Multiple sequence alignment - TraesCS5B01G220100

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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 TraesCS5B01G220100 chr5B 100.000 2884 0 0 1 2884 394573401 394570518 0.000000e+00 5326.0
1 TraesCS5B01G220100 chr5B 88.825 1226 103 19 834 2032 394628228 394627010 0.000000e+00 1474.0
2 TraesCS5B01G220100 chr5B 89.255 1182 76 20 827 1978 394581213 394580053 0.000000e+00 1432.0
3 TraesCS5B01G220100 chr5B 95.642 826 23 9 2069 2884 545594030 545593208 0.000000e+00 1314.0
4 TraesCS5B01G220100 chr5B 93.659 820 35 9 2072 2884 493971103 493970294 0.000000e+00 1210.0
5 TraesCS5B01G220100 chr5B 82.712 295 29 11 382 664 394628753 394628469 2.870000e-60 243.0
6 TraesCS5B01G220100 chr5B 88.095 126 10 4 684 808 394628414 394628293 8.330000e-31 145.0
7 TraesCS5B01G220100 chr5B 93.103 87 6 0 664 750 394581429 394581343 8.390000e-26 128.0
8 TraesCS5B01G220100 chr5A 92.474 1249 67 13 839 2073 437393316 437392081 0.000000e+00 1760.0
9 TraesCS5B01G220100 chr5A 83.465 1772 167 56 339 2043 437413348 437411636 0.000000e+00 1533.0
10 TraesCS5B01G220100 chr5A 89.337 1116 74 21 834 1929 437400123 437399033 0.000000e+00 1360.0
11 TraesCS5B01G220100 chr5A 83.155 374 43 12 296 664 437393915 437393557 9.970000e-85 324.0
12 TraesCS5B01G220100 chr5A 81.498 227 31 7 402 625 437400668 437400450 2.950000e-40 176.0
13 TraesCS5B01G220100 chr5A 91.304 69 2 2 721 789 437393461 437393397 1.100000e-14 91.6
14 TraesCS5B01G220100 chr5D 91.463 1230 77 13 837 2041 336314796 336316022 0.000000e+00 1664.0
15 TraesCS5B01G220100 chr5D 88.815 1198 92 20 859 2041 336381453 336380283 0.000000e+00 1432.0
16 TraesCS5B01G220100 chr5D 90.674 1083 77 13 834 1898 336239935 336238859 0.000000e+00 1419.0
17 TraesCS5B01G220100 chr5D 89.973 1107 76 13 834 1929 336338471 336339553 0.000000e+00 1397.0
18 TraesCS5B01G220100 chr5D 88.309 479 39 7 1577 2041 336257245 336256770 2.510000e-155 558.0
19 TraesCS5B01G220100 chr5D 91.129 372 22 6 837 1197 336258012 336257641 7.180000e-136 494.0
20 TraesCS5B01G220100 chr5D 82.836 402 44 14 274 664 336258638 336258251 1.280000e-88 337.0
21 TraesCS5B01G220100 chr5D 82.836 402 44 14 274 664 336314170 336314557 1.280000e-88 337.0
22 TraesCS5B01G220100 chr5D 81.507 292 34 10 376 664 336240469 336240195 3.740000e-54 222.0
23 TraesCS5B01G220100 chr5D 81.164 292 35 10 376 664 336337937 336338211 1.740000e-52 217.0
24 TraesCS5B01G220100 chr5D 81.271 299 29 14 382 664 336382031 336381744 1.740000e-52 217.0
25 TraesCS5B01G220100 chr5D 89.032 155 9 4 684 834 336381689 336381539 4.910000e-43 185.0
26 TraesCS5B01G220100 chr5D 88.000 150 12 5 664 811 336240141 336239996 3.820000e-39 172.0
27 TraesCS5B01G220100 chr5D 88.000 150 12 5 661 808 336338262 336338407 3.820000e-39 172.0
28 TraesCS5B01G220100 chr5D 93.043 115 5 2 1959 2073 336238866 336238755 6.390000e-37 165.0
29 TraesCS5B01G220100 chr5D 91.304 69 2 2 721 789 336258155 336258091 1.100000e-14 91.6
30 TraesCS5B01G220100 chr5D 91.304 69 2 2 721 789 336314653 336314717 1.100000e-14 91.6
31 TraesCS5B01G220100 chr6B 98.409 817 7 4 2072 2882 592137655 592138471 0.000000e+00 1432.0
32 TraesCS5B01G220100 chr6B 93.750 736 11 6 2072 2801 125722470 125721764 0.000000e+00 1072.0
33 TraesCS5B01G220100 chr6B 98.980 98 1 0 2787 2884 125721748 125721651 2.950000e-40 176.0
34 TraesCS5B01G220100 chr2B 98.049 820 10 4 2071 2884 23731714 23730895 0.000000e+00 1421.0
35 TraesCS5B01G220100 chr2B 79.338 755 111 32 2071 2796 794320237 794319499 3.340000e-134 488.0
36 TraesCS5B01G220100 chr3A 91.697 819 38 11 2071 2882 111081693 111082488 0.000000e+00 1109.0
37 TraesCS5B01G220100 chr7A 91.463 820 37 13 2072 2884 619019760 619020553 0.000000e+00 1096.0
38 TraesCS5B01G220100 chr4B 86.700 797 62 29 2110 2884 8381664 8382438 0.000000e+00 845.0
39 TraesCS5B01G220100 chr3B 85.613 848 69 30 2073 2884 620145637 620144807 0.000000e+00 841.0
