Multiple sequence alignment - TraesCS3B01G318200

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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 TraesCS3B01G318200 chr3B 100.000 2166 0 0 1847 4012 512863436 512861271 0.000000e+00 4000.0
1 TraesCS3B01G318200 chr3B 100.000 1559 0 0 1 1559 512865282 512863724 0.000000e+00 2880.0
2 TraesCS3B01G318200 chr3B 85.043 234 33 2 1853 2085 512863322 512863090 1.860000e-58 237.0
3 TraesCS3B01G318200 chr3B 85.043 234 33 2 1961 2193 512863430 512863198 1.860000e-58 237.0
4 TraesCS3B01G318200 chr3B 96.226 106 4 0 441 546 685149484 685149379 1.480000e-39 174.0
5 TraesCS3B01G318200 chr3D 93.516 1388 59 11 138 1502 393066626 393065247 0.000000e+00 2036.0
6 TraesCS3B01G318200 chr3D 89.134 1629 138 20 1872 3492 393064844 393063247 0.000000e+00 1991.0
7 TraesCS3B01G318200 chr3D 95.101 347 17 0 1847 2193 393064815 393064469 7.580000e-152 547.0
8 TraesCS3B01G318200 chr3D 84.241 349 50 3 1853 2197 393064701 393064354 6.420000e-88 335.0
9 TraesCS3B01G318200 chr3D 84.758 269 39 2 1926 2193 393064844 393064577 6.610000e-68 268.0
10 TraesCS3B01G318200 chr3D 94.118 51 1 2 2138 2187 393064848 393064799 4.300000e-10 76.8
11 TraesCS3B01G318200 chr3A 94.104 1289 32 17 2208 3477 512609980 512608717 0.000000e+00 1919.0
12 TraesCS3B01G318200 chr3A 90.373 1475 71 21 138 1559 512611999 512610543 0.000000e+00 1871.0
13 TraesCS3B01G318200 chr3A 89.048 210 23 0 2044 2253 512610109 512609900 1.110000e-65 261.0
14 TraesCS3B01G318200 chr3A 86.905 168 16 2 1305 1469 512610629 512610465 2.460000e-42 183.0
15 TraesCS3B01G318200 chr3A 84.667 150 23 0 1936 2085 512610109 512609960 2.500000e-32 150.0
16 TraesCS3B01G318200 chr3A 78.740 127 27 0 1847 1973 512610589 512610463 7.140000e-13 86.1
17 TraesCS3B01G318200 chr7B 90.164 244 20 2 3494 3734 38681580 38681822 8.370000e-82 315.0
18 TraesCS3B01G318200 chr7B 100.000 28 0 0 17 44 595784092 595784119 7.000000e-03 52.8
19 TraesCS3B01G318200 chr2B 85.563 284 35 3 3730 4012 283259361 283259083 3.920000e-75 292.0
20 TraesCS3B01G318200 chr2B 84.874 238 32 2 3500 3734 283259651 283259415 1.860000e-58 237.0
21 TraesCS3B01G318200 chr1D 85.772 246 30 3 3492 3734 62409068 62408825 5.150000e-64 255.0
22 TraesCS3B01G318200 chr7A 81.786 280 46 3 3731 4010 178020860 178021134 3.120000e-56 230.0
23 TraesCS3B01G318200 chr5D 81.071 280 48 3 3731 4010 487022312 487022038 6.750000e-53 219.0


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 TraesCS3B01G318200 chr3B 512861271 512865282 4011 True 1838.500000 4000 92.521500 1 4012 4 chr3B.!!$R2 4011
1 TraesCS3B01G318200 chr3D 393063247 393066626 3379 True 875.633333 2036 90.144667 138 3492 6 chr3D.!!$R1 3354
2 TraesCS3B01G318200 chr3A 512608717 512611999 3282 True 745.016667 1919 87.306167 138 3477 6 chr3A.!!$R1 3339
3 TraesCS3B01G318200 chr2B 283259083 283259651 568 True 264.500000 292 85.218500 3500 4012 2 chr2B.!!$R1 512

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
37 38 0.179129 GAGGCATGGTTTTGCATCCG 60.179 55.0 0.00 0.0 45.18 4.18 F
40 41 0.243365 GCATGGTTTTGCATCCGTGA 59.757 50.0 21.51 0.0 41.65 4.35 F
1462 1526 0.469331 AGTGACACCTCTCCGACCAA 60.469 55.0 0.84 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1589 0.607489 CAGGCAGTTTCCAGTCCCAG 60.607 60.000 0.0 0.0 0.00 4.45 R
1526 1590 1.455849 CAGGCAGTTTCCAGTCCCA 59.544 57.895 0.0 0.0 0.00 4.37 R
3229 4021 2.223021 CGTCCATACGCAGACCAAATTG 60.223 50.000 0.0 0.0 43.12 2.32 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
33 34 1.927487 ATGAGAGGCATGGTTTTGCA 58.073 45.000 0.00 0.00 44.59 4.08
34 35 1.927487 TGAGAGGCATGGTTTTGCAT 58.073 45.000 0.00 0.00 44.59 3.96
36 37 3.746900 GAGGCATGGTTTTGCATCC 57.253 52.632 0.00 0.00 45.18 3.51
37 38 0.179129 GAGGCATGGTTTTGCATCCG 60.179 55.000 0.00 0.00 45.18 4.18
38 39 0.899717 AGGCATGGTTTTGCATCCGT 60.900 50.000 0.00 0.00 44.59 4.69
39 40 0.737019 GGCATGGTTTTGCATCCGTG 60.737 55.000 16.15 16.15 44.59 4.94
40 41 0.243365 GCATGGTTTTGCATCCGTGA 59.757 50.000 21.51 0.00 41.65 4.35
41 42 1.733389 GCATGGTTTTGCATCCGTGAG 60.733 52.381 21.51 4.71 41.65 3.51
42 43 1.811965 CATGGTTTTGCATCCGTGAGA 59.188 47.619 15.68 0.00 41.65 3.27
43 44 1.522668 TGGTTTTGCATCCGTGAGAG 58.477 50.000 0.00 0.00 0.00 3.20
44 45 1.071542 TGGTTTTGCATCCGTGAGAGA 59.928 47.619 0.00 0.00 0.00 3.10
45 46 2.151202 GGTTTTGCATCCGTGAGAGAA 58.849 47.619 0.00 0.00 0.00 2.87
46 47 2.552315 GGTTTTGCATCCGTGAGAGAAA 59.448 45.455 0.00 0.00 0.00 2.52
47 48 3.555518 GTTTTGCATCCGTGAGAGAAAC 58.444 45.455 0.00 0.00 0.00 2.78
48 49 2.839486 TTGCATCCGTGAGAGAAACT 57.161 45.000 0.00 0.00 0.00 2.66
49 50 2.839486 TGCATCCGTGAGAGAAACTT 57.161 45.000 0.00 0.00 0.00 2.66
50 51 2.688507 TGCATCCGTGAGAGAAACTTC 58.311 47.619 0.00 0.00 0.00 3.01
51 52 2.003301 GCATCCGTGAGAGAAACTTCC 58.997 52.381 0.00 0.00 0.00 3.46
52 53 2.622436 CATCCGTGAGAGAAACTTCCC 58.378 52.381 0.00 0.00 0.00 3.97
53 54 1.712056 TCCGTGAGAGAAACTTCCCA 58.288 50.000 0.00 0.00 0.00 4.37
54 55 1.343465 TCCGTGAGAGAAACTTCCCAC 59.657 52.381 0.00 0.00 0.00 4.61
