Multiple sequence alignment - TraesCS3D01G021800

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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 TraesCS3D01G021800 chr3D 100.000 6811 0 0 1 6811 7128785 7135595 0.000000e+00 12578.0
1 TraesCS3D01G021800 chr3D 85.583 763 77 18 1 745 475866563 475867310 0.000000e+00 769.0
2 TraesCS3D01G021800 chr3B 94.901 3236 117 16 2839 6062 8734706 8737905 0.000000e+00 5018.0
3 TraesCS3D01G021800 chr3B 92.173 1316 73 16 918 2210 8733309 8734617 0.000000e+00 1832.0
4 TraesCS3D01G021800 chr3B 90.549 455 30 6 6356 6809 8738843 8739285 2.120000e-164 590.0
5 TraesCS3D01G021800 chr3B 86.312 263 22 8 6113 6369 8737905 8738159 2.420000e-69 274.0
6 TraesCS3D01G021800 chr3A 95.174 2466 74 22 2573 5030 13154418 13151990 0.000000e+00 3853.0
7 TraesCS3D01G021800 chr3A 93.169 1464 79 10 5355 6811 13151551 13150102 0.000000e+00 2130.0
8 TraesCS3D01G021800 chr3A 92.618 1314 65 21 918 2210 13155833 13154531 0.000000e+00 1860.0
9 TraesCS3D01G021800 chr3A 86.713 715 79 12 13 713 187231061 187231773 0.000000e+00 780.0
10 TraesCS3D01G021800 chr3A 90.811 370 26 5 4989 5355 13152002 13151638 7.940000e-134 488.0
11 TraesCS3D01G021800 chr3A 94.845 97 5 0 744 840 13186316 13186220 1.180000e-32 152.0
12 TraesCS3D01G021800 chr3A 95.506 89 2 1 837 925 13155942 13155856 2.560000e-29 141.0
13 TraesCS3D01G021800 chr3A 84.375 64 9 1 881 944 35843563 35843625 2.050000e-05 62.1
14 TraesCS3D01G021800 chr2D 83.622 1557 177 47 3638 5158 2472501 2470987 0.000000e+00 1391.0
15 TraesCS3D01G021800 chr2D 80.687 1165 129 41 1490 2575 2474383 2473236 0.000000e+00 817.0
16 TraesCS3D01G021800 chr2D 85.828 755 82 15 1 745 500661710 500662449 0.000000e+00 778.0
17 TraesCS3D01G021800 chr2D 85.771 759 78 20 1 745 608381616 608382358 0.000000e+00 776.0
18 TraesCS3D01G021800 chr2D 87.914 604 56 11 2639 3230 2473100 2472502 0.000000e+00 695.0
19 TraesCS3D01G021800 chr2D 82.898 421 50 9 2904 3305 2375266 2374849 6.490000e-95 359.0
20 TraesCS3D01G021800 chr2D 81.995 411 25 26 945 1325 2474902 2474511 3.090000e-78 303.0
21 TraesCS3D01G021800 chrUn 80.827 1742 185 72 944 2575 15905747 15907449 0.000000e+00 1229.0
22 TraesCS3D01G021800 chrUn 83.871 806 89 21 4373 5159 15908969 15909752 0.000000e+00 730.0
23 TraesCS3D01G021800 chrUn 86.333 600 60 16 2639 3230 15907585 15908170 9.640000e-178 634.0
24 TraesCS3D01G021800 chrUn 82.816 419 52 9 2904 3303 352147721 352148138 2.340000e-94 357.0
25 TraesCS3D01G021800 chrUn 83.880 366 47 8 2904 3262 15854362 15854002 8.460000e-89 339.0
26 TraesCS3D01G021800 chrUn 81.324 423 55 9 2904 3305 15637402 15636983 8.520000e-84 322.0
27 TraesCS3D01G021800 chrUn 93.103 203 10 3 3638 3836 15908171 15908373 1.860000e-75 294.0
28 TraesCS3D01G021800 chr2A 80.902 1220 142 38 1437 2575 2482436 2483645 0.000000e+00 878.0
29 TraesCS3D01G021800 chr2A 83.227 787 115 14 4373 5158 2485287 2486057 0.000000e+00 706.0
30 TraesCS3D01G021800 chr2A 87.049 610 55 15 2639 3230 2483982 2484585 0.000000e+00 667.0
31 TraesCS3D01G021800 chr2A 85.463 454 50 10 3638 4078 2484586 2485036 6.220000e-125 459.0
32 TraesCS3D01G021800 chr2A 88.110 328 15 17 1017 1325 2482030 2482352 1.080000e-97 368.0
33 TraesCS3D01G021800 chr6D 86.939 758 67 24 1 745 457327127 457326389 0.000000e+00 822.0
34 TraesCS3D01G021800 chr6D 87.681 690 74 9 33 713 59176308 59176995 0.000000e+00 793.0
35 TraesCS3D01G021800 chr1A 86.887 755 74 20 1 745 348727749 348728488 0.000000e+00 822.0
36 TraesCS3D01G021800 chr1D 85.714 756 81 16 7 745 199563813 199563068 0.000000e+00 773.0
37 TraesCS3D01G021800 chr1D 83.048 702 78 28 2573 3262 60430235 60430907 3.520000e-167 599.0
38 TraesCS3D01G021800 chr1D 86.777 121 11 3 1164 1280 60428911 60429030 5.540000e-26 130.0
39 TraesCS3D01G021800 chr5A 85.283 761 76 23 1 747 320936783 320937521 0.000000e+00 752.0
40 TraesCS3D01G021800 chr5A 84.576 389 53 5 5416 5801 456036745 456037129 4.990000e-101 379.0
41 TraesCS3D01G021800 chr2B 81.223 703 86 29 2573 3262 757833986 757834655 6.050000e-145 525.0
