Multiple sequence alignment - TraesCS2A01G132400

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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 TraesCS2A01G132400 chr2A 100.000 5129 0 0 1 5129 79350394 79355522 0.000000e+00 9472.0
1 TraesCS2A01G132400 chr2A 84.234 222 12 10 917 1138 79350412 79350610 1.460000e-45 195.0
2 TraesCS2A01G132400 chr2A 84.234 222 12 10 19 217 79351310 79351531 1.460000e-45 195.0
3 TraesCS2A01G132400 chr2D 95.063 3119 102 12 917 4013 79091777 79094865 0.000000e+00 4859.0
4 TraesCS2A01G132400 chr2D 92.701 548 29 5 4010 4551 79095023 79095565 0.000000e+00 780.0
5 TraesCS2A01G132400 chr2D 84.646 508 30 22 4595 5081 79095570 79096050 3.620000e-126 462.0
6 TraesCS2A01G132400 chr2D 88.341 223 14 6 1 217 79091759 79091975 1.830000e-64 257.0
7 TraesCS2A01G132400 chr2B 89.528 1633 93 21 1611 3191 123060573 123062179 0.000000e+00 1997.0
8 TraesCS2A01G132400 chr2B 85.614 855 58 24 4312 5129 123063414 123064240 0.000000e+00 837.0
9 TraesCS2A01G132400 chr2B 89.528 678 34 21 917 1590 123059855 123060499 0.000000e+00 824.0
10 TraesCS2A01G132400 chr2B 91.162 611 41 3 3184 3794 123062222 123062819 0.000000e+00 817.0
11 TraesCS2A01G132400 chr2B 92.698 493 26 6 3830 4314 123062821 123063311 0.000000e+00 702.0
12 TraesCS2A01G132400 chr3D 93.762 529 22 6 217 734 296425197 296425725 0.000000e+00 784.0
13 TraesCS2A01G132400 chr3D 87.059 170 17 4 744 913 296431355 296431519 2.440000e-43 187.0
14 TraesCS2A01G132400 chr7B 84.808 678 71 16 931 1606 615453220 615453867 0.000000e+00 652.0
15 TraesCS2A01G132400 chr5B 80.000 110 17 5 4955 5063 433548529 433548424 5.510000e-10 76.8
16 TraesCS2A01G132400 chr1B 100.000 28 0 0 5058 5085 310552785 310552812 9.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G132400 chr2A 79350394 79355522 5128 False 9472.0 9472 100.00000 1 5129 1 chr2A.!!$F1 5128
1 TraesCS2A01G132400 chr2D 79091759 79096050 4291 False 1589.5 4859 90.18775 1 5081 4 chr2D.!!$F1 5080
2 TraesCS2A01G132400 chr2B 123059855 123064240 4385 False 1035.4 1997 89.70600 917 5129 5 chr2B.!!$F1 4212
3 TraesCS2A01G132400 chr3D 296425197 296425725 528 False 784.0 784 93.76200 217 734 1 chr3D.!!$F1 517
4 TraesCS2A01G132400 chr7B 615453220 615453867 647 False 652.0 652 84.80800 931 1606 1 chr7B.!!$F1 675

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
754 766 0.097674 CGGCGGCATCAAGAGAAAAG 59.902 55.0 10.53 0.00 0.00 2.27 F
874 886 0.107312 AGTGATGAGGTGGATGCAGC 60.107 55.0 8.54 8.54 0.00 5.25 F
904 916 0.520412 CCTTTGCGCGACCGTTAATG 60.520 55.0 12.10 0.00 36.67 1.90 F
1755 1846 0.601311 GTGCGAGCTTCAGTTGGAGT 60.601 55.0 0.00 0.00 0.00 3.85 F
3229 3416 0.445436 GAGGCACAGCACATTTCTCG 59.555 55.0 0.00 0.00 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2237 0.962489 CTCCGCTCGATATCCAAGGT 59.038 55.000 0.00 0.0 0.00 3.50 R
2803 2916 2.298729 TGTAAGTTGATTTTGGCAGGGC 59.701 45.455 0.00 0.0 0.00 5.19 R
2841 2954 2.816087 CAGGCAGCAACTACAACAATCT 59.184 45.455 0.00 0.0 0.00 2.40 R
3503 3703 1.279840 GTGGTCGTCACAAGCAAGC 59.720 57.895 6.75 0.0 45.39 4.01 R
4996 5490 0.040692 CGTCGGTCGTCTGTTTCTCA 60.041 55.000 0.00 0.0 34.52 3.27 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
23 24 0.725117 CGTATTCCGGCACTTTGACC 59.275 55.000 0.00 0.00 0.00 4.02
24 25 1.816074 GTATTCCGGCACTTTGACCA 58.184 50.000 0.00 0.00 0.00 4.02
25 26 1.737793 GTATTCCGGCACTTTGACCAG 59.262 52.381 0.00 0.00 0.00 4.00
26 27 0.400213 ATTCCGGCACTTTGACCAGA 59.600 50.000 0.00 0.00 0.00 3.86
27 28 0.400213 TTCCGGCACTTTGACCAGAT 59.600 50.000 0.00 0.00 0.00 2.90
28 29 0.400213 TCCGGCACTTTGACCAGATT 59.600 50.000 0.00 0.00 0.00 2.40
29 30 0.804989 CCGGCACTTTGACCAGATTC 59.195 55.000 0.00 0.00 0.00 2.52
30 31 0.443869 CGGCACTTTGACCAGATTCG 59.556 55.000 0.00 0.00 0.00 3.34
31 32 1.808411 GGCACTTTGACCAGATTCGA 58.192 50.000 0.00 0.00 0.00 3.71
32 33 1.464997 GGCACTTTGACCAGATTCGAC 59.535 52.381 0.00 0.00 0.00 4.20
33 34 1.464997 GCACTTTGACCAGATTCGACC 59.535 52.381 0.00 0.00 0.00 4.79
34 35 1.726791 CACTTTGACCAGATTCGACCG 59.273 52.381 0.00 0.00 0.00 4.79
35 36 1.343465 ACTTTGACCAGATTCGACCGT 59.657 47.619 0.00 0.00 0.00 4.83
36 37 2.224209 ACTTTGACCAGATTCGACCGTT 60.224 45.455 0.00 0.00 0.00 4.44
37 38 2.074547 TTGACCAGATTCGACCGTTC 57.925 50.000 0.00 0.00 0.00 3.95
38 39 0.245539 TGACCAGATTCGACCGTTCC 59.754 55.000 0.00 0.00 0.00 3.62
39 40 0.801067 GACCAGATTCGACCGTTCCG 60.801 60.000 0.00 0.00 0.00 4.30
59 60 4.845580 CTGCTGCCGCTCCCGAAT 62.846 66.667 0.70 0.00 36.97 3.34
60 61 4.838152 TGCTGCCGCTCCCGAATC 62.838 66.667 0.70 0.00 36.97 2.52
61 62 4.537433 GCTGCCGCTCCCGAATCT 62.537 66.667 0.00 0.00 36.29 2.40
62 63 2.279784 CTGCCGCTCCCGAATCTC 60.280 66.667 0.00 0.00 36.29 2.75
63 64 4.207281 TGCCGCTCCCGAATCTCG 62.207 66.667 0.00 0.00 40.07 4.04
100 101 4.966787 GCACCCAGGAAACGGCCA 62.967 66.667 2.24 0.00 0.00 5.36
101 102 2.035626 CACCCAGGAAACGGCCAT 59.964 61.111 2.24 0.00 0.00 4.40
102 103 2.035626 ACCCAGGAAACGGCCATG 59.964 61.111 2.24 0.00 0.00 3.66
103 104 3.451894 CCCAGGAAACGGCCATGC 61.452 66.667 2.24 0.00 0.00 4.06
104 105 3.451894 CCAGGAAACGGCCATGCC 61.452 66.667 2.24 0.00 46.75 4.40
153 154 4.914420 CCGCGCGTGGAGCTAGAG 62.914 72.222 34.65 2.97 45.59 2.43
183 184 4.072088 GCGGTGCCGTTCGACTTG 62.072 66.667 12.46 0.00 42.09 3.16
184 185 3.411351 CGGTGCCGTTCGACTTGG 61.411 66.667 1.93 0.00 34.35 3.61
