Multiple sequence alignment - TraesCS2D01G516400

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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 TraesCS2D01G516400 chr2D 100.000 2801 0 0 1 2801 607682219 607679419 0.000000e+00 5173.0
1 TraesCS2D01G516400 chr2D 87.368 95 11 1 1 94 60794716 60794810 1.060000e-19 108.0
2 TraesCS2D01G516400 chr2B 90.956 1946 88 29 176 2109 741008149 741006280 0.000000e+00 2538.0
3 TraesCS2D01G516400 chr2B 80.429 746 72 34 2088 2801 741006255 741005552 4.170000e-138 501.0
4 TraesCS2D01G516400 chr2A 90.221 1626 70 36 207 1801 739379899 739378332 0.000000e+00 2039.0
5 TraesCS2D01G516400 chr2A 85.624 473 39 21 1864 2320 739378334 739377875 1.170000e-128 470.0
6 TraesCS2D01G516400 chr2A 76.463 735 85 47 2129 2801 739375273 739374565 4.500000e-83 318.0
7 TraesCS2D01G516400 chr2A 92.647 136 10 0 2349 2484 739377570 739377435 2.200000e-46 196.0
8 TraesCS2D01G516400 chr2A 88.889 81 8 1 19 99 703677774 703677853 6.390000e-17 99.0
9 TraesCS2D01G516400 chr4D 86.316 95 12 1 1 94 378448086 378448180 4.940000e-18 102.0
10 TraesCS2D01G516400 chr3B 85.149 101 14 1 1 100 790493936 790493836 4.940000e-18 102.0
11 TraesCS2D01G516400 chr5D 83.810 105 15 2 1 103 427372763 427372659 6.390000e-17 99.0
12 TraesCS2D01G516400 chr1B 85.263 95 12 2 1 94 308636400 308636493 2.300000e-16 97.1
13 TraesCS2D01G516400 chr7A 86.585 82 11 0 18 99 605167090 605167009 1.070000e-14 91.6
14 TraesCS2D01G516400 chr7D 85.542 83 11 1 19 100 142335005 142334923 4.970000e-13 86.1
15 TraesCS2D01G516400 chr1D 82.178 101 17 1 1 100 298359222 298359122 4.970000e-13 86.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G516400 chr2D 607679419 607682219 2800 True 5173.00 5173 100.00000 1 2801 1 chr2D.!!$R1 2800
1 TraesCS2D01G516400 chr2B 741005552 741008149 2597 True 1519.50 2538 85.69250 176 2801 2 chr2B.!!$R1 2625
2 TraesCS2D01G516400 chr2A 739374565 739379899 5334 True 755.75 2039 86.23875 207 2801 4 chr2A.!!$R1 2594

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
33 34 0.033504 ATGTATCATGTCCGCGGACC 59.966 55.0 45.59 32.2 43.97 4.46 F
545 564 0.167689 CTTTCTCCTTTGCGCTGCTC 59.832 55.0 9.73 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1850 0.318784 CTGCTATTCGGGCGACTACC 60.319 60.0 0.0 0.0 0.0 3.18 R
2337 2728 0.523966 CGGACTCTCTCTGACACCAC 59.476 60.0 0.0 0.0 0.0 4.16 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
24 25 6.429521 TGGATGACTCATCATGTATCATGT 57.570 37.500 18.77 0.00 46.01 3.21
25 26 6.461640 TGGATGACTCATCATGTATCATGTC 58.538 40.000 18.77 4.85 46.01 3.06
26 27 5.873712 GGATGACTCATCATGTATCATGTCC 59.126 44.000 18.77 5.04 46.01 4.02
27 28 4.874970 TGACTCATCATGTATCATGTCCG 58.125 43.478 9.13 1.25 0.00 4.79
28 29 3.657634 ACTCATCATGTATCATGTCCGC 58.342 45.455 9.13 0.00 0.00 5.54
29 30 2.665052 CTCATCATGTATCATGTCCGCG 59.335 50.000 0.00 0.00 0.00 6.46
30 31 1.728425 CATCATGTATCATGTCCGCGG 59.272 52.381 22.12 22.12 0.00 6.46
31 32 1.036707 TCATGTATCATGTCCGCGGA 58.963 50.000 27.28 27.28 0.00 5.54
32 33 1.139989 CATGTATCATGTCCGCGGAC 58.860 55.000 43.88 43.88 44.77 4.79
33 34 0.033504 ATGTATCATGTCCGCGGACC 59.966 55.000 45.59 32.20 43.97 4.46
34 35 1.324005 TGTATCATGTCCGCGGACCA 61.324 55.000 45.59 35.00 43.97 4.02
35 36 0.874607 GTATCATGTCCGCGGACCAC 60.875 60.000 45.59 31.78 43.97 4.16
36 37 2.344521 TATCATGTCCGCGGACCACG 62.345 60.000 45.59 34.59 43.97 4.94
37 38 4.735132 CATGTCCGCGGACCACGT 62.735 66.667 45.59 29.67 46.52 4.49
38 39 4.430765 ATGTCCGCGGACCACGTC 62.431 66.667 45.59 26.89 46.52 4.34
46 47 3.607163 GGACCACGTCCGGACATA 58.393 61.111 32.80 0.00 43.14 2.29
47 48 1.892338 GGACCACGTCCGGACATAA 59.108 57.895 32.80 0.00 43.14 1.90
48 49 0.247185 GGACCACGTCCGGACATAAA 59.753 55.000 32.80 0.00 43.14 1.40
49 50 1.338011 GGACCACGTCCGGACATAAAA 60.338 52.381 32.80 0.00 43.14 1.52
50 51 2.624636 GACCACGTCCGGACATAAAAT 58.375 47.619 32.80 13.56 0.00 1.82
51 52 2.350498 GACCACGTCCGGACATAAAATG 59.650 50.000 32.80 17.49 0.00 2.32
52 53 1.668751 CCACGTCCGGACATAAAATGG 59.331 52.381 32.80 23.16 33.60 3.16
53 54 1.668751 CACGTCCGGACATAAAATGGG 59.331 52.381 32.80 16.06 33.60 4.00
54 55 1.555992 ACGTCCGGACATAAAATGGGA 59.444 47.619 32.80 0.00 33.60 4.37
55 56 2.171870 ACGTCCGGACATAAAATGGGAT 59.828 45.455 32.80 3.07 33.60 3.85
56 57 3.388676 ACGTCCGGACATAAAATGGGATA 59.611 43.478 32.80 0.00 33.60 2.59
57 58 4.041198 ACGTCCGGACATAAAATGGGATAT 59.959 41.667 32.80 0.00 33.60 1.63
58 59 5.246656 ACGTCCGGACATAAAATGGGATATA 59.753 40.000 32.80 0.00 33.60 0.86
