Multiple sequence alignment - TraesCS3A01G460900

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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 TraesCS3A01G460900 chr3A 100.000 3392 0 0 1 3392 697015422 697012031 0.000000e+00 6264.0
1 TraesCS3A01G460900 chr3A 100.000 266 0 0 3726 3991 697011697 697011432 3.580000e-135 492.0
2 TraesCS3A01G460900 chr3B 89.544 1712 128 25 1689 3380 745610785 745609105 0.000000e+00 2122.0
3 TraesCS3A01G460900 chr3B 84.435 1619 111 67 24 1580 745612500 745610961 0.000000e+00 1463.0
4 TraesCS3A01G460900 chr3B 93.750 64 4 0 3726 3789 745609054 745608991 3.280000e-16 97.1
5 TraesCS3A01G460900 chr3D 89.246 1432 89 29 896 2293 560943691 560942291 0.000000e+00 1731.0
6 TraesCS3A01G460900 chr3D 88.740 1119 99 16 2288 3390 560942126 560941019 0.000000e+00 1343.0
7 TraesCS3A01G460900 chr3D 84.232 742 41 30 93 809 560944431 560943741 0.000000e+00 652.0
8 TraesCS3A01G460900 chr3D 91.912 136 11 0 3856 3991 560940482 560940347 1.460000e-44 191.0
9 TraesCS3A01G460900 chr3D 94.366 71 4 0 3728 3798 560940944 560940874 4.220000e-20 110.0
10 TraesCS3A01G460900 chrUn 86.775 431 35 14 1140 1567 362209026 362208615 1.010000e-125 460.0
11 TraesCS3A01G460900 chrUn 98.305 118 2 0 1687 1804 362208432 362208315 1.450000e-49 207.0
12 TraesCS3A01G460900 chrUn 86.813 91 11 1 893 982 362209112 362209022 2.540000e-17 100.0
13 TraesCS3A01G460900 chr1B 86.775 431 35 14 1140 1567 59503186 59503597 1.010000e-125 460.0
14 TraesCS3A01G460900 chr1B 86.775 431 35 14 1140 1567 59522878 59523289 1.010000e-125 460.0
15 TraesCS3A01G460900 chr1B 98.305 118 2 0 1687 1804 59503780 59503897 1.450000e-49 207.0
16 TraesCS3A01G460900 chr1B 98.305 118 2 0 1687 1804 59523472 59523589 1.450000e-49 207.0
17 TraesCS3A01G460900 chr1B 85.841 113 5 2 697 809 59502926 59503027 4.220000e-20 110.0
18 TraesCS3A01G460900 chr1B 86.813 91 11 1 893 982 59522792 59522882 2.540000e-17 100.0


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 TraesCS3A01G460900 chr3A 697011432 697015422 3990 True 3378.000000 6264 100.0000 1 3991 2 chr3A.!!$R1 3990
1 TraesCS3A01G460900 chr3B 745608991 745612500 3509 True 1227.366667 2122 89.2430 24 3789 3 chr3B.!!$R1 3765
2 TraesCS3A01G460900 chr3D 560940347 560944431 4084 True 805.400000 1731 89.6992 93 3991 5 chr3D.!!$R1 3898
3 TraesCS3A01G460900 chrUn 362208315 362209112 797 True 255.666667 460 90.6310 893 1804 3 chrUn.!!$R1 911
4 TraesCS3A01G460900 chr1B 59502926 59503897 971 False 259.000000 460 90.3070 697 1804 3 chr1B.!!$F1 1107
5 TraesCS3A01G460900 chr1B 59522792 59523589 797 False 255.666667 460 90.6310 893 1804 3 chr1B.!!$F2 911

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
447 455 0.036875 GTTGACAGCTAGCCCAAGGT 59.963 55.0 12.13 2.02 0.00 3.50 F
716 759 0.041833 TAGCTGCTCTGTTCCTCCCT 59.958 55.0 4.91 0.00 0.00 4.20 F
809 852 0.105964 TTAAAACACCCAGCCCAGCA 60.106 50.0 0.00 0.00 0.00 4.41 F
811 854 0.114168 AAAACACCCAGCCCAGCATA 59.886 50.0 0.00 0.00 0.00 3.14 F
829 872 0.318441 TAGCCACCATATCTCGCAGC 59.682 55.0 0.00 0.00 0.00 5.25 F
831 874 0.533755 GCCACCATATCTCGCAGCTT 60.534 55.0 0.00 0.00 0.00 3.74 F
837 880 0.533755 ATATCTCGCAGCTTGTGGCC 60.534 55.0 0.00 0.00 43.05 5.36 F
855 898 0.541863 CCGCAGACTCCCTACCATTT 59.458 55.0 0.00 0.00 0.00 2.32 F
1296 1384 0.734597 TGCTTCATGCGCTGCAATTG 60.735 50.0 9.73 0.00 43.62 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2350 0.033504 TGAAGTTCTCGTCCACCAGC 59.966 55.000 4.17 0.00 0.00 4.85 R
2414 2809 0.179089 CGGTGATGAGCTCCAGAAGG 60.179 60.000 12.15 0.00 0.00 3.46 R
2449 2844 2.488153 GTTGATTCCGGAGAAACCAAGG 59.512 50.000 3.34 0.00 38.90 3.61 R
2655 3064 3.677527 GTCTCCCGACGTCTCCAA 58.322 61.111 14.70 0.00 0.00 3.53 R
2819 3228 1.760029 GTCAGGGTCATCTCCTTCTCC 59.240 57.143 0.00 0.00 31.06 3.71 R
2843 3252 2.123726 GTGCCATCCCCCATGACC 60.124 66.667 0.00 0.00 33.80 4.02 R
2861 3270 1.456331 CCCAAGGGTGATGATGGCC 60.456 63.158 0.00 0.00 0.00 5.36 R
2876 3285 2.947532 CGTGAAGAGCTGGCTCCCA 61.948 63.158 17.60 13.35 43.70 4.37 R
3101 3511 0.252239 GCAACCATCCTTCCCCCTTT 60.252 55.000 0.00 0.00 0.00 3.11 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
18 19 2.357881 CTGCGCTGTGCTGGAGAA 60.358 61.111 14.92 0.00 46.63 2.87
19 20 2.357881 TGCGCTGTGCTGGAGAAG 60.358 61.111 14.92 0.00 46.63 2.85
20 21 2.358003 GCGCTGTGCTGGAGAAGT 60.358 61.111 5.84 0.00 41.73 3.01
