Multiple sequence alignment - TraesCS5B01G049800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G049800 chr5B 100.000 5551 0 0 1 5551 55306942 55312492 0.000000e+00 10251.0
1 TraesCS5B01G049800 chr5B 90.811 555 45 5 1 552 648756547 648755996 0.000000e+00 737.0
2 TraesCS5B01G049800 chr5D 94.021 2793 121 14 2350 5102 52255633 52258419 0.000000e+00 4191.0
3 TraesCS5B01G049800 chr5D 94.872 1443 47 8 919 2354 52253966 52255388 0.000000e+00 2230.0
4 TraesCS5B01G049800 chr5D 91.566 249 17 2 5305 5551 52260098 52260344 1.920000e-89 340.0
5 TraesCS5B01G049800 chr5D 92.135 89 4 3 4776 4863 481806104 481806190 7.550000e-24 122.0
6 TraesCS5B01G049800 chr5D 89.655 87 4 4 5202 5287 52258481 52258563 7.610000e-19 106.0
7 TraesCS5B01G049800 chr5D 94.737 57 2 1 556 612 52253918 52253973 2.750000e-13 87.9
8 TraesCS5B01G049800 chr5D 94.231 52 1 1 5100 5151 52258436 52258485 1.660000e-10 78.7
9 TraesCS5B01G049800 chr5A 94.201 2190 100 14 919 3098 41348468 41350640 0.000000e+00 3315.0
10 TraesCS5B01G049800 chr5A 96.535 1270 34 3 3528 4788 41350860 41352128 0.000000e+00 2093.0
11 TraesCS5B01G049800 chr5A 85.872 453 26 14 4837 5264 41352125 41352564 1.100000e-121 448.0
12 TraesCS5B01G049800 chr5A 92.544 228 15 1 3127 3352 41350639 41350866 5.360000e-85 326.0
13 TraesCS5B01G049800 chr5A 89.157 249 18 5 5305 5551 41354136 41354377 9.040000e-78 302.0
14 TraesCS5B01G049800 chr7A 92.266 556 39 3 1 553 725718229 725718783 0.000000e+00 785.0
15 TraesCS5B01G049800 chr7A 92.222 90 5 2 4775 4863 200703794 200703706 5.840000e-25 126.0
16 TraesCS5B01G049800 chr7A 91.111 90 6 2 4775 4863 460121980 460121892 2.720000e-23 121.0
17 TraesCS5B01G049800 chr6B 91.606 548 41 4 1 545 89066011 89065466 0.000000e+00 752.0
18 TraesCS5B01G049800 chr6D 92.453 159 10 1 389 545 456578384 456578226 5.600000e-55 226.0
19 TraesCS5B01G049800 chr4A 93.103 87 4 2 4779 4864 285485367 285485452 5.840000e-25 126.0
20 TraesCS5B01G049800 chr3D 93.023 86 5 1 4779 4863 278514945 278515030 2.100000e-24 124.0
21 TraesCS5B01G049800 chr2D 93.023 86 4 2 4779 4863 643235908 643235824 2.100000e-24 124.0
22 TraesCS5B01G049800 chr1D 93.023 86 5 1 4779 4863 349811153 349811068 2.100000e-24 124.0
23 TraesCS5B01G049800 chr7B 91.111 90 6 2 4775 4863 468196039 468195951 2.720000e-23 121.0


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 TraesCS5B01G049800 chr5B 55306942 55312492 5550 False 10251.000000 10251 100.000000 1 5551 1 chr5B.!!$F1 5550
1 TraesCS5B01G049800 chr5B 648755996 648756547 551 True 737.000000 737 90.811000 1 552 1 chr5B.!!$R1 551
2 TraesCS5B01G049800 chr5D 52253918 52260344 6426 False 1172.266667 4191 93.180333 556 5551 6 chr5D.!!$F2 4995
3 TraesCS5B01G049800 chr5A 41348468 41354377 5909 False 1296.800000 3315 91.661800 919 5551 5 chr5A.!!$F1 4632
4 TraesCS5B01G049800 chr7A 725718229 725718783 554 False 785.000000 785 92.266000 1 553 1 chr7A.!!$F1 552
5 TraesCS5B01G049800 chr6B 89065466 89066011 545 True 752.000000 752 91.606000 1 545 1 chr6B.!!$R1 544

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
634 637 0.035056 GACCTGTGCATGGGTAGCTT 60.035 55.0 12.51 0.0 35.77 3.74 F
838 841 0.037975 CTGTTCATGTGCTTTGGGCC 60.038 55.0 0.00 0.0 40.92 5.80 F
869 872 0.325203 GGCCTGGGCTTGGGATTTTA 60.325 55.0 13.80 0.0 41.60 1.52 F
916 919 0.822121 GCTCGGGGTTTGAACAGGTT 60.822 55.0 0.00 0.0 0.00 3.50 F
2315 2328 0.250166 GGACCTTGTGCCGTTGTACT 60.250 55.0 0.00 0.0 0.00 2.73 F
3356 3632 2.035961 CTGGACAGAAGAGTTCCGAACA 59.964 50.0 13.69 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1864 0.531753 TGCACGCAACAAGCAGACTA 60.532 50.000 0.00 0.00 46.13 2.59 R
1854 1865 1.375853 TTGCACGCAACAAGCAGACT 61.376 50.000 0.00 0.00 46.13 3.24 R
2095 2106 1.798813 CGGAGCAGTTAACTGACCAAC 59.201 52.381 34.43 18.47 46.59 3.77 R
2807 3069 3.952323 AGGTTGATCAATGCAATCCTGAG 59.048 43.478 12.12 0.00 30.78 3.35 R
3447 3744 1.220206 CTGACAGGCAGCTAGTGGG 59.780 63.158 0.00 0.00 37.90 4.61 R
4879 5187 1.511887 CCGCGGAAATTGTTGCTCG 60.512 57.895 24.07 0.00 33.62 5.03 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
17 18 4.577152 CACAACCTTGGTGCCTCA 57.423 55.556 0.00 0.00 0.00 3.86
35 36 1.770110 ACCCAAGCACTGGTCTCCA 60.770 57.895 4.33 0.00 44.76 3.86
65 66 1.899142 GGGTGGGCAAAGCTAAATTCA 59.101 47.619 0.00 0.00 0.00 2.57
81 82 6.982724 GCTAAATTCAGATGCAGCCTTTTTAT 59.017 34.615 0.00 0.00 0.00 1.40
85 86 3.949754 TCAGATGCAGCCTTTTTATCAGG 59.050 43.478 0.00 0.00 34.08 3.86
194 195 2.055042 AGTACAGGAGGCTGAGGCG 61.055 63.158 0.00 0.00 39.81 5.52
196 197 3.296842 TACAGGAGGCTGAGGCGGA 62.297 63.158 0.00 0.00 39.81 5.54
197 198 3.847602 CAGGAGGCTGAGGCGGAG 61.848 72.222 0.00 0.00 39.81 4.63
247 248 6.500684 TGCAAAGAGATACAATGGAAGAAC 57.499 37.500 0.00 0.00 0.00 3.01
292 293 6.596309 TTCAGTTGATAGAGAGCTGAGAAA 57.404 37.500 0.00 0.00 37.47 2.52
312 313 2.643551 ACACCACAGTTGGAGTTTCAG 58.356 47.619 0.00 0.00 43.62 3.02
326 327 3.879892 GAGTTTCAGAATGCTACCCCATC 59.120 47.826 0.00 0.00 34.76 3.51