59 60 6.070424 ACGTCCGGACATAAAATGGGATATAT 60.070 38.462 32.80 0.00 33.60 0.86
60 61 7.124599 ACGTCCGGACATAAAATGGGATATATA 59.875 37.037 32.80 0.00 33.60 0.86
61 62 7.437267 CGTCCGGACATAAAATGGGATATATAC 59.563 40.741 32.80 0.39 33.60 1.47
62 63 7.713942 GTCCGGACATAAAATGGGATATATACC 59.286 40.741 29.75 7.08 33.60 2.73
63 64 6.704493 CCGGACATAAAATGGGATATATACCG 59.296 42.308 9.54 0.00 31.47 4.02
64 65 7.418139 CCGGACATAAAATGGGATATATACCGA 60.418 40.741 9.54 0.00 33.16 4.69
65 66 7.982919 CGGACATAAAATGGGATATATACCGAA 59.017 37.037 9.54 0.00 33.16 4.30
66 67 9.326413 GGACATAAAATGGGATATATACCGAAG 57.674 37.037 9.54 0.00 31.47 3.79
68 69 9.886132 ACATAAAATGGGATATATACCGAAGAC 57.114 33.333 9.54 0.00 31.47 3.01
69 70 9.884636 CATAAAATGGGATATATACCGAAGACA 57.115 33.333 9.54 0.00 31.47 3.41
72 73 9.807921 AAAATGGGATATATACCGAAGACATTT 57.192 29.630 9.54 5.81 36.66 2.32
73 74 8.792830 AATGGGATATATACCGAAGACATTTG 57.207 34.615 9.54 0.00 31.47 2.32
74 75 6.170506 TGGGATATATACCGAAGACATTTGC 58.829 40.000 9.54 0.00 31.47 3.68
75 76 6.170506 GGGATATATACCGAAGACATTTGCA 58.829 40.000 0.00 0.00 0.00 4.08
76 77 6.313905 GGGATATATACCGAAGACATTTGCAG 59.686 42.308 0.00 0.00 0.00 4.41
77 78 6.313905 GGATATATACCGAAGACATTTGCAGG 59.686 42.308 0.00 0.00 0.00 4.85
78 79 2.851263 TACCGAAGACATTTGCAGGT 57.149 45.000 0.00 0.00 0.00 4.00
79 80 1.523758 ACCGAAGACATTTGCAGGTC 58.476 50.000 7.04 7.04 0.00 3.85
80 81 1.202758 ACCGAAGACATTTGCAGGTCA 60.203 47.619 14.93 0.00 36.50 4.02
81 82 1.466167 CCGAAGACATTTGCAGGTCAG 59.534 52.381 14.93 7.69 36.50 3.51
82 83 1.135859 CGAAGACATTTGCAGGTCAGC 60.136 52.381 14.93 7.33 36.50 4.26
83 84 0.877071 AAGACATTTGCAGGTCAGCG 59.123 50.000 14.93 0.00 36.50 5.18
84 85 0.250467 AGACATTTGCAGGTCAGCGT 60.250 50.000 14.93 0.00 36.50 5.07
85 86 0.593128 GACATTTGCAGGTCAGCGTT 59.407 50.000 9.53 0.00 37.31 4.84
86 87 1.804151 GACATTTGCAGGTCAGCGTTA 59.196 47.619 9.53 0.00 37.31 3.18
87 88 1.806542 ACATTTGCAGGTCAGCGTTAG 59.193 47.619 0.00 0.00 37.31 2.34
88 89 2.076100 CATTTGCAGGTCAGCGTTAGA 58.924 47.619 0.00 0.00 37.31 2.10
89 90 1.795768 TTTGCAGGTCAGCGTTAGAG 58.204 50.000 0.00 0.00 37.31 2.43
90 91 0.966179 TTGCAGGTCAGCGTTAGAGA 59.034 50.000 0.00 0.00 37.31 3.10
91 92 1.186200 TGCAGGTCAGCGTTAGAGAT 58.814 50.000 0.00 0.00 37.31 2.75
92 93 1.134995 TGCAGGTCAGCGTTAGAGATG 60.135 52.381 0.00 0.00 37.31 2.90
93 94 1.565305 CAGGTCAGCGTTAGAGATGC 58.435 55.000 0.00 0.00 40.73 3.91
108 109 7.646548 TTAGAGATGCTCTAAGCTAGTTCAA 57.353 36.000 11.70 0.00 44.85 2.69
109 110 5.901552 AGAGATGCTCTAAGCTAGTTCAAC 58.098 41.667 0.11 0.00 42.97 3.18
110 111 5.017294 AGATGCTCTAAGCTAGTTCAACC 57.983 43.478 0.11 0.00 42.97 3.77
111 112 4.714308 AGATGCTCTAAGCTAGTTCAACCT 59.286 41.667 0.11 0.00 42.97 3.50
112 113 4.457834 TGCTCTAAGCTAGTTCAACCTC 57.542 45.455 0.11 0.00 42.97 3.85
113 114 3.119459 TGCTCTAAGCTAGTTCAACCTCG 60.119 47.826 0.11 0.00 42.97 4.63
114 115 3.735514 GCTCTAAGCTAGTTCAACCTCGG 60.736 52.174 0.00 0.00 38.45 4.63
115 116 3.428532 TCTAAGCTAGTTCAACCTCGGT 58.571 45.455 0.00 0.00 0.00 4.69
116 117 3.830755 TCTAAGCTAGTTCAACCTCGGTT 59.169 43.478 0.00 0.00 39.13 4.44
117 118 2.745515 AGCTAGTTCAACCTCGGTTC 57.254 50.000 0.00 0.00 36.00 3.62
118 119 1.968493 AGCTAGTTCAACCTCGGTTCA 59.032 47.619 0.00 0.00 36.00 3.18
119 120 2.367567 AGCTAGTTCAACCTCGGTTCAA 59.632 45.455 0.00 0.00 36.00 2.69
120 121 3.135994 GCTAGTTCAACCTCGGTTCAAA 58.864 45.455 0.00 0.00 36.00 2.69
121 122 3.562557 GCTAGTTCAACCTCGGTTCAAAA 59.437 43.478 0.00 0.00 36.00 2.44
122 123 4.554134 GCTAGTTCAACCTCGGTTCAAAAC 60.554 45.833 0.00 4.63 36.00 2.43
123 124 3.617284 AGTTCAACCTCGGTTCAAAACT 58.383 40.909 11.87 11.87 36.00 2.66
124 125 3.377172 AGTTCAACCTCGGTTCAAAACTG 59.623 43.478 14.87 0.00 36.00 3.16
125 126 1.673920 TCAACCTCGGTTCAAAACTGC 59.326 47.619 0.00 0.00 37.69 4.40
126 127 0.661020 AACCTCGGTTCAAAACTGCG 59.339 50.000 0.00 0.00 37.69 5.18
127 128 0.179067 ACCTCGGTTCAAAACTGCGA 60.179 50.000 0.00 0.00 37.69 5.10
128 129 0.941542 CCTCGGTTCAAAACTGCGAA 59.058 50.000 0.00 0.00 37.69 4.70
129 130 1.332375 CCTCGGTTCAAAACTGCGAAA 59.668 47.619 0.00 0.00 37.69 3.46
130 131 2.372350 CTCGGTTCAAAACTGCGAAAC 58.628 47.619 0.00 0.00 37.69 2.78
131 132 2.011222 TCGGTTCAAAACTGCGAAACT 58.989 42.857 0.00 0.00 37.69 2.66
132 133 2.420722 TCGGTTCAAAACTGCGAAACTT 59.579 40.909 0.00 0.00 37.69 2.66
133 134 3.622163 TCGGTTCAAAACTGCGAAACTTA 59.378 39.130 0.00 0.00 37.69 2.24
134 135 4.273969 TCGGTTCAAAACTGCGAAACTTAT 59.726 37.500 0.00 0.00 37.69 1.73
