Multiple sequence alignment - TraesCS2A01G550900

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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 TraesCS2A01G550900 chr2A 100.000 6898 0 0 1 6898 757954327 757947430 0.000000e+00 12739.0
1 TraesCS2A01G550900 chr2D 97.040 2466 53 11 3992 6439 627253509 627251046 0.000000e+00 4132.0
2 TraesCS2A01G550900 chr2D 89.848 2492 113 44 26 2419 627257488 627255039 0.000000e+00 3072.0
3 TraesCS2A01G550900 chr2D 95.928 1498 33 10 2420 3909 627254993 627253516 0.000000e+00 2403.0
4 TraesCS2A01G550900 chr2D 94.118 187 9 1 6591 6777 627251028 627250844 4.070000e-72 283.0
5 TraesCS2A01G550900 chr2D 95.556 45 2 0 6854 6898 627250755 627250711 9.600000e-09 73.1
6 TraesCS2A01G550900 chr2B 90.438 1893 98 30 549 2418 769082837 769081005 0.000000e+00 2416.0
7 TraesCS2A01G550900 chr2B 92.269 1591 89 17 2423 4001 769080953 769079385 0.000000e+00 2226.0
8 TraesCS2A01G550900 chr2B 90.424 1013 55 17 4168 5148 769079382 769078380 0.000000e+00 1295.0
9 TraesCS2A01G550900 chr2B 88.558 638 51 14 5801 6437 769077339 769076723 0.000000e+00 754.0
10 TraesCS2A01G550900 chr2B 92.308 299 22 1 5440 5737 769077815 769077517 2.300000e-114 424.0
11 TraesCS2A01G550900 chr2B 90.045 221 19 3 5194 5414 769078384 769078167 4.070000e-72 283.0
12 TraesCS2A01G550900 chr2B 84.071 226 15 13 6563 6777 769076721 769076506 1.520000e-46 198.0
13 TraesCS2A01G550900 chr2B 93.103 116 7 1 6782 6897 769076421 769076307 1.190000e-37 169.0
14 TraesCS2A01G550900 chr2B 76.949 295 32 17 120 378 769083378 769083084 1.210000e-27 135.0
15 TraesCS2A01G550900 chr2B 79.375 160 23 7 6563 6715 769076183 769076027 3.400000e-18 104.0
16 TraesCS2A01G550900 chr7A 97.857 140 2 1 6428 6567 77440676 77440538 2.490000e-59 241.0
17 TraesCS2A01G550900 chr6A 97.810 137 3 0 6430 6566 617047912 617047776 3.220000e-58 237.0
18 TraesCS2A01G550900 chr6A 97.761 134 3 0 6438 6571 349575055 349574922 1.500000e-56 231.0
19 TraesCS2A01G550900 chr1A 97.163 141 3 1 6431 6571 213289385 213289524 3.220000e-58 237.0
20 TraesCS2A01G550900 chr1A 99.225 129 1 0 6437 6565 12159812 12159684 4.160000e-57 233.0
21 TraesCS2A01G550900 chr5A 97.810 137 2 1 6429 6565 668160086 668159951 1.160000e-57 235.0
22 TraesCS2A01G550900 chr4A 96.479 142 3 1 6437 6576 513376009 513375868 4.160000e-57 233.0
23 TraesCS2A01G550900 chr3A 97.761 134 2 1 6436 6569 569426422 569426554 5.380000e-56 230.0
24 TraesCS2A01G550900 chr3B 93.377 151 9 1 6415 6564 53574037 53573887 9.010000e-54 222.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G550900 chr2A 757947430 757954327 6897 True 12739.00 12739 100.000 1 6898 1 chr2A.!!$R1 6897
1 TraesCS2A01G550900 chr2D 627250711 627257488 6777 True 1992.62 4132 94.498 26 6898 5 chr2D.!!$R1 6872
2 TraesCS2A01G550900 chr2B 769076027 769083378 7351 True 800.40 2416 87.754 120 6897 10 chr2B.!!$R1 6777

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
28 29 0.673985 TCACCGGAATATCTCCAGCG 59.326 55.0 9.46 0.0 45.74 5.18 F
1108 1280 0.532573 GTGGCGACTGATCTCTTCCA 59.467 55.0 0.00 0.0 0.00 3.53 F
1301 1473 0.891373 CACCACCACCACAACAACAA 59.109 50.0 0.00 0.0 0.00 2.83 F
2829 3068 0.386476 AGCACATGCACACAAACCAG 59.614 50.0 6.64 0.0 45.16 4.00 F
3126 3368 0.397187 TGGCGCCTACCAACAACTTA 59.603 50.0 29.70 0.0 36.55 2.24 F
4152 4405 2.024176 TCAGTACAGCCCTTTGGAGA 57.976 50.0 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2202 0.247460 TCTCAAGCCAGATGGTGACG 59.753 55.000 0.00 0.0 37.57 4.35 R
2581 2820 2.285743 AGGGAGGGGCTCTTCCAC 60.286 66.667 15.93 6.1 44.03 4.02 R
3094 3336 2.722094 AGGCGCCATGTGAAAATTAGA 58.278 42.857 31.54 0.0 0.00 2.10 R
4485 4752 0.545171 CCATGTGCTCCCTGACTGAT 59.455 55.000 0.00 0.0 0.00 2.90 R
4587 4854 2.936202 ACCAGCAATATGACCATGTCC 58.064 47.619 0.00 0.0 0.00 4.02 R
6004 6778 1.766143 GCAACTATTCCTGGCGCTCG 61.766 60.000 7.64 0.0 0.00 5.03 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 4.506886 AATCGACTCTCACCGGAATATC 57.493 45.455 9.46 0.00 0.00 1.63
