Multiple sequence alignment - TraesCS2A01G256500

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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 TraesCS2A01G256500 chr2A 100.000 5249 0 0 1 5249 393192687 393197935 0.000000e+00 9694.0
1 TraesCS2A01G256500 chr2A 94.545 55 3 0 5195 5249 522443795 522443741 9.370000e-13 86.1
2 TraesCS2A01G256500 chr2A 95.918 49 2 0 3889 3937 28818807 28818759 4.360000e-11 80.5
3 TraesCS2A01G256500 chr2A 95.745 47 2 0 3887 3933 650624372 650624418 5.640000e-10 76.8
4 TraesCS2A01G256500 chr2B 96.051 2608 77 11 2178 4765 394001650 393999049 0.000000e+00 4222.0
5 TraesCS2A01G256500 chr2B 95.965 347 14 0 867 1213 394002012 394001666 9.870000e-157 564.0
6 TraesCS2A01G256500 chr2B 93.506 231 13 2 4824 5054 393998566 393998338 5.030000e-90 342.0
7 TraesCS2A01G256500 chr2B 90.610 213 13 2 5037 5249 393983858 393983653 5.180000e-70 276.0
8 TraesCS2A01G256500 chr2B 94.828 58 2 1 5193 5249 163227255 163227312 7.240000e-14 89.8
9 TraesCS2A01G256500 chr2D 96.095 2305 61 12 2484 4765 324916247 324913949 0.000000e+00 3731.0
10 TraesCS2A01G256500 chr2D 96.552 1682 44 6 810 2485 324918263 324916590 0.000000e+00 2772.0
11 TraesCS2A01G256500 chr2D 94.444 378 14 1 4840 5217 324913338 324912968 4.560000e-160 575.0
12 TraesCS2A01G256500 chr2D 93.651 63 3 1 5188 5249 112861979 112862041 5.600000e-15 93.5
13 TraesCS2A01G256500 chr6D 89.086 678 71 3 22 696 445280520 445281197 0.000000e+00 839.0
14 TraesCS2A01G256500 chr6D 88.382 680 73 6 1 676 261018008 261017331 0.000000e+00 813.0
15 TraesCS2A01G256500 chr6D 88.131 674 75 5 27 696 445212299 445212971 0.000000e+00 797.0
16 TraesCS2A01G256500 chr6D 89.474 76 4 3 3863 3936 103006191 103006118 5.600000e-15 93.5
17 TraesCS2A01G256500 chr7D 87.697 699 68 7 1 692 412765584 412766271 0.000000e+00 798.0
18 TraesCS2A01G256500 chr7D 84.536 194 20 4 4823 5011 311880594 311880782 3.230000e-42 183.0
19 TraesCS2A01G256500 chr7D 90.667 75 1 3 3862 3931 383219870 383219943 1.560000e-15 95.3
20 TraesCS2A01G256500 chr7D 90.476 63 5 1 5188 5249 96218971 96219033 1.210000e-11 82.4
21 TraesCS2A01G256500 chr6A 87.755 686 79 4 11 692 410344660 410343976 0.000000e+00 797.0
22 TraesCS2A01G256500 chr1D 87.464 702 66 18 1 690 240987771 240988462 0.000000e+00 789.0
23 TraesCS2A01G256500 chr1D 87.000 700 80 9 1 692 378876366 378875670 0.000000e+00 778.0
24 TraesCS2A01G256500 chr3A 87.074 704 80 8 1 694 669932070 669932772 0.000000e+00 785.0
25 TraesCS2A01G256500 chr3A 100.000 28 0 0 687 714 644383701 644383674 9.000000e-03 52.8
26 TraesCS2A01G256500 chr5B 86.733 701 87 6 1 695 523379690 523378990 0.000000e+00 774.0
27 TraesCS2A01G256500 chr7B 84.500 200 21 3 4823 5017 296332388 296332194 6.940000e-44 189.0
28 TraesCS2A01G256500 chr7B 89.744 78 1 6 3863 3934 413974957 413974881 5.600000e-15 93.5
29 TraesCS2A01G256500 chr7B 93.333 60 3 1 5191 5249 210857780 210857721 2.600000e-13 87.9
30 TraesCS2A01G256500 chr7B 97.959 49 1 0 3889 3937 219565079 219565031 9.370000e-13 86.1
31 TraesCS2A01G256500 chr7B 89.231 65 7 0 5185 5249 188976528 188976592 1.210000e-11 82.4
32 TraesCS2A01G256500 chr7B 97.778 45 1 0 3889 3933 639796243 639796287 1.570000e-10 78.7
33 TraesCS2A01G256500 chr7B 91.071 56 5 0 3889 3944 522138190 522138245 5.640000e-10 76.8
34 TraesCS2A01G256500 chr4A 93.333 75 0 2 3863 3932 595568233 595568159 7.190000e-19 106.0
35 TraesCS2A01G256500 chr5A 91.549 71 4 2 3863 3931 561531569 561531499 4.330000e-16 97.1
36 TraesCS2A01G256500 chr3B 90.541 74 3 2 3863 3932 822885425 822885352 1.560000e-15 95.3
37 TraesCS2A01G256500 chr3B 93.220 59 4 0 5191 5249 798324672 798324614 2.600000e-13 87.9
38 TraesCS2A01G256500 chr3B 91.803 61 3 2 5191 5249 416812506 416812446 3.370000e-12 84.2
39 TraesCS2A01G256500 chr3B 96.000 50 2 0 3889 3938 423791587 423791636 1.210000e-11 82.4
40 TraesCS2A01G256500 chr1A 87.654 81 6 3 3854 3932 583907791 583907869 2.010000e-14 91.6
41 TraesCS2A01G256500 chr1B 91.667 60 4 1 5191 5249 89903480 89903421 1.210000e-11 82.4


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 TraesCS2A01G256500 chr2A 393192687 393197935 5248 False 9694.000000 9694 100.000 1 5249 1 chr2A.!!$F1 5248
1 TraesCS2A01G256500 chr2B 393998338 394002012 3674 True 1709.333333 4222 95.174 867 5054 3 chr2B.!!$R2 4187
2 TraesCS2A01G256500 chr2D 324912968 324918263 5295 True 2359.333333 3731 95.697 810 5217 3 chr2D.!!$R1 4407
