Multiple sequence alignment - TraesCS5A01G243400

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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 TraesCS5A01G243400 chr5A 100.000 2578 0 0 1 2578 457914177 457916754 0.000000e+00 4761.0
1 TraesCS5A01G243400 chr5A 97.196 535 14 1 1 534 12186003 12186537 0.000000e+00 904.0
2 TraesCS5A01G243400 chr5A 97.328 524 14 0 1 524 242799711 242800234 0.000000e+00 891.0
3 TraesCS5A01G243400 chr5A 91.921 557 37 1 4 560 190372133 190371585 0.000000e+00 773.0
4 TraesCS5A01G243400 chr5A 78.932 674 81 34 958 1603 457908244 457908884 4.000000e-108 401.0
5 TraesCS5A01G243400 chr5A 79.915 234 24 14 958 1178 457905683 457905906 1.600000e-32 150.0
6 TraesCS5A01G243400 chr5D 83.702 1086 114 36 848 1917 356320292 356321330 0.000000e+00 966.0
7 TraesCS5A01G243400 chr5D 80.560 679 68 35 948 1603 356206542 356207179 5.020000e-127 464.0
8 TraesCS5A01G243400 chr5D 83.753 437 37 15 2165 2578 356321548 356321973 1.450000e-102 383.0
9 TraesCS5A01G243400 chr5D 82.432 74 7 5 1906 1977 346878365 346878296 2.770000e-05 60.2
10 TraesCS5A01G243400 chr3B 97.566 534 12 1 1 533 10648461 10648994 0.000000e+00 913.0
11 TraesCS5A01G243400 chr2A 94.614 557 22 3 1 557 744974722 744975270 0.000000e+00 856.0
12 TraesCS5A01G243400 chr5B 96.964 494 14 1 1 493 378027734 378028227 0.000000e+00 828.0
13 TraesCS5A01G243400 chr5B 84.816 652 66 19 848 1488 421275359 421275988 2.180000e-175 625.0
14 TraesCS5A01G243400 chr5B 80.938 682 65 34 948 1598 421187510 421188157 1.790000e-131 479.0
15 TraesCS5A01G243400 chr5B 77.824 717 91 41 1436 2138 421276005 421276667 5.210000e-102 381.0
16 TraesCS5A01G243400 chr5B 82.651 415 35 19 2165 2563 421276661 421277054 1.480000e-87 333.0
17 TraesCS5A01G243400 chr4B 90.809 544 33 4 1 534 530262428 530262964 0.000000e+00 712.0
18 TraesCS5A01G243400 chr4B 75.163 306 63 8 1824 2124 134205073 134205370 5.790000e-27 132.0
19 TraesCS5A01G243400 chr6D 90.073 413 32 2 6 409 19568042 19567630 6.320000e-146 527.0
20 TraesCS5A01G243400 chr6B 85.263 285 37 4 172 452 68696698 68696415 3.250000e-74 289.0
21 TraesCS5A01G243400 chr7D 75.926 432 83 19 1703 2124 127768126 127767706 4.350000e-48 202.0
22 TraesCS5A01G243400 chr3A 72.055 433 94 23 1698 2123 640837485 640837897 1.260000e-18 104.0
23 TraesCS5A01G243400 chr3A 74.274 241 34 14 598 836 674078371 674078585 2.750000e-10 76.8


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 TraesCS5A01G243400 chr5A 457914177 457916754 2577 False 4761.000000 4761 100.000000 1 2578 1 chr5A.!!$F3 2577
1 TraesCS5A01G243400 chr5A 12186003 12186537 534 False 904.000000 904 97.196000 1 534 1 chr5A.!!$F1 533
2 TraesCS5A01G243400 chr5A 242799711 242800234 523 False 891.000000 891 97.328000 1 524 1 chr5A.!!$F2 523
3 TraesCS5A01G243400 chr5A 190371585 190372133 548 True 773.000000 773 91.921000 4 560 1 chr5A.!!$R1 556
4 TraesCS5A01G243400 chr5A 457905683 457908884 3201 False 275.500000 401 79.423500 958 1603 2 chr5A.!!$F4 645
5 TraesCS5A01G243400 chr5D 356320292 356321973 1681 False 674.500000 966 83.727500 848 2578 2 chr5D.!!$F2 1730
6 TraesCS5A01G243400 chr5D 356206542 356207179 637 False 464.000000 464 80.560000 948 1603 1 chr5D.!!$F1 655
7 TraesCS5A01G243400 chr3B 10648461 10648994 533 False 913.000000 913 97.566000 1 533 1 chr3B.!!$F1 532
8 TraesCS5A01G243400 chr2A 744974722 744975270 548 False 856.000000 856 94.614000 1 557 1 chr2A.!!$F1 556
9 TraesCS5A01G243400 chr5B 421187510 421188157 647 False 479.000000 479 80.938000 948 1598 1 chr5B.!!$F2 650
10 TraesCS5A01G243400 chr5B 421275359 421277054 1695 False 446.333333 625 81.763667 848 2563 3 chr5B.!!$F3 1715
11 TraesCS5A01G243400 chr4B 530262428 530262964 536 False 712.000000 712 90.809000 1 534 1 chr4B.!!$F2 533

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
564 577 1.378119 GGTCGGGCCTGGGTTTTAG 60.378 63.158 12.87 0.0 0.0 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 4328 0.037326 CGGGACATATATGCAGCCGT 60.037 55.0 12.79 0.0 0.0 5.68 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
168 178 1.571773 GGCCAAGGTAGTGGATGGGT 61.572 60.000 0.00 0.00 41.65 4.51
246 258 1.677552 CTTGGAGTTGCCGTACCCT 59.322 57.895 0.00 0.00 40.66 4.34
369 381 5.163622 CGCAATGGAAATCCTGTAATCAAGT 60.164 40.000 0.44 0.00 36.82 3.16
453 465 7.874940 AGATCGTTGAATCAATGAAAAACTGA 58.125 30.769 20.15 0.00 41.73 3.41
562 575 4.295199 GGGTCGGGCCTGGGTTTT 62.295 66.667 12.87 0.00 37.43 2.43
563 576 2.758434 GGTCGGGCCTGGGTTTTA 59.242 61.111 12.87 0.00 0.00 1.52
564 577 1.378119 GGTCGGGCCTGGGTTTTAG 60.378 63.158 12.87 0.00 0.00 1.85
565 578 1.378119 GTCGGGCCTGGGTTTTAGG 60.378 63.158 12.87 0.00 38.39 2.69
572 585 2.604912 CCTGGGTTTTAGGCCTCTTT 57.395 50.000 9.68 0.00 0.00 2.52
573 586 2.447443 CCTGGGTTTTAGGCCTCTTTC 58.553 52.381 9.68 0.00 0.00 2.62
574 587 2.447443 CTGGGTTTTAGGCCTCTTTCC 58.553 52.381 9.68 8.57 0.00 3.13
575 588 2.041755 CTGGGTTTTAGGCCTCTTTCCT 59.958 50.000 9.68 0.00 37.72 3.36
576 589 2.449345 TGGGTTTTAGGCCTCTTTCCTT 59.551 45.455 9.68 0.00 35.21 3.36
577 590 3.116900 TGGGTTTTAGGCCTCTTTCCTTT 60.117 43.478 9.68 0.00 35.21 3.11
578 591 3.258372 GGGTTTTAGGCCTCTTTCCTTTG 59.742 47.826 9.68 0.00 35.21 2.77
579 592 4.149598 GGTTTTAGGCCTCTTTCCTTTGA 58.850 43.478 9.68 0.00 35.21 2.69
580 593 4.772624 GGTTTTAGGCCTCTTTCCTTTGAT 59.227 41.667 9.68 0.00 35.21 2.57
581 594 5.949952 GGTTTTAGGCCTCTTTCCTTTGATA 59.050 40.000 9.68 0.00 35.21 2.15