40 TraesCS5B01G220100 chr4A 85.313 783 69 28 2087 2852 35518850 35518097 0.000000e+00 767.0
41 TraesCS5B01G220100 chr4D 86.345 747 32 34 2070 2805 383872705 383873392 0.000000e+00 750.0
42 TraesCS5B01G220100 chr4D 92.964 469 28 2 2421 2884 383873792 383874260 0.000000e+00 678.0
43 TraesCS5B01G220100 chrUn 80.698 860 100 33 2071 2884 49812875 49813714 2.460000e-170 608.0


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 TraesCS5B01G220100 chr5B 394570518 394573401 2883 True 5326.000000 5326 100.000000 1 2884 1 chr5B.!!$R1 2883
1 TraesCS5B01G220100 chr5B 545593208 545594030 822 True 1314.000000 1314 95.642000 2069 2884 1 chr5B.!!$R3 815
2 TraesCS5B01G220100 chr5B 493970294 493971103 809 True 1210.000000 1210 93.659000 2072 2884 1 chr5B.!!$R2 812
3 TraesCS5B01G220100 chr5B 394580053 394581429 1376 True 780.000000 1432 91.179000 664 1978 2 chr5B.!!$R4 1314
4 TraesCS5B01G220100 chr5B 394627010 394628753 1743 True 620.666667 1474 86.544000 382 2032 3 chr5B.!!$R5 1650
5 TraesCS5B01G220100 chr5A 437411636 437413348 1712 True 1533.000000 1533 83.465000 339 2043 1 chr5A.!!$R1 1704
6 TraesCS5B01G220100 chr5A 437399033 437400668 1635 True 768.000000 1360 85.417500 402 1929 2 chr5A.!!$R3 1527
7 TraesCS5B01G220100 chr5A 437392081 437393915 1834 True 725.200000 1760 88.977667 296 2073 3 chr5A.!!$R2 1777
8 TraesCS5B01G220100 chr5D 336314170 336316022 1852 False 697.533333 1664 88.534333 274 2041 3 chr5D.!!$F1 1767
9 TraesCS5B01G220100 chr5D 336380283 336382031 1748 True 611.333333 1432 86.372667 382 2041 3 chr5D.!!$R3 1659
10 TraesCS5B01G220100 chr5D 336337937 336339553 1616 False 595.333333 1397 86.379000 376 1929 3 chr5D.!!$F2 1553
11 TraesCS5B01G220100 chr5D 336238755 336240469 1714 True 494.500000 1419 88.306000 376 2073 4 chr5D.!!$R1 1697
12 TraesCS5B01G220100 chr5D 336256770 336258638 1868 True 370.150000 558 88.394500 274 2041 4 chr5D.!!$R2 1767
13 TraesCS5B01G220100 chr6B 592137655 592138471 816 False 1432.000000 1432 98.409000 2072 2882 1 chr6B.!!$F1 810
14 TraesCS5B01G220100 chr6B 125721651 125722470 819 True 624.000000 1072 96.365000 2072 2884 2 chr6B.!!$R1 812
15 TraesCS5B01G220100 chr2B 23730895 23731714 819 True 1421.000000 1421 98.049000 2071 2884 1 chr2B.!!$R1 813
16 TraesCS5B01G220100 chr2B 794319499 794320237 738 True 488.000000 488 79.338000 2071 2796 1 chr2B.!!$R2 725
17 TraesCS5B01G220100 chr3A 111081693 111082488 795 False 1109.000000 1109 91.697000 2071 2882 1 chr3A.!!$F1 811
18 TraesCS5B01G220100 chr7A 619019760 619020553 793 False 1096.000000 1096 91.463000 2072 2884 1 chr7A.!!$F1 812
19 TraesCS5B01G220100 chr4B 8381664 8382438 774 False 845.000000 845 86.700000 2110 2884 1 chr4B.!!$F1 774
20 TraesCS5B01G220100 chr3B 620144807 620145637 830 True 841.000000 841 85.613000 2073 2884 1 chr3B.!!$R1 811
21 TraesCS5B01G220100 chr4A 35518097 35518850 753 True 767.000000 767 85.313000 2087 2852 1 chr4A.!!$R1 765
22 TraesCS5B01G220100 chr4D 383872705 383874260 1555 False 714.000000 750 89.654500 2070 2884 2 chr4D.!!$F1 814
23 TraesCS5B01G220100 chrUn 49812875 49813714 839 False 608.000000 608 80.698000 2071 2884 1 chrUn.!!$F1 813

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
475 497 0.244994 CTTCGTGTGAGGACTGAGGG 59.755 60.0 0.0 0.0 0.0 4.30 F
476 498 0.469331 TTCGTGTGAGGACTGAGGGT 60.469 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1807 0.456221 ACTCGGTGATCTTGGCGTAG 59.544 55.0 0.0 0.0 0.0 3.51 R
1941 2302 0.737219 GCAGGTTGTCATCTGGCATC 59.263 55.0 0.0 0.0 0.0 3.91 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 3.430473 AACGAATTGACTGGCCCAA 57.570 47.368 0.00 0.00 0.00 4.12
19 20 1.698506 AACGAATTGACTGGCCCAAA 58.301 45.000 0.00 0.00 0.00 3.28
20 21 1.698506 ACGAATTGACTGGCCCAAAA 58.301 45.000 0.00 0.00 0.00 2.44
21 22 2.247358 ACGAATTGACTGGCCCAAAAT 58.753 42.857 0.00 0.00 0.00 1.82
22 23 2.632512 ACGAATTGACTGGCCCAAAATT 59.367 40.909 0.00 1.03 0.00 1.82
