Multiple sequence alignment - TraesCS3B01G480100

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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 TraesCS3B01G480100 chr3B 100.000 2122 0 0 1 2122 728296259 728294138 0.000000e+00 3919
1 TraesCS3B01G480100 chr3B 98.428 509 6 1 1 507 19920593 19920085 0.000000e+00 894
2 TraesCS3B01G480100 chr3B 98.235 510 6 1 1 507 805353277 805352768 0.000000e+00 889
3 TraesCS3B01G480100 chr3B 100.000 125 0 0 2411 2535 728293849 728293725 5.450000e-57 231
4 TraesCS3B01G480100 chr3D 93.430 1035 47 10 812 1833 548999595 548998569 0.000000e+00 1515
5 TraesCS3B01G480100 chr3D 87.814 796 80 11 513 1297 553405696 553406485 0.000000e+00 917
6 TraesCS3B01G480100 chr3D 89.286 588 56 5 710 1291 553357478 553358064 0.000000e+00 730
7 TraesCS3B01G480100 chr3D 89.826 403 35 4 508 909 553357231 553357628 1.740000e-141 512
8 TraesCS3B01G480100 chr3D 86.777 363 32 6 1298 1653 553358107 553358460 8.500000e-105 390
9 TraesCS3B01G480100 chr3D 87.456 287 35 1 1833 2118 75798397 75798683 1.880000e-86 329
10 TraesCS3B01G480100 chr3D 92.857 126 8 1 2411 2535 548998557 548998432 5.570000e-42 182
11 TraesCS3B01G480100 chr1B 98.239 511 8 1 1 510 669264224 669263714 0.000000e+00 893
12 TraesCS3B01G480100 chr6B 98.054 514 6 1 1 510 4100593 4100080 0.000000e+00 891
13 TraesCS3B01G480100 chr4A 98.054 514 7 2 1 511 692066408 692066921 0.000000e+00 891
14 TraesCS3B01G480100 chr4A 98.232 509 8 1 1 508 690068911 690069419 0.000000e+00 889
15 TraesCS3B01G480100 chr4A 98.228 508 8 1 1 508 659405527 659405021 0.000000e+00 887
16 TraesCS3B01G480100 chr5B 98.232 509 7 1 1 507 634669116 634669624 0.000000e+00 889
17 TraesCS3B01G480100 chr5B 87.108 287 36 1 1833 2118 253631276 253630990 8.750000e-85 324
18 TraesCS3B01G480100 chr4B 98.232 509 8 1 1 508 243973106 243973614 0.000000e+00 889
19 TraesCS3B01G480100 chr3A 93.047 489 29 3 812 1295 686281142 686280654 0.000000e+00 710
20 TraesCS3B01G480100 chr3A 88.403 595 60 7 710 1297 689660002 689660594 0.000000e+00 708
21 TraesCS3B01G480100 chr3A 88.403 595 60 7 710 1297 689662839 689663431 0.000000e+00 708
22 TraesCS3B01G480100 chr3A 87.585 588 56 9 710 1291 689523734 689524310 0.000000e+00 665
23 TraesCS3B01G480100 chr3A 86.745 596 69 8 710 1297 689867232 689867825 0.000000e+00 654
24 TraesCS3B01G480100 chr3A 86.242 596 72 8 710 1297 689846918 689847511 2.750000e-179 638
25 TraesCS3B01G480100 chr3A 90.888 428 14 7 1298 1706 686280615 686280194 3.690000e-153 551
26 TraesCS3B01G480100 chr3A 88.889 405 38 5 508 909 689866932 689867332 2.270000e-135 492
27 TraesCS3B01G480100 chr3A 88.916 406 33 8 508 909 689578609 689579006 8.150000e-135 490
28 TraesCS3B01G480100 chr3A 88.916 406 33 7 508 909 689608387 689608784 8.150000e-135 490
29 TraesCS3B01G480100 chr3A 88.366 404 41 4 508 909 689846619 689847018 4.900000e-132 481
30 TraesCS3B01G480100 chr3A 88.395 405 38 6 508 909 689659754 689660152 1.760000e-131 479
31 TraesCS3B01G480100 chr3A 88.395 405 38 6 508 909 689662591 689662989 1.760000e-131 479
32 TraesCS3B01G480100 chr3A 88.395 405 38 6 508 909 689666406 689666804 1.760000e-131 479
33 TraesCS3B01G480100 chr3A 87.542 297 32 4 1828 2121 737596925 737596631 3.120000e-89 339
34 TraesCS3B01G480100 chr3A 85.666 293 32 5 1298 1583 689524353 689524642 1.470000e-77 300
35 TraesCS3B01G480100 chr3A 85.324 293 33 5 1298 1583 689579481 689579770 6.860000e-76 294
36 TraesCS3B01G480100 chr3A 85.324 293 33 5 1298 1583 689609259 689609548 6.860000e-76 294
37 TraesCS3B01G480100 chr3A 93.798 129 6 2 1706 1833 686279892 686279765 2.570000e-45 193
38 TraesCS3B01G480100 chr2A 89.347 291 29 2 1833 2122 87263755 87264044 5.150000e-97 364
39 TraesCS3B01G480100 chr7A 89.547 287 29 1 1833 2118 48584713 48584999 1.850000e-96 363
40 TraesCS3B01G480100 chr6D 88.153 287 33 1 1833 2118 362907908 362907622 8.690000e-90 340
41 TraesCS3B01G480100 chr2D 87.713 293 34 2 1829 2120 525903658 525903949 8.690000e-90 340
42 TraesCS3B01G480100 chr2D 86.735 294 32 5 1832 2120 273361396 273361687 1.130000e-83 320
43 TraesCS3B01G480100 chr1D 87.762 286 27 6 1832 2116 462262260 462262538 6.760000e-86 327


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 TraesCS3B01G480100 chr3B 728293725 728296259 2534 True 2075.000000 3919 100.000000 1 2535 2 chr3B.!!$R3 2534
1 TraesCS3B01G480100 chr3B 19920085 19920593 508 True 894.000000 894 98.428000 1 507 1 chr3B.!!$R1 506
