Multiple sequence alignment - TraesCS5A01G439100

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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 TraesCS5A01G439100 chr5A 100.000 4184 0 0 1 4184 620564109 620559926 0.000000e+00 7727.0
1 TraesCS5A01G439100 chr1D 93.712 1463 68 13 837 2285 360093263 360094715 0.000000e+00 2170.0
2 TraesCS5A01G439100 chr1D 87.602 492 35 10 2985 3459 360095324 360095806 7.910000e-152 547.0
3 TraesCS5A01G439100 chr1D 88.380 284 22 7 11 286 174846043 174845763 8.670000e-87 331.0
4 TraesCS5A01G439100 chr1D 80.397 403 39 21 2480 2872 360094868 360095240 1.920000e-68 270.0
5 TraesCS5A01G439100 chr1D 84.892 139 13 5 3994 4126 408071311 408071447 2.620000e-27 134.0
6 TraesCS5A01G439100 chr1B 93.379 1465 71 14 837 2285 482163884 482165338 0.000000e+00 2145.0
7 TraesCS5A01G439100 chr1B 86.916 428 40 10 2985 3407 482165948 482166364 2.280000e-127 466.0
8 TraesCS5A01G439100 chr1B 100.000 32 0 0 4021 4052 548621002 548621033 4.520000e-05 60.2
9 TraesCS5A01G439100 chr1B 97.059 34 1 0 3777 3810 466926177 466926210 1.620000e-04 58.4
10 TraesCS5A01G439100 chr5D 96.060 1269 41 6 962 2223 496589632 496588366 0.000000e+00 2058.0
11 TraesCS5A01G439100 chr5D 94.844 737 28 5 2923 3651 496587451 496586717 0.000000e+00 1142.0
12 TraesCS5A01G439100 chr5D 88.148 675 35 16 2267 2921 496588197 496587548 0.000000e+00 761.0
13 TraesCS5A01G439100 chr5D 88.103 311 27 6 321 621 496592269 496591959 1.110000e-95 361.0
14 TraesCS5A01G439100 chr5D 98.611 144 2 0 4041 4184 496586330 496586187 5.370000e-64 255.0
15 TraesCS5A01G439100 chr5D 79.496 278 25 18 638 914 496591978 496591732 7.190000e-38 169.0
16 TraesCS5A01G439100 chr5D 80.159 252 7 11 3777 3988 496586593 496586345 9.370000e-32 148.0
17 TraesCS5A01G439100 chr5D 97.015 67 2 0 2233 2299 496588264 496588198 3.420000e-21 113.0
18 TraesCS5A01G439100 chr5B 96.187 1259 44 2 984 2238 615201342 615200084 0.000000e+00 2056.0
19 TraesCS5A01G439100 chr5B 92.185 1446 79 14 2233 3651 615199930 615198492 0.000000e+00 2013.0
20 TraesCS5A01G439100 chr5B 86.408 309 31 6 322 620 615203984 615203677 1.120000e-85 327.0
21 TraesCS5A01G439100 chr5B 94.737 114 6 0 2233 2346 615199987 615199874 1.200000e-40 178.0
22 TraesCS5A01G439100 chr5B 79.195 298 30 18 638 914 615203695 615203409 1.200000e-40 178.0
23 TraesCS5A01G439100 chr5B 81.683 202 17 8 3851 4035 615198121 615197923 2.610000e-32 150.0
24 TraesCS5A01G439100 chr1A 95.531 1253 52 2 990 2238 537356828 537355576 0.000000e+00 2001.0
25 TraesCS5A01G439100 chr1A 89.420 293 19 6 3161 3448 537354583 537354298 3.980000e-95 359.0
26 TraesCS5A01G439100 chr1A 90.863 197 16 2 3006 3201 537354780 537354585 3.210000e-66 263.0
27 TraesCS5A01G439100 chr2A 83.064 803 132 4 989 1789 385906109 385906909 0.000000e+00 726.0
28 TraesCS5A01G439100 chr2A 82.192 146 13 7 3994 4126 40618581 40618436 3.420000e-21 113.0
29 TraesCS5A01G439100 chr3A 91.450 269 15 4 3922 4184 632551391 632551125 3.070000e-96 363.0
30 TraesCS5A01G439100 chr3A 89.109 101 9 2 3535 3634 632554564 632554465 1.580000e-24 124.0
31 TraesCS5A01G439100 chr3A 84.672 137 4 4 3652 3779 632554412 632554284 2.040000e-23 121.0
32 TraesCS5A01G439100 chr3D 88.498 313 17 4 3889 4184 489166033 489165723 1.110000e-95 361.0
33 TraesCS5A01G439100 chr3D 80.620 129 20 4 3652 3779 489176281 489176157 1.240000e-15 95.3
34 TraesCS5A01G439100 chr7B 86.408 309 30 7 2233 2534 421500828 421500525 1.120000e-85 327.0
35 TraesCS5A01G439100 chr7B 86.408 309 30 8 2233 2534 632609917 632610220 1.120000e-85 327.0
36 TraesCS5A01G439100 chr7B 89.552 201 15 3 2029 2223 421501187 421500987 2.500000e-62 250.0
37 TraesCS5A01G439100 chr7B 88.601 193 18 2 2029 2217 632609558 632609750 9.050000e-57 231.0
38 TraesCS5A01G439100 chr7B 92.105 114 9 0 2233 2346 421500885 421500772 1.200000e-35 161.0
39 TraesCS5A01G439100 chr7B 90.351 114 11 0 2233 2346 632609860 632609973 2.610000e-32 150.0
40 TraesCS5A01G439100 chr6B 86.149 296 22 7 3889 4184 136933900 136933624 6.800000e-78 302.0
41 TraesCS5A01G439100 chr3B 83.557 298 35 9 10 295 423321661 423321956 2.480000e-67 267.0
42 TraesCS5A01G439100 chr4A 84.120 233 18 12 3905 4126 27665952 27666176 1.520000e-49 207.0
43 TraesCS5A01G439100 chr4D 84.236 203 19 8 3929 4125 438208538 438208733 7.140000e-43 185.0
44 TraesCS5A01G439100 chr4B 80.000 130 10 8 3991 4120 541920089 541920202 9.640000e-12 82.4


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 TraesCS5A01G439100 chr5A 620559926 620564109 4183 True 7727.000000 7727 100.000000 1 4184 1 chr5A.!!$R1 4183
1 TraesCS5A01G439100 chr1D 360093263 360095806 2543 False 995.666667 2170 87.237000 837 3459 3 chr1D.!!$F2 2622
2 TraesCS5A01G439100 chr1B 482163884 482166364 2480 False 1305.500000 2145 90.147500 837 3407 2 chr1B.!!$F3 2570