351 352 1.338105 CGGACATCAGGCAAACTCTGA 60.338 52.381 0.00 0.00 44.19 3.27
369 370 7.573968 ACTCTGAAACTTTTTGCTGATTACT 57.426 32.000 0.00 0.00 0.00 2.24
370 371 7.420800 ACTCTGAAACTTTTTGCTGATTACTG 58.579 34.615 0.00 0.00 0.00 2.74
392 393 3.245122 GGATTAGTGTGGTTGGGAGGAAA 60.245 47.826 0.00 0.00 0.00 3.13
408 409 3.365472 AGGAAACTCAACAAACTGGCTT 58.635 40.909 0.00 0.00 32.90 4.35
454 455 0.322008 GCAGGCAACCAAGCTCTAGT 60.322 55.000 0.00 0.00 34.17 2.57
466 467 0.173708 GCTCTAGTTGGGTCAGTCCG 59.826 60.000 0.00 0.00 37.00 4.79
583 586 4.262463 GCGACCCATTCTATCCATCTACAA 60.262 45.833 0.00 0.00 0.00 2.41
604 607 1.167781 GGGCCGTTCCAACTTCGAAA 61.168 55.000 0.00 0.00 36.21 3.46
605 608 0.237498 GGCCGTTCCAACTTCGAAAG 59.763 55.000 0.00 0.00 34.01 2.62
606 609 0.385598 GCCGTTCCAACTTCGAAAGC 60.386 55.000 0.00 0.00 0.00 3.51
607 610 0.237498 CCGTTCCAACTTCGAAAGCC 59.763 55.000 0.00 0.00 0.00 4.35
608 611 0.237498 CGTTCCAACTTCGAAAGCCC 59.763 55.000 0.00 0.00 0.00 5.19
609 612 1.314730 GTTCCAACTTCGAAAGCCCA 58.685 50.000 0.00 0.00 0.00 5.36
610 613 1.679153 GTTCCAACTTCGAAAGCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
611 614 2.060050 TCCAACTTCGAAAGCCCAAA 57.940 45.000 0.00 0.00 0.00 3.28
612 615 1.679153 TCCAACTTCGAAAGCCCAAAC 59.321 47.619 0.00 0.00 0.00 2.93
613 616 1.681264 CCAACTTCGAAAGCCCAAACT 59.319 47.619 0.00 0.00 0.00 2.66
614 617 2.882137 CCAACTTCGAAAGCCCAAACTA 59.118 45.455 0.00 0.00 0.00 2.24
615 618 3.058224 CCAACTTCGAAAGCCCAAACTAG 60.058 47.826 0.00 0.00 0.00 2.57
616 619 3.764237 ACTTCGAAAGCCCAAACTAGA 57.236 42.857 0.00 0.00 0.00 2.43
617 620 3.400255 ACTTCGAAAGCCCAAACTAGAC 58.600 45.455 0.00 0.00 0.00 2.59
618 621 2.467566 TCGAAAGCCCAAACTAGACC 57.532 50.000 0.00 0.00 0.00 3.85
619 622 1.975680 TCGAAAGCCCAAACTAGACCT 59.024 47.619 0.00 0.00 0.00 3.85
620 623 2.076863 CGAAAGCCCAAACTAGACCTG 58.923 52.381 0.00 0.00 0.00 4.00
621 624 2.550208 CGAAAGCCCAAACTAGACCTGT 60.550 50.000 0.00 0.00 0.00 4.00
622 625 2.568623 AAGCCCAAACTAGACCTGTG 57.431 50.000 0.00 0.00 0.00 3.66
623 626 0.036875 AGCCCAAACTAGACCTGTGC 59.963 55.000 0.00 0.00 0.00 4.57
624 627 0.250727 GCCCAAACTAGACCTGTGCA 60.251 55.000 0.00 0.00 0.00 4.57
625 628 1.614317 GCCCAAACTAGACCTGTGCAT 60.614 52.381 0.00 0.00 0.00 3.96
626 629 2.086869 CCCAAACTAGACCTGTGCATG 58.913 52.381 0.00 0.00 0.00 4.06
627 630 2.086869 CCAAACTAGACCTGTGCATGG 58.913 52.381 0.00 7.10 0.00 3.66
628 631 2.086869 CAAACTAGACCTGTGCATGGG 58.913 52.381 12.39 9.49 0.00 4.00
629 632 1.362224 AACTAGACCTGTGCATGGGT 58.638 50.000 12.40 12.40 38.70 4.51
630 633 2.247699 ACTAGACCTGTGCATGGGTA 57.752 50.000 12.51 4.00 35.77 3.69
631 634 2.111384 ACTAGACCTGTGCATGGGTAG 58.889 52.381 12.51 13.24 35.77 3.18
632 635 0.830648 TAGACCTGTGCATGGGTAGC 59.169 55.000 12.51 3.37 35.77 3.58
633 636 0.911525 AGACCTGTGCATGGGTAGCT 60.912 55.000 12.51 0.00 35.77 3.32
634 637 0.035056 GACCTGTGCATGGGTAGCTT 60.035 55.000 12.51 0.00 35.77 3.74
635 638 0.322816 ACCTGTGCATGGGTAGCTTG 60.323 55.000 11.13 0.00 33.59 4.01
636 639 1.033746 CCTGTGCATGGGTAGCTTGG 61.034 60.000 0.00 0.00 0.00 3.61
637 640 0.322816 CTGTGCATGGGTAGCTTGGT 60.323 55.000 0.00 0.00 0.00 3.67
638 641 0.112218 TGTGCATGGGTAGCTTGGTT 59.888 50.000 0.00 0.00 0.00 3.67
639 642 0.811281 GTGCATGGGTAGCTTGGTTC 59.189 55.000 0.00 0.00 0.00 3.62
640 643 0.676466 TGCATGGGTAGCTTGGTTCG 60.676 55.000 0.00 0.00 0.00 3.95
641 644 1.376609 GCATGGGTAGCTTGGTTCGG 61.377 60.000 0.00 0.00 0.00 4.30
642 645 0.251916 CATGGGTAGCTTGGTTCGGA 59.748 55.000 0.00 0.00 0.00 4.55
643 646 0.541863 ATGGGTAGCTTGGTTCGGAG 59.458 55.000 0.00 0.00 0.00 4.63
644 647 1.221021 GGGTAGCTTGGTTCGGAGG 59.779 63.158 0.00 0.00 0.00 4.30
645 648 1.449778 GGTAGCTTGGTTCGGAGGC 60.450 63.158 0.00 0.00 0.00 4.70
646 649 1.449778 GTAGCTTGGTTCGGAGGCC 60.450 63.158 0.00 0.00 0.00 5.19
647 650 2.666098 TAGCTTGGTTCGGAGGCCC 61.666 63.158 0.00 0.00 0.00 5.80
675 678 4.181010 CCCGACATCTGGGCCAGG 62.181 72.222 32.23 19.93 40.47 4.45
676 679 4.864334 CCGACATCTGGGCCAGGC 62.864 72.222 32.23 17.89 31.51 4.85
688 691 3.747579 CCAGGCCTGGGCTCCATT 61.748 66.667 40.24 0.00 46.81 3.16
689 692 2.361771 CAGGCCTGGGCTCCATTT 59.638 61.111 26.14 0.00 41.60 2.32
690 693 2.056223 CAGGCCTGGGCTCCATTTG 61.056 63.158 26.14 5.09 41.60 2.32
691 694 3.464494 GGCCTGGGCTCCATTTGC 61.464 66.667 13.80 0.00 41.60 3.68
697 700 3.076916 GGCTCCATTTGCCCACCC 61.077 66.667 0.00 0.00 44.32 4.61
698 701 3.451894 GCTCCATTTGCCCACCCG 61.452 66.667 0.00 0.00 0.00 5.28
699 702 2.354729 CTCCATTTGCCCACCCGA 59.645 61.111 0.00 0.00 0.00 5.14
700 703 1.304052 CTCCATTTGCCCACCCGAA 60.304 57.895 0.00 0.00 0.00 4.30
701 704 1.304052 TCCATTTGCCCACCCGAAG 60.304 57.895 0.00 0.00 0.00 3.79
702 705 2.573340 CATTTGCCCACCCGAAGC 59.427 61.111 0.00 0.00 0.00 3.86
703 706 2.679996 ATTTGCCCACCCGAAGCC 60.680 61.111 0.00 0.00 0.00 4.35
704 707 3.224007 ATTTGCCCACCCGAAGCCT 62.224 57.895 0.00 0.00 0.00 4.58
705 708 4.659172 TTGCCCACCCGAAGCCTG 62.659 66.667 0.00 0.00 0.00 4.85
712 715 4.077184 CCCGAAGCCTGGCGTGTA 62.077 66.667 12.97 0.00 0.00 2.90
