Multiple sequence alignment - TraesCS2D01G509000

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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 TraesCS2D01G509000 chr2D 100.000 3533 0 0 1 3533 601635567 601632035 0.000000e+00 6525.0
1 TraesCS2D01G509000 chr2D 95.198 1916 70 14 1627 3533 405635494 405637396 0.000000e+00 3009.0
2 TraesCS2D01G509000 chr2D 93.220 59 1 2 2 60 601708330 601708275 2.260000e-12 84.2
3 TraesCS2D01G509000 chr1D 95.820 1914 71 6 1626 3533 147379853 147377943 0.000000e+00 3083.0
4 TraesCS2D01G509000 chr1D 94.781 1916 77 13 1630 3533 27538781 27536877 0.000000e+00 2963.0
5 TraesCS2D01G509000 chr7D 95.547 1909 78 4 1627 3533 592752377 592754280 0.000000e+00 3048.0
6 TraesCS2D01G509000 chr7D 94.961 1925 93 4 1611 3533 599196526 599198448 0.000000e+00 3014.0
7 TraesCS2D01G509000 chr7D 94.830 1915 91 8 1623 3533 35355951 35357861 0.000000e+00 2981.0
8 TraesCS2D01G509000 chr3D 95.241 1912 85 5 1626 3533 553011967 553010058 0.000000e+00 3022.0
9 TraesCS2D01G509000 chr6D 94.877 1913 85 10 1626 3533 28253645 28255549 0.000000e+00 2977.0
10 TraesCS2D01G509000 chr4D 94.564 1913 89 13 1627 3533 130556838 130558741 0.000000e+00 2942.0
11 TraesCS2D01G509000 chr2B 87.755 1274 96 39 373 1625 731935707 731934473 0.000000e+00 1434.0
12 TraesCS2D01G509000 chr2B 89.720 214 19 2 164 377 731936981 731936771 1.620000e-68 270.0
13 TraesCS2D01G509000 chr2B 91.525 59 2 2 2 60 732038772 732038717 1.050000e-10 78.7
14 TraesCS2D01G509000 chrUn 94.915 59 1 2 2 60 379978914 379978970 1.350000e-14 91.6
15 TraesCS2D01G509000 chrUn 82.178 101 5 7 2 102 258625418 258625505 1.360000e-09 75.0
16 TraesCS2D01G509000 chrUn 82.178 101 5 7 2 102 388793034 388793121 1.360000e-09 75.0
17 TraesCS2D01G509000 chrUn 81.553 103 5 8 2 103 15279645 15279734 4.890000e-09 73.1
18 TraesCS2D01G509000 chr2A 94.915 59 1 2 2 60 734912548 734912492 1.350000e-14 91.6
19 TraesCS2D01G509000 chr4A 95.556 45 2 0 2 46 741106823 741106779 4.890000e-09 73.1


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 TraesCS2D01G509000 chr2D 601632035 601635567 3532 True 6525 6525 100.0000 1 3533 1 chr2D.!!$R1 3532
1 TraesCS2D01G509000 chr2D 405635494 405637396 1902 False 3009 3009 95.1980 1627 3533 1 chr2D.!!$F1 1906
2 TraesCS2D01G509000 chr1D 147377943 147379853 1910 True 3083 3083 95.8200 1626 3533 1 chr1D.!!$R2 1907
3 TraesCS2D01G509000 chr1D 27536877 27538781 1904 True 2963 2963 94.7810 1630 3533 1 chr1D.!!$R1 1903
4 TraesCS2D01G509000 chr7D 592752377 592754280 1903 False 3048 3048 95.5470 1627 3533 1 chr7D.!!$F2 1906
5 TraesCS2D01G509000 chr7D 599196526 599198448 1922 False 3014 3014 94.9610 1611 3533 1 chr7D.!!$F3 1922
6 TraesCS2D01G509000 chr7D 35355951 35357861 1910 False 2981 2981 94.8300 1623 3533 1 chr7D.!!$F1 1910
7 TraesCS2D01G509000 chr3D 553010058 553011967 1909 True 3022 3022 95.2410 1626 3533 1 chr3D.!!$R1 1907
8 TraesCS2D01G509000 chr6D 28253645 28255549 1904 False 2977 2977 94.8770 1626 3533 1 chr6D.!!$F1 1907
9 TraesCS2D01G509000 chr4D 130556838 130558741 1903 False 2942 2942 94.5640 1627 3533 1 chr4D.!!$F1 1906
10 TraesCS2D01G509000 chr2B 731934473 731936981 2508 True 852 1434 88.7375 164 1625 2 chr2B.!!$R2 1461

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
382 383 0.107654 GGGCACCGCTATCTTCAGTT 60.108 55.0 0.0 0.0 40.86 3.16 F
1443 2523 0.178975 ACGGAAGAAATGGTTGGGCA 60.179 50.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2904 0.251787 GTGGATGCCTTTTGGTCCCT 60.252 55.000 0.0 0.0 42.99 4.20 R
3295 4396 2.598565 TCGACTAGCTTATCCCATGCT 58.401 47.619 0.0 0.0 40.53 3.79 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.982241 ACTTGGAGAAAGAGTTCATCCA 57.018 40.909 0.00 0.00 38.35 3.41
22 23 5.310409 ACTTGGAGAAAGAGTTCATCCAA 57.690 39.130 14.27 14.27 42.47 3.53
23 24 5.885465 ACTTGGAGAAAGAGTTCATCCAAT 58.115 37.500 14.89 7.81 43.02 3.16
24 25 5.942826 ACTTGGAGAAAGAGTTCATCCAATC 59.057 40.000 14.89 0.00 43.02 2.67
25 26 5.503634 TGGAGAAAGAGTTCATCCAATCA 57.496 39.130 0.00 0.00 37.75 2.57
26 27 6.070951 TGGAGAAAGAGTTCATCCAATCAT 57.929 37.500 0.00 0.00 37.75 2.45
27 28 6.118170 TGGAGAAAGAGTTCATCCAATCATC 58.882 40.000 0.00 0.00 37.75 2.92
28 29 6.069789 TGGAGAAAGAGTTCATCCAATCATCT 60.070 38.462 0.00 0.00 37.75 2.90
29 30 6.260493 GGAGAAAGAGTTCATCCAATCATCTG 59.740 42.308 0.00 0.00 36.09 2.90
30 31 6.955364 AGAAAGAGTTCATCCAATCATCTGA 58.045 36.000 0.00 0.00 36.09 3.27
