Multiple sequence alignment - TraesCS5A01G329900

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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 TraesCS5A01G329900 chr5A 100.000 2924 0 0 1 2924 539094485 539091562 0.000000e+00 5400.0
1 TraesCS5A01G329900 chr5A 83.969 131 19 2 1377 1506 214166890 214167019 1.100000e-24 124.0
2 TraesCS5A01G329900 chr5D 88.129 3041 140 89 1 2890 425078487 425075517 0.000000e+00 3411.0
3 TraesCS5A01G329900 chr5D 94.595 111 6 0 2777 2887 425040478 425040368 3.870000e-39 172.0
4 TraesCS5A01G329900 chr5D 83.969 131 19 2 1377 1506 200501539 200501668 1.100000e-24 124.0
5 TraesCS5A01G329900 chr5B 89.021 2277 103 61 1 2187 514280656 514278437 0.000000e+00 2684.0
6 TraesCS5A01G329900 chr5B 84.689 418 26 19 2185 2571 514278163 514277753 1.640000e-102 383.0
7 TraesCS5A01G329900 chr5B 83.969 131 19 2 1377 1506 211146510 211146639 1.100000e-24 124.0
8 TraesCS5A01G329900 chr5B 86.957 69 3 2 2823 2890 514077123 514077060 4.040000e-09 73.1
9 TraesCS5A01G329900 chr3A 92.857 266 19 0 1001 1266 633922101 633922366 1.270000e-103 387.0
10 TraesCS5A01G329900 chr3B 92.105 266 21 0 1001 1266 653152051 653152316 2.750000e-100 375.0
11 TraesCS5A01G329900 chr3D 91.729 266 22 0 1001 1266 492131424 492131689 1.280000e-98 370.0
12 TraesCS5A01G329900 chr1A 90.977 266 24 0 1001 1266 463461697 463461432 2.770000e-95 359.0
13 TraesCS5A01G329900 chr1A 91.837 49 4 0 2876 2924 32093603 32093555 5.230000e-08 69.4
14 TraesCS5A01G329900 chr1A 93.333 45 2 1 2879 2923 247414032 247414075 6.760000e-07 65.8
15 TraesCS5A01G329900 chr1B 88.968 281 31 0 1001 1281 487951482 487951202 6.000000e-92 348.0
16 TraesCS5A01G329900 chr1D 89.630 270 26 2 1001 1269 364625272 364625004 2.790000e-90 342.0
17 TraesCS5A01G329900 chr7D 88.679 265 30 0 1001 1265 262698956 262698692 1.010000e-84 324.0
18 TraesCS5A01G329900 chr7D 86.325 117 16 0 1382 1498 262698692 262698576 8.510000e-26 128.0
19 TraesCS5A01G329900 chr4B 74.550 389 76 20 1130 1506 100576660 100577037 6.530000e-32 148.0
20 TraesCS5A01G329900 chr7A 86.325 117 16 0 1382 1498 285576344 285576228 8.510000e-26 128.0
21 TraesCS5A01G329900 chr7B 85.470 117 17 0 1382 1498 241107945 241108061 3.960000e-24 122.0
22 TraesCS5A01G329900 chr4A 89.831 59 2 4 2866 2924 581914590 581914644 4.040000e-09 73.1
23 TraesCS5A01G329900 chr4A 87.273 55 4 3 2870 2923 645102663 645102611 3.150000e-05 60.2
24 TraesCS5A01G329900 chr2A 97.561 41 1 0 2884 2924 177683446 177683486 1.450000e-08 71.3
25 TraesCS5A01G329900 chr2A 86.154 65 5 4 2863 2923 5624099 5624163 1.880000e-07 67.6
26 TraesCS5A01G329900 chr2D 93.478 46 1 2 2878 2923 36071523 36071566 1.880000e-07 67.6
27 TraesCS5A01G329900 chr6B 88.889 54 4 2 2871 2923 362191801 362191853 6.760000e-07 65.8
28 TraesCS5A01G329900 chr6A 90.000 50 3 1 2877 2924 12327368 12327417 2.430000e-06 63.9


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 TraesCS5A01G329900 chr5A 539091562 539094485 2923 True 5400.0 5400 100.000 1 2924 1 chr5A.!!$R1 2923
1 TraesCS5A01G329900 chr5D 425075517 425078487 2970 True 3411.0 3411 88.129 1 2890 1 chr5D.!!$R2 2889
2 TraesCS5A01G329900 chr5B 514277753 514280656 2903 True 1533.5 2684 86.855 1 2571 2 chr5B.!!$R2 2570

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
