Multiple sequence alignment - TraesCS4B01G134500

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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 TraesCS4B01G134500 chr4B 100.000 3012 0 0 1 3012 175535975 175538986 0.000000e+00 5563.0
1 TraesCS4B01G134500 chr4B 100.000 1389 0 0 3291 4679 175539265 175540653 0.000000e+00 2566.0
2 TraesCS4B01G134500 chr4A 94.908 2219 91 9 759 2970 462219510 462217307 0.000000e+00 3452.0
3 TraesCS4B01G134500 chr4A 96.209 1398 41 6 3291 4679 462216889 462215495 0.000000e+00 2278.0
4 TraesCS4B01G134500 chr4A 90.323 93 8 1 142 233 704224549 704224641 2.290000e-23 121.0
5 TraesCS4B01G134500 chr4A 89.247 93 9 1 142 233 704170805 704170897 1.060000e-21 115.0
6 TraesCS4B01G134500 chr4D 93.780 2283 82 22 759 3010 115047849 115050102 0.000000e+00 3374.0
7 TraesCS4B01G134500 chr4D 97.135 1396 22 7 3291 4679 115050147 115051531 0.000000e+00 2340.0
8 TraesCS4B01G134500 chr2B 93.353 346 22 1 932 1277 275457918 275457574 1.160000e-140 510.0
9 TraesCS4B01G134500 chr2B 81.659 229 34 6 497 724 66521413 66521634 2.880000e-42 183.0
10 TraesCS4B01G134500 chr2B 96.000 75 2 1 1 74 58770366 58770292 2.290000e-23 121.0
11 TraesCS4B01G134500 chr2B 93.750 80 3 2 1 78 152507445 152507524 8.220000e-23 119.0
12 TraesCS4B01G134500 chr2B 94.805 77 2 2 1 76 197939060 197938985 8.220000e-23 119.0
13 TraesCS4B01G134500 chr5B 92.416 356 23 4 373 725 313435005 313434651 5.400000e-139 505.0
14 TraesCS4B01G134500 chr5B 94.262 244 12 2 1035 1277 25482881 25483123 5.720000e-99 372.0
15 TraesCS4B01G134500 chr5B 97.541 122 3 0 1035 1156 661259593 661259714 4.740000e-50 209.0
16 TraesCS4B01G134500 chr5B 95.833 72 3 0 1 72 95791236 95791307 2.960000e-22 117.0
17 TraesCS4B01G134500 chr5B 100.000 38 0 0 932 969 25482844 25482881 2.340000e-08 71.3
18 TraesCS4B01G134500 chr5A 91.292 356 27 4 373 725 530067907 530067553 2.530000e-132 483.0
19 TraesCS4B01G134500 chr5A 87.560 209 20 4 376 578 624121433 624121641 2.180000e-58 237.0
20 TraesCS4B01G134500 chr5A 82.511 223 34 4 484 703 640408311 640408091 1.720000e-44 191.0
21 TraesCS4B01G134500 chr5A 88.421 95 10 1 142 235 530068797 530068703 3.830000e-21 113.0
22 TraesCS4B01G134500 chr6B 96.296 243 9 0 1035 1277 651366685 651366443 2.620000e-107 399.0
23 TraesCS4B01G134500 chr6B 95.473 243 11 0 1035 1277 76227831 76227589 5.680000e-104 388.0
24 TraesCS4B01G134500 chr6B 95.041 242 12 0 1035 1276 671657596 671657837 9.500000e-102 381.0
25 TraesCS4B01G134500 chr6B 91.667 84 6 1 1 83 216900351 216900268 1.060000e-21 115.0
26 TraesCS4B01G134500 chr6B 97.368 38 1 0 477 514 68903361 68903324 1.090000e-06 65.8
27 TraesCS4B01G134500 chr3B 95.473 243 11 0 1035 1277 748485473 748485715 5.680000e-104 388.0
28 TraesCS4B01G134500 chr3B 92.683 82 6 0 1 82 775413736 775413817 8.220000e-23 119.0
29 TraesCS4B01G134500 chr3B 100.000 38 0 0 932 969 748485436 748485473 2.340000e-08 71.3
30 TraesCS4B01G134500 chr1D 82.707 266 42 4 462 725 367841515 367841778 2.820000e-57 233.0
31 TraesCS4B01G134500 chr1D 79.121 91 16 3 142 231 143249615 143249703 5.060000e-05 60.2
32 TraesCS4B01G134500 chr5D 78.723 329 45 20 381 700 5575991 5575679 3.690000e-46 196.0
33 TraesCS4B01G134500 chr6D 91.367 139 7 3 1033 1170 452249444 452249578 8.000000e-43 185.0
34 TraesCS4B01G134500 chr6D 92.593 81 4 2 1 79 288785750 288785670 1.060000e-21 115.0
35 TraesCS4B01G134500 chr1B 91.398 93 7 1 142 233 377263947 377264039 4.920000e-25 126.0
36 TraesCS4B01G134500 chr1B 89.109 101 8 2 142 239 576057660 576057560 6.360000e-24 122.0
37 TraesCS4B01G134500 chr7D 94.737 76 3 1 1 75 242903942 242903867 2.960000e-22 117.0
38 TraesCS4B01G134500 chr7B 92.683 82 3 3 1 79 175023796 175023877 1.060000e-21 115.0
39 TraesCS4B01G134500 chr7B 88.776 98 5 2 142 233 403410680 403410583 1.060000e-21 115.0
40 TraesCS4B01G134500 chr7B 83.333 66 8 3 142 206 718088223 718088160 1.820000e-04 58.4
41 TraesCS4B01G134500 chr7B 96.774 31 1 0 138 168 554169315 554169345 8.000000e-03 52.8


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 TraesCS4B01G134500 chr4B 175535975 175540653 4678 False 4064.5 5563 100.0000 1 4679 2 chr4B.!!$F1 4678
