Multiple sequence alignment - TraesCS7A01G330400

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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 TraesCS7A01G330400 chr7A 100.000 2903 0 0 1 2903 483752740 483749838 0.000000e+00 5361.0
1 TraesCS7A01G330400 chr3D 96.069 2493 71 3 412 2903 420455829 420458295 0.000000e+00 4036.0
2 TraesCS7A01G330400 chr2D 95.745 2491 78 4 414 2903 8943756 8946219 0.000000e+00 3988.0
3 TraesCS7A01G330400 chr2D 95.668 2493 81 3 412 2903 616986064 616988530 0.000000e+00 3980.0
4 TraesCS7A01G330400 chr2D 95.668 2493 79 5 412 2903 577711634 577709170 0.000000e+00 3978.0
5 TraesCS7A01G330400 chr2D 95.349 2494 100 4 411 2903 536086265 536083787 0.000000e+00 3949.0
6 TraesCS7A01G330400 chr7B 95.531 2484 105 5 422 2903 659929338 659926859 0.000000e+00 3967.0
7 TraesCS7A01G330400 chr5D 95.482 2501 84 5 405 2903 357882214 357884687 0.000000e+00 3965.0
8 TraesCS7A01G330400 chr2B 91.902 2519 161 21 409 2903 679650866 679648367 0.000000e+00 3482.0
9 TraesCS7A01G330400 chr2B 87.773 687 83 1 2216 2901 200723573 200722887 0.000000e+00 802.0
10 TraesCS7A01G330400 chr2A 84.493 2141 300 23 414 2536 594579026 594576900 0.000000e+00 2085.0
11 TraesCS7A01G330400 chr6B 90.608 1299 96 8 415 1688 671710449 671709152 0.000000e+00 1700.0
12 TraesCS7A01G330400 chr7D 92.746 193 13 1 221 413 418397778 418397587 7.920000e-71 278.0
13 TraesCS7A01G330400 chr3B 92.537 67 4 1 58 123 733454977 733454911 8.560000e-16 95.3


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 TraesCS7A01G330400 chr7A 483749838 483752740 2902 True 5361 5361 100.000 1 2903 1 chr7A.!!$R1 2902
1 TraesCS7A01G330400 chr3D 420455829 420458295 2466 False 4036 4036 96.069 412 2903 1 chr3D.!!$F1 2491
2 TraesCS7A01G330400 chr2D 8943756 8946219 2463 False 3988 3988 95.745 414 2903 1 chr2D.!!$F1 2489
3 TraesCS7A01G330400 chr2D 616986064 616988530 2466 False 3980 3980 95.668 412 2903 1 chr2D.!!$F2 2491
4 TraesCS7A01G330400 chr2D 577709170 577711634 2464 True 3978 3978 95.668 412 2903 1 chr2D.!!$R2 2491
5 TraesCS7A01G330400 chr2D 536083787 536086265 2478 True 3949 3949 95.349 411 2903 1 chr2D.!!$R1 2492
6 TraesCS7A01G330400 chr7B 659926859 659929338 2479 True 3967 3967 95.531 422 2903 1 chr7B.!!$R1 2481
7 TraesCS7A01G330400 chr5D 357882214 357884687 2473 False 3965 3965 95.482 405 2903 1 chr5D.!!$F1 2498
8 TraesCS7A01G330400 chr2B 679648367 679650866 2499 True 3482 3482 91.902 409 2903 1 chr2B.!!$R2 2494
9 TraesCS7A01G330400 chr2B 200722887 200723573 686 True 802 802 87.773 2216 2901 1 chr2B.!!$R1 685
10 TraesCS7A01G330400 chr2A 594576900 594579026 2126 True 2085 2085 84.493 414 2536 1 chr2A.!!$R1 2122
11 TraesCS7A01G330400 chr6B 671709152 671710449 1297 True 1700 1700 90.608 415 1688 1 chr6B.!!$R1 1273

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
36 37 0.031449 TCACGAGCAATCACACACGA 59.969 50.0 0.00 0.0 0.00 4.35 F
181 182 0.036164 AGCGCTGGTTGTGATTGGTA 59.964 50.0 10.39 0.0 0.00 3.25 F
311 312 0.036388 ACCCGAATGCTCAATCGTGT 60.036 50.0 6.59 0.0 37.36 4.49 F
318 319 0.037419 TGCTCAATCGTGTAGCTGCA 60.037 50.0 0.00 0.0 37.16 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1216 1.279271 TCAGCTAGTTCTTTCCCAGGC 59.721 52.381 0.0 0.0 0.0 4.85 R
1505 1524 2.082231 CTGCCACTTCATCAACCTCAG 58.918 52.381 0.0 0.0 0.0 3.35 R
1652 1692 2.106338 TCTGGTGGATTGTTGCTCTGAA 59.894 45.455 0.0 0.0 0.0 3.02 R
1953 1995 2.547211 GTGCCCATCAGAATCTTCATCG 59.453 50.000 0.0 0.0 0.0 3.84 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
17 18 3.702802 TGGCGACAGGTACGGAAT 58.297 55.556 0.00 0.00 35.01 3.01
18 19 1.514087 TGGCGACAGGTACGGAATC 59.486 57.895 0.00 0.00 35.01 2.52
19 20 1.252215 TGGCGACAGGTACGGAATCA 61.252 55.000 0.00 0.00 35.01 2.57
20 21 0.804933 GGCGACAGGTACGGAATCAC 60.805 60.000 0.00 0.00 0.00 3.06
21 22 1.138047 GCGACAGGTACGGAATCACG 61.138 60.000 0.00 0.00 40.31 4.35
22 23 0.448990 CGACAGGTACGGAATCACGA 59.551 55.000 0.00 0.00 37.61 4.35
23 24 1.531264 CGACAGGTACGGAATCACGAG 60.531 57.143 0.00 0.00 37.61 4.18
24 25 0.172803 ACAGGTACGGAATCACGAGC 59.827 55.000 0.00 0.00 37.61 5.03
25 26 0.172578 CAGGTACGGAATCACGAGCA 59.827 55.000 0.00 0.00 37.61 4.26
26 27 0.892755 AGGTACGGAATCACGAGCAA 59.107 50.000 0.00 0.00 37.61 3.91
27 28 1.480954 AGGTACGGAATCACGAGCAAT 59.519 47.619 0.00 0.00 37.61 3.56
28 29 1.859080 GGTACGGAATCACGAGCAATC 59.141 52.381 0.00 0.00 37.61 2.67
29 30 2.536365 GTACGGAATCACGAGCAATCA 58.464 47.619 0.00 0.00 37.61 2.57
30 31 1.359848 ACGGAATCACGAGCAATCAC 58.640 50.000 0.00 0.00 37.61 3.06
31 32 1.337728 ACGGAATCACGAGCAATCACA 60.338 47.619 0.00 0.00 37.61 3.58
32 33 1.061131 CGGAATCACGAGCAATCACAC 59.939 52.381 0.00 0.00 35.47 3.82
33 34 2.076100 GGAATCACGAGCAATCACACA 58.924 47.619 0.00 0.00 0.00 3.72
34 35 2.159653 GGAATCACGAGCAATCACACAC 60.160 50.000 0.00 0.00 0.00 3.82
35 36 1.070821 ATCACGAGCAATCACACACG 58.929 50.000 0.00 0.00 0.00 4.49
36 37 0.031449 TCACGAGCAATCACACACGA 59.969 50.000 0.00 0.00 0.00 4.35
37 38 1.070821 CACGAGCAATCACACACGAT 58.929 50.000 0.00 0.00 0.00 3.73
38 39 1.460743 CACGAGCAATCACACACGATT 59.539 47.619 0.00 0.00 36.00 3.34
