Multiple sequence alignment - TraesCS5B01G518300

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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 TraesCS5B01G518300 chr5B 100.000 2501 0 0 1 2501 681181789 681179289 0.000000e+00 4619.0
1 TraesCS5B01G518300 chr5B 95.848 1156 42 4 875 2028 532363619 532364770 0.000000e+00 1864.0
2 TraesCS5B01G518300 chr5B 96.552 725 21 2 875 1598 144592224 144591503 0.000000e+00 1197.0
3 TraesCS5B01G518300 chr5B 89.130 138 13 2 2058 2195 681179623 681179488 1.190000e-38 171.0
4 TraesCS5B01G518300 chr5B 89.130 138 13 2 2167 2302 681179732 681179595 1.190000e-38 171.0
5 TraesCS5B01G518300 chr5B 75.130 386 36 29 2082 2434 657653524 657653166 2.610000e-25 126.0
6 TraesCS5B01G518300 chr5B 85.039 127 13 5 2260 2384 12337066 12337188 9.390000e-25 124.0
7 TraesCS5B01G518300 chr4D 93.546 1193 38 8 875 2034 175106199 175107385 0.000000e+00 1740.0
8 TraesCS5B01G518300 chr7B 93.686 1172 54 4 883 2034 8966449 8967620 0.000000e+00 1736.0
9 TraesCS5B01G518300 chr7B 95.022 683 17 3 1355 2035 83918512 83919179 0.000000e+00 1057.0
10 TraesCS5B01G518300 chr7B 86.391 169 19 4 2051 2218 495000486 495000321 5.500000e-42 182.0
11 TraesCS5B01G518300 chr7B 82.390 159 18 7 2113 2263 10761683 10761839 2.020000e-26 130.0
12 TraesCS5B01G518300 chr1A 98.632 877 12 0 1 877 394598554 394599430 0.000000e+00 1554.0
13 TraesCS5B01G518300 chr1A 96.552 725 21 2 875 1598 394599989 394600710 0.000000e+00 1197.0
14 TraesCS5B01G518300 chr1B 98.518 877 13 0 1 877 70693259 70692383 0.000000e+00 1548.0
15 TraesCS5B01G518300 chr1B 96.414 725 22 2 875 1598 70691824 70691103 0.000000e+00 1192.0
16 TraesCS5B01G518300 chr1B 94.993 679 17 3 1358 2034 449256373 449255710 0.000000e+00 1050.0
17 TraesCS5B01G518300 chr1B 77.778 261 40 15 2055 2302 356238440 356238695 7.210000e-31 145.0
18 TraesCS5B01G518300 chrUn 98.404 877 14 0 1 877 278748569 278749445 0.000000e+00 1543.0
19 TraesCS5B01G518300 chr6A 98.404 877 14 0 1 877 81878903 81878027 0.000000e+00 1543.0
20 TraesCS5B01G518300 chr6A 98.176 877 16 0 1 877 539539853 539540729 0.000000e+00 1531.0
21 TraesCS5B01G518300 chr6A 96.414 725 22 2 875 1598 68986903 68987624 0.000000e+00 1192.0
22 TraesCS5B01G518300 chr3B 98.404 877 14 0 1 877 220779740 220780616 0.000000e+00 1543.0
23 TraesCS5B01G518300 chr3B 98.290 877 15 0 1 877 565442736 565441860 0.000000e+00 1537.0
24 TraesCS5B01G518300 chr3B 98.176 877 16 0 1 877 217965601 217964725 0.000000e+00 1531.0
25 TraesCS5B01G518300 chr3B 93.571 1011 62 3 875 1884 123987270 123988278 0.000000e+00 1504.0
26 TraesCS5B01G518300 chr3B 96.414 725 22 3 875 1598 217969105 217969826 0.000000e+00 1192.0
27 TraesCS5B01G518300 chr3B 77.333 225 38 10 2113 2327 59465974 59466195 1.220000e-23 121.0
28 TraesCS5B01G518300 chr3B 92.105 76 6 0 2035 2110 599087811 599087886 9.460000e-20 108.0
29 TraesCS5B01G518300 chr7A 98.062 877 17 0 1 877 594456285 594457161 0.000000e+00 1526.0
30 TraesCS5B01G518300 chr7A 94.993 679 17 3 1358 2034 376617078 376616415 0.000000e+00 1050.0
31 TraesCS5B01G518300 chr5A 95.140 679 16 3 1358 2034 695337329 695336666 0.000000e+00 1055.0
32 TraesCS5B01G518300 chr5A 95.140 679 16 3 1358 2034 695361902 695361239 0.000000e+00 1055.0
33 TraesCS5B01G518300 chr5A 84.916 179 20 7 2071 2248 451135075 451134903 9.200000e-40 174.0
34 TraesCS5B01G518300 chr4B 95.015 682 17 3 1355 2034 316995573 316996239 0.000000e+00 1055.0
35 TraesCS5B01G518300 chr4A 94.993 679 17 3 1358 2034 535867958 535867295 0.000000e+00 1050.0
36 TraesCS5B01G518300 chr4A 81.333 300 44 11 2139 2434 604173613 604173322 1.500000e-57 233.0
37 TraesCS5B01G518300 chr6D 88.166 169 16 4 2050 2218 365051010 365051174 5.460000e-47 198.0
38 TraesCS5B01G518300 chr7D 80.579 242 33 9 2198 2434 555230552 555230784 9.200000e-40 174.0
39 TraesCS5B01G518300 chr7D 80.583 206 30 9 2145 2347 192366197 192365999 1.550000e-32 150.0
40 TraesCS5B01G518300 chr5D 81.188 202 29 8 2106 2302 283106545 283106348 1.200000e-33 154.0
41 TraesCS5B01G518300 chr5D 82.682 179 22 9 2061 2234 548631608 548631782 1.550000e-32 150.0
42 TraesCS5B01G518300 chr1D 78.814 236 34 14 2118 2347 487590943 487590718 7.210000e-31 145.0
43 TraesCS5B01G518300 chr2A 89.535 86 6 3 2050 2134 89598660 89598743 3.400000e-19 106.0
44 TraesCS5B01G518300 chr2A 97.222 36 0 1 2106 2141 758288372 758288338 2.690000e-05 60.2


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 TraesCS5B01G518300 chr5B 681179289 681181789 2500 True 1653.666667 4619 92.753333 1 2501 3 chr5B.!!$R3 2500
1 TraesCS5B01G518300 chr5B 532363619 532364770 1151 False 1864.000000 1864 95.848000 875 2028 1 chr5B.!!$F2 1153
2 TraesCS5B01G518300 chr5B 144591503 144592224 721 True 1197.000000 1197 96.552000 875 1598 1 chr5B.!!$R1 723
3 TraesCS5B01G518300 chr4D 175106199 175107385 1186 False 1740.000000 1740 93.546000 875 2034 1 chr4D.!!$F1 1159
4 TraesCS5B01G518300 chr7B 8966449 8967620 1171 False 1736.000000 1736 93.686000 883 2034 1 chr7B.!!$F1 1151
5 TraesCS5B01G518300 chr7B 83918512 83919179 667 False 1057.000000 1057 95.022000 1355 2035 1 chr7B.!!$F3 680