55 56 1.608283 CCGTGAGAGAAACTTCCCACC 60.608 57.143 0.00 0.00 0.00 4.61
56 57 1.070134 CGTGAGAGAAACTTCCCACCA 59.930 52.381 0.00 0.00 0.00 4.17
57 58 2.289694 CGTGAGAGAAACTTCCCACCAT 60.290 50.000 0.00 0.00 0.00 3.55
58 59 3.756117 GTGAGAGAAACTTCCCACCATT 58.244 45.455 0.00 0.00 0.00 3.16
59 60 4.145052 GTGAGAGAAACTTCCCACCATTT 58.855 43.478 0.00 0.00 0.00 2.32
60 61 5.313712 GTGAGAGAAACTTCCCACCATTTA 58.686 41.667 0.00 0.00 0.00 1.40
61 62 5.181433 GTGAGAGAAACTTCCCACCATTTAC 59.819 44.000 0.00 0.00 0.00 2.01
62 63 4.663334 AGAGAAACTTCCCACCATTTACC 58.337 43.478 0.00 0.00 0.00 2.85
63 64 4.105697 AGAGAAACTTCCCACCATTTACCA 59.894 41.667 0.00 0.00 0.00 3.25
64 65 5.010708 AGAAACTTCCCACCATTTACCAT 57.989 39.130 0.00 0.00 0.00 3.55
65 66 4.772100 AGAAACTTCCCACCATTTACCATG 59.228 41.667 0.00 0.00 0.00 3.66
66 67 2.456577 ACTTCCCACCATTTACCATGC 58.543 47.619 0.00 0.00 0.00 4.06
67 68 2.225242 ACTTCCCACCATTTACCATGCA 60.225 45.455 0.00 0.00 0.00 3.96
68 69 2.844654 TCCCACCATTTACCATGCAT 57.155 45.000 0.00 0.00 0.00 3.96
69 70 2.665165 TCCCACCATTTACCATGCATC 58.335 47.619 0.00 0.00 0.00 3.91
70 71 2.244510 TCCCACCATTTACCATGCATCT 59.755 45.455 0.00 0.00 0.00 2.90
71 72 3.461458 TCCCACCATTTACCATGCATCTA 59.539 43.478 0.00 0.00 0.00 1.98
72 73 4.079500 TCCCACCATTTACCATGCATCTAA 60.080 41.667 0.00 0.00 0.00 2.10
73 74 4.648762 CCCACCATTTACCATGCATCTAAA 59.351 41.667 0.00 2.32 0.00 1.85
74 75 5.305128 CCCACCATTTACCATGCATCTAAAT 59.695 40.000 0.00 4.72 0.00 1.40
75 76 6.218019 CCACCATTTACCATGCATCTAAATG 58.782 40.000 24.49 24.49 37.50 2.32
77 78 5.786311 CCATTTACCATGCATCTAAATGGG 58.214 41.667 32.12 22.78 45.93 4.00
78 79 4.935352 TTTACCATGCATCTAAATGGGC 57.065 40.909 0.00 0.00 46.45 5.36
79 80 1.708341 ACCATGCATCTAAATGGGCC 58.292 50.000 0.00 0.00 46.45 5.80
80 81 0.599558 CCATGCATCTAAATGGGCCG 59.400 55.000 0.00 0.00 39.82 6.13
81 82 1.321474 CATGCATCTAAATGGGCCGT 58.679 50.000 0.00 0.00 33.19 5.68
82 83 2.503331 CATGCATCTAAATGGGCCGTA 58.497 47.619 0.00 0.00 33.19 4.02
83 84 2.254546 TGCATCTAAATGGGCCGTAG 57.745 50.000 0.00 0.01 33.19 3.51
84 85 1.765904 TGCATCTAAATGGGCCGTAGA 59.234 47.619 12.23 12.23 33.19 2.59
85 86 2.171659 TGCATCTAAATGGGCCGTAGAA 59.828 45.455 13.45 0.00 33.19 2.10
86 87 3.211045 GCATCTAAATGGGCCGTAGAAA 58.789 45.455 13.45 0.00 33.19 2.52
87 88 3.821033 GCATCTAAATGGGCCGTAGAAAT 59.179 43.478 13.45 0.00 33.19 2.17
88 89 4.278419 GCATCTAAATGGGCCGTAGAAATT 59.722 41.667 13.45 0.89 33.19 1.82
89 90 5.472137 GCATCTAAATGGGCCGTAGAAATTA 59.528 40.000 13.45 1.95 33.19 1.40
90 91 6.016610 GCATCTAAATGGGCCGTAGAAATTAA 60.017 38.462 13.45 0.00 33.19 1.40
91 92 7.584987 CATCTAAATGGGCCGTAGAAATTAAG 58.415 38.462 13.45 0.00 0.00 1.85
92 93 4.649088 AAATGGGCCGTAGAAATTAAGC 57.351 40.909 0.00 0.00 0.00 3.09
93 94 2.791347 TGGGCCGTAGAAATTAAGCA 57.209 45.000 0.00 0.00 0.00 3.91
94 95 2.639065 TGGGCCGTAGAAATTAAGCAG 58.361 47.619 0.00 0.00 0.00 4.24
95 96 1.947456 GGGCCGTAGAAATTAAGCAGG 59.053 52.381 0.00 0.00 0.00 4.85
96 97 1.947456 GGCCGTAGAAATTAAGCAGGG 59.053 52.381 0.00 0.00 0.00 4.45
97 98 1.947456 GCCGTAGAAATTAAGCAGGGG 59.053 52.381 0.00 0.00 0.00 4.79
98 99 2.420967 GCCGTAGAAATTAAGCAGGGGA 60.421 50.000 0.00 0.00 0.00 4.81
99 100 3.747708 GCCGTAGAAATTAAGCAGGGGAT 60.748 47.826 0.00 0.00 0.00 3.85
100 101 4.504340 GCCGTAGAAATTAAGCAGGGGATA 60.504 45.833 0.00 0.00 0.00 2.59
101 102 5.803470 GCCGTAGAAATTAAGCAGGGGATAT 60.803 44.000 0.00 0.00 0.00 1.63
102 103 6.238648 CCGTAGAAATTAAGCAGGGGATATT 58.761 40.000 0.00 0.00 0.00 1.28
103 104 6.149474 CCGTAGAAATTAAGCAGGGGATATTG 59.851 42.308 0.00 0.00 0.00 1.90
104 105 6.710744 CGTAGAAATTAAGCAGGGGATATTGT 59.289 38.462 0.00 0.00 0.00 2.71
105 106 7.876068 CGTAGAAATTAAGCAGGGGATATTGTA 59.124 37.037 0.00 0.00 0.00 2.41
106 107 9.740710 GTAGAAATTAAGCAGGGGATATTGTAT 57.259 33.333 0.00 0.00 0.00 2.29
110 111 9.875708 AAATTAAGCAGGGGATATTGTATTACA 57.124 29.630 0.00 0.00 0.00 2.41
112 113 8.862325 TTAAGCAGGGGATATTGTATTACATG 57.138 34.615 0.00 0.00 0.00 3.21
113 114 5.819991 AGCAGGGGATATTGTATTACATGG 58.180 41.667 0.00 0.00 0.00 3.66
114 115 4.949856 GCAGGGGATATTGTATTACATGGG 59.050 45.833 0.00 0.00 0.00 4.00
115 116 4.949856 CAGGGGATATTGTATTACATGGGC 59.050 45.833 0.00 0.00 0.00 5.36
116 117 4.017499 AGGGGATATTGTATTACATGGGCC 60.017 45.833 0.00 0.00 0.00 5.80
117 118 4.017499 GGGGATATTGTATTACATGGGCCT 60.017 45.833 4.53 0.00 0.00 5.19
118 119 5.192923 GGGGATATTGTATTACATGGGCCTA 59.807 44.000 4.53 0.00 0.00 3.93
119 120 6.297360 GGGGATATTGTATTACATGGGCCTAA 60.297 42.308 4.53 0.00 0.00 2.69
120 121 6.602009 GGGATATTGTATTACATGGGCCTAAC 59.398 42.308 4.53 0.00 0.00 2.34
121 122 6.602009 GGATATTGTATTACATGGGCCTAACC 59.398 42.308 4.53 0.00 37.93 2.85
132 133 2.180432 GGCCTAACCCATCCGTAATC 57.820 55.000 0.00 0.00 0.00 1.75
133 134 1.271217 GGCCTAACCCATCCGTAATCC 60.271 57.143 0.00 0.00 0.00 3.01
134 135 1.418637 GCCTAACCCATCCGTAATCCA 59.581 52.381 0.00 0.00 0.00 3.41
135 136 2.158726 GCCTAACCCATCCGTAATCCAA 60.159 50.000 0.00 0.00 0.00 3.53
136 137 3.473625 CCTAACCCATCCGTAATCCAAC 58.526 50.000 0.00 0.00 0.00 3.77
