Multiple sequence alignment - TraesCS3B01G287900

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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 TraesCS3B01G287900 chr3B 100.000 5618 0 0 1 5618 462651997 462657614 0.000000e+00 10375
1 TraesCS3B01G287900 chr3B 93.910 5123 252 24 184 5266 252150040 252155142 0.000000e+00 7677
2 TraesCS3B01G287900 chr3B 93.208 5212 288 41 184 5357 403961156 403966339 0.000000e+00 7603
3 TraesCS3B01G287900 chr3B 98.396 187 3 0 1 187 462644523 462644709 4.200000e-86 329
4 TraesCS3B01G287900 chr3B 97.861 187 4 0 1 187 167653842 167654028 1.950000e-84 324
5 TraesCS3B01G287900 chr3B 97.283 184 5 0 1 184 220639237 220639054 4.230000e-81 313
6 TraesCS3B01G287900 chr3B 96.791 187 6 0 1 187 509009493 509009679 4.230000e-81 313
7 TraesCS3B01G287900 chr3B 97.268 183 5 0 1 183 167660799 167660981 1.520000e-80 311
8 TraesCS3B01G287900 chr7B 95.043 5467 207 36 184 5618 197422614 197428048 0.000000e+00 8536
9 TraesCS3B01G287900 chr7B 93.578 5466 277 40 184 5618 571060692 571066114 0.000000e+00 8082
10 TraesCS3B01G287900 chr7B 93.567 5456 279 37 184 5611 17882809 17888220 0.000000e+00 8065
11 TraesCS3B01G287900 chr7B 91.696 5118 344 51 184 5263 73616855 73621929 0.000000e+00 7022
12 TraesCS3B01G287900 chr7B 94.511 3243 127 24 2388 5618 416730237 416727034 0.000000e+00 4955
13 TraesCS3B01G287900 chr7B 91.969 2428 152 25 184 2585 412001515 411999105 0.000000e+00 3363
14 TraesCS3B01G287900 chr7B 93.568 1508 75 14 4115 5618 206466922 206465433 0.000000e+00 2228
15 TraesCS3B01G287900 chr7B 90.714 1303 104 9 4057 5357 214334157 214332870 0.000000e+00 1720
16 TraesCS3B01G287900 chr7B 97.326 187 5 0 1 187 664366534 664366720 9.080000e-83 318
17 TraesCS3B01G287900 chr7B 97.312 186 5 0 1 186 408691759 408691574 3.270000e-82 316
18 TraesCS3B01G287900 chr6B 93.343 5468 261 41 184 5618 362246237 362240840 0.000000e+00 7986
19 TraesCS3B01G287900 chr6B 93.996 5213 248 36 184 5357 360446532 360441346 0.000000e+00 7832
20 TraesCS3B01G287900 chr6B 93.853 3042 167 16 2326 5357 216288769 216291800 0.000000e+00 4564
21 TraesCS3B01G287900 chr6B 92.647 2176 121 22 184 2335 216241923 216244083 0.000000e+00 3096
22 TraesCS3B01G287900 chr6B 96.791 187 6 0 1 187 408711132 408710946 4.230000e-81 313
23 TraesCS3B01G287900 chr2B 91.415 5207 359 52 184 5357 343964385 343969536 0.000000e+00 7059
24 TraesCS3B01G287900 chr2B 92.668 3805 215 27 184 3961 252805101 252808868 0.000000e+00 5422
25 TraesCS3B01G287900 chr2B 88.668 503 32 9 5119 5618 657957402 657956922 1.740000e-164 590
26 TraesCS3B01G287900 chr2B 96.791 187 6 0 1 187 237197519 237197705 4.230000e-81 313
27 TraesCS3B01G287900 chr1B 92.388 3941 204 40 184 4080 280909491 280905603 0.000000e+00 5528
28 TraesCS3B01G287900 chr4B 95.103 2818 124 9 2253 5063 427373516 427376326 0.000000e+00 4427
29 TraesCS3B01G287900 chr4B 92.036 2235 130 31 184 2390 427371189 427373403 0.000000e+00 3097
30 TraesCS3B01G287900 chr4B 89.710 2245 172 34 184 2390 421195188 421197411 0.000000e+00 2811
31 TraesCS3B01G287900 chr4B 91.481 493 17 8 5119 5607 427376321 427376792 0.000000e+00 654
32 TraesCS3B01G287900 chr4B 89.264 503 29 9 5119 5618 244233246 244232766 1.730000e-169 606
33 TraesCS3B01G287900 chr5B 90.258 503 25 7 5119 5618 90605679 90605198 2.210000e-178 636
34 TraesCS3B01G287900 chr5B 89.442 502 29 8 5119 5618 354135738 354135259 3.720000e-171 612
35 TraesCS3B01G287900 chrUn 89.901 505 23 11 5118 5618 86138290 86137810 4.780000e-175 625


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 TraesCS3B01G287900 chr3B 462651997 462657614 5617 False 10375 10375 100.000000 1 5618 1 chr3B.!!$F6 5617
1 TraesCS3B01G287900 chr3B 252150040 252155142 5102 False 7677 7677 93.910000 184 5266 1 chr3B.!!$F3 5082
2 TraesCS3B01G287900 chr3B 403961156 403966339 5183 False 7603 7603 93.208000 184 5357 1 chr3B.!!$F4 5173
3 TraesCS3B01G287900 chr7B 197422614 197428048 5434 False 8536 8536 95.043000 184 5618 1 chr7B.!!$F3 5434
4 TraesCS3B01G287900 chr7B 571060692 571066114 5422 False 8082 8082 93.578000 184 5618 1 chr7B.!!$F4 5434
5 TraesCS3B01G287900 chr7B 17882809 17888220 5411 False 8065 8065 93.567000 184 5611 1 chr7B.!!$F1 5427
