Multiple sequence alignment - TraesCS3A01G083800

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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 TraesCS3A01G083800 chr3A 100.000 5835 0 0 1 5835 53843020 53837186 0.000000e+00 10776.0
1 TraesCS3A01G083800 chr3A 85.859 99 10 4 712 809 697457857 697457952 1.030000e-17 102.0
2 TraesCS3A01G083800 chr3B 96.147 5269 154 17 598 5835 66190397 66185147 0.000000e+00 8560.0
3 TraesCS3A01G083800 chr3B 80.764 733 102 15 4303 5024 170804708 170805412 2.390000e-148 536.0
4 TraesCS3A01G083800 chr3B 77.056 754 129 25 4278 5019 126652954 126653675 1.520000e-105 394.0
5 TraesCS3A01G083800 chr3B 87.009 331 33 7 137 465 66190784 66190462 1.190000e-96 364.0
6 TraesCS3A01G083800 chr3B 82.895 76 9 4 527 598 549666224 549666299 1.360000e-06 65.8
7 TraesCS3A01G083800 chr3D 97.068 3684 87 9 871 4548 42498184 42494516 0.000000e+00 6185.0
8 TraesCS3A01G083800 chr3D 96.875 1280 23 7 4573 5835 42494518 42493239 0.000000e+00 2126.0
9 TraesCS3A01G083800 chr3D 83.784 148 18 5 2 145 523388750 523388605 1.020000e-27 135.0
10 TraesCS3A01G083800 chr3D 96.970 33 1 0 813 845 42498207 42498175 8.170000e-04 56.5
11 TraesCS3A01G083800 chr2D 84.176 752 96 13 4288 5024 612521397 612520654 0.000000e+00 708.0
12 TraesCS3A01G083800 chr2D 93.182 44 2 1 2267 2310 35800105 35800063 4.880000e-06 63.9
13 TraesCS3A01G083800 chr1A 83.979 749 100 13 4288 5024 308302570 308301830 0.000000e+00 701.0
14 TraesCS3A01G083800 chr4A 81.436 738 95 18 4303 5027 619159071 619158363 3.050000e-157 566.0
15 TraesCS3A01G083800 chr4A 86.567 134 13 4 2 131 642916631 642916499 6.100000e-30 143.0
16 TraesCS3A01G083800 chr1B 85.065 154 23 0 654 807 11900726 11900879 2.180000e-34 158.0
17 TraesCS3A01G083800 chr1B 84.962 133 15 4 2 130 74506576 74506445 4.750000e-26 130.0
18 TraesCS3A01G083800 chr1B 87.143 70 7 2 530 598 346163140 346163072 1.740000e-10 78.7
19 TraesCS3A01G083800 chrUn 83.108 148 19 5 2 145 297719378 297719523 4.750000e-26 130.0
20 TraesCS3A01G083800 chrUn 83.108 148 19 5 2 145 397425472 397425327 4.750000e-26 130.0
21 TraesCS3A01G083800 chrUn 83.108 148 19 5 2 145 428410492 428410637 4.750000e-26 130.0
22 TraesCS3A01G083800 chr5B 84.962 133 15 4 2 130 549426843 549426712 4.750000e-26 130.0
23 TraesCS3A01G083800 chr5B 84.962 133 15 4 2 130 549460499 549460368 4.750000e-26 130.0
24 TraesCS3A01G083800 chr5B 81.000 100 9 9 2274 2371 52647860 52647769 2.920000e-08 71.3
25 TraesCS3A01G083800 chr4D 82.836 134 19 4 678 809 503265150 503265281 3.690000e-22 117.0
26 TraesCS3A01G083800 chr2A 84.553 123 14 4 2 120 16491395 16491274 3.690000e-22 117.0
27 TraesCS3A01G083800 chr7D 96.667 60 2 0 750 809 140833586 140833527 3.720000e-17 100.0
28 TraesCS3A01G083800 chr7A 86.667 90 7 3 2276 2365 213113538 213113454 1.730000e-15 95.3
29 TraesCS3A01G083800 chr6B 94.643 56 1 1 542 597 732849 732902 1.040000e-12 86.1
30 TraesCS3A01G083800 chr6B 80.899 89 13 3 2276 2364 172738845 172738929 3.770000e-07 67.6
31 TraesCS3A01G083800 chr1D 83.696 92 8 4 2276 2366 246951994 246951909 4.850000e-11 80.5
32 TraesCS3A01G083800 chr6A 86.301 73 8 2 527 598 500437991 500437920 1.740000e-10 78.7
33 TraesCS3A01G083800 chr6D 82.022 89 12 3 2276 2364 90111901 90111817 8.110000e-09 73.1
34 TraesCS3A01G083800 chr5D 80.808 99 8 9 2274 2371 50037517 50037429 3.770000e-07 67.6


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 TraesCS3A01G083800 chr3A 53837186 53843020 5834 True 10776.000000 10776 100.000 1 5835 1 chr3A.!!$R1 5834
1 TraesCS3A01G083800 chr3B 66185147 66190784 5637 True 4462.000000 8560 91.578 137 5835 2 chr3B.!!$R1 5698
2 TraesCS3A01G083800 chr3B 170804708 170805412 704 False 536.000000 536 80.764 4303 5024 1 chr3B.!!$F2 721
3 TraesCS3A01G083800 chr3B 126652954 126653675 721 False 394.000000 394 77.056 4278 5019 1 chr3B.!!$F1 741
4 TraesCS3A01G083800 chr3D 42493239 42498207 4968 True 2789.166667 6185 96.971 813 5835 3 chr3D.!!$R2 5022
5 TraesCS3A01G083800 chr2D 612520654 612521397 743 True 708.000000 708 84.176 4288 5024 1 chr2D.!!$R2 736
6 TraesCS3A01G083800 chr1A 308301830 308302570 740 True 701.000000 701 83.979 4288 5024 1 chr1A.!!$R1 736
