Multiple sequence alignment - TraesCS1D01G358300

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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 TraesCS1D01G358300 chr1D 100.000 2291 0 0 1 2291 441957807 441960097 0.000000e+00 4231.0
1 TraesCS1D01G358300 chr1D 96.117 721 28 0 1319 2039 442440581 442439861 0.000000e+00 1177.0
2 TraesCS1D01G358300 chr1D 97.472 356 9 0 1 356 442440925 442440570 1.950000e-170 608.0
3 TraesCS1D01G358300 chr1D 97.628 253 5 1 2039 2291 441967388 441967639 1.260000e-117 433.0
4 TraesCS1D01G358300 chr1D 79.883 343 59 8 7 344 442449171 442448834 2.270000e-60 243.0
5 TraesCS1D01G358300 chr1D 77.747 364 51 17 1 355 442444419 442444077 1.800000e-46 196.0
6 TraesCS1D01G358300 chr1D 100.000 29 0 0 1986 2014 408870853 408870881 1.000000e-03 54.7
7 TraesCS1D01G358300 chr6D 98.506 937 12 2 385 1320 132301225 132302160 0.000000e+00 1652.0
8 TraesCS1D01G358300 chr6D 94.068 236 12 2 2056 2291 222245671 222245438 7.780000e-95 357.0
9 TraesCS1D01G358300 chr6D 100.000 35 0 0 356 390 132301174 132301140 5.280000e-07 65.8
10 TraesCS1D01G358300 chr3B 96.261 936 35 0 385 1320 534100837 534101772 0.000000e+00 1535.0
11 TraesCS1D01G358300 chr6A 96.257 935 35 0 385 1319 373083674 373082740 0.000000e+00 1533.0
12 TraesCS1D01G358300 chr6A 90.734 259 20 4 2034 2291 253485976 253485721 2.180000e-90 342.0
13 TraesCS1D01G358300 chr6A 100.000 33 0 0 356 388 373083725 373083757 6.830000e-06 62.1
14 TraesCS1D01G358300 chr5B 95.962 941 36 2 385 1324 138157377 138158316 0.000000e+00 1526.0
15 TraesCS1D01G358300 chr5B 88.841 932 100 4 392 1320 704295754 704294824 0.000000e+00 1142.0
16 TraesCS1D01G358300 chr5B 86.766 937 119 5 385 1319 612423439 612422506 0.000000e+00 1038.0
17 TraesCS1D01G358300 chr5B 97.258 547 15 0 774 1320 442850531 442851077 0.000000e+00 928.0
18 TraesCS1D01G358300 chr5B 95.556 405 15 3 385 788 442847617 442848019 0.000000e+00 645.0
19 TraesCS1D01G358300 chr5B 100.000 34 0 0 357 390 442847565 442847532 1.900000e-06 63.9
20 TraesCS1D01G358300 chr1A 91.475 739 44 6 1319 2039 536246855 536247592 0.000000e+00 998.0
21 TraesCS1D01G358300 chr1A 96.620 355 12 0 2 356 536246512 536246866 7.050000e-165 590.0
22 TraesCS1D01G358300 chr1A 81.174 579 96 9 1327 1896 536204689 536205263 9.650000e-124 453.0
23 TraesCS1D01G358300 chr1A 93.644 236 13 2 2056 2291 102534074 102534307 3.620000e-93 351.0
24 TraesCS1D01G358300 chr1A 94.000 50 3 0 1 50 536238448 536238497 2.440000e-10 76.8
25 TraesCS1D01G358300 chr1B 90.042 713 69 2 1327 2039 601087380 601086670 0.000000e+00 922.0
26 TraesCS1D01G358300 chr1B 77.384 367 48 19 1 355 602160140 602160483 3.890000e-43 185.0
27 TraesCS1D01G358300 chr1B 74.286 245 55 7 103 343 602222611 602222851 1.870000e-16 97.1
28 TraesCS1D01G358300 chr3A 76.415 954 202 20 381 1323 178990007 178989066 5.690000e-136 494.0
29 TraesCS1D01G358300 chr4A 75.840 952 206 19 378 1320 26542896 26543832 1.600000e-126 462.0
30 TraesCS1D01G358300 chr4A 91.732 254 18 3 2039 2291 370498059 370498310 1.300000e-92 350.0
31 TraesCS1D01G358300 chr7B 92.623 244 11 5 2049 2291 171945715 171945478 6.060000e-91 344.0
32 TraesCS1D01G358300 chr7A 92.562 242 15 3 2051 2291 683274821 683274582 6.060000e-91 344.0
33 TraesCS1D01G358300 chr7A 90.551 254 20 4 2039 2291 358302521 358302771 1.310000e-87 333.0
34 TraesCS1D01G358300 chr2D 91.093 247 18 4 2045 2290 482192933 482192690 4.720000e-87 331.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G358300 chr1D 441957807 441960097 2290 False 4231.000000 4231 100.000000 1 2291 1 chr1D.!!$F2 2290
1 TraesCS1D01G358300 chr1D 442439861 442444419 4558 True 660.333333 1177 90.445333 1 2039 3 chr1D.!!$R2 2038
2 TraesCS1D01G358300 chr6D 132301225 132302160 935 False 1652.000000 1652 98.506000 385 1320 1 chr6D.!!$F1 935
3 TraesCS1D01G358300 chr3B 534100837 534101772 935 False 1535.000000 1535 96.261000 385 1320 1 chr3B.!!$F1 935
4 TraesCS1D01G358300 chr6A 373082740 373083674 934 True 1533.000000 1533 96.257000 385 1319 1 chr6A.!!$R2 934
5 TraesCS1D01G358300 chr5B 138157377 138158316 939 False 1526.000000 1526 95.962000 385 1324 1 chr5B.!!$F1 939
6 TraesCS1D01G358300 chr5B 704294824 704295754 930 True 1142.000000 1142 88.841000 392 1320 1 chr5B.!!$R3 928
7 TraesCS1D01G358300 chr5B 612422506 612423439 933 True 1038.000000 1038 86.766000 385 1319 1 chr5B.!!$R2 934
8 TraesCS1D01G358300 chr5B 442847617 442851077 3460 False 786.500000 928 96.407000 385 1320 2 chr5B.!!$F2 935
9 TraesCS1D01G358300 chr1A 536246512 536247592 1080 False 794.000000 998 94.047500 2 2039 2 chr1A.!!$F4 2037
10 TraesCS1D01G358300 chr1A 536204689 536205263 574 False 453.000000 453 81.174000 1327 1896 1 chr1A.!!$F2 569
11 TraesCS1D01G358300 chr1B 601086670 601087380 710 True 922.000000 922 90.042000 1327 2039 1 chr1B.!!$R1 712
12 TraesCS1D01G358300 chr3A 178989066 178990007 941 True 494.000000 494 76.415000 381 1323 1 chr3A.!!$R1 942