6 TraesCS3B01G287900 chr7B 73616855 73621929 5074 False 7022 7022 91.696000 184 5263 1 chr7B.!!$F2 5079
7 TraesCS3B01G287900 chr7B 416727034 416730237 3203 True 4955 4955 94.511000 2388 5618 1 chr7B.!!$R5 3230
8 TraesCS3B01G287900 chr7B 411999105 412001515 2410 True 3363 3363 91.969000 184 2585 1 chr7B.!!$R4 2401
9 TraesCS3B01G287900 chr7B 206465433 206466922 1489 True 2228 2228 93.568000 4115 5618 1 chr7B.!!$R1 1503
10 TraesCS3B01G287900 chr7B 214332870 214334157 1287 True 1720 1720 90.714000 4057 5357 1 chr7B.!!$R2 1300
11 TraesCS3B01G287900 chr6B 362240840 362246237 5397 True 7986 7986 93.343000 184 5618 1 chr6B.!!$R2 5434
12 TraesCS3B01G287900 chr6B 360441346 360446532 5186 True 7832 7832 93.996000 184 5357 1 chr6B.!!$R1 5173
13 TraesCS3B01G287900 chr6B 216288769 216291800 3031 False 4564 4564 93.853000 2326 5357 1 chr6B.!!$F2 3031
14 TraesCS3B01G287900 chr6B 216241923 216244083 2160 False 3096 3096 92.647000 184 2335 1 chr6B.!!$F1 2151
15 TraesCS3B01G287900 chr2B 343964385 343969536 5151 False 7059 7059 91.415000 184 5357 1 chr2B.!!$F3 5173
16 TraesCS3B01G287900 chr2B 252805101 252808868 3767 False 5422 5422 92.668000 184 3961 1 chr2B.!!$F2 3777
17 TraesCS3B01G287900 chr1B 280905603 280909491 3888 True 5528 5528 92.388000 184 4080 1 chr1B.!!$R1 3896
18 TraesCS3B01G287900 chr4B 421195188 421197411 2223 False 2811 2811 89.710000 184 2390 1 chr4B.!!$F1 2206
19 TraesCS3B01G287900 chr4B 427371189 427376792 5603 False 2726 4427 92.873333 184 5607 3 chr4B.!!$F2 5423

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
27 28 0.034477 AACGGGGAAAATGCTCGGAT 60.034 50.000 0.00 0.00 0.00 4.18 F
1273 1321 0.040157 TTGAGTACGACAACGACCCG 60.040 55.000 0.00 0.00 42.66 5.28 F
1373 1421 0.179234 TGAAAGGTGCACCGTCTTCA 59.821 50.000 30.89 30.89 42.08 3.02 F
2479 2815 1.238439 CCACAGAAGGCGTGTCATTT 58.762 50.000 0.00 0.00 32.26 2.32 F
3323 3699 1.877443 ACAACGTTCCGGATTTCCAAG 59.123 47.619 4.15 0.00 35.14 3.61 F
3474 3853 2.034685 GGAGAAAACACAACTGCTTCCC 59.965 50.000 0.00 0.00 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1761 0.749818 TTCTCCAACTTTGCACGGCA 60.750 50.000 0.00 0.0 36.47 5.69 R
2713 3049 0.243095 GTTCGGGTAGTGAAGACGCT 59.757 55.000 0.00 0.0 40.21 5.07 R
2886 3226 3.060602 TGCATTTGTACGTTGACATCGA 58.939 40.909 12.66 0.0 0.00 3.59 R
3786 4170 1.067060 CTACGCATAGCTGTAGCACCA 59.933 52.381 6.65 0.0 45.16 4.17 R
4526 4925 1.353022 TGGTCCTCCTTGCGGTTAATT 59.647 47.619 0.00 0.0 34.23 1.40 R
5426 5884 0.974010 GGTGAGTCCGTCATACCCCA 60.974 60.000 0.00 0.0 37.56 4.96 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
21 22 1.211709 CGGACAACGGGGAAAATGC 59.788 57.895 0.00 0.00 39.42 3.56
22 23 1.241315 CGGACAACGGGGAAAATGCT 61.241 55.000 0.00 0.00 39.42 3.79
23 24 0.526211 GGACAACGGGGAAAATGCTC 59.474 55.000 0.00 0.00 0.00 4.26
24 25 0.168128 GACAACGGGGAAAATGCTCG 59.832 55.000 0.00 0.00 0.00 5.03
25 26 1.241315 ACAACGGGGAAAATGCTCGG 61.241 55.000 0.00 0.00 0.00 4.63
26 27 0.958382 CAACGGGGAAAATGCTCGGA 60.958 55.000 0.00 0.00 0.00 4.55
27 28 0.034477 AACGGGGAAAATGCTCGGAT 60.034 50.000 0.00 0.00 0.00 4.18
28 29 0.748005 ACGGGGAAAATGCTCGGATG 60.748 55.000 0.00 0.00 0.00 3.51
29 30 1.735973 GGGGAAAATGCTCGGATGC 59.264 57.895 0.00 0.00 0.00 3.91
31 32 0.817013 GGGAAAATGCTCGGATGCAA 59.183 50.000 0.00 0.00 46.61 4.08
32 33 1.202336 GGGAAAATGCTCGGATGCAAG 60.202 52.381 0.00 0.00 46.61 4.01
33 34 1.745087 GGAAAATGCTCGGATGCAAGA 59.255 47.619 0.00 0.00 46.61 3.02
34 35 2.164219 GGAAAATGCTCGGATGCAAGAA 59.836 45.455 0.00 0.00 46.61 2.52
35 36 3.367292 GGAAAATGCTCGGATGCAAGAAA 60.367 43.478 0.00 0.00 46.61 2.52
36 37 2.927553 AATGCTCGGATGCAAGAAAC 57.072 45.000 0.00 0.00 46.61 2.78
37 38 0.729116 ATGCTCGGATGCAAGAAACG 59.271 50.000 0.00 0.00 46.61 3.60
38 39 0.320334 TGCTCGGATGCAAGAAACGA 60.320 50.000 0.00 0.00 40.29 3.85
39 40 0.796312 GCTCGGATGCAAGAAACGAA 59.204 50.000 0.00 0.00 32.80 3.85
40 41 1.464189 GCTCGGATGCAAGAAACGAAC 60.464 52.381 0.00 0.00 32.80 3.95
41 42 1.798223 CTCGGATGCAAGAAACGAACA 59.202 47.619 0.00 0.00 32.80 3.18
42 43 1.529438 TCGGATGCAAGAAACGAACAC 59.471 47.619 0.00 0.00 0.00 3.32
43 44 1.721489 CGGATGCAAGAAACGAACACG 60.721 52.381 0.00 0.00 0.00 4.49
