Multiple sequence alignment - TraesCS4D01G014900

Loading Multiple Alignment...

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 TraesCS4D01G014900 chr4D 100.000 2312 0 0 1 2312 6665131 6662820 0.000000e+00 4270
1 TraesCS4D01G014900 chr4D 96.875 128 3 1 1161 1288 6673283 6673157 1.800000e-51 213
2 TraesCS4D01G014900 chr7A 85.025 1202 54 57 1181 2312 44268762 44269907 0.000000e+00 1107
3 TraesCS4D01G014900 chr4A 87.102 597 29 14 107 686 596742391 596742956 1.170000e-177 632
4 TraesCS4D01G014900 chr4A 82.456 798 31 49 766 1517 596742955 596743689 4.250000e-167 597
5 TraesCS4D01G014900 chr4A 84.632 475 28 22 844 1288 596737907 596738366 4.560000e-117 431
6 TraesCS4D01G014900 chr4A 86.701 391 25 11 1885 2261 596744052 596744429 2.140000e-110 409
7 TraesCS4D01G014900 chr4A 93.711 159 10 0 1149 1307 596725478 596725636 2.970000e-59 239
8 TraesCS4D01G014900 chr4A 88.000 100 12 0 1629 1728 596743814 596743913 4.040000e-23 119
9 TraesCS4D01G014900 chr4B 83.666 551 48 22 994 1526 11928571 11928045 4.470000e-132 481
10 TraesCS4D01G014900 chr4B 82.033 423 27 21 1858 2269 11927711 11927327 4.800000e-82 315


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 TraesCS4D01G014900 chr4D 6662820 6665131 2311 True 4270.00 4270 100.00000 1 2312 1 chr4D.!!$R1 2311
1 TraesCS4D01G014900 chr7A 44268762 44269907 1145 False 1107.00 1107 85.02500 1181 2312 1 chr7A.!!$F1 1131
2 TraesCS4D01G014900 chr4A 596742391 596744429 2038 False 439.25 632 86.06475 107 2261 4 chr4A.!!$F3 2154
3 TraesCS4D01G014900 chr4B 11927327 11928571 1244 True 398.00 481 82.84950 994 2269 2 chr4B.!!$R1 1275

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
998 1048 0.034059 CATAGCTTAGCCAGGTCGGG 59.966 60.0 0.0 0.0 34.13 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2235 0.379669 CGGCCAAGATCATCAGTTGC 59.62 55.0 2.24 0.0 0.0 4.17 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
18 19 3.976339 GGATAGCTGTCTCATGCGT 57.024 52.632 10.54 0.00 0.00 5.24
20 21 3.584406 GGATAGCTGTCTCATGCGTAT 57.416 47.619 10.54 0.00 0.00 3.06
21 22 3.249091 GGATAGCTGTCTCATGCGTATG 58.751 50.000 10.54 7.22 35.57 2.39
22 23 3.305676 GGATAGCTGTCTCATGCGTATGT 60.306 47.826 13.39 0.00 35.73 2.29
23 24 1.931906 AGCTGTCTCATGCGTATGTG 58.068 50.000 13.39 11.08 35.73 3.21
24 25 1.205655 AGCTGTCTCATGCGTATGTGT 59.794 47.619 13.39 0.00 35.73 3.72
25 26 1.590238 GCTGTCTCATGCGTATGTGTC 59.410 52.381 13.39 9.26 35.73 3.67
26 27 2.196749 CTGTCTCATGCGTATGTGTCC 58.803 52.381 13.39 7.10 35.73 4.02
27 28 1.200483 GTCTCATGCGTATGTGTCCG 58.800 55.000 13.39 0.00 35.73 4.79
35 36 2.554806 CGTATGTGTCCGCAGACTAA 57.445 50.000 1.05 0.00 43.91 2.24
36 37 3.079960 CGTATGTGTCCGCAGACTAAT 57.920 47.619 1.05 0.00 43.91 1.73
37 38 3.043586 CGTATGTGTCCGCAGACTAATC 58.956 50.000 1.05 0.00 43.91 1.75
38 39 3.488553 CGTATGTGTCCGCAGACTAATCA 60.489 47.826 1.05 0.00 43.91 2.57
39 40 3.827008 ATGTGTCCGCAGACTAATCAT 57.173 42.857 1.05 0.00 43.91 2.45
40 41 2.892374 TGTGTCCGCAGACTAATCATG 58.108 47.619 1.05 0.00 43.91 3.07
41 42 2.233676 TGTGTCCGCAGACTAATCATGT 59.766 45.455 1.05 0.00 43.91 3.21
42 43 2.860735 GTGTCCGCAGACTAATCATGTC 59.139 50.000 1.05 0.00 43.91 3.06
43 44 2.159099 TGTCCGCAGACTAATCATGTCC 60.159 50.000 1.05 0.00 43.91 4.02
44 45 2.107366 TCCGCAGACTAATCATGTCCA 58.893 47.619 0.00 0.00 35.21 4.02
45 46 2.700371 TCCGCAGACTAATCATGTCCAT 59.300 45.455 0.00 0.00 35.21 3.41
46 47 2.804527 CCGCAGACTAATCATGTCCATG 59.195 50.000 0.71 0.71 40.09 3.66
47 48 2.804527 CGCAGACTAATCATGTCCATGG 59.195 50.000 4.97 4.97 39.24 3.66
48 49 3.493176 CGCAGACTAATCATGTCCATGGA 60.493 47.826 11.44 11.44 39.24 3.41
49 50 4.454678 GCAGACTAATCATGTCCATGGAA 58.545 43.478 18.20 7.57 39.24 3.53
50 51 5.068636 GCAGACTAATCATGTCCATGGAAT 58.931 41.667 18.20 9.70 39.24 3.01
51 52 5.048921 GCAGACTAATCATGTCCATGGAATG 60.049 44.000 18.20 20.42 46.21 2.67
52 53 6.293698 CAGACTAATCATGTCCATGGAATGA 58.706 40.000 27.32 27.32 46.28 2.57
53 54 6.940867 CAGACTAATCATGTCCATGGAATGAT 59.059 38.462 28.50 28.50 46.28 2.45
54 55 6.940867 AGACTAATCATGTCCATGGAATGATG 59.059 38.462 31.44 25.85 46.28 3.07
55 56 7.421030 AGACTAATCATGTCCATGGAATGATGT 60.421 37.037 31.44 27.58 46.28 3.06
65 66 4.547886 ATGGAATGATGTGGGAGGAAAT 57.452 40.909 0.00 0.00 0.00 2.17
66 67 4.335735 TGGAATGATGTGGGAGGAAATT 57.664 40.909 0.00 0.00 0.00 1.82