3 TraesCS5A01G439100 chr5D 496586187 496592269 6082 True 625.875000 2058 90.304500 321 4184 8 chr5D.!!$R1 3863
4 TraesCS5A01G439100 chr5B 615197923 615203984 6061 True 817.000000 2056 88.399167 322 4035 6 chr5B.!!$R1 3713
5 TraesCS5A01G439100 chr1A 537354298 537356828 2530 True 874.333333 2001 91.938000 990 3448 3 chr1A.!!$R1 2458
6 TraesCS5A01G439100 chr2A 385906109 385906909 800 False 726.000000 726 83.064000 989 1789 1 chr2A.!!$F1 800
7 TraesCS5A01G439100 chr3A 632551125 632554564 3439 True 202.666667 363 88.410333 3535 4184 3 chr3A.!!$R1 649
8 TraesCS5A01G439100 chr7B 421500525 421501187 662 True 246.000000 327 89.355000 2029 2534 3 chr7B.!!$R1 505
9 TraesCS5A01G439100 chr7B 632609558 632610220 662 False 236.000000 327 88.453333 2029 2534 3 chr7B.!!$F1 505

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
44 45 0.107654 GGAAGAAGATGTGGGGTCGG 60.108 60.0 0.00 0.0 0.00 4.79 F
45 46 0.107654 GAAGAAGATGTGGGGTCGGG 60.108 60.0 0.00 0.0 0.00 5.14 F
876 909 0.179936 CTAAAGCCCAGAGAGCCCAG 59.820 60.0 0.00 0.0 0.00 4.45 F
2112 4288 1.101635 TCAGCGCGGTATGCTACTCT 61.102 55.0 11.92 0.0 41.72 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 4180 2.199652 CCTGCGGGCAGTTCCAAAA 61.200 57.895 18.48 0.0 42.15 2.44 R
2052 4228 2.642171 TCTTCTCCTTCCTGGCCTTA 57.358 50.000 3.32 0.0 35.26 2.69 R
2398 4757 0.658897 AAACGTACAACCACAAGGCG 59.341 50.000 0.00 0.0 39.06 5.52 R
3958 9746 0.320697 GAAGGGCCTCGTGTACAACT 59.679 55.000 6.46 0.0 0.00 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.562635 GTGCTCCGTGTGGCTTAC 58.437 61.111 0.00 0.00 34.14 2.34
18 19 2.048597 TGCTCCGTGTGGCTTACG 60.049 61.111 7.04 7.04 40.98 3.18
23 24 2.125673 CGTGTGGCTTACGGGAGG 60.126 66.667 6.27 0.00 37.86 4.30
24 25 2.642254 CGTGTGGCTTACGGGAGGA 61.642 63.158 6.27 0.00 37.86 3.71
25 26 1.218316 GTGTGGCTTACGGGAGGAG 59.782 63.158 0.00 0.00 0.00 3.69
26 27 1.987855 TGTGGCTTACGGGAGGAGG 60.988 63.158 0.00 0.00 0.00 4.30
27 28 1.684734 GTGGCTTACGGGAGGAGGA 60.685 63.158 0.00 0.00 0.00 3.71
28 29 1.079621 TGGCTTACGGGAGGAGGAA 59.920 57.895 0.00 0.00 0.00 3.36
29 30 0.976073 TGGCTTACGGGAGGAGGAAG 60.976 60.000 0.00 0.00 0.00 3.46
30 31 0.686769 GGCTTACGGGAGGAGGAAGA 60.687 60.000 0.00 0.00 0.00 2.87
31 32 1.192428 GCTTACGGGAGGAGGAAGAA 58.808 55.000 0.00 0.00 0.00 2.52
32 33 1.137282 GCTTACGGGAGGAGGAAGAAG 59.863 57.143 0.00 0.00 0.00 2.85
33 34 2.736347 CTTACGGGAGGAGGAAGAAGA 58.264 52.381 0.00 0.00 0.00 2.87
34 35 3.301274 CTTACGGGAGGAGGAAGAAGAT 58.699 50.000 0.00 0.00 0.00 2.40
35 36 1.490574 ACGGGAGGAGGAAGAAGATG 58.509 55.000 0.00 0.00 0.00 2.90
36 37 1.273324 ACGGGAGGAGGAAGAAGATGT 60.273 52.381 0.00 0.00 0.00 3.06
37 38 1.137872 CGGGAGGAGGAAGAAGATGTG 59.862 57.143 0.00 0.00 0.00 3.21
38 39 1.488393 GGGAGGAGGAAGAAGATGTGG 59.512 57.143 0.00 0.00 0.00 4.17
39 40 1.488393 GGAGGAGGAAGAAGATGTGGG 59.512 57.143 0.00 0.00 0.00 4.61
40 41 1.488393 GAGGAGGAAGAAGATGTGGGG 59.512 57.143 0.00 0.00 0.00 4.96
41 42 1.203492 AGGAGGAAGAAGATGTGGGGT 60.203 52.381 0.00 0.00 0.00 4.95
42 43 1.210722 GGAGGAAGAAGATGTGGGGTC 59.789 57.143 0.00 0.00 0.00 4.46
43 44 0.905357 AGGAAGAAGATGTGGGGTCG 59.095 55.000 0.00 0.00 0.00 4.79
44 45 0.107654 GGAAGAAGATGTGGGGTCGG 60.108 60.000 0.00 0.00 0.00 4.79
45 46 0.107654 GAAGAAGATGTGGGGTCGGG 60.108 60.000 0.00 0.00 0.00 5.14
46 47 2.124695 GAAGATGTGGGGTCGGGC 60.125 66.667 0.00 0.00 0.00 6.13
47 48 4.096003 AAGATGTGGGGTCGGGCG 62.096 66.667 0.00 0.00 0.00 6.13
49 50 4.832608 GATGTGGGGTCGGGCGTC 62.833 72.222 0.00 0.00 0.00 5.19
55 56 4.436998 GGGTCGGGCGTCAGTGAG 62.437 72.222 0.00 0.00 0.00 3.51
64 65 4.803426 GTCAGTGAGCGCGGGGAG 62.803 72.222 8.83 0.00 0.00 4.30
77 78 3.591835 GGGAGGCGAGCGAGAGAG 61.592 72.222 0.00 0.00 0.00 3.20
78 79 3.591835 GGAGGCGAGCGAGAGAGG 61.592 72.222 0.00 0.00 0.00 3.69
79 80 3.591835 GAGGCGAGCGAGAGAGGG 61.592 72.222 0.00 0.00 0.00 4.30
82 83 2.909965 GCGAGCGAGAGAGGGGAT 60.910 66.667 0.00 0.00 0.00 3.85
83 84 3.038280 CGAGCGAGAGAGGGGATG 58.962 66.667 0.00 0.00 0.00 3.51
84 85 2.560119 CGAGCGAGAGAGGGGATGG 61.560 68.421 0.00 0.00 0.00 3.51
85 86 2.123077 AGCGAGAGAGGGGATGGG 60.123 66.667 0.00 0.00 0.00 4.00
86 87 2.444895 GCGAGAGAGGGGATGGGT 60.445 66.667 0.00 0.00 0.00 4.51
87 88 2.801631 GCGAGAGAGGGGATGGGTG 61.802 68.421 0.00 0.00 0.00 4.61
88 89 2.801631 CGAGAGAGGGGATGGGTGC 61.802 68.421 0.00 0.00 0.00 5.01
89 90 2.765807 AGAGAGGGGATGGGTGCG 60.766 66.667 0.00 0.00 0.00 5.34
90 91 3.866582 GAGAGGGGATGGGTGCGG 61.867 72.222 0.00 0.00 0.00 5.69
108 109 3.200593 GCGACCGAGGCGAGAGTA 61.201 66.667 3.17 0.00 0.00 2.59
109 110 2.708255 CGACCGAGGCGAGAGTAC 59.292 66.667 0.00 0.00 0.00 2.73
110 111 2.821688 CGACCGAGGCGAGAGTACC 61.822 68.421 0.00 0.00 0.00 3.34
