Multiple sequence alignment - TraesCS3D01G188000

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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 TraesCS3D01G188000 chr3D 100.000 4166 0 0 1 4166 174454362 174458527 0.000000e+00 7694.0
1 TraesCS3D01G188000 chr3D 88.024 501 53 7 1525 2025 584112475 584111982 1.670000e-163 586.0
2 TraesCS3D01G188000 chr3D 86.538 104 9 1 3337 3440 564146260 564146162 4.400000e-20 110.0
3 TraesCS3D01G188000 chr3A 90.959 3484 191 61 744 4164 213256122 213259544 0.000000e+00 4575.0
4 TraesCS3D01G188000 chr3A 90.855 503 23 7 231 712 213250172 213250672 0.000000e+00 652.0
5 TraesCS3D01G188000 chr3A 80.943 530 81 15 3647 4166 727312315 727312834 6.490000e-108 401.0
6 TraesCS3D01G188000 chr3B 93.462 2799 114 32 610 3357 252956521 252959301 0.000000e+00 4091.0
7 TraesCS3D01G188000 chr3B 89.691 679 56 9 3389 4066 252959297 252959962 0.000000e+00 854.0
8 TraesCS3D01G188000 chr5B 84.608 1072 126 24 987 2040 446010246 446009196 0.000000e+00 1029.0
9 TraesCS3D01G188000 chr5B 84.351 1048 123 26 995 2025 446411462 446412485 0.000000e+00 989.0
10 TraesCS3D01G188000 chr5B 82.203 1062 136 20 995 2040 447207097 447206073 0.000000e+00 865.0
11 TraesCS3D01G188000 chr5B 81.693 874 126 27 2177 3023 446009032 446008166 0.000000e+00 697.0
12 TraesCS3D01G188000 chr5B 84.116 724 91 19 2305 3023 447205427 447204723 0.000000e+00 678.0
13 TraesCS3D01G188000 chr5B 83.724 725 100 17 2305 3023 446413272 446413984 0.000000e+00 669.0
14 TraesCS3D01G188000 chr5B 89.157 83 9 0 3338 3420 679149247 679149165 2.050000e-18 104.0
15 TraesCS3D01G188000 chr5B 81.600 125 15 4 3338 3462 288902561 288902445 3.430000e-16 97.1
16 TraesCS3D01G188000 chr5B 86.842 76 10 0 2177 2252 447205574 447205499 7.420000e-13 86.1
17 TraesCS3D01G188000 chr5A 84.112 1070 125 29 995 2037 476072857 476073908 0.000000e+00 992.0
18 TraesCS3D01G188000 chr5A 80.986 852 134 23 2177 3023 476074046 476074874 0.000000e+00 651.0
19 TraesCS3D01G188000 chr5D 83.865 1066 131 25 995 2041 374295430 374296473 0.000000e+00 977.0
20 TraesCS3D01G188000 chr5D 83.951 729 103 11 2305 3023 374296772 374297496 0.000000e+00 686.0
21 TraesCS3D01G188000 chr5D 77.654 537 81 22 3635 4166 486224986 486225488 1.470000e-74 291.0
22 TraesCS3D01G188000 chr5D 86.842 114 7 5 3337 3448 434400778 434400671 2.030000e-23 121.0
23 TraesCS3D01G188000 chr5D 85.714 70 9 1 2177 2245 374296641 374296710 5.780000e-09 73.1
24 TraesCS3D01G188000 chr7A 78.918 721 134 15 2312 3023 221740412 221739701 1.360000e-129 473.0
25 TraesCS3D01G188000 chr7A 82.353 527 83 8 1525 2045 221741288 221740766 2.280000e-122 449.0
26 TraesCS3D01G188000 chr7A 76.471 289 66 2 3682 3969 10093996 10093709 5.580000e-34 156.0
27 TraesCS3D01G188000 chr4D 83.205 518 82 5 3642 4156 502028475 502028990 1.750000e-128 470.0
28 TraesCS3D01G188000 chr7D 78.303 719 141 13 2312 3023 208655219 208654509 2.280000e-122 449.0
29 TraesCS3D01G188000 chr2B 81.682 535 82 10 3643 4166 13973141 13973670 8.270000e-117 431.0
30 TraesCS3D01G188000 chr2B 87.500 104 8 1 3338 3441 387075931 387076029 9.460000e-22 115.0
31 TraesCS3D01G188000 chr2B 82.716 81 6 6 3642 3717 57885375 57885298 9.670000e-07 65.8
32 TraesCS3D01G188000 chr4A 81.192 537 91 9 3635 4166 246716553 246717084 1.380000e-114 424.0
33 TraesCS3D01G188000 chr6A 79.206 529 99 8 3641 4166 35649742 35649222 1.420000e-94 357.0
34 TraesCS3D01G188000 chr2D 87.222 180 18 4 3990 4166 10392177 10392000 2.540000e-47 200.0
35 TraesCS3D01G188000 chr2D 82.716 81 6 6 3642 3717 35047861 35047784 9.670000e-07 65.8
36 TraesCS3D01G188000 chr2A 91.765 85 7 0 3336 3420 391841375 391841459 7.320000e-23 119.0
37 TraesCS3D01G188000 chr4B 91.667 84 7 0 3337 3420 403672021 403672104 2.630000e-22 117.0
38 TraesCS3D01G188000 chr6B 85.714 105 14 1 3336 3440 506760968 506761071 4.400000e-20 110.0


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 TraesCS3D01G188000 chr3D 174454362 174458527 4165 False 7694.000000 7694 100.0000 1 4166 1 chr3D.!!$F1 4165
1 TraesCS3D01G188000 chr3A 213256122 213259544 3422 False 4575.000000 4575 90.9590 744 4164 1 chr3A.!!$F2 3420
2 TraesCS3D01G188000 chr3A 213250172 213250672 500 False 652.000000 652 90.8550 231 712 1 chr3A.!!$F1 481