21 22 1.079819 GCGCTGTGCTGGAGAAGTA 60.080 57.895 5.84 0.00 41.73 2.24
22 23 1.080995 GCGCTGTGCTGGAGAAGTAG 61.081 60.000 5.84 0.00 41.73 2.57
30 31 0.461693 CTGGAGAAGTAGCAGCCAGC 60.462 60.000 0.00 0.00 39.60 4.85
72 73 1.489230 ACCTCGTTTTCCTCAAGGTGT 59.511 47.619 0.00 0.00 38.88 4.16
104 105 0.374758 GCATGTGTGATGACGCGATT 59.625 50.000 15.93 0.00 35.15 3.34
195 196 1.079612 CATGCTGGCTGTCACGAGA 60.080 57.895 0.00 0.00 0.00 4.04
241 245 2.998316 AGAAGTATCTGGAAGCAGGC 57.002 50.000 0.00 0.00 33.59 4.85
336 344 5.615544 GCCAAGTGCACGATATAATCATGAC 60.616 44.000 12.01 0.00 40.77 3.06
344 352 7.970614 TGCACGATATAATCATGACATCTCTAC 59.029 37.037 0.00 0.00 0.00 2.59
345 353 7.970614 GCACGATATAATCATGACATCTCTACA 59.029 37.037 0.00 0.00 0.00 2.74
355 363 7.215085 TCATGACATCTCTACAATCATCCTTG 58.785 38.462 0.00 0.00 0.00 3.61
358 366 5.609423 ACATCTCTACAATCATCCTTGCTC 58.391 41.667 0.00 0.00 0.00 4.26
359 367 4.313277 TCTCTACAATCATCCTTGCTCG 57.687 45.455 0.00 0.00 0.00 5.03
360 368 2.799412 CTCTACAATCATCCTTGCTCGC 59.201 50.000 0.00 0.00 0.00 5.03
381 389 2.045280 CTCGGGTCTCCAGCCTATG 58.955 63.158 0.00 0.00 38.13 2.23
443 451 1.005037 CACGTTGACAGCTAGCCCA 60.005 57.895 12.13 4.43 0.00 5.36
445 453 0.320771 ACGTTGACAGCTAGCCCAAG 60.321 55.000 12.13 9.65 0.00 3.61
447 455 0.036875 GTTGACAGCTAGCCCAAGGT 59.963 55.000 12.13 2.02 0.00 3.50
448 456 0.324943 TTGACAGCTAGCCCAAGGTC 59.675 55.000 12.13 11.89 0.00 3.85
450 458 2.258748 GACAGCTAGCCCAAGGTCCC 62.259 65.000 12.13 0.00 0.00 4.46
454 462 1.993391 CTAGCCCAAGGTCCCGGAA 60.993 63.158 0.73 0.00 0.00 4.30
455 463 1.307517 TAGCCCAAGGTCCCGGAAT 60.308 57.895 0.73 0.00 0.00 3.01
521 549 1.301401 CCGGTGCGGTGAAGAAGAA 60.301 57.895 0.00 0.00 42.73 2.52
529 557 1.069432 CGGTGAAGAAGAAGACGACGA 60.069 52.381 0.00 0.00 0.00 4.20
547 575 3.141038 CGACCCGTTCGTTCGTTC 58.859 61.111 5.65 0.00 43.24 3.95
548 576 2.700347 CGACCCGTTCGTTCGTTCG 61.700 63.158 5.65 8.01 43.24 3.95
549 577 1.658409 GACCCGTTCGTTCGTTCGT 60.658 57.895 2.67 0.00 0.00 3.85
552 580 2.700347 CCGTTCGTTCGTTCGTCCG 61.700 63.158 2.67 5.83 0.00 4.79
554 582 1.531522 CGTTCGTTCGTTCGTCCGTT 61.532 55.000 2.67 0.00 0.00 4.44
556 584 0.845768 TTCGTTCGTTCGTCCGTTTC 59.154 50.000 2.67 0.00 0.00 2.78
557 585 0.248417 TCGTTCGTTCGTCCGTTTCA 60.248 50.000 2.67 0.00 0.00 2.69
577 615 2.504681 GCCGCGGTGAAATGCTTG 60.505 61.111 28.70 0.00 0.00 4.01
579 617 2.254951 CGCGGTGAAATGCTTGCA 59.745 55.556 0.00 0.00 0.00 4.08
626 669 1.518056 CGTCCAAGTTGCCATGTGCT 61.518 55.000 0.00 0.00 42.00 4.40
627 670 0.242017 GTCCAAGTTGCCATGTGCTC 59.758 55.000 0.00 2.25 42.00 4.26
628 671 0.178995 TCCAAGTTGCCATGTGCTCA 60.179 50.000 0.00 0.00 42.00 4.26
629 672 0.892755 CCAAGTTGCCATGTGCTCAT 59.107 50.000 0.00 0.00 42.00 2.90
630 673 1.135199 CCAAGTTGCCATGTGCTCATC 60.135 52.381 0.00 0.00 42.00 2.92
631 674 1.816835 CAAGTTGCCATGTGCTCATCT 59.183 47.619 0.00 0.00 42.00 2.90
632 675 1.460504 AGTTGCCATGTGCTCATCTG 58.539 50.000 0.00 0.00 42.00 2.90
633 676 0.179145 GTTGCCATGTGCTCATCTGC 60.179 55.000 11.13 11.13 42.00 4.26
649 692 6.348295 GCTCATCTGCATTCATTTCATATCGT 60.348 38.462 0.00 0.00 0.00 3.73
654 697 5.125356 TGCATTCATTTCATATCGTCCACT 58.875 37.500 0.00 0.00 0.00 4.00
655 698 5.237127 TGCATTCATTTCATATCGTCCACTC 59.763 40.000 0.00 0.00 0.00 3.51
656 699 5.334414 GCATTCATTTCATATCGTCCACTCC 60.334 44.000 0.00 0.00 0.00 3.85
657 700 5.351948 TTCATTTCATATCGTCCACTCCA 57.648 39.130 0.00 0.00 0.00 3.86
658 701 4.693283 TCATTTCATATCGTCCACTCCAC 58.307 43.478 0.00 0.00 0.00 4.02
659 702 3.536956 TTTCATATCGTCCACTCCACC 57.463 47.619 0.00 0.00 0.00 4.61
660 703 2.153034 TCATATCGTCCACTCCACCA 57.847 50.000 0.00 0.00 0.00 4.17
661 704 1.754803 TCATATCGTCCACTCCACCAC 59.245 52.381 0.00 0.00 0.00 4.16
662 705 1.480545 CATATCGTCCACTCCACCACA 59.519 52.381 0.00 0.00 0.00 4.17
663 706 0.892755 TATCGTCCACTCCACCACAC 59.107 55.000 0.00 0.00 0.00 3.82
664 707 1.827399 ATCGTCCACTCCACCACACC 61.827 60.000 0.00 0.00 0.00 4.16
665 708 2.802724 CGTCCACTCCACCACACCA 61.803 63.158 0.00 0.00 0.00 4.17
666 709 1.227853 GTCCACTCCACCACACCAC 60.228 63.158 0.00 0.00 0.00 4.16
667 710 2.113139 CCACTCCACCACACCACC 59.887 66.667 0.00 0.00 0.00 4.61
668 711 2.452064 CCACTCCACCACACCACCT 61.452 63.158 0.00 0.00 0.00 4.00
669 712 1.227943 CACTCCACCACACCACCTG 60.228 63.158 0.00 0.00 0.00 4.00
670 713 2.281761 CTCCACCACACCACCTGC 60.282 66.667 0.00 0.00 0.00 4.85