13 TraesCS1D01G358300 chr4A 26542896 26543832 936 False 462.000000 462 75.840000 378 1320 1 chr4A.!!$F1 942

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
351 3846 0.323178 CACTGGCTCATCAAGGGCTT 60.323 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 8147 0.036732 TCCATCCTCTGTTGGTGCAC 59.963 55.0 8.8 8.8 33.73 4.57 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
152 3647 2.635338 GACGGCCACGAAAACCAC 59.365 61.111 2.24 0.00 44.60 4.16
209 3704 5.485353 GTCATCACCTTGGGATATCATAGGA 59.515 44.000 18.54 3.60 0.00 2.94
225 3720 1.486310 TAGGAGGCCTTACAGCATGTG 59.514 52.381 6.77 0.00 42.41 3.21
239 3734 1.881973 GCATGTGCACTTTCTCTTCCA 59.118 47.619 19.41 0.00 41.59 3.53
309 3804 1.002134 CCTTCGTCCATGGCAACCT 60.002 57.895 6.96 0.00 0.00 3.50
351 3846 0.323178 CACTGGCTCATCAAGGGCTT 60.323 55.000 0.00 0.00 0.00 4.35
352 3847 0.323178 ACTGGCTCATCAAGGGCTTG 60.323 55.000 0.00 0.00 41.71 4.01
353 3848 1.000521 TGGCTCATCAAGGGCTTGG 60.001 57.895 0.00 0.00 40.78 3.61
354 3849 1.755783 GGCTCATCAAGGGCTTGGG 60.756 63.158 0.00 0.00 40.78 4.12
355 3850 2.421399 GCTCATCAAGGGCTTGGGC 61.421 63.158 0.00 0.00 40.78 5.36
366 3861 3.520623 GCTTGGGCCATATGTTCCT 57.479 52.632 7.26 0.00 0.00 3.36
367 3862 1.322442 GCTTGGGCCATATGTTCCTC 58.678 55.000 7.26 0.00 0.00 3.71
368 3863 1.986882 CTTGGGCCATATGTTCCTCC 58.013 55.000 7.26 0.00 0.00 4.30
369 3864 1.215173 CTTGGGCCATATGTTCCTCCA 59.785 52.381 7.26 0.00 0.00 3.86
370 3865 1.303898 TGGGCCATATGTTCCTCCAA 58.696 50.000 0.00 0.00 0.00 3.53
371 3866 1.858910 TGGGCCATATGTTCCTCCAAT 59.141 47.619 0.00 0.00 0.00 3.16
372 3867 2.158475 TGGGCCATATGTTCCTCCAATC 60.158 50.000 0.00 0.00 0.00 2.67
373 3868 2.154462 GGCCATATGTTCCTCCAATCG 58.846 52.381 0.00 0.00 0.00 3.34
374 3869 2.224523 GGCCATATGTTCCTCCAATCGA 60.225 50.000 0.00 0.00 0.00 3.59
375 3870 3.560025 GGCCATATGTTCCTCCAATCGAT 60.560 47.826 0.00 0.00 0.00 3.59
376 3871 3.438087 GCCATATGTTCCTCCAATCGATG 59.562 47.826 0.00 0.00 0.00 3.84
377 3872 4.645535 CCATATGTTCCTCCAATCGATGT 58.354 43.478 0.00 0.00 0.00 3.06
378 3873 4.692625 CCATATGTTCCTCCAATCGATGTC 59.307 45.833 0.00 0.00 0.00 3.06
379 3874 3.912496 ATGTTCCTCCAATCGATGTCA 57.088 42.857 0.00 0.00 0.00 3.58
380 3875 2.972625 TGTTCCTCCAATCGATGTCAC 58.027 47.619 0.00 0.00 0.00 3.67
381 3876 2.280628 GTTCCTCCAATCGATGTCACC 58.719 52.381 0.00 0.00 0.00 4.02
382 3877 1.567357 TCCTCCAATCGATGTCACCA 58.433 50.000 0.00 0.00 0.00 4.17
383 3878 2.118679 TCCTCCAATCGATGTCACCAT 58.881 47.619 0.00 0.00 0.00 3.55
540 4035 4.327680 GAGCACTACAAATGGAAGAGGTT 58.672 43.478 0.00 0.00 0.00 3.50
566 4061 1.136690 CGTATGTGTGCGTGTTCTGT 58.863 50.000 0.00 0.00 0.00 3.41
1429 7462 5.048364 TGCGAATACAACAGCTTTAACCATT 60.048 36.000 0.00 0.00 0.00 3.16
1530 7566 5.471556 TTACATGTAAAGGTGACGAAGGA 57.528 39.130 15.92 0.00 0.00 3.36
1627 7663 2.158900 GCACTCTACATGTATGTGGGCT 60.159 50.000 26.41 2.35 41.89 5.19
1717 7753 0.394352 AATTGATGAGGTCACGGGCC 60.394 55.000 0.00 0.00 36.32 5.80
1721 7757 2.185310 GATGAGGTCACGGGCCTGTT 62.185 60.000 16.73 0.00 36.29 3.16
1725 7761 2.203294 GTCACGGGCCTGTTTGGT 60.203 61.111 16.73 0.00 38.35 3.67
1802 7838 1.305549 CCAGCTTGGAGGCCCATTT 60.306 57.895 0.00 0.00 43.12 2.32
1821 7858 5.353956 CCATTTAAATCATGTCGTGGACTCA 59.646 40.000 0.00 0.00 33.15 3.41
1878 7919 6.926280 TGCTTAATGTTGATTTTGTAAGCG 57.074 33.333 8.27 0.00 40.85 4.68
1911 7952 3.190744 GGCTAAAAGGTTACTGCAGGAAC 59.809 47.826 30.43 30.43 0.00 3.62
1947 7988 9.554395 TTTATGATCATTGGCGAAATCTACTAA 57.446 29.630 14.65 0.00 0.00 2.24
2079 8138 6.719365 GGATTGACAAAATCCTAACTCATCG 58.281 40.000 9.40 0.00 42.23 3.84
2080 8139 6.538742 GGATTGACAAAATCCTAACTCATCGA 59.461 38.462 9.40 0.00 42.23 3.59
2081 8140 7.227512 GGATTGACAAAATCCTAACTCATCGAT 59.772 37.037 9.40 0.00 42.23 3.59
2082 8141 7.539712 TTGACAAAATCCTAACTCATCGATC 57.460 36.000 0.00 0.00 0.00 3.69
2083 8142 5.748630 TGACAAAATCCTAACTCATCGATCG 59.251 40.000 9.36 9.36 0.00 3.69
2084 8143 5.902681 ACAAAATCCTAACTCATCGATCGA 58.097 37.500 21.86 21.86 0.00 3.59
2085 8144 6.338146 ACAAAATCCTAACTCATCGATCGAA 58.662 36.000 23.50 5.51 0.00 3.71
2086 8145 6.477033 ACAAAATCCTAACTCATCGATCGAAG 59.523 38.462 23.50 18.46 0.00 3.79
2087 8146 6.392625 AAATCCTAACTCATCGATCGAAGA 57.607 37.500 23.50 21.87 45.75 2.87
2088 8147 5.621197 ATCCTAACTCATCGATCGAAGAG 57.379 43.478 35.93 35.93 43.63 2.85
2091 8150 2.483583 ACTCATCGATCGAAGAGTGC 57.516 50.000 39.85 0.00 46.93 4.40
2092 8151 1.745653 ACTCATCGATCGAAGAGTGCA 59.254 47.619 39.85 14.91 46.93 4.57
2093 8152 2.115595 CTCATCGATCGAAGAGTGCAC 58.884 52.381 31.93 9.40 43.63 4.57
2094 8153 1.202302 TCATCGATCGAAGAGTGCACC 60.202 52.381 23.50 5.12 43.63 5.01
2095 8154 0.817654 ATCGATCGAAGAGTGCACCA 59.182 50.000 23.50 0.00 43.63 4.17
2096 8155 0.601057 TCGATCGAAGAGTGCACCAA 59.399 50.000 16.99 0.00 43.63 3.67
2097 8156 0.716108 CGATCGAAGAGTGCACCAAC 59.284 55.000 14.63 5.68 43.63 3.77
2098 8157 1.795768 GATCGAAGAGTGCACCAACA 58.204 50.000 14.63 0.00 43.63 3.33
2099 8158 1.728971 GATCGAAGAGTGCACCAACAG 59.271 52.381 14.63 2.90 43.63 3.16