6 TraesCS5B01G518300 chr1A 394598554 394600710 2156 False 1375.500000 1554 97.592000 1 1598 2 chr1A.!!$F1 1597
7 TraesCS5B01G518300 chr1B 70691103 70693259 2156 True 1370.000000 1548 97.466000 1 1598 2 chr1B.!!$R2 1597
8 TraesCS5B01G518300 chr1B 449255710 449256373 663 True 1050.000000 1050 94.993000 1358 2034 1 chr1B.!!$R1 676
9 TraesCS5B01G518300 chrUn 278748569 278749445 876 False 1543.000000 1543 98.404000 1 877 1 chrUn.!!$F1 876
10 TraesCS5B01G518300 chr6A 81878027 81878903 876 True 1543.000000 1543 98.404000 1 877 1 chr6A.!!$R1 876
11 TraesCS5B01G518300 chr6A 539539853 539540729 876 False 1531.000000 1531 98.176000 1 877 1 chr6A.!!$F2 876
12 TraesCS5B01G518300 chr6A 68986903 68987624 721 False 1192.000000 1192 96.414000 875 1598 1 chr6A.!!$F1 723
13 TraesCS5B01G518300 chr3B 220779740 220780616 876 False 1543.000000 1543 98.404000 1 877 1 chr3B.!!$F4 876
14 TraesCS5B01G518300 chr3B 565441860 565442736 876 True 1537.000000 1537 98.290000 1 877 1 chr3B.!!$R2 876
15 TraesCS5B01G518300 chr3B 217964725 217965601 876 True 1531.000000 1531 98.176000 1 877 1 chr3B.!!$R1 876
16 TraesCS5B01G518300 chr3B 123987270 123988278 1008 False 1504.000000 1504 93.571000 875 1884 1 chr3B.!!$F2 1009
17 TraesCS5B01G518300 chr3B 217969105 217969826 721 False 1192.000000 1192 96.414000 875 1598 1 chr3B.!!$F3 723
18 TraesCS5B01G518300 chr7A 594456285 594457161 876 False 1526.000000 1526 98.062000 1 877 1 chr7A.!!$F1 876
19 TraesCS5B01G518300 chr7A 376616415 376617078 663 True 1050.000000 1050 94.993000 1358 2034 1 chr7A.!!$R1 676
20 TraesCS5B01G518300 chr5A 695336666 695337329 663 True 1055.000000 1055 95.140000 1358 2034 1 chr5A.!!$R2 676
21 TraesCS5B01G518300 chr5A 695361239 695361902 663 True 1055.000000 1055 95.140000 1358 2034 1 chr5A.!!$R3 676
22 TraesCS5B01G518300 chr4B 316995573 316996239 666 False 1055.000000 1055 95.015000 1355 2034 1 chr4B.!!$F1 679
23 TraesCS5B01G518300 chr4A 535867295 535867958 663 True 1050.000000 1050 94.993000 1358 2034 1 chr4A.!!$R1 676

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
98 99 0.756294 TTTGAGGAGGCAACACGAGA 59.244 50.0 0.0 0.0 41.41 4.04 F
1024 1586 0.179023 ACGGTTTCAAAAGGGGCGTA 60.179 50.0 0.0 0.0 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1609 1.089920 CCTCAATGACCAAAGCCTCG 58.910 55.0 0.00 0.00 0.00 4.63 R
2212 2829 0.694771 ACATGACAGACTGCCATGGT 59.305 50.0 28.47 15.48 41.28 3.55 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
74 75 7.092716 GCTTAATGATTGTGTGAAGGAAACAT 58.907 34.615 0.00 0.00 0.00 2.71
98 99 0.756294 TTTGAGGAGGCAACACGAGA 59.244 50.000 0.00 0.00 41.41 4.04
240 241 2.358957 TGCCTCAAGTGTATGTCATGC 58.641 47.619 0.00 0.00 0.00 4.06
280 281 7.065563 GCTGATTTGCTTGAGAAGAGAATTCTA 59.934 37.037 8.25 0.00 31.96 2.10
430 431 6.174049 GGACCTAATGTTGGAAGATATAGGC 58.826 44.000 0.00 0.00 0.00 3.93
572 573 1.034838 AGCCACTCGTTTTGCCACAA 61.035 50.000 0.00 0.00 0.00 3.33
621 622 2.097825 GAACAAGGCTGCATTGAGGAT 58.902 47.619 30.65 14.72 0.00 3.24
633 634 8.359642 GGCTGCATTGAGGATTTTATTTACATA 58.640 33.333 0.50 0.00 0.00 2.29
706 707 7.977789 TGTGCAAGAGATTATACTTTCAACA 57.022 32.000 0.00 0.00 0.00 3.33
775 776 7.184106 CACTTCTTAGAGTTCTTAGAGTAGCG 58.816 42.308 0.00 0.00 33.79 4.26
979 1541 7.596621 GGAAAAGGTTGAATGATCTTGTCTTTC 59.403 37.037 0.00 0.00 39.94 2.62
1018 1580 5.469479 AGAATATGCAACGGTTTCAAAAGG 58.531 37.500 0.00 0.00 0.00 3.11
1024 1586 0.179023 ACGGTTTCAAAAGGGGCGTA 60.179 50.000 0.00 0.00 0.00 4.42
1047 1609 0.466124 AGGTGGGCGAGAATAGCTTC 59.534 55.000 0.00 0.00 36.74 3.86
1183 1745 3.701040 GGATGTTGATGTGGCTATTGGTT 59.299 43.478 0.00 0.00 0.00 3.67
1235 1797 4.820897 CATAGGACAGCAACTACACTTCA 58.179 43.478 0.00 0.00 0.00 3.02
1273 1838 1.218875 CCGTCTGCAACACTACGCAA 61.219 55.000 0.00 0.00 37.76 4.85
1309 1874 4.877378 ACAACACGACCTACAATTCCTA 57.123 40.909 0.00 0.00 0.00 2.94
1332 1897 2.090606 AGAAGATGAGGCAGAGGAGGAT 60.091 50.000 0.00 0.00 0.00 3.24
1367 1932 0.892755 CACTCAAGCATGCCCAATGT 59.107 50.000 15.66 4.58 38.65 2.71
1434 2002 2.743664 CAATGACGATCAAGAGCCAACA 59.256 45.455 0.00 0.00 0.00 3.33
1566 2135 2.834638 ATCCCTTTTGCTATGCTGGT 57.165 45.000 0.00 0.00 0.00 4.00
1638 2207 7.936847 ACTACTGGACTTGTGTCATTTGAATTA 59.063 33.333 0.00 0.00 44.61 1.40
1953 2567 1.927838 GCTTACAAGTCTCTAAGGCGC 59.072 52.381 0.00 0.00 0.00 6.53
1982 2596 0.830648 TTATGCCTCAGCGCTTAGGT 59.169 50.000 32.46 19.77 44.31 3.08
2035 2652 5.124297 GCCTTACCGCCTTAAAAACATAGAA 59.876 40.000 0.00 0.00 0.00 2.10
2036 2653 6.183360 GCCTTACCGCCTTAAAAACATAGAAT 60.183 38.462 0.00 0.00 0.00 2.40
2037 2654 7.012610 GCCTTACCGCCTTAAAAACATAGAATA 59.987 37.037 0.00 0.00 0.00 1.75
2038 2655 8.340443 CCTTACCGCCTTAAAAACATAGAATAC 58.660 37.037 0.00 0.00 0.00 1.89
2039 2656 8.789825 TTACCGCCTTAAAAACATAGAATACA 57.210 30.769 0.00 0.00 0.00 2.29
2040 2657 7.875327 ACCGCCTTAAAAACATAGAATACAT 57.125 32.000 0.00 0.00 0.00 2.29
2041 2658 8.288689 ACCGCCTTAAAAACATAGAATACATT 57.711 30.769 0.00 0.00 0.00 2.71
2042 2659 8.745590 ACCGCCTTAAAAACATAGAATACATTT 58.254 29.630 0.00 0.00 0.00 2.32
2043 2660 9.019764 CCGCCTTAAAAACATAGAATACATTTG 57.980 33.333 0.00 0.00 0.00 2.32
