Multiple sequence alignment - TraesCS3D01G117400

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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 TraesCS3D01G117400 chr3D 100.000 2314 0 0 1 2314 70898743 70901056 0.000000e+00 4274.0
1 TraesCS3D01G117400 chr3D 97.578 2023 45 4 43 2064 602873076 602875095 0.000000e+00 3461.0
2 TraesCS3D01G117400 chr3D 97.233 253 7 0 2062 2314 49585161 49585413 1.640000e-116 429.0
3 TraesCS3D01G117400 chr7B 97.923 2022 40 2 43 2064 644446456 644448475 0.000000e+00 3500.0
4 TraesCS3D01G117400 chr7B 97.923 2022 40 2 43 2064 743095919 743097938 0.000000e+00 3500.0
5 TraesCS3D01G117400 chrUn 97.923 2022 39 3 43 2064 170994988 170992970 0.000000e+00 3498.0
6 TraesCS3D01G117400 chrUn 100.000 43 0 0 1 43 370538204 370538246 1.910000e-11 80.5
7 TraesCS3D01G117400 chr7D 97.923 2022 39 2 43 2064 626724509 626726527 0.000000e+00 3498.0
8 TraesCS3D01G117400 chr7D 97.873 2022 41 2 43 2064 626630257 626632276 0.000000e+00 3494.0
9 TraesCS3D01G117400 chr7D 97.825 2023 41 3 43 2064 382073335 382071315 0.000000e+00 3489.0
10 TraesCS3D01G117400 chr1D 97.774 2022 43 2 43 2064 212458883 212460902 0.000000e+00 3483.0
11 TraesCS3D01G117400 chr1D 100.000 43 0 0 1 43 185765461 185765419 1.910000e-11 80.5
12 TraesCS3D01G117400 chr6B 97.725 2022 43 3 43 2064 307014494 307012476 0.000000e+00 3476.0
13 TraesCS3D01G117400 chr5D 97.233 253 7 0 2062 2314 8525370 8525622 1.640000e-116 429.0
14 TraesCS3D01G117400 chr5D 97.222 252 7 0 2062 2313 482357709 482357458 5.910000e-116 427.0
15 TraesCS3D01G117400 chr2D 97.233 253 7 0 2062 2314 348365932 348365680 1.640000e-116 429.0
16 TraesCS3D01G117400 chr6D 97.222 252 7 0 2062 2313 104925468 104925719 5.910000e-116 427.0
17 TraesCS3D01G117400 chr6D 96.838 253 8 0 2062 2314 107517999 107518251 7.640000e-115 424.0
18 TraesCS3D01G117400 chr6D 96.838 253 8 0 2062 2314 189548970 189548718 7.640000e-115 424.0
19 TraesCS3D01G117400 chr4D 96.838 253 8 0 2062 2314 230309630 230309378 7.640000e-115 424.0
20 TraesCS3D01G117400 chr4D 96.838 253 8 0 2062 2314 258826415 258826163 7.640000e-115 424.0
21 TraesCS3D01G117400 chr4D 100.000 43 0 0 1 43 123408888 123408846 1.910000e-11 80.5
22 TraesCS3D01G117400 chr4D 100.000 43 0 0 1 43 135002795 135002837 1.910000e-11 80.5
23 TraesCS3D01G117400 chr6A 100.000 43 0 0 1 43 84406400 84406442 1.910000e-11 80.5
24 TraesCS3D01G117400 chr6A 100.000 43 0 0 1 43 289124643 289124601 1.910000e-11 80.5
25 TraesCS3D01G117400 chr6A 100.000 43 0 0 1 43 608897969 608898011 1.910000e-11 80.5
26 TraesCS3D01G117400 chr5B 100.000 43 0 0 1 43 713029907 713029949 1.910000e-11 80.5
27 TraesCS3D01G117400 chr1A 100.000 43 0 0 1 43 94587697 94587655 1.910000e-11 80.5


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 TraesCS3D01G117400 chr3D 70898743 70901056 2313 False 4274 4274 100.000 1 2314 1 chr3D.!!$F2 2313
1 TraesCS3D01G117400 chr3D 602873076 602875095 2019 False 3461 3461 97.578 43 2064 1 chr3D.!!$F3 2021
2 TraesCS3D01G117400 chr7B 644446456 644448475 2019 False 3500 3500 97.923 43 2064 1 chr7B.!!$F1 2021
3 TraesCS3D01G117400 chr7B 743095919 743097938 2019 False 3500 3500 97.923 43 2064 1 chr7B.!!$F2 2021
4 TraesCS3D01G117400 chrUn 170992970 170994988 2018 True 3498 3498 97.923 43 2064 1 chrUn.!!$R1 2021
5 TraesCS3D01G117400 chr7D 626724509 626726527 2018 False 3498 3498 97.923 43 2064 1 chr7D.!!$F2 2021
6 TraesCS3D01G117400 chr7D 626630257 626632276 2019 False 3494 3494 97.873 43 2064 1 chr7D.!!$F1 2021
7 TraesCS3D01G117400 chr7D 382071315 382073335 2020 True 3489 3489 97.825 43 2064 1 chr7D.!!$R1 2021
8 TraesCS3D01G117400 chr1D 212458883 212460902 2019 False 3483 3483 97.774 43 2064 1 chr1D.!!$F1 2021
9 TraesCS3D01G117400 chr6B 307012476 307014494 2018 True 3476 3476 97.725 43 2064 1 chr6B.!!$R1 2021

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
524 525 0.318441 CTTCAGTGCTCTCCGAACCA 59.682 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2267 0.035152 CCACCTACTGCTTCATGGCA 60.035 55.0 0.0 0.0 40.15 4.92 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
19 20 2.464157 CCCTTTCTTTCGCTGTCTCT 57.536 50.000 0.00 0.00 0.00 3.10
20 21 3.594603 CCCTTTCTTTCGCTGTCTCTA 57.405 47.619 0.00 0.00 0.00 2.43
21 22 4.130286 CCCTTTCTTTCGCTGTCTCTAT 57.870 45.455 0.00 0.00 0.00 1.98
22 23 4.508662 CCCTTTCTTTCGCTGTCTCTATT 58.491 43.478 0.00 0.00 0.00 1.73
23 24 4.568760 CCCTTTCTTTCGCTGTCTCTATTC 59.431 45.833 0.00 0.00 0.00 1.75
24 25 5.415221 CCTTTCTTTCGCTGTCTCTATTCT 58.585 41.667 0.00 0.00 0.00 2.40
25 26 6.405953 CCCTTTCTTTCGCTGTCTCTATTCTA 60.406 42.308 0.00 0.00 0.00 2.10
26 27 7.206687 CCTTTCTTTCGCTGTCTCTATTCTAT 58.793 38.462 0.00 0.00 0.00 1.98
27 28 7.708752 CCTTTCTTTCGCTGTCTCTATTCTATT 59.291 37.037 0.00 0.00 0.00 1.73
28 29 7.993821 TTCTTTCGCTGTCTCTATTCTATTG 57.006 36.000 0.00 0.00 0.00 1.90
29 30 6.507900 TCTTTCGCTGTCTCTATTCTATTGG 58.492 40.000 0.00 0.00 0.00 3.16
30 31 5.854010 TTCGCTGTCTCTATTCTATTGGT 57.146 39.130 0.00 0.00 0.00 3.67
31 32 5.188327 TCGCTGTCTCTATTCTATTGGTG 57.812 43.478 0.00 0.00 0.00 4.17
32 33 4.038042 TCGCTGTCTCTATTCTATTGGTGG 59.962 45.833 0.00 0.00 0.00 4.61
33 34 4.038042 CGCTGTCTCTATTCTATTGGTGGA 59.962 45.833 0.00 0.00 0.00 4.02