671 714 4.248842 TCCACCACACCACCTGCG 62.249 66.667 0.00 0.00 0.00 5.18
672 715 4.562425 CCACCACACCACCTGCGT 62.562 66.667 0.00 0.00 0.00 5.24
713 756 0.179086 GCCTAGCTGCTCTGTTCCTC 60.179 60.000 4.91 0.00 0.00 3.71
714 757 0.463620 CCTAGCTGCTCTGTTCCTCC 59.536 60.000 4.91 0.00 0.00 4.30
715 758 0.463620 CTAGCTGCTCTGTTCCTCCC 59.536 60.000 4.91 0.00 0.00 4.30
716 759 0.041833 TAGCTGCTCTGTTCCTCCCT 59.958 55.000 4.91 0.00 0.00 4.20
739 782 1.709147 CTGATTGCGCACCAGCTACC 61.709 60.000 21.33 0.00 39.10 3.18
740 783 1.450312 GATTGCGCACCAGCTACCT 60.450 57.895 11.12 0.00 39.10 3.08
741 784 1.709147 GATTGCGCACCAGCTACCTG 61.709 60.000 11.12 0.00 39.10 4.00
778 821 3.151906 CATCCATCCCTCCCGTCC 58.848 66.667 0.00 0.00 0.00 4.79
785 828 2.937959 ATCCCTCCCGTCCTGCTCTC 62.938 65.000 0.00 0.00 0.00 3.20
809 852 0.105964 TTAAAACACCCAGCCCAGCA 60.106 50.000 0.00 0.00 0.00 4.41
811 854 0.114168 AAAACACCCAGCCCAGCATA 59.886 50.000 0.00 0.00 0.00 3.14
812 855 0.323725 AAACACCCAGCCCAGCATAG 60.324 55.000 0.00 0.00 0.00 2.23
813 856 2.517875 CACCCAGCCCAGCATAGC 60.518 66.667 0.00 0.00 0.00 2.97
814 857 3.813724 ACCCAGCCCAGCATAGCC 61.814 66.667 0.00 0.00 0.00 3.93
815 858 3.812544 CCCAGCCCAGCATAGCCA 61.813 66.667 0.00 0.00 0.00 4.75
817 860 2.517875 CAGCCCAGCATAGCCACC 60.518 66.667 0.00 0.00 0.00 4.61
818 861 3.016971 AGCCCAGCATAGCCACCA 61.017 61.111 0.00 0.00 0.00 4.17
819 862 2.196776 GCCCAGCATAGCCACCAT 59.803 61.111 0.00 0.00 0.00 3.55
820 863 1.061905 AGCCCAGCATAGCCACCATA 61.062 55.000 0.00 0.00 0.00 2.74
823 866 1.632409 CCCAGCATAGCCACCATATCT 59.368 52.381 0.00 0.00 0.00 1.98
824 867 2.355513 CCCAGCATAGCCACCATATCTC 60.356 54.545 0.00 0.00 0.00 2.75
825 868 2.614779 CAGCATAGCCACCATATCTCG 58.385 52.381 0.00 0.00 0.00 4.04
826 869 1.066573 AGCATAGCCACCATATCTCGC 60.067 52.381 0.00 0.00 0.00 5.03
827 870 1.338105 GCATAGCCACCATATCTCGCA 60.338 52.381 0.00 0.00 0.00 5.10
829 872 0.318441 TAGCCACCATATCTCGCAGC 59.682 55.000 0.00 0.00 0.00 5.25
830 873 1.070445 GCCACCATATCTCGCAGCT 59.930 57.895 0.00 0.00 0.00 4.24
831 874 0.533755 GCCACCATATCTCGCAGCTT 60.534 55.000 0.00 0.00 0.00 3.74
832 875 1.224075 CCACCATATCTCGCAGCTTG 58.776 55.000 0.00 0.00 0.00 4.01
833 876 1.473965 CCACCATATCTCGCAGCTTGT 60.474 52.381 0.00 0.00 0.00 3.16
834 877 1.596260 CACCATATCTCGCAGCTTGTG 59.404 52.381 0.00 0.00 0.00 3.33
835 878 1.224075 CCATATCTCGCAGCTTGTGG 58.776 55.000 0.00 0.00 0.00 4.17
836 879 0.585357 CATATCTCGCAGCTTGTGGC 59.415 55.000 0.00 0.00 42.19 5.01
837 880 0.533755 ATATCTCGCAGCTTGTGGCC 60.534 55.000 0.00 0.00 43.05 5.36
838 881 2.906182 TATCTCGCAGCTTGTGGCCG 62.906 60.000 0.00 0.00 43.05 6.13
843 886 3.730761 CAGCTTGTGGCCGCAGAC 61.731 66.667 20.15 15.33 43.05 3.51
844 887 3.946201 AGCTTGTGGCCGCAGACT 61.946 61.111 20.15 17.40 43.05 3.24
845 888 3.426568 GCTTGTGGCCGCAGACTC 61.427 66.667 20.15 6.27 34.27 3.36
846 889 2.743928 CTTGTGGCCGCAGACTCC 60.744 66.667 20.15 0.00 0.00 3.85
847 890 4.329545 TTGTGGCCGCAGACTCCC 62.330 66.667 20.15 0.00 0.00 4.30
849 892 3.075005 GTGGCCGCAGACTCCCTA 61.075 66.667 12.58 0.00 0.00 3.53
850 893 3.075005 TGGCCGCAGACTCCCTAC 61.075 66.667 0.00 0.00 0.00 3.18
851 894 3.851128 GGCCGCAGACTCCCTACC 61.851 72.222 0.00 0.00 0.00 3.18
852 895 3.075005 GCCGCAGACTCCCTACCA 61.075 66.667 0.00 0.00 0.00 3.25
853 896 2.435693 GCCGCAGACTCCCTACCAT 61.436 63.158 0.00 0.00 0.00 3.55
854 897 1.972660 GCCGCAGACTCCCTACCATT 61.973 60.000 0.00 0.00 0.00 3.16
855 898 0.541863 CCGCAGACTCCCTACCATTT 59.458 55.000 0.00 0.00 0.00 2.32
858 901 2.420022 CGCAGACTCCCTACCATTTTTG 59.580 50.000 0.00 0.00 0.00 2.44
859 902 2.755103 GCAGACTCCCTACCATTTTTGG 59.245 50.000 0.00 0.00 0.00 3.28
861 904 4.010349 CAGACTCCCTACCATTTTTGGTC 58.990 47.826 0.00 0.00 42.99 4.02
865 908 2.108601 TCCCTACCATTTTTGGTCGGTT 59.891 45.455 12.98 0.00 41.65 4.44
868 911 0.955905 ACCATTTTTGGTCGGTTCGG 59.044 50.000 0.00 0.00 37.74 4.30
880 929 2.741211 GTTCGGTCGGGTTGCTCC 60.741 66.667 0.00 0.00 0.00 4.70
882 931 2.809307 TTCGGTCGGGTTGCTCCAA 61.809 57.895 1.43 0.00 38.11 3.53
894 943 2.568612 CTCCAAGAGCAGTCGCGA 59.431 61.111 3.71 3.71 45.49 5.87
1001 1078 2.745100 CGGGACACGGACTCTCGA 60.745 66.667 0.00 0.00 39.42 4.04
1002 1079 2.113433 CGGGACACGGACTCTCGAT 61.113 63.158 0.00 0.00 39.42 3.59
1005 1082 1.297745 GACACGGACTCTCGATCGC 60.298 63.158 11.09 0.00 0.00 4.58
1212 1294 2.125633 GCCTCCGACGAAACTCCC 60.126 66.667 0.00 0.00 0.00 4.30