135 136 4.973663 CGGTTCAAAACTGCGAAACTTATT 59.026 37.500 0.00 0.00 0.00 1.40
136 137 6.018098 TCGGTTCAAAACTGCGAAACTTATTA 60.018 34.615 0.00 0.00 37.69 0.98
137 138 6.799925 CGGTTCAAAACTGCGAAACTTATTAT 59.200 34.615 0.00 0.00 0.00 1.28
138 139 7.201232 CGGTTCAAAACTGCGAAACTTATTATG 60.201 37.037 0.00 0.00 0.00 1.90
139 140 7.806014 GGTTCAAAACTGCGAAACTTATTATGA 59.194 33.333 0.00 0.00 0.00 2.15
140 141 9.341899 GTTCAAAACTGCGAAACTTATTATGAT 57.658 29.630 0.00 0.00 0.00 2.45
141 142 8.894409 TCAAAACTGCGAAACTTATTATGATG 57.106 30.769 0.00 0.00 0.00 3.07
142 143 7.967854 TCAAAACTGCGAAACTTATTATGATGG 59.032 33.333 0.00 0.00 0.00 3.51
143 144 7.624360 AAACTGCGAAACTTATTATGATGGA 57.376 32.000 0.00 0.00 0.00 3.41
144 145 7.807977 AACTGCGAAACTTATTATGATGGAT 57.192 32.000 0.00 0.00 0.00 3.41
145 146 8.902540 AACTGCGAAACTTATTATGATGGATA 57.097 30.769 0.00 0.00 0.00 2.59
146 147 8.539770 ACTGCGAAACTTATTATGATGGATAG 57.460 34.615 0.00 0.00 0.00 2.08
147 148 8.150945 ACTGCGAAACTTATTATGATGGATAGT 58.849 33.333 0.00 0.00 0.00 2.12
148 149 8.310406 TGCGAAACTTATTATGATGGATAGTG 57.690 34.615 0.00 0.00 0.00 2.74
149 150 7.095229 TGCGAAACTTATTATGATGGATAGTGC 60.095 37.037 0.00 0.00 0.00 4.40
150 151 7.118390 GCGAAACTTATTATGATGGATAGTGCT 59.882 37.037 0.00 0.00 0.00 4.40
151 152 9.639601 CGAAACTTATTATGATGGATAGTGCTA 57.360 33.333 0.00 0.00 0.00 3.49
159 160 9.983024 ATTATGATGGATAGTGCTACTACTAGT 57.017 33.333 0.00 0.00 36.66 2.57
162 163 9.983024 ATGATGGATAGTGCTACTACTAGTATT 57.017 33.333 2.33 0.00 36.66 1.89
163 164 9.809395 TGATGGATAGTGCTACTACTAGTATTT 57.191 33.333 2.33 0.00 36.66 1.40
165 166 7.883217 TGGATAGTGCTACTACTAGTATTTGC 58.117 38.462 16.16 16.16 36.66 3.68
166 167 7.039923 TGGATAGTGCTACTACTAGTATTTGCC 60.040 40.741 18.87 12.51 36.66 4.52
167 168 5.532664 AGTGCTACTACTAGTATTTGCCC 57.467 43.478 18.87 11.06 29.08 5.36
168 169 4.344390 AGTGCTACTACTAGTATTTGCCCC 59.656 45.833 18.87 12.04 29.08 5.80
169 170 4.344390 GTGCTACTACTAGTATTTGCCCCT 59.656 45.833 18.87 0.00 29.08 4.79
170 171 4.966805 TGCTACTACTAGTATTTGCCCCTT 59.033 41.667 18.87 0.00 29.08 3.95
171 172 5.427481 TGCTACTACTAGTATTTGCCCCTTT 59.573 40.000 18.87 0.00 29.08 3.11
172 173 6.069847 TGCTACTACTAGTATTTGCCCCTTTT 60.070 38.462 18.87 0.00 29.08 2.27
173 174 6.827251 GCTACTACTAGTATTTGCCCCTTTTT 59.173 38.462 13.28 0.00 29.08 1.94
226 227 3.195698 GCGCGGGGACTGAATGTC 61.196 66.667 8.83 0.00 44.63 3.06
302 304 1.336609 ACGACCAAGGCTACGACTTTC 60.337 52.381 9.48 0.00 0.00 2.62
303 305 1.336517 CGACCAAGGCTACGACTTTCA 60.337 52.381 0.00 0.00 0.00 2.69
304 306 2.338500 GACCAAGGCTACGACTTTCAG 58.662 52.381 0.00 0.00 0.00 3.02
305 307 1.968493 ACCAAGGCTACGACTTTCAGA 59.032 47.619 0.00 0.00 0.00 3.27
306 308 2.288886 ACCAAGGCTACGACTTTCAGAC 60.289 50.000 0.00 0.00 0.00 3.51
307 309 2.028930 CCAAGGCTACGACTTTCAGACT 60.029 50.000 0.00 0.00 0.00 3.24
308 310 3.555168 CCAAGGCTACGACTTTCAGACTT 60.555 47.826 0.00 0.00 38.18 3.01
309 311 4.058817 CAAGGCTACGACTTTCAGACTTT 58.941 43.478 0.00 0.00 35.42 2.66
310 312 3.654414 AGGCTACGACTTTCAGACTTTG 58.346 45.455 0.00 0.00 0.00 2.77
335 337 2.505982 CCAGTCATGCGGTAGGGG 59.494 66.667 0.00 0.00 0.00 4.79
449 461 2.360350 ATCCGCACCTGCACCAAG 60.360 61.111 0.00 0.00 42.21 3.61
490 502 3.299977 GCCAAAACCACCCCCGTC 61.300 66.667 0.00 0.00 0.00 4.79
491 503 2.599281 CCAAAACCACCCCCGTCC 60.599 66.667 0.00 0.00 0.00 4.79
512 531 1.834896 GTCTCCTCCCTCCTTTTCTCC 59.165 57.143 0.00 0.00 0.00 3.71
541 560 0.687354 TCTCCTTTCTCCTTTGCGCT 59.313 50.000 9.73 0.00 0.00 5.92
542 561 0.801251 CTCCTTTCTCCTTTGCGCTG 59.199 55.000 9.73 0.00 0.00 5.18
543 562 1.211190 CCTTTCTCCTTTGCGCTGC 59.789 57.895 9.73 0.00 0.00 5.25
544 563 1.239968 CCTTTCTCCTTTGCGCTGCT 61.240 55.000 9.73 0.00 0.00 4.24
545 564 0.167689 CTTTCTCCTTTGCGCTGCTC 59.832 55.000 9.73 0.00 0.00 4.26
546 565 0.534877 TTTCTCCTTTGCGCTGCTCA 60.535 50.000 9.73 0.00 0.00 4.26
547 566 0.952497 TTCTCCTTTGCGCTGCTCAG 60.952 55.000 9.73 0.00 0.00 3.35
577 597 2.285743 AGAACCCCCTCTGCCCTC 60.286 66.667 0.00 0.00 0.00 4.30
578 598 3.412408 GAACCCCCTCTGCCCTCC 61.412 72.222 0.00 0.00 0.00 4.30
590 610 0.325933 TGCCCTCCATGACAACTCTG 59.674 55.000 0.00 0.00 0.00 3.35
739 760 1.924731 AGCTTTTGGAAGGGCTAACC 58.075 50.000 0.00 0.00 40.67 2.85
800 821 4.876107 ACAAACAGTGGATTAGATTAGGCG 59.124 41.667 0.00 0.00 0.00 5.52
802 823 5.552870 AACAGTGGATTAGATTAGGCGAT 57.447 39.130 0.00 0.00 0.00 4.58
892 921 1.079819 CTGGCCAGTGACCACTACG 60.080 63.158 25.53 0.00 40.20 3.51
