Multiple sequence alignment - TraesCS5B01G236600

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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 TraesCS5B01G236600 chr5B 100.000 3838 0 0 1 3838 417803718 417807555 0.000000e+00 7088.0
1 TraesCS5B01G236600 chr5B 93.517 725 18 4 48 757 339094228 339093518 0.000000e+00 1051.0
2 TraesCS5B01G236600 chr5B 88.378 370 18 13 399 754 394757196 394756838 4.580000e-114 422.0
3 TraesCS5B01G236600 chr5B 86.943 314 35 5 3065 3373 645890077 645890389 7.890000e-92 348.0
4 TraesCS5B01G236600 chr5B 86.624 314 34 7 3065 3372 372722028 372722339 1.320000e-89 340.0
5 TraesCS5B01G236600 chr5B 85.893 319 39 5 3059 3372 182509855 182510172 6.140000e-88 335.0
6 TraesCS5B01G236600 chr5D 91.597 2142 71 45 814 2880 353654705 353656812 0.000000e+00 2857.0
7 TraesCS5B01G236600 chr5D 93.850 439 22 2 2567 3005 353664173 353664606 0.000000e+00 656.0
8 TraesCS5B01G236600 chr5D 86.486 481 41 5 3380 3838 353664639 353665117 1.230000e-139 507.0
9 TraesCS5B01G236600 chr5D 86.105 439 32 13 2877 3307 353657357 353657774 2.720000e-121 446.0
10 TraesCS5B01G236600 chr5D 86.667 315 32 7 3063 3370 269163258 269163569 1.320000e-89 340.0
11 TraesCS5B01G236600 chr5D 96.923 65 2 0 753 817 353654476 353654540 4.050000e-20 110.0
12 TraesCS5B01G236600 chr5A 89.385 2148 105 49 770 2852 454704138 454706227 0.000000e+00 2590.0
13 TraesCS5B01G236600 chr5A 86.702 188 10 4 2877 3064 454710461 454710633 1.090000e-45 195.0
14 TraesCS5B01G236600 chr1B 93.385 771 33 10 1 754 674469863 674470632 0.000000e+00 1125.0
15 TraesCS5B01G236600 chr1B 89.216 714 52 12 54 756 396579980 396580679 0.000000e+00 869.0
16 TraesCS5B01G236600 chr3B 93.377 755 32 9 15 754 56451454 56452205 0.000000e+00 1101.0
17 TraesCS5B01G236600 chr3B 91.720 785 25 8 5 753 617427398 617428178 0.000000e+00 1053.0
18 TraesCS5B01G236600 chr3B 91.451 772 41 15 5 756 816526772 816527538 0.000000e+00 1037.0
19 TraesCS5B01G236600 chr3B 91.747 727 40 13 41 761 771352013 771351301 0.000000e+00 992.0
20 TraesCS5B01G236600 chr3B 86.222 675 44 21 108 756 812568235 812568886 0.000000e+00 686.0
21 TraesCS5B01G236600 chr3B 90.244 41 3 1 3383 3423 481912996 481912957 7.000000e-03 52.8
22 TraesCS5B01G236600 chr6B 92.593 756 34 14 18 754 619730518 619729766 0.000000e+00 1066.0
23 TraesCS5B01G236600 chr6B 91.035 792 26 11 5 756 31584676 31585462 0.000000e+00 1027.0
24 TraesCS5B01G236600 chr6B 80.268 821 146 13 1489 2298 614312050 614312865 4.240000e-169 604.0
25 TraesCS5B01G236600 chr6B 80.024 821 148 13 1489 2298 614437360 614438175 9.180000e-166 593.0
26 TraesCS5B01G236600 chr6B 80.024 821 148 13 1489 2298 614582418 614583233 9.180000e-166 593.0
27 TraesCS5B01G236600 chr6B 79.976 824 143 17 1489 2298 636585585 636584770 4.270000e-164 588.0
28 TraesCS5B01G236600 chr4B 91.355 775 43 13 1 757 86057472 86058240 0.000000e+00 1038.0
29 TraesCS5B01G236600 chr4B 89.201 713 50 14 54 754 66110316 66111013 0.000000e+00 865.0
30 TraesCS5B01G236600 chr4B 80.906 817 142 12 1490 2299 568736079 568736888 1.950000e-177 632.0
31 TraesCS5B01G236600 chr4B 77.064 109 19 6 3382 3487 580942477 580942582 1.490000e-04 58.4
32 TraesCS5B01G236600 chr7B 91.429 770 25 12 5 738 400640614 400639850 0.000000e+00 1018.0
33 TraesCS5B01G236600 chr7B 92.806 695 20 3 72 754 508655693 508656369 0.000000e+00 979.0
34 TraesCS5B01G236600 chr7B 91.016 256 11 1 511 754 110697058 110697313 6.140000e-88 335.0
35 TraesCS5B01G236600 chr2B 92.152 739 28 5 45 753 755005153 755005891 0.000000e+00 1016.0
36 TraesCS5B01G236600 chr2B 85.938 320 38 6 3056 3370 20564085 20563768 6.140000e-88 335.0
37 TraesCS5B01G236600 chr4D 81.151 817 140 13 1490 2299 455693683 455694492 0.000000e+00 643.0
38 TraesCS5B01G236600 chr4D 85.531 311 39 5 3065 3370 335746044 335746353 1.720000e-83 320.0
39 TraesCS5B01G236600 chr4D 85.577 312 38 6 3065 3370 471779890 471779580 1.720000e-83 320.0
40 TraesCS5B01G236600 chr4D 86.149 296 34 6 3065 3354 280900479 280900185 2.880000e-81 313.0
41 TraesCS5B01G236600 chr4D 83.492 315 45 6 3065 3373 282141050 282140737 1.740000e-73 287.0
42 TraesCS5B01G236600 chr6A 79.928 832 149 15 1489 2308 554824924 554825749 2.550000e-166 595.0
43 TraesCS5B01G236600 chr6A 79.808 832 150 13 1489 2308 564975151 564975976 1.190000e-164 590.0
44 TraesCS5B01G236600 chr7A 79.469 828 151 17 1486 2299 559361803 559362625 1.550000e-158 569.0
45 TraesCS5B01G236600 chr6D 79.157 830 159 10 1489 2308 422191042 422191867 2.590000e-156 562.0
46 TraesCS5B01G236600 chr6D 88.055 293 31 4 3083 3372 129177791 129177500 1.020000e-90 344.0
47 TraesCS5B01G236600 chr6D 85.897 312 37 6 3065 3370 299594939 299594629 3.700000e-85 326.0