7 TraesCS3A01G083800 chr4A 619158363 619159071 708 True 566.000000 566 81.436 4303 5027 1 chr4A.!!$R1 724

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
417 419 0.528924 ATAGGCACGCGAACTACACA 59.471 50.0 15.93 0.0 0.00 3.72 F
609 643 0.773644 CCAGGCATATTGGGCTACCT 59.226 55.0 0.00 0.0 42.46 3.08 F
1838 1879 0.251787 GGGAAGTGCACCAAGGGAAT 60.252 55.0 14.63 0.0 0.00 3.01 F
2504 2547 0.742635 GGAAGCCGAGAAAGCTGAGG 60.743 60.0 0.00 0.0 40.49 3.86 F
3864 3907 0.099613 GATCAGCGCTCTTCTCGTCA 59.900 55.0 7.13 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1879 0.819259 GTGGCTGAACTTGCAGTCCA 60.819 55.000 0.00 0.0 39.72 4.02 R
2063 2104 3.495193 CGCACATGTTGAGAATTCCTTG 58.505 45.455 0.65 0.0 0.00 3.61 R
3823 3866 0.801251 GTGCTGGTGATGACTTGCTC 59.199 55.000 2.69 0.0 0.00 4.26 R
4131 4174 1.067142 TCTTGTCATACTCCACGGCAC 60.067 52.381 0.00 0.0 0.00 5.01 R
5162 5221 2.169789 CACCGCAGAATCAGCTCCG 61.170 63.158 0.00 0.0 0.00 4.63 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
34 35 8.401490 AGATTGATATTGAGGAATACAAAGGC 57.599 34.615 0.00 0.00 0.00 4.35
35 36 6.959639 TTGATATTGAGGAATACAAAGGCC 57.040 37.500 0.00 0.00 0.00 5.19
36 37 6.012337 TGATATTGAGGAATACAAAGGCCA 57.988 37.500 5.01 0.00 0.00 5.36
37 38 6.064060 TGATATTGAGGAATACAAAGGCCAG 58.936 40.000 5.01 0.00 0.00 4.85
38 39 3.806949 TTGAGGAATACAAAGGCCAGT 57.193 42.857 5.01 2.63 0.00 4.00
39 40 4.919774 TTGAGGAATACAAAGGCCAGTA 57.080 40.909 5.01 5.23 0.00 2.74
40 41 4.216411 TGAGGAATACAAAGGCCAGTAC 57.784 45.455 5.01 0.00 0.00 2.73
41 42 3.585289 TGAGGAATACAAAGGCCAGTACA 59.415 43.478 5.01 0.00 0.00 2.90
42 43 4.042311 TGAGGAATACAAAGGCCAGTACAA 59.958 41.667 5.01 0.00 0.00 2.41
43 44 5.193099 AGGAATACAAAGGCCAGTACAAT 57.807 39.130 5.01 0.00 0.00 2.71
44 45 4.949856 AGGAATACAAAGGCCAGTACAATG 59.050 41.667 5.01 0.00 0.00 2.82
45 46 4.097892 GGAATACAAAGGCCAGTACAATGG 59.902 45.833 5.01 0.00 43.72 3.16
46 47 2.969821 ACAAAGGCCAGTACAATGGA 57.030 45.000 5.01 0.00 43.57 3.41
47 48 3.456380 ACAAAGGCCAGTACAATGGAT 57.544 42.857 5.01 0.00 43.57 3.41
48 49 4.584638 ACAAAGGCCAGTACAATGGATA 57.415 40.909 5.01 0.00 43.57 2.59
49 50 4.526970 ACAAAGGCCAGTACAATGGATAG 58.473 43.478 5.01 0.00 43.57 2.08
50 51 4.227300 ACAAAGGCCAGTACAATGGATAGA 59.773 41.667 5.01 0.00 43.57 1.98
51 52 4.423625 AAGGCCAGTACAATGGATAGAC 57.576 45.455 5.01 0.00 43.57 2.59
52 53 3.384168 AGGCCAGTACAATGGATAGACA 58.616 45.455 5.01 0.00 43.57 3.41
53 54 3.780294 AGGCCAGTACAATGGATAGACAA 59.220 43.478 5.01 0.00 43.57 3.18
54 55 3.877508 GGCCAGTACAATGGATAGACAAC 59.122 47.826 0.00 0.00 43.57 3.32
55 56 4.384208 GGCCAGTACAATGGATAGACAACT 60.384 45.833 0.00 0.00 43.57 3.16
56 57 4.572389 GCCAGTACAATGGATAGACAACTG 59.428 45.833 5.35 0.00 43.57 3.16
57 58 5.626809 GCCAGTACAATGGATAGACAACTGA 60.627 44.000 5.35 0.00 43.57 3.41
58 59 6.406370 CCAGTACAATGGATAGACAACTGAA 58.594 40.000 0.00 0.00 43.57 3.02
59 60 6.313905 CCAGTACAATGGATAGACAACTGAAC 59.686 42.308 0.00 0.00 43.57 3.18
60 61 6.873605 CAGTACAATGGATAGACAACTGAACA 59.126 38.462 0.00 0.00 36.13 3.18
61 62 7.550551 CAGTACAATGGATAGACAACTGAACAT 59.449 37.037 0.00 0.00 36.13 2.71
62 63 8.758829 AGTACAATGGATAGACAACTGAACATA 58.241 33.333 0.00 0.00 0.00 2.29
63 64 9.035607 GTACAATGGATAGACAACTGAACATAG 57.964 37.037 0.00 0.00 0.00 2.23
64 65 7.851228 ACAATGGATAGACAACTGAACATAGA 58.149 34.615 0.00 0.00 0.00 1.98
65 66 8.321353 ACAATGGATAGACAACTGAACATAGAA 58.679 33.333 0.00 0.00 0.00 2.10
66 67 8.607459 CAATGGATAGACAACTGAACATAGAAC 58.393 37.037 0.00 0.00 0.00 3.01
67 68 7.239763 TGGATAGACAACTGAACATAGAACA 57.760 36.000 0.00 0.00 0.00 3.18
68 69 7.676004 TGGATAGACAACTGAACATAGAACAA 58.324 34.615 0.00 0.00 0.00 2.83
69 70 8.321353 TGGATAGACAACTGAACATAGAACAAT 58.679 33.333 0.00 0.00 0.00 2.71
70 71 8.821894 GGATAGACAACTGAACATAGAACAATC 58.178 37.037 0.00 0.00 0.00 2.67
71 72 9.371136 GATAGACAACTGAACATAGAACAATCA 57.629 33.333 0.00 0.00 0.00 2.57
72 73 7.664082 AGACAACTGAACATAGAACAATCAG 57.336 36.000 0.00 0.00 42.43 2.90
73 74 6.148480 AGACAACTGAACATAGAACAATCAGC 59.852 38.462 0.00 0.00 40.86 4.26
74 75 5.764686 ACAACTGAACATAGAACAATCAGCA 59.235 36.000 0.00 0.00 40.86 4.41
75 76 6.262944 ACAACTGAACATAGAACAATCAGCAA 59.737 34.615 0.00 0.00 40.86 3.91
76 77 6.882610 ACTGAACATAGAACAATCAGCAAA 57.117 33.333 0.00 0.00 40.86 3.68
