Multiple sequence alignment - TraesCS6D01G016000

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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 TraesCS6D01G016000 chr6D 100.000 3863 0 0 1 3863 6440826 6444688 0.000000e+00 7134.0
1 TraesCS6D01G016000 chr6D 95.234 1049 43 4 2819 3861 319747935 319746888 0.000000e+00 1653.0
2 TraesCS6D01G016000 chr6D 86.334 1383 161 17 908 2280 6425113 6426477 0.000000e+00 1482.0
3 TraesCS6D01G016000 chr6D 88.829 931 104 0 1889 2819 6352616 6353546 0.000000e+00 1144.0
4 TraesCS6D01G016000 chr6D 84.027 1033 115 29 832 1858 6496158 6497146 0.000000e+00 948.0
5 TraesCS6D01G016000 chr6D 89.100 633 66 2 2187 2819 6371318 6371947 0.000000e+00 784.0
6 TraesCS6D01G016000 chr6D 83.333 822 106 17 996 1808 6370259 6371058 0.000000e+00 730.0
7 TraesCS6D01G016000 chr6D 77.039 1324 244 34 989 2280 7032263 7033558 0.000000e+00 706.0
8 TraesCS6D01G016000 chr6D 84.370 659 77 12 832 1473 6351449 6352098 1.180000e-174 623.0
9 TraesCS6D01G016000 chr6D 91.011 356 31 1 1862 2217 6371065 6371419 2.700000e-131 479.0
10 TraesCS6D01G016000 chr6D 85.816 423 54 4 1439 1858 6352136 6352555 9.850000e-121 444.0
11 TraesCS6D01G016000 chr6D 89.666 329 33 1 1889 2217 6497207 6497534 5.970000e-113 418.0
12 TraesCS6D01G016000 chr6D 83.733 375 51 5 2445 2819 6426508 6426872 2.860000e-91 346.0
13 TraesCS6D01G016000 chr6D 81.351 370 65 4 2099 2466 6426368 6426735 8.110000e-77 298.0
14 TraesCS6D01G016000 chr6D 84.768 151 15 3 622 772 6496072 6496214 1.120000e-30 145.0
15 TraesCS6D01G016000 chr6D 90.909 88 8 0 2187 2274 6352842 6352929 6.780000e-23 119.0
16 TraesCS6D01G016000 chr6A 97.093 1204 21 3 1616 2819 5917085 5918274 0.000000e+00 2017.0
17 TraesCS6D01G016000 chr6A 95.856 917 34 3 5 921 5915570 5916482 0.000000e+00 1480.0
18 TraesCS6D01G016000 chr6A 82.791 1720 234 41 851 2546 5939429 5941110 0.000000e+00 1480.0
19 TraesCS6D01G016000 chr6A 83.468 1482 188 31 832 2271 5900559 5902025 0.000000e+00 1327.0
20 TraesCS6D01G016000 chr6A 98.033 610 9 1 964 1573 5916477 5917083 0.000000e+00 1057.0
21 TraesCS6D01G016000 chr6A 83.073 449 68 8 2375 2819 5901850 5902294 6.010000e-108 401.0
22 TraesCS6D01G016000 chr6A 84.267 375 49 5 2445 2819 5940875 5941239 1.320000e-94 357.0
23 TraesCS6D01G016000 chr6A 80.637 377 69 4 2099 2473 5940735 5941109 4.880000e-74 289.0
24 TraesCS6D01G016000 chr1D 95.157 1053 42 5 2818 3861 333745951 333744899 0.000000e+00 1653.0
25 TraesCS6D01G016000 chr1D 86.429 140 14 4 291 426 490075398 490075536 8.650000e-32 148.0
26 TraesCS6D01G016000 chr5D 95.143 1050 42 6 2820 3861 270713309 270712261 0.000000e+00 1648.0
27 TraesCS6D01G016000 chr5D 91.765 85 7 0 35 119 492185307 492185391 6.780000e-23 119.0
28 TraesCS6D01G016000 chr3D 94.972 1054 43 7 2820 3863 212007166 212008219 0.000000e+00 1644.0
29 TraesCS6D01G016000 chr3D 94.957 1051 44 5 2820 3861 346687213 346688263 0.000000e+00 1639.0
30 TraesCS6D01G016000 chr3D 94.862 1051 45 5 2820 3861 372979421 372980471 0.000000e+00 1633.0
31 TraesCS6D01G016000 chr3D 91.398 93 8 0 29 121 482504790 482504882 1.130000e-25 128.0
32 TraesCS6D01G016000 chr7D 94.957 1051 44 5 2820 3861 296757551 296758601 0.000000e+00 1639.0
33 TraesCS6D01G016000 chr7D 94.782 1054 46 7 2819 3863 243539643 243538590 0.000000e+00 1633.0
34 TraesCS6D01G016000 chr7D 94.777 1053 46 5 2818 3861 499093833 499094885 0.000000e+00 1631.0
35 TraesCS6D01G016000 chr7D 89.247 93 10 0 29 121 104018101 104018193 2.440000e-22 117.0
36 TraesCS6D01G016000 chr6B 84.547 906 109 21 832 1720 11592687 11593578 0.000000e+00 869.0
37 TraesCS6D01G016000 chr6B 84.323 606 60 19 832 1414 11792184 11792777 9.370000e-156 560.0
38 TraesCS6D01G016000 chr6B 87.166 374 45 2 2446 2819 11599187 11599557 4.610000e-114 422.0
39 TraesCS6D01G016000 chr6B 86.167 347 47 1 1513 1858 11792788 11793134 1.310000e-99 374.0
40 TraesCS6D01G016000 chr6B 86.061 330 38 1 1889 2218 11793195 11793516 7.940000e-92 348.0