48 TraesCS5B01G236600 chr6D 84.444 315 42 6 3065 3373 4112716 4112403 1.730000e-78 303.0
49 TraesCS5B01G236600 chr6D 85.085 295 38 5 3065 3354 202054192 202054485 2.900000e-76 296.0
50 TraesCS5B01G236600 chr6D 84.397 282 32 5 3103 3373 336963692 336963412 2.270000e-67 267.0
51 TraesCS5B01G236600 chr6D 82.736 307 42 8 3076 3374 25716013 25716316 2.940000e-66 263.0
52 TraesCS5B01G236600 chr6D 80.870 345 30 14 3063 3374 462621086 462620745 4.960000e-59 239.0
53 TraesCS5B01G236600 chr7D 78.986 828 155 17 1486 2299 493203703 493204525 7.250000e-152 547.0
54 TraesCS5B01G236600 chr7D 78.649 829 156 19 1486 2299 491873351 491872529 7.300000e-147 531.0
55 TraesCS5B01G236600 chr7D 86.859 312 34 6 3065 3370 156696033 156696343 3.670000e-90 342.0
56 TraesCS5B01G236600 chr7D 86.581 313 36 5 3063 3370 248468197 248468508 1.320000e-89 340.0
57 TraesCS5B01G236600 chr7D 86.032 315 38 5 3063 3372 638071224 638071537 2.210000e-87 333.0
58 TraesCS5B01G236600 chr7D 85.669 314 37 7 3067 3373 421451834 421452146 1.330000e-84 324.0
59 TraesCS5B01G236600 chr3D 86.408 309 36 5 3067 3370 536372178 536372485 2.210000e-87 333.0
60 TraesCS5B01G236600 chr3D 84.444 315 41 7 3065 3373 488227951 488228263 1.730000e-78 303.0
61 TraesCS5B01G236600 chr2D 86.262 313 35 6 3065 3370 107516451 107516762 2.210000e-87 333.0
62 TraesCS5B01G236600 chr2D 86.262 313 35 7 3065 3371 282539690 282539380 2.210000e-87 333.0
63 TraesCS5B01G236600 chr2D 85.759 316 38 6 3064 3373 553550022 553549708 1.030000e-85 327.0
64 TraesCS5B01G236600 chr2D 90.909 44 3 1 3380 3423 574823584 574823626 1.490000e-04 58.4
65 TraesCS5B01G236600 chr1D 84.228 298 38 8 3078 3368 319273859 319274154 8.120000e-72 281.0


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 TraesCS5B01G236600 chr5B 417803718 417807555 3837 False 7088.000000 7088 100.000000 1 3838 1 chr5B.!!$F3 3837
1 TraesCS5B01G236600 chr5B 339093518 339094228 710 True 1051.000000 1051 93.517000 48 757 1 chr5B.!!$R1 709
2 TraesCS5B01G236600 chr5D 353654476 353657774 3298 False 1137.666667 2857 91.541667 753 3307 3 chr5D.!!$F2 2554
3 TraesCS5B01G236600 chr5D 353664173 353665117 944 False 581.500000 656 90.168000 2567 3838 2 chr5D.!!$F3 1271
4 TraesCS5B01G236600 chr5A 454704138 454706227 2089 False 2590.000000 2590 89.385000 770 2852 1 chr5A.!!$F1 2082
5 TraesCS5B01G236600 chr1B 674469863 674470632 769 False 1125.000000 1125 93.385000 1 754 1 chr1B.!!$F2 753
6 TraesCS5B01G236600 chr1B 396579980 396580679 699 False 869.000000 869 89.216000 54 756 1 chr1B.!!$F1 702
7 TraesCS5B01G236600 chr3B 56451454 56452205 751 False 1101.000000 1101 93.377000 15 754 1 chr3B.!!$F1 739
8 TraesCS5B01G236600 chr3B 617427398 617428178 780 False 1053.000000 1053 91.720000 5 753 1 chr3B.!!$F2 748
9 TraesCS5B01G236600 chr3B 816526772 816527538 766 False 1037.000000 1037 91.451000 5 756 1 chr3B.!!$F4 751
10 TraesCS5B01G236600 chr3B 771351301 771352013 712 True 992.000000 992 91.747000 41 761 1 chr3B.!!$R2 720
11 TraesCS5B01G236600 chr3B 812568235 812568886 651 False 686.000000 686 86.222000 108 756 1 chr3B.!!$F3 648
12 TraesCS5B01G236600 chr6B 619729766 619730518 752 True 1066.000000 1066 92.593000 18 754 1 chr6B.!!$R1 736
13 TraesCS5B01G236600 chr6B 31584676 31585462 786 False 1027.000000 1027 91.035000 5 756 1 chr6B.!!$F1 751
14 TraesCS5B01G236600 chr6B 614312050 614312865 815 False 604.000000 604 80.268000 1489 2298 1 chr6B.!!$F2 809
15 TraesCS5B01G236600 chr6B 614437360 614438175 815 False 593.000000 593 80.024000 1489 2298 1 chr6B.!!$F3 809
16 TraesCS5B01G236600 chr6B 614582418 614583233 815 False 593.000000 593 80.024000 1489 2298 1 chr6B.!!$F4 809
17 TraesCS5B01G236600 chr6B 636584770 636585585 815 True 588.000000 588 79.976000 1489 2298 1 chr6B.!!$R2 809
18 TraesCS5B01G236600 chr4B 86057472 86058240 768 False 1038.000000 1038 91.355000 1 757 1 chr4B.!!$F2 756
19 TraesCS5B01G236600 chr4B 66110316 66111013 697 False 865.000000 865 89.201000 54 754 1 chr4B.!!$F1 700
20 TraesCS5B01G236600 chr4B 568736079 568736888 809 False 632.000000 632 80.906000 1490 2299 1 chr4B.!!$F3 809
21 TraesCS5B01G236600 chr7B 400639850 400640614 764 True 1018.000000 1018 91.429000 5 738 1 chr7B.!!$R1 733
22 TraesCS5B01G236600 chr7B 508655693 508656369 676 False 979.000000 979 92.806000 72 754 1 chr7B.!!$F2 682
23 TraesCS5B01G236600 chr2B 755005153 755005891 738 False 1016.000000 1016 92.152000 45 753 1 chr2B.!!$F1 708
24 TraesCS5B01G236600 chr4D 455693683 455694492 809 False 643.000000 643 81.151000 1490 2299 1 chr4D.!!$F2 809
25 TraesCS5B01G236600 chr6A 554824924 554825749 825 False 595.000000 595 79.928000 1489 2308 1 chr6A.!!$F1 819
