Multiple sequence alignment - TraesCS3A01G537800

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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 TraesCS3A01G537800 chr3A 100.000 5427 0 0 1 5427 749289021 749283595 0.000000e+00 10022.0
1 TraesCS3A01G537800 chr3A 96.392 970 29 5 1 964 660860880 660861849 0.000000e+00 1592.0
2 TraesCS3A01G537800 chr3A 96.711 912 27 3 1867 2777 101100255 101101164 0.000000e+00 1515.0
3 TraesCS3A01G537800 chr3A 74.242 594 121 19 3429 4017 749493092 749493658 2.540000e-53 220.0
4 TraesCS3A01G537800 chr3B 94.818 1563 66 7 2778 4336 822836675 822835124 0.000000e+00 2423.0
5 TraesCS3A01G537800 chr3B 88.072 830 68 14 4366 5173 822835123 822834303 0.000000e+00 955.0
6 TraesCS3A01G537800 chr3B 87.801 705 36 14 1198 1873 822837344 822836661 0.000000e+00 780.0
7 TraesCS3A01G537800 chr3B 96.104 77 3 0 1058 1134 822837499 822837423 5.710000e-25 126.0
8 TraesCS3A01G537800 chr3B 100.000 29 0 0 5079 5107 693600350 693600322 3.000000e-03 54.7
9 TraesCS3A01G537800 chr3D 94.061 1566 63 8 2778 4340 613632737 613631199 0.000000e+00 2350.0
10 TraesCS3A01G537800 chr3D 95.459 969 36 8 1 963 214959633 214958667 0.000000e+00 1539.0
11 TraesCS3A01G537800 chr3D 88.389 844 49 18 1058 1873 613633545 613632723 0.000000e+00 970.0
12 TraesCS3A01G537800 chr3D 87.004 454 38 7 4486 4932 613625965 613625526 4.880000e-135 492.0
13 TraesCS3A01G537800 chr3D 82.879 514 38 12 4936 5427 613625339 613624854 3.020000e-112 416.0
14 TraesCS3A01G537800 chr3D 75.620 726 157 13 3413 4131 513621318 513620606 5.210000e-90 342.0
15 TraesCS3A01G537800 chr3D 91.045 134 12 0 1323 1456 513623631 513623498 1.200000e-41 182.0
16 TraesCS3A01G537800 chr3D 88.889 144 16 0 1323 1466 513391138 513390995 1.550000e-40 178.0
17 TraesCS3A01G537800 chr3D 91.667 108 8 1 4388 4494 613627736 613627629 1.220000e-31 148.0
18 TraesCS3A01G537800 chr7D 96.000 975 32 7 1 969 114468242 114467269 0.000000e+00 1578.0
19 TraesCS3A01G537800 chr7D 95.643 964 39 3 1 961 151541038 151540075 0.000000e+00 1544.0
20 TraesCS3A01G537800 chr6A 96.074 968 33 5 1 963 26630943 26629976 0.000000e+00 1572.0
21 TraesCS3A01G537800 chr6A 95.267 972 40 6 1 967 460630068 460629098 0.000000e+00 1535.0
22 TraesCS3A01G537800 chr6A 93.202 912 35 12 1868 2777 10939051 10938165 0.000000e+00 1315.0
23 TraesCS3A01G537800 chr6B 97.162 916 21 4 1865 2778 51567743 51568655 0.000000e+00 1543.0
24 TraesCS3A01G537800 chr6B 79.032 186 29 8 1868 2046 710679619 710679437 9.550000e-23 119.0
25 TraesCS3A01G537800 chr2D 95.199 979 40 6 1 974 70391849 70390873 0.000000e+00 1541.0
26 TraesCS3A01G537800 chr2A 95.366 971 40 5 1 967 419483168 419484137 0.000000e+00 1539.0
27 TraesCS3A01G537800 chr7A 96.940 915 27 1 1866 2779 150181997 150182911 0.000000e+00 1533.0
28 TraesCS3A01G537800 chr7A 100.000 40 0 0 5298 5337 487261583 487261544 2.100000e-09 75.0
29 TraesCS3A01G537800 chr1D 95.253 969 37 8 1 963 84728937 84729902 0.000000e+00 1526.0
30 TraesCS3A01G537800 chr4A 96.393 915 32 1 1864 2777 607872067 607872981 0.000000e+00 1506.0
31 TraesCS3A01G537800 chr4A 96.053 912 31 4 1868 2777 647531786 647532694 0.000000e+00 1480.0
32 TraesCS3A01G537800 chr5A 84.664 952 90 26 1866 2775 706600554 706601491 0.000000e+00 898.0
33 TraesCS3A01G537800 chr6D 90.164 244 17 4 2020 2261 459043462 459043700 1.470000e-80 311.0
34 TraesCS3A01G537800 chr4D 76.617 201 35 10 1870 2062 31713937 31714133 3.460000e-17 100.0


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 TraesCS3A01G537800 chr3A 749283595 749289021 5426 True 10022.0 10022 100.00000 1 5427 1 chr3A.!!$R1 5426
1 TraesCS3A01G537800 chr3A 660860880 660861849 969 False 1592.0 1592 96.39200 1 964 1 chr3A.!!$F2 963
2 TraesCS3A01G537800 chr3A 101100255 101101164 909 False 1515.0 1515 96.71100 1867 2777 1 chr3A.!!$F1 910
3 TraesCS3A01G537800 chr3A 749493092 749493658 566 False 220.0 220 74.24200 3429 4017 1 chr3A.!!$F3 588
4 TraesCS3A01G537800 chr3B 822834303 822837499 3196 True 1071.0 2423 91.69875 1058 5173 4 chr3B.!!$R2 4115
5 TraesCS3A01G537800 chr3D 214958667 214959633 966 True 1539.0 1539 95.45900 1 963 1 chr3D.!!$R1 962
6 TraesCS3A01G537800 chr3D 613624854 613633545 8691 True 875.2 2350 88.80000 1058 5427 5 chr3D.!!$R4 4369
