Multiple sequence alignment - TraesCS7D01G056400

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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 TraesCS7D01G056400 chr7D 100.000 2408 0 0 1 2408 30242281 30239874 0.000000e+00 4447.0
1 TraesCS7D01G056400 chr7D 86.998 423 37 12 1995 2408 178506441 178506854 6.070000e-126 460.0
2 TraesCS7D01G056400 chr7A 90.057 1589 122 23 431 1997 30640333 30638759 0.000000e+00 2026.0
3 TraesCS7D01G056400 chr7A 91.304 69 5 1 359 427 30640456 30640389 2.550000e-15 93.5
4 TraesCS7D01G056400 chr4A 84.739 1684 160 47 1 1624 698174284 698175930 0.000000e+00 1596.0
5 TraesCS7D01G056400 chr4A 86.044 1082 73 36 567 1624 699003992 699005019 0.000000e+00 1090.0
6 TraesCS7D01G056400 chr4A 84.330 485 57 9 1239 1711 699007342 699007819 7.850000e-125 457.0
7 TraesCS7D01G056400 chr4A 84.179 335 23 17 1652 1977 699005015 699005328 5.030000e-77 298.0
8 TraesCS7D01G056400 chr4A 88.053 226 16 3 1652 1872 698175926 698176145 8.540000e-65 257.0
9 TraesCS7D01G056400 chr3A 86.600 403 39 9 1998 2394 455235396 455235003 4.760000e-117 431.0
10 TraesCS7D01G056400 chr3B 85.096 416 44 14 1999 2408 147659057 147659460 2.230000e-110 409.0
11 TraesCS7D01G056400 chr3B 85.195 385 41 10 1998 2372 733585817 733585439 4.860000e-102 381.0
12 TraesCS7D01G056400 chr3B 83.654 416 54 8 2000 2408 181750363 181749955 1.750000e-101 379.0
13 TraesCS7D01G056400 chr1D 84.507 426 44 13 1998 2408 379579159 379578741 3.730000e-108 401.0
14 TraesCS7D01G056400 chr3D 84.507 426 42 14 1998 2408 379244186 379243770 1.340000e-107 399.0
15 TraesCS7D01G056400 chr6D 83.693 417 45 14 2003 2408 407179734 407179330 2.920000e-99 372.0
16 TraesCS7D01G056400 chr2A 83.791 401 54 8 1998 2394 218146226 218146619 1.050000e-98 370.0


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 TraesCS7D01G056400 chr7D 30239874 30242281 2407 True 4447.00 4447 100.0000 1 2408 1 chr7D.!!$R1 2407
1 TraesCS7D01G056400 chr7A 30638759 30640456 1697 True 1059.75 2026 90.6805 359 1997 2 chr7A.!!$R1 1638
2 TraesCS7D01G056400 chr4A 698174284 698176145 1861 False 926.50 1596 86.3960 1 1872 2 chr4A.!!$F1 1871
3 TraesCS7D01G056400 chr4A 699003992 699007819 3827 False 615.00 1090 84.8510 567 1977 3 chr4A.!!$F2 1410

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
269 272 0.531532 TCCCTATCTCGACGACGTCC 60.532 60.0 21.63 5.01 40.69 4.79 F
1146 1253 0.949105 ACATCAAGACGGTGCGTTCC 60.949 55.0 0.00 0.00 41.37 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1481 0.108804 GAATCACAGGAGGTCGCGAA 60.109 55.0 12.06 0.0 0.0 4.70 R
2273 3165 0.177373 GGGTCTCGGGCGAAATAACT 59.823 55.0 0.00 0.0 0.0 2.24 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
22 23 4.409718 TTACTAGTTTGCAGTGTCACCA 57.590 40.909 0.00 0.00 0.00 4.17
47 48 4.762956 AGTACGAATACGCCTCCTATTC 57.237 45.455 0.00 0.00 43.96 1.75
52 53 4.202326 ACGAATACGCCTCCTATTCCAAAT 60.202 41.667 0.00 0.00 43.96 2.32
55 57 2.127708 ACGCCTCCTATTCCAAATCCT 58.872 47.619 0.00 0.00 0.00 3.24
59 61 4.202367 CGCCTCCTATTCCAAATCCTAGTT 60.202 45.833 0.00 0.00 0.00 2.24
63 65 4.476846 TCCTATTCCAAATCCTAGTTGCCA 59.523 41.667 0.00 0.00 0.00 4.92
87 89 4.980805 GTGTTCTCCACGCCGCCA 62.981 66.667 0.00 0.00 33.61 5.69
103 105 4.452733 CACCTCGGTCGCCTTCCC 62.453 72.222 0.00 0.00 0.00 3.97
154 156 1.181786 GAGGAGTGAGGACCTGTCTG 58.818 60.000 0.00 0.00 36.57 3.51
160 162 2.975489 AGTGAGGACCTGTCTGTTTCAT 59.025 45.455 0.00 0.00 0.00 2.57
200 203 2.359850 GTTCCCGTGGCAGCATCA 60.360 61.111 0.00 0.00 0.00 3.07
240 243 3.504863 TGTCGTGTTAGAATAAGGTCGC 58.495 45.455 0.00 0.00 0.00 5.19
242 245 3.790288 GTCGTGTTAGAATAAGGTCGCTC 59.210 47.826 0.00 0.00 0.00 5.03
252 255 3.844090 GGTCGCTCTGGCCTCTCC 61.844 72.222 3.32 0.00 34.44 3.71
256 259 1.532794 CGCTCTGGCCTCTCCCTAT 60.533 63.158 3.32 0.00 34.44 2.57
269 272 0.531532 TCCCTATCTCGACGACGTCC 60.532 60.000 21.63 5.01 40.69 4.79
276 279 2.102357 CGACGACGTCCCATCCAG 59.898 66.667 21.63 2.50 34.56 3.86
310 313 2.811873 GCATGTGGGAGTTTGTGTCTCT 60.812 50.000 0.00 0.00 33.06 3.10
315 318 5.330233 TGTGGGAGTTTGTGTCTCTAGATA 58.670 41.667 0.00 0.00 33.06 1.98
337 341 4.503741 TTTTGGCTTTCTTCGGATCTTG 57.496 40.909 0.00 0.00 0.00 3.02
349 353 3.588955 TCGGATCTTGACAGTTGATGTG 58.411 45.455 0.00 0.00 44.17 3.21
383 387 2.563702 ACAATTTGCTGGCTTTGGTTG 58.436 42.857 0.00 0.00 0.00 3.77
385 389 3.181452 ACAATTTGCTGGCTTTGGTTGAT 60.181 39.130 0.00 0.00 0.00 2.57
386 390 2.529780 TTTGCTGGCTTTGGTTGATG 57.470 45.000 0.00 0.00 0.00 3.07
442 497 3.798889 GCATGGTGATGGATTGATGCTTG 60.799 47.826 0.00 0.00 34.64 4.01
485 561 4.082679 ACTTCTAGATCTCGTTTCAAGCGT 60.083 41.667 0.00 0.00 0.00 5.07
486 562 4.436242 TCTAGATCTCGTTTCAAGCGTT 57.564 40.909 0.00 0.00 0.00 4.84
511 587 6.013842 AGCAACTATTGTGGTCTTTAAAGC 57.986 37.500 10.51 5.80 0.00 3.51
513 589 5.390613 CAACTATTGTGGTCTTTAAAGCCG 58.609 41.667 10.51 4.47 0.00 5.52
