Multiple sequence alignment - TraesCS2A01G506800

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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 TraesCS2A01G506800 chr2A 100.000 3661 0 0 1 3661 734530400 734526740 0.000000e+00 6761.0
1 TraesCS2A01G506800 chr2A 100.000 2964 0 0 3950 6913 734526451 734523488 0.000000e+00 5474.0
2 TraesCS2A01G506800 chr2A 95.297 2105 83 4 4819 6913 734622231 734624329 0.000000e+00 3325.0
3 TraesCS2A01G506800 chr2A 96.175 1464 46 7 40 1496 734617381 734618841 0.000000e+00 2385.0
4 TraesCS2A01G506800 chr2A 95.183 1308 36 11 1494 2780 734619094 734620395 0.000000e+00 2041.0
5 TraesCS2A01G506800 chr2A 96.942 883 17 5 2781 3661 734620436 734621310 0.000000e+00 1472.0
6 TraesCS2A01G506800 chr2A 92.172 792 40 8 3950 4737 734621459 734622232 0.000000e+00 1099.0
7 TraesCS2A01G506800 chr2A 96.000 50 1 1 2741 2789 141160671 141160622 5.750000e-11 80.5
8 TraesCS2A01G506800 chr2A 91.379 58 3 2 1 58 173796924 173796869 2.070000e-10 78.7
9 TraesCS2A01G506800 chr2D 91.762 1663 127 4 4819 6473 601183452 601185112 0.000000e+00 2303.0
10 TraesCS2A01G506800 chr2D 94.981 1056 25 5 2632 3661 601181481 601182534 0.000000e+00 1631.0
11 TraesCS2A01G506800 chr2D 91.909 791 29 8 1817 2578 601180419 601181203 0.000000e+00 1074.0
12 TraesCS2A01G506800 chr2D 91.024 791 43 6 3950 4737 601182684 601183449 0.000000e+00 1042.0
13 TraesCS2A01G506800 chr2D 91.463 656 40 11 849 1496 601178519 601179166 0.000000e+00 887.0
14 TraesCS2A01G506800 chr2D 94.494 563 19 4 302 856 601176664 601177222 0.000000e+00 857.0
15 TraesCS2A01G506800 chr2D 94.753 324 14 2 1494 1817 601179936 601180256 1.040000e-137 501.0
16 TraesCS2A01G506800 chr2D 89.247 279 18 5 40 316 601176378 601176646 8.590000e-89 339.0
17 TraesCS2A01G506800 chr2D 90.323 217 17 2 6697 6913 601188905 601189117 1.470000e-71 281.0
18 TraesCS2A01G506800 chr2D 90.588 85 8 0 4736 4820 301182445 301182529 5.670000e-21 113.0
19 TraesCS2A01G506800 chr2D 92.982 57 2 2 2724 2780 350755879 350755933 1.600000e-11 82.4
20 TraesCS2A01G506800 chr2B 95.280 1123 48 2 4819 5941 731311567 731312684 0.000000e+00 1775.0
21 TraesCS2A01G506800 chr2B 90.768 1094 91 4 5757 6841 731312694 731313786 0.000000e+00 1452.0
22 TraesCS2A01G506800 chr2B 92.386 788 45 6 1494 2281 731305536 731306308 0.000000e+00 1109.0
23 TraesCS2A01G506800 chr2B 90.559 805 56 13 705 1496 731303891 731304688 0.000000e+00 1048.0
24 TraesCS2A01G506800 chr2B 88.340 789 49 16 3950 4737 731310818 731311564 0.000000e+00 907.0
25 TraesCS2A01G506800 chr2B 93.348 451 25 2 3211 3661 731309928 731310373 0.000000e+00 662.0
26 TraesCS2A01G506800 chr2B 95.946 296 11 1 2278 2572 731306335 731306630 4.850000e-131 479.0
27 TraesCS2A01G506800 chr2B 91.061 358 24 4 2795 3148 731309577 731309930 1.740000e-130 477.0
28 TraesCS2A01G506800 chr2B 85.806 310 26 10 302 598 731271583 731271887 5.210000e-81 313.0
29 TraesCS2A01G506800 chr2B 92.661 109 6 2 2632 2739 731306892 731306999 9.280000e-34 156.0
30 TraesCS2A01G506800 chr2B 91.071 112 3 5 586 696 731284361 731284466 2.010000e-30 145.0
31 TraesCS2A01G506800 chr2B 94.118 85 5 0 4736 4820 86681143 86681059 5.630000e-26 130.0
32 TraesCS2A01G506800 chr2B 90.698 86 8 0 4735 4820 31160183 31160268 1.580000e-21 115.0
33 TraesCS2A01G506800 chr2B 82.540 126 6 7 193 316 731271454 731271565 5.710000e-16 97.1
34 TraesCS2A01G506800 chr2B 96.000 50 1 1 2741 2789 189599563 189599514 5.750000e-11 80.5
35 TraesCS2A01G506800 chr4B 80.451 266 46 5 3296 3558 1991128 1990866 1.520000e-46 198.0
36 TraesCS2A01G506800 chr4B 84.884 86 13 0 4735 4820 125833816 125833901 3.430000e-13 87.9
37 TraesCS2A01G506800 chr4B 84.884 86 13 0 4735 4820 573220426 573220341 3.430000e-13 87.9
38 TraesCS2A01G506800 chr4B 83.529 85 14 0 4736 4820 200799629 200799713 5.750000e-11 80.5
39 TraesCS2A01G506800 chr3A 94.505 91 4 1 4732 4821 100348268 100348358 9.350000e-29 139.0
40 TraesCS2A01G506800 chr3B 95.294 85 4 0 4735 4819 71400378 71400462 1.210000e-27 135.0
41 TraesCS2A01G506800 chr3B 90.909 88 8 0 4734 4821 217984916 217985003 1.220000e-22 119.0
42 TraesCS2A01G506800 chr4A 95.294 85 3 1 4736 4820 743181472 743181555 4.350000e-27 134.0
43 TraesCS2A01G506800 chr4A 95.294 85 3 1 4736 4820 743224617 743224700 4.350000e-27 134.0
44 TraesCS2A01G506800 chr4A 94.444 54 2 1 1 54 296623801 296623853 1.600000e-11 82.4
45 TraesCS2A01G506800 chr4A 94.340 53 2 1 2729 2780 119794968 119794916 5.750000e-11 80.5
46 TraesCS2A01G506800 chr1B 93.023 86 6 0 4735 4820 106864820 106864735 7.280000e-25 126.0
47 TraesCS2A01G506800 chr1B 89.130 92 9 1 4736 4826 141771963 141771872 5.670000e-21 113.0
48 TraesCS2A01G506800 chr1B 86.667 90 8 4 4732 4820 46089092 46089006 5.710000e-16 97.1