3 TraesCS3D01G188000 chr3A 727312315 727312834 519 False 401.000000 401 80.9430 3647 4166 1 chr3A.!!$F3 519
4 TraesCS3D01G188000 chr3B 252956521 252959962 3441 False 2472.500000 4091 91.5765 610 4066 2 chr3B.!!$F1 3456
5 TraesCS3D01G188000 chr5B 446008166 446010246 2080 True 863.000000 1029 83.1505 987 3023 2 chr5B.!!$R3 2036
6 TraesCS3D01G188000 chr5B 446411462 446413984 2522 False 829.000000 989 84.0375 995 3023 2 chr5B.!!$F1 2028
7 TraesCS3D01G188000 chr5B 447204723 447207097 2374 True 543.033333 865 84.3870 995 3023 3 chr5B.!!$R4 2028
8 TraesCS3D01G188000 chr5A 476072857 476074874 2017 False 821.500000 992 82.5490 995 3023 2 chr5A.!!$F1 2028
9 TraesCS3D01G188000 chr5D 374295430 374297496 2066 False 578.700000 977 84.5100 995 3023 3 chr5D.!!$F2 2028
10 TraesCS3D01G188000 chr5D 486224986 486225488 502 False 291.000000 291 77.6540 3635 4166 1 chr5D.!!$F1 531
11 TraesCS3D01G188000 chr7A 221739701 221741288 1587 True 461.000000 473 80.6355 1525 3023 2 chr7A.!!$R2 1498
12 TraesCS3D01G188000 chr4D 502028475 502028990 515 False 470.000000 470 83.2050 3642 4156 1 chr4D.!!$F1 514
13 TraesCS3D01G188000 chr7D 208654509 208655219 710 True 449.000000 449 78.3030 2312 3023 1 chr7D.!!$R1 711
14 TraesCS3D01G188000 chr2B 13973141 13973670 529 False 431.000000 431 81.6820 3643 4166 1 chr2B.!!$F1 523
15 TraesCS3D01G188000 chr4A 246716553 246717084 531 False 424.000000 424 81.1920 3635 4166 1 chr4A.!!$F1 531
16 TraesCS3D01G188000 chr6A 35649222 35649742 520 True 357.000000 357 79.2060 3641 4166 1 chr6A.!!$R1 525

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
485 486 0.318955 CAAAAAGGCCGCCTCACTTG 60.319 55.0 13.72 12.37 30.89 3.16 F
1374 1428 0.611062 TGGACGACGTCATCTCCCTT 60.611 55.0 27.77 0.00 33.68 3.95 F
2082 3137 0.884704 TGCTTCGCTTCAGGACCAAC 60.885 55.0 0.00 0.00 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2110 0.609957 TCCTGTCGAGGTAAGCCGAA 60.610 55.0 0.00 0.0 40.76 4.30 R
2970 4181 0.240945 CAACGCCCACCACTTTGATC 59.759 55.0 0.00 0.0 0.00 2.92 R
3229 4461 0.320771 GCCGAGCTCCTGTTCTTTCA 60.321 55.0 8.47 0.0 0.00 2.69 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
32 33 9.717942 TTTTCAAATACATGTTTAAATCCAGGG 57.282 29.630 2.30 0.00 0.00 4.45
33 34 8.429237 TTCAAATACATGTTTAAATCCAGGGT 57.571 30.769 2.30 0.00 0.00 4.34
34 35 8.429237 TCAAATACATGTTTAAATCCAGGGTT 57.571 30.769 2.30 0.00 0.00 4.11
35 36 9.535170 TCAAATACATGTTTAAATCCAGGGTTA 57.465 29.630 2.30 0.00 0.00 2.85
41 42 8.929487 ACATGTTTAAATCCAGGGTTAAAAAGA 58.071 29.630 9.41 2.76 32.52 2.52
42 43 9.942850 CATGTTTAAATCCAGGGTTAAAAAGAT 57.057 29.630 9.41 4.56 32.52 2.40
44 45 9.990360 TGTTTAAATCCAGGGTTAAAAAGATTC 57.010 29.630 9.41 0.85 32.52 2.52
45 46 9.431887 GTTTAAATCCAGGGTTAAAAAGATTCC 57.568 33.333 9.41 0.00 32.52 3.01
46 47 8.728596 TTAAATCCAGGGTTAAAAAGATTCCA 57.271 30.769 0.00 0.00 0.00 3.53
47 48 7.813087 AAATCCAGGGTTAAAAAGATTCCAT 57.187 32.000 0.00 0.00 0.00 3.41
48 49 6.796785 ATCCAGGGTTAAAAAGATTCCATG 57.203 37.500 0.00 0.00 0.00 3.66
49 50 5.898120 TCCAGGGTTAAAAAGATTCCATGA 58.102 37.500 0.00 0.00 32.70 3.07
50 51 6.502138 TCCAGGGTTAAAAAGATTCCATGAT 58.498 36.000 0.00 0.00 32.70 2.45
51 52 6.959366 TCCAGGGTTAAAAAGATTCCATGATT 59.041 34.615 0.00 0.00 32.70 2.57
52 53 8.119246 TCCAGGGTTAAAAAGATTCCATGATTA 58.881 33.333 0.00 0.00 32.70 1.75
53 54 8.757877 CCAGGGTTAAAAAGATTCCATGATTAA 58.242 33.333 0.00 0.00 32.70 1.40
54 55 9.807649 CAGGGTTAAAAAGATTCCATGATTAAG 57.192 33.333 0.00 0.00 32.70 1.85
55 56 9.768215 AGGGTTAAAAAGATTCCATGATTAAGA 57.232 29.630 0.00 0.00 0.00 2.10
92 93 9.480053 AACTGTTTTATGACCATGAAATTCTTG 57.520 29.630 0.00 2.28 30.66 3.02
93 94 8.090214 ACTGTTTTATGACCATGAAATTCTTGG 58.910 33.333 21.79 21.79 44.58 3.61
94 95 6.873076 TGTTTTATGACCATGAAATTCTTGGC 59.127 34.615 22.90 16.96 43.31 4.52
95 96 6.602410 TTTATGACCATGAAATTCTTGGCA 57.398 33.333 22.90 20.71 43.31 4.92
96 97 6.795144 TTATGACCATGAAATTCTTGGCAT 57.205 33.333 25.15 25.15 43.31 4.40
97 98 4.724074 TGACCATGAAATTCTTGGCATC 57.276 40.909 22.90 15.97 43.31 3.91
98 99 3.448301 TGACCATGAAATTCTTGGCATCC 59.552 43.478 22.90 12.78 43.31 3.51
99 100 3.703052 GACCATGAAATTCTTGGCATCCT 59.297 43.478 22.90 7.54 43.31 3.24
100 101 4.870636 ACCATGAAATTCTTGGCATCCTA 58.129 39.130 22.90 0.00 43.31 2.94
101 102 5.461327 ACCATGAAATTCTTGGCATCCTAT 58.539 37.500 22.90 4.04 43.31 2.57
