Multiple sequence alignment - TraesCS2B01G479400

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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 TraesCS2B01G479400 chr2B 100.000 4121 0 0 1 4121 676745595 676749715 0.000000e+00 7611
1 TraesCS2B01G479400 chr2B 95.184 706 31 2 3417 4121 551112863 551113566 0.000000e+00 1112
2 TraesCS2B01G479400 chr2B 80.808 198 33 5 654 847 94868946 94869142 2.570000e-32 150
3 TraesCS2B01G479400 chr2B 80.526 190 36 1 654 842 731563193 731563382 1.190000e-30 145
4 TraesCS2B01G479400 chr2A 93.157 2499 95 20 838 3298 705530707 705533167 0.000000e+00 3598
5 TraesCS2B01G479400 chr2D 92.340 2415 89 22 838 3199 565076268 565078639 0.000000e+00 3347
6 TraesCS2B01G479400 chr2D 93.900 2246 73 17 909 3135 565089726 565091926 0.000000e+00 3330
7 TraesCS2B01G479400 chr2D 93.072 2223 87 17 1005 3199 565051787 565053970 0.000000e+00 3190
8 TraesCS2B01G479400 chr2D 89.944 179 12 4 3126 3299 565091950 565092127 4.140000e-55 226
9 TraesCS2B01G479400 chr2D 93.388 121 7 1 3296 3416 192977568 192977449 1.180000e-40 178
10 TraesCS2B01G479400 chr2D 95.283 106 3 1 838 941 565051675 565051780 2.550000e-37 167
11 TraesCS2B01G479400 chr4A 82.246 1977 234 64 1113 3059 698171069 698169180 0.000000e+00 1598
12 TraesCS2B01G479400 chr4A 81.491 1972 245 57 1116 3057 698935404 698933523 0.000000e+00 1509
13 TraesCS2B01G479400 chr4A 80.880 1637 208 61 1484 3085 698804979 698803413 0.000000e+00 1192
14 TraesCS2B01G479400 chr4A 83.227 787 94 24 2322 3085 698926088 698925317 0.000000e+00 688
15 TraesCS2B01G479400 chr4A 82.242 794 111 16 1116 1906 698826680 698825914 0.000000e+00 658
16 TraesCS2B01G479400 chr4A 85.388 219 20 10 2853 3059 698800806 698800588 2.490000e-52 217
17 TraesCS2B01G479400 chr4A 83.598 189 28 3 2893 3079 699014171 699014358 1.520000e-39 174
18 TraesCS2B01G479400 chr4A 84.138 145 23 0 696 840 655671827 655671971 1.540000e-29 141
19 TraesCS2B01G479400 chr4A 80.864 162 30 1 650 811 701060988 701061148 4.320000e-25 126
20 TraesCS2B01G479400 chr7A 81.998 1972 227 71 1113 3059 30651193 30653061 0.000000e+00 1557
21 TraesCS2B01G479400 chr7D 81.463 1969 237 69 1113 3059 30264384 30266246 0.000000e+00 1496
22 TraesCS2B01G479400 chr7D 95.211 522 18 3 1 521 39032762 39033277 0.000000e+00 819
23 TraesCS2B01G479400 chr7D 93.204 309 18 3 545 851 39033457 39033764 6.280000e-123 451
24 TraesCS2B01G479400 chr4B 95.474 707 27 4 3417 4121 364222050 364222753 0.000000e+00 1123
25 TraesCS2B01G479400 chr4B 81.013 158 16 11 688 838 128034124 128033974 3.370000e-21 113
26 TraesCS2B01G479400 chr7B 95.332 707 29 3 3417 4121 638462643 638461939 0.000000e+00 1120
27 TraesCS2B01G479400 chr7B 94.201 707 38 2 3417 4121 64693161 64692456 0.000000e+00 1075
28 TraesCS2B01G479400 chr7B 96.016 502 14 2 1 501 702458324 702458820 0.000000e+00 811
29 TraesCS2B01G479400 chr7B 94.677 263 14 0 576 838 702459062 702459324 3.830000e-110 409
30 TraesCS2B01G479400 chrUn 94.915 708 29 4 3418 4121 39266746 39267450 0.000000e+00 1101
31 TraesCS2B01G479400 chr3B 94.774 708 30 6 3419 4121 171118271 171117566 0.000000e+00 1096
32 TraesCS2B01G479400 chr3B 93.935 709 37 3 3419 4121 6649187 6648479 0.000000e+00 1066
33 TraesCS2B01G479400 chr5B 93.768 706 38 3 3417 4121 522025692 522026392 0.000000e+00 1055
34 TraesCS2B01G479400 chr5B 90.805 522 20 5 1 521 693913887 693913393 0.000000e+00 673
35 TraesCS2B01G479400 chr5B 94.983 299 12 3 545 840 693913185 693912887 2.240000e-127 466
36 TraesCS2B01G479400 chr5A 93.362 708 42 3 3417 4121 71363410 71364115 0.000000e+00 1042
37 TraesCS2B01G479400 chr6D 95.211 522 18 3 1 521 319683526 319684041 0.000000e+00 819
38 TraesCS2B01G479400 chr6D 91.837 294 15 3 545 838 319684221 319684505 6.420000e-108 401
39 TraesCS2B01G479400 chr6D 75.904 664 137 13 2137 2799 134741436 134740795 6.650000e-83 318
40 TraesCS2B01G479400 chr6D 75.831 662 136 14 2137 2797 134336495 134335857 8.600000e-82 315
41 TraesCS2B01G479400 chr6B 75.789 665 132 19 2137 2797 233087917 233087278 4.000000e-80 309
42 TraesCS2B01G479400 chr6A 75.753 664 134 14 2137 2797 175996579 175995940 4.000000e-80 309
43 TraesCS2B01G479400 chr1B 95.041 121 6 0 3297 3417 61019154 61019274 1.510000e-44 191
44 TraesCS2B01G479400 chr3A 93.277 119 8 0 3297 3415 47050265 47050383 4.230000e-40 176


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 TraesCS2B01G479400 chr2B 676745595 676749715 4120 False 7611.0 7611 100.0000 1 4121 1 chr2B.!!$F3 4120
1 TraesCS2B01G479400 chr2B 551112863 551113566 703 False 1112.0 1112 95.1840 3417 4121 1 chr2B.!!$F2 704
2 TraesCS2B01G479400 chr2A 705530707 705533167 2460 False 3598.0 3598 93.1570 838 3298 1 chr2A.!!$F1 2460