23 24 3.829601 ACGAATTGACTGGCCCAAAATTA 59.170 39.130 0.00 0.00 0.00 1.40
24 25 4.282195 ACGAATTGACTGGCCCAAAATTAA 59.718 37.500 0.00 0.00 0.00 1.40
25 26 4.625311 CGAATTGACTGGCCCAAAATTAAC 59.375 41.667 0.00 0.00 0.00 2.01
26 27 3.651803 TTGACTGGCCCAAAATTAACG 57.348 42.857 0.00 0.00 0.00 3.18
27 28 2.588620 TGACTGGCCCAAAATTAACGT 58.411 42.857 0.00 0.00 0.00 3.99
28 29 2.554893 TGACTGGCCCAAAATTAACGTC 59.445 45.455 0.00 0.00 0.00 4.34
29 30 2.817844 GACTGGCCCAAAATTAACGTCT 59.182 45.455 0.00 0.00 0.00 4.18
30 31 2.817844 ACTGGCCCAAAATTAACGTCTC 59.182 45.455 0.00 0.00 0.00 3.36
31 32 3.081804 CTGGCCCAAAATTAACGTCTCT 58.918 45.455 0.00 0.00 0.00 3.10
32 33 3.492337 TGGCCCAAAATTAACGTCTCTT 58.508 40.909 0.00 0.00 0.00 2.85
33 34 4.653868 TGGCCCAAAATTAACGTCTCTTA 58.346 39.130 0.00 0.00 0.00 2.10
34 35 5.071370 TGGCCCAAAATTAACGTCTCTTAA 58.929 37.500 0.00 0.00 0.00 1.85
35 36 5.535406 TGGCCCAAAATTAACGTCTCTTAAA 59.465 36.000 0.00 0.00 0.00 1.52
36 37 6.040616 TGGCCCAAAATTAACGTCTCTTAAAA 59.959 34.615 0.00 0.00 0.00 1.52
37 38 6.924612 GGCCCAAAATTAACGTCTCTTAAAAA 59.075 34.615 0.00 0.00 0.00 1.94
38 39 7.601130 GGCCCAAAATTAACGTCTCTTAAAAAT 59.399 33.333 0.00 0.00 0.00 1.82
39 40 8.984764 GCCCAAAATTAACGTCTCTTAAAAATT 58.015 29.630 0.00 0.00 0.00 1.82
46 47 6.510879 AACGTCTCTTAAAAATTCCCATCC 57.489 37.500 0.00 0.00 0.00 3.51
47 48 4.948004 ACGTCTCTTAAAAATTCCCATCCC 59.052 41.667 0.00 0.00 0.00 3.85
48 49 4.947388 CGTCTCTTAAAAATTCCCATCCCA 59.053 41.667 0.00 0.00 0.00 4.37
49 50 5.417580 CGTCTCTTAAAAATTCCCATCCCAA 59.582 40.000 0.00 0.00 0.00 4.12
50 51 6.071616 CGTCTCTTAAAAATTCCCATCCCAAA 60.072 38.462 0.00 0.00 0.00 3.28
51 52 7.524698 CGTCTCTTAAAAATTCCCATCCCAAAA 60.525 37.037 0.00 0.00 0.00 2.44
52 53 7.602644 GTCTCTTAAAAATTCCCATCCCAAAAC 59.397 37.037 0.00 0.00 0.00 2.43
53 54 7.291182 TCTCTTAAAAATTCCCATCCCAAAACA 59.709 33.333 0.00 0.00 0.00 2.83
54 55 7.806180 TCTTAAAAATTCCCATCCCAAAACAA 58.194 30.769 0.00 0.00 0.00 2.83
55 56 7.936301 TCTTAAAAATTCCCATCCCAAAACAAG 59.064 33.333 0.00 0.00 0.00 3.16
56 57 5.903198 AAAATTCCCATCCCAAAACAAGA 57.097 34.783 0.00 0.00 0.00 3.02
57 58 4.890158 AATTCCCATCCCAAAACAAGAC 57.110 40.909 0.00 0.00 0.00 3.01
58 59 3.611025 TTCCCATCCCAAAACAAGACT 57.389 42.857 0.00 0.00 0.00 3.24
59 60 3.611025 TCCCATCCCAAAACAAGACTT 57.389 42.857 0.00 0.00 0.00 3.01
60 61 4.733077 TCCCATCCCAAAACAAGACTTA 57.267 40.909 0.00 0.00 0.00 2.24
61 62 4.403734 TCCCATCCCAAAACAAGACTTAC 58.596 43.478 0.00 0.00 0.00 2.34
62 63 3.509967 CCCATCCCAAAACAAGACTTACC 59.490 47.826 0.00 0.00 0.00 2.85
63 64 4.148838 CCATCCCAAAACAAGACTTACCA 58.851 43.478 0.00 0.00 0.00 3.25
64 65 4.022329 CCATCCCAAAACAAGACTTACCAC 60.022 45.833 0.00 0.00 0.00 4.16
65 66 4.237976 TCCCAAAACAAGACTTACCACA 57.762 40.909 0.00 0.00 0.00 4.17
66 67 3.949113 TCCCAAAACAAGACTTACCACAC 59.051 43.478 0.00 0.00 0.00 3.82
67 68 3.242936 CCCAAAACAAGACTTACCACACG 60.243 47.826 0.00 0.00 0.00 4.49
68 69 3.375922 CCAAAACAAGACTTACCACACGT 59.624 43.478 0.00 0.00 0.00 4.49
69 70 4.571580 CCAAAACAAGACTTACCACACGTA 59.428 41.667 0.00 0.00 0.00 3.57
70 71 5.495502 CAAAACAAGACTTACCACACGTAC 58.504 41.667 0.00 0.00 0.00 3.67
71 72 4.389890 AACAAGACTTACCACACGTACA 57.610 40.909 0.00 0.00 0.00 2.90
72 73 4.389890 ACAAGACTTACCACACGTACAA 57.610 40.909 0.00 0.00 0.00 2.41
73 74 4.114794 ACAAGACTTACCACACGTACAAC 58.885 43.478 0.00 0.00 0.00 3.32
74 75 4.142093 ACAAGACTTACCACACGTACAACT 60.142 41.667 0.00 0.00 0.00 3.16
75 76 3.973657 AGACTTACCACACGTACAACTG 58.026 45.455 0.00 0.00 0.00 3.16
76 77 3.633525 AGACTTACCACACGTACAACTGA 59.366 43.478 0.00 0.00 0.00 3.41
77 78 3.709987 ACTTACCACACGTACAACTGAC 58.290 45.455 0.00 0.00 0.00 3.51
78 79 3.130869 ACTTACCACACGTACAACTGACA 59.869 43.478 0.00 0.00 0.00 3.58
79 80 2.676632 ACCACACGTACAACTGACAA 57.323 45.000 0.00 0.00 0.00 3.18
80 81 2.975266 ACCACACGTACAACTGACAAA 58.025 42.857 0.00 0.00 0.00 2.83
81 82 3.336468 ACCACACGTACAACTGACAAAA 58.664 40.909 0.00 0.00 0.00 2.44
