Multiple sequence alignment - TraesCS3D01G290300

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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 TraesCS3D01G290300 chr3D 100.000 2834 0 0 1 2834 400446804 400449637 0.000000e+00 5234.0
1 TraesCS3D01G290300 chr3D 94.875 722 30 4 1 715 295638508 295639229 0.000000e+00 1122.0
2 TraesCS3D01G290300 chr3D 85.090 778 58 22 1867 2634 582149657 582148928 0.000000e+00 741.0
3 TraesCS3D01G290300 chr6D 95.423 721 27 3 1 715 266662878 266663598 0.000000e+00 1144.0
4 TraesCS3D01G290300 chr6D 83.626 171 15 6 753 914 459229253 459229419 6.330000e-32 148.0
5 TraesCS3D01G290300 chr6D 86.441 118 13 1 1888 2002 463885658 463885541 2.960000e-25 126.0
6 TraesCS3D01G290300 chr2D 95.125 718 31 3 1 715 125757053 125757769 0.000000e+00 1129.0
7 TraesCS3D01G290300 chr2D 94.868 721 30 4 1 715 134738101 134737382 0.000000e+00 1120.0
8 TraesCS3D01G290300 chr2D 94.979 717 30 4 5 715 322341191 322341907 0.000000e+00 1120.0
9 TraesCS3D01G290300 chr2D 94.730 721 32 5 1 715 76157464 76158184 0.000000e+00 1116.0
10 TraesCS3D01G290300 chr2D 84.961 778 59 22 1867 2634 42003443 42004172 0.000000e+00 736.0
11 TraesCS3D01G290300 chr2D 83.190 232 31 6 1592 1821 622912657 622912432 3.700000e-49 206.0
12 TraesCS3D01G290300 chr2D 88.235 153 15 3 716 868 628840678 628840827 2.240000e-41 180.0
13 TraesCS3D01G290300 chr2D 89.655 87 9 0 1731 1817 622878098 622878184 8.300000e-21 111.0
14 TraesCS3D01G290300 chr5D 95.007 721 30 3 1 715 324129060 324129780 0.000000e+00 1127.0
15 TraesCS3D01G290300 chr5D 95.007 721 30 3 1 715 415026797 415026077 0.000000e+00 1127.0
16 TraesCS3D01G290300 chr5D 85.090 778 58 24 1867 2634 476031404 476032133 0.000000e+00 741.0
17 TraesCS3D01G290300 chr5D 85.090 778 58 21 1867 2634 511133118 511132389 0.000000e+00 741.0
18 TraesCS3D01G290300 chr5D 89.139 267 24 4 717 982 483117165 483117427 7.570000e-86 327.0
19 TraesCS3D01G290300 chr5D 91.705 217 16 2 994 1209 483127124 483127339 1.650000e-77 300.0
20 TraesCS3D01G290300 chr5D 84.016 244 21 12 743 982 169785260 169785489 4.750000e-53 219.0
21 TraesCS3D01G290300 chr5D 85.167 209 20 10 743 947 156602825 156603026 1.330000e-48 204.0
22 TraesCS3D01G290300 chr5D 93.130 131 7 2 1395 1524 560356708 560356837 1.040000e-44 191.0
23 TraesCS3D01G290300 chr5D 93.023 129 9 0 1396 1524 28989719 28989847 3.730000e-44 189.0
24 TraesCS3D01G290300 chr5D 89.922 129 13 0 1396 1524 476030769 476030641 1.750000e-37 167.0
25 TraesCS3D01G290300 chr3A 89.732 896 69 9 994 1887 339108163 339109037 0.000000e+00 1123.0
26 TraesCS3D01G290300 chr3A 92.996 771 51 3 1867 2634 339110082 339110852 0.000000e+00 1122.0
27 TraesCS3D01G290300 chr7D 94.875 722 30 4 1 715 136230079 136229358 0.000000e+00 1122.0
28 TraesCS3D01G290300 chr7D 94.615 130 7 0 1395 1524 596556671 596556542 4.790000e-48 202.0
29 TraesCS3D01G290300 chr7A 90.285 772 55 9 1867 2634 296598055 296598810 0.000000e+00 992.0
30 TraesCS3D01G290300 chr7A 89.147 129 12 2 1267 1395 299434767 299434641 2.920000e-35 159.0
31 TraesCS3D01G290300 chr7A 87.952 83 10 0 1508 1590 299434565 299434647 6.460000e-17 99.0
32 TraesCS3D01G290300 chr7B 86.154 780 65 17 1867 2634 671814009 671813261 0.000000e+00 802.0
33 TraesCS3D01G290300 chr7B 93.651 126 8 0 1396 1521 671814649 671814774 3.730000e-44 189.0
34 TraesCS3D01G290300 chr6B 86.026 780 66 17 1867 2634 283380694 283379946 0.000000e+00 797.0
35 TraesCS3D01G290300 chr6B 93.846 130 8 0 1395 1524 283381333 283381462 2.230000e-46 196.0
36 TraesCS3D01G290300 chr6B 91.538 130 11 0 1395 1524 283382015 283382144 2.240000e-41 180.0
37 TraesCS3D01G290300 chr6B 89.157 83 9 0 1508 1590 78218576 78218658 1.390000e-18 104.0
38 TraesCS3D01G290300 chr6B 93.443 61 4 0 1335 1395 78218712 78218652 1.080000e-14 91.6
39 TraesCS3D01G290300 chr1D 84.704 778 61 22 1867 2634 393755196 393755925 0.000000e+00 725.0
40 TraesCS3D01G290300 chr1D 84.242 165 13 6 759 914 236040507 236040667 6.330000e-32 148.0
41 TraesCS3D01G290300 chr1B 93.367 196 13 0 1395 1590 647049609 647049804 9.930000e-75 291.0
42 TraesCS3D01G290300 chr1B 87.444 223 22 5 716 937 309495458 309495241 4.690000e-63 252.0
43 TraesCS3D01G290300 chr1B 89.055 201 18 2 1588 1787 647049440 647049243 2.180000e-61 246.0
44 TraesCS3D01G290300 chr1B 89.535 172 12 4 1043 1213 309494927 309494761 2.210000e-51 213.0
45 TraesCS3D01G290300 chr1B 86.667 120 14 2 1276 1395 647049915 647049798 6.370000e-27 132.0
46 TraesCS3D01G290300 chr1B 90.361 83 8 0 1508 1590 12933145 12933227 2.980000e-20 110.0
47 TraesCS3D01G290300 chr1B 89.157 83 9 0 1508 1590 360520002 360520084 1.390000e-18 104.0
48 TraesCS3D01G290300 chr1B 93.443 61 4 0 1335 1395 12933281 12933221 1.080000e-14 91.6
49 TraesCS3D01G290300 chr1B 93.443 61 4 0 1335 1395 360520138 360520078 1.080000e-14 91.6
50 TraesCS3D01G290300 chr2A 82.609 322 34 12 1586 1887 754346217 754345898 6.020000e-67 265.0
51 TraesCS3D01G290300 chr2A 84.239 184 19 4 740 914 488467854 488467672 1.350000e-38 171.0
52 TraesCS3D01G290300 chr2A 82.659 173 25 5 1224 1395 6471836 6472004 6.330000e-32 148.0
53 TraesCS3D01G290300 chr2A 93.750 80 5 0 1511 1590 6472077 6471998 1.380000e-23 121.0