185 186 2.029964 GGTGCCGTTCGACTTGGA 59.970 61.111 1.11 0.00 0.00 3.53
186 187 2.027625 GGTGCCGTTCGACTTGGAG 61.028 63.158 1.11 0.00 0.00 3.86
187 188 2.027625 GTGCCGTTCGACTTGGAGG 61.028 63.158 1.11 0.00 0.00 4.30
188 189 3.119096 GCCGTTCGACTTGGAGGC 61.119 66.667 1.11 0.00 37.61 4.70
194 195 4.473520 CGACTTGGAGGCGGCCAT 62.474 66.667 23.09 6.21 44.58 4.40
195 196 2.825836 GACTTGGAGGCGGCCATG 60.826 66.667 23.09 8.36 37.86 3.66
196 197 3.628646 GACTTGGAGGCGGCCATGT 62.629 63.158 23.09 16.70 45.68 3.21
197 198 3.136123 CTTGGAGGCGGCCATGTG 61.136 66.667 23.09 3.22 37.86 3.21
217 218 3.443045 GCCACGGGCTGTTCATGG 61.443 66.667 0.00 0.00 46.69 3.66
218 219 2.751436 CCACGGGCTGTTCATGGG 60.751 66.667 0.00 0.00 0.00 4.00
298 299 2.763215 GCTGGGGTGGATTGGACA 59.237 61.111 0.00 0.00 0.00 4.02
299 300 1.307647 GCTGGGGTGGATTGGACAT 59.692 57.895 0.00 0.00 0.00 3.06
329 341 1.000394 TGAAGACGATTTGACAGCCGA 60.000 47.619 0.00 0.00 0.00 5.54
381 393 4.240881 ACATCCAGGCAACATCATAGTT 57.759 40.909 0.00 0.00 41.41 2.24
430 442 0.108186 CTCCCACGCATAGTTGAGCA 60.108 55.000 0.00 0.00 0.00 4.26
517 529 0.847373 AGAGGAGCAGATCGAGGGTA 59.153 55.000 0.00 0.00 0.00 3.69
531 543 1.217244 GGGTAAGAAGAAGGCGCGA 59.783 57.895 12.10 0.00 0.00 5.87
572 584 0.250295 TCGTCTTTGCTTGGACCCTG 60.250 55.000 0.00 0.00 0.00 4.45
578 590 3.365265 GCTTGGACCCTGCAACCG 61.365 66.667 0.00 0.00 0.00 4.44
615 627 1.810030 CTTAGGAGCGACGGCCAAC 60.810 63.158 2.24 0.00 41.24 3.77
634 646 1.760480 GAGGAGAGGTGAGGAGGCC 60.760 68.421 0.00 0.00 0.00 5.19
636 648 2.043852 GAGAGGTGAGGAGGCCGA 60.044 66.667 0.00 0.00 0.00 5.54
715 727 2.354072 GCGCGAGGAGAATCGAGG 60.354 66.667 12.10 0.00 45.56 4.63
734 746 0.478507 GGAGAGGAGAGGAGAGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
735 747 0.178990 GAGAGGAGAGGAGAGGAGGC 60.179 65.000 0.00 0.00 0.00 4.70
736 748 1.528309 GAGGAGAGGAGAGGAGGCG 60.528 68.421 0.00 0.00 0.00 5.52
737 749 2.520741 GGAGAGGAGAGGAGGCGG 60.521 72.222 0.00 0.00 0.00 6.13
738 750 3.223589 GAGAGGAGAGGAGGCGGC 61.224 72.222 0.00 0.00 0.00 6.53
749 761 4.845580 AGGCGGCGGCATCAAGAG 62.846 66.667 34.87 0.00 42.47 2.85
750 762 4.838152 GGCGGCGGCATCAAGAGA 62.838 66.667 29.41 0.00 42.47 3.10
751 763 2.819595 GCGGCGGCATCAAGAGAA 60.820 61.111 9.78 0.00 39.62 2.87
752 764 2.398554 GCGGCGGCATCAAGAGAAA 61.399 57.895 9.78 0.00 39.62 2.52
753 765 1.922135 GCGGCGGCATCAAGAGAAAA 61.922 55.000 9.78 0.00 39.62 2.29
754 766 0.097674 CGGCGGCATCAAGAGAAAAG 59.902 55.000 10.53 0.00 0.00 2.27
755 767 0.453390 GGCGGCATCAAGAGAAAAGG 59.547 55.000 3.07 0.00 0.00 3.11
756 768 1.168714 GCGGCATCAAGAGAAAAGGT 58.831 50.000 0.00 0.00 0.00 3.50
757 769 1.135575 GCGGCATCAAGAGAAAAGGTG 60.136 52.381 0.00 0.00 0.00 4.00
758 770 1.470098 CGGCATCAAGAGAAAAGGTGG 59.530 52.381 0.00 0.00 0.00 4.61
759 771 1.821136 GGCATCAAGAGAAAAGGTGGG 59.179 52.381 0.00 0.00 0.00 4.61
760 772 1.203287 GCATCAAGAGAAAAGGTGGGC 59.797 52.381 0.00 0.00 0.00 5.36
761 773 1.470098 CATCAAGAGAAAAGGTGGGCG 59.530 52.381 0.00 0.00 0.00 6.13
762 774 0.472471 TCAAGAGAAAAGGTGGGCGT 59.528 50.000 0.00 0.00 0.00 5.68
763 775 0.593128 CAAGAGAAAAGGTGGGCGTG 59.407 55.000 0.00 0.00 0.00 5.34
764 776 1.172812 AAGAGAAAAGGTGGGCGTGC 61.173 55.000 0.00 0.00 0.00 5.34
765 777 2.966309 GAGAAAAGGTGGGCGTGCG 61.966 63.158 0.00 0.00 0.00 5.34
766 778 4.038080 GAAAAGGTGGGCGTGCGG 62.038 66.667 0.00 0.00 0.00 5.69
767 779 4.572571 AAAAGGTGGGCGTGCGGA 62.573 61.111 0.00 0.00 0.00 5.54
777 789 3.680786 CGTGCGGAGACCAGGTCA 61.681 66.667 22.31 0.00 34.60 4.02
778 790 2.982130 GTGCGGAGACCAGGTCAT 59.018 61.111 22.31 6.81 34.60 3.06
779 791 1.448540 GTGCGGAGACCAGGTCATG 60.449 63.158 22.31 11.41 34.60 3.07
780 792 2.512515 GCGGAGACCAGGTCATGC 60.513 66.667 22.31 17.16 34.60 4.06
781 793 2.187946 CGGAGACCAGGTCATGCC 59.812 66.667 22.31 17.29 34.60 4.40
782 794 2.592308 GGAGACCAGGTCATGCCC 59.408 66.667 22.31 12.57 38.26 5.36
783 795 2.300967 GGAGACCAGGTCATGCCCA 61.301 63.158 22.31 0.00 38.26 5.36
784 796 1.685224 GAGACCAGGTCATGCCCAA 59.315 57.895 22.31 0.00 38.26 4.12
785 797 0.257039 GAGACCAGGTCATGCCCAAT 59.743 55.000 22.31 0.00 38.26 3.16
786 798 0.257039 AGACCAGGTCATGCCCAATC 59.743 55.000 22.31 0.00 38.26 2.67
787 799 0.753111 GACCAGGTCATGCCCAATCC 60.753 60.000 15.43 0.00 38.26 3.01
788 800 1.456331 CCAGGTCATGCCCAATCCC 60.456 63.158 0.00 0.00 38.26 3.85
789 801 1.616921 CAGGTCATGCCCAATCCCT 59.383 57.895 0.00 0.00 38.26 4.20
790 802 0.466922 CAGGTCATGCCCAATCCCTC 60.467 60.000 0.00 0.00 38.26 4.30
791 803 1.152673 GGTCATGCCCAATCCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
792 804 1.649271 GGTCATGCCCAATCCCTCCT 61.649 60.000 0.00 0.00 0.00 3.69
793 805 0.179006 GTCATGCCCAATCCCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
794 806 0.327867 TCATGCCCAATCCCTCCTCT 60.328 55.000 0.00 0.00 0.00 3.69
795 807 0.178998 CATGCCCAATCCCTCCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
796 808 1.358830 ATGCCCAATCCCTCCTCTGG 61.359 60.000 0.00 0.00 0.00 3.86
797 809 2.003548 GCCCAATCCCTCCTCTGGT 61.004 63.158 0.00 0.00 0.00 4.00
798 810 1.575447 GCCCAATCCCTCCTCTGGTT 61.575 60.000 0.00 0.00 0.00 3.67
799 811 0.548510 CCCAATCCCTCCTCTGGTTC 59.451 60.000 0.00 0.00 0.00 3.62
800 812 1.589414 CCAATCCCTCCTCTGGTTCT 58.411 55.000 0.00 0.00 0.00 3.01
