Multiple sequence alignment - TraesCS3A01G306400

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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 TraesCS3A01G306400 chr3A 100.000 4208 0 0 1 4208 543181507 543177300 0.000000e+00 7771
1 TraesCS3A01G306400 chr3B 92.371 3408 166 36 512 3870 534190026 534193388 0.000000e+00 4767
2 TraesCS3A01G306400 chr3B 88.439 346 20 5 116 461 534189684 534190009 2.360000e-107 399
3 TraesCS3A01G306400 chr3B 89.058 329 24 9 890 1210 95456164 95456488 8.480000e-107 398
4 TraesCS3A01G306400 chr3B 85.404 322 29 9 3874 4193 534193508 534193813 6.790000e-83 318
5 TraesCS3A01G306400 chr3D 90.598 3510 178 59 171 3622 408314275 408317690 0.000000e+00 4514
6 TraesCS3A01G306400 chr3D 89.695 262 13 4 3815 4067 408317690 408317946 5.250000e-84 322
7 TraesCS3A01G306400 chr3D 95.833 96 4 0 4098 4193 408317950 408318045 5.630000e-34 156


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 TraesCS3A01G306400 chr3A 543177300 543181507 4207 True 7771 7771 100.000 1 4208 1 chr3A.!!$R1 4207
1 TraesCS3A01G306400 chr3B 534189684 534193813 4129 False 1828 4767 88.738 116 4193 3 chr3B.!!$F2 4077
2 TraesCS3A01G306400 chr3D 408314275 408318045 3770 False 1664 4514 92.042 171 4193 3 chr3D.!!$F1 4022

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
904 963 0.107459 GGCACAGATCTTCCCACTCC 60.107 60.0 0.00 0.00 0.00 3.85 F
1496 1564 0.107897 TTCACCGTGAACTGCAGTGT 60.108 50.0 22.49 10.78 30.26 3.55 F
3008 3098 0.038159 AGTCGAGGAAACAAGCTCCG 60.038 55.0 0.00 0.00 38.08 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2049 0.106918 CTACCTCTCCCTGCTCGACT 60.107 60.0 0.0 0.0 0.00 4.18 R
3013 3103 0.250234 CTCCTTTGGATGTGCCGAGA 59.750 55.0 0.0 0.0 40.66 4.04 R
4175 4402 0.833287 ATAGCATCGGCAGTGTCCTT 59.167 50.0 0.0 0.0 44.61 3.36 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
25 26 4.395583 GCAGCGTGCAGTTGAGGC 62.396 66.667 5.30 0.00 44.26 4.70
26 27 2.974148 CAGCGTGCAGTTGAGGCA 60.974 61.111 0.00 0.00 39.32 4.75
27 28 2.033141 AGCGTGCAGTTGAGGCAT 59.967 55.556 0.00 0.00 44.11 4.40
29 30 3.659334 CGTGCAGTTGAGGCATGT 58.341 55.556 0.00 0.00 44.11 3.21
30 31 2.839629 CGTGCAGTTGAGGCATGTA 58.160 52.632 0.00 0.00 44.11 2.29
31 32 0.443869 CGTGCAGTTGAGGCATGTAC 59.556 55.000 0.00 0.00 44.11 2.90
32 33 0.443869 GTGCAGTTGAGGCATGTACG 59.556 55.000 0.00 0.00 44.11 3.67
33 34 1.298157 TGCAGTTGAGGCATGTACGC 61.298 55.000 0.00 0.00 36.11 4.42
34 35 1.021390 GCAGTTGAGGCATGTACGCT 61.021 55.000 0.00 0.00 0.00 5.07
35 36 1.442769 CAGTTGAGGCATGTACGCTT 58.557 50.000 0.00 0.00 0.00 4.68
36 37 1.129251 CAGTTGAGGCATGTACGCTTG 59.871 52.381 0.00 0.00 0.00 4.01
37 38 1.156736 GTTGAGGCATGTACGCTTGT 58.843 50.000 0.00 0.00 0.00 3.16
38 39 1.128692 GTTGAGGCATGTACGCTTGTC 59.871 52.381 0.00 0.00 0.00 3.18
39 40 0.608130 TGAGGCATGTACGCTTGTCT 59.392 50.000 0.00 0.00 37.41 3.41
40 41 1.002366 GAGGCATGTACGCTTGTCTG 58.998 55.000 2.55 0.00 35.28 3.51
41 42 0.608130 AGGCATGTACGCTTGTCTGA 59.392 50.000 0.00 0.00 34.10 3.27
42 43 1.208052 AGGCATGTACGCTTGTCTGAT 59.792 47.619 0.00 0.00 34.10 2.90
43 44 1.328680 GGCATGTACGCTTGTCTGATG 59.671 52.381 0.00 0.00 0.00 3.07
44 45 1.267732 GCATGTACGCTTGTCTGATGC 60.268 52.381 0.00 0.00 0.00 3.91
45 46 1.328680 CATGTACGCTTGTCTGATGCC 59.671 52.381 0.00 0.00 0.00 4.40
46 47 0.391130 TGTACGCTTGTCTGATGCCC 60.391 55.000 0.00 0.00 0.00 5.36
47 48 1.090052 GTACGCTTGTCTGATGCCCC 61.090 60.000 0.00 0.00 0.00 5.80
48 49 2.572095 TACGCTTGTCTGATGCCCCG 62.572 60.000 0.00 0.00 0.00 5.73
49 50 3.512516 GCTTGTCTGATGCCCCGC 61.513 66.667 0.00 0.00 0.00 6.13
50 51 2.270205 CTTGTCTGATGCCCCGCT 59.730 61.111 0.00 0.00 0.00 5.52
51 52 2.046023 TTGTCTGATGCCCCGCTG 60.046 61.111 0.00 0.00 0.00 5.18
52 53 3.626996 TTGTCTGATGCCCCGCTGG 62.627 63.158 0.00 0.00 37.09 4.85
65 66 4.828296 GCTGGCCCAGGTCCCATG 62.828 72.222 13.78 0.00 31.21 3.66
66 67 3.341629 CTGGCCCAGGTCCCATGT 61.342 66.667 1.63 0.00 0.00 3.21
67 68 3.650298 CTGGCCCAGGTCCCATGTG 62.650 68.421 1.63 0.00 0.00 3.21
68 69 4.447342 GGCCCAGGTCCCATGTGG 62.447 72.222 0.00 0.00 0.00 4.17
70 71 4.802051 CCCAGGTCCCATGTGGCG 62.802 72.222 0.00 0.00 0.00 5.69
88 89 2.360350 CCAGCGCCACAGGAACAT 60.360 61.111 2.29 0.00 0.00 2.71
89 90 2.693762 CCAGCGCCACAGGAACATG 61.694 63.158 2.29 0.00 0.00 3.21
90 91 3.058160 AGCGCCACAGGAACATGC 61.058 61.111 2.29 0.00 0.00 4.06
91 92 4.120331 GCGCCACAGGAACATGCC 62.120 66.667 0.00 0.00 0.00 4.40
92 93 2.672651 CGCCACAGGAACATGCCA 60.673 61.111 0.00 0.00 0.00 4.92
93 94 2.048023 CGCCACAGGAACATGCCAT 61.048 57.895 0.00 0.00 0.00 4.40
94 95 1.514087 GCCACAGGAACATGCCATG 59.486 57.895 2.40 2.40 0.00 3.66
95 96 1.952102 GCCACAGGAACATGCCATGG 61.952 60.000 7.63 7.63 38.71 3.66
