Multiple sequence alignment - TraesCS3A01G282800

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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 TraesCS3A01G282800 chr3A 100.000 6182 0 0 1 6182 511079484 511073303 0.000000e+00 11417.0
1 TraesCS3A01G282800 chr3A 84.359 390 54 3 5800 6182 158163312 158163701 5.850000e-100 375.0
2 TraesCS3A01G282800 chr3D 95.163 4073 85 36 1427 5427 390669311 390665279 0.000000e+00 6327.0
3 TraesCS3A01G282800 chr3D 93.173 1245 58 11 106 1346 390670955 390669734 0.000000e+00 1803.0
4 TraesCS3A01G282800 chr3D 87.989 741 77 9 5444 6181 390665030 390664299 0.000000e+00 865.0
5 TraesCS3A01G282800 chr3D 81.262 507 73 9 5694 6182 529837890 529838392 2.090000e-104 390.0
6 TraesCS3A01G282800 chr3D 83.565 359 53 6 5830 6182 43564431 43564073 1.280000e-86 331.0
7 TraesCS3A01G282800 chr3D 90.476 42 3 1 1615 1656 292001078 292001038 3.000000e-03 54.7
8 TraesCS3A01G282800 chr3B 95.028 1770 37 25 1358 3083 508255682 508253920 0.000000e+00 2734.0
9 TraesCS3A01G282800 chr3B 95.068 1541 41 7 3122 4631 508253921 508252385 0.000000e+00 2392.0
10 TraesCS3A01G282800 chr3B 91.600 1250 69 16 106 1346 508256969 508255747 0.000000e+00 1694.0
11 TraesCS3A01G282800 chr3B 92.206 757 27 11 4656 5380 508252399 508251643 0.000000e+00 1042.0
12 TraesCS3A01G282800 chr3B 92.378 328 18 4 5344 5667 508251643 508251319 1.570000e-125 460.0
13 TraesCS3A01G282800 chr1D 79.161 739 109 37 2135 2849 439026835 439026118 2.610000e-128 470.0
14 TraesCS3A01G282800 chr1D 100.000 32 0 0 1616 1647 24929041 24929072 6.690000e-05 60.2
15 TraesCS3A01G282800 chr1D 94.444 36 2 0 1614 1649 382633931 382633896 8.660000e-04 56.5
16 TraesCS3A01G282800 chr1B 79.098 732 109 34 2140 2849 595182801 595182092 1.210000e-126 464.0
17 TraesCS3A01G282800 chr1B 79.699 532 66 22 5676 6182 334246995 334247509 4.590000e-91 346.0
18 TraesCS3A01G282800 chr1B 92.500 40 1 2 1614 1653 98724160 98724123 8.660000e-04 56.5
19 TraesCS3A01G282800 chr5D 82.008 528 73 13 5676 6182 62530578 62530052 4.430000e-116 429.0
20 TraesCS3A01G282800 chr2B 80.306 523 80 14 5681 6182 790374761 790374241 2.100000e-99 374.0
21 TraesCS3A01G282800 chr2B 87.500 48 3 3 1614 1658 551568383 551568336 1.100000e-02 52.8
22 TraesCS3A01G282800 chr2A 79.887 532 81 15 5676 6182 169336921 169337451 3.520000e-97 366.0
23 TraesCS3A01G282800 chr2A 88.235 68 7 1 2 68 565329530 565329597 5.140000e-11 80.5
24 TraesCS3A01G282800 chr5A 80.039 511 78 15 5694 6182 288258359 288257851 2.120000e-94 357.0
25 TraesCS3A01G282800 chr5A 96.970 33 0 1 1614 1646 397253496 397253527 3.000000e-03 54.7
26 TraesCS3A01G282800 chr7A 79.528 508 82 9 5695 6182 694104105 694104610 5.930000e-90 342.0
27 TraesCS3A01G282800 chr1A 81.517 422 64 11 2435 2849 535316581 535316167 9.930000e-88 335.0
28 TraesCS3A01G282800 chr1A 88.083 193 19 3 2140 2330 535316876 535316686 6.240000e-55 226.0
29 TraesCS3A01G282800 chr6D 89.720 107 11 0 5690 5796 412358534 412358428 3.010000e-28 137.0
30 TraesCS3A01G282800 chr4B 94.444 36 2 0 1614 1649 640002201 640002236 8.660000e-04 56.5


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 TraesCS3A01G282800 chr3A 511073303 511079484 6181 True 11417.000000 11417 100.000000 1 6182 1 chr3A.!!$R1 6181
1 TraesCS3A01G282800 chr3D 390664299 390670955 6656 True 2998.333333 6327 92.108333 106 6181 3 chr3D.!!$R3 6075
2 TraesCS3A01G282800 chr3D 529837890 529838392 502 False 390.000000 390 81.262000 5694 6182 1 chr3D.!!$F1 488
3 TraesCS3A01G282800 chr3B 508251319 508256969 5650 True 1664.400000 2734 93.256000 106 5667 5 chr3B.!!$R1 5561
4 TraesCS3A01G282800 chr1D 439026118 439026835 717 True 470.000000 470 79.161000 2135 2849 1 chr1D.!!$R2 714
5 TraesCS3A01G282800 chr1B 595182092 595182801 709 True 464.000000 464 79.098000 2140 2849 1 chr1B.!!$R2 709
6 TraesCS3A01G282800 chr1B 334246995 334247509 514 False 346.000000 346 79.699000 5676 6182 1 chr1B.!!$F1 506
7 TraesCS3A01G282800 chr5D 62530052 62530578 526 True 429.000000 429 82.008000 5676 6182 1 chr5D.!!$R1 506
8 TraesCS3A01G282800 chr2B 790374241 790374761 520 True 374.000000 374 80.306000 5681 6182 1 chr2B.!!$R2 501
9 TraesCS3A01G282800 chr2A 169336921 169337451 530 False 366.000000 366 79.887000 5676 6182 1 chr2A.!!$F1 506
10 TraesCS3A01G282800 chr5A 288257851 288258359 508 True 357.000000 357 80.039000 5694 6182 1 chr5A.!!$R1 488
11 TraesCS3A01G282800 chr7A 694104105 694104610 505 False 342.000000 342 79.528000 5695 6182 1 chr7A.!!$F1 487