801 813 1.918957 CCAATCCCTCCTCTGGTTCTT 59.081 52.381 0.00 0.00 0.00 2.52
802 814 2.310052 CCAATCCCTCCTCTGGTTCTTT 59.690 50.000 0.00 0.00 0.00 2.52
803 815 3.245407 CCAATCCCTCCTCTGGTTCTTTT 60.245 47.826 0.00 0.00 0.00 2.27
804 816 4.411013 CAATCCCTCCTCTGGTTCTTTTT 58.589 43.478 0.00 0.00 0.00 1.94
805 817 3.790089 TCCCTCCTCTGGTTCTTTTTC 57.210 47.619 0.00 0.00 0.00 2.29
806 818 2.375509 TCCCTCCTCTGGTTCTTTTTCC 59.624 50.000 0.00 0.00 0.00 3.13
807 819 2.555448 CCCTCCTCTGGTTCTTTTTCCC 60.555 54.545 0.00 0.00 0.00 3.97
808 820 2.376855 CCTCCTCTGGTTCTTTTTCCCT 59.623 50.000 0.00 0.00 0.00 4.20
809 821 3.560239 CCTCCTCTGGTTCTTTTTCCCTC 60.560 52.174 0.00 0.00 0.00 4.30
810 822 2.038557 TCCTCTGGTTCTTTTTCCCTCG 59.961 50.000 0.00 0.00 0.00 4.63
811 823 1.807142 CTCTGGTTCTTTTTCCCTCGC 59.193 52.381 0.00 0.00 0.00 5.03
812 824 1.420138 TCTGGTTCTTTTTCCCTCGCT 59.580 47.619 0.00 0.00 0.00 4.93
813 825 2.635915 TCTGGTTCTTTTTCCCTCGCTA 59.364 45.455 0.00 0.00 0.00 4.26
814 826 3.003480 CTGGTTCTTTTTCCCTCGCTAG 58.997 50.000 0.00 0.00 0.00 3.42
815 827 1.738350 GGTTCTTTTTCCCTCGCTAGC 59.262 52.381 4.06 4.06 0.00 3.42
816 828 2.423577 GTTCTTTTTCCCTCGCTAGCA 58.576 47.619 16.45 0.92 0.00 3.49
817 829 2.094762 TCTTTTTCCCTCGCTAGCAC 57.905 50.000 16.45 0.00 0.00 4.40
818 830 1.346395 TCTTTTTCCCTCGCTAGCACA 59.654 47.619 16.45 0.00 0.00 4.57
819 831 2.027192 TCTTTTTCCCTCGCTAGCACAT 60.027 45.455 16.45 0.00 0.00 3.21
820 832 2.489938 TTTTCCCTCGCTAGCACATT 57.510 45.000 16.45 0.00 0.00 2.71
821 833 3.620427 TTTTCCCTCGCTAGCACATTA 57.380 42.857 16.45 0.00 0.00 1.90
822 834 3.838244 TTTCCCTCGCTAGCACATTAT 57.162 42.857 16.45 0.00 0.00 1.28
823 835 3.838244 TTCCCTCGCTAGCACATTATT 57.162 42.857 16.45 0.00 0.00 1.40
824 836 3.838244 TCCCTCGCTAGCACATTATTT 57.162 42.857 16.45 0.00 0.00 1.40
825 837 4.150897 TCCCTCGCTAGCACATTATTTT 57.849 40.909 16.45 0.00 0.00 1.82
826 838 4.523083 TCCCTCGCTAGCACATTATTTTT 58.477 39.130 16.45 0.00 0.00 1.94
862 874 6.405278 TTTTACTCTGACTGACAGTGATGA 57.595 37.500 14.14 7.16 45.86 2.92
863 875 5.635417 TTACTCTGACTGACAGTGATGAG 57.365 43.478 14.14 17.57 45.86 2.90
864 876 2.824936 ACTCTGACTGACAGTGATGAGG 59.175 50.000 14.14 1.00 45.86 3.86
865 877 2.824936 CTCTGACTGACAGTGATGAGGT 59.175 50.000 14.14 0.00 45.86 3.85
866 878 2.560105 TCTGACTGACAGTGATGAGGTG 59.440 50.000 14.14 0.00 45.86 4.00
867 879 1.620323 TGACTGACAGTGATGAGGTGG 59.380 52.381 14.14 0.00 0.00 4.61
868 880 1.895798 GACTGACAGTGATGAGGTGGA 59.104 52.381 14.14 0.00 0.00 4.02
869 881 2.499289 GACTGACAGTGATGAGGTGGAT 59.501 50.000 14.14 0.00 0.00 3.41
870 882 2.235650 ACTGACAGTGATGAGGTGGATG 59.764 50.000 7.47 0.00 0.00 3.51
871 883 1.065926 TGACAGTGATGAGGTGGATGC 60.066 52.381 0.00 0.00 0.00 3.91
872 884 0.986527 ACAGTGATGAGGTGGATGCA 59.013 50.000 0.00 0.00 0.00 3.96
873 885 1.065636 ACAGTGATGAGGTGGATGCAG 60.066 52.381 0.00 0.00 0.00 4.41
874 886 0.107312 AGTGATGAGGTGGATGCAGC 60.107 55.000 8.54 8.54 0.00 5.25
875 887 1.153309 TGATGAGGTGGATGCAGCG 60.153 57.895 10.91 0.00 0.00 5.18
876 888 1.144716 GATGAGGTGGATGCAGCGA 59.855 57.895 10.91 2.25 0.00 4.93
877 889 0.879400 GATGAGGTGGATGCAGCGAG 60.879 60.000 10.91 0.00 0.00 5.03
878 890 2.202987 GAGGTGGATGCAGCGAGG 60.203 66.667 10.91 0.00 0.00 4.63
879 891 3.746949 GAGGTGGATGCAGCGAGGG 62.747 68.421 10.91 0.00 0.00 4.30
880 892 4.864334 GGTGGATGCAGCGAGGGG 62.864 72.222 0.00 0.00 0.00 4.79
881 893 4.864334 GTGGATGCAGCGAGGGGG 62.864 72.222 0.00 0.00 0.00 5.40
901 913 2.739287 CCCTTTGCGCGACCGTTA 60.739 61.111 12.10 0.00 36.67 3.18
902 914 2.319096 CCCTTTGCGCGACCGTTAA 61.319 57.895 12.10 0.00 36.67 2.01
903 915 1.641123 CCCTTTGCGCGACCGTTAAT 61.641 55.000 12.10 0.00 36.67 1.40
904 916 0.520412 CCTTTGCGCGACCGTTAATG 60.520 55.000 12.10 0.00 36.67 1.90
905 917 0.520412 CTTTGCGCGACCGTTAATGG 60.520 55.000 12.10 12.41 36.67 3.16
906 918 1.913451 TTTGCGCGACCGTTAATGGG 61.913 55.000 18.06 6.33 36.67 4.00
907 919 2.816520 GCGCGACCGTTAATGGGT 60.817 61.111 18.06 9.61 41.48 4.51
932 944 7.711339 GTCTAATTAATTGACCAGATTCGACCT 59.289 37.037 11.05 0.00 0.00 3.85
1273 1289 2.835895 GCTCCCTCCTCGTCTCCC 60.836 72.222 0.00 0.00 0.00 4.30
1276 1292 1.619975 TCCCTCCTCGTCTCCCTCT 60.620 63.158 0.00 0.00 0.00 3.69
1607 1629 4.564406 CCTCTGCTTTCCTCTGTATGTGTT 60.564 45.833 0.00 0.00 0.00 3.32
1633 1718 2.676839 AGCATCAGAATTCAGAAGTGCG 59.323 45.455 16.22 2.24 36.53 5.34
1641 1726 2.755836 TTCAGAAGTGCGCAGTTTTC 57.244 45.000 29.82 22.66 0.00 2.29
1698 1789 6.073981 TCTTATATTGCCATGTTATTGCCCA 58.926 36.000 0.00 0.00 0.00 5.36
1719 1810 3.087031 AGCAGATGGACAAGAACATTGG 58.913 45.455 0.00 0.00 0.00 3.16
1727 1818 1.972795 ACAAGAACATTGGCAATGGCT 59.027 42.857 35.77 29.29 43.21 4.75
1755 1846 0.601311 GTGCGAGCTTCAGTTGGAGT 60.601 55.000 0.00 0.00 0.00 3.85
1761 1852 3.063485 GAGCTTCAGTTGGAGTTGAGAC 58.937 50.000 0.00 0.00 0.00 3.36
1762 1853 2.435805 AGCTTCAGTTGGAGTTGAGACA 59.564 45.455 0.00 0.00 0.00 3.41
1780 1871 5.481824 TGAGACATTCATCTGGTACTGAAGT 59.518 40.000 0.00 0.00 40.32 3.01
1785 1876 6.652481 ACATTCATCTGGTACTGAAGTTCTTG 59.348 38.462 4.17 0.00 40.32 3.02
1837 1928 2.021931 GAAGCGCGGCAAGAATCG 59.978 61.111 8.83 0.00 0.00 3.34
1975 2087 6.423604 ACACATTTGGAAACGGATGAAAAATC 59.576 34.615 0.00 0.00 0.00 2.17
2091 2203 0.899720 TACTCCGGAAGAATTGGCGT 59.100 50.000 5.23 0.00 0.00 5.68
