Multiple sequence alignment - TraesCS4B01G223000

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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 TraesCS4B01G223000 chr4B 100.000 2729 0 0 1 2729 467716869 467719597 0.000000e+00 5040.0
1 TraesCS4B01G223000 chr4B 84.567 635 82 11 1977 2606 431568496 431567873 1.390000e-172 616.0
2 TraesCS4B01G223000 chr4B 94.186 86 4 1 2644 2729 6403231 6403147 2.210000e-26 130.0
3 TraesCS4B01G223000 chr4D 93.887 1963 67 22 1 1929 380294319 380296262 0.000000e+00 2911.0
4 TraesCS4B01G223000 chr4D 86.929 635 77 5 1977 2605 9482587 9481953 0.000000e+00 708.0
5 TraesCS4B01G223000 chr4A 91.579 1995 75 41 1 1931 83573147 83571182 0.000000e+00 2667.0
6 TraesCS4B01G223000 chr4A 77.076 602 84 30 2029 2606 144839625 144839054 5.710000e-77 298.0
7 TraesCS4B01G223000 chr4A 89.231 130 10 3 2480 2605 115882281 115882152 2.810000e-35 159.0
8 TraesCS4B01G223000 chr4A 98.765 81 1 0 2649 2729 592496587 592496507 7.880000e-31 145.0
9 TraesCS4B01G223000 chr4A 98.765 81 1 0 2649 2729 593063473 593063393 7.880000e-31 145.0
10 TraesCS4B01G223000 chr4A 94.253 87 4 1 2644 2729 609572461 609572375 6.130000e-27 132.0
11 TraesCS4B01G223000 chr4A 98.077 52 0 1 2602 2652 694655074 694655125 3.740000e-14 89.8
12 TraesCS4B01G223000 chr4A 93.103 58 4 0 2595 2652 650594183 650594240 4.840000e-13 86.1
13 TraesCS4B01G223000 chr6D 84.748 636 84 11 1977 2605 39087369 39086740 2.310000e-175 625.0
14 TraesCS4B01G223000 chr5B 82.596 339 48 9 1115 1452 438557310 438557638 3.440000e-74 289.0
15 TraesCS4B01G223000 chr5B 95.349 86 3 1 2643 2728 676245850 676245934 4.740000e-28 135.0
16 TraesCS4B01G223000 chr5D 82.006 339 50 9 1115 1452 369427996 369428324 7.440000e-71 278.0
17 TraesCS4B01G223000 chr5A 81.953 338 52 7 1115 1452 471946672 471947000 7.440000e-71 278.0
18 TraesCS4B01G223000 chr7D 75.123 611 93 33 2014 2605 82292016 82291446 5.880000e-57 231.0
19 TraesCS4B01G223000 chr7D 98.039 51 1 0 2602 2652 35397713 35397763 3.740000e-14 89.8
20 TraesCS4B01G223000 chr7D 96.296 54 2 0 2599 2652 584243944 584243997 3.740000e-14 89.8
21 TraesCS4B01G223000 chr7A 78.481 395 51 15 2217 2605 83908893 83908527 7.600000e-56 228.0
22 TraesCS4B01G223000 chr7A 76.415 424 76 17 2190 2605 681671362 681671769 9.900000e-50 207.0
23 TraesCS4B01G223000 chr7A 98.765 81 1 0 2649 2729 95817436 95817356 7.880000e-31 145.0
24 TraesCS4B01G223000 chr3B 76.096 502 71 28 2116 2605 621935266 621934802 1.650000e-52 217.0
25 TraesCS4B01G223000 chr3B 98.765 81 1 0 2649 2729 160643802 160643882 7.880000e-31 145.0
26 TraesCS4B01G223000 chr6B 98.765 81 1 0 2649 2729 672136842 672136762 7.880000e-31 145.0
27 TraesCS4B01G223000 chr6B 96.512 86 3 0 2644 2729 526200308 526200393 2.830000e-30 143.0
28 TraesCS4B01G223000 chr6B 100.000 50 0 0 2603 2652 688176113 688176064 2.890000e-15 93.5
29 TraesCS4B01G223000 chr3A 96.552 87 3 0 2643 2729 581367978 581368064 7.880000e-31 145.0
30 TraesCS4B01G223000 chr3A 94.253 87 5 0 2641 2727 704458533 704458447 1.700000e-27 134.0
31 TraesCS4B01G223000 chr2A 98.765 81 1 0 2649 2729 312042622 312042542 7.880000e-31 145.0
32 TraesCS4B01G223000 chr2A 91.935 62 3 2 2592 2652 639790918 639790858 4.840000e-13 86.1
33 TraesCS4B01G223000 chrUn 94.186 86 4 1 2644 2729 274800307 274800223 2.210000e-26 130.0
34 TraesCS4B01G223000 chr2B 93.258 89 5 1 2642 2729 555653860 555653772 2.210000e-26 130.0
