Multiple sequence alignment - TraesCS3A01G400900

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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 TraesCS3A01G400900 chr3A 100.000 2861 0 0 1 2861 647362366 647359506 0.000000e+00 5284.0
1 TraesCS3A01G400900 chr3A 86.959 1687 188 16 940 2604 647390517 647388841 0.000000e+00 1868.0
2 TraesCS3A01G400900 chr3A 96.855 636 18 2 297 930 662882600 662883235 0.000000e+00 1062.0
3 TraesCS3A01G400900 chr3B 94.894 940 35 7 1 929 775480133 775479196 0.000000e+00 1458.0
4 TraesCS3A01G400900 chr3B 89.939 1143 94 4 931 2062 672576532 672575400 0.000000e+00 1454.0
5 TraesCS3A01G400900 chr3B 83.573 1254 164 23 940 2161 672525588 672524345 0.000000e+00 1136.0
6 TraesCS3A01G400900 chr3B 89.429 700 50 8 159 834 101318891 101318192 0.000000e+00 861.0
7 TraesCS3A01G400900 chr3B 89.649 570 54 3 2163 2727 672517813 672517244 0.000000e+00 721.0
8 TraesCS3A01G400900 chr3B 93.333 405 25 2 2085 2488 672676806 672676403 5.280000e-167 597.0
9 TraesCS3A01G400900 chr3B 95.408 196 9 0 2532 2727 672563483 672563288 2.140000e-81 313.0
10 TraesCS3A01G400900 chr3B 93.296 179 12 0 2159 2337 672575405 672575227 6.080000e-67 265.0
11 TraesCS3A01G400900 chr3B 88.732 213 22 1 2325 2535 672563936 672563724 2.830000e-65 259.0
12 TraesCS3A01G400900 chr3B 91.111 180 14 2 1877 2056 672780386 672780209 2.850000e-60 243.0
13 TraesCS3A01G400900 chr3B 92.683 123 4 5 811 930 43197938 43197818 3.790000e-39 172.0
14 TraesCS3A01G400900 chr5D 94.574 940 28 12 1 930 548204628 548203702 0.000000e+00 1432.0
15 TraesCS3A01G400900 chr5D 92.369 249 11 3 464 705 425666599 425666352 5.870000e-92 348.0
16 TraesCS3A01G400900 chr5D 89.744 234 11 6 697 929 425665090 425664869 1.300000e-73 287.0
17 TraesCS3A01G400900 chr5D 85.030 167 17 6 1 159 472276328 472276494 2.280000e-36 163.0
18 TraesCS3A01G400900 chr7D 93.943 941 24 14 1 930 500905731 500906649 0.000000e+00 1391.0
19 TraesCS3A01G400900 chr7A 93.248 933 27 13 1 930 686149025 686149924 0.000000e+00 1341.0
20 TraesCS3A01G400900 chr4D 95.860 773 19 4 1 765 418535059 418535826 0.000000e+00 1238.0
21 TraesCS3A01G400900 chr3D 88.697 867 81 6 1212 2062 510830049 510829184 0.000000e+00 1042.0
22 TraesCS3A01G400900 chr3D 89.803 608 51 2 1466 2062 510909435 510908828 0.000000e+00 769.0
23 TraesCS3A01G400900 chr3D 91.807 476 37 2 915 1390 510925761 510925288 0.000000e+00 662.0
24 TraesCS3A01G400900 chr3D 91.878 394 21 7 2478 2861 510912281 510911889 9.020000e-150 540.0
25 TraesCS3A01G400900 chr3D 90.860 372 29 4 2388 2755 510908186 510907816 7.120000e-136 494.0
26 TraesCS3A01G400900 chr3D 88.550 393 37 6 2214 2604 510754437 510754051 1.200000e-128 470.0
27 TraesCS3A01G400900 chr3D 90.606 330 31 0 2159 2488 510913084 510912755 3.380000e-119 438.0
28 TraesCS3A01G400900 chr3D 93.277 238 16 0 2159 2396 510908833 510908596 4.540000e-93 351.0
29 TraesCS3A01G400900 chr3D 89.964 279 17 4 1795 2062 510913357 510913079 1.630000e-92 350.0
30 TraesCS3A01G400900 chr3D 95.652 161 7 0 2567 2727 511282857 511282697 2.830000e-65 259.0
31 TraesCS3A01G400900 chr3D 87.634 186 20 3 1877 2062 511324732 511324550 2.230000e-51 213.0
32 TraesCS3A01G400900 chr3D 90.991 111 10 0 2751 2861 510858484 510858374 1.780000e-32 150.0
33 TraesCS3A01G400900 chr3D 100.000 43 0 0 1174 1216 510857585 510857543 2.360000e-11 80.5
34 TraesCS3A01G400900 chr4A 91.837 686 43 10 159 835 738597846 738598527 0.000000e+00 944.0
35 TraesCS3A01G400900 chrUn 88.820 161 16 2 1877 2036 338412202 338412043 2.250000e-46 196.0
36 TraesCS3A01G400900 chrUn 93.913 115 5 2 817 930 352696638 352696525 3.790000e-39 172.0
37 TraesCS3A01G400900 chr5B 88.554 166 12 6 1 159 578592004 578592169 8.090000e-46 195.0
38 TraesCS3A01G400900 chr7B 92.623 122 5 4 811 930 458535805 458535924 3.790000e-39 172.0
39 TraesCS3A01G400900 chr7B 92.623 122 5 4 811 930 706833538 706833657 3.790000e-39 172.0
40 TraesCS3A01G400900 chr4B 92.623 122 5 4 811 930 429435477 429435596 3.790000e-39 172.0
41 TraesCS3A01G400900 chr2B 92.683 123 4 5 811 930 794935544 794935664 3.790000e-39 172.0
42 TraesCS3A01G400900 chr5A 86.250 160 17 3 3 159 591465448 591465605 4.900000e-38 169.0
43 TraesCS3A01G400900 chr1B 91.803 122 6 4 811 930 375924700 375924581 1.760000e-37 167.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G400900 chr3A 647359506 647362366 2860 True 5284.000000 5284 100.000000 1 2861 1 chr3A.!!$R1 2860
1 TraesCS3A01G400900 chr3A 647388841 647390517 1676 True 1868.000000 1868 86.959000 940 2604 1 chr3A.!!$R2 1664
2 TraesCS3A01G400900 chr3A 662882600 662883235 635 False 1062.000000 1062 96.855000 297 930 1 chr3A.!!$F1 633
3 TraesCS3A01G400900 chr3B 775479196 775480133 937 True 1458.000000 1458 94.894000 1 929 1 chr3B.!!$R7 928
4 TraesCS3A01G400900 chr3B 672524345 672525588 1243 True 1136.000000 1136 83.573000 940 2161 1 chr3B.!!$R4 1221
5 TraesCS3A01G400900 chr3B 101318192 101318891 699 True 861.000000 861 89.429000 159 834 1 chr3B.!!$R2 675
6 TraesCS3A01G400900 chr3B 672575227 672576532 1305 True 859.500000 1454 91.617500 931 2337 2 chr3B.!!$R9 1406
7 TraesCS3A01G400900 chr3B 672517244 672517813 569 True 721.000000 721 89.649000 2163 2727 1 chr3B.!!$R3 564
8 TraesCS3A01G400900 chr3B 672563288 672563936 648 True 286.000000 313 92.070000 2325 2727 2 chr3B.!!$R8 402
9 TraesCS3A01G400900 chr5D 548203702 548204628 926 True 1432.000000 1432 94.574000 1 930 1 chr5D.!!$R1 929