1 TraesCS4B01G134500 chr4A 462215495 462219510 4015 True 2865.0 3452 95.5585 759 4679 2 chr4A.!!$R1 3920
2 TraesCS4B01G134500 chr4D 115047849 115051531 3682 False 2857.0 3374 95.4575 759 4679 2 chr4D.!!$F1 3920
3 TraesCS4B01G134500 chr5A 530067553 530068797 1244 True 298.0 483 89.8565 142 725 2 chr5A.!!$R2 583

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
23 24 0.027848 GAGTCGATCCGAACCGAGTC 59.972 60.0 12.59 12.59 44.50 3.36 F
113 114 0.030235 GGTTTCCCAACAGTTGCGTC 59.970 55.0 7.88 0.00 34.15 5.19 F
381 577 0.107410 AGTTGCACCACTCAAACCGA 60.107 50.0 0.00 0.00 0.00 4.69 F
731 1394 0.301687 CGAGTTTGATTCCATCGCGG 59.698 55.0 6.13 0.00 0.00 6.46 F
1278 1955 0.453390 GCAAGGATTCCAAGAAGCGG 59.547 55.0 5.29 0.00 0.00 5.52 F
1279 1956 0.453390 CAAGGATTCCAAGAAGCGGC 59.547 55.0 5.29 0.00 0.00 6.53 F
1280 1957 0.681243 AAGGATTCCAAGAAGCGGCC 60.681 55.0 5.29 0.00 0.00 6.13 F
2930 3626 0.830648 ACCGTATGCAGCAGGTACAT 59.169 50.0 0.00 0.00 34.83 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 2303 0.178915 TTTCCTGGGAAGGGACGAGA 60.179 55.000 2.19 0.00 35.38 4.04 R
1933 2610 1.745653 TCCATGAGCTCTACAGTCACG 59.254 52.381 16.19 0.00 0.00 4.35 R
2217 2896 6.486993 GGTTAAGGCTATACTGCTTGCTAAAT 59.513 38.462 0.00 0.00 0.00 1.40 R
2597 3278 1.000827 ACTTCTCTGTCTGCACACTCG 60.001 52.381 0.00 0.00 0.00 4.18 R
2703 3385 3.120616 TCGAGTAATCAGCAAAACGTTCG 59.879 43.478 0.00 0.00 0.00 3.95 R
2833 3529 4.753610 TGAAGAGAGTTTCTGTGCTTCATG 59.246 41.667 0.00 0.00 37.43 3.07 R
2972 3668 4.818546 CCACATGTTCTCAGTTTGTCTTCT 59.181 41.667 0.00 0.00 0.00 2.85 R
4644 5461 1.337447 CCCTGCAAACAAATCCAGCTG 60.337 52.381 6.78 6.78 0.00 4.24 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
19 20 0.989890 GTTTGAGTCGATCCGAACCG 59.010 55.000 8.23 0.00 37.72 4.44
20 21 0.883153 TTTGAGTCGATCCGAACCGA 59.117 50.000 0.00 0.00 37.72 4.69
21 22 0.450583 TTGAGTCGATCCGAACCGAG 59.549 55.000 0.00 0.00 37.72 4.63
22 23 0.675837 TGAGTCGATCCGAACCGAGT 60.676 55.000 0.00 0.00 40.67 4.18
23 24 0.027848 GAGTCGATCCGAACCGAGTC 59.972 60.000 12.59 12.59 44.50 3.36
24 25 0.675837 AGTCGATCCGAACCGAGTCA 60.676 55.000 0.00 0.00 37.72 3.41
25 26 0.522915 GTCGATCCGAACCGAGTCAC 60.523 60.000 0.00 0.00 37.72 3.67
26 27 1.582937 CGATCCGAACCGAGTCACG 60.583 63.158 0.00 0.00 42.18 4.35
27 28 1.798735 GATCCGAACCGAGTCACGA 59.201 57.895 0.00 0.00 45.77 4.35
28 29 0.248134 GATCCGAACCGAGTCACGAG 60.248 60.000 0.00 0.00 45.77 4.18
29 30 2.267681 ATCCGAACCGAGTCACGAGC 62.268 60.000 0.00 0.00 45.77 5.03
30 31 2.561885 CGAACCGAGTCACGAGCT 59.438 61.111 0.00 0.00 45.77 4.09
31 32 1.642037 CCGAACCGAGTCACGAGCTA 61.642 60.000 0.00 0.00 45.77 3.32
32 33 0.520827 CGAACCGAGTCACGAGCTAC 60.521 60.000 0.00 0.00 45.77 3.58
33 34 0.803740 GAACCGAGTCACGAGCTACT 59.196 55.000 0.00 0.00 45.77 2.57
34 35 1.199558 GAACCGAGTCACGAGCTACTT 59.800 52.381 0.00 0.00 45.77 2.24
35 36 0.522180 ACCGAGTCACGAGCTACTTG 59.478 55.000 0.00 0.00 45.77 3.16
36 37 0.522180 CCGAGTCACGAGCTACTTGT 59.478 55.000 0.00 0.00 45.77 3.16
37 38 1.068472 CCGAGTCACGAGCTACTTGTT 60.068 52.381 0.00 0.00 45.77 2.83
38 39 2.607282 CCGAGTCACGAGCTACTTGTTT 60.607 50.000 0.00 0.00 45.77 2.83
39 40 3.365666 CCGAGTCACGAGCTACTTGTTTA 60.366 47.826 0.00 0.00 45.77 2.01
40 41 3.846896 CGAGTCACGAGCTACTTGTTTAG 59.153 47.826 0.00 0.00 45.77 1.85
41 42 3.576648 AGTCACGAGCTACTTGTTTAGC 58.423 45.455 0.00 0.00 44.27 3.09
47 48 1.625616 GCTACTTGTTTAGCTCGCGA 58.374 50.000 9.26 9.26 41.24 5.87
48 49 1.584308 GCTACTTGTTTAGCTCGCGAG 59.416 52.381 31.37 31.37 41.24 5.03
77 78 1.451449 TTTTTCCAGCCCTAGTCCCA 58.549 50.000 0.00 0.00 0.00 4.37
78 79 0.696501 TTTTCCAGCCCTAGTCCCAC 59.303 55.000 0.00 0.00 0.00 4.61
79 80 0.178873 TTTCCAGCCCTAGTCCCACT 60.179 55.000 0.00 0.00 0.00 4.00
80 81 0.617820 TTCCAGCCCTAGTCCCACTC 60.618 60.000 0.00 0.00 0.00 3.51
81 82 1.306141 CCAGCCCTAGTCCCACTCA 60.306 63.158 0.00 0.00 0.00 3.41
82 83 0.692419 CCAGCCCTAGTCCCACTCAT 60.692 60.000 0.00 0.00 0.00 2.90
83 84 0.467384 CAGCCCTAGTCCCACTCATG 59.533 60.000 0.00 0.00 0.00 3.07
84 85 0.043334 AGCCCTAGTCCCACTCATGT 59.957 55.000 0.00 0.00 0.00 3.21
85 86 0.179000 GCCCTAGTCCCACTCATGTG 59.821 60.000 0.00 0.00 43.45 3.21
86 87 1.866015 CCCTAGTCCCACTCATGTGA 58.134 55.000 0.94 0.00 46.55 3.58
