Multiple sequence alignment - TraesCS3D01G481600

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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 TraesCS3D01G481600 chr3D 100.000 3723 0 0 1 3723 579582051 579585773 0.000000e+00 6876.0
1 TraesCS3D01G481600 chr3D 94.591 721 30 2 1 718 579399247 579398533 0.000000e+00 1107.0
2 TraesCS3D01G481600 chr3D 93.074 693 41 3 1759 2445 579425733 579425042 0.000000e+00 1007.0
3 TraesCS3D01G481600 chr3D 91.139 553 49 0 3171 3723 579396258 579395706 0.000000e+00 750.0
4 TraesCS3D01G481600 chr3D 90.942 552 48 2 3171 3721 579423948 579423398 0.000000e+00 741.0
5 TraesCS3D01G481600 chr3D 86.598 194 22 3 1564 1756 579397906 579397716 1.050000e-50 211.0
6 TraesCS3D01G481600 chr3D 81.618 272 35 6 1607 1878 579426012 579425756 1.050000e-50 211.0
7 TraesCS3D01G481600 chr3D 87.597 129 13 3 1838 1965 579397684 579397558 3.000000e-31 147.0
8 TraesCS3D01G481600 chr3D 88.525 122 13 1 1299 1420 579426220 579426100 3.000000e-31 147.0
9 TraesCS3D01G481600 chr3D 78.605 215 34 9 387 593 568137081 568136871 8.390000e-27 132.0
10 TraesCS3D01G481600 chr3D 85.600 125 11 6 1299 1420 579398100 579397980 1.400000e-24 124.0
11 TraesCS3D01G481600 chr3D 78.453 181 30 5 1 178 567686992 567687166 3.930000e-20 110.0
12 TraesCS3D01G481600 chr3B 90.407 2210 141 25 1552 3721 773762805 773760627 0.000000e+00 2841.0
13 TraesCS3D01G481600 chr3B 88.354 1039 56 29 2713 3723 773898093 773899094 0.000000e+00 1188.0
14 TraesCS3D01G481600 chr3B 92.804 806 57 1 1816 2621 773897294 773898098 0.000000e+00 1166.0
15 TraesCS3D01G481600 chr3B 89.866 898 69 8 1556 2445 773746420 773745537 0.000000e+00 1134.0
16 TraesCS3D01G481600 chr3B 86.481 1043 95 25 2 1031 773747802 773746793 0.000000e+00 1103.0
17 TraesCS3D01G481600 chr3B 83.223 602 46 14 189 776 773882267 773882827 5.550000e-138 501.0
18 TraesCS3D01G481600 chr3B 77.178 482 79 18 227 697 756439833 756440294 6.170000e-63 252.0
19 TraesCS3D01G481600 chr3B 79.496 278 20 17 1553 1820 773883444 773883694 2.980000e-36 163.0
20 TraesCS3D01G481600 chr3B 85.185 81 12 0 98 178 684638408 684638488 2.380000e-12 84.2
21 TraesCS3D01G481600 chr3A 90.929 904 51 10 1550 2443 714603933 714603051 0.000000e+00 1186.0
22 TraesCS3D01G481600 chr3A 89.286 924 71 11 1547 2445 714624938 714625858 0.000000e+00 1133.0
23 TraesCS3D01G481600 chr3A 90.476 819 51 3 2 813 714596360 714595562 0.000000e+00 1055.0
24 TraesCS3D01G481600 chr3A 91.049 782 49 9 2955 3723 714643381 714644154 0.000000e+00 1037.0
25 TraesCS3D01G481600 chr3A 93.115 610 41 1 1836 2445 714594291 714593683 0.000000e+00 893.0
26 TraesCS3D01G481600 chr3A 91.139 553 49 0 3171 3723 714591755 714591203 0.000000e+00 750.0
27 TraesCS3D01G481600 chr3A 81.081 185 31 4 227 409 702421159 702421341 1.080000e-30 145.0
28 TraesCS3D01G481600 chr3A 97.260 73 1 1 2841 2913 714643148 714643219 5.050000e-24 122.0
29 TraesCS3D01G481600 chr3A 78.307 189 28 9 381 560 700441519 700441703 3.930000e-20 110.0
30 TraesCS3D01G481600 chr3A 75.124 201 32 12 994 1189 714595413 714595226 1.110000e-10 78.7
31 TraesCS3D01G481600 chr4A 81.039 385 37 16 1553 1928 714667505 714667862 1.320000e-69 274.0
32 TraesCS3D01G481600 chr4A 97.849 93 2 0 1182 1274 714667251 714667343 1.070000e-35 161.0
33 TraesCS3D01G481600 chr4B 80.051 396 43 17 1547 1933 430672397 430672765 1.030000e-65 261.0
34 TraesCS3D01G481600 chr4B 98.925 93 1 0 1182 1274 430672149 430672241 2.300000e-37 167.0
35 TraesCS3D01G481600 chr4B 85.593 118 15 2 1552 1667 622342137 622342020 5.050000e-24 122.0
36 TraesCS3D01G481600 chr4B 100.000 33 0 0 1151 1183 430672093 430672125 1.120000e-05 62.1
37 TraesCS3D01G481600 chr7D 89.560 182 8 6 2623 2794 263946172 263946352 1.740000e-53 220.0
38 TraesCS3D01G481600 chr7D 88.112 143 17 0 2656 2798 13018640 13018782 1.780000e-38 171.0
39 TraesCS3D01G481600 chr7D 89.855 69 5 2 2605 2673 137560870 137560936 1.840000e-13 87.9
40 TraesCS3D01G481600 chr2D 88.525 183 17 3 2612 2793 458156094 458156273 6.260000e-53 219.0
41 TraesCS3D01G481600 chr2B 88.636 176 9 2 2623 2788 411541456 411541282 1.750000e-48 204.0
42 TraesCS3D01G481600 chr2B 89.404 151 13 3 2612 2762 133025577 133025430 1.770000e-43 187.0
43 TraesCS3D01G481600 chr2B 87.500 120 13 2 1550 1667 315136538 315136657 1.800000e-28 137.0
44 TraesCS3D01G481600 chr2B 86.667 120 14 2 1550 1667 120491410 120491529 8.390000e-27 132.0
45 TraesCS3D01G481600 chr2A 88.816 152 14 3 2611 2762 601706804 601706952 2.280000e-42 183.0
46 TraesCS3D01G481600 chr2A 85.405 185 16 4 2614 2788 457912620 457912803 8.210000e-42 182.0
47 TraesCS3D01G481600 chr7B 88.742 151 12 4 2612 2762 323200938 323200793 2.950000e-41 180.0
48 TraesCS3D01G481600 chr4D 89.437 142 11 4 2622 2762 478248013 478247875 3.820000e-40 176.0