35 TraesCS4B01G223000 chr7B 100.000 49 0 0 2604 2652 744174762 744174714 1.040000e-14 91.6
36 TraesCS4B01G223000 chr1B 100.000 49 0 0 2604 2652 550457688 550457640 1.040000e-14 91.6
37 TraesCS4B01G223000 chr1B 100.000 49 0 0 2604 2652 676982035 676982083 1.040000e-14 91.6


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 TraesCS4B01G223000 chr4B 467716869 467719597 2728 False 5040 5040 100.000 1 2729 1 chr4B.!!$F1 2728
1 TraesCS4B01G223000 chr4B 431567873 431568496 623 True 616 616 84.567 1977 2606 1 chr4B.!!$R2 629
2 TraesCS4B01G223000 chr4D 380294319 380296262 1943 False 2911 2911 93.887 1 1929 1 chr4D.!!$F1 1928
3 TraesCS4B01G223000 chr4D 9481953 9482587 634 True 708 708 86.929 1977 2605 1 chr4D.!!$R1 628
4 TraesCS4B01G223000 chr4A 83571182 83573147 1965 True 2667 2667 91.579 1 1931 1 chr4A.!!$R1 1930
5 TraesCS4B01G223000 chr4A 144839054 144839625 571 True 298 298 77.076 2029 2606 1 chr4A.!!$R3 577
6 TraesCS4B01G223000 chr6D 39086740 39087369 629 True 625 625 84.748 1977 2605 1 chr6D.!!$R1 628
7 TraesCS4B01G223000 chr7D 82291446 82292016 570 True 231 231 75.123 2014 2605 1 chr7D.!!$R1 591

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
158 159 0.036022 AGCTCAAGTTCACAGAGGGC 59.964 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2056 0.388294 GCGGTAGGCGAAGGTTAGAT 59.612 55.0 0.0 0.0 0.0 1.98 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
40 41 2.031516 CGTGTCCTGCTGCTTCTGG 61.032 63.158 0.00 0.00 0.00 3.86
100 101 2.579201 GCAGGAGCTAGCCGTTCA 59.421 61.111 12.13 0.00 37.91 3.18
106 107 0.103937 GAGCTAGCCGTTCATGCTCT 59.896 55.000 12.13 0.00 44.52 4.09
107 108 0.539051 AGCTAGCCGTTCATGCTCTT 59.461 50.000 12.13 0.00 40.23 2.85
122 123 0.915364 CTCTTCTTCCCTCCCCTTGG 59.085 60.000 0.00 0.00 0.00 3.61
123 124 1.208165 TCTTCTTCCCTCCCCTTGGC 61.208 60.000 0.00 0.00 0.00 4.52
135 136 0.323178 CCCTTGGCATCTGAAGCAGT 60.323 55.000 7.22 0.00 32.61 4.40
140 141 3.257469 TGGCATCTGAAGCAGTAAGAG 57.743 47.619 7.22 0.00 32.61 2.85
147 148 3.576118 TCTGAAGCAGTAAGAGCTCAAGT 59.424 43.478 17.77 3.39 42.53 3.16
152 153 3.070159 AGCAGTAAGAGCTCAAGTTCACA 59.930 43.478 17.77 0.00 38.01 3.58
153 154 3.431572 GCAGTAAGAGCTCAAGTTCACAG 59.568 47.826 17.77 2.46 0.00 3.66
158 159 0.036022 AGCTCAAGTTCACAGAGGGC 59.964 55.000 0.00 0.00 0.00 5.19
166 168 2.430382 TTCACAGAGGGCGTTCGTCC 62.430 60.000 7.83 7.83 0.00 4.79
172 174 1.442526 GAGGGCGTTCGTCCGATCTA 61.443 60.000 10.15 0.00 34.60 1.98
207 209 2.490115 TGGTGTTTTATGATGGTTCGCC 59.510 45.455 0.00 0.00 37.92 5.54
446 448 5.246981 TGTTTTGATCCATCACTTCTCCT 57.753 39.130 0.00 0.00 36.36 3.69
460 462 3.571401 ACTTCTCCTGCCTTCATGTTTTG 59.429 43.478 0.00 0.00 0.00 2.44
578 580 7.873719 TTTGAACTAGTCCATTTTGTGAGAA 57.126 32.000 0.00 0.00 0.00 2.87
702 704 0.465705 TCTCTTGATCCGCCACATCC 59.534 55.000 0.00 0.00 0.00 3.51
703 705 0.467384 CTCTTGATCCGCCACATCCT 59.533 55.000 0.00 0.00 0.00 3.24
704 706 0.178767 TCTTGATCCGCCACATCCTG 59.821 55.000 0.00 0.00 0.00 3.86
705 707 0.816825 CTTGATCCGCCACATCCTGG 60.817 60.000 0.00 0.00 44.08 4.45
706 708 1.271127 TTGATCCGCCACATCCTGGA 61.271 55.000 0.00 0.00 43.95 3.86
707 709 1.056125 TGATCCGCCACATCCTGGAT 61.056 55.000 2.57 2.57 43.95 3.41
725 727 7.363031 TCCTGGATCTAGATAGTACCAAACTT 58.637 38.462 7.81 0.00 39.80 2.66
726 728 7.844779 TCCTGGATCTAGATAGTACCAAACTTT 59.155 37.037 7.81 0.00 39.80 2.66
