 0.00 0.00 0.00 3.51
101 103 8.887717 GCAATAGATCAAAAACTAGATGTCAGT 58.112 33.333 0.00 0.00 0.00 3.41
104 106 7.678947 AGATCAAAAACTAGATGTCAGTTGG 57.321 36.000 0.00 0.00 36.38 3.77
105 107 5.689383 TCAAAAACTAGATGTCAGTTGGC 57.311 39.130 0.00 0.00 36.38 4.52
106 108 5.376625 TCAAAAACTAGATGTCAGTTGGCT 58.623 37.500 0.00 0.00 36.38 4.75
107 109 5.827797 TCAAAAACTAGATGTCAGTTGGCTT 59.172 36.000 0.00 0.00 36.38 4.35
108 110 6.995686 TCAAAAACTAGATGTCAGTTGGCTTA 59.004 34.615 0.00 0.00 36.38 3.09
109 111 6.803154 AAAACTAGATGTCAGTTGGCTTAC 57.197 37.500 0.00 0.00 36.38 2.34
110 112 4.473477 ACTAGATGTCAGTTGGCTTACC 57.527 45.455 0.00 0.00 0.00 2.85
111 113 2.789409 AGATGTCAGTTGGCTTACCC 57.211 50.000 0.00 0.00 33.59 3.69
112 114 2.269940 AGATGTCAGTTGGCTTACCCT 58.730 47.619 0.00 0.00 33.59 4.34
113 115 3.450904 AGATGTCAGTTGGCTTACCCTA 58.549 45.455 0.00 0.00 33.59 3.53
114 116 3.844211 AGATGTCAGTTGGCTTACCCTAA 59.156 43.478 0.00 0.00 33.59 2.69
115 117 4.288626 AGATGTCAGTTGGCTTACCCTAAA 59.711 41.667 0.00 0.00 33.59 1.85
167 169 6.830873 AGGTGAAGAGGAATTTCAAATGAG 57.169 37.500 0.00 0.00 36.41 2.90
170 172 5.018809 TGAAGAGGAATTTCAAATGAGGGG 58.981 41.667 0.00 0.00 31.98 4.79
177 179 5.302823 GGAATTTCAAATGAGGGGTATCCAG 59.697 44.000 0.00 0.00 38.24 3.86
201 203 8.811378 CAGAAATTGGAGTTCACTTTTTCTTTC 58.189 33.333 1.97 0.00 32.03 2.62
247 253 3.118775 TGCGAGTGGTAGTAATGCAGAAT 60.119 43.478 0.00 0.00 0.00 2.40
269 275 6.867662 ATAAGATTGCTGGATCTAAAACCG 57.132 37.500 0.00 0.00 35.37 4.44
270 276 2.945668 AGATTGCTGGATCTAAAACCGC 59.054 45.455 0.00 0.00 34.68 5.68
324 333 5.995282 TGATGAAGTTGAACCGACATAGTTT 59.005 36.000 0.00 0.00 0.00 2.66
325 334 5.917541 TGAAGTTGAACCGACATAGTTTC 57.082 39.130 0.00 0.00 0.00 2.78
347 356 0.885879 ACAACACGACGAGCCAGATA 59.114 50.000 0.00 0.00 0.00 1.98
356 365 0.595588 CGAGCCAGATAGAGCACGAT 59.404 55.000 0.00 0.00 44.29 3.73
491 506 9.862371 ATCTTTCGATGGAAGTACATATATGTC 57.138 33.333 21.49 13.06 36.52 3.06
553 573 1.161843 TGTAAAAGCTTAGGCACGCC 58.838 50.000 0.00 0.00 41.70 5.68
563 584 0.885196 TAGGCACGCCATTTTTGGAC 59.115 50.000 11.35 0.00 38.92 4.02
573 594 6.201806 CACGCCATTTTTGGACAGAAATAAAA 59.798 34.615 1.17 0.00 0.00 1.52
