Multiple sequence alignment - TraesCS3D01G209000

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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 TraesCS3D01G209000 chr3D 100.000 2324 0 0 1 2324 276092589 276090266 0.000000e+00 4292
1 TraesCS3D01G209000 chr3D 99.597 1242 5 0 1 1242 276113724 276112483 0.000000e+00 2266
2 TraesCS3D01G209000 chr3B 93.025 1147 25 11 290 1400 375173048 375174175 0.000000e+00 1624
3 TraesCS3D01G209000 chr3B 96.581 468 6 5 1399 1866 375174203 375174660 0.000000e+00 767
4 TraesCS3D01G209000 chr3B 95.307 277 13 0 2048 2324 256150300 256150024 7.620000e-120 440
5 TraesCS3D01G209000 chr3B 95.270 148 5 2 1901 2047 375174836 375174982 1.390000e-57 233
6 TraesCS3D01G209000 chr3A 93.572 669 30 6 732 1400 364139593 364140248 0.000000e+00 985
7 TraesCS3D01G209000 chr3A 91.429 490 11 5 275 734 364133310 364133798 0.000000e+00 643
8 TraesCS3D01G209000 chr3A 91.418 268 20 2 1 267 364132911 364133176 4.720000e-97 364
9 TraesCS3D01G209000 chrUn 99.246 398 3 0 1927 2324 349572196 349572593 0.000000e+00 719
10 TraesCS3D01G209000 chr1D 95.088 285 14 0 2040 2324 76743626 76743910 1.270000e-122 449
11 TraesCS3D01G209000 chr1D 95.053 283 12 2 2043 2324 207663454 207663735 5.890000e-121 444
12 TraesCS3D01G209000 chr6D 96.000 275 11 0 2045 2319 329976780 329977054 4.560000e-122 448
13 TraesCS3D01G209000 chr7D 95.070 284 13 1 2042 2324 196368409 196368692 1.640000e-121 446
14 TraesCS3D01G209000 chr5D 95.668 277 12 0 2048 2324 440152542 440152266 1.640000e-121 446
15 TraesCS3D01G209000 chr5D 95.290 276 13 0 2049 2324 329903232 329902957 2.740000e-119 438
16 TraesCS3D01G209000 chr2D 95.018 281 14 0 2044 2324 109664835 109664555 2.120000e-120 442


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 TraesCS3D01G209000 chr3D 276090266 276092589 2323 True 4292.000000 4292 100.000000 1 2324 1 chr3D.!!$R1 2323
1 TraesCS3D01G209000 chr3D 276112483 276113724 1241 True 2266.000000 2266 99.597000 1 1242 1 chr3D.!!$R2 1241
2 TraesCS3D01G209000 chr3B 375173048 375174982 1934 False 874.666667 1624 94.958667 290 2047 3 chr3B.!!$F1 1757
3 TraesCS3D01G209000 chr3A 364139593 364140248 655 False 985.000000 985 93.572000 732 1400 1 chr3A.!!$F1 668
4 TraesCS3D01G209000 chr3A 364132911 364133798 887 False 503.500000 643 91.423500 1 734 2 chr3A.!!$F2 733

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
211 213 1.199097 CCGGGGTGATGTTTTCTTTCG 59.801 52.381 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2388 0.027979 TGTATAGCACCGACGCGTAC 59.972 55.0 13.97 3.47 36.85 3.67 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
211 213 1.199097 CCGGGGTGATGTTTTCTTTCG 59.801 52.381 0.00 0.00 0.00 3.46
1335 1504 2.989166 ACGCTTGTAGTTAAACGCCTAC 59.011 45.455 0.00 0.00 35.25 3.18
1373 1542 5.237779 TGTTTCGTTTTTCCAGATGTAGTCC 59.762 40.000 0.00 0.00 0.00 3.85
1501 1699 1.068588 GGTGTTTGGTTCAGGAAAGGC 59.931 52.381 0.00 0.00 0.00 4.35
1703 1901 0.179108 GAATCGAACCCTGACCTCGG 60.179 60.000 0.00 0.00 33.44 4.63
1721 1919 1.659098 CGGAATCCGTGAAACTGCTAC 59.341 52.381 14.46 0.00 42.73 3.58
1722 1920 2.674177 CGGAATCCGTGAAACTGCTACT 60.674 50.000 14.46 0.00 42.73 2.57
1724 1922 4.113354 GGAATCCGTGAAACTGCTACTAG 58.887 47.826 0.00 0.00 31.75 2.57
1725 1923 4.381718 GGAATCCGTGAAACTGCTACTAGT 60.382 45.833 0.00 0.00 31.75 2.57
1726 1924 5.163581 GGAATCCGTGAAACTGCTACTAGTA 60.164 44.000 1.89 1.89 31.75 1.82
1727 1925 4.959596 TCCGTGAAACTGCTACTAGTAG 57.040 45.455 23.25 23.25 33.91 2.57
1834 2032 0.099436 GTGGAAATCAGACGCCATGC 59.901 55.000 0.00 0.00 32.26 4.06
1866 2064 2.893637 CGGGTTCCACTCACTATTCAG 58.106 52.381 0.00 0.00 0.00 3.02
1867 2065 2.233922 CGGGTTCCACTCACTATTCAGT 59.766 50.000 0.00 0.00 34.42 3.41
1868 2066 3.306780 CGGGTTCCACTCACTATTCAGTT 60.307 47.826 0.00 0.00 30.46 3.16
1869 2067 4.081862 CGGGTTCCACTCACTATTCAGTTA 60.082 45.833 0.00 0.00 30.46 2.24
1870 2068 5.568023 CGGGTTCCACTCACTATTCAGTTAA 60.568 44.000 0.00 0.00 30.46 2.01
1871 2069 5.875359 GGGTTCCACTCACTATTCAGTTAAG 59.125 44.000 0.00 0.00 30.46 1.85
1872 2070 6.465084 GGTTCCACTCACTATTCAGTTAAGT 58.535 40.000 0.00 0.00 30.46 2.24
1873 2071 6.935208 GGTTCCACTCACTATTCAGTTAAGTT 59.065 38.462 0.00 0.00 30.46 2.66
1874 2072 7.095187 GGTTCCACTCACTATTCAGTTAAGTTG 60.095 40.741 0.00 0.00 30.46 3.16
1875 2073 5.932303 TCCACTCACTATTCAGTTAAGTTGC 59.068 40.000 0.00 0.00 30.46 4.17
1876 2074 5.700832 CCACTCACTATTCAGTTAAGTTGCA 59.299 40.000 0.00 0.00 30.46 4.08
1877 2075 6.128445 CCACTCACTATTCAGTTAAGTTGCAG 60.128 42.308 0.00 0.00 30.46 4.41
1878 2076 6.425114 CACTCACTATTCAGTTAAGTTGCAGT 59.575 38.462 0.00 0.00 30.46 4.40
1879 2077 6.425114 ACTCACTATTCAGTTAAGTTGCAGTG 59.575 38.462 0.00 0.00 30.46 3.66
1880 2078 5.700832 TCACTATTCAGTTAAGTTGCAGTGG 59.299 40.000 0.00 0.00 33.41 4.00
1881 2079 5.003804 ACTATTCAGTTAAGTTGCAGTGGG 58.996 41.667 0.00 0.00 0.00 4.61
1882 2080 3.290948 TTCAGTTAAGTTGCAGTGGGT 57.709 42.857 0.00 0.00 0.00 4.51
1883 2081 2.571212 TCAGTTAAGTTGCAGTGGGTG 58.429 47.619 0.00 0.00 0.00 4.61
