Multiple sequence alignment - TraesCS1D01G415100

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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 TraesCS1D01G415100 chr1D 100.000 2534 0 0 1 2534 474719144 474721677 0.000000e+00 4680.0
1 TraesCS1D01G415100 chr1A 86.418 2010 136 63 134 2115 570247503 570249403 0.000000e+00 2073.0
2 TraesCS1D01G415100 chr1B 85.399 2041 126 80 49 1999 659948007 659949965 0.000000e+00 1960.0
3 TraesCS1D01G415100 chr1B 89.189 259 20 3 2278 2534 659950024 659950276 1.460000e-82 316.0
4 TraesCS1D01G415100 chr1B 85.870 184 10 2 308 475 659913152 659913335 5.570000e-42 182.0
5 TraesCS1D01G415100 chr4D 97.297 37 1 0 2 38 137946298 137946262 2.100000e-06 63.9
6 TraesCS1D01G415100 chr5D 94.872 39 2 0 1 39 130139020 130139058 7.570000e-06 62.1


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 TraesCS1D01G415100 chr1D 474719144 474721677 2533 False 4680 4680 100.000 1 2534 1 chr1D.!!$F1 2533
1 TraesCS1D01G415100 chr1A 570247503 570249403 1900 False 2073 2073 86.418 134 2115 1 chr1A.!!$F1 1981
2 TraesCS1D01G415100 chr1B 659948007 659950276 2269 False 1138 1960 87.294 49 2534 2 chr1B.!!$F2 2485

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
122 123 0.03467 AGAAATCAGAGCCACCCAGC 60.035 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1730 0.032952 GGCAGACCGTACACACTGAA 59.967 55.0 12.29 0.0 32.9 3.02 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
25 26 8.813643 GATGTTATCACCTATGTTACTACCAC 57.186 38.462 0.00 0.00 0.00 4.16
26 27 7.966339 TGTTATCACCTATGTTACTACCACT 57.034 36.000 0.00 0.00 0.00 4.00
27 28 7.778083 TGTTATCACCTATGTTACTACCACTG 58.222 38.462 0.00 0.00 0.00 3.66
28 29 7.398047 TGTTATCACCTATGTTACTACCACTGT 59.602 37.037 0.00 0.00 0.00 3.55
29 30 5.654603 TCACCTATGTTACTACCACTGTG 57.345 43.478 0.00 0.00 0.00 3.66
30 31 4.464951 TCACCTATGTTACTACCACTGTGG 59.535 45.833 24.80 24.80 45.02 4.17
31 32 3.773119 ACCTATGTTACTACCACTGTGGG 59.227 47.826 29.05 15.61 43.37 4.61
32 33 3.773119 CCTATGTTACTACCACTGTGGGT 59.227 47.826 29.05 20.19 43.37 4.51
33 34 4.957954 CCTATGTTACTACCACTGTGGGTA 59.042 45.833 29.05 19.22 43.37 3.69
39 40 2.984435 TACCACTGTGGGTAGTCTGA 57.016 50.000 29.05 2.84 43.37 3.27
40 41 1.339097 ACCACTGTGGGTAGTCTGAC 58.661 55.000 29.05 0.00 43.37 3.51
41 42 1.338107 CCACTGTGGGTAGTCTGACA 58.662 55.000 19.23 0.00 32.67 3.58
42 43 1.000955 CCACTGTGGGTAGTCTGACAC 59.999 57.143 19.23 6.24 32.67 3.67
43 44 1.686587 CACTGTGGGTAGTCTGACACA 59.313 52.381 10.88 4.35 41.11 3.72
44 45 2.300152 CACTGTGGGTAGTCTGACACAT 59.700 50.000 10.88 0.00 42.27 3.21
45 46 2.563179 ACTGTGGGTAGTCTGACACATC 59.437 50.000 10.88 0.00 42.27 3.06
46 47 1.899814 TGTGGGTAGTCTGACACATCC 59.100 52.381 10.88 7.60 38.76 3.51
47 48 1.207329 GTGGGTAGTCTGACACATCCC 59.793 57.143 10.88 14.59 34.60 3.85
52 53 0.972983 AGTCTGACACATCCCTCCCG 60.973 60.000 10.88 0.00 0.00 5.14
58 59 1.221840 CACATCCCTCCCGACTTGG 59.778 63.158 0.00 0.00 37.55 3.61
62 63 1.139058 CATCCCTCCCGACTTGGTTAG 59.861 57.143 0.00 0.00 35.15 2.34
64 65 1.358787 TCCCTCCCGACTTGGTTAGTA 59.641 52.381 0.00 0.00 37.17 1.82
72 73 6.297582 TCCCGACTTGGTTAGTAAATTTTGA 58.702 36.000 0.00 0.00 37.17 2.69
111 112 8.707938 AAAACAAAAAGGAGTTCAGAAATCAG 57.292 30.769 12.50 0.00 0.00 2.90
112 113 7.645058 AACAAAAAGGAGTTCAGAAATCAGA 57.355 32.000 12.50 0.00 0.00 3.27
113 114 7.269477 ACAAAAAGGAGTTCAGAAATCAGAG 57.731 36.000 12.50 0.00 0.00 3.35
114 115 5.956068 AAAAGGAGTTCAGAAATCAGAGC 57.044 39.130 12.50 0.00 0.00 4.09
115 116 3.625649 AGGAGTTCAGAAATCAGAGCC 57.374 47.619 12.50 0.00 0.00 4.70
116 117 2.909006 AGGAGTTCAGAAATCAGAGCCA 59.091 45.455 12.50 0.00 0.00 4.75
117 118 3.006247 GGAGTTCAGAAATCAGAGCCAC 58.994 50.000 12.50 0.00 0.00 5.01
118 119 3.006247 GAGTTCAGAAATCAGAGCCACC 58.994 50.000 5.72 0.00 0.00 4.61
119 120 2.087646 GTTCAGAAATCAGAGCCACCC 58.912 52.381 0.00 0.00 0.00 4.61
120 121 1.361204 TCAGAAATCAGAGCCACCCA 58.639 50.000 0.00 0.00 0.00 4.51
121 122 1.280133 TCAGAAATCAGAGCCACCCAG 59.720 52.381 0.00 0.00 0.00 4.45
122 123 0.034670 AGAAATCAGAGCCACCCAGC 60.035 55.000 0.00 0.00 0.00 4.85
153 154 1.887854 TGTCCATCATTGCACACTTGG 59.112 47.619 0.00 0.00 0.00 3.61
199 212 3.964031 ACTCTGAACCTGTTCTTCACTCT 59.036 43.478 11.03 0.00 40.14 3.24
254 271 2.497138 CACACACTGGCAAATCTCTCA 58.503 47.619 0.00 0.00 0.00 3.27