2044 2661 8.531530 CGCCTTAAAAACATAGAATACATTTGC 58.468 33.333 0.00 0.00 0.00 3.68
2045 2662 8.817100 GCCTTAAAAACATAGAATACATTTGCC 58.183 33.333 0.00 0.00 0.00 4.52
2046 2663 9.868277 CCTTAAAAACATAGAATACATTTGCCA 57.132 29.630 0.00 0.00 0.00 4.92
2052 2669 9.553064 AAACATAGAATACATTTGCCAAAAACA 57.447 25.926 0.00 0.00 0.00 2.83
2053 2670 9.723601 AACATAGAATACATTTGCCAAAAACAT 57.276 25.926 0.00 0.00 0.00 2.71
2054 2671 9.369904 ACATAGAATACATTTGCCAAAAACATC 57.630 29.630 0.00 0.00 0.00 3.06
2055 2672 9.590451 CATAGAATACATTTGCCAAAAACATCT 57.410 29.630 0.00 0.00 0.00 2.90
2058 2675 9.995003 AGAATACATTTGCCAAAAACATCTTAA 57.005 25.926 0.00 0.00 0.00 1.85
2060 2677 9.777297 AATACATTTGCCAAAAACATCTTAAGT 57.223 25.926 1.63 0.00 0.00 2.24
2061 2678 9.777297 ATACATTTGCCAAAAACATCTTAAGTT 57.223 25.926 1.63 0.00 0.00 2.66
2062 2679 8.504812 ACATTTGCCAAAAACATCTTAAGTTT 57.495 26.923 1.63 0.00 40.66 2.66
2063 2680 8.397148 ACATTTGCCAAAAACATCTTAAGTTTG 58.603 29.630 1.63 5.56 39.02 2.93
2064 2681 5.982465 TGCCAAAAACATCTTAAGTTTGC 57.018 34.783 1.63 3.53 39.02 3.68
2065 2682 4.813697 TGCCAAAAACATCTTAAGTTTGCC 59.186 37.500 1.63 0.00 39.02 4.52
2066 2683 4.813697 GCCAAAAACATCTTAAGTTTGCCA 59.186 37.500 1.63 0.00 39.02 4.92
2067 2684 5.469760 GCCAAAAACATCTTAAGTTTGCCAT 59.530 36.000 1.63 0.00 39.02 4.40
2068 2685 6.566376 GCCAAAAACATCTTAAGTTTGCCATG 60.566 38.462 1.63 0.40 39.02 3.66
2069 2686 6.073112 CCAAAAACATCTTAAGTTTGCCATGG 60.073 38.462 7.63 7.63 39.02 3.66
2070 2687 5.806654 AAACATCTTAAGTTTGCCATGGT 57.193 34.783 14.67 0.00 37.76 3.55
2071 2688 6.909550 AAACATCTTAAGTTTGCCATGGTA 57.090 33.333 14.67 5.86 37.76 3.25
2072 2689 6.909550 AACATCTTAAGTTTGCCATGGTAA 57.090 33.333 11.68 11.68 0.00 2.85
2073 2690 6.515272 ACATCTTAAGTTTGCCATGGTAAG 57.485 37.500 15.25 12.29 0.00 2.34
2074 2691 6.010219 ACATCTTAAGTTTGCCATGGTAAGT 58.990 36.000 15.25 8.99 0.00 2.24
2075 2692 6.493458 ACATCTTAAGTTTGCCATGGTAAGTT 59.507 34.615 15.25 17.71 0.00 2.66
2076 2693 6.969993 TCTTAAGTTTGCCATGGTAAGTTT 57.030 33.333 15.25 14.93 0.00 2.66
2077 2694 6.744112 TCTTAAGTTTGCCATGGTAAGTTTG 58.256 36.000 15.25 12.68 0.00 2.93
2078 2695 3.385193 AGTTTGCCATGGTAAGTTTGC 57.615 42.857 15.25 5.46 0.00 3.68
2079 2696 2.037121 AGTTTGCCATGGTAAGTTTGCC 59.963 45.455 15.25 1.74 0.00 4.52
2080 2697 1.709578 TTGCCATGGTAAGTTTGCCA 58.290 45.000 11.68 4.14 46.95 4.92
2089 2706 5.344743 TGGTAAGTTTGCCATGTTTTTGA 57.655 34.783 0.00 0.00 38.05 2.69
2090 2707 5.734720 TGGTAAGTTTGCCATGTTTTTGAA 58.265 33.333 0.00 0.00 38.05 2.69
2091 2708 5.582665 TGGTAAGTTTGCCATGTTTTTGAAC 59.417 36.000 0.00 0.00 38.05 3.18
2092 2709 5.582665 GGTAAGTTTGCCATGTTTTTGAACA 59.417 36.000 0.00 0.00 37.05 3.18
2093 2710 6.259829 GGTAAGTTTGCCATGTTTTTGAACAT 59.740 34.615 0.00 0.00 43.64 2.71
2094 2711 5.989551 AGTTTGCCATGTTTTTGAACATC 57.010 34.783 2.02 0.00 41.12 3.06
2095 2712 5.673514 AGTTTGCCATGTTTTTGAACATCT 58.326 33.333 2.02 0.00 41.12 2.90
2096 2713 6.815089 AGTTTGCCATGTTTTTGAACATCTA 58.185 32.000 2.02 0.00 41.12 1.98
2097 2714 7.444299 AGTTTGCCATGTTTTTGAACATCTAT 58.556 30.769 2.02 0.00 41.12 1.98
2098 2715 8.584157 AGTTTGCCATGTTTTTGAACATCTATA 58.416 29.630 2.02 0.00 41.12 1.31
2099 2716 9.202273 GTTTGCCATGTTTTTGAACATCTATAA 57.798 29.630 2.02 0.00 41.12 0.98
2100 2717 8.755696 TTGCCATGTTTTTGAACATCTATAAC 57.244 30.769 2.02 0.00 41.12 1.89
2101 2718 8.121305 TGCCATGTTTTTGAACATCTATAACT 57.879 30.769 2.02 0.00 41.12 2.24
2102 2719 8.584157 TGCCATGTTTTTGAACATCTATAACTT 58.416 29.630 2.02 0.00 41.12 2.66
2103 2720 9.076596 GCCATGTTTTTGAACATCTATAACTTC 57.923 33.333 2.02 0.00 41.12 3.01
2107 2724 9.126151 TGTTTTTGAACATCTATAACTTCACCA 57.874 29.630 0.00 0.00 0.00 4.17
2110 2727 7.864108 TTGAACATCTATAACTTCACCATGG 57.136 36.000 11.19 11.19 0.00 3.66
2111 2728 5.822519 TGAACATCTATAACTTCACCATGGC 59.177 40.000 13.04 0.00 0.00 4.40
2112 2729 5.372343 ACATCTATAACTTCACCATGGCA 57.628 39.130 13.04 0.00 0.00 4.92
2113 2730 5.754782 ACATCTATAACTTCACCATGGCAA 58.245 37.500 13.04 3.89 0.00 4.52
2114 2731 5.824624 ACATCTATAACTTCACCATGGCAAG 59.175 40.000 13.04 16.49 0.00 4.01
2115 2732 5.435686 TCTATAACTTCACCATGGCAAGT 57.564 39.130 19.62 19.62 31.48 3.16
2116 2733 5.815581 TCTATAACTTCACCATGGCAAGTT 58.184 37.500 30.91 30.91 41.94 2.66
2117 2734 6.245408 TCTATAACTTCACCATGGCAAGTTT 58.755 36.000 32.30 24.52 40.18 2.66
2118 2735 3.457610 AACTTCACCATGGCAAGTTTG 57.542 42.857 26.35 12.56 37.09 2.93
2157 2774 9.165035 ACATCTATAAATTTGCCATGTTTTTGG 57.835 29.630 0.00 0.00 39.94 3.28
2158 2775 9.381033 CATCTATAAATTTGCCATGTTTTTGGA 57.619 29.630 0.00 0.00 39.25 3.53
2159 2776 8.770438 TCTATAAATTTGCCATGTTTTTGGAC 57.230 30.769 0.00 0.00 39.25 4.02
2160 2777 8.370940 TCTATAAATTTGCCATGTTTTTGGACA 58.629 29.630 0.00 0.00 39.25 4.02
2161 2778 7.999450 ATAAATTTGCCATGTTTTTGGACAT 57.001 28.000 0.00 0.00 40.76 3.06
2171 2788 6.923928 ATGTTTTTGGACATGGAAAAGTTG 57.076 33.333 0.00 0.00 38.75 3.16
2172 2789 6.042638 TGTTTTTGGACATGGAAAAGTTGA 57.957 33.333 0.00 0.00 0.00 3.18
2173 2790 5.872070 TGTTTTTGGACATGGAAAAGTTGAC 59.128 36.000 0.00 0.00 0.00 3.18
2174 2791 5.667539 TTTTGGACATGGAAAAGTTGACA 57.332 34.783 0.00 0.00 0.00 3.58
2175 2792 5.867903 TTTGGACATGGAAAAGTTGACAT 57.132 34.783 0.00 0.00 0.00 3.06