582 595 6.607600 GGTTTTAGGCCTCTTTCCTTTGATAT 59.392 38.462 9.68 0.00 35.21 1.63
583 596 7.416777 GGTTTTAGGCCTCTTTCCTTTGATATG 60.417 40.741 9.68 0.00 35.21 1.78
584 597 6.575244 TTAGGCCTCTTTCCTTTGATATGA 57.425 37.500 9.68 0.00 35.21 2.15
585 598 5.659849 AGGCCTCTTTCCTTTGATATGAT 57.340 39.130 0.00 0.00 0.00 2.45
586 599 6.770286 AGGCCTCTTTCCTTTGATATGATA 57.230 37.500 0.00 0.00 0.00 2.15
587 600 6.777782 AGGCCTCTTTCCTTTGATATGATAG 58.222 40.000 0.00 0.00 0.00 2.08
588 601 6.560304 AGGCCTCTTTCCTTTGATATGATAGA 59.440 38.462 0.00 0.00 0.00 1.98
589 602 7.072961 AGGCCTCTTTCCTTTGATATGATAGAA 59.927 37.037 0.00 0.00 0.00 2.10
590 603 7.174080 GGCCTCTTTCCTTTGATATGATAGAAC 59.826 40.741 0.00 0.00 0.00 3.01
591 604 7.936301 GCCTCTTTCCTTTGATATGATAGAACT 59.064 37.037 0.00 0.00 0.00 3.01
665 678 9.859427 TTTTTATAGAGAAAGACATGCCATTTG 57.141 29.630 0.00 0.00 0.00 2.32
666 679 8.806429 TTTATAGAGAAAGACATGCCATTTGA 57.194 30.769 0.00 0.00 0.00 2.69
667 680 8.985315 TTATAGAGAAAGACATGCCATTTGAT 57.015 30.769 0.00 0.00 0.00 2.57
669 682 6.690194 AGAGAAAGACATGCCATTTGATAC 57.310 37.500 0.00 0.00 0.00 2.24
670 683 6.182627 AGAGAAAGACATGCCATTTGATACA 58.817 36.000 0.00 0.00 0.00 2.29
671 684 6.832384 AGAGAAAGACATGCCATTTGATACAT 59.168 34.615 0.00 0.00 0.00 2.29
672 685 7.994911 AGAGAAAGACATGCCATTTGATACATA 59.005 33.333 0.00 0.00 0.00 2.29
673 686 8.162878 AGAAAGACATGCCATTTGATACATAG 57.837 34.615 0.00 0.00 0.00 2.23
674 687 7.994911 AGAAAGACATGCCATTTGATACATAGA 59.005 33.333 0.00 0.00 0.00 1.98
675 688 8.523915 AAAGACATGCCATTTGATACATAGAA 57.476 30.769 0.00 0.00 0.00 2.10
676 689 8.701908 AAGACATGCCATTTGATACATAGAAT 57.298 30.769 0.00 0.00 0.00 2.40
677 690 9.797642 AAGACATGCCATTTGATACATAGAATA 57.202 29.630 0.00 0.00 0.00 1.75
678 691 9.445878 AGACATGCCATTTGATACATAGAATAG 57.554 33.333 0.00 0.00 0.00 1.73
679 692 9.440773 GACATGCCATTTGATACATAGAATAGA 57.559 33.333 0.00 0.00 0.00 1.98
680 693 9.797642 ACATGCCATTTGATACATAGAATAGAA 57.202 29.630 0.00 0.00 0.00 2.10
780 793 7.334844 GAATTCATTCCTACTAACCAAAGGG 57.665 40.000 0.00 0.00 41.29 3.95
837 850 9.403583 TCATATCCTACAAAATTCCTACAAACC 57.596 33.333 0.00 0.00 0.00 3.27
838 851 9.184523 CATATCCTACAAAATTCCTACAAACCA 57.815 33.333 0.00 0.00 0.00 3.67
839 852 9.762381 ATATCCTACAAAATTCCTACAAACCAA 57.238 29.630 0.00 0.00 0.00 3.67
840 853 7.279750 TCCTACAAAATTCCTACAAACCAAC 57.720 36.000 0.00 0.00 0.00 3.77
841 854 6.265876 TCCTACAAAATTCCTACAAACCAACC 59.734 38.462 0.00 0.00 0.00 3.77
842 855 5.941555 ACAAAATTCCTACAAACCAACCA 57.058 34.783 0.00 0.00 0.00 3.67
843 856 5.912892 ACAAAATTCCTACAAACCAACCAG 58.087 37.500 0.00 0.00 0.00 4.00
844 857 5.659079 ACAAAATTCCTACAAACCAACCAGA 59.341 36.000 0.00 0.00 0.00 3.86
845 858 6.326323 ACAAAATTCCTACAAACCAACCAGAT 59.674 34.615 0.00 0.00 0.00 2.90
846 859 6.590234 AAATTCCTACAAACCAACCAGATC 57.410 37.500 0.00 0.00 0.00 2.75
852 865 6.443849 TCCTACAAACCAACCAGATCTTAGAT 59.556 38.462 0.00 0.00 0.00 1.98
858 871 4.536090 ACCAACCAGATCTTAGATTCCACA 59.464 41.667 0.00 0.00 0.00 4.17
859 872 5.121811 CCAACCAGATCTTAGATTCCACAG 58.878 45.833 0.00 0.00 0.00 3.66
866 879 2.768527 TCTTAGATTCCACAGAGCTGGG 59.231 50.000 0.00 0.00 34.19 4.45
894 907 6.071391 ACCTTTGCAGTTTATACATTTCCCTG 60.071 38.462 0.00 0.00 0.00 4.45
896 909 5.186256 TGCAGTTTATACATTTCCCTGGA 57.814 39.130 0.00 0.00 0.00 3.86
909 927 4.808414 TTCCCTGGAATCTATGCGATAG 57.192 45.455 0.00 0.00 0.00 2.08
911 929 2.419297 CCCTGGAATCTATGCGATAGGC 60.419 54.545 0.00 0.00 43.96 3.93
915 933 4.093743 TGGAATCTATGCGATAGGCCTTA 58.906 43.478 12.58 0.00 42.61 2.69
917 935 5.053145 GGAATCTATGCGATAGGCCTTATG 58.947 45.833 12.58 1.20 42.61 1.90
918 936 5.395768 GGAATCTATGCGATAGGCCTTATGT 60.396 44.000 12.58 0.00 42.61 2.29
919 937 4.456280 TCTATGCGATAGGCCTTATGTG 57.544 45.455 12.58 0.00 42.61 3.21
922 940 1.760029 TGCGATAGGCCTTATGTGTCA 59.240 47.619 12.58 0.00 42.61 3.58
933 951 8.451908 AGGCCTTATGTGTCACTTAAAATATC 57.548 34.615 0.00 2.77 0.00 1.63
938 956 9.373750 CTTATGTGTCACTTAAAATATCGCATG 57.626 33.333 11.29 0.00 0.00 4.06
939 957 6.117911 TGTGTCACTTAAAATATCGCATGG 57.882 37.500 4.27 0.00 0.00 3.66
940 958 4.970003 GTGTCACTTAAAATATCGCATGGC 59.030 41.667 0.00 0.00 0.00 4.40
955 975 2.202864 GGCGCAGAGCTTCCTCTC 60.203 66.667 10.83 0.00 45.21 3.20
956 976 2.581953 GCGCAGAGCTTCCTCTCG 60.582 66.667 0.30 0.00 45.21 4.04
999 3586 6.144563 GCAAACCTCTCAAATCAAGCTAAAAC 59.855 38.462 0.00 0.00 0.00 2.43
1002 3589 4.766891 CCTCTCAAATCAAGCTAAAACCCA 59.233 41.667 0.00 0.00 0.00 4.51
1026 3614 6.813649 CACAAGCAAGAAGAGTAGTAGCATTA 59.186 38.462 0.00 0.00 0.00 1.90
1027 3615 7.009999 CACAAGCAAGAAGAGTAGTAGCATTAG 59.990 40.741 0.00 0.00 0.00 1.73
1028 3616 5.596845 AGCAAGAAGAGTAGTAGCATTAGC 58.403 41.667 0.00 0.00 42.56 3.09
1029 3617 5.127845 AGCAAGAAGAGTAGTAGCATTAGCA 59.872 40.000 0.00 0.00 45.49 3.49
1030 3618 5.988561 GCAAGAAGAGTAGTAGCATTAGCAT 59.011 40.000 0.00 0.00 45.49 3.79
1031 3619 7.014711 AGCAAGAAGAGTAGTAGCATTAGCATA 59.985 37.037 0.00 0.00 45.49 3.14
1033 3621 6.904498 AGAAGAGTAGTAGCATTAGCATACG 58.096 40.000 0.00 0.00 45.49 3.06
1050 3638 1.446099 CGAGTGTGTACTGCCGCAT 60.446 57.895 0.00 0.00 37.25 4.73
1052 3640 1.560923 GAGTGTGTACTGCCGCATAG 58.439 55.000 0.00 0.00 37.25 2.23
1053 3641 0.175760 AGTGTGTACTGCCGCATAGG 59.824 55.000 0.00 0.00 44.97 2.57
1222 3842 2.695646 GCGAAGATCAACGGCGAC 59.304 61.111 16.62 0.00 0.00 5.19
1246 3866 0.322816 AGGCATGCAAATCGTCAGGT 60.323 50.000 21.36 0.00 0.00 4.00