3 TraesCS2B01G479400 chr2D 565076268 565078639 2371 False 3347.0 3347 92.3400 838 3199 1 chr2D.!!$F1 2361
4 TraesCS2B01G479400 chr2D 565089726 565092127 2401 False 1778.0 3330 91.9220 909 3299 2 chr2D.!!$F3 2390
5 TraesCS2B01G479400 chr2D 565051675 565053970 2295 False 1678.5 3190 94.1775 838 3199 2 chr2D.!!$F2 2361
6 TraesCS2B01G479400 chr4A 698169180 698171069 1889 True 1598.0 1598 82.2460 1113 3059 1 chr4A.!!$R1 1946
7 TraesCS2B01G479400 chr4A 698933523 698935404 1881 True 1509.0 1509 81.4910 1116 3057 1 chr4A.!!$R4 1941
8 TraesCS2B01G479400 chr4A 698800588 698804979 4391 True 704.5 1192 83.1340 1484 3085 2 chr4A.!!$R5 1601
9 TraesCS2B01G479400 chr4A 698925317 698926088 771 True 688.0 688 83.2270 2322 3085 1 chr4A.!!$R3 763
10 TraesCS2B01G479400 chr4A 698825914 698826680 766 True 658.0 658 82.2420 1116 1906 1 chr4A.!!$R2 790
11 TraesCS2B01G479400 chr7A 30651193 30653061 1868 False 1557.0 1557 81.9980 1113 3059 1 chr7A.!!$F1 1946
12 TraesCS2B01G479400 chr7D 30264384 30266246 1862 False 1496.0 1496 81.4630 1113 3059 1 chr7D.!!$F1 1946
13 TraesCS2B01G479400 chr7D 39032762 39033764 1002 False 635.0 819 94.2075 1 851 2 chr7D.!!$F2 850
14 TraesCS2B01G479400 chr4B 364222050 364222753 703 False 1123.0 1123 95.4740 3417 4121 1 chr4B.!!$F1 704
15 TraesCS2B01G479400 chr7B 638461939 638462643 704 True 1120.0 1120 95.3320 3417 4121 1 chr7B.!!$R2 704
16 TraesCS2B01G479400 chr7B 64692456 64693161 705 True 1075.0 1075 94.2010 3417 4121 1 chr7B.!!$R1 704
17 TraesCS2B01G479400 chr7B 702458324 702459324 1000 False 610.0 811 95.3465 1 838 2 chr7B.!!$F1 837
18 TraesCS2B01G479400 chrUn 39266746 39267450 704 False 1101.0 1101 94.9150 3418 4121 1 chrUn.!!$F1 703
19 TraesCS2B01G479400 chr3B 171117566 171118271 705 True 1096.0 1096 94.7740 3419 4121 1 chr3B.!!$R2 702
20 TraesCS2B01G479400 chr3B 6648479 6649187 708 True 1066.0 1066 93.9350 3419 4121 1 chr3B.!!$R1 702
21 TraesCS2B01G479400 chr5B 522025692 522026392 700 False 1055.0 1055 93.7680 3417 4121 1 chr5B.!!$F1 704
22 TraesCS2B01G479400 chr5B 693912887 693913887 1000 True 569.5 673 92.8940 1 840 2 chr5B.!!$R1 839
23 TraesCS2B01G479400 chr5A 71363410 71364115 705 False 1042.0 1042 93.3620 3417 4121 1 chr5A.!!$F1 704
24 TraesCS2B01G479400 chr6D 319683526 319684505 979 False 610.0 819 93.5240 1 838 2 chr6D.!!$F1 837
25 TraesCS2B01G479400 chr6D 134740795 134741436 641 True 318.0 318 75.9040 2137 2799 1 chr6D.!!$R2 662
26 TraesCS2B01G479400 chr6D 134335857 134336495 638 True 315.0 315 75.8310 2137 2797 1 chr6D.!!$R1 660
27 TraesCS2B01G479400 chr6B 233087278 233087917 639 True 309.0 309 75.7890 2137 2797 1 chr6B.!!$R1 660
28 TraesCS2B01G479400 chr6A 175995940 175996579 639 True 309.0 309 75.7530 2137 2797 1 chr6A.!!$R1 660

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
537 539 0.398696 TGCCAACGGTTGAGTGGTAT 59.601 50.0 21.88 0.0 0.0 2.73 F
1507 1758 0.030101 CTTCTCCATCTCGAGCGACC 59.970 60.0 7.81 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 2043 2.514824 GGCGGATCCTTGAGTGGC 60.515 66.667 10.75 3.44 0.0 5.01 R
3359 3802 0.037326 TTGCACGGTGGTCTCATCTC 60.037 55.000 10.60 0.00 0.0 2.75 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
437 439 6.097554 CCATTTTACCCCACAAGTGCATTATA 59.902 38.462 0.00 0.00 0.00 0.98
535 537 1.077357 TTGCCAACGGTTGAGTGGT 60.077 52.632 21.88 0.00 0.00 4.16
537 539 0.398696 TGCCAACGGTTGAGTGGTAT 59.601 50.000 21.88 0.00 0.00 2.73
538 540 0.802494 GCCAACGGTTGAGTGGTATG 59.198 55.000 21.88 4.00 0.00 2.39
540 542 1.804151 CCAACGGTTGAGTGGTATGTG 59.196 52.381 21.88 0.00 0.00 3.21
542 544 3.135225 CAACGGTTGAGTGGTATGTGAA 58.865 45.455 15.66 0.00 0.00 3.18
664 878 1.029947 TCTACCGATCGCTGACAGCA 61.030 55.000 26.32 14.14 42.58 4.41
703 917 2.181777 GCCTCGTCAGCATCGTGA 59.818 61.111 0.00 0.00 0.00 4.35
769 983 4.602340 AGTTGTAGAACCAGTTCGATGT 57.398 40.909 4.94 0.00 43.97 3.06
770 984 5.717078 AGTTGTAGAACCAGTTCGATGTA 57.283 39.130 4.94 0.00 43.97 2.29
771 985 6.282199 AGTTGTAGAACCAGTTCGATGTAT 57.718 37.500 4.94 0.00 43.97 2.29
772 986 6.698380 AGTTGTAGAACCAGTTCGATGTATT 58.302 36.000 4.94 0.00 43.97 1.89
773 987 7.159372 AGTTGTAGAACCAGTTCGATGTATTT 58.841 34.615 4.94 0.00 43.97 1.40
774 988 7.660208 AGTTGTAGAACCAGTTCGATGTATTTT 59.340 33.333 4.94 0.00 43.97 1.82
775 989 8.928733 GTTGTAGAACCAGTTCGATGTATTTTA 58.071 33.333 4.94 0.00 43.97 1.52
776 990 8.470040 TGTAGAACCAGTTCGATGTATTTTAC 57.530 34.615 4.94 0.71 43.97 2.01
777 991 8.089597 TGTAGAACCAGTTCGATGTATTTTACA 58.910 33.333 4.94 3.00 43.97 2.41
778 992 7.972832 AGAACCAGTTCGATGTATTTTACAA 57.027 32.000 4.94 0.00 43.97 2.41
779 993 8.029642 AGAACCAGTTCGATGTATTTTACAAG 57.970 34.615 4.94 0.00 43.97 3.16
780 994 7.660208 AGAACCAGTTCGATGTATTTTACAAGT 59.340 33.333 4.94 0.00 43.97 3.16
