Multiple sequence alignment - TraesCS1D01G392000

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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 TraesCS1D01G392000 chr1D 100.000 2519 0 0 1 2519 462308319 462310837 0.000000e+00 4652.0
1 TraesCS1D01G392000 chr1D 88.372 559 35 9 1067 1617 462356463 462356999 0.000000e+00 645.0
2 TraesCS1D01G392000 chr1D 92.128 343 11 7 1 336 462302865 462303198 1.050000e-128 470.0
3 TraesCS1D01G392000 chr1B 90.362 1380 77 23 322 1681 637371294 637372637 0.000000e+00 1760.0
4 TraesCS1D01G392000 chr1B 91.618 513 35 3 1067 1579 637475404 637475908 0.000000e+00 702.0
5 TraesCS1D01G392000 chr1B 83.216 709 74 18 1718 2423 637476215 637476881 2.140000e-170 608.0
6 TraesCS1D01G392000 chr1B 92.793 222 16 0 1 222 637371062 637371283 3.130000e-84 322.0
7 TraesCS1D01G392000 chr1B 90.476 147 7 3 1587 1726 637476005 637476151 1.190000e-43 187.0
8 TraesCS1D01G392000 chr1B 92.391 92 6 1 2422 2513 637477071 637477161 2.030000e-26 130.0
9 TraesCS1D01G392000 chr1B 91.304 92 7 1 2422 2513 637476943 637477033 9.460000e-25 124.0
10 TraesCS1D01G392000 chr1A 91.417 769 50 9 992 1753 554088699 554089458 0.000000e+00 1040.0
11 TraesCS1D01G392000 chr1A 88.857 350 23 2 3 336 554087315 554087664 1.390000e-112 416.0
12 TraesCS1D01G392000 chr1A 92.079 303 10 8 1294 1589 554123766 554124061 5.010000e-112 414.0
13 TraesCS1D01G392000 chr5A 87.027 185 14 7 928 1104 681865229 681865411 1.530000e-47 200.0
14 TraesCS1D01G392000 chr5A 86.875 160 12 5 928 1080 683664125 683663968 1.200000e-38 171.0
15 TraesCS1D01G392000 chr6B 78.346 254 36 15 1951 2193 193561 193316 2.020000e-31 147.0
16 TraesCS1D01G392000 chr6B 78.059 237 45 5 1951 2183 698446429 698446662 2.610000e-30 143.0
17 TraesCS1D01G392000 chr6B 78.059 237 45 5 1951 2183 698808035 698807802 2.610000e-30 143.0
18 TraesCS1D01G392000 chr2D 77.912 249 46 8 1951 2193 625455936 625455691 2.020000e-31 147.0
19 TraesCS1D01G392000 chr7B 77.912 249 44 8 1951 2193 742246638 742246881 7.260000e-31 145.0
20 TraesCS1D01G392000 chr7B 77.686 242 48 4 1920 2156 17353160 17353400 2.610000e-30 143.0
21 TraesCS1D01G392000 chr7B 89.655 58 3 3 335 390 199316787 199316731 1.250000e-08 71.3
22 TraesCS1D01G392000 chr3A 77.642 246 48 3 1952 2193 632034823 632034581 2.610000e-30 143.0
23 TraesCS1D01G392000 chr3B 77.778 243 45 5 1956 2193 710411727 710411965 9.390000e-30 141.0
24 TraesCS1D01G392000 chr4B 77.419 248 47 5 1951 2193 655052805 655053048 3.380000e-29 139.0
25 TraesCS1D01G392000 chr6D 97.619 42 1 0 334 375 269237043 269237084 3.480000e-09 73.1


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 TraesCS1D01G392000 chr1D 462308319 462310837 2518 False 4652.0 4652 100.0000 1 2519 1 chr1D.!!$F2 2518
1 TraesCS1D01G392000 chr1D 462356463 462356999 536 False 645.0 645 88.3720 1067 1617 1 chr1D.!!$F3 550
2 TraesCS1D01G392000 chr1B 637371062 637372637 1575 False 1041.0 1760 91.5775 1 1681 2 chr1B.!!$F1 1680
3 TraesCS1D01G392000 chr1B 637475404 637477161 1757 False 350.2 702 89.8010 1067 2513 5 chr1B.!!$F2 1446
4 TraesCS1D01G392000 chr1A 554087315 554089458 2143 False 728.0 1040 90.1370 3 1753 2 chr1A.!!$F2 1750

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