111 112 1.451747 GACCGAGGCGAGAGTACCT 60.452 63.158 0.00 0.00 39.65 3.08
115 116 3.906718 AGGCGAGAGTACCTCACG 58.093 61.111 6.70 6.70 44.73 4.35
116 117 1.749638 AGGCGAGAGTACCTCACGG 60.750 63.158 11.86 0.00 42.85 4.94
117 118 2.102553 GCGAGAGTACCTCACGGC 59.897 66.667 11.86 2.70 42.85 5.68
118 119 2.403987 CGAGAGTACCTCACGGCG 59.596 66.667 4.80 4.80 39.97 6.46
119 120 2.799371 GAGAGTACCTCACGGCGG 59.201 66.667 13.24 0.00 41.58 6.13
120 121 2.754658 AGAGTACCTCACGGCGGG 60.755 66.667 13.24 7.61 32.06 6.13
121 122 3.834799 GAGTACCTCACGGCGGGG 61.835 72.222 10.28 11.84 0.00 5.73
160 161 4.235762 GGCTGGGCCGAGCGATTA 62.236 66.667 30.36 0.00 39.62 1.75
161 162 2.663188 GCTGGGCCGAGCGATTAG 60.663 66.667 24.75 0.00 0.00 1.73
172 173 2.969238 CGATTAGCGCTGGCCTGG 60.969 66.667 22.90 0.00 41.24 4.45
173 174 3.282920 GATTAGCGCTGGCCTGGC 61.283 66.667 22.90 11.05 41.24 4.85
185 186 2.844362 CCTGGCCGGCTGGATCTA 60.844 66.667 28.56 3.34 37.49 1.98
186 187 2.219875 CCTGGCCGGCTGGATCTAT 61.220 63.158 28.56 0.00 37.49 1.98
187 188 1.294780 CTGGCCGGCTGGATCTATC 59.705 63.158 28.56 6.48 37.49 2.08
188 189 1.152247 TGGCCGGCTGGATCTATCT 60.152 57.895 28.56 0.00 37.49 1.98
189 190 0.764369 TGGCCGGCTGGATCTATCTT 60.764 55.000 28.56 0.00 37.49 2.40
190 191 0.398318 GGCCGGCTGGATCTATCTTT 59.602 55.000 28.56 0.00 37.49 2.52
191 192 1.202818 GGCCGGCTGGATCTATCTTTT 60.203 52.381 28.56 0.00 37.49 2.27
192 193 2.576615 GCCGGCTGGATCTATCTTTTT 58.423 47.619 22.15 0.00 37.49 1.94
318 319 6.240549 ACTCAAGTAACTCATATTCCTGGG 57.759 41.667 0.00 0.00 0.00 4.45
319 320 5.726793 ACTCAAGTAACTCATATTCCTGGGT 59.273 40.000 0.00 0.00 0.00 4.51
325 326 2.846206 ACTCATATTCCTGGGTTGAGCA 59.154 45.455 12.71 0.00 37.84 4.26
335 336 0.949105 GGGTTGAGCAACATCGTCGT 60.949 55.000 14.55 0.00 42.85 4.34
351 352 0.894184 TCGTTGGAGAAGACGAGGCT 60.894 55.000 0.00 0.00 42.67 4.58
359 360 1.006102 AAGACGAGGCTGACAACGG 60.006 57.895 0.00 0.00 0.00 4.44
365 366 2.028484 GGCTGACAACGGACACGA 59.972 61.111 0.00 0.00 44.60 4.35
366 367 2.308039 GGCTGACAACGGACACGAC 61.308 63.158 0.00 0.00 44.60 4.34
438 440 6.397272 ACAAGATTCTTGTTGCAAAAAGTCA 58.603 32.000 25.20 15.50 29.38 3.41
447 449 3.242549 TGCAAAAAGTCATGTGTGCAA 57.757 38.095 0.00 0.00 38.93 4.08
477 479 1.431243 AGGGTTGCAATAAGGTCCCAA 59.569 47.619 19.55 0.00 37.56 4.12
480 482 3.263170 GGGTTGCAATAAGGTCCCAATTT 59.737 43.478 14.13 0.00 35.43 1.82
606 616 3.217626 CTTAGCAGCCCCCTTGAAATAG 58.782 50.000 0.00 0.00 0.00 1.73
607 617 0.396278 AGCAGCCCCCTTGAAATAGC 60.396 55.000 0.00 0.00 0.00 2.97
608 618 0.684153 GCAGCCCCCTTGAAATAGCA 60.684 55.000 0.00 0.00 0.00 3.49
609 619 2.031097 GCAGCCCCCTTGAAATAGCAT 61.031 52.381 0.00 0.00 0.00 3.79
610 620 2.391678 CAGCCCCCTTGAAATAGCATT 58.608 47.619 0.00 0.00 0.00 3.56
611 621 3.565307 CAGCCCCCTTGAAATAGCATTA 58.435 45.455 0.00 0.00 0.00 1.90
612 622 3.319122 CAGCCCCCTTGAAATAGCATTAC 59.681 47.826 0.00 0.00 0.00 1.89
613 623 3.205282 AGCCCCCTTGAAATAGCATTACT 59.795 43.478 0.00 0.00 0.00 2.24
614 624 3.960755 GCCCCCTTGAAATAGCATTACTT 59.039 43.478 0.00 0.00 0.00 2.24
615 625 4.405680 GCCCCCTTGAAATAGCATTACTTT 59.594 41.667 0.00 0.00 0.00 2.66
616 626 5.104941 GCCCCCTTGAAATAGCATTACTTTT 60.105 40.000 0.00 0.00 0.00 2.27
617 627 6.576244 GCCCCCTTGAAATAGCATTACTTTTT 60.576 38.462 0.00 0.00 32.92 1.94
705 715 5.704053 TCTTTTCCACCGAGAAAAACTATCC 59.296 40.000 8.60 0.00 43.27 2.59
749 759 1.714541 TTTTGCTCAGGGCCATGAAA 58.285 45.000 22.26 11.10 40.92 2.69
754 764 1.396653 CTCAGGGCCATGAAACATCC 58.603 55.000 22.26 0.00 0.00 3.51
756 766 2.413406 AGGGCCATGAAACATCCCT 58.587 52.632 6.18 5.53 42.25 4.20
758 768 1.079323 AGGGCCATGAAACATCCCTTT 59.921 47.619 6.18 0.00 44.54 3.11
759 769 1.908619 GGGCCATGAAACATCCCTTTT 59.091 47.619 4.39 0.00 34.19 2.27
760 770 3.103742 GGGCCATGAAACATCCCTTTTA 58.896 45.455 4.39 0.00 34.19 1.52
762 772 3.769300 GGCCATGAAACATCCCTTTTACT 59.231 43.478 0.00 0.00 0.00 2.24
763 773 4.142160 GGCCATGAAACATCCCTTTTACTC 60.142 45.833 0.00 0.00 0.00 2.59
764 774 4.142160 GCCATGAAACATCCCTTTTACTCC 60.142 45.833 0.00 0.00 0.00 3.85
765 775 5.016173 CCATGAAACATCCCTTTTACTCCA 58.984 41.667 0.00 0.00 0.00 3.86
767 777 6.155049 CCATGAAACATCCCTTTTACTCCAAT 59.845 38.462 0.00 0.00 0.00 3.16
768 778 6.588719 TGAAACATCCCTTTTACTCCAATG 57.411 37.500 0.00 0.00 0.00 2.82
769 779 6.074648 TGAAACATCCCTTTTACTCCAATGT 58.925 36.000 0.00 0.00 0.00 2.71
771 781 5.520748 ACATCCCTTTTACTCCAATGTCT 57.479 39.130 0.00 0.00 0.00 3.41
772 782 5.501156 ACATCCCTTTTACTCCAATGTCTC 58.499 41.667 0.00 0.00 0.00 3.36
775 785 5.947663 TCCCTTTTACTCCAATGTCTCAAA 58.052 37.500 0.00 0.00 0.00 2.69
776 786 6.369629 TCCCTTTTACTCCAATGTCTCAAAA 58.630 36.000 0.00 0.00 0.00 2.44
777 787 6.264518 TCCCTTTTACTCCAATGTCTCAAAAC 59.735 38.462 0.00 0.00 0.00 2.43