102 103 5.901276 ACCATGAAATTCTTGGCATCCTATT 59.099 36.000 22.90 3.42 43.31 1.73
103 104 6.384886 ACCATGAAATTCTTGGCATCCTATTT 59.615 34.615 22.90 2.81 43.31 1.40
104 105 7.092757 ACCATGAAATTCTTGGCATCCTATTTT 60.093 33.333 22.90 2.19 43.31 1.82
105 106 7.225931 CCATGAAATTCTTGGCATCCTATTTTG 59.774 37.037 13.84 0.00 35.35 2.44
106 107 6.642430 TGAAATTCTTGGCATCCTATTTTGG 58.358 36.000 0.00 0.00 0.00 3.28
107 108 6.213195 TGAAATTCTTGGCATCCTATTTTGGT 59.787 34.615 0.00 0.00 0.00 3.67
108 109 5.859205 ATTCTTGGCATCCTATTTTGGTC 57.141 39.130 0.00 0.00 0.00 4.02
109 110 4.591321 TCTTGGCATCCTATTTTGGTCT 57.409 40.909 0.00 0.00 0.00 3.85
110 111 4.934356 TCTTGGCATCCTATTTTGGTCTT 58.066 39.130 0.00 0.00 0.00 3.01
111 112 6.073447 TCTTGGCATCCTATTTTGGTCTTA 57.927 37.500 0.00 0.00 0.00 2.10
112 113 6.489603 TCTTGGCATCCTATTTTGGTCTTAA 58.510 36.000 0.00 0.00 0.00 1.85
113 114 7.125391 TCTTGGCATCCTATTTTGGTCTTAAT 58.875 34.615 0.00 0.00 0.00 1.40
114 115 8.278639 TCTTGGCATCCTATTTTGGTCTTAATA 58.721 33.333 0.00 0.00 0.00 0.98
115 116 9.082313 CTTGGCATCCTATTTTGGTCTTAATAT 57.918 33.333 0.00 0.00 0.00 1.28
116 117 9.432982 TTGGCATCCTATTTTGGTCTTAATATT 57.567 29.630 0.00 0.00 0.00 1.28
117 118 9.432982 TGGCATCCTATTTTGGTCTTAATATTT 57.567 29.630 0.00 0.00 0.00 1.40
118 119 9.914131 GGCATCCTATTTTGGTCTTAATATTTC 57.086 33.333 0.00 0.00 0.00 2.17
198 199 9.974980 AATAAAAACAAATCCAAGATTACACGT 57.025 25.926 0.00 0.00 0.00 4.49
199 200 7.692908 AAAAACAAATCCAAGATTACACGTG 57.307 32.000 15.48 15.48 0.00 4.49
200 201 4.419522 ACAAATCCAAGATTACACGTGC 57.580 40.909 17.22 0.00 0.00 5.34
201 202 3.120338 ACAAATCCAAGATTACACGTGCG 60.120 43.478 17.22 0.00 0.00 5.34
202 203 2.380084 ATCCAAGATTACACGTGCGT 57.620 45.000 17.22 0.80 0.00 5.24
203 204 2.157834 TCCAAGATTACACGTGCGTT 57.842 45.000 17.22 0.00 0.00 4.84
204 205 1.795872 TCCAAGATTACACGTGCGTTG 59.204 47.619 17.22 11.58 0.00 4.10
205 206 1.591248 CAAGATTACACGTGCGTTGC 58.409 50.000 17.22 1.46 0.00 4.17
206 207 1.070242 CAAGATTACACGTGCGTTGCA 60.070 47.619 17.22 0.00 35.60 4.08
207 208 0.790207 AGATTACACGTGCGTTGCAG 59.210 50.000 17.22 0.00 40.08 4.41
214 215 3.342627 GTGCGTTGCAGGTGCGTA 61.343 61.111 0.00 0.00 45.83 4.42
215 216 2.358125 TGCGTTGCAGGTGCGTAT 60.358 55.556 0.00 0.00 45.83 3.06
216 217 1.963855 TGCGTTGCAGGTGCGTATT 60.964 52.632 0.00 0.00 45.83 1.89
217 218 1.209127 GCGTTGCAGGTGCGTATTT 59.791 52.632 0.00 0.00 45.83 1.40
218 219 0.444651 GCGTTGCAGGTGCGTATTTA 59.555 50.000 0.00 0.00 45.83 1.40
219 220 1.789054 GCGTTGCAGGTGCGTATTTAC 60.789 52.381 0.00 0.00 45.83 2.01
220 221 1.730064 CGTTGCAGGTGCGTATTTACT 59.270 47.619 0.00 0.00 45.83 2.24
221 222 2.924926 CGTTGCAGGTGCGTATTTACTA 59.075 45.455 0.00 0.00 45.83 1.82
222 223 3.000078 CGTTGCAGGTGCGTATTTACTAG 60.000 47.826 0.00 0.00 45.83 2.57
223 224 3.880047 TGCAGGTGCGTATTTACTAGT 57.120 42.857 0.00 0.00 45.83 2.57
224 225 4.987408 TGCAGGTGCGTATTTACTAGTA 57.013 40.909 0.00 0.00 45.83 1.82
225 226 5.327616 TGCAGGTGCGTATTTACTAGTAA 57.672 39.130 11.38 11.38 45.83 2.24
226 227 5.909477 TGCAGGTGCGTATTTACTAGTAAT 58.091 37.500 15.92 8.95 45.83 1.89
227 228 5.981315 TGCAGGTGCGTATTTACTAGTAATC 59.019 40.000 15.92 8.95 45.83 1.75
228 229 5.404667 GCAGGTGCGTATTTACTAGTAATCC 59.595 44.000 15.92 9.72 0.00 3.01
229 230 6.509656 CAGGTGCGTATTTACTAGTAATCCA 58.490 40.000 15.92 2.14 0.00 3.41
230 231 6.982141 CAGGTGCGTATTTACTAGTAATCCAA 59.018 38.462 15.92 1.78 0.00 3.53
231 232 7.493320 CAGGTGCGTATTTACTAGTAATCCAAA 59.507 37.037 15.92 3.27 0.00 3.28
232 233 8.042515 AGGTGCGTATTTACTAGTAATCCAAAA 58.957 33.333 15.92 2.54 0.00 2.44
233 234 8.118607 GGTGCGTATTTACTAGTAATCCAAAAC 58.881 37.037 15.92 10.61 0.00 2.43
234 235 8.658609 GTGCGTATTTACTAGTAATCCAAAACA 58.341 33.333 15.92 6.66 0.00 2.83
235 236 8.658609 TGCGTATTTACTAGTAATCCAAAACAC 58.341 33.333 15.92 0.97 0.00 3.32
260 261 1.133598 CACGGAACCTACGTCATAGCA 59.866 52.381 0.00 0.00 43.58 3.49
292 293 5.801350 TGCTACAACATGCATAAGAAGAC 57.199 39.130 0.00 0.00 33.94 3.01
353 354 0.959553 TCCGGATAAGATCTCACCGC 59.040 55.000 21.63 2.31 41.86 5.68
376 377 1.597854 TGGAGCAACTTGTCGGCTG 60.598 57.895 4.94 0.00 38.15 4.85
381 382 2.665185 AACTTGTCGGCTGGTCGC 60.665 61.111 0.00 0.00 38.13 5.19
450 451 3.150335 CGCTAGCTCCTGAGGCCA 61.150 66.667 13.93 0.00 0.00 5.36
