Multiple sequence alignment - TraesCS1D01G401100

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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 TraesCS1D01G401100 chr1D 100.000 2502 0 0 1 2502 467457655 467455154 0.000000e+00 4621.0
1 TraesCS1D01G401100 chr1D 92.564 1022 43 12 961 1974 122263780 122262784 0.000000e+00 1435.0
2 TraesCS1D01G401100 chr1D 96.015 527 21 0 1974 2500 122262753 122262227 0.000000e+00 857.0
3 TraesCS1D01G401100 chr1D 98.305 59 1 0 214 272 467466618 467466560 1.220000e-18 104.0
4 TraesCS1D01G401100 chr1D 94.915 59 3 0 214 272 467486753 467486695 2.650000e-15 93.5
5 TraesCS1D01G401100 chr6D 94.747 2151 99 12 357 2500 110324270 110322127 0.000000e+00 3334.0
6 TraesCS1D01G401100 chr6D 94.405 1680 68 10 428 2097 80068606 80070269 0.000000e+00 2558.0
7 TraesCS1D01G401100 chr6D 96.867 415 12 1 2087 2500 80081919 80082333 0.000000e+00 693.0
8 TraesCS1D01G401100 chr3D 94.700 2151 95 14 357 2500 46539858 46541996 0.000000e+00 3323.0
9 TraesCS1D01G401100 chr3D 93.938 1699 56 10 309 1974 585903860 585902176 0.000000e+00 2523.0
10 TraesCS1D01G401100 chr3D 96.986 365 9 1 2136 2500 585902013 585901651 1.650000e-171 612.0
11 TraesCS1D01G401100 chr7D 95.272 1671 59 9 308 1974 602775725 602777379 0.000000e+00 2630.0
12 TraesCS1D01G401100 chr7D 95.443 1141 37 7 837 1974 590072350 590071222 0.000000e+00 1805.0
13 TraesCS1D01G401100 chr7D 96.395 527 19 0 1974 2500 590071191 590070665 0.000000e+00 869.0
14 TraesCS1D01G401100 chr7D 97.260 365 10 0 2136 2500 602777542 602777906 9.830000e-174 619.0
15 TraesCS1D01G401100 chr5D 93.216 1754 85 24 357 2104 495476201 495477926 0.000000e+00 2549.0
16 TraesCS1D01G401100 chr5A 96.236 1541 50 5 437 1974 426307146 426305611 0.000000e+00 2518.0
17 TraesCS1D01G401100 chr5A 97.154 527 15 0 1974 2500 426305580 426305054 0.000000e+00 891.0
18 TraesCS1D01G401100 chr5A 94.000 50 3 0 1058 1107 426306289 426306240 2.670000e-10 76.8
19 TraesCS1D01G401100 chr2B 91.402 535 42 3 308 839 18196190 18195657 0.000000e+00 730.0
20 TraesCS1D01G401100 chr2B 88.930 271 25 3 1997 2262 746017605 746017875 1.860000e-86 329.0
21 TraesCS1D01G401100 chr2B 84.211 114 11 3 910 1016 649589696 649589809 1.220000e-18 104.0
22 TraesCS1D01G401100 chr2D 88.811 572 53 10 363 928 590221127 590221693 0.000000e+00 691.0
23 TraesCS1D01G401100 chr2D 100.000 31 0 0 1900 1930 41959257 41959287 9.670000e-05 58.4
24 TraesCS1D01G401100 chr3B 87.856 527 40 2 1974 2500 241927852 241927350 4.610000e-167 597.0
25 TraesCS1D01G401100 chr1A 90.705 312 21 2 1 308 559799677 559799370 2.320000e-110 409.0
26 TraesCS1D01G401100 chr1A 85.333 75 4 4 233 301 559834701 559834628 1.240000e-08 71.3
27 TraesCS1D01G401100 chr1B 96.364 165 6 0 308 472 682377294 682377130 3.170000e-69 272.0
28 TraesCS1D01G401100 chr1B 88.288 111 8 3 164 270 645269481 645269590 7.260000e-26 128.0
29 TraesCS1D01G401100 chr1B 88.172 93 4 4 214 300 645293084 645292993 1.220000e-18 104.0


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 TraesCS1D01G401100 chr1D 467455154 467457655 2501 True 4621.000000 4621 100.000000 1 2502 1 chr1D.!!$R1 2501
1 TraesCS1D01G401100 chr1D 122262227 122263780 1553 True 1146.000000 1435 94.289500 961 2500 2 chr1D.!!$R4 1539
2 TraesCS1D01G401100 chr6D 110322127 110324270 2143 True 3334.000000 3334 94.747000 357 2500 1 chr6D.!!$R1 2143
3 TraesCS1D01G401100 chr6D 80068606 80070269 1663 False 2558.000000 2558 94.405000 428 2097 1 chr6D.!!$F1 1669
4 TraesCS1D01G401100 chr3D 46539858 46541996 2138 False 3323.000000 3323 94.700000 357 2500 1 chr3D.!!$F1 2143
5 TraesCS1D01G401100 chr3D 585901651 585903860 2209 True 1567.500000 2523 95.462000 309 2500 2 chr3D.!!$R1 2191
6 TraesCS1D01G401100 chr7D 602775725 602777906 2181 False 1624.500000 2630 96.266000 308 2500 2 chr7D.!!$F1 2192
7 TraesCS1D01G401100 chr7D 590070665 590072350 1685 True 1337.000000 1805 95.919000 837 2500 2 chr7D.!!$R1 1663
8 TraesCS1D01G401100 chr5D 495476201 495477926 1725 False 2549.000000 2549 93.216000 357 2104 1 chr5D.!!$F1 1747
9 TraesCS1D01G401100 chr5A 426305054 426307146 2092 True 1161.933333 2518 95.796667 437 2500 3 chr5A.!!$R1 2063
10 TraesCS1D01G401100 chr2B 18195657 18196190 533 True 730.000000 730 91.402000 308 839 1 chr2B.!!$R1 531
11 TraesCS1D01G401100 chr2D 590221127 590221693 566 False 691.000000 691 88.811000 363 928 1 chr2D.!!$F2 565
12 TraesCS1D01G401100 chr3B 241927350 241927852 502 True 597.000000 597 87.856000 1974 2500 1 chr3B.!!$R1 526

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
264 265 0.036952 CTCGTGGAGTTGTGGATGCT 60.037 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2253 0.109153 TGAACCTGCACATGCTGACT 59.891 50.0 11.87 0.0 41.71 3.41 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 4.519610 GGTGTGGGTGCTGGATTT 57.480 55.556 0.00 0.00 0.00 2.17
18 19 2.745379 GGTGTGGGTGCTGGATTTT 58.255 52.632 0.00 0.00 0.00 1.82
19 20 0.318120 GGTGTGGGTGCTGGATTTTG 59.682 55.000 0.00 0.00 0.00 2.44
20 21 0.319813 GTGTGGGTGCTGGATTTTGC 60.320 55.000 0.00 0.00 0.00 3.68
21 22 0.469705 TGTGGGTGCTGGATTTTGCT 60.470 50.000 0.00 0.00 0.00 3.91
22 23 1.202989 TGTGGGTGCTGGATTTTGCTA 60.203 47.619 0.00 0.00 0.00 3.49
23 24 1.202348 GTGGGTGCTGGATTTTGCTAC 59.798 52.381 0.00 0.00 0.00 3.58
24 25 0.451783 GGGTGCTGGATTTTGCTACG 59.548 55.000 0.00 0.00 0.00 3.51