12 TraesCS3A01G282800 chr1A 535316167 535316876 709 True 280.500000 335 84.800000 2140 2849 2 chr1A.!!$R1 709

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
81 82 0.033208 TCATGGGCATTTGAGGGGTC 60.033 55.000 0.00 0.0 0.00 4.46 F
1193 1204 0.035439 TCGGGAAGGTCAAGATTGCC 60.035 55.000 0.00 0.0 33.87 4.52 F
2323 2719 1.113788 GCCCAAATTATGCAGCTCCA 58.886 50.000 0.00 0.0 0.00 3.86 F
3214 3614 0.979709 TCCAGATGGGAGCTGACAGG 60.980 60.000 4.26 0.0 42.15 4.00 F
4448 4879 1.408266 CCCCTGTTGCCATACACCTAC 60.408 57.143 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1222 1.227823 CTTGACGGCCACCTTGTGA 60.228 57.895 2.24 0.0 35.23 3.58 R
3111 3511 0.763652 CTCCCATGCATAGCCTCACT 59.236 55.000 0.00 0.0 0.00 3.41 R
3654 4056 4.349636 TCACTTGGAGTAATGGGTGAGAAA 59.650 41.667 0.00 0.0 31.43 2.52 R
5086 5539 0.261696 GTATGTCCCAAGGGGCCAAT 59.738 55.000 7.39 0.0 43.94 3.16 R
5778 6529 0.397941 CATCCACCACGCCTCCATAT 59.602 55.000 0.00 0.0 0.00 1.78 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
18 19 3.745723 AAGGGTCAGAATTTGCGGT 57.254 47.368 0.00 0.00 0.00 5.68
19 20 2.871096 AAGGGTCAGAATTTGCGGTA 57.129 45.000 0.00 0.00 0.00 4.02
20 21 3.366052 AAGGGTCAGAATTTGCGGTAT 57.634 42.857 0.00 0.00 0.00 2.73
21 22 2.643551 AGGGTCAGAATTTGCGGTATG 58.356 47.619 0.00 0.00 0.00 2.39
22 23 2.026262 AGGGTCAGAATTTGCGGTATGT 60.026 45.455 0.00 0.00 0.00 2.29
23 24 2.097466 GGGTCAGAATTTGCGGTATGTG 59.903 50.000 0.00 0.00 0.00 3.21
24 25 2.097466 GGTCAGAATTTGCGGTATGTGG 59.903 50.000 0.00 0.00 0.00 4.17
25 26 3.006940 GTCAGAATTTGCGGTATGTGGA 58.993 45.455 0.00 0.00 0.00 4.02
26 27 3.627577 GTCAGAATTTGCGGTATGTGGAT 59.372 43.478 0.00 0.00 0.00 3.41
27 28 3.627123 TCAGAATTTGCGGTATGTGGATG 59.373 43.478 0.00 0.00 0.00 3.51
28 29 3.378112 CAGAATTTGCGGTATGTGGATGT 59.622 43.478 0.00 0.00 0.00 3.06
29 30 3.378112 AGAATTTGCGGTATGTGGATGTG 59.622 43.478 0.00 0.00 0.00 3.21
30 31 0.808125 TTTGCGGTATGTGGATGTGC 59.192 50.000 0.00 0.00 0.00 4.57
31 32 0.322008 TTGCGGTATGTGGATGTGCA 60.322 50.000 0.00 0.00 0.00 4.57
32 33 0.322008 TGCGGTATGTGGATGTGCAA 60.322 50.000 0.00 0.00 0.00 4.08
33 34 0.098728 GCGGTATGTGGATGTGCAAC 59.901 55.000 0.00 0.00 37.35 4.17
34 35 0.373370 CGGTATGTGGATGTGCAACG 59.627 55.000 0.00 0.00 42.39 4.10
35 36 0.098728 GGTATGTGGATGTGCAACGC 59.901 55.000 0.00 0.00 42.39 4.84
36 37 0.801872 GTATGTGGATGTGCAACGCA 59.198 50.000 0.00 0.00 42.39 5.24
37 38 1.198867 GTATGTGGATGTGCAACGCAA 59.801 47.619 0.00 0.00 41.47 4.85
38 39 0.039256 ATGTGGATGTGCAACGCAAC 60.039 50.000 0.00 0.00 41.47 4.17
39 40 1.358402 GTGGATGTGCAACGCAACA 59.642 52.632 0.00 0.00 41.47 3.33
40 41 0.039256 GTGGATGTGCAACGCAACAT 60.039 50.000 0.00 0.00 41.47 2.71
41 42 0.672889 TGGATGTGCAACGCAACATT 59.327 45.000 0.00 0.00 41.47 2.71
42 43 1.068281 TGGATGTGCAACGCAACATTT 59.932 42.857 0.00 0.00 41.47 2.32
43 44 1.456544 GGATGTGCAACGCAACATTTG 59.543 47.619 0.00 0.00 41.47 2.32
44 45 2.392821 GATGTGCAACGCAACATTTGA 58.607 42.857 0.00 0.00 41.47 2.69
45 46 1.837648 TGTGCAACGCAACATTTGAG 58.162 45.000 0.00 0.00 41.47 3.02
46 47 1.403323 TGTGCAACGCAACATTTGAGA 59.597 42.857 0.00 0.00 41.47 3.27
47 48 1.780860 GTGCAACGCAACATTTGAGAC 59.219 47.619 0.00 0.00 41.47 3.36
48 49 1.044725 GCAACGCAACATTTGAGACG 58.955 50.000 0.00 0.00 34.37 4.18
49 50 1.596954 GCAACGCAACATTTGAGACGT 60.597 47.619 0.00 0.00 34.37 4.34
50 51 2.036217 CAACGCAACATTTGAGACGTG 58.964 47.619 0.00 0.00 34.37 4.49
51 52 1.577468 ACGCAACATTTGAGACGTGA 58.423 45.000 0.00 0.00 34.37 4.35
52 53 1.260561 ACGCAACATTTGAGACGTGAC 59.739 47.619 0.00 0.00 34.37 3.67
53 54 1.398451 CGCAACATTTGAGACGTGACC 60.398 52.381 0.00 0.00 31.66 4.02
54 55 1.398451 GCAACATTTGAGACGTGACCG 60.398 52.381 0.00 0.00 40.83 4.79
55 56 1.194547 CAACATTTGAGACGTGACCGG 59.805 52.381 0.00 0.00 38.78 5.28
56 57 0.677288 ACATTTGAGACGTGACCGGA 59.323 50.000 9.46 0.00 38.78 5.14
57 58 1.068474 CATTTGAGACGTGACCGGAC 58.932 55.000 9.46 1.07 38.78 4.79
58 59 0.388134 ATTTGAGACGTGACCGGACG 60.388 55.000 9.46 12.06 45.09 4.79
59 60 3.547249 TTGAGACGTGACCGGACGC 62.547 63.158 9.46 8.26 43.33 5.19
64 65 4.986587 CGTGACCGGACGCGTTCA 62.987 66.667 27.57 12.98 38.67 3.18
65 66 2.431942 GTGACCGGACGCGTTCAT 60.432 61.111 19.39 4.38 0.00 2.57
66 67 2.431771 TGACCGGACGCGTTCATG 60.432 61.111 19.39 10.51 0.00 3.07
67 68 3.186047 GACCGGACGCGTTCATGG 61.186 66.667 19.39 14.13 0.00 3.66
68 69 4.752879 ACCGGACGCGTTCATGGG 62.753 66.667 19.39 13.36 0.00 4.00
71 72 2.824041 GGACGCGTTCATGGGCAT 60.824 61.111 15.53 0.00 0.00 4.40
72 73 2.406616 GGACGCGTTCATGGGCATT 61.407 57.895 15.53 0.00 0.00 3.56