2096 2208 1.867233 CCGGAAGAATTGGCGTATCTG 59.133 52.381 0.00 0.00 0.00 2.90
2117 2229 5.047306 TCTGGATGAAGACTTCTTAGCGAAA 60.047 40.000 16.02 0.00 36.11 3.46
2118 2230 5.734720 TGGATGAAGACTTCTTAGCGAAAT 58.265 37.500 16.02 0.00 36.11 2.17
2576 2688 7.182817 TCAGTTCTTAGCATACTGGTATGTT 57.817 36.000 18.24 15.65 43.57 2.71
2577 2689 7.620880 TCAGTTCTTAGCATACTGGTATGTTT 58.379 34.615 18.24 11.54 43.57 2.83
2578 2690 8.100791 TCAGTTCTTAGCATACTGGTATGTTTT 58.899 33.333 18.24 9.70 43.57 2.43
2603 2715 6.463995 TTTTTCTGACACTGGCATTTAGTT 57.536 33.333 0.00 0.00 0.00 2.24
2700 2813 3.191162 TGACAAGCAATTTGGGAAGATCG 59.809 43.478 0.00 0.00 41.25 3.69
2841 2954 9.567776 TCAACTTACAACATAGAGGAATTTTGA 57.432 29.630 0.00 0.00 0.00 2.69
2882 2995 5.172205 CCTGTTCTAGTAAGCAGAAAGTCC 58.828 45.833 0.00 0.00 33.95 3.85
2918 3047 4.458295 CCCCTTCATGAATGCATCTCATAC 59.542 45.833 18.05 2.14 34.33 2.39
2970 3099 4.973168 AGTTTGTAGCATTCCAGACTGAA 58.027 39.130 3.32 0.00 0.00 3.02
2986 3115 6.536582 CCAGACTGAACTAATGTGTTATCAGG 59.463 42.308 3.32 0.00 30.69 3.86
3219 3406 1.202222 GCATACATTGTGAGGCACAGC 60.202 52.381 0.00 0.00 45.39 4.40
3226 3413 0.953727 TGTGAGGCACAGCACATTTC 59.046 50.000 0.00 0.00 39.62 2.17
3229 3416 0.445436 GAGGCACAGCACATTTCTCG 59.555 55.000 0.00 0.00 0.00 4.04
3233 3420 1.063174 GCACAGCACATTTCTCGATCC 59.937 52.381 0.00 0.00 0.00 3.36
3496 3696 3.483411 GCTTGTGTTTCAAACCAAAAGCG 60.483 43.478 13.01 2.07 35.48 4.68
3503 3703 3.145422 AAACCAAAAGCGGGGCGTG 62.145 57.895 0.00 0.00 0.00 5.34
3565 3765 7.372714 TGGATCTGTCACAAGAATTTGAATTG 58.627 34.615 0.00 0.00 37.73 2.32
3587 3787 3.939740 ATCAGAAGGCAGGCTCAAATA 57.060 42.857 0.00 0.00 0.00 1.40
3666 3866 4.617067 CGATAGGCTGAGGCACTGTATTAG 60.617 50.000 9.23 0.00 41.55 1.73
3798 3998 6.578919 GCAGCATTGTTCTAACTGAAACTTAC 59.421 38.462 0.00 0.00 36.30 2.34
3828 4028 6.944557 TCATGTCTACATAAACAAGTCACG 57.055 37.500 0.00 0.00 34.26 4.35
3985 4185 5.842907 TCGATTTCCACATACATCCTGTAG 58.157 41.667 0.00 0.00 36.14 2.74
3990 4192 4.030216 TCCACATACATCCTGTAGAGCAA 58.970 43.478 0.00 0.00 36.14 3.91
4035 4398 8.615360 AGATGGACTATATATGTGTGGCTTAT 57.385 34.615 0.00 0.00 0.00 1.73
4036 4399 9.715119 AGATGGACTATATATGTGTGGCTTATA 57.285 33.333 0.00 0.00 0.00 0.98
4069 4432 6.946340 AGGAAAAGAATGTTGTCCAGTTTTT 58.054 32.000 1.98 0.00 27.98 1.94
4123 4492 1.682323 TGCTCAAAAATGTCAGCTGCA 59.318 42.857 9.47 11.14 32.76 4.41
4144 4513 5.154222 GCAGGTAGTTCAAACTTGCAATAC 58.846 41.667 0.00 0.00 39.12 1.89
4223 4592 1.581934 CTCCACAGTTTGTTCGCAGA 58.418 50.000 0.00 0.00 0.00 4.26
4239 4608 1.340017 GCAGAGTGGGCAATTCACCTA 60.340 52.381 0.00 0.00 35.87 3.08
4246 4615 2.084546 GGGCAATTCACCTATATCCGC 58.915 52.381 0.00 0.00 0.00 5.54
4273 4642 8.594881 AATAAGAATCTGATTAGCGGTGTTAG 57.405 34.615 2.28 0.00 0.00 2.34
4296 4665 9.592196 TTAGGATTAGTAATACCGGAAGTACAT 57.408 33.333 9.46 0.00 32.46 2.29
4330 4804 7.976135 AAGATGTATATCTGTTGCCATCTTC 57.024 36.000 2.35 0.00 42.78 2.87
4358 4832 8.798859 AATCTATCCAGTGGTTATATGAATGC 57.201 34.615 9.54 0.00 0.00 3.56
4372 4846 4.603989 ATGAATGCATGTTTTCCACACA 57.396 36.364 0.00 0.00 38.61 3.72
4416 4891 5.862924 TGATCAAATCACCGAGTCTTTTC 57.137 39.130 0.00 0.00 33.59 2.29
4437 4912 1.153842 GGCACGCAGGTTATTTGGC 60.154 57.895 0.00 0.00 0.00 4.52
4452 4927 1.822114 TTGGCTACCGTAGTGCTGCA 61.822 55.000 0.00 0.00 0.00 4.41
4454 4929 2.167861 GCTACCGTAGTGCTGCAGC 61.168 63.158 31.89 31.89 42.50 5.25
4457 4932 0.738975 TACCGTAGTGCTGCAGCTAG 59.261 55.000 36.61 22.19 42.66 3.42
4551 5026 2.988010 TCACAGGCTATGCGAAGAAT 57.012 45.000 0.00 0.00 0.00 2.40
4553 5028 4.400529 TCACAGGCTATGCGAAGAATAA 57.599 40.909 0.00 0.00 0.00 1.40
4555 5030 3.248602 CACAGGCTATGCGAAGAATAACC 59.751 47.826 0.00 0.00 0.00 2.85
4556 5031 2.476619 CAGGCTATGCGAAGAATAACCG 59.523 50.000 0.00 0.00 0.00 4.44
4629 5104 8.025270 TCTGGATACGGTTATAATTTGGAGAA 57.975 34.615 0.00 0.00 45.94 2.87
4751 5226 0.860203 CAGAATGCAGCGCGATGTTG 60.860 55.000 26.61 12.51 0.00 3.33
4762 5237 1.359459 GCGATGTTGGGAGACGGAAC 61.359 60.000 0.00 0.00 0.00 3.62
4791 5266 5.383130 GGTTACTGAAGAAAATTCGCAGAC 58.617 41.667 19.01 11.26 37.66 3.51
4797 5272 5.985781 TGAAGAAAATTCGCAGACAAGTAC 58.014 37.500 0.00 0.00 34.32 2.73
4809 5284 4.096311 CAGACAAGTACGGTCAGTAATCG 58.904 47.826 18.73 0.00 37.02 3.34
4810 5285 3.128242 AGACAAGTACGGTCAGTAATCGG 59.872 47.826 18.73 0.00 37.02 4.18
4817 5292 0.727398 GGTCAGTAATCGGCAAGCAC 59.273 55.000 0.00 0.00 0.00 4.40
4846 5321 2.375509 GCCCCCAAGCACTACCTATATT 59.624 50.000 0.00 0.00 0.00 1.28
4894 5388 2.478292 CAGAGGGGGAAAAGGCTACTA 58.522 52.381 0.00 0.00 0.00 1.82
4895 5389 2.844348 CAGAGGGGGAAAAGGCTACTAA 59.156 50.000 0.00 0.00 0.00 2.24
4896 5390 3.459969 CAGAGGGGGAAAAGGCTACTAAT 59.540 47.826 0.00 0.00 0.00 1.73
4897 5391 4.658901 CAGAGGGGGAAAAGGCTACTAATA 59.341 45.833 0.00 0.00 0.00 0.98
4935 5429 7.281549 ACTGTAGTAAGTAAAAATATTGCCGGG 59.718 37.037 2.18 0.00 0.00 5.73
4936 5430 7.111466 TGTAGTAAGTAAAAATATTGCCGGGT 58.889 34.615 2.18 0.00 0.00 5.28
4952 5446 1.817740 CGGGTGGAAAGAGGAAAGCAA 60.818 52.381 0.00 0.00 0.00 3.91
4955 5449 3.696548 GGGTGGAAAGAGGAAAGCAATAG 59.303 47.826 0.00 0.00 0.00 1.73
4963 5457 8.693625 GGAAAGAGGAAAGCAATAGTACTACTA 58.306 37.037 4.31 0.00 34.82 1.82
4974 5468 9.712305 AGCAATAGTACTACTATTATTTGGCAG 57.288 33.333 17.52 7.39 46.48 4.85