67 68 4.686891 TGGAATGATGTGGGAGGAAATTT 58.313 39.130 0.00 0.00 0.00 1.82
68 69 5.836705 TGGAATGATGTGGGAGGAAATTTA 58.163 37.500 0.00 0.00 0.00 1.40
69 70 5.656416 TGGAATGATGTGGGAGGAAATTTAC 59.344 40.000 0.00 0.00 0.00 2.01
70 71 5.221048 GGAATGATGTGGGAGGAAATTTACG 60.221 44.000 0.00 0.00 0.00 3.18
71 72 3.616219 TGATGTGGGAGGAAATTTACGG 58.384 45.455 0.00 0.00 0.00 4.02
72 73 2.500392 TGTGGGAGGAAATTTACGGG 57.500 50.000 0.00 0.00 0.00 5.28
73 74 1.706305 TGTGGGAGGAAATTTACGGGT 59.294 47.619 0.00 0.00 0.00 5.28
74 75 2.290450 TGTGGGAGGAAATTTACGGGTC 60.290 50.000 0.00 0.00 0.00 4.46
75 76 1.065998 TGGGAGGAAATTTACGGGTCG 60.066 52.381 0.00 0.00 0.00 4.79
76 77 1.012086 GGAGGAAATTTACGGGTCGC 58.988 55.000 0.00 0.00 0.00 5.19
77 78 1.012086 GAGGAAATTTACGGGTCGCC 58.988 55.000 0.00 0.00 0.00 5.54
78 79 0.393402 AGGAAATTTACGGGTCGCCC 60.393 55.000 4.96 4.96 41.09 6.13
79 80 0.393402 GGAAATTTACGGGTCGCCCT 60.393 55.000 12.26 3.58 42.67 5.19
80 81 0.730840 GAAATTTACGGGTCGCCCTG 59.269 55.000 12.26 1.08 42.67 4.45
81 82 0.325602 AAATTTACGGGTCGCCCTGA 59.674 50.000 0.00 0.00 42.67 3.86
90 91 3.814577 GTCGCCCTGACGCATATAT 57.185 52.632 0.00 0.00 37.96 0.86
91 92 1.350193 GTCGCCCTGACGCATATATG 58.650 55.000 8.45 8.45 37.96 1.78
92 93 1.067846 GTCGCCCTGACGCATATATGA 60.068 52.381 17.10 0.00 37.96 2.15
93 94 1.824852 TCGCCCTGACGCATATATGAT 59.175 47.619 17.10 3.25 0.00 2.45
94 95 3.020984 TCGCCCTGACGCATATATGATA 58.979 45.455 17.10 0.00 0.00 2.15
95 96 3.636764 TCGCCCTGACGCATATATGATAT 59.363 43.478 17.10 0.25 0.00 1.63
96 97 4.825085 TCGCCCTGACGCATATATGATATA 59.175 41.667 17.10 0.00 0.00 0.86
97 98 5.476945 TCGCCCTGACGCATATATGATATAT 59.523 40.000 17.10 0.00 0.00 0.86
98 99 5.802451 CGCCCTGACGCATATATGATATATC 59.198 44.000 17.10 5.73 0.00 1.63
99 100 6.349694 CGCCCTGACGCATATATGATATATCT 60.350 42.308 17.10 2.68 0.00 1.98
100 101 7.148239 CGCCCTGACGCATATATGATATATCTA 60.148 40.741 17.10 4.68 0.00 1.98
101 102 7.971168 GCCCTGACGCATATATGATATATCTAC 59.029 40.741 17.10 0.00 0.00 2.59
102 103 8.178313 CCCTGACGCATATATGATATATCTACG 58.822 40.741 17.10 9.09 0.00 3.51
103 104 8.936864 CCTGACGCATATATGATATATCTACGA 58.063 37.037 17.10 0.00 0.00 3.43
104 105 9.965748 CTGACGCATATATGATATATCTACGAG 57.034 37.037 17.10 7.45 0.00 4.18
105 106 9.706691 TGACGCATATATGATATATCTACGAGA 57.293 33.333 17.10 7.64 0.00 4.04
136 137 1.399714 TCCTGTGGCTAGGACGTATG 58.600 55.000 6.93 0.00 41.85 2.39
137 138 0.249489 CCTGTGGCTAGGACGTATGC 60.249 60.000 2.68 0.00 40.42 3.14
138 139 0.747255 CTGTGGCTAGGACGTATGCT 59.253 55.000 0.00 0.00 0.00 3.79
139 140 0.744874 TGTGGCTAGGACGTATGCTC 59.255 55.000 0.00 0.00 0.00 4.26
140 141 0.744874 GTGGCTAGGACGTATGCTCA 59.255 55.000 0.00 0.00 0.00 4.26
144 151 2.194271 GCTAGGACGTATGCTCAACAC 58.806 52.381 0.00 0.00 0.00 3.32
160 167 5.177696 GCTCAACACGAGAGACTTGTTTAAT 59.822 40.000 0.00 0.00 45.45 1.40
163 170 8.651391 TCAACACGAGAGACTTGTTTAATTTA 57.349 30.769 0.00 0.00 38.58 1.40
164 171 8.545420 TCAACACGAGAGACTTGTTTAATTTAC 58.455 33.333 0.00 0.00 38.58 2.01
165 172 8.548721 CAACACGAGAGACTTGTTTAATTTACT 58.451 33.333 0.00 0.00 38.58 2.24
166 173 8.073355 ACACGAGAGACTTGTTTAATTTACTG 57.927 34.615 0.00 0.00 0.00 2.74
167 174 7.170998 ACACGAGAGACTTGTTTAATTTACTGG 59.829 37.037 0.00 0.00 0.00 4.00
168 175 7.170998 CACGAGAGACTTGTTTAATTTACTGGT 59.829 37.037 0.00 0.00 0.00 4.00
220 232 2.095372 CGAAAAGCTCCCACGGTTAATC 59.905 50.000 0.00 0.00 0.00 1.75
246 258 0.106335 TGTAACCGGTTCCTCGCAAA 59.894 50.000 26.16 0.00 0.00 3.68
248 260 1.603326 GTAACCGGTTCCTCGCAAAAA 59.397 47.619 26.16 0.00 0.00 1.94
249 261 0.666374 AACCGGTTCCTCGCAAAAAG 59.334 50.000 15.86 0.00 0.00 2.27
250 262 0.179040 ACCGGTTCCTCGCAAAAAGA 60.179 50.000 0.00 0.00 0.00 2.52
255 267 3.485743 CGGTTCCTCGCAAAAAGAAAAAG 59.514 43.478 0.00 0.00 0.00 2.27
274 286 7.439356 AGAAAAAGAGTAACTGTAACCGGTAAC 59.561 37.037 8.00 0.00 0.00 2.50
290 302 0.682852 TAACCACGGGTTGAGACCAG 59.317 55.000 15.93 0.00 46.35 4.00
291 303 1.758482 TAACCACGGGTTGAGACCAGA 60.758 52.381 15.93 0.00 46.35 3.86
292 304 3.923519 TAACCACGGGTTGAGACCAGAC 61.924 54.545 15.93 0.00 46.35 3.51
296 308 2.047179 GGTTGAGACCAGACGGCC 60.047 66.667 0.00 0.00 45.77 6.13
297 309 2.741092 GTTGAGACCAGACGGCCA 59.259 61.111 2.24 0.00 34.57 5.36
298 310 1.374758 GTTGAGACCAGACGGCCAG 60.375 63.158 2.24 0.00 34.57 4.85
299 311 1.533033 TTGAGACCAGACGGCCAGA 60.533 57.895 2.24 0.00 34.57 3.86