22 23 3.210232 TCGACTCTCACCGGAATATCT 57.790 47.619 9.46 0.00 0.00 1.98
23 24 3.139850 TCGACTCTCACCGGAATATCTC 58.860 50.000 9.46 0.00 0.00 2.75
24 25 2.226912 CGACTCTCACCGGAATATCTCC 59.773 54.545 9.46 0.00 41.40 3.71
25 26 3.223435 GACTCTCACCGGAATATCTCCA 58.777 50.000 9.46 0.00 45.74 3.86
26 27 3.226777 ACTCTCACCGGAATATCTCCAG 58.773 50.000 9.46 0.00 45.74 3.86
27 28 1.964223 TCTCACCGGAATATCTCCAGC 59.036 52.381 9.46 0.00 45.74 4.85
28 29 0.673985 TCACCGGAATATCTCCAGCG 59.326 55.000 9.46 0.00 45.74 5.18
29 30 0.946221 CACCGGAATATCTCCAGCGC 60.946 60.000 9.46 0.00 45.74 5.92
30 31 1.734477 CCGGAATATCTCCAGCGCG 60.734 63.158 0.00 0.00 45.74 6.86
31 32 1.007271 CGGAATATCTCCAGCGCGT 60.007 57.895 8.43 0.00 45.74 6.01
38 39 1.873270 ATCTCCAGCGCGTACACACA 61.873 55.000 8.43 0.00 0.00 3.72
54 59 0.877071 CACATCACCTCCAACAGTGC 59.123 55.000 0.00 0.00 33.90 4.40
126 145 1.377202 GCAAGAGATTCCCCACGCA 60.377 57.895 0.00 0.00 0.00 5.24
151 170 2.122413 AGATAGGCGGCCCATCCA 60.122 61.111 21.46 0.92 34.01 3.41
163 182 2.597340 CATCCAGCCCGGTTCCAT 59.403 61.111 0.00 0.00 35.57 3.41
170 189 3.334891 CCCGGTTCCATCCCACCA 61.335 66.667 0.00 0.00 31.84 4.17
188 207 4.664677 CCACCGCCCGATCCGATC 62.665 72.222 0.00 0.00 0.00 3.69
190 209 4.916314 ACCGCCCGATCCGATCCT 62.916 66.667 2.69 0.00 0.00 3.24
196 217 1.531840 CCGATCCGATCCTCCACCT 60.532 63.158 2.69 0.00 0.00 4.00
203 224 1.810606 CGATCCTCCACCTCATCCCG 61.811 65.000 0.00 0.00 0.00 5.14
248 281 4.692475 CCCCCGGAAGCGTTTCGT 62.692 66.667 0.73 0.00 33.98 3.85
316 368 3.023735 GGGGGCAGGAGGGTCATT 61.024 66.667 0.00 0.00 0.00 2.57
322 374 4.115199 AGGAGGGTCATTGCGCCC 62.115 66.667 4.18 0.00 45.16 6.13
375 430 1.336056 GCTAGCGCTGGTGGTATAGAC 60.336 57.143 22.90 0.00 0.00 2.59
391 458 9.786105 GTGGTATAGACTACTCTGTTTAAGAAC 57.214 37.037 0.00 0.00 34.36 3.01
464 551 4.247380 GCCTGCCCTCCTGGATCG 62.247 72.222 0.00 0.00 35.39 3.69
491 588 4.547859 CCAGAGGGATTTCGCAGG 57.452 61.111 0.00 0.00 35.59 4.85
494 591 1.616628 AGAGGGATTTCGCAGGGGT 60.617 57.895 0.00 0.00 0.00 4.95
506 620 4.070265 AGGGGTGATCCGGTCCGA 62.070 66.667 14.39 0.00 36.01 4.55
538 682 2.362120 AGGTTCGGGATCGGTCGT 60.362 61.111 0.00 0.00 36.95 4.34
539 683 2.103736 GGTTCGGGATCGGTCGTC 59.896 66.667 0.00 0.00 36.95 4.20
540 684 2.277756 GTTCGGGATCGGTCGTCG 60.278 66.667 4.03 4.03 40.90 5.12
541 685 4.183686 TTCGGGATCGGTCGTCGC 62.184 66.667 5.36 0.00 39.05 5.19
569 713 1.966451 GTTGGTGAGGGCGGAGTTG 60.966 63.158 0.00 0.00 0.00 3.16
570 714 3.190738 TTGGTGAGGGCGGAGTTGG 62.191 63.158 0.00 0.00 0.00 3.77
820 988 1.658686 TTTCGGCGTGGTTTGTTGCT 61.659 50.000 6.85 0.00 0.00 3.91
821 989 2.329678 TTCGGCGTGGTTTGTTGCTG 62.330 55.000 6.85 0.00 35.04 4.41
822 990 2.027460 GGCGTGGTTTGTTGCTGG 59.973 61.111 0.00 0.00 0.00 4.85
823 991 2.781158 GGCGTGGTTTGTTGCTGGT 61.781 57.895 0.00 0.00 0.00 4.00
848 1016 1.652563 GTTGGTTGGTCGGTTGCTC 59.347 57.895 0.00 0.00 0.00 4.26
864 1032 3.932545 TGCTCTTGTTGTTGTTGTTGT 57.067 38.095 0.00 0.00 0.00 3.32
906 1074 3.391382 GTGCCTCGCTAGTGGGGT 61.391 66.667 23.20 0.00 0.00 4.95
907 1075 3.390521 TGCCTCGCTAGTGGGGTG 61.391 66.667 23.20 0.00 0.00 4.61
908 1076 4.162690 GCCTCGCTAGTGGGGTGG 62.163 72.222 23.20 11.57 42.19 4.61
1088 1260 5.054390 GGATTGCTTGTTCCGTTGAATTA 57.946 39.130 0.00 0.00 31.98 1.40
1090 1262 5.335661 GGATTGCTTGTTCCGTTGAATTAGT 60.336 40.000 0.00 0.00 31.98 2.24
1108 1280 0.532573 GTGGCGACTGATCTCTTCCA 59.467 55.000 0.00 0.00 0.00 3.53
1113 1285 1.747924 CGACTGATCTCTTCCAGCTCA 59.252 52.381 0.00 0.00 33.90 4.26
1251 1423 1.078426 GTTCCACCAGGGGATCACG 60.078 63.158 0.00 0.00 36.67 4.35
1301 1473 0.891373 CACCACCACCACAACAACAA 59.109 50.000 0.00 0.00 0.00 2.83
1302 1474 0.892063 ACCACCACCACAACAACAAC 59.108 50.000 0.00 0.00 0.00 3.32
1303 1475 0.891373 CCACCACCACAACAACAACA 59.109 50.000 0.00 0.00 0.00 3.33
1306 1478 2.094286 CACCACCACAACAACAACATGT 60.094 45.455 0.00 0.00 34.24 3.21
1344 1516 3.311110 AGCGACGTCACCATGGGT 61.311 61.111 18.09 3.52 35.62 4.51
1480 1661 4.622456 GCAACGTGCCGGTGGTTG 62.622 66.667 22.07 22.07 45.43 3.77