781 995 7.739498 ACCAGTTCGATGTATTTTACAAGTT 57.261 32.000 0.00 0.00 42.76 2.66
782 996 7.803724 ACCAGTTCGATGTATTTTACAAGTTC 58.196 34.615 0.00 0.00 42.76 3.01
783 997 7.442969 ACCAGTTCGATGTATTTTACAAGTTCA 59.557 33.333 0.00 0.00 42.76 3.18
784 998 7.957484 CCAGTTCGATGTATTTTACAAGTTCAG 59.043 37.037 0.00 0.00 42.76 3.02
785 999 7.957484 CAGTTCGATGTATTTTACAAGTTCAGG 59.043 37.037 0.00 0.00 42.76 3.86
786 1000 6.417191 TCGATGTATTTTACAAGTTCAGGC 57.583 37.500 0.00 0.00 42.76 4.85
787 1001 5.935206 TCGATGTATTTTACAAGTTCAGGCA 59.065 36.000 0.00 0.00 42.76 4.75
788 1002 6.021596 CGATGTATTTTACAAGTTCAGGCAC 58.978 40.000 0.00 0.00 42.76 5.01
789 1003 6.128282 CGATGTATTTTACAAGTTCAGGCACT 60.128 38.462 0.00 0.00 42.76 4.40
790 1004 7.064134 CGATGTATTTTACAAGTTCAGGCACTA 59.936 37.037 0.00 0.00 42.76 2.74
791 1005 8.630054 ATGTATTTTACAAGTTCAGGCACTAA 57.370 30.769 0.00 0.00 42.76 2.24
792 1006 8.453238 TGTATTTTACAAGTTCAGGCACTAAA 57.547 30.769 0.00 0.00 33.36 1.85
793 1007 9.073475 TGTATTTTACAAGTTCAGGCACTAAAT 57.927 29.630 0.00 0.00 33.36 1.40
794 1008 9.908152 GTATTTTACAAGTTCAGGCACTAAATT 57.092 29.630 0.00 0.00 36.02 1.82
795 1009 8.816640 ATTTTACAAGTTCAGGCACTAAATTG 57.183 30.769 5.51 5.51 36.02 2.32
796 1010 4.243007 ACAAGTTCAGGCACTAAATTGC 57.757 40.909 6.59 0.00 42.18 3.56
797 1011 3.636300 ACAAGTTCAGGCACTAAATTGCA 59.364 39.130 6.59 0.00 44.94 4.08
798 1012 3.923017 AGTTCAGGCACTAAATTGCAC 57.077 42.857 0.00 0.00 44.94 4.57
799 1013 3.221771 AGTTCAGGCACTAAATTGCACA 58.778 40.909 0.00 0.00 44.94 4.57
800 1014 3.004734 AGTTCAGGCACTAAATTGCACAC 59.995 43.478 0.00 0.00 44.94 3.82
801 1015 2.862541 TCAGGCACTAAATTGCACACT 58.137 42.857 0.00 0.00 44.94 3.55
802 1016 3.221771 TCAGGCACTAAATTGCACACTT 58.778 40.909 0.00 0.00 44.94 3.16
803 1017 3.004629 TCAGGCACTAAATTGCACACTTG 59.995 43.478 0.00 0.00 44.94 3.16
804 1018 2.958355 AGGCACTAAATTGCACACTTGT 59.042 40.909 0.00 0.00 44.94 3.16
805 1019 3.052036 GGCACTAAATTGCACACTTGTG 58.948 45.455 4.92 4.92 44.94 3.33
806 1020 3.052036 GCACTAAATTGCACACTTGTGG 58.948 45.455 11.27 0.00 45.72 4.17
807 1021 3.052036 CACTAAATTGCACACTTGTGGC 58.948 45.455 11.27 7.00 45.72 5.01
808 1022 2.692557 ACTAAATTGCACACTTGTGGCA 59.307 40.909 11.27 9.25 45.72 4.92
809 1023 2.687700 AAATTGCACACTTGTGGCAA 57.312 40.000 21.98 21.98 45.72 4.52
810 1024 2.228138 AATTGCACACTTGTGGCAAG 57.772 45.000 23.10 7.27 45.72 4.01
811 1025 1.113788 ATTGCACACTTGTGGCAAGT 58.886 45.000 23.10 8.53 45.72 3.16
812 1026 0.894141 TTGCACACTTGTGGCAAGTT 59.106 45.000 18.49 2.37 45.72 2.66
813 1027 0.455410 TGCACACTTGTGGCAAGTTC 59.545 50.000 11.32 5.57 45.72 3.01
814 1028 0.455410 GCACACTTGTGGCAAGTTCA 59.545 50.000 11.32 0.00 45.72 3.18
815 1029 1.135141 GCACACTTGTGGCAAGTTCAA 60.135 47.619 11.32 0.00 45.72 2.69
816 1030 2.801063 CACACTTGTGGCAAGTTCAAG 58.199 47.619 11.32 12.46 42.10 3.02
817 1031 1.134946 ACACTTGTGGCAAGTTCAAGC 59.865 47.619 13.61 0.00 41.22 4.01
818 1032 1.134753 CACTTGTGGCAAGTTCAAGCA 59.865 47.619 13.61 0.00 41.22 3.91
819 1033 1.134946 ACTTGTGGCAAGTTCAAGCAC 59.865 47.619 13.61 0.00 41.22 4.40
820 1034 1.406539 CTTGTGGCAAGTTCAAGCACT 59.593 47.619 3.07 0.00 33.51 4.40
821 1035 2.340210 TGTGGCAAGTTCAAGCACTA 57.660 45.000 0.00 0.00 0.00 2.74
822 1036 2.221169 TGTGGCAAGTTCAAGCACTAG 58.779 47.619 0.00 0.00 0.00 2.57
823 1037 2.222027 GTGGCAAGTTCAAGCACTAGT 58.778 47.619 0.00 0.00 0.00 2.57
824 1038 2.031682 GTGGCAAGTTCAAGCACTAGTG 60.032 50.000 18.93 18.93 0.00 2.74
825 1039 1.537202 GGCAAGTTCAAGCACTAGTGG 59.463 52.381 23.95 8.08 0.00 4.00
826 1040 2.222027 GCAAGTTCAAGCACTAGTGGT 58.778 47.619 21.62 21.62 44.00 4.16
827 1041 3.399330 GCAAGTTCAAGCACTAGTGGTA 58.601 45.455 26.75 10.64 40.87 3.25
828 1042 4.003648 GCAAGTTCAAGCACTAGTGGTAT 58.996 43.478 26.75 14.49 40.87 2.73
829 1043 5.175859 GCAAGTTCAAGCACTAGTGGTATA 58.824 41.667 26.75 15.36 40.87 1.47
830 1044 5.642063 GCAAGTTCAAGCACTAGTGGTATAA 59.358 40.000 26.75 19.82 40.87 0.98
831 1045 6.316390 GCAAGTTCAAGCACTAGTGGTATAAT 59.684 38.462 26.75 9.52 40.87 1.28
832 1046 7.148239 GCAAGTTCAAGCACTAGTGGTATAATT 60.148 37.037 26.75 16.94 40.87 1.40
833 1047 9.378551 CAAGTTCAAGCACTAGTGGTATAATTA 57.621 33.333 26.75 7.84 40.87 1.40
834 1048 8.943909 AGTTCAAGCACTAGTGGTATAATTAC 57.056 34.615 26.75 17.47 40.87 1.89
836 1050 7.670605 TCAAGCACTAGTGGTATAATTACCT 57.329 36.000 26.75 6.16 46.96 3.08
998 1240 2.832201 GCATCCTGCAGGGGAAGC 60.832 66.667 32.23 24.42 44.26 3.86
1010 1252 0.526211 GGGGAAGCGATGAACCAAAC 59.474 55.000 0.00 0.00 0.00 2.93
1111 1353 2.497675 CTCCTCATTTCGTTCCTCCTCA 59.502 50.000 0.00 0.00 0.00 3.86
1118 1360 1.444553 CGTTCCTCCTCACGCTGTC 60.445 63.158 0.00 0.00 0.00 3.51
1233 1478 2.203195 AGCAAGAGCAACCACGCA 60.203 55.556 0.00 0.00 45.49 5.24