31 32 7.400439 AGAAAGAGTTCATCCAATCATCTGAA 58.600 34.615 0.00 0.00 36.09 3.02
32 33 7.886970 AGAAAGAGTTCATCCAATCATCTGAAA 59.113 33.333 0.00 0.00 36.09 2.69
33 34 8.591114 AAAGAGTTCATCCAATCATCTGAAAT 57.409 30.769 0.00 0.00 30.06 2.17
34 35 8.591114 AAGAGTTCATCCAATCATCTGAAATT 57.409 30.769 0.00 0.00 30.06 1.82
35 36 8.223177 AGAGTTCATCCAATCATCTGAAATTC 57.777 34.615 0.00 0.00 30.06 2.17
36 37 7.284944 AGAGTTCATCCAATCATCTGAAATTCC 59.715 37.037 0.00 0.00 30.06 3.01
37 38 6.893554 AGTTCATCCAATCATCTGAAATTCCA 59.106 34.615 0.00 0.00 30.06 3.53
38 39 7.398047 AGTTCATCCAATCATCTGAAATTCCAA 59.602 33.333 0.00 0.00 30.06 3.53
39 40 7.342769 TCATCCAATCATCTGAAATTCCAAG 57.657 36.000 0.00 0.00 0.00 3.61
40 41 7.120716 TCATCCAATCATCTGAAATTCCAAGA 58.879 34.615 0.00 0.00 0.00 3.02
41 42 7.783119 TCATCCAATCATCTGAAATTCCAAGAT 59.217 33.333 0.00 0.00 0.00 2.40
42 43 7.342769 TCCAATCATCTGAAATTCCAAGATG 57.657 36.000 13.88 13.88 38.08 2.90
43 44 7.120716 TCCAATCATCTGAAATTCCAAGATGA 58.879 34.615 20.87 20.87 45.96 2.92
47 48 7.949690 TCATCTGAAATTCCAAGATGATTGT 57.050 32.000 17.03 0.00 39.97 2.71
48 49 8.357290 TCATCTGAAATTCCAAGATGATTGTT 57.643 30.769 17.03 0.00 39.97 2.83
49 50 8.809066 TCATCTGAAATTCCAAGATGATTGTTT 58.191 29.630 17.03 0.00 39.97 2.83
50 51 9.431887 CATCTGAAATTCCAAGATGATTGTTTT 57.568 29.630 14.56 0.00 38.78 2.43
52 53 9.912634 TCTGAAATTCCAAGATGATTGTTTTAC 57.087 29.630 0.00 0.00 0.00 2.01
53 54 9.918630 CTGAAATTCCAAGATGATTGTTTTACT 57.081 29.630 0.00 0.00 0.00 2.24
76 77 8.902540 ACTTACATTACATGTTGAAGTGAAGA 57.097 30.769 2.30 0.00 41.63 2.87
77 78 8.993121 ACTTACATTACATGTTGAAGTGAAGAG 58.007 33.333 2.30 0.00 41.63 2.85
78 79 8.902540 TTACATTACATGTTGAAGTGAAGAGT 57.097 30.769 2.30 0.00 41.63 3.24
79 80 7.807977 ACATTACATGTTGAAGTGAAGAGTT 57.192 32.000 2.30 0.00 41.63 3.01
80 81 7.642669 ACATTACATGTTGAAGTGAAGAGTTG 58.357 34.615 2.30 0.00 41.63 3.16
81 82 4.558538 ACATGTTGAAGTGAAGAGTTGC 57.441 40.909 0.00 0.00 0.00 4.17
82 83 3.947196 ACATGTTGAAGTGAAGAGTTGCA 59.053 39.130 0.00 0.00 0.00 4.08
83 84 4.036027 ACATGTTGAAGTGAAGAGTTGCAG 59.964 41.667 0.00 0.00 0.00 4.41
84 85 3.609853 TGTTGAAGTGAAGAGTTGCAGT 58.390 40.909 0.00 0.00 0.00 4.40
85 86 4.009675 TGTTGAAGTGAAGAGTTGCAGTT 58.990 39.130 0.00 0.00 0.00 3.16
86 87 5.182487 TGTTGAAGTGAAGAGTTGCAGTTA 58.818 37.500 0.00 0.00 0.00 2.24
87 88 5.064707 TGTTGAAGTGAAGAGTTGCAGTTAC 59.935 40.000 0.00 0.00 0.00 2.50
88 89 5.023533 TGAAGTGAAGAGTTGCAGTTACT 57.976 39.130 0.00 0.00 0.00 2.24
89 90 6.156748 TGAAGTGAAGAGTTGCAGTTACTA 57.843 37.500 0.00 0.00 0.00 1.82
90 91 6.759272 TGAAGTGAAGAGTTGCAGTTACTAT 58.241 36.000 0.00 0.00 0.00 2.12
91 92 7.217200 TGAAGTGAAGAGTTGCAGTTACTATT 58.783 34.615 0.00 0.00 30.31 1.73
92 93 8.364894 TGAAGTGAAGAGTTGCAGTTACTATTA 58.635 33.333 0.00 0.00 27.99 0.98
93 94 9.372369 GAAGTGAAGAGTTGCAGTTACTATTAT 57.628 33.333 0.00 0.00 27.99 1.28
94 95 9.726438 AAGTGAAGAGTTGCAGTTACTATTATT 57.274 29.630 0.00 0.00 27.99 1.40
102 103 9.953565 AGTTGCAGTTACTATTATTAGTTTGGA 57.046 29.630 2.79 0.10 39.42 3.53
105 106 9.337396 TGCAGTTACTATTATTAGTTTGGATGG 57.663 33.333 2.79 0.00 39.42 3.51
106 107 8.290325 GCAGTTACTATTATTAGTTTGGATGGC 58.710 37.037 2.79 0.00 39.42 4.40
107 108 9.337396 CAGTTACTATTATTAGTTTGGATGGCA 57.663 33.333 2.79 0.00 39.42 4.92
118 119 8.685838 TTAGTTTGGATGGCATAACTATAACC 57.314 34.615 17.57 6.44 34.22 2.85
119 120 6.668645 AGTTTGGATGGCATAACTATAACCA 58.331 36.000 11.45 4.51 34.28 3.67
120 121 7.297614 AGTTTGGATGGCATAACTATAACCAT 58.702 34.615 11.45 0.00 43.72 3.55
121 122 7.231317 AGTTTGGATGGCATAACTATAACCATG 59.769 37.037 11.45 0.00 41.15 3.66
122 123 6.199557 TGGATGGCATAACTATAACCATGT 57.800 37.500 0.00 0.00 41.15 3.21
123 124 6.237901 TGGATGGCATAACTATAACCATGTC 58.762 40.000 0.00 0.00 41.15 3.06
124 125 6.044287 TGGATGGCATAACTATAACCATGTCT 59.956 38.462 0.00 0.00 41.15 3.41
125 126 7.236640 TGGATGGCATAACTATAACCATGTCTA 59.763 37.037 0.00 0.00 41.15 2.59
126 127 8.267894 GGATGGCATAACTATAACCATGTCTAT 58.732 37.037 0.00 0.00 41.15 1.98
129 130 9.321532 TGGCATAACTATAACCATGTCTATAGT 57.678 33.333 14.10 14.10 41.15 2.12
130 131 9.804758 GGCATAACTATAACCATGTCTATAGTC 57.195 37.037 17.75 9.78 39.38 2.59
131 132 9.804758 GCATAACTATAACCATGTCTATAGTCC 57.195 37.037 17.75 8.57 39.38 3.85
141 142 8.465798 ACCATGTCTATAGTCCCTATACTACT 57.534 38.462 0.00 0.00 34.87 2.57