2176 2793 4.852134 TGGACATGGAAAAGTTGACATG 57.148 40.909 11.14 11.14 44.61 3.21
2177 2794 3.573538 TGGACATGGAAAAGTTGACATGG 59.426 43.478 15.08 3.05 43.66 3.66
2178 2795 3.578688 GACATGGAAAAGTTGACATGGC 58.421 45.455 15.08 10.58 43.66 4.40
2179 2796 2.964464 ACATGGAAAAGTTGACATGGCA 59.036 40.909 0.00 0.00 43.66 4.92
2180 2797 3.387374 ACATGGAAAAGTTGACATGGCAA 59.613 39.130 10.79 10.79 43.66 4.52
2181 2798 3.731652 TGGAAAAGTTGACATGGCAAG 57.268 42.857 16.10 0.00 0.00 4.01
2182 2799 3.030291 TGGAAAAGTTGACATGGCAAGT 58.970 40.909 16.10 16.20 33.02 3.16
2183 2800 3.450457 TGGAAAAGTTGACATGGCAAGTT 59.550 39.130 25.76 25.76 41.76 2.66
2185 2802 4.270808 GGAAAAGTTGACATGGCAAGTTTG 59.729 41.667 36.33 0.00 45.63 2.93
2200 2817 5.542616 CAAGTTTGCCATGTTTTTGAACA 57.457 34.783 0.00 0.00 37.05 3.18
2201 2818 6.121613 CAAGTTTGCCATGTTTTTGAACAT 57.878 33.333 0.00 0.00 43.64 2.71
2202 2819 5.989551 AGTTTGCCATGTTTTTGAACATC 57.010 34.783 2.02 0.00 41.12 3.06
2203 2820 5.673514 AGTTTGCCATGTTTTTGAACATCT 58.326 33.333 2.02 0.00 41.12 2.90
2204 2821 6.815089 AGTTTGCCATGTTTTTGAACATCTA 58.185 32.000 2.02 0.00 41.12 1.98
2205 2822 7.444299 AGTTTGCCATGTTTTTGAACATCTAT 58.556 30.769 2.02 0.00 41.12 1.98
2206 2823 8.584157 AGTTTGCCATGTTTTTGAACATCTATA 58.416 29.630 2.02 0.00 41.12 1.31
2207 2824 9.202273 GTTTGCCATGTTTTTGAACATCTATAA 57.798 29.630 2.02 0.00 41.12 0.98
2208 2825 8.755696 TTGCCATGTTTTTGAACATCTATAAC 57.244 30.769 2.02 0.00 41.12 1.89
2209 2826 8.121305 TGCCATGTTTTTGAACATCTATAACT 57.879 30.769 2.02 0.00 41.12 2.24
2210 2827 8.584157 TGCCATGTTTTTGAACATCTATAACTT 58.416 29.630 2.02 0.00 41.12 2.66
2211 2828 9.076596 GCCATGTTTTTGAACATCTATAACTTC 57.923 33.333 2.02 0.00 41.12 3.01
2215 2832 9.126151 TGTTTTTGAACATCTATAACTTCACCA 57.874 29.630 0.00 0.00 0.00 4.17
2218 2835 7.864108 TTGAACATCTATAACTTCACCATGG 57.136 36.000 11.19 11.19 0.00 3.66
2219 2836 5.822519 TGAACATCTATAACTTCACCATGGC 59.177 40.000 13.04 0.00 0.00 4.40
2220 2837 5.372343 ACATCTATAACTTCACCATGGCA 57.628 39.130 13.04 0.00 0.00 4.92
2221 2838 5.371526 ACATCTATAACTTCACCATGGCAG 58.628 41.667 13.04 8.19 0.00 4.85
2222 2839 5.104360 ACATCTATAACTTCACCATGGCAGT 60.104 40.000 13.04 8.91 0.00 4.40
2223 2840 5.023533 TCTATAACTTCACCATGGCAGTC 57.976 43.478 13.04 0.00 0.00 3.51
2224 2841 4.716784 TCTATAACTTCACCATGGCAGTCT 59.283 41.667 13.04 5.76 0.00 3.24
2225 2842 1.901591 AACTTCACCATGGCAGTCTG 58.098 50.000 13.04 1.70 0.00 3.51
2226 2843 0.767375 ACTTCACCATGGCAGTCTGT 59.233 50.000 13.04 0.52 0.00 3.41
2227 2844 1.271054 ACTTCACCATGGCAGTCTGTC 60.271 52.381 13.04 0.00 0.00 3.51
2228 2845 0.764271 TTCACCATGGCAGTCTGTCA 59.236 50.000 13.04 10.09 35.91 3.58
2229 2846 0.986527 TCACCATGGCAGTCTGTCAT 59.013 50.000 14.33 14.33 44.65 3.06
2235 2852 2.936919 TGGCAGTCTGTCATGTTTCT 57.063 45.000 2.12 0.00 0.00 2.52
2236 2853 2.497138 TGGCAGTCTGTCATGTTTCTG 58.503 47.619 2.12 0.00 0.00 3.02
2237 2854 2.104622 TGGCAGTCTGTCATGTTTCTGA 59.895 45.455 2.12 0.00 0.00 3.27
2238 2855 3.141398 GGCAGTCTGTCATGTTTCTGAA 58.859 45.455 0.00 0.00 0.00 3.02
2239 2856 3.565482 GGCAGTCTGTCATGTTTCTGAAA 59.435 43.478 0.00 0.00 0.00 2.69
2240 2857 4.036734 GGCAGTCTGTCATGTTTCTGAAAA 59.963 41.667 4.09 0.00 0.00 2.29
2241 2858 5.278660 GGCAGTCTGTCATGTTTCTGAAAAT 60.279 40.000 4.09 0.00 0.00 1.82
2242 2859 5.855395 GCAGTCTGTCATGTTTCTGAAAATC 59.145 40.000 4.09 0.00 0.00 2.17
2243 2860 6.293845 GCAGTCTGTCATGTTTCTGAAAATCT 60.294 38.462 4.09 0.00 0.00 2.40
2244 2861 7.095060 GCAGTCTGTCATGTTTCTGAAAATCTA 60.095 37.037 4.09 0.00 0.00 1.98
2245 2862 8.944029 CAGTCTGTCATGTTTCTGAAAATCTAT 58.056 33.333 4.09 0.00 0.00 1.98
2303 2920 4.462508 TGGCAAGTTTGTCATGTTTTCA 57.537 36.364 0.00 0.00 37.97 2.69
2304 2921 4.431809 TGGCAAGTTTGTCATGTTTTCAG 58.568 39.130 0.00 0.00 37.97 3.02
2305 2922 4.159321 TGGCAAGTTTGTCATGTTTTCAGA 59.841 37.500 0.00 0.00 37.97 3.27
2306 2923 4.504097 GGCAAGTTTGTCATGTTTTCAGAC 59.496 41.667 0.00 0.00 31.86 3.51
2307 2924 5.101628 GCAAGTTTGTCATGTTTTCAGACA 58.898 37.500 0.00 0.00 36.74 3.41
2308 2925 5.576384 GCAAGTTTGTCATGTTTTCAGACAA 59.424 36.000 0.00 0.00 41.38 3.18
2309 2926 6.090628 GCAAGTTTGTCATGTTTTCAGACAAA 59.909 34.615 13.92 13.92 44.75 2.83
2310 2927 7.359933 GCAAGTTTGTCATGTTTTCAGACAAAA 60.360 33.333 18.06 4.23 46.17 2.44
2311 2928 8.494347 CAAGTTTGTCATGTTTTCAGACAAAAA 58.506 29.630 18.06 0.00 46.17 1.94
2338 2955 4.939271 TGCTATGGCAAATCACATGAATG 58.061 39.130 0.00 0.00 46.36 2.67
2339 2956 4.403113 TGCTATGGCAAATCACATGAATGT 59.597 37.500 0.00 0.00 46.36 2.71
2340 2957 5.105269 TGCTATGGCAAATCACATGAATGTT 60.105 36.000 0.00 0.00 46.36 2.71
2341 2958 5.233476 GCTATGGCAAATCACATGAATGTTG 59.767 40.000 0.00 0.00 37.37 3.33
2342 2959 4.603989 TGGCAAATCACATGAATGTTGT 57.396 36.364 0.00 0.00 39.39 3.32
2343 2960 4.558178 TGGCAAATCACATGAATGTTGTC 58.442 39.130 0.00 0.66 39.39 3.18
2344 2961 4.038883 TGGCAAATCACATGAATGTTGTCA 59.961 37.500 0.00 3.47 39.39 3.58
2345 2962 5.172934 GGCAAATCACATGAATGTTGTCAT 58.827 37.500 0.00 0.00 39.39 3.06
2346 2963 6.071503 TGGCAAATCACATGAATGTTGTCATA 60.072 34.615 0.00 0.00 39.39 2.15