39 40 1.726791 ACGAGCAATCACACACGATTC 59.273 47.619 0.00 0.00 33.27 2.52
40 41 1.726248 CGAGCAATCACACACGATTCA 59.274 47.619 0.00 0.00 33.27 2.57
41 42 2.157474 CGAGCAATCACACACGATTCAA 59.843 45.455 0.00 0.00 33.27 2.69
42 43 3.722957 CGAGCAATCACACACGATTCAAG 60.723 47.826 0.00 0.00 33.27 3.02
43 44 3.402110 AGCAATCACACACGATTCAAGA 58.598 40.909 0.00 0.00 33.27 3.02
44 45 3.814842 AGCAATCACACACGATTCAAGAA 59.185 39.130 0.00 0.00 33.27 2.52
45 46 4.083643 AGCAATCACACACGATTCAAGAAG 60.084 41.667 0.00 0.00 33.27 2.85
46 47 4.715896 CAATCACACACGATTCAAGAAGG 58.284 43.478 0.00 0.00 33.27 3.46
47 48 2.143122 TCACACACGATTCAAGAAGGC 58.857 47.619 0.00 0.00 0.00 4.35
48 49 1.872952 CACACACGATTCAAGAAGGCA 59.127 47.619 0.00 0.00 0.00 4.75
49 50 2.485426 CACACACGATTCAAGAAGGCAT 59.515 45.455 0.00 0.00 0.00 4.40
50 51 3.684305 CACACACGATTCAAGAAGGCATA 59.316 43.478 0.00 0.00 0.00 3.14
51 52 3.935203 ACACACGATTCAAGAAGGCATAG 59.065 43.478 0.00 0.00 0.00 2.23
52 53 2.939103 ACACGATTCAAGAAGGCATAGC 59.061 45.455 0.00 0.00 0.00 2.97
53 54 2.938451 CACGATTCAAGAAGGCATAGCA 59.062 45.455 0.00 0.00 0.00 3.49
54 55 3.374988 CACGATTCAAGAAGGCATAGCAA 59.625 43.478 0.00 0.00 0.00 3.91
55 56 4.009675 ACGATTCAAGAAGGCATAGCAAA 58.990 39.130 0.00 0.00 0.00 3.68
56 57 4.095483 ACGATTCAAGAAGGCATAGCAAAG 59.905 41.667 0.00 0.00 0.00 2.77
57 58 3.855689 TTCAAGAAGGCATAGCAAAGC 57.144 42.857 0.00 0.00 0.00 3.51
58 59 2.794103 TCAAGAAGGCATAGCAAAGCA 58.206 42.857 0.00 0.00 0.00 3.91
59 60 3.156293 TCAAGAAGGCATAGCAAAGCAA 58.844 40.909 0.00 0.00 0.00 3.91
60 61 3.573538 TCAAGAAGGCATAGCAAAGCAAA 59.426 39.130 0.00 0.00 0.00 3.68
61 62 4.039004 TCAAGAAGGCATAGCAAAGCAAAA 59.961 37.500 0.00 0.00 0.00 2.44
62 63 4.605640 AGAAGGCATAGCAAAGCAAAAA 57.394 36.364 0.00 0.00 0.00 1.94
80 81 3.293311 AAAACAGCAAGCTAGCACATG 57.707 42.857 18.83 13.63 36.85 3.21
81 82 0.524862 AACAGCAAGCTAGCACATGC 59.475 50.000 24.30 24.30 42.49 4.06
82 83 0.607217 ACAGCAAGCTAGCACATGCA 60.607 50.000 29.63 0.00 45.16 3.96
83 84 0.524414 CAGCAAGCTAGCACATGCAA 59.476 50.000 29.63 0.00 45.16 4.08
84 85 0.809385 AGCAAGCTAGCACATGCAAG 59.191 50.000 29.63 9.57 45.16 4.01
85 86 0.524862 GCAAGCTAGCACATGCAAGT 59.475 50.000 25.81 0.00 45.16 3.16
86 87 1.731424 GCAAGCTAGCACATGCAAGTG 60.731 52.381 25.81 17.48 45.16 3.16
95 96 3.670311 CACATGCAAGTGCTAGACATC 57.330 47.619 9.41 0.00 42.66 3.06
96 97 3.004862 CACATGCAAGTGCTAGACATCA 58.995 45.455 9.41 0.00 42.66 3.07
97 98 3.437741 CACATGCAAGTGCTAGACATCAA 59.562 43.478 9.41 0.00 42.66 2.57
98 99 3.438087 ACATGCAAGTGCTAGACATCAAC 59.562 43.478 4.69 0.00 42.66 3.18
99 100 2.068519 TGCAAGTGCTAGACATCAACG 58.931 47.619 4.69 0.00 42.66 4.10
100 101 1.201965 GCAAGTGCTAGACATCAACGC 60.202 52.381 0.00 0.00 38.21 4.84
101 102 2.068519 CAAGTGCTAGACATCAACGCA 58.931 47.619 0.00 0.00 0.00 5.24
103 104 0.721718 GTGCTAGACATCAACGCACC 59.278 55.000 0.00 0.00 43.68 5.01
104 105 0.320050 TGCTAGACATCAACGCACCA 59.680 50.000 0.00 0.00 0.00 4.17
105 106 1.002366 GCTAGACATCAACGCACCAG 58.998 55.000 0.00 0.00 0.00 4.00
106 107 1.002366 CTAGACATCAACGCACCAGC 58.998 55.000 0.00 0.00 37.42 4.85
107 108 0.320050 TAGACATCAACGCACCAGCA 59.680 50.000 0.00 0.00 42.27 4.41
108 109 0.534877 AGACATCAACGCACCAGCAA 60.535 50.000 0.00 0.00 42.27 3.91
109 110 0.385974 GACATCAACGCACCAGCAAC 60.386 55.000 0.00 0.00 42.27 4.17
110 111 0.819259 ACATCAACGCACCAGCAACT 60.819 50.000 0.00 0.00 42.27 3.16
111 112 0.311790 CATCAACGCACCAGCAACTT 59.688 50.000 0.00 0.00 42.27 2.66
112 113 1.032014 ATCAACGCACCAGCAACTTT 58.968 45.000 0.00 0.00 42.27 2.66
113 114 0.100325 TCAACGCACCAGCAACTTTG 59.900 50.000 0.00 0.00 42.27 2.77
124 125 3.663644 CAACTTTGCCATGCACACA 57.336 47.368 0.00 0.00 38.71 3.72
125 126 2.157834 CAACTTTGCCATGCACACAT 57.842 45.000 0.00 0.00 38.71 3.21
126 127 3.300852 CAACTTTGCCATGCACACATA 57.699 42.857 0.00 0.00 38.71 2.29
127 128 2.988493 CAACTTTGCCATGCACACATAC 59.012 45.455 0.00 0.00 38.71 2.39
128 129 1.199789 ACTTTGCCATGCACACATACG 59.800 47.619 0.00 0.00 38.71 3.06
129 130 0.109365 TTTGCCATGCACACATACGC 60.109 50.000 0.00 0.00 38.71 4.42
130 131 2.023181 GCCATGCACACATACGCG 59.977 61.111 3.53 3.53 33.67 6.01
131 132 2.023181 CCATGCACACATACGCGC 59.977 61.111 5.73 0.00 33.67 6.86
132 133 2.748843 CCATGCACACATACGCGCA 61.749 57.895 5.73 0.00 39.01 6.09
133 134 1.297085 CATGCACACATACGCGCAG 60.297 57.895 5.73 2.42 37.88 5.18
134 135 2.463620 ATGCACACATACGCGCAGG 61.464 57.895 5.73 0.00 37.88 4.85
135 136 4.520846 GCACACATACGCGCAGGC 62.521 66.667 5.73 0.00 0.00 4.85
136 137 2.815211 CACACATACGCGCAGGCT 60.815 61.111 5.73 0.00 36.88 4.58
137 138 1.518352 CACACATACGCGCAGGCTA 60.518 57.895 5.73 0.00 36.88 3.93
138 139 1.226974 ACACATACGCGCAGGCTAG 60.227 57.895 5.73 0.00 36.88 3.42
139 140 1.226974 CACATACGCGCAGGCTAGT 60.227 57.895 5.73 0.00 36.88 2.57
140 141 0.806102 CACATACGCGCAGGCTAGTT 60.806 55.000 5.73 0.00 36.88 2.24
141 142 0.806102 ACATACGCGCAGGCTAGTTG 60.806 55.000 5.73 0.46 36.88 3.16
142 143 0.806102 CATACGCGCAGGCTAGTTGT 60.806 55.000 5.73 0.00 36.88 3.32