815 1015 1.06909 AACACGGACATGCACGTCT 59.931 52.632 13.27 0.0 42.04 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2720 0.037303 CCACCACAAGGATGCTCTGT 59.963 55.0 0.0 0.0 38.69 3.41 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 49 3.317711 AGGTTCATACGAGAGATGAGCAG 59.682 47.826 0.00 0.00 36.54 4.24
218 219 2.274920 GCAAAGCAGCCTGAAATCTC 57.725 50.000 0.00 0.00 0.00 2.75
222 223 3.930634 AAGCAGCCTGAAATCTCAAAC 57.069 42.857 0.00 0.00 0.00 2.93
223 224 2.867624 AGCAGCCTGAAATCTCAAACA 58.132 42.857 0.00 0.00 0.00 2.83
232 234 7.343833 AGCCTGAAATCTCAAACATTTATGGAT 59.656 33.333 0.00 0.00 0.00 3.41
265 267 6.402981 AGTGGTTTTAGGGTCTTCCATTAT 57.597 37.500 0.00 0.00 38.24 1.28
268 270 8.566109 AGTGGTTTTAGGGTCTTCCATTATAAT 58.434 33.333 0.00 0.00 38.24 1.28
377 394 9.561069 AAATAAGTGACTCAACTTTGTACTCAT 57.439 29.630 0.00 0.00 40.77 2.90
446 469 2.416747 ACATGAATGTGTGTCCTGACG 58.583 47.619 0.00 0.00 40.03 4.35
458 489 2.738521 CTGACGAACAGTGGCGGG 60.739 66.667 11.50 0.00 41.30 6.13
459 490 4.308458 TGACGAACAGTGGCGGGG 62.308 66.667 11.50 0.00 0.00 5.73
462 493 4.077184 CGAACAGTGGCGGGGCTA 62.077 66.667 0.00 0.00 0.00 3.93
463 494 2.436115 GAACAGTGGCGGGGCTAC 60.436 66.667 0.00 0.00 40.33 3.58
468 499 4.162690 GTGGCGGGGCTACTGAGG 62.163 72.222 0.00 0.00 37.08 3.86
480 511 3.406764 GCTACTGAGGCATAAATGAGGG 58.593 50.000 0.00 0.00 0.00 4.30
592 781 3.457610 ACAAAAAGGACGACCGACTTA 57.542 42.857 0.00 0.00 41.83 2.24
669 862 1.722011 TTTCTTCGAACTGCCCGATC 58.278 50.000 0.00 0.00 35.84 3.69
757 957 1.127951 GATAAACAAGTGGCCGACGTG 59.872 52.381 15.70 15.70 39.72 4.49
815 1015 1.069090 AACACGGACATGCACGTCT 59.931 52.632 13.27 0.00 42.04 4.18
827 1027 2.910199 TGCACGTCTACGGAGTATACT 58.090 47.619 4.68 4.68 44.56 2.12
829 1029 2.868583 GCACGTCTACGGAGTATACTGA 59.131 50.000 10.90 0.00 44.56 3.41
835 1035 5.523188 CGTCTACGGAGTATACTGAGAAGTT 59.477 44.000 10.90 0.00 44.56 2.66
969 1492 4.022762 AGCTATTGTAGACAGCATCGTAGG 60.023 45.833 0.00 0.00 37.78 3.18
970 1493 4.261656 GCTATTGTAGACAGCATCGTAGGT 60.262 45.833 0.00 0.00 35.35 3.08
971 1494 5.048921 GCTATTGTAGACAGCATCGTAGGTA 60.049 44.000 0.00 0.00 35.35 3.08
972 1495 5.847111 ATTGTAGACAGCATCGTAGGTAA 57.153 39.130 0.00 0.00 0.00 2.85
973 1496 4.895224 TGTAGACAGCATCGTAGGTAAG 57.105 45.455 0.00 0.00 0.00 2.34
974 1497 2.873133 AGACAGCATCGTAGGTAAGC 57.127 50.000 0.00 0.00 0.00 3.09
975 1498 2.100197 AGACAGCATCGTAGGTAAGCA 58.900 47.619 0.00 0.00 0.00 3.91
988 1513 4.257267 AGGTAAGCAACAGCAAAAATCC 57.743 40.909 0.00 0.00 0.00 3.01
1179 1721 2.764314 GGACTACGGCGCCTTCGTA 61.764 63.158 26.68 19.87 41.38 3.43
1509 2051 3.329889 AATGTCTGGCCCGGCTCA 61.330 61.111 9.86 4.90 0.00 4.26
1738 2466 2.561373 GTTTTCCGGCGGCTTCTG 59.439 61.111 23.83 0.00 0.00 3.02
1759 2487 0.723981 GCTGACGATCTCTTGGTTGC 59.276 55.000 0.00 0.00 0.00 4.17
1769 2497 2.203280 TTGGTTGCCGGTGGTGAG 60.203 61.111 1.90 0.00 0.00 3.51
1770 2498 2.674563 CTTGGTTGCCGGTGGTGAGA 62.675 60.000 1.90 0.00 0.00 3.27
1796 2524 0.833287 ATCGGATCTCTTGTGTGGGG 59.167 55.000 0.00 0.00 0.00 4.96
1801 2529 0.608640 ATCTCTTGTGTGGGGACGTC 59.391 55.000 7.13 7.13 0.00 4.34
1802 2530 0.757561 TCTCTTGTGTGGGGACGTCA 60.758 55.000 18.91 0.00 0.00 4.35
1803 2531 0.319900 CTCTTGTGTGGGGACGTCAG 60.320 60.000 18.91 3.30 0.00 3.51