1233 1321 3.290710 CCCCACGCTAGGTAAGTAACTA 58.709 50.000 0.00 0.00 0.00 2.24
1239 1327 4.142600 ACGCTAGGTAAGTAACTAACACCG 60.143 45.833 0.00 0.00 34.36 4.94
1242 1330 2.094545 AGGTAAGTAACTAACACCGGCG 60.095 50.000 0.00 0.00 34.36 6.46
1246 1334 1.067354 AGTAACTAACACCGGCGAAGG 60.067 52.381 9.30 0.00 37.30 3.46
1249 1337 1.810030 CTAACACCGGCGAAGGAGC 60.810 63.158 9.30 0.00 34.73 4.70
1251 1339 2.221906 TAACACCGGCGAAGGAGCTC 62.222 60.000 9.30 4.71 37.29 4.09
1255 1343 2.024871 CGGCGAAGGAGCTCGTAG 59.975 66.667 9.76 8.27 40.99 3.51
1256 1344 2.278923 GGCGAAGGAGCTCGTAGC 60.279 66.667 21.36 21.36 42.84 3.58
1257 1345 2.490217 GCGAAGGAGCTCGTAGCA 59.510 61.111 23.32 0.00 45.56 3.49
1258 1346 1.153823 GCGAAGGAGCTCGTAGCAA 60.154 57.895 23.32 0.00 45.56 3.91
1262 1350 1.202582 GAAGGAGCTCGTAGCAAGTCA 59.797 52.381 9.76 0.00 45.56 3.41
1273 1361 4.170062 CAAGTCATGCCGCTGCCG 62.170 66.667 0.00 0.00 36.33 5.69
1285 1373 4.170062 CTGCCGGCGTGCTTCATG 62.170 66.667 23.90 0.00 0.00 3.07
1296 1384 0.734597 TGCTTCATGCGCTGCAATTG 60.735 50.000 9.73 0.00 43.62 2.32
1315 1425 3.357166 TGACGTTTTGTATGGTTTGGC 57.643 42.857 0.00 0.00 0.00 4.52
1548 1658 2.815211 TCGTCGACGAGGTACCCG 60.815 66.667 34.97 17.82 44.22 5.28
1581 1692 3.238108 ACTCTGCTACTTCATGAACGG 57.762 47.619 3.38 0.00 0.00 4.44
1585 1724 2.668457 CTGCTACTTCATGAACGGTCAC 59.332 50.000 4.62 0.00 36.31 3.67
1598 1737 5.047847 TGAACGGTCACTTAGTTTCTGAAG 58.952 41.667 0.00 0.00 0.00 3.02
1616 1759 3.629855 TGAAGTGCCAGATTTTCGTTTCA 59.370 39.130 0.00 0.00 0.00 2.69
1629 1772 7.913821 AGATTTTCGTTTCAACAAGGAAGTAAC 59.086 33.333 0.00 0.00 0.00 2.50
1646 1798 1.329256 AACTGCCTCTGTACTGACGT 58.671 50.000 0.00 0.00 0.00 4.34
1667 1819 5.694910 ACGTGAGAGTTCGTGAAATGTATTT 59.305 36.000 0.00 0.00 38.85 1.40
1684 1845 5.698832 TGTATTTTTGACTGAATTCGCCTG 58.301 37.500 0.04 0.00 0.00 4.85
1685 1846 3.641437 TTTTTGACTGAATTCGCCTGG 57.359 42.857 0.04 0.00 0.00 4.45
1855 2047 1.004044 ACAGCTCCATTCCTTGTCAGG 59.996 52.381 0.00 0.00 42.50 3.86
1857 2049 1.034292 GCTCCATTCCTTGTCAGGCC 61.034 60.000 0.00 0.00 40.58 5.19
1863 2055 1.923356 TTCCTTGTCAGGCCAATTCC 58.077 50.000 5.01 0.00 40.58 3.01
1905 2097 0.833287 AATGCGCAGACCCTACATCT 59.167 50.000 18.32 0.00 0.00 2.90
1925 2117 5.209818 TCTATTTACCAGATACCGGCAAG 57.790 43.478 0.00 0.00 0.00 4.01
2272 2489 3.646162 TCCAGAGTAAGCCTGTCTGAAAA 59.354 43.478 0.10 0.00 40.21 2.29
2285 2502 3.454447 TGTCTGAAAACTCTGAACCCTGA 59.546 43.478 0.00 0.00 0.00 3.86
2414 2809 2.287368 CGTGTACAGCTTTGGGGTTTTC 60.287 50.000 0.00 0.00 0.00 2.29
2498 2893 5.357257 TCTCTCGCTCATTGGGTAATTAAC 58.643 41.667 0.00 0.00 0.00 2.01
2499 2894 5.128827 TCTCTCGCTCATTGGGTAATTAACT 59.871 40.000 0.00 0.00 0.00 2.24
2500 2895 6.322969 TCTCTCGCTCATTGGGTAATTAACTA 59.677 38.462 0.00 0.00 0.00 2.24
2501 2896 6.513180 TCTCGCTCATTGGGTAATTAACTAG 58.487 40.000 0.00 0.00 0.00 2.57
2522 2918 7.099764 ACTAGTCAGTGATACCAATTTCAGTG 58.900 38.462 0.00 6.41 42.23 3.66
2528 2924 9.295825 TCAGTGATACCAATTTCAGTGTATTTT 57.704 29.630 10.89 0.00 41.78 1.82
2535 2931 7.090173 ACCAATTTCAGTGTATTTTCATTCCG 58.910 34.615 0.00 0.00 0.00 4.30
2536 2932 7.040062 ACCAATTTCAGTGTATTTTCATTCCGA 60.040 33.333 0.00 0.00 0.00 4.55
2537 2933 7.273381 CCAATTTCAGTGTATTTTCATTCCGAC 59.727 37.037 0.00 0.00 0.00 4.79
2539 2935 8.786826 ATTTCAGTGTATTTTCATTCCGACTA 57.213 30.769 0.00 0.00 0.00 2.59
2541 2937 8.610248 TTCAGTGTATTTTCATTCCGACTAAA 57.390 30.769 0.00 0.00 0.00 1.85
2544 2940 9.113876 CAGTGTATTTTCATTCCGACTAAAAAC 57.886 33.333 0.00 0.00 0.00 2.43
2545 2941 9.063615 AGTGTATTTTCATTCCGACTAAAAACT 57.936 29.630 0.00 0.00 0.00 2.66
2614 3020 9.874205 TTTCATCCAAAATTAAGCTAAATCCAG 57.126 29.630 0.00 0.00 0.00 3.86
2630 3039 9.219603 GCTAAATCCAGCTACATTATATTGACA 57.780 33.333 1.71 0.00 38.57 3.58
2639 3048 8.267894 AGCTACATTATATTGACACCAGTTTCT 58.732 33.333 1.71 0.00 0.00 2.52
2819 3228 2.279120 GAGCTCGACCGCATCCTG 60.279 66.667 0.00 0.00 0.00 3.86
2843 3252 1.032657 AGGAGATGACCCTGACGACG 61.033 60.000 0.00 0.00 31.66 5.12
2855 3264 2.365105 ACGACGGTCATGGGGGAT 60.365 61.111 9.10 0.00 0.00 3.85
2861 3270 2.516930 GTCATGGGGGATGGCACG 60.517 66.667 0.00 0.00 36.60 5.34
2876 3285 1.077501 CACGGCCATCATCACCCTT 60.078 57.895 2.24 0.00 0.00 3.95
2917 3326 8.558700 CACGTCATGATCATCCAATATTTGTTA 58.441 33.333 4.86 0.00 0.00 2.41
2919 3328 8.017373 CGTCATGATCATCCAATATTTGTTACC 58.983 37.037 4.86 0.00 0.00 2.85
