Multiple sequence alignment - TraesCS4A01G049100

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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 TraesCS4A01G049100 chr4A 100.000 2359 0 0 1 2359 40238191 40235833 0.000000e+00 4357
1 TraesCS4A01G049100 chr4A 98.636 220 2 1 2140 2359 498210780 498210998 2.840000e-104 388
2 TraesCS4A01G049100 chr4D 86.139 1782 100 53 467 2141 424572551 424574292 0.000000e+00 1786
3 TraesCS4A01G049100 chr4D 82.305 486 46 16 3 465 424571925 424572393 3.680000e-103 385
4 TraesCS4A01G049100 chr4B 87.896 1545 77 29 688 2150 520418815 520420331 0.000000e+00 1716
5 TraesCS4A01G049100 chr4B 91.696 289 20 2 166 453 520418429 520418714 4.720000e-107 398
6 TraesCS4A01G049100 chr4B 100.000 213 0 0 2147 2359 128540875 128541087 6.110000e-106 394
7 TraesCS4A01G049100 chr4B 98.643 221 3 0 2139 2359 461692729 461692949 2.200000e-105 392
8 TraesCS4A01G049100 chr4B 83.333 156 13 7 453 607 520418660 520418803 5.290000e-27 132
9 TraesCS4A01G049100 chr7A 100.000 213 0 0 2147 2359 317176315 317176103 6.110000e-106 394
10 TraesCS4A01G049100 chr3A 100.000 213 0 0 2147 2359 632556807 632556595 6.110000e-106 394
11 TraesCS4A01G049100 chr3A 98.624 218 3 0 2142 2359 94568673 94568456 1.020000e-103 387
12 TraesCS4A01G049100 chr2A 100.000 213 0 0 2147 2359 740400939 740400727 6.110000e-106 394
13 TraesCS4A01G049100 chr1A 100.000 213 0 0 2147 2359 341181116 341181328 6.110000e-106 394
14 TraesCS4A01G049100 chr3B 100.000 212 0 0 2148 2359 736494077 736493866 2.200000e-105 392


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 TraesCS4A01G049100 chr4A 40235833 40238191 2358 True 4357.000000 4357 100.000000 1 2359 1 chr4A.!!$R1 2358
1 TraesCS4A01G049100 chr4D 424571925 424574292 2367 False 1085.500000 1786 84.222000 3 2141 2 chr4D.!!$F1 2138
2 TraesCS4A01G049100 chr4B 520418429 520420331 1902 False 748.666667 1716 87.641667 166 2150 3 chr4B.!!$F3 1984

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
37 38 0.105760 ATGCCCCAGTTTTGTGGTGA 60.106 50.0 0.0 0.0 35.60 4.02 F
924 1165 0.116342 TGCCAAGAGGACTGGGTAGA 59.884 55.0 0.0 0.0 39.36 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 1441 0.178967 TCCACAGCCCTGCAAATCAA 60.179 50.0 0.0 0.0 0.0 2.57 R
2212 2548 0.178990 GTCAGGGGTGCTTGGAACTT 60.179 55.0 0.0 0.0 0.0 2.66 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
23 24 0.179045 ATAAGCTCACGACCATGCCC 60.179 55.000 0.00 0.00 0.00 5.36
25 26 4.408821 GCTCACGACCATGCCCCA 62.409 66.667 0.00 0.00 0.00 4.96
37 38 0.105760 ATGCCCCAGTTTTGTGGTGA 60.106 50.000 0.00 0.00 35.60 4.02
39 40 1.744320 GCCCCAGTTTTGTGGTGACC 61.744 60.000 0.00 0.00 35.60 4.02
40 41 1.112916 CCCCAGTTTTGTGGTGACCC 61.113 60.000 0.00 0.00 35.60 4.46
52 53 1.979308 TGGTGACCCCGTCAATCTAAA 59.021 47.619 0.00 0.00 44.49 1.85
53 54 2.574369 TGGTGACCCCGTCAATCTAAAT 59.426 45.455 0.00 0.00 44.49 1.40
56 57 3.013921 TGACCCCGTCAATCTAAATTGC 58.986 45.455 0.00 0.00 39.78 3.56
62 63 4.437390 CCCGTCAATCTAAATTGCTGTGTC 60.437 45.833 0.00 0.00 41.76 3.67
80 81 3.005897 GTGTCAGCTCAACAACCTAGAGA 59.994 47.826 0.10 0.00 0.00 3.10
91 92 7.394016 TCAACAACCTAGAGATGCTCATAAAA 58.606 34.615 0.00 0.00 32.06 1.52
95 96 7.225538 ACAACCTAGAGATGCTCATAAAAATCG 59.774 37.037 0.00 0.00 32.06 3.34
102 103 9.499479 AGAGATGCTCATAAAAATCGAATGTAT 57.501 29.630 0.00 0.00 32.06 2.29
111 112 8.684655 CATAAAAATCGAATGTATGTGCATGTC 58.315 33.333 0.00 0.00 0.00 3.06
112 113 6.441093 AAAATCGAATGTATGTGCATGTCT 57.559 33.333 0.00 0.00 0.00 3.41
115 116 5.004922 TCGAATGTATGTGCATGTCTACA 57.995 39.130 0.00 0.00 0.00 2.74
125 126 7.725818 ATGTGCATGTCTACATTCATAGAAG 57.274 36.000 0.00 0.00 34.00 2.85
126 127 6.643388 TGTGCATGTCTACATTCATAGAAGT 58.357 36.000 0.00 0.00 32.57 3.01
127 128 6.536224 TGTGCATGTCTACATTCATAGAAGTG 59.464 38.462 0.00 0.00 32.57 3.16
128 129 6.758416 GTGCATGTCTACATTCATAGAAGTGA 59.242 38.462 0.00 0.00 32.57 3.41
137 138 9.809096 CTACATTCATAGAAGTGAGTATGTGTT 57.191 33.333 0.00 0.00 33.73 3.32
139 140 8.939929 ACATTCATAGAAGTGAGTATGTGTTTG 58.060 33.333 0.00 0.00 31.66 2.93
143 144 9.639601 TCATAGAAGTGAGTATGTGTTTGTAAG 57.360 33.333 0.00 0.00 0.00 2.34
149 150 4.994852 TGAGTATGTGTTTGTAAGTGAGCC 59.005 41.667 0.00 0.00 0.00 4.70
151 152 6.014925 TGAGTATGTGTTTGTAAGTGAGCCTA 60.015 38.462 0.00 0.00 0.00 3.93
153 154 6.818644 AGTATGTGTTTGTAAGTGAGCCTATG 59.181 38.462 0.00 0.00 0.00 2.23
156 157 4.994852 GTGTTTGTAAGTGAGCCTATGTGA 59.005 41.667 0.00 0.00 0.00 3.58
157 158 4.994852 TGTTTGTAAGTGAGCCTATGTGAC 59.005 41.667 0.00 0.00 0.00 3.67
159 160 5.420725 TTGTAAGTGAGCCTATGTGACAT 57.579 39.130 2.65 2.65 0.00 3.06
