Multiple sequence alignment - TraesCS2D01G287900

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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 TraesCS2D01G287900 chr2D 100.000 3369 0 0 1 3369 368527209 368523841 0.000000e+00 6222.0
1 TraesCS2D01G287900 chr2D 97.407 270 6 1 142 411 535240300 535240032 3.060000e-125 459.0
2 TraesCS2D01G287900 chr2D 93.985 266 15 1 146 411 8321028 8321292 5.240000e-108 401.0
3 TraesCS2D01G287900 chr2B 92.335 2270 99 28 409 2623 437383539 437381290 0.000000e+00 3158.0
4 TraesCS2D01G287900 chr2B 86.247 778 36 30 2608 3357 437381273 437380539 0.000000e+00 778.0
5 TraesCS2D01G287900 chr2B 84.746 59 9 0 1094 1152 438458659 438458717 3.630000e-05 60.2
6 TraesCS2D01G287900 chr2A 90.630 2316 139 34 410 2671 498842454 498840163 0.000000e+00 3003.0
7 TraesCS2D01G287900 chr2A 88.714 700 28 26 2696 3357 498839794 498839108 0.000000e+00 808.0
8 TraesCS2D01G287900 chr2A 96.642 268 9 0 150 417 578488816 578489083 2.380000e-121 446.0
9 TraesCS2D01G287900 chr2A 89.610 231 24 0 1658 1888 188903341 188903111 9.140000e-76 294.0
10 TraesCS2D01G287900 chr2A 84.746 59 9 0 1094 1152 499578770 499578828 3.630000e-05 60.2
11 TraesCS2D01G287900 chr6D 97.710 262 5 1 151 412 444470974 444471234 1.840000e-122 449.0
12 TraesCS2D01G287900 chrUn 96.565 262 8 1 151 412 29714776 29715036 1.860000e-117 433.0
13 TraesCS2D01G287900 chrUn 94.245 139 8 0 2030 2168 77418652 77418790 2.630000e-51 213.0
14 TraesCS2D01G287900 chr5A 93.548 279 17 1 140 418 281122365 281122088 6.730000e-112 414.0
15 TraesCS2D01G287900 chr7A 94.656 262 14 0 151 412 435003837 435004098 1.130000e-109 407.0
16 TraesCS2D01G287900 chr7A 92.806 139 10 0 2030 2168 577614474 577614612 5.700000e-48 202.0
17 TraesCS2D01G287900 chr7A 92.086 139 11 0 2030 2168 49367113 49366975 2.650000e-46 196.0
18 TraesCS2D01G287900 chr7A 93.069 101 6 1 1694 1794 13394019 13394118 2.710000e-31 147.0
19 TraesCS2D01G287900 chr5D 94.275 262 15 0 150 411 529785019 529784758 5.240000e-108 401.0
20 TraesCS2D01G287900 chr5D 89.030 237 24 2 1671 1906 28994477 28994712 3.290000e-75 292.0
21 TraesCS2D01G287900 chr5D 91.579 95 8 0 2030 2124 28994709 28994803 7.580000e-27 132.0
22 TraesCS2D01G287900 chr3A 93.962 265 16 0 150 414 47377689 47377425 5.240000e-108 401.0
23 TraesCS2D01G287900 chr1A 89.610 231 24 0 1658 1888 464086768 464086538 9.140000e-76 294.0
24 TraesCS2D01G287900 chr1A 93.525 139 9 0 2030 2168 474165753 474165891 1.230000e-49 207.0
25 TraesCS2D01G287900 chr4B 88.745 231 24 1 1658 1888 211498271 211498499 7.120000e-72 281.0
26 TraesCS2D01G287900 chr4B 88.525 122 14 0 1780 1901 414711337 414711216 7.530000e-32 148.0
27 TraesCS2D01G287900 chr6A 86.916 214 17 3 1685 1897 602928514 602928311 2.610000e-56 230.0
28 TraesCS2D01G287900 chr6A 85.507 138 19 1 1658 1795 617204830 617204694 3.500000e-30 143.0
29 TraesCS2D01G287900 chr3B 85.135 222 22 3 1679 1900 749767736 749767946 2.040000e-52 217.0
30 TraesCS2D01G287900 chr6B 92.806 139 10 0 2030 2168 574503331 574503469 5.700000e-48 202.0
31 TraesCS2D01G287900 chr6B 87.805 123 15 0 1780 1902 22888114 22888236 9.740000e-31 145.0
32 TraesCS2D01G287900 chr1B 85.484 124 16 2 1780 1902 72992580 72992702 9.810000e-26 128.0
33 TraesCS2D01G287900 chr4A 82.407 108 12 5 2043 2145 626700132 626700237 1.670000e-13 87.9


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 TraesCS2D01G287900 chr2D 368523841 368527209 3368 True 6222.0 6222 100.000 1 3369 1 chr2D.!!$R1 3368
1 TraesCS2D01G287900 chr2B 437380539 437383539 3000 True 1968.0 3158 89.291 409 3357 2 chr2B.!!$R1 2948
2 TraesCS2D01G287900 chr2A 498839108 498842454 3346 True 1905.5 3003 89.672 410 3357 2 chr2A.!!$R2 2947

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
63 64 0.178995 TGCCTGCTTGATGAACCACA 60.179 50.0 0.00 0.00 0.00 4.17 F
64 65 0.242017 GCCTGCTTGATGAACCACAC 59.758 55.0 0.00 0.00 0.00 3.82 F
77 78 0.250727 ACCACACAAAGCCACGCTAT 60.251 50.0 0.00 0.00 38.25 2.97 F
1585 1674 0.712222 GTCGGTTTGTCGATCGGTTC 59.288 55.0 16.41 7.07 41.40 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1639 0.640768 CGACTCCAATCGCGAAGAAC 59.359 55.000 15.24 6.88 34.90 3.01 R
1585 1674 0.731417 AGTGAGATACCGTTCGACCG 59.269 55.000 0.00 0.00 0.00 4.79 R
1685 1775 2.047274 GCGCTCCACAGTAGCCAA 60.047 61.111 0.00 0.00 36.60 4.52 R
2512 2605 0.025898 CACGCATCGAGCAATCACAG 59.974 55.000 7.47 0.00 46.13 3.66 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
30 31 8.641499 AAAAATCTAGTTGAAATTTGCGTGAA 57.359 26.923 0.00 0.00 0.00 3.18