1884 2082 1.608590 CAGTTAAGTTGCAGTGGGTGG 59.391 52.381 0.00 0.00 0.00 4.61
1885 2083 0.958822 GTTAAGTTGCAGTGGGTGGG 59.041 55.000 0.00 0.00 0.00 4.61
1886 2084 0.178975 TTAAGTTGCAGTGGGTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
1887 2085 2.075355 TAAGTTGCAGTGGGTGGGGG 62.075 60.000 0.00 0.00 0.00 5.40
1888 2086 4.218686 GTTGCAGTGGGTGGGGGT 62.219 66.667 0.00 0.00 0.00 4.95
1889 2087 4.217210 TTGCAGTGGGTGGGGGTG 62.217 66.667 0.00 0.00 0.00 4.61
1915 2254 2.570302 GGTGAAACTAGGGCTTGAGGTA 59.430 50.000 0.00 0.00 36.74 3.08
1939 2278 1.296727 ATAAAACTAGGCTTCGCGGC 58.703 50.000 6.13 1.57 38.75 6.53
1961 2300 2.224066 CGGCTACAATTAGTGGAGGAGG 60.224 54.545 0.00 0.00 38.83 4.30
1988 2327 1.207089 TGCAGAGTTAGCGGCAACTAT 59.793 47.619 14.70 10.69 38.86 2.12
1999 2338 2.746472 GCGGCAACTATTTGGAGGAGAT 60.746 50.000 0.00 0.00 32.81 2.75
2048 2387 2.819595 CTCCCCCGACGCACATTG 60.820 66.667 0.00 0.00 0.00 2.82
2049 2388 4.402528 TCCCCCGACGCACATTGG 62.403 66.667 0.00 0.00 0.00 3.16
2050 2389 4.715523 CCCCCGACGCACATTGGT 62.716 66.667 0.00 0.00 0.00 3.67
2051 2390 2.266372 CCCCGACGCACATTGGTA 59.734 61.111 0.00 0.00 0.00 3.25
2052 2391 2.104253 CCCCGACGCACATTGGTAC 61.104 63.158 0.00 0.00 0.00 3.34
2053 2392 2.449525 CCCGACGCACATTGGTACG 61.450 63.158 0.00 0.00 39.68 3.67
2054 2393 2.394136 CGACGCACATTGGTACGC 59.606 61.111 0.00 0.00 37.29 4.42
2057 2396 2.394136 CGCACATTGGTACGCGTC 59.606 61.111 18.63 7.69 42.66 5.19
2058 2397 2.394136 GCACATTGGTACGCGTCG 59.606 61.111 18.63 0.60 0.00 5.12
2059 2398 3.077705 CACATTGGTACGCGTCGG 58.922 61.111 18.63 2.31 0.00 4.79
2060 2399 1.735198 CACATTGGTACGCGTCGGT 60.735 57.895 18.63 3.03 0.00 4.69
2061 2400 1.735198 ACATTGGTACGCGTCGGTG 60.735 57.895 18.63 11.64 0.00 4.94
2062 2401 2.812178 ATTGGTACGCGTCGGTGC 60.812 61.111 18.63 1.73 0.00 5.01
2063 2402 3.291101 ATTGGTACGCGTCGGTGCT 62.291 57.895 18.63 0.00 0.00 4.40
2064 2403 1.936436 ATTGGTACGCGTCGGTGCTA 61.936 55.000 18.63 0.00 0.00 3.49
2065 2404 1.936436 TTGGTACGCGTCGGTGCTAT 61.936 55.000 18.63 0.00 0.00 2.97
2066 2405 1.094650 TGGTACGCGTCGGTGCTATA 61.095 55.000 18.63 0.00 0.00 1.31
2067 2406 0.658536 GGTACGCGTCGGTGCTATAC 60.659 60.000 18.63 4.42 0.00 1.47
2068 2407 0.027979 GTACGCGTCGGTGCTATACA 59.972 55.000 18.63 0.00 0.00 2.29
2069 2408 0.731994 TACGCGTCGGTGCTATACAA 59.268 50.000 18.63 0.00 0.00 2.41
2070 2409 0.109179 ACGCGTCGGTGCTATACAAA 60.109 50.000 5.58 0.00 0.00 2.83
2071 2410 0.296642 CGCGTCGGTGCTATACAAAC 59.703 55.000 0.00 0.00 0.00 2.93
2072 2411 0.296642 GCGTCGGTGCTATACAAACG 59.703 55.000 0.00 0.00 39.95 3.60
2073 2412 0.918619 CGTCGGTGCTATACAAACGG 59.081 55.000 0.00 0.00 36.02 4.44
2074 2413 1.733389 CGTCGGTGCTATACAAACGGT 60.733 52.381 0.00 0.00 36.02 4.83
2075 2414 2.340337 GTCGGTGCTATACAAACGGTT 58.660 47.619 0.00 0.00 33.21 4.44
2076 2415 2.738314 GTCGGTGCTATACAAACGGTTT 59.262 45.455 0.00 0.00 33.21 3.27
2077 2416 3.187022 GTCGGTGCTATACAAACGGTTTT 59.813 43.478 2.79 0.00 33.21 2.43
2078 2417 4.388469 GTCGGTGCTATACAAACGGTTTTA 59.612 41.667 2.79 1.29 33.21 1.52
2079 2418 4.993584 TCGGTGCTATACAAACGGTTTTAA 59.006 37.500 2.79 0.00 33.21 1.52
2080 2419 5.468072 TCGGTGCTATACAAACGGTTTTAAA 59.532 36.000 2.79 0.00 33.21 1.52
2081 2420 5.564882 CGGTGCTATACAAACGGTTTTAAAC 59.435 40.000 2.79 0.00 0.00 2.01
2092 2431 3.374220 GGTTTTAAACCCCTTTCCACG 57.626 47.619 15.49 0.00 46.12 4.94
2093 2432 2.957680 GGTTTTAAACCCCTTTCCACGA 59.042 45.455 15.49 0.00 46.12 4.35
2094 2433 3.243501 GGTTTTAAACCCCTTTCCACGAC 60.244 47.826 15.49 0.00 46.12 4.34
2095 2434 1.881591 TTAAACCCCTTTCCACGACG 58.118 50.000 0.00 0.00 0.00 5.12
2096 2435 0.035176 TAAACCCCTTTCCACGACGG 59.965 55.000 0.00 0.00 0.00 4.79
2097 2436 3.837570 AACCCCTTTCCACGACGGC 62.838 63.158 0.00 0.00 33.14 5.68
2098 2437 4.323477 CCCCTTTCCACGACGGCA 62.323 66.667 0.00 0.00 33.14 5.69
2099 2438 2.046314 CCCTTTCCACGACGGCAT 60.046 61.111 0.00 0.00 33.14 4.40
2100 2439 1.674322 CCCTTTCCACGACGGCATT 60.674 57.895 0.00 0.00 33.14 3.56
2101 2440 1.241315 CCCTTTCCACGACGGCATTT 61.241 55.000 0.00 0.00 33.14 2.32
2102 2441 0.109781 CCTTTCCACGACGGCATTTG 60.110 55.000 0.00 0.00 33.14 2.32
2103 2442 0.109781 CTTTCCACGACGGCATTTGG 60.110 55.000 0.00 0.00 33.14 3.28
2104 2443 0.535328 TTTCCACGACGGCATTTGGA 60.535 50.000 0.00 0.00 36.31 3.53
2105 2444 0.535328 TTCCACGACGGCATTTGGAA 60.535 50.000 11.13 11.13 44.21 3.53
2106 2445 1.209127 CCACGACGGCATTTGGAAC 59.791 57.895 0.00 0.00 0.00 3.62
2107 2446 1.234615 CCACGACGGCATTTGGAACT 61.235 55.000 0.00 0.00 0.00 3.01
2108 2447 0.110238 CACGACGGCATTTGGAACTG 60.110 55.000 0.00 0.00 0.00 3.16
2109 2448 0.534203 ACGACGGCATTTGGAACTGT 60.534 50.000 0.00 0.00 0.00 3.55
2110 2449 0.165944 CGACGGCATTTGGAACTGTC 59.834 55.000 0.00 0.00 36.54 3.51
2111 2450 0.165944 GACGGCATTTGGAACTGTCG 59.834 55.000 2.60 2.60 45.46 4.35
2112 2451 1.154225 CGGCATTTGGAACTGTCGC 60.154 57.895 0.00 0.00 33.37 5.19
2113 2452 1.212751 GGCATTTGGAACTGTCGCC 59.787 57.895 0.00 0.00 0.00 5.54
2114 2453 1.244019 GGCATTTGGAACTGTCGCCT 61.244 55.000 0.00 0.00 35.17 5.52