779 789 7.417342 CCCTTTTACTCCAATGTCTCAAAACAA 60.417 37.037 0.00 0.00 31.81 2.83
800 830 9.803315 AAACAAAAAGATCTTTTACTCCACTTC 57.197 29.630 28.95 0.00 41.45 3.01
820 850 2.361104 GAACCATCTTGCGGCCCA 60.361 61.111 0.00 0.00 0.00 5.36
821 851 2.361610 AACCATCTTGCGGCCCAG 60.362 61.111 0.00 0.00 0.00 4.45
823 853 4.809496 CCATCTTGCGGCCCAGCT 62.809 66.667 0.00 0.00 38.13 4.24
824 854 3.207669 CATCTTGCGGCCCAGCTC 61.208 66.667 0.00 0.00 38.13 4.09
825 855 4.845580 ATCTTGCGGCCCAGCTCG 62.846 66.667 0.00 0.00 38.13 5.03
833 863 4.925861 GCCCAGCTCGGCTCCATC 62.926 72.222 15.96 0.00 46.10 3.51
834 864 4.247380 CCCAGCTCGGCTCCATCC 62.247 72.222 0.00 0.00 36.40 3.51
835 865 3.473647 CCAGCTCGGCTCCATCCA 61.474 66.667 0.00 0.00 36.40 3.41
861 894 1.626321 TCGCCCATTCAGTGACCTAAA 59.374 47.619 0.00 0.00 0.00 1.85
876 909 0.179936 CTAAAGCCCAGAGAGCCCAG 59.820 60.000 0.00 0.00 0.00 4.45
973 3149 4.426313 GCCCAAGCCGCTACCCTT 62.426 66.667 0.00 0.00 0.00 3.95
974 3150 2.355115 CCCAAGCCGCTACCCTTT 59.645 61.111 0.00 0.00 0.00 3.11
977 3153 1.299976 CAAGCCGCTACCCTTTCCT 59.700 57.895 0.00 0.00 0.00 3.36
979 3155 1.911702 AAGCCGCTACCCTTTCCTCC 61.912 60.000 0.00 0.00 0.00 4.30
980 3156 2.368011 GCCGCTACCCTTTCCTCCT 61.368 63.158 0.00 0.00 0.00 3.69
1038 3214 2.995872 GCTCGTCTCCGTCAAGGCT 61.996 63.158 0.00 0.00 40.77 4.58
1056 3232 3.716195 CTGGACGGGGACATGGCA 61.716 66.667 0.00 0.00 0.00 4.92
1720 3896 3.208884 AACGTCGAGCGCCTCAACT 62.209 57.895 2.29 0.00 46.11 3.16
1974 4150 3.558109 CCAGGAAGAACCCTCTGAAGAAC 60.558 52.174 0.00 0.00 40.05 3.01
1986 4162 3.016474 GAAGAACGCTGCTGCCGTC 62.016 63.158 10.24 7.45 35.36 4.79
1995 4171 3.123620 GCTGCCGTCCTCAAGCTG 61.124 66.667 0.00 0.00 0.00 4.24
2004 4180 1.840635 GTCCTCAAGCTGAACCCCTAT 59.159 52.381 0.00 0.00 0.00 2.57
2112 4288 1.101635 TCAGCGCGGTATGCTACTCT 61.102 55.000 11.92 0.00 41.72 3.24
2140 4318 6.064060 CCCTTTGCCATCTGTTTCATATCTA 58.936 40.000 0.00 0.00 0.00 1.98
2208 4388 4.329256 GGATGTTCGTACTAAGGTTTGAGC 59.671 45.833 0.00 0.00 0.00 4.26
2217 4397 5.757850 ACTAAGGTTTGAGCAAGTCTTTG 57.242 39.130 0.00 0.00 37.36 2.77
2299 4598 4.773674 ACAATTCTGGAATGCCTGATTCAA 59.226 37.500 0.00 0.00 42.22 2.69
2307 4606 6.851318 TGGAATGCCTGATTCAATAATAGGA 58.149 36.000 0.00 0.00 42.22 2.94
2398 4757 6.976925 ACTTTATGATGCTTGCTATTCAAAGC 59.023 34.615 0.52 0.52 43.08 3.51
2419 4780 1.862411 GCCTTGTGGTTGTACGTTTGC 60.862 52.381 0.00 0.00 35.27 3.68
2477 5031 8.770828 TGTTTTCTTTACATAGACTTGTAGTGC 58.229 33.333 0.00 0.00 33.81 4.40
2564 5162 9.722056 CCTGTCTTGATTTGTTAGTATATTTGC 57.278 33.333 0.00 0.00 0.00 3.68
2661 5259 3.042871 TGTGCAATTTCTTTGATGGCC 57.957 42.857 0.00 0.00 37.53 5.36
2676 5275 2.530460 TGGCCTGCCATACTGAATTT 57.470 45.000 6.80 0.00 41.89 1.82
2678 5277 3.172339 TGGCCTGCCATACTGAATTTTT 58.828 40.909 6.80 0.00 41.89 1.94
2789 5397 4.583871 ACTTTAGCACTGAATCTTCCTGG 58.416 43.478 0.00 0.00 0.00 4.45
2841 5449 5.564550 ACTGAAAATCTGAGGCAGTATTGT 58.435 37.500 0.00 0.00 37.98 2.71
2901 5538 9.739276 AAGAGTAGGAAATTGTATGTGATCAAA 57.261 29.630 0.00 0.00 0.00 2.69
2914 5551 5.375417 TGTGATCAAAGTTATTGCTGGTG 57.625 39.130 0.00 0.00 0.00 4.17
2921 5653 9.638239 GATCAAAGTTATTGCTGGTGAATTAAA 57.362 29.630 0.00 0.00 0.00 1.52
2959 5691 1.072266 TGGGTGCTTGGGATACTGTT 58.928 50.000 0.00 0.00 0.00 3.16
3001 5733 7.854557 TCAAAAGTTGTCTGATATCTGATGG 57.145 36.000 14.54 0.00 0.00 3.51
3024 5756 6.324512 TGGTTAAATTCCATATGCTGCATCTT 59.675 34.615 19.90 5.25 0.00 2.40
3304 6101 5.534654 TGCTGTTTTGGTAGCTGTTTATCTT 59.465 36.000 0.00 0.00 40.52 2.40
3306 6103 6.515035 GCTGTTTTGGTAGCTGTTTATCTTGT 60.515 38.462 0.00 0.00 36.99 3.16
3312 6109 5.468746 TGGTAGCTGTTTATCTTGTGTGTTC 59.531 40.000 0.00 0.00 0.00 3.18
3465 6266 0.962489 TTTTGTGGTTGGCATACCCG 59.038 50.000 13.78 0.00 37.39 5.28
3521 6322 6.913873 TCTTTGCAACGTTTTTAGTCTACT 57.086 33.333 0.00 0.00 0.00 2.57
3566 6367 9.409312 CACTGCTTTATCATTGTTGATTTTGTA 57.591 29.630 0.00 0.00 42.61 2.41
3567 6368 9.979578 ACTGCTTTATCATTGTTGATTTTGTAA 57.020 25.926 0.00 0.00 42.61 2.41
3606 6407 1.328279 CAGGTTGTGTTTTCTCCCCC 58.672 55.000 0.00 0.00 0.00 5.40
3625 6429 3.901222 CCCCCTTAAAAACCTGATGTTGT 59.099 43.478 0.00 0.00 37.23 3.32
3638 6442 6.574350 ACCTGATGTTGTTACTAGTAGATGC 58.426 40.000 3.59 0.00 0.00 3.91
3701 6537 2.319136 TGCTGTTTCTGTGGTAACGT 57.681 45.000 0.00 0.00 42.51 3.99
3742 6587 5.365021 AGGCACTGCATAGATCTAAGTTT 57.635 39.130 6.52 0.00 37.18 2.66
3743 6588 6.485830 AGGCACTGCATAGATCTAAGTTTA 57.514 37.500 6.52 0.00 37.18 2.01
3744 6589 6.520272 AGGCACTGCATAGATCTAAGTTTAG 58.480 40.000 6.52 5.68 37.18 1.85
3745 6590 6.098982 AGGCACTGCATAGATCTAAGTTTAGT 59.901 38.462 6.52 6.26 37.18 2.24
3746 6591 6.763610 GGCACTGCATAGATCTAAGTTTAGTT 59.236 38.462 6.52 0.00 32.61 2.24