1488 1669 2.825982 CCGGTGGTTGTCCAGTCA 59.174 61.111 0.00 0.00 45.24 3.41
1569 1753 4.070552 GTCACCGGCTCGCCTTCT 62.071 66.667 0.00 0.00 0.00 2.85
1578 1762 1.882989 GCTCGCCTTCTGAGTGGAGT 61.883 60.000 3.45 0.00 35.85 3.85
1702 1890 3.006752 TGATGGAGTTTGCCAATTTGGTC 59.993 43.478 16.62 9.59 42.16 4.02
1827 2015 2.094700 TCAGTTTCTAGCAGCACTACCG 60.095 50.000 0.00 0.00 0.00 4.02
1896 2084 3.363178 GAACTGCACTTGGTTTCTTTCG 58.637 45.455 0.00 0.00 0.00 3.46
1897 2085 1.676006 ACTGCACTTGGTTTCTTTCGG 59.324 47.619 0.00 0.00 0.00 4.30
2014 2202 7.032377 AGAAAGAAAGAGAACCATGTCAAAC 57.968 36.000 0.00 0.00 0.00 2.93
2052 2240 7.811713 GCTTGAGAATTGCTTCTAAGAAACAAT 59.188 33.333 0.00 0.00 41.87 2.71
2238 2426 6.647229 TGTCTAAGTATCTCTTCTCCGTACA 58.353 40.000 0.00 0.00 37.56 2.90
2250 2438 4.866508 TCTCCGTACATGTTCTGTTCTT 57.133 40.909 2.30 0.00 39.39 2.52
2284 2475 5.116882 GTGTTCTTACTGGTCTTGTTCTGT 58.883 41.667 0.00 0.00 0.00 3.41
2822 3061 3.684305 TCAGTATAACAGCACATGCACAC 59.316 43.478 6.64 0.00 45.16 3.82
2829 3068 0.386476 AGCACATGCACACAAACCAG 59.614 50.000 6.64 0.00 45.16 4.00
3094 3336 1.001020 TTTGCATCTGCCCCGATGT 60.001 52.632 0.00 0.00 42.14 3.06
3126 3368 0.397187 TGGCGCCTACCAACAACTTA 59.603 50.000 29.70 0.00 36.55 2.24
3337 3581 5.835257 AGATTTTGAATGGTGTCAACTGTG 58.165 37.500 0.00 0.00 37.24 3.66
3400 3646 4.160252 GGGCTACATGGTTCAAACATCAAT 59.840 41.667 0.00 0.00 0.00 2.57
3516 3762 7.623268 ATTCGAAACACACTTTATTTGCTTC 57.377 32.000 0.00 0.00 0.00 3.86
3518 3764 6.734137 TCGAAACACACTTTATTTGCTTCAT 58.266 32.000 0.00 0.00 0.00 2.57
3539 3785 8.523523 TTCATTTCTTGATGTTATGCTTGTTG 57.476 30.769 0.00 0.00 33.34 3.33
3697 3944 4.363138 GCCAGTAGCAATATTTTTGAGCC 58.637 43.478 0.00 0.00 42.97 4.70
3717 3964 5.550290 AGCCAAACATTTTTAACATGGGAG 58.450 37.500 0.00 0.00 0.00 4.30
3831 4083 3.686016 TGTAGGAGGCAAAGATTTCACC 58.314 45.455 0.00 0.00 0.00 4.02
3909 4161 8.499403 AACTTAGCCAAAAGTTTAATTTGCAA 57.501 26.923 0.00 0.00 45.20 4.08
3917 4169 7.696035 CCAAAAGTTTAATTTGCAACCTTGAAC 59.304 33.333 15.40 15.40 36.64 3.18
3970 4223 5.301805 CACTTTAGGTGGTTTCTCAAATGGT 59.698 40.000 0.00 0.00 41.90 3.55
3980 4233 5.047092 GGTTTCTCAAATGGTTCATGGTGAT 60.047 40.000 0.00 0.00 0.00 3.06
4152 4405 2.024176 TCAGTACAGCCCTTTGGAGA 57.976 50.000 0.00 0.00 0.00 3.71
4534 4801 6.315393 CGCCTATTGGTTTTACATCTTACACT 59.685 38.462 0.00 0.00 35.27 3.55
4571 4838 7.341445 TGGCTATTTGTTTTCACAACTAGTT 57.659 32.000 1.12 1.12 43.37 2.24
4575 4842 9.516314 GCTATTTGTTTTCACAACTAGTTCTTT 57.484 29.630 4.77 0.00 43.37 2.52
4690 4958 3.956199 AGCATATTTGGCAGTAGCACAAT 59.044 39.130 0.00 0.00 44.61 2.71
5419 5872 4.081420 TGCTGTCCTGAGATCTACCTTTTC 60.081 45.833 0.00 0.00 0.00 2.29
5422 5875 5.838955 TGTCCTGAGATCTACCTTTTCCTA 58.161 41.667 0.00 0.00 0.00 2.94
5460 6075 7.664318 TCGTATAATGTTCTAGAGCAGGATGTA 59.336 37.037 14.89 4.34 39.31 2.29
5539 6155 1.276705 TGTGCCAATGCCGAGTAACTA 59.723 47.619 0.00 0.00 36.33 2.24
5778 6552 6.601217 TGGTGCTAAAAATATGTATGCACTCA 59.399 34.615 13.52 8.18 45.63 3.41
5781 6555 8.184192 GTGCTAAAAATATGTATGCACTCAAGT 58.816 33.333 0.00 0.00 43.79 3.16
6004 6778 3.069729 CCCTACAGGCTGTTATACTGACC 59.930 52.174 27.24 0.00 36.17 4.02
6103 6881 0.107945 AGGAGCGGATTCTGCAGTTC 60.108 55.000 19.30 11.84 33.85 3.01
6303 7084 5.746245 CGTTTGCATTTTTACTTGTTCCAGA 59.254 36.000 0.00 0.00 0.00 3.86
6358 7139 4.312231 CGCTGTGCCGTGTTGGTG 62.312 66.667 0.00 0.00 41.21 4.17
6415 7196 7.362234 AGGGGTATCCTAGTTTTGCATAAATT 58.638 34.615 0.00 0.00 45.98 1.82
6421 7202 5.588648 TCCTAGTTTTGCATAAATTCCCTCG 59.411 40.000 0.00 0.00 0.00 4.63
6437 7218 3.025262 CCCTCGTCTAGTTTAGGCTTCT 58.975 50.000 0.00 0.00 0.00 2.85
6438 7219 4.080129 TCCCTCGTCTAGTTTAGGCTTCTA 60.080 45.833 0.00 0.00 0.00 2.10
6439 7220 4.036616 CCCTCGTCTAGTTTAGGCTTCTAC 59.963 50.000 0.00 0.00 0.00 2.59
6440 7221 4.883006 CCTCGTCTAGTTTAGGCTTCTACT 59.117 45.833 0.00 0.00 0.00 2.57
6441 7222 5.007921 CCTCGTCTAGTTTAGGCTTCTACTC 59.992 48.000 0.00 0.00 0.00 2.59