2115 2454 1.448985 GCATTTGGAACTGTCGCCTA 58.551 50.000 2.04 0.00 0.00 3.93
2116 2455 1.398390 GCATTTGGAACTGTCGCCTAG 59.602 52.381 2.04 0.00 0.00 3.02
2117 2456 2.699954 CATTTGGAACTGTCGCCTAGT 58.300 47.619 2.04 0.00 0.00 2.57
2118 2457 2.163818 TTTGGAACTGTCGCCTAGTG 57.836 50.000 2.04 0.00 0.00 2.74
2119 2458 1.334160 TTGGAACTGTCGCCTAGTGA 58.666 50.000 2.04 0.00 0.00 3.41
2120 2459 0.888619 TGGAACTGTCGCCTAGTGAG 59.111 55.000 2.04 0.00 0.00 3.51
2121 2460 0.889306 GGAACTGTCGCCTAGTGAGT 59.111 55.000 0.00 0.00 0.00 3.41
2122 2461 1.402984 GGAACTGTCGCCTAGTGAGTG 60.403 57.143 0.00 0.00 0.00 3.51
2123 2462 1.540267 GAACTGTCGCCTAGTGAGTGA 59.460 52.381 0.00 0.00 0.00 3.41
2124 2463 0.882474 ACTGTCGCCTAGTGAGTGAC 59.118 55.000 4.72 4.72 43.49 3.67
2125 2464 0.179187 CTGTCGCCTAGTGAGTGACG 60.179 60.000 6.67 0.00 45.60 4.35
2126 2465 1.136984 GTCGCCTAGTGAGTGACGG 59.863 63.158 0.00 0.00 35.27 4.79
2127 2466 2.044555 TCGCCTAGTGAGTGACGGG 61.045 63.158 0.00 0.00 0.00 5.28
2128 2467 2.893398 GCCTAGTGAGTGACGGGG 59.107 66.667 0.00 0.00 0.00 5.73
2129 2468 1.681327 GCCTAGTGAGTGACGGGGA 60.681 63.158 0.00 0.00 0.00 4.81
2130 2469 1.043673 GCCTAGTGAGTGACGGGGAT 61.044 60.000 0.00 0.00 0.00 3.85
2131 2470 1.753141 GCCTAGTGAGTGACGGGGATA 60.753 57.143 0.00 0.00 0.00 2.59
2132 2471 2.231529 CCTAGTGAGTGACGGGGATAG 58.768 57.143 0.00 0.00 0.00 2.08
2133 2472 2.231529 CTAGTGAGTGACGGGGATAGG 58.768 57.143 0.00 0.00 0.00 2.57
2134 2473 0.397254 AGTGAGTGACGGGGATAGGG 60.397 60.000 0.00 0.00 0.00 3.53
2135 2474 1.075525 TGAGTGACGGGGATAGGGG 60.076 63.158 0.00 0.00 0.00 4.79
2136 2475 1.837499 GAGTGACGGGGATAGGGGG 60.837 68.421 0.00 0.00 0.00 5.40
2153 2492 3.468063 GGTCCTTCCCACACGACT 58.532 61.111 0.00 0.00 0.00 4.18
2154 2493 1.292541 GGTCCTTCCCACACGACTC 59.707 63.158 0.00 0.00 0.00 3.36
2155 2494 1.469335 GGTCCTTCCCACACGACTCA 61.469 60.000 0.00 0.00 0.00 3.41
2156 2495 0.038159 GTCCTTCCCACACGACTCAG 60.038 60.000 0.00 0.00 0.00 3.35
2157 2496 0.178973 TCCTTCCCACACGACTCAGA 60.179 55.000 0.00 0.00 0.00 3.27
2158 2497 0.679505 CCTTCCCACACGACTCAGAA 59.320 55.000 0.00 0.00 0.00 3.02
2159 2498 1.070134 CCTTCCCACACGACTCAGAAA 59.930 52.381 0.00 0.00 0.00 2.52
2160 2499 2.135933 CTTCCCACACGACTCAGAAAC 58.864 52.381 0.00 0.00 0.00 2.78
2161 2500 0.391597 TCCCACACGACTCAGAAACC 59.608 55.000 0.00 0.00 0.00 3.27
2162 2501 0.944311 CCCACACGACTCAGAAACCG 60.944 60.000 0.00 0.00 0.00 4.44
2163 2502 0.249322 CCACACGACTCAGAAACCGT 60.249 55.000 0.00 0.00 35.46 4.83
2164 2503 1.129326 CACACGACTCAGAAACCGTC 58.871 55.000 0.00 0.00 32.50 4.79
2166 2505 4.148230 CGACTCAGAAACCGTCGG 57.852 61.111 10.48 10.48 44.75 4.79
2167 2506 1.443872 CGACTCAGAAACCGTCGGG 60.444 63.158 17.28 0.00 44.75 5.14
2168 2507 1.080025 GACTCAGAAACCGTCGGGG 60.080 63.158 17.28 0.00 43.62 5.73
2169 2508 1.530013 GACTCAGAAACCGTCGGGGA 61.530 60.000 17.28 4.13 39.97 4.81
2170 2509 0.903454 ACTCAGAAACCGTCGGGGAT 60.903 55.000 17.28 0.20 39.97 3.85
2171 2510 1.108776 CTCAGAAACCGTCGGGGATA 58.891 55.000 17.28 0.00 39.97 2.59
2172 2511 1.067212 CTCAGAAACCGTCGGGGATAG 59.933 57.143 17.28 2.55 39.97 2.08
2173 2512 0.104304 CAGAAACCGTCGGGGATAGG 59.896 60.000 17.28 0.00 39.97 2.57
2174 2513 1.047034 AGAAACCGTCGGGGATAGGG 61.047 60.000 17.28 0.00 39.97 3.53
2175 2514 1.002017 AAACCGTCGGGGATAGGGA 59.998 57.895 17.28 0.00 39.97 4.20
2176 2515 1.047034 AAACCGTCGGGGATAGGGAG 61.047 60.000 17.28 0.00 39.97 4.30
2177 2516 3.303928 CCGTCGGGGATAGGGAGC 61.304 72.222 2.34 0.00 38.47 4.70
2178 2517 3.303928 CGTCGGGGATAGGGAGCC 61.304 72.222 0.00 0.00 0.00 4.70
2179 2518 2.201771 GTCGGGGATAGGGAGCCT 59.798 66.667 0.00 0.00 37.71 4.58
2180 2519 1.459730 GTCGGGGATAGGGAGCCTT 60.460 63.158 0.00 0.00 34.61 4.35
2181 2520 1.459539 TCGGGGATAGGGAGCCTTG 60.460 63.158 0.00 0.00 34.61 3.61
2182 2521 1.459539 CGGGGATAGGGAGCCTTGA 60.460 63.158 0.00 0.00 34.61 3.02
2183 2522 0.838122 CGGGGATAGGGAGCCTTGAT 60.838 60.000 0.00 0.00 34.61 2.57
2184 2523 0.695347 GGGGATAGGGAGCCTTGATG 59.305 60.000 0.00 0.00 34.61 3.07
2185 2524 0.037447 GGGATAGGGAGCCTTGATGC 59.963 60.000 0.00 0.00 34.61 3.91
2186 2525 0.767375 GGATAGGGAGCCTTGATGCA 59.233 55.000 0.00 0.00 34.61 3.96
2187 2526 1.353694 GGATAGGGAGCCTTGATGCAT 59.646 52.381 0.00 0.00 34.61 3.96
2188 2527 2.573462 GGATAGGGAGCCTTGATGCATA 59.427 50.000 0.00 0.00 34.61 3.14
2189 2528 3.604582 GATAGGGAGCCTTGATGCATAC 58.395 50.000 0.00 0.00 34.61 2.39
2190 2529 1.216064 AGGGAGCCTTGATGCATACA 58.784 50.000 0.00 0.00 0.00 2.29
2191 2530 1.142465 AGGGAGCCTTGATGCATACAG 59.858 52.381 0.00 0.00 0.00 2.74
2192 2531 1.133976 GGGAGCCTTGATGCATACAGT 60.134 52.381 0.00 0.00 0.00 3.55
2193 2532 2.648059 GGAGCCTTGATGCATACAGTT 58.352 47.619 0.00 0.00 0.00 3.16
2194 2533 2.357009 GGAGCCTTGATGCATACAGTTG 59.643 50.000 0.00 0.00 0.00 3.16
2195 2534 3.012518 GAGCCTTGATGCATACAGTTGT 58.987 45.455 0.00 0.00 0.00 3.32
2196 2535 3.012518 AGCCTTGATGCATACAGTTGTC 58.987 45.455 0.00 0.00 0.00 3.18
2197 2536 2.098117 GCCTTGATGCATACAGTTGTCC 59.902 50.000 0.00 0.00 0.00 4.02