896 925 1.878656 GCCAGTGACCACTACGCTCT 61.879 60.000 1.95 0.00 40.20 4.09
1050 1083 2.351276 GGGGTGAGCGTCATGGTT 59.649 61.111 0.00 0.00 0.00 3.67
1481 1535 3.522731 CTCCTCCTCCTCCGCGTG 61.523 72.222 4.92 0.00 0.00 5.34
1607 1661 0.754217 TACGGGATCACGGAGGAAGG 60.754 60.000 23.42 0.00 38.39 3.46
1776 1830 0.318445 CCTCGTCGTCGTCCAACTTT 60.318 55.000 1.33 0.00 38.33 2.66
1796 1850 2.393362 CGCGCGCTTCTTCTCTTG 59.607 61.111 30.48 5.07 0.00 3.02
1806 1860 1.183549 TCTTCTCTTGGTAGTCGCCC 58.816 55.000 0.00 0.00 0.00 6.13
1809 1863 0.609957 TCTCTTGGTAGTCGCCCGAA 60.610 55.000 0.00 0.00 0.00 4.30
1823 1877 1.687123 GCCCGAATAGCAGACCTCTTA 59.313 52.381 0.00 0.00 0.00 2.10
1830 1884 5.545588 GAATAGCAGACCTCTTATGATGCA 58.454 41.667 0.00 0.00 36.15 3.96
1833 1887 3.129871 GCAGACCTCTTATGATGCAGTC 58.870 50.000 0.00 0.00 33.92 3.51
1848 1902 0.881796 CAGTCGAGTGTGGCTGAGTA 59.118 55.000 12.29 0.00 0.00 2.59
1854 1908 3.508402 TCGAGTGTGGCTGAGTAATGTAA 59.492 43.478 0.00 0.00 0.00 2.41
1862 1916 3.394719 GCTGAGTAATGTAAGCCCTAGC 58.605 50.000 0.00 0.00 40.32 3.42
1889 1950 8.737168 AGATCTTGATTCCATTCATCGTTTTA 57.263 30.769 0.00 0.00 0.00 1.52
1931 1999 5.163602 TGTTGTTCGTTGGATTTGCTAGTTT 60.164 36.000 0.00 0.00 0.00 2.66
1979 2047 4.968719 TGTACCCCACTTGATGATCTATGT 59.031 41.667 0.00 0.00 0.00 2.29
1985 2053 6.295011 CCCCACTTGATGATCTATGTCTAGAC 60.295 46.154 16.32 16.32 36.81 2.59
1997 2065 6.231211 TCTATGTCTAGACGATGCATCAGTA 58.769 40.000 25.70 12.40 0.00 2.74
2011 2079 4.168760 GCATCAGTATCTGGTTGCAAAAC 58.831 43.478 0.00 0.00 39.22 2.43
2049 2117 6.206634 TCCATGTTTGATCTACACAAAACTCC 59.793 38.462 3.80 0.00 38.63 3.85
2082 2150 5.246883 ACTCTAGGCCAAAATGCTCAAAAAT 59.753 36.000 5.01 0.00 0.00 1.82
2084 2152 4.354893 AGGCCAAAATGCTCAAAAATCA 57.645 36.364 5.01 0.00 0.00 2.57
2109 2224 5.416952 AGCTCTCTCTCTCTCTCTTTTTCTG 59.583 44.000 0.00 0.00 0.00 3.02
2116 2231 4.990526 TCTCTCTCTTTTTCTGGGCAAAT 58.009 39.130 0.00 0.00 0.00 2.32
2229 2349 8.990163 TTGGATAAAGAAAGGTAACAACTCTT 57.010 30.769 0.00 0.00 41.41 2.85
2235 2355 7.881775 AAGAAAGGTAACAACTCTTCAATGT 57.118 32.000 0.00 0.00 41.41 2.71
2247 2367 9.809096 ACAACTCTTCAATGTACTGATATACTG 57.191 33.333 0.00 0.00 0.00 2.74
2255 2375 9.481340 TCAATGTACTGATATACTGAAGATTGC 57.519 33.333 0.00 0.00 0.00 3.56
2257 2377 9.836864 AATGTACTGATATACTGAAGATTGCAA 57.163 29.630 0.00 0.00 0.00 4.08
2260 2380 9.967346 GTACTGATATACTGAAGATTGCAACTA 57.033 33.333 0.00 0.00 0.00 2.24
2261 2381 8.879342 ACTGATATACTGAAGATTGCAACTAC 57.121 34.615 0.00 0.00 0.00 2.73
2264 2384 8.144478 TGATATACTGAAGATTGCAACTACTCC 58.856 37.037 0.00 0.00 0.00 3.85
2320 2441 4.622701 AGTTTTGCACTGTTCTTCAGAC 57.377 40.909 1.79 0.00 46.27 3.51
2321 2442 3.063997 AGTTTTGCACTGTTCTTCAGACG 59.936 43.478 1.79 0.00 46.27 4.18
2322 2443 1.581934 TTGCACTGTTCTTCAGACGG 58.418 50.000 1.79 0.00 46.27 4.79
2323 2444 0.750249 TGCACTGTTCTTCAGACGGA 59.250 50.000 1.79 0.00 46.27 4.69
2337 2728 2.802816 CAGACGGACTTTTGTTCTGAGG 59.197 50.000 0.00 0.00 37.11 3.86
2376 2777 3.142951 CGAGGACTGATACAGTAGGGAG 58.857 54.545 4.36 0.00 45.44 4.30
2379 2780 1.609555 GACTGATACAGTAGGGAGCCG 59.390 57.143 4.36 0.00 45.44 5.52
2426 2827 1.610522 GAGTGGCTGTTGCTTTGTCAT 59.389 47.619 0.00 0.00 39.59 3.06
2483 5420 3.000819 CTGACCGGGGGCAGTGTA 61.001 66.667 12.62 0.00 0.00 2.90
2494 5431 2.027100 GGGGCAGTGTAAGCTTTACTCT 60.027 50.000 3.20 4.71 0.00 3.24
2571 5514 0.037605 AATGTTCACCCTCCGTCGAC 60.038 55.000 5.18 5.18 0.00 4.20
2582 5535 2.325761 CTCCGTCGACCAAACAACTAG 58.674 52.381 10.58 0.00 0.00 2.57
2584 5537 2.884012 TCCGTCGACCAAACAACTAGTA 59.116 45.455 10.58 0.00 0.00 1.82
2585 5538 3.058016 TCCGTCGACCAAACAACTAGTAG 60.058 47.826 10.58 0.00 0.00 2.57
2586 5539 3.304928 CCGTCGACCAAACAACTAGTAGT 60.305 47.826 10.58 0.00 0.00 2.73
2587 5540 4.083324 CCGTCGACCAAACAACTAGTAGTA 60.083 45.833 10.58 0.00 0.00 1.82
2588 5541 5.392380 CCGTCGACCAAACAACTAGTAGTAT 60.392 44.000 10.58 0.00 0.00 2.12
2589 5542 5.510674 CGTCGACCAAACAACTAGTAGTATG 59.489 44.000 10.58 7.03 0.00 2.39
2590 5543 5.287992 GTCGACCAAACAACTAGTAGTATGC 59.712 44.000 3.51 0.00 0.00 3.14
2591 5544 5.184479 TCGACCAAACAACTAGTAGTATGCT 59.816 40.000 2.50 0.00 33.55 3.79
2592 5545 5.515626 CGACCAAACAACTAGTAGTATGCTC 59.484 44.000 2.50 0.00 29.76 4.26
2593 5546 5.731591 ACCAAACAACTAGTAGTATGCTCC 58.268 41.667 2.50 0.00 29.76 4.70
2594 5547 5.247564 ACCAAACAACTAGTAGTATGCTCCA 59.752 40.000 2.50 0.00 29.76 3.86