77 78 7.275888 ACTGAACATAGAACAATCAGCAAAA 57.724 32.000 0.00 0.00 40.86 2.44
78 79 7.715657 ACTGAACATAGAACAATCAGCAAAAA 58.284 30.769 0.00 0.00 40.86 1.94
115 116 4.681074 GCATACTAGCCTTCTTCTTCCT 57.319 45.455 0.00 0.00 0.00 3.36
116 117 4.627058 GCATACTAGCCTTCTTCTTCCTC 58.373 47.826 0.00 0.00 0.00 3.71
117 118 4.343814 GCATACTAGCCTTCTTCTTCCTCT 59.656 45.833 0.00 0.00 0.00 3.69
118 119 5.738783 GCATACTAGCCTTCTTCTTCCTCTG 60.739 48.000 0.00 0.00 0.00 3.35
119 120 4.054359 ACTAGCCTTCTTCTTCCTCTGA 57.946 45.455 0.00 0.00 0.00 3.27
120 121 4.619679 ACTAGCCTTCTTCTTCCTCTGAT 58.380 43.478 0.00 0.00 0.00 2.90
121 122 5.029474 ACTAGCCTTCTTCTTCCTCTGATT 58.971 41.667 0.00 0.00 0.00 2.57
122 123 6.198639 ACTAGCCTTCTTCTTCCTCTGATTA 58.801 40.000 0.00 0.00 0.00 1.75
123 124 6.843861 ACTAGCCTTCTTCTTCCTCTGATTAT 59.156 38.462 0.00 0.00 0.00 1.28
124 125 8.007742 ACTAGCCTTCTTCTTCCTCTGATTATA 58.992 37.037 0.00 0.00 0.00 0.98
125 126 7.682787 AGCCTTCTTCTTCCTCTGATTATAA 57.317 36.000 0.00 0.00 0.00 0.98
126 127 7.734942 AGCCTTCTTCTTCCTCTGATTATAAG 58.265 38.462 0.00 0.00 0.00 1.73
127 128 6.426633 GCCTTCTTCTTCCTCTGATTATAAGC 59.573 42.308 0.00 0.00 0.00 3.09
128 129 7.689066 GCCTTCTTCTTCCTCTGATTATAAGCT 60.689 40.741 1.93 0.00 0.00 3.74
129 130 7.656948 CCTTCTTCTTCCTCTGATTATAAGCTG 59.343 40.741 1.93 1.70 0.00 4.24
130 131 6.520272 TCTTCTTCCTCTGATTATAAGCTGC 58.480 40.000 1.93 0.00 0.00 5.25
131 132 5.220710 TCTTCCTCTGATTATAAGCTGCC 57.779 43.478 1.93 0.00 0.00 4.85
132 133 4.904251 TCTTCCTCTGATTATAAGCTGCCT 59.096 41.667 1.93 0.00 0.00 4.75
133 134 4.613925 TCCTCTGATTATAAGCTGCCTG 57.386 45.455 1.93 0.00 0.00 4.85
134 135 3.969976 TCCTCTGATTATAAGCTGCCTGT 59.030 43.478 1.93 0.00 0.00 4.00
135 136 4.039730 TCCTCTGATTATAAGCTGCCTGTC 59.960 45.833 1.93 0.00 0.00 3.51
162 163 1.449778 GTAGGGCTCGGTTTGGCTC 60.450 63.158 0.00 0.00 0.00 4.70
187 188 4.864704 ACAAAACACACCTTCAGTTTGT 57.135 36.364 0.00 0.00 41.17 2.83
191 192 2.365582 ACACACCTTCAGTTTGTGGTC 58.634 47.619 5.97 0.00 44.11 4.02
195 196 0.868406 CCTTCAGTTTGTGGTCGCTC 59.132 55.000 0.00 0.00 0.00 5.03
212 213 1.068748 GCTCAATCACACACAAGCCAG 60.069 52.381 0.00 0.00 0.00 4.85
214 215 3.079578 CTCAATCACACACAAGCCAGAT 58.920 45.455 0.00 0.00 0.00 2.90
273 274 7.311364 TGTTAAACGAACTATAGGAAATGGC 57.689 36.000 4.43 0.00 38.98 4.40
274 275 6.316890 TGTTAAACGAACTATAGGAAATGGCC 59.683 38.462 4.43 0.00 38.98 5.36
275 276 4.497291 AACGAACTATAGGAAATGGCCA 57.503 40.909 8.56 8.56 0.00 5.36
353 355 1.002069 ATCAAACCTGGCCAGATGGA 58.998 50.000 34.91 23.90 37.39 3.41
354 356 1.002069 TCAAACCTGGCCAGATGGAT 58.998 50.000 34.91 10.68 37.39 3.41
357 359 1.987807 AACCTGGCCAGATGGATCGG 61.988 60.000 34.91 18.04 37.39 4.18
377 379 3.033764 CGACACAACACGACCCGG 61.034 66.667 0.00 0.00 0.00 5.73
381 383 4.619227 ACAACACGACCCGGCCTG 62.619 66.667 0.00 0.00 0.00 4.85
390 392 1.053424 GACCCGGCCTGGATTATACA 58.947 55.000 21.63 0.00 42.00 2.29
397 399 2.827604 CTGGATTATACAGGCGCGG 58.172 57.895 8.83 0.00 32.38 6.46
400 402 2.165641 CTGGATTATACAGGCGCGGATA 59.834 50.000 8.83 0.00 32.38 2.59
411 413 3.627218 GCGGATAGGCACGCGAAC 61.627 66.667 15.93 3.29 46.58 3.95
417 419 0.528924 ATAGGCACGCGAACTACACA 59.471 50.000 15.93 0.00 0.00 3.72
422 424 2.048597 CGCGAACTACACAGGCCA 60.049 61.111 5.01 0.00 0.00 5.36
426 428 1.695893 CGAACTACACAGGCCATGCG 61.696 60.000 5.01 0.31 0.00 4.73
476 478 4.416516 GCCCAGGCCCATTTAATATTAGT 58.583 43.478 0.00 0.00 34.56 2.24
477 479 4.220602 GCCCAGGCCCATTTAATATTAGTG 59.779 45.833 0.00 0.02 34.56 2.74
478 480 5.393866 CCCAGGCCCATTTAATATTAGTGT 58.606 41.667 0.00 0.00 0.00 3.55
479 481 6.548321 CCCAGGCCCATTTAATATTAGTGTA 58.452 40.000 0.00 0.00 0.00 2.90
480 482 7.182060 CCCAGGCCCATTTAATATTAGTGTAT 58.818 38.462 0.00 0.00 0.00 2.29
481 483 7.673926 CCCAGGCCCATTTAATATTAGTGTATT 59.326 37.037 0.00 0.00 0.00 1.89
482 484 8.522830 CCAGGCCCATTTAATATTAGTGTATTG 58.477 37.037 0.00 0.00 0.00 1.90
483 485 9.295825 CAGGCCCATTTAATATTAGTGTATTGA 57.704 33.333 0.00 0.00 0.00 2.57
484 486 9.297037 AGGCCCATTTAATATTAGTGTATTGAC 57.703 33.333 0.00 0.00 0.00 3.18
486 488 8.234546 GCCCATTTAATATTAGTGTATTGACGG 58.765 37.037 0.00 0.00 0.00 4.79
488 490 8.999431 CCATTTAATATTAGTGTATTGACGGCT 58.001 33.333 0.00 0.00 0.00 5.52