73 74 1.506262 GACGCGTTCATGGGCATTT 59.494 52.632 15.53 0.00 0.00 2.32
74 75 0.798009 GACGCGTTCATGGGCATTTG 60.798 55.000 15.53 0.00 0.00 2.32
75 76 1.240641 ACGCGTTCATGGGCATTTGA 61.241 50.000 5.58 0.00 0.00 2.69
76 77 0.523968 CGCGTTCATGGGCATTTGAG 60.524 55.000 0.00 0.00 0.00 3.02
77 78 0.179129 GCGTTCATGGGCATTTGAGG 60.179 55.000 0.00 0.00 0.00 3.86
78 79 0.457035 CGTTCATGGGCATTTGAGGG 59.543 55.000 0.00 0.00 0.00 4.30
79 80 0.826062 GTTCATGGGCATTTGAGGGG 59.174 55.000 0.00 0.00 0.00 4.79
80 81 0.413037 TTCATGGGCATTTGAGGGGT 59.587 50.000 0.00 0.00 0.00 4.95
81 82 0.033208 TCATGGGCATTTGAGGGGTC 60.033 55.000 0.00 0.00 0.00 4.46
82 83 1.076777 ATGGGCATTTGAGGGGTCG 60.077 57.895 0.00 0.00 0.00 4.79
83 84 2.440247 GGGCATTTGAGGGGTCGG 60.440 66.667 0.00 0.00 0.00 4.79
84 85 2.674754 GGCATTTGAGGGGTCGGA 59.325 61.111 0.00 0.00 0.00 4.55
85 86 1.227383 GGCATTTGAGGGGTCGGAT 59.773 57.895 0.00 0.00 0.00 4.18
86 87 0.395724 GGCATTTGAGGGGTCGGATT 60.396 55.000 0.00 0.00 0.00 3.01
87 88 1.025041 GCATTTGAGGGGTCGGATTC 58.975 55.000 0.00 0.00 0.00 2.52
88 89 1.299541 CATTTGAGGGGTCGGATTCG 58.700 55.000 0.00 0.00 37.82 3.34
89 90 0.180406 ATTTGAGGGGTCGGATTCGG 59.820 55.000 0.00 0.00 36.95 4.30
90 91 2.530958 TTTGAGGGGTCGGATTCGGC 62.531 60.000 0.00 0.00 40.80 5.54
91 92 3.467226 GAGGGGTCGGATTCGGCA 61.467 66.667 0.00 0.00 43.76 5.69
92 93 3.447025 GAGGGGTCGGATTCGGCAG 62.447 68.421 0.00 0.00 43.76 4.85
94 95 4.162690 GGGTCGGATTCGGCAGCT 62.163 66.667 0.00 0.00 43.76 4.24
95 96 2.892425 GGTCGGATTCGGCAGCTG 60.892 66.667 10.11 10.11 43.76 4.24
96 97 2.125512 GTCGGATTCGGCAGCTGT 60.126 61.111 16.64 0.00 41.24 4.40
97 98 1.141019 GTCGGATTCGGCAGCTGTA 59.859 57.895 16.64 0.00 41.24 2.74
98 99 0.872021 GTCGGATTCGGCAGCTGTAG 60.872 60.000 16.64 9.87 41.24 2.74
99 100 1.592669 CGGATTCGGCAGCTGTAGG 60.593 63.158 16.64 5.01 0.00 3.18
100 101 1.522569 GGATTCGGCAGCTGTAGGT 59.477 57.895 16.64 2.73 0.00 3.08
101 102 0.811616 GGATTCGGCAGCTGTAGGTG 60.812 60.000 16.64 6.71 45.58 4.00
120 121 4.113354 GGTGCTCTAATTTGGTCTCTACG 58.887 47.826 0.00 0.00 0.00 3.51
137 138 6.261381 GTCTCTACGGTGTCAGATATTCTCTT 59.739 42.308 0.00 0.00 29.16 2.85
239 243 3.994853 GGGAACGAACCGTCCCGT 61.995 66.667 9.84 0.00 34.32 5.28
240 244 2.431430 GGAACGAACCGTCCCGTC 60.431 66.667 0.00 0.00 39.99 4.79
241 245 2.802414 GAACGAACCGTCCCGTCG 60.802 66.667 0.00 0.00 39.99 5.12
315 319 3.918328 AATCCTCCCCGTCCCACGT 62.918 63.158 0.00 0.00 40.58 4.49
462 466 1.979389 AATCTCTCCTCCCCCTCCCC 61.979 65.000 0.00 0.00 0.00 4.81
585 589 4.517934 CTACGCCTCTCCCCGGGA 62.518 72.222 26.32 5.87 0.00 5.14
615 619 2.854523 GGCCAGGTAGGGGATCCC 60.855 72.222 23.95 23.95 45.90 3.85
645 649 4.548513 CCCCCTCTCTCCCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
694 698 2.664851 GCGCTTGGGTTTTTGGGC 60.665 61.111 0.00 0.00 0.00 5.36
724 728 2.480419 AGTTTTCGTTTCATCGCTCCAG 59.520 45.455 0.00 0.00 0.00 3.86
788 792 2.037620 CTCCCGAGCTTAGCATGGCT 62.038 60.000 7.07 0.00 43.41 4.75
868 873 2.037847 GCTCTGGGGGCAAATGGT 59.962 61.111 0.00 0.00 0.00 3.55
875 880 0.252239 GGGGGCAAATGGTCCTTCTT 60.252 55.000 0.00 0.00 42.62 2.52
878 883 2.529632 GGGCAAATGGTCCTTCTTCTT 58.470 47.619 0.00 0.00 38.65 2.52
881 886 3.573967 GGCAAATGGTCCTTCTTCTTTCA 59.426 43.478 0.00 0.00 0.00 2.69
914 919 1.077068 TGCCTGCCTTTTATCCCCG 60.077 57.895 0.00 0.00 0.00 5.73
1050 1061 5.490139 TTCGTACTAGTAGTGATTTCCCG 57.510 43.478 13.29 0.19 0.00 5.14
1072 1083 3.739810 GGTCTTCGTTTCCTGAAGTGTAC 59.260 47.826 3.00 0.00 42.68 2.90
1085 1096 5.995282 CCTGAAGTGTACTTTGGTGTGATTA 59.005 40.000 0.00 0.00 36.11 1.75
1107 1118 4.030913 ACGATTAAGGTGGAAGATGGAGA 58.969 43.478 0.00 0.00 0.00 3.71
1172 1183 1.077716 GACCCTGGGGATTGGTTCG 60.078 63.158 18.88 0.00 38.96 3.95
1193 1204 0.035439 TCGGGAAGGTCAAGATTGCC 60.035 55.000 0.00 0.00 33.87 4.52
1211 1222 3.616219 TGCCGAGCATATAAAAACTGGT 58.384 40.909 0.00 0.00 31.71 4.00
1280 1291 3.909995 TGGAGATGGAAGAGAAAGGTTGA 59.090 43.478 0.00 0.00 0.00 3.18
1287 1298 9.539194 AGATGGAAGAGAAAGGTTGATAATTTT 57.461 29.630 0.00 0.00 0.00 1.82
1293 1304 9.481340 AAGAGAAAGGTTGATAATTTTTCTTGC 57.519 29.630 2.93 0.00 36.55 4.01
1294 1305 8.864087 AGAGAAAGGTTGATAATTTTTCTTGCT 58.136 29.630 1.67 0.00 37.99 3.91
1295 1306 9.133627 GAGAAAGGTTGATAATTTTTCTTGCTC 57.866 33.333 0.00 0.00 37.99 4.26
1296 1307 8.864087 AGAAAGGTTGATAATTTTTCTTGCTCT 58.136 29.630 0.00 0.00 35.25 4.09
1322 1333 7.652524 TCTATTGAGCTCTTTCAGTGAGTAT 57.347 36.000 16.19 0.00 34.30 2.12
