Multiple sequence alignment - TraesCS2D01G144600

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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 TraesCS2D01G144600 chr2D 100.000 3669 0 0 1 3669 85930727 85927059 0.000000e+00 6776.0
1 TraesCS2D01G144600 chr2D 85.439 1868 229 26 829 2661 8695341 8697200 0.000000e+00 1903.0
2 TraesCS2D01G144600 chr2D 86.059 1657 197 17 1047 2684 9665347 9663706 0.000000e+00 1749.0
3 TraesCS2D01G144600 chr2D 81.844 2148 307 51 546 2657 19586434 19588534 0.000000e+00 1729.0
4 TraesCS2D01G144600 chr2D 83.676 1850 268 21 827 2649 9604425 9606267 0.000000e+00 1712.0
5 TraesCS2D01G144600 chr2D 82.941 1530 221 18 1140 2650 8670684 8672192 0.000000e+00 1343.0
6 TraesCS2D01G144600 chr2D 94.253 174 9 1 3441 3613 507432663 507432836 7.810000e-67 265.0
7 TraesCS2D01G144600 chr2B 95.635 3368 98 10 116 3461 138994294 138990954 0.000000e+00 5360.0
8 TraesCS2D01G144600 chr2B 83.428 1931 276 26 790 2684 12421947 12423869 0.000000e+00 1753.0
9 TraesCS2D01G144600 chr2B 83.377 1925 274 28 796 2684 11518678 11516764 0.000000e+00 1740.0
10 TraesCS2D01G144600 chr2B 85.938 1657 198 13 1047 2684 11445346 11446986 0.000000e+00 1736.0
11 TraesCS2D01G144600 chr2B 84.620 1775 237 25 973 2720 768807179 768805414 0.000000e+00 1733.0
12 TraesCS2D01G144600 chr2B 80.244 1559 239 33 1144 2684 11226427 11224920 0.000000e+00 1109.0
13 TraesCS2D01G144600 chr2B 95.763 118 5 0 1 118 138995912 138996029 1.340000e-44 191.0
14 TraesCS2D01G144600 chr2B 86.207 87 12 0 848 934 12996327 12996241 1.080000e-15 95.3
15 TraesCS2D01G144600 chr2B 85.366 82 12 0 842 923 13347762 13347681 6.530000e-13 86.1
16 TraesCS2D01G144600 chr2A 90.909 1353 97 12 902 2247 86432355 86431022 0.000000e+00 1794.0
17 TraesCS2D01G144600 chr2A 83.151 1828 275 21 883 2684 8707129 8708949 0.000000e+00 1639.0
18 TraesCS2D01G144600 chr2A 82.379 1572 236 22 1143 2693 9121997 9120446 0.000000e+00 1330.0
19 TraesCS2D01G144600 chr2A 94.105 475 20 4 2246 2716 86387305 86386835 0.000000e+00 715.0
20 TraesCS2D01G144600 chr2A 79.745 548 83 11 829 1357 9941530 9942068 4.470000e-99 372.0
21 TraesCS2D01G144600 chr2A 85.385 390 14 13 233 605 86432716 86432353 7.490000e-97 364.0
22 TraesCS2D01G144600 chr2A 75.181 415 65 22 3067 3449 8626121 8626529 1.050000e-35 161.0
23 TraesCS2D01G144600 chr7D 81.927 1920 254 53 840 2723 589391533 589389671 0.000000e+00 1537.0
24 TraesCS2D01G144600 chr7D 96.450 169 6 0 3444 3612 426432037 426431869 2.790000e-71 279.0
25 TraesCS2D01G144600 chr3D 96.364 165 6 0 3448 3612 396430167 396430331 4.670000e-69 272.0
26 TraesCS2D01G144600 chr3A 94.611 167 9 0 3446 3612 40914888 40915054 3.630000e-65 259.0
27 TraesCS2D01G144600 chr5A 92.655 177 13 0 3439 3615 662667879 662667703 4.700000e-64 255.0
28 TraesCS2D01G144600 chr4D 94.048 168 10 0 3446 3613 316527523 316527356 4.700000e-64 255.0
29 TraesCS2D01G144600 chr7A 93.064 173 12 0 3444 3616 77161732 77161560 1.690000e-63 254.0
30 TraesCS2D01G144600 chr7A 93.023 172 12 0 3441 3612 443397625 443397796 6.080000e-63 252.0
31 TraesCS2D01G144600 chr7B 90.957 188 16 1 3430 3616 517104786 517104973 6.080000e-63 252.0


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 TraesCS2D01G144600 chr2D 85927059 85930727 3668 True 6776 6776 100.000 1 3669 1 chr2D.!!$R2 3668
1 TraesCS2D01G144600 chr2D 8695341 8697200 1859 False 1903 1903 85.439 829 2661 1 chr2D.!!$F2 1832
2 TraesCS2D01G144600 chr2D 9663706 9665347 1641 True 1749 1749 86.059 1047 2684 1 chr2D.!!$R1 1637
3 TraesCS2D01G144600 chr2D 19586434 19588534 2100 False 1729 1729 81.844 546 2657 1 chr2D.!!$F4 2111
4 TraesCS2D01G144600 chr2D 9604425 9606267 1842 False 1712 1712 83.676 827 2649 1 chr2D.!!$F3 1822
5 TraesCS2D01G144600 chr2D 8670684 8672192 1508 False 1343 1343 82.941 1140 2650 1 chr2D.!!$F1 1510
6 TraesCS2D01G144600 chr2B 138990954 138994294 3340 True 5360 5360 95.635 116 3461 1 chr2B.!!$R5 3345
7 TraesCS2D01G144600 chr2B 12421947 12423869 1922 False 1753 1753 83.428 790 2684 1 chr2B.!!$F2 1894
8 TraesCS2D01G144600 chr2B 11516764 11518678 1914 True 1740 1740 83.377 796 2684 1 chr2B.!!$R2 1888
9 TraesCS2D01G144600 chr2B 11445346 11446986 1640 False 1736 1736 85.938 1047 2684 1 chr2B.!!$F1 1637
10 TraesCS2D01G144600 chr2B 768805414 768807179 1765 True 1733 1733 84.620 973 2720 1 chr2B.!!$R6 1747
11 TraesCS2D01G144600 chr2B 11224920 11226427 1507 True 1109 1109 80.244 1144 2684 1 chr2B.!!$R1 1540
12 TraesCS2D01G144600 chr2A 8707129 8708949 1820 False 1639 1639 83.151 883 2684 1 chr2A.!!$F2 1801
13 TraesCS2D01G144600 chr2A 9120446 9121997 1551 True 1330 1330 82.379 1143 2693 1 chr2A.!!$R1 1550
14 TraesCS2D01G144600 chr2A 86431022 86432716 1694 True 1079 1794 88.147 233 2247 2 chr2A.!!$R3 2014
15 TraesCS2D01G144600 chr2A 9941530 9942068 538 False 372 372 79.745 829 1357 1 chr2A.!!$F3 528