44 45 1.263217 GGATGCAAGAAACGAACACGT 59.737 47.619 0.00 0.00 42.17 4.49
45 46 2.477375 GGATGCAAGAAACGAACACGTA 59.523 45.455 0.00 0.00 39.39 3.57
46 47 3.124636 GGATGCAAGAAACGAACACGTAT 59.875 43.478 0.00 0.00 39.39 3.06
47 48 3.513462 TGCAAGAAACGAACACGTATG 57.487 42.857 0.00 0.00 39.39 2.39
48 49 2.230864 GCAAGAAACGAACACGTATGC 58.769 47.619 0.00 0.00 39.39 3.14
49 50 2.349060 GCAAGAAACGAACACGTATGCA 60.349 45.455 0.00 0.00 39.39 3.96
50 51 3.846744 GCAAGAAACGAACACGTATGCAA 60.847 43.478 0.00 0.00 39.39 4.08
51 52 4.275662 CAAGAAACGAACACGTATGCAAA 58.724 39.130 0.00 0.00 39.39 3.68
52 53 4.539509 AGAAACGAACACGTATGCAAAA 57.460 36.364 0.00 0.00 39.39 2.44
53 54 5.103290 AGAAACGAACACGTATGCAAAAT 57.897 34.783 0.00 0.00 39.39 1.82
54 55 4.909305 AGAAACGAACACGTATGCAAAATG 59.091 37.500 0.00 0.00 39.39 2.32
55 56 4.475763 AACGAACACGTATGCAAAATGA 57.524 36.364 0.00 0.00 39.39 2.57
56 57 4.475763 ACGAACACGTATGCAAAATGAA 57.524 36.364 0.00 0.00 38.51 2.57
57 58 4.849883 ACGAACACGTATGCAAAATGAAA 58.150 34.783 0.00 0.00 38.51 2.69
58 59 5.457140 ACGAACACGTATGCAAAATGAAAT 58.543 33.333 0.00 0.00 38.51 2.17
59 60 5.341993 ACGAACACGTATGCAAAATGAAATG 59.658 36.000 0.00 0.00 38.51 2.32
60 61 5.514059 AACACGTATGCAAAATGAAATGC 57.486 34.783 0.00 0.00 42.86 3.56
67 68 4.994220 TGCAAAATGAAATGCACATGAC 57.006 36.364 0.00 0.00 46.87 3.06
68 69 3.429207 TGCAAAATGAAATGCACATGACG 59.571 39.130 0.00 0.00 46.87 4.35
69 70 3.674281 GCAAAATGAAATGCACATGACGA 59.326 39.130 0.00 0.00 42.12 4.20
70 71 4.433283 GCAAAATGAAATGCACATGACGAC 60.433 41.667 0.00 0.00 42.12 4.34
71 72 4.502171 AAATGAAATGCACATGACGACA 57.498 36.364 0.00 0.00 0.00 4.35
72 73 4.707030 AATGAAATGCACATGACGACAT 57.293 36.364 0.00 0.00 37.19 3.06
73 74 9.896582 GCAAAATGAAATGCACATGACGACATG 62.897 40.741 23.22 23.22 44.17 3.21
86 87 6.812879 ATGACGACATGATATGAAATGCAT 57.187 33.333 0.00 0.00 36.87 3.96
87 88 7.910441 ATGACGACATGATATGAAATGCATA 57.090 32.000 0.00 0.00 38.30 3.14
88 89 7.727331 TGACGACATGATATGAAATGCATAA 57.273 32.000 0.00 0.00 42.45 1.90
89 90 7.799784 TGACGACATGATATGAAATGCATAAG 58.200 34.615 0.00 0.00 42.45 1.73
90 91 7.656948 TGACGACATGATATGAAATGCATAAGA 59.343 33.333 0.00 0.00 42.45 2.10
91 92 8.557592 ACGACATGATATGAAATGCATAAGAT 57.442 30.769 0.00 0.00 42.45 2.40
92 93 8.448615 ACGACATGATATGAAATGCATAAGATG 58.551 33.333 0.00 0.00 42.45 2.90
93 94 8.662141 CGACATGATATGAAATGCATAAGATGA 58.338 33.333 0.00 0.00 42.45 2.92
94 95 9.770503 GACATGATATGAAATGCATAAGATGAC 57.229 33.333 0.00 1.76 42.45 3.06
95 96 9.292195 ACATGATATGAAATGCATAAGATGACA 57.708 29.630 0.00 0.00 42.45 3.58
98 99 8.736244 TGATATGAAATGCATAAGATGACATGG 58.264 33.333 0.00 0.00 42.45 3.66
99 100 5.190992 TGAAATGCATAAGATGACATGGC 57.809 39.130 0.00 0.00 30.98 4.40
100 101 4.645588 TGAAATGCATAAGATGACATGGCA 59.354 37.500 2.18 2.18 30.98 4.92
101 102 5.127356 TGAAATGCATAAGATGACATGGCAA 59.873 36.000 4.70 0.00 30.98 4.52
102 103 5.601583 AATGCATAAGATGACATGGCAAA 57.398 34.783 4.70 0.00 30.98 3.68
103 104 4.642445 TGCATAAGATGACATGGCAAAG 57.358 40.909 4.70 0.00 0.00 2.77
104 105 4.018490 TGCATAAGATGACATGGCAAAGT 58.982 39.130 4.70 0.00 0.00 2.66
105 106 4.142337 TGCATAAGATGACATGGCAAAGTG 60.142 41.667 4.70 1.70 0.00 3.16
106 107 4.357142 CATAAGATGACATGGCAAAGTGC 58.643 43.478 4.70 0.00 44.08 4.40
123 124 2.884146 GCAACACGCAAGCAAATGA 58.116 47.368 0.00 0.00 45.62 2.57
124 125 0.503961 GCAACACGCAAGCAAATGAC 59.496 50.000 0.00 0.00 45.62 3.06
125 126 1.837648 CAACACGCAAGCAAATGACA 58.162 45.000 0.00 0.00 45.62 3.58
126 127 2.396601 CAACACGCAAGCAAATGACAT 58.603 42.857 0.00 0.00 45.62 3.06
127 128 2.054687 ACACGCAAGCAAATGACATG 57.945 45.000 0.00 0.00 45.62 3.21
128 129 1.336148 ACACGCAAGCAAATGACATGG 60.336 47.619 0.00 0.00 45.62 3.66
129 130 0.388907 ACGCAAGCAAATGACATGGC 60.389 50.000 0.00 0.00 45.62 4.40
130 131 0.388778 CGCAAGCAAATGACATGGCA 60.389 50.000 2.18 2.18 0.00 4.92
131 132 1.798283 GCAAGCAAATGACATGGCAA 58.202 45.000 4.70 0.00 0.00 4.52
132 133 1.461897 GCAAGCAAATGACATGGCAAC 59.538 47.619 4.70 0.00 0.00 4.17
133 134 1.722464 CAAGCAAATGACATGGCAACG 59.278 47.619 4.70 0.00 42.51 4.10
134 135 1.246649 AGCAAATGACATGGCAACGA 58.753 45.000 4.70 0.00 42.51 3.85