34 35 5.293560 GCTGTCTCTATTCTATTGGTGGAC 58.706 45.833 0.00 0.00 0.00 4.02
35 36 5.515797 TGTCTCTATTCTATTGGTGGACG 57.484 43.478 0.00 0.00 0.00 4.79
36 37 4.341235 TGTCTCTATTCTATTGGTGGACGG 59.659 45.833 0.00 0.00 0.00 4.79
37 38 4.341520 GTCTCTATTCTATTGGTGGACGGT 59.658 45.833 0.00 0.00 0.00 4.83
38 39 4.583489 TCTCTATTCTATTGGTGGACGGTC 59.417 45.833 0.00 0.00 0.00 4.79
39 40 2.596904 ATTCTATTGGTGGACGGTCG 57.403 50.000 1.43 0.00 0.00 4.79
40 41 1.259609 TTCTATTGGTGGACGGTCGT 58.740 50.000 1.43 0.00 0.00 4.34
41 42 2.127271 TCTATTGGTGGACGGTCGTA 57.873 50.000 1.43 0.00 0.00 3.43
215 216 8.894409 TGAATTAACAAATATGAAGCAAGACG 57.106 30.769 0.00 0.00 0.00 4.18
233 234 0.689745 CGTACTCCCTCCCATCCCAA 60.690 60.000 0.00 0.00 0.00 4.12
322 323 4.689612 ACACATAAATCGAGGGCTATGT 57.310 40.909 0.00 0.00 35.80 2.29
332 333 2.264455 GAGGGCTATGTGGATCCTCAT 58.736 52.381 27.56 27.56 42.49 2.90
436 437 7.441157 TCGAACACAGAGTCAAAAGTGAATTAT 59.559 33.333 10.64 0.00 34.87 1.28
524 525 0.318441 CTTCAGTGCTCTCCGAACCA 59.682 55.000 0.00 0.00 0.00 3.67
567 568 2.154462 CGGCTCACCAACTTGATCTTT 58.846 47.619 0.00 0.00 34.57 2.52
626 627 2.036862 AGTACGGTCTCGCTTTCCTTTT 59.963 45.455 0.00 0.00 40.63 2.27
635 636 3.283751 TCGCTTTCCTTTTCCACTCAAA 58.716 40.909 0.00 0.00 0.00 2.69
649 650 3.002791 CACTCAAATGTACGGCATCTGT 58.997 45.455 0.00 0.00 36.67 3.41
829 831 3.696518 TACGAGCCCTCTGCCCCAT 62.697 63.158 0.00 0.00 42.71 4.00
892 894 6.017275 ACGTCACCCTTAGATAGAGTTATTCG 60.017 42.308 0.00 0.00 0.00 3.34
1162 1164 1.696097 CCCCCTCGATTCCCGACATT 61.696 60.000 0.00 0.00 43.23 2.71
1212 1214 2.816360 CGAGTCCGTATCACCGCGA 61.816 63.158 8.23 0.00 0.00 5.87
1451 1453 5.017490 TCCTTCAGATCCTAGAAAACGTCT 58.983 41.667 0.00 0.00 40.71 4.18
1619 1624 3.814625 TGATTTGCAGTGGTCAGTTACA 58.185 40.909 0.00 0.00 0.00 2.41
1623 1628 2.285083 TGCAGTGGTCAGTTACACAAC 58.715 47.619 0.00 0.00 39.99 3.32
1659 1664 6.993308 AGTTTCCTTCTTCAGAGTCCTTTTAC 59.007 38.462 0.00 0.00 0.00 2.01
1671 1676 8.616598 TCAGAGTCCTTTTACCCCAATATTAAA 58.383 33.333 0.00 0.00 0.00 1.52
1693 1698 5.968676 AGATAATGTGTGGGCCTTTACTA 57.031 39.130 4.53 0.00 0.00 1.82
1718 1723 1.302907 AGATGGTTGATCCCCTTGCT 58.697 50.000 0.00 0.00 34.77 3.91
1822 1827 5.221803 CCAGCAATGGACTAAGGTATGAGAT 60.222 44.000 0.00 0.00 0.00 2.75
1946 1951 7.013655 CCACATAAGCAATAAAGCCAATAGACT 59.986 37.037 0.00 0.00 34.23 3.24
2064 2069 0.609131 CTGGTCTGCCCGGTCAAATT 60.609 55.000 0.00 0.00 34.56 1.82
2065 2070 0.693622 TGGTCTGCCCGGTCAAATTA 59.306 50.000 0.00 0.00 35.15 1.40
2066 2071 1.074084 TGGTCTGCCCGGTCAAATTAA 59.926 47.619 0.00 0.00 35.15 1.40
2067 2072 1.743394 GGTCTGCCCGGTCAAATTAAG 59.257 52.381 0.00 0.00 0.00 1.85
2068 2073 1.743394 GTCTGCCCGGTCAAATTAAGG 59.257 52.381 0.00 0.00 0.00 2.69
2069 2074 1.631388 TCTGCCCGGTCAAATTAAGGA 59.369 47.619 0.00 0.00 0.00 3.36
2070 2075 1.743394 CTGCCCGGTCAAATTAAGGAC 59.257 52.381 0.00 0.00 0.00 3.85
2071 2076 1.353022 TGCCCGGTCAAATTAAGGACT 59.647 47.619 0.00 0.00 34.49 3.85
2072 2077 1.743394 GCCCGGTCAAATTAAGGACTG 59.257 52.381 0.00 6.66 39.56 3.51
2073 2078 2.617021 GCCCGGTCAAATTAAGGACTGA 60.617 50.000 0.00 0.00 41.83 3.41
2074 2079 3.270877 CCCGGTCAAATTAAGGACTGAG 58.729 50.000 0.00 0.00 41.83 3.35
2075 2080 3.055385 CCCGGTCAAATTAAGGACTGAGA 60.055 47.826 0.00 0.00 41.83 3.27
2076 2081 4.564821 CCCGGTCAAATTAAGGACTGAGAA 60.565 45.833 0.00 0.00 41.83 2.87
2077 2082 4.392138 CCGGTCAAATTAAGGACTGAGAAC 59.608 45.833 12.69 0.00 41.83 3.01
2078 2083 4.091509 CGGTCAAATTAAGGACTGAGAACG 59.908 45.833 7.53 0.00 41.83 3.95
2079 2084 4.392138 GGTCAAATTAAGGACTGAGAACGG 59.608 45.833 0.00 0.00 34.49 4.44
2080 2085 4.392138 GTCAAATTAAGGACTGAGAACGGG 59.608 45.833 0.00 0.00 0.00 5.28
2081 2086 4.041198 TCAAATTAAGGACTGAGAACGGGT 59.959 41.667 0.00 0.00 0.00 5.28
2082 2087 3.889520 ATTAAGGACTGAGAACGGGTC 57.110 47.619 0.00 0.00 0.00 4.46
2083 2088 2.297698 TAAGGACTGAGAACGGGTCA 57.702 50.000 0.00 0.00 0.00 4.02
2084 2089 1.645710 AAGGACTGAGAACGGGTCAT 58.354 50.000 0.00 0.00 0.00 3.06
2085 2090 1.645710 AGGACTGAGAACGGGTCATT 58.354 50.000 0.00 0.00 0.00 2.57
2086 2091 1.978580 AGGACTGAGAACGGGTCATTT 59.021 47.619 0.00 0.00 0.00 2.32
2087 2092 2.372172 AGGACTGAGAACGGGTCATTTT 59.628 45.455 0.00 0.00 0.00 1.82
2088 2093 3.581332 AGGACTGAGAACGGGTCATTTTA 59.419 43.478 0.00 0.00 0.00 1.52
2089 2094 3.933332 GGACTGAGAACGGGTCATTTTAG 59.067 47.826 0.00 0.00 0.00 1.85
2090 2095 3.335579 ACTGAGAACGGGTCATTTTAGC 58.664 45.455 0.00 0.00 0.00 3.09
2091 2096 2.343101 TGAGAACGGGTCATTTTAGCG 58.657 47.619 0.00 0.00 0.00 4.26
2092 2097 2.289195 TGAGAACGGGTCATTTTAGCGT 60.289 45.455 0.00 0.00 0.00 5.07
2093 2098 2.344025 AGAACGGGTCATTTTAGCGTC 58.656 47.619 0.00 0.00 0.00 5.19
2094 2099 1.395954 GAACGGGTCATTTTAGCGTCC 59.604 52.381 0.00 0.00 0.00 4.79
2095 2100 0.322322 ACGGGTCATTTTAGCGTCCA 59.678 50.000 0.00 0.00 0.00 4.02
2096 2101 1.006832 CGGGTCATTTTAGCGTCCAG 58.993 55.000 0.00 0.00 0.00 3.86
2107 2112 2.887568 CGTCCAGCAGGTCATCGC 60.888 66.667 0.00 0.00 35.89 4.58
2108 2113 2.581354 GTCCAGCAGGTCATCGCT 59.419 61.111 0.00 0.00 39.66 4.93
2109 2114 1.816537 GTCCAGCAGGTCATCGCTA 59.183 57.895 0.00 0.00 36.50 4.26