802 857 0.042731 AGACCTTCTTCCCCGATCCA 59.957 55.0 0.0 0.0 0.0 3.41 F
917 979 0.178990 ACTTCCACTCCTGCAAACCC 60.179 55.0 0.0 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1749 0.107165 GTCCATCTGGGGGTTGCTAC 60.107 60.0 0.0 0.0 37.22 3.58 R
2239 2635 0.107752 GCTCTCCTCTCCTGCCAAAG 60.108 60.0 0.0 0.0 0.00 2.77 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
54 56 0.811281 GAGAATCAAAACAGCCCCCG 59.189 55.000 0.00 0.00 33.17 5.73
98 101 0.385974 GACACACGAATTGCACTGCC 60.386 55.000 0.00 0.00 0.00 4.85
99 102 1.081242 CACACGAATTGCACTGCCC 60.081 57.895 0.00 0.00 0.00 5.36
113 116 2.282462 GCCCCTGGGTCACAACTG 60.282 66.667 12.71 0.00 37.65 3.16
172 180 3.006940 TCCAACGTGGCACATATTCTTC 58.993 45.455 19.09 0.00 44.52 2.87
233 242 7.768582 TGAGTTTGTGTCTTACAGAAAGATTGA 59.231 33.333 2.94 0.00 45.84 2.57
345 355 0.808125 TTTGCTTGTGTTGCACGAGT 59.192 45.000 15.44 0.00 45.03 4.18
386 396 3.008330 CAGCATCAAGGGAAAGAGAGTG 58.992 50.000 0.00 0.00 0.00 3.51
387 397 2.026449 AGCATCAAGGGAAAGAGAGTGG 60.026 50.000 0.00 0.00 0.00 4.00
388 398 2.943199 GCATCAAGGGAAAGAGAGTGGG 60.943 54.545 0.00 0.00 0.00 4.61
389 399 2.415983 TCAAGGGAAAGAGAGTGGGA 57.584 50.000 0.00 0.00 0.00 4.37
408 418 1.001631 GGGAGGGGAAATTGGGTGG 59.998 63.158 0.00 0.00 0.00 4.61
488 507 6.596703 GGTTAGTTAGCTGTTAAAACCGAAG 58.403 40.000 0.00 0.00 27.91 3.79
610 636 3.046087 CTGTGGCTGGCTGTGTCG 61.046 66.667 2.00 0.00 0.00 4.35
627 653 3.071479 TGTCGTTGTTGCCTTTCTATCC 58.929 45.455 0.00 0.00 0.00 2.59
636 662 4.494091 TGCCTTTCTATCCTCCTCTTTG 57.506 45.455 0.00 0.00 0.00 2.77
637 663 3.846588 TGCCTTTCTATCCTCCTCTTTGT 59.153 43.478 0.00 0.00 0.00 2.83
638 664 4.195416 GCCTTTCTATCCTCCTCTTTGTG 58.805 47.826 0.00 0.00 0.00 3.33
639 665 4.323868 GCCTTTCTATCCTCCTCTTTGTGT 60.324 45.833 0.00 0.00 0.00 3.72
640 666 5.181748 CCTTTCTATCCTCCTCTTTGTGTG 58.818 45.833 0.00 0.00 0.00 3.82
641 667 5.280215 CCTTTCTATCCTCCTCTTTGTGTGT 60.280 44.000 0.00 0.00 0.00 3.72
642 668 4.808414 TCTATCCTCCTCTTTGTGTGTG 57.192 45.455 0.00 0.00 0.00 3.82
643 669 4.160329 TCTATCCTCCTCTTTGTGTGTGT 58.840 43.478 0.00 0.00 0.00 3.72
644 670 2.620251 TCCTCCTCTTTGTGTGTGTG 57.380 50.000 0.00 0.00 0.00 3.82
645 671 1.837439 TCCTCCTCTTTGTGTGTGTGT 59.163 47.619 0.00 0.00 0.00 3.72
646 672 1.942657 CCTCCTCTTTGTGTGTGTGTG 59.057 52.381 0.00 0.00 0.00 3.82
651 677 2.483877 CTCTTTGTGTGTGTGTGTGTGT 59.516 45.455 0.00 0.00 0.00 3.72
800 855 2.605837 GAAGACCTTCTTCCCCGATC 57.394 55.000 4.81 0.00 45.34 3.69
801 856 1.139256 GAAGACCTTCTTCCCCGATCC 59.861 57.143 4.81 0.00 45.34 3.36
802 857 0.042731 AGACCTTCTTCCCCGATCCA 59.957 55.000 0.00 0.00 0.00 3.41
803 858 0.466124 GACCTTCTTCCCCGATCCAG 59.534 60.000 0.00 0.00 0.00 3.86
804 859 0.252742 ACCTTCTTCCCCGATCCAGT 60.253 55.000 0.00 0.00 0.00 4.00
805 860 0.179000 CCTTCTTCCCCGATCCAGTG 59.821 60.000 0.00 0.00 0.00 3.66
847 903 1.059913 ATAAAGATCCAGCCTCCGGG 58.940 55.000 0.00 0.00 0.00 5.73
914 976 1.064017 ACCAACTTCCACTCCTGCAAA 60.064 47.619 0.00 0.00 0.00 3.68
915 977 1.338020 CCAACTTCCACTCCTGCAAAC 59.662 52.381 0.00 0.00 0.00 2.93
916 978 1.338020 CAACTTCCACTCCTGCAAACC 59.662 52.381 0.00 0.00 0.00 3.27
917 979 0.178990 ACTTCCACTCCTGCAAACCC 60.179 55.000 0.00 0.00 0.00 4.11
918 980 1.228124 TTCCACTCCTGCAAACCCG 60.228 57.895 0.00 0.00 0.00 5.28
