Multiple sequence alignment - TraesCS7A01G049300

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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 TraesCS7A01G049300 chr7A 100.000 3878 0 0 1 3878 22964857 22960980 0.000000e+00 7162.0
1 TraesCS7A01G049300 chr7A 97.083 617 16 2 1 616 121045869 121045254 0.000000e+00 1038.0
2 TraesCS7A01G049300 chr7A 96.921 617 17 2 1 616 657506259 657505644 0.000000e+00 1033.0
3 TraesCS7A01G049300 chr4A 90.515 2214 143 32 1104 3286 705539082 705536905 0.000000e+00 2863.0
4 TraesCS7A01G049300 chr4A 96.921 617 17 2 1 616 537234027 537234642 0.000000e+00 1033.0
5 TraesCS7A01G049300 chr4A 76.899 316 36 16 827 1106 705539445 705539131 1.120000e-30 145.0
6 TraesCS7A01G049300 chr4A 100.000 29 0 0 1102 1130 705539123 705539095 2.000000e-03 54.7
7 TraesCS7A01G049300 chr7D 89.564 2204 142 47 1123 3291 22613847 22611697 0.000000e+00 2715.0
8 TraesCS7A01G049300 chr7D 95.028 362 16 1 3245 3604 22610248 22609887 5.620000e-158 568.0
9 TraesCS7A01G049300 chr7D 94.737 266 12 2 3615 3878 22609913 22609648 2.790000e-111 412.0
10 TraesCS7A01G049300 chr7D 84.337 83 13 0 3612 3694 22611515 22611433 8.930000e-12 82.4
11 TraesCS7A01G049300 chr7D 78.014 141 13 9 975 1100 22614037 22613900 5.370000e-09 73.1
12 TraesCS7A01G049300 chr2B 97.407 617 14 2 1 616 39425702 39425087 0.000000e+00 1050.0
13 TraesCS7A01G049300 chr3A 97.083 617 16 2 1 616 604309896 604309281 0.000000e+00 1038.0
14 TraesCS7A01G049300 chr5A 96.921 617 17 2 1 616 22288348 22288963 0.000000e+00 1033.0
15 TraesCS7A01G049300 chr4B 96.921 617 17 2 1 616 489024631 489025246 0.000000e+00 1033.0
16 TraesCS7A01G049300 chr2A 96.926 618 16 3 1 616 145437219 145437835 0.000000e+00 1033.0
17 TraesCS7A01G049300 chr2A 84.615 78 12 0 1379 1456 11331253 11331176 1.160000e-10 78.7
18 TraesCS7A01G049300 chr6B 96.759 617 18 2 1 616 669342815 669342200 0.000000e+00 1027.0
19 TraesCS7A01G049300 chr2D 82.209 489 43 21 956 1408 476933599 476934079 7.860000e-102 381.0
20 TraesCS7A01G049300 chr5D 83.149 451 36 18 993 1408 515035848 515035403 3.660000e-100 375.0


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 TraesCS7A01G049300 chr7A 22960980 22964857 3877 True 7162.0 7162 100.000 1 3878 1 chr7A.!!$R1 3877
1 TraesCS7A01G049300 chr7A 121045254 121045869 615 True 1038.0 1038 97.083 1 616 1 chr7A.!!$R2 615
2 TraesCS7A01G049300 chr7A 657505644 657506259 615 True 1033.0 1033 96.921 1 616 1 chr7A.!!$R3 615
3 TraesCS7A01G049300 chr4A 537234027 537234642 615 False 1033.0 1033 96.921 1 616 1 chr4A.!!$F1 615
4 TraesCS7A01G049300 chr4A 705536905 705539445 2540 True 1020.9 2863 89.138 827 3286 3 chr4A.!!$R1 2459
5 TraesCS7A01G049300 chr7D 22609648 22614037 4389 True 770.1 2715 88.336 975 3878 5 chr7D.!!$R1 2903
6 TraesCS7A01G049300 chr2B 39425087 39425702 615 True 1050.0 1050 97.407 1 616 1 chr2B.!!$R1 615
7 TraesCS7A01G049300 chr3A 604309281 604309896 615 True 1038.0 1038 97.083 1 616 1 chr3A.!!$R1 615
8 TraesCS7A01G049300 chr5A 22288348 22288963 615 False 1033.0 1033 96.921 1 616 1 chr5A.!!$F1 615
9 TraesCS7A01G049300 chr4B 489024631 489025246 615 False 1033.0 1033 96.921 1 616 1 chr4B.!!$F1 615
10 TraesCS7A01G049300 chr2A 145437219 145437835 616 False 1033.0 1033 96.926 1 616 1 chr2A.!!$F1 615
11 TraesCS7A01G049300 chr6B 669342200 669342815 615 True 1027.0 1027 96.759 1 616 1 chr6B.!!$R1 615

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
802 805 0.032130 TTTATAGCCGCCGCTCTCAG 59.968 55.0 1.83 0.0 43.95 3.35 F
822 825 0.105760 TTTGCCTTCTCCTTGCCCAA 60.106 50.0 0.00 0.0 0.00 4.12 F
823 826 0.114954 TTGCCTTCTCCTTGCCCAAT 59.885 50.0 0.00 0.0 0.00 3.16 F
946 960 0.179140 CCGCCGCACAATTTTGCTAT 60.179 50.0 14.27 0.0 40.62 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2732 2880 0.036577 GCATGTCACACTCAGCCTCT 60.037 55.000 0.0 0.0 0.00 3.69 R
2791 2939 2.912956 AGTCCTTCTCTGCATAACCCAA 59.087 45.455 0.0 0.0 0.00 4.12 R
2797 2945 3.509967 TCGTCAAAGTCCTTCTCTGCATA 59.490 43.478 0.0 0.0 0.00 3.14 R
2920 3068 4.404507 GCAAAGTGCAGAAGATAACGAA 57.595 40.909 0.0 0.0 44.26 3.85 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
107 109 8.304596 CGGTACTACCAATATGAATACACATCT 58.695 37.037 6.06 0.00 38.47 2.90
493 496 1.600636 CCACGTTGGCAGGATGTGT 60.601 57.895 9.90 0.00 39.31 3.72
558 561 4.877619 TCGGGCGCCACACCAAAA 62.878 61.111 30.85 0.05 0.00 2.44
571 574 2.438021 ACACCAAAAGGTCAGCAGAGTA 59.562 45.455 0.00 0.00 0.00 2.59
616 619 4.687483 CAGTTTGTGATTTGATTTCTGCCC 59.313 41.667 0.00 0.00 0.00 5.36
617 620 3.959535 TTGTGATTTGATTTCTGCCCC 57.040 42.857 0.00 0.00 0.00 5.80
618 621 1.818060 TGTGATTTGATTTCTGCCCCG 59.182 47.619 0.00 0.00 0.00 5.73
619 622 0.817013 TGATTTGATTTCTGCCCCGC 59.183 50.000 0.00 0.00 0.00 6.13
620 623 0.248621 GATTTGATTTCTGCCCCGCG 60.249 55.000 0.00 0.00 0.00 6.46
621 624 2.283472 ATTTGATTTCTGCCCCGCGC 62.283 55.000 0.00 0.00 38.31 6.86
622 625 3.918253 TTGATTTCTGCCCCGCGCT 62.918 57.895 5.56 0.00 38.78 5.92
623 626 3.134127 GATTTCTGCCCCGCGCTT 61.134 61.111 5.56 0.00 38.78 4.68
624 627 3.401243 GATTTCTGCCCCGCGCTTG 62.401 63.158 5.56 0.00 38.78 4.01
625 628 3.918253 ATTTCTGCCCCGCGCTTGA 62.918 57.895 5.56 0.00 38.78 3.02
638 641 4.335647 CTTGACCCAGCCAGCCGT 62.336 66.667 0.00 0.00 0.00 5.68