4977 5471 9.930693 AATAGTACTACTATTATTTGGCAGCTC 57.069 33.333 16.75 0.00 46.38 4.09
4981 5475 6.448006 ACTACTATTATTTGGCAGCTCGTAG 58.552 40.000 0.00 0.00 0.00 3.51
4982 5476 4.058817 ACTATTATTTGGCAGCTCGTAGC 58.941 43.478 0.00 0.00 42.84 3.58
4988 5482 2.889503 GCAGCTCGTAGCCAGCAG 60.890 66.667 13.16 0.60 43.77 4.24
4989 5483 2.889503 CAGCTCGTAGCCAGCAGC 60.890 66.667 3.66 0.00 43.77 5.25
5001 5495 1.134580 GCCAGCAGCAGATAGTGAGAA 60.135 52.381 0.00 0.00 42.97 2.87
5008 5502 3.856521 CAGCAGATAGTGAGAAACAGACG 59.143 47.826 0.00 0.00 0.00 4.18
5010 5504 3.854809 GCAGATAGTGAGAAACAGACGAC 59.145 47.826 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.080286 ACGGTCGAATCTGGTCAAAG 57.920 50.000 0.00 0.00 0.00 2.77
18 19 1.337447 GGAACGGTCGAATCTGGTCAA 60.337 52.381 0.00 0.00 32.55 3.18
19 20 0.245539 GGAACGGTCGAATCTGGTCA 59.754 55.000 0.00 0.00 32.55 4.02
20 21 3.046280 GGAACGGTCGAATCTGGTC 57.954 57.895 0.00 0.00 0.00 4.02
44 45 4.537433 AGATTCGGGAGCGGCAGC 62.537 66.667 0.00 0.00 45.58 5.25
45 46 2.279784 GAGATTCGGGAGCGGCAG 60.280 66.667 1.45 0.00 0.00 4.85
46 47 4.207281 CGAGATTCGGGAGCGGCA 62.207 66.667 1.45 0.00 36.00 5.69
83 84 4.966787 TGGCCGTTTCCTGGGTGC 62.967 66.667 0.00 0.00 0.00 5.01
84 85 2.035626 ATGGCCGTTTCCTGGGTG 59.964 61.111 0.00 0.00 0.00 4.61
85 86 2.035626 CATGGCCGTTTCCTGGGT 59.964 61.111 0.00 0.00 0.00 4.51
86 87 3.451894 GCATGGCCGTTTCCTGGG 61.452 66.667 0.00 0.00 0.00 4.45
87 88 3.451894 GGCATGGCCGTTTCCTGG 61.452 66.667 8.35 0.00 39.62 4.45
136 137 4.914420 CTCTAGCTCCACGCGCGG 62.914 72.222 35.22 22.11 45.59 6.46
166 167 4.072088 CAAGTCGAACGGCACCGC 62.072 66.667 9.43 0.00 44.19 5.68
167 168 3.411351 CCAAGTCGAACGGCACCG 61.411 66.667 7.71 7.71 46.03 4.94
168 169 2.027625 CTCCAAGTCGAACGGCACC 61.028 63.158 1.04 0.00 0.00 5.01
169 170 2.027625 CCTCCAAGTCGAACGGCAC 61.028 63.158 1.04 0.00 0.00 5.01
170 171 2.342279 CCTCCAAGTCGAACGGCA 59.658 61.111 1.04 0.00 0.00 5.69
171 172 3.119096 GCCTCCAAGTCGAACGGC 61.119 66.667 0.00 0.00 0.00 5.68
172 173 2.809601 CGCCTCCAAGTCGAACGG 60.810 66.667 0.00 0.00 0.00 4.44
173 174 2.809601 CCGCCTCCAAGTCGAACG 60.810 66.667 0.00 0.00 0.00 3.95
174 175 3.119096 GCCGCCTCCAAGTCGAAC 61.119 66.667 0.00 0.00 0.00 3.95
175 176 4.388499 GGCCGCCTCCAAGTCGAA 62.388 66.667 0.71 0.00 0.00 3.71
177 178 4.473520 ATGGCCGCCTCCAAGTCG 62.474 66.667 11.61 0.00 39.96 4.18
178 179 2.825836 CATGGCCGCCTCCAAGTC 60.826 66.667 11.61 0.00 39.96 3.01
179 180 3.650950 ACATGGCCGCCTCCAAGT 61.651 61.111 11.61 0.00 39.96 3.16
180 181 3.136123 CACATGGCCGCCTCCAAG 61.136 66.667 11.61 0.00 39.96 3.61
201 202 2.751436 CCCATGAACAGCCCGTGG 60.751 66.667 0.00 0.00 39.74 4.94
202 203 2.751436 CCCCATGAACAGCCCGTG 60.751 66.667 0.00 0.00 0.00 4.94
203 204 3.256960 ACCCCATGAACAGCCCGT 61.257 61.111 0.00 0.00 0.00 5.28
204 205 2.438434 GACCCCATGAACAGCCCG 60.438 66.667 0.00 0.00 0.00 6.13
205 206 1.077429 GAGACCCCATGAACAGCCC 60.077 63.158 0.00 0.00 0.00 5.19
206 207 1.077429 GGAGACCCCATGAACAGCC 60.077 63.158 0.00 0.00 34.14 4.85
207 208 0.393537 CAGGAGACCCCATGAACAGC 60.394 60.000 0.00 0.00 37.41 4.40
208 209 0.393537 GCAGGAGACCCCATGAACAG 60.394 60.000 0.00 0.00 37.41 3.16
209 210 1.685224 GCAGGAGACCCCATGAACA 59.315 57.895 0.00 0.00 37.41 3.18
210 211 1.077429 GGCAGGAGACCCCATGAAC 60.077 63.158 0.00 0.00 37.41 3.18
211 212 0.846427 AAGGCAGGAGACCCCATGAA 60.846 55.000 0.00 0.00 37.41 2.57
212 213 1.229951 AAGGCAGGAGACCCCATGA 60.230 57.895 0.00 0.00 37.41 3.07
213 214 1.077212 CAAGGCAGGAGACCCCATG 60.077 63.158 0.00 0.00 37.41 3.66
214 215 2.988839 GCAAGGCAGGAGACCCCAT 61.989 63.158 0.00 0.00 37.41 4.00
215 216 3.650950 GCAAGGCAGGAGACCCCA 61.651 66.667 0.00 0.00 37.41 4.96
216 217 4.432741 GGCAAGGCAGGAGACCCC 62.433 72.222 0.00 0.00 0.00 4.95
217 218 2.988839 ATGGCAAGGCAGGAGACCC 61.989 63.158 2.05 0.00 0.00 4.46
218 219 1.751927 CATGGCAAGGCAGGAGACC 60.752 63.158 1.81 0.00 0.00 3.85
287 288 1.299541 CGCTGGTATGTCCAATCCAC 58.700 55.000 0.00 0.00 46.59 4.02
298 299 1.516386 CGTCTTCACGCGCTGGTAT 60.516 57.895 5.73 0.00 39.69 2.73
299 300 1.929806 ATCGTCTTCACGCGCTGGTA 61.930 55.000 5.73 0.00 46.28 3.25
308 320 1.126846 CGGCTGTCAAATCGTCTTCAC 59.873 52.381 0.00 0.00 0.00 3.18
320 332 4.400109 GCTCGTCGTCGGCTGTCA 62.400 66.667 1.55 0.00 37.69 3.58
324 336 3.329688 CTCAAGCTCGTCGTCGGCT 62.330 63.158 10.92 10.92 42.16 5.52
329 341 0.800012 GAGTCTCTCAAGCTCGTCGT 59.200 55.000 0.00 0.00 0.00 4.34
430 442 1.226888 GGCGACGTTTAGAGGCGAT 60.227 57.895 0.00 0.00 0.00 4.58
517 529 1.374758 CCAGTCGCGCCTTCTTCTT 60.375 57.895 0.00 0.00 0.00 2.52
531 543 0.419459 AGGAGACCCCAAGATCCAGT 59.581 55.000 0.00 0.00 37.41 4.00
615 627 2.124693 GCCTCCTCACCTCTCCTCG 61.125 68.421 0.00 0.00 0.00 4.63
634 646 2.202492 CTCTTCCTCGTGCCGTCG 60.202 66.667 0.00 0.00 0.00 5.12
636 648 2.282958 TCCTCTTCCTCGTGCCGT 60.283 61.111 0.00 0.00 0.00 5.68
672 684 1.893919 GCCGTTCTTCCTCTGCCTCT 61.894 60.000 0.00 0.00 0.00 3.69
715 727 0.478507 CCTCCTCTCCTCTCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
734 746 1.922135 TTTTCTCTTGATGCCGCCGC 61.922 55.000 0.00 0.00 0.00 6.53
735 747 0.097674 CTTTTCTCTTGATGCCGCCG 59.902 55.000 0.00 0.00 0.00 6.46
736 748 0.453390 CCTTTTCTCTTGATGCCGCC 59.547 55.000 0.00 0.00 0.00 6.13
737 749 1.135575 CACCTTTTCTCTTGATGCCGC 60.136 52.381 0.00 0.00 0.00 6.53