3 TraesCS2A01G256500 chr6D 445280520 445281197 677 False 839.000000 839 89.086 22 696 1 chr6D.!!$F2 674
4 TraesCS2A01G256500 chr6D 261017331 261018008 677 True 813.000000 813 88.382 1 676 1 chr6D.!!$R2 675
5 TraesCS2A01G256500 chr6D 445212299 445212971 672 False 797.000000 797 88.131 27 696 1 chr6D.!!$F1 669
6 TraesCS2A01G256500 chr7D 412765584 412766271 687 False 798.000000 798 87.697 1 692 1 chr7D.!!$F4 691
7 TraesCS2A01G256500 chr6A 410343976 410344660 684 True 797.000000 797 87.755 11 692 1 chr6A.!!$R1 681
8 TraesCS2A01G256500 chr1D 240987771 240988462 691 False 789.000000 789 87.464 1 690 1 chr1D.!!$F1 689
9 TraesCS2A01G256500 chr1D 378875670 378876366 696 True 778.000000 778 87.000 1 692 1 chr1D.!!$R1 691
10 TraesCS2A01G256500 chr3A 669932070 669932772 702 False 785.000000 785 87.074 1 694 1 chr3A.!!$F1 693
11 TraesCS2A01G256500 chr5B 523378990 523379690 700 True 774.000000 774 86.733 1 695 1 chr5B.!!$R1 694

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
772 789 0.249398 AGATGCGGGGTGTGTTAGAC 59.751 55.0 0.00 0.0 0.00 2.59 F
1384 1406 0.035056 CCACTGGGTCCTAGCTTTGG 60.035 60.0 1.33 0.0 0.00 3.28 F
1387 1409 0.035056 CTGGGTCCTAGCTTTGGTGG 60.035 60.0 0.00 0.0 0.00 4.61 F
1388 1410 0.770557 TGGGTCCTAGCTTTGGTGGT 60.771 55.0 0.00 0.0 0.00 4.16 F
2506 2873 1.102978 GGGCTTGTGTGTCACTTTGT 58.897 50.0 4.27 0.0 35.11 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2506 2873 0.175760 GGAGGCTACATTCGCACAGA 59.824 55.000 0.00 0.0 0.0 3.41 R
3060 3431 2.680312 TGGACTCACTCTGCTATTGC 57.320 50.000 0.00 0.0 40.2 3.56 R
3608 3979 0.541392 ATTCCTGCGCACACCTATCA 59.459 50.000 5.66 0.0 0.0 2.15 R
3619 3990 4.944962 TCTGTGTTTTCATATTCCTGCG 57.055 40.909 0.00 0.0 0.0 5.18 R
4405 4796 1.732259 GAAACACATCAGCTACACGGG 59.268 52.381 0.00 0.0 0.0 5.28 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
30 31 2.430244 TTCGGCGTGCTCGAAGTC 60.430 61.111 13.13 0.00 40.99 3.01
38 39 2.510238 GCTCGAAGTCAGCCGCAT 60.510 61.111 0.00 0.00 0.00 4.73
73 74 0.456142 GTCGTCGCACTGTATGAGCA 60.456 55.000 0.00 0.00 32.44 4.26
149 150 1.603236 GAATCCATGCCCGCAAACCA 61.603 55.000 0.00 0.00 0.00 3.67
316 320 1.091771 CAGATCTGCAAATCCGGCGT 61.092 55.000 10.38 0.00 0.00 5.68
377 388 4.697756 CCTTTCGGCGTGCTCCCA 62.698 66.667 6.85 0.00 0.00 4.37
562 579 1.906105 TAGGGCCGAGATTTTGCCGT 61.906 55.000 0.00 0.00 46.31 5.68
565 582 2.690778 GCCGAGATTTTGCCGTGCT 61.691 57.895 0.00 0.00 0.00 4.40
590 607 2.210711 AAAAATTTGCGGGCCGGGA 61.211 52.632 29.48 6.40 0.00 5.14
631 648 2.281970 AGGTTTTTCCGCCCGACC 60.282 61.111 0.00 0.00 41.99 4.79
640 657 2.820479 CGCCCGACCCGCATTTTA 60.820 61.111 0.00 0.00 0.00 1.52
641 658 2.400158 CGCCCGACCCGCATTTTAA 61.400 57.895 0.00 0.00 0.00 1.52
642 659 1.138036 GCCCGACCCGCATTTTAAC 59.862 57.895 0.00 0.00 0.00 2.01
643 660 1.426223 CCCGACCCGCATTTTAACG 59.574 57.895 0.00 0.00 0.00 3.18
654 671 6.232979 CCGCATTTTAACGGTTATTTTACG 57.767 37.500 0.73 4.23 44.46 3.18
655 672 5.227598 CCGCATTTTAACGGTTATTTTACGG 59.772 40.000 13.82 13.82 44.46 4.02
656 673 6.020372 CGCATTTTAACGGTTATTTTACGGA 58.980 36.000 0.73 0.00 0.00 4.69
657 674 6.687958 CGCATTTTAACGGTTATTTTACGGAT 59.312 34.615 0.73 0.00 0.00 4.18
658 675 7.097329 CGCATTTTAACGGTTATTTTACGGATC 60.097 37.037 0.73 0.00 0.00 3.36
659 676 7.097329 GCATTTTAACGGTTATTTTACGGATCG 60.097 37.037 0.73 0.00 0.00 3.69
660 677 5.964887 TTAACGGTTATTTTACGGATCGG 57.035 39.130 0.73 0.00 0.00 4.18
661 678 2.825205 ACGGTTATTTTACGGATCGGG 58.175 47.619 5.18 0.00 0.00 5.14
662 679 2.430332 ACGGTTATTTTACGGATCGGGA 59.570 45.455 5.18 0.00 0.00 5.14
663 680 2.796593 CGGTTATTTTACGGATCGGGAC 59.203 50.000 5.18 0.00 0.00 4.46
680 697 3.207354 CGAGATACGGGGTGTGCT 58.793 61.111 0.00 0.00 38.46 4.40
681 698 2.411535 CGAGATACGGGGTGTGCTA 58.588 57.895 0.00 0.00 38.46 3.49
682 699 0.311165 CGAGATACGGGGTGTGCTAG 59.689 60.000 0.00 0.00 38.46 3.42
683 700 1.688772 GAGATACGGGGTGTGCTAGA 58.311 55.000 0.00 0.00 0.00 2.43
684 701 1.337387 GAGATACGGGGTGTGCTAGAC 59.663 57.143 0.00 0.00 0.00 2.59
685 702 1.108776 GATACGGGGTGTGCTAGACA 58.891 55.000 0.00 0.00 0.00 3.41
686 703 1.687123 GATACGGGGTGTGCTAGACAT 59.313 52.381 0.00 0.00 36.78 3.06
687 704 0.821517 TACGGGGTGTGCTAGACATG 59.178 55.000 0.00 0.00 36.78 3.21
688 705 1.815421 CGGGGTGTGCTAGACATGC 60.815 63.158 0.00 0.00 36.78 4.06
689 706 1.604378 GGGGTGTGCTAGACATGCT 59.396 57.895 0.00 0.00 36.78 3.79
690 707 0.462759 GGGGTGTGCTAGACATGCTC 60.463 60.000 0.00 0.00 36.78 4.26
691 708 0.539051 GGGTGTGCTAGACATGCTCT 59.461 55.000 0.00 0.00 36.78 4.09