143 144 0.108329 ATACGCGCAGGCTAGTTGTT 60.108 50.000 5.73 0.00 36.88 2.83
144 145 1.011968 TACGCGCAGGCTAGTTGTTG 61.012 55.000 5.73 0.00 36.88 3.33
145 146 2.317609 CGCGCAGGCTAGTTGTTGT 61.318 57.895 8.75 0.00 36.88 3.32
146 147 1.497722 GCGCAGGCTAGTTGTTGTC 59.502 57.895 0.30 0.00 35.83 3.18
147 148 1.781555 CGCAGGCTAGTTGTTGTCG 59.218 57.895 0.00 0.00 0.00 4.35
148 149 0.666274 CGCAGGCTAGTTGTTGTCGA 60.666 55.000 0.00 0.00 0.00 4.20
149 150 1.726853 GCAGGCTAGTTGTTGTCGAT 58.273 50.000 0.00 0.00 0.00 3.59
150 151 1.394917 GCAGGCTAGTTGTTGTCGATG 59.605 52.381 0.00 0.00 0.00 3.84
151 152 2.002586 CAGGCTAGTTGTTGTCGATGG 58.997 52.381 0.00 0.00 0.00 3.51
152 153 1.066143 AGGCTAGTTGTTGTCGATGGG 60.066 52.381 0.00 0.00 0.00 4.00
153 154 1.369625 GCTAGTTGTTGTCGATGGGG 58.630 55.000 0.00 0.00 0.00 4.96
154 155 1.338769 GCTAGTTGTTGTCGATGGGGT 60.339 52.381 0.00 0.00 0.00 4.95
155 156 2.346803 CTAGTTGTTGTCGATGGGGTG 58.653 52.381 0.00 0.00 0.00 4.61
156 157 0.250727 AGTTGTTGTCGATGGGGTGG 60.251 55.000 0.00 0.00 0.00 4.61
157 158 1.074072 TTGTTGTCGATGGGGTGGG 59.926 57.895 0.00 0.00 0.00 4.61
158 159 1.710996 TTGTTGTCGATGGGGTGGGT 61.711 55.000 0.00 0.00 0.00 4.51
159 160 1.674322 GTTGTCGATGGGGTGGGTG 60.674 63.158 0.00 0.00 0.00 4.61
160 161 2.901281 TTGTCGATGGGGTGGGTGG 61.901 63.158 0.00 0.00 0.00 4.61
161 162 4.109675 GTCGATGGGGTGGGTGGG 62.110 72.222 0.00 0.00 0.00 4.61
162 163 4.340489 TCGATGGGGTGGGTGGGA 62.340 66.667 0.00 0.00 0.00 4.37
163 164 3.797353 CGATGGGGTGGGTGGGAG 61.797 72.222 0.00 0.00 0.00 4.30
164 165 4.129148 GATGGGGTGGGTGGGAGC 62.129 72.222 0.00 0.00 0.00 4.70
173 174 4.643387 GGTGGGAGCGCTGGTTGT 62.643 66.667 18.48 0.00 0.00 3.32
174 175 3.357079 GTGGGAGCGCTGGTTGTG 61.357 66.667 18.48 0.00 0.00 3.33
175 176 3.555324 TGGGAGCGCTGGTTGTGA 61.555 61.111 18.48 0.00 0.00 3.58
176 177 2.045926 GGGAGCGCTGGTTGTGAT 60.046 61.111 18.48 0.00 0.00 3.06
177 178 1.675641 GGGAGCGCTGGTTGTGATT 60.676 57.895 18.48 0.00 0.00 2.57
178 179 1.503542 GGAGCGCTGGTTGTGATTG 59.496 57.895 18.48 0.00 0.00 2.67
179 180 1.503542 GAGCGCTGGTTGTGATTGG 59.496 57.895 18.48 0.00 0.00 3.16
180 181 1.228245 AGCGCTGGTTGTGATTGGT 60.228 52.632 10.39 0.00 0.00 3.67
181 182 0.036164 AGCGCTGGTTGTGATTGGTA 59.964 50.000 10.39 0.00 0.00 3.25
182 183 0.447801 GCGCTGGTTGTGATTGGTAG 59.552 55.000 0.00 0.00 0.00 3.18
183 184 1.086696 CGCTGGTTGTGATTGGTAGG 58.913 55.000 0.00 0.00 0.00 3.18
184 185 1.610624 CGCTGGTTGTGATTGGTAGGT 60.611 52.381 0.00 0.00 0.00 3.08
185 186 2.354303 CGCTGGTTGTGATTGGTAGGTA 60.354 50.000 0.00 0.00 0.00 3.08
186 187 3.007635 GCTGGTTGTGATTGGTAGGTAC 58.992 50.000 0.00 0.00 0.00 3.34
187 188 3.259064 CTGGTTGTGATTGGTAGGTACG 58.741 50.000 0.00 0.00 0.00 3.67
188 189 2.004733 GGTTGTGATTGGTAGGTACGC 58.995 52.381 0.00 0.00 0.00 4.42
189 190 2.613474 GGTTGTGATTGGTAGGTACGCA 60.613 50.000 0.00 0.00 0.00 5.24
190 191 3.267483 GTTGTGATTGGTAGGTACGCAT 58.733 45.455 0.00 0.00 0.00 4.73
191 192 2.899976 TGTGATTGGTAGGTACGCATG 58.100 47.619 0.00 0.00 0.00 4.06
192 193 2.235155 TGTGATTGGTAGGTACGCATGT 59.765 45.455 0.00 0.00 0.00 3.21
193 194 3.447944 TGTGATTGGTAGGTACGCATGTA 59.552 43.478 0.00 0.00 0.00 2.29
194 195 4.100344 TGTGATTGGTAGGTACGCATGTAT 59.900 41.667 0.00 0.00 32.11 2.29
195 196 4.684703 GTGATTGGTAGGTACGCATGTATC 59.315 45.833 0.00 0.00 32.11 2.24
196 197 4.587262 TGATTGGTAGGTACGCATGTATCT 59.413 41.667 0.00 0.00 44.27 1.98
197 198 4.579454 TTGGTAGGTACGCATGTATCTC 57.421 45.455 0.00 0.00 41.18 2.75
198 199 2.551032 TGGTAGGTACGCATGTATCTCG 59.449 50.000 0.00 0.00 41.18 4.04
199 200 2.551459 GGTAGGTACGCATGTATCTCGT 59.449 50.000 0.00 0.00 41.18 4.18
200 201 2.776312 AGGTACGCATGTATCTCGTG 57.224 50.000 5.69 0.00 37.47 4.35
201 202 1.337071 AGGTACGCATGTATCTCGTGG 59.663 52.381 5.69 0.00 37.47 4.94
202 203 1.335810 GGTACGCATGTATCTCGTGGA 59.664 52.381 5.69 0.00 37.61 4.02
203 204 2.604855 GGTACGCATGTATCTCGTGGAG 60.605 54.545 5.69 0.00 37.61 3.86
204 205 0.249073 ACGCATGTATCTCGTGGAGC 60.249 55.000 0.00 0.00 34.92 4.70
205 206 0.249031 CGCATGTATCTCGTGGAGCA 60.249 55.000 0.00 0.00 33.96 4.26
206 207 1.495878 GCATGTATCTCGTGGAGCAG 58.504 55.000 0.00 0.00 33.96 4.24
207 208 1.202463 GCATGTATCTCGTGGAGCAGT 60.202 52.381 0.00 0.00 33.96 4.40
208 209 2.034685 GCATGTATCTCGTGGAGCAGTA 59.965 50.000 0.00 0.00 33.96 2.74
209 210 3.305676 GCATGTATCTCGTGGAGCAGTAT 60.306 47.826 0.00 0.00 33.96 2.12
210 211 4.797604 GCATGTATCTCGTGGAGCAGTATT 60.798 45.833 0.00 0.00 33.96 1.89
211 212 4.569761 TGTATCTCGTGGAGCAGTATTC 57.430 45.455 0.00 0.00 0.00 1.75
212 213 4.207955 TGTATCTCGTGGAGCAGTATTCT 58.792 43.478 0.00 0.00 0.00 2.40
213 214 5.374071 TGTATCTCGTGGAGCAGTATTCTA 58.626 41.667 0.00 0.00 0.00 2.10
214 215 5.470437 TGTATCTCGTGGAGCAGTATTCTAG 59.530 44.000 0.00 0.00 0.00 2.43
215 216 3.887352 TCTCGTGGAGCAGTATTCTAGT 58.113 45.455 0.00 0.00 0.00 2.57
216 217 3.878103 TCTCGTGGAGCAGTATTCTAGTC 59.122 47.826 0.00 0.00 0.00 2.59
217 218 2.612672 TCGTGGAGCAGTATTCTAGTCG 59.387 50.000 0.00 0.00 0.00 4.18
218 219 2.287069 CGTGGAGCAGTATTCTAGTCGG 60.287 54.545 0.00 0.00 0.00 4.79
