Multiple sequence alignment - TraesCS1B01G377900

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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 TraesCS1B01G377900 chr1B 100.000 2946 0 0 1 2946 610168602 610171547 0.000000e+00 5441.0
1 TraesCS1B01G377900 chr1B 96.078 51 1 1 2026 2076 61951686 61951735 6.770000e-12 82.4
2 TraesCS1B01G377900 chr1A 89.990 1039 47 23 732 1751 541997311 541998311 0.000000e+00 1290.0
3 TraesCS1B01G377900 chr1A 91.001 689 44 10 3 685 541996555 541997231 0.000000e+00 913.0
4 TraesCS1B01G377900 chr1A 92.675 628 30 8 2328 2946 541999817 542000437 0.000000e+00 891.0
5 TraesCS1B01G377900 chr1A 92.694 219 15 1 1815 2033 541998339 541998556 6.130000e-82 315.0
6 TraesCS1B01G377900 chr1D 93.228 694 20 9 1 694 446270791 446271457 0.000000e+00 996.0
7 TraesCS1B01G377900 chr1D 91.440 736 28 12 732 1446 446271528 446272249 0.000000e+00 977.0
8 TraesCS1B01G377900 chr1D 88.244 672 55 14 2164 2823 446273507 446274166 0.000000e+00 782.0
9 TraesCS1B01G377900 chr1D 89.576 566 44 8 1479 2033 446272330 446272891 0.000000e+00 704.0
10 TraesCS1B01G377900 chr1D 91.935 124 9 1 2822 2945 446274454 446274576 3.900000e-39 172.0
11 TraesCS1B01G377900 chr3B 80.000 230 36 6 2727 2946 54151912 54152141 8.450000e-36 161.0
12 TraesCS1B01G377900 chr3B 82.778 180 27 3 2771 2946 54075717 54075896 1.090000e-34 158.0
13 TraesCS1B01G377900 chr3B 94.000 50 2 1 2021 2069 513668910 513668959 1.130000e-09 75.0
14 TraesCS1B01G377900 chr4B 80.093 216 37 4 2732 2946 16705171 16704961 3.930000e-34 156.0
15 TraesCS1B01G377900 chr6D 89.189 111 6 3 2824 2934 126633560 126633456 1.840000e-27 134.0
16 TraesCS1B01G377900 chr6B 93.220 59 2 2 2026 2083 655780327 655780384 5.230000e-13 86.1
17 TraesCS1B01G377900 chr3A 97.959 49 1 0 2028 2076 620471321 620471369 5.230000e-13 86.1
18 TraesCS1B01G377900 chr2B 97.959 49 1 0 2028 2076 297438935 297438983 5.230000e-13 86.1
19 TraesCS1B01G377900 chr7B 97.917 48 1 0 2029 2076 48864200 48864153 1.880000e-12 84.2
20 TraesCS1B01G377900 chr5B 96.078 51 2 0 2026 2076 616513011 616512961 1.880000e-12 84.2
21 TraesCS1B01G377900 chr4D 96.078 51 2 0 2026 2076 16403543 16403493 1.880000e-12 84.2
22 TraesCS1B01G377900 chr2A 91.379 58 3 2 2019 2076 68248996 68249051 8.750000e-11 78.7


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 TraesCS1B01G377900 chr1B 610168602 610171547 2945 False 5441.00 5441 100.0000 1 2946 1 chr1B.!!$F2 2945
1 TraesCS1B01G377900 chr1A 541996555 542000437 3882 False 852.25 1290 91.5900 3 2946 4 chr1A.!!$F1 2943
2 TraesCS1B01G377900 chr1D 446270791 446274576 3785 False 726.20 996 90.8846 1 2945 5 chr1D.!!$F1 2944

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
699 706 0.179054 GGAAAGGCGTCCCCAGATAC 60.179 60.0 0.0 0.0 35.39 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 4148 0.178924 AATTTGCCTGTGCCCTCCTT 60.179 50.0 0.0 0.0 36.33 3.36 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
171 172 6.566197 AATCAACTCAGGCAAACTAAGAAG 57.434 37.500 0.00 0.00 0.00 2.85
176 177 4.101741 ACTCAGGCAAACTAAGAAGACACT 59.898 41.667 0.00 0.00 0.00 3.55
212 213 2.030262 GTGGGCGCAAATTTGGCA 59.970 55.556 23.93 9.49 0.00 4.92
213 214 2.028733 GTGGGCGCAAATTTGGCAG 61.029 57.895 23.93 13.09 0.00 4.85
214 215 2.343387 GGGCGCAAATTTGGCAGT 59.657 55.556 23.93 0.00 0.00 4.40
283 284 4.808649 GCACTAGGCGACCAGTAC 57.191 61.111 0.00 0.00 0.00 2.73
314 315 0.243907 CACCACACGAGGGTCTACAG 59.756 60.000 0.00 0.00 36.19 2.74
349 350 5.353678 CCAACCTAAGAAAGCAGATCTTCTG 59.646 44.000 0.00 0.08 46.90 3.02