26 TraesCS5B01G236600 chr6A 564975151 564975976 825 False 590.000000 590 79.808000 1489 2308 1 chr6A.!!$F2 819
27 TraesCS5B01G236600 chr7A 559361803 559362625 822 False 569.000000 569 79.469000 1486 2299 1 chr7A.!!$F1 813
28 TraesCS5B01G236600 chr6D 422191042 422191867 825 False 562.000000 562 79.157000 1489 2308 1 chr6D.!!$F3 819
29 TraesCS5B01G236600 chr7D 493203703 493204525 822 False 547.000000 547 78.986000 1486 2299 1 chr7D.!!$F4 813
30 TraesCS5B01G236600 chr7D 491872529 491873351 822 True 531.000000 531 78.649000 1486 2299 1 chr7D.!!$R1 813

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
202 263 1.226686 CTGACGCTATGGCTGCCATC 61.227 60.0 35.64 22.83 40.74 3.51 F
392 456 1.403814 AGATTCATCTTCGGAGGCGA 58.596 50.0 0.00 0.00 31.97 5.54 F
1465 1908 0.318784 ACTCTGCGACGACTGTTTCC 60.319 55.0 0.00 0.00 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1410 0.032815 TGTGTAGCGCTAACACTGCA 59.967 50.0 31.39 19.65 45.95 4.41 R
2338 2793 0.248743 CATGCATGCGTGACCATTCC 60.249 55.0 31.95 0.00 35.09 3.01 R
3092 4114 0.032515 TAATCCCCAGCTGACCGAGA 60.033 55.0 17.39 4.42 0.00 4.04 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
196 257 1.381872 ACCCTCTGACGCTATGGCT 60.382 57.895 0.00 0.00 36.09 4.75
202 263 1.226686 CTGACGCTATGGCTGCCATC 61.227 60.000 35.64 22.83 40.74 3.51
392 456 1.403814 AGATTCATCTTCGGAGGCGA 58.596 50.000 0.00 0.00 31.97 5.54
708 875 2.782615 GAAGCACGCGCGGTAAAT 59.217 55.556 35.22 15.95 45.49 1.40
744 916 3.195002 GCATAGCGCGGCTGTTGA 61.195 61.111 8.83 0.00 40.10 3.18
768 940 5.918608 AGATGCTCTAACAATGGATAACGT 58.081 37.500 0.00 0.00 0.00 3.99
801 973 4.194720 CGCTTCGTCCCTCCTCGG 62.195 72.222 0.00 0.00 0.00 4.63
848 1206 5.363373 AGTGTTAGCCAGCACAACGTAGT 62.363 47.826 1.63 0.00 38.28 2.73
853 1211 1.468565 GCCAGCACAACGTAGTCGATA 60.469 52.381 0.00 0.00 45.00 2.92
857 1215 3.857665 CAGCACAACGTAGTCGATATTGT 59.142 43.478 0.00 0.00 45.00 2.71
1042 1410 3.304928 GCCACAAGTACTACACACGTACT 60.305 47.826 0.00 0.00 46.93 2.73
1043 1411 4.224433 CCACAAGTACTACACACGTACTG 58.776 47.826 0.00 0.00 44.89 2.74
1044 1412 3.667261 CACAAGTACTACACACGTACTGC 59.333 47.826 0.00 0.00 44.89 4.40
1066 1434 0.665068 TGTTAGCGCTACACACACGG 60.665 55.000 18.63 0.00 0.00 4.94
1090 1480 0.471617 CAGAGTTATGGGGAGGCAGG 59.528 60.000 0.00 0.00 0.00 4.85
1162 1552 1.827344 TCAATGCACAGACGGAGATCT 59.173 47.619 0.00 0.00 0.00 2.75
1167 1557 1.996191 GCACAGACGGAGATCTTGTTC 59.004 52.381 0.00 0.00 0.00 3.18
1176 1574 3.384789 CGGAGATCTTGTTCCAGGTGATA 59.615 47.826 0.00 0.00 32.87 2.15
1178 1576 4.407296 GGAGATCTTGTTCCAGGTGATACT 59.593 45.833 0.00 0.00 33.55 2.12
1179 1577 5.598830 GGAGATCTTGTTCCAGGTGATACTA 59.401 44.000 0.00 0.00 33.55 1.82
1181 1579 4.737855 TCTTGTTCCAGGTGATACTAGC 57.262 45.455 0.00 0.00 0.00 3.42
1183 1581 4.716784 TCTTGTTCCAGGTGATACTAGCAT 59.283 41.667 0.00 0.00 0.00 3.79
1186 1584 2.397597 TCCAGGTGATACTAGCATGCA 58.602 47.619 21.98 5.01 0.00 3.96
1187 1585 2.103094 TCCAGGTGATACTAGCATGCAC 59.897 50.000 21.98 7.01 0.00 4.57
1188 1586 2.130395 CAGGTGATACTAGCATGCACG 58.870 52.381 21.98 12.56 0.00 5.34
1189 1587 1.757118 AGGTGATACTAGCATGCACGT 59.243 47.619 21.98 17.84 0.00 4.49
1207 1623 1.014352 GTACGGACCATTGATGTGCC 58.986 55.000 0.00 0.00 0.00 5.01
1230 1646 2.668625 ACTCCTAGTAGGCTAACTGGC 58.331 52.381 11.75 0.00 42.15 4.85
1273 1707 0.679505 TTCAACTGGGACTCGTGGAG 59.320 55.000 0.00 0.00 35.52 3.86
1280 1714 1.739562 GGACTCGTGGAGCAAGCAG 60.740 63.158 0.00 0.00 32.04 4.24
1283 1717 3.965539 CTCGTGGAGCAAGCAGGGG 62.966 68.421 0.00 0.00 0.00 4.79
1313 1747 1.304713 CATGCTCAAGGCCCAGGTT 60.305 57.895 0.00 0.00 40.92 3.50
1355 1789 4.008933 ACTCACGTCTGGCTGCCC 62.009 66.667 17.53 0.00 0.00 5.36
1364 1798 4.992982 TGGCTGCCCCCACCTACA 62.993 66.667 17.53 0.00 0.00 2.74
1391 1825 3.441572 CCGTTTCATCTCAAGGCAAATCT 59.558 43.478 0.00 0.00 0.00 2.40
1394 1828 5.352569 CGTTTCATCTCAAGGCAAATCTACT 59.647 40.000 0.00 0.00 0.00 2.57
1401 1843 7.898014 TCTCAAGGCAAATCTACTATCTACA 57.102 36.000 0.00 0.00 0.00 2.74
1464 1907 1.488527 AACTCTGCGACGACTGTTTC 58.511 50.000 0.00 0.00 0.00 2.78
1465 1908 0.318784 ACTCTGCGACGACTGTTTCC 60.319 55.000 0.00 0.00 0.00 3.13
1468 1911 1.202486 TCTGCGACGACTGTTTCCTTT 60.202 47.619 0.00 0.00 0.00 3.11
1474 1917 0.934496 CGACTGTTTCCTTTCGTGCA 59.066 50.000 0.00 0.00 0.00 4.57
1479 1922 1.612950 TGTTTCCTTTCGTGCATGCAT 59.387 42.857 25.64 0.00 0.00 3.96
1480 1923 1.987770 GTTTCCTTTCGTGCATGCATG 59.012 47.619 30.20 30.20 0.00 4.06
1575 2018 4.514577 CTCATCGCGGCCTTCGGT 62.515 66.667 6.13 4.45 39.69 4.69
1920 2363 2.503375 GTCGCCAGGACGTACGTG 60.503 66.667 28.16 12.57 35.61 4.49