6442 7223 4.880696 TCGTCTAGTTTAGGCTTCTACTCC 59.119 45.833 0.00 0.00 0.00 3.85
6443 7224 4.036616 CGTCTAGTTTAGGCTTCTACTCCC 59.963 50.000 0.00 0.00 0.00 4.30
6444 7225 5.202765 GTCTAGTTTAGGCTTCTACTCCCT 58.797 45.833 0.00 0.00 0.00 4.20
6445 7226 5.300034 GTCTAGTTTAGGCTTCTACTCCCTC 59.700 48.000 0.00 0.00 0.00 4.30
6446 7227 3.376636 AGTTTAGGCTTCTACTCCCTCC 58.623 50.000 0.00 0.00 0.00 4.30
6447 7228 2.068834 TTAGGCTTCTACTCCCTCCG 57.931 55.000 0.00 0.00 0.00 4.63
6448 7229 0.924823 TAGGCTTCTACTCCCTCCGT 59.075 55.000 0.00 0.00 0.00 4.69
6449 7230 0.041386 AGGCTTCTACTCCCTCCGTT 59.959 55.000 0.00 0.00 0.00 4.44
6450 7231 0.460722 GGCTTCTACTCCCTCCGTTC 59.539 60.000 0.00 0.00 0.00 3.95
6451 7232 0.460722 GCTTCTACTCCCTCCGTTCC 59.539 60.000 0.00 0.00 0.00 3.62
6452 7233 0.739561 CTTCTACTCCCTCCGTTCCG 59.260 60.000 0.00 0.00 0.00 4.30
6453 7234 0.329261 TTCTACTCCCTCCGTTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
6454 7235 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
6455 7236 1.064166 TCTACTCCCTCCGTTCCGAAT 60.064 52.381 0.00 0.00 0.00 3.34
6456 7237 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
6457 7238 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
6458 7239 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
6459 7240 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
6460 7241 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
6461 7242 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
6462 7243 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
6463 7244 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
6464 7245 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
6465 7246 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
6466 7247 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
6467 7248 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
6468 7249 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
6469 7250 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
6470 7251 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
6471 7252 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
6472 7253 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
6473 7254 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
6474 7255 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
6475 7256 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
6476 7257 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
6483 7264 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
6484 7265 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
6485 7266 8.155821 TGTCTTAGATTTGTCTAGATACGGAG 57.844 38.462 0.00 0.00 0.00 4.63
6486 7267 7.228906 TGTCTTAGATTTGTCTAGATACGGAGG 59.771 40.741 0.00 0.00 0.00 4.30
6487 7268 7.229106 GTCTTAGATTTGTCTAGATACGGAGGT 59.771 40.741 0.00 0.00 0.00 3.85
6488 7269 8.435187 TCTTAGATTTGTCTAGATACGGAGGTA 58.565 37.037 0.00 0.00 0.00 3.08
6489 7270 9.233649 CTTAGATTTGTCTAGATACGGAGGTAT 57.766 37.037 0.00 0.00 42.01 2.73
6502 7283 7.778185 ATACGGAGGTATCTAGCACTAAAAT 57.222 36.000 0.00 0.00 34.18 1.82
6503 7284 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
6504 7285 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
6505 7286 6.153067 CGGAGGTATCTAGCACTAAAATGAG 58.847 44.000 0.00 0.00 0.00 2.90
6506 7287 6.239064 CGGAGGTATCTAGCACTAAAATGAGT 60.239 42.308 0.00 0.00 0.00 3.41
6507 7288 7.149307 GGAGGTATCTAGCACTAAAATGAGTC 58.851 42.308 0.00 0.00 0.00 3.36
6508 7289 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
6509 7290 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
6510 7291 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
6511 7292 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
6515 7296 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
6518 7299 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
6519 7300 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
6520 7301 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