692 709 1.757118 GGGTGTGCTAGACATGCTCTA 59.243 52.381 0.00 0.00 36.78 2.43
693 710 2.168521 GGGTGTGCTAGACATGCTCTAA 59.831 50.000 0.00 0.00 36.78 2.10
694 711 3.452474 GGTGTGCTAGACATGCTCTAAG 58.548 50.000 0.00 0.00 36.78 2.18
695 712 2.863137 GTGTGCTAGACATGCTCTAAGC 59.137 50.000 0.00 6.30 42.82 3.09
696 713 2.159043 TGTGCTAGACATGCTCTAAGCC 60.159 50.000 0.00 2.29 41.51 4.35
697 714 1.414181 TGCTAGACATGCTCTAAGCCC 59.586 52.381 0.00 0.00 41.51 5.19
698 715 1.414181 GCTAGACATGCTCTAAGCCCA 59.586 52.381 0.00 0.00 41.51 5.36
699 716 2.804933 GCTAGACATGCTCTAAGCCCAC 60.805 54.545 0.00 0.00 41.51 4.61
700 717 1.577736 AGACATGCTCTAAGCCCACT 58.422 50.000 0.00 0.00 41.51 4.00
701 718 2.752030 AGACATGCTCTAAGCCCACTA 58.248 47.619 0.00 0.00 41.51 2.74
702 719 3.312890 AGACATGCTCTAAGCCCACTAT 58.687 45.455 0.00 0.00 41.51 2.12
703 720 3.713764 AGACATGCTCTAAGCCCACTATT 59.286 43.478 0.00 0.00 41.51 1.73
704 721 3.812053 GACATGCTCTAAGCCCACTATTG 59.188 47.826 0.00 0.00 41.51 1.90
705 722 3.200825 ACATGCTCTAAGCCCACTATTGT 59.799 43.478 0.00 0.00 41.51 2.71
706 723 4.408921 ACATGCTCTAAGCCCACTATTGTA 59.591 41.667 0.00 0.00 41.51 2.41
707 724 4.402056 TGCTCTAAGCCCACTATTGTAC 57.598 45.455 0.00 0.00 41.51 2.90
708 725 4.030913 TGCTCTAAGCCCACTATTGTACT 58.969 43.478 0.00 0.00 41.51 2.73
709 726 4.469945 TGCTCTAAGCCCACTATTGTACTT 59.530 41.667 0.00 0.00 41.51 2.24
710 727 4.811557 GCTCTAAGCCCACTATTGTACTTG 59.188 45.833 0.00 0.00 34.48 3.16
711 728 4.766375 TCTAAGCCCACTATTGTACTTGC 58.234 43.478 0.00 0.00 0.00 4.01
712 729 3.721087 AAGCCCACTATTGTACTTGCT 57.279 42.857 0.00 0.00 0.00 3.91
749 766 3.959535 ACAGTTATTTTACGGGTCGGA 57.040 42.857 0.00 0.00 0.00 4.55
753 770 1.102154 TATTTTACGGGTCGGAGCGA 58.898 50.000 0.53 0.00 0.00 4.93
767 784 4.760047 GCGAGATGCGGGGTGTGT 62.760 66.667 0.00 0.00 41.29 3.72
772 789 0.249398 AGATGCGGGGTGTGTTAGAC 59.751 55.000 0.00 0.00 0.00 2.59
783 800 4.322801 GGGTGTGTTAGACATGCTCTAAGT 60.323 45.833 14.28 0.00 41.37 2.24
784 801 4.865365 GGTGTGTTAGACATGCTCTAAGTC 59.135 45.833 14.28 11.64 41.37 3.01
785 802 4.865365 GTGTGTTAGACATGCTCTAAGTCC 59.135 45.833 14.28 7.24 41.37 3.85
786 803 4.526650 TGTGTTAGACATGCTCTAAGTCCA 59.473 41.667 14.28 8.98 41.37 4.02
787 804 4.865365 GTGTTAGACATGCTCTAAGTCCAC 59.135 45.833 14.28 14.27 41.37 4.02
788 805 4.772624 TGTTAGACATGCTCTAAGTCCACT 59.227 41.667 14.28 0.00 41.37 4.00
789 806 5.949952 TGTTAGACATGCTCTAAGTCCACTA 59.050 40.000 14.28 0.00 41.37 2.74
790 807 6.607600 TGTTAGACATGCTCTAAGTCCACTAT 59.392 38.462 14.28 0.00 41.37 2.12
791 808 7.124298 TGTTAGACATGCTCTAAGTCCACTATT 59.876 37.037 14.28 0.00 41.37 1.73
792 809 5.911752 AGACATGCTCTAAGTCCACTATTG 58.088 41.667 0.00 0.00 32.82 1.90
793 810 5.423610 AGACATGCTCTAAGTCCACTATTGT 59.576 40.000 0.00 0.00 32.82 2.71
794 811 6.607600 AGACATGCTCTAAGTCCACTATTGTA 59.392 38.462 0.00 0.00 32.82 2.41
795 812 6.574350 ACATGCTCTAAGTCCACTATTGTAC 58.426 40.000 0.00 0.00 0.00 2.90
796 813 6.381420 ACATGCTCTAAGTCCACTATTGTACT 59.619 38.462 0.00 0.00 0.00 2.73
797 814 6.852420 TGCTCTAAGTCCACTATTGTACTT 57.148 37.500 0.00 0.00 36.26 2.24
798 815 6.631016 TGCTCTAAGTCCACTATTGTACTTG 58.369 40.000 1.89 0.00 34.23 3.16
799 816 5.520649 GCTCTAAGTCCACTATTGTACTTGC 59.479 44.000 1.89 0.00 34.23 4.01
800 817 6.628398 GCTCTAAGTCCACTATTGTACTTGCT 60.628 42.308 1.89 0.00 34.23 3.91
801 818 6.864342 TCTAAGTCCACTATTGTACTTGCTC 58.136 40.000 1.89 0.00 34.23 4.26
802 819 5.746990 AAGTCCACTATTGTACTTGCTCT 57.253 39.130 0.00 0.00 31.20 4.09
803 820 5.746990 AGTCCACTATTGTACTTGCTCTT 57.253 39.130 0.00 0.00 0.00 2.85
804 821 6.852420 AGTCCACTATTGTACTTGCTCTTA 57.148 37.500 0.00 0.00 0.00 2.10
805 822 7.425224 AGTCCACTATTGTACTTGCTCTTAT 57.575 36.000 0.00 0.00 0.00 1.73
806 823 7.493367 AGTCCACTATTGTACTTGCTCTTATC 58.507 38.462 0.00 0.00 0.00 1.75
807 824 7.124298 AGTCCACTATTGTACTTGCTCTTATCA 59.876 37.037 0.00 0.00 0.00 2.15
808 825 7.436673 GTCCACTATTGTACTTGCTCTTATCAG 59.563 40.741 0.00 0.00 0.00 2.90
838 855 1.147376 TGGTGAACCAGTTCCACGG 59.853 57.895 8.01 0.00 42.01 4.94
840 857 2.112297 TGAACCAGTTCCACGGGC 59.888 61.111 8.01 0.00 36.91 6.13
848 865 0.252197 AGTTCCACGGGCTATCAACC 59.748 55.000 0.00 0.00 0.00 3.77
861 878 4.101790 CAACCGTGGGATGCGTGC 62.102 66.667 0.00 0.00 0.00 5.34
916 934 2.031120 CTTGTCCTTGCTTTTGGTCCA 58.969 47.619 0.00 0.00 0.00 4.02
921 939 2.430332 TCCTTGCTTTTGGTCCACTTTG 59.570 45.455 0.00 0.00 0.00 2.77