2328 2783 7.869016 TCGTCGAGCCATATTTTCTTATTAG 57.131 36.000 0.00 0.00 0.00 1.73
2329 2784 7.431249 TCGTCGAGCCATATTTTCTTATTAGT 58.569 34.615 0.00 0.00 0.00 2.24
2330 2785 8.570488 TCGTCGAGCCATATTTTCTTATTAGTA 58.430 33.333 0.00 0.00 0.00 1.82
2679 3134 2.553727 GCGGCGCTAGCTACCTAGT 61.554 63.158 26.86 0.00 42.51 2.57
2680 3135 1.233285 GCGGCGCTAGCTACCTAGTA 61.233 60.000 26.86 0.00 42.51 1.82
2681 3136 0.797542 CGGCGCTAGCTACCTAGTAG 59.202 60.000 13.93 0.00 42.51 2.57
2682 3137 1.607509 CGGCGCTAGCTACCTAGTAGA 60.608 57.143 13.93 0.00 42.51 2.59
2683 3138 1.805943 GGCGCTAGCTACCTAGTAGAC 59.194 57.143 13.93 0.00 42.51 2.59
2684 3139 1.460359 GCGCTAGCTACCTAGTAGACG 59.540 57.143 13.93 4.74 42.51 4.18
2685 3140 2.753296 CGCTAGCTACCTAGTAGACGT 58.247 52.381 13.93 0.00 42.51 4.34
2686 3141 3.129871 CGCTAGCTACCTAGTAGACGTT 58.870 50.000 13.93 0.00 42.51 3.99
2687 3142 4.302455 CGCTAGCTACCTAGTAGACGTTA 58.698 47.826 13.93 0.00 42.51 3.18
2688 3143 4.385447 CGCTAGCTACCTAGTAGACGTTAG 59.615 50.000 13.93 0.30 42.51 2.34
2689 3144 4.152223 GCTAGCTACCTAGTAGACGTTAGC 59.848 50.000 7.70 6.17 42.51 3.09
2690 3145 4.148128 AGCTACCTAGTAGACGTTAGCA 57.852 45.455 12.64 0.00 38.29 3.49
2691 3146 4.521146 AGCTACCTAGTAGACGTTAGCAA 58.479 43.478 12.64 0.00 38.29 3.91
2692 3147 4.335037 AGCTACCTAGTAGACGTTAGCAAC 59.665 45.833 12.64 0.00 38.29 4.17
2693 3148 4.335037 GCTACCTAGTAGACGTTAGCAACT 59.665 45.833 5.96 1.76 38.29 3.16
2694 3149 5.163673 GCTACCTAGTAGACGTTAGCAACTT 60.164 44.000 5.96 0.00 38.29 2.66
2778 3245 5.708697 ACTAGGCAATAAAGTTTGTACCACC 59.291 40.000 0.00 0.00 0.00 4.61
2796 3263 1.376037 CACCGCTCTCCTTCCAACC 60.376 63.158 0.00 0.00 0.00 3.77
2880 3895 6.539464 ACGTTGTTAATCCTGTGTTCACTTAA 59.461 34.615 4.59 0.00 0.00 1.85
2915 3936 5.642063 ACTACAGGAAAATTACATGTCACCG 59.358 40.000 0.00 0.00 34.28 4.94
2931 3952 0.319083 ACCGTGTGGCTCGATGTAAA 59.681 50.000 0.00 0.00 39.70 2.01
2933 3954 0.719465 CGTGTGGCTCGATGTAAACC 59.281 55.000 0.00 0.00 0.00 3.27
2948 3969 5.141355 TGTAAACCGAGTGTAAAAACACG 57.859 39.130 3.22 0.00 44.71 4.49
3074 4096 7.986320 TGGGCATTATTTTTATCAATGTTGAGG 59.014 33.333 1.65 0.00 41.08 3.86
3082 4104 7.800155 TTTTATCAATGTTGAGGATATCGCA 57.200 32.000 1.65 0.00 41.08 5.10
3084 4106 7.601073 TTATCAATGTTGAGGATATCGCATC 57.399 36.000 1.65 0.00 41.08 3.91
3085 4107 3.989817 TCAATGTTGAGGATATCGCATCG 59.010 43.478 0.00 0.00 32.50 3.84
3086 4108 3.667497 ATGTTGAGGATATCGCATCGT 57.333 42.857 0.00 0.00 0.00 3.73
3087 4109 3.452755 TGTTGAGGATATCGCATCGTT 57.547 42.857 0.00 0.00 0.00 3.85
3088 4110 4.577834 TGTTGAGGATATCGCATCGTTA 57.422 40.909 0.00 0.00 0.00 3.18
3089 4111 4.546570 TGTTGAGGATATCGCATCGTTAG 58.453 43.478 0.00 0.00 0.00 2.34
3090 4112 3.217599 TGAGGATATCGCATCGTTAGC 57.782 47.619 0.00 0.00 0.00 3.09
3091 4113 2.556622 TGAGGATATCGCATCGTTAGCA 59.443 45.455 0.00 0.00 0.00 3.49
3092 4114 3.193479 TGAGGATATCGCATCGTTAGCAT 59.807 43.478 0.00 0.00 0.00 3.79
3093 4115 3.775202 AGGATATCGCATCGTTAGCATC 58.225 45.455 0.00 0.00 0.00 3.91
3094 4116 3.445450 AGGATATCGCATCGTTAGCATCT 59.555 43.478 0.00 0.00 0.00 2.90
3095 4117 3.794028 GGATATCGCATCGTTAGCATCTC 59.206 47.826 0.00 0.00 0.00 2.75
3096 4118 1.691127 ATCGCATCGTTAGCATCTCG 58.309 50.000 0.00 0.00 0.00 4.04
3097 4119 0.317854 TCGCATCGTTAGCATCTCGG 60.318 55.000 0.00 0.00 0.00 4.63
3098 4120 0.595053 CGCATCGTTAGCATCTCGGT 60.595 55.000 0.00 0.00 0.00 4.69
3099 4121 1.132588 GCATCGTTAGCATCTCGGTC 58.867 55.000 0.00 0.00 0.00 4.79
3100 4122 1.536072 GCATCGTTAGCATCTCGGTCA 60.536 52.381 0.00 0.00 0.00 4.02
3101 4123 2.389059 CATCGTTAGCATCTCGGTCAG 58.611 52.381 0.00 0.00 0.00 3.51
3102 4124 0.100682 TCGTTAGCATCTCGGTCAGC 59.899 55.000 0.00 0.00 0.00 4.26
3103 4125 0.101399 CGTTAGCATCTCGGTCAGCT 59.899 55.000 0.00 0.00 40.92 4.24
3104 4126 1.565305 GTTAGCATCTCGGTCAGCTG 58.435 55.000 7.63 7.63 37.94 4.24
3105 4127 0.461548 TTAGCATCTCGGTCAGCTGG 59.538 55.000 15.13 0.00 37.94 4.85
3106 4128 1.395045 TAGCATCTCGGTCAGCTGGG 61.395 60.000 15.13 3.86 37.94 4.45
3107 4129 2.503061 CATCTCGGTCAGCTGGGG 59.497 66.667 15.13 3.48 0.00 4.96
3108 4130 2.060383 CATCTCGGTCAGCTGGGGA 61.060 63.158 15.13 3.34 0.00 4.81
3113 4135 0.325296 TCGGTCAGCTGGGGATTAGT 60.325 55.000 15.13 0.00 0.00 2.24
3164 4186 7.813148 ATCGATTTTATCGGTCGACTATCAATT 59.187 33.333 16.46 4.44 43.84 2.32
3205 4227 7.883391 TCACAGGTTTCCAACACTAAAATAA 57.117 32.000 0.00 0.00 0.00 1.40
3212 4234 9.999009 GGTTTCCAACACTAAAATAAGCTATAC 57.001 33.333 0.00 0.00 0.00 1.47
3271 4293 5.601662 TGATTACTAGCCTTTGAATCCTCG 58.398 41.667 0.00 0.00 0.00 4.63
3321 4344 7.568128 AGTACATATTGCATAATAGGGTCCA 57.432 36.000 0.00 0.00 35.45 4.02