787 827 0.929824 GTTTGAACGACGACGACGGA 60.930 55.000 22.36 4.69 44.46 4.69
788 828 0.929824 TTTGAACGACGACGACGGAC 60.930 55.000 22.36 15.55 44.46 4.79
802 842 3.703127 GGACGACGGCCCTTTCCT 61.703 66.667 9.18 0.00 0.00 3.36
803 843 2.346365 GACGACGGCCCTTTCCTT 59.654 61.111 0.00 0.00 0.00 3.36
804 844 1.740664 GACGACGGCCCTTTCCTTC 60.741 63.158 0.00 0.00 0.00 3.46
805 845 2.436115 CGACGGCCCTTTCCTTCC 60.436 66.667 0.00 0.00 0.00 3.46
849 896 1.340114 GCTTTCCAACTCCGATCCCTT 60.340 52.381 0.00 0.00 0.00 3.95
862 914 1.953686 GATCCCTTCTCTCTCCGACAG 59.046 57.143 0.00 0.00 0.00 3.51
922 974 2.031012 CTCGTGTCCTTGCCTGCA 59.969 61.111 0.00 0.00 0.00 4.41
1115 1176 3.360340 GCCTGCTGCCACTGTCAC 61.360 66.667 0.00 0.00 0.00 3.67
1131 1192 0.612174 TCACGGACAAGGAGGAGGAG 60.612 60.000 0.00 0.00 0.00 3.69
1132 1193 1.305381 ACGGACAAGGAGGAGGAGG 60.305 63.158 0.00 0.00 0.00 4.30
1133 1194 1.000486 CGGACAAGGAGGAGGAGGA 60.000 63.158 0.00 0.00 0.00 3.71
1134 1195 1.040339 CGGACAAGGAGGAGGAGGAG 61.040 65.000 0.00 0.00 0.00 3.69
1135 1196 0.689412 GGACAAGGAGGAGGAGGAGG 60.689 65.000 0.00 0.00 0.00 4.30
1136 1197 0.336737 GACAAGGAGGAGGAGGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
1137 1198 1.022903 ACAAGGAGGAGGAGGAGGAT 58.977 55.000 0.00 0.00 0.00 3.24
1138 1199 1.343884 ACAAGGAGGAGGAGGAGGATG 60.344 57.143 0.00 0.00 0.00 3.51
1139 1200 0.267356 AAGGAGGAGGAGGAGGATGG 59.733 60.000 0.00 0.00 0.00 3.51
1140 1201 0.933791 AGGAGGAGGAGGAGGATGGT 60.934 60.000 0.00 0.00 0.00 3.55
1141 1202 0.762461 GGAGGAGGAGGAGGATGGTG 60.762 65.000 0.00 0.00 0.00 4.17
1142 1203 0.031616 GAGGAGGAGGAGGATGGTGT 60.032 60.000 0.00 0.00 0.00 4.16
1170 1231 1.534235 ACTGAGGCTGTCCGACCTT 60.534 57.895 0.00 0.00 36.05 3.50
1228 1289 3.241530 TGACCAAGGTGCGCCTCT 61.242 61.111 21.49 7.24 46.33 3.69
1637 1707 1.828660 TCTCGCGGATCTTCTCCCC 60.829 63.158 6.13 0.00 41.49 4.81
1640 1710 2.838225 GCGGATCTTCTCCCCCGA 60.838 66.667 0.00 0.00 44.29 5.14
1643 1713 2.499827 GGATCTTCTCCCCCGACGG 61.500 68.421 6.99 6.99 38.19 4.79
1788 1870 0.832135 TCACCGTCCTGGAGCTCTTT 60.832 55.000 14.64 0.00 42.00 2.52
1794 1876 0.251341 TCCTGGAGCTCTTTTTGGGC 60.251 55.000 14.64 0.00 0.00 5.36