42 TraesCS3D01G021800 chr2B 82.182 275 37 8 1424 1690 757698093 757698363 6.870000e-55 226.0
43 TraesCS3D01G021800 chr2B 82.182 275 37 8 1424 1690 757699159 757699429 6.870000e-55 226.0
44 TraesCS3D01G021800 chr2B 82.182 275 37 8 1424 1690 757704792 757705062 6.870000e-55 226.0
45 TraesCS3D01G021800 chr2B 82.117 274 37 8 1424 1690 757832926 757833194 2.470000e-54 224.0
46 TraesCS3D01G021800 chr2B 86.777 121 11 3 1164 1280 757704553 757704672 5.540000e-26 130.0
47 TraesCS3D01G021800 chr4A 84.576 389 53 5 5416 5801 27189966 27189582 4.990000e-101 379.0
48 TraesCS3D01G021800 chr4B 87.500 120 11 2 1171 1286 623071257 623071138 1.190000e-27 135.0
49 TraesCS3D01G021800 chr5B 86.777 121 11 3 1164 1280 536510736 536510855 5.540000e-26 130.0


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 TraesCS3D01G021800 chr3D 7128785 7135595 6810 False 12578.00 12578 100.00000 1 6811 1 chr3D.!!$F1 6810
1 TraesCS3D01G021800 chr3D 475866563 475867310 747 False 769.00 769 85.58300 1 745 1 chr3D.!!$F2 744
2 TraesCS3D01G021800 chr3B 8733309 8739285 5976 False 1928.50 5018 90.98375 918 6809 4 chr3B.!!$F1 5891
3 TraesCS3D01G021800 chr3A 13150102 13155942 5840 True 1694.40 3853 93.45560 837 6811 5 chr3A.!!$R2 5974
4 TraesCS3D01G021800 chr3A 187231061 187231773 712 False 780.00 780 86.71300 13 713 1 chr3A.!!$F2 700
5 TraesCS3D01G021800 chr2D 2470987 2474902 3915 True 801.50 1391 83.55450 945 5158 4 chr2D.!!$R2 4213
6 TraesCS3D01G021800 chr2D 500661710 500662449 739 False 778.00 778 85.82800 1 745 1 chr2D.!!$F1 744
7 TraesCS3D01G021800 chr2D 608381616 608382358 742 False 776.00 776 85.77100 1 745 1 chr2D.!!$F2 744
8 TraesCS3D01G021800 chrUn 15905747 15909752 4005 False 721.75 1229 86.03350 944 5159 4 chrUn.!!$F2 4215
9 TraesCS3D01G021800 chr2A 2482030 2486057 4027 False 615.60 878 84.95020 1017 5158 5 chr2A.!!$F1 4141
10 TraesCS3D01G021800 chr6D 457326389 457327127 738 True 822.00 822 86.93900 1 745 1 chr6D.!!$R1 744
11 TraesCS3D01G021800 chr6D 59176308 59176995 687 False 793.00 793 87.68100 33 713 1 chr6D.!!$F1 680
12 TraesCS3D01G021800 chr1A 348727749 348728488 739 False 822.00 822 86.88700 1 745 1 chr1A.!!$F1 744
13 TraesCS3D01G021800 chr1D 199563068 199563813 745 True 773.00 773 85.71400 7 745 1 chr1D.!!$R1 738
14 TraesCS3D01G021800 chr1D 60428911 60430907 1996 False 364.50 599 84.91250 1164 3262 2 chr1D.!!$F1 2098
15 TraesCS3D01G021800 chr5A 320936783 320937521 738 False 752.00 752 85.28300 1 747 1 chr5A.!!$F1 746
16 TraesCS3D01G021800 chr2B 757832926 757834655 1729 False 374.50 525 81.67000 1424 3262 2 chr2B.!!$F3 1838
17 TraesCS3D01G021800 chr2B 757698093 757699429 1336 False 226.00 226 82.18200 1424 1690 2 chr2B.!!$F1 266

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
698 740 0.036388 GTCGCAATCTGAGGGGTTGA 60.036 55.000 0.00 0.0 0.0 3.18 F
787 829 0.679002 ATGACATGTCTGGGCTGTGC 60.679 55.000 25.55 0.0 0.0 4.57 F
1935 2719 0.746923 GTATCCCGCGCTTCCCTTTT 60.747 55.000 5.56 0.0 0.0 2.27 F
3524 4704 0.180406 AGTCACGCTTGTTTCCACCT 59.820 50.000 0.00 0.0 0.0 4.00 F
4510 5946 2.031245 TGTTCCAATTGTTGCTGCTACG 60.031 45.455 9.51 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 3091 0.677731 CCACCATTGAGACATGGCGT 60.678 55.000 0.0 0.00 41.53 5.68 R
2347 3216 1.261619 GAAACACAGAGGAAGCGTGTG 59.738 52.381 0.0 0.24 42.85 3.82 R
3636 4816 1.467374 GCGTTAAAATGGCGATGCACT 60.467 47.619 0.0 0.00 0.00 4.40 R
4564 6000 0.250901 GGGTGCTTTTCCTGCTCTCA 60.251 55.000 0.0 0.00 0.00 3.27 R
6125 7685 0.328258 ATACACCAACTCCACCTGCC 59.672 55.000 0.0 0.00 0.00 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 77 1.206831 GGTTTTGCTTCCGCGAGAC 59.793 57.895 8.23 0.00 39.65 3.36
75 78 1.503818 GGTTTTGCTTCCGCGAGACA 61.504 55.000 8.23 0.00 36.59 3.41
122 125 2.380410 CCGTGCCTCTCGAAAACGG 61.380 63.158 8.89 8.89 46.69 4.44
123 126 1.372499 CGTGCCTCTCGAAAACGGA 60.372 57.895 0.00 0.00 0.00 4.69
217 234 2.034532 TGGAGAGTCACGGCCGTA 59.965 61.111 33.70 16.87 0.00 4.02
482 520 4.023878 CGGTTCGGTCTTTTTGTCCAATTA 60.024 41.667 0.00 0.00 0.00 1.40