3747 6592 7.042389 GGCACTGCATAGATCTAAGTTTAGTTC 60.042 40.741 6.52 4.01 32.30 3.01
3774 6619 9.738832 TGTAGTTGCTTTTAGGTTGAAAATAAC 57.261 29.630 0.00 0.00 31.79 1.89
3813 9184 8.948631 TTAGCTCACTACTTTAATGATCCAAG 57.051 34.615 0.00 0.00 0.00 3.61
3844 9514 4.894784 ACATGTCTACAACAACACCCTAG 58.105 43.478 0.00 0.00 42.37 3.02
3861 9584 7.187676 ACACCCTAGTAGTAGAAATTACCAGT 58.812 38.462 6.14 0.00 0.00 4.00
3867 9590 9.790389 CTAGTAGTAGAAATTACCAGTGAACTG 57.210 37.037 3.35 3.35 43.40 3.16
3878 9601 3.328931 ACCAGTGAACTGATGAACCATCT 59.671 43.478 12.05 0.00 46.59 2.90
3879 9602 4.202503 ACCAGTGAACTGATGAACCATCTT 60.203 41.667 12.05 0.00 46.59 2.40
3880 9603 4.155462 CCAGTGAACTGATGAACCATCTTG 59.845 45.833 12.05 4.43 46.59 3.02
3881 9604 3.755378 AGTGAACTGATGAACCATCTTGC 59.245 43.478 8.22 0.00 41.06 4.01
3882 9605 3.503363 GTGAACTGATGAACCATCTTGCA 59.497 43.478 8.22 0.00 41.06 4.08
3884 9607 4.397103 TGAACTGATGAACCATCTTGCATC 59.603 41.667 8.22 0.00 41.06 3.91
3885 9608 4.232188 ACTGATGAACCATCTTGCATCT 57.768 40.909 8.22 0.00 41.06 2.90
3894 9671 2.224475 CCATCTTGCATCTAGGTCCAGG 60.224 54.545 0.00 0.00 0.00 4.45
3956 9744 8.037758 ACAACTGAACTACATCTTTCTGGATAG 58.962 37.037 0.00 0.00 0.00 2.08
3958 9746 8.824756 ACTGAACTACATCTTTCTGGATAGTA 57.175 34.615 0.00 0.00 0.00 1.82
3991 9779 4.110072 AGGCCCTTCATGCAGATCTATAT 58.890 43.478 0.00 0.00 0.00 0.86
3994 9782 5.104776 GGCCCTTCATGCAGATCTATATACA 60.105 44.000 0.00 0.00 0.00 2.29
3995 9783 5.814705 GCCCTTCATGCAGATCTATATACAC 59.185 44.000 0.00 0.00 0.00 2.90
4012 9807 2.830104 ACACTCACTTTACGTTGGGAC 58.170 47.619 0.00 0.00 0.00 4.46
4141 9941 2.295349 ACCACACTATACGATTAGGCCG 59.705 50.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.048597 CGTAAGCCACACGGAGCA 60.049 61.111 0.00 0.00 35.78 4.26
6 7 2.125673 CCTCCCGTAAGCCACACG 60.126 66.667 0.00 0.00 39.10 4.49
7 8 1.218316 CTCCTCCCGTAAGCCACAC 59.782 63.158 0.00 0.00 0.00 3.82
8 9 1.987855 CCTCCTCCCGTAAGCCACA 60.988 63.158 0.00 0.00 0.00 4.17
9 10 1.262640 TTCCTCCTCCCGTAAGCCAC 61.263 60.000 0.00 0.00 0.00 5.01
10 11 0.976073 CTTCCTCCTCCCGTAAGCCA 60.976 60.000 0.00 0.00 0.00 4.75
11 12 0.686769 TCTTCCTCCTCCCGTAAGCC 60.687 60.000 0.00 0.00 0.00 4.35
12 13 1.137282 CTTCTTCCTCCTCCCGTAAGC 59.863 57.143 0.00 0.00 0.00 3.09
13 14 2.736347 TCTTCTTCCTCCTCCCGTAAG 58.264 52.381 0.00 0.00 0.00 2.34
14 15 2.913603 TCTTCTTCCTCCTCCCGTAA 57.086 50.000 0.00 0.00 0.00 3.18
15 16 2.024273 ACATCTTCTTCCTCCTCCCGTA 60.024 50.000 0.00 0.00 0.00 4.02
16 17 1.273324 ACATCTTCTTCCTCCTCCCGT 60.273 52.381 0.00 0.00 0.00 5.28
17 18 1.137872 CACATCTTCTTCCTCCTCCCG 59.862 57.143 0.00 0.00 0.00 5.14
18 19 1.488393 CCACATCTTCTTCCTCCTCCC 59.512 57.143 0.00 0.00 0.00 4.30
19 20 1.488393 CCCACATCTTCTTCCTCCTCC 59.512 57.143 0.00 0.00 0.00 4.30
20 21 1.488393 CCCCACATCTTCTTCCTCCTC 59.512 57.143 0.00 0.00 0.00 3.71
21 22 1.203492 ACCCCACATCTTCTTCCTCCT 60.203 52.381 0.00 0.00 0.00 3.69
22 23 1.210722 GACCCCACATCTTCTTCCTCC 59.789 57.143 0.00 0.00 0.00 4.30
23 24 1.134670 CGACCCCACATCTTCTTCCTC 60.135 57.143 0.00 0.00 0.00 3.71
24 25 0.905357 CGACCCCACATCTTCTTCCT 59.095 55.000 0.00 0.00 0.00 3.36
25 26 0.107654 CCGACCCCACATCTTCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
26 27 0.107654 CCCGACCCCACATCTTCTTC 60.108 60.000 0.00 0.00 0.00 2.87
27 28 1.991230 CCCGACCCCACATCTTCTT 59.009 57.895 0.00 0.00 0.00 2.52
28 29 2.670148 GCCCGACCCCACATCTTCT 61.670 63.158 0.00 0.00 0.00 2.85
29 30 2.124695 GCCCGACCCCACATCTTC 60.125 66.667 0.00 0.00 0.00 2.87
30 31 4.096003 CGCCCGACCCCACATCTT 62.096 66.667 0.00 0.00 0.00 2.40
32 33 4.832608 GACGCCCGACCCCACATC 62.833 72.222 0.00 0.00 0.00 3.06
38 39 4.436998 CTCACTGACGCCCGACCC 62.437 72.222 0.00 0.00 0.00 4.46
47 48 4.803426 CTCCCCGCGCTCACTGAC 62.803 72.222 5.56 0.00 0.00 3.51
60 61 3.591835 CTCTCTCGCTCGCCTCCC 61.592 72.222 0.00 0.00 0.00 4.30
61 62 3.591835 CCTCTCTCGCTCGCCTCC 61.592 72.222 0.00 0.00 0.00 4.30
62 63 3.591835 CCCTCTCTCGCTCGCCTC 61.592 72.222 0.00 0.00 0.00 4.70
65 66 2.909965 ATCCCCTCTCTCGCTCGC 60.910 66.667 0.00 0.00 0.00 5.03
66 67 2.560119 CCATCCCCTCTCTCGCTCG 61.560 68.421 0.00 0.00 0.00 5.03
67 68 2.206536 CCCATCCCCTCTCTCGCTC 61.207 68.421 0.00 0.00 0.00 5.03
68 69 2.123077 CCCATCCCCTCTCTCGCT 60.123 66.667 0.00 0.00 0.00 4.93
69 70 2.444895 ACCCATCCCCTCTCTCGC 60.445 66.667 0.00 0.00 0.00 5.03
70 71 2.801631 GCACCCATCCCCTCTCTCG 61.802 68.421 0.00 0.00 0.00 4.04
71 72 2.801631 CGCACCCATCCCCTCTCTC 61.802 68.421 0.00 0.00 0.00 3.20
72 73 2.765807 CGCACCCATCCCCTCTCT 60.766 66.667 0.00 0.00 0.00 3.10
73 74 3.866582 CCGCACCCATCCCCTCTC 61.867 72.222 0.00 0.00 0.00 3.20
91 92 3.200593 TACTCTCGCCTCGGTCGC 61.201 66.667 0.00 0.00 0.00 5.19
