Multiple sequence alignment - TraesCS3D01G078600

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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 TraesCS3D01G078600 chr3D 100.000 4011 0 0 1 4011 39210381 39206371 0.000000e+00 7408.0
1 TraesCS3D01G078600 chr3D 86.205 1515 110 33 1480 2957 39302217 39300765 0.000000e+00 1548.0
2 TraesCS3D01G078600 chr3D 95.905 757 30 1 1 756 39245422 39244666 0.000000e+00 1225.0
3 TraesCS3D01G078600 chr3D 87.234 564 39 11 3447 3987 39300263 39299710 2.650000e-171 612.0
4 TraesCS3D01G078600 chr3D 89.234 483 28 12 2984 3450 39300766 39300292 2.080000e-162 582.0
5 TraesCS3D01G078600 chr3D 94.068 236 7 4 1196 1428 39302535 39302304 6.380000e-93 351.0
6 TraesCS3D01G078600 chr3D 97.826 46 1 0 1436 1481 12525700 12525745 3.320000e-11 80.5
7 TraesCS3D01G078600 chr3B 88.555 1433 109 25 1480 2877 62011934 62010522 0.000000e+00 1687.0
8 TraesCS3D01G078600 chr3B 87.909 1497 92 32 2006 3450 62216110 62214651 0.000000e+00 1679.0
9 TraesCS3D01G078600 chr3B 91.441 888 38 19 2875 3728 62010450 62009567 0.000000e+00 1184.0
10 TraesCS3D01G078600 chr3B 87.456 566 39 10 3447 3989 62214622 62214066 1.220000e-174 623.0
11 TraesCS3D01G078600 chr3B 88.802 509 30 19 1480 1977 62216604 62216112 2.060000e-167 599.0
12 TraesCS3D01G078600 chr3B 93.233 266 9 4 1151 1409 62012273 62012010 2.260000e-102 383.0
13 TraesCS3D01G078600 chr3B 79.304 517 86 18 111 619 127317407 127317910 3.840000e-90 342.0
14 TraesCS3D01G078600 chr3B 91.453 234 8 8 1196 1428 62216913 62216691 1.080000e-80 311.0
15 TraesCS3D01G078600 chr3B 91.371 197 12 1 3798 3989 62006508 62006312 8.550000e-67 265.0
16 TraesCS3D01G078600 chr3B 95.918 49 1 1 1046 1094 62013837 62013790 1.200000e-10 78.7
17 TraesCS3D01G078600 chr3B 95.833 48 2 0 1432 1479 774168312 774168359 1.200000e-10 78.7
18 TraesCS3D01G078600 chr3B 92.593 54 3 1 1432 1485 545380111 545380163 4.300000e-10 76.8
19 TraesCS3D01G078600 chr3A 89.921 1270 79 23 2221 3450 50547174 50545914 0.000000e+00 1591.0
20 TraesCS3D01G078600 chr3A 90.056 714 55 11 1480 2191 50547862 50547163 0.000000e+00 911.0
21 TraesCS3D01G078600 chr3A 89.432 757 31 15 2222 2956 50639573 50638844 0.000000e+00 909.0
22 TraesCS3D01G078600 chr3A 89.379 725 50 14 1480 2191 50640273 50639563 0.000000e+00 887.0
23 TraesCS3D01G078600 chr3A 90.947 475 29 8 960 1428 50548418 50547952 9.460000e-176 627.0
24 TraesCS3D01G078600 chr3A 87.216 485 35 10 2986 3450 50638842 50638365 9.870000e-146 527.0
25 TraesCS3D01G078600 chr3A 77.693 789 126 28 1 752 685363710 685362935 1.710000e-118 436.0
26 TraesCS3D01G078600 chr3A 85.132 417 28 11 3594 3989 50638217 50637814 2.910000e-106 396.0
27 TraesCS3D01G078600 chr3A 84.397 423 33 9 3518 3920 50545785 50545376 6.290000e-103 385.0
28 TraesCS3D01G078600 chr3A 94.850 233 9 2 1196 1428 50640589 50640360 1.060000e-95 361.0
29 TraesCS3D01G078600 chr3A 91.304 161 9 3 776 933 50558405 50558247 8.730000e-52 215.0
30 TraesCS3D01G078600 chr3A 92.105 76 5 1 262 337 569227682 569227608 5.480000e-19 106.0
31 TraesCS3D01G078600 chr2D 97.493 758 15 2 1 757 33323463 33324217 0.000000e+00 1291.0
32 TraesCS3D01G078600 chr2D 94.000 50 3 0 1432 1481 211200308 211200357 4.300000e-10 76.8
33 TraesCS3D01G078600 chr7D 90.562 498 25 4 262 757 135420622 135420145 1.220000e-179 640.0
34 TraesCS3D01G078600 chr7D 96.310 271 10 0 1 271 135420816 135420546 2.840000e-121 446.0
35 TraesCS3D01G078600 chr7D 86.275 153 19 2 51 202 135420863 135420712 8.920000e-37 165.0
36 TraesCS3D01G078600 chr1A 80.796 729 112 20 51 757 504706469 504707191 2.730000e-151 545.0
37 TraesCS3D01G078600 chr5A 82.033 423 46 10 1480 1897 632224300 632223903 2.310000e-87 333.0
38 TraesCS3D01G078600 chr5A 88.462 182 14 3 1248 1428 564680197 564680022 3.140000e-51 213.0
39 TraesCS3D01G078600 chr5A 85.246 183 16 5 1480 1658 564679936 564679761 1.150000e-40 178.0
40 TraesCS3D01G078600 chr5A 95.745 47 2 0 1433 1479 406022925 406022971 4.300000e-10 76.8
41 TraesCS3D01G078600 chrUn 92.683 205 15 0 1 205 294162213 294162009 3.030000e-76 296.0
42 TraesCS3D01G078600 chrUn 85.714 105 15 0 1 105 294162116 294162012 1.180000e-20 111.0
43 TraesCS3D01G078600 chr2B 92.718 206 14 1 1 205 594202241 594202036 3.030000e-76 296.0
44 TraesCS3D01G078600 chr2B 84.729 203 29 2 1 202 143637213 143637012 6.800000e-48 202.0
45 TraesCS3D01G078600 chr2B 81.773 203 37 0 2521 2723 84817752 84817954 1.920000e-38 171.0
46 TraesCS3D01G078600 chr5B 79.832 357 55 13 416 757 690876356 690876710 1.110000e-60 244.0
47 TraesCS3D01G078600 chr5B 89.011 182 13 3 1248 1428 385249834 385250009 6.750000e-53 219.0
48 TraesCS3D01G078600 chr5B 97.727 44 1 0 1438 1481 686200445 686200402 4.300000e-10 76.8
49 TraesCS3D01G078600 chr6B 88.660 194 11 6 1248 1440 68221069 68221252 4.030000e-55 226.0
50 TraesCS3D01G078600 chr7B 90.116 172 10 3 1258 1428 684165019 684165184 2.430000e-52 217.0
51 TraesCS3D01G078600 chr7B 87.978 183 11 2 1480 1658 614249237 614249062 5.250000e-49 206.0
52 TraesCS3D01G078600 chr7B 87.978 183 11 2 1480 1658 698630560 698630385 5.250000e-49 206.0
53 TraesCS3D01G078600 chr4A 87.432 183 12 2 1480 1658 661807697 661807522 2.440000e-47 200.0
54 TraesCS3D01G078600 chr4A 83.744 203 33 0 2522 2724 173932155 173931953 4.090000e-45 193.0
55 TraesCS3D01G078600 chr4B 86.982 169 18 3 593 757 37554008 37554176 1.900000e-43 187.0