2034 2116 1.369448 CCGCGTGCTACGAGAGATC 60.369 63.158 4.92 0.00 46.05 2.75
2052 2134 3.960755 AGATCATCGTGGAGACCATGTAA 59.039 43.478 9.39 0.00 41.03 2.41
2072 2154 5.655090 TGTAAGATATCGGGACAGAGACAAA 59.345 40.000 0.00 0.00 0.00 2.83
2078 2160 3.399330 TCGGGACAGAGACAAAATCAAC 58.601 45.455 0.00 0.00 0.00 3.18
2181 2263 7.054124 TCATCAACCTGAACTTTTAGACAAGT 58.946 34.615 0.00 0.00 38.74 3.16
2448 4785 7.488792 TCATGAACATTTATTGAATTGGCGAAG 59.511 33.333 0.00 0.00 0.00 3.79
2681 5025 6.262193 TGGAAATTTATTGAAGTCCCGAAC 57.738 37.500 0.00 0.00 0.00 3.95
2694 5038 7.325694 TGAAGTCCCGAACTATTTAAAGTAGG 58.674 38.462 0.00 0.00 37.17 3.18
2697 5041 7.326454 AGTCCCGAACTATTTAAAGTAGGAAC 58.674 38.462 0.00 0.00 36.07 3.62
2744 5117 1.047801 ATTTGAAAAACAGGCCGCCT 58.952 45.000 5.94 5.94 0.00 5.52
2789 5164 2.570284 TTGCGTCTTCTCCCAGCGA 61.570 57.895 0.00 0.00 0.00 4.93
2886 5262 8.815565 TTTTTATCACTTATAGGTGGCATTGA 57.184 30.769 14.38 0.00 37.75 2.57
2892 5268 4.079212 ACTTATAGGTGGCATTGATGGGTT 60.079 41.667 0.00 0.00 0.00 4.11
2908 5284 8.770438 TTGATGGGTTATATTTTGCAACTTTC 57.230 30.769 0.00 0.00 0.00 2.62
2912 5288 4.565166 GGTTATATTTTGCAACTTTCGGGC 59.435 41.667 0.00 0.00 0.00 6.13
2913 5289 3.951775 ATATTTTGCAACTTTCGGGCA 57.048 38.095 0.00 0.00 35.41 5.36
2918 5294 2.147436 TGCAACTTTCGGGCAAATTC 57.853 45.000 0.00 0.00 34.05 2.17
2923 5300 4.423732 CAACTTTCGGGCAAATTCTATGG 58.576 43.478 0.00 0.00 0.00 2.74
2926 5303 1.388547 TCGGGCAAATTCTATGGTGC 58.611 50.000 0.00 0.00 36.24 5.01
2931 5308 2.754552 GGCAAATTCTATGGTGCACTGA 59.245 45.455 17.98 4.00 38.78 3.41
2933 5310 3.728864 GCAAATTCTATGGTGCACTGACG 60.729 47.826 17.98 3.68 36.97 4.35
3028 5406 9.904198 AAAGGAAAAATCAATTATATGTTGGGG 57.096 29.630 3.70 0.00 0.00 4.96
3029 5407 8.033178 AGGAAAAATCAATTATATGTTGGGGG 57.967 34.615 3.70 0.00 0.00 5.40
3030 5408 7.627293 AGGAAAAATCAATTATATGTTGGGGGT 59.373 33.333 3.70 0.00 0.00 4.95
3031 5409 8.929487 GGAAAAATCAATTATATGTTGGGGGTA 58.071 33.333 3.70 0.00 0.00 3.69
3032 5410 9.981114 GAAAAATCAATTATATGTTGGGGGTAG 57.019 33.333 3.70 0.00 0.00 3.18
3033 5411 9.722317 AAAAATCAATTATATGTTGGGGGTAGA 57.278 29.630 3.70 0.00 0.00 2.59
3034 5412 9.897040 AAAATCAATTATATGTTGGGGGTAGAT 57.103 29.630 3.70 0.00 0.00 1.98