738 750 1.470098 CCACCTTTTCTCTTGATGCCG 59.530 52.381 0.00 0.00 0.00 5.69
739 751 1.821136 CCCACCTTTTCTCTTGATGCC 59.179 52.381 0.00 0.00 0.00 4.40
740 752 1.203287 GCCCACCTTTTCTCTTGATGC 59.797 52.381 0.00 0.00 0.00 3.91
741 753 1.470098 CGCCCACCTTTTCTCTTGATG 59.530 52.381 0.00 0.00 0.00 3.07
742 754 1.073923 ACGCCCACCTTTTCTCTTGAT 59.926 47.619 0.00 0.00 0.00 2.57
743 755 0.472471 ACGCCCACCTTTTCTCTTGA 59.528 50.000 0.00 0.00 0.00 3.02
744 756 0.593128 CACGCCCACCTTTTCTCTTG 59.407 55.000 0.00 0.00 0.00 3.02
745 757 1.172812 GCACGCCCACCTTTTCTCTT 61.173 55.000 0.00 0.00 0.00 2.85
746 758 1.600916 GCACGCCCACCTTTTCTCT 60.601 57.895 0.00 0.00 0.00 3.10
747 759 2.954611 GCACGCCCACCTTTTCTC 59.045 61.111 0.00 0.00 0.00 2.87
748 760 2.978010 CGCACGCCCACCTTTTCT 60.978 61.111 0.00 0.00 0.00 2.52
749 761 4.038080 CCGCACGCCCACCTTTTC 62.038 66.667 0.00 0.00 0.00 2.29
750 762 4.572571 TCCGCACGCCCACCTTTT 62.573 61.111 0.00 0.00 0.00 2.27
760 772 3.006756 ATGACCTGGTCTCCGCACG 62.007 63.158 26.03 0.00 33.15 5.34
761 773 1.448540 CATGACCTGGTCTCCGCAC 60.449 63.158 26.03 0.35 33.15 5.34
762 774 2.981302 CATGACCTGGTCTCCGCA 59.019 61.111 26.03 7.98 33.15 5.69
763 775 2.512515 GCATGACCTGGTCTCCGC 60.513 66.667 26.03 20.50 33.15 5.54
764 776 2.187946 GGCATGACCTGGTCTCCG 59.812 66.667 26.03 15.45 33.15 4.63
765 777 1.852157 TTGGGCATGACCTGGTCTCC 61.852 60.000 26.03 21.73 39.10 3.71
766 778 0.257039 ATTGGGCATGACCTGGTCTC 59.743 55.000 26.03 15.09 39.10 3.36
767 779 0.257039 GATTGGGCATGACCTGGTCT 59.743 55.000 26.03 10.26 39.10 3.85
768 780 0.753111 GGATTGGGCATGACCTGGTC 60.753 60.000 21.02 19.96 39.10 4.02
769 781 1.307647 GGATTGGGCATGACCTGGT 59.692 57.895 21.02 4.15 39.10 4.00
770 782 1.456331 GGGATTGGGCATGACCTGG 60.456 63.158 21.02 0.00 39.10 4.45
771 783 0.466922 GAGGGATTGGGCATGACCTG 60.467 60.000 21.02 0.00 39.10 4.00
772 784 1.649271 GGAGGGATTGGGCATGACCT 61.649 60.000 21.02 0.00 39.10 3.85
773 785 1.152673 GGAGGGATTGGGCATGACC 60.153 63.158 12.04 12.04 37.93 4.02
774 786 0.179006 GAGGAGGGATTGGGCATGAC 60.179 60.000 0.00 0.00 0.00 3.06
775 787 0.327867 AGAGGAGGGATTGGGCATGA 60.328 55.000 0.00 0.00 0.00 3.07
776 788 0.178998 CAGAGGAGGGATTGGGCATG 60.179 60.000 0.00 0.00 0.00 4.06
777 789 1.358830 CCAGAGGAGGGATTGGGCAT 61.359 60.000 0.00 0.00 0.00 4.40
778 790 2.002977 CCAGAGGAGGGATTGGGCA 61.003 63.158 0.00 0.00 0.00 5.36
779 791 1.575447 AACCAGAGGAGGGATTGGGC 61.575 60.000 0.00 0.00 34.99 5.36
780 792 0.548510 GAACCAGAGGAGGGATTGGG 59.451 60.000 0.00 0.00 34.99 4.12
781 793 1.589414 AGAACCAGAGGAGGGATTGG 58.411 55.000 0.00 0.00 36.76 3.16
782 794 3.728385 AAAGAACCAGAGGAGGGATTG 57.272 47.619 0.00 0.00 0.00 2.67
783 795 4.509302 GGAAAAAGAACCAGAGGAGGGATT 60.509 45.833 0.00 0.00 0.00 3.01
784 796 3.010696 GGAAAAAGAACCAGAGGAGGGAT 59.989 47.826 0.00 0.00 0.00 3.85
785 797 2.375509 GGAAAAAGAACCAGAGGAGGGA 59.624 50.000 0.00 0.00 0.00 4.20
786 798 2.555448 GGGAAAAAGAACCAGAGGAGGG 60.555 54.545 0.00 0.00 0.00 4.30
787 799 2.376855 AGGGAAAAAGAACCAGAGGAGG 59.623 50.000 0.00 0.00 0.00 4.30
788 800 3.680490 GAGGGAAAAAGAACCAGAGGAG 58.320 50.000 0.00 0.00 0.00 3.69
789 801 2.038557 CGAGGGAAAAAGAACCAGAGGA 59.961 50.000 0.00 0.00 0.00 3.71
790 802 2.427506 CGAGGGAAAAAGAACCAGAGG 58.572 52.381 0.00 0.00 0.00 3.69
791 803 1.807142 GCGAGGGAAAAAGAACCAGAG 59.193 52.381 0.00 0.00 0.00 3.35
792 804 1.420138 AGCGAGGGAAAAAGAACCAGA 59.580 47.619 0.00 0.00 0.00 3.86
793 805 1.897560 AGCGAGGGAAAAAGAACCAG 58.102 50.000 0.00 0.00 0.00 4.00
794 806 2.874457 GCTAGCGAGGGAAAAAGAACCA 60.874 50.000 0.00 0.00 0.00 3.67
795 807 1.738350 GCTAGCGAGGGAAAAAGAACC 59.262 52.381 0.00 0.00 0.00 3.62
796 808 2.159824 GTGCTAGCGAGGGAAAAAGAAC 59.840 50.000 10.77 0.00 0.00 3.01
797 809 2.224426 TGTGCTAGCGAGGGAAAAAGAA 60.224 45.455 10.77 0.00 0.00 2.52
798 810 1.346395 TGTGCTAGCGAGGGAAAAAGA 59.654 47.619 10.77 0.00 0.00 2.52
799 811 1.808411 TGTGCTAGCGAGGGAAAAAG 58.192 50.000 10.77 0.00 0.00 2.27
800 812 2.489938 ATGTGCTAGCGAGGGAAAAA 57.510 45.000 10.77 0.00 0.00 1.94
801 813 2.489938 AATGTGCTAGCGAGGGAAAA 57.510 45.000 10.77 0.00 0.00 2.29
802 814 3.838244 ATAATGTGCTAGCGAGGGAAA 57.162 42.857 10.77 0.00 0.00 3.13
803 815 3.838244 AATAATGTGCTAGCGAGGGAA 57.162 42.857 10.77 0.00 0.00 3.97
804 816 3.838244 AAATAATGTGCTAGCGAGGGA 57.162 42.857 10.77 0.00 0.00 4.20
805 817 4.900635 AAAAATAATGTGCTAGCGAGGG 57.099 40.909 10.77 0.00 0.00 4.30
838 850 6.816136 TCATCACTGTCAGTCAGAGTAAAAA 58.184 36.000 1.37 0.00 46.27 1.94
839 851 6.405278 TCATCACTGTCAGTCAGAGTAAAA 57.595 37.500 1.37 0.00 46.27 1.52
840 852 5.047731 CCTCATCACTGTCAGTCAGAGTAAA 60.048 44.000 17.83 0.00 46.27 2.01
841 853 4.460731 CCTCATCACTGTCAGTCAGAGTAA 59.539 45.833 17.83 1.17 46.27 2.24
842 854 4.013050 CCTCATCACTGTCAGTCAGAGTA 58.987 47.826 17.83 2.92 46.27 2.59
843 855 2.824936 CCTCATCACTGTCAGTCAGAGT 59.175 50.000 17.83 0.00 46.27 3.24
844 856 2.824936 ACCTCATCACTGTCAGTCAGAG 59.175 50.000 1.37 10.14 46.27 3.35
845 857 2.560105 CACCTCATCACTGTCAGTCAGA 59.440 50.000 1.37 0.00 46.27 3.27
847 859 1.620323 CCACCTCATCACTGTCAGTCA 59.380 52.381 1.37 0.00 0.00 3.41
848 860 1.895798 TCCACCTCATCACTGTCAGTC 59.104 52.381 1.37 0.00 0.00 3.51
849 861 2.015456 TCCACCTCATCACTGTCAGT 57.985 50.000 0.00 0.00 0.00 3.41
850 862 2.902523 CATCCACCTCATCACTGTCAG 58.097 52.381 0.00 0.00 0.00 3.51