56 TraesCS3D01G078600 chr2A 81.773 203 37 0 2521 2723 54817556 54817354 1.920000e-38 171.0
57 TraesCS3D01G078600 chr1B 78.010 191 27 12 779 964 488480812 488480992 5.480000e-19 106.0
58 TraesCS3D01G078600 chr5D 86.667 90 6 4 880 964 476786884 476786796 1.190000e-15 95.3
59 TraesCS3D01G078600 chr5D 95.745 47 2 0 1433 1479 290070548 290070502 4.300000e-10 76.8
60 TraesCS3D01G078600 chr6A 94.000 50 3 0 1432 1481 39864167 39864216 4.300000e-10 76.8
61 TraesCS3D01G078600 chr6A 95.556 45 2 0 883 927 615179518 615179474 5.560000e-09 73.1
62 TraesCS3D01G078600 chr7A 93.878 49 3 0 1433 1481 699921354 699921402 1.550000e-09 75.0


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 TraesCS3D01G078600 chr3D 39206371 39210381 4010 True 7408.00 7408 100.00000 1 4011 1 chr3D.!!$R1 4010
1 TraesCS3D01G078600 chr3D 39244666 39245422 756 True 1225.00 1225 95.90500 1 756 1 chr3D.!!$R2 755
2 TraesCS3D01G078600 chr3D 39299710 39302535 2825 True 773.25 1548 89.18525 1196 3987 4 chr3D.!!$R3 2791
3 TraesCS3D01G078600 chr3B 62214066 62216913 2847 True 803.00 1679 88.90500 1196 3989 4 chr3B.!!$R2 2793
4 TraesCS3D01G078600 chr3B 62006312 62013837 7525 True 719.54 1687 92.10360 1046 3989 5 chr3B.!!$R1 2943
5 TraesCS3D01G078600 chr3B 127317407 127317910 503 False 342.00 342 79.30400 111 619 1 chr3B.!!$F1 508
6 TraesCS3D01G078600 chr3A 50545376 50548418 3042 True 878.50 1591 88.83025 960 3920 4 chr3A.!!$R4 2960
7 TraesCS3D01G078600 chr3A 50637814 50640589 2775 True 616.00 909 89.20180 1196 3989 5 chr3A.!!$R5 2793
8 TraesCS3D01G078600 chr3A 685362935 685363710 775 True 436.00 436 77.69300 1 752 1 chr3A.!!$R3 751
9 TraesCS3D01G078600 chr2D 33323463 33324217 754 False 1291.00 1291 97.49300 1 757 1 chr2D.!!$F1 756
10 TraesCS3D01G078600 chr7D 135420145 135420863 718 True 417.00 640 91.04900 1 757 3 chr7D.!!$R1 756
11 TraesCS3D01G078600 chr1A 504706469 504707191 722 False 545.00 545 80.79600 51 757 1 chr1A.!!$F1 706

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
757 847 0.033228 CGCTGGGCTCTATCCTCTTG 59.967 60.0 0.00 0.0 0.00 3.02 F
799 889 0.107410 TTGCCACGACCTGTTGTCTT 60.107 50.0 0.00 0.0 42.13 3.01 F
800 890 0.107410 TGCCACGACCTGTTGTCTTT 60.107 50.0 0.00 0.0 42.13 2.52 F
957 1047 0.107703 TCCCTGCAGCGTCAAATAGG 60.108 55.0 8.66 0.3 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2732 4447 1.066303 CAAGCGCAGGAGTAGAGTAGG 59.934 57.143 11.47 0.0 0.00 3.18 R
2812 4533 3.300009 CATGAGAAGAAACAAACGGCAC 58.700 45.455 0.00 0.0 0.00 5.01 R
2924 4720 2.037902 TCGTTCCTGCCATCAGTACAAA 59.962 45.455 0.00 0.0 38.66 2.83 R
3225 5040 9.250624 CCGCCAAAAGCTAAGATATATAGATAC 57.749 37.037 0.00 0.0 40.39 2.24 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
204 261 3.366883 GGCGATGATTTTTGCTACAACCA 60.367 43.478 0.00 0.00 0.00 3.67
234 291 1.681793 GGAGCTAGAACCGATAGTGCA 59.318 52.381 0.00 0.00 0.00 4.57
452 512 0.250727 GGTGGGAGCTACAAGCAACA 60.251 55.000 0.00 0.00 45.56 3.33
757 847 0.033228 CGCTGGGCTCTATCCTCTTG 59.967 60.000 0.00 0.00 0.00 3.02
758 848 1.418334 GCTGGGCTCTATCCTCTTGA 58.582 55.000 0.00 0.00 0.00 3.02
759 849 1.765314 GCTGGGCTCTATCCTCTTGAA 59.235 52.381 0.00 0.00 0.00 2.69
760 850 2.484594 GCTGGGCTCTATCCTCTTGAAC 60.485 54.545 0.00 0.00 0.00 3.18
761 851 2.103941 CTGGGCTCTATCCTCTTGAACC 59.896 54.545 0.00 0.00 0.00 3.62
762 852 1.069358 GGGCTCTATCCTCTTGAACCG 59.931 57.143 0.00 0.00 0.00 4.44
763 853 1.069358 GGCTCTATCCTCTTGAACCGG 59.931 57.143 0.00 0.00 0.00 5.28
764 854 1.757699 GCTCTATCCTCTTGAACCGGT 59.242 52.381 0.00 0.00 0.00 5.28
765 855 2.482142 GCTCTATCCTCTTGAACCGGTG 60.482 54.545 8.52 0.00 0.00 4.94
766 856 1.480954 TCTATCCTCTTGAACCGGTGC 59.519 52.381 8.52 6.80 0.00 5.01
767 857 0.174845 TATCCTCTTGAACCGGTGCG 59.825 55.000 8.52 0.00 0.00 5.34
768 858 3.423154 CCTCTTGAACCGGTGCGC 61.423 66.667 8.52 0.00 0.00 6.09
769 859 3.423154 CTCTTGAACCGGTGCGCC 61.423 66.667 8.52 6.11 0.00 6.53
790 880 4.811761 GCGCGAATTGCCACGACC 62.812 66.667 12.10 0.00 42.08 4.79
791 881 3.118454 CGCGAATTGCCACGACCT 61.118 61.111 0.00 0.00 42.08 3.85
792 882 2.480555 GCGAATTGCCACGACCTG 59.519 61.111 0.00 0.00 37.76 4.00
793 883 2.325082 GCGAATTGCCACGACCTGT 61.325 57.895 0.00 0.00 37.76 4.00
794 884 1.852067 GCGAATTGCCACGACCTGTT 61.852 55.000 0.00 0.00 37.76 3.16
795 885 0.110238 CGAATTGCCACGACCTGTTG 60.110 55.000 0.00 0.00 0.00 3.33
796 886 0.951558 GAATTGCCACGACCTGTTGT 59.048 50.000 0.00 0.00 0.00 3.32
797 887 0.951558 AATTGCCACGACCTGTTGTC 59.048 50.000 0.00 0.00 40.81 3.18
798 888 0.108585 ATTGCCACGACCTGTTGTCT 59.891 50.000 0.00 0.00 42.13 3.41
799 889 0.107410 TTGCCACGACCTGTTGTCTT 60.107 50.000 0.00 0.00 42.13 3.01
800 890 0.107410 TGCCACGACCTGTTGTCTTT 60.107 50.000 0.00 0.00 42.13 2.52
801 891 0.586802 GCCACGACCTGTTGTCTTTC 59.413 55.000 0.00 0.00 42.13 2.62
802 892 1.226746 CCACGACCTGTTGTCTTTCC 58.773 55.000 0.00 0.00 42.13 3.13
803 893 0.859232 CACGACCTGTTGTCTTTCCG 59.141 55.000 0.00 0.00 42.13 4.30
804 894 0.249741 ACGACCTGTTGTCTTTCCGG 60.250 55.000 0.00 0.00 42.13 5.14
805 895 0.949105 CGACCTGTTGTCTTTCCGGG 60.949 60.000 0.00 0.00 42.13 5.73
806 896 0.108019 GACCTGTTGTCTTTCCGGGT 59.892 55.000 0.00 0.00 41.03 5.28
807 897 0.549469 ACCTGTTGTCTTTCCGGGTT 59.451 50.000 0.00 0.00 34.11 4.11
808 898 0.951558 CCTGTTGTCTTTCCGGGTTG 59.048 55.000 0.00 0.00 0.00 3.77
