Multiple sequence alignment - TraesCS1A01G384800

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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 TraesCS1A01G384800 chr1A 100.000 2936 0 0 1 2936 554462530 554465465 0 5422
1 TraesCS1A01G384800 chr1A 99.442 538 2 1 2399 2936 554464398 554464934 0 976
2 TraesCS1A01G384800 chr1A 99.071 538 4 1 2399 2936 532087144 532087680 0 965
3 TraesCS1A01G384800 chr2A 99.088 1535 13 1 877 2411 726903290 726901757 0 2756
4 TraesCS1A01G384800 chr2A 97.465 868 20 2 1 867 32526028 32526894 0 1480
5 TraesCS1A01G384800 chr2A 99.257 538 3 1 2399 2936 726902299 726901763 0 970
6 TraesCS1A01G384800 chr3D 98.762 1535 17 1 877 2411 589260362 589258830 0 2728
7 TraesCS1A01G384800 chr3D 99.257 538 3 1 2399 2936 589259372 589258836 0 970
8 TraesCS1A01G384800 chr7B 98.695 1532 18 2 877 2408 662730079 662731608 0 2717
9 TraesCS1A01G384800 chr7B 98.306 1535 24 2 877 2411 663096260 663094728 0 2689
10 TraesCS1A01G384800 chr7B 99.442 538 2 1 2399 2936 622433814 622433278 0 976
11 TraesCS1A01G384800 chr3B 98.567 1535 21 1 877 2411 201571622 201570089 0 2712
12 TraesCS1A01G384800 chr3B 99.071 538 4 1 2399 2936 201570631 201570095 0 965
13 TraesCS1A01G384800 chr7A 98.502 1535 21 1 877 2411 258307648 258306116 0 2706
14 TraesCS1A01G384800 chr7A 99.257 538 3 1 2399 2936 258306658 258306122 0 970
15 TraesCS1A01G384800 chr5D 98.564 1532 20 2 877 2408 503248436 503249965 0 2706
16 TraesCS1A01G384800 chr5D 98.962 867 8 1 1 867 6177449 6176584 0 1550
17 TraesCS1A01G384800 chr5D 98.736 870 8 1 1 867 503290825 503291694 0 1543
18 TraesCS1A01G384800 chr4A 98.241 1535 23 3 877 2411 583865741 583864211 0 2682
19 TraesCS1A01G384800 chr4A 96.774 868 25 2 1 867 309490332 309489467 0 1445
20 TraesCS1A01G384800 chr2D 98.241 1535 23 4 877 2411 272809082 272807552 0 2682
21 TraesCS1A01G384800 chr2D 98.731 867 7 2 1 867 638423975 638424837 0 1537
22 TraesCS1A01G384800 chr2D 99.071 538 3 1 2399 2936 591989829 591990364 0 965
23 TraesCS1A01G384800 chr1D 98.962 867 9 0 1 867 254434500 254435366 0 1552
24 TraesCS1A01G384800 chr6D 98.737 871 7 1 1 867 45508051 45507181 0 1544
25 TraesCS1A01G384800 chr4B 97.809 867 18 1 1 867 308680301 308679436 0 1495
26 TraesCS1A01G384800 chr5A 97.959 833 15 2 36 867 657451090 657451921 0 1443
27 TraesCS1A01G384800 chr3A 99.257 538 3 1 2399 2936 66001324 66000788 0 970


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 TraesCS1A01G384800 chr1A 554462530 554465465 2935 False 3199.0 5422 99.7210 1 2936 2 chr1A.!!$F2 2935
1 TraesCS1A01G384800 chr1A 532087144 532087680 536 False 965.0 965 99.0710 2399 2936 1 chr1A.!!$F1 537
2 TraesCS1A01G384800 chr2A 726901757 726903290 1533 True 1863.0 2756 99.1725 877 2936 2 chr2A.!!$R1 2059
3 TraesCS1A01G384800 chr2A 32526028 32526894 866 False 1480.0 1480 97.4650 1 867 1 chr2A.!!$F1 866
4 TraesCS1A01G384800 chr3D 589258830 589260362 1532 True 1849.0 2728 99.0095 877 2936 2 chr3D.!!$R1 2059
5 TraesCS1A01G384800 chr7B 662730079 662731608 1529 False 2717.0 2717 98.6950 877 2408 1 chr7B.!!$F1 1531
6 TraesCS1A01G384800 chr7B 663094728 663096260 1532 True 2689.0 2689 98.3060 877 2411 1 chr7B.!!$R2 1534
7 TraesCS1A01G384800 chr7B 622433278 622433814 536 True 976.0 976 99.4420 2399 2936 1 chr7B.!!$R1 537
8 TraesCS1A01G384800 chr3B 201570089 201571622 1533 True 1838.5 2712 98.8190 877 2936 2 chr3B.!!$R1 2059
9 TraesCS1A01G384800 chr7A 258306116 258307648 1532 True 1838.0 2706 98.8795 877 2936 2 chr7A.!!$R1 2059
10 TraesCS1A01G384800 chr5D 503248436 503249965 1529 False 2706.0 2706 98.5640 877 2408 1 chr5D.!!$F1 1531
11 TraesCS1A01G384800 chr5D 6176584 6177449 865 True 1550.0 1550 98.9620 1 867 1 chr5D.!!$R1 866
12 TraesCS1A01G384800 chr5D 503290825 503291694 869 False 1543.0 1543 98.7360 1 867 1 chr5D.!!$F2 866
13 TraesCS1A01G384800 chr4A 583864211 583865741 1530 True 2682.0 2682 98.2410 877 2411 1 chr4A.!!$R2 1534
14 TraesCS1A01G384800 chr4A 309489467 309490332 865 True 1445.0 1445 96.7740 1 867 1 chr4A.!!$R1 866
15 TraesCS1A01G384800 chr2D 272807552 272809082 1530 True 2682.0 2682 98.2410 877 2411 1 chr2D.!!$R1 1534
16 TraesCS1A01G384800 chr2D 638423975 638424837 862 False 1537.0 1537 98.7310 1 867 1 chr2D.!!$F2 866
17 TraesCS1A01G384800 chr2D 591989829 591990364 535 False 965.0 965 99.0710 2399 2936 1 chr2D.!!$F1 537
18 TraesCS1A01G384800 chr1D 254434500 254435366 866 False 1552.0 1552 98.9620 1 867 1 chr1D.!!$F1 866
19 TraesCS1A01G384800 chr6D 45507181 45508051 870 True 1544.0 1544 98.7370 1 867 1 chr6D.!!$R1 866
20 TraesCS1A01G384800 chr4B 308679436 308680301 865 True 1495.0 1495 97.8090 1 867 1 chr4B.!!$R1 866
21 TraesCS1A01G384800 chr5A 657451090 657451921 831 False 1443.0 1443 97.9590 36 867 1 chr5A.!!$F1 831
22 TraesCS1A01G384800 chr3A 66000788 66001324 536 True 970.0 970 99.2570 2399 2936 1 chr3A.!!$R1 537

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
986 998 0.249868 CACAGGTCTCCGCAAAGTCA 60.25 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2145 0.107508 GTTAGGATGCCTCAGCTGCA 60.108 55.0 9.47 3.83 43.97 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 441 9.575783 GTCTTTGGTTTTATCACTTGTTGTTTA 57.424 29.630 0.00 0.00 0.00 2.01
654 665 1.407618 GTTTTTGGGACCTTCGTGCTT 59.592 47.619 0.00 0.00 0.00 3.91
867 879 7.969536 TCAACTTCTCATTTTGTTCTAGGAG 57.030 36.000 0.00 0.00 0.00 3.69