851 863 1.065926 GCATCCACCTCATCACTGTCA 60.066 52.381 0.00 0.00 0.00 3.58
852 864 1.065926 TGCATCCACCTCATCACTGTC 60.066 52.381 0.00 0.00 0.00 3.51
853 865 0.986527 TGCATCCACCTCATCACTGT 59.013 50.000 0.00 0.00 0.00 3.55
854 866 1.664873 CTGCATCCACCTCATCACTG 58.335 55.000 0.00 0.00 0.00 3.66
855 867 0.107312 GCTGCATCCACCTCATCACT 60.107 55.000 0.00 0.00 0.00 3.41
856 868 1.434622 CGCTGCATCCACCTCATCAC 61.435 60.000 0.00 0.00 0.00 3.06
857 869 1.153309 CGCTGCATCCACCTCATCA 60.153 57.895 0.00 0.00 0.00 3.07
858 870 0.879400 CTCGCTGCATCCACCTCATC 60.879 60.000 0.00 0.00 0.00 2.92
859 871 1.145598 CTCGCTGCATCCACCTCAT 59.854 57.895 0.00 0.00 0.00 2.90
860 872 2.580815 CTCGCTGCATCCACCTCA 59.419 61.111 0.00 0.00 0.00 3.86
861 873 2.202987 CCTCGCTGCATCCACCTC 60.203 66.667 0.00 0.00 0.00 3.85
862 874 3.790437 CCCTCGCTGCATCCACCT 61.790 66.667 0.00 0.00 0.00 4.00
863 875 4.864334 CCCCTCGCTGCATCCACC 62.864 72.222 0.00 0.00 0.00 4.61
864 876 4.864334 CCCCCTCGCTGCATCCAC 62.864 72.222 0.00 0.00 0.00 4.02
884 896 1.641123 ATTAACGGTCGCGCAAAGGG 61.641 55.000 8.75 0.00 0.00 3.95
885 897 0.520412 CATTAACGGTCGCGCAAAGG 60.520 55.000 8.75 0.00 0.00 3.11
886 898 0.520412 CCATTAACGGTCGCGCAAAG 60.520 55.000 8.75 0.00 0.00 2.77
887 899 1.498166 CCATTAACGGTCGCGCAAA 59.502 52.632 8.75 0.00 0.00 3.68
888 900 2.392181 CCCATTAACGGTCGCGCAA 61.392 57.895 8.75 0.00 0.00 4.85
889 901 2.816083 CCCATTAACGGTCGCGCA 60.816 61.111 8.75 0.00 0.00 6.09
890 902 2.805807 GACCCATTAACGGTCGCGC 61.806 63.158 0.00 0.00 40.46 6.86
891 903 3.391355 GACCCATTAACGGTCGCG 58.609 61.111 0.00 0.00 40.46 5.87
895 907 7.283807 GGTCAATTAATTAGACCCATTAACGGT 59.716 37.037 24.65 0.00 44.72 4.83
896 908 7.645402 GGTCAATTAATTAGACCCATTAACGG 58.355 38.462 24.65 3.50 44.72 4.44
906 918 7.711339 AGGTCGAATCTGGTCAATTAATTAGAC 59.289 37.037 16.22 16.22 33.74 2.59
907 919 7.792032 AGGTCGAATCTGGTCAATTAATTAGA 58.208 34.615 0.00 0.69 0.00 2.10
908 920 8.438676 AAGGTCGAATCTGGTCAATTAATTAG 57.561 34.615 0.00 0.00 0.00 1.73
909 921 8.801882 AAAGGTCGAATCTGGTCAATTAATTA 57.198 30.769 0.00 0.00 0.00 1.40
910 922 7.148069 GGAAAGGTCGAATCTGGTCAATTAATT 60.148 37.037 0.00 0.00 0.00 1.40
911 923 6.318900 GGAAAGGTCGAATCTGGTCAATTAAT 59.681 38.462 0.00 0.00 0.00 1.40
912 924 5.646360 GGAAAGGTCGAATCTGGTCAATTAA 59.354 40.000 0.00 0.00 0.00 1.40
913 925 5.183228 GGAAAGGTCGAATCTGGTCAATTA 58.817 41.667 0.00 0.00 0.00 1.40
914 926 4.010349 GGAAAGGTCGAATCTGGTCAATT 58.990 43.478 0.00 0.00 0.00 2.32
915 927 3.610911 GGAAAGGTCGAATCTGGTCAAT 58.389 45.455 0.00 0.00 0.00 2.57
1258 1274 1.215679 AAGAGGGAGACGAGGAGGGA 61.216 60.000 0.00 0.00 0.00 4.20
1607 1629 6.104665 CACTTCTGAATTCTGATGCTCAGTA 58.895 40.000 20.98 4.61 44.58 2.74
1698 1789 3.087031 CCAATGTTCTTGTCCATCTGCT 58.913 45.455 0.00 0.00 0.00 4.24
1719 1810 2.401766 ACAGCGCAGTAGCCATTGC 61.402 57.895 11.47 0.00 37.52 3.56
1755 1846 6.014242 ACTTCAGTACCAGATGAATGTCTCAA 60.014 38.462 6.00 0.00 37.67 3.02
1761 1852 6.875726 TCAAGAACTTCAGTACCAGATGAATG 59.124 38.462 6.00 0.00 35.04 2.67
1762 1853 7.009179 TCAAGAACTTCAGTACCAGATGAAT 57.991 36.000 6.00 0.00 35.04 2.57
1780 1871 3.971305 TGGAGGTGTCCTTAACTCAAGAA 59.029 43.478 0.00 0.00 44.30 2.52
1785 1876 4.508662 CTGATTGGAGGTGTCCTTAACTC 58.491 47.826 0.00 0.00 44.30 3.01
1837 1928 2.094182 TCTAGCTTGACACGGACATTCC 60.094 50.000 0.00 0.00 0.00 3.01
1907 2019 2.169789 CACTCTTGCATCCTCCGCG 61.170 63.158 0.00 0.00 0.00 6.46
2078 2190 3.194005 TCCAGATACGCCAATTCTTCC 57.806 47.619 0.00 0.00 0.00 3.46
2091 2203 5.828328 TCGCTAAGAAGTCTTCATCCAGATA 59.172 40.000 14.97 0.00 37.40 1.98
2096 2208 5.503194 GCATTTCGCTAAGAAGTCTTCATCC 60.503 44.000 14.97 0.00 40.40 3.51
2117 2229 4.800914 GCTCGATATCCAAGGTTACAGCAT 60.801 45.833 0.00 0.00 0.00 3.79
2118 2230 3.492656 GCTCGATATCCAAGGTTACAGCA 60.493 47.826 0.00 0.00 0.00 4.41
2124 2236 1.341531 CTCCGCTCGATATCCAAGGTT 59.658 52.381 0.00 0.00 0.00 3.50
2125 2237 0.962489 CTCCGCTCGATATCCAAGGT 59.038 55.000 0.00 0.00 0.00 3.50
2191 2303 9.814899 TTTTCTGCATTTCTTCAAGATTTTGTA 57.185 25.926 0.00 0.00 35.73 2.41
2585 2697 6.741992 TGATAAACTAAATGCCAGTGTCAG 57.258 37.500 0.00 0.00 0.00 3.51
2603 2715 5.945191 TGTCAGCATGTCAAAAGGATGATAA 59.055 36.000 0.00 0.00 37.40 1.75
2803 2916 2.298729 TGTAAGTTGATTTTGGCAGGGC 59.701 45.455 0.00 0.00 0.00 5.19
2841 2954 2.816087 CAGGCAGCAACTACAACAATCT 59.184 45.455 0.00 0.00 0.00 2.40
2882 2995 3.553828 TGAAGGGGAAAATAGGCTACG 57.446 47.619 0.00 0.00 0.00 3.51
2918 3047 2.355209 GCAGGACTCTGTTCCCCTAAAG 60.355 54.545 0.00 0.00 42.78 1.85
2970 3099 9.959721 AATTGAAGTACCTGATAACACATTAGT 57.040 29.630 0.00 0.00 0.00 2.24
3033 3166 6.699204 TCATTTCAACAAATTGCGCTCTTTAA 59.301 30.769 9.73 0.00 35.63 1.52
3086 3223 7.334921 TGTTGTTAATGATAGACCTTTTACGGG 59.665 37.037 0.00 0.00 0.00 5.28
3219 3406 2.293677 TCACCGGATCGAGAAATGTG 57.706 50.000 9.46 0.00 0.00 3.21
3226 3413 2.871182 TCAGAAATCACCGGATCGAG 57.129 50.000 9.46 0.00 31.88 4.04
3229 3416 7.378966 TGTAGAATATCAGAAATCACCGGATC 58.621 38.462 9.46 0.00 31.88 3.36
3233 3420 6.931281 ACCATGTAGAATATCAGAAATCACCG 59.069 38.462 0.00 0.00 0.00 4.94
3261 3461 9.567776 TTATTCCTTGAGTAATGTTCAGAACAA 57.432 29.630 19.92 1.62 45.86 2.83
3359 3559 3.436704 AGTTGTAATGATGTTCACCGCAG 59.563 43.478 0.00 0.00 0.00 5.18
3496 3696 4.347453 CACAAGCAAGCACGCCCC 62.347 66.667 0.00 0.00 0.00 5.80