2100 8159 0.750249 TCGAAGAGTGCACCAACAGA 59.250 50.000 14.63 5.50 0.00 3.41
2101 8160 1.143305 CGAAGAGTGCACCAACAGAG 58.857 55.000 14.63 0.00 0.00 3.35
2102 8161 1.517242 GAAGAGTGCACCAACAGAGG 58.483 55.000 14.63 0.00 0.00 3.69
2103 8162 1.070758 GAAGAGTGCACCAACAGAGGA 59.929 52.381 14.63 0.00 0.00 3.71
2104 8163 1.356124 AGAGTGCACCAACAGAGGAT 58.644 50.000 14.63 0.00 0.00 3.24
2105 8164 1.002888 AGAGTGCACCAACAGAGGATG 59.997 52.381 14.63 0.00 0.00 3.51
2106 8165 0.037303 AGTGCACCAACAGAGGATGG 59.963 55.000 14.63 0.00 42.37 3.51
2107 8166 0.036732 GTGCACCAACAGAGGATGGA 59.963 55.000 5.22 0.00 39.20 3.41
2108 8167 0.036732 TGCACCAACAGAGGATGGAC 59.963 55.000 0.00 0.00 39.20 4.02
2109 8168 0.326264 GCACCAACAGAGGATGGACT 59.674 55.000 0.00 0.00 39.20 3.85
2110 8169 1.555075 GCACCAACAGAGGATGGACTA 59.445 52.381 0.00 0.00 39.20 2.59
2111 8170 2.419297 GCACCAACAGAGGATGGACTAG 60.419 54.545 0.00 0.00 39.20 2.57
2112 8171 2.169352 CACCAACAGAGGATGGACTAGG 59.831 54.545 0.00 0.00 39.20 3.02
2113 8172 2.225650 ACCAACAGAGGATGGACTAGGT 60.226 50.000 0.00 0.00 39.20 3.08
2114 8173 3.012502 ACCAACAGAGGATGGACTAGGTA 59.987 47.826 0.00 0.00 39.20 3.08
2115 8174 3.639094 CCAACAGAGGATGGACTAGGTAG 59.361 52.174 0.00 0.00 39.20 3.18
2116 8175 2.952116 ACAGAGGATGGACTAGGTAGC 58.048 52.381 0.00 0.00 0.00 3.58
2117 8176 2.245028 ACAGAGGATGGACTAGGTAGCA 59.755 50.000 0.00 0.00 0.00 3.49
2118 8177 2.625790 CAGAGGATGGACTAGGTAGCAC 59.374 54.545 0.00 0.00 0.00 4.40
2119 8178 1.609555 GAGGATGGACTAGGTAGCACG 59.390 57.143 0.00 0.00 0.00 5.34
2120 8179 1.214673 AGGATGGACTAGGTAGCACGA 59.785 52.381 0.00 0.00 0.00 4.35
2121 8180 2.158445 AGGATGGACTAGGTAGCACGAT 60.158 50.000 0.00 0.00 0.00 3.73
2122 8181 2.229302 GGATGGACTAGGTAGCACGATC 59.771 54.545 0.00 0.00 0.00 3.69
2123 8182 2.430248 TGGACTAGGTAGCACGATCA 57.570 50.000 0.00 0.00 0.00 2.92
2124 8183 2.298610 TGGACTAGGTAGCACGATCAG 58.701 52.381 0.00 0.00 0.00 2.90
2125 8184 2.299521 GGACTAGGTAGCACGATCAGT 58.700 52.381 0.00 0.00 0.00 3.41
2126 8185 2.291190 GGACTAGGTAGCACGATCAGTC 59.709 54.545 0.00 0.00 0.00 3.51
2127 8186 2.291190 GACTAGGTAGCACGATCAGTCC 59.709 54.545 0.00 0.00 0.00 3.85
2128 8187 2.092321 ACTAGGTAGCACGATCAGTCCT 60.092 50.000 0.00 0.00 0.00 3.85
2129 8188 2.730934 AGGTAGCACGATCAGTCCTA 57.269 50.000 0.00 0.00 0.00 2.94
2130 8189 2.577700 AGGTAGCACGATCAGTCCTAG 58.422 52.381 0.00 0.00 0.00 3.02
2131 8190 2.172930 AGGTAGCACGATCAGTCCTAGA 59.827 50.000 0.00 0.00 0.00 2.43
2132 8191 2.950309 GGTAGCACGATCAGTCCTAGAA 59.050 50.000 0.00 0.00 0.00 2.10
2133 8192 3.570550 GGTAGCACGATCAGTCCTAGAAT 59.429 47.826 0.00 0.00 0.00 2.40
2134 8193 4.760715 GGTAGCACGATCAGTCCTAGAATA 59.239 45.833 0.00 0.00 0.00 1.75
2135 8194 5.106475 GGTAGCACGATCAGTCCTAGAATAG 60.106 48.000 0.00 0.00 38.80 1.73
2136 8195 4.465886 AGCACGATCAGTCCTAGAATAGT 58.534 43.478 0.00 0.00 36.82 2.12
2137 8196 4.277174 AGCACGATCAGTCCTAGAATAGTG 59.723 45.833 0.00 0.00 36.82 2.74
2138 8197 4.276183 GCACGATCAGTCCTAGAATAGTGA 59.724 45.833 0.00 0.00 36.82 3.41
2139 8198 5.048364 GCACGATCAGTCCTAGAATAGTGAT 60.048 44.000 8.79 8.79 35.43 3.06
2140 8199 6.515862 GCACGATCAGTCCTAGAATAGTGATT 60.516 42.308 9.84 0.00 33.63 2.57
2141 8200 7.081349 CACGATCAGTCCTAGAATAGTGATTC 58.919 42.308 9.84 0.00 41.69 2.52
2142 8201 6.072948 ACGATCAGTCCTAGAATAGTGATTCG 60.073 42.308 9.84 13.71 45.34 3.34
2143 8202 6.147985 CGATCAGTCCTAGAATAGTGATTCGA 59.852 42.308 9.84 0.00 45.34 3.71
2144 8203 7.148323 CGATCAGTCCTAGAATAGTGATTCGAT 60.148 40.741 9.84 0.00 45.34 3.59
2145 8204 9.168451 GATCAGTCCTAGAATAGTGATTCGATA 57.832 37.037 9.84 0.00 45.34 2.92
2146 8205 8.919777 TCAGTCCTAGAATAGTGATTCGATAA 57.080 34.615 0.00 0.00 45.34 1.75
2147 8206 8.784994 TCAGTCCTAGAATAGTGATTCGATAAC 58.215 37.037 0.00 0.00 45.34 1.89
2148 8207 8.024285 CAGTCCTAGAATAGTGATTCGATAACC 58.976 40.741 0.00 0.00 45.34 2.85
2149 8208 7.724506 AGTCCTAGAATAGTGATTCGATAACCA 59.275 37.037 0.00 0.00 45.34 3.67
2150 8209 8.358148 GTCCTAGAATAGTGATTCGATAACCAA 58.642 37.037 0.00 0.00 45.34 3.67
2151 8210 8.358148 TCCTAGAATAGTGATTCGATAACCAAC 58.642 37.037 0.00 0.00 45.34 3.77
2152 8211 8.141909 CCTAGAATAGTGATTCGATAACCAACA 58.858 37.037 0.00 0.00 45.34 3.33
2153 8212 7.772332 AGAATAGTGATTCGATAACCAACAC 57.228 36.000 0.00 0.00 45.34 3.32
2154 8213 6.475727 AGAATAGTGATTCGATAACCAACACG 59.524 38.462 0.00 0.00 45.34 4.49
2155 8214 2.671396 AGTGATTCGATAACCAACACGC 59.329 45.455 0.00 0.00 33.00 5.34
2156 8215 2.671396 GTGATTCGATAACCAACACGCT 59.329 45.455 0.00 0.00 0.00 5.07
2157 8216 3.861113 GTGATTCGATAACCAACACGCTA 59.139 43.478 0.00 0.00 0.00 4.26
2158 8217 4.327898 GTGATTCGATAACCAACACGCTAA 59.672 41.667 0.00 0.00 0.00 3.09
2159 8218 4.565166 TGATTCGATAACCAACACGCTAAG 59.435 41.667 0.00 0.00 0.00 2.18
2160 8219 3.853831 TCGATAACCAACACGCTAAGA 57.146 42.857 0.00 0.00 0.00 2.10
2161 8220 4.177165 TCGATAACCAACACGCTAAGAA 57.823 40.909 0.00 0.00 0.00 2.52
2162 8221 4.751060 TCGATAACCAACACGCTAAGAAT 58.249 39.130 0.00 0.00 0.00 2.40