531 607 1.308998 CGGGTACAATGAGGGCATTC 58.691 55.000 0.00 0.00 42.66 2.67
535 611 3.496160 GGGTACAATGAGGGCATTCGTAT 60.496 47.826 0.00 0.00 42.66 3.06
536 612 3.746492 GGTACAATGAGGGCATTCGTATC 59.254 47.826 0.00 0.00 42.66 2.24
560 636 5.942961 TGTCCATTTCCTTTACTGTTGGTA 58.057 37.500 0.00 0.00 0.00 3.25
587 663 5.124936 GTGTAATTTTTAATCTCCGGCTGGT 59.875 40.000 12.43 0.00 36.30 4.00
656 734 9.872757 ATGTAGTTTTATGTTTTACTTGTCGTG 57.127 29.630 0.00 0.00 0.00 4.35
673 751 4.106197 GTCGTGATGTATCTGGTTGTCTC 58.894 47.826 0.00 0.00 0.00 3.36
684 762 8.038944 TGTATCTGGTTGTCTCTTTATTGTACC 58.961 37.037 0.00 0.00 0.00 3.34
695 773 9.704098 GTCTCTTTATTGTACCGATCATTTTTC 57.296 33.333 0.00 0.00 0.00 2.29
704 783 9.757227 TTGTACCGATCATTTTTCTTTTTCATT 57.243 25.926 0.00 0.00 0.00 2.57
705 784 9.190858 TGTACCGATCATTTTTCTTTTTCATTG 57.809 29.630 0.00 0.00 0.00 2.82
706 785 7.656707 ACCGATCATTTTTCTTTTTCATTGG 57.343 32.000 0.00 0.00 0.00 3.16
707 786 7.216494 ACCGATCATTTTTCTTTTTCATTGGT 58.784 30.769 0.00 0.00 0.00 3.67
708 787 7.714813 ACCGATCATTTTTCTTTTTCATTGGTT 59.285 29.630 0.00 0.00 0.00 3.67
1146 1253 0.949105 ACATCAAGACGGTGCGTTCC 60.949 55.000 0.00 0.00 41.37 3.62
1149 1256 2.027625 CAAGACGGTGCGTTCCCTC 61.028 63.158 0.00 0.00 41.37 4.30
1177 1285 2.517402 CGTCTCCCCCTCTCTCCG 60.517 72.222 0.00 0.00 0.00 4.63
1193 1302 1.131826 CCGTTGATTGGTTCGTCGC 59.868 57.895 0.00 0.00 0.00 5.19
1213 1322 1.663074 GTCGCTGAGGATCCATCGC 60.663 63.158 15.82 11.53 0.00 4.58
1363 1472 3.689002 CTCCTCTTCAAGGCCGCCC 62.689 68.421 5.55 0.00 45.78 6.13
1397 1506 1.519455 CCTCCTGTGATTCGTCGGC 60.519 63.158 0.00 0.00 0.00 5.54
1399 1508 2.885644 CCTGTGATTCGTCGGCGG 60.886 66.667 10.62 0.00 38.89 6.13
1422 1531 2.259917 TCTTGATCTGCTCCTGTCCAA 58.740 47.619 0.00 0.00 0.00 3.53
1427 1538 0.108585 TCTGCTCCTGTCCAACCAAC 59.891 55.000 0.00 0.00 0.00 3.77
1432 1543 1.903404 CCTGTCCAACCAACCCTGC 60.903 63.158 0.00 0.00 0.00 4.85
1447 1558 1.066573 CCCTGCAGAGTCTCATTCGTT 60.067 52.381 17.39 0.00 0.00 3.85
1462 1579 1.081556 TCGTTGGCGATGACGGATTG 61.082 55.000 0.00 0.00 42.81 2.67
1463 1580 1.081556 CGTTGGCGATGACGGATTGA 61.082 55.000 0.00 0.00 41.33 2.57
1473 1594 0.179171 GACGGATTGAGCGTCGAGAA 60.179 55.000 0.00 0.00 0.00 2.87
1537 1658 1.284657 CCTGTATGCTCTGCTGAACG 58.715 55.000 0.00 0.00 0.00 3.95
1539 1660 1.078201 TGTATGCTCTGCTGAACGCG 61.078 55.000 3.53 3.53 43.27 6.01
1544 1665 1.664649 CTCTGCTGAACGCGAACCA 60.665 57.895 15.93 6.38 43.27 3.67
1570 1691 5.824624 CCAGATTTTGTACATAGACCATGCT 59.175 40.000 0.00 0.00 38.29 3.79
1584 1709 2.756760 ACCATGCTCAGTAAATTGCAGG 59.243 45.455 0.00 0.00 38.87 4.85
1585 1710 3.431922 CATGCTCAGTAAATTGCAGGG 57.568 47.619 0.00 0.00 38.87 4.45
1646 1771 1.135373 GCCGATCTCAACTCGTGAAGA 60.135 52.381 0.00 0.00 35.22 2.87
1692 1819 7.259290 TCCTAACATTCAGTTCAGTTTGTTC 57.741 36.000 0.00 0.00 41.64 3.18
1753 1885 2.855963 GCGATTCAAATCAGCCAATGTG 59.144 45.455 3.81 0.00 35.11 3.21
1754 1886 3.427909 GCGATTCAAATCAGCCAATGTGA 60.428 43.478 3.81 0.00 35.11 3.58
1755 1887 4.735985 CGATTCAAATCAGCCAATGTGAA 58.264 39.130 4.48 4.48 37.30 3.18
1756 1888 5.345702 CGATTCAAATCAGCCAATGTGAAT 58.654 37.500 12.08 12.08 43.29 2.57
1757 1889 5.231357 CGATTCAAATCAGCCAATGTGAATG 59.769 40.000 15.58 7.48 41.55 2.67
1758 1890 5.471556 TTCAAATCAGCCAATGTGAATGT 57.528 34.783 0.00 0.00 29.73 2.71
1766 1898 1.619827 CCAATGTGAATGTGGTTGCCT 59.380 47.619 0.00 0.00 0.00 4.75
1776 1908 4.789012 ATGTGGTTGCCTCTGTATTTTG 57.211 40.909 0.00 0.00 0.00 2.44
1777 1909 3.561143 TGTGGTTGCCTCTGTATTTTGT 58.439 40.909 0.00 0.00 0.00 2.83
1778 1910 3.957497 TGTGGTTGCCTCTGTATTTTGTT 59.043 39.130 0.00 0.00 0.00 2.83
1798 1934 8.851541 TTTGTTTAATAATCAGTAGGTCCGTT 57.148 30.769 0.00 0.00 0.00 4.44
1809 1945 3.695060 AGTAGGTCCGTTGTGTCTGATAG 59.305 47.826 0.00 0.00 0.00 2.08
1850 1986 1.760613 TCCGACTTGATATGACCCACC 59.239 52.381 0.00 0.00 0.00 4.61
1851 1987 1.538204 CCGACTTGATATGACCCACCG 60.538 57.143 0.00 0.00 0.00 4.94
1964 2108 2.037136 GCCGCTGTTGAGCTGTCAT 61.037 57.895 0.00 0.00 43.77 3.06
1992 2136 0.967380 CATTTGGCCTCAGGTCACCC 60.967 60.000 0.00 0.00 36.87 4.61
1997 2141 4.135153 CCTCAGGTCACCCGAGCG 62.135 72.222 0.83 0.00 44.60 5.03
2004 2896 2.033448 TCACCCGAGCGGCAAAAT 59.967 55.556 1.45 0.00 33.26 1.82
2006 2898 1.175983 TCACCCGAGCGGCAAAATTT 61.176 50.000 1.45 0.00 33.26 1.82
2007 2899 0.732538 CACCCGAGCGGCAAAATTTC 60.733 55.000 1.45 0.00 33.26 2.17
2008 2900 1.175983 ACCCGAGCGGCAAAATTTCA 61.176 50.000 1.45 0.00 33.26 2.69
2010 2902 1.270971 CCGAGCGGCAAAATTTCATG 58.729 50.000 1.45 0.00 0.00 3.07
2013 2905 2.730928 CGAGCGGCAAAATTTCATGTTT 59.269 40.909 1.45 0.00 0.00 2.83
2014 2906 3.184178 CGAGCGGCAAAATTTCATGTTTT 59.816 39.130 1.45 0.00 0.00 2.43
2017 2909 4.024977 AGCGGCAAAATTTCATGTTTTGAC 60.025 37.500 18.93 16.20 46.27 3.18
2018 2910 4.771360 CGGCAAAATTTCATGTTTTGACC 58.229 39.130 18.93 17.03 46.77 4.02
2022 2914 5.901336 GCAAAATTTCATGTTTTGACCGTTC 59.099 36.000 18.93 2.43 45.02 3.95
