Multiple sequence alignment - TraesCS3D01G518100

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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 TraesCS3D01G518100 chr3D 100.000 2393 0 0 1 2393 600664541 600666933 0.000000e+00 4420.0
1 TraesCS3D01G518100 chr3D 82.494 794 52 43 863 1606 600655078 600655834 1.220000e-172 616.0
2 TraesCS3D01G518100 chr3D 83.256 215 24 9 429 633 600654682 600654894 1.130000e-43 187.0
3 TraesCS3D01G518100 chr3D 79.227 207 17 9 658 854 600654964 600655154 1.160000e-23 121.0
4 TraesCS3D01G518100 chr3D 97.619 42 0 1 1619 1660 600666123 600666163 1.190000e-08 71.3
5 TraesCS3D01G518100 chr3D 87.500 56 4 3 108 161 550538374 550538320 7.140000e-06 62.1
6 TraesCS3D01G518100 chr5D 95.726 585 7 3 1827 2393 6376278 6376862 0.000000e+00 926.0
7 TraesCS3D01G518100 chr3A 86.364 836 47 17 1 828 730091173 730091949 0.000000e+00 850.0
8 TraesCS3D01G518100 chr3A 86.305 774 57 22 863 1623 730032157 730031420 0.000000e+00 797.0
9 TraesCS3D01G518100 chr3A 86.305 774 57 22 863 1623 730442750 730443487 0.000000e+00 797.0
10 TraesCS3D01G518100 chr3A 86.305 774 57 22 863 1623 730590956 730591693 0.000000e+00 797.0
11 TraesCS3D01G518100 chr3A 86.176 774 58 24 863 1623 730463175 730463912 0.000000e+00 791.0
12 TraesCS3D01G518100 chr3A 86.047 774 59 22 863 1623 730012313 730011576 0.000000e+00 785.0
13 TraesCS3D01G518100 chr3A 85.990 778 57 24 863 1623 730091895 730092637 0.000000e+00 785.0
14 TraesCS3D01G518100 chr3A 92.197 487 18 9 349 828 730590537 730591010 0.000000e+00 671.0
15 TraesCS3D01G518100 chr3A 91.992 487 19 9 349 828 730012732 730012259 0.000000e+00 665.0
16 TraesCS3D01G518100 chr3A 91.992 487 19 9 349 828 730032576 730032103 0.000000e+00 665.0
17 TraesCS3D01G518100 chr3A 91.992 487 19 9 349 828 730462756 730463229 0.000000e+00 665.0
18 TraesCS3D01G518100 chr3A 90.144 487 19 11 349 828 730442340 730442804 7.320000e-170 606.0
19 TraesCS3D01G518100 chr3A 85.824 522 45 16 1021 1516 730085774 730086292 5.860000e-146 527.0
20 TraesCS3D01G518100 chr3A 93.696 349 14 3 349 690 730511742 730512089 1.270000e-142 516.0
21 TraesCS3D01G518100 chr3A 88.444 225 19 5 1 223 730441707 730441926 5.070000e-67 265.0
22 TraesCS3D01G518100 chr3A 88.444 225 19 5 1 223 730589904 730590123 5.070000e-67 265.0
23 TraesCS3D01G518100 chr3A 88.000 225 20 5 1 223 730013364 730013145 2.360000e-65 259.0
24 TraesCS3D01G518100 chr3A 88.000 225 20 5 1 223 730033209 730032990 2.360000e-65 259.0
25 TraesCS3D01G518100 chr3A 88.000 225 20 5 1 223 730511109 730511328 2.360000e-65 259.0
26 TraesCS3D01G518100 chr3A 87.556 225 21 5 1 223 730462123 730462342 1.100000e-63 254.0
27 TraesCS3D01G518100 chr3A 88.764 178 10 6 1619 1788 730092597 730092772 2.410000e-50 209.0
28 TraesCS3D01G518100 chr3A 87.640 178 12 6 1619 1788 730463872 730464047 5.220000e-47 198.0
29 TraesCS3D01G518100 chr3A 87.151 179 12 6 1619 1788 730031460 730031284 2.430000e-45 193.0
30 TraesCS3D01G518100 chr3A 87.151 179 12 6 1619 1788 730443447 730443623 2.430000e-45 193.0
31 TraesCS3D01G518100 chr3A 86.592 179 13 6 1619 1788 730011616 730011440 1.130000e-43 187.0
32 TraesCS3D01G518100 chr3A 86.592 179 13 6 1619 1788 730591653 730591829 1.130000e-43 187.0
33 TraesCS3D01G518100 chr3A 92.982 57 0 2 1554 1606 730086300 730086356 1.970000e-11 80.5
34 TraesCS3D01G518100 chrUn 85.895 631 58 14 863 1480 358203082 358203694 0.000000e+00 643.0
35 TraesCS3D01G518100 chrUn 90.144 487 19 11 349 828 358202672 358203136 7.320000e-170 606.0
36 TraesCS3D01G518100 chrUn 88.444 225 19 5 1 223 358202039 358202258 5.070000e-67 265.0
37 TraesCS3D01G518100 chr3B 84.932 657 59 21 863 1492 697683124 697683767 1.560000e-176 628.0
38 TraesCS3D01G518100 chr3B 84.789 664 46 23 868 1492 808019582 808020229 1.220000e-172 616.0
39 TraesCS3D01G518100 chr3B 81.731 208 18 12 659 854 808019452 808019651 3.180000e-34 156.0
40 TraesCS3D01G518100 chr3B 92.727 55 1 1 1555 1606 697706343 697706397 2.550000e-10 76.8
41 TraesCS3D01G518100 chr4A 89.286 504 36 6 1836 2321 674905717 674905214 1.220000e-172 616.0
42 TraesCS3D01G518100 chr7B 89.474 76 4 4 1823 1897 685665740 685665668 2.530000e-15 93.5
43 TraesCS3D01G518100 chr7B 88.732 71 4 4 1825 1894 498876597 498876664 1.520000e-12 84.2
44 TraesCS3D01G518100 chr1B 92.308 65 2 3 1829 1893 645352755 645352694 3.280000e-14 89.8
45 TraesCS3D01G518100 chr1B 89.552 67 3 4 1828 1891 7336047 7335982 5.480000e-12 82.4
46 TraesCS3D01G518100 chr6D 92.188 64 2 3 1829 1889 16629415 16629352 1.180000e-13 87.9
47 TraesCS3D01G518100 chr1D 90.909 66 3 3 1827 1889 227642031 227641966 4.240000e-13 86.1
48 TraesCS3D01G518100 chr5B 91.803 61 3 2 1828 1886 17711820 17711760 1.520000e-12 84.2
49 TraesCS3D01G518100 chr5A 87.013 77 7 3 1828 1904 424240339 424240266 1.520000e-12 84.2
50 TraesCS3D01G518100 chr2B 80.342 117 16 7 163 275 704755588 704755475 5.480000e-12 82.4