31 32 8.816640 AAAATCTAGTTGAAATTTGCGTGAAT 57.183 26.923 0.00 0.00 0.00 2.57
32 33 9.906660 AAAATCTAGTTGAAATTTGCGTGAATA 57.093 25.926 0.00 0.00 0.00 1.75
33 34 9.906660 AAATCTAGTTGAAATTTGCGTGAATAA 57.093 25.926 0.00 0.00 0.00 1.40
34 35 8.895932 ATCTAGTTGAAATTTGCGTGAATAAC 57.104 30.769 0.00 0.00 0.00 1.89
35 36 7.866729 TCTAGTTGAAATTTGCGTGAATAACA 58.133 30.769 0.00 0.00 0.00 2.41
36 37 6.747659 AGTTGAAATTTGCGTGAATAACAC 57.252 33.333 0.00 0.00 45.11 3.32
54 55 4.329545 GTCCCCGTGCCTGCTTGA 62.330 66.667 0.00 0.00 0.00 3.02
55 56 3.329889 TCCCCGTGCCTGCTTGAT 61.330 61.111 0.00 0.00 0.00 2.57
56 57 3.136123 CCCCGTGCCTGCTTGATG 61.136 66.667 0.00 0.00 0.00 3.07
57 58 2.046023 CCCGTGCCTGCTTGATGA 60.046 61.111 0.00 0.00 0.00 2.92
58 59 1.675310 CCCGTGCCTGCTTGATGAA 60.675 57.895 0.00 0.00 0.00 2.57
59 60 1.503542 CCGTGCCTGCTTGATGAAC 59.496 57.895 0.00 0.00 0.00 3.18
60 61 1.503542 CGTGCCTGCTTGATGAACC 59.496 57.895 0.00 0.00 0.00 3.62
61 62 1.236616 CGTGCCTGCTTGATGAACCA 61.237 55.000 0.00 0.00 0.00 3.67
62 63 0.242017 GTGCCTGCTTGATGAACCAC 59.758 55.000 0.00 0.00 0.00 4.16
63 64 0.178995 TGCCTGCTTGATGAACCACA 60.179 50.000 0.00 0.00 0.00 4.17
64 65 0.242017 GCCTGCTTGATGAACCACAC 59.758 55.000 0.00 0.00 0.00 3.82
65 66 1.608055 CCTGCTTGATGAACCACACA 58.392 50.000 0.00 0.00 0.00 3.72
66 67 1.955778 CCTGCTTGATGAACCACACAA 59.044 47.619 0.00 0.00 0.00 3.33
67 68 2.361757 CCTGCTTGATGAACCACACAAA 59.638 45.455 0.00 0.00 0.00 2.83
68 69 3.551454 CCTGCTTGATGAACCACACAAAG 60.551 47.826 0.00 0.00 0.00 2.77
69 70 2.223782 TGCTTGATGAACCACACAAAGC 60.224 45.455 0.00 0.00 44.04 3.51
70 71 2.863704 GCTTGATGAACCACACAAAGCC 60.864 50.000 0.00 0.00 40.94 4.35
71 72 2.064434 TGATGAACCACACAAAGCCA 57.936 45.000 0.00 0.00 0.00 4.75
72 73 1.680735 TGATGAACCACACAAAGCCAC 59.319 47.619 0.00 0.00 0.00 5.01
73 74 0.667993 ATGAACCACACAAAGCCACG 59.332 50.000 0.00 0.00 0.00 4.94
74 75 1.299089 GAACCACACAAAGCCACGC 60.299 57.895 0.00 0.00 0.00 5.34
75 76 1.724582 GAACCACACAAAGCCACGCT 61.725 55.000 0.00 0.00 42.56 5.07
76 77 0.464735 AACCACACAAAGCCACGCTA 60.465 50.000 0.00 0.00 38.25 4.26
77 78 0.250727 ACCACACAAAGCCACGCTAT 60.251 50.000 0.00 0.00 38.25 2.97
78 79 1.002659 ACCACACAAAGCCACGCTATA 59.997 47.619 0.00 0.00 38.25 1.31
79 80 2.288666 CCACACAAAGCCACGCTATAT 58.711 47.619 0.00 0.00 38.25 0.86
80 81 2.682856 CCACACAAAGCCACGCTATATT 59.317 45.455 0.00 0.00 38.25 1.28
81 82 3.487376 CCACACAAAGCCACGCTATATTG 60.487 47.826 0.00 0.00 38.25 1.90
82 83 3.373748 CACACAAAGCCACGCTATATTGA 59.626 43.478 4.10 0.00 38.25 2.57
83 84 4.006989 ACACAAAGCCACGCTATATTGAA 58.993 39.130 4.10 0.00 38.25 2.69
84 85 4.094887 ACACAAAGCCACGCTATATTGAAG 59.905 41.667 4.10 0.36 38.25 3.02
85 86 4.332543 CACAAAGCCACGCTATATTGAAGA 59.667 41.667 4.10 0.00 38.25 2.87
86 87 4.572389 ACAAAGCCACGCTATATTGAAGAG 59.428 41.667 4.10 0.00 38.25 2.85
87 88 4.408182 AAGCCACGCTATATTGAAGAGT 57.592 40.909 0.00 0.00 38.25 3.24
88 89 3.722147 AGCCACGCTATATTGAAGAGTG 58.278 45.455 1.96 1.96 42.35 3.51
89 90 3.133003 AGCCACGCTATATTGAAGAGTGT 59.867 43.478 6.98 0.00 41.49 3.55
90 91 4.341235 AGCCACGCTATATTGAAGAGTGTA 59.659 41.667 6.98 0.00 41.49 2.90
91 92 5.047847 GCCACGCTATATTGAAGAGTGTAA 58.952 41.667 6.98 0.00 41.49 2.41
92 93 5.522460 GCCACGCTATATTGAAGAGTGTAAA 59.478 40.000 6.98 0.00 41.49 2.01
93 94 6.202954 GCCACGCTATATTGAAGAGTGTAAAT 59.797 38.462 6.98 0.00 41.49 1.40
94 95 7.254795 GCCACGCTATATTGAAGAGTGTAAATT 60.255 37.037 6.98 0.00 41.49 1.82
95 96 9.256477 CCACGCTATATTGAAGAGTGTAAATTA 57.744 33.333 6.98 0.00 41.49 1.40
102 103 7.596749 ATTGAAGAGTGTAAATTACTGTCGG 57.403 36.000 4.67 0.00 0.00 4.79
103 104 4.927425 TGAAGAGTGTAAATTACTGTCGGC 59.073 41.667 4.67 0.00 0.00 5.54
104 105 4.803098 AGAGTGTAAATTACTGTCGGCT 57.197 40.909 4.67 0.00 0.00 5.52
105 106 5.148651 AGAGTGTAAATTACTGTCGGCTT 57.851 39.130 4.67 0.00 0.00 4.35
106 107 5.548406 AGAGTGTAAATTACTGTCGGCTTT 58.452 37.500 4.67 0.00 0.00 3.51
107 108 6.694447 AGAGTGTAAATTACTGTCGGCTTTA 58.306 36.000 4.67 0.00 0.00 1.85
108 109 7.156673 AGAGTGTAAATTACTGTCGGCTTTAA 58.843 34.615 4.67 0.00 0.00 1.52
109 110 7.822822 AGAGTGTAAATTACTGTCGGCTTTAAT 59.177 33.333 4.67 0.00 0.00 1.40
110 111 9.090692 GAGTGTAAATTACTGTCGGCTTTAATA 57.909 33.333 4.67 0.00 0.00 0.98
111 112 9.439500 AGTGTAAATTACTGTCGGCTTTAATAA 57.561 29.630 4.67 0.00 0.00 1.40
126 127 9.417284 CGGCTTTAATAAATAAAACTACAGTCG 57.583 33.333 0.00 0.00 33.20 4.18
127 128 9.218359 GGCTTTAATAAATAAAACTACAGTCGC 57.782 33.333 0.00 0.00 33.20 5.19