135 136 1.068333 AGCAAATGACATGGCAACGAC 60.068 47.619 4.70 0.00 42.51 4.34
136 137 1.605500 CAAATGACATGGCAACGACG 58.394 50.000 4.70 0.00 42.51 5.12
137 138 0.521291 AAATGACATGGCAACGACGG 59.479 50.000 4.70 0.00 42.51 4.79
138 139 1.922135 AATGACATGGCAACGACGGC 61.922 55.000 4.70 0.00 42.51 5.68
139 140 4.147322 GACATGGCAACGACGGCG 62.147 66.667 10.39 10.39 44.79 6.46
140 141 4.673298 ACATGGCAACGACGGCGA 62.673 61.111 22.49 0.00 41.64 5.54
141 142 3.418913 CATGGCAACGACGGCGAA 61.419 61.111 22.49 0.00 41.64 4.70
142 143 2.435938 ATGGCAACGACGGCGAAT 60.436 55.556 22.49 1.56 41.64 3.34
143 144 1.153529 ATGGCAACGACGGCGAATA 60.154 52.632 22.49 0.00 41.64 1.75
144 145 0.741574 ATGGCAACGACGGCGAATAA 60.742 50.000 22.49 0.00 41.64 1.40
145 146 1.059838 GGCAACGACGGCGAATAAC 59.940 57.895 22.49 0.67 41.64 1.89
146 147 1.356527 GGCAACGACGGCGAATAACT 61.357 55.000 22.49 0.00 41.64 2.24
147 148 0.247145 GCAACGACGGCGAATAACTG 60.247 55.000 22.49 5.42 41.64 3.16
148 149 0.368907 CAACGACGGCGAATAACTGG 59.631 55.000 22.49 0.00 41.64 4.00
149 150 1.356527 AACGACGGCGAATAACTGGC 61.357 55.000 22.49 0.00 41.64 4.85
150 151 1.807981 CGACGGCGAATAACTGGCA 60.808 57.895 16.62 0.00 40.82 4.92
151 152 1.752501 CGACGGCGAATAACTGGCAG 61.753 60.000 16.62 14.16 40.82 4.85
152 153 0.459585 GACGGCGAATAACTGGCAGA 60.460 55.000 23.66 0.00 0.00 4.26
153 154 0.739813 ACGGCGAATAACTGGCAGAC 60.740 55.000 23.66 5.99 0.00 3.51
154 155 0.739462 CGGCGAATAACTGGCAGACA 60.739 55.000 23.66 8.46 0.00 3.41
155 156 0.727398 GGCGAATAACTGGCAGACAC 59.273 55.000 23.66 6.68 0.00 3.67
156 157 0.727398 GCGAATAACTGGCAGACACC 59.273 55.000 23.66 5.14 0.00 4.16
157 158 1.676014 GCGAATAACTGGCAGACACCT 60.676 52.381 23.66 0.74 0.00 4.00
158 159 2.002586 CGAATAACTGGCAGACACCTG 58.997 52.381 23.66 2.78 43.22 4.00
159 160 2.359900 GAATAACTGGCAGACACCTGG 58.640 52.381 23.66 0.00 40.72 4.45
165 166 3.503363 GCAGACACCTGGCGCATC 61.503 66.667 10.83 0.00 40.72 3.91
166 167 3.190849 CAGACACCTGGCGCATCG 61.191 66.667 10.83 0.00 36.77 3.84
167 168 3.381983 AGACACCTGGCGCATCGA 61.382 61.111 10.83 0.00 0.00 3.59
168 169 2.434185 GACACCTGGCGCATCGAA 60.434 61.111 10.83 0.00 0.00 3.71
169 170 1.815421 GACACCTGGCGCATCGAAT 60.815 57.895 10.83 0.00 0.00 3.34
170 171 1.766143 GACACCTGGCGCATCGAATC 61.766 60.000 10.83 0.00 0.00 2.52
171 172 2.203070 ACCTGGCGCATCGAATCC 60.203 61.111 10.83 0.00 0.00 3.01
172 173 3.341043 CCTGGCGCATCGAATCCG 61.341 66.667 10.83 0.00 37.07 4.18
173 174 3.341043 CTGGCGCATCGAATCCGG 61.341 66.667 10.83 0.00 36.24 5.14
174 175 4.908687 TGGCGCATCGAATCCGGG 62.909 66.667 10.83 0.00 36.24 5.73
178 179 4.910585 GCATCGAATCCGGGGCGT 62.911 66.667 0.00 0.00 36.24 5.68
179 180 2.203015 CATCGAATCCGGGGCGTT 60.203 61.111 0.00 0.00 36.24 4.84
180 181 1.068417 CATCGAATCCGGGGCGTTA 59.932 57.895 0.00 0.00 36.24 3.18
181 182 1.068585 ATCGAATCCGGGGCGTTAC 59.931 57.895 0.00 0.00 36.24 2.50
182 183 1.678598 ATCGAATCCGGGGCGTTACA 61.679 55.000 0.00 0.00 36.24 2.41
329 331 5.163447 CGAGATGGGACTAAACATTAGGACA 60.163 44.000 2.53 0.00 0.00 4.02
601 631 2.354729 TGGCAATCCAGTTCCCGG 59.645 61.111 0.00 0.00 37.47 5.73
605 635 1.092348 GCAATCCAGTTCCCGGTTAC 58.908 55.000 0.00 0.00 0.00 2.50
725 758 4.553351 CGAATGCAGTTCATTATCGCACAT 60.553 41.667 0.00 0.00 44.95 3.21
769 807 1.169661 ATGCCCGTTCGCACAGAAAA 61.170 50.000 0.00 0.00 42.70 2.29
770 808 1.082104 GCCCGTTCGCACAGAAAAG 60.082 57.895 0.00 0.00 41.10 2.27
771 809 1.782028 GCCCGTTCGCACAGAAAAGT 61.782 55.000 0.00 0.00 41.10 2.66
773 811 0.041312 CCGTTCGCACAGAAAAGTGG 60.041 55.000 0.00 0.00 41.10 4.00
774 812 0.655733 CGTTCGCACAGAAAAGTGGT 59.344 50.000 0.00 0.00 41.10 4.16
776 814 1.021202 TTCGCACAGAAAAGTGGTGG 58.979 50.000 0.00 0.00 39.87 4.61
778 816 0.738389 CGCACAGAAAAGTGGTGGTT 59.262 50.000 0.00 0.00 39.87 3.67
779 817 1.944024 CGCACAGAAAAGTGGTGGTTA 59.056 47.619 0.00 0.00 39.87 2.85
1034 1082 6.299922 TCCACAACAACACAAGTATCCATTA 58.700 36.000 0.00 0.00 0.00 1.90
1054 1102 2.354729 CTCCCACCAAATCGCCCA 59.645 61.111 0.00 0.00 0.00 5.36
1120 1168 1.210931 CGACGAGTACAAGGGCGAA 59.789 57.895 0.00 0.00 0.00 4.70
1273 1321 0.040157 TTGAGTACGACAACGACCCG 60.040 55.000 0.00 0.00 42.66 5.28
1278 1326 1.172180 TACGACAACGACCCGGAAGT 61.172 55.000 0.73 0.00 42.66 3.01