300 312 1.118965 TTGAGACCAGACGGCCAGAA 61.119 55.000 2.24 0.00 34.57 3.02
301 313 1.118965 TGAGACCAGACGGCCAGAAA 61.119 55.000 2.24 0.00 34.57 2.52
302 314 0.670854 GAGACCAGACGGCCAGAAAC 60.671 60.000 2.24 0.00 34.57 2.78
303 315 1.070786 GACCAGACGGCCAGAAACA 59.929 57.895 2.24 0.00 34.57 2.83
304 316 1.227853 ACCAGACGGCCAGAAACAC 60.228 57.895 2.24 0.00 34.57 3.32
305 317 1.966451 CCAGACGGCCAGAAACACC 60.966 63.158 2.24 0.00 0.00 4.16
309 321 2.281208 CGGCCAGAAACACCGGAA 60.281 61.111 9.46 0.00 43.23 4.30
310 322 2.325082 CGGCCAGAAACACCGGAAG 61.325 63.158 9.46 1.96 43.23 3.46
311 323 1.228154 GGCCAGAAACACCGGAAGT 60.228 57.895 9.46 2.78 0.00 3.01
378 391 1.108776 GGAGGCATGGACGTACTGTA 58.891 55.000 0.00 0.00 0.00 2.74
418 431 3.753434 ACCTCGTCAGCTCCTGCG 61.753 66.667 0.00 0.00 45.42 5.18
419 432 3.753434 CCTCGTCAGCTCCTGCGT 61.753 66.667 0.00 0.00 45.42 5.24
460 473 0.179081 GGGTACGCCTGTTCCAGATC 60.179 60.000 0.00 0.00 37.28 2.75
461 474 0.527817 GGTACGCCTGTTCCAGATCG 60.528 60.000 0.00 0.00 35.72 3.69
465 478 1.153349 GCCTGTTCCAGATCGGGAC 60.153 63.158 14.73 10.72 44.83 4.46
523 536 2.045926 GGCCGCTGTTCTCCACAT 60.046 61.111 0.00 0.00 33.76 3.21
551 564 3.359523 ACAGTGCTCGCGTACCGA 61.360 61.111 5.77 6.34 45.15 4.69
552 565 2.102357 CAGTGCTCGCGTACCGAT 59.898 61.111 5.77 0.00 46.31 4.18
580 593 2.178273 CTGTCCGTGATCGTGCGA 59.822 61.111 0.00 0.00 35.01 5.10
601 614 5.286082 GCGAAATGCACGTAGAAAAATTGAT 59.714 36.000 0.00 0.00 45.45 2.57
616 629 7.564660 AGAAAAATTGATATGAATACTGGCCCA 59.435 33.333 0.00 0.00 0.00 5.36
620 633 3.138098 TGATATGAATACTGGCCCAAGCA 59.862 43.478 0.00 0.00 42.56 3.91
621 634 1.767759 ATGAATACTGGCCCAAGCAC 58.232 50.000 0.00 0.00 42.56 4.40
623 636 1.202989 TGAATACTGGCCCAAGCACAA 60.203 47.619 0.00 0.00 42.56 3.33
624 637 2.102578 GAATACTGGCCCAAGCACAAT 58.897 47.619 0.00 0.00 42.56 2.71
625 638 1.477553 ATACTGGCCCAAGCACAATG 58.522 50.000 0.00 0.00 42.56 2.82
626 639 0.112218 TACTGGCCCAAGCACAATGT 59.888 50.000 0.00 0.00 42.56 2.71
630 643 2.234414 CTGGCCCAAGCACAATGTAAAT 59.766 45.455 0.00 0.00 42.56 1.40
662 680 2.037902 TGCAGTTCTCCCACGTTAATCA 59.962 45.455 0.00 0.00 0.00 2.57
664 682 3.063997 GCAGTTCTCCCACGTTAATCATG 59.936 47.826 0.00 0.00 0.00 3.07
686 704 5.587289 TGAGAAGAAACAACGAAAAATGGG 58.413 37.500 0.00 0.00 0.00 4.00
687 705 4.944048 AGAAGAAACAACGAAAAATGGGG 58.056 39.130 0.00 0.00 0.00 4.96
688 706 3.744238 AGAAACAACGAAAAATGGGGG 57.256 42.857 0.00 0.00 0.00 5.40
689 707 3.035363 AGAAACAACGAAAAATGGGGGT 58.965 40.909 0.00 0.00 0.00 4.95
690 708 2.900716 AACAACGAAAAATGGGGGTG 57.099 45.000 0.00 0.00 0.00 4.61
691 709 2.074729 ACAACGAAAAATGGGGGTGA 57.925 45.000 0.00 0.00 0.00 4.02
692 710 1.684450 ACAACGAAAAATGGGGGTGAC 59.316 47.619 0.00 0.00 0.00 3.67
693 711 1.683917 CAACGAAAAATGGGGGTGACA 59.316 47.619 0.00 0.00 0.00 3.58
694 712 1.324383 ACGAAAAATGGGGGTGACAC 58.676 50.000 0.00 0.00 0.00 3.67
702 720 4.813346 GGGGTGACACCGTGAATT 57.187 55.556 18.40 0.00 39.83 2.17
703 721 3.030415 GGGGTGACACCGTGAATTT 57.970 52.632 18.40 0.00 39.83 1.82
704 722 0.879090 GGGGTGACACCGTGAATTTC 59.121 55.000 18.40 1.73 39.83 2.17
705 723 0.515564 GGGTGACACCGTGAATTTCG 59.484 55.000 18.40 0.00 39.83 3.46
706 724 0.110373 GGTGACACCGTGAATTTCGC 60.110 55.000 9.33 0.00 0.00 4.70
712 730 2.399611 CGTGAATTTCGCGCTCCC 59.600 61.111 18.20 0.00 43.59 4.30
713 731 2.399611 GTGAATTTCGCGCTCCCG 59.600 61.111 5.56 0.00 37.57 5.14
714 732 2.817834 TGAATTTCGCGCTCCCGG 60.818 61.111 5.56 0.00 34.32 5.73
741 759 2.143925 GTCGAGGGACACAAAAAGAGG 58.856 52.381 0.00 0.00 42.91 3.69
742 760 2.043992 TCGAGGGACACAAAAAGAGGA 58.956 47.619 0.00 0.00 0.00 3.71
743 761 2.037251 TCGAGGGACACAAAAAGAGGAG 59.963 50.000 0.00 0.00 0.00 3.69
744 762 2.784347 GAGGGACACAAAAAGAGGAGG 58.216 52.381 0.00 0.00 0.00 4.30
745 763 2.372172 GAGGGACACAAAAAGAGGAGGA 59.628 50.000 0.00 0.00 0.00 3.71
746 764 2.373502 AGGGACACAAAAAGAGGAGGAG 59.626 50.000 0.00 0.00 0.00 3.69
747 765 2.106684 GGGACACAAAAAGAGGAGGAGT 59.893 50.000 0.00 0.00 0.00 3.85
748 766 3.403968 GGACACAAAAAGAGGAGGAGTC 58.596 50.000 0.00 0.00 0.00 3.36
749 767 3.403968 GACACAAAAAGAGGAGGAGTCC 58.596 50.000 0.00 0.00 44.33 3.85
757 775 4.554036 GGAGGAGTCCGGCATGGC 62.554 72.222 9.69 9.69 37.80 4.40
758 776 3.785859 GAGGAGTCCGGCATGGCA 61.786 66.667 20.37 0.00 37.80 4.92