2023 2915 6.238076 GCAAAATTTCATGTTTTGACCGTTCT 60.238 34.615 18.93 0.00 45.02 3.01
2029 2921 1.130955 GTTTTGACCGTTCTCGCGTA 58.869 50.000 5.77 0.00 35.54 4.42
2034 2926 0.457337 GACCGTTCTCGCGTACCAAT 60.457 55.000 5.77 0.00 35.54 3.16
2035 2927 0.037975 ACCGTTCTCGCGTACCAATT 60.038 50.000 5.77 0.00 35.54 2.32
2037 2929 1.342555 CGTTCTCGCGTACCAATTCA 58.657 50.000 5.77 0.00 0.00 2.57
2040 2932 1.179152 TCTCGCGTACCAATTCAGGA 58.821 50.000 5.77 0.00 0.00 3.86
2041 2933 1.754803 TCTCGCGTACCAATTCAGGAT 59.245 47.619 5.77 0.00 0.00 3.24
2042 2934 2.128035 CTCGCGTACCAATTCAGGATC 58.872 52.381 5.77 0.00 0.00 3.36
2043 2935 1.754803 TCGCGTACCAATTCAGGATCT 59.245 47.619 5.77 0.00 0.00 2.75
2044 2936 1.860950 CGCGTACCAATTCAGGATCTG 59.139 52.381 0.00 0.00 0.00 2.90
2045 2937 2.481276 CGCGTACCAATTCAGGATCTGA 60.481 50.000 0.00 0.00 38.87 3.27
2046 2938 3.733337 GCGTACCAATTCAGGATCTGAT 58.267 45.455 0.00 0.00 40.39 2.90
2047 2939 3.743396 GCGTACCAATTCAGGATCTGATC 59.257 47.826 9.18 9.18 40.39 2.92
2087 2979 6.554334 TGGATTTGACTCTTTTTCTTACCG 57.446 37.500 0.00 0.00 0.00 4.02
2088 2980 5.048991 TGGATTTGACTCTTTTTCTTACCGC 60.049 40.000 0.00 0.00 0.00 5.68
2089 2981 4.823790 TTTGACTCTTTTTCTTACCGCC 57.176 40.909 0.00 0.00 0.00 6.13
2090 2982 3.478857 TGACTCTTTTTCTTACCGCCA 57.521 42.857 0.00 0.00 0.00 5.69
2091 2983 3.399330 TGACTCTTTTTCTTACCGCCAG 58.601 45.455 0.00 0.00 0.00 4.85
2093 2985 3.665190 ACTCTTTTTCTTACCGCCAGAG 58.335 45.455 0.00 0.00 33.83 3.35
2094 2986 3.003480 CTCTTTTTCTTACCGCCAGAGG 58.997 50.000 0.00 0.00 37.30 3.69
2096 2988 2.178912 TTTTCTTACCGCCAGAGGTG 57.821 50.000 3.03 0.00 45.54 4.00
2097 2989 0.321298 TTTCTTACCGCCAGAGGTGC 60.321 55.000 3.03 0.00 45.54 5.01
2099 2991 1.448540 CTTACCGCCAGAGGTGCTG 60.449 63.158 3.03 0.00 45.54 4.41
2106 2998 2.185350 CAGAGGTGCTGGCGGTAG 59.815 66.667 0.00 0.00 41.07 3.18
2107 2999 3.077556 AGAGGTGCTGGCGGTAGG 61.078 66.667 0.00 0.00 0.00 3.18
2108 3000 4.162690 GAGGTGCTGGCGGTAGGG 62.163 72.222 0.00 0.00 0.00 3.53
2111 3003 2.662070 GGTGCTGGCGGTAGGGTTA 61.662 63.158 0.00 0.00 0.00 2.85
2112 3004 1.153429 GTGCTGGCGGTAGGGTTAG 60.153 63.158 0.00 0.00 0.00 2.34
2113 3005 1.305465 TGCTGGCGGTAGGGTTAGA 60.305 57.895 0.00 0.00 0.00 2.10
2114 3006 1.143401 GCTGGCGGTAGGGTTAGAC 59.857 63.158 0.00 0.00 0.00 2.59
2115 3007 1.610554 GCTGGCGGTAGGGTTAGACA 61.611 60.000 0.00 0.00 0.00 3.41
2116 3008 0.460311 CTGGCGGTAGGGTTAGACAG 59.540 60.000 0.00 0.00 0.00 3.51
2117 3009 1.143401 GGCGGTAGGGTTAGACAGC 59.857 63.158 0.00 0.00 36.22 4.40
2118 3010 1.143401 GCGGTAGGGTTAGACAGCC 59.857 63.158 0.00 0.00 44.40 4.85
2123 3015 2.901042 GGGTTAGACAGCCTCCCG 59.099 66.667 0.00 0.00 40.32 5.14
2124 3016 2.187163 GGTTAGACAGCCTCCCGC 59.813 66.667 0.00 0.00 37.98 6.13
2125 3017 2.187163 GTTAGACAGCCTCCCGCC 59.813 66.667 0.00 0.00 38.78 6.13
2126 3018 2.284331 TTAGACAGCCTCCCGCCA 60.284 61.111 0.00 0.00 38.78 5.69
2127 3019 2.359169 TTAGACAGCCTCCCGCCAG 61.359 63.158 0.00 0.00 38.78 4.85
2146 3038 1.686800 GGAACCTGGCGGTAGGGTA 60.687 63.158 0.00 0.00 44.73 3.69
2147 3039 1.519246 GAACCTGGCGGTAGGGTAC 59.481 63.158 0.00 0.00 44.73 3.34
2148 3040 0.974525 GAACCTGGCGGTAGGGTACT 60.975 60.000 0.00 0.00 44.73 2.73
2149 3041 0.336048 AACCTGGCGGTAGGGTACTA 59.664 55.000 0.00 0.00 44.73 1.82
2150 3042 0.336048 ACCTGGCGGTAGGGTACTAA 59.664 55.000 0.00 0.00 43.29 2.24
2151 3043 1.062658 ACCTGGCGGTAGGGTACTAAT 60.063 52.381 0.00 0.00 43.29 1.73
2152 3044 1.617357 CCTGGCGGTAGGGTACTAATC 59.383 57.143 0.00 0.00 34.06 1.75
2155 3047 1.342496 GGCGGTAGGGTACTAATCCAC 59.658 57.143 0.00 0.00 0.00 4.02
2156 3048 1.000938 GCGGTAGGGTACTAATCCACG 60.001 57.143 0.00 0.00 0.00 4.94
2158 3050 2.291741 CGGTAGGGTACTAATCCACGTC 59.708 54.545 0.00 0.00 0.00 4.34
2159 3051 3.290710 GGTAGGGTACTAATCCACGTCA 58.709 50.000 0.00 0.00 0.00 4.35
2160 3052 3.317430 GGTAGGGTACTAATCCACGTCAG 59.683 52.174 0.00 0.00 0.00 3.51
2161 3053 1.755380 AGGGTACTAATCCACGTCAGC 59.245 52.381 0.00 0.00 0.00 4.26
2162 3054 1.479323 GGGTACTAATCCACGTCAGCA 59.521 52.381 0.00 0.00 0.00 4.41
2163 3055 2.102588 GGGTACTAATCCACGTCAGCAT 59.897 50.000 0.00 0.00 0.00 3.79
2164 3056 3.123804 GGTACTAATCCACGTCAGCATG 58.876 50.000 0.00 0.00 37.54 4.06
2165 3057 3.430374 GGTACTAATCCACGTCAGCATGT 60.430 47.826 0.00 0.00 37.40 3.21
2171 3063 2.449548 CACGTCAGCATGTGGAGAC 58.550 57.895 0.00 0.00 36.06 3.36
2172 3064 3.772636 CGTCAGCATGTGGAGACG 58.227 61.111 13.71 13.71 46.12 4.18
2173 3065 4.192000 GTCAGCATGTGGAGACGG 57.808 61.111 0.00 0.00 37.40 4.79
2174 3066 1.293498 GTCAGCATGTGGAGACGGT 59.707 57.895 0.00 0.00 37.40 4.83
2175 3067 1.016130 GTCAGCATGTGGAGACGGTG 61.016 60.000 0.00 0.00 37.40 4.94
2177 3069 1.016130 CAGCATGTGGAGACGGTGAC 61.016 60.000 0.00 0.00 0.00 3.67
2223 3115 4.530857 CCGCTAGGGTCCTTGGCG 62.531 72.222 22.61 22.61 42.19 5.69
2224 3116 4.530857 CGCTAGGGTCCTTGGCGG 62.531 72.222 21.96 5.47 40.47 6.13