87 88 2.402564 CCCTAGTCCCACTCATGTGAT 58.597 52.381 0.94 0.00 46.55 3.06
88 89 2.103771 CCCTAGTCCCACTCATGTGATG 59.896 54.545 0.94 0.00 46.55 3.07
89 90 2.103771 CCTAGTCCCACTCATGTGATGG 59.896 54.545 0.94 5.73 46.55 3.51
91 92 4.247781 CCCACTCATGTGATGGGC 57.752 61.111 17.01 0.00 46.52 5.36
92 93 1.820906 CCCACTCATGTGATGGGCG 60.821 63.158 17.01 2.40 46.52 6.13
93 94 1.078214 CCACTCATGTGATGGGCGT 60.078 57.895 0.94 0.00 46.55 5.68
94 95 1.371337 CCACTCATGTGATGGGCGTG 61.371 60.000 0.94 0.00 46.55 5.34
95 96 1.078214 ACTCATGTGATGGGCGTGG 60.078 57.895 0.94 0.00 32.68 4.94
96 97 1.078214 CTCATGTGATGGGCGTGGT 60.078 57.895 0.00 0.00 0.00 4.16
97 98 0.677731 CTCATGTGATGGGCGTGGTT 60.678 55.000 0.00 0.00 0.00 3.67
98 99 0.251121 TCATGTGATGGGCGTGGTTT 60.251 50.000 0.00 0.00 0.00 3.27
99 100 0.171007 CATGTGATGGGCGTGGTTTC 59.829 55.000 0.00 0.00 0.00 2.78
100 101 0.965363 ATGTGATGGGCGTGGTTTCC 60.965 55.000 0.00 0.00 0.00 3.13
101 102 2.034999 TGATGGGCGTGGTTTCCC 59.965 61.111 0.00 0.00 42.93 3.97
105 106 2.519780 GGGCGTGGTTTCCCAACA 60.520 61.111 0.00 0.00 44.15 3.33
106 107 2.561037 GGGCGTGGTTTCCCAACAG 61.561 63.158 0.00 0.00 44.15 3.16
107 108 1.826487 GGCGTGGTTTCCCAACAGT 60.826 57.895 0.00 0.00 44.15 3.55
108 109 1.388837 GGCGTGGTTTCCCAACAGTT 61.389 55.000 0.00 0.00 44.15 3.16
109 110 0.248866 GCGTGGTTTCCCAACAGTTG 60.249 55.000 6.28 6.28 44.15 3.16
110 111 0.248866 CGTGGTTTCCCAACAGTTGC 60.249 55.000 7.88 0.00 44.15 4.17
111 112 0.248866 GTGGTTTCCCAACAGTTGCG 60.249 55.000 7.88 0.00 44.15 4.85
112 113 0.681564 TGGTTTCCCAACAGTTGCGT 60.682 50.000 7.88 0.00 37.98 5.24
113 114 0.030235 GGTTTCCCAACAGTTGCGTC 59.970 55.000 7.88 0.00 34.15 5.19
114 115 1.021968 GTTTCCCAACAGTTGCGTCT 58.978 50.000 7.88 0.00 32.54 4.18
115 116 1.002792 GTTTCCCAACAGTTGCGTCTC 60.003 52.381 7.88 0.00 32.54 3.36
116 117 0.878523 TTCCCAACAGTTGCGTCTCG 60.879 55.000 7.88 0.00 0.00 4.04
117 118 1.594293 CCCAACAGTTGCGTCTCGT 60.594 57.895 7.88 0.00 0.00 4.18
118 119 1.157870 CCCAACAGTTGCGTCTCGTT 61.158 55.000 7.88 0.00 0.00 3.85
119 120 0.655733 CCAACAGTTGCGTCTCGTTT 59.344 50.000 7.88 0.00 0.00 3.60
120 121 1.063469 CCAACAGTTGCGTCTCGTTTT 59.937 47.619 7.88 0.00 0.00 2.43
121 122 2.477189 CCAACAGTTGCGTCTCGTTTTT 60.477 45.455 7.88 0.00 0.00 1.94
140 141 5.930837 TTTTTCAGGGTCAACAATTGAGT 57.069 34.783 13.59 0.00 41.01 3.41
148 149 4.379652 GGTCAACAATTGAGTGGCATTTT 58.620 39.130 13.59 0.00 41.01 1.82
153 154 7.599998 GTCAACAATTGAGTGGCATTTTCTATT 59.400 33.333 13.59 0.00 41.01 1.73
159 160 1.926510 GTGGCATTTTCTATTTGGCGC 59.073 47.619 0.00 0.00 38.65 6.53
162 163 1.589779 GCATTTTCTATTTGGCGCTGC 59.410 47.619 7.64 0.00 0.00 5.25
184 185 1.574134 GCGCCGTTTATAGCCTGTTA 58.426 50.000 0.00 0.00 0.00 2.41
186 187 1.862827 CGCCGTTTATAGCCTGTTACC 59.137 52.381 0.00 0.00 0.00 2.85
188 189 2.476821 CCGTTTATAGCCTGTTACCGG 58.523 52.381 0.00 0.00 0.00 5.28
252 447 2.287668 GCTCGCTTAGCCTATCTTTCGA 60.288 50.000 0.00 0.00 46.25 3.71
254 449 4.551388 CTCGCTTAGCCTATCTTTCGATT 58.449 43.478 0.00 0.00 0.00 3.34
256 451 4.037565 TCGCTTAGCCTATCTTTCGATTGA 59.962 41.667 0.00 0.00 0.00 2.57
267 462 7.764443 CCTATCTTTCGATTGAGTTACCAAAGA 59.236 37.037 0.00 0.00 33.98 2.52
285 480 7.091443 ACCAAAGAACAAAAATTACACGACAA 58.909 30.769 0.00 0.00 0.00 3.18
288 483 7.964545 AAGAACAAAAATTACACGACAACTC 57.035 32.000 0.00 0.00 0.00 3.01
290 485 4.839796 ACAAAAATTACACGACAACTCGG 58.160 39.130 0.00 0.00 44.80 4.63
295 490 1.596603 TACACGACAACTCGGAGTCA 58.403 50.000 11.71 0.00 44.80 3.41
306 501 1.344763 CTCGGAGTCAAACCAAGGACT 59.655 52.381 0.00 0.00 46.51 3.85
321 516 3.662247 AGGACTTCCTACTTCACAACG 57.338 47.619 0.00 0.00 46.48 4.10
327 523 1.684450 TCCTACTTCACAACGCACTCA 59.316 47.619 0.00 0.00 0.00 3.41
337 533 1.263217 CAACGCACTCAAGTAACCACC 59.737 52.381 0.00 0.00 0.00 4.61
346 542 2.359478 GTAACCACCCCGCCACAG 60.359 66.667 0.00 0.00 0.00 3.66
353 549 2.751436 CCCCGCCACAGGAACATG 60.751 66.667 0.00 0.00 0.00 3.21
358 554 1.081242 GCCACAGGAACATGTTGCG 60.081 57.895 22.31 18.82 32.91 4.85
376 572 1.225855 CGCTAAGTTGCACCACTCAA 58.774 50.000 0.00 0.00 0.00 3.02
377 573 1.601903 CGCTAAGTTGCACCACTCAAA 59.398 47.619 0.00 0.00 0.00 2.69