178 179 2.004733 TCTCACATTTCTGCTGCATCG 58.995 47.619 1.31 0.00 0.00 3.84
223 224 6.844696 AACATAACTAGAACGTGCCATATG 57.155 37.500 0.00 0.00 0.00 1.78
321 323 0.826715 ACTGCATGCGACTCCTATGT 59.173 50.000 14.09 0.00 0.00 2.29
390 404 5.248477 ACCTACAGCAGTCAATTTAAGGAGA 59.752 40.000 0.00 0.00 0.00 3.71
394 408 3.008049 AGCAGTCAATTTAAGGAGACGGT 59.992 43.478 0.00 0.00 36.18 4.83
397 411 3.007635 GTCAATTTAAGGAGACGGTGGG 58.992 50.000 0.00 0.00 0.00 4.61
398 412 2.640826 TCAATTTAAGGAGACGGTGGGT 59.359 45.455 0.00 0.00 0.00 4.51
399 413 3.839490 TCAATTTAAGGAGACGGTGGGTA 59.161 43.478 0.00 0.00 0.00 3.69
400 414 4.081309 TCAATTTAAGGAGACGGTGGGTAG 60.081 45.833 0.00 0.00 0.00 3.18
401 415 2.610438 TTAAGGAGACGGTGGGTAGT 57.390 50.000 0.00 0.00 0.00 2.73
402 416 1.843368 TAAGGAGACGGTGGGTAGTG 58.157 55.000 0.00 0.00 0.00 2.74
421 443 4.156477 AGTGTTCCACTAGAGAAGAGCTT 58.844 43.478 0.00 0.00 43.46 3.74
422 444 4.021544 AGTGTTCCACTAGAGAAGAGCTTG 60.022 45.833 0.00 0.00 43.46 4.01
423 445 3.258228 GTTCCACTAGAGAAGAGCTTGC 58.742 50.000 0.00 0.00 0.00 4.01
424 446 2.529632 TCCACTAGAGAAGAGCTTGCA 58.470 47.619 0.00 0.00 0.00 4.08
476 500 2.309755 TGCTCATTCATTCAAGGAGGGT 59.690 45.455 0.00 0.00 42.26 4.34
490 514 1.353022 GGAGGGTCACCATTAACACCA 59.647 52.381 0.00 0.00 40.13 4.17
752 789 2.615227 AAATGGAGCCGGCTAGCCTG 62.615 60.000 32.97 25.35 0.00 4.85
797 836 1.372997 ATCGCGTGACTGTGTCCAC 60.373 57.895 5.77 0.00 0.00 4.02
800 839 1.227556 GCGTGACTGTGTCCACCTT 60.228 57.895 0.00 0.00 0.00 3.50
995 1044 1.125202 GAAGCTCTCTTTGCGAACGAC 59.875 52.381 0.00 0.00 35.28 4.34
1093 1153 2.990967 ACGGCGGGAACTTCGGTA 60.991 61.111 13.24 0.00 0.00 4.02
1124 1187 4.722700 CCCTCCTGGCAACACCGG 62.723 72.222 0.00 0.00 46.17 5.28
1183 1246 2.533266 CGTACATAACACCTCCCGTTC 58.467 52.381 0.00 0.00 0.00 3.95
1186 1249 1.975680 ACATAACACCTCCCGTTCACT 59.024 47.619 0.00 0.00 0.00 3.41
1189 1252 0.683412 AACACCTCCCGTTCACTACC 59.317 55.000 0.00 0.00 0.00 3.18
1191 1254 1.076024 ACACCTCCCGTTCACTACCTA 59.924 52.381 0.00 0.00 0.00 3.08
1206 1269 2.738013 ACCTACAGTCCGTTACAAGC 57.262 50.000 0.00 0.00 0.00 4.01
1218 1281 6.312918 AGTCCGTTACAAGCAGTATATTTGTG 59.687 38.462 0.88 0.00 36.52 3.33
1220 1283 5.163804 CCGTTACAAGCAGTATATTTGTGCA 60.164 40.000 6.45 0.00 39.80 4.57
1221 1284 6.310960 CGTTACAAGCAGTATATTTGTGCAA 58.689 36.000 0.00 0.00 39.80 4.08
1224 1287 8.638565 GTTACAAGCAGTATATTTGTGCAAAAG 58.361 33.333 1.26 0.00 39.80 2.27
1236 1299 5.557891 TTGTGCAAAAGTTTTGGGATTTG 57.442 34.783 25.65 3.93 36.19 2.32
1239 1302 4.633565 GTGCAAAAGTTTTGGGATTTGACA 59.366 37.500 25.65 12.18 35.34 3.58
1243 1306 6.717413 CAAAAGTTTTGGGATTTGACATGTG 58.283 36.000 18.80 0.00 35.34 3.21
1250 1314 4.222336 TGGGATTTGACATGTGTTTTCCT 58.778 39.130 1.15 0.00 0.00 3.36
1462 1526 0.469331 AGTGACACCTCTCCGACCAA 60.469 55.000 0.84 0.00 0.00 3.67
1532 1596 3.953775 CCAACCACGCCTGGGACT 61.954 66.667 6.69 0.00 42.74 3.85
1533 1597 2.669569 CAACCACGCCTGGGACTG 60.670 66.667 6.69 0.00 42.74 3.51
1543 1980 1.763770 CTGGGACTGGAAACTGCCT 59.236 57.895 0.00 0.00 0.00 4.75
1544 1981 0.607489 CTGGGACTGGAAACTGCCTG 60.607 60.000 0.00 0.00 0.00 4.85
1550 1987 2.747855 GGAAACTGCCTGCCCTCG 60.748 66.667 0.00 0.00 0.00 4.63
1907 2344 3.905678 CGCCGGCACCTCTCCTAG 61.906 72.222 28.98 0.98 0.00 3.02
1993 2430 3.003763 GGAACTGCCCTCCCTCGT 61.004 66.667 0.00 0.00 0.00 4.18
2036 2473 2.038329 ACCTGGCGGTGGCTACTA 59.962 61.111 0.00 0.00 43.51 1.82
2212 2986 3.324108 GCTACCCACCGTCCCCAA 61.324 66.667 0.00 0.00 0.00 4.12
2213 2987 2.666812 CTACCCACCGTCCCCAAC 59.333 66.667 0.00 0.00 0.00 3.77
2214 2988 2.122503 TACCCACCGTCCCCAACA 60.123 61.111 0.00 0.00 0.00 3.33
2215 2989 1.769295 TACCCACCGTCCCCAACAA 60.769 57.895 0.00 0.00 0.00 2.83
2216 2990 2.054473 TACCCACCGTCCCCAACAAC 62.054 60.000 0.00 0.00 0.00 3.32
2217 2991 2.975799 CCACCGTCCCCAACAACG 60.976 66.667 0.00 0.00 38.58 4.10
2218 2992 3.656045 CACCGTCCCCAACAACGC 61.656 66.667 0.00 0.00 37.56 4.84
2219 2993 4.941309 ACCGTCCCCAACAACGCC 62.941 66.667 0.00 0.00 37.56 5.68
2495 3269 2.635338 GCCGTTCGACCCAAACAC 59.365 61.111 0.00 0.00 0.00 3.32
2517 3291 3.470888 CCCTACTCCCCGCTGGTG 61.471 72.222 0.00 0.00 34.77 4.17
2577 3351 3.246880 ACCCCACCGTTCTCCACC 61.247 66.667 0.00 0.00 0.00 4.61
2891 3671 4.329545 GTCAGCAGCGGGTTCCCA 62.330 66.667 8.70 0.00 0.00 4.37
3025 3805 2.125673 CTAGGCGTGGGTTCGTGG 60.126 66.667 0.00 0.00 0.00 4.94
3125 3909 2.105821 TGACTCGTTTGATCCTGGGTTT 59.894 45.455 0.00 0.00 0.00 3.27
3177 3968 1.591594 CGTGCACGTGACCTCTGTT 60.592 57.895 30.50 0.00 34.11 3.16
3185 3976 1.327460 CGTGACCTCTGTTTGTGTGTG 59.673 52.381 0.00 0.00 0.00 3.82
3186 3977 2.356135 GTGACCTCTGTTTGTGTGTGT 58.644 47.619 0.00 0.00 0.00 3.72
3187 3978 3.527533 GTGACCTCTGTTTGTGTGTGTA 58.472 45.455 0.00 0.00 0.00 2.90
3188 3979 3.936453 GTGACCTCTGTTTGTGTGTGTAA 59.064 43.478 0.00 0.00 0.00 2.41
3229 4021 5.001232 TCTAAAGTGTTTATGTGGCCTGTC 58.999 41.667 3.32 0.00 0.00 3.51
3245 4037 3.009723 CCTGTCAATTTGGTCTGCGTAT 58.990 45.455 0.00 0.00 0.00 3.06