7 TraesCS3A01G537800 chr3D 513620606 513623631 3025 True 262.0 342 83.33250 1323 4131 2 chr3D.!!$R3 2808
8 TraesCS3A01G537800 chr7D 114467269 114468242 973 True 1578.0 1578 96.00000 1 969 1 chr7D.!!$R1 968
9 TraesCS3A01G537800 chr7D 151540075 151541038 963 True 1544.0 1544 95.64300 1 961 1 chr7D.!!$R2 960
10 TraesCS3A01G537800 chr6A 26629976 26630943 967 True 1572.0 1572 96.07400 1 963 1 chr6A.!!$R2 962
11 TraesCS3A01G537800 chr6A 460629098 460630068 970 True 1535.0 1535 95.26700 1 967 1 chr6A.!!$R3 966
12 TraesCS3A01G537800 chr6A 10938165 10939051 886 True 1315.0 1315 93.20200 1868 2777 1 chr6A.!!$R1 909
13 TraesCS3A01G537800 chr6B 51567743 51568655 912 False 1543.0 1543 97.16200 1865 2778 1 chr6B.!!$F1 913
14 TraesCS3A01G537800 chr2D 70390873 70391849 976 True 1541.0 1541 95.19900 1 974 1 chr2D.!!$R1 973
15 TraesCS3A01G537800 chr2A 419483168 419484137 969 False 1539.0 1539 95.36600 1 967 1 chr2A.!!$F1 966
16 TraesCS3A01G537800 chr7A 150181997 150182911 914 False 1533.0 1533 96.94000 1866 2779 1 chr7A.!!$F1 913
17 TraesCS3A01G537800 chr1D 84728937 84729902 965 False 1526.0 1526 95.25300 1 963 1 chr1D.!!$F1 962
18 TraesCS3A01G537800 chr4A 607872067 607872981 914 False 1506.0 1506 96.39300 1864 2777 1 chr4A.!!$F1 913
19 TraesCS3A01G537800 chr4A 647531786 647532694 908 False 1480.0 1480 96.05300 1868 2777 1 chr4A.!!$F2 909
20 TraesCS3A01G537800 chr5A 706600554 706601491 937 False 898.0 898 84.66400 1866 2775 1 chr5A.!!$F1 909

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
660 672 0.597118 GCAAAACGCATGGCAACTGA 60.597 50.0 0.00 0.00 41.79 3.41 F
1009 1022 0.105039 GTTCTGATGTAGAGGCCGGG 59.895 60.0 2.18 0.00 36.61 5.73 F
1858 2127 0.105709 TATCCTCGACATCAGGGGCA 60.106 55.0 0.00 0.00 0.00 5.36 F
2042 2423 0.397254 ATAGTGGCCGGCAGTAGACT 60.397 55.0 30.85 21.54 0.00 3.24 F
3120 3547 0.391263 CTAGCTTCCAACGTGGTCCC 60.391 60.0 0.00 0.00 39.03 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2443 0.321034 GAGATGCTGGCACTGTGTGA 60.321 55.0 9.86 0.0 35.23 3.58 R
2781 3208 0.109039 TCATGATTGGCGTCGTCGAA 60.109 50.0 6.17 0.0 39.71 3.71 R
2782 3209 0.800683 GTCATGATTGGCGTCGTCGA 60.801 55.0 6.17 0.0 39.71 4.20 R
3860 5128 0.535102 CCACCAACAAGGAAGAGCGT 60.535 55.0 0.00 0.0 41.22 5.07 R
4759 11126 0.987294 CCTCTTCCCCTTCTCTTGCA 59.013 55.0 0.00 0.0 0.00 4.08 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
484 491 1.293498 CTCACAAGCACGCTAGGGT 59.707 57.895 6.62 6.62 0.00 4.34
569 577 4.490899 ACCATGCAAAACATATGGCAAT 57.509 36.364 7.80 0.00 44.06 3.56
660 672 0.597118 GCAAAACGCATGGCAACTGA 60.597 50.000 0.00 0.00 41.79 3.41
663 675 0.743688 AAACGCATGGCAACTGACAA 59.256 45.000 0.00 0.00 36.16 3.18
808 821 2.873472 GTGTGGTAAAACGGATGTGTGA 59.127 45.455 0.00 0.00 0.00 3.58
810 823 3.135994 GTGGTAAAACGGATGTGTGAGT 58.864 45.455 0.00 0.00 0.00 3.41
856 869 2.416296 CGAGTTGTCCTACGTGGCATAA 60.416 50.000 0.00 0.00 35.26 1.90
896 909 3.375299 GCCAAGATTCGTGCAGAAGTTAT 59.625 43.478 0.00 0.00 42.92 1.89
904 917 2.223340 CGTGCAGAAGTTATTGGATGGC 60.223 50.000 0.00 0.00 0.00 4.40
967 980 5.048921 TGTGGGCGTTAACATTTTCGATTTA 60.049 36.000 6.39 0.00 0.00 1.40
969 982 6.528774 GTGGGCGTTAACATTTTCGATTTAAT 59.471 34.615 6.39 0.00 0.00 1.40
970 983 7.697291 GTGGGCGTTAACATTTTCGATTTAATA 59.303 33.333 6.39 0.00 0.00 0.98
971 984 8.242053 TGGGCGTTAACATTTTCGATTTAATAA 58.758 29.630 6.39 0.00 0.00 1.40
972 985 9.074443 GGGCGTTAACATTTTCGATTTAATAAA 57.926 29.630 6.39 0.00 0.00 1.40
979 992 8.460831 ACATTTTCGATTTAATAAAGTGTGGC 57.539 30.769 2.13 0.00 33.49 5.01
980 993 7.544217 ACATTTTCGATTTAATAAAGTGTGGCC 59.456 33.333 0.00 0.00 33.49 5.36
981 994 4.868450 TCGATTTAATAAAGTGTGGCCG 57.132 40.909 0.00 0.00 0.00 6.13
982 995 4.255301 TCGATTTAATAAAGTGTGGCCGT 58.745 39.130 0.00 0.00 0.00 5.68
983 996 5.417811 TCGATTTAATAAAGTGTGGCCGTA 58.582 37.500 0.00 0.00 0.00 4.02
984 997 6.050432 TCGATTTAATAAAGTGTGGCCGTAT 58.950 36.000 0.00 0.00 0.00 3.06
985 998 6.018588 TCGATTTAATAAAGTGTGGCCGTATG 60.019 38.462 0.00 0.00 0.00 2.39
986 999 6.238266 CGATTTAATAAAGTGTGGCCGTATGT 60.238 38.462 0.00 0.00 0.00 2.29
987 1000 7.042590 CGATTTAATAAAGTGTGGCCGTATGTA 60.043 37.037 0.00 0.00 0.00 2.29