987 1068 2.279517 CGGCGGCAGACCATCTAC 60.280 66.667 10.53 0.00 34.57 2.59
1269 1350 0.470766 TCCTGGGCAACAAGTACGTT 59.529 50.000 0.00 0.00 39.74 3.99
1282 1371 7.306632 GCAACAAGTACGTTCATCTATCCATAC 60.307 40.741 0.00 0.00 0.00 2.39
1318 1407 5.124457 CCAATGAATGAACGATCCTCTGTTT 59.876 40.000 0.00 0.00 0.00 2.83
1404 1498 1.202830 TCTCTGATAGCCGGGAGACTC 60.203 57.143 2.18 0.00 31.02 3.36
1546 1640 4.202253 CCAACATCACCATATCCTTCGAGA 60.202 45.833 0.00 0.00 0.00 4.04
1652 1746 2.784371 TGGACCACCATCACCATCA 58.216 52.632 0.00 0.00 41.77 3.07
1654 1748 0.394352 GGACCACCATCACCATCACC 60.394 60.000 0.00 0.00 35.97 4.02
1655 1749 0.744414 GACCACCATCACCATCACCG 60.744 60.000 0.00 0.00 0.00 4.94
1656 1750 1.299648 CCACCATCACCATCACCGT 59.700 57.895 0.00 0.00 0.00 4.83
1657 1751 0.539518 CCACCATCACCATCACCGTA 59.460 55.000 0.00 0.00 0.00 4.02
1658 1752 1.473257 CCACCATCACCATCACCGTAG 60.473 57.143 0.00 0.00 0.00 3.51
1660 1754 0.177836 CCATCACCATCACCGTAGCA 59.822 55.000 0.00 0.00 0.00 3.49
1664 1758 1.024579 CACCATCACCGTAGCAACCC 61.025 60.000 0.00 0.00 0.00 4.11
1931 2025 2.167075 TCGAGATGAAATGAGCAGAGCA 59.833 45.455 0.00 0.00 0.00 4.26
1932 2026 2.540516 CGAGATGAAATGAGCAGAGCAG 59.459 50.000 0.00 0.00 0.00 4.24
1933 2027 3.737355 CGAGATGAAATGAGCAGAGCAGA 60.737 47.826 0.00 0.00 0.00 4.26
1934 2028 3.799366 AGATGAAATGAGCAGAGCAGAG 58.201 45.455 0.00 0.00 0.00 3.35
1935 2029 1.735386 TGAAATGAGCAGAGCAGAGC 58.265 50.000 0.00 0.00 0.00 4.09
2015 2126 6.091441 GTGAAAATACAGCGAGTGAAAGAGAT 59.909 38.462 0.00 0.00 0.00 2.75
2016 2127 6.091305 TGAAAATACAGCGAGTGAAAGAGATG 59.909 38.462 0.00 0.00 0.00 2.90
2026 2137 5.178252 CGAGTGAAAGAGATGCAAGAAGAAA 59.822 40.000 0.00 0.00 0.00 2.52
2028 2139 6.294473 AGTGAAAGAGATGCAAGAAGAAAGA 58.706 36.000 0.00 0.00 0.00 2.52
2029 2140 6.427547 AGTGAAAGAGATGCAAGAAGAAAGAG 59.572 38.462 0.00 0.00 0.00 2.85
2030 2141 5.180868 TGAAAGAGATGCAAGAAGAAAGAGC 59.819 40.000 0.00 0.00 0.00 4.09
2041 2154 5.083533 AGAAGAAAGAGCGATGATCTTGT 57.916 39.130 0.00 0.00 37.30 3.16
2042 2155 4.869297 AGAAGAAAGAGCGATGATCTTGTG 59.131 41.667 0.00 0.00 37.30 3.33
2043 2156 3.529533 AGAAAGAGCGATGATCTTGTGG 58.470 45.455 0.00 0.00 37.30 4.17
2044 2157 3.055530 AGAAAGAGCGATGATCTTGTGGT 60.056 43.478 0.00 0.00 37.30 4.16
2045 2158 2.306341 AGAGCGATGATCTTGTGGTG 57.694 50.000 0.00 0.00 0.00 4.17
2046 2159 0.654683 GAGCGATGATCTTGTGGTGC 59.345 55.000 0.00 0.00 0.00 5.01
2047 2160 0.745845 AGCGATGATCTTGTGGTGCC 60.746 55.000 0.00 0.00 0.00 5.01
2048 2161 1.718757 GCGATGATCTTGTGGTGCCC 61.719 60.000 0.00 0.00 0.00 5.36
2059 2172 3.365265 GGTGCCCTGTTTCGCCAG 61.365 66.667 0.00 0.00 33.28 4.85
2083 2196 7.742556 GGATCATCTCCTTTCCTTCTTTATG 57.257 40.000 0.00 0.00 41.29 1.90
2090 2209 4.080299 TCCTTTCCTTCTTTATGCCCTCTC 60.080 45.833 0.00 0.00 0.00 3.20
2112 2232 2.791383 TGCTCCATTTTGTTTGTCCG 57.209 45.000 0.00 0.00 0.00 4.79
2149 2269 8.980143 AAAAATTACCGTTTGACTAATCATGG 57.020 30.769 0.00 0.00 33.85 3.66
2171 2291 2.880890 GCAATAATACTCTGGTGCTGGG 59.119 50.000 0.00 0.00 0.00 4.45
2194 2590 5.527582 GGTGGCTCACTGTATAAATTACAGG 59.472 44.000 15.12 6.39 46.70 4.00
2232 2628 7.807977 AAGTGCAATAGTAATATGAAGGTGG 57.192 36.000 0.00 0.00 0.00 4.61