2595 5548 5.581085 CCAAACAACTAGTAGTATGCTCCAC 59.419 44.000 2.50 0.00 29.76 4.02
2596 5549 6.398918 CAAACAACTAGTAGTATGCTCCACT 58.601 40.000 2.50 0.00 29.76 4.00
2597 5550 7.363530 CCAAACAACTAGTAGTATGCTCCACTA 60.364 40.741 2.50 0.00 29.76 2.74
2598 5551 6.696441 ACAACTAGTAGTATGCTCCACTAC 57.304 41.667 2.50 12.40 45.74 2.73
2599 5552 5.593502 ACAACTAGTAGTATGCTCCACTACC 59.406 44.000 2.50 3.56 46.29 3.18
2606 5559 2.770164 ATGCTCCACTACCACACTTC 57.230 50.000 0.00 0.00 0.00 3.01
2612 5565 0.389948 CACTACCACACTTCTCCCGC 60.390 60.000 0.00 0.00 0.00 6.13
2628 5581 2.825836 GCTGGCCATTGGTCTCCG 60.826 66.667 5.51 0.00 0.00 4.63
2696 5662 1.448013 CGGGTTCTCGGAAAGGAGC 60.448 63.158 0.00 0.00 33.98 4.70
2697 5663 1.078356 GGGTTCTCGGAAAGGAGCC 60.078 63.158 0.00 0.00 43.93 4.70
2698 5664 1.078356 GGTTCTCGGAAAGGAGCCC 60.078 63.158 0.00 0.00 33.98 5.19
2699 5665 1.448013 GTTCTCGGAAAGGAGCCCG 60.448 63.158 0.00 0.00 46.57 6.13
2701 5667 4.840005 CTCGGAAAGGAGCCCGCC 62.840 72.222 0.00 0.00 44.96 6.13
2705 5671 4.176752 GAAAGGAGCCCGCCCGAT 62.177 66.667 0.00 0.00 0.00 4.18
2706 5672 4.176752 AAAGGAGCCCGCCCGATC 62.177 66.667 0.00 0.00 0.00 3.69
2716 5682 2.272146 GCCCGATCCTGGCTTTCA 59.728 61.111 12.56 0.00 45.70 2.69
2717 5683 1.821332 GCCCGATCCTGGCTTTCAG 60.821 63.158 12.56 0.00 45.70 3.02
2718 5684 1.604378 CCCGATCCTGGCTTTCAGT 59.396 57.895 0.00 0.00 41.83 3.41
2719 5685 0.035056 CCCGATCCTGGCTTTCAGTT 60.035 55.000 0.00 0.00 41.83 3.16
2720 5686 1.614317 CCCGATCCTGGCTTTCAGTTT 60.614 52.381 0.00 0.00 41.83 2.66
2726 5692 1.532868 CCTGGCTTTCAGTTTCAGACG 59.467 52.381 0.00 0.00 41.83 4.18
2734 5700 0.798776 CAGTTTCAGACGACCATGGC 59.201 55.000 13.04 3.65 0.00 4.40
2736 5702 0.321653 GTTTCAGACGACCATGGCCT 60.322 55.000 13.04 0.80 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.834107 ACATGATACATGATGAGTCATCCAA 58.166 36.000 26.58 12.38 43.14 3.53
1 2 6.429521 ACATGATACATGATGAGTCATCCA 57.570 37.500 26.58 17.42 43.14 3.41
2 3 5.873712 GGACATGATACATGATGAGTCATCC 59.126 44.000 26.58 12.86 43.14 3.51
3 4 5.575995 CGGACATGATACATGATGAGTCATC 59.424 44.000 23.75 23.75 43.14 2.92
4 5 5.476614 CGGACATGATACATGATGAGTCAT 58.523 41.667 16.86 4.98 45.87 3.06
5 6 4.797275 GCGGACATGATACATGATGAGTCA 60.797 45.833 16.86 3.21 39.04 3.41
6 7 3.677121 GCGGACATGATACATGATGAGTC 59.323 47.826 16.86 5.12 0.00 3.36
7 8 3.657634 GCGGACATGATACATGATGAGT 58.342 45.455 16.86 0.00 0.00 3.41
8 9 2.665052 CGCGGACATGATACATGATGAG 59.335 50.000 16.86 7.48 0.00 2.90
9 10 2.610232 CCGCGGACATGATACATGATGA 60.610 50.000 24.07 0.00 0.00 2.92
10 11 1.728425 CCGCGGACATGATACATGATG 59.272 52.381 24.07 0.00 0.00 3.07
11 12 1.618343 TCCGCGGACATGATACATGAT 59.382 47.619 27.28 3.36 0.00 2.45
12 13 1.036707 TCCGCGGACATGATACATGA 58.963 50.000 27.28 0.00 0.00 3.07
13 14 1.139989 GTCCGCGGACATGATACATG 58.860 55.000 44.88 8.65 44.02 3.21
14 15 3.588277 GTCCGCGGACATGATACAT 57.412 52.632 44.88 0.00 44.02 2.29
30 31 2.083167 TTTTATGTCCGGACGTGGTC 57.917 50.000 34.65 10.06 0.00 4.02
31 32 2.352388 CATTTTATGTCCGGACGTGGT 58.648 47.619 34.65 20.21 0.00 4.16
32 33 1.668751 CCATTTTATGTCCGGACGTGG 59.331 52.381 34.65 23.99 0.00 4.94
33 34 1.668751 CCCATTTTATGTCCGGACGTG 59.331 52.381 34.65 19.55 0.00 4.49
34 35 1.555992 TCCCATTTTATGTCCGGACGT 59.444 47.619 31.01 31.01 0.00 4.34
35 36 2.319136 TCCCATTTTATGTCCGGACG 57.681 50.000 28.70 12.84 0.00 4.79
36 37 7.713942 GGTATATATCCCATTTTATGTCCGGAC 59.286 40.741 28.17 28.17 0.00 4.79
37 38 7.418139 CGGTATATATCCCATTTTATGTCCGGA 60.418 40.741 0.00 0.00 0.00 5.14
38 39 6.704493 CGGTATATATCCCATTTTATGTCCGG 59.296 42.308 0.00 0.00 0.00 5.14
39 40 7.494211 TCGGTATATATCCCATTTTATGTCCG 58.506 38.462 0.00 0.00 0.00 4.79
40 41 9.326413 CTTCGGTATATATCCCATTTTATGTCC 57.674 37.037 0.00 0.00 0.00 4.02
42 43 9.886132 GTCTTCGGTATATATCCCATTTTATGT 57.114 33.333 0.00 0.00 0.00 2.29
43 44 9.884636 TGTCTTCGGTATATATCCCATTTTATG 57.115 33.333 0.00 0.00 0.00 1.90
46 47 9.807921 AAATGTCTTCGGTATATATCCCATTTT 57.192 29.630 0.00 0.00 0.00 1.82
47 48 9.231297 CAAATGTCTTCGGTATATATCCCATTT 57.769 33.333 0.00 0.00 31.14 2.32
48 49 7.336931 GCAAATGTCTTCGGTATATATCCCATT 59.663 37.037 0.00 0.00 0.00 3.16
49 50 6.823689 GCAAATGTCTTCGGTATATATCCCAT 59.176 38.462 0.00 0.00 0.00 4.00
50 51 6.170506 GCAAATGTCTTCGGTATATATCCCA 58.829 40.000 0.00 0.00 0.00 4.37
51 52 6.170506 TGCAAATGTCTTCGGTATATATCCC 58.829 40.000 0.00 0.00 0.00 3.85
52 53 6.313905 CCTGCAAATGTCTTCGGTATATATCC 59.686 42.308 0.00 0.00 0.00 2.59
53 54 6.874134 ACCTGCAAATGTCTTCGGTATATATC 59.126 38.462 0.00 0.00 0.00 1.63