727 729 7.928706 CCTGGATCTAGATAGTACCAAACTTTG 59.071 40.741 7.81 0.00 39.80 2.77
728 730 8.375493 TGGATCTAGATAGTACCAAACTTTGT 57.625 34.615 4.89 0.00 39.80 2.83
729 731 9.483489 TGGATCTAGATAGTACCAAACTTTGTA 57.517 33.333 4.89 0.00 39.80 2.41
757 759 9.658799 ATTATAATGAAGATTATCCACACCTCG 57.341 33.333 0.00 0.00 36.38 4.63
758 760 5.359194 AATGAAGATTATCCACACCTCGT 57.641 39.130 0.00 0.00 0.00 4.18
770 803 0.736053 CACCTCGTCCTCTCTACTGC 59.264 60.000 0.00 0.00 0.00 4.40
811 844 3.426695 GGTTCTCGCCATTCTTTGACATG 60.427 47.826 0.00 0.00 0.00 3.21
846 879 0.930310 GCAAGCGTCGCATCATCTAA 59.070 50.000 21.09 0.00 0.00 2.10
880 914 9.924650 AAGTATATATTTTGAACTAGGTAGCCG 57.075 33.333 0.00 0.00 0.00 5.52
921 955 6.127925 TGGTGCACAGATCATTCATTTCTAAC 60.128 38.462 20.43 0.00 0.00 2.34
922 956 6.127925 GGTGCACAGATCATTCATTTCTAACA 60.128 38.462 20.43 0.00 0.00 2.41
923 957 6.744537 GTGCACAGATCATTCATTTCTAACAC 59.255 38.462 13.17 0.00 0.00 3.32
924 958 5.961843 GCACAGATCATTCATTTCTAACACG 59.038 40.000 0.00 0.00 0.00 4.49
928 962 9.383519 ACAGATCATTCATTTCTAACACGTAAT 57.616 29.630 0.00 0.00 0.00 1.89
957 998 3.442625 TCTTGATTTTCTCCATGCAGCTG 59.557 43.478 10.11 10.11 0.00 4.24
967 1008 0.812811 CATGCAGCTGTACATCGCCT 60.813 55.000 16.64 0.00 0.00 5.52
998 1039 3.296322 GCAGATCGCAAGCTAGATAGT 57.704 47.619 0.00 0.00 41.79 2.12
1434 1475 2.100631 CCTCGTCGACATTGTGCCC 61.101 63.158 17.16 0.00 0.00 5.36
1710 1751 3.011517 GCTGGCTTCCCTCCTGGA 61.012 66.667 0.00 0.00 43.18 3.86
1715 1756 1.306568 GCTTCCCTCCTGGACCTCT 60.307 63.158 0.00 0.00 45.11 3.69
1793 1853 2.573167 CACGGCGCGCAATGTAAC 60.573 61.111 34.42 12.59 0.00 2.50
1861 1932 8.630054 ACTAACAACAAGCAGTTATTTATCCA 57.370 30.769 0.00 0.00 38.74 3.41
1866 1937 8.584157 ACAACAAGCAGTTATTTATCCATTTGA 58.416 29.630 0.00 0.00 38.74 2.69
1907 1985 5.762179 ACTACCATGAGTTTGAATCCAGA 57.238 39.130 0.00 0.00 0.00 3.86
1934 2012 3.558829 CAGGATATGCATCATCCGTATGC 59.441 47.826 20.30 7.75 45.64 3.14
1947 2025 2.490328 CGTATGCGGCCAAATTTCAT 57.510 45.000 2.24 0.00 0.00 2.57
1948 2026 2.118683 CGTATGCGGCCAAATTTCATG 58.881 47.619 2.24 0.00 0.00 3.07
1949 2027 2.479389 CGTATGCGGCCAAATTTCATGT 60.479 45.455 2.24 0.00 0.00 3.21
1950 2028 2.766345 ATGCGGCCAAATTTCATGTT 57.234 40.000 2.24 0.00 0.00 2.71
1951 2029 2.540265 TGCGGCCAAATTTCATGTTT 57.460 40.000 2.24 0.00 0.00 2.83
1952 2030 2.843701 TGCGGCCAAATTTCATGTTTT 58.156 38.095 2.24 0.00 0.00 2.43
1953 2031 2.547211 TGCGGCCAAATTTCATGTTTTG 59.453 40.909 2.24 9.88 33.58 2.44
1954 2032 2.805099 GCGGCCAAATTTCATGTTTTGA 59.195 40.909 2.24 0.00 35.34 2.69
1955 2033 3.363871 GCGGCCAAATTTCATGTTTTGAC 60.364 43.478 2.24 7.68 35.34 3.18
1956 2034 3.186205 CGGCCAAATTTCATGTTTTGACC 59.814 43.478 2.24 13.19 35.34 4.02
1957 2035 4.388485 GGCCAAATTTCATGTTTTGACCT 58.612 39.130 15.34 0.00 33.91 3.85
1958 2036 4.821260 GGCCAAATTTCATGTTTTGACCTT 59.179 37.500 15.34 0.00 33.91 3.50
1959 2037 5.299028 GGCCAAATTTCATGTTTTGACCTTT 59.701 36.000 15.34 0.00 33.91 3.11
1960 2038 6.183360 GGCCAAATTTCATGTTTTGACCTTTT 60.183 34.615 15.34 0.00 33.91 2.27
1961 2039 7.257003 GCCAAATTTCATGTTTTGACCTTTTT 58.743 30.769 15.34 0.00 35.34 1.94
1962 2040 8.401709 GCCAAATTTCATGTTTTGACCTTTTTA 58.598 29.630 15.34 0.00 35.34 1.52
1963 2041 9.934190 CCAAATTTCATGTTTTGACCTTTTTAG 57.066 29.630 15.34 0.00 35.34 1.85
1964 2042 9.934190 CAAATTTCATGTTTTGACCTTTTTAGG 57.066 29.630 10.84 0.00 35.34 2.69