142 143 8.330247 ACCATGTCTATAGTCCCTATACTACTG 58.670 40.741 0.00 0.00 34.87 2.74
143 144 8.549731 CCATGTCTATAGTCCCTATACTACTGA 58.450 40.741 0.00 0.00 34.87 3.41
146 147 8.476447 TGTCTATAGTCCCTATACTACTGATCG 58.524 40.741 0.00 0.00 34.87 3.69
147 148 7.927629 GTCTATAGTCCCTATACTACTGATCGG 59.072 44.444 0.00 0.00 34.87 4.18
148 149 4.997545 AGTCCCTATACTACTGATCGGT 57.002 45.455 12.79 12.79 0.00 4.69
149 150 4.909001 AGTCCCTATACTACTGATCGGTC 58.091 47.826 11.34 0.00 0.00 4.79
150 151 4.350225 AGTCCCTATACTACTGATCGGTCA 59.650 45.833 11.34 0.00 0.00 4.02
151 152 5.014333 AGTCCCTATACTACTGATCGGTCAT 59.986 44.000 11.34 6.06 32.98 3.06
152 153 5.124138 GTCCCTATACTACTGATCGGTCATG 59.876 48.000 11.34 5.63 32.98 3.07
153 154 5.010933 CCCTATACTACTGATCGGTCATGT 58.989 45.833 11.34 11.19 32.98 3.21
154 155 6.013119 TCCCTATACTACTGATCGGTCATGTA 60.013 42.308 11.34 12.92 32.98 2.29
155 156 6.316640 CCCTATACTACTGATCGGTCATGTAG 59.683 46.154 22.79 22.79 39.42 2.74
156 157 7.104290 CCTATACTACTGATCGGTCATGTAGA 58.896 42.308 27.47 16.08 37.78 2.59
157 158 7.606839 CCTATACTACTGATCGGTCATGTAGAA 59.393 40.741 27.47 17.18 37.78 2.10
158 159 5.502153 ACTACTGATCGGTCATGTAGAAC 57.498 43.478 27.47 0.00 37.78 3.01
159 160 5.194432 ACTACTGATCGGTCATGTAGAACT 58.806 41.667 27.47 12.88 37.78 3.01
160 161 6.354938 ACTACTGATCGGTCATGTAGAACTA 58.645 40.000 27.47 4.92 37.78 2.24
161 162 6.999272 ACTACTGATCGGTCATGTAGAACTAT 59.001 38.462 27.47 12.39 37.78 2.12
162 163 6.078202 ACTGATCGGTCATGTAGAACTATG 57.922 41.667 0.00 0.00 32.98 2.23
236 237 2.507484 TGTCTTCCTGGCAGTGAATTG 58.493 47.619 14.43 6.26 0.00 2.32
238 239 1.202915 TCTTCCTGGCAGTGAATTGCA 60.203 47.619 14.43 0.00 45.86 4.08
239 240 1.614903 CTTCCTGGCAGTGAATTGCAA 59.385 47.619 14.43 0.00 45.86 4.08
296 297 4.357947 GTCAGTGCCGTCTGCCGA 62.358 66.667 0.00 0.00 40.16 5.54
323 324 6.422776 AAAGTATACTTTTGGTGCTCGATG 57.577 37.500 22.49 0.00 43.07 3.84
343 344 4.210724 TGGGTTATACAACACCACTAGC 57.789 45.455 0.00 0.00 37.25 3.42
363 364 5.108385 AGCTACAAAGTGGAAAATTGACG 57.892 39.130 0.00 0.00 0.00 4.35
366 367 2.223947 ACAAAGTGGAAAATTGACGGGC 60.224 45.455 0.00 0.00 0.00 6.13
381 382 1.522569 GGGCACCGCTATCTTCAGT 59.477 57.895 0.00 0.00 40.86 3.41
382 383 0.107654 GGGCACCGCTATCTTCAGTT 60.108 55.000 0.00 0.00 40.86 3.16
383 384 1.679032 GGGCACCGCTATCTTCAGTTT 60.679 52.381 0.00 0.00 40.86 2.66
384 385 1.398390 GGCACCGCTATCTTCAGTTTG 59.602 52.381 0.00 0.00 0.00 2.93
385 386 2.076863 GCACCGCTATCTTCAGTTTGT 58.923 47.619 0.00 0.00 0.00 2.83
387 388 3.058224 GCACCGCTATCTTCAGTTTGTTT 60.058 43.478 0.00 0.00 0.00 2.83
389 390 5.334569 GCACCGCTATCTTCAGTTTGTTTTA 60.335 40.000 0.00 0.00 0.00 1.52
391 392 6.797033 CACCGCTATCTTCAGTTTGTTTTAAG 59.203 38.462 0.00 0.00 0.00 1.85
392 393 6.485648 ACCGCTATCTTCAGTTTGTTTTAAGT 59.514 34.615 0.00 0.00 0.00 2.24
393 394 7.012989 ACCGCTATCTTCAGTTTGTTTTAAGTT 59.987 33.333 0.00 0.00 0.00 2.66
412 1452 8.948631 TTAAGTTAGTGCCTTATCTTCAGATG 57.051 34.615 0.00 0.00 36.05 2.90
413 1453 5.923204 AGTTAGTGCCTTATCTTCAGATGG 58.077 41.667 0.00 0.00 36.05 3.51
414 1454 3.853355 AGTGCCTTATCTTCAGATGGG 57.147 47.619 0.00 3.51 36.05 4.00
415 1455 2.158696 AGTGCCTTATCTTCAGATGGGC 60.159 50.000 20.01 20.01 45.74 5.36
418 1458 3.326006 TGCCTTATCTTCAGATGGGCTAG 59.674 47.826 23.84 0.00 45.73 3.42
419 1459 3.326297 GCCTTATCTTCAGATGGGCTAGT 59.674 47.826 19.74 0.00 44.03 2.57
420 1460 4.802248 GCCTTATCTTCAGATGGGCTAGTG 60.802 50.000 19.74 0.00 44.03 2.74
421 1461 4.590647 CCTTATCTTCAGATGGGCTAGTGA 59.409 45.833 0.00 0.00 36.05 3.41
422 1462 5.279406 CCTTATCTTCAGATGGGCTAGTGAG 60.279 48.000 0.00 0.00 36.05 3.51
423 1463 3.107402 TCTTCAGATGGGCTAGTGAGT 57.893 47.619 0.00 0.00 0.00 3.41
424 1464 4.251103 TCTTCAGATGGGCTAGTGAGTA 57.749 45.455 0.00 0.00 0.00 2.59
426 1466 3.671740 TCAGATGGGCTAGTGAGTAGT 57.328 47.619 0.00 0.00 0.00 2.73
427 1467 3.982516 TCAGATGGGCTAGTGAGTAGTT 58.017 45.455 0.00 0.00 0.00 2.24
428 1468 5.125367 TCAGATGGGCTAGTGAGTAGTTA 57.875 43.478 0.00 0.00 0.00 2.24
429 1469 5.516044 TCAGATGGGCTAGTGAGTAGTTAA 58.484 41.667 0.00 0.00 0.00 2.01
433 1491 7.278868 CAGATGGGCTAGTGAGTAGTTAAAAAG 59.721 40.741 0.00 0.00 0.00 2.27
435 1493 5.308759 TGGGCTAGTGAGTAGTTAAAAAGGT 59.691 40.000 0.00 0.00 0.00 3.50
465 1523 8.950208 AAAAGAGAACACTATATTAGCTGGAC 57.050 34.615 0.00 0.00 0.00 4.02
511 1584 4.144555 GCTGCACGCGATTTATTTAGATC 58.855 43.478 15.93 0.00 0.00 2.75