219 220 2.034812 GTGGAGCAGTATTCTAGTCGGG 59.965 54.545 0.00 0.00 0.00 5.14
220 221 2.308690 GGAGCAGTATTCTAGTCGGGT 58.691 52.381 0.00 0.00 0.00 5.28
221 222 2.694109 GGAGCAGTATTCTAGTCGGGTT 59.306 50.000 0.00 0.00 0.00 4.11
222 223 3.132467 GGAGCAGTATTCTAGTCGGGTTT 59.868 47.826 0.00 0.00 0.00 3.27
223 224 4.382793 GGAGCAGTATTCTAGTCGGGTTTT 60.383 45.833 0.00 0.00 0.00 2.43
224 225 5.161943 AGCAGTATTCTAGTCGGGTTTTT 57.838 39.130 0.00 0.00 0.00 1.94
249 250 8.780846 TTTCGGAGCTACTTTAAAATATGTCA 57.219 30.769 0.00 0.00 0.00 3.58
250 251 8.958119 TTCGGAGCTACTTTAAAATATGTCAT 57.042 30.769 0.00 0.00 0.00 3.06
251 252 8.589335 TCGGAGCTACTTTAAAATATGTCATC 57.411 34.615 0.00 0.00 0.00 2.92
252 253 7.656137 TCGGAGCTACTTTAAAATATGTCATCC 59.344 37.037 0.00 0.00 0.00 3.51
253 254 7.657761 CGGAGCTACTTTAAAATATGTCATCCT 59.342 37.037 0.00 0.00 0.00 3.24
254 255 9.343539 GGAGCTACTTTAAAATATGTCATCCTT 57.656 33.333 0.00 0.00 0.00 3.36
256 257 9.125026 AGCTACTTTAAAATATGTCATCCTTGG 57.875 33.333 0.00 0.00 0.00 3.61
257 258 8.352942 GCTACTTTAAAATATGTCATCCTTGGG 58.647 37.037 0.00 0.00 0.00 4.12
258 259 9.627123 CTACTTTAAAATATGTCATCCTTGGGA 57.373 33.333 0.00 0.00 35.55 4.37
267 268 5.596836 TGTCATCCTTGGGATAAAAATGC 57.403 39.130 0.00 0.00 40.98 3.56
268 269 4.405358 TGTCATCCTTGGGATAAAAATGCC 59.595 41.667 0.00 0.00 40.98 4.40
269 270 4.405358 GTCATCCTTGGGATAAAAATGCCA 59.595 41.667 0.00 0.00 40.98 4.92
270 271 5.070847 GTCATCCTTGGGATAAAAATGCCAT 59.929 40.000 0.00 0.00 40.98 4.40
271 272 5.070714 TCATCCTTGGGATAAAAATGCCATG 59.929 40.000 0.00 2.63 40.98 3.66
272 273 4.618635 TCCTTGGGATAAAAATGCCATGA 58.381 39.130 11.70 4.61 41.74 3.07
273 274 5.028802 TCCTTGGGATAAAAATGCCATGAA 58.971 37.500 11.70 0.00 41.74 2.57
274 275 5.104982 TCCTTGGGATAAAAATGCCATGAAC 60.105 40.000 11.70 0.00 41.74 3.18
275 276 5.338219 CCTTGGGATAAAAATGCCATGAACA 60.338 40.000 11.70 0.00 41.74 3.18
276 277 5.752036 TGGGATAAAAATGCCATGAACAA 57.248 34.783 0.00 0.00 37.11 2.83
277 278 6.119240 TGGGATAAAAATGCCATGAACAAA 57.881 33.333 0.00 0.00 37.11 2.83
278 279 6.537355 TGGGATAAAAATGCCATGAACAAAA 58.463 32.000 0.00 0.00 37.11 2.44
279 280 7.000472 TGGGATAAAAATGCCATGAACAAAAA 59.000 30.769 0.00 0.00 37.11 1.94
308 309 2.919666 AAAACCCGAATGCTCAATCG 57.080 45.000 0.69 0.69 38.74 3.34
309 310 1.821216 AAACCCGAATGCTCAATCGT 58.179 45.000 6.59 0.00 37.36 3.73
310 311 1.086696 AACCCGAATGCTCAATCGTG 58.913 50.000 6.59 0.00 37.36 4.35
311 312 0.036388 ACCCGAATGCTCAATCGTGT 60.036 50.000 6.59 0.00 37.36 4.49
312 313 1.206132 ACCCGAATGCTCAATCGTGTA 59.794 47.619 6.59 0.00 37.36 2.90
313 314 1.860950 CCCGAATGCTCAATCGTGTAG 59.139 52.381 6.59 0.00 37.36 2.74
314 315 1.258982 CCGAATGCTCAATCGTGTAGC 59.741 52.381 6.59 0.00 37.36 3.58
315 316 2.196749 CGAATGCTCAATCGTGTAGCT 58.803 47.619 0.00 0.00 37.16 3.32
316 317 2.034254 CGAATGCTCAATCGTGTAGCTG 60.034 50.000 0.00 0.00 37.16 4.24
317 318 1.293924 ATGCTCAATCGTGTAGCTGC 58.706 50.000 0.00 0.00 37.16 5.25
318 319 0.037419 TGCTCAATCGTGTAGCTGCA 60.037 50.000 0.00 0.00 37.16 4.41
319 320 0.371645 GCTCAATCGTGTAGCTGCAC 59.628 55.000 23.43 23.43 36.12 4.57
327 328 1.606606 GTGTAGCTGCACGATTTTGC 58.393 50.000 19.38 0.00 43.31 3.68
328 329 0.165727 TGTAGCTGCACGATTTTGCG 59.834 50.000 0.00 0.00 46.20 4.85
329 330 0.442310 GTAGCTGCACGATTTTGCGA 59.558 50.000 1.02 0.00 46.20 5.10
330 331 1.062587 GTAGCTGCACGATTTTGCGAT 59.937 47.619 1.02 0.00 46.20 4.58
331 332 0.097674 AGCTGCACGATTTTGCGATC 59.902 50.000 1.02 0.00 46.20 3.69
360 361 2.951745 CGACTCAGCCGTGCGATC 60.952 66.667 0.00 0.00 0.00 3.69
361 362 2.583593 GACTCAGCCGTGCGATCC 60.584 66.667 0.00 0.00 0.00 3.36
362 363 4.498520 ACTCAGCCGTGCGATCCG 62.499 66.667 0.00 0.00 0.00 4.18
368 369 4.221422 CCGTGCGATCCGGTGGAT 62.221 66.667 0.00 0.00 46.28 3.41
375 376 4.286320 ATCCGGTGGATCTCGCGC 62.286 66.667 0.00 0.00 38.09 6.86
383 384 4.508128 GATCTCGCGCGGGTGGAA 62.508 66.667 31.23 11.07 0.00 3.53
384 385 4.814294 ATCTCGCGCGGGTGGAAC 62.814 66.667 31.23 0.00 0.00 3.62
395 396 3.590824 GTGGAACCAATCAGGCCG 58.409 61.111 0.00 0.00 43.14 6.13
396 397 2.361104 TGGAACCAATCAGGCCGC 60.361 61.111 0.00 0.00 43.14 6.53
397 398 2.361104 GGAACCAATCAGGCCGCA 60.361 61.111 0.00 0.00 43.14 5.69
398 399 2.409870 GGAACCAATCAGGCCGCAG 61.410 63.158 0.00 0.00 43.14 5.18
399 400 3.056313 GAACCAATCAGGCCGCAGC 62.056 63.158 0.00 0.00 43.14 5.25
402 403 3.869272 CAATCAGGCCGCAGCGTC 61.869 66.667 15.05 0.00 41.24 5.19
635 640 2.190313 CATAAGGCCCAGAGCGCA 59.810 61.111 11.47 0.00 45.17 6.09
688 695 2.696864 GGAAGTCCATCCCCACTCA 58.303 57.895 0.00 0.00 33.05 3.41
850 857 2.163815 GCAATTGAAGCTCTGACTGCAT 59.836 45.455 10.34 0.00 0.00 3.96
870 877 5.594725 TGCATTGTTACTGTTAGGGTTTCAA 59.405 36.000 0.00 0.00 0.00 2.69
991 1005 8.094548 TGTAGTGATATACTCTTGTTTGTTGCT 58.905 33.333 0.00 0.00 40.89 3.91
1197 1216 8.900511 AATCGATGAAGTTGTATTTTCATGTG 57.099 30.769 0.00 0.00 42.43 3.21
1282 1301 5.432645 TGTCAGACTACATTTGTGTTGGAA 58.567 37.500 1.31 0.00 0.00 3.53
1335 1354 2.619332 GGAGCAGGACAGTGAGAGTAGA 60.619 54.545 0.00 0.00 0.00 2.59
1427 1446 4.256920 GACATGGTCATTACTGCAGAACT 58.743 43.478 23.35 0.00 32.09 3.01