809 899 0.951558 CTGTTGTCTTTCCGGGTTGG 59.048 55.000 0.00 0.00 40.09 3.77
810 900 1.104577 TGTTGTCTTTCCGGGTTGGC 61.105 55.000 0.00 0.00 37.80 4.52
811 901 0.822121 GTTGTCTTTCCGGGTTGGCT 60.822 55.000 0.00 0.00 37.80 4.75
812 902 0.821711 TTGTCTTTCCGGGTTGGCTG 60.822 55.000 0.00 0.00 37.80 4.85
813 903 1.072505 GTCTTTCCGGGTTGGCTGA 59.927 57.895 0.00 0.00 37.80 4.26
814 904 0.322546 GTCTTTCCGGGTTGGCTGAT 60.323 55.000 0.00 0.00 37.80 2.90
815 905 0.322456 TCTTTCCGGGTTGGCTGATG 60.322 55.000 0.00 0.00 37.80 3.07
816 906 1.937546 CTTTCCGGGTTGGCTGATGC 61.938 60.000 0.00 0.00 37.80 3.91
817 907 4.776322 TCCGGGTTGGCTGATGCG 62.776 66.667 0.00 0.00 40.82 4.73
818 908 4.776322 CCGGGTTGGCTGATGCGA 62.776 66.667 0.00 0.00 40.82 5.10
819 909 2.514592 CGGGTTGGCTGATGCGAT 60.515 61.111 0.00 0.00 40.82 4.58
820 910 2.114670 CGGGTTGGCTGATGCGATT 61.115 57.895 0.00 0.00 40.82 3.34
821 911 1.434696 GGGTTGGCTGATGCGATTG 59.565 57.895 0.00 0.00 40.82 2.67
822 912 1.434696 GGTTGGCTGATGCGATTGG 59.565 57.895 0.00 0.00 40.82 3.16
823 913 1.031571 GGTTGGCTGATGCGATTGGA 61.032 55.000 0.00 0.00 40.82 3.53
824 914 0.379669 GTTGGCTGATGCGATTGGAG 59.620 55.000 0.00 0.00 40.82 3.86
825 915 1.378882 TTGGCTGATGCGATTGGAGC 61.379 55.000 0.00 0.00 40.82 4.70
826 916 1.525535 GGCTGATGCGATTGGAGCT 60.526 57.895 0.00 0.00 40.82 4.09
827 917 1.099879 GGCTGATGCGATTGGAGCTT 61.100 55.000 0.00 0.00 40.82 3.74
828 918 1.586422 GCTGATGCGATTGGAGCTTA 58.414 50.000 0.00 0.00 35.28 3.09
829 919 1.262683 GCTGATGCGATTGGAGCTTAC 59.737 52.381 0.00 0.00 35.28 2.34
830 920 2.831333 CTGATGCGATTGGAGCTTACT 58.169 47.619 0.00 0.00 35.28 2.24
831 921 3.800261 GCTGATGCGATTGGAGCTTACTA 60.800 47.826 0.00 0.00 35.28 1.82
832 922 3.717707 TGATGCGATTGGAGCTTACTAC 58.282 45.455 0.00 0.00 35.28 2.73
833 923 2.596904 TGCGATTGGAGCTTACTACC 57.403 50.000 0.00 0.00 35.28 3.18
834 924 1.202371 TGCGATTGGAGCTTACTACCG 60.202 52.381 0.00 0.00 35.28 4.02
835 925 1.868519 GCGATTGGAGCTTACTACCGG 60.869 57.143 0.00 0.00 0.00 5.28
836 926 1.407979 CGATTGGAGCTTACTACCGGT 59.592 52.381 13.98 13.98 0.00 5.28
837 927 2.543238 CGATTGGAGCTTACTACCGGTC 60.543 54.545 12.40 0.00 0.00 4.79
838 928 0.813184 TTGGAGCTTACTACCGGTCG 59.187 55.000 12.40 7.75 0.00 4.79
839 929 1.065436 GGAGCTTACTACCGGTCGC 59.935 63.158 12.40 7.54 0.00 5.19
840 930 1.298190 GAGCTTACTACCGGTCGCG 60.298 63.158 12.40 0.00 32.23 5.87
841 931 2.278401 GCTTACTACCGGTCGCGG 60.278 66.667 12.40 2.41 0.00 6.46
842 932 2.410469 CTTACTACCGGTCGCGGG 59.590 66.667 12.40 1.35 0.00 6.13
843 933 2.361104 TTACTACCGGTCGCGGGT 60.361 61.111 12.40 8.73 40.20 5.28
844 934 1.937546 CTTACTACCGGTCGCGGGTT 61.938 60.000 12.40 0.00 38.10 4.11
845 935 1.933115 TTACTACCGGTCGCGGGTTC 61.933 60.000 12.40 0.00 38.10 3.62
846 936 4.842091 CTACCGGTCGCGGGTTCG 62.842 72.222 12.40 7.47 38.10 3.95
849 939 4.807039 CCGGTCGCGGGTTCGAAT 62.807 66.667 6.13 0.00 40.43 3.34
850 940 3.252484 CGGTCGCGGGTTCGAATC 61.252 66.667 6.13 0.00 40.43 2.52
851 941 2.183555 GGTCGCGGGTTCGAATCT 59.816 61.111 8.59 0.00 40.43 2.40
852 942 1.877165 GGTCGCGGGTTCGAATCTC 60.877 63.158 8.59 0.00 40.43 2.75
853 943 1.139095 GTCGCGGGTTCGAATCTCT 59.861 57.895 8.59 0.00 40.43 3.10
854 944 0.866483 GTCGCGGGTTCGAATCTCTC 60.866 60.000 8.59 0.00 40.43 3.20
855 945 1.589196 CGCGGGTTCGAATCTCTCC 60.589 63.158 8.59 0.41 39.00 3.71
856 946 1.515954 GCGGGTTCGAATCTCTCCA 59.484 57.895 8.59 0.00 39.00 3.86
857 947 0.528684 GCGGGTTCGAATCTCTCCAG 60.529 60.000 8.59 3.02 39.00 3.86
858 948 0.528684 CGGGTTCGAATCTCTCCAGC 60.529 60.000 8.59 0.00 39.00 4.85
859 949 0.537188 GGGTTCGAATCTCTCCAGCA 59.463 55.000 8.59 0.00 0.00 4.41
860 950 1.066143 GGGTTCGAATCTCTCCAGCAA 60.066 52.381 8.59 0.00 0.00 3.91
861 951 2.275318 GGTTCGAATCTCTCCAGCAAG 58.725 52.381 0.00 0.00 0.00 4.01
862 952 1.663135 GTTCGAATCTCTCCAGCAAGC 59.337 52.381 0.00 0.00 0.00 4.01
863 953 0.176680 TCGAATCTCTCCAGCAAGCC 59.823 55.000 0.00 0.00 0.00 4.35
864 954 0.107993 CGAATCTCTCCAGCAAGCCA 60.108 55.000 0.00 0.00 0.00 4.75
865 955 1.666054 GAATCTCTCCAGCAAGCCAG 58.334 55.000 0.00 0.00 0.00 4.85
866 956 1.209019 GAATCTCTCCAGCAAGCCAGA 59.791 52.381 0.00 0.00 0.00 3.86
867 957 1.283347 ATCTCTCCAGCAAGCCAGAA 58.717 50.000 0.00 0.00 0.00 3.02
868 958 1.283347 TCTCTCCAGCAAGCCAGAAT 58.717 50.000 0.00 0.00 0.00 2.40
869 959 2.470990 TCTCTCCAGCAAGCCAGAATA 58.529 47.619 0.00 0.00 0.00 1.75
870 960 2.840038 TCTCTCCAGCAAGCCAGAATAA 59.160 45.455 0.00 0.00 0.00 1.40
871 961 3.264193 TCTCTCCAGCAAGCCAGAATAAA 59.736 43.478 0.00 0.00 0.00 1.40
872 962 4.012374 CTCTCCAGCAAGCCAGAATAAAA 58.988 43.478 0.00 0.00 0.00 1.52
873 963 4.603131 TCTCCAGCAAGCCAGAATAAAAT 58.397 39.130 0.00 0.00 0.00 1.82
874 964 4.400251 TCTCCAGCAAGCCAGAATAAAATG 59.600 41.667 0.00 0.00 0.00 2.32
875 965 4.088634 TCCAGCAAGCCAGAATAAAATGT 58.911 39.130 0.00 0.00 0.00 2.71
876 966 4.082081 TCCAGCAAGCCAGAATAAAATGTG 60.082 41.667 0.00 0.00 0.00 3.21
877 967 4.322198 CCAGCAAGCCAGAATAAAATGTGT 60.322 41.667 0.00 0.00 0.00 3.72
878 968 4.624024 CAGCAAGCCAGAATAAAATGTGTG 59.376 41.667 0.00 0.00 0.00 3.82
879 969 4.523943 AGCAAGCCAGAATAAAATGTGTGA 59.476 37.500 0.00 0.00 0.00 3.58
880 970 4.860907 GCAAGCCAGAATAAAATGTGTGAG 59.139 41.667 0.00 0.00 0.00 3.51
881 971 5.335897 GCAAGCCAGAATAAAATGTGTGAGA 60.336 40.000 0.00 0.00 0.00 3.27