639 642 2.925706 TTGACCCAGCCAGCCGTA 60.926 61.111 0.00 0.00 0.00 4.02
640 643 2.859273 CTTGACCCAGCCAGCCGTAG 62.859 65.000 0.00 0.00 0.00 3.51
641 644 4.840005 GACCCAGCCAGCCGTAGC 62.840 72.222 0.00 0.00 40.32 3.58
644 647 4.393155 CCAGCCAGCCGTAGCACA 62.393 66.667 0.00 0.00 43.56 4.57
645 648 2.358615 CAGCCAGCCGTAGCACAA 60.359 61.111 0.00 0.00 43.56 3.33
646 649 2.358737 AGCCAGCCGTAGCACAAC 60.359 61.111 0.00 0.00 43.56 3.32
647 650 3.431725 GCCAGCCGTAGCACAACC 61.432 66.667 0.00 0.00 43.56 3.77
648 651 3.118454 CCAGCCGTAGCACAACCG 61.118 66.667 0.00 0.00 43.56 4.44
649 652 3.788766 CAGCCGTAGCACAACCGC 61.789 66.667 0.00 0.00 43.56 5.68
652 655 3.773630 CCGTAGCACAACCGCGTG 61.774 66.667 4.92 0.00 40.00 5.34
681 684 2.507324 GAGCAAGTCGAGCCGGAC 60.507 66.667 5.05 0.00 37.19 4.79
682 685 4.421479 AGCAAGTCGAGCCGGACG 62.421 66.667 5.05 10.80 41.81 4.79
684 687 4.796231 CAAGTCGAGCCGGACGGG 62.796 72.222 5.05 3.74 41.81 5.28
696 699 4.137872 GACGGGGGCAATCGACGA 62.138 66.667 0.00 0.00 0.00 4.20
697 700 4.446413 ACGGGGGCAATCGACGAC 62.446 66.667 0.00 0.00 0.00 4.34
698 701 4.444838 CGGGGGCAATCGACGACA 62.445 66.667 0.00 0.00 0.00 4.35
699 702 2.818274 GGGGGCAATCGACGACAC 60.818 66.667 0.00 0.00 0.00 3.67
700 703 3.186047 GGGGCAATCGACGACACG 61.186 66.667 0.00 0.00 0.00 4.49
701 704 2.126228 GGGCAATCGACGACACGA 60.126 61.111 0.00 0.00 46.04 4.35
702 705 2.442188 GGGCAATCGACGACACGAC 61.442 63.158 0.00 0.00 44.84 4.34
703 706 2.442188 GGCAATCGACGACACGACC 61.442 63.158 0.00 0.00 44.84 4.79
704 707 2.774951 GCAATCGACGACACGACCG 61.775 63.158 0.00 0.00 44.84 4.79
705 708 2.150218 CAATCGACGACACGACCGG 61.150 63.158 0.00 0.00 44.84 5.28
706 709 3.332493 AATCGACGACACGACCGGG 62.332 63.158 6.32 0.00 44.84 5.73
708 711 4.748679 CGACGACACGACCGGGTC 62.749 72.222 17.38 17.38 44.52 4.46
709 712 4.410743 GACGACACGACCGGGTCC 62.411 72.222 21.06 6.35 45.12 4.46
713 716 4.948080 ACACGACCGGGTCCCCTT 62.948 66.667 21.06 0.65 0.00 3.95
714 717 4.078516 CACGACCGGGTCCCCTTC 62.079 72.222 21.06 0.00 0.00 3.46
723 726 4.040198 GTCCCCTTCCCCTCCCCT 62.040 72.222 0.00 0.00 0.00 4.79
724 727 3.707189 TCCCCTTCCCCTCCCCTC 61.707 72.222 0.00 0.00 0.00 4.30
725 728 4.845307 CCCCTTCCCCTCCCCTCC 62.845 77.778 0.00 0.00 0.00 4.30
726 729 4.845307 CCCTTCCCCTCCCCTCCC 62.845 77.778 0.00 0.00 0.00 4.30
727 730 4.845307 CCTTCCCCTCCCCTCCCC 62.845 77.778 0.00 0.00 0.00 4.81
752 755 4.154347 GGTCTCGGCCTGCTCCTG 62.154 72.222 0.00 0.00 0.00 3.86
753 756 4.828925 GTCTCGGCCTGCTCCTGC 62.829 72.222 0.00 0.00 40.20 4.85
759 762 4.737177 GCCTGCTCCTGCCTGCTT 62.737 66.667 0.00 0.00 38.71 3.91
760 763 2.438075 CCTGCTCCTGCCTGCTTC 60.438 66.667 0.00 0.00 38.71 3.86
761 764 2.350134 CTGCTCCTGCCTGCTTCA 59.650 61.111 0.00 0.00 38.71 3.02
762 765 1.077644 CTGCTCCTGCCTGCTTCAT 60.078 57.895 0.00 0.00 38.71 2.57
763 766 1.377366 CTGCTCCTGCCTGCTTCATG 61.377 60.000 0.00 0.00 38.71 3.07
764 767 2.772691 GCTCCTGCCTGCTTCATGC 61.773 63.158 0.00 0.00 43.25 4.06
765 768 1.077644 CTCCTGCCTGCTTCATGCT 60.078 57.895 0.00 0.00 43.37 3.79
766 769 0.179702 CTCCTGCCTGCTTCATGCTA 59.820 55.000 0.00 0.00 43.37 3.49
767 770 0.107508 TCCTGCCTGCTTCATGCTAC 60.108 55.000 0.00 0.00 43.37 3.58
768 771 0.107312 CCTGCCTGCTTCATGCTACT 60.107 55.000 0.00 0.00 43.37 2.57
769 772 1.139654 CCTGCCTGCTTCATGCTACTA 59.860 52.381 0.00 0.00 43.37 1.82
770 773 2.481854 CTGCCTGCTTCATGCTACTAG 58.518 52.381 0.00 0.00 43.37 2.57
771 774 1.833630 TGCCTGCTTCATGCTACTAGT 59.166 47.619 0.00 0.00 43.37 2.57
772 775 3.031013 TGCCTGCTTCATGCTACTAGTA 58.969 45.455 1.89 1.89 43.37 1.82
773 776 3.181475 TGCCTGCTTCATGCTACTAGTAC 60.181 47.826 0.00 0.00 43.37 2.73
774 777 3.068873 GCCTGCTTCATGCTACTAGTACT 59.931 47.826 0.00 0.00 43.37 2.73
775 778 4.278669 GCCTGCTTCATGCTACTAGTACTA 59.721 45.833 1.89 1.89 43.37 1.82
776 779 5.764131 CCTGCTTCATGCTACTAGTACTAC 58.236 45.833 0.00 0.00 43.37 2.73
777 780 5.533154 CCTGCTTCATGCTACTAGTACTACT 59.467 44.000 0.00 0.00 43.37 2.57
778 781 6.293735 CCTGCTTCATGCTACTAGTACTACTC 60.294 46.154 0.00 0.00 43.37 2.59
779 782 5.531659 TGCTTCATGCTACTAGTACTACTCC 59.468 44.000 0.00 0.00 43.37 3.85
780 783 5.766174 GCTTCATGCTACTAGTACTACTCCT 59.234 44.000 0.00 0.00 38.95 3.69
781 784 6.293735 GCTTCATGCTACTAGTACTACTCCTG 60.294 46.154 0.00 0.00 38.95 3.86
782 785 6.249911 TCATGCTACTAGTACTACTCCTGT 57.750 41.667 0.00 0.00 0.00 4.00
783 786 6.660800 TCATGCTACTAGTACTACTCCTGTT 58.339 40.000 0.00 0.00 0.00 3.16
784 787 7.117397 TCATGCTACTAGTACTACTCCTGTTT 58.883 38.462 0.00 0.00 0.00 2.83
785 788 7.614583 TCATGCTACTAGTACTACTCCTGTTTT 59.385 37.037 0.00 0.00 0.00 2.43
786 789 8.900781 CATGCTACTAGTACTACTCCTGTTTTA 58.099 37.037 0.00 0.00 0.00 1.52
787 790 9.643735 ATGCTACTAGTACTACTCCTGTTTTAT 57.356 33.333 0.00 0.00 0.00 1.40
791 794 8.462589 ACTAGTACTACTCCTGTTTTATAGCC 57.537 38.462 0.00 0.00 0.00 3.93
792 795 6.388435 AGTACTACTCCTGTTTTATAGCCG 57.612 41.667 0.00 0.00 0.00 5.52
793 796 4.056092 ACTACTCCTGTTTTATAGCCGC 57.944 45.455 0.00 0.00 0.00 6.53
794 797 2.327200 ACTCCTGTTTTATAGCCGCC 57.673 50.000 0.00 0.00 0.00 6.13
795 798 1.217882 CTCCTGTTTTATAGCCGCCG 58.782 55.000 0.00 0.00 0.00 6.46
796 799 0.812412 TCCTGTTTTATAGCCGCCGC 60.812 55.000 0.00 0.00 0.00 6.53
798 801 0.582005 CTGTTTTATAGCCGCCGCTC 59.418 55.000 1.83 0.00 43.95 5.03