96 97 0.323633 CCACAGGAACATGCCATGGA 60.324 55.000 18.40 0.31 38.22 3.41
97 98 1.687054 CCACAGGAACATGCCATGGAT 60.687 52.381 18.40 3.14 38.22 3.41
98 99 1.407618 CACAGGAACATGCCATGGATG 59.592 52.381 18.40 17.85 33.60 3.51
99 100 0.387929 CAGGAACATGCCATGGATGC 59.612 55.000 18.40 0.00 33.60 3.91
100 101 1.105167 AGGAACATGCCATGGATGCG 61.105 55.000 18.40 2.33 33.60 4.73
101 102 1.386525 GGAACATGCCATGGATGCGT 61.387 55.000 18.40 8.10 33.60 5.24
103 104 2.027024 CATGCCATGGATGCGTGC 59.973 61.111 18.40 0.00 38.74 5.34
104 105 3.221389 ATGCCATGGATGCGTGCC 61.221 61.111 18.40 0.00 0.00 5.01
105 106 4.737177 TGCCATGGATGCGTGCCA 62.737 61.111 18.40 0.00 40.24 4.92
106 107 3.221389 GCCATGGATGCGTGCCAT 61.221 61.111 18.40 0.00 46.76 4.40
107 108 1.898094 GCCATGGATGCGTGCCATA 60.898 57.895 18.40 0.00 44.08 2.74
108 109 1.859427 GCCATGGATGCGTGCCATAG 61.859 60.000 18.40 4.67 44.08 2.23
109 110 0.250424 CCATGGATGCGTGCCATAGA 60.250 55.000 5.56 0.00 44.08 1.98
110 111 1.154197 CATGGATGCGTGCCATAGAG 58.846 55.000 8.88 0.00 44.08 2.43
111 112 1.051008 ATGGATGCGTGCCATAGAGA 58.949 50.000 7.80 0.00 44.07 3.10
112 113 0.829990 TGGATGCGTGCCATAGAGAA 59.170 50.000 0.00 0.00 33.29 2.87
113 114 1.417517 TGGATGCGTGCCATAGAGAAT 59.582 47.619 0.00 0.00 33.29 2.40
114 115 2.072298 GGATGCGTGCCATAGAGAATC 58.928 52.381 0.00 0.00 33.29 2.52
138 139 3.872511 TCGTAATTTAACGAGCCCAGA 57.127 42.857 0.00 0.00 46.29 3.86
147 148 2.044555 CGAGCCCAGACCGTCACTA 61.045 63.158 0.40 0.00 0.00 2.74
154 155 3.555586 GCCCAGACCGTCACTAAAAGTTA 60.556 47.826 0.40 0.00 0.00 2.24
158 159 5.396484 CAGACCGTCACTAAAAGTTATCGA 58.604 41.667 0.40 0.00 0.00 3.59
159 160 5.860182 CAGACCGTCACTAAAAGTTATCGAA 59.140 40.000 0.40 0.00 0.00 3.71
193 194 3.910767 GCATTGTTTTGCTCGAAGAAGAG 59.089 43.478 0.00 0.00 39.57 2.85
206 213 4.512198 TCGAAGAAGAGCGTAGGATAGAAG 59.488 45.833 0.00 0.00 0.00 2.85
236 243 5.342806 TCGCAGTGAAAAAGTAGAATGTG 57.657 39.130 0.00 0.00 0.00 3.21
237 244 3.908382 CGCAGTGAAAAAGTAGAATGTGC 59.092 43.478 0.00 0.00 0.00 4.57
247 254 7.801716 AAAAGTAGAATGTGCAAACAGTAGA 57.198 32.000 0.00 0.00 0.00 2.59
273 283 2.869801 TGCAAATTATTAGGCGACCGAG 59.130 45.455 0.00 0.00 0.00 4.63
298 308 4.466726 CCTGCTCCATCAGATCATCAGATA 59.533 45.833 0.00 0.00 36.19 1.98
299 309 5.046520 CCTGCTCCATCAGATCATCAGATAA 60.047 44.000 0.00 0.00 36.19 1.75
315 325 7.341769 TCATCAGATAATAAACAAACCAAGGGG 59.658 37.037 0.00 0.00 41.29 4.79
352 362 3.649073 TCCTACTCAATTCACACACACG 58.351 45.455 0.00 0.00 0.00 4.49
354 364 0.581529 ACTCAATTCACACACACGCG 59.418 50.000 3.53 3.53 0.00 6.01
407 417 1.709147 CGTGCCTGCCTGCTTCATAC 61.709 60.000 0.00 0.00 0.00 2.39
408 418 0.677731 GTGCCTGCCTGCTTCATACA 60.678 55.000 0.00 0.00 0.00 2.29
409 419 0.393402 TGCCTGCCTGCTTCATACAG 60.393 55.000 0.00 0.00 34.82 2.74
410 420 0.393537 GCCTGCCTGCTTCATACAGT 60.394 55.000 0.00 0.00 33.09 3.55
411 421 1.134401 GCCTGCCTGCTTCATACAGTA 60.134 52.381 0.00 0.00 33.09 2.74
462 492 3.073062 ACACCAAGCACAGTAGGAGAATT 59.927 43.478 0.00 0.00 0.00 2.17
463 493 4.074970 CACCAAGCACAGTAGGAGAATTT 58.925 43.478 0.00 0.00 0.00 1.82
464 494 5.221843 ACACCAAGCACAGTAGGAGAATTTA 60.222 40.000 0.00 0.00 0.00 1.40
465 495 5.882557 CACCAAGCACAGTAGGAGAATTTAT 59.117 40.000 0.00 0.00 0.00 1.40
466 496 7.047891 CACCAAGCACAGTAGGAGAATTTATA 58.952 38.462 0.00 0.00 0.00 0.98
468 498 7.770897 ACCAAGCACAGTAGGAGAATTTATAAG 59.229 37.037 0.00 0.00 0.00 1.73
469 499 7.770897 CCAAGCACAGTAGGAGAATTTATAAGT 59.229 37.037 0.00 0.00 0.00 2.24
470 500 9.817809 CAAGCACAGTAGGAGAATTTATAAGTA 57.182 33.333 0.00 0.00 0.00 2.24
472 502 8.978472 AGCACAGTAGGAGAATTTATAAGTACA 58.022 33.333 0.00 0.00 0.00 2.90
492 524 0.980231 AAAACAAACAGGGCAGGGCA 60.980 50.000 0.00 0.00 0.00 5.36
502 534 3.224324 GCAGGGCAGCCATGGATG 61.224 66.667 27.03 25.84 35.67 3.51
509 541 1.517694 CAGCCATGGATGCGTTTGC 60.518 57.895 18.60 0.00 43.20 3.68
510 542 2.202783 GCCATGGATGCGTTTGCC 60.203 61.111 18.40 0.00 41.78 4.52
514 546 1.377202 ATGGATGCGTTTGCCGAGT 60.377 52.632 0.00 0.00 41.78 4.18
524 556 0.454600 TTTGCCGAGTAGAGTAGCCG 59.545 55.000 0.00 0.00 0.00 5.52
537 569 0.731855 GTAGCCGTCGAACACTGGAC 60.732 60.000 0.00 0.00 0.00 4.02
538 570 0.892358 TAGCCGTCGAACACTGGACT 60.892 55.000 0.00 0.00 0.00 3.85
539 571 0.892358 AGCCGTCGAACACTGGACTA 60.892 55.000 0.00 0.00 0.00 2.59
540 572 0.456312 GCCGTCGAACACTGGACTAG 60.456 60.000 0.00 0.00 0.00 2.57
541 573 1.162698 CCGTCGAACACTGGACTAGA 58.837 55.000 0.00 0.00 0.00 2.43
590 622 1.788344 GCAGATCGCGCAGACTTTTTC 60.788 52.381 8.75 0.12 0.00 2.29
606 638 4.715130 TCCTCCCCAGTCCCCACG 62.715 72.222 0.00 0.00 0.00 4.94
634 673 4.980805 TTGACGCGAGCACCCACC 62.981 66.667 15.93 0.00 0.00 4.61