54 TraesCS3D01G290300 chrUn 89.147 129 12 2 1267 1395 347152118 347151992 2.920000e-35 159.0
55 TraesCS3D01G290300 chr4A 89.147 129 12 2 1267 1395 420023105 420022979 2.920000e-35 159.0
56 TraesCS3D01G290300 chr4A 91.566 83 7 0 1508 1590 420022903 420022985 6.420000e-22 115.0


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 TraesCS3D01G290300 chr3D 400446804 400449637 2833 False 5234.0 5234 100.0000 1 2834 1 chr3D.!!$F2 2833
1 TraesCS3D01G290300 chr3D 295638508 295639229 721 False 1122.0 1122 94.8750 1 715 1 chr3D.!!$F1 714
2 TraesCS3D01G290300 chr3D 582148928 582149657 729 True 741.0 741 85.0900 1867 2634 1 chr3D.!!$R1 767
3 TraesCS3D01G290300 chr6D 266662878 266663598 720 False 1144.0 1144 95.4230 1 715 1 chr6D.!!$F1 714
4 TraesCS3D01G290300 chr2D 125757053 125757769 716 False 1129.0 1129 95.1250 1 715 1 chr2D.!!$F3 714
5 TraesCS3D01G290300 chr2D 134737382 134738101 719 True 1120.0 1120 94.8680 1 715 1 chr2D.!!$R1 714
6 TraesCS3D01G290300 chr2D 322341191 322341907 716 False 1120.0 1120 94.9790 5 715 1 chr2D.!!$F4 710
7 TraesCS3D01G290300 chr2D 76157464 76158184 720 False 1116.0 1116 94.7300 1 715 1 chr2D.!!$F2 714
8 TraesCS3D01G290300 chr2D 42003443 42004172 729 False 736.0 736 84.9610 1867 2634 1 chr2D.!!$F1 767
9 TraesCS3D01G290300 chr5D 324129060 324129780 720 False 1127.0 1127 95.0070 1 715 1 chr5D.!!$F4 714
10 TraesCS3D01G290300 chr5D 415026077 415026797 720 True 1127.0 1127 95.0070 1 715 1 chr5D.!!$R1 714
11 TraesCS3D01G290300 chr5D 476031404 476032133 729 False 741.0 741 85.0900 1867 2634 1 chr5D.!!$F5 767
12 TraesCS3D01G290300 chr5D 511132389 511133118 729 True 741.0 741 85.0900 1867 2634 1 chr5D.!!$R3 767
13 TraesCS3D01G290300 chr3A 339108163 339110852 2689 False 1122.5 1123 91.3640 994 2634 2 chr3A.!!$F1 1640
14 TraesCS3D01G290300 chr7D 136229358 136230079 721 True 1122.0 1122 94.8750 1 715 1 chr7D.!!$R1 714
15 TraesCS3D01G290300 chr7A 296598055 296598810 755 False 992.0 992 90.2850 1867 2634 1 chr7A.!!$F1 767
16 TraesCS3D01G290300 chr7B 671813261 671814009 748 True 802.0 802 86.1540 1867 2634 1 chr7B.!!$R1 767
17 TraesCS3D01G290300 chr6B 283379946 283380694 748 True 797.0 797 86.0260 1867 2634 1 chr6B.!!$R2 767
18 TraesCS3D01G290300 chr1D 393755196 393755925 729 False 725.0 725 84.7040 1867 2634 1 chr1D.!!$F2 767
19 TraesCS3D01G290300 chr1B 309494761 309495458 697 True 232.5 252 88.4895 716 1213 2 chr1B.!!$R3 497

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
988 1186 0.250081 GAATCGCCATCTCCCTGGAC 60.25 60.0 0.0 0.0 38.69 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 4071 0.108329 AACTCCGGCGTGTAGGATTG 60.108 55.0 6.01 0.0 35.75 2.67 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
117 119 4.382754 GCAGGACATTGTTTTCGAATGAAC 59.617 41.667 0.00 1.84 35.23 3.18
125 127 5.155509 TGTTTTCGAATGAACACACTCAG 57.844 39.130 10.60 0.00 39.27 3.35
133 135 5.007234 CGAATGAACACACTCAGGTTTTGTA 59.993 40.000 0.00 0.00 0.00 2.41
356 364 2.086869 CAACGAACCAGGCAATCAGAT 58.913 47.619 0.00 0.00 0.00 2.90
576 586 2.027653 GGCTTTCTCTACTGAGGTGCTT 60.028 50.000 0.00 0.00 40.58 3.91
628 638 6.320926 CAGTAGTTCTCCCTTTACTACCCTAC 59.679 46.154 0.00 0.00 43.22 3.18
699 709 8.472413 CCCAACTATTGATCAAAGACATGATTT 58.528 33.333 13.09 0.00 40.08 2.17
719 729 0.399454 AGAGCCAATGCATATCCGCT 59.601 50.000 0.00 4.43 41.13 5.52
728 738 1.730902 CATATCCGCTCGCTCACCG 60.731 63.158 0.00 0.00 38.61 4.94
730 740 2.131294 ATATCCGCTCGCTCACCGTC 62.131 60.000 0.00 0.00 38.35 4.79
736 746 4.400109 TCGCTCACCGTCGTCAGC 62.400 66.667 0.00 0.00 38.35 4.26
738 748 2.049063 GCTCACCGTCGTCAGCTT 60.049 61.111 0.00 0.00 0.00 3.74
742 752 1.174078 TCACCGTCGTCAGCTTACCA 61.174 55.000 0.00 0.00 0.00 3.25
745 755 2.029623 ACCGTCGTCAGCTTACCATAT 58.970 47.619 0.00 0.00 0.00 1.78
747 757 3.825014 ACCGTCGTCAGCTTACCATATAT 59.175 43.478 0.00 0.00 0.00 0.86
778 788 9.758651 ATTTTTGAGGTGGTACTAAAATTGTTC 57.241 29.630 0.00 0.00 31.53 3.18
779 789 8.528044 TTTTGAGGTGGTACTAAAATTGTTCT 57.472 30.769 0.00 0.00 0.00 3.01
780 790 7.504924 TTGAGGTGGTACTAAAATTGTTCTG 57.495 36.000 0.00 0.00 0.00 3.02
781 791 6.833041 TGAGGTGGTACTAAAATTGTTCTGA 58.167 36.000 0.00 0.00 0.00 3.27
782 792 6.934645 TGAGGTGGTACTAAAATTGTTCTGAG 59.065 38.462 0.00 0.00 0.00 3.35
783 793 7.074653 AGGTGGTACTAAAATTGTTCTGAGA 57.925 36.000 0.00 0.00 0.00 3.27
786 796 7.307811 GGTGGTACTAAAATTGTTCTGAGACAC 60.308 40.741 0.00 0.00 0.00 3.67
798 808 5.007626 TGTTCTGAGACACAAAAGAATTCGG 59.992 40.000 0.00 0.00 31.73 4.30
811 821 1.463444 GAATTCGGCTGTTACAACGCT 59.537 47.619 4.58 0.00 0.00 5.07
812 822 1.076332 ATTCGGCTGTTACAACGCTC 58.924 50.000 4.58 0.00 0.00 5.03
813 823 1.279527 TTCGGCTGTTACAACGCTCG 61.280 55.000 4.58 3.60 0.00 5.03
814 824 2.474712 GGCTGTTACAACGCTCGC 59.525 61.111 8.18 0.00 0.00 5.03
815 825 2.474712 GCTGTTACAACGCTCGCC 59.525 61.111 0.00 0.00 0.00 5.54
849 860 1.103398 AGCGTCAATGCTAATGGGCC 61.103 55.000 0.00 0.00 45.14 5.80
870 881 3.055021 CCTTTAGAAACCTCCTCTCACCC 60.055 52.174 0.00 0.00 0.00 4.61
871 882 2.249309 TAGAAACCTCCTCTCACCCC 57.751 55.000 0.00 0.00 0.00 4.95
914 925 1.148310 CGAACAAGGAGCAACGACAT 58.852 50.000 0.00 0.00 0.00 3.06
915 926 1.136252 CGAACAAGGAGCAACGACATG 60.136 52.381 0.00 0.00 0.00 3.21
