Multiple sequence alignment - TraesCS6A01G145800

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 TraesCS6A01G145800 chr6A 100.000 4417 0 0 1 4417 124299115 124303531 0.000000e+00 8157.0
1 TraesCS6A01G145800 chr6D 91.851 1902 66 32 740 2602 103008819 103010670 0.000000e+00 2571.0
2 TraesCS6A01G145800 chr6D 91.752 1758 77 35 2605 4339 103010980 103012692 0.000000e+00 2381.0
3 TraesCS6A01G145800 chr6D 87.900 438 39 11 2631 3057 455535582 455536016 1.830000e-138 503.0
4 TraesCS6A01G145800 chr6D 97.778 45 1 0 4373 4417 103012690 103012734 1.320000e-10 78.7
5 TraesCS6A01G145800 chr6B 87.916 1473 112 37 779 2230 188680467 188681894 0.000000e+00 1674.0
6 TraesCS6A01G145800 chr6B 91.186 590 37 8 3831 4417 188683778 188684355 0.000000e+00 787.0
7 TraesCS6A01G145800 chr6B 81.037 849 92 42 2384 3223 188682379 188683167 2.920000e-171 612.0
8 TraesCS6A01G145800 chr6B 85.640 383 33 10 3272 3642 188683355 188683727 2.490000e-102 383.0
9 TraesCS6A01G145800 chr6B 90.566 106 10 0 2769 2874 46969214 46969319 1.660000e-29 141.0
10 TraesCS6A01G145800 chr2B 86.588 932 94 21 1090 2018 434718748 434719651 0.000000e+00 1000.0
11 TraesCS6A01G145800 chr2B 88.716 257 28 1 1877 2133 434719671 434719926 3.320000e-81 313.0
12 TraesCS6A01G145800 chr2B 82.692 156 17 9 120 270 448579726 448579576 3.590000e-26 130.0
13 TraesCS6A01G145800 chr4A 86.639 479 59 3 1068 1544 375825200 375824725 3.910000e-145 525.0
14 TraesCS6A01G145800 chr4A 86.247 429 43 9 1594 2018 375824722 375824306 6.740000e-123 451.0
15 TraesCS6A01G145800 chr4A 79.388 490 71 18 192 674 123256512 123256978 7.130000e-83 318.0
16 TraesCS6A01G145800 chr4A 88.073 218 23 2 1913 2129 375824263 375824048 5.670000e-64 255.0
17 TraesCS6A01G145800 chr2D 88.128 438 38 10 2631 3057 520580170 520579736 3.940000e-140 508.0
18 TraesCS6A01G145800 chr2D 90.909 99 7 2 1 97 294500527 294500429 9.970000e-27 132.0
19 TraesCS6A01G145800 chr4D 87.900 438 39 10 2631 3057 95123383 95122949 1.830000e-138 503.0
20 TraesCS6A01G145800 chr4D 81.316 471 73 13 140 604 507239532 507239993 6.980000e-98 368.0
21 TraesCS6A01G145800 chr4B 78.628 627 102 25 120 734 424697384 424696778 1.930000e-103 387.0
22 TraesCS6A01G145800 chr3D 82.838 437 45 11 2631 3057 533430017 533429601 9.030000e-97 364.0
23 TraesCS6A01G145800 chr3D 93.548 93 3 3 1 90 81673026 81673118 7.710000e-28 135.0
24 TraesCS6A01G145800 chr5A 80.453 486 71 17 140 611 293436199 293436674 2.530000e-92 350.0
25 TraesCS6A01G145800 chr5A 81.311 412 54 16 206 601 41456547 41456143 3.320000e-81 313.0
26 TraesCS6A01G145800 chr5A 77.905 525 82 28 120 629 434522936 434523441 3.340000e-76 296.0
27 TraesCS6A01G145800 chr5A 77.843 510 88 18 121 612 550648031 550648533 4.320000e-75 292.0
28 TraesCS6A01G145800 chr5A 92.473 93 5 2 4 94 674286222 674286130 9.970000e-27 132.0
29 TraesCS6A01G145800 chr5A 81.884 138 23 1 124 261 531393867 531394002 1.000000e-21 115.0
30 TraesCS6A01G145800 chr7D 81.441 458 54 21 1088 1542 613546473 613546902 3.270000e-91 346.0
31 TraesCS6A01G145800 chr7D 78.692 535 78 28 120 639 191565300 191565813 1.530000e-84 324.0
32 TraesCS6A01G145800 chr7A 82.033 423 55 18 1123 1542 705123783 705124187 1.520000e-89 340.0
33 TraesCS6A01G145800 chr7A 94.845 97 3 2 1 95 9325076 9325172 2.750000e-32 150.0
34 TraesCS6A01G145800 chr7A 91.667 96 6 2 5 98 517300289 517300194 9.970000e-27 132.0
35 TraesCS6A01G145800 chr7A 90.099 101 8 2 1 99 495395442 495395542 3.590000e-26 130.0
36 TraesCS6A01G145800 chr5D 82.057 418 53 15 206 606 548794565 548794153 1.970000e-88 337.0
37 TraesCS6A01G145800 chr1A 80.405 444 64 18 86 517 61124298 61123866 2.560000e-82 316.0
38 TraesCS6A01G145800 chr1A 87.611 113 9 5 1 110 34718754 34718864 4.640000e-25 126.0
39 TraesCS6A01G145800 chr7B 93.684 190 12 0 1123 1312 704037862 704038051 7.230000e-73 285.0
40 TraesCS6A01G145800 chr7B 90.598 117 11 0 1426 1542 704038135 704038251 5.920000e-34 156.0
41 TraesCS6A01G145800 chr1B 90.566 106 10 0 2769 2874 500419653 500419758 1.660000e-29 141.0
42 TraesCS6A01G145800 chr1B 88.034 117 7 5 4 113 299055409 299055293 9.970000e-27 132.0
43 TraesCS6A01G145800 chrUn 86.667 120 13 3 4 121 79573433 79573315 3.590000e-26 130.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G145800 chr6A 124299115 124303531 4416 False 8157.000000 8157 100.000000 1 4417 1 chr6A.!!$F1 4416
1 TraesCS6A01G145800 chr6D 103008819 103012734 3915 False 1676.900000 2571 93.793667 740 4417 3 chr6D.!!$F2 3677
2 TraesCS6A01G145800 chr6B 188680467 188684355 3888 False 864.000000 1674 86.444750 779 4417 4 chr6B.!!$F2 3638
3 TraesCS6A01G145800 chr2B 434718748 434719926 1178 False 656.500000 1000 87.652000 1090 2133 2 chr2B.!!$F1 1043