2233 2629 5.765182 AGTGCAATAGTAATATGAAGGTGGC 59.235 40.000 0.00 0.00 0.00 5.01
2239 2635 8.299570 CAATAGTAATATGAAGGTGGCAATTCC 58.700 37.037 10.27 0.00 0.00 3.01
2475 2885 6.814644 GGCGGCTACATACATACATACATAAA 59.185 38.462 0.00 0.00 0.00 1.40
2503 2930 2.276732 TCTCTTGCCAAAAGGTCCAG 57.723 50.000 0.00 0.00 0.00 3.86
2519 2946 5.186198 AGGTCCAGGTGAATATTTTTCGAG 58.814 41.667 0.00 0.00 0.00 4.04
2545 2981 8.689069 GTCGATCTAAGTAATTTTACATCCGTC 58.311 37.037 3.50 0.00 36.12 4.79
2555 2991 7.424227 AATTTTACATCCGTCGTTAAACAGA 57.576 32.000 0.00 0.00 0.00 3.41
2556 2992 7.605410 ATTTTACATCCGTCGTTAAACAGAT 57.395 32.000 0.00 0.00 0.00 2.90
2568 3005 5.685954 TCGTTAAACAGATAGATGATGACGC 59.314 40.000 0.00 0.00 0.00 5.19
2570 3007 4.679373 AAACAGATAGATGATGACGCCT 57.321 40.909 0.00 0.00 0.00 5.52
2576 3013 5.861251 CAGATAGATGATGACGCCTAACTTC 59.139 44.000 0.00 0.00 0.00 3.01
2588 3025 5.236282 ACGCCTAACTTCTCTAACCTTTTC 58.764 41.667 0.00 0.00 0.00 2.29
2591 3028 7.093421 ACGCCTAACTTCTCTAACCTTTTCTAT 60.093 37.037 0.00 0.00 0.00 1.98
2592 3029 7.435784 CGCCTAACTTCTCTAACCTTTTCTATC 59.564 40.741 0.00 0.00 0.00 2.08
2593 3030 7.435784 GCCTAACTTCTCTAACCTTTTCTATCG 59.564 40.741 0.00 0.00 0.00 2.92
2594 3031 7.921745 CCTAACTTCTCTAACCTTTTCTATCGG 59.078 40.741 0.00 0.00 0.00 4.18
2596 3033 4.303086 TCTCTAACCTTTTCTATCGGCG 57.697 45.455 0.00 0.00 0.00 6.46
2597 3034 3.067742 TCTCTAACCTTTTCTATCGGCGG 59.932 47.826 7.21 0.00 0.00 6.13
2600 3037 2.311124 ACCTTTTCTATCGGCGGAAG 57.689 50.000 7.21 4.94 0.00 3.46
2626 3063 3.728385 AAGCTTCTCTAACCATGGCTT 57.272 42.857 13.04 8.20 34.36 4.35
2668 3124 2.116238 AGTAATCCATACGCAGGTGGT 58.884 47.619 0.00 0.00 39.62 4.16
2671 3127 2.910688 ATCCATACGCAGGTGGTTAG 57.089 50.000 0.00 0.00 38.34 2.34
2675 3131 1.754803 CATACGCAGGTGGTTAGAGGA 59.245 52.381 0.00 0.00 0.00 3.71
2680 3136 2.093447 CGCAGGTGGTTAGAGGAAAGAT 60.093 50.000 0.00 0.00 0.00 2.40
2688 3144 3.927142 GGTTAGAGGAAAGATCGTGTGTG 59.073 47.826 0.00 0.00 0.00 3.82
2689 3145 4.557205 GTTAGAGGAAAGATCGTGTGTGT 58.443 43.478 0.00 0.00 0.00 3.72
2692 3148 7.415989 GGTTAGAGGAAAGATCGTGTGTGTATA 60.416 40.741 0.00 0.00 0.00 1.47
2709 3165 6.016610 GTGTGTATATGAAACCAGGTGTGTTT 60.017 38.462 0.00 0.00 38.57 2.83
2710 3166 7.173562 GTGTGTATATGAAACCAGGTGTGTTTA 59.826 37.037 0.00 0.00 36.13 2.01
2713 3169 9.303116 TGTATATGAAACCAGGTGTGTTTATTT 57.697 29.630 0.00 0.00 36.13 1.40
2717 3173 6.130569 TGAAACCAGGTGTGTTTATTTAGGT 58.869 36.000 0.00 0.00 36.13 3.08
2718 3174 6.039941 TGAAACCAGGTGTGTTTATTTAGGTG 59.960 38.462 0.00 0.00 36.13 4.00
2730 3186 6.716173 TGTTTATTTAGGTGGAAGGTGGTAAC 59.284 38.462 0.00 0.00 0.00 2.50
2744 3200 3.253230 GTGGTAACGCGTGGTATTTAGT 58.747 45.455 14.98 0.00 42.51 2.24
2746 3202 5.043248 GTGGTAACGCGTGGTATTTAGTAT 58.957 41.667 14.98 0.00 42.51 2.12
2747 3203 5.173854 GTGGTAACGCGTGGTATTTAGTATC 59.826 44.000 14.98 0.00 42.51 2.24
2751 3228 3.231965 CGCGTGGTATTTAGTATCGGAG 58.768 50.000 0.00 0.00 0.00 4.63
2752 3229 3.058708 CGCGTGGTATTTAGTATCGGAGA 60.059 47.826 0.00 0.00 45.75 3.71
2754 3231 5.467705 GCGTGGTATTTAGTATCGGAGAAT 58.532 41.667 0.00 0.00 43.58 2.40
2774 3251 1.810030 GGCTAACCACGGCGAGAAG 60.810 63.158 16.62 5.42 35.26 2.85
2775 3252 1.214589 GCTAACCACGGCGAGAAGA 59.785 57.895 16.62 0.00 0.00 2.87