949 971 1.202510 CCTCTTCCTCCTCTCGCATTG 60.203 57.143 0.00 0.00 0.00 2.82
950 972 0.826715 TCTTCCTCCTCTCGCATTGG 59.173 55.000 0.00 0.00 0.00 3.16
961 983 2.949644 TCTCGCATTGGAGTAGAATCGA 59.050 45.455 0.00 0.00 35.52 3.59
962 984 3.570125 TCTCGCATTGGAGTAGAATCGAT 59.430 43.478 0.00 0.00 35.52 3.59
964 986 4.051237 TCGCATTGGAGTAGAATCGATTG 58.949 43.478 16.96 0.00 0.00 2.67
967 989 2.910688 TGGAGTAGAATCGATTGGGC 57.089 50.000 16.96 0.79 0.00 5.36
1155 1177 3.209812 TCACTCCGGATCCGCGAG 61.210 66.667 33.15 33.15 40.19 5.03
1290 1312 3.290948 TCCTATACATGTTTGTGCCCC 57.709 47.619 2.30 0.00 36.53 5.80
1355 1377 0.659427 ACATGCGTGCATCATACTGC 59.341 50.000 5.64 0.00 42.62 4.40
1383 1405 3.558674 CCACTGGGTCCTAGCTTTG 57.441 57.895 1.33 0.00 0.00 2.77
1384 1406 0.035056 CCACTGGGTCCTAGCTTTGG 60.035 60.000 1.33 0.00 0.00 3.28
1385 1407 0.693049 CACTGGGTCCTAGCTTTGGT 59.307 55.000 1.33 0.00 0.00 3.67
1386 1408 0.693049 ACTGGGTCCTAGCTTTGGTG 59.307 55.000 1.33 0.00 0.00 4.17
1387 1409 0.035056 CTGGGTCCTAGCTTTGGTGG 60.035 60.000 0.00 0.00 0.00 4.61
1388 1410 0.770557 TGGGTCCTAGCTTTGGTGGT 60.771 55.000 0.00 0.00 0.00 4.16
1432 1454 4.623167 GCCACTCGCTATTGTGTATATCAG 59.377 45.833 0.00 0.00 32.76 2.90
1485 1507 5.080337 TGGATGATAGGGTCTCACTACATC 58.920 45.833 0.00 0.00 33.35 3.06
1495 1517 3.017442 TCTCACTACATCCAGTCTTCCG 58.983 50.000 0.00 0.00 0.00 4.30
1602 1625 9.845740 TTTCAGTTGCTTAAATCAGGCTATATA 57.154 29.630 0.00 0.00 0.00 0.86
1609 1632 8.935844 TGCTTAAATCAGGCTATATATTTGTCG 58.064 33.333 0.00 0.00 0.00 4.35
1719 1742 5.707298 TCACTGTTTCCTCATCATTTCCTTC 59.293 40.000 0.00 0.00 0.00 3.46
2024 2047 7.402941 AGAGGGCAAAAGTTATATGGGATTTTT 59.597 33.333 0.00 0.00 0.00 1.94
2267 2290 9.638239 TGTCCTTAACATTGCAAATATCTTTTC 57.362 29.630 1.71 0.00 31.20 2.29
2277 2300 4.625311 GCAAATATCTTTTCACGGGTTTGG 59.375 41.667 0.00 0.00 0.00 3.28
2306 2329 4.092383 GCATGTTGCAATTCCTAAAGCTTG 59.908 41.667 0.59 0.00 44.26 4.01
2332 2355 3.181429 ACCTGCATATGTTATTCCCCAGG 60.181 47.826 15.92 15.92 43.16 4.45
2383 2406 5.857471 AATATTAGCAGCATGGCTTCAAA 57.143 34.783 1.62 0.00 42.71 2.69
2506 2873 1.102978 GGGCTTGTGTGTCACTTTGT 58.897 50.000 4.27 0.00 35.11 2.83
2560 2927 6.546034 GCCCTTGTATTATGCTCTTCCTTTTA 59.454 38.462 0.00 0.00 0.00 1.52
2561 2928 7.231519 GCCCTTGTATTATGCTCTTCCTTTTAT 59.768 37.037 0.00 0.00 0.00 1.40
2596 2963 2.899900 TCCAGCCTCTATCGCAATATGT 59.100 45.455 0.00 0.00 0.00 2.29
2882 3252 9.638239 TGGAACATTTTAGTGCATTAATTCTTC 57.362 29.630 2.17 2.63 0.00 2.87
2963 3334 7.723324 AGTAATATTTGTATCAGCTACACCGT 58.277 34.615 0.00 0.00 40.06 4.83
2967 3338 3.770263 TGTATCAGCTACACCGTACAC 57.230 47.619 0.00 0.00 35.38 2.90
3060 3431 7.016072 AGGGACATATTCTGATTCTAACCAGAG 59.984 40.741 0.00 0.00 40.13 3.35
3077 3448 3.446799 CAGAGCAATAGCAGAGTGAGTC 58.553 50.000 0.00 0.00 45.49 3.36
3130 3501 7.997223 ACATGTATGGTCAATTGATCTCAGAAT 59.003 33.333 19.21 6.94 0.00 2.40
3475 3846 5.263968 ACCTATTATGTTGTCGAGACCAG 57.736 43.478 0.34 0.00 0.00 4.00
3484 3855 4.020573 TGTTGTCGAGACCAGAACCATAAT 60.021 41.667 0.34 0.00 0.00 1.28
3608 3979 4.660303 TGGTTGAGAACTCCAGCCATATAT 59.340 41.667 0.00 0.00 39.47 0.86
3619 3990 4.080919 TCCAGCCATATATGATAGGTGTGC 60.081 45.833 14.54 6.29 0.00 4.57
3647 4018 5.911280 GGAATATGAAAACACAGATGCATCG 59.089 40.000 20.67 17.08 0.00 3.84
3675 4046 7.761249 GCAAATCTTTAATTTGTCTGCCATACT 59.239 33.333 11.03 0.00 40.19 2.12
3722 4093 5.104776 TCCCAGGAATAGACTGAATTGTGAG 60.105 44.000 0.00 0.00 38.20 3.51
3723 4094 5.338708 CCCAGGAATAGACTGAATTGTGAGT 60.339 44.000 0.00 0.00 38.20 3.41
3724 4095 6.176183 CCAGGAATAGACTGAATTGTGAGTT 58.824 40.000 0.00 0.00 38.20 3.01
3852 4225 7.010339 AGAAGCAGGTAGTCTTTATCTGTTT 57.990 36.000 0.00 0.00 32.97 2.83
4008 4384 6.317140 TCTTCAATCACAAATATGAGCAGGAC 59.683 38.462 0.00 0.00 30.46 3.85
4070 4446 1.702401 TCCTGGTTATGGTTGCTGTCA 59.298 47.619 0.00 0.00 0.00 3.58
4396 4787 3.193479 GTGGCAAGTTTATTTCTCTGGGG 59.807 47.826 0.00 0.00 0.00 4.96
4405 4796 6.603599 AGTTTATTTCTCTGGGGAATAGTTGC 59.396 38.462 0.00 0.00 0.00 4.17
4417 4808 1.191535 ATAGTTGCCCGTGTAGCTGA 58.808 50.000 0.00 0.00 0.00 4.26
4558 4949 2.480555 GCGATGCCTGGAACAACG 59.519 61.111 0.00 0.00 38.70 4.10
4577 4968 2.093128 ACGGTTTTGGCGGAGAGATTAT 60.093 45.455 0.00 0.00 0.00 1.28
4624 5015 3.596214 TGCTTCCGTGTCTCCTTTAATC 58.404 45.455 0.00 0.00 0.00 1.75
4771 5165 6.418585 AAAACGAGTTATGTAGCTTTAGCC 57.581 37.500 0.00 0.00 43.38 3.93