25 26 0.451783 GGTGCTGGATTTTGCTACGG 59.548 55.000 0.00 0.00 0.00 4.02
26 27 1.448985 GTGCTGGATTTTGCTACGGA 58.551 50.000 0.00 0.00 0.00 4.69
27 28 2.017049 GTGCTGGATTTTGCTACGGAT 58.983 47.619 0.00 0.00 0.00 4.18
28 29 2.016318 TGCTGGATTTTGCTACGGATG 58.984 47.619 0.00 0.00 0.00 3.51
29 30 1.268743 GCTGGATTTTGCTACGGATGC 60.269 52.381 0.00 0.00 0.00 3.91
30 31 2.016318 CTGGATTTTGCTACGGATGCA 58.984 47.619 0.00 0.00 38.80 3.96
31 32 2.620115 CTGGATTTTGCTACGGATGCAT 59.380 45.455 0.00 0.00 40.34 3.96
32 33 3.814625 TGGATTTTGCTACGGATGCATA 58.185 40.909 0.00 0.00 40.34 3.14
33 34 3.563808 TGGATTTTGCTACGGATGCATAC 59.436 43.478 0.00 0.00 40.34 2.39
34 35 3.563808 GGATTTTGCTACGGATGCATACA 59.436 43.478 10.18 0.00 40.34 2.29
35 36 4.216257 GGATTTTGCTACGGATGCATACAT 59.784 41.667 10.18 0.00 40.34 2.29
36 37 5.411361 GGATTTTGCTACGGATGCATACATA 59.589 40.000 10.18 0.00 40.34 2.29
37 38 5.666969 TTTTGCTACGGATGCATACATAC 57.333 39.130 10.18 0.00 40.34 2.39
38 39 4.329462 TTGCTACGGATGCATACATACA 57.671 40.909 10.18 0.00 36.88 2.29
39 40 4.535526 TGCTACGGATGCATACATACAT 57.464 40.909 10.18 0.00 36.88 2.29
40 41 5.652994 TGCTACGGATGCATACATACATA 57.347 39.130 10.18 0.00 36.88 2.29
41 42 5.407502 TGCTACGGATGCATACATACATAC 58.592 41.667 10.18 0.00 36.88 2.39
42 43 5.047660 TGCTACGGATGCATACATACATACA 60.048 40.000 10.18 0.00 36.88 2.29
43 44 6.042777 GCTACGGATGCATACATACATACAT 58.957 40.000 10.18 0.00 36.88 2.29
44 45 6.019559 GCTACGGATGCATACATACATACATG 60.020 42.308 10.18 0.00 36.88 3.21
45 46 5.178061 ACGGATGCATACATACATACATGG 58.822 41.667 10.18 0.00 36.88 3.66
46 47 4.571984 CGGATGCATACATACATACATGGG 59.428 45.833 10.18 0.00 36.88 4.00
47 48 4.336433 GGATGCATACATACATACATGGGC 59.664 45.833 3.28 0.00 37.06 5.36
48 49 4.639078 TGCATACATACATACATGGGCT 57.361 40.909 0.00 0.00 0.00 5.19
49 50 4.325972 TGCATACATACATACATGGGCTG 58.674 43.478 0.00 0.00 0.00 4.85
50 51 4.041444 TGCATACATACATACATGGGCTGA 59.959 41.667 0.00 0.00 0.00 4.26
51 52 5.003160 GCATACATACATACATGGGCTGAA 58.997 41.667 0.00 0.00 0.00 3.02
52 53 5.649395 GCATACATACATACATGGGCTGAAT 59.351 40.000 0.00 0.00 0.00 2.57
53 54 6.403964 GCATACATACATACATGGGCTGAATG 60.404 42.308 0.00 0.00 0.00 2.67
54 55 3.822735 ACATACATACATGGGCTGAATGC 59.177 43.478 0.00 0.00 41.94 3.56
64 65 1.065928 GCTGAATGCCTGCATCAGC 59.934 57.895 25.79 25.79 43.17 4.26
65 66 1.384989 GCTGAATGCCTGCATCAGCT 61.385 55.000 28.96 10.21 44.42 4.24
66 67 1.963172 CTGAATGCCTGCATCAGCTA 58.037 50.000 4.89 0.00 42.74 3.32
67 68 2.505405 CTGAATGCCTGCATCAGCTAT 58.495 47.619 4.89 0.00 42.74 2.97
68 69 2.885266 CTGAATGCCTGCATCAGCTATT 59.115 45.455 4.89 2.36 42.74 1.73
69 70 2.882761 TGAATGCCTGCATCAGCTATTC 59.117 45.455 4.89 14.53 42.74 1.75
70 71 2.651382 ATGCCTGCATCAGCTATTCA 57.349 45.000 0.00 0.00 42.74 2.57
71 72 2.423446 TGCCTGCATCAGCTATTCAA 57.577 45.000 5.28 0.00 42.74 2.69
72 73 2.725637 TGCCTGCATCAGCTATTCAAA 58.274 42.857 5.28 0.00 42.74 2.69
73 74 3.293337 TGCCTGCATCAGCTATTCAAAT 58.707 40.909 5.28 0.00 42.74 2.32
74 75 3.702548 TGCCTGCATCAGCTATTCAAATT 59.297 39.130 5.28 0.00 42.74 1.82
75 76 4.202080 TGCCTGCATCAGCTATTCAAATTC 60.202 41.667 5.28 0.00 42.74 2.17
76 77 4.534168 CCTGCATCAGCTATTCAAATTCG 58.466 43.478 0.00 0.00 42.74 3.34
77 78 4.036027 CCTGCATCAGCTATTCAAATTCGT 59.964 41.667 0.00 0.00 42.74 3.85
78 79 4.912214 TGCATCAGCTATTCAAATTCGTG 58.088 39.130 0.00 0.00 42.74 4.35
79 80 4.395854 TGCATCAGCTATTCAAATTCGTGT 59.604 37.500 0.00 0.00 42.74 4.49
80 81 5.106197 TGCATCAGCTATTCAAATTCGTGTT 60.106 36.000 0.00 0.00 42.74 3.32
81 82 5.801947 GCATCAGCTATTCAAATTCGTGTTT 59.198 36.000 0.00 0.00 37.91 2.83
82 83 6.021153 GCATCAGCTATTCAAATTCGTGTTTC 60.021 38.462 0.00 0.00 37.91 2.78
83 84 6.801539 TCAGCTATTCAAATTCGTGTTTCT 57.198 33.333 0.00 0.00 0.00 2.52
84 85 6.831769 TCAGCTATTCAAATTCGTGTTTCTC 58.168 36.000 0.00 0.00 0.00 2.87
85 86 6.426633 TCAGCTATTCAAATTCGTGTTTCTCA 59.573 34.615 0.00 0.00 0.00 3.27
86 87 7.041440 TCAGCTATTCAAATTCGTGTTTCTCAA 60.041 33.333 0.00 0.00 0.00 3.02
87 88 7.591057 CAGCTATTCAAATTCGTGTTTCTCAAA 59.409 33.333 0.00 0.00 0.00 2.69
88 89 8.134895 AGCTATTCAAATTCGTGTTTCTCAAAA 58.865 29.630 0.00 0.00 0.00 2.44
89 90 8.751335 GCTATTCAAATTCGTGTTTCTCAAAAA 58.249 29.630 0.00 0.00 0.00 1.94
114 115 3.891056 AAAATCAAGTTCGTCCGTTCC 57.109 42.857 0.00 0.00 0.00 3.62
115 116 1.804601 AATCAAGTTCGTCCGTTCCC 58.195 50.000 0.00 0.00 0.00 3.97
116 117 0.974383 ATCAAGTTCGTCCGTTCCCT 59.026 50.000 0.00 0.00 0.00 4.20
117 118 0.754472 TCAAGTTCGTCCGTTCCCTT 59.246 50.000 0.00 0.00 0.00 3.95
118 119 1.139455 TCAAGTTCGTCCGTTCCCTTT 59.861 47.619 0.00 0.00 0.00 3.11
119 120 1.944709 CAAGTTCGTCCGTTCCCTTTT 59.055 47.619 0.00 0.00 0.00 2.27
120 121 3.132925 CAAGTTCGTCCGTTCCCTTTTA 58.867 45.455 0.00 0.00 0.00 1.52
121 122 3.473923 AGTTCGTCCGTTCCCTTTTAA 57.526 42.857 0.00 0.00 0.00 1.52
122 123 3.807553 AGTTCGTCCGTTCCCTTTTAAA 58.192 40.909 0.00 0.00 0.00 1.52
123 124 4.198530 AGTTCGTCCGTTCCCTTTTAAAA 58.801 39.130 0.00 0.00 0.00 1.52
124 125 4.639755 AGTTCGTCCGTTCCCTTTTAAAAA 59.360 37.500 1.66 0.00 0.00 1.94
145 146 6.754702 AAAACAAGATCAGGATCATGTGAG 57.245 37.500 17.72 0.00 45.54 3.51
146 147 5.432680 AACAAGATCAGGATCATGTGAGT 57.567 39.130 17.72 3.49 45.54 3.41
147 148 4.767478 ACAAGATCAGGATCATGTGAGTG 58.233 43.478 16.65 5.03 44.85 3.51