2163 8222 4.565166 TCGATAACCAACACGCTAAGAATG 59.435 41.667 0.00 0.00 0.00 2.67
2164 8223 4.565166 CGATAACCAACACGCTAAGAATGA 59.435 41.667 0.00 0.00 0.00 2.57
2165 8224 5.276395 CGATAACCAACACGCTAAGAATGAG 60.276 44.000 0.00 0.00 0.00 2.90
2166 8225 3.678056 ACCAACACGCTAAGAATGAGA 57.322 42.857 0.00 0.00 0.00 3.27
2167 8226 4.207891 ACCAACACGCTAAGAATGAGAT 57.792 40.909 0.00 0.00 0.00 2.75
2168 8227 4.579869 ACCAACACGCTAAGAATGAGATT 58.420 39.130 0.00 0.00 0.00 2.40
2169 8228 5.730550 ACCAACACGCTAAGAATGAGATTA 58.269 37.500 0.00 0.00 0.00 1.75
2170 8229 6.349300 ACCAACACGCTAAGAATGAGATTAT 58.651 36.000 0.00 0.00 0.00 1.28
2171 8230 6.823689 ACCAACACGCTAAGAATGAGATTATT 59.176 34.615 0.00 0.00 0.00 1.40
2172 8231 7.128331 CCAACACGCTAAGAATGAGATTATTG 58.872 38.462 0.00 0.00 0.00 1.90
2173 8232 7.201644 CCAACACGCTAAGAATGAGATTATTGT 60.202 37.037 0.00 0.00 0.00 2.71
2174 8233 7.470289 ACACGCTAAGAATGAGATTATTGTC 57.530 36.000 0.00 0.00 0.00 3.18
2175 8234 6.480320 ACACGCTAAGAATGAGATTATTGTCC 59.520 38.462 0.00 0.00 0.00 4.02
2176 8235 6.479990 CACGCTAAGAATGAGATTATTGTCCA 59.520 38.462 0.00 0.00 0.00 4.02
2177 8236 7.172190 CACGCTAAGAATGAGATTATTGTCCAT 59.828 37.037 0.00 0.00 0.00 3.41
2178 8237 7.716998 ACGCTAAGAATGAGATTATTGTCCATT 59.283 33.333 0.00 0.00 0.00 3.16
2179 8238 9.208022 CGCTAAGAATGAGATTATTGTCCATTA 57.792 33.333 0.00 0.00 0.00 1.90
2188 8247 9.613428 TGAGATTATTGTCCATTAACTACCAAG 57.387 33.333 0.00 0.00 0.00 3.61
2189 8248 8.451908 AGATTATTGTCCATTAACTACCAAGC 57.548 34.615 0.00 0.00 0.00 4.01
2190 8249 8.052748 AGATTATTGTCCATTAACTACCAAGCA 58.947 33.333 0.00 0.00 0.00 3.91
2191 8250 8.588290 ATTATTGTCCATTAACTACCAAGCAA 57.412 30.769 0.00 0.00 0.00 3.91
2192 8251 5.699097 TTGTCCATTAACTACCAAGCAAC 57.301 39.130 0.00 0.00 0.00 4.17
2193 8252 4.720046 TGTCCATTAACTACCAAGCAACA 58.280 39.130 0.00 0.00 0.00 3.33
2194 8253 4.759693 TGTCCATTAACTACCAAGCAACAG 59.240 41.667 0.00 0.00 0.00 3.16
2195 8254 4.156008 GTCCATTAACTACCAAGCAACAGG 59.844 45.833 0.00 0.00 0.00 4.00
2196 8255 3.443681 CCATTAACTACCAAGCAACAGGG 59.556 47.826 0.00 0.00 0.00 4.45
2197 8256 3.868619 TTAACTACCAAGCAACAGGGT 57.131 42.857 0.00 0.00 38.70 4.34
2198 8257 2.748209 AACTACCAAGCAACAGGGTT 57.252 45.000 0.00 0.00 37.82 4.11
2206 8265 2.859992 GCAACAGGGTTGCTAGGAG 58.140 57.895 22.81 0.00 41.87 3.69
2207 8266 0.036875 GCAACAGGGTTGCTAGGAGT 59.963 55.000 22.81 0.00 41.87 3.85
2208 8267 1.278127 GCAACAGGGTTGCTAGGAGTA 59.722 52.381 22.81 0.00 41.87 2.59
2209 8268 2.092914 GCAACAGGGTTGCTAGGAGTAT 60.093 50.000 22.81 0.00 41.87 2.12
2210 8269 3.622455 GCAACAGGGTTGCTAGGAGTATT 60.622 47.826 22.81 0.00 41.87 1.89
2211 8270 3.914426 ACAGGGTTGCTAGGAGTATTG 57.086 47.619 0.00 0.00 0.00 1.90
2212 8271 3.450904 ACAGGGTTGCTAGGAGTATTGA 58.549 45.455 0.00 0.00 0.00 2.57
2213 8272 4.040755 ACAGGGTTGCTAGGAGTATTGAT 58.959 43.478 0.00 0.00 0.00 2.57
2214 8273 4.475016 ACAGGGTTGCTAGGAGTATTGATT 59.525 41.667 0.00 0.00 0.00 2.57
2215 8274 5.059833 CAGGGTTGCTAGGAGTATTGATTC 58.940 45.833 0.00 0.00 0.00 2.52
2216 8275 4.103311 AGGGTTGCTAGGAGTATTGATTCC 59.897 45.833 0.00 0.00 0.00 3.01
2217 8276 4.141482 GGGTTGCTAGGAGTATTGATTCCA 60.141 45.833 0.00 0.00 33.85 3.53
2218 8277 4.816925 GGTTGCTAGGAGTATTGATTCCAC 59.183 45.833 0.00 0.00 33.85 4.02
2219 8278 5.428253 GTTGCTAGGAGTATTGATTCCACA 58.572 41.667 0.00 0.00 33.85 4.17
2220 8279 5.023533 TGCTAGGAGTATTGATTCCACAC 57.976 43.478 0.00 0.00 33.85 3.82
2221 8280 4.469586 TGCTAGGAGTATTGATTCCACACA 59.530 41.667 0.00 0.00 33.85 3.72
2222 8281 5.130975 TGCTAGGAGTATTGATTCCACACAT 59.869 40.000 0.00 0.00 33.85 3.21
2223 8282 5.698545 GCTAGGAGTATTGATTCCACACATC 59.301 44.000 0.00 0.00 33.85 3.06
2224 8283 5.698741 AGGAGTATTGATTCCACACATCA 57.301 39.130 0.00 0.00 33.85 3.07
2225 8284 5.431765 AGGAGTATTGATTCCACACATCAC 58.568 41.667 0.00 0.00 33.85 3.06
2226 8285 4.271049 GGAGTATTGATTCCACACATCACG 59.729 45.833 0.00 0.00 31.70 4.35
2227 8286 4.191544 AGTATTGATTCCACACATCACGG 58.808 43.478 0.00 0.00 30.09 4.94
2228 8287 2.559698 TTGATTCCACACATCACGGT 57.440 45.000 0.00 0.00 30.09 4.83
2229 8288 2.559698 TGATTCCACACATCACGGTT 57.440 45.000 0.00 0.00 0.00 4.44
2230 8289 2.422597 TGATTCCACACATCACGGTTC 58.577 47.619 0.00 0.00 0.00 3.62
2231 8290 2.224402 TGATTCCACACATCACGGTTCA 60.224 45.455 0.00 0.00 0.00 3.18
2232 8291 1.588674 TTCCACACATCACGGTTCAC 58.411 50.000 0.00 0.00 0.00 3.18
2233 8292 0.250124 TCCACACATCACGGTTCACC 60.250 55.000 0.00 0.00 0.00 4.02
2234 8293 0.250295 CCACACATCACGGTTCACCT 60.250 55.000 0.00 0.00 0.00 4.00
2235 8294 0.867746 CACACATCACGGTTCACCTG 59.132 55.000 0.00 0.00 0.00 4.00
2236 8295 0.468226 ACACATCACGGTTCACCTGT 59.532 50.000 0.00 0.00 0.00 4.00
2237 8296 1.148310 CACATCACGGTTCACCTGTC 58.852 55.000 0.00 0.00 0.00 3.51
2238 8297 0.319555 ACATCACGGTTCACCTGTCG 60.320 55.000 0.00 0.00 0.00 4.35
2239 8298 1.014044 CATCACGGTTCACCTGTCGG 61.014 60.000 0.00 0.00 0.00 4.79
2240 8299 2.781595 ATCACGGTTCACCTGTCGGC 62.782 60.000 0.00 0.00 0.00 5.54