49 TraesCS3D01G481600 chrUn 97.849 93 2 0 1182 1274 230759811 230759903 1.070000e-35 161.0
50 TraesCS3D01G481600 chr1B 85.000 120 16 2 1550 1667 670761575 670761694 1.820000e-23 121.0
51 TraesCS3D01G481600 chr6B 92.857 70 4 1 2605 2673 274211494 274211563 2.370000e-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 TraesCS3D01G481600 chr3D 579582051 579585773 3722 False 6876.000 6876 100.00000 1 3723 1 chr3D.!!$F2 3722
1 TraesCS3D01G481600 chr3D 579423398 579426220 2822 True 526.500 1007 88.53975 1299 3721 4 chr3D.!!$R3 2422
2 TraesCS3D01G481600 chr3D 579395706 579399247 3541 True 467.800 1107 89.10500 1 3723 5 chr3D.!!$R2 3722
3 TraesCS3D01G481600 chr3B 773760627 773762805 2178 True 2841.000 2841 90.40700 1552 3721 1 chr3B.!!$R1 2169
4 TraesCS3D01G481600 chr3B 773897294 773899094 1800 False 1177.000 1188 90.57900 1816 3723 2 chr3B.!!$F4 1907
5 TraesCS3D01G481600 chr3B 773745537 773747802 2265 True 1118.500 1134 88.17350 2 2445 2 chr3B.!!$R2 2443
6 TraesCS3D01G481600 chr3B 773882267 773883694 1427 False 332.000 501 81.35950 189 1820 2 chr3B.!!$F3 1631
7 TraesCS3D01G481600 chr3A 714603051 714603933 882 True 1186.000 1186 90.92900 1550 2443 1 chr3A.!!$R1 893
8 TraesCS3D01G481600 chr3A 714624938 714625858 920 False 1133.000 1133 89.28600 1547 2445 1 chr3A.!!$F3 898
9 TraesCS3D01G481600 chr3A 714591203 714596360 5157 True 694.175 1055 87.46350 2 3723 4 chr3A.!!$R2 3721
10 TraesCS3D01G481600 chr3A 714643148 714644154 1006 False 579.500 1037 94.15450 2841 3723 2 chr3A.!!$F4 882
11 TraesCS3D01G481600 chr4A 714667251 714667862 611 False 217.500 274 89.44400 1182 1928 2 chr4A.!!$F1 746

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
118 119 0.037975 GTACCTCCGCGTCAAGGAAA 60.038 55.0 21.85 9.69 37.32 3.13 F
1455 1661 0.027194 CTTCACGCGATGCATTGGAG 59.973 55.0 15.93 8.29 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1750 0.036577 CCCCTGTCTTCAGTCTGCAG 60.037 60.0 7.63 7.63 39.82 4.41 R
3183 5967 0.980423 GACCAAGTGGAGAGAAGGCT 59.020 55.0 3.83 0.00 38.94 4.58 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
94 95 3.515901 ACAGGAGAGATCCAAAGGTGTAC 59.484 47.826 0.00 0.00 0.00 2.90
100 101 2.897969 AGATCCAAAGGTGTACGTCAGT 59.102 45.455 0.00 0.00 0.00 3.41
109 110 1.061570 GTACGTCAGTACCTCCGCG 59.938 63.158 0.00 0.00 45.59 6.46
112 113 2.683859 CGTCAGTACCTCCGCGTCA 61.684 63.158 4.92 0.00 0.00 4.35
118 119 0.037975 GTACCTCCGCGTCAAGGAAA 60.038 55.000 21.85 9.69 37.32 3.13
178 179 0.898326 TGTAGGAGCCGTCTTGAGCA 60.898 55.000 0.00 0.00 0.00 4.26
742 761 4.430423 GTTGCTCTTGCGGCGTCG 62.430 66.667 4.29 4.29 43.34 5.12
776 827 0.318441 CGTCCAGCAAGAGGAGTGAA 59.682 55.000 0.00 0.00 35.42 3.18
777 828 1.802069 GTCCAGCAAGAGGAGTGAAC 58.198 55.000 0.00 0.00 35.42 3.18
778 829 1.346068 GTCCAGCAAGAGGAGTGAACT 59.654 52.381 0.00 0.00 35.42 3.01
779 830 1.345741 TCCAGCAAGAGGAGTGAACTG 59.654 52.381 0.00 0.00 0.00 3.16
780 831 1.345741 CCAGCAAGAGGAGTGAACTGA 59.654 52.381 0.00 0.00 0.00 3.41
781 832 2.612471 CCAGCAAGAGGAGTGAACTGAG 60.612 54.545 0.00 0.00 0.00 3.35
782 833 2.036992 CAGCAAGAGGAGTGAACTGAGT 59.963 50.000 0.00 0.00 0.00 3.41
783 834 2.036992 AGCAAGAGGAGTGAACTGAGTG 59.963 50.000 0.00 0.00 0.00 3.51
784 835 2.869636 GCAAGAGGAGTGAACTGAGTGG 60.870 54.545 0.00 0.00 0.00 4.00
785 836 2.366916 CAAGAGGAGTGAACTGAGTGGT 59.633 50.000 0.00 0.00 0.00 4.16
786 837 1.967066 AGAGGAGTGAACTGAGTGGTG 59.033 52.381 0.00 0.00 0.00 4.17
787 838 1.001406 GAGGAGTGAACTGAGTGGTGG 59.999 57.143 0.00 0.00 0.00 4.61
788 839 1.048601 GGAGTGAACTGAGTGGTGGA 58.951 55.000 0.00 0.00 0.00 4.02
789 840 1.270358 GGAGTGAACTGAGTGGTGGAC 60.270 57.143 0.00 0.00 0.00 4.02
790 841 1.689273 GAGTGAACTGAGTGGTGGACT 59.311 52.381 0.00 0.00 37.76 3.85
791 842 1.414181 AGTGAACTGAGTGGTGGACTG 59.586 52.381 0.00 0.00 33.83 3.51
792 843 0.106708 TGAACTGAGTGGTGGACTGC 59.893 55.000 0.00 0.00 33.83 4.40
793 844 0.603975 GAACTGAGTGGTGGACTGCC 60.604 60.000 0.00 0.00 33.83 4.85
794 845 1.056700 AACTGAGTGGTGGACTGCCT 61.057 55.000 0.00 0.00 33.83 4.75
795 846 1.004080 CTGAGTGGTGGACTGCCTG 60.004 63.158 0.00 0.00 33.83 4.85
796 847 1.762522 CTGAGTGGTGGACTGCCTGT 61.763 60.000 0.00 0.00 33.83 4.00
797 848 1.302033 GAGTGGTGGACTGCCTGTG 60.302 63.158 0.00 0.00 33.83 3.66
798 849 1.758440 GAGTGGTGGACTGCCTGTGA 61.758 60.000 0.00 0.00 33.83 3.58
799 850 1.598130 GTGGTGGACTGCCTGTGAC 60.598 63.158 0.00 0.00 34.31 3.67
800 851 2.069430 TGGTGGACTGCCTGTGACA 61.069 57.895 0.00 0.00 34.31 3.58
844 897 0.392595 GGAGCGGAGGTAGGTTTTGG 60.393 60.000 0.00 0.00 39.88 3.28
948 1014 0.038744 CCTTCAACTGGCCCAGACAT 59.961 55.000 19.90 0.00 35.18 3.06
949 1015 1.457346 CTTCAACTGGCCCAGACATC 58.543 55.000 19.90 0.00 35.18 3.06
950 1016 1.004044 CTTCAACTGGCCCAGACATCT 59.996 52.381 19.90 0.00 35.18 2.90
951 1017 0.615331 TCAACTGGCCCAGACATCTC 59.385 55.000 19.90 0.00 35.18 2.75