310 328 3.121544 GGAAGCGAAGGAAATAGTACGG 58.878 50.000 0.00 0.00 0.00 4.02
480 499 2.718563 GGAAGCGTGGGAGGATAAAAA 58.281 47.619 0.00 0.00 0.00 1.94
484 503 1.953311 GCGTGGGAGGATAAAAAGGCA 60.953 52.381 0.00 0.00 0.00 4.75
543 562 2.101575 CCGTCCTCGCGAAATCGA 59.898 61.111 21.62 8.85 43.02 3.59
558 577 0.674534 ATCGAACGCTATCACCCCTC 59.325 55.000 0.00 0.00 0.00 4.30
559 578 1.299165 CGAACGCTATCACCCCTCG 60.299 63.158 0.00 0.00 0.00 4.63
584 603 3.894547 CTTGTACCCGCGCCCAAGT 62.895 63.158 0.00 0.00 31.79 3.16
650 673 3.518998 ACGCCCACGATCGAGAGG 61.519 66.667 24.34 18.89 43.93 3.69
653 676 3.227276 CCCACGATCGAGAGGGGG 61.227 72.222 26.42 20.89 37.66 5.40
673 696 1.936547 GGTGAATCTCTTGGATGCGTC 59.063 52.381 0.00 0.00 32.58 5.19
857 906 4.383770 CGAACCCCACCTACAATCTACAAT 60.384 45.833 0.00 0.00 0.00 2.71
889 947 0.240945 GTGTGCCATTTCCTCCGTTG 59.759 55.000 0.00 0.00 0.00 4.10
890 948 1.212751 GTGCCATTTCCTCCGTTGC 59.787 57.895 0.00 0.00 0.00 4.17
891 949 1.976474 TGCCATTTCCTCCGTTGCC 60.976 57.895 0.00 0.00 0.00 4.52
920 978 2.931105 TGCGGTTCCCCAGGCTAA 60.931 61.111 0.00 0.00 0.00 3.09
922 980 3.074281 CGGTTCCCCAGGCTAACA 58.926 61.111 0.77 0.00 0.00 2.41
923 981 1.078426 CGGTTCCCCAGGCTAACAG 60.078 63.158 0.77 0.00 0.00 3.16
930 988 1.413077 CCCCAGGCTAACAGCTACTAC 59.587 57.143 0.00 0.00 41.99 2.73
931 989 2.389715 CCCAGGCTAACAGCTACTACT 58.610 52.381 0.00 0.00 41.99 2.57
932 990 3.563223 CCCAGGCTAACAGCTACTACTA 58.437 50.000 0.00 0.00 41.99 1.82
934 992 3.004944 CCAGGCTAACAGCTACTACTAGC 59.995 52.174 0.00 0.00 45.30 3.42
980 1047 2.811317 GCTTGGCTCCGTCTGACG 60.811 66.667 22.49 22.49 42.11 4.35
1361 1440 2.047274 CGGCATCCACGACAAGGT 60.047 61.111 0.00 0.00 0.00 3.50
1373 1452 2.156051 GACAAGGTCGCCGAGAAGGT 62.156 60.000 0.00 0.00 43.70 3.50
1381 1460 3.068881 CCGAGAAGGTGGAAGGCA 58.931 61.111 0.00 0.00 34.51 4.75
1412 1491 1.253999 GTGGATACGACGTCAACGAC 58.746 55.000 17.16 6.97 40.54 4.34
1571 1659 3.962421 GATCCAGCGCCTGCATGC 61.962 66.667 11.82 11.82 46.23 4.06
1603 1701 3.692406 GCGGGTCAACCTCGGAGT 61.692 66.667 4.02 0.00 36.97 3.85
1604 1702 2.345760 GCGGGTCAACCTCGGAGTA 61.346 63.158 4.02 0.00 36.97 2.59
1605 1703 1.807886 CGGGTCAACCTCGGAGTAG 59.192 63.158 4.02 0.00 36.97 2.57
1615 1723 3.277715 ACCTCGGAGTAGTTAGCAGTAC 58.722 50.000 4.02 0.00 0.00 2.73
1618 1726 3.276857 TCGGAGTAGTTAGCAGTACTGG 58.723 50.000 23.95 6.49 39.01 4.00
1619 1727 3.015327 CGGAGTAGTTAGCAGTACTGGT 58.985 50.000 28.84 28.84 39.01 4.00
1620 1728 4.080919 TCGGAGTAGTTAGCAGTACTGGTA 60.081 45.833 26.76 26.76 39.01 3.25
1621 1729 4.272991 CGGAGTAGTTAGCAGTACTGGTAG 59.727 50.000 28.19 14.63 43.34 3.18
1622 1730 5.192176 GGAGTAGTTAGCAGTACTGGTAGT 58.808 45.833 28.19 22.63 43.34 2.73
1624 1732 6.183360 GGAGTAGTTAGCAGTACTGGTAGTTC 60.183 46.154 28.19 22.35 43.34 3.01
1628 1736 3.944055 AGCAGTACTGGTAGTTCAGTG 57.056 47.619 25.49 0.00 46.29 3.66
1629 1737 3.231818 AGCAGTACTGGTAGTTCAGTGT 58.768 45.455 25.49 0.00 46.29 3.55
1635 1743 2.295349 ACTGGTAGTTCAGTGTGTACGG 59.705 50.000 0.00 0.00 45.27 4.02
1638 1746 2.555757 GGTAGTTCAGTGTGTACGGTCT 59.444 50.000 0.00 0.00 0.00 3.85
1642 1750 1.374252 CAGTGTGTACGGTCTGCCC 60.374 63.158 0.00 0.00 0.00 5.36
1760 1870 7.320443 TGACATGTTATCTTCATTTGCCTAC 57.680 36.000 0.00 0.00 0.00 3.18
1761 1871 7.112122 TGACATGTTATCTTCATTTGCCTACT 58.888 34.615 0.00 0.00 0.00 2.57
1766 1876 7.857456 TGTTATCTTCATTTGCCTACTCCTAA 58.143 34.615 0.00 0.00 0.00 2.69
1767 1877 7.987458 TGTTATCTTCATTTGCCTACTCCTAAG 59.013 37.037 0.00 0.00 0.00 2.18
1768 1878 6.567602 ATCTTCATTTGCCTACTCCTAAGT 57.432 37.500 0.00 0.00 39.66 2.24
1769 1879 7.676683 ATCTTCATTTGCCTACTCCTAAGTA 57.323 36.000 0.00 0.00 36.92 2.24
1866 1983 4.985538 ACTTCTTACATCTTCCTTTGGCA 58.014 39.130 0.00 0.00 0.00 4.92
2028 2160 7.472334 AAAATGAAATGCTCATGGTAACTCT 57.528 32.000 0.00 0.00 44.43 3.24
2069 2201 9.171701 CAAATTGCTTTTGTGATTTGGTAAATG 57.828 29.630 4.99 0.00 39.93 2.32
2070 2202 8.449251 AATTGCTTTTGTGATTTGGTAAATGT 57.551 26.923 0.00 0.00 0.00 2.71
2071 2203 7.856145 TTGCTTTTGTGATTTGGTAAATGTT 57.144 28.000 0.00 0.00 0.00 2.71
2072 2204 7.244166 TGCTTTTGTGATTTGGTAAATGTTG 57.756 32.000 0.00 0.00 0.00 3.33
2115 2247 0.951558 AAGCAATTTGGAGCGAACGT 59.048 45.000 0.00 0.00 35.48 3.99