92 93 2.708255 GTACTCTCGCCTCGGTCG 59.292 66.667 0.00 0.00 0.00 4.79
93 94 1.451747 AGGTACTCTCGCCTCGGTC 60.452 63.158 0.00 0.00 0.00 4.79
94 95 2.675989 AGGTACTCTCGCCTCGGT 59.324 61.111 0.00 0.00 0.00 4.69
126 127 4.760047 CAGACCTTCGGCCCACGG 62.760 72.222 0.00 0.00 44.45 4.94
127 128 4.760047 CCAGACCTTCGGCCCACG 62.760 72.222 0.00 0.00 46.11 4.94
133 134 4.785453 GCCCAGCCAGACCTTCGG 62.785 72.222 0.00 0.00 0.00 4.30
143 144 4.235762 TAATCGCTCGGCCCAGCC 62.236 66.667 17.36 0.00 46.75 4.85
144 145 2.663188 CTAATCGCTCGGCCCAGC 60.663 66.667 13.04 13.04 35.90 4.85
145 146 2.663188 GCTAATCGCTCGGCCCAG 60.663 66.667 0.00 0.00 35.14 4.45
146 147 4.585526 CGCTAATCGCTCGGCCCA 62.586 66.667 0.00 0.00 36.13 5.36
155 156 2.969238 CCAGGCCAGCGCTAATCG 60.969 66.667 10.99 0.00 42.12 3.34
156 157 3.282920 GCCAGGCCAGCGCTAATC 61.283 66.667 10.99 1.71 34.44 1.75
168 169 2.177594 GATAGATCCAGCCGGCCAGG 62.178 65.000 26.15 25.80 44.97 4.45
169 170 1.190833 AGATAGATCCAGCCGGCCAG 61.191 60.000 26.15 16.88 0.00 4.85
170 171 0.764369 AAGATAGATCCAGCCGGCCA 60.764 55.000 26.15 8.02 0.00 5.36
171 172 0.398318 AAAGATAGATCCAGCCGGCC 59.602 55.000 26.15 7.28 0.00 6.13
172 173 2.262423 AAAAGATAGATCCAGCCGGC 57.738 50.000 21.89 21.89 0.00 6.13
292 293 9.090103 CCCAGGAATATGAGTTACTTGAGTATA 57.910 37.037 0.00 0.00 0.00 1.47
293 294 7.569111 ACCCAGGAATATGAGTTACTTGAGTAT 59.431 37.037 0.00 0.00 0.00 2.12
294 295 6.901300 ACCCAGGAATATGAGTTACTTGAGTA 59.099 38.462 0.00 0.00 0.00 2.59
295 296 5.726793 ACCCAGGAATATGAGTTACTTGAGT 59.273 40.000 0.00 0.00 0.00 3.41
296 297 6.240549 ACCCAGGAATATGAGTTACTTGAG 57.759 41.667 0.00 0.00 0.00 3.02
297 298 6.214615 TCAACCCAGGAATATGAGTTACTTGA 59.785 38.462 0.00 0.00 0.00 3.02
298 299 6.414732 TCAACCCAGGAATATGAGTTACTTG 58.585 40.000 0.00 0.00 0.00 3.16
299 300 6.636454 TCAACCCAGGAATATGAGTTACTT 57.364 37.500 0.00 0.00 0.00 2.24
300 301 5.396884 GCTCAACCCAGGAATATGAGTTACT 60.397 44.000 10.56 0.00 39.68 2.24
301 302 4.816925 GCTCAACCCAGGAATATGAGTTAC 59.183 45.833 10.56 0.00 39.68 2.50
302 303 4.473196 TGCTCAACCCAGGAATATGAGTTA 59.527 41.667 10.56 1.79 39.68 2.24
303 304 3.266772 TGCTCAACCCAGGAATATGAGTT 59.733 43.478 10.56 0.00 39.68 3.01
304 305 2.846206 TGCTCAACCCAGGAATATGAGT 59.154 45.455 10.56 0.00 39.68 3.41
305 306 3.565764 TGCTCAACCCAGGAATATGAG 57.434 47.619 0.00 0.00 40.30 2.90
306 307 3.010027 TGTTGCTCAACCCAGGAATATGA 59.990 43.478 9.92 0.00 40.46 2.15
307 308 3.355378 TGTTGCTCAACCCAGGAATATG 58.645 45.455 9.92 0.00 40.46 1.78
308 309 3.737559 TGTTGCTCAACCCAGGAATAT 57.262 42.857 9.92 0.00 40.46 1.28
309 310 3.620488 GATGTTGCTCAACCCAGGAATA 58.380 45.455 9.92 0.00 40.46 1.75
310 311 2.450476 GATGTTGCTCAACCCAGGAAT 58.550 47.619 9.92 0.00 40.46 3.01
311 312 1.881925 CGATGTTGCTCAACCCAGGAA 60.882 52.381 9.92 0.00 40.46 3.36
312 313 0.321564 CGATGTTGCTCAACCCAGGA 60.322 55.000 9.92 0.00 40.46 3.86
313 314 0.606401 ACGATGTTGCTCAACCCAGG 60.606 55.000 9.92 0.84 40.46 4.45
314 315 0.798776 GACGATGTTGCTCAACCCAG 59.201 55.000 9.92 4.21 40.46 4.45
315 316 0.948623 CGACGATGTTGCTCAACCCA 60.949 55.000 9.92 0.00 40.46 4.51
316 317 0.949105 ACGACGATGTTGCTCAACCC 60.949 55.000 0.00 2.18 40.46 4.11
317 318 0.865769 AACGACGATGTTGCTCAACC 59.134 50.000 0.00 0.00 40.46 3.77
318 319 1.398451 CCAACGACGATGTTGCTCAAC 60.398 52.381 15.72 5.84 46.14 3.18
319 320 0.865111 CCAACGACGATGTTGCTCAA 59.135 50.000 15.72 0.00 46.14 3.02
325 326 2.673833 GTCTTCTCCAACGACGATGTT 58.326 47.619 0.00 0.00 0.00 2.71
335 336 0.603569 GTCAGCCTCGTCTTCTCCAA 59.396 55.000 0.00 0.00 0.00 3.53
349 350 2.645510 CGTCGTGTCCGTTGTCAGC 61.646 63.158 0.00 0.00 35.01 4.26
351 352 1.009335 CTCGTCGTGTCCGTTGTCA 60.009 57.895 0.00 0.00 35.01 3.58
359 360 0.524392 CATCTCTGGCTCGTCGTGTC 60.524 60.000 0.00 0.00 0.00 3.67
459 461 4.020662 TGAAATTGGGACCTTATTGCAACC 60.021 41.667 0.00 0.00 0.00 3.77
460 462 5.146010 TGAAATTGGGACCTTATTGCAAC 57.854 39.130 0.00 0.00 0.00 4.17
472 474 3.450457 ACTTGTTGCAACTGAAATTGGGA 59.550 39.130 28.61 2.96 0.00 4.37
477 479 4.989279 AGACACTTGTTGCAACTGAAAT 57.011 36.364 28.61 12.75 0.00 2.17
480 482 3.081061 ACAAGACACTTGTTGCAACTGA 58.919 40.909 28.61 16.75 0.00 3.41
571 576 2.043652 TAAGCGTCGGCCTACCCT 60.044 61.111 0.00 0.00 41.24 4.34
619 629 6.702282 GGTTTATTCACGTCCAAATCCAAAAA 59.298 34.615 0.00 0.00 0.00 1.94
620 630 6.183360 TGGTTTATTCACGTCCAAATCCAAAA 60.183 34.615 0.00 0.00 0.00 2.44
621 631 5.302059 TGGTTTATTCACGTCCAAATCCAAA 59.698 36.000 0.00 0.00 0.00 3.28
622 632 4.827835 TGGTTTATTCACGTCCAAATCCAA 59.172 37.500 0.00 0.00 0.00 3.53
623 633 4.399219 TGGTTTATTCACGTCCAAATCCA 58.601 39.130 0.00 0.00 0.00 3.41
624 634 5.124776 TGATGGTTTATTCACGTCCAAATCC 59.875 40.000 0.00 0.00 0.00 3.01
625 635 6.027749 GTGATGGTTTATTCACGTCCAAATC 58.972 40.000 0.00 0.00 0.00 2.17