1248 1493 2.347490 GCAAACTCCTCCTCGGCA 59.653 61.111 0.00 0.00 0.00 5.69
1498 1749 3.655615 ACGAGACCTACTTCTCCATCT 57.344 47.619 0.00 0.00 39.18 2.90
1507 1758 0.030101 CTTCTCCATCTCGAGCGACC 59.970 60.000 7.81 0.00 0.00 4.79
1868 2135 3.771160 ACCAGCACCGTCCGATCC 61.771 66.667 0.00 0.00 0.00 3.36
1999 2272 2.414825 GTGCTTGCTCTCTTCTTGCTAC 59.585 50.000 0.00 0.00 0.00 3.58
2127 2418 3.134127 GCGTCCTTGATGTGGCCC 61.134 66.667 0.00 0.00 0.00 5.80
2399 2717 3.110178 GGTGTTCGAGTTCGCCGG 61.110 66.667 0.00 0.00 39.60 6.13
2636 2960 4.470170 CGCGATCACCACGGACGA 62.470 66.667 0.00 0.00 0.00 4.20
2637 2961 2.879462 GCGATCACCACGGACGAC 60.879 66.667 0.00 0.00 0.00 4.34
2725 3055 2.035312 AGTACCTCGAGCACGGGT 59.965 61.111 17.49 17.49 42.40 5.28
2815 3145 1.828832 GGCTAGACAAGACGATGACG 58.171 55.000 0.00 0.00 45.75 4.35
3051 3426 2.711922 GCTCCTTTCGCTCTCGGGA 61.712 63.158 0.00 0.00 36.13 5.14
3107 3493 4.351938 TGACGGCACCGGAACTCG 62.352 66.667 9.46 9.13 44.69 4.18
3132 3558 5.421056 TCACGAACAATAGGTCCAGATTACT 59.579 40.000 0.00 0.00 0.00 2.24
3133 3559 6.604396 TCACGAACAATAGGTCCAGATTACTA 59.396 38.462 0.00 0.00 0.00 1.82
3134 3560 6.696148 CACGAACAATAGGTCCAGATTACTAC 59.304 42.308 0.00 0.00 0.00 2.73
3135 3561 6.606395 ACGAACAATAGGTCCAGATTACTACT 59.394 38.462 0.00 0.00 0.00 2.57
3136 3562 6.918569 CGAACAATAGGTCCAGATTACTACTG 59.081 42.308 0.00 0.00 35.43 2.74
3137 3563 7.416438 CGAACAATAGGTCCAGATTACTACTGT 60.416 40.741 0.00 0.00 34.04 3.55
3138 3564 7.113658 ACAATAGGTCCAGATTACTACTGTG 57.886 40.000 0.00 0.00 34.04 3.66
3139 3565 5.793030 ATAGGTCCAGATTACTACTGTGC 57.207 43.478 0.00 0.00 34.04 4.57
3180 3607 4.950744 ACCGTCGGTGTACTTTCG 57.049 55.556 18.08 0.00 32.98 3.46
3209 3640 5.128171 ACGTAGGCATCTTATGGACTTGTAA 59.872 40.000 0.00 0.00 0.00 2.41
3213 3644 4.319766 GGCATCTTATGGACTTGTAATGCG 60.320 45.833 0.00 0.00 32.68 4.73
3218 3649 6.345298 TCTTATGGACTTGTAATGCGATCAA 58.655 36.000 0.00 0.00 0.00 2.57
3227 3658 6.257411 ACTTGTAATGCGATCAAGATCAGAAG 59.743 38.462 10.39 6.74 40.35 2.85
3235 3666 5.582665 GCGATCAAGATCAGAAGTAAACCTT 59.417 40.000 10.39 0.00 37.69 3.50
3254 3685 3.499918 CCTTGGCACTGAAGTAAACTCAG 59.500 47.826 0.00 0.00 37.50 3.35
3301 3744 8.636213 TCTTGTTAGTATTAAGATCGTTAGGGG 58.364 37.037 0.00 0.00 0.00 4.79
3303 3746 6.324512 TGTTAGTATTAAGATCGTTAGGGGCA 59.675 38.462 0.00 0.00 0.00 5.36
3304 3747 7.015877 TGTTAGTATTAAGATCGTTAGGGGCAT 59.984 37.037 0.00 0.00 0.00 4.40
3306 3749 4.706842 ATTAAGATCGTTAGGGGCATGT 57.293 40.909 0.00 0.00 0.00 3.21
3307 3750 5.818678 ATTAAGATCGTTAGGGGCATGTA 57.181 39.130 0.00 0.00 0.00 2.29
3308 3751 3.470645 AAGATCGTTAGGGGCATGTAC 57.529 47.619 0.00 0.00 0.00 2.90
3309 3752 2.394632 AGATCGTTAGGGGCATGTACA 58.605 47.619 0.00 0.00 0.00 2.90
3310 3753 2.769663 AGATCGTTAGGGGCATGTACAA 59.230 45.455 0.00 0.00 0.00 2.41
3311 3754 3.391296 AGATCGTTAGGGGCATGTACAAT 59.609 43.478 0.00 0.00 0.00 2.71
3312 3755 2.912771 TCGTTAGGGGCATGTACAATG 58.087 47.619 0.00 0.12 0.00 2.82
3313 3756 1.946768 CGTTAGGGGCATGTACAATGG 59.053 52.381 0.00 0.00 0.00 3.16
3314 3757 2.682563 CGTTAGGGGCATGTACAATGGT 60.683 50.000 0.00 0.00 0.00 3.55
3315 3758 3.432467 CGTTAGGGGCATGTACAATGGTA 60.432 47.826 0.00 0.00 0.00 3.25
3316 3759 4.134563 GTTAGGGGCATGTACAATGGTAG 58.865 47.826 0.00 0.00 0.00 3.18
3317 3760 2.205342 AGGGGCATGTACAATGGTAGT 58.795 47.619 0.00 0.00 0.00 2.73
3318 3761 3.389866 AGGGGCATGTACAATGGTAGTA 58.610 45.455 0.00 0.00 0.00 1.82
3319 3762 3.980698 AGGGGCATGTACAATGGTAGTAT 59.019 43.478 0.00 0.00 0.00 2.12
3320 3763 4.415512 AGGGGCATGTACAATGGTAGTATT 59.584 41.667 0.00 0.00 0.00 1.89
3322 3765 5.704053 GGGGCATGTACAATGGTAGTATTAC 59.296 44.000 0.00 0.00 0.00 1.89
3335 3778 4.102681 GGTAGTATTACCTTGGTGATGCCT 59.897 45.833 7.17 5.83 45.01 4.75
3336 3779 4.423625 AGTATTACCTTGGTGATGCCTC 57.576 45.455 7.25 0.00 38.35 4.70
3337 3780 3.780294 AGTATTACCTTGGTGATGCCTCA 59.220 43.478 7.25 0.00 38.35 3.86
3338 3781 2.787473 TTACCTTGGTGATGCCTCAG 57.213 50.000 2.03 0.00 38.35 3.35
3339 3782 1.656587 TACCTTGGTGATGCCTCAGT 58.343 50.000 2.03 0.00 38.35 3.41
3340 3783 1.656587 ACCTTGGTGATGCCTCAGTA 58.343 50.000 0.00 0.00 38.35 2.74
3341 3784 1.279271 ACCTTGGTGATGCCTCAGTAC 59.721 52.381 0.00 0.00 38.35 2.73
3342 3785 1.278985 CCTTGGTGATGCCTCAGTACA 59.721 52.381 0.00 0.00 38.35 2.90
3343 3786 2.625737 CTTGGTGATGCCTCAGTACAG 58.374 52.381 0.00 0.00 38.35 2.74
3344 3787 0.250234 TGGTGATGCCTCAGTACAGC 59.750 55.000 0.00 0.00 38.35 4.40
3345 3788 0.462759 GGTGATGCCTCAGTACAGCC 60.463 60.000 0.00 0.00 30.18 4.85
3347 3790 0.250234 TGATGCCTCAGTACAGCCAC 59.750 55.000 0.00 0.00 0.00 5.01
3349 3792 1.544825 ATGCCTCAGTACAGCCACGT 61.545 55.000 0.00 0.00 0.00 4.49