2 TraesCS3B01G480100 chr3B 805352768 805353277 509 True 889.000000 889 98.235000 1 507 1 chr3B.!!$R2 506
3 TraesCS3B01G480100 chr3D 553405696 553406485 789 False 917.000000 917 87.814000 513 1297 1 chr3D.!!$F2 784
4 TraesCS3B01G480100 chr3D 548998432 548999595 1163 True 848.500000 1515 93.143500 812 2535 2 chr3D.!!$R1 1723
5 TraesCS3B01G480100 chr3D 553357231 553358460 1229 False 544.000000 730 88.629667 508 1653 3 chr3D.!!$F3 1145
6 TraesCS3B01G480100 chr1B 669263714 669264224 510 True 893.000000 893 98.239000 1 510 1 chr1B.!!$R1 509
7 TraesCS3B01G480100 chr6B 4100080 4100593 513 True 891.000000 891 98.054000 1 510 1 chr6B.!!$R1 509
8 TraesCS3B01G480100 chr4A 692066408 692066921 513 False 891.000000 891 98.054000 1 511 1 chr4A.!!$F2 510
9 TraesCS3B01G480100 chr4A 690068911 690069419 508 False 889.000000 889 98.232000 1 508 1 chr4A.!!$F1 507
10 TraesCS3B01G480100 chr4A 659405021 659405527 506 True 887.000000 887 98.228000 1 508 1 chr4A.!!$R1 507
11 TraesCS3B01G480100 chr5B 634669116 634669624 508 False 889.000000 889 98.232000 1 507 1 chr5B.!!$F1 506
12 TraesCS3B01G480100 chr4B 243973106 243973614 508 False 889.000000 889 98.232000 1 508 1 chr4B.!!$F1 507
13 TraesCS3B01G480100 chr3A 689866932 689867825 893 False 573.000000 654 87.817000 508 1297 2 chr3A.!!$F6 789
14 TraesCS3B01G480100 chr3A 689659754 689666804 7050 False 570.600000 708 88.398200 508 1297 5 chr3A.!!$F4 789
15 TraesCS3B01G480100 chr3A 689846619 689847511 892 False 559.500000 638 87.304000 508 1297 2 chr3A.!!$F5 789
16 TraesCS3B01G480100 chr3A 686279765 686281142 1377 True 484.666667 710 92.577667 812 1833 3 chr3A.!!$R2 1021
17 TraesCS3B01G480100 chr3A 689523734 689524642 908 False 482.500000 665 86.625500 710 1583 2 chr3A.!!$F1 873
18 TraesCS3B01G480100 chr3A 689578609 689579770 1161 False 392.000000 490 87.120000 508 1583 2 chr3A.!!$F2 1075
19 TraesCS3B01G480100 chr3A 689608387 689609548 1161 False 392.000000 490 87.120000 508 1583 2 chr3A.!!$F3 1075

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
637 645 0.25064 CACCAAGAGCCAGCAGAAGT 60.251 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 6145 0.041833 TGAGTTGGAGGAGGGAGAGG 59.958 60.0 0.0 0.0 0.0 3.69 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
211 212 9.784531 AGCTAGCTAACACAATATATGAAACAT 57.215 29.630 17.69 0.00 0.00 2.71
297 303 1.024046 AATGCTAACGCGTGGATGCA 61.024 50.000 23.37 23.37 39.65 3.96
532 538 2.296831 TGTTTTCCACGACGAGTTCA 57.703 45.000 0.00 0.00 0.00 3.18
537 543 1.244816 TCCACGACGAGTTCACTCAT 58.755 50.000 0.00 0.00 43.00 2.90
540 546 2.161808 CCACGACGAGTTCACTCATAGT 59.838 50.000 0.00 0.00 43.00 2.12
541 547 3.418094 CACGACGAGTTCACTCATAGTC 58.582 50.000 0.00 5.77 43.00 2.59
570 578 7.987750 TTTGCATGTAACCAACTATGAGTAA 57.012 32.000 0.00 0.00 0.00 2.24
600 608 9.216117 AGTATAATTTCTGTTTTGCTCTTACGT 57.784 29.630 0.00 0.00 0.00 3.57
637 645 0.250640 CACCAAGAGCCAGCAGAAGT 60.251 55.000 0.00 0.00 0.00 3.01
641 652 2.030451 CCAAGAGCCAGCAGAAGTTTTC 60.030 50.000 0.00 0.00 0.00 2.29
646 660 4.403752 AGAGCCAGCAGAAGTTTTCTTTTT 59.596 37.500 0.00 0.00 40.61 1.94
756 770 7.823745 TTTGGATTTCCATATCTTCTAAGCC 57.176 36.000 0.00 0.00 46.97 4.35
757 771 6.514012 TGGATTTCCATATCTTCTAAGCCA 57.486 37.500 0.00 0.00 42.01 4.75
758 772 7.095183 TGGATTTCCATATCTTCTAAGCCAT 57.905 36.000 0.00 0.00 42.01 4.40
759 773 7.529555 TGGATTTCCATATCTTCTAAGCCATT 58.470 34.615 0.00 0.00 42.01 3.16
760 774 7.449395 TGGATTTCCATATCTTCTAAGCCATTG 59.551 37.037 0.00 0.00 42.01 2.82
761 775 6.639632 TTTCCATATCTTCTAAGCCATTGC 57.360 37.500 0.00 0.00 37.95 3.56
762 776 5.308976 TCCATATCTTCTAAGCCATTGCA 57.691 39.130 0.00 0.00 41.13 4.08
763 777 5.065914 TCCATATCTTCTAAGCCATTGCAC 58.934 41.667 0.00 0.00 41.13 4.57
764 778 4.823442 CCATATCTTCTAAGCCATTGCACA 59.177 41.667 0.00 0.00 41.13 4.57
766 780 6.183360 CCATATCTTCTAAGCCATTGCACAAA 60.183 38.462 0.00 0.00 41.13 2.83
767 781 5.927281 ATCTTCTAAGCCATTGCACAAAT 57.073 34.783 0.00 0.00 41.13 2.32
768 782 5.063180 TCTTCTAAGCCATTGCACAAATG 57.937 39.130 0.00 0.00 44.60 2.32
786 800 5.933463 ACAAATGCTTGTATCCAACATTTGG 59.067 36.000 24.85 8.42 46.93 3.28
802 816 6.029492 ACATTTGGATTTCCATATCCTCCA 57.971 37.500 0.00 0.00 46.97 3.86
803 817 6.442961 ACATTTGGATTTCCATATCCTCCAA 58.557 36.000 0.00 0.00 46.97 3.53
804 818 6.552350 ACATTTGGATTTCCATATCCTCCAAG 59.448 38.462 0.00 0.00 46.97 3.61
806 820 5.310409 TGGATTTCCATATCCTCCAAGAC 57.690 43.478 0.00 0.00 43.75 3.01