1804 2532 0.757561 TCTTGTGTGGGGACGTCAGA 60.758 55.000 18.91 5.87 0.00 3.27
1805 2533 0.600255 CTTGTGTGGGGACGTCAGAC 60.600 60.000 18.91 10.61 0.00 3.51
1820 2548 3.554731 CGTCAGACGTGTGTAGCTATAGA 59.445 47.826 15.21 0.00 36.74 1.98
1847 2575 8.584063 TTAAGGCCCTATTAGTTTAGGTTTTG 57.416 34.615 0.00 0.00 37.62 2.44
1850 2578 5.718130 GGCCCTATTAGTTTAGGTTTTGGTT 59.282 40.000 0.00 0.00 37.62 3.67
1852 2580 6.209986 GCCCTATTAGTTTAGGTTTTGGTTGT 59.790 38.462 0.00 0.00 37.62 3.32
1853 2581 7.256048 GCCCTATTAGTTTAGGTTTTGGTTGTT 60.256 37.037 0.00 0.00 37.62 2.83
1855 2583 8.852135 CCTATTAGTTTAGGTTTTGGTTGTTGA 58.148 33.333 0.00 0.00 35.06 3.18
1856 2584 9.673454 CTATTAGTTTAGGTTTTGGTTGTTGAC 57.327 33.333 0.00 0.00 0.00 3.18
1857 2585 4.989044 AGTTTAGGTTTTGGTTGTTGACG 58.011 39.130 0.00 0.00 0.00 4.35
1859 2587 4.619437 TTAGGTTTTGGTTGTTGACGTC 57.381 40.909 9.11 9.11 0.00 4.34
1860 2588 2.718563 AGGTTTTGGTTGTTGACGTCT 58.281 42.857 17.92 0.00 0.00 4.18
1861 2589 3.086282 AGGTTTTGGTTGTTGACGTCTT 58.914 40.909 17.92 0.00 0.00 3.01
1862 2590 3.119637 AGGTTTTGGTTGTTGACGTCTTG 60.120 43.478 17.92 0.00 0.00 3.02
1863 2591 3.175929 GTTTTGGTTGTTGACGTCTTGG 58.824 45.455 17.92 0.00 0.00 3.61
1864 2592 2.404923 TTGGTTGTTGACGTCTTGGA 57.595 45.000 17.92 0.00 0.00 3.53
1865 2593 2.631160 TGGTTGTTGACGTCTTGGAT 57.369 45.000 17.92 0.00 0.00 3.41
1866 2594 2.925724 TGGTTGTTGACGTCTTGGATT 58.074 42.857 17.92 0.00 0.00 3.01
1867 2595 2.875933 TGGTTGTTGACGTCTTGGATTC 59.124 45.455 17.92 2.09 0.00 2.52
1868 2596 2.096417 GGTTGTTGACGTCTTGGATTCG 60.096 50.000 17.92 0.00 0.00 3.34
1869 2597 1.790755 TGTTGACGTCTTGGATTCGG 58.209 50.000 17.92 0.00 0.00 4.30
1870 2598 0.442699 GTTGACGTCTTGGATTCGGC 59.557 55.000 17.92 0.00 0.00 5.54
1871 2599 1.011968 TTGACGTCTTGGATTCGGCG 61.012 55.000 17.92 0.00 35.16 6.46
1872 2600 2.125673 ACGTCTTGGATTCGGCGG 60.126 61.111 7.21 0.00 0.00 6.13
1873 2601 3.564027 CGTCTTGGATTCGGCGGC 61.564 66.667 7.21 0.00 0.00 6.53
1874 2602 3.564027 GTCTTGGATTCGGCGGCG 61.564 66.667 27.15 27.15 0.00 6.46
1875 2603 4.830765 TCTTGGATTCGGCGGCGG 62.831 66.667 31.73 13.38 0.00 6.13
1899 2627 3.197790 CGACTGCGGCCCAGAATG 61.198 66.667 23.24 11.14 44.64 2.67
1901 2629 1.817099 GACTGCGGCCCAGAATGAG 60.817 63.158 23.24 0.00 44.64 2.90
1906 2634 0.453390 GCGGCCCAGAATGAGAAAAG 59.547 55.000 0.00 0.00 39.69 2.27
1907 2635 0.453390 CGGCCCAGAATGAGAAAAGC 59.547 55.000 0.00 0.00 39.69 3.51
1908 2636 1.844687 GGCCCAGAATGAGAAAAGCT 58.155 50.000 0.00 0.00 39.69 3.74
1911 2639 2.821969 GCCCAGAATGAGAAAAGCTTCA 59.178 45.455 0.00 0.00 39.69 3.02
1912 2640 3.119566 GCCCAGAATGAGAAAAGCTTCAG 60.120 47.826 0.00 0.00 39.69 3.02
1913 2641 3.442977 CCCAGAATGAGAAAAGCTTCAGG 59.557 47.826 0.00 0.00 39.69 3.86
1914 2642 3.119566 CCAGAATGAGAAAAGCTTCAGGC 60.120 47.826 0.00 0.00 39.69 4.85
1915 2643 3.425892 CAGAATGAGAAAAGCTTCAGGCG 60.426 47.826 0.00 0.00 42.84 5.52
1936 2665 0.319555 TTCTCCAACGAGGCGTCTTG 60.320 55.000 1.72 1.72 39.99 3.02
1939 2668 2.383527 CCAACGAGGCGTCTTGCTC 61.384 63.158 3.56 0.00 45.43 4.26
1954 2683 4.514441 GTCTTGCTCTATGGTCATTGATGG 59.486 45.833 0.00 0.00 0.00 3.51
1967 2696 8.187913 TGGTCATTGATGGATTTGAAAACTAA 57.812 30.769 0.00 0.00 0.00 2.24
1978 2707 8.825745 TGGATTTGAAAACTAATTTGTTCAAGC 58.174 29.630 5.74 4.18 30.16 4.01