2110 2115 0.390860 GTCCAGCAGGTCATCGCTAT 59.609 55.000 0.00 0.00 36.50 2.97
2111 2116 1.123077 TCCAGCAGGTCATCGCTATT 58.877 50.000 0.00 0.00 36.50 1.73
2112 2117 1.202568 TCCAGCAGGTCATCGCTATTG 60.203 52.381 0.00 0.00 36.50 1.90
2113 2118 1.473965 CCAGCAGGTCATCGCTATTGT 60.474 52.381 0.00 0.00 36.50 2.71
2114 2119 1.863454 CAGCAGGTCATCGCTATTGTC 59.137 52.381 0.00 0.00 36.50 3.18
2115 2120 1.759445 AGCAGGTCATCGCTATTGTCT 59.241 47.619 0.00 0.00 36.50 3.41
2116 2121 2.959030 AGCAGGTCATCGCTATTGTCTA 59.041 45.455 0.00 0.00 36.50 2.59
2117 2122 3.384789 AGCAGGTCATCGCTATTGTCTAA 59.615 43.478 0.00 0.00 36.50 2.10
2118 2123 3.491267 GCAGGTCATCGCTATTGTCTAAC 59.509 47.826 0.00 0.00 0.00 2.34
2119 2124 4.682787 CAGGTCATCGCTATTGTCTAACA 58.317 43.478 0.00 0.00 0.00 2.41
2120 2125 4.742167 CAGGTCATCGCTATTGTCTAACAG 59.258 45.833 0.00 0.00 0.00 3.16
2121 2126 4.402793 AGGTCATCGCTATTGTCTAACAGT 59.597 41.667 0.00 0.00 0.00 3.55
2122 2127 5.105310 AGGTCATCGCTATTGTCTAACAGTT 60.105 40.000 0.00 0.00 0.00 3.16
2123 2128 5.581085 GGTCATCGCTATTGTCTAACAGTTT 59.419 40.000 0.00 0.00 0.00 2.66
2124 2129 6.092259 GGTCATCGCTATTGTCTAACAGTTTT 59.908 38.462 0.00 0.00 0.00 2.43
2125 2130 7.360946 GGTCATCGCTATTGTCTAACAGTTTTT 60.361 37.037 0.00 0.00 0.00 1.94
2126 2131 7.478667 GTCATCGCTATTGTCTAACAGTTTTTG 59.521 37.037 0.00 0.00 0.00 2.44
2127 2132 7.386573 TCATCGCTATTGTCTAACAGTTTTTGA 59.613 33.333 0.00 0.00 0.00 2.69
2128 2133 7.117241 TCGCTATTGTCTAACAGTTTTTGAG 57.883 36.000 0.00 0.00 0.00 3.02
2129 2134 6.704493 TCGCTATTGTCTAACAGTTTTTGAGT 59.296 34.615 0.00 0.00 0.00 3.41
2130 2135 7.868922 TCGCTATTGTCTAACAGTTTTTGAGTA 59.131 33.333 0.00 0.00 0.00 2.59
2131 2136 8.656849 CGCTATTGTCTAACAGTTTTTGAGTAT 58.343 33.333 0.00 0.00 0.00 2.12
2132 2137 9.760660 GCTATTGTCTAACAGTTTTTGAGTATG 57.239 33.333 0.00 0.00 0.00 2.39
2136 2141 8.149973 TGTCTAACAGTTTTTGAGTATGTTCC 57.850 34.615 0.00 0.00 35.77 3.62
2137 2142 7.771361 TGTCTAACAGTTTTTGAGTATGTTCCA 59.229 33.333 0.00 0.00 35.77 3.53
2138 2143 8.784043 GTCTAACAGTTTTTGAGTATGTTCCAT 58.216 33.333 0.00 0.00 35.77 3.41
2141 2146 7.145932 ACAGTTTTTGAGTATGTTCCATAGC 57.854 36.000 0.00 0.00 0.00 2.97
2142 2147 6.942576 ACAGTTTTTGAGTATGTTCCATAGCT 59.057 34.615 0.00 0.00 0.00 3.32
2143 2148 7.448469 ACAGTTTTTGAGTATGTTCCATAGCTT 59.552 33.333 0.00 0.00 0.00 3.74
2144 2149 8.299570 CAGTTTTTGAGTATGTTCCATAGCTTT 58.700 33.333 0.00 0.00 0.00 3.51
2145 2150 8.515414 AGTTTTTGAGTATGTTCCATAGCTTTC 58.485 33.333 0.00 0.00 0.00 2.62
2146 2151 8.515414 GTTTTTGAGTATGTTCCATAGCTTTCT 58.485 33.333 0.00 0.00 0.00 2.52
2147 2152 7.615582 TTTGAGTATGTTCCATAGCTTTCTG 57.384 36.000 0.00 0.00 0.00 3.02
2148 2153 6.299805 TGAGTATGTTCCATAGCTTTCTGT 57.700 37.500 0.00 0.00 0.00 3.41
2149 2154 6.711277 TGAGTATGTTCCATAGCTTTCTGTT 58.289 36.000 0.00 0.00 0.00 3.16
2150 2155 6.595326 TGAGTATGTTCCATAGCTTTCTGTTG 59.405 38.462 0.00 0.00 0.00 3.33
2151 2156 6.476378 AGTATGTTCCATAGCTTTCTGTTGT 58.524 36.000 0.00 0.00 0.00 3.32
2152 2157 6.942576 AGTATGTTCCATAGCTTTCTGTTGTT 59.057 34.615 0.00 0.00 0.00 2.83
2153 2158 5.689383 TGTTCCATAGCTTTCTGTTGTTC 57.311 39.130 0.00 0.00 0.00 3.18
2154 2159 5.129634 TGTTCCATAGCTTTCTGTTGTTCA 58.870 37.500 0.00 0.00 0.00 3.18
2155 2160 5.239306 TGTTCCATAGCTTTCTGTTGTTCAG 59.761 40.000 0.00 0.00 44.85 3.02
2156 2161 4.973168 TCCATAGCTTTCTGTTGTTCAGT 58.027 39.130 0.00 0.00 43.97 3.41
2157 2162 5.376625 TCCATAGCTTTCTGTTGTTCAGTT 58.623 37.500 0.00 0.00 43.97 3.16
2158 2163 5.239306 TCCATAGCTTTCTGTTGTTCAGTTG 59.761 40.000 0.00 0.00 43.97 3.16
2159 2164 3.427161 AGCTTTCTGTTGTTCAGTTGC 57.573 42.857 0.00 0.00 43.97 4.17
2160 2165 2.754552 AGCTTTCTGTTGTTCAGTTGCA 59.245 40.909 0.00 0.00 43.97 4.08
2161 2166 3.193267 AGCTTTCTGTTGTTCAGTTGCAA 59.807 39.130 0.00 0.00 43.97 4.08
2162 2167 4.114794 GCTTTCTGTTGTTCAGTTGCAAT 58.885 39.130 0.59 0.00 43.97 3.56
2163 2168 4.567959 GCTTTCTGTTGTTCAGTTGCAATT 59.432 37.500 0.59 0.00 43.97 2.32
2164 2169 5.063817 GCTTTCTGTTGTTCAGTTGCAATTT 59.936 36.000 0.59 0.00 43.97 1.82
2165 2170 6.402442 GCTTTCTGTTGTTCAGTTGCAATTTT 60.402 34.615 0.59 0.00 43.97 1.82
2166 2171 7.201513 GCTTTCTGTTGTTCAGTTGCAATTTTA 60.202 33.333 0.59 0.00 43.97 1.52
2167 2172 7.754069 TTCTGTTGTTCAGTTGCAATTTTAG 57.246 32.000 0.59 0.00 43.97 1.85
2168 2173 5.748152 TCTGTTGTTCAGTTGCAATTTTAGC 59.252 36.000 0.59 0.00 43.97 3.09
2169 2174 5.414360 TGTTGTTCAGTTGCAATTTTAGCA 58.586 33.333 0.59 0.00 40.85 3.49
2170 2175 6.035866 CTGTTGTTCAGTTGCAATTTTAGCAA 59.964 34.615 0.59 0.94 41.03 3.91
2179 2184 6.734104 TTGCAATTTTAGCAAGTGTTTTGT 57.266 29.167 0.00 0.00 46.13 2.83
2180 2185 7.834068 TTGCAATTTTAGCAAGTGTTTTGTA 57.166 28.000 0.00 0.00 46.13 2.41
2181 2186 7.462109 TGCAATTTTAGCAAGTGTTTTGTAG 57.538 32.000 0.00 0.00 39.39 2.74
2182 2187 6.019156 TGCAATTTTAGCAAGTGTTTTGTAGC 60.019 34.615 0.00 0.00 39.39 3.58
2183 2188 6.200854 GCAATTTTAGCAAGTGTTTTGTAGCT 59.799 34.615 0.00 0.00 36.20 3.32
2184 2189 7.558137 CAATTTTAGCAAGTGTTTTGTAGCTG 58.442 34.615 0.00 0.00 33.83 4.24
2185 2190 4.829064 TTAGCAAGTGTTTTGTAGCTGG 57.171 40.909 0.00 0.00 33.83 4.85
2186 2191 1.956477 AGCAAGTGTTTTGTAGCTGGG 59.044 47.619 0.00 0.00 0.00 4.45