82 83 3.752222 ACCACACGTACAACTGACAAAAA 59.248 39.130 0.00 0.00 0.00 1.94
102 103 4.954092 AAATGAGAACGAATCTTGGAGC 57.046 40.909 0.00 0.00 38.96 4.70
103 104 3.616956 ATGAGAACGAATCTTGGAGCA 57.383 42.857 0.00 0.00 38.96 4.26
104 105 2.964740 TGAGAACGAATCTTGGAGCAG 58.035 47.619 0.00 0.00 38.96 4.24
105 106 1.663135 GAGAACGAATCTTGGAGCAGC 59.337 52.381 0.00 0.00 38.96 5.25
106 107 1.002430 AGAACGAATCTTGGAGCAGCA 59.998 47.619 0.00 0.00 33.39 4.41
107 108 1.806542 GAACGAATCTTGGAGCAGCAA 59.193 47.619 0.00 0.00 0.00 3.91
108 109 2.119801 ACGAATCTTGGAGCAGCAAT 57.880 45.000 0.00 0.00 0.00 3.56
109 110 2.012673 ACGAATCTTGGAGCAGCAATC 58.987 47.619 0.00 0.00 0.00 2.67
110 111 2.011947 CGAATCTTGGAGCAGCAATCA 58.988 47.619 0.00 0.00 0.00 2.57
111 112 2.421073 CGAATCTTGGAGCAGCAATCAA 59.579 45.455 0.00 0.00 0.00 2.57
112 113 3.730061 CGAATCTTGGAGCAGCAATCAAC 60.730 47.826 0.00 0.00 0.00 3.18
113 114 2.275134 TCTTGGAGCAGCAATCAACA 57.725 45.000 0.00 0.00 0.00 3.33
114 115 2.156917 TCTTGGAGCAGCAATCAACAG 58.843 47.619 0.00 0.00 0.00 3.16
115 116 0.599558 TTGGAGCAGCAATCAACAGC 59.400 50.000 0.00 0.00 0.00 4.40
116 117 1.246056 TGGAGCAGCAATCAACAGCC 61.246 55.000 0.00 0.00 0.00 4.85
117 118 1.246056 GGAGCAGCAATCAACAGCCA 61.246 55.000 0.00 0.00 0.00 4.75
118 119 0.599558 GAGCAGCAATCAACAGCCAA 59.400 50.000 0.00 0.00 0.00 4.52
119 120 1.000060 GAGCAGCAATCAACAGCCAAA 60.000 47.619 0.00 0.00 0.00 3.28
120 121 1.413445 AGCAGCAATCAACAGCCAAAA 59.587 42.857 0.00 0.00 0.00 2.44
121 122 2.158928 AGCAGCAATCAACAGCCAAAAA 60.159 40.909 0.00 0.00 0.00 1.94
165 166 6.995511 TTTTTAGGCGAATTACATGTAGCT 57.004 33.333 12.84 0.00 0.00 3.32
167 168 8.495361 TTTTTAGGCGAATTACATGTAGCTAA 57.505 30.769 12.84 8.00 0.00 3.09
168 169 8.495361 TTTTAGGCGAATTACATGTAGCTAAA 57.505 30.769 12.84 11.88 0.00 1.85
169 170 7.709269 TTAGGCGAATTACATGTAGCTAAAG 57.291 36.000 12.84 3.71 0.00 1.85
170 171 5.671493 AGGCGAATTACATGTAGCTAAAGT 58.329 37.500 12.84 0.00 0.00 2.66
171 172 5.523916 AGGCGAATTACATGTAGCTAAAGTG 59.476 40.000 12.84 0.00 0.00 3.16
172 173 5.522460 GGCGAATTACATGTAGCTAAAGTGA 59.478 40.000 12.84 0.00 0.00 3.41
173 174 6.036735 GGCGAATTACATGTAGCTAAAGTGAA 59.963 38.462 12.84 0.00 0.00 3.18
174 175 7.413657 GGCGAATTACATGTAGCTAAAGTGAAA 60.414 37.037 12.84 0.00 0.00 2.69
175 176 8.122952 GCGAATTACATGTAGCTAAAGTGAAAT 58.877 33.333 5.56 0.00 0.00 2.17
176 177 9.988350 CGAATTACATGTAGCTAAAGTGAAATT 57.012 29.630 5.56 0.38 0.00 1.82
287 288 9.643693 CATTTTCCCCTTATAATTGTATGATGC 57.356 33.333 0.00 0.00 0.00 3.91
288 289 7.447374 TTTCCCCTTATAATTGTATGATGCG 57.553 36.000 0.00 0.00 0.00 4.73
290 291 6.957631 TCCCCTTATAATTGTATGATGCGAT 58.042 36.000 0.00 0.00 0.00 4.58
362 372 4.074259 AGTACTTGCATGCACTTGATGAA 58.926 39.130 22.58 1.44 0.00 2.57
364 374 3.909430 ACTTGCATGCACTTGATGAAAG 58.091 40.909 22.58 14.15 40.91 2.62
380 390 9.282247 CTTGATGAAAGTAAGTGTTTGCATATC 57.718 33.333 0.00 0.00 0.00 1.63
398 408 6.261603 TGCATATCTGTGCTCCAAAATAAGAG 59.738 38.462 0.64 0.00 45.27 2.85
441 455 7.584987 AGGAACAGTTTCAATTTTATGTCGAG 58.415 34.615 0.00 0.00 32.80 4.04
446 460 6.797033 CAGTTTCAATTTTATGTCGAGTGGTC 59.203 38.462 0.00 0.00 0.00 4.02
471 493 2.509052 TGTTCTTCGTGTGAGGACTG 57.491 50.000 0.00 0.00 28.70 3.51
475 497 0.244994 CTTCGTGTGAGGACTGAGGG 59.755 60.000 0.00 0.00 0.00 4.30
476 498 0.469331 TTCGTGTGAGGACTGAGGGT 60.469 55.000 0.00 0.00 0.00 4.34
477 499 0.894184 TCGTGTGAGGACTGAGGGTC 60.894 60.000 0.00 0.00 43.79 4.46
478 500 0.896019 CGTGTGAGGACTGAGGGTCT 60.896 60.000 0.00 0.00 43.97 3.85
479 501 1.343069 GTGTGAGGACTGAGGGTCTT 58.657 55.000 0.00 0.00 43.97 3.01
480 502 1.001406 GTGTGAGGACTGAGGGTCTTG 59.999 57.143 0.00 0.00 43.97 3.02
526 551 9.586435 GCTGCTAATTATTACTTCCAAAACAAT 57.414 29.630 0.00 0.00 0.00 2.71
545 570 6.715344 ACAATAAGAAAGCACGACGATTTA 57.285 33.333 0.00 0.00 0.00 1.40
548 574 7.692291 ACAATAAGAAAGCACGACGATTTATTG 59.308 33.333 0.00 11.96 40.44 1.90