3350 3793 1.446272 GCCTCAGTACAGCCACGTC 60.446 63.158 0.00 0.00 0.00 4.34
3351 3794 1.154016 CCTCAGTACAGCCACGTCG 60.154 63.158 0.00 0.00 0.00 5.12
3352 3795 1.154016 CTCAGTACAGCCACGTCGG 60.154 63.158 0.00 0.00 38.11 4.79
3353 3796 1.863662 CTCAGTACAGCCACGTCGGT 61.864 60.000 0.00 0.00 36.97 4.69
3354 3797 1.443872 CAGTACAGCCACGTCGGTC 60.444 63.158 0.00 0.03 36.97 4.79
3355 3798 1.900016 AGTACAGCCACGTCGGTCA 60.900 57.895 0.00 0.00 36.97 4.02
3356 3799 1.443872 GTACAGCCACGTCGGTCAG 60.444 63.158 0.00 0.48 36.97 3.51
3357 3800 2.632544 TACAGCCACGTCGGTCAGG 61.633 63.158 0.00 0.00 36.97 3.86
3358 3801 3.680786 CAGCCACGTCGGTCAGGA 61.681 66.667 0.00 0.00 36.97 3.86
3359 3802 3.374402 AGCCACGTCGGTCAGGAG 61.374 66.667 0.00 0.00 36.97 3.69
3360 3803 3.371063 GCCACGTCGGTCAGGAGA 61.371 66.667 0.00 0.00 36.97 3.71
3361 3804 2.878429 CCACGTCGGTCAGGAGAG 59.122 66.667 0.00 0.00 0.00 3.20
3362 3805 1.674651 CCACGTCGGTCAGGAGAGA 60.675 63.158 0.00 0.00 0.00 3.10
3363 3806 1.032657 CCACGTCGGTCAGGAGAGAT 61.033 60.000 0.00 0.00 0.00 2.75
3364 3807 0.099613 CACGTCGGTCAGGAGAGATG 59.900 60.000 0.00 0.00 0.00 2.90
3365 3808 0.035343 ACGTCGGTCAGGAGAGATGA 60.035 55.000 0.00 0.00 0.00 2.92
3367 3810 1.744114 CGTCGGTCAGGAGAGATGAGA 60.744 57.143 0.00 0.00 0.00 3.27
3368 3811 1.673920 GTCGGTCAGGAGAGATGAGAC 59.326 57.143 0.00 0.00 0.00 3.36
3369 3812 1.028905 CGGTCAGGAGAGATGAGACC 58.971 60.000 0.00 0.00 44.05 3.85
3370 3813 2.151502 GGTCAGGAGAGATGAGACCA 57.848 55.000 0.00 0.00 46.15 4.02
3371 3814 1.754226 GGTCAGGAGAGATGAGACCAC 59.246 57.143 0.00 0.00 46.15 4.16
3372 3815 1.754226 GTCAGGAGAGATGAGACCACC 59.246 57.143 0.00 0.00 0.00 4.61
3376 3819 0.179124 GAGAGATGAGACCACCGTGC 60.179 60.000 0.00 0.00 0.00 5.34
3377 3820 0.900182 AGAGATGAGACCACCGTGCA 60.900 55.000 0.00 0.00 0.00 4.57
3379 3822 0.615331 AGATGAGACCACCGTGCAAT 59.385 50.000 0.00 0.00 0.00 3.56
3381 3824 1.812571 GATGAGACCACCGTGCAATTT 59.187 47.619 0.00 0.00 0.00 1.82
3382 3825 1.234821 TGAGACCACCGTGCAATTTC 58.765 50.000 0.00 0.00 0.00 2.17
3383 3826 1.234821 GAGACCACCGTGCAATTTCA 58.765 50.000 0.00 0.00 0.00 2.69
3384 3827 0.951558 AGACCACCGTGCAATTTCAC 59.048 50.000 0.00 0.00 0.00 3.18
3385 3828 0.665835 GACCACCGTGCAATTTCACA 59.334 50.000 8.92 0.00 36.80 3.58
3386 3829 0.383949 ACCACCGTGCAATTTCACAC 59.616 50.000 8.92 1.49 36.80 3.82
3387 3830 0.318614 CCACCGTGCAATTTCACACC 60.319 55.000 8.92 0.00 36.80 4.16
3388 3831 0.667993 CACCGTGCAATTTCACACCT 59.332 50.000 8.92 0.00 36.80 4.00
3389 3832 1.876799 CACCGTGCAATTTCACACCTA 59.123 47.619 8.92 0.00 36.80 3.08
3390 3833 2.487762 CACCGTGCAATTTCACACCTAT 59.512 45.455 8.92 0.00 36.80 2.57
3391 3834 2.747446 ACCGTGCAATTTCACACCTATC 59.253 45.455 8.92 0.00 36.80 2.08
3392 3835 2.097466 CCGTGCAATTTCACACCTATCC 59.903 50.000 8.92 0.00 36.80 2.59
3393 3836 2.746904 CGTGCAATTTCACACCTATCCA 59.253 45.455 8.92 0.00 36.80 3.41
3394 3837 3.190327 CGTGCAATTTCACACCTATCCAA 59.810 43.478 8.92 0.00 36.80 3.53
3395 3838 4.142403 CGTGCAATTTCACACCTATCCAAT 60.142 41.667 8.92 0.00 36.80 3.16
3396 3839 5.104374 GTGCAATTTCACACCTATCCAATG 58.896 41.667 3.17 0.00 36.97 2.82
3397 3840 4.114794 GCAATTTCACACCTATCCAATGC 58.885 43.478 0.00 0.00 0.00 3.56
3398 3841 4.381825 GCAATTTCACACCTATCCAATGCA 60.382 41.667 0.00 0.00 0.00 3.96
3399 3842 5.722263 CAATTTCACACCTATCCAATGCAA 58.278 37.500 0.00 0.00 0.00 4.08
3400 3843 4.782019 TTTCACACCTATCCAATGCAAC 57.218 40.909 0.00 0.00 0.00 4.17
3401 3844 3.431673 TCACACCTATCCAATGCAACA 57.568 42.857 0.00 0.00 0.00 3.33
3402 3845 3.346315 TCACACCTATCCAATGCAACAG 58.654 45.455 0.00 0.00 0.00 3.16
3403 3846 2.094675 ACACCTATCCAATGCAACAGC 58.905 47.619 0.00 0.00 0.00 4.40
3404 3847 2.093890 CACCTATCCAATGCAACAGCA 58.906 47.619 0.00 0.00 43.41 4.41
3405 3848 2.098607 CACCTATCCAATGCAACAGCAG 59.901 50.000 0.00 0.00 42.36 4.24
3406 3849 1.066605 CCTATCCAATGCAACAGCAGC 59.933 52.381 0.00 0.00 42.36 5.25
3407 3850 1.066605 CTATCCAATGCAACAGCAGCC 59.933 52.381 0.00 0.00 42.36 4.85
3408 3851 1.610554 ATCCAATGCAACAGCAGCCC 61.611 55.000 0.00 0.00 42.36 5.19
3409 3852 2.263540 CAATGCAACAGCAGCCCC 59.736 61.111 0.00 0.00 42.36 5.80
3410 3853 2.203669 AATGCAACAGCAGCCCCA 60.204 55.556 0.00 0.00 42.36 4.96
3411 3854 2.576832 AATGCAACAGCAGCCCCAC 61.577 57.895 0.00 0.00 42.36 4.61
3414 3857 3.357079 CAACAGCAGCCCCACGAC 61.357 66.667 0.00 0.00 0.00 4.34
3415 3858 4.988598 AACAGCAGCCCCACGACG 62.989 66.667 0.00 0.00 0.00 5.12
3477 3924 3.608316 AAAATGCATACGGCCACATTT 57.392 38.095 2.24 7.64 42.81 2.32
3478 3925 4.727507 AAAATGCATACGGCCACATTTA 57.272 36.364 2.24 0.00 40.77 1.40
3595 4051 0.109132 CCGGCTGGCAAAAGATGAAC 60.109 55.000 0.00 0.00 0.00 3.18
3597 4053 1.203052 CGGCTGGCAAAAGATGAACAT 59.797 47.619 1.08 0.00 0.00 2.71