16 TraesCS2D01G144600 chr7D 589389671 589391533 1862 True 1537 1537 81.927 840 2723 1 chr7D.!!$R2 1883

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
77 78 0.035915 GAAGAGGTCCCAGTCTTGCC 60.036 60.0 0.00 0.0 33.04 4.52 F
112 113 0.183492 AACTGCAGGTTGGAGCAAGA 59.817 50.0 19.93 0.0 39.63 3.02 F
113 114 0.183492 ACTGCAGGTTGGAGCAAGAA 59.817 50.0 19.93 0.0 39.63 2.52 F
2001 2082 0.674895 ATGAGCGGTGGAAGCAAGAC 60.675 55.0 0.00 0.0 37.01 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1191 1.338389 GCTTCCATGGCAAGCAACAAT 60.338 47.619 29.01 0.0 44.87 2.71 R
1870 1948 6.039969 GGTCCTTCCATGGTCAAGTATTGTT 61.040 44.000 12.58 0.0 40.89 2.83 R
2050 2131 7.086685 AGACAAAACACCTAGGAAAATAGGA 57.913 36.000 17.98 0.0 44.50 2.94 R
2932 3042 0.250989 TTGGATGGAACGGTTGGGAC 60.251 55.000 0.00 0.0 0.00 4.46 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 1.297689 TGAGCATGCACCAGTCTCC 59.702 57.895 21.98 0.00 0.00 3.71
19 20 1.297689 GAGCATGCACCAGTCTCCA 59.702 57.895 21.98 0.00 0.00 3.86
20 21 0.107312 GAGCATGCACCAGTCTCCAT 60.107 55.000 21.98 0.00 0.00 3.41
21 22 0.107312 AGCATGCACCAGTCTCCATC 60.107 55.000 21.98 0.00 0.00 3.51
22 23 0.393402 GCATGCACCAGTCTCCATCA 60.393 55.000 14.21 0.00 0.00 3.07
23 24 1.664873 CATGCACCAGTCTCCATCAG 58.335 55.000 0.00 0.00 0.00 2.90
24 25 1.065636 CATGCACCAGTCTCCATCAGT 60.066 52.381 0.00 0.00 0.00 3.41
25 26 0.322648 TGCACCAGTCTCCATCAGTG 59.677 55.000 0.00 0.00 0.00 3.66
26 27 0.610174 GCACCAGTCTCCATCAGTGA 59.390 55.000 0.00 0.00 0.00 3.41
27 28 1.209019 GCACCAGTCTCCATCAGTGAT 59.791 52.381 0.00 0.00 0.00 3.06
28 29 2.741228 GCACCAGTCTCCATCAGTGATC 60.741 54.545 1.56 0.00 0.00 2.92
29 30 2.114616 ACCAGTCTCCATCAGTGATCC 58.885 52.381 1.56 0.00 0.00 3.36
30 31 2.292785 ACCAGTCTCCATCAGTGATCCT 60.293 50.000 1.56 0.00 0.00 3.24
31 32 2.364970 CCAGTCTCCATCAGTGATCCTC 59.635 54.545 1.56 0.00 0.00 3.71
32 33 3.298619 CAGTCTCCATCAGTGATCCTCT 58.701 50.000 1.56 0.00 0.00 3.69
33 34 3.068448 CAGTCTCCATCAGTGATCCTCTG 59.932 52.174 1.56 8.22 0.00 3.35
34 35 2.037901 TCTCCATCAGTGATCCTCTGC 58.962 52.381 1.56 0.00 33.48 4.26
35 36 1.761198 CTCCATCAGTGATCCTCTGCA 59.239 52.381 1.56 0.00 33.48 4.41
36 37 2.369203 CTCCATCAGTGATCCTCTGCAT 59.631 50.000 1.56 3.54 33.48 3.96
37 38 2.104281 TCCATCAGTGATCCTCTGCATG 59.896 50.000 1.56 11.90 33.48 4.06
38 39 2.158798 CCATCAGTGATCCTCTGCATGT 60.159 50.000 1.56 0.00 33.48 3.21
39 40 2.975732 TCAGTGATCCTCTGCATGTC 57.024 50.000 9.31 0.00 33.48 3.06
40 41 2.464782 TCAGTGATCCTCTGCATGTCT 58.535 47.619 9.31 0.00 33.48 3.41
41 42 3.635591 TCAGTGATCCTCTGCATGTCTA 58.364 45.455 9.31 0.00 33.48 2.59
42 43 3.382865 TCAGTGATCCTCTGCATGTCTAC 59.617 47.826 9.31 0.00 33.48 2.59
43 44 3.131755 CAGTGATCCTCTGCATGTCTACA 59.868 47.826 0.00 0.00 0.00 2.74
44 45 3.966006 AGTGATCCTCTGCATGTCTACAT 59.034 43.478 0.00 0.00 36.96 2.29
45 46 4.039004 AGTGATCCTCTGCATGTCTACATC 59.961 45.833 0.00 0.00 33.61 3.06
46 47 3.005155 TGATCCTCTGCATGTCTACATCG 59.995 47.826 0.00 0.00 33.61 3.84
47 48 2.654863 TCCTCTGCATGTCTACATCGA 58.345 47.619 0.00 0.00 33.61 3.59
48 49 2.620585 TCCTCTGCATGTCTACATCGAG 59.379 50.000 0.00 0.70 33.61 4.04
49 50 2.288091 CCTCTGCATGTCTACATCGAGG 60.288 54.545 13.74 13.74 33.61 4.63
50 51 2.620585 CTCTGCATGTCTACATCGAGGA 59.379 50.000 3.06 0.00 33.61 3.71
51 52 3.225940 TCTGCATGTCTACATCGAGGAT 58.774 45.455 3.06 0.00 33.61 3.24
52 53 4.398319 TCTGCATGTCTACATCGAGGATA 58.602 43.478 3.06 0.00 33.61 2.59
53 54 5.012893 TCTGCATGTCTACATCGAGGATAT 58.987 41.667 3.06 0.00 33.61 1.63
54 55 5.064441 TGCATGTCTACATCGAGGATATG 57.936 43.478 3.06 8.20 33.61 1.78
55 56 4.082026 TGCATGTCTACATCGAGGATATGG 60.082 45.833 3.06 0.00 33.61 2.74
56 57 4.679106 GCATGTCTACATCGAGGATATGGG 60.679 50.000 3.06 0.00 33.61 4.00
57 58 4.382386 TGTCTACATCGAGGATATGGGA 57.618 45.455 3.06 0.00 0.00 4.37
58 59 4.336280 TGTCTACATCGAGGATATGGGAG 58.664 47.826 3.06 0.00 0.00 4.30
59 60 4.042934 TGTCTACATCGAGGATATGGGAGA 59.957 45.833 3.06 0.00 0.00 3.71
60 61 5.010933 GTCTACATCGAGGATATGGGAGAA 58.989 45.833 3.06 0.00 0.00 2.87
61 62 5.124776 GTCTACATCGAGGATATGGGAGAAG 59.875 48.000 3.06 0.00 0.00 2.85
62 63 4.119556 ACATCGAGGATATGGGAGAAGA 57.880 45.455 3.06 0.00 0.00 2.87
63 64 4.085733 ACATCGAGGATATGGGAGAAGAG 58.914 47.826 3.06 0.00 0.00 2.85
64 65 3.162147 TCGAGGATATGGGAGAAGAGG 57.838 52.381 0.00 0.00 0.00 3.69
65 66 2.447429 TCGAGGATATGGGAGAAGAGGT 59.553 50.000 0.00 0.00 0.00 3.85
66 67 2.823154 CGAGGATATGGGAGAAGAGGTC 59.177 54.545 0.00 0.00 0.00 3.85
67 68 3.169908 GAGGATATGGGAGAAGAGGTCC 58.830 54.545 0.00 0.00 0.00 4.46
73 74 3.701800 GGAGAAGAGGTCCCAGTCT 57.298 57.895 0.00 0.00 0.00 3.24
74 75 1.945580 GGAGAAGAGGTCCCAGTCTT 58.054 55.000 0.00 0.00 35.67 3.01
75 76 1.552792 GGAGAAGAGGTCCCAGTCTTG 59.447 57.143 0.00 0.00 33.04 3.02
76 77 0.980423 AGAAGAGGTCCCAGTCTTGC 59.020 55.000 0.00 0.00 33.04 4.01
77 78 0.035915 GAAGAGGTCCCAGTCTTGCC 60.036 60.000 0.00 0.00 33.04 4.52