799 802 0.177141 TGTTTTATAGCCGCCGCTCT 59.823 50.000 1.83 0.00 43.95 4.09
800 803 0.859882 GTTTTATAGCCGCCGCTCTC 59.140 55.000 1.83 0.00 43.95 3.20
801 804 0.462375 TTTTATAGCCGCCGCTCTCA 59.538 50.000 1.83 0.00 43.95 3.27
802 805 0.032130 TTTATAGCCGCCGCTCTCAG 59.968 55.000 1.83 0.00 43.95 3.35
803 806 1.107538 TTATAGCCGCCGCTCTCAGT 61.108 55.000 1.83 0.00 43.95 3.41
804 807 1.107538 TATAGCCGCCGCTCTCAGTT 61.108 55.000 1.83 0.00 43.95 3.16
805 808 1.961180 ATAGCCGCCGCTCTCAGTTT 61.961 55.000 1.83 0.00 43.95 2.66
806 809 2.835701 TAGCCGCCGCTCTCAGTTTG 62.836 60.000 1.83 0.00 43.95 2.93
807 810 3.793144 CCGCCGCTCTCAGTTTGC 61.793 66.667 0.00 0.00 0.00 3.68
808 811 3.793144 CGCCGCTCTCAGTTTGCC 61.793 66.667 0.00 0.00 0.00 4.52
809 812 2.359230 GCCGCTCTCAGTTTGCCT 60.359 61.111 0.00 0.00 0.00 4.75
810 813 1.968540 GCCGCTCTCAGTTTGCCTT 60.969 57.895 0.00 0.00 0.00 4.35
811 814 1.916697 GCCGCTCTCAGTTTGCCTTC 61.917 60.000 0.00 0.00 0.00 3.46
812 815 0.321122 CCGCTCTCAGTTTGCCTTCT 60.321 55.000 0.00 0.00 0.00 2.85
813 816 1.074752 CGCTCTCAGTTTGCCTTCTC 58.925 55.000 0.00 0.00 0.00 2.87
814 817 1.447945 GCTCTCAGTTTGCCTTCTCC 58.552 55.000 0.00 0.00 0.00 3.71
815 818 1.003003 GCTCTCAGTTTGCCTTCTCCT 59.997 52.381 0.00 0.00 0.00 3.69
816 819 2.551938 GCTCTCAGTTTGCCTTCTCCTT 60.552 50.000 0.00 0.00 0.00 3.36
817 820 3.072944 CTCTCAGTTTGCCTTCTCCTTG 58.927 50.000 0.00 0.00 0.00 3.61
818 821 1.538950 CTCAGTTTGCCTTCTCCTTGC 59.461 52.381 0.00 0.00 0.00 4.01
819 822 0.600057 CAGTTTGCCTTCTCCTTGCC 59.400 55.000 0.00 0.00 0.00 4.52
820 823 0.540597 AGTTTGCCTTCTCCTTGCCC 60.541 55.000 0.00 0.00 0.00 5.36
821 824 0.827507 GTTTGCCTTCTCCTTGCCCA 60.828 55.000 0.00 0.00 0.00 5.36
822 825 0.105760 TTTGCCTTCTCCTTGCCCAA 60.106 50.000 0.00 0.00 0.00 4.12
823 826 0.114954 TTGCCTTCTCCTTGCCCAAT 59.885 50.000 0.00 0.00 0.00 3.16
824 827 0.323725 TGCCTTCTCCTTGCCCAATC 60.324 55.000 0.00 0.00 0.00 2.67
825 828 1.039785 GCCTTCTCCTTGCCCAATCC 61.040 60.000 0.00 0.00 0.00 3.01
836 839 2.517919 CCAATCCCCAGGCTAGCC 59.482 66.667 27.19 27.19 0.00 3.93
838 841 1.649271 CCAATCCCCAGGCTAGCCTT 61.649 60.000 34.20 16.71 45.70 4.35
871 874 3.966104 CGGCGCTCGCTCCATCTA 61.966 66.667 7.64 0.00 41.60 1.98
887 890 0.975556 TCTAATCCACCCAGCTGCGA 60.976 55.000 8.66 0.57 0.00 5.10
893 896 3.706373 ACCCAGCTGCGATCCGTT 61.706 61.111 8.66 0.00 0.00 4.44
895 898 2.892425 CCAGCTGCGATCCGTTCC 60.892 66.667 8.66 0.00 0.00 3.62
900 903 1.218047 CTGCGATCCGTTCCTTCCA 59.782 57.895 0.00 0.00 0.00 3.53
902 905 2.174319 GCGATCCGTTCCTTCCAGC 61.174 63.158 0.00 0.00 0.00 4.85
905 908 0.528684 GATCCGTTCCTTCCAGCGAG 60.529 60.000 0.00 0.00 0.00 5.03
915 918 2.354259 CTTCCAGCGAGCATTTCTTCT 58.646 47.619 0.00 0.00 0.00 2.85
921 924 4.380233 CCAGCGAGCATTTCTTCTGAATTT 60.380 41.667 0.00 0.00 31.51 1.82
923 926 5.060569 CAGCGAGCATTTCTTCTGAATTTTG 59.939 40.000 0.00 0.00 31.51 2.44
935 949 4.722855 ATTTTGCTGCCGCCGCAC 62.723 61.111 9.19 0.00 41.12 5.34
942 956 2.355599 TGCCGCCGCACAATTTTG 60.356 55.556 0.00 0.00 41.12 2.44
945 959 1.211449 CCGCCGCACAATTTTGCTA 59.789 52.632 14.27 0.00 40.62 3.49
946 960 0.179140 CCGCCGCACAATTTTGCTAT 60.179 50.000 14.27 0.00 40.62 2.97
947 961 1.191096 CGCCGCACAATTTTGCTATC 58.809 50.000 14.27 2.98 40.62 2.08
949 963 2.187707 GCCGCACAATTTTGCTATCTG 58.812 47.619 14.27 0.00 40.62 2.90
951 965 3.489738 GCCGCACAATTTTGCTATCTGAT 60.490 43.478 14.27 0.00 40.62 2.90
953 967 4.036027 CCGCACAATTTTGCTATCTGATCT 59.964 41.667 14.27 0.00 40.62 2.75
954 968 5.449588 CCGCACAATTTTGCTATCTGATCTT 60.450 40.000 14.27 0.00 40.62 2.40
955 969 6.238456 CCGCACAATTTTGCTATCTGATCTTA 60.238 38.462 14.27 0.00 40.62 2.10
956 970 6.849811 CGCACAATTTTGCTATCTGATCTTAG 59.150 38.462 14.27 0.00 40.62 2.18
957 971 6.636044 GCACAATTTTGCTATCTGATCTTAGC 59.364 38.462 9.34 12.93 40.97 3.09
1029 1050 1.446272 CAGGTCGTCCTTCTTCGCC 60.446 63.158 0.00 0.00 43.07 5.54
1033 1054 1.605451 TCGTCCTTCTTCGCCTCCA 60.605 57.895 0.00 0.00 0.00 3.86
1040 1061 1.503818 TTCTTCGCCTCCAACAACGC 61.504 55.000 0.00 0.00 0.00 4.84
1050 1071 1.673920 TCCAACAACGCCAAGAAGAAC 59.326 47.619 0.00 0.00 0.00 3.01
1054 1075 0.537371 CAACGCCAAGAAGAACCCCT 60.537 55.000 0.00 0.00 0.00 4.79
1055 1076 0.185175 AACGCCAAGAAGAACCCCTT 59.815 50.000 0.00 0.00 37.93 3.95
1074 1113 2.462782 CGACTCCGACTCCGACTCC 61.463 68.421 0.00 0.00 38.22 3.85
1153 1243 2.646175 CGGAACTCCCTCTTCGCCA 61.646 63.158 0.00 0.00 0.00 5.69
1154 1244 1.079057 GGAACTCCCTCTTCGCCAC 60.079 63.158 0.00 0.00 0.00 5.01
1157 1247 3.068691 CTCCCTCTTCGCCACCGA 61.069 66.667 0.00 0.00 42.66 4.69
1161 1263 4.796231 CTCTTCGCCACCGACCCG 62.796 72.222 0.00 0.00 44.30 5.28
1200 1302 1.152839 CTCCTCCTCCTCCTCGTCC 60.153 68.421 0.00 0.00 0.00 4.79
1284 1386 4.106925 GTGCAGGAGCTGGAGGGG 62.107 72.222 0.00 0.00 42.74 4.79
1464 1566 4.893829 GGATCTATCCAGGGTAAGGAAC 57.106 50.000 4.04 0.00 46.38 3.62
1512 1617 8.319143 GGATACTACTTGCTAGTTGTTTTTCA 57.681 34.615 18.50 3.29 40.18 2.69
1516 1621 8.220755 ACTACTTGCTAGTTGTTTTTCATTGA 57.779 30.769 6.03 0.00 37.08 2.57
1537 1642 8.702438 CATTGACAAACTTGCCAATTAAGTTAG 58.298 33.333 5.48 0.00 44.98 2.34
1538 1643 7.341445 TGACAAACTTGCCAATTAAGTTAGT 57.659 32.000 5.48 0.00 44.98 2.24
1550 1662 7.683463 GCCAATTAAGTTAGTTCCTGTTGTTGT 60.683 37.037 0.00 0.00 0.00 3.32