3037 5415 8.751215 TCAATTATATGTTGGGGGTAGATAGT 57.249 34.615 3.70 0.00 0.00 2.12
3038 5416 8.602424 TCAATTATATGTTGGGGGTAGATAGTG 58.398 37.037 3.70 0.00 0.00 2.74
3039 5417 8.383175 CAATTATATGTTGGGGGTAGATAGTGT 58.617 37.037 0.00 0.00 0.00 3.55
3040 5418 7.549147 TTATATGTTGGGGGTAGATAGTGTC 57.451 40.000 0.00 0.00 0.00 3.67
3041 5419 2.104967 TGTTGGGGGTAGATAGTGTCG 58.895 52.381 0.00 0.00 0.00 4.35
3042 5420 1.411612 GTTGGGGGTAGATAGTGTCGG 59.588 57.143 0.00 0.00 0.00 4.79
3043 5421 0.928505 TGGGGGTAGATAGTGTCGGA 59.071 55.000 0.00 0.00 0.00 4.55
3044 5422 1.288633 TGGGGGTAGATAGTGTCGGAA 59.711 52.381 0.00 0.00 0.00 4.30
3045 5423 2.292389 TGGGGGTAGATAGTGTCGGAAA 60.292 50.000 0.00 0.00 0.00 3.13
3046 5424 2.970640 GGGGGTAGATAGTGTCGGAAAT 59.029 50.000 0.00 0.00 0.00 2.17
3047 5425 3.244112 GGGGGTAGATAGTGTCGGAAATG 60.244 52.174 0.00 0.00 0.00 2.32
3048 5426 3.244112 GGGGTAGATAGTGTCGGAAATGG 60.244 52.174 0.00 0.00 0.00 3.16
3049 5427 3.640029 GGGTAGATAGTGTCGGAAATGGA 59.360 47.826 0.00 0.00 0.00 3.41
3050 5428 4.283722 GGGTAGATAGTGTCGGAAATGGAT 59.716 45.833 0.00 0.00 0.00 3.41
3051 5429 5.479375 GGGTAGATAGTGTCGGAAATGGATA 59.521 44.000 0.00 0.00 0.00 2.59
3052 5430 6.154706 GGGTAGATAGTGTCGGAAATGGATAT 59.845 42.308 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.036992 TCATGCATGGAAAAACACCCAC 59.963 45.455 25.97 0.00 34.92 4.61
1 2 2.323599 TCATGCATGGAAAAACACCCA 58.676 42.857 25.97 0.00 36.79 4.51
2 3 3.615224 ATCATGCATGGAAAAACACCC 57.385 42.857 25.97 0.00 0.00 4.61
3 4 4.932268 CAATCATGCATGGAAAAACACC 57.068 40.909 25.97 0.00 0.00 4.16
79 81 7.334421 GCCAACTGACATCTAGTTTTTGATCTA 59.666 37.037 0.00 0.00 36.29 1.98
80 82 6.150140 GCCAACTGACATCTAGTTTTTGATCT 59.850 38.462 0.00 0.00 36.29 2.75
81 83 6.150140 AGCCAACTGACATCTAGTTTTTGATC 59.850 38.462 0.00 0.00 36.29 2.92
82 84 6.006449 AGCCAACTGACATCTAGTTTTTGAT 58.994 36.000 0.00 0.00 36.29 2.57
83 85 5.376625 AGCCAACTGACATCTAGTTTTTGA 58.623 37.500 0.00 0.00 36.29 2.69
84 86 5.695851 AGCCAACTGACATCTAGTTTTTG 57.304 39.130 0.00 0.00 36.29 2.44
85 87 6.206829 GGTAAGCCAACTGACATCTAGTTTTT 59.793 38.462 0.00 0.00 36.29 1.94
86 88 5.705905 GGTAAGCCAACTGACATCTAGTTTT 59.294 40.000 0.00 0.00 36.29 2.43