3322 4345 7.394816 AGTACATATTGCATAATAGGGTCCAC 58.605 38.462 0.00 0.00 35.45 4.02
3323 4346 6.199557 ACATATTGCATAATAGGGTCCACA 57.800 37.500 0.00 0.00 35.45 4.17
3324 4347 6.609876 ACATATTGCATAATAGGGTCCACAA 58.390 36.000 0.00 0.00 35.45 3.33
3325 4348 7.066142 ACATATTGCATAATAGGGTCCACAAA 58.934 34.615 0.00 0.00 35.45 2.83
3326 4349 7.563188 ACATATTGCATAATAGGGTCCACAAAA 59.437 33.333 0.00 0.00 35.45 2.44
3327 4350 6.865834 ATTGCATAATAGGGTCCACAAAAA 57.134 33.333 0.00 0.00 0.00 1.94
3328 4351 5.652994 TGCATAATAGGGTCCACAAAAAC 57.347 39.130 0.00 0.00 0.00 2.43
3329 4352 5.080337 TGCATAATAGGGTCCACAAAAACA 58.920 37.500 0.00 0.00 0.00 2.83
3330 4353 5.719085 TGCATAATAGGGTCCACAAAAACAT 59.281 36.000 0.00 0.00 0.00 2.71
3331 4354 6.892456 TGCATAATAGGGTCCACAAAAACATA 59.108 34.615 0.00 0.00 0.00 2.29
3332 4355 7.397476 TGCATAATAGGGTCCACAAAAACATAA 59.603 33.333 0.00 0.00 0.00 1.90
3333 4356 8.254508 GCATAATAGGGTCCACAAAAACATAAA 58.745 33.333 0.00 0.00 0.00 1.40
3339 4362 8.024145 AGGGTCCACAAAAACATAAATAAACA 57.976 30.769 0.00 0.00 0.00 2.83
3340 4363 8.655901 AGGGTCCACAAAAACATAAATAAACAT 58.344 29.630 0.00 0.00 0.00 2.71
3341 4364 9.930693 GGGTCCACAAAAACATAAATAAACATA 57.069 29.630 0.00 0.00 0.00 2.29
3363 4386 8.772705 ACATAATTTTGCAAACACAATGTTAGG 58.227 29.630 12.39 7.04 40.14 2.69
3364 4387 8.986847 CATAATTTTGCAAACACAATGTTAGGA 58.013 29.630 12.39 0.00 40.14 2.94
3365 4388 7.856145 AATTTTGCAAACACAATGTTAGGAA 57.144 28.000 12.39 0.00 40.14 3.36
3366 4389 8.449251 AATTTTGCAAACACAATGTTAGGAAT 57.551 26.923 12.39 0.00 40.14 3.01
3367 4390 9.553064 AATTTTGCAAACACAATGTTAGGAATA 57.447 25.926 12.39 0.00 40.14 1.75
3368 4391 8.586570 TTTTGCAAACACAATGTTAGGAATAG 57.413 30.769 12.39 0.00 40.14 1.73
3369 4392 6.266168 TGCAAACACAATGTTAGGAATAGG 57.734 37.500 0.00 0.00 40.14 2.57
3370 4393 5.102313 GCAAACACAATGTTAGGAATAGGC 58.898 41.667 0.00 0.00 40.14 3.93
3371 4394 5.650543 CAAACACAATGTTAGGAATAGGCC 58.349 41.667 0.00 0.00 40.14 5.19
3372 4395 3.898482 ACACAATGTTAGGAATAGGCCC 58.102 45.455 0.00 0.00 0.00 5.80
3373 4396 3.268334 ACACAATGTTAGGAATAGGCCCA 59.732 43.478 0.00 0.00 0.00 5.36
3374 4397 3.632145 CACAATGTTAGGAATAGGCCCAC 59.368 47.826 0.00 0.00 0.00 4.61
3375 4398 3.222603 CAATGTTAGGAATAGGCCCACC 58.777 50.000 0.00 0.00 0.00 4.61
3376 4399 1.218844 TGTTAGGAATAGGCCCACCC 58.781 55.000 0.00 0.00 36.11 4.61
3377 4400 0.108019 GTTAGGAATAGGCCCACCCG 59.892 60.000 0.00 0.00 39.21 5.28
3378 4401 1.057851 TTAGGAATAGGCCCACCCGG 61.058 60.000 0.00 0.00 39.21 5.73
3379 4402 1.963761 TAGGAATAGGCCCACCCGGA 61.964 60.000 0.73 0.00 39.21 5.14
3380 4403 2.154074 GGAATAGGCCCACCCGGAT 61.154 63.158 0.73 0.00 39.21 4.18
3381 4404 1.716028 GGAATAGGCCCACCCGGATT 61.716 60.000 0.73 0.00 39.21 3.01
3382 4405 0.185175 GAATAGGCCCACCCGGATTT 59.815 55.000 0.73 0.00 39.21 2.17
3383 4406 0.634465 AATAGGCCCACCCGGATTTT 59.366 50.000 0.73 0.00 39.21 1.82
3384 4407 0.634465 ATAGGCCCACCCGGATTTTT 59.366 50.000 0.73 0.00 39.21 1.94
3385 4408 1.296984 TAGGCCCACCCGGATTTTTA 58.703 50.000 0.73 0.00 39.21 1.52
3386 4409 0.634465 AGGCCCACCCGGATTTTTAT 59.366 50.000 0.73 0.00 39.21 1.40
3387 4410 1.854280 AGGCCCACCCGGATTTTTATA 59.146 47.619 0.73 0.00 39.21 0.98
3394 4417 5.531287 CCCACCCGGATTTTTATAGAAGAAG 59.469 44.000 0.73 0.00 0.00 2.85
3412 4435 3.151906 CCCACCCGGATGAGATCC 58.848 66.667 0.73 0.00 46.22 3.36
3429 4452 2.961531 TCCCGAAAAATTCACCCTCA 57.038 45.000 0.00 0.00 0.00 3.86
3434 4457 2.292292 CGAAAAATTCACCCTCAACGGT 59.708 45.455 0.00 0.00 36.18 4.83
3439 4462 0.599558 TTCACCCTCAACGGTAGTCG 59.400 55.000 0.00 0.00 45.88 4.18
3443 4466 0.108945 CCCTCAACGGTAGTCGAACC 60.109 60.000 0.00 0.00 42.43 3.62
3452 4475 2.345760 TAGTCGAACCCCGGTCTGC 61.346 63.158 0.00 0.00 39.14 4.26
3456 4479 2.747686 GAACCCCGGTCTGCAAGA 59.252 61.111 0.00 0.00 43.69 3.02
3480 4503 0.099968 CCACTGCGATCTTGCCATTG 59.900 55.000 0.00 0.00 0.00 2.82
3519 4555 1.079612 GCAACTGGAAAGGCATGGC 60.080 57.895 12.14 12.14 0.00 4.40
3538 4574 2.673368 GGCAGTTTCACGGTAAGATCAG 59.327 50.000 0.00 0.00 0.00 2.90
3562 4598 0.103755 CTGAGCCATCTTAGCTGCGA 59.896 55.000 0.00 0.00 41.75 5.10
3563 4599 0.103755 TGAGCCATCTTAGCTGCGAG 59.896 55.000 0.00 0.00 41.75 5.03
3564 4600 0.387202 GAGCCATCTTAGCTGCGAGA 59.613 55.000 10.38 10.38 41.75 4.04
3590 4626 5.416271 AATTCAATTGCTTCCAGCTCATT 57.584 34.783 0.00 0.00 42.97 2.57
3596 4632 1.687660 TGCTTCCAGCTCATTTGCAAA 59.312 42.857 15.44 15.44 42.97 3.68
3599 4635 3.863400 GCTTCCAGCTCATTTGCAAACAT 60.863 43.478 15.41 0.00 38.45 2.71
3606 4642 8.093307 TCCAGCTCATTTGCAAACATTAAATTA 58.907 29.630 15.41 0.00 34.99 1.40
3615 4651 9.985318 TTTGCAAACATTAAATTAATAGCATGC 57.015 25.926 10.51 10.51 0.00 4.06