4772 5166 4.730949 ACGAGTTATGTAGCTTTAGCCA 57.269 40.909 0.00 0.00 43.38 4.75
4774 5168 5.671493 ACGAGTTATGTAGCTTTAGCCATT 58.329 37.500 0.00 0.00 43.38 3.16
4775 5169 5.523916 ACGAGTTATGTAGCTTTAGCCATTG 59.476 40.000 0.00 0.00 43.38 2.82
4777 5171 6.292381 CGAGTTATGTAGCTTTAGCCATTGTC 60.292 42.308 0.00 0.00 43.38 3.18
4778 5172 6.414732 AGTTATGTAGCTTTAGCCATTGTCA 58.585 36.000 0.00 0.00 43.38 3.58
4781 5175 4.393834 TGTAGCTTTAGCCATTGTCACAA 58.606 39.130 0.00 0.00 43.38 3.33
4782 5176 4.455533 TGTAGCTTTAGCCATTGTCACAAG 59.544 41.667 0.00 0.00 43.38 3.16
4783 5177 3.754965 AGCTTTAGCCATTGTCACAAGA 58.245 40.909 0.00 0.00 43.38 3.02
4784 5178 3.755378 AGCTTTAGCCATTGTCACAAGAG 59.245 43.478 0.00 0.00 43.38 2.85
4785 5179 3.503748 GCTTTAGCCATTGTCACAAGAGT 59.496 43.478 0.00 0.00 34.31 3.24
4787 5181 5.437289 TTTAGCCATTGTCACAAGAGTTG 57.563 39.130 0.00 0.00 0.00 3.16
4788 5182 2.936202 AGCCATTGTCACAAGAGTTGT 58.064 42.857 0.00 0.00 46.75 3.32
4798 5192 3.275617 ACAAGAGTTGTGTTGCCTGTA 57.724 42.857 0.00 0.00 43.48 2.74
4799 5193 3.206150 ACAAGAGTTGTGTTGCCTGTAG 58.794 45.455 0.00 0.00 43.48 2.74
4800 5194 3.206150 CAAGAGTTGTGTTGCCTGTAGT 58.794 45.455 0.00 0.00 0.00 2.73
4802 5196 4.891992 AGAGTTGTGTTGCCTGTAGTAT 57.108 40.909 0.00 0.00 0.00 2.12
4803 5197 4.822026 AGAGTTGTGTTGCCTGTAGTATC 58.178 43.478 0.00 0.00 0.00 2.24
4805 5199 5.046304 AGAGTTGTGTTGCCTGTAGTATCAT 60.046 40.000 0.00 0.00 0.00 2.45
4806 5200 6.154534 AGAGTTGTGTTGCCTGTAGTATCATA 59.845 38.462 0.00 0.00 0.00 2.15
4807 5201 6.707290 AGTTGTGTTGCCTGTAGTATCATAA 58.293 36.000 0.00 0.00 0.00 1.90
4808 5202 7.165485 AGTTGTGTTGCCTGTAGTATCATAAA 58.835 34.615 0.00 0.00 0.00 1.40
4809 5203 7.663905 AGTTGTGTTGCCTGTAGTATCATAAAA 59.336 33.333 0.00 0.00 0.00 1.52
4810 5204 7.987750 TGTGTTGCCTGTAGTATCATAAAAA 57.012 32.000 0.00 0.00 0.00 1.94
4849 5814 7.829211 ACATGCATATTTATAGGCTAAACCGAT 59.171 33.333 0.00 0.00 46.52 4.18
4861 5826 3.004944 GCTAAACCGATCTAGACCTCCAG 59.995 52.174 0.00 0.00 0.00 3.86
4943 5908 7.492352 ACCAGTACAAACAACTCATTTACTC 57.508 36.000 0.00 0.00 0.00 2.59
4981 5946 1.858041 CAGCTGACAGAACACGCAG 59.142 57.895 8.42 0.00 0.00 5.18
5060 6025 4.417437 ACCGATCTATACTAATGCCCAGT 58.583 43.478 0.00 0.00 0.00 4.00
5061 6026 4.838986 ACCGATCTATACTAATGCCCAGTT 59.161 41.667 0.00 0.00 0.00 3.16
5062 6027 6.014647 ACCGATCTATACTAATGCCCAGTTA 58.985 40.000 0.00 0.00 0.00 2.24
5063 6028 6.495872 ACCGATCTATACTAATGCCCAGTTAA 59.504 38.462 0.00 0.00 0.00 2.01
5064 6029 6.812160 CCGATCTATACTAATGCCCAGTTAAC 59.188 42.308 0.00 0.00 0.00 2.01
5065 6030 7.309867 CCGATCTATACTAATGCCCAGTTAACT 60.310 40.741 1.12 1.12 0.00 2.24
5066 6031 8.737175 CGATCTATACTAATGCCCAGTTAACTA 58.263 37.037 8.04 0.00 0.00 2.24
5128 6093 1.148310 CTTGTGTGCTACCTTGACCG 58.852 55.000 0.00 0.00 0.00 4.79
5184 6149 1.135489 GCATCACACCATGCTTGTCAG 60.135 52.381 0.00 0.00 45.03 3.51
5189 6154 2.225019 CACACCATGCTTGTCAGTCTTC 59.775 50.000 0.00 0.00 0.00 2.87
5235 6200 4.790765 GCTCAAAGCCCAACTAAAATCT 57.209 40.909 0.00 0.00 34.48 2.40
5236 6201 4.488879 GCTCAAAGCCCAACTAAAATCTG 58.511 43.478 0.00 0.00 34.48 2.90
5237 6202 4.218417 GCTCAAAGCCCAACTAAAATCTGA 59.782 41.667 0.00 0.00 34.48 3.27
5238 6203 5.278957 GCTCAAAGCCCAACTAAAATCTGAA 60.279 40.000 0.00 0.00 34.48 3.02
5239 6204 6.723298 TCAAAGCCCAACTAAAATCTGAAA 57.277 33.333 0.00 0.00 0.00 2.69
5240 6205 7.301868 TCAAAGCCCAACTAAAATCTGAAAT 57.698 32.000 0.00 0.00 0.00 2.17
5241 6206 7.734942 TCAAAGCCCAACTAAAATCTGAAATT 58.265 30.769 0.00 0.00 0.00 1.82
5242 6207 7.872483 TCAAAGCCCAACTAAAATCTGAAATTC 59.128 33.333 0.00 0.00 0.00 2.17
5243 6208 7.544804 AAGCCCAACTAAAATCTGAAATTCT 57.455 32.000 0.00 0.00 0.00 2.40
5244 6209 7.163001 AGCCCAACTAAAATCTGAAATTCTC 57.837 36.000 0.00 0.00 0.00 2.87
5245 6210 6.030228 GCCCAACTAAAATCTGAAATTCTCG 58.970 40.000 0.00 0.00 0.00 4.04
5246 6211 6.349363 GCCCAACTAAAATCTGAAATTCTCGT 60.349 38.462 0.00 0.00 0.00 4.18
5247 6212 7.023575 CCCAACTAAAATCTGAAATTCTCGTG 58.976 38.462 0.00 0.00 0.00 4.35
5248 6213 7.023575 CCAACTAAAATCTGAAATTCTCGTGG 58.976 38.462 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.932580 TTCGAGCACGCCGAAGCAT 62.933 57.895 10.07 0.00 40.56 3.79
23 24 1.446099 GTGATGCGGCTGACTTCGA 60.446 57.895 0.00 0.00 0.00 3.71
30 31 3.190849 CGGACAGTGATGCGGCTG 61.191 66.667 0.00 0.00 38.58 4.85
38 39 3.841379 GACTGCACGCGGACAGTGA 62.841 63.158 32.23 3.93 46.82 3.41
73 74 4.827087 CTGTGGCTCGCCGATGCT 62.827 66.667 3.14 0.00 39.42 3.79