3503 3703 1.279840 GTGGTCGTCACAAGCAAGC 59.720 57.895 6.75 0.00 45.39 4.01
3565 3765 2.698855 TTGAGCCTGCCTTCTGATAC 57.301 50.000 0.00 0.00 0.00 2.24
3587 3787 8.414003 TGTATTTCTATCGTCACAGCTAATTCT 58.586 33.333 0.00 0.00 0.00 2.40
3666 3866 9.914131 AGTTGCAGTTTTTAGATAAAAATCCTC 57.086 29.630 12.29 2.26 44.16 3.71
3798 3998 8.939929 ACTTGTTTATGTAGACATGATTCAGTG 58.060 33.333 0.00 0.00 37.15 3.66
3828 4028 6.639632 ACATGGAACCTTATATTGATGCAC 57.360 37.500 0.00 0.00 0.00 4.57
3985 4185 9.243637 CTCTGTCTAACTATATGAGTTTTGCTC 57.756 37.037 0.70 0.00 46.79 4.26
3990 4192 9.647918 TCCATCTCTGTCTAACTATATGAGTTT 57.352 33.333 0.70 0.00 46.79 2.66
4036 4399 9.325198 GGACAACATTCTTTTCCTTAAAACATT 57.675 29.630 0.00 0.00 31.37 2.71
4044 4407 6.544928 AAACTGGACAACATTCTTTTCCTT 57.455 33.333 0.00 0.00 0.00 3.36
4081 4444 7.307632 GAGCATCAGGTGTGAATGTATTCATAC 60.308 40.741 19.85 19.85 44.36 2.39
4123 4492 5.473504 CCAGTATTGCAAGTTTGAACTACCT 59.526 40.000 4.94 0.00 38.57 3.08
4144 4513 1.870055 AAAGGATGCTTGCGTGCCAG 61.870 55.000 0.00 0.00 0.00 4.85
4223 4592 3.244561 CGGATATAGGTGAATTGCCCACT 60.245 47.826 0.00 0.00 35.05 4.00
4239 4608 8.887717 GCTAATCAGATTCTTATTTGCGGATAT 58.112 33.333 9.98 0.00 0.00 1.63
4246 4615 7.251704 ACACCGCTAATCAGATTCTTATTTG 57.748 36.000 0.00 0.00 0.00 2.32
4358 4832 6.144402 GTCTTATGCTTTGTGTGGAAAACATG 59.856 38.462 0.00 0.00 41.97 3.21
4372 4846 6.175471 TCATCATGTCAGTGTCTTATGCTTT 58.825 36.000 0.00 0.00 0.00 3.51
4437 4912 0.738975 TAGCTGCAGCACTACGGTAG 59.261 55.000 38.24 13.49 45.16 3.18
4452 4927 6.892658 AGATCGTTCTGACATAATCTAGCT 57.107 37.500 0.00 0.00 0.00 3.32
4454 4929 8.511321 AGCTAAGATCGTTCTGACATAATCTAG 58.489 37.037 0.00 0.00 30.72 2.43
4457 4932 6.920758 ACAGCTAAGATCGTTCTGACATAATC 59.079 38.462 14.20 0.00 30.72 1.75
4551 5026 5.584649 CACATTTTCATTCTCCTAGCGGTTA 59.415 40.000 0.00 0.00 0.00 2.85
4553 5028 3.941483 CACATTTTCATTCTCCTAGCGGT 59.059 43.478 0.00 0.00 0.00 5.68
4555 5030 4.728882 GCACACATTTTCATTCTCCTAGCG 60.729 45.833 0.00 0.00 0.00 4.26
4556 5031 4.156556 TGCACACATTTTCATTCTCCTAGC 59.843 41.667 0.00 0.00 0.00 3.42
4557 5032 5.885230 TGCACACATTTTCATTCTCCTAG 57.115 39.130 0.00 0.00 0.00 3.02
4558 5033 6.883756 TGTATGCACACATTTTCATTCTCCTA 59.116 34.615 0.00 0.00 37.74 2.94
4629 5104 2.394632 TGATAACCATGCTCCGGTACT 58.605 47.619 0.00 0.00 34.99 2.73
4751 5226 3.198582 CGAGAGGTTCCGTCTCCC 58.801 66.667 8.01 0.00 40.83 4.30
4791 5266 2.190981 GCCGATTACTGACCGTACTTG 58.809 52.381 0.00 0.00 0.00 3.16
4797 5272 0.739462 TGCTTGCCGATTACTGACCG 60.739 55.000 0.00 0.00 0.00 4.79
4809 5284 1.080298 GGCATGTCTTGTGCTTGCC 60.080 57.895 6.48 6.48 45.45 4.52
4810 5285 1.080298 GGGCATGTCTTGTGCTTGC 60.080 57.895 0.00 0.00 42.16 4.01
4817 5292 1.607178 TGCTTGGGGGCATGTCTTG 60.607 57.895 0.00 0.00 37.29 3.02
4876 5367 5.132312 AGTTATTAGTAGCCTTTTCCCCCTC 59.868 44.000 0.00 0.00 0.00 4.30
4919 5413 4.722361 TTCCACCCGGCAATATTTTTAC 57.278 40.909 0.00 0.00 0.00 2.01
4920 5414 5.017490 TCTTTCCACCCGGCAATATTTTTA 58.983 37.500 0.00 0.00 0.00 1.52
4921 5415 3.835395 TCTTTCCACCCGGCAATATTTTT 59.165 39.130 0.00 0.00 0.00 1.94
4922 5416 3.436243 TCTTTCCACCCGGCAATATTTT 58.564 40.909 0.00 0.00 0.00 1.82
4935 5429 6.174049 AGTACTATTGCTTTCCTCTTTCCAC 58.826 40.000 0.00 0.00 0.00 4.02
4936 5430 6.374417 AGTACTATTGCTTTCCTCTTTCCA 57.626 37.500 0.00 0.00 0.00 3.53
4952 5446 8.244802 CGAGCTGCCAAATAATAGTAGTACTAT 58.755 37.037 15.79 15.79 42.86 2.12
4955 5449 6.214399 ACGAGCTGCCAAATAATAGTAGTAC 58.786 40.000 0.00 0.00 0.00 2.73
4971 5465 2.889503 CTGCTGGCTACGAGCTGC 60.890 66.667 0.00 10.70 41.99 5.25
4973 5467 3.368190 CTGCTGCTGGCTACGAGCT 62.368 63.158 0.00 0.00 41.99 4.09
4974 5468 2.641439 ATCTGCTGCTGGCTACGAGC 62.641 60.000 6.69 0.00 42.39 5.03
4977 5471 0.387202 ACTATCTGCTGCTGGCTACG 59.613 55.000 6.69 0.00 42.39 3.51
4981 5475 0.463204 TCTCACTATCTGCTGCTGGC 59.537 55.000 6.69 0.00 42.22 4.85
4982 5476 2.935201 GTTTCTCACTATCTGCTGCTGG 59.065 50.000 6.69 0.00 0.00 4.85
4983 5477 3.593096 TGTTTCTCACTATCTGCTGCTG 58.407 45.455 0.00 0.00 0.00 4.41
4984 5478 3.513119 TCTGTTTCTCACTATCTGCTGCT 59.487 43.478 0.00 0.00 0.00 4.24
4985 5479 3.616379 GTCTGTTTCTCACTATCTGCTGC 59.384 47.826 0.00 0.00 0.00 5.25
4986 5480 3.856521 CGTCTGTTTCTCACTATCTGCTG 59.143 47.826 0.00 0.00 0.00 4.41
4987 5481 3.759086 TCGTCTGTTTCTCACTATCTGCT 59.241 43.478 0.00 0.00 0.00 4.24
4988 5482 3.854809 GTCGTCTGTTTCTCACTATCTGC 59.145 47.826 0.00 0.00 0.00 4.26
4989 5483 4.416620 GGTCGTCTGTTTCTCACTATCTG 58.583 47.826 0.00 0.00 0.00 2.90
4990 5484 3.127203 CGGTCGTCTGTTTCTCACTATCT 59.873 47.826 0.00 0.00 0.00 1.98
4991 5485 3.126514 TCGGTCGTCTGTTTCTCACTATC 59.873 47.826 0.00 0.00 0.00 2.08
4992 5486 3.079578 TCGGTCGTCTGTTTCTCACTAT 58.920 45.455 0.00 0.00 0.00 2.12
4993 5487 2.225019 GTCGGTCGTCTGTTTCTCACTA 59.775 50.000 0.00 0.00 0.00 2.74
4994 5488 1.001597 GTCGGTCGTCTGTTTCTCACT 60.002 52.381 0.00 0.00 0.00 3.41
4995 5489 1.406447 GTCGGTCGTCTGTTTCTCAC 58.594 55.000 0.00 0.00 0.00 3.51
4996 5490 0.040692 CGTCGGTCGTCTGTTTCTCA 60.041 55.000 0.00 0.00 34.52 3.27
4997 5491 0.728466 CCGTCGGTCGTCTGTTTCTC 60.728 60.000 2.08 0.00 37.94 2.87
5001 5495 4.695231 CGCCGTCGGTCGTCTGTT 62.695 66.667 13.94 0.00 37.94 3.16
5023 5517 1.262640 TGGTAACCTTCCGGCCTCTC 61.263 60.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.