988 1001 8.685838 ATTTAATAAAGTGTGGCCGTATGTAT 57.314 30.769 0.00 0.00 0.00 2.29
989 1002 7.718272 TTAATAAAGTGTGGCCGTATGTATC 57.282 36.000 0.00 0.00 0.00 2.24
990 1003 2.218953 AAGTGTGGCCGTATGTATCG 57.781 50.000 0.00 0.00 0.00 2.92
991 1004 1.108776 AGTGTGGCCGTATGTATCGT 58.891 50.000 0.00 0.00 0.00 3.73
992 1005 1.479323 AGTGTGGCCGTATGTATCGTT 59.521 47.619 0.00 0.00 0.00 3.85
993 1006 1.856597 GTGTGGCCGTATGTATCGTTC 59.143 52.381 0.00 0.00 0.00 3.95
994 1007 1.752498 TGTGGCCGTATGTATCGTTCT 59.248 47.619 0.00 0.00 0.00 3.01
995 1008 2.124903 GTGGCCGTATGTATCGTTCTG 58.875 52.381 0.00 0.00 0.00 3.02
996 1009 2.025898 TGGCCGTATGTATCGTTCTGA 58.974 47.619 0.00 0.00 0.00 3.27
997 1010 2.626266 TGGCCGTATGTATCGTTCTGAT 59.374 45.455 0.00 0.00 41.30 2.90
998 1011 2.987149 GGCCGTATGTATCGTTCTGATG 59.013 50.000 0.00 0.00 37.99 3.07
999 1012 3.552273 GGCCGTATGTATCGTTCTGATGT 60.552 47.826 0.00 0.00 37.99 3.06
1000 1013 4.320714 GGCCGTATGTATCGTTCTGATGTA 60.321 45.833 0.00 0.00 37.99 2.29
1001 1014 4.852104 GCCGTATGTATCGTTCTGATGTAG 59.148 45.833 0.00 0.00 37.99 2.74
1002 1015 5.334646 GCCGTATGTATCGTTCTGATGTAGA 60.335 44.000 0.00 0.00 37.99 2.59
1003 1016 6.307915 CCGTATGTATCGTTCTGATGTAGAG 58.692 44.000 0.00 0.00 37.99 2.43
1004 1017 6.307915 CGTATGTATCGTTCTGATGTAGAGG 58.692 44.000 0.00 0.00 37.99 3.69
1005 1018 4.569761 TGTATCGTTCTGATGTAGAGGC 57.430 45.455 0.00 0.00 37.99 4.70
1006 1019 3.318275 TGTATCGTTCTGATGTAGAGGCC 59.682 47.826 0.00 0.00 37.99 5.19
1007 1020 0.738975 TCGTTCTGATGTAGAGGCCG 59.261 55.000 0.00 0.00 36.61 6.13
1008 1021 0.249073 CGTTCTGATGTAGAGGCCGG 60.249 60.000 0.00 0.00 36.61 6.13
1009 1022 0.105039 GTTCTGATGTAGAGGCCGGG 59.895 60.000 2.18 0.00 36.61 5.73
1010 1023 1.048724 TTCTGATGTAGAGGCCGGGG 61.049 60.000 2.18 0.00 36.61 5.73
1011 1024 1.762460 CTGATGTAGAGGCCGGGGT 60.762 63.158 2.18 0.00 0.00 4.95
1012 1025 2.032860 CTGATGTAGAGGCCGGGGTG 62.033 65.000 2.18 0.00 0.00 4.61
1013 1026 2.040606 ATGTAGAGGCCGGGGTGT 59.959 61.111 2.18 0.00 0.00 4.16
1014 1027 2.029307 GATGTAGAGGCCGGGGTGTC 62.029 65.000 2.18 0.00 0.00 3.67
1015 1028 3.468140 GTAGAGGCCGGGGTGTCC 61.468 72.222 2.18 0.00 0.00 4.02
1030 1043 4.746535 GGTGTCCCCTTTTTGAAAGAAA 57.253 40.909 2.15 0.00 0.00 2.52
1031 1044 5.092554 GGTGTCCCCTTTTTGAAAGAAAA 57.907 39.130 2.15 0.00 0.00 2.29
1032 1045 5.492895 GGTGTCCCCTTTTTGAAAGAAAAA 58.507 37.500 2.15 0.00 0.00 1.94
1089 1102 4.679662 AGGTCGTACTGTAATTGGATTCG 58.320 43.478 0.00 0.00 0.00 3.34
1134 1147 5.989477 TCCGAGATGGAATTGAATTGTAGT 58.011 37.500 0.00 0.00 46.38 2.73
1135 1148 6.414732 TCCGAGATGGAATTGAATTGTAGTT 58.585 36.000 0.00 0.00 46.38 2.24
1136 1149 6.316140 TCCGAGATGGAATTGAATTGTAGTTG 59.684 38.462 0.00 0.00 46.38 3.16
1137 1150 6.094048 CCGAGATGGAATTGAATTGTAGTTGT 59.906 38.462 0.00 0.00 42.00 3.32
1138 1151 7.279981 CCGAGATGGAATTGAATTGTAGTTGTA 59.720 37.037 0.00 0.00 42.00 2.41
1139 1152 8.331022 CGAGATGGAATTGAATTGTAGTTGTAG 58.669 37.037 0.00 0.00 0.00 2.74
1147 1160 5.790593 TGAATTGTAGTTGTAGGAGTCCAC 58.209 41.667 12.86 8.29 0.00 4.02
1156 1169 0.622136 TAGGAGTCCACGTCCAGCTA 59.378 55.000 12.86 0.00 36.43 3.32
1157 1170 0.681564 AGGAGTCCACGTCCAGCTAG 60.682 60.000 12.86 0.00 36.43 3.42
1158 1171 1.668101 GGAGTCCACGTCCAGCTAGG 61.668 65.000 3.60 0.00 39.47 3.02
1161 1174 0.455005 GTCCACGTCCAGCTAGGTAC 59.545 60.000 0.00 0.00 39.02 3.34
1163 1176 0.739561 CCACGTCCAGCTAGGTACTC 59.260 60.000 0.00 0.00 41.75 2.59
1164 1177 1.682394 CCACGTCCAGCTAGGTACTCT 60.682 57.143 0.00 0.00 41.75 3.24
1166 1179 3.478509 CACGTCCAGCTAGGTACTCTAT 58.521 50.000 0.00 0.00 41.75 1.98
1167 1180 3.251245 CACGTCCAGCTAGGTACTCTATG 59.749 52.174 0.00 0.00 41.75 2.23
1169 1182 3.223435 GTCCAGCTAGGTACTCTATGCA 58.777 50.000 0.00 0.00 41.75 3.96
1170 1183 3.637229 GTCCAGCTAGGTACTCTATGCAA 59.363 47.826 0.00 0.00 41.75 4.08
1172 1185 4.524714 TCCAGCTAGGTACTCTATGCAATC 59.475 45.833 0.00 0.00 41.75 2.67
1173 1186 4.526262 CCAGCTAGGTACTCTATGCAATCT 59.474 45.833 0.00 0.00 41.75 2.40
1174 1187 5.712446 CCAGCTAGGTACTCTATGCAATCTA 59.288 44.000 0.00 0.00 41.75 1.98
1175 1188 6.379703 CCAGCTAGGTACTCTATGCAATCTAT 59.620 42.308 0.00 0.00 41.75 1.98