1323 1334 8.753497 TCTATTGAGCTCTTTCAGTGAGTATA 57.247 34.615 16.19 0.00 34.30 1.47
1349 1360 8.432805 AGAGTTTCCTATTCTGTACATATTGGG 58.567 37.037 14.27 8.27 0.00 4.12
1350 1361 8.102484 AGTTTCCTATTCTGTACATATTGGGT 57.898 34.615 14.27 0.00 0.00 4.51
1351 1362 9.220906 AGTTTCCTATTCTGTACATATTGGGTA 57.779 33.333 14.27 1.69 0.00 3.69
1381 1448 6.668541 AGTATGCTGCTGTTGTAGTAATTG 57.331 37.500 0.00 0.00 0.00 2.32
1403 1470 4.155826 TGTCGCTCATAAATGGAAAGTTGG 59.844 41.667 0.00 0.00 0.00 3.77
1515 1868 9.230122 TGTTTTTCTATCTTTGCATGATGTAGA 57.770 29.630 11.53 6.01 0.00 2.59
1535 1918 2.068837 AAATTGTGAATGCAGCACCG 57.931 45.000 16.93 0.00 35.43 4.94
1546 1929 1.303309 GCAGCACCGCTCTTGATTAT 58.697 50.000 0.00 0.00 36.40 1.28
1547 1930 2.158971 TGCAGCACCGCTCTTGATTATA 60.159 45.455 0.00 0.00 36.40 0.98
1676 2059 5.592282 TGTTTGGTCTAAAATGAAGCACTCA 59.408 36.000 0.00 0.00 38.81 3.41
1681 2064 6.321181 TGGTCTAAAATGAAGCACTCAAGTTT 59.679 34.615 0.00 0.00 37.67 2.66
1747 2139 9.812347 AAGATATTAAGATTATTCATGCACCCA 57.188 29.630 0.00 0.00 0.00 4.51
1828 2220 6.878923 TGGAGTATGTTAAGTCTGGTGAATTG 59.121 38.462 0.00 0.00 32.45 2.32
1834 2226 7.581213 TGTTAAGTCTGGTGAATTGTTTGAT 57.419 32.000 0.00 0.00 32.45 2.57
2036 2432 3.002038 TGTATCAGCAATGGCATGTGA 57.998 42.857 0.00 5.30 44.61 3.58
2109 2505 8.890718 GTTTATCATTCCACTTAGACCCTTAAC 58.109 37.037 0.00 0.00 0.00 2.01
2323 2719 1.113788 GCCCAAATTATGCAGCTCCA 58.886 50.000 0.00 0.00 0.00 3.86
2366 2762 7.453393 ACTATTTTCAGACAGAAAGGACATGA 58.547 34.615 0.00 0.00 46.24 3.07
2376 2772 6.475504 ACAGAAAGGACATGACATCATTGTA 58.524 36.000 0.00 0.00 35.79 2.41
2377 2773 6.372659 ACAGAAAGGACATGACATCATTGTAC 59.627 38.462 0.00 0.00 35.79 2.90
2379 2775 6.820656 AGAAAGGACATGACATCATTGTACTC 59.179 38.462 0.00 1.53 35.79 2.59
2380 2776 5.028549 AGGACATGACATCATTGTACTCC 57.971 43.478 0.00 0.00 35.79 3.85
2885 3284 5.708948 CACCGCTTCCTTTATGAAAATCAA 58.291 37.500 0.00 0.00 0.00 2.57
2948 3347 3.706594 TGCCAAATATTCCGCCCATAAAA 59.293 39.130 4.71 0.00 0.00 1.52
3111 3511 2.170166 CCTTCTGCCTTGTGCCATTTA 58.830 47.619 0.00 0.00 40.16 1.40
3116 3516 2.161855 TGCCTTGTGCCATTTAGTGAG 58.838 47.619 0.00 0.00 40.16 3.51
3214 3614 0.979709 TCCAGATGGGAGCTGACAGG 60.980 60.000 4.26 0.00 42.15 4.00
3215 3615 0.979709 CCAGATGGGAGCTGACAGGA 60.980 60.000 4.26 0.00 40.01 3.86
3250 3651 9.958180 TCATGTATTTCTTCATTTAAGTCCTCA 57.042 29.630 0.00 0.00 36.51 3.86
3442 3844 7.218204 GTGCAAATTAACGACCATGACTAATTC 59.782 37.037 0.00 0.00 0.00 2.17
3599 4001 7.331934 CCGATTCTGTTTTAATCTTCTGACTGA 59.668 37.037 0.00 0.00 32.29 3.41
3654 4056 2.787473 TTGGCATCAAGGAATCGTCT 57.213 45.000 0.00 0.00 0.00 4.18
3804 4206 9.383519 CTTCAGGTAATCTATGTTTAGCTTTGA 57.616 33.333 0.00 0.00 35.74 2.69
4019 4421 7.389053 GGTCAGGAGAATATGAATCATACCAAC 59.611 40.741 4.93 5.25 0.00 3.77
4351 4782 4.348863 ACTCTTCACATATCCCTGCATC 57.651 45.455 0.00 0.00 0.00 3.91
4369 4800 6.744537 CCTGCATCTCTTTTACTTTGAAATCG 59.255 38.462 0.00 0.00 0.00 3.34
4373 4804 3.817238 TCTTTTACTTTGAAATCGGCGC 58.183 40.909 0.00 0.00 0.00 6.53
4448 4879 1.408266 CCCCTGTTGCCATACACCTAC 60.408 57.143 0.00 0.00 0.00 3.18
4493 4924 5.052481 TGTCTATTGCAGTCACTATCATGC 58.948 41.667 0.00 0.00 39.14 4.06
4654 5087 4.746729 TCCTTATTTCGCTTACGCACTTA 58.253 39.130 0.00 0.00 39.84 2.24
4695 5128 2.742053 TCCGTGTTGCATTCTTCTTAGC 59.258 45.455 0.00 0.00 0.00 3.09
4914 5361 2.386661 TTCTCCAGCGGATCAAAGTC 57.613 50.000 0.00 0.00 0.00 3.01
5112 5570 3.047695 CCCTTGGGACATACTCCTACT 57.952 52.381 0.00 0.00 39.30 2.57
5115 5573 4.140994 CCCTTGGGACATACTCCTACTCTA 60.141 50.000 0.00 0.00 39.30 2.43
5119 5577 3.822167 GGGACATACTCCTACTCTACTGC 59.178 52.174 0.00 0.00 39.39 4.40
5120 5578 4.446600 GGGACATACTCCTACTCTACTGCT 60.447 50.000 0.00 0.00 39.39 4.24
5121 5579 4.517453 GGACATACTCCTACTCTACTGCTG 59.483 50.000 0.00 0.00 35.89 4.41
5243 5701 2.480845 GGGCCACAGACAATCGTATAC 58.519 52.381 4.39 0.00 0.00 1.47
5244 5702 2.159014 GGGCCACAGACAATCGTATACA 60.159 50.000 4.39 0.00 0.00 2.29
5245 5703 3.123804 GGCCACAGACAATCGTATACAG 58.876 50.000 0.00 0.00 0.00 2.74
5246 5704 3.430374 GGCCACAGACAATCGTATACAGT 60.430 47.826 0.00 0.00 0.00 3.55
5250 5708 6.534059 CCACAGACAATCGTATACAGTTTTG 58.466 40.000 3.32 3.59 0.00 2.44
5251 5709 6.147164 CCACAGACAATCGTATACAGTTTTGT 59.853 38.462 3.32 6.56 41.39 2.83
5253 5711 7.740346 CACAGACAATCGTATACAGTTTTGTTC 59.260 37.037 3.32 2.63 38.76 3.18
5254 5712 7.656137 ACAGACAATCGTATACAGTTTTGTTCT 59.344 33.333 3.32 4.40 38.76 3.01
5256 5714 8.709646 AGACAATCGTATACAGTTTTGTTCTTC 58.290 33.333 3.32 0.00 38.76 2.87