161 162 5.178061 TGTAAGTGAGCCTATGTGACATTG 58.822 41.667 2.29 0.93 0.00 2.82
229 252 7.752239 CCAGAAAGTTATCTAACATTTGCAGTG 59.248 37.037 3.15 0.14 38.62 3.66
252 275 4.811557 GGAAAGACCTAGATTCATCCAACG 59.188 45.833 0.00 0.00 35.41 4.10
254 277 3.643237 AGACCTAGATTCATCCAACGGA 58.357 45.455 0.00 0.00 35.55 4.69
258 281 4.282195 ACCTAGATTCATCCAACGGAGATC 59.718 45.833 0.00 0.00 34.05 2.75
295 318 1.661341 AACCATCGCAGCTCATCTTC 58.339 50.000 0.00 0.00 0.00 2.87
326 349 0.953960 GTGTCACGGTGACCCCATTC 60.954 60.000 31.93 15.06 46.40 2.67
418 442 7.955864 CGACGATGAATAGTACGAAATATCTGA 59.044 37.037 0.00 0.00 0.00 3.27
435 460 8.915871 AATATCTGAAAAACCAATCATCAACG 57.084 30.769 0.00 0.00 0.00 4.10
487 668 0.534203 TCTGGAAAACCCGTCAGCAC 60.534 55.000 0.00 0.00 37.93 4.40
545 726 0.610232 GCAGCTGACAAGGACCCAAT 60.610 55.000 20.43 0.00 0.00 3.16
546 727 1.915141 CAGCTGACAAGGACCCAATT 58.085 50.000 8.42 0.00 0.00 2.32
547 728 1.542915 CAGCTGACAAGGACCCAATTG 59.457 52.381 8.42 0.00 0.00 2.32
548 729 0.244721 GCTGACAAGGACCCAATTGC 59.755 55.000 0.00 0.00 0.00 3.56
549 730 1.915141 CTGACAAGGACCCAATTGCT 58.085 50.000 0.00 0.00 0.00 3.91
638 844 2.890474 CGCCACATACCCGCACTC 60.890 66.667 0.00 0.00 0.00 3.51
642 848 1.449601 CACATACCCGCACTCCCAC 60.450 63.158 0.00 0.00 0.00 4.61
684 890 4.752879 CGCCTACGTGTGGGTGGG 62.753 72.222 7.97 0.00 41.16 4.61
685 891 3.633116 GCCTACGTGTGGGTGGGT 61.633 66.667 0.00 0.00 40.41 4.51
745 951 1.972752 CCCCGTTAACAAACCCCCG 60.973 63.158 6.39 0.00 0.00 5.73
873 1114 0.179108 AATACGAGCGCCCAGAAGAC 60.179 55.000 2.29 0.00 0.00 3.01
899 1140 2.124445 GCCCCGGTGTCATAACCC 60.124 66.667 0.00 0.00 36.84 4.11
908 1149 1.153229 GTCATAACCCGGGAGTGCC 60.153 63.158 32.02 8.75 0.00 5.01
919 1160 1.298014 GGAGTGCCAAGAGGACTGG 59.702 63.158 0.00 0.00 36.89 4.00
920 1161 1.298014 GAGTGCCAAGAGGACTGGG 59.702 63.158 0.00 0.00 40.12 4.45
923 1164 0.250513 GTGCCAAGAGGACTGGGTAG 59.749 60.000 0.00 0.00 39.36 3.18
924 1165 0.116342 TGCCAAGAGGACTGGGTAGA 59.884 55.000 0.00 0.00 39.36 2.59
925 1166 1.276622 GCCAAGAGGACTGGGTAGAA 58.723 55.000 0.00 0.00 39.36 2.10
926 1167 1.208293 GCCAAGAGGACTGGGTAGAAG 59.792 57.143 0.00 0.00 39.36 2.85
927 1168 1.834263 CCAAGAGGACTGGGTAGAAGG 59.166 57.143 0.00 0.00 36.89 3.46
956 1197 1.608717 CCTCCGAGGGTCTGGTCTTG 61.609 65.000 6.53 0.00 0.00 3.02
960 1201 0.951040 CGAGGGTCTGGTCTTGTTGC 60.951 60.000 0.00 0.00 0.00 4.17
1116 1365 3.255379 CGCTAGCTCGCCGTTTCC 61.255 66.667 13.93 0.00 0.00 3.13
1155 1424 2.678934 TAGGCTGACTCCGGCGTT 60.679 61.111 6.01 0.00 45.55 4.84
1159 1428 2.357517 CTGACTCCGGCGTTGCTT 60.358 61.111 6.01 0.00 0.00 3.91
1160 1429 1.961277 CTGACTCCGGCGTTGCTTT 60.961 57.895 6.01 0.00 0.00 3.51
1164 1433 1.371635 CTCCGGCGTTGCTTTTTGG 60.372 57.895 6.01 0.00 0.00 3.28
1167 1436 1.486644 CCGGCGTTGCTTTTTGGTTG 61.487 55.000 6.01 0.00 0.00 3.77
1168 1437 1.641140 GGCGTTGCTTTTTGGTTGC 59.359 52.632 0.00 0.00 0.00 4.17
1172 1441 1.999024 CGTTGCTTTTTGGTTGCTTGT 59.001 42.857 0.00 0.00 0.00 3.16
1173 1442 2.414825 CGTTGCTTTTTGGTTGCTTGTT 59.585 40.909 0.00 0.00 0.00 2.83
1174 1443 3.724422 CGTTGCTTTTTGGTTGCTTGTTG 60.724 43.478 0.00 0.00 0.00 3.33
1175 1444 3.325293 TGCTTTTTGGTTGCTTGTTGA 57.675 38.095 0.00 0.00 0.00 3.18
1176 1445 3.871485 TGCTTTTTGGTTGCTTGTTGAT 58.129 36.364 0.00 0.00 0.00 2.57
1361 1630 0.755698 TCTGCCGGGACATCTAGACC 60.756 60.000 2.18 0.00 0.00 3.85
1422 1691 1.168714 GGCTTACTGCTTGGTCTTGG 58.831 55.000 0.00 0.00 42.39 3.61
1425 1694 2.154462 CTTACTGCTTGGTCTTGGTGG 58.846 52.381 0.00 0.00 0.00 4.61
1508 1779 4.880537 CCTCTGCTACCGCCGCTG 62.881 72.222 0.00 0.00 34.43 5.18
1509 1780 4.135153 CTCTGCTACCGCCGCTGT 62.135 66.667 0.00 0.00 34.43 4.40
1510 1781 2.752640 TCTGCTACCGCCGCTGTA 60.753 61.111 0.00 0.00 34.43 2.74
1517 1788 0.319211 TACCGCCGCTGTATGTATGC 60.319 55.000 0.00 0.00 0.00 3.14
1662 1936 2.224314 CACGACTCCTTTCTTCTTTGCC 59.776 50.000 0.00 0.00 0.00 4.52
1680 1959 2.819608 TGCCTGCAAACTTTGATCTACC 59.180 45.455 5.65 0.00 0.00 3.18
1702 2013 7.466746 ACCACAAATATTTATGTTCTGCAGT 57.533 32.000 14.67 0.00 0.00 4.40
1729 2040 6.486320 TGTTTGTTCATGCTTCAGATAGACAA 59.514 34.615 0.00 0.00 0.00 3.18
1759 2072 4.326826 TGTTTGTTCAGGCTTCAGATAGG 58.673 43.478 0.00 0.00 0.00 2.57
1779 2092 2.945668 GGCAAAACCTAGTATCAGCAGG 59.054 50.000 0.00 0.00 34.51 4.85
1780 2093 2.945668 GCAAAACCTAGTATCAGCAGGG 59.054 50.000 0.00 0.00 33.48 4.45
1781 2094 3.622455 GCAAAACCTAGTATCAGCAGGGT 60.622 47.826 0.00 0.00 33.48 4.34
1825 2138 1.168714 GTCAGGTTTGATGCTCCACC 58.831 55.000 0.00 0.00 35.39 4.61
1893 2207 2.287608 GCCGACCTGCCAATTAATTAGC 60.288 50.000 11.16 11.16 0.00 3.09