522 560 8.877864 AGTTTATCAAAACCTATCAACATGGA 57.122 30.769 0.00 0.00 45.11 3.41
539 577 9.300681 TCAACATGGAATCTAGTTTTGAAGATT 57.699 29.630 0.00 0.00 34.17 2.40
555 593 3.252974 AGATTTTGACGCGAGGAATCT 57.747 42.857 15.93 17.74 33.49 2.40
653 694 1.193874 GAAAACTACCAGGTTGCGACG 59.806 52.381 0.00 0.00 0.00 5.12
693 735 1.089920 CCTTTGTCGCAATCTGAGGG 58.910 55.000 0.00 0.00 0.00 4.30
698 740 0.036388 GTCGCAATCTGAGGGGTTGA 60.036 55.000 0.00 0.00 0.00 3.18
709 751 4.844085 TCTGAGGGGTTGAAGTGATCTTTA 59.156 41.667 0.00 0.00 33.64 1.85
713 755 5.316987 AGGGGTTGAAGTGATCTTTACAAG 58.683 41.667 0.00 0.00 33.64 3.16
714 756 4.459337 GGGGTTGAAGTGATCTTTACAAGG 59.541 45.833 0.00 0.00 33.64 3.61
715 757 5.313712 GGGTTGAAGTGATCTTTACAAGGA 58.686 41.667 0.00 0.00 33.64 3.36
716 758 5.768164 GGGTTGAAGTGATCTTTACAAGGAA 59.232 40.000 0.00 0.00 33.64 3.36
717 759 6.434340 GGGTTGAAGTGATCTTTACAAGGAAT 59.566 38.462 0.00 0.00 33.64 3.01
718 760 7.610305 GGGTTGAAGTGATCTTTACAAGGAATA 59.390 37.037 0.00 0.00 33.64 1.75
719 761 8.669243 GGTTGAAGTGATCTTTACAAGGAATAG 58.331 37.037 0.00 0.00 33.64 1.73
727 769 9.268282 TGATCTTTACAAGGAATAGGAGTACTT 57.732 33.333 0.00 0.00 0.00 2.24
747 789 4.021016 ACTTCTCAACTAGTGATTTCGGCT 60.021 41.667 0.00 0.00 35.07 5.52
748 790 5.185249 ACTTCTCAACTAGTGATTTCGGCTA 59.815 40.000 0.00 0.00 35.07 3.93
749 791 5.654603 TCTCAACTAGTGATTTCGGCTAA 57.345 39.130 0.00 0.00 35.07 3.09
750 792 6.032956 TCTCAACTAGTGATTTCGGCTAAA 57.967 37.500 0.00 0.00 35.07 1.85
751 793 5.867716 TCTCAACTAGTGATTTCGGCTAAAC 59.132 40.000 0.00 0.00 35.07 2.01
752 794 5.543714 TCAACTAGTGATTTCGGCTAAACA 58.456 37.500 0.00 0.00 0.00 2.83
753 795 5.637810 TCAACTAGTGATTTCGGCTAAACAG 59.362 40.000 0.00 0.00 0.00 3.16
754 796 4.504858 ACTAGTGATTTCGGCTAAACAGG 58.495 43.478 0.00 0.00 0.00 4.00
755 797 2.084546 AGTGATTTCGGCTAAACAGGC 58.915 47.619 0.00 0.00 0.00 4.85
756 798 1.132453 GTGATTTCGGCTAAACAGGCC 59.868 52.381 0.00 0.00 45.57 5.19
761 803 2.359975 GGCTAAACAGGCCGTGCT 60.360 61.111 0.00 0.00 40.19 4.40
762 804 1.078708 GGCTAAACAGGCCGTGCTA 60.079 57.895 0.00 0.00 40.19 3.49
763 805 1.090052 GGCTAAACAGGCCGTGCTAG 61.090 60.000 0.00 5.14 40.19 3.42
764 806 1.090052 GCTAAACAGGCCGTGCTAGG 61.090 60.000 0.00 0.00 0.00 3.02
774 816 2.533266 CCGTGCTAGGCTTATGACAT 57.467 50.000 0.00 0.00 0.00 3.06
775 817 2.138320 CCGTGCTAGGCTTATGACATG 58.862 52.381 0.00 0.00 0.00 3.21
776 818 2.483714 CCGTGCTAGGCTTATGACATGT 60.484 50.000 0.00 0.00 0.00 3.21
777 819 2.797156 CGTGCTAGGCTTATGACATGTC 59.203 50.000 19.27 19.27 0.00 3.06
778 820 3.491619 CGTGCTAGGCTTATGACATGTCT 60.492 47.826 25.55 13.92 0.00 3.41
779 821 3.806521 GTGCTAGGCTTATGACATGTCTG 59.193 47.826 25.55 14.04 0.00 3.51
780 822 3.181462 TGCTAGGCTTATGACATGTCTGG 60.181 47.826 25.55 13.67 0.00 3.86
781 823 3.805108 GCTAGGCTTATGACATGTCTGGG 60.805 52.174 25.55 13.98 0.00 4.45
782 824 1.133976 AGGCTTATGACATGTCTGGGC 60.134 52.381 25.55 21.18 0.00 5.36
783 825 1.133976 GGCTTATGACATGTCTGGGCT 60.134 52.381 25.55 8.62 0.00 5.19
784 826 1.945394 GCTTATGACATGTCTGGGCTG 59.055 52.381 25.55 12.17 0.00 4.85
785 827 2.681976 GCTTATGACATGTCTGGGCTGT 60.682 50.000 25.55 6.63 0.00 4.40
786 828 2.696989 TATGACATGTCTGGGCTGTG 57.303 50.000 25.55 0.00 0.00 3.66
787 829 0.679002 ATGACATGTCTGGGCTGTGC 60.679 55.000 25.55 0.00 0.00 4.57
826 868 4.579127 GGCATGGCCCGTTTATCT 57.421 55.556 8.35 0.00 44.06 1.98
827 869 2.807247 GGCATGGCCCGTTTATCTT 58.193 52.632 8.35 0.00 44.06 2.40
828 870 1.111277 GGCATGGCCCGTTTATCTTT 58.889 50.000 8.35 0.00 44.06 2.52
829 871 1.480545 GGCATGGCCCGTTTATCTTTT 59.519 47.619 8.35 0.00 44.06 2.27
830 872 2.093711 GGCATGGCCCGTTTATCTTTTT 60.094 45.455 8.35 0.00 44.06 1.94
831 873 3.186909 GCATGGCCCGTTTATCTTTTTC 58.813 45.455 0.00 0.00 0.00 2.29
832 874 3.119137 GCATGGCCCGTTTATCTTTTTCT 60.119 43.478 0.00 0.00 0.00 2.52
833 875 4.423732 CATGGCCCGTTTATCTTTTTCTG 58.576 43.478 0.00 0.00 0.00 3.02
834 876 3.757270 TGGCCCGTTTATCTTTTTCTGA 58.243 40.909 0.00 0.00 0.00 3.27
835 877 3.504520 TGGCCCGTTTATCTTTTTCTGAC 59.495 43.478 0.00 0.00 0.00 3.51