759 777 4.101448 AGGAGTCCGGCATGGCAC 62.101 66.667 20.37 10.80 37.80 5.01
793 811 1.757306 CAGTCCCACCTGAGCTTGT 59.243 57.895 0.00 0.00 34.23 3.16
810 839 3.948719 TGCCCTCCACCCGACAAC 61.949 66.667 0.00 0.00 0.00 3.32
813 842 4.029809 CCTCCACCCGACAACCCC 62.030 72.222 0.00 0.00 0.00 4.95
991 1041 1.273606 GCTCGGATCATAGCTTAGCCA 59.726 52.381 0.00 0.00 35.80 4.75
998 1048 0.034059 CATAGCTTAGCCAGGTCGGG 59.966 60.000 0.00 0.00 34.13 5.14
1026 1076 4.899239 CTGATCCGGCGGCTGTCC 62.899 72.222 23.83 8.42 0.00 4.02
1313 1392 2.528743 CCGCCGACTGCTGCTAATG 61.529 63.158 0.00 0.00 38.05 1.90
1315 1394 1.450312 GCCGACTGCTGCTAATGGT 60.450 57.895 0.00 0.00 36.87 3.55
1316 1395 0.179084 GCCGACTGCTGCTAATGGTA 60.179 55.000 0.00 0.00 36.87 3.25
1368 1469 3.354645 GGCGCGGCCCTATTTAGC 61.355 66.667 23.89 0.00 44.06 3.09
1369 1470 2.590575 GCGCGGCCCTATTTAGCA 60.591 61.111 8.83 0.00 0.00 3.49
1370 1471 2.607892 GCGCGGCCCTATTTAGCAG 61.608 63.158 8.83 0.00 0.00 4.24
1459 1574 5.140177 CCGTAGTATTATCGTTCGGTGTAC 58.860 45.833 0.00 0.00 33.20 2.90
1460 1575 4.835463 CGTAGTATTATCGTTCGGTGTACG 59.165 45.833 0.00 0.00 46.11 3.67
1461 1576 4.882671 AGTATTATCGTTCGGTGTACGT 57.117 40.909 0.00 0.00 44.69 3.57
1462 1577 5.984233 AGTATTATCGTTCGGTGTACGTA 57.016 39.130 0.00 0.00 44.69 3.57
1463 1578 5.738370 AGTATTATCGTTCGGTGTACGTAC 58.262 41.667 18.90 18.90 44.69 3.67
1464 1579 4.882671 ATTATCGTTCGGTGTACGTACT 57.117 40.909 25.12 5.50 44.69 2.73
1465 1580 5.984233 ATTATCGTTCGGTGTACGTACTA 57.016 39.130 25.12 10.10 44.69 1.82
1466 1581 5.984233 TTATCGTTCGGTGTACGTACTAT 57.016 39.130 25.12 9.11 44.69 2.12
1467 1582 3.656651 TCGTTCGGTGTACGTACTATG 57.343 47.619 25.12 14.59 44.69 2.23
1468 1583 3.000041 TCGTTCGGTGTACGTACTATGT 59.000 45.455 25.12 0.00 44.69 2.29
1469 1584 4.177783 TCGTTCGGTGTACGTACTATGTA 58.822 43.478 25.12 2.87 44.69 2.29
1484 1599 6.916387 CGTACTATGTAATGTACCACCTGAAG 59.084 42.308 0.00 0.00 36.59 3.02
1502 1617 2.113860 AGCGACGGGTAGTGTACTAA 57.886 50.000 0.00 0.00 0.00 2.24
1506 1621 3.265791 CGACGGGTAGTGTACTAAGAGT 58.734 50.000 0.00 0.00 0.00 3.24
1523 1645 5.718724 AAGAGTACCACCAGTAGTTGTAC 57.281 43.478 0.00 0.00 44.28 2.90
1527 1649 4.802999 GTACCACCAGTAGTTGTACTCAC 58.197 47.826 0.00 0.00 41.93 3.51
1528 1650 2.631545 ACCACCAGTAGTTGTACTCACC 59.368 50.000 0.00 0.00 37.40 4.02
1529 1651 2.028385 CCACCAGTAGTTGTACTCACCC 60.028 54.545 0.00 0.00 37.40 4.61
1530 1652 2.028385 CACCAGTAGTTGTACTCACCCC 60.028 54.545 0.00 0.00 37.40 4.95
1531 1653 2.158204 ACCAGTAGTTGTACTCACCCCT 60.158 50.000 0.00 0.00 37.40 4.79
1532 1654 2.496470 CCAGTAGTTGTACTCACCCCTC 59.504 54.545 0.00 0.00 37.40 4.30
1533 1655 3.162666 CAGTAGTTGTACTCACCCCTCA 58.837 50.000 0.00 0.00 37.40 3.86
1534 1656 3.576982 CAGTAGTTGTACTCACCCCTCAA 59.423 47.826 0.00 0.00 37.40 3.02
1535 1657 4.039973 CAGTAGTTGTACTCACCCCTCAAA 59.960 45.833 0.00 0.00 37.40 2.69
1536 1658 4.657039 AGTAGTTGTACTCACCCCTCAAAA 59.343 41.667 0.00 0.00 34.00 2.44
1537 1659 4.513406 AGTTGTACTCACCCCTCAAAAA 57.487 40.909 0.00 0.00 0.00 1.94
1592 1714 3.187227 GGCTACTGGTTTATGATGATGCG 59.813 47.826 0.00 0.00 0.00 4.73
1615 1763 4.197750 CTCTGTAGCATGAAGAAATGGCT 58.802 43.478 0.00 0.00 0.00 4.75
1616 1764 5.357742 TCTGTAGCATGAAGAAATGGCTA 57.642 39.130 0.00 0.00 0.00 3.93
1617 1765 5.118990 TCTGTAGCATGAAGAAATGGCTAC 58.881 41.667 13.51 13.51 37.50 3.58
1618 1766 5.102953 TGTAGCATGAAGAAATGGCTACT 57.897 39.130 19.09 0.00 37.67 2.57
1619 1767 4.877823 TGTAGCATGAAGAAATGGCTACTG 59.122 41.667 19.09 0.00 37.67 2.74
1622 1770 3.445096 GCATGAAGAAATGGCTACTGGTT 59.555 43.478 0.00 0.00 0.00 3.67
1861 2140 1.415200 GTTGGCCCTAGCTAGCTACT 58.585 55.000 20.67 0.00 39.73 2.57
1921 2200 2.101380 GTGAGAGGCGACGAGAGC 59.899 66.667 0.00 0.00 0.00 4.09
1922 2201 2.045829 TGAGAGGCGACGAGAGCT 60.046 61.111 0.00 0.00 34.52 4.09
1923 2202 1.090625 GTGAGAGGCGACGAGAGCTA 61.091 60.000 0.00 0.00 34.52 3.32
1924 2203 0.812014 TGAGAGGCGACGAGAGCTAG 60.812 60.000 0.00 0.00 34.52 3.42
1928 2207 1.161563 AGGCGACGAGAGCTAGTAGC 61.162 60.000 14.62 14.62 42.84 3.58
1955 2235 0.179936 CTAGCTTTGGGAGGAGCCAG 59.820 60.000 0.00 0.00 39.71 4.85
2098 2417 3.418047 ACAGTATTACAGTTTGGGTGGC 58.582 45.455 0.00 0.00 0.00 5.01
2176 2504 3.443925 GGCCGCCTTTCCTCTTGC 61.444 66.667 0.71 0.00 0.00 4.01
2302 2637 1.887854 TCAGTCCGTCACCATTACGAA 59.112 47.619 0.00 0.00 42.90 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.672397 CACATACGCATGAGACAGCTATC 59.328 47.826 2.50 0.00 35.96 2.08