484 491 1.123928 AGTAAATGGAGGAGAGGCCG 58.876 55.000 0.00 0.00 43.43 6.13
495 502 4.394712 GAGGCCGTGTGGGTCAGG 62.395 72.222 0.00 0.00 45.54 3.86
685 692 1.803334 TTCGAATGTGACGGGGAAAG 58.197 50.000 0.00 0.00 0.00 2.62
697 704 2.998949 GGAAAGGCGTCCCCAGAT 59.001 61.111 0.00 0.00 35.39 2.90
698 705 2.218066 GGAAAGGCGTCCCCAGATA 58.782 57.895 0.00 0.00 35.39 1.98
699 706 0.179054 GGAAAGGCGTCCCCAGATAC 60.179 60.000 0.00 0.00 35.39 2.24
700 707 0.831307 GAAAGGCGTCCCCAGATACT 59.169 55.000 0.00 0.00 35.39 2.12
701 708 0.831307 AAAGGCGTCCCCAGATACTC 59.169 55.000 0.00 0.00 35.39 2.59
702 709 1.049289 AAGGCGTCCCCAGATACTCC 61.049 60.000 0.00 0.00 35.39 3.85
703 710 2.728817 GCGTCCCCAGATACTCCG 59.271 66.667 0.00 0.00 0.00 4.63
704 711 2.728817 CGTCCCCAGATACTCCGC 59.271 66.667 0.00 0.00 0.00 5.54
705 712 2.857744 CGTCCCCAGATACTCCGCC 61.858 68.421 0.00 0.00 0.00 6.13
706 713 2.520982 TCCCCAGATACTCCGCCG 60.521 66.667 0.00 0.00 0.00 6.46
707 714 2.520982 CCCCAGATACTCCGCCGA 60.521 66.667 0.00 0.00 0.00 5.54
708 715 2.131709 CCCCAGATACTCCGCCGAA 61.132 63.158 0.00 0.00 0.00 4.30
709 716 1.067582 CCCAGATACTCCGCCGAAC 59.932 63.158 0.00 0.00 0.00 3.95
710 717 1.672854 CCCAGATACTCCGCCGAACA 61.673 60.000 0.00 0.00 0.00 3.18
721 728 1.883021 GCCGAACAAATCCACAGGG 59.117 57.895 0.00 0.00 0.00 4.45
725 732 2.290071 CCGAACAAATCCACAGGGTACT 60.290 50.000 0.00 0.00 34.93 2.73
726 733 3.000727 CGAACAAATCCACAGGGTACTC 58.999 50.000 0.00 0.00 34.93 2.59
727 734 3.556213 CGAACAAATCCACAGGGTACTCA 60.556 47.826 0.00 0.00 34.93 3.41
728 735 4.589908 GAACAAATCCACAGGGTACTCAT 58.410 43.478 0.00 0.00 34.93 2.90
729 736 3.955471 ACAAATCCACAGGGTACTCATG 58.045 45.455 0.00 0.00 34.93 3.07
730 737 3.282021 CAAATCCACAGGGTACTCATGG 58.718 50.000 9.34 9.34 33.20 3.66
734 790 2.290287 ACAGGGTACTCATGGCGCA 61.290 57.895 10.83 0.00 0.00 6.09
746 802 3.050275 GGCGCACTCACCTTGACC 61.050 66.667 10.83 0.00 0.00 4.02
906 977 1.750341 CGTGGTACATATGGGCCGGA 61.750 60.000 5.05 0.00 44.52 5.14
1256 1332 0.543749 GCTCTACAAGGTCAGGCCAT 59.456 55.000 5.01 0.00 40.61 4.40
1371 1451 4.453093 GCTCAGGATAGCACAGCC 57.547 61.111 0.00 0.00 42.30 4.85
1372 1452 1.227793 GCTCAGGATAGCACAGCCC 60.228 63.158 0.00 0.00 42.30 5.19
1373 1453 1.068753 CTCAGGATAGCACAGCCCG 59.931 63.158 0.00 0.00 30.64 6.13
1374 1454 1.680522 CTCAGGATAGCACAGCCCGT 61.681 60.000 0.00 0.00 30.64 5.28
1402 1482 4.098349 GCATCATAAAATTGTCCAGCTCCA 59.902 41.667 0.00 0.00 0.00 3.86
1441 1525 3.795688 TTCTTCACTTGCCAGATTCCT 57.204 42.857 0.00 0.00 0.00 3.36
1471 1592 2.315925 ACGGTGATATGTGGCTTCAG 57.684 50.000 0.00 0.00 0.00 3.02
1481 1613 6.767902 TGATATGTGGCTTCAGATTTAGGAAC 59.232 38.462 0.00 0.00 0.00 3.62
1532 1664 3.711190 TGATACTGCATTGGAGAGGCTTA 59.289 43.478 12.54 0.00 35.70 3.09
1536 1668 2.941720 CTGCATTGGAGAGGCTTAGTTC 59.058 50.000 0.00 0.00 35.70 3.01
1559 1693 1.017387 GTGCTTAAATCGCCTCTGGG 58.983 55.000 0.00 0.00 0.00 4.45
1560 1694 0.618458 TGCTTAAATCGCCTCTGGGT 59.382 50.000 0.00 0.00 34.45 4.51
1736 1870 1.606737 GGAAGCTAAGCCGGCATAGAG 60.607 57.143 36.10 23.58 0.00 2.43
1739 1873 0.669012 GCTAAGCCGGCATAGAGCTC 60.669 60.000 36.10 18.25 44.79 4.09
1743 1877 1.301322 GCCGGCATAGAGCTCCTTC 60.301 63.158 24.80 0.00 44.79 3.46
1747 1881 1.036707 GGCATAGAGCTCCTTCGAGT 58.963 55.000 10.93 0.00 44.79 4.18
1759 1893 4.506039 TCGAGTTCGAAGGGGTCA 57.494 55.556 0.00 0.00 46.30 4.02
1760 1894 2.971676 TCGAGTTCGAAGGGGTCAT 58.028 52.632 0.00 0.00 46.30 3.06
1761 1895 0.530744 TCGAGTTCGAAGGGGTCATG 59.469 55.000 0.00 0.00 46.30 3.07