5278 5740 9.788889 TCTTCATATACTAATTCGAGGTGTCTA 57.211 33.333 0.00 0.00 0.00 2.59
5302 5767 1.739466 TCTTCTGCGTCCATTGATTGC 59.261 47.619 0.00 0.00 0.00 3.56
5303 5768 0.447406 TTCTGCGTCCATTGATTGCG 59.553 50.000 0.00 0.00 0.00 4.85
5304 5769 0.390998 TCTGCGTCCATTGATTGCGA 60.391 50.000 0.00 0.00 0.00 5.10
5305 5770 0.447406 CTGCGTCCATTGATTGCGAA 59.553 50.000 0.00 0.00 0.00 4.70
5399 5912 0.527565 GAGAACAATGCGGCAACCAT 59.472 50.000 6.82 0.00 0.00 3.55
5411 5924 1.064463 GGCAACCATCATGGAAGGAGA 60.064 52.381 11.90 0.00 40.96 3.71
5412 5925 2.295885 GCAACCATCATGGAAGGAGAG 58.704 52.381 11.90 0.00 40.96 3.20
5475 6220 6.904954 AAATACGTTCAATTTGTTACTGCG 57.095 33.333 0.00 0.00 0.00 5.18
5525 6273 2.190578 CGATGGGAGGGCACTTCC 59.809 66.667 6.24 6.24 43.38 3.46
5527 6275 1.225704 GATGGGAGGGCACTTCCTG 59.774 63.158 16.35 0.00 43.48 3.86
5580 6328 1.531739 GGAGAAAACGCCCCATGCAA 61.532 55.000 0.00 0.00 41.33 4.08
5583 6331 1.066929 AGAAAACGCCCCATGCAAATC 60.067 47.619 0.00 0.00 41.33 2.17
5629 6377 4.429212 TCCACGCACCGGTCATCG 62.429 66.667 2.59 11.73 38.88 3.84
5669 6418 3.978855 GGCTTGTTAATTTGAACGGTGTC 59.021 43.478 0.00 0.00 31.59 3.67
5674 6423 6.150396 TGTTAATTTGAACGGTGTCCATTT 57.850 33.333 0.00 0.00 31.59 2.32
5708 6459 1.465188 TGGGAAGAAAGAGGGCCCA 60.465 57.895 27.56 0.00 46.10 5.36
5771 6522 3.276857 GTCTACCTCGTCTCATGTGGTA 58.723 50.000 0.00 0.00 32.74 3.25
5778 6529 3.889538 CTCGTCTCATGTGGTATTAGGGA 59.110 47.826 0.00 0.00 0.00 4.20
5779 6530 4.480115 TCGTCTCATGTGGTATTAGGGAT 58.520 43.478 0.00 0.00 0.00 3.85
5812 6577 1.694133 GGATGGACCAGAGGGCTCAG 61.694 65.000 0.00 0.00 37.90 3.35
5834 6600 8.687824 TCAGTTTTTCATGTTCTTTTGAGTTC 57.312 30.769 0.00 0.00 0.00 3.01
5836 6602 9.143631 CAGTTTTTCATGTTCTTTTGAGTTCTT 57.856 29.630 0.00 0.00 0.00 2.52
5909 6683 2.282180 GGTTCTTCCCGCCTTGCA 60.282 61.111 0.00 0.00 0.00 4.08
5945 6719 1.107538 TTCTAGCATCGTCGGAGGGG 61.108 60.000 0.00 0.00 0.00 4.79
6028 6803 2.159226 CCAGGTGGATCTTGTAGTCGTC 60.159 54.545 0.00 0.00 37.39 4.20
6055 6830 7.464844 CGTTTGTGTTCATGTGTCTACAAGTTA 60.465 37.037 0.00 0.00 40.84 2.24
6092 6867 1.196808 GCTTCTTTTCATTGGCGACGA 59.803 47.619 0.00 0.00 0.00 4.20
6093 6869 2.839474 CTTCTTTTCATTGGCGACGAC 58.161 47.619 0.00 0.00 0.00 4.34
6115 6891 0.464036 TTGTTCTCGTGTGCTGGTCT 59.536 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.871096 TACCGCAAATTCTGACCCTT 57.129 45.000 0.00 0.00 0.00 3.95
1 2 2.026262 ACATACCGCAAATTCTGACCCT 60.026 45.455 0.00 0.00 0.00 4.34
2 3 2.097466 CACATACCGCAAATTCTGACCC 59.903 50.000 0.00 0.00 0.00 4.46
3 4 2.097466 CCACATACCGCAAATTCTGACC 59.903 50.000 0.00 0.00 0.00 4.02
4 5 3.006940 TCCACATACCGCAAATTCTGAC 58.993 45.455 0.00 0.00 0.00 3.51
5 6 3.342377 TCCACATACCGCAAATTCTGA 57.658 42.857 0.00 0.00 0.00 3.27
6 7 3.378112 ACATCCACATACCGCAAATTCTG 59.622 43.478 0.00 0.00 0.00 3.02
7 8 3.378112 CACATCCACATACCGCAAATTCT 59.622 43.478 0.00 0.00 0.00 2.40
8 9 3.694734 CACATCCACATACCGCAAATTC 58.305 45.455 0.00 0.00 0.00 2.17
9 10 2.159254 GCACATCCACATACCGCAAATT 60.159 45.455 0.00 0.00 0.00 1.82
10 11 1.405105 GCACATCCACATACCGCAAAT 59.595 47.619 0.00 0.00 0.00 2.32
11 12 0.808125 GCACATCCACATACCGCAAA 59.192 50.000 0.00 0.00 0.00 3.68
12 13 0.322008 TGCACATCCACATACCGCAA 60.322 50.000 0.00 0.00 0.00 4.85
13 14 0.322008 TTGCACATCCACATACCGCA 60.322 50.000 0.00 0.00 0.00 5.69
14 15 0.098728 GTTGCACATCCACATACCGC 59.901 55.000 0.00 0.00 0.00 5.68
15 16 0.373370 CGTTGCACATCCACATACCG 59.627 55.000 0.00 0.00 0.00 4.02
16 17 0.098728 GCGTTGCACATCCACATACC 59.901 55.000 0.00 0.00 0.00 2.73
17 18 0.801872 TGCGTTGCACATCCACATAC 59.198 50.000 0.00 0.00 31.71 2.39
18 19 1.198867 GTTGCGTTGCACATCCACATA 59.801 47.619 0.00 0.00 38.71 2.29
19 20 0.039256 GTTGCGTTGCACATCCACAT 60.039 50.000 0.00 0.00 38.71 3.21
20 21 1.358402 GTTGCGTTGCACATCCACA 59.642 52.632 0.00 0.00 38.71 4.17
21 22 0.039256 ATGTTGCGTTGCACATCCAC 60.039 50.000 0.00 0.00 38.71 4.02
22 23 0.672889 AATGTTGCGTTGCACATCCA 59.327 45.000 0.00 0.00 38.71 3.41
23 24 1.456544 CAAATGTTGCGTTGCACATCC 59.543 47.619 0.00 0.00 38.71 3.51
24 25 2.392821 TCAAATGTTGCGTTGCACATC 58.607 42.857 0.00 0.00 38.71 3.06
25 26 2.034432 TCTCAAATGTTGCGTTGCACAT 59.966 40.909 0.00 0.00 38.71 3.21
26 27 1.403323 TCTCAAATGTTGCGTTGCACA 59.597 42.857 0.00 0.00 38.71 4.57
27 28 1.780860 GTCTCAAATGTTGCGTTGCAC 59.219 47.619 0.00 0.00 38.71 4.57
28 29 1.596709 CGTCTCAAATGTTGCGTTGCA 60.597 47.619 0.00 0.00 36.47 4.08
29 30 1.044725 CGTCTCAAATGTTGCGTTGC 58.955 50.000 0.00 0.00 0.00 4.17