54 55 6.769512 ACCTGCAAATGTCTTCGGTATATAT 58.230 36.000 0.00 0.00 0.00 0.86
55 56 6.169557 ACCTGCAAATGTCTTCGGTATATA 57.830 37.500 0.00 0.00 0.00 0.86
56 57 5.036117 ACCTGCAAATGTCTTCGGTATAT 57.964 39.130 0.00 0.00 0.00 0.86
57 58 4.081365 TGACCTGCAAATGTCTTCGGTATA 60.081 41.667 10.82 0.00 32.67 1.47
58 59 3.270877 GACCTGCAAATGTCTTCGGTAT 58.729 45.455 4.01 0.00 0.00 2.73
59 60 2.037902 TGACCTGCAAATGTCTTCGGTA 59.962 45.455 10.82 0.00 32.67 4.02
60 61 1.202758 TGACCTGCAAATGTCTTCGGT 60.203 47.619 10.82 0.80 32.67 4.69
61 62 1.466167 CTGACCTGCAAATGTCTTCGG 59.534 52.381 10.82 0.00 32.67 4.30
62 63 1.135859 GCTGACCTGCAAATGTCTTCG 60.136 52.381 10.82 3.12 32.67 3.79
63 64 1.135859 CGCTGACCTGCAAATGTCTTC 60.136 52.381 10.82 3.74 32.67 2.87
64 65 0.877071 CGCTGACCTGCAAATGTCTT 59.123 50.000 10.82 0.00 32.67 3.01
65 66 0.250467 ACGCTGACCTGCAAATGTCT 60.250 50.000 10.82 0.00 32.67 3.41
66 67 0.593128 AACGCTGACCTGCAAATGTC 59.407 50.000 4.24 4.24 0.00 3.06
67 68 1.806542 CTAACGCTGACCTGCAAATGT 59.193 47.619 0.00 0.00 0.00 2.71
68 69 2.076100 TCTAACGCTGACCTGCAAATG 58.924 47.619 0.00 0.00 0.00 2.32
69 70 2.028112 TCTCTAACGCTGACCTGCAAAT 60.028 45.455 0.00 0.00 0.00 2.32
70 71 1.343142 TCTCTAACGCTGACCTGCAAA 59.657 47.619 0.00 0.00 0.00 3.68
71 72 0.966179 TCTCTAACGCTGACCTGCAA 59.034 50.000 0.00 0.00 0.00 4.08
72 73 1.134995 CATCTCTAACGCTGACCTGCA 60.135 52.381 0.00 0.00 0.00 4.41
73 74 1.565305 CATCTCTAACGCTGACCTGC 58.435 55.000 0.00 0.00 0.00 4.85
74 75 1.135915 AGCATCTCTAACGCTGACCTG 59.864 52.381 0.00 0.00 33.91 4.00
75 76 1.407258 GAGCATCTCTAACGCTGACCT 59.593 52.381 0.00 0.00 35.75 3.85
76 77 1.846541 GAGCATCTCTAACGCTGACC 58.153 55.000 0.00 0.00 35.75 4.02
89 90 5.017294 AGGTTGAACTAGCTTAGAGCATC 57.983 43.478 0.00 0.00 45.56 3.91
90 91 4.440802 CGAGGTTGAACTAGCTTAGAGCAT 60.441 45.833 0.00 0.00 45.56 3.79
91 92 3.119459 CGAGGTTGAACTAGCTTAGAGCA 60.119 47.826 0.00 0.00 45.56 4.26
92 93 3.440228 CGAGGTTGAACTAGCTTAGAGC 58.560 50.000 0.00 0.00 42.84 4.09
93 94 3.444388 ACCGAGGTTGAACTAGCTTAGAG 59.556 47.826 0.00 0.00 0.00 2.43
94 95 3.428532 ACCGAGGTTGAACTAGCTTAGA 58.571 45.455 0.00 0.00 0.00 2.10
95 96 3.870633 ACCGAGGTTGAACTAGCTTAG 57.129 47.619 0.00 0.00 0.00 2.18
96 97 3.575256 TGAACCGAGGTTGAACTAGCTTA 59.425 43.478 12.80 0.00 38.60 3.09
97 98 2.367567 TGAACCGAGGTTGAACTAGCTT 59.632 45.455 12.80 0.00 38.60 3.74
98 99 1.968493 TGAACCGAGGTTGAACTAGCT 59.032 47.619 12.80 0.00 38.60 3.32
99 100 2.450609 TGAACCGAGGTTGAACTAGC 57.549 50.000 12.80 0.00 38.60 3.42
100 101 4.814771 AGTTTTGAACCGAGGTTGAACTAG 59.185 41.667 12.80 0.00 38.60 2.57
101 102 4.573201 CAGTTTTGAACCGAGGTTGAACTA 59.427 41.667 12.80 0.00 38.60 2.24
102 103 3.377172 CAGTTTTGAACCGAGGTTGAACT 59.623 43.478 12.80 14.85 38.60 3.01
103 104 3.691498 CAGTTTTGAACCGAGGTTGAAC 58.309 45.455 12.80 13.09 38.60 3.18
104 105 2.098443 GCAGTTTTGAACCGAGGTTGAA 59.902 45.455 12.80 7.56 38.60 2.69
105 106 1.673920 GCAGTTTTGAACCGAGGTTGA 59.326 47.619 12.80 0.27 38.60 3.18
106 107 1.596954 CGCAGTTTTGAACCGAGGTTG 60.597 52.381 12.80 0.00 38.60 3.77
107 108 0.661020 CGCAGTTTTGAACCGAGGTT 59.339 50.000 7.30 7.30 41.54 3.50
108 109 0.179067 TCGCAGTTTTGAACCGAGGT 60.179 50.000 0.00 0.00 0.00 3.85
109 110 0.941542 TTCGCAGTTTTGAACCGAGG 59.058 50.000 0.00 0.00 0.00 4.63
110 111 2.031683 AGTTTCGCAGTTTTGAACCGAG 59.968 45.455 0.00 0.00 0.00 4.63
111 112 2.011222 AGTTTCGCAGTTTTGAACCGA 58.989 42.857 0.00 0.00 0.00 4.69
112 113 2.468532 AGTTTCGCAGTTTTGAACCG 57.531 45.000 0.00 0.00 0.00 4.44
113 114 7.806014 TCATAATAAGTTTCGCAGTTTTGAACC 59.194 33.333 0.00 0.00 0.00 3.62
114 115 8.722342 TCATAATAAGTTTCGCAGTTTTGAAC 57.278 30.769 0.00 0.00 0.00 3.18
115 116 9.340695 CATCATAATAAGTTTCGCAGTTTTGAA 57.659 29.630 0.00 0.00 0.00 2.69
116 117 7.967854 CCATCATAATAAGTTTCGCAGTTTTGA 59.032 33.333 0.00 0.00 0.00 2.69
117 118 7.967854 TCCATCATAATAAGTTTCGCAGTTTTG 59.032 33.333 0.00 0.00 0.00 2.44
118 119 8.050778 TCCATCATAATAAGTTTCGCAGTTTT 57.949 30.769 0.00 0.00 0.00 2.43
119 120 7.624360 TCCATCATAATAAGTTTCGCAGTTT 57.376 32.000 0.00 0.00 0.00 2.66
120 121 7.807977 ATCCATCATAATAAGTTTCGCAGTT 57.192 32.000 0.00 0.00 0.00 3.16
121 122 8.150945 ACTATCCATCATAATAAGTTTCGCAGT 58.849 33.333 0.00 0.00 0.00 4.40
122 123 8.438513 CACTATCCATCATAATAAGTTTCGCAG 58.561 37.037 0.00 0.00 0.00 5.18
123 124 7.095229 GCACTATCCATCATAATAAGTTTCGCA 60.095 37.037 0.00 0.00 0.00 5.10
124 125 7.118390 AGCACTATCCATCATAATAAGTTTCGC 59.882 37.037 0.00 0.00 0.00 4.70