1763 1897 0.107654 GAGTTCGAAGGGGTCATGGG 60.108 60.000 0.00 0.00 0.00 4.00
1764 1898 0.546747 AGTTCGAAGGGGTCATGGGA 60.547 55.000 0.00 0.00 0.00 4.37
1765 1899 0.107654 GTTCGAAGGGGTCATGGGAG 60.108 60.000 0.00 0.00 0.00 4.30
1766 1900 0.546747 TTCGAAGGGGTCATGGGAGT 60.547 55.000 0.00 0.00 0.00 3.85
1768 1902 0.753262 CGAAGGGGTCATGGGAGTAG 59.247 60.000 0.00 0.00 0.00 2.57
1769 1903 1.880941 GAAGGGGTCATGGGAGTAGT 58.119 55.000 0.00 0.00 0.00 2.73
1775 1910 2.633488 GGTCATGGGAGTAGTTTGCTC 58.367 52.381 0.00 0.00 0.00 4.26
1785 1920 5.309638 GGAGTAGTTTGCTCTTCTCCTTTT 58.690 41.667 16.11 0.00 43.75 2.27
1799 1934 2.680339 CTCCTTTTTCTTGATCGGAGGC 59.320 50.000 0.00 0.00 35.54 4.70
1876 2011 8.739039 TCTTGTAATTTACATTCTGGTGATTGG 58.261 33.333 9.95 0.00 38.68 3.16
1905 2040 4.097892 GCCGTGGAATCATAATGGTCTTTT 59.902 41.667 0.00 0.00 0.00 2.27
1989 2132 9.608617 CATTTTATCGATTTGATGATCTTCCAG 57.391 33.333 1.71 0.00 37.99 3.86
2011 2154 2.354203 GCGAAATAGATAGGGCTGGGAG 60.354 54.545 0.00 0.00 0.00 4.30
2033 2176 3.491447 GGCACCCATTTTGCATCATCTAC 60.491 47.826 0.00 0.00 42.12 2.59
2034 2177 3.382546 GCACCCATTTTGCATCATCTACT 59.617 43.478 0.00 0.00 39.93 2.57
2035 2178 4.498682 GCACCCATTTTGCATCATCTACTC 60.499 45.833 0.00 0.00 39.93 2.59
2036 2179 4.037208 CACCCATTTTGCATCATCTACTCC 59.963 45.833 0.00 0.00 0.00 3.85
2037 2180 3.571401 CCCATTTTGCATCATCTACTCCC 59.429 47.826 0.00 0.00 0.00 4.30
2038 2181 4.467769 CCATTTTGCATCATCTACTCCCT 58.532 43.478 0.00 0.00 0.00 4.20
2039 2182 4.518211 CCATTTTGCATCATCTACTCCCTC 59.482 45.833 0.00 0.00 0.00 4.30
2040 2183 3.845781 TTTGCATCATCTACTCCCTCC 57.154 47.619 0.00 0.00 0.00 4.30
2041 2184 1.332195 TGCATCATCTACTCCCTCCG 58.668 55.000 0.00 0.00 0.00 4.63
2042 2185 1.333177 GCATCATCTACTCCCTCCGT 58.667 55.000 0.00 0.00 0.00 4.69
2043 2186 1.689273 GCATCATCTACTCCCTCCGTT 59.311 52.381 0.00 0.00 0.00 4.44
2044 2187 2.288518 GCATCATCTACTCCCTCCGTTC 60.289 54.545 0.00 0.00 0.00 3.95
2045 2188 2.068834 TCATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
2046 2189 0.669077 CATCTACTCCCTCCGTTCCG 59.331 60.000 0.00 0.00 0.00 4.30
2047 2190 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
2048 2191 0.549950 TCTACTCCCTCCGTTCCGAT 59.450 55.000 0.00 0.00 0.00 4.18
2049 2192 1.064166 TCTACTCCCTCCGTTCCGATT 60.064 52.381 0.00 0.00 0.00 3.34
2050 2193 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
2051 2194 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
2052 2195 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
2053 2196 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
2054 2197 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2056 2199 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
2057 2200 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
2058 2201 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
2059 2202 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
2060 2203 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
2061 2204 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
2062 2205 0.452987 TCCGATTTACTCGTCGTGGG 59.547 55.000 0.00 0.00 46.18 4.61
2063 2206 0.171903 CCGATTTACTCGTCGTGGGT 59.828 55.000 0.00 0.00 46.18 4.51
2064 2207 1.403249 CCGATTTACTCGTCGTGGGTT 60.403 52.381 0.00 0.00 46.18 4.11
2065 2208 2.331194 CGATTTACTCGTCGTGGGTTT 58.669 47.619 0.00 0.00 42.56 3.27
2066 2209 3.500982 CGATTTACTCGTCGTGGGTTTA 58.499 45.455 0.00 0.00 42.56 2.01
2067 2210 3.545078 CGATTTACTCGTCGTGGGTTTAG 59.455 47.826 0.00 0.00 42.56 1.85
2068 2211 4.488879 GATTTACTCGTCGTGGGTTTAGT 58.511 43.478 0.00 0.00 0.00 2.24