49 TraesCS2A01G506800 chr7B 91.954 87 7 0 4736 4822 84634864 84634778 9.420000e-24 122.0
50 TraesCS2A01G506800 chr7B 90.476 63 1 4 1 61 746488132 746488191 2.070000e-10 78.7
51 TraesCS2A01G506800 chr5B 91.860 86 7 0 4735 4820 431070540 431070455 3.390000e-23 121.0
52 TraesCS2A01G506800 chr6D 89.011 91 9 1 4731 4821 95724152 95724063 2.040000e-20 111.0
53 TraesCS2A01G506800 chr6D 94.444 54 2 1 1 54 216847318 216847266 1.600000e-11 82.4
54 TraesCS2A01G506800 chr6D 100.000 34 0 0 4735 4768 99923413 99923446 5.790000e-06 63.9
55 TraesCS2A01G506800 chr4D 89.655 87 9 0 4736 4822 31338435 31338349 2.040000e-20 111.0
56 TraesCS2A01G506800 chr4D 94.340 53 2 1 2729 2780 346123360 346123412 5.750000e-11 80.5
57 TraesCS2A01G506800 chr4D 82.353 85 9 4 4733 4817 436894473 436894395 1.240000e-07 69.4
58 TraesCS2A01G506800 chr5D 89.535 86 9 0 4736 4821 325476209 325476124 7.330000e-20 110.0
59 TraesCS2A01G506800 chr5D 88.372 86 8 2 4719 4804 3563185 3563268 1.230000e-17 102.0
60 TraesCS2A01G506800 chr5D 100.000 47 0 0 1 47 253168184 253168138 3.430000e-13 87.9
61 TraesCS2A01G506800 chr5D 95.349 43 2 0 4734 4776 510162359 510162401 1.240000e-07 69.4
62 TraesCS2A01G506800 chr5D 95.122 41 2 0 4736 4776 3563307 3563267 1.610000e-06 65.8
63 TraesCS2A01G506800 chr6A 88.636 88 10 0 4735 4822 532658450 532658363 2.640000e-19 108.0
64 TraesCS2A01G506800 chr6A 86.517 89 12 0 4733 4821 250692225 250692313 1.590000e-16 99.0
65 TraesCS2A01G506800 chr7D 87.640 89 11 0 4732 4820 617803215 617803303 3.410000e-18 104.0
66 TraesCS2A01G506800 chr7D 85.227 88 10 3 4736 4822 576889643 576889558 3.430000e-13 87.9
67 TraesCS2A01G506800 chr1A 84.270 89 12 2 4733 4820 573325345 573325432 1.240000e-12 86.1
68 TraesCS2A01G506800 chr1A 92.857 56 3 1 1 55 13490989 13490934 5.750000e-11 80.5
69 TraesCS2A01G506800 chrUn 96.154 52 1 1 1 51 48472349 48472298 4.440000e-12 84.2
70 TraesCS2A01G506800 chrUn 96.154 52 1 1 1 51 235114450 235114399 4.440000e-12 84.2
71 TraesCS2A01G506800 chrUn 96.154 52 1 1 1 51 433967154 433967205 4.440000e-12 84.2
72 TraesCS2A01G506800 chrUn 91.489 47 3 1 4734 4779 32245794 32245748 5.790000e-06 63.9
73 TraesCS2A01G506800 chr1D 97.826 46 1 0 2741 2786 326476813 326476768 5.750000e-11 80.5
74 TraesCS2A01G506800 chr1D 100.000 33 0 0 4736 4768 65904845 65904813 2.080000e-05 62.1
75 TraesCS2A01G506800 chr7A 92.593 54 2 2 2741 2794 31708899 31708950 7.440000e-10 76.8


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 TraesCS2A01G506800 chr2A 734523488 734530400 6912 True 6117.500000 6761 100.000000 1 6913 2 chr2A.!!$R3 6912
1 TraesCS2A01G506800 chr2A 734617381 734624329 6948 False 2064.400000 3325 95.153800 40 6913 5 chr2A.!!$F1 6873
2 TraesCS2A01G506800 chr2D 601176378 601189117 12739 False 990.555556 2303 92.217333 40 6913 9 chr2D.!!$F3 6873
3 TraesCS2A01G506800 chr2B 731303891 731313786 9895 False 896.111111 1775 92.261000 705 6841 9 chr2B.!!$F4 6136

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
186 190 2.985896 ACGACACCATGGAGTATTTGG 58.014 47.619 21.47 6.96 36.56 3.28 F
257 261 8.112822 TGATCAAGGATATTTGTTTCCACCTTA 58.887 33.333 0.00 0.00 35.02 2.69 F
1179 2535 1.067071 GTACGTGCTTCCTTGCCTACT 60.067 52.381 0.00 0.00 0.00 2.57 F
1219 2575 0.246360 GCCACGGCAAGCCTTTATTT 59.754 50.000 9.73 0.00 41.49 1.40 F
2256 4659 0.935196 GTCAACCGAAACACGAGCTT 59.065 50.000 0.00 0.00 45.77 3.74 F
3452 8700 0.334676 TTGGTGAGGCTTATTGGGGG 59.665 55.000 0.00 0.00 0.00 5.40 F
4531 9940 1.421646 AGCAGGGTATTGGATAGTGGC 59.578 52.381 0.00 0.00 0.00 5.01 F
5267 10680 0.309922 CAGGAAGTGTTGCAGCTGTG 59.690 55.000 16.64 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 2535 0.173481 GGAGCACATCTAGACGCACA 59.827 55.000 11.89 0.00 0.00 4.57 R
1186 2542 1.227380 GTGGCCGGAGCACATCTAG 60.227 63.158 5.05 0.00 42.56 2.43 R
2534 4968 1.089920 GTGCTGGTGAATGGCTACAG 58.910 55.000 0.00 0.00 0.00 2.74 R
3049 8294 5.592104 TGTAGTCTTTGTTGACTGAGTCA 57.408 39.130 11.93 11.93 45.70 3.41 R
3603 8851 0.037303 ACATCACAGAACTGCAGGGG 59.963 55.000 19.93 6.65 0.00 4.79 R
4828 10241 0.037326 TGAACCATGCACGAGGACTC 60.037 55.000 8.53 5.48 0.00 3.36 R
5511 10924 0.037447 GTCTCCTTGGCTTGCTCCTT 59.963 55.000 0.00 0.00 0.00 3.36 R
6221 11836 0.309302 CGAACCAAATTGACACGGCA 59.691 50.000 0.00 0.00 0.00 5.69 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
27 28 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
28 29 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
29 30 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
30 31 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
31 32 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
32 33 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
33 34 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