2116 2248 0.951558 AGCAATTTGGAGCGAACGTT 59.048 45.000 0.00 0.00 35.48 3.99
2117 2249 1.052287 GCAATTTGGAGCGAACGTTG 58.948 50.000 5.00 0.00 0.00 4.10
2118 2250 1.685302 CAATTTGGAGCGAACGTTGG 58.315 50.000 5.00 5.50 0.00 3.77
2119 2251 0.039527 AATTTGGAGCGAACGTTGGC 60.040 50.000 25.54 25.54 0.00 4.52
2120 2252 1.862602 ATTTGGAGCGAACGTTGGCC 61.863 55.000 28.41 19.93 31.78 5.36
2122 2254 4.699522 GGAGCGAACGTTGGCCCT 62.700 66.667 28.41 13.74 31.78 5.19
2123 2255 3.119096 GAGCGAACGTTGGCCCTC 61.119 66.667 28.41 18.09 31.78 4.30
2126 2258 2.356553 CGAACGTTGGCCCTCGAA 60.357 61.111 20.56 0.00 33.13 3.71
2127 2259 1.740296 CGAACGTTGGCCCTCGAAT 60.740 57.895 20.56 10.44 33.13 3.34
2128 2260 1.794222 GAACGTTGGCCCTCGAATG 59.206 57.895 20.56 7.35 0.00 2.67
2129 2261 0.672401 GAACGTTGGCCCTCGAATGA 60.672 55.000 20.56 0.00 0.00 2.57
2130 2262 0.250553 AACGTTGGCCCTCGAATGAA 60.251 50.000 20.56 0.00 0.00 2.57
2131 2263 0.673644 ACGTTGGCCCTCGAATGAAG 60.674 55.000 20.56 0.00 0.00 3.02
2132 2264 1.803289 GTTGGCCCTCGAATGAAGC 59.197 57.895 0.00 0.00 0.00 3.86
2133 2265 0.960364 GTTGGCCCTCGAATGAAGCA 60.960 55.000 0.00 0.00 0.00 3.91
2134 2266 0.960364 TTGGCCCTCGAATGAAGCAC 60.960 55.000 0.00 0.00 0.00 4.40
2135 2267 1.377202 GGCCCTCGAATGAAGCACA 60.377 57.895 0.00 0.00 0.00 4.57
2136 2268 0.749454 GGCCCTCGAATGAAGCACAT 60.749 55.000 0.00 0.00 41.45 3.21
2137 2269 0.379669 GCCCTCGAATGAAGCACATG 59.620 55.000 0.00 0.00 39.39 3.21
2138 2270 1.742761 CCCTCGAATGAAGCACATGT 58.257 50.000 0.00 0.00 39.39 3.21
2139 2271 2.905075 CCCTCGAATGAAGCACATGTA 58.095 47.619 0.00 0.00 39.39 2.29
2140 2272 3.470709 CCCTCGAATGAAGCACATGTAT 58.529 45.455 0.00 0.00 39.39 2.29
2141 2273 3.496130 CCCTCGAATGAAGCACATGTATC 59.504 47.826 0.00 0.00 39.39 2.24
2142 2274 4.375272 CCTCGAATGAAGCACATGTATCT 58.625 43.478 0.00 0.00 39.39 1.98
2143 2275 4.813161 CCTCGAATGAAGCACATGTATCTT 59.187 41.667 11.08 11.08 39.39 2.40
2144 2276 5.277202 CCTCGAATGAAGCACATGTATCTTG 60.277 44.000 14.88 0.00 39.39 3.02
2145 2277 4.571984 TCGAATGAAGCACATGTATCTTGG 59.428 41.667 14.88 0.00 39.39 3.61
2146 2278 4.571984 CGAATGAAGCACATGTATCTTGGA 59.428 41.667 14.88 4.73 39.39 3.53
2147 2279 5.277202 CGAATGAAGCACATGTATCTTGGAG 60.277 44.000 14.88 0.00 39.39 3.86
2148 2280 3.273434 TGAAGCACATGTATCTTGGAGC 58.727 45.455 14.88 5.07 0.00 4.70
2149 2281 3.273434 GAAGCACATGTATCTTGGAGCA 58.727 45.455 14.88 0.00 0.00 4.26
2150 2282 3.354948 AGCACATGTATCTTGGAGCAA 57.645 42.857 0.00 0.00 0.00 3.91
2151 2283 3.276857 AGCACATGTATCTTGGAGCAAG 58.723 45.455 0.00 0.00 42.25 4.01
2152 2284 2.357009 GCACATGTATCTTGGAGCAAGG 59.643 50.000 0.00 0.00 41.33 3.61
2153 2285 2.947652 CACATGTATCTTGGAGCAAGGG 59.052 50.000 0.00 0.00 41.33 3.95
2154 2286 1.952296 CATGTATCTTGGAGCAAGGGC 59.048 52.381 0.00 0.00 41.33 5.19
2155 2287 0.255890 TGTATCTTGGAGCAAGGGCC 59.744 55.000 0.00 0.00 41.33 5.80
2156 2288 0.255890 GTATCTTGGAGCAAGGGCCA 59.744 55.000 6.18 0.00 41.33 5.36
2157 2289 0.255890 TATCTTGGAGCAAGGGCCAC 59.744 55.000 6.18 0.00 41.33 5.01
2158 2290 2.826777 ATCTTGGAGCAAGGGCCACG 62.827 60.000 6.18 0.00 41.33 4.94
2159 2291 3.850098 CTTGGAGCAAGGGCCACGT 62.850 63.158 6.18 0.00 42.56 4.49
2160 2292 3.842925 TTGGAGCAAGGGCCACGTC 62.843 63.158 6.18 0.00 42.56 4.34
2161 2293 4.329545 GGAGCAAGGGCCACGTCA 62.330 66.667 6.18 0.00 42.56 4.35
2162 2294 2.743928 GAGCAAGGGCCACGTCAG 60.744 66.667 6.18 0.00 42.56 3.51
2163 2295 3.537206 GAGCAAGGGCCACGTCAGT 62.537 63.158 6.18 0.00 42.56 3.41
2164 2296 2.594592 GCAAGGGCCACGTCAGTT 60.595 61.111 6.18 0.00 0.00 3.16
2165 2297 2.193536 GCAAGGGCCACGTCAGTTT 61.194 57.895 6.18 0.00 0.00 2.66
2166 2298 1.734388 GCAAGGGCCACGTCAGTTTT 61.734 55.000 6.18 0.00 0.00 2.43
2167 2299 0.310854 CAAGGGCCACGTCAGTTTTC 59.689 55.000 6.18 0.00 0.00 2.29
2168 2300 1.164041 AAGGGCCACGTCAGTTTTCG 61.164 55.000 6.18 0.00 0.00 3.46
2169 2301 2.613506 GGGCCACGTCAGTTTTCGG 61.614 63.158 4.39 0.00 0.00 4.30
2170 2302 1.595929 GGCCACGTCAGTTTTCGGA 60.596 57.895 0.00 0.00 0.00 4.55
2171 2303 1.566018 GGCCACGTCAGTTTTCGGAG 61.566 60.000 0.00 0.00 0.00 4.63
2172 2304 1.566018 GCCACGTCAGTTTTCGGAGG 61.566 60.000 0.00 0.00 36.34 4.30
2173 2305 1.566018 CCACGTCAGTTTTCGGAGGC 61.566 60.000 0.00 0.00 34.31 4.70
2174 2306 1.663702 ACGTCAGTTTTCGGAGGCG 60.664 57.895 0.00 0.00 34.31 5.52