808 822 5.373555 TGGATTTCCATATCCTCCAAGACAT 59.626 40.000 0.00 0.00 43.75 3.06
810 824 4.607293 TTCCATATCCTCCAAGACATCG 57.393 45.455 0.00 0.00 0.00 3.84
811 825 2.300152 TCCATATCCTCCAAGACATCGC 59.700 50.000 0.00 0.00 0.00 4.58
812 826 2.037641 CCATATCCTCCAAGACATCGCA 59.962 50.000 0.00 0.00 0.00 5.10
813 827 2.890808 TATCCTCCAAGACATCGCAC 57.109 50.000 0.00 0.00 0.00 5.34
814 828 0.904649 ATCCTCCAAGACATCGCACA 59.095 50.000 0.00 0.00 0.00 4.57
988 3896 7.872483 ACACCATCATTCCAACAACTTATTTTC 59.128 33.333 0.00 0.00 0.00 2.29
998 3906 7.123547 TCCAACAACTTATTTTCAGAACTTGGT 59.876 33.333 0.00 0.00 0.00 3.67
1190 4100 2.603473 ACGCAGGTGTGGAGGCTA 60.603 61.111 0.00 0.00 0.00 3.93
1191 4101 2.214216 ACGCAGGTGTGGAGGCTAA 61.214 57.895 0.00 0.00 0.00 3.09
1193 4103 1.888436 CGCAGGTGTGGAGGCTAAGA 61.888 60.000 0.00 0.00 0.00 2.10
1354 4303 4.112634 AGACGTGCATGTGTACATATGAC 58.887 43.478 30.14 22.77 34.26 3.06
1358 4307 3.873361 GTGCATGTGTACATATGACTGCT 59.127 43.478 30.14 0.00 34.26 4.24
1747 5031 2.620115 CTCATACAACACCATGCATCCC 59.380 50.000 0.00 0.00 0.00 3.85
1748 5032 1.682854 CATACAACACCATGCATCCCC 59.317 52.381 0.00 0.00 0.00 4.81
1768 5053 3.222603 CCTAGCCAACACCTGTTTTTCT 58.777 45.455 0.00 0.00 35.83 2.52
1772 5057 2.430694 GCCAACACCTGTTTTTCTCCTT 59.569 45.455 0.00 0.00 35.83 3.36
1773 5058 3.634910 GCCAACACCTGTTTTTCTCCTTA 59.365 43.478 0.00 0.00 35.83 2.69
1833 5119 6.210287 ACGAAACCTTCCATCTCTAACTAG 57.790 41.667 0.00 0.00 0.00 2.57
1834 5120 5.950549 ACGAAACCTTCCATCTCTAACTAGA 59.049 40.000 0.00 0.00 0.00 2.43
1850 5136 9.988815 CTCTAACTAGAGCATGGTTAATAATGT 57.011 33.333 0.00 0.00 42.83 2.71
1853 5139 8.608844 AACTAGAGCATGGTTAATAATGTAGC 57.391 34.615 0.00 0.00 29.53 3.58
1854 5140 7.162082 ACTAGAGCATGGTTAATAATGTAGCC 58.838 38.462 0.00 0.00 0.00 3.93
1855 5141 5.940617 AGAGCATGGTTAATAATGTAGCCA 58.059 37.500 0.00 0.00 38.54 4.75
1857 5143 4.520492 AGCATGGTTAATAATGTAGCCAGC 59.480 41.667 0.00 0.00 37.72 4.85
1858 5144 4.520492 GCATGGTTAATAATGTAGCCAGCT 59.480 41.667 0.00 0.00 37.72 4.24
1859 5145 5.563475 GCATGGTTAATAATGTAGCCAGCTG 60.563 44.000 6.78 6.78 37.72 4.24
1870 5156 4.291047 CCAGCTGCGGCCTATATG 57.709 61.111 15.55 5.19 39.73 1.78
1871 5157 1.376424 CCAGCTGCGGCCTATATGG 60.376 63.158 15.55 11.38 39.73 2.74
1872 5158 1.372683 CAGCTGCGGCCTATATGGT 59.627 57.895 15.55 0.00 39.73 3.55
1873 5159 0.671781 CAGCTGCGGCCTATATGGTC 60.672 60.000 15.55 0.00 39.73 4.02
1874 5160 0.833834 AGCTGCGGCCTATATGGTCT 60.834 55.000 15.55 0.00 38.58 3.85
1875 5161 0.035458 GCTGCGGCCTATATGGTCTT 59.965 55.000 6.12 0.00 38.58 3.01
1877 5163 1.070758 CTGCGGCCTATATGGTCTTGT 59.929 52.381 0.00 0.00 38.58 3.16
1879 5165 1.070134 GCGGCCTATATGGTCTTGTCA 59.930 52.381 0.00 0.00 38.58 3.58
1880 5166 2.755650 CGGCCTATATGGTCTTGTCAC 58.244 52.381 0.00 0.00 38.58 3.67
1881 5167 2.102420 CGGCCTATATGGTCTTGTCACA 59.898 50.000 0.00 0.00 38.58 3.58
1883 5169 4.319177 GGCCTATATGGTCTTGTCACATC 58.681 47.826 0.00 0.00 37.49 3.06
1884 5170 4.202357 GGCCTATATGGTCTTGTCACATCA 60.202 45.833 0.00 0.00 37.49 3.07
1885 5171 5.513788 GGCCTATATGGTCTTGTCACATCAT 60.514 44.000 0.00 0.00 37.49 2.45
1886 5172 5.641209 GCCTATATGGTCTTGTCACATCATC 59.359 44.000 0.00 0.00 38.35 2.92
1888 5174 7.310052 GCCTATATGGTCTTGTCACATCATCTA 60.310 40.741 0.00 0.00 38.35 1.98
1889 5175 8.756927 CCTATATGGTCTTGTCACATCATCTAT 58.243 37.037 0.00 0.00 0.00 1.98
1892 5178 5.847304 TGGTCTTGTCACATCATCTATAGC 58.153 41.667 0.00 0.00 0.00 2.97
1893 5179 5.221521 TGGTCTTGTCACATCATCTATAGCC 60.222 44.000 0.00 0.00 0.00 3.93
1894 5180 5.221521 GGTCTTGTCACATCATCTATAGCCA 60.222 44.000 0.00 0.00 0.00 4.75
1895 5181 6.283694 GTCTTGTCACATCATCTATAGCCAA 58.716 40.000 0.00 0.00 0.00 4.52
1897 5183 4.635223 TGTCACATCATCTATAGCCAAGC 58.365 43.478 0.00 0.00 0.00 4.01
1899 5185 5.163269 TGTCACATCATCTATAGCCAAGCTT 60.163 40.000 0.00 0.00 40.44 3.74
1900 5186 6.041979 TGTCACATCATCTATAGCCAAGCTTA 59.958 38.462 0.00 0.00 40.44 3.09
1903 6010 8.473219 TCACATCATCTATAGCCAAGCTTATAG 58.527 37.037 0.00 3.01 40.44 1.31
1904 6011 7.224362 CACATCATCTATAGCCAAGCTTATAGC 59.776 40.741 0.00 2.58 40.44 2.97
1920 6027 5.066505 GCTTATAGCTGGCAAATACAACAGT 59.933 40.000 0.00 0.00 38.45 3.55
1921 6028 6.404734 GCTTATAGCTGGCAAATACAACAGTT 60.405 38.462 0.00 0.00 38.45 3.16
1922 6029 3.648339 AGCTGGCAAATACAACAGTTG 57.352 42.857 12.03 12.03 35.31 3.16
1934 6041 7.872163 AATACAACAGTTGCATGTAAATGTG 57.128 32.000 26.24 21.23 38.66 3.21