515 1588 5.176774 TGCACGCGATTTATTTAGATCGAAT 59.823 36.000 15.93 3.42 45.90 3.34
526 1599 6.906157 ATTTAGATCGAATCATTTGCCCAT 57.094 33.333 0.00 0.00 0.00 4.00
528 1601 7.815840 TTTAGATCGAATCATTTGCCCATTA 57.184 32.000 0.00 0.00 0.00 1.90
529 1602 7.815840 TTAGATCGAATCATTTGCCCATTAA 57.184 32.000 0.00 0.00 0.00 1.40
530 1603 6.906157 AGATCGAATCATTTGCCCATTAAT 57.094 33.333 0.00 0.00 0.00 1.40
532 1605 8.408043 AGATCGAATCATTTGCCCATTAATTA 57.592 30.769 0.00 0.00 0.00 1.40
533 1606 9.028284 AGATCGAATCATTTGCCCATTAATTAT 57.972 29.630 0.00 0.00 0.00 1.28
534 1607 9.294030 GATCGAATCATTTGCCCATTAATTATC 57.706 33.333 0.00 0.00 0.00 1.75
535 1608 8.408043 TCGAATCATTTGCCCATTAATTATCT 57.592 30.769 0.00 0.00 0.00 1.98
536 1609 8.298854 TCGAATCATTTGCCCATTAATTATCTG 58.701 33.333 0.00 0.00 0.00 2.90
538 1611 6.728089 TCATTTGCCCATTAATTATCTGCA 57.272 33.333 0.00 0.00 0.00 4.41
539 1612 7.305813 TCATTTGCCCATTAATTATCTGCAT 57.694 32.000 0.00 0.00 0.00 3.96
540 1613 7.156000 TCATTTGCCCATTAATTATCTGCATG 58.844 34.615 0.00 0.00 0.00 4.06
541 1614 5.471556 TTGCCCATTAATTATCTGCATGG 57.528 39.130 6.25 6.25 35.13 3.66
542 1615 3.258872 TGCCCATTAATTATCTGCATGGC 59.741 43.478 7.38 7.21 34.17 4.40
545 1618 4.022068 CCCATTAATTATCTGCATGGCGTT 60.022 41.667 7.38 0.00 34.17 4.84
546 1619 5.182950 CCCATTAATTATCTGCATGGCGTTA 59.817 40.000 7.38 0.00 34.17 3.18
580 1655 4.299547 TGCACTTCACGGCTCGCT 62.300 61.111 0.00 0.00 0.00 4.93
687 1762 4.261781 CGGTACTACGCCTCCGCC 62.262 72.222 0.00 0.00 38.22 6.13
704 1779 0.931005 GCCATCGACTTCTTTAGCCG 59.069 55.000 0.00 0.00 0.00 5.52
784 1859 2.612221 GCAGAGGCGTTGGTTTACTACT 60.612 50.000 0.00 0.00 0.00 2.57
795 1870 2.287849 GGTTTACTACTACCCGATCGCC 60.288 54.545 10.32 0.00 0.00 5.54
843 1918 2.607892 GCTCGTGGTTGACTGCACC 61.608 63.158 0.00 0.00 0.00 5.01
941 2016 3.998156 CGAGGAGTTCGTCTGGGA 58.002 61.111 1.02 0.00 44.27 4.37
944 2019 1.475403 GAGGAGTTCGTCTGGGATGA 58.525 55.000 0.00 0.00 0.00 2.92
955 2030 2.202756 GGGATGACGTGGTCGAGC 60.203 66.667 7.89 7.89 40.62 5.03
1011 2086 3.491619 CGCTCTTCTACATGCAGGTATGT 60.492 47.826 12.22 3.59 43.34 2.29
1044 2119 1.816074 TTTTGACCTCGCATGGTACC 58.184 50.000 4.43 4.43 41.00 3.34
1047 2122 1.144057 GACCTCGCATGGTACCAGG 59.856 63.158 22.17 22.17 41.00 4.45
1048 2123 1.612442 ACCTCGCATGGTACCAGGT 60.612 57.895 26.22 20.59 38.79 4.00
1049 2124 0.324923 ACCTCGCATGGTACCAGGTA 60.325 55.000 26.22 14.64 38.79 3.08
1050 2125 0.389391 CCTCGCATGGTACCAGGTAG 59.611 60.000 26.22 21.86 0.00 3.18
1051 2126 1.112113 CTCGCATGGTACCAGGTAGT 58.888 55.000 26.22 3.58 0.00 2.73
1052 2127 2.304092 CTCGCATGGTACCAGGTAGTA 58.696 52.381 26.22 9.68 0.00 1.82
1053 2128 2.891580 CTCGCATGGTACCAGGTAGTAT 59.108 50.000 26.22 1.98 0.00 2.12
1054 2129 4.077108 CTCGCATGGTACCAGGTAGTATA 58.923 47.826 26.22 6.47 0.00 1.47
1055 2130 4.669700 TCGCATGGTACCAGGTAGTATAT 58.330 43.478 26.22 0.40 0.00 0.86
1056 2131 4.461431 TCGCATGGTACCAGGTAGTATATG 59.539 45.833 26.22 14.19 0.00 1.78
1057 2132 4.219944 CGCATGGTACCAGGTAGTATATGT 59.780 45.833 26.22 0.00 0.00 2.29
1058 2133 5.416639 CGCATGGTACCAGGTAGTATATGTA 59.583 44.000 26.22 0.00 0.00 2.29
1059 2134 6.404403 CGCATGGTACCAGGTAGTATATGTAG 60.404 46.154 26.22 8.51 0.00 2.74
1060 2135 6.436532 GCATGGTACCAGGTAGTATATGTAGT 59.563 42.308 26.22 0.00 0.00 2.73
1061 2136 7.613022 GCATGGTACCAGGTAGTATATGTAGTA 59.387 40.741 26.22 0.00 0.00 1.82
1062 2137 8.954350 CATGGTACCAGGTAGTATATGTAGTAC 58.046 40.741 21.41 6.04 36.43 2.73
1063 2138 8.280258 TGGTACCAGGTAGTATATGTAGTACT 57.720 38.462 11.60 0.00 37.06 2.73
1064 2139 8.727149 TGGTACCAGGTAGTATATGTAGTACTT 58.273 37.037 11.60 4.32 37.06 2.24
1068 2143 8.910944 ACCAGGTAGTATATGTAGTACTTGTTG 58.089 37.037 18.84 11.02 39.96 3.33
1069 2144 8.358148 CCAGGTAGTATATGTAGTACTTGTTGG 58.642 40.741 18.84 14.27 39.96 3.77
1070 2145 8.910944 CAGGTAGTATATGTAGTACTTGTTGGT 58.089 37.037 14.67 0.00 38.25 3.67
1079 2154 7.174107 TGTAGTACTTGTTGGTATACTTCCC 57.826 40.000 0.00 0.00 0.00 3.97
1080 2155 5.334724 AGTACTTGTTGGTATACTTCCCG 57.665 43.478 2.25 0.00 0.00 5.14
1081 2156 2.981898 ACTTGTTGGTATACTTCCCGC 58.018 47.619 2.25 0.00 0.00 6.13
1082 2157 2.303600 ACTTGTTGGTATACTTCCCGCA 59.696 45.455 2.25 0.00 0.00 5.69
1083 2158 3.244630 ACTTGTTGGTATACTTCCCGCAA 60.245 43.478 2.25 0.00 0.00 4.85
1084 2159 3.420300 TGTTGGTATACTTCCCGCAAA 57.580 42.857 2.25 0.00 0.00 3.68