4 TraesCS6A01G145800 chr4A 375824048 375825200 1152 True 410.333333 525 86.986333 1068 2129 3 chr4A.!!$R1 1061
5 TraesCS6A01G145800 chr4B 424696778 424697384 606 True 387.000000 387 78.628000 120 734 1 chr4B.!!$R1 614
6 TraesCS6A01G145800 chr5A 434522936 434523441 505 False 296.000000 296 77.905000 120 629 1 chr5A.!!$F2 509
7 TraesCS6A01G145800 chr5A 550648031 550648533 502 False 292.000000 292 77.843000 121 612 1 chr5A.!!$F4 491
8 TraesCS6A01G145800 chr7D 191565300 191565813 513 False 324.000000 324 78.692000 120 639 1 chr7D.!!$F1 519

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
748 782 0.036388 CGCCCTCTCTAAGCAAACCA 60.036 55.0 0.00 0.00 0.00 3.67 F
1492 1535 0.985490 AGGAGAGGGACATGAAGCCC 60.985 60.0 13.01 13.01 45.04 5.19 F
1870 1928 0.315251 TCCTCTTGTCGCAGTCTGTG 59.685 55.0 7.09 7.09 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1748 0.451783 CAATAGAAGGCACGCCAACC 59.548 55.0 11.35 0.00 38.92 3.77 R
3096 3989 0.392706 ATTGTGAGTCGGTCAGCACA 59.607 50.0 0.00 0.00 39.27 4.57 R
3810 4873 0.178992 TAGGCACAGTGCTTTGGCTT 60.179 50.0 24.75 5.32 45.81 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.245159 CTGAGAGTGGCAAAGTGACA 57.755 50.000 0.00 0.00 29.15 3.58
20 21 2.775890 CTGAGAGTGGCAAAGTGACAT 58.224 47.619 0.00 0.00 37.93 3.06
21 22 2.483106 CTGAGAGTGGCAAAGTGACATG 59.517 50.000 0.00 0.00 37.93 3.21
22 23 2.158769 TGAGAGTGGCAAAGTGACATGT 60.159 45.455 0.00 0.00 37.93 3.21
23 24 2.481952 GAGAGTGGCAAAGTGACATGTC 59.518 50.000 19.27 19.27 37.93 3.06
24 25 2.158769 AGAGTGGCAAAGTGACATGTCA 60.159 45.455 24.56 24.56 37.93 3.58
25 26 2.618241 GAGTGGCAAAGTGACATGTCAA 59.382 45.455 29.42 10.05 37.93 3.18
26 27 3.023119 AGTGGCAAAGTGACATGTCAAA 58.977 40.909 29.42 5.89 37.93 2.69
27 28 3.638160 AGTGGCAAAGTGACATGTCAAAT 59.362 39.130 29.42 18.31 37.93 2.32
28 29 4.099881 AGTGGCAAAGTGACATGTCAAATT 59.900 37.500 29.42 22.66 37.93 1.82
29 30 4.445385 GTGGCAAAGTGACATGTCAAATTC 59.555 41.667 29.42 17.04 37.93 2.17
30 31 4.341806 TGGCAAAGTGACATGTCAAATTCT 59.658 37.500 29.42 19.00 41.85 2.40
31 32 5.534278 TGGCAAAGTGACATGTCAAATTCTA 59.466 36.000 29.42 12.92 41.85 2.10
32 33 6.088824 GGCAAAGTGACATGTCAAATTCTAG 58.911 40.000 29.42 17.53 41.85 2.43
33 34 6.072508 GGCAAAGTGACATGTCAAATTCTAGA 60.073 38.462 29.42 1.05 41.85 2.43
34 35 7.020010 GCAAAGTGACATGTCAAATTCTAGAG 58.980 38.462 29.42 14.82 41.85 2.43
35 36 7.308229 GCAAAGTGACATGTCAAATTCTAGAGT 60.308 37.037 29.42 9.01 41.85 3.24
36 37 7.664082 AAGTGACATGTCAAATTCTAGAGTG 57.336 36.000 29.42 0.00 41.85 3.51
37 38 6.169094 AGTGACATGTCAAATTCTAGAGTGG 58.831 40.000 29.42 0.00 41.85 4.00
38 39 4.937620 TGACATGTCAAATTCTAGAGTGGC 59.062 41.667 26.02 0.00 36.53 5.01
39 40 4.910195 ACATGTCAAATTCTAGAGTGGCA 58.090 39.130 9.14 9.14 0.00 4.92
40 41 5.503927 ACATGTCAAATTCTAGAGTGGCAT 58.496 37.500 12.12 12.12 36.78 4.40
41 42 6.653020 ACATGTCAAATTCTAGAGTGGCATA 58.347 36.000 15.69 0.00 34.18 3.14
42 43 7.112122 ACATGTCAAATTCTAGAGTGGCATAA 58.888 34.615 15.69 0.00 34.18 1.90
43 44 7.281774 ACATGTCAAATTCTAGAGTGGCATAAG 59.718 37.037 15.69 9.90 34.18 1.73
44 45 5.586243 TGTCAAATTCTAGAGTGGCATAAGC 59.414 40.000 3.98 0.00 41.10 3.09
45 46 5.586243 GTCAAATTCTAGAGTGGCATAAGCA 59.414 40.000 0.00 0.00 44.61 3.91
46 47 6.094048 GTCAAATTCTAGAGTGGCATAAGCAA 59.906 38.462 0.00 0.00 44.61 3.91
47 48 6.658816 TCAAATTCTAGAGTGGCATAAGCAAA 59.341 34.615 0.00 0.00 44.61 3.68
48 49 6.690194 AATTCTAGAGTGGCATAAGCAAAG 57.310 37.500 0.00 0.00 44.61 2.77
49 50 4.826274 TCTAGAGTGGCATAAGCAAAGT 57.174 40.909 0.00 0.00 44.61 2.66
50 51 5.932619 TCTAGAGTGGCATAAGCAAAGTA 57.067 39.130 0.00 0.00 44.61 2.24
51 52 5.907207 TCTAGAGTGGCATAAGCAAAGTAG 58.093 41.667 0.00 0.00 44.61 2.57
52 53 3.878778 AGAGTGGCATAAGCAAAGTAGG 58.121 45.455 0.00 0.00 44.61 3.18
53 54 2.356069 GAGTGGCATAAGCAAAGTAGGC 59.644 50.000 0.00 0.00 44.61 3.93
54 55 2.091541 GTGGCATAAGCAAAGTAGGCA 58.908 47.619 0.00 0.00 44.61 4.75
55 56 2.491693 GTGGCATAAGCAAAGTAGGCAA 59.508 45.455 0.00 0.00 44.61 4.52
56 57 3.056891 GTGGCATAAGCAAAGTAGGCAAA 60.057 43.478 0.00 0.00 44.61 3.68
57 58 3.576118 TGGCATAAGCAAAGTAGGCAAAA 59.424 39.130 0.00 0.00 44.61 2.44
58 59 4.176271 GGCATAAGCAAAGTAGGCAAAAG 58.824 43.478 0.00 0.00 44.61 2.27
59 60 3.614176 GCATAAGCAAAGTAGGCAAAAGC 59.386 43.478 0.00 0.00 41.58 3.51
60 61 4.619160 GCATAAGCAAAGTAGGCAAAAGCT 60.619 41.667 0.00 0.00 41.58 3.74
61 62 5.393027 GCATAAGCAAAGTAGGCAAAAGCTA 60.393 40.000 0.00 0.00 41.58 3.32
62 63 4.773323 AAGCAAAGTAGGCAAAAGCTAG 57.227 40.909 0.00 0.00 0.00 3.42
63 64 4.021102 AGCAAAGTAGGCAAAAGCTAGA 57.979 40.909 0.00 0.00 0.00 2.43