6521 7302 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
6538 7319 8.651589 ACATCCGTATCTAGATAAATCCAAGA 57.348 34.615 14.09 4.52 0.00 3.02
6539 7320 8.524487 ACATCCGTATCTAGATAAATCCAAGAC 58.476 37.037 14.09 0.57 0.00 3.01
6540 7321 8.523658 CATCCGTATCTAGATAAATCCAAGACA 58.476 37.037 14.09 0.00 0.00 3.41
6541 7322 8.473358 TCCGTATCTAGATAAATCCAAGACAA 57.527 34.615 14.09 0.00 0.00 3.18
6542 7323 8.577296 TCCGTATCTAGATAAATCCAAGACAAG 58.423 37.037 14.09 0.00 0.00 3.16
6543 7324 8.361139 CCGTATCTAGATAAATCCAAGACAAGT 58.639 37.037 14.09 0.00 0.00 3.16
6550 7331 8.438676 AGATAAATCCAAGACAAGTAATTCGG 57.561 34.615 0.00 0.00 0.00 4.30
6551 7332 8.265055 AGATAAATCCAAGACAAGTAATTCGGA 58.735 33.333 0.00 0.00 0.00 4.55
6552 7333 8.801882 ATAAATCCAAGACAAGTAATTCGGAA 57.198 30.769 0.00 0.00 0.00 4.30
6553 7334 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
6606 7387 7.624360 TGTTTTCTTCAACAGCTAAAGAGAA 57.376 32.000 0.00 0.00 32.70 2.87
6681 7462 6.304356 TGACAAGAGTTGCACTATTTTCTG 57.696 37.500 9.55 0.00 30.08 3.02
6727 7508 1.216064 TATTCCATGGCAGTGGCTCT 58.784 50.000 18.53 2.27 39.19 4.09
6728 7509 0.106819 ATTCCATGGCAGTGGCTCTC 60.107 55.000 18.53 0.00 39.19 3.20
6777 7568 8.460428 ACAAAATGTGAAGAAACGTTAAACCTA 58.540 29.630 0.00 0.00 0.00 3.08
6778 7569 9.458374 CAAAATGTGAAGAAACGTTAAACCTAT 57.542 29.630 0.00 0.00 0.00 2.57
6779 7570 9.458374 AAAATGTGAAGAAACGTTAAACCTATG 57.542 29.630 0.00 0.00 0.00 2.23
6780 7571 5.992729 TGTGAAGAAACGTTAAACCTATGC 58.007 37.500 0.00 0.00 0.00 3.14
6799 7670 4.241590 TGCTGAATTTGTGATGGTTGTC 57.758 40.909 0.00 0.00 0.00 3.18
6809 7680 1.003580 TGATGGTTGTCTTCCCAGAGC 59.996 52.381 0.00 0.00 33.39 4.09
6845 7716 5.465390 CACATCTCACGGAAACTAGTTGAAA 59.535 40.000 9.34 0.00 0.00 2.69
6846 7717 5.696724 ACATCTCACGGAAACTAGTTGAAAG 59.303 40.000 9.34 4.16 0.00 2.62
6847 7718 5.524971 TCTCACGGAAACTAGTTGAAAGA 57.475 39.130 9.34 4.39 0.00 2.52
6848 7719 5.287226 TCTCACGGAAACTAGTTGAAAGAC 58.713 41.667 9.34 0.00 0.00 3.01
6850 7721 4.807304 TCACGGAAACTAGTTGAAAGACAC 59.193 41.667 9.34 0.00 0.00 3.67
6851 7722 4.809426 CACGGAAACTAGTTGAAAGACACT 59.191 41.667 9.34 0.00 0.00 3.55
6852 7723 4.809426 ACGGAAACTAGTTGAAAGACACTG 59.191 41.667 9.34 2.19 0.00 3.66
6866 7737 0.892358 ACACTGTCCCAATGCTGCTG 60.892 55.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.754323 GAGATATTCCGGTGAGAGTCGAT 59.246 47.826 0.00 0.00 0.00 3.59
2 3 3.139850 GAGATATTCCGGTGAGAGTCGA 58.860 50.000 0.00 0.00 0.00 4.20
3 4 2.226912 GGAGATATTCCGGTGAGAGTCG 59.773 54.545 0.00 0.00 35.91 4.18
14 15 1.000607 TGTACGCGCTGGAGATATTCC 60.001 52.381 5.73 0.00 46.98 3.01
15 16 2.052157 GTGTACGCGCTGGAGATATTC 58.948 52.381 5.73 0.00 0.00 1.75
16 17 1.407618 TGTGTACGCGCTGGAGATATT 59.592 47.619 5.73 0.00 0.00 1.28
17 18 1.029681 TGTGTACGCGCTGGAGATAT 58.970 50.000 5.73 0.00 0.00 1.63
18 19 0.099968 GTGTGTACGCGCTGGAGATA 59.900 55.000 5.73 0.00 0.00 1.98
19 20 1.153823 GTGTGTACGCGCTGGAGAT 60.154 57.895 5.73 0.00 0.00 2.75
20 21 1.873270 ATGTGTGTACGCGCTGGAGA 61.873 55.000 19.84 0.63 0.00 3.71
21 22 1.413767 GATGTGTGTACGCGCTGGAG 61.414 60.000 19.84 0.00 0.00 3.86
22 23 1.445410 GATGTGTGTACGCGCTGGA 60.445 57.895 19.84 1.37 0.00 3.86
23 24 1.736282 TGATGTGTGTACGCGCTGG 60.736 57.895 19.84 0.00 0.00 4.85
24 25 1.416049 GTGATGTGTGTACGCGCTG 59.584 57.895 19.84 1.02 0.00 5.18
25 26 1.736645 GGTGATGTGTGTACGCGCT 60.737 57.895 19.84 6.59 0.00 5.92
26 27 1.683790 GAGGTGATGTGTGTACGCGC 61.684 60.000 13.02 13.02 0.00 6.86
27 28 1.076533 GGAGGTGATGTGTGTACGCG 61.077 60.000 3.53 3.53 0.00 6.01
28 29 0.037697 TGGAGGTGATGTGTGTACGC 60.038 55.000 0.00 0.00 0.00 4.42
29 30 2.066262 GTTGGAGGTGATGTGTGTACG 58.934 52.381 0.00 0.00 0.00 3.67
30 31 3.067106 CTGTTGGAGGTGATGTGTGTAC 58.933 50.000 0.00 0.00 0.00 2.90
31 32 2.703536 ACTGTTGGAGGTGATGTGTGTA 59.296 45.455 0.00 0.00 0.00 2.90
38 39 0.326264 GGAGCACTGTTGGAGGTGAT 59.674 55.000 0.00 0.00 35.69 3.06
151 170 3.728373 GTGGGATGGAACCGGGCT 61.728 66.667 6.32 0.00 0.00 5.19