1085 2160 3.752665 TGTTGGTATACTTCCCGCAAAA 58.247 40.909 2.25 0.00 0.00 2.44
1086 2161 4.142790 TGTTGGTATACTTCCCGCAAAAA 58.857 39.130 2.25 0.00 0.00 1.94
1125 2205 7.721842 TGGTATATATTCAAGGAAAATCGCCAA 59.278 33.333 0.00 0.00 0.00 4.52
1134 2214 4.936891 AGGAAAATCGCCAATTTATCTGC 58.063 39.130 0.00 0.00 36.54 4.26
1195 2275 1.040339 TGGGTTTCCAAGTGTGCCAC 61.040 55.000 0.00 0.00 40.73 5.01
1203 2283 1.667830 AAGTGTGCCACGTCATCGG 60.668 57.895 0.00 0.00 39.64 4.18
1232 2312 1.003839 GGCGTGACCCAGTTCATCA 60.004 57.895 0.00 0.00 0.00 3.07
1282 2362 2.428569 CATCCGTCCGTATCGCCG 60.429 66.667 0.00 0.00 0.00 6.46
1312 2392 3.577313 GGGATCTTCAAGGCGCGC 61.577 66.667 25.94 25.94 0.00 6.86
1354 2434 1.607628 GACGTCTACCCAGCGTATGAT 59.392 52.381 8.70 0.00 35.59 2.45
1358 2438 2.364324 GTCTACCCAGCGTATGATCCAA 59.636 50.000 0.00 0.00 0.00 3.53
1375 2455 0.788391 CAACGTCGCCAAGTAGAACC 59.212 55.000 0.00 0.00 0.00 3.62
1408 2488 2.798262 GACGACGTTGACGACCCG 60.798 66.667 10.51 12.07 43.02 5.28
1443 2523 0.178975 ACGGAAGAAATGGTTGGGCA 60.179 50.000 0.00 0.00 0.00 5.36
1461 2541 2.406616 AATACCTGCGCTTTGGCCG 61.407 57.895 9.73 0.00 34.44 6.13
1480 2560 1.137825 GAAGGAGGTCGTCGCTCTG 59.862 63.158 0.81 0.00 0.00 3.35
1496 2576 3.229271 TGCGCAGGCATCTGGATA 58.771 55.556 5.66 0.00 46.21 2.59
1531 2611 1.257539 CGACGTTCGAGCTCTTAACC 58.742 55.000 12.85 4.05 43.74 2.85
1545 2625 2.105134 TCTTAACCGCTTTCCTGTGGAA 59.895 45.455 0.85 0.00 40.27 3.53
1665 2745 0.758123 TTTGTCCCGGTTCGTAAGGT 59.242 50.000 0.00 0.00 38.47 3.50
1667 2747 0.540365 TGTCCCGGTTCGTAAGGTCT 60.540 55.000 0.00 0.00 38.47 3.85
1674 2754 3.129988 CCGGTTCGTAAGGTCTATCTGTT 59.870 47.826 0.00 0.00 38.47 3.16
1704 2784 2.176314 AACCGGGACTAAAGGGTCGC 62.176 60.000 6.32 0.00 42.98 5.19
1745 2825 1.271656 AGTCCCGGTTCTTACACGAAG 59.728 52.381 0.00 0.00 36.38 3.79
1758 2838 1.982395 ACGAAGCGGGACAGATGGA 60.982 57.895 0.00 0.00 0.00 3.41
1819 2899 1.710996 TTGGTCCCGGTTGGTGACAT 61.711 55.000 0.00 0.00 42.32 3.06
1824 2904 0.536233 CCCGGTTGGTGACATCAACA 60.536 55.000 28.13 4.74 44.38 3.33
1844 2924 0.541764 GGGACCAAAAGGCATCCACA 60.542 55.000 0.00 0.00 32.45 4.17
2124 3220 3.069872 TGCATGTTGCCTTCACTTCAATT 59.930 39.130 0.00 0.00 44.23 2.32
2185 3281 0.109735 CATGCTCGCATCATGCATCC 60.110 55.000 11.00 0.00 45.36 3.51
2286 3383 4.341235 TCATAGTCATCGAACCAACCCTAG 59.659 45.833 0.00 0.00 0.00 3.02
2346 3443 7.566509 GGTAGGACCTAAATACCCTCTTTAAGA 59.433 40.741 1.75 0.00 34.73 2.10
2505 3602 7.587037 TCTTTGATTTTCATGTCTCCACTTT 57.413 32.000 0.00 0.00 0.00 2.66
2952 4051 9.860898 GAAAATAAGCTGTCAATGGAAATAAGT 57.139 29.630 0.00 0.00 0.00 2.24
3242 4343 8.194769 GTCCTTAGGTGAATTTTCTTTGTTTCA 58.805 33.333 0.00 0.00 0.00 2.69
3322 4423 6.085555 TGGGATAAGCTAGTCGAATTGTAG 57.914 41.667 0.00 0.00 0.00 2.74
3478 4584 1.725557 GCCTATCGCACAGACCTCGA 61.726 60.000 0.00 0.00 37.47 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.942236 TGATTGGATGAACTCTTTCTCCAAG 59.058 40.000 16.43 0.00 44.01 3.61
4 5 6.260493 CAGATGATTGGATGAACTCTTTCTCC 59.740 42.308 0.00 0.00 33.19 3.71
6 7 6.955364 TCAGATGATTGGATGAACTCTTTCT 58.045 36.000 0.00 0.00 32.36 2.52
7 8 7.621428 TTCAGATGATTGGATGAACTCTTTC 57.379 36.000 0.00 0.00 0.00 2.62
10 11 7.284944 GGAATTTCAGATGATTGGATGAACTCT 59.715 37.037 0.00 0.00 31.72 3.24
11 12 7.067859 TGGAATTTCAGATGATTGGATGAACTC 59.932 37.037 0.00 0.00 31.72 3.01
12 13 6.893554 TGGAATTTCAGATGATTGGATGAACT 59.106 34.615 0.00 0.00 31.72 3.01
13 14 7.104043 TGGAATTTCAGATGATTGGATGAAC 57.896 36.000 0.00 0.00 31.72 3.18
14 15 7.616542 TCTTGGAATTTCAGATGATTGGATGAA 59.383 33.333 0.00 0.00 0.00 2.57
15 16 7.120716 TCTTGGAATTTCAGATGATTGGATGA 58.879 34.615 0.00 0.00 0.00 2.92
16 17 7.342769 TCTTGGAATTTCAGATGATTGGATG 57.657 36.000 0.00 0.00 0.00 3.51
17 18 7.783119 TCATCTTGGAATTTCAGATGATTGGAT 59.217 33.333 18.50 1.00 39.97 3.41
18 19 7.120716 TCATCTTGGAATTTCAGATGATTGGA 58.879 34.615 18.50 4.30 39.97 3.53
19 20 7.342769 TCATCTTGGAATTTCAGATGATTGG 57.657 36.000 18.50 2.12 39.97 3.16
23 24 7.949690 ACAATCATCTTGGAATTTCAGATGA 57.050 32.000 22.03 22.03 45.96 2.92
24 25 8.997621 AAACAATCATCTTGGAATTTCAGATG 57.002 30.769 15.61 15.61 38.08 2.90
26 27 9.912634 GTAAAACAATCATCTTGGAATTTCAGA 57.087 29.630 0.00 0.00 0.00 3.27
27 28 9.918630 AGTAAAACAATCATCTTGGAATTTCAG 57.081 29.630 0.00 0.00 0.00 3.02
57 58 6.262944 TGCAACTCTTCACTTCAACATGTAAT 59.737 34.615 0.00 0.00 0.00 1.89