378 574 2.602217 CGCTAAGTTGCACCACTCAAAC 60.602 50.000 0.00 0.00 0.00 2.93
379 575 2.287608 GCTAAGTTGCACCACTCAAACC 60.288 50.000 0.00 0.00 0.00 3.27
380 576 0.738389 AAGTTGCACCACTCAAACCG 59.262 50.000 0.00 0.00 0.00 4.44
381 577 0.107410 AGTTGCACCACTCAAACCGA 60.107 50.000 0.00 0.00 0.00 4.69
383 579 0.950836 TTGCACCACTCAAACCGATG 59.049 50.000 0.00 0.00 0.00 3.84
393 933 5.221048 CCACTCAAACCGATGAACTTTTTCT 60.221 40.000 0.00 0.00 32.36 2.52
394 934 5.682862 CACTCAAACCGATGAACTTTTTCTG 59.317 40.000 0.00 0.00 32.36 3.02
399 939 7.978975 TCAAACCGATGAACTTTTTCTGAAAAT 59.021 29.630 15.63 2.02 34.45 1.82
505 1166 8.947055 TGATGAACTATTTCTCAAATCGATGA 57.053 30.769 0.00 0.00 32.36 2.92
507 1168 9.643652 GATGAACTATTTCTCAAATCGATGAAC 57.356 33.333 0.00 0.00 32.36 3.18
541 1203 8.118893 ACTTTGTGAATTTTGTCTCAAAATCG 57.881 30.769 16.99 0.00 39.31 3.34
546 1208 8.134261 TGTGAATTTTGTCTCAAAATCGATGAA 58.866 29.630 16.99 3.77 0.00 2.57
610 1272 4.811555 AAATGATAAATAAGCAGCGCGA 57.188 36.364 12.10 0.00 0.00 5.87
625 1287 1.463805 CGCGACCATACTAGTTCACG 58.536 55.000 0.00 2.19 0.00 4.35
658 1320 3.684305 GCCATTAAAAATCACAAGTGGCC 59.316 43.478 0.00 0.00 43.76 5.36
666 1329 0.687920 TCACAAGTGGCCAATCGGTA 59.312 50.000 7.24 0.00 33.28 4.02
684 1347 2.547826 GTATGGTGGTCGGCTAAGTTC 58.452 52.381 0.00 0.00 0.00 3.01
701 1364 0.951558 TTCGAACAAGCCTTGCCTTC 59.048 50.000 3.88 1.10 0.00 3.46
704 1367 2.027192 TCGAACAAGCCTTGCCTTCTAT 60.027 45.455 3.88 0.00 0.00 1.98
718 1381 3.679083 GCCTTCTATAGTGGTGCGAGTTT 60.679 47.826 13.30 0.00 0.00 2.66
725 1388 1.202758 AGTGGTGCGAGTTTGATTCCA 60.203 47.619 0.00 0.00 0.00 3.53
726 1389 1.812571 GTGGTGCGAGTTTGATTCCAT 59.187 47.619 0.00 0.00 0.00 3.41
727 1390 2.083774 TGGTGCGAGTTTGATTCCATC 58.916 47.619 0.00 0.00 0.00 3.51
728 1391 1.062587 GGTGCGAGTTTGATTCCATCG 59.937 52.381 0.00 0.00 36.51 3.84
730 1393 3.786955 CGAGTTTGATTCCATCGCG 57.213 52.632 0.00 0.00 0.00 5.87
731 1394 0.301687 CGAGTTTGATTCCATCGCGG 59.698 55.000 6.13 0.00 0.00 6.46
732 1395 0.657840 GAGTTTGATTCCATCGCGGG 59.342 55.000 6.13 0.00 34.36 6.13
733 1396 1.064134 GTTTGATTCCATCGCGGGC 59.936 57.895 6.13 0.00 34.36 6.13
734 1397 2.118404 TTTGATTCCATCGCGGGCC 61.118 57.895 6.13 0.00 34.36 5.80
735 1398 4.908687 TGATTCCATCGCGGGCCG 62.909 66.667 24.35 24.35 38.61 6.13
754 1417 3.604667 CCCAACAAAGGCGCTGCA 61.605 61.111 7.64 0.00 0.00 4.41
755 1418 2.049802 CCAACAAAGGCGCTGCAG 60.050 61.111 10.11 10.11 0.00 4.41
756 1419 2.049802 CAACAAAGGCGCTGCAGG 60.050 61.111 17.12 6.85 0.00 4.85
757 1420 2.203337 AACAAAGGCGCTGCAGGA 60.203 55.556 17.12 0.00 0.00 3.86
795 1459 1.568504 TCTAACTGAATGGGCCGAGT 58.431 50.000 0.00 0.00 0.00 4.18
876 1553 1.103398 CCATCCGTTCTGGCCAATCC 61.103 60.000 7.01 0.00 37.80 3.01
896 1573 2.363975 ATTCTCGCCGGCCCTGTTA 61.364 57.895 23.46 1.48 0.00 2.41
981 1658 1.018910 GCCGTTGTGTGTTAGGTTGT 58.981 50.000 0.00 0.00 0.00 3.32
1265 1942 1.273606 CCACGAGAAGAAGAGCAAGGA 59.726 52.381 0.00 0.00 0.00 3.36
1277 1954 1.399791 GAGCAAGGATTCCAAGAAGCG 59.600 52.381 5.29 0.00 0.00 4.68
1278 1955 0.453390 GCAAGGATTCCAAGAAGCGG 59.547 55.000 5.29 0.00 0.00 5.52
1279 1956 0.453390 CAAGGATTCCAAGAAGCGGC 59.547 55.000 5.29 0.00 0.00 6.53
1280 1957 0.681243 AAGGATTCCAAGAAGCGGCC 60.681 55.000 5.29 0.00 0.00 6.13
1281 1958 2.472909 GGATTCCAAGAAGCGGCCG 61.473 63.158 24.05 24.05 0.00 6.13
1282 1959 3.113386 GATTCCAAGAAGCGGCCGC 62.113 63.158 42.34 42.34 42.33 6.53
1334 2011 1.906824 TGCGGAAGAAGGAGACGGT 60.907 57.895 0.00 0.00 0.00 4.83
1365 2042 2.125961 GGAGTATGACCGGCCGTCT 61.126 63.158 26.12 8.60 42.49 4.18
1392 2069 3.414700 GTGGTCTGCCTCAACGCG 61.415 66.667 3.53 3.53 35.27 6.01
1401 2078 2.417516 CTCAACGCGATCCGGGAT 59.582 61.111 15.93 9.85 42.31 3.85
1626 2303 1.224120 TCATGCCCCTTCCTCCTCTAT 59.776 52.381 0.00 0.00 0.00 1.98
1650 2327 1.305297 CCCTTCCCAGGAAAAGGCC 60.305 63.158 12.98 0.00 44.19 5.19
1742 2419 4.306600 CACCAGGAACAAGGTTTAATTGC 58.693 43.478 0.00 0.00 36.89 3.56
1947 2624 5.008217 GTGAATATCTCGTGACTGTAGAGCT 59.992 44.000 0.00 0.00 32.42 4.09
2295 2976 3.265791 CTGTCAAGTCCTAGCATTGTCC 58.734 50.000 0.00 0.00 0.00 4.02
2357 3038 5.505181 ACAGGTCATTGATGGACTAAAGT 57.495 39.130 0.00 0.00 35.61 2.66