1437 4131 5.041940 CGGGTACAGAGCTCTTGTTTATAC 58.958 45.833 15.27 10.22 0.00 1.47
1440 4134 5.972382 GGTACAGAGCTCTTGTTTATACGAG 59.028 44.000 15.27 0.15 37.16 4.18
1456 4154 8.443937 GTTTATACGAGCTGTTCTCTTGATTTT 58.556 33.333 0.00 0.00 39.70 1.82
1466 4164 7.377766 TGTTCTCTTGATTTTTATTCCTCGG 57.622 36.000 0.00 0.00 0.00 4.63
1467 4165 6.374333 TGTTCTCTTGATTTTTATTCCTCGGG 59.626 38.462 0.00 0.00 0.00 5.14
1468 4166 6.062258 TCTCTTGATTTTTATTCCTCGGGT 57.938 37.500 0.00 0.00 0.00 5.28
1469 4167 6.113411 TCTCTTGATTTTTATTCCTCGGGTC 58.887 40.000 0.00 0.00 0.00 4.46
1498 4205 2.437359 ATGCAGAGCCTGGCGAAC 60.437 61.111 13.96 9.12 31.21 3.95
1499 4206 2.964310 ATGCAGAGCCTGGCGAACT 61.964 57.895 13.96 11.31 31.21 3.01
1516 4223 5.064707 GGCGAACTTGTGTGATGTGTATATT 59.935 40.000 0.00 0.00 0.00 1.28
1567 4277 7.232330 TGTGATGTGTATTTCCTTTTCATTGGA 59.768 33.333 0.00 0.00 0.00 3.53
1568 4278 8.087750 GTGATGTGTATTTCCTTTTCATTGGAA 58.912 33.333 0.00 0.00 40.21 3.53
1569 4279 8.814931 TGATGTGTATTTCCTTTTCATTGGAAT 58.185 29.630 0.00 0.00 41.36 3.01
1570 4280 9.657419 GATGTGTATTTCCTTTTCATTGGAATT 57.343 29.630 0.00 0.00 41.36 2.17
1608 4318 1.273886 GCCTTCTCTTCTTCGAGGTGT 59.726 52.381 0.00 0.00 0.00 4.16
1617 4328 6.998673 TCTCTTCTTCGAGGTGTCATATATCA 59.001 38.462 0.00 0.00 0.00 2.15
1619 4330 5.358298 TCTTCGAGGTGTCATATATCACG 57.642 43.478 0.00 0.00 35.67 4.35
1620 4331 4.215613 TCTTCGAGGTGTCATATATCACGG 59.784 45.833 0.00 0.00 35.67 4.94
1623 4334 3.579709 GAGGTGTCATATATCACGGCTG 58.420 50.000 0.00 0.00 35.67 4.85
1694 4406 3.961729 GGTTGAAACCCTCGTCCG 58.038 61.111 0.36 0.00 43.43 4.79
1696 4408 1.226030 GGTTGAAACCCTCGTCCGTG 61.226 60.000 0.36 0.00 43.43 4.94
1699 4411 1.666872 GAAACCCTCGTCCGTGGTG 60.667 63.158 6.99 1.99 31.32 4.17
1712 4424 3.017442 TCCGTGGTGTCATTGTTTTTCA 58.983 40.909 0.00 0.00 0.00 2.69
1719 4431 5.065731 TGGTGTCATTGTTTTTCAAAATGGC 59.934 36.000 0.00 0.00 39.62 4.40
1721 4433 6.238703 GGTGTCATTGTTTTTCAAAATGGCAT 60.239 34.615 5.34 0.00 44.88 4.40
1722 4434 7.041508 GGTGTCATTGTTTTTCAAAATGGCATA 60.042 33.333 0.00 0.00 44.88 3.14
1729 4441 9.784531 TTGTTTTTCAAAATGGCATAATTCCTA 57.215 25.926 0.00 0.00 32.64 2.94
1731 4443 9.213799 GTTTTTCAAAATGGCATAATTCCTACA 57.786 29.630 0.00 0.00 0.00 2.74
1773 4486 4.635765 TGCTGATTCATTAGAGAAAACCGG 59.364 41.667 0.00 0.00 0.00 5.28
1774 4487 4.496507 GCTGATTCATTAGAGAAAACCGGC 60.497 45.833 0.00 0.00 0.00 6.13
1777 4490 1.551430 TCATTAGAGAAAACCGGCCGA 59.449 47.619 30.73 1.48 0.00 5.54
1782 4495 0.949397 GAGAAAACCGGCCGAAAACT 59.051 50.000 30.73 18.41 0.00 2.66
1784 4497 2.549329 GAGAAAACCGGCCGAAAACTAA 59.451 45.455 30.73 0.00 0.00 2.24
1789 4502 1.068125 ACCGGCCGAAAACTAAATTGC 60.068 47.619 30.73 0.00 0.00 3.56
1791 4504 1.201414 CGGCCGAAAACTAAATTGCCT 59.799 47.619 24.07 0.00 35.28 4.75
1793 4506 3.119779 CGGCCGAAAACTAAATTGCCTAA 60.120 43.478 24.07 0.00 35.28 2.69
1814 4527 9.394477 GCCTAATTAATTATGAAAAACTAGGCG 57.606 33.333 12.94 0.00 38.61 5.52
1837 4550 4.974368 AAAAATGTCACAACCGTTGAGA 57.026 36.364 18.19 12.50 0.00 3.27
1838 4551 4.552166 AAAATGTCACAACCGTTGAGAG 57.448 40.909 18.19 7.40 30.95 3.20
1839 4552 3.469008 AATGTCACAACCGTTGAGAGA 57.531 42.857 18.19 13.86 30.95 3.10
1840 4553 2.509052 TGTCACAACCGTTGAGAGAG 57.491 50.000 18.19 2.86 30.95 3.20
1845 4558 1.006102 AACCGTTGAGAGAGGCACG 60.006 57.895 0.00 0.00 0.00 5.34
1851 4564 2.346803 GTTGAGAGAGGCACGCATAAA 58.653 47.619 0.00 0.00 0.00 1.40
1856 4569 4.141937 TGAGAGAGGCACGCATAAAATACT 60.142 41.667 0.00 0.00 0.00 2.12
1866 4579 5.294306 CACGCATAAAATACTCCACTCACAT 59.706 40.000 0.00 0.00 0.00 3.21
1871 4584 7.254590 GCATAAAATACTCCACTCACATCACTC 60.255 40.741 0.00 0.00 0.00 3.51
1878 4591 5.719085 ACTCCACTCACATCACTCTAAAGAT 59.281 40.000 0.00 0.00 0.00 2.40
1885 4598 4.574013 CACATCACTCTAAAGATGGCCTTC 59.426 45.833 10.66 10.66 44.50 3.46
1887 4600 2.505819 TCACTCTAAAGATGGCCTTCCC 59.494 50.000 14.77 0.00 33.02 3.97
1897 4610 2.586792 GCCTTCCCGAGACAGCAT 59.413 61.111 0.00 0.00 0.00 3.79
1898 4611 1.817099 GCCTTCCCGAGACAGCATG 60.817 63.158 0.00 0.00 46.00 4.06
1911 4624 4.420143 GCATGTAGCCGTCATCGT 57.580 55.556 0.00 0.00 37.23 3.73
1917 4630 1.681264 TGTAGCCGTCATCGTCATCAT 59.319 47.619 0.00 0.00 35.01 2.45
1919 4632 2.315925 AGCCGTCATCGTCATCATTT 57.684 45.000 0.00 0.00 35.01 2.32
1920 4633 2.205074 AGCCGTCATCGTCATCATTTC 58.795 47.619 0.00 0.00 35.01 2.17
1921 4634 2.159043 AGCCGTCATCGTCATCATTTCT 60.159 45.455 0.00 0.00 35.01 2.52
1922 4635 2.033407 GCCGTCATCGTCATCATTTCTG 60.033 50.000 0.00 0.00 35.01 3.02
1923 4636 3.447742 CCGTCATCGTCATCATTTCTGA 58.552 45.455 0.00 0.00 33.66 3.27
1924 4637 3.865164 CCGTCATCGTCATCATTTCTGAA 59.135 43.478 0.00 0.00 33.17 3.02
1925 4638 4.509230 CCGTCATCGTCATCATTTCTGAAT 59.491 41.667 0.00 0.00 33.17 2.57
1926 4639 5.691754 CCGTCATCGTCATCATTTCTGAATA 59.308 40.000 0.00 0.00 33.17 1.75
1927 4640 6.128982 CCGTCATCGTCATCATTTCTGAATAG 60.129 42.308 0.00 0.00 33.17 1.73
1928 4641 6.638468 CGTCATCGTCATCATTTCTGAATAGA 59.362 38.462 0.00 0.00 34.37 1.98
1929 4642 7.357941 CGTCATCGTCATCATTTCTGAATAGAC 60.358 40.741 0.00 0.00 34.37 2.59
1930 4643 6.638468 TCATCGTCATCATTTCTGAATAGACG 59.362 38.462 16.87 16.87 45.89 4.18
1931 4644 4.740205 TCGTCATCATTTCTGAATAGACGC 59.260 41.667 17.58 4.27 45.12 5.19
1932 4645 4.374409 CGTCATCATTTCTGAATAGACGCG 60.374 45.833 3.53 3.53 42.56 6.01
1933 4646 4.504461 GTCATCATTTCTGAATAGACGCGT 59.496 41.667 13.85 13.85 34.37 6.01