2920 3329 8.849168 GTCATGATCATCCAATATTTGTTACCA 58.151 33.333 4.86 0.00 0.00 3.25
2923 3332 8.586879 TGATCATCCAATATTTGTTACCACAA 57.413 30.769 0.00 0.00 41.39 3.33
2947 3356 4.750952 TGGATATTTTTGTGTTTCGCGA 57.249 36.364 3.71 3.71 0.00 5.87
2974 3383 7.145323 TGCTAAACTTTAGTTGCCTGAAAATC 58.855 34.615 9.77 0.00 38.44 2.17
2999 3408 3.985127 TGAGCATCAATTGAATTCCCCT 58.015 40.909 13.09 2.76 45.97 4.79
3029 3438 2.672714 CTGGAAATCAAGACGACGTGA 58.327 47.619 4.58 5.98 38.66 4.35
3050 3459 1.076192 TCTTCGACGGAGGGGAGTT 59.924 57.895 2.65 0.00 0.00 3.01
3052 3461 1.228644 TTCGACGGAGGGGAGTTCA 60.229 57.895 0.00 0.00 0.00 3.18
3061 3470 0.771755 AGGGGAGTTCAAGGGTTGAC 59.228 55.000 0.00 0.00 39.87 3.18
3062 3471 0.771755 GGGGAGTTCAAGGGTTGACT 59.228 55.000 0.00 0.00 39.87 3.41
3078 3488 4.442706 GTTGACTGATATGGGTGTGGTAG 58.557 47.826 0.00 0.00 0.00 3.18
3095 3505 0.997363 TAGAGGAGGACTTCACCGGA 59.003 55.000 9.46 0.00 34.73 5.14
3098 3508 2.283529 GGAGGACTTCACCGGAGCA 61.284 63.158 9.46 0.00 34.73 4.26
3101 3511 0.472471 AGGACTTCACCGGAGCAAAA 59.528 50.000 9.46 0.00 34.73 2.44
3119 3531 2.325661 AAAAGGGGGAAGGATGGTTG 57.674 50.000 0.00 0.00 0.00 3.77
3120 3532 0.252239 AAAGGGGGAAGGATGGTTGC 60.252 55.000 0.00 0.00 0.00 4.17
3195 3609 2.038690 GGGACGATGAGGCGACATA 58.961 57.895 0.00 0.00 34.83 2.29
3213 3627 2.808761 TAGGCTGAAGGTGGCGGGTA 62.809 60.000 0.00 0.00 35.01 3.69
3259 3674 0.537143 TGGCTCAACAATGGAAGCGT 60.537 50.000 0.00 0.00 0.00 5.07
3276 3691 1.176527 CGTTTGTCAGCAATGGGGAT 58.823 50.000 0.00 0.00 34.18 3.85
3377 3821 9.373743 TTGCATATAAAGCAACTGCGTGTGTAA 62.374 37.037 10.79 0.00 46.13 2.41
3385 3829 4.702392 CAACTGCGTGTGTAATTTCTCTC 58.298 43.478 0.00 0.00 0.00 3.20
3387 3831 4.632153 ACTGCGTGTGTAATTTCTCTCTT 58.368 39.130 0.00 0.00 0.00 2.85
3388 3832 5.057149 ACTGCGTGTGTAATTTCTCTCTTT 58.943 37.500 0.00 0.00 0.00 2.52
3767 4211 0.107703 CCATGGACTCGCAAGGCTAA 60.108 55.000 5.56 0.00 38.47 3.09
3814 4275 5.522460 TCAAGTCTAACAAAGTTTCCAGACG 59.478 40.000 12.00 0.00 37.93 4.18
3839 4300 2.959465 ACTTCCCCTCTGAGGTTTTG 57.041 50.000 21.70 11.61 31.93 2.44
3844 4305 0.961753 CCCTCTGAGGTTTTGTTGGC 59.038 55.000 21.70 0.00 31.93 4.52
3853 4314 0.858583 GTTTTGTTGGCGGCAACATC 59.141 50.000 44.93 34.26 43.54 3.06
3863 4645 2.412089 GGCGGCAACATCGTATAAGATC 59.588 50.000 3.07 0.00 0.00 2.75
3893 4675 3.811031 TGGAACAACGGGTTGATGT 57.189 47.368 17.72 3.18 42.93 3.06
3983 4765 3.702330 GCAAAAGAAAGTTGCGGTAGTT 58.298 40.909 0.00 0.00 41.74 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.357881 TTCTCCAGCACAGCGCAG 60.358 61.111 11.47 3.33 46.13 5.18
2 3 1.815817 TACTTCTCCAGCACAGCGCA 61.816 55.000 11.47 0.00 46.13 6.09
3 4 1.079819 TACTTCTCCAGCACAGCGC 60.080 57.895 0.00 0.00 42.91 5.92
4 5 1.080995 GCTACTTCTCCAGCACAGCG 61.081 60.000 0.00 0.00 37.73 5.18
5 6 0.036952 TGCTACTTCTCCAGCACAGC 60.037 55.000 0.00 0.00 42.68 4.40
6 7 2.007360 CTGCTACTTCTCCAGCACAG 57.993 55.000 0.00 0.00 42.68 3.66
11 12 0.461693 GCTGGCTGCTACTTCTCCAG 60.462 60.000 9.31 2.43 45.26 3.86
12 13 1.599047 GCTGGCTGCTACTTCTCCA 59.401 57.895 9.31 0.00 38.95 3.86
13 14 1.153269 GGCTGGCTGCTACTTCTCC 60.153 63.158 16.14 0.00 42.39 3.71
14 15 0.461693 CTGGCTGGCTGCTACTTCTC 60.462 60.000 16.14 0.00 42.39 2.87
15 16 1.601171 CTGGCTGGCTGCTACTTCT 59.399 57.895 16.14 0.00 42.39 2.85
16 17 1.451028 CCTGGCTGGCTGCTACTTC 60.451 63.158 16.14 0.00 42.39 3.01
17 18 2.673523 CCTGGCTGGCTGCTACTT 59.326 61.111 16.14 0.00 42.39 2.24
43 44 4.660938 AAACGAGGTGGCCTGGGC 62.661 66.667 14.23 14.23 33.54 5.36
44 45 1.971695 GAAAACGAGGTGGCCTGGG 60.972 63.158 3.32 0.00 33.54 4.45
45 46 1.971695 GGAAAACGAGGTGGCCTGG 60.972 63.158 3.32 0.00 35.43 4.45
104 105 2.034939 CCGGTATCGTGCCAAGTACATA 59.965 50.000 0.00 0.00 33.95 2.29
195 196 8.545472 TCTATAAACTAGTGCAAATTGGGTAGT 58.455 33.333 0.00 0.00 0.00 2.73
241 245 0.890542 TGCCTTGTGGTTGCTAGCTG 60.891 55.000 17.23 0.00 35.27 4.24
245 249 0.825840 GGGTTGCCTTGTGGTTGCTA 60.826 55.000 0.00 0.00 35.27 3.49
247 251 2.133641 AGGGTTGCCTTGTGGTTGC 61.134 57.895 0.00 0.00 35.27 4.17
248 252 1.741525 CAGGGTTGCCTTGTGGTTG 59.258 57.895 0.00 0.00 35.27 3.77
249 253 2.133641 GCAGGGTTGCCTTGTGGTT 61.134 57.895 0.00 0.00 44.74 3.67
250 254 2.521708 GCAGGGTTGCCTTGTGGT 60.522 61.111 0.00 0.00 44.74 4.16
336 344 4.685165 CGAGCAAGGATGATTGTAGAGATG 59.315 45.833 0.00 0.00 32.56 2.90