125 126 8.539770 AGCACTATCCATCATAATAAGTTTCG 57.460 34.615 0.00 0.00 0.00 3.46
133 134 9.983024 ACTAGTAGTAGCACTATCCATCATAAT 57.017 33.333 0.00 0.00 32.65 1.28
136 137 9.983024 AATACTAGTAGTAGCACTATCCATCAT 57.017 33.333 15.08 0.00 33.66 2.45
137 138 9.809395 AAATACTAGTAGTAGCACTATCCATCA 57.191 33.333 15.08 0.00 33.66 3.07
139 140 8.524487 GCAAATACTAGTAGTAGCACTATCCAT 58.476 37.037 15.08 0.00 33.66 3.41
140 141 7.039923 GGCAAATACTAGTAGTAGCACTATCCA 60.040 40.741 15.08 0.00 33.66 3.41
141 142 7.314393 GGCAAATACTAGTAGTAGCACTATCC 58.686 42.308 15.08 6.58 33.66 2.59
142 143 7.314393 GGGCAAATACTAGTAGTAGCACTATC 58.686 42.308 15.08 1.81 33.66 2.08
143 144 6.210984 GGGGCAAATACTAGTAGTAGCACTAT 59.789 42.308 17.22 0.04 33.66 2.12
144 145 5.537674 GGGGCAAATACTAGTAGTAGCACTA 59.462 44.000 17.22 0.00 33.66 2.74
145 146 4.344390 GGGGCAAATACTAGTAGTAGCACT 59.656 45.833 17.22 0.11 33.66 4.40
146 147 4.344390 AGGGGCAAATACTAGTAGTAGCAC 59.656 45.833 15.08 13.36 33.66 4.40
147 148 4.553678 AGGGGCAAATACTAGTAGTAGCA 58.446 43.478 15.08 0.00 33.66 3.49
148 149 5.548181 AAGGGGCAAATACTAGTAGTAGC 57.452 43.478 15.08 12.44 33.66 3.58
238 239 3.189285 TGCAGCTTTGCTTCAAACTTTC 58.811 40.909 0.00 0.00 36.40 2.62
260 261 2.481952 GCTCGTGCTCATTCTTCAAACT 59.518 45.455 1.41 0.00 36.03 2.66
310 312 1.517694 CGCATGACTGGCATTTGGC 60.518 57.895 0.00 0.00 43.74 4.52
335 337 2.726691 CCATTGACCGTCGACGTGC 61.727 63.158 33.49 24.78 37.74 5.34
390 394 2.279069 CCTCTGACCACACGAGGCT 61.279 63.158 0.00 0.00 35.97 4.58
391 395 2.262915 CCTCTGACCACACGAGGC 59.737 66.667 0.00 0.00 35.97 4.70
392 396 2.973899 CCCTCTGACCACACGAGG 59.026 66.667 0.00 0.00 39.18 4.63
487 499 2.829458 GGAGGGAGGAGACGGACG 60.829 72.222 0.00 0.00 0.00 4.79
488 500 0.615261 AAAGGAGGGAGGAGACGGAC 60.615 60.000 0.00 0.00 0.00 4.79
489 501 0.116541 AAAAGGAGGGAGGAGACGGA 59.883 55.000 0.00 0.00 0.00 4.69
490 502 0.537653 GAAAAGGAGGGAGGAGACGG 59.462 60.000 0.00 0.00 0.00 4.79
491 503 1.478916 GAGAAAAGGAGGGAGGAGACG 59.521 57.143 0.00 0.00 0.00 4.18
512 531 0.314302 AGAAAGGAGACGGTCGTGTG 59.686 55.000 0.00 0.00 0.00 3.82
543 562 3.947132 CTGCGGGGTGAGCACTGAG 62.947 68.421 0.16 0.00 40.01 3.35
544 563 4.007644 CTGCGGGGTGAGCACTGA 62.008 66.667 0.16 0.00 40.01 3.41
545 564 3.535629 TTCTGCGGGGTGAGCACTG 62.536 63.158 0.16 0.00 40.01 3.66
546 565 3.241530 TTCTGCGGGGTGAGCACT 61.242 61.111 0.16 0.00 40.01 4.40
547 566 3.050275 GTTCTGCGGGGTGAGCAC 61.050 66.667 0.00 0.00 40.01 4.40
566 585 1.565390 TTGTCATGGAGGGCAGAGGG 61.565 60.000 0.00 0.00 0.00 4.30
571 590 0.325933 CAGAGTTGTCATGGAGGGCA 59.674 55.000 0.00 0.00 0.00 5.36
577 597 1.740380 CGTAGGGCAGAGTTGTCATGG 60.740 57.143 0.00 0.00 0.00 3.66
578 598 1.645034 CGTAGGGCAGAGTTGTCATG 58.355 55.000 0.00 0.00 0.00 3.07
623 643 2.991540 GCCGAGCCCTTTGCCTTT 60.992 61.111 0.00 0.00 42.71 3.11
800 821 8.226448 CGGCTATCTCATTGTCTAATCAAAATC 58.774 37.037 0.00 0.00 0.00 2.17
802 823 6.017934 GCGGCTATCTCATTGTCTAATCAAAA 60.018 38.462 0.00 0.00 0.00 2.44
896 925 2.354510 GTGAGTGTGCTGTACTTGCAAA 59.645 45.455 13.92 7.72 42.41 3.68
1068 1101 2.168521 GAGGATGACGATGGTGAGGAAA 59.831 50.000 0.00 0.00 0.00 3.13
1481 1535 3.716539 TACATGAGGCCGTCGCTGC 62.717 63.158 0.00 0.00 34.44 5.25
1776 1830 2.202570 GAGAAGAAGCGCGCGGTA 60.203 61.111 36.14 0.00 0.00 4.02
1796 1850 0.318784 CTGCTATTCGGGCGACTACC 60.319 60.000 0.00 0.00 0.00 3.18
1806 1860 4.624882 GCATCATAAGAGGTCTGCTATTCG 59.375 45.833 0.00 0.00 0.00 3.34
1809 1863 4.592351 ACTGCATCATAAGAGGTCTGCTAT 59.408 41.667 0.00 0.00 0.00 2.97
1823 1877 0.742281 GCCACACTCGACTGCATCAT 60.742 55.000 0.00 0.00 0.00 2.45
1830 1884 1.617322 TTACTCAGCCACACTCGACT 58.383 50.000 0.00 0.00 0.00 4.18
1833 1887 2.370281 ACATTACTCAGCCACACTCG 57.630 50.000 0.00 0.00 0.00 4.18
1857 1911 7.002250 TGAATGGAATCAAGATCTAGCTAGG 57.998 40.000 20.58 4.32 0.00 3.02
1862 1916 7.959689 AACGATGAATGGAATCAAGATCTAG 57.040 36.000 0.00 0.00 32.06 2.43
1889 1950 1.077625 AGAACCGAGGAGCCAGAGT 59.922 57.895 0.00 0.00 0.00 3.24
1931 1999 2.027745 TCCTGGCAAAAACAAGTGCAAA 60.028 40.909 0.00 0.00 42.74 3.68
1979 2047 4.457257 CCAGATACTGATGCATCGTCTAGA 59.543 45.833 21.34 7.97 32.44 2.43
1985 2053 2.222678 GCAACCAGATACTGATGCATCG 59.777 50.000 21.34 17.42 40.83 3.84
2049 2117 2.738587 TGGCCTAGAGTGAGAGTAGG 57.261 55.000 3.32 0.00 37.05 3.18
2082 2150 4.574674 AAGAGAGAGAGAGAGAGCTTGA 57.425 45.455 0.00 0.00 0.00 3.02
2084 2152 6.012745 AGAAAAAGAGAGAGAGAGAGAGCTT 58.987 40.000 0.00 0.00 0.00 3.74