34 35 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
35 36 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
36 37 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
37 38 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
38 39 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
53 54 4.683400 CGGAGGGAGTATTAAGCACACATT 60.683 45.833 0.00 0.00 0.00 2.71
111 113 8.557029 AGTTGTCTATTTGCAGTAACTGTAAAC 58.443 33.333 0.00 0.00 45.49 2.01
124 126 3.399330 ACTGTAAACCAGGATGTCGTTG 58.601 45.455 0.00 0.00 46.06 4.10
173 177 3.318886 GGAAGAGAGAAGAAACGACACC 58.681 50.000 0.00 0.00 0.00 4.16
174 178 3.243771 GGAAGAGAGAAGAAACGACACCA 60.244 47.826 0.00 0.00 0.00 4.17
186 190 2.985896 ACGACACCATGGAGTATTTGG 58.014 47.619 21.47 6.96 36.56 3.28
257 261 8.112822 TGATCAAGGATATTTGTTTCCACCTTA 58.887 33.333 0.00 0.00 35.02 2.69
1178 2534 1.356938 GTACGTGCTTCCTTGCCTAC 58.643 55.000 0.00 0.00 0.00 3.18
1179 2535 1.067071 GTACGTGCTTCCTTGCCTACT 60.067 52.381 0.00 0.00 0.00 2.57
1186 2542 0.320421 TTCCTTGCCTACTGTGCGTC 60.320 55.000 0.00 0.00 0.00 5.19
1189 2545 1.469940 CCTTGCCTACTGTGCGTCTAG 60.470 57.143 0.00 0.00 0.00 2.43
1190 2546 1.472878 CTTGCCTACTGTGCGTCTAGA 59.527 52.381 0.00 0.00 0.00 2.43
1216 2572 2.675075 GGCCACGGCAAGCCTTTA 60.675 61.111 10.83 0.00 46.14 1.85
1217 2573 2.052104 GGCCACGGCAAGCCTTTAT 61.052 57.895 10.83 0.00 46.14 1.40
1218 2574 1.604147 GGCCACGGCAAGCCTTTATT 61.604 55.000 10.83 0.00 46.14 1.40
1219 2575 0.246360 GCCACGGCAAGCCTTTATTT 59.754 50.000 9.73 0.00 41.49 1.40
1220 2576 1.337728 GCCACGGCAAGCCTTTATTTT 60.338 47.619 9.73 0.00 41.49 1.82
1221 2577 2.606108 CCACGGCAAGCCTTTATTTTC 58.394 47.619 9.73 0.00 0.00 2.29
1222 2578 2.606108 CACGGCAAGCCTTTATTTTCC 58.394 47.619 9.73 0.00 0.00 3.13
1223 2579 2.231235 CACGGCAAGCCTTTATTTTCCT 59.769 45.455 9.73 0.00 0.00 3.36
1224 2580 2.492088 ACGGCAAGCCTTTATTTTCCTC 59.508 45.455 9.73 0.00 0.00 3.71
1225 2581 2.755103 CGGCAAGCCTTTATTTTCCTCT 59.245 45.455 9.73 0.00 0.00 3.69
1226 2582 3.181496 CGGCAAGCCTTTATTTTCCTCTC 60.181 47.826 9.73 0.00 0.00 3.20
1227 2583 4.019858 GGCAAGCCTTTATTTTCCTCTCT 58.980 43.478 3.29 0.00 0.00 3.10
1291 2663 7.484140 ACTTCTTTTGGATGAAACAACTCTTC 58.516 34.615 0.00 0.00 0.00 2.87
1298 2670 8.421249 TTGGATGAAACAACTCTTCCATTATT 57.579 30.769 8.53 0.00 44.65 1.40
1307 2679 7.318141 ACAACTCTTCCATTATTTGCATTGAG 58.682 34.615 0.00 0.00 0.00 3.02
1374 2746 6.083098 TGTCCGTTTTGTGATGAAATTCAT 57.917 33.333 8.39 8.39 40.34 2.57
1377 2749 6.088085 GTCCGTTTTGTGATGAAATTCATGTC 59.912 38.462 13.82 6.62 37.20 3.06
1470 2842 4.094830 TGAAGGACTTTGGGTTTAGGAC 57.905 45.455 0.00 0.00 0.00 3.85
1489 2861 5.256474 AGGACCTTTCATCGAATTTCACAT 58.744 37.500 0.00 0.00 0.00 3.21
1507 3734 9.838339 ATTTCACATAAGAATTACTAGGGAGTG 57.162 33.333 0.00 0.00 36.28 3.51
1595 3825 2.836262 TGCAGTTGGAAAATTGCAAGG 58.164 42.857 4.94 0.00 43.03 3.61
1987 4383 6.000246 TGCCTCACTTCAAATATATGACCA 58.000 37.500 0.00 0.00 0.00 4.02
1989 4385 6.889177 TGCCTCACTTCAAATATATGACCAAA 59.111 34.615 0.00 0.00 0.00 3.28
2040 4438 7.109501 TGGAAAACTAGCTACTTCAATATGCA 58.890 34.615 0.00 0.00 0.00 3.96
2045 4443 6.586344 ACTAGCTACTTCAATATGCACATGT 58.414 36.000 0.00 0.00 0.00 3.21
2153 4551 7.064966 TGTGCTGCATATGTGAATATACTATGC 59.935 37.037 5.27 6.02 43.05 3.14
2252 4655 2.200792 TTACGTCAACCGAAACACGA 57.799 45.000 0.00 0.00 45.77 4.35
2256 4659 0.935196 GTCAACCGAAACACGAGCTT 59.065 50.000 0.00 0.00 45.77 3.74
2478 4911 6.980416 ATAGAGCTAGTCCTATTTCCGTTT 57.020 37.500 0.00 0.00 0.00 3.60
2534 4968 5.328691 CAAATGGACATTGCATGCAAAATC 58.671 37.500 34.84 30.36 39.55 2.17
3049 8294 4.749310 CTTGCCTCGTCGCTGCCT 62.749 66.667 0.00 0.00 0.00 4.75
3452 8700 0.334676 TTGGTGAGGCTTATTGGGGG 59.665 55.000 0.00 0.00 0.00 5.40
3525 8773 1.544691 GGTGACATCTACTGTGACGGT 59.455 52.381 1.37 1.37 42.28 4.83
3602 8850 9.717942 AATATGATCTAGCTTGTACATCTTTCC 57.282 33.333 0.00 0.00 0.00 3.13
3603 8851 5.918608 TGATCTAGCTTGTACATCTTTCCC 58.081 41.667 0.00 0.00 0.00 3.97
3604 8852 4.755266 TCTAGCTTGTACATCTTTCCCC 57.245 45.455 0.00 0.00 0.00 4.81
3605 8853 2.808906 AGCTTGTACATCTTTCCCCC 57.191 50.000 0.00 0.00 0.00 5.40
3984 9389 7.851822 CATATGATGCCGGTTTGTTATTAAC 57.148 36.000 1.90 0.00 0.00 2.01
3987 9392 4.523173 TGATGCCGGTTTGTTATTAACCAA 59.477 37.500 1.90 0.00 44.24 3.67
4003 9408 6.546428 TTAACCAATGGTCAAAACTCCAAA 57.454 33.333 4.95 0.00 37.27 3.28
4005 9410 4.030216 ACCAATGGTCAAAACTCCAAAGT 58.970 39.130 0.00 0.00 37.27 2.66
4054 9459 8.385491 TCTCATCCTTAATTATACATGGCATGT 58.615 33.333 33.18 33.18 46.92 3.21
4073 9478 5.688823 CATGTGTTTCTCGCTCACATTTTA 58.311 37.500 7.19 0.00 46.26 1.52
4145 9550 4.004982 GGCTTTGGTCGTTAGATAAACCA 58.995 43.478 0.00 0.00 39.96 3.67