2175 2307 1.663702 CGTCAGTTTTCGGAGGCGT 60.664 57.895 0.00 0.00 0.00 5.68
2176 2308 1.219522 CGTCAGTTTTCGGAGGCGTT 61.220 55.000 0.00 0.00 0.00 4.84
2177 2309 0.511653 GTCAGTTTTCGGAGGCGTTC 59.488 55.000 0.00 0.00 0.00 3.95
2178 2310 0.942410 TCAGTTTTCGGAGGCGTTCG 60.942 55.000 0.00 0.00 0.00 3.95
2179 2311 2.172659 GTTTTCGGAGGCGTTCGC 59.827 61.111 8.75 8.75 0.00 4.70
2180 2312 2.029964 TTTTCGGAGGCGTTCGCT 59.970 55.556 16.40 3.31 0.00 4.93
2181 2313 2.025418 TTTTCGGAGGCGTTCGCTC 61.025 57.895 16.40 11.40 0.00 5.03
2182 2314 3.927163 TTTCGGAGGCGTTCGCTCC 62.927 63.158 16.40 17.57 0.00 4.70
2184 2316 4.735132 CGGAGGCGTTCGCTCCAA 62.735 66.667 23.60 0.00 37.12 3.53
2185 2317 2.125106 GGAGGCGTTCGCTCCAAT 60.125 61.111 21.20 5.45 37.24 3.16
2186 2318 2.174319 GGAGGCGTTCGCTCCAATC 61.174 63.158 21.20 11.64 37.24 2.67
2187 2319 2.509336 AGGCGTTCGCTCCAATCG 60.509 61.111 16.40 0.00 0.00 3.34
2188 2320 3.564027 GGCGTTCGCTCCAATCGG 61.564 66.667 16.40 0.00 0.00 4.18
2189 2321 3.564027 GCGTTCGCTCCAATCGGG 61.564 66.667 9.99 0.00 38.37 5.14
2190 2322 3.564027 CGTTCGCTCCAATCGGGC 61.564 66.667 0.00 0.00 36.21 6.13
2191 2323 3.564027 GTTCGCTCCAATCGGGCG 61.564 66.667 0.00 0.00 46.87 6.13
2195 2327 3.564027 GCTCCAATCGGGCGAACG 61.564 66.667 0.00 0.00 36.21 3.95
2196 2328 3.564027 CTCCAATCGGGCGAACGC 61.564 66.667 10.81 10.81 41.06 4.84
2206 2338 2.432972 GCGAACGCGTTCCCCTTA 60.433 61.111 38.04 0.00 40.36 2.69
2207 2339 1.812507 GCGAACGCGTTCCCCTTAT 60.813 57.895 38.04 11.11 40.36 1.73
2208 2340 1.759293 GCGAACGCGTTCCCCTTATC 61.759 60.000 38.04 18.24 40.36 1.75
2209 2341 1.149964 CGAACGCGTTCCCCTTATCC 61.150 60.000 38.04 17.16 36.27 2.59
2210 2342 0.177373 GAACGCGTTCCCCTTATCCT 59.823 55.000 35.88 6.00 33.64 3.24
2211 2343 1.410153 GAACGCGTTCCCCTTATCCTA 59.590 52.381 35.88 0.00 33.64 2.94
2212 2344 1.713297 ACGCGTTCCCCTTATCCTAT 58.287 50.000 5.58 0.00 0.00 2.57
2213 2345 1.343465 ACGCGTTCCCCTTATCCTATG 59.657 52.381 5.58 0.00 0.00 2.23
2214 2346 1.337823 CGCGTTCCCCTTATCCTATGG 60.338 57.143 0.00 0.00 0.00 2.74
2215 2347 1.003233 GCGTTCCCCTTATCCTATGGG 59.997 57.143 0.00 0.00 41.57 4.00
2221 2353 3.441500 CCCTTATCCTATGGGGCTTTC 57.558 52.381 0.00 0.00 39.00 2.62
2222 2354 2.041755 CCCTTATCCTATGGGGCTTTCC 59.958 54.545 0.00 0.00 39.00 3.13
2223 2355 2.989571 CCTTATCCTATGGGGCTTTCCT 59.010 50.000 0.00 0.00 35.33 3.36
2224 2356 3.009584 CCTTATCCTATGGGGCTTTCCTC 59.990 52.174 0.00 0.00 35.33 3.71
2245 2377 1.620819 ACTCGCTGATTCACTCAACCT 59.379 47.619 0.00 0.00 32.14 3.50
2247 2379 3.449018 ACTCGCTGATTCACTCAACCTAT 59.551 43.478 0.00 0.00 32.14 2.57
2249 2381 3.447229 TCGCTGATTCACTCAACCTATCA 59.553 43.478 0.00 0.00 32.14 2.15
2254 2386 5.674525 TGATTCACTCAACCTATCATCACC 58.325 41.667 0.00 0.00 0.00 4.02
2260 2392 4.161189 ACTCAACCTATCATCACCTGACTG 59.839 45.833 0.00 0.00 36.48 3.51
2261 2393 3.452264 TCAACCTATCATCACCTGACTGG 59.548 47.826 0.00 0.00 36.48 4.00
2262 2394 1.765314 ACCTATCATCACCTGACTGGC 59.235 52.381 0.00 0.00 40.22 4.85
2263 2395 1.071385 CCTATCATCACCTGACTGGCC 59.929 57.143 0.00 0.00 40.22 5.36
2264 2396 0.752658 TATCATCACCTGACTGGCCG 59.247 55.000 0.00 0.00 40.22 6.13
2265 2397 2.599645 ATCATCACCTGACTGGCCGC 62.600 60.000 0.00 0.00 40.22 6.53
2266 2398 4.101448 ATCACCTGACTGGCCGCC 62.101 66.667 1.04 1.04 40.22 6.13
2289 2421 4.431131 CAGCGGGCCTCCACCATT 62.431 66.667 0.84 0.00 0.00 3.16
2323 2456 2.402564 CCCTTCTCCTAGGCAGATTGA 58.597 52.381 2.96 0.00 33.73 2.57
2330 2463 4.041321 TCTCCTAGGCAGATTGATCAATGG 59.959 45.833 25.37 17.12 0.00 3.16
2339 2472 5.234329 GCAGATTGATCAATGGCATTCTTTG 59.766 40.000 25.37 6.62 31.69 2.77
2347 2480 6.855763 TCAATGGCATTCTTTGTAGGAAAT 57.144 33.333 10.36 0.00 33.69 2.17
2377 2510 8.757982 ATCTCTATAACATGGCAAGTTTGAAT 57.242 30.769 13.77 4.17 0.00 2.57
2378 2511 9.851686 ATCTCTATAACATGGCAAGTTTGAATA 57.148 29.630 13.77 5.10 0.00 1.75
2416 2549 6.165577 GGTCACATGGCAAATTAAGAACATT 58.834 36.000 0.00 0.00 0.00 2.71
2417 2550 7.319646 GGTCACATGGCAAATTAAGAACATTA 58.680 34.615 0.00 0.00 0.00 1.90
2418 2551 7.981225 GGTCACATGGCAAATTAAGAACATTAT 59.019 33.333 0.00 0.00 0.00 1.28
2420 2553 8.530311 TCACATGGCAAATTAAGAACATTATGT 58.470 29.630 0.00 0.00 0.00 2.29
2421 2554 9.153721 CACATGGCAAATTAAGAACATTATGTT 57.846 29.630 10.64 10.64 44.37 2.71
2422 2555 9.723601 ACATGGCAAATTAAGAACATTATGTTT 57.276 25.926 12.13 0.00 41.28 2.83