868 880 7.509546 TCAACTTCTCATTTTGTTCTAGGAGT 58.490 34.615 0.00 0.00 0.00 3.85
869 881 8.647796 TCAACTTCTCATTTTGTTCTAGGAGTA 58.352 33.333 0.00 0.00 0.00 2.59
870 882 9.442047 CAACTTCTCATTTTGTTCTAGGAGTAT 57.558 33.333 0.00 0.00 0.00 2.12
986 998 0.249868 CACAGGTCTCCGCAAAGTCA 60.250 55.000 0.00 0.00 0.00 3.41
1120 1132 0.813821 AACGGTCCTAAGGTAGCGAC 59.186 55.000 10.62 6.18 39.72 5.19
1126 1138 2.037144 TCCTAAGGTAGCGACATTCCC 58.963 52.381 0.00 0.00 30.80 3.97
1632 1646 7.256286 GCTCAACGGATAAAAGTTACTCTAGA 58.744 38.462 0.00 0.00 0.00 2.43
2054 2068 1.006102 CATACGGGGATGGAGCGAC 60.006 63.158 0.00 0.00 0.00 5.19
2055 2069 1.456892 ATACGGGGATGGAGCGACA 60.457 57.895 0.00 0.00 0.00 4.35
2056 2070 1.464376 ATACGGGGATGGAGCGACAG 61.464 60.000 0.00 0.00 0.00 3.51
2057 2071 2.561467 TACGGGGATGGAGCGACAGA 62.561 60.000 0.00 0.00 0.00 3.41
2058 2072 2.721167 CGGGGATGGAGCGACAGAA 61.721 63.158 0.00 0.00 0.00 3.02
2059 2073 1.144936 GGGGATGGAGCGACAGAAG 59.855 63.158 0.00 0.00 0.00 2.85
2060 2074 1.617947 GGGGATGGAGCGACAGAAGT 61.618 60.000 0.00 0.00 0.00 3.01
2061 2075 1.112113 GGGATGGAGCGACAGAAGTA 58.888 55.000 0.00 0.00 0.00 2.24
2062 2076 1.689273 GGGATGGAGCGACAGAAGTAT 59.311 52.381 0.00 0.00 0.00 2.12
2063 2077 2.546795 GGGATGGAGCGACAGAAGTATG 60.547 54.545 0.00 0.00 0.00 2.39
2064 2078 2.546795 GGATGGAGCGACAGAAGTATGG 60.547 54.545 0.00 0.00 0.00 2.74
2065 2079 1.847328 TGGAGCGACAGAAGTATGGA 58.153 50.000 0.00 0.00 0.00 3.41
2066 2080 2.176045 TGGAGCGACAGAAGTATGGAA 58.824 47.619 0.00 0.00 0.00 3.53
2067 2081 2.565391 TGGAGCGACAGAAGTATGGAAA 59.435 45.455 0.00 0.00 0.00 3.13
2068 2082 3.197766 TGGAGCGACAGAAGTATGGAAAT 59.802 43.478 0.00 0.00 0.00 2.17
2069 2083 4.404394 TGGAGCGACAGAAGTATGGAAATA 59.596 41.667 0.00 0.00 0.00 1.40
2070 2084 4.985409 GGAGCGACAGAAGTATGGAAATAG 59.015 45.833 0.00 0.00 0.00 1.73
2071 2085 4.950050 AGCGACAGAAGTATGGAAATAGG 58.050 43.478 0.00 0.00 0.00 2.57
2072 2086 4.649674 AGCGACAGAAGTATGGAAATAGGA 59.350 41.667 0.00 0.00 0.00 2.94
2073 2087 5.305644 AGCGACAGAAGTATGGAAATAGGAT 59.694 40.000 0.00 0.00 0.00 3.24
2074 2088 6.493802 AGCGACAGAAGTATGGAAATAGGATA 59.506 38.462 0.00 0.00 0.00 2.59
2075 2089 7.015292 AGCGACAGAAGTATGGAAATAGGATAA 59.985 37.037 0.00 0.00 0.00 1.75
2076 2090 7.329717 GCGACAGAAGTATGGAAATAGGATAAG 59.670 40.741 0.00 0.00 0.00 1.73
2077 2091 7.815068 CGACAGAAGTATGGAAATAGGATAAGG 59.185 40.741 0.00 0.00 0.00 2.69
2078 2092 8.568617 ACAGAAGTATGGAAATAGGATAAGGT 57.431 34.615 0.00 0.00 0.00 3.50
2079 2093 9.670442 ACAGAAGTATGGAAATAGGATAAGGTA 57.330 33.333 0.00 0.00 0.00 3.08
2081 2095 8.817876 AGAAGTATGGAAATAGGATAAGGTAGC 58.182 37.037 0.00 0.00 0.00 3.58
2082 2096 7.171630 AGTATGGAAATAGGATAAGGTAGCG 57.828 40.000 0.00 0.00 0.00 4.26
2083 2097 4.884668 TGGAAATAGGATAAGGTAGCGG 57.115 45.455 0.00 0.00 0.00 5.52
2084 2098 4.228824 TGGAAATAGGATAAGGTAGCGGT 58.771 43.478 0.00 0.00 0.00 5.68
2085 2099 4.039973 TGGAAATAGGATAAGGTAGCGGTG 59.960 45.833 0.00 0.00 0.00 4.94
2086 2100 4.282703 GGAAATAGGATAAGGTAGCGGTGA 59.717 45.833 0.00 0.00 0.00 4.02
2087 2101 5.470047 AAATAGGATAAGGTAGCGGTGAG 57.530 43.478 0.00 0.00 0.00 3.51
2088 2102 2.750141 AGGATAAGGTAGCGGTGAGA 57.250 50.000 0.00 0.00 0.00 3.27
2089 2103 2.308690 AGGATAAGGTAGCGGTGAGAC 58.691 52.381 0.00 0.00 0.00 3.36
2090 2104 1.001597 GGATAAGGTAGCGGTGAGACG 60.002 57.143 0.00 0.00 0.00 4.18
2091 2105 1.945394 GATAAGGTAGCGGTGAGACGA 59.055 52.381 0.00 0.00 35.47 4.20
2092 2106 1.376543 TAAGGTAGCGGTGAGACGAG 58.623 55.000 0.00 0.00 35.47 4.18
2093 2107 1.935327 AAGGTAGCGGTGAGACGAGC 61.935 60.000 0.00 0.00 35.47 5.03
2094 2108 2.102553 GTAGCGGTGAGACGAGCC 59.897 66.667 0.00 0.00 35.47 4.70
2097 2111 4.719369 GCGGTGAGACGAGCCGTT 62.719 66.667 4.16 0.00 46.41 4.44
2098 2112 2.049433 CGGTGAGACGAGCCGTTT 60.049 61.111 1.80 0.00 41.37 3.60
2099 2113 1.210931 CGGTGAGACGAGCCGTTTA 59.789 57.895 1.80 0.00 41.37 2.01
2100 2114 0.387622 CGGTGAGACGAGCCGTTTAA 60.388 55.000 1.80 0.00 41.37 1.52
2101 2115 1.787012 GGTGAGACGAGCCGTTTAAA 58.213 50.000 1.80 0.00 41.37 1.52
2102 2116 2.344025 GGTGAGACGAGCCGTTTAAAT 58.656 47.619 1.80 0.00 41.37 1.40
2103 2117 3.514645 GGTGAGACGAGCCGTTTAAATA 58.485 45.455 1.80 0.00 41.37 1.40
2104 2118 3.550678 GGTGAGACGAGCCGTTTAAATAG 59.449 47.826 1.80 0.00 41.37 1.73
2105 2119 3.550678 GTGAGACGAGCCGTTTAAATAGG 59.449 47.826 7.96 7.96 41.37 2.57
2106 2120 3.194116 TGAGACGAGCCGTTTAAATAGGT 59.806 43.478 12.38 3.81 41.37 3.08
2107 2121 3.518590 AGACGAGCCGTTTAAATAGGTG 58.481 45.455 12.38 7.10 41.37 4.00
2108 2122 3.056322 AGACGAGCCGTTTAAATAGGTGT 60.056 43.478 12.38 9.40 41.37 4.16
2109 2123 3.256558 ACGAGCCGTTTAAATAGGTGTC 58.743 45.455 12.38 9.36 36.35 3.67
2110 2124 3.255725 CGAGCCGTTTAAATAGGTGTCA 58.744 45.455 12.38 0.00 0.00 3.58
2111 2125 3.680937 CGAGCCGTTTAAATAGGTGTCAA 59.319 43.478 12.38 0.00 0.00 3.18
2112 2126 4.201685 CGAGCCGTTTAAATAGGTGTCAAG 60.202 45.833 12.38 0.00 0.00 3.02
2113 2127 4.648651 AGCCGTTTAAATAGGTGTCAAGT 58.351 39.130 12.38 0.00 0.00 3.16
2114 2128 4.454504 AGCCGTTTAAATAGGTGTCAAGTG 59.545 41.667 12.38 0.00 0.00 3.16
2115 2129 4.379082 GCCGTTTAAATAGGTGTCAAGTGG 60.379 45.833 12.38 0.00 0.00 4.00
2116 2130 4.998672 CCGTTTAAATAGGTGTCAAGTGGA 59.001 41.667 0.00 0.00 0.00 4.02
2117 2131 5.470777 CCGTTTAAATAGGTGTCAAGTGGAA 59.529 40.000 0.00 0.00 0.00 3.53