882 972 6.626623 GCAAGCCAGAATAAAATGTGTGAGAT 60.627 38.462 0.00 0.00 0.00 2.75
883 973 6.446781 AGCCAGAATAAAATGTGTGAGATG 57.553 37.500 0.00 0.00 0.00 2.90
884 974 5.359009 AGCCAGAATAAAATGTGTGAGATGG 59.641 40.000 0.00 0.00 0.00 3.51
885 975 5.357878 GCCAGAATAAAATGTGTGAGATGGA 59.642 40.000 0.00 0.00 0.00 3.41
886 976 6.678900 GCCAGAATAAAATGTGTGAGATGGAC 60.679 42.308 0.00 0.00 0.00 4.02
887 977 6.183360 CCAGAATAAAATGTGTGAGATGGACC 60.183 42.308 0.00 0.00 0.00 4.46
888 978 5.586243 AGAATAAAATGTGTGAGATGGACCG 59.414 40.000 0.00 0.00 0.00 4.79
889 979 2.113860 AAATGTGTGAGATGGACCGG 57.886 50.000 0.00 0.00 0.00 5.28
890 980 0.392998 AATGTGTGAGATGGACCGGC 60.393 55.000 0.00 0.00 0.00 6.13
891 981 2.125106 GTGTGAGATGGACCGGCC 60.125 66.667 0.00 4.32 37.10 6.13
892 982 3.399181 TGTGAGATGGACCGGCCC 61.399 66.667 0.00 0.00 34.97 5.80
893 983 3.399181 GTGAGATGGACCGGCCCA 61.399 66.667 13.59 13.59 41.05 5.36
894 984 3.083349 TGAGATGGACCGGCCCAG 61.083 66.667 16.91 0.00 39.97 4.45
895 985 4.554036 GAGATGGACCGGCCCAGC 62.554 72.222 18.38 18.38 42.62 4.85
921 1011 3.503363 GCTGCAGGCGCCTGTTAG 61.503 66.667 46.58 41.30 45.24 2.34
922 1012 3.503363 CTGCAGGCGCCTGTTAGC 61.503 66.667 46.58 36.19 45.24 3.09
923 1013 4.328025 TGCAGGCGCCTGTTAGCA 62.328 61.111 46.58 38.11 45.24 3.49
924 1014 3.055719 GCAGGCGCCTGTTAGCAA 61.056 61.111 46.58 0.00 45.24 3.91
925 1015 2.625823 GCAGGCGCCTGTTAGCAAA 61.626 57.895 46.58 0.00 45.24 3.68
926 1016 1.956043 CAGGCGCCTGTTAGCAAAA 59.044 52.632 42.09 0.00 39.10 2.44
927 1017 0.313672 CAGGCGCCTGTTAGCAAAAA 59.686 50.000 42.09 0.00 39.10 1.94
947 1037 6.396829 AAAAATGATATAACTCCCTGCAGC 57.603 37.500 8.66 0.00 0.00 5.25
948 1038 2.820059 TGATATAACTCCCTGCAGCG 57.180 50.000 8.66 0.00 0.00 5.18
949 1039 2.039418 TGATATAACTCCCTGCAGCGT 58.961 47.619 8.66 1.64 0.00 5.07
950 1040 2.035961 TGATATAACTCCCTGCAGCGTC 59.964 50.000 8.66 0.00 0.00 5.19
951 1041 1.480789 TATAACTCCCTGCAGCGTCA 58.519 50.000 8.66 0.00 0.00 4.35
952 1042 0.613260 ATAACTCCCTGCAGCGTCAA 59.387 50.000 8.66 0.00 0.00 3.18
953 1043 0.394938 TAACTCCCTGCAGCGTCAAA 59.605 50.000 8.66 0.00 0.00 2.69
954 1044 0.250901 AACTCCCTGCAGCGTCAAAT 60.251 50.000 8.66 0.00 0.00 2.32
955 1045 0.613260 ACTCCCTGCAGCGTCAAATA 59.387 50.000 8.66 0.00 0.00 1.40
956 1046 1.293924 CTCCCTGCAGCGTCAAATAG 58.706 55.000 8.66 0.00 0.00 1.73
957 1047 0.107703 TCCCTGCAGCGTCAAATAGG 60.108 55.000 8.66 0.30 0.00 2.57
958 1048 1.097547 CCCTGCAGCGTCAAATAGGG 61.098 60.000 8.66 0.00 38.96 3.53
969 1059 4.095782 GCGTCAAATAGGGTTTGCTTATGA 59.904 41.667 0.00 0.00 0.00 2.15
972 1062 6.692681 CGTCAAATAGGGTTTGCTTATGAATG 59.307 38.462 0.00 0.00 0.00 2.67
1428 3022 1.004044 GCTTCCATGATCCCGATCCAT 59.996 52.381 0.00 0.00 37.02 3.41
1429 3023 2.938756 GCTTCCATGATCCCGATCCATC 60.939 54.545 0.00 0.00 37.02 3.51
1430 3024 1.279496 TCCATGATCCCGATCCATCC 58.721 55.000 0.00 0.00 37.02 3.51
1431 3025 0.986527 CCATGATCCCGATCCATCCA 59.013 55.000 0.00 0.00 37.02 3.41
1441 3035 4.905456 TCCCGATCCATCCAAAATAGTACT 59.095 41.667 0.00 0.00 0.00 2.73
1442 3036 5.011738 TCCCGATCCATCCAAAATAGTACTC 59.988 44.000 0.00 0.00 0.00 2.59
1443 3037 5.238583 CCGATCCATCCAAAATAGTACTCC 58.761 45.833 0.00 0.00 0.00 3.85
1444 3038 5.238583 CGATCCATCCAAAATAGTACTCCC 58.761 45.833 0.00 0.00 0.00 4.30
1445 3039 5.012148 CGATCCATCCAAAATAGTACTCCCT 59.988 44.000 0.00 0.00 0.00 4.20
1447 3041 6.248569 TCCATCCAAAATAGTACTCCCTTC 57.751 41.667 0.00 0.00 0.00 3.46
1448 3042 5.057149 CCATCCAAAATAGTACTCCCTTCG 58.943 45.833 0.00 0.00 0.00 3.79
1449 3043 5.396436 CCATCCAAAATAGTACTCCCTTCGT 60.396 44.000 0.00 0.00 0.00 3.85
1451 3045 4.161001 TCCAAAATAGTACTCCCTTCGTCC 59.839 45.833 0.00 0.00 0.00 4.79
1452 3046 4.439968 CAAAATAGTACTCCCTTCGTCCC 58.560 47.826 0.00 0.00 0.00 4.46
1453 3047 3.393426 AATAGTACTCCCTTCGTCCCA 57.607 47.619 0.00 0.00 0.00 4.37
1454 3048 3.614568 ATAGTACTCCCTTCGTCCCAT 57.385 47.619 0.00 0.00 0.00 4.00
1455 3049 4.736611 ATAGTACTCCCTTCGTCCCATA 57.263 45.455 0.00 0.00 0.00 2.74
1458 3052 5.070823 AGTACTCCCTTCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
1459 3053 5.652324 AGTACTCCCTTCGTCCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
1460 3054 6.797707 AGTACTCCCTTCGTCCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
1461 3055 7.243824 AGTACTCCCTTCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
1462 3056 6.607004 ACTCCCTTCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
1463 3057 6.320518 ACTCCCTTCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
1464 3058 6.437793 ACTCCCTTCGTCCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
1465 3059 5.187186 TCCCTTCGTCCCATAATATAAGAGC 59.813 44.000 0.00 0.00 0.00 4.09
1467 3061 5.336531 CCTTCGTCCCATAATATAAGAGCGT 60.337 44.000 0.00 0.00 0.00 5.07
1468 3062 5.717078 TCGTCCCATAATATAAGAGCGTT 57.283 39.130 0.00 0.00 0.00 4.84
1469 3063 6.092955 TCGTCCCATAATATAAGAGCGTTT 57.907 37.500 0.00 0.00 0.00 3.60
1470 3064 6.518493 TCGTCCCATAATATAAGAGCGTTTT 58.482 36.000 0.00 0.00 0.00 2.43
1496 3134 4.159506 ACACTAGTTTGGCTTTTGCTCAAA 59.840 37.500 0.00 0.00 46.54 2.69
1498 3136 2.996691 GTTTGGCTTTTGCTCAAACG 57.003 45.000 14.26 0.00 46.09 3.60
1727 3369 5.848369 TCCTTCAGTTCATCCATCCATCTAT 59.152 40.000 0.00 0.00 0.00 1.98
1731 3373 8.496534 TTCAGTTCATCCATCCATCTATCTTA 57.503 34.615 0.00 0.00 0.00 2.10