41 TraesCS6D01G016000 chr6B 89.130 138 13 2 292 428 12974385 12974249 1.850000e-38 171.0
42 TraesCS6D01G016000 chr6B 78.261 207 24 14 582 772 11762152 11762353 3.150000e-21 113.0
43 TraesCS6D01G016000 chr2B 85.484 186 21 2 53 233 526885442 526885258 5.090000e-44 189.0
44 TraesCS6D01G016000 chr2B 85.906 149 15 6 283 428 672647389 672647244 1.860000e-33 154.0
45 TraesCS6D01G016000 chr4D 91.304 138 10 2 301 437 465420918 465420782 1.830000e-43 187.0
46 TraesCS6D01G016000 chr4D 89.844 128 12 1 301 428 108214066 108213940 3.090000e-36 163.0
47 TraesCS6D01G016000 chr7A 88.571 140 13 2 289 428 468937575 468937711 2.390000e-37 167.0
48 TraesCS6D01G016000 chr7B 87.050 139 14 3 291 428 733872717 733872852 1.860000e-33 154.0
49 TraesCS6D01G016000 chr5B 88.281 128 14 1 301 428 710335580 710335706 6.680000e-33 152.0
50 TraesCS6D01G016000 chr4B 90.805 87 8 0 35 121 525268175 525268261 2.440000e-22 117.0
51 TraesCS6D01G016000 chr4B 90.805 87 8 0 35 121 525304754 525304668 2.440000e-22 117.0
52 TraesCS6D01G016000 chr4B 90.805 87 8 0 35 121 525389929 525390015 2.440000e-22 117.0
53 TraesCS6D01G016000 chr4A 90.217 92 6 3 31 121 719904769 719904680 2.440000e-22 117.0
54 TraesCS6D01G016000 chr2A 80.000 115 23 0 121 235 586901125 586901011 6.880000e-13 86.1


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 TraesCS6D01G016000 chr6D 6440826 6444688 3862 False 7134.000000 7134 100.000000 1 3863 1 chr6D.!!$F1 3862
1 TraesCS6D01G016000 chr6D 319746888 319747935 1047 True 1653.000000 1653 95.234000 2819 3861 1 chr6D.!!$R1 1042
2 TraesCS6D01G016000 chr6D 6425113 6426872 1759 False 708.666667 1482 83.806000 908 2819 3 chr6D.!!$F5 1911
3 TraesCS6D01G016000 chr6D 7032263 7033558 1295 False 706.000000 706 77.039000 989 2280 1 chr6D.!!$F2 1291
4 TraesCS6D01G016000 chr6D 6370259 6371947 1688 False 664.333333 784 87.814667 996 2819 3 chr6D.!!$F4 1823
5 TraesCS6D01G016000 chr6D 6351449 6353546 2097 False 582.500000 1144 87.481000 832 2819 4 chr6D.!!$F3 1987
6 TraesCS6D01G016000 chr6D 6496072 6497534 1462 False 503.666667 948 86.153667 622 2217 3 chr6D.!!$F6 1595
7 TraesCS6D01G016000 chr6A 5915570 5918274 2704 False 1518.000000 2017 96.994000 5 2819 3 chr6A.!!$F2 2814
8 TraesCS6D01G016000 chr6A 5900559 5902294 1735 False 864.000000 1327 83.270500 832 2819 2 chr6A.!!$F1 1987
9 TraesCS6D01G016000 chr6A 5939429 5941239 1810 False 708.666667 1480 82.565000 851 2819 3 chr6A.!!$F3 1968
10 TraesCS6D01G016000 chr1D 333744899 333745951 1052 True 1653.000000 1653 95.157000 2818 3861 1 chr1D.!!$R1 1043
11 TraesCS6D01G016000 chr5D 270712261 270713309 1048 True 1648.000000 1648 95.143000 2820 3861 1 chr5D.!!$R1 1041
12 TraesCS6D01G016000 chr3D 212007166 212008219 1053 False 1644.000000 1644 94.972000 2820 3863 1 chr3D.!!$F1 1043
13 TraesCS6D01G016000 chr3D 346687213 346688263 1050 False 1639.000000 1639 94.957000 2820 3861 1 chr3D.!!$F2 1041
14 TraesCS6D01G016000 chr3D 372979421 372980471 1050 False 1633.000000 1633 94.862000 2820 3861 1 chr3D.!!$F3 1041
15 TraesCS6D01G016000 chr7D 296757551 296758601 1050 False 1639.000000 1639 94.957000 2820 3861 1 chr7D.!!$F2 1041
16 TraesCS6D01G016000 chr7D 243538590 243539643 1053 True 1633.000000 1633 94.782000 2819 3863 1 chr7D.!!$R1 1044
17 TraesCS6D01G016000 chr7D 499093833 499094885 1052 False 1631.000000 1631 94.777000 2818 3861 1 chr7D.!!$F3 1043
18 TraesCS6D01G016000 chr6B 11592687 11593578 891 False 869.000000 869 84.547000 832 1720 1 chr6B.!!$F1 888
19 TraesCS6D01G016000 chr6B 11792184 11793516 1332 False 427.333333 560 85.517000 832 2218 3 chr6B.!!$F4 1386

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
760 761 0.108662 TCCACACATACGCAGCTCTG 60.109 55.0 0.00 0.00 0.00 3.35 F
775 776 0.248134 CTCTGCTCTACGTACGTGCC 60.248 60.0 30.25 15.21 0.00 5.01 F
844 845 0.319469 CCACCACCATGGAAAAACGC 60.319 55.0 21.47 0.00 43.02 4.84 F
1607 1919 0.034186 TCAATTGCGGATTGGCCTCT 60.034 50.0 3.32 0.00 44.30 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1900 0.034186 AGAGGCCAATCCGCAATTGA 60.034 50.0 10.34 0.00 46.54 2.57 R