1289 1337 1.291877 CCCGGAAGTGACGCAGAAAG 61.292 60.000 0.73 0.00 0.00 2.62
1328 1376 3.383229 TCGGCAAGAATCACCCGA 58.617 55.556 5.15 5.15 46.50 5.14
1373 1421 0.179234 TGAAAGGTGCACCGTCTTCA 59.821 50.000 30.89 30.89 42.08 3.02
1387 1435 2.484889 GTCTTCAACAACTTCCTCGCT 58.515 47.619 0.00 0.00 0.00 4.93
1390 1438 2.839486 TCAACAACTTCCTCGCTGAT 57.161 45.000 0.00 0.00 0.00 2.90
1562 1610 1.533965 GCATGCTCATCGACGACTACA 60.534 52.381 11.37 0.00 0.00 2.74
1581 1630 7.251704 ACTACAACAACAACATGAAGAAGAG 57.748 36.000 0.00 0.00 0.00 2.85
1603 1652 3.598715 ACCGACGACGAGCACCAA 61.599 61.111 9.28 0.00 42.66 3.67
1712 1761 2.852075 TCACCCAGGACGGCCTTT 60.852 61.111 7.41 0.00 43.90 3.11
1891 1947 9.389570 GTTGTTTGCTTATGTATCGTTAGTTTT 57.610 29.630 0.00 0.00 0.00 2.43
2028 2085 1.246056 ATGCAAACAGGACGCATGCT 61.246 50.000 17.13 2.38 44.41 3.79
2164 2222 5.904080 CACAAAAAGAAAAACGCAAAACACA 59.096 32.000 0.00 0.00 0.00 3.72
2166 2224 7.742089 CACAAAAAGAAAAACGCAAAACACATA 59.258 29.630 0.00 0.00 0.00 2.29
2251 2334 8.463930 AAGTACATGTATGATTTACATTGGGG 57.536 34.615 9.18 0.00 40.07 4.96
2375 2706 2.765122 CACGCCCCAACATTGAAAAAT 58.235 42.857 0.00 0.00 0.00 1.82
2472 2808 3.832237 CTGCACCCACAGAAGGCGT 62.832 63.158 0.00 0.00 40.25 5.68
2479 2815 1.238439 CCACAGAAGGCGTGTCATTT 58.762 50.000 0.00 0.00 32.26 2.32
2585 2921 6.092259 CCAAATAAGTAACAAGAGGAGTTCGG 59.908 42.308 0.00 0.00 0.00 4.30
3134 3500 6.874288 AAGAAAGAACACCATCAAGAGAAG 57.126 37.500 0.00 0.00 0.00 2.85
3323 3699 1.877443 ACAACGTTCCGGATTTCCAAG 59.123 47.619 4.15 0.00 35.14 3.61
3473 3852 2.952310 AGGAGAAAACACAACTGCTTCC 59.048 45.455 0.00 0.00 0.00 3.46
3474 3853 2.034685 GGAGAAAACACAACTGCTTCCC 59.965 50.000 0.00 0.00 0.00 3.97
3786 4170 2.947938 AAGAAGCCACAGCGTGCAGT 62.948 55.000 0.00 0.00 46.67 4.40
4228 4622 9.443283 GATATTCATATTGCAGTTCAGTTTCAC 57.557 33.333 0.00 0.00 0.00 3.18
4320 4719 4.438744 GCCAATGGAACTAGACAAATTCCG 60.439 45.833 2.05 0.00 44.17 4.30
4323 4722 4.202245 TGGAACTAGACAAATTCCGGAG 57.798 45.455 3.34 0.00 44.17 4.63
4345 4744 4.223032 AGGAATGATGAGTACACCTTCGTT 59.777 41.667 0.00 2.43 0.00 3.85
4366 4765 4.753516 TGGATTCGCTATTGAAGGAGAA 57.246 40.909 0.00 0.00 0.00 2.87
4814 5217 7.715657 TGTATGCAAGATTTTGATAATGTCCC 58.284 34.615 0.00 0.00 36.36 4.46
5293 5750 0.753479 TTTCGTGTGGTGCCCAACAT 60.753 50.000 0.00 0.00 34.18 2.71
5306 5763 2.817258 GCCCAACATACACACTTGCTAA 59.183 45.455 0.00 0.00 0.00 3.09
5382 5839 1.832719 TTCCATCAAAGGGGACGCGA 61.833 55.000 15.93 0.00 31.59 5.87
5443 5901 1.410004 GATGGGGTATGACGGACTCA 58.590 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.338655 CATTTTCCCCGTTGTCCGTTT 59.661 47.619 0.00 0.00 33.66 3.60
1 2 0.955905 CATTTTCCCCGTTGTCCGTT 59.044 50.000 0.00 0.00 33.66 4.44
2 3 1.520600 GCATTTTCCCCGTTGTCCGT 61.521 55.000 0.00 0.00 33.66 4.69
3 4 1.211709 GCATTTTCCCCGTTGTCCG 59.788 57.895 0.00 0.00 0.00 4.79
4 5 0.526211 GAGCATTTTCCCCGTTGTCC 59.474 55.000 0.00 0.00 0.00 4.02
5 6 0.168128 CGAGCATTTTCCCCGTTGTC 59.832 55.000 0.00 0.00 0.00 3.18
6 7 1.241315 CCGAGCATTTTCCCCGTTGT 61.241 55.000 0.00 0.00 0.00 3.32
7 8 0.958382 TCCGAGCATTTTCCCCGTTG 60.958 55.000 0.00 0.00 0.00 4.10
8 9 0.034477 ATCCGAGCATTTTCCCCGTT 60.034 50.000 0.00 0.00 0.00 4.44
9 10 0.748005 CATCCGAGCATTTTCCCCGT 60.748 55.000 0.00 0.00 0.00 5.28
10 11 2.024918 CATCCGAGCATTTTCCCCG 58.975 57.895 0.00 0.00 0.00 5.73
11 12 1.037030 TGCATCCGAGCATTTTCCCC 61.037 55.000 0.00 0.00 40.11 4.81
12 13 0.817013 TTGCATCCGAGCATTTTCCC 59.183 50.000 0.00 0.00 45.19 3.97
13 14 1.745087 TCTTGCATCCGAGCATTTTCC 59.255 47.619 0.00 0.00 45.19 3.13
14 15 3.492421 TTCTTGCATCCGAGCATTTTC 57.508 42.857 0.00 0.00 45.19 2.29
15 16 3.578688 GTTTCTTGCATCCGAGCATTTT 58.421 40.909 0.00 0.00 45.19 1.82
16 17 2.414559 CGTTTCTTGCATCCGAGCATTT 60.415 45.455 0.00 0.00 45.19 2.32
17 18 1.131126 CGTTTCTTGCATCCGAGCATT 59.869 47.619 0.00 0.00 45.19 3.56
18 19 0.729116 CGTTTCTTGCATCCGAGCAT 59.271 50.000 0.00 0.00 45.19 3.79
19 20 0.320334 TCGTTTCTTGCATCCGAGCA 60.320 50.000 0.00 0.00 43.99 4.26
20 21 0.796312 TTCGTTTCTTGCATCCGAGC 59.204 50.000 0.00 0.00 0.00 5.03
21 22 1.798223 TGTTCGTTTCTTGCATCCGAG 59.202 47.619 0.00 0.00 0.00 4.63