1732 3374 7.901029 TCAGTTCATCCATCCATCTATCTTAC 58.099 38.462 0.00 0.00 0.00 2.34
1759 3403 1.904852 GCTATCCGATGCATGCGTGG 61.905 60.000 19.18 16.53 0.00 4.94
1804 3466 9.859427 TTTTGGCAAATATAGACATTTCAGAAG 57.141 29.630 14.29 0.00 0.00 2.85
1805 3467 8.579850 TTGGCAAATATAGACATTTCAGAAGT 57.420 30.769 0.00 0.00 0.00 3.01
1806 3468 9.679661 TTGGCAAATATAGACATTTCAGAAGTA 57.320 29.630 0.00 0.00 0.00 2.24
1854 3525 6.599244 CACATTCCAAATGCCTACTTTCTCTA 59.401 38.462 0.00 0.00 0.00 2.43
1910 3584 6.506500 AACAGAATGGATAAGCTTGAACAG 57.493 37.500 9.86 0.00 43.62 3.16
2106 3785 4.168014 ACATTGCAAATTATGTCAGCGTG 58.832 39.130 1.71 0.00 0.00 5.34
2113 3792 5.174761 GCAAATTATGTCAGCGTGAAAAACA 59.825 36.000 0.00 0.00 0.00 2.83
2122 3801 6.142817 GTCAGCGTGAAAAACATAAATCTGT 58.857 36.000 0.00 0.00 0.00 3.41
2206 3885 1.266718 GCTCTGTCATGTTCCGCAAAA 59.733 47.619 0.00 0.00 0.00 2.44
2289 3978 3.064408 GCATCCATGTGCACATATATCGG 59.936 47.826 30.92 25.59 44.43 4.18
2374 4065 4.046462 CGGTGAACTCGTTAGACAAAAGA 58.954 43.478 0.00 0.00 0.00 2.52
2409 4102 6.204882 GGTTCCAGAATAATTTGCTACGCTAT 59.795 38.462 0.00 0.00 0.00 2.97
2533 4248 2.989824 ACCCTGGACGAGTCGGTG 60.990 66.667 18.30 3.59 0.00 4.94
2557 4272 3.343788 GACCGAGAGCAGGGACGTG 62.344 68.421 0.00 0.00 0.00 4.49
2732 4447 5.086104 TGCCTGGTGTAAGTTCTTCTATC 57.914 43.478 0.00 0.00 0.00 2.08
2812 4533 7.919690 TCACTAGAACAGTTTGATTTGTCAAG 58.080 34.615 0.00 0.00 34.26 3.02
2924 4720 5.565455 ACAATTGGGGATTGATTTGTGTT 57.435 34.783 10.83 0.00 46.59 3.32
3225 5040 7.226523 TCCAATCATATTGTTGTAACGGAGATG 59.773 37.037 0.00 0.00 0.00 2.90
3363 5191 5.957842 TTGCAAATCTCTACGGTGAAAAT 57.042 34.783 0.00 0.00 0.00 1.82
3367 5195 5.447818 GCAAATCTCTACGGTGAAAATCCAG 60.448 44.000 0.00 0.00 0.00 3.86
3401 5229 4.326009 CAGTACAAAAACAAGTTGTGTGCC 59.674 41.667 9.79 3.62 40.60 5.01
3424 5252 1.388547 TTTCTGGCGCTTCAACTGTT 58.611 45.000 7.64 0.00 0.00 3.16
3466 5340 7.594758 GCACAACTGTATGAACATGTACAAAAT 59.405 33.333 0.00 0.00 34.37 1.82
3553 5444 1.423584 TGGTGTGATCTGTGAGGTGT 58.576 50.000 0.00 0.00 0.00 4.16
3660 5555 4.635765 TGTACTCAAGGTCAATTGCTATGC 59.364 41.667 0.00 0.00 0.00 3.14
3662 5557 2.360165 CTCAAGGTCAATTGCTATGCCC 59.640 50.000 0.00 0.00 0.00 5.36
3687 5582 6.485648 CCTTCTCATGCAGTTGATATGATTCA 59.514 38.462 0.00 0.00 31.11 2.57
3709 5604 5.010922 TCAATCCAGTTGCTGCTTTATTTGT 59.989 36.000 0.00 0.00 37.74 2.83
3860 8749 0.603065 TATGCCGATGACCGATCCAG 59.397 55.000 0.00 0.00 41.76 3.86
3885 8774 1.942776 CCCTTTCAAATCTGGGGCTT 58.057 50.000 0.00 0.00 36.15 4.35
3983 8872 2.591571 AGGTTTAACGCGGGATACTC 57.408 50.000 12.47 0.00 0.00 2.59
3989 8878 1.477553 AACGCGGGATACTCTTGGTA 58.522 50.000 12.47 0.00 34.62 3.25
3990 8879 0.743097 ACGCGGGATACTCTTGGTAC 59.257 55.000 12.47 0.00 32.72 3.34
3991 8880 0.742505 CGCGGGATACTCTTGGTACA 59.257 55.000 0.00 0.00 32.72 2.90
3992 8881 1.340248 CGCGGGATACTCTTGGTACAT 59.660 52.381 0.00 0.00 39.30 2.29
3993 8882 2.555325 CGCGGGATACTCTTGGTACATA 59.445 50.000 0.00 0.00 39.30 2.29
3994 8883 3.611057 CGCGGGATACTCTTGGTACATAC 60.611 52.174 0.00 0.00 39.30 2.39
3995 8884 3.305881 GCGGGATACTCTTGGTACATACC 60.306 52.174 0.75 0.75 46.62 2.73
3996 8885 4.150359 CGGGATACTCTTGGTACATACCT 58.850 47.826 9.46 0.00 46.58 3.08
3997 8886 5.319453 CGGGATACTCTTGGTACATACCTA 58.681 45.833 9.46 1.07 46.58 3.08
3998 8887 5.950549 CGGGATACTCTTGGTACATACCTAT 59.049 44.000 9.46 0.00 46.58 2.57
3999 8888 6.127703 CGGGATACTCTTGGTACATACCTATG 60.128 46.154 9.46 1.57 46.58 2.23
4000 8889 6.724905 GGGATACTCTTGGTACATACCTATGT 59.275 42.308 9.46 3.50 46.58 2.29
4001 8890 7.234988 GGGATACTCTTGGTACATACCTATGTT 59.765 40.741 9.46 0.00 43.99 2.71
4002 8891 9.305555 GGATACTCTTGGTACATACCTATGTTA 57.694 37.037 9.46 0.00 43.99 2.41
4004 8893 9.878737 ATACTCTTGGTACATACCTATGTTACT 57.121 33.333 9.46 0.00 43.99 2.24
4005 8894 8.605325 ACTCTTGGTACATACCTATGTTACTT 57.395 34.615 9.46 0.00 43.99 2.24
4006 8895 9.043548 ACTCTTGGTACATACCTATGTTACTTT 57.956 33.333 9.46 0.00 43.99 2.66
4007 8896 9.886132 CTCTTGGTACATACCTATGTTACTTTT 57.114 33.333 9.46 0.00 43.99 2.27
4010 8899 9.585099 TTGGTACATACCTATGTTACTTTTACG 57.415 33.333 9.46 0.00 43.99 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 277 1.134670 GCTCCTTGCACTATCGGTTCT 60.135 52.381 0.00 0.00 42.31 3.01
234 291 1.608717 CTGCCCACTCGTAGCTCCTT 61.609 60.000 0.00 0.00 0.00 3.36
314 371 0.987613 TGTAGCATCCCCATCTGCCA 60.988 55.000 0.00 0.00 39.22 4.92
383 443 0.320858 TTGTAGCATCGCCGTTTGGA 60.321 50.000 0.00 0.00 37.49 3.53
452 512 1.066143 ACGACTTTCCATCTCGCCATT 60.066 47.619 0.00 0.00 0.00 3.16
641 728 4.012895 CGCTTGCGTCGGTTGCTT 62.013 61.111 6.86 0.00 0.00 3.91
718 808 1.982395 AACCGCTCGTCCTCATCCA 60.982 57.895 0.00 0.00 0.00 3.41
773 863 4.811761 GGTCGTGGCAATTCGCGC 62.812 66.667 0.00 0.00 43.84 6.86
774 864 3.118454 AGGTCGTGGCAATTCGCG 61.118 61.111 0.00 0.00 43.84 5.87
775 865 1.852067 AACAGGTCGTGGCAATTCGC 61.852 55.000 0.00 0.00 41.28 4.70
776 866 0.110238 CAACAGGTCGTGGCAATTCG 60.110 55.000 0.00 0.00 0.00 3.34
777 867 0.951558 ACAACAGGTCGTGGCAATTC 59.048 50.000 0.00 0.00 0.00 2.17
778 868 0.951558 GACAACAGGTCGTGGCAATT 59.048 50.000 0.00 0.00 36.65 2.32
779 869 2.629002 GACAACAGGTCGTGGCAAT 58.371 52.632 0.00 0.00 36.65 3.56
780 870 4.134623 GACAACAGGTCGTGGCAA 57.865 55.556 0.00 0.00 36.65 4.52