1176 1189 7.093552 CCAGCTAGGTACTCTATGCAATCTATT 60.094 40.741 0.00 0.00 41.75 1.73
1177 1190 7.758980 CAGCTAGGTACTCTATGCAATCTATTG 59.241 40.741 0.00 0.00 41.75 1.90
1179 1192 8.740906 GCTAGGTACTCTATGCAATCTATTGTA 58.259 37.037 0.00 0.45 41.75 2.41
1182 1195 9.148879 AGGTACTCTATGCAATCTATTGTACTT 57.851 33.333 0.00 0.00 39.88 2.24
1261 1312 0.516120 GAAGAGACGACGACGACGAC 60.516 60.000 25.15 18.88 42.66 4.34
1399 1472 1.549170 GACGAGACCAAGTACACCCAT 59.451 52.381 0.00 0.00 0.00 4.00
1517 1590 3.615509 GATTGGGACGCGGGGTTCA 62.616 63.158 12.47 2.38 0.00 3.18
1723 1990 8.906636 CTTTGAAGCATATATATTGATGGTGC 57.093 34.615 1.83 1.07 34.17 5.01
1858 2127 0.105709 TATCCTCGACATCAGGGGCA 60.106 55.000 0.00 0.00 0.00 5.36
1877 2146 2.389866 ATCTTCGACGGACGCGGATC 62.390 60.000 12.47 0.00 42.26 3.36
1920 2292 1.227943 TGCTATCTTGGCCATCCGC 60.228 57.895 6.09 6.15 34.14 5.54
2042 2423 0.397254 ATAGTGGCCGGCAGTAGACT 60.397 55.000 30.85 21.54 0.00 3.24
2047 2428 0.464452 GGCCGGCAGTAGACTTGTAT 59.536 55.000 30.85 0.00 0.00 2.29
2062 2443 9.361315 GTAGACTTGTATGGTTTTGTTGTTTTT 57.639 29.630 0.00 0.00 0.00 1.94
2158 2550 3.086282 TGTCACATGCATGCTCAATCTT 58.914 40.909 26.53 1.08 0.00 2.40
2648 3075 5.425217 TGATCACAGTGGACAACCTGTATAT 59.575 40.000 0.00 0.00 37.04 0.86
2779 3206 5.304686 TGCCTTCTCAAATATTATCCCGT 57.695 39.130 0.00 0.00 0.00 5.28
2780 3207 5.305585 TGCCTTCTCAAATATTATCCCGTC 58.694 41.667 0.00 0.00 0.00 4.79
2781 3208 5.071788 TGCCTTCTCAAATATTATCCCGTCT 59.928 40.000 0.00 0.00 0.00 4.18
2782 3209 5.998363 GCCTTCTCAAATATTATCCCGTCTT 59.002 40.000 0.00 0.00 0.00 3.01
2783 3210 6.147985 GCCTTCTCAAATATTATCCCGTCTTC 59.852 42.308 0.00 0.00 0.00 2.87
2904 3331 5.386958 TGCTTTCAAGTGTAGTCGATACT 57.613 39.130 0.00 0.00 39.91 2.12
2955 3382 3.079960 TCGACAAAGAGTGTGAGTGTC 57.920 47.619 0.00 0.00 41.96 3.67
2957 3384 3.079960 GACAAAGAGTGTGAGTGTCGA 57.920 47.619 0.00 0.00 41.96 4.20
2958 3385 3.643763 GACAAAGAGTGTGAGTGTCGAT 58.356 45.455 0.00 0.00 41.96 3.59
2959 3386 4.795268 GACAAAGAGTGTGAGTGTCGATA 58.205 43.478 0.00 0.00 41.96 2.92
2960 3387 4.547532 ACAAAGAGTGTGAGTGTCGATAC 58.452 43.478 3.80 3.80 39.72 2.24
2961 3388 3.851976 AAGAGTGTGAGTGTCGATACC 57.148 47.619 8.86 1.51 0.00 2.73
3037 3464 7.953710 CACTGCACGACACAATATCAATATATG 59.046 37.037 0.00 0.00 0.00 1.78
3072 3499 7.604164 TGTGTTACATGTTGGTTTTGATTTGTT 59.396 29.630 2.30 0.00 0.00 2.83
3085 3512 9.213799 GGTTTTGATTTGTTATCATGGCTTTTA 57.786 29.630 0.00 0.00 0.00 1.52
3120 3547 0.391263 CTAGCTTCCAACGTGGTCCC 60.391 60.000 0.00 0.00 39.03 4.46
3156 3586 0.530744 CTTCACCCGAGTCGATCCAA 59.469 55.000 15.64 0.53 0.00 3.53
3190 3620 2.254546 TGTCATTTCTGTCAAGGCGT 57.745 45.000 0.00 0.00 0.00 5.68
3385 3816 5.659440 ATATCATTCCACCGTTTTTGCTT 57.341 34.783 0.00 0.00 0.00 3.91
3757 5025 2.373836 TCCCGGAAACTTCAAGGATCAA 59.626 45.455 0.73 0.00 0.00 2.57
3765 5033 5.629079 AACTTCAAGGATCAAATCGTTCC 57.371 39.130 0.00 0.00 35.40 3.62
3768 5036 5.124457 ACTTCAAGGATCAAATCGTTCCATG 59.876 40.000 0.00 0.00 36.12 3.66
3808 5076 1.065928 GGTAGTCGGCGATGGTGAG 59.934 63.158 14.79 0.00 0.00 3.51
3852 5120 3.062909 GTGGTAGCTATCTCGCTAGATCG 59.937 52.174 3.64 0.00 42.69 3.69
3860 5128 2.640184 TCTCGCTAGATCGGAAGTTGA 58.360 47.619 0.00 0.00 0.00 3.18
3914 5182 1.008938 ACCTTGCCCTCACTCTAGGAT 59.991 52.381 0.00 0.00 39.15 3.24
3999 5267 5.028549 ACATATGTGCCGAAAAGAGAGAT 57.971 39.130 7.78 0.00 0.00 2.75
4017 5285 8.497910 AGAGAGATGCCTAATATGTTTAAGGA 57.502 34.615 0.00 0.00 0.00 3.36
4059 5327 2.906389 TCTTGCTGTGAGAAGGTATGGT 59.094 45.455 0.00 0.00 0.00 3.55
4093 5361 7.104939 AGGCCACGTATTAGTTGTTTGTATAA 58.895 34.615 5.01 0.00 0.00 0.98
4340 5614 9.736414 TGGGTCTTGACTACTATACATATACTC 57.264 37.037 0.61 0.00 0.00 2.59
4342 5616 9.434420 GGTCTTGACTACTATACATATACTCGT 57.566 37.037 0.61 0.00 0.00 4.18
4344 5618 9.433153 TCTTGACTACTATACATATACTCGTGG 57.567 37.037 0.00 0.00 0.00 4.94
4347 5621 8.370182 TGACTACTATACATATACTCGTGGTGA 58.630 37.037 0.00 0.00 0.00 4.02
4348 5622 9.381033 GACTACTATACATATACTCGTGGTGAT 57.619 37.037 0.00 0.00 0.00 3.06
4351 5625 8.734218 ACTATACATATACTCGTGGTGATAGG 57.266 38.462 0.00 0.00 0.00 2.57
4352 5626 8.546322 ACTATACATATACTCGTGGTGATAGGA 58.454 37.037 0.00 0.00 0.00 2.94