918 929 1.070758 ACAAGGAGCAACGACATGAGT 59.929 47.619 0.00 0.00 0.00 3.41
928 939 1.135546 ACGACATGAGTGCTTCTCTCG 60.136 52.381 0.00 13.39 43.13 4.04
937 948 4.051922 GAGTGCTTCTCTCGAACAGAAAA 58.948 43.478 7.66 0.00 39.86 2.29
938 949 4.442706 AGTGCTTCTCTCGAACAGAAAAA 58.557 39.130 7.66 0.00 29.36 1.94
940 951 3.809832 TGCTTCTCTCGAACAGAAAAAGG 59.190 43.478 7.66 0.00 29.87 3.11
947 1145 4.036380 TCTCGAACAGAAAAAGGAAAAGGC 59.964 41.667 0.00 0.00 0.00 4.35
952 1150 2.884639 CAGAAAAAGGAAAAGGCCGAGA 59.115 45.455 0.00 0.00 0.00 4.04
953 1151 3.317993 CAGAAAAAGGAAAAGGCCGAGAA 59.682 43.478 0.00 0.00 0.00 2.87
954 1152 4.021981 CAGAAAAAGGAAAAGGCCGAGAAT 60.022 41.667 0.00 0.00 0.00 2.40
955 1153 5.183140 CAGAAAAAGGAAAAGGCCGAGAATA 59.817 40.000 0.00 0.00 0.00 1.75
957 1155 3.283259 AAGGAAAAGGCCGAGAATAGG 57.717 47.619 0.00 0.00 0.00 2.57
959 1157 2.436173 AGGAAAAGGCCGAGAATAGGAG 59.564 50.000 0.00 0.00 29.15 3.69
960 1158 2.214347 GAAAAGGCCGAGAATAGGAGC 58.786 52.381 0.00 0.00 29.15 4.70
963 1161 1.917872 AGGCCGAGAATAGGAGCTAG 58.082 55.000 0.00 0.00 29.15 3.42
964 1162 0.892063 GGCCGAGAATAGGAGCTAGG 59.108 60.000 0.00 0.00 29.15 3.02
965 1163 0.892063 GCCGAGAATAGGAGCTAGGG 59.108 60.000 0.00 0.00 29.15 3.53
966 1164 1.824045 GCCGAGAATAGGAGCTAGGGT 60.824 57.143 0.00 0.00 29.15 4.34
967 1165 2.599677 CCGAGAATAGGAGCTAGGGTT 58.400 52.381 0.00 0.00 29.15 4.11
968 1166 2.966516 CCGAGAATAGGAGCTAGGGTTT 59.033 50.000 0.00 0.00 29.15 3.27
970 1168 3.637229 CGAGAATAGGAGCTAGGGTTTGA 59.363 47.826 0.00 0.00 0.00 2.69
971 1169 4.099573 CGAGAATAGGAGCTAGGGTTTGAA 59.900 45.833 0.00 0.00 0.00 2.69
972 1170 5.221541 CGAGAATAGGAGCTAGGGTTTGAAT 60.222 44.000 0.00 0.00 0.00 2.57
974 1172 2.990066 AGGAGCTAGGGTTTGAATCG 57.010 50.000 0.00 0.00 0.00 3.34
975 1173 1.134371 AGGAGCTAGGGTTTGAATCGC 60.134 52.381 0.00 0.00 0.00 4.58
976 1174 1.300481 GAGCTAGGGTTTGAATCGCC 58.700 55.000 0.00 0.00 0.00 5.54
977 1175 0.618458 AGCTAGGGTTTGAATCGCCA 59.382 50.000 0.00 0.00 0.00 5.69
978 1176 1.212935 AGCTAGGGTTTGAATCGCCAT 59.787 47.619 0.00 0.00 0.00 4.40
979 1177 1.604278 GCTAGGGTTTGAATCGCCATC 59.396 52.381 0.00 0.00 0.00 3.51
980 1178 2.746472 GCTAGGGTTTGAATCGCCATCT 60.746 50.000 0.00 0.00 0.00 2.90
981 1179 2.044123 AGGGTTTGAATCGCCATCTC 57.956 50.000 0.00 0.00 0.00 2.75
982 1180 1.025041 GGGTTTGAATCGCCATCTCC 58.975 55.000 0.00 0.00 0.00 3.71
983 1181 1.025041 GGTTTGAATCGCCATCTCCC 58.975 55.000 0.00 0.00 0.00 4.30
984 1182 1.408822 GGTTTGAATCGCCATCTCCCT 60.409 52.381 0.00 0.00 0.00 4.20
987 1185 0.690744 TGAATCGCCATCTCCCTGGA 60.691 55.000 0.00 0.00 38.69 3.86
988 1186 0.250081 GAATCGCCATCTCCCTGGAC 60.250 60.000 0.00 0.00 38.69 4.02
990 1188 0.982852 ATCGCCATCTCCCTGGACAA 60.983 55.000 0.00 0.00 38.69 3.18
992 1190 1.225704 GCCATCTCCCTGGACAAGG 59.774 63.158 0.00 0.00 46.94 3.61
1003 1262 1.526917 GGACAAGGGGATGCGATGG 60.527 63.158 0.00 0.00 0.00 3.51
1154 1414 4.719369 CTACGCCGGCCGCCTATC 62.719 72.222 22.85 4.53 41.76 2.08
1209 1470 2.689034 CTCCTCCGAAAGCCCCCT 60.689 66.667 0.00 0.00 0.00 4.79
1210 1471 2.687566 TCCTCCGAAAGCCCCCTC 60.688 66.667 0.00 0.00 0.00 4.30
1211 1472 2.689034 CCTCCGAAAGCCCCCTCT 60.689 66.667 0.00 0.00 0.00 3.69
1212 1473 2.586792 CTCCGAAAGCCCCCTCTG 59.413 66.667 0.00 0.00 0.00 3.35
1213 1474 3.689002 CTCCGAAAGCCCCCTCTGC 62.689 68.421 0.00 0.00 0.00 4.26
1240 1501 4.447342 CCACCATCAGCCCCACCC 62.447 72.222 0.00 0.00 0.00 4.61
1326 1587 2.308118 TACCCTCCTCCCATCGGGAC 62.308 65.000 0.00 0.00 46.17 4.46
1373 1634 2.202756 GTCCTCGCCGCGATTTCT 60.203 61.111 17.22 0.00 34.61 2.52
1378 1639 1.192534 CCTCGCCGCGATTTCTAAATC 59.807 52.381 17.22 5.52 41.02 2.17
1389 1650 5.902051 GATTTCTAAATCGAACCTACCGG 57.098 43.478 0.00 0.00 35.88 5.28
1392 1653 2.100252 TCTAAATCGAACCTACCGGCAG 59.900 50.000 0.00 0.00 0.00 4.85
1431 1692 0.644380 TGGGGAGAGATCCAGATGGT 59.356 55.000 0.00 0.00 36.34 3.55
1436 1697 1.339610 GAGAGATCCAGATGGTGACGG 59.660 57.143 0.00 0.00 36.34 4.79
1442 1703 3.771160 AGATGGTGACGGCGGACC 61.771 66.667 19.97 19.97 0.00 4.46
1516 1777 3.868200 GAGGGGTGGGCTGGTGTTG 62.868 68.421 0.00 0.00 0.00 3.33
1525 1786 2.935955 CTGGTGTTGGCGACGAAC 59.064 61.111 0.00 0.00 0.00 3.95
1560 1821 4.504916 CTCGGTGAGGCAGAGGCG 62.505 72.222 0.00 0.00 42.47 5.52
1621 1882 3.818787 CCCTCAGCACGCCAATGC 61.819 66.667 0.00 0.00 46.50 3.56
1658 1919 1.162800 GGCGGCCTTGACATCTCATC 61.163 60.000 12.87 0.00 0.00 2.92
1703 1964 0.889186 GAGCGTGAGGGCAAGGAAAA 60.889 55.000 0.00 0.00 34.64 2.29
1713 1974 1.269448 GGCAAGGAAAACATCGAGCAA 59.731 47.619 0.00 0.00 0.00 3.91
1770 2031 0.759959 AGCATGCAGAGGAGGAGATG 59.240 55.000 21.98 0.00 0.00 2.90
1776 2037 1.270412 GCAGAGGAGGAGATGCATCTG 60.270 57.143 33.33 18.48 37.25 2.90
1781 2042 2.158986 AGGAGGAGATGCATCTGAAACG 60.159 50.000 33.33 0.00 37.25 3.60
1794 2055 1.398390 CTGAAACGCCTTACCATGAGC 59.602 52.381 0.00 0.00 0.00 4.26
1816 2077 4.260538 GCAGACTGCCGAAATTCTTCATAG 60.261 45.833 17.01 0.00 37.42 2.23
1848 2109 4.558226 TGACTGACAGAGGTATGCAATT 57.442 40.909 10.08 0.00 0.00 2.32
1859 2120 5.365025 AGAGGTATGCAATTTCTCTGCTCTA 59.635 40.000 10.17 0.00 40.59 2.43
1864 2125 4.835678 TGCAATTTCTCTGCTCTACATCA 58.164 39.130 0.00 0.00 40.59 3.07
1870 3196 8.386606 CAATTTCTCTGCTCTACATCACTAAAC 58.613 37.037 0.00 0.00 0.00 2.01