344 352 1.645455 CGGCGAGCAAGGATGATTG 59.355 57.895 0.00 0.00 0.00 2.67
345 353 4.131376 CGGCGAGCAAGGATGATT 57.869 55.556 0.00 0.00 0.00 2.57
381 389 3.423154 CGCTTTGACCCGGCTGTC 61.423 66.667 0.00 0.00 35.77 3.51
443 451 2.267961 GTGCGATTCCGGGACCTT 59.732 61.111 0.00 0.00 36.06 3.50
445 453 4.137872 TCGTGCGATTCCGGGACC 62.138 66.667 0.00 0.00 36.06 4.46
447 455 4.137872 GGTCGTGCGATTCCGGGA 62.138 66.667 0.00 0.00 36.06 5.14
506 532 0.784778 CGTCTTCTTCTTCACCGCAC 59.215 55.000 0.00 0.00 0.00 5.34
507 533 0.671796 TCGTCTTCTTCTTCACCGCA 59.328 50.000 0.00 0.00 0.00 5.69
508 534 1.061485 GTCGTCTTCTTCTTCACCGC 58.939 55.000 0.00 0.00 0.00 5.68
509 535 1.069432 TCGTCGTCTTCTTCTTCACCG 60.069 52.381 0.00 0.00 0.00 4.94
510 536 2.317684 GTCGTCGTCTTCTTCTTCACC 58.682 52.381 0.00 0.00 0.00 4.02
521 549 2.959357 GAACGGGTCGTCGTCGTCT 61.959 63.158 1.33 3.65 43.07 4.18
626 669 6.148315 GGACGATATGAAATGAATGCAGATGA 59.852 38.462 0.00 0.00 0.00 2.92
627 670 6.072893 TGGACGATATGAAATGAATGCAGATG 60.073 38.462 0.00 0.00 0.00 2.90
628 671 5.999600 TGGACGATATGAAATGAATGCAGAT 59.000 36.000 0.00 0.00 0.00 2.90
629 672 5.237127 GTGGACGATATGAAATGAATGCAGA 59.763 40.000 0.00 0.00 0.00 4.26
630 673 5.237996 AGTGGACGATATGAAATGAATGCAG 59.762 40.000 0.00 0.00 0.00 4.41
631 674 5.125356 AGTGGACGATATGAAATGAATGCA 58.875 37.500 0.00 0.00 0.00 3.96
632 675 5.334414 GGAGTGGACGATATGAAATGAATGC 60.334 44.000 0.00 0.00 0.00 3.56
633 676 5.759763 TGGAGTGGACGATATGAAATGAATG 59.240 40.000 0.00 0.00 0.00 2.67
649 692 2.448582 GGTGGTGTGGTGGAGTGGA 61.449 63.158 0.00 0.00 0.00 4.02
654 697 4.248842 CGCAGGTGGTGTGGTGGA 62.249 66.667 0.00 0.00 32.53 4.02
655 698 4.562425 ACGCAGGTGGTGTGGTGG 62.562 66.667 0.00 0.00 41.38 4.61
656 699 2.972505 GACGCAGGTGGTGTGGTG 60.973 66.667 0.00 0.00 41.19 4.17
657 700 4.602259 CGACGCAGGTGGTGTGGT 62.602 66.667 0.00 0.00 41.19 4.16
658 701 4.602259 ACGACGCAGGTGGTGTGG 62.602 66.667 0.00 0.00 41.19 4.17
659 702 2.971428 AAGACGACGCAGGTGGTGTG 62.971 60.000 0.00 0.00 41.19 3.82
660 703 2.694829 GAAGACGACGCAGGTGGTGT 62.695 60.000 0.00 0.00 44.56 4.16
661 704 2.022129 GAAGACGACGCAGGTGGTG 61.022 63.158 0.00 0.00 35.05 4.17
662 705 1.745320 AAGAAGACGACGCAGGTGGT 61.745 55.000 0.00 0.00 37.85 4.16
663 706 1.006102 AAGAAGACGACGCAGGTGG 60.006 57.895 0.00 0.00 0.00 4.61
664 707 1.284982 CCAAGAAGACGACGCAGGTG 61.285 60.000 0.00 0.00 0.00 4.00
665 708 1.006102 CCAAGAAGACGACGCAGGT 60.006 57.895 0.00 0.00 0.00 4.00
666 709 2.383527 GCCAAGAAGACGACGCAGG 61.384 63.158 0.00 0.00 0.00 4.85
667 710 2.383527 GGCCAAGAAGACGACGCAG 61.384 63.158 0.00 0.00 0.00 5.18
668 711 2.357034 GGCCAAGAAGACGACGCA 60.357 61.111 0.00 0.00 0.00 5.24
669 712 2.048127 AGGCCAAGAAGACGACGC 60.048 61.111 5.01 0.00 0.00 5.19
670 713 1.738099 CCAGGCCAAGAAGACGACG 60.738 63.158 5.01 0.00 0.00 5.12
671 714 2.035442 GCCAGGCCAAGAAGACGAC 61.035 63.158 5.01 0.00 0.00 4.34
672 715 2.172483 GAGCCAGGCCAAGAAGACGA 62.172 60.000 8.22 0.00 0.00 4.20
713 756 1.817099 GTGCGCAATCAGAGGAGGG 60.817 63.158 14.00 0.00 0.00 4.30
714 757 1.817099 GGTGCGCAATCAGAGGAGG 60.817 63.158 14.00 0.00 0.00 4.30
715 758 1.078918 TGGTGCGCAATCAGAGGAG 60.079 57.895 14.00 0.00 0.00 3.69
716 759 1.078918 CTGGTGCGCAATCAGAGGA 60.079 57.895 27.82 3.26 0.00 3.71
739 782 2.563013 ATTGGGGCAGCTACCAGCAG 62.563 60.000 5.07 0.00 45.56 4.24
740 783 2.153898 AATTGGGGCAGCTACCAGCA 62.154 55.000 5.07 0.00 45.56 4.41
741 784 1.380380 AATTGGGGCAGCTACCAGC 60.380 57.895 5.07 0.00 42.84 4.85
742 785 1.669999 GCAATTGGGGCAGCTACCAG 61.670 60.000 5.07 0.00 38.16 4.00
751 794 1.750297 GGATGGATGCAATTGGGGC 59.250 57.895 7.72 0.00 0.00 5.80
778 821 3.753797 GGGTGTTTTAAAGAGGAGAGCAG 59.246 47.826 0.00 0.00 0.00 4.24
785 828 1.893137 GGGCTGGGTGTTTTAAAGAGG 59.107 52.381 0.00 0.00 0.00 3.69
809 852 1.066573 GCTGCGAGATATGGTGGCTAT 60.067 52.381 0.00 0.00 0.00 2.97
811 854 1.070445 GCTGCGAGATATGGTGGCT 59.930 57.895 0.00 0.00 0.00 4.75
812 855 0.533755 AAGCTGCGAGATATGGTGGC 60.534 55.000 0.00 0.00 0.00 5.01
813 856 1.224075 CAAGCTGCGAGATATGGTGG 58.776 55.000 0.00 0.00 0.00 4.61
814 857 1.596260 CACAAGCTGCGAGATATGGTG 59.404 52.381 0.00 0.00 0.00 4.17
815 858 1.473965 CCACAAGCTGCGAGATATGGT 60.474 52.381 0.00 0.00 0.00 3.55
817 860 0.585357 GCCACAAGCTGCGAGATATG 59.415 55.000 0.00 0.00 38.99 1.78
818 861 0.533755 GGCCACAAGCTGCGAGATAT 60.534 55.000 0.00 0.00 43.05 1.63
819 862 1.153369 GGCCACAAGCTGCGAGATA 60.153 57.895 0.00 0.00 43.05 1.98