1940 6047 8.849490 CAACAGTTGCATGTAAATGTGTATTAC 58.151 33.333 26.24 0.00 38.66 1.89
1941 6048 8.335532 ACAGTTGCATGTAAATGTGTATTACT 57.664 30.769 25.23 1.75 37.46 2.24
1942 6049 8.792633 ACAGTTGCATGTAAATGTGTATTACTT 58.207 29.630 25.23 1.08 37.46 2.24
1943 6050 9.624697 CAGTTGCATGTAAATGTGTATTACTTT 57.375 29.630 14.71 0.00 34.94 2.66
1965 6072 5.596836 TTTTGATACATGGCCCATCTTTC 57.403 39.130 0.00 0.00 0.00 2.62
1966 6073 4.524802 TTGATACATGGCCCATCTTTCT 57.475 40.909 0.00 0.00 0.00 2.52
1967 6074 4.090761 TGATACATGGCCCATCTTTCTC 57.909 45.455 0.00 0.00 0.00 2.87
1968 6075 3.718434 TGATACATGGCCCATCTTTCTCT 59.282 43.478 0.00 0.00 0.00 3.10
1969 6076 2.725221 ACATGGCCCATCTTTCTCTC 57.275 50.000 0.00 0.00 0.00 3.20
1970 6077 2.203584 ACATGGCCCATCTTTCTCTCT 58.796 47.619 0.00 0.00 0.00 3.10
1971 6078 2.172293 ACATGGCCCATCTTTCTCTCTC 59.828 50.000 0.00 0.00 0.00 3.20
1973 6080 1.556911 TGGCCCATCTTTCTCTCTCAC 59.443 52.381 0.00 0.00 0.00 3.51
1974 6081 1.556911 GGCCCATCTTTCTCTCTCACA 59.443 52.381 0.00 0.00 0.00 3.58
1976 6083 3.006247 GCCCATCTTTCTCTCTCACAAC 58.994 50.000 0.00 0.00 0.00 3.32
1979 6086 4.634883 CCCATCTTTCTCTCTCACAACATG 59.365 45.833 0.00 0.00 0.00 3.21
1982 6089 6.206243 CCATCTTTCTCTCTCACAACATGTTT 59.794 38.462 8.77 0.00 0.00 2.83
1984 6091 7.953158 TCTTTCTCTCTCACAACATGTTTAG 57.047 36.000 8.77 7.15 0.00 1.85
1985 6092 6.931281 TCTTTCTCTCTCACAACATGTTTAGG 59.069 38.462 8.77 0.07 0.00 2.69
1986 6093 6.419484 TTCTCTCTCACAACATGTTTAGGA 57.581 37.500 8.77 5.93 0.00 2.94
1988 6095 4.569943 TCTCTCACAACATGTTTAGGAGC 58.430 43.478 8.77 0.00 0.00 4.70
1989 6096 4.040339 TCTCTCACAACATGTTTAGGAGCA 59.960 41.667 8.77 3.89 0.00 4.26
1990 6097 4.065088 TCTCACAACATGTTTAGGAGCAC 58.935 43.478 8.77 0.00 0.00 4.40
1992 6099 2.548057 CACAACATGTTTAGGAGCACGT 59.452 45.455 8.77 0.00 0.00 4.49
1993 6100 2.548057 ACAACATGTTTAGGAGCACGTG 59.452 45.455 12.28 12.28 36.21 4.49
1994 6101 2.805671 CAACATGTTTAGGAGCACGTGA 59.194 45.455 22.23 0.00 34.52 4.35
1995 6102 3.334583 ACATGTTTAGGAGCACGTGAT 57.665 42.857 22.23 14.87 34.52 3.06
1996 6103 3.002791 ACATGTTTAGGAGCACGTGATG 58.997 45.455 22.23 12.80 34.52 3.07
2005 6112 2.745100 CACGTGATGCAGCCAGCT 60.745 61.111 10.90 0.00 45.94 4.24
2006 6113 2.745100 ACGTGATGCAGCCAGCTG 60.745 61.111 15.34 15.34 45.94 4.24
2007 6114 2.745100 CGTGATGCAGCCAGCTGT 60.745 61.111 20.11 1.89 45.24 4.40
2008 6115 2.330372 CGTGATGCAGCCAGCTGTT 61.330 57.895 20.11 8.96 45.24 3.16
2009 6116 1.020861 CGTGATGCAGCCAGCTGTTA 61.021 55.000 20.11 10.72 45.24 2.41
2010 6117 1.386533 GTGATGCAGCCAGCTGTTAT 58.613 50.000 20.11 14.62 45.24 1.89
2012 6119 1.065272 TGATGCAGCCAGCTGTTATCA 60.065 47.619 24.72 24.72 45.24 2.15
2013 6120 1.602851 GATGCAGCCAGCTGTTATCAG 59.397 52.381 20.11 0.00 45.24 2.90
2014 6121 0.325933 TGCAGCCAGCTGTTATCAGT 59.674 50.000 20.11 0.00 45.24 3.41
2015 6122 1.554617 TGCAGCCAGCTGTTATCAGTA 59.445 47.619 20.11 0.00 45.24 2.74
2016 6123 2.208431 GCAGCCAGCTGTTATCAGTAG 58.792 52.381 20.11 0.00 45.24 2.57
2017 6124 2.208431 CAGCCAGCTGTTATCAGTAGC 58.792 52.381 13.81 5.31 43.05 3.58
2018 6125 1.139853 AGCCAGCTGTTATCAGTAGCC 59.860 52.381 13.81 0.00 43.05 3.93
2019 6126 1.811941 GCCAGCTGTTATCAGTAGCCC 60.812 57.143 13.81 0.00 43.05 5.19
2020 6127 1.539065 CCAGCTGTTATCAGTAGCCCG 60.539 57.143 13.81 0.00 43.05 6.13
2021 6128 0.105039 AGCTGTTATCAGTAGCCCGC 59.895 55.000 2.85 0.00 43.05 6.13
2022 6129 0.105039 GCTGTTATCAGTAGCCCGCT 59.895 55.000 2.85 0.00 43.05 5.52
2024 6131 2.474816 CTGTTATCAGTAGCCCGCTTC 58.525 52.381 0.00 0.00 36.97 3.86
2025 6132 1.138266 TGTTATCAGTAGCCCGCTTCC 59.862 52.381 0.00 0.00 0.00 3.46
2028 6135 0.983378 ATCAGTAGCCCGCTTCCCTT 60.983 55.000 0.00 0.00 0.00 3.95
2029 6136 1.153349 CAGTAGCCCGCTTCCCTTC 60.153 63.158 0.00 0.00 0.00 3.46
2030 6137 1.306226 AGTAGCCCGCTTCCCTTCT 60.306 57.895 0.00 0.00 0.00 2.85
2031 6138 1.144276 GTAGCCCGCTTCCCTTCTC 59.856 63.158 0.00 0.00 0.00 2.87
2032 6139 1.001760 TAGCCCGCTTCCCTTCTCT 59.998 57.895 0.00 0.00 0.00 3.10
2033 6140 1.043673 TAGCCCGCTTCCCTTCTCTC 61.044 60.000 0.00 0.00 0.00 3.20
2034 6141 2.363172 GCCCGCTTCCCTTCTCTCT 61.363 63.158 0.00 0.00 0.00 3.10
2035 6142 1.904990 GCCCGCTTCCCTTCTCTCTT 61.905 60.000 0.00 0.00 0.00 2.85
2036 6143 0.176910 CCCGCTTCCCTTCTCTCTTC 59.823 60.000 0.00 0.00 0.00 2.87
2037 6144 1.190643 CCGCTTCCCTTCTCTCTTCT 58.809 55.000 0.00 0.00 0.00 2.85
2038 6145 1.136110 CCGCTTCCCTTCTCTCTTCTC 59.864 57.143 0.00 0.00 0.00 2.87