713 716 2.047655 CCGAAGCCTGGCGTGTAA 60.048 61.111 12.97 0.00 0.00 2.41
714 717 2.100631 CCGAAGCCTGGCGTGTAAG 61.101 63.158 12.97 2.37 0.00 2.34
715 718 2.740714 CGAAGCCTGGCGTGTAAGC 61.741 63.158 12.97 0.00 0.00 3.09
745 748 7.748691 AAAAGCTCAAAATGGCAATAAATGT 57.251 28.000 0.00 0.00 0.00 2.71
746 749 8.845413 AAAAGCTCAAAATGGCAATAAATGTA 57.155 26.923 0.00 0.00 0.00 2.29
747 750 9.452287 AAAAGCTCAAAATGGCAATAAATGTAT 57.548 25.926 0.00 0.00 0.00 2.29
825 828 8.948631 TTTTAATTACAAAATGGCACTGTTCA 57.051 26.923 4.29 0.00 0.00 3.18
826 829 9.553064 TTTTAATTACAAAATGGCACTGTTCAT 57.447 25.926 4.29 0.00 0.00 2.57
827 830 8.531622 TTAATTACAAAATGGCACTGTTCATG 57.468 30.769 4.29 0.00 0.00 3.07
828 831 5.528043 TTACAAAATGGCACTGTTCATGT 57.472 34.783 4.29 1.36 0.00 3.21
829 832 3.719924 ACAAAATGGCACTGTTCATGTG 58.280 40.909 0.00 0.00 38.36 3.21
836 839 2.427232 CACTGTTCATGTGCTTTGGG 57.573 50.000 0.00 0.00 0.00 4.12
837 840 0.675633 ACTGTTCATGTGCTTTGGGC 59.324 50.000 0.00 0.00 42.22 5.36
838 841 0.037975 CTGTTCATGTGCTTTGGGCC 60.038 55.000 0.00 0.00 40.92 5.80
839 842 1.080569 GTTCATGTGCTTTGGGCCG 60.081 57.895 0.00 0.00 40.92 6.13
840 843 2.274645 TTCATGTGCTTTGGGCCGG 61.275 57.895 0.00 0.00 40.92 6.13
841 844 3.762247 CATGTGCTTTGGGCCGGG 61.762 66.667 2.18 0.00 40.92 5.73
865 868 3.747579 CAGGCCTGGGCTTGGGAT 61.748 66.667 26.14 0.00 43.25 3.85
866 869 2.948924 AGGCCTGGGCTTGGGATT 60.949 61.111 18.27 0.00 41.60 3.01
867 870 2.039462 GGCCTGGGCTTGGGATTT 59.961 61.111 13.80 0.00 41.60 2.17
868 871 1.613332 GGCCTGGGCTTGGGATTTT 60.613 57.895 13.80 0.00 41.60 1.82
869 872 0.325203 GGCCTGGGCTTGGGATTTTA 60.325 55.000 13.80 0.00 41.60 1.52
870 873 1.114627 GCCTGGGCTTGGGATTTTAG 58.885 55.000 4.12 0.00 38.26 1.85
871 874 1.619704 GCCTGGGCTTGGGATTTTAGT 60.620 52.381 4.12 0.00 38.26 2.24
872 875 2.820178 CCTGGGCTTGGGATTTTAGTT 58.180 47.619 0.00 0.00 0.00 2.24
873 876 3.173151 CCTGGGCTTGGGATTTTAGTTT 58.827 45.455 0.00 0.00 0.00 2.66
874 877 3.195610 CCTGGGCTTGGGATTTTAGTTTC 59.804 47.826 0.00 0.00 0.00 2.78
875 878 2.823154 TGGGCTTGGGATTTTAGTTTCG 59.177 45.455 0.00 0.00 0.00 3.46
876 879 2.165641 GGGCTTGGGATTTTAGTTTCGG 59.834 50.000 0.00 0.00 0.00 4.30
877 880 2.165641 GGCTTGGGATTTTAGTTTCGGG 59.834 50.000 0.00 0.00 0.00 5.14
878 881 2.416836 GCTTGGGATTTTAGTTTCGGGC 60.417 50.000 0.00 0.00 0.00 6.13
879 882 2.891191 TGGGATTTTAGTTTCGGGCT 57.109 45.000 0.00 0.00 0.00 5.19
880 883 3.163616 TGGGATTTTAGTTTCGGGCTT 57.836 42.857 0.00 0.00 0.00 4.35
881 884 3.502356 TGGGATTTTAGTTTCGGGCTTT 58.498 40.909 0.00 0.00 0.00 3.51
882 885 4.664392 TGGGATTTTAGTTTCGGGCTTTA 58.336 39.130 0.00 0.00 0.00 1.85
883 886 4.460034 TGGGATTTTAGTTTCGGGCTTTAC 59.540 41.667 0.00 0.00 0.00 2.01
884 887 4.460034 GGGATTTTAGTTTCGGGCTTTACA 59.540 41.667 0.00 0.00 0.00 2.41
885 888 5.047872 GGGATTTTAGTTTCGGGCTTTACAA 60.048 40.000 0.00 0.00 0.00 2.41
886 889 6.448852 GGATTTTAGTTTCGGGCTTTACAAA 58.551 36.000 0.00 0.00 0.00 2.83
887 890 6.584942 GGATTTTAGTTTCGGGCTTTACAAAG 59.415 38.462 0.00 0.00 39.03 2.77
895 898 3.284336 CTTTACAAAGCCCGGCCC 58.716 61.111 5.55 0.00 0.00 5.80
896 899 2.673687 TTTACAAAGCCCGGCCCG 60.674 61.111 5.55 0.00 0.00 6.13
911 914 3.053896 CCGGCTCGGGGTTTGAAC 61.054 66.667 5.79 0.00 44.15 3.18
912 915 2.281208 CGGCTCGGGGTTTGAACA 60.281 61.111 0.00 0.00 0.00 3.18
913 916 2.325082 CGGCTCGGGGTTTGAACAG 61.325 63.158 0.00 0.00 0.00 3.16
914 917 1.971695 GGCTCGGGGTTTGAACAGG 60.972 63.158 0.00 0.00 0.00 4.00
915 918 1.228154 GCTCGGGGTTTGAACAGGT 60.228 57.895 0.00 0.00 0.00 4.00
916 919 0.822121 GCTCGGGGTTTGAACAGGTT 60.822 55.000 0.00 0.00 0.00 3.50
917 920 1.687563 CTCGGGGTTTGAACAGGTTT 58.312 50.000 0.00 0.00 0.00 3.27
926 929 4.116961 GTTTGAACAGGTTTAGCCCAAAC 58.883 43.478 9.27 9.27 44.94 2.93
1014 1021 4.049640 GAAATGGCCGGCGCAACA 62.050 61.111 22.54 13.51 36.38 3.33
1287 1294 3.371063 ATCACCACCGTCGAGCGT 61.371 61.111 0.00 0.00 39.32 5.07
1317 1324 1.390926 GTACCTGTGGGAGGAGGGA 59.609 63.158 0.00 0.00 46.33 4.20
1429 1436 5.786392 GTGTACAGAATGATGTAAACGCTC 58.214 41.667 0.00 0.00 39.69 5.03
1580 1591 2.617532 GCCTTTCTTCAGCCTCATGAGT 60.618 50.000 21.11 0.60 0.00 3.41
1586 1597 2.783379 TCAGCCTCATGAGTATCCCT 57.217 50.000 21.11 6.62 0.00 4.20
1660 1671 2.229543 TGTGTGCTGCATTCTTGATTCC 59.770 45.455 5.27 0.00 0.00 3.01
1687 1698 2.593346 ATTTGTTGCTTTGCCGTCAA 57.407 40.000 0.00 0.00 0.00 3.18
1853 1864 6.437928 CGCAATGCCTGTTTGTTACATATAT 58.562 36.000 0.00 0.00 35.85 0.86
1854 1865 7.580600 CGCAATGCCTGTTTGTTACATATATA 58.419 34.615 0.00 0.00 35.85 0.86
1859 1870 8.887036 TGCCTGTTTGTTACATATATAGTCTG 57.113 34.615 0.00 0.00 35.85 3.51
1890 1901 2.492088 TGCAACGACTGTGATAGCTAGT 59.508 45.455 0.00 0.00 0.00 2.57
1947 1958 1.677217 GCTGGTGATCCTTCGAAGCTT 60.677 52.381 19.99 8.67 34.23 3.74
2081 2092 2.434702 GGGATCCGTAAGTGAAGACCAT 59.565 50.000 5.45 0.00 0.00 3.55
2111 2122 9.738832 TTTTTATTTAGTTGGTCAGTTAACTGC 57.261 29.630 27.49 21.55 43.46 4.40