1934 4647 4.740205 TCATCATTTCTGAATAGACGCGTC 59.260 41.667 31.30 31.30 34.37 5.19
1935 4648 4.104696 TCATTTCTGAATAGACGCGTCA 57.895 40.909 37.85 24.72 31.21 4.35
1936 4649 4.682787 TCATTTCTGAATAGACGCGTCAT 58.317 39.130 37.85 25.71 31.21 3.06
1937 4650 4.504097 TCATTTCTGAATAGACGCGTCATG 59.496 41.667 37.85 27.18 31.21 3.07
1948 4661 1.211181 CGCGTCATGCATCGTCATCT 61.211 55.000 9.25 0.00 46.97 2.90
1955 4668 5.046529 GTCATGCATCGTCATCTCTAAACT 58.953 41.667 0.00 0.00 0.00 2.66
1957 4670 4.046938 TGCATCGTCATCTCTAAACTCC 57.953 45.455 0.00 0.00 0.00 3.85
1970 4683 1.499049 AAACTCCGAGCAAACGACTC 58.501 50.000 0.00 0.00 35.09 3.36
1977 4690 1.499049 GAGCAAACGACTCCGACTTT 58.501 50.000 0.00 0.00 39.50 2.66
1978 4691 2.669364 GAGCAAACGACTCCGACTTTA 58.331 47.619 0.00 0.00 39.50 1.85
1979 4692 3.054878 GAGCAAACGACTCCGACTTTAA 58.945 45.455 0.00 0.00 39.50 1.52
1980 4693 2.798847 AGCAAACGACTCCGACTTTAAC 59.201 45.455 0.00 0.00 39.50 2.01
1983 4696 2.322371 ACGACTCCGACTTTAACGTC 57.678 50.000 2.07 2.07 39.50 4.34
1991 4704 2.414768 GACTTTAACGTCGGCGATTG 57.585 50.000 20.03 11.95 42.00 2.67
1992 4705 1.723003 GACTTTAACGTCGGCGATTGT 59.277 47.619 20.03 12.69 42.00 2.71
1993 4706 1.723003 ACTTTAACGTCGGCGATTGTC 59.277 47.619 20.03 0.00 42.00 3.18
1994 4707 1.722464 CTTTAACGTCGGCGATTGTCA 59.278 47.619 20.03 0.00 42.00 3.58
1995 4708 1.342555 TTAACGTCGGCGATTGTCAG 58.657 50.000 20.03 3.45 42.00 3.51
1996 4709 1.074319 TAACGTCGGCGATTGTCAGC 61.074 55.000 20.03 0.00 42.00 4.26
1997 4710 2.507102 CGTCGGCGATTGTCAGCT 60.507 61.111 14.79 0.00 41.33 4.24
2006 4719 1.609061 CGATTGTCAGCTCAACCCACT 60.609 52.381 0.00 0.00 0.00 4.00
2008 4721 0.249868 TTGTCAGCTCAACCCACTCG 60.250 55.000 0.00 0.00 0.00 4.18
2097 4853 0.039798 TCCGACTCCGACAAAGAACG 60.040 55.000 0.00 0.00 38.22 3.95
2110 4866 1.605753 AAGAACGGCAAAGGAGAACC 58.394 50.000 0.00 0.00 0.00 3.62
2130 4886 1.391157 AAACACGGCTGGCACACAAT 61.391 50.000 1.08 0.00 0.00 2.71
2134 4890 2.260154 CGGCTGGCACACAATCACA 61.260 57.895 1.08 0.00 0.00 3.58
2135 4891 1.582968 GGCTGGCACACAATCACAG 59.417 57.895 0.00 0.00 0.00 3.66
2136 4892 0.890542 GGCTGGCACACAATCACAGA 60.891 55.000 0.00 0.00 0.00 3.41
2137 4893 0.953727 GCTGGCACACAATCACAGAA 59.046 50.000 0.00 0.00 0.00 3.02
2138 4894 1.337703 GCTGGCACACAATCACAGAAA 59.662 47.619 0.00 0.00 0.00 2.52
2139 4895 2.223782 GCTGGCACACAATCACAGAAAA 60.224 45.455 0.00 0.00 0.00 2.29
2140 4896 3.374745 CTGGCACACAATCACAGAAAAC 58.625 45.455 0.00 0.00 0.00 2.43
2141 4897 2.223456 TGGCACACAATCACAGAAAACG 60.223 45.455 0.00 0.00 0.00 3.60
2142 4898 2.384382 GCACACAATCACAGAAAACGG 58.616 47.619 0.00 0.00 0.00 4.44
2143 4899 2.223479 GCACACAATCACAGAAAACGGT 60.223 45.455 0.00 0.00 0.00 4.83
2144 4900 3.362295 CACACAATCACAGAAAACGGTG 58.638 45.455 0.00 0.00 36.36 4.94
2145 4901 3.013921 ACACAATCACAGAAAACGGTGT 58.986 40.909 0.00 0.00 36.43 4.16
2146 4902 4.034626 CACACAATCACAGAAAACGGTGTA 59.965 41.667 0.00 0.00 36.57 2.90
2147 4903 4.034742 ACACAATCACAGAAAACGGTGTAC 59.965 41.667 0.00 0.00 36.57 2.90
2148 4904 4.272504 CACAATCACAGAAAACGGTGTACT 59.727 41.667 0.00 0.00 36.43 2.73
2149 4905 4.510340 ACAATCACAGAAAACGGTGTACTC 59.490 41.667 0.00 0.00 36.43 2.59
2150 4906 4.602340 ATCACAGAAAACGGTGTACTCT 57.398 40.909 0.00 0.00 36.43 3.24
2151 4907 3.973657 TCACAGAAAACGGTGTACTCTC 58.026 45.455 0.00 0.00 36.43 3.20
2152 4908 2.724690 CACAGAAAACGGTGTACTCTCG 59.275 50.000 0.00 0.00 0.00 4.04
2153 4909 2.288030 ACAGAAAACGGTGTACTCTCGG 60.288 50.000 0.00 0.00 0.00 4.63
2154 4910 1.271656 AGAAAACGGTGTACTCTCGGG 59.728 52.381 0.00 0.00 0.00 5.14
2155 4911 1.270550 GAAAACGGTGTACTCTCGGGA 59.729 52.381 0.00 0.00 0.00 5.14
2156 4912 0.600057 AAACGGTGTACTCTCGGGAC 59.400 55.000 0.00 0.00 0.00 4.46
2157 4913 0.251077 AACGGTGTACTCTCGGGACT 60.251 55.000 0.00 0.00 0.00 3.85
2158 4914 0.615331 ACGGTGTACTCTCGGGACTA 59.385 55.000 0.00 0.00 0.00 2.59
2159 4915 1.003580 ACGGTGTACTCTCGGGACTAA 59.996 52.381 0.00 0.00 0.00 2.24
2160 4916 2.086869 CGGTGTACTCTCGGGACTAAA 58.913 52.381 0.00 0.00 0.00 1.85
2161 4917 2.159462 CGGTGTACTCTCGGGACTAAAC 60.159 54.545 0.00 0.00 0.00 2.01
2162 4918 3.087781 GGTGTACTCTCGGGACTAAACT 58.912 50.000 0.00 0.00 0.00 2.66
2163 4919 3.119566 GGTGTACTCTCGGGACTAAACTG 60.120 52.174 0.00 0.00 0.00 3.16
2164 4920 2.490903 TGTACTCTCGGGACTAAACTGC 59.509 50.000 0.00 0.00 0.00 4.40
2165 4921 1.629043 ACTCTCGGGACTAAACTGCA 58.371 50.000 0.00 0.00 0.00 4.41
2166 4922 1.968493 ACTCTCGGGACTAAACTGCAA 59.032 47.619 0.00 0.00 0.00 4.08
2183 4939 3.347216 TGCAAAGAAGTTCATCTAGCCC 58.653 45.455 5.50 0.00 32.60 5.19
2199 4955 0.672711 GCCCAGGAAACGGTGTACTC 60.673 60.000 0.00 0.00 0.00 2.59
2211 4967 1.801178 GGTGTACTCTCAGCACAAAGC 59.199 52.381 0.00 0.00 46.19 3.51
2240 4996 1.398958 GGGGACACAAGCCAGCAAAA 61.399 55.000 0.00 0.00 0.00 2.44
2241 4997 0.032540 GGGACACAAGCCAGCAAAAG 59.967 55.000 0.00 0.00 0.00 2.27
2242 4998 0.598419 GGACACAAGCCAGCAAAAGC 60.598 55.000 0.00 0.00 0.00 3.51
2243 4999 0.598419 GACACAAGCCAGCAAAAGCC 60.598 55.000 0.00 0.00 0.00 4.35
2286 5042 4.158384 GCACATGAAGGTCATACAAAACG 58.842 43.478 0.00 0.00 34.28 3.60
2287 5043 4.083537 GCACATGAAGGTCATACAAAACGA 60.084 41.667 0.00 0.00 34.28 3.85
2316 5072 7.484035 ACAAATCTAAGAAACGATATGAGGC 57.516 36.000 0.00 0.00 0.00 4.70
2317 5073 6.201044 ACAAATCTAAGAAACGATATGAGGCG 59.799 38.462 0.00 0.00 0.00 5.52