87 89 5.246307 GGTAAGCCAACTGACATCTAGTTT 58.754 41.667 0.00 0.00 36.29 2.66
88 90 4.323562 GGGTAAGCCAACTGACATCTAGTT 60.324 45.833 0.00 0.00 38.84 2.24
89 91 3.197983 GGGTAAGCCAACTGACATCTAGT 59.802 47.826 0.00 0.00 36.17 2.57
90 92 3.452627 AGGGTAAGCCAACTGACATCTAG 59.547 47.826 0.00 0.00 36.17 2.43
91 93 3.450904 AGGGTAAGCCAACTGACATCTA 58.549 45.455 0.00 0.00 36.17 1.98
92 94 2.269940 AGGGTAAGCCAACTGACATCT 58.730 47.619 0.00 0.00 36.17 2.90
93 95 2.789409 AGGGTAAGCCAACTGACATC 57.211 50.000 0.00 0.00 36.17 3.06
94 96 4.650972 TTTAGGGTAAGCCAACTGACAT 57.349 40.909 0.00 0.00 36.17 3.06
95 97 4.440826 TTTTAGGGTAAGCCAACTGACA 57.559 40.909 0.00 0.00 36.17 3.58
120 122 1.202976 ACCAAGCCAGCTGACATCTTT 60.203 47.619 17.39 0.00 0.00 2.52
121 123 0.403271 ACCAAGCCAGCTGACATCTT 59.597 50.000 17.39 9.73 0.00 2.40
130 132 1.616159 TCACCTTTAACCAAGCCAGC 58.384 50.000 0.00 0.00 0.00 4.85
177 179 7.043391 CCGAAAGAAAAAGTGAACTCCAATTTC 60.043 37.037 0.00 0.00 41.57 2.17
194 196 2.241176 AGGCATGTATCCCCGAAAGAAA 59.759 45.455 0.00 0.00 0.00 2.52
195 197 1.843851 AGGCATGTATCCCCGAAAGAA 59.156 47.619 0.00 0.00 0.00 2.52
196 198 1.507140 AGGCATGTATCCCCGAAAGA 58.493 50.000 0.00 0.00 0.00 2.52
197 199 2.348411 AAGGCATGTATCCCCGAAAG 57.652 50.000 0.00 0.00 0.00 2.62
201 203 1.140852 TCTCAAAGGCATGTATCCCCG 59.859 52.381 0.00 0.00 0.00 5.73
247 253 4.574828 GCGGTTTTAGATCCAGCAATCTTA 59.425 41.667 2.17 0.00 37.24 2.10
270 276 0.319555 TCAAAGGCGAGTCTGTTCGG 60.320 55.000 0.00 0.00 40.79 4.30
324 333 2.050714 GCTCGTCGTGTTGTCCGA 60.051 61.111 0.00 0.00 0.00 4.55
325 334 3.103911 GGCTCGTCGTGTTGTCCG 61.104 66.667 0.00 0.00 0.00 4.79
356 365 4.058732 ATGTGGCGTCGCACCGTA 62.059 61.111 20.50 0.33 36.09 4.02
397 406 2.366167 CAGCCTCTCCTCTGGGGA 59.634 66.667 0.00 0.00 42.77 4.81
553 573 8.764287 GTCCACTTTTATTTCTGTCCAAAAATG 58.236 33.333 0.00 0.00 0.00 2.32
563 584 8.846211 TCTACTTTTGGTCCACTTTTATTTCTG 58.154 33.333 0.00 0.00 0.00 3.02
573 594 2.375509 CCCCTTCTACTTTTGGTCCACT 59.624 50.000 0.00 0.00 0.00 4.00
707 747 3.033185 CGATTGTCGCGTTTCACTTTTT 58.967 40.909 5.77 0.00 31.14 1.94
754 794 2.656560 TCAAACCAAACCAAACCGTG 57.343 45.000 0.00 0.00 0.00 4.94