4356 5630 8.453238 ACATATACTCGTGGTGATAGGATATC 57.547 38.462 0.00 0.00 26.44 1.63
4357 5631 8.053355 ACATATACTCGTGGTGATAGGATATCA 58.947 37.037 4.83 0.00 26.44 2.15
4358 5632 9.072375 CATATACTCGTGGTGATAGGATATCAT 57.928 37.037 4.83 0.00 26.44 2.45
4363 5637 7.451877 ACTCGTGGTGATAGGATATCATTAGTT 59.548 37.037 4.83 0.00 0.00 2.24
4364 5638 8.190326 TCGTGGTGATAGGATATCATTAGTTT 57.810 34.615 4.83 0.00 0.00 2.66
4421 9110 9.665719 TGCTCTCAACAACTTGTATTCATATAA 57.334 29.630 0.00 0.00 0.00 0.98
4462 9157 5.998454 ATGAAACGAATTGCATAGAGAGG 57.002 39.130 0.00 0.00 0.00 3.69
4529 10896 5.751990 GGAGAAAAGTAGAAGAAACACACGA 59.248 40.000 0.00 0.00 0.00 4.35
4597 10964 7.173907 AGACAAAAGGACATGTTGTTAGATCAG 59.826 37.037 0.00 0.00 35.67 2.90
4617 10984 3.681417 CAGACACACACATATCCACACAG 59.319 47.826 0.00 0.00 0.00 3.66
4646 11013 1.203075 AGCTAGCGGGTTCTATAGCCT 60.203 52.381 9.55 0.00 42.48 4.58
4651 11018 1.962100 GCGGGTTCTATAGCCTAGTGT 59.038 52.381 0.00 0.00 42.48 3.55
4655 11022 3.958798 GGGTTCTATAGCCTAGTGTGACA 59.041 47.826 0.00 0.00 41.39 3.58
4713 11080 4.966965 TCAAAGACAAACCTAACGCAAA 57.033 36.364 0.00 0.00 0.00 3.68
4714 11081 5.508200 TCAAAGACAAACCTAACGCAAAT 57.492 34.783 0.00 0.00 0.00 2.32
4747 11114 0.237235 CAAACAATCGTCACGGTGGG 59.763 55.000 8.50 1.04 0.00 4.61
4759 11126 3.661648 GGTGGGCAGATGGGTGGT 61.662 66.667 0.00 0.00 0.00 4.16
4791 11158 2.290387 GGGAAGAGGAGGAAGGAAACAC 60.290 54.545 0.00 0.00 0.00 3.32
4802 11169 4.072839 GGAAGGAAACACGAAGAAGGATT 58.927 43.478 0.00 0.00 0.00 3.01
4872 11246 1.068250 GAGTCGGGCATAGAGGCAC 59.932 63.158 0.00 0.00 46.44 5.01
4876 11250 1.221840 CGGGCATAGAGGCACTGTT 59.778 57.895 0.00 0.00 46.44 3.16
4944 11501 3.060363 GTGACAACAAGCTAATACGACGG 59.940 47.826 0.00 0.00 0.00 4.79
5014 11576 3.766545 TGCAGATAAAAGGCAAAGGTCT 58.233 40.909 0.00 0.00 34.05 3.85
5136 11709 5.068198 GGAGGAAGCAAAAGCAATATGATGA 59.932 40.000 0.00 0.00 0.00 2.92
5137 11710 6.239232 GGAGGAAGCAAAAGCAATATGATGAT 60.239 38.462 0.00 0.00 0.00 2.45
5138 11711 7.040201 GGAGGAAGCAAAAGCAATATGATGATA 60.040 37.037 0.00 0.00 0.00 2.15
5139 11712 8.418597 AGGAAGCAAAAGCAATATGATGATAT 57.581 30.769 0.00 0.00 0.00 1.63
5204 11790 5.423290 TCATCATCCACTACTCACTCAATGT 59.577 40.000 0.00 0.00 0.00 2.71
5205 11791 5.745312 TCATCCACTACTCACTCAATGTT 57.255 39.130 0.00 0.00 0.00 2.71
5209 11795 6.850752 TCCACTACTCACTCAATGTTGATA 57.149 37.500 0.00 0.00 36.46 2.15
5210 11796 7.423844 TCCACTACTCACTCAATGTTGATAT 57.576 36.000 0.00 0.00 36.46 1.63
5211 11797 8.533569 TCCACTACTCACTCAATGTTGATATA 57.466 34.615 0.00 0.00 36.46 0.86
5212 11798 9.147732 TCCACTACTCACTCAATGTTGATATAT 57.852 33.333 0.00 0.00 36.46 0.86
5256 11844 0.035343 TCCTCCTCGTGTCGACATCT 60.035 55.000 23.12 0.00 0.00 2.90
5264 11852 4.260294 CCTCGTGTCGACATCTTCTACTAC 60.260 50.000 23.12 3.39 0.00 2.73
5331 11922 8.592998 GCTCAATCAATCATTCATTCAACTTTC 58.407 33.333 0.00 0.00 0.00 2.62
5344 11935 4.558538 TCAACTTTCTTTGAGCAGCTTC 57.441 40.909 0.00 0.00 31.68 3.86
5346 11937 2.565841 ACTTTCTTTGAGCAGCTTCGT 58.434 42.857 0.00 0.00 0.00 3.85
5347 11938 3.728845 ACTTTCTTTGAGCAGCTTCGTA 58.271 40.909 0.00 0.00 0.00 3.43
5348 11939 4.319177 ACTTTCTTTGAGCAGCTTCGTAT 58.681 39.130 0.00 0.00 0.00 3.06
5349 11940 4.390297 ACTTTCTTTGAGCAGCTTCGTATC 59.610 41.667 0.00 0.00 0.00 2.24
5350 11941 2.893637 TCTTTGAGCAGCTTCGTATCC 58.106 47.619 0.00 0.00 0.00 2.59
5351 11942 2.233676 TCTTTGAGCAGCTTCGTATCCA 59.766 45.455 0.00 0.00 0.00 3.41
5352 11943 2.010145 TTGAGCAGCTTCGTATCCAC 57.990 50.000 0.00 0.00 0.00 4.02
5381 11976 1.139163 CGGCTGCACAAAATTGGAAC 58.861 50.000 0.50 0.00 0.00 3.62
5385 11980 2.664916 CTGCACAAAATTGGAACGAGG 58.335 47.619 0.00 0.00 0.00 4.63
5390 11985 3.490526 CACAAAATTGGAACGAGGCAAAG 59.509 43.478 0.00 0.00 0.00 2.77
5391 11986 3.383185 ACAAAATTGGAACGAGGCAAAGA 59.617 39.130 0.00 0.00 0.00 2.52
5392 11987 3.643159 AAATTGGAACGAGGCAAAGAC 57.357 42.857 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 2.813908 GCACGCGTGTAAGAGGGG 60.814 66.667 36.80 11.99 0.00 4.79
88 91 4.849329 CGAGGCCTGACGTACCGC 62.849 72.222 12.00 0.00 0.00 5.68
174 178 3.059461 GCACTTAAACGAACATGGACGAA 60.059 43.478 17.79 4.27 0.00 3.85
660 672 0.474184 CTCTCCCACACCCAAGTTGT 59.526 55.000 1.45 0.00 0.00 3.32