598 632 4.648007 CCTCTAGGCCCAGGCATA 57.352 61.111 11.50 6.97 44.11 3.14
599 633 3.095262 CCTCTAGGCCCAGGCATAT 57.905 57.895 11.50 0.00 44.11 1.78
600 634 1.366319 CCTCTAGGCCCAGGCATATT 58.634 55.000 11.50 0.00 44.11 1.28
601 635 1.004044 CCTCTAGGCCCAGGCATATTG 59.996 57.143 11.50 3.68 44.11 1.90
602 636 1.004044 CTCTAGGCCCAGGCATATTGG 59.996 57.143 11.50 0.00 44.11 3.16
608 642 3.346426 CCAGGCATATTGGGCTACC 57.654 57.895 0.00 0.00 42.46 3.18
609 643 0.773644 CCAGGCATATTGGGCTACCT 59.226 55.000 0.00 0.00 42.46 3.08
610 644 1.985159 CCAGGCATATTGGGCTACCTA 59.015 52.381 0.00 0.00 42.46 3.08
611 645 2.578021 CCAGGCATATTGGGCTACCTAT 59.422 50.000 0.00 0.00 42.46 2.57
612 646 3.010584 CCAGGCATATTGGGCTACCTATT 59.989 47.826 0.00 0.00 42.46 1.73
613 647 4.227300 CCAGGCATATTGGGCTACCTATTA 59.773 45.833 0.00 0.00 42.46 0.98
614 648 5.431765 CAGGCATATTGGGCTACCTATTAG 58.568 45.833 0.00 0.00 42.46 1.73
661 695 8.544597 AATTTAAAATAAATAAATCCGGCACGC 58.455 29.630 0.00 0.00 40.11 5.34
674 708 4.988598 CACGCGTGCCCAACCTCT 62.989 66.667 28.16 0.00 0.00 3.69
675 709 3.307906 ACGCGTGCCCAACCTCTA 61.308 61.111 12.93 0.00 0.00 2.43
676 710 2.509336 CGCGTGCCCAACCTCTAG 60.509 66.667 0.00 0.00 0.00 2.43
677 711 2.125106 GCGTGCCCAACCTCTAGG 60.125 66.667 0.00 0.00 42.17 3.02
679 713 2.272471 GTGCCCAACCTCTAGGCC 59.728 66.667 0.00 0.00 46.55 5.19
680 714 3.015145 TGCCCAACCTCTAGGCCC 61.015 66.667 0.00 0.00 46.55 5.80
681 715 3.015145 GCCCAACCTCTAGGCCCA 61.015 66.667 0.00 0.00 41.00 5.36
682 716 3.049080 GCCCAACCTCTAGGCCCAG 62.049 68.421 0.00 0.00 41.00 4.45
683 717 2.378634 CCCAACCTCTAGGCCCAGG 61.379 68.421 10.85 10.85 39.32 4.45
684 718 2.592308 CAACCTCTAGGCCCAGGC 59.408 66.667 12.12 0.00 39.32 4.85
685 719 2.124996 AACCTCTAGGCCCAGGCA 59.875 61.111 11.50 0.00 44.11 4.75
705 739 2.590007 GCTCTATGCGGGCCACAG 60.590 66.667 4.39 0.00 0.00 3.66
841 875 0.818296 CCGTCGTCCTCTGATTCCTT 59.182 55.000 0.00 0.00 0.00 3.36
845 879 1.831736 TCGTCCTCTGATTCCTTTCCC 59.168 52.381 0.00 0.00 0.00 3.97
958 993 2.980246 AGCCAAACCCTAGAAAGCTT 57.020 45.000 0.00 0.00 0.00 3.74
1572 1613 3.181967 CCGGTCTTCTTCAGCGCG 61.182 66.667 0.00 0.00 33.39 6.86
1689 1730 0.881118 CCAACATGCCAAACTACGCT 59.119 50.000 0.00 0.00 0.00 5.07
1838 1879 0.251787 GGGAAGTGCACCAAGGGAAT 60.252 55.000 14.63 0.00 0.00 3.01
2016 2057 1.063764 GCTGCTAAGATGCAAGCTGAC 59.936 52.381 16.44 6.47 42.83 3.51
2052 2093 3.713764 AGCAGGCTTCATCAGGTAATACT 59.286 43.478 0.00 0.00 0.00 2.12
2063 2104 6.767902 TCATCAGGTAATACTTGCCAATTCTC 59.232 38.462 0.00 0.00 37.96 2.87
2107 2150 6.736243 GCGCTCTATTGTTGAACTAGTAGGAT 60.736 42.308 0.00 0.00 0.00 3.24
2189 2232 1.933853 CATGTTAGGTCGCAAGCCTAC 59.066 52.381 0.00 0.00 42.85 3.18
2237 2280 4.628333 TCTTAAATTACACTGCACGCCTAC 59.372 41.667 0.00 0.00 0.00 3.18
2284 2327 5.957771 TGATGCTATTTTGTACTCCCTCT 57.042 39.130 0.00 0.00 0.00 3.69
2338 2381 3.524763 TTAGCCTACAAAAACGAACGC 57.475 42.857 0.00 0.00 0.00 4.84
2504 2547 0.742635 GGAAGCCGAGAAAGCTGAGG 60.743 60.000 0.00 0.00 40.49 3.86
2822 2865 1.242076 GCAATTCCAGCAGTCACTGT 58.758 50.000 6.68 0.00 35.83 3.55
2959 3002 1.398958 GCTTTGGTGGGGAAAGTGCA 61.399 55.000 0.00 0.00 33.66 4.57
3110 3153 6.311445 ACATTACAACGTGAGATTAGAAGCAG 59.689 38.462 0.00 0.00 0.00 4.24
3156 3199 7.422399 TCTTTAGTTATTGGTTGTGTGAAAGC 58.578 34.615 0.00 0.00 0.00 3.51
3373 3416 8.729805 TCAACAGCATAATTTCTTTTGGTTTT 57.270 26.923 0.00 0.00 0.00 2.43
3790 3833 2.393271 AATCAAGAAGGTCAGCTCGG 57.607 50.000 0.00 0.00 0.00 4.63
3823 3866 2.936498 GTCACCACGACATCATAAAGGG 59.064 50.000 0.00 0.00 44.69 3.95
3839 3882 0.617413 AGGGAGCAAGTCATCACCAG 59.383 55.000 0.00 0.00 0.00 4.00
3853 3896 3.857854 CCAGCACGTGATCAGCGC 61.858 66.667 22.23 0.00 0.00 5.92
3864 3907 0.099613 GATCAGCGCTCTTCTCGTCA 59.900 55.000 7.13 0.00 0.00 4.35
3933 3976 7.678947 ACAGTGATAAGAAGGATGTCAAAAG 57.321 36.000 0.00 0.00 0.00 2.27
4003 4046 2.886523 TGGCAAAGATGAAAGGTCTGTG 59.113 45.455 0.00 0.00 34.66 3.66
4032 4075 4.388165 CGCAGTGGATAAGAATGCAGATAG 59.612 45.833 0.00 0.00 33.66 2.08
4131 4174 2.904697 TCTAGACATGATGCTGCTGG 57.095 50.000 0.00 0.00 0.00 4.85
4180 4223 7.628234 AGAATGAAGACAGTATTGAGGATGTT 58.372 34.615 0.00 0.00 0.00 2.71