2118 2132 6.348213 CCGTTTAAATAGGTGTCAAGTGGAAG 60.348 42.308 0.00 0.00 0.00 3.46
2119 2133 6.204108 CGTTTAAATAGGTGTCAAGTGGAAGT 59.796 38.462 0.00 0.00 0.00 3.01
2120 2134 7.360361 GTTTAAATAGGTGTCAAGTGGAAGTG 58.640 38.462 0.00 0.00 0.00 3.16
2121 2135 2.543777 TAGGTGTCAAGTGGAAGTGC 57.456 50.000 0.00 0.00 0.00 4.40
2122 2136 0.546122 AGGTGTCAAGTGGAAGTGCA 59.454 50.000 0.00 0.00 0.00 4.57
2123 2137 0.947244 GGTGTCAAGTGGAAGTGCAG 59.053 55.000 0.00 0.00 0.00 4.41
2124 2138 1.668419 GTGTCAAGTGGAAGTGCAGT 58.332 50.000 0.00 0.00 0.00 4.40
2125 2139 1.331756 GTGTCAAGTGGAAGTGCAGTG 59.668 52.381 0.00 0.00 0.00 3.66
2126 2140 1.209261 TGTCAAGTGGAAGTGCAGTGA 59.791 47.619 0.00 0.00 0.00 3.41
2127 2141 2.158769 TGTCAAGTGGAAGTGCAGTGAT 60.159 45.455 0.00 0.00 0.00 3.06
2128 2142 2.225019 GTCAAGTGGAAGTGCAGTGATG 59.775 50.000 0.00 0.00 0.00 3.07
2129 2143 2.158769 TCAAGTGGAAGTGCAGTGATGT 60.159 45.455 0.00 0.00 0.00 3.06
2130 2144 3.070878 TCAAGTGGAAGTGCAGTGATGTA 59.929 43.478 0.00 0.00 0.00 2.29
2131 2145 3.988976 AGTGGAAGTGCAGTGATGTAT 57.011 42.857 0.00 0.00 0.00 2.29
2132 2146 3.603532 AGTGGAAGTGCAGTGATGTATG 58.396 45.455 0.00 0.00 0.00 2.39
2133 2147 2.096496 GTGGAAGTGCAGTGATGTATGC 59.904 50.000 0.00 0.00 42.86 3.14
2137 2151 3.867549 TGCAGTGATGTATGCAGCT 57.132 47.368 0.00 0.00 46.97 4.24
2138 2152 1.375551 TGCAGTGATGTATGCAGCTG 58.624 50.000 10.11 10.11 46.97 4.24
2139 2153 1.065998 TGCAGTGATGTATGCAGCTGA 60.066 47.619 20.43 2.70 46.97 4.26
2140 2154 1.598132 GCAGTGATGTATGCAGCTGAG 59.402 52.381 20.43 0.00 42.11 3.35
2141 2155 2.210961 CAGTGATGTATGCAGCTGAGG 58.789 52.381 20.43 0.00 31.27 3.86
2142 2156 0.942962 GTGATGTATGCAGCTGAGGC 59.057 55.000 20.43 1.90 39.06 4.70
2143 2157 0.542805 TGATGTATGCAGCTGAGGCA 59.457 50.000 20.43 9.12 46.66 4.75
2148 2162 4.055178 TGCAGCTGAGGCATCCTA 57.945 55.556 20.43 0.00 41.70 2.94
2149 2163 2.299975 TGCAGCTGAGGCATCCTAA 58.700 52.632 20.43 0.00 41.70 2.69
2150 2164 0.107508 TGCAGCTGAGGCATCCTAAC 60.108 55.000 20.43 0.00 41.70 2.34
2151 2165 1.156645 GCAGCTGAGGCATCCTAACG 61.157 60.000 20.43 0.00 41.70 3.18
2152 2166 0.461548 CAGCTGAGGCATCCTAACGA 59.538 55.000 8.42 0.00 41.70 3.85
2153 2167 1.134699 CAGCTGAGGCATCCTAACGAA 60.135 52.381 8.42 0.00 41.70 3.85
2154 2168 1.134670 AGCTGAGGCATCCTAACGAAC 60.135 52.381 0.00 0.00 41.70 3.95
2155 2169 1.560923 CTGAGGCATCCTAACGAACG 58.439 55.000 0.00 0.00 31.76 3.95
2156 2170 1.134367 CTGAGGCATCCTAACGAACGA 59.866 52.381 0.00 0.00 31.76 3.85
2157 2171 1.546923 TGAGGCATCCTAACGAACGAA 59.453 47.619 0.00 0.00 31.76 3.85
2158 2172 1.925185 GAGGCATCCTAACGAACGAAC 59.075 52.381 0.14 0.00 31.76 3.95
2159 2173 0.643820 GGCATCCTAACGAACGAACG 59.356 55.000 0.14 0.00 39.31 3.95
2160 2174 1.621107 GCATCCTAACGAACGAACGA 58.379 50.000 11.97 0.00 37.03 3.85
2161 2175 2.190981 GCATCCTAACGAACGAACGAT 58.809 47.619 11.97 4.02 37.03 3.73
2162 2176 2.601763 GCATCCTAACGAACGAACGATT 59.398 45.455 11.97 6.20 37.03 3.34
2163 2177 3.061697 GCATCCTAACGAACGAACGATTT 59.938 43.478 11.97 1.45 37.03 2.17
2164 2178 4.565229 CATCCTAACGAACGAACGATTTG 58.435 43.478 11.97 0.00 37.03 2.32
2165 2179 3.899734 TCCTAACGAACGAACGATTTGA 58.100 40.909 11.97 2.51 37.03 2.69
2166 2180 4.297510 TCCTAACGAACGAACGATTTGAA 58.702 39.130 11.97 0.00 37.03 2.69
2167 2181 4.148696 TCCTAACGAACGAACGATTTGAAC 59.851 41.667 11.97 0.00 37.03 3.18
2168 2182 2.936050 ACGAACGAACGATTTGAACC 57.064 45.000 11.97 0.00 37.03 3.62
2169 2183 2.476821 ACGAACGAACGATTTGAACCT 58.523 42.857 11.97 0.00 37.03 3.50
2170 2184 2.867975 ACGAACGAACGATTTGAACCTT 59.132 40.909 11.97 0.00 37.03 3.50
2171 2185 3.215244 CGAACGAACGATTTGAACCTTG 58.785 45.455 0.14 0.00 35.09 3.61
2172 2186 3.302870 CGAACGAACGATTTGAACCTTGT 60.303 43.478 0.14 0.00 35.09 3.16
2173 2187 4.594136 GAACGAACGATTTGAACCTTGTT 58.406 39.130 0.14 0.00 0.00 2.83
2174 2188 4.205323 ACGAACGATTTGAACCTTGTTC 57.795 40.909 0.14 0.07 34.00 3.18
2175 2189 3.002965 ACGAACGATTTGAACCTTGTTCC 59.997 43.478 0.14 0.00 33.86 3.62
2176 2190 3.250040 CGAACGATTTGAACCTTGTTCCT 59.750 43.478 4.65 0.00 33.86 3.36
2177 2191 4.449743 CGAACGATTTGAACCTTGTTCCTA 59.550 41.667 4.65 0.00 33.86 2.94
2178 2192 5.614013 CGAACGATTTGAACCTTGTTCCTAC 60.614 44.000 4.65 0.00 33.86 3.18
2179 2193 4.710324 ACGATTTGAACCTTGTTCCTACA 58.290 39.130 4.65 0.00 0.00 2.74
2180 2194 4.514066 ACGATTTGAACCTTGTTCCTACAC 59.486 41.667 4.65 0.00 32.98 2.90
2181 2195 4.377022 CGATTTGAACCTTGTTCCTACACG 60.377 45.833 4.65 1.83 32.98 4.49
2182 2196 2.536761 TGAACCTTGTTCCTACACGG 57.463 50.000 4.65 0.00 46.34 4.94
2183 2197 1.154197 GAACCTTGTTCCTACACGGC 58.846 55.000 0.00 0.00 45.17 5.68
2184 2198 0.250597 AACCTTGTTCCTACACGGCC 60.251 55.000 0.00 0.00 45.17 6.13
2185 2199 1.125711 ACCTTGTTCCTACACGGCCT 61.126 55.000 0.00 0.00 45.17 5.19
2186 2200 0.673644 CCTTGTTCCTACACGGCCTG 60.674 60.000 0.00 0.21 36.94 4.85
2187 2201 0.320374 CTTGTTCCTACACGGCCTGA 59.680 55.000 0.00 0.00 32.98 3.86
2188 2202 0.981183 TTGTTCCTACACGGCCTGAT 59.019 50.000 0.00 0.00 32.98 2.90
2189 2203 0.535335 TGTTCCTACACGGCCTGATC 59.465 55.000 0.00 0.00 0.00 2.92
2190 2204 0.535335 GTTCCTACACGGCCTGATCA 59.465 55.000 0.00 0.00 0.00 2.92
2191 2205 1.066430 GTTCCTACACGGCCTGATCAA 60.066 52.381 0.00 0.00 0.00 2.57
2192 2206 1.271856 TCCTACACGGCCTGATCAAA 58.728 50.000 0.00 0.00 0.00 2.69
2193 2207 1.837439 TCCTACACGGCCTGATCAAAT 59.163 47.619 0.00 0.00 0.00 2.32