2187 2192 1.681264 GCAAGTGTTTTGTAGCTGGGT 59.319 47.619 0.00 0.00 0.00 4.51
2188 2193 2.100749 GCAAGTGTTTTGTAGCTGGGTT 59.899 45.455 0.00 0.00 0.00 4.11
2189 2194 3.430236 GCAAGTGTTTTGTAGCTGGGTTT 60.430 43.478 0.00 0.00 0.00 3.27
2190 2195 4.111916 CAAGTGTTTTGTAGCTGGGTTTG 58.888 43.478 0.00 0.00 0.00 2.93
2191 2196 2.693074 AGTGTTTTGTAGCTGGGTTTGG 59.307 45.455 0.00 0.00 0.00 3.28
2192 2197 2.691011 GTGTTTTGTAGCTGGGTTTGGA 59.309 45.455 0.00 0.00 0.00 3.53
2193 2198 3.320826 GTGTTTTGTAGCTGGGTTTGGAT 59.679 43.478 0.00 0.00 0.00 3.41
2194 2199 3.964031 TGTTTTGTAGCTGGGTTTGGATT 59.036 39.130 0.00 0.00 0.00 3.01
2195 2200 4.038642 TGTTTTGTAGCTGGGTTTGGATTC 59.961 41.667 0.00 0.00 0.00 2.52
2196 2201 3.517296 TTGTAGCTGGGTTTGGATTCA 57.483 42.857 0.00 0.00 0.00 2.57
2197 2202 2.790433 TGTAGCTGGGTTTGGATTCAC 58.210 47.619 0.00 0.00 0.00 3.18
2198 2203 2.107378 TGTAGCTGGGTTTGGATTCACA 59.893 45.455 0.00 0.00 0.00 3.58
2199 2204 2.380064 AGCTGGGTTTGGATTCACAA 57.620 45.000 0.00 0.00 0.00 3.33
2200 2205 2.893424 AGCTGGGTTTGGATTCACAAT 58.107 42.857 0.00 0.00 0.00 2.71
2201 2206 2.827921 AGCTGGGTTTGGATTCACAATC 59.172 45.455 0.00 0.00 37.17 2.67
2202 2207 2.562298 GCTGGGTTTGGATTCACAATCA 59.438 45.455 0.00 0.00 39.71 2.57
2203 2208 3.367703 GCTGGGTTTGGATTCACAATCAG 60.368 47.826 0.00 0.00 39.71 2.90
2204 2209 4.081406 CTGGGTTTGGATTCACAATCAGA 58.919 43.478 0.00 0.00 39.71 3.27
2205 2210 4.478203 TGGGTTTGGATTCACAATCAGAA 58.522 39.130 0.00 0.00 39.71 3.02
2206 2211 5.085920 TGGGTTTGGATTCACAATCAGAAT 58.914 37.500 0.00 0.00 39.71 2.40
2207 2212 5.185635 TGGGTTTGGATTCACAATCAGAATC 59.814 40.000 7.24 7.24 46.66 2.52
2216 2221 8.211116 GATTCACAATCAGAATCATCTTCACT 57.789 34.615 10.17 0.00 46.63 3.41
2217 2222 9.322773 GATTCACAATCAGAATCATCTTCACTA 57.677 33.333 10.17 0.00 46.63 2.74
2218 2223 8.713737 TTCACAATCAGAATCATCTTCACTAG 57.286 34.615 0.00 0.00 32.03 2.57
2219 2224 8.071177 TCACAATCAGAATCATCTTCACTAGA 57.929 34.615 0.00 0.00 37.28 2.43
2220 2225 8.702819 TCACAATCAGAATCATCTTCACTAGAT 58.297 33.333 0.00 0.00 44.60 1.98
2235 2240 9.283768 TCTTCACTAGATGTTTGAAATTAAGCA 57.716 29.630 0.00 0.00 0.00 3.91
2238 2243 8.390354 TCACTAGATGTTTGAAATTAAGCATCG 58.610 33.333 10.38 3.29 46.44 3.84
2239 2244 7.164826 CACTAGATGTTTGAAATTAAGCATCGC 59.835 37.037 10.38 0.00 46.44 4.58
2240 2245 5.030295 AGATGTTTGAAATTAAGCATCGCG 58.970 37.500 0.00 0.00 46.44 5.87
2241 2246 4.153958 TGTTTGAAATTAAGCATCGCGT 57.846 36.364 5.77 0.00 0.00 6.01
2242 2247 3.911365 TGTTTGAAATTAAGCATCGCGTG 59.089 39.130 5.77 5.06 0.00 5.34
2243 2248 4.155449 GTTTGAAATTAAGCATCGCGTGA 58.845 39.130 5.77 0.00 0.00 4.35
2244 2249 4.614555 TTGAAATTAAGCATCGCGTGAT 57.385 36.364 5.43 5.43 34.28 3.06
2245 2250 4.614555 TGAAATTAAGCATCGCGTGATT 57.385 36.364 9.17 11.50 40.14 2.57
2246 2251 4.980590 TGAAATTAAGCATCGCGTGATTT 58.019 34.783 9.17 4.91 38.40 2.17
2247 2252 5.398169 TGAAATTAAGCATCGCGTGATTTT 58.602 33.333 9.17 9.44 36.69 1.82
2248 2253 6.547283 TGAAATTAAGCATCGCGTGATTTTA 58.453 32.000 9.17 8.46 36.69 1.52
2249 2254 6.467682 TGAAATTAAGCATCGCGTGATTTTAC 59.532 34.615 9.17 0.00 36.69 2.01
2250 2255 2.825086 AAGCATCGCGTGATTTTACC 57.175 45.000 9.17 0.00 30.99 2.85
2251 2256 2.024176 AGCATCGCGTGATTTTACCT 57.976 45.000 9.17 0.00 30.49 3.08
2252 2257 2.356135 AGCATCGCGTGATTTTACCTT 58.644 42.857 9.17 0.00 30.49 3.50
2253 2258 2.095853 AGCATCGCGTGATTTTACCTTG 59.904 45.455 9.17 0.00 30.49 3.61
2254 2259 2.791158 GCATCGCGTGATTTTACCTTGG 60.791 50.000 9.17 0.00 30.49 3.61
2255 2260 0.800012 TCGCGTGATTTTACCTTGGC 59.200 50.000 5.77 0.00 0.00 4.52
2256 2261 0.519519 CGCGTGATTTTACCTTGGCA 59.480 50.000 0.00 0.00 0.00 4.92
2257 2262 1.727857 CGCGTGATTTTACCTTGGCAC 60.728 52.381 0.00 0.00 0.00 5.01
2258 2263 1.402325 GCGTGATTTTACCTTGGCACC 60.402 52.381 0.00 0.00 0.00 5.01
2259 2264 1.883275 CGTGATTTTACCTTGGCACCA 59.117 47.619 0.00 0.00 0.00 4.17
2260 2265 2.351350 CGTGATTTTACCTTGGCACCAC 60.351 50.000 0.00 0.00 0.00 4.16
2261 2266 1.883275 TGATTTTACCTTGGCACCACG 59.117 47.619 0.00 0.00 0.00 4.94
2262 2267 1.883926 GATTTTACCTTGGCACCACGT 59.116 47.619 0.00 0.00 0.00 4.49
2263 2268 1.025812 TTTTACCTTGGCACCACGTG 58.974 50.000 9.08 9.08 36.51 4.49
2272 2277 2.562912 CACCACGTGCCATGAAGC 59.437 61.111 10.91 0.00 0.00 3.86
2273 2278 2.112928 ACCACGTGCCATGAAGCA 59.887 55.556 10.91 0.00 41.46 3.91
2274 2279 1.968017 ACCACGTGCCATGAAGCAG 60.968 57.895 10.91 0.00 45.14 4.24
2275 2280 1.968017 CCACGTGCCATGAAGCAGT 60.968 57.895 10.91 0.00 45.14 4.40
2276 2281 0.673333 CCACGTGCCATGAAGCAGTA 60.673 55.000 10.91 0.00 45.14 2.74
2277 2282 0.723414 CACGTGCCATGAAGCAGTAG 59.277 55.000 0.82 0.00 45.14 2.57
2278 2283 0.391661 ACGTGCCATGAAGCAGTAGG 60.392 55.000 0.00 0.00 45.14 3.18
2279 2284 0.391661 CGTGCCATGAAGCAGTAGGT 60.392 55.000 0.00 0.00 45.14 3.08
2280 2285 1.089920 GTGCCATGAAGCAGTAGGTG 58.910 55.000 0.00 0.00 45.14 4.00
2281 2286 0.035152 TGCCATGAAGCAGTAGGTGG 60.035 55.000 0.00 0.00 38.00 4.61
2282 2287 0.749454 GCCATGAAGCAGTAGGTGGG 60.749 60.000 0.00 0.00 0.00 4.61
2283 2288 0.911769 CCATGAAGCAGTAGGTGGGA 59.088 55.000 0.00 0.00 0.00 4.37
2284 2289 1.134280 CCATGAAGCAGTAGGTGGGAG 60.134 57.143 0.00 0.00 0.00 4.30
2285 2290 0.543749 ATGAAGCAGTAGGTGGGAGC 59.456 55.000 0.00 0.00 0.00 4.70