2424 2557 8.770438 TGGCAAATTAAGAACATTATGTTTCC 57.230 30.769 12.13 0.51 41.28 3.13
2425 2558 8.370940 TGGCAAATTAAGAACATTATGTTTCCA 58.629 29.630 12.13 6.12 41.28 3.53
2426 2559 8.872845 GGCAAATTAAGAACATTATGTTTCCAG 58.127 33.333 12.13 0.00 41.28 3.86
2462 2595 5.584649 ACTGAAATATGTAATGGTCACACGG 59.415 40.000 0.00 0.00 0.00 4.94
2485 2618 6.608610 GGCATTTTTACGATTACACTTGTCT 58.391 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.639761 AGTGGTAGTAACATAGGTGATAACATC 58.360 37.037 0.00 0.00 0.00 3.06
1 2 8.421784 CAGTGGTAGTAACATAGGTGATAACAT 58.578 37.037 0.00 0.00 0.00 2.71
2 3 7.398047 ACAGTGGTAGTAACATAGGTGATAACA 59.602 37.037 0.00 0.00 0.00 2.41
3 4 7.705325 CACAGTGGTAGTAACATAGGTGATAAC 59.295 40.741 9.85 0.00 0.00 1.89
4 5 7.147794 CCACAGTGGTAGTAACATAGGTGATAA 60.148 40.741 11.99 0.00 31.35 1.75
5 6 6.322969 CCACAGTGGTAGTAACATAGGTGATA 59.677 42.308 11.99 0.00 31.35 2.15
6 7 5.128827 CCACAGTGGTAGTAACATAGGTGAT 59.871 44.000 11.99 0.00 31.35 3.06
7 8 4.464951 CCACAGTGGTAGTAACATAGGTGA 59.535 45.833 11.99 0.00 31.35 4.02
8 9 4.382685 CCCACAGTGGTAGTAACATAGGTG 60.383 50.000 18.82 8.89 35.17 4.00
9 10 3.773119 CCCACAGTGGTAGTAACATAGGT 59.227 47.826 18.82 0.00 35.17 3.08
10 11 3.773119 ACCCACAGTGGTAGTAACATAGG 59.227 47.826 18.82 0.84 36.67 2.57
20 21 2.158430 TGTCAGACTACCCACAGTGGTA 60.158 50.000 18.82 9.76 40.84 3.25
21 22 1.339097 GTCAGACTACCCACAGTGGT 58.661 55.000 18.82 9.12 43.95 4.16
22 23 1.000955 GTGTCAGACTACCCACAGTGG 59.999 57.143 13.35 13.35 37.25 4.00
23 24 1.686587 TGTGTCAGACTACCCACAGTG 59.313 52.381 1.31 0.00 33.19 3.66
24 25 2.082140 TGTGTCAGACTACCCACAGT 57.918 50.000 1.31 0.00 33.19 3.55
25 26 2.093973 GGATGTGTCAGACTACCCACAG 60.094 54.545 1.31 0.00 40.76 3.66
26 27 1.899814 GGATGTGTCAGACTACCCACA 59.100 52.381 1.31 0.00 41.58 4.17
27 28 1.207329 GGGATGTGTCAGACTACCCAC 59.793 57.143 15.18 1.86 39.13 4.61
28 29 1.078823 AGGGATGTGTCAGACTACCCA 59.921 52.381 19.36 6.52 40.64 4.51
29 30 1.757699 GAGGGATGTGTCAGACTACCC 59.242 57.143 1.31 9.03 39.40 3.69
30 31 1.757699 GGAGGGATGTGTCAGACTACC 59.242 57.143 1.31 0.00 0.00 3.18
31 32 1.757699 GGGAGGGATGTGTCAGACTAC 59.242 57.143 1.31 0.00 0.00 2.73
32 33 1.685180 CGGGAGGGATGTGTCAGACTA 60.685 57.143 1.31 0.00 0.00 2.59
33 34 0.972983 CGGGAGGGATGTGTCAGACT 60.973 60.000 1.31 0.00 0.00 3.24
34 35 0.970937 TCGGGAGGGATGTGTCAGAC 60.971 60.000 0.00 0.00 0.00 3.51
35 36 0.970937 GTCGGGAGGGATGTGTCAGA 60.971 60.000 0.00 0.00 0.00 3.27
36 37 0.972983 AGTCGGGAGGGATGTGTCAG 60.973 60.000 0.00 0.00 0.00 3.51
37 38 0.544357 AAGTCGGGAGGGATGTGTCA 60.544 55.000 0.00 0.00 0.00 3.58
38 39 0.108138 CAAGTCGGGAGGGATGTGTC 60.108 60.000 0.00 0.00 0.00 3.67
39 40 1.553690 CCAAGTCGGGAGGGATGTGT 61.554 60.000 0.00 0.00 0.00 3.72
40 41 1.221840 CCAAGTCGGGAGGGATGTG 59.778 63.158 0.00 0.00 0.00 3.21
41 42 0.840722 AACCAAGTCGGGAGGGATGT 60.841 55.000 0.00 0.00 40.22 3.06
42 43 1.139058 CTAACCAAGTCGGGAGGGATG 59.861 57.143 0.00 0.00 40.22 3.51
43 44 1.273666 ACTAACCAAGTCGGGAGGGAT 60.274 52.381 0.00 0.00 40.22 3.85
44 45 0.115745 ACTAACCAAGTCGGGAGGGA 59.884 55.000 0.00 0.00 40.22 4.20
45 46 1.856629 TACTAACCAAGTCGGGAGGG 58.143 55.000 0.00 0.00 39.80 4.30
46 47 3.967332 TTTACTAACCAAGTCGGGAGG 57.033 47.619 0.00 0.00 39.80 4.30
47 48 6.428771 TCAAAATTTACTAACCAAGTCGGGAG 59.571 38.462 0.00 0.00 39.80 4.30
72 73 9.945904 TCCTTTTTGTTTTAGTTTACCAACAAT 57.054 25.926 0.00 0.00 38.56 2.71
87 88 8.066612 TCTGATTTCTGAACTCCTTTTTGTTT 57.933 30.769 5.45 0.00 0.00 2.83
95 96 2.909006 TGGCTCTGATTTCTGAACTCCT 59.091 45.455 5.45 0.00 0.00 3.69
114 115 2.836360 GATGGCCATGCTGGGTGG 60.836 66.667 26.56 0.00 38.19 4.61
115 116 2.836360 GGATGGCCATGCTGGGTG 60.836 66.667 28.45 0.00 38.19 4.61
116 117 3.025599 AGGATGGCCATGCTGGGT 61.026 61.111 36.04 14.85 38.11 4.51
153 154 8.356657 AGTAGTAGTACATTGATCAGAAGATGC 58.643 37.037 10.33 0.00 33.72 3.91
242 256 1.101331 CCAAGGCTGAGAGATTTGCC 58.899 55.000 0.00 0.00 45.21 4.52
243 257 1.101331 CCCAAGGCTGAGAGATTTGC 58.899 55.000 0.00 0.00 0.00 3.68
310 328 1.470632 CGCCTGTCTGATCCTCTTGTC 60.471 57.143 0.00 0.00 0.00 3.18
431 449 2.235761 TGGGTGGAGTTAAGGGCCC 61.236 63.158 16.46 16.46 36.73 5.80
543 562 3.217231 CCGAGGGGTGATAGCGTT 58.783 61.111 0.00 0.00 0.00 4.84
558 577 0.868602 CGCGGGTACAAGATACACCG 60.869 60.000 0.00 0.00 43.81 4.94