1872 3198 6.201226 TCTCTGCTCTACATCACTAAACTG 57.799 41.667 0.00 0.00 0.00 3.16
1876 3202 7.615403 TCTGCTCTACATCACTAAACTGAAAT 58.385 34.615 0.00 0.00 0.00 2.17
1882 3208 9.534565 TCTACATCACTAAACTGAAATATCTGC 57.465 33.333 0.00 0.00 0.00 4.26
1883 3209 9.317936 CTACATCACTAAACTGAAATATCTGCA 57.682 33.333 0.00 0.00 0.00 4.41
1885 3211 8.043113 ACATCACTAAACTGAAATATCTGCAGA 58.957 33.333 20.79 20.79 33.94 4.26
1886 3212 9.053840 CATCACTAAACTGAAATATCTGCAGAT 57.946 33.333 30.85 30.85 38.51 2.90
1930 3257 2.802787 ATGTGAGATAGTAGCCGTGC 57.197 50.000 0.00 0.00 0.00 5.34
2042 3369 2.552315 CTGCCACAGGTACGAAAACAAT 59.448 45.455 0.00 0.00 0.00 2.71
2102 3429 4.468095 AGCACTAACACAATCACGTTTC 57.532 40.909 0.00 0.00 0.00 2.78
2139 3466 2.695666 AGTAGTCAATGGGTCATCTCCG 59.304 50.000 0.00 0.00 0.00 4.63
2170 3497 5.473504 AGGTTCAGCACTAATTACTGTTTGG 59.526 40.000 2.54 0.00 33.12 3.28
2174 3501 8.347035 GTTCAGCACTAATTACTGTTTGGTTAA 58.653 33.333 2.54 0.00 33.12 2.01
2208 3535 4.379082 CCGAAAACAATAGTACCAAGCACC 60.379 45.833 0.00 0.00 0.00 5.01
2243 3570 7.397476 CACCTGAGTATATCACATGGGTATAGT 59.603 40.741 0.00 0.08 32.47 2.12
2416 3750 6.040391 TGGCAAATAGACACTGCTTTACTTTT 59.960 34.615 0.00 0.00 36.32 2.27
2425 3759 9.569167 AGACACTGCTTTACTTTTAACTTTTTC 57.431 29.630 0.00 0.00 0.00 2.29
2634 3974 6.816640 GCATACACTAGAACATTGTAACAGGA 59.183 38.462 0.00 0.00 29.78 3.86
2635 3975 7.495934 GCATACACTAGAACATTGTAACAGGAT 59.504 37.037 0.00 0.00 29.78 3.24
2638 3978 8.135382 ACACTAGAACATTGTAACAGGATAGT 57.865 34.615 0.00 0.00 0.00 2.12
2639 3979 8.035394 ACACTAGAACATTGTAACAGGATAGTG 58.965 37.037 0.00 0.00 41.19 2.74
2640 3980 8.251026 CACTAGAACATTGTAACAGGATAGTGA 58.749 37.037 0.00 0.00 38.97 3.41
2641 3981 8.470805 ACTAGAACATTGTAACAGGATAGTGAG 58.529 37.037 0.00 0.00 0.00 3.51
2642 3982 6.644347 AGAACATTGTAACAGGATAGTGAGG 58.356 40.000 0.00 0.00 0.00 3.86
2643 3983 4.770795 ACATTGTAACAGGATAGTGAGGC 58.229 43.478 0.00 0.00 0.00 4.70
2644 3984 3.520290 TTGTAACAGGATAGTGAGGCG 57.480 47.619 0.00 0.00 0.00 5.52
2645 3985 2.730382 TGTAACAGGATAGTGAGGCGA 58.270 47.619 0.00 0.00 0.00 5.54
2646 3986 3.093814 TGTAACAGGATAGTGAGGCGAA 58.906 45.455 0.00 0.00 0.00 4.70
2647 3987 2.969628 AACAGGATAGTGAGGCGAAG 57.030 50.000 0.00 0.00 0.00 3.79
2648 3988 2.145397 ACAGGATAGTGAGGCGAAGA 57.855 50.000 0.00 0.00 0.00 2.87
2649 3989 2.672098 ACAGGATAGTGAGGCGAAGAT 58.328 47.619 0.00 0.00 0.00 2.40
2650 3990 2.363680 ACAGGATAGTGAGGCGAAGATG 59.636 50.000 0.00 0.00 0.00 2.90
2651 3991 2.363680 CAGGATAGTGAGGCGAAGATGT 59.636 50.000 0.00 0.00 0.00 3.06
2652 3992 3.034635 AGGATAGTGAGGCGAAGATGTT 58.965 45.455 0.00 0.00 0.00 2.71
2653 3993 3.126831 GGATAGTGAGGCGAAGATGTTG 58.873 50.000 0.00 0.00 0.00 3.33
2654 3994 3.181475 GGATAGTGAGGCGAAGATGTTGA 60.181 47.826 0.00 0.00 0.00 3.18
2655 3995 4.502259 GGATAGTGAGGCGAAGATGTTGAT 60.502 45.833 0.00 0.00 0.00 2.57
2656 3996 2.625737 AGTGAGGCGAAGATGTTGATG 58.374 47.619 0.00 0.00 0.00 3.07
2657 3997 1.063174 GTGAGGCGAAGATGTTGATGC 59.937 52.381 0.00 0.00 0.00 3.91
2658 3998 1.338960 TGAGGCGAAGATGTTGATGCA 60.339 47.619 0.00 0.00 0.00 3.96
2659 3999 1.329906 GAGGCGAAGATGTTGATGCAG 59.670 52.381 0.00 0.00 0.00 4.41
2660 4000 1.089920 GGCGAAGATGTTGATGCAGT 58.910 50.000 0.00 0.00 0.00 4.40
2661 4001 2.093500 AGGCGAAGATGTTGATGCAGTA 60.093 45.455 0.00 0.00 0.00 2.74
2662 4002 2.677836 GGCGAAGATGTTGATGCAGTAA 59.322 45.455 0.00 0.00 0.00 2.24
2663 4003 3.313526 GGCGAAGATGTTGATGCAGTAAT 59.686 43.478 0.00 0.00 0.00 1.89
2664 4004 4.277258 GCGAAGATGTTGATGCAGTAATG 58.723 43.478 0.00 0.00 0.00 1.90
2665 4005 4.277258 CGAAGATGTTGATGCAGTAATGC 58.723 43.478 8.51 8.51 0.00 3.56
2672 4012 2.047750 TGCAGTAATGCACGCGGA 60.048 55.556 14.87 0.00 40.23 5.54
2673 4013 2.387445 TGCAGTAATGCACGCGGAC 61.387 57.895 14.87 1.50 40.23 4.79
2674 4014 2.387445 GCAGTAATGCACGCGGACA 61.387 57.895 12.47 8.69 34.41 4.02
2675 4015 1.419922 CAGTAATGCACGCGGACAC 59.580 57.895 12.47 0.00 0.00 3.67
2676 4016 2.092291 AGTAATGCACGCGGACACG 61.092 57.895 12.47 0.00 44.63 4.49
2677 4017 2.811747 TAATGCACGCGGACACGG 60.812 61.111 12.47 0.00 41.36 4.94
2686 4026 4.351938 CGGACACGGCAAGGACGA 62.352 66.667 0.00 0.00 35.20 4.20
2687 4027 2.432628 GGACACGGCAAGGACGAG 60.433 66.667 0.00 0.00 35.20 4.18
2688 4028 2.649034 GACACGGCAAGGACGAGA 59.351 61.111 0.00 0.00 35.20 4.04
2689 4029 1.006571 GACACGGCAAGGACGAGAA 60.007 57.895 0.00 0.00 35.20 2.87
2690 4030 1.006102 ACACGGCAAGGACGAGAAG 60.006 57.895 0.00 0.00 35.20 2.85
2691 4031 2.048127 ACGGCAAGGACGAGAAGC 60.048 61.111 0.00 0.00 35.20 3.86
2693 4033 2.815647 GGCAAGGACGAGAAGCGG 60.816 66.667 0.00 0.00 46.49 5.52
2694 4034 2.815647 GCAAGGACGAGAAGCGGG 60.816 66.667 0.00 0.00 46.49 6.13
2695 4035 2.125512 CAAGGACGAGAAGCGGGG 60.126 66.667 0.00 0.00 46.49 5.73
2696 4036 4.083862 AAGGACGAGAAGCGGGGC 62.084 66.667 0.00 0.00 46.49 5.80
2698 4038 4.821589 GGACGAGAAGCGGGGCTG 62.822 72.222 0.00 0.00 46.49 4.85
2708 4048 4.641645 CGGGGCTGCTTGGACACA 62.642 66.667 0.00 0.00 0.00 3.72
2709 4049 2.985847 GGGGCTGCTTGGACACAC 60.986 66.667 0.00 0.00 0.00 3.82
2710 4050 2.985847 GGGCTGCTTGGACACACC 60.986 66.667 0.00 0.00 39.54 4.16
2711 4051 3.357079 GGCTGCTTGGACACACCG 61.357 66.667 0.00 0.00 42.61 4.94