552 578 5.178623 AGAAAGCACGACGATTTATTGAACA 59.821 36.000 0.00 0.00 0.00 3.18
562 595 2.396590 TTATTGAACACGGAGAGCCC 57.603 50.000 0.00 0.00 0.00 5.19
563 596 0.539986 TATTGAACACGGAGAGCCCC 59.460 55.000 0.00 0.00 0.00 5.80
564 597 2.198304 ATTGAACACGGAGAGCCCCC 62.198 60.000 0.00 0.00 0.00 5.40
596 630 0.994995 CAGTGATCTTGAACGGCTCG 59.005 55.000 0.00 0.00 0.00 5.03
613 653 2.288518 GCTCGTTGACAAAGTCTCCTCT 60.289 50.000 0.98 0.00 33.15 3.69
615 655 4.558898 GCTCGTTGACAAAGTCTCCTCTAA 60.559 45.833 0.98 0.00 33.15 2.10
627 693 6.232581 AGTCTCCTCTAAAAGACCATGATG 57.767 41.667 0.00 0.00 42.34 3.07
629 695 6.441924 AGTCTCCTCTAAAAGACCATGATGAA 59.558 38.462 0.00 0.00 42.34 2.57
647 713 3.259064 TGAAACGGCTGCTGACTAATAC 58.741 45.455 16.72 0.32 0.00 1.89
763 929 0.516877 ATGTTGCATTGGTCGTGTCG 59.483 50.000 0.00 0.00 0.00 4.35
764 930 0.530870 TGTTGCATTGGTCGTGTCGA 60.531 50.000 0.00 0.00 0.00 4.20
765 931 0.796312 GTTGCATTGGTCGTGTCGAT 59.204 50.000 0.00 0.00 38.42 3.59
766 932 1.075542 TTGCATTGGTCGTGTCGATC 58.924 50.000 0.00 0.00 38.42 3.69
767 933 1.075979 TGCATTGGTCGTGTCGATCG 61.076 55.000 9.36 9.36 40.17 3.69
778 945 1.927174 GTGTCGATCGGACCAAGAATG 59.073 52.381 16.41 0.00 45.46 2.67
811 978 2.162408 GCTCGACCATCCAAAAAGAAGG 59.838 50.000 0.00 0.00 0.00 3.46
814 983 3.326588 TCGACCATCCAAAAAGAAGGAGA 59.673 43.478 0.00 0.00 37.34 3.71
816 985 3.759086 GACCATCCAAAAAGAAGGAGACC 59.241 47.826 0.00 0.00 37.34 3.85
991 1274 1.696832 GCTGCAAGAACCGATCCGAC 61.697 60.000 0.00 0.00 34.07 4.79
1347 1666 2.587194 CTCGGCATCTGCTTCGGG 60.587 66.667 1.70 0.00 41.70 5.14
1636 1971 3.315949 GCCACCCGGAGTACACCA 61.316 66.667 0.73 0.00 0.00 4.17
1637 1972 2.886134 GCCACCCGGAGTACACCAA 61.886 63.158 0.73 0.00 0.00 3.67
1671 2006 4.225340 CTCGTCGACCGCCTCTCG 62.225 72.222 10.58 0.00 36.19 4.04
1722 2074 3.306364 CCCTCTAGCTATGTGGTGCATAC 60.306 52.174 0.00 0.00 38.94 2.39
1745 2105 3.496870 GCCATTGTTACTCCAGGATAGGG 60.497 52.174 0.00 0.00 0.00 3.53
1755 2115 3.048600 TCCAGGATAGGGTCTGATTTGG 58.951 50.000 0.00 0.00 33.11 3.28
1864 2224 4.202050 GCTCTGCAAAAGTTTCCTCAAGAA 60.202 41.667 0.00 0.00 0.00 2.52
1879 2239 8.728337 TTCCTCAAGAATGAAGAATCATACTG 57.272 34.615 0.00 0.00 45.60 2.74
1941 2302 2.357034 ACTAGCGGCGTGGTGTTG 60.357 61.111 9.37 0.00 0.00 3.33
1964 2329 1.162698 CCAGATGACAACCTGCAGTG 58.837 55.000 13.81 7.93 0.00 3.66
2361 2798 9.661563 TTTCTTCTTCTCTTTACTGTGTGTTAA 57.338 29.630 0.00 0.00 0.00 2.01
2362 2799 9.832445 TTCTTCTTCTCTTTACTGTGTGTTAAT 57.168 29.630 0.00 0.00 0.00 1.40
2589 3468 7.828508 AATGTTCAATGCCTATATCACACAT 57.171 32.000 0.00 0.00 0.00 3.21
2616 3901 9.643693 ATGTTCAGTGCCTATTTAGAAATTTTG 57.356 29.630 0.00 0.00 0.00 2.44
2743 4052 6.200286 CGCACCGAATTAATCACTAGTATTGT 59.800 38.462 0.00 0.00 0.00 2.71
2768 4077 5.538813 TGAGCTCAACTGGTAAAGAAGACTA 59.461 40.000 15.67 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.698506 TTTGGGCCAGTCAATTCGTT 58.301 45.000 6.23 0.00 0.00 3.85
1 2 1.698506 TTTTGGGCCAGTCAATTCGT 58.301 45.000 6.23 0.00 0.00 3.85
3 4 4.625311 CGTTAATTTTGGGCCAGTCAATTC 59.375 41.667 18.46 8.92 0.00 2.17
4 5 4.039852 ACGTTAATTTTGGGCCAGTCAATT 59.960 37.500 18.75 18.75 0.00 2.32
5 6 3.576550 ACGTTAATTTTGGGCCAGTCAAT 59.423 39.130 6.23 4.02 0.00 2.57
6 7 2.959707 ACGTTAATTTTGGGCCAGTCAA 59.040 40.909 6.23 1.40 0.00 3.18
7 8 2.554893 GACGTTAATTTTGGGCCAGTCA 59.445 45.455 6.23 0.00 0.00 3.41
8 9 2.817844 AGACGTTAATTTTGGGCCAGTC 59.182 45.455 6.23 8.29 0.00 3.51
9 10 2.817844 GAGACGTTAATTTTGGGCCAGT 59.182 45.455 6.23 0.00 0.00 4.00
10 11 3.081804 AGAGACGTTAATTTTGGGCCAG 58.918 45.455 6.23 0.00 0.00 4.85
11 12 3.149005 AGAGACGTTAATTTTGGGCCA 57.851 42.857 0.00 0.00 0.00 5.36
12 13 5.632244 TTAAGAGACGTTAATTTTGGGCC 57.368 39.130 0.00 0.00 0.00 5.80
13 14 7.933728 TTTTTAAGAGACGTTAATTTTGGGC 57.066 32.000 0.00 0.00 0.00 5.36
20 21 8.683615 GGATGGGAATTTTTAAGAGACGTTAAT 58.316 33.333 0.00 0.00 0.00 1.40