1560 1672 3.211045 TCCTGTTGTTGTTCCTTACTGC 58.789 45.455 0.00 0.00 0.00 4.40
1564 1682 5.277828 CCTGTTGTTGTTCCTTACTGCTTAC 60.278 44.000 0.00 0.00 0.00 2.34
1593 1711 7.208225 AGCCTAATTTTGTTCTTCTCAACTC 57.792 36.000 0.00 0.00 0.00 3.01
1601 1719 7.864108 TTTGTTCTTCTCAACTCAGATCAAA 57.136 32.000 0.00 0.00 35.40 2.69
1612 1730 6.263842 TCAACTCAGATCAAATGTTTCAAGCT 59.736 34.615 0.00 0.00 0.00 3.74
1636 1759 4.776349 TGGTAGTACAGTTTATGGCATGG 58.224 43.478 10.98 0.00 0.00 3.66
1657 1780 4.642885 TGGCTGCAAATATTAGTTACCCAC 59.357 41.667 0.50 0.00 0.00 4.61
1659 1782 5.126384 GGCTGCAAATATTAGTTACCCACAA 59.874 40.000 0.50 0.00 0.00 3.33
1660 1783 6.350612 GGCTGCAAATATTAGTTACCCACAAA 60.351 38.462 0.50 0.00 0.00 2.83
1663 1786 7.822658 TGCAAATATTAGTTACCCACAAACTC 58.177 34.615 0.00 0.00 38.18 3.01
1665 1788 7.753580 GCAAATATTAGTTACCCACAAACTCAC 59.246 37.037 0.00 0.00 38.18 3.51
1668 1791 2.132686 AGTTACCCACAAACTCACCCT 58.867 47.619 0.00 0.00 31.56 4.34
1675 1798 3.243737 CCCACAAACTCACCCTTAAAAGC 60.244 47.826 0.00 0.00 0.00 3.51
1687 1810 9.739276 CTCACCCTTAAAAGCCATCATATATTA 57.261 33.333 0.00 0.00 0.00 0.98
1723 1846 5.537300 TCTGGAACTATATGCTGAGGAAC 57.463 43.478 0.00 0.00 0.00 3.62
1736 1859 3.491619 GCTGAGGAACATCTAGATTGCGA 60.492 47.826 1.33 0.00 0.00 5.10
1737 1860 4.798924 GCTGAGGAACATCTAGATTGCGAT 60.799 45.833 1.33 0.00 0.00 4.58
1744 1874 5.914085 ACATCTAGATTGCGATGTTAAGC 57.086 39.130 1.33 0.00 45.75 3.09
1754 1884 5.378292 TGCGATGTTAAGCCAAATTTACA 57.622 34.783 0.00 0.00 0.00 2.41
1796 1929 5.749596 TTACATGGACAAGTTTGTGACAG 57.250 39.130 1.62 0.21 42.43 3.51
1799 1932 1.742831 TGGACAAGTTTGTGACAGTGC 59.257 47.619 1.62 0.00 42.43 4.40
1809 1942 3.502191 TGTGACAGTGCCTTTTTGTTC 57.498 42.857 0.00 0.00 0.00 3.18
1811 1944 3.119531 TGTGACAGTGCCTTTTTGTTCTG 60.120 43.478 0.00 0.00 0.00 3.02
1817 1950 3.055891 AGTGCCTTTTTGTTCTGCAAACT 60.056 39.130 11.34 0.00 45.70 2.66
1822 1955 5.794945 GCCTTTTTGTTCTGCAAACTTTTTC 59.205 36.000 11.34 0.00 45.70 2.29
1861 1994 1.557099 GGGATCTTGGGGGTTTGTTC 58.443 55.000 0.00 0.00 0.00 3.18
1894 2027 1.457346 AGCCAAAGAAGAATGGAGCG 58.543 50.000 0.00 0.00 39.12 5.03
1945 2078 8.034804 GGTAATTTCCAGTGCAATCTTAAACAT 58.965 33.333 0.00 0.00 0.00 2.71
1993 2136 4.142609 AGAAACACATGTGTCTGACTGT 57.857 40.909 30.64 11.51 44.13 3.55
1994 2137 5.276461 AGAAACACATGTGTCTGACTGTA 57.724 39.130 30.64 0.00 44.13 2.74
1999 2142 5.798132 ACACATGTGTCTGACTGTAATGAT 58.202 37.500 25.76 0.00 40.24 2.45
2013 2159 9.056005 TGACTGTAATGATAAAATATGGACTGC 57.944 33.333 0.00 0.00 0.00 4.40
2115 2261 0.888285 GCCATATGGAGCAGAGGCAC 60.888 60.000 26.47 0.00 41.63 5.01
2215 2362 4.938080 AGTCGAGGTACATAGAATTGCTG 58.062 43.478 0.00 0.00 0.00 4.41
2234 2381 6.647334 TGCTGTGAATGAATACCTCAAAAA 57.353 33.333 0.00 0.00 37.67 1.94
2239 2386 9.918630 CTGTGAATGAATACCTCAAAAATTTCT 57.081 29.630 0.00 0.00 37.67 2.52
2248 2395 9.539194 AATACCTCAAAAATTTCTTCTCAGGAT 57.461 29.630 0.00 0.00 0.00 3.24
2452 2599 7.921214 TGACACTTCACTCTTAGTTCTTACTTG 59.079 37.037 0.00 0.00 35.78 3.16
2478 2625 6.649155 TGCTCATAGCCTAATAAACACTTCA 58.351 36.000 0.00 0.00 41.51 3.02
2479 2626 7.109501 TGCTCATAGCCTAATAAACACTTCAA 58.890 34.615 0.00 0.00 41.51 2.69
2531 2678 6.479001 ACGTGCTGTTAATCACTAATCCATAC 59.521 38.462 0.00 0.00 0.00 2.39
2572 2720 2.198827 TCCATTGCACATTTCCGTCT 57.801 45.000 0.00 0.00 0.00 4.18
2573 2721 1.811965 TCCATTGCACATTTCCGTCTG 59.188 47.619 0.00 0.00 0.00 3.51
2574 2722 1.621107 CATTGCACATTTCCGTCTGC 58.379 50.000 0.00 0.00 0.00 4.26
2598 2746 3.685550 GCTGCCCATGGAAATACTGTAGT 60.686 47.826 15.22 0.00 0.00 2.73
2599 2747 4.444306 GCTGCCCATGGAAATACTGTAGTA 60.444 45.833 15.22 0.00 34.67 1.82
2600 2748 5.290493 TGCCCATGGAAATACTGTAGTAG 57.710 43.478 15.22 0.00 33.52 2.57
2601 2749 4.065789 GCCCATGGAAATACTGTAGTAGC 58.934 47.826 15.22 0.00 33.52 3.58
2602 2750 4.202367 GCCCATGGAAATACTGTAGTAGCT 60.202 45.833 15.22 0.00 33.52 3.32
2603 2751 5.542779 CCCATGGAAATACTGTAGTAGCTC 58.457 45.833 15.22 0.00 33.52 4.09
2604 2752 5.070446 CCCATGGAAATACTGTAGTAGCTCA 59.930 44.000 15.22 0.00 33.52 4.26
2605 2753 5.986135 CCATGGAAATACTGTAGTAGCTCAC 59.014 44.000 5.56 0.00 33.52 3.51
2606 2754 6.406961 CCATGGAAATACTGTAGTAGCTCACA 60.407 42.308 5.56 0.00 33.52 3.58
2607 2755 6.599356 TGGAAATACTGTAGTAGCTCACAA 57.401 37.500 0.00 0.00 33.52 3.33
2608 2756 6.999950 TGGAAATACTGTAGTAGCTCACAAA 58.000 36.000 0.00 0.00 33.52 2.83
2609 2757 7.097192 TGGAAATACTGTAGTAGCTCACAAAG 58.903 38.462 0.00 0.00 33.52 2.77
2630 2778 4.003648 AGTAGCTCCAAAATCCAGAAACG 58.996 43.478 0.00 0.00 0.00 3.60
2650 2798 6.817765 AACGATTTACCATCTGACATTGTT 57.182 33.333 0.00 0.00 0.00 2.83
2724 2872 3.243501 GCTTCATTCTTCAAGGTGCAACA 60.244 43.478 3.64 0.00 39.98 3.33
2731 2879 5.843673 TCTTCAAGGTGCAACATTTACAA 57.156 34.783 3.64 0.00 37.74 2.41
2732 2880 6.214191 TCTTCAAGGTGCAACATTTACAAA 57.786 33.333 3.64 0.00 37.74 2.83
2733 2881 6.272318 TCTTCAAGGTGCAACATTTACAAAG 58.728 36.000 3.64 0.00 37.74 2.77
2791 2939 3.454082 TGGTTTCAGGCAAACAAAGGATT 59.546 39.130 3.29 0.00 45.66 3.01
2844 2992 1.923395 CTACAGGGTCAAGGGGGCA 60.923 63.158 0.00 0.00 0.00 5.36
2880 3028 2.028130 CGTCTGCTTGGGAGATAGACT 58.972 52.381 0.00 0.00 36.91 3.24
2902 3050 5.299028 ACTGAAAGCATATGTTGTTGTCACA 59.701 36.000 4.29 0.00 37.60 3.58