866 908 1.723128 ATATGCCTGGGCCTCAAGGG 61.723 60.000 17.81 8.04 41.09 3.95
955 1027 1.985895 CCAGGTCTGGTTAAACCCTCT 59.014 52.381 8.78 0.00 45.53 3.69
1142 1233 2.443577 GTCCGTACCCTCCCTCCC 60.444 72.222 0.00 0.00 0.00 4.30
1143 1234 2.619484 TCCGTACCCTCCCTCCCT 60.619 66.667 0.00 0.00 0.00 4.20
1144 1235 2.251386 TCCGTACCCTCCCTCCCTT 61.251 63.158 0.00 0.00 0.00 3.95
1145 1236 1.306739 CCGTACCCTCCCTCCCTTT 60.307 63.158 0.00 0.00 0.00 3.11
1149 1240 2.204459 TACCCTCCCTCCCTTTCCCC 62.204 65.000 0.00 0.00 0.00 4.81
1161 1252 2.563406 CCTTTCCCCTCCCTCTTTAGT 58.437 52.381 0.00 0.00 0.00 2.24
1164 1255 4.202684 CCTTTCCCCTCCCTCTTTAGTTTT 60.203 45.833 0.00 0.00 0.00 2.43
1388 1491 6.947733 TGTTTTCTTCCAGTCCATTGATGTAT 59.052 34.615 0.00 0.00 0.00 2.29
1654 2423 8.345565 TCTGCTCTCTGTTTTAACAAGATTTTC 58.654 33.333 0.00 0.00 38.66 2.29
1768 2539 5.411781 GTGTTCTCACAGGTTAGTATCAGG 58.588 45.833 0.00 0.00 43.37 3.86
1769 2540 4.081642 TGTTCTCACAGGTTAGTATCAGGC 60.082 45.833 0.00 0.00 0.00 4.85
1862 2642 6.460953 GGTTGCAGGAGAAATACAAACTGAAA 60.461 38.462 0.00 0.00 0.00 2.69
1935 2719 0.746923 GTATCCCGCGCTTCCCTTTT 60.747 55.000 5.56 0.00 0.00 2.27
2022 2815 9.643693 CTGTATAGTATGACAATCACATATGCA 57.356 33.333 1.58 0.00 33.70 3.96
2023 2816 9.643693 TGTATAGTATGACAATCACATATGCAG 57.356 33.333 1.58 0.00 33.70 4.41
2024 2817 9.645059 GTATAGTATGACAATCACATATGCAGT 57.355 33.333 1.58 0.00 33.70 4.40
2025 2818 6.856135 AGTATGACAATCACATATGCAGTG 57.144 37.500 1.58 1.89 38.32 3.66
2026 2819 6.351711 AGTATGACAATCACATATGCAGTGT 58.648 36.000 1.58 5.34 38.16 3.55
2028 2821 5.963176 TGACAATCACATATGCAGTGTTT 57.037 34.783 1.58 0.71 38.16 2.83
2029 2822 5.701855 TGACAATCACATATGCAGTGTTTG 58.298 37.500 19.15 19.15 45.38 2.93
2030 2823 5.710513 ACAATCACATATGCAGTGTTTGT 57.289 34.783 20.07 20.07 46.68 2.83
2091 2904 3.650942 AGTGGATGTCTGGTCCAAAGTAA 59.349 43.478 0.00 0.00 46.67 2.24
2167 2994 2.412089 GTGTGAATGACGTAGGACAAGC 59.588 50.000 0.00 0.00 0.00 4.01
2176 3003 3.391049 ACGTAGGACAAGCAAGAAAGAC 58.609 45.455 0.00 0.00 0.00 3.01
2185 3014 2.288666 AGCAAGAAAGACTTCGTTGCA 58.711 42.857 25.17 0.00 42.23 4.08
2228 3072 5.567037 AACATCTAGCATATGGGCTGTTA 57.433 39.130 4.56 0.00 45.44 2.41
2247 3091 7.094377 GGCTGTTACTTTCTATTTCCACATCAA 60.094 37.037 0.00 0.00 0.00 2.57
2254 3098 2.945447 ATTTCCACATCAACGCCATG 57.055 45.000 0.00 0.00 0.00 3.66
2259 3103 1.441738 CACATCAACGCCATGTCTCA 58.558 50.000 0.00 0.00 31.83 3.27
2279 3123 2.338577 ATGGTGGCAATCTAGTCTGC 57.661 50.000 9.47 9.47 37.86 4.26
2290 3134 3.594603 TCTAGTCTGCTGTGCCTAAAC 57.405 47.619 0.00 0.00 0.00 2.01
2298 3143 5.642063 GTCTGCTGTGCCTAAACTTACATAA 59.358 40.000 0.00 0.00 0.00 1.90
2299 3144 6.316390 GTCTGCTGTGCCTAAACTTACATAAT 59.684 38.462 0.00 0.00 0.00 1.28
2308 3153 7.715249 TGCCTAAACTTACATAATCCAGCTAAG 59.285 37.037 0.00 0.00 0.00 2.18
2347 3216 7.656707 ACATACAATTTGAAGGCATTTGAAC 57.343 32.000 2.79 0.00 0.00 3.18
2367 3236 1.261619 CACACGCTTCCTCTGTGTTTC 59.738 52.381 0.00 0.00 43.90 2.78
2371 3242 1.457303 CGCTTCCTCTGTGTTTCTTCG 59.543 52.381 0.00 0.00 0.00 3.79
2387 3259 2.165234 TCTTCGAGAGATGCAGGAACAG 59.835 50.000 0.00 0.00 41.60 3.16
2426 3298 6.707608 GCTATCATCATTCATCAGTACAACCA 59.292 38.462 0.00 0.00 0.00 3.67
2430 3302 8.352137 TCATCATTCATCAGTACAACCAAATT 57.648 30.769 0.00 0.00 0.00 1.82
2444 3316 9.040939 GTACAACCAAATTTGTGCTTCTTAATT 57.959 29.630 16.73 0.00 40.04 1.40
2445 3317 8.141835 ACAACCAAATTTGTGCTTCTTAATTC 57.858 30.769 16.73 0.00 38.31 2.17
2449 3321 7.708752 ACCAAATTTGTGCTTCTTAATTCGAAA 59.291 29.630 16.73 0.00 0.00 3.46
2450 3322 8.711457 CCAAATTTGTGCTTCTTAATTCGAAAT 58.289 29.630 16.73 0.00 0.00 2.17
2451 3323 9.731519 CAAATTTGTGCTTCTTAATTCGAAATC 57.268 29.630 10.15 0.00 0.00 2.17
2452 3324 9.474920 AAATTTGTGCTTCTTAATTCGAAATCA 57.525 25.926 0.00 0.00 0.00 2.57
2513 3385 7.619965 AGAGAGGGAAAATAAGAAGAAGACTG 58.380 38.462 0.00 0.00 0.00 3.51
2545 3417 7.759489 ATGTTTTTGAACTTACAGCCTATGA 57.241 32.000 0.00 0.00 0.00 2.15
2935 4101 5.193679 ACATATTTCAAGAAGTACCCAGCC 58.806 41.667 0.00 0.00 0.00 4.85