2778 3255 1.993370 CTAACCACGGCGAGAAGAAAG 59.007 52.381 16.62 0.00 0.00 2.62
2779 3256 0.602905 AACCACGGCGAGAAGAAAGG 60.603 55.000 16.62 4.46 0.00 3.11
2780 3257 1.292223 CCACGGCGAGAAGAAAGGA 59.708 57.895 16.62 0.00 0.00 3.36
2815 3304 2.230660 GTGACAAAGGGACAAGGGAAG 58.769 52.381 0.00 0.00 0.00 3.46
2824 3313 4.687976 AGGGACAAGGGAAGCATTTTAAT 58.312 39.130 0.00 0.00 0.00 1.40
2826 3315 6.443832 AGGGACAAGGGAAGCATTTTAATAT 58.556 36.000 0.00 0.00 0.00 1.28
2902 3394 9.357161 TCTAATCTAATCTACTTCCTCTGTTCC 57.643 37.037 0.00 0.00 0.00 3.62
2903 3395 9.362151 CTAATCTAATCTACTTCCTCTGTTCCT 57.638 37.037 0.00 0.00 0.00 3.36
2905 3397 9.716556 AATCTAATCTACTTCCTCTGTTCCTAA 57.283 33.333 0.00 0.00 0.00 2.69
2906 3398 9.716556 ATCTAATCTACTTCCTCTGTTCCTAAA 57.283 33.333 0.00 0.00 0.00 1.85
2907 3399 9.716556 TCTAATCTACTTCCTCTGTTCCTAAAT 57.283 33.333 0.00 0.00 0.00 1.40
2913 3405 9.892130 CTACTTCCTCTGTTCCTAAATATTTGT 57.108 33.333 11.05 0.00 0.00 2.83
2914 3406 8.794335 ACTTCCTCTGTTCCTAAATATTTGTC 57.206 34.615 11.05 0.00 0.00 3.18
2915 3407 8.606830 ACTTCCTCTGTTCCTAAATATTTGTCT 58.393 33.333 11.05 0.00 0.00 3.41
2916 3408 9.454859 CTTCCTCTGTTCCTAAATATTTGTCTT 57.545 33.333 11.05 0.00 0.00 3.01
2917 3409 9.807921 TTCCTCTGTTCCTAAATATTTGTCTTT 57.192 29.630 11.05 0.00 0.00 2.52
2918 3410 9.449719 TCCTCTGTTCCTAAATATTTGTCTTTC 57.550 33.333 11.05 0.00 0.00 2.62
2919 3411 9.454859 CCTCTGTTCCTAAATATTTGTCTTTCT 57.545 33.333 11.05 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 5.440234 ACATGATGTCGTCTATGGACTAC 57.560 43.478 7.68 7.26 40.10 2.73
98 101 4.800554 GTCAGTTGTGACCCAGGG 57.199 61.111 2.85 2.85 46.58 4.45
117 120 2.774809 AGCCATTTTCTAGGACCTCTCC 59.225 50.000 0.00 0.00 36.71 3.71
118 121 3.491792 CGAGCCATTTTCTAGGACCTCTC 60.492 52.174 0.00 0.00 0.00 3.20
119 122 2.432510 CGAGCCATTTTCTAGGACCTCT 59.567 50.000 0.00 0.00 0.00 3.69
172 180 9.859427 TTGTCTGCCAAGAATTTTATTTAGATG 57.141 29.630 0.00 0.00 33.05 2.90
224 233 8.527810 AGATCGGATATAGAACCTCAATCTTTC 58.472 37.037 0.00 0.00 0.00 2.62
345 355 1.283905 GCCCTCCCTGCCTAAAAACTA 59.716 52.381 0.00 0.00 0.00 2.24
386 396 1.620818 CCAATTTCCCCTCCCTCCC 59.379 63.158 0.00 0.00 0.00 4.30
387 397 1.221909 ACCCAATTTCCCCTCCCTCC 61.222 60.000 0.00 0.00 0.00 4.30
388 398 0.033109 CACCCAATTTCCCCTCCCTC 60.033 60.000 0.00 0.00 0.00 4.30
389 399 1.518431 CCACCCAATTTCCCCTCCCT 61.518 60.000 0.00 0.00 0.00 4.20
408 418 4.862371 TGTTTGTGGGGGATTATTAGGTC 58.138 43.478 0.00 0.00 0.00 3.85
488 507 4.858680 GCCTACCCTCTTGGCGCC 62.859 72.222 22.73 22.73 37.11 6.53
610 636 3.942115 GAGGAGGATAGAAAGGCAACAAC 59.058 47.826 0.00 0.00 41.41 3.32
627 653 2.352651 CACACACACACACAAAGAGGAG 59.647 50.000 0.00 0.00 0.00 3.69
636 662 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
637 663 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
638 664 5.472320 TTATTACACACACACACACACAC 57.528 39.130 0.00 0.00 0.00 3.82
639 665 5.644206 AGTTTATTACACACACACACACACA 59.356 36.000 0.00 0.00 0.00 3.72
640 666 5.963004 CAGTTTATTACACACACACACACAC 59.037 40.000 0.00 0.00 0.00 3.82
641 667 5.065346 CCAGTTTATTACACACACACACACA 59.935 40.000 0.00 0.00 0.00 3.72
642 668 5.065474 ACCAGTTTATTACACACACACACAC 59.935 40.000 0.00 0.00 0.00 3.82
643 669 5.186942 ACCAGTTTATTACACACACACACA 58.813 37.500 0.00 0.00 0.00 3.72