128 129 9.763465 GCTTTAATAAATAAAACTACAGTCGCA 57.237 29.630 0.00 0.00 33.20 5.10
154 155 5.888412 TTTTTCCTGAAACGTACGTACTC 57.112 39.130 23.12 20.41 0.00 2.59
155 156 3.559238 TTCCTGAAACGTACGTACTCC 57.441 47.619 23.12 11.31 0.00 3.85
156 157 1.812571 TCCTGAAACGTACGTACTCCC 59.187 52.381 23.12 9.56 0.00 4.30
157 158 1.815003 CCTGAAACGTACGTACTCCCT 59.185 52.381 23.12 0.97 0.00 4.20
158 159 3.009723 CCTGAAACGTACGTACTCCCTA 58.990 50.000 23.12 5.23 0.00 3.53
159 160 3.181506 CCTGAAACGTACGTACTCCCTAC 60.182 52.174 23.12 9.97 0.00 3.18
173 174 8.108716 CGTACTCCCTACGTTTTTATTTACTC 57.891 38.462 0.00 0.00 42.90 2.59
174 175 7.970614 CGTACTCCCTACGTTTTTATTTACTCT 59.029 37.037 0.00 0.00 42.90 3.24
175 176 9.080915 GTACTCCCTACGTTTTTATTTACTCTG 57.919 37.037 0.00 0.00 0.00 3.35
176 177 6.592994 ACTCCCTACGTTTTTATTTACTCTGC 59.407 38.462 0.00 0.00 0.00 4.26
177 178 6.465948 TCCCTACGTTTTTATTTACTCTGCA 58.534 36.000 0.00 0.00 0.00 4.41
178 179 7.107542 TCCCTACGTTTTTATTTACTCTGCAT 58.892 34.615 0.00 0.00 0.00 3.96
179 180 8.259411 TCCCTACGTTTTTATTTACTCTGCATA 58.741 33.333 0.00 0.00 0.00 3.14
180 181 9.052759 CCCTACGTTTTTATTTACTCTGCATAT 57.947 33.333 0.00 0.00 0.00 1.78
195 196 7.697352 CTCTGCATATTAGAGTTGACTGAAG 57.303 40.000 5.84 0.00 37.48 3.02
196 197 7.175347 TCTGCATATTAGAGTTGACTGAAGT 57.825 36.000 0.00 0.00 0.00 3.01
197 198 7.261325 TCTGCATATTAGAGTTGACTGAAGTC 58.739 38.462 3.41 3.41 44.97 3.01
223 224 6.505044 ACTTCGTAAAGTTTGACCAAGTTT 57.495 33.333 0.00 0.00 43.28 2.66
224 225 7.614124 ACTTCGTAAAGTTTGACCAAGTTTA 57.386 32.000 0.00 0.00 43.28 2.01
225 226 8.217131 ACTTCGTAAAGTTTGACCAAGTTTAT 57.783 30.769 0.00 0.00 43.28 1.40
226 227 9.328845 ACTTCGTAAAGTTTGACCAAGTTTATA 57.671 29.630 0.00 0.00 43.28 0.98
227 228 9.807386 CTTCGTAAAGTTTGACCAAGTTTATAG 57.193 33.333 0.00 2.48 40.73 1.31
228 229 8.314143 TCGTAAAGTTTGACCAAGTTTATAGG 57.686 34.615 0.00 0.00 40.73 2.57
229 230 8.149647 TCGTAAAGTTTGACCAAGTTTATAGGA 58.850 33.333 0.00 0.84 40.73 2.94
230 231 8.776470 CGTAAAGTTTGACCAAGTTTATAGGAA 58.224 33.333 0.00 0.00 40.73 3.36
233 234 8.990163 AAGTTTGACCAAGTTTATAGGAAAGA 57.010 30.769 0.00 0.00 0.00 2.52
234 235 8.990163 AGTTTGACCAAGTTTATAGGAAAGAA 57.010 30.769 0.00 0.00 0.00 2.52
235 236 9.588096 AGTTTGACCAAGTTTATAGGAAAGAAT 57.412 29.630 0.00 0.00 0.00 2.40
277 278 8.842942 ACATATCTATATGATGCGAAAGTACG 57.157 34.615 15.23 0.00 42.05 3.67
278 279 8.459635 ACATATCTATATGATGCGAAAGTACGT 58.540 33.333 15.23 0.00 42.05 3.57
279 280 9.290483 CATATCTATATGATGCGAAAGTACGTT 57.710 33.333 0.00 0.00 42.05 3.99
280 281 7.798486 ATCTATATGATGCGAAAGTACGTTC 57.202 36.000 11.06 11.06 33.43 3.95
281 282 6.731164 TCTATATGATGCGAAAGTACGTTCA 58.269 36.000 19.40 4.18 34.35 3.18
282 283 7.197703 TCTATATGATGCGAAAGTACGTTCAA 58.802 34.615 19.40 8.88 33.89 2.69
283 284 6.844696 ATATGATGCGAAAGTACGTTCAAT 57.155 33.333 19.40 12.70 33.89 2.57
284 285 7.940178 ATATGATGCGAAAGTACGTTCAATA 57.060 32.000 19.40 9.93 33.89 1.90
285 286 6.656314 ATGATGCGAAAGTACGTTCAATAA 57.344 33.333 19.40 7.73 33.89 1.40
286 287 6.656314 TGATGCGAAAGTACGTTCAATAAT 57.344 33.333 19.40 8.18 35.59 1.28
287 288 6.474364 TGATGCGAAAGTACGTTCAATAATG 58.526 36.000 19.40 5.23 35.59 1.90
288 289 6.311690 TGATGCGAAAGTACGTTCAATAATGA 59.688 34.615 19.40 1.44 35.59 2.57
289 290 6.469139 TGCGAAAGTACGTTCAATAATGAA 57.531 33.333 19.40 0.00 43.18 2.57
290 291 7.067532 TGCGAAAGTACGTTCAATAATGAAT 57.932 32.000 19.40 0.00 46.67 2.57
291 292 7.177407 TGCGAAAGTACGTTCAATAATGAATC 58.823 34.615 19.40 0.00 46.67 2.52
292 293 7.064134 TGCGAAAGTACGTTCAATAATGAATCT 59.936 33.333 19.40 0.00 46.67 2.40
293 294 8.537223 GCGAAAGTACGTTCAATAATGAATCTA 58.463 33.333 19.40 0.00 46.67 1.98
366 367 9.736023 CTTTGTCAAAGTTTATAAAGCTTGACT 57.264 29.630 30.01 13.37 39.29 3.41
388 389 6.189677 CTTTGACCAAAGTTAATATGCGGA 57.810 37.500 12.91 0.00 42.02 5.54
389 390 5.811399 TTGACCAAAGTTAATATGCGGAG 57.189 39.130 0.00 0.00 0.00 4.63
390 391 4.839121 TGACCAAAGTTAATATGCGGAGT 58.161 39.130 0.00 0.00 0.00 3.85
391 392 5.979993 TGACCAAAGTTAATATGCGGAGTA 58.020 37.500 0.00 0.00 0.00 2.59
392 393 6.408035 TGACCAAAGTTAATATGCGGAGTAA 58.592 36.000 0.00 0.00 0.00 2.24
393 394 6.879993 TGACCAAAGTTAATATGCGGAGTAAA 59.120 34.615 0.00 0.00 0.00 2.01
394 395 7.554835 TGACCAAAGTTAATATGCGGAGTAAAT 59.445 33.333 0.00 0.00 0.00 1.40
395 396 8.967664 ACCAAAGTTAATATGCGGAGTAAATA 57.032 30.769 0.00 0.00 0.00 1.40
396 397 9.398538 ACCAAAGTTAATATGCGGAGTAAATAA 57.601 29.630 0.00 0.00 0.00 1.40
401 402 9.925268 AGTTAATATGCGGAGTAAATAAAAACG 57.075 29.630 0.00 0.00 0.00 3.60