953 1019 1.903877 AACTGGCCCAGACATCTCGG 61.904 60.000 19.90 0.00 35.18 4.63
958 1024 1.758440 GCCCAGACATCTCGGCCATA 61.758 60.000 6.27 0.00 43.28 2.74
960 1026 0.752658 CCAGACATCTCGGCCATACA 59.247 55.000 2.24 0.00 0.00 2.29
961 1027 1.539065 CCAGACATCTCGGCCATACAC 60.539 57.143 2.24 0.00 0.00 2.90
962 1028 1.136891 CAGACATCTCGGCCATACACA 59.863 52.381 2.24 0.00 0.00 3.72
963 1029 1.137086 AGACATCTCGGCCATACACAC 59.863 52.381 2.24 0.00 0.00 3.82
975 1041 3.483421 CCATACACACTGATGGATGCAT 58.517 45.455 0.00 0.00 44.72 3.96
977 1043 1.660167 ACACACTGATGGATGCATCG 58.340 50.000 20.61 17.05 34.46 3.84
980 1046 1.419012 ACACTGATGGATGCATCGGAT 59.581 47.619 34.71 22.11 39.65 4.18
992 1058 1.111116 CATCGGATGCCAGCCCATTT 61.111 55.000 4.84 0.00 0.00 2.32
1035 1102 2.494918 CTCTGAACCCTACCGCGG 59.505 66.667 26.86 26.86 0.00 6.46
1036 1103 3.718210 CTCTGAACCCTACCGCGGC 62.718 68.421 28.58 7.50 0.00 6.53
1092 1177 4.517815 GTCCGCCGCAATCCCGTA 62.518 66.667 0.00 0.00 0.00 4.02
1096 1181 4.825252 GCCGCAATCCCGTACCGT 62.825 66.667 0.00 0.00 0.00 4.83
1097 1182 2.584143 CCGCAATCCCGTACCGTC 60.584 66.667 0.00 0.00 0.00 4.79
1098 1183 2.493030 CGCAATCCCGTACCGTCT 59.507 61.111 0.00 0.00 0.00 4.18
1099 1184 1.876714 CGCAATCCCGTACCGTCTG 60.877 63.158 0.00 0.00 0.00 3.51
1100 1185 1.520787 GCAATCCCGTACCGTCTGG 60.521 63.158 0.00 0.00 42.84 3.86
1124 1209 1.047002 ATCTCCTCATCGAAGGGCAG 58.953 55.000 3.32 0.00 37.02 4.85
1125 1210 1.045350 TCTCCTCATCGAAGGGCAGG 61.045 60.000 3.32 0.00 37.02 4.85
1126 1211 2.203126 CCTCATCGAAGGGCAGGC 60.203 66.667 0.00 0.00 32.35 4.85
1127 1212 2.586245 CTCATCGAAGGGCAGGCA 59.414 61.111 0.00 0.00 0.00 4.75
1128 1213 1.523258 CTCATCGAAGGGCAGGCAG 60.523 63.158 0.00 0.00 0.00 4.85
1129 1214 3.207669 CATCGAAGGGCAGGCAGC 61.208 66.667 0.00 0.00 44.65 5.25
1264 1421 6.250951 GTGTTGTACTGTTAGATTAGCTCGTC 59.749 42.308 0.00 0.00 0.00 4.20
1265 1422 6.072342 TGTTGTACTGTTAGATTAGCTCGTCA 60.072 38.462 0.00 0.00 0.00 4.35
1281 1438 4.602995 CTCGTCACCTTCAGTTAGATAGC 58.397 47.826 0.00 0.00 0.00 2.97
1283 1440 3.381908 CGTCACCTTCAGTTAGATAGCCT 59.618 47.826 0.00 0.00 0.00 4.58
1284 1441 4.688021 GTCACCTTCAGTTAGATAGCCTG 58.312 47.826 0.00 0.00 0.00 4.85
1285 1442 4.160626 GTCACCTTCAGTTAGATAGCCTGT 59.839 45.833 0.00 0.00 0.00 4.00
1286 1443 5.360144 GTCACCTTCAGTTAGATAGCCTGTA 59.640 44.000 0.00 0.00 0.00 2.74
1287 1444 6.041069 GTCACCTTCAGTTAGATAGCCTGTAT 59.959 42.308 0.00 0.00 0.00 2.29
1288 1445 6.265649 TCACCTTCAGTTAGATAGCCTGTATC 59.734 42.308 0.00 0.00 0.00 2.24
1289 1446 5.540719 ACCTTCAGTTAGATAGCCTGTATCC 59.459 44.000 0.00 0.00 0.00 2.59
1290 1447 5.046950 CCTTCAGTTAGATAGCCTGTATCCC 60.047 48.000 0.00 0.00 0.00 3.85
1291 1448 5.340891 TCAGTTAGATAGCCTGTATCCCT 57.659 43.478 0.00 0.00 0.00 4.20
1292 1449 5.080337 TCAGTTAGATAGCCTGTATCCCTG 58.920 45.833 0.00 0.00 0.00 4.45
1293 1450 4.835615 CAGTTAGATAGCCTGTATCCCTGT 59.164 45.833 0.00 0.00 0.00 4.00
1294 1451 5.305644 CAGTTAGATAGCCTGTATCCCTGTT 59.694 44.000 0.00 0.00 0.00 3.16
1295 1452 6.493802 CAGTTAGATAGCCTGTATCCCTGTTA 59.506 42.308 0.00 0.00 0.00 2.41
1296 1453 6.722129 AGTTAGATAGCCTGTATCCCTGTTAG 59.278 42.308 0.00 0.00 0.00 2.34
1297 1454 3.835395 AGATAGCCTGTATCCCTGTTAGC 59.165 47.826 0.00 0.00 0.00 3.09
1308 1465 4.737855 TCCCTGTTAGCTTCAGTACATC 57.262 45.455 14.51 0.00 0.00 3.06
1313 1470 5.126222 CCTGTTAGCTTCAGTACATCTCTGA 59.874 44.000 14.51 0.00 39.71 3.27
1316 1473 8.293699 TGTTAGCTTCAGTACATCTCTGATTA 57.706 34.615 0.00 0.00 40.83 1.75
1318 1475 9.405587 GTTAGCTTCAGTACATCTCTGATTATC 57.594 37.037 0.00 0.00 40.83 1.75
1326 1496 7.812191 CAGTACATCTCTGATTATCTAACTGCC 59.188 40.741 0.00 0.00 35.20 4.85
1394 1566 2.631062 AGTCAACCGTTCATCCTGTGTA 59.369 45.455 0.00 0.00 0.00 2.90
1403 1583 7.110155 ACCGTTCATCCTGTGTATTAGATTTT 58.890 34.615 0.00 0.00 0.00 1.82
1415 1621 9.599866 TGTGTATTAGATTTTATCAGTCTGTGG 57.400 33.333 0.00 0.00 0.00 4.17
1440 1646 1.078918 CCCACGCTGATCTGCTTCA 60.079 57.895 20.58 0.00 0.00 3.02
1449 1655 1.423721 GATCTGCTTCACGCGATGCA 61.424 55.000 15.93 15.80 46.70 3.96
1451 1657 3.577229 TGCTTCACGCGATGCATT 58.423 50.000 15.93 0.00 44.74 3.56
1452 1658 1.135108 TGCTTCACGCGATGCATTG 59.865 52.632 15.93 9.80 44.74 2.82
1453 1659 1.584483 GCTTCACGCGATGCATTGG 60.584 57.895 15.93 8.25 40.97 3.16
1454 1660 1.980951 GCTTCACGCGATGCATTGGA 61.981 55.000 15.93 1.81 40.97 3.53
1455 1661 0.027194 CTTCACGCGATGCATTGGAG 59.973 55.000 15.93 8.29 0.00 3.86
1456 1662 0.390998 TTCACGCGATGCATTGGAGA 60.391 50.000 15.93 7.16 0.00 3.71
1457 1663 1.083806 TCACGCGATGCATTGGAGAC 61.084 55.000 15.93 0.00 0.00 3.36
1458 1664 1.079197 ACGCGATGCATTGGAGACA 60.079 52.632 15.93 0.00 39.83 3.41
1459 1665 0.462581 ACGCGATGCATTGGAGACAT 60.463 50.000 15.93 0.00 42.32 3.06
1460 1666 0.041576 CGCGATGCATTGGAGACATG 60.042 55.000 15.85 0.00 42.32 3.21