148 149 3.472283 AGATCAGGATCATGTGAGTGC 57.528 47.619 7.33 0.00 40.22 4.40
149 150 2.133553 GATCAGGATCATGTGAGTGCG 58.866 52.381 7.33 0.00 37.74 5.34
150 151 0.897621 TCAGGATCATGTGAGTGCGT 59.102 50.000 7.33 0.00 0.00 5.24
151 152 1.004595 CAGGATCATGTGAGTGCGTG 58.995 55.000 0.00 0.00 0.00 5.34
152 153 0.610174 AGGATCATGTGAGTGCGTGT 59.390 50.000 0.00 0.00 0.00 4.49
153 154 1.824852 AGGATCATGTGAGTGCGTGTA 59.175 47.619 0.00 0.00 0.00 2.90
154 155 2.432146 AGGATCATGTGAGTGCGTGTAT 59.568 45.455 0.00 0.00 0.00 2.29
155 156 2.797156 GGATCATGTGAGTGCGTGTATC 59.203 50.000 0.00 0.00 0.00 2.24
156 157 3.447742 GATCATGTGAGTGCGTGTATCA 58.552 45.455 0.00 0.00 0.00 2.15
157 158 2.606108 TCATGTGAGTGCGTGTATCAC 58.394 47.619 0.00 0.00 42.90 3.06
158 159 2.231235 TCATGTGAGTGCGTGTATCACT 59.769 45.455 6.17 3.61 46.46 3.41
159 160 2.064573 TGTGAGTGCGTGTATCACTG 57.935 50.000 0.00 0.00 44.09 3.66
160 161 1.336795 TGTGAGTGCGTGTATCACTGG 60.337 52.381 0.00 0.00 44.09 4.00
161 162 1.067846 GTGAGTGCGTGTATCACTGGA 60.068 52.381 0.00 0.00 44.09 3.86
162 163 1.824852 TGAGTGCGTGTATCACTGGAT 59.175 47.619 0.00 0.00 44.09 3.41
163 164 2.233676 TGAGTGCGTGTATCACTGGATT 59.766 45.455 0.00 0.00 44.09 3.01
164 165 2.604914 GAGTGCGTGTATCACTGGATTG 59.395 50.000 0.00 0.00 44.09 2.67
165 166 1.665679 GTGCGTGTATCACTGGATTGG 59.334 52.381 0.00 0.00 34.89 3.16
166 167 1.552792 TGCGTGTATCACTGGATTGGA 59.447 47.619 0.00 0.00 34.89 3.53
167 168 2.170397 TGCGTGTATCACTGGATTGGAT 59.830 45.455 0.00 0.00 34.89 3.41
168 169 3.386402 TGCGTGTATCACTGGATTGGATA 59.614 43.478 0.00 0.00 34.89 2.59
169 170 4.040339 TGCGTGTATCACTGGATTGGATAT 59.960 41.667 0.00 0.00 34.89 1.63
170 171 4.389992 GCGTGTATCACTGGATTGGATATG 59.610 45.833 0.00 0.00 34.89 1.78
171 172 4.389992 CGTGTATCACTGGATTGGATATGC 59.610 45.833 0.00 0.00 34.89 3.14
172 173 5.555017 GTGTATCACTGGATTGGATATGCT 58.445 41.667 0.00 0.00 34.89 3.79
173 174 5.641209 GTGTATCACTGGATTGGATATGCTC 59.359 44.000 0.00 0.00 34.89 4.26
174 175 5.545335 TGTATCACTGGATTGGATATGCTCT 59.455 40.000 0.00 0.00 34.89 4.09
175 176 5.579753 ATCACTGGATTGGATATGCTCTT 57.420 39.130 0.00 0.00 0.00 2.85
176 177 4.711399 TCACTGGATTGGATATGCTCTTG 58.289 43.478 0.00 0.00 0.00 3.02
177 178 4.164796 TCACTGGATTGGATATGCTCTTGT 59.835 41.667 0.00 0.00 0.00 3.16
178 179 4.275196 CACTGGATTGGATATGCTCTTGTG 59.725 45.833 0.00 0.00 0.00 3.33
179 180 4.164796 ACTGGATTGGATATGCTCTTGTGA 59.835 41.667 0.00 0.00 0.00 3.58
180 181 4.454678 TGGATTGGATATGCTCTTGTGAC 58.545 43.478 0.00 0.00 0.00 3.67
181 182 3.496130 GGATTGGATATGCTCTTGTGACG 59.504 47.826 0.00 0.00 0.00 4.35
182 183 3.610040 TTGGATATGCTCTTGTGACGT 57.390 42.857 0.00 0.00 0.00 4.34
183 184 3.165058 TGGATATGCTCTTGTGACGTC 57.835 47.619 9.11 9.11 0.00 4.34
184 185 2.159099 TGGATATGCTCTTGTGACGTCC 60.159 50.000 14.12 5.06 0.00 4.79
185 186 2.159099 GGATATGCTCTTGTGACGTCCA 60.159 50.000 14.12 7.88 0.00 4.02
186 187 2.654749 TATGCTCTTGTGACGTCCAG 57.345 50.000 14.12 6.63 0.00 3.86
187 188 0.681733 ATGCTCTTGTGACGTCCAGT 59.318 50.000 14.12 0.00 0.00 4.00
195 196 4.361827 GACGTCCAGTCGATCGTG 57.638 61.111 15.94 6.88 40.43 4.35
196 197 1.500844 GACGTCCAGTCGATCGTGT 59.499 57.895 15.94 0.05 40.43 4.49
197 198 0.109873 GACGTCCAGTCGATCGTGTT 60.110 55.000 15.94 0.00 40.43 3.32
198 199 0.386858 ACGTCCAGTCGATCGTGTTG 60.387 55.000 15.94 11.47 35.24 3.33
199 200 1.071019 CGTCCAGTCGATCGTGTTGG 61.071 60.000 15.94 19.22 0.00 3.77
200 201 0.038526 GTCCAGTCGATCGTGTTGGT 60.039 55.000 23.95 2.76 0.00 3.67
201 202 0.677288 TCCAGTCGATCGTGTTGGTT 59.323 50.000 23.95 2.52 0.00 3.67
202 203 1.069513 TCCAGTCGATCGTGTTGGTTT 59.930 47.619 23.95 1.69 0.00 3.27
203 204 1.194547 CCAGTCGATCGTGTTGGTTTG 59.805 52.381 15.94 3.51 0.00 2.93
204 205 2.131972 CAGTCGATCGTGTTGGTTTGA 58.868 47.619 15.94 0.00 0.00 2.69
205 206 2.096909 CAGTCGATCGTGTTGGTTTGAC 60.097 50.000 15.94 1.42 0.00 3.18
206 207 1.133407 TCGATCGTGTTGGTTTGACG 58.867 50.000 15.94 0.00 34.38 4.35
207 208 0.856641 CGATCGTGTTGGTTTGACGT 59.143 50.000 7.03 0.00 34.69 4.34
208 209 1.259507 CGATCGTGTTGGTTTGACGTT 59.740 47.619 7.03 0.00 34.69 3.99
209 210 2.635444 GATCGTGTTGGTTTGACGTTG 58.365 47.619 0.00 0.00 34.69 4.10
210 211 1.440708 TCGTGTTGGTTTGACGTTGT 58.559 45.000 0.00 0.00 34.69 3.32
211 212 2.614779 TCGTGTTGGTTTGACGTTGTA 58.385 42.857 0.00 0.00 34.69 2.41
212 213 2.348059 TCGTGTTGGTTTGACGTTGTAC 59.652 45.455 0.00 0.00 34.69 2.90
223 224 3.875813 CGTTGTACGTGCATGGATG 57.124 52.632 7.30 4.68 36.74 3.51
224 225 1.075542 CGTTGTACGTGCATGGATGT 58.924 50.000 16.75 16.75 36.74 3.06
225 226 1.201910 CGTTGTACGTGCATGGATGTG 60.202 52.381 21.09 1.08 36.74 3.21
226 227 0.801872 TTGTACGTGCATGGATGTGC 59.198 50.000 21.09 19.74 45.25 4.57
232 233 4.469883 GCATGGATGTGCGAGGAT 57.530 55.556 0.00 0.00 35.10 3.24
233 234 3.612517 GCATGGATGTGCGAGGATA 57.387 52.632 0.00 0.00 35.10 2.59
234 235 1.882912 GCATGGATGTGCGAGGATAA 58.117 50.000 0.00 0.00 35.10 1.75
235 236 2.430465 GCATGGATGTGCGAGGATAAT 58.570 47.619 0.00 0.00 35.10 1.28
236 237 3.599343 GCATGGATGTGCGAGGATAATA 58.401 45.455 0.00 0.00 35.10 0.98
237 238 4.002982 GCATGGATGTGCGAGGATAATAA 58.997 43.478 0.00 0.00 35.10 1.40
238 239 4.093998 GCATGGATGTGCGAGGATAATAAG 59.906 45.833 0.00 0.00 35.10 1.73
239 240 3.664107 TGGATGTGCGAGGATAATAAGC 58.336 45.455 0.00 0.00 0.00 3.09