2 3 3.068732 ACACATACGCATGAGACAGCTAT 59.931 43.478 2.50 0.00 35.96 2.97
3 4 2.427095 ACACATACGCATGAGACAGCTA 59.573 45.455 2.50 0.00 35.96 3.32
4 5 1.205655 ACACATACGCATGAGACAGCT 59.794 47.619 2.50 0.00 35.96 4.24
5 6 1.590238 GACACATACGCATGAGACAGC 59.410 52.381 2.50 0.00 35.96 4.40
6 7 2.196749 GGACACATACGCATGAGACAG 58.803 52.381 2.50 0.00 35.96 3.51
7 8 1.469079 CGGACACATACGCATGAGACA 60.469 52.381 2.50 0.00 35.96 3.41
8 9 1.200483 CGGACACATACGCATGAGAC 58.800 55.000 2.50 0.00 35.96 3.36
9 10 3.641031 CGGACACATACGCATGAGA 57.359 52.632 2.50 0.00 35.96 3.27
16 17 2.554806 TTAGTCTGCGGACACATACG 57.445 50.000 27.02 0.00 44.36 3.06
17 18 4.041740 TGATTAGTCTGCGGACACATAC 57.958 45.455 27.02 14.00 44.36 2.39
18 19 4.099419 ACATGATTAGTCTGCGGACACATA 59.901 41.667 27.02 8.66 44.36 2.29
19 20 3.118629 ACATGATTAGTCTGCGGACACAT 60.119 43.478 27.02 20.58 44.36 3.21
20 21 2.233676 ACATGATTAGTCTGCGGACACA 59.766 45.455 27.02 19.43 44.36 3.72
21 22 2.860735 GACATGATTAGTCTGCGGACAC 59.139 50.000 27.02 14.95 44.36 3.67
22 23 2.159099 GGACATGATTAGTCTGCGGACA 60.159 50.000 27.02 8.35 44.36 4.02
23 24 2.159099 TGGACATGATTAGTCTGCGGAC 60.159 50.000 18.39 18.39 42.41 4.79
24 25 2.107366 TGGACATGATTAGTCTGCGGA 58.893 47.619 0.00 0.00 36.29 5.54
25 26 2.602257 TGGACATGATTAGTCTGCGG 57.398 50.000 0.00 0.00 36.29 5.69
26 27 2.804527 CCATGGACATGATTAGTCTGCG 59.195 50.000 5.56 0.00 41.20 5.18
27 28 4.077300 TCCATGGACATGATTAGTCTGC 57.923 45.455 11.44 0.00 41.20 4.26
28 29 6.293698 TCATTCCATGGACATGATTAGTCTG 58.706 40.000 24.15 5.20 41.20 3.51
29 30 6.505048 TCATTCCATGGACATGATTAGTCT 57.495 37.500 24.15 0.00 41.20 3.24
30 31 6.713903 ACATCATTCCATGGACATGATTAGTC 59.286 38.462 30.06 0.00 41.20 2.59
31 32 6.489022 CACATCATTCCATGGACATGATTAGT 59.511 38.462 30.06 25.54 41.20 2.24
32 33 6.072119 CCACATCATTCCATGGACATGATTAG 60.072 42.308 30.06 25.91 41.20 1.73
33 34 5.771165 CCACATCATTCCATGGACATGATTA 59.229 40.000 30.06 17.15 41.20 1.75
34 35 4.587262 CCACATCATTCCATGGACATGATT 59.413 41.667 30.06 23.06 41.20 2.57
35 36 4.149598 CCACATCATTCCATGGACATGAT 58.850 43.478 28.50 28.50 41.20 2.45
36 37 3.558033 CCACATCATTCCATGGACATGA 58.442 45.455 27.32 27.32 41.20 3.07
37 38 2.626266 CCCACATCATTCCATGGACATG 59.374 50.000 15.91 19.69 38.51 3.21
38 39 2.515005 TCCCACATCATTCCATGGACAT 59.485 45.455 15.91 8.72 33.80 3.06
39 40 1.921748 TCCCACATCATTCCATGGACA 59.078 47.619 15.91 6.51 33.80 4.02
40 41 2.579873 CTCCCACATCATTCCATGGAC 58.420 52.381 15.91 0.00 33.80 4.02
41 42 1.496001 CCTCCCACATCATTCCATGGA 59.504 52.381 11.44 11.44 33.80 3.41
42 43 1.496001 TCCTCCCACATCATTCCATGG 59.504 52.381 4.97 4.97 0.00 3.66
43 44 3.301794 TTCCTCCCACATCATTCCATG 57.698 47.619 0.00 0.00 0.00 3.66
44 45 4.547886 ATTTCCTCCCACATCATTCCAT 57.452 40.909 0.00 0.00 0.00 3.41
45 46 4.335735 AATTTCCTCCCACATCATTCCA 57.664 40.909 0.00 0.00 0.00 3.53
46 47 5.221048 CGTAAATTTCCTCCCACATCATTCC 60.221 44.000 0.00 0.00 0.00 3.01
47 48 5.221048 CCGTAAATTTCCTCCCACATCATTC 60.221 44.000 0.00 0.00 0.00 2.67
48 49 4.644685 CCGTAAATTTCCTCCCACATCATT 59.355 41.667 0.00 0.00 0.00 2.57
49 50 4.207165 CCGTAAATTTCCTCCCACATCAT 58.793 43.478 0.00 0.00 0.00 2.45
50 51 3.616219 CCGTAAATTTCCTCCCACATCA 58.384 45.455 0.00 0.00 0.00 3.07
51 52 2.949644 CCCGTAAATTTCCTCCCACATC 59.050 50.000 0.00 0.00 0.00 3.06
52 53 2.310647 ACCCGTAAATTTCCTCCCACAT 59.689 45.455 0.00 0.00 0.00 3.21
53 54 1.706305 ACCCGTAAATTTCCTCCCACA 59.294 47.619 0.00 0.00 0.00 4.17
54 55 2.362736 GACCCGTAAATTTCCTCCCAC 58.637 52.381 0.00 0.00 0.00 4.61
55 56 1.065998 CGACCCGTAAATTTCCTCCCA 60.066 52.381 0.00 0.00 0.00 4.37
56 57 1.660167 CGACCCGTAAATTTCCTCCC 58.340 55.000 0.00 0.00 0.00 4.30
57 58 1.012086 GCGACCCGTAAATTTCCTCC 58.988 55.000 0.00 0.00 0.00 4.30
58 59 1.012086 GGCGACCCGTAAATTTCCTC 58.988 55.000 0.00 0.00 0.00 3.71
59 60 3.164026 GGCGACCCGTAAATTTCCT 57.836 52.632 0.00 0.00 0.00 3.36
72 73 1.067846 TCATATATGCGTCAGGGCGAC 60.068 52.381 7.92 0.00 41.62 5.19
73 74 1.253100 TCATATATGCGTCAGGGCGA 58.747 50.000 7.92 0.00 35.06 5.54
74 75 2.299993 ATCATATATGCGTCAGGGCG 57.700 50.000 7.92 0.00 35.06 6.13
75 76 6.929625 AGATATATCATATATGCGTCAGGGC 58.070 40.000 15.08 0.00 0.00 5.19
76 77 8.178313 CGTAGATATATCATATATGCGTCAGGG 58.822 40.741 15.08 0.00 0.00 4.45