1965 2043 9.679661 AAATTTCATGTTTTGACCTTTTTAGGT 57.320 25.926 0.00 0.00 46.40 3.08
1966 2044 9.679661 AATTTCATGTTTTGACCTTTTTAGGTT 57.320 25.926 0.00 0.00 43.24 3.50
1967 2045 8.485976 TTTCATGTTTTGACCTTTTTAGGTTG 57.514 30.769 0.00 0.00 43.24 3.77
1968 2046 6.045955 TCATGTTTTGACCTTTTTAGGTTGC 58.954 36.000 0.00 0.00 43.24 4.17
1969 2047 5.669164 TGTTTTGACCTTTTTAGGTTGCT 57.331 34.783 0.00 0.00 43.24 3.91
1970 2048 6.043854 TGTTTTGACCTTTTTAGGTTGCTT 57.956 33.333 0.00 0.00 43.24 3.91
1971 2049 5.872070 TGTTTTGACCTTTTTAGGTTGCTTG 59.128 36.000 0.00 0.00 43.24 4.01
1972 2050 5.923733 TTTGACCTTTTTAGGTTGCTTGA 57.076 34.783 0.00 0.00 43.24 3.02
1973 2051 5.514274 TTGACCTTTTTAGGTTGCTTGAG 57.486 39.130 0.00 0.00 43.24 3.02
1974 2052 3.317993 TGACCTTTTTAGGTTGCTTGAGC 59.682 43.478 0.00 0.00 43.24 4.26
1988 2066 4.873768 GCTTGAGCAAGATCTAACCTTC 57.126 45.455 14.04 0.00 40.79 3.46
1998 2076 0.682209 TCTAACCTTCGCCTACCGCT 60.682 55.000 0.00 0.00 36.73 5.52
2088 2178 3.131478 CCGCCGTTTGTGGGATCC 61.131 66.667 1.92 1.92 41.22 3.36
2092 2182 1.175983 GCCGTTTGTGGGATCCAACA 61.176 55.000 18.69 18.69 34.18 3.33
2114 2204 0.539986 CCTACCGCCAAGGCTTAAGA 59.460 55.000 6.67 0.00 46.52 2.10
2122 2212 1.066430 CCAAGGCTTAAGACGGTAGCA 60.066 52.381 6.67 0.00 36.64 3.49
2142 2232 2.679199 GGCTAAAGCTACTGCCGAC 58.321 57.895 7.82 0.00 41.70 4.79
2145 2235 0.454600 CTAAAGCTACTGCCGACGGA 59.545 55.000 20.50 1.60 40.80 4.69
2146 2236 0.171903 TAAAGCTACTGCCGACGGAC 59.828 55.000 20.50 9.82 40.80 4.79
2147 2237 1.812686 AAAGCTACTGCCGACGGACA 61.813 55.000 20.50 14.19 40.80 4.02
2164 2265 4.157120 ACGGCGGTGAGGTATGGC 62.157 66.667 13.24 0.00 0.00 4.40
2170 2271 4.530857 GTGAGGTATGGCGCGCCT 62.531 66.667 45.79 33.35 36.94 5.52
2171 2272 3.781307 TGAGGTATGGCGCGCCTT 61.781 61.111 45.79 40.89 36.94 4.35
2172 2273 3.272334 GAGGTATGGCGCGCCTTG 61.272 66.667 45.79 0.33 36.94 3.61
2173 2274 4.096003 AGGTATGGCGCGCCTTGT 62.096 61.111 45.79 33.27 36.94 3.16
2180 2281 4.135493 GCGCGCCTTGTCTTCGTC 62.135 66.667 23.24 0.00 0.00 4.20
2184 2285 0.095417 GCGCCTTGTCTTCGTCAATC 59.905 55.000 0.00 0.00 0.00 2.67
2321 2424 3.071479 GTTCTGTGCGGTAGGATTTCAA 58.929 45.455 0.00 0.00 0.00 2.69
2391 2494 3.684369 TACCTGGCGGTAGGGTCCC 62.684 68.421 0.00 0.00 43.29 4.46
2472 2576 7.174772 TGTTTGCATATGACAGATAAACACACT 59.825 33.333 6.97 0.00 33.27 3.55
2476 2580 6.403527 GCATATGACAGATAAACACACTGCAA 60.404 38.462 6.97 0.00 35.38 4.08
2518 2623 7.943079 ATGAAAATATGATGACCTCACACAA 57.057 32.000 0.00 0.00 36.48 3.33
2606 2715 4.817464 AGCAATAACACAAAACCGAGTACA 59.183 37.500 0.00 0.00 0.00 2.90
2607 2716 4.907582 GCAATAACACAAAACCGAGTACAC 59.092 41.667 0.00 0.00 0.00 2.90
2608 2717 5.277634 GCAATAACACAAAACCGAGTACACT 60.278 40.000 0.00 0.00 0.00 3.55
2609 2718 6.073657 GCAATAACACAAAACCGAGTACACTA 60.074 38.462 0.00 0.00 0.00 2.74
2610 2719 7.507304 CAATAACACAAAACCGAGTACACTAG 58.493 38.462 0.00 0.00 0.00 2.57
2611 2720 4.660789 ACACAAAACCGAGTACACTAGT 57.339 40.909 0.00 0.00 0.00 2.57
2612 2721 5.772825 ACACAAAACCGAGTACACTAGTA 57.227 39.130 0.00 0.00 0.00 1.82
2613 2722 5.766222 ACACAAAACCGAGTACACTAGTAG 58.234 41.667 0.00 0.00 0.00 2.57
2614 2723 5.532406 ACACAAAACCGAGTACACTAGTAGA 59.468 40.000 3.59 0.00 0.00 2.59
2615 2724 6.208204 ACACAAAACCGAGTACACTAGTAGAT 59.792 38.462 3.59 0.00 0.00 1.98
2616 2725 7.391554 ACACAAAACCGAGTACACTAGTAGATA 59.608 37.037 3.59 0.00 0.00 1.98