430 442 1.072930 ACCAACCACCTCCCCTCTT 60.073 57.895 0.00 0.00 0.00 2.85
544 561 2.438434 CGGCAAAATCTCGGCCCT 60.438 61.111 0.00 0.00 44.90 5.19
590 607 3.147629 CTGATTAGACCCCGTATCTCGT 58.852 50.000 0.00 0.00 37.94 4.18
606 623 0.603065 GCGGAAAAACCTGCCTGATT 59.397 50.000 0.00 0.00 36.31 2.57
638 655 4.808364 CCCGATCCGTAAAATAACCGTTAA 59.192 41.667 0.00 0.00 0.00 2.01
639 656 4.098654 TCCCGATCCGTAAAATAACCGTTA 59.901 41.667 0.00 0.00 0.00 3.18
640 657 3.118811 TCCCGATCCGTAAAATAACCGTT 60.119 43.478 0.00 0.00 0.00 4.44
641 658 2.430332 TCCCGATCCGTAAAATAACCGT 59.570 45.455 0.00 0.00 0.00 4.83
642 659 2.796593 GTCCCGATCCGTAAAATAACCG 59.203 50.000 0.00 0.00 0.00 4.44
643 660 2.796593 CGTCCCGATCCGTAAAATAACC 59.203 50.000 0.00 0.00 0.00 2.85
644 661 3.705604 TCGTCCCGATCCGTAAAATAAC 58.294 45.455 0.00 0.00 0.00 1.89
645 662 3.631686 TCTCGTCCCGATCCGTAAAATAA 59.368 43.478 0.00 0.00 34.61 1.40
646 663 3.213506 TCTCGTCCCGATCCGTAAAATA 58.786 45.455 0.00 0.00 34.61 1.40
647 664 2.026641 TCTCGTCCCGATCCGTAAAAT 58.973 47.619 0.00 0.00 34.61 1.82
648 665 1.462616 TCTCGTCCCGATCCGTAAAA 58.537 50.000 0.00 0.00 34.61 1.52
649 666 1.683943 ATCTCGTCCCGATCCGTAAA 58.316 50.000 0.00 0.00 34.61 2.01
650 667 2.146342 GTATCTCGTCCCGATCCGTAA 58.854 52.381 0.00 0.00 34.61 3.18
651 668 1.800805 GTATCTCGTCCCGATCCGTA 58.199 55.000 0.00 0.00 34.61 4.02
652 669 1.226686 CGTATCTCGTCCCGATCCGT 61.227 60.000 0.00 0.00 34.61 4.69
653 670 1.496393 CGTATCTCGTCCCGATCCG 59.504 63.158 0.00 0.00 34.61 4.18
654 671 1.584380 CCCGTATCTCGTCCCGATCC 61.584 65.000 0.00 0.00 34.61 3.36
655 672 1.584380 CCCCGTATCTCGTCCCGATC 61.584 65.000 0.00 0.00 34.61 3.69
656 673 1.602888 CCCCGTATCTCGTCCCGAT 60.603 63.158 0.00 0.00 34.61 4.18
657 674 2.203252 CCCCGTATCTCGTCCCGA 60.203 66.667 0.00 0.00 37.94 5.14
658 675 2.517875 ACCCCGTATCTCGTCCCG 60.518 66.667 0.00 0.00 37.94 5.14
659 676 1.755783 ACACCCCGTATCTCGTCCC 60.756 63.158 0.00 0.00 37.94 4.46
660 677 1.436336 CACACCCCGTATCTCGTCC 59.564 63.158 0.00 0.00 37.94 4.79
661 678 1.226888 GCACACCCCGTATCTCGTC 60.227 63.158 0.00 0.00 37.94 4.20
662 679 0.394762 TAGCACACCCCGTATCTCGT 60.395 55.000 0.00 0.00 37.94 4.18
663 680 0.311165 CTAGCACACCCCGTATCTCG 59.689 60.000 0.00 0.00 39.52 4.04
664 681 1.337387 GTCTAGCACACCCCGTATCTC 59.663 57.143 0.00 0.00 0.00 2.75
665 682 1.341679 TGTCTAGCACACCCCGTATCT 60.342 52.381 0.00 0.00 0.00 1.98
666 683 1.108776 TGTCTAGCACACCCCGTATC 58.891 55.000 0.00 0.00 0.00 2.24
667 684 1.412710 CATGTCTAGCACACCCCGTAT 59.587 52.381 0.00 0.00 38.04 3.06
668 685 0.821517 CATGTCTAGCACACCCCGTA 59.178 55.000 0.00 0.00 38.04 4.02
669 686 1.596934 CATGTCTAGCACACCCCGT 59.403 57.895 0.00 0.00 38.04 5.28
670 687 1.815421 GCATGTCTAGCACACCCCG 60.815 63.158 0.00 0.00 38.04 5.73
671 688 0.462759 GAGCATGTCTAGCACACCCC 60.463 60.000 0.00 0.00 38.04 4.95
672 689 0.539051 AGAGCATGTCTAGCACACCC 59.461 55.000 0.00 0.00 38.04 4.61
673 690 3.452474 CTTAGAGCATGTCTAGCACACC 58.548 50.000 0.00 0.00 39.05 4.16
674 691 2.863137 GCTTAGAGCATGTCTAGCACAC 59.137 50.000 0.00 0.00 41.89 3.82
675 692 2.159043 GGCTTAGAGCATGTCTAGCACA 60.159 50.000 17.47 0.00 44.75 4.57
676 693 2.478831 GGCTTAGAGCATGTCTAGCAC 58.521 52.381 17.47 0.00 44.75 4.40
677 694 1.414181 GGGCTTAGAGCATGTCTAGCA 59.586 52.381 17.47 0.00 44.75 3.49
678 695 1.414181 TGGGCTTAGAGCATGTCTAGC 59.586 52.381 2.04 6.45 44.75 3.42
679 696 2.697751 AGTGGGCTTAGAGCATGTCTAG 59.302 50.000 2.04 0.00 44.75 2.43
680 697 2.752030 AGTGGGCTTAGAGCATGTCTA 58.248 47.619 2.04 0.00 44.75 2.59
681 698 1.577736 AGTGGGCTTAGAGCATGTCT 58.422 50.000 2.04 0.00 44.75 3.41
682 699 3.760580 ATAGTGGGCTTAGAGCATGTC 57.239 47.619 2.04 0.00 44.75 3.06
683 700 3.200825 ACAATAGTGGGCTTAGAGCATGT 59.799 43.478 2.04 0.00 44.75 3.21
684 701 3.813443 ACAATAGTGGGCTTAGAGCATG 58.187 45.455 2.04 0.00 44.75 4.06
685 702 4.656112 AGTACAATAGTGGGCTTAGAGCAT 59.344 41.667 2.04 0.00 44.75 3.79
686 703 4.030913 AGTACAATAGTGGGCTTAGAGCA 58.969 43.478 2.04 0.00 44.75 4.26
687 704 4.674281 AGTACAATAGTGGGCTTAGAGC 57.326 45.455 0.00 0.00 41.46 4.09
688 705 4.811557 GCAAGTACAATAGTGGGCTTAGAG 59.188 45.833 0.00 0.00 0.00 2.43
689 706 4.469945 AGCAAGTACAATAGTGGGCTTAGA 59.530 41.667 0.00 0.00 0.00 2.10
690 707 4.770795 AGCAAGTACAATAGTGGGCTTAG 58.229 43.478 0.00 0.00 0.00 2.18
691 708 4.383770 GGAGCAAGTACAATAGTGGGCTTA 60.384 45.833 0.00 0.00 0.00 3.09
692 709 3.610911 GAGCAAGTACAATAGTGGGCTT 58.389 45.455 0.00 0.00 0.00 4.35
693 710 2.092914 GGAGCAAGTACAATAGTGGGCT 60.093 50.000 0.00 0.00 0.00 5.19