2286 2291 0.835971 TGAAGCAGTAGGTGGGAGCA 60.836 55.000 0.00 0.00 0.00 4.26
2287 2292 0.107945 GAAGCAGTAGGTGGGAGCAG 60.108 60.000 0.00 0.00 0.00 4.24
2288 2293 0.545309 AAGCAGTAGGTGGGAGCAGA 60.545 55.000 0.00 0.00 0.00 4.26
2289 2294 0.975040 AGCAGTAGGTGGGAGCAGAG 60.975 60.000 0.00 0.00 0.00 3.35
2290 2295 1.261238 GCAGTAGGTGGGAGCAGAGT 61.261 60.000 0.00 0.00 0.00 3.24
2291 2296 0.820871 CAGTAGGTGGGAGCAGAGTC 59.179 60.000 0.00 0.00 0.00 3.36
2292 2297 0.681564 AGTAGGTGGGAGCAGAGTCG 60.682 60.000 0.00 0.00 0.00 4.18
2293 2298 0.966370 GTAGGTGGGAGCAGAGTCGT 60.966 60.000 0.00 0.00 0.00 4.34
2294 2299 0.680280 TAGGTGGGAGCAGAGTCGTC 60.680 60.000 0.00 0.00 0.00 4.20
2295 2300 2.574399 GTGGGAGCAGAGTCGTCC 59.426 66.667 1.60 1.60 0.00 4.79
2296 2301 1.979693 GTGGGAGCAGAGTCGTCCT 60.980 63.158 8.57 0.00 0.00 3.85
2297 2302 1.228894 TGGGAGCAGAGTCGTCCTT 60.229 57.895 8.57 0.00 0.00 3.36
2298 2303 1.216710 GGGAGCAGAGTCGTCCTTG 59.783 63.158 8.57 0.00 0.00 3.61
2299 2304 1.446966 GGAGCAGAGTCGTCCTTGC 60.447 63.158 2.81 0.00 0.00 4.01
2300 2305 1.446966 GAGCAGAGTCGTCCTTGCC 60.447 63.158 0.00 0.00 0.00 4.52
2301 2306 2.159819 GAGCAGAGTCGTCCTTGCCA 62.160 60.000 0.00 0.00 0.00 4.92
2302 2307 1.078848 GCAGAGTCGTCCTTGCCAT 60.079 57.895 0.00 0.00 0.00 4.40
2303 2308 0.674895 GCAGAGTCGTCCTTGCCATT 60.675 55.000 0.00 0.00 0.00 3.16
2304 2309 1.405526 GCAGAGTCGTCCTTGCCATTA 60.406 52.381 0.00 0.00 0.00 1.90
2305 2310 2.544685 CAGAGTCGTCCTTGCCATTAG 58.455 52.381 0.00 0.00 0.00 1.73
2306 2311 1.134670 AGAGTCGTCCTTGCCATTAGC 60.135 52.381 0.00 0.00 44.14 3.09
2307 2312 0.905357 AGTCGTCCTTGCCATTAGCT 59.095 50.000 0.00 0.00 44.23 3.32
2308 2313 1.279271 AGTCGTCCTTGCCATTAGCTT 59.721 47.619 0.00 0.00 44.23 3.74
2309 2314 1.666189 GTCGTCCTTGCCATTAGCTTC 59.334 52.381 0.00 0.00 44.23 3.86
2310 2315 1.277842 TCGTCCTTGCCATTAGCTTCA 59.722 47.619 0.00 0.00 44.23 3.02
2311 2316 1.667724 CGTCCTTGCCATTAGCTTCAG 59.332 52.381 0.00 0.00 44.23 3.02
2312 2317 1.403323 GTCCTTGCCATTAGCTTCAGC 59.597 52.381 0.00 0.00 44.23 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.464157 AGAGACAGCGAAAGAAAGGG 57.536 50.000 0.00 0.00 0.00 3.95
1 2 5.415221 AGAATAGAGACAGCGAAAGAAAGG 58.585 41.667 0.00 0.00 0.00 3.11
2 3 8.538856 CAATAGAATAGAGACAGCGAAAGAAAG 58.461 37.037 0.00 0.00 0.00 2.62
3 4 7.492669 CCAATAGAATAGAGACAGCGAAAGAAA 59.507 37.037 0.00 0.00 0.00 2.52
4 5 6.980978 CCAATAGAATAGAGACAGCGAAAGAA 59.019 38.462 0.00 0.00 0.00 2.52
5 6 6.096987 ACCAATAGAATAGAGACAGCGAAAGA 59.903 38.462 0.00 0.00 0.00 2.52
6 7 6.199908 CACCAATAGAATAGAGACAGCGAAAG 59.800 42.308 0.00 0.00 0.00 2.62
7 8 6.042777 CACCAATAGAATAGAGACAGCGAAA 58.957 40.000 0.00 0.00 0.00 3.46
8 9 5.451937 CCACCAATAGAATAGAGACAGCGAA 60.452 44.000 0.00 0.00 0.00 4.70
9 10 4.038042 CCACCAATAGAATAGAGACAGCGA 59.962 45.833 0.00 0.00 0.00 4.93
10 11 4.038042 TCCACCAATAGAATAGAGACAGCG 59.962 45.833 0.00 0.00 0.00 5.18
11 12 5.293560 GTCCACCAATAGAATAGAGACAGC 58.706 45.833 0.00 0.00 0.00 4.40
12 13 5.508153 CCGTCCACCAATAGAATAGAGACAG 60.508 48.000 0.00 0.00 0.00 3.51
13 14 4.341235 CCGTCCACCAATAGAATAGAGACA 59.659 45.833 0.00 0.00 0.00 3.41
14 15 4.341520 ACCGTCCACCAATAGAATAGAGAC 59.658 45.833 0.00 0.00 0.00 3.36
15 16 4.543689 ACCGTCCACCAATAGAATAGAGA 58.456 43.478 0.00 0.00 0.00 3.10
16 17 4.556898 CGACCGTCCACCAATAGAATAGAG 60.557 50.000 0.00 0.00 0.00 2.43
17 18 3.317149 CGACCGTCCACCAATAGAATAGA 59.683 47.826 0.00 0.00 0.00 1.98
18 19 3.067742 ACGACCGTCCACCAATAGAATAG 59.932 47.826 0.00 0.00 0.00 1.73
19 20 3.025978 ACGACCGTCCACCAATAGAATA 58.974 45.455 0.00 0.00 0.00 1.75
20 21 1.829222 ACGACCGTCCACCAATAGAAT 59.171 47.619 0.00 0.00 0.00 2.40
21 22 1.259609 ACGACCGTCCACCAATAGAA 58.740 50.000 0.00 0.00 0.00 2.10
22 23 2.127271 TACGACCGTCCACCAATAGA 57.873 50.000 0.00 0.00 0.00 1.98
23 24 2.805845 CTTACGACCGTCCACCAATAG 58.194 52.381 0.00 0.00 0.00 1.73
24 25 1.135024 GCTTACGACCGTCCACCAATA 60.135 52.381 0.00 0.00 0.00 1.90
25 26 0.390735 GCTTACGACCGTCCACCAAT 60.391 55.000 0.00 0.00 0.00 3.16
26 27 1.005867 GCTTACGACCGTCCACCAA 60.006 57.895 0.00 0.00 0.00 3.67
27 28 2.201708 TGCTTACGACCGTCCACCA 61.202 57.895 0.00 0.00 0.00 4.17
28 29 1.735559 GTGCTTACGACCGTCCACC 60.736 63.158 0.00 0.00 0.00 4.61
29 30 0.598158 TTGTGCTTACGACCGTCCAC 60.598 55.000 0.00 6.21 0.00 4.02
30 31 0.319211 CTTGTGCTTACGACCGTCCA 60.319 55.000 0.00 0.00 0.00 4.02
31 32 1.623973 GCTTGTGCTTACGACCGTCC 61.624 60.000 0.00 0.00 36.03 4.79
32 33 0.942410 TGCTTGTGCTTACGACCGTC 60.942 55.000 0.00 0.00 40.48 4.79
33 34 0.531090 TTGCTTGTGCTTACGACCGT 60.531 50.000 0.00 0.00 40.48 4.83
34 35 0.584396 TTTGCTTGTGCTTACGACCG 59.416 50.000 0.00 0.00 40.48 4.79
35 36 2.766970 TTTTGCTTGTGCTTACGACC 57.233 45.000 0.00 0.00 40.48 4.79
36 37 3.425193 CCATTTTTGCTTGTGCTTACGAC 59.575 43.478 0.00 0.00 40.48 4.34
37 38 3.067461 ACCATTTTTGCTTGTGCTTACGA 59.933 39.130 0.00 0.00 40.48 3.43
38 39 3.380142 ACCATTTTTGCTTGTGCTTACG 58.620 40.909 0.00 0.00 40.48 3.18
39 40 4.808364 TCAACCATTTTTGCTTGTGCTTAC 59.192 37.500 0.00 0.00 40.48 2.34
40 41 5.016051 TCAACCATTTTTGCTTGTGCTTA 57.984 34.783 0.00 0.00 40.48 3.09
41 42 3.871485 TCAACCATTTTTGCTTGTGCTT 58.129 36.364 0.00 0.00 40.48 3.91