2039 6146 1.136110 CGCTTCCCTTCTCTCTTCTCC 59.864 57.143 0.00 0.00 0.00 3.71
2040 6147 2.466846 GCTTCCCTTCTCTCTTCTCCT 58.533 52.381 0.00 0.00 0.00 3.69
2041 6148 2.430694 GCTTCCCTTCTCTCTTCTCCTC 59.569 54.545 0.00 0.00 0.00 3.71
2043 6150 3.662759 TCCCTTCTCTCTTCTCCTCTC 57.337 52.381 0.00 0.00 0.00 3.20
2044 6151 2.243736 TCCCTTCTCTCTTCTCCTCTCC 59.756 54.545 0.00 0.00 0.00 3.71
2045 6152 2.666317 CCTTCTCTCTTCTCCTCTCCC 58.334 57.143 0.00 0.00 0.00 4.30
2046 6153 2.244769 CCTTCTCTCTTCTCCTCTCCCT 59.755 54.545 0.00 0.00 0.00 4.20
2047 6154 3.555966 CTTCTCTCTTCTCCTCTCCCTC 58.444 54.545 0.00 0.00 0.00 4.30
2048 6155 1.850345 TCTCTCTTCTCCTCTCCCTCC 59.150 57.143 0.00 0.00 0.00 4.30
2049 6156 1.852965 CTCTCTTCTCCTCTCCCTCCT 59.147 57.143 0.00 0.00 0.00 3.69
2050 6157 1.850345 TCTCTTCTCCTCTCCCTCCTC 59.150 57.143 0.00 0.00 0.00 3.71
2051 6158 0.930726 TCTTCTCCTCTCCCTCCTCC 59.069 60.000 0.00 0.00 0.00 4.30
2052 6159 0.633921 CTTCTCCTCTCCCTCCTCCA 59.366 60.000 0.00 0.00 0.00 3.86
2053 6160 1.007721 CTTCTCCTCTCCCTCCTCCAA 59.992 57.143 0.00 0.00 0.00 3.53
2054 6161 0.336737 TCTCCTCTCCCTCCTCCAAC 59.663 60.000 0.00 0.00 0.00 3.77
2055 6162 0.338120 CTCCTCTCCCTCCTCCAACT 59.662 60.000 0.00 0.00 0.00 3.16
2056 6163 0.336737 TCCTCTCCCTCCTCCAACTC 59.663 60.000 0.00 0.00 0.00 3.01
2057 6164 0.041833 CCTCTCCCTCCTCCAACTCA 59.958 60.000 0.00 0.00 0.00 3.41
2058 6165 1.343884 CCTCTCCCTCCTCCAACTCAT 60.344 57.143 0.00 0.00 0.00 2.90
2059 6166 2.038659 CTCTCCCTCCTCCAACTCATC 58.961 57.143 0.00 0.00 0.00 2.92
2060 6167 1.127343 CTCCCTCCTCCAACTCATCC 58.873 60.000 0.00 0.00 0.00 3.51
2061 6168 0.417437 TCCCTCCTCCAACTCATCCA 59.583 55.000 0.00 0.00 0.00 3.41
2062 6169 1.203428 TCCCTCCTCCAACTCATCCAA 60.203 52.381 0.00 0.00 0.00 3.53
2063 6170 1.635487 CCCTCCTCCAACTCATCCAAA 59.365 52.381 0.00 0.00 0.00 3.28
2064 6171 2.041620 CCCTCCTCCAACTCATCCAAAA 59.958 50.000 0.00 0.00 0.00 2.44
2065 6172 3.309410 CCCTCCTCCAACTCATCCAAAAT 60.309 47.826 0.00 0.00 0.00 1.82
2066 6173 4.079787 CCCTCCTCCAACTCATCCAAAATA 60.080 45.833 0.00 0.00 0.00 1.40
2067 6174 5.399497 CCCTCCTCCAACTCATCCAAAATAT 60.399 44.000 0.00 0.00 0.00 1.28
2068 6175 6.183361 CCCTCCTCCAACTCATCCAAAATATA 60.183 42.308 0.00 0.00 0.00 0.86
2069 6176 7.290061 CCTCCTCCAACTCATCCAAAATATAA 58.710 38.462 0.00 0.00 0.00 0.98
2070 6177 7.946776 CCTCCTCCAACTCATCCAAAATATAAT 59.053 37.037 0.00 0.00 0.00 1.28
2097 6204 3.788672 GCTTACAGCCTGCCTATGT 57.211 52.632 0.00 0.00 34.48 2.29
2098 6205 1.587547 GCTTACAGCCTGCCTATGTC 58.412 55.000 0.00 0.00 34.48 3.06
2099 6206 1.134401 GCTTACAGCCTGCCTATGTCA 60.134 52.381 0.00 0.00 34.48 3.58
2100 6207 2.486191 GCTTACAGCCTGCCTATGTCAT 60.486 50.000 0.00 0.00 34.48 3.06
2101 6208 3.397482 CTTACAGCCTGCCTATGTCATC 58.603 50.000 0.00 0.00 0.00 2.92
2102 6209 1.504912 ACAGCCTGCCTATGTCATCT 58.495 50.000 0.00 0.00 0.00 2.90
2103 6210 1.842562 ACAGCCTGCCTATGTCATCTT 59.157 47.619 0.00 0.00 0.00 2.40
2104 6211 3.041211 ACAGCCTGCCTATGTCATCTTA 58.959 45.455 0.00 0.00 0.00 2.10
2105 6212 3.649981 ACAGCCTGCCTATGTCATCTTAT 59.350 43.478 0.00 0.00 0.00 1.73
2106 6213 4.103785 ACAGCCTGCCTATGTCATCTTATT 59.896 41.667 0.00 0.00 0.00 1.40
2107 6214 5.307976 ACAGCCTGCCTATGTCATCTTATTA 59.692 40.000 0.00 0.00 0.00 0.98
2108 6215 6.013032 ACAGCCTGCCTATGTCATCTTATTAT 60.013 38.462 0.00 0.00 0.00 1.28
2109 6216 7.180946 ACAGCCTGCCTATGTCATCTTATTATA 59.819 37.037 0.00 0.00 0.00 0.98
2110 6217 7.493971 CAGCCTGCCTATGTCATCTTATTATAC 59.506 40.741 0.00 0.00 0.00 1.47
2111 6218 7.401493 AGCCTGCCTATGTCATCTTATTATACT 59.599 37.037 0.00 0.00 0.00 2.12
2112 6219 8.043710 GCCTGCCTATGTCATCTTATTATACTT 58.956 37.037 0.00 0.00 0.00 2.24
2113 6220 9.376075 CCTGCCTATGTCATCTTATTATACTTG 57.624 37.037 0.00 0.00 0.00 3.16
2114 6221 8.777865 TGCCTATGTCATCTTATTATACTTGC 57.222 34.615 0.00 0.00 0.00 4.01
2115 6222 8.597167 TGCCTATGTCATCTTATTATACTTGCT 58.403 33.333 0.00 0.00 0.00 3.91
2116 6223 9.092876 GCCTATGTCATCTTATTATACTTGCTC 57.907 37.037 0.00 0.00 0.00 4.26
2433 6540 4.498009 CCTGAATTTCATTACGGGCATGTC 60.498 45.833 0.00 0.00 0.00 3.06
2434 6541 3.064682 TGAATTTCATTACGGGCATGTCG 59.935 43.478 8.61 8.61 0.00 4.35
2474 6582 7.004086 TCAAAACCTTCCATGTTAACTCTCAT 58.996 34.615 7.22 0.00 0.00 2.90
2479 6587 7.458397 ACCTTCCATGTTAACTCTCATGTAAA 58.542 34.615 7.22 0.00 39.53 2.01
2505 6613 9.846248 AGTATGTCAAAAGATTTTTGTAGATGC 57.154 29.630 12.44 8.14 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