2194 2208 2.158957 TCCTACACGGCCTGATCAAATC 60.159 50.000 0.00 0.00 0.00 2.17
2195 2209 1.860950 CTACACGGCCTGATCAAATCG 59.139 52.381 0.00 3.36 0.00 3.34
2196 2210 0.249120 ACACGGCCTGATCAAATCGA 59.751 50.000 15.12 0.00 0.00 3.59
2197 2211 1.134401 ACACGGCCTGATCAAATCGAT 60.134 47.619 15.12 0.00 36.91 3.59
2208 2222 1.739466 TCAAATCGATCAGGCACTTGC 59.261 47.619 0.00 0.00 34.60 4.01
2223 2237 4.856664 GCACTTGCCATCTATCTTCATTG 58.143 43.478 0.00 0.00 34.31 2.82
2224 2238 4.337555 GCACTTGCCATCTATCTTCATTGT 59.662 41.667 0.00 0.00 34.31 2.71
2225 2239 5.163581 GCACTTGCCATCTATCTTCATTGTT 60.164 40.000 0.00 0.00 34.31 2.83
2226 2240 6.493116 CACTTGCCATCTATCTTCATTGTTC 58.507 40.000 0.00 0.00 0.00 3.18
2227 2241 6.094464 CACTTGCCATCTATCTTCATTGTTCA 59.906 38.462 0.00 0.00 0.00 3.18
2228 2242 6.660521 ACTTGCCATCTATCTTCATTGTTCAA 59.339 34.615 0.00 0.00 0.00 2.69
2229 2243 6.441093 TGCCATCTATCTTCATTGTTCAAC 57.559 37.500 0.00 0.00 0.00 3.18
2230 2244 6.182627 TGCCATCTATCTTCATTGTTCAACT 58.817 36.000 0.00 0.00 0.00 3.16
2231 2245 6.317140 TGCCATCTATCTTCATTGTTCAACTC 59.683 38.462 0.00 0.00 0.00 3.01
2232 2246 6.541641 GCCATCTATCTTCATTGTTCAACTCT 59.458 38.462 0.00 0.00 0.00 3.24
2233 2247 7.066766 GCCATCTATCTTCATTGTTCAACTCTT 59.933 37.037 0.00 0.00 0.00 2.85
2234 2248 8.954350 CCATCTATCTTCATTGTTCAACTCTTT 58.046 33.333 0.00 0.00 0.00 2.52
2235 2249 9.770503 CATCTATCTTCATTGTTCAACTCTTTG 57.229 33.333 0.00 0.00 0.00 2.77
2236 2250 9.730705 ATCTATCTTCATTGTTCAACTCTTTGA 57.269 29.630 0.00 0.00 40.14 2.69
2237 2251 9.730705 TCTATCTTCATTGTTCAACTCTTTGAT 57.269 29.630 0.00 0.00 41.50 2.57
2238 2252 9.770503 CTATCTTCATTGTTCAACTCTTTGATG 57.229 33.333 0.00 0.00 41.50 3.07
2239 2253 7.806409 TCTTCATTGTTCAACTCTTTGATGA 57.194 32.000 0.00 0.00 41.50 2.92
2240 2254 8.224389 TCTTCATTGTTCAACTCTTTGATGAA 57.776 30.769 0.00 0.00 41.50 2.57
2241 2255 8.685427 TCTTCATTGTTCAACTCTTTGATGAAA 58.315 29.630 0.00 0.00 41.50 2.69
2242 2256 9.304731 CTTCATTGTTCAACTCTTTGATGAAAA 57.695 29.630 0.00 0.00 41.50 2.29
2243 2257 8.861033 TCATTGTTCAACTCTTTGATGAAAAG 57.139 30.769 0.00 0.00 45.76 2.27
2276 2290 3.848353 AAAAAGCTCTGCCCTTCCA 57.152 47.368 0.00 0.00 0.00 3.53
2277 2291 2.315720 AAAAAGCTCTGCCCTTCCAT 57.684 45.000 0.00 0.00 0.00 3.41
2278 2292 1.844687 AAAAGCTCTGCCCTTCCATC 58.155 50.000 0.00 0.00 0.00 3.51
2279 2293 0.998145 AAAGCTCTGCCCTTCCATCT 59.002 50.000 0.00 0.00 0.00 2.90
2280 2294 0.545646 AAGCTCTGCCCTTCCATCTC 59.454 55.000 0.00 0.00 0.00 2.75
2281 2295 0.326427 AGCTCTGCCCTTCCATCTCT 60.326 55.000 0.00 0.00 0.00 3.10
2282 2296 0.545646 GCTCTGCCCTTCCATCTCTT 59.454 55.000 0.00 0.00 0.00 2.85
2283 2297 1.746516 GCTCTGCCCTTCCATCTCTTG 60.747 57.143 0.00 0.00 0.00 3.02
2299 2313 6.730447 CATCTCTTGGATAGATAGAGAGGGA 58.270 44.000 0.00 0.00 45.34 4.20
2300 2314 6.387192 TCTCTTGGATAGATAGAGAGGGAG 57.613 45.833 0.00 0.00 39.46 4.30
2301 2315 5.252863 TCTCTTGGATAGATAGAGAGGGAGG 59.747 48.000 0.00 0.00 39.46 4.30
2302 2316 4.293634 TCTTGGATAGATAGAGAGGGAGGG 59.706 50.000 0.00 0.00 0.00 4.30
2303 2317 2.313342 TGGATAGATAGAGAGGGAGGGC 59.687 54.545 0.00 0.00 0.00 5.19
2304 2318 2.313342 GGATAGATAGAGAGGGAGGGCA 59.687 54.545 0.00 0.00 0.00 5.36
2305 2319 3.627237 GGATAGATAGAGAGGGAGGGCAG 60.627 56.522 0.00 0.00 0.00 4.85
2306 2320 1.540115 AGATAGAGAGGGAGGGCAGA 58.460 55.000 0.00 0.00 0.00 4.26
2307 2321 1.428912 AGATAGAGAGGGAGGGCAGAG 59.571 57.143 0.00 0.00 0.00 3.35
2308 2322 0.486879 ATAGAGAGGGAGGGCAGAGG 59.513 60.000 0.00 0.00 0.00 3.69
2309 2323 2.305314 TAGAGAGGGAGGGCAGAGGC 62.305 65.000 0.00 0.00 40.13 4.70
2319 2333 3.673599 GCAGAGGCCTTTGGTGTC 58.326 61.111 23.77 4.23 0.00 3.67
2320 2334 1.973812 GCAGAGGCCTTTGGTGTCC 60.974 63.158 23.77 3.86 0.00 4.02
2321 2335 1.303643 CAGAGGCCTTTGGTGTCCC 60.304 63.158 15.60 0.00 0.00 4.46
2322 2336 1.464198 AGAGGCCTTTGGTGTCCCT 60.464 57.895 6.77 0.00 0.00 4.20
2323 2337 1.068352 AGAGGCCTTTGGTGTCCCTT 61.068 55.000 6.77 0.00 0.00 3.95
2324 2338 0.178961 GAGGCCTTTGGTGTCCCTTT 60.179 55.000 6.77 0.00 0.00 3.11
2325 2339 0.178961 AGGCCTTTGGTGTCCCTTTC 60.179 55.000 0.00 0.00 0.00 2.62
2326 2340 0.469144 GGCCTTTGGTGTCCCTTTCA 60.469 55.000 0.00 0.00 0.00 2.69
2327 2341 0.961753 GCCTTTGGTGTCCCTTTCAG 59.038 55.000 0.00 0.00 0.00 3.02
2328 2342 1.754201 GCCTTTGGTGTCCCTTTCAGT 60.754 52.381 0.00 0.00 0.00 3.41
2329 2343 2.230660 CCTTTGGTGTCCCTTTCAGTC 58.769 52.381 0.00 0.00 0.00 3.51
2330 2344 2.422803 CCTTTGGTGTCCCTTTCAGTCA 60.423 50.000 0.00 0.00 0.00 3.41
2331 2345 3.287222 CTTTGGTGTCCCTTTCAGTCAA 58.713 45.455 0.00 0.00 0.00 3.18
2332 2346 2.638480 TGGTGTCCCTTTCAGTCAAG 57.362 50.000 0.00 0.00 0.00 3.02
2333 2347 2.123589 TGGTGTCCCTTTCAGTCAAGA 58.876 47.619 0.00 0.00 0.00 3.02
2334 2348 2.507886 TGGTGTCCCTTTCAGTCAAGAA 59.492 45.455 0.00 0.00 0.00 2.52
2335 2349 3.138283 TGGTGTCCCTTTCAGTCAAGAAT 59.862 43.478 0.00 0.00 0.00 2.40
2336 2350 4.145052 GGTGTCCCTTTCAGTCAAGAATT 58.855 43.478 0.00 0.00 0.00 2.17
2349 2363 3.967332 CAAGAATTGGGGCTTCACAAT 57.033 42.857 0.00 0.00 43.94 2.71
2350 2364 4.276058 CAAGAATTGGGGCTTCACAATT 57.724 40.909 6.33 6.33 46.61 2.32
2351 2365 5.404466 CAAGAATTGGGGCTTCACAATTA 57.596 39.130 6.58 0.00 44.68 1.40
2352 2366 5.170748 CAAGAATTGGGGCTTCACAATTAC 58.829 41.667 6.58 2.38 44.68 1.89
2353 2367 4.677182 AGAATTGGGGCTTCACAATTACT 58.323 39.130 6.58 4.23 44.68 2.24