215 216 1.132500 CTTGGGATGGGAGGGAGTAC 58.868 60.000 0.00 0.00 0.00 2.73
322 323 9.282905 TCCATTTCATATATGTATGAGGATCCA 57.717 33.333 15.82 0.00 45.44 3.41
436 437 1.078918 CGCAGATTGGCCTGACTCA 60.079 57.895 3.32 0.00 36.29 3.41
567 568 3.985019 TCTTACATAAGGTTCCCGCAA 57.015 42.857 0.00 0.00 34.14 4.85
626 627 2.236146 AGATGCCGTACATTTGAGTGGA 59.764 45.455 0.00 0.00 39.84 4.02
635 636 0.806102 GCACGACAGATGCCGTACAT 60.806 55.000 0.00 0.00 43.54 2.29
649 650 1.198759 AAGAAGGGGCCTAAGCACGA 61.199 55.000 0.84 0.00 46.55 4.35
710 711 4.020928 CACGCCATACCTATACCCATACAA 60.021 45.833 0.00 0.00 0.00 2.41
829 831 1.519234 CGCGAGCTGGTTAGATGCA 60.519 57.895 0.00 0.00 0.00 3.96
892 894 0.312416 AGCGCATCTCTGTATCGACC 59.688 55.000 11.47 0.00 0.00 4.79
1212 1214 2.542907 CCGGACGCTGCAGTTGTTT 61.543 57.895 16.64 0.00 0.00 2.83
1272 1274 0.967380 CTTGGGGCTTCTTTGGCGAT 60.967 55.000 0.00 0.00 0.00 4.58
1619 1624 2.484947 GGAAACTCTCTTCCCGTGTTGT 60.485 50.000 0.00 0.00 39.26 3.32
1623 1628 2.300437 AGAAGGAAACTCTCTTCCCGTG 59.700 50.000 0.00 0.00 45.28 4.94
1659 1664 7.525360 GCCCACACATTATCTTTAATATTGGGG 60.525 40.741 14.35 0.00 38.85 4.96
1671 1676 4.862641 AGTAAAGGCCCACACATTATCT 57.137 40.909 0.00 0.00 0.00 1.98
1693 1698 4.682021 AGGGGATCAACCATCTTCTTTT 57.318 40.909 8.23 0.00 41.20 2.27
1718 1723 1.511613 GGGGAGGATGGAATGAGTCA 58.488 55.000 0.00 0.00 0.00 3.41
1822 1827 4.079958 GGCCCCTTCTCTTTACCTTTATCA 60.080 45.833 0.00 0.00 0.00 2.15
1946 1951 8.447833 CAAGTTATTTCGTACAGGCTATTCAAA 58.552 33.333 0.00 0.00 0.00 2.69
2064 2069 2.297698 TGACCCGTTCTCAGTCCTTA 57.702 50.000 0.00 0.00 0.00 2.69
2065 2070 1.645710 ATGACCCGTTCTCAGTCCTT 58.354 50.000 0.00 0.00 0.00 3.36
2066 2071 1.645710 AATGACCCGTTCTCAGTCCT 58.354 50.000 0.00 0.00 0.00 3.85
2067 2072 2.474410 AAATGACCCGTTCTCAGTCC 57.526 50.000 0.00 0.00 0.00 3.85
2068 2073 3.371285 GCTAAAATGACCCGTTCTCAGTC 59.629 47.826 0.00 0.00 0.00 3.51
2069 2074 3.335579 GCTAAAATGACCCGTTCTCAGT 58.664 45.455 0.00 0.00 0.00 3.41
2070 2075 2.348666 CGCTAAAATGACCCGTTCTCAG 59.651 50.000 0.00 0.00 0.00 3.35
2071 2076 2.289195 ACGCTAAAATGACCCGTTCTCA 60.289 45.455 0.00 0.00 0.00 3.27
2072 2077 2.344025 ACGCTAAAATGACCCGTTCTC 58.656 47.619 0.00 0.00 0.00 2.87
2073 2078 2.344025 GACGCTAAAATGACCCGTTCT 58.656 47.619 0.00 0.00 31.65 3.01
2074 2079 1.395954 GGACGCTAAAATGACCCGTTC 59.604 52.381 0.00 0.00 31.65 3.95
2075 2080 1.270947 TGGACGCTAAAATGACCCGTT 60.271 47.619 0.00 0.00 31.65 4.44
2076 2081 0.322322 TGGACGCTAAAATGACCCGT 59.678 50.000 0.00 0.00 34.52 5.28
2077 2082 1.006832 CTGGACGCTAAAATGACCCG 58.993 55.000 0.00 0.00 0.00 5.28
2078 2083 0.733150 GCTGGACGCTAAAATGACCC 59.267 55.000 0.00 0.00 35.14 4.46
2079 2084 1.398390 CTGCTGGACGCTAAAATGACC 59.602 52.381 0.00 0.00 40.11 4.02
2080 2085 1.398390 CCTGCTGGACGCTAAAATGAC 59.602 52.381 2.92 0.00 40.11 3.06
2081 2086 1.003118 ACCTGCTGGACGCTAAAATGA 59.997 47.619 17.64 0.00 40.11 2.57
2082 2087 1.398390 GACCTGCTGGACGCTAAAATG 59.602 52.381 17.64 0.00 40.11 2.32
2083 2088 1.003118 TGACCTGCTGGACGCTAAAAT 59.997 47.619 17.64 0.00 40.11 1.82
2084 2089 0.394938 TGACCTGCTGGACGCTAAAA 59.605 50.000 17.64 0.00 40.11 1.52
2085 2090 0.613260 ATGACCTGCTGGACGCTAAA 59.387 50.000 17.64 0.00 40.11 1.85
2086 2091 0.175760 GATGACCTGCTGGACGCTAA 59.824 55.000 17.64 0.00 40.11 3.09
2087 2092 1.816537 GATGACCTGCTGGACGCTA 59.183 57.895 17.64 0.00 40.11 4.26
2088 2093 2.581354 GATGACCTGCTGGACGCT 59.419 61.111 17.64 1.66 40.11 5.07
2089 2094 2.887568 CGATGACCTGCTGGACGC 60.888 66.667 17.64 5.75 37.04 5.19
2090 2095 2.004808 TAGCGATGACCTGCTGGACG 62.005 60.000 17.64 15.49 42.46 4.79
2091 2096 0.390860 ATAGCGATGACCTGCTGGAC 59.609 55.000 17.64 11.05 42.46 4.02
2092 2097 1.123077 AATAGCGATGACCTGCTGGA 58.877 50.000 17.64 0.00 42.46 3.86
2093 2098 1.224075 CAATAGCGATGACCTGCTGG 58.776 55.000 8.29 8.29 42.46 4.85
2094 2099 1.863454 GACAATAGCGATGACCTGCTG 59.137 52.381 0.00 0.00 42.46 4.41
2095 2100 1.759445 AGACAATAGCGATGACCTGCT 59.241 47.619 0.00 0.00 45.04 4.24
2096 2101 2.231215 AGACAATAGCGATGACCTGC 57.769 50.000 0.00 0.00 0.00 4.85
2097 2102 4.682787 TGTTAGACAATAGCGATGACCTG 58.317 43.478 0.00 0.00 0.00 4.00
2098 2103 4.402793 ACTGTTAGACAATAGCGATGACCT 59.597 41.667 0.00 0.00 0.00 3.85
2099 2104 4.683832 ACTGTTAGACAATAGCGATGACC 58.316 43.478 0.00 0.00 0.00 4.02
2100 2105 6.648725 AAACTGTTAGACAATAGCGATGAC 57.351 37.500 0.00 0.00 0.00 3.06
2101 2106 7.386573 TCAAAAACTGTTAGACAATAGCGATGA 59.613 33.333 0.00 0.00 0.00 2.92
2102 2107 7.518161 TCAAAAACTGTTAGACAATAGCGATG 58.482 34.615 0.00 0.00 0.00 3.84
2103 2108 7.387948 ACTCAAAAACTGTTAGACAATAGCGAT 59.612 33.333 0.00 0.00 0.00 4.58
2104 2109 6.704493 ACTCAAAAACTGTTAGACAATAGCGA 59.296 34.615 0.00 0.00 0.00 4.93
2105 2110 6.888430 ACTCAAAAACTGTTAGACAATAGCG 58.112 36.000 0.00 0.00 0.00 4.26
2106 2111 9.760660 CATACTCAAAAACTGTTAGACAATAGC 57.239 33.333 0.00 0.00 0.00 2.97
2110 2115 8.617809 GGAACATACTCAAAAACTGTTAGACAA 58.382 33.333 0.00 0.00 30.63 3.18
2111 2116 7.771361 TGGAACATACTCAAAAACTGTTAGACA 59.229 33.333 0.00 0.00 30.63 3.41
2112 2117 8.149973 TGGAACATACTCAAAAACTGTTAGAC 57.850 34.615 0.00 0.00 30.63 2.59