402 403 9.161684 GTTAATATGCGGAGTAAATAAAAACGG 57.838 33.333 0.00 0.00 0.00 4.44
403 404 7.556733 AATATGCGGAGTAAATAAAAACGGA 57.443 32.000 0.00 0.00 0.00 4.69
404 405 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
405 406 4.567971 TGCGGAGTAAATAAAAACGGAGA 58.432 39.130 0.00 0.00 0.00 3.71
406 407 4.628333 TGCGGAGTAAATAAAAACGGAGAG 59.372 41.667 0.00 0.00 0.00 3.20
407 408 4.866486 GCGGAGTAAATAAAAACGGAGAGA 59.134 41.667 0.00 0.00 0.00 3.10
427 428 9.703892 GGAGAGAGTACGTATATTGTAGAGTAA 57.296 37.037 0.00 0.00 0.00 2.24
624 631 1.524621 CCCCCGCATCTCACATCAC 60.525 63.158 0.00 0.00 0.00 3.06
625 632 1.524002 CCCCGCATCTCACATCACT 59.476 57.895 0.00 0.00 0.00 3.41
787 807 2.819595 CGTCCAACCCATCCGCTG 60.820 66.667 0.00 0.00 0.00 5.18
790 810 2.751436 CCAACCCATCCGCTGTGG 60.751 66.667 0.00 0.00 40.09 4.17
791 811 3.443045 CAACCCATCCGCTGTGGC 61.443 66.667 1.39 0.00 37.80 5.01
792 812 3.650950 AACCCATCCGCTGTGGCT 61.651 61.111 1.39 0.00 37.80 4.75
1146 1211 1.296715 CTTCCCCCACGACCTCAAG 59.703 63.158 0.00 0.00 0.00 3.02
1152 1217 1.338136 CCCACGACCTCAAGGCCTAT 61.338 60.000 5.16 0.00 39.32 2.57
1164 1229 2.915604 CAAGGCCTATAGGTCCATGGAT 59.084 50.000 25.16 5.24 41.83 3.41
1168 1233 2.555664 CCTATAGGTCCATGGATGCCT 58.444 52.381 23.58 23.58 35.28 4.75
1571 1660 1.153823 CTTCGCGATTGGAGTCGGT 60.154 57.895 10.88 0.00 41.72 4.69
1585 1674 0.712222 GTCGGTTTGTCGATCGGTTC 59.288 55.000 16.41 7.07 41.40 3.62
1778 1868 2.207924 AACGGCGAACTGGAGGAGT 61.208 57.895 16.62 0.00 35.94 3.85
2171 2261 1.279496 CTGACCATCCAACTCCAGGA 58.721 55.000 0.00 0.00 39.97 3.86
2240 2330 0.235665 GTCGTCCGTGTCGTGTTCTA 59.764 55.000 0.00 0.00 0.00 2.10
2391 2484 4.382386 AGGTAGGTTGCCTGTTAATGTT 57.618 40.909 0.00 0.00 34.61 2.71
2413 2506 7.810658 TGTTCTGAACTAACCTTAGTAGTACG 58.189 38.462 20.18 0.00 42.86 3.67
2414 2507 7.661437 TGTTCTGAACTAACCTTAGTAGTACGA 59.339 37.037 20.18 0.00 42.86 3.43
2428 2521 0.526954 GTACGAGTATGTGGGTGGCG 60.527 60.000 0.00 0.00 0.00 5.69
2464 2557 2.721425 AAGTTGTTTCGTCCTTGGGA 57.279 45.000 0.00 0.00 0.00 4.37
2512 2605 3.697982 CACTAAAACCGTGTTGTTTCCC 58.302 45.455 0.00 0.00 37.46 3.97
2524 2617 1.522668 TGTTTCCCTGTGATTGCTCG 58.477 50.000 0.00 0.00 0.00 5.03
2581 2682 1.593196 TACTGCCACACTTGCTGTTC 58.407 50.000 0.00 0.00 40.66 3.18
2614 2748 7.551585 AGATGCTATGCTATGTTGAGTATACC 58.448 38.462 0.00 0.00 0.00 2.73
2640 2774 4.024218 CCGGATCGTAGTAGTTCTACTTGG 60.024 50.000 16.10 9.67 44.80 3.61
2658 2795 9.639563 TCTACTTGGGCATCATCAATATTTTTA 57.360 29.630 0.00 0.00 0.00 1.52
2669 2806 6.429692 TCATCAATATTTTTATGCCCGTCGAT 59.570 34.615 0.00 0.00 0.00 3.59
2670 2807 6.236017 TCAATATTTTTATGCCCGTCGATC 57.764 37.500 0.00 0.00 0.00 3.69
2671 2808 5.180492 TCAATATTTTTATGCCCGTCGATCC 59.820 40.000 0.00 0.00 0.00 3.36
2672 2809 1.670791 TTTTTATGCCCGTCGATCCC 58.329 50.000 0.00 0.00 0.00 3.85
2673 2810 0.531090 TTTTATGCCCGTCGATCCCG 60.531 55.000 0.00 0.00 37.07 5.14
2693 2830 3.119602 CCGTCGATCTTGACCAGTCTAAA 60.120 47.826 0.00 0.00 35.40 1.85
2694 2831 3.852536 CGTCGATCTTGACCAGTCTAAAC 59.147 47.826 0.00 0.00 35.40 2.01
2696 2833 4.082136 GTCGATCTTGACCAGTCTAAACCT 60.082 45.833 0.00 0.00 32.61 3.50
2697 2834 4.082190 TCGATCTTGACCAGTCTAAACCTG 60.082 45.833 0.00 0.00 0.00 4.00
2699 2836 4.602340 TCTTGACCAGTCTAAACCTGTC 57.398 45.455 0.00 0.00 0.00 3.51
2700 2837 3.323979 TCTTGACCAGTCTAAACCTGTCC 59.676 47.826 0.00 0.00 0.00 4.02
2701 2838 2.972348 TGACCAGTCTAAACCTGTCCT 58.028 47.619 0.00 0.00 0.00 3.85
2702 2839 2.632996 TGACCAGTCTAAACCTGTCCTG 59.367 50.000 0.00 0.00 0.00 3.86
2907 3400 6.948228 CGACAGTATATTGAACGTTTCACTTG 59.052 38.462 0.46 0.00 39.87 3.16
2952 3445 1.969923 TCCATGTTTTTGCCCAAGGAG 59.030 47.619 0.00 0.00 0.00 3.69
2955 3448 0.753479 TGTTTTTGCCCAAGGAGCGA 60.753 50.000 0.00 0.00 0.00 4.93
2956 3449 0.039165 GTTTTTGCCCAAGGAGCGAG 60.039 55.000 0.00 0.00 0.00 5.03
2969 3477 1.936547 GGAGCGAGAGTAATTGCTTGG 59.063 52.381 0.00 0.00 40.12 3.61
3006 3516 1.883926 GCCATCGTTTTTACCTGTGGT 59.116 47.619 0.00 0.00 40.16 4.16
3007 3517 2.351350 GCCATCGTTTTTACCTGTGGTG 60.351 50.000 0.00 0.00 36.19 4.17
3008 3518 3.142951 CCATCGTTTTTACCTGTGGTGA 58.857 45.455 0.00 0.00 36.19 4.02
3009 3519 3.756434 CCATCGTTTTTACCTGTGGTGAT 59.244 43.478 0.00 0.00 36.19 3.06
3010 3520 4.379394 CCATCGTTTTTACCTGTGGTGATG 60.379 45.833 0.00 3.14 36.19 3.07
3011 3521 3.142951 TCGTTTTTACCTGTGGTGATGG 58.857 45.455 0.00 0.00 36.19 3.51
3012 3522 2.227865 CGTTTTTACCTGTGGTGATGGG 59.772 50.000 0.00 0.00 36.19 4.00