644 670 5.744666 ACCAGTTTATTACACACACACAC 57.255 39.130 0.00 0.00 0.00 3.82
645 671 7.336176 TGTTTACCAGTTTATTACACACACACA 59.664 33.333 0.00 0.00 0.00 3.72
646 672 7.695820 TGTTTACCAGTTTATTACACACACAC 58.304 34.615 0.00 0.00 0.00 3.82
651 677 7.416022 CGGTTTGTTTACCAGTTTATTACACA 58.584 34.615 0.00 0.00 38.12 3.72
685 711 2.564504 TCATGACCTCACCTCAACTCAG 59.435 50.000 0.00 0.00 0.00 3.35
711 747 3.368501 CTCCCCCTCCCTCTCCCA 61.369 72.222 0.00 0.00 0.00 4.37
742 797 2.745821 GGAAAAAGGTTAGGCTGGTACG 59.254 50.000 0.00 0.00 0.00 3.67
800 855 1.512996 CTGCACTTGACTGGCACTGG 61.513 60.000 0.00 0.00 33.34 4.00
801 856 0.816825 ACTGCACTTGACTGGCACTG 60.817 55.000 0.00 0.00 33.34 3.66
802 857 0.816825 CACTGCACTTGACTGGCACT 60.817 55.000 0.00 0.00 33.34 4.40
803 858 1.650912 CACTGCACTTGACTGGCAC 59.349 57.895 0.00 0.00 33.34 5.01
804 859 2.188829 GCACTGCACTTGACTGGCA 61.189 57.895 0.00 0.00 35.96 4.92
805 860 2.641559 GCACTGCACTTGACTGGC 59.358 61.111 0.00 0.00 0.00 4.85
914 976 3.893399 GGTTGGGTTGGGTCGGGT 61.893 66.667 0.00 0.00 0.00 5.28
915 977 4.671590 GGGTTGGGTTGGGTCGGG 62.672 72.222 0.00 0.00 0.00 5.14
916 978 3.438615 TTGGGTTGGGTTGGGTCGG 62.439 63.158 0.00 0.00 0.00 4.79
917 979 2.196229 TTGGGTTGGGTTGGGTCG 59.804 61.111 0.00 0.00 0.00 4.79
918 980 1.835267 GGTTGGGTTGGGTTGGGTC 60.835 63.158 0.00 0.00 0.00 4.46
987 1068 3.164268 CCTCCCCATCTCACTATCTCTG 58.836 54.545 0.00 0.00 0.00 3.35
1215 1296 0.034089 TGATGAGCTCGTCCTCCTCA 60.034 55.000 28.83 10.61 39.65 3.86
1269 1350 9.760926 GGAGCTATATATGGTATGGATAGATGA 57.239 37.037 0.00 0.00 0.00 2.92
1282 1371 7.765819 TCGTTCATTCATTGGAGCTATATATGG 59.234 37.037 0.00 0.00 0.00 2.74
1318 1407 2.212812 TCACAAGGCCATGCATGTAA 57.787 45.000 24.58 0.00 31.03 2.41
1404 1498 2.606519 TTGTCCGTCCTCCCTGGG 60.607 66.667 6.33 6.33 36.20 4.45
1407 1501 1.977544 CTCGTTGTCCGTCCTCCCT 60.978 63.158 0.00 0.00 37.94 4.20
1635 1729 0.394352 GGTGATGGTGATGGTGGTCC 60.394 60.000 0.00 0.00 0.00 4.46
1649 1743 1.910580 CTGGGGGTTGCTACGGTGAT 61.911 60.000 0.00 0.00 0.00 3.06
1651 1745 1.910580 ATCTGGGGGTTGCTACGGTG 61.911 60.000 0.00 0.00 0.00 4.94
1652 1746 1.615424 ATCTGGGGGTTGCTACGGT 60.615 57.895 0.00 0.00 0.00 4.83
1654 1748 1.153168 CCATCTGGGGGTTGCTACG 60.153 63.158 0.00 0.00 0.00 3.51
1655 1749 0.107165 GTCCATCTGGGGGTTGCTAC 60.107 60.000 0.00 0.00 37.22 3.58
1656 1750 0.253160 AGTCCATCTGGGGGTTGCTA 60.253 55.000 0.00 0.00 37.22 3.49
1657 1751 1.542375 AGTCCATCTGGGGGTTGCT 60.542 57.895 0.00 0.00 37.22 3.91
1658 1752 1.379044 CAGTCCATCTGGGGGTTGC 60.379 63.158 0.00 0.00 40.23 4.17
1692 1786 2.526873 AGGTCCGGGCACTTGAGT 60.527 61.111 9.07 0.00 0.00 3.41
1931 2025 2.686835 GAGGGGGTGCTCTGCTCT 60.687 66.667 0.00 0.00 0.00 4.09
1932 2026 3.791586 GGAGGGGGTGCTCTGCTC 61.792 72.222 0.00 0.00 0.00 4.26
1935 2029 3.086600 GAGGGAGGGGGTGCTCTG 61.087 72.222 0.00 0.00 0.00 3.35
2015 2126 3.044235 TCATCGCTCTTTCTTCTTGCA 57.956 42.857 0.00 0.00 0.00 4.08
2016 2127 3.870419 AGATCATCGCTCTTTCTTCTTGC 59.130 43.478 0.00 0.00 0.00 4.01
2026 2137 1.741732 GCACCACAAGATCATCGCTCT 60.742 52.381 0.00 0.00 0.00 4.09
2028 2139 0.745845 GGCACCACAAGATCATCGCT 60.746 55.000 0.00 0.00 0.00 4.93
2029 2140 1.723870 GGCACCACAAGATCATCGC 59.276 57.895 0.00 0.00 0.00 4.58