1979 2708 8.003784 GGATTTGAAAACTAATTTGTTCAAGCG 58.996 33.333 5.74 0.00 30.16 4.68
1986 2715 3.855689 AATTTGTTCAAGCGAGGATGG 57.144 42.857 0.00 0.00 0.00 3.51
1994 2723 2.887568 GCGAGGATGGCGTGACAG 60.888 66.667 0.00 0.00 0.00 3.51
1995 2724 2.885113 CGAGGATGGCGTGACAGA 59.115 61.111 0.00 0.00 0.00 3.41
2001 2730 1.153289 ATGGCGTGACAGAGCATCC 60.153 57.895 5.36 0.00 33.66 3.51
2011 2740 0.037303 CAGAGCATCCTTGTGGTGGT 59.963 55.000 0.00 0.00 33.66 4.16
2026 2755 0.668535 GTGGTCTTGTGTCTTTGGCC 59.331 55.000 0.00 0.00 0.00 5.36
2028 2757 1.064017 TGGTCTTGTGTCTTTGGCCTT 60.064 47.619 3.32 0.00 0.00 4.35
2030 2759 2.297701 GTCTTGTGTCTTTGGCCTTCA 58.702 47.619 3.32 0.00 0.00 3.02
2032 2761 1.338020 CTTGTGTCTTTGGCCTTCACC 59.662 52.381 3.32 0.00 0.00 4.02
2059 2788 2.320805 CAATGTTTGCTCCAGTGTCG 57.679 50.000 0.00 0.00 0.00 4.35
2075 2804 2.743928 CGGCACAGAGCTTGGGAC 60.744 66.667 2.78 0.00 44.79 4.46
2105 2836 2.089980 GAGCAGATGCAGATTGTGGTT 58.910 47.619 7.68 0.00 45.16 3.67
2109 2840 0.247814 GATGCAGATTGTGGTTCGCG 60.248 55.000 0.00 0.00 0.00 5.87
2125 2856 2.881441 GCGTCGGCGATATCTGAAA 58.119 52.632 16.53 0.00 41.33 2.69
2158 2889 1.944024 TGTGTTGGATTCGTGGTTGAC 59.056 47.619 0.00 0.00 0.00 3.18
2173 2904 4.637534 GTGGTTGACGACTAGTAGGTATGA 59.362 45.833 7.94 0.00 0.00 2.15
2180 2911 6.485984 TGACGACTAGTAGGTATGATTTCCTC 59.514 42.308 7.94 0.00 35.51 3.71
2185 2916 5.426325 AGTAGGTATGATTTCCTCCTCCT 57.574 43.478 0.00 0.00 35.51 3.69
2188 2919 4.153411 AGGTATGATTTCCTCCTCCTACG 58.847 47.826 0.00 0.00 0.00 3.51
2192 2923 3.709587 TGATTTCCTCCTCCTACGTCTT 58.290 45.455 0.00 0.00 0.00 3.01
2194 2925 4.159879 TGATTTCCTCCTCCTACGTCTTTC 59.840 45.833 0.00 0.00 0.00 2.62
2196 2927 3.453059 TCCTCCTCCTACGTCTTTCTT 57.547 47.619 0.00 0.00 0.00 2.52
2205 2936 1.374758 CGTCTTTCTTGAGCGGGCT 60.375 57.895 0.00 0.00 0.00 5.19
2219 2950 3.721706 GGCTGGAGGTGGGAGGTG 61.722 72.222 0.00 0.00 0.00 4.00
2220 2951 3.721706 GCTGGAGGTGGGAGGTGG 61.722 72.222 0.00 0.00 0.00 4.61
2221 2952 3.011517 CTGGAGGTGGGAGGTGGG 61.012 72.222 0.00 0.00 0.00 4.61
2222 2953 3.537506 TGGAGGTGGGAGGTGGGA 61.538 66.667 0.00 0.00 0.00 4.37
2232 2963 1.150135 GGGAGGTGGGAGGAGATATGA 59.850 57.143 0.00 0.00 0.00 2.15
2243 2974 5.163152 GGGAGGAGATATGAACTTTGATGGT 60.163 44.000 0.00 0.00 0.00 3.55
2264 2995 2.297701 GTGTTCGGGGATGTGCATATT 58.702 47.619 0.00 0.00 0.00 1.28
2265 2996 3.118223 TGTGTTCGGGGATGTGCATATTA 60.118 43.478 0.00 0.00 0.00 0.98
2266 2997 3.498397 GTGTTCGGGGATGTGCATATTAG 59.502 47.826 0.00 0.00 0.00 1.73
2267 2998 3.389656 TGTTCGGGGATGTGCATATTAGA 59.610 43.478 0.00 0.00 0.00 2.10
2268 2999 4.041567 TGTTCGGGGATGTGCATATTAGAT 59.958 41.667 0.00 0.00 0.00 1.98
2269 3000 4.908601 TCGGGGATGTGCATATTAGATT 57.091 40.909 0.00 0.00 0.00 2.40
2270 3001 5.241403 TCGGGGATGTGCATATTAGATTT 57.759 39.130 0.00 0.00 0.00 2.17
2271 3002 6.367374 TCGGGGATGTGCATATTAGATTTA 57.633 37.500 0.00 0.00 0.00 1.40
2272 3003 6.406370 TCGGGGATGTGCATATTAGATTTAG 58.594 40.000 0.00 0.00 0.00 1.85
2273 3004 6.212589 TCGGGGATGTGCATATTAGATTTAGA 59.787 38.462 0.00 0.00 0.00 2.10
2274 3005 7.050377 CGGGGATGTGCATATTAGATTTAGAT 58.950 38.462 0.00 0.00 0.00 1.98
2275 3006 8.204160 CGGGGATGTGCATATTAGATTTAGATA 58.796 37.037 0.00 0.00 0.00 1.98