2198 2537 2.684881 CCTTGATGCATACAGTTGTCCC 59.315 50.000 0.00 0.00 0.00 4.46
2199 2538 3.614092 CTTGATGCATACAGTTGTCCCT 58.386 45.455 0.00 0.00 0.00 4.20
2200 2539 4.384098 CCTTGATGCATACAGTTGTCCCTA 60.384 45.833 0.00 0.00 0.00 3.53
2201 2540 5.371526 CTTGATGCATACAGTTGTCCCTAT 58.628 41.667 0.00 0.00 0.00 2.57
2202 2541 6.464322 CCTTGATGCATACAGTTGTCCCTATA 60.464 42.308 0.00 0.00 0.00 1.31
2203 2542 6.686484 TGATGCATACAGTTGTCCCTATAT 57.314 37.500 0.00 0.00 0.00 0.86
2204 2543 7.790782 TGATGCATACAGTTGTCCCTATATA 57.209 36.000 0.00 0.00 0.00 0.86
2205 2544 8.201242 TGATGCATACAGTTGTCCCTATATAA 57.799 34.615 0.00 0.00 0.00 0.98
2206 2545 8.094548 TGATGCATACAGTTGTCCCTATATAAC 58.905 37.037 0.00 0.00 0.00 1.89
2207 2546 6.765403 TGCATACAGTTGTCCCTATATAACC 58.235 40.000 0.00 0.00 0.00 2.85
2208 2547 5.867716 GCATACAGTTGTCCCTATATAACCG 59.132 44.000 0.00 0.00 0.00 4.44
2209 2548 6.517864 GCATACAGTTGTCCCTATATAACCGT 60.518 42.308 0.00 0.00 0.00 4.83
2210 2549 5.945144 ACAGTTGTCCCTATATAACCGTT 57.055 39.130 0.00 0.00 0.00 4.44
2211 2550 6.303903 ACAGTTGTCCCTATATAACCGTTT 57.696 37.500 0.00 0.00 0.00 3.60
2212 2551 6.343703 ACAGTTGTCCCTATATAACCGTTTC 58.656 40.000 0.00 0.00 0.00 2.78
2213 2552 5.756833 CAGTTGTCCCTATATAACCGTTTCC 59.243 44.000 0.00 0.00 0.00 3.13
2214 2553 4.589216 TGTCCCTATATAACCGTTTCCG 57.411 45.455 0.00 0.00 0.00 4.30
2215 2554 4.214310 TGTCCCTATATAACCGTTTCCGA 58.786 43.478 0.00 0.00 35.63 4.55
2216 2555 4.834496 TGTCCCTATATAACCGTTTCCGAT 59.166 41.667 0.00 0.00 35.63 4.18
2217 2556 6.009589 TGTCCCTATATAACCGTTTCCGATA 58.990 40.000 0.00 0.00 35.63 2.92
2218 2557 6.664816 TGTCCCTATATAACCGTTTCCGATAT 59.335 38.462 0.00 0.00 35.63 1.63
2219 2558 7.148018 TGTCCCTATATAACCGTTTCCGATATC 60.148 40.741 0.00 0.00 35.63 1.63
2220 2559 7.067981 GTCCCTATATAACCGTTTCCGATATCT 59.932 40.741 0.34 0.00 35.63 1.98
2221 2560 7.284034 TCCCTATATAACCGTTTCCGATATCTC 59.716 40.741 0.34 0.00 35.63 2.75
2222 2561 7.130917 CCTATATAACCGTTTCCGATATCTCG 58.869 42.308 0.34 0.00 44.62 4.04
2236 2575 5.704217 GATATCTCGAATATCCCAAACGC 57.296 43.478 12.72 0.00 0.00 4.84
2237 2576 3.753294 ATCTCGAATATCCCAAACGCT 57.247 42.857 0.00 0.00 0.00 5.07
2238 2577 3.536956 TCTCGAATATCCCAAACGCTT 57.463 42.857 0.00 0.00 0.00 4.68
2239 2578 3.454375 TCTCGAATATCCCAAACGCTTC 58.546 45.455 0.00 0.00 0.00 3.86
2240 2579 2.198406 TCGAATATCCCAAACGCTTCG 58.802 47.619 0.00 0.00 37.43 3.79
2241 2580 1.931172 CGAATATCCCAAACGCTTCGT 59.069 47.619 0.00 0.00 43.97 3.85
2242 2581 2.034001 CGAATATCCCAAACGCTTCGTC 60.034 50.000 0.00 0.00 39.99 4.20
2243 2582 1.949465 ATATCCCAAACGCTTCGTCC 58.051 50.000 0.00 0.00 39.99 4.79
2244 2583 0.899720 TATCCCAAACGCTTCGTCCT 59.100 50.000 0.00 0.00 39.99 3.85
2245 2584 0.036306 ATCCCAAACGCTTCGTCCTT 59.964 50.000 0.00 0.00 39.99 3.36
2246 2585 0.882927 TCCCAAACGCTTCGTCCTTG 60.883 55.000 0.00 0.00 39.99 3.61
2247 2586 1.082104 CCAAACGCTTCGTCCTTGC 60.082 57.895 0.00 0.00 39.99 4.01
2248 2587 1.507141 CCAAACGCTTCGTCCTTGCT 61.507 55.000 0.00 0.00 39.99 3.91
2249 2588 1.144969 CAAACGCTTCGTCCTTGCTA 58.855 50.000 0.00 0.00 39.99 3.49
2250 2589 1.136336 CAAACGCTTCGTCCTTGCTAC 60.136 52.381 0.00 0.00 39.99 3.58
2251 2590 0.317479 AACGCTTCGTCCTTGCTACT 59.683 50.000 0.00 0.00 39.99 2.57
2252 2591 0.109226 ACGCTTCGTCCTTGCTACTC 60.109 55.000 0.00 0.00 33.69 2.59
2253 2592 1.134530 CGCTTCGTCCTTGCTACTCG 61.135 60.000 0.00 0.00 0.00 4.18
2254 2593 0.109226 GCTTCGTCCTTGCTACTCGT 60.109 55.000 0.00 0.00 0.00 4.18
2255 2594 1.669211 GCTTCGTCCTTGCTACTCGTT 60.669 52.381 0.00 0.00 0.00 3.85
2256 2595 2.673833 CTTCGTCCTTGCTACTCGTTT 58.326 47.619 0.00 0.00 0.00 3.60
2257 2596 2.060326 TCGTCCTTGCTACTCGTTTG 57.940 50.000 0.00 0.00 0.00 2.93
2258 2597 1.338973 TCGTCCTTGCTACTCGTTTGT 59.661 47.619 0.00 0.00 0.00 2.83
2259 2598 1.455786 CGTCCTTGCTACTCGTTTGTG 59.544 52.381 0.00 0.00 0.00 3.33
2260 2599 1.194772 GTCCTTGCTACTCGTTTGTGC 59.805 52.381 0.00 0.00 0.00 4.57
2261 2600 1.070134 TCCTTGCTACTCGTTTGTGCT 59.930 47.619 0.00 0.00 0.00 4.40
2262 2601 1.461127 CCTTGCTACTCGTTTGTGCTC 59.539 52.381 0.00 0.00 0.00 4.26
2263 2602 1.125021 CTTGCTACTCGTTTGTGCTCG 59.875 52.381 0.00 0.00 0.00 5.03
2264 2603 1.282248 TGCTACTCGTTTGTGCTCGC 61.282 55.000 0.00 0.00 0.00 5.03
2265 2604 1.282248 GCTACTCGTTTGTGCTCGCA 61.282 55.000 0.00 0.00 0.00 5.10
2266 2605 1.350193 CTACTCGTTTGTGCTCGCAT 58.650 50.000 0.00 0.00 0.00 4.73
2267 2606 1.726791 CTACTCGTTTGTGCTCGCATT 59.273 47.619 0.00 0.00 0.00 3.56
2268 2607 0.235665 ACTCGTTTGTGCTCGCATTG 59.764 50.000 0.00 0.00 0.00 2.82
2269 2608 1.061799 CTCGTTTGTGCTCGCATTGC 61.062 55.000 0.00 0.00 0.00 3.56
2270 2609 2.082366 CGTTTGTGCTCGCATTGCC 61.082 57.895 2.41 0.00 0.00 4.52
2271 2610 1.007502 GTTTGTGCTCGCATTGCCA 60.008 52.632 2.41 0.00 0.00 4.92
2272 2611 0.388907 GTTTGTGCTCGCATTGCCAT 60.389 50.000 2.41 0.00 0.00 4.40
2273 2612 0.109179 TTTGTGCTCGCATTGCCATC 60.109 50.000 2.41 0.00 0.00 3.51
2274 2613 2.023741 GTGCTCGCATTGCCATCG 59.976 61.111 2.41 0.00 0.00 3.84
2275 2614 3.879682 TGCTCGCATTGCCATCGC 61.880 61.111 2.41 1.45 0.00 4.58