30 31 2.036217 CACGTCTCAAATGTTGCGTTG 58.964 47.619 0.00 0.00 0.00 4.10
31 32 1.937223 TCACGTCTCAAATGTTGCGTT 59.063 42.857 0.00 0.00 0.00 4.84
32 33 1.260561 GTCACGTCTCAAATGTTGCGT 59.739 47.619 0.00 0.00 0.00 5.24
33 34 1.398451 GGTCACGTCTCAAATGTTGCG 60.398 52.381 0.00 0.00 0.00 4.85
34 35 1.398451 CGGTCACGTCTCAAATGTTGC 60.398 52.381 0.00 0.00 34.81 4.17
35 36 1.194547 CCGGTCACGTCTCAAATGTTG 59.805 52.381 0.00 0.00 38.78 3.33
36 37 1.069513 TCCGGTCACGTCTCAAATGTT 59.930 47.619 0.00 0.00 38.78 2.71
37 38 0.677288 TCCGGTCACGTCTCAAATGT 59.323 50.000 0.00 0.00 38.78 2.71
38 39 1.068474 GTCCGGTCACGTCTCAAATG 58.932 55.000 0.00 0.00 38.78 2.32
39 40 0.388134 CGTCCGGTCACGTCTCAAAT 60.388 55.000 7.49 0.00 38.78 2.32
40 41 1.008194 CGTCCGGTCACGTCTCAAA 60.008 57.895 7.49 0.00 38.78 2.69
41 42 2.640989 CGTCCGGTCACGTCTCAA 59.359 61.111 7.49 0.00 38.78 3.02
42 43 4.034258 GCGTCCGGTCACGTCTCA 62.034 66.667 16.07 0.00 42.04 3.27
45 46 4.988486 AACGCGTCCGGTCACGTC 62.988 66.667 14.44 7.46 42.04 4.34
51 52 4.752879 CCCATGAACGCGTCCGGT 62.753 66.667 14.44 0.00 39.22 5.28
54 55 1.933115 AAATGCCCATGAACGCGTCC 61.933 55.000 14.44 0.00 0.00 4.79
55 56 0.798009 CAAATGCCCATGAACGCGTC 60.798 55.000 14.44 7.01 0.00 5.19
56 57 1.212490 CAAATGCCCATGAACGCGT 59.788 52.632 5.58 5.58 0.00 6.01
57 58 0.523968 CTCAAATGCCCATGAACGCG 60.524 55.000 3.53 3.53 0.00 6.01
58 59 0.179129 CCTCAAATGCCCATGAACGC 60.179 55.000 0.00 0.00 0.00 4.84
59 60 0.457035 CCCTCAAATGCCCATGAACG 59.543 55.000 0.00 0.00 0.00 3.95
60 61 0.826062 CCCCTCAAATGCCCATGAAC 59.174 55.000 0.00 0.00 0.00 3.18
61 62 0.413037 ACCCCTCAAATGCCCATGAA 59.587 50.000 0.00 0.00 0.00 2.57
62 63 0.033208 GACCCCTCAAATGCCCATGA 60.033 55.000 0.00 0.00 0.00 3.07
63 64 1.386525 CGACCCCTCAAATGCCCATG 61.387 60.000 0.00 0.00 0.00 3.66
64 65 1.076777 CGACCCCTCAAATGCCCAT 60.077 57.895 0.00 0.00 0.00 4.00
65 66 2.354729 CGACCCCTCAAATGCCCA 59.645 61.111 0.00 0.00 0.00 5.36
66 67 2.284515 ATCCGACCCCTCAAATGCCC 62.285 60.000 0.00 0.00 0.00 5.36
67 68 0.395724 AATCCGACCCCTCAAATGCC 60.396 55.000 0.00 0.00 0.00 4.40
68 69 1.025041 GAATCCGACCCCTCAAATGC 58.975 55.000 0.00 0.00 0.00 3.56
69 70 1.299541 CGAATCCGACCCCTCAAATG 58.700 55.000 0.00 0.00 38.22 2.32
70 71 0.180406 CCGAATCCGACCCCTCAAAT 59.820 55.000 0.00 0.00 38.22 2.32
71 72 1.600107 CCGAATCCGACCCCTCAAA 59.400 57.895 0.00 0.00 38.22 2.69
72 73 3.026431 GCCGAATCCGACCCCTCAA 62.026 63.158 0.00 0.00 38.22 3.02
73 74 3.467226 GCCGAATCCGACCCCTCA 61.467 66.667 0.00 0.00 38.22 3.86
74 75 3.447025 CTGCCGAATCCGACCCCTC 62.447 68.421 0.00 0.00 38.22 4.30
75 76 3.470888 CTGCCGAATCCGACCCCT 61.471 66.667 0.00 0.00 38.22 4.79
77 78 4.162690 AGCTGCCGAATCCGACCC 62.163 66.667 0.00 0.00 38.22 4.46
78 79 2.292794 TACAGCTGCCGAATCCGACC 62.293 60.000 15.27 0.00 38.22 4.79
79 80 0.872021 CTACAGCTGCCGAATCCGAC 60.872 60.000 15.27 0.00 38.22 4.79
80 81 1.437573 CTACAGCTGCCGAATCCGA 59.562 57.895 15.27 0.00 38.22 4.55
81 82 1.592669 CCTACAGCTGCCGAATCCG 60.593 63.158 15.27 0.00 0.00 4.18
82 83 0.811616 CACCTACAGCTGCCGAATCC 60.812 60.000 15.27 0.00 0.00 3.01
83 84 1.432270 GCACCTACAGCTGCCGAATC 61.432 60.000 15.27 0.00 0.00 2.52
84 85 1.450312 GCACCTACAGCTGCCGAAT 60.450 57.895 15.27 0.00 0.00 3.34
85 86 2.047274 GCACCTACAGCTGCCGAA 60.047 61.111 15.27 0.00 0.00 4.30
86 87 2.997315 AGCACCTACAGCTGCCGA 60.997 61.111 15.27 0.00 41.61 5.54
87 88 1.667154 TAGAGCACCTACAGCTGCCG 61.667 60.000 15.27 4.58 43.58 5.69
88 89 0.537188 TTAGAGCACCTACAGCTGCC 59.463 55.000 15.27 0.00 43.58 4.85
89 90 2.611225 ATTAGAGCACCTACAGCTGC 57.389 50.000 15.27 0.00 43.58 5.25
90 91 3.624861 CCAAATTAGAGCACCTACAGCTG 59.375 47.826 13.48 13.48 43.58 4.24
91 92 3.264450 ACCAAATTAGAGCACCTACAGCT 59.736 43.478 0.00 0.00 46.82 4.24
92 93 3.610911 ACCAAATTAGAGCACCTACAGC 58.389 45.455 0.00 0.00 0.00 4.40
93 94 5.091261 AGACCAAATTAGAGCACCTACAG 57.909 43.478 0.00 0.00 0.00 2.74
94 95 4.777896 AGAGACCAAATTAGAGCACCTACA 59.222 41.667 0.00 0.00 0.00 2.74
95 96 5.346181 AGAGACCAAATTAGAGCACCTAC 57.654 43.478 0.00 0.00 0.00 3.18
96 97 5.067413 CGTAGAGACCAAATTAGAGCACCTA 59.933 44.000 0.00 0.00 0.00 3.08
97 98 4.142138 CGTAGAGACCAAATTAGAGCACCT 60.142 45.833 0.00 0.00 0.00 4.00
98 99 4.113354 CGTAGAGACCAAATTAGAGCACC 58.887 47.826 0.00 0.00 0.00 5.01
99 100 4.113354 CCGTAGAGACCAAATTAGAGCAC 58.887 47.826 0.00 0.00 0.00 4.40
100 101 3.767673 ACCGTAGAGACCAAATTAGAGCA 59.232 43.478 0.00 0.00 0.00 4.26
101 102 4.113354 CACCGTAGAGACCAAATTAGAGC 58.887 47.826 0.00 0.00 0.00 4.09