10 TraesCS3A01G400900 chr5D 425664869 425666599 1730 True 317.500000 348 91.056500 464 929 2 chr5D.!!$R2 465
11 TraesCS3A01G400900 chr7D 500905731 500906649 918 False 1391.000000 1391 93.943000 1 930 1 chr7D.!!$F1 929
12 TraesCS3A01G400900 chr7A 686149025 686149924 899 False 1341.000000 1341 93.248000 1 930 1 chr7A.!!$F1 929
13 TraesCS3A01G400900 chr4D 418535059 418535826 767 False 1238.000000 1238 95.860000 1 765 1 chr4D.!!$F1 764
14 TraesCS3A01G400900 chr3D 510829184 510830049 865 True 1042.000000 1042 88.697000 1212 2062 1 chr3D.!!$R2 850
15 TraesCS3A01G400900 chr3D 510907816 510913357 5541 True 490.333333 769 91.064667 1466 2861 6 chr3D.!!$R7 1395
16 TraesCS3A01G400900 chr4A 738597846 738598527 681 False 944.000000 944 91.837000 159 835 1 chr4A.!!$F1 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
627 632 2.121042 AGGTGGGGAATGGGGTGT 60.121 61.111 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 4624 0.038892 CAAAGCATGGACACACTGCC 60.039 55.0 0.0 0.0 34.07 4.85 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
244 248 2.231964 GCTTGATGGATGCAAAACTGGA 59.768 45.455 0.00 0.00 0.00 3.86
308 312 2.268920 GGCTTGTGAGGATGGCGA 59.731 61.111 0.00 0.00 0.00 5.54
627 632 2.121042 AGGTGGGGAATGGGGTGT 60.121 61.111 0.00 0.00 0.00 4.16
781 2085 2.260434 CGATGGGTTGTCGGTCGT 59.740 61.111 0.00 0.00 35.55 4.34
938 2275 8.774183 TCCATTAGGAGTAGAGATAGAGTATCC 58.226 40.741 0.00 0.00 39.61 2.59
1023 2360 0.036388 ATGGCTACACGAGGTTGGTG 60.036 55.000 0.00 0.00 41.15 4.17
1065 2402 1.338973 AGCTGTTCGTCGTACTTTGGA 59.661 47.619 3.61 0.00 0.00 3.53
1070 2407 3.054878 GTTCGTCGTACTTTGGACATGT 58.945 45.455 0.00 0.00 32.74 3.21
1073 2410 4.229096 TCGTCGTACTTTGGACATGTAAC 58.771 43.478 0.00 0.00 32.74 2.50
1116 2459 3.745797 GCTTGAAGGACCTCAAACAGTCT 60.746 47.826 0.00 0.00 34.96 3.24
1119 2462 3.199946 TGAAGGACCTCAAACAGTCTGTT 59.800 43.478 12.62 12.62 43.41 3.16
1189 2553 1.459592 GCATCGACGGTTACATATGCC 59.540 52.381 1.58 0.00 34.95 4.40
1280 2644 0.466124 CTCGAAGGTCCATTCCCTCC 59.534 60.000 0.00 0.00 0.00 4.30
1318 2682 0.994995 CTTCATGACCGCTCTTGACG 59.005 55.000 0.00 0.00 31.87 4.35
1390 2754 2.172679 TGGCGTACACAACCTATCTGA 58.827 47.619 0.00 0.00 0.00 3.27
1436 2800 1.022735 GTGATCCCTGCAAGCATCAG 58.977 55.000 0.00 0.00 0.00 2.90
1468 2832 4.742201 TGAGCACGCTCGCCCTTC 62.742 66.667 14.00 0.00 45.48 3.46
1469 2833 4.742201 GAGCACGCTCGCCCTTCA 62.742 66.667 2.78 0.00 33.06 3.02
1542 4000 1.455786 CTCATTTCGTTCAACGTCGCT 59.544 47.619 10.31 0.00 43.14 4.93
1562 4020 3.618507 GCTGATAACTCACTGTCAAGCCT 60.619 47.826 0.00 0.00 0.00 4.58
1588 4046 1.215117 GACTCTCTGCAGCGCTTCT 59.785 57.895 7.50 0.00 0.00 2.85
1599 4057 3.049674 CGCTTCTCGGCTGCCAAA 61.050 61.111 20.29 8.61 33.78 3.28
1605 4063 0.250684 TCTCGGCTGCCAAATTCACA 60.251 50.000 20.29 0.00 0.00 3.58
1620 4078 2.690881 ACAGGCAATCCGGGGCTA 60.691 61.111 0.00 0.00 39.39 3.93
1623 4081 2.078665 AGGCAATCCGGGGCTATGT 61.079 57.895 0.00 0.00 39.65 2.29
1627 4085 3.133365 AATCCGGGGCTATGTGGGC 62.133 63.158 0.00 0.00 0.00 5.36
1663 4121 1.072331 GGTGCAAGAAGAGGTTCAGGA 59.928 52.381 0.00 0.00 34.82 3.86
1675 4133 3.239449 AGGTTCAGGATGCGGATACATA 58.761 45.455 0.58 0.00 34.76 2.29
1687 4145 3.861131 GCGGATACATATTCGGCTTGTCT 60.861 47.826 1.89 0.00 35.27 3.41
1694 4152 0.400213 ATTCGGCTTGTCTGGGTTCA 59.600 50.000 0.00 0.00 0.00 3.18
1695 4153 0.181587 TTCGGCTTGTCTGGGTTCAA 59.818 50.000 0.00 0.00 0.00 2.69
1697 4155 0.535102 CGGCTTGTCTGGGTTCAAGT 60.535 55.000 0.00 0.00 41.83 3.16
1722 4180 2.386661 TTGTCCGGATTCAGAAGCTC 57.613 50.000 7.81 0.00 0.00 4.09
1727 4185 1.150567 CGGATTCAGAAGCTCCTGCG 61.151 60.000 0.00 0.00 45.42 5.18
1728 4186 0.107945 GGATTCAGAAGCTCCTGCGT 60.108 55.000 0.00 0.00 45.42 5.24
1731 4189 1.257743 TTCAGAAGCTCCTGCGTAGT 58.742 50.000 0.00 0.00 45.42 2.73
1751 4209 1.290203 ATCAATGACGCGTCCATCAC 58.710 50.000 34.34 11.70 0.00 3.06
1752 4210 0.037790 TCAATGACGCGTCCATCACA 60.038 50.000 34.34 17.38 0.00 3.58
1830 4288 1.140312 TCTTGTTCTGTGGGAGGCTT 58.860 50.000 0.00 0.00 0.00 4.35
1875 4333 3.293714 TGACGGCGGGTACACGAA 61.294 61.111 24.33 0.00 35.47 3.85
2003 4476 9.436957 AATATTACGAATATCTCATGGTCCAAC 57.563 33.333 0.00 0.00 33.04 3.77
2045 4518 2.481568 ACTTCTCATGTTGATGTGCGTG 59.518 45.455 0.00 0.00 0.00 5.34
2056 4529 4.391405 TGATGTGCGTGTATCTGATCTT 57.609 40.909 0.00 0.00 0.00 2.40
2057 4530 4.114794 TGATGTGCGTGTATCTGATCTTG 58.885 43.478 0.00 0.00 0.00 3.02
2058 4531 3.592898 TGTGCGTGTATCTGATCTTGT 57.407 42.857 0.00 0.00 0.00 3.16
2059 4532 4.712122 TGTGCGTGTATCTGATCTTGTA 57.288 40.909 0.00 0.00 0.00 2.41
2060 4533 4.421058 TGTGCGTGTATCTGATCTTGTAC 58.579 43.478 0.00 0.00 0.00 2.90
2061 4534 4.082463 TGTGCGTGTATCTGATCTTGTACA 60.082 41.667 0.00 0.00 0.00 2.90
2062 4535 4.862574 GTGCGTGTATCTGATCTTGTACAA 59.137 41.667 8.28 8.28 0.00 2.41
2063 4536 5.520288 GTGCGTGTATCTGATCTTGTACAAT 59.480 40.000 9.13 0.00 0.00 2.71
2064 4537 5.519927 TGCGTGTATCTGATCTTGTACAATG 59.480 40.000 9.13 3.87 0.00 2.82
2065 4538 5.050769 GCGTGTATCTGATCTTGTACAATGG 60.051 44.000 9.13 0.00 0.00 3.16
2066 4539 5.463392 CGTGTATCTGATCTTGTACAATGGG 59.537 44.000 9.13 0.00 0.00 4.00
2067 4540 5.237344 GTGTATCTGATCTTGTACAATGGGC 59.763 44.000 9.13 0.21 0.00 5.36
2068 4541 4.785346 ATCTGATCTTGTACAATGGGCT 57.215 40.909 9.13 0.00 0.00 5.19
2069 4542 3.877559 TCTGATCTTGTACAATGGGCTG 58.122 45.455 9.13 4.06 0.00 4.85