284 290 0.388391 CCAAAATGCATCCACGCGTT 60.388 50.000 10.22 0.00 42.89 4.84
297 303 0.898326 GCTCCAACCGGGACCAAAAT 60.898 55.000 6.32 0.00 42.15 1.82
549 557 5.584649 TGCTTACTCATAGTTGGTTACATGC 59.415 40.000 0.00 0.00 0.00 4.06
579 587 5.458779 GCAACGTAAGAGCAAAACAGAAATT 59.541 36.000 0.00 0.00 40.54 1.82
584 592 2.032799 TGGCAACGTAAGAGCAAAACAG 59.967 45.455 0.00 0.00 42.08 3.16
599 607 3.618150 GGTGCAATTACATTGATGGCAAC 59.382 43.478 0.00 0.00 42.83 4.17
600 608 3.260128 TGGTGCAATTACATTGATGGCAA 59.740 39.130 0.00 0.00 42.83 4.52
637 645 3.769844 TGTGCTACCCCACAAAAAGAAAA 59.230 39.130 0.00 0.00 42.33 2.29
671 685 9.624373 ATCTCCAGCAATTAATCATATGTATCC 57.376 33.333 1.90 0.00 0.00 2.59
748 762 3.258872 AGCATTTGTGCAATGGCTTAGAA 59.741 39.130 3.03 0.00 42.51 2.10
752 766 2.147958 CAAGCATTTGTGCAATGGCTT 58.852 42.857 13.90 13.90 42.51 4.35
753 767 1.071071 ACAAGCATTTGTGCAATGGCT 59.929 42.857 3.03 5.42 45.54 4.75
754 768 1.515081 ACAAGCATTTGTGCAATGGC 58.485 45.000 3.03 0.00 45.54 4.40
755 769 3.866910 GGATACAAGCATTTGTGCAATGG 59.133 43.478 3.03 0.00 46.63 3.16
785 799 5.310409 TGTCTTGGAGGATATGGAAATCC 57.690 43.478 0.00 0.00 45.06 3.01
786 800 5.641209 CGATGTCTTGGAGGATATGGAAATC 59.359 44.000 0.00 0.00 0.00 2.17
787 801 5.555017 CGATGTCTTGGAGGATATGGAAAT 58.445 41.667 0.00 0.00 0.00 2.17
788 802 4.743651 GCGATGTCTTGGAGGATATGGAAA 60.744 45.833 0.00 0.00 0.00 3.13
789 803 3.244215 GCGATGTCTTGGAGGATATGGAA 60.244 47.826 0.00 0.00 0.00 3.53
790 804 2.300152 GCGATGTCTTGGAGGATATGGA 59.700 50.000 0.00 0.00 0.00 3.41
791 805 2.037641 TGCGATGTCTTGGAGGATATGG 59.962 50.000 0.00 0.00 0.00 2.74
792 806 3.062763 GTGCGATGTCTTGGAGGATATG 58.937 50.000 0.00 0.00 0.00 1.78
793 807 2.700371 TGTGCGATGTCTTGGAGGATAT 59.300 45.455 0.00 0.00 0.00 1.63
795 809 0.904649 TGTGCGATGTCTTGGAGGAT 59.095 50.000 0.00 0.00 0.00 3.24
796 810 0.684535 TTGTGCGATGTCTTGGAGGA 59.315 50.000 0.00 0.00 0.00 3.71
797 811 1.522668 TTTGTGCGATGTCTTGGAGG 58.477 50.000 0.00 0.00 0.00 4.30
798 812 2.730090 GCATTTGTGCGATGTCTTGGAG 60.730 50.000 0.00 0.00 0.00 3.86
802 816 2.294233 ACAAGCATTTGTGCGATGTCTT 59.706 40.909 8.40 0.00 45.54 3.01
803 817 1.881973 ACAAGCATTTGTGCGATGTCT 59.118 42.857 8.40 0.00 45.54 3.41
804 818 2.336554 ACAAGCATTTGTGCGATGTC 57.663 45.000 8.40 0.00 45.54 3.06
806 820 3.365832 GGATACAAGCATTTGTGCGATG 58.634 45.455 1.78 7.40 46.63 3.84
840 3744 7.348080 TGTGTAATGTCTTAGAGGGTATGAG 57.652 40.000 0.00 0.00 0.00 2.90
846 3750 5.882557 AGCATTTGTGTAATGTCTTAGAGGG 59.117 40.000 0.00 0.00 44.52 4.30
988 3896 1.197721 GAACGCCATGACCAAGTTCTG 59.802 52.381 0.00 0.00 38.40 3.02
998 3906 2.741985 CACCGCTGAACGCCATGA 60.742 61.111 0.00 0.00 41.76 3.07
1014 3922 2.124983 GCAGCGAGAATCTGGGCA 60.125 61.111 5.81 0.00 32.41 5.36
1146 4056 6.488344 TGACTTAGAATTAATGTGTGCACCAA 59.512 34.615 15.69 2.17 0.00 3.67
1190 4100 0.687354 CTAGGGGCCGTGCATATCTT 59.313 55.000 9.43 0.00 0.00 2.40
1191 4101 1.831652 GCTAGGGGCCGTGCATATCT 61.832 60.000 9.43 0.00 34.27 1.98
1193 4103 1.705002 TTGCTAGGGGCCGTGCATAT 61.705 55.000 19.00 0.00 40.92 1.78
1358 4307 0.688087 GTGGTGGTGGGGTTTTTCCA 60.688 55.000 0.00 0.00 38.11 3.53
1583 4544 6.154534 TGCATATGTACAAGTCAAGTAGGAGT 59.845 38.462 0.00 0.00 0.00 3.85
1584 4545 6.573434 TGCATATGTACAAGTCAAGTAGGAG 58.427 40.000 0.00 0.00 0.00 3.69
1585 4546 6.538945 TGCATATGTACAAGTCAAGTAGGA 57.461 37.500 0.00 0.00 0.00 2.94
1586 4547 8.887036 TTATGCATATGTACAAGTCAAGTAGG 57.113 34.615 7.36 0.00 0.00 3.18
1589 4550 9.394767 TCAATTATGCATATGTACAAGTCAAGT 57.605 29.630 7.36 0.00 0.00 3.16
1747 5031 3.222603 AGAAAAACAGGTGTTGGCTAGG 58.777 45.455 0.00 0.00 38.44 3.02
1748 5032 3.253432 GGAGAAAAACAGGTGTTGGCTAG 59.747 47.826 0.00 0.00 38.44 3.42
1833 5119 5.335191 GCTGGCTACATTATTAACCATGCTC 60.335 44.000 0.00 0.00 0.00 4.26
1834 5120 4.520492 GCTGGCTACATTATTAACCATGCT 59.480 41.667 0.00 0.00 0.00 3.79
1835 5121 4.520492 AGCTGGCTACATTATTAACCATGC 59.480 41.667 0.00 0.00 0.00 4.06
1839 5125 3.058914 CGCAGCTGGCTACATTATTAACC 60.059 47.826 17.12 0.00 41.67 2.85
1840 5126 3.058914 CCGCAGCTGGCTACATTATTAAC 60.059 47.826 17.12 0.00 41.67 2.01
1843 5129 1.597742 CCGCAGCTGGCTACATTATT 58.402 50.000 17.12 0.00 41.67 1.40
1844 5130 3.312404 CCGCAGCTGGCTACATTAT 57.688 52.632 17.12 0.00 41.67 1.28
1853 5139 1.376424 CCATATAGGCCGCAGCTGG 60.376 63.158 17.12 5.50 39.73 4.85
1854 5140 0.671781 GACCATATAGGCCGCAGCTG 60.672 60.000 10.11 10.11 43.14 4.24
1855 5141 0.833834 AGACCATATAGGCCGCAGCT 60.834 55.000 0.00 0.00 43.14 4.24