2241 8300 3.542676 ACGGTTCACCTGTCGGCA 61.543 61.111 0.00 0.00 0.00 5.69
2242 8301 2.047274 CGGTTCACCTGTCGGCAT 60.047 61.111 0.00 0.00 0.00 4.40
2243 8302 1.671054 CGGTTCACCTGTCGGCATT 60.671 57.895 0.00 0.00 0.00 3.56
2244 8303 1.635663 CGGTTCACCTGTCGGCATTC 61.636 60.000 0.00 0.00 0.00 2.67
2245 8304 1.305930 GGTTCACCTGTCGGCATTCC 61.306 60.000 0.00 0.00 0.00 3.01
2267 8326 1.869132 GTTACAACCAACACGGAGACC 59.131 52.381 0.00 0.00 38.63 3.85
2268 8327 1.121378 TACAACCAACACGGAGACCA 58.879 50.000 0.00 0.00 38.63 4.02
2269 8328 0.253610 ACAACCAACACGGAGACCAA 59.746 50.000 0.00 0.00 38.63 3.67
2270 8329 0.944386 CAACCAACACGGAGACCAAG 59.056 55.000 0.00 0.00 38.63 3.61
2271 8330 0.834612 AACCAACACGGAGACCAAGA 59.165 50.000 0.00 0.00 38.63 3.02
2272 8331 0.834612 ACCAACACGGAGACCAAGAA 59.165 50.000 0.00 0.00 38.63 2.52
2273 8332 1.210967 ACCAACACGGAGACCAAGAAA 59.789 47.619 0.00 0.00 38.63 2.52
2274 8333 2.158667 ACCAACACGGAGACCAAGAAAT 60.159 45.455 0.00 0.00 38.63 2.17
2275 8334 2.226437 CCAACACGGAGACCAAGAAATG 59.774 50.000 0.00 0.00 36.56 2.32
2276 8335 3.138304 CAACACGGAGACCAAGAAATGA 58.862 45.455 0.00 0.00 0.00 2.57
2277 8336 3.485463 ACACGGAGACCAAGAAATGAA 57.515 42.857 0.00 0.00 0.00 2.57
2278 8337 4.021102 ACACGGAGACCAAGAAATGAAT 57.979 40.909 0.00 0.00 0.00 2.57
2279 8338 5.160607 ACACGGAGACCAAGAAATGAATA 57.839 39.130 0.00 0.00 0.00 1.75
2280 8339 5.556915 ACACGGAGACCAAGAAATGAATAA 58.443 37.500 0.00 0.00 0.00 1.40
2281 8340 6.180472 ACACGGAGACCAAGAAATGAATAAT 58.820 36.000 0.00 0.00 0.00 1.28
2282 8341 6.094048 ACACGGAGACCAAGAAATGAATAATG 59.906 38.462 0.00 0.00 0.00 1.90
2283 8342 6.316140 CACGGAGACCAAGAAATGAATAATGA 59.684 38.462 0.00 0.00 0.00 2.57
2284 8343 7.012704 CACGGAGACCAAGAAATGAATAATGAT 59.987 37.037 0.00 0.00 0.00 2.45
2285 8344 7.012704 ACGGAGACCAAGAAATGAATAATGATG 59.987 37.037 0.00 0.00 0.00 3.07
2286 8345 7.521099 CGGAGACCAAGAAATGAATAATGATGG 60.521 40.741 0.00 0.00 0.00 3.51
2287 8346 7.047460 AGACCAAGAAATGAATAATGATGGC 57.953 36.000 0.00 0.00 0.00 4.40
2288 8347 5.835257 ACCAAGAAATGAATAATGATGGCG 58.165 37.500 0.00 0.00 0.00 5.69
2289 8348 5.593909 ACCAAGAAATGAATAATGATGGCGA 59.406 36.000 0.00 0.00 0.00 5.54
2290 8349 6.096705 ACCAAGAAATGAATAATGATGGCGAA 59.903 34.615 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 3647 1.470098 GAATGTTGTGTAGCCTGGCAG 59.530 52.381 22.65 7.75 0.00 4.85
192 3687 2.507471 GGCCTCCTATGATATCCCAAGG 59.493 54.545 0.00 4.67 0.00 3.61
209 3704 0.962356 GTGCACATGCTGTAAGGCCT 60.962 55.000 13.17 0.00 42.66 5.19
225 3720 3.063485 GACTCAGTGGAAGAGAAAGTGC 58.937 50.000 0.00 0.00 36.91 4.40
239 3734 1.581954 CGCTCCAACTCGACTCAGT 59.418 57.895 0.00 0.00 0.00 3.41
309 3804 2.709125 CTTGCCCCGAGACACGACAA 62.709 60.000 0.00 0.00 45.77 3.18
351 3846 1.303898 TTGGAGGAACATATGGCCCA 58.696 50.000 7.80 3.97 0.00 5.36
352 3847 2.519013 GATTGGAGGAACATATGGCCC 58.481 52.381 7.80 7.55 0.00 5.80
353 3848 2.154462 CGATTGGAGGAACATATGGCC 58.846 52.381 7.80 8.15 0.00 5.36
354 3849 3.126001 TCGATTGGAGGAACATATGGC 57.874 47.619 7.80 0.00 0.00 4.40
355 3850 4.645535 ACATCGATTGGAGGAACATATGG 58.354 43.478 7.80 0.00 0.00 2.74
356 3851 5.178252 GTGACATCGATTGGAGGAACATATG 59.822 44.000 0.00 0.00 0.00 1.78
357 3852 5.300752 GTGACATCGATTGGAGGAACATAT 58.699 41.667 0.00 0.00 0.00 1.78
358 3853 4.442893 GGTGACATCGATTGGAGGAACATA 60.443 45.833 0.00 0.00 0.00 2.29
359 3854 3.535561 GTGACATCGATTGGAGGAACAT 58.464 45.455 0.00 0.00 0.00 2.71
360 3855 2.354704 GGTGACATCGATTGGAGGAACA 60.355 50.000 0.00 0.00 0.00 3.18
361 3856 2.280628 GGTGACATCGATTGGAGGAAC 58.719 52.381 0.00 0.00 0.00 3.62
362 3857 1.905894 TGGTGACATCGATTGGAGGAA 59.094 47.619 0.00 0.00 33.40 3.36
363 3858 1.567357 TGGTGACATCGATTGGAGGA 58.433 50.000 0.00 0.00 33.40 3.71
376 3871 1.160137 GGCAGACTGTTGATGGTGAC 58.840 55.000 3.99 0.00 0.00 3.67
377 3872 1.059098 AGGCAGACTGTTGATGGTGA 58.941 50.000 3.99 0.00 0.00 4.02
378 3873 1.901591 AAGGCAGACTGTTGATGGTG 58.098 50.000 3.99 0.00 0.00 4.17
379 3874 2.233271 CAAAGGCAGACTGTTGATGGT 58.767 47.619 3.99 0.00 0.00 3.55
380 3875 1.068055 GCAAAGGCAGACTGTTGATGG 60.068 52.381 3.99 0.00 40.72 3.51
381 3876 1.884579 AGCAAAGGCAGACTGTTGATG 59.115 47.619 3.99 0.72 44.61 3.07
382 3877 2.283145 AGCAAAGGCAGACTGTTGAT 57.717 45.000 3.99 0.00 44.61 2.57
383 3878 2.057137 AAGCAAAGGCAGACTGTTGA 57.943 45.000 3.99 0.00 44.61 3.18
540 4035 2.813474 GCACACATACGCAGCCGA 60.813 61.111 0.00 0.00 38.29 5.54
566 4061 6.206634 CAGTAATTTAACCACTCCTCTTGCAA 59.793 38.462 0.00 0.00 0.00 4.08
1323 7356 1.471829 GGGTCCAAAAGTTGCCCAGG 61.472 60.000 0.00 0.00 39.13 4.45
1429 7462 1.885157 CCACGCTAAGTACCGGTGA 59.115 57.895 19.93 0.00 0.00 4.02
1530 7566 0.892755 CAGCAACACCATTGCCATCT 59.107 50.000 7.97 0.00 45.98 2.90
1627 7663 2.181777 CAGTGCCGCGCTCTTCTA 59.818 61.111 5.56 0.00 29.56 2.10
1717 7753 8.294577 GGTATGTCCTTTAAAGTAACCAAACAG 58.705 37.037 14.03 0.00 0.00 3.16
1721 7757 6.532826 ACGGTATGTCCTTTAAAGTAACCAA 58.467 36.000 14.03 1.19 0.00 3.67