2347 2964 6.254157 GGCAAATCACATGAATGTTGTCATAC 59.746 38.462 0.00 0.00 39.39 2.39
2348 2965 6.807720 GCAAATCACATGAATGTTGTCATACA 59.192 34.615 0.00 0.00 39.39 2.29
2349 2966 7.490079 GCAAATCACATGAATGTTGTCATACAT 59.510 33.333 0.00 0.00 39.39 2.29
2353 2970 8.558973 TCACATGAATGTTGTCATACATAACA 57.441 30.769 0.00 0.00 40.11 2.41
2354 2971 9.007901 TCACATGAATGTTGTCATACATAACAA 57.992 29.630 0.00 0.00 39.34 2.83
2355 2972 9.623350 CACATGAATGTTGTCATACATAACAAA 57.377 29.630 0.00 0.00 39.34 2.83
2359 2976 9.138062 TGAATGTTGTCATACATAACAAATTGC 57.862 29.630 0.00 0.00 39.34 3.56
2360 2977 8.477984 AATGTTGTCATACATAACAAATTGCC 57.522 30.769 0.00 0.00 39.34 4.52
2361 2978 6.986250 TGTTGTCATACATAACAAATTGCCA 58.014 32.000 0.00 0.00 37.15 4.92
2362 2979 7.609960 TGTTGTCATACATAACAAATTGCCAT 58.390 30.769 0.00 0.00 37.15 4.40
2363 2980 8.093307 TGTTGTCATACATAACAAATTGCCATT 58.907 29.630 0.00 0.00 37.15 3.16
2364 2981 8.382130 GTTGTCATACATAACAAATTGCCATTG 58.618 33.333 0.00 0.00 37.15 2.82
2365 2982 7.609960 TGTCATACATAACAAATTGCCATTGT 58.390 30.769 0.00 0.00 42.56 2.71
2367 2984 8.934825 GTCATACATAACAAATTGCCATTGTTT 58.065 29.630 14.28 0.95 45.97 2.83
2372 2989 9.153721 ACATAACAAATTGCCATTGTTTATGAG 57.846 29.630 20.40 10.11 45.97 2.90
2373 2990 6.484818 AACAAATTGCCATTGTTTATGAGC 57.515 33.333 5.95 0.00 45.97 4.26
2374 2991 5.549347 ACAAATTGCCATTGTTTATGAGCA 58.451 33.333 0.00 0.00 37.74 4.26
2375 2992 5.996513 ACAAATTGCCATTGTTTATGAGCAA 59.003 32.000 12.58 12.58 45.65 3.91
2376 2993 6.148150 ACAAATTGCCATTGTTTATGAGCAAG 59.852 34.615 14.35 7.68 45.23 4.01
2377 2994 3.872511 TGCCATTGTTTATGAGCAAGG 57.127 42.857 0.00 0.00 37.43 3.61
2378 2995 3.429492 TGCCATTGTTTATGAGCAAGGA 58.571 40.909 0.36 0.00 37.43 3.36
2379 2996 3.193267 TGCCATTGTTTATGAGCAAGGAC 59.807 43.478 0.36 0.00 37.43 3.85
2380 2997 3.193267 GCCATTGTTTATGAGCAAGGACA 59.807 43.478 0.36 0.00 36.26 4.02
2381 2998 4.321899 GCCATTGTTTATGAGCAAGGACAA 60.322 41.667 0.36 0.00 36.26 3.18
2382 2999 5.782047 CCATTGTTTATGAGCAAGGACAAA 58.218 37.500 0.36 0.00 36.26 2.83
2383 3000 5.865552 CCATTGTTTATGAGCAAGGACAAAG 59.134 40.000 0.36 0.00 36.26 2.77
2384 3001 6.294675 CCATTGTTTATGAGCAAGGACAAAGA 60.295 38.462 0.36 0.00 36.26 2.52
2385 3002 6.899393 TTGTTTATGAGCAAGGACAAAGAT 57.101 33.333 0.00 0.00 0.00 2.40
2386 3003 6.258230 TGTTTATGAGCAAGGACAAAGATG 57.742 37.500 0.00 0.00 0.00 2.90
2387 3004 6.003326 TGTTTATGAGCAAGGACAAAGATGA 58.997 36.000 0.00 0.00 0.00 2.92
2388 3005 6.489700 TGTTTATGAGCAAGGACAAAGATGAA 59.510 34.615 0.00 0.00 0.00 2.57
2389 3006 7.014134 TGTTTATGAGCAAGGACAAAGATGAAA 59.986 33.333 0.00 0.00 0.00 2.69
2390 3007 7.523293 TTATGAGCAAGGACAAAGATGAAAA 57.477 32.000 0.00 0.00 0.00 2.29
2391 3008 5.850557 TGAGCAAGGACAAAGATGAAAAA 57.149 34.783 0.00 0.00 0.00 1.94
2417 3034 8.859517 AAAATCCATGAACTTTGCAAAATTTG 57.140 26.923 13.84 5.75 0.00 2.32
2482 3099 7.935338 ATGACAAATGACAATTGAACAAGAC 57.065 32.000 13.59 7.56 0.00 3.01
2483 3100 6.861144 TGACAAATGACAATTGAACAAGACA 58.139 32.000 13.59 9.56 0.00 3.41
2484 3101 6.751425 TGACAAATGACAATTGAACAAGACAC 59.249 34.615 13.59 6.44 0.00 3.67
2485 3102 6.629128 ACAAATGACAATTGAACAAGACACA 58.371 32.000 13.59 0.00 0.00 3.72
2486 3103 7.095910 ACAAATGACAATTGAACAAGACACAA 58.904 30.769 13.59 0.00 0.00 3.33
2487 3104 7.601886 ACAAATGACAATTGAACAAGACACAAA 59.398 29.630 13.59 0.00 0.00 2.83
2488 3105 8.441608 CAAATGACAATTGAACAAGACACAAAA 58.558 29.630 13.59 0.00 0.00 2.44
2489 3106 8.545229 AATGACAATTGAACAAGACACAAAAA 57.455 26.923 13.59 0.00 0.00 1.94
2490 3107 7.344910 TGACAATTGAACAAGACACAAAAAC 57.655 32.000 13.59 0.00 0.00 2.43
2491 3108 6.925718 TGACAATTGAACAAGACACAAAAACA 59.074 30.769 13.59 0.00 0.00 2.83
2492 3109 7.116090 TGACAATTGAACAAGACACAAAAACAG 59.884 33.333 13.59 0.00 0.00 3.16
2493 3110 7.151308 ACAATTGAACAAGACACAAAAACAGA 58.849 30.769 13.59 0.00 0.00 3.41
2494 3111 7.655328 ACAATTGAACAAGACACAAAAACAGAA 59.345 29.630 13.59 0.00 0.00 3.02
2495 3112 8.494347 CAATTGAACAAGACACAAAAACAGAAA 58.506 29.630 0.00 0.00 0.00 2.52
2496 3113 8.776376 ATTGAACAAGACACAAAAACAGAAAT 57.224 26.923 0.00 0.00 0.00 2.17
2497 3114 8.600449 TTGAACAAGACACAAAAACAGAAATT 57.400 26.923 0.00 0.00 0.00 1.82
2498 3115 8.600449 TGAACAAGACACAAAAACAGAAATTT 57.400 26.923 0.00 0.00 0.00 1.82
2499 3116 9.050601 TGAACAAGACACAAAAACAGAAATTTT 57.949 25.926 0.00 0.00 33.13 1.82
2500 3117 9.528847 GAACAAGACACAAAAACAGAAATTTTC 57.471 29.630 0.66 0.66 31.35 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.260884 CACTAGGAGGCTTGTAACCTGAA 59.739 47.826 2.11 0.00 37.77 3.02
74 75 2.297701 GTGTTGCCTCCTCAAAAGTCA 58.702 47.619 0.00 0.00 0.00 3.41
240 241 5.938710 AGCAAATCAGCTATCATATCACCAG 59.061 40.000 0.00 0.00 44.50 4.00
280 281 5.388654 ACCACATTCTCTTTTCCAACATCT 58.611 37.500 0.00 0.00 0.00 2.90
430 431 4.925646 GGCTTCTTAAATGCCTTCAACTTG 59.074 41.667 0.00 0.00 43.05 3.16
572 573 3.191888 ACTCCTAAGTGTGAGGATGGT 57.808 47.619 0.00 0.00 42.31 3.55
633 634 4.901250 ACTTGTTTCCAACCCATTCTTCAT 59.099 37.500 0.00 0.00 0.00 2.57
706 707 0.957395 CAATTGCGCTCCACCACTCT 60.957 55.000 9.73 0.00 0.00 3.24
775 776 1.964552 CAGGCTTCTCATCACCATCC 58.035 55.000 0.00 0.00 0.00 3.51