3601 4057 4.168760 GCTGGCAAAAGATGAACATGTAC 58.831 43.478 0.00 0.00 0.00 2.90
3700 4156 1.225855 TGCAGTAACCAAACGCTCTG 58.774 50.000 0.00 0.00 0.00 3.35
3757 4213 2.363711 TAGCGCAGTAGCCCGGAATG 62.364 60.000 11.47 0.00 37.52 2.67
3758 4214 3.272334 CGCAGTAGCCCGGAATGC 61.272 66.667 0.73 2.89 37.52 3.56
3900 5468 0.030638 CAACCAGCCACGTTCCAAAG 59.969 55.000 0.00 0.00 0.00 2.77
3941 5509 4.281657 GGAGGAGGAATGTTAAAGGCAAT 58.718 43.478 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
382 383 3.992643 TCAGCCCATTTTCAATGTGTTG 58.007 40.909 0.00 0.00 36.65 3.33
517 519 0.180642 TACCACTCAACCGTTGGCAA 59.819 50.000 11.35 0.00 0.00 4.52
521 523 2.761559 TCACATACCACTCAACCGTTG 58.238 47.619 4.78 4.78 0.00 4.10
522 524 3.478857 TTCACATACCACTCAACCGTT 57.521 42.857 0.00 0.00 0.00 4.44
523 525 3.478857 TTTCACATACCACTCAACCGT 57.521 42.857 0.00 0.00 0.00 4.83
524 526 5.371115 AAATTTCACATACCACTCAACCG 57.629 39.130 0.00 0.00 0.00 4.44
525 527 8.281212 AGATAAATTTCACATACCACTCAACC 57.719 34.615 0.00 0.00 0.00 3.77
526 528 8.398665 GGAGATAAATTTCACATACCACTCAAC 58.601 37.037 0.00 0.00 0.00 3.18
527 529 8.106462 TGGAGATAAATTTCACATACCACTCAA 58.894 33.333 0.00 0.00 0.00 3.02
528 530 7.629157 TGGAGATAAATTTCACATACCACTCA 58.371 34.615 0.00 0.00 0.00 3.41
529 531 8.506168 TTGGAGATAAATTTCACATACCACTC 57.494 34.615 0.00 0.00 0.00 3.51
530 532 7.557719 CCTTGGAGATAAATTTCACATACCACT 59.442 37.037 0.00 0.00 0.00 4.00
531 533 7.339466 ACCTTGGAGATAAATTTCACATACCAC 59.661 37.037 0.00 0.00 0.00 4.16
532 534 7.410174 ACCTTGGAGATAAATTTCACATACCA 58.590 34.615 0.00 0.00 0.00 3.25
533 535 7.881775 ACCTTGGAGATAAATTTCACATACC 57.118 36.000 0.00 0.00 0.00 2.73
567 779 5.682234 AGCCCCCTGAAATTATTTTCTTG 57.318 39.130 10.54 4.88 41.54 3.02
703 917 7.548075 ACGGTTCAAATCTCATCTTTATACGTT 59.452 33.333 0.00 0.00 0.00 3.99
769 983 9.906660 CAATTTAGTGCCTGAACTTGTAAAATA 57.093 29.630 0.00 0.00 0.00 1.40
770 984 7.384932 GCAATTTAGTGCCTGAACTTGTAAAAT 59.615 33.333 0.00 0.00 38.66 1.82
771 985 6.699642 GCAATTTAGTGCCTGAACTTGTAAAA 59.300 34.615 0.00 0.00 38.66 1.52
772 986 6.183360 TGCAATTTAGTGCCTGAACTTGTAAA 60.183 34.615 0.00 0.00 44.26 2.01
773 987 5.300539 TGCAATTTAGTGCCTGAACTTGTAA 59.699 36.000 0.00 0.00 44.26 2.41
774 988 4.824537 TGCAATTTAGTGCCTGAACTTGTA 59.175 37.500 0.00 0.00 44.26 2.41
775 989 3.636300 TGCAATTTAGTGCCTGAACTTGT 59.364 39.130 0.00 0.00 44.26 3.16
776 990 3.983344 GTGCAATTTAGTGCCTGAACTTG 59.017 43.478 0.00 0.00 44.26 3.16
777 991 3.636300 TGTGCAATTTAGTGCCTGAACTT 59.364 39.130 0.00 0.00 44.26 2.66
778 992 3.004734 GTGTGCAATTTAGTGCCTGAACT 59.995 43.478 0.00 0.00 44.26 3.01
779 993 3.004734 AGTGTGCAATTTAGTGCCTGAAC 59.995 43.478 0.00 0.00 44.26 3.18
780 994 3.221771 AGTGTGCAATTTAGTGCCTGAA 58.778 40.909 0.00 0.00 44.26 3.02
781 995 2.862541 AGTGTGCAATTTAGTGCCTGA 58.137 42.857 0.00 0.00 44.26 3.86
782 996 3.243501 ACAAGTGTGCAATTTAGTGCCTG 60.244 43.478 0.00 0.00 44.26 4.85
783 997 2.958355 ACAAGTGTGCAATTTAGTGCCT 59.042 40.909 0.00 0.00 44.26 4.75
784 998 3.052036 CACAAGTGTGCAATTTAGTGCC 58.948 45.455 0.00 0.00 44.26 5.01
785 999 3.052036 CCACAAGTGTGCAATTTAGTGC 58.948 45.455 5.89 0.00 44.34 4.40
786 1000 3.052036 GCCACAAGTGTGCAATTTAGTG 58.948 45.455 5.89 0.00 44.34 2.74
787 1001 2.692557 TGCCACAAGTGTGCAATTTAGT 59.307 40.909 5.89 0.00 44.34 2.24
788 1002 3.367992 TGCCACAAGTGTGCAATTTAG 57.632 42.857 5.89 0.00 44.34 1.85
789 1003 3.131933 ACTTGCCACAAGTGTGCAATTTA 59.868 39.130 20.99 7.25 44.34 1.40
790 1004 2.093553 ACTTGCCACAAGTGTGCAATTT 60.094 40.909 20.99 13.01 44.34 1.82
791 1005 1.481772 ACTTGCCACAAGTGTGCAATT 59.518 42.857 20.99 15.93 44.34 2.32
792 1006 1.113788 ACTTGCCACAAGTGTGCAAT 58.886 45.000 20.99 12.99 44.34 3.56
793 1007 0.894141 AACTTGCCACAAGTGTGCAA 59.106 45.000 20.11 20.11 44.34 4.08
794 1008 0.455410 GAACTTGCCACAAGTGTGCA 59.545 50.000 13.32 10.80 44.34 4.57
795 1009 0.455410 TGAACTTGCCACAAGTGTGC 59.545 50.000 13.32 7.33 44.34 4.57
796 1010 2.801063 CTTGAACTTGCCACAAGTGTG 58.199 47.619 13.32 4.38 45.23 3.82
797 1011 1.134946 GCTTGAACTTGCCACAAGTGT 59.865 47.619 13.32 4.68 41.73 3.55
798 1012 1.134753 TGCTTGAACTTGCCACAAGTG 59.865 47.619 13.32 2.97 41.73 3.16
799 1013 1.134946 GTGCTTGAACTTGCCACAAGT 59.865 47.619 7.15 7.15 41.73 3.16
800 1014 1.406539 AGTGCTTGAACTTGCCACAAG 59.593 47.619 5.80 5.80 42.33 3.16
801 1015 1.473258 AGTGCTTGAACTTGCCACAA 58.527 45.000 0.00 0.00 0.00 3.33
802 1016 2.221169 CTAGTGCTTGAACTTGCCACA 58.779 47.619 0.00 0.00 0.00 4.17
803 1017 2.031682 CACTAGTGCTTGAACTTGCCAC 60.032 50.000 10.54 0.00 0.00 5.01
804 1018 2.221169 CACTAGTGCTTGAACTTGCCA 58.779 47.619 10.54 0.00 0.00 4.92
805 1019 1.537202 CCACTAGTGCTTGAACTTGCC 59.463 52.381 17.86 0.00 0.00 4.52