2132 2137 5.689383 TGAACAACAGAAAGCTATGGAAC 57.311 39.130 0.00 0.00 0.00 3.62
2143 2148 8.056173 TGCTAAAATTGCAACTGAACAACAGAA 61.056 33.333 0.00 0.00 41.98 3.02
2144 2149 6.626844 TGCTAAAATTGCAACTGAACAACAGA 60.627 34.615 0.00 0.00 41.98 3.41
2145 2150 5.519566 TGCTAAAATTGCAACTGAACAACAG 59.480 36.000 0.00 0.00 42.56 3.16
2146 2151 5.414360 TGCTAAAATTGCAACTGAACAACA 58.586 33.333 0.00 0.00 37.51 3.33
2147 2152 5.964887 TGCTAAAATTGCAACTGAACAAC 57.035 34.783 0.00 0.00 37.51 3.32
2148 2153 6.035866 CACTTGCTAAAATTGCAACTGAACAA 59.964 34.615 0.00 1.90 44.24 2.83
2149 2154 5.519566 CACTTGCTAAAATTGCAACTGAACA 59.480 36.000 0.00 0.00 44.24 3.18
2150 2155 5.519927 ACACTTGCTAAAATTGCAACTGAAC 59.480 36.000 0.00 0.00 44.24 3.18
2151 2156 5.659463 ACACTTGCTAAAATTGCAACTGAA 58.341 33.333 0.00 0.00 44.24 3.02
2152 2157 5.261209 ACACTTGCTAAAATTGCAACTGA 57.739 34.783 0.00 0.00 44.24 3.41
2153 2158 5.971895 AACACTTGCTAAAATTGCAACTG 57.028 34.783 0.00 3.26 44.24 3.16
2154 2159 6.371271 ACAAAACACTTGCTAAAATTGCAACT 59.629 30.769 0.00 0.00 44.24 3.16
2155 2160 6.541969 ACAAAACACTTGCTAAAATTGCAAC 58.458 32.000 0.00 0.00 44.24 4.17
2156 2161 6.734104 ACAAAACACTTGCTAAAATTGCAA 57.266 29.167 0.00 0.00 46.48 4.08
2157 2162 6.019156 GCTACAAAACACTTGCTAAAATTGCA 60.019 34.615 0.00 0.00 38.80 4.08
2158 2163 6.200854 AGCTACAAAACACTTGCTAAAATTGC 59.799 34.615 0.00 0.00 0.00 3.56
2159 2164 7.306749 CCAGCTACAAAACACTTGCTAAAATTG 60.307 37.037 0.00 0.00 0.00 2.32
2160 2165 6.701400 CCAGCTACAAAACACTTGCTAAAATT 59.299 34.615 0.00 0.00 0.00 1.82
2161 2166 6.215845 CCAGCTACAAAACACTTGCTAAAAT 58.784 36.000 0.00 0.00 0.00 1.82
2162 2167 5.451242 CCCAGCTACAAAACACTTGCTAAAA 60.451 40.000 0.00 0.00 0.00 1.52
2163 2168 4.037446 CCCAGCTACAAAACACTTGCTAAA 59.963 41.667 0.00 0.00 0.00 1.85
2164 2169 3.568007 CCCAGCTACAAAACACTTGCTAA 59.432 43.478 0.00 0.00 0.00 3.09
2165 2170 3.146066 CCCAGCTACAAAACACTTGCTA 58.854 45.455 0.00 0.00 0.00 3.49
2166 2171 1.956477 CCCAGCTACAAAACACTTGCT 59.044 47.619 0.00 0.00 0.00 3.91
2167 2172 1.681264 ACCCAGCTACAAAACACTTGC 59.319 47.619 0.00 0.00 0.00 4.01
2168 2173 4.111916 CAAACCCAGCTACAAAACACTTG 58.888 43.478 0.00 0.00 0.00 3.16
2169 2174 3.132111 CCAAACCCAGCTACAAAACACTT 59.868 43.478 0.00 0.00 0.00 3.16
2170 2175 2.693074 CCAAACCCAGCTACAAAACACT 59.307 45.455 0.00 0.00 0.00 3.55
2171 2176 2.691011 TCCAAACCCAGCTACAAAACAC 59.309 45.455 0.00 0.00 0.00 3.32
2172 2177 3.019799 TCCAAACCCAGCTACAAAACA 57.980 42.857 0.00 0.00 0.00 2.83
2173 2178 4.038642 TGAATCCAAACCCAGCTACAAAAC 59.961 41.667 0.00 0.00 0.00 2.43
2174 2179 4.038642 GTGAATCCAAACCCAGCTACAAAA 59.961 41.667 0.00 0.00 0.00 2.44
2175 2180 3.572255 GTGAATCCAAACCCAGCTACAAA 59.428 43.478 0.00 0.00 0.00 2.83
2176 2181 3.153919 GTGAATCCAAACCCAGCTACAA 58.846 45.455 0.00 0.00 0.00 2.41
2177 2182 2.107378 TGTGAATCCAAACCCAGCTACA 59.893 45.455 0.00 0.00 0.00 2.74
2178 2183 2.790433 TGTGAATCCAAACCCAGCTAC 58.210 47.619 0.00 0.00 0.00 3.58
2179 2184 3.517296 TTGTGAATCCAAACCCAGCTA 57.483 42.857 0.00 0.00 0.00 3.32
2180 2185 2.380064 TTGTGAATCCAAACCCAGCT 57.620 45.000 0.00 0.00 0.00 4.24
2181 2186 2.562298 TGATTGTGAATCCAAACCCAGC 59.438 45.455 0.00 0.00 37.09 4.85
2182 2187 4.081406 TCTGATTGTGAATCCAAACCCAG 58.919 43.478 0.00 0.00 37.09 4.45
2183 2188 4.111255 TCTGATTGTGAATCCAAACCCA 57.889 40.909 0.00 0.00 37.09 4.51
2184 2189 5.185635 TGATTCTGATTGTGAATCCAAACCC 59.814 40.000 12.14 0.00 45.34 4.11
2185 2190 6.271488 TGATTCTGATTGTGAATCCAAACC 57.729 37.500 12.14 0.00 45.34 3.27
2186 2191 7.769220 AGATGATTCTGATTGTGAATCCAAAC 58.231 34.615 12.14 3.91 45.34 2.93
2187 2192 7.949690 AGATGATTCTGATTGTGAATCCAAA 57.050 32.000 12.14 0.00 45.34 3.28
2188 2193 7.612633 TGAAGATGATTCTGATTGTGAATCCAA 59.387 33.333 12.14 0.00 45.34 3.53
2189 2194 7.066645 GTGAAGATGATTCTGATTGTGAATCCA 59.933 37.037 12.14 2.60 45.34 3.41
2190 2195 7.282675 AGTGAAGATGATTCTGATTGTGAATCC 59.717 37.037 12.14 1.13 45.34 3.01
2191 2196 8.211116 AGTGAAGATGATTCTGATTGTGAATC 57.789 34.615 8.89 8.89 45.83 2.52
2192 2197 9.327628 CTAGTGAAGATGATTCTGATTGTGAAT 57.672 33.333 0.00 0.00 36.91 2.57
2193 2198 8.534496 TCTAGTGAAGATGATTCTGATTGTGAA 58.466 33.333 0.00 0.00 30.72 3.18
2194 2199 8.071177 TCTAGTGAAGATGATTCTGATTGTGA 57.929 34.615 0.00 0.00 30.72 3.58
2195 2200 8.890124 ATCTAGTGAAGATGATTCTGATTGTG 57.110 34.615 0.00 0.00 43.62 3.33
2209 2214 9.283768 TGCTTAATTTCAAACATCTAGTGAAGA 57.716 29.630 0.00 0.00 39.02 2.87
2212 2217 8.390354 CGATGCTTAATTTCAAACATCTAGTGA 58.610 33.333 0.00 0.00 33.43 3.41
2213 2218 7.164826 GCGATGCTTAATTTCAAACATCTAGTG 59.835 37.037 0.00 0.00 33.43 2.74
2214 2219 7.189512 GCGATGCTTAATTTCAAACATCTAGT 58.810 34.615 0.00 0.00 33.43 2.57
2215 2220 6.355405 CGCGATGCTTAATTTCAAACATCTAG 59.645 38.462 0.00 0.00 33.43 2.43
2216 2221 6.183360 ACGCGATGCTTAATTTCAAACATCTA 60.183 34.615 15.93 0.00 33.43 1.98
2217 2222 5.030295 CGCGATGCTTAATTTCAAACATCT 58.970 37.500 0.00 0.00 33.43 2.90
2218 2223 4.793216 ACGCGATGCTTAATTTCAAACATC 59.207 37.500 15.93 0.00 0.00 3.06
2219 2224 4.558470 CACGCGATGCTTAATTTCAAACAT 59.442 37.500 15.93 0.00 0.00 2.71
2220 2225 3.911365 CACGCGATGCTTAATTTCAAACA 59.089 39.130 15.93 0.00 0.00 2.83
2221 2226 4.155449 TCACGCGATGCTTAATTTCAAAC 58.845 39.130 15.93 0.00 0.00 2.93