559 578 1.149964 GCGCGGGTACAAGATACACC 61.150 60.000 8.83 0.00 0.00 4.16
562 581 1.593479 GGGCGCGGGTACAAGATAC 60.593 63.158 8.83 0.00 0.00 2.24
650 673 1.752084 GCATCCAAGAGATTCACCCCC 60.752 57.143 0.00 0.00 30.59 5.40
653 676 1.936547 GACGCATCCAAGAGATTCACC 59.063 52.381 0.00 0.00 30.59 4.02
934 992 3.589495 TTGTGATCAGTCAGCTCTCAG 57.411 47.619 0.00 0.00 34.36 3.35
935 993 3.070015 TGTTTGTGATCAGTCAGCTCTCA 59.930 43.478 0.00 0.00 34.36 3.27
936 994 3.431572 GTGTTTGTGATCAGTCAGCTCTC 59.568 47.826 0.00 0.00 34.36 3.20
937 995 3.397482 GTGTTTGTGATCAGTCAGCTCT 58.603 45.455 0.00 0.00 34.36 4.09
938 996 2.481952 GGTGTTTGTGATCAGTCAGCTC 59.518 50.000 0.00 0.00 34.36 4.09
939 997 2.105477 AGGTGTTTGTGATCAGTCAGCT 59.895 45.455 0.00 5.54 34.36 4.24
940 998 2.498167 AGGTGTTTGTGATCAGTCAGC 58.502 47.619 0.00 3.25 34.36 4.26
944 1002 3.290710 AGCAAAGGTGTTTGTGATCAGT 58.709 40.909 0.00 0.00 44.37 3.41
1249 1325 4.113815 CCGCCTGGCCCTGATCAA 62.114 66.667 14.12 0.00 0.00 2.57
1344 1423 2.047274 ACCTTGTCGTGGATGCCG 60.047 61.111 0.00 0.00 0.00 5.69
1356 1435 1.738099 CACCTTCTCGGCGACCTTG 60.738 63.158 4.99 0.00 35.61 3.61
1361 1440 2.646175 CCTTCCACCTTCTCGGCGA 61.646 63.158 10.14 10.14 35.61 5.54
1426 1505 1.006805 GATCATCGACGCCTCCCAG 60.007 63.158 0.00 0.00 0.00 4.45
1433 1521 2.296480 GCCTCGTGATCATCGACGC 61.296 63.158 17.91 17.91 35.53 5.19
1596 1694 3.312973 CCAGTACTGCTAACTACTCCGAG 59.687 52.174 17.86 0.00 0.00 4.63
1599 1697 5.192176 ACTACCAGTACTGCTAACTACTCC 58.808 45.833 17.86 0.00 0.00 3.85
1603 1701 6.150641 CACTGAACTACCAGTACTGCTAACTA 59.849 42.308 17.86 0.13 44.87 2.24
1604 1702 5.047943 CACTGAACTACCAGTACTGCTAACT 60.048 44.000 17.86 1.09 44.87 2.24
1605 1703 5.162075 CACTGAACTACCAGTACTGCTAAC 58.838 45.833 17.86 6.69 44.87 2.34
1615 1723 2.295349 ACCGTACACACTGAACTACCAG 59.705 50.000 0.00 0.00 39.93 4.00
1618 1726 3.562505 CAGACCGTACACACTGAACTAC 58.437 50.000 0.00 0.00 32.90 2.73
1619 1727 2.030540 GCAGACCGTACACACTGAACTA 60.031 50.000 12.29 0.00 32.90 2.24
1620 1728 1.269621 GCAGACCGTACACACTGAACT 60.270 52.381 12.29 0.00 32.90 3.01
1621 1729 1.137513 GCAGACCGTACACACTGAAC 58.862 55.000 12.29 0.00 32.90 3.18
1622 1730 0.032952 GGCAGACCGTACACACTGAA 59.967 55.000 12.29 0.00 32.90 3.02
1624 1732 1.374252 GGGCAGACCGTACACACTG 60.374 63.158 0.00 0.00 36.48 3.66
1760 1870 2.273370 TCGCACGCTTTACTTAGGAG 57.727 50.000 0.00 0.00 0.00 3.69
1761 1871 2.728690 TTCGCACGCTTTACTTAGGA 57.271 45.000 0.00 0.00 0.00 2.94
1766 1876 2.363788 TCAGATTCGCACGCTTTACT 57.636 45.000 0.00 0.00 0.00 2.24
1767 1877 2.412089 AGTTCAGATTCGCACGCTTTAC 59.588 45.455 0.00 0.00 0.00 2.01
1768 1878 2.411748 CAGTTCAGATTCGCACGCTTTA 59.588 45.455 0.00 0.00 0.00 1.85
1769 1879 1.195448 CAGTTCAGATTCGCACGCTTT 59.805 47.619 0.00 0.00 0.00 3.51
1972 2097 4.673968 TCGCTAGGGACCATATCATTACT 58.326 43.478 5.20 0.00 0.00 2.24
1999 2131 8.938906 GTTACCATGAGCATTTCATTTTTGATT 58.061 29.630 0.00 0.00 44.14 2.57
2000 2132 8.316214 AGTTACCATGAGCATTTCATTTTTGAT 58.684 29.630 0.00 0.00 44.14 2.57
2001 2133 7.669427 AGTTACCATGAGCATTTCATTTTTGA 58.331 30.769 0.00 0.00 44.14 2.69
2002 2134 7.816031 AGAGTTACCATGAGCATTTCATTTTTG 59.184 33.333 0.00 0.00 44.14 2.44
2004 2136 7.472334 AGAGTTACCATGAGCATTTCATTTT 57.528 32.000 0.00 0.00 44.14 1.82
2005 2137 7.472334 AAGAGTTACCATGAGCATTTCATTT 57.528 32.000 0.00 0.00 44.14 2.32
2006 2138 8.579850 TTAAGAGTTACCATGAGCATTTCATT 57.420 30.769 0.00 0.00 44.14 2.57
2008 2140 7.994425 TTTAAGAGTTACCATGAGCATTTCA 57.006 32.000 0.00 0.00 40.85 2.69
2009 2141 7.970614 CCTTTTAAGAGTTACCATGAGCATTTC 59.029 37.037 0.00 0.00 0.00 2.17
2010 2142 7.669722 TCCTTTTAAGAGTTACCATGAGCATTT 59.330 33.333 0.00 0.00 0.00 2.32
2011 2143 7.175104 TCCTTTTAAGAGTTACCATGAGCATT 58.825 34.615 0.00 0.00 0.00 3.56
2012 2144 6.721318 TCCTTTTAAGAGTTACCATGAGCAT 58.279 36.000 0.00 0.00 0.00 3.79
2014 2146 6.879458 TCTTCCTTTTAAGAGTTACCATGAGC 59.121 38.462 0.00 0.00 31.85 4.26
2091 2223 4.442733 CGTTCGCTCCAAATTGCTTAAAAA 59.557 37.500 0.00 0.00 0.00 1.94
2115 2247 0.960364 GTGCTTCATTCGAGGGCCAA 60.960 55.000 6.18 0.00 0.00 4.52
2116 2248 1.377202 GTGCTTCATTCGAGGGCCA 60.377 57.895 6.18 0.00 0.00 5.36
2117 2249 0.749454 ATGTGCTTCATTCGAGGGCC 60.749 55.000 0.00 0.00 32.08 5.80
2118 2250 0.379669 CATGTGCTTCATTCGAGGGC 59.620 55.000 0.00 0.00 34.09 5.19