1949 2271 2.566036 CGTCTCAATACGAGCTCGATC 58.434 52.381 40.58 18.56 45.68 3.69
2016 2338 1.556591 CGATCACCACACCACACACG 61.557 60.000 0.00 0.00 0.00 4.49
2071 2404 8.409358 AATAATTGCCTCCAACCAATATCTAC 57.591 34.615 0.00 0.00 32.95 2.59
2115 2451 4.330074 CGCACTTCAACTAACCTAAGATGG 59.670 45.833 0.00 0.00 0.00 3.51
2117 2453 4.636206 CACTTCAACTAACCTAAGATGGCC 59.364 45.833 0.00 0.00 0.00 5.36
2118 2454 4.288626 ACTTCAACTAACCTAAGATGGCCA 59.711 41.667 8.56 8.56 0.00 5.36
2120 2456 3.844211 TCAACTAACCTAAGATGGCCACT 59.156 43.478 8.16 4.50 0.00 4.00
2122 2458 5.128827 TCAACTAACCTAAGATGGCCACTAG 59.871 44.000 8.16 9.55 0.00 2.57
2124 2460 2.868964 ACCTAAGATGGCCACTAGGA 57.131 50.000 30.76 9.49 36.89 2.94
2141 2477 0.798776 GGACTGTCGACCAAGCAATG 59.201 55.000 14.12 0.00 0.00 2.82
2150 2486 3.006430 TCGACCAAGCAATGTGAGTTAGA 59.994 43.478 0.00 0.00 0.00 2.10
2151 2487 3.369147 CGACCAAGCAATGTGAGTTAGAG 59.631 47.826 0.00 0.00 0.00 2.43
2152 2488 3.679389 ACCAAGCAATGTGAGTTAGAGG 58.321 45.455 0.00 0.00 0.00 3.69
2153 2489 3.012518 CCAAGCAATGTGAGTTAGAGGG 58.987 50.000 0.00 0.00 0.00 4.30
2154 2490 3.560025 CCAAGCAATGTGAGTTAGAGGGT 60.560 47.826 0.00 0.00 0.00 4.34
2155 2491 3.340814 AGCAATGTGAGTTAGAGGGTG 57.659 47.619 0.00 0.00 0.00 4.61
2156 2492 1.740025 GCAATGTGAGTTAGAGGGTGC 59.260 52.381 0.00 0.00 0.00 5.01
2157 2493 2.616510 GCAATGTGAGTTAGAGGGTGCT 60.617 50.000 0.00 0.00 0.00 4.40
2158 2494 3.679389 CAATGTGAGTTAGAGGGTGCTT 58.321 45.455 0.00 0.00 0.00 3.91
2159 2495 2.839486 TGTGAGTTAGAGGGTGCTTG 57.161 50.000 0.00 0.00 0.00 4.01
2160 2496 1.347707 TGTGAGTTAGAGGGTGCTTGG 59.652 52.381 0.00 0.00 0.00 3.61
2161 2497 1.623811 GTGAGTTAGAGGGTGCTTGGA 59.376 52.381 0.00 0.00 0.00 3.53
2162 2498 2.237392 GTGAGTTAGAGGGTGCTTGGAT 59.763 50.000 0.00 0.00 0.00 3.41
2163 2499 3.451178 GTGAGTTAGAGGGTGCTTGGATA 59.549 47.826 0.00 0.00 0.00 2.59
2164 2500 3.451178 TGAGTTAGAGGGTGCTTGGATAC 59.549 47.826 0.00 0.00 0.00 2.24
2184 2520 8.664211 GGATACAAGGGACTATTTTTAGTCTG 57.336 38.462 11.69 6.32 44.35 3.51
2185 2521 8.483758 GGATACAAGGGACTATTTTTAGTCTGA 58.516 37.037 11.69 0.00 44.35 3.27
2186 2522 9.315525 GATACAAGGGACTATTTTTAGTCTGAC 57.684 37.037 11.69 0.00 44.35 3.51
2187 2523 7.317722 ACAAGGGACTATTTTTAGTCTGACT 57.682 36.000 15.57 15.57 44.35 3.41
2188 2524 8.431910 ACAAGGGACTATTTTTAGTCTGACTA 57.568 34.615 13.34 13.34 44.35 2.59
2189 2525 8.877195 ACAAGGGACTATTTTTAGTCTGACTAA 58.123 33.333 22.80 22.80 44.35 2.24
2190 2526 9.720769 CAAGGGACTATTTTTAGTCTGACTAAA 57.279 33.333 29.65 29.65 42.90 1.85
2209 2545 9.654663 TGACTAAAAATAGTCTCTTTTAGAGGC 57.345 33.333 22.30 14.20 46.94 4.70
2218 2554 6.971527 GTCTCTTTTAGAGGCTAAAGTTCC 57.028 41.667 7.84 0.00 43.38 3.62
2219 2555 6.465084 GTCTCTTTTAGAGGCTAAAGTTCCA 58.535 40.000 7.84 0.00 43.38 3.53
2220 2556 6.935208 GTCTCTTTTAGAGGCTAAAGTTCCAA 59.065 38.462 7.84 0.00 43.38 3.53
2221 2557 7.118535 GTCTCTTTTAGAGGCTAAAGTTCCAAG 59.881 40.741 7.84 0.00 43.38 3.61
2222 2558 5.705905 TCTTTTAGAGGCTAAAGTTCCAAGC 59.294 40.000 7.84 0.00 33.97 4.01
2223 2559 4.634012 TTAGAGGCTAAAGTTCCAAGCA 57.366 40.909 0.00 0.00 38.01 3.91
2224 2560 2.784347 AGAGGCTAAAGTTCCAAGCAC 58.216 47.619 0.00 2.09 38.01 4.40
2225 2561 1.813178 GAGGCTAAAGTTCCAAGCACC 59.187 52.381 0.00 0.00 38.01 5.01
2226 2562 0.888619 GGCTAAAGTTCCAAGCACCC 59.111 55.000 7.02 0.00 38.01 4.61
2227 2563 0.888619 GCTAAAGTTCCAAGCACCCC 59.111 55.000 0.00 0.00 36.26 4.95
2228 2564 1.547901 GCTAAAGTTCCAAGCACCCCT 60.548 52.381 0.00 0.00 36.26 4.79
2229 2565 2.162681 CTAAAGTTCCAAGCACCCCTG 58.837 52.381 0.00 0.00 0.00 4.45
2230 2566 0.555769 AAAGTTCCAAGCACCCCTGA 59.444 50.000 0.00 0.00 0.00 3.86
2231 2567 0.178990 AAGTTCCAAGCACCCCTGAC 60.179 55.000 0.00 0.00 0.00 3.51
2232 2568 1.062488 AGTTCCAAGCACCCCTGACT 61.062 55.000 0.00 0.00 0.00 3.41
2233 2569 0.690762 GTTCCAAGCACCCCTGACTA 59.309 55.000 0.00 0.00 0.00 2.59
2234 2570 1.073284 GTTCCAAGCACCCCTGACTAA 59.927 52.381 0.00 0.00 0.00 2.24
2235 2571 1.440618 TCCAAGCACCCCTGACTAAA 58.559 50.000 0.00 0.00 0.00 1.85
2236 2572 1.351017 TCCAAGCACCCCTGACTAAAG 59.649 52.381 0.00 0.00 0.00 1.85
2237 2573 1.351017 CCAAGCACCCCTGACTAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
2238 2574 2.616510 CCAAGCACCCCTGACTAAAGAG 60.617 54.545 0.00 0.00 0.00 2.85
2239 2575 2.303022 CAAGCACCCCTGACTAAAGAGA 59.697 50.000 0.00 0.00 0.00 3.10
2240 2576 2.183679 AGCACCCCTGACTAAAGAGAG 58.816 52.381 0.00 0.00 0.00 3.20
2241 2577 1.208293 GCACCCCTGACTAAAGAGAGG 59.792 57.143 0.00 0.00 0.00 3.69
2242 2578 1.208293 CACCCCTGACTAAAGAGAGGC 59.792 57.143 0.00 0.00 0.00 4.70
2243 2579 1.079658 ACCCCTGACTAAAGAGAGGCT 59.920 52.381 0.00 0.00 0.00 4.58