77 78 8.936864 TCGTAGATATATCATATATGCGTCAGG 58.063 37.037 15.08 0.00 0.00 3.86
78 79 9.965748 CTCGTAGATATATCATATATGCGTCAG 57.034 37.037 15.08 0.97 33.89 3.51
79 80 9.706691 TCTCGTAGATATATCATATATGCGTCA 57.293 33.333 15.08 0.00 33.89 4.35
136 137 2.141535 ACAAGTCTCTCGTGTTGAGC 57.858 50.000 0.00 0.00 44.86 4.26
137 138 6.771188 ATTAAACAAGTCTCTCGTGTTGAG 57.229 37.500 0.75 0.00 45.07 3.02
138 139 7.548196 AAATTAAACAAGTCTCTCGTGTTGA 57.452 32.000 0.75 0.00 45.07 3.18
139 140 8.548721 AGTAAATTAAACAAGTCTCTCGTGTTG 58.451 33.333 0.75 0.00 45.07 3.33
144 151 7.510630 CACCAGTAAATTAAACAAGTCTCTCG 58.489 38.462 0.00 0.00 0.00 4.04
160 167 2.805295 CGTCCACTCTTGCACCAGTAAA 60.805 50.000 0.00 0.00 0.00 2.01
163 170 1.069765 CGTCCACTCTTGCACCAGT 59.930 57.895 0.00 0.00 0.00 4.00
164 171 1.669115 CCGTCCACTCTTGCACCAG 60.669 63.158 0.00 0.00 0.00 4.00
165 172 2.377628 GACCGTCCACTCTTGCACCA 62.378 60.000 0.00 0.00 0.00 4.17
166 173 1.668151 GACCGTCCACTCTTGCACC 60.668 63.158 0.00 0.00 0.00 5.01
167 174 1.668151 GGACCGTCCACTCTTGCAC 60.668 63.158 13.05 0.00 36.28 4.57
168 175 2.137528 TGGACCGTCCACTCTTGCA 61.138 57.895 16.73 0.00 42.67 4.08
220 232 3.582780 GAGGAACCGGTTACAGTTACTG 58.417 50.000 30.96 11.21 37.28 2.74
246 258 6.825213 ACCGGTTACAGTTACTCTTTTTCTTT 59.175 34.615 0.00 0.00 0.00 2.52
248 260 5.922053 ACCGGTTACAGTTACTCTTTTTCT 58.078 37.500 0.00 0.00 0.00 2.52
249 261 7.307396 GGTTACCGGTTACAGTTACTCTTTTTC 60.307 40.741 23.92 0.00 0.00 2.29
250 262 6.483307 GGTTACCGGTTACAGTTACTCTTTTT 59.517 38.462 23.92 0.00 0.00 1.94
255 267 4.237724 GTGGTTACCGGTTACAGTTACTC 58.762 47.826 23.92 6.52 0.00 2.59
274 286 1.004918 GTCTGGTCTCAACCCGTGG 60.005 63.158 0.00 0.00 45.83 4.94
290 302 2.999739 TTCCGGTGTTTCTGGCCGTC 63.000 60.000 0.00 0.00 43.56 4.79
291 303 3.109592 TTCCGGTGTTTCTGGCCGT 62.110 57.895 0.00 0.00 43.56 5.68
292 304 2.281208 TTCCGGTGTTTCTGGCCG 60.281 61.111 0.00 0.00 42.13 6.13
293 305 1.228154 ACTTCCGGTGTTTCTGGCC 60.228 57.895 0.00 0.00 42.13 5.36
294 306 0.534203 TCACTTCCGGTGTTTCTGGC 60.534 55.000 0.00 0.00 45.50 4.85
295 307 1.226746 GTCACTTCCGGTGTTTCTGG 58.773 55.000 0.00 0.00 45.50 3.86
296 308 0.859232 CGTCACTTCCGGTGTTTCTG 59.141 55.000 0.00 0.00 45.50 3.02
297 309 0.249741 CCGTCACTTCCGGTGTTTCT 60.250 55.000 0.00 0.00 45.50 2.52
298 310 2.231820 CCGTCACTTCCGGTGTTTC 58.768 57.895 0.00 0.00 45.50 2.78
299 311 4.449391 CCGTCACTTCCGGTGTTT 57.551 55.556 0.00 0.00 45.50 2.83
305 317 3.751246 TACCGGCCGTCACTTCCG 61.751 66.667 26.12 8.44 42.58 4.30
306 318 2.125793 GTACCGGCCGTCACTTCC 60.126 66.667 26.12 0.12 0.00 3.46
307 319 1.445582 CTGTACCGGCCGTCACTTC 60.446 63.158 26.12 8.59 0.00 3.01
308 320 2.654877 CTGTACCGGCCGTCACTT 59.345 61.111 26.12 5.01 0.00 3.16
309 321 4.065281 GCTGTACCGGCCGTCACT 62.065 66.667 26.12 5.72 0.00 3.41
342 354 1.746615 CCTCGGCCAGTGATTGTGG 60.747 63.158 2.24 0.00 38.21 4.17
366 379 1.588824 CGGCCAGTACAGTACGTCCA 61.589 60.000 2.24 0.00 0.00 4.02
460 473 2.525248 CGTCGCCATTGATGTCCCG 61.525 63.158 0.00 0.00 0.00 5.14
461 474 1.153449 TCGTCGCCATTGATGTCCC 60.153 57.895 0.00 0.00 0.00 4.46
465 478 2.525248 CCCGTCGTCGCCATTGATG 61.525 63.158 0.00 0.00 35.54 3.07
501 514 2.435059 GAGAACAGCGGCCACTCC 60.435 66.667 2.24 0.00 0.00 3.85
551 564 1.126488 ACGGACAGGCTCATCATGAT 58.874 50.000 1.18 1.18 0.00 2.45
552 565 0.176449 CACGGACAGGCTCATCATGA 59.824 55.000 0.00 0.00 0.00 3.07
580 593 9.853555 TTCATATCAATTTTTCTACGTGCATTT 57.146 25.926 0.00 0.00 0.00 2.32
590 603 7.564660 TGGGCCAGTATTCATATCAATTTTTCT 59.435 33.333 0.00 0.00 0.00 2.52
596 609 4.768968 GCTTGGGCCAGTATTCATATCAAT 59.231 41.667 6.23 0.00 0.00 2.57
601 614 2.240921 TGTGCTTGGGCCAGTATTCATA 59.759 45.455 6.23 0.00 37.74 2.15
610 623 1.709578 TTTACATTGTGCTTGGGCCA 58.290 45.000 0.00 0.00 37.74 5.36
616 629 6.922957 ACGTTGAAATGATTTACATTGTGCTT 59.077 30.769 0.00 0.00 46.90 3.91
620 633 6.212235 TGCACGTTGAAATGATTTACATTGT 58.788 32.000 0.00 0.00 46.90 2.71
621 634 6.363088 ACTGCACGTTGAAATGATTTACATTG 59.637 34.615 0.00 0.00 46.90 2.82
623 636 6.012658 ACTGCACGTTGAAATGATTTACAT 57.987 33.333 0.00 0.00 41.45 2.29
624 637 5.431420 ACTGCACGTTGAAATGATTTACA 57.569 34.783 0.00 0.00 0.00 2.41
625 638 6.142817 AGAACTGCACGTTGAAATGATTTAC 58.857 36.000 6.31 0.00 35.56 2.01
626 639 6.312399 AGAACTGCACGTTGAAATGATTTA 57.688 33.333 6.31 0.00 35.56 1.40
630 643 2.548057 GGAGAACTGCACGTTGAAATGA 59.452 45.455 6.31 0.00 35.56 2.57