2226 3118 2.062177 GCTAGGGTCCTTGGCGGTA 61.062 63.158 0.00 0.00 0.00 4.02
2227 3119 2.029307 GCTAGGGTCCTTGGCGGTAG 62.029 65.000 0.00 0.00 0.00 3.18
2228 3120 1.382146 TAGGGTCCTTGGCGGTAGG 60.382 63.158 0.00 0.00 0.00 3.18
2229 3121 4.484872 GGGTCCTTGGCGGTAGGC 62.485 72.222 0.00 0.00 44.11 3.93
2233 3125 2.125106 CCTTGGCGGTAGGCTGTC 60.125 66.667 0.00 0.00 44.18 3.51
2235 3127 1.327690 CCTTGGCGGTAGGCTGTCTA 61.328 60.000 0.00 0.00 44.18 2.59
2236 3128 0.535335 CTTGGCGGTAGGCTGTCTAA 59.465 55.000 0.00 0.00 44.18 2.10
2237 3129 0.248289 TTGGCGGTAGGCTGTCTAAC 59.752 55.000 0.00 0.00 44.18 2.34
2238 3130 1.143401 GGCGGTAGGCTGTCTAACC 59.857 63.158 0.00 0.00 42.94 2.85
2239 3131 1.143401 GCGGTAGGCTGTCTAACCC 59.857 63.158 0.00 0.00 39.11 4.11
2240 3132 1.328430 GCGGTAGGCTGTCTAACCCT 61.328 60.000 0.00 0.00 39.11 4.34
2242 3134 1.680207 CGGTAGGCTGTCTAACCCTAC 59.320 57.143 0.00 7.39 46.60 3.18
2244 3136 1.680207 GTAGGCTGTCTAACCCTACCG 59.320 57.143 0.00 0.00 43.31 4.02
2245 3137 1.143401 GGCTGTCTAACCCTACCGC 59.857 63.158 0.00 0.00 0.00 5.68
2247 3139 1.396653 GCTGTCTAACCCTACCGCTA 58.603 55.000 0.00 0.00 0.00 4.26
2248 3140 1.337387 GCTGTCTAACCCTACCGCTAG 59.663 57.143 0.00 0.00 0.00 3.42
2249 3141 1.337387 CTGTCTAACCCTACCGCTAGC 59.663 57.143 4.06 4.06 0.00 3.42
2250 3142 1.341285 TGTCTAACCCTACCGCTAGCA 60.341 52.381 16.45 0.00 0.00 3.49
2251 3143 1.962100 GTCTAACCCTACCGCTAGCAT 59.038 52.381 16.45 4.48 0.00 3.79
2252 3144 2.030096 GTCTAACCCTACCGCTAGCATC 60.030 54.545 16.45 0.00 0.00 3.91
2253 3145 1.272769 CTAACCCTACCGCTAGCATCC 59.727 57.143 16.45 0.00 0.00 3.51
2256 3148 1.668294 CCTACCGCTAGCATCCCTG 59.332 63.158 16.45 0.00 0.00 4.45
2257 3149 1.668294 CTACCGCTAGCATCCCTGG 59.332 63.158 16.45 9.04 0.00 4.45
2258 3150 2.441822 CTACCGCTAGCATCCCTGGC 62.442 65.000 16.45 0.00 43.92 4.85
2261 3153 3.866582 GCTAGCATCCCTGGCGGT 61.867 66.667 10.63 0.00 38.32 5.68
2263 3155 1.668294 CTAGCATCCCTGGCGGTAG 59.332 63.158 0.00 0.00 36.08 3.18
2264 3156 1.821061 CTAGCATCCCTGGCGGTAGG 61.821 65.000 0.00 0.00 37.59 3.18
2271 3163 4.514577 CTGGCGGTAGGGTGCGAG 62.515 72.222 0.00 0.00 0.00 5.03
2275 3167 3.760035 CGGTAGGGTGCGAGCAGT 61.760 66.667 0.00 0.00 0.00 4.40
2276 3168 2.663196 GGTAGGGTGCGAGCAGTT 59.337 61.111 0.00 0.00 0.00 3.16
2277 3169 1.895238 GGTAGGGTGCGAGCAGTTA 59.105 57.895 0.00 0.00 0.00 2.24
2280 3172 2.629051 GTAGGGTGCGAGCAGTTATTT 58.371 47.619 0.00 0.00 0.00 1.40
2281 3173 1.739067 AGGGTGCGAGCAGTTATTTC 58.261 50.000 0.00 0.00 0.00 2.17
2286 3178 1.636340 CGAGCAGTTATTTCGCCCG 59.364 57.895 0.00 0.00 0.00 6.13
2287 3179 0.804544 CGAGCAGTTATTTCGCCCGA 60.805 55.000 0.00 0.00 0.00 5.14
2288 3180 0.931005 GAGCAGTTATTTCGCCCGAG 59.069 55.000 0.00 0.00 0.00 4.63
2289 3181 0.535335 AGCAGTTATTTCGCCCGAGA 59.465 50.000 0.00 0.00 0.00 4.04
2290 3182 0.651031 GCAGTTATTTCGCCCGAGAC 59.349 55.000 0.00 0.00 0.00 3.36
2291 3183 1.287425 CAGTTATTTCGCCCGAGACC 58.713 55.000 0.00 0.00 0.00 3.85
2292 3184 0.177373 AGTTATTTCGCCCGAGACCC 59.823 55.000 0.00 0.00 0.00 4.46
2295 3187 2.287457 TATTTCGCCCGAGACCCGTG 62.287 60.000 0.00 0.00 36.31 4.94
2310 3202 3.076916 GTGCCCCTGCCCATTTCC 61.077 66.667 0.00 0.00 36.33 3.13
2311 3203 4.397010 TGCCCCTGCCCATTTCCC 62.397 66.667 0.00 0.00 36.33 3.97
2314 3206 2.364186 CCCTGCCCATTTCCCCAC 60.364 66.667 0.00 0.00 0.00 4.61
2315 3207 2.364186 CCTGCCCATTTCCCCACC 60.364 66.667 0.00 0.00 0.00 4.61
2316 3208 2.364186 CTGCCCATTTCCCCACCC 60.364 66.667 0.00 0.00 0.00 4.61
2317 3209 3.982258 CTGCCCATTTCCCCACCCC 62.982 68.421 0.00 0.00 0.00 4.95
2319 3211 2.689813 CCCATTTCCCCACCCCTC 59.310 66.667 0.00 0.00 0.00 4.30
2320 3212 2.689813 CCATTTCCCCACCCCTCC 59.310 66.667 0.00 0.00 0.00 4.30
2321 3213 2.689813 CATTTCCCCACCCCTCCC 59.310 66.667 0.00 0.00 0.00 4.30
2340 4194 4.016706 CTCCCCCGTCGGCAGTTT 62.017 66.667 5.50 0.00 0.00 2.66
2343 4197 2.046314 CCCCGTCGGCAGTTTCAT 60.046 61.111 5.50 0.00 0.00 2.57
2345 4199 1.079127 CCCGTCGGCAGTTTCATCT 60.079 57.895 5.50 0.00 0.00 2.90
2346 4200 1.084370 CCCGTCGGCAGTTTCATCTC 61.084 60.000 5.50 0.00 0.00 2.75
2348 4202 1.084370 CGTCGGCAGTTTCATCTCCC 61.084 60.000 0.00 0.00 0.00 4.30
2369 4223 3.024356 TCGCCCCTCTCTCCCTCT 61.024 66.667 0.00 0.00 0.00 3.69
2370 4224 2.520741 CGCCCCTCTCTCCCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
2371 4225 3.024217 GCCCCTCTCTCCCTCTCT 58.976 66.667 0.00 0.00 0.00 3.10
2374 4228 0.859760 CCCCTCTCTCCCTCTCTCAT 59.140 60.000 0.00 0.00 0.00 2.90
2378 4232 2.224867 CCTCTCTCCCTCTCTCATCTCC 60.225 59.091 0.00 0.00 0.00 3.71
2379 4233 2.713167 CTCTCTCCCTCTCTCATCTCCT 59.287 54.545 0.00 0.00 0.00 3.69
2380 4234 3.130450 TCTCTCCCTCTCTCATCTCCTT 58.870 50.000 0.00 0.00 0.00 3.36
2381 4235 3.138283 TCTCTCCCTCTCTCATCTCCTTC 59.862 52.174 0.00 0.00 0.00 3.46
2382 4236 2.855599 TCTCCCTCTCTCATCTCCTTCA 59.144 50.000 0.00 0.00 0.00 3.02
2384 4238 2.584965 TCCCTCTCTCATCTCCTTCACT 59.415 50.000 0.00 0.00 0.00 3.41