2354 2368 5.826643 AGAATTGGGGCTTCACAATTACTA 58.173 37.500 6.58 0.00 44.68 1.82
2355 2369 5.888161 AGAATTGGGGCTTCACAATTACTAG 59.112 40.000 6.58 0.00 44.68 2.57
2356 2370 2.999331 TGGGGCTTCACAATTACTAGC 58.001 47.619 0.00 0.00 0.00 3.42
2374 2388 8.792830 TTACTAGCCAATATTTATCTCATGCC 57.207 34.615 0.00 0.00 0.00 4.40
2375 2389 7.025520 ACTAGCCAATATTTATCTCATGCCT 57.974 36.000 0.00 0.00 0.00 4.75
2376 2390 7.465116 ACTAGCCAATATTTATCTCATGCCTT 58.535 34.615 0.00 0.00 0.00 4.35
2377 2391 7.946776 ACTAGCCAATATTTATCTCATGCCTTT 59.053 33.333 0.00 0.00 0.00 3.11
2378 2392 7.224522 AGCCAATATTTATCTCATGCCTTTC 57.775 36.000 0.00 0.00 0.00 2.62
2379 2393 6.210185 AGCCAATATTTATCTCATGCCTTTCC 59.790 38.462 0.00 0.00 0.00 3.13
2380 2394 6.210185 GCCAATATTTATCTCATGCCTTTCCT 59.790 38.462 0.00 0.00 0.00 3.36
2381 2395 7.576477 GCCAATATTTATCTCATGCCTTTCCTC 60.576 40.741 0.00 0.00 0.00 3.71
2382 2396 7.361542 CCAATATTTATCTCATGCCTTTCCTCG 60.362 40.741 0.00 0.00 0.00 4.63
2383 2397 4.487714 TTTATCTCATGCCTTTCCTCGT 57.512 40.909 0.00 0.00 0.00 4.18
2384 2398 4.487714 TTATCTCATGCCTTTCCTCGTT 57.512 40.909 0.00 0.00 0.00 3.85
2385 2399 2.386661 TCTCATGCCTTTCCTCGTTC 57.613 50.000 0.00 0.00 0.00 3.95
2386 2400 1.623311 TCTCATGCCTTTCCTCGTTCA 59.377 47.619 0.00 0.00 0.00 3.18
2387 2401 2.237143 TCTCATGCCTTTCCTCGTTCAT 59.763 45.455 0.00 0.00 0.00 2.57
2388 2402 2.353889 CTCATGCCTTTCCTCGTTCATG 59.646 50.000 0.00 0.00 34.32 3.07
2389 2403 1.402968 CATGCCTTTCCTCGTTCATGG 59.597 52.381 0.00 0.00 0.00 3.66
2390 2404 0.400213 TGCCTTTCCTCGTTCATGGT 59.600 50.000 0.00 0.00 0.00 3.55
2391 2405 1.202879 TGCCTTTCCTCGTTCATGGTT 60.203 47.619 0.00 0.00 0.00 3.67
2392 2406 1.468914 GCCTTTCCTCGTTCATGGTTC 59.531 52.381 0.00 0.00 0.00 3.62
2393 2407 1.732259 CCTTTCCTCGTTCATGGTTCG 59.268 52.381 0.00 0.00 0.00 3.95
2394 2408 2.611971 CCTTTCCTCGTTCATGGTTCGA 60.612 50.000 0.00 0.36 0.00 3.71
2395 2409 3.262420 CTTTCCTCGTTCATGGTTCGAT 58.738 45.455 7.85 0.00 33.26 3.59
2396 2410 4.430007 CTTTCCTCGTTCATGGTTCGATA 58.570 43.478 7.85 0.00 33.26 2.92
2397 2411 4.665833 TTCCTCGTTCATGGTTCGATAT 57.334 40.909 7.85 0.00 33.26 1.63
2406 2420 4.693283 TCATGGTTCGATATTCTGGTGTC 58.307 43.478 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 441 9.726438 GGATAAGCTGTATTATTGAACCATACT 57.274 33.333 0.00 0.00 0.00 2.12
986 998 2.376518 CAGCCCCCATACATGGTCTTAT 59.623 50.000 7.46 0.00 46.65 1.73
1632 1646 4.570926 TGGGGAAGATCATCCTGTTATCT 58.429 43.478 16.22 0.00 39.57 1.98
1642 1656 2.507471 GTGGACTCTTGGGGAAGATCAT 59.493 50.000 0.00 0.00 0.00 2.45
2055 2069 8.817876 GCTACCTTATCCTATTTCCATACTTCT 58.182 37.037 0.00 0.00 0.00 2.85
2056 2070 7.760340 CGCTACCTTATCCTATTTCCATACTTC 59.240 40.741 0.00 0.00 0.00 3.01
2057 2071 7.310485 CCGCTACCTTATCCTATTTCCATACTT 60.310 40.741 0.00 0.00 0.00 2.24
2058 2072 6.154706 CCGCTACCTTATCCTATTTCCATACT 59.845 42.308 0.00 0.00 0.00 2.12
2059 2073 6.070938 ACCGCTACCTTATCCTATTTCCATAC 60.071 42.308 0.00 0.00 0.00 2.39
2060 2074 6.021030 ACCGCTACCTTATCCTATTTCCATA 58.979 40.000 0.00 0.00 0.00 2.74
2061 2075 4.844655 ACCGCTACCTTATCCTATTTCCAT 59.155 41.667 0.00 0.00 0.00 3.41
2062 2076 4.039973 CACCGCTACCTTATCCTATTTCCA 59.960 45.833 0.00 0.00 0.00 3.53
2063 2077 4.282703 TCACCGCTACCTTATCCTATTTCC 59.717 45.833 0.00 0.00 0.00 3.13
2064 2078 5.243283 TCTCACCGCTACCTTATCCTATTTC 59.757 44.000 0.00 0.00 0.00 2.17
2065 2079 5.010820 GTCTCACCGCTACCTTATCCTATTT 59.989 44.000 0.00 0.00 0.00 1.40
2066 2080 4.523558 GTCTCACCGCTACCTTATCCTATT 59.476 45.833 0.00 0.00 0.00 1.73
2067 2081 4.080687 GTCTCACCGCTACCTTATCCTAT 58.919 47.826 0.00 0.00 0.00 2.57
2068 2082 3.484407 GTCTCACCGCTACCTTATCCTA 58.516 50.000 0.00 0.00 0.00 2.94
2069 2083 2.308690 GTCTCACCGCTACCTTATCCT 58.691 52.381 0.00 0.00 0.00 3.24
2070 2084 1.001597 CGTCTCACCGCTACCTTATCC 60.002 57.143 0.00 0.00 0.00 2.59
2071 2085 1.945394 TCGTCTCACCGCTACCTTATC 59.055 52.381 0.00 0.00 0.00 1.75
2072 2086 1.948145 CTCGTCTCACCGCTACCTTAT 59.052 52.381 0.00 0.00 0.00 1.73
2073 2087 1.376543 CTCGTCTCACCGCTACCTTA 58.623 55.000 0.00 0.00 0.00 2.69
2074 2088 1.935327 GCTCGTCTCACCGCTACCTT 61.935 60.000 0.00 0.00 0.00 3.50
2075 2089 2.408241 GCTCGTCTCACCGCTACCT 61.408 63.158 0.00 0.00 0.00 3.08
2076 2090 2.102553 GCTCGTCTCACCGCTACC 59.897 66.667 0.00 0.00 0.00 3.18
2077 2091 2.102553 GGCTCGTCTCACCGCTAC 59.897 66.667 0.00 0.00 0.00 3.58
2078 2092 3.506096 CGGCTCGTCTCACCGCTA 61.506 66.667 0.00 0.00 40.55 4.26
2082 2096 1.787012 TTTAAACGGCTCGTCTCACC 58.213 50.000 0.69 0.00 39.99 4.02
2083 2097 3.550678 CCTATTTAAACGGCTCGTCTCAC 59.449 47.826 0.69 0.00 39.99 3.51
2084 2098 3.194116 ACCTATTTAAACGGCTCGTCTCA 59.806 43.478 5.50 0.00 39.99 3.27
2085 2099 3.550678 CACCTATTTAAACGGCTCGTCTC 59.449 47.826 5.50 0.00 39.99 3.36
2086 2100 3.056322 ACACCTATTTAAACGGCTCGTCT 60.056 43.478 5.50 0.00 39.99 4.18
2087 2101 3.256558 ACACCTATTTAAACGGCTCGTC 58.743 45.455 5.50 0.00 39.99 4.20
2088 2102 3.256558 GACACCTATTTAAACGGCTCGT 58.743 45.455 5.50 0.00 43.97 4.18
2089 2103 3.255725 TGACACCTATTTAAACGGCTCG 58.744 45.455 5.50 0.00 0.00 5.03
2090 2104 4.694037 ACTTGACACCTATTTAAACGGCTC 59.306 41.667 5.50 2.50 0.00 4.70
2091 2105 4.454504 CACTTGACACCTATTTAAACGGCT 59.545 41.667 5.50 0.00 0.00 5.52
2092 2106 4.379082 CCACTTGACACCTATTTAAACGGC 60.379 45.833 5.50 0.00 0.00 5.68