1505 1524 0.175531 AGCAAAACCACAGTGGCAAC 59.824 50.000 20.48 5.09 42.67 4.17
1537 1556 0.109342 AGTGGCAGGAACTCAGTTGG 59.891 55.000 0.00 0.00 34.60 3.77
1642 1682 3.095332 CAGAGGAATGTGAGGACAGAGA 58.905 50.000 0.00 0.00 34.87 3.10
1652 1692 3.070302 GTGAGGACAGAGAAAGTGAAGGT 59.930 47.826 0.00 0.00 0.00 3.50
1864 1904 4.946157 CAGGTGATTCAACAGCTCCTATTT 59.054 41.667 4.20 0.00 44.98 1.40
1934 1974 2.200081 ACAGTGGGGCTATGACTCATT 58.800 47.619 0.00 0.00 0.00 2.57
2091 2133 5.736358 GCTTGTGAAAGCATCGAAGAAATAG 59.264 40.000 5.60 0.00 44.85 1.73
2104 2146 4.941263 CGAAGAAATAGGGAATTGTGACCA 59.059 41.667 0.00 0.00 0.00 4.02
2144 2186 6.320494 TCTTGAAGTCAGAGAGTAACAGAC 57.680 41.667 0.00 0.00 0.00 3.51
2172 2214 1.207488 AAGTGTGGATGGCCTGGCTA 61.207 55.000 19.68 13.97 34.31 3.93
2202 2244 5.351458 GCTTATTTATGGAGCCAAAACCTG 58.649 41.667 0.00 0.00 0.00 4.00
2366 2408 4.340381 AGAGCATGAAAGCAACAGTTCTTT 59.660 37.500 0.00 9.28 36.85 2.52
2641 2686 7.433680 AGTGATTGGTTTAGATGGTTGTTTTC 58.566 34.615 0.00 0.00 0.00 2.29
2675 2720 4.040339 TGTCAAAGGAGAGCTATTGTGTGA 59.960 41.667 0.00 0.00 0.00 3.58
2708 2753 8.289939 AGAGATGCAAACAATCAAATGTATCT 57.710 30.769 5.15 5.15 44.41 1.98
2769 2814 1.707989 TGGAAGTGGTTCATTGCCCTA 59.292 47.619 0.00 0.00 33.93 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.252215 TGATTCCGTACCTGTCGCCA 61.252 55.000 0.00 0.00 0.00 5.69
3 4 0.448990 TCGTGATTCCGTACCTGTCG 59.551 55.000 0.00 0.00 0.00 4.35
5 6 0.172803 GCTCGTGATTCCGTACCTGT 59.827 55.000 0.00 0.00 0.00 4.00
6 7 0.172578 TGCTCGTGATTCCGTACCTG 59.827 55.000 0.00 0.00 0.00 4.00
7 8 0.892755 TTGCTCGTGATTCCGTACCT 59.107 50.000 0.00 0.00 0.00 3.08
8 9 1.859080 GATTGCTCGTGATTCCGTACC 59.141 52.381 0.00 0.00 0.00 3.34
9 10 2.281762 GTGATTGCTCGTGATTCCGTAC 59.718 50.000 0.00 0.00 0.00 3.67
10 11 2.094442 TGTGATTGCTCGTGATTCCGTA 60.094 45.455 0.00 0.00 0.00 4.02
11 12 1.337728 TGTGATTGCTCGTGATTCCGT 60.338 47.619 0.00 0.00 0.00 4.69
12 13 1.061131 GTGTGATTGCTCGTGATTCCG 59.939 52.381 0.00 0.00 0.00 4.30
13 14 2.076100 TGTGTGATTGCTCGTGATTCC 58.924 47.619 0.00 0.00 0.00 3.01
14 15 2.472886 CGTGTGTGATTGCTCGTGATTC 60.473 50.000 0.00 0.00 0.00 2.52
15 16 1.460743 CGTGTGTGATTGCTCGTGATT 59.539 47.619 0.00 0.00 0.00 2.57
16 17 1.070821 CGTGTGTGATTGCTCGTGAT 58.929 50.000 0.00 0.00 0.00 3.06
17 18 0.031449 TCGTGTGTGATTGCTCGTGA 59.969 50.000 0.00 0.00 0.00 4.35
18 19 1.070821 ATCGTGTGTGATTGCTCGTG 58.929 50.000 0.00 0.00 0.00 4.35
19 20 1.726791 GAATCGTGTGTGATTGCTCGT 59.273 47.619 0.00 0.00 38.65 4.18
20 21 1.726248 TGAATCGTGTGTGATTGCTCG 59.274 47.619 0.00 0.00 38.65 5.03
21 22 3.433274 TCTTGAATCGTGTGTGATTGCTC 59.567 43.478 0.00 0.00 38.65 4.26
22 23 3.402110 TCTTGAATCGTGTGTGATTGCT 58.598 40.909 0.00 0.00 38.65 3.91
23 24 3.811722 TCTTGAATCGTGTGTGATTGC 57.188 42.857 0.00 0.00 38.65 3.56
24 25 4.715896 CCTTCTTGAATCGTGTGTGATTG 58.284 43.478 0.00 0.00 38.65 2.67
25 26 3.189287 GCCTTCTTGAATCGTGTGTGATT 59.811 43.478 0.00 0.00 41.16 2.57
26 27 2.744202 GCCTTCTTGAATCGTGTGTGAT 59.256 45.455 0.00 0.00 0.00 3.06
27 28 2.143122 GCCTTCTTGAATCGTGTGTGA 58.857 47.619 0.00 0.00 0.00 3.58
28 29 1.872952 TGCCTTCTTGAATCGTGTGTG 59.127 47.619 0.00 0.00 0.00 3.82
29 30 2.254546 TGCCTTCTTGAATCGTGTGT 57.745 45.000 0.00 0.00 0.00 3.72
30 31 3.242543 GCTATGCCTTCTTGAATCGTGTG 60.243 47.826 0.00 0.00 0.00 3.82
31 32 2.939103 GCTATGCCTTCTTGAATCGTGT 59.061 45.455 0.00 0.00 0.00 4.49
32 33 2.938451 TGCTATGCCTTCTTGAATCGTG 59.062 45.455 0.00 0.00 0.00 4.35
33 34 3.266510 TGCTATGCCTTCTTGAATCGT 57.733 42.857 0.00 0.00 0.00 3.73
34 35 4.595116 CTTTGCTATGCCTTCTTGAATCG 58.405 43.478 0.00 0.00 0.00 3.34
35 36 4.142315 TGCTTTGCTATGCCTTCTTGAATC 60.142 41.667 3.74 0.00 0.00 2.52
36 37 3.765511 TGCTTTGCTATGCCTTCTTGAAT 59.234 39.130 3.74 0.00 0.00 2.57
37 38 3.156293 TGCTTTGCTATGCCTTCTTGAA 58.844 40.909 3.74 0.00 0.00 2.69
38 39 2.794103 TGCTTTGCTATGCCTTCTTGA 58.206 42.857 3.74 0.00 0.00 3.02
39 40 3.581024 TTGCTTTGCTATGCCTTCTTG 57.419 42.857 3.74 0.00 0.00 3.02
40 41 4.605640 TTTTGCTTTGCTATGCCTTCTT 57.394 36.364 3.74 0.00 0.00 2.52
41 42 4.605640 TTTTTGCTTTGCTATGCCTTCT 57.394 36.364 3.74 0.00 0.00 2.85
59 60 3.645884 CATGTGCTAGCTTGCTGTTTTT 58.354 40.909 20.64 0.00 0.00 1.94
60 61 2.608752 GCATGTGCTAGCTTGCTGTTTT 60.609 45.455 20.64 0.00 36.83 2.43
61 62 1.068055 GCATGTGCTAGCTTGCTGTTT 60.068 47.619 20.64 1.18 36.83 2.83
62 63 0.524862 GCATGTGCTAGCTTGCTGTT 59.475 50.000 20.64 2.91 36.83 3.16
63 64 0.607217 TGCATGTGCTAGCTTGCTGT 60.607 50.000 26.63 4.41 42.66 4.40
64 65 0.524414 TTGCATGTGCTAGCTTGCTG 59.476 50.000 26.63 11.93 42.66 4.41
65 66 0.809385 CTTGCATGTGCTAGCTTGCT 59.191 50.000 26.63 0.00 42.66 3.91
66 67 0.524862 ACTTGCATGTGCTAGCTTGC 59.475 50.000 22.69 22.69 45.47 4.01
67 68 2.257974 CACTTGCATGTGCTAGCTTG 57.742 50.000 18.52 11.85 45.47 4.01
75 76 3.004862 TGATGTCTAGCACTTGCATGTG 58.995 45.455 24.37 24.37 45.16 3.21
76 77 3.339253 TGATGTCTAGCACTTGCATGT 57.661 42.857 3.62 0.00 45.16 3.21
77 78 3.484721 CGTTGATGTCTAGCACTTGCATG 60.485 47.826 3.62 0.00 45.16 4.06
78 79 2.674852 CGTTGATGTCTAGCACTTGCAT 59.325 45.455 3.62 0.00 45.16 3.96