788 878 0.549469 AACCCGGAAAGACAACAGGT 59.451 50.000 0.73 0.00 0.00 4.00
789 879 0.951558 CAACCCGGAAAGACAACAGG 59.048 55.000 0.73 0.00 0.00 4.00
790 880 0.951558 CCAACCCGGAAAGACAACAG 59.048 55.000 0.73 0.00 36.56 3.16
791 881 1.104577 GCCAACCCGGAAAGACAACA 61.105 55.000 0.73 0.00 36.56 3.33
792 882 0.822121 AGCCAACCCGGAAAGACAAC 60.822 55.000 0.73 0.00 36.56 3.32
793 883 0.821711 CAGCCAACCCGGAAAGACAA 60.822 55.000 0.73 0.00 36.56 3.18
794 884 1.228124 CAGCCAACCCGGAAAGACA 60.228 57.895 0.73 0.00 36.56 3.41
795 885 0.322546 ATCAGCCAACCCGGAAAGAC 60.323 55.000 0.73 0.00 36.56 3.01
796 886 0.322456 CATCAGCCAACCCGGAAAGA 60.322 55.000 0.73 0.00 36.56 2.52
797 887 1.937546 GCATCAGCCAACCCGGAAAG 61.938 60.000 0.73 0.00 36.56 2.62
798 888 1.976474 GCATCAGCCAACCCGGAAA 60.976 57.895 0.73 0.00 36.56 3.13
799 889 2.361104 GCATCAGCCAACCCGGAA 60.361 61.111 0.73 0.00 36.56 4.30
800 890 4.776322 CGCATCAGCCAACCCGGA 62.776 66.667 0.73 0.00 36.56 5.14
801 891 4.776322 TCGCATCAGCCAACCCGG 62.776 66.667 0.00 0.00 37.52 5.73
802 892 2.114670 AATCGCATCAGCCAACCCG 61.115 57.895 0.00 0.00 37.52 5.28
803 893 1.434696 CAATCGCATCAGCCAACCC 59.565 57.895 0.00 0.00 37.52 4.11
804 894 1.031571 TCCAATCGCATCAGCCAACC 61.032 55.000 0.00 0.00 37.52 3.77
805 895 0.379669 CTCCAATCGCATCAGCCAAC 59.620 55.000 0.00 0.00 37.52 3.77
806 896 1.378882 GCTCCAATCGCATCAGCCAA 61.379 55.000 0.00 0.00 37.52 4.52
807 897 1.820906 GCTCCAATCGCATCAGCCA 60.821 57.895 0.00 0.00 37.52 4.75
808 898 1.099879 AAGCTCCAATCGCATCAGCC 61.100 55.000 0.00 0.00 37.52 4.85
809 899 1.262683 GTAAGCTCCAATCGCATCAGC 59.737 52.381 0.00 0.00 37.42 4.26
810 900 2.831333 AGTAAGCTCCAATCGCATCAG 58.169 47.619 0.00 0.00 0.00 2.90
811 901 2.988010 AGTAAGCTCCAATCGCATCA 57.012 45.000 0.00 0.00 0.00 3.07
812 902 3.060602 GGTAGTAAGCTCCAATCGCATC 58.939 50.000 0.00 0.00 0.00 3.91
813 903 2.545952 CGGTAGTAAGCTCCAATCGCAT 60.546 50.000 0.00 0.00 0.00 4.73
814 904 1.202371 CGGTAGTAAGCTCCAATCGCA 60.202 52.381 0.00 0.00 0.00 5.10
815 905 1.488527 CGGTAGTAAGCTCCAATCGC 58.511 55.000 0.00 0.00 0.00 4.58
816 906 1.407979 ACCGGTAGTAAGCTCCAATCG 59.592 52.381 4.49 0.00 0.00 3.34
817 907 2.543238 CGACCGGTAGTAAGCTCCAATC 60.543 54.545 7.34 0.00 0.00 2.67
818 908 1.407979 CGACCGGTAGTAAGCTCCAAT 59.592 52.381 7.34 0.00 0.00 3.16
819 909 0.813184 CGACCGGTAGTAAGCTCCAA 59.187 55.000 7.34 0.00 0.00 3.53
820 910 1.660560 GCGACCGGTAGTAAGCTCCA 61.661 60.000 16.51 0.00 31.55 3.86
821 911 1.065436 GCGACCGGTAGTAAGCTCC 59.935 63.158 16.51 0.00 31.55 4.70
822 912 1.298190 CGCGACCGGTAGTAAGCTC 60.298 63.158 16.51 0.00 31.93 4.09
823 913 2.796651 CGCGACCGGTAGTAAGCT 59.203 61.111 16.51 0.00 31.93 3.74
833 923 3.252484 GATTCGAACCCGCGACCG 61.252 66.667 8.23 5.30 40.42 4.79
834 924 1.877165 GAGATTCGAACCCGCGACC 60.877 63.158 8.23 0.00 40.42 4.79
835 925 0.866483 GAGAGATTCGAACCCGCGAC 60.866 60.000 8.23 0.00 40.42 5.19
836 926 1.432251 GAGAGATTCGAACCCGCGA 59.568 57.895 8.23 0.00 38.72 5.87
837 927 1.589196 GGAGAGATTCGAACCCGCG 60.589 63.158 0.00 0.00 35.37 6.46
838 928 0.528684 CTGGAGAGATTCGAACCCGC 60.529 60.000 0.00 0.00 35.37 6.13
839 929 0.528684 GCTGGAGAGATTCGAACCCG 60.529 60.000 0.00 0.00 37.07 5.28
840 930 0.537188 TGCTGGAGAGATTCGAACCC 59.463 55.000 0.00 0.00 0.00 4.11
841 931 2.275318 CTTGCTGGAGAGATTCGAACC 58.725 52.381 0.00 0.00 0.00 3.62
842 932 1.663135 GCTTGCTGGAGAGATTCGAAC 59.337 52.381 0.00 0.00 0.00 3.95
843 933 1.406069 GGCTTGCTGGAGAGATTCGAA 60.406 52.381 0.00 0.00 0.00 3.71
844 934 0.176680 GGCTTGCTGGAGAGATTCGA 59.823 55.000 0.00 0.00 0.00 3.71
845 935 0.107993 TGGCTTGCTGGAGAGATTCG 60.108 55.000 0.00 0.00 0.00 3.34
846 936 1.209019 TCTGGCTTGCTGGAGAGATTC 59.791 52.381 0.00 0.00 0.00 2.52
847 937 1.283347 TCTGGCTTGCTGGAGAGATT 58.717 50.000 0.00 0.00 0.00 2.40
848 938 1.283347 TTCTGGCTTGCTGGAGAGAT 58.717 50.000 0.00 0.00 0.00 2.75
849 939 1.283347 ATTCTGGCTTGCTGGAGAGA 58.717 50.000 0.00 0.00 0.00 3.10
850 940 2.996249 TATTCTGGCTTGCTGGAGAG 57.004 50.000 0.00 0.00 0.00 3.20
851 941 3.719268 TTTATTCTGGCTTGCTGGAGA 57.281 42.857 0.00 0.00 0.00 3.71
852 942 4.159135 ACATTTTATTCTGGCTTGCTGGAG 59.841 41.667 0.00 0.00 0.00 3.86
853 943 4.082081 CACATTTTATTCTGGCTTGCTGGA 60.082 41.667 0.00 0.00 0.00 3.86
854 944 4.178540 CACATTTTATTCTGGCTTGCTGG 58.821 43.478 0.00 0.00 0.00 4.85
855 945 4.624024 CACACATTTTATTCTGGCTTGCTG 59.376 41.667 0.00 0.00 0.00 4.41
856 946 4.523943 TCACACATTTTATTCTGGCTTGCT 59.476 37.500 0.00 0.00 0.00 3.91
857 947 4.808558 TCACACATTTTATTCTGGCTTGC 58.191 39.130 0.00 0.00 0.00 4.01
858 948 6.258230 TCTCACACATTTTATTCTGGCTTG 57.742 37.500 0.00 0.00 0.00 4.01
859 949 6.127535 CCATCTCACACATTTTATTCTGGCTT 60.128 38.462 0.00 0.00 0.00 4.35
860 950 5.359009 CCATCTCACACATTTTATTCTGGCT 59.641 40.000 0.00 0.00 0.00 4.75
861 951 5.357878 TCCATCTCACACATTTTATTCTGGC 59.642 40.000 0.00 0.00 0.00 4.85
862 952 6.183360 GGTCCATCTCACACATTTTATTCTGG 60.183 42.308 0.00 0.00 0.00 3.86
863 953 6.457392 CGGTCCATCTCACACATTTTATTCTG 60.457 42.308 0.00 0.00 0.00 3.02
864 954 5.586243 CGGTCCATCTCACACATTTTATTCT 59.414 40.000 0.00 0.00 0.00 2.40
865 955 5.220854 CCGGTCCATCTCACACATTTTATTC 60.221 44.000 0.00 0.00 0.00 1.75
866 956 4.640201 CCGGTCCATCTCACACATTTTATT 59.360 41.667 0.00 0.00 0.00 1.40
867 957 4.199310 CCGGTCCATCTCACACATTTTAT 58.801 43.478 0.00 0.00 0.00 1.40