797 836 1.622173 CCTGCCTCTTCCTCTTCCTCT 60.622 57.143 0.00 0.00 0.00 3.69
895 944 4.457496 CGGGCACGGCACAGATCT 62.457 66.667 0.00 0.00 36.18 2.75
896 945 2.045926 GGGCACGGCACAGATCTT 60.046 61.111 0.00 0.00 0.00 2.40
904 963 0.107459 GGCACAGATCTTCCCACTCC 60.107 60.000 0.00 0.00 0.00 3.85
905 964 0.615331 GCACAGATCTTCCCACTCCA 59.385 55.000 0.00 0.00 0.00 3.86
1413 1481 2.131067 GCGGAAGGAGGAGGAGGAG 61.131 68.421 0.00 0.00 0.00 3.69
1414 1482 1.456705 CGGAAGGAGGAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1415 1483 1.939082 CGGAAGGAGGAGGAGGAGGA 61.939 65.000 0.00 0.00 0.00 3.71
1418 1486 2.835895 GGAGGAGGAGGAGGACGC 60.836 72.222 0.00 0.00 0.00 5.19
1496 1564 0.107897 TTCACCGTGAACTGCAGTGT 60.108 50.000 22.49 10.78 30.26 3.55
1497 1565 0.529773 TCACCGTGAACTGCAGTGTC 60.530 55.000 22.49 19.08 0.00 3.67
1498 1566 0.809636 CACCGTGAACTGCAGTGTCA 60.810 55.000 22.49 21.32 0.00 3.58
1499 1567 0.530650 ACCGTGAACTGCAGTGTCAG 60.531 55.000 22.49 15.78 39.86 3.51
1500 1568 1.566563 CGTGAACTGCAGTGTCAGC 59.433 57.895 22.49 16.73 37.59 4.26
1501 1569 1.566563 GTGAACTGCAGTGTCAGCG 59.433 57.895 22.49 0.00 37.59 5.18
1502 1570 1.595109 TGAACTGCAGTGTCAGCGG 60.595 57.895 22.49 0.00 43.90 5.52
1749 1820 0.316522 ATGATGATCGCGTCAGGAGG 59.683 55.000 5.77 0.00 42.90 4.30
1779 1850 2.507471 CCAGCTCCCTTACCAGAATCTT 59.493 50.000 0.00 0.00 0.00 2.40
1838 1909 2.367512 GCATGGGGAGGAGGAGGT 60.368 66.667 0.00 0.00 0.00 3.85
1845 1916 0.252742 GGGAGGAGGAGGTGGAAGAA 60.253 60.000 0.00 0.00 0.00 2.52
1851 1922 3.044894 GGAGGAGGTGGAAGAAGATGAT 58.955 50.000 0.00 0.00 0.00 2.45
1944 2015 8.048514 TGTGTAAAAACCTCCTTGTTACTACTT 58.951 33.333 0.00 0.00 0.00 2.24
1977 2048 1.304381 GATGAAGGGTGGCAAGGCA 60.304 57.895 0.00 0.00 0.00 4.75
1978 2049 0.899717 GATGAAGGGTGGCAAGGCAA 60.900 55.000 0.00 0.00 0.00 4.52
1983 2054 2.281484 GGTGGCAAGGCAAGTCGA 60.281 61.111 0.00 0.00 0.00 4.20
1985 2056 2.669569 TGGCAAGGCAAGTCGAGC 60.670 61.111 0.00 0.00 0.00 5.03
1995 2066 1.077625 AAGTCGAGCAGGGAGAGGT 59.922 57.895 0.00 0.00 0.00 3.85
2117 2188 2.206815 TGCACACAACAATGCTTCAC 57.793 45.000 0.00 0.00 42.55 3.18
2130 2201 5.009010 ACAATGCTTCACGAATTCAGAGTTT 59.991 36.000 6.22 0.00 0.00 2.66
2132 2203 6.801539 ATGCTTCACGAATTCAGAGTTTTA 57.198 33.333 6.22 0.00 0.00 1.52
2139 2229 7.151976 TCACGAATTCAGAGTTTTATGAGTGA 58.848 34.615 6.22 3.40 29.19 3.41
2161 2251 9.030452 AGTGATAGTTCTAAACATCTCAGTCTT 57.970 33.333 0.00 0.00 0.00 3.01
2205 2295 4.096532 GGGAGGAAGTTTATAAGCACAAGC 59.903 45.833 1.97 0.00 42.56 4.01
2380 2470 2.290008 ACGTTGCCTTATCACCATCACA 60.290 45.455 0.00 0.00 0.00 3.58
2567 2657 6.724893 TTGCATGAAGATTCAATGGATCAT 57.275 33.333 4.10 0.00 41.13 2.45
2588 2678 6.276091 TCATCGTTCAGGTATTGATTCAGAG 58.724 40.000 0.00 0.00 35.27 3.35
2589 2679 5.914898 TCGTTCAGGTATTGATTCAGAGA 57.085 39.130 0.00 0.00 35.27 3.10
2594 2684 6.398234 TCAGGTATTGATTCAGAGACTAGC 57.602 41.667 0.00 0.00 0.00 3.42
2603 2693 3.162147 TCAGAGACTAGCCAGTTGACT 57.838 47.619 0.00 0.00 34.21 3.41
2604 2694 2.822561 TCAGAGACTAGCCAGTTGACTG 59.177 50.000 4.15 4.15 43.40 3.51
2607 2697 1.620819 AGACTAGCCAGTTGACTGTGG 59.379 52.381 10.03 0.00 42.27 4.17
2608 2698 1.344763 GACTAGCCAGTTGACTGTGGT 59.655 52.381 10.03 9.19 42.27 4.16
2610 2700 2.299297 ACTAGCCAGTTGACTGTGGTAC 59.701 50.000 10.03 0.00 42.27 3.34
2657 2747 2.158475 AGGGTGTGATGTTCAACATGGT 60.158 45.455 8.05 0.00 39.27 3.55
2662 2752 2.095768 GTGATGTTCAACATGGTGGACG 60.096 50.000 17.43 0.00 39.27 4.79
2663 2753 1.468520 GATGTTCAACATGGTGGACGG 59.531 52.381 17.43 0.00 39.27 4.79
2695 2785 4.331168 CAGAAGTAACAGCATAGTGGAAGC 59.669 45.833 0.00 0.00 0.00 3.86
2711 2801 4.937620 GTGGAAGCTCAAGACAATGATACA 59.062 41.667 0.00 0.00 0.00 2.29
2718 2808 6.315642 AGCTCAAGACAATGATACATTGACAG 59.684 38.462 24.67 16.64 33.51 3.51
2722 2812 9.065798 TCAAGACAATGATACATTGACAGAAAA 57.934 29.630 24.67 7.17 33.51 2.29
2723 2813 9.338291 CAAGACAATGATACATTGACAGAAAAG 57.662 33.333 24.67 7.95 33.51 2.27
2735 2825 6.707440 TTGACAGAAAAGATTGCCAAAGTA 57.293 33.333 0.00 0.00 0.00 2.24
2738 2828 4.023193 ACAGAAAAGATTGCCAAAGTACCG 60.023 41.667 0.00 0.00 0.00 4.02
2746 2836 1.712018 GCCAAAGTACCGGAATCCGC 61.712 60.000 17.50 2.56 46.86 5.54
2768 2858 5.238650 CGCTTCATTAATACCTTCCGGAAAT 59.761 40.000 19.39 11.96 0.00 2.17
2782 2872 2.614057 CCGGAAATGCAGGATCAGTAAC 59.386 50.000 0.00 0.00 33.08 2.50
2800 2890 8.777865 TCAGTAACACTGGATGATAGAAAAAG 57.222 34.615 6.48 0.00 45.94 2.27
2826 2916 6.611236 TCATGATAGTAGTCAGGATGTTCCAA 59.389 38.462 0.00 0.00 39.61 3.53
2834 2924 6.065976 AGTCAGGATGTTCCAATACATTCA 57.934 37.500 0.00 0.00 39.61 2.57
2849 2939 9.376075 CCAATACATTCAGAAGATAATATCGCT 57.624 33.333 0.00 0.00 0.00 4.93