22 23 1.529438 GTGTTCGTTTCTTGCATCCGA 59.471 47.619 0.00 0.00 0.00 4.55
23 24 1.721489 CGTGTTCGTTTCTTGCATCCG 60.721 52.381 0.00 0.00 0.00 4.18
24 25 1.950472 CGTGTTCGTTTCTTGCATCC 58.050 50.000 0.00 0.00 0.00 3.51
34 35 9.386110 GCATTTCATTTTGCATACGTGTTCGTT 62.386 37.037 0.00 0.00 43.07 3.85
35 36 8.017529 GCATTTCATTTTGCATACGTGTTCGT 62.018 38.462 0.00 0.00 44.23 3.85
36 37 5.718290 GCATTTCATTTTGCATACGTGTTCG 60.718 40.000 0.00 0.00 38.72 3.95
37 38 5.118357 TGCATTTCATTTTGCATACGTGTTC 59.882 36.000 0.00 0.00 43.54 3.18
38 39 4.987285 TGCATTTCATTTTGCATACGTGTT 59.013 33.333 0.00 0.00 43.54 3.32
39 40 4.554292 TGCATTTCATTTTGCATACGTGT 58.446 34.783 0.00 0.00 43.54 4.49
46 47 3.429207 CGTCATGTGCATTTCATTTTGCA 59.571 39.130 0.00 0.00 46.03 4.08
47 48 3.674281 TCGTCATGTGCATTTCATTTTGC 59.326 39.130 0.00 0.00 39.33 3.68
48 49 4.680567 TGTCGTCATGTGCATTTCATTTTG 59.319 37.500 0.00 0.00 0.00 2.44
49 50 4.869215 TGTCGTCATGTGCATTTCATTTT 58.131 34.783 0.00 0.00 0.00 1.82
50 51 4.502171 TGTCGTCATGTGCATTTCATTT 57.498 36.364 0.00 0.00 0.00 2.32
51 52 4.417506 CATGTCGTCATGTGCATTTCATT 58.582 39.130 13.58 0.00 44.37 2.57
52 53 4.023739 CATGTCGTCATGTGCATTTCAT 57.976 40.909 13.58 0.00 44.37 2.57
53 54 3.474693 CATGTCGTCATGTGCATTTCA 57.525 42.857 13.58 0.00 44.37 2.69
60 61 7.784049 ATGCATTTCATATCATGTCGTCATGTG 60.784 37.037 19.65 12.35 41.56 3.21
61 62 6.206048 ATGCATTTCATATCATGTCGTCATGT 59.794 34.615 19.65 11.23 41.56 3.21
62 63 6.608610 ATGCATTTCATATCATGTCGTCATG 58.391 36.000 15.34 15.34 41.85 3.07
63 64 6.812879 ATGCATTTCATATCATGTCGTCAT 57.187 33.333 0.00 0.00 32.59 3.06
64 65 7.656948 TCTTATGCATTTCATATCATGTCGTCA 59.343 33.333 3.54 0.00 37.49 4.35
65 66 8.021955 TCTTATGCATTTCATATCATGTCGTC 57.978 34.615 3.54 0.00 37.49 4.20
66 67 7.967890 TCTTATGCATTTCATATCATGTCGT 57.032 32.000 3.54 0.00 37.49 4.34
67 68 8.662141 TCATCTTATGCATTTCATATCATGTCG 58.338 33.333 3.54 0.00 37.49 4.35
68 69 9.770503 GTCATCTTATGCATTTCATATCATGTC 57.229 33.333 3.54 0.00 37.49 3.06
69 70 9.292195 TGTCATCTTATGCATTTCATATCATGT 57.708 29.630 3.54 0.00 37.49 3.21
72 73 8.736244 CCATGTCATCTTATGCATTTCATATCA 58.264 33.333 3.54 0.00 37.49 2.15
73 74 7.701078 GCCATGTCATCTTATGCATTTCATATC 59.299 37.037 3.54 0.00 37.49 1.63
74 75 7.177744 TGCCATGTCATCTTATGCATTTCATAT 59.822 33.333 3.54 0.00 37.49 1.78
75 76 6.490721 TGCCATGTCATCTTATGCATTTCATA 59.509 34.615 3.54 0.00 36.63 2.15
76 77 5.303333 TGCCATGTCATCTTATGCATTTCAT 59.697 36.000 3.54 0.00 39.17 2.57
77 78 4.645588 TGCCATGTCATCTTATGCATTTCA 59.354 37.500 3.54 0.00 0.00 2.69
78 79 5.190992 TGCCATGTCATCTTATGCATTTC 57.809 39.130 3.54 0.00 0.00 2.17
79 80 5.601583 TTGCCATGTCATCTTATGCATTT 57.398 34.783 3.54 0.00 0.00 2.32
80 81 5.128171 ACTTTGCCATGTCATCTTATGCATT 59.872 36.000 3.54 0.00 0.00 3.56
81 82 4.647853 ACTTTGCCATGTCATCTTATGCAT 59.352 37.500 3.79 3.79 0.00 3.96
82 83 4.018490 ACTTTGCCATGTCATCTTATGCA 58.982 39.130 0.00 0.00 0.00 3.96
83 84 4.357142 CACTTTGCCATGTCATCTTATGC 58.643 43.478 0.00 0.00 0.00 3.14
84 85 4.142337 TGCACTTTGCCATGTCATCTTATG 60.142 41.667 0.00 0.00 44.23 1.90
85 86 4.018490 TGCACTTTGCCATGTCATCTTAT 58.982 39.130 0.00 0.00 44.23 1.73
86 87 3.419943 TGCACTTTGCCATGTCATCTTA 58.580 40.909 0.00 0.00 44.23 2.10
87 88 2.241160 TGCACTTTGCCATGTCATCTT 58.759 42.857 0.00 0.00 44.23 2.40
88 89 1.913778 TGCACTTTGCCATGTCATCT 58.086 45.000 0.00 0.00 44.23 2.90
89 90 2.288334 TGTTGCACTTTGCCATGTCATC 60.288 45.455 0.00 0.00 44.23 2.92
90 91 1.687660 TGTTGCACTTTGCCATGTCAT 59.312 42.857 0.00 0.00 44.23 3.06
91 92 1.109609 TGTTGCACTTTGCCATGTCA 58.890 45.000 0.00 0.00 44.23 3.58
92 93 1.490621 GTGTTGCACTTTGCCATGTC 58.509 50.000 0.00 0.00 44.23 3.06
93 94 0.248990 CGTGTTGCACTTTGCCATGT 60.249 50.000 0.00 0.00 44.23 3.21
94 95 1.550659 GCGTGTTGCACTTTGCCATG 61.551 55.000 0.00 0.00 44.23 3.66
95 96 1.300080 GCGTGTTGCACTTTGCCAT 60.300 52.632 0.00 0.00 44.23 4.40
96 97 2.103934 GCGTGTTGCACTTTGCCA 59.896 55.556 0.00 0.00 44.23 4.92
105 106 0.503961 GTCATTTGCTTGCGTGTTGC 59.496 50.000 0.00 0.00 46.70 4.17
106 107 1.837648 TGTCATTTGCTTGCGTGTTG 58.162 45.000 0.00 0.00 0.00 3.33
107 108 2.396601 CATGTCATTTGCTTGCGTGTT 58.603 42.857 0.00 0.00 0.00 3.32
108 109 1.336148 CCATGTCATTTGCTTGCGTGT 60.336 47.619 0.00 0.00 0.00 4.49