663 675 0.838122 CTCCTCTCCCACACCCAAGT 60.838 60.000 0.00 0.00 0.00 3.16
808 821 1.333177 GGTGTGTGAGAGAGGTCACT 58.667 55.000 5.65 0.00 46.06 3.41
810 823 1.040646 GTGGTGTGTGAGAGAGGTCA 58.959 55.000 0.00 0.00 0.00 4.02
856 869 4.782019 TGGCACGAATTAGCTGATTTTT 57.218 36.364 5.07 0.00 0.00 1.94
896 909 2.192979 GCCTCCATCGCCATCCAA 59.807 61.111 0.00 0.00 0.00 3.53
904 917 2.509336 GTCCACACGCCTCCATCG 60.509 66.667 0.00 0.00 0.00 3.84
967 980 4.748102 CGATACATACGGCCACACTTTATT 59.252 41.667 2.24 0.00 0.00 1.40
969 982 3.130869 ACGATACATACGGCCACACTTTA 59.869 43.478 2.24 0.00 34.93 1.85
970 983 2.093869 ACGATACATACGGCCACACTTT 60.094 45.455 2.24 0.00 34.93 2.66
971 984 1.479323 ACGATACATACGGCCACACTT 59.521 47.619 2.24 0.00 34.93 3.16
972 985 1.108776 ACGATACATACGGCCACACT 58.891 50.000 2.24 0.00 34.93 3.55
973 986 1.856597 GAACGATACATACGGCCACAC 59.143 52.381 2.24 0.00 34.93 3.82
974 987 1.752498 AGAACGATACATACGGCCACA 59.248 47.619 2.24 0.00 34.93 4.17
975 988 2.124903 CAGAACGATACATACGGCCAC 58.875 52.381 2.24 0.00 34.93 5.01
976 989 2.025898 TCAGAACGATACATACGGCCA 58.974 47.619 2.24 0.00 34.93 5.36
977 990 2.787601 TCAGAACGATACATACGGCC 57.212 50.000 0.00 0.00 34.93 6.13
978 991 3.639538 ACATCAGAACGATACATACGGC 58.360 45.455 0.00 0.00 31.20 5.68
979 992 6.237313 TCTACATCAGAACGATACATACGG 57.763 41.667 0.00 0.00 31.20 4.02
980 993 6.307915 CCTCTACATCAGAACGATACATACG 58.692 44.000 0.00 0.00 31.12 3.06
981 994 6.087522 GCCTCTACATCAGAACGATACATAC 58.912 44.000 0.00 0.00 31.12 2.39
982 995 5.183331 GGCCTCTACATCAGAACGATACATA 59.817 44.000 0.00 0.00 31.12 2.29
983 996 4.021894 GGCCTCTACATCAGAACGATACAT 60.022 45.833 0.00 0.00 31.12 2.29
984 997 3.318275 GGCCTCTACATCAGAACGATACA 59.682 47.826 0.00 0.00 31.12 2.29
985 998 3.609644 CGGCCTCTACATCAGAACGATAC 60.610 52.174 0.00 0.00 31.12 2.24
986 999 2.552743 CGGCCTCTACATCAGAACGATA 59.447 50.000 0.00 0.00 31.12 2.92
987 1000 1.338337 CGGCCTCTACATCAGAACGAT 59.662 52.381 0.00 0.00 31.12 3.73
988 1001 0.738975 CGGCCTCTACATCAGAACGA 59.261 55.000 0.00 0.00 31.12 3.85
989 1002 0.249073 CCGGCCTCTACATCAGAACG 60.249 60.000 0.00 0.00 31.12 3.95
990 1003 0.105039 CCCGGCCTCTACATCAGAAC 59.895 60.000 0.00 0.00 31.12 3.01
991 1004 1.048724 CCCCGGCCTCTACATCAGAA 61.049 60.000 0.00 0.00 31.12 3.02
992 1005 1.457643 CCCCGGCCTCTACATCAGA 60.458 63.158 0.00 0.00 0.00 3.27
993 1006 1.762460 ACCCCGGCCTCTACATCAG 60.762 63.158 0.00 0.00 0.00 2.90
994 1007 2.063979 CACCCCGGCCTCTACATCA 61.064 63.158 0.00 0.00 0.00 3.07
995 1008 2.029307 GACACCCCGGCCTCTACATC 62.029 65.000 0.00 0.00 0.00 3.06
996 1009 2.040606 ACACCCCGGCCTCTACAT 59.959 61.111 0.00 0.00 0.00 2.29
997 1010 2.682494 GACACCCCGGCCTCTACA 60.682 66.667 0.00 0.00 0.00 2.74
998 1011 3.468140 GGACACCCCGGCCTCTAC 61.468 72.222 0.00 0.00 0.00 2.59
999 1012 4.791069 GGGACACCCCGGCCTCTA 62.791 72.222 0.00 0.00 44.02 2.43
1009 1022 4.746535 TTTCTTTCAAAAAGGGGACACC 57.253 40.909 0.00 0.00 40.67 4.16
1033 1046 9.494271 ACTGCTTTTTCTTTTCTTTTCTTTTCT 57.506 25.926 0.00 0.00 0.00 2.52
1036 1049 9.929180 AGTACTGCTTTTTCTTTTCTTTTCTTT 57.071 25.926 0.00 0.00 0.00 2.52
1037 1050 9.929180 AAGTACTGCTTTTTCTTTTCTTTTCTT 57.071 25.926 0.00 0.00 32.57 2.52
1038 1051 9.358872 CAAGTACTGCTTTTTCTTTTCTTTTCT 57.641 29.630 0.00 0.00 34.69 2.52
1070 1083 4.735578 GCTCCGAATCCAATTACAGTACGA 60.736 45.833 0.00 0.00 0.00 3.43
1134 1147 1.254026 CTGGACGTGGACTCCTACAA 58.746 55.000 0.00 0.00 0.00 2.41
1135 1148 1.248785 GCTGGACGTGGACTCCTACA 61.249 60.000 0.00 0.00 0.00 2.74
1136 1149 0.966370 AGCTGGACGTGGACTCCTAC 60.966 60.000 0.00 0.00 0.00 3.18
1137 1150 0.622136 TAGCTGGACGTGGACTCCTA 59.378 55.000 0.00 0.00 0.00 2.94
1138 1151 0.681564 CTAGCTGGACGTGGACTCCT 60.682 60.000 0.00 0.00 0.00 3.69
1139 1152 1.668101 CCTAGCTGGACGTGGACTCC 61.668 65.000 0.00 0.00 38.35 3.85
1147 1160 2.226912 GCATAGAGTACCTAGCTGGACG 59.773 54.545 0.00 0.00 39.71 4.79
1156 1169 8.713708 AGTACAATAGATTGCATAGAGTACCT 57.286 34.615 2.09 0.00 41.38 3.08
1157 1170 9.197694 CAAGTACAATAGATTGCATAGAGTACC 57.802 37.037 2.09 0.00 41.38 3.34
1158 1171 9.751542 ACAAGTACAATAGATTGCATAGAGTAC 57.248 33.333 2.09 0.00 41.38 2.73