2069 2212 4.320608 TTTACTCGTCGTGGGTTTAGTT 57.679 40.909 0.00 0.00 0.00 2.24
2070 2213 2.428888 ACTCGTCGTGGGTTTAGTTC 57.571 50.000 0.00 0.00 0.00 3.01
2071 2214 1.682854 ACTCGTCGTGGGTTTAGTTCA 59.317 47.619 0.00 0.00 0.00 3.18
2072 2215 2.101249 ACTCGTCGTGGGTTTAGTTCAA 59.899 45.455 0.00 0.00 0.00 2.69
2073 2216 3.125316 CTCGTCGTGGGTTTAGTTCAAA 58.875 45.455 0.00 0.00 0.00 2.69
2074 2217 3.731089 TCGTCGTGGGTTTAGTTCAAAT 58.269 40.909 0.00 0.00 0.00 2.32
2075 2218 4.128643 TCGTCGTGGGTTTAGTTCAAATT 58.871 39.130 0.00 0.00 0.00 1.82
2076 2219 4.211794 TCGTCGTGGGTTTAGTTCAAATTC 59.788 41.667 0.00 0.00 0.00 2.17
2077 2220 4.024725 CGTCGTGGGTTTAGTTCAAATTCA 60.025 41.667 0.00 0.00 0.00 2.57
2078 2221 5.504337 CGTCGTGGGTTTAGTTCAAATTCAA 60.504 40.000 0.00 0.00 0.00 2.69
2091 2234 8.846943 AGTTCAAATTCAAAAACAAAGGTTCT 57.153 26.923 0.00 0.00 35.82 3.01
2114 2257 4.651778 AGTCATTGCCAGCTTAACAGTTA 58.348 39.130 0.00 0.00 0.00 2.24
2124 2267 6.676456 GCCAGCTTAACAGTTATCATGTTCTG 60.676 42.308 0.00 0.61 41.08 3.02
2125 2268 6.183360 CCAGCTTAACAGTTATCATGTTCTGG 60.183 42.308 9.34 9.34 40.65 3.86
2127 2270 7.119699 CAGCTTAACAGTTATCATGTTCTGGAA 59.880 37.037 0.00 0.00 41.08 3.53
2129 2272 9.109393 GCTTAACAGTTATCATGTTCTGGAATA 57.891 33.333 0.00 0.00 41.08 1.75
2133 2276 8.668510 ACAGTTATCATGTTCTGGAATACATC 57.331 34.615 0.00 0.00 32.88 3.06
2134 2277 8.267183 ACAGTTATCATGTTCTGGAATACATCA 58.733 33.333 0.00 0.00 32.88 3.07
2135 2278 9.112725 CAGTTATCATGTTCTGGAATACATCAA 57.887 33.333 0.00 0.00 32.88 2.57
2136 2279 9.685276 AGTTATCATGTTCTGGAATACATCAAA 57.315 29.630 0.00 0.00 32.88 2.69
2139 2282 8.585471 ATCATGTTCTGGAATACATCAAAAGT 57.415 30.769 0.00 0.00 32.88 2.66
2141 2284 8.514594 TCATGTTCTGGAATACATCAAAAGTTC 58.485 33.333 0.00 0.00 32.88 3.01
2155 2806 0.535102 AAGTTCCCAACGCTCACTGG 60.535 55.000 0.00 0.00 36.23 4.00
2164 2815 2.620112 CGCTCACTGGGCAAGGTTG 61.620 63.158 0.87 0.00 0.00 3.77
2165 2816 2.270986 GCTCACTGGGCAAGGTTGG 61.271 63.158 0.00 0.00 0.00 3.77
2242 2917 3.802685 GGCAATGTCACGAGACCTAATAC 59.197 47.826 10.58 0.00 44.33 1.89
2243 2918 3.486108 GCAATGTCACGAGACCTAATACG 59.514 47.826 10.58 0.00 44.33 3.06
2258 2936 8.529476 AGACCTAATACGTGAAGTAACTGAAAT 58.471 33.333 0.00 0.00 39.04 2.17
2269 2947 6.443849 TGAAGTAACTGAAATGGAGGGAGTAT 59.556 38.462 0.00 0.00 0.00 2.12
2270 2948 7.622081 TGAAGTAACTGAAATGGAGGGAGTATA 59.378 37.037 0.00 0.00 0.00 1.47
2272 2950 9.670442 AAGTAACTGAAATGGAGGGAGTATATA 57.330 33.333 0.00 0.00 0.00 0.86
2273 2951 9.091220 AGTAACTGAAATGGAGGGAGTATATAC 57.909 37.037 4.60 4.60 0.00 1.47
2274 2952 9.091220 GTAACTGAAATGGAGGGAGTATATACT 57.909 37.037 15.37 15.37 39.71 2.12
2275 2953 8.568617 AACTGAAATGGAGGGAGTATATACTT 57.431 34.615 16.46 1.01 36.50 2.24
2276 2954 8.568617 ACTGAAATGGAGGGAGTATATACTTT 57.431 34.615 16.46 4.57 36.50 2.66
2277 2955 9.004231 ACTGAAATGGAGGGAGTATATACTTTT 57.996 33.333 16.46 10.72 36.50 2.27
2278 2956 9.495572 CTGAAATGGAGGGAGTATATACTTTTC 57.504 37.037 16.46 17.79 36.50 2.29
2296 2976 0.179076 TCATGTATGCAGCACCGGAG 60.179 55.000 9.46 0.00 0.00 4.63
2318 4132 2.327343 CCACGAGCACACCACCATG 61.327 63.158 0.00 0.00 0.00 3.66
2323 4137 1.069022 CGAGCACACCACCATGAAAAG 60.069 52.381 0.00 0.00 0.00 2.27
2324 4138 1.956477 GAGCACACCACCATGAAAAGT 59.044 47.619 0.00 0.00 0.00 2.66
2325 4139 2.362077 GAGCACACCACCATGAAAAGTT 59.638 45.455 0.00 0.00 0.00 2.66
2326 4140 2.101249 AGCACACCACCATGAAAAGTTG 59.899 45.455 0.00 0.00 0.00 3.16
2327 4141 2.100584 GCACACCACCATGAAAAGTTGA 59.899 45.455 0.00 0.00 0.00 3.18