240 241 3.070878 TGGATGTGCGAGGATAATAAGCA 59.929 43.478 0.00 0.00 35.27 3.91
241 242 4.065088 GGATGTGCGAGGATAATAAGCAA 58.935 43.478 0.00 0.00 39.67 3.91
242 243 4.153117 GGATGTGCGAGGATAATAAGCAAG 59.847 45.833 0.00 0.00 39.67 4.01
243 244 2.872245 TGTGCGAGGATAATAAGCAAGC 59.128 45.455 0.00 0.00 39.67 4.01
244 245 2.872245 GTGCGAGGATAATAAGCAAGCA 59.128 45.455 0.00 0.00 39.67 3.91
245 246 2.872245 TGCGAGGATAATAAGCAAGCAC 59.128 45.455 0.00 0.00 34.66 4.40
246 247 3.134458 GCGAGGATAATAAGCAAGCACT 58.866 45.455 0.00 0.00 0.00 4.40
247 248 3.185391 GCGAGGATAATAAGCAAGCACTC 59.815 47.826 0.00 0.00 0.00 3.51
248 249 3.426859 CGAGGATAATAAGCAAGCACTCG 59.573 47.826 0.00 0.00 39.16 4.18
249 250 4.372656 GAGGATAATAAGCAAGCACTCGT 58.627 43.478 0.00 0.00 0.00 4.18
250 251 4.122776 AGGATAATAAGCAAGCACTCGTG 58.877 43.478 0.00 0.00 0.00 4.35
251 252 3.248602 GGATAATAAGCAAGCACTCGTGG 59.751 47.826 0.00 0.00 0.00 4.94
252 253 2.472695 AATAAGCAAGCACTCGTGGA 57.527 45.000 0.00 0.00 0.00 4.02
253 254 2.015736 ATAAGCAAGCACTCGTGGAG 57.984 50.000 0.00 0.00 35.52 3.86
254 255 0.679505 TAAGCAAGCACTCGTGGAGT 59.320 50.000 0.00 0.00 44.44 3.85
255 256 0.179045 AAGCAAGCACTCGTGGAGTT 60.179 50.000 0.00 0.00 41.37 3.01
256 257 0.882042 AGCAAGCACTCGTGGAGTTG 60.882 55.000 0.00 0.00 41.37 3.16
257 258 1.160329 GCAAGCACTCGTGGAGTTGT 61.160 55.000 0.00 0.00 41.37 3.32
258 259 0.583438 CAAGCACTCGTGGAGTTGTG 59.417 55.000 0.00 0.00 41.37 3.33
259 260 0.532862 AAGCACTCGTGGAGTTGTGG 60.533 55.000 0.00 0.00 41.37 4.17
260 261 1.069090 GCACTCGTGGAGTTGTGGA 59.931 57.895 0.00 0.00 41.37 4.02
261 262 0.320771 GCACTCGTGGAGTTGTGGAT 60.321 55.000 0.00 0.00 41.37 3.41
262 263 1.432514 CACTCGTGGAGTTGTGGATG 58.567 55.000 0.00 0.00 41.37 3.51
263 264 0.320771 ACTCGTGGAGTTGTGGATGC 60.321 55.000 0.00 0.00 40.28 3.91
264 265 0.036952 CTCGTGGAGTTGTGGATGCT 60.037 55.000 0.00 0.00 0.00 3.79
265 266 0.320683 TCGTGGAGTTGTGGATGCTG 60.321 55.000 0.00 0.00 0.00 4.41
266 267 0.320683 CGTGGAGTTGTGGATGCTGA 60.321 55.000 0.00 0.00 0.00 4.26
267 268 1.446907 GTGGAGTTGTGGATGCTGAG 58.553 55.000 0.00 0.00 0.00 3.35
268 269 0.321919 TGGAGTTGTGGATGCTGAGC 60.322 55.000 0.00 0.00 0.00 4.26
269 270 0.321919 GGAGTTGTGGATGCTGAGCA 60.322 55.000 10.59 10.59 44.86 4.26
270 271 0.801251 GAGTTGTGGATGCTGAGCAC 59.199 55.000 10.33 3.67 43.04 4.40
271 272 0.109153 AGTTGTGGATGCTGAGCACA 59.891 50.000 10.33 0.28 43.04 4.57
272 273 1.171308 GTTGTGGATGCTGAGCACAT 58.829 50.000 10.33 0.00 43.04 3.21
273 274 1.135489 GTTGTGGATGCTGAGCACATG 60.135 52.381 10.33 0.00 43.04 3.21
274 275 0.037160 TGTGGATGCTGAGCACATGT 59.963 50.000 10.33 0.00 43.04 3.21
275 276 1.171308 GTGGATGCTGAGCACATGTT 58.829 50.000 10.33 0.00 43.04 2.71
276 277 1.542915 GTGGATGCTGAGCACATGTTT 59.457 47.619 10.33 0.00 43.04 2.83
277 278 2.029649 GTGGATGCTGAGCACATGTTTT 60.030 45.455 10.33 0.00 43.04 2.43
278 279 2.229543 TGGATGCTGAGCACATGTTTTC 59.770 45.455 10.33 0.54 43.04 2.29
279 280 2.416431 GGATGCTGAGCACATGTTTTCC 60.416 50.000 10.33 7.32 43.04 3.13
280 281 1.689984 TGCTGAGCACATGTTTTCCA 58.310 45.000 1.40 0.00 31.71 3.53
281 282 2.241160 TGCTGAGCACATGTTTTCCAT 58.759 42.857 1.40 0.00 31.71 3.41
282 283 2.629137 TGCTGAGCACATGTTTTCCATT 59.371 40.909 1.40 0.00 31.71 3.16
283 284 3.069872 TGCTGAGCACATGTTTTCCATTT 59.930 39.130 1.40 0.00 31.71 2.32
284 285 4.060205 GCTGAGCACATGTTTTCCATTTT 58.940 39.130 0.00 0.00 0.00 1.82
285 286 4.151157 GCTGAGCACATGTTTTCCATTTTC 59.849 41.667 0.00 0.00 0.00 2.29
286 287 5.273674 TGAGCACATGTTTTCCATTTTCA 57.726 34.783 0.00 0.00 0.00 2.69
287 288 5.856156 TGAGCACATGTTTTCCATTTTCAT 58.144 33.333 0.00 0.00 0.00 2.57
288 289 6.289834 TGAGCACATGTTTTCCATTTTCATT 58.710 32.000 0.00 0.00 0.00 2.57
289 290 6.424509 TGAGCACATGTTTTCCATTTTCATTC 59.575 34.615 0.00 0.00 0.00 2.67
290 291 6.289834 AGCACATGTTTTCCATTTTCATTCA 58.710 32.000 0.00 0.00 0.00 2.57
291 292 6.938030 AGCACATGTTTTCCATTTTCATTCAT 59.062 30.769 0.00 0.00 0.00 2.57
292 293 8.095792 AGCACATGTTTTCCATTTTCATTCATA 58.904 29.630 0.00 0.00 0.00 2.15
293 294 8.885722 GCACATGTTTTCCATTTTCATTCATAT 58.114 29.630 0.00 0.00 0.00 1.78
366 367 2.024918 CGATTTGGGATTCCTGGCG 58.975 57.895 2.01 0.00 0.00 5.69
468 469 7.852263 AGTTACTGCTGGAATGAATAGTTACT 58.148 34.615 0.00 0.00 0.00 2.24
469 470 7.982354 AGTTACTGCTGGAATGAATAGTTACTC 59.018 37.037 0.00 0.00 0.00 2.59
470 471 5.675538 ACTGCTGGAATGAATAGTTACTCC 58.324 41.667 0.00 0.00 0.00 3.85
485 487 3.818121 CTCCCGTTTCGTGCCACCA 62.818 63.158 0.00 0.00 0.00 4.17
487 489 2.590575 CCGTTTCGTGCCACCACT 60.591 61.111 0.00 0.00 39.86 4.00
490 492 2.970324 TTTCGTGCCACCACTCGC 60.970 61.111 0.00 0.00 39.86 5.03
505 507 2.824041 CGCAATTACGCTGCCCCT 60.824 61.111 0.00 0.00 36.40 4.79
509 511 3.400599 AATTACGCTGCCCCTCCGG 62.401 63.158 0.00 0.00 0.00 5.14
552 557 0.182775 CTGGGGTATAAAAGGCGGCT 59.817 55.000 5.25 5.25 0.00 5.52
958 1003 4.856801 GCCATGGCCGATGACCGT 62.857 66.667 27.24 0.00 33.31 4.83
1099 1146 2.021068 GCTCGATCTGTGCCAGCCTA 62.021 60.000 0.00 0.00 0.00 3.93
1148 1195 0.600782 GACGCCGGTGTTCCTTGTTA 60.601 55.000 23.85 0.00 0.00 2.41
1493 1552 1.826385 GGTCTATTGTGTGCAGGCTT 58.174 50.000 0.00 0.00 0.00 4.35
1577 1643 7.661847 CCTTAATTCCTGGATTATAGGTGTGTC 59.338 40.741 0.00 0.00 36.67 3.67
1857 1931 7.613551 ATTTAGTGATTATACCTCCTTCGGT 57.386 36.000 0.00 0.00 41.10 4.69