4223 9628 4.558226 TGCAGATGACATTCAGGTTAGT 57.442 40.909 0.00 0.00 0.00 2.24
4288 9694 2.038557 TGAGGTTACCAAGAGCTTCACC 59.961 50.000 3.51 0.00 0.00 4.02
4356 9765 7.660208 ACAGTTTAGGATTGTTCGTAGTTTCAT 59.340 33.333 0.00 0.00 0.00 2.57
4507 9916 3.140623 GTGGCGGGTTTTTCAGTTAGTA 58.859 45.455 0.00 0.00 0.00 1.82
4531 9940 1.421646 AGCAGGGTATTGGATAGTGGC 59.578 52.381 0.00 0.00 0.00 5.01
4553 9962 2.036346 GGGTTTTTCAGCATGCTCTGTT 59.964 45.455 19.68 0.00 35.63 3.16
4569 9978 4.632153 CTCTGTTGTTACAAGCAGGTAGT 58.368 43.478 19.45 0.00 32.92 2.73
4570 9979 5.031066 TCTGTTGTTACAAGCAGGTAGTT 57.969 39.130 19.45 0.00 32.92 2.24
4571 9980 6.164417 TCTGTTGTTACAAGCAGGTAGTTA 57.836 37.500 19.45 5.01 32.92 2.24
4572 9981 6.220930 TCTGTTGTTACAAGCAGGTAGTTAG 58.779 40.000 19.45 2.58 32.92 2.34
4573 9982 6.041182 TCTGTTGTTACAAGCAGGTAGTTAGA 59.959 38.462 19.45 4.21 32.92 2.10
4574 9983 6.765403 TGTTGTTACAAGCAGGTAGTTAGAT 58.235 36.000 0.00 0.00 0.00 1.98
4575 9984 6.872020 TGTTGTTACAAGCAGGTAGTTAGATC 59.128 38.462 0.00 0.00 0.00 2.75
4576 9985 6.599356 TGTTACAAGCAGGTAGTTAGATCA 57.401 37.500 0.00 0.00 0.00 2.92
4577 9986 6.631016 TGTTACAAGCAGGTAGTTAGATCAG 58.369 40.000 0.00 0.00 0.00 2.90
4578 9987 4.130286 ACAAGCAGGTAGTTAGATCAGC 57.870 45.455 0.00 0.00 0.00 4.26
4579 9988 3.515502 ACAAGCAGGTAGTTAGATCAGCA 59.484 43.478 0.00 0.00 0.00 4.41
4580 9989 4.163078 ACAAGCAGGTAGTTAGATCAGCAT 59.837 41.667 0.00 0.00 0.00 3.79
4581 9990 4.333913 AGCAGGTAGTTAGATCAGCATG 57.666 45.455 0.00 0.00 37.54 4.06
4582 9991 3.708631 AGCAGGTAGTTAGATCAGCATGT 59.291 43.478 0.00 0.00 37.40 3.21
4583 9992 4.163078 AGCAGGTAGTTAGATCAGCATGTT 59.837 41.667 0.00 0.00 37.40 2.71
4584 9993 4.878397 GCAGGTAGTTAGATCAGCATGTTT 59.122 41.667 0.00 0.00 37.40 2.83
4585 9994 5.355350 GCAGGTAGTTAGATCAGCATGTTTT 59.645 40.000 0.00 0.00 37.40 2.43
4586 9995 6.127897 GCAGGTAGTTAGATCAGCATGTTTTT 60.128 38.462 0.00 0.00 37.40 1.94
4587 9996 7.467623 CAGGTAGTTAGATCAGCATGTTTTTC 58.532 38.462 0.00 0.00 37.40 2.29
4623 10032 3.960571 AGCCAATGACATGCTACTTCTT 58.039 40.909 0.00 0.00 32.56 2.52
4660 10069 4.315803 TGCTCTTCTACTTTGGTTGTAGC 58.684 43.478 0.00 0.00 37.78 3.58
4666 10075 8.135382 TCTTCTACTTTGGTTGTAGCTAGATT 57.865 34.615 0.00 0.00 37.78 2.40
4701 10110 2.879026 GAGCCTGTTTTCGTTTCTCCTT 59.121 45.455 0.00 0.00 0.00 3.36
4741 10150 8.915036 TCTGACTTTATGTTTCTATCTACTCCC 58.085 37.037 0.00 0.00 0.00 4.30
4742 10151 8.840200 TGACTTTATGTTTCTATCTACTCCCT 57.160 34.615 0.00 0.00 0.00 4.20
4743 10152 8.915036 TGACTTTATGTTTCTATCTACTCCCTC 58.085 37.037 0.00 0.00 0.00 4.30
4744 10153 9.138596 GACTTTATGTTTCTATCTACTCCCTCT 57.861 37.037 0.00 0.00 0.00 3.69
4745 10154 8.919145 ACTTTATGTTTCTATCTACTCCCTCTG 58.081 37.037 0.00 0.00 0.00 3.35
4746 10155 8.840200 TTTATGTTTCTATCTACTCCCTCTGT 57.160 34.615 0.00 0.00 0.00 3.41
4747 10156 8.840200 TTATGTTTCTATCTACTCCCTCTGTT 57.160 34.615 0.00 0.00 0.00 3.16
4748 10157 6.777213 TGTTTCTATCTACTCCCTCTGTTC 57.223 41.667 0.00 0.00 0.00 3.18
4749 10158 5.657302 TGTTTCTATCTACTCCCTCTGTTCC 59.343 44.000 0.00 0.00 0.00 3.62
4750 10159 5.467668 TTCTATCTACTCCCTCTGTTCCA 57.532 43.478 0.00 0.00 0.00 3.53
4751 10160 5.671463 TCTATCTACTCCCTCTGTTCCAT 57.329 43.478 0.00 0.00 0.00 3.41
4752 10161 6.781857 TCTATCTACTCCCTCTGTTCCATA 57.218 41.667 0.00 0.00 0.00 2.74
4753 10162 7.162973 TCTATCTACTCCCTCTGTTCCATAA 57.837 40.000 0.00 0.00 0.00 1.90
4754 10163 7.770662 TCTATCTACTCCCTCTGTTCCATAAT 58.229 38.462 0.00 0.00 0.00 1.28
4755 10164 8.901841 TCTATCTACTCCCTCTGTTCCATAATA 58.098 37.037 0.00 0.00 0.00 0.98
4756 10165 9.707957 CTATCTACTCCCTCTGTTCCATAATAT 57.292 37.037 0.00 0.00 0.00 1.28
4759 10168 9.535170 TCTACTCCCTCTGTTCCATAATATAAG 57.465 37.037 0.00 0.00 0.00 1.73
4760 10169 9.535170 CTACTCCCTCTGTTCCATAATATAAGA 57.465 37.037 0.00 0.00 0.00 2.10
4761 10170 8.798975 ACTCCCTCTGTTCCATAATATAAGAA 57.201 34.615 0.00 0.00 0.00 2.52
4762 10171 8.652290 ACTCCCTCTGTTCCATAATATAAGAAC 58.348 37.037 7.86 7.86 39.22 3.01
4763 10172 7.667557 TCCCTCTGTTCCATAATATAAGAACG 58.332 38.462 9.40 0.00 41.17 3.95
4764 10173 7.289317 TCCCTCTGTTCCATAATATAAGAACGT 59.711 37.037 9.40 0.00 41.17 3.99
4765 10174 7.931948 CCCTCTGTTCCATAATATAAGAACGTT 59.068 37.037 0.00 0.00 41.17 3.99
4766 10175 9.326413 CCTCTGTTCCATAATATAAGAACGTTT 57.674 33.333 0.46 0.00 41.17 3.60
4782 10191 8.556517 AAGAACGTTTTTCAAACTATGTTAGC 57.443 30.769 0.46 0.00 0.00 3.09
4783 10192 7.927048 AGAACGTTTTTCAAACTATGTTAGCT 58.073 30.769 0.46 0.00 0.00 3.32
4784 10193 8.403236 AGAACGTTTTTCAAACTATGTTAGCTT 58.597 29.630 0.46 0.00 0.00 3.74
4785 10194 7.908193 ACGTTTTTCAAACTATGTTAGCTTG 57.092 32.000 0.00 0.00 34.13 4.01
4786 10195 6.915843 ACGTTTTTCAAACTATGTTAGCTTGG 59.084 34.615 0.00 0.00 33.75 3.61