694 711 2.289565 GGAGCAAGTACAATAGTGGGC 58.710 52.381 0.00 0.00 0.00 5.36
695 712 2.741878 CGGGAGCAAGTACAATAGTGGG 60.742 54.545 0.00 0.00 0.00 4.61
696 713 2.550978 CGGGAGCAAGTACAATAGTGG 58.449 52.381 0.00 0.00 0.00 4.00
697 714 2.550978 CCGGGAGCAAGTACAATAGTG 58.449 52.381 0.00 0.00 0.00 2.74
698 715 1.134491 GCCGGGAGCAAGTACAATAGT 60.134 52.381 2.18 0.00 42.97 2.12
699 716 1.583054 GCCGGGAGCAAGTACAATAG 58.417 55.000 2.18 0.00 42.97 1.73
700 717 0.179468 GGCCGGGAGCAAGTACAATA 59.821 55.000 2.18 0.00 46.50 1.90
701 718 1.077716 GGCCGGGAGCAAGTACAAT 60.078 57.895 2.18 0.00 46.50 2.71
702 719 2.349755 GGCCGGGAGCAAGTACAA 59.650 61.111 2.18 0.00 46.50 2.41
703 720 3.712907 GGGCCGGGAGCAAGTACA 61.713 66.667 2.18 0.00 46.50 2.90
704 721 4.832608 CGGGCCGGGAGCAAGTAC 62.833 72.222 20.56 0.00 46.50 2.73
711 728 1.751162 TTAAAATGCGGGCCGGGAG 60.751 57.895 29.48 0.00 0.00 4.30
712 729 2.047443 GTTAAAATGCGGGCCGGGA 61.047 57.895 29.48 10.10 0.00 5.14
749 766 4.457496 CACACCCCGCATCTCGCT 62.457 66.667 0.00 0.00 39.08 4.93
753 770 0.249398 GTCTAACACACCCCGCATCT 59.751 55.000 0.00 0.00 0.00 2.90
764 781 4.865365 GTGGACTTAGAGCATGTCTAACAC 59.135 45.833 11.41 13.04 41.97 3.32
767 784 7.124298 ACAATAGTGGACTTAGAGCATGTCTAA 59.876 37.037 13.56 13.56 44.19 2.10
783 800 7.418337 TGATAAGAGCAAGTACAATAGTGGA 57.582 36.000 0.00 0.00 0.00 4.02
784 801 6.201806 GCTGATAAGAGCAAGTACAATAGTGG 59.798 42.308 0.00 0.00 38.95 4.00
785 802 6.758416 TGCTGATAAGAGCAAGTACAATAGTG 59.242 38.462 0.00 0.00 46.05 2.74
786 803 6.878317 TGCTGATAAGAGCAAGTACAATAGT 58.122 36.000 0.00 0.00 46.05 2.12
798 815 4.746115 CACTCTCTGAATGCTGATAAGAGC 59.254 45.833 0.00 0.00 39.62 4.09
799 816 5.163426 ACCACTCTCTGAATGCTGATAAGAG 60.163 44.000 0.00 0.00 36.53 2.85
800 817 4.713814 ACCACTCTCTGAATGCTGATAAGA 59.286 41.667 0.00 0.00 0.00 2.10
801 818 4.809958 CACCACTCTCTGAATGCTGATAAG 59.190 45.833 0.00 0.00 0.00 1.73
802 819 4.467438 TCACCACTCTCTGAATGCTGATAA 59.533 41.667 0.00 0.00 0.00 1.75
803 820 4.026052 TCACCACTCTCTGAATGCTGATA 58.974 43.478 0.00 0.00 0.00 2.15
804 821 2.836372 TCACCACTCTCTGAATGCTGAT 59.164 45.455 0.00 0.00 0.00 2.90
805 822 2.250924 TCACCACTCTCTGAATGCTGA 58.749 47.619 0.00 0.00 0.00 4.26
806 823 2.740981 GTTCACCACTCTCTGAATGCTG 59.259 50.000 0.00 0.00 0.00 4.41
807 824 2.289945 GGTTCACCACTCTCTGAATGCT 60.290 50.000 0.00 0.00 35.64 3.79
808 825 2.079925 GGTTCACCACTCTCTGAATGC 58.920 52.381 0.00 0.00 35.64 3.56
815 832 1.416401 TGGAACTGGTTCACCACTCTC 59.584 52.381 14.25 0.00 42.01 3.20
838 855 1.166531 GCATCCCACGGTTGATAGCC 61.167 60.000 0.00 0.00 0.00 3.93
840 857 0.179084 ACGCATCCCACGGTTGATAG 60.179 55.000 0.00 0.00 34.00 2.08
852 869 0.963355 TTTAAGGGGTGCACGCATCC 60.963 55.000 31.75 19.60 46.13 3.51
861 878 2.391926 AAGTTGGGGTTTAAGGGGTG 57.608 50.000 0.00 0.00 0.00 4.61
916 934 1.705745 GGAAGAGGGGAAGGACAAAGT 59.294 52.381 0.00 0.00 0.00 2.66
921 939 0.043485 AGGAGGAAGAGGGGAAGGAC 59.957 60.000 0.00 0.00 0.00 3.85
949 971 2.760374 CAGCCCAATCGATTCTACTCC 58.240 52.381 7.92 0.00 0.00 3.85
950 972 2.139118 GCAGCCCAATCGATTCTACTC 58.861 52.381 7.92 0.00 0.00 2.59
961 983 0.704076 TCAAACCCTAGCAGCCCAAT 59.296 50.000 0.00 0.00 0.00 3.16
962 984 0.704076 ATCAAACCCTAGCAGCCCAA 59.296 50.000 0.00 0.00 0.00 4.12
964 986 0.466372 GGATCAAACCCTAGCAGCCC 60.466 60.000 0.00 0.00 0.00 5.19
1155 1177 1.032114 CGTCCATCCAGGGGAAAAGC 61.032 60.000 0.00 0.00 35.88 3.51
1259 1281 9.912634 ACAAACATGTATAGGAAACAATTTCAG 57.087 29.630 0.00 0.00 41.43 3.02
1260 1282 9.689976 CACAAACATGTATAGGAAACAATTTCA 57.310 29.630 0.00 0.00 41.43 2.69
1261 1283 8.647226 GCACAAACATGTATAGGAAACAATTTC 58.353 33.333 0.00 0.00 38.94 2.17
1290 1312 9.071276 AGACATAAATTGGGAAACATATAGCAG 57.929 33.333 0.00 0.00 0.00 4.24
1355 1377 2.366469 ACCCAGTGGTGCTAGTGAG 58.634 57.895 8.74 0.00 45.58 3.51
1375 1397 0.598065 GCACCAACCACCAAAGCTAG 59.402 55.000 0.00 0.00 0.00 3.42
1485 1507 8.488651 AAACATATAGTAAAACGGAAGACTGG 57.511 34.615 0.00 0.00 0.00 4.00
1602 1625 5.296035 GGGTAATCGGAGAAAATCGACAAAT 59.704 40.000 0.00 0.00 43.58 2.32
1609 1632 6.693315 TTGATTGGGTAATCGGAGAAAATC 57.307 37.500 0.00 0.00 44.55 2.17
1612 1635 6.262273 GCTATTTGATTGGGTAATCGGAGAAA 59.738 38.462 0.00 0.00 44.55 2.52
1719 1742 3.240069 GCTGTCACAAGCTGCATTTTAG 58.760 45.455 1.02 0.00 40.20 1.85
1891 1914 4.554960 ATCATCATCAGGACCAGCATAG 57.445 45.455 0.00 0.00 0.00 2.23
2267 2290 1.801309 ATGCCGAAACCAAACCCGTG 61.801 55.000 0.00 0.00 0.00 4.94