102 103 5.105877 TGACACCGTAGAGACCAAATTAGAG 60.106 44.000 0.00 0.00 0.00 2.43
103 104 4.768448 TGACACCGTAGAGACCAAATTAGA 59.232 41.667 0.00 0.00 0.00 2.10
104 105 5.068234 TGACACCGTAGAGACCAAATTAG 57.932 43.478 0.00 0.00 0.00 1.73
120 121 7.849804 TTTTAGCAAGAGAATATCTGACACC 57.150 36.000 0.00 0.00 38.67 4.16
147 151 1.881252 CTGCGATTAACGTCCGGGG 60.881 63.158 0.00 0.00 44.60 5.73
315 319 0.904865 ATCAGACAACGGGCAGAGGA 60.905 55.000 0.00 0.00 0.00 3.71
501 505 2.450243 GGGGGTGGAGAGACTGGA 59.550 66.667 0.00 0.00 0.00 3.86
655 659 3.845259 CGGAATTCTCGGGCGGGA 61.845 66.667 5.23 0.00 0.00 5.14
661 665 2.962253 GCCTCGCGGAATTCTCGG 60.962 66.667 6.13 9.75 0.00 4.63
694 698 0.932399 AAACGAAAACTCACGGTCCG 59.068 50.000 10.48 10.48 0.00 4.79
746 750 1.068753 CGGATCTGCAGGCTAGGTG 59.931 63.158 15.13 0.00 0.00 4.00
788 792 1.602323 ATCGCCGGAAAACCAGCAA 60.602 52.632 5.05 0.00 0.00 3.91
793 797 2.332654 ACAGCATCGCCGGAAAACC 61.333 57.895 5.05 0.00 0.00 3.27
852 857 1.380380 GGACCATTTGCCCCCAGAG 60.380 63.158 0.00 0.00 0.00 3.35
881 886 3.131755 GGCAGGCAGAAATGCTTAATTCT 59.868 43.478 0.00 0.00 42.19 2.40
990 999 1.008538 GGCGGGCATGAATAAAGCG 60.009 57.895 0.00 0.00 0.00 4.68
1019 1028 9.871238 AATCACTACTAGTACGAAATTTCACAT 57.129 29.630 17.99 5.55 0.00 3.21
1050 1061 2.835027 ACACTTCAGGAAACGAAGACC 58.165 47.619 6.89 0.00 40.81 3.85
1072 1083 6.403200 CCACCTTAATCGTAATCACACCAAAG 60.403 42.308 0.00 0.00 0.00 2.77
1085 1096 4.030913 TCTCCATCTTCCACCTTAATCGT 58.969 43.478 0.00 0.00 0.00 3.73
1107 1118 3.064324 GCCATCTTTGCCGCCTGT 61.064 61.111 0.00 0.00 0.00 4.00
1172 1183 1.468914 GCAATCTTGACCTTCCCGAAC 59.531 52.381 0.00 0.00 0.00 3.95
1193 1204 5.794687 TGTGACCAGTTTTTATATGCTCG 57.205 39.130 0.00 0.00 0.00 5.03
1211 1222 1.227823 CTTGACGGCCACCTTGTGA 60.228 57.895 2.24 0.00 35.23 3.58
1293 1304 7.939782 TCACTGAAAGAGCTCAATAGATAGAG 58.060 38.462 17.77 3.86 37.43 2.43
1294 1305 7.559533 ACTCACTGAAAGAGCTCAATAGATAGA 59.440 37.037 17.77 3.98 37.43 1.98
1295 1306 7.715657 ACTCACTGAAAGAGCTCAATAGATAG 58.284 38.462 17.77 12.25 37.43 2.08
1296 1307 7.652524 ACTCACTGAAAGAGCTCAATAGATA 57.347 36.000 17.77 2.30 37.43 1.98
1323 1334 8.432805 CCCAATATGTACAGAATAGGAAACTCT 58.567 37.037 0.33 0.00 43.67 3.24
1346 1357 6.253758 ACAGCAGCATACTACTATATACCCA 58.746 40.000 0.00 0.00 0.00 4.51
1347 1358 6.777213 ACAGCAGCATACTACTATATACCC 57.223 41.667 0.00 0.00 0.00 3.69
1348 1359 7.603651 ACAACAGCAGCATACTACTATATACC 58.396 38.462 0.00 0.00 0.00 2.73
1349 1360 9.776158 CTACAACAGCAGCATACTACTATATAC 57.224 37.037 0.00 0.00 0.00 1.47
1350 1361 9.516546 ACTACAACAGCAGCATACTACTATATA 57.483 33.333 0.00 0.00 0.00 0.86
1351 1362 8.410673 ACTACAACAGCAGCATACTACTATAT 57.589 34.615 0.00 0.00 0.00 0.86
1354 1421 7.634671 TTACTACAACAGCAGCATACTACTA 57.365 36.000 0.00 0.00 0.00 1.82
1356 1423 7.277981 ACAATTACTACAACAGCAGCATACTAC 59.722 37.037 0.00 0.00 0.00 2.73
1363 1430 3.725010 GCGACAATTACTACAACAGCAGC 60.725 47.826 0.00 0.00 0.00 5.25
1381 1448 4.662145 CCAACTTTCCATTTATGAGCGAC 58.338 43.478 0.00 0.00 0.00 5.19
1515 1868 2.406130 CGGTGCTGCATTCACAATTTT 58.594 42.857 17.48 0.00 36.22 1.82
1747 2139 5.702670 CACTTCATAAAGGCGGATGATATGT 59.297 40.000 0.85 0.00 36.78 2.29
1828 2220 9.612620 CTACCTTTCTCAACAATGTAATCAAAC 57.387 33.333 0.00 0.00 0.00 2.93
1834 2226 5.876357 AGCCTACCTTTCTCAACAATGTAA 58.124 37.500 0.00 0.00 0.00 2.41
2036 2432 7.319646 TGCAATTTCCGAGCAAACTATATTTT 58.680 30.769 0.00 0.00 34.97 1.82
2098 2494 1.176527 CCCGTCACGTTAAGGGTCTA 58.823 55.000 12.13 0.00 39.05 2.59
2109 2505 3.310501 AGAAAACAAAGTAACCCGTCACG 59.689 43.478 0.00 0.00 0.00 4.35
2366 2762 6.054860 ACAAAGCTAGGAGTACAATGATGT 57.945 37.500 0.00 0.00 43.74 3.06
2376 2772 2.303311 GTCTGGGAACAAAGCTAGGAGT 59.697 50.000 0.00 0.00 42.06 3.85
2377 2773 2.569404 AGTCTGGGAACAAAGCTAGGAG 59.431 50.000 0.00 0.00 42.06 3.69
2379 2775 2.569404 AGAGTCTGGGAACAAAGCTAGG 59.431 50.000 0.00 0.00 42.06 3.02
2380 2776 3.971245 AGAGTCTGGGAACAAAGCTAG 57.029 47.619 0.00 0.00 42.06 3.42
2587 2984 2.241160 TGCACCATTCAAATGCAGACT 58.759 42.857 0.00 0.00 44.17 3.24
3111 3511 0.763652 CTCCCATGCATAGCCTCACT 59.236 55.000 0.00 0.00 0.00 3.41
3116 3516 3.755434 GCACTCCCATGCATAGCC 58.245 61.111 0.00 0.00 45.39 3.93
3250 3651 7.004086 TCATGAGAGAAACCAACACCTTATTT 58.996 34.615 0.00 0.00 0.00 1.40
3256 3657 5.712152 AAATCATGAGAGAAACCAACACC 57.288 39.130 0.09 0.00 0.00 4.16
3599 4001 6.947644 TCAATAATCTAACAGCACATGCAT 57.052 33.333 6.64 0.00 45.16 3.96
3654 4056 4.349636 TCACTTGGAGTAATGGGTGAGAAA 59.650 41.667 0.00 0.00 31.43 2.52