806 1020 2.222027 ACCACTAGTGCTTGAACTTGC 58.778 47.619 17.86 0.00 0.00 4.01
807 1021 7.849804 ATTATACCACTAGTGCTTGAACTTG 57.150 36.000 17.86 3.01 0.00 3.16
808 1022 9.379791 GTAATTATACCACTAGTGCTTGAACTT 57.620 33.333 17.86 7.47 0.00 2.66
809 1023 8.943909 GTAATTATACCACTAGTGCTTGAACT 57.056 34.615 17.86 1.71 0.00 3.01
886 1100 1.066136 GTTGACGTAGACGGAAAGCC 58.934 55.000 7.04 0.00 44.95 4.35
991 1233 0.526211 GTTTGGTTCATCGCTTCCCC 59.474 55.000 0.00 0.00 0.00 4.81
993 1235 4.201920 GGAATAGTTTGGTTCATCGCTTCC 60.202 45.833 0.00 0.00 0.00 3.46
995 1237 4.331968 TGGAATAGTTTGGTTCATCGCTT 58.668 39.130 0.00 0.00 0.00 4.68
997 1239 4.156008 ACTTGGAATAGTTTGGTTCATCGC 59.844 41.667 0.00 0.00 0.00 4.58
998 1240 5.163754 GGACTTGGAATAGTTTGGTTCATCG 60.164 44.000 0.00 0.00 0.00 3.84
1010 1252 6.817765 TTTGCTTACTTGGACTTGGAATAG 57.182 37.500 0.00 0.00 0.00 1.73
1039 1281 1.729470 CCATGGAGACGAGGACGAGG 61.729 65.000 5.56 0.00 42.66 4.63
1040 1282 1.730487 CCATGGAGACGAGGACGAG 59.270 63.158 5.56 0.00 42.66 4.18
1041 1283 2.415608 GCCATGGAGACGAGGACGA 61.416 63.158 18.40 0.00 42.66 4.20
1042 1284 2.105128 GCCATGGAGACGAGGACG 59.895 66.667 18.40 0.00 45.75 4.79
1043 1285 2.501610 GGCCATGGAGACGAGGAC 59.498 66.667 18.40 0.00 0.00 3.85
1044 1286 3.147595 CGGCCATGGAGACGAGGA 61.148 66.667 18.40 0.00 0.00 3.71
1072 1314 2.359850 GTGGTGGATGGCAAGCGA 60.360 61.111 0.00 0.00 0.00 4.93
1140 1382 2.572284 GCGTTGGCCTCGTACTCT 59.428 61.111 18.60 0.00 0.00 3.24
1233 1478 2.943978 CGGTGCCGAGGAGGAGTTT 61.944 63.158 4.35 0.00 45.00 2.66
1791 2043 2.514824 GGCGGATCCTTGAGTGGC 60.515 66.667 10.75 3.44 0.00 5.01
2430 2748 4.150454 CCCTCCTCCTCCTCGCCT 62.150 72.222 0.00 0.00 0.00 5.52
2630 2954 4.495939 CGTCGTCCTCGTCGTCCG 62.496 72.222 0.00 0.00 41.73 4.79
2631 2955 3.114616 TCGTCGTCCTCGTCGTCC 61.115 66.667 7.05 0.00 45.27 4.79
2632 2956 2.095469 GTCGTCGTCCTCGTCGTC 59.905 66.667 7.05 0.00 45.27 4.20
2633 2957 3.418068 GGTCGTCGTCCTCGTCGT 61.418 66.667 0.91 0.00 45.27 4.34
2634 2958 4.495939 CGGTCGTCGTCCTCGTCG 62.496 72.222 6.94 1.62 46.06 5.12
2635 2959 4.808238 GCGGTCGTCGTCCTCGTC 62.808 72.222 6.94 0.00 41.72 4.20
2691 3021 2.762459 TCGGGCGCCAGATAACCT 60.762 61.111 30.85 0.00 0.00 3.50
2725 3055 3.797353 GAGCTGGGGGCCGATCAA 61.797 66.667 0.00 0.00 43.05 2.57
2823 3153 4.065281 ACCTTCCCGTTCTCGCCG 62.065 66.667 0.00 0.00 35.54 6.46
2824 3154 2.434359 CACCTTCCCGTTCTCGCC 60.434 66.667 0.00 0.00 35.54 5.54
2825 3155 1.880819 TACCACCTTCCCGTTCTCGC 61.881 60.000 0.00 0.00 35.54 5.03
3051 3426 8.820831 TCCCAATTTATTGTCCAATTGTACATT 58.179 29.630 4.55 4.42 38.29 2.71
3107 3493 3.587797 TCTGGACCTATTGTTCGTGAC 57.412 47.619 0.00 0.00 0.00 3.67
3138 3564 2.461110 CCGTGTTGGATGCGGTAGC 61.461 63.158 0.00 0.00 42.00 3.58
3139 3565 2.461110 GCCGTGTTGGATGCGGTAG 61.461 63.158 4.16 0.00 46.41 3.18
3209 3640 5.525378 GGTTTACTTCTGATCTTGATCGCAT 59.475 40.000 6.19 0.00 0.00 4.73
3213 3644 6.183360 GCCAAGGTTTACTTCTGATCTTGATC 60.183 42.308 3.82 3.82 37.29 2.92
3218 3649 4.042187 AGTGCCAAGGTTTACTTCTGATCT 59.958 41.667 0.00 0.00 37.29 2.75
3227 3658 5.298527 AGTTTACTTCAGTGCCAAGGTTTAC 59.701 40.000 0.00 0.00 0.00 2.01
3235 3666 3.838244 ACTGAGTTTACTTCAGTGCCA 57.162 42.857 7.07 0.00 42.37 4.92
3254 3685 7.816031 ACAAGAAAATGACATGATGATTGGAAC 59.184 33.333 0.00 0.00 0.00 3.62
3286 3726 4.406326 TGTACATGCCCCTAACGATCTTAA 59.594 41.667 0.00 0.00 0.00 1.85
3299 3742 5.704053 GGTAATACTACCATTGTACATGCCC 59.296 44.000 0.00 0.00 46.23 5.36
3300 3743 6.796705 GGTAATACTACCATTGTACATGCC 57.203 41.667 0.00 0.00 46.23 4.40
3308 3751 8.862894 GGCATCACCAAGGTAATACTACCATTG 61.863 44.444 2.74 4.71 43.75 2.82
3309 3752 6.915590 GGCATCACCAAGGTAATACTACCATT 60.916 42.308 2.74 0.00 43.75 3.16
3310 3753 5.456186 GGCATCACCAAGGTAATACTACCAT 60.456 44.000 2.74 0.00 43.75 3.55
3311 3754 4.141574 GGCATCACCAAGGTAATACTACCA 60.142 45.833 2.74 0.00 43.75 3.25
3312 3755 4.102681 AGGCATCACCAAGGTAATACTACC 59.897 45.833 0.00 0.00 44.26 3.18
3313 3756 5.163343 TGAGGCATCACCAAGGTAATACTAC 60.163 44.000 0.00 0.00 43.14 2.73
3314 3757 4.966168 TGAGGCATCACCAAGGTAATACTA 59.034 41.667 0.00 0.00 43.14 1.82
3315 3758 3.780294 TGAGGCATCACCAAGGTAATACT 59.220 43.478 0.00 0.00 43.14 2.12
3316 3759 4.130118 CTGAGGCATCACCAAGGTAATAC 58.870 47.826 0.00 0.00 43.14 1.89
3317 3760 3.780294 ACTGAGGCATCACCAAGGTAATA 59.220 43.478 0.00 0.00 43.14 0.98
3318 3761 2.578021 ACTGAGGCATCACCAAGGTAAT 59.422 45.455 0.00 0.00 43.14 1.89
3319 3762 1.985159 ACTGAGGCATCACCAAGGTAA 59.015 47.619 0.00 0.00 43.14 2.85
3320 3763 1.656587 ACTGAGGCATCACCAAGGTA 58.343 50.000 0.00 0.00 43.14 3.08
3322 3765 1.278985 TGTACTGAGGCATCACCAAGG 59.721 52.381 0.00 0.00 43.14 3.61
3323 3766 2.625737 CTGTACTGAGGCATCACCAAG 58.374 52.381 0.00 0.00 43.14 3.61