3013 3523 1.917872 TTTTACCTGTGGTGATGGGC 58.082 50.000 0.00 0.00 36.19 5.36
3026 3536 0.743097 GATGGGCTGATGGCAAACTC 59.257 55.000 0.00 0.00 44.01 3.01
3036 3549 0.671251 TGGCAAACTCCGCGAAATTT 59.329 45.000 8.23 1.04 0.00 1.82
3045 3558 4.510571 ACTCCGCGAAATTTACAAGGTAT 58.489 39.130 8.23 0.00 0.00 2.73
3046 3559 5.663456 ACTCCGCGAAATTTACAAGGTATA 58.337 37.500 8.23 0.00 0.00 1.47
3054 3567 8.139989 GCGAAATTTACAAGGTATAGTAGGAGA 58.860 37.037 0.00 0.00 0.00 3.71
3066 3579 7.769044 AGGTATAGTAGGAGAACGTACGTTTTA 59.231 37.037 32.14 19.30 40.77 1.52
3078 3591 9.321590 AGAACGTACGTTTTATTTTATTTGAGC 57.678 29.630 32.14 14.67 38.60 4.26
3090 3603 4.439305 TTATTTGAGCGGTGTACGTACT 57.561 40.909 25.12 5.69 46.52 2.73
3091 3604 5.559427 TTATTTGAGCGGTGTACGTACTA 57.441 39.130 25.12 10.10 46.52 1.82
3092 3605 4.644103 ATTTGAGCGGTGTACGTACTAT 57.356 40.909 25.12 7.69 46.52 2.12
3098 3611 3.191162 AGCGGTGTACGTACTATGTTTGA 59.809 43.478 25.12 0.60 46.52 2.69
3147 3672 3.366052 ACTGACGGGGAGCAAAATTAT 57.634 42.857 0.00 0.00 0.00 1.28
3348 3885 2.434884 CCGGCACCACAGCACTAG 60.435 66.667 0.00 0.00 35.83 2.57
3366 3903 4.285003 CACTAGCTCTACCTAGAGGCTAGA 59.715 50.000 26.88 14.07 46.22 2.43
3367 3904 4.530946 ACTAGCTCTACCTAGAGGCTAGAG 59.469 50.000 26.88 20.18 46.22 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.641499 TTCACGCAAATTTCAACTAGATTTTT 57.359 26.923 0.00 0.00 0.00 1.94
6 7 8.816640 ATTCACGCAAATTTCAACTAGATTTT 57.183 26.923 0.00 0.00 0.00 1.82
7 8 9.906660 TTATTCACGCAAATTTCAACTAGATTT 57.093 25.926 0.00 0.00 0.00 2.17
8 9 9.341899 GTTATTCACGCAAATTTCAACTAGATT 57.658 29.630 0.00 0.00 0.00 2.40
9 10 8.511321 TGTTATTCACGCAAATTTCAACTAGAT 58.489 29.630 0.00 0.00 0.00 1.98
10 11 7.801315 GTGTTATTCACGCAAATTTCAACTAGA 59.199 33.333 0.00 0.00 37.31 2.43
11 12 7.928402 GTGTTATTCACGCAAATTTCAACTAG 58.072 34.615 0.00 0.00 37.31 2.57
12 13 7.845617 GTGTTATTCACGCAAATTTCAACTA 57.154 32.000 0.00 0.00 37.31 2.24
13 14 6.747659 GTGTTATTCACGCAAATTTCAACT 57.252 33.333 0.00 0.00 37.31 3.16
37 38 3.628646 ATCAAGCAGGCACGGGGAC 62.629 63.158 0.00 0.00 0.00 4.46
38 39 3.329889 ATCAAGCAGGCACGGGGA 61.330 61.111 0.00 0.00 0.00 4.81
39 40 3.136123 CATCAAGCAGGCACGGGG 61.136 66.667 0.00 0.00 0.00 5.73
40 41 1.675310 TTCATCAAGCAGGCACGGG 60.675 57.895 0.00 0.00 0.00 5.28
41 42 1.503542 GTTCATCAAGCAGGCACGG 59.496 57.895 0.00 0.00 0.00 4.94
42 43 1.236616 TGGTTCATCAAGCAGGCACG 61.237 55.000 0.00 0.00 35.03 5.34
43 44 0.242017 GTGGTTCATCAAGCAGGCAC 59.758 55.000 0.00 0.00 40.69 5.01
44 45 0.178995 TGTGGTTCATCAAGCAGGCA 60.179 50.000 0.00 0.00 40.69 4.75
45 46 0.242017 GTGTGGTTCATCAAGCAGGC 59.758 55.000 0.00 0.00 40.69 4.85
46 47 1.608055 TGTGTGGTTCATCAAGCAGG 58.392 50.000 0.00 0.00 40.69 4.85
47 48 3.635331 CTTTGTGTGGTTCATCAAGCAG 58.365 45.455 0.00 0.00 40.69 4.24
48 49 2.223782 GCTTTGTGTGGTTCATCAAGCA 60.224 45.455 0.00 0.00 40.55 3.91
49 50 2.397549 GCTTTGTGTGGTTCATCAAGC 58.602 47.619 0.00 0.00 37.05 4.01
50 51 2.361757 TGGCTTTGTGTGGTTCATCAAG 59.638 45.455 0.00 0.00 0.00 3.02
51 52 2.100584 GTGGCTTTGTGTGGTTCATCAA 59.899 45.455 0.00 0.00 0.00 2.57
52 53 1.680735 GTGGCTTTGTGTGGTTCATCA 59.319 47.619 0.00 0.00 0.00 3.07
53 54 1.334960 CGTGGCTTTGTGTGGTTCATC 60.335 52.381 0.00 0.00 0.00 2.92
54 55 0.667993 CGTGGCTTTGTGTGGTTCAT 59.332 50.000 0.00 0.00 0.00 2.57
55 56 1.999071 GCGTGGCTTTGTGTGGTTCA 61.999 55.000 0.00 0.00 0.00 3.18
56 57 1.299089 GCGTGGCTTTGTGTGGTTC 60.299 57.895 0.00 0.00 0.00 3.62
57 58 0.464735 TAGCGTGGCTTTGTGTGGTT 60.465 50.000 0.00 0.00 40.44 3.67
58 59 0.250727 ATAGCGTGGCTTTGTGTGGT 60.251 50.000 0.00 0.00 40.44 4.16
59 60 1.732941 TATAGCGTGGCTTTGTGTGG 58.267 50.000 0.00 0.00 40.44 4.17
60 61 3.373748 TCAATATAGCGTGGCTTTGTGTG 59.626 43.478 0.00 0.00 40.44 3.82
61 62 3.605634 TCAATATAGCGTGGCTTTGTGT 58.394 40.909 0.00 0.00 40.44 3.72
62 63 4.332543 TCTTCAATATAGCGTGGCTTTGTG 59.667 41.667 0.00 0.00 40.44 3.33
63 64 4.513442 TCTTCAATATAGCGTGGCTTTGT 58.487 39.130 0.00 0.00 40.44 2.83
64 65 4.572389 ACTCTTCAATATAGCGTGGCTTTG 59.428 41.667 0.00 0.00 40.44 2.77
65 66 4.572389 CACTCTTCAATATAGCGTGGCTTT 59.428 41.667 0.00 0.00 40.44 3.51
66 67 4.122776 CACTCTTCAATATAGCGTGGCTT 58.877 43.478 0.00 0.00 40.44 4.35
67 68 3.133003 ACACTCTTCAATATAGCGTGGCT 59.867 43.478 0.00 0.00 43.41 4.75
68 69 3.458189 ACACTCTTCAATATAGCGTGGC 58.542 45.455 0.00 0.00 33.72 5.01
69 70 7.715265 ATTTACACTCTTCAATATAGCGTGG 57.285 36.000 0.00 0.00 33.72 4.94
76 77 9.314321 CCGACAGTAATTTACACTCTTCAATAT 57.686 33.333 9.15 0.00 0.00 1.28