2488 3169 5.238583 ACAGTGGCAAGAAATCTACTACAC 58.761 41.667 0.00 0.00 0.00 2.90
2597 3278 7.334858 AGAGGAGAAGACATCAAAGGTAATTC 58.665 38.462 0.00 0.00 0.00 2.17
2634 3315 5.950549 AGAGAAGTCCCGTTCATTCTTACTA 59.049 40.000 0.00 0.00 32.31 1.82
2635 3316 6.436532 AGAGAAGTCCCGTTCATTCTTACTAA 59.563 38.462 0.00 0.00 32.31 2.24
2640 3321 9.901172 AAGTCCCGTTCATTCTTACTAAATTAT 57.099 29.630 0.00 0.00 0.00 1.28
2681 3362 7.970614 GTCCTGAATTCATGGTTCATAGTTTTC 59.029 37.037 8.96 0.00 35.26 2.29
2686 3368 6.899393 TTCATGGTTCATAGTTTTCAGCTT 57.101 33.333 0.00 0.00 0.00 3.74
2724 3406 3.120616 TCGAACGTTTTGCTGATTACTCG 59.879 43.478 0.46 0.00 0.00 4.18
2725 3407 3.120616 CGAACGTTTTGCTGATTACTCGA 59.879 43.478 0.46 0.00 0.00 4.04
2726 3408 4.375606 CGAACGTTTTGCTGATTACTCGAA 60.376 41.667 0.46 0.00 0.00 3.71
2727 3409 4.385244 ACGTTTTGCTGATTACTCGAAC 57.615 40.909 0.00 0.00 0.00 3.95
2728 3410 3.805422 ACGTTTTGCTGATTACTCGAACA 59.195 39.130 0.00 0.00 0.00 3.18
2729 3411 4.141680 CGTTTTGCTGATTACTCGAACAC 58.858 43.478 0.00 0.00 0.00 3.32
2730 3412 4.084537 CGTTTTGCTGATTACTCGAACACT 60.085 41.667 0.00 0.00 0.00 3.55
2731 3413 4.990543 TTTGCTGATTACTCGAACACTG 57.009 40.909 0.00 0.00 0.00 3.66
2732 3414 2.337583 TGCTGATTACTCGAACACTGC 58.662 47.619 0.00 0.00 0.00 4.40
2733 3415 2.288763 TGCTGATTACTCGAACACTGCA 60.289 45.455 0.00 0.00 33.04 4.41
2735 3417 3.372206 GCTGATTACTCGAACACTGCAAT 59.628 43.478 0.00 0.00 0.00 3.56
2736 3418 4.726021 GCTGATTACTCGAACACTGCAATG 60.726 45.833 0.00 0.00 0.00 2.82
2737 3419 4.314961 TGATTACTCGAACACTGCAATGT 58.685 39.130 0.00 0.00 0.00 2.71
2738 3420 4.388773 TGATTACTCGAACACTGCAATGTC 59.611 41.667 0.00 0.00 30.55 3.06
2739 3421 2.533266 ACTCGAACACTGCAATGTCT 57.467 45.000 0.00 0.00 30.55 3.41
2757 3453 9.129209 GCAATGTCTTTTACTTATTTTCAGGTC 57.871 33.333 0.00 0.00 0.00 3.85
2826 3522 3.967332 AAGGTTTTGCTAGTAGCCGTA 57.033 42.857 19.41 2.31 41.51 4.02
2833 3529 6.419771 GTTTTGCTAGTAGCCGTAAATGATC 58.580 40.000 19.41 2.90 41.51 2.92
2841 3537 3.544684 AGCCGTAAATGATCATGAAGCA 58.455 40.909 9.46 1.25 0.00 3.91
2880 3576 6.200878 TCCCTTAAACTGGAAATTCTCACT 57.799 37.500 0.00 0.00 0.00 3.41
2895 3591 2.568509 TCTCACTGTGAATGATGGCTCA 59.431 45.455 12.16 0.00 35.41 4.26
2930 3626 0.830648 ACCGTATGCAGCAGGTACAT 59.169 50.000 0.00 0.00 34.83 2.29
2935 3631 3.561310 CGTATGCAGCAGGTACATTGAAT 59.439 43.478 0.00 0.00 0.00 2.57
2971 3667 7.687941 TTCTTTTTGTGACATTCCCTATCTC 57.312 36.000 0.00 0.00 0.00 2.75
2972 3668 6.778821 TCTTTTTGTGACATTCCCTATCTCA 58.221 36.000 0.00 0.00 0.00 3.27
2979 3675 5.127845 GTGACATTCCCTATCTCAGAAGACA 59.872 44.000 0.00 0.00 33.32 3.41
2995 3691 4.818546 AGAAGACAAACTGAGAACATGTGG 59.181 41.667 0.00 0.00 0.00 4.17
3328 4136 3.921119 TGATTTTTAGCTGCACCACTG 57.079 42.857 1.02 0.00 0.00 3.66
3333 4141 5.584253 TTTTTAGCTGCACCACTGTTTTA 57.416 34.783 1.02 0.00 0.00 1.52
3733 4542 2.721090 GAGCAATTTTGTCAGCGTCAAC 59.279 45.455 0.00 0.00 0.00 3.18
3753 4562 6.368791 GTCAACTGTTTTGCCTTCTTCTTTTT 59.631 34.615 0.00 0.00 0.00 1.94
3800 4609 3.920231 ATCTCTTGCCTTGATGTAGCA 57.080 42.857 0.00 0.00 33.97 3.49
3904 4716 3.632145 AGGAACTGTTGCGATGAGTTTTT 59.368 39.130 6.39 0.00 37.18 1.94
3972 4784 6.671190 TGTATGTTCTGACAGAATTTTGCAG 58.329 36.000 20.43 11.60 39.58 4.41
3976 4788 2.031769 TCTGACAGAATTTTGCAGCACG 60.032 45.455 1.64 0.00 0.00 5.34
4026 4838 2.416893 GTCTTCTTGAATGGAAGGCGTC 59.583 50.000 0.00 0.00 40.17 5.19
4030 4843 3.420893 TCTTGAATGGAAGGCGTCATTT 58.579 40.909 2.23 0.00 34.18 2.32
4644 5461 1.875963 CGGAAATGCCACACTGACC 59.124 57.895 0.00 0.00 35.94 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.989890 CGGTTCGGATCGACTCAAAC 59.010 55.000 0.00 0.00 34.89 2.93
1 2 0.883153 TCGGTTCGGATCGACTCAAA 59.117 50.000 0.00 0.00 34.89 2.69
2 3 0.450583 CTCGGTTCGGATCGACTCAA 59.549 55.000 0.00 0.00 34.89 3.02
3 4 0.675837 ACTCGGTTCGGATCGACTCA 60.676 55.000 0.00 0.00 34.89 3.41
4 5 0.027848 GACTCGGTTCGGATCGACTC 59.972 60.000 0.00 0.00 34.89 3.36
5 6 0.675837 TGACTCGGTTCGGATCGACT 60.676 55.000 0.00 0.00 34.89 4.18
6 7 0.522915 GTGACTCGGTTCGGATCGAC 60.523 60.000 0.00 0.00 34.89 4.20
7 8 1.798735 GTGACTCGGTTCGGATCGA 59.201 57.895 0.00 0.00 0.00 3.59
8 9 1.582937 CGTGACTCGGTTCGGATCG 60.583 63.158 0.00 0.00 35.71 3.69