917 1479 5.828747 TCCTTTTCTTCGTATGGATCTACG 58.171 41.667 7.93 7.93 44.48 3.51
979 1541 6.038161 TGCATATTCTTCCGGTTGTATGAAAG 59.962 38.462 0.00 0.00 0.00 2.62
1018 1580 2.437895 GCCCACCTTCTTACGCCC 60.438 66.667 0.00 0.00 0.00 6.13
1024 1586 1.134371 GCTATTCTCGCCCACCTTCTT 60.134 52.381 0.00 0.00 0.00 2.52
1047 1609 1.089920 CCTCAATGACCAAAGCCTCG 58.910 55.000 0.00 0.00 0.00 4.63
1147 1709 4.525996 TCAACATCCTCCCATGTAATGTG 58.474 43.478 0.00 0.00 44.81 3.21
1183 1745 2.615493 GGCCTCGAAGGTTTGAAGATGA 60.615 50.000 0.00 0.00 37.80 2.92
1235 1797 1.215423 GGACATTTGTCTGGCCCCTAT 59.785 52.381 10.32 0.00 44.20 2.57
1273 1838 3.057456 CGTGTTGTAGTAGGTCTCTTGCT 60.057 47.826 0.00 0.00 0.00 3.91
1309 1874 2.504996 CCTCCTCTGCCTCATCTTCTTT 59.495 50.000 0.00 0.00 0.00 2.52
1332 1897 1.949525 GAGTGTTGCTCTTGCTCCAAA 59.050 47.619 0.00 0.00 40.98 3.28
1356 1921 1.759299 CCCCTCCACATTGGGCATG 60.759 63.158 0.00 0.00 42.03 4.06
1367 1932 1.585592 AGTATGAATCCTCCCCCTCCA 59.414 52.381 0.00 0.00 0.00 3.86
1638 2207 7.308348 GCACGGCATATTACATAACCATTAACT 60.308 37.037 0.00 0.00 0.00 2.24
1661 2230 5.088739 GTGTAACTGCAATCTACAATGCAC 58.911 41.667 0.00 0.00 46.87 4.57
1681 2250 7.550906 GGAAAGAAAGATAGCAAGTATGAGTGT 59.449 37.037 0.00 0.00 0.00 3.55
1876 2490 4.891992 ACTAGGCATACATCCATACACC 57.108 45.455 0.00 0.00 0.00 4.16
1930 2544 4.184629 CGCCTTAGAGACTTGTAAGCAAT 58.815 43.478 0.00 0.00 33.65 3.56
2035 2652 9.777297 AACTTAAGATGTTTTTGGCAAATGTAT 57.223 25.926 14.29 8.12 0.00 2.29
2036 2653 9.606631 AAACTTAAGATGTTTTTGGCAAATGTA 57.393 25.926 14.29 3.37 34.40 2.29
2037 2654 8.397148 CAAACTTAAGATGTTTTTGGCAAATGT 58.603 29.630 14.29 0.14 35.71 2.71
2038 2655 7.376601 GCAAACTTAAGATGTTTTTGGCAAATG 59.623 33.333 14.29 4.89 35.71 2.32
2039 2656 7.416817 GCAAACTTAAGATGTTTTTGGCAAAT 58.583 30.769 14.29 0.00 35.71 2.32
2040 2657 6.183360 GGCAAACTTAAGATGTTTTTGGCAAA 60.183 34.615 24.77 8.93 46.46 3.68
2041 2658 5.295540 GGCAAACTTAAGATGTTTTTGGCAA 59.704 36.000 24.77 0.00 46.46 4.52
2042 2659 4.813697 GGCAAACTTAAGATGTTTTTGGCA 59.186 37.500 24.77 0.00 46.46 4.92
2043 2660 5.342806 GGCAAACTTAAGATGTTTTTGGC 57.657 39.130 19.36 19.36 42.94 4.52
2044 2661 6.073112 CCATGGCAAACTTAAGATGTTTTTGG 60.073 38.462 10.09 9.65 35.71 3.28
2045 2662 6.482973 ACCATGGCAAACTTAAGATGTTTTTG 59.517 34.615 13.04 9.95 35.71 2.44
2046 2663 6.591001 ACCATGGCAAACTTAAGATGTTTTT 58.409 32.000 13.04 0.00 35.71 1.94
2047 2664 6.173427 ACCATGGCAAACTTAAGATGTTTT 57.827 33.333 13.04 0.00 35.71 2.43
2048 2665 5.806654 ACCATGGCAAACTTAAGATGTTT 57.193 34.783 13.04 0.00 38.04 2.83
2049 2666 6.493458 ACTTACCATGGCAAACTTAAGATGTT 59.507 34.615 19.22 0.00 0.00 2.71
2050 2667 6.010219 ACTTACCATGGCAAACTTAAGATGT 58.990 36.000 19.22 0.81 0.00 3.06
2051 2668 6.515272 ACTTACCATGGCAAACTTAAGATG 57.485 37.500 19.22 8.90 0.00 2.90
2052 2669 7.378181 CAAACTTACCATGGCAAACTTAAGAT 58.622 34.615 19.22 8.78 0.00 2.40
2053 2670 6.737346 GCAAACTTACCATGGCAAACTTAAGA 60.737 38.462 19.22 0.00 0.00 2.10
2054 2671 5.405269 GCAAACTTACCATGGCAAACTTAAG 59.595 40.000 13.04 13.25 0.00 1.85
2055 2672 5.293560 GCAAACTTACCATGGCAAACTTAA 58.706 37.500 13.04 0.55 0.00 1.85
2056 2673 4.262249 GGCAAACTTACCATGGCAAACTTA 60.262 41.667 13.04 0.00 39.25 2.24
2057 2674 3.494223 GGCAAACTTACCATGGCAAACTT 60.494 43.478 13.04 0.00 39.25 2.66
2058 2675 2.037121 GGCAAACTTACCATGGCAAACT 59.963 45.455 13.04 0.00 39.25 2.66
2059 2676 2.224161 TGGCAAACTTACCATGGCAAAC 60.224 45.455 13.04 0.00 45.18 2.93
2060 2677 2.042464 TGGCAAACTTACCATGGCAAA 58.958 42.857 13.04 5.75 45.18 3.68
2061 2678 1.709578 TGGCAAACTTACCATGGCAA 58.290 45.000 13.04 3.96 45.18 4.52
2062 2679 3.446658 TGGCAAACTTACCATGGCA 57.553 47.368 13.04 0.00 45.85 4.92
2067 2684 5.344743 TCAAAAACATGGCAAACTTACCA 57.655 34.783 0.00 0.00 41.06 3.25
2068 2685 5.582665 TGTTCAAAAACATGGCAAACTTACC 59.417 36.000 0.00 0.00 40.45 2.85
2069 2686 6.654793 TGTTCAAAAACATGGCAAACTTAC 57.345 33.333 0.00 0.00 40.45 2.34
2084 2701 8.739039 CCATGGTGAAGTTATAGATGTTCAAAA 58.261 33.333 2.57 0.00 30.94 2.44
2085 2702 7.148086 GCCATGGTGAAGTTATAGATGTTCAAA 60.148 37.037 14.67 0.00 30.94 2.69
2086 2703 6.318648 GCCATGGTGAAGTTATAGATGTTCAA 59.681 38.462 14.67 0.00 30.94 2.69
2087 2704 5.822519 GCCATGGTGAAGTTATAGATGTTCA 59.177 40.000 14.67 0.00 0.00 3.18
2088 2705 5.822519 TGCCATGGTGAAGTTATAGATGTTC 59.177 40.000 14.67 0.00 0.00 3.18
2089 2706 5.754782 TGCCATGGTGAAGTTATAGATGTT 58.245 37.500 14.67 0.00 0.00 2.71
2090 2707 5.372343 TGCCATGGTGAAGTTATAGATGT 57.628 39.130 14.67 0.00 0.00 3.06
2091 2708 5.824624 ACTTGCCATGGTGAAGTTATAGATG 59.175 40.000 19.95 1.61 0.00 2.90
2092 2709 6.006275 ACTTGCCATGGTGAAGTTATAGAT 57.994 37.500 19.95 2.55 0.00 1.98
2093 2710 5.435686 ACTTGCCATGGTGAAGTTATAGA 57.564 39.130 19.95 0.00 0.00 1.98
2094 2711 6.324819 CAAACTTGCCATGGTGAAGTTATAG 58.675 40.000 29.40 22.04 38.64 1.31
2095 2712 6.266168 CAAACTTGCCATGGTGAAGTTATA 57.734 37.500 29.40 3.68 38.64 0.98
2096 2713 5.138125 CAAACTTGCCATGGTGAAGTTAT 57.862 39.130 29.40 21.07 38.64 1.89
2097 2714 4.582701 CAAACTTGCCATGGTGAAGTTA 57.417 40.909 29.40 5.74 38.64 2.24
2098 2715 3.457610 CAAACTTGCCATGGTGAAGTT 57.542 42.857 26.27 26.27 40.77 2.66