3650 4688 5.479306 TCACAATAAGCACTGAACCTACTC 58.521 41.667 0.00 0.00 0.00 2.59
3692 4730 1.848388 AGATGAGACCATTGCCCATGA 59.152 47.619 0.00 0.00 34.31 3.07
3696 4734 3.443052 TGAGACCATTGCCCATGAATTT 58.557 40.909 0.00 0.00 34.31 1.82
3703 4742 5.416326 ACCATTGCCCATGAATTTTTGAATG 59.584 36.000 0.00 0.00 34.31 2.67
3751 4790 1.839424 ATTAAGGAGTTGGCTGGTGC 58.161 50.000 0.00 0.00 38.76 5.01
3762 4801 0.676782 GGCTGGTGCGAAACTACCAT 60.677 55.000 0.00 0.00 45.28 3.55
3766 4805 3.377172 GCTGGTGCGAAACTACCATAATT 59.623 43.478 0.00 0.00 45.28 1.40
3789 4834 0.974010 ACCTGCTTGGGCCATTCATG 60.974 55.000 7.26 8.10 41.11 3.07
3825 4870 6.072783 CGATATAGTGTCATCAGAGAGAGCAA 60.073 42.308 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 263 0.179111 TAGCGAAACTCATGCCTCCG 60.179 55.000 0.00 0.00 0.00 4.63
392 456 5.073311 TCATCTTCCGAAGACGATTCTTT 57.927 39.130 13.12 0.00 42.53 2.52
801 973 1.063469 CCAATCCGTTATCGTGCAACC 59.937 52.381 0.00 0.00 35.01 3.77
848 1206 1.136110 TCTTCCGCAGCACAATATCGA 59.864 47.619 0.00 0.00 0.00 3.59
853 1211 2.034879 CCGTCTTCCGCAGCACAAT 61.035 57.895 0.00 0.00 34.38 2.71
952 1315 2.374170 CGGGGCAAGGTATTTATAGGGT 59.626 50.000 0.00 0.00 0.00 4.34
986 1350 6.830324 TGGATATAGAGCTTGCTTTTTGTGAT 59.170 34.615 0.00 0.00 0.00 3.06
1042 1410 0.032815 TGTGTAGCGCTAACACTGCA 59.967 50.000 31.39 19.65 45.95 4.41
1043 1411 0.438830 GTGTGTAGCGCTAACACTGC 59.561 55.000 32.46 25.29 45.95 4.40
1044 1412 1.455786 GTGTGTGTAGCGCTAACACTG 59.544 52.381 35.33 0.00 45.95 3.66
1066 1434 0.181350 CTCCCCATAACTCTGGTGCC 59.819 60.000 0.00 0.00 34.23 5.01
1140 1530 0.678950 TCTCCGTCTGTGCATTGACA 59.321 50.000 17.91 0.00 33.18 3.58
1162 1552 4.769688 CATGCTAGTATCACCTGGAACAA 58.230 43.478 0.00 0.00 38.70 2.83
1167 1557 2.487934 GTGCATGCTAGTATCACCTGG 58.512 52.381 20.33 0.00 0.00 4.45
1176 1574 0.179145 GTCCGTACGTGCATGCTAGT 60.179 55.000 20.33 19.70 0.00 2.57
1178 1576 1.140161 GGTCCGTACGTGCATGCTA 59.860 57.895 20.33 2.15 0.00 3.49
1179 1577 2.125673 GGTCCGTACGTGCATGCT 60.126 61.111 20.33 0.40 0.00 3.79
1181 1579 0.373370 CAATGGTCCGTACGTGCATG 59.627 55.000 15.21 3.82 0.00 4.06
1183 1581 0.248012 ATCAATGGTCCGTACGTGCA 59.752 50.000 15.21 1.06 0.00 4.57
1186 1584 2.004583 CACATCAATGGTCCGTACGT 57.995 50.000 15.21 0.00 0.00 3.57
1187 1585 0.650512 GCACATCAATGGTCCGTACG 59.349 55.000 8.69 8.69 0.00 3.67
1188 1586 1.014352 GGCACATCAATGGTCCGTAC 58.986 55.000 0.00 0.00 0.00 3.67
1189 1587 0.461163 CGGCACATCAATGGTCCGTA 60.461 55.000 13.54 0.00 39.90 4.02
1207 1623 3.814283 CCAGTTAGCCTACTAGGAGTACG 59.186 52.174 6.26 0.00 37.67 3.67
1283 1717 0.322456 TGAGCATGTTGTACCAGCCC 60.322 55.000 0.00 0.00 0.00 5.19
1355 1789 0.395312 AAACGGAGTGTGTAGGTGGG 59.605 55.000 0.00 0.00 45.00 4.61
1364 1798 2.872038 GCCTTGAGATGAAACGGAGTGT 60.872 50.000 0.00 0.00 45.00 3.55
1391 1825 4.582869 ACACACGTGACCTGTAGATAGTA 58.417 43.478 25.01 0.00 0.00 1.82
1394 1828 3.570975 ACAACACACGTGACCTGTAGATA 59.429 43.478 25.01 0.00 0.00 1.98
1401 1843 0.392461 AGCAACAACACACGTGACCT 60.392 50.000 25.01 2.03 0.00 3.85
1440 1883 2.488545 ACAGTCGTCGCAGAGTTAGAAT 59.511 45.455 0.00 0.00 36.95 2.40
1442 1885 1.520494 ACAGTCGTCGCAGAGTTAGA 58.480 50.000 0.00 0.00 36.95 2.10
1453 1896 1.070776 GCACGAAAGGAAACAGTCGTC 60.071 52.381 0.00 0.00 46.27 4.20
1480 1923 1.601162 CGGCATGTATCCTGCAATTGC 60.601 52.381 23.69 23.69 41.47 3.56
1481 1924 1.001048 CCGGCATGTATCCTGCAATTG 60.001 52.381 0.00 0.00 41.47 2.32
1482 1925 1.321474 CCGGCATGTATCCTGCAATT 58.679 50.000 0.00 0.00 41.47 2.32
1483 1926 0.538057 CCCGGCATGTATCCTGCAAT 60.538 55.000 0.00 0.00 41.47 3.56
1484 1927 1.152984 CCCGGCATGTATCCTGCAA 60.153 57.895 0.00 0.00 41.47 4.08
2328 2783 3.181510 GCGTGACCATTCCAGAAATGTAC 60.182 47.826 0.00 0.00 42.80 2.90
2329 2784 3.006940 GCGTGACCATTCCAGAAATGTA 58.993 45.455 0.00 0.00 42.80 2.29
2330 2785 1.812571 GCGTGACCATTCCAGAAATGT 59.187 47.619 0.00 0.00 42.80 2.71
2338 2793 0.248743 CATGCATGCGTGACCATTCC 60.249 55.000 31.95 0.00 35.09 3.01
2674 3129 4.341099 CGAAGTTGCTAACGTCTACTAGG 58.659 47.826 11.02 0.00 37.68 3.02
2679 3134 2.322161 GTGCGAAGTTGCTAACGTCTA 58.678 47.619 11.02 0.00 37.68 2.59
2680 3135 1.137513 GTGCGAAGTTGCTAACGTCT 58.862 50.000 11.02 0.00 37.68 4.18
2681 3136 0.163146 GGTGCGAAGTTGCTAACGTC 59.837 55.000 0.00 0.00 36.68 4.34
2682 3137 1.554042 CGGTGCGAAGTTGCTAACGT 61.554 55.000 0.00 0.00 36.23 3.99
2683 3138 1.129809 CGGTGCGAAGTTGCTAACG 59.870 57.895 0.00 0.00 36.23 3.18
2684 3139 1.495951 CCGGTGCGAAGTTGCTAAC 59.504 57.895 0.00 0.00 35.36 2.34
2685 3140 2.322081 GCCGGTGCGAAGTTGCTAA 61.322 57.895 1.90 0.00 35.36 3.09
2686 3141 2.740826 GCCGGTGCGAAGTTGCTA 60.741 61.111 1.90 0.00 35.36 3.49