868 958 3.605634 CCGGTCCATCTCACACATTTTA 58.394 45.455 0.00 0.00 0.00 1.52
869 959 2.436417 CCGGTCCATCTCACACATTTT 58.564 47.619 0.00 0.00 0.00 1.82
870 960 1.950484 GCCGGTCCATCTCACACATTT 60.950 52.381 1.90 0.00 0.00 2.32
871 961 0.392998 GCCGGTCCATCTCACACATT 60.393 55.000 1.90 0.00 0.00 2.71
872 962 1.221840 GCCGGTCCATCTCACACAT 59.778 57.895 1.90 0.00 0.00 3.21
873 963 2.662596 GCCGGTCCATCTCACACA 59.337 61.111 1.90 0.00 0.00 3.72
874 964 2.125106 GGCCGGTCCATCTCACAC 60.125 66.667 1.90 0.00 34.01 3.82
875 965 3.399181 GGGCCGGTCCATCTCACA 61.399 66.667 23.50 0.00 36.21 3.58
876 966 3.391665 CTGGGCCGGTCCATCTCAC 62.392 68.421 31.80 0.00 36.05 3.51
877 967 3.083349 CTGGGCCGGTCCATCTCA 61.083 66.667 31.80 4.70 36.05 3.27
878 968 4.554036 GCTGGGCCGGTCCATCTC 62.554 72.222 31.80 17.26 36.05 2.75
909 999 2.727103 TTTTTGCTAACAGGCGCCT 58.273 47.368 27.08 27.08 34.52 5.52
924 1014 5.009010 CGCTGCAGGGAGTTATATCATTTTT 59.991 40.000 25.55 0.00 0.00 1.94
925 1015 4.516698 CGCTGCAGGGAGTTATATCATTTT 59.483 41.667 25.55 0.00 0.00 1.82
926 1016 4.067896 CGCTGCAGGGAGTTATATCATTT 58.932 43.478 25.55 0.00 0.00 2.32
927 1017 3.071602 ACGCTGCAGGGAGTTATATCATT 59.928 43.478 34.63 7.02 0.00 2.57
928 1018 2.634940 ACGCTGCAGGGAGTTATATCAT 59.365 45.455 34.63 7.55 0.00 2.45
929 1019 2.035961 GACGCTGCAGGGAGTTATATCA 59.964 50.000 34.63 0.00 0.00 2.15
930 1020 2.035961 TGACGCTGCAGGGAGTTATATC 59.964 50.000 34.63 20.29 0.00 1.63
931 1021 2.039418 TGACGCTGCAGGGAGTTATAT 58.961 47.619 34.63 12.50 0.00 0.86
932 1022 1.480789 TGACGCTGCAGGGAGTTATA 58.519 50.000 34.63 12.29 0.00 0.98
933 1023 0.613260 TTGACGCTGCAGGGAGTTAT 59.387 50.000 34.63 14.02 0.00 1.89
934 1024 0.394938 TTTGACGCTGCAGGGAGTTA 59.605 50.000 34.63 15.53 0.00 2.24
935 1025 0.250901 ATTTGACGCTGCAGGGAGTT 60.251 50.000 34.63 14.79 0.00 3.01
936 1026 0.613260 TATTTGACGCTGCAGGGAGT 59.387 50.000 34.63 15.56 0.00 3.85
937 1027 1.293924 CTATTTGACGCTGCAGGGAG 58.706 55.000 34.63 17.64 0.00 4.30
938 1028 0.107703 CCTATTTGACGCTGCAGGGA 60.108 55.000 34.63 14.71 0.00 4.20
939 1029 1.097547 CCCTATTTGACGCTGCAGGG 61.098 60.000 27.57 27.57 37.01 4.45
940 1030 0.392998 ACCCTATTTGACGCTGCAGG 60.393 55.000 17.12 8.27 0.00 4.85
941 1031 1.453155 AACCCTATTTGACGCTGCAG 58.547 50.000 10.11 10.11 0.00 4.41
942 1032 1.539388 CAAACCCTATTTGACGCTGCA 59.461 47.619 0.00 0.00 0.00 4.41
943 1033 1.732405 GCAAACCCTATTTGACGCTGC 60.732 52.381 3.62 0.00 0.00 5.25
944 1034 1.812571 AGCAAACCCTATTTGACGCTG 59.187 47.619 3.62 0.00 0.00 5.18
945 1035 2.200373 AGCAAACCCTATTTGACGCT 57.800 45.000 3.62 0.00 0.00 5.07
946 1036 4.095782 TCATAAGCAAACCCTATTTGACGC 59.904 41.667 3.62 0.00 0.00 5.19
947 1037 5.811399 TCATAAGCAAACCCTATTTGACG 57.189 39.130 3.62 0.00 0.00 4.35
948 1038 7.771183 TCATTCATAAGCAAACCCTATTTGAC 58.229 34.615 3.62 0.00 0.00 3.18
949 1039 7.833682 TCTCATTCATAAGCAAACCCTATTTGA 59.166 33.333 3.62 0.00 0.00 2.69
950 1040 7.999679 TCTCATTCATAAGCAAACCCTATTTG 58.000 34.615 0.00 0.00 0.00 2.32
951 1041 8.773033 ATCTCATTCATAAGCAAACCCTATTT 57.227 30.769 0.00 0.00 0.00 1.40
952 1042 8.773033 AATCTCATTCATAAGCAAACCCTATT 57.227 30.769 0.00 0.00 0.00 1.73
953 1043 9.512588 CTAATCTCATTCATAAGCAAACCCTAT 57.487 33.333 0.00 0.00 0.00 2.57
954 1044 7.445402 GCTAATCTCATTCATAAGCAAACCCTA 59.555 37.037 0.00 0.00 0.00 3.53
955 1045 6.264067 GCTAATCTCATTCATAAGCAAACCCT 59.736 38.462 0.00 0.00 0.00 4.34
956 1046 6.442112 GCTAATCTCATTCATAAGCAAACCC 58.558 40.000 0.00 0.00 0.00 4.11
957 1047 6.264067 AGGCTAATCTCATTCATAAGCAAACC 59.736 38.462 0.00 0.00 0.00 3.27
958 1048 7.137426 CAGGCTAATCTCATTCATAAGCAAAC 58.863 38.462 0.00 0.00 0.00 2.93
969 1059 7.800092 AGTGATTAAGACAGGCTAATCTCATT 58.200 34.615 8.08 0.00 32.01 2.57
972 1062 7.049799 AGAGTGATTAAGACAGGCTAATCTC 57.950 40.000 8.08 5.16 32.01 2.75
1428 3022 4.161001 GGACGAAGGGAGTACTATTTTGGA 59.839 45.833 0.00 0.00 0.00 3.53
1429 3023 4.439968 GGACGAAGGGAGTACTATTTTGG 58.560 47.826 0.00 0.00 0.00 3.28
1430 3024 4.081309 TGGGACGAAGGGAGTACTATTTTG 60.081 45.833 0.00 0.00 0.00 2.44
1431 3025 4.098894 TGGGACGAAGGGAGTACTATTTT 58.901 43.478 0.00 0.00 0.00 1.82
1441 3035 5.187186 GCTCTTATATTATGGGACGAAGGGA 59.813 44.000 0.00 0.00 0.00 4.20
1442 3036 5.420409 GCTCTTATATTATGGGACGAAGGG 58.580 45.833 0.00 0.00 0.00 3.95
1443 3037 5.103000 CGCTCTTATATTATGGGACGAAGG 58.897 45.833 0.00 0.00 0.00 3.46
1444 3038 5.710984 ACGCTCTTATATTATGGGACGAAG 58.289 41.667 0.00 0.00 0.00 3.79
1445 3039 5.717078 ACGCTCTTATATTATGGGACGAA 57.283 39.130 0.00 0.00 0.00 3.85
1447 3041 6.399669 CGAAAACGCTCTTATATTATGGGACG 60.400 42.308 0.00 0.00 0.00 4.79
1448 3042 6.643770 TCGAAAACGCTCTTATATTATGGGAC 59.356 38.462 0.00 0.00 0.00 4.46
1449 3043 6.643770 GTCGAAAACGCTCTTATATTATGGGA 59.356 38.462 0.00 0.00 0.00 4.37
1451 3045 7.169308 AGTGTCGAAAACGCTCTTATATTATGG 59.831 37.037 0.00 0.00 45.69 2.74
1452 3046 8.062231 AGTGTCGAAAACGCTCTTATATTATG 57.938 34.615 0.00 0.00 45.69 1.90
1453 3047 9.395707 CTAGTGTCGAAAACGCTCTTATATTAT 57.604 33.333 0.00 0.00 45.69 1.28
1454 3048 8.400947 ACTAGTGTCGAAAACGCTCTTATATTA 58.599 33.333 0.00 0.00 45.69 0.98
1455 3049 7.256286 ACTAGTGTCGAAAACGCTCTTATATT 58.744 34.615 0.00 0.00 45.69 1.28
1458 3052 5.056894 ACTAGTGTCGAAAACGCTCTTAT 57.943 39.130 0.00 0.00 45.69 1.73
1459 3053 4.494350 ACTAGTGTCGAAAACGCTCTTA 57.506 40.909 0.00 0.00 45.69 2.10