1461 1667 1.302366 GCGATGCATTGGAGACATGA 58.698 50.000 15.85 0.00 42.32 3.07
1462 1668 1.263484 GCGATGCATTGGAGACATGAG 59.737 52.381 15.85 0.00 42.32 2.90
1463 1669 1.263484 CGATGCATTGGAGACATGAGC 59.737 52.381 5.98 0.00 42.32 4.26
1464 1670 1.263484 GATGCATTGGAGACATGAGCG 59.737 52.381 0.00 0.00 42.32 5.03
1465 1671 0.249955 TGCATTGGAGACATGAGCGA 59.750 50.000 0.00 0.00 42.32 4.93
1466 1672 0.654683 GCATTGGAGACATGAGCGAC 59.345 55.000 0.00 0.00 42.32 5.19
1467 1673 0.926155 CATTGGAGACATGAGCGACG 59.074 55.000 0.00 0.00 42.32 5.12
1468 1674 0.807667 ATTGGAGACATGAGCGACGC 60.808 55.000 13.03 13.03 42.32 5.19
1469 1675 2.583593 GGAGACATGAGCGACGCC 60.584 66.667 17.79 8.82 0.00 5.68
1470 1676 2.181777 GAGACATGAGCGACGCCA 59.818 61.111 17.79 14.61 0.00 5.69
1471 1677 1.227089 GAGACATGAGCGACGCCAT 60.227 57.895 17.79 16.27 0.00 4.40
1472 1678 1.485838 GAGACATGAGCGACGCCATG 61.486 60.000 31.77 31.77 40.42 3.66
1473 1679 2.512286 ACATGAGCGACGCCATGG 60.512 61.111 34.04 23.73 39.61 3.66
1474 1680 2.512286 CATGAGCGACGCCATGGT 60.512 61.111 28.71 10.16 35.32 3.55
1475 1681 2.108514 CATGAGCGACGCCATGGTT 61.109 57.895 28.71 9.52 35.32 3.67
1476 1682 1.377202 ATGAGCGACGCCATGGTTT 60.377 52.632 17.79 0.00 0.00 3.27
1477 1683 1.647545 ATGAGCGACGCCATGGTTTG 61.648 55.000 17.79 6.42 0.00 2.93
1478 1684 3.667429 GAGCGACGCCATGGTTTGC 62.667 63.158 17.79 15.68 0.00 3.68
1479 1685 3.737172 GCGACGCCATGGTTTGCT 61.737 61.111 14.67 0.00 0.00 3.91
1480 1686 2.176546 CGACGCCATGGTTTGCTG 59.823 61.111 14.67 0.00 0.00 4.41
1481 1687 2.126346 GACGCCATGGTTTGCTGC 60.126 61.111 14.67 0.00 0.00 5.25
1482 1688 2.911509 ACGCCATGGTTTGCTGCA 60.912 55.556 14.67 0.00 0.00 4.41
1483 1689 2.126228 CGCCATGGTTTGCTGCAG 60.126 61.111 14.67 10.11 0.00 4.41
1484 1690 2.922950 CGCCATGGTTTGCTGCAGT 61.923 57.895 16.64 0.00 0.00 4.40
1485 1691 1.080298 GCCATGGTTTGCTGCAGTC 60.080 57.895 16.64 8.39 0.00 3.51
1486 1692 1.530013 GCCATGGTTTGCTGCAGTCT 61.530 55.000 16.64 0.00 0.00 3.24
1487 1693 0.242825 CCATGGTTTGCTGCAGTCTG 59.757 55.000 16.64 0.00 0.00 3.51
1488 1694 1.241165 CATGGTTTGCTGCAGTCTGA 58.759 50.000 16.64 0.00 0.00 3.27
1489 1695 1.610038 CATGGTTTGCTGCAGTCTGAA 59.390 47.619 16.64 2.46 0.00 3.02
1490 1696 1.985473 TGGTTTGCTGCAGTCTGAAT 58.015 45.000 16.64 0.00 0.00 2.57
1491 1697 3.138884 TGGTTTGCTGCAGTCTGAATA 57.861 42.857 16.64 0.00 0.00 1.75
1492 1698 3.485394 TGGTTTGCTGCAGTCTGAATAA 58.515 40.909 16.64 0.00 0.00 1.40
1493 1699 4.081406 TGGTTTGCTGCAGTCTGAATAAT 58.919 39.130 16.64 0.00 0.00 1.28
1494 1700 5.252547 TGGTTTGCTGCAGTCTGAATAATA 58.747 37.500 16.64 0.00 0.00 0.98
1495 1701 5.887598 TGGTTTGCTGCAGTCTGAATAATAT 59.112 36.000 16.64 0.00 0.00 1.28
1496 1702 6.377996 TGGTTTGCTGCAGTCTGAATAATATT 59.622 34.615 16.64 0.00 0.00 1.28
1497 1703 6.914757 GGTTTGCTGCAGTCTGAATAATATTC 59.085 38.462 16.64 6.07 0.00 1.75
1498 1704 7.201767 GGTTTGCTGCAGTCTGAATAATATTCT 60.202 37.037 16.64 0.00 0.00 2.40
1499 1705 7.488187 TTGCTGCAGTCTGAATAATATTCTC 57.512 36.000 16.64 5.32 0.00 2.87
1500 1706 6.824553 TGCTGCAGTCTGAATAATATTCTCT 58.175 36.000 16.64 7.15 0.00 3.10
1501 1707 6.704937 TGCTGCAGTCTGAATAATATTCTCTG 59.295 38.462 16.64 16.66 0.00 3.35
1502 1708 6.927936 GCTGCAGTCTGAATAATATTCTCTGA 59.072 38.462 22.97 13.83 0.00 3.27
1503 1709 7.440556 GCTGCAGTCTGAATAATATTCTCTGAA 59.559 37.037 22.97 17.13 0.00 3.02
1504 1710 9.322773 CTGCAGTCTGAATAATATTCTCTGAAA 57.677 33.333 22.97 15.11 0.00 2.69
1505 1711 9.102757 TGCAGTCTGAATAATATTCTCTGAAAC 57.897 33.333 22.97 13.62 0.00 2.78
1506 1712 8.555361 GCAGTCTGAATAATATTCTCTGAAACC 58.445 37.037 22.97 11.27 0.00 3.27
1507 1713 9.605275 CAGTCTGAATAATATTCTCTGAAACCA 57.395 33.333 13.45 0.00 0.00 3.67
1510 1716 9.396022 TCTGAATAATATTCTCTGAAACCAACC 57.604 33.333 13.45 0.00 0.00 3.77
1511 1717 9.177608 CTGAATAATATTCTCTGAAACCAACCA 57.822 33.333 13.45 0.00 0.00 3.67
1512 1718 9.527157 TGAATAATATTCTCTGAAACCAACCAA 57.473 29.630 13.45 0.00 0.00 3.67
1517 1723 9.753674 AATATTCTCTGAAACCAACCAATTAGA 57.246 29.630 0.00 0.00 0.00 2.10
1518 1724 9.753674 ATATTCTCTGAAACCAACCAATTAGAA 57.246 29.630 0.00 0.00 0.00 2.10
1519 1725 8.655935 ATTCTCTGAAACCAACCAATTAGAAT 57.344 30.769 0.00 0.00 0.00 2.40
1520 1726 7.687941 TCTCTGAAACCAACCAATTAGAATC 57.312 36.000 0.00 0.00 0.00 2.52
1521 1727 7.461749 TCTCTGAAACCAACCAATTAGAATCT 58.538 34.615 0.00 0.00 0.00 2.40
1522 1728 7.391554 TCTCTGAAACCAACCAATTAGAATCTG 59.608 37.037 0.00 0.00 0.00 2.90
1523 1729 7.230747 TCTGAAACCAACCAATTAGAATCTGA 58.769 34.615 0.00 0.00 0.00 3.27
1524 1730 7.723616 TCTGAAACCAACCAATTAGAATCTGAA 59.276 33.333 0.00 0.00 0.00 3.02
1525 1731 8.243961 TGAAACCAACCAATTAGAATCTGAAA 57.756 30.769 0.00 0.00 0.00 2.69
1526 1732 8.141268 TGAAACCAACCAATTAGAATCTGAAAC 58.859 33.333 0.00 0.00 0.00 2.78
1527 1733 6.590234 ACCAACCAATTAGAATCTGAAACC 57.410 37.500 0.00 0.00 0.00 3.27