2617 2726 8.239314 CACAAAACCGAGTACACTAGTAGATAA 58.761 37.037 3.59 0.00 0.00 1.75
2618 2727 8.796475 ACAAAACCGAGTACACTAGTAGATAAA 58.204 33.333 3.59 0.00 0.00 1.40
2619 2728 9.286946 CAAAACCGAGTACACTAGTAGATAAAG 57.713 37.037 3.59 0.00 0.00 1.85
2620 2729 7.565323 AACCGAGTACACTAGTAGATAAAGG 57.435 40.000 3.59 0.00 0.00 3.11
2621 2730 6.060788 ACCGAGTACACTAGTAGATAAAGGG 58.939 44.000 3.59 0.00 0.00 3.95
2622 2731 5.472820 CCGAGTACACTAGTAGATAAAGGGG 59.527 48.000 3.59 0.00 0.00 4.79
2623 2732 5.048852 CGAGTACACTAGTAGATAAAGGGGC 60.049 48.000 3.59 0.00 0.00 5.80
2624 2733 6.028258 AGTACACTAGTAGATAAAGGGGCT 57.972 41.667 3.59 0.00 0.00 5.19
2625 2734 6.442091 AGTACACTAGTAGATAAAGGGGCTT 58.558 40.000 3.59 0.00 0.00 4.35
2626 2735 6.901857 AGTACACTAGTAGATAAAGGGGCTTT 59.098 38.462 3.59 0.00 37.46 3.51
2627 2736 6.638021 ACACTAGTAGATAAAGGGGCTTTT 57.362 37.500 3.59 0.00 35.21 2.27
2628 2737 6.415573 ACACTAGTAGATAAAGGGGCTTTTG 58.584 40.000 3.59 0.00 35.21 2.44
2629 2738 6.012771 ACACTAGTAGATAAAGGGGCTTTTGT 60.013 38.462 3.59 0.00 35.21 2.83
2630 2739 6.539103 CACTAGTAGATAAAGGGGCTTTTGTC 59.461 42.308 3.59 4.51 35.21 3.18
2631 2740 4.856509 AGTAGATAAAGGGGCTTTTGTCC 58.143 43.478 0.00 0.00 45.31 4.02
2637 2746 3.047735 GGGCTTTTGTCCCGGTTG 58.952 61.111 0.00 0.00 38.54 3.77
2638 2747 2.570284 GGGCTTTTGTCCCGGTTGG 61.570 63.158 0.00 0.00 38.54 3.77
2639 2748 1.830847 GGCTTTTGTCCCGGTTGGT 60.831 57.895 0.00 0.00 34.77 3.67
2640 2749 0.537828 GGCTTTTGTCCCGGTTGGTA 60.538 55.000 0.00 0.00 34.77 3.25
2641 2750 1.320507 GCTTTTGTCCCGGTTGGTAA 58.679 50.000 0.00 0.00 34.77 2.85
2642 2751 1.268625 GCTTTTGTCCCGGTTGGTAAG 59.731 52.381 0.00 0.00 34.77 2.34
2643 2752 1.883926 CTTTTGTCCCGGTTGGTAAGG 59.116 52.381 0.00 0.00 34.77 2.69
2644 2753 0.537828 TTTGTCCCGGTTGGTAAGGC 60.538 55.000 0.00 0.00 34.77 4.35
2645 2754 2.045634 GTCCCGGTTGGTAAGGCC 60.046 66.667 0.00 0.00 34.77 5.19
2646 2755 3.332385 TCCCGGTTGGTAAGGCCC 61.332 66.667 0.00 0.00 36.04 5.80
2647 2756 3.335729 CCCGGTTGGTAAGGCCCT 61.336 66.667 0.00 0.00 36.04 5.19
2648 2757 2.761160 CCGGTTGGTAAGGCCCTT 59.239 61.111 0.00 0.00 36.04 3.95
2649 2758 1.076014 CCGGTTGGTAAGGCCCTTT 59.924 57.895 0.00 0.00 36.04 3.11
2650 2759 0.328926 CCGGTTGGTAAGGCCCTTTA 59.671 55.000 0.00 0.00 36.04 1.85
2651 2760 1.680860 CCGGTTGGTAAGGCCCTTTAG 60.681 57.143 0.00 0.00 36.04 1.85
2652 2761 1.680860 CGGTTGGTAAGGCCCTTTAGG 60.681 57.143 0.00 0.00 36.04 2.69
2664 2773 2.058593 CCTTTAGGGCATCTCCAACC 57.941 55.000 0.00 0.00 36.21 3.77
2665 2774 1.668419 CTTTAGGGCATCTCCAACCG 58.332 55.000 0.00 0.00 36.21 4.44
2666 2775 0.988832 TTTAGGGCATCTCCAACCGT 59.011 50.000 0.00 0.00 36.21 4.83
2667 2776 0.988832 TTAGGGCATCTCCAACCGTT 59.011 50.000 0.00 0.00 36.21 4.44
2668 2777 0.251916 TAGGGCATCTCCAACCGTTG 59.748 55.000 4.12 4.12 36.21 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.234884 GCTTCAGCACACACGGTAAC 59.765 55.000 0.00 0.00 41.59 2.50
88 89 0.539051 AAGAGCATGAACGGCTAGCT 59.461 50.000 15.72 0.00 42.78 3.32
89 90 0.933796 GAAGAGCATGAACGGCTAGC 59.066 55.000 6.04 6.04 42.78 3.42
90 91 2.593346 AGAAGAGCATGAACGGCTAG 57.407 50.000 0.00 0.00 42.78 3.42
91 92 2.418746 GGAAGAAGAGCATGAACGGCTA 60.419 50.000 0.00 0.00 42.78 3.93
100 101 0.045469 AGGGGAGGGAAGAAGAGCAT 59.955 55.000 0.00 0.00 0.00 3.79
106 107 0.850883 ATGCCAAGGGGAGGGAAGAA 60.851 55.000 0.00 0.00 35.59 2.52
107 108 1.230281 ATGCCAAGGGGAGGGAAGA 60.230 57.895 0.00 0.00 35.59 2.87