2070 4543 3.519107 TCTGATCTTGTACAATGGGCTGA 59.481 43.478 9.13 1.98 0.00 4.26
2071 4544 3.609853 TGATCTTGTACAATGGGCTGAC 58.390 45.455 9.13 0.00 0.00 3.51
2072 4545 3.008923 TGATCTTGTACAATGGGCTGACA 59.991 43.478 9.13 1.17 0.00 3.58
2073 4546 3.500448 TCTTGTACAATGGGCTGACAA 57.500 42.857 9.13 0.00 0.00 3.18
2074 4547 3.411446 TCTTGTACAATGGGCTGACAAG 58.589 45.455 9.13 6.71 45.37 3.16
2075 4548 2.198827 TGTACAATGGGCTGACAAGG 57.801 50.000 0.00 0.00 0.00 3.61
2076 4549 1.702401 TGTACAATGGGCTGACAAGGA 59.298 47.619 0.00 0.00 0.00 3.36
2077 4550 2.308570 TGTACAATGGGCTGACAAGGAT 59.691 45.455 0.00 0.00 0.00 3.24
2078 4551 3.521531 TGTACAATGGGCTGACAAGGATA 59.478 43.478 0.00 0.00 0.00 2.59
2079 4552 3.959495 ACAATGGGCTGACAAGGATAT 57.041 42.857 0.00 0.00 0.00 1.63
2080 4553 3.559069 ACAATGGGCTGACAAGGATATG 58.441 45.455 0.00 0.00 0.00 1.78
2081 4554 3.202818 ACAATGGGCTGACAAGGATATGA 59.797 43.478 0.00 0.00 0.00 2.15
2082 4555 4.209538 CAATGGGCTGACAAGGATATGAA 58.790 43.478 0.00 0.00 0.00 2.57
2083 4556 4.736611 ATGGGCTGACAAGGATATGAAT 57.263 40.909 0.00 0.00 0.00 2.57
2084 4557 4.524802 TGGGCTGACAAGGATATGAATT 57.475 40.909 0.00 0.00 0.00 2.17
2085 4558 4.870636 TGGGCTGACAAGGATATGAATTT 58.129 39.130 0.00 0.00 0.00 1.82
2086 4559 5.271598 TGGGCTGACAAGGATATGAATTTT 58.728 37.500 0.00 0.00 0.00 1.82
2087 4560 6.430864 TGGGCTGACAAGGATATGAATTTTA 58.569 36.000 0.00 0.00 0.00 1.52
2088 4561 6.321181 TGGGCTGACAAGGATATGAATTTTAC 59.679 38.462 0.00 0.00 0.00 2.01
2089 4562 6.547510 GGGCTGACAAGGATATGAATTTTACT 59.452 38.462 0.00 0.00 0.00 2.24
2090 4563 7.420800 GGCTGACAAGGATATGAATTTTACTG 58.579 38.462 0.00 0.00 0.00 2.74
2091 4564 7.067494 GGCTGACAAGGATATGAATTTTACTGT 59.933 37.037 0.00 0.00 0.00 3.55
2092 4565 7.912250 GCTGACAAGGATATGAATTTTACTGTG 59.088 37.037 0.00 0.00 0.00 3.66
2093 4566 7.761409 TGACAAGGATATGAATTTTACTGTGC 58.239 34.615 0.00 0.00 0.00 4.57
2094 4567 6.785191 ACAAGGATATGAATTTTACTGTGCG 58.215 36.000 0.00 0.00 0.00 5.34
2095 4568 6.374333 ACAAGGATATGAATTTTACTGTGCGT 59.626 34.615 0.00 0.00 0.00 5.24
2096 4569 7.094377 ACAAGGATATGAATTTTACTGTGCGTT 60.094 33.333 0.00 0.00 0.00 4.84
2097 4570 8.394877 CAAGGATATGAATTTTACTGTGCGTTA 58.605 33.333 0.00 0.00 0.00 3.18
2098 4571 8.142994 AGGATATGAATTTTACTGTGCGTTAG 57.857 34.615 0.00 0.00 0.00 2.34
2099 4572 6.851330 GGATATGAATTTTACTGTGCGTTAGC 59.149 38.462 0.00 0.00 45.41 3.09
2100 4573 5.880054 ATGAATTTTACTGTGCGTTAGCT 57.120 34.783 0.00 0.00 45.42 3.32
2101 4574 5.029650 TGAATTTTACTGTGCGTTAGCTG 57.970 39.130 0.00 0.00 45.42 4.24
2102 4575 2.961522 TTTTACTGTGCGTTAGCTGC 57.038 45.000 0.00 0.00 45.42 5.25
2103 4576 0.787787 TTTACTGTGCGTTAGCTGCG 59.212 50.000 0.00 1.72 45.42 5.18
2104 4577 1.011968 TTACTGTGCGTTAGCTGCGG 61.012 55.000 13.07 0.00 45.42 5.69
2105 4578 2.829043 TACTGTGCGTTAGCTGCGGG 62.829 60.000 13.07 0.00 45.42 6.13
2110 4583 4.451150 CGTTAGCTGCGGGCCTGA 62.451 66.667 18.31 0.00 43.05 3.86
2111 4584 2.190578 GTTAGCTGCGGGCCTGAT 59.809 61.111 18.31 0.00 43.05 2.90
2112 4585 1.445942 GTTAGCTGCGGGCCTGATA 59.554 57.895 18.31 1.65 43.05 2.15
2113 4586 0.601311 GTTAGCTGCGGGCCTGATAG 60.601 60.000 18.31 13.84 43.05 2.08
2114 4587 1.758440 TTAGCTGCGGGCCTGATAGG 61.758 60.000 18.31 2.29 43.05 2.57
2115 4588 2.656698 TAGCTGCGGGCCTGATAGGA 62.657 60.000 18.31 0.00 43.05 2.94
2116 4589 3.106986 GCTGCGGGCCTGATAGGAA 62.107 63.158 18.31 0.00 37.67 3.36
2117 4590 1.526887 CTGCGGGCCTGATAGGAAA 59.473 57.895 18.31 0.00 37.67 3.13
2118 4591 0.107214 CTGCGGGCCTGATAGGAAAA 60.107 55.000 18.31 0.00 37.67 2.29
2119 4592 0.329931 TGCGGGCCTGATAGGAAAAA 59.670 50.000 18.31 0.00 37.67 1.94
2120 4593 0.738975 GCGGGCCTGATAGGAAAAAC 59.261 55.000 18.31 0.00 37.67 2.43
2121 4594 1.953311 GCGGGCCTGATAGGAAAAACA 60.953 52.381 18.31 0.00 37.67 2.83
2122 4595 2.654863 CGGGCCTGATAGGAAAAACAT 58.345 47.619 5.28 0.00 37.67 2.71
2123 4596 3.023832 CGGGCCTGATAGGAAAAACATT 58.976 45.455 5.28 0.00 37.67 2.71
2124 4597 3.447229 CGGGCCTGATAGGAAAAACATTT 59.553 43.478 5.28 0.00 37.67 2.32
2125 4598 4.677779 CGGGCCTGATAGGAAAAACATTTG 60.678 45.833 5.28 0.00 37.67 2.32
2126 4599 4.383010 GGGCCTGATAGGAAAAACATTTGG 60.383 45.833 0.84 0.00 37.67 3.28
2127 4600 4.183865 GCCTGATAGGAAAAACATTTGGC 58.816 43.478 0.00 0.00 37.67 4.52
2128 4601 4.322650 GCCTGATAGGAAAAACATTTGGCA 60.323 41.667 0.00 0.00 37.67 4.92
2129 4602 5.170748 CCTGATAGGAAAAACATTTGGCAC 58.829 41.667 0.00 0.00 37.67 5.01
2130 4603 5.279406 CCTGATAGGAAAAACATTTGGCACA 60.279 40.000 0.00 0.00 37.67 4.57
2131 4604 5.537188 TGATAGGAAAAACATTTGGCACAC 58.463 37.500 0.00 0.00 39.29 3.82
2132 4605 3.902881 AGGAAAAACATTTGGCACACA 57.097 38.095 0.00 0.00 39.29 3.72
2133 4606 3.795877 AGGAAAAACATTTGGCACACAG 58.204 40.909 0.00 0.00 39.29 3.66
2134 4607 3.450457 AGGAAAAACATTTGGCACACAGA 59.550 39.130 0.00 0.00 39.29 3.41
2135 4608 4.081198 AGGAAAAACATTTGGCACACAGAA 60.081 37.500 0.00 0.00 39.29 3.02
2136 4609 4.633565 GGAAAAACATTTGGCACACAGAAA 59.366 37.500 0.00 0.00 39.29 2.52
2137 4610 5.123027 GGAAAAACATTTGGCACACAGAAAA 59.877 36.000 0.00 0.00 39.29 2.29
2138 4611 6.183360 GGAAAAACATTTGGCACACAGAAAAT 60.183 34.615 0.00 0.00 39.29 1.82
2139 4612 6.756299 AAAACATTTGGCACACAGAAAATT 57.244 29.167 0.00 0.00 39.29 1.82
2140 4613 6.756299 AAACATTTGGCACACAGAAAATTT 57.244 29.167 0.00 0.00 39.29 1.82
2141 4614 6.756299 AACATTTGGCACACAGAAAATTTT 57.244 29.167 2.28 2.28 39.29 1.82
2142 4615 6.756299 ACATTTGGCACACAGAAAATTTTT 57.244 29.167 4.63 0.00 39.29 1.94