4228 4271 0.465278 GAAGCTTGGGAGAGGATGGC 60.465 60.000 2.10 0.00 0.00 4.40
4254 4297 9.425893 CGATAATATTCAGAAACATGACACAAC 57.574 33.333 0.00 0.00 0.00 3.32
4264 4307 4.803098 ACATGACACAACTAGGAGTACC 57.197 45.455 0.00 0.00 0.00 3.34
4269 4312 4.280174 TGACACAACTAGGAGTACCAAGAC 59.720 45.833 0.00 0.00 38.94 3.01
4434 4478 9.175577 CAGGGATAAATATCATAGGGATGGTAT 57.824 37.037 3.07 0.00 40.49 2.73
4491 4539 5.585047 GCACTCGACCTAGGAAATACAATTT 59.415 40.000 17.98 0.00 0.00 1.82
4594 4644 2.289882 TGGTTCAGACTCTGATGGCTTG 60.290 50.000 9.63 0.00 40.39 4.01
4668 4721 0.460987 GTCATCCAGGAAGACCAGCG 60.461 60.000 13.15 0.00 38.94 5.18
4691 4745 5.334802 CGATTTGCTGATGAAACTGGTACAA 60.335 40.000 0.00 0.00 38.70 2.41
4980 5039 5.472820 GCAGGATATGAAGATCTTTTGGAGG 59.527 44.000 9.87 0.00 0.00 4.30
5162 5221 1.265365 GTTGCAGGCTTGTGAAGAGTC 59.735 52.381 0.00 0.00 0.00 3.36
5454 5515 6.936900 AGCAGCTTAATTGATCCGTATGTTAT 59.063 34.615 0.00 0.00 0.00 1.89
5477 5538 9.841295 TTATGTTCAGTAGTTGTTTACTCCTTT 57.159 29.630 0.00 0.00 38.33 3.11
5496 5557 7.671398 ACTCCTTTGGATGAATGTAGACAATTT 59.329 33.333 0.00 0.00 0.00 1.82
5713 5799 4.141018 ACATTTACTCCAGGGTGTTCCTTT 60.141 41.667 0.00 0.00 45.47 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.507329 GCCTTTGTATTCCTCAATATCAATCTA 57.493 33.333 0.00 0.00 0.00 1.98
9 10 7.449704 GGCCTTTGTATTCCTCAATATCAATCT 59.550 37.037 0.00 0.00 0.00 2.40
10 11 7.231317 TGGCCTTTGTATTCCTCAATATCAATC 59.769 37.037 3.32 0.00 0.00 2.67
11 12 7.068702 TGGCCTTTGTATTCCTCAATATCAAT 58.931 34.615 3.32 0.00 0.00 2.57
12 13 6.430864 TGGCCTTTGTATTCCTCAATATCAA 58.569 36.000 3.32 0.00 0.00 2.57
13 14 6.012337 TGGCCTTTGTATTCCTCAATATCA 57.988 37.500 3.32 0.00 0.00 2.15
14 15 6.064717 ACTGGCCTTTGTATTCCTCAATATC 58.935 40.000 3.32 0.00 0.00 1.63
15 16 6.018433 ACTGGCCTTTGTATTCCTCAATAT 57.982 37.500 3.32 0.00 0.00 1.28
16 17 5.450818 ACTGGCCTTTGTATTCCTCAATA 57.549 39.130 3.32 0.00 0.00 1.90
17 18 4.322057 ACTGGCCTTTGTATTCCTCAAT 57.678 40.909 3.32 0.00 0.00 2.57
18 19 3.806949 ACTGGCCTTTGTATTCCTCAA 57.193 42.857 3.32 0.00 0.00 3.02
19 20 3.585289 TGTACTGGCCTTTGTATTCCTCA 59.415 43.478 3.32 0.00 0.00 3.86
20 21 4.216411 TGTACTGGCCTTTGTATTCCTC 57.784 45.455 3.32 0.00 0.00 3.71
21 22 4.650972 TTGTACTGGCCTTTGTATTCCT 57.349 40.909 3.32 0.00 0.00 3.36
22 23 4.097892 CCATTGTACTGGCCTTTGTATTCC 59.902 45.833 3.32 0.00 0.00 3.01
23 24 4.947388 TCCATTGTACTGGCCTTTGTATTC 59.053 41.667 3.32 0.00 36.16 1.75
24 25 4.929479 TCCATTGTACTGGCCTTTGTATT 58.071 39.130 3.32 0.00 36.16 1.89
25 26 4.584638 TCCATTGTACTGGCCTTTGTAT 57.415 40.909 3.32 0.00 36.16 2.29
26 27 4.584638 ATCCATTGTACTGGCCTTTGTA 57.415 40.909 3.32 1.75 36.16 2.41
27 28 2.969821 TCCATTGTACTGGCCTTTGT 57.030 45.000 3.32 2.84 36.16 2.83
28 29 4.576463 GTCTATCCATTGTACTGGCCTTTG 59.424 45.833 3.32 0.00 36.16 2.77
29 30 4.227300 TGTCTATCCATTGTACTGGCCTTT 59.773 41.667 3.32 0.00 36.16 3.11
30 31 3.780294 TGTCTATCCATTGTACTGGCCTT 59.220 43.478 3.32 0.00 36.16 4.35
31 32 3.384168 TGTCTATCCATTGTACTGGCCT 58.616 45.455 3.32 0.00 36.16 5.19
32 33 3.838244 TGTCTATCCATTGTACTGGCC 57.162 47.619 0.00 0.00 36.16 5.36
33 34 4.572389 CAGTTGTCTATCCATTGTACTGGC 59.428 45.833 0.00 0.00 36.16 4.85
34 35 5.977635 TCAGTTGTCTATCCATTGTACTGG 58.022 41.667 0.00 0.00 37.66 4.00
35 36 6.873605 TGTTCAGTTGTCTATCCATTGTACTG 59.126 38.462 0.00 0.00 34.55 2.74
36 37 7.004555 TGTTCAGTTGTCTATCCATTGTACT 57.995 36.000 0.00 0.00 0.00 2.73
37 38 7.849804 ATGTTCAGTTGTCTATCCATTGTAC 57.150 36.000 0.00 0.00 0.00 2.90
38 39 8.977412 TCTATGTTCAGTTGTCTATCCATTGTA 58.023 33.333 0.00 0.00 0.00 2.41
39 40 7.851228 TCTATGTTCAGTTGTCTATCCATTGT 58.149 34.615 0.00 0.00 0.00 2.71
40 41 8.607459 GTTCTATGTTCAGTTGTCTATCCATTG 58.393 37.037 0.00 0.00 0.00 2.82
41 42 8.321353 TGTTCTATGTTCAGTTGTCTATCCATT 58.679 33.333 0.00 0.00 0.00 3.16
42 43 7.851228 TGTTCTATGTTCAGTTGTCTATCCAT 58.149 34.615 0.00 0.00 0.00 3.41
43 44 7.239763 TGTTCTATGTTCAGTTGTCTATCCA 57.760 36.000 0.00 0.00 0.00 3.41
44 45 8.723942 ATTGTTCTATGTTCAGTTGTCTATCC 57.276 34.615 0.00 0.00 0.00 2.59
45 46 9.371136 TGATTGTTCTATGTTCAGTTGTCTATC 57.629 33.333 0.00 0.00 0.00 2.08
46 47 9.376075 CTGATTGTTCTATGTTCAGTTGTCTAT 57.624 33.333 0.00 0.00 31.36 1.98