9 10 0.248134 CTCGTGACTCGGTTCGGATC 60.248 60.000 0.00 0.00 40.32 3.36
10 11 1.801332 CTCGTGACTCGGTTCGGAT 59.199 57.895 0.00 0.00 40.32 4.18
11 12 2.974489 GCTCGTGACTCGGTTCGGA 61.974 63.158 0.00 0.00 40.32 4.55
12 13 1.642037 TAGCTCGTGACTCGGTTCGG 61.642 60.000 0.00 0.00 40.32 4.30
13 14 0.520827 GTAGCTCGTGACTCGGTTCG 60.521 60.000 0.00 0.00 40.32 3.95
14 15 0.803740 AGTAGCTCGTGACTCGGTTC 59.196 55.000 0.00 0.00 40.32 3.62
15 16 1.068472 CAAGTAGCTCGTGACTCGGTT 60.068 52.381 0.00 0.00 40.32 4.44
16 17 0.522180 CAAGTAGCTCGTGACTCGGT 59.478 55.000 0.00 0.00 40.32 4.69
17 18 0.522180 ACAAGTAGCTCGTGACTCGG 59.478 55.000 0.00 0.00 40.32 4.63
18 19 2.333389 AACAAGTAGCTCGTGACTCG 57.667 50.000 0.00 0.00 41.41 4.18
19 20 3.608939 GCTAAACAAGTAGCTCGTGACTC 59.391 47.826 0.00 0.00 42.73 3.36
20 21 3.576648 GCTAAACAAGTAGCTCGTGACT 58.423 45.455 0.00 0.00 42.73 3.41
21 22 3.974585 GCTAAACAAGTAGCTCGTGAC 57.025 47.619 0.00 0.00 42.73 3.67
28 29 1.584308 CTCGCGAGCTAAACAAGTAGC 59.416 52.381 25.07 0.00 45.77 3.58
58 59 1.074889 GTGGGACTAGGGCTGGAAAAA 59.925 52.381 0.00 0.00 0.00 1.94
59 60 0.696501 GTGGGACTAGGGCTGGAAAA 59.303 55.000 0.00 0.00 0.00 2.29
60 61 0.178873 AGTGGGACTAGGGCTGGAAA 60.179 55.000 0.00 0.00 0.00 3.13
61 62 0.617820 GAGTGGGACTAGGGCTGGAA 60.618 60.000 0.00 0.00 0.00 3.53
62 63 1.001760 GAGTGGGACTAGGGCTGGA 59.998 63.158 0.00 0.00 0.00 3.86
63 64 0.692419 ATGAGTGGGACTAGGGCTGG 60.692 60.000 0.00 0.00 0.00 4.85
64 65 0.467384 CATGAGTGGGACTAGGGCTG 59.533 60.000 0.00 0.00 0.00 4.85
65 66 0.043334 ACATGAGTGGGACTAGGGCT 59.957 55.000 0.00 0.00 0.00 5.19
66 67 0.179000 CACATGAGTGGGACTAGGGC 59.821 60.000 0.00 0.00 42.13 5.19
67 68 1.866015 TCACATGAGTGGGACTAGGG 58.134 55.000 0.00 0.00 45.91 3.53
68 69 2.103771 CCATCACATGAGTGGGACTAGG 59.896 54.545 0.00 0.00 41.43 3.02
69 70 3.465742 CCATCACATGAGTGGGACTAG 57.534 52.381 0.00 0.00 41.43 2.57
75 76 1.078214 ACGCCCATCACATGAGTGG 60.078 57.895 0.00 4.23 45.91 4.00
77 78 1.078214 CCACGCCCATCACATGAGT 60.078 57.895 0.00 0.00 0.00 3.41
78 79 0.677731 AACCACGCCCATCACATGAG 60.678 55.000 0.00 0.00 0.00 2.90
79 80 0.251121 AAACCACGCCCATCACATGA 60.251 50.000 0.00 0.00 0.00 3.07
80 81 0.171007 GAAACCACGCCCATCACATG 59.829 55.000 0.00 0.00 0.00 3.21
81 82 0.965363 GGAAACCACGCCCATCACAT 60.965 55.000 0.00 0.00 0.00 3.21
82 83 1.602323 GGAAACCACGCCCATCACA 60.602 57.895 0.00 0.00 0.00 3.58
83 84 3.274067 GGAAACCACGCCCATCAC 58.726 61.111 0.00 0.00 0.00 3.06
95 96 1.002792 GAGACGCAACTGTTGGGAAAC 60.003 52.381 34.78 25.11 45.47 2.78
96 97 1.305201 GAGACGCAACTGTTGGGAAA 58.695 50.000 34.78 0.00 45.47 3.13
97 98 0.878523 CGAGACGCAACTGTTGGGAA 60.879 55.000 34.78 0.00 45.47 3.97
98 99 1.300620 CGAGACGCAACTGTTGGGA 60.301 57.895 34.78 0.00 45.47 4.37
100 101 0.655733 AAACGAGACGCAACTGTTGG 59.344 50.000 21.01 13.53 0.00 3.77
101 102 2.452006 AAAACGAGACGCAACTGTTG 57.548 45.000 15.98 15.98 0.00 3.33
118 119 5.395103 CCACTCAATTGTTGACCCTGAAAAA 60.395 40.000 5.13 0.00 35.46 1.94
119 120 4.099266 CCACTCAATTGTTGACCCTGAAAA 59.901 41.667 5.13 0.00 35.46 2.29
120 121 3.636300 CCACTCAATTGTTGACCCTGAAA 59.364 43.478 5.13 0.00 35.46 2.69
121 122 3.221771 CCACTCAATTGTTGACCCTGAA 58.778 45.455 5.13 0.00 35.46 3.02
122 123 2.862541 CCACTCAATTGTTGACCCTGA 58.137 47.619 5.13 0.00 35.46 3.86
123 124 1.270550 GCCACTCAATTGTTGACCCTG 59.729 52.381 5.13 0.00 35.46 4.45
124 125 1.133513 TGCCACTCAATTGTTGACCCT 60.134 47.619 5.13 0.00 35.46 4.34
125 126 1.327303 TGCCACTCAATTGTTGACCC 58.673 50.000 5.13 0.00 35.46 4.46
126 127 3.665745 AATGCCACTCAATTGTTGACC 57.334 42.857 5.13 0.71 35.46 4.02
127 128 5.291971 AGAAAATGCCACTCAATTGTTGAC 58.708 37.500 5.13 0.00 35.46 3.18
128 129 5.534207 AGAAAATGCCACTCAATTGTTGA 57.466 34.783 5.13 0.00 38.17 3.18
129 130 7.894376 AATAGAAAATGCCACTCAATTGTTG 57.106 32.000 5.13 4.23 0.00 3.33
130 131 7.388500 CCAAATAGAAAATGCCACTCAATTGTT 59.612 33.333 5.13 0.00 0.00 2.83
131 132 6.875195 CCAAATAGAAAATGCCACTCAATTGT 59.125 34.615 5.13 0.00 0.00 2.71
132 133 6.183360 GCCAAATAGAAAATGCCACTCAATTG 60.183 38.462 0.00 0.00 0.00 2.32
133 134 5.876460 GCCAAATAGAAAATGCCACTCAATT 59.124 36.000 0.00 0.00 0.00 2.32