2143 4616 6.784176 ACATTTGGCACACAGAAAATTTTTC 58.216 32.000 12.94 12.94 39.29 2.29
2144 4617 6.598850 ACATTTGGCACACAGAAAATTTTTCT 59.401 30.769 16.82 16.82 39.29 2.52
2156 4629 6.643388 AGAAAATTTTTCTGTTTCTGGCAGT 58.357 32.000 20.74 0.00 39.52 4.40
2157 4630 6.536224 AGAAAATTTTTCTGTTTCTGGCAGTG 59.464 34.615 20.74 1.56 39.52 3.66
2231 4805 7.872138 AGTCCTGGTTTGATCCTGAATTAATA 58.128 34.615 0.00 0.00 0.00 0.98
2251 4825 2.616524 ACAAGTGCCTACTAGGACCAA 58.383 47.619 6.26 0.00 37.67 3.67
2262 4836 4.048970 ACTAGGACCAAGAGAAGCACTA 57.951 45.455 0.00 0.00 0.00 2.74
2265 4839 3.445008 AGGACCAAGAGAAGCACTATCA 58.555 45.455 0.00 0.00 0.00 2.15
2282 4856 6.541086 CACTATCATTGCTCTTGACAAAGTC 58.459 40.000 0.00 0.00 34.78 3.01
2297 4871 5.473846 TGACAAAGTCGTAGATGTCTCTCTT 59.526 40.000 12.65 0.00 42.55 2.85
2439 5432 3.064900 AGTGAGCTGGTCAATCTTTCC 57.935 47.619 11.60 0.00 36.74 3.13
2440 5433 2.373169 AGTGAGCTGGTCAATCTTTCCA 59.627 45.455 11.60 0.00 36.74 3.53
2443 5436 0.804989 GCTGGTCAATCTTTCCACCG 59.195 55.000 0.00 0.00 0.00 4.94
2445 5438 2.614481 GCTGGTCAATCTTTCCACCGTA 60.614 50.000 0.00 0.00 0.00 4.02
2461 5454 2.106857 ACCGTATGCTAGCTACTCTCCT 59.893 50.000 17.23 0.00 0.00 3.69
2462 5455 2.486203 CCGTATGCTAGCTACTCTCCTG 59.514 54.545 17.23 2.84 0.00 3.86
2467 5460 3.431415 TGCTAGCTACTCTCCTGTTCAA 58.569 45.455 17.23 0.00 0.00 2.69
2469 5462 4.142071 TGCTAGCTACTCTCCTGTTCAATG 60.142 45.833 17.23 0.00 0.00 2.82
2491 5486 4.141251 TGGGACCTGAGGAATTAATTAGCC 60.141 45.833 4.99 0.00 0.00 3.93
2520 5515 0.603975 GTCTGTGTTCCAGTGGAGGC 60.604 60.000 12.67 10.17 42.19 4.70
2582 5825 1.086696 GCGGCTTCTGCTTTGTATCA 58.913 50.000 0.00 0.00 39.59 2.15
2755 5998 4.717877 TCAGCAGGAATCAACTTTTCTGA 58.282 39.130 0.00 0.00 0.00 3.27
2756 5999 4.516698 TCAGCAGGAATCAACTTTTCTGAC 59.483 41.667 0.00 0.00 0.00 3.51
2757 6000 3.499918 AGCAGGAATCAACTTTTCTGACG 59.500 43.478 0.00 0.00 0.00 4.35
2758 6001 3.498397 GCAGGAATCAACTTTTCTGACGA 59.502 43.478 0.00 0.00 0.00 4.20
2759 6002 4.154918 GCAGGAATCAACTTTTCTGACGAT 59.845 41.667 0.00 0.00 0.00 3.73
2760 6003 5.351465 GCAGGAATCAACTTTTCTGACGATA 59.649 40.000 0.00 0.00 0.00 2.92
2761 6004 6.456181 GCAGGAATCAACTTTTCTGACGATAG 60.456 42.308 0.00 0.00 46.19 2.08
2762 6005 5.582665 AGGAATCAACTTTTCTGACGATAGC 59.417 40.000 0.00 0.00 42.67 2.97
2763 6006 5.456192 AATCAACTTTTCTGACGATAGCG 57.544 39.130 0.00 0.00 44.79 4.26
2764 6007 4.168922 TCAACTTTTCTGACGATAGCGA 57.831 40.909 7.69 0.00 41.64 4.93
2765 6008 4.166523 TCAACTTTTCTGACGATAGCGAG 58.833 43.478 7.69 0.00 41.64 5.03
2766 6009 4.082949 TCAACTTTTCTGACGATAGCGAGA 60.083 41.667 7.69 0.00 41.64 4.04
2767 6010 4.640789 ACTTTTCTGACGATAGCGAGAT 57.359 40.909 7.69 0.00 41.64 2.75
2768 6011 5.752892 ACTTTTCTGACGATAGCGAGATA 57.247 39.130 7.69 0.00 41.64 1.98
2769 6012 5.512473 ACTTTTCTGACGATAGCGAGATAC 58.488 41.667 7.69 0.00 41.64 2.24
2770 6013 5.066117 ACTTTTCTGACGATAGCGAGATACA 59.934 40.000 7.69 0.00 41.64 2.29
2771 6014 5.690997 TTTCTGACGATAGCGAGATACAT 57.309 39.130 7.69 0.00 41.64 2.29
2772 6015 4.670227 TCTGACGATAGCGAGATACATG 57.330 45.455 7.69 0.00 41.64 3.21
2773 6016 4.065789 TCTGACGATAGCGAGATACATGT 58.934 43.478 7.69 2.69 41.64 3.21
2774 6017 4.083802 TCTGACGATAGCGAGATACATGTG 60.084 45.833 7.69 0.00 41.64 3.21
2775 6018 3.813166 TGACGATAGCGAGATACATGTGA 59.187 43.478 7.69 0.00 41.64 3.58
2776 6019 4.455877 TGACGATAGCGAGATACATGTGAT 59.544 41.667 7.69 0.00 41.64 3.06
2777 6020 4.727475 ACGATAGCGAGATACATGTGATG 58.273 43.478 7.69 0.00 41.64 3.07
2778 6021 4.455877 ACGATAGCGAGATACATGTGATGA 59.544 41.667 7.69 0.00 41.64 2.92
2779 6022 4.790651 CGATAGCGAGATACATGTGATGAC 59.209 45.833 9.11 0.00 40.82 3.06
2780 6023 5.391416 CGATAGCGAGATACATGTGATGACT 60.391 44.000 9.11 1.62 40.82 3.41
2781 6024 4.662468 AGCGAGATACATGTGATGACTT 57.338 40.909 9.11 0.00 0.00 3.01
2782 6025 4.615949 AGCGAGATACATGTGATGACTTC 58.384 43.478 9.11 0.00 0.00 3.01
2783 6026 4.340666 AGCGAGATACATGTGATGACTTCT 59.659 41.667 9.11 0.00 0.00 2.85
2784 6027 5.046529 GCGAGATACATGTGATGACTTCTT 58.953 41.667 9.11 0.00 0.00 2.52
2785 6028 5.174761 GCGAGATACATGTGATGACTTCTTC 59.825 44.000 9.11 0.00 0.00 2.87
2786 6029 6.268566 CGAGATACATGTGATGACTTCTTCA 58.731 40.000 9.11 0.00 39.11 3.02
2787 6030 6.753744 CGAGATACATGTGATGACTTCTTCAA 59.246 38.462 9.11 0.00 37.92 2.69
2788 6031 7.437565 CGAGATACATGTGATGACTTCTTCAAT 59.562 37.037 9.11 0.00 37.92 2.57
2789 6032 8.659925 AGATACATGTGATGACTTCTTCAATC 57.340 34.615 9.11 0.00 37.92 2.67
2790 6033 8.484575 AGATACATGTGATGACTTCTTCAATCT 58.515 33.333 9.11 0.31 37.92 2.40
2791 6034 9.107177 GATACATGTGATGACTTCTTCAATCTT 57.893 33.333 9.11 0.00 37.92 2.40
2792 6035 7.375106 ACATGTGATGACTTCTTCAATCTTC 57.625 36.000 0.00 0.00 37.92 2.87
2793 6036 6.938596 ACATGTGATGACTTCTTCAATCTTCA 59.061 34.615 0.00 0.00 37.92 3.02
2794 6037 7.446319 ACATGTGATGACTTCTTCAATCTTCAA 59.554 33.333 0.00 0.00 37.92 2.69
2795 6038 7.430992 TGTGATGACTTCTTCAATCTTCAAG 57.569 36.000 0.00 0.00 37.92 3.02
2796 6039 6.072838 TGTGATGACTTCTTCAATCTTCAAGC 60.073 38.462 0.00 0.00 37.92 4.01
2797 6040 6.149142 GTGATGACTTCTTCAATCTTCAAGCT 59.851 38.462 0.00 0.00 37.92 3.74
2798 6041 6.370994 TGATGACTTCTTCAATCTTCAAGCTC 59.629 38.462 0.00 0.00 37.92 4.09
2799 6042 4.999950 TGACTTCTTCAATCTTCAAGCTCC 59.000 41.667 0.00 0.00 0.00 4.70
2800 6043 3.999663 ACTTCTTCAATCTTCAAGCTCCG 59.000 43.478 0.00 0.00 0.00 4.63
2801 6044 2.350522 TCTTCAATCTTCAAGCTCCGC 58.649 47.619 0.00 0.00 0.00 5.54