177 196 2.574955 GGTGGAGGATCGGATCGGG 61.575 68.421 11.62 0.00 34.37 5.14
188 207 3.866582 GCCGGGATGAGGTGGAGG 61.867 72.222 2.18 0.00 0.00 4.30
234 267 1.808390 CCCTACGAAACGCTTCCGG 60.808 63.158 0.00 0.00 39.22 5.14
236 269 3.482809 GCCCTACGAAACGCTTCC 58.517 61.111 0.00 0.00 0.00 3.46
375 430 5.535333 TGGGTTCGTTCTTAAACAGAGTAG 58.465 41.667 0.00 0.00 34.93 2.57
455 542 0.326927 GGTTTGGGTTCGATCCAGGA 59.673 55.000 14.36 0.00 35.48 3.86
464 551 0.704664 ATCCCTCTGGGTTTGGGTTC 59.295 55.000 2.25 0.00 44.74 3.62
489 586 3.390671 ATCGGACCGGATCACCCCT 62.391 63.158 15.25 0.00 0.00 4.79
491 588 2.735237 GATCGGACCGGATCACCC 59.265 66.667 15.25 0.00 41.93 4.61
820 988 0.252284 ACCAACCAACCAACCAACCA 60.252 50.000 0.00 0.00 0.00 3.67
821 989 0.462375 GACCAACCAACCAACCAACC 59.538 55.000 0.00 0.00 0.00 3.77
822 990 0.101579 CGACCAACCAACCAACCAAC 59.898 55.000 0.00 0.00 0.00 3.77
823 991 1.038130 CCGACCAACCAACCAACCAA 61.038 55.000 0.00 0.00 0.00 3.67
848 1016 1.653114 CCGCACAACAACAACAACAAG 59.347 47.619 0.00 0.00 0.00 3.16
1088 1260 0.820871 GGAAGAGATCAGTCGCCACT 59.179 55.000 0.00 0.00 0.00 4.00
1090 1262 0.820226 CTGGAAGAGATCAGTCGCCA 59.180 55.000 0.00 0.00 34.07 5.69
1108 1280 1.160137 GACCTGCACGAAATTGAGCT 58.840 50.000 0.00 0.00 0.00 4.09
1113 1285 0.953960 GGACCGACCTGCACGAAATT 60.954 55.000 0.00 0.00 35.41 1.82
1301 1473 1.971357 ACGACTGGAAGGAGAACATGT 59.029 47.619 0.00 0.00 39.30 3.21
1302 1474 2.611518 GACGACTGGAAGGAGAACATG 58.388 52.381 0.00 0.00 39.30 3.21
1303 1475 1.550976 GGACGACTGGAAGGAGAACAT 59.449 52.381 0.00 0.00 39.30 2.71
1306 1478 1.257743 CTGGACGACTGGAAGGAGAA 58.742 55.000 0.00 0.00 39.30 2.87
1395 1576 1.562783 GAGAAGAGTGGTACAGGCCT 58.437 55.000 0.00 0.00 41.80 5.19
1480 1661 1.446966 GCGAGCTCCTTGACTGGAC 60.447 63.158 8.47 0.00 31.94 4.02
1569 1753 2.596338 TCGCGGTCACTCCACTCA 60.596 61.111 6.13 0.00 35.57 3.41
1578 1762 1.954382 AGTATATTCAGCTCGCGGTCA 59.046 47.619 6.13 0.00 0.00 4.02
1677 1865 0.813184 ATTGGCAAACTCCATCAGCG 59.187 50.000 3.01 0.00 35.77 5.18
1702 1890 1.343506 GAAAAGAAGCTTGCCGCATG 58.656 50.000 2.10 0.00 42.61 4.06
1844 2032 2.473376 CCAAATAACGACGAAAGCGACC 60.473 50.000 0.00 0.00 41.64 4.79
1896 2084 1.001378 CGGCTGTTAATGCTTATGGCC 60.001 52.381 0.00 0.00 40.92 5.36
1897 2085 1.600413 GCGGCTGTTAATGCTTATGGC 60.600 52.381 0.00 0.00 42.22 4.40
1964 2152 6.494491 AGGATTCCTTTGACACAAATTCATCA 59.506 34.615 0.00 0.00 0.00 3.07
2014 2202 0.247460 TCTCAAGCCAGATGGTGACG 59.753 55.000 0.00 0.00 37.57 4.35
2052 2240 8.940397 AGAATTAGAACCTCAAAGGAAATGAA 57.060 30.769 0.00 0.00 37.67 2.57
2238 2426 9.066892 ACACACATTAATACAAGAACAGAACAT 57.933 29.630 0.00 0.00 0.00 2.71
2250 2438 8.372459 AGACCAGTAAGAACACACATTAATACA 58.628 33.333 0.00 0.00 0.00 2.29
2284 2475 6.570672 AGATTGACGTTCTCACACTAAGTA 57.429 37.500 0.00 0.00 0.00 2.24
2546 2785 4.166144 CACCCCTATAAACTTCATCCAGGT 59.834 45.833 0.00 0.00 0.00 4.00
2581 2820 2.285743 AGGGAGGGGCTCTTCCAC 60.286 66.667 15.93 6.10 44.03 4.02
2822 3061 6.549061 CATGTCATCAGAACATACTGGTTTG 58.451 40.000 0.00 0.00 38.31 2.93
2829 3068 4.864916 AACGCATGTCATCAGAACATAC 57.135 40.909 0.00 0.00 0.00 2.39
3094 3336 2.722094 AGGCGCCATGTGAAAATTAGA 58.278 42.857 31.54 0.00 0.00 2.10
3126 3368 4.412199 TCCATCGATATTGAGAAAGGGGTT 59.588 41.667 0.00 0.00 0.00 4.11
3337 3581 1.002544 AGTGAGGCTAGCTGGTTTGTC 59.997 52.381 15.72 0.00 0.00 3.18
3339 3583 1.271054 ACAGTGAGGCTAGCTGGTTTG 60.271 52.381 15.72 10.58 34.79 2.93
3516 3762 7.811236 AGTCAACAAGCATAACATCAAGAAATG 59.189 33.333 0.00 0.00 0.00 2.32
3518 3764 7.275888 AGTCAACAAGCATAACATCAAGAAA 57.724 32.000 0.00 0.00 0.00 2.52
3530 3776 7.931948 AGTACTAACTACAAAGTCAACAAGCAT 59.068 33.333 0.00 0.00 33.75 3.79
3565 3811 3.087031 CAAGGTTGCTTCCAGATGATGT 58.913 45.455 1.12 0.00 0.00 3.06
3657 3903 0.950116 GCTTGTCTTCTGTGCTGCTT 59.050 50.000 0.00 0.00 0.00 3.91
3697 3944 8.310382 TCCATACTCCCATGTTAAAAATGTTTG 58.690 33.333 0.00 0.00 0.00 2.93
3733 3980 5.136068 ACCTTCAGGACATCTCTCATAGA 57.864 43.478 0.00 0.00 37.34 1.98