1591 1903 0.323725 ACAAGAGGCCAATCCGCAAT 60.324 50.0 5.01 0.00 40.77 3.56 R
2173 2587 1.826385 CCAGTAAGAAGGTTGCTGGG 58.174 55.0 12.59 0.00 44.99 4.45 R
3118 3533 0.456221 CGGACACTCTTATGAGCCGT 59.544 55.0 12.24 7.63 43.85 5.68 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
148 149 5.601313 TCAGAGGTATAATTTTAGCTCCCGT 59.399 40.000 23.20 9.38 44.20 5.28
165 166 1.730593 CGTCGCAATCGGTCTCGTTC 61.731 60.000 0.00 0.00 37.69 3.95
166 167 1.513373 TCGCAATCGGTCTCGTTCG 60.513 57.895 0.00 0.00 37.69 3.95
195 196 3.505464 ACGGTCGAACTTAGATCTTGG 57.495 47.619 0.00 0.00 0.00 3.61
196 197 3.087031 ACGGTCGAACTTAGATCTTGGA 58.913 45.455 0.00 0.00 0.00 3.53
202 203 3.242123 CGAACTTAGATCTTGGAAAGCGC 60.242 47.826 0.00 0.00 45.70 5.92
218 219 2.399611 GCGGACGCACTACATTGC 59.600 61.111 12.31 0.00 41.49 3.56
278 279 1.243902 TTGGATTGTCCGTCTTTGCC 58.756 50.000 0.00 0.00 40.17 4.52
282 283 2.296190 GGATTGTCCGTCTTTGCCTTTT 59.704 45.455 0.00 0.00 0.00 2.27
338 339 3.291584 TGTTTGGTTGTGTGCATCCTAA 58.708 40.909 0.00 0.00 35.89 2.69
343 344 5.833406 TGGTTGTGTGCATCCTAATTATG 57.167 39.130 0.00 0.00 35.89 1.90
370 371 1.835531 CCGGGTGGGTACTCTAAATGT 59.164 52.381 0.00 0.00 0.00 2.71
387 388 8.039603 TCTAAATGTTTTGTATCGCTTGATGT 57.960 30.769 0.00 0.00 33.40 3.06
396 397 8.446489 TTTGTATCGCTTGATGTTACATTTTG 57.554 30.769 0.00 0.00 33.40 2.44
415 416 9.474313 ACATTTTGAGATAATAAAAGCACCCTA 57.526 29.630 0.00 0.00 0.00 3.53
420 421 9.653287 TTGAGATAATAAAAGCACCCTATATCG 57.347 33.333 0.00 0.00 0.00 2.92
509 510 3.083848 AACGACCTCCACACACGCA 62.084 57.895 0.00 0.00 0.00 5.24
510 511 2.048222 CGACCTCCACACACGCAT 60.048 61.111 0.00 0.00 0.00 4.73
712 713 3.490759 GTCTGCGCCCACACATCG 61.491 66.667 4.18 0.00 0.00 3.84
718 719 3.520862 GCCCACACATCGGCCATG 61.521 66.667 2.24 8.60 39.39 3.66
719 720 2.271821 CCCACACATCGGCCATGA 59.728 61.111 18.41 2.61 36.21 3.07
720 721 1.378382 CCCACACATCGGCCATGAA 60.378 57.895 18.41 0.00 36.21 2.57
721 722 0.752743 CCCACACATCGGCCATGAAT 60.753 55.000 18.41 6.27 36.21 2.57
722 723 1.476652 CCCACACATCGGCCATGAATA 60.477 52.381 18.41 0.00 36.21 1.75
723 724 2.296792 CCACACATCGGCCATGAATAA 58.703 47.619 18.41 0.00 36.21 1.40
724 725 2.687425 CCACACATCGGCCATGAATAAA 59.313 45.455 18.41 0.00 36.21 1.40
725 726 3.489059 CCACACATCGGCCATGAATAAAC 60.489 47.826 18.41 0.00 36.21 2.01
726 727 2.354510 ACACATCGGCCATGAATAAACG 59.645 45.455 18.41 0.00 36.21 3.60
727 728 2.611751 CACATCGGCCATGAATAAACGA 59.388 45.455 18.41 0.04 36.21 3.85
728 729 2.872245 ACATCGGCCATGAATAAACGAG 59.128 45.455 18.41 0.00 36.21 4.18
729 730 2.684001 TCGGCCATGAATAAACGAGT 57.316 45.000 2.24 0.00 0.00 4.18
730 731 3.804786 TCGGCCATGAATAAACGAGTA 57.195 42.857 2.24 0.00 0.00 2.59
731 732 3.450578 TCGGCCATGAATAAACGAGTAC 58.549 45.455 2.24 0.00 0.00 2.73
732 733 2.542595 CGGCCATGAATAAACGAGTACC 59.457 50.000 2.24 0.00 0.00 3.34
733 734 2.876550 GGCCATGAATAAACGAGTACCC 59.123 50.000 0.00 0.00 0.00 3.69
734 735 3.433173 GGCCATGAATAAACGAGTACCCT 60.433 47.826 0.00 0.00 0.00 4.34
735 736 3.808174 GCCATGAATAAACGAGTACCCTC 59.192 47.826 0.00 0.00 0.00 4.30
736 737 4.682320 GCCATGAATAAACGAGTACCCTCA 60.682 45.833 0.00 0.00 37.59 3.86
737 738 5.611374 CCATGAATAAACGAGTACCCTCAT 58.389 41.667 0.00 0.00 37.59 2.90
738 739 5.696724 CCATGAATAAACGAGTACCCTCATC 59.303 44.000 0.00 0.00 37.59 2.92
739 740 5.272283 TGAATAAACGAGTACCCTCATCC 57.728 43.478 0.00 0.00 37.59 3.51
740 741 4.712829 TGAATAAACGAGTACCCTCATCCA 59.287 41.667 0.00 0.00 37.59 3.41
741 742 5.365605 TGAATAAACGAGTACCCTCATCCAT 59.634 40.000 0.00 0.00 37.59 3.41
742 743 3.821421 AAACGAGTACCCTCATCCATC 57.179 47.619 0.00 0.00 37.59 3.51
743 744 1.705873 ACGAGTACCCTCATCCATCC 58.294 55.000 0.00 0.00 37.59 3.51
744 745 1.063190 ACGAGTACCCTCATCCATCCA 60.063 52.381 0.00 0.00 37.59 3.41
745 746 1.341531 CGAGTACCCTCATCCATCCAC 59.658 57.143 0.00 0.00 37.59 4.02
746 747 2.398588 GAGTACCCTCATCCATCCACA 58.601 52.381 0.00 0.00 37.67 4.17