21 22 7.121611 GGGATGGGAATTTTTAAGAGACGTTAA 59.878 37.037 0.00 0.00 0.00 2.01
22 23 6.600427 GGGATGGGAATTTTTAAGAGACGTTA 59.400 38.462 0.00 0.00 0.00 3.18
23 24 5.417894 GGGATGGGAATTTTTAAGAGACGTT 59.582 40.000 0.00 0.00 0.00 3.99
24 25 4.948004 GGGATGGGAATTTTTAAGAGACGT 59.052 41.667 0.00 0.00 0.00 4.34
25 26 4.947388 TGGGATGGGAATTTTTAAGAGACG 59.053 41.667 0.00 0.00 0.00 4.18
26 27 6.850752 TTGGGATGGGAATTTTTAAGAGAC 57.149 37.500 0.00 0.00 0.00 3.36
27 28 7.291182 TGTTTTGGGATGGGAATTTTTAAGAGA 59.709 33.333 0.00 0.00 0.00 3.10
28 29 7.449247 TGTTTTGGGATGGGAATTTTTAAGAG 58.551 34.615 0.00 0.00 0.00 2.85
29 30 7.380423 TGTTTTGGGATGGGAATTTTTAAGA 57.620 32.000 0.00 0.00 0.00 2.10
30 31 7.936301 TCTTGTTTTGGGATGGGAATTTTTAAG 59.064 33.333 0.00 0.00 0.00 1.85
31 32 7.717436 GTCTTGTTTTGGGATGGGAATTTTTAA 59.283 33.333 0.00 0.00 0.00 1.52
32 33 7.071824 AGTCTTGTTTTGGGATGGGAATTTTTA 59.928 33.333 0.00 0.00 0.00 1.52
33 34 6.061441 GTCTTGTTTTGGGATGGGAATTTTT 58.939 36.000 0.00 0.00 0.00 1.94
34 35 5.369404 AGTCTTGTTTTGGGATGGGAATTTT 59.631 36.000 0.00 0.00 0.00 1.82
35 36 4.907269 AGTCTTGTTTTGGGATGGGAATTT 59.093 37.500 0.00 0.00 0.00 1.82
36 37 4.492646 AGTCTTGTTTTGGGATGGGAATT 58.507 39.130 0.00 0.00 0.00 2.17
37 38 4.132122 AGTCTTGTTTTGGGATGGGAAT 57.868 40.909 0.00 0.00 0.00 3.01
38 39 3.611025 AGTCTTGTTTTGGGATGGGAA 57.389 42.857 0.00 0.00 0.00 3.97
39 40 3.611025 AAGTCTTGTTTTGGGATGGGA 57.389 42.857 0.00 0.00 0.00 4.37
40 41 3.509967 GGTAAGTCTTGTTTTGGGATGGG 59.490 47.826 0.00 0.00 0.00 4.00
41 42 4.022329 GTGGTAAGTCTTGTTTTGGGATGG 60.022 45.833 0.00 0.00 0.00 3.51
42 43 4.582656 TGTGGTAAGTCTTGTTTTGGGATG 59.417 41.667 0.00 0.00 0.00 3.51
43 44 4.583073 GTGTGGTAAGTCTTGTTTTGGGAT 59.417 41.667 0.00 0.00 0.00 3.85
44 45 3.949113 GTGTGGTAAGTCTTGTTTTGGGA 59.051 43.478 0.00 0.00 0.00 4.37
45 46 3.242936 CGTGTGGTAAGTCTTGTTTTGGG 60.243 47.826 0.00 0.00 0.00 4.12
46 47 3.375922 ACGTGTGGTAAGTCTTGTTTTGG 59.624 43.478 0.00 0.00 0.00 3.28
47 48 4.609691 ACGTGTGGTAAGTCTTGTTTTG 57.390 40.909 0.00 0.00 0.00 2.44
48 49 5.177326 TGTACGTGTGGTAAGTCTTGTTTT 58.823 37.500 0.00 0.00 31.61 2.43
49 50 4.757594 TGTACGTGTGGTAAGTCTTGTTT 58.242 39.130 0.00 0.00 31.61 2.83
50 51 4.389890 TGTACGTGTGGTAAGTCTTGTT 57.610 40.909 0.00 0.00 31.61 2.83
51 52 4.114794 GTTGTACGTGTGGTAAGTCTTGT 58.885 43.478 0.00 0.00 31.61 3.16
52 53 4.208460 CAGTTGTACGTGTGGTAAGTCTTG 59.792 45.833 0.00 0.00 31.61 3.02
53 54 4.098349 TCAGTTGTACGTGTGGTAAGTCTT 59.902 41.667 0.00 0.00 31.61 3.01
54 55 3.633525 TCAGTTGTACGTGTGGTAAGTCT 59.366 43.478 0.00 0.00 31.61 3.24
55 56 3.732721 GTCAGTTGTACGTGTGGTAAGTC 59.267 47.826 0.00 0.00 31.61 3.01
56 57 3.130869 TGTCAGTTGTACGTGTGGTAAGT 59.869 43.478 0.00 0.00 31.61 2.24
57 58 3.708890 TGTCAGTTGTACGTGTGGTAAG 58.291 45.455 0.00 0.00 31.61 2.34
58 59 3.797451 TGTCAGTTGTACGTGTGGTAA 57.203 42.857 0.00 0.00 31.61 2.85
59 60 3.797451 TTGTCAGTTGTACGTGTGGTA 57.203 42.857 0.00 0.00 0.00 3.25
60 61 2.676632 TTGTCAGTTGTACGTGTGGT 57.323 45.000 0.00 0.00 0.00 4.16
61 62 4.343811 TTTTTGTCAGTTGTACGTGTGG 57.656 40.909 0.00 0.00 0.00 4.17
79 80 5.241506 TGCTCCAAGATTCGTTCTCATTTTT 59.758 36.000 0.00 0.00 31.78 1.94
80 81 4.761739 TGCTCCAAGATTCGTTCTCATTTT 59.238 37.500 0.00 0.00 31.78 1.82
81 82 4.326826 TGCTCCAAGATTCGTTCTCATTT 58.673 39.130 0.00 0.00 31.78 2.32
82 83 3.937706 CTGCTCCAAGATTCGTTCTCATT 59.062 43.478 0.00 0.00 31.78 2.57
83 84 3.529533 CTGCTCCAAGATTCGTTCTCAT 58.470 45.455 0.00 0.00 31.78 2.90
84 85 2.932622 GCTGCTCCAAGATTCGTTCTCA 60.933 50.000 0.00 0.00 31.78 3.27
85 86 1.663135 GCTGCTCCAAGATTCGTTCTC 59.337 52.381 0.00 0.00 31.78 2.87
86 87 1.002430 TGCTGCTCCAAGATTCGTTCT 59.998 47.619 0.00 0.00 35.70 3.01
87 88 1.442769 TGCTGCTCCAAGATTCGTTC 58.557 50.000 0.00 0.00 0.00 3.95
88 89 1.896220 TTGCTGCTCCAAGATTCGTT 58.104 45.000 0.00 0.00 0.00 3.85
89 90 2.012673 GATTGCTGCTCCAAGATTCGT 58.987 47.619 0.00 0.00 0.00 3.85
90 91 2.011947 TGATTGCTGCTCCAAGATTCG 58.988 47.619 0.00 0.00 0.00 3.34