662 680 6.215845 CCCATTTTTCGTTGTTTCTTCTCAT 58.784 36.000 0.00 0.00 0.00 2.90
664 682 4.982295 CCCCATTTTTCGTTGTTTCTTCTC 59.018 41.667 0.00 0.00 0.00 2.87
686 704 0.515564 CGAAATTCACGGTGTCACCC 59.484 55.000 16.60 0.00 33.75 4.61
687 705 0.110373 GCGAAATTCACGGTGTCACC 60.110 55.000 12.40 12.40 34.05 4.02
688 706 0.450482 CGCGAAATTCACGGTGTCAC 60.450 55.000 0.00 0.00 0.00 3.67
689 707 1.856688 CGCGAAATTCACGGTGTCA 59.143 52.632 0.00 0.00 0.00 3.58
690 708 1.509162 GCGCGAAATTCACGGTGTC 60.509 57.895 12.10 0.00 0.00 3.67
691 709 1.897398 GAGCGCGAAATTCACGGTGT 61.897 55.000 12.10 0.00 32.56 4.16
692 710 1.225745 GAGCGCGAAATTCACGGTG 60.226 57.895 12.10 0.56 32.56 4.94
693 711 2.388232 GGAGCGCGAAATTCACGGT 61.388 57.895 12.10 7.85 35.24 4.83
694 712 2.399611 GGAGCGCGAAATTCACGG 59.600 61.111 12.10 0.00 0.00 4.94
695 713 2.399611 GGGAGCGCGAAATTCACG 59.600 61.111 12.10 0.00 0.00 4.35
696 714 2.399611 CGGGAGCGCGAAATTCAC 59.600 61.111 12.10 0.81 0.00 3.18
697 715 2.817834 CCGGGAGCGCGAAATTCA 60.818 61.111 12.10 0.00 0.00 2.57
698 716 3.573491 CCCGGGAGCGCGAAATTC 61.573 66.667 18.48 0.38 0.00 2.17
720 738 2.484770 CCTCTTTTTGTGTCCCTCGACA 60.485 50.000 0.00 0.00 46.91 4.35
721 739 2.143925 CCTCTTTTTGTGTCCCTCGAC 58.856 52.381 0.00 0.00 39.66 4.20
722 740 2.037251 CTCCTCTTTTTGTGTCCCTCGA 59.963 50.000 0.00 0.00 0.00 4.04
723 741 2.417719 CTCCTCTTTTTGTGTCCCTCG 58.582 52.381 0.00 0.00 0.00 4.63
724 742 2.372172 TCCTCCTCTTTTTGTGTCCCTC 59.628 50.000 0.00 0.00 0.00 4.30
725 743 2.373502 CTCCTCCTCTTTTTGTGTCCCT 59.626 50.000 0.00 0.00 0.00 4.20
726 744 2.106684 ACTCCTCCTCTTTTTGTGTCCC 59.893 50.000 0.00 0.00 0.00 4.46
727 745 3.403968 GACTCCTCCTCTTTTTGTGTCC 58.596 50.000 0.00 0.00 0.00 4.02
728 746 3.403968 GGACTCCTCCTCTTTTTGTGTC 58.596 50.000 0.00 0.00 33.07 3.67
729 747 2.224305 CGGACTCCTCCTCTTTTTGTGT 60.224 50.000 0.00 0.00 33.79 3.72
730 748 2.417719 CGGACTCCTCCTCTTTTTGTG 58.582 52.381 0.00 0.00 33.79 3.33
731 749 1.348036 CCGGACTCCTCCTCTTTTTGT 59.652 52.381 0.00 0.00 33.79 2.83
732 750 1.946283 GCCGGACTCCTCCTCTTTTTG 60.946 57.143 5.05 0.00 33.79 2.44
733 751 0.325272 GCCGGACTCCTCCTCTTTTT 59.675 55.000 5.05 0.00 33.79 1.94
734 752 0.836400 TGCCGGACTCCTCCTCTTTT 60.836 55.000 5.05 0.00 33.79 2.27
735 753 0.618968 ATGCCGGACTCCTCCTCTTT 60.619 55.000 5.05 0.00 33.79 2.52
736 754 1.002274 ATGCCGGACTCCTCCTCTT 59.998 57.895 5.05 0.00 33.79 2.85
737 755 1.760086 CATGCCGGACTCCTCCTCT 60.760 63.158 5.05 0.00 33.79 3.69
738 756 2.801631 CCATGCCGGACTCCTCCTC 61.802 68.421 5.05 0.00 36.56 3.71
739 757 2.765807 CCATGCCGGACTCCTCCT 60.766 66.667 5.05 0.00 36.56 3.69
740 758 4.554036 GCCATGCCGGACTCCTCC 62.554 72.222 5.05 0.00 36.56 4.30
741 759 3.785859 TGCCATGCCGGACTCCTC 61.786 66.667 5.05 0.00 36.56 3.71
742 760 4.101448 GTGCCATGCCGGACTCCT 62.101 66.667 5.05 0.00 36.56 3.69
793 811 3.948719 GTTGTCGGGTGGAGGGCA 61.949 66.667 0.00 0.00 0.00 5.36
824 853 2.357517 GTGTGACTGTGAGCCCCG 60.358 66.667 0.00 0.00 0.00 5.73
828 857 1.004440 GGGAGGTGTGACTGTGAGC 60.004 63.158 0.00 0.00 0.00 4.26
831 860 2.343758 CGGGGAGGTGTGACTGTG 59.656 66.667 0.00 0.00 0.00 3.66
832 861 2.923035 CCGGGGAGGTGTGACTGT 60.923 66.667 0.00 0.00 34.51 3.55
833 862 4.394712 GCCGGGGAGGTGTGACTG 62.395 72.222 2.18 0.00 43.70 3.51
902 937 2.262915 GAGCTGACCGGTGACCAG 59.737 66.667 14.63 15.28 0.00 4.00
903 938 3.311110 GGAGCTGACCGGTGACCA 61.311 66.667 14.63 2.16 0.00 4.02
904 939 3.311110 TGGAGCTGACCGGTGACC 61.311 66.667 14.63 0.83 0.00 4.02
905 940 2.048127 GTGGAGCTGACCGGTGAC 60.048 66.667 14.63 0.00 0.00 3.67
906 941 2.203640 AGTGGAGCTGACCGGTGA 60.204 61.111 14.63 0.65 0.00 4.02
908 943 3.374402 CGAGTGGAGCTGACCGGT 61.374 66.667 6.92 6.92 0.00 5.28
969 1019 1.068194 GCTAAGCTATGATCCGAGCGT 60.068 52.381 9.59 9.23 43.72 5.07
980 1030 1.122019 CCCCGACCTGGCTAAGCTAT 61.122 60.000 0.00 0.00 35.87 2.97
991 1041 2.765807 CTGCCTCATCCCCGACCT 60.766 66.667 0.00 0.00 0.00 3.85
998 1048 1.301558 CGGATCAGCTGCCTCATCC 60.302 63.158 18.10 18.10 32.75 3.51
1206 1285 3.511595 TACCCGTACTCCTGCGCG 61.512 66.667 0.00 0.00 0.00 6.86
1380 1481 0.249911 ATAATCTTCCAGGCGGCGAC 60.250 55.000 12.98 8.50 0.00 5.19
1381 1482 0.468226 AATAATCTTCCAGGCGGCGA 59.532 50.000 12.98 0.00 0.00 5.54
1434 1544 3.250762 CACCGAACGATAATACTACGGGA 59.749 47.826 0.00 0.00 42.54 5.14