2758 3225 4.552355 GTGGTGGTACAAACTTTATTGCC 58.448 43.478 0.00 0.00 44.16 4.52
2778 3245 1.376037 GGTTGGAAGGAGAGCGGTG 60.376 63.158 0.00 0.00 0.00 4.94
2796 3263 2.048222 TCACGCTCCTTCCGCAAG 60.048 61.111 0.00 0.00 0.00 4.01
2880 3895 9.908152 GTAATTTTCCTGTAGTGTTAGCAATTT 57.092 29.630 0.00 0.00 0.00 1.82
2915 3936 0.719465 CGGTTTACATCGAGCCACAC 59.281 55.000 0.00 0.00 0.00 3.82
2933 3954 0.938713 TGCCCGTGTTTTTACACTCG 59.061 50.000 6.83 0.00 38.40 4.18
2948 3969 0.038310 AGGAAGTAAGCCAAGTGCCC 59.962 55.000 0.00 0.00 42.71 5.36
3006 4027 2.915079 CCATGCCCACGTATCCCA 59.085 61.111 0.00 0.00 0.00 4.37
3074 4096 3.480308 CGAGATGCTAACGATGCGATATC 59.520 47.826 0.00 0.00 0.00 1.63
3077 4099 1.667177 CCGAGATGCTAACGATGCGAT 60.667 52.381 0.00 0.00 0.00 4.58
3082 4104 1.269309 GCTGACCGAGATGCTAACGAT 60.269 52.381 0.00 0.00 0.00 3.73
3084 4106 0.101399 AGCTGACCGAGATGCTAACG 59.899 55.000 0.00 0.00 33.64 3.18
3085 4107 1.565305 CAGCTGACCGAGATGCTAAC 58.435 55.000 8.42 0.00 29.56 2.34
3086 4108 0.461548 CCAGCTGACCGAGATGCTAA 59.538 55.000 17.39 0.00 36.71 3.09
3087 4109 1.395045 CCCAGCTGACCGAGATGCTA 61.395 60.000 17.39 0.00 36.71 3.49
3088 4110 2.729479 CCCAGCTGACCGAGATGCT 61.729 63.158 17.39 0.00 36.71 3.79
3089 4111 2.202987 CCCAGCTGACCGAGATGC 60.203 66.667 17.39 0.00 36.71 3.91
3090 4112 1.406065 ATCCCCAGCTGACCGAGATG 61.406 60.000 17.39 0.00 37.87 2.90
3091 4113 0.692419 AATCCCCAGCTGACCGAGAT 60.692 55.000 17.39 6.68 0.00 2.75
3092 4114 0.032515 TAATCCCCAGCTGACCGAGA 60.033 55.000 17.39 4.42 0.00 4.04
3093 4115 0.390860 CTAATCCCCAGCTGACCGAG 59.609 60.000 17.39 0.00 0.00 4.63
3094 4116 0.325296 ACTAATCCCCAGCTGACCGA 60.325 55.000 17.39 7.57 0.00 4.69
3095 4117 0.179073 CACTAATCCCCAGCTGACCG 60.179 60.000 17.39 1.40 0.00 4.79
3096 4118 1.204146 TCACTAATCCCCAGCTGACC 58.796 55.000 17.39 0.00 0.00 4.02
3097 4119 3.567478 AATCACTAATCCCCAGCTGAC 57.433 47.619 17.39 0.00 0.00 3.51
3098 4120 5.912149 ATTAATCACTAATCCCCAGCTGA 57.088 39.130 17.39 0.00 0.00 4.26
3099 4121 8.463930 TTTTATTAATCACTAATCCCCAGCTG 57.536 34.615 6.78 6.78 32.28 4.24
3148 4170 2.953648 TGGCTAATTGATAGTCGACCGA 59.046 45.455 13.01 0.16 39.19 4.69
3212 4234 8.322906 TCTGTCAATATTGTTTTGGTGTAGAG 57.677 34.615 14.97 1.31 0.00 2.43
3215 4237 8.349245 CACTTCTGTCAATATTGTTTTGGTGTA 58.651 33.333 14.97 0.00 0.00 2.90
3221 4243 8.908903 TGGTAACACTTCTGTCAATATTGTTTT 58.091 29.630 14.97 0.00 46.17 2.43
3297 4320 7.017155 TGTGGACCCTATTATGCAATATGTACT 59.983 37.037 0.00 0.00 0.00 2.73
3307 4330 5.652994 TGTTTTTGTGGACCCTATTATGC 57.347 39.130 0.00 0.00 0.00 3.14
3313 4336 9.144298 TGTTTATTTATGTTTTTGTGGACCCTA 57.856 29.630 0.00 0.00 0.00 3.53
3314 4337 8.024145 TGTTTATTTATGTTTTTGTGGACCCT 57.976 30.769 0.00 0.00 0.00 4.34
3315 4338 8.840833 ATGTTTATTTATGTTTTTGTGGACCC 57.159 30.769 0.00 0.00 0.00 4.46
3337 4360 8.772705 CCTAACATTGTGTTTGCAAAATTATGT 58.227 29.630 14.67 16.63 41.45 2.29
3338 4361 8.986847 TCCTAACATTGTGTTTGCAAAATTATG 58.013 29.630 14.67 16.05 41.45 1.90
3339 4362 9.553064 TTCCTAACATTGTGTTTGCAAAATTAT 57.447 25.926 14.67 2.66 41.45 1.28
3340 4363 8.948631 TTCCTAACATTGTGTTTGCAAAATTA 57.051 26.923 14.67 0.40 41.45 1.40
3341 4364 7.856145 TTCCTAACATTGTGTTTGCAAAATT 57.144 28.000 14.67 2.97 41.45 1.82
3342 4365 9.206870 CTATTCCTAACATTGTGTTTGCAAAAT 57.793 29.630 14.67 0.26 41.45 1.82
3343 4366 7.655328 CCTATTCCTAACATTGTGTTTGCAAAA 59.345 33.333 14.67 0.00 41.45 2.44
3344 4367 7.151308 CCTATTCCTAACATTGTGTTTGCAAA 58.849 34.615 8.05 8.05 41.45 3.68
3345 4368 6.686630 CCTATTCCTAACATTGTGTTTGCAA 58.313 36.000 0.00 0.00 41.45 4.08
3346 4369 5.336372 GCCTATTCCTAACATTGTGTTTGCA 60.336 40.000 0.20 0.00 41.45 4.08
3347 4370 5.102313 GCCTATTCCTAACATTGTGTTTGC 58.898 41.667 0.20 0.00 41.45 3.68
3348 4371 5.394115 GGGCCTATTCCTAACATTGTGTTTG 60.394 44.000 0.84 0.00 41.45 2.93
3349 4372 4.709886 GGGCCTATTCCTAACATTGTGTTT 59.290 41.667 0.84 0.00 41.45 2.83
3350 4373 4.264172 TGGGCCTATTCCTAACATTGTGTT 60.264 41.667 4.53 0.67 43.88 3.32
3351 4374 3.268334 TGGGCCTATTCCTAACATTGTGT 59.732 43.478 4.53 0.00 0.00 3.72
3352 4375 3.632145 GTGGGCCTATTCCTAACATTGTG 59.368 47.826 4.53 0.00 0.00 3.33
3353 4376 3.372675 GGTGGGCCTATTCCTAACATTGT 60.373 47.826 4.53 0.00 0.00 2.71
3354 4377 3.222603 GGTGGGCCTATTCCTAACATTG 58.777 50.000 4.53 0.00 0.00 2.82
3355 4378 2.177016 GGGTGGGCCTATTCCTAACATT 59.823 50.000 4.53 0.00 34.45 2.71
3356 4379 1.780919 GGGTGGGCCTATTCCTAACAT 59.219 52.381 4.53 0.00 34.45 2.71
3357 4380 1.218844 GGGTGGGCCTATTCCTAACA 58.781 55.000 4.53 0.00 34.45 2.41
3358 4381 0.108019 CGGGTGGGCCTATTCCTAAC 59.892 60.000 4.53 0.00 34.45 2.34
3359 4382 1.057851 CCGGGTGGGCCTATTCCTAA 61.058 60.000 4.53 0.00 34.45 2.69