1528 1734 6.314917 ACCAACCAATTAGAATCTGAAACCT 58.685 36.000 0.00 0.00 0.00 3.50
1529 1735 6.434340 ACCAACCAATTAGAATCTGAAACCTC 59.566 38.462 0.00 0.00 0.00 3.85
1530 1736 6.434028 CCAACCAATTAGAATCTGAAACCTCA 59.566 38.462 0.00 0.00 0.00 3.86
1531 1737 7.123247 CCAACCAATTAGAATCTGAAACCTCAT 59.877 37.037 0.00 0.00 0.00 2.90
1532 1738 7.636150 ACCAATTAGAATCTGAAACCTCATG 57.364 36.000 0.00 0.00 0.00 3.07
1533 1739 6.604795 ACCAATTAGAATCTGAAACCTCATGG 59.395 38.462 0.00 0.00 39.83 3.66
1542 1748 2.351276 ACCTCATGGTCAACCGCC 59.649 61.111 0.00 0.00 44.78 6.13
1543 1749 2.819595 CCTCATGGTCAACCGCCG 60.820 66.667 0.00 0.00 39.43 6.46
1544 1750 3.499737 CTCATGGTCAACCGCCGC 61.500 66.667 0.00 0.00 39.43 6.53
1545 1751 3.958147 CTCATGGTCAACCGCCGCT 62.958 63.158 0.00 0.00 39.43 5.52
1608 1827 7.596248 CAGAATCTGAAACCAACCAATTAACTG 59.404 37.037 3.77 0.00 32.44 3.16
1612 1831 3.385193 AACCAACCAATTAACTGCAGC 57.615 42.857 15.27 0.00 0.00 5.25
1704 1925 8.421002 TCATGTATCTCTATTTTGTTGGATCGA 58.579 33.333 0.00 0.00 0.00 3.59
1713 1934 9.389755 TCTATTTTGTTGGATCGATAAATGTCA 57.610 29.630 0.00 0.00 0.00 3.58
1749 1970 3.003068 CCATAGCTGTGCAATTGAGCTAC 59.997 47.826 22.62 10.98 45.62 3.58
1764 1994 4.331968 TGAGCTACAGTTGTTTTATGGGG 58.668 43.478 0.00 0.00 0.00 4.96
1774 2004 7.343574 ACAGTTGTTTTATGGGGTACTTTTCTT 59.656 33.333 0.00 0.00 0.00 2.52
1820 2198 0.967380 CCCGGCTTGCTTGAATCCTT 60.967 55.000 0.00 0.00 0.00 3.36
1824 2202 1.403780 GGCTTGCTTGAATCCTTGCTG 60.404 52.381 0.00 0.00 0.00 4.41
1882 2654 8.841444 ACTTTCGTCATGTATGATAAAAATGC 57.159 30.769 0.00 0.00 39.30 3.56
1996 2782 2.604686 TGGCTGCCGACCTTCTCT 60.605 61.111 14.98 0.00 0.00 3.10
2022 2808 1.744320 CTCCCCGACATACATCGCCA 61.744 60.000 0.00 0.00 40.87 5.69
2460 3645 3.002759 GCTCTGTGTTTCTTTCTGTGGTC 59.997 47.826 0.00 0.00 0.00 4.02
2490 3709 7.384439 TGAGCCAAACATCGTTAATCAAATA 57.616 32.000 0.00 0.00 0.00 1.40
2543 3762 6.543831 ACTTCATTTATGCATTAGGGTCAGTC 59.456 38.462 3.54 0.00 0.00 3.51
2629 3849 3.505464 ATCAAGGTTTAGGAGTCGACG 57.495 47.619 10.46 0.00 0.00 5.12
2633 3853 2.083002 AGGTTTAGGAGTCGACGAGTC 58.917 52.381 21.91 21.91 0.00 3.36
2673 3903 5.807344 TCATAGACTAATCGTGACAAGTCG 58.193 41.667 7.43 0.00 42.51 4.18
2679 3909 2.051879 ATCGTGACAAGTCGACACTG 57.948 50.000 19.50 16.43 38.03 3.66
2686 3916 3.187700 GACAAGTCGACACTGAAGTTGT 58.812 45.455 19.50 16.64 32.71 3.32
2689 3919 2.810650 AGTCGACACTGAAGTTGTGAC 58.189 47.619 19.50 0.00 38.65 3.67
2785 4015 3.930336 TGACTAGTCCTTCGACTCGTAA 58.070 45.455 20.11 0.00 46.90 3.18
2960 5718 9.113838 GTGATGTATTAGAATCCAATGTTGAGT 57.886 33.333 0.00 0.00 0.00 3.41
2970 5728 8.321353 AGAATCCAATGTTGAGTCACATAGTAA 58.679 33.333 0.00 0.00 36.30 2.24
3009 5767 1.605712 CCCTCCGTTCACACTTCACTC 60.606 57.143 0.00 0.00 0.00 3.51
3010 5768 1.341531 CCTCCGTTCACACTTCACTCT 59.658 52.381 0.00 0.00 0.00 3.24
3011 5769 2.557056 CCTCCGTTCACACTTCACTCTA 59.443 50.000 0.00 0.00 0.00 2.43
3012 5770 3.005472 CCTCCGTTCACACTTCACTCTAA 59.995 47.826 0.00 0.00 0.00 2.10
3013 5771 4.500887 CCTCCGTTCACACTTCACTCTAAA 60.501 45.833 0.00 0.00 0.00 1.85
3014 5772 5.209818 TCCGTTCACACTTCACTCTAAAT 57.790 39.130 0.00 0.00 0.00 1.40
3015 5773 5.607477 TCCGTTCACACTTCACTCTAAATT 58.393 37.500 0.00 0.00 0.00 1.82
3016 5774 6.053005 TCCGTTCACACTTCACTCTAAATTT 58.947 36.000 0.00 0.00 0.00 1.82
3077 5859 3.314080 TCAACTGCAAGGTTAGTTTTCGG 59.686 43.478 0.00 0.00 39.30 4.30
3145 5929 1.397672 TCTCTGCTCCTGATTCCTCG 58.602 55.000 0.00 0.00 0.00 4.63
3156 5940 4.082190 TCCTGATTCCTCGTCACTTGTTAG 60.082 45.833 0.00 0.00 0.00 2.34
3183 5967 0.630673 AAGGGGGTAAGCATGCATCA 59.369 50.000 21.98 0.47 0.00 3.07
3204 5988 0.390472 CCTTCTCTCCACTTGGTCGC 60.390 60.000 0.00 0.00 36.34 5.19
3365 6149 5.221702 ACCCCCTCAAATTCAACTGAAAATG 60.222 40.000 0.00 0.00 37.61 2.32
3599 6383 8.267620 TGGAAATCTTGTAGTCCTATCATCAT 57.732 34.615 0.00 0.00 0.00 2.45
3605 6389 7.455891 TCTTGTAGTCCTATCATCATACGGTA 58.544 38.462 0.00 0.00 0.00 4.02
3651 6435 1.594293 CAAGCGACACCGTCCTTGT 60.594 57.895 13.02 0.00 36.76 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.621520 GTGTTCGACACCACGACC 58.378 61.111 6.82 0.00 43.05 4.79
94 95 2.099831 GACGCGGAGGTACTGACG 59.900 66.667 12.47 0.00 41.55 4.35
100 101 0.037975 GTTTCCTTGACGCGGAGGTA 60.038 55.000 20.17 11.55 34.57 3.08
109 110 3.010420 GAGGCACATAGGTTTCCTTGAC 58.990 50.000 0.29 0.00 34.61 3.18
112 113 1.065418 CCGAGGCACATAGGTTTCCTT 60.065 52.381 0.29 0.00 34.61 3.36
118 119 3.309582 CCACCGAGGCACATAGGT 58.690 61.111 0.00 0.00 37.49 3.08
148 149 2.868583 CGGCTCCTACATCTTCACATTG 59.131 50.000 0.00 0.00 0.00 2.82
151 152 1.476891 GACGGCTCCTACATCTTCACA 59.523 52.381 0.00 0.00 0.00 3.58
187 188 1.536940 TGATGCATGGTGAACTGGTG 58.463 50.000 2.46 0.00 0.00 4.17
316 317 0.106819 ACCCCGCTACTCGTCAGTAT 60.107 55.000 0.00 0.00 34.44 2.12