4787 10196 7.136119 CGTTTTTCAAACTATGTTAGCTTGGA 58.864 34.615 0.00 0.00 33.75 3.53
4788 10197 7.646130 CGTTTTTCAAACTATGTTAGCTTGGAA 59.354 33.333 0.00 0.00 33.75 3.53
4789 10198 9.308318 GTTTTTCAAACTATGTTAGCTTGGAAA 57.692 29.630 0.00 1.73 37.49 3.13
4790 10199 9.877178 TTTTTCAAACTATGTTAGCTTGGAAAA 57.123 25.926 10.61 10.61 42.53 2.29
4791 10200 8.865590 TTTCAAACTATGTTAGCTTGGAAAAC 57.134 30.769 0.00 0.00 33.75 2.43
4792 10201 6.664515 TCAAACTATGTTAGCTTGGAAAACG 58.335 36.000 0.00 0.00 33.75 3.60
4793 10202 6.261381 TCAAACTATGTTAGCTTGGAAAACGT 59.739 34.615 0.00 0.00 33.75 3.99
4794 10203 6.628919 AACTATGTTAGCTTGGAAAACGTT 57.371 33.333 0.00 0.00 0.00 3.99
4795 10204 6.237313 ACTATGTTAGCTTGGAAAACGTTC 57.763 37.500 0.00 0.00 0.00 3.95
4811 10220 7.941795 AAAACGTTCCTATATTATGAGACGG 57.058 36.000 0.00 0.00 33.95 4.79
4812 10221 6.889301 AACGTTCCTATATTATGAGACGGA 57.111 37.500 0.00 0.00 33.95 4.69
4813 10222 6.497785 ACGTTCCTATATTATGAGACGGAG 57.502 41.667 0.00 0.00 33.95 4.63
4814 10223 5.415077 ACGTTCCTATATTATGAGACGGAGG 59.585 44.000 0.00 0.00 33.95 4.30
4815 10224 5.163642 CGTTCCTATATTATGAGACGGAGGG 60.164 48.000 0.00 0.00 0.00 4.30
4816 10225 5.791303 TCCTATATTATGAGACGGAGGGA 57.209 43.478 0.00 0.00 0.00 4.20
4817 10226 5.756918 TCCTATATTATGAGACGGAGGGAG 58.243 45.833 0.00 0.00 0.00 4.30
4818 10227 5.253330 TCCTATATTATGAGACGGAGGGAGT 59.747 44.000 0.00 0.00 0.00 3.85
4819 10228 6.446110 TCCTATATTATGAGACGGAGGGAGTA 59.554 42.308 0.00 0.00 0.00 2.59
4828 10241 4.145807 AGACGGAGGGAGTATTCACATAG 58.854 47.826 0.00 0.00 0.00 2.23
4921 10334 6.594159 AGATAGTCCAACAGATTGTTTTACGG 59.406 38.462 0.00 0.00 38.77 4.02
5081 10494 5.654603 ACATGAAACTACACGATCAGGTA 57.345 39.130 0.00 0.00 35.33 3.08
5267 10680 0.309922 CAGGAAGTGTTGCAGCTGTG 59.690 55.000 16.64 0.00 0.00 3.66
5486 10899 2.955881 GCACCGTAAGCTGGAGGGT 61.956 63.158 7.31 7.31 35.46 4.34
5508 10921 6.887002 GGGTTCAGAGGAGAAGAATAAAATGT 59.113 38.462 0.00 0.00 0.00 2.71
5511 10924 7.257790 TCAGAGGAGAAGAATAAAATGTCCA 57.742 36.000 0.00 0.00 0.00 4.02
5548 10961 5.725822 AGGAGACAGAGAAGGAGATGAAAAT 59.274 40.000 0.00 0.00 0.00 1.82
5550 10963 6.315891 GGAGACAGAGAAGGAGATGAAAATTG 59.684 42.308 0.00 0.00 0.00 2.32
5576 10989 5.412594 TCTGGATGACAATGTGAAACTAAGC 59.587 40.000 0.00 0.00 38.04 3.09
5601 11014 9.301153 GCGGTCAGATTCAAAAATTAAATATGT 57.699 29.630 0.00 0.00 0.00 2.29
5697 11110 1.061346 TGGATAAGAAGGGGGAGGAGG 60.061 57.143 0.00 0.00 0.00 4.30
5712 11125 0.328258 GGAGGGAGCTACTTTGCCAA 59.672 55.000 0.00 0.00 0.00 4.52
5719 11132 4.270008 GGAGCTACTTTGCCAAATAAGGA 58.730 43.478 0.00 0.00 0.00 3.36
6034 11648 1.833630 TGGCATTTTGTGTTTCACCCA 59.166 42.857 0.00 0.00 32.73 4.51
6128 11742 3.737850 GAGAGGGTCTCCATGCTATTTG 58.262 50.000 0.00 0.00 37.55 2.32
6141 11755 2.171659 TGCTATTTGGCCTTGATCCGTA 59.828 45.455 3.32 0.00 0.00 4.02
6146 11760 2.973694 TGGCCTTGATCCGTAAGTAC 57.026 50.000 3.32 0.00 0.00 2.73
6181 11796 9.251440 ACTCCTGTCATTATATTATACGGCTTA 57.749 33.333 0.00 0.00 0.00 3.09
6214 11829 1.209128 GATAATGTGGCGGTGTCGAG 58.791 55.000 0.00 0.00 39.00 4.04
6221 11836 1.668151 GGCGGTGTCGAGCTTTCTT 60.668 57.895 0.00 0.00 39.00 2.52
6284 11899 0.390603 CCCTTCGTGGTCGTGCAATA 60.391 55.000 0.00 0.00 38.33 1.90
6302 11917 0.036671 TAGCGACGACAGACCTCTGA 60.037 55.000 9.35 0.00 46.59 3.27
6338 11953 0.109342 CTGCTTGTTGTGTCCCTCCT 59.891 55.000 0.00 0.00 0.00 3.69
6342 11957 2.027192 GCTTGTTGTGTCCCTCCTATGA 60.027 50.000 0.00 0.00 0.00 2.15
6421 12036 2.741878 CGGTGCGGTATCCTTTTGATCT 60.742 50.000 0.00 0.00 34.76 2.75
6509 12124 0.679505 GGAGCCCCCAACAAGTTTTC 59.320 55.000 0.00 0.00 34.14 2.29
6791 15976 3.181499 GCTCGGACGATGTCTTCTTCTAA 60.181 47.826 0.00 0.00 32.47 2.10
6823 16008 7.039011 AGGACTCTGACAATACACATCTTAACA 60.039 37.037 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
2 3 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
3 4 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
4 5 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
5 6 7.094549 CGTTCCAAAATAGATGACCCAACTTTA 60.095 37.037 0.00 0.00 0.00 1.85
6 7 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
7 8 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
8 9 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
9 10 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
10 11 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
11 12 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
12 13 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
13 14 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
14 15 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
15 16 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
16 17 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