58 59 5.588246 TGCAACTCTTCACTTCAACATGTAA 59.412 36.000 0.00 0.00 0.00 2.41
59 60 5.122519 TGCAACTCTTCACTTCAACATGTA 58.877 37.500 0.00 0.00 0.00 2.29
60 61 3.947196 TGCAACTCTTCACTTCAACATGT 59.053 39.130 0.00 0.00 0.00 3.21
61 62 4.036027 ACTGCAACTCTTCACTTCAACATG 59.964 41.667 0.00 0.00 0.00 3.21
62 63 4.202441 ACTGCAACTCTTCACTTCAACAT 58.798 39.130 0.00 0.00 0.00 2.71
63 64 3.609853 ACTGCAACTCTTCACTTCAACA 58.390 40.909 0.00 0.00 0.00 3.33
64 65 4.622701 AACTGCAACTCTTCACTTCAAC 57.377 40.909 0.00 0.00 0.00 3.18
65 66 5.428253 AGTAACTGCAACTCTTCACTTCAA 58.572 37.500 0.00 0.00 0.00 2.69
66 67 5.023533 AGTAACTGCAACTCTTCACTTCA 57.976 39.130 0.00 0.00 0.00 3.02
67 68 7.659652 AATAGTAACTGCAACTCTTCACTTC 57.340 36.000 0.00 0.00 0.00 3.01
68 69 9.726438 AATAATAGTAACTGCAACTCTTCACTT 57.274 29.630 0.00 0.00 0.00 3.16
76 77 9.953565 TCCAAACTAATAATAGTAACTGCAACT 57.046 29.630 0.00 0.00 41.57 3.16
79 80 9.337396 CCATCCAAACTAATAATAGTAACTGCA 57.663 33.333 0.00 0.00 41.57 4.41
80 81 8.290325 GCCATCCAAACTAATAATAGTAACTGC 58.710 37.037 0.00 0.00 41.57 4.40
81 82 9.337396 TGCCATCCAAACTAATAATAGTAACTG 57.663 33.333 0.00 0.00 41.57 3.16
92 93 9.297037 GGTTATAGTTATGCCATCCAAACTAAT 57.703 33.333 3.38 0.00 37.80 1.73
93 94 8.275758 TGGTTATAGTTATGCCATCCAAACTAA 58.724 33.333 3.38 0.00 37.80 2.24
94 95 7.807198 TGGTTATAGTTATGCCATCCAAACTA 58.193 34.615 2.02 2.02 38.43 2.24
95 96 6.668645 TGGTTATAGTTATGCCATCCAAACT 58.331 36.000 0.00 0.00 36.26 2.66
96 97 6.952773 TGGTTATAGTTATGCCATCCAAAC 57.047 37.500 0.00 0.00 0.00 2.93
97 98 7.066142 ACATGGTTATAGTTATGCCATCCAAA 58.934 34.615 0.00 0.00 37.80 3.28
98 99 6.609876 ACATGGTTATAGTTATGCCATCCAA 58.390 36.000 0.00 0.00 37.80 3.53
99 100 6.044287 AGACATGGTTATAGTTATGCCATCCA 59.956 38.462 0.00 0.00 37.80 3.41
100 101 6.476378 AGACATGGTTATAGTTATGCCATCC 58.524 40.000 0.00 0.00 37.80 3.51
103 104 9.321532 ACTATAGACATGGTTATAGTTATGCCA 57.678 33.333 18.39 0.00 39.06 4.92
104 105 9.804758 GACTATAGACATGGTTATAGTTATGCC 57.195 37.037 22.11 12.03 41.05 4.40
105 106 9.804758 GGACTATAGACATGGTTATAGTTATGC 57.195 37.037 22.11 14.18 41.05 3.14
125 126 7.092354 ATGACCGATCAGTAGTATAGGGACTAT 60.092 40.741 0.00 0.00 46.15 2.12
126 127 6.215023 ATGACCGATCAGTAGTATAGGGACTA 59.785 42.308 0.00 0.00 41.72 2.59
127 128 4.350225 TGACCGATCAGTAGTATAGGGACT 59.650 45.833 0.00 0.00 46.37 3.85
128 129 4.649692 TGACCGATCAGTAGTATAGGGAC 58.350 47.826 0.00 0.00 0.00 4.46
129 130 4.987963 TGACCGATCAGTAGTATAGGGA 57.012 45.455 0.00 0.00 0.00 4.20
130 131 5.010933 ACATGACCGATCAGTAGTATAGGG 58.989 45.833 0.00 0.00 38.57 3.53
131 132 7.104290 TCTACATGACCGATCAGTAGTATAGG 58.896 42.308 13.02 0.00 38.57 2.57
132 133 8.444715 GTTCTACATGACCGATCAGTAGTATAG 58.555 40.741 13.02 0.00 38.57 1.31
133 134 8.155510 AGTTCTACATGACCGATCAGTAGTATA 58.844 37.037 13.02 0.00 38.57 1.47
134 135 6.999272 AGTTCTACATGACCGATCAGTAGTAT 59.001 38.462 13.02 2.76 38.57 2.12
135 136 6.354938 AGTTCTACATGACCGATCAGTAGTA 58.645 40.000 13.02 3.75 38.57 1.82
136 137 5.194432 AGTTCTACATGACCGATCAGTAGT 58.806 41.667 13.02 2.89 38.57 2.73
137 138 5.759506 AGTTCTACATGACCGATCAGTAG 57.240 43.478 0.00 9.08 38.57 2.57
138 139 6.771267 ACATAGTTCTACATGACCGATCAGTA 59.229 38.462 0.00 0.00 38.57 2.74
139 140 5.594725 ACATAGTTCTACATGACCGATCAGT 59.405 40.000 0.00 0.00 38.57 3.41
140 141 5.917447 CACATAGTTCTACATGACCGATCAG 59.083 44.000 0.00 0.00 38.57 2.90
141 142 5.592688 TCACATAGTTCTACATGACCGATCA 59.407 40.000 0.00 0.00 39.83 2.92
142 143 6.073327 TCACATAGTTCTACATGACCGATC 57.927 41.667 0.00 0.00 0.00 3.69
143 144 6.127451 TGTTCACATAGTTCTACATGACCGAT 60.127 38.462 0.00 0.00 0.00 4.18
144 145 5.184287 TGTTCACATAGTTCTACATGACCGA 59.816 40.000 0.00 0.00 0.00 4.69
145 146 5.407502 TGTTCACATAGTTCTACATGACCG 58.592 41.667 0.00 0.00 0.00 4.79
146 147 8.942338 TTATGTTCACATAGTTCTACATGACC 57.058 34.615 0.00 0.00 39.69 4.02
148 149 9.936759 TGTTTATGTTCACATAGTTCTACATGA 57.063 29.630 0.00 0.00 39.69 3.07
154 155 8.567948 CCACTTTGTTTATGTTCACATAGTTCT 58.432 33.333 0.10 0.00 39.69 3.01
155 156 8.349983 ACCACTTTGTTTATGTTCACATAGTTC 58.650 33.333 0.10 0.00 39.69 3.01
156 157 8.232913 ACCACTTTGTTTATGTTCACATAGTT 57.767 30.769 0.10 0.00 39.69 2.24
157 158 7.817418 ACCACTTTGTTTATGTTCACATAGT 57.183 32.000 0.10 0.00 39.69 2.12
160 161 8.691797 ACTTAACCACTTTGTTTATGTTCACAT 58.308 29.630 0.00 0.00 40.22 3.21