2333 5089 2.534903 GCGGGCATAAAGTCGCTCC 61.535 63.158 0.00 0.00 44.10 4.70
2334 5090 1.887707 CGGGCATAAAGTCGCTCCC 60.888 63.158 0.00 0.00 0.00 4.30
2383 5139 0.237498 CATATGCATGGCTGTCAGCG 59.763 55.000 18.44 6.31 43.62 5.18
2389 5145 0.725686 CATGGCTGTCAGCGAAAGAG 59.274 55.000 18.44 3.57 43.62 2.85
2408 5165 2.559785 GCCATGCCATATTCTCCCG 58.440 57.895 0.00 0.00 0.00 5.14
2433 5190 0.446222 CATGGTACGTGCCCTTTTCG 59.554 55.000 20.66 0.00 0.00 3.46
2436 5193 1.293963 GGTACGTGCCCTTTTCGTCC 61.294 60.000 12.25 0.00 38.69 4.79
2466 5241 3.950397 TCAATTACGCCAACCTTCTCAT 58.050 40.909 0.00 0.00 0.00 2.90
2502 5277 2.064387 CGTGTGTAAACCGCGGTAG 58.936 57.895 34.44 11.50 32.48 3.18
2520 5295 2.747855 GGAACCTGAAGGCGCTGG 60.748 66.667 7.64 4.89 39.32 4.85
2539 5314 1.575576 GCTTGCTGCAGGAGACACTG 61.576 60.000 17.12 1.87 42.31 3.66
2545 5320 2.262915 CAGGAGACACTGCCGACC 59.737 66.667 0.00 0.00 0.00 4.79
2558 5335 2.031360 CCGACCGGAGAGATACCAC 58.969 63.158 9.46 0.00 37.50 4.16
2561 5338 1.033574 GACCGGAGAGATACCACCAG 58.966 60.000 9.46 0.00 0.00 4.00
2562 5339 1.043673 ACCGGAGAGATACCACCAGC 61.044 60.000 9.46 0.00 0.00 4.85
2566 5343 1.139853 GGAGAGATACCACCAGCAAGG 59.860 57.143 0.00 0.00 45.67 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 99 0.750546 TCATAGCTCGTAGGCCGTGT 60.751 55.000 0.00 0.00 37.94 4.49
246 258 1.869342 CGCCACACATCGAGATATGCA 60.869 52.381 0.00 0.00 0.00 3.96
387 399 1.352156 CGTAAGCCACAGCGAGAACC 61.352 60.000 0.00 0.00 46.67 3.62
453 465 1.064685 GGCCCAAAGTAGTGTAGGCAT 60.065 52.381 0.00 0.00 42.29 4.40
548 561 3.083386 CCTAAAACCCAGGCCCGA 58.917 61.111 0.00 0.00 0.00 5.14
553 566 2.447443 GAAAGAGGCCTAAAACCCAGG 58.553 52.381 4.42 0.00 36.16 4.45
554 567 2.041755 AGGAAAGAGGCCTAAAACCCAG 59.958 50.000 4.42 0.00 32.92 4.45
555 568 2.070573 AGGAAAGAGGCCTAAAACCCA 58.929 47.619 4.42 0.00 32.92 4.51
556 569 2.901338 AGGAAAGAGGCCTAAAACCC 57.099 50.000 4.42 3.65 32.92 4.11
557 570 4.149598 TCAAAGGAAAGAGGCCTAAAACC 58.850 43.478 4.42 7.90 33.76 3.27
558 571 5.984695 ATCAAAGGAAAGAGGCCTAAAAC 57.015 39.130 4.42 0.00 33.76 2.43
559 572 7.410174 TCATATCAAAGGAAAGAGGCCTAAAA 58.590 34.615 4.42 0.00 33.76 1.52
560 573 6.969043 TCATATCAAAGGAAAGAGGCCTAAA 58.031 36.000 4.42 0.00 33.76 1.85
561 574 6.575244 TCATATCAAAGGAAAGAGGCCTAA 57.425 37.500 4.42 0.00 33.76 2.69
562 575 6.770286 ATCATATCAAAGGAAAGAGGCCTA 57.230 37.500 4.42 0.00 33.76 3.93
563 576 5.659849 ATCATATCAAAGGAAAGAGGCCT 57.340 39.130 3.86 3.86 37.35 5.19
564 577 6.773638 TCTATCATATCAAAGGAAAGAGGCC 58.226 40.000 0.00 0.00 0.00 5.19
565 578 7.936301 AGTTCTATCATATCAAAGGAAAGAGGC 59.064 37.037 0.00 0.00 0.00 4.70
639 652 9.859427 CAAATGGCATGTCTTTCTCTATAAAAA 57.141 29.630 0.00 0.00 0.00 1.94
640 653 9.241919 TCAAATGGCATGTCTTTCTCTATAAAA 57.758 29.630 0.00 0.00 0.00 1.52
641 654 8.806429 TCAAATGGCATGTCTTTCTCTATAAA 57.194 30.769 0.00 0.00 0.00 1.40
642 655 8.985315 ATCAAATGGCATGTCTTTCTCTATAA 57.015 30.769 0.00 0.00 0.00 0.98
643 656 9.494271 GTATCAAATGGCATGTCTTTCTCTATA 57.506 33.333 0.00 0.00 0.00 1.31
644 657 7.994911 TGTATCAAATGGCATGTCTTTCTCTAT 59.005 33.333 0.00 0.00 0.00 1.98
645 658 7.337938 TGTATCAAATGGCATGTCTTTCTCTA 58.662 34.615 0.00 0.00 0.00 2.43
646 659 6.182627 TGTATCAAATGGCATGTCTTTCTCT 58.817 36.000 0.00 0.00 0.00 3.10
647 660 6.441093 TGTATCAAATGGCATGTCTTTCTC 57.559 37.500 0.00 0.00 0.00 2.87
648 661 7.994911 TCTATGTATCAAATGGCATGTCTTTCT 59.005 33.333 0.00 0.00 0.00 2.52
649 662 8.158169 TCTATGTATCAAATGGCATGTCTTTC 57.842 34.615 0.00 0.00 0.00 2.62
650 663 8.523915 TTCTATGTATCAAATGGCATGTCTTT 57.476 30.769 0.00 0.00 0.00 2.52
651 664 8.701908 ATTCTATGTATCAAATGGCATGTCTT 57.298 30.769 0.00 0.00 0.00 3.01
652 665 9.445878 CTATTCTATGTATCAAATGGCATGTCT 57.554 33.333 0.00 0.00 0.00 3.41
653 666 9.440773 TCTATTCTATGTATCAAATGGCATGTC 57.559 33.333 0.00 0.00 0.00 3.06
654 667 9.797642 TTCTATTCTATGTATCAAATGGCATGT 57.202 29.630 0.00 0.00 0.00 3.21
756 769 6.890268 ACCCTTTGGTTAGTAGGAATGAATTC 59.110 38.462 0.00 0.00 44.75 2.17
757 770 6.800890 ACCCTTTGGTTAGTAGGAATGAATT 58.199 36.000 0.00 0.00 44.75 2.17
758 771 6.402981 ACCCTTTGGTTAGTAGGAATGAAT 57.597 37.500 0.00 0.00 44.75 2.57
759 772 5.853572 ACCCTTTGGTTAGTAGGAATGAA 57.146 39.130 0.00 0.00 44.75 2.57
811 824 9.403583 GGTTTGTAGGAATTTTGTAGGATATGA 57.596 33.333 0.00 0.00 0.00 2.15
812 825 9.184523 TGGTTTGTAGGAATTTTGTAGGATATG 57.815 33.333 0.00 0.00 0.00 1.78
813 826 9.762381 TTGGTTTGTAGGAATTTTGTAGGATAT 57.238 29.630 0.00 0.00 0.00 1.63
814 827 9.016438 GTTGGTTTGTAGGAATTTTGTAGGATA 57.984 33.333 0.00 0.00 0.00 2.59
815 828 7.039293 GGTTGGTTTGTAGGAATTTTGTAGGAT 60.039 37.037 0.00 0.00 0.00 3.24
816 829 6.265876 GGTTGGTTTGTAGGAATTTTGTAGGA 59.734 38.462 0.00 0.00 0.00 2.94
817 830 6.041069 TGGTTGGTTTGTAGGAATTTTGTAGG 59.959 38.462 0.00 0.00 0.00 3.18
818 831 7.013846 TCTGGTTGGTTTGTAGGAATTTTGTAG 59.986 37.037 0.00 0.00 0.00 2.74
819 832 6.834451 TCTGGTTGGTTTGTAGGAATTTTGTA 59.166 34.615 0.00 0.00 0.00 2.41
820 833 5.659079 TCTGGTTGGTTTGTAGGAATTTTGT 59.341 36.000 0.00 0.00 0.00 2.83
821 834 6.155475 TCTGGTTGGTTTGTAGGAATTTTG 57.845 37.500 0.00 0.00 0.00 2.44
822 835 6.782494 AGATCTGGTTGGTTTGTAGGAATTTT 59.218 34.615 0.00 0.00 0.00 1.82
823 836 6.314917 AGATCTGGTTGGTTTGTAGGAATTT 58.685 36.000 0.00 0.00 0.00 1.82
824 837 5.892348 AGATCTGGTTGGTTTGTAGGAATT 58.108 37.500 0.00 0.00 0.00 2.17
825 838 5.520748 AGATCTGGTTGGTTTGTAGGAAT 57.479 39.130 0.00 0.00 0.00 3.01