78 79 0.768221 AAGAGGTCCCAGTCTTGCCA 60.768 55.000 0.00 0.00 31.63 4.92
79 80 0.548682 AGAGGTCCCAGTCTTGCCAT 60.549 55.000 0.00 0.00 0.00 4.40
80 81 0.329596 GAGGTCCCAGTCTTGCCATT 59.670 55.000 0.00 0.00 0.00 3.16
81 82 0.329596 AGGTCCCAGTCTTGCCATTC 59.670 55.000 0.00 0.00 0.00 2.67
82 83 0.681243 GGTCCCAGTCTTGCCATTCC 60.681 60.000 0.00 0.00 0.00 3.01
83 84 0.681243 GTCCCAGTCTTGCCATTCCC 60.681 60.000 0.00 0.00 0.00 3.97
84 85 0.846427 TCCCAGTCTTGCCATTCCCT 60.846 55.000 0.00 0.00 0.00 4.20
85 86 0.394899 CCCAGTCTTGCCATTCCCTC 60.395 60.000 0.00 0.00 0.00 4.30
86 87 0.329261 CCAGTCTTGCCATTCCCTCA 59.671 55.000 0.00 0.00 0.00 3.86
87 88 1.064166 CCAGTCTTGCCATTCCCTCAT 60.064 52.381 0.00 0.00 0.00 2.90
88 89 2.173356 CCAGTCTTGCCATTCCCTCATA 59.827 50.000 0.00 0.00 0.00 2.15
89 90 3.181436 CCAGTCTTGCCATTCCCTCATAT 60.181 47.826 0.00 0.00 0.00 1.78
90 91 4.467769 CAGTCTTGCCATTCCCTCATATT 58.532 43.478 0.00 0.00 0.00 1.28
91 92 4.891756 CAGTCTTGCCATTCCCTCATATTT 59.108 41.667 0.00 0.00 0.00 1.40
92 93 6.064060 CAGTCTTGCCATTCCCTCATATTTA 58.936 40.000 0.00 0.00 0.00 1.40
93 94 6.547141 CAGTCTTGCCATTCCCTCATATTTAA 59.453 38.462 0.00 0.00 0.00 1.52
94 95 7.068593 CAGTCTTGCCATTCCCTCATATTTAAA 59.931 37.037 0.00 0.00 0.00 1.52
95 96 7.068716 AGTCTTGCCATTCCCTCATATTTAAAC 59.931 37.037 0.00 0.00 0.00 2.01
96 97 7.068716 GTCTTGCCATTCCCTCATATTTAAACT 59.931 37.037 0.00 0.00 0.00 2.66
97 98 6.713762 TGCCATTCCCTCATATTTAAACTG 57.286 37.500 0.00 0.00 0.00 3.16
98 99 5.068987 TGCCATTCCCTCATATTTAAACTGC 59.931 40.000 0.00 0.00 0.00 4.40
99 100 5.068987 GCCATTCCCTCATATTTAAACTGCA 59.931 40.000 0.00 0.00 0.00 4.41
100 101 6.736794 GCCATTCCCTCATATTTAAACTGCAG 60.737 42.308 13.48 13.48 0.00 4.41
101 102 6.239120 CCATTCCCTCATATTTAAACTGCAGG 60.239 42.308 19.93 0.00 0.00 4.85
102 103 5.450818 TCCCTCATATTTAAACTGCAGGT 57.549 39.130 19.93 9.19 0.00 4.00
103 104 5.826643 TCCCTCATATTTAAACTGCAGGTT 58.173 37.500 22.75 22.75 40.28 3.50
104 105 5.652014 TCCCTCATATTTAAACTGCAGGTTG 59.348 40.000 27.29 10.00 38.29 3.77
105 106 5.163519 CCCTCATATTTAAACTGCAGGTTGG 60.164 44.000 27.29 15.88 38.29 3.77
106 107 5.652014 CCTCATATTTAAACTGCAGGTTGGA 59.348 40.000 27.29 15.09 38.29 3.53
107 108 6.183360 CCTCATATTTAAACTGCAGGTTGGAG 60.183 42.308 27.29 19.73 41.93 3.86
108 109 3.942130 ATTTAAACTGCAGGTTGGAGC 57.058 42.857 27.29 0.00 39.63 4.70
109 110 2.356665 TTAAACTGCAGGTTGGAGCA 57.643 45.000 27.29 3.14 39.63 4.26
110 111 2.356665 TAAACTGCAGGTTGGAGCAA 57.643 45.000 27.29 2.30 39.63 3.91
111 112 1.035139 AAACTGCAGGTTGGAGCAAG 58.965 50.000 18.18 0.00 39.63 4.01
112 113 0.183492 AACTGCAGGTTGGAGCAAGA 59.817 50.000 19.93 0.00 39.63 3.02
113 114 0.183492 ACTGCAGGTTGGAGCAAGAA 59.817 50.000 19.93 0.00 39.63 2.52
114 115 1.202976 ACTGCAGGTTGGAGCAAGAAT 60.203 47.619 19.93 0.00 39.63 2.40
130 131 5.010415 AGCAAGAATTCAAACTTCCTTGAGG 59.990 40.000 8.44 0.00 36.69 3.86
154 155 6.425114 GGAAAATGGAAAAGAAAAAGGAGAGC 59.575 38.462 0.00 0.00 0.00 4.09
156 157 3.551846 TGGAAAAGAAAAAGGAGAGCGT 58.448 40.909 0.00 0.00 0.00 5.07
159 160 0.868406 AAGAAAAAGGAGAGCGTGCG 59.132 50.000 0.00 0.00 0.00 5.34
163 164 2.660258 AAAAGGAGAGCGTGCGGTGT 62.660 55.000 0.00 0.00 0.00 4.16
173 174 2.040544 GTGCGGTGTCCTCCAATGG 61.041 63.158 0.00 0.00 0.00 3.16
204 205 5.629435 CGGGCTAGAAATTTTGAACAGAAAC 59.371 40.000 0.00 0.00 0.00 2.78
239 240 4.718940 AGTTTGACACAAACTTGAAGGG 57.281 40.909 19.66 0.00 37.18 3.95
478 497 1.374758 CAAGTCACGCCACCTCCTC 60.375 63.158 0.00 0.00 0.00 3.71
482 501 4.457496 CACGCCACCTCCTCGCAT 62.457 66.667 0.00 0.00 0.00 4.73
624 643 2.040213 CTTGCCAATGAGTAGCGCCG 62.040 60.000 2.29 0.00 0.00 6.46
730 751 5.815233 TGCCATGGAAAATGTAAAAGGAA 57.185 34.783 18.40 0.00 0.00 3.36
753 774 7.595130 GGAATCCAACACAAAAGAGAAATACAC 59.405 37.037 0.00 0.00 0.00 2.90
929 960 4.222810 GGAGCCCAACTTTTGTATTCCATT 59.777 41.667 0.00 0.00 0.00 3.16
1020 1064 0.944311 CCACCCTTGAACTCGTCACG 60.944 60.000 0.00 0.00 35.39 4.35
1026 1072 1.521423 CTTGAACTCGTCACGGTCAAC 59.479 52.381 0.00 0.00 35.39 3.18
1076 1127 2.232452 TCTGTAAGACTTGCAGAGGCTC 59.768 50.000 26.34 6.34 45.50 4.70
1132 1191 3.054139 AGCAGCTTCCCTCATCAATTGTA 60.054 43.478 5.13 0.00 0.00 2.41
1644 1717 2.029020 TGTCTCGTAGGCCATATGATGC 60.029 50.000 5.01 0.00 0.00 3.91
1870 1948 6.381133 TGCACTTGAATGGAGATAGACTCTTA 59.619 38.462 0.00 0.00 44.37 2.10
1945 2026 4.973168 AGTTTGCTTCTGATGTAGGTGAA 58.027 39.130 0.00 0.00 0.00 3.18
2001 2082 0.674895 ATGAGCGGTGGAAGCAAGAC 60.675 55.000 0.00 0.00 37.01 3.01
2050 2131 1.955208 GCCCGGTTTGGATCTGTGAAT 60.955 52.381 0.00 0.00 42.00 2.57
2115 2196 2.542020 TTCAAGACACTGGCATTCGA 57.458 45.000 0.00 0.00 0.00 3.71
2403 2493 6.429692 CCACTTACCATGACAAGTAATGTTCA 59.570 38.462 10.44 0.00 44.12 3.18
2717 2827 8.958119 AGTTAAACGGATGTGTTCATGTATAT 57.042 30.769 0.00 0.00 34.06 0.86