2864 2954 1.512926 TCGCTGTCAAGAAGGAAAGC 58.487 50.000 0.00 0.00 43.37 3.51
2889 2979 2.604462 CCTTTGCAATTTCTAATGCCGC 59.396 45.455 0.00 0.00 41.87 6.53
2900 2990 2.023414 TAATGCCGCTACCTGTCCCG 62.023 60.000 0.00 0.00 0.00 5.14
2918 3008 1.281899 CGAAGTCGCCTTCAGATTCC 58.718 55.000 7.03 0.00 46.19 3.01
2932 3022 1.012841 GATTCCTGGCTTTCTCGCAG 58.987 55.000 0.00 0.00 0.00 5.18
2961 3051 5.355350 CCATCTGTGAAGAATAAACCACCTC 59.645 44.000 0.00 0.00 0.00 3.85
2963 3053 4.597507 TCTGTGAAGAATAAACCACCTCCT 59.402 41.667 0.00 0.00 0.00 3.69
2995 3085 3.868757 TGGAATCCAAGTACAGTCGAG 57.131 47.619 0.00 0.00 0.00 4.04
3008 3098 0.038159 AGTCGAGGAAACAAGCTCCG 60.038 55.000 0.00 0.00 38.08 4.63
3013 3103 1.228154 GGAAACAAGCTCCGTGGGT 60.228 57.895 0.00 0.00 0.00 4.51
3017 3107 2.125912 CAAGCTCCGTGGGTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
3054 3144 3.584733 ATGATCTTAAACCTCCCAGGC 57.415 47.619 0.00 0.00 39.63 4.85
3083 3173 8.075574 CGCCAAATAAGATTTGCAGATGTAATA 58.924 33.333 0.00 0.00 0.00 0.98
3115 3205 4.391216 CACTCTGTTCTGCCTATGTTTCTG 59.609 45.833 0.00 0.00 0.00 3.02
3190 3282 3.138468 GGTGGTGGAGAGGCCTTATTATT 59.862 47.826 6.77 0.00 37.63 1.40
3216 3308 8.774546 TGGATACTGAGATATGATATCTTCCC 57.225 38.462 19.80 13.59 37.61 3.97
3547 3639 6.943981 TCTGTAAAAACGTTGAGTTGATCTG 58.056 36.000 0.00 0.00 43.37 2.90
3592 3684 5.835113 TCCAATATAAGTCAGCCTTTTGC 57.165 39.130 0.00 0.00 41.71 3.68
3622 3714 7.701539 AGACATTTCCTGTGCAATGTAAATA 57.298 32.000 0.00 0.00 42.46 1.40
3644 3736 1.874231 CATCTCTCTGGTGATGCATGC 59.126 52.381 11.82 11.82 36.89 4.06
3685 3777 4.650754 ACTGGCATTACCTACTAGAACG 57.349 45.455 0.00 0.00 40.22 3.95
3693 3785 7.318141 GCATTACCTACTAGAACGGCATATAA 58.682 38.462 0.00 0.00 0.00 0.98
3718 3810 5.648092 GTGCCTTATCTGGTTTTGTGTAGAT 59.352 40.000 0.00 0.00 34.51 1.98
3720 3812 7.335924 GTGCCTTATCTGGTTTTGTGTAGATAA 59.664 37.037 0.00 0.00 38.88 1.75
3722 3814 8.736244 GCCTTATCTGGTTTTGTGTAGATAAAA 58.264 33.333 0.00 0.00 39.97 1.52
3799 3891 7.781056 TCAGTGTATGTCATGTCTAGCAATTA 58.219 34.615 0.00 0.00 0.00 1.40
3809 3901 7.440556 GTCATGTCTAGCAATTACATCTGTCAT 59.559 37.037 0.00 0.00 31.60 3.06
3814 3906 8.454106 GTCTAGCAATTACATCTGTCATGTTTT 58.546 33.333 0.00 0.00 33.76 2.43
3844 3936 7.234371 TGGTGATTGGTTTTGAGATGGAAAATA 59.766 33.333 0.00 0.00 0.00 1.40
3898 4107 1.959747 CACAACTCGCATGCAGAAAG 58.040 50.000 19.57 11.27 0.00 2.62
3899 4108 0.239347 ACAACTCGCATGCAGAAAGC 59.761 50.000 19.57 0.00 45.96 3.51
3900 4109 0.455633 CAACTCGCATGCAGAAAGCC 60.456 55.000 19.57 0.00 44.83 4.35
3944 4153 5.800296 TGTGCTCTACAAAACAGCCTATAA 58.200 37.500 0.00 0.00 36.06 0.98
3945 4154 5.874810 TGTGCTCTACAAAACAGCCTATAAG 59.125 40.000 0.00 0.00 36.06 1.73
3961 4170 8.367911 CAGCCTATAAGTTTGGTGTATGATCTA 58.632 37.037 0.00 0.00 0.00 1.98
3971 4180 8.660373 GTTTGGTGTATGATCTAAGTTCTCAAG 58.340 37.037 0.00 0.00 0.00 3.02
3972 4181 7.482169 TGGTGTATGATCTAAGTTCTCAAGT 57.518 36.000 0.00 0.00 0.00 3.16
3973 4182 8.589701 TGGTGTATGATCTAAGTTCTCAAGTA 57.410 34.615 0.00 0.00 0.00 2.24
3974 4183 8.467598 TGGTGTATGATCTAAGTTCTCAAGTAC 58.532 37.037 0.00 0.00 0.00 2.73
3975 4184 8.467598 GGTGTATGATCTAAGTTCTCAAGTACA 58.532 37.037 0.00 0.00 0.00 2.90
3976 4185 9.509855 GTGTATGATCTAAGTTCTCAAGTACAG 57.490 37.037 0.00 0.00 0.00 2.74
4032 4241 3.922240 CCACATATGCACTCTTGTTTTGC 59.078 43.478 1.58 0.00 36.76 3.68
4042 4251 3.108144 CTCTTGTTTTGCGTTGACTTGG 58.892 45.455 0.00 0.00 0.00 3.61
4067 4276 7.546667 GGTACATTCTGTTTATCGAAGTGGTTA 59.453 37.037 0.00 0.00 0.00 2.85
4068 4277 9.095065 GTACATTCTGTTTATCGAAGTGGTTAT 57.905 33.333 0.00 0.00 0.00 1.89
4070 4279 7.280205 ACATTCTGTTTATCGAAGTGGTTATCC 59.720 37.037 0.00 0.00 0.00 2.59
4071 4280 6.288941 TCTGTTTATCGAAGTGGTTATCCA 57.711 37.500 0.00 0.00 42.05 3.41
4086 4295 6.542821 TGGTTATCCACTCAATCTTTCTTGT 58.457 36.000 0.00 0.00 39.03 3.16
4087 4296 7.004086 TGGTTATCCACTCAATCTTTCTTGTT 58.996 34.615 0.00 0.00 39.03 2.83
4088 4297 7.505585 TGGTTATCCACTCAATCTTTCTTGTTT 59.494 33.333 0.00 0.00 39.03 2.83
4089 4298 7.809806 GGTTATCCACTCAATCTTTCTTGTTTG 59.190 37.037 0.00 0.00 0.00 2.93
4090 4299 8.567948 GTTATCCACTCAATCTTTCTTGTTTGA 58.432 33.333 0.00 0.00 0.00 2.69
4091 4300 7.771927 ATCCACTCAATCTTTCTTGTTTGAT 57.228 32.000 0.00 0.00 0.00 2.57
4092 4301 7.587037 TCCACTCAATCTTTCTTGTTTGATT 57.413 32.000 0.00 0.00 0.00 2.57
4093 4302 8.010733 TCCACTCAATCTTTCTTGTTTGATTT 57.989 30.769 0.00 0.00 0.00 2.17
4094 4303 8.477256 TCCACTCAATCTTTCTTGTTTGATTTT 58.523 29.630 0.00 0.00 0.00 1.82
4095 4304 9.748708 CCACTCAATCTTTCTTGTTTGATTTTA 57.251 29.630 0.00 0.00 0.00 1.52
4140 4367 5.504501 CGTTATTTTACGGGGAAGTATTGGC 60.505 44.000 0.00 0.00 37.86 4.52