1725 7761 5.863397 CACGACGGTATGTCCTTTAAAGTAA 59.137 40.000 14.03 0.00 45.23 2.24
1802 7838 9.423061 CAATATATGAGTCCACGACATGATTTA 57.577 33.333 0.00 0.00 34.60 1.40
1878 7919 1.202031 CCTTTTAGCCGCAATGTCGTC 60.202 52.381 0.00 0.00 0.00 4.20
1911 7952 5.276270 CCAATGATCATAAAGAACTTGCGG 58.724 41.667 9.04 0.00 0.00 5.69
2039 8098 6.653020 TGTCAATCCTTGCTCTATTGTACAT 58.347 36.000 0.00 0.00 33.35 2.29
2040 8099 6.048732 TGTCAATCCTTGCTCTATTGTACA 57.951 37.500 0.00 0.00 33.35 2.90
2041 8100 6.985188 TTGTCAATCCTTGCTCTATTGTAC 57.015 37.500 0.00 0.00 33.35 2.90
2042 8101 7.994425 TTTTGTCAATCCTTGCTCTATTGTA 57.006 32.000 0.00 0.00 33.35 2.41
2043 8102 6.899393 TTTTGTCAATCCTTGCTCTATTGT 57.101 33.333 0.00 0.00 33.35 2.71
2044 8103 6.976925 GGATTTTGTCAATCCTTGCTCTATTG 59.023 38.462 6.38 0.00 42.23 1.90
2045 8104 7.105241 GGATTTTGTCAATCCTTGCTCTATT 57.895 36.000 6.38 0.00 42.23 1.73
2046 8105 6.705863 GGATTTTGTCAATCCTTGCTCTAT 57.294 37.500 6.38 0.00 42.23 1.98
2055 8114 6.538742 TCGATGAGTTAGGATTTTGTCAATCC 59.461 38.462 5.58 5.58 45.08 3.01
2056 8115 7.539712 TCGATGAGTTAGGATTTTGTCAATC 57.460 36.000 0.00 0.00 0.00 2.67
2057 8116 7.042456 CGATCGATGAGTTAGGATTTTGTCAAT 60.042 37.037 10.26 0.00 0.00 2.57
2058 8117 6.255670 CGATCGATGAGTTAGGATTTTGTCAA 59.744 38.462 10.26 0.00 0.00 3.18
2059 8118 5.748630 CGATCGATGAGTTAGGATTTTGTCA 59.251 40.000 10.26 0.00 0.00 3.58
2060 8119 5.977725 TCGATCGATGAGTTAGGATTTTGTC 59.022 40.000 15.15 0.00 0.00 3.18
2061 8120 5.902681 TCGATCGATGAGTTAGGATTTTGT 58.097 37.500 15.15 0.00 0.00 2.83
2062 8121 6.697455 TCTTCGATCGATGAGTTAGGATTTTG 59.303 38.462 24.91 0.00 0.00 2.44
2063 8122 6.806751 TCTTCGATCGATGAGTTAGGATTTT 58.193 36.000 24.91 0.00 0.00 1.82
2064 8123 6.392625 TCTTCGATCGATGAGTTAGGATTT 57.607 37.500 24.91 0.00 0.00 2.17
2065 8124 6.007936 CTCTTCGATCGATGAGTTAGGATT 57.992 41.667 35.34 0.00 39.84 3.01
2066 8125 5.621197 CTCTTCGATCGATGAGTTAGGAT 57.379 43.478 35.34 0.00 39.84 3.24
2073 8132 2.115595 GTGCACTCTTCGATCGATGAG 58.884 52.381 38.77 38.77 45.89 2.90
2074 8133 1.202302 GGTGCACTCTTCGATCGATGA 60.202 52.381 26.31 26.31 0.00 2.92
2075 8134 1.203928 GGTGCACTCTTCGATCGATG 58.796 55.000 20.18 20.94 0.00 3.84
2076 8135 0.817654 TGGTGCACTCTTCGATCGAT 59.182 50.000 20.18 0.00 0.00 3.59
2077 8136 0.601057 TTGGTGCACTCTTCGATCGA 59.399 50.000 15.15 15.15 0.00 3.59
2078 8137 0.716108 GTTGGTGCACTCTTCGATCG 59.284 55.000 17.98 9.36 0.00 3.69
2079 8138 1.728971 CTGTTGGTGCACTCTTCGATC 59.271 52.381 17.98 0.00 0.00 3.69
2080 8139 1.344438 TCTGTTGGTGCACTCTTCGAT 59.656 47.619 17.98 0.00 0.00 3.59
2081 8140 0.750249 TCTGTTGGTGCACTCTTCGA 59.250 50.000 17.98 5.74 0.00 3.71
2082 8141 1.143305 CTCTGTTGGTGCACTCTTCG 58.857 55.000 17.98 3.31 0.00 3.79
2083 8142 1.070758 TCCTCTGTTGGTGCACTCTTC 59.929 52.381 17.98 0.00 0.00 2.87
2084 8143 1.131638 TCCTCTGTTGGTGCACTCTT 58.868 50.000 17.98 0.00 0.00 2.85
2085 8144 1.002888 CATCCTCTGTTGGTGCACTCT 59.997 52.381 17.98 0.00 0.00 3.24
2086 8145 1.446907 CATCCTCTGTTGGTGCACTC 58.553 55.000 17.98 7.60 0.00 3.51
2087 8146 0.037303 CCATCCTCTGTTGGTGCACT 59.963 55.000 17.98 0.00 0.00 4.40
2088 8147 0.036732 TCCATCCTCTGTTGGTGCAC 59.963 55.000 8.80 8.80 33.73 4.57
2089 8148 0.036732 GTCCATCCTCTGTTGGTGCA 59.963 55.000 0.00 0.00 33.73 4.57
2090 8149 0.326264 AGTCCATCCTCTGTTGGTGC 59.674 55.000 0.00 0.00 33.73 5.01
2091 8150 2.169352 CCTAGTCCATCCTCTGTTGGTG 59.831 54.545 0.00 0.00 33.73 4.17
2092 8151 2.225650 ACCTAGTCCATCCTCTGTTGGT 60.226 50.000 0.00 0.00 33.73 3.67
2093 8152 2.472029 ACCTAGTCCATCCTCTGTTGG 58.528 52.381 0.00 0.00 33.35 3.77
2094 8153 3.068873 GCTACCTAGTCCATCCTCTGTTG 59.931 52.174 0.00 0.00 0.00 3.33
2095 8154 3.301274 GCTACCTAGTCCATCCTCTGTT 58.699 50.000 0.00 0.00 0.00 3.16
2096 8155 2.245028 TGCTACCTAGTCCATCCTCTGT 59.755 50.000 0.00 0.00 0.00 3.41
2097 8156 2.625790 GTGCTACCTAGTCCATCCTCTG 59.374 54.545 0.00 0.00 0.00 3.35
2098 8157 2.750135 CGTGCTACCTAGTCCATCCTCT 60.750 54.545 0.00 0.00 0.00 3.69
2099 8158 1.609555 CGTGCTACCTAGTCCATCCTC 59.390 57.143 0.00 0.00 0.00 3.71
2100 8159 1.214673 TCGTGCTACCTAGTCCATCCT 59.785 52.381 0.00 0.00 0.00 3.24
2101 8160 1.688772 TCGTGCTACCTAGTCCATCC 58.311 55.000 0.00 0.00 0.00 3.51
2102 8161 2.885266 TGATCGTGCTACCTAGTCCATC 59.115 50.000 0.00 0.00 0.00 3.51
2103 8162 2.887783 CTGATCGTGCTACCTAGTCCAT 59.112 50.000 0.00 0.00 0.00 3.41
2104 8163 2.298610 CTGATCGTGCTACCTAGTCCA 58.701 52.381 0.00 0.00 0.00 4.02
2105 8164 2.291190 GACTGATCGTGCTACCTAGTCC 59.709 54.545 0.00 0.00 0.00 3.85
2106 8165 2.291190 GGACTGATCGTGCTACCTAGTC 59.709 54.545 0.00 0.00 34.01 2.59
2107 8166 2.092321 AGGACTGATCGTGCTACCTAGT 60.092 50.000 9.29 0.00 43.06 2.57
2108 8167 2.577700 AGGACTGATCGTGCTACCTAG 58.422 52.381 9.29 0.00 43.06 3.02
2109 8168 2.730934 AGGACTGATCGTGCTACCTA 57.269 50.000 9.29 0.00 43.06 3.08
2110 8169 2.172930 TCTAGGACTGATCGTGCTACCT 59.827 50.000 12.40 7.47 43.06 3.08
2111 8170 2.573369 TCTAGGACTGATCGTGCTACC 58.427 52.381 12.40 1.70 43.06 3.18