2276 2615 3.879682 GCTCGCATTGCCATCGCA 61.880 61.111 2.41 0.00 45.49 5.10
2284 2623 3.381983 TGCCATCGCAGTCGGAGT 61.382 61.111 0.00 0.00 41.12 3.85
2285 2624 2.125512 GCCATCGCAGTCGGAGTT 60.126 61.111 0.00 0.00 36.13 3.01
2286 2625 1.741770 GCCATCGCAGTCGGAGTTT 60.742 57.895 0.00 0.00 36.13 2.66
2287 2626 1.298859 GCCATCGCAGTCGGAGTTTT 61.299 55.000 0.00 0.00 36.13 2.43
2288 2627 0.443869 CCATCGCAGTCGGAGTTTTG 59.556 55.000 0.00 0.00 36.13 2.44
2289 2628 1.148310 CATCGCAGTCGGAGTTTTGT 58.852 50.000 0.00 0.00 36.13 2.83
2290 2629 1.136252 CATCGCAGTCGGAGTTTTGTG 60.136 52.381 0.00 0.00 36.13 3.33
2291 2630 0.878523 TCGCAGTCGGAGTTTTGTGG 60.879 55.000 0.00 0.00 36.13 4.17
2292 2631 1.157870 CGCAGTCGGAGTTTTGTGGT 61.158 55.000 0.00 0.00 0.00 4.16
2293 2632 1.021968 GCAGTCGGAGTTTTGTGGTT 58.978 50.000 0.00 0.00 0.00 3.67
2294 2633 1.404035 GCAGTCGGAGTTTTGTGGTTT 59.596 47.619 0.00 0.00 0.00 3.27
2295 2634 2.159296 GCAGTCGGAGTTTTGTGGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
2296 2635 3.065648 GCAGTCGGAGTTTTGTGGTTTTA 59.934 43.478 0.00 0.00 0.00 1.52
2297 2636 4.594136 CAGTCGGAGTTTTGTGGTTTTAC 58.406 43.478 0.00 0.00 0.00 2.01
2298 2637 3.628942 AGTCGGAGTTTTGTGGTTTTACC 59.371 43.478 0.00 0.00 39.22 2.85
2299 2638 3.628942 GTCGGAGTTTTGTGGTTTTACCT 59.371 43.478 0.00 0.00 39.58 3.08
2300 2639 4.815846 GTCGGAGTTTTGTGGTTTTACCTA 59.184 41.667 0.00 0.00 39.58 3.08
2301 2640 5.296531 GTCGGAGTTTTGTGGTTTTACCTAA 59.703 40.000 0.00 0.00 39.58 2.69
2302 2641 5.884792 TCGGAGTTTTGTGGTTTTACCTAAA 59.115 36.000 0.00 0.00 39.58 1.85
2303 2642 6.376581 TCGGAGTTTTGTGGTTTTACCTAAAA 59.623 34.615 0.00 0.00 39.58 1.52
2313 2652 5.977489 GTTTTACCTAAAACCAGGCAGAT 57.023 39.130 8.83 0.00 45.62 2.90
2314 2653 6.340962 GTTTTACCTAAAACCAGGCAGATT 57.659 37.500 8.83 0.00 45.62 2.40
2315 2654 6.387465 GTTTTACCTAAAACCAGGCAGATTC 58.613 40.000 8.83 0.00 45.62 2.52
2316 2655 3.087370 ACCTAAAACCAGGCAGATTCC 57.913 47.619 0.00 0.00 39.53 3.01
2317 2656 2.378547 ACCTAAAACCAGGCAGATTCCA 59.621 45.455 0.00 0.00 39.53 3.53
2318 2657 3.019564 CCTAAAACCAGGCAGATTCCAG 58.980 50.000 0.00 0.00 0.00 3.86
2319 2658 2.978156 AAAACCAGGCAGATTCCAGA 57.022 45.000 0.00 0.00 0.00 3.86
2320 2659 2.206576 AAACCAGGCAGATTCCAGAC 57.793 50.000 0.00 0.00 0.00 3.51
2321 2660 1.067295 AACCAGGCAGATTCCAGACA 58.933 50.000 0.00 0.00 0.00 3.41
2322 2661 0.326264 ACCAGGCAGATTCCAGACAC 59.674 55.000 0.00 0.00 0.00 3.67
2323 2662 0.742281 CCAGGCAGATTCCAGACACG 60.742 60.000 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
211 213 2.149973 AACCCATGAAATCTCAGCCC 57.850 50.000 0.00 0.00 34.23 5.19
1246 1414 3.112709 GGAGTTGCTCCGCGTCAC 61.113 66.667 4.92 0.00 41.08 3.67
1373 1542 8.622948 AACAGACCAAGTAAGGAAGAAATAAG 57.377 34.615 0.00 0.00 0.00 1.73
1501 1699 3.567576 TCCCACATTGCGTTTACATTG 57.432 42.857 0.00 0.00 0.00 2.82
1703 1901 4.745649 ACTAGTAGCAGTTTCACGGATTC 58.254 43.478 0.00 0.00 0.00 2.52
1721 1919 5.239525 GGGATTGCCTAAAACATGCTACTAG 59.760 44.000 0.00 0.00 0.00 2.57
1722 1920 5.130350 GGGATTGCCTAAAACATGCTACTA 58.870 41.667 0.00 0.00 0.00 1.82
1724 1922 3.243068 CGGGATTGCCTAAAACATGCTAC 60.243 47.826 0.00 0.00 0.00 3.58
1725 1923 2.948979 CGGGATTGCCTAAAACATGCTA 59.051 45.455 0.00 0.00 0.00 3.49
1726 1924 1.750778 CGGGATTGCCTAAAACATGCT 59.249 47.619 0.00 0.00 0.00 3.79
1727 1925 1.202405 CCGGGATTGCCTAAAACATGC 60.202 52.381 0.00 0.00 0.00 4.06
1728 1926 2.099405 ACCGGGATTGCCTAAAACATG 58.901 47.619 6.32 0.00 0.00 3.21
1729 1927 2.525105 ACCGGGATTGCCTAAAACAT 57.475 45.000 6.32 0.00 0.00 2.71
1730 1928 2.296073 AACCGGGATTGCCTAAAACA 57.704 45.000 6.32 0.00 0.00 2.83
1731 1929 4.202080 GGATAAACCGGGATTGCCTAAAAC 60.202 45.833 6.32 0.00 0.00 2.43
1732 1930 3.955551 GGATAAACCGGGATTGCCTAAAA 59.044 43.478 6.32 0.00 0.00 1.52
1866 2064 0.958822 CCCACCCACTGCAACTTAAC 59.041 55.000 0.00 0.00 0.00 2.01
1867 2065 0.178975 CCCCACCCACTGCAACTTAA 60.179 55.000 0.00 0.00 0.00 1.85
1868 2066 1.458486 CCCCACCCACTGCAACTTA 59.542 57.895 0.00 0.00 0.00 2.24
1869 2067 2.198426 CCCCACCCACTGCAACTT 59.802 61.111 0.00 0.00 0.00 2.66
1870 2068 3.902112 CCCCCACCCACTGCAACT 61.902 66.667 0.00 0.00 0.00 3.16
1871 2069 4.218686 ACCCCCACCCACTGCAAC 62.219 66.667 0.00 0.00 0.00 4.17
1872 2070 4.217210 CACCCCCACCCACTGCAA 62.217 66.667 0.00 0.00 0.00 4.08
1891 2089 0.323451 CAAGCCCTAGTTTCACCCCC 60.323 60.000 0.00 0.00 0.00 5.40
1892 2090 0.696501 TCAAGCCCTAGTTTCACCCC 59.303 55.000 0.00 0.00 0.00 4.95
1893 2091 1.340114 CCTCAAGCCCTAGTTTCACCC 60.340 57.143 0.00 0.00 0.00 4.61
1894 2092 1.351350 ACCTCAAGCCCTAGTTTCACC 59.649 52.381 0.00 0.00 0.00 4.02
1895 2093 2.861147 ACCTCAAGCCCTAGTTTCAC 57.139 50.000 0.00 0.00 0.00 3.18
1896 2094 2.838202 CCTACCTCAAGCCCTAGTTTCA 59.162 50.000 0.00 0.00 0.00 2.69
1897 2095 2.170817 CCCTACCTCAAGCCCTAGTTTC 59.829 54.545 0.00 0.00 0.00 2.78
1898 2096 2.197465 CCCTACCTCAAGCCCTAGTTT 58.803 52.381 0.00 0.00 0.00 2.66
1899 2097 1.365028 TCCCTACCTCAAGCCCTAGTT 59.635 52.381 0.00 0.00 0.00 2.24
1939 2278 1.760613 TCCTCCACTAATTGTAGCCGG 59.239 52.381 0.00 0.00 0.00 6.13