3013 4189 7.452880 TTTCCTTGTCATCCTAGTCAATTTG 57.547 36.000 0.00 0.00 0.00 2.32
3109 4288 4.389374 CCCAGGTTTATGCGAGTTGATAT 58.611 43.478 0.00 0.00 0.00 1.63
3327 4507 5.689383 TTTTGAACTGTAGATTGTGCTCC 57.311 39.130 0.00 0.00 0.00 4.70
3328 4508 4.350368 TTGAACTGTAGATTGTGCTCCA 57.650 40.909 0.00 0.00 0.00 3.86
3329 4509 4.558226 TGAACTGTAGATTGTGCTCCAT 57.442 40.909 0.00 0.00 0.00 3.41
3330 4510 4.910195 TGAACTGTAGATTGTGCTCCATT 58.090 39.130 0.00 0.00 0.00 3.16
3331 4511 5.316167 TGAACTGTAGATTGTGCTCCATTT 58.684 37.500 0.00 0.00 0.00 2.32
3332 4512 5.769662 TGAACTGTAGATTGTGCTCCATTTT 59.230 36.000 0.00 0.00 0.00 1.82
3333 4513 6.265196 TGAACTGTAGATTGTGCTCCATTTTT 59.735 34.615 0.00 0.00 0.00 1.94
3524 4704 0.180406 AGTCACGCTTGTTTCCACCT 59.820 50.000 0.00 0.00 0.00 4.00
3537 4717 7.201821 GCTTGTTTCCACCTAACTGCAATATAT 60.202 37.037 0.00 0.00 0.00 0.86
3636 4816 9.048446 GTAAAGTAAACCTGATTCTTGTGTGTA 57.952 33.333 0.00 0.00 0.00 2.90
3654 4834 4.095610 GTGTAGTGCATCGCCATTTTAAC 58.904 43.478 0.00 0.00 0.00 2.01
4341 5660 9.221775 GCAAAACCAATTAATACAGAAGTATCG 57.778 33.333 0.00 0.00 40.00 2.92
4362 5681 3.494924 CGGATGGGAATGCTCAGTCAATA 60.495 47.826 0.00 0.00 0.00 1.90
4363 5682 4.660168 GGATGGGAATGCTCAGTCAATAT 58.340 43.478 0.00 0.00 0.00 1.28
4497 5933 3.559242 CCACAAAAACGCAATGTTCCAAT 59.441 39.130 0.00 0.00 40.84 3.16
4510 5946 2.031245 TGTTCCAATTGTTGCTGCTACG 60.031 45.455 9.51 0.00 0.00 3.51
4873 6310 4.572389 CGAAGCATGGCAGTTCTTACTAAT 59.428 41.667 0.00 0.00 31.96 1.73
4875 6312 6.403636 CGAAGCATGGCAGTTCTTACTAATTT 60.404 38.462 0.00 0.00 31.96 1.82
4876 6313 6.840780 AGCATGGCAGTTCTTACTAATTTT 57.159 33.333 0.00 0.00 31.96 1.82
5164 6635 6.072948 CGAGAGTATCAGGTCAGTACATTAGG 60.073 46.154 0.00 0.00 37.82 2.69
5223 6694 8.306761 ACTTCAGAGTTTTGTTTGAGTTTTCAT 58.693 29.630 0.00 0.00 29.49 2.57
5299 6771 4.124851 ACCTATCTGACGCCTAAACTTG 57.875 45.455 0.00 0.00 0.00 3.16
5345 6817 4.984161 CACTTTTGGTTGCCATTCTACTTG 59.016 41.667 0.00 0.00 31.53 3.16
5517 7076 6.806751 TGATCTGTCATTAGTGCTTACTACC 58.193 40.000 0.00 0.00 0.00 3.18
5573 7132 1.040646 TCTCGCTTTCTGGTCTGTGT 58.959 50.000 0.00 0.00 0.00 3.72
5707 7266 4.452825 CCAGAGAAGTCATCTTGCATGAT 58.547 43.478 9.20 9.20 38.96 2.45
5819 7378 3.709987 CTTTTTCTGCAGGTTTCAGTGG 58.290 45.455 15.13 0.00 33.48 4.00
5961 7520 1.481363 TGGTGTTGTAACTGTGGTCGA 59.519 47.619 0.00 0.00 0.00 4.20
5962 7521 2.093606 TGGTGTTGTAACTGTGGTCGAA 60.094 45.455 0.00 0.00 0.00 3.71
6011 7570 7.759489 ATTTTCTACAAGCAGTGGAACATTA 57.241 32.000 7.45 0.00 45.83 1.90
6051 7611 3.939740 ATAGGATGATATGCGGCCATT 57.060 42.857 2.24 0.00 32.85 3.16
6067 7627 1.694169 ATTGGAGGAGCATCGGGGT 60.694 57.895 0.00 0.00 34.37 4.95
6069 7629 3.866582 GGAGGAGCATCGGGGTGG 61.867 72.222 0.00 0.00 34.37 4.61
6100 7660 2.684499 GGGAGGAGGGGGAAAGCTG 61.684 68.421 0.00 0.00 0.00 4.24
6119 7679 2.176273 CCGGATCTTGCTTGCCTCG 61.176 63.158 0.00 0.00 0.00 4.63
6122 7682 2.046892 ATCTTGCTTGCCTCGCGT 60.047 55.556 5.77 0.00 0.00 6.01
6125 7685 3.020026 CTTGCTTGCCTCGCGTGAG 62.020 63.158 19.15 19.15 42.18 3.51
6156 7716 2.100605 TGGTGTATACGCACATGCAA 57.899 45.000 17.76 0.00 40.89 4.08
6160 7720 4.636206 TGGTGTATACGCACATGCAAATTA 59.364 37.500 17.76 0.00 40.89 1.40
6253 7819 5.791666 TGCATTGAACATATGAAAGCCAAA 58.208 33.333 10.38 0.00 0.00 3.28
6267 7833 2.336088 CAAAAGGCAGTGCACCGG 59.664 61.111 18.61 7.56 0.00 5.28
6399 8662 8.980143 AATTGTTCCAATTCCTACGTTATTTG 57.020 30.769 0.00 0.00 0.00 2.32
6472 8735 5.856455 ACAAACAAAAACTCAGTTTCGTCAG 59.144 36.000 2.45 3.69 34.43 3.51
6479 8742 3.220110 ACTCAGTTTCGTCAGGACTACA 58.780 45.455 0.00 0.00 0.00 2.74
6516 8779 7.816995 TGCCAAACAGATTTGTGGTTAAATATC 59.183 33.333 0.00 0.00 43.23 1.63
6582 8846 8.469200 TGAGTGTTCAAAACTTGATGAAAGAAT 58.531 29.630 0.00 0.00 39.84 2.40
6677 8943 9.726438 ACATTCTAAGCTACAACTCTGTAAATT 57.274 29.630 0.00 0.00 37.58 1.82
6684 8950 8.261492 AGCTACAACTCTGTAAATTTCATCAG 57.739 34.615 0.00 3.00 37.58 2.90
6721 8987 2.033299 CCAGCACAACGAGAAAATGTGT 59.967 45.455 6.95 0.00 44.79 3.72