468 469 2.524306 CCATCAAGGGCTGGTTAACAA 58.476 47.619 8.10 0.00 0.00 2.83
470 471 3.323403 CCATCAAGGGCTGGTTAACAAAA 59.677 43.478 8.10 0.00 0.00 2.44
472 473 4.664150 TCAAGGGCTGGTTAACAAAAAG 57.336 40.909 8.10 0.58 0.00 2.27
473 474 3.386402 TCAAGGGCTGGTTAACAAAAAGG 59.614 43.478 8.10 0.00 0.00 3.11
474 475 1.691976 AGGGCTGGTTAACAAAAAGGC 59.308 47.619 8.10 10.65 0.00 4.35
475 476 1.270625 GGGCTGGTTAACAAAAAGGCC 60.271 52.381 19.47 19.47 45.01 5.19
479 480 0.677288 GGTTAACAAAAAGGCCGCCT 59.323 50.000 5.94 5.94 33.87 5.52
480 481 1.336517 GGTTAACAAAAAGGCCGCCTC 60.337 52.381 13.72 0.00 30.89 4.70
481 482 1.338655 GTTAACAAAAAGGCCGCCTCA 59.661 47.619 13.72 0.00 30.89 3.86
482 483 0.955905 TAACAAAAAGGCCGCCTCAC 59.044 50.000 13.72 0.00 30.89 3.51
483 484 0.755327 AACAAAAAGGCCGCCTCACT 60.755 50.000 13.72 0.00 30.89 3.41
484 485 0.755327 ACAAAAAGGCCGCCTCACTT 60.755 50.000 13.72 0.00 30.89 3.16
485 486 0.318955 CAAAAAGGCCGCCTCACTTG 60.319 55.000 13.72 12.37 30.89 3.16
486 487 1.463553 AAAAAGGCCGCCTCACTTGG 61.464 55.000 13.72 0.00 30.89 3.61
487 488 2.640581 AAAAGGCCGCCTCACTTGGT 62.641 55.000 13.72 0.00 30.89 3.67
488 489 2.640581 AAAGGCCGCCTCACTTGGTT 62.641 55.000 13.72 0.00 30.89 3.67
489 490 3.056328 GGCCGCCTCACTTGGTTC 61.056 66.667 0.71 0.00 0.00 3.62
504 507 1.399440 TGGTTCGAGTCTTATCCGTCG 59.601 52.381 0.00 0.00 0.00 5.12
505 508 1.464821 GTTCGAGTCTTATCCGTCGC 58.535 55.000 0.00 0.00 32.41 5.19
531 534 0.673985 CCCGATCGTGCTTATCTGGA 59.326 55.000 15.09 0.00 31.36 3.86
608 611 1.183549 ACTAGTCCAACTGGTAGCGG 58.816 55.000 0.00 0.00 38.19 5.52
736 756 4.864334 CTTGCTAGGCGCCAGGGG 62.864 72.222 31.54 15.94 38.05 4.79
739 759 4.237207 GCTAGGCGCCAGGGGTAC 62.237 72.222 31.54 6.53 0.00 3.34
760 792 4.894784 ACCGTCACTTCAATATTGTGTCT 58.105 39.130 14.97 0.00 33.82 3.41
794 826 4.465632 TGTATGAGGCGTAATCACAGTT 57.534 40.909 0.00 0.00 0.00 3.16
795 827 5.585820 TGTATGAGGCGTAATCACAGTTA 57.414 39.130 0.00 0.00 0.00 2.24
796 828 5.345702 TGTATGAGGCGTAATCACAGTTAC 58.654 41.667 0.00 0.00 0.00 2.50
910 952 2.822764 CCGCGCCTATAAGAAAGACTT 58.177 47.619 0.00 0.00 42.04 3.01
1329 1383 2.956964 GCGTTCGGCATCTCCTCG 60.957 66.667 0.00 0.00 42.87 4.63
1374 1428 0.611062 TGGACGACGTCATCTCCCTT 60.611 55.000 27.77 0.00 33.68 3.95
1971 2110 1.961277 CAACACCGGAAGAGCGCTT 60.961 57.895 13.26 0.95 36.96 4.68
2071 3126 1.001378 GTCAAACCATGTTGCTTCGCT 60.001 47.619 0.00 0.00 0.00 4.93
2082 3137 0.884704 TGCTTCGCTTCAGGACCAAC 60.885 55.000 0.00 0.00 0.00 3.77
2085 3140 1.466167 CTTCGCTTCAGGACCAACATG 59.534 52.381 0.00 0.00 0.00 3.21
2214 3325 2.169352 GCAGAGAAGATGGTTCTAGCCA 59.831 50.000 0.00 0.00 43.48 4.75
2246 3368 5.294552 GGTATGTTTCTACATTCTCAGCCAC 59.705 44.000 0.00 0.00 42.29 5.01
3025 4236 1.486211 ACTGCCAACGCTAGGTATCT 58.514 50.000 0.00 0.00 35.36 1.98
3028 4239 3.449737 ACTGCCAACGCTAGGTATCTAAA 59.550 43.478 0.00 0.00 35.36 1.85
3044 4255 8.329502 AGGTATCTAAATTAACTTGCAGTCCTT 58.670 33.333 0.00 0.00 0.00 3.36
3072 4283 4.326826 ACCATTAACACTGACCATGACAG 58.673 43.478 14.98 14.98 40.68 3.51
3081 4309 0.530744 GACCATGACAGTACTGCCGA 59.469 55.000 22.90 7.15 0.00 5.54
3091 4319 0.528684 GTACTGCCGATGCTCCTGTC 60.529 60.000 0.00 0.00 38.71 3.51
3104 4332 2.418884 GCTCCTGTCCTTACTACTTGCC 60.419 54.545 0.00 0.00 0.00 4.52
3172 4401 4.082190 TGGATCAGAAGTTGTAGGAACTCG 60.082 45.833 0.00 0.00 41.75 4.18
3229 4461 4.870021 AGAATTGGTTATCCTCTGCCTT 57.130 40.909 0.00 0.00 34.23 4.35
3273 4505 1.052617 GCTATGAGAGGGGGAAGGAC 58.947 60.000 0.00 0.00 0.00 3.85
3329 4562 6.755607 GCAGTAGGATGTTTAGGTTGTACTAC 59.244 42.308 0.00 0.00 0.00 2.73
3335 4568 7.622479 AGGATGTTTAGGTTGTACTACCATACT 59.378 37.037 25.29 14.05 40.82 2.12
3350 4583 2.959707 CCATACTGTACTCCCTCTGTCC 59.040 54.545 0.00 0.00 0.00 4.02
3359 4592 5.311121 TGTACTCCCTCTGTCCCAAAATAAA 59.689 40.000 0.00 0.00 0.00 1.40
3365 4598 5.716703 CCCTCTGTCCCAAAATAAATGTCTT 59.283 40.000 0.00 0.00 0.00 3.01
3368 4601 8.462016 CCTCTGTCCCAAAATAAATGTCTTAAG 58.538 37.037 0.00 0.00 0.00 1.85
3369 4602 8.934023 TCTGTCCCAAAATAAATGTCTTAAGT 57.066 30.769 1.63 0.00 0.00 2.24
3441 4674 4.476628 TTTTGGGACGGAAGGAGTATAC 57.523 45.455 0.00 0.00 0.00 1.47
3442 4675 2.832643 TGGGACGGAAGGAGTATACA 57.167 50.000 5.50 0.00 0.00 2.29
3446 4679 3.567585 GGGACGGAAGGAGTATACAGTAC 59.432 52.174 5.50 0.00 0.00 2.73