1940 2279 2.224066 CCTCCTCCACTAATTGTAGCCG 60.224 54.545 0.00 0.00 0.00 5.52
1961 2300 1.709147 CGCTAACTCTGCATGCCCAC 61.709 60.000 16.68 0.00 0.00 4.61
1988 2327 1.299648 CACCCGCATCTCCTCCAAA 59.700 57.895 0.00 0.00 0.00 3.28
1999 2338 2.992817 AATTGCTCCCAACACCCGCA 62.993 55.000 0.00 0.00 32.95 5.69
2044 2383 3.077705 CACCGACGCGTACCAATG 58.922 61.111 13.97 2.57 0.00 2.82
2045 2384 1.936436 TAGCACCGACGCGTACCAAT 61.936 55.000 13.97 0.00 36.85 3.16
2046 2385 1.936436 ATAGCACCGACGCGTACCAA 61.936 55.000 13.97 0.00 36.85 3.67
2048 2387 0.658536 GTATAGCACCGACGCGTACC 60.659 60.000 13.97 0.00 36.85 3.34
2049 2388 0.027979 TGTATAGCACCGACGCGTAC 59.972 55.000 13.97 3.47 36.85 3.67
2050 2389 0.731994 TTGTATAGCACCGACGCGTA 59.268 50.000 13.97 0.00 36.85 4.42
2051 2390 0.109179 TTTGTATAGCACCGACGCGT 60.109 50.000 13.85 13.85 36.85 6.01
2052 2391 0.296642 GTTTGTATAGCACCGACGCG 59.703 55.000 3.53 3.53 36.85 6.01
2053 2392 0.296642 CGTTTGTATAGCACCGACGC 59.703 55.000 0.00 0.00 30.90 5.19
2054 2393 0.918619 CCGTTTGTATAGCACCGACG 59.081 55.000 0.00 0.00 35.44 5.12
2055 2394 2.000429 ACCGTTTGTATAGCACCGAC 58.000 50.000 0.00 0.00 0.00 4.79
2056 2395 2.747396 AACCGTTTGTATAGCACCGA 57.253 45.000 0.00 0.00 0.00 4.69
2057 2396 3.817148 AAAACCGTTTGTATAGCACCG 57.183 42.857 0.00 0.00 0.00 4.94
2058 2397 5.858049 GGTTTAAAACCGTTTGTATAGCACC 59.142 40.000 0.00 0.00 42.62 5.01
2059 2398 6.916401 GGTTTAAAACCGTTTGTATAGCAC 57.084 37.500 0.00 0.00 42.62 4.40
2073 2412 3.548616 CGTCGTGGAAAGGGGTTTAAAAC 60.549 47.826 0.00 0.00 0.00 2.43
2074 2413 2.617774 CGTCGTGGAAAGGGGTTTAAAA 59.382 45.455 0.00 0.00 0.00 1.52
2075 2414 2.220313 CGTCGTGGAAAGGGGTTTAAA 58.780 47.619 0.00 0.00 0.00 1.52
2076 2415 1.542987 CCGTCGTGGAAAGGGGTTTAA 60.543 52.381 0.00 0.00 42.00 1.52
2077 2416 0.035176 CCGTCGTGGAAAGGGGTTTA 59.965 55.000 0.00 0.00 42.00 2.01
2078 2417 1.228033 CCGTCGTGGAAAGGGGTTT 60.228 57.895 0.00 0.00 42.00 3.27
2079 2418 2.428622 CCGTCGTGGAAAGGGGTT 59.571 61.111 0.00 0.00 42.00 4.11
2080 2419 4.324991 GCCGTCGTGGAAAGGGGT 62.325 66.667 0.51 0.00 42.00 4.95
2081 2420 3.622060 ATGCCGTCGTGGAAAGGGG 62.622 63.158 0.51 0.00 42.00 4.79
2082 2421 1.241315 AAATGCCGTCGTGGAAAGGG 61.241 55.000 0.51 0.00 42.00 3.95
2083 2422 0.109781 CAAATGCCGTCGTGGAAAGG 60.110 55.000 0.51 0.00 42.00 3.11
2084 2423 0.109781 CCAAATGCCGTCGTGGAAAG 60.110 55.000 0.51 0.00 42.00 2.62
2085 2424 0.535328 TCCAAATGCCGTCGTGGAAA 60.535 50.000 0.00 0.00 42.00 3.13
2086 2425 0.535328 TTCCAAATGCCGTCGTGGAA 60.535 50.000 9.51 9.51 45.62 3.53
2087 2426 1.071642 TTCCAAATGCCGTCGTGGA 59.928 52.632 0.00 0.00 42.00 4.02
2088 2427 1.209127 GTTCCAAATGCCGTCGTGG 59.791 57.895 0.00 0.00 42.50 4.94
2089 2428 0.110238 CAGTTCCAAATGCCGTCGTG 60.110 55.000 0.00 0.00 0.00 4.35
2090 2429 0.534203 ACAGTTCCAAATGCCGTCGT 60.534 50.000 0.00 0.00 0.00 4.34
2091 2430 0.165944 GACAGTTCCAAATGCCGTCG 59.834 55.000 0.00 0.00 0.00 5.12
2092 2431 0.165944 CGACAGTTCCAAATGCCGTC 59.834 55.000 0.00 0.00 0.00 4.79
2093 2432 1.852067 GCGACAGTTCCAAATGCCGT 61.852 55.000 0.00 0.00 32.64 5.68
2094 2433 1.154225 GCGACAGTTCCAAATGCCG 60.154 57.895 0.00 0.00 33.18 5.69
2095 2434 1.212751 GGCGACAGTTCCAAATGCC 59.787 57.895 0.00 0.00 0.00 4.40
2096 2435 1.398390 CTAGGCGACAGTTCCAAATGC 59.602 52.381 0.00 0.00 0.00 3.56
2097 2436 2.416547 CACTAGGCGACAGTTCCAAATG 59.583 50.000 0.00 0.00 0.00 2.32
2098 2437 2.301870 TCACTAGGCGACAGTTCCAAAT 59.698 45.455 0.00 0.00 0.00 2.32
2099 2438 1.689813 TCACTAGGCGACAGTTCCAAA 59.310 47.619 0.00 0.00 0.00 3.28
2100 2439 1.272490 CTCACTAGGCGACAGTTCCAA 59.728 52.381 0.00 0.00 0.00 3.53
2101 2440 0.888619 CTCACTAGGCGACAGTTCCA 59.111 55.000 0.00 0.00 0.00 3.53
2102 2441 0.889306 ACTCACTAGGCGACAGTTCC 59.111 55.000 0.00 0.00 0.00 3.62
2103 2442 1.540267 TCACTCACTAGGCGACAGTTC 59.460 52.381 0.00 0.00 0.00 3.01
2104 2443 1.269998 GTCACTCACTAGGCGACAGTT 59.730 52.381 0.00 0.00 32.38 3.16
2105 2444 0.882474 GTCACTCACTAGGCGACAGT 59.118 55.000 0.00 0.00 32.38 3.55
2106 2445 0.179187 CGTCACTCACTAGGCGACAG 60.179 60.000 0.00 0.00 31.87 3.51
2107 2446 1.583495 CCGTCACTCACTAGGCGACA 61.583 60.000 0.00 0.00 31.87 4.35
2108 2447 1.136984 CCGTCACTCACTAGGCGAC 59.863 63.158 0.00 0.00 0.00 5.19
2109 2448 2.044555 CCCGTCACTCACTAGGCGA 61.045 63.158 0.00 0.00 0.00 5.54
2110 2449 2.490217 CCCGTCACTCACTAGGCG 59.510 66.667 0.00 0.00 0.00 5.52
2111 2450 1.043673 ATCCCCGTCACTCACTAGGC 61.044 60.000 0.00 0.00 0.00 3.93
2112 2451 2.231529 CTATCCCCGTCACTCACTAGG 58.768 57.143 0.00 0.00 0.00 3.02
2113 2452 2.231529 CCTATCCCCGTCACTCACTAG 58.768 57.143 0.00 0.00 0.00 2.57
2114 2453 1.133575 CCCTATCCCCGTCACTCACTA 60.134 57.143 0.00 0.00 0.00 2.74
2115 2454 0.397254 CCCTATCCCCGTCACTCACT 60.397 60.000 0.00 0.00 0.00 3.41
2116 2455 1.400530 CCCCTATCCCCGTCACTCAC 61.401 65.000 0.00 0.00 0.00 3.51
2117 2456 1.075525 CCCCTATCCCCGTCACTCA 60.076 63.158 0.00 0.00 0.00 3.41
2118 2457 1.837499 CCCCCTATCCCCGTCACTC 60.837 68.421 0.00 0.00 0.00 3.51
2119 2458 2.285868 CCCCCTATCCCCGTCACT 59.714 66.667 0.00 0.00 0.00 3.41