2962 3110 3.610821 GCTTCCGTGGGTTGTTAATTCAC 60.611 47.826 0.00 0.00 0.00 3.18
2980 3128 9.926158 TTAATTCACATCATTTTGTGCATAAGT 57.074 25.926 0.00 0.00 45.29 2.24
2996 3144 4.567971 CATAAGTCTCTGATCAGGATGGC 58.432 47.826 22.42 13.95 36.16 4.40
3060 3208 0.039437 ATATGCTAGACGGCGGTTCG 60.039 55.000 13.24 0.00 34.52 3.95
3266 3416 1.464997 GGCTTTGAGATCCGTGTTGTC 59.535 52.381 0.00 0.00 0.00 3.18
3274 4919 3.919216 AGATCCGTGTTGTCTTCTTCTG 58.081 45.455 0.00 0.00 0.00 3.02
3307 4952 8.677148 TGTTCACTTATATGGATAGGCTTTTC 57.323 34.615 0.00 0.00 0.00 2.29
3361 5006 0.029300 CTGTTTGTGTGTTGGGCTCG 59.971 55.000 0.00 0.00 0.00 5.03
3428 5073 4.887748 TCAAACTGCTGGAAACACAAAAA 58.112 34.783 0.00 0.00 35.60 1.94
3432 5077 3.189285 CTGCTGGAAACACAAAAACTGG 58.811 45.455 0.00 0.00 35.60 4.00
3437 5082 5.733373 GCTGGAAACACAAAAACTGGTCTAG 60.733 44.000 0.00 0.00 35.60 2.43
3454 5099 4.560128 GTCTAGAAGACATCAGTTGCACA 58.440 43.478 0.00 0.00 44.45 4.57
3463 5108 4.536065 ACATCAGTTGCACATTTGTTACG 58.464 39.130 0.00 0.00 0.00 3.18
3478 5123 4.465632 TGTTACGGTCAGAGTTGCATAT 57.534 40.909 0.00 0.00 0.00 1.78
3479 5124 4.827692 TGTTACGGTCAGAGTTGCATATT 58.172 39.130 0.00 0.00 0.00 1.28
3576 5223 3.871006 TGCTATAAGCGTTCACTTCCATG 59.129 43.478 0.00 0.00 46.26 3.66
3577 5224 3.303395 GCTATAAGCGTTCACTTCCATGC 60.303 47.826 0.00 0.00 0.00 4.06
3594 5241 2.804986 TGCTGCATAAGACCAATGGA 57.195 45.000 6.16 0.00 0.00 3.41
3600 5247 5.389859 TGCATAAGACCAATGGAAGTTTG 57.610 39.130 6.16 0.00 0.00 2.93
3601 5248 4.832266 TGCATAAGACCAATGGAAGTTTGT 59.168 37.500 6.16 0.00 0.00 2.83
3602 5249 5.304101 TGCATAAGACCAATGGAAGTTTGTT 59.696 36.000 6.16 0.00 0.00 2.83
3603 5250 6.183360 TGCATAAGACCAATGGAAGTTTGTTT 60.183 34.615 6.16 0.00 0.00 2.83
3604 5251 6.705825 GCATAAGACCAATGGAAGTTTGTTTT 59.294 34.615 6.16 0.00 0.00 2.43
3605 5252 7.226523 GCATAAGACCAATGGAAGTTTGTTTTT 59.773 33.333 6.16 0.00 0.00 1.94
3624 5271 4.519540 TTTTCTGTGATTTGCTAAGGCC 57.480 40.909 0.00 0.00 37.74 5.19
3625 5272 2.877097 TCTGTGATTTGCTAAGGCCA 57.123 45.000 5.01 0.00 37.74 5.36
3626 5273 3.153369 TCTGTGATTTGCTAAGGCCAA 57.847 42.857 5.01 0.00 37.74 4.52
3627 5274 3.700538 TCTGTGATTTGCTAAGGCCAAT 58.299 40.909 5.01 0.00 36.67 3.16
3628 5275 3.444742 TCTGTGATTTGCTAAGGCCAATG 59.555 43.478 5.01 0.00 34.57 2.82
3629 5276 2.496871 TGTGATTTGCTAAGGCCAATGG 59.503 45.455 5.01 0.00 34.57 3.16
3630 5277 2.109774 TGATTTGCTAAGGCCAATGGG 58.890 47.619 5.01 0.00 34.57 4.00
3631 5278 2.292126 TGATTTGCTAAGGCCAATGGGA 60.292 45.455 5.01 0.00 34.57 4.37
3632 5279 1.851304 TTTGCTAAGGCCAATGGGAG 58.149 50.000 5.01 0.00 37.74 4.30
3633 5280 0.704076 TTGCTAAGGCCAATGGGAGT 59.296 50.000 5.01 0.00 37.74 3.85
3634 5281 1.590591 TGCTAAGGCCAATGGGAGTA 58.409 50.000 5.01 0.00 37.74 2.59
3635 5282 2.135189 TGCTAAGGCCAATGGGAGTAT 58.865 47.619 5.01 0.00 37.74 2.12
3664 5311 9.866798 TTCATGTATACAAAATTTTGCTGCATA 57.133 25.926 26.94 16.86 41.79 3.14
3693 5340 6.032775 GTGTCTGAAATGTTGCGACAATATTG 59.967 38.462 11.67 14.01 39.66 1.90
3716 5363 7.265647 TGGAAACGTTCTCAATTGAATACAA 57.734 32.000 9.88 0.00 40.42 2.41
3717 5364 7.359595 TGGAAACGTTCTCAATTGAATACAAG 58.640 34.615 9.88 0.00 39.46 3.16
3750 5397 2.294233 GTGAGGATTTTCTGCAGCAACA 59.706 45.455 9.47 0.00 0.00 3.33
3805 5452 5.163913 CGCTAGCCATAATAATTGCAGAGAC 60.164 44.000 9.66 0.00 0.00 3.36
3811 5458 7.941238 AGCCATAATAATTGCAGAGACTGTAAT 59.059 33.333 8.73 8.73 45.77 1.89
3838 5486 3.134574 TGTCTATTTTGTTCCTGCGGT 57.865 42.857 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 109 6.980978 TGATTTGTTTGGTTTGCTCGATTTAA 59.019 30.769 0.00 0.00 0.00 1.52
314 317 5.129634 TCTTCATCTCTTCGCTCTCTGTAT 58.870 41.667 0.00 0.00 0.00 2.29
326 329 2.641815 ACCAGGCAGTTCTTCATCTCTT 59.358 45.455 0.00 0.00 0.00 2.85
480 483 1.965930 GCGTCACACATCCTGCCAA 60.966 57.895 0.00 0.00 0.00 4.52
621 624 2.859273 CTACGGCTGGCTGGGTCAAG 62.859 65.000 6.36 0.00 0.00 3.02
622 625 2.925706 TACGGCTGGCTGGGTCAA 60.926 61.111 6.36 0.00 0.00 3.18
623 626 3.390521 CTACGGCTGGCTGGGTCA 61.391 66.667 6.36 0.00 0.00 4.02
624 627 4.840005 GCTACGGCTGGCTGGGTC 62.840 72.222 6.36 0.00 35.22 4.46
627 630 3.899981 TTGTGCTACGGCTGGCTGG 62.900 63.158 6.36 0.00 39.59 4.85
628 631 2.358615 TTGTGCTACGGCTGGCTG 60.359 61.111 0.00 0.00 39.59 4.85
629 632 2.358737 GTTGTGCTACGGCTGGCT 60.359 61.111 0.00 0.00 39.59 4.75
630 633 3.431725 GGTTGTGCTACGGCTGGC 61.432 66.667 0.00 0.00 39.59 4.85
631 634 3.118454 CGGTTGTGCTACGGCTGG 61.118 66.667 0.00 0.00 39.59 4.85
632 635 3.788766 GCGGTTGTGCTACGGCTG 61.789 66.667 8.47 0.00 40.14 4.85
635 638 3.773630 CACGCGGTTGTGCTACGG 61.774 66.667 12.47 0.00 32.31 4.02
663 666 4.116328 TCCGGCTCGACTTGCTCG 62.116 66.667 0.00 0.00 44.44 5.03
664 667 2.507324 GTCCGGCTCGACTTGCTC 60.507 66.667 0.00 0.00 0.00 4.26
665 668 4.421479 CGTCCGGCTCGACTTGCT 62.421 66.667 12.27 0.00 0.00 3.91
667 670 4.796231 CCCGTCCGGCTCGACTTG 62.796 72.222 17.76 3.89 0.00 3.16
679 682 4.137872 TCGTCGATTGCCCCCGTC 62.138 66.667 0.00 0.00 0.00 4.79
680 683 4.446413 GTCGTCGATTGCCCCCGT 62.446 66.667 0.00 0.00 0.00 5.28
681 684 4.444838 TGTCGTCGATTGCCCCCG 62.445 66.667 0.00 0.00 0.00 5.73
682 685 2.818274 GTGTCGTCGATTGCCCCC 60.818 66.667 0.00 0.00 0.00 5.40
683 686 3.186047 CGTGTCGTCGATTGCCCC 61.186 66.667 0.00 0.00 0.00 5.80