64 65 4.006319 AGCAAAGTAGGCAAAAGCTAGAG 58.994 43.478 0.00 0.00 0.00 2.43
65 66 3.753797 GCAAAGTAGGCAAAAGCTAGAGT 59.246 43.478 0.00 0.00 0.00 3.24
66 67 4.378874 GCAAAGTAGGCAAAAGCTAGAGTG 60.379 45.833 0.00 0.00 0.00 3.51
67 68 3.618690 AGTAGGCAAAAGCTAGAGTGG 57.381 47.619 0.00 0.00 0.00 4.00
68 69 2.010497 GTAGGCAAAAGCTAGAGTGGC 58.990 52.381 0.00 0.00 36.84 5.01
69 70 0.401738 AGGCAAAAGCTAGAGTGGCA 59.598 50.000 12.75 0.00 38.91 4.92
70 71 1.202927 AGGCAAAAGCTAGAGTGGCAA 60.203 47.619 12.75 0.00 38.91 4.52
71 72 1.613437 GGCAAAAGCTAGAGTGGCAAA 59.387 47.619 0.00 0.00 36.61 3.68
72 73 2.035832 GGCAAAAGCTAGAGTGGCAAAA 59.964 45.455 0.00 0.00 36.61 2.44
73 74 3.492482 GGCAAAAGCTAGAGTGGCAAAAA 60.492 43.478 0.00 0.00 36.61 1.94
74 75 3.490896 GCAAAAGCTAGAGTGGCAAAAAC 59.509 43.478 0.00 0.00 0.00 2.43
75 76 4.681744 CAAAAGCTAGAGTGGCAAAAACA 58.318 39.130 0.00 0.00 0.00 2.83
76 77 5.108517 CAAAAGCTAGAGTGGCAAAAACAA 58.891 37.500 0.00 0.00 0.00 2.83
77 78 5.337578 AAAGCTAGAGTGGCAAAAACAAA 57.662 34.783 0.00 0.00 0.00 2.83
78 79 5.535753 AAGCTAGAGTGGCAAAAACAAAT 57.464 34.783 0.00 0.00 0.00 2.32
79 80 5.535753 AGCTAGAGTGGCAAAAACAAATT 57.464 34.783 0.00 0.00 0.00 1.82
80 81 5.917462 AGCTAGAGTGGCAAAAACAAATTT 58.083 33.333 0.00 0.00 0.00 1.82
81 82 5.985530 AGCTAGAGTGGCAAAAACAAATTTC 59.014 36.000 0.00 0.00 0.00 2.17
82 83 5.177511 GCTAGAGTGGCAAAAACAAATTTCC 59.822 40.000 0.00 0.00 0.00 3.13
83 84 4.450976 AGAGTGGCAAAAACAAATTTCCC 58.549 39.130 0.00 0.00 0.00 3.97
84 85 3.550820 AGTGGCAAAAACAAATTTCCCC 58.449 40.909 0.00 0.00 0.00 4.81
85 86 3.201930 AGTGGCAAAAACAAATTTCCCCT 59.798 39.130 0.00 0.00 0.00 4.79
86 87 3.951037 GTGGCAAAAACAAATTTCCCCTT 59.049 39.130 0.00 0.00 0.00 3.95
87 88 4.400884 GTGGCAAAAACAAATTTCCCCTTT 59.599 37.500 0.00 0.00 0.00 3.11
88 89 5.019470 TGGCAAAAACAAATTTCCCCTTTT 58.981 33.333 0.00 0.00 0.00 2.27
89 90 5.481824 TGGCAAAAACAAATTTCCCCTTTTT 59.518 32.000 0.00 0.00 0.00 1.94
90 91 5.809562 GGCAAAAACAAATTTCCCCTTTTTG 59.190 36.000 18.00 18.00 41.54 2.44
91 92 6.350528 GGCAAAAACAAATTTCCCCTTTTTGA 60.351 34.615 22.23 0.00 41.31 2.69
92 93 7.093354 GCAAAAACAAATTTCCCCTTTTTGAA 58.907 30.769 22.23 0.00 41.31 2.69
93 94 7.600375 GCAAAAACAAATTTCCCCTTTTTGAAA 59.400 29.630 22.23 0.00 41.31 2.69
94 95 9.481340 CAAAAACAAATTTCCCCTTTTTGAAAA 57.519 25.926 17.73 0.00 41.31 2.29
95 96 9.703892 AAAAACAAATTTCCCCTTTTTGAAAAG 57.296 25.926 8.83 8.83 43.82 2.27
96 97 6.449635 ACAAATTTCCCCTTTTTGAAAAGC 57.550 33.333 10.06 0.00 43.07 3.51
97 98 6.186957 ACAAATTTCCCCTTTTTGAAAAGCT 58.813 32.000 10.06 0.00 43.07 3.74
98 99 6.663093 ACAAATTTCCCCTTTTTGAAAAGCTT 59.337 30.769 10.06 0.00 43.07 3.74
99 100 6.698008 AATTTCCCCTTTTTGAAAAGCTTG 57.302 33.333 0.00 2.43 43.07 4.01
100 101 5.428184 TTTCCCCTTTTTGAAAAGCTTGA 57.572 34.783 0.00 4.35 43.07 3.02
101 102 5.628797 TTCCCCTTTTTGAAAAGCTTGAT 57.371 34.783 0.00 0.00 43.07 2.57
102 103 5.628797 TCCCCTTTTTGAAAAGCTTGATT 57.371 34.783 0.00 0.00 43.07 2.57
103 104 6.739331 TCCCCTTTTTGAAAAGCTTGATTA 57.261 33.333 0.00 0.00 43.07 1.75
104 105 7.130681 TCCCCTTTTTGAAAAGCTTGATTAA 57.869 32.000 0.00 0.00 43.07 1.40
105 106 6.989759 TCCCCTTTTTGAAAAGCTTGATTAAC 59.010 34.615 0.00 0.00 43.07 2.01
106 107 6.765512 CCCCTTTTTGAAAAGCTTGATTAACA 59.234 34.615 0.00 0.00 43.07 2.41
107 108 7.445096 CCCCTTTTTGAAAAGCTTGATTAACAT 59.555 33.333 0.00 0.00 43.07 2.71
108 109 8.839343 CCCTTTTTGAAAAGCTTGATTAACATT 58.161 29.630 0.00 0.00 43.07 2.71
512 543 8.498054 TTTCAAATGCTTGGTCAACATTTTTA 57.502 26.923 15.00 8.70 40.94 1.52
652 686 4.316205 AAAAACGAGGTTGAATGTTCCC 57.684 40.909 0.00 0.00 0.00 3.97
653 687 1.519408 AACGAGGTTGAATGTTCCCG 58.481 50.000 0.00 0.00 0.00 5.14
654 688 0.682852 ACGAGGTTGAATGTTCCCGA 59.317 50.000 0.00 0.00 0.00 5.14
655 689 1.337823 ACGAGGTTGAATGTTCCCGAG 60.338 52.381 0.00 0.00 0.00 4.63
656 690 1.337823 CGAGGTTGAATGTTCCCGAGT 60.338 52.381 0.00 0.00 0.00 4.18
657 691 2.076863 GAGGTTGAATGTTCCCGAGTG 58.923 52.381 0.00 0.00 0.00 3.51
658 692 1.420138 AGGTTGAATGTTCCCGAGTGT 59.580 47.619 0.00 0.00 0.00 3.55
659 693 1.804748 GGTTGAATGTTCCCGAGTGTC 59.195 52.381 0.00 0.00 0.00 3.67
660 694 2.550208 GGTTGAATGTTCCCGAGTGTCT 60.550 50.000 0.00 0.00 0.00 3.41
662 696 1.001974 TGAATGTTCCCGAGTGTCTGG 59.998 52.381 0.00 0.00 0.00 3.86
686 720 2.249309 CAACTCGTGCCACGCTTG 59.751 61.111 13.39 12.18 42.21 4.01
688 722 1.956170 AACTCGTGCCACGCTTGAG 60.956 57.895 13.39 7.26 42.21 3.02
700 734 2.450619 GCTTGAGCGAGACTTGTCC 58.549 57.895 0.00 0.00 0.00 4.02
701 735 0.037790 GCTTGAGCGAGACTTGTCCT 60.038 55.000 0.00 0.00 0.00 3.85
702 736 1.707632 CTTGAGCGAGACTTGTCCTG 58.292 55.000 0.00 0.00 0.00 3.86
710 744 0.827925 AGACTTGTCCTGGTCTCGCA 60.828 55.000 0.00 0.00 38.25 5.10