2112 8171 4.839668 ATTCTAGGACTGATCGTGCTAC 57.160 45.455 12.40 0.00 43.06 3.58
2113 8172 5.470437 CACTATTCTAGGACTGATCGTGCTA 59.530 44.000 14.54 14.54 43.06 3.49
2114 8173 4.277174 CACTATTCTAGGACTGATCGTGCT 59.723 45.833 13.97 13.97 46.78 4.40
2115 8174 4.276183 TCACTATTCTAGGACTGATCGTGC 59.724 45.833 0.00 2.00 0.00 5.34
2116 8175 6.567687 ATCACTATTCTAGGACTGATCGTG 57.432 41.667 0.00 0.00 0.00 4.35
2117 8176 6.072948 CGAATCACTATTCTAGGACTGATCGT 60.073 42.308 0.00 0.00 39.56 3.73
2118 8177 6.147985 TCGAATCACTATTCTAGGACTGATCG 59.852 42.308 0.00 0.00 39.56 3.69
2119 8178 7.441890 TCGAATCACTATTCTAGGACTGATC 57.558 40.000 0.00 0.00 39.56 2.92
2120 8179 9.521841 TTATCGAATCACTATTCTAGGACTGAT 57.478 33.333 0.00 0.00 39.56 2.90
2121 8180 8.784994 GTTATCGAATCACTATTCTAGGACTGA 58.215 37.037 0.00 0.00 39.56 3.41
2122 8181 8.024285 GGTTATCGAATCACTATTCTAGGACTG 58.976 40.741 0.00 0.00 39.56 3.51
2123 8182 7.724506 TGGTTATCGAATCACTATTCTAGGACT 59.275 37.037 0.00 0.00 39.56 3.85
2124 8183 7.883217 TGGTTATCGAATCACTATTCTAGGAC 58.117 38.462 0.00 0.00 39.56 3.85
2125 8184 8.358148 GTTGGTTATCGAATCACTATTCTAGGA 58.642 37.037 0.00 0.00 39.56 2.94
2126 8185 8.141909 TGTTGGTTATCGAATCACTATTCTAGG 58.858 37.037 0.00 0.00 39.56 3.02
2127 8186 8.969267 GTGTTGGTTATCGAATCACTATTCTAG 58.031 37.037 0.00 0.00 39.56 2.43
2128 8187 7.646526 CGTGTTGGTTATCGAATCACTATTCTA 59.353 37.037 0.00 0.00 39.56 2.10
2129 8188 6.475727 CGTGTTGGTTATCGAATCACTATTCT 59.524 38.462 0.00 0.00 39.56 2.40
2130 8189 6.637365 CGTGTTGGTTATCGAATCACTATTC 58.363 40.000 0.00 0.00 38.53 1.75
2131 8190 5.006358 GCGTGTTGGTTATCGAATCACTATT 59.994 40.000 0.00 0.00 0.00 1.73
2132 8191 4.506654 GCGTGTTGGTTATCGAATCACTAT 59.493 41.667 0.00 0.00 0.00 2.12
2133 8192 3.861113 GCGTGTTGGTTATCGAATCACTA 59.139 43.478 0.00 0.00 0.00 2.74
2134 8193 2.671396 GCGTGTTGGTTATCGAATCACT 59.329 45.455 0.00 0.00 0.00 3.41
2135 8194 2.671396 AGCGTGTTGGTTATCGAATCAC 59.329 45.455 0.00 0.00 0.00 3.06
2136 8195 2.967362 AGCGTGTTGGTTATCGAATCA 58.033 42.857 0.00 0.00 0.00 2.57
2137 8196 4.802039 TCTTAGCGTGTTGGTTATCGAATC 59.198 41.667 0.00 0.00 0.00 2.52
2138 8197 4.751060 TCTTAGCGTGTTGGTTATCGAAT 58.249 39.130 0.00 0.00 0.00 3.34
2139 8198 4.177165 TCTTAGCGTGTTGGTTATCGAA 57.823 40.909 0.00 0.00 0.00 3.71
2140 8199 3.853831 TCTTAGCGTGTTGGTTATCGA 57.146 42.857 0.00 0.00 0.00 3.59
2141 8200 4.565166 TCATTCTTAGCGTGTTGGTTATCG 59.435 41.667 0.00 0.00 0.00 2.92
2142 8201 5.810587 TCTCATTCTTAGCGTGTTGGTTATC 59.189 40.000 0.00 0.00 0.00 1.75
2143 8202 5.730550 TCTCATTCTTAGCGTGTTGGTTAT 58.269 37.500 0.00 0.00 0.00 1.89
2144 8203 5.142061 TCTCATTCTTAGCGTGTTGGTTA 57.858 39.130 0.00 0.00 0.00 2.85
2145 8204 4.002906 TCTCATTCTTAGCGTGTTGGTT 57.997 40.909 0.00 0.00 0.00 3.67
2146 8205 3.678056 TCTCATTCTTAGCGTGTTGGT 57.322 42.857 0.00 0.00 0.00 3.67
2147 8206 6.851222 ATAATCTCATTCTTAGCGTGTTGG 57.149 37.500 0.00 0.00 0.00 3.77
2148 8207 7.688372 ACAATAATCTCATTCTTAGCGTGTTG 58.312 34.615 0.00 0.00 0.00 3.33
2149 8208 7.011482 GGACAATAATCTCATTCTTAGCGTGTT 59.989 37.037 0.00 0.00 0.00 3.32
2150 8209 6.480320 GGACAATAATCTCATTCTTAGCGTGT 59.520 38.462 0.00 0.00 0.00 4.49
2151 8210 6.479990 TGGACAATAATCTCATTCTTAGCGTG 59.520 38.462 0.00 0.00 0.00 5.34
2152 8211 6.582636 TGGACAATAATCTCATTCTTAGCGT 58.417 36.000 0.00 0.00 0.00 5.07
2153 8212 7.664082 ATGGACAATAATCTCATTCTTAGCG 57.336 36.000 0.00 0.00 0.00 4.26
2162 8221 9.613428 CTTGGTAGTTAATGGACAATAATCTCA 57.387 33.333 0.00 0.00 0.00 3.27
2163 8222 8.560374 GCTTGGTAGTTAATGGACAATAATCTC 58.440 37.037 0.00 0.00 0.00 2.75
2164 8223 8.052748 TGCTTGGTAGTTAATGGACAATAATCT 58.947 33.333 0.00 0.00 0.00 2.40
2165 8224 8.220755 TGCTTGGTAGTTAATGGACAATAATC 57.779 34.615 0.00 0.00 0.00 1.75
2166 8225 8.466798 GTTGCTTGGTAGTTAATGGACAATAAT 58.533 33.333 0.00 0.00 0.00 1.28
2167 8226 7.448777 TGTTGCTTGGTAGTTAATGGACAATAA 59.551 33.333 0.00 0.00 0.00 1.40
2168 8227 6.943146 TGTTGCTTGGTAGTTAATGGACAATA 59.057 34.615 0.00 0.00 0.00 1.90
2169 8228 5.772672 TGTTGCTTGGTAGTTAATGGACAAT 59.227 36.000 0.00 0.00 0.00 2.71
2170 8229 5.133941 TGTTGCTTGGTAGTTAATGGACAA 58.866 37.500 0.00 0.00 0.00 3.18
2171 8230 4.720046 TGTTGCTTGGTAGTTAATGGACA 58.280 39.130 0.00 0.00 0.00 4.02
2172 8231 4.156008 CCTGTTGCTTGGTAGTTAATGGAC 59.844 45.833 0.00 0.00 0.00 4.02
2173 8232 4.331968 CCTGTTGCTTGGTAGTTAATGGA 58.668 43.478 0.00 0.00 0.00 3.41
2174 8233 3.443681 CCCTGTTGCTTGGTAGTTAATGG 59.556 47.826 0.00 0.00 0.00 3.16
2175 8234 4.079253 ACCCTGTTGCTTGGTAGTTAATG 58.921 43.478 0.00 0.00 0.00 1.90
2176 8235 4.382386 ACCCTGTTGCTTGGTAGTTAAT 57.618 40.909 0.00 0.00 0.00 1.40
2177 8236 3.868619 ACCCTGTTGCTTGGTAGTTAA 57.131 42.857 0.00 0.00 0.00 2.01
2178 8237 3.482436 CAACCCTGTTGCTTGGTAGTTA 58.518 45.455 0.00 0.00 0.00 2.24
2179 8238 2.306847 CAACCCTGTTGCTTGGTAGTT 58.693 47.619 0.00 0.00 0.00 2.24
2180 8239 1.981256 CAACCCTGTTGCTTGGTAGT 58.019 50.000 0.00 0.00 0.00 2.73
2181 8240 0.598065 GCAACCCTGTTGCTTGGTAG 59.402 55.000 21.26 0.00 41.87 3.18