17 18 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
18 19 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
19 20 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
20 21 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
21 22 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
22 23 5.493809 CTTAATACTCCCTCCGTTCCAAAA 58.506 41.667 0.00 0.00 0.00 2.44
23 24 4.624604 GCTTAATACTCCCTCCGTTCCAAA 60.625 45.833 0.00 0.00 0.00 3.28
24 25 3.118519 GCTTAATACTCCCTCCGTTCCAA 60.119 47.826 0.00 0.00 0.00 3.53
25 26 2.433239 GCTTAATACTCCCTCCGTTCCA 59.567 50.000 0.00 0.00 0.00 3.53
26 27 2.433239 TGCTTAATACTCCCTCCGTTCC 59.567 50.000 0.00 0.00 0.00 3.62
27 28 3.118884 TGTGCTTAATACTCCCTCCGTTC 60.119 47.826 0.00 0.00 0.00 3.95
28 29 2.835764 TGTGCTTAATACTCCCTCCGTT 59.164 45.455 0.00 0.00 0.00 4.44
29 30 2.167900 GTGTGCTTAATACTCCCTCCGT 59.832 50.000 0.00 0.00 0.00 4.69
30 31 2.167693 TGTGTGCTTAATACTCCCTCCG 59.832 50.000 0.00 0.00 0.00 4.63
31 32 3.906720 TGTGTGCTTAATACTCCCTCC 57.093 47.619 0.00 0.00 0.00 4.30
32 33 4.576463 CCAATGTGTGCTTAATACTCCCTC 59.424 45.833 0.00 0.00 0.00 4.30
33 34 4.018415 ACCAATGTGTGCTTAATACTCCCT 60.018 41.667 0.00 0.00 0.00 4.20
34 35 4.096382 CACCAATGTGTGCTTAATACTCCC 59.904 45.833 0.00 0.00 37.72 4.30
35 36 4.941263 TCACCAATGTGTGCTTAATACTCC 59.059 41.667 0.00 0.00 43.26 3.85
36 37 5.643777 AGTCACCAATGTGTGCTTAATACTC 59.356 40.000 0.00 0.00 43.26 2.59
37 38 5.560724 AGTCACCAATGTGTGCTTAATACT 58.439 37.500 0.00 0.00 43.26 2.12
38 39 5.880054 AGTCACCAATGTGTGCTTAATAC 57.120 39.130 0.00 0.00 43.26 1.89
53 54 8.356657 CAAAAACATGGAAATAGTTAGTCACCA 58.643 33.333 0.00 0.00 0.00 4.17
61 63 8.626526 ACTCGTAACAAAAACATGGAAATAGTT 58.373 29.630 0.00 0.00 0.00 2.24
69 71 5.816919 AGACAACTCGTAACAAAAACATGG 58.183 37.500 0.00 0.00 0.00 3.66
83 85 5.405571 ACAGTTACTGCAAATAGACAACTCG 59.594 40.000 12.80 0.00 34.37 4.18
111 113 3.627577 CCCTATTTTCAACGACATCCTGG 59.372 47.826 0.00 0.00 0.00 4.45
124 126 4.007659 TCTTTCAGAACCGCCCTATTTTC 58.992 43.478 0.00 0.00 0.00 2.29
186 190 0.031994 AGTGCCGCACAATTGGAAAC 59.968 50.000 24.97 0.00 36.74 2.78
257 261 0.390866 CACGTGCATCTCTCCAGCTT 60.391 55.000 0.82 0.00 0.00 3.74
1178 2534 1.554392 GAGCACATCTAGACGCACAG 58.446 55.000 11.89 0.00 0.00 3.66
1179 2535 0.173481 GGAGCACATCTAGACGCACA 59.827 55.000 11.89 0.00 0.00 4.57
1186 2542 1.227380 GTGGCCGGAGCACATCTAG 60.227 63.158 5.05 0.00 42.56 2.43
1291 2663 6.151663 TGTCATCCTCAATGCAAATAATGG 57.848 37.500 0.00 0.00 35.17 3.16
1298 2670 5.945191 TCTTGTATTGTCATCCTCAATGCAA 59.055 36.000 16.40 16.40 46.74 4.08
1307 2679 9.643693 ATCAACAAATTTCTTGTATTGTCATCC 57.356 29.630 6.15 0.00 35.09 3.51
1374 2746 3.202097 TGATGCTCAACTTTTGACGACA 58.798 40.909 0.00 0.00 35.46 4.35
1377 2749 4.083643 AGTGATGATGCTCAACTTTTGACG 60.084 41.667 0.00 0.00 35.46 4.35
1397 2769 9.731819 TTTTCAGAAGCGTAATATAGTCTAGTG 57.268 33.333 0.00 0.00 0.00 2.74
1470 2842 9.793252 AATTCTTATGTGAAATTCGATGAAAGG 57.207 29.630 0.00 0.00 0.00 3.11
1595 3825 3.372206 CCATCTGTAGCAGTACTGTTTGC 59.628 47.826 23.44 15.56 40.57 3.68
1987 4383 6.025539 AGGCAGGGAGAGGAAATTAAATTTT 58.974 36.000 0.00 0.00 31.47 1.82
1989 4385 5.204292 GAGGCAGGGAGAGGAAATTAAATT 58.796 41.667 0.00 0.00 0.00 1.82
2182 4580 4.141846 ACTTTTGCTCAGTTCAGTCAGAGA 60.142 41.667 0.00 0.00 0.00 3.10
2183 4581 4.125703 ACTTTTGCTCAGTTCAGTCAGAG 58.874 43.478 0.00 0.00 0.00 3.35
2239 4642 1.329292 TGAAAGCTCGTGTTTCGGTTG 59.671 47.619 0.00 0.00 36.81 3.77
2252 4655 9.553064 ACGAGAGAAAAATATATCATGAAAGCT 57.447 29.630 0.00 0.00 0.00 3.74
2478 4911 5.630121 AGTACTCAAAATGACCATGTGGAA 58.370 37.500 5.96 0.00 38.94 3.53
2534 4968 1.089920 GTGCTGGTGAATGGCTACAG 58.910 55.000 0.00 0.00 0.00 2.74
2878 8123 9.950680 TTGAACACTTTTGAAGATGAATTCTAC 57.049 29.630 7.05 0.89 33.05 2.59
3049 8294 5.592104 TGTAGTCTTTGTTGACTGAGTCA 57.408 39.130 11.93 11.93 45.70 3.41
3331 8578 5.187772 TGCACTCTTCTCTTGAAGCCTATTA 59.812 40.000 1.31 0.00 46.81 0.98
3452 8700 2.223377 ACAAGAATCGAAACACGCTTCC 59.777 45.455 0.00 0.00 44.71 3.46
3525 8773 7.735917 TCTTCTTTCTCACTTGGATAAAGACA 58.264 34.615 4.90 0.00 43.97 3.41
3602 8850 0.679002 CATCACAGAACTGCAGGGGG 60.679 60.000 19.93 5.75 0.00 5.40
3603 8851 0.037303 ACATCACAGAACTGCAGGGG 59.963 55.000 19.93 6.65 0.00 4.79
3604 8852 1.901591 AACATCACAGAACTGCAGGG 58.098 50.000 19.93 7.03 0.00 4.45
3605 8853 2.620115 ACAAACATCACAGAACTGCAGG 59.380 45.455 19.93 1.96 0.00 4.85
3984 9389 4.099266 TCACTTTGGAGTTTTGACCATTGG 59.901 41.667 0.00 0.00 36.02 3.16
3987 9392 5.739935 GCATTCACTTTGGAGTTTTGACCAT 60.740 40.000 0.00 0.00 36.02 3.55
4003 9408 7.886629 AAATCACACATTATAGGCATTCACT 57.113 32.000 0.00 0.00 0.00 3.41
4005 9410 8.523915 AGAAAATCACACATTATAGGCATTCA 57.476 30.769 0.00 0.00 0.00 2.57