2244 2580 2.315155 ACCCCTGACTAAAGAGAGGCTA 59.685 50.000 0.00 0.00 0.00 3.93
2245 2581 2.962421 CCCCTGACTAAAGAGAGGCTAG 59.038 54.545 0.00 0.00 0.00 3.42
2246 2582 2.962421 CCCTGACTAAAGAGAGGCTAGG 59.038 54.545 0.00 0.00 0.00 3.02
2247 2583 3.373220 CCCTGACTAAAGAGAGGCTAGGA 60.373 52.174 0.00 0.00 29.08 2.94
2248 2584 3.634910 CCTGACTAAAGAGAGGCTAGGAC 59.365 52.174 0.00 0.00 29.08 3.85
2249 2585 4.532834 CTGACTAAAGAGAGGCTAGGACT 58.467 47.826 0.00 0.00 0.00 3.85
2250 2586 5.398126 CCTGACTAAAGAGAGGCTAGGACTA 60.398 48.000 0.00 0.00 29.08 2.59
2251 2587 5.686753 TGACTAAAGAGAGGCTAGGACTAG 58.313 45.833 1.98 1.98 36.29 2.57
2252 2588 5.192121 TGACTAAAGAGAGGCTAGGACTAGT 59.808 44.000 0.00 0.00 35.65 2.57
2253 2589 5.687780 ACTAAAGAGAGGCTAGGACTAGTC 58.312 45.833 14.87 14.87 38.03 2.59
2259 2595 3.306472 AGGCTAGGACTAGTCTTGAGG 57.694 52.381 21.88 10.56 45.03 3.86
2260 2596 1.684450 GGCTAGGACTAGTCTTGAGGC 59.316 57.143 21.88 21.38 35.06 4.70
2261 2597 2.661718 GCTAGGACTAGTCTTGAGGCT 58.338 52.381 21.88 11.79 35.65 4.58
2262 2598 3.435313 GGCTAGGACTAGTCTTGAGGCTA 60.435 52.174 24.87 16.06 35.06 3.93
2263 2599 4.208746 GCTAGGACTAGTCTTGAGGCTAA 58.791 47.826 21.88 0.00 35.65 3.09
2264 2600 4.645588 GCTAGGACTAGTCTTGAGGCTAAA 59.354 45.833 21.88 0.00 35.65 1.85
2265 2601 5.127356 GCTAGGACTAGTCTTGAGGCTAAAA 59.873 44.000 21.88 0.00 35.65 1.52
2266 2602 6.183360 GCTAGGACTAGTCTTGAGGCTAAAAT 60.183 42.308 21.88 0.00 35.65 1.82
2267 2603 6.228616 AGGACTAGTCTTGAGGCTAAAATC 57.771 41.667 21.88 0.73 0.00 2.17
2268 2604 5.961421 AGGACTAGTCTTGAGGCTAAAATCT 59.039 40.000 21.88 3.06 0.00 2.40
2269 2605 6.442244 AGGACTAGTCTTGAGGCTAAAATCTT 59.558 38.462 21.88 0.00 0.00 2.40
2270 2606 7.037945 AGGACTAGTCTTGAGGCTAAAATCTTT 60.038 37.037 21.88 0.00 0.00 2.52
2271 2607 7.608376 GGACTAGTCTTGAGGCTAAAATCTTTT 59.392 37.037 21.88 0.00 0.00 2.27
2272 2608 9.654663 GACTAGTCTTGAGGCTAAAATCTTTTA 57.345 33.333 15.91 0.00 0.00 1.52
2286 2622 9.025041 CTAAAATCTTTTAGTCATGGGAAACCT 57.975 33.333 12.31 0.00 45.91 3.50
2316 2652 9.600432 AAAATATGTATTAGCTCTCTCTCTCCT 57.400 33.333 0.00 0.00 0.00 3.69
2317 2653 8.807948 AATATGTATTAGCTCTCTCTCTCCTC 57.192 38.462 0.00 0.00 0.00 3.71
2318 2654 5.638530 TGTATTAGCTCTCTCTCTCCTCA 57.361 43.478 0.00 0.00 0.00 3.86
2319 2655 6.199557 TGTATTAGCTCTCTCTCTCCTCAT 57.800 41.667 0.00 0.00 0.00 2.90
2320 2656 6.609876 TGTATTAGCTCTCTCTCTCCTCATT 58.390 40.000 0.00 0.00 0.00 2.57
2321 2657 7.066142 TGTATTAGCTCTCTCTCTCCTCATTT 58.934 38.462 0.00 0.00 0.00 2.32
2322 2658 8.221251 TGTATTAGCTCTCTCTCTCCTCATTTA 58.779 37.037 0.00 0.00 0.00 1.40
2323 2659 9.073475 GTATTAGCTCTCTCTCTCCTCATTTAA 57.927 37.037 0.00 0.00 0.00 1.52
2324 2660 8.725606 ATTAGCTCTCTCTCTCCTCATTTAAT 57.274 34.615 0.00 0.00 0.00 1.40
2325 2661 8.546083 TTAGCTCTCTCTCTCCTCATTTAATT 57.454 34.615 0.00 0.00 0.00 1.40
2326 2662 7.054491 AGCTCTCTCTCTCCTCATTTAATTC 57.946 40.000 0.00 0.00 0.00 2.17
2327 2663 6.041979 AGCTCTCTCTCTCCTCATTTAATTCC 59.958 42.308 0.00 0.00 0.00 3.01
2328 2664 6.041979 GCTCTCTCTCTCCTCATTTAATTCCT 59.958 42.308 0.00 0.00 0.00 3.36
2329 2665 7.595819 TCTCTCTCTCCTCATTTAATTCCTC 57.404 40.000 0.00 0.00 0.00 3.71
2330 2666 7.361438 TCTCTCTCTCCTCATTTAATTCCTCT 58.639 38.462 0.00 0.00 0.00 3.69
2331 2667 7.505585 TCTCTCTCTCCTCATTTAATTCCTCTC 59.494 40.741 0.00 0.00 0.00 3.20
2332 2668 6.553100 TCTCTCTCCTCATTTAATTCCTCTCC 59.447 42.308 0.00 0.00 0.00 3.71
2333 2669 6.448202 TCTCTCCTCATTTAATTCCTCTCCT 58.552 40.000 0.00 0.00 0.00 3.69
2334 2670 6.905776 TCTCTCCTCATTTAATTCCTCTCCTT 59.094 38.462 0.00 0.00 0.00 3.36
2335 2671 8.068110 TCTCTCCTCATTTAATTCCTCTCCTTA 58.932 37.037 0.00 0.00 0.00 2.69
2336 2672 8.256356 TCTCCTCATTTAATTCCTCTCCTTAG 57.744 38.462 0.00 0.00 0.00 2.18
2337 2673 7.846823 TCTCCTCATTTAATTCCTCTCCTTAGT 59.153 37.037 0.00 0.00 0.00 2.24
2338 2674 8.393959 TCCTCATTTAATTCCTCTCCTTAGTT 57.606 34.615 0.00 0.00 0.00 2.24
2339 2675 8.487028 TCCTCATTTAATTCCTCTCCTTAGTTC 58.513 37.037 0.00 0.00 0.00 3.01
2340 2676 8.490311 CCTCATTTAATTCCTCTCCTTAGTTCT 58.510 37.037 0.00 0.00 0.00 3.01
2341 2677 9.323985 CTCATTTAATTCCTCTCCTTAGTTCTG 57.676 37.037 0.00 0.00 0.00 3.02
2342 2678 8.267894 TCATTTAATTCCTCTCCTTAGTTCTGG 58.732 37.037 0.00 0.00 0.00 3.86
2343 2679 7.808279 TTTAATTCCTCTCCTTAGTTCTGGA 57.192 36.000 0.00 0.00 0.00 3.86
2344 2680 7.996758 TTAATTCCTCTCCTTAGTTCTGGAT 57.003 36.000 0.00 0.00 0.00 3.41
2345 2681 6.899892 AATTCCTCTCCTTAGTTCTGGATT 57.100 37.500 0.00 0.00 0.00 3.01
2346 2682 5.683876 TTCCTCTCCTTAGTTCTGGATTG 57.316 43.478 0.00 0.00 0.00 2.67
2347 2683 4.033709 TCCTCTCCTTAGTTCTGGATTGG 58.966 47.826 0.00 0.00 0.00 3.16