2093 2107 4.998672 TCCACTTGACACCTATTTAAACGG 59.001 41.667 0.00 0.00 0.00 4.44
2094 2108 6.204108 ACTTCCACTTGACACCTATTTAAACG 59.796 38.462 0.00 0.00 0.00 3.60
2095 2109 7.360361 CACTTCCACTTGACACCTATTTAAAC 58.640 38.462 0.00 0.00 0.00 2.01
2096 2110 6.016610 GCACTTCCACTTGACACCTATTTAAA 60.017 38.462 0.00 0.00 0.00 1.52
2097 2111 5.472137 GCACTTCCACTTGACACCTATTTAA 59.528 40.000 0.00 0.00 0.00 1.52
2098 2112 5.001232 GCACTTCCACTTGACACCTATTTA 58.999 41.667 0.00 0.00 0.00 1.40
2099 2113 3.821033 GCACTTCCACTTGACACCTATTT 59.179 43.478 0.00 0.00 0.00 1.40
2100 2114 3.181445 TGCACTTCCACTTGACACCTATT 60.181 43.478 0.00 0.00 0.00 1.73
2101 2115 2.371841 TGCACTTCCACTTGACACCTAT 59.628 45.455 0.00 0.00 0.00 2.57
2102 2116 1.765904 TGCACTTCCACTTGACACCTA 59.234 47.619 0.00 0.00 0.00 3.08
2103 2117 0.546122 TGCACTTCCACTTGACACCT 59.454 50.000 0.00 0.00 0.00 4.00
2104 2118 0.947244 CTGCACTTCCACTTGACACC 59.053 55.000 0.00 0.00 0.00 4.16
2105 2119 1.331756 CACTGCACTTCCACTTGACAC 59.668 52.381 0.00 0.00 0.00 3.67
2106 2120 1.209261 TCACTGCACTTCCACTTGACA 59.791 47.619 0.00 0.00 0.00 3.58
2107 2121 1.953559 TCACTGCACTTCCACTTGAC 58.046 50.000 0.00 0.00 0.00 3.18
2108 2122 2.158769 ACATCACTGCACTTCCACTTGA 60.159 45.455 0.00 0.00 0.00 3.02
2109 2123 2.224606 ACATCACTGCACTTCCACTTG 58.775 47.619 0.00 0.00 0.00 3.16
2110 2124 2.645838 ACATCACTGCACTTCCACTT 57.354 45.000 0.00 0.00 0.00 3.16
2111 2125 3.603532 CATACATCACTGCACTTCCACT 58.396 45.455 0.00 0.00 0.00 4.00
2112 2126 2.096496 GCATACATCACTGCACTTCCAC 59.904 50.000 0.00 0.00 38.28 4.02
2113 2127 2.290197 TGCATACATCACTGCACTTCCA 60.290 45.455 0.00 0.00 43.11 3.53
2114 2128 2.353889 CTGCATACATCACTGCACTTCC 59.646 50.000 0.00 0.00 43.11 3.46
2115 2129 2.223203 GCTGCATACATCACTGCACTTC 60.223 50.000 0.00 0.00 43.11 3.01
2116 2130 1.741706 GCTGCATACATCACTGCACTT 59.258 47.619 0.00 0.00 43.11 3.16
2117 2131 1.065636 AGCTGCATACATCACTGCACT 60.066 47.619 1.02 0.00 43.11 4.40
2118 2132 1.063616 CAGCTGCATACATCACTGCAC 59.936 52.381 0.00 0.00 43.11 4.57
2119 2133 1.065998 TCAGCTGCATACATCACTGCA 60.066 47.619 9.47 0.00 45.60 4.41
2120 2134 1.598132 CTCAGCTGCATACATCACTGC 59.402 52.381 9.47 0.00 38.87 4.40
2121 2135 2.210961 CCTCAGCTGCATACATCACTG 58.789 52.381 9.47 0.00 0.00 3.66
2122 2136 1.474677 GCCTCAGCTGCATACATCACT 60.475 52.381 9.47 0.00 35.50 3.41
2123 2137 0.942962 GCCTCAGCTGCATACATCAC 59.057 55.000 9.47 0.00 35.50 3.06
2124 2138 0.542805 TGCCTCAGCTGCATACATCA 59.457 50.000 9.47 0.00 40.80 3.07
2125 2139 3.391736 TGCCTCAGCTGCATACATC 57.608 52.632 9.47 0.00 40.80 3.06
2131 2145 0.107508 GTTAGGATGCCTCAGCTGCA 60.108 55.000 9.47 3.83 43.97 4.41
2132 2146 1.156645 CGTTAGGATGCCTCAGCTGC 61.157 60.000 9.47 0.00 40.80 5.25
2133 2147 0.461548 TCGTTAGGATGCCTCAGCTG 59.538 55.000 7.63 7.63 40.80 4.24
2134 2148 1.134670 GTTCGTTAGGATGCCTCAGCT 60.135 52.381 0.00 0.00 40.80 4.24
2135 2149 1.291132 GTTCGTTAGGATGCCTCAGC 58.709 55.000 0.00 0.00 34.61 4.26
2136 2150 1.134367 TCGTTCGTTAGGATGCCTCAG 59.866 52.381 0.00 0.00 34.61 3.35
2137 2151 1.179152 TCGTTCGTTAGGATGCCTCA 58.821 50.000 0.00 0.00 34.61 3.86
2138 2152 1.925185 GTTCGTTCGTTAGGATGCCTC 59.075 52.381 0.00 0.00 34.61 4.70
2139 2153 1.734707 CGTTCGTTCGTTAGGATGCCT 60.735 52.381 0.00 0.00 37.71 4.75
2140 2154 0.643820 CGTTCGTTCGTTAGGATGCC 59.356 55.000 0.00 0.00 0.00 4.40
2141 2155 1.621107 TCGTTCGTTCGTTAGGATGC 58.379 50.000 2.67 0.00 0.00 3.91
2142 2156 4.325204 TCAAATCGTTCGTTCGTTAGGATG 59.675 41.667 2.67 0.00 0.00 3.51
2143 2157 4.487948 TCAAATCGTTCGTTCGTTAGGAT 58.512 39.130 2.67 0.00 0.00 3.24
2144 2158 3.899734 TCAAATCGTTCGTTCGTTAGGA 58.100 40.909 2.67 0.00 0.00 2.94
2145 2159 4.380290 GTTCAAATCGTTCGTTCGTTAGG 58.620 43.478 2.67 0.00 0.00 2.69
2146 2160 4.149396 AGGTTCAAATCGTTCGTTCGTTAG 59.851 41.667 2.67 0.00 0.00 2.34
2147 2161 4.050553 AGGTTCAAATCGTTCGTTCGTTA 58.949 39.130 2.67 0.00 0.00 3.18
2148 2162 2.867975 AGGTTCAAATCGTTCGTTCGTT 59.132 40.909 2.67 0.00 0.00 3.85
2149 2163 2.476821 AGGTTCAAATCGTTCGTTCGT 58.523 42.857 2.67 0.00 0.00 3.85
2150 2164 3.215244 CAAGGTTCAAATCGTTCGTTCG 58.785 45.455 0.00 0.00 0.00 3.95
2151 2165 4.205323 ACAAGGTTCAAATCGTTCGTTC 57.795 40.909 0.00 0.00 0.00 3.95
2152 2166 4.496840 GGAACAAGGTTCAAATCGTTCGTT 60.497 41.667 10.86 0.00 34.87 3.85
2153 2167 3.002965 GGAACAAGGTTCAAATCGTTCGT 59.997 43.478 10.86 0.00 34.87 3.85
2154 2168 3.250040 AGGAACAAGGTTCAAATCGTTCG 59.750 43.478 10.86 0.00 34.87 3.95
2155 2169 4.830826 AGGAACAAGGTTCAAATCGTTC 57.169 40.909 10.86 0.00 33.62 3.95
2156 2170 5.008316 GTGTAGGAACAAGGTTCAAATCGTT 59.992 40.000 10.86 0.00 37.36 3.85
2157 2171 4.514066 GTGTAGGAACAAGGTTCAAATCGT 59.486 41.667 10.86 0.00 37.36 3.73
2158 2172 4.377022 CGTGTAGGAACAAGGTTCAAATCG 60.377 45.833 10.86 5.41 37.36 3.34
2159 2173 4.083484 CCGTGTAGGAACAAGGTTCAAATC 60.083 45.833 10.86 0.39 46.59 2.17
2160 2174 3.818773 CCGTGTAGGAACAAGGTTCAAAT 59.181 43.478 10.86 0.02 46.59 2.32
2161 2175 3.207778 CCGTGTAGGAACAAGGTTCAAA 58.792 45.455 10.86 0.00 46.59 2.69
2162 2176 2.841215 CCGTGTAGGAACAAGGTTCAA 58.159 47.619 10.86 0.00 46.59 2.69
2163 2177 2.536761 CCGTGTAGGAACAAGGTTCA 57.463 50.000 10.86 0.00 46.59 3.18
2168 2182 0.320374 TCAGGCCGTGTAGGAACAAG 59.680 55.000 0.00 0.00 45.00 3.16
2169 2183 0.981183 ATCAGGCCGTGTAGGAACAA 59.019 50.000 0.00 0.00 45.00 2.83
2170 2184 0.535335 GATCAGGCCGTGTAGGAACA 59.465 55.000 0.00 0.00 45.00 3.18