1911 1987 5.102953 TGCTACCTATTCAGTCAATGCTT 57.897 39.130 0.00 0.00 0.00 3.91
1979 2117 0.250727 CTCTCCTTCCGGCCACAAAA 60.251 55.000 2.24 0.00 0.00 2.44
2027 2165 5.435686 ACTAGATTATGTGTTCTGCCCAA 57.564 39.130 0.00 0.00 0.00 4.12
2097 2235 2.918712 AAGGTCAGTTCACCTCTGTG 57.081 50.000 0.00 0.00 46.97 3.66
2104 2242 3.135712 TCAGTTCACCTCTGTGGCTTTTA 59.864 43.478 0.00 0.00 42.98 1.52
2105 2243 4.074970 CAGTTCACCTCTGTGGCTTTTAT 58.925 43.478 0.00 0.00 42.98 1.40
2106 2244 4.520492 CAGTTCACCTCTGTGGCTTTTATT 59.480 41.667 0.00 0.00 42.98 1.40
2107 2245 4.520492 AGTTCACCTCTGTGGCTTTTATTG 59.480 41.667 0.00 0.00 42.98 1.90
2108 2246 4.098914 TCACCTCTGTGGCTTTTATTGT 57.901 40.909 0.00 0.00 42.98 2.71
2109 2247 4.469657 TCACCTCTGTGGCTTTTATTGTT 58.530 39.130 0.00 0.00 42.98 2.83
2110 2248 4.892934 TCACCTCTGTGGCTTTTATTGTTT 59.107 37.500 0.00 0.00 42.98 2.83
2111 2249 6.065374 TCACCTCTGTGGCTTTTATTGTTTA 58.935 36.000 0.00 0.00 42.98 2.01
2112 2250 6.547880 TCACCTCTGTGGCTTTTATTGTTTAA 59.452 34.615 0.00 0.00 42.98 1.52
2113 2251 7.232534 TCACCTCTGTGGCTTTTATTGTTTAAT 59.767 33.333 0.00 0.00 42.98 1.40
2114 2252 7.872483 CACCTCTGTGGCTTTTATTGTTTAATT 59.128 33.333 0.00 0.00 38.90 1.40
2115 2253 9.084533 ACCTCTGTGGCTTTTATTGTTTAATTA 57.915 29.630 0.00 0.00 40.22 1.40
2116 2254 9.573133 CCTCTGTGGCTTTTATTGTTTAATTAG 57.427 33.333 0.00 0.00 0.00 1.73
2119 2257 9.906660 CTGTGGCTTTTATTGTTTAATTAGTCA 57.093 29.630 0.00 0.00 0.00 3.41
2120 2258 9.906660 TGTGGCTTTTATTGTTTAATTAGTCAG 57.093 29.630 0.00 0.00 0.00 3.51
2121 2259 8.860128 GTGGCTTTTATTGTTTAATTAGTCAGC 58.140 33.333 0.00 0.00 0.00 4.26
2122 2260 8.580720 TGGCTTTTATTGTTTAATTAGTCAGCA 58.419 29.630 0.00 0.00 0.00 4.41
2123 2261 9.586435 GGCTTTTATTGTTTAATTAGTCAGCAT 57.414 29.630 0.00 0.00 0.00 3.79
2127 2265 8.909708 TTATTGTTTAATTAGTCAGCATGTGC 57.090 30.769 0.00 0.00 42.49 4.57
2128 2266 5.956068 TGTTTAATTAGTCAGCATGTGCA 57.044 34.783 7.83 0.00 45.16 4.57
2129 2267 5.941733 TGTTTAATTAGTCAGCATGTGCAG 58.058 37.500 7.83 0.00 45.16 4.41
2130 2268 5.106197 TGTTTAATTAGTCAGCATGTGCAGG 60.106 40.000 7.83 0.00 45.16 4.85
2131 2269 2.795231 ATTAGTCAGCATGTGCAGGT 57.205 45.000 7.83 0.00 45.16 4.00
2132 2270 2.566833 TTAGTCAGCATGTGCAGGTT 57.433 45.000 7.83 0.00 45.16 3.50
2133 2271 2.099141 TAGTCAGCATGTGCAGGTTC 57.901 50.000 7.83 0.00 45.16 3.62
2134 2272 0.109153 AGTCAGCATGTGCAGGTTCA 59.891 50.000 7.83 0.00 45.16 3.18
2274 2442 5.642919 TGATAAATTTTGCCCACAAGAATGC 59.357 36.000 0.00 0.00 37.04 3.56
2290 2458 8.902806 CACAAGAATGCCCTAACAAATCTTATA 58.097 33.333 0.00 0.00 32.03 0.98
2500 2668 5.534207 TTCAGCCTTGTTGATTTGAATGT 57.466 34.783 0.00 0.00 0.00 2.71
2501 2669 5.534207 TCAGCCTTGTTGATTTGAATGTT 57.466 34.783 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.318120 CAAAATCCAGCACCCACACC 59.682 55.000 0.00 0.00 0.00 4.16
2 3 0.469705 AGCAAAATCCAGCACCCACA 60.470 50.000 0.00 0.00 0.00 4.17
4 5 1.544724 GTAGCAAAATCCAGCACCCA 58.455 50.000 0.00 0.00 0.00 4.51
5 6 0.451783 CGTAGCAAAATCCAGCACCC 59.548 55.000 0.00 0.00 0.00 4.61
6 7 0.451783 CCGTAGCAAAATCCAGCACC 59.548 55.000 0.00 0.00 0.00 5.01
7 8 1.448985 TCCGTAGCAAAATCCAGCAC 58.551 50.000 0.00 0.00 0.00 4.40
8 9 2.016318 CATCCGTAGCAAAATCCAGCA 58.984 47.619 0.00 0.00 0.00 4.41
9 10 1.268743 GCATCCGTAGCAAAATCCAGC 60.269 52.381 0.00 0.00 0.00 4.85
10 11 2.016318 TGCATCCGTAGCAAAATCCAG 58.984 47.619 0.00 0.00 39.39 3.86
11 12 2.121291 TGCATCCGTAGCAAAATCCA 57.879 45.000 0.00 0.00 39.39 3.41
12 13 3.563808 TGTATGCATCCGTAGCAAAATCC 59.436 43.478 0.19 0.00 46.27 3.01
13 14 4.811555 TGTATGCATCCGTAGCAAAATC 57.188 40.909 0.19 0.00 46.27 2.17
14 15 5.762711 TGTATGTATGCATCCGTAGCAAAAT 59.237 36.000 0.19 0.00 46.27 1.82
15 16 5.119694 TGTATGTATGCATCCGTAGCAAAA 58.880 37.500 0.19 0.00 46.27 2.44
16 17 4.698575 TGTATGTATGCATCCGTAGCAAA 58.301 39.130 0.19 0.00 46.27 3.68
17 18 4.329462 TGTATGTATGCATCCGTAGCAA 57.671 40.909 0.19 0.00 46.27 3.91
19 20 5.407502 TGTATGTATGTATGCATCCGTAGC 58.592 41.667 0.19 0.00 36.58 3.58
20 21 6.476706 CCATGTATGTATGTATGCATCCGTAG 59.523 42.308 0.19 0.00 36.58 3.51
21 22 6.337356 CCATGTATGTATGTATGCATCCGTA 58.663 40.000 0.19 0.00 36.58 4.02
22 23 5.178061 CCATGTATGTATGTATGCATCCGT 58.822 41.667 0.19 0.00 36.58 4.69
23 24 4.571984 CCCATGTATGTATGTATGCATCCG 59.428 45.833 0.19 0.00 36.58 4.18
24 25 4.336433 GCCCATGTATGTATGTATGCATCC 59.664 45.833 0.19 0.00 36.58 3.51
25 26 5.065602 CAGCCCATGTATGTATGTATGCATC 59.934 44.000 0.19 0.00 36.58 3.91
26 27 4.945543 CAGCCCATGTATGTATGTATGCAT 59.054 41.667 3.79 3.79 39.03 3.96
27 28 4.041444 TCAGCCCATGTATGTATGTATGCA 59.959 41.667 0.00 0.00 0.00 3.96
28 29 4.578871 TCAGCCCATGTATGTATGTATGC 58.421 43.478 0.00 0.00 0.00 3.14
29 30 6.403964 GCATTCAGCCCATGTATGTATGTATG 60.404 42.308 0.00 0.00 38.55 2.39
30 31 5.649395 GCATTCAGCCCATGTATGTATGTAT 59.351 40.000 0.00 0.00 38.55 2.29
31 32 5.003160 GCATTCAGCCCATGTATGTATGTA 58.997 41.667 0.00 0.00 38.55 2.29
32 33 3.822735 GCATTCAGCCCATGTATGTATGT 59.177 43.478 0.00 0.00 38.55 2.29
33 34 4.430137 GCATTCAGCCCATGTATGTATG 57.570 45.455 0.00 0.00 38.55 2.39
46 47 1.065928 GCTGATGCAGGCATTCAGC 59.934 57.895 26.83 26.83 43.17 4.26
47 48 1.963172 TAGCTGATGCAGGCATTCAG 58.037 50.000 19.96 19.96 42.74 3.02
48 49 2.651382 ATAGCTGATGCAGGCATTCA 57.349 45.000 8.34 7.12 42.74 2.57