91 92 3.192001 TGTTGATTGCTGCTCCAAGATTC 59.808 43.478 0.00 0.00 0.00 2.52
92 93 3.159472 TGTTGATTGCTGCTCCAAGATT 58.841 40.909 0.00 0.00 0.00 2.40
93 94 2.753452 CTGTTGATTGCTGCTCCAAGAT 59.247 45.455 0.00 0.00 0.00 2.40
94 95 2.156917 CTGTTGATTGCTGCTCCAAGA 58.843 47.619 0.00 0.59 0.00 3.02
95 96 1.402456 GCTGTTGATTGCTGCTCCAAG 60.402 52.381 0.00 0.00 0.00 3.61
96 97 0.599558 GCTGTTGATTGCTGCTCCAA 59.400 50.000 0.00 0.00 0.00 3.53
97 98 1.246056 GGCTGTTGATTGCTGCTCCA 61.246 55.000 0.00 0.00 0.00 3.86
98 99 1.246056 TGGCTGTTGATTGCTGCTCC 61.246 55.000 0.00 0.00 0.00 4.70
99 100 0.599558 TTGGCTGTTGATTGCTGCTC 59.400 50.000 0.00 0.00 0.00 4.26
100 101 1.042229 TTTGGCTGTTGATTGCTGCT 58.958 45.000 0.00 0.00 0.00 4.24
101 102 1.868469 TTTTGGCTGTTGATTGCTGC 58.132 45.000 0.00 0.00 0.00 5.25
142 143 6.995511 AGCTACATGTAATTCGCCTAAAAA 57.004 33.333 7.06 0.00 0.00 1.94
143 144 8.495361 TTTAGCTACATGTAATTCGCCTAAAA 57.505 30.769 7.06 5.55 0.00 1.52
144 145 7.767198 ACTTTAGCTACATGTAATTCGCCTAAA 59.233 33.333 7.06 11.10 0.00 1.85
145 146 7.223971 CACTTTAGCTACATGTAATTCGCCTAA 59.776 37.037 7.06 5.25 0.00 2.69
146 147 6.700081 CACTTTAGCTACATGTAATTCGCCTA 59.300 38.462 7.06 0.00 0.00 3.93
147 148 5.523916 CACTTTAGCTACATGTAATTCGCCT 59.476 40.000 7.06 0.71 0.00 5.52
148 149 5.522460 TCACTTTAGCTACATGTAATTCGCC 59.478 40.000 7.06 0.00 0.00 5.54
149 150 6.583912 TCACTTTAGCTACATGTAATTCGC 57.416 37.500 7.06 6.86 0.00 4.70
150 151 9.988350 AATTTCACTTTAGCTACATGTAATTCG 57.012 29.630 7.06 0.00 0.00 3.34
246 247 9.859152 AAGGGGAAAATGTTTTTCATTCAATTA 57.141 25.926 13.09 0.00 44.85 1.40
247 248 8.765488 AAGGGGAAAATGTTTTTCATTCAATT 57.235 26.923 13.09 0.00 44.85 2.32
261 262 9.643693 GCATCATACAATTATAAGGGGAAAATG 57.356 33.333 0.00 0.00 0.00 2.32
262 263 8.522830 CGCATCATACAATTATAAGGGGAAAAT 58.477 33.333 0.00 0.00 0.00 1.82
263 264 7.721842 TCGCATCATACAATTATAAGGGGAAAA 59.278 33.333 0.00 0.00 0.00 2.29
264 265 7.227873 TCGCATCATACAATTATAAGGGGAAA 58.772 34.615 0.00 0.00 0.00 3.13
265 266 6.774673 TCGCATCATACAATTATAAGGGGAA 58.225 36.000 0.00 0.00 0.00 3.97
266 267 6.367374 TCGCATCATACAATTATAAGGGGA 57.633 37.500 0.00 0.00 0.00 4.81
267 268 6.038603 CCATCGCATCATACAATTATAAGGGG 59.961 42.308 0.00 0.00 0.00 4.79
268 269 6.823182 TCCATCGCATCATACAATTATAAGGG 59.177 38.462 0.00 0.00 0.00 3.95
269 270 7.848223 TCCATCGCATCATACAATTATAAGG 57.152 36.000 0.00 0.00 0.00 2.69
270 271 9.712359 CATTCCATCGCATCATACAATTATAAG 57.288 33.333 0.00 0.00 0.00 1.73
271 272 8.183536 GCATTCCATCGCATCATACAATTATAA 58.816 33.333 0.00 0.00 0.00 0.98
272 273 7.553760 AGCATTCCATCGCATCATACAATTATA 59.446 33.333 0.00 0.00 0.00 0.98
277 278 3.479489 AGCATTCCATCGCATCATACAA 58.521 40.909 0.00 0.00 0.00 2.41
284 285 3.598019 AAAACAAGCATTCCATCGCAT 57.402 38.095 0.00 0.00 0.00 4.73
320 327 5.272405 ACTCCGTATCCTATATCCACCTT 57.728 43.478 0.00 0.00 0.00 3.50
322 329 5.753716 AGTACTCCGTATCCTATATCCACC 58.246 45.833 0.00 0.00 0.00 4.61
362 372 5.942872 GCACAGATATGCAAACACTTACTT 58.057 37.500 0.00 0.00 45.39 2.24
380 390 6.151648 TCCATTTCTCTTATTTTGGAGCACAG 59.848 38.462 0.00 0.00 0.00 3.66
398 408 5.765182 TGTTCCTTGAAGAGTTCTCCATTTC 59.235 40.000 0.00 0.00 0.00 2.17
441 455 3.621715 ACACGAAGAACAAAGAAGACCAC 59.378 43.478 0.00 0.00 0.00 4.16
446 460 4.025647 GTCCTCACACGAAGAACAAAGAAG 60.026 45.833 0.00 0.00 0.00 2.85
471 493 3.181456 CCAATGGAGAGATCAAGACCCTC 60.181 52.174 0.00 0.00 0.00 4.30
475 497 4.161189 TGAGACCAATGGAGAGATCAAGAC 59.839 45.833 6.16 0.00 0.00 3.01
476 498 4.356436 TGAGACCAATGGAGAGATCAAGA 58.644 43.478 6.16 0.00 0.00 3.02
477 499 4.443175 CCTGAGACCAATGGAGAGATCAAG 60.443 50.000 6.16 0.00 0.00 3.02
478 500 3.453717 CCTGAGACCAATGGAGAGATCAA 59.546 47.826 6.16 0.00 0.00 2.57
479 501 3.036819 CCTGAGACCAATGGAGAGATCA 58.963 50.000 6.16 1.62 0.00 2.92
480 502 2.224257 GCCTGAGACCAATGGAGAGATC 60.224 54.545 6.16 0.00 0.00 2.75
526 551 6.954616 TCAATAAATCGTCGTGCTTTCTTA 57.045 33.333 0.00 0.00 0.00 2.10