47 48 7.331934 GCTGATTGTTCTATGTTCAGTTGTCTA 59.668 37.037 0.00 0.00 36.91 2.59
48 49 6.148480 GCTGATTGTTCTATGTTCAGTTGTCT 59.852 38.462 0.00 0.00 36.91 3.41
49 50 6.073058 TGCTGATTGTTCTATGTTCAGTTGTC 60.073 38.462 0.00 0.00 36.91 3.18
50 51 5.764686 TGCTGATTGTTCTATGTTCAGTTGT 59.235 36.000 0.00 0.00 36.91 3.32
51 52 6.245115 TGCTGATTGTTCTATGTTCAGTTG 57.755 37.500 0.00 0.00 36.91 3.16
52 53 6.882610 TTGCTGATTGTTCTATGTTCAGTT 57.117 33.333 0.00 0.00 36.91 3.16
53 54 6.882610 TTTGCTGATTGTTCTATGTTCAGT 57.117 33.333 0.00 0.00 36.91 3.41
94 95 4.343814 AGAGGAAGAAGAAGGCTAGTATGC 59.656 45.833 0.00 0.00 0.00 3.14
95 96 5.596361 TCAGAGGAAGAAGAAGGCTAGTATG 59.404 44.000 0.00 0.00 0.00 2.39
96 97 5.772004 TCAGAGGAAGAAGAAGGCTAGTAT 58.228 41.667 0.00 0.00 0.00 2.12
97 98 5.194473 TCAGAGGAAGAAGAAGGCTAGTA 57.806 43.478 0.00 0.00 0.00 1.82
98 99 4.054359 TCAGAGGAAGAAGAAGGCTAGT 57.946 45.455 0.00 0.00 0.00 2.57
99 100 5.612725 AATCAGAGGAAGAAGAAGGCTAG 57.387 43.478 0.00 0.00 0.00 3.42
100 101 8.783660 TTATAATCAGAGGAAGAAGAAGGCTA 57.216 34.615 0.00 0.00 0.00 3.93
101 102 7.682787 TTATAATCAGAGGAAGAAGAAGGCT 57.317 36.000 0.00 0.00 0.00 4.58
102 103 6.426633 GCTTATAATCAGAGGAAGAAGAAGGC 59.573 42.308 0.00 0.00 0.00 4.35
103 104 7.656948 CAGCTTATAATCAGAGGAAGAAGAAGG 59.343 40.741 0.00 0.00 0.00 3.46
104 105 7.171337 GCAGCTTATAATCAGAGGAAGAAGAAG 59.829 40.741 0.00 0.00 0.00 2.85
105 106 6.989169 GCAGCTTATAATCAGAGGAAGAAGAA 59.011 38.462 0.00 0.00 0.00 2.52
106 107 6.463614 GGCAGCTTATAATCAGAGGAAGAAGA 60.464 42.308 0.00 0.00 0.00 2.87
107 108 5.700373 GGCAGCTTATAATCAGAGGAAGAAG 59.300 44.000 0.00 0.00 0.00 2.85
108 109 5.367937 AGGCAGCTTATAATCAGAGGAAGAA 59.632 40.000 0.00 0.00 0.00 2.52
109 110 4.904251 AGGCAGCTTATAATCAGAGGAAGA 59.096 41.667 0.00 0.00 0.00 2.87
110 111 4.996122 CAGGCAGCTTATAATCAGAGGAAG 59.004 45.833 0.00 0.00 0.00 3.46
111 112 4.410228 ACAGGCAGCTTATAATCAGAGGAA 59.590 41.667 0.00 0.00 0.00 3.36
112 113 3.969976 ACAGGCAGCTTATAATCAGAGGA 59.030 43.478 0.00 0.00 0.00 3.71
113 114 4.314121 GACAGGCAGCTTATAATCAGAGG 58.686 47.826 0.00 0.00 0.00 3.69
114 115 3.986572 CGACAGGCAGCTTATAATCAGAG 59.013 47.826 0.00 0.00 0.00 3.35
115 116 3.243873 CCGACAGGCAGCTTATAATCAGA 60.244 47.826 0.00 0.00 0.00 3.27
116 117 3.062763 CCGACAGGCAGCTTATAATCAG 58.937 50.000 0.00 0.00 0.00 2.90
117 118 2.698274 TCCGACAGGCAGCTTATAATCA 59.302 45.455 0.00 0.00 37.47 2.57
118 119 3.321497 CTCCGACAGGCAGCTTATAATC 58.679 50.000 0.00 0.00 37.47 1.75
119 120 2.037772 CCTCCGACAGGCAGCTTATAAT 59.962 50.000 0.00 0.00 34.56 1.28
120 121 1.412710 CCTCCGACAGGCAGCTTATAA 59.587 52.381 0.00 0.00 34.56 0.98
121 122 1.040646 CCTCCGACAGGCAGCTTATA 58.959 55.000 0.00 0.00 34.56 0.98
122 123 0.687757 TCCTCCGACAGGCAGCTTAT 60.688 55.000 0.00 0.00 43.08 1.73
123 124 0.687757 ATCCTCCGACAGGCAGCTTA 60.688 55.000 0.00 0.00 43.08 3.09
124 125 1.557269 AATCCTCCGACAGGCAGCTT 61.557 55.000 0.00 0.00 43.08 3.74
125 126 1.992277 AATCCTCCGACAGGCAGCT 60.992 57.895 0.00 0.00 43.08 4.24
126 127 1.817099 CAATCCTCCGACAGGCAGC 60.817 63.158 0.00 0.00 43.08 5.25
127 128 0.824109 TACAATCCTCCGACAGGCAG 59.176 55.000 0.00 0.00 43.08 4.85
128 129 0.824109 CTACAATCCTCCGACAGGCA 59.176 55.000 0.00 0.00 43.08 4.75
129 130 0.105039 CCTACAATCCTCCGACAGGC 59.895 60.000 0.00 0.00 43.08 4.85
130 131 0.753262 CCCTACAATCCTCCGACAGG 59.247 60.000 0.00 0.00 45.15 4.00
131 132 0.105039 GCCCTACAATCCTCCGACAG 59.895 60.000 0.00 0.00 0.00 3.51
132 133 0.325296 AGCCCTACAATCCTCCGACA 60.325 55.000 0.00 0.00 0.00 4.35
133 134 0.389757 GAGCCCTACAATCCTCCGAC 59.610 60.000 0.00 0.00 0.00 4.79
134 135 1.107538 CGAGCCCTACAATCCTCCGA 61.108 60.000 0.00 0.00 0.00 4.55
135 136 1.364171 CGAGCCCTACAATCCTCCG 59.636 63.158 0.00 0.00 0.00 4.63
162 163 6.018343 ACAAACTGAAGGTGTGTTTTGTTTTG 60.018 34.615 0.00 0.00 43.31 2.44
187 188 0.105778 TGTGTGTGATTGAGCGACCA 59.894 50.000 0.00 0.00 0.00 4.02
191 192 0.110056 GGCTTGTGTGTGATTGAGCG 60.110 55.000 0.00 0.00 0.00 5.03
195 196 3.928727 AATCTGGCTTGTGTGTGATTG 57.071 42.857 0.00 0.00 0.00 2.67
230 231 9.160496 GTTTAACATTTATTTTCATGATGCCCA 57.840 29.630 0.00 0.00 0.00 5.36
260 261 5.183904 GGCTTACATTGGCCATTTCCTATAG 59.816 44.000 6.09 0.00 46.84 1.31
261 262 5.076873 GGCTTACATTGGCCATTTCCTATA 58.923 41.667 6.09 0.00 46.84 1.31