134 135 5.422145 GCCAAATAGAAAATGCCACTCAAT 58.578 37.500 0.00 0.00 0.00 2.57
135 136 4.617995 CGCCAAATAGAAAATGCCACTCAA 60.618 41.667 0.00 0.00 0.00 3.02
136 137 3.119531 CGCCAAATAGAAAATGCCACTCA 60.120 43.478 0.00 0.00 0.00 3.41
137 138 3.438360 CGCCAAATAGAAAATGCCACTC 58.562 45.455 0.00 0.00 0.00 3.51
138 139 2.417243 GCGCCAAATAGAAAATGCCACT 60.417 45.455 0.00 0.00 0.00 4.00
139 140 1.926510 GCGCCAAATAGAAAATGCCAC 59.073 47.619 0.00 0.00 0.00 5.01
140 141 1.824230 AGCGCCAAATAGAAAATGCCA 59.176 42.857 2.29 0.00 0.00 4.92
148 149 2.114670 GCCTGCAGCGCCAAATAGA 61.115 57.895 8.66 0.00 0.00 1.98
159 160 1.934463 CTATAAACGGCGCCTGCAG 59.066 57.895 26.68 11.62 45.35 4.41
162 163 3.330275 GGCTATAAACGGCGCCTG 58.670 61.111 26.68 20.24 39.42 4.85
171 172 4.516323 GGTTTCCGGTAACAGGCTATAAA 58.484 43.478 23.28 0.00 0.00 1.40
197 198 1.821332 AGCTAAATCGGCTGCAGGC 60.821 57.895 29.31 29.31 38.73 4.85
254 449 9.575783 GTGTAATTTTTGTTCTTTGGTAACTCA 57.424 29.630 0.00 0.00 37.61 3.41
256 451 8.460428 TCGTGTAATTTTTGTTCTTTGGTAACT 58.540 29.630 0.00 0.00 37.61 2.24
267 462 5.064962 TCCGAGTTGTCGTGTAATTTTTGTT 59.935 36.000 0.00 0.00 45.30 2.83
279 474 1.537562 GGTTTGACTCCGAGTTGTCGT 60.538 52.381 1.71 0.00 45.30 4.34
285 480 1.070289 GTCCTTGGTTTGACTCCGAGT 59.930 52.381 0.00 0.00 35.33 4.18
288 483 2.143925 GAAGTCCTTGGTTTGACTCCG 58.856 52.381 0.00 0.00 40.84 4.63
290 485 3.493767 AGGAAGTCCTTGGTTTGACTC 57.506 47.619 0.00 0.00 46.09 3.36
295 490 4.165372 TGTGAAGTAGGAAGTCCTTGGTTT 59.835 41.667 4.91 0.00 46.09 3.27
306 501 2.101750 TGAGTGCGTTGTGAAGTAGGAA 59.898 45.455 0.00 0.00 0.00 3.36
311 506 2.024176 ACTTGAGTGCGTTGTGAAGT 57.976 45.000 0.00 0.00 0.00 3.01
320 515 0.953960 GGGGTGGTTACTTGAGTGCG 60.954 60.000 0.00 0.00 0.00 5.34
321 516 0.953960 CGGGGTGGTTACTTGAGTGC 60.954 60.000 0.00 0.00 0.00 4.40
327 523 2.406002 CTGTGGCGGGGTGGTTACTT 62.406 60.000 0.00 0.00 0.00 2.24
337 533 1.603455 AACATGTTCCTGTGGCGGG 60.603 57.895 4.92 0.00 0.00 6.13
346 542 2.584791 CAACTTAGCGCAACATGTTCC 58.415 47.619 11.47 0.00 0.00 3.62
353 549 0.660300 GTGGTGCAACTTAGCGCAAC 60.660 55.000 11.47 5.45 46.43 4.17
358 554 2.287608 GGTTTGAGTGGTGCAACTTAGC 60.288 50.000 2.04 0.00 36.74 3.09
376 572 6.701400 CCATTTTCAGAAAAAGTTCATCGGTT 59.299 34.615 12.38 0.00 37.76 4.44
377 573 6.183360 ACCATTTTCAGAAAAAGTTCATCGGT 60.183 34.615 12.38 6.50 37.76 4.69
378 574 6.144402 CACCATTTTCAGAAAAAGTTCATCGG 59.856 38.462 12.38 5.98 37.76 4.18
379 575 6.917477 TCACCATTTTCAGAAAAAGTTCATCG 59.083 34.615 12.38 2.40 37.76 3.84
380 576 8.542953 GTTCACCATTTTCAGAAAAAGTTCATC 58.457 33.333 12.38 0.00 37.76 2.92
381 577 8.260114 AGTTCACCATTTTCAGAAAAAGTTCAT 58.740 29.630 12.38 0.00 37.76 2.57
383 579 8.479313 AAGTTCACCATTTTCAGAAAAAGTTC 57.521 30.769 12.38 6.56 37.76 3.01
515 1177 9.232082 CGATTTTGAGACAAAATTCACAAAGTA 57.768 29.630 18.85 0.00 37.37 2.24
610 1272 6.038050 GCTAAGAGTACGTGAACTAGTATGGT 59.962 42.308 0.00 0.00 0.00 3.55
625 1287 6.905609 GTGATTTTTAATGGCGCTAAGAGTAC 59.094 38.462 7.64 0.00 0.00 2.73
658 1320 1.157870 GCCGACCACCATACCGATTG 61.158 60.000 0.00 0.00 0.00 2.67
666 1329 0.108329 CGAACTTAGCCGACCACCAT 60.108 55.000 0.00 0.00 0.00 3.55
684 1347 1.808411 TAGAAGGCAAGGCTTGTTCG 58.192 50.000 26.71 3.46 0.00 3.95
701 1364 4.508124 GGAATCAAACTCGCACCACTATAG 59.492 45.833 0.00 0.00 0.00 1.31
704 1367 2.037902 TGGAATCAAACTCGCACCACTA 59.962 45.455 0.00 0.00 0.00 2.74
718 1381 4.908687 CGGCCCGCGATGGAATCA 62.909 66.667 8.23 0.00 45.97 2.57
735 1398 4.362476 CAGCGCCTTTGTTGGGCC 62.362 66.667 2.29 0.00 46.24 5.80
737 1400 3.562779 CTGCAGCGCCTTTGTTGGG 62.563 63.158 2.29 0.00 0.00 4.12
738 1401 2.049802 CTGCAGCGCCTTTGTTGG 60.050 61.111 2.29 0.00 0.00 3.77
739 1402 2.049802 CCTGCAGCGCCTTTGTTG 60.050 61.111 8.66 0.00 0.00 3.33
740 1403 2.203337 TCCTGCAGCGCCTTTGTT 60.203 55.556 8.66 0.00 0.00 2.83
741 1404 2.670934 CTCCTGCAGCGCCTTTGT 60.671 61.111 8.66 0.00 0.00 2.83
742 1405 4.112341 GCTCCTGCAGCGCCTTTG 62.112 66.667 8.66 0.00 38.76 2.77
750 1413 2.435586 CCCAACGAGCTCCTGCAG 60.436 66.667 6.78 6.78 42.74 4.41
751 1414 4.704833 GCCCAACGAGCTCCTGCA 62.705 66.667 8.47 0.00 42.74 4.41
752 1415 2.914777 CTAGCCCAACGAGCTCCTGC 62.915 65.000 8.47 3.88 41.83 4.85