2171 2185 0.535335 TGATCAGGCCGTGTAGGAAC 59.465 55.000 0.00 0.00 45.00 3.62
2172 2186 1.271856 TTGATCAGGCCGTGTAGGAA 58.728 50.000 0.00 0.00 45.00 3.36
2173 2187 1.271856 TTTGATCAGGCCGTGTAGGA 58.728 50.000 0.00 0.00 45.00 2.94
2174 2188 2.213499 GATTTGATCAGGCCGTGTAGG 58.787 52.381 0.00 0.00 44.97 3.18
2175 2189 1.860950 CGATTTGATCAGGCCGTGTAG 59.139 52.381 0.00 0.00 0.00 2.74
2176 2190 1.478916 TCGATTTGATCAGGCCGTGTA 59.521 47.619 0.00 0.00 0.00 2.90
2177 2191 0.249120 TCGATTTGATCAGGCCGTGT 59.751 50.000 0.00 0.00 0.00 4.49
2178 2192 1.586422 ATCGATTTGATCAGGCCGTG 58.414 50.000 0.00 0.00 28.49 4.94
2186 2200 3.547613 GCAAGTGCCTGATCGATTTGATC 60.548 47.826 0.00 6.92 43.56 2.92
2187 2201 2.357009 GCAAGTGCCTGATCGATTTGAT 59.643 45.455 0.00 0.00 35.87 2.57
2188 2202 1.739466 GCAAGTGCCTGATCGATTTGA 59.261 47.619 0.00 0.00 34.31 2.69
2189 2203 2.184385 GCAAGTGCCTGATCGATTTG 57.816 50.000 0.00 0.00 34.31 2.32
2201 2215 4.337555 ACAATGAAGATAGATGGCAAGTGC 59.662 41.667 0.00 0.00 41.14 4.40
2202 2216 6.094464 TGAACAATGAAGATAGATGGCAAGTG 59.906 38.462 0.00 0.00 0.00 3.16
2203 2217 6.182627 TGAACAATGAAGATAGATGGCAAGT 58.817 36.000 0.00 0.00 0.00 3.16
2204 2218 6.688637 TGAACAATGAAGATAGATGGCAAG 57.311 37.500 0.00 0.00 0.00 4.01
2205 2219 6.660521 AGTTGAACAATGAAGATAGATGGCAA 59.339 34.615 0.00 0.00 0.00 4.52
2206 2220 6.182627 AGTTGAACAATGAAGATAGATGGCA 58.817 36.000 0.00 0.00 0.00 4.92
2207 2221 6.541641 AGAGTTGAACAATGAAGATAGATGGC 59.458 38.462 0.00 0.00 0.00 4.40
2208 2222 8.503458 AAGAGTTGAACAATGAAGATAGATGG 57.497 34.615 0.00 0.00 0.00 3.51
2209 2223 9.770503 CAAAGAGTTGAACAATGAAGATAGATG 57.229 33.333 0.00 0.00 36.83 2.90
2210 2224 9.730705 TCAAAGAGTTGAACAATGAAGATAGAT 57.269 29.630 0.00 0.00 40.87 1.98
2211 2225 9.730705 ATCAAAGAGTTGAACAATGAAGATAGA 57.269 29.630 0.00 0.00 46.66 1.98
2212 2226 9.770503 CATCAAAGAGTTGAACAATGAAGATAG 57.229 33.333 0.00 0.00 46.66 2.08
2213 2227 9.506018 TCATCAAAGAGTTGAACAATGAAGATA 57.494 29.630 0.00 0.00 46.66 1.98
2214 2228 8.400184 TCATCAAAGAGTTGAACAATGAAGAT 57.600 30.769 0.00 0.00 46.66 2.40
2215 2229 7.806409 TCATCAAAGAGTTGAACAATGAAGA 57.194 32.000 0.00 0.00 46.66 2.87
2216 2230 8.861033 TTTCATCAAAGAGTTGAACAATGAAG 57.139 30.769 0.00 0.00 46.66 3.02
2217 2231 9.304731 CTTTTCATCAAAGAGTTGAACAATGAA 57.695 29.630 0.00 1.05 46.66 2.57
2218 2232 8.685427 TCTTTTCATCAAAGAGTTGAACAATGA 58.315 29.630 0.00 0.00 46.66 2.57
2219 2233 8.861033 TCTTTTCATCAAAGAGTTGAACAATG 57.139 30.769 0.00 0.00 46.66 2.82
2258 2272 2.174360 GATGGAAGGGCAGAGCTTTTT 58.826 47.619 0.00 0.00 0.00 1.94
2259 2273 1.357079 AGATGGAAGGGCAGAGCTTTT 59.643 47.619 0.00 0.00 0.00 2.27
2260 2274 0.998145 AGATGGAAGGGCAGAGCTTT 59.002 50.000 0.00 0.00 0.00 3.51
2261 2275 0.545646 GAGATGGAAGGGCAGAGCTT 59.454 55.000 0.00 0.00 0.00 3.74
2262 2276 0.326427 AGAGATGGAAGGGCAGAGCT 60.326 55.000 0.00 0.00 0.00 4.09
2263 2277 0.545646 AAGAGATGGAAGGGCAGAGC 59.454 55.000 0.00 0.00 0.00 4.09
2264 2278 2.328819 CAAGAGATGGAAGGGCAGAG 57.671 55.000 0.00 0.00 0.00 3.35
2275 2289 6.730447 TCCCTCTCTATCTATCCAAGAGATG 58.270 44.000 2.02 0.35 43.52 2.90
2276 2290 6.068853 CCTCCCTCTCTATCTATCCAAGAGAT 60.069 46.154 2.02 0.00 43.52 2.75
2277 2291 5.252863 CCTCCCTCTCTATCTATCCAAGAGA 59.747 48.000 0.00 1.69 42.60 3.10
2278 2292 5.509498 CCTCCCTCTCTATCTATCCAAGAG 58.491 50.000 0.00 0.00 37.74 2.85
2279 2293 4.293634 CCCTCCCTCTCTATCTATCCAAGA 59.706 50.000 0.00 0.00 39.02 3.02
2280 2294 4.609301 CCCTCCCTCTCTATCTATCCAAG 58.391 52.174 0.00 0.00 0.00 3.61
2281 2295 3.245803 GCCCTCCCTCTCTATCTATCCAA 60.246 52.174 0.00 0.00 0.00 3.53
2282 2296 2.313342 GCCCTCCCTCTCTATCTATCCA 59.687 54.545 0.00 0.00 0.00 3.41
2283 2297 2.313342 TGCCCTCCCTCTCTATCTATCC 59.687 54.545 0.00 0.00 0.00 2.59
2284 2298 3.268334 TCTGCCCTCCCTCTCTATCTATC 59.732 52.174 0.00 0.00 0.00 2.08
2285 2299 3.269381 CTCTGCCCTCCCTCTCTATCTAT 59.731 52.174 0.00 0.00 0.00 1.98
2286 2300 2.647299 CTCTGCCCTCCCTCTCTATCTA 59.353 54.545 0.00 0.00 0.00 1.98
2287 2301 1.428912 CTCTGCCCTCCCTCTCTATCT 59.571 57.143 0.00 0.00 0.00 1.98
2288 2302 1.549950 CCTCTGCCCTCCCTCTCTATC 60.550 61.905 0.00 0.00 0.00 2.08
2289 2303 0.486879 CCTCTGCCCTCCCTCTCTAT 59.513 60.000 0.00 0.00 0.00 1.98
2290 2304 1.934410 CCTCTGCCCTCCCTCTCTA 59.066 63.158 0.00 0.00 0.00 2.43
2291 2305 2.695597 CCTCTGCCCTCCCTCTCT 59.304 66.667 0.00 0.00 0.00 3.10
2292 2306 3.160748 GCCTCTGCCCTCCCTCTC 61.161 72.222 0.00 0.00 0.00 3.20
2302 2316 1.973812 GGACACCAAAGGCCTCTGC 60.974 63.158 5.23 0.00 0.00 4.26
2303 2317 1.303643 GGGACACCAAAGGCCTCTG 60.304 63.158 5.23 0.54 36.50 3.35
2304 2318 1.068352 AAGGGACACCAAAGGCCTCT 61.068 55.000 5.23 0.00 40.13 3.69
2305 2319 0.178961 AAAGGGACACCAAAGGCCTC 60.179 55.000 5.23 0.00 40.13 4.70
2306 2320 0.178961 GAAAGGGACACCAAAGGCCT 60.179 55.000 0.00 0.00 40.13 5.19
2307 2321 0.469144 TGAAAGGGACACCAAAGGCC 60.469 55.000 0.00 0.00 40.13 5.19
2308 2322 0.961753 CTGAAAGGGACACCAAAGGC 59.038 55.000 0.00 0.00 40.13 4.35
2309 2323 2.230660 GACTGAAAGGGACACCAAAGG 58.769 52.381 0.00 0.00 39.30 3.11
2310 2324 2.930950 TGACTGAAAGGGACACCAAAG 58.069 47.619 0.00 0.00 39.30 2.77
2311 2325 3.053991 TCTTGACTGAAAGGGACACCAAA 60.054 43.478 0.00 0.00 39.30 3.28
2312 2326 2.507886 TCTTGACTGAAAGGGACACCAA 59.492 45.455 0.00 0.00 39.30 3.67
2313 2327 2.123589 TCTTGACTGAAAGGGACACCA 58.876 47.619 0.00 0.00 39.30 4.17