3503 4736 3.517296 TTTTGAATGGTGCCTCCTGTA 57.483 42.857 0.00 0.00 37.07 2.74
3508 4741 0.615331 ATGGTGCCTCCTGTACACTG 59.385 55.000 0.00 0.00 37.07 3.66
3547 4780 2.448926 TCCTCATGTGGTTGTACACG 57.551 50.000 13.34 0.00 44.21 4.49
3553 4786 0.530211 TGTGGTTGTACACGGTTCCG 60.530 55.000 9.81 9.81 44.21 4.30
3564 4797 2.046700 GGTTCCGATCCCACGCAA 60.047 61.111 0.00 0.00 0.00 4.85
3591 4824 8.519526 GTTTCAACATTTTGTATGGATCACCTA 58.480 33.333 0.00 0.00 34.09 3.08
3652 4886 1.144691 TGTCTTTGGATGGGTGGTGA 58.855 50.000 0.00 0.00 0.00 4.02
3656 4890 1.205417 CTTTGGATGGGTGGTGATTGC 59.795 52.381 0.00 0.00 0.00 3.56
3871 5108 1.299316 CTGGTGCAAGCGTGTTTGG 60.299 57.895 0.59 0.00 36.92 3.28
3880 5117 2.302230 GCGTGTTTGGTGCACATGC 61.302 57.895 20.43 10.91 46.89 4.06
3956 5200 7.693951 GCAGTGATTATGCCGTTATTGAATATC 59.306 37.037 0.00 0.00 37.73 1.63
3980 5224 0.524862 CCTGCTTGTGTCTGAATGCC 59.475 55.000 0.00 0.00 0.00 4.40
3981 5225 1.241165 CTGCTTGTGTCTGAATGCCA 58.759 50.000 0.00 0.00 0.00 4.92
3982 5226 1.816835 CTGCTTGTGTCTGAATGCCAT 59.183 47.619 0.00 0.00 0.00 4.40
3983 5227 3.011818 CTGCTTGTGTCTGAATGCCATA 58.988 45.455 0.00 0.00 0.00 2.74
3994 5238 8.786898 GTGTCTGAATGCCATATATTATGTTGT 58.213 33.333 0.00 0.00 0.00 3.32
4037 5289 3.133542 CAGGGATGATGACACAGAGCTTA 59.866 47.826 0.00 0.00 0.00 3.09
4047 5299 5.918608 TGACACAGAGCTTAAGAAGTCTTT 58.081 37.500 6.67 0.00 37.40 2.52
4070 5322 4.141846 TGCATTTTGCTGGTTGTTTTAGGA 60.142 37.500 0.75 0.00 45.31 2.94
4071 5323 4.448732 GCATTTTGCTGGTTGTTTTAGGAG 59.551 41.667 0.00 0.00 40.96 3.69
4094 5346 8.258708 GGAGGCTCTCTGTTATTCTAGTTTTTA 58.741 37.037 15.23 0.00 0.00 1.52
4102 5354 7.960738 TCTGTTATTCTAGTTTTTAATGCGTGC 59.039 33.333 0.00 0.00 0.00 5.34
4117 5370 1.574428 GTGCGTTAGGTGTGCTTGG 59.426 57.895 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.717942 CCCTGGATTTAAACATGTATTTGAAAA 57.282 29.630 0.00 0.00 0.00 2.29
7 8 8.875168 ACCCTGGATTTAAACATGTATTTGAAA 58.125 29.630 0.00 0.00 0.00 2.69
8 9 8.429237 ACCCTGGATTTAAACATGTATTTGAA 57.571 30.769 0.00 0.00 0.00 2.69
9 10 8.429237 AACCCTGGATTTAAACATGTATTTGA 57.571 30.769 0.00 0.00 0.00 2.69
15 16 8.929487 TCTTTTTAACCCTGGATTTAAACATGT 58.071 29.630 10.83 0.00 29.06 3.21
16 17 9.942850 ATCTTTTTAACCCTGGATTTAAACATG 57.057 29.630 10.83 0.00 29.06 3.21
18 19 9.990360 GAATCTTTTTAACCCTGGATTTAAACA 57.010 29.630 10.83 6.16 29.06 2.83
19 20 9.431887 GGAATCTTTTTAACCCTGGATTTAAAC 57.568 33.333 10.83 2.53 29.06 2.01
20 21 9.160412 TGGAATCTTTTTAACCCTGGATTTAAA 57.840 29.630 0.00 2.31 0.00 1.52
21 22 8.728596 TGGAATCTTTTTAACCCTGGATTTAA 57.271 30.769 0.00 0.00 0.00 1.52
22 23 8.757877 CATGGAATCTTTTTAACCCTGGATTTA 58.242 33.333 0.00 0.00 0.00 1.40
23 24 7.457535 TCATGGAATCTTTTTAACCCTGGATTT 59.542 33.333 0.00 0.00 0.00 2.17
24 25 6.959366 TCATGGAATCTTTTTAACCCTGGATT 59.041 34.615 0.00 0.00 0.00 3.01
25 26 6.502138 TCATGGAATCTTTTTAACCCTGGAT 58.498 36.000 0.00 0.00 0.00 3.41
26 27 5.898120 TCATGGAATCTTTTTAACCCTGGA 58.102 37.500 0.00 0.00 0.00 3.86
27 28 6.796785 ATCATGGAATCTTTTTAACCCTGG 57.203 37.500 0.00 0.00 0.00 4.45
28 29 9.807649 CTTAATCATGGAATCTTTTTAACCCTG 57.192 33.333 0.00 0.00 0.00 4.45
29 30 9.768215 TCTTAATCATGGAATCTTTTTAACCCT 57.232 29.630 0.00 0.00 0.00 4.34
66 67 9.480053 CAAGAATTTCATGGTCATAAAACAGTT 57.520 29.630 0.00 0.00 0.00 3.16
67 68 8.090214 CCAAGAATTTCATGGTCATAAAACAGT 58.910 33.333 11.65 0.00 31.05 3.55
68 69 7.063780 GCCAAGAATTTCATGGTCATAAAACAG 59.936 37.037 18.97 0.00 37.54 3.16
69 70 6.873076 GCCAAGAATTTCATGGTCATAAAACA 59.127 34.615 18.97 0.00 37.54 2.83
70 71 6.873076 TGCCAAGAATTTCATGGTCATAAAAC 59.127 34.615 18.97 3.90 37.54 2.43
71 72 7.002250 TGCCAAGAATTTCATGGTCATAAAA 57.998 32.000 18.97 0.00 37.54 1.52
72 73 6.602410 TGCCAAGAATTTCATGGTCATAAA 57.398 33.333 18.97 0.38 37.54 1.40
73 74 6.183360 GGATGCCAAGAATTTCATGGTCATAA 60.183 38.462 18.97 4.35 37.54 1.90
74 75 5.302568 GGATGCCAAGAATTTCATGGTCATA 59.697 40.000 18.97 6.91 37.54 2.15
75 76 4.100498 GGATGCCAAGAATTTCATGGTCAT 59.900 41.667 20.44 20.44 37.54 3.06
76 77 3.448301 GGATGCCAAGAATTTCATGGTCA 59.552 43.478 18.97 16.90 37.54 4.02
77 78 3.703052 AGGATGCCAAGAATTTCATGGTC 59.297 43.478 18.97 11.14 37.54 4.02
78 79 3.716431 AGGATGCCAAGAATTTCATGGT 58.284 40.909 18.97 3.52 37.54 3.55