49 50 2.882761 TGAATAGCTGATGCAGGCATTC 59.117 45.455 8.34 14.57 42.74 2.67
50 51 2.940158 TGAATAGCTGATGCAGGCATT 58.060 42.857 8.34 8.37 42.74 3.56
51 52 2.651382 TGAATAGCTGATGCAGGCAT 57.349 45.000 6.44 6.44 42.74 4.40
52 53 2.423446 TTGAATAGCTGATGCAGGCA 57.577 45.000 0.00 0.00 42.74 4.75
53 54 4.296690 GAATTTGAATAGCTGATGCAGGC 58.703 43.478 0.00 0.00 42.74 4.85
54 55 4.036027 ACGAATTTGAATAGCTGATGCAGG 59.964 41.667 0.00 0.00 42.74 4.85
55 56 4.968181 CACGAATTTGAATAGCTGATGCAG 59.032 41.667 0.00 0.00 42.74 4.41
56 57 4.395854 ACACGAATTTGAATAGCTGATGCA 59.604 37.500 0.00 0.00 42.74 3.96
57 58 4.913376 ACACGAATTTGAATAGCTGATGC 58.087 39.130 0.00 0.00 40.05 3.91
58 59 7.246311 AGAAACACGAATTTGAATAGCTGATG 58.754 34.615 0.00 0.00 0.00 3.07
59 60 7.119699 TGAGAAACACGAATTTGAATAGCTGAT 59.880 33.333 0.00 0.00 0.00 2.90
60 61 6.426633 TGAGAAACACGAATTTGAATAGCTGA 59.573 34.615 0.00 0.00 0.00 4.26
61 62 6.602179 TGAGAAACACGAATTTGAATAGCTG 58.398 36.000 0.00 0.00 0.00 4.24
62 63 6.801539 TGAGAAACACGAATTTGAATAGCT 57.198 33.333 0.00 0.00 0.00 3.32
63 64 7.851822 TTTGAGAAACACGAATTTGAATAGC 57.148 32.000 0.00 0.00 0.00 2.97
93 94 3.004002 GGGAACGGACGAACTTGATTTTT 59.996 43.478 0.00 0.00 0.00 1.94
94 95 2.551032 GGGAACGGACGAACTTGATTTT 59.449 45.455 0.00 0.00 0.00 1.82
95 96 2.148768 GGGAACGGACGAACTTGATTT 58.851 47.619 0.00 0.00 0.00 2.17
96 97 1.346722 AGGGAACGGACGAACTTGATT 59.653 47.619 0.00 0.00 0.00 2.57
97 98 0.974383 AGGGAACGGACGAACTTGAT 59.026 50.000 0.00 0.00 0.00 2.57
98 99 0.754472 AAGGGAACGGACGAACTTGA 59.246 50.000 0.00 0.00 0.00 3.02
99 100 1.589803 AAAGGGAACGGACGAACTTG 58.410 50.000 0.00 0.00 0.00 3.16
100 101 2.336945 AAAAGGGAACGGACGAACTT 57.663 45.000 0.00 0.00 0.00 2.66
101 102 3.473923 TTAAAAGGGAACGGACGAACT 57.526 42.857 0.00 0.00 0.00 3.01
102 103 4.550577 TTTTAAAAGGGAACGGACGAAC 57.449 40.909 0.00 0.00 0.00 3.95
126 127 3.560481 GCACTCACATGATCCTGATCTTG 59.440 47.826 16.96 16.96 44.10 3.02
127 128 3.740452 CGCACTCACATGATCCTGATCTT 60.740 47.826 0.00 0.00 38.60 2.40
128 129 2.223994 CGCACTCACATGATCCTGATCT 60.224 50.000 0.00 0.00 38.60 2.75
129 130 2.133553 CGCACTCACATGATCCTGATC 58.866 52.381 0.00 0.06 38.29 2.92
130 131 1.483827 ACGCACTCACATGATCCTGAT 59.516 47.619 0.00 0.00 0.00 2.90
131 132 0.897621 ACGCACTCACATGATCCTGA 59.102 50.000 0.00 0.00 0.00 3.86
132 133 1.004595 CACGCACTCACATGATCCTG 58.995 55.000 0.00 0.00 0.00 3.86
133 134 0.610174 ACACGCACTCACATGATCCT 59.390 50.000 0.00 0.00 0.00 3.24
134 135 2.293677 TACACGCACTCACATGATCC 57.706 50.000 0.00 0.00 0.00 3.36
135 136 3.243877 GTGATACACGCACTCACATGATC 59.756 47.826 0.00 0.00 39.24 2.92
136 137 3.118992 AGTGATACACGCACTCACATGAT 60.119 43.478 0.00 0.00 42.62 2.45
137 138 2.231235 AGTGATACACGCACTCACATGA 59.769 45.455 0.00 0.00 42.62 3.07
138 139 2.346545 CAGTGATACACGCACTCACATG 59.653 50.000 9.67 0.00 44.28 3.21
139 140 2.610433 CAGTGATACACGCACTCACAT 58.390 47.619 9.67 0.00 44.28 3.21
140 141 1.336795 CCAGTGATACACGCACTCACA 60.337 52.381 9.67 0.00 44.28 3.58
141 142 1.067846 TCCAGTGATACACGCACTCAC 60.068 52.381 0.00 0.00 44.28 3.51
142 143 1.253100 TCCAGTGATACACGCACTCA 58.747 50.000 0.00 0.00 44.28 3.41
143 144 2.586258 ATCCAGTGATACACGCACTC 57.414 50.000 0.00 0.00 44.28 3.51
144 145 2.621338 CAATCCAGTGATACACGCACT 58.379 47.619 0.00 0.00 46.86 4.40
145 146 1.665679 CCAATCCAGTGATACACGCAC 59.334 52.381 0.00 0.00 39.64 5.34
146 147 1.552792 TCCAATCCAGTGATACACGCA 59.447 47.619 0.00 0.00 39.64 5.24
147 148 2.309528 TCCAATCCAGTGATACACGC 57.690 50.000 0.00 0.00 39.64 5.34
148 149 4.389992 GCATATCCAATCCAGTGATACACG 59.610 45.833 0.00 0.00 39.64 4.49
149 150 5.555017 AGCATATCCAATCCAGTGATACAC 58.445 41.667 0.00 0.00 34.10 2.90
150 151 5.545335 AGAGCATATCCAATCCAGTGATACA 59.455 40.000 0.00 0.00 0.00 2.29
151 152 6.047511 AGAGCATATCCAATCCAGTGATAC 57.952 41.667 0.00 0.00 0.00 2.24
152 153 6.043590 ACAAGAGCATATCCAATCCAGTGATA 59.956 38.462 0.00 0.00 0.00 2.15
153 154 5.163120 ACAAGAGCATATCCAATCCAGTGAT 60.163 40.000 0.00 0.00 0.00 3.06
154 155 4.164796 ACAAGAGCATATCCAATCCAGTGA 59.835 41.667 0.00 0.00 0.00 3.41
155 156 4.275196 CACAAGAGCATATCCAATCCAGTG 59.725 45.833 0.00 0.00 0.00 3.66
156 157 4.164796 TCACAAGAGCATATCCAATCCAGT 59.835 41.667 0.00 0.00 0.00 4.00
157 158 4.514441 GTCACAAGAGCATATCCAATCCAG 59.486 45.833 0.00 0.00 0.00 3.86
158 159 4.454678 GTCACAAGAGCATATCCAATCCA 58.545 43.478 0.00 0.00 0.00 3.41
159 160 3.496130 CGTCACAAGAGCATATCCAATCC 59.504 47.826 0.00 0.00 0.00 3.01
160 161 4.122776 ACGTCACAAGAGCATATCCAATC 58.877 43.478 0.00 0.00 0.00 2.67
161 162 4.122776 GACGTCACAAGAGCATATCCAAT 58.877 43.478 11.55 0.00 0.00 3.16
162 163 3.521560 GACGTCACAAGAGCATATCCAA 58.478 45.455 11.55 0.00 0.00 3.53
163 164 2.159099 GGACGTCACAAGAGCATATCCA 60.159 50.000 18.91 0.00 0.00 3.41
164 165 2.159099 TGGACGTCACAAGAGCATATCC 60.159 50.000 18.91 0.00 0.00 2.59
165 166 3.119291 CTGGACGTCACAAGAGCATATC 58.881 50.000 18.91 0.00 0.00 1.63
166 167 2.497675 ACTGGACGTCACAAGAGCATAT 59.502 45.455 18.91 0.00 0.00 1.78
167 168 1.893137 ACTGGACGTCACAAGAGCATA 59.107 47.619 18.91 0.00 0.00 3.14
168 169 0.681733 ACTGGACGTCACAAGAGCAT 59.318 50.000 18.91 0.00 0.00 3.79
169 170 0.032130 GACTGGACGTCACAAGAGCA 59.968 55.000 18.91 2.99 42.37 4.26
170 171 1.004277 CGACTGGACGTCACAAGAGC 61.004 60.000 18.91 8.34 42.98 4.09
171 172 0.591659 TCGACTGGACGTCACAAGAG 59.408 55.000 18.91 10.81 42.98 2.85