2214 2225 2.680974 TAGCCATGCTCCCGAATGCC 62.681 60.000 0.00 0.00 40.44 4.40
2245 2256 6.894828 TCTAGGTTTGTTATCGTTTCTTTGC 58.105 36.000 0.00 0.00 0.00 3.68
2315 2328 0.250166 GGACCTTGTGCCGTTGTACT 60.250 55.000 0.00 0.00 0.00 2.73
2346 2359 5.529800 TGATCATGAACCAGCAATGATGTAG 59.470 40.000 0.00 0.00 32.72 2.74
2348 2361 5.988287 TCATGAACCAGCAATGATGTAGTA 58.012 37.500 0.00 0.00 0.00 1.82
2368 2630 8.108999 TGTAGTACTAGGTGTCACTTAACCATA 58.891 37.037 1.87 0.00 39.05 2.74
2398 2660 5.010282 TCTGTATTTCCTTCTTTTCCAGGC 58.990 41.667 0.00 0.00 0.00 4.85
2618 2880 7.442666 TCTTGTTTTAAAAATACATTGGGCCAC 59.557 33.333 5.23 0.00 0.00 5.01
2635 2897 6.200114 TGGGCCACTACTACTATTACTCTTT 58.800 40.000 0.00 0.00 0.00 2.52
2637 2899 7.840716 TGGGCCACTACTACTATTACTCTTTAA 59.159 37.037 0.00 0.00 0.00 1.52
2638 2900 8.140628 GGGCCACTACTACTATTACTCTTTAAC 58.859 40.741 4.39 0.00 0.00 2.01
2807 3069 4.978580 GCAGGAAGTTGTGATTTTTCAGAC 59.021 41.667 0.00 0.00 0.00 3.51
2843 3115 3.358111 TCAACCTGGTCAAACTGTTCA 57.642 42.857 0.00 0.00 0.00 3.18
2844 3116 3.278574 TCAACCTGGTCAAACTGTTCAG 58.721 45.455 0.00 0.00 0.00 3.02
2891 3163 7.703328 TCTTCAACAACCAAACTCTATGTTTC 58.297 34.615 0.00 0.00 46.11 2.78
3107 3381 5.613358 AGCACAAATAAGACTAACAGCAC 57.387 39.130 0.00 0.00 0.00 4.40
3109 3383 4.455877 GCACAAATAAGACTAACAGCACCT 59.544 41.667 0.00 0.00 0.00 4.00
3115 3389 3.851976 AGACTAACAGCACCTACTTCG 57.148 47.619 0.00 0.00 0.00 3.79
3119 3393 2.902705 AACAGCACCTACTTCGTTGA 57.097 45.000 0.00 0.00 0.00 3.18
3125 3399 3.961408 AGCACCTACTTCGTTGATAGGAT 59.039 43.478 3.58 0.00 38.20 3.24
3135 3409 5.139435 TCGTTGATAGGATGATGCCTTAG 57.861 43.478 0.00 0.00 39.50 2.18
3138 3412 4.897509 TGATAGGATGATGCCTTAGTGG 57.102 45.455 0.00 0.00 39.50 4.00
3178 3452 7.121168 TCACTTTGCTATCTTAATTGAACCTGG 59.879 37.037 0.00 0.00 0.00 4.45
3236 3510 9.601217 CTTACAAGGTGCACTAGATTACTTTAT 57.399 33.333 17.98 3.19 0.00 1.40
3238 3512 6.316390 ACAAGGTGCACTAGATTACTTTATGC 59.684 38.462 17.98 0.00 0.00 3.14
3262 3536 6.485648 GCGATATTTGGTATTTTCCCTACACT 59.514 38.462 0.00 0.00 0.00 3.55
3263 3537 7.658575 GCGATATTTGGTATTTTCCCTACACTA 59.341 37.037 0.00 0.00 0.00 2.74
3264 3538 9.204570 CGATATTTGGTATTTTCCCTACACTAG 57.795 37.037 0.00 0.00 0.00 2.57
3265 3539 9.503399 GATATTTGGTATTTTCCCTACACTAGG 57.497 37.037 0.00 0.00 45.81 3.02
3272 3548 3.771071 TTCCCTACACTAGGTAGCCTT 57.229 47.619 11.05 0.00 46.73 4.35
3290 3566 5.625150 AGCCTTCCCTATCATGTATGTTTC 58.375 41.667 0.00 0.00 0.00 2.78
3318 3594 2.107950 TCTTTTCTACGTGGCATGGG 57.892 50.000 12.05 3.72 0.00 4.00
3345 3621 5.248640 TGCTTATTTCTTCCTGGACAGAAG 58.751 41.667 15.79 4.64 30.68 2.85
3356 3632 2.035961 CTGGACAGAAGAGTTCCGAACA 59.964 50.000 13.69 0.00 0.00 3.18
3380 3656 9.436957 ACATTCTACATGAAGTTAACTAGTTGG 57.563 33.333 18.56 0.92 38.18 3.77
3382 3658 6.999950 TCTACATGAAGTTAACTAGTTGGCA 58.000 36.000 18.56 8.85 0.00 4.92
3383 3659 7.446769 TCTACATGAAGTTAACTAGTTGGCAA 58.553 34.615 18.56 0.00 0.00 4.52
3384 3660 6.952773 ACATGAAGTTAACTAGTTGGCAAA 57.047 33.333 18.56 1.25 0.00 3.68
3385 3661 6.735130 ACATGAAGTTAACTAGTTGGCAAAC 58.265 36.000 18.56 13.65 36.47 2.93
3447 3744 5.693104 TGTTACACAGTAAACGGAATCTGTC 59.307 40.000 0.00 0.00 38.79 3.51
3485 3782 2.029743 GCGTTTCAAGCCTGGTTCA 58.970 52.632 0.00 0.00 0.00 3.18
3503 3800 2.428491 TCAACGTACCATTTGGCGAAT 58.572 42.857 0.00 0.00 39.32 3.34
3508 3805 5.856126 ACGTACCATTTGGCGAATATATG 57.144 39.130 0.00 4.49 39.32 1.78
3513 3810 4.213270 ACCATTTGGCGAATATATGTGTCG 59.787 41.667 0.00 1.68 39.32 4.35
4097 4403 5.015178 TCACCTATGTCTTCCTTTGGGATTT 59.985 40.000 0.00 0.00 41.87 2.17
4098 4404 5.126061 CACCTATGTCTTCCTTTGGGATTTG 59.874 44.000 0.00 0.00 41.87 2.32
4178 4484 1.531149 CGAACCACTTGTTAGGTGCTG 59.469 52.381 0.00 0.00 38.37 4.41
4270 4576 4.095782 GCAGACTGAGAGTGACTTAGTAGG 59.904 50.000 6.65 0.00 43.82 3.18
4420 4726 2.353858 CAAAATCTGCACTGGGCCA 58.646 52.632 5.85 5.85 43.89 5.36
4586 4892 7.916977 TGCATCTCTTCATTTTGTTGCATATAC 59.083 33.333 0.00 0.00 34.24 1.47
4809 5116 7.545965 CCTCTGAAAAGAAATAGAAGAGCGTTA 59.454 37.037 0.00 0.00 0.00 3.18
4810 5117 8.467402 TCTGAAAAGAAATAGAAGAGCGTTAG 57.533 34.615 0.00 0.00 0.00 2.34
4811 5118 8.304596 TCTGAAAAGAAATAGAAGAGCGTTAGA 58.695 33.333 0.00 0.00 0.00 2.10
4812 5119 9.092876 CTGAAAAGAAATAGAAGAGCGTTAGAT 57.907 33.333 0.00 0.00 0.00 1.98
4813 5120 9.088512 TGAAAAGAAATAGAAGAGCGTTAGATC 57.911 33.333 0.00 0.00 0.00 2.75
4814 5121 9.088512 GAAAAGAAATAGAAGAGCGTTAGATCA 57.911 33.333 0.00 0.00 34.73 2.92
4815 5122 7.995463 AAGAAATAGAAGAGCGTTAGATCAC 57.005 36.000 0.00 0.00 34.73 3.06
4816 5123 7.341445 AGAAATAGAAGAGCGTTAGATCACT 57.659 36.000 0.00 0.00 34.73 3.41
4817 5124 8.453238 AGAAATAGAAGAGCGTTAGATCACTA 57.547 34.615 0.00 0.00 34.73 2.74
4818 5125 8.347035 AGAAATAGAAGAGCGTTAGATCACTAC 58.653 37.037 0.00 0.00 34.73 2.73
4819 5126 7.811117 AATAGAAGAGCGTTAGATCACTACT 57.189 36.000 0.00 0.00 34.73 2.57
4820 5127 7.811117 ATAGAAGAGCGTTAGATCACTACTT 57.189 36.000 0.00 0.00 34.73 2.24
4821 5128 6.518208 AGAAGAGCGTTAGATCACTACTTT 57.482 37.500 0.00 0.00 34.73 2.66