3360 4383 1.460689 CCGGGTGGGCCTATTCCTA 60.461 63.158 4.53 0.00 34.45 2.94
3361 4384 2.638025 ATCCGGGTGGGCCTATTCCT 62.638 60.000 4.53 0.00 35.24 3.36
3362 4385 1.716028 AATCCGGGTGGGCCTATTCC 61.716 60.000 4.53 1.57 35.24 3.01
3363 4386 0.185175 AAATCCGGGTGGGCCTATTC 59.815 55.000 4.53 0.00 35.24 1.75
3364 4387 0.634465 AAAATCCGGGTGGGCCTATT 59.366 50.000 4.53 0.00 35.24 1.73
3365 4388 0.634465 AAAAATCCGGGTGGGCCTAT 59.366 50.000 4.53 0.00 35.24 2.57
3366 4389 1.296984 TAAAAATCCGGGTGGGCCTA 58.703 50.000 4.53 0.00 35.24 3.93
3367 4390 0.634465 ATAAAAATCCGGGTGGGCCT 59.366 50.000 4.53 0.00 35.24 5.19
3368 4391 2.158579 TCTATAAAAATCCGGGTGGGCC 60.159 50.000 0.00 0.00 35.24 5.80
3369 4392 3.217681 TCTATAAAAATCCGGGTGGGC 57.782 47.619 0.00 0.00 35.24 5.36
3370 4393 5.043737 TCTTCTATAAAAATCCGGGTGGG 57.956 43.478 0.00 0.00 35.24 4.61
3371 4394 5.008712 GCTTCTTCTATAAAAATCCGGGTGG 59.991 44.000 0.00 0.00 0.00 4.61
3372 4395 5.008712 GGCTTCTTCTATAAAAATCCGGGTG 59.991 44.000 0.00 0.00 0.00 4.61
3373 4396 5.131067 GGCTTCTTCTATAAAAATCCGGGT 58.869 41.667 0.00 0.00 0.00 5.28
3374 4397 4.519350 GGGCTTCTTCTATAAAAATCCGGG 59.481 45.833 0.00 0.00 0.00 5.73
3375 4398 5.008712 GTGGGCTTCTTCTATAAAAATCCGG 59.991 44.000 0.00 0.00 0.00 5.14
3376 4399 5.008712 GGTGGGCTTCTTCTATAAAAATCCG 59.991 44.000 0.00 0.00 0.00 4.18
3377 4400 5.302059 GGGTGGGCTTCTTCTATAAAAATCC 59.698 44.000 0.00 0.00 0.00 3.01
3378 4401 5.008712 CGGGTGGGCTTCTTCTATAAAAATC 59.991 44.000 0.00 0.00 0.00 2.17
3379 4402 4.887655 CGGGTGGGCTTCTTCTATAAAAAT 59.112 41.667 0.00 0.00 0.00 1.82
3380 4403 4.266714 CGGGTGGGCTTCTTCTATAAAAA 58.733 43.478 0.00 0.00 0.00 1.94
3381 4404 3.371166 CCGGGTGGGCTTCTTCTATAAAA 60.371 47.826 0.00 0.00 0.00 1.52
3382 4405 2.171870 CCGGGTGGGCTTCTTCTATAAA 59.828 50.000 0.00 0.00 0.00 1.40
3383 4406 1.766496 CCGGGTGGGCTTCTTCTATAA 59.234 52.381 0.00 0.00 0.00 0.98
3384 4407 1.062734 TCCGGGTGGGCTTCTTCTATA 60.063 52.381 0.00 0.00 35.24 1.31
3385 4408 0.326238 TCCGGGTGGGCTTCTTCTAT 60.326 55.000 0.00 0.00 35.24 1.98
3386 4409 0.326238 ATCCGGGTGGGCTTCTTCTA 60.326 55.000 0.00 0.00 35.24 2.10
3387 4410 1.616628 ATCCGGGTGGGCTTCTTCT 60.617 57.895 0.00 0.00 35.24 2.85
3394 4417 2.427753 GATCTCATCCGGGTGGGC 59.572 66.667 16.41 0.00 35.24 5.36
3412 4435 2.351350 CCGTTGAGGGTGAATTTTTCGG 60.351 50.000 0.00 0.00 35.97 4.30
3414 4437 4.517832 ACTACCGTTGAGGGTGAATTTTTC 59.482 41.667 5.67 0.00 46.96 2.29
3421 4444 0.250858 TCGACTACCGTTGAGGGTGA 60.251 55.000 5.67 0.00 46.96 4.02
3423 4446 0.600057 GTTCGACTACCGTTGAGGGT 59.400 55.000 0.66 0.66 46.96 4.34
3429 4452 2.639327 CCGGGGTTCGACTACCGTT 61.639 63.158 16.58 0.00 44.57 4.44
3434 4457 2.345760 GCAGACCGGGGTTCGACTA 61.346 63.158 6.32 0.00 42.43 2.59
3439 4462 1.026718 CATCTTGCAGACCGGGGTTC 61.027 60.000 6.32 0.00 0.00 3.62
3465 4488 3.923013 CCCAATGGCAAGATCGCA 58.077 55.556 0.00 0.00 0.00 5.10
3488 4511 0.038744 CAGTTGCCAGAGGATTGGGT 59.961 55.000 0.00 0.00 38.72 4.51
3493 4516 1.005215 CCTTTCCAGTTGCCAGAGGAT 59.995 52.381 0.00 0.00 0.00 3.24
3519 4555 3.589988 AGCTGATCTTACCGTGAAACTG 58.410 45.455 0.00 0.00 31.75 3.16
3544 4580 0.103755 CTCGCAGCTAAGATGGCTCA 59.896 55.000 0.00 0.00 38.03 4.26
3555 4591 0.037326 TTGAATTCGGTCTCGCAGCT 60.037 50.000 0.04 0.00 36.13 4.24
3562 4598 3.420893 TGGAAGCAATTGAATTCGGTCT 58.579 40.909 10.34 0.00 0.00 3.85
3563 4599 3.762779 CTGGAAGCAATTGAATTCGGTC 58.237 45.455 10.34 1.43 0.00 4.79
3564 4600 3.855689 CTGGAAGCAATTGAATTCGGT 57.144 42.857 10.34 0.00 0.00 4.69
3590 4626 8.610896 GGCATGCTATTAATTTAATGTTTGCAA 58.389 29.630 18.92 0.00 31.25 4.08
3596 4632 8.236585 TGAGTGGCATGCTATTAATTTAATGT 57.763 30.769 18.92 0.00 0.00 2.71
3599 4635 7.013274 GGACTGAGTGGCATGCTATTAATTTAA 59.987 37.037 18.92 0.00 0.00 1.52
3606 4642 1.842562 AGGACTGAGTGGCATGCTATT 59.157 47.619 18.92 8.51 0.00 1.73
3610 4646 0.321919 TGAAGGACTGAGTGGCATGC 60.322 55.000 9.90 9.90 0.00 4.06
3615 4651 3.686726 GCTTATTGTGAAGGACTGAGTGG 59.313 47.826 0.00 0.00 0.00 4.00
3671 4709 2.158711 TCATGGGCAATGGTCTCATCTC 60.159 50.000 1.15 0.00 36.86 2.75
3673 4711 2.353357 TCATGGGCAATGGTCTCATC 57.647 50.000 1.15 0.00 36.86 2.92
3692 4730 3.818180 TGCCCAAGTGCATTCAAAAATT 58.182 36.364 0.00 0.00 36.04 1.82
3696 4734 2.550423 CCATTGCCCAAGTGCATTCAAA 60.550 45.455 0.00 0.00 41.70 2.69
3703 4742 1.070601 AGAAAACCATTGCCCAAGTGC 59.929 47.619 0.00 0.00 0.00 4.40
3751 4790 4.574828 CAGGTCCCAATTATGGTAGTTTCG 59.425 45.833 0.00 0.00 46.01 3.46
3762 4801 0.324275 GCCCAAGCAGGTCCCAATTA 60.324 55.000 0.00 0.00 39.53 1.40
3810 4855 5.188555 ACATAAAGGTTGCTCTCTCTGATGA 59.811 40.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.