3734 3981 5.867903 AACCTTCAGGACATCTCTCATAG 57.132 43.478 0.00 0.00 38.94 2.23
3831 4083 1.992233 AAGCAGGTGTGTGCAACGTG 61.992 55.000 5.54 5.54 46.60 4.49
3917 4169 8.738645 AGTGGCCTATTTCAATAGTTTTAGAG 57.261 34.615 3.32 0.00 37.30 2.43
3970 4223 2.492881 GTGGCATTCACATCACCATGAA 59.507 45.455 0.00 0.00 45.39 2.57
4113 4366 9.944663 GTACTGAATCACAATCAAGTAAAAACA 57.055 29.630 0.00 0.00 0.00 2.83
4118 4371 6.371548 GGCTGTACTGAATCACAATCAAGTAA 59.628 38.462 3.61 0.00 0.00 2.24
4312 4568 3.914312 TCAGAACGGAACAGAATGAGAC 58.086 45.455 0.00 0.00 39.69 3.36
4313 4569 4.560128 CTTCAGAACGGAACAGAATGAGA 58.440 43.478 0.00 0.00 39.69 3.27
4485 4752 0.545171 CCATGTGCTCCCTGACTGAT 59.455 55.000 0.00 0.00 0.00 2.90
4534 4801 6.839124 ACAAATAGCCATGAGAATTTCACA 57.161 33.333 0.00 0.00 38.99 3.58
4587 4854 2.936202 ACCAGCAATATGACCATGTCC 58.064 47.619 0.00 0.00 0.00 4.02
4594 4862 9.627395 CACTAACTACTATACCAGCAATATGAC 57.373 37.037 0.00 0.00 0.00 3.06
5572 6188 4.406069 CTCATTCTGCAACAACAATACGG 58.594 43.478 0.00 0.00 0.00 4.02
5778 6552 5.818857 ACATCGTTGTTACTTGTTACCACTT 59.181 36.000 0.00 0.00 29.55 3.16
5781 6555 5.603596 AGACATCGTTGTTACTTGTTACCA 58.396 37.500 0.00 0.00 35.79 3.25
5790 6564 5.404366 TGCTTAGTTGAGACATCGTTGTTAC 59.596 40.000 0.00 0.00 35.79 2.50
6004 6778 1.766143 GCAACTATTCCTGGCGCTCG 61.766 60.000 7.64 0.00 0.00 5.03
6303 7084 5.396436 GGCTCATTACTGTACAGGGTACAAT 60.396 44.000 26.12 13.54 0.00 2.71
6358 7139 1.211190 CCCTCGCTGCTTTGCTTTC 59.789 57.895 0.00 0.00 0.00 2.62
6415 7196 2.822707 AGCCTAAACTAGACGAGGGA 57.177 50.000 0.00 0.00 0.00 4.20
6421 7202 5.202765 AGGGAGTAGAAGCCTAAACTAGAC 58.797 45.833 0.00 0.00 0.00 2.59
6447 7228 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
6448 7229 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
6449 7230 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
6450 7231 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
6457 7238 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
6458 7239 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
6459 7240 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
6460 7241 7.228906 CCTCCGTATCTAGACAAATCTAAGACA 59.771 40.741 0.00 0.00 36.98 3.41
6461 7242 7.229106 ACCTCCGTATCTAGACAAATCTAAGAC 59.771 40.741 0.00 0.00 36.98 3.01
6462 7243 7.288560 ACCTCCGTATCTAGACAAATCTAAGA 58.711 38.462 0.00 0.00 36.98 2.10
6463 7244 7.513371 ACCTCCGTATCTAGACAAATCTAAG 57.487 40.000 0.00 0.00 36.98 2.18
6464 7245 9.228949 GATACCTCCGTATCTAGACAAATCTAA 57.771 37.037 0.00 0.00 45.11 2.10
6465 7246 8.789825 GATACCTCCGTATCTAGACAAATCTA 57.210 38.462 0.00 0.00 45.11 1.98
6466 7247 7.690952 GATACCTCCGTATCTAGACAAATCT 57.309 40.000 0.00 0.00 45.11 2.40
6478 7259 7.450634 TCATTTTAGTGCTAGATACCTCCGTAT 59.549 37.037 0.00 0.00 37.92 3.06
6479 7260 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
6480 7261 5.597182 TCATTTTAGTGCTAGATACCTCCGT 59.403 40.000 0.00 0.00 0.00 4.69
6481 7262 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
6482 7263 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
6483 7264 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
6484 7265 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
6485 7266 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
6489 7270 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
6492 7273 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
6493 7274 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
6494 7275 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
6495 7276 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
6512 7293 9.749340 TCTTGGATTTATCTAGATACGGATGTA 57.251 33.333 12.12 0.00 34.45 2.29
6513 7294 8.524487 GTCTTGGATTTATCTAGATACGGATGT 58.476 37.037 12.12 0.00 0.00 3.06
6514 7295 8.523658 TGTCTTGGATTTATCTAGATACGGATG 58.476 37.037 12.12 1.08 0.00 3.51
6515 7296 8.651589 TGTCTTGGATTTATCTAGATACGGAT 57.348 34.615 12.12 6.99 0.00 4.18
6516 7297 8.473358 TTGTCTTGGATTTATCTAGATACGGA 57.527 34.615 12.12 2.46 0.00 4.69