826 839 4.993705 AGATCTGGTTGGTTTGTAGGAA 57.006 40.909 0.00 0.00 0.00 3.36
827 840 4.993705 AAGATCTGGTTGGTTTGTAGGA 57.006 40.909 0.00 0.00 0.00 2.94
828 841 6.049955 TCTAAGATCTGGTTGGTTTGTAGG 57.950 41.667 0.00 0.00 0.00 3.18
829 842 7.281100 GGAATCTAAGATCTGGTTGGTTTGTAG 59.719 40.741 0.00 0.00 0.00 2.74
830 843 7.110155 GGAATCTAAGATCTGGTTGGTTTGTA 58.890 38.462 0.00 0.00 0.00 2.41
831 844 5.946377 GGAATCTAAGATCTGGTTGGTTTGT 59.054 40.000 0.00 0.00 0.00 2.83
832 845 5.945784 TGGAATCTAAGATCTGGTTGGTTTG 59.054 40.000 0.00 0.00 0.00 2.93
833 846 5.946377 GTGGAATCTAAGATCTGGTTGGTTT 59.054 40.000 0.00 0.00 0.00 3.27
834 847 5.014123 TGTGGAATCTAAGATCTGGTTGGTT 59.986 40.000 0.00 0.00 0.00 3.67
835 848 4.536090 TGTGGAATCTAAGATCTGGTTGGT 59.464 41.667 0.00 0.00 0.00 3.67
836 849 5.102953 TGTGGAATCTAAGATCTGGTTGG 57.897 43.478 0.00 0.00 0.00 3.77
837 850 5.982356 TCTGTGGAATCTAAGATCTGGTTG 58.018 41.667 0.00 0.00 0.00 3.77
838 851 5.396213 GCTCTGTGGAATCTAAGATCTGGTT 60.396 44.000 0.00 0.00 0.00 3.67
839 852 4.100808 GCTCTGTGGAATCTAAGATCTGGT 59.899 45.833 0.00 0.00 0.00 4.00
840 853 4.344679 AGCTCTGTGGAATCTAAGATCTGG 59.655 45.833 0.00 0.00 0.00 3.86
841 854 5.291178 CAGCTCTGTGGAATCTAAGATCTG 58.709 45.833 0.00 0.00 29.57 2.90
842 855 4.344679 CCAGCTCTGTGGAATCTAAGATCT 59.655 45.833 0.00 0.00 40.44 2.75
843 856 4.502950 CCCAGCTCTGTGGAATCTAAGATC 60.503 50.000 0.00 0.00 40.44 2.75
844 857 3.390639 CCCAGCTCTGTGGAATCTAAGAT 59.609 47.826 0.00 0.00 40.44 2.40
845 858 2.768527 CCCAGCTCTGTGGAATCTAAGA 59.231 50.000 0.00 0.00 40.44 2.10
846 859 2.158842 CCCCAGCTCTGTGGAATCTAAG 60.159 54.545 0.00 0.00 40.44 2.18
852 865 1.198759 GGTACCCCAGCTCTGTGGAA 61.199 60.000 0.00 0.00 40.44 3.53
858 871 1.133809 TGCAAAGGTACCCCAGCTCT 61.134 55.000 8.74 0.00 32.46 4.09
859 872 0.678048 CTGCAAAGGTACCCCAGCTC 60.678 60.000 8.74 0.00 32.46 4.09
866 879 7.255569 GGAAATGTATAAACTGCAAAGGTACC 58.744 38.462 2.73 2.73 0.00 3.34
867 880 7.122204 AGGGAAATGTATAAACTGCAAAGGTAC 59.878 37.037 0.00 0.00 0.00 3.34
874 887 5.186256 TCCAGGGAAATGTATAAACTGCA 57.814 39.130 0.00 0.00 0.00 4.41
875 888 6.547510 AGATTCCAGGGAAATGTATAAACTGC 59.452 38.462 4.63 0.00 37.69 4.40
876 889 9.799106 ATAGATTCCAGGGAAATGTATAAACTG 57.201 33.333 4.63 0.00 37.69 3.16
888 901 3.515502 CCTATCGCATAGATTCCAGGGAA 59.484 47.826 2.75 2.75 40.66 3.97
889 902 3.099905 CCTATCGCATAGATTCCAGGGA 58.900 50.000 5.15 0.00 40.66 4.20
894 907 3.618690 AAGGCCTATCGCATAGATTCC 57.381 47.619 5.16 4.13 40.66 3.01
896 909 5.046304 ACACATAAGGCCTATCGCATAGATT 60.046 40.000 5.16 0.00 40.66 2.40
909 927 7.352739 CGATATTTTAAGTGACACATAAGGCC 58.647 38.462 8.59 0.00 0.00 5.19
911 929 7.915508 TGCGATATTTTAAGTGACACATAAGG 58.084 34.615 8.59 0.00 0.00 2.69
915 933 6.728200 CCATGCGATATTTTAAGTGACACAT 58.272 36.000 8.59 0.00 0.00 3.21
917 935 4.970003 GCCATGCGATATTTTAAGTGACAC 59.030 41.667 0.00 0.00 0.00 3.67
918 936 5.168526 GCCATGCGATATTTTAAGTGACA 57.831 39.130 0.00 0.00 0.00 3.58
938 956 2.202864 GAGAGGAAGCTCTGCGCC 60.203 66.667 4.18 0.00 40.39 6.53
939 957 2.581953 CGAGAGGAAGCTCTGCGC 60.582 66.667 0.00 0.00 39.57 6.09
940 958 1.719725 TAGCGAGAGGAAGCTCTGCG 61.720 60.000 0.00 0.00 43.44 5.18
941 959 0.673437 ATAGCGAGAGGAAGCTCTGC 59.327 55.000 0.00 0.00 43.44 4.26
944 962 5.293560 ACAATTTATAGCGAGAGGAAGCTC 58.706 41.667 0.00 0.00 43.44 4.09
955 975 2.942376 TGCCCAGTGACAATTTATAGCG 59.058 45.455 0.00 0.00 0.00 4.26
956 976 4.981806 TTGCCCAGTGACAATTTATAGC 57.018 40.909 0.00 0.00 0.00 2.97
999 3586 3.409026 ACTACTCTTCTTGCTTGTGGG 57.591 47.619 0.00 0.00 0.00 4.61
1002 3589 4.873746 TGCTACTACTCTTCTTGCTTGT 57.126 40.909 0.00 0.00 0.00 3.16
1026 3614 1.135083 GGCAGTACACACTCGTATGCT 60.135 52.381 0.00 0.00 30.46 3.79
1027 3615 1.278238 GGCAGTACACACTCGTATGC 58.722 55.000 0.00 0.00 30.46 3.14
1028 3616 1.545759 CGGCAGTACACACTCGTATG 58.454 55.000 0.00 0.00 30.46 2.39
1029 3617 0.179145 GCGGCAGTACACACTCGTAT 60.179 55.000 0.00 0.00 30.46 3.06
1030 3618 1.210931 GCGGCAGTACACACTCGTA 59.789 57.895 0.00 0.00 30.46 3.43
1031 3619 2.049433 GCGGCAGTACACACTCGT 60.049 61.111 0.00 0.00 30.46 4.18
1033 3621 1.560923 CTATGCGGCAGTACACACTC 58.439 55.000 9.25 0.00 30.46 3.51
1053 3641 1.553690 TAAGACTCCTGGGGCACAGC 61.554 60.000 12.38 0.00 46.14 4.40
1141 3755 3.738282 GGCTCGACACTAGCAAGATTATG 59.262 47.826 0.00 0.00 41.93 1.90
1222 3842 1.011904 CGATTTGCATGCCTCGTCG 60.012 57.895 16.68 15.27 0.00 5.12
1223 3843 2.089854 ACGATTTGCATGCCTCGTC 58.910 52.632 25.21 14.05 40.00 4.20
1224 3844 0.673333 TGACGATTTGCATGCCTCGT 60.673 50.000 28.73 28.73 46.09 4.18
1225 3845 0.027194 CTGACGATTTGCATGCCTCG 59.973 55.000 24.19 24.19 37.17 4.63
1404 4027 1.414181 CTCTGTACCCGATCCAGCATT 59.586 52.381 0.00 0.00 0.00 3.56
1411 4034 1.751924 ACAAGAGCTCTGTACCCGATC 59.248 52.381 19.06 0.00 0.00 3.69
1412 4035 1.853963 ACAAGAGCTCTGTACCCGAT 58.146 50.000 19.06 0.00 0.00 4.18
1413 4036 1.629043 AACAAGAGCTCTGTACCCGA 58.371 50.000 19.06 0.00 0.00 5.14
1414 4037 2.457366 AAACAAGAGCTCTGTACCCG 57.543 50.000 19.06 4.59 0.00 5.28
1440 4134 6.963805 CGAGGAATAAAAATCAAGAGAACAGC 59.036 38.462 0.00 0.00 0.00 4.40
1456 4154 1.143183 GCAGCGACCCGAGGAATAA 59.857 57.895 0.00 0.00 0.00 1.40
1516 4223 7.966204 CACGTTTTTCCTTCTCTTTCTAAAACA 59.034 33.333 0.00 0.00 35.07 2.83
1567 4277 6.220201 AGGCAACGCACAAACTTTATTAATT 58.780 32.000 0.00 0.00 46.39 1.40
1568 4278 5.778862 AGGCAACGCACAAACTTTATTAAT 58.221 33.333 0.00 0.00 46.39 1.40
1569 4279 5.189659 AGGCAACGCACAAACTTTATTAA 57.810 34.783 0.00 0.00 46.39 1.40