820 863 2.437359 GGCCACAAGCTGCGAGAT 60.437 61.111 0.00 0.00 43.05 2.75
827 870 3.890936 GAGTCTGCGGCCACAAGCT 62.891 63.158 2.24 0.00 43.05 3.74
829 872 2.743928 GGAGTCTGCGGCCACAAG 60.744 66.667 2.24 0.00 0.00 3.16
830 873 4.329545 GGGAGTCTGCGGCCACAA 62.330 66.667 2.24 0.00 0.00 3.33
831 874 3.897681 TAGGGAGTCTGCGGCCACA 62.898 63.158 2.24 0.00 0.00 4.17
832 875 3.075005 TAGGGAGTCTGCGGCCAC 61.075 66.667 2.24 0.00 0.00 5.01
833 876 3.075005 GTAGGGAGTCTGCGGCCA 61.075 66.667 2.24 0.00 0.00 5.36
834 877 3.851128 GGTAGGGAGTCTGCGGCC 61.851 72.222 0.00 0.00 0.00 6.13
835 878 1.972660 AATGGTAGGGAGTCTGCGGC 61.973 60.000 0.00 0.00 0.00 6.53
836 879 0.541863 AAATGGTAGGGAGTCTGCGG 59.458 55.000 0.00 0.00 0.00 5.69
837 880 2.403252 AAAATGGTAGGGAGTCTGCG 57.597 50.000 0.00 0.00 0.00 5.18
838 881 2.755103 CCAAAAATGGTAGGGAGTCTGC 59.245 50.000 0.00 0.00 0.00 4.26
839 882 4.010349 GACCAAAAATGGTAGGGAGTCTG 58.990 47.826 0.00 0.00 43.24 3.51
840 883 3.307480 CGACCAAAAATGGTAGGGAGTCT 60.307 47.826 0.00 0.00 43.24 3.24
841 884 3.007635 CGACCAAAAATGGTAGGGAGTC 58.992 50.000 0.00 0.00 43.24 3.36
842 885 2.290705 CCGACCAAAAATGGTAGGGAGT 60.291 50.000 16.64 0.00 46.71 3.85
843 886 2.365582 CCGACCAAAAATGGTAGGGAG 58.634 52.381 16.64 1.16 46.71 4.30
844 887 2.500392 CCGACCAAAAATGGTAGGGA 57.500 50.000 16.64 0.00 46.71 4.20
847 890 2.160813 CCGAACCGACCAAAAATGGTAG 59.839 50.000 0.00 0.69 43.24 3.18
848 891 2.152830 CCGAACCGACCAAAAATGGTA 58.847 47.619 0.00 0.00 43.24 3.25
849 892 0.955905 CCGAACCGACCAAAAATGGT 59.044 50.000 0.00 0.00 46.40 3.55
850 893 0.955905 ACCGAACCGACCAAAAATGG 59.044 50.000 0.00 0.00 0.00 3.16
851 894 1.399215 CGACCGAACCGACCAAAAATG 60.399 52.381 0.00 0.00 0.00 2.32
852 895 0.869730 CGACCGAACCGACCAAAAAT 59.130 50.000 0.00 0.00 0.00 1.82
853 896 1.159098 CCGACCGAACCGACCAAAAA 61.159 55.000 0.00 0.00 0.00 1.94
854 897 1.594836 CCGACCGAACCGACCAAAA 60.595 57.895 0.00 0.00 0.00 2.44
855 898 2.029369 CCGACCGAACCGACCAAA 59.971 61.111 0.00 0.00 0.00 3.28
858 901 3.994853 AACCCGACCGAACCGACC 61.995 66.667 0.00 0.00 0.00 4.79
859 902 2.735857 CAACCCGACCGAACCGAC 60.736 66.667 0.00 0.00 0.00 4.79
861 904 4.675029 AGCAACCCGACCGAACCG 62.675 66.667 0.00 0.00 0.00 4.44
865 908 3.234630 CTTGGAGCAACCCGACCGA 62.235 63.158 0.00 0.00 38.00 4.69
868 911 4.285851 CTCTTGGAGCAACCCGAC 57.714 61.111 0.00 0.00 38.00 4.79
880 929 2.126149 AGCTCGCGACTGCTCTTG 60.126 61.111 16.29 0.08 39.65 3.02
988 1065 2.762234 GGCGATCGAGAGTCCGTGT 61.762 63.158 21.57 0.00 0.00 4.49
1072 1154 4.114997 GACCGCGGTTGGCAATGG 62.115 66.667 34.65 6.22 43.84 3.16
1212 1294 2.105766 AGTTACTTACCTAGCGTGGGG 58.894 52.381 3.24 0.00 0.00 4.96
1233 1321 3.591254 GAGCTCCTTCGCCGGTGTT 62.591 63.158 16.01 0.00 0.00 3.32
1239 1327 2.278923 GCTACGAGCTCCTTCGCC 60.279 66.667 8.47 0.00 44.15 5.54
1242 1330 1.202582 TGACTTGCTACGAGCTCCTTC 59.797 52.381 8.47 0.00 42.97 3.46
1256 1344 4.170062 CGGCAGCGGCATGACTTG 62.170 66.667 11.88 0.00 43.71 3.16
1275 1363 2.860690 ATTGCAGCGCATGAAGCACG 62.861 55.000 11.47 7.32 46.13 5.34
1276 1364 0.734942 AATTGCAGCGCATGAAGCAC 60.735 50.000 11.47 7.71 46.13 4.40
1277 1365 0.734597 CAATTGCAGCGCATGAAGCA 60.735 50.000 11.47 8.86 46.13 3.91
1285 1373 0.159345 CAAAACGTCAATTGCAGCGC 59.841 50.000 0.00 0.00 0.00 5.92
1296 1384 2.295070 AGGCCAAACCATACAAAACGTC 59.705 45.455 5.01 0.00 43.14 4.34
1547 1657 3.070018 AGCAGAGTTTCAGATGGTTTCG 58.930 45.455 0.00 0.00 0.00 3.46
1548 1658 5.241662 AGTAGCAGAGTTTCAGATGGTTTC 58.758 41.667 0.00 0.00 0.00 2.78
1585 1724 6.566197 AAATCTGGCACTTCAGAAACTAAG 57.434 37.500 0.00 0.00 45.54 2.18
1598 1737 3.701241 TGTTGAAACGAAAATCTGGCAC 58.299 40.909 0.00 0.00 0.00 5.01
1616 1759 3.136626 ACAGAGGCAGTTACTTCCTTGTT 59.863 43.478 4.86 0.00 0.00 2.83
1629 1772 0.881796 TCACGTCAGTACAGAGGCAG 59.118 55.000 7.77 2.15 0.00 4.85
1646 1798 8.067784 GTCAAAAATACATTTCACGAACTCTCA 58.932 33.333 0.00 0.00 0.00 3.27
1667 1819 1.533625 CCCAGGCGAATTCAGTCAAA 58.466 50.000 6.22 0.00 0.00 2.69
1855 2047 1.150827 GTTTGCTGCTTGGAATTGGC 58.849 50.000 0.00 0.00 0.00 4.52
1857 2049 1.796459 GCTGTTTGCTGCTTGGAATTG 59.204 47.619 0.00 0.00 38.95 2.32
1905 2097 3.968649 TCCTTGCCGGTATCTGGTAAATA 59.031 43.478 1.90 0.00 30.44 1.40
1925 2117 0.460987 CCAGCCTTGTCATCGACTCC 60.461 60.000 0.00 0.00 33.15 3.85
1931 2123 2.479566 TGAACTCCAGCCTTGTCATC 57.520 50.000 0.00 0.00 0.00 2.92