6517 7298 8.361139 ACTTGTCTTGGATTTATCTAGATACGG 58.639 37.037 12.12 1.13 0.00 4.02
6524 7305 9.542462 CCGAATTACTTGTCTTGGATTTATCTA 57.458 33.333 0.00 0.00 0.00 1.98
6525 7306 8.265055 TCCGAATTACTTGTCTTGGATTTATCT 58.735 33.333 0.00 0.00 0.00 1.98
6526 7307 8.433421 TCCGAATTACTTGTCTTGGATTTATC 57.567 34.615 0.00 0.00 0.00 1.75
6527 7308 8.674607 GTTCCGAATTACTTGTCTTGGATTTAT 58.325 33.333 0.00 0.00 0.00 1.40
6528 7309 7.148540 CGTTCCGAATTACTTGTCTTGGATTTA 60.149 37.037 0.00 0.00 0.00 1.40
6529 7310 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
6530 7311 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
6531 7312 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
6532 7313 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
6533 7314 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
6534 7315 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
6535 7316 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
6536 7317 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
6537 7318 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
6538 7319 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
6539 7320 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
6540 7321 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
6541 7322 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
6542 7323 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
6543 7324 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
6544 7325 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
6545 7326 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
6546 7327 1.318158 GCTACTCCCTCCGTTCCGAA 61.318 60.000 0.00 0.00 0.00 4.30
6547 7328 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
6548 7329 0.465097 TAGCTACTCCCTCCGTTCCG 60.465 60.000 0.00 0.00 0.00 4.30
6549 7330 1.998222 ATAGCTACTCCCTCCGTTCC 58.002 55.000 0.00 0.00 0.00 3.62
6550 7331 3.492829 CCAAATAGCTACTCCCTCCGTTC 60.493 52.174 0.00 0.00 0.00 3.95
6551 7332 2.434702 CCAAATAGCTACTCCCTCCGTT 59.565 50.000 0.00 0.00 0.00 4.44
6552 7333 2.040178 CCAAATAGCTACTCCCTCCGT 58.960 52.381 0.00 0.00 0.00 4.69
6553 7334 1.344763 CCCAAATAGCTACTCCCTCCG 59.655 57.143 0.00 0.00 0.00 4.63
6554 7335 2.369203 GACCCAAATAGCTACTCCCTCC 59.631 54.545 0.00 0.00 0.00 4.30
6555 7336 3.039011 TGACCCAAATAGCTACTCCCTC 58.961 50.000 0.00 0.00 0.00 4.30
6556 7337 3.130734 TGACCCAAATAGCTACTCCCT 57.869 47.619 0.00 0.00 0.00 4.20
6557 7338 4.137543 CAATGACCCAAATAGCTACTCCC 58.862 47.826 0.00 0.00 0.00 4.30
6558 7339 3.565902 GCAATGACCCAAATAGCTACTCC 59.434 47.826 0.00 0.00 0.00 3.85
6559 7340 3.565902 GGCAATGACCCAAATAGCTACTC 59.434 47.826 0.00 0.00 0.00 2.59
6560 7341 3.203040 AGGCAATGACCCAAATAGCTACT 59.797 43.478 0.00 0.00 0.00 2.57
6561 7342 3.316308 CAGGCAATGACCCAAATAGCTAC 59.684 47.826 0.00 0.00 0.00 3.58
6606 7387 8.940397 TCCTACATTTTCTTTTCTCATCCTTT 57.060 30.769 0.00 0.00 0.00 3.11
6695 7476 9.420118 ACTGCCATGGAATAAAAATGATACTTA 57.580 29.630 18.40 0.00 0.00 2.24
6705 7486 2.760092 GAGCCACTGCCATGGAATAAAA 59.240 45.455 18.40 0.00 43.02 1.52
6727 7508 7.014230 TGTGTAGATAGTACTGCATTGCATAGA 59.986 37.037 12.53 0.00 38.13 1.98
6728 7509 7.147976 TGTGTAGATAGTACTGCATTGCATAG 58.852 38.462 12.53 3.97 38.13 2.23
6772 7563 5.018809 ACCATCACAAATTCAGCATAGGTT 58.981 37.500 0.00 0.00 0.00 3.50
6777 7568 4.525487 AGACAACCATCACAAATTCAGCAT 59.475 37.500 0.00 0.00 0.00 3.79
6778 7569 3.890756 AGACAACCATCACAAATTCAGCA 59.109 39.130 0.00 0.00 0.00 4.41
6779 7570 4.510038 AGACAACCATCACAAATTCAGC 57.490 40.909 0.00 0.00 0.00 4.26
6780 7571 5.464168 GGAAGACAACCATCACAAATTCAG 58.536 41.667 0.00 0.00 0.00 3.02
6850 7721 0.963962 AAACAGCAGCATTGGGACAG 59.036 50.000 0.00 0.00 42.39 3.51
6851 7722 0.961019 GAAACAGCAGCATTGGGACA 59.039 50.000 0.00 0.00 0.00 4.02
6852 7723 0.961019 TGAAACAGCAGCATTGGGAC 59.039 50.000 0.00 0.00 0.00 4.46
6866 7737 7.326789 CCAACATCTTGTGTGAATATGTGAAAC 59.673 37.037 0.00 0.00 41.14 2.78


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

AutoCloner maintained by Alex Coulton.