2328 4142 3.430098 GCACACCACCATGAAAAGTTGAA 60.430 43.478 0.00 0.00 0.00 2.69
2329 4143 4.753233 CACACCACCATGAAAAGTTGAAA 58.247 39.130 0.00 0.00 0.00 2.69
2330 4144 5.174395 CACACCACCATGAAAAGTTGAAAA 58.826 37.500 0.00 0.00 0.00 2.29
2514 4329 3.788797 GCACTGAACCACGAGTTTTTCAG 60.789 47.826 16.26 16.26 46.91 3.02
2564 4380 2.324541 CTCACTTGATAGGGAGGGGAG 58.675 57.143 0.00 0.00 46.34 4.30
2566 4382 2.045885 TCACTTGATAGGGAGGGGAGTT 59.954 50.000 0.00 0.00 0.00 3.01
2567 4383 2.436173 CACTTGATAGGGAGGGGAGTTC 59.564 54.545 0.00 0.00 0.00 3.01
2581 4397 6.070710 GGAGGGGAGTTCCTATTCATGTATAC 60.071 46.154 0.00 0.00 37.25 1.47
2582 4398 5.480772 AGGGGAGTTCCTATTCATGTATACG 59.519 44.000 0.00 0.00 34.92 3.06
2589 4405 1.053424 ATTCATGTATACGCCGGGGT 58.947 50.000 28.40 28.40 0.00 4.95
2715 4533 0.105224 TTCTGGCTTTTGTCGACGGA 59.895 50.000 11.62 0.00 0.00 4.69
2807 4625 5.678483 CAGACAAGTTTGATTGTTTCTGTCG 59.322 40.000 0.00 0.00 43.32 4.35
2813 4633 2.131972 TGATTGTTTCTGTCGGTCGTG 58.868 47.619 0.00 0.00 0.00 4.35
2931 5046 1.915489 TGTCAACATACTCCCCTGCAT 59.085 47.619 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.430925 AGCAGTTGTGAGATAATAGCAAACAA 59.569 34.615 0.00 0.00 0.00 2.83
13 14 5.939883 AGCAGTTGTGAGATAATAGCAAACA 59.060 36.000 0.00 0.00 0.00 2.83
171 172 5.063880 CCCTTGGGCATATAAGTTAGTGTC 58.936 45.833 0.00 0.00 0.00 3.67
212 213 4.223923 AGAAGATTGTTGCAGTAGGCTACT 59.776 41.667 21.30 21.30 46.50 2.57
213 214 4.508662 AGAAGATTGTTGCAGTAGGCTAC 58.491 43.478 16.93 16.93 46.54 3.58
214 215 4.826274 AGAAGATTGTTGCAGTAGGCTA 57.174 40.909 0.00 0.00 45.15 3.93
314 315 4.645863 TCTTAGGTTGGGTTTAGGGTTC 57.354 45.455 0.00 0.00 0.00 3.62
449 452 8.025243 TCCATTTACTGTTTGTTTCTCGTATC 57.975 34.615 0.00 0.00 0.00 2.24
495 502 0.178843 TATAGCCCCCATTCTCCCCC 60.179 60.000 0.00 0.00 0.00 5.40
496 503 0.992695 GTATAGCCCCCATTCTCCCC 59.007 60.000 0.00 0.00 0.00 4.81
618 625 2.353406 GCTGTAGGGTTTGACGAAGCTA 60.353 50.000 4.67 0.00 36.04 3.32
685 692 2.857744 CGGAGTATCTGGGGACGCC 61.858 68.421 0.53 0.53 38.01 5.68
694 701 2.483188 GGATTTGTTCGGCGGAGTATCT 60.483 50.000 7.21 0.00 33.73 1.98
695 702 1.865340 GGATTTGTTCGGCGGAGTATC 59.135 52.381 7.21 1.12 0.00 2.24
696 703 1.208535 TGGATTTGTTCGGCGGAGTAT 59.791 47.619 7.21 0.00 0.00 2.12
697 704 0.609151 TGGATTTGTTCGGCGGAGTA 59.391 50.000 7.21 0.00 0.00 2.59
698 705 0.953960 GTGGATTTGTTCGGCGGAGT 60.954 55.000 7.21 0.00 0.00 3.85
699 706 0.953471 TGTGGATTTGTTCGGCGGAG 60.953 55.000 7.21 0.00 0.00 4.63
700 707 0.953471 CTGTGGATTTGTTCGGCGGA 60.953 55.000 7.21 0.00 0.00 5.54
701 708 1.501741 CTGTGGATTTGTTCGGCGG 59.498 57.895 7.21 0.00 0.00 6.13
702 709 1.501741 CCTGTGGATTTGTTCGGCG 59.498 57.895 0.00 0.00 0.00 6.46
703 710 0.893727 ACCCTGTGGATTTGTTCGGC 60.894 55.000 0.00 0.00 34.81 5.54
704 711 2.081462 GTACCCTGTGGATTTGTTCGG 58.919 52.381 0.00 0.00 34.81 4.30
705 712 3.000727 GAGTACCCTGTGGATTTGTTCG 58.999 50.000 0.00 0.00 34.81 3.95
706 713 4.015872 TGAGTACCCTGTGGATTTGTTC 57.984 45.455 0.00 0.00 34.81 3.18
707 714 4.335416 CATGAGTACCCTGTGGATTTGTT 58.665 43.478 0.00 0.00 34.81 2.83
708 715 3.308402 CCATGAGTACCCTGTGGATTTGT 60.308 47.826 0.00 0.00 34.81 2.83
709 716 3.282021 CCATGAGTACCCTGTGGATTTG 58.718 50.000 0.00 0.00 34.81 2.32
710 717 2.357154 GCCATGAGTACCCTGTGGATTT 60.357 50.000 0.00 0.00 34.81 2.17
721 728 1.084370 GGTGAGTGCGCCATGAGTAC 61.084 60.000 4.18 0.00 44.29 2.73
725 732 1.672030 CAAGGTGAGTGCGCCATGA 60.672 57.895 4.18 0.00 44.06 3.07
729 736 3.050275 GGTCAAGGTGAGTGCGCC 61.050 66.667 4.18 0.00 45.26 6.53