3247 4039 2.746904 TGTCAATTTGGTCTGCGTATGG 59.253 45.455 0.00 0.00 0.00 2.74
3338 4133 0.323302 TGCAGCTAATGTTGGACGGA 59.677 50.000 0.00 0.00 0.00 4.69
3351 4146 0.109412 GGACGGAGAATCGACACGTT 60.109 55.000 0.00 0.00 37.96 3.99
3421 4220 3.282021 GTCATTGATGCCACACCATACT 58.718 45.455 0.00 0.00 0.00 2.12
3422 4221 3.065786 GTCATTGATGCCACACCATACTG 59.934 47.826 0.00 0.00 0.00 2.74
3433 4232 5.702865 CCACACCATACTGTGAATTTCAAG 58.297 41.667 0.00 4.24 43.77 3.02
3471 4270 1.137872 CCCTTCCTCGAGACATTCAGG 59.862 57.143 15.71 8.98 0.00 3.86
3492 4291 3.003897 GGGTATTTGTTTGCACGTGAAGA 59.996 43.478 22.23 0.00 0.00 2.87
3493 4292 3.972502 GGTATTTGTTTGCACGTGAAGAC 59.027 43.478 22.23 15.75 0.00 3.01
3494 4293 4.261031 GGTATTTGTTTGCACGTGAAGACT 60.261 41.667 22.23 0.81 0.00 3.24
3495 4294 5.049954 GGTATTTGTTTGCACGTGAAGACTA 60.050 40.000 22.23 8.69 0.00 2.59
3496 4295 4.530094 TTTGTTTGCACGTGAAGACTAG 57.470 40.909 22.23 0.00 0.00 2.57
3497 4296 3.446310 TGTTTGCACGTGAAGACTAGA 57.554 42.857 22.23 0.00 0.00 2.43
3498 4297 3.990092 TGTTTGCACGTGAAGACTAGAT 58.010 40.909 22.23 0.00 0.00 1.98
3499 4298 5.128992 TGTTTGCACGTGAAGACTAGATA 57.871 39.130 22.23 0.00 0.00 1.98
3500 4299 4.921515 TGTTTGCACGTGAAGACTAGATAC 59.078 41.667 22.23 4.25 0.00 2.24
3501 4300 3.400505 TGCACGTGAAGACTAGATACG 57.599 47.619 22.23 2.31 40.30 3.06
3502 4301 2.096980 TGCACGTGAAGACTAGATACGG 59.903 50.000 22.23 0.00 38.92 4.02
3503 4302 2.353889 GCACGTGAAGACTAGATACGGA 59.646 50.000 22.23 0.00 38.92 4.69
3504 4303 3.546417 GCACGTGAAGACTAGATACGGAG 60.546 52.174 22.23 0.00 38.92 4.63
3505 4304 3.002451 CACGTGAAGACTAGATACGGAGG 59.998 52.174 10.90 0.00 38.92 4.30
3506 4305 3.118482 ACGTGAAGACTAGATACGGAGGA 60.118 47.826 0.00 0.00 38.92 3.71
3507 4306 3.495377 CGTGAAGACTAGATACGGAGGAG 59.505 52.174 0.00 0.00 0.00 3.69
3508 4307 4.706035 GTGAAGACTAGATACGGAGGAGA 58.294 47.826 0.00 0.00 0.00 3.71
3509 4308 5.124645 GTGAAGACTAGATACGGAGGAGAA 58.875 45.833 0.00 0.00 0.00 2.87
3510 4309 5.766174 GTGAAGACTAGATACGGAGGAGAAT 59.234 44.000 0.00 0.00 0.00 2.40
3511 4310 6.263617 GTGAAGACTAGATACGGAGGAGAATT 59.736 42.308 0.00 0.00 0.00 2.17
3512 4311 7.444792 GTGAAGACTAGATACGGAGGAGAATTA 59.555 40.741 0.00 0.00 0.00 1.40
3527 4326 4.082949 GGAGAATTACCACCCGTTTTTGAG 60.083 45.833 0.00 0.00 0.00 3.02
3528 4327 4.466827 AGAATTACCACCCGTTTTTGAGT 58.533 39.130 0.00 0.00 0.00 3.41
3538 4337 4.867608 ACCCGTTTTTGAGTTGTCAATTTG 59.132 37.500 0.00 0.00 42.41 2.32
3539 4338 5.105752 CCCGTTTTTGAGTTGTCAATTTGA 58.894 37.500 0.00 0.00 42.41 2.69
3540 4339 5.752955 CCCGTTTTTGAGTTGTCAATTTGAT 59.247 36.000 1.78 0.00 42.41 2.57
3564 4363 6.882610 AGAGATTTATATGCGAAAATGGCA 57.117 33.333 0.00 0.00 45.71 4.92
3595 4394 4.158025 GGAGACTTCCTCGACTACAATCAA 59.842 45.833 0.00 0.00 42.89 2.57
3600 4399 6.574350 ACTTCCTCGACTACAATCAAATAGG 58.426 40.000 0.00 0.00 0.00 2.57
3601 4400 6.154706 ACTTCCTCGACTACAATCAAATAGGT 59.845 38.462 0.00 0.00 0.00 3.08
3622 4421 3.249189 TGCGGGAAGGAGTGGCTT 61.249 61.111 0.00 0.00 0.00 4.35
3624 4423 2.960688 GCGGGAAGGAGTGGCTTCT 61.961 63.158 0.00 0.00 0.00 2.85
3625 4424 1.078848 CGGGAAGGAGTGGCTTCTG 60.079 63.158 0.00 0.00 0.00 3.02
3631 4430 1.352083 AGGAGTGGCTTCTGCAGTTA 58.648 50.000 14.67 2.24 41.91 2.24
3650 4449 1.251251 ACTTGCACCAAGGAATGAGC 58.749 50.000 9.50 0.00 44.81 4.26
3658 4457 1.134159 CCAAGGAATGAGCTGGAGAGG 60.134 57.143 0.00 0.00 0.00 3.69
3673 4475 4.093743 TGGAGAGGTGTATGCTTCTTGTA 58.906 43.478 0.00 0.00 0.00 2.41
3682 4484 6.341316 GTGTATGCTTCTTGTATTCTGGAGA 58.659 40.000 0.00 0.00 0.00 3.71
3691 4493 6.698380 TCTTGTATTCTGGAGAAGTTGGTAC 58.302 40.000 0.00 0.00 37.48 3.34
3700 4502 3.370061 GGAGAAGTTGGTACATACGCAAC 59.630 47.826 12.04 12.04 39.30 4.17
3712 4514 2.443260 TACGCAACGAGGTGGTGCAT 62.443 55.000 5.70 0.00 0.00 3.96
3715 4517 1.868997 CAACGAGGTGGTGCATCAC 59.131 57.895 22.26 22.26 36.95 3.06
3718 4520 0.603707 ACGAGGTGGTGCATCACAAG 60.604 55.000 30.19 21.52 39.27 3.16
3721 4523 2.562912 GTGGTGCATCACAAGCCG 59.437 61.111 25.18 0.00 37.57 5.52
3740 4600 1.732077 CGGTTCCGCAAATGACAATGG 60.732 52.381 0.00 0.00 0.00 3.16
3741 4601 1.272212 GGTTCCGCAAATGACAATGGT 59.728 47.619 0.00 0.00 0.00 3.55
3750 4610 3.377253 AATGACAATGGTGCTGATCCT 57.623 42.857 0.00 0.00 0.00 3.24
3752 4612 0.737219 GACAATGGTGCTGATCCTGC 59.263 55.000 1.38 1.38 0.00 4.85
3774 4635 5.770663 TGCAAAGGGTAAAGCTTACATTACA 59.229 36.000 0.00 0.00 32.78 2.41
3775 4636 6.265649 TGCAAAGGGTAAAGCTTACATTACAA 59.734 34.615 0.00 0.00 32.78 2.41
3804 4665 1.654023 GGGTGCAGCCGGTTATTCAC 61.654 60.000 20.97 6.15 38.44 3.18
3807 4668 1.135689 GTGCAGCCGGTTATTCACAAG 60.136 52.381 1.90 0.00 0.00 3.16
3809 4670 0.451783 CAGCCGGTTATTCACAAGGC 59.548 55.000 1.90 0.00 45.96 4.35
3810 4671 0.679960 AGCCGGTTATTCACAAGGCC 60.680 55.000 1.90 0.00 46.48 5.19
3826 4687 2.048603 GCCAAGTTGCCTAGCTGGG 61.049 63.158 12.68 12.68 36.00 4.45
3827 4688 1.685224 CCAAGTTGCCTAGCTGGGA 59.315 57.895 22.15 6.28 29.99 4.37
3839 4700 4.855340 CCTAGCTGGGAAAAACCTAATCA 58.145 43.478 11.42 0.00 38.98 2.57