2385 4239 2.958355 CCCTCTCTCATCTCCTTCACTC 59.042 54.545 0.00 0.00 0.00 3.51
2386 4240 3.373001 CCCTCTCTCATCTCCTTCACTCT 60.373 52.174 0.00 0.00 0.00 3.24
2388 4242 3.885297 CTCTCTCATCTCCTTCACTCTCC 59.115 52.174 0.00 0.00 0.00 3.71
2390 4244 2.038659 CTCATCTCCTTCACTCTCCCC 58.961 57.143 0.00 0.00 0.00 4.81
2391 4245 1.127343 CATCTCCTTCACTCTCCCCC 58.873 60.000 0.00 0.00 0.00 5.40
2392 4246 1.022903 ATCTCCTTCACTCTCCCCCT 58.977 55.000 0.00 0.00 0.00 4.79
2393 4247 0.336737 TCTCCTTCACTCTCCCCCTC 59.663 60.000 0.00 0.00 0.00 4.30
2394 4248 0.689412 CTCCTTCACTCTCCCCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
2396 4250 1.000486 CTTCACTCTCCCCCTCCGA 60.000 63.158 0.00 0.00 0.00 4.55
2398 4252 1.801302 TTCACTCTCCCCCTCCGACT 61.801 60.000 0.00 0.00 0.00 4.18
2399 4253 1.305381 CACTCTCCCCCTCCGACTT 60.305 63.158 0.00 0.00 0.00 3.01
2401 4255 1.000486 CTCTCCCCCTCCGACTTCA 60.000 63.158 0.00 0.00 0.00 3.02
2402 4256 1.305046 TCTCCCCCTCCGACTTCAC 60.305 63.158 0.00 0.00 0.00 3.18
2404 4258 3.771160 CCCCCTCCGACTTCACCG 61.771 72.222 0.00 0.00 0.00 4.94
2405 4259 2.995574 CCCCTCCGACTTCACCGT 60.996 66.667 0.00 0.00 0.00 4.83
2406 4260 2.580601 CCCCTCCGACTTCACCGTT 61.581 63.158 0.00 0.00 0.00 4.44
2407 4261 1.370064 CCCTCCGACTTCACCGTTT 59.630 57.895 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.275617 TTGGTGACACTGCAAACTAGT 57.724 42.857 5.39 0.00 42.67 2.57
6 7 3.258123 ACTTTTTGGTGACACTGCAAACT 59.742 39.130 5.39 0.00 42.67 2.66
14 15 5.368374 CGTATTCGTACTTTTTGGTGACAC 58.632 41.667 0.00 0.00 42.67 3.67
20 21 3.063045 GGAGGCGTATTCGTACTTTTTGG 59.937 47.826 0.00 0.00 39.49 3.28
22 23 4.198028 AGGAGGCGTATTCGTACTTTTT 57.802 40.909 0.00 0.00 39.49 1.94
47 48 2.214376 TGGTGGCAACTAGGATTTGG 57.786 50.000 3.27 0.00 37.61 3.28
52 53 1.145571 ACCTTTGGTGGCAACTAGGA 58.854 50.000 24.67 0.00 32.98 2.94
99 101 4.772231 CCGGACGAGGGAGGGGAA 62.772 72.222 0.00 0.00 0.00 3.97
126 128 1.153939 CTCACTCCTCTTGTCGCCG 60.154 63.158 0.00 0.00 0.00 6.46
131 133 1.133009 ACAGGTCCTCACTCCTCTTGT 60.133 52.381 0.00 0.00 30.91 3.16
167 170 6.149633 CACGGGAACAAATTCTAAGAAAAGG 58.850 40.000 0.00 0.00 34.98 3.11
174 177 2.817258 CTGCCACGGGAACAAATTCTAA 59.183 45.455 0.00 0.00 34.98 2.10
178 181 1.112315 TGCTGCCACGGGAACAAATT 61.112 50.000 0.00 0.00 0.00 1.82
179 182 0.899717 ATGCTGCCACGGGAACAAAT 60.900 50.000 0.00 0.00 0.00 2.32
200 203 1.619827 CATTGTTGCCACCACCTCATT 59.380 47.619 0.00 0.00 0.00 2.57
217 220 4.565564 GCGACCTTATTCTAACACGACATT 59.434 41.667 0.00 0.00 0.00 2.71
220 223 3.767278 AGCGACCTTATTCTAACACGAC 58.233 45.455 0.00 0.00 0.00 4.34
226 229 2.102588 GGCCAGAGCGACCTTATTCTAA 59.897 50.000 0.00 0.00 41.24 2.10
240 243 1.886222 CGAGATAGGGAGAGGCCAGAG 60.886 61.905 5.01 0.00 38.95 3.35
242 245 0.111446 TCGAGATAGGGAGAGGCCAG 59.889 60.000 5.01 0.00 38.95 4.85
252 255 0.812811 TGGGACGTCGTCGAGATAGG 60.813 60.000 18.61 0.00 40.62 2.57
256 259 2.110967 GGATGGGACGTCGTCGAGA 61.111 63.158 18.61 5.75 40.62 4.04
276 279 3.443045 CATGCCCTTCGGTGCCAC 61.443 66.667 0.00 0.00 0.00 5.01
284 287 0.890683 CAAACTCCCACATGCCCTTC 59.109 55.000 0.00 0.00 0.00 3.46
310 313 7.509546 AGATCCGAAGAAAGCCAAAATATCTA 58.490 34.615 0.00 0.00 0.00 1.98
315 318 4.766891 TCAAGATCCGAAGAAAGCCAAAAT 59.233 37.500 0.00 0.00 0.00 1.82
337 341 3.119291 CTCGATAGGCACATCAACTGTC 58.881 50.000 0.00 0.00 35.29 3.51
349 353 3.002759 GCAAATTGTTCTCCTCGATAGGC 59.997 47.826 0.00 0.00 43.31 3.93
369 373 1.667151 GCATCAACCAAAGCCAGCA 59.333 52.632 0.00 0.00 0.00 4.41
371 375 0.109597 GTCGCATCAACCAAAGCCAG 60.110 55.000 0.00 0.00 0.00 4.85
383 387 2.803451 AGAAGATGTCGAAGTCGCATC 58.197 47.619 20.60 20.60 44.81 3.91
385 389 2.596452 GAAGAAGATGTCGAAGTCGCA 58.404 47.619 0.00 0.00 39.60 5.10
386 390 1.921230 GGAAGAAGATGTCGAAGTCGC 59.079 52.381 0.00 0.00 39.60 5.19
460 536 5.403246 GCTTGAAACGAGATCTAGAAGTCA 58.597 41.667 10.07 6.77 0.00 3.41
463 539 4.416620 ACGCTTGAAACGAGATCTAGAAG 58.583 43.478 10.07 4.02 0.00 2.85
485 561 7.575414 TTTAAAGACCACAATAGTTGCTCAA 57.425 32.000 0.00 0.00 0.00 3.02
486 562 6.293955 GCTTTAAAGACCACAATAGTTGCTCA 60.294 38.462 19.48 0.00 0.00 4.26
499 575 1.698532 TGTACCCGGCTTTAAAGACCA 59.301 47.619 19.48 6.14 0.00 4.02
500 576 2.477845 TGTACCCGGCTTTAAAGACC 57.522 50.000 19.48 16.80 0.00 3.85
511 587 0.106719 AATGCCCTCATTGTACCCGG 60.107 55.000 0.00 0.00 41.12 5.73
513 589 1.308998 CGAATGCCCTCATTGTACCC 58.691 55.000 0.00 0.00 42.60 3.69
531 607 6.106673 ACAGTAAAGGAAATGGACAGATACG 58.893 40.000 0.00 0.00 0.00 3.06
535 611 5.070001 CCAACAGTAAAGGAAATGGACAGA 58.930 41.667 0.00 0.00 0.00 3.41
536 612 4.827284 ACCAACAGTAAAGGAAATGGACAG 59.173 41.667 0.00 0.00 0.00 3.51
560 636 5.949952 AGCCGGAGATTAAAAATTACACCTT 59.050 36.000 5.05 0.00 0.00 3.50
587 663 4.099113 TGTTGTTCTTGCCATTGATTGTCA 59.901 37.500 0.00 0.00 0.00 3.58
630 708 9.872757 CACGACAAGTAAAACATAAAACTACAT 57.127 29.630 0.00 0.00 0.00 2.29