2277 2300 1.726248 GGAATTGCAACATGCCGAAAC 59.274 47.619 0.00 0.00 44.23 2.78
2332 2355 3.706055 TGGTGCAAGAAGAGACCAC 57.294 52.632 0.00 0.00 33.44 4.16
2383 2406 9.213777 TGGATGATTAAGAATTACTGTACTCCT 57.786 33.333 0.00 0.00 0.00 3.69
2506 2873 0.175760 GGAGGCTACATTCGCACAGA 59.824 55.000 0.00 0.00 0.00 3.41
2882 3252 5.003692 TGAGAATTAGCTCAGCACTAGTG 57.996 43.478 18.93 18.93 39.84 2.74
2944 3315 5.105473 AGTGTACGGTGTAGCTGATACAAAT 60.105 40.000 7.42 0.00 45.88 2.32
2963 3334 9.554395 TTGACTCTGACATTAATGAAAAGTGTA 57.446 29.630 22.16 7.94 0.00 2.90
3060 3431 2.680312 TGGACTCACTCTGCTATTGC 57.320 50.000 0.00 0.00 40.20 3.56
3608 3979 0.541392 ATTCCTGCGCACACCTATCA 59.459 50.000 5.66 0.00 0.00 2.15
3619 3990 4.944962 TCTGTGTTTTCATATTCCTGCG 57.055 40.909 0.00 0.00 0.00 5.18
3647 4018 5.695816 TGGCAGACAAATTAAAGATTTGCAC 59.304 36.000 10.47 6.37 41.36 4.57
3722 4093 5.659463 TGATGCCCTGCAAATACATAAAAC 58.341 37.500 0.00 0.00 43.62 2.43
3723 4094 5.681954 GCTGATGCCCTGCAAATACATAAAA 60.682 40.000 0.00 0.00 43.62 1.52
3724 4095 4.202141 GCTGATGCCCTGCAAATACATAAA 60.202 41.667 0.00 0.00 43.62 1.40
3852 4225 2.979678 ACAGAGGGAGTAGAAGGCAAAA 59.020 45.455 0.00 0.00 0.00 2.44
4008 4384 2.220653 AGTCCACACCATTCCATTGG 57.779 50.000 0.00 0.00 42.82 3.16
4070 4446 3.775316 ACCAAGAATGTTAGGATCCTCGT 59.225 43.478 20.22 3.02 0.00 4.18
4375 4766 3.075283 TCCCCAGAGAAATAAACTTGCCA 59.925 43.478 0.00 0.00 0.00 4.92
4396 4787 1.933853 CAGCTACACGGGCAACTATTC 59.066 52.381 0.00 0.00 0.00 1.75
4405 4796 1.732259 GAAACACATCAGCTACACGGG 59.268 52.381 0.00 0.00 0.00 5.28
4412 4803 5.779529 ACAAAATGAGAAACACATCAGCT 57.220 34.783 0.00 0.00 0.00 4.24
4417 4808 5.291614 GTGCACAACAAAATGAGAAACACAT 59.708 36.000 13.17 0.00 0.00 3.21
4558 4949 4.640647 AGAAATAATCTCTCCGCCAAAACC 59.359 41.667 0.00 0.00 30.46 3.27
4593 4984 3.057174 AGACACGGAAGCAAAACAAACAA 60.057 39.130 0.00 0.00 0.00 2.83
4624 5015 3.190849 CACATCTCTGGGTGCGCG 61.191 66.667 0.00 0.00 0.00 6.86
4762 5156 3.754965 TCTTGTGACAATGGCTAAAGCT 58.245 40.909 0.00 0.00 41.70 3.74
4765 5159 4.887071 ACAACTCTTGTGACAATGGCTAAA 59.113 37.500 0.00 0.00 43.48 1.85
4767 5161 4.085357 ACAACTCTTGTGACAATGGCTA 57.915 40.909 0.00 0.00 43.48 3.93
4778 5172 2.128771 ACAGGCAACACAACTCTTGT 57.871 45.000 0.00 0.00 46.75 3.16
4781 5175 4.283467 TGATACTACAGGCAACACAACTCT 59.717 41.667 0.00 0.00 41.41 3.24
4782 5176 4.566004 TGATACTACAGGCAACACAACTC 58.434 43.478 0.00 0.00 41.41 3.01
4783 5177 4.617253 TGATACTACAGGCAACACAACT 57.383 40.909 0.00 0.00 41.41 3.16
4784 5178 6.978343 TTATGATACTACAGGCAACACAAC 57.022 37.500 0.00 0.00 41.41 3.32
4785 5179 7.987750 TTTTATGATACTACAGGCAACACAA 57.012 32.000 0.00 0.00 41.41 3.33
4822 5216 8.315482 TCGGTTTAGCCTATAAATATGCATGTA 58.685 33.333 10.16 0.00 34.25 2.29
4849 5814 1.221909 TGGAGCCCTGGAGGTCTAGA 61.222 60.000 12.11 0.00 38.26 2.43
4861 5826 2.359975 CAGGTCGGTTTGGAGCCC 60.360 66.667 0.00 0.00 35.06 5.19
4981 5946 3.494045 GCCTGTAGTCAATTTGGCTTC 57.506 47.619 9.10 4.73 32.64 3.86
5011 5976 7.440255 TCAGACCAACACTTAGCTAGTAAAAAC 59.560 37.037 0.00 0.00 34.56 2.43
5060 6025 0.035598 TGCGTGCTGGGCTTAGTTAA 59.964 50.000 0.00 0.00 0.00 2.01
5061 6026 0.035598 TTGCGTGCTGGGCTTAGTTA 59.964 50.000 0.00 0.00 0.00 2.24
5062 6027 1.228124 TTGCGTGCTGGGCTTAGTT 60.228 52.632 0.00 0.00 0.00 2.24
5063 6028 1.672356 CTTGCGTGCTGGGCTTAGT 60.672 57.895 0.00 0.00 0.00 2.24
5064 6029 2.401766 CCTTGCGTGCTGGGCTTAG 61.402 63.158 0.00 0.00 0.00 2.18
5065 6030 2.359850 CCTTGCGTGCTGGGCTTA 60.360 61.111 0.00 0.00 0.00 3.09
5066 6031 4.586235 ACCTTGCGTGCTGGGCTT 62.586 61.111 8.73 0.00 0.00 4.35
5128 6093 2.027653 AGCTTAGAGCAAGGACTGGAAC 60.028 50.000 2.47 0.00 45.56 3.62
5184 6149 5.065346 GCCTACTAGCAAAATCCAAGAAGAC 59.935 44.000 0.00 0.00 0.00 3.01
5189 6154 5.904362 AAAGCCTACTAGCAAAATCCAAG 57.096 39.130 0.00 0.00 34.23 3.61
5217 6182 7.874528 AGAATTTCAGATTTTAGTTGGGCTTTG 59.125 33.333 0.00 0.00 0.00 2.77
5218 6183 7.966812 AGAATTTCAGATTTTAGTTGGGCTTT 58.033 30.769 0.00 0.00 0.00 3.51
5219 6184 7.544804 AGAATTTCAGATTTTAGTTGGGCTT 57.455 32.000 0.00 0.00 0.00 4.35
5220 6185 6.127897 CGAGAATTTCAGATTTTAGTTGGGCT 60.128 38.462 0.00 0.00 0.00 5.19
5221 6186 6.030228 CGAGAATTTCAGATTTTAGTTGGGC 58.970 40.000 0.00 0.00 0.00 5.36
5222 6187 7.023575 CACGAGAATTTCAGATTTTAGTTGGG 58.976 38.462 0.00 0.00 0.00 4.12
5223 6188 7.023575 CCACGAGAATTTCAGATTTTAGTTGG 58.976 38.462 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.