747 748 2.103263 GAGTACCCTCATCCATCCACAC 59.897 54.545 0.00 0.00 37.67 3.82
748 749 1.837439 GTACCCTCATCCATCCACACA 59.163 52.381 0.00 0.00 0.00 3.72
749 750 1.600058 ACCCTCATCCATCCACACAT 58.400 50.000 0.00 0.00 0.00 3.21
750 751 2.775418 ACCCTCATCCATCCACACATA 58.225 47.619 0.00 0.00 0.00 2.29
751 752 2.439507 ACCCTCATCCATCCACACATAC 59.560 50.000 0.00 0.00 0.00 2.39
752 753 2.548707 CCCTCATCCATCCACACATACG 60.549 54.545 0.00 0.00 0.00 3.06
753 754 2.138320 CTCATCCATCCACACATACGC 58.862 52.381 0.00 0.00 0.00 4.42
754 755 1.484240 TCATCCATCCACACATACGCA 59.516 47.619 0.00 0.00 0.00 5.24
755 756 1.869132 CATCCATCCACACATACGCAG 59.131 52.381 0.00 0.00 0.00 5.18
756 757 0.461870 TCCATCCACACATACGCAGC 60.462 55.000 0.00 0.00 0.00 5.25
757 758 0.462581 CCATCCACACATACGCAGCT 60.463 55.000 0.00 0.00 0.00 4.24
758 759 0.933097 CATCCACACATACGCAGCTC 59.067 55.000 0.00 0.00 0.00 4.09
759 760 0.826715 ATCCACACATACGCAGCTCT 59.173 50.000 0.00 0.00 0.00 4.09
760 761 0.108662 TCCACACATACGCAGCTCTG 60.109 55.000 0.00 0.00 0.00 3.35
771 772 3.518017 CAGCTCTGCTCTACGTACG 57.482 57.895 15.01 15.01 36.40 3.67
772 773 0.727970 CAGCTCTGCTCTACGTACGT 59.272 55.000 25.98 25.98 36.40 3.57
773 774 0.727970 AGCTCTGCTCTACGTACGTG 59.272 55.000 30.25 19.22 30.62 4.49
774 775 0.862283 GCTCTGCTCTACGTACGTGC 60.862 60.000 30.25 24.11 0.00 5.34
775 776 0.248134 CTCTGCTCTACGTACGTGCC 60.248 60.000 30.25 15.21 0.00 5.01
776 777 1.226603 CTGCTCTACGTACGTGCCC 60.227 63.158 30.25 15.54 0.00 5.36
777 778 1.929806 CTGCTCTACGTACGTGCCCA 61.930 60.000 30.25 18.85 0.00 5.36
778 779 1.317431 TGCTCTACGTACGTGCCCAT 61.317 55.000 30.25 5.02 0.00 4.00
779 780 0.870307 GCTCTACGTACGTGCCCATG 60.870 60.000 30.25 14.46 0.00 3.66
780 781 0.870307 CTCTACGTACGTGCCCATGC 60.870 60.000 30.25 0.00 38.26 4.06
791 792 2.388310 TGCCCATGCATTTTCATGTG 57.612 45.000 0.00 0.00 44.23 3.21
792 793 1.011333 GCCCATGCATTTTCATGTGC 58.989 50.000 0.00 0.00 41.60 4.57
797 798 2.151881 TGCATTTTCATGTGCACCAC 57.848 45.000 15.69 0.00 45.60 4.16
807 808 2.677971 GTGCACCACACTATAGCCG 58.322 57.895 5.22 0.00 46.41 5.52
808 809 1.153449 TGCACCACACTATAGCCGC 60.153 57.895 0.00 0.00 0.00 6.53
809 810 1.887707 GCACCACACTATAGCCGCC 60.888 63.158 0.00 0.00 0.00 6.13
810 811 1.520192 CACCACACTATAGCCGCCA 59.480 57.895 0.00 0.00 0.00 5.69
811 812 0.810031 CACCACACTATAGCCGCCAC 60.810 60.000 0.00 0.00 0.00 5.01
812 813 1.227556 CCACACTATAGCCGCCACC 60.228 63.158 0.00 0.00 0.00 4.61
813 814 1.520192 CACACTATAGCCGCCACCA 59.480 57.895 0.00 0.00 0.00 4.17
814 815 0.810031 CACACTATAGCCGCCACCAC 60.810 60.000 0.00 0.00 0.00 4.16
815 816 1.227556 CACTATAGCCGCCACCACC 60.228 63.158 0.00 0.00 0.00 4.61
816 817 2.426023 CTATAGCCGCCACCACCC 59.574 66.667 0.00 0.00 0.00 4.61
817 818 3.165685 TATAGCCGCCACCACCCC 61.166 66.667 0.00 0.00 0.00 4.95
822 823 3.407967 CCGCCACCACCCCACTAT 61.408 66.667 0.00 0.00 0.00 2.12
823 824 2.189521 CGCCACCACCCCACTATC 59.810 66.667 0.00 0.00 0.00 2.08
824 825 2.189521 GCCACCACCCCACTATCG 59.810 66.667 0.00 0.00 0.00 2.92
825 826 2.189521 CCACCACCCCACTATCGC 59.810 66.667 0.00 0.00 0.00 4.58
826 827 2.189521 CACCACCCCACTATCGCC 59.810 66.667 0.00 0.00 0.00 5.54
827 828 2.285069 ACCACCCCACTATCGCCA 60.285 61.111 0.00 0.00 0.00 5.69
828 829 2.189521 CCACCCCACTATCGCCAC 59.810 66.667 0.00 0.00 0.00 5.01
829 830 2.189521 CACCCCACTATCGCCACC 59.810 66.667 0.00 0.00 0.00 4.61
830 831 2.285069 ACCCCACTATCGCCACCA 60.285 61.111 0.00 0.00 0.00 4.17
844 845 0.319469 CCACCACCATGGAAAAACGC 60.319 55.000 21.47 0.00 43.02 4.84
947 1085 2.747135 CGTTGCCCCGGGAAAATATACT 60.747 50.000 26.32 0.00 0.00 2.12
949 1087 1.071071 TGCCCCGGGAAAATATACTCG 59.929 52.381 26.32 0.30 0.00 4.18
952 1090 2.564062 CCCCGGGAAAATATACTCGCTA 59.436 50.000 26.32 0.00 0.00 4.26
955 1093 4.159879 CCCGGGAAAATATACTCGCTATCT 59.840 45.833 18.48 0.00 0.00 1.98
960 1099 7.036829 GGGAAAATATACTCGCTATCTCTTCC 58.963 42.308 0.00 0.00 0.00 3.46
1072 1238 4.459089 GCTTCTTCCTCGCCGCCT 62.459 66.667 0.00 0.00 0.00 5.52