6734 9000 6.506500 AGAAAATGTGTTGCCTAGATTGAG 57.493 37.500 0.00 0.00 0.00 3.02
6786 9052 2.618045 CCCCAACCATGTAGAACAGTCC 60.618 54.545 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 218 2.488820 GTACGGCCGTGACTCTCC 59.511 66.667 40.02 14.64 0.00 3.71
522 560 6.797033 CGCGTCAAAATCTTCAAAACTAGATT 59.203 34.615 0.00 0.00 33.01 2.40
539 577 2.256174 CGTTAGATTCCTCGCGTCAAA 58.744 47.619 5.77 0.00 0.00 2.69
555 593 1.868498 CTCAAACCGCTTTCACCGTTA 59.132 47.619 0.00 0.00 0.00 3.18
640 681 2.029073 CACTCGTCGCAACCTGGT 59.971 61.111 0.00 0.00 0.00 4.00
665 706 2.176546 CGACAAAGGCGCACATGG 59.823 61.111 10.83 0.00 0.00 3.66
676 717 0.400213 ACCCCTCAGATTGCGACAAA 59.600 50.000 0.00 0.00 0.00 2.83
686 728 2.907892 AGATCACTTCAACCCCTCAGA 58.092 47.619 0.00 0.00 0.00 3.27
709 751 6.726764 AGTTGAGAAGTACTCCTATTCCTTGT 59.273 38.462 0.00 0.00 44.34 3.16
713 755 7.556996 TCACTAGTTGAGAAGTACTCCTATTCC 59.443 40.741 0.00 0.00 44.34 3.01
714 756 8.508883 TCACTAGTTGAGAAGTACTCCTATTC 57.491 38.462 0.00 0.00 44.34 1.75
715 757 9.482175 AATCACTAGTTGAGAAGTACTCCTATT 57.518 33.333 0.00 0.00 44.34 1.73
716 758 9.482175 AAATCACTAGTTGAGAAGTACTCCTAT 57.518 33.333 0.00 0.00 44.34 2.57
717 759 8.880991 AAATCACTAGTTGAGAAGTACTCCTA 57.119 34.615 0.00 0.00 44.34 2.94
718 760 7.362229 CGAAATCACTAGTTGAGAAGTACTCCT 60.362 40.741 0.00 0.00 44.34 3.69
719 761 6.748198 CGAAATCACTAGTTGAGAAGTACTCC 59.252 42.308 0.00 0.00 44.34 3.85
727 769 5.654603 TTAGCCGAAATCACTAGTTGAGA 57.345 39.130 0.00 0.00 37.77 3.27
747 789 1.078708 GCCTAGCACGGCCTGTTTA 60.079 57.895 0.00 0.00 44.41 2.01
748 790 2.359975 GCCTAGCACGGCCTGTTT 60.360 61.111 0.00 0.00 44.41 2.83
755 797 2.138320 CATGTCATAAGCCTAGCACGG 58.862 52.381 0.00 0.00 0.00 4.94
756 798 2.797156 GACATGTCATAAGCCTAGCACG 59.203 50.000 21.07 0.00 0.00 5.34
757 799 3.806521 CAGACATGTCATAAGCCTAGCAC 59.193 47.826 27.02 0.00 0.00 4.40
758 800 3.181462 CCAGACATGTCATAAGCCTAGCA 60.181 47.826 27.02 0.00 0.00 3.49
759 801 3.397482 CCAGACATGTCATAAGCCTAGC 58.603 50.000 27.02 0.00 0.00 3.42
760 802 3.805108 GCCCAGACATGTCATAAGCCTAG 60.805 52.174 27.02 6.69 0.00 3.02
761 803 2.104792 GCCCAGACATGTCATAAGCCTA 59.895 50.000 27.02 0.00 0.00 3.93
762 804 1.133976 GCCCAGACATGTCATAAGCCT 60.134 52.381 27.02 1.97 0.00 4.58
763 805 1.133976 AGCCCAGACATGTCATAAGCC 60.134 52.381 27.02 10.24 0.00 4.35
764 806 1.945394 CAGCCCAGACATGTCATAAGC 59.055 52.381 27.02 21.53 0.00 3.09
765 807 2.941064 CACAGCCCAGACATGTCATAAG 59.059 50.000 27.02 13.57 0.00 1.73
766 808 2.940971 GCACAGCCCAGACATGTCATAA 60.941 50.000 27.02 0.00 0.00 1.90
767 809 1.407299 GCACAGCCCAGACATGTCATA 60.407 52.381 27.02 0.00 0.00 2.15
768 810 0.679002 GCACAGCCCAGACATGTCAT 60.679 55.000 27.02 10.02 0.00 3.06
769 811 1.302752 GCACAGCCCAGACATGTCA 60.303 57.895 27.02 0.00 0.00 3.58
770 812 2.042831 GGCACAGCCCAGACATGTC 61.043 63.158 18.47 18.47 44.06 3.06
771 813 2.034687 GGCACAGCCCAGACATGT 59.965 61.111 0.00 0.00 44.06 3.21
810 852 2.959507 AAAAGATAAACGGGCCATGC 57.040 45.000 4.39 0.00 0.00 4.06
811 853 4.157656 TCAGAAAAAGATAAACGGGCCATG 59.842 41.667 4.39 0.00 0.00 3.66
812 854 4.157840 GTCAGAAAAAGATAAACGGGCCAT 59.842 41.667 4.39 0.00 0.00 4.40
813 855 3.504520 GTCAGAAAAAGATAAACGGGCCA 59.495 43.478 4.39 0.00 0.00 5.36
814 856 3.756963 AGTCAGAAAAAGATAAACGGGCC 59.243 43.478 0.00 0.00 0.00 5.80
815 857 5.372547 AAGTCAGAAAAAGATAAACGGGC 57.627 39.130 0.00 0.00 0.00 6.13
816 858 9.908152 AATAAAAGTCAGAAAAAGATAAACGGG 57.092 29.630 0.00 0.00 0.00 5.28
846 888 1.067295 CCTTGAGGCCCAGGCATATA 58.933 55.000 11.50 0.00 44.11 0.86
847 889 1.723128 CCCTTGAGGCCCAGGCATAT 61.723 60.000 11.50 0.00 44.11 1.78
955 1027 1.258445 GGAGGGAGACGGAAGCAGAA 61.258 60.000 0.00 0.00 0.00 3.02
1142 1233 4.659529 AAACTAAAGAGGGAGGGGAAAG 57.340 45.455 0.00 0.00 0.00 2.62
1143 1234 4.668335 AGAAAACTAAAGAGGGAGGGGAAA 59.332 41.667 0.00 0.00 0.00 3.13
1144 1235 4.042934 CAGAAAACTAAAGAGGGAGGGGAA 59.957 45.833 0.00 0.00 0.00 3.97
1145 1236 3.587506 CAGAAAACTAAAGAGGGAGGGGA 59.412 47.826 0.00 0.00 0.00 4.81
1149 1240 4.257731 GGAGCAGAAAACTAAAGAGGGAG 58.742 47.826 0.00 0.00 0.00 4.30