172 173 1.199327 GATCGACTGGACGTCACAAGA 59.801 52.381 18.91 9.90 42.98 3.02
173 174 1.618861 GATCGACTGGACGTCACAAG 58.381 55.000 18.91 13.61 42.98 3.16
174 175 0.109919 CGATCGACTGGACGTCACAA 60.110 55.000 18.91 1.00 42.98 3.33
175 176 1.232621 ACGATCGACTGGACGTCACA 61.233 55.000 24.34 11.87 42.98 3.58
176 177 0.793478 CACGATCGACTGGACGTCAC 60.793 60.000 24.34 7.49 42.98 3.67
177 178 1.232621 ACACGATCGACTGGACGTCA 61.233 55.000 24.34 2.63 42.98 4.35
178 179 0.109873 AACACGATCGACTGGACGTC 60.110 55.000 24.34 7.13 36.86 4.34
179 180 0.386858 CAACACGATCGACTGGACGT 60.387 55.000 24.34 3.95 39.53 4.34
180 181 1.071019 CCAACACGATCGACTGGACG 61.071 60.000 24.34 3.48 0.00 4.79
181 182 0.038526 ACCAACACGATCGACTGGAC 60.039 55.000 28.74 0.00 0.00 4.02
182 183 0.677288 AACCAACACGATCGACTGGA 59.323 50.000 28.74 0.00 0.00 3.86
183 184 1.194547 CAAACCAACACGATCGACTGG 59.805 52.381 24.34 23.95 0.00 4.00
184 185 2.096909 GTCAAACCAACACGATCGACTG 60.097 50.000 24.34 13.35 0.00 3.51
185 186 2.132762 GTCAAACCAACACGATCGACT 58.867 47.619 24.34 2.40 0.00 4.18
186 187 1.136721 CGTCAAACCAACACGATCGAC 60.137 52.381 24.34 4.07 35.49 4.20
187 188 1.133407 CGTCAAACCAACACGATCGA 58.867 50.000 24.34 0.00 35.49 3.59
188 189 0.856641 ACGTCAAACCAACACGATCG 59.143 50.000 14.88 14.88 37.00 3.69
189 190 2.031191 ACAACGTCAAACCAACACGATC 59.969 45.455 0.00 0.00 37.00 3.69
190 191 2.011222 ACAACGTCAAACCAACACGAT 58.989 42.857 0.00 0.00 37.00 3.73
191 192 1.440708 ACAACGTCAAACCAACACGA 58.559 45.000 0.00 0.00 37.00 4.35
192 193 2.696255 GTACAACGTCAAACCAACACG 58.304 47.619 0.00 0.00 39.48 4.49
193 194 2.696255 CGTACAACGTCAAACCAACAC 58.304 47.619 0.00 0.00 36.74 3.32
205 206 4.908966 GCACATCCATGCACGTACAACG 62.909 54.545 0.00 0.00 45.39 4.10
206 207 1.465689 GCACATCCATGCACGTACAAC 60.466 52.381 0.00 0.00 45.39 3.32
207 208 0.801872 GCACATCCATGCACGTACAA 59.198 50.000 0.00 0.00 45.39 2.41
208 209 1.357991 CGCACATCCATGCACGTACA 61.358 55.000 0.00 0.00 46.47 2.90
209 210 1.081556 TCGCACATCCATGCACGTAC 61.082 55.000 0.00 0.00 46.47 3.67
210 211 0.805711 CTCGCACATCCATGCACGTA 60.806 55.000 0.00 0.00 46.47 3.57
211 212 2.047370 TCGCACATCCATGCACGT 60.047 55.556 0.00 0.00 46.47 4.49
212 213 2.705220 CTCGCACATCCATGCACG 59.295 61.111 0.00 0.00 46.47 5.34
213 214 0.816825 ATCCTCGCACATCCATGCAC 60.817 55.000 0.00 0.00 46.47 4.57
214 215 0.758123 TATCCTCGCACATCCATGCA 59.242 50.000 0.00 0.00 46.47 3.96
215 216 1.882912 TTATCCTCGCACATCCATGC 58.117 50.000 0.00 0.00 42.48 4.06
216 217 4.093998 GCTTATTATCCTCGCACATCCATG 59.906 45.833 0.00 0.00 0.00 3.66
217 218 4.256920 GCTTATTATCCTCGCACATCCAT 58.743 43.478 0.00 0.00 0.00 3.41
218 219 3.070878 TGCTTATTATCCTCGCACATCCA 59.929 43.478 0.00 0.00 0.00 3.41
219 220 3.664107 TGCTTATTATCCTCGCACATCC 58.336 45.455 0.00 0.00 0.00 3.51
220 221 4.377841 GCTTGCTTATTATCCTCGCACATC 60.378 45.833 0.00 0.00 0.00 3.06
221 222 3.499918 GCTTGCTTATTATCCTCGCACAT 59.500 43.478 0.00 0.00 0.00 3.21
222 223 2.872245 GCTTGCTTATTATCCTCGCACA 59.128 45.455 0.00 0.00 0.00 4.57
223 224 2.872245 TGCTTGCTTATTATCCTCGCAC 59.128 45.455 0.00 0.00 0.00 5.34
224 225 2.872245 GTGCTTGCTTATTATCCTCGCA 59.128 45.455 0.00 0.00 0.00 5.10
225 226 3.134458 AGTGCTTGCTTATTATCCTCGC 58.866 45.455 0.00 0.00 0.00 5.03
226 227 3.426859 CGAGTGCTTGCTTATTATCCTCG 59.573 47.826 0.00 0.00 34.22 4.63
227 228 4.210120 CACGAGTGCTTGCTTATTATCCTC 59.790 45.833 0.00 0.00 0.00 3.71
228 229 4.122776 CACGAGTGCTTGCTTATTATCCT 58.877 43.478 0.00 0.00 0.00 3.24
229 230 3.248602 CCACGAGTGCTTGCTTATTATCC 59.751 47.826 0.00 0.00 0.00 2.59
230 231 4.119862 TCCACGAGTGCTTGCTTATTATC 58.880 43.478 0.00 0.00 0.00 1.75
231 232 4.122776 CTCCACGAGTGCTTGCTTATTAT 58.877 43.478 0.00 0.00 0.00 1.28
232 233 3.056107 ACTCCACGAGTGCTTGCTTATTA 60.056 43.478 0.00 0.00 41.76 0.98
233 234 2.289694 ACTCCACGAGTGCTTGCTTATT 60.290 45.455 0.00 0.00 41.76 1.40
234 235 1.276421 ACTCCACGAGTGCTTGCTTAT 59.724 47.619 0.00 0.00 41.76 1.73
235 236 0.679505 ACTCCACGAGTGCTTGCTTA 59.320 50.000 0.00 0.00 41.76 3.09
236 237 0.179045 AACTCCACGAGTGCTTGCTT 60.179 50.000 0.00 0.00 42.59 3.91
237 238 0.882042 CAACTCCACGAGTGCTTGCT 60.882 55.000 0.00 0.00 42.59 3.91
238 239 1.160329 ACAACTCCACGAGTGCTTGC 61.160 55.000 0.00 0.00 42.59 4.01
239 240 0.583438 CACAACTCCACGAGTGCTTG 59.417 55.000 0.00 2.16 42.59 4.01
240 241 0.532862 CCACAACTCCACGAGTGCTT 60.533 55.000 0.00 0.00 42.59 3.91
241 242 1.069765 CCACAACTCCACGAGTGCT 59.930 57.895 0.00 0.00 42.59 4.40
242 243 0.320771 ATCCACAACTCCACGAGTGC 60.321 55.000 0.00 0.00 42.59 4.40
243 244 1.432514 CATCCACAACTCCACGAGTG 58.567 55.000 0.00 0.00 42.59 3.51
244 245 0.320771 GCATCCACAACTCCACGAGT 60.321 55.000 0.00 0.00 45.64 4.18
245 246 0.036952 AGCATCCACAACTCCACGAG 60.037 55.000 0.00 0.00 35.52 4.18
246 247 0.320683 CAGCATCCACAACTCCACGA 60.321 55.000 0.00 0.00 0.00 4.35
247 248 0.320683 TCAGCATCCACAACTCCACG 60.321 55.000 0.00 0.00 0.00 4.94
248 249 1.446907 CTCAGCATCCACAACTCCAC 58.553 55.000 0.00 0.00 0.00 4.02
249 250 0.321919 GCTCAGCATCCACAACTCCA 60.322 55.000 0.00 0.00 0.00 3.86
250 251 0.321919 TGCTCAGCATCCACAACTCC 60.322 55.000 0.00 0.00 31.71 3.85
251 252 0.801251 GTGCTCAGCATCCACAACTC 59.199 55.000 0.54 0.00 41.91 3.01
252 253 0.109153 TGTGCTCAGCATCCACAACT 59.891 50.000 0.54 0.00 41.91 3.16