1299 1471 3.071602 GCCAGATAAGTCCATCCTTGCTA 59.928 47.826 0.00 0.00 0.00 3.49
1422 1594 2.965147 TCTTGATCTATCCGGCATGTCA 59.035 45.455 0.00 0.00 0.00 3.58
1491 1735 6.617784 TGGAATACCTTGACCTATCCAACATA 59.382 38.462 0.00 0.00 37.04 2.29
1492 1736 6.935208 GGAATACCTTGACCTATCCAACATAC 59.065 42.308 0.00 0.00 0.00 2.39
1493 1737 7.202102 GGAATACCTTGACCTATCCAACATACT 60.202 40.741 0.00 0.00 0.00 2.12
1573 1885 5.255687 TGTTGGTGCATCTTGATATGAGTT 58.744 37.500 0.00 0.00 0.00 3.01
1574 1886 5.124297 TGTTGGTGCATCTTGATATGAGTTG 59.876 40.000 0.00 0.00 0.00 3.16
1575 1887 4.201657 TGGTGCATCTTGATATGAGTTGG 58.798 43.478 0.00 0.00 0.00 3.77
1576 1888 3.567164 GGTGCATCTTGATATGAGTTGGG 59.433 47.826 0.00 0.00 0.00 4.12
1577 1889 4.202441 GTGCATCTTGATATGAGTTGGGT 58.798 43.478 0.00 0.00 0.00 4.51
1578 1890 4.274459 GTGCATCTTGATATGAGTTGGGTC 59.726 45.833 0.00 0.00 0.00 4.46
1579 1891 4.080413 TGCATCTTGATATGAGTTGGGTCA 60.080 41.667 0.00 0.00 0.00 4.02
1580 1892 4.883585 GCATCTTGATATGAGTTGGGTCAA 59.116 41.667 0.00 0.00 0.00 3.18
1581 1893 5.533903 GCATCTTGATATGAGTTGGGTCAAT 59.466 40.000 0.00 0.00 0.00 2.57
1582 1894 6.293845 GCATCTTGATATGAGTTGGGTCAATC 60.294 42.308 0.00 0.00 0.00 2.67
1583 1895 6.566079 TCTTGATATGAGTTGGGTCAATCT 57.434 37.500 0.00 0.00 0.00 2.40
1584 1896 6.586344 TCTTGATATGAGTTGGGTCAATCTC 58.414 40.000 0.00 0.00 0.00 2.75
1585 1897 5.955961 TGATATGAGTTGGGTCAATCTCA 57.044 39.130 11.92 11.92 36.64 3.27
1586 1898 5.922053 TGATATGAGTTGGGTCAATCTCAG 58.078 41.667 13.68 0.00 36.15 3.35
1587 1899 2.479566 TGAGTTGGGTCAATCTCAGC 57.520 50.000 8.01 0.00 31.78 4.26
1588 1900 1.980765 TGAGTTGGGTCAATCTCAGCT 59.019 47.619 8.01 0.00 40.75 4.24
1589 1901 2.626840 GAGTTGGGTCAATCTCAGCTC 58.373 52.381 0.00 0.00 44.94 4.09
1590 1902 1.980765 AGTTGGGTCAATCTCAGCTCA 59.019 47.619 0.00 0.00 32.65 4.26
1591 1903 2.373169 AGTTGGGTCAATCTCAGCTCAA 59.627 45.455 0.00 0.00 32.65 3.02
1592 1904 3.009916 AGTTGGGTCAATCTCAGCTCAAT 59.990 43.478 0.00 0.00 32.65 2.57
1593 1905 3.726557 TGGGTCAATCTCAGCTCAATT 57.273 42.857 0.00 0.00 0.00 2.32
1594 1906 3.349927 TGGGTCAATCTCAGCTCAATTG 58.650 45.455 0.00 0.00 0.00 2.32
1595 1907 2.098770 GGGTCAATCTCAGCTCAATTGC 59.901 50.000 0.00 0.00 31.84 3.56
1596 1908 2.223203 GGTCAATCTCAGCTCAATTGCG 60.223 50.000 0.00 0.00 38.13 4.85
1597 1909 2.011947 TCAATCTCAGCTCAATTGCGG 58.988 47.619 0.00 0.00 38.13 5.69
1598 1910 2.011947 CAATCTCAGCTCAATTGCGGA 58.988 47.619 0.00 0.00 38.13 5.54
1599 1911 2.617308 CAATCTCAGCTCAATTGCGGAT 59.383 45.455 0.00 0.00 36.65 4.18
1600 1912 2.408271 TCTCAGCTCAATTGCGGATT 57.592 45.000 0.00 0.00 36.65 3.01
1601 1913 2.011947 TCTCAGCTCAATTGCGGATTG 58.988 47.619 0.00 6.34 45.31 2.67
1602 1914 1.065102 CTCAGCTCAATTGCGGATTGG 59.935 52.381 0.00 5.29 44.30 3.16
1603 1915 0.526954 CAGCTCAATTGCGGATTGGC 60.527 55.000 0.00 12.46 44.30 4.52
1604 1916 1.227060 GCTCAATTGCGGATTGGCC 60.227 57.895 0.00 0.00 44.30 5.36
1605 1917 1.669999 GCTCAATTGCGGATTGGCCT 61.670 55.000 3.32 0.00 44.30 5.19
1606 1918 0.383231 CTCAATTGCGGATTGGCCTC 59.617 55.000 3.32 0.00 44.30 4.70
1607 1919 0.034186 TCAATTGCGGATTGGCCTCT 60.034 50.000 3.32 0.00 44.30 3.69
1608 1920 0.819582 CAATTGCGGATTGGCCTCTT 59.180 50.000 3.32 0.00 41.19 2.85
1609 1921 0.819582 AATTGCGGATTGGCCTCTTG 59.180 50.000 3.32 0.00 0.00 3.02
1610 1922 0.323725 ATTGCGGATTGGCCTCTTGT 60.324 50.000 3.32 0.00 0.00 3.16
1611 1923 0.539438 TTGCGGATTGGCCTCTTGTT 60.539 50.000 3.32 0.00 0.00 2.83
1612 1924 0.326595 TGCGGATTGGCCTCTTGTTA 59.673 50.000 3.32 0.00 0.00 2.41
1613 1925 1.064758 TGCGGATTGGCCTCTTGTTAT 60.065 47.619 3.32 0.00 0.00 1.89
1693 2005 1.909302 ACCAATCCCTCACACACCTAG 59.091 52.381 0.00 0.00 0.00 3.02
2139 2481 1.135333 GGAGCTATACCGCTAGGCATC 59.865 57.143 0.00 0.00 41.08 3.91
2168 2582 6.426646 TCTGTCTTCTTTAGAAAGCCTTCT 57.573 37.500 2.55 2.55 44.37 2.85
2173 2587 7.442666 TGTCTTCTTTAGAAAGCCTTCTTCTTC 59.557 37.037 2.23 0.00 42.17 2.87
2328 2742 7.519032 TCTTTCCAATAACAAACTTAGTGGG 57.481 36.000 6.71 0.00 39.73 4.61