415 416 0.680061 AAGACTCCGACTTCCACCAC 59.320 55.000 0.00 0.00 0.00 4.16
641 648 1.441729 CCAAATCGCTCCTCCGCTA 59.558 57.895 0.00 0.00 0.00 4.26
776 827 1.460305 AGGCAGTCCACCACTCAGT 60.460 57.895 0.00 0.00 30.26 3.41
777 828 1.004080 CAGGCAGTCCACCACTCAG 60.004 63.158 0.00 0.00 30.26 3.35
778 829 1.766059 ACAGGCAGTCCACCACTCA 60.766 57.895 0.00 0.00 30.26 3.41
779 830 1.302033 CACAGGCAGTCCACCACTC 60.302 63.158 0.00 0.00 30.26 3.51
780 831 1.766059 TCACAGGCAGTCCACCACT 60.766 57.895 0.00 0.00 34.67 4.00
781 832 1.598130 GTCACAGGCAGTCCACCAC 60.598 63.158 0.00 0.00 33.74 4.16
782 833 2.043604 CTGTCACAGGCAGTCCACCA 62.044 60.000 0.00 0.00 33.74 4.17
783 834 1.302033 CTGTCACAGGCAGTCCACC 60.302 63.158 0.00 0.00 33.74 4.61
784 835 0.882042 CACTGTCACAGGCAGTCCAC 60.882 60.000 10.28 0.00 44.43 4.02
785 836 1.048160 TCACTGTCACAGGCAGTCCA 61.048 55.000 10.28 0.00 44.43 4.02
786 837 0.601311 GTCACTGTCACAGGCAGTCC 60.601 60.000 10.28 0.00 44.43 3.85
787 838 0.941463 CGTCACTGTCACAGGCAGTC 60.941 60.000 10.28 0.00 44.43 3.51
788 839 1.068083 CGTCACTGTCACAGGCAGT 59.932 57.895 10.28 0.00 46.86 4.40
789 840 1.665916 CCGTCACTGTCACAGGCAG 60.666 63.158 10.28 0.00 39.67 4.85
790 841 2.421314 CCGTCACTGTCACAGGCA 59.579 61.111 10.28 0.00 35.51 4.75
791 842 3.044305 GCCGTCACTGTCACAGGC 61.044 66.667 10.28 0.00 35.51 4.85
792 843 2.734723 CGCCGTCACTGTCACAGG 60.735 66.667 10.28 0.00 35.51 4.00
793 844 2.734723 CCGCCGTCACTGTCACAG 60.735 66.667 2.22 2.22 37.52 3.66
794 845 4.961511 GCCGCCGTCACTGTCACA 62.962 66.667 0.00 0.00 0.00 3.58
822 873 4.835891 ACCTACCTCCGCTCCCCG 62.836 72.222 0.00 0.00 0.00 5.73
844 897 1.000163 TGTTTCCACGAGAGAGCAGAC 60.000 52.381 0.00 0.00 0.00 3.51
948 1014 1.136891 CATCAGTGTGTATGGCCGAGA 59.863 52.381 0.00 0.00 0.00 4.04
949 1015 1.575244 CATCAGTGTGTATGGCCGAG 58.425 55.000 0.00 0.00 0.00 4.63
950 1016 0.177836 CCATCAGTGTGTATGGCCGA 59.822 55.000 0.00 0.00 36.50 5.54
951 1017 0.177836 TCCATCAGTGTGTATGGCCG 59.822 55.000 0.00 0.00 42.08 6.13
953 1019 1.605710 GCATCCATCAGTGTGTATGGC 59.394 52.381 4.75 0.00 42.08 4.40
958 1024 1.660167 CGATGCATCCATCAGTGTGT 58.340 50.000 20.87 0.00 46.59 3.72
960 1026 0.832626 TCCGATGCATCCATCAGTGT 59.167 50.000 20.87 0.00 46.59 3.55
961 1027 1.804748 CATCCGATGCATCCATCAGTG 59.195 52.381 20.87 4.89 46.59 3.66
962 1028 2.180432 CATCCGATGCATCCATCAGT 57.820 50.000 20.87 0.00 46.59 3.41
975 1041 1.453745 GAAATGGGCTGGCATCCGA 60.454 57.895 2.88 0.00 0.00 4.55
977 1043 3.122850 CGAAATGGGCTGGCATCC 58.877 61.111 2.88 0.00 0.00 3.51
1011 1078 1.406205 GGTAGGGTTCAGAGCTCAAGC 60.406 57.143 17.77 11.76 42.49 4.01
1015 1082 1.142097 GCGGTAGGGTTCAGAGCTC 59.858 63.158 5.27 5.27 0.00 4.09
1090 1175 0.179108 GAGATGCCACCAGACGGTAC 60.179 60.000 0.00 0.00 46.94 3.34
1091 1176 1.327690 GGAGATGCCACCAGACGGTA 61.328 60.000 0.00 0.00 46.94 4.02
1095 1180 0.835941 ATGAGGAGATGCCACCAGAC 59.164 55.000 0.00 0.00 40.02 3.51
1096 1181 1.126488 GATGAGGAGATGCCACCAGA 58.874 55.000 0.00 0.00 40.02 3.86
1097 1182 0.249784 CGATGAGGAGATGCCACCAG 60.250 60.000 0.00 0.00 40.02 4.00
1098 1183 0.687427 TCGATGAGGAGATGCCACCA 60.687 55.000 0.00 0.00 40.02 4.17
1099 1184 0.465705 TTCGATGAGGAGATGCCACC 59.534 55.000 0.00 0.00 40.02 4.61
1100 1185 1.539929 CCTTCGATGAGGAGATGCCAC 60.540 57.143 0.00 0.00 39.25 5.01
1101 1186 0.755079 CCTTCGATGAGGAGATGCCA 59.245 55.000 0.00 0.00 39.25 4.92
1126 1211 3.716006 CAGTTGACGCGGGTGCTG 61.716 66.667 10.96 11.53 39.65 4.41
1127 1212 2.933878 TTTCAGTTGACGCGGGTGCT 62.934 55.000 10.96 2.29 39.65 4.40
1128 1213 1.852067 ATTTCAGTTGACGCGGGTGC 61.852 55.000 10.96 2.32 37.91 5.01
1129 1214 0.165944 GATTTCAGTTGACGCGGGTG 59.834 55.000 10.96 0.00 0.00 4.61
1130 1215 0.953960 GGATTTCAGTTGACGCGGGT 60.954 55.000 12.47 4.12 0.00 5.28
1131 1216 0.953471 TGGATTTCAGTTGACGCGGG 60.953 55.000 12.47 0.00 0.00 6.13
1132 1217 0.443869 CTGGATTTCAGTTGACGCGG 59.556 55.000 12.47 0.00 38.64 6.46
1133 1218 1.391485 CTCTGGATTTCAGTTGACGCG 59.609 52.381 3.53 3.53 43.76 6.01
1134 1219 1.129437 GCTCTGGATTTCAGTTGACGC 59.871 52.381 0.00 0.00 43.76 5.19
1135 1220 2.416747 TGCTCTGGATTTCAGTTGACG 58.583 47.619 0.00 0.00 43.76 4.35
1136 1221 3.190118 CCTTGCTCTGGATTTCAGTTGAC 59.810 47.826 0.00 0.00 43.76 3.18
1141 1226 3.063510 TCACCTTGCTCTGGATTTCAG 57.936 47.619 0.00 0.00 44.68 3.02
1261 1418 3.381908 AGGCTATCTAACTGAAGGTGACG 59.618 47.826 0.00 0.00 0.00 4.35
1264 1421 4.744795 ACAGGCTATCTAACTGAAGGTG 57.255 45.455 0.00 0.00 36.17 4.00
1265 1422 5.540719 GGATACAGGCTATCTAACTGAAGGT 59.459 44.000 0.00 0.00 36.17 3.50
1281 1438 3.452627 ACTGAAGCTAACAGGGATACAGG 59.547 47.826 19.99 0.00 39.38 4.00
1283 1440 5.020795 TGTACTGAAGCTAACAGGGATACA 58.979 41.667 19.99 16.44 39.38 2.29
1284 1441 5.593679 TGTACTGAAGCTAACAGGGATAC 57.406 43.478 19.99 14.75 39.38 2.24