2136 2475 1.292541 GAGTCGTGTGGGAAGGACC 59.707 63.158 0.00 0.00 35.94 4.46
2137 2476 0.038159 CTGAGTCGTGTGGGAAGGAC 60.038 60.000 0.00 0.00 35.64 3.85
2138 2477 0.178973 TCTGAGTCGTGTGGGAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
2139 2478 0.679505 TTCTGAGTCGTGTGGGAAGG 59.320 55.000 0.00 0.00 0.00 3.46
2140 2479 2.135933 GTTTCTGAGTCGTGTGGGAAG 58.864 52.381 0.00 0.00 0.00 3.46
2141 2480 1.202604 GGTTTCTGAGTCGTGTGGGAA 60.203 52.381 0.00 0.00 0.00 3.97
2142 2481 0.391597 GGTTTCTGAGTCGTGTGGGA 59.608 55.000 0.00 0.00 0.00 4.37
2143 2482 0.944311 CGGTTTCTGAGTCGTGTGGG 60.944 60.000 0.00 0.00 0.00 4.61
2144 2483 0.249322 ACGGTTTCTGAGTCGTGTGG 60.249 55.000 0.00 0.00 34.40 4.17
2145 2484 1.129326 GACGGTTTCTGAGTCGTGTG 58.871 55.000 6.72 0.00 35.91 3.82
2146 2485 3.564455 GACGGTTTCTGAGTCGTGT 57.436 52.632 6.72 0.00 35.91 4.49
2150 2489 1.080025 CCCCGACGGTTTCTGAGTC 60.080 63.158 13.94 0.00 0.00 3.36
2151 2490 0.903454 ATCCCCGACGGTTTCTGAGT 60.903 55.000 13.94 0.00 0.00 3.41
2152 2491 1.067212 CTATCCCCGACGGTTTCTGAG 59.933 57.143 13.94 0.00 0.00 3.35
2153 2492 1.108776 CTATCCCCGACGGTTTCTGA 58.891 55.000 13.94 1.59 0.00 3.27
2154 2493 0.104304 CCTATCCCCGACGGTTTCTG 59.896 60.000 13.94 0.00 0.00 3.02
2155 2494 1.047034 CCCTATCCCCGACGGTTTCT 61.047 60.000 13.94 0.00 0.00 2.52
2156 2495 1.044790 TCCCTATCCCCGACGGTTTC 61.045 60.000 13.94 0.00 0.00 2.78
2157 2496 1.002017 TCCCTATCCCCGACGGTTT 59.998 57.895 13.94 0.00 0.00 3.27
2158 2497 1.457079 CTCCCTATCCCCGACGGTT 60.457 63.158 13.94 0.00 0.00 4.44
2159 2498 2.197875 CTCCCTATCCCCGACGGT 59.802 66.667 13.94 0.00 0.00 4.83
2160 2499 3.303928 GCTCCCTATCCCCGACGG 61.304 72.222 6.99 6.99 0.00 4.79
2161 2500 3.303928 GGCTCCCTATCCCCGACG 61.304 72.222 0.00 0.00 0.00 5.12
2162 2501 1.459730 AAGGCTCCCTATCCCCGAC 60.460 63.158 0.00 0.00 31.13 4.79
2163 2502 1.459539 CAAGGCTCCCTATCCCCGA 60.460 63.158 0.00 0.00 31.13 5.14
2164 2503 0.838122 ATCAAGGCTCCCTATCCCCG 60.838 60.000 0.00 0.00 31.13 5.73
2165 2504 0.695347 CATCAAGGCTCCCTATCCCC 59.305 60.000 0.00 0.00 31.13 4.81
2166 2505 0.037447 GCATCAAGGCTCCCTATCCC 59.963 60.000 0.00 0.00 31.13 3.85
2167 2506 0.767375 TGCATCAAGGCTCCCTATCC 59.233 55.000 0.00 0.00 31.13 2.59
2168 2507 2.875094 ATGCATCAAGGCTCCCTATC 57.125 50.000 0.00 0.00 31.13 2.08
2169 2508 2.981784 TGTATGCATCAAGGCTCCCTAT 59.018 45.455 0.19 0.00 31.13 2.57
2170 2509 2.369860 CTGTATGCATCAAGGCTCCCTA 59.630 50.000 0.19 0.00 31.13 3.53
2171 2510 1.142465 CTGTATGCATCAAGGCTCCCT 59.858 52.381 0.19 0.00 33.87 4.20
2172 2511 1.133976 ACTGTATGCATCAAGGCTCCC 60.134 52.381 0.19 0.00 34.04 4.30
2173 2512 2.338577 ACTGTATGCATCAAGGCTCC 57.661 50.000 0.19 0.00 34.04 4.70
2174 2513 3.012518 ACAACTGTATGCATCAAGGCTC 58.987 45.455 0.19 0.00 34.04 4.70
2175 2514 3.012518 GACAACTGTATGCATCAAGGCT 58.987 45.455 0.19 0.00 34.04 4.58
2176 2515 2.098117 GGACAACTGTATGCATCAAGGC 59.902 50.000 0.19 0.00 0.00 4.35
2177 2516 2.684881 GGGACAACTGTATGCATCAAGG 59.315 50.000 0.19 0.00 0.00 3.61
2178 2517 3.614092 AGGGACAACTGTATGCATCAAG 58.386 45.455 0.19 4.57 0.00 3.02
2179 2518 3.719268 AGGGACAACTGTATGCATCAA 57.281 42.857 0.19 0.00 0.00 2.57
2180 2519 6.686484 ATATAGGGACAACTGTATGCATCA 57.314 37.500 0.19 0.10 0.00 3.07
2181 2520 7.549488 GGTTATATAGGGACAACTGTATGCATC 59.451 40.741 0.19 0.00 0.00 3.91
2182 2521 7.394816 GGTTATATAGGGACAACTGTATGCAT 58.605 38.462 3.79 3.79 0.00 3.96
2183 2522 6.517697 CGGTTATATAGGGACAACTGTATGCA 60.518 42.308 0.00 0.00 0.00 3.96
2184 2523 5.867716 CGGTTATATAGGGACAACTGTATGC 59.132 44.000 0.00 0.00 0.00 3.14
2185 2524 6.989659 ACGGTTATATAGGGACAACTGTATG 58.010 40.000 0.00 0.00 38.41 2.39
2186 2525 7.607615 AACGGTTATATAGGGACAACTGTAT 57.392 36.000 0.00 0.00 39.06 2.29
2187 2526 7.417797 GGAAACGGTTATATAGGGACAACTGTA 60.418 40.741 0.00 0.00 39.06 2.74
2188 2527 5.945144 AACGGTTATATAGGGACAACTGT 57.055 39.130 0.00 0.00 41.14 3.55
2189 2528 5.756833 GGAAACGGTTATATAGGGACAACTG 59.243 44.000 0.00 0.00 34.21 3.16
2190 2529 5.922053 GGAAACGGTTATATAGGGACAACT 58.078 41.667 0.00 0.00 0.00 3.16
2208 2547 5.962433 TGGGATATTCGAGATATCGGAAAC 58.038 41.667 10.26 9.56 33.08 2.78
2209 2548 6.599356 TTGGGATATTCGAGATATCGGAAA 57.401 37.500 10.26 0.00 33.08 3.13
2210 2549 6.395629 GTTTGGGATATTCGAGATATCGGAA 58.604 40.000 10.26 12.62 33.08 4.30
2211 2550 5.392703 CGTTTGGGATATTCGAGATATCGGA 60.393 44.000 10.26 0.23 33.08 4.55
2212 2551 4.798907 CGTTTGGGATATTCGAGATATCGG 59.201 45.833 10.26 0.00 33.08 4.18
2213 2552 4.265556 GCGTTTGGGATATTCGAGATATCG 59.734 45.833 2.64 2.64 33.08 2.92
2214 2553 5.411781 AGCGTTTGGGATATTCGAGATATC 58.588 41.667 14.28 14.28 0.00 1.63
2215 2554 5.407407 AGCGTTTGGGATATTCGAGATAT 57.593 39.130 0.00 0.00 0.00 1.63
2216 2555 4.866508 AGCGTTTGGGATATTCGAGATA 57.133 40.909 0.00 0.00 0.00 1.98
2217 2556 3.753294 AGCGTTTGGGATATTCGAGAT 57.247 42.857 0.00 0.00 0.00 2.75
2218 2557 3.454375 GAAGCGTTTGGGATATTCGAGA 58.546 45.455 0.00 0.00 0.00 4.04
2219 2558 2.218759 CGAAGCGTTTGGGATATTCGAG 59.781 50.000 0.00 0.00 41.37 4.04
2220 2559 2.198406 CGAAGCGTTTGGGATATTCGA 58.802 47.619 0.00 0.00 41.37 3.71