2590 3004 7.668469 TGAGTTGTACTACATTAGAAGTCCTCA 59.332 37.037 10.09 0.00 0.00 3.86
2707 3121 2.693069 GGCATGTCCCATCTAAGATCG 58.307 52.381 0.00 0.00 0.00 3.69
3090 3505 3.836562 TCGTTCCTTTATATAGGGAGGCC 59.163 47.826 9.12 0.00 35.90 5.19
3118 3533 1.379176 CAGCTCTCAGAGTCCCGGA 60.379 63.158 0.73 0.00 31.39 5.14
3168 3583 5.105146 ACTCTCAACTATCCTTGCCTTACAG 60.105 44.000 0.00 0.00 0.00 2.74
3180 3595 5.869888 CCTTGCCTTACAGTACAAGTTCTAG 59.130 44.000 0.00 0.00 38.24 2.43
3206 3621 7.119262 GCATAATAATGATTACAACTACGGGCT 59.881 37.037 0.00 0.00 34.84 5.19
3447 3867 2.202756 GGCGTGACGTCATCCTCC 60.203 66.667 23.12 15.71 0.00 4.30
3676 4100 0.109689 CTTCGTCTTCTTCCTCGCGT 60.110 55.000 5.77 0.00 0.00 6.01
3678 4102 1.863880 CGTCTTCTTCCTCGCGTCG 60.864 63.158 5.77 0.00 0.00 5.12
3784 4208 1.009900 CCAGAGATACGCGACGACC 60.010 63.158 15.93 0.00 0.00 4.79
3836 4260 0.833287 TGCCCTGCTAGAACAGATCC 59.167 55.000 0.00 0.00 40.25 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.774894 AAGCTACCGGGCAACTCCAA 61.775 55.000 6.32 0.00 36.21 3.53
2 3 1.774894 AAAGCTACCGGGCAACTCCA 61.775 55.000 6.32 0.00 36.21 3.86
3 4 0.608308 AAAAGCTACCGGGCAACTCC 60.608 55.000 6.32 0.00 34.17 3.85
51 52 2.695055 CGCGGACGCACTACATTG 59.305 61.111 17.35 0.00 42.06 2.82
148 149 1.513373 CGAACGAGACCGATTGCGA 60.513 57.895 0.00 0.00 40.82 5.10
165 166 7.264448 TCTAAGTTCGACCGTAAATTTAACG 57.736 36.000 0.00 6.38 40.01 3.18
166 167 9.080915 AGATCTAAGTTCGACCGTAAATTTAAC 57.919 33.333 0.00 0.00 0.00 2.01
218 219 7.394816 ACAATATAAATACTCCCTCCATTCCG 58.605 38.462 0.00 0.00 0.00 4.30
315 316 3.495331 AGGATGCACACAACCAAACATA 58.505 40.909 0.00 0.00 41.12 2.29
316 317 2.318908 AGGATGCACACAACCAAACAT 58.681 42.857 0.00 0.00 41.12 2.71
338 339 1.149174 CACCCGGCCTCTGCATAAT 59.851 57.895 0.00 0.00 40.13 1.28
370 371 8.910666 CAAAATGTAACATCAAGCGATACAAAA 58.089 29.630 0.00 0.00 0.00 2.44
396 397 9.871238 TTCGATATAGGGTGCTTTTATTATCTC 57.129 33.333 0.00 0.00 0.00 2.75
428 429 5.482163 TCAAGGATCACTGTCACACATAA 57.518 39.130 0.00 0.00 0.00 1.90
429 430 5.422145 CATCAAGGATCACTGTCACACATA 58.578 41.667 0.00 0.00 0.00 2.29
433 434 2.038820 TGCATCAAGGATCACTGTCACA 59.961 45.455 0.00 0.00 0.00 3.58
444 445 2.236146 ACGTACAGGATTGCATCAAGGA 59.764 45.455 0.00 0.00 0.00 3.36
712 713 2.876550 GGGTACTCGTTTATTCATGGCC 59.123 50.000 0.00 0.00 0.00 5.36
726 727 2.103263 GTGTGGATGGATGAGGGTACTC 59.897 54.545 0.00 0.00 44.23 2.59
727 728 2.119495 GTGTGGATGGATGAGGGTACT 58.881 52.381 0.00 0.00 0.00 2.73
728 729 1.837439 TGTGTGGATGGATGAGGGTAC 59.163 52.381 0.00 0.00 0.00 3.34
729 730 2.262266 TGTGTGGATGGATGAGGGTA 57.738 50.000 0.00 0.00 0.00 3.69
730 731 1.600058 ATGTGTGGATGGATGAGGGT 58.400 50.000 0.00 0.00 0.00 4.34
731 732 2.548707 CGTATGTGTGGATGGATGAGGG 60.549 54.545 0.00 0.00 0.00 4.30
732 733 2.759191 CGTATGTGTGGATGGATGAGG 58.241 52.381 0.00 0.00 0.00 3.86
733 734 2.138320 GCGTATGTGTGGATGGATGAG 58.862 52.381 0.00 0.00 0.00 2.90
734 735 1.484240 TGCGTATGTGTGGATGGATGA 59.516 47.619 0.00 0.00 0.00 2.92
735 736 1.869132 CTGCGTATGTGTGGATGGATG 59.131 52.381 0.00 0.00 0.00 3.51
736 737 1.811558 GCTGCGTATGTGTGGATGGAT 60.812 52.381 0.00 0.00 0.00 3.41
737 738 0.461870 GCTGCGTATGTGTGGATGGA 60.462 55.000 0.00 0.00 0.00 3.41
738 739 0.462581 AGCTGCGTATGTGTGGATGG 60.463 55.000 0.00 0.00 0.00 3.51
739 740 0.933097 GAGCTGCGTATGTGTGGATG 59.067 55.000 0.00 0.00 0.00 3.51
740 741 0.826715 AGAGCTGCGTATGTGTGGAT 59.173 50.000 0.00 0.00 0.00 3.41
741 742 0.108662 CAGAGCTGCGTATGTGTGGA 60.109 55.000 0.00 0.00 0.00 4.02
742 743 2.377004 CAGAGCTGCGTATGTGTGG 58.623 57.895 0.00 0.00 0.00 4.17
753 754 0.727970 ACGTACGTAGAGCAGAGCTG 59.272 55.000 21.41 0.00 39.88 4.24
754 755 0.727970 CACGTACGTAGAGCAGAGCT 59.272 55.000 22.34 0.00 43.88 4.09
755 756 0.862283 GCACGTACGTAGAGCAGAGC 60.862 60.000 22.34 13.78 0.00 4.09
756 757 0.248134 GGCACGTACGTAGAGCAGAG 60.248 60.000 22.34 7.18 0.00 3.35
757 758 1.651240 GGGCACGTACGTAGAGCAGA 61.651 60.000 22.34 0.00 0.00 4.26