3324 3767 1.339055 GCTGTACTGAGGCATCACCAA 60.339 52.381 0.00 0.00 43.14 3.67
3325 3768 0.250234 GCTGTACTGAGGCATCACCA 59.750 55.000 0.00 0.00 43.14 4.17
3326 3769 0.462759 GGCTGTACTGAGGCATCACC 60.463 60.000 0.00 0.00 38.40 4.02
3327 3770 0.250234 TGGCTGTACTGAGGCATCAC 59.750 55.000 0.00 0.00 43.18 3.06
3328 3771 2.682631 TGGCTGTACTGAGGCATCA 58.317 52.632 0.00 0.00 43.18 3.07
3331 3774 2.154798 GACGTGGCTGTACTGAGGCA 62.155 60.000 5.47 5.47 45.64 4.75
3332 3775 1.446272 GACGTGGCTGTACTGAGGC 60.446 63.158 3.61 1.78 38.99 4.70
3333 3776 1.154016 CGACGTGGCTGTACTGAGG 60.154 63.158 3.61 0.00 0.00 3.86
3335 3778 1.859427 GACCGACGTGGCTGTACTGA 61.859 60.000 3.61 0.00 43.94 3.41
3336 3779 1.443872 GACCGACGTGGCTGTACTG 60.444 63.158 0.00 0.00 43.94 2.74
3337 3780 1.863662 CTGACCGACGTGGCTGTACT 61.864 60.000 0.00 0.00 43.94 2.73
3338 3781 1.443872 CTGACCGACGTGGCTGTAC 60.444 63.158 0.00 0.00 43.94 2.90
3339 3782 2.632544 CCTGACCGACGTGGCTGTA 61.633 63.158 0.00 0.00 43.94 2.74
3340 3783 3.991051 CCTGACCGACGTGGCTGT 61.991 66.667 0.00 0.00 43.94 4.40
3341 3784 3.633094 CTCCTGACCGACGTGGCTG 62.633 68.421 0.00 0.00 43.94 4.85
3342 3785 3.374402 CTCCTGACCGACGTGGCT 61.374 66.667 0.00 0.00 43.94 4.75
3343 3786 3.343788 CTCTCCTGACCGACGTGGC 62.344 68.421 0.00 0.00 43.94 5.01
3344 3787 1.032657 ATCTCTCCTGACCGACGTGG 61.033 60.000 0.00 0.00 46.41 4.94
3345 3788 0.099613 CATCTCTCCTGACCGACGTG 59.900 60.000 0.00 0.00 0.00 4.49
3347 3790 0.660488 CTCATCTCTCCTGACCGACG 59.340 60.000 0.00 0.00 0.00 5.12
3349 3792 1.408961 GGTCTCATCTCTCCTGACCGA 60.409 57.143 0.00 0.00 37.93 4.69
3350 3793 1.028905 GGTCTCATCTCTCCTGACCG 58.971 60.000 0.00 0.00 37.93 4.79
3351 3794 1.754226 GTGGTCTCATCTCTCCTGACC 59.246 57.143 0.00 0.00 45.22 4.02
3352 3795 1.754226 GGTGGTCTCATCTCTCCTGAC 59.246 57.143 0.00 0.00 0.00 3.51
3353 3796 1.683319 CGGTGGTCTCATCTCTCCTGA 60.683 57.143 0.00 0.00 0.00 3.86
3354 3797 0.743688 CGGTGGTCTCATCTCTCCTG 59.256 60.000 0.00 0.00 0.00 3.86
3355 3798 0.333312 ACGGTGGTCTCATCTCTCCT 59.667 55.000 0.00 0.00 0.00 3.69
3356 3799 0.457851 CACGGTGGTCTCATCTCTCC 59.542 60.000 0.00 0.00 0.00 3.71
3357 3800 0.179124 GCACGGTGGTCTCATCTCTC 60.179 60.000 10.60 0.00 0.00 3.20
3358 3801 0.900182 TGCACGGTGGTCTCATCTCT 60.900 55.000 10.60 0.00 0.00 3.10
3359 3802 0.037326 TTGCACGGTGGTCTCATCTC 60.037 55.000 10.60 0.00 0.00 2.75
3360 3803 0.615331 ATTGCACGGTGGTCTCATCT 59.385 50.000 10.60 0.00 0.00 2.90
3361 3804 1.453155 AATTGCACGGTGGTCTCATC 58.547 50.000 10.60 0.00 0.00 2.92
3362 3805 1.812571 GAAATTGCACGGTGGTCTCAT 59.187 47.619 10.60 0.00 0.00 2.90
3363 3806 1.234821 GAAATTGCACGGTGGTCTCA 58.765 50.000 10.60 0.00 0.00 3.27
3364 3807 1.069227 GTGAAATTGCACGGTGGTCTC 60.069 52.381 10.60 0.00 0.00 3.36
3365 3808 0.951558 GTGAAATTGCACGGTGGTCT 59.048 50.000 10.60 0.00 0.00 3.85
3367 3810 0.383949 GTGTGAAATTGCACGGTGGT 59.616 50.000 12.02 0.00 41.63 4.16
3368 3811 0.318614 GGTGTGAAATTGCACGGTGG 60.319 55.000 12.02 0.00 41.63 4.61
3369 3812 0.667993 AGGTGTGAAATTGCACGGTG 59.332 50.000 12.02 3.15 41.63 4.94
3370 3813 2.264005 TAGGTGTGAAATTGCACGGT 57.736 45.000 12.02 1.58 41.63 4.83
3371 3814 2.097466 GGATAGGTGTGAAATTGCACGG 59.903 50.000 12.02 0.00 41.63 4.94
3372 3815 2.746904 TGGATAGGTGTGAAATTGCACG 59.253 45.455 12.02 0.00 41.63 5.34
3376 3819 5.327616 TGCATTGGATAGGTGTGAAATTG 57.672 39.130 0.00 0.00 0.00 2.32
3377 3820 5.245751 TGTTGCATTGGATAGGTGTGAAATT 59.754 36.000 0.00 0.00 0.00 1.82
3379 3822 4.148079 TGTTGCATTGGATAGGTGTGAAA 58.852 39.130 0.00 0.00 0.00 2.69
3381 3824 3.346315 CTGTTGCATTGGATAGGTGTGA 58.654 45.455 0.00 0.00 0.00 3.58
3382 3825 2.159338 GCTGTTGCATTGGATAGGTGTG 60.159 50.000 0.00 0.00 39.41 3.82
3383 3826 2.094675 GCTGTTGCATTGGATAGGTGT 58.905 47.619 0.00 0.00 39.41 4.16
3384 3827 2.093890 TGCTGTTGCATTGGATAGGTG 58.906 47.619 0.00 0.00 45.31 4.00
3385 3828 2.512692 TGCTGTTGCATTGGATAGGT 57.487 45.000 0.00 0.00 45.31 3.08
3397 3840 3.357079 GTCGTGGGGCTGCTGTTG 61.357 66.667 0.00 0.00 0.00 3.33
3398 3841 4.988598 CGTCGTGGGGCTGCTGTT 62.989 66.667 0.00 0.00 0.00 3.16
3400 3843 4.988598 AACGTCGTGGGGCTGCTG 62.989 66.667 0.00 0.00 0.00 4.41
3401 3844 3.767630 AAAACGTCGTGGGGCTGCT 62.768 57.895 0.00 0.00 0.00 4.24
3402 3845 2.841160 AAAAACGTCGTGGGGCTGC 61.841 57.895 0.00 0.00 0.00 5.25
3403 3846 3.427670 AAAAACGTCGTGGGGCTG 58.572 55.556 0.00 0.00 0.00 4.85
3682 4138 1.069906 CACAGAGCGTTTGGTTACTGC 60.070 52.381 0.00 0.00 0.00 4.40
3859 5007 4.650754 GGATAGAGTCCGAAACAGCTAA 57.349 45.455 0.00 0.00 37.23 3.09
3900 5468 1.683790 CGCATTCGGTCAGGTCGTTC 61.684 60.000 0.00 0.00 0.00 3.95
3941 5509 0.519519 CTTATGGCGTTCGGTGCAAA 59.480 50.000 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.