3855 4716 1.843368 ATCATGGGTGGACAAAGCTG 58.157 50.000 0.00 0.00 0.00 4.24
3867 4728 1.202758 ACAAAGCTGAACACGGATGGA 60.203 47.619 0.00 0.00 0.00 3.41
3870 4731 1.078848 GCTGAACACGGATGGAGCT 60.079 57.895 0.00 0.00 0.00 4.09
3876 4737 1.238439 ACACGGATGGAGCTTTTGTG 58.762 50.000 0.00 0.00 0.00 3.33
3894 4755 0.107557 TGTCATGCGATGATGCTGGT 60.108 50.000 2.80 0.00 42.04 4.00
3906 4767 1.174712 ATGCTGGTGCGGGCATAATC 61.175 55.000 0.00 0.00 45.74 1.75
3910 4771 1.360192 GGTGCGGGCATAATCTTGC 59.640 57.895 0.00 0.00 42.01 4.01
3961 4822 1.699730 TCAGCTTGTAGGGCGCTATA 58.300 50.000 14.20 8.56 31.80 1.31
3964 4825 3.071023 TCAGCTTGTAGGGCGCTATATTT 59.929 43.478 14.20 0.00 31.80 1.40
3965 4826 3.815401 CAGCTTGTAGGGCGCTATATTTT 59.185 43.478 14.20 0.00 31.80 1.82
3968 4829 4.537015 CTTGTAGGGCGCTATATTTTTGC 58.463 43.478 14.20 0.00 0.00 3.68
3977 4838 4.555313 GCGCTATATTTTTGCAGAGATGCA 60.555 41.667 0.00 0.00 43.81 3.96
3978 4839 4.908156 CGCTATATTTTTGCAGAGATGCAC 59.092 41.667 1.74 0.00 45.32 4.57
3980 4841 6.073602 CGCTATATTTTTGCAGAGATGCACTA 60.074 38.462 1.74 0.00 45.32 2.74
3985 4846 1.857965 TGCAGAGATGCACTAGAGGT 58.142 50.000 0.00 0.00 40.23 3.85
3992 4853 2.584673 TGCACTAGAGGTGGAGCTC 58.415 57.895 4.71 4.71 45.44 4.09
3994 4855 1.285078 TGCACTAGAGGTGGAGCTCTA 59.715 52.381 14.64 13.53 45.44 2.43
3998 4859 1.892474 CTAGAGGTGGAGCTCTATGCC 59.108 57.143 14.64 6.13 44.23 4.40
4001 4862 1.227793 GGTGGAGCTCTATGCCTGC 60.228 63.158 14.64 0.00 44.23 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.927487 TGCAAAACCATGCCTCTCAT 58.073 45.000 0.00 0.00 45.83 2.90
15 16 1.820519 GATGCAAAACCATGCCTCTCA 59.179 47.619 0.00 0.00 45.83 3.27
16 17 1.135721 GGATGCAAAACCATGCCTCTC 59.864 52.381 0.00 0.00 45.83 3.20
17 18 1.188863 GGATGCAAAACCATGCCTCT 58.811 50.000 0.00 0.00 45.83 3.69
18 19 0.179129 CGGATGCAAAACCATGCCTC 60.179 55.000 0.00 0.00 45.83 4.70
19 20 0.899717 ACGGATGCAAAACCATGCCT 60.900 50.000 0.00 0.00 45.83 4.75
20 21 0.737019 CACGGATGCAAAACCATGCC 60.737 55.000 0.00 0.00 45.83 4.40
21 22 0.243365 TCACGGATGCAAAACCATGC 59.757 50.000 0.00 0.00 46.58 4.06
22 23 1.811965 TCTCACGGATGCAAAACCATG 59.188 47.619 0.00 0.00 0.00 3.66
23 24 2.086869 CTCTCACGGATGCAAAACCAT 58.913 47.619 0.00 0.00 0.00 3.55
24 25 1.071542 TCTCTCACGGATGCAAAACCA 59.928 47.619 0.00 0.00 0.00 3.67
25 26 1.808411 TCTCTCACGGATGCAAAACC 58.192 50.000 0.00 0.00 0.00 3.27
26 27 3.251004 AGTTTCTCTCACGGATGCAAAAC 59.749 43.478 0.00 0.00 0.00 2.43
27 28 3.476552 AGTTTCTCTCACGGATGCAAAA 58.523 40.909 0.00 0.00 0.00 2.44
28 29 3.126001 AGTTTCTCTCACGGATGCAAA 57.874 42.857 0.00 0.00 0.00 3.68
29 30 2.839486 AGTTTCTCTCACGGATGCAA 57.161 45.000 0.00 0.00 0.00 4.08
30 31 2.612972 GGAAGTTTCTCTCACGGATGCA 60.613 50.000 0.00 0.00 0.00 3.96
31 32 2.003301 GGAAGTTTCTCTCACGGATGC 58.997 52.381 0.00 0.00 0.00 3.91
32 33 2.028112 TGGGAAGTTTCTCTCACGGATG 60.028 50.000 0.00 0.00 0.00 3.51
33 34 2.028020 GTGGGAAGTTTCTCTCACGGAT 60.028 50.000 0.00 0.00 0.00 4.18
34 35 1.343465 GTGGGAAGTTTCTCTCACGGA 59.657 52.381 0.00 0.00 0.00 4.69
35 36 1.608283 GGTGGGAAGTTTCTCTCACGG 60.608 57.143 0.00 0.00 0.00 4.94
36 37 1.070134 TGGTGGGAAGTTTCTCTCACG 59.930 52.381 0.00 0.00 0.00 4.35
37 38 2.930826 TGGTGGGAAGTTTCTCTCAC 57.069 50.000 0.00 0.00 0.00 3.51
38 39 4.453480 AAATGGTGGGAAGTTTCTCTCA 57.547 40.909 0.00 0.00 0.00 3.27
39 40 4.700692 GGTAAATGGTGGGAAGTTTCTCTC 59.299 45.833 0.00 0.00 0.00 3.20
40 41 4.105697 TGGTAAATGGTGGGAAGTTTCTCT 59.894 41.667 0.00 0.00 0.00 3.10
41 42 4.403734 TGGTAAATGGTGGGAAGTTTCTC 58.596 43.478 0.00 0.00 0.00 2.87
42 43 4.463050 TGGTAAATGGTGGGAAGTTTCT 57.537 40.909 0.00 0.00 0.00 2.52
43 44 4.620567 GCATGGTAAATGGTGGGAAGTTTC 60.621 45.833 0.00 0.00 0.00 2.78
44 45 3.260632 GCATGGTAAATGGTGGGAAGTTT 59.739 43.478 0.00 0.00 0.00 2.66
45 46 2.831526 GCATGGTAAATGGTGGGAAGTT 59.168 45.455 0.00 0.00 0.00 2.66
46 47 2.225242 TGCATGGTAAATGGTGGGAAGT 60.225 45.455 0.00 0.00 0.00 3.01
47 48 2.455557 TGCATGGTAAATGGTGGGAAG 58.544 47.619 0.00 0.00 0.00 3.46
48 49 2.612285 TGCATGGTAAATGGTGGGAA 57.388 45.000 0.00 0.00 0.00 3.97
49 50 2.244510 AGATGCATGGTAAATGGTGGGA 59.755 45.455 2.46 0.00 0.00 4.37
50 51 2.669781 AGATGCATGGTAAATGGTGGG 58.330 47.619 2.46 0.00 0.00 4.61
51 52 5.850557 TTTAGATGCATGGTAAATGGTGG 57.149 39.130 2.46 0.00 0.00 4.61
55 56 5.232463 GCCCATTTAGATGCATGGTAAATG 58.768 41.667 26.80 26.80 41.08 2.32
56 57 4.284234 GGCCCATTTAGATGCATGGTAAAT 59.716 41.667 2.46 10.59 38.72 1.40
57 58 3.640967 GGCCCATTTAGATGCATGGTAAA 59.359 43.478 2.46 8.59 38.72 2.01
58 59 3.230134 GGCCCATTTAGATGCATGGTAA 58.770 45.455 2.46 0.00 38.72 2.85
59 60 2.813726 CGGCCCATTTAGATGCATGGTA 60.814 50.000 2.46 0.00 38.72 3.25
60 61 1.708341 GGCCCATTTAGATGCATGGT 58.292 50.000 2.46 0.00 38.72 3.55
61 62 0.599558 CGGCCCATTTAGATGCATGG 59.400 55.000 2.46 0.00 39.92 3.66
62 63 1.321474 ACGGCCCATTTAGATGCATG 58.679 50.000 2.46 0.00 31.67 4.06
63 64 2.371841 TCTACGGCCCATTTAGATGCAT 59.628 45.455 0.00 0.00 31.67 3.96
64 65 1.765904 TCTACGGCCCATTTAGATGCA 59.234 47.619 0.00 0.00 31.67 3.96