2276 3007 9.331282 GGGGATGTGCATATTAGATTTAGATAC 57.669 37.037 0.00 0.00 0.00 2.24
2307 3038 9.696917 CAAAATTGCTTTTCTATCCTACAAACT 57.303 29.630 0.00 0.00 32.21 2.66
2320 3051 9.915629 CTATCCTACAAACTAATCATGTCCTAC 57.084 37.037 0.00 0.00 0.00 3.18
2344 3075 4.762251 AGGAAAACTCACAAGCAATAGGAC 59.238 41.667 0.00 0.00 0.00 3.85
2345 3076 4.762251 GGAAAACTCACAAGCAATAGGACT 59.238 41.667 0.00 0.00 0.00 3.85
2352 3083 6.096423 ACTCACAAGCAATAGGACTATCGTTA 59.904 38.462 0.00 0.00 0.00 3.18
2377 3108 7.450074 AGTACATGTAGGAATGAGTTCAACAA 58.550 34.615 5.62 0.00 36.20 2.83
2378 3109 6.560253 ACATGTAGGAATGAGTTCAACAAC 57.440 37.500 0.00 0.00 36.20 3.32
2379 3110 6.061441 ACATGTAGGAATGAGTTCAACAACA 58.939 36.000 0.00 0.00 36.20 3.33
2430 3352 1.274447 ACCAGCGTAGGGTGTTCTTAC 59.726 52.381 13.08 0.00 40.03 2.34
2452 3374 5.876357 ACTTCAAGTTAGACAATTAGCCCA 58.124 37.500 0.00 0.00 0.00 5.36
2483 3405 7.786030 ACTAATATCAGGATATTCATGGTCGG 58.214 38.462 15.74 3.70 41.60 4.79
2492 3414 5.163723 GGATATTCATGGTCGGCATAATGTG 60.164 44.000 0.00 0.00 0.00 3.21
2501 3423 5.779806 GTCGGCATAATGTGACCATATAC 57.220 43.478 0.00 0.00 29.16 1.47
2505 3427 6.209788 TCGGCATAATGTGACCATATACTGTA 59.790 38.462 0.00 0.00 29.16 2.74
2506 3428 6.310467 CGGCATAATGTGACCATATACTGTAC 59.690 42.308 0.00 0.00 29.16 2.90
2507 3429 7.386851 GGCATAATGTGACCATATACTGTACT 58.613 38.462 0.00 0.00 0.00 2.73
2508 3430 7.545965 GGCATAATGTGACCATATACTGTACTC 59.454 40.741 0.00 0.00 0.00 2.59
2509 3431 7.545965 GCATAATGTGACCATATACTGTACTCC 59.454 40.741 0.00 0.00 0.00 3.85
2511 3433 7.676683 AATGTGACCATATACTGTACTCCTT 57.323 36.000 0.00 0.00 0.00 3.36
2512 3434 6.710597 TGTGACCATATACTGTACTCCTTC 57.289 41.667 0.00 0.00 0.00 3.46
2513 3435 5.597182 TGTGACCATATACTGTACTCCTTCC 59.403 44.000 0.00 0.00 0.00 3.46
2514 3436 4.825634 TGACCATATACTGTACTCCTTCCG 59.174 45.833 0.00 0.00 0.00 4.30
2515 3437 4.801164 ACCATATACTGTACTCCTTCCGT 58.199 43.478 0.00 0.00 0.00 4.69
2516 3438 5.206587 ACCATATACTGTACTCCTTCCGTT 58.793 41.667 0.00 0.00 0.00 4.44
2517 3439 5.301298 ACCATATACTGTACTCCTTCCGTTC 59.699 44.000 0.00 0.00 0.00 3.95
2518 3440 5.450171 CATATACTGTACTCCTTCCGTTCG 58.550 45.833 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.611006 GGCTGCTCATCTCTCGTATGA 59.389 52.381 0.00 0.00 32.56 2.15
35 36 2.009424 TTCGGGCTGCTCATCTCTCG 62.009 60.000 0.00 0.00 0.00 4.04
48 49 8.871686 AATCATAATAATTCAAACTTTCGGGC 57.128 30.769 0.00 0.00 0.00 6.13
302 319 4.268405 GTGAAGAAAATGTTGTTGGTGCTG 59.732 41.667 0.00 0.00 0.00 4.41
373 390 3.873361 TCAGCGAGCTTATCCAAAATGAG 59.127 43.478 0.00 0.00 0.00 2.90
375 392 3.374988 TGTCAGCGAGCTTATCCAAAATG 59.625 43.478 0.00 0.00 0.00 2.32
377 394 2.742053 GTGTCAGCGAGCTTATCCAAAA 59.258 45.455 0.00 0.00 0.00 2.44
446 469 2.436115 GTAGCCCCGCCACTGTTC 60.436 66.667 0.00 0.00 0.00 3.18
458 489 3.406764 CCTCATTTATGCCTCAGTAGCC 58.593 50.000 0.00 0.00 0.00 3.93
459 490 3.406764 CCCTCATTTATGCCTCAGTAGC 58.593 50.000 0.00 0.00 0.00 3.58
460 491 3.244700 CCCCCTCATTTATGCCTCAGTAG 60.245 52.174 0.00 0.00 0.00 2.57
461 492 2.711009 CCCCCTCATTTATGCCTCAGTA 59.289 50.000 0.00 0.00 0.00 2.74
462 493 1.496429 CCCCCTCATTTATGCCTCAGT 59.504 52.381 0.00 0.00 0.00 3.41
463 494 1.820877 GCCCCCTCATTTATGCCTCAG 60.821 57.143 0.00 0.00 0.00 3.35