1285 1442 6.136857 AGATGTACTGAAGCTAACAGGGATA 58.863 40.000 19.99 9.81 39.38 2.59
1286 1443 4.965532 AGATGTACTGAAGCTAACAGGGAT 59.034 41.667 19.99 11.20 39.38 3.85
1287 1444 4.353777 AGATGTACTGAAGCTAACAGGGA 58.646 43.478 19.99 8.81 39.38 4.20
1288 1445 4.404073 AGAGATGTACTGAAGCTAACAGGG 59.596 45.833 19.99 3.21 39.38 4.45
1289 1446 5.126222 TCAGAGATGTACTGAAGCTAACAGG 59.874 44.000 19.99 7.06 40.70 4.00
1290 1447 6.201226 TCAGAGATGTACTGAAGCTAACAG 57.799 41.667 16.08 16.08 40.70 3.16
1291 1448 6.782082 ATCAGAGATGTACTGAAGCTAACA 57.218 37.500 0.00 0.00 45.44 2.41
1292 1449 9.405587 GATAATCAGAGATGTACTGAAGCTAAC 57.594 37.037 0.00 0.00 45.44 2.34
1293 1450 9.360901 AGATAATCAGAGATGTACTGAAGCTAA 57.639 33.333 0.00 0.00 45.44 3.09
1294 1451 8.932434 AGATAATCAGAGATGTACTGAAGCTA 57.068 34.615 0.00 0.00 45.44 3.32
1295 1452 7.838079 AGATAATCAGAGATGTACTGAAGCT 57.162 36.000 0.00 0.00 45.44 3.74
1296 1453 9.405587 GTTAGATAATCAGAGATGTACTGAAGC 57.594 37.037 0.00 0.00 45.44 3.86
1308 1465 5.236047 GCTTGTGGCAGTTAGATAATCAGAG 59.764 44.000 0.00 0.00 41.35 3.35
1326 1496 4.639334 AGATACATATGGCTCTGCTTGTG 58.361 43.478 7.80 0.00 0.00 3.33
1338 1510 9.591792 TTGAAGTTCAGAACAGAGATACATATG 57.408 33.333 15.85 0.00 0.00 1.78
1394 1566 9.965902 AGAAACCACAGACTGATAAAATCTAAT 57.034 29.630 10.08 0.00 0.00 1.73
1403 1583 2.838202 GGGGAGAAACCACAGACTGATA 59.162 50.000 10.08 0.00 42.69 2.15
1415 1621 0.250513 AGATCAGCGTGGGGAGAAAC 59.749 55.000 0.00 0.00 0.00 2.78
1440 1646 0.462581 ATGTCTCCAATGCATCGCGT 60.463 50.000 5.77 0.00 0.00 6.01
1449 1655 0.807667 GCGTCGCTCATGTCTCCAAT 60.808 55.000 10.68 0.00 0.00 3.16
1450 1656 1.446099 GCGTCGCTCATGTCTCCAA 60.446 57.895 10.68 0.00 0.00 3.53
1451 1657 2.181777 GCGTCGCTCATGTCTCCA 59.818 61.111 10.68 0.00 0.00 3.86
1452 1658 2.583593 GGCGTCGCTCATGTCTCC 60.584 66.667 18.11 0.00 0.00 3.71
1453 1659 1.227089 ATGGCGTCGCTCATGTCTC 60.227 57.895 18.11 0.00 0.00 3.36
1454 1660 1.520120 CATGGCGTCGCTCATGTCT 60.520 57.895 26.93 6.97 34.75 3.41
1455 1661 2.528743 CCATGGCGTCGCTCATGTC 61.529 63.158 29.88 12.80 36.34 3.06
1456 1662 2.512286 CCATGGCGTCGCTCATGT 60.512 61.111 29.88 10.34 36.34 3.21
1457 1663 1.647545 AAACCATGGCGTCGCTCATG 61.648 55.000 27.69 27.69 37.15 3.07
1458 1664 1.377202 AAACCATGGCGTCGCTCAT 60.377 52.632 18.11 15.31 0.00 2.90
1459 1665 2.031919 AAACCATGGCGTCGCTCA 59.968 55.556 18.11 13.64 0.00 4.26
1460 1666 2.480555 CAAACCATGGCGTCGCTC 59.519 61.111 18.11 7.95 0.00 5.03
1461 1667 3.737172 GCAAACCATGGCGTCGCT 61.737 61.111 18.11 0.00 0.00 4.93
1462 1668 3.737172 AGCAAACCATGGCGTCGC 61.737 61.111 13.04 9.22 34.54 5.19
1463 1669 2.176546 CAGCAAACCATGGCGTCG 59.823 61.111 13.04 0.00 34.54 5.12
1464 1670 2.126346 GCAGCAAACCATGGCGTC 60.126 61.111 13.04 0.00 34.54 5.19
1465 1671 2.911509 TGCAGCAAACCATGGCGT 60.912 55.556 13.04 0.00 34.54 5.68
1466 1672 2.126228 CTGCAGCAAACCATGGCG 60.126 61.111 13.04 1.24 34.54 5.69
1467 1673 1.080298 GACTGCAGCAAACCATGGC 60.080 57.895 15.27 0.00 0.00 4.40
1468 1674 0.242825 CAGACTGCAGCAAACCATGG 59.757 55.000 15.27 11.19 0.00 3.66
1469 1675 1.241165 TCAGACTGCAGCAAACCATG 58.759 50.000 15.27 2.44 0.00 3.66
1470 1676 1.985473 TTCAGACTGCAGCAAACCAT 58.015 45.000 15.27 0.00 0.00 3.55
1471 1677 1.985473 ATTCAGACTGCAGCAAACCA 58.015 45.000 15.27 0.00 0.00 3.67
1472 1678 4.708726 ATTATTCAGACTGCAGCAAACC 57.291 40.909 15.27 0.00 0.00 3.27
1473 1679 7.701445 AGAATATTATTCAGACTGCAGCAAAC 58.299 34.615 15.27 3.07 0.00 2.93
1474 1680 7.772292 AGAGAATATTATTCAGACTGCAGCAAA 59.228 33.333 15.27 3.27 0.00 3.68
1475 1681 7.226128 CAGAGAATATTATTCAGACTGCAGCAA 59.774 37.037 15.27 1.77 0.00 3.91
1476 1682 6.704937 CAGAGAATATTATTCAGACTGCAGCA 59.295 38.462 15.27 0.00 0.00 4.41
1477 1683 6.927936 TCAGAGAATATTATTCAGACTGCAGC 59.072 38.462 15.27 6.85 0.00 5.25
1478 1684 8.883954 TTCAGAGAATATTATTCAGACTGCAG 57.116 34.615 13.48 13.48 0.00 4.41
1479 1685 9.102757 GTTTCAGAGAATATTATTCAGACTGCA 57.897 33.333 16.68 10.84 0.00 4.41
1480 1686 8.555361 GGTTTCAGAGAATATTATTCAGACTGC 58.445 37.037 16.68 10.25 0.00 4.40
1481 1687 9.605275 TGGTTTCAGAGAATATTATTCAGACTG 57.395 33.333 16.68 18.65 0.00 3.51
1484 1690 9.396022 GGTTGGTTTCAGAGAATATTATTCAGA 57.604 33.333 16.68 9.60 0.00 3.27
1485 1691 9.177608 TGGTTGGTTTCAGAGAATATTATTCAG 57.822 33.333 16.68 7.79 0.00 3.02
1486 1692 9.527157 TTGGTTGGTTTCAGAGAATATTATTCA 57.473 29.630 16.68 0.00 0.00 2.57
1491 1697 9.753674 TCTAATTGGTTGGTTTCAGAGAATATT 57.246 29.630 0.00 0.00 0.00 1.28
1492 1698 9.753674 TTCTAATTGGTTGGTTTCAGAGAATAT 57.246 29.630 0.00 0.00 0.00 1.28
1493 1699 9.753674 ATTCTAATTGGTTGGTTTCAGAGAATA 57.246 29.630 0.00 0.00 30.28 1.75
1494 1700 8.655935 ATTCTAATTGGTTGGTTTCAGAGAAT 57.344 30.769 0.00 0.00 0.00 2.40
1495 1701 7.944554 AGATTCTAATTGGTTGGTTTCAGAGAA 59.055 33.333 0.00 0.00 0.00 2.87
1496 1702 7.391554 CAGATTCTAATTGGTTGGTTTCAGAGA 59.608 37.037 0.00 0.00 0.00 3.10