272 273 1.478105 CCTTCTTGGGCTTACATTGGC 59.522 52.381 0.00 0.00 0.00 4.52
273 274 2.493278 CACCTTCTTGGGCTTACATTGG 59.507 50.000 0.00 0.00 41.11 3.16
274 275 2.094545 GCACCTTCTTGGGCTTACATTG 60.095 50.000 0.00 0.00 41.11 2.82
275 276 2.171003 GCACCTTCTTGGGCTTACATT 58.829 47.619 0.00 0.00 41.11 2.71
315 316 0.824109 TACTGTCATGCCTTCTCGGG 59.176 55.000 0.00 0.00 0.00 5.14
316 317 2.101415 TGATACTGTCATGCCTTCTCGG 59.899 50.000 0.00 0.00 0.00 4.63
326 327 2.308570 TGGCCAGGTTTGATACTGTCAT 59.691 45.455 0.00 0.00 36.54 3.06
329 331 1.985159 TCTGGCCAGGTTTGATACTGT 59.015 47.619 32.23 0.00 32.90 3.55
353 355 2.307309 CGTGTTGTGTCGTGCCGAT 61.307 57.895 0.67 0.00 38.42 4.18
354 356 2.957489 CGTGTTGTGTCGTGCCGA 60.957 61.111 0.00 0.00 0.00 5.54
357 359 2.624264 GGTCGTGTTGTGTCGTGC 59.376 61.111 0.00 0.00 0.00 5.34
362 364 4.922026 GGCCGGGTCGTGTTGTGT 62.922 66.667 2.18 0.00 0.00 3.72
370 372 0.037605 GTATAATCCAGGCCGGGTCG 60.038 60.000 22.25 0.00 34.36 4.79
381 383 2.481449 CCTATCCGCGCCTGTATAATCC 60.481 54.545 0.00 0.00 0.00 3.01
383 385 1.134788 GCCTATCCGCGCCTGTATAAT 60.135 52.381 0.00 0.00 0.00 1.28
394 396 2.672908 TAGTTCGCGTGCCTATCCGC 62.673 60.000 5.77 0.00 46.10 5.54
397 399 1.197910 GTGTAGTTCGCGTGCCTATC 58.802 55.000 5.77 1.56 0.00 2.08
400 402 1.372997 CTGTGTAGTTCGCGTGCCT 60.373 57.895 5.77 2.91 0.00 4.75
411 413 2.514592 CCCGCATGGCCTGTGTAG 60.515 66.667 3.32 2.17 33.29 2.74
457 459 9.295825 TCAATACACTAATATTAAATGGGCCTG 57.704 33.333 4.53 0.00 0.00 4.85
458 460 9.297037 GTCAATACACTAATATTAAATGGGCCT 57.703 33.333 4.53 0.00 0.00 5.19
460 462 8.234546 CCGTCAATACACTAATATTAAATGGGC 58.765 37.037 9.91 0.00 0.00 5.36
461 463 8.234546 GCCGTCAATACACTAATATTAAATGGG 58.765 37.037 9.91 0.00 0.00 4.00
467 469 9.184062 CGTTTAGCCGTCAATACACTAATATTA 57.816 33.333 0.00 0.00 0.00 0.98
468 470 7.707893 ACGTTTAGCCGTCAATACACTAATATT 59.292 33.333 0.00 0.00 35.95 1.28
471 473 5.290158 CACGTTTAGCCGTCAATACACTAAT 59.710 40.000 0.00 0.00 39.45 1.73
472 474 4.622313 CACGTTTAGCCGTCAATACACTAA 59.378 41.667 0.00 0.00 39.45 2.24
474 476 2.991190 CACGTTTAGCCGTCAATACACT 59.009 45.455 0.00 0.00 39.45 3.55
475 477 2.733026 ACACGTTTAGCCGTCAATACAC 59.267 45.455 0.00 0.00 39.45 2.90
476 478 2.988493 GACACGTTTAGCCGTCAATACA 59.012 45.455 0.00 0.00 39.45 2.29
477 479 2.988493 TGACACGTTTAGCCGTCAATAC 59.012 45.455 2.01 0.00 39.45 1.89
478 480 3.300852 TGACACGTTTAGCCGTCAATA 57.699 42.857 2.01 0.00 39.45 1.90
479 481 2.157834 TGACACGTTTAGCCGTCAAT 57.842 45.000 2.01 0.00 39.45 2.57
480 482 1.937278 TTGACACGTTTAGCCGTCAA 58.063 45.000 11.53 11.53 43.96 3.18
481 483 2.157834 ATTGACACGTTTAGCCGTCA 57.842 45.000 0.44 0.44 39.45 4.35
482 484 2.988493 TGTATTGACACGTTTAGCCGTC 59.012 45.455 0.00 0.00 39.45 4.79
483 485 2.733026 GTGTATTGACACGTTTAGCCGT 59.267 45.455 0.00 0.00 46.23 5.68
484 486 3.363788 GTGTATTGACACGTTTAGCCG 57.636 47.619 0.00 0.00 46.23 5.52
570 604 4.880537 CTAGAGGCTGGGCACGCG 62.881 72.222 3.53 3.53 0.00 6.01
571 605 4.537433 CCTAGAGGCTGGGCACGC 62.537 72.222 0.00 0.00 0.00 5.34
635 669 8.544597 GCGTGCCGGATTTATTTATTTTAAATT 58.455 29.630 5.05 0.00 31.19 1.82
636 670 7.096394 CGCGTGCCGGATTTATTTATTTTAAAT 60.096 33.333 5.05 0.00 33.16 1.40
637 671 6.196724 CGCGTGCCGGATTTATTTATTTTAAA 59.803 34.615 5.05 0.00 0.00 1.52
638 672 5.681982 CGCGTGCCGGATTTATTTATTTTAA 59.318 36.000 5.05 0.00 0.00 1.52
639 673 5.206299 CGCGTGCCGGATTTATTTATTTTA 58.794 37.500 5.05 0.00 0.00 1.52
640 674 4.039032 CGCGTGCCGGATTTATTTATTTT 58.961 39.130 5.05 0.00 0.00 1.82
641 675 3.065648 ACGCGTGCCGGATTTATTTATTT 59.934 39.130 12.93 0.00 42.52 1.40
642 676 2.614983 ACGCGTGCCGGATTTATTTATT 59.385 40.909 12.93 0.00 42.52 1.40
643 677 2.032377 CACGCGTGCCGGATTTATTTAT 60.032 45.455 28.16 0.00 42.52 1.40
644 678 1.328069 CACGCGTGCCGGATTTATTTA 59.672 47.619 28.16 0.00 42.52 1.40
645 679 0.098025 CACGCGTGCCGGATTTATTT 59.902 50.000 28.16 0.00 42.52 1.40
646 680 1.719117 CACGCGTGCCGGATTTATT 59.281 52.632 28.16 0.00 42.52 1.40
647 681 3.405464 CACGCGTGCCGGATTTAT 58.595 55.556 28.16 0.00 42.52 1.40
657 691 3.583276 TAGAGGTTGGGCACGCGTG 62.583 63.158 34.01 34.01 0.00 5.34
658 692 3.296709 CTAGAGGTTGGGCACGCGT 62.297 63.158 5.58 5.58 0.00 6.01