2048 2161 2.208431 GAGATGATCCTGGCGAAACAG 58.792 52.381 0.00 0.00 38.21 3.16
2070 2183 3.263425 ACGAGAGGGCATAAAGAAGGAAA 59.737 43.478 0.00 0.00 0.00 3.13
2072 2185 2.467880 ACGAGAGGGCATAAAGAAGGA 58.532 47.619 0.00 0.00 0.00 3.36
2073 2186 2.939103 CAACGAGAGGGCATAAAGAAGG 59.061 50.000 0.00 0.00 0.00 3.46
2074 2187 2.352960 GCAACGAGAGGGCATAAAGAAG 59.647 50.000 0.00 0.00 35.87 2.85
2075 2188 2.027192 AGCAACGAGAGGGCATAAAGAA 60.027 45.455 0.00 0.00 37.88 2.52
2078 2191 1.406887 GGAGCAACGAGAGGGCATAAA 60.407 52.381 0.00 0.00 37.88 1.40
2080 2193 0.975556 TGGAGCAACGAGAGGGCATA 60.976 55.000 0.00 0.00 37.88 3.14
2081 2194 1.630126 ATGGAGCAACGAGAGGGCAT 61.630 55.000 0.00 0.00 37.88 4.40
2082 2195 1.841302 AATGGAGCAACGAGAGGGCA 61.841 55.000 0.00 0.00 37.88 5.36
2083 2196 0.678048 AAATGGAGCAACGAGAGGGC 60.678 55.000 0.00 0.00 36.02 5.19
2090 2209 2.794350 GGACAAACAAAATGGAGCAACG 59.206 45.455 0.00 0.00 0.00 4.10
2126 2246 6.405397 GCCCATGATTAGTCAAACGGTAATTT 60.405 38.462 0.00 0.00 38.01 1.82
2127 2247 5.067283 GCCCATGATTAGTCAAACGGTAATT 59.933 40.000 0.00 0.00 38.01 1.40
2128 2248 4.578928 GCCCATGATTAGTCAAACGGTAAT 59.421 41.667 0.00 0.00 38.01 1.89
2149 2269 2.880890 CCAGCACCAGAGTATTATTGCC 59.119 50.000 0.00 0.00 0.00 4.52
2171 2291 6.346096 TCCTGTAATTTATACAGTGAGCCAC 58.654 40.000 12.99 0.00 42.37 5.01
2194 2590 3.698029 TGCACTTTCTTGAAAGCACTC 57.302 42.857 19.40 9.19 33.18 3.51
2213 2609 8.299570 GGAATTGCCACCTTCATATTACTATTG 58.700 37.037 0.00 0.00 36.34 1.90
2239 2635 0.107752 GCTCTCCTCTCCTGCCAAAG 60.108 60.000 0.00 0.00 0.00 2.77
2404 2806 2.585869 CGCAAAGCGTGTCACGAGT 61.586 57.895 28.83 12.02 46.05 4.18
2451 2854 7.201496 GGTTTATGTATGTATGTATGTAGCCGC 60.201 40.741 0.00 0.00 0.00 6.53
2452 2855 8.033038 AGGTTTATGTATGTATGTATGTAGCCG 58.967 37.037 0.00 0.00 0.00 5.52
2485 2895 1.251251 CCTGGACCTTTTGGCAAGAG 58.749 55.000 10.64 10.64 45.59 2.85
2487 2897 0.675633 CACCTGGACCTTTTGGCAAG 59.324 55.000 0.00 0.00 45.59 4.01
2488 2898 0.260230 TCACCTGGACCTTTTGGCAA 59.740 50.000 0.00 0.00 45.59 4.52
2489 2899 0.260230 TTCACCTGGACCTTTTGGCA 59.740 50.000 0.00 0.00 45.59 4.92
2490 2900 1.632589 ATTCACCTGGACCTTTTGGC 58.367 50.000 0.00 0.00 45.59 4.52
2492 2902 6.586082 CGAAAAATATTCACCTGGACCTTTTG 59.414 38.462 0.00 0.00 0.00 2.44
2497 2907 4.941873 ACTCGAAAAATATTCACCTGGACC 59.058 41.667 0.00 0.00 0.00 4.46
2503 2930 6.830114 AGATCGACTCGAAAAATATTCACC 57.170 37.500 5.00 0.00 39.99 4.02
2519 2946 8.571461 ACGGATGTAAAATTACTTAGATCGAC 57.429 34.615 5.05 0.00 34.12 4.20
2545 2981 5.107837 GGCGTCATCATCTATCTGTTTAACG 60.108 44.000 0.00 0.00 0.00 3.18
2555 2991 5.772672 AGAGAAGTTAGGCGTCATCATCTAT 59.227 40.000 0.00 0.00 0.00 1.98
2556 2992 5.133941 AGAGAAGTTAGGCGTCATCATCTA 58.866 41.667 0.00 0.00 0.00 1.98
2568 3005 7.921745 CCGATAGAAAAGGTTAGAGAAGTTAGG 59.078 40.741 0.00 0.00 39.76 2.69
2570 3007 7.263496 GCCGATAGAAAAGGTTAGAGAAGTTA 58.737 38.462 0.00 0.00 39.76 2.24
2576 3013 3.067742 TCCGCCGATAGAAAAGGTTAGAG 59.932 47.826 0.00 0.00 39.76 2.43
2657 3113 1.927487 TTCCTCTAACCACCTGCGTA 58.073 50.000 0.00 0.00 0.00 4.42
2663 3119 3.056035 ACACGATCTTTCCTCTAACCACC 60.056 47.826 0.00 0.00 0.00 4.61
2668 3124 4.866508 ACACACACGATCTTTCCTCTAA 57.133 40.909 0.00 0.00 0.00 2.10
2671 3127 6.504398 TCATATACACACACGATCTTTCCTC 58.496 40.000 0.00 0.00 0.00 3.71