4822 5129 6.926313 AGAAGAGCGTTAGATCACTACTTTT 58.074 36.000 0.00 0.00 34.73 2.27
4823 5130 8.053026 AGAAGAGCGTTAGATCACTACTTTTA 57.947 34.615 0.00 0.00 34.73 1.52
4879 5187 2.541762 GAGTAGATCGCTTCAATGTGCC 59.458 50.000 0.00 0.00 0.00 5.01
5015 5326 9.444600 ACTACATTTTACTACGAATTGAATGGT 57.555 29.630 0.00 0.00 0.00 3.55
5016 5327 9.916397 CTACATTTTACTACGAATTGAATGGTC 57.084 33.333 0.00 0.00 0.00 4.02
5022 5333 9.887406 TTTACTACGAATTGAATGGTCTTTTTC 57.113 29.630 0.00 0.00 0.00 2.29
5041 5353 5.643379 TTTCTTTGACATGTAATCCCTGC 57.357 39.130 0.00 0.00 0.00 4.85
5089 5403 3.770666 CTGATCCTCGAAATACGTGTGT 58.229 45.455 0.00 0.00 43.13 3.72
5090 5404 3.507786 TGATCCTCGAAATACGTGTGTG 58.492 45.455 0.00 0.00 43.13 3.82
5091 5405 1.705256 TCCTCGAAATACGTGTGTGC 58.295 50.000 0.00 0.00 43.13 4.57
5092 5406 0.719465 CCTCGAAATACGTGTGTGCC 59.281 55.000 0.00 0.00 43.13 5.01
5093 5407 1.424403 CTCGAAATACGTGTGTGCCA 58.576 50.000 0.00 0.00 43.13 4.92
5095 5409 1.729517 TCGAAATACGTGTGTGCCATG 59.270 47.619 0.00 0.00 43.13 3.66
5096 5410 1.463056 CGAAATACGTGTGTGCCATGT 59.537 47.619 0.00 0.00 45.31 3.21
5098 5412 3.123790 CGAAATACGTGTGTGCCATGTAA 59.876 43.478 0.00 0.00 46.03 2.41
5147 5480 4.032960 ACCACTATGTTGATGGAAGCAA 57.967 40.909 0.00 0.00 41.67 3.91
5177 5512 5.951148 TGAGAGCATTTGATATGTTTGGGAA 59.049 36.000 0.00 0.00 0.00 3.97
5214 5549 8.682936 ACTTCAAACCATATATGACCAAGATC 57.317 34.615 14.54 0.00 0.00 2.75
5238 5573 9.642343 ATCATACAACTGGACTATTACTGTCTA 57.358 33.333 0.00 0.00 35.04 2.59
5300 5635 7.703058 AAATTATTGTTCTCAGTTACCAGGG 57.297 36.000 0.00 0.00 0.00 4.45
5302 5637 3.764237 TTGTTCTCAGTTACCAGGGTC 57.236 47.619 0.00 0.00 0.00 4.46
5303 5638 1.975680 TGTTCTCAGTTACCAGGGTCC 59.024 52.381 0.00 0.00 0.00 4.46
5342 7293 3.066064 AGCTAACTCGAGAGCATACACAG 59.934 47.826 23.49 7.43 41.36 3.66
5423 7374 5.323371 TGGCAAATAATAAGAGCAACCAC 57.677 39.130 0.00 0.00 0.00 4.16
5425 7376 5.105797 TGGCAAATAATAAGAGCAACCACTG 60.106 40.000 0.00 0.00 0.00 3.66
5451 7402 9.542462 GGCTGTACTATTAACTGTGATTCATAA 57.458 33.333 0.00 0.00 0.00 1.90
5497 7450 9.407380 TGAATTTTAGAATGTATGTATGCACCT 57.593 29.630 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 0.604511 CAGCAGTCACATGTGCCTGA 60.605 55.000 34.47 10.82 40.81 3.86
85 86 2.338015 CCCCAGCAGTCACATGTGC 61.338 63.158 21.38 15.51 40.17 4.57
141 142 0.250901 AGGCGTTGGCAAACTGAGAT 60.251 50.000 0.00 0.00 42.47 2.75
180 181 3.847602 CTCCGCCTCAGCCTCCTG 61.848 72.222 0.00 0.00 40.54 3.86
194 195 0.466124 GACCACACAGGATAGCCTCC 59.534 60.000 0.00 0.00 44.80 4.30
197 198 1.195115 TCAGACCACACAGGATAGCC 58.805 55.000 0.00 0.00 41.22 3.93
206 207 1.604278 GCAAGTTCCTTCAGACCACAC 59.396 52.381 0.00 0.00 0.00 3.82
247 248 2.609459 GCGTTGTCAGTCTCCAATATGG 59.391 50.000 0.00 0.00 39.43 2.74
277 278 3.834813 TGTGGTGTTTCTCAGCTCTCTAT 59.165 43.478 0.00 0.00 43.97 1.98
306 307 2.952310 GGATGGGGTAGCATTCTGAAAC 59.048 50.000 0.00 0.00 0.00 2.78
312 313 1.541233 CGTCAGGATGGGGTAGCATTC 60.541 57.143 0.00 0.00 36.16 2.67
351 352 8.860088 ACTAATCCAGTAATCAGCAAAAAGTTT 58.140 29.630 0.00 0.00 34.98 2.66
369 370 1.633432 CCTCCCAACCACACTAATCCA 59.367 52.381 0.00 0.00 0.00 3.41
370 371 1.913419 TCCTCCCAACCACACTAATCC 59.087 52.381 0.00 0.00 0.00 3.01
392 393 3.503748 GCTCATAAGCCAGTTTGTTGAGT 59.496 43.478 0.00 0.00 43.10 3.41
423 424 0.034756 TTGCCTGCTGTTCTCGCTAA 59.965 50.000 0.00 0.00 0.00 3.09
454 455 1.825474 GATTCTCTCGGACTGACCCAA 59.175 52.381 0.00 0.00 34.64 4.12
483 484 6.360370 AGGATTACACTCAGCTAGAAACAA 57.640 37.500 0.00 0.00 0.00 2.83
553 556 4.200092 GGATAGAATGGGTCGCTTTCTTT 58.800 43.478 19.06 13.32 32.28 2.52
554 557 3.199946 TGGATAGAATGGGTCGCTTTCTT 59.800 43.478 19.06 10.05 32.28 2.52
555 558 2.771943 TGGATAGAATGGGTCGCTTTCT 59.228 45.455 18.23 18.23 34.29 2.52
556 559 3.194005 TGGATAGAATGGGTCGCTTTC 57.806 47.619 7.27 7.27 0.00 2.62
557 560 3.392616 AGATGGATAGAATGGGTCGCTTT 59.607 43.478 0.00 0.00 0.00 3.51
558 561 2.975489 AGATGGATAGAATGGGTCGCTT 59.025 45.455 0.00 0.00 0.00 4.68
559 562 2.614259 AGATGGATAGAATGGGTCGCT 58.386 47.619 0.00 0.00 0.00 4.93
560 563 3.258372 TGTAGATGGATAGAATGGGTCGC 59.742 47.826 0.00 0.00 0.00 5.19
561 564 5.468540 TTGTAGATGGATAGAATGGGTCG 57.531 43.478 0.00 0.00 0.00 4.79
562 565 6.176183 CCATTGTAGATGGATAGAATGGGTC 58.824 44.000 12.50 0.00 45.87 4.46
563 566 6.131972 CCATTGTAGATGGATAGAATGGGT 57.868 41.667 12.50 0.00 45.87 4.51
583 586 1.674322 CGAAGTTGGAACGGCCCAT 60.674 57.895 0.00 0.00 35.87 4.00
604 607 0.036875 GCACAGGTCTAGTTTGGGCT 59.963 55.000 9.73 0.00 38.20 5.19
605 608 0.250727 TGCACAGGTCTAGTTTGGGC 60.251 55.000 9.98 9.98 41.53 5.36
606 609 2.086869 CATGCACAGGTCTAGTTTGGG 58.913 52.381 0.00 0.00 0.00 4.12
607 610 2.086869 CCATGCACAGGTCTAGTTTGG 58.913 52.381 0.00 0.00 0.00 3.28
608 611 2.086869 CCCATGCACAGGTCTAGTTTG 58.913 52.381 6.30 0.00 0.00 2.93
609 612 1.705186 ACCCATGCACAGGTCTAGTTT 59.295 47.619 3.60 0.00 0.00 2.66
610 613 1.362224 ACCCATGCACAGGTCTAGTT 58.638 50.000 3.60 0.00 0.00 2.24