79 80 2.068519 CGTTGATGTCTAGCACTTGCA 58.931 47.619 3.62 0.00 45.16 4.08
80 81 1.201965 GCGTTGATGTCTAGCACTTGC 60.202 52.381 0.00 0.00 42.49 4.01
81 82 2.068519 TGCGTTGATGTCTAGCACTTG 58.931 47.619 0.00 0.00 32.43 3.16
82 83 2.455674 TGCGTTGATGTCTAGCACTT 57.544 45.000 0.00 0.00 32.43 3.16
85 86 0.320050 TGGTGCGTTGATGTCTAGCA 59.680 50.000 0.00 0.00 35.27 3.49
86 87 1.002366 CTGGTGCGTTGATGTCTAGC 58.998 55.000 0.00 0.00 0.00 3.42
87 88 1.002366 GCTGGTGCGTTGATGTCTAG 58.998 55.000 0.00 0.00 0.00 2.43
88 89 0.320050 TGCTGGTGCGTTGATGTCTA 59.680 50.000 0.00 0.00 43.34 2.59
89 90 0.534877 TTGCTGGTGCGTTGATGTCT 60.535 50.000 0.00 0.00 43.34 3.41
90 91 0.385974 GTTGCTGGTGCGTTGATGTC 60.386 55.000 0.00 0.00 43.34 3.06
91 92 0.819259 AGTTGCTGGTGCGTTGATGT 60.819 50.000 0.00 0.00 43.34 3.06
92 93 0.311790 AAGTTGCTGGTGCGTTGATG 59.688 50.000 0.00 0.00 43.34 3.07
93 94 1.032014 AAAGTTGCTGGTGCGTTGAT 58.968 45.000 0.00 0.00 43.34 2.57
94 95 0.100325 CAAAGTTGCTGGTGCGTTGA 59.900 50.000 0.00 0.00 43.34 3.18
95 96 2.580661 CAAAGTTGCTGGTGCGTTG 58.419 52.632 0.00 0.00 43.34 4.10
103 104 6.867304 TATGTGTGCATGGCAAAGTTGCTG 62.867 45.833 15.20 8.20 43.49 4.41
104 105 4.871600 TATGTGTGCATGGCAAAGTTGCT 61.872 43.478 15.20 0.00 43.49 3.91
105 106 2.609984 TATGTGTGCATGGCAAAGTTGC 60.610 45.455 7.51 7.51 41.47 4.17
106 107 2.157834 ATGTGTGCATGGCAAAGTTG 57.842 45.000 0.00 0.00 41.47 3.16
107 108 2.351641 CGTATGTGTGCATGGCAAAGTT 60.352 45.455 0.00 0.00 41.47 2.66
108 109 1.199789 CGTATGTGTGCATGGCAAAGT 59.800 47.619 0.00 0.00 41.47 2.66
109 110 1.898938 CGTATGTGTGCATGGCAAAG 58.101 50.000 0.00 0.00 41.47 2.77
110 111 0.109365 GCGTATGTGTGCATGGCAAA 60.109 50.000 0.00 0.00 41.47 3.68
111 112 1.505807 GCGTATGTGTGCATGGCAA 59.494 52.632 0.00 0.00 41.47 4.52
112 113 2.748843 CGCGTATGTGTGCATGGCA 61.749 57.895 0.00 0.00 36.38 4.92
113 114 2.023181 CGCGTATGTGTGCATGGC 59.977 61.111 0.00 0.00 36.58 4.40
114 115 2.023181 GCGCGTATGTGTGCATGG 59.977 61.111 8.43 0.00 44.59 3.66
118 119 4.520846 GCCTGCGCGTATGTGTGC 62.521 66.667 8.43 0.00 45.41 4.57
119 120 1.482621 CTAGCCTGCGCGTATGTGTG 61.483 60.000 8.43 0.00 41.18 3.82
120 121 1.226974 CTAGCCTGCGCGTATGTGT 60.227 57.895 8.43 0.00 41.18 3.72
121 122 0.806102 AACTAGCCTGCGCGTATGTG 60.806 55.000 8.43 0.00 41.18 3.21
122 123 0.806102 CAACTAGCCTGCGCGTATGT 60.806 55.000 8.43 0.00 41.18 2.29
123 124 0.806102 ACAACTAGCCTGCGCGTATG 60.806 55.000 8.43 0.31 41.18 2.39
124 125 0.108329 AACAACTAGCCTGCGCGTAT 60.108 50.000 8.43 0.00 41.18 3.06
125 126 1.011968 CAACAACTAGCCTGCGCGTA 61.012 55.000 8.43 0.71 41.18 4.42
126 127 2.030562 AACAACTAGCCTGCGCGT 59.969 55.556 8.43 0.00 41.18 6.01
127 128 2.227968 GACAACAACTAGCCTGCGCG 62.228 60.000 0.00 0.00 41.18 6.86
128 129 1.497722 GACAACAACTAGCCTGCGC 59.502 57.895 0.00 0.00 0.00 6.09
129 130 0.666274 TCGACAACAACTAGCCTGCG 60.666 55.000 0.00 0.00 0.00 5.18
130 131 1.394917 CATCGACAACAACTAGCCTGC 59.605 52.381 0.00 0.00 0.00 4.85
131 132 2.002586 CCATCGACAACAACTAGCCTG 58.997 52.381 0.00 0.00 0.00 4.85
132 133 1.066143 CCCATCGACAACAACTAGCCT 60.066 52.381 0.00 0.00 0.00 4.58
133 134 1.369625 CCCATCGACAACAACTAGCC 58.630 55.000 0.00 0.00 0.00 3.93
134 135 1.338769 ACCCCATCGACAACAACTAGC 60.339 52.381 0.00 0.00 0.00 3.42
135 136 2.346803 CACCCCATCGACAACAACTAG 58.653 52.381 0.00 0.00 0.00 2.57
136 137 1.002659 CCACCCCATCGACAACAACTA 59.997 52.381 0.00 0.00 0.00 2.24
137 138 0.250727 CCACCCCATCGACAACAACT 60.251 55.000 0.00 0.00 0.00 3.16
138 139 1.241315 CCCACCCCATCGACAACAAC 61.241 60.000 0.00 0.00 0.00 3.32
139 140 1.074072 CCCACCCCATCGACAACAA 59.926 57.895 0.00 0.00 0.00 2.83
140 141 2.150719 ACCCACCCCATCGACAACA 61.151 57.895 0.00 0.00 0.00 3.33
141 142 1.674322 CACCCACCCCATCGACAAC 60.674 63.158 0.00 0.00 0.00 3.32
142 143 2.753701 CACCCACCCCATCGACAA 59.246 61.111 0.00 0.00 0.00 3.18
143 144 3.326578 CCACCCACCCCATCGACA 61.327 66.667 0.00 0.00 0.00 4.35
144 145 4.109675 CCCACCCACCCCATCGAC 62.110 72.222 0.00 0.00 0.00 4.20
145 146 4.340489 TCCCACCCACCCCATCGA 62.340 66.667 0.00 0.00 0.00 3.59
146 147 3.797353 CTCCCACCCACCCCATCG 61.797 72.222 0.00 0.00 0.00 3.84
147 148 4.129148 GCTCCCACCCACCCCATC 62.129 72.222 0.00 0.00 0.00 3.51
156 157 4.643387 ACAACCAGCGCTCCCACC 62.643 66.667 7.13 0.00 0.00 4.61
157 158 3.357079 CACAACCAGCGCTCCCAC 61.357 66.667 7.13 0.00 0.00 4.61
158 159 2.410322 AATCACAACCAGCGCTCCCA 62.410 55.000 7.13 0.00 0.00 4.37
159 160 1.675641 AATCACAACCAGCGCTCCC 60.676 57.895 7.13 0.00 0.00 4.30
160 161 1.503542 CAATCACAACCAGCGCTCC 59.496 57.895 7.13 0.00 0.00 4.70
161 162 1.237285 ACCAATCACAACCAGCGCTC 61.237 55.000 7.13 0.00 0.00 5.03
162 163 0.036164 TACCAATCACAACCAGCGCT 59.964 50.000 2.64 2.64 0.00 5.92
163 164 0.447801 CTACCAATCACAACCAGCGC 59.552 55.000 0.00 0.00 0.00 5.92
164 165 1.086696 CCTACCAATCACAACCAGCG 58.913 55.000 0.00 0.00 0.00 5.18
165 166 2.200373 ACCTACCAATCACAACCAGC 57.800 50.000 0.00 0.00 0.00 4.85
166 167 3.259064 CGTACCTACCAATCACAACCAG 58.741 50.000 0.00 0.00 0.00 4.00
167 168 2.613474 GCGTACCTACCAATCACAACCA 60.613 50.000 0.00 0.00 0.00 3.67