626 636 5.710099 AGTGATGGTTTATTCACGTCCAAAT 59.290 36.000 0.00 0.00 38.07 2.32
627 637 5.067273 AGTGATGGTTTATTCACGTCCAAA 58.933 37.500 0.00 0.00 38.07 3.28
628 638 4.647611 AGTGATGGTTTATTCACGTCCAA 58.352 39.130 0.00 0.00 38.07 3.53
629 639 4.280436 AGTGATGGTTTATTCACGTCCA 57.720 40.909 0.00 0.00 38.07 4.02
630 640 5.622770 AAAGTGATGGTTTATTCACGTCC 57.377 39.130 0.00 0.00 38.07 4.79
666 676 8.840321 CGGTGGAAAAGAAGTGATGATTTATAT 58.160 33.333 0.00 0.00 0.00 0.86
667 677 8.044309 TCGGTGGAAAAGAAGTGATGATTTATA 58.956 33.333 0.00 0.00 0.00 0.98
673 683 3.323691 TCTCGGTGGAAAAGAAGTGATGA 59.676 43.478 0.00 0.00 0.00 2.92
705 715 2.417516 CTGGTCCATCTACGGCCG 59.582 66.667 26.86 26.86 0.00 6.13
733 743 0.040058 ATGTTTCATGGCCCTGAGCA 59.960 50.000 10.81 13.68 46.50 4.26
734 744 0.743097 GATGTTTCATGGCCCTGAGC 59.257 55.000 10.81 8.85 42.60 4.26
739 749 1.571955 AAAGGGATGTTTCATGGCCC 58.428 50.000 0.00 0.00 39.12 5.80
749 759 5.014123 TGAGACATTGGAGTAAAAGGGATGT 59.986 40.000 0.00 0.00 0.00 3.06
754 764 7.038154 TGTTTTGAGACATTGGAGTAAAAGG 57.962 36.000 0.00 0.00 0.00 3.11
756 766 9.712305 TTTTTGTTTTGAGACATTGGAGTAAAA 57.288 25.926 0.00 0.00 0.00 1.52
758 768 8.744652 TCTTTTTGTTTTGAGACATTGGAGTAA 58.255 29.630 0.00 0.00 0.00 2.24
759 769 8.287439 TCTTTTTGTTTTGAGACATTGGAGTA 57.713 30.769 0.00 0.00 0.00 2.59
760 770 7.169158 TCTTTTTGTTTTGAGACATTGGAGT 57.831 32.000 0.00 0.00 0.00 3.85
762 772 8.010733 AGATCTTTTTGTTTTGAGACATTGGA 57.989 30.769 0.00 0.00 0.00 3.53
763 773 8.652810 AAGATCTTTTTGTTTTGAGACATTGG 57.347 30.769 0.88 0.00 0.00 3.16
771 781 9.581099 GTGGAGTAAAAGATCTTTTTGTTTTGA 57.419 29.630 32.37 14.41 42.22 2.69
772 782 9.586435 AGTGGAGTAAAAGATCTTTTTGTTTTG 57.414 29.630 32.37 0.00 42.22 2.44
775 785 8.966868 TGAAGTGGAGTAAAAGATCTTTTTGTT 58.033 29.630 32.37 20.22 42.22 2.83
776 786 8.406297 GTGAAGTGGAGTAAAAGATCTTTTTGT 58.594 33.333 32.37 21.83 42.22 2.83
777 787 7.587757 CGTGAAGTGGAGTAAAAGATCTTTTTG 59.412 37.037 32.37 3.70 42.22 2.44
779 789 6.990349 TCGTGAAGTGGAGTAAAAGATCTTTT 59.010 34.615 30.61 30.61 44.16 2.27
800 830 2.480555 GCCGCAAGATGGTTCGTG 59.519 61.111 0.00 0.00 43.02 4.35
820 850 2.515071 GGATGGATGGAGCCGAGCT 61.515 63.158 0.00 0.00 43.88 4.09
821 851 2.031768 GGATGGATGGAGCCGAGC 59.968 66.667 0.00 0.00 0.00 5.03
822 852 0.399454 AATGGATGGATGGAGCCGAG 59.601 55.000 0.00 0.00 0.00 4.63
823 853 0.397941 GAATGGATGGATGGAGCCGA 59.602 55.000 0.00 0.00 0.00 5.54
824 854 0.952497 CGAATGGATGGATGGAGCCG 60.952 60.000 0.00 0.00 0.00 5.52
825 855 1.239968 GCGAATGGATGGATGGAGCC 61.240 60.000 0.00 0.00 0.00 4.70
826 856 1.239968 GGCGAATGGATGGATGGAGC 61.240 60.000 0.00 0.00 0.00 4.70
828 858 1.351850 TGGGCGAATGGATGGATGGA 61.352 55.000 0.00 0.00 0.00 3.41
829 859 0.251474 ATGGGCGAATGGATGGATGG 60.251 55.000 0.00 0.00 0.00 3.51
831 861 1.145531 TGAATGGGCGAATGGATGGAT 59.854 47.619 0.00 0.00 0.00 3.41
832 862 0.550432 TGAATGGGCGAATGGATGGA 59.450 50.000 0.00 0.00 0.00 3.41
833 863 0.956633 CTGAATGGGCGAATGGATGG 59.043 55.000 0.00 0.00 0.00 3.51
834 864 1.335810 CACTGAATGGGCGAATGGATG 59.664 52.381 0.00 0.00 0.00 3.51
835 865 1.212688 TCACTGAATGGGCGAATGGAT 59.787 47.619 0.00 0.00 0.00 3.41
861 894 4.737476 AGCTGGGCTCTCTGGGCT 62.737 66.667 0.00 0.00 30.62 5.19
960 3136 1.602771 GAGGAAAGGGTAGCGGCTT 59.397 57.895 8.26 0.00 0.00 4.35
961 3137 2.368011 GGAGGAAAGGGTAGCGGCT 61.368 63.158 7.98 7.98 0.00 5.52
962 3138 2.189784 GGAGGAAAGGGTAGCGGC 59.810 66.667 0.00 0.00 0.00 6.53
963 3139 1.687297 GGAGGAGGAAAGGGTAGCGG 61.687 65.000 0.00 0.00 0.00 5.52
964 3140 1.687297 GGGAGGAGGAAAGGGTAGCG 61.687 65.000 0.00 0.00 0.00 4.26
965 3141 1.346479 GGGGAGGAGGAAAGGGTAGC 61.346 65.000 0.00 0.00 0.00 3.58
966 3142 1.049289 CGGGGAGGAGGAAAGGGTAG 61.049 65.000 0.00 0.00 0.00 3.18
967 3143 1.002533 CGGGGAGGAGGAAAGGGTA 59.997 63.158 0.00 0.00 0.00 3.69
1038 3214 3.399181 GCCATGTCCCCGTCCAGA 61.399 66.667 0.00 0.00 0.00 3.86
1720 3896 3.249189 AGGGGCAAGGTCGAGCAA 61.249 61.111 18.15 0.00 0.00 3.91
1986 4162 3.372440 AAATAGGGGTTCAGCTTGAGG 57.628 47.619 0.00 0.00 0.00 3.86
1995 4171 2.496070 GGCAGTTCCAAAATAGGGGTTC 59.504 50.000 0.00 0.00 34.01 3.62
2004 4180 2.199652 CCTGCGGGCAGTTCCAAAA 61.200 57.895 18.48 0.00 42.15 2.44
2052 4228 2.642171 TCTTCTCCTTCCTGGCCTTA 57.358 50.000 3.32 0.00 35.26 2.69
2112 4288 2.978156 AACAGATGGCAAAGGGAAGA 57.022 45.000 0.00 0.00 0.00 2.87
2170 4348 5.995282 ACGAACATCCAACAATTACTTCAGA 59.005 36.000 0.00 0.00 0.00 3.27
2173 4353 7.360575 AGTACGAACATCCAACAATTACTTC 57.639 36.000 0.00 0.00 0.00 3.01
2174 4354 8.836268 TTAGTACGAACATCCAACAATTACTT 57.164 30.769 0.00 0.00 0.00 2.24
2186 4366 4.927425 TGCTCAAACCTTAGTACGAACATC 59.073 41.667 0.00 0.00 0.00 3.06
2208 4388 6.090898 GCTACATACCACTACACAAAGACTTG 59.909 42.308 0.00 0.00 38.61 3.16