1161 1174 9.416794 CCTACAAGTACAATAGATTGCATAGAG 57.583 37.037 2.09 0.00 41.38 2.43
1163 1176 7.657354 TGCCTACAAGTACAATAGATTGCATAG 59.343 37.037 2.09 0.00 41.38 2.23
1164 1177 7.505258 TGCCTACAAGTACAATAGATTGCATA 58.495 34.615 2.09 0.00 41.38 3.14
1166 1179 5.739959 TGCCTACAAGTACAATAGATTGCA 58.260 37.500 2.09 0.00 41.38 4.08
1167 1180 5.277538 GCTGCCTACAAGTACAATAGATTGC 60.278 44.000 2.09 0.00 41.38 3.56
1169 1182 5.368989 GGCTGCCTACAAGTACAATAGATT 58.631 41.667 12.43 0.00 0.00 2.40
1170 1183 4.202367 GGGCTGCCTACAAGTACAATAGAT 60.202 45.833 19.68 0.00 0.00 1.98
1172 1185 3.134804 AGGGCTGCCTACAAGTACAATAG 59.865 47.826 19.68 0.00 0.00 1.73
1173 1186 3.112263 AGGGCTGCCTACAAGTACAATA 58.888 45.455 19.68 0.00 0.00 1.90
1174 1187 1.916181 AGGGCTGCCTACAAGTACAAT 59.084 47.619 19.68 0.00 0.00 2.71
1175 1188 1.003118 CAGGGCTGCCTACAAGTACAA 59.997 52.381 19.68 0.00 0.00 2.41
1176 1189 0.613260 CAGGGCTGCCTACAAGTACA 59.387 55.000 19.68 0.00 0.00 2.90
1177 1190 3.460648 CAGGGCTGCCTACAAGTAC 57.539 57.895 19.68 0.00 0.00 2.73
1261 1312 0.031314 CACCATCTCCATCCTCGTCG 59.969 60.000 0.00 0.00 0.00 5.12
1264 1315 1.070445 GCCACCATCTCCATCCTCG 59.930 63.158 0.00 0.00 0.00 4.63
1501 1574 3.615509 GATGAACCCCGCGTCCCAA 62.616 63.158 4.92 0.00 0.00 4.12
1512 1585 3.554692 CGACGCTGCCGATGAACC 61.555 66.667 0.00 0.00 38.29 3.62
1517 1590 4.194720 GAGGTCGACGCTGCCGAT 62.195 66.667 9.92 0.00 38.38 4.18
1676 1942 4.889409 AGCTCAAAAGTTGAATTGTCTCCA 59.111 37.500 0.00 0.00 39.58 3.86
1677 1943 5.444663 AGCTCAAAAGTTGAATTGTCTCC 57.555 39.130 0.00 0.00 39.58 3.71
1713 1980 8.807948 ATTTAACAGTAACTAGCACCATCAAT 57.192 30.769 0.00 0.00 0.00 2.57
1714 1981 7.064134 CGATTTAACAGTAACTAGCACCATCAA 59.936 37.037 0.00 0.00 0.00 2.57
1719 1986 4.628333 TGCGATTTAACAGTAACTAGCACC 59.372 41.667 0.00 0.00 29.62 5.01
1723 1990 5.109903 AGCCTGCGATTTAACAGTAACTAG 58.890 41.667 0.00 0.00 31.76 2.57
1858 2127 2.389866 GATCCGCGTCCGTCGAAGAT 62.390 60.000 4.92 0.00 40.67 2.40
1920 2292 1.067060 TCTCGAGACACACAACAGTGG 59.933 52.381 12.08 0.00 43.72 4.00
1961 2333 5.419471 ACTCCTGCTAATCGAGAGTTTAAGT 59.581 40.000 0.00 0.00 34.17 2.24
2042 2423 7.441157 TGTGTGAAAAACAACAAAACCATACAA 59.559 29.630 0.00 0.00 41.57 2.41
2047 2428 5.235186 CACTGTGTGAAAAACAACAAAACCA 59.765 36.000 0.00 0.00 41.57 3.67
2062 2443 0.321034 GAGATGCTGGCACTGTGTGA 60.321 55.000 9.86 0.00 35.23 3.58
2158 2550 6.763355 AGAAAAGAGATAGCTTGTGTGAGAA 58.237 36.000 0.00 0.00 0.00 2.87
2779 3206 0.172578 ATGATTGGCGTCGTCGAAGA 59.827 50.000 12.54 0.00 39.71 2.87
2780 3207 0.298707 CATGATTGGCGTCGTCGAAG 59.701 55.000 6.17 3.62 39.71 3.79
2781 3208 0.109039 TCATGATTGGCGTCGTCGAA 60.109 50.000 6.17 0.00 39.71 3.71
2782 3209 0.800683 GTCATGATTGGCGTCGTCGA 60.801 55.000 6.17 0.00 39.71 4.20
2783 3210 1.631072 GTCATGATTGGCGTCGTCG 59.369 57.895 0.00 0.00 40.37 5.12
2904 3331 5.307196 AGAAGGCTAGGTTCTCAAAGTTGTA 59.693 40.000 0.00 0.00 27.32 2.41
2972 3399 6.718454 AGAAGAACAAGTTTGATGATGGTGAT 59.282 34.615 0.00 0.00 0.00 3.06
2988 3415 7.070074 AGTGAAGACCTAGAAGAAGAAGAACAA 59.930 37.037 0.00 0.00 0.00 2.83
2989 3416 6.551601 AGTGAAGACCTAGAAGAAGAAGAACA 59.448 38.462 0.00 0.00 0.00 3.18
2990 3417 6.866248 CAGTGAAGACCTAGAAGAAGAAGAAC 59.134 42.308 0.00 0.00 0.00 3.01
3072 3499 9.695526 GCACATGAATAAATAAAAGCCATGATA 57.304 29.630 0.00 0.00 35.32 2.15
3085 3512 5.009410 GGAAGCTAGCTGCACATGAATAAAT 59.991 40.000 24.45 0.00 45.94 1.40
3120 3547 4.296265 GGTAACTTGTGGAGCGGG 57.704 61.111 0.00 0.00 0.00 6.13
3156 3586 5.824624 AGAAATGACATTGAGGCAATATCGT 59.175 36.000 0.34 0.00 39.98 3.73
3190 3620 3.466836 GATAGCCAACATCCGATTCACA 58.533 45.455 0.00 0.00 0.00 3.58
3385 3816 3.003897 GTCAAACACGCCTTACATTTCCA 59.996 43.478 0.00 0.00 0.00 3.53
3670 4938 1.927487 TGATTGCAATGGTGGCTTCT 58.073 45.000 18.59 0.00 0.00 2.85
3757 5025 1.331756 GCTGATTCGCATGGAACGATT 59.668 47.619 0.00 0.00 39.65 3.34
3765 5033 3.177272 CTGCCCGCTGATTCGCATG 62.177 63.158 0.00 0.00 0.00 4.06
3768 5036 3.567797 GACTGCCCGCTGATTCGC 61.568 66.667 0.16 0.00 0.00 4.70
3788 5056 2.438975 ACCATCGCCGACTACCGA 60.439 61.111 0.00 0.00 41.76 4.69
3860 5128 0.535102 CCACCAACAAGGAAGAGCGT 60.535 55.000 0.00 0.00 41.22 5.07
3914 5182 4.447724 GCGAATAAGCACTTGATCGGAATA 59.552 41.667 16.28 0.00 34.66 1.75