2908 3018 7.834068 ATGTATTATCACCATCGCATAGTTC 57.166 36.000 0.00 0.00 0.00 3.01
2932 3042 8.485976 TCTGGTTCAAATTTTGTTTTTACTGG 57.514 30.769 8.89 1.12 0.00 4.00
3029 3139 3.383620 TTGTGTCAATTTGGATGCCAC 57.616 42.857 0.00 0.00 30.78 5.01
3055 3165 9.630098 CAAAAACTTATTGTCATGCTCTAACAT 57.370 29.630 0.00 0.00 0.00 2.71
3118 3228 1.000283 CTAGGCATCAGGTCGGATCAC 60.000 57.143 0.00 0.00 0.00 3.06
3138 3249 1.682344 GCGCCTCCCCCAAAAATCT 60.682 57.895 0.00 0.00 0.00 2.40
3187 3298 6.596497 ACAGGTTTATTGAAATTACCGACGAT 59.404 34.615 0.00 0.00 34.09 3.73
3195 3306 3.651562 AATTACCGACGATTGCGAAAG 57.348 42.857 0.00 0.00 41.64 2.62
3330 3449 3.034635 GTGCATCTCTTCCCTTCCTCTA 58.965 50.000 0.00 0.00 0.00 2.43
3449 3574 8.023128 TCTGCTTTTTCATGCATTAGTTTCTAC 58.977 33.333 0.00 0.00 38.59 2.59
3451 3576 8.023128 TGCTTTTTCATGCATTAGTTTCTACTC 58.977 33.333 0.00 0.00 33.54 2.59
3455 3580 5.918608 TCATGCATTAGTTTCTACTCCCTC 58.081 41.667 0.00 0.00 35.78 4.30
3457 3582 4.101114 TGCATTAGTTTCTACTCCCTCCA 58.899 43.478 0.00 0.00 35.78 3.86
3461 3586 6.261158 GCATTAGTTTCTACTCCCTCCATTTC 59.739 42.308 0.00 0.00 35.78 2.17
3462 3587 6.945636 TTAGTTTCTACTCCCTCCATTTCA 57.054 37.500 0.00 0.00 35.78 2.69
3463 3588 5.843019 AGTTTCTACTCCCTCCATTTCAA 57.157 39.130 0.00 0.00 0.00 2.69
3464 3589 6.200878 AGTTTCTACTCCCTCCATTTCAAA 57.799 37.500 0.00 0.00 0.00 2.69
3465 3590 6.610830 AGTTTCTACTCCCTCCATTTCAAAA 58.389 36.000 0.00 0.00 0.00 2.44
3466 3591 7.241628 AGTTTCTACTCCCTCCATTTCAAAAT 58.758 34.615 0.00 0.00 0.00 1.82
3467 3592 8.390921 AGTTTCTACTCCCTCCATTTCAAAATA 58.609 33.333 0.00 0.00 0.00 1.40
3468 3593 9.190317 GTTTCTACTCCCTCCATTTCAAAATAT 57.810 33.333 0.00 0.00 0.00 1.28
3472 3597 9.853177 CTACTCCCTCCATTTCAAAATATAAGT 57.147 33.333 0.00 0.00 0.00 2.24
3473 3598 8.753497 ACTCCCTCCATTTCAAAATATAAGTC 57.247 34.615 0.00 0.00 0.00 3.01
3474 3599 8.560903 ACTCCCTCCATTTCAAAATATAAGTCT 58.439 33.333 0.00 0.00 0.00 3.24
3475 3600 9.413734 CTCCCTCCATTTCAAAATATAAGTCTT 57.586 33.333 0.00 0.00 0.00 3.01
3476 3601 9.768215 TCCCTCCATTTCAAAATATAAGTCTTT 57.232 29.630 0.00 0.00 0.00 2.52
3495 3620 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
3496 3621 9.136323 AGTCTTTTTAGACATTTCAAATGGACT 57.864 29.630 14.70 14.18 41.02 3.85
3501 3626 9.959749 TTTTAGACATTTCAAATGGACTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
3502 3627 8.684386 TTAGACATTTCAAATGGACTACAACA 57.316 30.769 14.70 1.25 0.00 3.33
3503 3628 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
3504 3629 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
3505 3630 9.466497 AGACATTTCAAATGGACTACAACATAT 57.534 29.630 14.70 0.00 0.00 1.78
3506 3631 9.507280 GACATTTCAAATGGACTACAACATATG 57.493 33.333 14.70 0.00 0.00 1.78
3507 3632 9.241919 ACATTTCAAATGGACTACAACATATGA 57.758 29.630 14.70 0.00 0.00 2.15
3512 3637 9.898152 TCAAATGGACTACAACATATGAATGTA 57.102 29.630 10.38 15.73 45.79 2.29
3515 3640 9.851686 AATGGACTACAACATATGAATGTATGT 57.148 29.630 19.26 18.14 45.79 2.29
3517 3642 9.981114 TGGACTACAACATATGAATGTATGTAG 57.019 33.333 22.32 22.32 45.79 2.74
3552 3677 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3553 3678 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3554 3679 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3555 3680 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3556 3681 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3557 3682 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3558 3683 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3559 3684 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3560 3685 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3561 3686 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3562 3687 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3563 3688 5.351465 CACTCATTTTGCTCCGTATGTAGTT 59.649 40.000 0.00 0.00 0.00 2.24
3564 3689 6.533723 CACTCATTTTGCTCCGTATGTAGTTA 59.466 38.462 0.00 0.00 0.00 2.24
3565 3690 7.224753 CACTCATTTTGCTCCGTATGTAGTTAT 59.775 37.037 0.00 0.00 0.00 1.89
3566 3691 7.438459 ACTCATTTTGCTCCGTATGTAGTTATC 59.562 37.037 0.00 0.00 0.00 1.75
3567 3692 7.497595 TCATTTTGCTCCGTATGTAGTTATCT 58.502 34.615 0.00 0.00 0.00 1.98
3568 3693 8.635328 TCATTTTGCTCCGTATGTAGTTATCTA 58.365 33.333 0.00 0.00 0.00 1.98
3569 3694 9.424319 CATTTTGCTCCGTATGTAGTTATCTAT 57.576 33.333 0.00 0.00 0.00 1.98
3570 3695 9.998106 ATTTTGCTCCGTATGTAGTTATCTATT 57.002 29.630 0.00 0.00 0.00 1.73
3571 3696 8.812147 TTTGCTCCGTATGTAGTTATCTATTG 57.188 34.615 0.00 0.00 0.00 1.90
3572 3697 6.920817 TGCTCCGTATGTAGTTATCTATTGG 58.079 40.000 0.00 0.00 0.00 3.16
3573 3698 6.717997 TGCTCCGTATGTAGTTATCTATTGGA 59.282 38.462 0.00 0.00 0.00 3.53
3574 3699 7.231925 TGCTCCGTATGTAGTTATCTATTGGAA 59.768 37.037 0.00 0.00 0.00 3.53
3575 3700 8.251721 GCTCCGTATGTAGTTATCTATTGGAAT 58.748 37.037 0.00 0.00 0.00 3.01
3576 3701 9.790389 CTCCGTATGTAGTTATCTATTGGAATC 57.210 37.037 0.00 0.00 0.00 2.52