4054 9459 6.552859 TGATTAAAATGTGAGCGAGAAACA 57.447 33.333 0.00 0.00 0.00 2.83
4073 9478 5.426504 TGCCACTGAACAAAACAATTGATT 58.573 33.333 13.59 3.30 0.00 2.57
4145 9550 3.075882 TCCTCCAAATCCATGGTTTCTGT 59.924 43.478 12.58 0.00 41.46 3.41
4223 9628 7.177568 TGGATCATTAAAGAACGGGAATTTTCA 59.822 33.333 0.00 0.00 0.00 2.69
4288 9694 2.402388 CAAAGAGCGCGCATCTGG 59.598 61.111 35.10 21.56 0.00 3.86
4366 9775 9.097257 GCATTTGTGCCTATATTTGTTAACATT 57.903 29.630 9.56 3.03 0.00 2.71
4507 9916 4.526970 CACTATCCAATACCCTGCTTGTT 58.473 43.478 0.00 0.00 0.00 2.83
4531 9940 0.883833 AGAGCATGCTGAAAAACCCG 59.116 50.000 28.27 0.00 0.00 5.28
4553 9962 6.599356 TGATCTAACTACCTGCTTGTAACA 57.401 37.500 0.00 0.00 0.00 2.41
4570 9979 9.844790 CTAAATGTTGAAAAACATGCTGATCTA 57.155 29.630 4.94 0.00 42.13 1.98
4571 9980 7.816031 CCTAAATGTTGAAAAACATGCTGATCT 59.184 33.333 4.94 0.00 42.13 2.75
4572 9981 7.599998 ACCTAAATGTTGAAAAACATGCTGATC 59.400 33.333 4.94 0.00 42.13 2.92
4573 9982 7.385752 CACCTAAATGTTGAAAAACATGCTGAT 59.614 33.333 4.94 0.00 42.13 2.90
4574 9983 6.700960 CACCTAAATGTTGAAAAACATGCTGA 59.299 34.615 4.94 0.00 42.13 4.26
4575 9984 6.564499 GCACCTAAATGTTGAAAAACATGCTG 60.564 38.462 4.94 0.00 42.13 4.41
4576 9985 5.466393 GCACCTAAATGTTGAAAAACATGCT 59.534 36.000 4.94 0.00 42.13 3.79
4577 9986 5.466393 AGCACCTAAATGTTGAAAAACATGC 59.534 36.000 4.94 5.00 42.13 4.06
4578 9987 7.148755 GCTAGCACCTAAATGTTGAAAAACATG 60.149 37.037 10.63 0.00 42.13 3.21
4579 9988 6.868339 GCTAGCACCTAAATGTTGAAAAACAT 59.132 34.615 10.63 0.00 44.63 2.71
4580 9989 6.212955 GCTAGCACCTAAATGTTGAAAAACA 58.787 36.000 10.63 0.00 37.05 2.83
4581 9990 5.633601 GGCTAGCACCTAAATGTTGAAAAAC 59.366 40.000 18.24 0.00 0.00 2.43
4582 9991 5.303078 TGGCTAGCACCTAAATGTTGAAAAA 59.697 36.000 18.24 0.00 0.00 1.94
4583 9992 4.830046 TGGCTAGCACCTAAATGTTGAAAA 59.170 37.500 18.24 0.00 0.00 2.29
4584 9993 4.402829 TGGCTAGCACCTAAATGTTGAAA 58.597 39.130 18.24 0.00 0.00 2.69
4585 9994 4.027674 TGGCTAGCACCTAAATGTTGAA 57.972 40.909 18.24 0.00 0.00 2.69
4586 9995 3.712016 TGGCTAGCACCTAAATGTTGA 57.288 42.857 18.24 0.00 0.00 3.18
4587 9996 4.398988 TCATTGGCTAGCACCTAAATGTTG 59.601 41.667 18.24 1.93 0.00 3.33
4623 10032 0.602106 GAGCAGTTGCACAGCAGAGA 60.602 55.000 6.90 0.00 45.16 3.10
4660 10069 5.278463 GGCTCTCTGAAGACTGCTAATCTAG 60.278 48.000 0.00 0.00 0.00 2.43
4666 10075 2.098614 CAGGCTCTCTGAAGACTGCTA 58.901 52.381 8.93 0.00 45.10 3.49
4701 10110 1.899814 AGTCAGATTACAAGCGACCCA 59.100 47.619 0.00 0.00 0.00 4.51
4756 10165 9.654417 GCTAACATAGTTTGAAAAACGTTCTTA 57.346 29.630 0.00 0.00 0.00 2.10
4757 10166 8.403236 AGCTAACATAGTTTGAAAAACGTTCTT 58.597 29.630 0.00 0.00 0.00 2.52
4758 10167 7.927048 AGCTAACATAGTTTGAAAAACGTTCT 58.073 30.769 0.00 0.00 0.00 3.01
4759 10168 8.469125 CAAGCTAACATAGTTTGAAAAACGTTC 58.531 33.333 0.00 0.00 46.07 3.95
4760 10169 7.434013 CCAAGCTAACATAGTTTGAAAAACGTT 59.566 33.333 13.43 0.00 46.07 3.99
4761 10170 6.915843 CCAAGCTAACATAGTTTGAAAAACGT 59.084 34.615 13.43 0.00 46.07 3.99
4762 10171 7.136119 TCCAAGCTAACATAGTTTGAAAAACG 58.864 34.615 13.43 0.00 46.07 3.60
4763 10172 8.865590 TTCCAAGCTAACATAGTTTGAAAAAC 57.134 30.769 13.43 0.00 46.07 2.43
4764 10173 9.877178 TTTTCCAAGCTAACATAGTTTGAAAAA 57.123 25.926 13.43 10.05 46.07 1.94
4765 10174 9.308318 GTTTTCCAAGCTAACATAGTTTGAAAA 57.692 29.630 13.43 13.43 46.07 2.29
4766 10175 7.646130 CGTTTTCCAAGCTAACATAGTTTGAAA 59.354 33.333 13.43 9.76 46.07 2.69
4767 10176 7.136119 CGTTTTCCAAGCTAACATAGTTTGAA 58.864 34.615 13.43 5.61 46.07 2.69
4768 10177 6.261381 ACGTTTTCCAAGCTAACATAGTTTGA 59.739 34.615 13.43 0.86 46.07 2.69
4769 10178 6.435428 ACGTTTTCCAAGCTAACATAGTTTG 58.565 36.000 6.91 6.91 43.80 2.93
4770 10179 6.628919 ACGTTTTCCAAGCTAACATAGTTT 57.371 33.333 0.00 0.00 0.00 2.66
4771 10180 6.628919 AACGTTTTCCAAGCTAACATAGTT 57.371 33.333 0.00 0.00 0.00 2.24
4772 10181 6.237313 GAACGTTTTCCAAGCTAACATAGT 57.763 37.500 0.46 0.00 0.00 2.12
4786 10195 7.864379 TCCGTCTCATAATATAGGAACGTTTTC 59.136 37.037 0.46 0.00 0.00 2.29
4787 10196 7.719483 TCCGTCTCATAATATAGGAACGTTTT 58.281 34.615 0.46 0.00 0.00 2.43
4788 10197 7.281040 TCCGTCTCATAATATAGGAACGTTT 57.719 36.000 0.46 0.00 0.00 3.60
4789 10198 6.072064 CCTCCGTCTCATAATATAGGAACGTT 60.072 42.308 0.00 0.00 0.00 3.99
4790 10199 5.415077 CCTCCGTCTCATAATATAGGAACGT 59.585 44.000 0.00 0.00 0.00 3.99
4791 10200 5.163642 CCCTCCGTCTCATAATATAGGAACG 60.164 48.000 0.00 0.00 0.00 3.95
4792 10201 5.950549 TCCCTCCGTCTCATAATATAGGAAC 59.049 44.000 0.00 0.00 0.00 3.62
4793 10202 6.148735 TCCCTCCGTCTCATAATATAGGAA 57.851 41.667 0.00 0.00 0.00 3.36
4794 10203 5.253330 ACTCCCTCCGTCTCATAATATAGGA 59.747 44.000 0.00 0.00 0.00 2.94
4795 10204 5.511363 ACTCCCTCCGTCTCATAATATAGG 58.489 45.833 0.00 0.00 0.00 2.57