4017 5285 5.437060 AGAGGCGTGTATGTTTTCCAATAT 58.563 37.500 0.00 0.00 0.00 1.28
4340 5614 8.307483 AGAAACTAATGATATCCTATCACCACG 58.693 37.037 0.00 0.00 0.00 4.94
4343 5617 9.810545 GCTAGAAACTAATGATATCCTATCACC 57.189 37.037 0.00 0.00 0.00 4.02
4372 5646 6.333416 CACTCTAAAGTGCAATCTAGCTACA 58.667 40.000 0.00 0.00 46.01 2.74
4421 9110 8.707839 CGTTTCATTTTGTGCAATACCTTTATT 58.292 29.630 0.00 0.00 0.00 1.40
4505 10872 5.751990 TCGTGTGTTTCTTCTACTTTTCTCC 59.248 40.000 0.00 0.00 0.00 3.71
4597 10964 3.664107 ACTGTGTGGATATGTGTGTGTC 58.336 45.455 0.00 0.00 0.00 3.67
4617 10984 1.320507 ACCCGCTAGCTAGCTAAGAC 58.679 55.000 36.02 15.48 46.85 3.01
4633 11000 3.958798 TGTCACACTAGGCTATAGAACCC 59.041 47.826 3.21 0.00 0.00 4.11
4646 11013 3.069016 ACGTGGAGTTCAATGTCACACTA 59.931 43.478 0.00 0.00 0.00 2.74
4651 11018 2.159028 TGACACGTGGAGTTCAATGTCA 60.159 45.455 21.57 13.48 44.62 3.58
4655 11022 2.910688 AGTGACACGTGGAGTTCAAT 57.089 45.000 21.57 10.70 0.00 2.57
4697 11064 4.621034 CCAATCATTTGCGTTAGGTTTGTC 59.379 41.667 0.00 0.00 0.00 3.18
4707 11074 1.952990 TGTGTGTCCAATCATTTGCGT 59.047 42.857 0.00 0.00 0.00 5.24
4713 11080 4.998671 TTGTTTGTGTGTGTCCAATCAT 57.001 36.364 0.00 0.00 0.00 2.45
4714 11081 4.497173 CGATTGTTTGTGTGTGTCCAATCA 60.497 41.667 0.00 0.00 38.56 2.57
4747 11114 1.303561 TCTTGCACCACCCATCTGC 60.304 57.895 0.00 0.00 0.00 4.26
4759 11126 0.987294 CCTCTTCCCCTTCTCTTGCA 59.013 55.000 0.00 0.00 0.00 4.08
4791 11158 1.281899 GTCTCGCCAATCCTTCTTCG 58.718 55.000 0.00 0.00 0.00 3.79
4802 11169 1.522668 CATTTGACCTTGTCTCGCCA 58.477 50.000 0.00 0.00 33.15 5.69
4872 11246 1.021202 TCAACGCCTTGACCAAACAG 58.979 50.000 0.00 0.00 31.00 3.16
4876 11250 1.781025 CGCTTCAACGCCTTGACCAA 61.781 55.000 0.00 0.00 36.06 3.67
4916 11290 6.480651 TCGTATTAGCTTGTTGTCACTTTTGA 59.519 34.615 0.00 0.00 0.00 2.69
4918 11292 6.563381 CGTCGTATTAGCTTGTTGTCACTTTT 60.563 38.462 0.00 0.00 0.00 2.27
4923 11297 3.247442 CCGTCGTATTAGCTTGTTGTCA 58.753 45.455 0.00 0.00 0.00 3.58
4944 11501 1.208293 CCTCCACCCTCTCTTTGTAGC 59.792 57.143 0.00 0.00 0.00 3.58
5014 11576 3.584834 TCTTCAATTCAATGACGAGCGA 58.415 40.909 0.00 0.00 0.00 4.93
5054 11616 4.276926 GCACATCCTCTAACCAATTCATCC 59.723 45.833 0.00 0.00 0.00 3.51
5212 11798 9.939802 GAGACTTTTCCTCCTAATACAAAAGTA 57.060 33.333 7.82 0.00 43.82 2.24
5213 11799 7.883833 GGAGACTTTTCCTCCTAATACAAAAGT 59.116 37.037 7.61 7.61 45.52 2.66
5295 11886 9.708092 TGAATGATTGATTGAGCACAATTTTAA 57.292 25.926 10.81 7.50 45.30 1.52
5296 11887 9.878667 ATGAATGATTGATTGAGCACAATTTTA 57.121 25.926 10.81 0.69 45.30 1.52
5297 11888 8.786826 ATGAATGATTGATTGAGCACAATTTT 57.213 26.923 10.81 0.00 45.30 1.82
5298 11889 8.786826 AATGAATGATTGATTGAGCACAATTT 57.213 26.923 10.81 0.24 45.30 1.82
5299 11890 8.038351 TGAATGAATGATTGATTGAGCACAATT 58.962 29.630 10.81 0.00 45.30 2.32
5301 11892 6.926313 TGAATGAATGATTGATTGAGCACAA 58.074 32.000 0.00 0.00 40.42 3.33
5314 11905 7.663827 TGCTCAAAGAAAGTTGAATGAATGAT 58.336 30.769 0.00 0.00 37.08 2.45
5331 11922 2.349886 GTGGATACGAAGCTGCTCAAAG 59.650 50.000 1.00 0.00 42.51 2.77
5344 11935 0.243907 CGCCCTGGATAGTGGATACG 59.756 60.000 0.00 0.00 42.51 3.06
5346 11937 1.192146 GCCGCCCTGGATAGTGGATA 61.192 60.000 5.35 0.00 42.00 2.59
5347 11938 2.520536 GCCGCCCTGGATAGTGGAT 61.521 63.158 5.35 0.00 42.00 3.41
5348 11939 3.161450 GCCGCCCTGGATAGTGGA 61.161 66.667 5.35 0.00 42.00 4.02
5349 11940 3.164269 AGCCGCCCTGGATAGTGG 61.164 66.667 0.00 0.00 42.00 4.00
5350 11941 2.109799 CAGCCGCCCTGGATAGTG 59.890 66.667 0.00 0.00 42.00 2.74
5351 11942 3.866582 GCAGCCGCCCTGGATAGT 61.867 66.667 0.00 0.00 42.03 2.12
5352 11943 3.865383 TGCAGCCGCCCTGGATAG 61.865 66.667 0.00 0.00 42.03 2.08
5370 11961 3.735746 GTCTTTGCCTCGTTCCAATTTTG 59.264 43.478 0.00 0.00 0.00 2.44
5381 11976 1.371267 TGTCGTCGTCTTTGCCTCG 60.371 57.895 0.00 0.00 0.00 4.63
5385 11980 1.136690 TCATGTGTCGTCGTCTTTGC 58.863 50.000 0.00 0.00 0.00 3.68
5390 11985 3.242091 CCAATGATTCATGTGTCGTCGTC 60.242 47.826 0.00 0.00 0.00 4.20
5391 11986 2.672874 CCAATGATTCATGTGTCGTCGT 59.327 45.455 0.00 0.00 0.00 4.34
5392 11987 2.030823 CCCAATGATTCATGTGTCGTCG 59.969 50.000 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.