734 768 1.662608 CGAGACATATCAGCGCCCT 59.337 57.895 2.29 0.00 0.00 5.19
735 769 0.387878 CGAGACATATCAGCGCCCTC 60.388 60.000 2.29 0.00 0.00 4.30
736 770 0.965439 GAGACATATCAGCGCCCTCT 59.035 55.000 2.29 0.00 0.00 3.69
737 771 0.965439 AGACATATCAGCGCCCTCTC 59.035 55.000 2.29 0.00 0.00 3.20
738 772 0.965439 GACATATCAGCGCCCTCTCT 59.035 55.000 2.29 0.00 0.00 3.10
748 782 0.036388 CGCCCTCTCTAAGCAAACCA 60.036 55.000 0.00 0.00 0.00 3.67
750 784 2.293170 GCCCTCTCTAAGCAAACCATC 58.707 52.381 0.00 0.00 0.00 3.51
764 798 6.264528 AGCAAACCATCTAGGCCTCTATATA 58.735 40.000 9.68 0.00 43.14 0.86
765 799 6.155393 AGCAAACCATCTAGGCCTCTATATAC 59.845 42.308 9.68 0.00 43.14 1.47
1324 1365 1.026718 CGCTGTGGGTCTTCAATCCC 61.027 60.000 0.00 0.00 43.67 3.85
1407 1448 2.154462 GGTTTGGGTCTGATGTCTGTG 58.846 52.381 0.00 0.00 0.00 3.66
1408 1449 2.487265 GGTTTGGGTCTGATGTCTGTGT 60.487 50.000 0.00 0.00 0.00 3.72
1492 1535 0.985490 AGGAGAGGGACATGAAGCCC 60.985 60.000 13.01 13.01 45.04 5.19
1525 1568 2.756283 CTCGTCTCCGCCCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
1615 1658 2.288213 TGTGGTCGTGTTAAGAGCAGAG 60.288 50.000 0.00 0.00 45.19 3.35
1698 1748 5.407407 ACTGGTTGACTATGTGAAGTAGG 57.593 43.478 0.00 0.00 0.00 3.18
1704 1754 3.055385 TGACTATGTGAAGTAGGGTTGGC 60.055 47.826 0.00 0.00 0.00 4.52
1723 1773 1.940613 GCGTGCCTTCTATTGGGTTAG 59.059 52.381 0.00 0.00 0.00 2.34
1853 1911 5.581126 TGATGTAATTGTGCAATTCCTCC 57.419 39.130 12.72 4.09 40.99 4.30
1860 1918 2.783135 TGTGCAATTCCTCCTCTTGTC 58.217 47.619 0.00 0.00 0.00 3.18
1870 1928 0.315251 TCCTCTTGTCGCAGTCTGTG 59.685 55.000 7.09 7.09 0.00 3.66
1875 1937 1.458445 CTTGTCGCAGTCTGTGTCATG 59.542 52.381 12.99 11.63 0.00 3.07
1987 2209 7.933577 CCACCTCTTATATTTGCTGAACTATGA 59.066 37.037 0.00 0.00 0.00 2.15
2189 2415 7.931275 ACTTCCTTCTCAAAAGTACAATTGAC 58.069 34.615 13.59 6.20 31.68 3.18
2231 2737 8.850156 GGCTATGTTTTATTCACATACTTCCAT 58.150 33.333 0.00 0.00 36.28 3.41
2331 2867 5.181811 TGCTTATTGTCAACTGTCATCCAAG 59.818 40.000 0.00 0.00 0.00 3.61
2332 2868 5.182001 GCTTATTGTCAACTGTCATCCAAGT 59.818 40.000 0.00 0.00 0.00 3.16
2333 2869 6.371548 GCTTATTGTCAACTGTCATCCAAGTA 59.628 38.462 0.00 0.00 0.00 2.24
2334 2870 7.066284 GCTTATTGTCAACTGTCATCCAAGTAT 59.934 37.037 0.00 0.00 0.00 2.12
2335 2871 8.862325 TTATTGTCAACTGTCATCCAAGTATT 57.138 30.769 0.00 0.00 0.00 1.89
2411 2985 6.065374 TCAGAAAACACCAAACAAGGCTATA 58.935 36.000 0.00 0.00 0.00 1.31
2542 3116 9.329913 CAAAGTTGTATTGTTAATGTAGACAGC 57.670 33.333 0.00 0.00 0.00 4.40
2544 3118 8.792830 AGTTGTATTGTTAATGTAGACAGCAT 57.207 30.769 0.00 0.00 0.00 3.79
2545 3119 8.668353 AGTTGTATTGTTAATGTAGACAGCATG 58.332 33.333 0.00 0.00 46.00 4.06
2621 3507 5.063186 CAGTGCTTCATGTCTCTTGATACAC 59.937 44.000 0.00 0.00 33.13 2.90
2629 3515 4.936891 TGTCTCTTGATACACGATGATGG 58.063 43.478 0.00 0.00 0.00 3.51
2643 3531 3.001634 CGATGATGGTGATTCTTGAACCG 59.998 47.826 0.00 0.00 36.73 4.44
2664 3552 0.959372 ATGCTGACTTCCTGTGCAGC 60.959 55.000 0.00 0.00 43.49 5.25
2819 3707 3.240884 GGTTCGTTTCCTTACTCGAGAC 58.759 50.000 21.68 3.57 33.98 3.36
2988 3881 2.820059 TGCTGTCTTCTGTTGATCGT 57.180 45.000 0.00 0.00 0.00 3.73
3094 3987 0.737367 ATGCGAGTGTGTGACCATCG 60.737 55.000 0.00 0.00 36.51 3.84
3096 3989 1.080501 CGAGTGTGTGACCATCGCT 60.081 57.895 0.00 0.00 0.00 4.93
3097 3990 1.347097 CGAGTGTGTGACCATCGCTG 61.347 60.000 0.00 0.00 0.00 5.18
3110 4003 2.549611 ATCGCTGTGCTGACCGACTC 62.550 60.000 0.00 0.00 32.07 3.36
3148 4046 6.777091 TCATTATTAGGGCACTTTGTATGCAT 59.223 34.615 3.79 3.79 45.27 3.96
3152 4050 3.290710 AGGGCACTTTGTATGCATAAGG 58.709 45.455 8.28 0.00 45.27 2.69
3192 4091 6.876257 GCTAATCCCAGGAAGATGTGTTATAG 59.124 42.308 0.00 0.00 0.00 1.31
3247 4146 7.315247 TGAACCAACATGTGCTATTATACAC 57.685 36.000 0.00 0.00 37.31 2.90
3305 4353 3.180507 AGAGATCAGAGGAAGGTGCTTT 58.819 45.455 0.00 0.00 0.00 3.51
3306 4354 3.055240 AGAGATCAGAGGAAGGTGCTTTG 60.055 47.826 0.00 0.00 0.00 2.77
3430 4478 2.037902 TGGACTGATTTCGCAACACCTA 59.962 45.455 0.00 0.00 0.00 3.08
3446 4494 3.573110 ACACCTACAGTCCTAGTTCACAC 59.427 47.826 0.00 0.00 0.00 3.82
3486 4544 4.618920 AAACCCGTGTGATCTACTCTTT 57.381 40.909 0.00 0.00 0.00 2.52
3487 4545 3.870633 ACCCGTGTGATCTACTCTTTC 57.129 47.619 0.00 0.00 0.00 2.62
3488 4546 3.432378 ACCCGTGTGATCTACTCTTTCT 58.568 45.455 0.00 0.00 0.00 2.52
3489 4547 3.193691 ACCCGTGTGATCTACTCTTTCTG 59.806 47.826 0.00 0.00 0.00 3.02
3517 4575 3.058639 GCTCAAGCACTTCTTTGTTCGAT 60.059 43.478 0.00 0.00 41.59 3.59
3518 4576 4.461405 CTCAAGCACTTCTTTGTTCGATG 58.539 43.478 0.00 0.00 31.27 3.84
3531 4589 3.734463 TGTTCGATGCTACAACTTGGAA 58.266 40.909 0.00 0.00 0.00 3.53