684 687 2.126228 TCGTGTCGTCGATTGCCC 60.126 61.111 0.00 0.00 34.85 5.36
685 688 2.442188 GGTCGTGTCGTCGATTGCC 61.442 63.158 0.00 0.00 41.78 4.52
686 689 2.774951 CGGTCGTGTCGTCGATTGC 61.775 63.158 0.00 0.00 41.78 3.56
687 690 2.150218 CCGGTCGTGTCGTCGATTG 61.150 63.158 0.00 0.00 41.78 2.67
688 691 2.177531 CCGGTCGTGTCGTCGATT 59.822 61.111 0.00 0.00 41.78 3.34
689 692 3.807538 CCCGGTCGTGTCGTCGAT 61.808 66.667 0.00 0.00 41.78 3.59
691 694 4.748679 GACCCGGTCGTGTCGTCG 62.749 72.222 0.65 0.00 0.00 5.12
692 695 4.410743 GGACCCGGTCGTGTCGTC 62.411 72.222 11.55 0.00 32.65 4.20
706 709 4.040198 AGGGGAGGGGAAGGGGAC 62.040 72.222 0.00 0.00 0.00 4.46
707 710 3.707189 GAGGGGAGGGGAAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
708 711 4.845307 GGAGGGGAGGGGAAGGGG 62.845 77.778 0.00 0.00 0.00 4.79
709 712 4.845307 GGGAGGGGAGGGGAAGGG 62.845 77.778 0.00 0.00 0.00 3.95
710 713 4.845307 GGGGAGGGGAGGGGAAGG 62.845 77.778 0.00 0.00 0.00 3.46
735 738 4.154347 CAGGAGCAGGCCGAGACC 62.154 72.222 0.00 0.00 0.00 3.85
736 739 4.828925 GCAGGAGCAGGCCGAGAC 62.829 72.222 0.00 0.00 41.58 3.36
742 745 4.737177 AAGCAGGCAGGAGCAGGC 62.737 66.667 0.00 0.00 44.61 4.85
743 746 2.438075 GAAGCAGGCAGGAGCAGG 60.438 66.667 0.00 0.00 44.61 4.85
744 747 1.077644 ATGAAGCAGGCAGGAGCAG 60.078 57.895 0.00 0.00 44.61 4.24
745 748 1.378119 CATGAAGCAGGCAGGAGCA 60.378 57.895 0.00 0.00 44.61 4.26
746 749 2.772691 GCATGAAGCAGGCAGGAGC 61.773 63.158 0.00 0.00 41.05 4.70
747 750 3.510846 GCATGAAGCAGGCAGGAG 58.489 61.111 0.00 0.00 41.05 3.69
756 759 5.766174 AGGAGTAGTACTAGTAGCATGAAGC 59.234 44.000 10.28 0.00 46.19 3.86
757 760 6.768861 ACAGGAGTAGTACTAGTAGCATGAAG 59.231 42.308 10.28 0.00 0.00 3.02
758 761 6.660800 ACAGGAGTAGTACTAGTAGCATGAA 58.339 40.000 10.28 0.00 0.00 2.57
759 762 6.249911 ACAGGAGTAGTACTAGTAGCATGA 57.750 41.667 10.28 0.00 0.00 3.07
760 763 6.945938 AACAGGAGTAGTACTAGTAGCATG 57.054 41.667 10.28 9.34 0.00 4.06
761 764 7.957992 AAAACAGGAGTAGTACTAGTAGCAT 57.042 36.000 10.28 0.00 0.00 3.79
765 768 9.566432 GGCTATAAAACAGGAGTAGTACTAGTA 57.434 37.037 10.28 0.00 0.00 1.82
766 769 7.228308 CGGCTATAAAACAGGAGTAGTACTAGT 59.772 40.741 10.09 10.09 0.00 2.57
767 770 7.583230 CGGCTATAAAACAGGAGTAGTACTAG 58.417 42.308 1.87 0.00 0.00 2.57
768 771 6.016777 GCGGCTATAAAACAGGAGTAGTACTA 60.017 42.308 1.88 0.00 0.00 1.82
769 772 5.221204 GCGGCTATAAAACAGGAGTAGTACT 60.221 44.000 1.37 1.37 0.00 2.73
770 773 4.981054 GCGGCTATAAAACAGGAGTAGTAC 59.019 45.833 0.00 0.00 0.00 2.73
771 774 4.038402 GGCGGCTATAAAACAGGAGTAGTA 59.962 45.833 0.00 0.00 0.00 1.82
772 775 3.181468 GGCGGCTATAAAACAGGAGTAGT 60.181 47.826 0.00 0.00 0.00 2.73
773 776 3.391049 GGCGGCTATAAAACAGGAGTAG 58.609 50.000 0.00 0.00 0.00 2.57
774 777 2.223876 CGGCGGCTATAAAACAGGAGTA 60.224 50.000 7.61 0.00 0.00 2.59
775 778 1.472728 CGGCGGCTATAAAACAGGAGT 60.473 52.381 7.61 0.00 0.00 3.85
776 779 1.217882 CGGCGGCTATAAAACAGGAG 58.782 55.000 7.61 0.00 0.00 3.69
777 780 0.812412 GCGGCGGCTATAAAACAGGA 60.812 55.000 9.78 0.00 35.83 3.86
778 781 1.647084 GCGGCGGCTATAAAACAGG 59.353 57.895 9.78 0.00 35.83 4.00
789 792 3.793144 CAAACTGAGAGCGGCGGC 61.793 66.667 9.78 8.43 40.37 6.53
790 793 3.793144 GCAAACTGAGAGCGGCGG 61.793 66.667 9.78 0.00 0.00 6.13
791 794 3.793144 GGCAAACTGAGAGCGGCG 61.793 66.667 0.51 0.51 0.00 6.46
792 795 1.916697 GAAGGCAAACTGAGAGCGGC 61.917 60.000 0.00 0.00 0.00 6.53
793 796 0.321122 AGAAGGCAAACTGAGAGCGG 60.321 55.000 0.00 0.00 0.00 5.52
794 797 1.074752 GAGAAGGCAAACTGAGAGCG 58.925 55.000 0.00 0.00 0.00 5.03
795 798 1.003003 AGGAGAAGGCAAACTGAGAGC 59.997 52.381 0.00 0.00 0.00 4.09
796 799 3.072944 CAAGGAGAAGGCAAACTGAGAG 58.927 50.000 0.00 0.00 0.00 3.20
797 800 2.811873 GCAAGGAGAAGGCAAACTGAGA 60.812 50.000 0.00 0.00 0.00 3.27
798 801 1.538950 GCAAGGAGAAGGCAAACTGAG 59.461 52.381 0.00 0.00 0.00 3.35
799 802 1.609208 GCAAGGAGAAGGCAAACTGA 58.391 50.000 0.00 0.00 0.00 3.41
800 803 0.600057 GGCAAGGAGAAGGCAAACTG 59.400 55.000 0.00 0.00 0.00 3.16
801 804 0.540597 GGGCAAGGAGAAGGCAAACT 60.541 55.000 0.00 0.00 0.00 2.66
802 805 0.827507 TGGGCAAGGAGAAGGCAAAC 60.828 55.000 0.00 0.00 0.00 2.93
803 806 0.105760 TTGGGCAAGGAGAAGGCAAA 60.106 50.000 0.00 0.00 0.00 3.68
804 807 0.114954 ATTGGGCAAGGAGAAGGCAA 59.885 50.000 0.00 0.00 0.00 4.52
805 808 0.323725 GATTGGGCAAGGAGAAGGCA 60.324 55.000 0.00 0.00 0.00 4.75
806 809 1.039785 GGATTGGGCAAGGAGAAGGC 61.040 60.000 0.00 0.00 0.00 4.35
807 810 0.396278 GGGATTGGGCAAGGAGAAGG 60.396 60.000 0.00 0.00 0.00 3.46
808 811 0.396278 GGGGATTGGGCAAGGAGAAG 60.396 60.000 0.00 0.00 0.00 2.85
809 812 1.145900 TGGGGATTGGGCAAGGAGAA 61.146 55.000 0.00 0.00 0.00 2.87
810 813 1.543642 TGGGGATTGGGCAAGGAGA 60.544 57.895 0.00 0.00 0.00 3.71
811 814 1.076485 CTGGGGATTGGGCAAGGAG 60.076 63.158 0.00 0.00 0.00 3.69
812 815 2.625460 CCTGGGGATTGGGCAAGGA 61.625 63.158 0.00 0.00 0.00 3.36
813 816 2.042639 CCTGGGGATTGGGCAAGG 60.043 66.667 0.00 0.00 0.00 3.61
814 817 1.936767 TAGCCTGGGGATTGGGCAAG 61.937 60.000 5.99 0.00 0.00 4.01
815 818 1.933284 TAGCCTGGGGATTGGGCAA 60.933 57.895 5.99 0.00 0.00 4.52
816 819 2.286808 TAGCCTGGGGATTGGGCA 60.287 61.111 5.99 0.00 0.00 5.36
817 820 2.517919 CTAGCCTGGGGATTGGGC 59.482 66.667 0.00 0.00 0.00 5.36