755 795 2.671632 CGTTCAAACCAAACCAAACCGT 60.672 45.455 0.00 0.00 0.00 4.83
756 796 1.921230 CGTTCAAACCAAACCAAACCG 59.079 47.619 0.00 0.00 0.00 4.44
757 797 2.924926 GTCGTTCAAACCAAACCAAACC 59.075 45.455 0.00 0.00 0.00 3.27
758 798 2.595095 CGTCGTTCAAACCAAACCAAAC 59.405 45.455 0.00 0.00 0.00 2.93
759 799 2.486982 TCGTCGTTCAAACCAAACCAAA 59.513 40.909 0.00 0.00 0.00 3.28
760 800 2.082231 TCGTCGTTCAAACCAAACCAA 58.918 42.857 0.00 0.00 0.00 3.67
761 801 1.397692 GTCGTCGTTCAAACCAAACCA 59.602 47.619 0.00 0.00 0.00 3.67
787 827 2.346365 GAAGGAAAGGGCCGTCGT 59.654 61.111 0.00 0.00 0.00 4.34
788 828 2.436115 GGAAGGAAAGGGCCGTCG 60.436 66.667 0.00 0.00 37.31 5.12
802 842 3.181410 TGGAGTAGAGACCAAGGAAGGAA 60.181 47.826 0.00 0.00 32.93 3.36
803 843 2.382305 TGGAGTAGAGACCAAGGAAGGA 59.618 50.000 0.00 0.00 32.93 3.36
804 844 2.821437 TGGAGTAGAGACCAAGGAAGG 58.179 52.381 0.00 0.00 32.93 3.46
922 974 2.125106 CTTCGGCTTTAGCGGCCT 60.125 61.111 0.00 0.00 46.73 5.19
1104 1165 1.227527 CTTGTCCGTGACAGTGGCA 60.228 57.895 0.00 0.00 43.69 4.92
1108 1169 0.469331 TCCTCCTTGTCCGTGACAGT 60.469 55.000 6.79 0.00 43.69 3.55
1112 1173 0.612174 CTCCTCCTCCTTGTCCGTGA 60.612 60.000 0.00 0.00 0.00 4.35
1115 1176 1.000486 TCCTCCTCCTCCTTGTCCG 60.000 63.158 0.00 0.00 0.00 4.79
1131 1192 2.187946 CGCTCCACACCATCCTCC 59.812 66.667 0.00 0.00 0.00 4.30
1132 1193 2.512515 GCGCTCCACACCATCCTC 60.513 66.667 0.00 0.00 0.00 3.71
1133 1194 4.101448 GGCGCTCCACACCATCCT 62.101 66.667 7.64 0.00 0.00 3.24
1135 1196 4.451150 TCGGCGCTCCACACCATC 62.451 66.667 7.64 0.00 0.00 3.51
1136 1197 4.760047 GTCGGCGCTCCACACCAT 62.760 66.667 7.64 0.00 0.00 3.55
1139 1200 4.357947 TCAGTCGGCGCTCCACAC 62.358 66.667 7.64 0.00 0.00 3.82
1140 1201 4.056125 CTCAGTCGGCGCTCCACA 62.056 66.667 7.64 0.00 0.00 4.17
1141 1202 4.803426 CCTCAGTCGGCGCTCCAC 62.803 72.222 7.64 1.05 0.00 4.02
1152 1213 1.534235 AAGGTCGGACAGCCTCAGT 60.534 57.895 10.76 0.00 33.24 3.41
1170 1231 3.897681 TAGGTCGGCCAGCCACTCA 62.898 63.158 9.71 0.00 37.19 3.41
1207 1268 3.414700 GCGCACCTTGGTCACGAG 61.415 66.667 0.30 0.00 0.00 4.18
1547 1617 1.375908 GGCTTGATGTCGAGGTGCA 60.376 57.895 0.00 0.00 0.00 4.57
1558 1628 1.675641 GCAGGTTGTCGGGCTTGAT 60.676 57.895 0.00 0.00 0.00 2.57