1570 4280 4.839668 AGGCAACGCACAAACTTTATTA 57.160 36.364 0.00 0.00 46.39 0.98
1608 4318 7.054491 ACATATATGCAGCCGTGATATATGA 57.946 36.000 24.28 0.00 41.51 2.15
1617 4328 0.037326 CGGGACATATATGCAGCCGT 60.037 55.000 12.79 0.00 0.00 5.68
1619 4330 2.418746 CCTACGGGACATATATGCAGCC 60.419 54.545 12.79 11.18 33.58 4.85
1620 4331 2.496070 TCCTACGGGACATATATGCAGC 59.504 50.000 12.79 2.78 36.57 5.25
1623 4334 4.219944 TGAACTCCTACGGGACATATATGC 59.780 45.833 12.79 5.71 36.57 3.14
1694 4406 6.485393 CCATTTTGAAAAACAATGACACCAC 58.515 36.000 0.00 0.00 38.36 4.16
1696 4408 5.065731 TGCCATTTTGAAAAACAATGACACC 59.934 36.000 0.00 0.00 38.36 4.16
1699 4411 9.896263 AATTATGCCATTTTGAAAAACAATGAC 57.104 25.926 0.00 0.00 38.36 3.06
1740 4452 7.667219 TCTCTAATGAATCAGCAACTCCTTTTT 59.333 33.333 0.00 0.00 0.00 1.94
1745 4457 6.992063 TTTCTCTAATGAATCAGCAACTCC 57.008 37.500 0.00 0.00 0.00 3.85
1746 4458 7.247019 GGTTTTCTCTAATGAATCAGCAACTC 58.753 38.462 0.00 0.00 0.00 3.01
1748 4460 6.024049 CGGTTTTCTCTAATGAATCAGCAAC 58.976 40.000 0.00 0.00 0.00 4.17
1749 4461 5.123820 CCGGTTTTCTCTAATGAATCAGCAA 59.876 40.000 0.00 0.00 0.00 3.91
1751 4463 4.496507 GCCGGTTTTCTCTAATGAATCAGC 60.497 45.833 1.90 0.00 0.00 4.26
1752 4464 4.035675 GGCCGGTTTTCTCTAATGAATCAG 59.964 45.833 1.90 0.00 0.00 2.90
1754 4466 3.002348 CGGCCGGTTTTCTCTAATGAATC 59.998 47.826 20.10 0.00 0.00 2.52
1755 4467 2.943033 CGGCCGGTTTTCTCTAATGAAT 59.057 45.455 20.10 0.00 0.00 2.57
1756 4468 2.027929 TCGGCCGGTTTTCTCTAATGAA 60.028 45.455 27.83 0.00 0.00 2.57
1757 4469 1.551430 TCGGCCGGTTTTCTCTAATGA 59.449 47.619 27.83 0.00 0.00 2.57
1759 4471 2.773993 TTCGGCCGGTTTTCTCTAAT 57.226 45.000 27.83 0.00 0.00 1.73
1760 4472 2.547299 TTTCGGCCGGTTTTCTCTAA 57.453 45.000 27.83 5.54 0.00 2.10
1761 4473 2.145536 GTTTTCGGCCGGTTTTCTCTA 58.854 47.619 27.83 0.00 0.00 2.43
1762 4474 0.949397 GTTTTCGGCCGGTTTTCTCT 59.051 50.000 27.83 0.00 0.00 3.10
1763 4475 0.949397 AGTTTTCGGCCGGTTTTCTC 59.051 50.000 27.83 9.66 0.00 2.87
1773 4486 8.642908 ATTAATTAGGCAATTTAGTTTTCGGC 57.357 30.769 0.00 0.00 35.88 5.54
1819 4532 3.393800 CTCTCTCAACGGTTGTGACATT 58.606 45.455 19.47 0.00 0.00 2.71
1820 4533 2.289072 CCTCTCTCAACGGTTGTGACAT 60.289 50.000 19.47 0.00 0.00 3.06
1821 4534 1.068588 CCTCTCTCAACGGTTGTGACA 59.931 52.381 19.47 10.12 0.00 3.58
1829 4542 2.811317 GCGTGCCTCTCTCAACGG 60.811 66.667 0.00 0.00 0.00 4.44
1837 4550 3.118408 TGGAGTATTTTATGCGTGCCTCT 60.118 43.478 0.00 0.00 0.00 3.69
1838 4551 3.002348 GTGGAGTATTTTATGCGTGCCTC 59.998 47.826 0.00 0.00 0.00 4.70
1839 4552 2.943033 GTGGAGTATTTTATGCGTGCCT 59.057 45.455 0.00 0.00 0.00 4.75
1840 4553 2.943033 AGTGGAGTATTTTATGCGTGCC 59.057 45.455 0.00 0.00 0.00 5.01
1845 4558 6.540189 AGTGATGTGAGTGGAGTATTTTATGC 59.460 38.462 0.00 0.00 0.00 3.14
1851 4564 7.397476 TCTTTAGAGTGATGTGAGTGGAGTATT 59.603 37.037 0.00 0.00 0.00 1.89
1856 4569 5.105187 CCATCTTTAGAGTGATGTGAGTGGA 60.105 44.000 0.00 0.00 38.59 4.02
1866 4579 2.505819 GGGAAGGCCATCTTTAGAGTGA 59.494 50.000 5.01 0.00 35.50 3.41
1871 4584 1.762957 TCTCGGGAAGGCCATCTTTAG 59.237 52.381 5.01 1.53 35.50 1.85
1878 4591 3.706373 GCTGTCTCGGGAAGGCCA 61.706 66.667 5.01 0.00 35.15 5.36
1885 4598 1.227380 GGCTACATGCTGTCTCGGG 60.227 63.158 0.00 0.00 42.39 5.14
1887 4600 4.003534 CGGCTACATGCTGTCTCG 57.996 61.111 0.00 0.00 42.87 4.04
1902 4615 3.447742 TCAGAAATGATGACGATGACGG 58.552 45.455 0.00 0.00 44.46 4.79
1903 4616 5.648033 ATTCAGAAATGATGACGATGACG 57.352 39.130 0.00 0.00 45.75 4.35
1911 4624 4.682787 ACGCGTCTATTCAGAAATGATGA 58.317 39.130 5.58 0.00 30.85 2.92
1917 4630 2.603110 GCATGACGCGTCTATTCAGAAA 59.397 45.455 36.27 16.10 30.85 2.52
1919 4632 1.134175 TGCATGACGCGTCTATTCAGA 59.866 47.619 36.27 17.59 46.97 3.27
1920 4633 1.559831 TGCATGACGCGTCTATTCAG 58.440 50.000 36.27 20.69 46.97 3.02
1921 4634 2.223537 ATGCATGACGCGTCTATTCA 57.776 45.000 36.27 26.59 46.97 2.57
1928 4641 1.482621 GATGACGATGCATGACGCGT 61.483 55.000 13.85 13.85 46.97 6.01
1929 4642 1.200103 GATGACGATGCATGACGCG 59.800 57.895 2.46 3.53 46.97 6.01
1930 4643 0.506080 GAGATGACGATGCATGACGC 59.494 55.000 2.46 0.00 42.89 5.19
1931 4644 2.131281 AGAGATGACGATGCATGACG 57.869 50.000 2.46 4.83 0.00 4.35
1932 4645 5.046529 AGTTTAGAGATGACGATGCATGAC 58.953 41.667 2.46 0.00 0.00 3.06
1933 4646 5.268118 AGTTTAGAGATGACGATGCATGA 57.732 39.130 2.46 0.00 0.00 3.07
1934 4647 4.447054 GGAGTTTAGAGATGACGATGCATG 59.553 45.833 2.46 0.00 0.00 4.06
1935 4648 4.626042 GGAGTTTAGAGATGACGATGCAT 58.374 43.478 0.00 0.00 0.00 3.96
1936 4649 3.489229 CGGAGTTTAGAGATGACGATGCA 60.489 47.826 0.00 0.00 0.00 3.96
1937 4650 3.046390 CGGAGTTTAGAGATGACGATGC 58.954 50.000 0.00 0.00 0.00 3.91
1948 4661 2.295349 AGTCGTTTGCTCGGAGTTTAGA 59.705 45.455 6.90 0.00 0.00 2.10
1955 4668 2.257371 CGGAGTCGTTTGCTCGGA 59.743 61.111 0.00 0.00 35.99 4.55
1957 4670 0.663568 AAGTCGGAGTCGTTTGCTCG 60.664 55.000 0.00 0.00 37.69 5.03
1977 4690 1.074319 GCTGACAATCGCCGACGTTA 61.074 55.000 0.00 0.00 41.18 3.18
1978 4691 2.380410 GCTGACAATCGCCGACGTT 61.380 57.895 0.00 0.00 41.18 3.99
1979 4692 2.809601 GCTGACAATCGCCGACGT 60.810 61.111 0.00 0.00 41.18 4.34
1980 4693 2.507102 AGCTGACAATCGCCGACG 60.507 61.111 0.00 0.00 42.01 5.12
1983 4696 1.421485 GTTGAGCTGACAATCGCCG 59.579 57.895 0.00 0.00 32.36 6.46
1986 4699 0.798776 GTGGGTTGAGCTGACAATCG 59.201 55.000 0.00 0.00 32.36 3.34
1990 4703 1.367471 CGAGTGGGTTGAGCTGACA 59.633 57.895 0.00 0.00 0.00 3.58