2221 2560 1.931172 ACGAAGCGTTTGGGATATTCG 59.069 47.619 3.82 3.82 43.67 3.34
2222 2561 2.287103 GGACGAAGCGTTTGGGATATTC 59.713 50.000 0.00 0.00 41.37 1.75
2223 2562 2.093128 AGGACGAAGCGTTTGGGATATT 60.093 45.455 0.00 0.00 41.37 1.28
2224 2563 1.485066 AGGACGAAGCGTTTGGGATAT 59.515 47.619 0.00 0.00 41.37 1.63
2225 2564 0.899720 AGGACGAAGCGTTTGGGATA 59.100 50.000 0.00 0.00 41.37 2.59
2226 2565 0.036306 AAGGACGAAGCGTTTGGGAT 59.964 50.000 0.00 0.00 41.37 3.85
2227 2566 0.882927 CAAGGACGAAGCGTTTGGGA 60.883 55.000 0.00 0.00 41.37 4.37
2228 2567 1.574428 CAAGGACGAAGCGTTTGGG 59.426 57.895 0.00 0.00 41.37 4.12
2229 2568 1.082104 GCAAGGACGAAGCGTTTGG 60.082 57.895 0.00 0.00 41.37 3.28
2230 2569 1.136336 GTAGCAAGGACGAAGCGTTTG 60.136 52.381 0.00 0.00 41.37 2.93
2231 2570 1.145803 GTAGCAAGGACGAAGCGTTT 58.854 50.000 0.00 0.00 41.37 3.60
2232 2571 0.317479 AGTAGCAAGGACGAAGCGTT 59.683 50.000 0.00 0.00 41.37 4.84
2233 2572 0.109226 GAGTAGCAAGGACGAAGCGT 60.109 55.000 0.00 0.00 45.10 5.07
2234 2573 1.134530 CGAGTAGCAAGGACGAAGCG 61.135 60.000 0.00 0.00 0.00 4.68
2235 2574 0.109226 ACGAGTAGCAAGGACGAAGC 60.109 55.000 0.00 0.00 0.00 3.86
2236 2575 2.349297 AACGAGTAGCAAGGACGAAG 57.651 50.000 0.00 0.00 0.00 3.79
2237 2576 2.223876 ACAAACGAGTAGCAAGGACGAA 60.224 45.455 0.00 0.00 0.00 3.85
2238 2577 1.338973 ACAAACGAGTAGCAAGGACGA 59.661 47.619 0.00 0.00 0.00 4.20
2239 2578 1.455786 CACAAACGAGTAGCAAGGACG 59.544 52.381 0.00 0.00 0.00 4.79
2240 2579 1.194772 GCACAAACGAGTAGCAAGGAC 59.805 52.381 0.00 0.00 0.00 3.85
2241 2580 1.070134 AGCACAAACGAGTAGCAAGGA 59.930 47.619 0.00 0.00 0.00 3.36
2242 2581 1.461127 GAGCACAAACGAGTAGCAAGG 59.539 52.381 0.00 0.00 0.00 3.61
2243 2582 1.125021 CGAGCACAAACGAGTAGCAAG 59.875 52.381 0.00 0.00 0.00 4.01
2244 2583 1.136690 CGAGCACAAACGAGTAGCAA 58.863 50.000 0.00 0.00 0.00 3.91
2245 2584 1.282248 GCGAGCACAAACGAGTAGCA 61.282 55.000 0.00 0.00 0.00 3.49
2246 2585 1.282248 TGCGAGCACAAACGAGTAGC 61.282 55.000 0.00 0.00 0.00 3.58
2247 2586 1.350193 ATGCGAGCACAAACGAGTAG 58.650 50.000 0.00 0.00 0.00 2.57
2248 2587 1.459209 CAATGCGAGCACAAACGAGTA 59.541 47.619 0.00 0.00 0.00 2.59
2249 2588 0.235665 CAATGCGAGCACAAACGAGT 59.764 50.000 0.00 0.00 0.00 4.18
2250 2589 1.061799 GCAATGCGAGCACAAACGAG 61.062 55.000 0.00 0.00 0.00 4.18
2251 2590 1.082169 GCAATGCGAGCACAAACGA 60.082 52.632 0.00 0.00 0.00 3.85
2252 2591 2.082366 GGCAATGCGAGCACAAACG 61.082 57.895 0.00 0.00 0.00 3.60
2253 2592 0.388907 ATGGCAATGCGAGCACAAAC 60.389 50.000 0.00 0.00 0.00 2.93
2254 2593 0.109179 GATGGCAATGCGAGCACAAA 60.109 50.000 0.00 0.00 0.00 2.83
2255 2594 1.507630 GATGGCAATGCGAGCACAA 59.492 52.632 0.00 0.00 0.00 3.33
2256 2595 2.752939 CGATGGCAATGCGAGCACA 61.753 57.895 6.29 0.00 0.00 4.57
2257 2596 2.023741 CGATGGCAATGCGAGCAC 59.976 61.111 6.29 0.00 0.00 4.40
2258 2597 3.879682 GCGATGGCAATGCGAGCA 61.880 61.111 6.29 0.00 39.62 4.26
2268 2607 1.298859 AAAACTCCGACTGCGATGGC 61.299 55.000 0.00 0.00 40.82 4.40
2269 2608 0.443869 CAAAACTCCGACTGCGATGG 59.556 55.000 0.00 0.00 40.82 3.51
2270 2609 1.136252 CACAAAACTCCGACTGCGATG 60.136 52.381 0.00 0.00 40.82 3.84
2271 2610 1.148310 CACAAAACTCCGACTGCGAT 58.852 50.000 0.00 0.00 40.82 4.58
2272 2611 0.878523 CCACAAAACTCCGACTGCGA 60.879 55.000 0.00 0.00 40.82 5.10
2273 2612 1.157870 ACCACAAAACTCCGACTGCG 61.158 55.000 0.00 0.00 37.24 5.18
2274 2613 1.021968 AACCACAAAACTCCGACTGC 58.978 50.000 0.00 0.00 0.00 4.40
2275 2614 3.775661 AAAACCACAAAACTCCGACTG 57.224 42.857 0.00 0.00 0.00 3.51
2276 2615 3.628942 GGTAAAACCACAAAACTCCGACT 59.371 43.478 0.00 0.00 38.42 4.18
2277 2616 3.628942 AGGTAAAACCACAAAACTCCGAC 59.371 43.478 0.00 0.00 41.95 4.79
2278 2617 3.888583 AGGTAAAACCACAAAACTCCGA 58.111 40.909 0.00 0.00 41.95 4.55
2279 2618 5.754543 TTAGGTAAAACCACAAAACTCCG 57.245 39.130 0.00 0.00 41.95 4.63
2280 2619 7.760131 GTTTTAGGTAAAACCACAAAACTCC 57.240 36.000 20.54 5.96 45.62 3.85
2292 2631 5.479027 GGAATCTGCCTGGTTTTAGGTAAAA 59.521 40.000 0.00 0.00 40.11 1.52
2293 2632 5.014202 GGAATCTGCCTGGTTTTAGGTAAA 58.986 41.667 0.00 0.00 40.11 2.01
2294 2633 4.043561 TGGAATCTGCCTGGTTTTAGGTAA 59.956 41.667 0.00 0.00 40.11 2.85
2295 2634 3.589735 TGGAATCTGCCTGGTTTTAGGTA 59.410 43.478 0.00 0.00 40.11 3.08
2296 2635 2.378547 TGGAATCTGCCTGGTTTTAGGT 59.621 45.455 0.00 0.00 40.11 3.08
2297 2636 3.019564 CTGGAATCTGCCTGGTTTTAGG 58.980 50.000 0.00 0.00 40.95 2.69
2298 2637 3.691609 GTCTGGAATCTGCCTGGTTTTAG 59.308 47.826 0.00 0.00 0.00 1.85
2299 2638 3.073798 TGTCTGGAATCTGCCTGGTTTTA 59.926 43.478 0.00 0.00 0.00 1.52
2300 2639 2.158475 TGTCTGGAATCTGCCTGGTTTT 60.158 45.455 0.00 0.00 0.00 2.43
2301 2640 1.425066 TGTCTGGAATCTGCCTGGTTT 59.575 47.619 0.00 0.00 0.00 3.27
2302 2641 1.067295 TGTCTGGAATCTGCCTGGTT 58.933 50.000 0.00 0.00 0.00 3.67
2303 2642 0.326264 GTGTCTGGAATCTGCCTGGT 59.674 55.000 0.00 0.00 0.00 4.00
2304 2643 0.742281 CGTGTCTGGAATCTGCCTGG 60.742 60.000 0.00 0.00 0.00 4.45
2305 2644 2.759783 CGTGTCTGGAATCTGCCTG 58.240 57.895 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.