753 1416 1.142748 CTAGCCCAACGAGCTCCTG 59.857 63.158 8.47 5.80 41.83 3.86
754 1417 2.060980 CCTAGCCCAACGAGCTCCT 61.061 63.158 8.47 0.27 41.83 3.69
755 1418 2.501610 CCTAGCCCAACGAGCTCC 59.498 66.667 8.47 0.00 41.83 4.70
756 1419 2.202946 GCCTAGCCCAACGAGCTC 60.203 66.667 2.73 2.73 41.83 4.09
757 1420 3.787001 GGCCTAGCCCAACGAGCT 61.787 66.667 0.00 0.00 44.06 4.09
896 1573 1.001517 TCTCCTCTGCTCTCGCACT 60.002 57.895 0.00 0.00 42.25 4.40
1265 1942 3.134127 GCGGCCGCTTCTTGGAAT 61.134 61.111 41.71 0.00 38.26 3.01
1300 1977 0.812014 CGCACGGGTATGGCATTACA 60.812 55.000 4.78 0.00 0.00 2.41
1301 1978 1.503818 CCGCACGGGTATGGCATTAC 61.504 60.000 4.78 1.89 0.00 1.89
1334 2011 1.882189 ATACTCCACCCGGTCCTCCA 61.882 60.000 0.00 0.00 0.00 3.86
1345 2022 2.106332 CGGCCGGTCATACTCCAC 59.894 66.667 20.10 0.00 0.00 4.02
1365 2042 0.690762 GGCAGACCACCAGGAACTTA 59.309 55.000 0.00 0.00 38.69 2.24
1407 2084 2.444706 TCCTCCTCAGATGCCCCG 60.445 66.667 0.00 0.00 0.00 5.73
1626 2303 0.178915 TTTCCTGGGAAGGGACGAGA 60.179 55.000 2.19 0.00 35.38 4.04
1650 2327 4.259810 CGGATGTTAATACTCACTTGCACG 60.260 45.833 0.00 0.00 0.00 5.34
1933 2610 1.745653 TCCATGAGCTCTACAGTCACG 59.254 52.381 16.19 0.00 0.00 4.35
1972 2649 9.928236 GATAGAGACAACAGAAAATGAATTAGC 57.072 33.333 0.00 0.00 0.00 3.09
2217 2896 6.486993 GGTTAAGGCTATACTGCTTGCTAAAT 59.513 38.462 0.00 0.00 0.00 1.40
2488 3169 4.094442 GTGGTAAGCTTTGTAATTCTCCCG 59.906 45.833 3.20 0.00 0.00 5.14
2597 3278 1.000827 ACTTCTCTGTCTGCACACTCG 60.001 52.381 0.00 0.00 0.00 4.18
2634 3315 9.060347 CAGGACATGCATGTAAGTAGATAATTT 57.940 33.333 31.45 4.26 41.95 1.82
2635 3316 8.432013 TCAGGACATGCATGTAAGTAGATAATT 58.568 33.333 31.45 4.73 41.95 1.40
2640 3321 5.675684 TTCAGGACATGCATGTAAGTAGA 57.324 39.130 31.45 20.54 41.95 2.59
2681 3362 6.658831 TCGAAAGTTTAATCAACTGAAGCTG 58.341 36.000 0.00 0.00 45.77 4.24
2686 3368 6.592798 ACGTTCGAAAGTTTAATCAACTGA 57.407 33.333 11.11 0.00 45.77 3.41
2703 3385 3.120616 TCGAGTAATCAGCAAAACGTTCG 59.879 43.478 0.00 0.00 0.00 3.95
2724 3406 9.463443 AAATAAGTAAAAGACATTGCAGTGTTC 57.537 29.630 16.63 9.55 31.16 3.18
2725 3407 9.816354 AAAATAAGTAAAAGACATTGCAGTGTT 57.184 25.926 16.63 2.90 31.16 3.32
2726 3408 9.463443 GAAAATAAGTAAAAGACATTGCAGTGT 57.537 29.630 15.46 15.46 34.39 3.55
2727 3409 9.462174 TGAAAATAAGTAAAAGACATTGCAGTG 57.538 29.630 7.79 7.79 0.00 3.66
2728 3410 9.683069 CTGAAAATAAGTAAAAGACATTGCAGT 57.317 29.630 0.00 0.00 0.00 4.40
2729 3411 9.132521 CCTGAAAATAAGTAAAAGACATTGCAG 57.867 33.333 0.00 0.00 0.00 4.41
2730 3412 8.637986 ACCTGAAAATAAGTAAAAGACATTGCA 58.362 29.630 0.00 0.00 0.00 4.08
2731 3413 9.129209 GACCTGAAAATAAGTAAAAGACATTGC 57.871 33.333 0.00 0.00 0.00 3.56
2735 3417 8.846211 CCTTGACCTGAAAATAAGTAAAAGACA 58.154 33.333 0.00 0.00 0.00 3.41
2736 3418 9.063615 TCCTTGACCTGAAAATAAGTAAAAGAC 57.936 33.333 0.00 0.00 0.00 3.01
2737 3419 9.635404 TTCCTTGACCTGAAAATAAGTAAAAGA 57.365 29.630 0.00 0.00 0.00 2.52
2826 3522 6.433404 AGAGTTTCTGTGCTTCATGATCATTT 59.567 34.615 5.16 0.00 0.00 2.32
2833 3529 4.753610 TGAAGAGAGTTTCTGTGCTTCATG 59.246 41.667 0.00 0.00 37.43 3.07
2841 3537 6.688073 TTAAGGGATGAAGAGAGTTTCTGT 57.312 37.500 0.00 0.00 35.91 3.41
2971 3667 5.277683 CCACATGTTCTCAGTTTGTCTTCTG 60.278 44.000 0.00 0.00 0.00 3.02
2972 3668 4.818546 CCACATGTTCTCAGTTTGTCTTCT 59.181 41.667 0.00 0.00 0.00 2.85
2979 3675 5.182001 GCTATGTTCCACATGTTCTCAGTTT 59.818 40.000 0.00 0.00 39.53 2.66
3309 4117 3.923017 ACAGTGGTGCAGCTAAAAATC 57.077 42.857 18.08 0.00 0.00 2.17
3328 4136 9.250624 TGCCACAACACAGTTATTAATTAAAAC 57.749 29.630 1.21 8.20 0.00 2.43
3333 4141 6.040391 ACAGTGCCACAACACAGTTATTAATT 59.960 34.615 0.00 0.00 43.23 1.40
3753 4562 3.967401 TCGACACACGAGAATTACACAA 58.033 40.909 0.00 0.00 46.45 3.33
3754 4563 3.629438 TCGACACACGAGAATTACACA 57.371 42.857 0.00 0.00 46.45 3.72
3904 4716 8.376942 GCAAAAACTTACATTTCGTCTTCAAAA 58.623 29.630 0.00 0.00 0.00 2.44
3972 4784 6.074569 ACAACATAAACTATTTTTGTGCGTGC 60.075 34.615 0.00 0.00 0.00 5.34
4026 4838 5.336878 CGTACAACGCGGATTTTAAAATG 57.663 39.130 17.98 6.08 33.65 2.32
4644 5461 1.337447 CCCTGCAAACAAATCCAGCTG 60.337 52.381 6.78 6.78 0.00 4.24


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

AutoCloner maintained by Alex Coulton.