2119 2251 1.742761 ACATGTGCTTCATTCGAGGG 58.257 50.000 0.00 0.00 34.09 4.30
2120 2252 4.375272 AGATACATGTGCTTCATTCGAGG 58.625 43.478 9.11 0.00 34.09 4.63
2121 2253 5.277202 CCAAGATACATGTGCTTCATTCGAG 60.277 44.000 9.11 0.00 34.09 4.04
2122 2254 4.571984 CCAAGATACATGTGCTTCATTCGA 59.428 41.667 9.11 0.00 34.09 3.71
2123 2255 4.571984 TCCAAGATACATGTGCTTCATTCG 59.428 41.667 9.11 0.42 34.09 3.34
2124 2256 5.505324 GCTCCAAGATACATGTGCTTCATTC 60.505 44.000 9.11 0.00 34.09 2.67
2125 2257 4.337555 GCTCCAAGATACATGTGCTTCATT 59.662 41.667 9.11 0.00 34.09 2.57
2126 2258 3.881688 GCTCCAAGATACATGTGCTTCAT 59.118 43.478 9.11 0.00 37.22 2.57
2127 2259 3.273434 GCTCCAAGATACATGTGCTTCA 58.727 45.455 9.11 0.81 0.00 3.02
2128 2260 3.273434 TGCTCCAAGATACATGTGCTTC 58.727 45.455 9.11 2.89 0.00 3.86
2129 2261 3.354948 TGCTCCAAGATACATGTGCTT 57.645 42.857 9.11 9.21 0.00 3.91
2130 2262 3.276857 CTTGCTCCAAGATACATGTGCT 58.723 45.455 9.11 2.67 43.42 4.40
2131 2263 2.357009 CCTTGCTCCAAGATACATGTGC 59.643 50.000 9.11 0.63 43.42 4.57
2132 2264 2.947652 CCCTTGCTCCAAGATACATGTG 59.052 50.000 9.11 0.00 43.42 3.21
2133 2265 2.684927 GCCCTTGCTCCAAGATACATGT 60.685 50.000 2.69 2.69 43.42 3.21
2134 2266 1.952296 GCCCTTGCTCCAAGATACATG 59.048 52.381 6.54 0.00 43.42 3.21
2135 2267 1.133668 GGCCCTTGCTCCAAGATACAT 60.134 52.381 6.54 0.00 43.42 2.29
2136 2268 0.255890 GGCCCTTGCTCCAAGATACA 59.744 55.000 6.54 0.00 43.42 2.29
2137 2269 0.255890 TGGCCCTTGCTCCAAGATAC 59.744 55.000 0.00 0.00 43.42 2.24
2138 2270 0.255890 GTGGCCCTTGCTCCAAGATA 59.744 55.000 0.00 0.00 43.42 1.98
2139 2271 1.000396 GTGGCCCTTGCTCCAAGAT 60.000 57.895 0.00 0.00 43.42 2.40
2140 2272 2.436109 GTGGCCCTTGCTCCAAGA 59.564 61.111 0.00 0.00 43.42 3.02
2141 2273 3.058160 CGTGGCCCTTGCTCCAAG 61.058 66.667 0.00 0.00 40.75 3.61
2142 2274 3.842925 GACGTGGCCCTTGCTCCAA 62.843 63.158 0.00 0.00 37.74 3.53
2143 2275 4.329545 GACGTGGCCCTTGCTCCA 62.330 66.667 0.00 0.00 37.74 3.86
2144 2276 4.329545 TGACGTGGCCCTTGCTCC 62.330 66.667 0.00 0.00 37.74 4.70
2145 2277 2.743928 CTGACGTGGCCCTTGCTC 60.744 66.667 0.00 0.00 37.74 4.26
2146 2278 2.624674 AAACTGACGTGGCCCTTGCT 62.625 55.000 0.00 0.00 37.74 3.91
2147 2279 1.734388 AAAACTGACGTGGCCCTTGC 61.734 55.000 0.00 0.00 0.00 4.01
2148 2280 0.310854 GAAAACTGACGTGGCCCTTG 59.689 55.000 0.00 0.00 0.00 3.61
2149 2281 1.164041 CGAAAACTGACGTGGCCCTT 61.164 55.000 0.00 0.00 0.00 3.95
2150 2282 1.597027 CGAAAACTGACGTGGCCCT 60.597 57.895 0.00 0.00 0.00 5.19
2151 2283 2.613506 CCGAAAACTGACGTGGCCC 61.614 63.158 0.00 0.00 0.00 5.80
2152 2284 1.566018 CTCCGAAAACTGACGTGGCC 61.566 60.000 0.00 0.00 0.00 5.36
2153 2285 1.566018 CCTCCGAAAACTGACGTGGC 61.566 60.000 0.00 0.00 0.00 5.01
2154 2286 1.566018 GCCTCCGAAAACTGACGTGG 61.566 60.000 0.00 0.00 0.00 4.94
2155 2287 1.860078 GCCTCCGAAAACTGACGTG 59.140 57.895 0.00 0.00 0.00 4.49
2156 2288 1.663702 CGCCTCCGAAAACTGACGT 60.664 57.895 0.00 0.00 36.29 4.34
2157 2289 1.219522 AACGCCTCCGAAAACTGACG 61.220 55.000 0.00 0.00 38.29 4.35
2158 2290 0.511653 GAACGCCTCCGAAAACTGAC 59.488 55.000 0.00 0.00 38.29 3.51
2159 2291 0.942410 CGAACGCCTCCGAAAACTGA 60.942 55.000 0.00 0.00 38.29 3.41
2160 2292 1.491563 CGAACGCCTCCGAAAACTG 59.508 57.895 0.00 0.00 38.29 3.16
2161 2293 2.315386 GCGAACGCCTCCGAAAACT 61.315 57.895 8.03 0.00 38.29 2.66
2162 2294 2.172659 GCGAACGCCTCCGAAAAC 59.827 61.111 8.03 0.00 38.29 2.43
2163 2295 2.025418 GAGCGAACGCCTCCGAAAA 61.025 57.895 15.44 0.00 43.17 2.29
2164 2296 2.431942 GAGCGAACGCCTCCGAAA 60.432 61.111 15.44 0.00 43.17 3.46
2165 2297 4.430765 GGAGCGAACGCCTCCGAA 62.431 66.667 15.44 0.00 43.17 4.30
2167 2299 4.735132 TTGGAGCGAACGCCTCCG 62.735 66.667 21.94 0.00 43.17 4.63
2168 2300 2.125106 ATTGGAGCGAACGCCTCC 60.125 61.111 21.27 21.27 43.17 4.30
2169 2301 2.517450 CGATTGGAGCGAACGCCTC 61.517 63.158 15.44 11.67 43.17 4.70
2170 2302 2.509336 CGATTGGAGCGAACGCCT 60.509 61.111 15.44 3.43 43.17 5.52
2171 2303 3.564027 CCGATTGGAGCGAACGCC 61.564 66.667 15.44 7.27 43.17 5.68
2172 2304 3.564027 CCCGATTGGAGCGAACGC 61.564 66.667 11.31 11.31 42.33 4.84
2173 2305 3.564027 GCCCGATTGGAGCGAACG 61.564 66.667 0.00 0.00 37.49 3.95
2178 2310 3.564027 CGTTCGCCCGATTGGAGC 61.564 66.667 0.00 1.25 37.49 4.70
2179 2311 3.564027 GCGTTCGCCCGATTGGAG 61.564 66.667 0.00 0.00 37.49 3.86