79 80 6.415206 AATAGGATGCCAAGAATTTCATGG 57.585 37.500 14.84 14.84 38.22 3.66
80 81 7.225931 CCAAAATAGGATGCCAAGAATTTCATG 59.774 37.037 0.00 0.00 0.00 3.07
81 82 7.092757 ACCAAAATAGGATGCCAAGAATTTCAT 60.093 33.333 0.00 0.00 0.00 2.57
82 83 6.213195 ACCAAAATAGGATGCCAAGAATTTCA 59.787 34.615 0.00 0.00 0.00 2.69
83 84 6.643388 ACCAAAATAGGATGCCAAGAATTTC 58.357 36.000 0.00 0.00 0.00 2.17
84 85 6.441604 AGACCAAAATAGGATGCCAAGAATTT 59.558 34.615 0.00 0.00 0.00 1.82
85 86 5.960202 AGACCAAAATAGGATGCCAAGAATT 59.040 36.000 0.00 0.00 0.00 2.17
86 87 5.522641 AGACCAAAATAGGATGCCAAGAAT 58.477 37.500 0.00 0.00 0.00 2.40
87 88 4.934356 AGACCAAAATAGGATGCCAAGAA 58.066 39.130 0.00 0.00 0.00 2.52
88 89 4.591321 AGACCAAAATAGGATGCCAAGA 57.409 40.909 0.00 0.00 0.00 3.02
89 90 6.773976 TTAAGACCAAAATAGGATGCCAAG 57.226 37.500 0.00 0.00 0.00 3.61
90 91 9.432982 AATATTAAGACCAAAATAGGATGCCAA 57.567 29.630 0.00 0.00 0.00 4.52
91 92 9.432982 AAATATTAAGACCAAAATAGGATGCCA 57.567 29.630 0.00 0.00 0.00 4.92
92 93 9.914131 GAAATATTAAGACCAAAATAGGATGCC 57.086 33.333 0.00 0.00 0.00 4.40
172 173 9.974980 ACGTGTAATCTTGGATTTGTTTTTATT 57.025 25.926 0.00 0.00 0.00 1.40
173 174 9.405587 CACGTGTAATCTTGGATTTGTTTTTAT 57.594 29.630 7.58 0.00 0.00 1.40
174 175 7.380065 GCACGTGTAATCTTGGATTTGTTTTTA 59.620 33.333 18.38 0.00 0.00 1.52
175 176 6.200097 GCACGTGTAATCTTGGATTTGTTTTT 59.800 34.615 18.38 0.00 0.00 1.94
176 177 5.689961 GCACGTGTAATCTTGGATTTGTTTT 59.310 36.000 18.38 0.00 0.00 2.43
177 178 5.219633 GCACGTGTAATCTTGGATTTGTTT 58.780 37.500 18.38 0.00 0.00 2.83
178 179 4.612712 CGCACGTGTAATCTTGGATTTGTT 60.613 41.667 18.38 0.00 0.00 2.83
179 180 3.120338 CGCACGTGTAATCTTGGATTTGT 60.120 43.478 18.38 0.00 0.00 2.83
180 181 3.120338 ACGCACGTGTAATCTTGGATTTG 60.120 43.478 18.38 0.00 0.00 2.32
181 182 3.071479 ACGCACGTGTAATCTTGGATTT 58.929 40.909 18.38 0.00 0.00 2.17
182 183 2.695359 ACGCACGTGTAATCTTGGATT 58.305 42.857 18.38 0.00 0.00 3.01
183 184 2.380084 ACGCACGTGTAATCTTGGAT 57.620 45.000 18.38 0.00 0.00 3.41
184 185 1.795872 CAACGCACGTGTAATCTTGGA 59.204 47.619 18.38 0.00 0.00 3.53
185 186 1.724654 GCAACGCACGTGTAATCTTGG 60.725 52.381 18.38 0.50 0.00 3.61
186 187 1.070242 TGCAACGCACGTGTAATCTTG 60.070 47.619 18.38 11.84 31.71 3.02
187 188 1.194547 CTGCAACGCACGTGTAATCTT 59.805 47.619 18.38 0.00 33.79 2.40
188 189 0.790207 CTGCAACGCACGTGTAATCT 59.210 50.000 18.38 0.00 33.79 2.40
189 190 0.179225 CCTGCAACGCACGTGTAATC 60.179 55.000 18.38 0.00 33.79 1.75
190 191 0.882927 ACCTGCAACGCACGTGTAAT 60.883 50.000 18.38 0.00 33.79 1.89
191 192 1.521906 ACCTGCAACGCACGTGTAA 60.522 52.632 18.38 0.00 33.79 2.41
192 193 2.107343 ACCTGCAACGCACGTGTA 59.893 55.556 18.38 0.00 33.79 2.90
193 194 3.572539 CACCTGCAACGCACGTGT 61.573 61.111 18.38 0.00 39.45 4.49
194 195 4.962122 GCACCTGCAACGCACGTG 62.962 66.667 12.28 12.28 44.21 4.49
197 198 2.182614 AATACGCACCTGCAACGCAC 62.183 55.000 0.00 0.00 42.21 5.34
198 199 1.511318 AAATACGCACCTGCAACGCA 61.511 50.000 0.00 0.00 42.21 5.24
199 200 0.444651 TAAATACGCACCTGCAACGC 59.555 50.000 0.00 0.00 42.21 4.84
200 201 1.730064 AGTAAATACGCACCTGCAACG 59.270 47.619 0.00 0.00 42.21 4.10
201 202 3.930848 ACTAGTAAATACGCACCTGCAAC 59.069 43.478 0.00 0.00 42.21 4.17
202 203 4.196626 ACTAGTAAATACGCACCTGCAA 57.803 40.909 0.00 0.00 42.21 4.08
203 204 3.880047 ACTAGTAAATACGCACCTGCA 57.120 42.857 0.00 0.00 42.21 4.41
204 205 5.404667 GGATTACTAGTAAATACGCACCTGC 59.595 44.000 18.88 1.59 37.78 4.85
205 206 6.509656 TGGATTACTAGTAAATACGCACCTG 58.490 40.000 18.88 0.00 0.00 4.00
206 207 6.720112 TGGATTACTAGTAAATACGCACCT 57.280 37.500 18.88 0.00 0.00 4.00
207 208 7.775397 TTTGGATTACTAGTAAATACGCACC 57.225 36.000 18.88 12.95 0.00 5.01
208 209 8.658609 TGTTTTGGATTACTAGTAAATACGCAC 58.341 33.333 18.88 12.20 0.00 5.34
209 210 8.658609 GTGTTTTGGATTACTAGTAAATACGCA 58.341 33.333 18.88 9.63 0.00 5.24
210 211 8.658609 TGTGTTTTGGATTACTAGTAAATACGC 58.341 33.333 18.88 13.49 0.00 4.42
211 212 9.962759 GTGTGTTTTGGATTACTAGTAAATACG 57.037 33.333 18.88 0.00 0.00 3.06
214 215 8.789762 GTGGTGTGTTTTGGATTACTAGTAAAT 58.210 33.333 18.88 8.11 0.00 1.40
215 216 7.774157 TGTGGTGTGTTTTGGATTACTAGTAAA 59.226 33.333 18.88 1.55 0.00 2.01
216 217 7.227116 GTGTGGTGTGTTTTGGATTACTAGTAA 59.773 37.037 17.41 17.41 0.00 2.24