4149 4376 2.749621 GGGAAGTATTGGCACTGAACTG 59.250 50.000 0.00 0.00 0.00 3.16
4186 4413 2.030805 GTGATTCAACAAGGACACTGCC 60.031 50.000 0.00 0.00 0.00 4.85
4193 4420 0.108186 CAAGGACACTGCCGATGCTA 60.108 55.000 0.00 0.00 38.71 3.49
4194 4421 0.833287 AAGGACACTGCCGATGCTAT 59.167 50.000 0.00 0.00 38.71 2.97
4195 4422 0.833287 AGGACACTGCCGATGCTATT 59.167 50.000 0.00 0.00 38.71 1.73
4196 4423 1.210478 AGGACACTGCCGATGCTATTT 59.790 47.619 0.00 0.00 38.71 1.40
4197 4424 2.017049 GGACACTGCCGATGCTATTTT 58.983 47.619 0.00 0.00 38.71 1.82
4198 4425 2.032178 GGACACTGCCGATGCTATTTTC 59.968 50.000 0.00 0.00 38.71 2.29
4199 4426 2.939103 GACACTGCCGATGCTATTTTCT 59.061 45.455 0.00 0.00 38.71 2.52
4200 4427 3.347216 ACACTGCCGATGCTATTTTCTT 58.653 40.909 0.00 0.00 38.71 2.52
4201 4428 3.127548 ACACTGCCGATGCTATTTTCTTG 59.872 43.478 0.00 0.00 38.71 3.02
4202 4429 3.127548 CACTGCCGATGCTATTTTCTTGT 59.872 43.478 0.00 0.00 38.71 3.16
4203 4430 3.127548 ACTGCCGATGCTATTTTCTTGTG 59.872 43.478 0.00 0.00 38.71 3.33
4204 4431 2.423185 TGCCGATGCTATTTTCTTGTGG 59.577 45.455 0.00 0.00 38.71 4.17
4205 4432 2.796032 GCCGATGCTATTTTCTTGTGGC 60.796 50.000 0.00 0.00 33.53 5.01
4206 4433 2.684881 CCGATGCTATTTTCTTGTGGCT 59.315 45.455 0.00 0.00 0.00 4.75
4207 4434 3.876914 CCGATGCTATTTTCTTGTGGCTA 59.123 43.478 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.395583 GCCTCAACTGCACGCTGC 62.396 66.667 3.44 3.44 45.29 5.25
9 10 2.330372 ATGCCTCAACTGCACGCTG 61.330 57.895 0.00 0.00 42.38 5.18
10 11 2.033141 ATGCCTCAACTGCACGCT 59.967 55.556 0.00 0.00 42.38 5.07
11 12 1.298157 TACATGCCTCAACTGCACGC 61.298 55.000 0.00 0.00 42.38 5.34
12 13 0.443869 GTACATGCCTCAACTGCACG 59.556 55.000 0.00 0.00 42.38 5.34
13 14 0.443869 CGTACATGCCTCAACTGCAC 59.556 55.000 0.00 0.00 42.38 4.57
14 15 1.298157 GCGTACATGCCTCAACTGCA 61.298 55.000 0.00 0.00 43.97 4.41
15 16 1.021390 AGCGTACATGCCTCAACTGC 61.021 55.000 0.00 0.00 34.65 4.40
16 17 1.129251 CAAGCGTACATGCCTCAACTG 59.871 52.381 0.00 0.00 34.65 3.16
17 18 1.270839 ACAAGCGTACATGCCTCAACT 60.271 47.619 0.00 0.00 34.65 3.16
18 19 1.128692 GACAAGCGTACATGCCTCAAC 59.871 52.381 0.00 0.00 34.65 3.18
19 20 1.001974 AGACAAGCGTACATGCCTCAA 59.998 47.619 0.00 0.00 34.65 3.02
20 21 0.608130 AGACAAGCGTACATGCCTCA 59.392 50.000 0.00 0.00 34.65 3.86
21 22 1.002366 CAGACAAGCGTACATGCCTC 58.998 55.000 0.00 0.00 34.65 4.70
22 23 0.608130 TCAGACAAGCGTACATGCCT 59.392 50.000 0.00 0.00 34.65 4.75
23 24 1.328680 CATCAGACAAGCGTACATGCC 59.671 52.381 0.00 0.00 34.65 4.40
24 25 1.267732 GCATCAGACAAGCGTACATGC 60.268 52.381 0.00 0.00 0.00 4.06
25 26 1.328680 GGCATCAGACAAGCGTACATG 59.671 52.381 0.00 0.00 0.00 3.21
26 27 1.656652 GGCATCAGACAAGCGTACAT 58.343 50.000 0.00 0.00 0.00 2.29
27 28 0.391130 GGGCATCAGACAAGCGTACA 60.391 55.000 0.00 0.00 0.00 2.90
28 29 1.090052 GGGGCATCAGACAAGCGTAC 61.090 60.000 0.00 0.00 0.00 3.67
29 30 1.220749 GGGGCATCAGACAAGCGTA 59.779 57.895 0.00 0.00 0.00 4.42
30 31 2.045926 GGGGCATCAGACAAGCGT 60.046 61.111 0.00 0.00 0.00 5.07
31 32 3.197790 CGGGGCATCAGACAAGCG 61.198 66.667 0.00 0.00 0.00 4.68
32 33 3.512516 GCGGGGCATCAGACAAGC 61.513 66.667 0.00 0.00 0.00 4.01
33 34 2.110967 CAGCGGGGCATCAGACAAG 61.111 63.158 0.00 0.00 0.00 3.16
34 35 2.046023 CAGCGGGGCATCAGACAA 60.046 61.111 0.00 0.00 0.00 3.18
35 36 4.100084 CCAGCGGGGCATCAGACA 62.100 66.667 0.00 0.00 0.00 3.41
48 49 4.828296 CATGGGACCTGGGCCAGC 62.828 72.222 28.51 15.21 0.00 4.85
49 50 3.341629 ACATGGGACCTGGGCCAG 61.342 66.667 27.04 27.04 0.00 4.85
50 51 3.660571 CACATGGGACCTGGGCCA 61.661 66.667 22.83 5.85 0.00 5.36
51 52 4.447342 CCACATGGGACCTGGGCC 62.447 72.222 11.22 11.22 40.01 5.80
53 54 4.802051 CGCCACATGGGACCTGGG 62.802 72.222 0.00 0.00 40.01 4.45
71 72 2.360350 ATGTTCCTGTGGCGCTGG 60.360 61.111 16.98 16.98 37.52 4.85
72 73 2.872557 CATGTTCCTGTGGCGCTG 59.127 61.111 7.64 0.00 0.00 5.18
73 74 3.058160 GCATGTTCCTGTGGCGCT 61.058 61.111 7.64 0.00 0.00 5.92
74 75 4.120331 GGCATGTTCCTGTGGCGC 62.120 66.667 0.00 0.00 0.00 6.53
75 76 2.048023 ATGGCATGTTCCTGTGGCG 61.048 57.895 0.00 0.00 43.15 5.69
76 77 1.514087 CATGGCATGTTCCTGTGGC 59.486 57.895 19.32 0.00 40.89 5.01
77 78 0.323633 TCCATGGCATGTTCCTGTGG 60.324 55.000 24.80 9.82 35.39 4.17
78 79 1.407618 CATCCATGGCATGTTCCTGTG 59.592 52.381 24.80 8.80 0.00 3.66
79 80 1.771565 CATCCATGGCATGTTCCTGT 58.228 50.000 24.80 2.70 0.00 4.00
80 81 0.387929 GCATCCATGGCATGTTCCTG 59.612 55.000 24.80 16.31 0.00 3.86
81 82 1.105167 CGCATCCATGGCATGTTCCT 61.105 55.000 24.80 4.80 0.00 3.36
82 83 1.361271 CGCATCCATGGCATGTTCC 59.639 57.895 24.80 10.00 0.00 3.62
83 84 0.248743 CACGCATCCATGGCATGTTC 60.249 55.000 24.80 10.31 0.00 3.18