2131 2748 9.165035 CCAAAAACATGGCAAATTTATAGATGT 57.835 29.630 0.00 0.00 32.78 3.06
2132 2749 9.381033 TCCAAAAACATGGCAAATTTATAGATG 57.619 29.630 0.00 0.00 40.46 2.90
2133 2750 9.382275 GTCCAAAAACATGGCAAATTTATAGAT 57.618 29.630 0.00 0.00 40.46 1.98
2134 2751 8.370940 TGTCCAAAAACATGGCAAATTTATAGA 58.629 29.630 0.00 0.00 40.46 1.98
2135 2752 8.545229 TGTCCAAAAACATGGCAAATTTATAG 57.455 30.769 0.00 0.00 40.46 1.31
2137 2754 7.999450 ATGTCCAAAAACATGGCAAATTTAT 57.001 28.000 0.00 0.00 38.43 1.40
2148 2765 6.538381 GTCAACTTTTCCATGTCCAAAAACAT 59.462 34.615 0.00 0.00 40.49 2.71
2149 2766 5.872070 GTCAACTTTTCCATGTCCAAAAACA 59.128 36.000 0.00 0.00 0.00 2.83
2150 2767 5.872070 TGTCAACTTTTCCATGTCCAAAAAC 59.128 36.000 0.00 0.00 0.00 2.43
2151 2768 6.042638 TGTCAACTTTTCCATGTCCAAAAA 57.957 33.333 0.00 0.00 0.00 1.94
2152 2769 5.667539 TGTCAACTTTTCCATGTCCAAAA 57.332 34.783 0.00 0.00 0.00 2.44
2153 2770 5.453057 CCATGTCAACTTTTCCATGTCCAAA 60.453 40.000 0.00 0.00 34.30 3.28
2154 2771 4.039004 CCATGTCAACTTTTCCATGTCCAA 59.961 41.667 0.00 0.00 34.30 3.53
2155 2772 3.573538 CCATGTCAACTTTTCCATGTCCA 59.426 43.478 0.00 0.00 34.30 4.02
2156 2773 3.614870 GCCATGTCAACTTTTCCATGTCC 60.615 47.826 0.00 0.00 34.30 4.02
2157 2774 3.005684 TGCCATGTCAACTTTTCCATGTC 59.994 43.478 0.00 0.00 34.30 3.06
2158 2775 2.964464 TGCCATGTCAACTTTTCCATGT 59.036 40.909 0.00 0.00 34.30 3.21
2159 2776 3.663995 TGCCATGTCAACTTTTCCATG 57.336 42.857 0.00 0.00 35.56 3.66
2160 2777 3.642848 ACTTGCCATGTCAACTTTTCCAT 59.357 39.130 0.00 0.00 0.00 3.41
2161 2778 3.030291 ACTTGCCATGTCAACTTTTCCA 58.970 40.909 0.00 0.00 0.00 3.53
2162 2779 3.733443 ACTTGCCATGTCAACTTTTCC 57.267 42.857 0.00 0.00 0.00 3.13
2163 2780 5.393902 CAAACTTGCCATGTCAACTTTTC 57.606 39.130 0.00 0.00 0.00 2.29
2177 2794 4.142730 TGTTCAAAAACATGGCAAACTTGC 60.143 37.500 5.85 5.85 45.44 4.01
2178 2795 5.542616 TGTTCAAAAACATGGCAAACTTG 57.457 34.783 0.00 0.00 40.45 3.16
2192 2809 8.739039 CCATGGTGAAGTTATAGATGTTCAAAA 58.261 33.333 2.57 0.00 30.94 2.44
2193 2810 7.148086 GCCATGGTGAAGTTATAGATGTTCAAA 60.148 37.037 14.67 0.00 30.94 2.69
2194 2811 6.318648 GCCATGGTGAAGTTATAGATGTTCAA 59.681 38.462 14.67 0.00 30.94 2.69
2195 2812 5.822519 GCCATGGTGAAGTTATAGATGTTCA 59.177 40.000 14.67 0.00 0.00 3.18
2196 2813 5.822519 TGCCATGGTGAAGTTATAGATGTTC 59.177 40.000 14.67 0.00 0.00 3.18
2197 2814 5.754782 TGCCATGGTGAAGTTATAGATGTT 58.245 37.500 14.67 0.00 0.00 2.71
2198 2815 5.104360 ACTGCCATGGTGAAGTTATAGATGT 60.104 40.000 14.67 0.00 0.00 3.06
2199 2816 5.371526 ACTGCCATGGTGAAGTTATAGATG 58.628 41.667 14.67 0.00 0.00 2.90
2200 2817 5.367937 AGACTGCCATGGTGAAGTTATAGAT 59.632 40.000 14.67 0.00 0.00 1.98
2201 2818 4.716784 AGACTGCCATGGTGAAGTTATAGA 59.283 41.667 14.67 0.00 0.00 1.98
2202 2819 4.813161 CAGACTGCCATGGTGAAGTTATAG 59.187 45.833 14.67 3.54 0.00 1.31
2203 2820 4.225042 ACAGACTGCCATGGTGAAGTTATA 59.775 41.667 14.67 0.00 0.00 0.98
2204 2821 3.009473 ACAGACTGCCATGGTGAAGTTAT 59.991 43.478 14.67 5.60 0.00 1.89
2205 2822 2.371841 ACAGACTGCCATGGTGAAGTTA 59.628 45.455 14.67 0.00 0.00 2.24
2206 2823 1.143684 ACAGACTGCCATGGTGAAGTT 59.856 47.619 14.67 3.99 0.00 2.66
2207 2824 0.767375 ACAGACTGCCATGGTGAAGT 59.233 50.000 14.67 14.51 0.00 3.01
2208 2825 1.271001 TGACAGACTGCCATGGTGAAG 60.271 52.381 14.67 11.31 0.00 3.02
2209 2826 0.764271 TGACAGACTGCCATGGTGAA 59.236 50.000 14.67 0.00 0.00 3.18
2210 2827 0.986527 ATGACAGACTGCCATGGTGA 59.013 50.000 14.67 0.00 0.00 4.02
2211 2828 1.092348 CATGACAGACTGCCATGGTG 58.908 55.000 20.61 9.43 35.34 4.17
2212 2829 0.694771 ACATGACAGACTGCCATGGT 59.305 50.000 28.47 15.48 41.28 3.55
2213 2830 1.830279 AACATGACAGACTGCCATGG 58.170 50.000 28.47 7.63 41.28 3.66
2214 2831 3.079578 AGAAACATGACAGACTGCCATG 58.920 45.455 25.02 25.02 42.32 3.66
2215 2832 3.079578 CAGAAACATGACAGACTGCCAT 58.920 45.455 0.00 0.00 0.00 4.40
2216 2833 2.104622 TCAGAAACATGACAGACTGCCA 59.895 45.455 0.00 0.00 0.00 4.92
2217 2834 2.771089 TCAGAAACATGACAGACTGCC 58.229 47.619 0.00 0.00 0.00 4.85
2218 2835 4.818534 TTTCAGAAACATGACAGACTGC 57.181 40.909 0.00 0.00 0.00 4.40
2219 2836 7.199541 AGATTTTCAGAAACATGACAGACTG 57.800 36.000 0.00 0.00 0.00 3.51
2278 2895 1.717194 CATGACAAACTTGCCATGGC 58.283 50.000 30.54 30.54 42.84 4.40
2281 2898 5.021033 TGAAAACATGACAAACTTGCCAT 57.979 34.783 0.00 0.00 31.11 4.40
2282 2899 4.159321 TCTGAAAACATGACAAACTTGCCA 59.841 37.500 0.00 0.00 0.00 4.92
2283 2900 4.504097 GTCTGAAAACATGACAAACTTGCC 59.496 41.667 0.00 0.00 0.00 4.52
2284 2901 5.101628 TGTCTGAAAACATGACAAACTTGC 58.898 37.500 0.00 0.00 37.71 4.01
2313 2930 7.849816 ACATTCATGTGATTTGCCATAGCATTT 60.850 33.333 0.00 0.00 44.04 2.32
2314 2931 6.407639 ACATTCATGTGATTTGCCATAGCATT 60.408 34.615 0.00 0.00 44.04 3.56
2315 2932 5.069914 ACATTCATGTGATTTGCCATAGCAT 59.930 36.000 0.00 0.00 44.04 3.79
2316 2933 4.403113 ACATTCATGTGATTTGCCATAGCA 59.597 37.500 0.00 0.00 43.37 3.49
2317 2934 4.940463 ACATTCATGTGATTTGCCATAGC 58.060 39.130 0.00 0.00 40.03 2.97
2318 2935 6.334989 ACAACATTCATGTGATTTGCCATAG 58.665 36.000 0.00 0.00 41.61 2.23
2319 2936 6.071503 TGACAACATTCATGTGATTTGCCATA 60.072 34.615 0.00 0.00 41.61 2.74