1497 1703 7.391554 TCAGATTCTAATTGGTTGGTTTCAGAG 59.608 37.037 0.00 0.00 0.00 3.35
1498 1704 7.230747 TCAGATTCTAATTGGTTGGTTTCAGA 58.769 34.615 0.00 0.00 0.00 3.27
1499 1705 7.452880 TCAGATTCTAATTGGTTGGTTTCAG 57.547 36.000 0.00 0.00 0.00 3.02
1500 1706 7.831691 TTCAGATTCTAATTGGTTGGTTTCA 57.168 32.000 0.00 0.00 0.00 2.69
1501 1707 7.598869 GGTTTCAGATTCTAATTGGTTGGTTTC 59.401 37.037 0.00 0.00 0.00 2.78
1502 1708 7.290014 AGGTTTCAGATTCTAATTGGTTGGTTT 59.710 33.333 0.00 0.00 0.00 3.27
1503 1709 6.782494 AGGTTTCAGATTCTAATTGGTTGGTT 59.218 34.615 0.00 0.00 0.00 3.67
1504 1710 6.314917 AGGTTTCAGATTCTAATTGGTTGGT 58.685 36.000 0.00 0.00 0.00 3.67
1505 1711 6.434028 TGAGGTTTCAGATTCTAATTGGTTGG 59.566 38.462 0.00 0.00 0.00 3.77
1506 1712 7.452880 TGAGGTTTCAGATTCTAATTGGTTG 57.547 36.000 0.00 0.00 0.00 3.77
1507 1713 7.123247 CCATGAGGTTTCAGATTCTAATTGGTT 59.877 37.037 0.00 0.00 36.61 3.67
1508 1714 6.604795 CCATGAGGTTTCAGATTCTAATTGGT 59.395 38.462 0.00 0.00 36.61 3.67
1509 1715 7.035840 CCATGAGGTTTCAGATTCTAATTGG 57.964 40.000 0.00 0.00 36.61 3.16
1526 1732 2.819595 CGGCGGTTGACCATGAGG 60.820 66.667 0.00 0.00 42.21 3.86
1527 1733 3.499737 GCGGCGGTTGACCATGAG 61.500 66.667 9.78 0.00 35.14 2.90
1528 1734 4.015406 AGCGGCGGTTGACCATGA 62.015 61.111 5.44 0.00 35.14 3.07
1529 1735 3.803082 CAGCGGCGGTTGACCATG 61.803 66.667 9.73 0.00 35.14 3.66
1539 1745 3.485431 CTTCAGTCTGCAGCGGCG 61.485 66.667 9.47 0.51 45.35 6.46
1540 1746 2.047844 TCTTCAGTCTGCAGCGGC 60.048 61.111 9.47 0.31 41.68 6.53
1541 1747 1.005748 TGTCTTCAGTCTGCAGCGG 60.006 57.895 9.47 5.39 0.00 5.52
1542 1748 1.013005 CCTGTCTTCAGTCTGCAGCG 61.013 60.000 9.47 0.00 39.82 5.18
1543 1749 0.673022 CCCTGTCTTCAGTCTGCAGC 60.673 60.000 9.47 4.26 39.82 5.25
1544 1750 0.036577 CCCCTGTCTTCAGTCTGCAG 60.037 60.000 7.63 7.63 39.82 4.41
1545 1751 2.061220 CCCCTGTCTTCAGTCTGCA 58.939 57.895 0.00 0.00 39.82 4.41
1548 1754 1.484444 GGTGCCCCTGTCTTCAGTCT 61.484 60.000 0.00 0.00 39.82 3.24
1608 1827 0.445436 CACGAGGTTTCAGATGCTGC 59.555 55.000 0.00 0.00 0.00 5.25
1612 1831 3.393800 ACTGAACACGAGGTTTCAGATG 58.606 45.455 16.37 0.00 40.63 2.90
1686 1906 9.869844 GACATTTATCGATCCAACAAAATAGAG 57.130 33.333 0.00 0.00 0.00 2.43
1713 1934 7.775093 TGCACAGCTATGGTAGAATTAGAAATT 59.225 33.333 0.00 0.00 0.00 1.82
1749 1970 7.284919 AGAAAAGTACCCCATAAAACAACTG 57.715 36.000 0.00 0.00 0.00 3.16
1882 2654 3.290308 AGATATCCAACTAGCGCTTCG 57.710 47.619 18.68 10.39 0.00 3.79
1888 2660 7.049799 AGTTCAGAGAAGATATCCAACTAGC 57.950 40.000 0.00 0.00 0.00 3.42
1895 2667 6.204495 GGCAATGAAGTTCAGAGAAGATATCC 59.796 42.308 11.91 0.00 0.00 2.59
1899 2671 5.176741 AGGCAATGAAGTTCAGAGAAGAT 57.823 39.130 11.91 0.00 0.00 2.40
1996 2782 1.077285 TATGTCGGGGAGTCAGCGA 60.077 57.895 0.00 0.00 0.00 4.93
2022 2808 1.308998 CACAGCGAACAAAGGAAGGT 58.691 50.000 0.00 0.00 0.00 3.50
2100 2886 2.162681 ACCAGGAAGCGGAGAAATTTG 58.837 47.619 0.00 0.00 0.00 2.32
2103 2889 1.351017 TCAACCAGGAAGCGGAGAAAT 59.649 47.619 0.00 0.00 0.00 2.17
2460 3645 1.603802 ACGATGTTTGGCTCAACAGTG 59.396 47.619 8.47 0.00 0.00 3.66
2543 3762 6.687105 GCATTAGACCTTATAAAACAGTTGCG 59.313 38.462 0.00 0.00 0.00 4.85
2551 3771 6.062095 GGCCTCTGCATTAGACCTTATAAAA 58.938 40.000 0.00 0.00 40.13 1.52
2629 3849 2.095161 AGTCTCAACATCCGAACGACTC 60.095 50.000 0.00 0.00 0.00 3.36
2633 3853 2.347697 TGAGTCTCAACATCCGAACG 57.652 50.000 0.00 0.00 0.00 3.95
2634 3854 5.038033 GTCTATGAGTCTCAACATCCGAAC 58.962 45.833 6.64 0.00 0.00 3.95
2638 3858 7.081349 CGATTAGTCTATGAGTCTCAACATCC 58.919 42.308 6.64 0.00 0.00 3.51
2639 3859 7.589587 CACGATTAGTCTATGAGTCTCAACATC 59.410 40.741 6.64 0.97 0.00 3.06
2673 3903 5.631512 GTCTATGAGTCACAACTTCAGTGTC 59.368 44.000 0.00 0.00 38.16 3.67
2679 3909 6.092396 TCGACTAGTCTATGAGTCACAACTTC 59.908 42.308 20.34 0.00 41.87 3.01
2686 3916 4.870991 CAGTGTCGACTAGTCTATGAGTCA 59.129 45.833 20.34 6.02 41.87 3.41
2689 3919 5.583061 ACTTCAGTGTCGACTAGTCTATGAG 59.417 44.000 20.34 4.93 0.00 2.90
2785 4015 3.788142 ACCCACTCATTACTTCCATGGAT 59.212 43.478 17.06 3.82 0.00 3.41
2970 5728 6.627953 CGGAGGGCAGTATTTCAAATTTTCAT 60.628 38.462 0.00 0.00 0.00 2.57
3077 5859 8.311109 AGAGAGAGGAAAATTTAGAGTGAACTC 58.689 37.037 2.06 2.06 43.17 3.01
3145 5929 4.214332 CCCTTCTTTGAGCTAACAAGTGAC 59.786 45.833 0.00 0.00 0.00 3.67
3156 5940 1.271926 TGCTTACCCCCTTCTTTGAGC 60.272 52.381 0.00 0.00 0.00 4.26
3183 5967 0.980423 GACCAAGTGGAGAGAAGGCT 59.020 55.000 3.83 0.00 38.94 4.58
3204 5988 2.885266 CAAGGAATCAGGAGCATGATGG 59.115 50.000 0.00 0.00 39.84 3.51
3401 6185 3.231736 AACCCAGACGACGGTGCT 61.232 61.111 0.00 0.00 30.96 4.40
3427 6211 2.562738 AGCATCGGTGATCGGATTATCA 59.437 45.455 0.00 0.00 39.77 2.15
3475 6259 3.477530 GGACAACACAAGGCTAGAGTTT 58.522 45.455 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.