730 737 3.050275 GGGTCAAGGTGAGTGCGC 61.050 66.667 0.00 0.00 0.00 6.09
734 790 0.178861 AGATGGGGGTCAAGGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
916 987 3.400599 CTATTTGAGCCCGCCCGGT 62.401 63.158 0.00 0.00 0.00 5.28
941 1012 2.747855 CTGGACGCTTTCCTGCCC 60.748 66.667 3.14 0.00 46.10 5.36
1256 1332 2.974489 GCGTCGGTCCGAGAGTGAA 61.974 63.158 15.95 0.00 36.23 3.18
1369 1449 1.436195 TTTATGATGCGAGCACGGGC 61.436 55.000 0.00 0.00 40.15 6.13
1370 1450 1.013596 TTTTATGATGCGAGCACGGG 58.986 50.000 5.52 0.00 40.15 5.28
1371 1451 3.038017 CAATTTTATGATGCGAGCACGG 58.962 45.455 5.52 0.00 40.15 4.94
1372 1452 3.683989 ACAATTTTATGATGCGAGCACG 58.316 40.909 0.00 0.00 42.93 5.34
1373 1453 4.037690 GGACAATTTTATGATGCGAGCAC 58.962 43.478 0.00 0.00 0.00 4.40
1374 1454 3.693578 TGGACAATTTTATGATGCGAGCA 59.306 39.130 0.00 0.00 0.00 4.26
1426 1510 2.775911 TCAGAGGAATCTGGCAAGTG 57.224 50.000 5.48 0.00 38.23 3.16
1430 1514 2.045524 GGAGATCAGAGGAATCTGGCA 58.954 52.381 5.48 0.00 38.23 4.92
1471 1592 8.458843 TCCGATTTTCAAATGAGTTCCTAAATC 58.541 33.333 0.00 0.00 0.00 2.17
1481 1613 4.966366 GCGATCTTCCGATTTTCAAATGAG 59.034 41.667 0.00 0.00 0.00 2.90
1532 1664 2.484264 GGCGATTTAAGCACACAGAACT 59.516 45.455 0.00 0.00 36.08 3.01
1536 1668 2.094894 CAGAGGCGATTTAAGCACACAG 59.905 50.000 0.00 0.00 36.08 3.66
1559 1693 3.115554 GCAACACACAATCAGGTGAAAC 58.884 45.455 0.00 0.00 41.32 2.78
1560 1694 3.023119 AGCAACACACAATCAGGTGAAA 58.977 40.909 0.00 0.00 41.32 2.69
1743 1877 0.460284 CCATGACCCCTTCGAACTCG 60.460 60.000 0.00 0.00 41.45 4.18
1747 1881 0.546747 ACTCCCATGACCCCTTCGAA 60.547 55.000 0.00 0.00 0.00 3.71
1751 1885 2.308866 CAAACTACTCCCATGACCCCTT 59.691 50.000 0.00 0.00 0.00 3.95
1752 1886 1.916181 CAAACTACTCCCATGACCCCT 59.084 52.381 0.00 0.00 0.00 4.79
1757 1891 3.840666 AGAAGAGCAAACTACTCCCATGA 59.159 43.478 0.00 0.00 34.56 3.07
1758 1892 4.187694 GAGAAGAGCAAACTACTCCCATG 58.812 47.826 0.00 0.00 34.56 3.66
1759 1893 3.198853 GGAGAAGAGCAAACTACTCCCAT 59.801 47.826 0.00 0.00 36.06 4.00
1760 1894 2.567615 GGAGAAGAGCAAACTACTCCCA 59.432 50.000 0.00 0.00 36.06 4.37
1761 1895 2.835156 AGGAGAAGAGCAAACTACTCCC 59.165 50.000 0.00 0.00 39.55 4.30
1763 1897 6.708502 AGAAAAAGGAGAAGAGCAAACTACTC 59.291 38.462 0.00 0.00 0.00 2.59
1764 1898 6.596621 AGAAAAAGGAGAAGAGCAAACTACT 58.403 36.000 0.00 0.00 0.00 2.57
1765 1899 6.869315 AGAAAAAGGAGAAGAGCAAACTAC 57.131 37.500 0.00 0.00 0.00 2.73
1766 1900 7.054124 TCAAGAAAAAGGAGAAGAGCAAACTA 58.946 34.615 0.00 0.00 0.00 2.24
1768 1902 6.136541 TCAAGAAAAAGGAGAAGAGCAAAC 57.863 37.500 0.00 0.00 0.00 2.93
1769 1903 6.293626 CGATCAAGAAAAAGGAGAAGAGCAAA 60.294 38.462 0.00 0.00 0.00 3.68
1775 1910 4.633565 CCTCCGATCAAGAAAAAGGAGAAG 59.366 45.833 10.54 0.00 45.88 2.85
1785 1920 1.115467 GAGAGGCCTCCGATCAAGAA 58.885 55.000 29.54 0.00 33.30 2.52
1799 1934 6.091441 GCAAACAGTGAGTTACTTATGAGAGG 59.909 42.308 0.00 0.00 40.26 3.69
1876 2011 0.463654 TATGATTCCACGGCACTGCC 60.464 55.000 10.35 10.35 46.75 4.85
1989 2132 1.339151 CCCAGCCCTATCTATTTCGCC 60.339 57.143 0.00 0.00 0.00 5.54
2011 2154 1.483415 AGATGATGCAAAATGGGTGCC 59.517 47.619 0.00 0.00 41.49 5.01
2046 2189 4.488879 ACTAAACCCACGACGAGTAAATC 58.511 43.478 0.00 0.00 0.00 2.17
2047 2190 4.525912 ACTAAACCCACGACGAGTAAAT 57.474 40.909 0.00 0.00 0.00 1.40
2048 2191 4.202101 TGAACTAAACCCACGACGAGTAAA 60.202 41.667 0.00 0.00 0.00 2.01
2049 2192 3.317711 TGAACTAAACCCACGACGAGTAA 59.682 43.478 0.00 0.00 0.00 2.24
2050 2193 2.884012 TGAACTAAACCCACGACGAGTA 59.116 45.455 0.00 0.00 0.00 2.59
2051 2194 1.682854 TGAACTAAACCCACGACGAGT 59.317 47.619 0.00 0.00 0.00 4.18