659 693 2.509336 CTAGAGGTTGGGCACGCG 60.509 66.667 3.53 3.53 0.00 6.01
660 694 2.125106 CCTAGAGGTTGGGCACGC 60.125 66.667 0.00 0.00 0.00 5.34
665 699 2.378634 CCTGGGCCTAGAGGTTGGG 61.379 68.421 19.36 0.00 37.57 4.12
666 700 3.049080 GCCTGGGCCTAGAGGTTGG 62.049 68.421 19.36 0.85 37.57 3.77
667 701 2.300967 TGCCTGGGCCTAGAGGTTG 61.301 63.158 19.36 0.77 41.09 3.77
668 702 2.124996 TGCCTGGGCCTAGAGGTT 59.875 61.111 19.36 0.00 41.09 3.50
669 703 2.689034 GTGCCTGGGCCTAGAGGT 60.689 66.667 19.36 0.00 41.09 3.85
670 704 3.854669 CGTGCCTGGGCCTAGAGG 61.855 72.222 19.36 14.26 41.09 3.69
671 705 3.854669 CCGTGCCTGGGCCTAGAG 61.855 72.222 19.36 8.96 41.09 2.43
678 712 2.109799 CATAGAGCCGTGCCTGGG 59.890 66.667 0.00 0.00 0.00 4.45
679 713 2.590007 GCATAGAGCCGTGCCTGG 60.590 66.667 0.00 0.00 37.23 4.45
680 714 2.963854 CGCATAGAGCCGTGCCTG 60.964 66.667 0.00 0.00 41.38 4.85
681 715 4.227134 CCGCATAGAGCCGTGCCT 62.227 66.667 0.00 0.00 41.38 4.75
690 724 4.175337 GCCTGTGGCCCGCATAGA 62.175 66.667 0.00 0.00 44.06 1.98
807 841 1.816074 GACGGTGATACTGCCCAAAA 58.184 50.000 0.00 0.00 0.00 2.44
808 842 0.390603 CGACGGTGATACTGCCCAAA 60.391 55.000 0.00 0.00 0.00 3.28
958 993 1.822613 CGACGGCAGAGCTAGGGTA 60.823 63.158 0.00 0.00 0.00 3.69
1422 1463 2.331805 CCATCTAGGTCGTCGCCG 59.668 66.667 0.00 0.00 0.00 6.46
1557 1598 3.491652 GCCGCGCTGAAGAAGACC 61.492 66.667 5.56 0.00 0.00 3.85
1640 1681 3.626930 TGGTTGAGCATATTGGGGTAAC 58.373 45.455 0.00 0.00 0.00 2.50
1641 1682 3.525609 TCTGGTTGAGCATATTGGGGTAA 59.474 43.478 0.00 0.00 0.00 2.85
1701 1742 2.856988 AAGCCCGGGAAGGAACCA 60.857 61.111 29.31 0.00 45.00 3.67
1838 1879 0.819259 GTGGCTGAACTTGCAGTCCA 60.819 55.000 0.00 0.00 39.72 4.02
2063 2104 3.495193 CGCACATGTTGAGAATTCCTTG 58.505 45.455 0.65 0.00 0.00 3.61
2107 2150 8.040132 CAGGACCATCAGGCAAATTTTAATTAA 58.960 33.333 0.00 0.00 39.06 1.40
2237 2280 5.408604 AGATTTTGTAACTGGACTTGCTACG 59.591 40.000 0.00 0.00 0.00 3.51
2405 2448 8.454106 AGTGCATGAAATAACTCATAAGAACAC 58.546 33.333 0.00 0.00 34.20 3.32
2635 2678 5.003804 GCTTCTTCTGGTTTGGAATACTCA 58.996 41.667 0.00 0.00 0.00 3.41
2822 2865 2.279741 GGCTATTGACGTCTGCATCAA 58.720 47.619 17.92 3.10 39.09 2.57
2959 3002 4.990526 TCTCTTTGGCATCCTTTTCTTCT 58.009 39.130 0.00 0.00 0.00 2.85
3223 3266 7.551974 TCATCAAAAAGGAAGCTATCTCTTCAG 59.448 37.037 5.96 0.00 43.14 3.02
3373 3416 2.708861 TCAGGGTTCCTTCTGCAGTTTA 59.291 45.455 14.67 0.00 0.00 2.01
3790 3833 1.150536 TGGTGACCTTGAACCAGCC 59.849 57.895 2.11 0.00 41.56 4.85
3823 3866 0.801251 GTGCTGGTGATGACTTGCTC 59.199 55.000 2.69 0.00 0.00 4.26
3839 3882 2.018582 GAAGAGCGCTGATCACGTGC 62.019 60.000 18.48 17.58 38.13 5.34
3853 3896 1.406898 TGCCTGCTATGACGAGAAGAG 59.593 52.381 0.00 0.00 0.00 2.85
3864 3907 3.393609 TCTGGATCTTGAATGCCTGCTAT 59.606 43.478 0.00 0.00 0.00 2.97
3904 3947 5.661458 ACATCCTTCTTATCACTGTTACGG 58.339 41.667 0.00 0.00 0.00 4.02
3933 3976 1.483827 TGTCATCCTGCACCTCAGATC 59.516 52.381 0.00 0.00 45.72 2.75
4003 4046 2.961526 TCTTATCCACTGCGTCCTTC 57.038 50.000 0.00 0.00 0.00 3.46
4081 4124 5.068198 GTGATTGCCATTGTCAATATCCAGT 59.932 40.000 0.00 0.00 34.59 4.00
4131 4174 1.067142 TCTTGTCATACTCCACGGCAC 60.067 52.381 0.00 0.00 0.00 5.01
4180 4223 5.879763 TCAGATTTTGACCTTGGAGAATCA 58.120 37.500 0.00 0.00 36.25 2.57
4228 4271 9.425893 GTTGTGTCATGTTTCTGAATATTATCG 57.574 33.333 0.00 0.00 0.00 2.92
4254 4297 4.008330 TGTCTTCGTCTTGGTACTCCTAG 58.992 47.826 0.00 0.00 37.80 3.02
4264 4307 2.084610 TGCCATCTGTCTTCGTCTTG 57.915 50.000 0.00 0.00 0.00 3.02
4269 4312 2.693069 ACTTCTTGCCATCTGTCTTCG 58.307 47.619 0.00 0.00 0.00 3.79
4434 4478 1.618343 TCTTCGACTCATGCTGGTCAA 59.382 47.619 11.65 6.27 33.19 3.18
4491 4539 3.845992 TGAAGACAAGGGATCATCAAGGA 59.154 43.478 0.00 0.00 0.00 3.36
4594 4644 3.126000 GCCTAACTTCAGTGTCATGCTTC 59.874 47.826 0.00 0.00 0.00 3.86
4668 4721 5.627499 TGTACCAGTTTCATCAGCAAATC 57.373 39.130 0.00 0.00 0.00 2.17
5162 5221 2.169789 CACCGCAGAATCAGCTCCG 61.170 63.158 0.00 0.00 0.00 4.63
5477 5538 6.209192 ACAGCAAAATTGTCTACATTCATCCA 59.791 34.615 0.00 0.00 0.00 3.41
5596 5669 4.445735 GGGGAAAAGGAAAAAGGAAAAGGG 60.446 45.833 0.00 0.00 0.00 3.95
5713 5799 6.695429 CATGCTGCTTATCTCTGGAACTATA 58.305 40.000 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.