168 169 2.004733 GCGTACCTACCAATCACAACC 58.995 52.381 0.00 0.00 0.00 3.77
169 170 2.690786 TGCGTACCTACCAATCACAAC 58.309 47.619 0.00 0.00 0.00 3.32
170 171 3.266636 CATGCGTACCTACCAATCACAA 58.733 45.455 0.00 0.00 0.00 3.33
171 172 2.235155 ACATGCGTACCTACCAATCACA 59.765 45.455 0.00 0.00 0.00 3.58
172 173 2.901249 ACATGCGTACCTACCAATCAC 58.099 47.619 0.00 0.00 0.00 3.06
173 174 4.587262 AGATACATGCGTACCTACCAATCA 59.413 41.667 0.00 0.00 0.00 2.57
174 175 5.135508 AGATACATGCGTACCTACCAATC 57.864 43.478 0.00 0.00 0.00 2.67
175 176 4.321008 CGAGATACATGCGTACCTACCAAT 60.321 45.833 0.00 0.00 0.00 3.16
176 177 3.004002 CGAGATACATGCGTACCTACCAA 59.996 47.826 0.00 0.00 0.00 3.67
177 178 2.551032 CGAGATACATGCGTACCTACCA 59.449 50.000 0.00 0.00 0.00 3.25
178 179 2.551459 ACGAGATACATGCGTACCTACC 59.449 50.000 0.00 0.00 36.37 3.18
179 180 3.552541 CACGAGATACATGCGTACCTAC 58.447 50.000 0.00 0.00 36.37 3.18
180 181 2.551032 CCACGAGATACATGCGTACCTA 59.449 50.000 0.00 0.00 36.37 3.08
181 182 1.337071 CCACGAGATACATGCGTACCT 59.663 52.381 0.00 0.00 36.37 3.08
182 183 1.335810 TCCACGAGATACATGCGTACC 59.664 52.381 0.00 0.00 36.37 3.34
183 184 2.651701 CTCCACGAGATACATGCGTAC 58.348 52.381 0.00 0.00 36.37 3.67
184 185 1.001706 GCTCCACGAGATACATGCGTA 60.002 52.381 0.00 0.00 36.37 4.42
185 186 0.249073 GCTCCACGAGATACATGCGT 60.249 55.000 0.00 0.00 39.04 5.24
186 187 0.249031 TGCTCCACGAGATACATGCG 60.249 55.000 0.00 0.00 0.00 4.73
187 188 1.202463 ACTGCTCCACGAGATACATGC 60.202 52.381 0.00 0.00 0.00 4.06
188 189 2.879002 ACTGCTCCACGAGATACATG 57.121 50.000 0.00 0.00 0.00 3.21
189 190 4.830046 AGAATACTGCTCCACGAGATACAT 59.170 41.667 0.00 0.00 0.00 2.29
190 191 4.207955 AGAATACTGCTCCACGAGATACA 58.792 43.478 0.00 0.00 0.00 2.29
191 192 4.839668 AGAATACTGCTCCACGAGATAC 57.160 45.455 0.00 0.00 0.00 2.24
192 193 5.622180 ACTAGAATACTGCTCCACGAGATA 58.378 41.667 0.00 0.00 0.00 1.98
193 194 4.465886 ACTAGAATACTGCTCCACGAGAT 58.534 43.478 0.00 0.00 0.00 2.75
194 195 3.878103 GACTAGAATACTGCTCCACGAGA 59.122 47.826 0.00 0.00 0.00 4.04
195 196 3.303461 CGACTAGAATACTGCTCCACGAG 60.303 52.174 0.00 0.00 0.00 4.18
196 197 2.612672 CGACTAGAATACTGCTCCACGA 59.387 50.000 0.00 0.00 0.00 4.35
197 198 2.287069 CCGACTAGAATACTGCTCCACG 60.287 54.545 0.00 0.00 0.00 4.94
198 199 2.034812 CCCGACTAGAATACTGCTCCAC 59.965 54.545 0.00 0.00 0.00 4.02
199 200 2.307768 CCCGACTAGAATACTGCTCCA 58.692 52.381 0.00 0.00 0.00 3.86
200 201 2.308690 ACCCGACTAGAATACTGCTCC 58.691 52.381 0.00 0.00 0.00 4.70
201 202 4.388378 AAACCCGACTAGAATACTGCTC 57.612 45.455 0.00 0.00 0.00 4.26
202 203 4.820894 AAAACCCGACTAGAATACTGCT 57.179 40.909 0.00 0.00 0.00 4.24
223 224 9.221933 TGACATATTTTAAAGTAGCTCCGAAAA 57.778 29.630 0.00 0.00 0.00 2.29
224 225 8.780846 TGACATATTTTAAAGTAGCTCCGAAA 57.219 30.769 0.00 0.00 0.00 3.46
225 226 8.958119 ATGACATATTTTAAAGTAGCTCCGAA 57.042 30.769 0.00 0.00 0.00 4.30
226 227 7.656137 GGATGACATATTTTAAAGTAGCTCCGA 59.344 37.037 0.00 0.00 0.00 4.55
227 228 7.657761 AGGATGACATATTTTAAAGTAGCTCCG 59.342 37.037 0.00 0.00 0.00 4.63
228 229 8.910351 AGGATGACATATTTTAAAGTAGCTCC 57.090 34.615 0.00 0.00 0.00 4.70
230 231 9.125026 CCAAGGATGACATATTTTAAAGTAGCT 57.875 33.333 0.00 0.00 0.00 3.32
231 232 8.352942 CCCAAGGATGACATATTTTAAAGTAGC 58.647 37.037 0.00 0.00 0.00 3.58
232 233 9.627123 TCCCAAGGATGACATATTTTAAAGTAG 57.373 33.333 0.00 0.00 0.00 2.57
241 242 8.370182 GCATTTTTATCCCAAGGATGACATATT 58.630 33.333 6.38 0.00 43.06 1.28
242 243 7.038799 GGCATTTTTATCCCAAGGATGACATAT 60.039 37.037 6.38 0.00 43.06 1.78
243 244 6.267471 GGCATTTTTATCCCAAGGATGACATA 59.733 38.462 6.38 0.00 43.06 2.29
244 245 5.070847 GGCATTTTTATCCCAAGGATGACAT 59.929 40.000 6.38 0.00 43.06 3.06
245 246 4.405358 GGCATTTTTATCCCAAGGATGACA 59.595 41.667 6.38 0.00 43.06 3.58
246 247 4.405358 TGGCATTTTTATCCCAAGGATGAC 59.595 41.667 6.38 0.00 43.06 3.06
247 248 4.618635 TGGCATTTTTATCCCAAGGATGA 58.381 39.130 6.38 0.00 43.06 2.92
248 249 5.070714 TCATGGCATTTTTATCCCAAGGATG 59.929 40.000 6.38 0.00 43.06 3.51
249 250 5.218179 TCATGGCATTTTTATCCCAAGGAT 58.782 37.500 0.00 1.08 45.40 3.24
250 251 4.618635 TCATGGCATTTTTATCCCAAGGA 58.381 39.130 0.00 0.00 35.55 3.36
251 252 5.118286 GTTCATGGCATTTTTATCCCAAGG 58.882 41.667 0.00 0.00 0.00 3.61
252 253 5.732633 TGTTCATGGCATTTTTATCCCAAG 58.267 37.500 0.00 0.00 0.00 3.61
253 254 5.752036 TGTTCATGGCATTTTTATCCCAA 57.248 34.783 0.00 0.00 0.00 4.12
254 255 5.752036 TTGTTCATGGCATTTTTATCCCA 57.248 34.783 0.00 0.00 0.00 4.37
255 256 7.446001 TTTTTGTTCATGGCATTTTTATCCC 57.554 32.000 0.00 0.00 0.00 3.85
288 289 2.556622 ACGATTGAGCATTCGGGTTTTT 59.443 40.909 16.11 0.00 38.18 1.94
289 290 2.095263 CACGATTGAGCATTCGGGTTTT 60.095 45.455 16.11 0.00 38.18 2.43
290 291 1.468520 CACGATTGAGCATTCGGGTTT 59.531 47.619 16.11 0.00 38.18 3.27
291 292 1.086696 CACGATTGAGCATTCGGGTT 58.913 50.000 16.11 0.00 38.18 4.11
292 293 0.036388 ACACGATTGAGCATTCGGGT 60.036 50.000 14.64 14.64 43.34 5.28
293 294 1.860950 CTACACGATTGAGCATTCGGG 59.139 52.381 13.52 13.52 41.66 5.14
294 295 1.258982 GCTACACGATTGAGCATTCGG 59.741 52.381 16.11 9.40 38.18 4.30