3804 4206 4.916183 AGAGCTTAAGAAAAGCACCAGAT 58.084 39.130 6.67 0.00 45.30 2.90
4019 4421 4.399004 AGGCTCTGCACTGAAGTTATAG 57.601 45.455 0.00 0.00 0.00 1.31
4318 4747 9.988815 GGATATGTGAAGAGTTATCTTGTGTAT 57.011 33.333 0.00 0.00 45.98 2.29
4319 4748 8.421784 GGGATATGTGAAGAGTTATCTTGTGTA 58.578 37.037 0.00 0.00 45.98 2.90
4320 4749 7.126421 AGGGATATGTGAAGAGTTATCTTGTGT 59.874 37.037 0.00 0.00 45.98 3.72
4321 4750 7.440556 CAGGGATATGTGAAGAGTTATCTTGTG 59.559 40.741 0.00 0.00 45.98 3.33
4322 4751 7.504403 CAGGGATATGTGAAGAGTTATCTTGT 58.496 38.462 0.00 0.00 45.98 3.16
4323 4752 6.426328 GCAGGGATATGTGAAGAGTTATCTTG 59.574 42.308 0.00 0.00 45.98 3.02
4325 4754 5.604231 TGCAGGGATATGTGAAGAGTTATCT 59.396 40.000 0.00 0.00 37.39 1.98
4351 4782 3.846335 GCGCCGATTTCAAAGTAAAAGAG 59.154 43.478 0.00 0.00 0.00 2.85
4369 4800 0.733150 GTTCCTGAACCTATTGCGCC 59.267 55.000 4.18 0.00 35.36 6.53
4448 4879 1.248785 AAGTGGAGGCATGCAAGCAG 61.249 55.000 21.36 0.00 35.83 4.24
4493 4924 5.181690 TGGGAGTTGAATTTCAGTTTTCG 57.818 39.130 0.00 0.00 0.00 3.46
4627 5060 4.303086 CGTAAGCGAAATAAGGAGGAGA 57.697 45.455 0.00 0.00 41.33 3.71
4643 5076 7.748847 AGAACATATGGTTTTAAGTGCGTAAG 58.251 34.615 7.80 0.00 40.63 2.34
4654 5087 7.556275 ACACGGATAATGAGAACATATGGTTTT 59.444 33.333 7.80 0.00 40.63 2.43
4695 5128 7.307278 GCTGCAATATCAGAAATACAGAGACAG 60.307 40.741 0.00 0.00 36.19 3.51
4914 5361 2.385315 CGCATGTCTACATACTCCACG 58.615 52.381 0.00 0.00 34.26 4.94
5086 5539 0.261696 GTATGTCCCAAGGGGCCAAT 59.738 55.000 7.39 0.00 43.94 3.16
5107 5565 4.865365 GCAAGTAAACAGCAGTAGAGTAGG 59.135 45.833 0.00 0.00 0.00 3.18
5110 5568 4.336889 TGCAAGTAAACAGCAGTAGAGT 57.663 40.909 0.00 0.00 33.75 3.24
5111 5569 4.692625 ACATGCAAGTAAACAGCAGTAGAG 59.307 41.667 0.00 0.00 42.14 2.43
5112 5570 4.641396 ACATGCAAGTAAACAGCAGTAGA 58.359 39.130 0.00 0.00 42.14 2.59
5115 5573 5.964958 ATTACATGCAAGTAAACAGCAGT 57.035 34.783 17.54 0.00 42.14 4.40
5250 5708 9.182933 GACACCTCGAATTAGTATATGAAGAAC 57.817 37.037 0.00 0.00 0.00 3.01
5251 5709 9.132923 AGACACCTCGAATTAGTATATGAAGAA 57.867 33.333 0.00 0.00 0.00 2.52
5278 5740 3.616956 TCAATGGACGCAGAAGAGATT 57.383 42.857 0.00 0.00 0.00 2.40
5302 5767 0.937699 TTCTCAACGGACGTGCTTCG 60.938 55.000 5.27 0.56 46.00 3.79
5303 5768 1.390463 GATTCTCAACGGACGTGCTTC 59.610 52.381 5.27 0.00 0.00 3.86
5304 5769 1.000955 AGATTCTCAACGGACGTGCTT 59.999 47.619 5.27 0.00 0.00 3.91
5305 5770 0.603569 AGATTCTCAACGGACGTGCT 59.396 50.000 5.27 0.00 0.00 4.40
5399 5912 0.841961 CCATGCCTCTCCTTCCATGA 59.158 55.000 0.00 0.00 37.78 3.07
5455 6200 5.654317 TTCGCAGTAACAAATTGAACGTA 57.346 34.783 0.00 0.00 0.00 3.57
5544 6292 2.621998 TCTCCTACTACCAACATAGCGC 59.378 50.000 0.00 0.00 0.00 5.92
5545 6293 4.913335 TTCTCCTACTACCAACATAGCG 57.087 45.455 0.00 0.00 0.00 4.26
5546 6294 5.519206 CGTTTTCTCCTACTACCAACATAGC 59.481 44.000 0.00 0.00 0.00 2.97
5580 6328 1.207791 ACAGGCGAATGGAGAGGATT 58.792 50.000 0.00 0.00 0.00 3.01
5583 6331 0.539051 AGAACAGGCGAATGGAGAGG 59.461 55.000 0.00 0.00 0.00 3.69
5629 6377 4.972514 AGCCTTTAATAGCTTGCTTGAC 57.027 40.909 0.00 0.00 35.22 3.18
5669 6418 6.991531 TCCCATGAAAGAAAGAAAACAAATGG 59.008 34.615 0.00 0.00 0.00 3.16
5674 6423 7.416964 TTCTTCCCATGAAAGAAAGAAAACA 57.583 32.000 16.33 0.00 0.00 2.83
5708 6459 1.679032 GCACGAGAAACCCTAGCCAAT 60.679 52.381 0.00 0.00 0.00 3.16
5771 6522 1.909302 CCACGCCTCCATATCCCTAAT 59.091 52.381 0.00 0.00 0.00 1.73
5778 6529 0.397941 CATCCACCACGCCTCCATAT 59.602 55.000 0.00 0.00 0.00 1.78
5779 6530 1.695114 CCATCCACCACGCCTCCATA 61.695 60.000 0.00 0.00 0.00 2.74
5834 6600 6.650807 TCTGAGCTAGACACAAACCATAAAAG 59.349 38.462 0.00 0.00 0.00 2.27
5836 6602 6.109156 TCTGAGCTAGACACAAACCATAAA 57.891 37.500 0.00 0.00 0.00 1.40
5875 6644 6.688073 AAGAACCTTATCTTCAGAGAACCA 57.312 37.500 0.00 0.00 34.60 3.67
5945 6719 2.222027 CTGAAGACAAACCTCCACACC 58.778 52.381 0.00 0.00 0.00 4.16
6022 6797 1.864711 CATGAACACAAACGGACGACT 59.135 47.619 0.00 0.00 0.00 4.18
6023 6798 1.595794 ACATGAACACAAACGGACGAC 59.404 47.619 0.00 0.00 0.00 4.34
6028 6803 3.558006 TGTAGACACATGAACACAAACGG 59.442 43.478 0.00 0.00 0.00 4.44
6063 6838 4.566759 CCAATGAAAAGAAGCGTAGATCGA 59.433 41.667 0.00 0.00 42.86 3.59
6078 6853 1.262950 CAACAGTCGTCGCCAATGAAA 59.737 47.619 0.00 0.00 0.00 2.69
6092 6867 1.290203 CAGCACACGAGAACAACAGT 58.710 50.000 0.00 0.00 0.00 3.55
6093 6869 0.583438 CCAGCACACGAGAACAACAG 59.417 55.000 0.00 0.00 0.00 3.16
6115 6891 1.545136 TCGTCGTACAAGGCCACATAA 59.455 47.619 5.01 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.