2348 2684 4.033709 CCTCTCCTTAGTTCTGGATTGGA 58.966 47.826 0.00 0.00 31.05 3.53
2349 2685 4.100808 CCTCTCCTTAGTTCTGGATTGGAG 59.899 50.000 0.00 0.00 40.47 3.86
2350 2686 4.033709 TCTCCTTAGTTCTGGATTGGAGG 58.966 47.826 0.00 0.00 39.80 4.30
2351 2687 3.115390 TCCTTAGTTCTGGATTGGAGGG 58.885 50.000 0.00 0.00 0.00 4.30
2352 2688 2.846827 CCTTAGTTCTGGATTGGAGGGT 59.153 50.000 0.00 0.00 0.00 4.34
2353 2689 3.267031 CCTTAGTTCTGGATTGGAGGGTT 59.733 47.826 0.00 0.00 0.00 4.11
2354 2690 4.263949 CCTTAGTTCTGGATTGGAGGGTTT 60.264 45.833 0.00 0.00 0.00 3.27
2355 2691 3.160679 AGTTCTGGATTGGAGGGTTTG 57.839 47.619 0.00 0.00 0.00 2.93
2356 2692 2.171003 GTTCTGGATTGGAGGGTTTGG 58.829 52.381 0.00 0.00 0.00 3.28
2357 2693 1.753903 TCTGGATTGGAGGGTTTGGA 58.246 50.000 0.00 0.00 0.00 3.53
2358 2694 1.635487 TCTGGATTGGAGGGTTTGGAG 59.365 52.381 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.389391 ATGGTCGTGAGCTTATCCGG 59.611 55.000 0.00 0.00 0.00 5.14
1 2 1.491670 CATGGTCGTGAGCTTATCCG 58.508 55.000 0.39 0.00 0.00 4.18
6 7 2.045926 GGGCATGGTCGTGAGCTT 60.046 61.111 0.00 0.00 0.00 3.74
8 9 4.408821 TGGGGCATGGTCGTGAGC 62.409 66.667 0.00 0.00 0.00 4.26
13 14 1.178534 ACAAAACTGGGGCATGGTCG 61.179 55.000 0.00 0.00 0.00 4.79
23 24 1.452145 CGGGGTCACCACAAAACTGG 61.452 60.000 0.00 0.00 40.22 4.00
25 26 0.464916 GACGGGGTCACCACAAAACT 60.465 55.000 0.00 0.00 40.22 2.66
37 38 3.016736 CAGCAATTTAGATTGACGGGGT 58.983 45.455 10.05 0.00 44.37 4.95
39 40 3.440173 ACACAGCAATTTAGATTGACGGG 59.560 43.478 10.05 3.46 44.37 5.28
40 41 4.154015 TGACACAGCAATTTAGATTGACGG 59.846 41.667 10.05 5.01 44.37 4.79
56 57 1.959042 AGGTTGTTGAGCTGACACAG 58.041 50.000 0.00 0.00 34.08 3.66
62 63 2.935201 GCATCTCTAGGTTGTTGAGCTG 59.065 50.000 0.00 0.00 37.30 4.24
69 70 7.225538 CGATTTTTATGAGCATCTCTAGGTTGT 59.774 37.037 0.00 0.00 34.92 3.32
70 71 7.439356 TCGATTTTTATGAGCATCTCTAGGTTG 59.561 37.037 0.00 0.00 34.92 3.77
74 75 8.986847 ACATTCGATTTTTATGAGCATCTCTAG 58.013 33.333 1.16 0.00 34.92 2.43
80 81 7.592533 GCACATACATTCGATTTTTATGAGCAT 59.407 33.333 15.63 0.00 36.98 3.79
91 92 6.048509 TGTAGACATGCACATACATTCGATT 58.951 36.000 0.00 0.00 0.00 3.34
102 103 6.536224 CACTTCTATGAATGTAGACATGCACA 59.464 38.462 5.43 3.30 44.19 4.57
111 112 9.809096 AACACATACTCACTTCTATGAATGTAG 57.191 33.333 0.00 0.00 31.33 2.74
125 126 5.107065 GGCTCACTTACAAACACATACTCAC 60.107 44.000 0.00 0.00 0.00 3.51
126 127 4.994852 GGCTCACTTACAAACACATACTCA 59.005 41.667 0.00 0.00 0.00 3.41
127 128 5.238583 AGGCTCACTTACAAACACATACTC 58.761 41.667 0.00 0.00 0.00 2.59
128 129 5.228945 AGGCTCACTTACAAACACATACT 57.771 39.130 0.00 0.00 0.00 2.12
137 138 4.882842 TGTCACATAGGCTCACTTACAA 57.117 40.909 0.00 0.00 0.00 2.41
139 140 4.034510 GCAATGTCACATAGGCTCACTTAC 59.965 45.833 7.03 0.00 0.00 2.34
143 144 1.328680 CGCAATGTCACATAGGCTCAC 59.671 52.381 11.40 0.00 0.00 3.51
149 150 1.085893 TGGTGCGCAATGTCACATAG 58.914 50.000 14.00 0.00 35.04 2.23
151 152 1.580942 GTGGTGCGCAATGTCACAT 59.419 52.632 14.00 0.00 35.04 3.21
153 154 2.255252 GGTGGTGCGCAATGTCAC 59.745 61.111 14.00 17.73 0.00 3.67
229 252 4.811557 CGTTGGATGAATCTAGGTCTTTCC 59.188 45.833 0.00 0.91 0.00 3.13
252 275 1.120530 TAAAGCTCCCGTGGATCTCC 58.879 55.000 0.00 0.00 27.07 3.71
254 277 3.713826 TTTTAAAGCTCCCGTGGATCT 57.286 42.857 0.00 0.00 28.42 2.75
258 281 3.759618 TGGTTATTTTAAAGCTCCCGTGG 59.240 43.478 0.00 0.00 0.00 4.94
295 318 1.868997 GTGACACCGTTGATGGCTG 59.131 57.895 0.00 0.00 0.00 4.85
326 349 1.452145 GGCAGAGCTCGAGGTAGAGG 61.452 65.000 18.63 8.39 38.63 3.69
356 380 2.105128 CCTCGTCACTCGGCATCC 59.895 66.667 0.00 0.00 40.32 3.51
357 381 2.583593 GCCTCGTCACTCGGCATC 60.584 66.667 0.00 0.00 43.25 3.91
375 399 2.580470 CGAGCGATGACGATGCACC 61.580 63.158 0.00 0.00 42.66 5.01
390 414 8.169910 AGATATTTCGTACTATTCATCGTCGAG 58.830 37.037 0.00 0.00 0.00 4.04
406 430 8.739039 TGATGATTGGTTTTTCAGATATTTCGT 58.261 29.630 0.00 0.00 0.00 3.85
407 431 9.571810 TTGATGATTGGTTTTTCAGATATTTCG 57.428 29.630 0.00 0.00 0.00 3.46
425 450 9.912634 AACACTGATTTTTATTCGTTGATGATT 57.087 25.926 0.00 0.00 0.00 2.57
465 490 2.238646 TGCTGACGGGTTTTCCAGATAT 59.761 45.455 0.00 0.00 42.91 1.63
576 757 1.003839 GGCGTGTCAGTGGATGGAA 60.004 57.895 0.00 0.00 0.00 3.53
648 854 1.227556 CGGGGTCCTGATAAAGCGG 60.228 63.158 0.00 0.00 0.00 5.52
782 988 4.910585 CGGTGGTCTATGGCGGGC 62.911 72.222 0.00 0.00 0.00 6.13
899 1140 2.266055 GTCCTCTTGGCACTCCCG 59.734 66.667 0.00 0.00 35.87 5.14
908 1149 1.834263 CCCTTCTACCCAGTCCTCTTG 59.166 57.143 0.00 0.00 0.00 3.02
919 1160 1.346479 GGCTCCCCTTCCCTTCTACC 61.346 65.000 0.00 0.00 0.00 3.18
920 1161 0.326713 AGGCTCCCCTTCCCTTCTAC 60.327 60.000 0.00 0.00 38.74 2.59