1435 1545 3.003689 ACACCGAACGATAATACTACGGG 59.996 47.826 0.00 0.00 42.54 5.28
1436 1546 4.214980 ACACCGAACGATAATACTACGG 57.785 45.455 0.00 0.00 43.61 4.02
1438 1548 5.738370 ACGTACACCGAACGATAATACTAC 58.262 41.667 2.27 0.00 42.90 2.73
1440 1550 4.882671 ACGTACACCGAACGATAATACT 57.117 40.909 2.27 0.00 42.90 2.12
1441 1551 5.738370 AGTACGTACACCGAACGATAATAC 58.262 41.667 26.55 0.00 42.90 1.89
1459 1574 6.381481 TCAGGTGGTACATTACATAGTACG 57.619 41.667 0.00 0.00 44.52 3.67
1460 1575 6.700520 GCTTCAGGTGGTACATTACATAGTAC 59.299 42.308 0.00 0.00 44.52 2.73
1461 1576 6.460537 CGCTTCAGGTGGTACATTACATAGTA 60.461 42.308 0.00 0.00 44.52 1.82
1462 1577 5.671493 GCTTCAGGTGGTACATTACATAGT 58.329 41.667 0.00 0.00 44.52 2.12
1463 1578 4.745125 CGCTTCAGGTGGTACATTACATAG 59.255 45.833 0.00 0.00 44.52 2.23
1464 1579 4.403113 TCGCTTCAGGTGGTACATTACATA 59.597 41.667 0.00 0.00 44.52 2.29
1465 1580 3.196901 TCGCTTCAGGTGGTACATTACAT 59.803 43.478 0.00 0.00 44.52 2.29
1466 1581 2.563620 TCGCTTCAGGTGGTACATTACA 59.436 45.455 0.00 0.00 44.52 2.41
1467 1582 2.928116 GTCGCTTCAGGTGGTACATTAC 59.072 50.000 0.00 0.00 44.52 1.89
1468 1583 2.416296 CGTCGCTTCAGGTGGTACATTA 60.416 50.000 0.00 0.00 44.52 1.90
1469 1584 1.671850 CGTCGCTTCAGGTGGTACATT 60.672 52.381 0.00 0.00 44.52 2.71
1484 1599 2.009774 TCTTAGTACACTACCCGTCGC 58.990 52.381 0.00 0.00 0.00 5.19
1506 1621 3.828451 GGTGAGTACAACTACTGGTGGTA 59.172 47.826 0.00 0.00 32.96 3.25
1508 1623 2.028385 GGGTGAGTACAACTACTGGTGG 60.028 54.545 0.00 0.00 32.96 4.61
1509 1624 2.028385 GGGGTGAGTACAACTACTGGTG 60.028 54.545 0.00 0.00 32.96 4.17
1534 1656 7.335924 TGCAGAGTACAACTACTGTTTCTTTTT 59.664 33.333 0.00 0.00 39.64 1.94
1535 1657 6.821665 TGCAGAGTACAACTACTGTTTCTTTT 59.178 34.615 0.00 0.00 39.64 2.27
1536 1658 6.346096 TGCAGAGTACAACTACTGTTTCTTT 58.654 36.000 0.00 0.00 39.64 2.52
1537 1659 5.914033 TGCAGAGTACAACTACTGTTTCTT 58.086 37.500 0.00 0.00 39.64 2.52
1538 1660 5.302059 TCTGCAGAGTACAACTACTGTTTCT 59.698 40.000 13.74 0.00 39.64 2.52
1539 1661 5.529791 TCTGCAGAGTACAACTACTGTTTC 58.470 41.667 13.74 0.00 39.64 2.78
1540 1662 5.531122 TCTGCAGAGTACAACTACTGTTT 57.469 39.130 13.74 0.00 39.64 2.83
1541 1663 5.531122 TTCTGCAGAGTACAACTACTGTT 57.469 39.130 17.43 0.00 39.64 3.16
1542 1664 5.730296 ATTCTGCAGAGTACAACTACTGT 57.270 39.130 17.43 0.00 42.47 3.55
1616 1764 9.686683 ATAAACAGAGCAAGATAATAAACCAGT 57.313 29.630 0.00 0.00 0.00 4.00
1617 1765 9.941664 CATAAACAGAGCAAGATAATAAACCAG 57.058 33.333 0.00 0.00 0.00 4.00
1618 1766 8.405531 GCATAAACAGAGCAAGATAATAAACCA 58.594 33.333 0.00 0.00 0.00 3.67
1619 1767 8.405531 TGCATAAACAGAGCAAGATAATAAACC 58.594 33.333 0.00 0.00 34.97 3.27
1774 2047 1.183549 GTGACAGTACGTCCCTGGAT 58.816 55.000 16.73 0.32 44.71 3.41
1777 2050 3.794690 CAGTGACAGTACGTCCCTG 57.205 57.895 12.26 12.26 42.58 4.45
1778 2051 0.959553 CACAGTGACAGTACGTCCCT 59.040 55.000 12.97 6.30 44.71 4.20
1780 2053 1.607628 ACTCACAGTGACAGTACGTCC 59.392 52.381 0.00 6.74 44.71 4.79
1839 2118 0.760945 AGCTAGCTAGGGCCAACGAT 60.761 55.000 17.69 0.00 39.73 3.73
1861 2140 2.662866 CCTTCATGGACCGGACTACTA 58.337 52.381 9.46 0.00 38.35 1.82
1922 2201 5.071370 CCAAAGCTAGCTACTAGGCTACTA 58.929 45.833 19.70 0.00 42.97 1.82
1923 2202 3.892588 CCAAAGCTAGCTACTAGGCTACT 59.107 47.826 19.70 0.00 42.97 2.57
1924 2203 3.006003 CCCAAAGCTAGCTACTAGGCTAC 59.994 52.174 19.70 0.00 42.97 3.58
1928 2207 2.630580 CCTCCCAAAGCTAGCTACTAGG 59.369 54.545 19.70 16.19 34.88 3.02
1955 2235 0.379669 CGGCCAAGATCATCAGTTGC 59.620 55.000 2.24 0.00 0.00 4.17
1991 2301 1.397390 AAGTGACAAGACCCGTCCGT 61.397 55.000 0.00 0.00 32.15 4.69
1992 2302 0.666577 GAAGTGACAAGACCCGTCCG 60.667 60.000 0.00 0.00 32.15 4.79
1993 2303 0.666577 CGAAGTGACAAGACCCGTCC 60.667 60.000 0.00 0.00 32.15 4.79
1994 2304 1.282930 GCGAAGTGACAAGACCCGTC 61.283 60.000 0.00 0.00 0.00 4.79
2118 2437 3.942748 CGGAAAGGGACGGATCATAAAAA 59.057 43.478 0.00 0.00 0.00 1.94
2119 2438 3.537580 CGGAAAGGGACGGATCATAAAA 58.462 45.455 0.00 0.00 0.00 1.52
2120 2439 2.743838 GCGGAAAGGGACGGATCATAAA 60.744 50.000 0.00 0.00 0.00 1.40
2121 2440 1.202604 GCGGAAAGGGACGGATCATAA 60.203 52.381 0.00 0.00 0.00 1.90
2122 2441 0.391597 GCGGAAAGGGACGGATCATA 59.608 55.000 0.00 0.00 0.00 2.15
2123 2442 1.146263 GCGGAAAGGGACGGATCAT 59.854 57.895 0.00 0.00 0.00 2.45
2124 2443 2.582436 GCGGAAAGGGACGGATCA 59.418 61.111 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.