2182 8241 2.727103 GCAACCCTGTTGCTTGGTA 58.273 52.632 21.26 0.00 41.87 3.25
2183 8242 3.537388 GCAACCCTGTTGCTTGGT 58.463 55.556 21.26 0.00 41.87 3.67
2188 8247 0.036875 ACTCCTAGCAACCCTGTTGC 59.963 55.000 21.06 21.06 45.22 4.17
2189 8248 3.914426 ATACTCCTAGCAACCCTGTTG 57.086 47.619 2.65 2.65 0.00 3.33
2190 8249 3.844211 TCAATACTCCTAGCAACCCTGTT 59.156 43.478 0.00 0.00 0.00 3.16
2191 8250 3.450904 TCAATACTCCTAGCAACCCTGT 58.549 45.455 0.00 0.00 0.00 4.00
2192 8251 4.696479 ATCAATACTCCTAGCAACCCTG 57.304 45.455 0.00 0.00 0.00 4.45
2193 8252 4.103311 GGAATCAATACTCCTAGCAACCCT 59.897 45.833 0.00 0.00 0.00 4.34
2194 8253 4.141482 TGGAATCAATACTCCTAGCAACCC 60.141 45.833 0.00 0.00 32.51 4.11
2195 8254 4.816925 GTGGAATCAATACTCCTAGCAACC 59.183 45.833 0.00 0.00 32.51 3.77
2196 8255 5.294552 GTGTGGAATCAATACTCCTAGCAAC 59.705 44.000 0.00 0.00 32.51 4.17
2197 8256 5.045942 TGTGTGGAATCAATACTCCTAGCAA 60.046 40.000 0.00 0.00 32.51 3.91
2198 8257 4.469586 TGTGTGGAATCAATACTCCTAGCA 59.530 41.667 0.00 0.00 32.51 3.49
2199 8258 5.023533 TGTGTGGAATCAATACTCCTAGC 57.976 43.478 0.00 0.00 32.51 3.42
2200 8259 6.703607 GTGATGTGTGGAATCAATACTCCTAG 59.296 42.308 0.00 0.00 35.87 3.02
2201 8260 6.582636 GTGATGTGTGGAATCAATACTCCTA 58.417 40.000 0.00 0.00 35.87 2.94
2202 8261 5.431765 GTGATGTGTGGAATCAATACTCCT 58.568 41.667 0.00 0.00 35.87 3.69
2203 8262 4.271049 CGTGATGTGTGGAATCAATACTCC 59.729 45.833 0.00 0.00 35.87 3.85
2204 8263 4.271049 CCGTGATGTGTGGAATCAATACTC 59.729 45.833 0.00 0.00 35.87 2.59
2205 8264 4.191544 CCGTGATGTGTGGAATCAATACT 58.808 43.478 0.00 0.00 35.87 2.12
2206 8265 3.938963 ACCGTGATGTGTGGAATCAATAC 59.061 43.478 0.00 0.00 35.87 1.89
2207 8266 4.214986 ACCGTGATGTGTGGAATCAATA 57.785 40.909 0.00 0.00 35.87 1.90
2208 8267 3.071874 ACCGTGATGTGTGGAATCAAT 57.928 42.857 0.00 0.00 35.87 2.57
2209 8268 2.559698 ACCGTGATGTGTGGAATCAA 57.440 45.000 0.00 0.00 35.87 2.57
2210 8269 2.224402 TGAACCGTGATGTGTGGAATCA 60.224 45.455 0.00 0.00 0.00 2.57
2211 8270 2.159627 GTGAACCGTGATGTGTGGAATC 59.840 50.000 0.00 0.00 0.00 2.52
2212 8271 2.151202 GTGAACCGTGATGTGTGGAAT 58.849 47.619 0.00 0.00 0.00 3.01
2213 8272 1.588674 GTGAACCGTGATGTGTGGAA 58.411 50.000 0.00 0.00 0.00 3.53
2214 8273 0.250124 GGTGAACCGTGATGTGTGGA 60.250 55.000 0.00 0.00 0.00 4.02
2215 8274 0.250295 AGGTGAACCGTGATGTGTGG 60.250 55.000 0.00 0.00 42.08 4.17
2216 8275 0.867746 CAGGTGAACCGTGATGTGTG 59.132 55.000 0.00 0.00 42.08 3.82
2217 8276 0.468226 ACAGGTGAACCGTGATGTGT 59.532 50.000 6.10 0.00 42.08 3.72
2218 8277 1.148310 GACAGGTGAACCGTGATGTG 58.852 55.000 0.00 0.00 42.08 3.21
2219 8278 0.319555 CGACAGGTGAACCGTGATGT 60.320 55.000 2.43 0.00 42.08 3.06
2220 8279 1.014044 CCGACAGGTGAACCGTGATG 61.014 60.000 2.43 0.00 42.08 3.07
2221 8280 1.292223 CCGACAGGTGAACCGTGAT 59.708 57.895 2.43 0.00 42.08 3.06
2222 8281 2.732016 CCGACAGGTGAACCGTGA 59.268 61.111 2.43 0.00 42.08 4.35
2223 8282 3.041940 GCCGACAGGTGAACCGTG 61.042 66.667 2.43 0.86 42.08 4.94
2224 8283 2.391724 AATGCCGACAGGTGAACCGT 62.392 55.000 0.00 0.00 42.08 4.83
2225 8284 1.635663 GAATGCCGACAGGTGAACCG 61.636 60.000 0.00 0.00 42.08 4.44
2226 8285 1.305930 GGAATGCCGACAGGTGAACC 61.306 60.000 0.00 0.00 40.50 3.62
2227 8286 2.171635 GGAATGCCGACAGGTGAAC 58.828 57.895 0.00 0.00 40.50 3.18
2228 8287 4.713946 GGAATGCCGACAGGTGAA 57.286 55.556 0.00 0.00 40.50 3.18
2247 8306 1.869132 GGTCTCCGTGTTGGTTGTAAC 59.131 52.381 0.00 0.00 39.52 2.50
2248 8307 1.485480 TGGTCTCCGTGTTGGTTGTAA 59.515 47.619 0.00 0.00 39.52 2.41
2249 8308 1.121378 TGGTCTCCGTGTTGGTTGTA 58.879 50.000 0.00 0.00 39.52 2.41
2250 8309 0.253610 TTGGTCTCCGTGTTGGTTGT 59.746 50.000 0.00 0.00 39.52 3.32
2251 8310 0.944386 CTTGGTCTCCGTGTTGGTTG 59.056 55.000 0.00 0.00 39.52 3.77
2252 8311 0.834612 TCTTGGTCTCCGTGTTGGTT 59.165 50.000 0.00 0.00 39.52 3.67
2253 8312 0.834612 TTCTTGGTCTCCGTGTTGGT 59.165 50.000 0.00 0.00 39.52 3.67
2254 8313 1.961793 TTTCTTGGTCTCCGTGTTGG 58.038 50.000 0.00 0.00 40.09 3.77
2255 8314 3.138304 TCATTTCTTGGTCTCCGTGTTG 58.862 45.455 0.00 0.00 0.00 3.33
2256 8315 3.485463 TCATTTCTTGGTCTCCGTGTT 57.515 42.857 0.00 0.00 0.00 3.32
2257 8316 3.485463 TTCATTTCTTGGTCTCCGTGT 57.515 42.857 0.00 0.00 0.00 4.49
2258 8317 6.316140 TCATTATTCATTTCTTGGTCTCCGTG 59.684 38.462 0.00 0.00 0.00 4.94
2259 8318 6.414732 TCATTATTCATTTCTTGGTCTCCGT 58.585 36.000 0.00 0.00 0.00 4.69
2260 8319 6.925610 TCATTATTCATTTCTTGGTCTCCG 57.074 37.500 0.00 0.00 0.00 4.63
2261 8320 7.655490 CCATCATTATTCATTTCTTGGTCTCC 58.345 38.462 0.00 0.00 0.00 3.71
2262 8321 7.144000 GCCATCATTATTCATTTCTTGGTCTC 58.856 38.462 0.00 0.00 0.00 3.36
2263 8322 6.238842 CGCCATCATTATTCATTTCTTGGTCT 60.239 38.462 0.00 0.00 0.00 3.85
2264 8323 5.916883 CGCCATCATTATTCATTTCTTGGTC 59.083 40.000 0.00 0.00 0.00 4.02
2265 8324 5.593909 TCGCCATCATTATTCATTTCTTGGT 59.406 36.000 0.00 0.00 0.00 3.67
2266 8325 6.075762 TCGCCATCATTATTCATTTCTTGG 57.924 37.500 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.