122 123 2.865551 GAGCTCTTACTGCTTCAGATGC 59.134 50.000 6.43 1.18 41.30 3.91
123 124 4.120792 TGAGCTCTTACTGCTTCAGATG 57.879 45.455 16.19 0.00 41.30 2.90
135 136 3.259374 CCCTCTGTGAACTTGAGCTCTTA 59.741 47.826 16.19 1.96 0.00 2.10
140 141 1.294659 CGCCCTCTGTGAACTTGAGC 61.295 60.000 0.00 0.00 0.00 4.26
147 148 1.006571 GACGAACGCCCTCTGTGAA 60.007 57.895 0.00 0.00 0.00 3.18
152 153 2.754658 ATCGGACGAACGCCCTCT 60.755 61.111 0.00 0.00 0.00 3.69
153 154 1.442526 TAGATCGGACGAACGCCCTC 61.443 60.000 0.00 0.00 0.00 4.30
158 159 1.582502 GCTTTGTAGATCGGACGAACG 59.417 52.381 0.00 0.00 0.00 3.95
166 168 1.482593 AGACCTGGGCTTTGTAGATCG 59.517 52.381 0.00 0.00 0.00 3.69
207 209 4.305989 TGAAACTTAAGCTGGCACAAAG 57.694 40.909 1.29 0.00 38.70 2.77
446 448 0.033781 GCAGGCAAAACATGAAGGCA 59.966 50.000 0.00 0.00 0.00 4.75
578 580 6.399743 TGCATATTTCTGCATGTGAACAATT 58.600 32.000 0.00 0.00 46.76 2.32
702 704 8.478877 ACAAAGTTTGGTACTATCTAGATCCAG 58.521 37.037 19.45 4.67 35.54 3.86
703 705 8.375493 ACAAAGTTTGGTACTATCTAGATCCA 57.625 34.615 19.45 7.65 35.54 3.41
731 733 9.658799 CGAGGTGTGGATAATCTTCATTATAAT 57.341 33.333 0.00 0.00 35.63 1.28
752 754 0.328592 TGCAGTAGAGAGGACGAGGT 59.671 55.000 0.00 0.00 0.00 3.85
753 755 1.686355 ATGCAGTAGAGAGGACGAGG 58.314 55.000 0.00 0.00 0.00 4.63
754 756 4.393680 GGTATATGCAGTAGAGAGGACGAG 59.606 50.000 0.00 0.00 0.00 4.18
755 757 4.325119 GGTATATGCAGTAGAGAGGACGA 58.675 47.826 0.00 0.00 0.00 4.20
756 758 3.440872 GGGTATATGCAGTAGAGAGGACG 59.559 52.174 0.00 0.00 0.00 4.79
757 759 4.668636 AGGGTATATGCAGTAGAGAGGAC 58.331 47.826 0.00 0.00 0.00 3.85
758 760 4.565861 CGAGGGTATATGCAGTAGAGAGGA 60.566 50.000 0.00 0.00 0.00 3.71
880 914 2.417586 GCACCATCCCGTAAGTAACAAC 59.582 50.000 0.00 0.00 0.00 3.32
921 955 7.530010 AGAAAATCAAGATGGTTCATTACGTG 58.470 34.615 0.00 0.00 0.00 4.49
922 956 7.148239 GGAGAAAATCAAGATGGTTCATTACGT 60.148 37.037 0.00 0.00 0.00 3.57
923 957 7.148255 TGGAGAAAATCAAGATGGTTCATTACG 60.148 37.037 8.56 0.00 0.00 3.18
924 958 8.055279 TGGAGAAAATCAAGATGGTTCATTAC 57.945 34.615 8.56 0.00 0.00 1.89
928 962 5.105635 GCATGGAGAAAATCAAGATGGTTCA 60.106 40.000 0.00 0.00 0.00 3.18
957 998 3.053455 CAAGCTAGCTAAGGCGATGTAC 58.947 50.000 19.70 0.00 44.37 2.90
967 1008 1.858091 GCGATCTGCAAGCTAGCTAA 58.142 50.000 19.70 6.08 45.45 3.09
998 1039 1.340017 GCAGCTGGTGGTTCTCCATTA 60.340 52.381 17.12 0.00 46.20 1.90
1710 1751 2.303175 GATCACTCGGAGCTTAGAGGT 58.697 52.381 19.25 8.39 38.72 3.85
1715 1756 1.001268 GCATCGATCACTCGGAGCTTA 60.001 52.381 4.58 0.00 45.10 3.09
1770 1830 3.317153 ATTGCGCGCCGTGGTAAAC 62.317 57.895 30.77 0.00 0.00 2.01
1793 1853 9.056005 ACATGCCATATACTTACACAATTACAG 57.944 33.333 0.00 0.00 0.00 2.74
1829 1900 6.373186 AACTGCTTGTTGTTAGTCCTTAAC 57.627 37.500 0.00 0.00 41.68 2.01
1931 2009 2.766345 AACATGAAATTTGGCCGCAT 57.234 40.000 0.00 0.00 0.00 4.73
1932 2010 2.540265 AAACATGAAATTTGGCCGCA 57.460 40.000 0.00 0.00 0.00 5.69
1933 2011 2.805099 TCAAAACATGAAATTTGGCCGC 59.195 40.909 17.10 0.00 37.19 6.53
1934 2012 4.388189 GTCAAAACATGAAATTTGGCCG 57.612 40.909 17.10 0.00 40.50 6.13
1936 2014 6.375945 AAAGGTCAAAACATGAAATTTGGC 57.624 33.333 17.10 16.04 40.50 4.52
1937 2015 9.934190 CTAAAAAGGTCAAAACATGAAATTTGG 57.066 29.630 17.10 0.99 40.50 3.28
1938 2016 9.934190 CCTAAAAAGGTCAAAACATGAAATTTG 57.066 29.630 0.00 8.25 40.50 2.32
1939 2017 9.679661 ACCTAAAAAGGTCAAAACATGAAATTT 57.320 25.926 0.00 0.00 40.50 1.82