1686 1768 2.737180 CGCTCGGGGCTCATGTAT 59.263 61.111 0.00 0.00 39.13 2.29
1933 2015 1.443828 GCCTCCGAGGATCCTTGAC 59.556 63.158 28.24 9.63 37.67 3.18
1934 2016 2.127869 CGCCTCCGAGGATCCTTGA 61.128 63.158 28.24 19.86 37.67 3.02
1935 2017 2.419198 CGCCTCCGAGGATCCTTG 59.581 66.667 20.95 20.95 37.67 3.61
2021 2103 1.604278 CCACGATGATCTCTCGTAGCA 59.396 52.381 18.96 0.00 46.85 3.49
2034 2116 3.801114 TCTTACATGGTCTCCACGATG 57.199 47.619 0.00 0.00 42.80 3.84
2052 2134 5.363868 TGATTTTGTCTCTGTCCCGATATCT 59.636 40.000 0.34 0.00 0.00 1.98
2072 2154 9.160496 GAGTTCATCTCAAGAATACAGTTGATT 57.840 33.333 0.00 0.00 42.34 2.57
2078 2160 9.944663 GTAGTAGAGTTCATCTCAAGAATACAG 57.055 37.037 0.00 0.00 44.98 2.74
2147 2229 6.581171 AGTTCAGGTTGATGAAAGAAATCC 57.419 37.500 0.00 0.00 40.72 3.01
2227 4557 7.403312 TTGTCAAATCCAAAAAGAGAGACAA 57.597 32.000 0.00 0.00 40.06 3.18
2228 4558 7.587037 ATTGTCAAATCCAAAAAGAGAGACA 57.413 32.000 0.00 0.00 0.00 3.41
2383 4718 9.796120 CCTGAAAATTCAAAAACTGTTAGTGTA 57.204 29.630 0.00 0.00 36.64 2.90
2384 4719 8.527810 TCCTGAAAATTCAAAAACTGTTAGTGT 58.472 29.630 0.00 0.00 36.64 3.55
2590 4933 9.598517 AAATCATAAAATGTTTGCGGATACAAT 57.401 25.926 4.10 0.00 0.00 2.71
2717 5083 5.498159 GGCCTGTTTTTCAAATTTCGTTTC 58.502 37.500 0.00 0.00 0.00 2.78
2763 5138 3.335534 GAAGACGCAACGTGCCGT 61.336 61.111 12.72 12.72 41.37 5.68
2764 5139 3.000080 GAGAAGACGCAACGTGCCG 62.000 63.158 0.00 6.57 41.37 5.69
2768 5143 1.006102 CTGGGAGAAGACGCAACGT 60.006 57.895 0.00 0.00 45.10 3.99
2789 5164 2.106857 ACCTCCTATACTGCGCTCTACT 59.893 50.000 9.73 0.00 0.00 2.57
2886 5262 6.337356 CCGAAAGTTGCAAAATATAACCCAT 58.663 36.000 0.00 0.00 0.00 4.00
2892 5268 5.392767 TTGCCCGAAAGTTGCAAAATATA 57.607 34.783 0.00 0.00 41.80 0.86
2908 5284 1.102154 TGCACCATAGAATTTGCCCG 58.898 50.000 0.00 0.00 33.86 6.13
2912 5288 3.181507 CCGTCAGTGCACCATAGAATTTG 60.182 47.826 14.63 1.54 0.00 2.32
2913 5289 3.009723 CCGTCAGTGCACCATAGAATTT 58.990 45.455 14.63 0.00 0.00 1.82
2918 5294 1.645034 CTTCCGTCAGTGCACCATAG 58.355 55.000 14.63 2.98 0.00 2.23
2923 5300 1.394917 CTATTGCTTCCGTCAGTGCAC 59.605 52.381 9.40 9.40 35.01 4.57
2926 5303 1.009829 GGCTATTGCTTCCGTCAGTG 58.990 55.000 0.00 0.00 39.59 3.66