77 78 7.277098 GCCGACAGTAATTTACACTCTTCAATA 59.723 37.037 9.15 0.00 0.00 1.90
78 79 6.092259 GCCGACAGTAATTTACACTCTTCAAT 59.908 38.462 9.15 0.00 0.00 2.57
79 80 5.407387 GCCGACAGTAATTTACACTCTTCAA 59.593 40.000 9.15 0.00 0.00 2.69
80 81 4.927425 GCCGACAGTAATTTACACTCTTCA 59.073 41.667 9.15 0.00 0.00 3.02
81 82 5.169295 AGCCGACAGTAATTTACACTCTTC 58.831 41.667 9.15 0.00 0.00 2.87
82 83 5.148651 AGCCGACAGTAATTTACACTCTT 57.851 39.130 9.15 0.00 0.00 2.85
83 84 4.803098 AGCCGACAGTAATTTACACTCT 57.197 40.909 9.15 0.00 0.00 3.24
84 85 5.857822 AAAGCCGACAGTAATTTACACTC 57.142 39.130 9.15 2.27 0.00 3.51
85 86 7.916914 ATTAAAGCCGACAGTAATTTACACT 57.083 32.000 9.15 0.00 0.00 3.55
100 101 9.417284 CGACTGTAGTTTTATTTATTAAAGCCG 57.583 33.333 0.00 0.00 32.96 5.52
101 102 9.218359 GCGACTGTAGTTTTATTTATTAAAGCC 57.782 33.333 0.00 0.00 32.96 4.35
102 103 9.763465 TGCGACTGTAGTTTTATTTATTAAAGC 57.237 29.630 0.00 0.00 31.57 3.51
132 133 4.744631 GGAGTACGTACGTTTCAGGAAAAA 59.255 41.667 27.92 0.43 31.33 1.94
133 134 4.298332 GGAGTACGTACGTTTCAGGAAAA 58.702 43.478 27.92 1.29 31.33 2.29
134 135 3.305335 GGGAGTACGTACGTTTCAGGAAA 60.305 47.826 27.92 2.14 0.00 3.13
135 136 2.228822 GGGAGTACGTACGTTTCAGGAA 59.771 50.000 27.92 3.00 0.00 3.36
136 137 1.812571 GGGAGTACGTACGTTTCAGGA 59.187 52.381 27.92 3.86 0.00 3.86
137 138 1.815003 AGGGAGTACGTACGTTTCAGG 59.185 52.381 27.92 0.00 0.00 3.86
138 139 4.008539 GTAGGGAGTACGTACGTTTCAG 57.991 50.000 27.92 0.00 31.59 3.02
149 150 9.080915 CAGAGTAAATAAAAACGTAGGGAGTAC 57.919 37.037 0.00 0.00 0.00 2.73
150 151 7.761249 GCAGAGTAAATAAAAACGTAGGGAGTA 59.239 37.037 0.00 0.00 0.00 2.59
151 152 6.592994 GCAGAGTAAATAAAAACGTAGGGAGT 59.407 38.462 0.00 0.00 0.00 3.85
152 153 6.592607 TGCAGAGTAAATAAAAACGTAGGGAG 59.407 38.462 0.00 0.00 0.00 4.30
153 154 6.465948 TGCAGAGTAAATAAAAACGTAGGGA 58.534 36.000 0.00 0.00 0.00 4.20
154 155 6.730960 TGCAGAGTAAATAAAAACGTAGGG 57.269 37.500 0.00 0.00 0.00 3.53
171 172 7.264221 ACTTCAGTCAACTCTAATATGCAGAG 58.736 38.462 11.37 11.37 44.28 3.35
172 173 7.175347 ACTTCAGTCAACTCTAATATGCAGA 57.825 36.000 0.00 0.00 0.00 4.26
173 174 7.462109 GACTTCAGTCAACTCTAATATGCAG 57.538 40.000 1.86 0.00 44.18 4.41
201 202 9.807386 CTATAAACTTGGTCAAACTTTACGAAG 57.193 33.333 0.00 0.00 37.43 3.79
202 203 8.776470 CCTATAAACTTGGTCAAACTTTACGAA 58.224 33.333 0.00 0.00 0.00 3.85
203 204 8.149647 TCCTATAAACTTGGTCAAACTTTACGA 58.850 33.333 0.00 0.00 0.00 3.43
204 205 8.314143 TCCTATAAACTTGGTCAAACTTTACG 57.686 34.615 0.00 0.00 0.00 3.18
207 208 9.416284 TCTTTCCTATAAACTTGGTCAAACTTT 57.584 29.630 0.00 0.00 0.00 2.66
208 209 8.990163 TCTTTCCTATAAACTTGGTCAAACTT 57.010 30.769 0.00 0.00 0.00 2.66
209 210 8.990163 TTCTTTCCTATAAACTTGGTCAAACT 57.010 30.769 0.00 0.00 0.00 2.66
251 252 9.290483 CGTACTTTCGCATCATATAGATATGTT 57.710 33.333 8.92 0.00 40.69 2.71
252 253 8.459635 ACGTACTTTCGCATCATATAGATATGT 58.540 33.333 8.92 0.00 40.69 2.29
253 254 8.842942 ACGTACTTTCGCATCATATAGATATG 57.157 34.615 3.50 3.50 41.10 1.78
254 255 9.504710 GAACGTACTTTCGCATCATATAGATAT 57.495 33.333 0.00 0.00 34.43 1.63
255 256 8.508875 TGAACGTACTTTCGCATCATATAGATA 58.491 33.333 7.51 0.00 34.43 1.98
256 257 7.368059 TGAACGTACTTTCGCATCATATAGAT 58.632 34.615 7.51 0.00 37.48 1.98
257 258 6.731164 TGAACGTACTTTCGCATCATATAGA 58.269 36.000 7.51 0.00 0.00 1.98
258 259 6.986424 TGAACGTACTTTCGCATCATATAG 57.014 37.500 7.51 0.00 0.00 1.31
259 260 7.940178 ATTGAACGTACTTTCGCATCATATA 57.060 32.000 7.51 0.00 32.87 0.86
260 261 6.844696 ATTGAACGTACTTTCGCATCATAT 57.155 33.333 7.51 0.00 32.87 1.78
261 262 7.758613 TTATTGAACGTACTTTCGCATCATA 57.241 32.000 7.51 0.00 32.87 2.15
262 263 6.656314 TTATTGAACGTACTTTCGCATCAT 57.344 33.333 7.51 0.00 32.87 2.45
263 264 6.311690 TCATTATTGAACGTACTTTCGCATCA 59.688 34.615 7.51 0.00 0.00 3.07
264 265 6.701937 TCATTATTGAACGTACTTTCGCATC 58.298 36.000 7.51 0.00 0.00 3.91
265 266 6.656314 TCATTATTGAACGTACTTTCGCAT 57.344 33.333 7.51 5.10 0.00 4.73
266 267 6.469139 TTCATTATTGAACGTACTTTCGCA 57.531 33.333 7.51 0.00 36.94 5.10
267 268 7.399523 AGATTCATTATTGAACGTACTTTCGC 58.600 34.615 7.51 0.00 44.36 4.70
340 341 9.736023 AGTCAAGCTTTATAAACTTTGACAAAG 57.264 29.630 29.41 23.41 44.10 2.77
347 348 8.691797 TGGTCAAAGTCAAGCTTTATAAACTTT 58.308 29.630 0.00 5.64 44.95 2.66
348 349 8.232913 TGGTCAAAGTCAAGCTTTATAAACTT 57.767 30.769 0.00 0.00 44.95 2.66
349 350 7.817418 TGGTCAAAGTCAAGCTTTATAAACT 57.183 32.000 0.00 0.00 44.95 2.66
350 351 8.865590 TTTGGTCAAAGTCAAGCTTTATAAAC 57.134 30.769 0.00 0.00 44.95 2.01
366 367 5.708230 ACTCCGCATATTAACTTTGGTCAAA 59.292 36.000 0.00 0.00 0.00 2.69