2109 2224 1.970640 AGGACTTGGTTTCATTTGCCC 59.029 47.619 0.00 0.00 0.00 5.36
2116 2231 4.645535 CTCTGATTCAGGACTTGGTTTCA 58.354 43.478 13.59 0.00 31.51 2.69
2229 2349 9.481340 GCAATCTTCAGTATATCAGTACATTGA 57.519 33.333 0.00 0.00 0.00 2.57
2235 2355 9.967346 GTAGTTGCAATCTTCAGTATATCAGTA 57.033 33.333 0.59 0.00 0.00 2.74
2246 2366 4.040339 TCAGTGGAGTAGTTGCAATCTTCA 59.960 41.667 0.59 4.32 0.00 3.02
2247 2367 4.569943 TCAGTGGAGTAGTTGCAATCTTC 58.430 43.478 0.59 1.54 0.00 2.87
2248 2368 4.623932 TCAGTGGAGTAGTTGCAATCTT 57.376 40.909 0.59 0.00 0.00 2.40
2250 2370 4.569943 TCTTCAGTGGAGTAGTTGCAATC 58.430 43.478 0.59 0.00 0.00 2.67
2251 2371 4.623932 TCTTCAGTGGAGTAGTTGCAAT 57.376 40.909 0.59 0.00 0.00 3.56
2252 2372 4.623932 ATCTTCAGTGGAGTAGTTGCAA 57.376 40.909 0.00 0.00 0.00 4.08
2254 2374 7.617041 AATTAATCTTCAGTGGAGTAGTTGC 57.383 36.000 0.00 0.00 0.00 4.17
2255 2375 9.877178 ACTAATTAATCTTCAGTGGAGTAGTTG 57.123 33.333 0.00 0.00 0.00 3.16
2288 2409 1.599542 GTGCAAAACTGAGAACGCTCT 59.400 47.619 0.00 0.00 41.84 4.09
2320 2441 1.873591 CCACCTCAGAACAAAAGTCCG 59.126 52.381 0.00 0.00 0.00 4.79
2321 2442 2.618709 CACCACCTCAGAACAAAAGTCC 59.381 50.000 0.00 0.00 0.00 3.85
2322 2443 3.279434 ACACCACCTCAGAACAAAAGTC 58.721 45.455 0.00 0.00 0.00 3.01
2323 2444 3.279434 GACACCACCTCAGAACAAAAGT 58.721 45.455 0.00 0.00 0.00 2.66
2337 2728 0.523966 CGGACTCTCTCTGACACCAC 59.476 60.000 0.00 0.00 0.00 4.16
2379 2780 4.947147 TCCAGCACCACAACGGCC 62.947 66.667 0.00 0.00 39.03 6.13
2394 2795 2.888863 CCACTCTGGTCGAGCTCC 59.111 66.667 16.64 0.00 43.85 4.70
2426 2827 1.213430 GGATTGGATACCAAACCCCGA 59.787 52.381 15.74 0.00 46.51 5.14
2483 5420 5.297029 GGAGTGTTTCACAAGAGTAAAGCTT 59.703 40.000 0.00 0.00 36.74 3.74
2494 5431 6.072508 GCATTATTCAGAGGAGTGTTTCACAA 60.073 38.462 2.80 0.00 36.74 3.33
2571 5514 5.581085 GTGGAGCATACTACTAGTTGTTTGG 59.419 44.000 22.04 11.81 0.00 3.28
2582 5535 4.043037 GTGTGGTAGTGGAGCATACTAC 57.957 50.000 13.57 13.57 46.11 2.73
2585 5538 3.195825 AGAAGTGTGGTAGTGGAGCATAC 59.804 47.826 0.00 0.00 45.22 2.39
2586 5539 3.441101 AGAAGTGTGGTAGTGGAGCATA 58.559 45.455 0.00 0.00 37.99 3.14
2587 5540 2.234908 GAGAAGTGTGGTAGTGGAGCAT 59.765 50.000 0.00 0.00 37.99 3.79
2588 5541 1.618837 GAGAAGTGTGGTAGTGGAGCA 59.381 52.381 0.00 0.00 0.00 4.26
2589 5542 1.066787 GGAGAAGTGTGGTAGTGGAGC 60.067 57.143 0.00 0.00 0.00 4.70
2590 5543 1.550976 GGGAGAAGTGTGGTAGTGGAG 59.449 57.143 0.00 0.00 0.00 3.86
2591 5544 1.640917 GGGAGAAGTGTGGTAGTGGA 58.359 55.000 0.00 0.00 0.00 4.02
2592 5545 0.246635 CGGGAGAAGTGTGGTAGTGG 59.753 60.000 0.00 0.00 0.00 4.00
2593 5546 0.389948 GCGGGAGAAGTGTGGTAGTG 60.390 60.000 0.00 0.00 0.00 2.74
2594 5547 0.542232 AGCGGGAGAAGTGTGGTAGT 60.542 55.000 0.00 0.00 0.00 2.73
2595 5548 0.108615 CAGCGGGAGAAGTGTGGTAG 60.109 60.000 0.00 0.00 0.00 3.18
2596 5549 1.541310 CCAGCGGGAGAAGTGTGGTA 61.541 60.000 0.00 0.00 35.59 3.25
2597 5550 2.743718 CAGCGGGAGAAGTGTGGT 59.256 61.111 0.00 0.00 0.00 4.16
2598 5551 2.046892 CCAGCGGGAGAAGTGTGG 60.047 66.667 0.00 0.00 35.59 4.17
2599 5552 2.743928 GCCAGCGGGAGAAGTGTG 60.744 66.667 7.23 0.00 35.59 3.82
2606 5559 4.431131 ACCAATGGCCAGCGGGAG 62.431 66.667 23.54 7.20 35.59 4.30
2612 5565 1.746615 CACGGAGACCAATGGCCAG 60.747 63.158 13.05 0.00 0.00 4.85
2634 5587 4.021925 GCACGCTCCCCTGGAACT 62.022 66.667 0.00 0.00 0.00 3.01
2667 5633 1.068194 CGAGAACCCGAGATATGCTCC 60.068 57.143 0.00 0.00 40.70 4.70
2668 5634 1.068194 CCGAGAACCCGAGATATGCTC 60.068 57.143 0.00 0.00 40.38 4.26
2669 5635 0.962489 CCGAGAACCCGAGATATGCT 59.038 55.000 0.00 0.00 0.00 3.79
2708 5674 2.210116 GTCGTCTGAAACTGAAAGCCA 58.790 47.619 0.00 0.00 37.60 4.75
2709 5675 1.531578 GGTCGTCTGAAACTGAAAGCC 59.468 52.381 0.00 0.00 37.60 4.35
2711 5677 3.187227 CCATGGTCGTCTGAAACTGAAAG 59.813 47.826 2.57 0.00 42.29 2.62
2712 5678 3.138304 CCATGGTCGTCTGAAACTGAAA 58.862 45.455 2.57 0.00 0.00 2.69
2713 5679 2.766313 CCATGGTCGTCTGAAACTGAA 58.234 47.619 2.57 0.00 0.00 3.02
2714 5680 1.608025 GCCATGGTCGTCTGAAACTGA 60.608 52.381 14.67 0.00 0.00 3.41
2716 5682 0.321653 GGCCATGGTCGTCTGAAACT 60.322 55.000 14.67 0.00 0.00 2.66
2717 5683 0.321653 AGGCCATGGTCGTCTGAAAC 60.322 55.000 14.67 0.00 0.00 2.78
2718 5684 0.036388 GAGGCCATGGTCGTCTGAAA 60.036 55.000 14.67 0.00 0.00 2.69
2719 5685 1.596934 GAGGCCATGGTCGTCTGAA 59.403 57.895 14.67 0.00 0.00 3.02
2720 5686 2.710902 CGAGGCCATGGTCGTCTGA 61.711 63.158 14.67 0.00 0.00 3.27
2767 5745 1.004398 TCGTGCGGCTAAATAATTGCG 60.004 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.