1857 5143 1.070758 ACAAGACCATATAGGCCGCAG 59.929 52.381 0.00 0.00 43.14 5.18
1858 5144 1.070134 GACAAGACCATATAGGCCGCA 59.930 52.381 0.00 0.00 43.14 5.69
1859 5145 1.070134 TGACAAGACCATATAGGCCGC 59.930 52.381 0.00 0.00 43.14 6.53
1861 5147 3.838244 TGTGACAAGACCATATAGGCC 57.162 47.619 0.00 0.00 43.14 5.19
1862 5148 4.960938 TGATGTGACAAGACCATATAGGC 58.039 43.478 0.00 0.00 43.14 3.93
1863 5149 7.002250 AGATGATGTGACAAGACCATATAGG 57.998 40.000 0.00 0.00 45.67 2.57
1866 5152 8.256605 GCTATAGATGATGTGACAAGACCATAT 58.743 37.037 3.21 0.00 0.00 1.78
1868 5154 6.462500 GCTATAGATGATGTGACAAGACCAT 58.538 40.000 3.21 0.00 0.00 3.55
1870 5156 5.221521 TGGCTATAGATGATGTGACAAGACC 60.222 44.000 3.21 0.00 0.00 3.85
1871 5157 5.847304 TGGCTATAGATGATGTGACAAGAC 58.153 41.667 3.21 0.00 0.00 3.01
1872 5158 6.484364 TTGGCTATAGATGATGTGACAAGA 57.516 37.500 3.21 0.00 0.00 3.02
1873 5159 5.178996 GCTTGGCTATAGATGATGTGACAAG 59.821 44.000 3.21 0.00 39.50 3.16
1874 5160 5.059161 GCTTGGCTATAGATGATGTGACAA 58.941 41.667 3.21 0.00 0.00 3.18
1875 5161 4.346127 AGCTTGGCTATAGATGATGTGACA 59.654 41.667 3.21 0.00 36.99 3.58
1877 5163 5.557576 AAGCTTGGCTATAGATGATGTGA 57.442 39.130 3.21 0.00 38.25 3.58
1879 5165 7.271511 GCTATAAGCTTGGCTATAGATGATGT 58.728 38.462 9.86 0.00 38.25 3.06
1880 5166 7.712264 GCTATAAGCTTGGCTATAGATGATG 57.288 40.000 9.86 0.00 38.25 3.07
1897 5183 6.683974 ACTGTTGTATTTGCCAGCTATAAG 57.316 37.500 0.00 0.00 0.00 1.73
1899 5185 5.163663 GCAACTGTTGTATTTGCCAGCTATA 60.164 40.000 20.57 0.00 38.58 1.31
1900 5186 4.380867 GCAACTGTTGTATTTGCCAGCTAT 60.381 41.667 20.57 0.00 38.58 2.97
1903 6010 2.061028 GCAACTGTTGTATTTGCCAGC 58.939 47.619 20.57 0.00 38.58 4.85
1904 6011 3.367992 TGCAACTGTTGTATTTGCCAG 57.632 42.857 20.57 0.00 42.44 4.85
1907 6014 6.761731 TTTACATGCAACTGTTGTATTTGC 57.238 33.333 19.39 7.12 43.15 3.68
1909 6016 7.925483 ACACATTTACATGCAACTGTTGTATTT 59.075 29.630 19.39 16.19 33.54 1.40
1912 6019 6.384258 ACACATTTACATGCAACTGTTGTA 57.616 33.333 20.57 17.22 33.05 2.41
1914 6021 7.872163 AATACACATTTACATGCAACTGTTG 57.128 32.000 15.98 15.98 33.05 3.33
1917 6024 9.624697 AAAGTAATACACATTTACATGCAACTG 57.375 29.630 0.00 0.00 33.05 3.16
1942 6049 5.721000 AGAAAGATGGGCCATGTATCAAAAA 59.279 36.000 26.77 0.00 0.00 1.94
1943 6050 5.271598 AGAAAGATGGGCCATGTATCAAAA 58.728 37.500 26.77 0.00 0.00 2.44
1944 6051 4.870636 AGAAAGATGGGCCATGTATCAAA 58.129 39.130 26.77 0.00 0.00 2.69
1945 6052 4.166725 AGAGAAAGATGGGCCATGTATCAA 59.833 41.667 26.77 0.00 0.00 2.57
1946 6053 3.718434 AGAGAAAGATGGGCCATGTATCA 59.282 43.478 26.77 0.00 0.00 2.15
1947 6054 4.041444 AGAGAGAAAGATGGGCCATGTATC 59.959 45.833 26.77 17.99 0.00 2.24
1951 6058 2.172082 TGAGAGAGAAAGATGGGCCATG 59.828 50.000 26.77 0.00 0.00 3.66
1954 6061 1.556911 TGTGAGAGAGAAAGATGGGCC 59.443 52.381 0.00 0.00 0.00 5.80
1955 6062 3.006247 GTTGTGAGAGAGAAAGATGGGC 58.994 50.000 0.00 0.00 0.00 5.36
1956 6063 4.277515 TGTTGTGAGAGAGAAAGATGGG 57.722 45.455 0.00 0.00 0.00 4.00
1957 6064 5.243981 ACATGTTGTGAGAGAGAAAGATGG 58.756 41.667 0.00 0.00 29.99 3.51
1958 6065 6.798315 AACATGTTGTGAGAGAGAAAGATG 57.202 37.500 11.07 0.00 31.55 2.90
1962 6069 6.826668 TCCTAAACATGTTGTGAGAGAGAAA 58.173 36.000 12.82 0.00 0.00 2.52
1964 6071 5.567623 GCTCCTAAACATGTTGTGAGAGAGA 60.568 44.000 25.00 11.57 0.00 3.10
1965 6072 4.629200 GCTCCTAAACATGTTGTGAGAGAG 59.371 45.833 25.00 21.07 0.00 3.20
1966 6073 4.040339 TGCTCCTAAACATGTTGTGAGAGA 59.960 41.667 25.00 15.33 0.00 3.10
1967 6074 4.153117 GTGCTCCTAAACATGTTGTGAGAG 59.847 45.833 25.00 21.25 0.00 3.20
1968 6075 4.065088 GTGCTCCTAAACATGTTGTGAGA 58.935 43.478 25.00 14.69 0.00 3.27
1969 6076 3.120546 CGTGCTCCTAAACATGTTGTGAG 60.121 47.826 12.82 17.51 0.00 3.51
1970 6077 2.805671 CGTGCTCCTAAACATGTTGTGA 59.194 45.455 12.82 8.17 0.00 3.58
1971 6078 2.548057 ACGTGCTCCTAAACATGTTGTG 59.452 45.455 12.82 7.91 32.12 3.33
1973 6080 2.805671 TCACGTGCTCCTAAACATGTTG 59.194 45.455 12.82 0.00 33.82 3.33
1974 6081 3.120321 TCACGTGCTCCTAAACATGTT 57.880 42.857 11.67 4.92 33.82 2.71
1976 6083 3.663464 CATCACGTGCTCCTAAACATG 57.337 47.619 11.67 2.02 0.00 3.21
1988 6095 2.745100 AGCTGGCTGCATCACGTG 60.745 61.111 18.84 9.94 45.94 4.49
1989 6096 2.745100 CAGCTGGCTGCATCACGT 60.745 61.111 18.84 0.00 45.94 4.49
1997 6104 2.208431 GCTACTGATAACAGCTGGCTG 58.792 52.381 19.93 19.42 46.95 4.85
1998 6105 1.139853 GGCTACTGATAACAGCTGGCT 59.860 52.381 19.93 7.27 46.95 4.75