642 720 6.367969 ACCAGATACATCACGACAAGTAAAAC 59.632 38.462 0.00 0.00 0.00 2.43
656 734 8.723942 ACAATAAAGAGACAACCAGATACATC 57.276 34.615 0.00 0.00 0.00 3.06
695 773 9.490663 GAGACGTCATAATAACCAATGAAAAAG 57.509 33.333 19.50 0.00 34.06 2.27
776 873 6.999272 GGTCCTCCTTTTTAGGGAATCTTATC 59.001 42.308 0.00 0.00 34.66 1.75
824 922 2.595463 GGTGGCTGTTGCTCTGCA 60.595 61.111 11.57 0.00 41.72 4.41
890 994 2.179517 GGAGACGGTGAGCGAGTG 59.820 66.667 12.27 0.00 0.00 3.51
900 1004 1.527370 GAGGAAATGGGGGAGACGG 59.473 63.158 0.00 0.00 0.00 4.79
1193 1302 1.006805 GATGGATCCTCAGCGACGG 60.007 63.158 14.23 0.00 0.00 4.79
1372 1481 0.108804 GAATCACAGGAGGTCGCGAA 60.109 55.000 12.06 0.00 0.00 4.70
1373 1482 1.511305 GAATCACAGGAGGTCGCGA 59.489 57.895 3.71 3.71 0.00 5.87
1397 1506 2.363680 ACAGGAGCAGATCAAGATACCG 59.636 50.000 0.00 0.00 0.00 4.02
1399 1508 3.386078 TGGACAGGAGCAGATCAAGATAC 59.614 47.826 0.00 0.00 0.00 2.24
1422 1531 0.764369 TGAGACTCTGCAGGGTTGGT 60.764 55.000 22.78 8.91 0.00 3.67
1427 1538 0.534412 ACGAATGAGACTCTGCAGGG 59.466 55.000 13.44 13.44 0.00 4.45
1432 1543 0.994995 CGCCAACGAATGAGACTCTG 59.005 55.000 3.68 0.00 43.93 3.35
1447 1558 1.521457 GCTCAATCCGTCATCGCCA 60.521 57.895 0.00 0.00 35.54 5.69
1456 1573 0.179161 ACTTCTCGACGCTCAATCCG 60.179 55.000 0.00 0.00 0.00 4.18
1462 1579 0.456995 CCTTCCACTTCTCGACGCTC 60.457 60.000 0.00 0.00 0.00 5.03
1463 1580 1.587054 CCTTCCACTTCTCGACGCT 59.413 57.895 0.00 0.00 0.00 5.07
1537 1658 3.438781 TGTACAAAATCTGGATGGTTCGC 59.561 43.478 0.00 0.00 0.00 4.70
1539 1660 7.012421 GGTCTATGTACAAAATCTGGATGGTTC 59.988 40.741 0.00 0.00 0.00 3.62
1544 1665 6.488006 GCATGGTCTATGTACAAAATCTGGAT 59.512 38.462 0.00 0.00 39.08 3.41
1570 1691 2.295909 GCAACACCCTGCAATTTACTGA 59.704 45.455 0.00 0.00 42.17 3.41
1646 1771 2.292016 TCAAACGAACGAAATGTGGCAT 59.708 40.909 0.14 0.00 0.00 4.40
1692 1819 2.148768 GTATTCCCTAATTTCGGGCGG 58.851 52.381 7.47 0.00 41.69 6.13
1753 1885 5.163513 CAAAATACAGAGGCAACCACATTC 58.836 41.667 0.00 0.00 37.17 2.67
1754 1886 4.588528 ACAAAATACAGAGGCAACCACATT 59.411 37.500 0.00 0.00 37.17 2.71
1755 1887 4.151883 ACAAAATACAGAGGCAACCACAT 58.848 39.130 0.00 0.00 37.17 3.21
1756 1888 3.561143 ACAAAATACAGAGGCAACCACA 58.439 40.909 0.00 0.00 37.17 4.17
1757 1889 4.584327 AACAAAATACAGAGGCAACCAC 57.416 40.909 0.00 0.00 37.17 4.16
1758 1890 6.716934 TTAAACAAAATACAGAGGCAACCA 57.283 33.333 0.00 0.00 37.17 3.67
1776 1908 7.332678 ACACAACGGACCTACTGATTATTAAAC 59.667 37.037 0.00 0.00 0.00 2.01
1777 1909 7.388437 ACACAACGGACCTACTGATTATTAAA 58.612 34.615 0.00 0.00 0.00 1.52
1778 1910 6.938507 ACACAACGGACCTACTGATTATTAA 58.061 36.000 0.00 0.00 0.00 1.40
1798 1934 5.409520 GCAACTTGAACATCTATCAGACACA 59.590 40.000 0.00 0.00 0.00 3.72
1809 1945 0.452784 GCGACGGCAACTTGAACATC 60.453 55.000 0.00 0.00 39.62 3.06
1850 1986 1.811266 CAGACGTGGGGAATCAGCG 60.811 63.158 0.00 0.00 0.00 5.18
1851 1987 2.109126 GCAGACGTGGGGAATCAGC 61.109 63.158 0.00 0.00 0.00 4.26
1964 2108 0.396139 GAGGCCAAATGCATCCTCCA 60.396 55.000 17.53 0.00 44.88 3.86
1992 2136 1.981254 ACATGAAATTTTGCCGCTCG 58.019 45.000 0.00 0.00 0.00 5.03
1997 2141 4.272261 ACGGTCAAAACATGAAATTTTGCC 59.728 37.500 12.74 14.37 43.62 4.52
2004 2896 3.547214 GCGAGAACGGTCAAAACATGAAA 60.547 43.478 1.87 0.00 38.80 2.69
2006 2898 1.529438 GCGAGAACGGTCAAAACATGA 59.471 47.619 1.87 0.00 40.15 3.07
2007 2899 1.721489 CGCGAGAACGGTCAAAACATG 60.721 52.381 0.00 0.00 40.15 3.21
2008 2900 0.511221 CGCGAGAACGGTCAAAACAT 59.489 50.000 0.00 0.00 40.15 2.71
2010 2902 1.130955 TACGCGAGAACGGTCAAAAC 58.869 50.000 15.93 0.00 40.15 2.43
2013 2905 1.081242 GGTACGCGAGAACGGTCAA 60.081 57.895 15.93 0.00 40.15 3.18
2014 2906 1.794151 TTGGTACGCGAGAACGGTCA 61.794 55.000 15.93 0.00 40.15 4.02
2017 2909 0.643820 GAATTGGTACGCGAGAACGG 59.356 55.000 15.93 0.00 40.15 4.44
2018 2910 1.320555 CTGAATTGGTACGCGAGAACG 59.679 52.381 15.93 0.00 42.93 3.95
2022 2914 2.128035 GATCCTGAATTGGTACGCGAG 58.872 52.381 15.93 0.00 0.00 5.03
2023 2915 1.754803 AGATCCTGAATTGGTACGCGA 59.245 47.619 15.93 0.00 0.00 5.87
2060 2952 9.594478 GGTAAGAAAAAGAGTCAAATCCAAAAA 57.406 29.630 0.00 0.00 0.00 1.94
2061 2953 7.918562 CGGTAAGAAAAAGAGTCAAATCCAAAA 59.081 33.333 0.00 0.00 0.00 2.44
2062 2954 7.422399 CGGTAAGAAAAAGAGTCAAATCCAAA 58.578 34.615 0.00 0.00 0.00 3.28
2063 2955 6.514376 GCGGTAAGAAAAAGAGTCAAATCCAA 60.514 38.462 0.00 0.00 0.00 3.53
2064 2956 5.048991 GCGGTAAGAAAAAGAGTCAAATCCA 60.049 40.000 0.00 0.00 0.00 3.41
2065 2957 5.391449 GCGGTAAGAAAAAGAGTCAAATCC 58.609 41.667 0.00 0.00 0.00 3.01
2066 2958 5.048991 TGGCGGTAAGAAAAAGAGTCAAATC 60.049 40.000 0.00 0.00 0.00 2.17
2067 2959 4.825085 TGGCGGTAAGAAAAAGAGTCAAAT 59.175 37.500 0.00 0.00 0.00 2.32
2068 2960 4.200874 TGGCGGTAAGAAAAAGAGTCAAA 58.799 39.130 0.00 0.00 0.00 2.69
2069 2961 3.811083 TGGCGGTAAGAAAAAGAGTCAA 58.189 40.909 0.00 0.00 0.00 3.18
2070 2962 3.070446 TCTGGCGGTAAGAAAAAGAGTCA 59.930 43.478 0.00 0.00 0.00 3.41