611 614 2.111384 CTACCCATGCACAGGTCTAGT 58.889 52.381 12.62 2.88 37.59 2.57
612 615 1.202580 GCTACCCATGCACAGGTCTAG 60.203 57.143 12.62 7.44 37.59 2.43
613 616 0.830648 GCTACCCATGCACAGGTCTA 59.169 55.000 12.62 0.00 37.59 2.59
614 617 0.911525 AGCTACCCATGCACAGGTCT 60.912 55.000 12.62 2.95 37.59 3.85
615 618 0.035056 AAGCTACCCATGCACAGGTC 60.035 55.000 12.62 0.67 37.59 3.85
616 619 0.322816 CAAGCTACCCATGCACAGGT 60.323 55.000 13.67 13.67 40.31 4.00
617 620 1.033746 CCAAGCTACCCATGCACAGG 61.034 60.000 2.24 2.24 0.00 4.00
618 621 0.322816 ACCAAGCTACCCATGCACAG 60.323 55.000 0.00 0.00 0.00 3.66
619 622 0.112218 AACCAAGCTACCCATGCACA 59.888 50.000 0.00 0.00 0.00 4.57
620 623 0.811281 GAACCAAGCTACCCATGCAC 59.189 55.000 0.00 0.00 0.00 4.57
621 624 0.676466 CGAACCAAGCTACCCATGCA 60.676 55.000 0.00 0.00 0.00 3.96
622 625 1.376609 CCGAACCAAGCTACCCATGC 61.377 60.000 0.00 0.00 0.00 4.06
623 626 0.251916 TCCGAACCAAGCTACCCATG 59.748 55.000 0.00 0.00 0.00 3.66
624 627 0.541863 CTCCGAACCAAGCTACCCAT 59.458 55.000 0.00 0.00 0.00 4.00
625 628 1.550130 CCTCCGAACCAAGCTACCCA 61.550 60.000 0.00 0.00 0.00 4.51
626 629 1.221021 CCTCCGAACCAAGCTACCC 59.779 63.158 0.00 0.00 0.00 3.69
627 630 1.449778 GCCTCCGAACCAAGCTACC 60.450 63.158 0.00 0.00 0.00 3.18
628 631 1.449778 GGCCTCCGAACCAAGCTAC 60.450 63.158 0.00 0.00 0.00 3.58
629 632 2.666098 GGGCCTCCGAACCAAGCTA 61.666 63.158 0.84 0.00 0.00 3.32
630 633 4.035102 GGGCCTCCGAACCAAGCT 62.035 66.667 0.84 0.00 0.00 3.74
659 662 4.864334 GCCTGGCCCAGATGTCGG 62.864 72.222 13.74 0.00 32.44 4.79
660 663 4.864334 GGCCTGGCCCAGATGTCG 62.864 72.222 27.77 0.00 44.06 4.35
672 675 2.056223 CAAATGGAGCCCAGGCCTG 61.056 63.158 26.87 26.87 43.17 4.85
673 676 2.361771 CAAATGGAGCCCAGGCCT 59.638 61.111 0.00 0.00 43.17 5.19
674 677 3.464494 GCAAATGGAGCCCAGGCC 61.464 66.667 4.70 0.00 43.17 5.19
675 678 3.464494 GGCAAATGGAGCCCAGGC 61.464 66.667 0.00 0.00 46.50 4.85
681 684 3.451894 CGGGTGGGCAAATGGAGC 61.452 66.667 0.00 0.00 0.00 4.70
682 685 1.304052 TTCGGGTGGGCAAATGGAG 60.304 57.895 0.00 0.00 0.00 3.86
683 686 1.304052 CTTCGGGTGGGCAAATGGA 60.304 57.895 0.00 0.00 0.00 3.41
684 687 3.005540 GCTTCGGGTGGGCAAATGG 62.006 63.158 0.00 0.00 0.00 3.16
685 688 2.573340 GCTTCGGGTGGGCAAATG 59.427 61.111 0.00 0.00 0.00 2.32
686 689 2.679996 GGCTTCGGGTGGGCAAAT 60.680 61.111 0.00 0.00 0.00 2.32
687 690 3.897122 AGGCTTCGGGTGGGCAAA 61.897 61.111 0.00 0.00 0.00 3.68
688 691 4.659172 CAGGCTTCGGGTGGGCAA 62.659 66.667 0.00 0.00 0.00 4.52
695 698 3.599285 TTACACGCCAGGCTTCGGG 62.599 63.158 10.54 6.63 34.86 5.14
696 699 2.047655 TTACACGCCAGGCTTCGG 60.048 61.111 10.54 0.00 0.00 4.30
697 700 2.740714 GCTTACACGCCAGGCTTCG 61.741 63.158 10.54 0.00 0.00 3.79
698 701 3.178539 GCTTACACGCCAGGCTTC 58.821 61.111 10.54 0.00 0.00 3.86
720 723 8.168790 ACATTTATTGCCATTTTGAGCTTTTT 57.831 26.923 0.00 0.00 0.00 1.94
721 724 7.748691 ACATTTATTGCCATTTTGAGCTTTT 57.251 28.000 0.00 0.00 0.00 2.27
799 802 9.553064 TGAACAGTGCCATTTTGTAATTAAAAT 57.447 25.926 0.00 0.00 40.00 1.82
800 803 8.948631 TGAACAGTGCCATTTTGTAATTAAAA 57.051 26.923 0.00 0.00 34.39 1.52
801 804 8.986847 CATGAACAGTGCCATTTTGTAATTAAA 58.013 29.630 0.00 0.00 0.00 1.52
802 805 8.147058 ACATGAACAGTGCCATTTTGTAATTAA 58.853 29.630 0.00 0.00 0.00 1.40
803 806 7.598118 CACATGAACAGTGCCATTTTGTAATTA 59.402 33.333 0.00 0.00 0.00 1.40
804 807 6.424509 CACATGAACAGTGCCATTTTGTAATT 59.575 34.615 0.00 0.00 0.00 1.40
805 808 5.927689 CACATGAACAGTGCCATTTTGTAAT 59.072 36.000 0.00 0.00 0.00 1.89
806 809 5.288015 CACATGAACAGTGCCATTTTGTAA 58.712 37.500 0.00 0.00 0.00 2.41
807 810 4.869215 CACATGAACAGTGCCATTTTGTA 58.131 39.130 0.00 0.00 0.00 2.41
808 811 3.719924 CACATGAACAGTGCCATTTTGT 58.280 40.909 0.00 0.00 0.00 2.83
817 820 1.603678 GCCCAAAGCACATGAACAGTG 60.604 52.381 0.00 0.00 42.97 3.66
818 821 0.675633 GCCCAAAGCACATGAACAGT 59.324 50.000 0.00 0.00 42.97 3.55
819 822 0.037975 GGCCCAAAGCACATGAACAG 60.038 55.000 0.00 0.00 46.50 3.16
820 823 1.804396 CGGCCCAAAGCACATGAACA 61.804 55.000 0.00 0.00 46.50 3.18
821 824 1.080569 CGGCCCAAAGCACATGAAC 60.081 57.895 0.00 0.00 46.50 3.18
822 825 2.274645 CCGGCCCAAAGCACATGAA 61.275 57.895 0.00 0.00 46.50 2.57
823 826 2.676121 CCGGCCCAAAGCACATGA 60.676 61.111 0.00 0.00 46.50 3.07
824 827 3.762247 CCCGGCCCAAAGCACATG 61.762 66.667 0.00 0.00 46.50 3.21
848 851 2.810488 AAATCCCAAGCCCAGGCCTG 62.810 60.000 26.87 26.87 43.17 4.85
849 852 2.110782 AAAATCCCAAGCCCAGGCCT 62.111 55.000 0.00 0.00 43.17 5.19
850 853 0.325203 TAAAATCCCAAGCCCAGGCC 60.325 55.000 4.70 0.00 43.17 5.19
851 854 1.114627 CTAAAATCCCAAGCCCAGGC 58.885 55.000 0.00 0.00 42.33 4.85
852 855 2.532250 ACTAAAATCCCAAGCCCAGG 57.468 50.000 0.00 0.00 0.00 4.45
853 856 3.119495 CGAAACTAAAATCCCAAGCCCAG 60.119 47.826 0.00 0.00 0.00 4.45
854 857 2.823154 CGAAACTAAAATCCCAAGCCCA 59.177 45.455 0.00 0.00 0.00 5.36
855 858 2.165641 CCGAAACTAAAATCCCAAGCCC 59.834 50.000 0.00 0.00 0.00 5.19
856 859 2.165641 CCCGAAACTAAAATCCCAAGCC 59.834 50.000 0.00 0.00 0.00 4.35