1460 3054 3.366440 ACTAGTGTCGAAAACGCTCTT 57.634 42.857 0.00 0.00 45.69 2.85
1461 3055 3.366440 AACTAGTGTCGAAAACGCTCT 57.634 42.857 0.00 0.00 45.69 4.09
1462 3056 3.362693 CCAAACTAGTGTCGAAAACGCTC 60.363 47.826 0.00 0.00 45.69 5.03
1464 3058 2.899977 CCAAACTAGTGTCGAAAACGC 58.100 47.619 0.00 0.00 38.74 4.84
1465 3059 2.542595 AGCCAAACTAGTGTCGAAAACG 59.457 45.455 0.00 0.00 0.00 3.60
1467 3061 5.336744 CAAAAGCCAAACTAGTGTCGAAAA 58.663 37.500 0.00 0.00 0.00 2.29
1468 3062 4.732355 GCAAAAGCCAAACTAGTGTCGAAA 60.732 41.667 0.00 0.00 0.00 3.46
1469 3063 3.242936 GCAAAAGCCAAACTAGTGTCGAA 60.243 43.478 0.00 0.00 0.00 3.71
1470 3064 2.289547 GCAAAAGCCAAACTAGTGTCGA 59.710 45.455 0.00 0.00 0.00 4.20
1472 3066 3.315191 TGAGCAAAAGCCAAACTAGTGTC 59.685 43.478 0.00 0.00 0.00 3.67
1473 3067 3.287222 TGAGCAAAAGCCAAACTAGTGT 58.713 40.909 0.00 0.00 0.00 3.55
1474 3068 3.988379 TGAGCAAAAGCCAAACTAGTG 57.012 42.857 0.00 0.00 0.00 2.74
1475 3069 4.682787 GTTTGAGCAAAAGCCAAACTAGT 58.317 39.130 18.50 0.00 43.54 2.57
1477 3071 3.378742 TCGTTTGAGCAAAAGCCAAACTA 59.621 39.130 20.94 13.70 44.26 2.24
1478 3072 2.165437 TCGTTTGAGCAAAAGCCAAACT 59.835 40.909 20.94 0.00 44.26 2.66
1520 3162 4.783560 TCCATCAACCACATGATCAGAT 57.216 40.909 0.00 0.00 37.96 2.90
1727 3369 6.094742 TGCATCGGATAGCAAAAATTGTAAGA 59.905 34.615 11.07 0.00 37.90 2.10
1731 3373 4.717233 TGCATCGGATAGCAAAAATTGT 57.283 36.364 11.07 0.00 37.90 2.71
1732 3374 4.084745 GCATGCATCGGATAGCAAAAATTG 60.085 41.667 14.21 11.29 44.88 2.32
1759 3403 6.292919 GCCAAAATCATGTAAGATCTACCGTC 60.293 42.308 0.00 0.00 0.00 4.79
1803 3465 4.813161 GTGTGTGATATGCTTGCAGATACT 59.187 41.667 2.56 0.00 0.00 2.12
1804 3466 4.024556 GGTGTGTGATATGCTTGCAGATAC 60.025 45.833 2.56 0.00 0.00 2.24
1805 3467 4.129380 GGTGTGTGATATGCTTGCAGATA 58.871 43.478 2.56 0.00 0.00 1.98
1806 3468 2.947652 GGTGTGTGATATGCTTGCAGAT 59.052 45.455 2.15 2.15 0.00 2.90
1817 3479 3.778954 TGGAATGTGTGGTGTGTGATA 57.221 42.857 0.00 0.00 0.00 2.15
1854 3525 4.987285 CAGAATCGCTGCTAGTATGAATGT 59.013 41.667 0.00 0.00 37.90 2.71
1910 3584 5.860716 CCAATTAGCTCAAAGTGCTTCTTTC 59.139 40.000 0.00 0.00 43.57 2.62
1929 3603 1.321474 CACAGGTCACACTGCCAATT 58.679 50.000 0.00 0.00 42.21 2.32
2086 3765 4.700268 TCACGCTGACATAATTTGCAAT 57.300 36.364 0.00 0.00 0.00 3.56
2090 3769 6.746104 TGTTTTTCACGCTGACATAATTTG 57.254 33.333 0.00 0.00 0.00 2.32
2103 3782 8.775884 CATCGTAACAGATTTATGTTTTTCACG 58.224 33.333 0.00 1.16 40.47 4.35
2188 3867 4.202101 ACAAATTTTGCGGAACATGACAGA 60.202 37.500 9.04 0.00 0.00 3.41
2230 3917 5.394553 CCATACTAGATCACAGTCACAGCAA 60.395 44.000 0.00 0.00 0.00 3.91
2289 3978 4.510038 TGGACAACCGTTAGAACTACTC 57.490 45.455 0.00 0.00 39.42 2.59
2352 4043 4.046462 TCTTTTGTCTAACGAGTTCACCG 58.954 43.478 0.00 0.00 0.00 4.94
2433 4126 4.676196 GCAAATTCACAATACTGGAGCTGG 60.676 45.833 0.00 0.00 0.00 4.85
2481 4196 4.016479 ACCTGGTCAGAAGAACCTAGGATA 60.016 45.833 17.98 0.00 0.00 2.59
2533 4248 1.743252 CCTGCTCTCGGTCCAAAGC 60.743 63.158 1.12 1.12 35.31 3.51
2557 4272 4.176752 CAGCGGTAGCCTTCCCCC 62.177 72.222 0.00 0.00 46.67 5.40
2650 4365 2.154462 CACAGAATGAGTGTGGTTCCC 58.846 52.381 0.00 0.00 41.43 3.97
2659 4374 1.625818 GTCCACTCCCACAGAATGAGT 59.374 52.381 0.00 0.00 39.69 3.41
2732 4447 1.066303 CAAGCGCAGGAGTAGAGTAGG 59.934 57.143 11.47 0.00 0.00 3.18
2812 4533 3.300009 CATGAGAAGAAACAAACGGCAC 58.700 45.455 0.00 0.00 0.00 5.01
2924 4720 2.037902 TCGTTCCTGCCATCAGTACAAA 59.962 45.455 0.00 0.00 38.66 2.83
3225 5040 9.250624 CCGCCAAAAGCTAAGATATATAGATAC 57.749 37.037 0.00 0.00 40.39 2.24
3242 5057 4.142924 GCCAAATTGAATAACCGCCAAAAG 60.143 41.667 0.00 0.00 0.00 2.27
3330 5150 7.172190 CCGTAGAGATTTGCAAATGACATCTAT 59.828 37.037 28.67 18.45 0.00 1.98
3363 5191 1.066430 GTACTGGTCGAAATGCCTGGA 60.066 52.381 0.00 0.00 0.00 3.86
3367 5195 3.907894 TTTTGTACTGGTCGAAATGCC 57.092 42.857 0.00 0.00 0.00 4.40
3401 5229 3.189287 ACAGTTGAAGCGCCAGAAAATAG 59.811 43.478 2.29 0.00 0.00 1.73
3466 5340 6.636562 TGCGAAACCAACTTTAAAAGGATA 57.363 33.333 7.72 0.00 0.00 2.59
3478 5365 4.849111 TTCAAACAAATGCGAAACCAAC 57.151 36.364 0.00 0.00 0.00 3.77
3479 5366 6.128172 ACAAATTCAAACAAATGCGAAACCAA 60.128 30.769 0.00 0.00 0.00 3.67
3539 5430 2.488153 CGTGTCTACACCTCACAGATCA 59.512 50.000 7.63 0.00 43.66 2.92
3545 5436 2.787601 TCAACGTGTCTACACCTCAC 57.212 50.000 7.63 0.00 43.66 3.51
3560 5451 3.539604 CCTGATCCCAGACAAGATCAAC 58.460 50.000 4.44 0.00 46.11 3.18
3614 5507 5.746990 TTTCTTTTTGTTTTGGAGGGACA 57.253 34.783 0.00 0.00 0.00 4.02
3660 5555 2.431954 ATCAACTGCATGAGAAGGGG 57.568 50.000 0.00 0.00 31.76 4.79
3662 5557 6.485648 TGAATCATATCAACTGCATGAGAAGG 59.514 38.462 0.00 0.00 32.51 3.46
3687 5582 5.473066 ACAAATAAAGCAGCAACTGGATT 57.527 34.783 0.00 0.00 31.21 3.01
3709 5604 5.819991 AGCTGGAATGAGAAAAGTGGAATA 58.180 37.500 0.00 0.00 0.00 1.75
3789 8290 3.053917 ACGGTGATTTATTTACCAGGGCT 60.054 43.478 0.00 0.00 34.10 5.19
3791 8292 7.576861 ATTTACGGTGATTTATTTACCAGGG 57.423 36.000 0.00 0.00 34.10 4.45
3792 8293 9.296400 CAAATTTACGGTGATTTATTTACCAGG 57.704 33.333 0.00 0.00 34.10 4.45
3860 8749 1.821136 CCAGATTTGAAAGGGCTCCAC 59.179 52.381 0.00 0.00 0.00 4.02
3885 8774 5.046591 ACAATTAAGAGTCCGAACAGATGGA 60.047 40.000 0.00 0.00 0.00 3.41
3936 8825 8.994429 TGCTATGTTTGTTTCTTTCTTTTTGA 57.006 26.923 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.