2802 6045 2.079158 CTTCAATCTTCAAGCTCCGCA 58.921 47.619 0.00 0.00 0.00 5.69
2803 6046 2.183478 TCAATCTTCAAGCTCCGCAA 57.817 45.000 0.00 0.00 0.00 4.85
2804 6047 2.079158 TCAATCTTCAAGCTCCGCAAG 58.921 47.619 0.00 0.00 0.00 4.01
2805 6048 1.808945 CAATCTTCAAGCTCCGCAAGT 59.191 47.619 0.00 0.00 0.00 3.16
2806 6049 1.731720 ATCTTCAAGCTCCGCAAGTC 58.268 50.000 0.00 0.00 0.00 3.01
2807 6050 0.681733 TCTTCAAGCTCCGCAAGTCT 59.318 50.000 0.00 0.00 0.00 3.24
2808 6051 1.893137 TCTTCAAGCTCCGCAAGTCTA 59.107 47.619 0.00 0.00 0.00 2.59
2809 6052 2.299013 TCTTCAAGCTCCGCAAGTCTAA 59.701 45.455 0.00 0.00 0.00 2.10
2810 6053 3.055819 TCTTCAAGCTCCGCAAGTCTAAT 60.056 43.478 0.00 0.00 0.00 1.73
2811 6054 2.893637 TCAAGCTCCGCAAGTCTAATC 58.106 47.619 0.00 0.00 0.00 1.75
2812 6055 2.497675 TCAAGCTCCGCAAGTCTAATCT 59.502 45.455 0.00 0.00 0.00 2.40
2813 6056 3.055819 TCAAGCTCCGCAAGTCTAATCTT 60.056 43.478 0.00 0.00 0.00 2.40
2814 6057 3.618690 AGCTCCGCAAGTCTAATCTTT 57.381 42.857 0.00 0.00 0.00 2.52
2815 6058 4.737855 AGCTCCGCAAGTCTAATCTTTA 57.262 40.909 0.00 0.00 0.00 1.85
2816 6059 5.086104 AGCTCCGCAAGTCTAATCTTTAA 57.914 39.130 0.00 0.00 0.00 1.52
2817 6060 5.675538 AGCTCCGCAAGTCTAATCTTTAAT 58.324 37.500 0.00 0.00 0.00 1.40
2818 6061 6.116126 AGCTCCGCAAGTCTAATCTTTAATT 58.884 36.000 0.00 0.00 0.00 1.40
2819 6062 6.037610 AGCTCCGCAAGTCTAATCTTTAATTG 59.962 38.462 0.00 0.00 0.00 2.32
2820 6063 6.037172 GCTCCGCAAGTCTAATCTTTAATTGA 59.963 38.462 0.00 0.00 0.00 2.57
2821 6064 7.303634 TCCGCAAGTCTAATCTTTAATTGAC 57.696 36.000 0.00 0.00 0.00 3.18
2822 6065 6.035650 TCCGCAAGTCTAATCTTTAATTGACG 59.964 38.462 0.00 0.00 0.00 4.35
2823 6066 6.183360 CCGCAAGTCTAATCTTTAATTGACGT 60.183 38.462 0.00 0.00 0.00 4.34
2824 6067 7.234384 CGCAAGTCTAATCTTTAATTGACGTT 58.766 34.615 0.00 0.00 0.00 3.99
2825 6068 7.214449 CGCAAGTCTAATCTTTAATTGACGTTG 59.786 37.037 0.00 0.00 0.00 4.10
2826 6069 8.015658 GCAAGTCTAATCTTTAATTGACGTTGT 58.984 33.333 0.00 0.00 0.00 3.32
2827 6070 9.530129 CAAGTCTAATCTTTAATTGACGTTGTC 57.470 33.333 0.00 0.00 0.00 3.18
2828 6071 9.490379 AAGTCTAATCTTTAATTGACGTTGTCT 57.510 29.630 0.00 0.00 33.15 3.41
2829 6072 8.926710 AGTCTAATCTTTAATTGACGTTGTCTG 58.073 33.333 0.00 0.00 33.15 3.51
2830 6073 8.709646 GTCTAATCTTTAATTGACGTTGTCTGT 58.290 33.333 0.00 0.00 33.15 3.41
2831 6074 8.708742 TCTAATCTTTAATTGACGTTGTCTGTG 58.291 33.333 0.00 0.00 33.15 3.66
2832 6075 6.861065 ATCTTTAATTGACGTTGTCTGTGT 57.139 33.333 0.00 0.00 33.15 3.72
2833 6076 6.281848 TCTTTAATTGACGTTGTCTGTGTC 57.718 37.500 0.00 0.00 33.15 3.67
2834 6077 6.046593 TCTTTAATTGACGTTGTCTGTGTCT 58.953 36.000 0.00 0.00 33.15 3.41
2835 6078 7.204604 TCTTTAATTGACGTTGTCTGTGTCTA 58.795 34.615 0.00 0.00 33.15 2.59
2836 6079 7.870954 TCTTTAATTGACGTTGTCTGTGTCTAT 59.129 33.333 0.00 0.00 33.15 1.98
2837 6080 5.845985 AATTGACGTTGTCTGTGTCTATG 57.154 39.130 0.00 0.00 33.15 2.23
2838 6081 3.297830 TGACGTTGTCTGTGTCTATGG 57.702 47.619 0.00 0.00 33.15 2.74
2839 6082 2.626266 TGACGTTGTCTGTGTCTATGGT 59.374 45.455 0.00 0.00 33.15 3.55
2840 6083 3.243336 GACGTTGTCTGTGTCTATGGTC 58.757 50.000 0.00 0.00 0.00 4.02
2841 6084 2.891580 ACGTTGTCTGTGTCTATGGTCT 59.108 45.455 0.00 0.00 0.00 3.85
2842 6085 4.077108 ACGTTGTCTGTGTCTATGGTCTA 58.923 43.478 0.00 0.00 0.00 2.59
2843 6086 4.156190 ACGTTGTCTGTGTCTATGGTCTAG 59.844 45.833 0.00 0.00 0.00 2.43
2844 6087 4.425520 GTTGTCTGTGTCTATGGTCTAGC 58.574 47.826 0.00 0.00 0.00 3.42
2845 6088 2.683362 TGTCTGTGTCTATGGTCTAGCG 59.317 50.000 0.00 0.00 0.00 4.26
2846 6089 2.943690 GTCTGTGTCTATGGTCTAGCGA 59.056 50.000 0.00 0.00 0.00 4.93
2847 6090 3.566322 GTCTGTGTCTATGGTCTAGCGAT 59.434 47.826 0.00 0.00 0.00 4.58
2848 6091 3.565902 TCTGTGTCTATGGTCTAGCGATG 59.434 47.826 0.00 0.00 0.00 3.84
2849 6092 3.288092 TGTGTCTATGGTCTAGCGATGT 58.712 45.455 0.00 0.00 0.00 3.06
2850 6093 3.699538 TGTGTCTATGGTCTAGCGATGTT 59.300 43.478 0.00 0.00 0.00 2.71
2851 6094 4.159693 TGTGTCTATGGTCTAGCGATGTTT 59.840 41.667 0.00 0.00 0.00 2.83
2852 6095 4.740695 GTGTCTATGGTCTAGCGATGTTTC 59.259 45.833 0.00 0.00 0.00 2.78
2853 6096 4.645136 TGTCTATGGTCTAGCGATGTTTCT 59.355 41.667 0.00 0.00 0.00 2.52
2854 6097 5.127194 TGTCTATGGTCTAGCGATGTTTCTT 59.873 40.000 0.00 0.00 0.00 2.52
2855 6098 6.320418 TGTCTATGGTCTAGCGATGTTTCTTA 59.680 38.462 0.00 0.00 0.00 2.10
2856 6099 7.014326 TGTCTATGGTCTAGCGATGTTTCTTAT 59.986 37.037 0.00 0.00 0.00 1.73
2857 6100 8.512956 GTCTATGGTCTAGCGATGTTTCTTATA 58.487 37.037 0.00 0.00 0.00 0.98
2858 6101 9.074576 TCTATGGTCTAGCGATGTTTCTTATAA 57.925 33.333 0.00 0.00 0.00 0.98
2859 6102 9.692749 CTATGGTCTAGCGATGTTTCTTATAAA 57.307 33.333 0.00 0.00 0.00 1.40
2860 6103 8.958119 ATGGTCTAGCGATGTTTCTTATAAAA 57.042 30.769 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 248 0.035036 CAGCTGCGAGATCCATCCAT 59.965 55.000 0.00 0.00 0.00 3.41
308 312 4.657824 CGGGCTGACAACCGTCGT 62.658 66.667 9.47 0.00 45.80 4.34
834 2142 3.531538 TCGTAGGTTAACCGTCGTAGAT 58.468 45.455 28.99 12.26 40.67 1.98
836 2144 3.740044 TTCGTAGGTTAACCGTCGTAG 57.260 47.619 28.99 16.62 42.08 3.51
838 2146 3.363341 TTTTCGTAGGTTAACCGTCGT 57.637 42.857 28.99 14.31 42.08 4.34
931 2268 2.431057 ACACACGATCAAGGGGATACTC 59.569 50.000 0.00 0.00 36.00 2.59
933 2270 2.981859 ACACACGATCAAGGGGATAC 57.018 50.000 0.00 0.00 36.00 2.24
935 2272 4.503714 AAATACACACGATCAAGGGGAT 57.496 40.909 0.00 0.00 39.53 3.85
937 2274 4.006989 TCAAAATACACACGATCAAGGGG 58.993 43.478 0.00 0.00 0.00 4.79