2314 2328 2.930826 TCTTGACTGAAAGGGACACC 57.069 50.000 0.00 0.00 39.30 4.16
2315 2329 4.022849 CCAATTCTTGACTGAAAGGGACAC 60.023 45.833 0.00 0.00 39.30 3.67
2316 2330 4.144297 CCAATTCTTGACTGAAAGGGACA 58.856 43.478 0.00 0.00 39.30 4.02
2317 2331 3.507622 CCCAATTCTTGACTGAAAGGGAC 59.492 47.826 10.61 0.00 42.75 4.46
2318 2332 3.500289 CCCCAATTCTTGACTGAAAGGGA 60.500 47.826 15.18 0.00 42.75 4.20
2319 2333 2.827921 CCCCAATTCTTGACTGAAAGGG 59.172 50.000 0.00 0.00 41.26 3.95
2320 2334 2.232208 GCCCCAATTCTTGACTGAAAGG 59.768 50.000 0.00 0.00 39.30 3.11
2321 2335 3.160269 AGCCCCAATTCTTGACTGAAAG 58.840 45.455 0.00 0.00 42.29 2.62
2322 2336 3.243359 AGCCCCAATTCTTGACTGAAA 57.757 42.857 0.00 0.00 0.00 2.69
2323 2337 2.978156 AGCCCCAATTCTTGACTGAA 57.022 45.000 0.00 0.00 0.00 3.02
2324 2338 2.108075 TGAAGCCCCAATTCTTGACTGA 59.892 45.455 0.00 0.00 0.00 3.41
2325 2339 2.229784 GTGAAGCCCCAATTCTTGACTG 59.770 50.000 0.00 0.00 0.00 3.51
2326 2340 2.158475 TGTGAAGCCCCAATTCTTGACT 60.158 45.455 0.00 0.00 29.73 3.41
2327 2341 2.238521 TGTGAAGCCCCAATTCTTGAC 58.761 47.619 0.00 0.00 0.00 3.18
2328 2342 2.673775 TGTGAAGCCCCAATTCTTGA 57.326 45.000 0.00 0.00 0.00 3.02
2329 2343 3.967332 ATTGTGAAGCCCCAATTCTTG 57.033 42.857 0.00 0.00 0.00 3.02
2330 2344 5.086621 AGTAATTGTGAAGCCCCAATTCTT 58.913 37.500 0.00 0.00 40.64 2.52
2331 2345 4.677182 AGTAATTGTGAAGCCCCAATTCT 58.323 39.130 0.00 0.00 40.64 2.40
2332 2346 5.450550 GCTAGTAATTGTGAAGCCCCAATTC 60.451 44.000 0.00 0.00 40.64 2.17
2333 2347 4.402474 GCTAGTAATTGTGAAGCCCCAATT 59.598 41.667 0.00 0.00 42.33 2.32
2334 2348 3.954258 GCTAGTAATTGTGAAGCCCCAAT 59.046 43.478 0.00 0.00 32.83 3.16
2335 2349 3.352648 GCTAGTAATTGTGAAGCCCCAA 58.647 45.455 0.00 0.00 0.00 4.12
2336 2350 2.356741 GGCTAGTAATTGTGAAGCCCCA 60.357 50.000 10.29 0.00 45.69 4.96
2337 2351 2.298610 GGCTAGTAATTGTGAAGCCCC 58.701 52.381 10.29 0.00 45.69 5.80
2348 2362 9.401058 GGCATGAGATAAATATTGGCTAGTAAT 57.599 33.333 0.00 0.00 0.00 1.89
2349 2363 8.605947 AGGCATGAGATAAATATTGGCTAGTAA 58.394 33.333 0.00 0.00 0.00 2.24
2350 2364 8.150827 AGGCATGAGATAAATATTGGCTAGTA 57.849 34.615 0.00 0.00 0.00 1.82
2351 2365 7.025520 AGGCATGAGATAAATATTGGCTAGT 57.974 36.000 0.00 0.00 0.00 2.57
2352 2366 7.934855 AAGGCATGAGATAAATATTGGCTAG 57.065 36.000 0.00 0.00 0.00 3.42
2353 2367 7.394359 GGAAAGGCATGAGATAAATATTGGCTA 59.606 37.037 0.00 0.00 0.00 3.93
2354 2368 6.210185 GGAAAGGCATGAGATAAATATTGGCT 59.790 38.462 0.00 0.00 0.00 4.75
2355 2369 6.210185 AGGAAAGGCATGAGATAAATATTGGC 59.790 38.462 0.00 0.00 0.00 4.52
2356 2370 7.361542 CGAGGAAAGGCATGAGATAAATATTGG 60.362 40.741 0.00 0.00 0.00 3.16
2357 2371 7.173907 ACGAGGAAAGGCATGAGATAAATATTG 59.826 37.037 0.00 0.00 0.00 1.90
2358 2372 7.227156 ACGAGGAAAGGCATGAGATAAATATT 58.773 34.615 0.00 0.00 0.00 1.28
2359 2373 6.773638 ACGAGGAAAGGCATGAGATAAATAT 58.226 36.000 0.00 0.00 0.00 1.28
2360 2374 6.174720 ACGAGGAAAGGCATGAGATAAATA 57.825 37.500 0.00 0.00 0.00 1.40
2361 2375 5.041191 ACGAGGAAAGGCATGAGATAAAT 57.959 39.130 0.00 0.00 0.00 1.40
2362 2376 4.487714 ACGAGGAAAGGCATGAGATAAA 57.512 40.909 0.00 0.00 0.00 1.40
2363 2377 4.081142 TGAACGAGGAAAGGCATGAGATAA 60.081 41.667 0.00 0.00 0.00 1.75
2364 2378 3.450817 TGAACGAGGAAAGGCATGAGATA 59.549 43.478 0.00 0.00 0.00 1.98
2365 2379 2.237143 TGAACGAGGAAAGGCATGAGAT 59.763 45.455 0.00 0.00 0.00 2.75
2366 2380 1.623311 TGAACGAGGAAAGGCATGAGA 59.377 47.619 0.00 0.00 0.00 3.27
2367 2381 2.099141 TGAACGAGGAAAGGCATGAG 57.901 50.000 0.00 0.00 0.00 2.90
2368 2382 2.358957 CATGAACGAGGAAAGGCATGA 58.641 47.619 0.00 0.00 36.20 3.07
2369 2383 1.402968 CCATGAACGAGGAAAGGCATG 59.597 52.381 0.00 0.00 34.47 4.06
2370 2384 1.004745 ACCATGAACGAGGAAAGGCAT 59.995 47.619 0.00 0.00 0.00 4.40
2371 2385 0.400213 ACCATGAACGAGGAAAGGCA 59.600 50.000 0.00 0.00 0.00 4.75
2372 2386 1.468914 GAACCATGAACGAGGAAAGGC 59.531 52.381 0.00 0.00 0.00 4.35
2373 2387 1.732259 CGAACCATGAACGAGGAAAGG 59.268 52.381 0.00 0.00 0.00 3.11
2374 2388 2.683968 TCGAACCATGAACGAGGAAAG 58.316 47.619 0.00 0.00 0.00 2.62
2375 2389 2.823924 TCGAACCATGAACGAGGAAA 57.176 45.000 0.00 0.00 0.00 3.13
2376 2390 4.665833 ATATCGAACCATGAACGAGGAA 57.334 40.909 12.42 4.23 39.31 3.36
2377 2391 4.341235 AGAATATCGAACCATGAACGAGGA 59.659 41.667 12.42 5.86 39.31 3.71
2378 2392 4.445718 CAGAATATCGAACCATGAACGAGG 59.554 45.833 12.42 0.00 39.31 4.63
2379 2393 4.445718 CCAGAATATCGAACCATGAACGAG 59.554 45.833 12.42 1.68 39.31 4.18
2380 2394 4.142026 ACCAGAATATCGAACCATGAACGA 60.142 41.667 10.14 10.14 40.18 3.85
2381 2395 4.025730 CACCAGAATATCGAACCATGAACG 60.026 45.833 0.00 0.00 0.00 3.95
2382 2396 4.876107 ACACCAGAATATCGAACCATGAAC 59.124 41.667 0.00 0.00 0.00 3.18
2383 2397 5.097742 ACACCAGAATATCGAACCATGAA 57.902 39.130 0.00 0.00 0.00 2.57
2384 2398 4.442893 GGACACCAGAATATCGAACCATGA 60.443 45.833 0.00 0.00 0.00 3.07
2385 2399 3.809832 GGACACCAGAATATCGAACCATG 59.190 47.826 0.00 0.00 0.00 3.66
2386 2400 3.181454 GGGACACCAGAATATCGAACCAT 60.181 47.826 0.00 0.00 36.50 3.55
2387 2401 2.169769 GGGACACCAGAATATCGAACCA 59.830 50.000 0.00 0.00 36.50 3.67
2388 2402 2.169769 TGGGACACCAGAATATCGAACC 59.830 50.000 0.00 0.00 43.37 3.62
2389 2403 3.536956 TGGGACACCAGAATATCGAAC 57.463 47.619 0.00 0.00 43.37 3.95


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

AutoCloner maintained by Alex Coulton.