4796 10205 8.754991 AATACTCCCTCCGTCTCATAATATAG 57.245 38.462 0.00 0.00 0.00 1.31
4797 10206 8.333984 TGAATACTCCCTCCGTCTCATAATATA 58.666 37.037 0.00 0.00 0.00 0.86
4798 10207 7.122948 GTGAATACTCCCTCCGTCTCATAATAT 59.877 40.741 0.00 0.00 0.00 1.28
4799 10208 6.433404 GTGAATACTCCCTCCGTCTCATAATA 59.567 42.308 0.00 0.00 0.00 0.98
4800 10209 5.244178 GTGAATACTCCCTCCGTCTCATAAT 59.756 44.000 0.00 0.00 0.00 1.28
4801 10210 4.583489 GTGAATACTCCCTCCGTCTCATAA 59.417 45.833 0.00 0.00 0.00 1.90
4802 10211 4.142790 GTGAATACTCCCTCCGTCTCATA 58.857 47.826 0.00 0.00 0.00 2.15
4803 10212 2.959707 GTGAATACTCCCTCCGTCTCAT 59.040 50.000 0.00 0.00 0.00 2.90
4804 10213 2.291346 TGTGAATACTCCCTCCGTCTCA 60.291 50.000 0.00 0.00 0.00 3.27
4805 10214 2.376109 TGTGAATACTCCCTCCGTCTC 58.624 52.381 0.00 0.00 0.00 3.36
4806 10215 2.526888 TGTGAATACTCCCTCCGTCT 57.473 50.000 0.00 0.00 0.00 4.18
4807 10216 4.142790 TCTATGTGAATACTCCCTCCGTC 58.857 47.826 0.00 0.00 0.00 4.79
4808 10217 4.145807 CTCTATGTGAATACTCCCTCCGT 58.854 47.826 0.00 0.00 0.00 4.69
4809 10218 4.145807 ACTCTATGTGAATACTCCCTCCG 58.854 47.826 0.00 0.00 0.00 4.63
4810 10219 4.525100 GGACTCTATGTGAATACTCCCTCC 59.475 50.000 0.00 0.00 0.00 4.30
4811 10220 5.390387 AGGACTCTATGTGAATACTCCCTC 58.610 45.833 0.00 0.00 0.00 4.30
4812 10221 5.390387 GAGGACTCTATGTGAATACTCCCT 58.610 45.833 0.00 0.00 0.00 4.20
4813 10222 4.216687 CGAGGACTCTATGTGAATACTCCC 59.783 50.000 0.00 0.00 0.00 4.30
4814 10223 4.822896 ACGAGGACTCTATGTGAATACTCC 59.177 45.833 0.00 0.00 0.00 3.85
4815 10224 5.753744 CACGAGGACTCTATGTGAATACTC 58.246 45.833 0.00 0.00 33.69 2.59
4816 10225 4.036971 GCACGAGGACTCTATGTGAATACT 59.963 45.833 9.16 0.00 33.69 2.12
4817 10226 4.202020 TGCACGAGGACTCTATGTGAATAC 60.202 45.833 9.16 0.00 33.69 1.89
4818 10227 3.951680 TGCACGAGGACTCTATGTGAATA 59.048 43.478 9.16 0.00 33.69 1.75
4819 10228 2.760650 TGCACGAGGACTCTATGTGAAT 59.239 45.455 9.16 0.00 33.69 2.57
4828 10241 0.037326 TGAACCATGCACGAGGACTC 60.037 55.000 8.53 5.48 0.00 3.36
4881 10294 7.360113 TGGACTATCTACAAGTGCATTATGA 57.640 36.000 0.00 0.00 39.94 2.15
4883 10296 7.564793 TGTTGGACTATCTACAAGTGCATTAT 58.435 34.615 0.00 0.00 43.57 1.28
4921 10334 9.290483 GTTCTACCTGCAAGAAATTTAATTAGC 57.710 33.333 0.92 0.00 34.86 3.09
5081 10494 7.896496 TCCTTCTTATCTCTCTTTAACTCCTGT 59.104 37.037 0.00 0.00 0.00 4.00
5267 10680 7.760794 TCAATCTTATTGTGCAAATCCATGTTC 59.239 33.333 0.00 0.00 0.00 3.18
5333 10746 3.575687 CCATTTCACTTTCTGCCTCCTTT 59.424 43.478 0.00 0.00 0.00 3.11
5486 10899 7.689299 TGGACATTTTATTCTTCTCCTCTGAA 58.311 34.615 0.00 0.00 0.00 3.02
5508 10921 1.075482 CCTTGGCTTGCTCCTTGGA 59.925 57.895 0.00 0.00 0.00 3.53
5511 10924 0.037447 GTCTCCTTGGCTTGCTCCTT 59.963 55.000 0.00 0.00 0.00 3.36
5548 10961 5.593909 AGTTTCACATTGTCATCCAGAACAA 59.406 36.000 0.00 0.00 0.00 2.83
5550 10963 5.695851 AGTTTCACATTGTCATCCAGAAC 57.304 39.130 0.00 0.00 0.00 3.01
5599 11012 8.455682 CAAAGGCGGTAATCTCTTTATTTAACA 58.544 33.333 0.00 0.00 0.00 2.41
5601 11014 7.477494 GCAAAGGCGGTAATCTCTTTATTTAA 58.523 34.615 0.00 0.00 0.00 1.52
5697 11110 4.270008 TCCTTATTTGGCAAAGTAGCTCC 58.730 43.478 18.61 0.00 34.17 4.70
5712 11125 5.081032 TCCAACGGTTTCCAATTCCTTATT 58.919 37.500 0.00 0.00 0.00 1.40
5719 11132 3.292460 TCAACTCCAACGGTTTCCAATT 58.708 40.909 0.00 0.00 0.00 2.32
5728 11141 1.666700 TCACGTTTTCAACTCCAACGG 59.333 47.619 8.38 0.00 45.99 4.44
5729 11142 3.350912 CTTCACGTTTTCAACTCCAACG 58.649 45.455 2.29 2.29 46.87 4.10
5745 11158 3.161866 TGCCTTGTAATTTCCCCTTCAC 58.838 45.455 0.00 0.00 0.00 3.18
6087 11701 3.130450 TCCAACAGGGGTGGATCAATAT 58.870 45.455 0.00 0.00 37.22 1.28
6128 11742 1.849097 CGTACTTACGGATCAAGGCC 58.151 55.000 0.00 0.00 45.30 5.19
6141 11755 6.579666 TGACAGGAGTAAACATACGTACTT 57.420 37.500 0.00 0.00 30.65 2.24
6174 11789 1.275573 GACCCTGAAGAACTAAGCCGT 59.724 52.381 0.00 0.00 0.00 5.68
6181 11796 4.383118 CCACATTATCGACCCTGAAGAACT 60.383 45.833 0.00 0.00 0.00 3.01
6214 11829 2.422276 AATTGACACGGCAAGAAAGC 57.578 45.000 0.00 0.00 0.00 3.51
6221 11836 0.309302 CGAACCAAATTGACACGGCA 59.691 50.000 0.00 0.00 0.00 5.69
6284 11899 0.678366 ATCAGAGGTCTGTCGTCGCT 60.678 55.000 6.87 0.00 44.12 4.93
6302 11917 1.065854 GCAGACCACAGTTAGCTCCAT 60.066 52.381 0.00 0.00 0.00 3.41
6338 11953 1.148273 GGCAACCGGGAGCATCATA 59.852 57.895 19.97 0.00 36.25 2.15
6342 11957 3.965258 TGTGGCAACCGGGAGCAT 61.965 61.111 19.97 0.00 0.00 3.79
6408 12023 6.707608 CGACATCCATTCAGATCAAAAGGATA 59.292 38.462 13.88 0.00 36.00 2.59
6421 12036 1.667236 GGCACATCGACATCCATTCA 58.333 50.000 0.00 0.00 0.00 2.57
6509 12124 2.538437 CTAGCACTAGACAAGCAGCAG 58.462 52.381 0.00 0.00 35.21 4.24
6791 15976 9.167311 GATGTGTATTGTCAGAGTCCTTATTTT 57.833 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.