938 2275 5.449041 CCATCAAAATACACACGATCAAGGG 60.449 44.000 0.00 0.00 0.00 3.95
983 2320 3.258228 ATCGCAGAACCTGGCAGCA 62.258 57.895 9.56 0.00 43.58 4.41
1023 2360 1.903877 TTAGGAGCAGCAGCCAGACC 61.904 60.000 0.00 0.00 43.56 3.85
1049 2386 3.054878 ACATGTCCAAAGTACGACGAAC 58.945 45.455 0.00 0.00 0.00 3.95
1065 2402 3.596214 GTCGGAATCACTGGTTACATGT 58.404 45.455 2.69 2.69 0.00 3.21
1070 2407 1.203052 GGACGTCGGAATCACTGGTTA 59.797 52.381 9.92 0.00 0.00 2.85
1073 2410 0.037697 TTGGACGTCGGAATCACTGG 60.038 55.000 9.92 0.00 0.00 4.00
1116 2459 3.649073 CACGCCATTAGGATCGATAACA 58.351 45.455 0.00 0.00 36.89 2.41
1119 2462 1.893137 AGCACGCCATTAGGATCGATA 59.107 47.619 0.00 0.00 36.89 2.92
1280 2644 2.282674 TGCAAAGCTGGAGGCCTG 60.283 61.111 12.00 0.00 43.05 4.85
1318 2682 2.288666 TGAGAAGTTGTTGCCAGACAC 58.711 47.619 0.00 0.00 0.00 3.67
1379 2743 4.082190 TGTTCGAGAGGTTCAGATAGGTTG 60.082 45.833 0.00 0.00 0.00 3.77
1390 2754 4.120589 GAGAAACTGTTGTTCGAGAGGTT 58.879 43.478 0.00 0.00 34.96 3.50
1436 2800 2.939103 GTGCTCAGGTATGTCATGTTCC 59.061 50.000 0.00 0.00 0.00 3.62
1465 2829 1.261619 GTCGAACTGGTTGTGCTGAAG 59.738 52.381 0.00 0.00 0.00 3.02
1466 2830 1.295792 GTCGAACTGGTTGTGCTGAA 58.704 50.000 0.00 0.00 0.00 3.02
1468 2832 1.564622 CGTCGAACTGGTTGTGCTG 59.435 57.895 0.00 0.00 0.00 4.41
1469 2833 1.594293 CCGTCGAACTGGTTGTGCT 60.594 57.895 0.00 0.00 0.00 4.40
1542 4000 4.202357 ACAAGGCTTGACAGTGAGTTATCA 60.202 41.667 32.50 0.00 0.00 2.15
1562 4020 1.533033 TGCAGAGAGTCCGGGACAA 60.533 57.895 27.87 2.82 34.60 3.18
1588 4046 1.243342 CCTGTGAATTTGGCAGCCGA 61.243 55.000 7.03 0.62 0.00 5.54
1599 4057 1.076777 CCCCGGATTGCCTGTGAAT 60.077 57.895 0.73 0.00 0.00 2.57
1605 4063 2.078665 ACATAGCCCCGGATTGCCT 61.079 57.895 0.73 0.00 0.00 4.75
1643 4101 1.072331 TCCTGAACCTCTTCTTGCACC 59.928 52.381 0.00 0.00 0.00 5.01
1663 4121 3.002791 CAAGCCGAATATGTATCCGCAT 58.997 45.455 0.00 0.00 0.00 4.73
1675 4133 0.400213 TGAACCCAGACAAGCCGAAT 59.600 50.000 0.00 0.00 0.00 3.34
1687 4145 2.955660 GGACAAACATCACTTGAACCCA 59.044 45.455 0.00 0.00 0.00 4.51
1694 4152 3.750371 TGAATCCGGACAAACATCACTT 58.250 40.909 6.12 0.00 0.00 3.16
1695 4153 3.007940 TCTGAATCCGGACAAACATCACT 59.992 43.478 6.12 0.00 0.00 3.41
1697 4155 3.694043 TCTGAATCCGGACAAACATCA 57.306 42.857 6.12 4.03 0.00 3.07
1727 4185 3.074504 TGGACGCGTCATTGATACTAC 57.925 47.619 37.26 18.06 0.00 2.73
1728 4186 3.316868 TGATGGACGCGTCATTGATACTA 59.683 43.478 37.26 10.20 0.00 1.82
1731 4189 2.159170 TGTGATGGACGCGTCATTGATA 60.159 45.455 37.26 18.18 0.00 2.15
1830 4288 0.320374 CACGAAAGGTGTAGGGCTGA 59.680 55.000 0.00 0.00 41.89 4.26
1875 4333 3.446570 GGCAGCTGGCGCATTCTT 61.447 61.111 25.69 0.00 46.16 2.52
2045 4518 5.468072 CAGCCCATTGTACAAGATCAGATAC 59.532 44.000 14.65 0.00 0.00 2.24
2056 4529 1.702401 TCCTTGTCAGCCCATTGTACA 59.298 47.619 0.00 0.00 0.00 2.90
2057 4530 2.489938 TCCTTGTCAGCCCATTGTAC 57.510 50.000 0.00 0.00 0.00 2.90
2058 4531 4.411869 TCATATCCTTGTCAGCCCATTGTA 59.588 41.667 0.00 0.00 0.00 2.41
2059 4532 3.202818 TCATATCCTTGTCAGCCCATTGT 59.797 43.478 0.00 0.00 0.00 2.71
2060 4533 3.824133 TCATATCCTTGTCAGCCCATTG 58.176 45.455 0.00 0.00 0.00 2.82
2061 4534 4.524802 TTCATATCCTTGTCAGCCCATT 57.475 40.909 0.00 0.00 0.00 3.16
2062 4535 4.736611 ATTCATATCCTTGTCAGCCCAT 57.263 40.909 0.00 0.00 0.00 4.00
2063 4536 4.524802 AATTCATATCCTTGTCAGCCCA 57.475 40.909 0.00 0.00 0.00 5.36
2064 4537 5.859205 AAAATTCATATCCTTGTCAGCCC 57.141 39.130 0.00 0.00 0.00 5.19
2065 4538 7.067494 ACAGTAAAATTCATATCCTTGTCAGCC 59.933 37.037 0.00 0.00 0.00 4.85
2066 4539 7.912250 CACAGTAAAATTCATATCCTTGTCAGC 59.088 37.037 0.00 0.00 0.00 4.26
2067 4540 7.912250 GCACAGTAAAATTCATATCCTTGTCAG 59.088 37.037 0.00 0.00 0.00 3.51
2068 4541 7.413988 CGCACAGTAAAATTCATATCCTTGTCA 60.414 37.037 0.00 0.00 0.00 3.58
2069 4542 6.907212 CGCACAGTAAAATTCATATCCTTGTC 59.093 38.462 0.00 0.00 0.00 3.18
2070 4543 6.374333 ACGCACAGTAAAATTCATATCCTTGT 59.626 34.615 0.00 0.00 0.00 3.16
2071 4544 6.785191 ACGCACAGTAAAATTCATATCCTTG 58.215 36.000 0.00 0.00 0.00 3.61
2072 4545 7.391148 AACGCACAGTAAAATTCATATCCTT 57.609 32.000 0.00 0.00 0.00 3.36
2073 4546 7.254795 GCTAACGCACAGTAAAATTCATATCCT 60.255 37.037 0.00 0.00 35.78 3.24
2074 4547 6.851330 GCTAACGCACAGTAAAATTCATATCC 59.149 38.462 0.00 0.00 35.78 2.59
2075 4548 7.584123 CAGCTAACGCACAGTAAAATTCATATC 59.416 37.037 0.00 0.00 39.10 1.63
2076 4549 7.409697 CAGCTAACGCACAGTAAAATTCATAT 58.590 34.615 0.00 0.00 39.10 1.78
2077 4550 6.674519 GCAGCTAACGCACAGTAAAATTCATA 60.675 38.462 0.00 0.00 39.10 2.15
2078 4551 5.631026 CAGCTAACGCACAGTAAAATTCAT 58.369 37.500 0.00 0.00 39.10 2.57
2079 4552 4.612712 GCAGCTAACGCACAGTAAAATTCA 60.613 41.667 0.00 0.00 39.10 2.57
2080 4553 3.846335 GCAGCTAACGCACAGTAAAATTC 59.154 43.478 0.00 0.00 39.10 2.17
2081 4554 3.666902 CGCAGCTAACGCACAGTAAAATT 60.667 43.478 0.00 0.00 39.10 1.82
2082 4555 2.159707 CGCAGCTAACGCACAGTAAAAT 60.160 45.455 0.00 0.00 39.10 1.82
2083 4556 1.193650 CGCAGCTAACGCACAGTAAAA 59.806 47.619 0.00 0.00 39.10 1.52
2084 4557 0.787787 CGCAGCTAACGCACAGTAAA 59.212 50.000 0.00 0.00 39.10 2.01
2085 4558 1.011968 CCGCAGCTAACGCACAGTAA 61.012 55.000 2.88 0.00 39.10 2.24
2086 4559 1.445410 CCGCAGCTAACGCACAGTA 60.445 57.895 2.88 0.00 39.10 2.74
2087 4560 2.738521 CCGCAGCTAACGCACAGT 60.739 61.111 2.88 0.00 39.10 3.55
2088 4561 3.490759 CCCGCAGCTAACGCACAG 61.491 66.667 2.88 0.00 39.10 3.66