65 66 2.543777 TCTACGGCCCATTTAGATGC 57.456 50.000 0.00 0.00 31.67 3.91
66 67 7.504924 TTAATTTCTACGGCCCATTTAGATG 57.495 36.000 0.00 0.00 0.00 2.90
67 68 6.206829 GCTTAATTTCTACGGCCCATTTAGAT 59.793 38.462 0.00 0.00 0.00 1.98
68 69 5.529800 GCTTAATTTCTACGGCCCATTTAGA 59.470 40.000 0.00 0.00 0.00 2.10
69 70 5.298276 TGCTTAATTTCTACGGCCCATTTAG 59.702 40.000 0.00 0.00 0.00 1.85
70 71 5.194432 TGCTTAATTTCTACGGCCCATTTA 58.806 37.500 0.00 0.00 0.00 1.40
71 72 4.020543 TGCTTAATTTCTACGGCCCATTT 58.979 39.130 0.00 0.00 0.00 2.32
72 73 3.626930 TGCTTAATTTCTACGGCCCATT 58.373 40.909 0.00 0.00 0.00 3.16
73 74 3.214328 CTGCTTAATTTCTACGGCCCAT 58.786 45.455 0.00 0.00 0.00 4.00
74 75 2.639065 CTGCTTAATTTCTACGGCCCA 58.361 47.619 0.00 0.00 0.00 5.36
75 76 1.947456 CCTGCTTAATTTCTACGGCCC 59.053 52.381 0.00 0.00 0.00 5.80
76 77 1.947456 CCCTGCTTAATTTCTACGGCC 59.053 52.381 0.00 0.00 0.00 6.13
77 78 1.947456 CCCCTGCTTAATTTCTACGGC 59.053 52.381 0.00 0.00 0.00 5.68
78 79 3.553828 TCCCCTGCTTAATTTCTACGG 57.446 47.619 0.00 0.00 0.00 4.02
79 80 6.710744 ACAATATCCCCTGCTTAATTTCTACG 59.289 38.462 0.00 0.00 0.00 3.51
80 81 9.740710 ATACAATATCCCCTGCTTAATTTCTAC 57.259 33.333 0.00 0.00 0.00 2.59
84 85 9.875708 TGTAATACAATATCCCCTGCTTAATTT 57.124 29.630 0.00 0.00 0.00 1.82
86 87 9.466497 CATGTAATACAATATCCCCTGCTTAAT 57.534 33.333 0.00 0.00 0.00 1.40
87 88 7.888021 CCATGTAATACAATATCCCCTGCTTAA 59.112 37.037 0.00 0.00 0.00 1.85
88 89 7.402054 CCATGTAATACAATATCCCCTGCTTA 58.598 38.462 0.00 0.00 0.00 3.09
89 90 6.248433 CCATGTAATACAATATCCCCTGCTT 58.752 40.000 0.00 0.00 0.00 3.91
90 91 5.281193 CCCATGTAATACAATATCCCCTGCT 60.281 44.000 0.00 0.00 0.00 4.24
91 92 4.949856 CCCATGTAATACAATATCCCCTGC 59.050 45.833 0.00 0.00 0.00 4.85
92 93 4.949856 GCCCATGTAATACAATATCCCCTG 59.050 45.833 0.00 0.00 0.00 4.45
93 94 4.017499 GGCCCATGTAATACAATATCCCCT 60.017 45.833 0.00 0.00 0.00 4.79
94 95 4.017499 AGGCCCATGTAATACAATATCCCC 60.017 45.833 0.00 0.00 0.00 4.81
95 96 5.193099 AGGCCCATGTAATACAATATCCC 57.807 43.478 0.00 0.00 0.00 3.85
96 97 6.602009 GGTTAGGCCCATGTAATACAATATCC 59.398 42.308 0.00 0.00 0.00 2.59
97 98 7.625828 GGTTAGGCCCATGTAATACAATATC 57.374 40.000 0.00 0.00 0.00 1.63
113 114 1.271217 GGATTACGGATGGGTTAGGCC 60.271 57.143 0.00 0.00 0.00 5.19
114 115 1.418637 TGGATTACGGATGGGTTAGGC 59.581 52.381 0.00 0.00 0.00 3.93
115 116 3.118186 TGTTGGATTACGGATGGGTTAGG 60.118 47.826 0.00 0.00 0.00 2.69
116 117 3.875134 GTGTTGGATTACGGATGGGTTAG 59.125 47.826 0.00 0.00 0.00 2.34
117 118 3.370739 GGTGTTGGATTACGGATGGGTTA 60.371 47.826 0.00 0.00 0.00 2.85
118 119 2.619590 GGTGTTGGATTACGGATGGGTT 60.620 50.000 0.00 0.00 0.00 4.11
119 120 1.064979 GGTGTTGGATTACGGATGGGT 60.065 52.381 0.00 0.00 0.00 4.51
120 121 1.211949 AGGTGTTGGATTACGGATGGG 59.788 52.381 0.00 0.00 0.00 4.00
121 122 2.710096 AGGTGTTGGATTACGGATGG 57.290 50.000 0.00 0.00 0.00 3.51
122 123 4.217550 ACAAAAGGTGTTGGATTACGGATG 59.782 41.667 0.00 0.00 37.01 3.51
123 124 4.403734 ACAAAAGGTGTTGGATTACGGAT 58.596 39.130 0.00 0.00 37.01 4.18
124 125 3.822940 ACAAAAGGTGTTGGATTACGGA 58.177 40.909 0.00 0.00 37.01 4.69
135 136 2.542595 GACATCGACGAACAAAAGGTGT 59.457 45.455 0.00 0.00 44.64 4.16
136 137 2.800544 AGACATCGACGAACAAAAGGTG 59.199 45.455 0.00 0.00 0.00 4.00
178 179 1.712977 CCTGCATTTCTGGCTCGCTC 61.713 60.000 0.00 0.00 0.00 5.03
223 224 2.661866 ACGTTCGCCTGCACACTC 60.662 61.111 0.00 0.00 0.00 3.51
255 256 1.824230 GGCCATGTGTCATTTTGCCTA 59.176 47.619 0.00 0.00 34.61 3.93
258 259 0.038343 ACGGCCATGTGTCATTTTGC 60.038 50.000 2.24 0.00 0.00 3.68
321 323 2.418692 CACCTACCAACGTTGTGCATA 58.581 47.619 25.63 11.88 0.00 3.14
390 404 4.299009 TGGAACACTACCCACCGT 57.701 55.556 0.00 0.00 0.00 4.83
401 415 3.306364 GCAAGCTCTTCTCTAGTGGAACA 60.306 47.826 0.00 0.00 41.43 3.18
402 416 3.258228 GCAAGCTCTTCTCTAGTGGAAC 58.742 50.000 0.00 0.00 0.00 3.62
409 431 3.203716 CATGCATGCAAGCTCTTCTCTA 58.796 45.455 26.68 0.00 34.99 2.43
476 500 1.880221 CGCAGGTGGTGTTAATGGTGA 60.880 52.381 0.00 0.00 0.00 4.02
559 596 3.677648 AACGTCGTGTCCTCGGGG 61.678 66.667 0.00 0.00 0.00 5.73
560 597 2.430244 CAACGTCGTGTCCTCGGG 60.430 66.667 0.00 0.00 0.00 5.14
565 602 3.165498 GATGGCAACGTCGTGTCC 58.835 61.111 0.00 3.81 44.02 4.02
758 795 2.046314 TGAAGCTAGGGTTGCGCC 60.046 61.111 4.18 0.00 35.28 6.53
761 798 0.394899 ATGCCTGAAGCTAGGGTTGC 60.395 55.000 4.68 0.00 44.23 4.17
797 836 1.405933 CGTAAAGGGAACGGGGTAAGG 60.406 57.143 0.00 0.00 36.71 2.69
800 839 1.190833 TGCGTAAAGGGAACGGGGTA 61.191 55.000 0.00 0.00 40.64 3.69
880 919 5.416326 GTGTTTACCTTTGCATGTATACCCA 59.584 40.000 0.00 0.00 0.00 4.51
995 1044 4.662961 TAGCCATCGCCATCGCCG 62.663 66.667 0.00 0.00 34.57 6.46
1093 1153 2.284699 AGGGTAGTCCTTGCGGCT 60.285 61.111 0.00 0.00 45.47 5.52
1124 1187 2.041153 CTTGGTGAGTGGTTTGGGC 58.959 57.895 0.00 0.00 0.00 5.36
1183 1246 4.730657 CTTGTAACGGACTGTAGGTAGTG 58.269 47.826 0.00 0.00 0.00 2.74
1186 1249 3.156293 TGCTTGTAACGGACTGTAGGTA 58.844 45.455 0.00 0.00 0.00 3.08
1189 1252 3.299340 ACTGCTTGTAACGGACTGTAG 57.701 47.619 0.00 0.00 0.00 2.74