3577 3702 9.529823 TCCGTATGTAGTTATCTATTGGAATCT 57.470 33.333 0.00 0.00 0.00 2.40
3578 3703 9.790389 CCGTATGTAGTTATCTATTGGAATCTC 57.210 37.037 0.00 0.00 0.00 2.75
3606 3731 9.819267 AGAAAGACTTATATTTTAGAACGGAGG 57.181 33.333 0.00 0.00 0.00 4.30
3607 3732 8.959705 AAAGACTTATATTTTAGAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
3608 3733 7.909485 AGACTTATATTTTAGAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
3609 3734 7.953752 AGACTTATATTTTAGAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
3610 3735 7.564292 AGACTTATATTTTAGAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
3611 3736 8.773033 ACTTATATTTTAGAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
3612 3737 9.377238 ACTTATATTTTAGAACGGAGGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
3616 3741 5.349061 TTTAGAACGGAGGGAGTATTTCC 57.651 43.478 0.00 0.00 46.00 3.13
3617 3742 3.117552 AGAACGGAGGGAGTATTTCCT 57.882 47.619 0.00 0.00 45.98 3.36
3618 3743 3.451890 AGAACGGAGGGAGTATTTCCTT 58.548 45.455 0.00 0.00 45.98 3.36
3619 3744 3.844804 AGAACGGAGGGAGTATTTCCTTT 59.155 43.478 0.00 0.00 45.98 3.11
3620 3745 4.288887 AGAACGGAGGGAGTATTTCCTTTT 59.711 41.667 0.00 0.00 45.98 2.27
3621 3746 4.652679 ACGGAGGGAGTATTTCCTTTTT 57.347 40.909 0.00 0.00 45.98 1.94
3653 3778 4.708868 GCATTGTGCATCATAAGCAATG 57.291 40.909 15.76 15.76 44.64 2.82
3654 3779 4.364860 GCATTGTGCATCATAAGCAATGA 58.635 39.130 21.45 4.45 45.22 2.57
3655 3780 4.208460 GCATTGTGCATCATAAGCAATGAC 59.792 41.667 21.45 12.32 45.22 3.06
3656 3781 5.963334 GCATTGTGCATCATAAGCAATGACT 60.963 40.000 21.45 0.00 45.22 3.41
3657 3782 7.392483 GCATTGTGCATCATAAGCAATGACTT 61.392 38.462 21.45 0.00 45.22 3.01
3658 3783 9.295251 GCATTGTGCATCATAAGCAATGACTTG 62.295 40.741 21.45 3.63 45.22 3.16
3667 3792 8.962884 TCATAAGCAATGACTTGTATGTACAT 57.037 30.769 13.93 13.93 39.77 2.29
3668 3793 9.045223 TCATAAGCAATGACTTGTATGTACATC 57.955 33.333 12.68 5.06 39.77 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.297689 GGAGACTGGTGCATGCTCA 59.702 57.895 20.33 15.66 0.00 4.26
1 2 0.107312 ATGGAGACTGGTGCATGCTC 60.107 55.000 20.33 15.68 0.00 4.26
2 3 0.107312 GATGGAGACTGGTGCATGCT 60.107 55.000 20.33 0.00 0.00 3.79
4 5 1.065636 ACTGATGGAGACTGGTGCATG 60.066 52.381 0.00 0.00 0.00 4.06
5 6 1.065636 CACTGATGGAGACTGGTGCAT 60.066 52.381 0.00 0.00 0.00 3.96
6 7 0.322648 CACTGATGGAGACTGGTGCA 59.677 55.000 0.00 0.00 0.00 4.57
7 8 0.610174 TCACTGATGGAGACTGGTGC 59.390 55.000 0.00 0.00 0.00 5.01
8 9 2.158986 GGATCACTGATGGAGACTGGTG 60.159 54.545 0.00 0.00 0.00 4.17
9 10 2.114616 GGATCACTGATGGAGACTGGT 58.885 52.381 0.00 0.00 0.00 4.00
10 11 2.364970 GAGGATCACTGATGGAGACTGG 59.635 54.545 0.00 0.00 33.17 4.00
11 12 3.068448 CAGAGGATCACTGATGGAGACTG 59.932 52.174 11.98 0.00 37.82 3.51
12 13 3.298619 CAGAGGATCACTGATGGAGACT 58.701 50.000 11.98 0.00 37.82 3.24
13 14 2.224018 GCAGAGGATCACTGATGGAGAC 60.224 54.545 18.85 1.04 37.82 3.36
14 15 2.037901 GCAGAGGATCACTGATGGAGA 58.962 52.381 18.85 0.00 37.82 3.71
15 16 1.761198 TGCAGAGGATCACTGATGGAG 59.239 52.381 18.85 0.00 37.82 3.86
16 17 1.870064 TGCAGAGGATCACTGATGGA 58.130 50.000 18.85 4.12 37.82 3.41
17 18 2.158798 ACATGCAGAGGATCACTGATGG 60.159 50.000 18.85 10.88 37.82 3.51
18 19 3.132160 GACATGCAGAGGATCACTGATG 58.868 50.000 18.85 18.40 37.82 3.07
19 20 3.039743 AGACATGCAGAGGATCACTGAT 58.960 45.455 18.85 0.00 37.82 2.90
20 21 2.464782 AGACATGCAGAGGATCACTGA 58.535 47.619 18.85 7.95 37.82 3.41
21 22 2.983907 AGACATGCAGAGGATCACTG 57.016 50.000 12.74 12.74 37.82 3.66
22 23 3.369175 TGTAGACATGCAGAGGATCACT 58.631 45.455 0.00 0.00 37.82 3.41
23 24 3.808466 TGTAGACATGCAGAGGATCAC 57.192 47.619 0.00 0.00 37.82 3.06
24 25 3.005155 CGATGTAGACATGCAGAGGATCA 59.995 47.826 0.00 0.00 35.06 2.92
25 26 3.254411 TCGATGTAGACATGCAGAGGATC 59.746 47.826 0.00 0.00 36.57 3.36
26 27 3.225940 TCGATGTAGACATGCAGAGGAT 58.774 45.455 0.00 0.00 36.57 3.24
27 28 2.620585 CTCGATGTAGACATGCAGAGGA 59.379 50.000 0.00 0.00 36.57 3.71
28 29 2.288091 CCTCGATGTAGACATGCAGAGG 60.288 54.545 17.05 17.05 39.94 3.69
29 30 2.620585 TCCTCGATGTAGACATGCAGAG 59.379 50.000 0.00 6.23 36.57 3.35
30 31 2.654863 TCCTCGATGTAGACATGCAGA 58.345 47.619 0.00 0.00 36.57 4.26
31 32 3.657015 ATCCTCGATGTAGACATGCAG 57.343 47.619 0.00 0.00 36.57 4.41
32 33 4.082026 CCATATCCTCGATGTAGACATGCA 60.082 45.833 0.00 0.00 36.57 3.96
33 34 4.428209 CCATATCCTCGATGTAGACATGC 58.572 47.826 0.00 0.00 36.57 4.06
34 35 4.706962 TCCCATATCCTCGATGTAGACATG 59.293 45.833 0.00 0.00 36.57 3.21
35 36 4.935578 TCCCATATCCTCGATGTAGACAT 58.064 43.478 0.00 0.00 39.70 3.06
36 37 4.042934 TCTCCCATATCCTCGATGTAGACA 59.957 45.833 0.00 0.00 0.00 3.41
37 38 4.590918 TCTCCCATATCCTCGATGTAGAC 58.409 47.826 0.00 0.00 0.00 2.59
38 39 4.929146 TCTCCCATATCCTCGATGTAGA 57.071 45.455 0.00 0.00 0.00 2.59
39 40 5.257262 TCTTCTCCCATATCCTCGATGTAG 58.743 45.833 0.00 0.00 0.00 2.74