2071 2963 3.660865 TCTGGCGGTAAGAAAAAGAGTC 58.339 45.455 0.00 0.00 0.00 3.36
2072 2964 3.557264 CCTCTGGCGGTAAGAAAAAGAGT 60.557 47.826 0.00 0.00 0.00 3.24
2073 2965 3.003480 CCTCTGGCGGTAAGAAAAAGAG 58.997 50.000 0.00 0.00 0.00 2.85
2075 2967 2.484264 CACCTCTGGCGGTAAGAAAAAG 59.516 50.000 0.00 0.00 34.94 2.27
2076 2968 2.500229 CACCTCTGGCGGTAAGAAAAA 58.500 47.619 0.00 0.00 34.94 1.94
2077 2969 1.880646 GCACCTCTGGCGGTAAGAAAA 60.881 52.381 0.00 0.00 34.94 2.29
2078 2970 0.321298 GCACCTCTGGCGGTAAGAAA 60.321 55.000 0.00 0.00 34.94 2.52
2079 2971 1.192146 AGCACCTCTGGCGGTAAGAA 61.192 55.000 0.00 0.00 34.94 2.52
2080 2972 1.609501 AGCACCTCTGGCGGTAAGA 60.610 57.895 0.00 0.00 34.94 2.10
2081 2973 1.448540 CAGCACCTCTGGCGGTAAG 60.449 63.158 0.00 0.00 39.15 2.34
2082 2974 2.662596 CAGCACCTCTGGCGGTAA 59.337 61.111 0.00 0.00 39.15 2.85
2089 2981 2.185350 CTACCGCCAGCACCTCTG 59.815 66.667 0.00 0.00 42.49 3.35
2090 2982 3.077556 CCTACCGCCAGCACCTCT 61.078 66.667 0.00 0.00 0.00 3.69
2091 2983 4.162690 CCCTACCGCCAGCACCTC 62.163 72.222 0.00 0.00 0.00 3.85
2093 2985 2.588856 CTAACCCTACCGCCAGCACC 62.589 65.000 0.00 0.00 0.00 5.01
2094 2986 1.153429 CTAACCCTACCGCCAGCAC 60.153 63.158 0.00 0.00 0.00 4.40
2095 2987 1.305465 TCTAACCCTACCGCCAGCA 60.305 57.895 0.00 0.00 0.00 4.41
2096 2988 1.143401 GTCTAACCCTACCGCCAGC 59.857 63.158 0.00 0.00 0.00 4.85
2097 2989 0.460311 CTGTCTAACCCTACCGCCAG 59.540 60.000 0.00 0.00 0.00 4.85
2099 2991 1.143401 GCTGTCTAACCCTACCGCC 59.857 63.158 0.00 0.00 0.00 6.13
2101 2993 0.745468 GAGGCTGTCTAACCCTACCG 59.255 60.000 0.00 0.00 0.00 4.02
2102 2994 1.121378 GGAGGCTGTCTAACCCTACC 58.879 60.000 0.00 0.00 0.00 3.18
2103 2995 1.121378 GGGAGGCTGTCTAACCCTAC 58.879 60.000 0.00 0.00 37.75 3.18
2104 2996 0.396695 CGGGAGGCTGTCTAACCCTA 60.397 60.000 4.71 0.00 38.51 3.53
2105 2997 1.686110 CGGGAGGCTGTCTAACCCT 60.686 63.158 4.71 0.00 38.51 4.34
2106 2998 2.901042 CGGGAGGCTGTCTAACCC 59.099 66.667 0.00 0.00 37.42 4.11
2107 2999 2.187163 GCGGGAGGCTGTCTAACC 59.813 66.667 0.00 0.00 39.11 2.85
2132 3024 1.617357 GATTAGTACCCTACCGCCAGG 59.383 57.143 0.00 0.00 45.13 4.45
2133 3025 1.617357 GGATTAGTACCCTACCGCCAG 59.383 57.143 0.00 0.00 0.00 4.85
2134 3026 1.063038 TGGATTAGTACCCTACCGCCA 60.063 52.381 0.00 0.00 0.00 5.69
2135 3027 1.342496 GTGGATTAGTACCCTACCGCC 59.658 57.143 0.00 0.00 0.00 6.13
2136 3028 1.000938 CGTGGATTAGTACCCTACCGC 60.001 57.143 0.00 0.00 0.00 5.68
2138 3030 3.290710 TGACGTGGATTAGTACCCTACC 58.709 50.000 0.00 0.00 0.00 3.18
2139 3031 3.243334 GCTGACGTGGATTAGTACCCTAC 60.243 52.174 0.00 0.00 0.00 3.18
2140 3032 2.954318 GCTGACGTGGATTAGTACCCTA 59.046 50.000 0.00 0.00 0.00 3.53
2141 3033 1.755380 GCTGACGTGGATTAGTACCCT 59.245 52.381 0.00 0.00 0.00 4.34
2142 3034 1.479323 TGCTGACGTGGATTAGTACCC 59.521 52.381 0.00 0.00 0.00 3.69
2143 3035 2.953466 TGCTGACGTGGATTAGTACC 57.047 50.000 0.00 0.00 0.00 3.34
2144 3036 3.551890 CACATGCTGACGTGGATTAGTAC 59.448 47.826 0.00 0.00 37.10 2.73
2146 3038 2.621338 CACATGCTGACGTGGATTAGT 58.379 47.619 0.00 0.00 37.10 2.24
2155 3047 3.772636 CGTCTCCACATGCTGACG 58.227 61.111 13.14 13.14 44.41 4.35
2156 3048 1.016130 CACCGTCTCCACATGCTGAC 61.016 60.000 0.00 0.00 0.00 3.51
2158 3050 1.016130 GTCACCGTCTCCACATGCTG 61.016 60.000 0.00 0.00 0.00 4.41
2159 3051 1.293498 GTCACCGTCTCCACATGCT 59.707 57.895 0.00 0.00 0.00 3.79
2160 3052 2.094659 CGTCACCGTCTCCACATGC 61.095 63.158 0.00 0.00 0.00 4.06
2161 3053 1.446099 CCGTCACCGTCTCCACATG 60.446 63.158 0.00 0.00 0.00 3.21
2162 3054 2.970639 CCGTCACCGTCTCCACAT 59.029 61.111 0.00 0.00 0.00 3.21
2163 3055 3.986006 GCCGTCACCGTCTCCACA 61.986 66.667 0.00 0.00 0.00 4.17
2164 3056 4.736896 GGCCGTCACCGTCTCCAC 62.737 72.222 0.00 0.00 0.00 4.02
2195 3087 4.625781 CTAGCGGTAGGGCGCGAC 62.626 72.222 12.10 6.99 38.18 5.19
2206 3098 4.530857 CGCCAAGGACCCTAGCGG 62.531 72.222 19.61 9.23 41.88 5.52
2208 3100 2.029307 CTACCGCCAAGGACCCTAGC 62.029 65.000 0.00 0.00 45.00 3.42
2209 3101 1.400530 CCTACCGCCAAGGACCCTAG 61.401 65.000 0.00 0.00 45.00 3.02
2210 3102 1.382146 CCTACCGCCAAGGACCCTA 60.382 63.158 0.00 0.00 45.00 3.53
2212 3104 4.484872 GCCTACCGCCAAGGACCC 62.485 72.222 0.54 0.00 45.00 4.46
2213 3105 3.400054 AGCCTACCGCCAAGGACC 61.400 66.667 0.54 0.00 45.00 4.46
2214 3106 2.125106 CAGCCTACCGCCAAGGAC 60.125 66.667 0.54 0.00 45.00 3.85
2215 3107 2.606519 ACAGCCTACCGCCAAGGA 60.607 61.111 0.54 0.00 45.00 3.36
2217 3109 0.535335 TTAGACAGCCTACCGCCAAG 59.465 55.000 0.00 0.00 38.78 3.61
2218 3110 0.248289 GTTAGACAGCCTACCGCCAA 59.752 55.000 0.00 0.00 38.78 4.52
2219 3111 1.610554 GGTTAGACAGCCTACCGCCA 61.611 60.000 0.00 0.00 38.78 5.69
2220 3112 1.143401 GGTTAGACAGCCTACCGCC 59.857 63.158 0.00 0.00 38.78 6.13
2221 3113 1.143401 GGGTTAGACAGCCTACCGC 59.857 63.158 0.00 0.00 40.32 5.68
2227 3119 1.143401 GCGGTAGGGTTAGACAGCC 59.857 63.158 0.00 0.00 44.40 4.85
2228 3120 1.337387 CTAGCGGTAGGGTTAGACAGC 59.663 57.143 13.90 0.00 37.07 4.40