2675 3131 6.876789 TGGTTTCATATACACACACGATCTTT 59.123 34.615 0.00 0.00 0.00 2.52
2680 3136 4.020928 ACCTGGTTTCATATACACACACGA 60.021 41.667 0.00 0.00 0.00 4.35
2692 3148 6.780522 ACCTAAATAAACACACCTGGTTTCAT 59.219 34.615 0.00 0.00 39.12 2.57
2709 3165 4.623647 GCGTTACCACCTTCCACCTAAATA 60.624 45.833 0.00 0.00 0.00 1.40
2710 3166 3.871074 GCGTTACCACCTTCCACCTAAAT 60.871 47.826 0.00 0.00 0.00 1.40
2713 3169 0.609662 GCGTTACCACCTTCCACCTA 59.390 55.000 0.00 0.00 0.00 3.08
2717 3173 1.301087 CACGCGTTACCACCTTCCA 60.301 57.895 10.22 0.00 0.00 3.53
2718 3174 2.030958 CCACGCGTTACCACCTTCC 61.031 63.158 10.22 0.00 0.00 3.46
2730 3186 3.058708 TCTCCGATACTAAATACCACGCG 60.059 47.826 3.53 3.53 0.00 6.01
2732 3188 5.793952 CGATTCTCCGATACTAAATACCACG 59.206 44.000 0.00 0.00 0.00 4.94
2733 3189 6.091437 CCGATTCTCCGATACTAAATACCAC 58.909 44.000 0.00 0.00 0.00 4.16
2734 3190 5.336213 GCCGATTCTCCGATACTAAATACCA 60.336 44.000 0.00 0.00 0.00 3.25
2735 3191 5.100943 GCCGATTCTCCGATACTAAATACC 58.899 45.833 0.00 0.00 0.00 2.73
2736 3192 5.952033 AGCCGATTCTCCGATACTAAATAC 58.048 41.667 0.00 0.00 0.00 1.89
2737 3193 7.362401 GGTTAGCCGATTCTCCGATACTAAATA 60.362 40.741 0.00 0.00 0.00 1.40
2738 3194 6.388278 GTTAGCCGATTCTCCGATACTAAAT 58.612 40.000 0.00 0.00 0.00 1.40
2740 3196 4.217118 GGTTAGCCGATTCTCCGATACTAA 59.783 45.833 0.00 0.00 0.00 2.24
2742 3198 2.557490 GGTTAGCCGATTCTCCGATACT 59.443 50.000 0.00 0.00 0.00 2.12
2744 3200 2.295349 GTGGTTAGCCGATTCTCCGATA 59.705 50.000 0.00 0.00 37.67 2.92
2746 3202 0.458669 GTGGTTAGCCGATTCTCCGA 59.541 55.000 0.00 0.00 37.67 4.55
2747 3203 0.870307 CGTGGTTAGCCGATTCTCCG 60.870 60.000 0.00 0.00 37.67 4.63
2751 3228 2.522638 CGCCGTGGTTAGCCGATTC 61.523 63.158 0.00 0.00 37.67 2.52
2752 3229 2.510691 CGCCGTGGTTAGCCGATT 60.511 61.111 0.00 0.00 37.67 3.34
2754 3231 4.124351 CTCGCCGTGGTTAGCCGA 62.124 66.667 0.00 0.00 37.67 5.54
2769 3246 3.055458 CCTGTCCTCCTTCCTTTCTTCTC 60.055 52.174 0.00 0.00 0.00 2.87
2771 3248 2.907042 TCCTGTCCTCCTTCCTTTCTTC 59.093 50.000 0.00 0.00 0.00 2.87
2774 3251 2.026729 CCTTCCTGTCCTCCTTCCTTTC 60.027 54.545 0.00 0.00 0.00 2.62
2775 3252 1.988846 CCTTCCTGTCCTCCTTCCTTT 59.011 52.381 0.00 0.00 0.00 3.11
2778 3255 0.615850 CACCTTCCTGTCCTCCTTCC 59.384 60.000 0.00 0.00 0.00 3.46
2779 3256 1.276705 GTCACCTTCCTGTCCTCCTTC 59.723 57.143 0.00 0.00 0.00 3.46
2780 3257 1.353091 GTCACCTTCCTGTCCTCCTT 58.647 55.000 0.00 0.00 0.00 3.36
2815 3304 4.060205 CAGCAAGCCCCATATTAAAATGC 58.940 43.478 0.00 0.00 0.00 3.56
2824 3313 0.550914 CCTAACCAGCAAGCCCCATA 59.449 55.000 0.00 0.00 0.00 2.74
2826 3315 0.842905 TACCTAACCAGCAAGCCCCA 60.843 55.000 0.00 0.00 0.00 4.96
2887 3379 9.892130 ACAAATATTTAGGAACAGAGGAAGTAG 57.108 33.333 0.00 0.00 0.00 2.57
2888 3380 9.886132 GACAAATATTTAGGAACAGAGGAAGTA 57.114 33.333 0.00 0.00 0.00 2.24
2889 3381 8.606830 AGACAAATATTTAGGAACAGAGGAAGT 58.393 33.333 0.00 0.00 0.00 3.01
2890 3382 9.454859 AAGACAAATATTTAGGAACAGAGGAAG 57.545 33.333 0.00 0.00 0.00 3.46
2891 3383 9.807921 AAAGACAAATATTTAGGAACAGAGGAA 57.192 29.630 0.00 0.00 0.00 3.36
2892 3384 9.449719 GAAAGACAAATATTTAGGAACAGAGGA 57.550 33.333 0.00 0.00 0.00 3.71
2893 3385 9.454859 AGAAAGACAAATATTTAGGAACAGAGG 57.545 33.333 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.