1161 1252 2.874457 GCTAGGGTTTCGGAGCAGAAAA 60.874 50.000 4.07 0.00 41.18 2.29
1164 1255 0.614979 AGCTAGGGTTTCGGAGCAGA 60.615 55.000 0.00 0.00 37.40 4.26
1488 2246 1.606889 GTCCCTGGTCTCGTCCTGT 60.607 63.158 0.00 0.00 0.00 4.00
1548 2306 0.752009 TCGCCTCTATGTCCTCGCTT 60.752 55.000 0.00 0.00 0.00 4.68
1654 2423 4.571580 TCCCTATTAAAACCGCGTAACATG 59.428 41.667 4.92 0.00 0.00 3.21
1768 2539 6.091441 CAGTAAGGAATCAAACTAGACAGTGC 59.909 42.308 0.00 0.00 34.36 4.40
1769 2540 7.155328 ACAGTAAGGAATCAAACTAGACAGTG 58.845 38.462 0.00 0.00 34.36 3.66
1862 2642 7.494298 ACTTTCGGTGCATATTTCTTTTGTTTT 59.506 29.630 0.00 0.00 0.00 2.43
1935 2719 5.465532 TGTGATATTTTTCCTGCTGCAAA 57.534 34.783 3.02 0.00 0.00 3.68
2059 2872 3.306989 CCAGACATCCACTACAAAGAGCA 60.307 47.826 0.00 0.00 0.00 4.26
2091 2904 9.995003 GAAGATACTTCAGAGATATTGGTTCAT 57.005 33.333 6.63 0.00 0.00 2.57
2167 2994 7.379529 ACAAATAATGCAACGAAGTCTTTCTTG 59.620 33.333 0.00 0.00 45.00 3.02
2176 3003 9.128107 AGTGAAATTACAAATAATGCAACGAAG 57.872 29.630 0.00 0.00 31.07 3.79
2228 3072 4.156008 GGCGTTGATGTGGAAATAGAAAGT 59.844 41.667 0.00 0.00 0.00 2.66
2247 3091 0.677731 CCACCATTGAGACATGGCGT 60.678 55.000 0.00 0.00 41.53 5.68
2254 3098 3.873952 GACTAGATTGCCACCATTGAGAC 59.126 47.826 0.00 0.00 0.00 3.36
2259 3103 2.240667 AGCAGACTAGATTGCCACCATT 59.759 45.455 16.03 0.00 41.17 3.16
2279 3123 6.238484 GCTGGATTATGTAAGTTTAGGCACAG 60.238 42.308 0.00 0.00 0.00 3.66
2290 3134 7.445945 ACCTAAGCTTAGCTGGATTATGTAAG 58.554 38.462 25.38 10.63 39.62 2.34
2298 3143 3.107601 TGTGACCTAAGCTTAGCTGGAT 58.892 45.455 25.38 9.48 39.62 3.41
2299 3144 2.233922 GTGTGACCTAAGCTTAGCTGGA 59.766 50.000 25.38 8.04 39.62 3.86
2308 3153 3.670625 TGTATGTTGGTGTGACCTAAGC 58.329 45.455 0.00 0.00 39.58 3.09
2347 3216 1.261619 GAAACACAGAGGAAGCGTGTG 59.738 52.381 0.00 0.24 42.85 3.82
2367 3236 2.165234 TCTGTTCCTGCATCTCTCGAAG 59.835 50.000 0.00 0.00 0.00 3.79
2371 3242 4.134379 TCATTCTGTTCCTGCATCTCTC 57.866 45.455 0.00 0.00 0.00 3.20
2418 3290 7.995463 TTAAGAAGCACAAATTTGGTTGTAC 57.005 32.000 21.74 8.77 39.73 2.90
2426 3298 9.474920 TGATTTCGAATTAAGAAGCACAAATTT 57.525 25.926 0.00 0.00 0.00 1.82
2430 3302 7.421599 TGTTGATTTCGAATTAAGAAGCACAA 58.578 30.769 0.00 0.00 0.00 3.33
2444 3316 7.622893 TCAATATGTTCCATGTTGATTTCGA 57.377 32.000 10.99 0.00 0.00 3.71
2445 3317 8.861033 ATTCAATATGTTCCATGTTGATTTCG 57.139 30.769 14.44 0.00 31.07 3.46
2449 3321 7.716560 TCTCGATTCAATATGTTCCATGTTGAT 59.283 33.333 14.44 7.40 31.07 2.57
2450 3322 7.047271 TCTCGATTCAATATGTTCCATGTTGA 58.953 34.615 10.99 10.99 0.00 3.18
2451 3323 7.225341 TCTCTCGATTCAATATGTTCCATGTTG 59.775 37.037 7.21 7.21 0.00 3.33
2452 3324 7.275183 TCTCTCGATTCAATATGTTCCATGTT 58.725 34.615 0.00 0.00 0.00 2.71
2464 3336 6.240549 ACCCACTTTATCTCTCGATTCAAT 57.759 37.500 0.00 0.00 0.00 2.57
2465 3337 5.677319 ACCCACTTTATCTCTCGATTCAA 57.323 39.130 0.00 0.00 0.00 2.69
2468 3340 6.366340 TCTCTACCCACTTTATCTCTCGATT 58.634 40.000 0.00 0.00 0.00 3.34
2472 3344 4.830600 CCCTCTCTACCCACTTTATCTCTC 59.169 50.000 0.00 0.00 0.00 3.20
2474 3346 4.805744 TCCCTCTCTACCCACTTTATCTC 58.194 47.826 0.00 0.00 0.00 2.75
2475 3347 4.901785 TCCCTCTCTACCCACTTTATCT 57.098 45.455 0.00 0.00 0.00 1.98
2513 3385 9.636965 GCTGTAAGTTCAAAAACATTTCATTTC 57.363 29.630 0.00 0.00 37.88 2.17
2536 3408 4.096984 GTGGGACTCAAATTTCATAGGCTG 59.903 45.833 0.00 0.00 0.00 4.85
2545 3417 2.949447 ACAGCAGTGGGACTCAAATTT 58.051 42.857 0.00 0.00 0.00 1.82
2585 3710 7.956943 GCACTGCGAATTTTATAAAGCAAAAAT 59.043 29.630 10.10 0.00 36.98 1.82
2935 4101 9.749340 AAGGGAAATAATAATTACCCTATTCGG 57.251 33.333 9.01 0.00 45.66 4.30
3002 4176 7.522725 AGGCAACAAGATCAACAAATTGACTAG 60.523 37.037 0.00 0.00 43.90 2.57
3013 4189 5.689383 TGTTTCTAGGCAACAAGATCAAC 57.311 39.130 6.07 0.00 41.41 3.18
3109 4288 1.722034 AGACAACAAGAGGGAGAGCA 58.278 50.000 0.00 0.00 0.00 4.26
3309 4489 5.886960 AAATGGAGCACAATCTACAGTTC 57.113 39.130 0.00 0.00 30.13 3.01
3310 4490 6.655078 AAAAATGGAGCACAATCTACAGTT 57.345 33.333 0.00 0.00 36.85 3.16