1191 1254 3.955650 ATACTGCTTGTAACGGACTGT 57.044 42.857 0.00 0.00 34.45 3.55
1206 1269 7.655328 TCCCAAAACTTTTGCACAAATATACTG 59.345 33.333 8.53 0.00 0.00 2.74
1218 1281 5.296531 ACATGTCAAATCCCAAAACTTTTGC 59.703 36.000 8.53 0.00 0.00 3.68
1220 1283 6.413892 ACACATGTCAAATCCCAAAACTTTT 58.586 32.000 0.00 0.00 0.00 2.27
1221 1284 5.988287 ACACATGTCAAATCCCAAAACTTT 58.012 33.333 0.00 0.00 0.00 2.66
1224 1287 6.238347 GGAAAACACATGTCAAATCCCAAAAC 60.238 38.462 0.00 0.00 0.00 2.43
1236 1299 3.503363 TCATCTGCAGGAAAACACATGTC 59.497 43.478 15.13 0.00 0.00 3.06
1239 1302 4.159135 GGAATCATCTGCAGGAAAACACAT 59.841 41.667 15.13 0.00 0.00 3.21
1243 1306 3.091545 TGGGAATCATCTGCAGGAAAAC 58.908 45.455 15.13 1.74 0.00 2.43
1250 1314 1.224315 CCCGTGGGAATCATCTGCA 59.776 57.895 0.00 0.00 37.50 4.41
1523 1587 1.973812 GCAGTTTCCAGTCCCAGGC 60.974 63.158 0.00 0.00 0.00 4.85
1524 1588 1.303643 GGCAGTTTCCAGTCCCAGG 60.304 63.158 0.00 0.00 0.00 4.45
1525 1589 0.607489 CAGGCAGTTTCCAGTCCCAG 60.607 60.000 0.00 0.00 0.00 4.45
1526 1590 1.455849 CAGGCAGTTTCCAGTCCCA 59.544 57.895 0.00 0.00 0.00 4.37
1527 1591 1.973812 GCAGGCAGTTTCCAGTCCC 60.974 63.158 0.00 0.00 0.00 4.46
1528 1592 1.973812 GGCAGGCAGTTTCCAGTCC 60.974 63.158 0.00 0.00 0.00 3.85
1529 1593 1.973812 GGGCAGGCAGTTTCCAGTC 60.974 63.158 0.00 0.00 0.00 3.51
1530 1594 2.116125 GGGCAGGCAGTTTCCAGT 59.884 61.111 0.00 0.00 0.00 4.00
1531 1595 1.676967 GAGGGCAGGCAGTTTCCAG 60.677 63.158 0.00 0.00 0.00 3.86
1532 1596 2.436109 GAGGGCAGGCAGTTTCCA 59.564 61.111 0.00 0.00 0.00 3.53
1533 1597 2.747855 CGAGGGCAGGCAGTTTCC 60.748 66.667 0.00 0.00 0.00 3.13
1534 1598 3.435186 GCGAGGGCAGGCAGTTTC 61.435 66.667 0.00 0.00 39.62 2.78
1890 2327 3.905678 CTAGGAGAGGTGCCGGCG 61.906 72.222 23.90 0.00 0.00 6.46
2085 2859 2.709883 CGGCGATGGTGGGCAATTT 61.710 57.895 0.00 0.00 0.00 1.82
2197 2971 1.769295 TTGTTGGGGACGGTGGGTA 60.769 57.895 0.00 0.00 0.00 3.69
2198 2972 3.097830 TTGTTGGGGACGGTGGGT 61.098 61.111 0.00 0.00 0.00 4.51
2199 2973 2.596338 GTTGTTGGGGACGGTGGG 60.596 66.667 0.00 0.00 0.00 4.61
2200 2974 2.975799 CGTTGTTGGGGACGGTGG 60.976 66.667 0.00 0.00 35.74 4.61
2201 2975 3.656045 GCGTTGTTGGGGACGGTG 61.656 66.667 0.00 0.00 39.52 4.94
2202 2976 4.941309 GGCGTTGTTGGGGACGGT 62.941 66.667 0.00 0.00 39.52 4.83
2219 2993 4.446413 GGTAGTCACCGCCACCCG 62.446 72.222 0.00 0.00 34.36 5.28
2220 2994 4.091939 GGGTAGTCACCGCCACCC 62.092 72.222 0.00 0.00 46.86 4.61
2221 2995 4.446413 CGGGTAGTCACCGCCACC 62.446 72.222 0.00 0.00 46.86 4.61
2227 3001 2.504519 GGATGGCGGGTAGTCACC 59.495 66.667 0.00 0.00 44.96 4.02
2228 3002 2.504519 GGGATGGCGGGTAGTCAC 59.495 66.667 0.00 0.00 37.24 3.67
2229 3003 2.766651 GGGGATGGCGGGTAGTCA 60.767 66.667 0.00 0.00 39.68 3.41
2230 3004 3.925090 CGGGGATGGCGGGTAGTC 61.925 72.222 0.00 0.00 0.00 2.59
2231 3005 4.468769 TCGGGGATGGCGGGTAGT 62.469 66.667 0.00 0.00 0.00 2.73
2232 3006 3.925090 GTCGGGGATGGCGGGTAG 61.925 72.222 0.00 0.00 0.00 3.18
2534 3308 4.067913 CAAATGGCGTGGGGGTGC 62.068 66.667 0.00 0.00 0.00 5.01
2631 3407 3.585862 AGTGCGTGGTAAACTAGTCATG 58.414 45.455 0.00 0.00 0.00 3.07
2891 3671 4.329545 ACCTGCGCCGTGGTGAAT 62.330 61.111 14.59 0.00 34.90 2.57
3075 3855 6.321690 ACGTACTTTAACTGCTAGAGATCCAT 59.678 38.462 0.00 0.00 0.00 3.41
3125 3909 7.865889 CCTAATACAAGCACGACATAACATCTA 59.134 37.037 0.00 0.00 0.00 1.98
3170 3954 4.693283 TCTCTTACACACACAAACAGAGG 58.307 43.478 0.00 0.00 0.00 3.69
3177 3968 5.009110 CACTCTCTCTCTCTTACACACACAA 59.991 44.000 0.00 0.00 0.00 3.33
3185 3976 5.001232 AGACACACACTCTCTCTCTCTTAC 58.999 45.833 0.00 0.00 0.00 2.34
3186 3977 5.235850 AGACACACACTCTCTCTCTCTTA 57.764 43.478 0.00 0.00 0.00 2.10
3187 3978 4.098914 AGACACACACTCTCTCTCTCTT 57.901 45.455 0.00 0.00 0.00 2.85
3188 3979 3.788227 AGACACACACTCTCTCTCTCT 57.212 47.619 0.00 0.00 0.00 3.10
3229 4021 2.223021 CGTCCATACGCAGACCAAATTG 60.223 50.000 0.00 0.00 43.12 2.32
3338 4133 5.152097 CACAAGTACTAACGTGTCGATTCT 58.848 41.667 0.00 0.00 44.98 2.40
3351 4146 2.924926 CGGCGTAAATGCACAAGTACTA 59.075 45.455 0.00 0.00 36.28 1.82
3421 4220 6.646240 GCCTATTTTTCTGCTTGAAATTCACA 59.354 34.615 0.00 0.00 43.34 3.58
3422 4221 6.091305 GGCCTATTTTTCTGCTTGAAATTCAC 59.909 38.462 0.00 0.00 43.34 3.18
3471 4270 3.972502 GTCTTCACGTGCAAACAAATACC 59.027 43.478 11.67 0.00 0.00 2.73
3492 4291 5.769162 GTGGTAATTCTCCTCCGTATCTAGT 59.231 44.000 0.00 0.00 0.00 2.57
3493 4292 5.183522 GGTGGTAATTCTCCTCCGTATCTAG 59.816 48.000 5.38 0.00 0.00 2.43
3494 4293 5.075493 GGTGGTAATTCTCCTCCGTATCTA 58.925 45.833 5.38 0.00 0.00 1.98
3495 4294 3.896272 GGTGGTAATTCTCCTCCGTATCT 59.104 47.826 5.38 0.00 0.00 1.98
3496 4295 3.006644 GGGTGGTAATTCTCCTCCGTATC 59.993 52.174 11.82 0.01 38.91 2.24
3497 4296 2.970640 GGGTGGTAATTCTCCTCCGTAT 59.029 50.000 11.82 0.00 38.91 3.06
3498 4297 2.391678 GGGTGGTAATTCTCCTCCGTA 58.608 52.381 11.82 0.00 38.91 4.02
3499 4298 1.201424 GGGTGGTAATTCTCCTCCGT 58.799 55.000 11.82 0.00 38.91 4.69
3500 4299 0.104304 CGGGTGGTAATTCTCCTCCG 59.896 60.000 14.54 14.54 38.91 4.63