2052 2195 2.427232 TGAACTAAACCCACGACGAG 57.573 50.000 0.00 0.00 0.00 4.18
2053 2196 2.886862 TTGAACTAAACCCACGACGA 57.113 45.000 0.00 0.00 0.00 4.20
2054 2197 4.024725 TGAATTTGAACTAAACCCACGACG 60.025 41.667 0.00 0.00 0.00 5.12
2055 2198 5.427036 TGAATTTGAACTAAACCCACGAC 57.573 39.130 0.00 0.00 0.00 4.34
2056 2199 6.452494 TTTGAATTTGAACTAAACCCACGA 57.548 33.333 0.00 0.00 0.00 4.35
2057 2200 7.063544 TGTTTTTGAATTTGAACTAAACCCACG 59.936 33.333 0.00 0.00 0.00 4.94
2058 2201 8.257830 TGTTTTTGAATTTGAACTAAACCCAC 57.742 30.769 0.00 0.00 0.00 4.61
2059 2202 8.848474 TTGTTTTTGAATTTGAACTAAACCCA 57.152 26.923 0.00 0.00 0.00 4.51
2060 2203 9.767684 CTTTGTTTTTGAATTTGAACTAAACCC 57.232 29.630 0.00 0.00 0.00 4.11
2061 2204 9.767684 CCTTTGTTTTTGAATTTGAACTAAACC 57.232 29.630 0.00 0.00 0.00 3.27
2065 2208 9.936759 AGAACCTTTGTTTTTGAATTTGAACTA 57.063 25.926 0.00 0.00 33.97 2.24
2066 2209 8.846943 AGAACCTTTGTTTTTGAATTTGAACT 57.153 26.923 0.00 0.00 33.97 3.01
2068 2211 9.936759 ACTAGAACCTTTGTTTTTGAATTTGAA 57.063 25.926 0.00 0.00 33.97 2.69
2069 2212 9.581099 GACTAGAACCTTTGTTTTTGAATTTGA 57.419 29.630 0.00 0.00 33.97 2.69
2070 2213 9.364989 TGACTAGAACCTTTGTTTTTGAATTTG 57.635 29.630 0.00 0.00 33.97 2.32
2073 2216 9.533253 CAATGACTAGAACCTTTGTTTTTGAAT 57.467 29.630 0.00 0.00 33.97 2.57
2074 2217 7.491048 GCAATGACTAGAACCTTTGTTTTTGAA 59.509 33.333 0.00 0.00 33.97 2.69
2075 2218 6.978080 GCAATGACTAGAACCTTTGTTTTTGA 59.022 34.615 0.00 0.00 33.97 2.69
2076 2219 6.200854 GGCAATGACTAGAACCTTTGTTTTTG 59.799 38.462 0.00 0.00 33.97 2.44
2077 2220 6.127196 TGGCAATGACTAGAACCTTTGTTTTT 60.127 34.615 0.00 0.00 33.97 1.94
2078 2221 5.362430 TGGCAATGACTAGAACCTTTGTTTT 59.638 36.000 0.00 0.00 33.97 2.43
2091 2234 4.286297 ACTGTTAAGCTGGCAATGACTA 57.714 40.909 0.00 0.00 0.00 2.59
2114 2257 8.585471 ACTTTTGATGTATTCCAGAACATGAT 57.415 30.769 0.00 0.00 36.48 2.45
2124 2267 5.399013 CGTTGGGAACTTTTGATGTATTCC 58.601 41.667 0.00 0.00 38.50 3.01
2125 2268 4.857037 GCGTTGGGAACTTTTGATGTATTC 59.143 41.667 0.00 0.00 0.00 1.75
2127 2270 4.079253 AGCGTTGGGAACTTTTGATGTAT 58.921 39.130 0.00 0.00 0.00 2.29
2129 2272 2.293399 GAGCGTTGGGAACTTTTGATGT 59.707 45.455 0.00 0.00 0.00 3.06
2130 2273 2.293122 TGAGCGTTGGGAACTTTTGATG 59.707 45.455 0.00 0.00 0.00 3.07
2132 2275 1.673920 GTGAGCGTTGGGAACTTTTGA 59.326 47.619 0.00 0.00 0.00 2.69
2133 2276 1.676006 AGTGAGCGTTGGGAACTTTTG 59.324 47.619 0.00 0.00 0.00 2.44
2134 2277 1.676006 CAGTGAGCGTTGGGAACTTTT 59.324 47.619 0.00 0.00 0.00 2.27
2135 2278 1.308998 CAGTGAGCGTTGGGAACTTT 58.691 50.000 0.00 0.00 0.00 2.66
2136 2279 0.535102 CCAGTGAGCGTTGGGAACTT 60.535 55.000 0.00 0.00 0.00 2.66
2137 2280 1.071471 CCAGTGAGCGTTGGGAACT 59.929 57.895 0.00 0.00 0.00 3.01
2155 2806 0.389025 CAACCTTGTCCAACCTTGCC 59.611 55.000 0.00 0.00 0.00 4.52
2156 2807 1.338020 CTCAACCTTGTCCAACCTTGC 59.662 52.381 0.00 0.00 0.00 4.01
2164 2815 2.859165 TCACCATCTCAACCTTGTCC 57.141 50.000 0.00 0.00 0.00 4.02
2165 2816 3.942829 TGATCACCATCTCAACCTTGTC 58.057 45.455 0.00 0.00 0.00 3.18
2191 2865 3.004629 TGGCTGCACACTACAAATTTCTG 59.995 43.478 0.50 0.00 0.00 3.02
2196 2870 1.266718 CGTTGGCTGCACACTACAAAT 59.733 47.619 0.50 0.00 0.00 2.32
2197 2871 0.660488 CGTTGGCTGCACACTACAAA 59.340 50.000 0.50 0.00 0.00 2.83
2202 2876 0.391661 CCTATCGTTGGCTGCACACT 60.392 55.000 0.50 0.00 0.00 3.55
2230 2905 5.964168 CAGTTACTTCACGTATTAGGTCTCG 59.036 44.000 0.00 0.00 0.00 4.04
2242 2917 3.684788 CCCTCCATTTCAGTTACTTCACG 59.315 47.826 0.00 0.00 0.00 4.35