857 860 2.416836 GCCCGAAACTAAAATCCCAAGC 60.417 50.000 0.00 0.00 0.00 4.01
858 861 3.089284 AGCCCGAAACTAAAATCCCAAG 58.911 45.455 0.00 0.00 0.00 3.61
859 862 3.163616 AGCCCGAAACTAAAATCCCAA 57.836 42.857 0.00 0.00 0.00 4.12
860 863 2.891191 AGCCCGAAACTAAAATCCCA 57.109 45.000 0.00 0.00 0.00 4.37
861 864 4.460034 TGTAAAGCCCGAAACTAAAATCCC 59.540 41.667 0.00 0.00 0.00 3.85
862 865 5.632244 TGTAAAGCCCGAAACTAAAATCC 57.368 39.130 0.00 0.00 0.00 3.01
863 866 7.562640 CTTTGTAAAGCCCGAAACTAAAATC 57.437 36.000 0.00 0.00 0.00 2.17
878 881 2.696759 CGGGCCGGGCTTTGTAAAG 61.697 63.158 28.80 5.53 39.03 1.85
879 882 2.673687 CGGGCCGGGCTTTGTAAA 60.674 61.111 28.80 0.00 0.00 2.01
880 883 4.726304 CCGGGCCGGGCTTTGTAA 62.726 66.667 37.27 0.00 44.15 2.41
895 898 2.281208 TGTTCAAACCCCGAGCCG 60.281 61.111 0.00 0.00 0.00 5.52
896 899 1.971695 CCTGTTCAAACCCCGAGCC 60.972 63.158 0.00 0.00 0.00 4.70
897 900 0.822121 AACCTGTTCAAACCCCGAGC 60.822 55.000 0.00 0.00 0.00 5.03
898 901 1.687563 AAACCTGTTCAAACCCCGAG 58.312 50.000 0.00 0.00 0.00 4.63
899 902 2.853705 CTAAACCTGTTCAAACCCCGA 58.146 47.619 0.00 0.00 0.00 5.14
900 903 1.268625 GCTAAACCTGTTCAAACCCCG 59.731 52.381 0.00 0.00 0.00 5.73
901 904 1.616865 GGCTAAACCTGTTCAAACCCC 59.383 52.381 0.00 0.00 34.51 4.95
902 905 1.616865 GGGCTAAACCTGTTCAAACCC 59.383 52.381 0.00 0.00 39.10 4.11
903 906 2.312390 TGGGCTAAACCTGTTCAAACC 58.688 47.619 0.00 0.00 39.10 3.27
904 907 4.116961 GTTTGGGCTAAACCTGTTCAAAC 58.883 43.478 14.81 4.36 42.25 2.93
905 908 4.394439 GTTTGGGCTAAACCTGTTCAAA 57.606 40.909 14.81 0.00 42.25 2.69
914 917 3.199677 GGTTTGTTGGTTTGGGCTAAAC 58.800 45.455 17.11 17.11 46.30 2.01
915 918 2.838202 TGGTTTGTTGGTTTGGGCTAAA 59.162 40.909 0.00 0.00 0.00 1.85
916 919 2.467880 TGGTTTGTTGGTTTGGGCTAA 58.532 42.857 0.00 0.00 0.00 3.09
917 920 2.160721 TGGTTTGTTGGTTTGGGCTA 57.839 45.000 0.00 0.00 0.00 3.93
926 929 0.527385 CGGCTGTGTTGGTTTGTTGG 60.527 55.000 0.00 0.00 0.00 3.77
1580 1591 3.247424 CCTGAGCTTCCCAGGGATA 57.753 57.895 9.80 0.00 45.66 2.59
1660 1671 4.318263 CGGCAAAGCAACAAATTCAGAAAG 60.318 41.667 0.00 0.00 0.00 2.62
1687 1698 1.452651 CGCTCAGGCCCATCAATGT 60.453 57.895 0.00 0.00 34.44 2.71
1769 1780 2.048222 CGCTCAAAGACCTCGGCA 60.048 61.111 0.00 0.00 0.00 5.69
1812 1823 5.572896 GCATTGCGCATTATAATAAGGGAAC 59.427 40.000 12.75 0.00 41.79 3.62
1853 1864 0.531753 TGCACGCAACAAGCAGACTA 60.532 50.000 0.00 0.00 46.13 2.59
1854 1865 1.375853 TTGCACGCAACAAGCAGACT 61.376 50.000 0.00 0.00 46.13 3.24
1947 1958 3.201930 TCCCAAATGCAGCCTTCATACTA 59.798 43.478 0.00 0.00 0.00 1.82
2090 2101 5.705905 GGAGCAGTTAACTGACCAACTAAAT 59.294 40.000 34.43 10.68 46.59 1.40
2095 2106 1.798813 CGGAGCAGTTAACTGACCAAC 59.201 52.381 34.43 18.47 46.59 3.77
2111 2122 5.050567 GTGAAAACAGGTTAGTACAACGGAG 60.051 44.000 0.00 0.00 0.00 4.63
2214 2225 4.745125 ACGATAACAAACCTAGATGCGATG 59.255 41.667 0.00 0.00 0.00 3.84
2315 2328 5.101648 TGCTGGTTCATGATCATGTCTAA 57.898 39.130 30.01 17.50 39.72 2.10
2346 2359 8.693625 AGAATATGGTTAAGTGACACCTAGTAC 58.306 37.037 0.84 0.00 33.76 2.73
2348 2361 7.180408 ACAGAATATGGTTAAGTGACACCTAGT 59.820 37.037 0.84 0.00 33.76 2.57
2368 2630 8.797438 GGAAAAGAAGGAAATACAGAACAGAAT 58.203 33.333 0.00 0.00 0.00 2.40
2398 2660 4.246458 GACAGCTTGACTTTACTACCCAG 58.754 47.826 0.00 0.00 0.00 4.45
2590 2852 8.286800 GGCCCAATGTATTTTTAAAACAAGAAC 58.713 33.333 0.00 0.00 0.00 3.01
2594 2856 7.283329 AGTGGCCCAATGTATTTTTAAAACAA 58.717 30.769 0.00 0.00 0.00 2.83
2601 2863 6.490492 AGTAGTAGTGGCCCAATGTATTTTT 58.510 36.000 0.00 0.00 0.00 1.94
2724 2986 5.391312 AAATGGTTGTTAAGATGCAGTCC 57.609 39.130 0.00 0.00 0.00 3.85
2778 3040 6.667007 AAAATCACAACTTCCTGCAAAAAG 57.333 33.333 6.26 6.26 0.00 2.27
2807 3069 3.952323 AGGTTGATCAATGCAATCCTGAG 59.048 43.478 12.12 0.00 30.78 3.35
2839 3111 4.982916 AGTACGACTTGTGAATCACTGAAC 59.017 41.667 14.97 3.54 35.11 3.18
2843 3115 8.453238 AGATATAGTACGACTTGTGAATCACT 57.547 34.615 14.97 0.00 35.11 3.41
2844 3116 9.171701 GAAGATATAGTACGACTTGTGAATCAC 57.828 37.037 6.41 6.41 34.56 3.06
2949 3223 2.786027 CGCATACTGATGTCTTGTCTCG 59.214 50.000 0.00 0.00 35.30 4.04
3107 3381 4.926238 GCATCATCCTATCAACGAAGTAGG 59.074 45.833 0.00 0.00 45.00 3.18
3109 3383 4.588951 AGGCATCATCCTATCAACGAAGTA 59.411 41.667 0.00 0.00 34.78 2.24
3115 3389 4.999950 CCACTAAGGCATCATCCTATCAAC 59.000 45.833 0.00 0.00 34.82 3.18
3119 3393 5.103940 ACAAACCACTAAGGCATCATCCTAT 60.104 40.000 0.00 0.00 43.14 2.57
3125 3399 4.469657 AGAAACAAACCACTAAGGCATCA 58.530 39.130 0.00 0.00 43.14 3.07
3135 3409 4.983671 AGTGAAAGGAGAAACAAACCAC 57.016 40.909 0.00 0.00 0.00 4.16
3138 3412 5.410924 AGCAAAGTGAAAGGAGAAACAAAC 58.589 37.500 0.00 0.00 0.00 2.93
3178 3452 1.530013 AACAGCATGGAGTGGCTTGC 61.530 55.000 0.00 0.00 43.62 4.01
3236 3510 6.261381 GTGTAGGGAAAATACCAAATATCGCA 59.739 38.462 0.00 0.00 0.00 5.10
3238 3512 9.204570 CTAGTGTAGGGAAAATACCAAATATCG 57.795 37.037 0.00 0.00 0.00 2.92
3262 3536 4.487282 ACATGATAGGGAAGGCTACCTA 57.513 45.455 17.19 17.19 43.08 3.08