2712 4052 3.357079 GCTGCTTGGACACACCGG 61.357 66.667 0.00 0.00 42.61 5.28
2713 4053 3.357079 CTGCTTGGACACACCGGC 61.357 66.667 0.00 0.00 42.61 6.13
2716 4056 3.345808 CTTGGACACACCGGCGTG 61.346 66.667 20.85 20.85 46.11 5.34
2717 4057 3.800685 CTTGGACACACCGGCGTGA 62.801 63.158 28.57 3.84 43.14 4.35
2718 4058 3.387225 TTGGACACACCGGCGTGAA 62.387 57.895 28.57 10.21 43.14 3.18
2719 4059 2.358247 GGACACACCGGCGTGAAT 60.358 61.111 28.57 7.57 43.14 2.57
2720 4060 1.079681 GGACACACCGGCGTGAATA 60.080 57.895 28.57 0.00 43.14 1.75
2721 4061 1.356527 GGACACACCGGCGTGAATAC 61.357 60.000 28.57 15.19 43.14 1.89
2733 4073 3.447752 CGTGAATACGTGTTGATGCAA 57.552 42.857 0.91 0.00 44.99 4.08
2734 4074 4.002267 CGTGAATACGTGTTGATGCAAT 57.998 40.909 0.91 0.00 44.99 3.56
2735 4075 4.021822 CGTGAATACGTGTTGATGCAATC 58.978 43.478 0.91 0.00 44.99 2.67
2736 4076 4.342772 GTGAATACGTGTTGATGCAATCC 58.657 43.478 0.91 0.00 44.73 3.01
2737 4077 4.094887 GTGAATACGTGTTGATGCAATCCT 59.905 41.667 0.91 0.00 44.73 3.24
2738 4078 5.293324 GTGAATACGTGTTGATGCAATCCTA 59.707 40.000 0.91 0.00 44.73 2.94
2739 4079 5.293324 TGAATACGTGTTGATGCAATCCTAC 59.707 40.000 0.91 0.00 44.73 3.18
2740 4080 3.052455 ACGTGTTGATGCAATCCTACA 57.948 42.857 0.00 0.00 44.73 2.74
2741 4081 2.742053 ACGTGTTGATGCAATCCTACAC 59.258 45.455 15.92 15.92 46.07 2.90
2742 4082 3.389687 GTGTTGATGCAATCCTACACG 57.610 47.619 12.81 0.00 44.73 4.49
2743 4083 1.737236 TGTTGATGCAATCCTACACGC 59.263 47.619 0.00 0.00 44.73 5.34
2744 4084 1.064060 GTTGATGCAATCCTACACGCC 59.936 52.381 0.00 0.00 44.73 5.68
2745 4085 0.809636 TGATGCAATCCTACACGCCG 60.810 55.000 0.00 0.00 44.73 6.46
2746 4086 1.498865 GATGCAATCCTACACGCCGG 61.499 60.000 0.00 0.00 37.38 6.13
2747 4087 1.966901 ATGCAATCCTACACGCCGGA 61.967 55.000 5.05 0.00 0.00 5.14
2748 4088 1.883084 GCAATCCTACACGCCGGAG 60.883 63.158 5.05 3.72 31.82 4.63
2749 4089 1.515954 CAATCCTACACGCCGGAGT 59.484 57.895 5.05 4.71 31.82 3.85
2750 4090 0.108329 CAATCCTACACGCCGGAGTT 60.108 55.000 8.62 3.08 31.82 3.01
2751 4091 0.108329 AATCCTACACGCCGGAGTTG 60.108 55.000 8.62 7.17 31.82 3.16
2752 4092 1.255667 ATCCTACACGCCGGAGTTGT 61.256 55.000 8.62 12.91 31.82 3.32
2753 4093 0.608856 TCCTACACGCCGGAGTTGTA 60.609 55.000 8.62 13.35 0.00 2.41
2754 4094 0.179145 CCTACACGCCGGAGTTGTAG 60.179 60.000 26.02 26.02 34.06 2.74
2755 4095 0.179145 CTACACGCCGGAGTTGTAGG 60.179 60.000 25.63 13.16 31.55 3.18
2756 4096 2.216750 TACACGCCGGAGTTGTAGGC 62.217 60.000 8.62 0.00 46.88 3.93
2759 4099 3.766691 GCCGGAGTTGTAGGCGGA 61.767 66.667 5.05 0.00 41.53 5.54
2760 4100 2.183555 CCGGAGTTGTAGGCGGAC 59.816 66.667 0.00 0.00 0.00 4.79
2761 4101 2.642254 CCGGAGTTGTAGGCGGACA 61.642 63.158 0.00 0.00 0.00 4.02
2762 4102 1.445582 CGGAGTTGTAGGCGGACAC 60.446 63.158 0.00 0.00 0.00 3.67
2763 4103 1.445582 GGAGTTGTAGGCGGACACG 60.446 63.158 0.00 0.00 44.63 4.49
2764 4104 1.445582 GAGTTGTAGGCGGACACGG 60.446 63.158 0.00 0.00 41.36 4.94
2773 4113 4.351938 CGGACACGGCAAGGACGA 62.352 66.667 0.00 0.00 35.20 4.20
2774 4114 2.264794 GGACACGGCAAGGACGAT 59.735 61.111 0.00 0.00 35.20 3.73
2775 4115 2.100631 GGACACGGCAAGGACGATG 61.101 63.158 0.00 0.00 35.20 3.84
2776 4116 2.740714 GACACGGCAAGGACGATGC 61.741 63.158 0.00 0.00 43.08 3.91
2777 4117 2.434884 CACGGCAAGGACGATGCT 60.435 61.111 0.00 0.00 43.34 3.79
2779 4119 3.197790 CGGCAAGGACGATGCTGG 61.198 66.667 0.00 0.00 44.60 4.85
2780 4120 2.825836 GGCAAGGACGATGCTGGG 60.826 66.667 0.00 0.00 43.34 4.45
2781 4121 3.512516 GCAAGGACGATGCTGGGC 61.513 66.667 0.00 0.00 40.64 5.36
2782 4122 2.270205 CAAGGACGATGCTGGGCT 59.730 61.111 0.00 0.00 0.00 5.19
2783 4123 2.110967 CAAGGACGATGCTGGGCTG 61.111 63.158 0.00 0.00 0.00 4.85
2784 4124 3.984193 AAGGACGATGCTGGGCTGC 62.984 63.158 0.00 0.00 0.00 5.25
2785 4125 4.479993 GGACGATGCTGGGCTGCT 62.480 66.667 0.00 0.00 0.00 4.24
2786 4126 2.894387 GACGATGCTGGGCTGCTC 60.894 66.667 0.00 0.00 0.00 4.26
2787 4127 4.827087 ACGATGCTGGGCTGCTCG 62.827 66.667 0.00 2.14 38.52 5.03
2789 4129 4.166888 GATGCTGGGCTGCTCGGA 62.167 66.667 13.69 0.00 0.00 4.55
2790 4130 4.479993 ATGCTGGGCTGCTCGGAC 62.480 66.667 13.69 4.13 0.00 4.79
2793 4133 4.007644 CTGGGCTGCTCGGACACA 62.008 66.667 0.88 0.00 0.00 3.72
2794 4134 3.535629 CTGGGCTGCTCGGACACAA 62.536 63.158 0.88 0.00 0.00 3.33
2795 4135 3.050275 GGGCTGCTCGGACACAAC 61.050 66.667 0.00 0.00 0.00 3.32
2796 4136 3.414700 GGCTGCTCGGACACAACG 61.415 66.667 0.00 0.00 0.00 4.10
2797 4137 3.414700 GCTGCTCGGACACAACGG 61.415 66.667 0.00 0.00 0.00 4.44
2798 4138 3.414700 CTGCTCGGACACAACGGC 61.415 66.667 0.00 0.00 0.00 5.68
2801 4141 3.403057 CTCGGACACAACGGCGTG 61.403 66.667 15.70 10.75 42.81 5.34
2802 4142 3.834447 CTCGGACACAACGGCGTGA 62.834 63.158 15.70 3.17 39.34 4.35
2803 4143 2.962786 CGGACACAACGGCGTGAA 60.963 61.111 15.70 0.00 39.34 3.18
2804 4144 2.935955 GGACACAACGGCGTGAAG 59.064 61.111 15.70 9.75 39.34 3.02
2805 4145 1.593209 GGACACAACGGCGTGAAGA 60.593 57.895 15.70 0.00 39.34 2.87
2806 4146 1.563173 GACACAACGGCGTGAAGAC 59.437 57.895 15.70 2.79 39.34 3.01
2816 4156 3.639222 CGTGAAGACGTGTTCATGC 57.361 52.632 28.10 17.31 40.91 4.06
2817 4157 0.858583 CGTGAAGACGTGTTCATGCA 59.141 50.000 28.10 7.49 40.91 3.96