1991 4704 1.374758 CCGAGTGGGTTGAGCTGAC 60.375 63.158 0.00 0.00 0.00 3.51
1992 4705 3.059982 CCGAGTGGGTTGAGCTGA 58.940 61.111 0.00 0.00 0.00 4.26
2006 4719 2.016393 CTTCGCATGGCCTCTACCGA 62.016 60.000 3.32 2.20 0.00 4.69
2008 4721 1.889573 GCTTCGCATGGCCTCTACC 60.890 63.158 3.32 0.00 0.00 3.18
2015 4728 5.007136 GGATCTTTATATAGCTTCGCATGGC 59.993 44.000 0.00 0.00 0.00 4.40
2021 4734 9.307121 CCTAATGTGGATCTTTATATAGCTTCG 57.693 37.037 0.00 0.00 0.00 3.79
2039 4752 1.556911 AGGTGGCTGAGTCCTAATGTG 59.443 52.381 0.00 0.00 0.00 3.21
2042 4797 0.543749 GCAGGTGGCTGAGTCCTAAT 59.456 55.000 0.00 0.00 40.25 1.73
2044 4799 2.351244 CGCAGGTGGCTGAGTCCTA 61.351 63.158 0.00 0.00 41.67 2.94
2097 4853 1.269051 CGTGTTTGGTTCTCCTTTGCC 60.269 52.381 0.00 0.00 34.23 4.52
2110 4866 2.026014 GTGTGCCAGCCGTGTTTG 59.974 61.111 0.00 0.00 0.00 2.93
2130 4886 3.549423 CGAGAGTACACCGTTTTCTGTGA 60.549 47.826 0.00 0.00 38.19 3.58
2134 4890 1.271656 CCCGAGAGTACACCGTTTTCT 59.728 52.381 0.00 0.00 0.00 2.52
2135 4891 1.270550 TCCCGAGAGTACACCGTTTTC 59.729 52.381 0.00 0.00 0.00 2.29
2136 4892 1.000171 GTCCCGAGAGTACACCGTTTT 60.000 52.381 0.00 0.00 0.00 2.43
2137 4893 0.600057 GTCCCGAGAGTACACCGTTT 59.400 55.000 0.00 0.00 0.00 3.60
2138 4894 0.251077 AGTCCCGAGAGTACACCGTT 60.251 55.000 0.00 0.00 0.00 4.44
2139 4895 0.615331 TAGTCCCGAGAGTACACCGT 59.385 55.000 0.00 0.00 0.00 4.83
2140 4896 1.742761 TTAGTCCCGAGAGTACACCG 58.257 55.000 0.00 0.00 0.00 4.94
2141 4897 3.087781 AGTTTAGTCCCGAGAGTACACC 58.912 50.000 0.00 0.00 31.53 4.16
2142 4898 3.672781 GCAGTTTAGTCCCGAGAGTACAC 60.673 52.174 0.00 0.00 31.39 2.90
2143 4899 2.490903 GCAGTTTAGTCCCGAGAGTACA 59.509 50.000 0.00 0.00 0.00 2.90
2144 4900 2.490903 TGCAGTTTAGTCCCGAGAGTAC 59.509 50.000 0.00 0.00 0.00 2.73
2145 4901 2.799017 TGCAGTTTAGTCCCGAGAGTA 58.201 47.619 0.00 0.00 0.00 2.59
2146 4902 1.629043 TGCAGTTTAGTCCCGAGAGT 58.371 50.000 0.00 0.00 0.00 3.24
2147 4903 2.743636 TTGCAGTTTAGTCCCGAGAG 57.256 50.000 0.00 0.00 0.00 3.20
2148 4904 2.631062 TCTTTGCAGTTTAGTCCCGAGA 59.369 45.455 0.00 0.00 0.00 4.04
2149 4905 3.040147 TCTTTGCAGTTTAGTCCCGAG 57.960 47.619 0.00 0.00 0.00 4.63
2150 4906 3.181458 ACTTCTTTGCAGTTTAGTCCCGA 60.181 43.478 0.00 0.00 0.00 5.14
2151 4907 3.139077 ACTTCTTTGCAGTTTAGTCCCG 58.861 45.455 0.00 0.00 0.00 5.14
2152 4908 4.578928 TGAACTTCTTTGCAGTTTAGTCCC 59.421 41.667 0.00 0.00 34.49 4.46
2153 4909 5.751243 TGAACTTCTTTGCAGTTTAGTCC 57.249 39.130 0.00 0.00 34.49 3.85
2154 4910 7.195839 AGATGAACTTCTTTGCAGTTTAGTC 57.804 36.000 0.00 0.00 34.49 2.59
2155 4911 7.095017 GCTAGATGAACTTCTTTGCAGTTTAGT 60.095 37.037 0.00 0.00 34.49 2.24
2156 4912 7.239972 GCTAGATGAACTTCTTTGCAGTTTAG 58.760 38.462 0.00 0.00 34.49 1.85
2157 4913 6.149474 GGCTAGATGAACTTCTTTGCAGTTTA 59.851 38.462 0.00 0.00 34.49 2.01
2158 4914 5.048434 GGCTAGATGAACTTCTTTGCAGTTT 60.048 40.000 0.00 0.00 34.49 2.66
2159 4915 4.457257 GGCTAGATGAACTTCTTTGCAGTT 59.543 41.667 0.00 0.00 37.18 3.16
2160 4916 4.006319 GGCTAGATGAACTTCTTTGCAGT 58.994 43.478 0.00 0.00 0.00 4.40
2161 4917 3.376546 GGGCTAGATGAACTTCTTTGCAG 59.623 47.826 0.00 0.00 0.00 4.41
2162 4918 3.244875 TGGGCTAGATGAACTTCTTTGCA 60.245 43.478 0.00 0.00 0.00 4.08
2163 4919 3.347216 TGGGCTAGATGAACTTCTTTGC 58.653 45.455 0.00 0.00 0.00 3.68
2164 4920 3.944015 CCTGGGCTAGATGAACTTCTTTG 59.056 47.826 0.00 0.00 0.00 2.77
2165 4921 3.846588 TCCTGGGCTAGATGAACTTCTTT 59.153 43.478 0.00 0.00 0.00 2.52
2166 4922 3.454858 TCCTGGGCTAGATGAACTTCTT 58.545 45.455 0.00 0.00 0.00 2.52
2183 4939 2.927014 GCTGAGAGTACACCGTTTCCTG 60.927 54.545 0.00 0.00 0.00 3.86
2199 4955 1.800315 GCATGCGCTTTGTGCTGAG 60.800 57.895 9.73 0.00 40.03 3.35
2248 5004 2.126734 GCATTGACAGCCACGCAC 60.127 61.111 0.00 0.00 0.00 5.34
2312 5068 2.534903 GCGACTTTATGCCCGCCTC 61.535 63.158 0.00 0.00 41.59 4.70
2316 5072 1.887707 GGGAGCGACTTTATGCCCG 60.888 63.158 0.00 0.00 0.00 6.13
2317 5073 0.107165 AAGGGAGCGACTTTATGCCC 60.107 55.000 0.00 0.00 35.79 5.36
2333 5089 3.055719 ATGTTGGCCGCACGAAGG 61.056 61.111 0.00 0.00 0.00 3.46
2334 5090 2.176546 CATGTTGGCCGCACGAAG 59.823 61.111 0.00 0.00 0.00 3.79
2389 5145 3.337517 TCGGGAGAATATGGCATGGCC 62.338 57.143 17.72 8.02 42.85 5.36
2406 5163 1.809619 CACGTACCATGTGCCTCGG 60.810 63.158 0.00 0.00 0.00 4.63
2433 5190 1.268032 CGTAATTGATTGCTGCGGGAC 60.268 52.381 0.00 0.00 0.00 4.46
2436 5193 0.592247 GGCGTAATTGATTGCTGCGG 60.592 55.000 0.00 0.00 0.00 5.69
2474 5249 2.067013 GTTTACACACGGAGCTTCTCC 58.933 52.381 2.83 2.83 46.44 3.71
2475 5250 2.067013 GGTTTACACACGGAGCTTCTC 58.933 52.381 0.00 0.00 0.00 2.87
2502 5277 2.747855 CAGCGCCTTCAGGTTCCC 60.748 66.667 2.29 0.00 37.57 3.97
2516 5291 3.441290 CTCCTGCAGCAAGCCAGC 61.441 66.667 8.66 0.75 44.83 4.85
2517 5292 2.039405 GTCTCCTGCAGCAAGCCAG 61.039 63.158 8.66 0.00 44.83 4.85
2518 5293 2.033141 GTCTCCTGCAGCAAGCCA 59.967 61.111 8.66 0.00 44.83 4.75
2519 5294 2.033141 TGTCTCCTGCAGCAAGCC 59.967 61.111 8.66 0.00 44.83 4.35
2520 5295 1.302351 AGTGTCTCCTGCAGCAAGC 60.302 57.895 8.66 5.22 45.96 4.01
2530 5305 4.436998 CCGGTCGGCAGTGTCTCC 62.437 72.222 0.00 0.00 0.00 3.71
2539 5314 1.826921 TGGTATCTCTCCGGTCGGC 60.827 63.158 0.00 0.00 34.68 5.54
2545 5320 0.824109 TTGCTGGTGGTATCTCTCCG 59.176 55.000 0.00 0.00 0.00 4.63
2558 5335 1.207791 ATACTCCCACTCCTTGCTGG 58.792 55.000 0.00 0.00 37.10 4.85


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

AutoCloner maintained by Alex Coulton.