367 368 5.250200 ACTCCGCATATTAACTTTGGTCAA 58.750 37.500 0.00 0.00 0.00 3.18
368 369 4.839121 ACTCCGCATATTAACTTTGGTCA 58.161 39.130 0.00 0.00 0.00 4.02
369 370 6.913873 TTACTCCGCATATTAACTTTGGTC 57.086 37.500 0.00 0.00 0.00 4.02
370 371 7.875327 ATTTACTCCGCATATTAACTTTGGT 57.125 32.000 0.00 0.00 0.00 3.67
375 376 9.925268 CGTTTTTATTTACTCCGCATATTAACT 57.075 29.630 0.00 0.00 0.00 2.24
376 377 9.161684 CCGTTTTTATTTACTCCGCATATTAAC 57.838 33.333 0.00 0.00 0.00 2.01
377 378 9.107177 TCCGTTTTTATTTACTCCGCATATTAA 57.893 29.630 0.00 0.00 0.00 1.40
378 379 8.659925 TCCGTTTTTATTTACTCCGCATATTA 57.340 30.769 0.00 0.00 0.00 0.98
379 380 7.496591 TCTCCGTTTTTATTTACTCCGCATATT 59.503 33.333 0.00 0.00 0.00 1.28
380 381 6.987992 TCTCCGTTTTTATTTACTCCGCATAT 59.012 34.615 0.00 0.00 0.00 1.78
381 382 6.339730 TCTCCGTTTTTATTTACTCCGCATA 58.660 36.000 0.00 0.00 0.00 3.14
382 383 5.180271 TCTCCGTTTTTATTTACTCCGCAT 58.820 37.500 0.00 0.00 0.00 4.73
383 384 4.567971 TCTCCGTTTTTATTTACTCCGCA 58.432 39.130 0.00 0.00 0.00 5.69
384 385 4.866486 TCTCTCCGTTTTTATTTACTCCGC 59.134 41.667 0.00 0.00 0.00 5.54
385 386 6.098017 ACTCTCTCCGTTTTTATTTACTCCG 58.902 40.000 0.00 0.00 0.00 4.63
386 387 7.219726 CGTACTCTCTCCGTTTTTATTTACTCC 59.780 40.741 0.00 0.00 0.00 3.85
387 388 7.752686 ACGTACTCTCTCCGTTTTTATTTACTC 59.247 37.037 0.00 0.00 0.00 2.59
388 389 7.597386 ACGTACTCTCTCCGTTTTTATTTACT 58.403 34.615 0.00 0.00 0.00 2.24
389 390 7.803079 ACGTACTCTCTCCGTTTTTATTTAC 57.197 36.000 0.00 0.00 0.00 2.01
393 394 9.674824 CAATATACGTACTCTCTCCGTTTTTAT 57.325 33.333 0.00 0.00 36.12 1.40
394 395 8.677300 ACAATATACGTACTCTCTCCGTTTTTA 58.323 33.333 0.00 0.00 36.12 1.52
395 396 7.542025 ACAATATACGTACTCTCTCCGTTTTT 58.458 34.615 0.00 0.00 36.12 1.94
396 397 7.093322 ACAATATACGTACTCTCTCCGTTTT 57.907 36.000 0.00 0.00 36.12 2.43
397 398 6.690194 ACAATATACGTACTCTCTCCGTTT 57.310 37.500 0.00 0.00 36.12 3.60
398 399 7.212976 TCTACAATATACGTACTCTCTCCGTT 58.787 38.462 0.00 0.00 36.12 4.44
399 400 6.753180 TCTACAATATACGTACTCTCTCCGT 58.247 40.000 0.00 0.00 38.53 4.69
400 401 6.867816 ACTCTACAATATACGTACTCTCTCCG 59.132 42.308 0.00 0.00 0.00 4.63
401 402 9.703892 TTACTCTACAATATACGTACTCTCTCC 57.296 37.037 0.00 0.00 0.00 3.71
624 631 2.791567 CTTGATTCGTCGTGGAGAGAG 58.208 52.381 0.00 0.00 0.00 3.20
625 632 1.135373 GCTTGATTCGTCGTGGAGAGA 60.135 52.381 0.00 0.00 0.00 3.10
790 810 4.811364 GGGAAGGGAGGCAGCAGC 62.811 72.222 0.00 0.00 41.10 5.25
791 811 4.120755 GGGGAAGGGAGGCAGCAG 62.121 72.222 0.00 0.00 0.00 4.24
858 892 2.124693 GGTTGGGTGTGTGGGTGTG 61.125 63.158 0.00 0.00 0.00 3.82
859 893 2.277404 GGTTGGGTGTGTGGGTGT 59.723 61.111 0.00 0.00 0.00 4.16
860 894 2.520741 GGGTTGGGTGTGTGGGTG 60.521 66.667 0.00 0.00 0.00 4.61
861 895 2.627476 TTGGGTTGGGTGTGTGGGT 61.627 57.895 0.00 0.00 0.00 4.51
862 896 2.131067 GTTGGGTTGGGTGTGTGGG 61.131 63.158 0.00 0.00 0.00 4.61
943 987 7.344093 AGTTGTGATGGATAGAAAGAGAGATGA 59.656 37.037 0.00 0.00 0.00 2.92
986 1030 1.538876 TGAGGAGTTGGGAGTGGGG 60.539 63.158 0.00 0.00 0.00 4.96
990 1034 1.194781 ATGCGTGAGGAGTTGGGAGT 61.195 55.000 0.00 0.00 32.19 3.85
992 1036 1.596934 GATGCGTGAGGAGTTGGGA 59.403 57.895 0.00 0.00 32.19 4.37
1146 1211 1.065126 GCATCCATGGACCTATAGGCC 60.065 57.143 18.99 19.54 39.32 5.19
1152 1217 1.121407 CCGAGGCATCCATGGACCTA 61.121 60.000 21.03 0.00 30.95 3.08
1233 1322 2.107953 GGGAGATCGCTGAGCACC 59.892 66.667 4.88 0.00 0.00 5.01
1389 1478 1.077930 ATCGCAAGGCAGCATGAGT 60.078 52.632 0.00 0.00 38.34 3.41
1548 1637 1.656095 GACTCCAATCGCGAAGAACAG 59.344 52.381 15.24 8.40 0.00 3.16
1550 1639 0.640768 CGACTCCAATCGCGAAGAAC 59.359 55.000 15.24 6.88 34.90 3.01
1585 1674 0.731417 AGTGAGATACCGTTCGACCG 59.269 55.000 0.00 0.00 0.00 4.79
1681 1771 2.048597 TCCACAGTAGCCAACGCG 60.049 61.111 3.53 3.53 41.18 6.01
1683 1773 2.094659 CGCTCCACAGTAGCCAACG 61.095 63.158 0.00 0.00 36.60 4.10
1685 1775 2.047274 GCGCTCCACAGTAGCCAA 60.047 61.111 0.00 0.00 36.60 4.52
1778 1868 3.785859 GGTCATCTGCCGGAGCCA 61.786 66.667 5.05 0.00 38.69 4.75
1904 1994 4.479993 GGCATCGCCCTCAGCAGT 62.480 66.667 0.00 0.00 44.06 4.40
2240 2330 6.904543 GCAGCAAAAACAAAAACAAATATCGT 59.095 30.769 0.00 0.00 0.00 3.73
2242 2332 8.683774 CATGCAGCAAAAACAAAAACAAATATC 58.316 29.630 0.00 0.00 0.00 1.63
2363 2453 7.499200 TTAACAGGCAACCTACCTATAAAGA 57.501 36.000 0.00 0.00 35.10 2.52
2364 2454 7.773690 ACATTAACAGGCAACCTACCTATAAAG 59.226 37.037 0.00 0.00 35.10 1.85
2391 2484 7.390027 ACTCGTACTACTAAGGTTAGTTCAGA 58.610 38.462 7.68 1.89 40.96 3.27