2229 3121 1.337387 GCTAGCGGTAGGGTTAGACAG 59.663 57.143 22.24 0.00 0.00 3.51
2233 3125 1.272769 GGATGCTAGCGGTAGGGTTAG 59.727 57.143 22.24 0.00 0.00 2.34
2235 3127 1.408453 GGGATGCTAGCGGTAGGGTT 61.408 60.000 22.24 0.00 0.00 4.11
2236 3128 1.837499 GGGATGCTAGCGGTAGGGT 60.837 63.158 22.24 0.00 0.00 4.34
2237 3129 1.534235 AGGGATGCTAGCGGTAGGG 60.534 63.158 22.24 0.00 0.00 3.53
2238 3130 1.668294 CAGGGATGCTAGCGGTAGG 59.332 63.158 22.24 5.38 0.00 3.18
2239 3131 1.668294 CCAGGGATGCTAGCGGTAG 59.332 63.158 17.24 17.24 0.00 3.18
2240 3132 2.507854 GCCAGGGATGCTAGCGGTA 61.508 63.158 10.77 0.00 0.00 4.02
2242 3134 4.976925 CGCCAGGGATGCTAGCGG 62.977 72.222 10.77 4.92 42.93 5.52
2243 3135 4.976925 CCGCCAGGGATGCTAGCG 62.977 72.222 10.77 8.57 46.04 4.26
2244 3136 2.441822 CTACCGCCAGGGATGCTAGC 62.442 65.000 8.10 8.10 43.47 3.42
2245 3137 1.668294 CTACCGCCAGGGATGCTAG 59.332 63.158 0.00 0.00 43.47 3.42
2247 3139 3.164269 CCTACCGCCAGGGATGCT 61.164 66.667 0.00 0.00 43.47 3.79
2258 3150 1.940883 TAACTGCTCGCACCCTACCG 61.941 60.000 0.00 0.00 0.00 4.02
2259 3151 0.464452 ATAACTGCTCGCACCCTACC 59.536 55.000 0.00 0.00 0.00 3.18
2260 3152 2.311124 AATAACTGCTCGCACCCTAC 57.689 50.000 0.00 0.00 0.00 3.18
2261 3153 2.737359 CGAAATAACTGCTCGCACCCTA 60.737 50.000 0.00 0.00 0.00 3.53
2263 3155 0.373716 CGAAATAACTGCTCGCACCC 59.626 55.000 0.00 0.00 0.00 4.61
2264 3156 3.877801 CGAAATAACTGCTCGCACC 57.122 52.632 0.00 0.00 0.00 5.01
2268 3160 1.636340 CGGGCGAAATAACTGCTCG 59.364 57.895 0.00 0.00 46.98 5.03
2269 3161 0.931005 CTCGGGCGAAATAACTGCTC 59.069 55.000 0.00 0.00 0.00 4.26
2270 3162 0.535335 TCTCGGGCGAAATAACTGCT 59.465 50.000 0.00 0.00 0.00 4.24
2271 3163 0.651031 GTCTCGGGCGAAATAACTGC 59.349 55.000 0.00 0.00 0.00 4.40
2272 3164 1.287425 GGTCTCGGGCGAAATAACTG 58.713 55.000 0.00 0.00 0.00 3.16
2273 3165 0.177373 GGGTCTCGGGCGAAATAACT 59.823 55.000 0.00 0.00 0.00 2.24
2274 3166 1.149964 CGGGTCTCGGGCGAAATAAC 61.150 60.000 0.00 0.00 34.75 1.89
2275 3167 1.142314 CGGGTCTCGGGCGAAATAA 59.858 57.895 0.00 0.00 34.75 1.40
2276 3168 2.053865 ACGGGTCTCGGGCGAAATA 61.054 57.895 0.00 0.00 44.45 1.40
2277 3169 3.387947 ACGGGTCTCGGGCGAAAT 61.388 61.111 0.00 0.00 44.45 2.17
2297 3189 2.364186 GTGGGGAAATGGGCAGGG 60.364 66.667 0.00 0.00 0.00 4.45
2299 3191 2.364186 GGGTGGGGAAATGGGCAG 60.364 66.667 0.00 0.00 0.00 4.85
2301 3193 3.679199 GAGGGGTGGGGAAATGGGC 62.679 68.421 0.00 0.00 0.00 5.36
2302 3194 2.689813 GAGGGGTGGGGAAATGGG 59.310 66.667 0.00 0.00 0.00 4.00
2303 3195 2.689813 GGAGGGGTGGGGAAATGG 59.310 66.667 0.00 0.00 0.00 3.16
2305 3197 2.620464 GGGGAGGGGTGGGGAAAT 60.620 66.667 0.00 0.00 0.00 2.17
2324 3216 4.011517 GAAACTGCCGACGGGGGA 62.012 66.667 17.22 0.00 35.78 4.81
2325 3217 3.622060 ATGAAACTGCCGACGGGGG 62.622 63.158 17.22 0.00 35.78 5.40
2326 3218 2.046314 ATGAAACTGCCGACGGGG 60.046 61.111 17.22 0.00 39.58 5.73
2327 3219 1.079127 AGATGAAACTGCCGACGGG 60.079 57.895 17.22 1.81 0.00 5.28
2328 3220 1.084370 GGAGATGAAACTGCCGACGG 61.084 60.000 10.29 10.29 0.00 4.79
2329 3221 1.084370 GGGAGATGAAACTGCCGACG 61.084 60.000 0.00 0.00 38.50 5.12
2330 3222 0.744771 GGGGAGATGAAACTGCCGAC 60.745 60.000 0.00 0.00 46.89 4.79
2331 3223 1.602237 GGGGAGATGAAACTGCCGA 59.398 57.895 0.00 0.00 46.89 5.54
2332 3224 1.452108 GGGGGAGATGAAACTGCCG 60.452 63.158 0.00 0.00 46.89 5.69
2333 3225 4.666105 GGGGGAGATGAAACTGCC 57.334 61.111 0.00 0.00 45.55 4.85
2351 4205 2.520741 GAGGGAGAGAGGGGCGAG 60.521 72.222 0.00 0.00 0.00 5.03
2355 4209 0.859760 ATGAGAGAGGGAGAGAGGGG 59.140 60.000 0.00 0.00 0.00 4.79
2357 4211 2.224867 GGAGATGAGAGAGGGAGAGAGG 60.225 59.091 0.00 0.00 0.00 3.69
2358 4212 2.713167 AGGAGATGAGAGAGGGAGAGAG 59.287 54.545 0.00 0.00 0.00 3.20
2359 4213 2.787956 AGGAGATGAGAGAGGGAGAGA 58.212 52.381 0.00 0.00 0.00 3.10
2360 4214 3.117550 TGAAGGAGATGAGAGAGGGAGAG 60.118 52.174 0.00 0.00 0.00 3.20
2369 4223 2.358721 GGGGAGAGTGAAGGAGATGAGA 60.359 54.545 0.00 0.00 0.00 3.27
2370 4224 2.038659 GGGGAGAGTGAAGGAGATGAG 58.961 57.143 0.00 0.00 0.00 2.90
2371 4225 1.343478 GGGGGAGAGTGAAGGAGATGA 60.343 57.143 0.00 0.00 0.00 2.92
2374 4228 0.336737 GAGGGGGAGAGTGAAGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
2378 4232 1.000486 TCGGAGGGGGAGAGTGAAG 60.000 63.158 0.00 0.00 0.00 3.02
2379 4233 1.305046 GTCGGAGGGGGAGAGTGAA 60.305 63.158 0.00 0.00 0.00 3.18
2380 4234 1.801302 AAGTCGGAGGGGGAGAGTGA 61.801 60.000 0.00 0.00 0.00 3.41
2381 4235 1.305381 AAGTCGGAGGGGGAGAGTG 60.305 63.158 0.00 0.00 0.00 3.51
2382 4236 1.000612 GAAGTCGGAGGGGGAGAGT 59.999 63.158 0.00 0.00 0.00 3.24
2384 4238 1.305046 GTGAAGTCGGAGGGGGAGA 60.305 63.158 0.00 0.00 0.00 3.71
2385 4239 2.359967 GGTGAAGTCGGAGGGGGAG 61.360 68.421 0.00 0.00 0.00 4.30
2386 4240 2.284405 GGTGAAGTCGGAGGGGGA 60.284 66.667 0.00 0.00 0.00 4.81
2388 4242 2.108278 AAACGGTGAAGTCGGAGGGG 62.108 60.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.