161 162 8.057536 ACTTAACCACTTTGTTTATGTTCACA 57.942 30.769 0.00 0.00 0.00 3.58
205 206 4.187694 GCCAGGAAGACAAGAACTAGATG 58.812 47.826 0.00 0.00 0.00 2.90
208 209 3.007398 ACTGCCAGGAAGACAAGAACTAG 59.993 47.826 0.00 0.00 0.00 2.57
210 211 1.771255 ACTGCCAGGAAGACAAGAACT 59.229 47.619 0.00 0.00 0.00 3.01
211 212 1.876156 CACTGCCAGGAAGACAAGAAC 59.124 52.381 0.00 0.00 0.00 3.01
221 222 1.702182 TTTGCAATTCACTGCCAGGA 58.298 45.000 0.00 0.00 41.90 3.86
236 237 4.746611 ACTTGTATTCTTGCAAGCTTTTGC 59.253 37.500 21.99 3.32 46.09 3.68
238 239 6.476706 GTCAACTTGTATTCTTGCAAGCTTTT 59.523 34.615 21.99 8.32 46.09 2.27
239 240 5.979517 GTCAACTTGTATTCTTGCAAGCTTT 59.020 36.000 21.99 10.73 46.09 3.51
316 317 2.870411 GGTGTTGTATAACCCATCGAGC 59.130 50.000 0.00 0.00 35.92 5.03
323 324 4.482952 AGCTAGTGGTGTTGTATAACCC 57.517 45.455 0.00 1.99 35.92 4.11
343 344 4.794169 CCCGTCAATTTTCCACTTTGTAG 58.206 43.478 0.00 0.00 0.00 2.74
363 364 0.107654 AACTGAAGATAGCGGTGCCC 60.108 55.000 0.00 0.00 0.00 5.36
366 367 4.749245 AAACAAACTGAAGATAGCGGTG 57.251 40.909 0.00 0.00 0.00 4.94
374 375 7.338449 AGGCACTAACTTAAAACAAACTGAAGA 59.662 33.333 0.00 0.00 36.02 2.87
377 378 7.399245 AAGGCACTAACTTAAAACAAACTGA 57.601 32.000 0.00 0.00 38.49 3.41
378 379 9.394477 GATAAGGCACTAACTTAAAACAAACTG 57.606 33.333 0.00 0.00 38.49 3.16
379 380 9.350951 AGATAAGGCACTAACTTAAAACAAACT 57.649 29.630 0.00 0.00 38.49 2.66
382 383 9.344772 TGAAGATAAGGCACTAACTTAAAACAA 57.655 29.630 0.00 0.00 38.49 2.83
383 384 8.911918 TGAAGATAAGGCACTAACTTAAAACA 57.088 30.769 0.00 0.00 38.49 2.83
384 385 9.216117 TCTGAAGATAAGGCACTAACTTAAAAC 57.784 33.333 0.00 0.00 38.49 2.43
385 386 9.959721 ATCTGAAGATAAGGCACTAACTTAAAA 57.040 29.630 0.00 0.00 38.49 1.52
387 388 7.987458 CCATCTGAAGATAAGGCACTAACTTAA 59.013 37.037 0.00 0.00 34.42 1.85
389 390 6.352516 CCATCTGAAGATAAGGCACTAACTT 58.647 40.000 0.00 0.00 31.77 2.66
391 392 5.059833 CCCATCTGAAGATAAGGCACTAAC 58.940 45.833 0.00 0.00 31.77 2.34
392 393 4.444876 GCCCATCTGAAGATAAGGCACTAA 60.445 45.833 20.72 0.00 45.38 2.24
393 394 3.071602 GCCCATCTGAAGATAAGGCACTA 59.928 47.826 20.72 0.00 45.38 2.74
412 1452 5.802465 ACCTTTTTAACTACTCACTAGCCC 58.198 41.667 0.00 0.00 0.00 5.19
413 1453 7.741027 AAACCTTTTTAACTACTCACTAGCC 57.259 36.000 0.00 0.00 0.00 3.93
442 1500 7.201956 CCTGTCCAGCTAATATAGTGTTCTCTT 60.202 40.741 0.00 0.00 0.00 2.85
449 1507 3.324846 TGCCCTGTCCAGCTAATATAGTG 59.675 47.826 0.00 0.00 0.00 2.74
511 1584 7.062605 GCAGATAATTAATGGGCAAATGATTCG 59.937 37.037 0.00 0.00 0.00 3.34
515 1588 6.728089 TGCAGATAATTAATGGGCAAATGA 57.272 33.333 0.00 0.00 0.00 2.57
526 1599 5.682943 GGTAACGCCATGCAGATAATTAA 57.317 39.130 0.00 0.00 37.17 1.40
627 1702 4.821589 GAGAGCGTCTTGGCCCCG 62.822 72.222 0.00 0.00 0.00 5.73
628 1703 4.475135 GGAGAGCGTCTTGGCCCC 62.475 72.222 0.00 0.00 0.00 5.80
629 1704 4.821589 CGGAGAGCGTCTTGGCCC 62.822 72.222 0.00 0.00 0.00 5.80
724 1799 2.668550 GGCTGGGTGGACGTTGTC 60.669 66.667 0.00 0.00 0.00 3.18
725 1800 3.476031 CTGGCTGGGTGGACGTTGT 62.476 63.158 0.00 0.00 0.00 3.32
726 1801 2.469465 ATCTGGCTGGGTGGACGTTG 62.469 60.000 0.00 0.00 0.00 4.10
727 1802 2.185310 GATCTGGCTGGGTGGACGTT 62.185 60.000 0.00 0.00 0.00 3.99
728 1803 2.607750 ATCTGGCTGGGTGGACGT 60.608 61.111 0.00 0.00 0.00 4.34
729 1804 2.184020 TTGATCTGGCTGGGTGGACG 62.184 60.000 0.00 0.00 0.00 4.79
730 1805 0.257039 ATTGATCTGGCTGGGTGGAC 59.743 55.000 0.00 0.00 0.00 4.02
772 1847 3.181487 GCGATCGGGTAGTAGTAAACCAA 60.181 47.826 18.30 0.00 37.51 3.67
774 1849 2.287849 GGCGATCGGGTAGTAGTAAACC 60.288 54.545 18.30 0.24 34.85 3.27
843 1918 4.636435 AACACCACCCCTTCGCCG 62.636 66.667 0.00 0.00 0.00 6.46
939 2014 2.579787 CGCTCGACCACGTCATCC 60.580 66.667 0.00 0.00 40.69 3.51
975 2050 3.291101 GAGCGGTCGGCCAACTACA 62.291 63.158 6.96 0.00 45.17 2.74
1024 2099 2.156098 GGTACCATGCGAGGTCAAAAA 58.844 47.619 7.15 0.00 42.06 1.94
1029 2104 1.144057 CCTGGTACCATGCGAGGTC 59.856 63.158 16.75 0.00 42.06 3.85
1030 2105 0.324923 TACCTGGTACCATGCGAGGT 60.325 55.000 22.39 22.39 45.05 3.85
1031 2106 0.389391 CTACCTGGTACCATGCGAGG 59.611 60.000 16.75 15.20 37.76 4.63
1032 2107 1.112113 ACTACCTGGTACCATGCGAG 58.888 55.000 16.75 15.31 0.00 5.03
1033 2108 2.440517 TACTACCTGGTACCATGCGA 57.559 50.000 16.75 3.66 0.00 5.10
1034 2109 4.219944 ACATATACTACCTGGTACCATGCG 59.780 45.833 16.75 10.01 0.00 4.73
1035 2110 5.740290 ACATATACTACCTGGTACCATGC 57.260 43.478 16.75 0.00 0.00 4.06