3331 4511 7.397892 TGGAACACAATCTACAGTTCAAAAA 57.602 32.000 0.00 0.00 41.49 1.94
3406 4586 3.849574 TCCCACTGAAATCAGGGTGATTA 59.150 43.478 14.50 0.00 45.57 1.75
3537 4717 7.313646 GCCTATAGCTTTCATGTTCGTAGATA 58.686 38.462 0.00 0.00 38.99 1.98
3636 4816 1.467374 GCGTTAAAATGGCGATGCACT 60.467 47.619 0.00 0.00 0.00 4.40
3654 4834 9.321590 CAATAATGATTGTAACTGACATATGCG 57.678 33.333 1.58 0.00 38.07 4.73
4341 5660 2.425143 TTGACTGAGCATTCCCATCC 57.575 50.000 0.00 0.00 0.00 3.51
4362 5681 5.387788 TCCATATTAATTGGCTGCACTGAT 58.612 37.500 0.50 0.00 34.06 2.90
4363 5682 4.790937 TCCATATTAATTGGCTGCACTGA 58.209 39.130 0.50 0.00 34.06 3.41
4448 5884 7.639162 AGTTCTTAGTGTTAGTTTGATCACG 57.361 36.000 0.00 0.00 36.16 4.35
4497 5933 2.480037 CAGATCAACGTAGCAGCAACAA 59.520 45.455 0.00 0.00 0.00 2.83
4510 5946 6.150140 ACTTCCTTTGCAATCTACAGATCAAC 59.850 38.462 0.00 0.00 32.75 3.18
4564 6000 0.250901 GGGTGCTTTTCCTGCTCTCA 60.251 55.000 0.00 0.00 0.00 3.27
4828 6265 9.529325 CTTCGGTGTCAATTGTAGAGAATAATA 57.471 33.333 5.13 0.00 0.00 0.98
4837 6274 3.181507 CCATGCTTCGGTGTCAATTGTAG 60.182 47.826 5.13 0.00 0.00 2.74
4875 6312 0.309612 GAAGCGCCGAGAACCAAAAA 59.690 50.000 2.29 0.00 0.00 1.94
4876 6313 0.534203 AGAAGCGCCGAGAACCAAAA 60.534 50.000 2.29 0.00 0.00 2.44
4884 6321 2.825726 TTCTCTGCAGAAGCGCCGAG 62.826 60.000 18.85 3.31 46.23 4.63
4885 6322 2.931068 TTCTCTGCAGAAGCGCCGA 61.931 57.895 18.85 7.45 46.23 5.54
4932 6369 8.000780 AGGCAAGTGACAGGATAATAATTTTC 57.999 34.615 0.00 0.00 0.00 2.29
5164 6635 5.811399 TTTCCGGTGTAACATCATCATTC 57.189 39.130 0.00 0.00 39.98 2.67
5195 6666 8.965986 AAAACTCAAACAAAACTCTGAAGTAC 57.034 30.769 0.00 0.00 33.48 2.73
5197 6668 7.657336 TGAAAACTCAAACAAAACTCTGAAGT 58.343 30.769 0.00 0.00 37.32 3.01
5254 6725 3.719268 ACATTCCTTACTGGCATGACA 57.281 42.857 0.00 0.00 41.13 3.58
5273 6744 5.067544 AGTTTAGGCGTCAGATAGGTTCTAC 59.932 44.000 0.00 0.00 31.77 2.59
5517 7076 7.759433 AGGAATCACAACTTTTTACACACAAAG 59.241 33.333 0.00 0.00 36.28 2.77
5550 7109 2.005451 CAGACCAGAAAGCGAGATTGG 58.995 52.381 0.00 0.00 35.07 3.16
5573 7132 2.484770 GCGCAATGGAAGGACCTGTATA 60.485 50.000 0.30 0.00 39.86 1.47
5707 7266 1.376466 GAGACAAGCTTGCCCTCCA 59.624 57.895 26.27 0.00 0.00 3.86
5819 7378 3.781162 GGCGCGACCAAACCGTAC 61.781 66.667 12.10 0.00 38.86 3.67
5961 7520 7.348815 TGAATAGATCAAACTGGGATGTGATT 58.651 34.615 0.00 0.00 34.30 2.57
5962 7521 6.903516 TGAATAGATCAAACTGGGATGTGAT 58.096 36.000 0.00 0.00 34.30 3.06
6051 7611 3.083349 CACCCCGATGCTCCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
6100 7660 2.439156 AGGCAAGCAAGATCCGGC 60.439 61.111 0.00 0.00 0.00 6.13
6119 7679 3.537206 AACTCCACCTGCCTCACGC 62.537 63.158 0.00 0.00 38.31 5.34
6122 7682 1.770110 ACCAACTCCACCTGCCTCA 60.770 57.895 0.00 0.00 0.00 3.86
6125 7685 0.328258 ATACACCAACTCCACCTGCC 59.672 55.000 0.00 0.00 0.00 4.85
6134 7694 2.006888 GCATGTGCGTATACACCAACT 58.993 47.619 3.32 0.00 39.93 3.16
6232 7798 7.298507 CCTTTTGGCTTTCATATGTTCAATG 57.701 36.000 1.90 0.00 0.00 2.82
6253 7819 0.960364 CATTACCGGTGCACTGCCTT 60.960 55.000 19.93 8.87 0.00 4.35
6267 7833 8.658609 AGTGCATTGCAATTATCAAAACATTAC 58.341 29.630 13.94 0.00 41.47 1.89
6433 8696 1.818674 GTTTGTGCGGGGAGATGAAAT 59.181 47.619 0.00 0.00 0.00 2.17
6472 8735 2.032290 GGCAAACGTTCTGTTGTAGTCC 60.032 50.000 0.00 0.00 40.84 3.85
6479 8742 2.490115 TCTGTTTGGCAAACGTTCTGTT 59.510 40.909 31.23 0.00 44.28 3.16
6516 8779 5.927115 GGTAACGATTTAGATAGCCCTTCAG 59.073 44.000 0.00 0.00 0.00 3.02
6677 8943 8.634335 TGGTTTTGTCTATGAATTCTGATGAA 57.366 30.769 7.05 0.49 36.54 2.57
6678 8944 7.148188 GCTGGTTTTGTCTATGAATTCTGATGA 60.148 37.037 7.05 0.00 0.00 2.92
6684 8950 6.012658 TGTGCTGGTTTTGTCTATGAATTC 57.987 37.500 0.00 0.00 0.00 2.17
6721 8987 3.943381 CTGAATGTGCTCAATCTAGGCAA 59.057 43.478 5.51 0.00 37.73 4.52
6734 9000 1.212751 GGCGGGTTTCTGAATGTGC 59.787 57.895 0.00 0.00 0.00 4.57
6786 9052 0.393077 ACCGAGTCTTGGACAGTTGG 59.607 55.000 13.57 0.00 34.60 3.77


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

AutoCloner maintained by Alex Coulton.