2818 4158 1.260297 CGTGAAGACGTGTTCATGCAA 59.740 47.619 28.10 6.52 40.91 4.08
2819 4159 2.096268 CGTGAAGACGTGTTCATGCAAT 60.096 45.455 28.10 0.00 40.91 3.56
2820 4160 3.482786 GTGAAGACGTGTTCATGCAATC 58.517 45.455 28.12 12.59 38.68 2.67
2821 4161 2.483877 TGAAGACGTGTTCATGCAATCC 59.516 45.455 22.84 0.00 31.31 3.01
2822 4162 2.479566 AGACGTGTTCATGCAATCCT 57.520 45.000 0.00 0.00 0.00 3.24
2823 4163 2.079158 AGACGTGTTCATGCAATCCTG 58.921 47.619 0.00 0.00 0.00 3.86
2833 4173 3.197790 CAATCCTGCACGCCGGAG 61.198 66.667 5.05 3.72 31.82 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 3.243068 GGCAAGTACAAAACCTGAGTGTG 60.243 47.826 0.00 0.00 0.00 3.82
125 127 8.757789 GTTTTTATACAAGGCAAGTACAAAACC 58.242 33.333 17.23 6.26 35.04 3.27
258 264 2.165030 CGAACACCTCCGTACTACCAAT 59.835 50.000 0.00 0.00 0.00 3.16
260 266 1.167851 CGAACACCTCCGTACTACCA 58.832 55.000 0.00 0.00 0.00 3.25
685 695 6.405065 GCATTGGCTCTAAATCATGTCTTTGA 60.405 38.462 0.00 0.00 36.96 2.69
699 709 1.625315 AGCGGATATGCATTGGCTCTA 59.375 47.619 3.54 0.00 41.91 2.43
700 710 0.399454 AGCGGATATGCATTGGCTCT 59.601 50.000 3.54 0.00 41.91 4.09
719 729 4.400109 GCTGACGACGGTGAGCGA 62.400 66.667 12.27 0.00 43.36 4.93
757 767 6.833041 TCAGAACAATTTTAGTACCACCTCA 58.167 36.000 0.00 0.00 0.00 3.86
758 768 7.117956 GTCTCAGAACAATTTTAGTACCACCTC 59.882 40.741 0.00 0.00 0.00 3.85
778 788 3.499918 AGCCGAATTCTTTTGTGTCTCAG 59.500 43.478 3.52 0.00 0.00 3.35
779 789 3.250762 CAGCCGAATTCTTTTGTGTCTCA 59.749 43.478 3.52 0.00 0.00 3.27
780 790 3.251004 ACAGCCGAATTCTTTTGTGTCTC 59.749 43.478 3.52 0.00 0.00 3.36
781 791 3.214328 ACAGCCGAATTCTTTTGTGTCT 58.786 40.909 3.52 0.00 0.00 3.41
782 792 3.626028 ACAGCCGAATTCTTTTGTGTC 57.374 42.857 3.52 0.00 0.00 3.67
783 793 4.336993 TGTAACAGCCGAATTCTTTTGTGT 59.663 37.500 3.52 0.00 0.00 3.72
786 796 4.378616 CGTTGTAACAGCCGAATTCTTTTG 59.621 41.667 3.52 1.56 0.00 2.44
798 808 2.474712 GGCGAGCGTTGTAACAGC 59.525 61.111 0.00 0.44 0.00 4.40
849 860 3.055021 GGGGTGAGAGGAGGTTTCTAAAG 60.055 52.174 0.00 0.00 0.00 1.85
887 898 0.322546 GCTCCTTGTTCGGGTGGAAT 60.323 55.000 0.00 0.00 36.92 3.01
898 909 1.070758 ACTCATGTCGTTGCTCCTTGT 59.929 47.619 0.00 0.00 0.00 3.16
928 939 3.067601 TCGGCCTTTTCCTTTTTCTGTTC 59.932 43.478 0.00 0.00 0.00 3.18
937 948 2.844348 TCCTATTCTCGGCCTTTTCCTT 59.156 45.455 0.00 0.00 0.00 3.36
938 949 2.436173 CTCCTATTCTCGGCCTTTTCCT 59.564 50.000 0.00 0.00 0.00 3.36
940 951 2.158885 AGCTCCTATTCTCGGCCTTTTC 60.159 50.000 0.00 0.00 0.00 2.29
947 1145 2.296073 ACCCTAGCTCCTATTCTCGG 57.704 55.000 0.00 0.00 0.00 4.63
952 1150 4.743955 GCGATTCAAACCCTAGCTCCTATT 60.744 45.833 0.00 0.00 0.00 1.73
953 1151 3.244249 GCGATTCAAACCCTAGCTCCTAT 60.244 47.826 0.00 0.00 0.00 2.57
954 1152 2.102588 GCGATTCAAACCCTAGCTCCTA 59.897 50.000 0.00 0.00 0.00 2.94
955 1153 1.134371 GCGATTCAAACCCTAGCTCCT 60.134 52.381 0.00 0.00 0.00 3.69
957 1155 1.300481 GGCGATTCAAACCCTAGCTC 58.700 55.000 0.00 0.00 0.00 4.09
959 1157 1.604278 GATGGCGATTCAAACCCTAGC 59.396 52.381 0.00 0.00 0.00 3.42
960 1158 3.134458 GAGATGGCGATTCAAACCCTAG 58.866 50.000 0.00 0.00 0.00 3.02
963 1161 1.025041 GGAGATGGCGATTCAAACCC 58.975 55.000 0.00 0.00 0.00 4.11
964 1162 1.025041 GGGAGATGGCGATTCAAACC 58.975 55.000 0.00 0.00 0.00 3.27
965 1163 1.672881 CAGGGAGATGGCGATTCAAAC 59.327 52.381 0.00 0.00 0.00 2.93
966 1164 1.408683 CCAGGGAGATGGCGATTCAAA 60.409 52.381 0.00 0.00 32.48 2.69
967 1165 0.181114 CCAGGGAGATGGCGATTCAA 59.819 55.000 0.00 0.00 32.48 2.69
968 1166 0.690744 TCCAGGGAGATGGCGATTCA 60.691 55.000 0.00 0.00 40.41 2.57
970 1168 0.982852 TGTCCAGGGAGATGGCGATT 60.983 55.000 0.00 0.00 40.41 3.34
971 1169 0.982852 TTGTCCAGGGAGATGGCGAT 60.983 55.000 0.00 0.00 40.41 4.58
972 1170 1.612146 TTGTCCAGGGAGATGGCGA 60.612 57.895 0.00 0.00 40.41 5.54
974 1172 1.225704 CCTTGTCCAGGGAGATGGC 59.774 63.158 4.73 0.00 40.41 4.40
982 1180 1.987807 ATCGCATCCCCTTGTCCAGG 61.988 60.000 0.00 0.00 43.49 4.45
983 1181 0.816825 CATCGCATCCCCTTGTCCAG 60.817 60.000 0.00 0.00 0.00 3.86
984 1182 1.224315 CATCGCATCCCCTTGTCCA 59.776 57.895 0.00 0.00 0.00 4.02
987 1185 2.597340 CCCATCGCATCCCCTTGT 59.403 61.111 0.00 0.00 0.00 3.16
988 1186 2.203394 CCCCATCGCATCCCCTTG 60.203 66.667 0.00 0.00 0.00 3.61
1373 1634 1.472026 GCTGCCGGTAGGTTCGATTTA 60.472 52.381 21.82 0.00 40.50 1.40
1406 1667 2.073101 GGATCTCTCCCCACACCCC 61.073 68.421 0.00 0.00 35.28 4.95
1431 1692 4.988716 ACCTCTGGTCCGCCGTCA 62.989 66.667 0.00 0.00 37.67 4.35
1442 1703 4.504916 CGCTGCCTCCGACCTCTG 62.505 72.222 0.00 0.00 0.00 3.35
1500 1761 4.994756 CCAACACCAGCCCACCCC 62.995 72.222 0.00 0.00 0.00 4.95
1511 1772 2.248431 GCTGTTCGTCGCCAACAC 59.752 61.111 0.00 0.00 30.49 3.32
1542 1803 4.828925 GCCTCTGCCTCACCGAGC 62.829 72.222 0.00 0.00 0.00 5.03
1600 1861 4.641645 TGGCGTGCTGAGGGGTTG 62.642 66.667 0.00 0.00 0.00 3.77
1606 1867 3.818787 GGGCATTGGCGTGCTGAG 61.819 66.667 13.29 0.00 44.45 3.35
1703 1964 0.807667 GATGACCGCTTGCTCGATGT 60.808 55.000 0.00 0.00 0.00 3.06
1737 1998 3.382803 ATGCTCCACGAGGCTCTGC 62.383 63.158 13.50 9.22 33.74 4.26
1770 2031 1.448985 TGGTAAGGCGTTTCAGATGC 58.551 50.000 0.00 0.00 39.65 3.91
1776 2037 1.398390 CTGCTCATGGTAAGGCGTTTC 59.602 52.381 0.00 0.00 0.00 2.78
1781 2042 1.661341 CAGTCTGCTCATGGTAAGGC 58.339 55.000 0.00 0.00 0.00 4.35