464 495 0.185901 GCCCCCTCATTTATGCCTCA 59.814 55.000 0.00 0.00 0.00 3.86
465 496 0.185901 TGCCCCCTCATTTATGCCTC 59.814 55.000 0.00 0.00 0.00 4.70
466 497 0.636101 TTGCCCCCTCATTTATGCCT 59.364 50.000 0.00 0.00 0.00 4.75
467 498 1.494960 TTTGCCCCCTCATTTATGCC 58.505 50.000 0.00 0.00 0.00 4.40
468 499 2.699846 TCATTTGCCCCCTCATTTATGC 59.300 45.455 0.00 0.00 0.00 3.14
469 500 3.243501 CGTCATTTGCCCCCTCATTTATG 60.244 47.826 0.00 0.00 0.00 1.90
470 501 2.958355 CGTCATTTGCCCCCTCATTTAT 59.042 45.455 0.00 0.00 0.00 1.40
471 502 2.025793 TCGTCATTTGCCCCCTCATTTA 60.026 45.455 0.00 0.00 0.00 1.40
472 503 1.185315 CGTCATTTGCCCCCTCATTT 58.815 50.000 0.00 0.00 0.00 2.32
473 504 0.331278 TCGTCATTTGCCCCCTCATT 59.669 50.000 0.00 0.00 0.00 2.57
474 505 0.331278 TTCGTCATTTGCCCCCTCAT 59.669 50.000 0.00 0.00 0.00 2.90
475 506 0.111446 TTTCGTCATTTGCCCCCTCA 59.889 50.000 0.00 0.00 0.00 3.86
476 507 1.474330 ATTTCGTCATTTGCCCCCTC 58.526 50.000 0.00 0.00 0.00 4.30
477 508 2.818751 TATTTCGTCATTTGCCCCCT 57.181 45.000 0.00 0.00 0.00 4.79
478 509 4.400529 AAATATTTCGTCATTTGCCCCC 57.599 40.909 0.00 0.00 0.00 5.40
515 546 6.372659 TGGCAGAAATTGAGAGAAATAGTGTC 59.627 38.462 0.00 0.00 0.00 3.67
592 781 4.254709 TCAAGCTGCTGTGGGCGT 62.255 61.111 1.35 0.00 45.43 5.68
669 862 4.505556 GCAAGAGCAAACAAAAAGGAAGAG 59.494 41.667 0.00 0.00 41.58 2.85
801 1001 1.872234 CCGTAGACGTGCATGTCCG 60.872 63.158 30.77 26.47 39.77 4.79
815 1015 6.018425 CGCTAAACTTCTCAGTATACTCCGTA 60.018 42.308 1.26 0.00 30.68 4.02
827 1027 1.068055 GGGTCGTCGCTAAACTTCTCA 60.068 52.381 0.00 0.00 0.00 3.27
829 1029 0.963962 TGGGTCGTCGCTAAACTTCT 59.036 50.000 0.00 0.00 0.00 2.85
835 1035 3.281240 GACCTGGGTCGTCGCTAA 58.719 61.111 3.88 0.00 35.30 3.09
920 1437 4.623002 TGCAACTATTTATGCATGCCATG 58.377 39.130 16.68 0.00 46.87 3.66
969 1492 4.627035 GGATGGATTTTTGCTGTTGCTTAC 59.373 41.667 0.00 0.00 40.48 2.34
970 1493 4.282957 TGGATGGATTTTTGCTGTTGCTTA 59.717 37.500 0.00 0.00 40.48 3.09
971 1494 3.071312 TGGATGGATTTTTGCTGTTGCTT 59.929 39.130 0.00 0.00 40.48 3.91
972 1495 2.633967 TGGATGGATTTTTGCTGTTGCT 59.366 40.909 0.00 0.00 40.48 3.91
973 1496 3.042871 TGGATGGATTTTTGCTGTTGC 57.957 42.857 0.00 0.00 40.20 4.17
974 1497 3.861113 CGATGGATGGATTTTTGCTGTTG 59.139 43.478 0.00 0.00 0.00 3.33
975 1498 3.763360 TCGATGGATGGATTTTTGCTGTT 59.237 39.130 0.00 0.00 0.00 3.16
988 1513 1.541889 CCCAGACATGGTCGATGGATG 60.542 57.143 0.00 0.79 46.10 3.51
1179 1721 1.382629 GTTGGCCCACACCAGGTAT 59.617 57.895 0.00 0.00 41.82 2.73
1256 1798 3.295462 CGTCGTCATCGTCGTCGC 61.295 66.667 0.00 0.00 41.73 5.19
1257 1799 2.643790 CCGTCGTCATCGTCGTCG 60.644 66.667 0.00 0.00 44.09 5.12
1258 1800 2.277120 CCCGTCGTCATCGTCGTC 60.277 66.667 6.54 0.00 44.09 4.20
1263 1805 4.873129 CTGCCCCCGTCGTCATCG 62.873 72.222 0.00 0.00 38.55 3.84
1362 1904 4.309950 ACGCCGACCTTCCCACAC 62.310 66.667 0.00 0.00 0.00 3.82
1509 2051 3.842923 CCGGCAGCTCAGTCCGAT 61.843 66.667 13.00 0.00 45.53 4.18
1593 2232 0.095245 CACGATGCTTACAGTTGCCG 59.905 55.000 0.00 0.00 0.00 5.69
1714 2367 2.426752 CGCCGGAAAACGTTGCTG 60.427 61.111 5.05 2.15 42.24 4.41
1738 2466 1.728971 CAACCAAGAGATCGTCAGCAC 59.271 52.381 0.00 0.00 0.00 4.40
1759 2487 1.553690 ATTGACCCTCTCACCACCGG 61.554 60.000 0.00 0.00 0.00 5.28