109 110 1.342555 CCATGTCATTTGCTTGCGTG 58.657 50.000 0.00 0.00 0.00 5.34
110 111 0.388907 GCCATGTCATTTGCTTGCGT 60.389 50.000 0.00 0.00 0.00 5.24
111 112 0.388778 TGCCATGTCATTTGCTTGCG 60.389 50.000 5.85 0.00 0.00 4.85
112 113 1.461897 GTTGCCATGTCATTTGCTTGC 59.538 47.619 5.85 0.00 0.00 4.01
113 114 1.722464 CGTTGCCATGTCATTTGCTTG 59.278 47.619 5.85 0.00 0.00 4.01
114 115 1.612950 TCGTTGCCATGTCATTTGCTT 59.387 42.857 5.85 0.00 0.00 3.91
115 116 1.068333 GTCGTTGCCATGTCATTTGCT 60.068 47.619 5.85 0.00 0.00 3.91
116 117 1.339711 GTCGTTGCCATGTCATTTGC 58.660 50.000 0.00 0.00 0.00 3.68
117 118 1.605500 CGTCGTTGCCATGTCATTTG 58.394 50.000 0.00 0.00 0.00 2.32
118 119 0.521291 CCGTCGTTGCCATGTCATTT 59.479 50.000 0.00 0.00 0.00 2.32
119 120 1.922135 GCCGTCGTTGCCATGTCATT 61.922 55.000 0.00 0.00 0.00 2.57
120 121 2.398554 GCCGTCGTTGCCATGTCAT 61.399 57.895 0.00 0.00 0.00 3.06
121 122 3.047280 GCCGTCGTTGCCATGTCA 61.047 61.111 0.00 0.00 0.00 3.58
122 123 4.147322 CGCCGTCGTTGCCATGTC 62.147 66.667 0.00 0.00 0.00 3.06
123 124 4.673298 TCGCCGTCGTTGCCATGT 62.673 61.111 0.00 0.00 36.96 3.21
124 125 1.425267 TATTCGCCGTCGTTGCCATG 61.425 55.000 0.00 0.00 36.96 3.66
125 126 0.741574 TTATTCGCCGTCGTTGCCAT 60.742 50.000 0.00 0.00 36.96 4.40
126 127 1.374378 TTATTCGCCGTCGTTGCCA 60.374 52.632 0.00 0.00 36.96 4.92
127 128 1.059838 GTTATTCGCCGTCGTTGCC 59.940 57.895 0.00 0.00 36.96 4.52
128 129 0.247145 CAGTTATTCGCCGTCGTTGC 60.247 55.000 0.00 0.00 36.96 4.17
129 130 0.368907 CCAGTTATTCGCCGTCGTTG 59.631 55.000 0.00 0.00 36.96 4.10
130 131 1.356527 GCCAGTTATTCGCCGTCGTT 61.357 55.000 0.00 0.00 36.96 3.85
131 132 1.808390 GCCAGTTATTCGCCGTCGT 60.808 57.895 0.00 0.00 36.96 4.34
132 133 1.752501 CTGCCAGTTATTCGCCGTCG 61.753 60.000 0.00 0.00 0.00 5.12
133 134 0.459585 TCTGCCAGTTATTCGCCGTC 60.460 55.000 0.00 0.00 0.00 4.79
134 135 0.739813 GTCTGCCAGTTATTCGCCGT 60.740 55.000 0.00 0.00 0.00 5.68
135 136 0.739462 TGTCTGCCAGTTATTCGCCG 60.739 55.000 0.00 0.00 0.00 6.46
136 137 0.727398 GTGTCTGCCAGTTATTCGCC 59.273 55.000 0.00 0.00 0.00 5.54
137 138 0.727398 GGTGTCTGCCAGTTATTCGC 59.273 55.000 0.00 0.00 0.00 4.70
138 139 2.002586 CAGGTGTCTGCCAGTTATTCG 58.997 52.381 0.00 0.00 33.86 3.34
139 140 2.359900 CCAGGTGTCTGCCAGTTATTC 58.640 52.381 0.00 0.00 39.61 1.75
140 141 1.614317 GCCAGGTGTCTGCCAGTTATT 60.614 52.381 0.00 0.00 39.61 1.40
141 142 0.035056 GCCAGGTGTCTGCCAGTTAT 60.035 55.000 0.00 0.00 39.61 1.89
142 143 1.374947 GCCAGGTGTCTGCCAGTTA 59.625 57.895 0.00 0.00 39.61 2.24
143 144 2.113986 GCCAGGTGTCTGCCAGTT 59.886 61.111 0.00 0.00 39.61 3.16
144 145 4.320456 CGCCAGGTGTCTGCCAGT 62.320 66.667 0.00 0.00 39.61 4.00
148 149 3.503363 GATGCGCCAGGTGTCTGC 61.503 66.667 4.18 0.00 39.61 4.26
149 150 3.190849 CGATGCGCCAGGTGTCTG 61.191 66.667 4.18 0.00 40.59 3.51
150 151 2.244117 ATTCGATGCGCCAGGTGTCT 62.244 55.000 4.18 0.00 0.00 3.41
151 152 1.766143 GATTCGATGCGCCAGGTGTC 61.766 60.000 4.18 0.00 0.00 3.67
152 153 1.815421 GATTCGATGCGCCAGGTGT 60.815 57.895 4.18 0.00 0.00 4.16
153 154 2.537560 GGATTCGATGCGCCAGGTG 61.538 63.158 4.18 0.00 0.00 4.00
154 155 2.203070 GGATTCGATGCGCCAGGT 60.203 61.111 4.18 0.00 0.00 4.00
155 156 3.341043 CGGATTCGATGCGCCAGG 61.341 66.667 4.18 0.00 37.28 4.45
156 157 3.341043 CCGGATTCGATGCGCCAG 61.341 66.667 4.18 0.00 43.11 4.85
157 158 4.908687 CCCGGATTCGATGCGCCA 62.909 66.667 0.73 0.00 43.11 5.69
161 162 2.981977 TAACGCCCCGGATTCGATGC 62.982 60.000 0.73 0.00 39.00 3.91
162 163 1.068417 TAACGCCCCGGATTCGATG 59.932 57.895 0.73 0.00 39.00 3.84
163 164 1.068585 GTAACGCCCCGGATTCGAT 59.931 57.895 0.73 0.02 39.00 3.59
164 165 2.349672 TGTAACGCCCCGGATTCGA 61.350 57.895 0.73 0.00 39.00 3.71
165 166 2.169146 GTGTAACGCCCCGGATTCG 61.169 63.158 0.73 5.63 0.00 3.34
166 167 1.816679 GGTGTAACGCCCCGGATTC 60.817 63.158 0.73 0.00 38.12 2.52
167 168 2.269883 GGTGTAACGCCCCGGATT 59.730 61.111 0.73 0.00 38.12 3.01
168 169 3.004354 TGGTGTAACGCCCCGGAT 61.004 61.111 0.73 0.00 38.12 4.18
169 170 4.006357 GTGGTGTAACGCCCCGGA 62.006 66.667 0.73 0.00 38.12 5.14
170 171 4.317444 TGTGGTGTAACGCCCCGG 62.317 66.667 0.00 0.00 38.12 5.73
171 172 2.740826 CTGTGGTGTAACGCCCCG 60.741 66.667 0.00 0.00 38.12 5.73