3561 4619 5.381174 TGCCACTGAAATCTGAAATTGAG 57.619 39.130 0.00 0.00 0.00 3.02
3595 4653 4.044336 TGTGCACTTTGTTCCAGAATTG 57.956 40.909 19.41 0.00 0.00 2.32
3716 4774 2.094182 CGTGTACTATGCTTGTCACCCT 60.094 50.000 0.00 0.00 0.00 4.34
3717 4775 3.522553 GTGTACTATGCTTGTCACCCTC 58.477 50.000 0.00 0.00 0.00 4.30
3739 4802 8.071177 CCTCTGGGAGTTTGATAAATTTGATT 57.929 34.615 0.00 0.00 33.58 2.57
3740 4803 7.977853 CCTCTGGGAGTTTGATAAATTTGATTG 59.022 37.037 0.00 0.00 33.58 2.67
3741 4804 8.648698 TCTGGGAGTTTGATAAATTTGATTGA 57.351 30.769 0.00 0.00 0.00 2.57
3742 4805 9.258629 TCTGGGAGTTTGATAAATTTGATTGAT 57.741 29.630 0.00 0.00 0.00 2.57
3756 4819 5.852282 TTGATTGATCAGTGAGGATCGTA 57.148 39.130 0.00 0.00 45.31 3.43
3758 4821 7.524717 TTGATTGATCAGTGAGGATCGTATA 57.475 36.000 0.00 0.00 45.31 1.47
3759 4822 6.914259 TGATTGATCAGTGAGGATCGTATAC 58.086 40.000 0.00 0.00 45.31 1.47
3760 4823 6.717084 TGATTGATCAGTGAGGATCGTATACT 59.283 38.462 0.00 0.00 45.31 2.12
3761 4824 6.561737 TTGATCAGTGAGGATCGTATACTC 57.438 41.667 0.00 1.41 45.31 2.59
3762 4825 4.691216 TGATCAGTGAGGATCGTATACTCG 59.309 45.833 0.00 0.00 43.47 4.18
3763 4826 4.069300 TCAGTGAGGATCGTATACTCGT 57.931 45.455 0.56 0.00 43.47 4.18
3764 4827 5.205759 TCAGTGAGGATCGTATACTCGTA 57.794 43.478 0.56 0.00 43.47 3.43
3765 4828 5.791666 TCAGTGAGGATCGTATACTCGTAT 58.208 41.667 0.56 0.00 43.47 3.06
3766 4829 5.638234 TCAGTGAGGATCGTATACTCGTATG 59.362 44.000 0.56 2.95 43.47 2.39
3767 4830 4.392445 AGTGAGGATCGTATACTCGTATGC 59.608 45.833 0.56 0.00 43.47 3.14
3768 4831 3.688185 TGAGGATCGTATACTCGTATGCC 59.312 47.826 0.56 0.00 43.47 4.40
3769 4832 3.940221 GAGGATCGTATACTCGTATGCCT 59.060 47.826 0.56 0.00 28.97 4.75
3770 4833 3.690139 AGGATCGTATACTCGTATGCCTG 59.310 47.826 0.56 0.00 0.00 4.85
3771 4834 3.439476 GGATCGTATACTCGTATGCCTGT 59.561 47.826 0.56 0.00 0.00 4.00
3772 4835 4.082895 GGATCGTATACTCGTATGCCTGTT 60.083 45.833 0.56 0.00 0.00 3.16
3773 4836 5.122869 GGATCGTATACTCGTATGCCTGTTA 59.877 44.000 0.56 0.00 0.00 2.41
3774 4837 5.348418 TCGTATACTCGTATGCCTGTTAC 57.652 43.478 0.56 0.00 0.00 2.50
3775 4838 5.059161 TCGTATACTCGTATGCCTGTTACT 58.941 41.667 0.56 0.00 0.00 2.24
3776 4839 5.528690 TCGTATACTCGTATGCCTGTTACTT 59.471 40.000 0.56 0.00 0.00 2.24
3777 4840 6.705825 TCGTATACTCGTATGCCTGTTACTTA 59.294 38.462 0.56 0.00 0.00 2.24
3778 4841 6.794158 CGTATACTCGTATGCCTGTTACTTAC 59.206 42.308 0.56 0.00 0.00 2.34
3779 4842 6.704289 ATACTCGTATGCCTGTTACTTACA 57.296 37.500 0.00 0.00 34.95 2.41
3810 4873 7.996066 TGTGGTAAGATTGCTTTTATATAGGCA 59.004 33.333 0.00 0.00 35.56 4.75
3859 4922 7.713073 TGACGACCTATATTATGCATTTTGACA 59.287 33.333 3.54 0.00 0.00 3.58
3871 4934 2.245795 TTTTGACATGCATTCTCGCG 57.754 45.000 0.00 0.00 33.35 5.87
3974 5040 4.934797 ATCCTAATCCCATGTACCCATG 57.065 45.455 0.00 0.00 46.65 3.66
4001 5067 6.859112 TGCCTTATCTCCTCAAGATATACC 57.141 41.667 0.00 0.00 44.59 2.73
4039 5106 1.337150 CACACGAACGCGATCTTCG 59.663 57.895 23.42 23.42 44.90 3.79
4251 5318 0.810031 ACACGGCACACAGAACACTC 60.810 55.000 0.00 0.00 0.00 3.51
4259 5326 1.485066 ACACAGAACACTCCTCCGTTT 59.515 47.619 0.00 0.00 0.00 3.60
4300 5367 1.045350 TCATGGGAGAGCGGGAGAAG 61.045 60.000 0.00 0.00 0.00 2.85
4301 5368 1.045350 CATGGGAGAGCGGGAGAAGA 61.045 60.000 0.00 0.00 0.00 2.87
4302 5369 0.325671 ATGGGAGAGCGGGAGAAGAA 60.326 55.000 0.00 0.00 0.00 2.52
4317 5384 2.385417 AGAAGAAGGGAGGAGGAGAAGT 59.615 50.000 0.00 0.00 0.00 3.01
4318 5385 3.178046 GAAGAAGGGAGGAGGAGAAGTT 58.822 50.000 0.00 0.00 0.00 2.66
4408 5475 2.123251 GAGGGATCTCTCCGGCCA 60.123 66.667 11.95 0.00 43.11 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.245159 TGTCACTTTGCCACTCTCAG 57.755 50.000 0.00 0.00 0.00 3.35
1 2 2.158769 ACATGTCACTTTGCCACTCTCA 60.159 45.455 0.00 0.00 0.00 3.27
2 3 2.481952 GACATGTCACTTTGCCACTCTC 59.518 50.000 21.07 0.00 0.00 3.20
4 5 2.221169 TGACATGTCACTTTGCCACTC 58.779 47.619 24.56 0.00 34.14 3.51
6 7 3.435105 TTTGACATGTCACTTTGCCAC 57.565 42.857 27.88 0.00 39.66 5.01
7 8 4.341806 AGAATTTGACATGTCACTTTGCCA 59.658 37.500 27.88 9.05 39.66 4.92
8 9 4.874970 AGAATTTGACATGTCACTTTGCC 58.125 39.130 27.88 14.36 39.66 4.52
9 10 6.902341 TCTAGAATTTGACATGTCACTTTGC 58.098 36.000 27.88 13.84 39.66 3.68
10 11 8.013947 CACTCTAGAATTTGACATGTCACTTTG 58.986 37.037 27.88 16.04 39.66 2.77
11 12 7.173907 CCACTCTAGAATTTGACATGTCACTTT 59.826 37.037 27.88 22.13 39.66 2.66
12 13 6.652481 CCACTCTAGAATTTGACATGTCACTT 59.348 38.462 27.88 22.33 39.66 3.16
13 14 6.169094 CCACTCTAGAATTTGACATGTCACT 58.831 40.000 27.88 22.00 39.66 3.41
14 15 5.163814 GCCACTCTAGAATTTGACATGTCAC 60.164 44.000 27.88 16.20 39.66 3.67
16 17 4.937620 TGCCACTCTAGAATTTGACATGTC 59.062 41.667 19.27 19.27 0.00 3.06