84 85 1.811195 CACGCATCCATGGCATGTT 59.189 52.632 24.80 10.25 0.00 2.71
85 86 2.777972 GCACGCATCCATGGCATGT 61.778 57.895 24.80 5.73 0.00 3.21
86 87 2.027024 GCACGCATCCATGGCATG 59.973 61.111 20.56 20.56 0.00 4.06
87 88 3.221389 GGCACGCATCCATGGCAT 61.221 61.111 6.96 0.00 40.91 4.40
89 90 1.859427 CTATGGCACGCATCCATGGC 61.859 60.000 6.96 0.00 43.67 4.40
90 91 0.250424 TCTATGGCACGCATCCATGG 60.250 55.000 4.97 4.97 43.67 3.66
91 92 1.154197 CTCTATGGCACGCATCCATG 58.846 55.000 12.31 0.00 43.67 3.66
92 93 1.051008 TCTCTATGGCACGCATCCAT 58.949 50.000 8.45 8.45 45.60 3.41
93 94 0.829990 TTCTCTATGGCACGCATCCA 59.170 50.000 0.00 0.00 38.09 3.41
94 95 2.072298 GATTCTCTATGGCACGCATCC 58.928 52.381 0.00 0.00 0.00 3.51
95 96 2.759191 TGATTCTCTATGGCACGCATC 58.241 47.619 0.00 0.00 0.00 3.91
96 97 2.916702 TGATTCTCTATGGCACGCAT 57.083 45.000 0.00 0.00 0.00 4.73
97 98 2.366590 AGATGATTCTCTATGGCACGCA 59.633 45.455 0.00 0.00 0.00 5.24
98 99 2.992543 GAGATGATTCTCTATGGCACGC 59.007 50.000 0.00 0.00 44.29 5.34
99 100 3.240884 CGAGATGATTCTCTATGGCACG 58.759 50.000 0.00 0.00 45.30 5.34
100 101 4.250116 ACGAGATGATTCTCTATGGCAC 57.750 45.455 0.00 0.00 45.30 5.01
101 102 6.596309 ATTACGAGATGATTCTCTATGGCA 57.404 37.500 0.00 0.00 45.30 4.92
102 103 7.897575 AAATTACGAGATGATTCTCTATGGC 57.102 36.000 0.00 0.00 45.30 4.40
120 121 2.606272 CGGTCTGGGCTCGTTAAATTAC 59.394 50.000 0.00 0.00 0.00 1.89
127 128 2.915659 TGACGGTCTGGGCTCGTT 60.916 61.111 9.88 0.00 37.25 3.85
136 137 5.633830 TCGATAACTTTTAGTGACGGTCT 57.366 39.130 9.88 0.00 0.00 3.85
138 139 7.385752 TCATTTTCGATAACTTTTAGTGACGGT 59.614 33.333 0.00 0.00 0.00 4.83
147 148 9.474920 TGCAAGAATTCATTTTCGATAACTTTT 57.525 25.926 8.44 0.00 0.00 2.27
154 155 7.894376 AACAATGCAAGAATTCATTTTCGAT 57.106 28.000 8.44 0.00 31.15 3.59
158 159 7.917720 GCAAAACAATGCAAGAATTCATTTT 57.082 28.000 8.44 0.00 45.70 1.82
193 194 5.556570 GCGAATTTTCACTTCTATCCTACGC 60.557 44.000 0.00 0.00 0.00 4.42
206 213 5.949233 ACTTTTTCACTGCGAATTTTCAC 57.051 34.783 0.00 0.00 32.32 3.18
247 254 5.518487 CGGTCGCCTAATAATTTGCATTTTT 59.482 36.000 0.00 0.00 0.00 1.94
273 283 0.400975 ATGATCTGATGGAGCAGGGC 59.599 55.000 0.00 0.00 43.90 5.19
298 308 4.416516 CTCTCCCCCTTGGTTTGTTTATT 58.583 43.478 0.00 0.00 34.77 1.40
299 309 3.817931 GCTCTCCCCCTTGGTTTGTTTAT 60.818 47.826 0.00 0.00 34.77 1.40
315 325 1.045911 AGGAATCTGGTCGGCTCTCC 61.046 60.000 0.00 0.00 0.00 3.71
365 375 4.514577 CCACTCCAGGCGCCTACG 62.515 72.222 32.30 22.43 44.07 3.51
366 376 4.840005 GCCACTCCAGGCGCCTAC 62.840 72.222 32.30 8.89 46.12 3.18
407 417 1.473434 GGATCGGAGGCCAAGTTACTG 60.473 57.143 5.01 0.00 0.00 2.74
408 418 0.831307 GGATCGGAGGCCAAGTTACT 59.169 55.000 5.01 0.00 0.00 2.24
409 419 0.529992 CGGATCGGAGGCCAAGTTAC 60.530 60.000 5.01 0.00 0.00 2.50
410 420 1.820581 CGGATCGGAGGCCAAGTTA 59.179 57.895 5.01 0.00 0.00 2.24
411 421 2.584608 CGGATCGGAGGCCAAGTT 59.415 61.111 5.01 0.00 0.00 2.66
462 492 8.008513 TGCCCTGTTTGTTTTTGTACTTATAA 57.991 30.769 0.00 0.00 0.00 0.98
463 493 7.255660 CCTGCCCTGTTTGTTTTTGTACTTATA 60.256 37.037 0.00 0.00 0.00 0.98
464 494 6.462347 CCTGCCCTGTTTGTTTTTGTACTTAT 60.462 38.462 0.00 0.00 0.00 1.73
465 495 5.163499 CCTGCCCTGTTTGTTTTTGTACTTA 60.163 40.000 0.00 0.00 0.00 2.24
466 496 4.382577 CCTGCCCTGTTTGTTTTTGTACTT 60.383 41.667 0.00 0.00 0.00 2.24
468 498 3.453424 CCTGCCCTGTTTGTTTTTGTAC 58.547 45.455 0.00 0.00 0.00 2.90
469 499 2.432510 CCCTGCCCTGTTTGTTTTTGTA 59.567 45.455 0.00 0.00 0.00 2.41
470 500 1.209261 CCCTGCCCTGTTTGTTTTTGT 59.791 47.619 0.00 0.00 0.00 2.83
472 502 0.180171 GCCCTGCCCTGTTTGTTTTT 59.820 50.000 0.00 0.00 0.00 1.94
474 504 1.382420 TGCCCTGCCCTGTTTGTTT 60.382 52.632 0.00 0.00 0.00 2.83
477 507 3.688159 GCTGCCCTGCCCTGTTTG 61.688 66.667 0.00 0.00 0.00 2.93
492 524 2.713967 GGCAAACGCATCCATGGCT 61.714 57.895 6.96 0.00 35.66 4.75
502 534 1.546834 CTACTCTACTCGGCAAACGC 58.453 55.000 0.00 0.00 43.86 4.84
503 535 1.546834 GCTACTCTACTCGGCAAACG 58.453 55.000 0.00 0.00 46.11 3.60
504 536 1.798079 CGGCTACTCTACTCGGCAAAC 60.798 57.143 0.00 0.00 0.00 2.93
505 537 0.454600 CGGCTACTCTACTCGGCAAA 59.545 55.000 0.00 0.00 0.00 3.68
506 538 0.679002 ACGGCTACTCTACTCGGCAA 60.679 55.000 0.00 0.00 0.00 4.52
507 539 1.077930 ACGGCTACTCTACTCGGCA 60.078 57.895 0.00 0.00 0.00 5.69
509 541 0.529337 TCGACGGCTACTCTACTCGG 60.529 60.000 0.00 0.00 0.00 4.63
510 542 1.005137 GTTCGACGGCTACTCTACTCG 60.005 57.143 0.00 0.00 0.00 4.18
514 546 1.736126 CAGTGTTCGACGGCTACTCTA 59.264 52.381 0.00 0.00 0.00 2.43
524 556 1.135344 GGCTCTAGTCCAGTGTTCGAC 60.135 57.143 0.00 0.00 0.00 4.20
537 569 1.068753 CCAGCACCATCGGCTCTAG 59.931 63.158 0.00 0.00 40.23 2.43
538 570 3.094062 GCCAGCACCATCGGCTCTA 62.094 63.158 0.00 0.00 42.78 2.43