2222 2227 4.411993 TCACGCGATGCTTAATTTCAAA 57.588 36.364 15.93 0.00 0.00 2.69
2223 2228 4.614555 ATCACGCGATGCTTAATTTCAA 57.385 36.364 15.93 0.00 0.00 2.69
2224 2229 4.614555 AATCACGCGATGCTTAATTTCA 57.385 36.364 15.93 0.00 30.13 2.69
2225 2230 5.932021 AAAATCACGCGATGCTTAATTTC 57.068 34.783 15.93 0.00 30.13 2.17
2226 2231 5.741982 GGTAAAATCACGCGATGCTTAATTT 59.258 36.000 15.93 6.67 30.13 1.82
2227 2232 5.065988 AGGTAAAATCACGCGATGCTTAATT 59.934 36.000 15.93 0.52 30.13 1.40
2228 2233 4.574828 AGGTAAAATCACGCGATGCTTAAT 59.425 37.500 15.93 1.57 30.13 1.40
2229 2234 3.936453 AGGTAAAATCACGCGATGCTTAA 59.064 39.130 15.93 0.00 30.13 1.85
2230 2235 3.527533 AGGTAAAATCACGCGATGCTTA 58.472 40.909 15.93 0.45 30.13 3.09
2231 2236 2.356135 AGGTAAAATCACGCGATGCTT 58.644 42.857 15.93 2.24 30.13 3.91
2232 2237 2.024176 AGGTAAAATCACGCGATGCT 57.976 45.000 15.93 0.00 30.13 3.79
2233 2238 2.440501 CAAGGTAAAATCACGCGATGC 58.559 47.619 15.93 0.00 30.13 3.91
2234 2239 2.791158 GCCAAGGTAAAATCACGCGATG 60.791 50.000 15.93 7.85 30.13 3.84
2235 2240 1.400494 GCCAAGGTAAAATCACGCGAT 59.600 47.619 15.93 0.00 0.00 4.58
2236 2241 0.800012 GCCAAGGTAAAATCACGCGA 59.200 50.000 15.93 0.00 0.00 5.87
2237 2242 0.519519 TGCCAAGGTAAAATCACGCG 59.480 50.000 3.53 3.53 0.00 6.01
2238 2243 1.402325 GGTGCCAAGGTAAAATCACGC 60.402 52.381 0.00 0.00 0.00 5.34
2239 2244 1.883275 TGGTGCCAAGGTAAAATCACG 59.117 47.619 0.00 0.00 0.00 4.35
2240 2245 2.351350 CGTGGTGCCAAGGTAAAATCAC 60.351 50.000 0.00 0.00 0.00 3.06
2241 2246 1.883275 CGTGGTGCCAAGGTAAAATCA 59.117 47.619 0.00 0.00 0.00 2.57
2242 2247 1.883926 ACGTGGTGCCAAGGTAAAATC 59.116 47.619 8.85 0.00 0.00 2.17
2243 2248 1.611491 CACGTGGTGCCAAGGTAAAAT 59.389 47.619 7.95 0.00 0.00 1.82
2244 2249 1.025812 CACGTGGTGCCAAGGTAAAA 58.974 50.000 7.95 0.00 0.00 1.52
2245 2250 2.709170 CACGTGGTGCCAAGGTAAA 58.291 52.632 7.95 0.00 0.00 2.01
2246 2251 4.466133 CACGTGGTGCCAAGGTAA 57.534 55.556 7.95 0.00 0.00 2.85
2255 2260 2.191354 CTGCTTCATGGCACGTGGTG 62.191 60.000 18.88 0.00 37.29 4.17
2256 2261 1.968017 CTGCTTCATGGCACGTGGT 60.968 57.895 18.88 0.00 37.29 4.16
2257 2262 0.673333 TACTGCTTCATGGCACGTGG 60.673 55.000 18.88 0.00 37.29 4.94
2258 2263 0.723414 CTACTGCTTCATGGCACGTG 59.277 55.000 12.28 12.28 37.29 4.49
2259 2264 0.391661 CCTACTGCTTCATGGCACGT 60.392 55.000 0.00 0.00 37.29 4.49
2260 2265 0.391661 ACCTACTGCTTCATGGCACG 60.392 55.000 0.00 0.00 37.29 5.34
2261 2266 1.089920 CACCTACTGCTTCATGGCAC 58.910 55.000 0.00 0.00 37.29 5.01
2262 2267 0.035152 CCACCTACTGCTTCATGGCA 60.035 55.000 0.00 0.00 40.15 4.92
2263 2268 0.749454 CCCACCTACTGCTTCATGGC 60.749 60.000 0.00 0.00 0.00 4.40
2264 2269 0.911769 TCCCACCTACTGCTTCATGG 59.088 55.000 0.00 0.00 0.00 3.66
2265 2270 1.745141 GCTCCCACCTACTGCTTCATG 60.745 57.143 0.00 0.00 0.00 3.07
2266 2271 0.543749 GCTCCCACCTACTGCTTCAT 59.456 55.000 0.00 0.00 0.00 2.57
2267 2272 0.835971 TGCTCCCACCTACTGCTTCA 60.836 55.000 0.00 0.00 0.00 3.02
2268 2273 0.107945 CTGCTCCCACCTACTGCTTC 60.108 60.000 0.00 0.00 0.00 3.86
2269 2274 0.545309 TCTGCTCCCACCTACTGCTT 60.545 55.000 0.00 0.00 0.00 3.91
2270 2275 0.975040 CTCTGCTCCCACCTACTGCT 60.975 60.000 0.00 0.00 0.00 4.24
2271 2276 1.261238 ACTCTGCTCCCACCTACTGC 61.261 60.000 0.00 0.00 0.00 4.40
2272 2277 0.820871 GACTCTGCTCCCACCTACTG 59.179 60.000 0.00 0.00 0.00 2.74
2273 2278 0.681564 CGACTCTGCTCCCACCTACT 60.682 60.000 0.00 0.00 0.00 2.57
2274 2279 0.966370 ACGACTCTGCTCCCACCTAC 60.966 60.000 0.00 0.00 0.00 3.18
2275 2280 0.680280 GACGACTCTGCTCCCACCTA 60.680 60.000 0.00 0.00 0.00 3.08
2276 2281 1.979693 GACGACTCTGCTCCCACCT 60.980 63.158 0.00 0.00 0.00 4.00
2277 2282 2.574399 GACGACTCTGCTCCCACC 59.426 66.667 0.00 0.00 0.00 4.61
2278 2283 1.536943 AAGGACGACTCTGCTCCCAC 61.537 60.000 0.00 0.00 0.00 4.61
2279 2284 1.228894 AAGGACGACTCTGCTCCCA 60.229 57.895 0.00 0.00 0.00 4.37
2280 2285 1.216710 CAAGGACGACTCTGCTCCC 59.783 63.158 0.00 0.00 0.00 4.30
2281 2286 1.446966 GCAAGGACGACTCTGCTCC 60.447 63.158 0.00 0.00 33.37 4.70
2282 2287 1.446966 GGCAAGGACGACTCTGCTC 60.447 63.158 10.26 0.62 35.19 4.26
2283 2288 1.548357 ATGGCAAGGACGACTCTGCT 61.548 55.000 0.00 0.00 35.19 4.24
2284 2289 0.674895 AATGGCAAGGACGACTCTGC 60.675 55.000 0.00 0.00 34.54 4.26
2285 2290 2.544685 CTAATGGCAAGGACGACTCTG 58.455 52.381 0.00 0.00 0.00 3.35
2286 2291 1.134670 GCTAATGGCAAGGACGACTCT 60.135 52.381 0.00 0.00 41.35 3.24
2287 2292 1.134670 AGCTAATGGCAAGGACGACTC 60.135 52.381 0.00 0.00 44.79 3.36
2288 2293 0.905357 AGCTAATGGCAAGGACGACT 59.095 50.000 0.00 0.00 44.79 4.18
2289 2294 1.666189 GAAGCTAATGGCAAGGACGAC 59.334 52.381 0.00 0.00 44.79 4.34
2290 2295 1.277842 TGAAGCTAATGGCAAGGACGA 59.722 47.619 0.00 0.00 44.79 4.20
2291 2296 1.667724 CTGAAGCTAATGGCAAGGACG 59.332 52.381 0.00 0.00 44.79 4.79
2292 2297 1.403323 GCTGAAGCTAATGGCAAGGAC 59.597 52.381 0.00 0.00 44.79 3.85
2293 2298 1.755179 GCTGAAGCTAATGGCAAGGA 58.245 50.000 0.00 0.00 44.79 3.36
2294 2299 0.379669 CGCTGAAGCTAATGGCAAGG 59.620 55.000 0.00 0.00 44.79 3.61
2295 2300 3.911989 CGCTGAAGCTAATGGCAAG 57.088 52.632 0.00 0.00 44.79 4.01


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

AutoCloner maintained by Alex Coulton.