17 18 4.910195 TGCCACTCTAGAATTTGACATGT 58.090 39.130 0.00 0.00 0.00 3.21
18 19 7.558161 TTATGCCACTCTAGAATTTGACATG 57.442 36.000 7.37 0.00 0.00 3.21
19 20 6.261826 GCTTATGCCACTCTAGAATTTGACAT 59.738 38.462 0.00 0.00 0.00 3.06
20 21 5.586243 GCTTATGCCACTCTAGAATTTGACA 59.414 40.000 0.00 0.00 0.00 3.58
21 22 5.586243 TGCTTATGCCACTCTAGAATTTGAC 59.414 40.000 0.00 0.00 38.71 3.18
22 23 5.744171 TGCTTATGCCACTCTAGAATTTGA 58.256 37.500 0.00 0.00 38.71 2.69
23 24 6.441093 TTGCTTATGCCACTCTAGAATTTG 57.559 37.500 0.00 0.00 38.71 2.32
24 25 6.660949 ACTTTGCTTATGCCACTCTAGAATTT 59.339 34.615 0.00 0.00 38.71 1.82
25 26 6.183347 ACTTTGCTTATGCCACTCTAGAATT 58.817 36.000 0.00 0.00 38.71 2.17
26 27 5.749462 ACTTTGCTTATGCCACTCTAGAAT 58.251 37.500 0.00 0.00 38.71 2.40
27 28 5.165961 ACTTTGCTTATGCCACTCTAGAA 57.834 39.130 0.00 0.00 38.71 2.10
28 29 4.826274 ACTTTGCTTATGCCACTCTAGA 57.174 40.909 0.00 0.00 38.71 2.43
29 30 5.053145 CCTACTTTGCTTATGCCACTCTAG 58.947 45.833 0.00 0.00 38.71 2.43
30 31 4.683400 GCCTACTTTGCTTATGCCACTCTA 60.683 45.833 0.00 0.00 38.71 2.43
31 32 3.878778 CCTACTTTGCTTATGCCACTCT 58.121 45.455 0.00 0.00 38.71 3.24
32 33 2.356069 GCCTACTTTGCTTATGCCACTC 59.644 50.000 0.00 0.00 38.71 3.51
33 34 2.290896 TGCCTACTTTGCTTATGCCACT 60.291 45.455 0.00 0.00 38.71 4.00
34 35 2.091541 TGCCTACTTTGCTTATGCCAC 58.908 47.619 0.00 0.00 38.71 5.01
35 36 2.505650 TGCCTACTTTGCTTATGCCA 57.494 45.000 0.00 0.00 38.71 4.92
36 37 3.866883 TTTGCCTACTTTGCTTATGCC 57.133 42.857 0.00 0.00 38.71 4.40
37 38 3.614176 GCTTTTGCCTACTTTGCTTATGC 59.386 43.478 0.00 0.00 40.15 3.14
53 54 4.681744 TGTTTTTGCCACTCTAGCTTTTG 58.318 39.130 0.00 0.00 0.00 2.44
54 55 5.337578 TTGTTTTTGCCACTCTAGCTTTT 57.662 34.783 0.00 0.00 0.00 2.27
55 56 5.337578 TTTGTTTTTGCCACTCTAGCTTT 57.662 34.783 0.00 0.00 0.00 3.51
56 57 5.535753 ATTTGTTTTTGCCACTCTAGCTT 57.464 34.783 0.00 0.00 0.00 3.74
57 58 5.535753 AATTTGTTTTTGCCACTCTAGCT 57.464 34.783 0.00 0.00 0.00 3.32
58 59 5.177511 GGAAATTTGTTTTTGCCACTCTAGC 59.822 40.000 0.00 0.00 0.00 3.42
59 60 5.696270 GGGAAATTTGTTTTTGCCACTCTAG 59.304 40.000 0.00 0.00 44.10 2.43
60 61 5.454045 GGGGAAATTTGTTTTTGCCACTCTA 60.454 40.000 9.25 0.00 45.84 2.43
61 62 4.450976 GGGAAATTTGTTTTTGCCACTCT 58.549 39.130 0.00 0.00 44.10 3.24
62 63 3.563808 GGGGAAATTTGTTTTTGCCACTC 59.436 43.478 9.25 0.00 45.84 3.51
63 64 3.201930 AGGGGAAATTTGTTTTTGCCACT 59.798 39.130 9.25 0.00 45.84 4.00
64 65 3.550820 AGGGGAAATTTGTTTTTGCCAC 58.449 40.909 9.25 0.00 45.84 5.01
65 66 3.941704 AGGGGAAATTTGTTTTTGCCA 57.058 38.095 9.25 0.00 45.84 4.92
66 67 5.590530 AAAAGGGGAAATTTGTTTTTGCC 57.409 34.783 0.00 0.00 43.98 4.52
67 68 6.625362 TCAAAAAGGGGAAATTTGTTTTTGC 58.375 32.000 20.08 0.00 43.21 3.68
68 69 9.481340 TTTTCAAAAAGGGGAAATTTGTTTTTG 57.519 25.926 19.47 19.47 44.15 2.44
69 70 9.703892 CTTTTCAAAAAGGGGAAATTTGTTTTT 57.296 25.926 0.00 0.34 41.23 1.94
70 71 7.816995 GCTTTTCAAAAAGGGGAAATTTGTTTT 59.183 29.630 15.09 0.00 44.24 2.43
71 72 7.178274 AGCTTTTCAAAAAGGGGAAATTTGTTT 59.822 29.630 15.09 0.00 44.24 2.83
72 73 6.663093 AGCTTTTCAAAAAGGGGAAATTTGTT 59.337 30.769 15.09 0.00 44.24 2.83
73 74 6.186957 AGCTTTTCAAAAAGGGGAAATTTGT 58.813 32.000 15.09 0.00 44.24 2.83
74 75 6.698008 AGCTTTTCAAAAAGGGGAAATTTG 57.302 33.333 15.09 0.00 44.24 2.32
75 76 6.889177 TCAAGCTTTTCAAAAAGGGGAAATTT 59.111 30.769 15.09 0.00 44.24 1.82
76 77 6.422333 TCAAGCTTTTCAAAAAGGGGAAATT 58.578 32.000 15.09 0.00 44.24 1.82
77 78 6.000246 TCAAGCTTTTCAAAAAGGGGAAAT 58.000 33.333 15.09 0.00 44.24 2.17
78 79 5.428184 TCAAGCTTTTCAAAAAGGGGAAA 57.572 34.783 15.09 0.00 44.24 3.13
79 80 5.628797 ATCAAGCTTTTCAAAAAGGGGAA 57.371 34.783 15.09 0.00 44.24 3.97
80 81 5.628797 AATCAAGCTTTTCAAAAAGGGGA 57.371 34.783 15.09 0.00 44.24 4.81
81 82 6.765512 TGTTAATCAAGCTTTTCAAAAAGGGG 59.234 34.615 15.09 0.00 44.24 4.79
82 83 7.784633 TGTTAATCAAGCTTTTCAAAAAGGG 57.215 32.000 15.09 0.00 44.24 3.95
644 678 0.321653 GCCAGACACTCGGGAACATT 60.322 55.000 0.00 0.00 33.29 2.71
645 679 1.296715 GCCAGACACTCGGGAACAT 59.703 57.895 0.00 0.00 33.29 2.71
646 680 2.741092 GCCAGACACTCGGGAACA 59.259 61.111 0.00 0.00 33.29 3.18
647 681 2.047179 GGCCAGACACTCGGGAAC 60.047 66.667 0.00 0.00 33.29 3.62
682 716 0.037790 AGGACAAGTCTCGCTCAAGC 60.038 55.000 0.00 0.00 37.78 4.01
686 720 0.109039 GACCAGGACAAGTCTCGCTC 60.109 60.000 0.00 0.00 0.00 5.03
688 722 0.109039 GAGACCAGGACAAGTCTCGC 60.109 60.000 4.56 0.00 46.82 5.03
691 725 0.827925 TGCGAGACCAGGACAAGTCT 60.828 55.000 0.00 0.00 45.90 3.24
693 727 0.036952 CATGCGAGACCAGGACAAGT 60.037 55.000 0.00 0.00 0.00 3.16
694 728 0.247460 TCATGCGAGACCAGGACAAG 59.753 55.000 0.00 0.00 0.00 3.16