1992 2187 7.563270 CATTGTGTAATAAGTTTTGTGTTGCC 58.437 34.615 0.00 0.00 0.00 4.52
1993 2188 7.062848 GCATTGTGTAATAAGTTTTGTGTTGC 58.937 34.615 0.00 0.00 0.00 4.17
1994 2189 8.055402 GTGCATTGTGTAATAAGTTTTGTGTTG 58.945 33.333 0.00 0.00 0.00 3.33
2060 2277 3.455469 GGTCCAGGCCTGCATTGC 61.455 66.667 28.39 13.56 0.00 3.56
2070 2287 1.748122 GCTGTGCAGATGGTCCAGG 60.748 63.158 3.02 0.00 0.00 4.45
2100 2317 1.909700 TGAAGCCCTTGTGGATCAAC 58.090 50.000 0.00 0.00 35.39 3.18
2133 2350 0.033504 TGAAGTTCTCGTCCACCAGC 59.966 55.000 4.17 0.00 0.00 4.85
2272 2489 4.288105 AGAATGATGTTCAGGGTTCAGAGT 59.712 41.667 0.00 0.00 0.00 3.24
2285 2502 6.849502 CAGACATAAACTGCAGAATGATGTT 58.150 36.000 23.35 10.85 39.69 2.71
2315 2702 2.103263 GTCAGATAAGAGCGGGGTTGAT 59.897 50.000 0.00 0.00 0.00 2.57
2414 2809 0.179089 CGGTGATGAGCTCCAGAAGG 60.179 60.000 12.15 0.00 0.00 3.46
2449 2844 2.488153 GTTGATTCCGGAGAAACCAAGG 59.512 50.000 3.34 0.00 38.90 3.61
2498 2893 7.099764 ACACTGAAATTGGTATCACTGACTAG 58.900 38.462 0.00 0.00 0.00 2.57
2499 2894 7.004555 ACACTGAAATTGGTATCACTGACTA 57.995 36.000 0.00 0.00 0.00 2.59
2500 2895 5.869579 ACACTGAAATTGGTATCACTGACT 58.130 37.500 0.00 0.00 0.00 3.41
2501 2896 7.849804 ATACACTGAAATTGGTATCACTGAC 57.150 36.000 0.00 0.00 0.00 3.51
2528 2924 9.806203 TTCGATATTAGTTTTTAGTCGGAATGA 57.194 29.630 0.00 0.00 0.00 2.57
2614 3020 8.438676 AGAAACTGGTGTCAATATAATGTAGC 57.561 34.615 0.00 0.00 0.00 3.58
2655 3064 3.677527 GTCTCCCGACGTCTCCAA 58.322 61.111 14.70 0.00 0.00 3.53
2819 3228 1.760029 GTCAGGGTCATCTCCTTCTCC 59.240 57.143 0.00 0.00 31.06 3.71
2843 3252 2.123726 GTGCCATCCCCCATGACC 60.124 66.667 0.00 0.00 33.80 4.02
2861 3270 1.456331 CCCAAGGGTGATGATGGCC 60.456 63.158 0.00 0.00 0.00 5.36
2876 3285 2.947532 CGTGAAGAGCTGGCTCCCA 61.948 63.158 17.60 13.35 43.70 4.37
2923 3332 6.153067 TCGCGAAACACAAAAATATCCATTT 58.847 32.000 6.20 0.00 35.84 2.32
2987 3396 3.808618 GCTCGATGCTAGGGGAATTCAAT 60.809 47.826 7.93 0.00 38.95 2.57
3034 3443 0.828762 TTGAACTCCCCTCCGTCGAA 60.829 55.000 0.00 0.00 0.00 3.71
3050 3459 3.054434 CACCCATATCAGTCAACCCTTGA 60.054 47.826 0.00 0.00 37.33 3.02
3052 3461 2.919602 ACACCCATATCAGTCAACCCTT 59.080 45.455 0.00 0.00 0.00 3.95
3061 3470 3.576118 CTCCTCTACCACACCCATATCAG 59.424 52.174 0.00 0.00 0.00 2.90
3062 3471 3.576861 CTCCTCTACCACACCCATATCA 58.423 50.000 0.00 0.00 0.00 2.15
3078 3488 1.950973 GCTCCGGTGAAGTCCTCCTC 61.951 65.000 7.92 0.00 0.00 3.71
3101 3511 0.252239 GCAACCATCCTTCCCCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
3119 3531 4.489771 CACCCCGGTCATCCCTGC 62.490 72.222 0.00 0.00 0.00 4.85
3120 3532 2.687200 TCACCCCGGTCATCCCTG 60.687 66.667 0.00 0.00 0.00 4.45
3144 3556 2.520536 GCCTCCTATGCCGGTCCAT 61.521 63.158 1.90 0.81 0.00 3.41
3145 3557 3.161450 GCCTCCTATGCCGGTCCA 61.161 66.667 1.90 0.00 0.00 4.02
3164 3576 4.115199 GTCCCGCCCTGCCTGAAT 62.115 66.667 0.00 0.00 0.00 2.57
3193 3607 2.746375 CCCGCCACCTTCAGCCTAT 61.746 63.158 0.00 0.00 0.00 2.57
3240 3655 0.537143 ACGCTTCCATTGTTGAGCCA 60.537 50.000 0.00 0.00 0.00 4.75
3259 3674 2.601240 TCATCCCCATTGCTGACAAA 57.399 45.000 0.00 0.00 39.77 2.83
3276 3691 2.041081 ACATTGGTCGATTTCCCCTTCA 59.959 45.455 0.00 0.00 0.00 3.02
3767 4211 2.489329 AGTATGTTTCAAGCTGCGCAAT 59.511 40.909 13.05 0.00 0.00 3.56
3774 4218 9.372369 GTTAGACTTGATAGTATGTTTCAAGCT 57.628 33.333 10.84 10.93 46.55 3.74
3826 4287 0.593128 CGCCAACAAAACCTCAGAGG 59.407 55.000 15.72 15.72 42.49 3.69
3827 4288 0.593128 CCGCCAACAAAACCTCAGAG 59.407 55.000 0.00 0.00 0.00 3.35
3828 4289 1.452145 GCCGCCAACAAAACCTCAGA 61.452 55.000 0.00 0.00 0.00 3.27
3829 4290 1.007387 GCCGCCAACAAAACCTCAG 60.007 57.895 0.00 0.00 0.00 3.35
3844 4305 7.525688 AATATGATCTTATACGATGTTGCCG 57.474 36.000 0.00 0.00 0.00 5.69
3853 4314 8.255394 TCCATGCACAAATATGATCTTATACG 57.745 34.615 1.79 0.09 0.00 3.06
3863 4645 3.858812 CCGTTGTTCCATGCACAAATATG 59.141 43.478 9.58 2.69 35.91 1.78
3887 4669 7.066645 TCCATTTCAAACAATTTGCAACATCAA 59.933 29.630 0.00 0.00 40.43 2.57
3893 4675 6.544931 TGGATTCCATTTCAAACAATTTGCAA 59.455 30.769 0.00 0.00 40.43 4.08
3939 4721 5.474825 CGGGGTTGCAACTTTAATAACAAT 58.525 37.500 27.64 0.00 0.00 2.71
3942 4724 3.247442 GCGGGGTTGCAACTTTAATAAC 58.753 45.455 27.64 9.37 34.15 1.89
3958 4740 2.899153 GCAACTTTCTTTTGCGGGG 58.101 52.632 0.00 0.00 40.01 5.73


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

AutoCloner maintained by Alex Coulton.