1999 6106 1.587547 GGCTACTGATAACAGCTGGC 58.412 55.000 19.93 7.97 46.95 4.85
2000 6107 1.539065 CGGGCTACTGATAACAGCTGG 60.539 57.143 19.93 0.72 46.95 4.85
2001 6108 1.858091 CGGGCTACTGATAACAGCTG 58.142 55.000 13.48 13.48 46.95 4.24
2002 6109 0.105039 GCGGGCTACTGATAACAGCT 59.895 55.000 0.00 0.00 46.95 4.24
2005 6112 1.138266 GGAAGCGGGCTACTGATAACA 59.862 52.381 0.00 0.00 0.00 2.41
2006 6113 1.540580 GGGAAGCGGGCTACTGATAAC 60.541 57.143 0.00 0.00 0.00 1.89
2007 6114 0.756903 GGGAAGCGGGCTACTGATAA 59.243 55.000 0.00 0.00 0.00 1.75
2008 6115 0.105658 AGGGAAGCGGGCTACTGATA 60.106 55.000 0.00 0.00 0.00 2.15
2009 6116 0.983378 AAGGGAAGCGGGCTACTGAT 60.983 55.000 0.00 0.00 0.00 2.90
2010 6117 1.612442 AAGGGAAGCGGGCTACTGA 60.612 57.895 0.00 0.00 0.00 3.41
2012 6119 1.306226 AGAAGGGAAGCGGGCTACT 60.306 57.895 0.00 0.00 0.00 2.57
2013 6120 1.144276 GAGAAGGGAAGCGGGCTAC 59.856 63.158 0.00 0.00 0.00 3.58
2014 6121 1.001760 AGAGAAGGGAAGCGGGCTA 59.998 57.895 0.00 0.00 0.00 3.93
2015 6122 2.284995 AGAGAAGGGAAGCGGGCT 60.285 61.111 0.00 0.00 0.00 5.19
2016 6123 1.904990 AAGAGAGAAGGGAAGCGGGC 61.905 60.000 0.00 0.00 0.00 6.13
2017 6124 0.176910 GAAGAGAGAAGGGAAGCGGG 59.823 60.000 0.00 0.00 0.00 6.13
2018 6125 1.136110 GAGAAGAGAGAAGGGAAGCGG 59.864 57.143 0.00 0.00 0.00 5.52
2019 6126 1.136110 GGAGAAGAGAGAAGGGAAGCG 59.864 57.143 0.00 0.00 0.00 4.68
2020 6127 2.430694 GAGGAGAAGAGAGAAGGGAAGC 59.569 54.545 0.00 0.00 0.00 3.86
2021 6128 3.954258 GAGAGGAGAAGAGAGAAGGGAAG 59.046 52.174 0.00 0.00 0.00 3.46
2022 6129 3.309556 GGAGAGGAGAAGAGAGAAGGGAA 60.310 52.174 0.00 0.00 0.00 3.97
2024 6131 2.666317 GGAGAGGAGAAGAGAGAAGGG 58.334 57.143 0.00 0.00 0.00 3.95
2025 6132 2.244769 AGGGAGAGGAGAAGAGAGAAGG 59.755 54.545 0.00 0.00 0.00 3.46
2028 6135 1.850345 GGAGGGAGAGGAGAAGAGAGA 59.150 57.143 0.00 0.00 0.00 3.10
2029 6136 1.852965 AGGAGGGAGAGGAGAAGAGAG 59.147 57.143 0.00 0.00 0.00 3.20
2030 6137 1.850345 GAGGAGGGAGAGGAGAAGAGA 59.150 57.143 0.00 0.00 0.00 3.10
2031 6138 1.133482 GGAGGAGGGAGAGGAGAAGAG 60.133 61.905 0.00 0.00 0.00 2.85
2032 6139 0.930726 GGAGGAGGGAGAGGAGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
2033 6140 0.633921 TGGAGGAGGGAGAGGAGAAG 59.366 60.000 0.00 0.00 0.00 2.85
2034 6141 1.093408 TTGGAGGAGGGAGAGGAGAA 58.907 55.000 0.00 0.00 0.00 2.87
2035 6142 0.336737 GTTGGAGGAGGGAGAGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
2036 6143 0.338120 AGTTGGAGGAGGGAGAGGAG 59.662 60.000 0.00 0.00 0.00 3.69
2037 6144 0.336737 GAGTTGGAGGAGGGAGAGGA 59.663 60.000 0.00 0.00 0.00 3.71
2038 6145 0.041833 TGAGTTGGAGGAGGGAGAGG 59.958 60.000 0.00 0.00 0.00 3.69
2039 6146 2.038659 GATGAGTTGGAGGAGGGAGAG 58.961 57.143 0.00 0.00 0.00 3.20
2040 6147 1.343478 GGATGAGTTGGAGGAGGGAGA 60.343 57.143 0.00 0.00 0.00 3.71
2041 6148 1.127343 GGATGAGTTGGAGGAGGGAG 58.873 60.000 0.00 0.00 0.00 4.30
2043 6150 1.289160 TTGGATGAGTTGGAGGAGGG 58.711 55.000 0.00 0.00 0.00 4.30
2044 6151 3.439857 TTTTGGATGAGTTGGAGGAGG 57.560 47.619 0.00 0.00 0.00 4.30
2045 6152 8.930846 ATTATATTTTGGATGAGTTGGAGGAG 57.069 34.615 0.00 0.00 0.00 3.69
2080 6187 2.988010 TGACATAGGCAGGCTGTAAG 57.012 50.000 17.16 1.11 0.00 2.34
2081 6188 3.041211 AGATGACATAGGCAGGCTGTAA 58.959 45.455 17.16 2.06 0.00 2.41
2082 6189 2.682594 AGATGACATAGGCAGGCTGTA 58.317 47.619 17.16 1.41 0.00 2.74
2083 6190 1.504912 AGATGACATAGGCAGGCTGT 58.495 50.000 17.16 0.00 0.00 4.40
2084 6191 2.634815 AAGATGACATAGGCAGGCTG 57.365 50.000 10.94 10.94 0.00 4.85
2085 6192 4.989875 AATAAGATGACATAGGCAGGCT 57.010 40.909 0.38 0.38 0.00 4.58
2086 6193 7.560368 AGTATAATAAGATGACATAGGCAGGC 58.440 38.462 0.00 0.00 0.00 4.85
2087 6194 9.376075 CAAGTATAATAAGATGACATAGGCAGG 57.624 37.037 0.00 0.00 0.00 4.85
2088 6195 8.877779 GCAAGTATAATAAGATGACATAGGCAG 58.122 37.037 0.00 0.00 0.00 4.85
2089 6196 8.597167 AGCAAGTATAATAAGATGACATAGGCA 58.403 33.333 0.00 0.00 0.00 4.75
2090 6197 9.092876 GAGCAAGTATAATAAGATGACATAGGC 57.907 37.037 0.00 0.00 0.00 3.93
2429 6536 3.826157 TGATTGGAAAGGAAAAGCGACAT 59.174 39.130 0.00 0.00 0.00 3.06
2433 6540 4.211164 GGTTTTGATTGGAAAGGAAAAGCG 59.789 41.667 0.00 0.00 32.44 4.68
2434 6541 5.368145 AGGTTTTGATTGGAAAGGAAAAGC 58.632 37.500 0.00 0.00 38.02 3.51
2479 6587 9.846248 GCATCTACAAAAATCTTTTGACATACT 57.154 29.630 16.56 0.00 33.83 2.12
2504 6612 2.092323 AGGGAAAAAGGATAACGCTGC 58.908 47.619 0.00 0.00 0.00 5.25
2505 6613 3.506067 ACAAGGGAAAAAGGATAACGCTG 59.494 43.478 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.