697 731 1.086634 GCTTCATGCGAGACCAGGAC 61.087 60.000 0.00 0.00 0.00 3.85
698 732 1.219124 GCTTCATGCGAGACCAGGA 59.781 57.895 0.00 0.00 0.00 3.86
710 744 2.670479 CGCTGATATGTCTCGCTTCAT 58.330 47.619 0.00 0.00 0.00 2.57
725 759 1.257750 TTGCTTAGAGAGGGCGCTGA 61.258 55.000 8.56 0.00 0.00 4.26
726 760 0.391661 TTTGCTTAGAGAGGGCGCTG 60.392 55.000 8.56 0.00 0.00 5.18
727 761 0.391793 GTTTGCTTAGAGAGGGCGCT 60.392 55.000 7.64 1.38 0.00 5.92
734 768 3.134804 GGCCTAGATGGTTTGCTTAGAGA 59.865 47.826 0.00 0.00 38.35 3.10
735 769 3.135530 AGGCCTAGATGGTTTGCTTAGAG 59.864 47.826 1.29 0.00 38.35 2.43
736 770 3.115390 AGGCCTAGATGGTTTGCTTAGA 58.885 45.455 1.29 0.00 38.35 2.10
737 771 3.135530 AGAGGCCTAGATGGTTTGCTTAG 59.864 47.826 4.42 0.00 38.35 2.18
738 772 3.115390 AGAGGCCTAGATGGTTTGCTTA 58.885 45.455 4.42 0.00 38.35 3.09
748 782 4.836255 GGGGGTATATAGAGGCCTAGAT 57.164 50.000 4.42 4.38 32.18 1.98
1117 1158 0.681564 ACTCGAAGATCTGCGGAGGT 60.682 55.000 22.96 15.57 33.89 3.85
1118 1159 1.002251 GTACTCGAAGATCTGCGGAGG 60.002 57.143 22.96 14.97 33.89 4.30
1119 1160 1.671328 TGTACTCGAAGATCTGCGGAG 59.329 52.381 22.96 19.13 33.89 4.63
1407 1448 3.261951 ACACGTGACGCAGCACAC 61.262 61.111 25.01 9.01 38.69 3.82
1408 1449 3.261216 CACACGTGACGCAGCACA 61.261 61.111 25.01 0.00 38.69 4.57
1525 1568 4.602340 AGCTTCTCACCTTTTCTCGTAA 57.398 40.909 0.00 0.00 0.00 3.18
1592 1635 2.869801 CTGCTCTTAACACGACCACAAA 59.130 45.455 0.00 0.00 0.00 2.83
1615 1658 1.016627 TTCAGCGCTGGTTCATATGC 58.983 50.000 35.36 0.00 0.00 3.14
1698 1748 0.451783 CAATAGAAGGCACGCCAACC 59.548 55.000 11.35 0.00 38.92 3.77
1704 1754 3.118738 AGACTAACCCAATAGAAGGCACG 60.119 47.826 0.00 0.00 0.00 5.34
1750 1800 6.542735 GCACCAGCTATATCATCAATCATCAT 59.457 38.462 0.00 0.00 37.91 2.45
1853 1911 1.269257 TGACACAGACTGCGACAAGAG 60.269 52.381 1.25 0.00 0.00 2.85
1860 1918 2.000429 TGATCATGACACAGACTGCG 58.000 50.000 1.25 0.00 0.00 5.18
1941 2003 8.024145 AGGTGGTAATAAGACAGAAGGATAAG 57.976 38.462 0.00 0.00 0.00 1.73
1987 2209 6.360370 TGAAATAACTCTGTTAGCTGTCCT 57.640 37.500 0.00 0.00 0.00 3.85
2122 2345 9.099454 GTAACGGAAAAGATCACAGAAAGATAT 57.901 33.333 0.00 0.00 0.00 1.63
2189 2415 2.604046 AGCCTACAGCCGTATTCAAG 57.396 50.000 0.00 0.00 45.47 3.02
2231 2737 5.724854 GCCCATGGGAGATAGGTACTATAAA 59.275 44.000 36.00 0.00 44.92 1.40
2232 2738 5.222673 TGCCCATGGGAGATAGGTACTATAA 60.223 44.000 36.00 0.00 44.92 0.98
2331 2867 6.303839 TCCCATACCTTAGAATTGCCAATAC 58.696 40.000 0.00 0.00 0.00 1.89
2332 2868 6.523035 TCCCATACCTTAGAATTGCCAATA 57.477 37.500 0.00 0.00 0.00 1.90
2333 2869 5.402054 TCCCATACCTTAGAATTGCCAAT 57.598 39.130 0.00 0.00 0.00 3.16
2334 2870 4.871871 TCCCATACCTTAGAATTGCCAA 57.128 40.909 0.00 0.00 0.00 4.52
2335 2871 5.402054 AATCCCATACCTTAGAATTGCCA 57.598 39.130 0.00 0.00 0.00 4.92
2336 2872 9.178758 CTATAAATCCCATACCTTAGAATTGCC 57.821 37.037 0.00 0.00 0.00 4.52
2337 2873 9.178758 CCTATAAATCCCATACCTTAGAATTGC 57.821 37.037 0.00 0.00 0.00 3.56
2338 2874 9.686683 CCCTATAAATCCCATACCTTAGAATTG 57.313 37.037 0.00 0.00 0.00 2.32
2339 2875 9.643778 TCCCTATAAATCCCATACCTTAGAATT 57.356 33.333 0.00 0.00 0.00 2.17
2340 2876 9.285359 CTCCCTATAAATCCCATACCTTAGAAT 57.715 37.037 0.00 0.00 0.00 2.40
2341 2877 8.246615 ACTCCCTATAAATCCCATACCTTAGAA 58.753 37.037 0.00 0.00 0.00 2.10
2342 2878 7.678598 CACTCCCTATAAATCCCATACCTTAGA 59.321 40.741 0.00 0.00 0.00 2.10
2343 2879 7.678598 TCACTCCCTATAAATCCCATACCTTAG 59.321 40.741 0.00 0.00 0.00 2.18
2344 2880 7.550042 TCACTCCCTATAAATCCCATACCTTA 58.450 38.462 0.00 0.00 0.00 2.69
2345 2881 6.399013 TCACTCCCTATAAATCCCATACCTT 58.601 40.000 0.00 0.00 0.00 3.50
2346 2882 5.989717 TCACTCCCTATAAATCCCATACCT 58.010 41.667 0.00 0.00 0.00 3.08
2347 2883 6.697641 TTCACTCCCTATAAATCCCATACC 57.302 41.667 0.00 0.00 0.00 2.73
2542 3116 6.036083 GGAACGGTATATTAGCATAGCACATG 59.964 42.308 0.00 0.00 0.00 3.21
2544 3118 5.475719 GGAACGGTATATTAGCATAGCACA 58.524 41.667 0.00 0.00 0.00 4.57
2545 3119 4.868734 GGGAACGGTATATTAGCATAGCAC 59.131 45.833 0.00 0.00 0.00 4.40
2621 3507 3.001634 CGGTTCAAGAATCACCATCATCG 59.998 47.826 0.00 0.00 0.00 3.84
2629 3515 3.932710 TCAGCATACGGTTCAAGAATCAC 59.067 43.478 0.00 0.00 0.00 3.06
2643 3531 2.005451 CTGCACAGGAAGTCAGCATAC 58.995 52.381 0.00 0.00 34.35 2.39
2819 3707 8.998989 CATAAAAGAAATTAGCGTGTACACATG 58.001 33.333 24.98 11.29 36.01 3.21
2988 3881 1.619654 CCCAACCACTCAAGCAATCA 58.380 50.000 0.00 0.00 0.00 2.57
3094 3987 2.024319 GTGAGTCGGTCAGCACAGC 61.024 63.158 0.00 0.00 35.13 4.40
3096 3989 0.392706 ATTGTGAGTCGGTCAGCACA 59.607 50.000 0.00 0.00 39.27 4.57
3097 3990 2.363788 TATTGTGAGTCGGTCAGCAC 57.636 50.000 0.00 0.00 35.13 4.40