2217 4397 4.939052 ATCAGGCTACATACCACTACAC 57.061 45.455 0.00 0.00 0.00 2.90
2398 4757 0.658897 AAACGTACAACCACAAGGCG 59.341 50.000 0.00 0.00 39.06 5.52
2419 4780 4.272018 GTGCTTGCTCCATATAGAACAGTG 59.728 45.833 0.00 0.00 0.00 3.66
2470 5023 3.720949 AGTACACAGAAACGCACTACA 57.279 42.857 0.00 0.00 0.00 2.74
2477 5031 5.464965 ACAAACTGAAGTACACAGAAACG 57.535 39.130 21.16 11.63 38.55 3.60
2636 5234 5.638657 GCCATCAAAGAAATTGCACATTGTA 59.361 36.000 0.00 0.00 38.98 2.41
2639 5237 4.004982 GGCCATCAAAGAAATTGCACATT 58.995 39.130 0.00 0.00 38.98 2.71
2661 5259 8.902806 TGGATACTTAAAAATTCAGTATGGCAG 58.097 33.333 0.00 0.00 34.50 4.85
2789 5397 2.508526 ACCAAGCAGTTCATGTCCTTC 58.491 47.619 0.00 0.00 0.00 3.46
2859 5467 5.241506 CCTACTCTTGGAGTTTCAAATGCAA 59.758 40.000 5.50 0.00 40.28 4.08
2901 5538 6.991938 TGCTTTTAATTCACCAGCAATAACT 58.008 32.000 0.00 0.00 37.54 2.24
2921 5653 5.528320 CACCCAAACATGAAAAGAAATGCTT 59.472 36.000 0.00 0.00 38.88 3.91
2959 5691 4.543590 TTGAAAGGGCAACAGAAAAACA 57.456 36.364 0.00 0.00 39.74 2.83
3001 5733 7.205297 ACAAGATGCAGCATATGGAATTTAAC 58.795 34.615 11.58 0.00 30.55 2.01
3015 5747 7.475015 TGAGAATAACAAATACAAGATGCAGC 58.525 34.615 0.00 0.00 0.00 5.25
3048 5783 6.428083 TCCTACAATAACAAGTGTTCCTCA 57.572 37.500 0.00 0.00 39.31 3.86
3049 5787 5.875359 CCTCCTACAATAACAAGTGTTCCTC 59.125 44.000 0.00 0.00 39.31 3.71
3304 6101 3.445805 TGCGTCCATAGATAGAACACACA 59.554 43.478 0.00 0.00 0.00 3.72
3306 6103 4.937201 ATGCGTCCATAGATAGAACACA 57.063 40.909 0.00 0.00 0.00 3.72
3347 6144 0.920664 CGACGACGATAAAGCATGCA 59.079 50.000 21.98 0.00 42.66 3.96
3411 6211 9.107177 TGCCAAAAATTATTTCGCATTCATAAT 57.893 25.926 3.86 0.00 32.10 1.28
3429 6229 5.106396 CCACAAAACTTCACAATGCCAAAAA 60.106 36.000 0.00 0.00 0.00 1.94
3465 6266 1.758783 CCGTGCAAGAAAGAAACTGC 58.241 50.000 0.00 0.00 0.00 4.40
3521 6322 3.255888 AGTGTCTCTTGAACGTCTATGCA 59.744 43.478 0.00 0.00 0.00 3.96
3580 6381 3.088532 AGAAAACACAACCTGCAAGTGA 58.911 40.909 13.17 0.00 37.05 3.41
3606 6407 9.063615 ACTAGTAACAACATCAGGTTTTTAAGG 57.936 33.333 0.00 0.00 37.72 2.69
3614 6415 6.154534 TGCATCTACTAGTAACAACATCAGGT 59.845 38.462 3.76 0.00 0.00 4.00
3616 6417 9.750125 TTATGCATCTACTAGTAACAACATCAG 57.250 33.333 0.19 0.00 0.00 2.90
3638 6442 9.553759 CATGCGAAAAAGCGTAATTATTTTATG 57.446 29.630 0.00 0.00 40.67 1.90
3701 6537 0.816018 TGGGCGAGCTTGAACGAAAA 60.816 50.000 4.70 0.00 0.00 2.29
3733 6578 9.780186 AAAGCAACTACAGAACTAAACTTAGAT 57.220 29.630 3.50 0.00 34.84 1.98
3740 6585 8.617809 CAACCTAAAAGCAACTACAGAACTAAA 58.382 33.333 0.00 0.00 0.00 1.85
3741 6586 7.988599 TCAACCTAAAAGCAACTACAGAACTAA 59.011 33.333 0.00 0.00 0.00 2.24
3742 6587 7.502696 TCAACCTAAAAGCAACTACAGAACTA 58.497 34.615 0.00 0.00 0.00 2.24
3743 6588 6.354130 TCAACCTAAAAGCAACTACAGAACT 58.646 36.000 0.00 0.00 0.00 3.01
3744 6589 6.613755 TCAACCTAAAAGCAACTACAGAAC 57.386 37.500 0.00 0.00 0.00 3.01
3745 6590 7.633193 TTTCAACCTAAAAGCAACTACAGAA 57.367 32.000 0.00 0.00 0.00 3.02
3746 6591 7.633193 TTTTCAACCTAAAAGCAACTACAGA 57.367 32.000 0.00 0.00 0.00 3.41
3747 6592 9.959749 TTATTTTCAACCTAAAAGCAACTACAG 57.040 29.630 0.00 0.00 32.20 2.74
3813 9184 6.368791 TGTTGTTGTAGACATGTCTTAGCATC 59.631 38.462 32.14 23.98 40.93 3.91
3844 9514 9.088512 CATCAGTTCACTGGTAATTTCTACTAC 57.911 37.037 7.11 0.00 43.91 2.73
3861 9584 3.753815 TGCAAGATGGTTCATCAGTTCA 58.246 40.909 10.08 1.03 42.72 3.18
3867 9590 4.712476 ACCTAGATGCAAGATGGTTCATC 58.288 43.478 0.00 0.00 40.80 2.92
3878 9601 2.912956 AGTTTCCTGGACCTAGATGCAA 59.087 45.455 0.00 0.00 0.00 4.08
3879 9602 2.237143 CAGTTTCCTGGACCTAGATGCA 59.763 50.000 0.00 0.00 34.90 3.96
3880 9603 2.911484 CAGTTTCCTGGACCTAGATGC 58.089 52.381 0.00 0.00 34.90 3.91
3881 9604 2.237143 TGCAGTTTCCTGGACCTAGATG 59.763 50.000 0.00 0.00 39.22 2.90
3882 9605 2.503356 CTGCAGTTTCCTGGACCTAGAT 59.497 50.000 5.25 0.00 39.22 1.98
3884 9607 1.065854 CCTGCAGTTTCCTGGACCTAG 60.066 57.143 13.81 0.00 39.22 3.02
3885 9608 0.984230 CCTGCAGTTTCCTGGACCTA 59.016 55.000 13.81 0.00 39.22 3.08
3894 9671 3.343617 TGCTATGGTAACCTGCAGTTTC 58.656 45.455 13.81 5.20 40.05 2.78
3956 9744 0.893447 AGGGCCTCGTGTACAACTAC 59.107 55.000 0.00 0.00 0.00 2.73
3958 9746 0.320697 GAAGGGCCTCGTGTACAACT 59.679 55.000 6.46 0.00 0.00 3.16
3991 9779 3.243839 GGTCCCAACGTAAAGTGAGTGTA 60.244 47.826 0.00 0.00 0.00 2.90
3994 9782 1.269936 CGGTCCCAACGTAAAGTGAGT 60.270 52.381 0.00 0.00 0.00 3.41
3995 9783 1.269936 ACGGTCCCAACGTAAAGTGAG 60.270 52.381 0.00 0.00 43.60 3.51
4012 9807 2.486918 AGGTCGGTGTTTTTCTTACGG 58.513 47.619 0.00 0.00 0.00 4.02
4141 9941 4.823989 TGAGTATAAGCTACGGTCCTTACC 59.176 45.833 0.00 0.00 42.95 2.85
4150 9950 5.915758 GTGAATGAGGTGAGTATAAGCTACG 59.084 44.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.