295 296 2.034254 CAGCTACACGATTGAGCATTCG 60.034 50.000 11.76 11.76 38.73 3.34
296 297 2.286067 GCAGCTACACGATTGAGCATTC 60.286 50.000 0.00 0.00 38.73 2.67
297 298 1.667724 GCAGCTACACGATTGAGCATT 59.332 47.619 0.00 0.00 38.73 3.56
298 299 1.293924 GCAGCTACACGATTGAGCAT 58.706 50.000 0.00 0.00 38.73 3.79
299 300 0.037419 TGCAGCTACACGATTGAGCA 60.037 50.000 0.00 0.00 38.73 4.26
300 301 0.371645 GTGCAGCTACACGATTGAGC 59.628 55.000 0.25 0.00 36.42 4.26
308 309 1.606606 GCAAAATCGTGCAGCTACAC 58.393 50.000 7.04 7.04 44.29 2.90
309 310 0.165727 CGCAAAATCGTGCAGCTACA 59.834 50.000 0.00 0.00 45.19 2.74
310 311 0.442310 TCGCAAAATCGTGCAGCTAC 59.558 50.000 0.00 0.00 45.19 3.58
311 312 1.327460 GATCGCAAAATCGTGCAGCTA 59.673 47.619 0.00 0.00 45.19 3.32
312 313 0.097674 GATCGCAAAATCGTGCAGCT 59.902 50.000 0.00 0.00 45.19 4.24
313 314 1.189989 CGATCGCAAAATCGTGCAGC 61.190 55.000 0.26 0.00 45.19 5.25
314 315 2.832640 CGATCGCAAAATCGTGCAG 58.167 52.632 0.26 0.00 45.19 4.41
333 334 4.126390 CTGAGTCGCGTGCGCTTG 62.126 66.667 9.73 1.22 39.59 4.01
343 344 2.951745 GATCGCACGGCTGAGTCG 60.952 66.667 4.31 4.31 36.42 4.18
344 345 2.583593 GGATCGCACGGCTGAGTC 60.584 66.667 0.00 0.00 0.00 3.36
345 346 4.498520 CGGATCGCACGGCTGAGT 62.499 66.667 0.00 0.00 0.00 3.41
358 359 4.286320 GCGCGAGATCCACCGGAT 62.286 66.667 12.10 0.00 46.28 4.18
366 367 4.508128 TTCCACCCGCGCGAGATC 62.508 66.667 34.63 0.00 0.00 2.75
367 368 4.814294 GTTCCACCCGCGCGAGAT 62.814 66.667 34.63 13.53 0.00 2.75
372 373 3.810896 GATTGGTTCCACCCGCGC 61.811 66.667 0.00 0.00 37.50 6.86
373 374 2.359354 TGATTGGTTCCACCCGCG 60.359 61.111 0.00 0.00 37.50 6.46
374 375 2.046285 CCTGATTGGTTCCACCCGC 61.046 63.158 0.00 0.00 37.50 6.13
375 376 2.046285 GCCTGATTGGTTCCACCCG 61.046 63.158 0.00 0.00 37.50 5.28
376 377 1.682344 GGCCTGATTGGTTCCACCC 60.682 63.158 0.00 0.00 37.50 4.61
377 378 2.046285 CGGCCTGATTGGTTCCACC 61.046 63.158 0.00 0.00 39.22 4.61
378 379 2.700773 GCGGCCTGATTGGTTCCAC 61.701 63.158 0.00 0.00 38.35 4.02
379 380 2.361104 GCGGCCTGATTGGTTCCA 60.361 61.111 0.00 0.00 38.35 3.53
380 381 2.361104 TGCGGCCTGATTGGTTCC 60.361 61.111 0.00 0.00 38.35 3.62
381 382 3.056313 GCTGCGGCCTGATTGGTTC 62.056 63.158 6.12 0.00 38.35 3.62
382 383 3.064324 GCTGCGGCCTGATTGGTT 61.064 61.111 6.12 0.00 38.35 3.67
385 386 3.869272 GACGCTGCGGCCTGATTG 61.869 66.667 26.95 0.00 34.44 2.67
400 401 2.414806 GACTTTTTCCTCTGTCGGGAC 58.585 52.381 0.00 0.00 31.94 4.46
401 402 1.346722 GGACTTTTTCCTCTGTCGGGA 59.653 52.381 0.00 0.00 41.95 5.14
402 403 1.071699 TGGACTTTTTCCTCTGTCGGG 59.928 52.381 0.00 0.00 46.10 5.14
403 404 2.543777 TGGACTTTTTCCTCTGTCGG 57.456 50.000 0.00 0.00 46.10 4.79
404 405 4.893424 TTTTGGACTTTTTCCTCTGTCG 57.107 40.909 0.00 0.00 46.10 4.35
405 406 7.652105 GGTTTATTTTGGACTTTTTCCTCTGTC 59.348 37.037 0.00 0.00 46.10 3.51
406 407 7.418597 GGGTTTATTTTGGACTTTTTCCTCTGT 60.419 37.037 0.00 0.00 46.10 3.41
409 410 6.929049 CAGGGTTTATTTTGGACTTTTTCCTC 59.071 38.462 0.00 0.00 46.10 3.71
656 663 2.931105 TTCCCCTTGCGTGGGCTA 60.931 61.111 8.21 0.00 45.78 3.93
672 679 0.921896 CCATGAGTGGGGATGGACTT 59.078 55.000 0.00 0.00 41.63 3.01
688 695 1.474330 GGAATTTCAAGGGACGCCAT 58.526 50.000 0.00 0.00 0.00 4.40
756 763 3.282745 AAGCCGTCACGATCGCTGT 62.283 57.895 16.60 0.00 0.00 4.40
786 793 0.735287 GGAGACCGTACCTTTGACGC 60.735 60.000 0.00 0.00 38.99 5.19
811 818 0.470833 GCAGCCATAGGAGGAGGAGA 60.471 60.000 0.00 0.00 0.00 3.71
850 857 7.340256 TCTCTTTGAAACCCTAACAGTAACAA 58.660 34.615 0.00 0.00 0.00 2.83
870 877 5.130975 ACAGAAAAGCCCCAATTTTTCTCTT 59.869 36.000 8.73 0.00 45.58 2.85
915 922 6.093532 ACAAAAACGAACAGAAAATTGCTG 57.906 33.333 0.00 0.00 39.26 4.41
991 1005 2.171237 CACTAGGGTCCATGATTGAGCA 59.829 50.000 0.00 0.00 31.96 4.26
1103 1122 2.996621 GACAACTTGTCCCTCTCAATCG 59.003 50.000 10.42 0.00 41.37 3.34
1197 1216 1.279271 TCAGCTAGTTCTTTCCCAGGC 59.721 52.381 0.00 0.00 0.00 4.85
1335 1354 4.019858 TCTCATAGTCACTAGCACTGCTT 58.980 43.478 9.30 0.00 40.44 3.91
1427 1446 5.363580 TGAGTGAGCACACCATTATCATCTA 59.636 40.000 10.88 0.00 46.99 1.98
1505 1524 2.082231 CTGCCACTTCATCAACCTCAG 58.918 52.381 0.00 0.00 0.00 3.35
1642 1682 3.620488 TGTTGCTCTGAACCTTCACTTT 58.380 40.909 0.00 0.00 32.90 2.66
1652 1692 2.106338 TCTGGTGGATTGTTGCTCTGAA 59.894 45.455 0.00 0.00 0.00 3.02
1900 1940 2.559931 CCCACTGTTTCTCCTCTCCCTA 60.560 54.545 0.00 0.00 0.00 3.53
1953 1995 2.547211 GTGCCCATCAGAATCTTCATCG 59.453 50.000 0.00 0.00 0.00 3.84
2081 2123 4.941263 TGGTCACAATTCCCTATTTCTTCG 59.059 41.667 0.00 0.00 0.00 3.79
2144 2186 2.746472 GCCATCCACACTTAGCCCTAAG 60.746 54.545 12.31 12.31 45.95 2.18
2172 2214 3.566351 GCTCCATAAATAAGCCAAGGGT 58.434 45.455 0.00 0.00 0.00 4.34
2202 2244 7.647907 ATGATTTGAAACATGCTTGTTCTTC 57.352 32.000 17.34 12.82 45.30 2.87
2366 2408 5.988287 TGATACATCAGCAAACATGTCCTA 58.012 37.500 0.00 0.00 34.92 2.94
2641 2686 4.389374 TCTCCTTTGACAGCACCTTTAAG 58.611 43.478 0.00 0.00 0.00 1.85
2708 2753 0.112218 AACAACTGCCCATGCCACTA 59.888 50.000 0.00 0.00 36.33 2.74


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

AutoCloner maintained by Alex Coulton.