3148 4046 9.561069 GGATTAGCAAATTTAGAGATGACCTTA 57.439 33.333 0.00 0.00 0.00 2.69
3152 4050 7.040823 CCTGGGATTAGCAAATTTAGAGATGAC 60.041 40.741 0.00 0.00 0.00 3.06
3210 4109 8.810427 CACATGTTGGTTCAATAAATCTAATGC 58.190 33.333 0.00 0.00 0.00 3.56
3244 4143 7.101054 TCGCAAAATTACTACTCTTATGGTGT 58.899 34.615 0.00 0.00 0.00 4.16
3247 4146 8.197988 ACTTCGCAAAATTACTACTCTTATGG 57.802 34.615 0.00 0.00 0.00 2.74
3305 4353 4.019321 ACTTCAAAGGCATACTAGAAGGCA 60.019 41.667 0.00 0.00 41.81 4.75
3306 4354 4.518249 ACTTCAAAGGCATACTAGAAGGC 58.482 43.478 0.00 0.00 41.81 4.35
3310 4358 5.104900 GGAAGGACTTCAAAGGCATACTAGA 60.105 44.000 13.51 0.00 41.20 2.43
3311 4359 5.104735 AGGAAGGACTTCAAAGGCATACTAG 60.105 44.000 13.51 0.00 41.20 2.57
3312 4360 4.783227 AGGAAGGACTTCAAAGGCATACTA 59.217 41.667 13.51 0.00 41.20 1.82
3313 4361 3.589288 AGGAAGGACTTCAAAGGCATACT 59.411 43.478 13.51 0.00 41.20 2.12
3314 4362 3.691609 CAGGAAGGACTTCAAAGGCATAC 59.308 47.826 13.51 0.00 41.20 2.39
3430 4478 4.152647 TCTCATGTGTGAACTAGGACTGT 58.847 43.478 0.00 0.00 33.05 3.55
3446 4494 6.389906 GGGTTTTAGGTTGAACAATCTCATG 58.610 40.000 3.49 0.00 33.15 3.07
3517 4575 6.155827 GCATGTTAAATTCCAAGTTGTAGCA 58.844 36.000 1.45 0.00 0.00 3.49
3518 4576 5.576774 GGCATGTTAAATTCCAAGTTGTAGC 59.423 40.000 1.45 0.00 0.00 3.58
3531 4589 6.839124 TCAGATTTCAGTGGCATGTTAAAT 57.161 33.333 0.00 0.00 0.00 1.40
3595 4653 2.125188 GCTCAGACTGGAGGCTGC 60.125 66.667 4.46 0.00 35.41 5.25
3716 4774 8.648698 TCAATCAAATTTATCAAACTCCCAGA 57.351 30.769 0.00 0.00 0.00 3.86
3717 4775 9.525409 GATCAATCAAATTTATCAAACTCCCAG 57.475 33.333 0.00 0.00 0.00 4.45
3739 4802 4.691216 CGAGTATACGATCCTCACTGATCA 59.309 45.833 0.00 0.00 41.00 2.92
3740 4803 4.691685 ACGAGTATACGATCCTCACTGATC 59.308 45.833 0.00 0.00 38.21 2.92
3741 4804 4.643463 ACGAGTATACGATCCTCACTGAT 58.357 43.478 0.00 0.00 37.03 2.90
3742 4805 4.069300 ACGAGTATACGATCCTCACTGA 57.931 45.455 0.00 0.00 37.03 3.41
3746 4809 3.688185 GGCATACGAGTATACGATCCTCA 59.312 47.826 0.00 0.00 37.03 3.86
3756 4819 6.704289 TGTAAGTAACAGGCATACGAGTAT 57.296 37.500 0.00 0.00 33.01 2.12
3758 4821 5.395682 TTGTAAGTAACAGGCATACGAGT 57.604 39.130 0.00 0.00 39.87 4.18
3759 4822 6.715344 TTTTGTAAGTAACAGGCATACGAG 57.285 37.500 0.00 0.00 39.87 4.18
3760 4823 7.173562 ACAATTTTGTAAGTAACAGGCATACGA 59.826 33.333 0.00 0.00 40.16 3.43
3761 4824 7.270365 CACAATTTTGTAAGTAACAGGCATACG 59.730 37.037 0.00 0.00 39.91 3.06
3762 4825 7.540745 CCACAATTTTGTAAGTAACAGGCATAC 59.459 37.037 0.00 0.00 39.91 2.39
3763 4826 7.231722 ACCACAATTTTGTAAGTAACAGGCATA 59.768 33.333 0.00 0.00 39.91 3.14
3764 4827 6.041523 ACCACAATTTTGTAAGTAACAGGCAT 59.958 34.615 0.00 0.00 39.91 4.40
3765 4828 5.361285 ACCACAATTTTGTAAGTAACAGGCA 59.639 36.000 0.00 0.00 39.91 4.75
3766 4829 5.838529 ACCACAATTTTGTAAGTAACAGGC 58.161 37.500 0.00 0.00 39.91 4.85
3767 4830 8.842280 TCTTACCACAATTTTGTAAGTAACAGG 58.158 33.333 13.88 3.63 41.27 4.00
3771 4834 9.685828 GCAATCTTACCACAATTTTGTAAGTAA 57.314 29.630 13.88 13.35 41.27 2.24
3772 4835 9.073475 AGCAATCTTACCACAATTTTGTAAGTA 57.927 29.630 13.88 0.00 41.27 2.24
3773 4836 7.951591 AGCAATCTTACCACAATTTTGTAAGT 58.048 30.769 13.88 0.34 41.27 2.24
3774 4837 8.816640 AAGCAATCTTACCACAATTTTGTAAG 57.183 30.769 10.30 10.30 39.91 2.34
3775 4838 9.606631 AAAAGCAATCTTACCACAATTTTGTAA 57.393 25.926 0.00 0.00 33.94 2.41
3777 4840 9.777297 ATAAAAGCAATCTTACCACAATTTTGT 57.223 25.926 0.00 0.00 35.20 2.83
3810 4873 0.178992 TAGGCACAGTGCTTTGGCTT 60.179 50.000 24.75 5.32 45.81 4.35
3859 4922 1.091771 CAAGGGTCGCGAGAATGCAT 61.092 55.000 10.24 0.00 45.01 3.96
3862 4925 2.225068 ATACAAGGGTCGCGAGAATG 57.775 50.000 10.24 9.38 45.01 2.67
3868 4931 2.035449 TCATTCCTATACAAGGGTCGCG 59.965 50.000 0.00 0.00 46.55 5.87
3871 4934 6.238759 GCATGTTTCATTCCTATACAAGGGTC 60.239 42.308 0.00 0.00 46.55 4.46
3974 5040 4.744795 TCTTGAGGAGATAAGGCAAGTC 57.255 45.455 0.00 0.00 37.71 3.01
4001 5067 5.814705 GTGTGGGAGATCTCATTTTCTACTG 59.185 44.000 23.85 0.00 0.00 2.74
4039 5106 4.980805 TGGTCGGCTGACGCAACC 62.981 66.667 19.26 6.82 46.49 3.77
4074 5141 1.289109 TTTACGTGCTCTGCTTCCGC 61.289 55.000 0.00 0.00 0.00 5.54
4083 5150 2.349532 GCAGTGGTTTCTTTACGTGCTC 60.350 50.000 0.00 0.00 0.00 4.26
4179 5246 2.618241 TGTATGATTTGAGCGAATGGCC 59.382 45.455 0.00 0.00 45.17 5.36
4259 5326 0.988832 AAGCAAGATACCAACCGGGA 59.011 50.000 6.32 0.00 41.15 5.14
4300 5367 1.834896 GGAACTTCTCCTCCTCCCTTC 59.165 57.143 0.00 0.00 41.61 3.46
4301 5368 1.556002 GGGAACTTCTCCTCCTCCCTT 60.556 57.143 0.00 0.00 44.68 3.95
4302 5369 0.043485 GGGAACTTCTCCTCCTCCCT 59.957 60.000 0.00 0.00 44.68 4.20


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

AutoCloner maintained by Alex Coulton.