1940 2018 9.679661 AACCTAAAAAGGTCAAAACATGAAATT 57.320 25.926 0.00 0.00 42.20 1.82
1941 2019 9.108284 CAACCTAAAAAGGTCAAAACATGAAAT 57.892 29.630 0.00 0.00 42.20 2.17
1942 2020 7.065204 GCAACCTAAAAAGGTCAAAACATGAAA 59.935 33.333 0.00 0.00 42.20 2.69
1943 2021 6.536941 GCAACCTAAAAAGGTCAAAACATGAA 59.463 34.615 0.00 0.00 42.20 2.57
1944 2022 6.045955 GCAACCTAAAAAGGTCAAAACATGA 58.954 36.000 0.00 0.00 42.20 3.07
1945 2023 6.048509 AGCAACCTAAAAAGGTCAAAACATG 58.951 36.000 0.00 0.00 42.20 3.21
1946 2024 6.233905 AGCAACCTAAAAAGGTCAAAACAT 57.766 33.333 0.00 0.00 42.20 2.71
1947 2025 5.669164 AGCAACCTAAAAAGGTCAAAACA 57.331 34.783 0.00 0.00 42.20 2.83
1948 2026 6.103330 TCAAGCAACCTAAAAAGGTCAAAAC 58.897 36.000 0.00 0.00 42.20 2.43
1949 2027 6.287589 TCAAGCAACCTAAAAAGGTCAAAA 57.712 33.333 0.00 0.00 42.20 2.44
1950 2028 5.681179 GCTCAAGCAACCTAAAAAGGTCAAA 60.681 40.000 0.00 0.00 42.20 2.69
1951 2029 4.202111 GCTCAAGCAACCTAAAAAGGTCAA 60.202 41.667 0.00 0.00 42.20 3.18
1952 2030 3.317993 GCTCAAGCAACCTAAAAAGGTCA 59.682 43.478 0.00 0.00 42.20 4.02
1953 2031 3.902150 GCTCAAGCAACCTAAAAAGGTC 58.098 45.455 0.00 0.00 42.20 3.85
1967 2045 3.308323 CGAAGGTTAGATCTTGCTCAAGC 59.692 47.826 0.00 0.00 38.28 4.01
1968 2046 3.308323 GCGAAGGTTAGATCTTGCTCAAG 59.692 47.826 0.00 3.32 39.71 3.02
1969 2047 3.262420 GCGAAGGTTAGATCTTGCTCAA 58.738 45.455 0.00 0.00 0.00 3.02
1970 2048 2.418746 GGCGAAGGTTAGATCTTGCTCA 60.419 50.000 0.00 0.00 0.00 4.26
1971 2049 2.159028 AGGCGAAGGTTAGATCTTGCTC 60.159 50.000 0.00 0.00 0.00 4.26
1972 2050 1.834263 AGGCGAAGGTTAGATCTTGCT 59.166 47.619 0.00 0.00 0.00 3.91
1973 2051 2.317530 AGGCGAAGGTTAGATCTTGC 57.682 50.000 0.00 0.00 0.00 4.01
1974 2052 3.718815 GGTAGGCGAAGGTTAGATCTTG 58.281 50.000 0.00 0.00 0.00 3.02
1975 2053 2.361438 CGGTAGGCGAAGGTTAGATCTT 59.639 50.000 0.00 0.00 0.00 2.40
1976 2054 1.955080 CGGTAGGCGAAGGTTAGATCT 59.045 52.381 0.00 0.00 0.00 2.75
1977 2055 1.602416 GCGGTAGGCGAAGGTTAGATC 60.602 57.143 0.00 0.00 0.00 2.75
1978 2056 0.388294 GCGGTAGGCGAAGGTTAGAT 59.612 55.000 0.00 0.00 0.00 1.98
1979 2057 1.811860 GCGGTAGGCGAAGGTTAGA 59.188 57.895 0.00 0.00 0.00 2.10
1980 2058 4.414732 GCGGTAGGCGAAGGTTAG 57.585 61.111 0.00 0.00 0.00 2.34
1998 2076 2.439960 CCTACCGCCAGGGCACATA 61.440 63.158 11.42 0.00 43.47 2.29
2088 2178 1.241315 CCTTGGCGGTAGGGTTGTTG 61.241 60.000 0.00 0.00 0.00 3.33
2092 2182 2.535331 AAGCCTTGGCGGTAGGGTT 61.535 57.895 5.95 10.56 45.91 4.11
2114 2204 0.541863 AGCTTTAGCCATGCTACCGT 59.458 50.000 0.00 0.00 41.12 4.83
2145 2235 2.577059 CATACCTCACCGCCGTGT 59.423 61.111 5.09 0.00 41.09 4.49
2146 2236 2.202878 CCATACCTCACCGCCGTG 60.203 66.667 0.00 0.00 41.72 4.94
2147 2237 4.157120 GCCATACCTCACCGCCGT 62.157 66.667 0.00 0.00 0.00 5.68
2163 2264 4.135493 GACGAAGACAAGGCGCGC 62.135 66.667 25.94 25.94 0.00 6.86
2164 2265 1.626654 ATTGACGAAGACAAGGCGCG 61.627 55.000 0.00 0.00 45.96 6.86
2166 2267 0.721718 GGATTGACGAAGACAAGGCG 59.278 55.000 0.00 0.00 45.96 5.52
2167 2268 1.808411 TGGATTGACGAAGACAAGGC 58.192 50.000 0.00 0.00 45.96 4.35
2168 2269 4.093998 CAGAATGGATTGACGAAGACAAGG 59.906 45.833 0.00 0.00 45.96 3.61
2169 2270 4.692625 ACAGAATGGATTGACGAAGACAAG 59.307 41.667 0.00 0.00 43.35 3.16
2170 2271 4.452114 CACAGAATGGATTGACGAAGACAA 59.548 41.667 0.00 0.00 43.97 3.18
2171 2272 3.996363 CACAGAATGGATTGACGAAGACA 59.004 43.478 0.00 0.00 43.62 3.41