2320 2937 5.155278 ACAACATTCATGTGATTTGCCAT 57.845 34.783 0.00 0.00 41.61 4.40
2321 2938 4.038883 TGACAACATTCATGTGATTTGCCA 59.961 37.500 0.00 0.00 41.61 4.92
2322 2939 4.558178 TGACAACATTCATGTGATTTGCC 58.442 39.130 0.00 0.00 41.61 4.52
2323 2940 6.807720 TGTATGACAACATTCATGTGATTTGC 59.192 34.615 0.00 0.00 41.61 3.68
2324 2941 8.920509 ATGTATGACAACATTCATGTGATTTG 57.079 30.769 0.00 0.00 40.92 2.32
2327 2944 9.176460 TGTTATGTATGACAACATTCATGTGAT 57.824 29.630 10.81 0.00 41.89 3.06
2328 2945 8.558973 TGTTATGTATGACAACATTCATGTGA 57.441 30.769 10.81 0.00 41.89 3.58
2329 2946 9.623350 TTTGTTATGTATGACAACATTCATGTG 57.377 29.630 10.81 0.00 41.89 3.21
2333 2950 9.138062 GCAATTTGTTATGTATGACAACATTCA 57.862 29.630 2.17 0.00 40.52 2.57
2334 2951 8.594687 GGCAATTTGTTATGTATGACAACATTC 58.405 33.333 2.17 0.00 40.52 2.67
2335 2952 8.093307 TGGCAATTTGTTATGTATGACAACATT 58.907 29.630 2.17 4.03 40.52 2.71
2336 2953 7.609960 TGGCAATTTGTTATGTATGACAACAT 58.390 30.769 2.17 7.91 42.62 2.71
2337 2954 6.986250 TGGCAATTTGTTATGTATGACAACA 58.014 32.000 2.17 0.00 36.24 3.33
2338 2955 8.382130 CAATGGCAATTTGTTATGTATGACAAC 58.618 33.333 0.00 0.00 36.24 3.32
2339 2956 8.093307 ACAATGGCAATTTGTTATGTATGACAA 58.907 29.630 0.70 0.00 33.64 3.18
2340 2957 7.609960 ACAATGGCAATTTGTTATGTATGACA 58.390 30.769 0.70 0.00 33.64 3.58
2341 2958 8.477984 AACAATGGCAATTTGTTATGTATGAC 57.522 30.769 15.55 0.00 43.52 3.06
2346 2963 9.153721 CTCATAAACAATGGCAATTTGTTATGT 57.846 29.630 16.98 7.01 44.32 2.29
2347 2964 8.117988 GCTCATAAACAATGGCAATTTGTTATG 58.882 33.333 16.98 17.65 44.32 1.90
2348 2965 7.823310 TGCTCATAAACAATGGCAATTTGTTAT 59.177 29.630 16.98 11.06 44.32 1.89
2349 2966 7.157347 TGCTCATAAACAATGGCAATTTGTTA 58.843 30.769 16.98 8.29 44.32 2.41
2350 2967 5.996513 TGCTCATAAACAATGGCAATTTGTT 59.003 32.000 12.25 12.25 46.38 2.83
2351 2968 5.549347 TGCTCATAAACAATGGCAATTTGT 58.451 33.333 0.70 0.70 38.22 2.83
2352 2969 6.402766 CCTTGCTCATAAACAATGGCAATTTG 60.403 38.462 11.57 0.00 44.02 2.32
2353 2970 5.644636 CCTTGCTCATAAACAATGGCAATTT 59.355 36.000 11.57 0.00 44.02 1.82
2354 2971 5.046448 TCCTTGCTCATAAACAATGGCAATT 60.046 36.000 11.57 0.00 44.02 2.32
2355 2972 4.467082 TCCTTGCTCATAAACAATGGCAAT 59.533 37.500 11.57 0.00 44.02 3.56
2356 2973 3.831333 TCCTTGCTCATAAACAATGGCAA 59.169 39.130 0.00 11.00 43.45 4.52
2357 2974 3.193267 GTCCTTGCTCATAAACAATGGCA 59.807 43.478 0.00 0.00 38.91 4.92
2358 2975 3.193267 TGTCCTTGCTCATAAACAATGGC 59.807 43.478 0.00 0.00 36.15 4.40
2359 2976 5.389859 TTGTCCTTGCTCATAAACAATGG 57.610 39.130 0.00 0.00 36.15 3.16
2360 2977 6.680810 TCTTTGTCCTTGCTCATAAACAATG 58.319 36.000 0.00 0.00 36.88 2.82
2361 2978 6.899393 TCTTTGTCCTTGCTCATAAACAAT 57.101 33.333 0.00 0.00 0.00 2.71
2362 2979 6.489700 TCATCTTTGTCCTTGCTCATAAACAA 59.510 34.615 0.00 0.00 0.00 2.83
2363 2980 6.003326 TCATCTTTGTCCTTGCTCATAAACA 58.997 36.000 0.00 0.00 0.00 2.83
2364 2981 6.500684 TCATCTTTGTCCTTGCTCATAAAC 57.499 37.500 0.00 0.00 0.00 2.01
2365 2982 7.523293 TTTCATCTTTGTCCTTGCTCATAAA 57.477 32.000 0.00 0.00 0.00 1.40
2366 2983 7.523293 TTTTCATCTTTGTCCTTGCTCATAA 57.477 32.000 0.00 0.00 0.00 1.90
2367 2984 7.523293 TTTTTCATCTTTGTCCTTGCTCATA 57.477 32.000 0.00 0.00 0.00 2.15
2368 2985 6.409524 TTTTTCATCTTTGTCCTTGCTCAT 57.590 33.333 0.00 0.00 0.00 2.90
2369 2986 5.850557 TTTTTCATCTTTGTCCTTGCTCA 57.149 34.783 0.00 0.00 0.00 4.26
2391 3008 9.303537 CAAATTTTGCAAAGTTCATGGATTTTT 57.696 25.926 18.78 0.00 0.00 1.94
2392 3009 8.859517 CAAATTTTGCAAAGTTCATGGATTTT 57.140 26.923 18.78 0.00 0.00 1.82
2456 3073 9.630098 GTCTTGTTCAATTGTCATTTGTCATAT 57.370 29.630 5.13 0.00 0.00 1.78
2457 3074 8.628280 TGTCTTGTTCAATTGTCATTTGTCATA 58.372 29.630 5.13 0.00 0.00 2.15
2458 3075 7.436080 GTGTCTTGTTCAATTGTCATTTGTCAT 59.564 33.333 5.13 0.00 0.00 3.06
2459 3076 6.751425 GTGTCTTGTTCAATTGTCATTTGTCA 59.249 34.615 5.13 5.96 0.00 3.58
2460 3077 6.751425 TGTGTCTTGTTCAATTGTCATTTGTC 59.249 34.615 5.13 4.00 0.00 3.18
2461 3078 6.629128 TGTGTCTTGTTCAATTGTCATTTGT 58.371 32.000 5.13 0.00 0.00 2.83
2462 3079 7.522901 TTGTGTCTTGTTCAATTGTCATTTG 57.477 32.000 5.13 1.72 0.00 2.32
2463 3080 8.545229 TTTTGTGTCTTGTTCAATTGTCATTT 57.455 26.923 5.13 0.00 0.00 2.32
2464 3081 8.442384 GTTTTTGTGTCTTGTTCAATTGTCATT 58.558 29.630 5.13 0.00 0.00 2.57
2465 3082 7.601886 TGTTTTTGTGTCTTGTTCAATTGTCAT 59.398 29.630 5.13 0.00 0.00 3.06
2466 3083 6.925718 TGTTTTTGTGTCTTGTTCAATTGTCA 59.074 30.769 5.13 3.83 0.00 3.58
2467 3084 7.328249 TCTGTTTTTGTGTCTTGTTCAATTGTC 59.672 33.333 5.13 1.16 0.00 3.18
2468 3085 7.151308 TCTGTTTTTGTGTCTTGTTCAATTGT 58.849 30.769 5.13 0.00 0.00 2.71
2469 3086 7.579589 TCTGTTTTTGTGTCTTGTTCAATTG 57.420 32.000 0.00 0.00 0.00 2.32
2470 3087 8.600449 TTTCTGTTTTTGTGTCTTGTTCAATT 57.400 26.923 0.00 0.00 0.00 2.32
2471 3088 8.776376 ATTTCTGTTTTTGTGTCTTGTTCAAT 57.224 26.923 0.00 0.00 0.00 2.57
2472 3089 8.600449 AATTTCTGTTTTTGTGTCTTGTTCAA 57.400 26.923 0.00 0.00 0.00 2.69
2473 3090 8.600449 AAATTTCTGTTTTTGTGTCTTGTTCA 57.400 26.923 0.00 0.00 0.00 3.18
2474 3091 9.528847 GAAAATTTCTGTTTTTGTGTCTTGTTC 57.471 29.630 0.00 0.00 31.80 3.18


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

AutoCloner maintained by Alex Coulton.