2093 4566 2.363711 TATCAGGCCCGCAGCTAACG 62.364 60.000 0.00 1.45 43.05 3.18
2094 4567 0.601311 CTATCAGGCCCGCAGCTAAC 60.601 60.000 0.00 0.00 43.05 2.34
2095 4568 1.748403 CTATCAGGCCCGCAGCTAA 59.252 57.895 0.00 0.00 43.05 3.09
2096 4569 2.210013 CCTATCAGGCCCGCAGCTA 61.210 63.158 0.00 0.00 43.05 3.32
2097 4570 3.554342 CCTATCAGGCCCGCAGCT 61.554 66.667 0.00 0.00 43.05 4.24
2098 4571 2.608970 TTTCCTATCAGGCCCGCAGC 62.609 60.000 0.00 0.00 42.60 5.25
2099 4572 0.107214 TTTTCCTATCAGGCCCGCAG 60.107 55.000 0.00 0.00 34.61 5.18
2100 4573 0.329931 TTTTTCCTATCAGGCCCGCA 59.670 50.000 0.00 0.00 34.61 5.69
2101 4574 0.738975 GTTTTTCCTATCAGGCCCGC 59.261 55.000 0.00 0.00 34.61 6.13
2102 4575 2.122783 TGTTTTTCCTATCAGGCCCG 57.877 50.000 0.00 0.00 34.61 6.13
2103 4576 4.383010 CCAAATGTTTTTCCTATCAGGCCC 60.383 45.833 0.00 0.00 34.61 5.80
2104 4577 4.758688 CCAAATGTTTTTCCTATCAGGCC 58.241 43.478 0.00 0.00 34.61 5.19
2105 4578 4.183865 GCCAAATGTTTTTCCTATCAGGC 58.816 43.478 0.00 0.00 34.61 4.85
2106 4579 5.170748 GTGCCAAATGTTTTTCCTATCAGG 58.829 41.667 0.00 0.00 36.46 3.86
2107 4580 5.634859 GTGTGCCAAATGTTTTTCCTATCAG 59.365 40.000 0.00 0.00 0.00 2.90
2108 4581 5.069648 TGTGTGCCAAATGTTTTTCCTATCA 59.930 36.000 0.00 0.00 0.00 2.15
2109 4582 5.537188 TGTGTGCCAAATGTTTTTCCTATC 58.463 37.500 0.00 0.00 0.00 2.08
2110 4583 5.304101 TCTGTGTGCCAAATGTTTTTCCTAT 59.696 36.000 0.00 0.00 0.00 2.57
2111 4584 4.646945 TCTGTGTGCCAAATGTTTTTCCTA 59.353 37.500 0.00 0.00 0.00 2.94
2112 4585 3.450457 TCTGTGTGCCAAATGTTTTTCCT 59.550 39.130 0.00 0.00 0.00 3.36
2113 4586 3.791245 TCTGTGTGCCAAATGTTTTTCC 58.209 40.909 0.00 0.00 0.00 3.13
2114 4587 5.793026 TTTCTGTGTGCCAAATGTTTTTC 57.207 34.783 0.00 0.00 0.00 2.29
2115 4588 6.756299 ATTTTCTGTGTGCCAAATGTTTTT 57.244 29.167 0.00 0.00 0.00 1.94
2116 4589 6.756299 AATTTTCTGTGTGCCAAATGTTTT 57.244 29.167 0.00 0.00 0.00 2.43
2117 4590 6.756299 AAATTTTCTGTGTGCCAAATGTTT 57.244 29.167 0.00 0.00 0.00 2.83
2118 4591 6.756299 AAAATTTTCTGTGTGCCAAATGTT 57.244 29.167 0.00 0.00 0.00 2.71
2119 4592 6.598850 AGAAAAATTTTCTGTGTGCCAAATGT 59.401 30.769 18.99 0.00 0.00 2.71
2120 4593 6.908284 CAGAAAAATTTTCTGTGTGCCAAATG 59.092 34.615 30.12 9.87 40.63 2.32
2121 4594 7.018635 CAGAAAAATTTTCTGTGTGCCAAAT 57.981 32.000 30.12 2.29 40.63 2.32
2122 4595 6.419980 CAGAAAAATTTTCTGTGTGCCAAA 57.580 33.333 30.12 0.00 40.63 3.28
2132 4605 6.536224 CACTGCCAGAAACAGAAAAATTTTCT 59.464 34.615 14.63 14.63 39.62 2.52
2133 4606 6.313658 ACACTGCCAGAAACAGAAAAATTTTC 59.686 34.615 10.26 10.26 38.55 2.29
2134 4607 6.092533 CACACTGCCAGAAACAGAAAAATTTT 59.907 34.615 0.00 0.00 38.55 1.82
2135 4608 5.581874 CACACTGCCAGAAACAGAAAAATTT 59.418 36.000 0.00 0.00 38.55 1.82
2136 4609 5.111293 CACACTGCCAGAAACAGAAAAATT 58.889 37.500 0.00 0.00 38.55 1.82
2137 4610 4.160252 ACACACTGCCAGAAACAGAAAAAT 59.840 37.500 0.00 0.00 38.55 1.82
2138 4611 3.509575 ACACACTGCCAGAAACAGAAAAA 59.490 39.130 0.00 0.00 38.55 1.94
2139 4612 3.088532 ACACACTGCCAGAAACAGAAAA 58.911 40.909 0.00 0.00 38.55 2.29
2140 4613 2.682856 GACACACTGCCAGAAACAGAAA 59.317 45.455 0.00 0.00 38.55 2.52
2141 4614 2.288666 GACACACTGCCAGAAACAGAA 58.711 47.619 0.00 0.00 38.55 3.02
2142 4615 1.475034 GGACACACTGCCAGAAACAGA 60.475 52.381 0.00 0.00 38.55 3.41
2143 4616 0.947244 GGACACACTGCCAGAAACAG 59.053 55.000 0.00 0.00 41.08 3.16
2144 4617 0.254462 TGGACACACTGCCAGAAACA 59.746 50.000 0.00 0.00 0.00 2.83
2145 4618 1.267806 CATGGACACACTGCCAGAAAC 59.732 52.381 0.00 0.00 37.64 2.78
2146 4619 1.608055 CATGGACACACTGCCAGAAA 58.392 50.000 0.00 0.00 37.64 2.52
2147 4620 0.890542 GCATGGACACACTGCCAGAA 60.891 55.000 0.00 0.00 37.64 3.02
2148 4621 1.302752 GCATGGACACACTGCCAGA 60.303 57.895 0.00 0.00 37.64 3.86
2149 4622 0.892358 AAGCATGGACACACTGCCAG 60.892 55.000 0.00 0.00 37.64 4.85
2150 4623 0.467844 AAAGCATGGACACACTGCCA 60.468 50.000 0.00 0.00 38.78 4.92
2151 4624 0.038892 CAAAGCATGGACACACTGCC 60.039 55.000 0.00 0.00 34.07 4.85
2152 4625 0.665369 GCAAAGCATGGACACACTGC 60.665 55.000 0.00 0.00 33.89 4.40
2153 4626 0.038892 GGCAAAGCATGGACACACTG 60.039 55.000 0.00 0.00 0.00 3.66
2154 4627 1.181098 GGGCAAAGCATGGACACACT 61.181 55.000 0.00 0.00 0.00 3.55
2155 4628 1.290009 GGGCAAAGCATGGACACAC 59.710 57.895 0.00 0.00 0.00 3.82
2156 4629 0.758310 TTGGGCAAAGCATGGACACA 60.758 50.000 0.00 0.00 0.00 3.72
2157 4630 0.609662 ATTGGGCAAAGCATGGACAC 59.390 50.000 0.00 0.00 0.00 3.67
2231 4805 2.320681 TGGTCCTAGTAGGCACTTGT 57.679 50.000 11.75 0.00 41.75 3.16
2262 4836 4.067896 ACGACTTTGTCAAGAGCAATGAT 58.932 39.130 0.00 0.00 33.72 2.45
2265 4839 4.883083 TCTACGACTTTGTCAAGAGCAAT 58.117 39.130 0.00 0.00 33.72 3.56
2439 5432 2.226912 GGAGAGTAGCTAGCATACGGTG 59.773 54.545 18.83 0.00 0.00 4.94
2440 5433 2.106857 AGGAGAGTAGCTAGCATACGGT 59.893 50.000 18.83 8.85 0.00 4.83
2443 5436 4.580995 TGAACAGGAGAGTAGCTAGCATAC 59.419 45.833 18.83 15.46 0.00 2.39
2445 5438 3.636679 TGAACAGGAGAGTAGCTAGCAT 58.363 45.455 18.83 1.59 0.00 3.79
2461 5454 1.741028 TCCTCAGGTCCCATTGAACA 58.259 50.000 0.00 0.00 30.86 3.18
2462 5455 2.879103 TTCCTCAGGTCCCATTGAAC 57.121 50.000 0.00 0.00 0.00 3.18
2467 5460 5.458215 GGCTAATTAATTCCTCAGGTCCCAT 60.458 44.000 3.39 0.00 0.00 4.00
2469 5462 4.399219 GGCTAATTAATTCCTCAGGTCCC 58.601 47.826 3.39 0.00 0.00 4.46
2491 5486 4.875544 TGGAACACAGACTTTTTCTTCG 57.124 40.909 0.00 0.00 28.96 3.79
2520 5515 3.303791 GCACAACTCTTAAAGGGACAACG 60.304 47.826 0.00 0.00 0.00 4.10