40 41 5.256806 TCTTCTCCCATATCCTCGATGTA 57.743 43.478 0.00 0.00 0.00 2.29
41 42 4.085733 CTCTTCTCCCATATCCTCGATGT 58.914 47.826 0.00 0.00 0.00 3.06
42 43 3.446873 CCTCTTCTCCCATATCCTCGATG 59.553 52.174 0.00 0.00 0.00 3.84
43 44 3.076785 ACCTCTTCTCCCATATCCTCGAT 59.923 47.826 0.00 0.00 0.00 3.59
44 45 2.447429 ACCTCTTCTCCCATATCCTCGA 59.553 50.000 0.00 0.00 0.00 4.04
45 46 2.823154 GACCTCTTCTCCCATATCCTCG 59.177 54.545 0.00 0.00 0.00 4.63
46 47 3.169908 GGACCTCTTCTCCCATATCCTC 58.830 54.545 0.00 0.00 0.00 3.71
47 48 2.158081 GGGACCTCTTCTCCCATATCCT 60.158 54.545 0.00 0.00 46.30 3.24
48 49 2.261729 GGGACCTCTTCTCCCATATCC 58.738 57.143 0.00 0.00 46.30 2.59
55 56 1.552792 CAAGACTGGGACCTCTTCTCC 59.447 57.143 0.00 0.00 0.00 3.71
56 57 1.066502 GCAAGACTGGGACCTCTTCTC 60.067 57.143 0.00 0.00 0.00 2.87
57 58 0.980423 GCAAGACTGGGACCTCTTCT 59.020 55.000 0.00 0.00 0.00 2.85
58 59 0.035915 GGCAAGACTGGGACCTCTTC 60.036 60.000 0.00 0.00 0.00 2.87
59 60 0.768221 TGGCAAGACTGGGACCTCTT 60.768 55.000 0.00 0.00 0.00 2.85
60 61 0.548682 ATGGCAAGACTGGGACCTCT 60.549 55.000 0.00 0.00 0.00 3.69
61 62 0.329596 AATGGCAAGACTGGGACCTC 59.670 55.000 0.00 0.00 0.00 3.85
62 63 0.329596 GAATGGCAAGACTGGGACCT 59.670 55.000 0.00 0.00 0.00 3.85
63 64 0.681243 GGAATGGCAAGACTGGGACC 60.681 60.000 0.00 0.00 0.00 4.46
64 65 0.681243 GGGAATGGCAAGACTGGGAC 60.681 60.000 0.00 0.00 0.00 4.46
65 66 0.846427 AGGGAATGGCAAGACTGGGA 60.846 55.000 0.00 0.00 0.00 4.37
66 67 0.394899 GAGGGAATGGCAAGACTGGG 60.395 60.000 0.00 0.00 0.00 4.45
67 68 0.329261 TGAGGGAATGGCAAGACTGG 59.671 55.000 0.00 0.00 0.00 4.00
68 69 2.431954 ATGAGGGAATGGCAAGACTG 57.568 50.000 0.00 0.00 0.00 3.51
69 70 4.803329 AATATGAGGGAATGGCAAGACT 57.197 40.909 0.00 0.00 0.00 3.24
70 71 6.959639 TTAAATATGAGGGAATGGCAAGAC 57.040 37.500 0.00 0.00 0.00 3.01
71 72 7.068593 CAGTTTAAATATGAGGGAATGGCAAGA 59.931 37.037 0.00 0.00 0.00 3.02
72 73 7.205297 CAGTTTAAATATGAGGGAATGGCAAG 58.795 38.462 0.00 0.00 0.00 4.01
73 74 6.406849 GCAGTTTAAATATGAGGGAATGGCAA 60.407 38.462 0.00 0.00 0.00 4.52
74 75 5.068987 GCAGTTTAAATATGAGGGAATGGCA 59.931 40.000 7.38 0.00 0.00 4.92
75 76 5.068987 TGCAGTTTAAATATGAGGGAATGGC 59.931 40.000 7.38 0.00 0.00 4.40
76 77 6.239120 CCTGCAGTTTAAATATGAGGGAATGG 60.239 42.308 13.81 0.00 0.00 3.16
77 78 6.322201 ACCTGCAGTTTAAATATGAGGGAATG 59.678 38.462 13.81 0.00 0.00 2.67
78 79 6.435164 ACCTGCAGTTTAAATATGAGGGAAT 58.565 36.000 13.81 4.25 0.00 3.01
79 80 5.826643 ACCTGCAGTTTAAATATGAGGGAA 58.173 37.500 13.81 0.00 0.00 3.97
80 81 5.450818 ACCTGCAGTTTAAATATGAGGGA 57.549 39.130 13.81 0.00 0.00 4.20
81 82 5.163519 CCAACCTGCAGTTTAAATATGAGGG 60.164 44.000 13.81 13.84 36.18 4.30
82 83 5.652014 TCCAACCTGCAGTTTAAATATGAGG 59.348 40.000 13.81 0.00 36.18 3.86
83 84 6.678900 GCTCCAACCTGCAGTTTAAATATGAG 60.679 42.308 13.81 6.82 36.18 2.90
84 85 5.125417 GCTCCAACCTGCAGTTTAAATATGA 59.875 40.000 13.81 0.00 36.18 2.15
85 86 5.105797 TGCTCCAACCTGCAGTTTAAATATG 60.106 40.000 13.81 0.00 36.18 1.78
86 87 5.016173 TGCTCCAACCTGCAGTTTAAATAT 58.984 37.500 13.81 0.00 36.18 1.28
87 88 4.402829 TGCTCCAACCTGCAGTTTAAATA 58.597 39.130 13.81 0.00 36.18 1.40
88 89 3.230134 TGCTCCAACCTGCAGTTTAAAT 58.770 40.909 13.81 0.00 36.18 1.40
89 90 2.660572 TGCTCCAACCTGCAGTTTAAA 58.339 42.857 13.81 0.00 36.18 1.52
90 91 2.356665 TGCTCCAACCTGCAGTTTAA 57.643 45.000 13.81 0.00 36.18 1.52
91 92 2.158682 TCTTGCTCCAACCTGCAGTTTA 60.159 45.455 13.81 0.00 40.46 2.01
92 93 1.035139 CTTGCTCCAACCTGCAGTTT 58.965 50.000 13.81 0.52 40.46 2.66
93 94 0.183492 TCTTGCTCCAACCTGCAGTT 59.817 50.000 13.81 4.33 40.46 3.16
94 95 0.183492 TTCTTGCTCCAACCTGCAGT 59.817 50.000 13.81 0.00 40.46 4.40
95 96 1.542492 ATTCTTGCTCCAACCTGCAG 58.458 50.000 6.78 6.78 40.46 4.41
96 97 1.888512 GAATTCTTGCTCCAACCTGCA 59.111 47.619 0.00 0.00 37.42 4.41
97 98 1.888512 TGAATTCTTGCTCCAACCTGC 59.111 47.619 7.05 0.00 0.00 4.85
98 99 4.038402 AGTTTGAATTCTTGCTCCAACCTG 59.962 41.667 7.05 0.00 0.00 4.00
99 100 4.218312 AGTTTGAATTCTTGCTCCAACCT 58.782 39.130 7.05 0.00 0.00 3.50
100 101 4.590850 AGTTTGAATTCTTGCTCCAACC 57.409 40.909 7.05 0.00 0.00 3.77
101 102 4.984785 GGAAGTTTGAATTCTTGCTCCAAC 59.015 41.667 7.05 0.00 0.00 3.77
102 103 4.895297 AGGAAGTTTGAATTCTTGCTCCAA 59.105 37.500 7.05 0.00 37.72 3.53
103 104 4.473444 AGGAAGTTTGAATTCTTGCTCCA 58.527 39.130 7.05 0.00 37.72 3.86
104 105 5.010012 TCAAGGAAGTTTGAATTCTTGCTCC 59.990 40.000 7.05 6.54 40.41 4.70
105 106 6.076981 TCAAGGAAGTTTGAATTCTTGCTC 57.923 37.500 7.05 0.00 40.41 4.26
106 107 5.010415 CCTCAAGGAAGTTTGAATTCTTGCT 59.990 40.000 7.05 0.23 42.42 3.91
107 108 5.010012 TCCTCAAGGAAGTTTGAATTCTTGC 59.990 40.000 7.05 0.00 42.18 4.01
108 109 6.639632 TCCTCAAGGAAGTTTGAATTCTTG 57.360 37.500 7.05 0.51 42.18 3.02
130 131 6.144563 CGCTCTCCTTTTTCTTTTCCATTTTC 59.855 38.462 0.00 0.00 0.00 2.29