3263 3537 3.352611 ACATGATAGGGAAGGCTACCT 57.647 47.619 14.25 14.25 40.89 3.08
3264 3538 4.532521 ACATACATGATAGGGAAGGCTACC 59.467 45.833 0.00 0.10 0.00 3.18
3265 3539 5.746990 ACATACATGATAGGGAAGGCTAC 57.253 43.478 0.00 0.00 0.00 3.58
3272 3548 6.296432 GGCCATAGAAACATACATGATAGGGA 60.296 42.308 0.00 0.00 0.00 4.20
3290 3566 3.809832 CCACGTAGAAAAGATGGCCATAG 59.190 47.826 20.84 4.35 0.00 2.23
3318 3594 4.943705 TGTCCAGGAAGAAATAAGCATGTC 59.056 41.667 0.00 0.00 0.00 3.06
3345 3621 5.869888 ACTTCATGTAGAATGTTCGGAACTC 59.130 40.000 20.53 11.42 35.25 3.01
3356 3632 8.100791 TGCCAACTAGTTAACTTCATGTAGAAT 58.899 33.333 14.49 0.00 35.25 2.40
3378 3654 1.484240 CCCACCAGAAAAAGTTTGCCA 59.516 47.619 0.00 0.00 0.00 4.92
3379 3655 1.484653 ACCCACCAGAAAAAGTTTGCC 59.515 47.619 0.00 0.00 0.00 4.52
3380 3656 2.549926 CACCCACCAGAAAAAGTTTGC 58.450 47.619 0.00 0.00 0.00 3.68
3382 3658 2.466846 AGCACCCACCAGAAAAAGTTT 58.533 42.857 0.00 0.00 0.00 2.66
3383 3659 2.159179 AGCACCCACCAGAAAAAGTT 57.841 45.000 0.00 0.00 0.00 2.66
3384 3660 2.159179 AAGCACCCACCAGAAAAAGT 57.841 45.000 0.00 0.00 0.00 2.66
3385 3661 4.321974 GGAATAAGCACCCACCAGAAAAAG 60.322 45.833 0.00 0.00 0.00 2.27
3447 3744 1.220206 CTGACAGGCAGCTAGTGGG 59.780 63.158 0.00 0.00 37.90 4.61
3480 3777 1.400500 CGCCAAATGGTACGTTGAACC 60.400 52.381 0.00 0.00 37.57 3.62
3485 3782 5.761234 ACATATATTCGCCAAATGGTACGTT 59.239 36.000 0.00 0.00 37.57 3.99
3503 3800 5.756347 GCAAACTATGGGTTCGACACATATA 59.244 40.000 9.43 3.37 42.95 0.86
3508 3805 2.147958 TGCAAACTATGGGTTCGACAC 58.852 47.619 0.00 0.00 37.12 3.67
3513 3810 2.946564 GCAACTGCAAACTATGGGTTC 58.053 47.619 0.00 0.00 41.59 3.62
3820 4125 6.942532 ACAAAGAAGCAAGAGTAATGTTCA 57.057 33.333 0.00 0.00 0.00 3.18
4097 4403 9.190858 GAAATATGCAGTCAAATTGTTTACACA 57.809 29.630 0.00 0.00 0.00 3.72
4098 4404 9.190858 TGAAATATGCAGTCAAATTGTTTACAC 57.809 29.630 0.00 0.00 0.00 2.90
4158 4464 1.531149 CAGCACCTAACAAGTGGTTCG 59.469 52.381 0.00 0.00 43.05 3.95
4178 4484 5.314923 ACAATACCATCACAACTGAATGC 57.685 39.130 0.00 0.00 0.00 3.56
4226 4532 7.917505 GTCTGCAAATAAAATAGGATCAACAGG 59.082 37.037 0.00 0.00 0.00 4.00
4586 4892 1.519751 CCGATCCTAGCCTCACCTCG 61.520 65.000 0.00 0.00 0.00 4.63
4777 5084 9.101325 TCTTCTATTTCTTTTCAGAGGGAGTAA 57.899 33.333 0.00 0.00 0.00 2.24
4799 5106 8.684973 TTAAAAGTAGTGATCTAACGCTCTTC 57.315 34.615 0.00 0.00 32.69 2.87
4834 5142 7.788026 TCCCTTCGTAAAGAAATATAAGAGCA 58.212 34.615 0.00 0.00 38.57 4.26
4854 5162 3.452627 ACATTGAAGCGATCTACTCCCTT 59.547 43.478 0.00 0.00 0.00 3.95
4879 5187 1.511887 CCGCGGAAATTGTTGCTCG 60.512 57.895 24.07 0.00 33.62 5.03
4993 5304 9.840427 AAAGACCATTCAATTCGTAGTAAAATG 57.160 29.630 0.00 0.00 0.00 2.32
5015 5326 7.523709 GCAGGGATTACATGTCAAAGAAAAAGA 60.524 37.037 0.00 0.00 0.00 2.52
5016 5327 6.587608 GCAGGGATTACATGTCAAAGAAAAAG 59.412 38.462 0.00 0.00 0.00 2.27
5022 5333 5.047802 ACAAAGCAGGGATTACATGTCAAAG 60.048 40.000 0.00 0.00 0.00 2.77
5089 5403 8.759481 TCAGGATTATTTGTATTTACATGGCA 57.241 30.769 0.00 0.00 35.89 4.92
5090 5404 8.850156 ACTCAGGATTATTTGTATTTACATGGC 58.150 33.333 0.00 0.00 35.89 4.40
5153 5486 5.508567 TCCCAAACATATCAAATGCTCTCA 58.491 37.500 0.00 0.00 0.00 3.27
5177 5512 5.499004 TGGTTTGAAGTTATAGCAGAGGT 57.501 39.130 0.00 0.00 0.00 3.85
5238 5573 7.966339 TTGAATCCCAGATTTCATCAGAATT 57.034 32.000 0.00 0.00 32.27 2.17
5287 5622 4.290942 AGATAAGGACCCTGGTAACTGAG 58.709 47.826 0.00 0.00 37.83 3.35
5288 5623 4.348020 AGATAAGGACCCTGGTAACTGA 57.652 45.455 0.00 0.00 37.83 3.41
5289 5624 5.437191 AAAGATAAGGACCCTGGTAACTG 57.563 43.478 0.00 0.00 37.61 3.16
5290 5625 7.017850 TGTTAAAAGATAAGGACCCTGGTAACT 59.982 37.037 0.00 0.00 37.61 2.24
5291 5626 7.170277 TGTTAAAAGATAAGGACCCTGGTAAC 58.830 38.462 0.00 0.00 0.00 2.50
5292 5627 7.332433 TGTTAAAAGATAAGGACCCTGGTAA 57.668 36.000 0.00 0.00 0.00 2.85
5293 5628 6.956102 TGTTAAAAGATAAGGACCCTGGTA 57.044 37.500 0.00 0.00 0.00 3.25
5294 5629 5.853572 TGTTAAAAGATAAGGACCCTGGT 57.146 39.130 0.00 0.00 0.00 4.00
5295 5630 6.663734 AGATGTTAAAAGATAAGGACCCTGG 58.336 40.000 0.00 0.00 0.00 4.45
5296 5631 7.442666 GCTAGATGTTAAAAGATAAGGACCCTG 59.557 40.741 0.00 0.00 0.00 4.45
5297 5632 7.348537 AGCTAGATGTTAAAAGATAAGGACCCT 59.651 37.037 0.00 0.00 0.00 4.34
5298 5633 7.510407 AGCTAGATGTTAAAAGATAAGGACCC 58.490 38.462 0.00 0.00 0.00 4.46
5342 7293 6.916387 GCTACCAGTTCACTAAAAAGGAAAAC 59.084 38.462 0.00 0.00 0.00 2.43
5383 7334 6.935741 TTGCCATGTCTAATTGTGTATACC 57.064 37.500 0.00 0.00 0.00 2.73
5416 7367 2.403252 ATAGTACAGCCAGTGGTTGC 57.597 50.000 24.51 10.38 37.43 4.17
5423 7374 7.041721 TGAATCACAGTTAATAGTACAGCCAG 58.958 38.462 0.00 0.00 0.00 4.85
5425 7376 9.542462 TTATGAATCACAGTTAATAGTACAGCC 57.458 33.333 0.00 0.00 0.00 4.85
5451 7402 9.484806 AAATTCATTCTAAGATCTGTTCCCAAT 57.515 29.630 0.00 0.00 0.00 3.16
5452 7403 8.884124 AAATTCATTCTAAGATCTGTTCCCAA 57.116 30.769 0.00 0.00 0.00 4.12
5453 7404 8.884124 AAAATTCATTCTAAGATCTGTTCCCA 57.116 30.769 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.