2582 5825 5.440610 ACTCAGAAAACTCACCAGTTGATT 58.559 37.500 0.00 0.00 42.45 2.57
2624 5867 9.856488 GTAAGAATACTTGATCACTGTACTTGA 57.144 33.333 9.20 0.00 37.53 3.02
2631 5874 6.311445 ACTTGCGTAAGAATACTTGATCACTG 59.689 38.462 20.61 0.00 43.02 3.66
2755 5998 4.455877 TCATCACATGTATCTCGCTATCGT 59.544 41.667 0.00 0.00 36.96 3.73
2756 5999 4.790651 GTCATCACATGTATCTCGCTATCG 59.209 45.833 0.00 0.00 0.00 2.92
2757 6000 5.948588 AGTCATCACATGTATCTCGCTATC 58.051 41.667 0.00 0.00 0.00 2.08
2758 6001 5.973899 AGTCATCACATGTATCTCGCTAT 57.026 39.130 0.00 0.00 0.00 2.97
2759 6002 5.532779 AGAAGTCATCACATGTATCTCGCTA 59.467 40.000 0.00 0.00 0.00 4.26
2760 6003 4.340666 AGAAGTCATCACATGTATCTCGCT 59.659 41.667 0.00 0.00 0.00 4.93
2761 6004 4.615949 AGAAGTCATCACATGTATCTCGC 58.384 43.478 0.00 0.00 0.00 5.03
2762 6005 6.268566 TGAAGAAGTCATCACATGTATCTCG 58.731 40.000 0.00 0.00 0.00 4.04
2763 6006 8.659925 ATTGAAGAAGTCATCACATGTATCTC 57.340 34.615 0.00 0.00 35.70 2.75
2764 6007 8.484575 AGATTGAAGAAGTCATCACATGTATCT 58.515 33.333 0.00 0.00 35.70 1.98
2765 6008 8.659925 AGATTGAAGAAGTCATCACATGTATC 57.340 34.615 0.00 0.00 35.70 2.24
2766 6009 9.107177 GAAGATTGAAGAAGTCATCACATGTAT 57.893 33.333 0.00 0.00 35.70 2.29
2767 6010 8.096414 TGAAGATTGAAGAAGTCATCACATGTA 58.904 33.333 0.00 0.00 35.70 2.29
2768 6011 6.938596 TGAAGATTGAAGAAGTCATCACATGT 59.061 34.615 0.00 0.00 35.70 3.21
2769 6012 7.373778 TGAAGATTGAAGAAGTCATCACATG 57.626 36.000 0.00 0.00 35.70 3.21
2770 6013 7.361885 GCTTGAAGATTGAAGAAGTCATCACAT 60.362 37.037 0.00 0.00 35.70 3.21
2771 6014 6.072838 GCTTGAAGATTGAAGAAGTCATCACA 60.073 38.462 0.00 0.00 35.70 3.58
2772 6015 6.149142 AGCTTGAAGATTGAAGAAGTCATCAC 59.851 38.462 0.00 0.00 35.70 3.06
2773 6016 6.236409 AGCTTGAAGATTGAAGAAGTCATCA 58.764 36.000 0.00 0.00 35.70 3.07
2774 6017 6.183360 GGAGCTTGAAGATTGAAGAAGTCATC 60.183 42.308 0.00 0.00 35.70 2.92
2775 6018 5.647225 GGAGCTTGAAGATTGAAGAAGTCAT 59.353 40.000 0.00 0.00 35.70 3.06
2776 6019 4.999950 GGAGCTTGAAGATTGAAGAAGTCA 59.000 41.667 0.00 0.00 0.00 3.41
2777 6020 4.092675 CGGAGCTTGAAGATTGAAGAAGTC 59.907 45.833 0.00 0.00 0.00 3.01
2778 6021 3.999663 CGGAGCTTGAAGATTGAAGAAGT 59.000 43.478 0.00 0.00 0.00 3.01
2779 6022 4.596801 CGGAGCTTGAAGATTGAAGAAG 57.403 45.455 0.00 0.00 0.00 2.85
2796 6039 7.402640 GTCAATTAAAGATTAGACTTGCGGAG 58.597 38.462 0.00 0.00 0.00 4.63
2797 6040 6.035650 CGTCAATTAAAGATTAGACTTGCGGA 59.964 38.462 0.00 0.00 0.00 5.54
2798 6041 6.183360 ACGTCAATTAAAGATTAGACTTGCGG 60.183 38.462 0.00 0.00 0.00 5.69
2799 6042 6.762108 ACGTCAATTAAAGATTAGACTTGCG 58.238 36.000 0.00 0.00 0.00 4.85
2800 6043 8.015658 ACAACGTCAATTAAAGATTAGACTTGC 58.984 33.333 0.00 0.00 0.00 4.01
2801 6044 9.530129 GACAACGTCAATTAAAGATTAGACTTG 57.470 33.333 0.00 0.00 32.09 3.16
2802 6045 9.490379 AGACAACGTCAATTAAAGATTAGACTT 57.510 29.630 0.00 0.00 34.60 3.01
2803 6046 8.926710 CAGACAACGTCAATTAAAGATTAGACT 58.073 33.333 0.00 0.00 34.60 3.24
2804 6047 8.709646 ACAGACAACGTCAATTAAAGATTAGAC 58.290 33.333 0.00 0.00 34.60 2.59
2805 6048 8.708742 CACAGACAACGTCAATTAAAGATTAGA 58.291 33.333 0.00 0.00 34.60 2.10
2806 6049 8.495949 ACACAGACAACGTCAATTAAAGATTAG 58.504 33.333 0.00 0.00 34.60 1.73
2807 6050 8.373048 ACACAGACAACGTCAATTAAAGATTA 57.627 30.769 0.00 0.00 34.60 1.75
2808 6051 7.226720 AGACACAGACAACGTCAATTAAAGATT 59.773 33.333 0.00 0.00 34.60 2.40
2809 6052 6.706270 AGACACAGACAACGTCAATTAAAGAT 59.294 34.615 0.00 0.00 34.60 2.40
2810 6053 6.046593 AGACACAGACAACGTCAATTAAAGA 58.953 36.000 0.00 0.00 34.60 2.52
2811 6054 6.287107 AGACACAGACAACGTCAATTAAAG 57.713 37.500 0.00 0.00 34.60 1.85
2812 6055 7.095397 CCATAGACACAGACAACGTCAATTAAA 60.095 37.037 0.00 0.00 34.60 1.52
2813 6056 6.367695 CCATAGACACAGACAACGTCAATTAA 59.632 38.462 0.00 0.00 34.60 1.40
2814 6057 5.867174 CCATAGACACAGACAACGTCAATTA 59.133 40.000 0.00 0.00 34.60 1.40
2815 6058 4.690748 CCATAGACACAGACAACGTCAATT 59.309 41.667 0.00 0.00 34.60 2.32
2816 6059 4.245660 CCATAGACACAGACAACGTCAAT 58.754 43.478 0.00 0.00 34.60 2.57
2817 6060 3.069016 ACCATAGACACAGACAACGTCAA 59.931 43.478 0.00 0.00 34.60 3.18
2818 6061 2.626266 ACCATAGACACAGACAACGTCA 59.374 45.455 0.00 0.00 34.60 4.35
2819 6062 3.057456 AGACCATAGACACAGACAACGTC 60.057 47.826 0.00 0.00 0.00 4.34
2820 6063 2.891580 AGACCATAGACACAGACAACGT 59.108 45.455 0.00 0.00 0.00 3.99
2821 6064 3.577649 AGACCATAGACACAGACAACG 57.422 47.619 0.00 0.00 0.00 4.10
2822 6065 4.425520 GCTAGACCATAGACACAGACAAC 58.574 47.826 0.00 0.00 0.00 3.32
2823 6066 3.128764 CGCTAGACCATAGACACAGACAA 59.871 47.826 0.00 0.00 0.00 3.18
2824 6067 2.683362 CGCTAGACCATAGACACAGACA 59.317 50.000 0.00 0.00 0.00 3.41
2825 6068 2.943690 TCGCTAGACCATAGACACAGAC 59.056 50.000 0.00 0.00 0.00 3.51
2826 6069 3.277142 TCGCTAGACCATAGACACAGA 57.723 47.619 0.00 0.00 0.00 3.41
2827 6070 3.316588 ACATCGCTAGACCATAGACACAG 59.683 47.826 0.00 0.00 0.00 3.66
2828 6071 3.288092 ACATCGCTAGACCATAGACACA 58.712 45.455 0.00 0.00 0.00 3.72
2829 6072 3.992260 ACATCGCTAGACCATAGACAC 57.008 47.619 0.00 0.00 0.00 3.67
2830 6073 4.645136 AGAAACATCGCTAGACCATAGACA 59.355 41.667 0.00 0.00 0.00 3.41
2831 6074 5.189659 AGAAACATCGCTAGACCATAGAC 57.810 43.478 0.00 0.00 0.00 2.59
2832 6075 5.854010 AAGAAACATCGCTAGACCATAGA 57.146 39.130 0.00 0.00 0.00 1.98
2833 6076 9.692749 TTTATAAGAAACATCGCTAGACCATAG 57.307 33.333 0.00 0.00 0.00 2.23
2835 6078 8.958119 TTTTATAAGAAACATCGCTAGACCAT 57.042 30.769 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.