139 140 1.264288 CGCACGCTCTCCTTTTTCTTT 59.736 47.619 0.00 0.00 0.00 2.52
154 155 2.047274 ATTGGAGGACACCGCACG 60.047 61.111 0.00 0.00 0.00 5.34
156 157 2.350895 CCATTGGAGGACACCGCA 59.649 61.111 0.00 0.00 0.00 5.69
159 160 2.763215 TGGCCATTGGAGGACACC 59.237 61.111 0.00 0.00 43.33 4.16
163 164 0.897863 CCGTTTTGGCCATTGGAGGA 60.898 55.000 6.09 0.00 0.00 3.71
204 205 9.734620 TTTGTGTCAAACTAATCTTGAATTCTG 57.265 29.630 7.05 0.00 34.68 3.02
239 240 8.074370 GTGTTTACCATCAAGGAAGTTAAGTTC 58.926 37.037 13.71 13.71 41.22 3.01
478 497 1.153289 AAGCTACTGGCCAGATGCG 60.153 57.895 39.19 22.25 42.61 4.73
482 501 1.896220 CAAACAAGCTACTGGCCAGA 58.104 50.000 39.19 20.75 43.05 3.86
570 589 2.546789 CCGTTTTACCTTGGTCAGTGAC 59.453 50.000 15.24 15.24 0.00 3.67
624 643 6.531240 CAGATGAACTTCTCTAGAGAAAGCAC 59.469 42.308 30.08 21.75 45.75 4.40
730 751 7.502226 TCTGTGTATTTCTCTTTTGTGTTGGAT 59.498 33.333 0.00 0.00 0.00 3.41
777 798 3.003897 GTGTACATGTTCCCTCGCAAAAA 59.996 43.478 2.30 0.00 0.00 1.94
778 799 2.550606 GTGTACATGTTCCCTCGCAAAA 59.449 45.455 2.30 0.00 0.00 2.44
779 800 2.147958 GTGTACATGTTCCCTCGCAAA 58.852 47.619 2.30 0.00 0.00 3.68
780 801 1.803334 GTGTACATGTTCCCTCGCAA 58.197 50.000 2.30 0.00 0.00 4.85
781 802 0.389296 CGTGTACATGTTCCCTCGCA 60.389 55.000 2.30 0.00 0.00 5.10
782 803 0.389426 ACGTGTACATGTTCCCTCGC 60.389 55.000 15.10 0.00 0.00 5.03
783 804 1.724623 CAACGTGTACATGTTCCCTCG 59.275 52.381 26.83 14.01 38.39 4.63
784 805 2.073816 CCAACGTGTACATGTTCCCTC 58.926 52.381 26.83 0.00 38.39 4.30
785 806 1.418637 ACCAACGTGTACATGTTCCCT 59.581 47.619 26.83 11.83 38.39 4.20
786 807 1.886886 ACCAACGTGTACATGTTCCC 58.113 50.000 26.83 0.00 38.39 3.97
787 808 3.372822 CCATACCAACGTGTACATGTTCC 59.627 47.826 26.83 0.36 38.39 3.62
788 809 4.092383 GTCCATACCAACGTGTACATGTTC 59.908 45.833 26.83 12.10 38.39 3.18
929 960 2.826128 CTCTGCACTTGTCTACTACCCA 59.174 50.000 0.00 0.00 0.00 4.51
982 1020 1.478137 GTGATAGACGGCTGCTAACG 58.522 55.000 0.00 0.00 0.00 3.18
1020 1064 4.932200 CAGTAGAAATGTCTCCAGTTGACC 59.068 45.833 0.00 0.00 35.12 4.02
1026 1072 6.875726 TCATCAAACAGTAGAAATGTCTCCAG 59.124 38.462 0.00 0.00 35.12 3.86
1076 1127 3.670625 TGGAGTCTGGACAATTTAACCG 58.329 45.455 3.51 0.00 0.00 4.44
1132 1191 1.338389 GCTTCCATGGCAAGCAACAAT 60.338 47.619 29.01 0.00 44.87 2.71
1870 1948 6.039969 GGTCCTTCCATGGTCAAGTATTGTT 61.040 44.000 12.58 0.00 40.89 2.83
2050 2131 7.086685 AGACAAAACACCTAGGAAAATAGGA 57.913 36.000 17.98 0.00 44.50 2.94
2115 2196 4.227134 CTGCGGGGTCTGCGCTAT 62.227 66.667 9.73 0.00 34.24 2.97
2180 2261 4.474226 CAAGTGAACCTTGCTTACTGTC 57.526 45.455 0.00 0.00 43.84 3.51
2403 2493 4.768968 CACTTGGTGATTCCTCCTTGATTT 59.231 41.667 0.00 0.00 35.23 2.17
2658 2760 4.138290 TGAACACACCCATTTATCACGTT 58.862 39.130 0.00 0.00 0.00 3.99
2661 2767 5.401550 CACATGAACACACCCATTTATCAC 58.598 41.667 0.00 0.00 0.00 3.06
2664 2773 3.195396 GCCACATGAACACACCCATTTAT 59.805 43.478 0.00 0.00 0.00 1.40
2665 2774 2.560542 GCCACATGAACACACCCATTTA 59.439 45.455 0.00 0.00 0.00 1.40
2668 2777 0.112995 AGCCACATGAACACACCCAT 59.887 50.000 0.00 0.00 0.00 4.00
2899 3009 5.920273 ACAAAATTTGAACCAGAACTATGCG 59.080 36.000 13.19 0.00 0.00 4.73
2908 3018 8.262715 ACCAGTAAAAACAAAATTTGAACCAG 57.737 30.769 13.19 0.81 0.00 4.00
2932 3042 0.250989 TTGGATGGAACGGTTGGGAC 60.251 55.000 0.00 0.00 0.00 4.46
3029 3139 9.630098 ATGTTAGAGCATGACAATAAGTTTTTG 57.370 29.630 0.00 4.70 30.19 2.44
3118 3228 1.948721 GATTTTTGGGGGAGGCGCTG 61.949 60.000 7.64 0.00 0.00 5.18
3195 3306 3.117171 CTGTGCTCGGTGCTCTGC 61.117 66.667 3.53 0.00 43.37 4.26
3330 3449 3.574396 CAGTATCCCATCATACCTCGTGT 59.426 47.826 0.00 0.00 30.49 4.49
3411 3536 6.645700 TGAAAAAGCAGACAAACAATTCAC 57.354 33.333 0.00 0.00 0.00 3.18
3449 3574 8.986929 AGACTTATATTTTGAAATGGAGGGAG 57.013 34.615 0.00 0.00 0.00 4.30
3469 3594 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
3470 3595 9.136323 AGTCCATTTGAAATGTCTAAAAAGACT 57.864 29.630 15.93 14.21 39.41 3.24
3475 3600 9.959749 GTTGTAGTCCATTTGAAATGTCTAAAA 57.040 29.630 15.93 14.59 0.00 1.52
3476 3601 9.126151 TGTTGTAGTCCATTTGAAATGTCTAAA 57.874 29.630 15.93 10.39 0.00 1.85
3477 3602 8.684386 TGTTGTAGTCCATTTGAAATGTCTAA 57.316 30.769 15.93 4.89 0.00 2.10
3478 3603 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
3479 3604 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
3480 3605 9.507280 CATATGTTGTAGTCCATTTGAAATGTC 57.493 33.333 15.93 9.10 0.00 3.06
3481 3606 9.241919 TCATATGTTGTAGTCCATTTGAAATGT 57.758 29.630 15.93 1.43 29.81 2.71
3485 3610 9.241919 ACATTCATATGTTGTAGTCCATTTGAA 57.758 29.630 10.88 7.58 42.29 2.69
3486 3611 8.806429 ACATTCATATGTTGTAGTCCATTTGA 57.194 30.769 10.88 0.00 42.29 2.69
3489 3614 9.851686 ACATACATTCATATGTTGTAGTCCATT 57.148 29.630 19.00 6.13 41.98 3.16
3491 3616 9.981114 CTACATACATTCATATGTTGTAGTCCA 57.019 33.333 19.00 5.83 41.98 4.02