1794 2055 5.111989 TCTATGAAGAATTTCGGCAGTCTG 58.888 41.667 0.00 0.00 36.04 3.51
1816 2077 1.188219 TGTCAGTCAGTGGAGGCCTC 61.188 60.000 25.59 25.59 0.00 4.70
1845 2106 8.317679 AGTTTAGTGATGTAGAGCAGAGAAATT 58.682 33.333 0.00 0.00 0.00 1.82
1848 2109 6.434340 TCAGTTTAGTGATGTAGAGCAGAGAA 59.566 38.462 0.00 0.00 0.00 2.87
1859 2120 8.043113 TCTGCAGATATTTCAGTTTAGTGATGT 58.957 33.333 13.74 0.00 0.00 3.06
1864 2125 9.624373 AATCATCTGCAGATATTTCAGTTTAGT 57.376 29.630 28.27 0.00 32.63 2.24
1870 3196 6.711194 ACTGGAATCATCTGCAGATATTTCAG 59.289 38.462 33.52 33.52 37.28 3.02
1872 3198 7.658982 TGTACTGGAATCATCTGCAGATATTTC 59.341 37.037 28.27 27.63 32.63 2.17
1876 3202 6.098838 ACTTGTACTGGAATCATCTGCAGATA 59.901 38.462 28.27 16.75 32.63 1.98
1882 3208 8.954950 AATCTTACTTGTACTGGAATCATCTG 57.045 34.615 0.00 0.00 0.00 2.90
1883 3209 9.965902 AAAATCTTACTTGTACTGGAATCATCT 57.034 29.630 0.00 0.00 0.00 2.90
1955 3282 5.392057 GGCACAAAACATTAGACTTAGGAGC 60.392 44.000 0.00 0.00 0.00 4.70
2015 3342 1.674057 GTACCTGTGGCAGAGCAGT 59.326 57.895 6.05 2.46 32.44 4.40
2042 3369 4.413495 CCTTTTCGGCAAAGAATTACGA 57.587 40.909 1.57 0.00 44.40 3.43
2064 3391 8.065407 TGTTAGTGCTTAGTACAATTGTTTTCG 58.935 33.333 17.78 3.56 0.00 3.46
2139 3466 3.955650 TTAGTGCTGAACCTGGAGTAC 57.044 47.619 0.00 0.00 0.00 2.73
2170 3497 5.462405 TGTTTTCGGCAATACCACATTAAC 58.538 37.500 0.00 0.00 39.03 2.01
2174 3501 4.799564 ATTGTTTTCGGCAATACCACAT 57.200 36.364 0.00 0.00 39.03 3.21
2208 3535 6.818142 TGTGATATACTCAGGTGATTGTGTTG 59.182 38.462 0.00 0.00 33.51 3.33
2416 3750 4.756135 GGACACACCCATACGAAAAAGTTA 59.244 41.667 0.00 0.00 0.00 2.24
2425 3759 6.596497 ACTTAATAAAAGGACACACCCATACG 59.404 38.462 0.00 0.00 40.05 3.06
2462 3797 8.594687 GTCACAAATGCAAAACCAACATATATC 58.405 33.333 0.00 0.00 0.00 1.63
2464 3799 7.383572 GTGTCACAAATGCAAAACCAACATATA 59.616 33.333 0.00 0.00 0.00 0.86
2634 3974 4.375272 CATCAACATCTTCGCCTCACTAT 58.625 43.478 0.00 0.00 0.00 2.12
2635 3975 3.785486 CATCAACATCTTCGCCTCACTA 58.215 45.455 0.00 0.00 0.00 2.74
2636 3976 2.625737 CATCAACATCTTCGCCTCACT 58.374 47.619 0.00 0.00 0.00 3.41
2637 3977 1.063174 GCATCAACATCTTCGCCTCAC 59.937 52.381 0.00 0.00 0.00 3.51
2638 3978 1.338960 TGCATCAACATCTTCGCCTCA 60.339 47.619 0.00 0.00 0.00 3.86
2639 3979 1.329906 CTGCATCAACATCTTCGCCTC 59.670 52.381 0.00 0.00 0.00 4.70
2640 3980 1.339438 ACTGCATCAACATCTTCGCCT 60.339 47.619 0.00 0.00 0.00 5.52
2641 3981 1.089920 ACTGCATCAACATCTTCGCC 58.910 50.000 0.00 0.00 0.00 5.54
2642 3982 4.277258 CATTACTGCATCAACATCTTCGC 58.723 43.478 0.00 0.00 0.00 4.70
2657 3997 1.419922 GTGTCCGCGTGCATTACTG 59.580 57.895 4.92 0.00 0.00 2.74
2658 3998 2.092291 CGTGTCCGCGTGCATTACT 61.092 57.895 4.92 0.00 0.00 2.24
2659 3999 2.394136 CGTGTCCGCGTGCATTAC 59.606 61.111 4.92 0.00 0.00 1.89
2660 4000 2.811747 CCGTGTCCGCGTGCATTA 60.812 61.111 4.92 0.00 0.00 1.90
2669 4009 4.351938 TCGTCCTTGCCGTGTCCG 62.352 66.667 0.00 0.00 0.00 4.79
2670 4010 2.430382 TTCTCGTCCTTGCCGTGTCC 62.430 60.000 0.00 0.00 0.00 4.02
2671 4011 1.006571 TTCTCGTCCTTGCCGTGTC 60.007 57.895 0.00 0.00 0.00 3.67
2672 4012 1.006102 CTTCTCGTCCTTGCCGTGT 60.006 57.895 0.00 0.00 0.00 4.49
2673 4013 2.383527 GCTTCTCGTCCTTGCCGTG 61.384 63.158 0.00 0.00 0.00 4.94
2674 4014 2.048127 GCTTCTCGTCCTTGCCGT 60.048 61.111 0.00 0.00 0.00 5.68
2675 4015 3.181967 CGCTTCTCGTCCTTGCCG 61.182 66.667 0.00 0.00 0.00 5.69
2676 4016 2.815647 CCGCTTCTCGTCCTTGCC 60.816 66.667 0.00 0.00 36.19 4.52
2677 4017 2.815647 CCCGCTTCTCGTCCTTGC 60.816 66.667 0.00 0.00 36.19 4.01
2678 4018 2.125512 CCCCGCTTCTCGTCCTTG 60.126 66.667 0.00 0.00 36.19 3.61
2679 4019 4.083862 GCCCCGCTTCTCGTCCTT 62.084 66.667 0.00 0.00 36.19 3.36
2681 4021 4.821589 CAGCCCCGCTTCTCGTCC 62.822 72.222 0.00 0.00 36.40 4.79
2691 4031 4.641645 TGTGTCCAAGCAGCCCCG 62.642 66.667 0.00 0.00 0.00 5.73
2692 4032 2.985847 GTGTGTCCAAGCAGCCCC 60.986 66.667 0.00 0.00 0.00 5.80
2693 4033 2.985847 GGTGTGTCCAAGCAGCCC 60.986 66.667 0.00 0.00 35.97 5.19
2694 4034 3.357079 CGGTGTGTCCAAGCAGCC 61.357 66.667 0.00 0.00 35.57 4.85
2695 4035 3.357079 CCGGTGTGTCCAAGCAGC 61.357 66.667 0.00 0.00 35.57 5.25
2696 4036 3.357079 GCCGGTGTGTCCAAGCAG 61.357 66.667 1.90 0.00 35.81 4.24
2699 4039 3.345808 CACGCCGGTGTGTCCAAG 61.346 66.667 34.81 12.93 39.38 3.61
2700 4040 2.668185 ATTCACGCCGGTGTGTCCAA 62.668 55.000 39.09 29.11 44.68 3.53
2701 4041 1.817911 TATTCACGCCGGTGTGTCCA 61.818 55.000 39.09 27.15 44.68 4.02
2702 4042 1.079681 TATTCACGCCGGTGTGTCC 60.080 57.895 39.09 6.22 44.68 4.02
2703 4043 1.680105 CGTATTCACGCCGGTGTGTC 61.680 60.000 39.09 27.01 44.68 3.67
2704 4044 1.735198 CGTATTCACGCCGGTGTGT 60.735 57.895 39.09 27.26 44.68 3.72
2705 4045 3.077705 CGTATTCACGCCGGTGTG 58.922 61.111 36.83 36.83 44.68 3.82
2714 4054 4.094887 AGGATTGCATCAACACGTATTCAC 59.905 41.667 0.00 0.00 0.00 3.18
2715 4055 4.260985 AGGATTGCATCAACACGTATTCA 58.739 39.130 0.00 0.00 0.00 2.57
2716 4056 4.882671 AGGATTGCATCAACACGTATTC 57.117 40.909 0.00 0.00 0.00 1.75
2717 4057 5.064707 GTGTAGGATTGCATCAACACGTATT 59.935 40.000 13.12 0.00 37.69 1.89
2718 4058 4.570772 GTGTAGGATTGCATCAACACGTAT 59.429 41.667 13.12 0.00 37.69 3.06
2719 4059 3.930229 GTGTAGGATTGCATCAACACGTA 59.070 43.478 13.12 0.00 37.69 3.57