527 552 5.856126 TCAATAAATCGTCGTGCTTTCTT 57.144 34.783 0.00 0.00 0.00 2.52
528 553 5.178623 TGTTCAATAAATCGTCGTGCTTTCT 59.821 36.000 0.00 0.00 0.00 2.52
529 554 5.280678 GTGTTCAATAAATCGTCGTGCTTTC 59.719 40.000 0.00 0.00 0.00 2.62
530 555 5.144359 GTGTTCAATAAATCGTCGTGCTTT 58.856 37.500 0.00 0.00 0.00 3.51
533 558 3.081445 CGTGTTCAATAAATCGTCGTGC 58.919 45.455 0.00 0.00 0.00 5.34
534 559 3.365520 TCCGTGTTCAATAAATCGTCGTG 59.634 43.478 0.00 0.00 0.00 4.35
535 560 3.577667 TCCGTGTTCAATAAATCGTCGT 58.422 40.909 0.00 0.00 0.00 4.34
545 570 1.299976 GGGGCTCTCCGTGTTCAAT 59.700 57.895 0.00 0.00 36.01 2.57
572 605 4.579869 AGCCGTTCAAGATCACTGTTTAT 58.420 39.130 0.00 0.00 0.00 1.40
574 607 2.808543 GAGCCGTTCAAGATCACTGTTT 59.191 45.455 0.00 0.00 0.00 2.83
575 608 2.417719 GAGCCGTTCAAGATCACTGTT 58.582 47.619 0.00 0.00 0.00 3.16
596 630 6.203145 GGTCTTTTAGAGGAGACTTTGTCAAC 59.797 42.308 3.83 0.00 44.43 3.18
613 653 4.155826 CAGCCGTTTCATCATGGTCTTTTA 59.844 41.667 0.00 0.00 0.00 1.52
615 655 2.489329 CAGCCGTTTCATCATGGTCTTT 59.511 45.455 0.00 0.00 0.00 2.52
627 693 2.281762 CGTATTAGTCAGCAGCCGTTTC 59.718 50.000 0.00 0.00 0.00 2.78
629 695 1.470979 CCGTATTAGTCAGCAGCCGTT 60.471 52.381 0.00 0.00 0.00 4.44
647 713 2.274232 TATGGTCGTCTTGGTCGCCG 62.274 60.000 0.00 0.00 0.00 6.46
763 929 1.401905 GGTTGCATTCTTGGTCCGATC 59.598 52.381 0.00 0.00 0.00 3.69
764 930 1.271871 TGGTTGCATTCTTGGTCCGAT 60.272 47.619 0.00 0.00 0.00 4.18
765 931 0.109532 TGGTTGCATTCTTGGTCCGA 59.890 50.000 0.00 0.00 0.00 4.55
766 932 1.135315 CATGGTTGCATTCTTGGTCCG 60.135 52.381 0.00 0.00 0.00 4.79
767 933 2.660189 CATGGTTGCATTCTTGGTCC 57.340 50.000 0.00 0.00 0.00 4.46
811 978 0.108585 TGCACACTTTGGAGGGTCTC 59.891 55.000 0.00 0.00 37.45 3.36
814 983 1.181098 GCATGCACACTTTGGAGGGT 61.181 55.000 14.21 0.00 41.23 4.34
816 985 1.588082 GGCATGCACACTTTGGAGG 59.412 57.895 21.36 0.00 0.00 4.30
825 995 2.356278 GGGAGAAGGGCATGCACA 59.644 61.111 24.51 0.00 0.00 4.57
884 1147 1.580845 GCTGTGGTGTGTGATCTGCC 61.581 60.000 0.00 0.00 0.00 4.85
887 1150 0.473755 TTGGCTGTGGTGTGTGATCT 59.526 50.000 0.00 0.00 0.00 2.75
991 1274 2.223641 CCACAATCTTCATGGCGGATTG 60.224 50.000 22.28 22.28 46.60 2.67
1202 1521 1.077930 TACTGTCCGAGGTCCTCCG 60.078 63.158 13.54 7.10 39.05 4.63
1206 1525 1.799383 GTCGTACTGTCCGAGGTCC 59.201 63.158 0.00 0.00 34.56 4.46
1210 1529 1.919956 AAGCCGTCGTACTGTCCGAG 61.920 60.000 0.00 0.00 34.56 4.63
1347 1666 2.546494 GCGGCATATCACCTGGTGC 61.546 63.158 22.02 9.78 36.88 5.01
1452 1771 2.125512 GCGTCGAGGAACCTGCAT 60.126 61.111 9.75 0.00 0.00 3.96
1488 1807 0.456221 ACTCGGTGATCTTGGCGTAG 59.544 55.000 0.00 0.00 0.00 3.51
1636 1971 1.751924 GAGGCTGAGGAGTATGTCGTT 59.248 52.381 0.00 0.00 0.00 3.85
1637 1972 1.394618 GAGGCTGAGGAGTATGTCGT 58.605 55.000 0.00 0.00 0.00 4.34
1672 2007 3.455469 GGTGATGGCTTGGCTGGC 61.455 66.667 0.00 0.00 0.00 4.85
1722 2074 2.332063 ATCCTGGAGTAACAATGGCG 57.668 50.000 1.52 0.00 0.00 5.69
1745 2105 2.397549 GTGCAAAGTGCCAAATCAGAC 58.602 47.619 0.00 0.00 44.23 3.51
1864 2224 5.938710 CCATGCTAGCAGTATGATTCTTCAT 59.061 40.000 23.89 0.00 40.18 2.57
1879 2239 4.256110 TCATATATGTGCACCATGCTAGC 58.744 43.478 15.69 8.10 45.31 3.42
1941 2302 0.737219 GCAGGTTGTCATCTGGCATC 59.263 55.000 0.00 0.00 0.00 3.91
1964 2329 4.051237 GACCAAGCTTTGTTCAATCCAAC 58.949 43.478 4.46 0.00 0.00 3.77
2044 2411 7.872881 TGCCTGTTAACGACAACATTTTATAA 58.127 30.769 0.26 0.00 37.75 0.98
2361 2798 9.729281 TTTCGTAATAGGAGGTGAACTTTTTAT 57.271 29.630 0.00 0.00 0.00 1.40
2362 2799 9.558396 TTTTCGTAATAGGAGGTGAACTTTTTA 57.442 29.630 0.00 0.00 0.00 1.52
2363 2800 8.454570 TTTTCGTAATAGGAGGTGAACTTTTT 57.545 30.769 0.00 0.00 0.00 1.94
2743 4052 5.057149 GTCTTCTTTACCAGTTGAGCTCAA 58.943 41.667 25.16 25.16 0.00 3.02
2768 4077 0.038892 AACACGCGACCAACGATACT 60.039 50.000 15.93 0.00 45.77 2.12


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

AutoCloner maintained by Alex Coulton.