217 218 6.707161 GTGTGGTGTGTTTTGGATTACTAGTA 59.293 38.462 0.00 0.00 0.00 1.82
218 219 5.529800 GTGTGGTGTGTTTTGGATTACTAGT 59.470 40.000 0.00 0.00 0.00 2.57
219 220 5.333798 CGTGTGGTGTGTTTTGGATTACTAG 60.334 44.000 0.00 0.00 0.00 2.57
220 221 4.512198 CGTGTGGTGTGTTTTGGATTACTA 59.488 41.667 0.00 0.00 0.00 1.82
221 222 3.314080 CGTGTGGTGTGTTTTGGATTACT 59.686 43.478 0.00 0.00 0.00 2.24
222 223 3.549221 CCGTGTGGTGTGTTTTGGATTAC 60.549 47.826 0.00 0.00 0.00 1.89
223 224 2.619177 CCGTGTGGTGTGTTTTGGATTA 59.381 45.455 0.00 0.00 0.00 1.75
224 225 1.407258 CCGTGTGGTGTGTTTTGGATT 59.593 47.619 0.00 0.00 0.00 3.01
225 226 1.028905 CCGTGTGGTGTGTTTTGGAT 58.971 50.000 0.00 0.00 0.00 3.41
226 227 0.035343 TCCGTGTGGTGTGTTTTGGA 60.035 50.000 0.00 0.00 36.30 3.53
227 228 0.811915 TTCCGTGTGGTGTGTTTTGG 59.188 50.000 0.00 0.00 36.30 3.28
228 229 1.468395 GGTTCCGTGTGGTGTGTTTTG 60.468 52.381 0.00 0.00 36.30 2.44
229 230 0.812549 GGTTCCGTGTGGTGTGTTTT 59.187 50.000 0.00 0.00 36.30 2.43
230 231 0.034863 AGGTTCCGTGTGGTGTGTTT 60.035 50.000 0.00 0.00 36.30 2.83
231 232 0.831966 TAGGTTCCGTGTGGTGTGTT 59.168 50.000 0.00 0.00 36.30 3.32
232 233 0.105408 GTAGGTTCCGTGTGGTGTGT 59.895 55.000 0.00 0.00 36.30 3.72
233 234 0.942410 CGTAGGTTCCGTGTGGTGTG 60.942 60.000 0.00 0.00 36.30 3.82
234 235 1.364901 CGTAGGTTCCGTGTGGTGT 59.635 57.895 0.00 0.00 36.30 4.16
235 236 0.665369 GACGTAGGTTCCGTGTGGTG 60.665 60.000 0.00 0.00 38.92 4.17
274 275 3.009723 CCCGTCTTCTTATGCATGTTGT 58.990 45.455 10.16 0.00 0.00 3.32
285 286 5.330233 ACCATTTTTAATCCCCGTCTTCTT 58.670 37.500 0.00 0.00 0.00 2.52
287 288 4.201881 CGACCATTTTTAATCCCCGTCTTC 60.202 45.833 0.00 0.00 0.00 2.87
292 293 4.084223 CGATACGACCATTTTTAATCCCCG 60.084 45.833 0.00 0.00 0.00 5.73
353 354 0.583438 CGACAAGTTGCTCCACTGTG 59.417 55.000 1.81 0.00 0.00 3.66
436 437 1.126488 CTTGATGGCCTCAGGAGCTA 58.874 55.000 3.32 0.00 32.85 3.32
450 451 4.040339 CCTTTTTGTTAACCAGCCCTTGAT 59.960 41.667 2.48 0.00 0.00 2.57
461 462 1.338655 TGAGGCGGCCTTTTTGTTAAC 59.661 47.619 24.71 7.32 31.76 2.01
464 465 0.755327 AGTGAGGCGGCCTTTTTGTT 60.755 50.000 24.71 0.00 31.76 2.83
465 466 0.755327 AAGTGAGGCGGCCTTTTTGT 60.755 50.000 24.71 5.17 31.76 2.83
466 467 0.318955 CAAGTGAGGCGGCCTTTTTG 60.319 55.000 24.71 21.46 31.76 2.44
468 469 1.903404 CCAAGTGAGGCGGCCTTTT 60.903 57.895 24.71 14.95 31.76 2.27
470 471 3.133365 AACCAAGTGAGGCGGCCTT 62.133 57.895 24.71 4.05 31.76 4.35
472 473 3.056328 GAACCAAGTGAGGCGGCC 61.056 66.667 12.11 12.11 0.00 6.13
473 474 3.423154 CGAACCAAGTGAGGCGGC 61.423 66.667 0.00 0.00 0.00 6.53
474 475 1.738099 CTCGAACCAAGTGAGGCGG 60.738 63.158 0.00 0.00 0.00 6.13
475 476 1.006102 ACTCGAACCAAGTGAGGCG 60.006 57.895 0.00 0.00 34.03 5.52
479 480 3.119602 CGGATAAGACTCGAACCAAGTGA 60.120 47.826 0.00 0.00 0.00 3.41
480 481 3.179830 CGGATAAGACTCGAACCAAGTG 58.820 50.000 0.00 0.00 0.00 3.16
481 482 2.824341 ACGGATAAGACTCGAACCAAGT 59.176 45.455 0.00 0.00 0.00 3.16
482 483 3.436496 GACGGATAAGACTCGAACCAAG 58.564 50.000 0.00 0.00 0.00 3.61
483 484 2.159476 CGACGGATAAGACTCGAACCAA 60.159 50.000 0.00 0.00 0.00 3.67
484 485 1.399440 CGACGGATAAGACTCGAACCA 59.601 52.381 0.00 0.00 0.00 3.67
485 486 1.859197 GCGACGGATAAGACTCGAACC 60.859 57.143 0.00 0.00 0.00 3.62
486 487 1.464821 GCGACGGATAAGACTCGAAC 58.535 55.000 0.00 0.00 0.00 3.95
487 488 0.379669 GGCGACGGATAAGACTCGAA 59.620 55.000 0.00 0.00 0.00 3.71
488 489 0.463295 AGGCGACGGATAAGACTCGA 60.463 55.000 0.00 0.00 0.00 4.04
489 490 0.041135 GAGGCGACGGATAAGACTCG 60.041 60.000 0.00 0.00 0.00 4.18
712 732 3.791539 CGCCTAGCAAGAGCAGTG 58.208 61.111 0.00 0.00 45.49 3.66
736 756 5.867716 AGACACAATATTGAAGTGACGGTAC 59.132 40.000 22.16 6.43 37.05 3.34
737 757 5.867174 CAGACACAATATTGAAGTGACGGTA 59.133 40.000 22.16 0.00 37.05 4.02
739 759 4.929211 TCAGACACAATATTGAAGTGACGG 59.071 41.667 22.16 10.64 37.05 4.79
740 760 5.443301 CGTCAGACACAATATTGAAGTGACG 60.443 44.000 29.67 29.67 40.79 4.35
742 762 5.405269 CACGTCAGACACAATATTGAAGTGA 59.595 40.000 22.16 14.36 46.10 3.41
748 780 2.222796 CGCCACGTCAGACACAATATTG 60.223 50.000 14.01 14.01 0.00 1.90
760 792 1.739929 CATACAAGGCGCCACGTCA 60.740 57.895 31.54 9.91 32.13 4.35
785 817 4.737855 ATGGCGAGTAGTAACTGTGATT 57.262 40.909 0.00 0.00 35.56 2.57
794 826 4.156556 ACGTAGTCAAAATGGCGAGTAGTA 59.843 41.667 0.00 0.00 29.74 1.82