1769 2497 2.432510 ACAAGAGATCCGATTGACCCTC 59.567 50.000 8.64 0.00 0.00 4.30
1770 2498 2.169352 CACAAGAGATCCGATTGACCCT 59.831 50.000 8.64 0.00 0.00 4.34
1801 2529 7.591795 CCTTAAATCTATAGCTACACACGTCTG 59.408 40.741 0.00 0.00 0.00 3.51
1802 2530 7.649973 CCTTAAATCTATAGCTACACACGTCT 58.350 38.462 0.00 0.00 0.00 4.18
1803 2531 6.362820 GCCTTAAATCTATAGCTACACACGTC 59.637 42.308 0.00 0.00 0.00 4.34
1804 2532 6.214399 GCCTTAAATCTATAGCTACACACGT 58.786 40.000 0.00 0.00 0.00 4.49
1805 2533 5.634020 GGCCTTAAATCTATAGCTACACACG 59.366 44.000 0.00 0.00 0.00 4.49
1806 2534 5.932883 GGGCCTTAAATCTATAGCTACACAC 59.067 44.000 0.84 0.00 0.00 3.82
1807 2535 5.844516 AGGGCCTTAAATCTATAGCTACACA 59.155 40.000 0.00 0.00 0.00 3.72
1820 2548 9.778479 AAAACCTAAACTAATAGGGCCTTAAAT 57.222 29.630 13.45 0.00 45.69 1.40
1847 2575 2.096417 CGAATCCAAGACGTCAACAACC 60.096 50.000 19.50 0.21 0.00 3.77
1850 2578 1.790755 CCGAATCCAAGACGTCAACA 58.209 50.000 19.50 0.00 0.00 3.33
1852 2580 1.011968 CGCCGAATCCAAGACGTCAA 61.012 55.000 19.50 0.01 0.00 3.18
1853 2581 1.445410 CGCCGAATCCAAGACGTCA 60.445 57.895 19.50 0.00 0.00 4.35
1855 2583 2.125673 CCGCCGAATCCAAGACGT 60.126 61.111 0.00 0.00 0.00 4.34
1856 2584 3.564027 GCCGCCGAATCCAAGACG 61.564 66.667 0.00 0.00 0.00 4.18
1857 2585 3.564027 CGCCGCCGAATCCAAGAC 61.564 66.667 0.00 0.00 36.29 3.01
1886 2614 0.251121 TTTTCTCATTCTGGGCCGCA 60.251 50.000 0.00 0.00 0.00 5.69
1893 2621 3.425892 CGCCTGAAGCTTTTCTCATTCTG 60.426 47.826 0.00 0.00 40.39 3.02
1906 2634 0.238553 GTTGGAGAAACGCCTGAAGC 59.761 55.000 0.00 0.00 38.52 3.86
1915 2643 0.319641 AGACGCCTCGTTGGAGAAAC 60.320 55.000 7.74 0.00 43.27 2.78
1926 2655 0.461961 ACCATAGAGCAAGACGCCTC 59.538 55.000 0.00 0.00 44.04 4.70
1936 2665 5.766670 TCAAATCCATCAATGACCATAGAGC 59.233 40.000 0.00 0.00 0.00 4.09
1939 2668 8.472413 AGTTTTCAAATCCATCAATGACCATAG 58.528 33.333 0.00 0.00 0.00 2.23
1954 2683 8.751335 TCGCTTGAACAAATTAGTTTTCAAATC 58.249 29.630 0.00 0.00 28.81 2.17
1967 2696 1.474077 GCCATCCTCGCTTGAACAAAT 59.526 47.619 0.00 0.00 0.00 2.32
1978 2707 1.226802 CTCTGTCACGCCATCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
1979 2708 1.520342 GCTCTGTCACGCCATCCTC 60.520 63.158 0.00 0.00 0.00 3.71
1986 2715 0.671781 ACAAGGATGCTCTGTCACGC 60.672 55.000 0.00 0.00 0.00 5.34
1991 2720 0.037303 CCACCACAAGGATGCTCTGT 59.963 55.000 0.00 0.00 38.69 3.41
1993 2722 0.326264 GACCACCACAAGGATGCTCT 59.674 55.000 0.00 0.00 38.69 4.09
1994 2723 0.326264 AGACCACCACAAGGATGCTC 59.674 55.000 0.00 0.00 38.69 4.26
1995 2724 0.773644 AAGACCACCACAAGGATGCT 59.226 50.000 0.00 0.00 38.69 3.79
2001 2730 2.332063 AGACACAAGACCACCACAAG 57.668 50.000 0.00 0.00 0.00 3.16
2011 2740 2.297701 GTGAAGGCCAAAGACACAAGA 58.702 47.619 5.01 0.00 0.00 3.02
2043 2772 1.891919 GCCGACACTGGAGCAAACA 60.892 57.895 0.00 0.00 0.00 2.83
2059 2788 2.167398 TACGTCCCAAGCTCTGTGCC 62.167 60.000 0.00 0.00 44.23 5.01
2075 2804 0.249238 GCATCTGCTCCTGGACTACG 60.249 60.000 0.00 0.00 38.21 3.51
2083 2812 1.408405 CCACAATCTGCATCTGCTCCT 60.408 52.381 3.53 0.00 42.66 3.69
2109 2840 2.989840 CCATCTTTCAGATATCGCCGAC 59.010 50.000 0.00 0.00 32.12 4.79
2117 2848 2.766263 ACGACCTGCCATCTTTCAGATA 59.234 45.455 0.00 0.00 32.12 1.98