818 821 2.517919 GCTAGCCTGGGGATTGGG 59.482 66.667 2.29 0.00 0.00 4.12
819 822 2.081161 AGGCTAGCCTGGGGATTGG 61.081 63.158 35.59 0.00 46.22 3.16
820 823 3.666122 AGGCTAGCCTGGGGATTG 58.334 61.111 35.59 0.00 46.22 2.67
832 835 2.752807 GGAATGGCGGGGAAGGCTA 61.753 63.158 0.00 0.00 37.59 3.93
836 839 2.830370 GCTGGAATGGCGGGGAAG 60.830 66.667 0.00 0.00 0.00 3.46
837 840 4.440829 GGCTGGAATGGCGGGGAA 62.441 66.667 0.00 0.00 0.00 3.97
863 866 2.053244 AGCTGGGTGGATTAGATGGAG 58.947 52.381 0.00 0.00 0.00 3.86
866 869 1.602311 GCAGCTGGGTGGATTAGATG 58.398 55.000 17.12 0.00 0.00 2.90
868 871 0.975556 TCGCAGCTGGGTGGATTAGA 60.976 55.000 27.76 5.59 0.00 2.10
870 873 0.106708 GATCGCAGCTGGGTGGATTA 59.893 55.000 27.76 10.15 0.00 1.75
871 874 1.153086 GATCGCAGCTGGGTGGATT 60.153 57.895 27.76 10.78 0.00 3.01
887 890 1.517832 CTCGCTGGAAGGAACGGAT 59.482 57.895 0.00 0.00 0.00 4.18
891 894 1.131315 GAAATGCTCGCTGGAAGGAAC 59.869 52.381 0.00 0.00 0.00 3.62
893 896 0.615331 AGAAATGCTCGCTGGAAGGA 59.385 50.000 0.00 0.00 0.00 3.36
895 898 2.095532 CAGAAGAAATGCTCGCTGGAAG 59.904 50.000 0.00 0.00 31.51 3.46
900 903 5.159209 CAAAATTCAGAAGAAATGCTCGCT 58.841 37.500 0.00 0.00 37.29 4.93
902 905 5.060569 CAGCAAAATTCAGAAGAAATGCTCG 59.939 40.000 10.83 5.78 43.86 5.03
905 908 4.142966 GGCAGCAAAATTCAGAAGAAATGC 60.143 41.667 0.00 5.34 39.84 3.56
935 949 7.170489 TCTCGCTAAGATCAGATAGCAAAATTG 59.830 37.037 19.04 7.25 43.71 2.32
937 951 6.753180 TCTCGCTAAGATCAGATAGCAAAAT 58.247 36.000 19.04 0.00 43.71 1.82
988 1009 2.203126 GCTCATGGCGGAAGGAGG 60.203 66.667 0.00 0.00 0.00 4.30
1029 1050 1.593196 TCTTCTTGGCGTTGTTGGAG 58.407 50.000 0.00 0.00 0.00 3.86
1033 1054 1.029681 GGGTTCTTCTTGGCGTTGTT 58.970 50.000 0.00 0.00 0.00 2.83
1055 1076 1.447489 GAGTCGGAGTCGGAGTCGA 60.447 63.158 16.95 2.46 43.86 4.20
1058 1079 2.436292 CGGAGTCGGAGTCGGAGT 60.436 66.667 13.45 7.71 36.95 3.85
1059 1080 2.125229 TCGGAGTCGGAGTCGGAG 60.125 66.667 16.41 7.01 36.95 4.63
1293 1395 0.970937 TGGTCTCCTCGGCCTTGTAG 60.971 60.000 0.00 0.00 0.00 2.74
1461 1563 6.260936 TCCTGAATTCACTGTTCTTCTTGTTC 59.739 38.462 3.38 0.00 0.00 3.18
1463 1565 5.684704 TCCTGAATTCACTGTTCTTCTTGT 58.315 37.500 3.38 0.00 0.00 3.16
1464 1566 5.180868 CCTCCTGAATTCACTGTTCTTCTTG 59.819 44.000 3.38 0.00 0.00 3.02
1515 1620 7.381408 GGAACTAACTTAATTGGCAAGTTTGTC 59.619 37.037 5.17 5.66 45.05 3.18
1516 1621 7.069455 AGGAACTAACTTAATTGGCAAGTTTGT 59.931 33.333 5.17 8.18 46.55 2.83
1537 1642 4.497507 GCAGTAAGGAACAACAACAGGAAC 60.498 45.833 0.00 0.00 0.00 3.62
1538 1643 3.630312 GCAGTAAGGAACAACAACAGGAA 59.370 43.478 0.00 0.00 0.00 3.36
1550 1662 5.516984 AGGCTACTAGTAAGCAGTAAGGAA 58.483 41.667 19.36 0.00 0.00 3.36
1564 1682 9.436957 TTGAGAAGAACAAAATTAGGCTACTAG 57.563 33.333 0.00 0.00 0.00 2.57
1588 1706 6.444633 AGCTTGAAACATTTGATCTGAGTTG 58.555 36.000 0.00 0.00 0.00 3.16
1593 1711 5.987347 ACCAAAGCTTGAAACATTTGATCTG 59.013 36.000 0.00 0.00 35.19 2.90
1601 1719 6.062095 ACTGTACTACCAAAGCTTGAAACAT 58.938 36.000 0.00 0.00 0.00 2.71
1612 1730 5.650266 CCATGCCATAAACTGTACTACCAAA 59.350 40.000 0.00 0.00 0.00 3.28
1636 1759 5.828299 TGTGGGTAACTAATATTTGCAGC 57.172 39.130 0.00 0.00 0.00 5.25
1657 1780 4.280677 TGATGGCTTTTAAGGGTGAGTTTG 59.719 41.667 0.00 0.00 0.00 2.93
1659 1782 4.112634 TGATGGCTTTTAAGGGTGAGTT 57.887 40.909 0.00 0.00 0.00 3.01
1660 1783 3.806949 TGATGGCTTTTAAGGGTGAGT 57.193 42.857 0.00 0.00 0.00 3.41
1663 1786 8.960591 CCTAATATATGATGGCTTTTAAGGGTG 58.039 37.037 0.00 0.00 0.00 4.61
1665 1788 8.336235 TCCCTAATATATGATGGCTTTTAAGGG 58.664 37.037 0.00 0.00 0.00 3.95
1675 1798 8.615878 TTGAACGTTTCCCTAATATATGATGG 57.384 34.615 0.46 0.00 0.00 3.51
1687 1810 3.146847 GTTCCAGATTGAACGTTTCCCT 58.853 45.455 0.46 0.00 35.70 4.20
1723 1846 4.751600 TGGCTTAACATCGCAATCTAGATG 59.248 41.667 5.86 2.06 46.95 2.90
1744 1874 3.367630 GCAATTCGCCACTGTAAATTTGG 59.632 43.478 0.00 0.00 32.94 3.28
1754 1884 1.589716 GCAAGGAGCAATTCGCCACT 61.590 55.000 0.00 0.00 44.04 4.00
1809 1942 1.070601 CCCCCTGGAAAAAGTTTGCAG 59.929 52.381 13.46 13.46 37.57 4.41
1811 1944 1.419381 TCCCCCTGGAAAAAGTTTGC 58.581 50.000 0.00 0.00 37.86 3.68
1822 1955 1.490910 CCTAGTAGCTTTTCCCCCTGG 59.509 57.143 0.00 0.00 0.00 4.45
1894 2027 1.130054 TCAGCATAGGGCCCCTGATC 61.130 60.000 21.43 4.12 46.50 2.92
1965 2098 7.552687 AGTCAGACACATGTGTTTCTTTAAGAA 59.447 33.333 31.03 2.94 45.05 2.52
2028 2174 6.503524 TCCATTGAGTTACAAAACAGAAAGC 58.496 36.000 0.00 0.00 42.03 3.51
2030 2176 6.922957 GCATCCATTGAGTTACAAAACAGAAA 59.077 34.615 0.00 0.00 42.03 2.52
2115 2261 1.457346 GATCTGACAGCCCCAGTTTG 58.543 55.000 0.00 0.00 33.57 2.93
2234 2381 5.427806 TCCAGATGTGATCCTGAGAAGAAAT 59.572 40.000 0.00 0.00 32.37 2.17
2239 2386 5.503634 TTTTCCAGATGTGATCCTGAGAA 57.496 39.130 0.00 0.00 32.37 2.87
2452 2599 5.059833 AGTGTTTATTAGGCTATGAGCAGC 58.940 41.667 0.00 0.00 44.75 5.25
2478 2625 5.197451 TGTGTAAGTTGAACAATCTGGGTT 58.803 37.500 0.00 0.00 0.00 4.11
2479 2626 4.787551 TGTGTAAGTTGAACAATCTGGGT 58.212 39.130 0.00 0.00 0.00 4.51
2547 2695 6.545666 AGACGGAAATGTGCAATGGATATTTA 59.454 34.615 9.17 0.00 0.00 1.40
2548 2696 5.360714 AGACGGAAATGTGCAATGGATATTT 59.639 36.000 8.97 8.97 0.00 1.40
2572 2720 2.564561 TATTTCCATGGGCAGCCGCA 62.565 55.000 13.02 5.12 41.24 5.69
2573 2721 1.827789 TATTTCCATGGGCAGCCGC 60.828 57.895 13.02 0.00 37.44 6.53