758 759 1.226603 GGGCACGTACGTAGAGCAG 60.227 63.158 22.34 8.75 0.00 4.24
759 760 1.317431 ATGGGCACGTACGTAGAGCA 61.317 55.000 22.34 6.16 0.00 4.26
760 761 0.870307 CATGGGCACGTACGTAGAGC 60.870 60.000 22.34 19.81 0.00 4.09
761 762 0.870307 GCATGGGCACGTACGTAGAG 60.870 60.000 22.34 10.34 40.72 2.43
762 763 1.140161 GCATGGGCACGTACGTAGA 59.860 57.895 22.34 5.45 40.72 2.59
763 764 3.700961 GCATGGGCACGTACGTAG 58.299 61.111 22.34 16.04 40.72 3.51
779 780 1.794116 GTGTGGTGCACATGAAAATGC 59.206 47.619 20.43 0.00 46.32 3.56
790 791 1.153449 GCGGCTATAGTGTGGTGCA 60.153 57.895 0.84 0.00 0.00 4.57
791 792 1.887707 GGCGGCTATAGTGTGGTGC 60.888 63.158 0.00 0.00 0.00 5.01
792 793 0.810031 GTGGCGGCTATAGTGTGGTG 60.810 60.000 11.43 0.00 0.00 4.17
793 794 1.520666 GTGGCGGCTATAGTGTGGT 59.479 57.895 11.43 0.00 0.00 4.16
794 795 1.227556 GGTGGCGGCTATAGTGTGG 60.228 63.158 11.43 0.00 0.00 4.17
795 796 0.810031 GTGGTGGCGGCTATAGTGTG 60.810 60.000 11.43 0.00 0.00 3.82
796 797 1.520666 GTGGTGGCGGCTATAGTGT 59.479 57.895 11.43 0.00 0.00 3.55
797 798 1.227556 GGTGGTGGCGGCTATAGTG 60.228 63.158 11.43 0.00 0.00 2.74
798 799 2.440817 GGGTGGTGGCGGCTATAGT 61.441 63.158 11.43 0.00 0.00 2.12
799 800 2.426023 GGGTGGTGGCGGCTATAG 59.574 66.667 11.43 0.00 0.00 1.31
800 801 3.165685 GGGGTGGTGGCGGCTATA 61.166 66.667 11.43 0.00 0.00 1.31
805 806 3.400599 GATAGTGGGGTGGTGGCGG 62.401 68.421 0.00 0.00 0.00 6.13
806 807 2.189521 GATAGTGGGGTGGTGGCG 59.810 66.667 0.00 0.00 0.00 5.69
807 808 2.189521 CGATAGTGGGGTGGTGGC 59.810 66.667 0.00 0.00 0.00 5.01
808 809 2.189521 GCGATAGTGGGGTGGTGG 59.810 66.667 0.00 0.00 39.35 4.61
809 810 2.189521 GGCGATAGTGGGGTGGTG 59.810 66.667 0.00 0.00 39.35 4.17
810 811 2.285069 TGGCGATAGTGGGGTGGT 60.285 61.111 0.00 0.00 39.35 4.16
811 812 2.189521 GTGGCGATAGTGGGGTGG 59.810 66.667 0.00 0.00 39.35 4.61
812 813 2.189521 GGTGGCGATAGTGGGGTG 59.810 66.667 0.00 0.00 39.35 4.61
813 814 2.285069 TGGTGGCGATAGTGGGGT 60.285 61.111 0.00 0.00 39.35 4.95
814 815 2.189521 GTGGTGGCGATAGTGGGG 59.810 66.667 0.00 0.00 39.35 4.96
815 816 1.983119 ATGGTGGTGGCGATAGTGGG 61.983 60.000 0.00 0.00 39.35 4.61
816 817 0.815213 CATGGTGGTGGCGATAGTGG 60.815 60.000 0.00 0.00 39.35 4.00
817 818 0.815213 CCATGGTGGTGGCGATAGTG 60.815 60.000 2.57 0.00 32.69 2.74
818 819 0.980754 TCCATGGTGGTGGCGATAGT 60.981 55.000 12.58 0.00 39.03 2.12
819 820 0.180171 TTCCATGGTGGTGGCGATAG 59.820 55.000 12.58 0.00 39.03 2.08
820 821 0.621082 TTTCCATGGTGGTGGCGATA 59.379 50.000 12.58 0.00 39.03 2.92
821 822 0.251564 TTTTCCATGGTGGTGGCGAT 60.252 50.000 12.58 0.00 39.03 4.58
822 823 0.468214 TTTTTCCATGGTGGTGGCGA 60.468 50.000 12.58 0.00 39.03 5.54
823 824 0.319469 GTTTTTCCATGGTGGTGGCG 60.319 55.000 12.58 0.00 39.03 5.69
824 825 0.319469 CGTTTTTCCATGGTGGTGGC 60.319 55.000 12.58 0.00 39.03 5.01
825 826 0.319469 GCGTTTTTCCATGGTGGTGG 60.319 55.000 12.58 0.00 39.03 4.61
826 827 0.662970 CGCGTTTTTCCATGGTGGTG 60.663 55.000 12.58 0.00 39.03 4.17
827 828 1.104577 ACGCGTTTTTCCATGGTGGT 61.105 50.000 12.58 0.00 39.03 4.16
828 829 0.875728 TACGCGTTTTTCCATGGTGG 59.124 50.000 20.78 0.00 39.43 4.61
829 830 1.400500 GGTACGCGTTTTTCCATGGTG 60.400 52.381 20.78 0.00 0.00 4.17
830 831 0.876399 GGTACGCGTTTTTCCATGGT 59.124 50.000 20.78 0.00 0.00 3.55
844 845 1.536072 CGTGTGGATGGATGAGGTACG 60.536 57.143 0.00 0.00 0.00 3.67
906 1026 2.277084 GTCGGGTGGTGCACTTATAAG 58.723 52.381 17.98 11.05 34.40 1.73
932 1070 2.833631 AGCGAGTATATTTTCCCGGG 57.166 50.000 16.85 16.85 0.00 5.73
947 1085 2.231529 GGTGCTAGGAAGAGATAGCGA 58.768 52.381 0.00 0.00 45.97 4.93
949 1087 3.801983 GCTTGGTGCTAGGAAGAGATAGC 60.802 52.174 0.00 0.00 43.81 2.97
952 1090 2.191400 TGCTTGGTGCTAGGAAGAGAT 58.809 47.619 0.00 0.00 43.37 2.75
955 1093 1.271379 GGTTGCTTGGTGCTAGGAAGA 60.271 52.381 0.00 0.00 43.37 2.87
960 1099 1.009829 GATCGGTTGCTTGGTGCTAG 58.990 55.000 0.00 0.00 43.37 3.42
1072 1238 3.774528 CTGGAGCCTGCCTGCGTA 61.775 66.667 0.00 0.00 34.08 4.42
1299 1471 4.286032 AGGTACTCGAGATGCTCTAGAGAT 59.714 45.833 24.24 13.32 45.38 2.75