2125 2856 0.603707 CAACACACGACCTGCCATCT 60.604 55.000 0.00 0.00 0.00 2.90
2131 2862 0.790207 CGAATCCAACACACGACCTG 59.210 55.000 0.00 0.00 0.00 4.00
2134 2865 0.511221 CCACGAATCCAACACACGAC 59.489 55.000 0.00 0.00 0.00 4.34
2136 2867 0.941542 AACCACGAATCCAACACACG 59.058 50.000 0.00 0.00 0.00 4.49
2158 2889 6.005198 AGGAGGAAATCATACCTACTAGTCG 58.995 44.000 0.00 0.00 44.70 4.18
2161 2892 6.557568 AGGAGGAGGAAATCATACCTACTAG 58.442 44.000 0.00 0.00 46.29 2.57
2165 2896 5.163012 ACGTAGGAGGAGGAAATCATACCTA 60.163 44.000 0.00 0.00 36.57 3.08
2173 2904 4.354662 AGAAAGACGTAGGAGGAGGAAAT 58.645 43.478 0.00 0.00 0.00 2.17
2180 2911 2.732597 CGCTCAAGAAAGACGTAGGAGG 60.733 54.545 0.00 0.00 0.00 4.30
2185 2916 0.389426 GCCCGCTCAAGAAAGACGTA 60.389 55.000 0.00 0.00 0.00 3.57
2188 2919 1.301677 CCAGCCCGCTCAAGAAAGAC 61.302 60.000 0.00 0.00 0.00 3.01
2192 2923 2.665000 CTCCAGCCCGCTCAAGAA 59.335 61.111 0.00 0.00 0.00 2.52
2194 2925 3.710722 ACCTCCAGCCCGCTCAAG 61.711 66.667 0.00 0.00 0.00 3.02
2205 2936 3.537506 TCCCACCTCCCACCTCCA 61.538 66.667 0.00 0.00 0.00 3.86
2215 2946 3.715648 AGTTCATATCTCCTCCCACCT 57.284 47.619 0.00 0.00 0.00 4.00
2216 2947 4.164221 TCAAAGTTCATATCTCCTCCCACC 59.836 45.833 0.00 0.00 0.00 4.61
2217 2948 5.359194 TCAAAGTTCATATCTCCTCCCAC 57.641 43.478 0.00 0.00 0.00 4.61
2218 2949 5.163163 CCATCAAAGTTCATATCTCCTCCCA 60.163 44.000 0.00 0.00 0.00 4.37
2219 2950 5.163152 ACCATCAAAGTTCATATCTCCTCCC 60.163 44.000 0.00 0.00 0.00 4.30
2220 2951 5.762218 CACCATCAAAGTTCATATCTCCTCC 59.238 44.000 0.00 0.00 0.00 4.30
2221 2952 6.259608 CACACCATCAAAGTTCATATCTCCTC 59.740 42.308 0.00 0.00 0.00 3.71
2222 2953 6.118170 CACACCATCAAAGTTCATATCTCCT 58.882 40.000 0.00 0.00 0.00 3.69
2232 2963 1.953686 CCCGAACACACCATCAAAGTT 59.046 47.619 0.00 0.00 0.00 2.66
2243 2974 0.615850 TATGCACATCCCCGAACACA 59.384 50.000 0.00 0.00 0.00 3.72
2273 3004 9.860898 GGATAGAAAAGCAATTTTGTTCTGTAT 57.139 29.630 3.42 0.00 0.00 2.29
2274 3005 9.077885 AGGATAGAAAAGCAATTTTGTTCTGTA 57.922 29.630 3.42 0.00 0.00 2.74
2275 3006 7.955918 AGGATAGAAAAGCAATTTTGTTCTGT 58.044 30.769 3.42 0.00 0.00 3.41
2276 3007 9.346725 GTAGGATAGAAAAGCAATTTTGTTCTG 57.653 33.333 3.42 0.00 0.00 3.02
2281 3012 9.696917 AGTTTGTAGGATAGAAAAGCAATTTTG 57.303 29.630 0.00 0.00 35.48 2.44
2286 3017 9.733556 TGATTAGTTTGTAGGATAGAAAAGCAA 57.266 29.630 0.00 0.00 35.48 3.91
2307 3038 7.103641 GTGAGTTTTCCTGTAGGACATGATTA 58.896 38.462 0.00 0.00 45.39 1.75
2310 3041 4.346709 TGTGAGTTTTCCTGTAGGACATGA 59.653 41.667 0.00 0.00 45.39 3.07
2311 3042 4.641396 TGTGAGTTTTCCTGTAGGACATG 58.359 43.478 0.00 0.00 45.39 3.21
2320 3051 4.761739 TCCTATTGCTTGTGAGTTTTCCTG 59.238 41.667 0.00 0.00 0.00 3.86
2344 3075 8.784994 ACTCATTCCTACATGTACTAACGATAG 58.215 37.037 0.08 0.00 46.19 2.08
2345 3076 8.687292 ACTCATTCCTACATGTACTAACGATA 57.313 34.615 0.08 0.00 0.00 2.92
2352 3083 7.004555 TGTTGAACTCATTCCTACATGTACT 57.995 36.000 0.08 0.00 33.49 2.73
2412 3143 3.251571 GAAGTAAGAACACCCTACGCTG 58.748 50.000 0.00 0.00 0.00 5.18
2430 3352 7.552687 TGTATGGGCTAATTGTCTAACTTGAAG 59.447 37.037 0.00 0.00 0.00 3.02
2483 3405 7.545965 GGAGTACAGTATATGGTCACATTATGC 59.454 40.741 0.00 0.00 38.53 3.14
2492 3414 4.826183 ACGGAAGGAGTACAGTATATGGTC 59.174 45.833 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.