253 254 1.135489 CATGTGCTCAGCATCCACAAC 60.135 52.381 0.54 0.00 42.10 3.32
254 255 1.170442 CATGTGCTCAGCATCCACAA 58.830 50.000 0.54 0.00 42.10 3.33
255 256 0.037160 ACATGTGCTCAGCATCCACA 59.963 50.000 0.54 0.00 41.91 4.17
256 257 1.171308 AACATGTGCTCAGCATCCAC 58.829 50.000 0.54 0.00 41.91 4.02
257 258 1.913778 AAACATGTGCTCAGCATCCA 58.086 45.000 0.54 0.00 41.91 3.41
258 259 2.416431 GGAAAACATGTGCTCAGCATCC 60.416 50.000 0.54 0.00 41.91 3.51
259 260 2.229543 TGGAAAACATGTGCTCAGCATC 59.770 45.455 0.54 0.00 41.91 3.91
260 261 2.241160 TGGAAAACATGTGCTCAGCAT 58.759 42.857 0.54 0.00 41.91 3.79
261 262 1.689984 TGGAAAACATGTGCTCAGCA 58.310 45.000 0.00 0.00 35.60 4.41
262 263 3.308438 AATGGAAAACATGTGCTCAGC 57.692 42.857 0.00 0.00 40.44 4.26
263 264 5.291178 TGAAAATGGAAAACATGTGCTCAG 58.709 37.500 0.00 0.00 40.44 3.35
264 265 5.273674 TGAAAATGGAAAACATGTGCTCA 57.726 34.783 0.00 0.00 40.44 4.26
265 266 6.424509 TGAATGAAAATGGAAAACATGTGCTC 59.575 34.615 0.00 0.00 40.44 4.26
266 267 6.289834 TGAATGAAAATGGAAAACATGTGCT 58.710 32.000 0.00 0.00 40.44 4.40
267 268 6.542574 TGAATGAAAATGGAAAACATGTGC 57.457 33.333 0.00 0.00 40.44 4.57
306 307 9.386122 AGGAGCTTCTATTCTTATTTCTGGATA 57.614 33.333 0.00 0.00 0.00 2.59
346 347 1.738346 GCCAGGAATCCCAAATCGCC 61.738 60.000 0.00 0.00 33.88 5.54
366 367 0.036388 TCAAGCAACCAGATCCGACC 60.036 55.000 0.00 0.00 0.00 4.79
468 469 3.862991 TGGTGGCACGAAACGGGA 61.863 61.111 12.17 0.00 28.17 5.14
469 470 3.656045 GTGGTGGCACGAAACGGG 61.656 66.667 12.17 0.00 0.00 5.28
470 471 2.590575 AGTGGTGGCACGAAACGG 60.591 61.111 12.17 0.00 0.00 4.44
485 487 2.106683 GGGCAGCGTAATTGCGAGT 61.107 57.895 20.50 2.66 42.42 4.18
487 489 2.822255 GGGGCAGCGTAATTGCGA 60.822 61.111 20.50 0.00 42.42 5.10
490 492 2.180204 CGGAGGGGCAGCGTAATTG 61.180 63.158 0.00 0.00 0.00 2.32
505 507 2.045731 GACGAAAATGCCCCCGGA 60.046 61.111 0.73 0.00 0.00 5.14
509 511 1.731709 GCAAAATGACGAAAATGCCCC 59.268 47.619 0.00 0.00 0.00 5.80
552 557 2.030862 GGTTTCACCACGGGCGTA 59.969 61.111 0.00 0.00 38.42 4.42
1148 1195 2.433491 TAGCGCAACGACGGCAAT 60.433 55.556 11.47 0.00 0.00 3.56
1577 1643 3.492102 TCCAGACAAGGAACAAGAAGG 57.508 47.619 0.00 0.00 33.93 3.46
1621 1690 3.855379 CCAGAATCATGTGCAAATGAACG 59.145 43.478 23.17 11.44 39.90 3.95
1911 1987 5.681179 GCCCAAAGAAACTAAAACTGAGCAA 60.681 40.000 0.00 0.00 0.00 3.91
1979 2117 5.298777 CGGTATAACACTGACTAAGCCTAGT 59.701 44.000 0.00 0.00 41.28 2.57
2027 2165 4.759782 AGAAGCACAGATAAATACGCTGT 58.240 39.130 0.00 0.00 43.16 4.40
2097 2235 8.980143 TGCTGACTAATTAAACAATAAAAGCC 57.020 30.769 0.00 0.00 0.00 4.35
2104 2242 6.923012 TGCACATGCTGACTAATTAAACAAT 58.077 32.000 5.31 0.00 42.66 2.71
2105 2243 6.324561 TGCACATGCTGACTAATTAAACAA 57.675 33.333 5.31 0.00 42.66 2.83
2106 2244 5.106197 CCTGCACATGCTGACTAATTAAACA 60.106 40.000 11.87 0.00 41.71 2.83
2107 2245 5.106157 ACCTGCACATGCTGACTAATTAAAC 60.106 40.000 11.87 0.00 41.71 2.01
2108 2246 5.009631 ACCTGCACATGCTGACTAATTAAA 58.990 37.500 11.87 0.00 41.71 1.52
2109 2247 4.588899 ACCTGCACATGCTGACTAATTAA 58.411 39.130 11.87 0.00 41.71 1.40
2110 2248 4.220693 ACCTGCACATGCTGACTAATTA 57.779 40.909 11.87 0.00 41.71 1.40
2111 2249 3.077484 ACCTGCACATGCTGACTAATT 57.923 42.857 11.87 0.00 41.71 1.40
2112 2250 2.795231 ACCTGCACATGCTGACTAAT 57.205 45.000 11.87 0.00 41.71 1.73
2113 2251 2.224499 TGAACCTGCACATGCTGACTAA 60.224 45.455 11.87 0.00 41.71 2.24
2114 2252 1.347378 TGAACCTGCACATGCTGACTA 59.653 47.619 11.87 0.00 41.71 2.59
2115 2253 0.109153 TGAACCTGCACATGCTGACT 59.891 50.000 11.87 0.00 41.71 3.41
2116 2254 1.171308 ATGAACCTGCACATGCTGAC 58.829 50.000 11.87 4.55 41.71 3.51
2117 2255 2.785540 TATGAACCTGCACATGCTGA 57.214 45.000 11.87 0.00 41.71 4.26
2118 2256 3.058432 GCTATATGAACCTGCACATGCTG 60.058 47.826 5.31 4.56 42.66 4.41
2119 2257 3.144506 GCTATATGAACCTGCACATGCT 58.855 45.455 5.31 0.00 42.66 3.79
2120 2258 2.880268 TGCTATATGAACCTGCACATGC 59.120 45.455 0.00 0.00 42.50 4.06
2121 2259 4.132336 ACTGCTATATGAACCTGCACATG 58.868 43.478 0.00 0.00 0.00 3.21
2122 2260 4.428294 ACTGCTATATGAACCTGCACAT 57.572 40.909 0.00 0.00 0.00 3.21
2123 2261 3.912496 ACTGCTATATGAACCTGCACA 57.088 42.857 0.00 0.00 0.00 4.57
2124 2262 4.508124 GTGTACTGCTATATGAACCTGCAC 59.492 45.833 0.00 0.00 0.00 4.57
2125 2263 4.161377 TGTGTACTGCTATATGAACCTGCA 59.839 41.667 0.00 0.00 0.00 4.41
2126 2264 4.693283 TGTGTACTGCTATATGAACCTGC 58.307 43.478 0.00 0.00 0.00 4.85
2127 2265 6.201615 CACATGTGTACTGCTATATGAACCTG 59.798 42.308 18.03 0.00 0.00 4.00
2128 2266 6.127054 ACACATGTGTACTGCTATATGAACCT 60.127 38.462 29.66 0.00 42.90 3.50
2129 2267 6.018751 CACACATGTGTACTGCTATATGAACC 60.019 42.308 30.11 0.00 42.83 3.62
2130 2268 6.756542 TCACACATGTGTACTGCTATATGAAC 59.243 38.462 30.11 0.00 45.76 3.18
2131 2269 6.872920 TCACACATGTGTACTGCTATATGAA 58.127 36.000 30.11 3.19 45.76 2.57
2132 2270 6.463995 TCACACATGTGTACTGCTATATGA 57.536 37.500 30.11 16.31 45.76 2.15
2133 2271 7.719778 ATTCACACATGTGTACTGCTATATG 57.280 36.000 30.11 14.30 45.76 1.78
2134 2272 8.860088 TCTATTCACACATGTGTACTGCTATAT 58.140 33.333 30.11 15.68 45.76 0.86
2195 2363 5.646360 GCTTGTAGTGCCTAAGGTAAAATCA 59.354 40.000 0.00 0.00 0.00 2.57
2290 2458 5.648572 GCTCTCTTTTAGCTGCAATCAAAT 58.351 37.500 1.02 0.00 37.01 2.32


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

AutoCloner maintained by Alex Coulton.