923 1164 2.379459 GGAGGCTCCCCTTCCCTTC 61.379 68.421 23.49 0.00 43.12 3.46
924 1165 2.286502 GGAGGCTCCCCTTCCCTT 60.287 66.667 23.49 0.00 43.12 3.95
925 1166 4.806339 CGGAGGCTCCCCTTCCCT 62.806 72.222 27.36 0.00 43.12 4.20
926 1167 4.798682 TCGGAGGCTCCCCTTCCC 62.799 72.222 27.36 1.65 43.12 3.97
927 1168 3.157949 CTCGGAGGCTCCCCTTCC 61.158 72.222 27.36 2.77 43.12 3.46
1071 1320 4.728102 TTACCGGACTGGCGCACG 62.728 66.667 9.46 5.17 43.94 5.34
1114 1363 4.056125 CTCTGCAGCACGTCGGGA 62.056 66.667 9.47 0.00 0.00 5.14
1121 1370 0.461693 CTAGGAAGCCTCTGCAGCAC 60.462 60.000 9.47 0.02 41.13 4.40
1155 1424 3.325293 TCAACAAGCAACCAAAAAGCA 57.675 38.095 0.00 0.00 0.00 3.91
1159 1428 4.005650 TGCAAATCAACAAGCAACCAAAA 58.994 34.783 0.00 0.00 33.48 2.44
1160 1429 3.603532 TGCAAATCAACAAGCAACCAAA 58.396 36.364 0.00 0.00 33.48 3.28
1164 1433 2.137523 CCCTGCAAATCAACAAGCAAC 58.862 47.619 0.00 0.00 36.44 4.17
1167 1436 0.319405 AGCCCTGCAAATCAACAAGC 59.681 50.000 0.00 0.00 0.00 4.01
1168 1437 1.342174 ACAGCCCTGCAAATCAACAAG 59.658 47.619 0.00 0.00 0.00 3.16
1172 1441 0.178967 TCCACAGCCCTGCAAATCAA 60.179 50.000 0.00 0.00 0.00 2.57
1173 1442 0.609957 CTCCACAGCCCTGCAAATCA 60.610 55.000 0.00 0.00 0.00 2.57
1174 1443 1.318158 CCTCCACAGCCCTGCAAATC 61.318 60.000 0.00 0.00 0.00 2.17
1175 1444 1.304713 CCTCCACAGCCCTGCAAAT 60.305 57.895 0.00 0.00 0.00 2.32
1176 1445 2.115910 CCTCCACAGCCCTGCAAA 59.884 61.111 0.00 0.00 0.00 3.68
1422 1691 3.621558 AGAAGCTAATTAACCAGGCCAC 58.378 45.455 5.01 0.00 0.00 5.01
1425 1694 5.825151 AGATCAAGAAGCTAATTAACCAGGC 59.175 40.000 0.00 0.00 0.00 4.85
1576 1850 3.967326 CCAGAGGTATCACCCATCTACAA 59.033 47.826 0.00 0.00 39.75 2.41
1623 1897 4.203764 GTCGTGTAAGATGTATTCGAACGG 59.796 45.833 0.00 0.00 0.00 4.44
1662 1936 5.437289 TTGTGGTAGATCAAAGTTTGCAG 57.563 39.130 10.90 0.00 0.00 4.41
1680 1959 8.239314 ACAGACTGCAGAACATAAATATTTGTG 58.761 33.333 23.35 19.82 35.68 3.33
1702 2013 6.369890 GTCTATCTGAAGCATGAACAAACAGA 59.630 38.462 0.00 0.00 37.33 3.41
1759 2072 2.945668 CCCTGCTGATACTAGGTTTTGC 59.054 50.000 0.00 0.00 0.00 3.68
1769 2082 1.452108 GGCACCACCCTGCTGATAC 60.452 63.158 0.00 0.00 37.33 2.24
1806 2119 1.168714 GGTGGAGCATCAAACCTGAC 58.831 55.000 0.00 0.00 39.52 3.51
1825 2138 2.826725 GGGTCTAGGATATTCCAGTCCG 59.173 54.545 0.00 0.00 39.61 4.79
1893 2207 2.146342 AGACGTCAAATCTTGGTGCTG 58.854 47.619 19.50 0.00 0.00 4.41
1949 2271 3.536498 GAAAACCACAGCACGGCGG 62.536 63.158 13.24 0.66 0.00 6.13
2016 2338 2.126189 GCGTCCGGTACAGTGTCC 60.126 66.667 0.00 0.00 0.00 4.02
2071 2404 2.076863 GTTCACGGGAGATTGTCAAGG 58.923 52.381 0.00 0.00 0.00 3.61
2115 2451 1.248785 TGGTCGACAGTCCTAGTGGC 61.249 60.000 18.91 0.00 0.00 5.01
2117 2453 1.402984 GCTTGGTCGACAGTCCTAGTG 60.403 57.143 18.91 0.00 32.97 2.74
2118 2454 0.889306 GCTTGGTCGACAGTCCTAGT 59.111 55.000 18.91 0.00 32.97 2.57
2120 2456 1.334160 TTGCTTGGTCGACAGTCCTA 58.666 50.000 18.91 0.00 0.00 2.94
2122 2458 0.798776 CATTGCTTGGTCGACAGTCC 59.201 55.000 18.91 0.00 0.00 3.85
2124 2460 1.202639 TCACATTGCTTGGTCGACAGT 60.203 47.619 18.91 0.00 0.00 3.55
2141 2477 1.623811 TCCAAGCACCCTCTAACTCAC 59.376 52.381 0.00 0.00 0.00 3.51
2150 2486 0.625849 CCCTTGTATCCAAGCACCCT 59.374 55.000 0.00 0.00 45.57 4.34
2151 2487 0.623723 TCCCTTGTATCCAAGCACCC 59.376 55.000 0.00 0.00 45.57 4.61
2152 2488 1.282157 AGTCCCTTGTATCCAAGCACC 59.718 52.381 0.00 0.00 45.57 5.01
2153 2489 2.789409 AGTCCCTTGTATCCAAGCAC 57.211 50.000 0.00 0.00 45.57 4.40
2154 2490 5.450818 AAATAGTCCCTTGTATCCAAGCA 57.549 39.130 0.00 0.00 45.57 3.91
2155 2491 6.775594 AAAAATAGTCCCTTGTATCCAAGC 57.224 37.500 0.00 0.00 45.57 4.01
2156 2492 9.110502 GACTAAAAATAGTCCCTTGTATCCAAG 57.889 37.037 4.96 0.00 40.86 3.61
2157 2493 8.832735 AGACTAAAAATAGTCCCTTGTATCCAA 58.167 33.333 11.35 0.00 45.66 3.53
2158 2494 8.265055 CAGACTAAAAATAGTCCCTTGTATCCA 58.735 37.037 11.35 0.00 45.66 3.41
2159 2495 8.483758 TCAGACTAAAAATAGTCCCTTGTATCC 58.516 37.037 11.35 0.00 45.66 2.59
2160 2496 9.315525 GTCAGACTAAAAATAGTCCCTTGTATC 57.684 37.037 11.35 0.00 45.66 2.24
2161 2497 9.047947 AGTCAGACTAAAAATAGTCCCTTGTAT 57.952 33.333 0.00 0.00 45.66 2.29
2162 2498 8.431910 AGTCAGACTAAAAATAGTCCCTTGTA 57.568 34.615 0.00 0.00 45.66 2.41
2163 2499 7.317722 AGTCAGACTAAAAATAGTCCCTTGT 57.682 36.000 0.00 0.00 45.66 3.16
2164 2500 9.720769 TTTAGTCAGACTAAAAATAGTCCCTTG 57.279 33.333 26.93 5.29 44.84 3.61
2183 2519 9.654663 GCCTCTAAAAGAGACTATTTTTAGTCA 57.345 33.333 12.70 4.01 45.07 3.41
2184 2520 9.878667 AGCCTCTAAAAGAGACTATTTTTAGTC 57.121 33.333 12.70 5.24 45.07 2.59
2191 2527 9.878667 GAACTTTAGCCTCTAAAAGAGACTATT 57.121 33.333 5.50 0.00 45.07 1.73