2720 4060 2.742053 GTGTAGGATTGCATCAACACGT 59.258 45.455 13.12 0.00 37.69 4.49
2721 4061 3.389687 GTGTAGGATTGCATCAACACG 57.610 47.619 13.12 0.00 37.69 4.49
2722 4062 2.476185 GCGTGTAGGATTGCATCAACAC 60.476 50.000 15.78 15.78 40.96 3.32
2723 4063 1.737236 GCGTGTAGGATTGCATCAACA 59.263 47.619 0.00 0.00 0.00 3.33
2724 4064 1.064060 GGCGTGTAGGATTGCATCAAC 59.936 52.381 0.00 0.00 0.00 3.18
2725 4065 1.378531 GGCGTGTAGGATTGCATCAA 58.621 50.000 0.00 0.00 0.00 2.57
2726 4066 0.809636 CGGCGTGTAGGATTGCATCA 60.810 55.000 0.00 0.00 0.00 3.07
2727 4067 1.498865 CCGGCGTGTAGGATTGCATC 61.499 60.000 6.01 0.00 0.00 3.91
2728 4068 1.523711 CCGGCGTGTAGGATTGCAT 60.524 57.895 6.01 0.00 0.00 3.96
2729 4069 2.125310 CCGGCGTGTAGGATTGCA 60.125 61.111 6.01 0.00 0.00 4.08
2730 4070 1.883084 CTCCGGCGTGTAGGATTGC 60.883 63.158 6.01 0.00 35.75 3.56
2731 4071 0.108329 AACTCCGGCGTGTAGGATTG 60.108 55.000 6.01 0.00 35.75 2.67
2732 4072 0.108329 CAACTCCGGCGTGTAGGATT 60.108 55.000 6.01 0.00 35.75 3.01
2733 4073 1.255667 ACAACTCCGGCGTGTAGGAT 61.256 55.000 6.01 0.00 35.75 3.24
2734 4074 0.608856 TACAACTCCGGCGTGTAGGA 60.609 55.000 6.01 0.00 34.93 2.94
2735 4075 0.179145 CTACAACTCCGGCGTGTAGG 60.179 60.000 21.09 11.68 31.55 3.18
2736 4076 0.179145 CCTACAACTCCGGCGTGTAG 60.179 60.000 21.61 21.61 34.06 2.74
2737 4077 1.885157 CCTACAACTCCGGCGTGTA 59.115 57.895 6.01 7.03 0.00 2.90
2738 4078 2.654877 CCTACAACTCCGGCGTGT 59.345 61.111 6.01 6.09 0.00 4.49
2739 4079 2.813908 GCCTACAACTCCGGCGTG 60.814 66.667 6.01 0.00 33.64 5.34
2742 4082 3.766691 TCCGCCTACAACTCCGGC 61.767 66.667 0.00 0.00 40.49 6.13
2743 4083 2.183555 GTCCGCCTACAACTCCGG 59.816 66.667 0.00 0.00 41.97 5.14
2744 4084 1.445582 GTGTCCGCCTACAACTCCG 60.446 63.158 0.00 0.00 0.00 4.63
2745 4085 1.445582 CGTGTCCGCCTACAACTCC 60.446 63.158 0.00 0.00 0.00 3.85
2746 4086 1.445582 CCGTGTCCGCCTACAACTC 60.446 63.158 0.00 0.00 0.00 3.01
2747 4087 2.654877 CCGTGTCCGCCTACAACT 59.345 61.111 0.00 0.00 0.00 3.16
2748 4088 3.116531 GCCGTGTCCGCCTACAAC 61.117 66.667 0.00 0.00 0.00 3.32
2749 4089 3.166490 TTGCCGTGTCCGCCTACAA 62.166 57.895 0.00 0.00 0.00 2.41
2750 4090 3.583276 CTTGCCGTGTCCGCCTACA 62.583 63.158 0.00 0.00 0.00 2.74
2751 4091 2.813908 CTTGCCGTGTCCGCCTAC 60.814 66.667 0.00 0.00 0.00 3.18
2752 4092 4.077184 CCTTGCCGTGTCCGCCTA 62.077 66.667 0.00 0.00 0.00 3.93
2756 4096 3.642778 ATCGTCCTTGCCGTGTCCG 62.643 63.158 0.00 0.00 0.00 4.79
2757 4097 2.100631 CATCGTCCTTGCCGTGTCC 61.101 63.158 0.00 0.00 0.00 4.02
2758 4098 2.740714 GCATCGTCCTTGCCGTGTC 61.741 63.158 0.00 0.00 33.95 3.67
2759 4099 2.742372 GCATCGTCCTTGCCGTGT 60.742 61.111 0.00 0.00 33.95 4.49
2760 4100 2.434884 AGCATCGTCCTTGCCGTG 60.435 61.111 0.00 0.00 41.06 4.94
2761 4101 2.434884 CAGCATCGTCCTTGCCGT 60.435 61.111 0.00 0.00 41.06 5.68
2762 4102 3.197790 CCAGCATCGTCCTTGCCG 61.198 66.667 0.00 0.00 41.06 5.69
2763 4103 2.825836 CCCAGCATCGTCCTTGCC 60.826 66.667 0.00 0.00 41.06 4.52
2764 4104 3.512516 GCCCAGCATCGTCCTTGC 61.513 66.667 0.00 0.00 40.45 4.01
2765 4105 2.110967 CAGCCCAGCATCGTCCTTG 61.111 63.158 0.00 0.00 0.00 3.61
2766 4106 2.270205 CAGCCCAGCATCGTCCTT 59.730 61.111 0.00 0.00 0.00 3.36
2767 4107 4.479993 GCAGCCCAGCATCGTCCT 62.480 66.667 0.00 0.00 0.00 3.85
2768 4108 4.479993 AGCAGCCCAGCATCGTCC 62.480 66.667 0.00 0.00 36.85 4.79
2769 4109 2.894387 GAGCAGCCCAGCATCGTC 60.894 66.667 0.00 0.00 36.85 4.20
2770 4110 4.827087 CGAGCAGCCCAGCATCGT 62.827 66.667 0.00 0.00 36.85 3.73
2772 4112 4.166888 TCCGAGCAGCCCAGCATC 62.167 66.667 0.00 0.00 36.85 3.91
2773 4113 4.479993 GTCCGAGCAGCCCAGCAT 62.480 66.667 0.00 0.00 36.85 3.79
2776 4116 3.535629 TTGTGTCCGAGCAGCCCAG 62.536 63.158 0.00 0.00 0.00 4.45
2777 4117 3.555324 TTGTGTCCGAGCAGCCCA 61.555 61.111 0.00 0.00 0.00 5.36
2778 4118 3.050275 GTTGTGTCCGAGCAGCCC 61.050 66.667 0.00 0.00 0.00 5.19
2779 4119 3.414700 CGTTGTGTCCGAGCAGCC 61.415 66.667 0.00 0.00 0.00 4.85
2780 4120 3.414700 CCGTTGTGTCCGAGCAGC 61.415 66.667 0.00 0.00 0.00 5.25
2781 4121 3.414700 GCCGTTGTGTCCGAGCAG 61.415 66.667 0.00 0.00 0.00 4.24
2784 4124 3.403057 CACGCCGTTGTGTCCGAG 61.403 66.667 0.00 0.00 35.12 4.63
2785 4125 3.427598 TTCACGCCGTTGTGTCCGA 62.428 57.895 0.00 0.00 40.74 4.55
2786 4126 2.938823 CTTCACGCCGTTGTGTCCG 61.939 63.158 0.00 0.00 40.74 4.79
2787 4127 1.593209 TCTTCACGCCGTTGTGTCC 60.593 57.895 0.00 0.00 40.74 4.02
2788 4128 1.563173 GTCTTCACGCCGTTGTGTC 59.437 57.895 0.00 0.00 40.74 3.67
2789 4129 2.235016 CGTCTTCACGCCGTTGTGT 61.235 57.895 0.00 0.00 39.69 3.72
2790 4130 2.544359 CGTCTTCACGCCGTTGTG 59.456 61.111 0.00 0.00 39.69 3.33
2799 4139 3.482786 GATTGCATGAACACGTCTTCAC 58.517 45.455 8.49 0.00 32.95 3.18
2800 4140 2.483877 GGATTGCATGAACACGTCTTCA 59.516 45.455 8.74 8.74 34.65 3.02
2801 4141 2.744202 AGGATTGCATGAACACGTCTTC 59.256 45.455 0.00 0.00 0.00 2.87
2802 4142 2.485426 CAGGATTGCATGAACACGTCTT 59.515 45.455 0.00 0.00 0.00 3.01
2803 4143 2.079158 CAGGATTGCATGAACACGTCT 58.921 47.619 0.00 0.00 0.00 4.18
2804 4144 2.532531 CAGGATTGCATGAACACGTC 57.467 50.000 0.00 0.00 0.00 4.34
2816 4156 3.197790 CTCCGGCGTGCAGGATTG 61.198 66.667 14.05 0.25 39.43 2.67


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

AutoCloner maintained by Alex Coulton.