172 173 2.359478 CCTGTGGTGTAACGCCCC 60.359 66.667 0.00 0.00 38.12 5.80
173 174 1.670083 GACCTGTGGTGTAACGCCC 60.670 63.158 0.00 0.00 38.12 6.13
174 175 0.321298 ATGACCTGTGGTGTAACGCC 60.321 55.000 0.00 0.00 38.12 5.68
175 176 2.268298 CTATGACCTGTGGTGTAACGC 58.732 52.381 0.00 0.00 38.12 4.84
176 177 2.418197 CCCTATGACCTGTGGTGTAACG 60.418 54.545 0.00 0.00 38.12 3.18
177 178 2.679930 GCCCTATGACCTGTGGTGTAAC 60.680 54.545 0.00 0.00 35.25 2.50
178 179 1.557832 GCCCTATGACCTGTGGTGTAA 59.442 52.381 0.00 0.00 35.25 2.41
179 180 1.200519 GCCCTATGACCTGTGGTGTA 58.799 55.000 0.00 0.00 35.25 2.90
180 181 0.840288 TGCCCTATGACCTGTGGTGT 60.840 55.000 0.00 0.00 35.25 4.16
181 182 0.548031 ATGCCCTATGACCTGTGGTG 59.452 55.000 0.00 0.00 35.25 4.17
182 183 2.190398 TATGCCCTATGACCTGTGGT 57.810 50.000 0.00 0.00 39.44 4.16
309 311 5.013704 TGTGTGTCCTAATGTTTAGTCCCAT 59.986 40.000 0.00 0.00 0.00 4.00
329 331 0.391395 TCCCGTTTCGTTGTGTGTGT 60.391 50.000 0.00 0.00 0.00 3.72
633 666 5.229469 GTGTATACATGTGCGTACTTCACTC 59.771 44.000 9.11 0.00 35.58 3.51
725 758 9.847706 ATTTTGTTACGTTTTATACATGCATCA 57.152 25.926 0.00 0.00 0.00 3.07
827 870 1.335506 GGTGGTTGTATGCAAACGTGG 60.336 52.381 7.10 0.00 44.90 4.94
970 1016 2.581246 GGGTCTGAATTTAAGGGGAGGT 59.419 50.000 0.00 0.00 0.00 3.85
1034 1082 2.746277 GCGATTTGGTGGGAGCGT 60.746 61.111 0.00 0.00 0.00 5.07
1120 1168 4.555709 TGCGCCTCCACGGTGTTT 62.556 61.111 4.18 0.00 45.36 2.83
1273 1321 1.869690 GGCTTTCTGCGTCACTTCC 59.130 57.895 0.00 0.00 44.05 3.46
1328 1376 2.753452 CACTCATTTGGAAGAGCAGCAT 59.247 45.455 0.00 0.00 35.28 3.79
1373 1421 1.339151 GGGATCAGCGAGGAAGTTGTT 60.339 52.381 0.00 0.00 0.00 2.83
1562 1610 6.016777 GTGATCCTCTTCTTCATGTTGTTGTT 60.017 38.462 0.00 0.00 0.00 2.83
1581 1630 2.278013 GCTCGTCGTCGGTGATCC 60.278 66.667 1.55 0.00 37.69 3.36
1712 1761 0.749818 TTCTCCAACTTTGCACGGCA 60.750 50.000 0.00 0.00 36.47 5.69
1724 1773 1.616628 GGGGCTCCTCCTTCTCCAA 60.617 63.158 0.00 0.00 34.39 3.53
1891 1947 3.838244 AACTAGGTTCAGCACACAAGA 57.162 42.857 0.00 0.00 0.00 3.02
2166 2224 8.303876 ACTTCCGCACTGTATTGAATTATTTTT 58.696 29.630 0.00 0.00 0.00 1.94
2438 2774 3.243134 GGTGCAGACCTATTACGAGACTC 60.243 52.174 0.00 0.00 39.47 3.36
2472 2808 3.277715 TGCACTGTGACTCAAAATGACA 58.722 40.909 12.86 0.00 0.00 3.58
2479 2815 0.250858 CCCCATGCACTGTGACTCAA 60.251 55.000 12.86 0.00 0.00 3.02
2585 2921 2.360475 GTGGGAAGGCCTCTGTGC 60.360 66.667 5.23 0.00 0.00 4.57
2598 2934 2.286833 CGACATGTTTATAAGCGGTGGG 59.713 50.000 0.00 0.00 0.00 4.61
2713 3049 0.243095 GTTCGGGTAGTGAAGACGCT 59.757 55.000 0.00 0.00 40.21 5.07
2886 3226 3.060602 TGCATTTGTACGTTGACATCGA 58.939 40.909 12.66 0.00 0.00 3.59
3372 3749 5.005628 TGGTGGGGCTCTATTTTAAGTTT 57.994 39.130 0.00 0.00 0.00 2.66
3786 4170 1.067060 CTACGCATAGCTGTAGCACCA 59.933 52.381 6.65 0.00 45.16 4.17
4102 4496 4.297510 TGCATGTTTTGTGTATGCTTGTC 58.702 39.130 9.47 0.00 45.53 3.18
4184 4578 8.283699 TGAATATCTGAATCTGTTGCATTGAA 57.716 30.769 0.00 0.00 0.00 2.69
4283 4682 6.782000 AGTTCCATTGGCCTGCAATATATTTA 59.218 34.615 3.32 0.00 0.00 1.40
4320 4719 4.698575 GAAGGTGTACTCATCATTCCTCC 58.301 47.826 0.00 0.00 0.00 4.30
4323 4722 4.124851 ACGAAGGTGTACTCATCATTCC 57.875 45.455 0.00 0.00 0.00 3.01
4345 4744 4.753516 TTCTCCTTCAATAGCGAATCCA 57.246 40.909 0.00 0.00 0.00 3.41
4366 4765 4.219288 CCAGATACCTTCAGCTTGCTTTTT 59.781 41.667 0.00 0.00 0.00 1.94
4526 4925 1.353022 TGGTCCTCCTTGCGGTTAATT 59.647 47.619 0.00 0.00 34.23 1.40
4613 5012 8.661752 AGATGATTCTCCATGACTCATATGTA 57.338 34.615 1.90 0.00 42.64 2.29
4814 5217 8.581263 CAAAAGAAATGTTCGATATGAAGCAAG 58.419 33.333 0.00 0.00 37.23 4.01
4847 5250 6.631971 TTGATCACAAGCAAACTGACATTA 57.368 33.333 0.00 0.00 0.00 1.90
5293 5750 4.396478 TGCACTTTGTTTAGCAAGTGTGTA 59.604 37.500 12.34 9.64 41.22 2.90
5306 5763 6.096282 ACCAACATTAAGTACTGCACTTTGTT 59.904 34.615 0.00 2.30 45.54 2.83
5322 5779 3.481453 TGTACTGCTTGCACCAACATTA 58.519 40.909 0.00 0.00 0.00 1.90
5325 5782 1.756430 TTGTACTGCTTGCACCAACA 58.244 45.000 0.00 0.00 0.00 3.33
5426 5884 0.974010 GGTGAGTCCGTCATACCCCA 60.974 60.000 0.00 0.00 37.56 4.96


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

AutoCloner maintained by Alex Coulton.