1037 2112 8.898728 AGTACTACATATACTACCTGGTACCAT 58.101 37.037 16.75 3.80 30.94 3.55
1038 2113 8.280258 AGTACTACATATACTACCTGGTACCA 57.720 38.462 15.39 15.39 30.94 3.25
1040 2115 9.566432 ACAAGTACTACATATACTACCTGGTAC 57.434 37.037 1.49 0.00 32.47 3.34
1042 2117 8.910944 CAACAAGTACTACATATACTACCTGGT 58.089 37.037 4.05 4.05 32.47 4.00
1043 2118 8.358148 CCAACAAGTACTACATATACTACCTGG 58.642 40.741 0.00 0.00 32.47 4.45
1044 2119 8.910944 ACCAACAAGTACTACATATACTACCTG 58.089 37.037 0.00 0.00 32.47 4.00
1053 2128 8.917088 GGGAAGTATACCAACAAGTACTACATA 58.083 37.037 0.00 0.00 0.00 2.29
1054 2129 7.417116 CGGGAAGTATACCAACAAGTACTACAT 60.417 40.741 0.00 0.00 0.00 2.29
1055 2130 6.127647 CGGGAAGTATACCAACAAGTACTACA 60.128 42.308 0.00 0.00 0.00 2.74
1056 2131 6.268566 CGGGAAGTATACCAACAAGTACTAC 58.731 44.000 0.00 0.00 0.00 2.73
1057 2132 5.163519 GCGGGAAGTATACCAACAAGTACTA 60.164 44.000 0.00 0.00 0.00 1.82
1058 2133 4.382362 GCGGGAAGTATACCAACAAGTACT 60.382 45.833 0.00 0.00 0.00 2.73
1059 2134 3.867493 GCGGGAAGTATACCAACAAGTAC 59.133 47.826 0.00 0.00 0.00 2.73
1060 2135 3.514706 TGCGGGAAGTATACCAACAAGTA 59.485 43.478 0.00 0.00 0.00 2.24
1061 2136 2.303600 TGCGGGAAGTATACCAACAAGT 59.696 45.455 0.00 0.00 0.00 3.16
1062 2137 2.980568 TGCGGGAAGTATACCAACAAG 58.019 47.619 0.00 0.00 0.00 3.16
1063 2138 3.420300 TTGCGGGAAGTATACCAACAA 57.580 42.857 0.00 0.00 0.00 2.83
1064 2139 3.420300 TTTGCGGGAAGTATACCAACA 57.580 42.857 0.00 0.00 0.00 3.33
1096 2171 8.564574 GCGATTTTCCTTGAATATATACCAACA 58.435 33.333 0.00 0.00 0.00 3.33
1097 2172 8.021396 GGCGATTTTCCTTGAATATATACCAAC 58.979 37.037 0.00 0.00 0.00 3.77
1110 2185 5.232838 GCAGATAAATTGGCGATTTTCCTTG 59.767 40.000 17.45 11.86 38.80 3.61
1121 2201 8.400947 CACCTGTATATATGCAGATAAATTGGC 58.599 37.037 26.80 0.00 42.19 4.52
1125 2205 8.749354 TCGTCACCTGTATATATGCAGATAAAT 58.251 33.333 26.80 8.43 42.19 1.40
1134 2214 9.613957 CTTTTAGTCTCGTCACCTGTATATATG 57.386 37.037 0.00 0.00 0.00 1.78
1222 2302 1.875576 GCTATCGCCCTGATGAACTGG 60.876 57.143 0.00 0.00 37.99 4.00
1264 2344 2.733593 GGCGATACGGACGGATGC 60.734 66.667 0.00 0.00 0.00 3.91
1282 2362 2.042930 ATCCCCCTCTCCCACACC 59.957 66.667 0.00 0.00 0.00 4.16
1296 2376 3.929948 CGCGCGCCTTGAAGATCC 61.930 66.667 27.72 0.00 0.00 3.36
1335 2415 1.607628 GATCATACGCTGGGTAGACGT 59.392 52.381 10.41 0.00 39.08 4.34
1336 2416 1.068472 GGATCATACGCTGGGTAGACG 60.068 57.143 10.41 2.33 33.84 4.18
1354 2434 0.675083 TTCTACTTGGCGACGTTGGA 59.325 50.000 4.64 0.00 0.00 3.53
1358 2438 1.080974 CGGTTCTACTTGGCGACGT 60.081 57.895 0.00 0.00 0.00 4.34
1375 2455 3.359523 TCGTGGTCACCGAGGACG 61.360 66.667 0.00 0.00 38.70 4.79
1443 2523 2.406616 CGGCCAAAGCGCAGGTATT 61.407 57.895 11.47 0.00 41.24 1.89
1461 2541 2.047443 AGAGCGACGACCTCCTTCC 61.047 63.158 0.00 0.00 0.00 3.46
1480 2560 2.313172 CGTATCCAGATGCCTGCGC 61.313 63.158 0.00 0.00 39.07 6.09
1483 2563 1.665916 CGCCGTATCCAGATGCCTG 60.666 63.158 0.00 0.00 40.09 4.85
1485 2565 3.044305 GCGCCGTATCCAGATGCC 61.044 66.667 0.00 0.00 0.00 4.40
1622 2702 4.017126 GGCCCTTTTTCTACTAATGTGCT 58.983 43.478 0.00 0.00 0.00 4.40
1665 2745 2.531771 TCCACAACCGGAACAGATAGA 58.468 47.619 9.46 0.00 29.93 1.98
1721 2801 3.320541 TCGTGTAAGAACCGGGACTAAAA 59.679 43.478 6.32 0.00 0.00 1.52
1745 2825 2.501610 GAGGTCCATCTGTCCCGC 59.498 66.667 0.00 0.00 0.00 6.13
1819 2899 0.260230 TGCCTTTTGGTCCCTGTTGA 59.740 50.000 0.00 0.00 42.99 3.18
1824 2904 0.251787 GTGGATGCCTTTTGGTCCCT 60.252 55.000 0.00 0.00 42.99 4.20
1844 2924 4.694233 CCTGCCAGCTGCTGACGT 62.694 66.667 30.10 0.00 41.11 4.34
1889 2978 1.132977 CCAAAACCCCTAAACCACCCT 60.133 52.381 0.00 0.00 0.00 4.34
2124 3220 4.220382 GTGGGTGAAATGAACATGGATTGA 59.780 41.667 0.00 0.00 0.00 2.57
2286 3383 9.443283 GATGATCATGTGCTAAGAACAATTAAC 57.557 33.333 14.30 0.00 0.00 2.01
2352 3449 8.275040 AGTCAGGGTCTATATTGTTTTATGCTT 58.725 33.333 0.00 0.00 0.00 3.91
2479 3576 6.974965 AGTGGAGACATGAAAATCAAAGAAC 58.025 36.000 0.00 0.00 46.14 3.01
2505 3602 8.792633 CAACTGTCCATACCAGATTTCTAAAAA 58.207 33.333 0.00 0.00 34.04 1.94
3242 4343 6.112734 GGGTTTTGAAGACCATGAAAGTTTT 58.887 36.000 7.23 0.00 38.98 2.43
3295 4396 2.598565 TCGACTAGCTTATCCCATGCT 58.401 47.619 0.00 0.00 40.53 3.79
3463 4569 1.356979 CGATCGAGGTCTGTGCGAT 59.643 57.895 10.26 0.00 46.22 4.58
3478 4584 2.261671 GACTGGTGCCACGACGAT 59.738 61.111 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.