2931 5308 3.577805 ATAAAGGGCTATTGCTTCCGT 57.422 42.857 0.00 0.00 39.59 4.69
2933 5310 7.670140 ACCTAATAATAAAGGGCTATTGCTTCC 59.330 37.037 0.00 0.00 37.18 3.46
3002 5380 9.904198 CCCCAACATATAATTGATTTTTCCTTT 57.096 29.630 2.43 0.00 0.00 3.11
3003 5381 8.493607 CCCCCAACATATAATTGATTTTTCCTT 58.506 33.333 2.43 0.00 0.00 3.36
3004 5382 7.627293 ACCCCCAACATATAATTGATTTTTCCT 59.373 33.333 2.43 0.00 0.00 3.36
3005 5383 7.801104 ACCCCCAACATATAATTGATTTTTCC 58.199 34.615 2.43 0.00 0.00 3.13
3006 5384 9.981114 CTACCCCCAACATATAATTGATTTTTC 57.019 33.333 2.43 0.00 0.00 2.29
3007 5385 9.722317 TCTACCCCCAACATATAATTGATTTTT 57.278 29.630 2.43 0.00 0.00 1.94
3008 5386 9.897040 ATCTACCCCCAACATATAATTGATTTT 57.103 29.630 2.43 0.00 0.00 1.82
3011 5389 9.351572 ACTATCTACCCCCAACATATAATTGAT 57.648 33.333 2.43 0.00 0.00 2.57
3012 5390 8.602424 CACTATCTACCCCCAACATATAATTGA 58.398 37.037 2.43 0.00 0.00 2.57
3013 5391 8.383175 ACACTATCTACCCCCAACATATAATTG 58.617 37.037 0.00 0.00 0.00 2.32
3014 5392 8.520119 ACACTATCTACCCCCAACATATAATT 57.480 34.615 0.00 0.00 0.00 1.40
3015 5393 7.093465 CGACACTATCTACCCCCAACATATAAT 60.093 40.741 0.00 0.00 0.00 1.28
3016 5394 6.209986 CGACACTATCTACCCCCAACATATAA 59.790 42.308 0.00 0.00 0.00 0.98
3017 5395 5.713389 CGACACTATCTACCCCCAACATATA 59.287 44.000 0.00 0.00 0.00 0.86
3018 5396 4.527038 CGACACTATCTACCCCCAACATAT 59.473 45.833 0.00 0.00 0.00 1.78
3019 5397 3.893200 CGACACTATCTACCCCCAACATA 59.107 47.826 0.00 0.00 0.00 2.29
3020 5398 2.698797 CGACACTATCTACCCCCAACAT 59.301 50.000 0.00 0.00 0.00 2.71
3021 5399 2.104967 CGACACTATCTACCCCCAACA 58.895 52.381 0.00 0.00 0.00 3.33
3022 5400 1.411612 CCGACACTATCTACCCCCAAC 59.588 57.143 0.00 0.00 0.00 3.77
3023 5401 1.288633 TCCGACACTATCTACCCCCAA 59.711 52.381 0.00 0.00 0.00 4.12
3024 5402 0.928505 TCCGACACTATCTACCCCCA 59.071 55.000 0.00 0.00 0.00 4.96
3025 5403 2.077687 TTCCGACACTATCTACCCCC 57.922 55.000 0.00 0.00 0.00 5.40
3026 5404 3.244112 CCATTTCCGACACTATCTACCCC 60.244 52.174 0.00 0.00 0.00 4.95
3027 5405 3.640029 TCCATTTCCGACACTATCTACCC 59.360 47.826 0.00 0.00 0.00 3.69
3028 5406 4.931661 TCCATTTCCGACACTATCTACC 57.068 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.