3530 3655 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3531 3656 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3532 3657 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3533 3658 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3534 3659 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3535 3660 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3536 3661 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3537 3662 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3538 3663 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3539 3664 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3540 3665 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3541 3666 7.653713 AGATAACTACATACGGAGCAAAATGAG 59.346 37.037 0.00 0.00 0.00 2.90
3542 3667 7.497595 AGATAACTACATACGGAGCAAAATGA 58.502 34.615 0.00 0.00 0.00 2.57
3543 3668 7.715265 AGATAACTACATACGGAGCAAAATG 57.285 36.000 0.00 0.00 0.00 2.32
3544 3669 9.998106 AATAGATAACTACATACGGAGCAAAAT 57.002 29.630 0.00 0.00 0.00 1.82
3545 3670 9.256477 CAATAGATAACTACATACGGAGCAAAA 57.744 33.333 0.00 0.00 0.00 2.44
3546 3671 7.870954 CCAATAGATAACTACATACGGAGCAAA 59.129 37.037 0.00 0.00 0.00 3.68
3547 3672 7.231925 TCCAATAGATAACTACATACGGAGCAA 59.768 37.037 0.00 0.00 0.00 3.91
3548 3673 6.717997 TCCAATAGATAACTACATACGGAGCA 59.282 38.462 0.00 0.00 0.00 4.26
3549 3674 7.154435 TCCAATAGATAACTACATACGGAGC 57.846 40.000 0.00 0.00 0.00 4.70
3550 3675 9.790389 GATTCCAATAGATAACTACATACGGAG 57.210 37.037 0.00 0.00 0.00 4.63
3551 3676 9.529823 AGATTCCAATAGATAACTACATACGGA 57.470 33.333 0.00 0.00 0.00 4.69
3552 3677 9.790389 GAGATTCCAATAGATAACTACATACGG 57.210 37.037 0.00 0.00 0.00 4.02
3580 3705 9.819267 CCTCCGTTCTAAAATATAAGTCTTTCT 57.181 33.333 0.00 0.00 0.00 2.52
3581 3706 9.043079 CCCTCCGTTCTAAAATATAAGTCTTTC 57.957 37.037 0.00 0.00 0.00 2.62
3582 3707 8.765517 TCCCTCCGTTCTAAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
3583 3708 8.315220 TCCCTCCGTTCTAAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
3584 3709 7.564292 ACTCCCTCCGTTCTAAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3585 3710 7.724287 ACTCCCTCCGTTCTAAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3586 3711 7.672122 ACTCCCTCCGTTCTAAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3590 3715 8.155510 GGAAATACTCCCTCCGTTCTAAAATAT 58.844 37.037 0.00 0.00 38.44 1.28
3591 3716 7.346436 AGGAAATACTCCCTCCGTTCTAAAATA 59.654 37.037 0.00 0.00 46.81 1.40
3592 3717 6.158169 AGGAAATACTCCCTCCGTTCTAAAAT 59.842 38.462 0.00 0.00 46.81 1.82
3593 3718 5.486419 AGGAAATACTCCCTCCGTTCTAAAA 59.514 40.000 0.00 0.00 46.81 1.52
3594 3719 5.028131 AGGAAATACTCCCTCCGTTCTAAA 58.972 41.667 0.00 0.00 46.81 1.85
3595 3720 4.617593 AGGAAATACTCCCTCCGTTCTAA 58.382 43.478 0.00 0.00 46.81 2.10
3596 3721 4.261411 AGGAAATACTCCCTCCGTTCTA 57.739 45.455 0.00 0.00 46.81 2.10
3597 3722 3.117552 AGGAAATACTCCCTCCGTTCT 57.882 47.619 0.00 0.00 46.81 3.01
3598 3723 3.908643 AAGGAAATACTCCCTCCGTTC 57.091 47.619 0.00 0.00 46.81 3.95
3599 3724 4.652679 AAAAGGAAATACTCCCTCCGTT 57.347 40.909 0.00 0.00 46.81 4.44
3600 3725 4.652679 AAAAAGGAAATACTCCCTCCGT 57.347 40.909 0.00 0.00 46.81 4.69
3623 3748 8.506437 GCTTATGATGCACAATGCTATAAGTAA 58.494 33.333 20.71 8.17 45.31 2.24
3624 3749 7.661027 TGCTTATGATGCACAATGCTATAAGTA 59.339 33.333 20.71 17.37 45.31 2.24
3625 3750 6.487668 TGCTTATGATGCACAATGCTATAAGT 59.512 34.615 20.71 3.75 45.31 2.24
3626 3751 6.905578 TGCTTATGATGCACAATGCTATAAG 58.094 36.000 18.25 18.25 45.31 1.73
3627 3752 6.880942 TGCTTATGATGCACAATGCTATAA 57.119 33.333 2.02 4.55 45.31 0.98
3628 3753 6.880942 TTGCTTATGATGCACAATGCTATA 57.119 33.333 2.02 0.00 45.31 1.31
3629 3754 5.777850 TTGCTTATGATGCACAATGCTAT 57.222 34.783 2.02 0.00 45.31 2.97
3630 3755 5.299782 TCATTGCTTATGATGCACAATGCTA 59.700 36.000 15.43 7.89 44.50 3.49
3631 3756 4.098807 TCATTGCTTATGATGCACAATGCT 59.901 37.500 15.43 0.00 44.50 3.79
3632 3757 4.208460 GTCATTGCTTATGATGCACAATGC 59.792 41.667 15.43 9.40 44.75 3.56
3633 3758 5.588240 AGTCATTGCTTATGATGCACAATG 58.412 37.500 14.52 14.52 44.75 2.82
3634 3759 5.847111 AGTCATTGCTTATGATGCACAAT 57.153 34.783 0.00 0.00 44.75 2.71
3635 3760 5.047872 ACAAGTCATTGCTTATGATGCACAA 60.048 36.000 0.00 0.00 44.75 3.33
3636 3761 4.460034 ACAAGTCATTGCTTATGATGCACA 59.540 37.500 0.00 0.00 44.75 4.57
3637 3762 4.990257 ACAAGTCATTGCTTATGATGCAC 58.010 39.130 0.00 0.00 44.75 4.57
3638 3763 6.319405 ACATACAAGTCATTGCTTATGATGCA 59.681 34.615 5.57 0.00 44.75 3.96
3639 3764 6.732154 ACATACAAGTCATTGCTTATGATGC 58.268 36.000 5.57 0.00 44.75 3.91
3640 3765 8.829612 TGTACATACAAGTCATTGCTTATGATG 58.170 33.333 0.00 4.22 38.16 3.07
3641 3766 8.962884 TGTACATACAAGTCATTGCTTATGAT 57.037 30.769 0.00 0.00 38.16 2.45
3642 3767 8.962884 ATGTACATACAAGTCATTGCTTATGA 57.037 30.769 6.56 0.00 40.27 2.15


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

AutoCloner maintained by Alex Coulton.