2409 2502 0.526954 CGCCACCCACATACTCGTAC 60.527 60.000 0.00 0.00 0.00 3.67
2412 2505 0.390603 TTTCGCCACCCACATACTCG 60.391 55.000 0.00 0.00 0.00 4.18
2413 2506 2.038387 ATTTCGCCACCCACATACTC 57.962 50.000 0.00 0.00 0.00 2.59
2414 2507 2.507407 AATTTCGCCACCCACATACT 57.493 45.000 0.00 0.00 0.00 2.12
2428 2521 7.997107 AACAACTTTTAACTCGGGAAATTTC 57.003 32.000 9.83 9.83 0.00 2.17
2488 2581 1.752683 ACAACACGGTTTTAGTGCCA 58.247 45.000 0.00 0.00 42.94 4.92
2490 2583 3.110358 GGAAACAACACGGTTTTAGTGC 58.890 45.455 0.00 0.00 40.85 4.40
2491 2584 3.379057 AGGGAAACAACACGGTTTTAGTG 59.621 43.478 0.00 0.00 40.85 2.74
2492 2585 3.379057 CAGGGAAACAACACGGTTTTAGT 59.621 43.478 0.00 0.00 40.85 2.24
2494 2587 3.128938 CACAGGGAAACAACACGGTTTTA 59.871 43.478 0.00 0.00 40.85 1.52
2512 2605 0.025898 CACGCATCGAGCAATCACAG 59.974 55.000 7.47 0.00 46.13 3.66
2547 2640 4.970003 GTGGCAGTAAAATATTGCGATCAC 59.030 41.667 0.00 0.00 41.70 3.06
2567 2668 3.781079 TTTTGAGAACAGCAAGTGTGG 57.219 42.857 0.00 0.00 40.26 4.17
2604 2705 0.963962 GATCCGGCGGGTATACTCAA 59.036 55.000 27.98 2.79 33.83 3.02
2606 2707 1.239968 ACGATCCGGCGGGTATACTC 61.240 60.000 27.98 5.27 35.12 2.59
2614 2748 0.040603 GAACTACTACGATCCGGCGG 60.041 60.000 22.51 22.51 35.12 6.13
2658 2795 3.912907 GACGGGATCGACGGGCAT 61.913 66.667 12.19 0.00 40.11 4.40
2669 2806 0.611062 ACTGGTCAAGATCGACGGGA 60.611 55.000 0.00 0.00 36.73 5.14
2670 2807 0.179134 GACTGGTCAAGATCGACGGG 60.179 60.000 0.00 0.00 36.73 5.28
2671 2808 0.811915 AGACTGGTCAAGATCGACGG 59.188 55.000 3.51 0.00 36.73 4.79
2672 2809 3.759527 TTAGACTGGTCAAGATCGACG 57.240 47.619 3.51 0.00 36.73 5.12
2673 2810 4.082136 AGGTTTAGACTGGTCAAGATCGAC 60.082 45.833 3.51 0.00 35.03 4.20
2693 2830 1.202651 GCACAGTTGTACAGGACAGGT 60.203 52.381 0.00 0.00 39.88 4.00
2694 2831 1.512926 GCACAGTTGTACAGGACAGG 58.487 55.000 0.00 0.00 39.88 4.00
2696 2833 0.107831 GGGCACAGTTGTACAGGACA 59.892 55.000 0.00 0.00 35.78 4.02
2697 2834 0.107831 TGGGCACAGTTGTACAGGAC 59.892 55.000 0.00 0.00 0.00 3.85
2699 2836 1.227999 CGTGGGCACAGTTGTACAGG 61.228 60.000 0.00 0.00 0.00 4.00
2700 2837 1.841663 GCGTGGGCACAGTTGTACAG 61.842 60.000 0.00 0.00 39.62 2.74
2701 2838 1.890041 GCGTGGGCACAGTTGTACA 60.890 57.895 0.00 0.00 39.62 2.90
2702 2839 1.890041 TGCGTGGGCACAGTTGTAC 60.890 57.895 0.00 0.00 46.21 2.90
2893 3386 1.353804 GCCGCAAGTGAAACGTTCA 59.646 52.632 0.00 0.00 45.86 3.18
2934 3427 1.799544 GCTCCTTGGGCAAAAACATG 58.200 50.000 0.00 0.00 0.00 3.21
2952 3445 2.605366 GAGACCAAGCAATTACTCTCGC 59.395 50.000 0.00 0.00 0.00 5.03
2955 3448 4.327680 GGTTGAGACCAAGCAATTACTCT 58.672 43.478 0.00 0.00 46.77 3.24
2956 3449 4.686839 GGTTGAGACCAAGCAATTACTC 57.313 45.455 0.00 0.00 46.77 2.59
2969 3477 2.743928 CTGGCTGGCGGTTGAGAC 60.744 66.667 1.18 0.00 0.00 3.36
3006 3516 0.040058 AGTTTGCCATCAGCCCATCA 59.960 50.000 0.00 0.00 42.71 3.07
3007 3517 0.743097 GAGTTTGCCATCAGCCCATC 59.257 55.000 0.00 0.00 42.71 3.51
3008 3518 0.685458 GGAGTTTGCCATCAGCCCAT 60.685 55.000 0.00 0.00 42.71 4.00
3009 3519 1.304381 GGAGTTTGCCATCAGCCCA 60.304 57.895 0.00 0.00 42.71 5.36
3010 3520 2.409870 CGGAGTTTGCCATCAGCCC 61.410 63.158 0.00 0.00 42.71 5.19
3011 3521 3.056313 GCGGAGTTTGCCATCAGCC 62.056 63.158 0.00 0.00 42.71 4.85
3012 3522 2.486966 GCGGAGTTTGCCATCAGC 59.513 61.111 0.00 0.00 44.14 4.26
3013 3523 1.298157 TTCGCGGAGTTTGCCATCAG 61.298 55.000 6.13 0.00 0.00 2.90
3026 3536 5.978934 ACTATACCTTGTAAATTTCGCGG 57.021 39.130 6.13 0.00 0.00 6.46
3036 3549 6.701841 CGTACGTTCTCCTACTATACCTTGTA 59.298 42.308 7.22 0.00 0.00 2.41
3046 3559 9.860898 ATAAAATAAAACGTACGTTCTCCTACT 57.139 29.630 31.79 13.38 37.35 2.57
3054 3567 7.268872 CCGCTCAAATAAAATAAAACGTACGTT 59.731 33.333 27.15 27.15 40.45 3.99
3066 3579 5.870978 AGTACGTACACCGCTCAAATAAAAT 59.129 36.000 26.55 0.00 41.42 1.82
3071 3584 4.142315 ACATAGTACGTACACCGCTCAAAT 60.142 41.667 26.55 5.34 41.42 2.32
3078 3591 5.334319 TCATCAAACATAGTACGTACACCG 58.666 41.667 26.55 15.85 44.03 4.94
3090 3603 6.874664 TGGTTAGTAGCGTTTCATCAAACATA 59.125 34.615 0.00 0.00 41.94 2.29
3091 3604 5.703592 TGGTTAGTAGCGTTTCATCAAACAT 59.296 36.000 0.00 0.00 41.94 2.71
3092 3605 5.057819 TGGTTAGTAGCGTTTCATCAAACA 58.942 37.500 0.00 0.00 41.94 2.83
3098 3611 3.522553 GAGCTGGTTAGTAGCGTTTCAT 58.477 45.455 0.00 0.00 45.61 2.57
3147 3672 3.294493 GCTGCGTTGCTTCCCCAA 61.294 61.111 0.00 0.00 0.00 4.12
3251 3776 1.226491 GAATCATGCACCTGCGCAC 60.226 57.895 5.66 0.00 46.56 5.34


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

AutoCloner maintained by Alex Coulton.