2182 2314 3.695933 GAACGCGTTCGCCCGATTG 62.696 63.158 33.47 0.00 39.84 2.67
2183 2315 3.484547 GAACGCGTTCGCCCGATT 61.485 61.111 33.47 4.92 39.84 3.34
2194 2326 4.562142 CCCATAGGATAAGGGGAACGCG 62.562 59.091 3.53 3.53 45.75 6.01
2195 2327 1.003233 CCCATAGGATAAGGGGAACGC 59.997 57.143 0.00 0.00 45.75 4.84
2202 2334 2.989571 AGGAAAGCCCCATAGGATAAGG 59.010 50.000 0.00 0.00 38.24 2.69
2203 2335 3.652869 TGAGGAAAGCCCCATAGGATAAG 59.347 47.826 0.00 0.00 38.24 1.73
2204 2336 3.394606 GTGAGGAAAGCCCCATAGGATAA 59.605 47.826 0.00 0.00 38.24 1.75
2205 2337 2.979678 GTGAGGAAAGCCCCATAGGATA 59.020 50.000 0.00 0.00 38.24 2.59
2206 2338 1.777272 GTGAGGAAAGCCCCATAGGAT 59.223 52.381 0.00 0.00 38.24 3.24
2207 2339 1.213296 GTGAGGAAAGCCCCATAGGA 58.787 55.000 0.00 0.00 38.24 2.94
2208 2340 1.141858 GAGTGAGGAAAGCCCCATAGG 59.858 57.143 0.00 0.00 39.47 2.57
2209 2341 1.202580 CGAGTGAGGAAAGCCCCATAG 60.203 57.143 0.00 0.00 34.66 2.23
2210 2342 0.830648 CGAGTGAGGAAAGCCCCATA 59.169 55.000 0.00 0.00 34.66 2.74
2211 2343 1.604378 CGAGTGAGGAAAGCCCCAT 59.396 57.895 0.00 0.00 34.66 4.00
2212 2344 3.068881 CGAGTGAGGAAAGCCCCA 58.931 61.111 0.00 0.00 34.66 4.96
2213 2345 2.436824 GCGAGTGAGGAAAGCCCC 60.437 66.667 0.00 0.00 34.66 5.80
2214 2346 1.743252 CAGCGAGTGAGGAAAGCCC 60.743 63.158 0.00 0.00 33.31 5.19
2215 2347 0.107945 ATCAGCGAGTGAGGAAAGCC 60.108 55.000 0.00 0.00 39.07 4.35
2216 2348 1.663135 GAATCAGCGAGTGAGGAAAGC 59.337 52.381 0.00 0.00 39.07 3.51
2217 2349 2.670414 GTGAATCAGCGAGTGAGGAAAG 59.330 50.000 0.00 0.00 39.07 2.62
2218 2350 2.300152 AGTGAATCAGCGAGTGAGGAAA 59.700 45.455 0.00 0.00 39.07 3.13
2219 2351 1.895798 AGTGAATCAGCGAGTGAGGAA 59.104 47.619 0.00 0.00 39.07 3.36
2220 2352 1.474478 GAGTGAATCAGCGAGTGAGGA 59.526 52.381 0.00 0.00 39.07 3.71
2221 2353 1.203287 TGAGTGAATCAGCGAGTGAGG 59.797 52.381 0.00 0.00 39.07 3.86
2222 2354 2.643933 TGAGTGAATCAGCGAGTGAG 57.356 50.000 0.00 0.00 39.07 3.51
2223 2355 2.610479 GGTTGAGTGAATCAGCGAGTGA 60.610 50.000 0.00 0.00 39.88 3.41
2224 2356 1.728971 GGTTGAGTGAATCAGCGAGTG 59.271 52.381 0.00 0.00 39.88 3.51
2225 2357 1.620819 AGGTTGAGTGAATCAGCGAGT 59.379 47.619 0.00 0.00 39.88 4.18
2226 2358 2.376808 AGGTTGAGTGAATCAGCGAG 57.623 50.000 0.00 0.00 39.88 5.03
2227 2359 3.447229 TGATAGGTTGAGTGAATCAGCGA 59.553 43.478 0.00 0.00 39.88 4.93
2245 2377 0.752658 CGGCCAGTCAGGTGATGATA 59.247 55.000 2.24 0.00 40.92 2.15
2247 2379 2.981302 CGGCCAGTCAGGTGATGA 59.019 61.111 2.24 0.00 40.61 2.92
2249 2381 4.101448 GGCGGCCAGTCAGGTGAT 62.101 66.667 15.62 0.00 40.61 3.06
2272 2404 4.431131 AATGGTGGAGGCCCGCTG 62.431 66.667 0.00 0.00 42.54 5.18
2273 2405 4.431131 CAATGGTGGAGGCCCGCT 62.431 66.667 0.00 0.00 42.54 5.52
2301 2434 0.944999 ATCTGCCTAGGAGAAGGGGA 59.055 55.000 14.75 0.00 37.11 4.81
2323 2456 6.855763 TTTCCTACAAAGAATGCCATTGAT 57.144 33.333 0.00 0.00 0.00 2.57
2377 2510 7.094334 TGCCATGTGACCGTTAAAAACATATTA 60.094 33.333 0.00 0.00 30.55 0.98
2378 2511 6.096695 GCCATGTGACCGTTAAAAACATATT 58.903 36.000 0.00 0.00 30.55 1.28
2383 2516 3.357166 TGCCATGTGACCGTTAAAAAC 57.643 42.857 0.00 0.00 0.00 2.43
2392 2525 5.132897 TGTTCTTAATTTGCCATGTGACC 57.867 39.130 0.00 0.00 0.00 4.02
2393 2526 8.810427 CATAATGTTCTTAATTTGCCATGTGAC 58.190 33.333 0.00 0.00 0.00 3.67
2398 2531 9.382275 GGAAACATAATGTTCTTAATTTGCCAT 57.618 29.630 0.00 0.00 40.14 4.40
2420 2553 3.703556 TCAGTTTGCCATGTTTCTGGAAA 59.296 39.130 0.00 0.00 38.69 3.13
2421 2554 3.295093 TCAGTTTGCCATGTTTCTGGAA 58.705 40.909 0.00 0.00 38.69 3.53
2422 2555 2.942804 TCAGTTTGCCATGTTTCTGGA 58.057 42.857 0.00 0.00 38.69 3.86
2423 2556 3.731652 TTCAGTTTGCCATGTTTCTGG 57.268 42.857 0.00 0.00 39.45 3.86
2424 2557 6.869913 ACATATTTCAGTTTGCCATGTTTCTG 59.130 34.615 0.00 0.00 0.00 3.02
2425 2558 6.996509 ACATATTTCAGTTTGCCATGTTTCT 58.003 32.000 0.00 0.00 0.00 2.52
2426 2559 8.755696 TTACATATTTCAGTTTGCCATGTTTC 57.244 30.769 0.00 0.00 0.00 2.78
2434 2567 7.273381 GTGTGACCATTACATATTTCAGTTTGC 59.727 37.037 0.00 0.00 0.00 3.68
2439 2572 5.504010 GCCGTGTGACCATTACATATTTCAG 60.504 44.000 0.00 0.00 0.00 3.02
2462 2595 7.295201 TGAGACAAGTGTAATCGTAAAAATGC 58.705 34.615 0.00 0.00 0.00 3.56
2485 2618 1.539388 GAATTTGCCGTGGACACATGA 59.461 47.619 0.00 0.00 35.58 3.07


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

AutoCloner maintained by Alex Coulton.