2192 2528 8.479689 GGAACTTTAGCCTCTAAAAGAGACTAT 58.520 37.037 5.50 0.00 45.07 2.12
2193 2529 7.453752 TGGAACTTTAGCCTCTAAAAGAGACTA 59.546 37.037 5.50 0.91 45.07 2.59
2194 2530 6.270231 TGGAACTTTAGCCTCTAAAAGAGACT 59.730 38.462 5.50 1.89 45.07 3.24
2195 2531 6.465084 TGGAACTTTAGCCTCTAAAAGAGAC 58.535 40.000 5.50 0.00 45.07 3.36
2196 2532 6.681729 TGGAACTTTAGCCTCTAAAAGAGA 57.318 37.500 5.50 0.00 45.07 3.10
2197 2533 6.128145 GCTTGGAACTTTAGCCTCTAAAAGAG 60.128 42.308 2.08 0.00 41.96 2.85
2198 2534 5.705905 GCTTGGAACTTTAGCCTCTAAAAGA 59.294 40.000 2.08 0.00 36.43 2.52
2199 2535 5.473504 TGCTTGGAACTTTAGCCTCTAAAAG 59.526 40.000 0.00 0.00 38.41 2.27
2200 2536 5.240844 GTGCTTGGAACTTTAGCCTCTAAAA 59.759 40.000 0.00 0.00 34.03 1.52
2201 2537 4.760204 GTGCTTGGAACTTTAGCCTCTAAA 59.240 41.667 0.00 0.00 34.03 1.85
2202 2538 4.324267 GTGCTTGGAACTTTAGCCTCTAA 58.676 43.478 0.00 0.00 34.03 2.10
2203 2539 3.307480 GGTGCTTGGAACTTTAGCCTCTA 60.307 47.826 0.00 0.00 34.03 2.43
2204 2540 2.553247 GGTGCTTGGAACTTTAGCCTCT 60.553 50.000 0.00 0.00 34.03 3.69
2205 2541 1.813178 GGTGCTTGGAACTTTAGCCTC 59.187 52.381 0.00 0.00 34.03 4.70
2206 2542 1.547901 GGGTGCTTGGAACTTTAGCCT 60.548 52.381 0.00 0.00 34.03 4.58
2207 2543 0.888619 GGGTGCTTGGAACTTTAGCC 59.111 55.000 0.00 0.00 34.03 3.93
2208 2544 0.888619 GGGGTGCTTGGAACTTTAGC 59.111 55.000 0.00 0.00 35.50 3.09
2209 2545 2.162681 CAGGGGTGCTTGGAACTTTAG 58.837 52.381 0.00 0.00 0.00 1.85
2210 2546 1.777878 TCAGGGGTGCTTGGAACTTTA 59.222 47.619 0.00 0.00 0.00 1.85
2211 2547 0.555769 TCAGGGGTGCTTGGAACTTT 59.444 50.000 0.00 0.00 0.00 2.66
2212 2548 0.178990 GTCAGGGGTGCTTGGAACTT 60.179 55.000 0.00 0.00 0.00 2.66
2213 2549 1.062488 AGTCAGGGGTGCTTGGAACT 61.062 55.000 0.00 0.00 0.00 3.01
2214 2550 0.690762 TAGTCAGGGGTGCTTGGAAC 59.309 55.000 0.00 0.00 0.00 3.62
2215 2551 1.440618 TTAGTCAGGGGTGCTTGGAA 58.559 50.000 0.00 0.00 0.00 3.53
2216 2552 1.351017 CTTTAGTCAGGGGTGCTTGGA 59.649 52.381 0.00 0.00 0.00 3.53
2217 2553 1.351017 TCTTTAGTCAGGGGTGCTTGG 59.649 52.381 0.00 0.00 0.00 3.61
2218 2554 2.303022 TCTCTTTAGTCAGGGGTGCTTG 59.697 50.000 0.00 0.00 0.00 4.01
2219 2555 2.569404 CTCTCTTTAGTCAGGGGTGCTT 59.431 50.000 0.00 0.00 0.00 3.91
2220 2556 2.183679 CTCTCTTTAGTCAGGGGTGCT 58.816 52.381 0.00 0.00 0.00 4.40
2221 2557 1.208293 CCTCTCTTTAGTCAGGGGTGC 59.792 57.143 0.00 0.00 0.00 5.01
2222 2558 1.208293 GCCTCTCTTTAGTCAGGGGTG 59.792 57.143 0.00 0.00 0.00 4.61
2223 2559 1.079658 AGCCTCTCTTTAGTCAGGGGT 59.920 52.381 0.00 0.00 0.00 4.95
2224 2560 1.872773 AGCCTCTCTTTAGTCAGGGG 58.127 55.000 0.00 0.00 0.00 4.79
2225 2561 2.962421 CCTAGCCTCTCTTTAGTCAGGG 59.038 54.545 0.00 0.00 0.00 4.45
2226 2562 3.634910 GTCCTAGCCTCTCTTTAGTCAGG 59.365 52.174 0.00 0.00 0.00 3.86
2227 2563 4.532834 AGTCCTAGCCTCTCTTTAGTCAG 58.467 47.826 0.00 0.00 0.00 3.51
2228 2564 4.594675 AGTCCTAGCCTCTCTTTAGTCA 57.405 45.455 0.00 0.00 0.00 3.41
2229 2565 5.687780 ACTAGTCCTAGCCTCTCTTTAGTC 58.312 45.833 1.22 0.00 36.66 2.59
2230 2566 5.430745 AGACTAGTCCTAGCCTCTCTTTAGT 59.569 44.000 19.38 0.00 36.66 2.24
2231 2567 5.937111 AGACTAGTCCTAGCCTCTCTTTAG 58.063 45.833 19.38 0.00 36.66 1.85
2232 2568 5.979656 AGACTAGTCCTAGCCTCTCTTTA 57.020 43.478 19.38 0.00 36.66 1.85
2233 2569 4.873724 AGACTAGTCCTAGCCTCTCTTT 57.126 45.455 19.38 0.00 36.66 2.52
2234 2570 4.228666 TCAAGACTAGTCCTAGCCTCTCTT 59.771 45.833 19.38 0.17 36.66 2.85
2235 2571 3.783642 TCAAGACTAGTCCTAGCCTCTCT 59.216 47.826 19.38 0.00 36.66 3.10
2236 2572 4.134563 CTCAAGACTAGTCCTAGCCTCTC 58.865 52.174 19.38 0.00 36.66 3.20
2237 2573 3.117663 CCTCAAGACTAGTCCTAGCCTCT 60.118 52.174 19.38 0.00 36.66 3.69
2238 2574 3.219281 CCTCAAGACTAGTCCTAGCCTC 58.781 54.545 19.38 0.00 36.66 4.70
2239 2575 2.688515 GCCTCAAGACTAGTCCTAGCCT 60.689 54.545 19.38 0.00 36.66 4.58
2240 2576 1.684450 GCCTCAAGACTAGTCCTAGCC 59.316 57.143 19.38 0.89 36.66 3.93
2241 2577 2.661718 AGCCTCAAGACTAGTCCTAGC 58.338 52.381 19.38 14.54 36.66 3.42
2242 2578 6.777213 TTTTAGCCTCAAGACTAGTCCTAG 57.223 41.667 19.38 13.33 39.04 3.02
2243 2579 7.126733 AGATTTTAGCCTCAAGACTAGTCCTA 58.873 38.462 19.38 9.39 0.00 2.94
2244 2580 5.961421 AGATTTTAGCCTCAAGACTAGTCCT 59.039 40.000 19.38 10.36 0.00 3.85
2245 2581 6.228616 AGATTTTAGCCTCAAGACTAGTCC 57.771 41.667 19.38 2.89 0.00 3.85
2246 2582 8.554835 AAAAGATTTTAGCCTCAAGACTAGTC 57.445 34.615 15.41 15.41 0.00 2.59
2247 2583 9.660180 CTAAAAGATTTTAGCCTCAAGACTAGT 57.340 33.333 11.10 0.00 41.97 2.57
2261 2597 8.950007 AGGTTTCCCATGACTAAAAGATTTTA 57.050 30.769 0.00 0.00 0.00 1.52
2262 2598 7.855784 AGGTTTCCCATGACTAAAAGATTTT 57.144 32.000 0.00 0.00 0.00 1.82
2263 2599 8.170730 AGTAGGTTTCCCATGACTAAAAGATTT 58.829 33.333 0.00 0.00 0.00 2.17