539 571 4.479993 GCCAGCACCATCGGCTCT 62.480 66.667 0.00 0.00 42.78 4.09
540 572 4.783621 TGCCAGCACCATCGGCTC 62.784 66.667 0.00 0.00 46.39 4.70
541 573 4.119363 ATGCCAGCACCATCGGCT 62.119 61.111 0.00 0.00 46.39 5.52
638 677 4.901123 TGGTGACACGGGTGCGTG 62.901 66.667 0.00 0.00 44.56 5.34
1059 1118 3.388841 AGGTCGGCCTTGTGGTAG 58.611 61.111 0.35 0.00 44.18 3.18
1217 1282 4.814294 CCAGGGCGTCGTGGTAGC 62.814 72.222 20.36 0.00 42.32 3.58
1218 1283 4.143333 CCCAGGGCGTCGTGGTAG 62.143 72.222 25.66 9.16 44.93 3.18
1377 1445 4.457496 AGCACATCGGCCACGGAG 62.457 66.667 2.24 0.00 41.39 4.63
1418 1486 3.187699 CTCTCCTCGTCATCGCCGG 62.188 68.421 0.00 0.00 36.96 6.13
1496 1564 3.749064 GACCGCTGAGACCGCTGA 61.749 66.667 0.00 0.00 0.00 4.26
1497 1565 3.691744 GAGACCGCTGAGACCGCTG 62.692 68.421 0.00 0.00 0.00 5.18
1498 1566 3.444805 GAGACCGCTGAGACCGCT 61.445 66.667 0.00 0.00 0.00 5.52
1499 1567 3.691744 CTGAGACCGCTGAGACCGC 62.692 68.421 0.00 0.00 0.00 5.68
1500 1568 2.487428 CTGAGACCGCTGAGACCG 59.513 66.667 0.00 0.00 0.00 4.79
1501 1569 2.183046 GCTGAGACCGCTGAGACC 59.817 66.667 0.00 0.00 0.00 3.85
1502 1570 2.202544 CGCTGAGACCGCTGAGAC 60.203 66.667 0.00 0.00 0.00 3.36
1503 1571 3.443925 CCGCTGAGACCGCTGAGA 61.444 66.667 0.00 0.00 0.00 3.27
1755 1826 0.617820 TCTGGTAAGGGAGCTGGACC 60.618 60.000 0.00 0.00 0.00 4.46
1779 1850 4.671831 TGCAAGACAAATAATTGGGAGGA 58.328 39.130 0.00 0.00 41.01 3.71
1826 1897 0.252742 TTCTTCCACCTCCTCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
1827 1898 1.199615 CTTCTTCCACCTCCTCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
1838 1909 5.127682 TCGAAGTCATCATCATCTTCTTCCA 59.872 40.000 0.00 0.00 35.55 3.53
1845 1916 4.335594 TGTACGTCGAAGTCATCATCATCT 59.664 41.667 7.43 0.00 0.00 2.90
1851 1922 5.007039 GGTACTATGTACGTCGAAGTCATCA 59.993 44.000 7.43 6.82 0.00 3.07
1944 2015 5.074929 ACCCTTCATCATAGGCATTGGATTA 59.925 40.000 0.00 0.00 0.00 1.75
1977 2048 0.331954 TACCTCTCCCTGCTCGACTT 59.668 55.000 0.00 0.00 0.00 3.01
1978 2049 0.106918 CTACCTCTCCCTGCTCGACT 60.107 60.000 0.00 0.00 0.00 4.18
1983 2054 1.307976 ATCCCCTACCTCTCCCTGCT 61.308 60.000 0.00 0.00 0.00 4.24
1985 2056 1.428869 CAATCCCCTACCTCTCCCTG 58.571 60.000 0.00 0.00 0.00 4.45
2028 2099 4.400961 GCAAGAGGGCTCGGTGCT 62.401 66.667 1.77 0.00 40.21 4.40
2117 2188 9.307121 ACTATCACTCATAAAACTCTGAATTCG 57.693 33.333 0.04 0.00 0.00 3.34
2132 2203 8.976353 ACTGAGATGTTTAGAACTATCACTCAT 58.024 33.333 0.00 0.00 0.00 2.90
2157 2247 7.182761 CAGTATTGCTGCAGTGTAAATAAGAC 58.817 38.462 16.64 7.09 38.52 3.01
2161 2251 4.881273 CCCAGTATTGCTGCAGTGTAAATA 59.119 41.667 16.64 11.45 43.71 1.40
2162 2252 3.696051 CCCAGTATTGCTGCAGTGTAAAT 59.304 43.478 16.64 12.38 43.71 1.40
2163 2253 3.081061 CCCAGTATTGCTGCAGTGTAAA 58.919 45.455 16.64 5.70 43.71 2.01
2167 2257 1.376543 CTCCCAGTATTGCTGCAGTG 58.623 55.000 16.64 4.06 43.71 3.66
2169 2259 0.543277 TCCTCCCAGTATTGCTGCAG 59.457 55.000 10.11 10.11 43.71 4.41
2205 2295 7.013846 TCCTTGGTTAATGTACTTTTGTTCCAG 59.986 37.037 0.00 0.73 0.00 3.86
2213 2303 6.697641 TCCTCTCCTTGGTTAATGTACTTT 57.302 37.500 0.00 0.00 0.00 2.66
2369 2459 5.163385 CCCATTTGCTTTATGTGATGGTGAT 60.163 40.000 0.00 0.00 33.79 3.06
2567 2657 5.419155 AGTCTCTGAATCAATACCTGAACGA 59.581 40.000 0.00 0.00 37.67 3.85
2603 2693 1.004277 GCCTTTGGATCCAGTACCACA 59.996 52.381 15.53 0.00 35.81 4.17
2604 2694 1.004277 TGCCTTTGGATCCAGTACCAC 59.996 52.381 15.53 4.70 35.81 4.16
2607 2697 3.567478 AGATGCCTTTGGATCCAGTAC 57.433 47.619 15.53 6.85 0.00 2.73
2608 2698 4.591321 AAAGATGCCTTTGGATCCAGTA 57.409 40.909 15.53 3.45 40.83 2.74
2657 2747 1.751351 CTTCTGACTATCTGCCGTCCA 59.249 52.381 0.00 0.00 0.00 4.02
2662 2752 4.116238 GCTGTTACTTCTGACTATCTGCC 58.884 47.826 0.00 0.00 0.00 4.85
2663 2753 4.748892 TGCTGTTACTTCTGACTATCTGC 58.251 43.478 0.00 0.00 0.00 4.26
2695 2785 7.838771 TCTGTCAATGTATCATTGTCTTGAG 57.161 36.000 17.93 9.36 0.00 3.02
2711 2801 6.165700 ACTTTGGCAATCTTTTCTGTCAAT 57.834 33.333 0.00 0.00 37.04 2.57
2718 2808 3.504520 TCCGGTACTTTGGCAATCTTTTC 59.495 43.478 0.00 0.00 0.00 2.29
2722 2812 2.871096 TTCCGGTACTTTGGCAATCT 57.129 45.000 0.00 0.00 0.00 2.40
2723 2813 2.357952 GGATTCCGGTACTTTGGCAATC 59.642 50.000 0.00 0.00 0.00 2.67
2726 2816 0.391927 CGGATTCCGGTACTTTGGCA 60.392 55.000 17.53 0.00 44.15 4.92
2738 2828 5.181433 GGAAGGTATTAATGAAGCGGATTCC 59.819 44.000 3.23 0.00 37.08 3.01
2782 2872 7.854557 TCATGACTTTTTCTATCATCCAGTG 57.145 36.000 0.00 0.00 30.58 3.66
2800 2890 6.040955 TGGAACATCCTGACTACTATCATGAC 59.959 42.308 0.00 0.00 37.46 3.06
2826 2916 9.579768 GACAGCGATATTATCTTCTGAATGTAT 57.420 33.333 20.30 5.88 34.12 2.29
2834 2924 7.014711 TCCTTCTTGACAGCGATATTATCTTCT 59.985 37.037 2.36 0.00 0.00 2.85