3501 4300 1.201424 ACGGGTGGTAATTCTCCTCC 58.799 55.000 10.44 10.44 37.74 4.30
3502 4301 3.345508 AAACGGGTGGTAATTCTCCTC 57.654 47.619 0.00 0.00 0.00 3.71
3503 4302 3.801307 AAAACGGGTGGTAATTCTCCT 57.199 42.857 0.00 0.00 0.00 3.69
3504 4303 3.822167 TCAAAAACGGGTGGTAATTCTCC 59.178 43.478 0.00 0.00 0.00 3.71
3505 4304 4.517832 ACTCAAAAACGGGTGGTAATTCTC 59.482 41.667 0.00 0.00 0.00 2.87
3506 4305 4.466827 ACTCAAAAACGGGTGGTAATTCT 58.533 39.130 0.00 0.00 0.00 2.40
3507 4306 4.841443 ACTCAAAAACGGGTGGTAATTC 57.159 40.909 0.00 0.00 0.00 2.17
3508 4307 4.403113 ACAACTCAAAAACGGGTGGTAATT 59.597 37.500 0.00 0.00 0.00 1.40
3509 4308 3.955551 ACAACTCAAAAACGGGTGGTAAT 59.044 39.130 0.00 0.00 0.00 1.89
3510 4309 3.354467 ACAACTCAAAAACGGGTGGTAA 58.646 40.909 0.00 0.00 0.00 2.85
3511 4310 2.944349 GACAACTCAAAAACGGGTGGTA 59.056 45.455 0.00 0.00 0.00 3.25
3512 4311 1.746787 GACAACTCAAAAACGGGTGGT 59.253 47.619 0.00 0.00 0.00 4.16
3538 4337 8.668353 TGCCATTTTCGCATATAAATCTCTATC 58.332 33.333 0.00 0.00 0.00 2.08
3539 4338 8.565896 TGCCATTTTCGCATATAAATCTCTAT 57.434 30.769 0.00 0.00 0.00 1.98
3540 4339 7.977789 TGCCATTTTCGCATATAAATCTCTA 57.022 32.000 0.00 0.00 0.00 2.43
3547 4346 8.986847 CCATATTTTTGCCATTTTCGCATATAA 58.013 29.630 0.00 0.00 35.83 0.98
3554 4353 6.332630 AGTCTCCATATTTTTGCCATTTTCG 58.667 36.000 0.00 0.00 0.00 3.46
3564 4363 6.301169 AGTCGAGGAAGTCTCCATATTTTT 57.699 37.500 0.00 0.00 45.24 1.94
3595 4394 2.434702 CTCCTTCCCGCAGTTACCTATT 59.565 50.000 0.00 0.00 0.00 1.73
3600 4399 0.391263 CCACTCCTTCCCGCAGTTAC 60.391 60.000 0.00 0.00 0.00 2.50
3601 4400 1.980052 CCACTCCTTCCCGCAGTTA 59.020 57.895 0.00 0.00 0.00 2.24
3607 4406 1.078848 CAGAAGCCACTCCTTCCCG 60.079 63.158 0.00 0.00 41.65 5.14
3625 4424 1.604604 TCCTTGGTGCAAGTAACTGC 58.395 50.000 0.00 0.00 39.58 4.40
3631 4430 1.202976 AGCTCATTCCTTGGTGCAAGT 60.203 47.619 0.00 0.00 39.58 3.16
3639 4438 1.558756 ACCTCTCCAGCTCATTCCTTG 59.441 52.381 0.00 0.00 0.00 3.61
3643 4442 3.726607 CATACACCTCTCCAGCTCATTC 58.273 50.000 0.00 0.00 0.00 2.67
3650 4449 3.055530 ACAAGAAGCATACACCTCTCCAG 60.056 47.826 0.00 0.00 0.00 3.86
3658 4457 6.341316 TCTCCAGAATACAAGAAGCATACAC 58.659 40.000 0.00 0.00 0.00 2.90
3673 4475 5.661458 CGTATGTACCAACTTCTCCAGAAT 58.339 41.667 0.00 0.00 33.01 2.40
3682 4484 2.991190 CTCGTTGCGTATGTACCAACTT 59.009 45.455 15.75 0.00 36.30 2.66
3691 4493 1.966493 GCACCACCTCGTTGCGTATG 61.966 60.000 0.00 0.00 0.00 2.39
3700 4502 1.915614 GCTTGTGATGCACCACCTCG 61.916 60.000 9.22 0.00 36.26 4.63
3712 4514 3.758973 TTGCGGAACCGGCTTGTGA 62.759 57.895 15.01 0.00 40.19 3.58
3715 4517 1.444212 CATTTGCGGAACCGGCTTG 60.444 57.895 15.01 0.00 40.19 4.01
3718 4520 2.136196 TTGTCATTTGCGGAACCGGC 62.136 55.000 15.01 7.86 40.19 6.13
3721 4523 1.272212 ACCATTGTCATTTGCGGAACC 59.728 47.619 0.00 0.00 0.00 3.62
3740 4600 0.610232 ACCCTTTGCAGGATCAGCAC 60.610 55.000 11.13 0.00 44.19 4.40
3741 4601 0.991146 TACCCTTTGCAGGATCAGCA 59.009 50.000 7.87 7.87 44.19 4.41
3750 4610 5.770663 TGTAATGTAAGCTTTACCCTTTGCA 59.229 36.000 3.20 2.93 35.56 4.08
3752 4612 7.759433 CCATTGTAATGTAAGCTTTACCCTTTG 59.241 37.037 3.20 0.00 35.56 2.77
3774 4635 0.106519 GCTGCACCCTGGTATCCATT 60.107 55.000 0.00 0.00 30.82 3.16
3775 4636 1.533711 GCTGCACCCTGGTATCCAT 59.466 57.895 0.00 0.00 30.82 3.41
3826 4687 4.770010 TGTCCACCCATGATTAGGTTTTTC 59.230 41.667 0.00 0.00 32.72 2.29
3827 4688 4.746466 TGTCCACCCATGATTAGGTTTTT 58.254 39.130 0.00 0.00 32.72 1.94
3839 4700 1.133513 TGTTCAGCTTTGTCCACCCAT 60.134 47.619 0.00 0.00 0.00 4.00
3855 4716 1.880027 ACAAAAGCTCCATCCGTGTTC 59.120 47.619 0.00 0.00 0.00 3.18
3867 4728 2.153645 TCATCGCATGACACAAAAGCT 58.846 42.857 0.00 0.00 33.59 3.74
3870 4731 2.488937 AGCATCATCGCATGACACAAAA 59.511 40.909 0.00 0.00 43.01 2.44
3876 4737 0.306840 CACCAGCATCATCGCATGAC 59.693 55.000 0.00 0.00 43.01 3.06
3894 4755 2.186160 CCGCAAGATTATGCCCGCA 61.186 57.895 0.00 0.00 43.47 5.69
3902 4763 1.116308 TCCATCGTCCCGCAAGATTA 58.884 50.000 0.00 0.00 43.02 1.75
3903 4764 0.469917 ATCCATCGTCCCGCAAGATT 59.530 50.000 0.00 0.00 43.02 2.40
3906 4767 0.877649 CTGATCCATCGTCCCGCAAG 60.878 60.000 0.00 0.00 0.00 4.01
3910 4771 0.464036 TTTCCTGATCCATCGTCCCG 59.536 55.000 0.00 0.00 0.00 5.14
3942 4803 1.699730 TATAGCGCCCTACAAGCTGA 58.300 50.000 2.29 0.00 41.80 4.26
3943 4804 2.751166 ATATAGCGCCCTACAAGCTG 57.249 50.000 2.29 0.00 41.80 4.24
3950 4811 4.065088 CTCTGCAAAAATATAGCGCCCTA 58.935 43.478 2.29 0.00 0.00 3.53
3968 4829 2.361757 CTCCACCTCTAGTGCATCTCTG 59.638 54.545 0.00 0.00 45.83 3.35
3977 4838 2.593026 GCATAGAGCTCCACCTCTAGT 58.407 52.381 10.93 0.00 44.96 2.57
3978 4839 1.892474 GGCATAGAGCTCCACCTCTAG 59.108 57.143 10.93 0.00 44.96 2.43
3980 4841 0.264359 AGGCATAGAGCTCCACCTCT 59.736 55.000 10.93 0.13 44.12 3.69
3985 4846 0.179702 CAAGCAGGCATAGAGCTCCA 59.820 55.000 10.93 0.00 44.79 3.86
3992 4853 0.769873 ATCCCTCCAAGCAGGCATAG 59.230 55.000 0.00 0.00 37.29 2.23
3994 4855 3.765491 ATCCCTCCAAGCAGGCAT 58.235 55.556 0.00 0.00 37.29 4.40


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

AutoCloner maintained by Alex Coulton.