2243 2918 4.906618 TCCCTCCATTTCAGTTACTTCAC 58.093 43.478 0.00 0.00 0.00 3.18
2246 2921 6.893020 ATACTCCCTCCATTTCAGTTACTT 57.107 37.500 0.00 0.00 0.00 2.24
2247 2922 9.091220 GTATATACTCCCTCCATTTCAGTTACT 57.909 37.037 5.58 0.00 0.00 2.24
2248 2923 9.091220 AGTATATACTCCCTCCATTTCAGTTAC 57.909 37.037 9.71 0.00 0.00 2.50
2249 2924 9.670442 AAGTATATACTCCCTCCATTTCAGTTA 57.330 33.333 15.72 0.00 34.99 2.24
2258 2936 7.931015 ACATGAAAAGTATATACTCCCTCCA 57.069 36.000 15.72 9.93 34.99 3.86
2269 2947 5.236263 CGGTGCTGCATACATGAAAAGTATA 59.764 40.000 5.27 0.00 31.32 1.47
2270 2948 4.035558 CGGTGCTGCATACATGAAAAGTAT 59.964 41.667 5.27 0.00 32.62 2.12
2272 2950 2.162208 CGGTGCTGCATACATGAAAAGT 59.838 45.455 5.27 0.00 0.00 2.66
2273 2951 2.478370 CCGGTGCTGCATACATGAAAAG 60.478 50.000 5.27 0.00 0.00 2.27
2274 2952 1.472082 CCGGTGCTGCATACATGAAAA 59.528 47.619 5.27 0.00 0.00 2.29
2275 2953 1.093972 CCGGTGCTGCATACATGAAA 58.906 50.000 5.27 0.00 0.00 2.69
2276 2954 0.251634 TCCGGTGCTGCATACATGAA 59.748 50.000 5.27 0.00 0.00 2.57
2277 2955 0.179076 CTCCGGTGCTGCATACATGA 60.179 55.000 5.27 1.52 0.00 3.07
2278 2956 1.779025 GCTCCGGTGCTGCATACATG 61.779 60.000 20.97 0.00 0.00 3.21
2280 2958 2.125147 GCTCCGGTGCTGCATACA 60.125 61.111 20.97 0.00 0.00 2.29
2318 4132 5.109210 CCCTCCTTGTGTTTTCAACTTTTC 58.891 41.667 0.00 0.00 0.00 2.29
2323 4137 1.754226 TGCCCTCCTTGTGTTTTCAAC 59.246 47.619 0.00 0.00 0.00 3.18
2324 4138 1.754226 GTGCCCTCCTTGTGTTTTCAA 59.246 47.619 0.00 0.00 0.00 2.69
2325 4139 1.341482 TGTGCCCTCCTTGTGTTTTCA 60.341 47.619 0.00 0.00 0.00 2.69
2326 4140 1.338020 CTGTGCCCTCCTTGTGTTTTC 59.662 52.381 0.00 0.00 0.00 2.29
2327 4141 1.402787 CTGTGCCCTCCTTGTGTTTT 58.597 50.000 0.00 0.00 0.00 2.43
2328 4142 0.468029 CCTGTGCCCTCCTTGTGTTT 60.468 55.000 0.00 0.00 0.00 2.83
2329 4143 1.151450 CCTGTGCCCTCCTTGTGTT 59.849 57.895 0.00 0.00 0.00 3.32
2330 4144 2.839098 CCTGTGCCCTCCTTGTGT 59.161 61.111 0.00 0.00 0.00 3.72
2331 4145 2.674380 GCCTGTGCCCTCCTTGTG 60.674 66.667 0.00 0.00 0.00 3.33
2332 4146 2.296945 TTTGCCTGTGCCCTCCTTGT 62.297 55.000 0.00 0.00 36.33 3.16
2333 4147 0.901580 ATTTGCCTGTGCCCTCCTTG 60.902 55.000 0.00 0.00 36.33 3.61
2334 4148 0.178924 AATTTGCCTGTGCCCTCCTT 60.179 50.000 0.00 0.00 36.33 3.36
2335 4149 0.901580 CAATTTGCCTGTGCCCTCCT 60.902 55.000 0.00 0.00 36.33 3.69
2336 4150 1.593265 CAATTTGCCTGTGCCCTCC 59.407 57.895 0.00 0.00 36.33 4.30
2337 4151 1.079612 GCAATTTGCCTGTGCCCTC 60.080 57.895 10.34 0.00 37.42 4.30
2364 4178 4.154918 CCTGGTGTTATTGAAGTGCTTCTC 59.845 45.833 12.44 1.08 40.14 2.87
2399 4214 3.148412 GCATTTGGGGCTTTGAATGTTT 58.852 40.909 0.00 0.00 33.25 2.83
2503 4318 7.167468 CACCTATTTTGGTTTCTGAAAAACTCG 59.833 37.037 4.09 0.00 38.45 4.18
2514 4329 2.562738 AGCTGGCACCTATTTTGGTTTC 59.437 45.455 0.00 0.00 38.45 2.78
2564 4380 3.924686 CCGGCGTATACATGAATAGGAAC 59.075 47.826 6.01 0.00 0.00 3.62
2566 4382 2.494471 CCCGGCGTATACATGAATAGGA 59.506 50.000 6.01 0.00 0.00 2.94
2567 4383 2.418197 CCCCGGCGTATACATGAATAGG 60.418 54.545 6.01 0.00 0.00 2.57
2581 4397 1.465777 CAAACTTTAACTACCCCGGCG 59.534 52.381 0.00 0.00 0.00 6.46
2582 4398 2.485426 GACAAACTTTAACTACCCCGGC 59.515 50.000 0.00 0.00 0.00 6.13
2650 4468 1.739067 GGAATGGGTTTCTGAGGTCG 58.261 55.000 0.00 0.00 34.56 4.79
2730 4548 0.036732 TGATGACAACCACAGAGGCC 59.963 55.000 0.00 0.00 43.14 5.19
2807 4625 0.802494 CCATGTACCTTTGCACGACC 59.198 55.000 0.00 0.00 0.00 4.79
2813 4633 5.246307 AGTTCTCTAACCATGTACCTTTGC 58.754 41.667 0.00 0.00 36.15 3.68


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

AutoCloner maintained by Alex Coulton.