2849 2939 1.888512 GGCATGCTTTCCTTCTTGACA 59.111 47.619 18.92 0.00 0.00 3.58
2889 2979 1.139095 GCGACTTCGGGACAGGTAG 59.861 63.158 0.02 0.00 40.23 3.18
2918 3008 0.386478 GCAAACTGCGAGAAAGCCAG 60.386 55.000 0.00 0.00 31.71 4.85
2932 3022 5.863935 GGTTTATTCTTCACAGATGGCAAAC 59.136 40.000 0.00 0.00 0.00 2.93
2961 3051 4.603131 TGGATTCCAAGAAAAGATGGAGG 58.397 43.478 1.94 0.00 45.94 4.30
2995 3085 1.228154 ACCCACGGAGCTTGTTTCC 60.228 57.895 0.00 0.00 0.00 3.13
3008 3098 2.125106 GGATGTGCCGAGACCCAC 60.125 66.667 0.00 0.00 0.00 4.61
3013 3103 0.250234 CTCCTTTGGATGTGCCGAGA 59.750 55.000 0.00 0.00 40.66 4.04
3017 3107 2.726821 TCATTCTCCTTTGGATGTGCC 58.273 47.619 0.00 0.00 37.10 5.01
3054 3144 3.119531 TCTGCAAATCTTATTTGGCGTGG 60.120 43.478 12.82 3.12 0.00 4.94
3083 3173 4.040952 AGGCAGAACAGAGTGAAGTTATGT 59.959 41.667 0.00 0.00 38.73 2.29
3115 3205 5.078411 TGGCTCTGAGAAGTAAGATGAAC 57.922 43.478 9.28 0.00 0.00 3.18
3190 3282 9.206690 GGGAAGATATCATATCTCAGTATCCAA 57.793 37.037 18.33 0.00 0.00 3.53
3355 3447 3.438781 TCGAATTTACCAACATGCTGGAC 59.561 43.478 21.94 5.04 38.96 4.02
3547 3639 5.954296 ATTGCATCCTATGATACAACTGC 57.046 39.130 0.00 0.00 37.14 4.40
3592 3684 2.886523 TGCACAGGAAATGTCTTGGAAG 59.113 45.455 0.00 0.00 41.41 3.46
3594 3686 2.655090 TGCACAGGAAATGTCTTGGA 57.345 45.000 0.00 0.00 41.41 3.53
3644 3736 6.910536 CAGTATTACTGGAAACTAGCAAGG 57.089 41.667 14.86 0.00 42.35 3.61
3769 3861 7.093945 TGCTAGACATGACATACACTGAGTAAA 60.094 37.037 0.00 0.00 36.05 2.01
3773 3865 5.254339 TGCTAGACATGACATACACTGAG 57.746 43.478 0.00 0.00 0.00 3.35
3799 3891 5.126869 TCACCAACAAAAACATGACAGATGT 59.873 36.000 0.00 0.00 0.00 3.06
3809 3901 5.997746 TCAAAACCAATCACCAACAAAAACA 59.002 32.000 0.00 0.00 0.00 2.83
3814 3906 5.453057 CCATCTCAAAACCAATCACCAACAA 60.453 40.000 0.00 0.00 0.00 2.83
3898 4107 0.877743 GAAGCTCACAGTTTCCAGGC 59.122 55.000 0.00 0.00 30.44 4.85
3899 4108 2.149578 CTGAAGCTCACAGTTTCCAGG 58.850 52.381 11.26 0.00 34.99 4.45
3900 4109 3.117491 TCTGAAGCTCACAGTTTCCAG 57.883 47.619 16.70 0.00 34.99 3.86
3930 4139 6.084326 ACACCAAACTTATAGGCTGTTTTG 57.916 37.500 0.00 0.00 32.42 2.44
3944 4153 7.907389 TGAGAACTTAGATCATACACCAAACT 58.093 34.615 0.00 0.00 0.00 2.66
3945 4154 8.547967 TTGAGAACTTAGATCATACACCAAAC 57.452 34.615 0.00 0.00 0.00 2.93
3961 4170 8.524487 CCTATGTCTTACTGTACTTGAGAACTT 58.476 37.037 0.00 0.00 0.00 2.66
3973 4182 8.353684 CGTTATGAGAATCCTATGTCTTACTGT 58.646 37.037 0.00 0.00 0.00 3.55
3974 4183 8.568794 TCGTTATGAGAATCCTATGTCTTACTG 58.431 37.037 0.00 0.00 0.00 2.74
3975 4184 8.693120 TCGTTATGAGAATCCTATGTCTTACT 57.307 34.615 0.00 0.00 0.00 2.24
3976 4185 9.400638 CTTCGTTATGAGAATCCTATGTCTTAC 57.599 37.037 0.00 0.00 0.00 2.34
4016 4225 2.098934 TCAACGCAAAACAAGAGTGCAT 59.901 40.909 0.00 0.00 38.19 3.96
4067 4276 7.771927 ATCAAACAAGAAAGATTGAGTGGAT 57.228 32.000 0.00 0.00 34.46 3.41
4068 4277 7.587037 AATCAAACAAGAAAGATTGAGTGGA 57.413 32.000 0.00 0.00 34.46 4.02
4077 4286 8.825745 GCACCAAATAAAATCAAACAAGAAAGA 58.174 29.630 0.00 0.00 0.00 2.52
4078 4287 8.610896 TGCACCAAATAAAATCAAACAAGAAAG 58.389 29.630 0.00 0.00 0.00 2.62
4079 4288 8.498054 TGCACCAAATAAAATCAAACAAGAAA 57.502 26.923 0.00 0.00 0.00 2.52
4080 4289 8.674263 ATGCACCAAATAAAATCAAACAAGAA 57.326 26.923 0.00 0.00 0.00 2.52
4081 4290 8.674263 AATGCACCAAATAAAATCAAACAAGA 57.326 26.923 0.00 0.00 0.00 3.02
4084 4293 9.499479 ACATAATGCACCAAATAAAATCAAACA 57.501 25.926 0.00 0.00 0.00 2.83
4085 4294 9.971744 GACATAATGCACCAAATAAAATCAAAC 57.028 29.630 0.00 0.00 0.00 2.93
4086 4295 9.941325 AGACATAATGCACCAAATAAAATCAAA 57.059 25.926 0.00 0.00 0.00 2.69
4087 4296 9.585099 GAGACATAATGCACCAAATAAAATCAA 57.415 29.630 0.00 0.00 0.00 2.57
4088 4297 8.970020 AGAGACATAATGCACCAAATAAAATCA 58.030 29.630 0.00 0.00 0.00 2.57
4089 4298 9.455847 GAGAGACATAATGCACCAAATAAAATC 57.544 33.333 0.00 0.00 0.00 2.17
4090 4299 8.416329 GGAGAGACATAATGCACCAAATAAAAT 58.584 33.333 0.00 0.00 0.00 1.82
4091 4300 7.415095 CGGAGAGACATAATGCACCAAATAAAA 60.415 37.037 0.00 0.00 0.00 1.52
4092 4301 6.038161 CGGAGAGACATAATGCACCAAATAAA 59.962 38.462 0.00 0.00 0.00 1.40
4093 4302 5.527214 CGGAGAGACATAATGCACCAAATAA 59.473 40.000 0.00 0.00 0.00 1.40
4094 4303 5.056480 CGGAGAGACATAATGCACCAAATA 58.944 41.667 0.00 0.00 0.00 1.40
4095 4304 3.879295 CGGAGAGACATAATGCACCAAAT 59.121 43.478 0.00 0.00 0.00 2.32
4096 4305 3.270027 CGGAGAGACATAATGCACCAAA 58.730 45.455 0.00 0.00 0.00 3.28
4140 4367 8.873830 ACTCGTTCAATAATAATCAGTTCAGTG 58.126 33.333 0.00 0.00 0.00 3.66
4175 4402 0.833287 ATAGCATCGGCAGTGTCCTT 59.167 50.000 0.00 0.00 44.61 3.36


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

AutoCloner maintained by Alex Coulton.