2264 2600 7.699878 AGTAGGTTTCCCATGACTAAAAGATT 58.300 34.615 0.00 0.00 0.00 2.40
2265 2601 7.272144 AGTAGGTTTCCCATGACTAAAAGAT 57.728 36.000 0.00 0.00 0.00 2.40
2266 2602 6.697641 AGTAGGTTTCCCATGACTAAAAGA 57.302 37.500 0.00 0.00 0.00 2.52
2267 2603 8.857694 TTTAGTAGGTTTCCCATGACTAAAAG 57.142 34.615 8.74 0.00 38.44 2.27
2268 2604 9.816787 ATTTTAGTAGGTTTCCCATGACTAAAA 57.183 29.630 19.00 19.00 45.07 1.52
2272 2608 8.557450 ACATATTTTAGTAGGTTTCCCATGACT 58.443 33.333 0.00 0.00 0.00 3.41
2273 2609 8.747538 ACATATTTTAGTAGGTTTCCCATGAC 57.252 34.615 0.00 0.00 0.00 3.06
2290 2626 9.600432 AGGAGAGAGAGAGCTAATACATATTTT 57.400 33.333 0.00 0.00 0.00 1.82
2291 2627 9.243105 GAGGAGAGAGAGAGCTAATACATATTT 57.757 37.037 0.00 0.00 0.00 1.40
2292 2628 8.390143 TGAGGAGAGAGAGAGCTAATACATATT 58.610 37.037 0.00 0.00 0.00 1.28
2293 2629 7.927788 TGAGGAGAGAGAGAGCTAATACATAT 58.072 38.462 0.00 0.00 0.00 1.78
2294 2630 7.323052 TGAGGAGAGAGAGAGCTAATACATA 57.677 40.000 0.00 0.00 0.00 2.29
2295 2631 6.199557 TGAGGAGAGAGAGAGCTAATACAT 57.800 41.667 0.00 0.00 0.00 2.29
2296 2632 5.638530 TGAGGAGAGAGAGAGCTAATACA 57.361 43.478 0.00 0.00 0.00 2.29
2297 2633 7.524717 AAATGAGGAGAGAGAGAGCTAATAC 57.475 40.000 0.00 0.00 0.00 1.89
2298 2634 9.821240 ATTAAATGAGGAGAGAGAGAGCTAATA 57.179 33.333 0.00 0.00 0.00 0.98
2299 2635 8.725606 ATTAAATGAGGAGAGAGAGAGCTAAT 57.274 34.615 0.00 0.00 0.00 1.73
2300 2636 8.546083 AATTAAATGAGGAGAGAGAGAGCTAA 57.454 34.615 0.00 0.00 0.00 3.09
2301 2637 7.232534 GGAATTAAATGAGGAGAGAGAGAGCTA 59.767 40.741 0.00 0.00 0.00 3.32
2302 2638 6.041979 GGAATTAAATGAGGAGAGAGAGAGCT 59.958 42.308 0.00 0.00 0.00 4.09
2303 2639 6.041979 AGGAATTAAATGAGGAGAGAGAGAGC 59.958 42.308 0.00 0.00 0.00 4.09
2304 2640 7.506938 AGAGGAATTAAATGAGGAGAGAGAGAG 59.493 40.741 0.00 0.00 0.00 3.20
2305 2641 7.361438 AGAGGAATTAAATGAGGAGAGAGAGA 58.639 38.462 0.00 0.00 0.00 3.10
2306 2642 7.255942 GGAGAGGAATTAAATGAGGAGAGAGAG 60.256 44.444 0.00 0.00 0.00 3.20
2307 2643 6.553100 GGAGAGGAATTAAATGAGGAGAGAGA 59.447 42.308 0.00 0.00 0.00 3.10
2308 2644 6.554605 AGGAGAGGAATTAAATGAGGAGAGAG 59.445 42.308 0.00 0.00 0.00 3.20
2309 2645 6.448202 AGGAGAGGAATTAAATGAGGAGAGA 58.552 40.000 0.00 0.00 0.00 3.10
2310 2646 6.745794 AGGAGAGGAATTAAATGAGGAGAG 57.254 41.667 0.00 0.00 0.00 3.20
2311 2647 7.846823 ACTAAGGAGAGGAATTAAATGAGGAGA 59.153 37.037 0.00 0.00 0.00 3.71
2312 2648 8.028652 ACTAAGGAGAGGAATTAAATGAGGAG 57.971 38.462 0.00 0.00 0.00 3.69
2313 2649 7.996758 ACTAAGGAGAGGAATTAAATGAGGA 57.003 36.000 0.00 0.00 0.00 3.71
2314 2650 8.490311 AGAACTAAGGAGAGGAATTAAATGAGG 58.510 37.037 0.00 0.00 0.00 3.86
2315 2651 9.323985 CAGAACTAAGGAGAGGAATTAAATGAG 57.676 37.037 0.00 0.00 0.00 2.90
2316 2652 8.267894 CCAGAACTAAGGAGAGGAATTAAATGA 58.732 37.037 0.00 0.00 0.00 2.57
2317 2653 8.267894 TCCAGAACTAAGGAGAGGAATTAAATG 58.732 37.037 0.00 0.00 0.00 2.32
2318 2654 8.393959 TCCAGAACTAAGGAGAGGAATTAAAT 57.606 34.615 0.00 0.00 0.00 1.40
2319 2655 7.808279 TCCAGAACTAAGGAGAGGAATTAAA 57.192 36.000 0.00 0.00 0.00 1.52
2320 2656 7.996758 ATCCAGAACTAAGGAGAGGAATTAA 57.003 36.000 0.00 0.00 37.34 1.40
2321 2657 7.147479 CCAATCCAGAACTAAGGAGAGGAATTA 60.147 40.741 0.00 0.00 37.34 1.40
2322 2658 6.353429 CCAATCCAGAACTAAGGAGAGGAATT 60.353 42.308 0.00 0.00 37.34 2.17
2323 2659 5.131809 CCAATCCAGAACTAAGGAGAGGAAT 59.868 44.000 0.00 0.00 37.34 3.01
2324 2660 4.471386 CCAATCCAGAACTAAGGAGAGGAA 59.529 45.833 0.00 0.00 37.34 3.36
2325 2661 4.033709 CCAATCCAGAACTAAGGAGAGGA 58.966 47.826 0.00 0.00 37.34 3.71
2326 2662 4.033709 TCCAATCCAGAACTAAGGAGAGG 58.966 47.826 0.00 0.00 37.34 3.69
2327 2663 4.100808 CCTCCAATCCAGAACTAAGGAGAG 59.899 50.000 7.12 0.00 42.87 3.20
2328 2664 4.033709 CCTCCAATCCAGAACTAAGGAGA 58.966 47.826 7.12 0.00 42.87 3.71
2329 2665 3.135530 CCCTCCAATCCAGAACTAAGGAG 59.864 52.174 0.00 0.00 40.58 3.69
2330 2666 3.115390 CCCTCCAATCCAGAACTAAGGA 58.885 50.000 0.00 0.00 38.50 3.36
2331 2667 2.846827 ACCCTCCAATCCAGAACTAAGG 59.153 50.000 0.00 0.00 0.00 2.69
2332 2668 4.576330 AACCCTCCAATCCAGAACTAAG 57.424 45.455 0.00 0.00 0.00 2.18
2333 2669 4.508405 CCAAACCCTCCAATCCAGAACTAA 60.508 45.833 0.00 0.00 0.00 2.24
2334 2670 3.010138 CCAAACCCTCCAATCCAGAACTA 59.990 47.826 0.00 0.00 0.00 2.24
2335 2671 2.225117 CCAAACCCTCCAATCCAGAACT 60.225 50.000 0.00 0.00 0.00 3.01
2336 2672 2.171003 CCAAACCCTCCAATCCAGAAC 58.829 52.381 0.00 0.00 0.00 3.01
2337 2673 2.041620 CTCCAAACCCTCCAATCCAGAA 59.958 50.000 0.00 0.00 0.00 3.02
2338 2674 1.635487 CTCCAAACCCTCCAATCCAGA 59.365 52.381 0.00 0.00 0.00 3.86
2339 2675 2.134789 CTCCAAACCCTCCAATCCAG 57.865 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.