1422 1594 1.485895 GGAGGCAAGAGAGCAGAGAAT 59.514 52.381 0.00 0.00 35.83 2.40
1491 1735 8.561738 AGACAATCCGTTTATTGAAATGTAGT 57.438 30.769 8.77 0.00 38.84 2.73
1573 1885 3.349927 CAATTGAGCTGAGATTGACCCA 58.650 45.455 0.00 0.00 33.67 4.51
1574 1886 2.098770 GCAATTGAGCTGAGATTGACCC 59.901 50.000 10.34 0.00 33.67 4.46
1575 1887 2.223203 CGCAATTGAGCTGAGATTGACC 60.223 50.000 10.34 1.42 33.67 4.02
1576 1888 2.223203 CCGCAATTGAGCTGAGATTGAC 60.223 50.000 10.34 7.22 33.67 3.18
1577 1889 2.011947 CCGCAATTGAGCTGAGATTGA 58.988 47.619 10.34 0.00 33.67 2.57
1578 1890 2.011947 TCCGCAATTGAGCTGAGATTG 58.988 47.619 10.34 0.00 34.67 2.67
1579 1891 2.408271 TCCGCAATTGAGCTGAGATT 57.592 45.000 10.34 0.00 0.00 2.40
1580 1892 2.617308 CAATCCGCAATTGAGCTGAGAT 59.383 45.455 10.34 1.24 46.54 2.75
1581 1893 2.011947 CAATCCGCAATTGAGCTGAGA 58.988 47.619 10.34 0.00 46.54 3.27
1582 1894 1.065102 CCAATCCGCAATTGAGCTGAG 59.935 52.381 10.34 0.00 46.54 3.35
1583 1895 1.097232 CCAATCCGCAATTGAGCTGA 58.903 50.000 10.34 0.00 46.54 4.26
1584 1896 0.526954 GCCAATCCGCAATTGAGCTG 60.527 55.000 10.34 3.62 46.54 4.24
1585 1897 1.669999 GGCCAATCCGCAATTGAGCT 61.670 55.000 10.34 0.00 46.54 4.09
1586 1898 1.227060 GGCCAATCCGCAATTGAGC 60.227 57.895 10.34 10.42 46.54 4.26
1587 1899 0.383231 GAGGCCAATCCGCAATTGAG 59.617 55.000 10.34 5.80 46.54 3.02
1588 1900 0.034186 AGAGGCCAATCCGCAATTGA 60.034 50.000 10.34 0.00 46.54 2.57
1589 1901 0.819582 AAGAGGCCAATCCGCAATTG 59.180 50.000 5.01 0.00 43.77 2.32
1590 1902 0.819582 CAAGAGGCCAATCCGCAATT 59.180 50.000 5.01 0.00 40.77 2.32
1591 1903 0.323725 ACAAGAGGCCAATCCGCAAT 60.324 50.000 5.01 0.00 40.77 3.56
1592 1904 0.539438 AACAAGAGGCCAATCCGCAA 60.539 50.000 5.01 0.00 40.77 4.85
1593 1905 0.326595 TAACAAGAGGCCAATCCGCA 59.673 50.000 5.01 0.00 40.77 5.69
1594 1906 1.334869 CATAACAAGAGGCCAATCCGC 59.665 52.381 5.01 0.00 40.77 5.54
1595 1907 2.917933 TCATAACAAGAGGCCAATCCG 58.082 47.619 5.01 0.00 40.77 4.18
1596 1908 6.772716 TCTTATTCATAACAAGAGGCCAATCC 59.227 38.462 5.01 0.00 0.00 3.01
1597 1909 7.807977 TCTTATTCATAACAAGAGGCCAATC 57.192 36.000 5.01 0.00 0.00 2.67
1598 1910 8.773033 AATCTTATTCATAACAAGAGGCCAAT 57.227 30.769 5.01 0.00 32.16 3.16
1599 1911 7.285401 GGAATCTTATTCATAACAAGAGGCCAA 59.715 37.037 5.01 0.00 32.16 4.52
1600 1912 6.772716 GGAATCTTATTCATAACAAGAGGCCA 59.227 38.462 5.01 0.00 32.16 5.36
1601 1913 6.772716 TGGAATCTTATTCATAACAAGAGGCC 59.227 38.462 0.00 0.00 32.16 5.19
1602 1914 7.807977 TGGAATCTTATTCATAACAAGAGGC 57.192 36.000 2.36 0.00 32.16 4.70
1693 2005 5.216614 AGGAAGTGAAGAGTTGTTAGGTC 57.783 43.478 0.00 0.00 0.00 3.85
2139 2481 6.093357 GGCTTTCTAAAGAAGACAGATTCCTG 59.907 42.308 6.64 0.00 41.02 3.86
2168 2582 3.394606 AGTAAGAAGGTTGCTGGGAAGAA 59.605 43.478 0.00 0.00 0.00 2.52
2173 2587 1.826385 CCAGTAAGAAGGTTGCTGGG 58.174 55.000 12.59 0.00 44.99 4.45
2328 2742 6.486941 AGTCTCTATCCCTAGTTGTATAGGC 58.513 44.000 0.00 0.00 41.00 3.93
2490 2904 4.980573 ACTGCAAACTAGTGTAATTCCCA 58.019 39.130 0.00 0.00 0.00 4.37
2590 3004 7.942341 TCCAGTAATATTGTTGTCAGAAAGGTT 59.058 33.333 0.00 0.00 0.00 3.50
3020 3435 3.496875 CTCATCGAGAGCCGGGCAG 62.497 68.421 23.09 9.53 37.59 4.85
3072 3487 3.438183 GTCGGCCTCCCTATATAAAGGA 58.562 50.000 0.00 5.63 39.15 3.36
3090 3505 2.811317 GAGAGCTGTTGGGCGTCG 60.811 66.667 0.00 0.00 37.29 5.12
3099 3514 1.680651 CCGGGACTCTGAGAGCTGT 60.681 63.158 12.44 0.00 32.04 4.40
3118 3533 0.456221 CGGACACTCTTATGAGCCGT 59.544 55.000 12.24 7.63 43.85 5.68
3180 3595 7.119262 AGCCCGTAGTTGTAATCATTATTATGC 59.881 37.037 0.00 0.00 30.42 3.14
3206 3621 4.504340 GCTAAGACCCGGATATGGCTTAAA 60.504 45.833 0.73 0.00 0.00 1.52
3678 4102 4.527583 CTCGGGCAGAGGAGCAGC 62.528 72.222 6.77 0.00 43.20 5.25
3686 4110 3.767806 CAGCAGAGCTCGGGCAGA 61.768 66.667 27.56 0.00 36.40 4.26
3784 4208 4.803426 GGCTGGTGAGTCGCGGAG 62.803 72.222 6.13 0.00 0.00 4.63
3836 4260 1.354506 CTACTCGAACCCTACCGCG 59.645 63.158 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.