2172 2273 4.092091 GTCACAGAATGGATTGACGAAGAC 59.908 45.833 0.00 0.00 43.62 3.01
2173 2274 4.245660 GTCACAGAATGGATTGACGAAGA 58.754 43.478 0.00 0.00 43.62 2.87
2224 2326 1.019278 GTGTGGCGGTAGGATGTGTG 61.019 60.000 0.00 0.00 0.00 3.82
2230 2332 4.682334 TCGGGTGTGGCGGTAGGA 62.682 66.667 0.00 0.00 0.00 2.94
2274 2376 2.354510 CCTTTTCAGTCACAGAACGCAA 59.645 45.455 0.00 0.00 0.00 4.85
2321 2424 3.043999 GCACCCTGGCGGTAGGATT 62.044 63.158 2.18 0.00 46.14 3.01
2472 2576 4.852134 ATGCAGACACTATTTTGTTGCA 57.148 36.364 12.29 12.29 42.37 4.08
2488 2592 8.235226 GTGAGGTCATCATATTTTCATATGCAG 58.765 37.037 0.00 0.00 41.55 4.41
2606 2715 6.352823 GGACAAAAGCCCCTTTATCTACTAGT 60.353 42.308 0.00 0.00 31.99 2.57
2607 2716 6.056236 GGACAAAAGCCCCTTTATCTACTAG 58.944 44.000 0.00 0.00 31.99 2.57
2608 2717 5.104235 GGGACAAAAGCCCCTTTATCTACTA 60.104 44.000 0.00 0.00 39.81 1.82
2609 2718 4.325109 GGGACAAAAGCCCCTTTATCTACT 60.325 45.833 0.00 0.00 39.81 2.57
2610 2719 3.952323 GGGACAAAAGCCCCTTTATCTAC 59.048 47.826 0.00 0.00 39.81 2.59
2611 2720 3.371166 CGGGACAAAAGCCCCTTTATCTA 60.371 47.826 0.00 0.00 42.92 1.98
2612 2721 2.620627 CGGGACAAAAGCCCCTTTATCT 60.621 50.000 0.00 0.00 42.92 1.98
2613 2722 1.749063 CGGGACAAAAGCCCCTTTATC 59.251 52.381 0.00 0.00 42.92 1.75
2614 2723 1.618616 CCGGGACAAAAGCCCCTTTAT 60.619 52.381 0.00 0.00 42.92 1.40
2615 2724 0.251430 CCGGGACAAAAGCCCCTTTA 60.251 55.000 0.00 0.00 42.92 1.85
2616 2725 1.533033 CCGGGACAAAAGCCCCTTT 60.533 57.895 0.00 0.00 42.92 3.11
2617 2726 2.117423 CCGGGACAAAAGCCCCTT 59.883 61.111 0.00 0.00 42.92 3.95
2618 2727 2.774633 AACCGGGACAAAAGCCCCT 61.775 57.895 6.32 0.00 42.92 4.79
2619 2728 2.203582 AACCGGGACAAAAGCCCC 60.204 61.111 6.32 0.00 42.92 5.80
2620 2729 2.570284 CCAACCGGGACAAAAGCCC 61.570 63.158 6.32 0.00 42.41 5.19
2621 2730 0.537828 TACCAACCGGGACAAAAGCC 60.538 55.000 6.32 0.00 41.15 4.35
2622 2731 1.268625 CTTACCAACCGGGACAAAAGC 59.731 52.381 6.32 0.00 41.15 3.51
2623 2732 1.883926 CCTTACCAACCGGGACAAAAG 59.116 52.381 6.32 3.70 41.15 2.27
2624 2733 1.984066 CCTTACCAACCGGGACAAAA 58.016 50.000 6.32 0.00 41.15 2.44
2625 2734 0.537828 GCCTTACCAACCGGGACAAA 60.538 55.000 6.32 0.00 41.15 2.83
2626 2735 1.073548 GCCTTACCAACCGGGACAA 59.926 57.895 6.32 0.00 41.15 3.18
2627 2736 2.751688 GCCTTACCAACCGGGACA 59.248 61.111 6.32 0.00 41.15 4.02
2628 2737 2.045634 GGCCTTACCAACCGGGAC 60.046 66.667 6.32 0.00 41.15 4.46
2629 2738 3.332385 GGGCCTTACCAACCGGGA 61.332 66.667 6.32 0.00 42.05 5.14
2630 2739 2.435120 AAAGGGCCTTACCAACCGGG 62.435 60.000 21.25 0.00 42.05 5.73
2631 2740 0.328926 TAAAGGGCCTTACCAACCGG 59.671 55.000 21.25 0.00 42.05 5.28
2632 2741 1.680860 CCTAAAGGGCCTTACCAACCG 60.681 57.143 21.25 3.06 42.05 4.44
2633 2742 2.139323 CCTAAAGGGCCTTACCAACC 57.861 55.000 21.25 0.00 42.05 3.77
2645 2754 1.747206 CGGTTGGAGATGCCCTAAAGG 60.747 57.143 0.00 0.00 39.47 3.11
2646 2755 1.065418 ACGGTTGGAGATGCCCTAAAG 60.065 52.381 0.00 0.00 34.97 1.85
2647 2756 0.988832 ACGGTTGGAGATGCCCTAAA 59.011 50.000 0.00 0.00 34.97 1.85
2648 2757 0.988832 AACGGTTGGAGATGCCCTAA 59.011 50.000 0.00 0.00 34.97 2.69
2649 2758 0.251916 CAACGGTTGGAGATGCCCTA 59.748 55.000 13.03 0.00 34.97 3.53
2650 2759 1.002134 CAACGGTTGGAGATGCCCT 60.002 57.895 13.03 0.00 34.97 5.19
2651 2760 3.590824 CAACGGTTGGAGATGCCC 58.409 61.111 13.03 0.00 34.97 5.36


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

AutoCloner maintained by Alex Coulton.