2574 2722 0.466189 AGTATTTCCATGGGCAGCCG 60.466 55.000 13.02 0.00 0.00 5.52
2578 2726 4.444306 GCTACTACAGTATTTCCATGGGCA 60.444 45.833 13.02 0.00 0.00 5.36
2600 2748 4.379918 GGATTTTGGAGCTACTTTGTGAGC 60.380 45.833 0.00 0.00 39.08 4.26
2601 2749 4.761739 TGGATTTTGGAGCTACTTTGTGAG 59.238 41.667 0.00 0.00 0.00 3.51
2602 2750 4.724399 TGGATTTTGGAGCTACTTTGTGA 58.276 39.130 0.00 0.00 0.00 3.58
2603 2751 4.761739 TCTGGATTTTGGAGCTACTTTGTG 59.238 41.667 0.00 0.00 0.00 3.33
2604 2752 4.985538 TCTGGATTTTGGAGCTACTTTGT 58.014 39.130 0.00 0.00 0.00 2.83
2605 2753 5.964958 TTCTGGATTTTGGAGCTACTTTG 57.035 39.130 0.00 0.00 0.00 2.77
2606 2754 5.048713 CGTTTCTGGATTTTGGAGCTACTTT 60.049 40.000 0.00 0.00 0.00 2.66
2607 2755 4.455877 CGTTTCTGGATTTTGGAGCTACTT 59.544 41.667 0.00 0.00 0.00 2.24
2608 2756 4.003648 CGTTTCTGGATTTTGGAGCTACT 58.996 43.478 0.00 0.00 0.00 2.57
2609 2757 4.000988 TCGTTTCTGGATTTTGGAGCTAC 58.999 43.478 0.00 0.00 0.00 3.58
2724 2872 4.757149 GTCACACTCAGCCTCTTTGTAAAT 59.243 41.667 0.00 0.00 0.00 1.40
2731 2879 1.610102 GCATGTCACACTCAGCCTCTT 60.610 52.381 0.00 0.00 0.00 2.85
2732 2880 0.036577 GCATGTCACACTCAGCCTCT 60.037 55.000 0.00 0.00 0.00 3.69
2733 2881 0.036577 AGCATGTCACACTCAGCCTC 60.037 55.000 0.00 0.00 0.00 4.70
2791 2939 2.912956 AGTCCTTCTCTGCATAACCCAA 59.087 45.455 0.00 0.00 0.00 4.12
2797 2945 3.509967 TCGTCAAAGTCCTTCTCTGCATA 59.490 43.478 0.00 0.00 0.00 3.14
2880 3028 5.278414 CCTGTGACAACAACATATGCTTTCA 60.278 40.000 1.58 0.00 35.37 2.69
2920 3068 4.404507 GCAAAGTGCAGAAGATAACGAA 57.595 40.909 0.00 0.00 44.26 3.85
2962 3110 7.080353 TCAGAGACTTATGCACAAAATGATG 57.920 36.000 0.00 0.00 0.00 3.07
2980 3128 2.475155 ACAAGCCATCCTGATCAGAGA 58.525 47.619 24.62 18.50 0.00 3.10
2996 3144 0.250901 CCAGTCACCTCCCCAACAAG 60.251 60.000 0.00 0.00 0.00 3.16
3060 3208 7.857569 TGTACTACAACTGCAACATAGAAAAC 58.142 34.615 0.00 0.00 0.00 2.43
3361 5006 5.302313 AGCCTGGTAAACTATAGACTGCTAC 59.698 44.000 6.78 0.73 0.00 3.58
3413 5058 3.119137 AGACCAGTTTTTGTGTTTCCAGC 60.119 43.478 0.00 0.00 0.00 4.85
3428 5073 4.322349 GCAACTGATGTCTTCTAGACCAGT 60.322 45.833 10.84 10.84 44.44 4.00
3432 5077 4.560128 TGTGCAACTGATGTCTTCTAGAC 58.440 43.478 0.00 0.00 41.17 2.59
3437 5082 4.863491 ACAAATGTGCAACTGATGTCTTC 58.137 39.130 0.00 0.00 38.04 2.87
3454 5099 3.472652 TGCAACTCTGACCGTAACAAAT 58.527 40.909 0.00 0.00 0.00 2.32
3533 5180 2.104281 ACCTCTAATTCATACGGGTGGC 59.896 50.000 0.00 0.00 0.00 5.01
3576 5223 3.019564 ACTTCCATTGGTCTTATGCAGC 58.980 45.455 1.86 0.00 0.00 5.25
3577 5224 5.047802 ACAAACTTCCATTGGTCTTATGCAG 60.048 40.000 1.86 0.00 32.02 4.41
3602 5249 4.343526 TGGCCTTAGCAAATCACAGAAAAA 59.656 37.500 3.32 0.00 42.56 1.94
3603 5250 3.894427 TGGCCTTAGCAAATCACAGAAAA 59.106 39.130 3.32 0.00 42.56 2.29
3604 5251 3.495331 TGGCCTTAGCAAATCACAGAAA 58.505 40.909 3.32 0.00 42.56 2.52
3605 5252 3.153369 TGGCCTTAGCAAATCACAGAA 57.847 42.857 3.32 0.00 42.56 3.02
3606 5253 2.877097 TGGCCTTAGCAAATCACAGA 57.123 45.000 3.32 0.00 42.56 3.41
3607 5254 3.429822 CCATTGGCCTTAGCAAATCACAG 60.430 47.826 3.32 0.00 40.91 3.66
3608 5255 2.496871 CCATTGGCCTTAGCAAATCACA 59.503 45.455 3.32 0.00 40.91 3.58
3609 5256 2.159057 CCCATTGGCCTTAGCAAATCAC 60.159 50.000 3.32 0.00 40.91 3.06
3610 5257 2.109774 CCCATTGGCCTTAGCAAATCA 58.890 47.619 3.32 0.00 40.91 2.57
3611 5258 2.363359 CTCCCATTGGCCTTAGCAAATC 59.637 50.000 3.32 0.00 40.91 2.17
3612 5259 2.292455 ACTCCCATTGGCCTTAGCAAAT 60.292 45.455 3.32 0.00 43.85 2.32
3613 5260 1.077005 ACTCCCATTGGCCTTAGCAAA 59.923 47.619 3.32 0.00 42.56 3.68
3614 5261 0.704076 ACTCCCATTGGCCTTAGCAA 59.296 50.000 3.32 0.00 42.56 3.91
3615 5262 1.590591 TACTCCCATTGGCCTTAGCA 58.409 50.000 3.32 0.00 42.56 3.49
3616 5263 2.158608 ACATACTCCCATTGGCCTTAGC 60.159 50.000 3.32 0.00 38.76 3.09
3617 5264 3.864789 ACATACTCCCATTGGCCTTAG 57.135 47.619 3.32 0.00 0.00 2.18
3618 5265 4.017958 TGAAACATACTCCCATTGGCCTTA 60.018 41.667 3.32 0.00 0.00 2.69
3619 5266 3.245586 TGAAACATACTCCCATTGGCCTT 60.246 43.478 3.32 0.00 0.00 4.35
3620 5267 2.311542 TGAAACATACTCCCATTGGCCT 59.688 45.455 3.32 0.00 0.00 5.19
3621 5268 2.733956 TGAAACATACTCCCATTGGCC 58.266 47.619 0.00 0.00 0.00 5.36
3622 5269 3.701040 ACATGAAACATACTCCCATTGGC 59.299 43.478 0.00 0.00 0.00 4.52
3623 5270 7.719193 TGTATACATGAAACATACTCCCATTGG 59.281 37.037 0.08 0.00 0.00 3.16
3624 5271 8.675705 TGTATACATGAAACATACTCCCATTG 57.324 34.615 0.08 0.00 0.00 2.82
3625 5272 9.693739 TTTGTATACATGAAACATACTCCCATT 57.306 29.630 6.36 0.00 0.00 3.16
3626 5273 9.693739 TTTTGTATACATGAAACATACTCCCAT 57.306 29.630 6.36 0.00 0.00 4.00
3627 5274 9.693739 ATTTTGTATACATGAAACATACTCCCA 57.306 29.630 6.36 0.00 0.00 4.37
3635 5282 8.494347 GCAGCAAAATTTTGTATACATGAAACA 58.506 29.630 27.13 0.00 40.24 2.83
3664 5311 2.877786 TCGCAACATTTCAGACACACAT 59.122 40.909 0.00 0.00 0.00 3.21
3693 5340 7.581476 TCTTGTATTCAATTGAGAACGTTTCC 58.419 34.615 8.41 0.00 32.82 3.13
3716 5363 6.944862 AGAAAATCCTCACTTGTAGCATTTCT 59.055 34.615 0.00 0.00 0.00 2.52
3717 5364 7.025963 CAGAAAATCCTCACTTGTAGCATTTC 58.974 38.462 0.00 0.00 0.00 2.17
3750 5397 2.489329 CACGACCTTGAGCCATTTGAAT 59.511 45.455 0.00 0.00 0.00 2.57
3811 5458 6.695278 CGCAGGAACAAAATAGACAAAGAAAA 59.305 34.615 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.