795 827 3.057033 ACGTAGTCAAAATGGCGAGTAGT 60.057 43.478 0.00 0.00 29.74 2.73
796 828 3.303495 CACGTAGTCAAAATGGCGAGTAG 59.697 47.826 0.00 0.00 41.61 2.57
890 927 2.510768 AGTCTTTCTTATAGGCGCGG 57.489 50.000 8.83 0.00 0.00 6.46
891 928 3.707793 AGAAGTCTTTCTTATAGGCGCG 58.292 45.455 0.00 0.00 40.79 6.86
892 929 4.683832 TGAGAAGTCTTTCTTATAGGCGC 58.316 43.478 0.00 0.00 43.63 6.53
893 930 6.036191 GGTTTGAGAAGTCTTTCTTATAGGCG 59.964 42.308 0.00 0.00 43.63 5.52
894 931 7.106890 AGGTTTGAGAAGTCTTTCTTATAGGC 58.893 38.462 0.00 0.00 43.63 3.93
910 952 5.890985 TCTTGATGTCCAAAAAGGTTTGAGA 59.109 36.000 0.81 0.00 45.99 3.27
948 990 3.170585 GCGTTCTCGGTCGGTTCG 61.171 66.667 0.00 0.00 37.56 3.95
1374 1428 1.112113 GGATGAAGCTACCGAGGACA 58.888 55.000 0.00 0.00 0.00 4.02
1971 2110 0.609957 TCCTGTCGAGGTAAGCCGAA 60.610 55.000 0.00 0.00 40.76 4.30
2071 3126 1.962807 CCAAAGCATGTTGGTCCTGAA 59.037 47.619 6.88 0.00 42.74 3.02
2082 3137 1.608055 TGACCACTGACCAAAGCATG 58.392 50.000 0.00 0.00 0.00 4.06
2085 3140 1.604278 GAGTTGACCACTGACCAAAGC 59.396 52.381 0.00 0.00 35.01 3.51
2214 3325 8.664669 AGAATGTAGAAACATACCCCAAAAAT 57.335 30.769 0.00 0.00 45.79 1.82
2301 3447 1.203100 AGGCCCTGCAAGAACTCATTT 60.203 47.619 0.00 0.00 34.07 2.32
2307 3488 2.094545 CACAATTAGGCCCTGCAAGAAC 60.095 50.000 0.00 0.00 34.07 3.01
2970 4181 0.240945 CAACGCCCACCACTTTGATC 59.759 55.000 0.00 0.00 0.00 2.92
3044 4255 2.026636 GGTCAGTGTTAATGGTAGGGCA 60.027 50.000 0.00 0.00 0.00 5.36
3047 4258 4.876107 GTCATGGTCAGTGTTAATGGTAGG 59.124 45.833 0.00 0.00 0.00 3.18
3050 4261 4.202461 ACTGTCATGGTCAGTGTTAATGGT 60.202 41.667 18.54 0.00 43.32 3.55
3051 4262 4.326826 ACTGTCATGGTCAGTGTTAATGG 58.673 43.478 18.54 0.00 43.32 3.16
3072 4283 0.528684 GACAGGAGCATCGGCAGTAC 60.529 60.000 0.00 0.00 44.61 2.73
3081 4309 3.118592 GCAAGTAGTAAGGACAGGAGCAT 60.119 47.826 0.00 0.00 0.00 3.79
3104 4332 5.783111 CACAAGACAATAAGAAAAAGGGGG 58.217 41.667 0.00 0.00 0.00 5.40
3116 4345 3.814842 CACAGAACCTGCACAAGACAATA 59.185 43.478 0.00 0.00 34.37 1.90
3117 4346 2.620115 CACAGAACCTGCACAAGACAAT 59.380 45.455 0.00 0.00 34.37 2.71
3229 4461 0.320771 GCCGAGCTCCTGTTCTTTCA 60.321 55.000 8.47 0.00 0.00 2.69
3273 4505 7.872993 TCTGTTGTCTAAAATGTACAGGAGAAG 59.127 37.037 0.33 0.00 35.06 2.85
3329 4562 2.959707 GGACAGAGGGAGTACAGTATGG 59.040 54.545 0.00 0.00 43.62 2.74
3335 4568 2.409064 TTTGGGACAGAGGGAGTACA 57.591 50.000 0.00 0.00 42.39 2.90
3404 4637 8.247562 CCGTCCCAAAATAAAATAAATGTCTCA 58.752 33.333 0.00 0.00 0.00 3.27
3441 4674 8.653338 GGTGTTTGTTATACATAGTGTGTACTG 58.347 37.037 1.38 0.00 45.59 2.74
3442 4675 8.369424 TGGTGTTTGTTATACATAGTGTGTACT 58.631 33.333 1.38 0.00 45.59 2.73
3446 4679 7.484641 GCAATGGTGTTTGTTATACATAGTGTG 59.515 37.037 0.00 0.00 0.00 3.82
3459 4692 2.036217 CACATGAGGCAATGGTGTTTGT 59.964 45.455 0.00 0.00 31.46 2.83
3503 4736 3.646162 TGTACAGAGTTCCAATCCAGTGT 59.354 43.478 0.00 0.00 0.00 3.55
3508 4741 5.501156 AGGAAATGTACAGAGTTCCAATCC 58.499 41.667 25.86 11.18 41.73 3.01
3547 4780 2.046700 TTGCGTGGGATCGGAACC 60.047 61.111 0.00 0.00 36.37 3.62
3553 4786 1.606668 TGTTGAAACTTGCGTGGGATC 59.393 47.619 0.00 0.00 0.00 3.36
3564 4797 7.233348 AGGTGATCCATACAAAATGTTGAAACT 59.767 33.333 1.62 0.00 35.94 2.66
3591 4824 1.383248 CATTCCCGACCCCTCTCCT 60.383 63.158 0.00 0.00 0.00 3.69
3652 4886 2.093973 AGAATCTTCGTCTCCACGCAAT 60.094 45.455 0.00 0.00 46.28 3.56
3656 4890 3.839293 AAGAAGAATCTTCGTCTCCACG 58.161 45.455 16.35 0.00 42.26 4.94
3745 4982 1.528309 CCAACCACCCGAGCAAAGT 60.528 57.895 0.00 0.00 0.00 2.66
3811 5048 2.903784 TCAATACCACTATATGCGCCCT 59.096 45.455 4.18 0.00 0.00 5.19
3840 5077 3.626924 ACCAGCCTTCGCCGTCTT 61.627 61.111 0.00 0.00 34.57 3.01
3861 5098 1.359833 CATGTGCACCAAACACGCT 59.640 52.632 15.69 0.00 41.03 5.07
3946 5190 6.057533 CACAAGCAGGTCCTGATATTCAATA 58.942 40.000 23.77 0.00 32.44 1.90
3956 5200 0.394192 TCAGACACAAGCAGGTCCTG 59.606 55.000 15.15 15.15 34.58 3.86
3980 5224 8.380742 AGGAGACCCCTACAACATAATATATG 57.619 38.462 0.00 0.00 45.48 1.78
4094 5346 1.866237 CACACCTAACGCACGCATT 59.134 52.632 0.00 0.00 0.00 3.56
4102 5354 1.289109 CCGACCAAGCACACCTAACG 61.289 60.000 0.00 0.00 0.00 3.18
4117 5370 8.260270 ACATAATACAAAGTTCTTAACCCGAC 57.740 34.615 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.