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 TraesCS3D01G518100 chr3D 600664541 600666933 2392 False 2245.650000 4420 98.809500 1 2393 2 chr3D.!!$F2 2392
1 TraesCS3D01G518100 chr3D 600654682 600655834 1152 False 308.000000 616 81.659000 429 1606 3 chr3D.!!$F1 1177
2 TraesCS3D01G518100 chr5D 6376278 6376862 584 False 926.000000 926 95.726000 1827 2393 1 chr5D.!!$F1 566
3 TraesCS3D01G518100 chr3A 730091173 730092772 1599 False 614.666667 850 87.039333 1 1788 3 chr3A.!!$F2 1787
4 TraesCS3D01G518100 chr3A 730589904 730591829 1925 False 480.000000 797 88.384500 1 1788 4 chr3A.!!$F6 1787
5 TraesCS3D01G518100 chr3A 730031284 730033209 1925 True 478.500000 797 88.362000 1 1788 4 chr3A.!!$R2 1787
6 TraesCS3D01G518100 chr3A 730462123 730464047 1924 False 477.000000 791 88.341000 1 1788 4 chr3A.!!$F4 1787
7 TraesCS3D01G518100 chr3A 730011440 730013364 1924 True 474.000000 785 88.157750 1 1788 4 chr3A.!!$R1 1787
8 TraesCS3D01G518100 chr3A 730441707 730443623 1916 False 465.250000 797 88.011000 1 1788 4 chr3A.!!$F3 1787
9 TraesCS3D01G518100 chr3A 730511109 730512089 980 False 387.500000 516 90.848000 1 690 2 chr3A.!!$F5 689
10 TraesCS3D01G518100 chr3A 730085774 730086356 582 False 303.750000 527 89.403000 1021 1606 2 chr3A.!!$F1 585
11 TraesCS3D01G518100 chrUn 358202039 358203694 1655 False 504.666667 643 88.161000 1 1480 3 chrUn.!!$F1 1479
12 TraesCS3D01G518100 chr3B 697683124 697683767 643 False 628.000000 628 84.932000 863 1492 1 chr3B.!!$F1 629
13 TraesCS3D01G518100 chr3B 808019452 808020229 777 False 386.000000 616 83.260000 659 1492 2 chr3B.!!$F3 833
14 TraesCS3D01G518100 chr4A 674905214 674905717 503 True 616.000000 616 89.286000 1836 2321 1 chr4A.!!$R1 485

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
329 651 0.027848 GAGCTAGCGACACGTAGGTC 59.972 60.0 9.55 0.0 36.81 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 2111 0.537188 GAGGAGATGTGCCCGAAAGA 59.463 55.0 0.0 0.0 0.0 2.52 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
47 48 1.106944 ACAGGTTGGTTCGCCTTTGG 61.107 55.000 0.00 0.00 38.36 3.28
60 61 2.483876 GCCTTTGGCTCCTTTTTGTTC 58.516 47.619 0.73 0.00 46.69 3.18
61 62 2.103094 GCCTTTGGCTCCTTTTTGTTCT 59.897 45.455 0.73 0.00 46.69 3.01
68 69 4.706476 TGGCTCCTTTTTGTTCTATGGATG 59.294 41.667 0.00 0.00 0.00 3.51
86 87 9.639563 CTATGGATGGATACTGTAGATGATACT 57.360 37.037 0.00 0.00 37.61 2.12
99 100 7.455891 TGTAGATGATACTTCAGGTACGGATA 58.544 38.462 0.00 0.00 34.73 2.59
196 200 8.836413 TCTTCGTTTCAAAATAAGTGTCTCAAT 58.164 29.630 0.00 0.00 0.00 2.57
326 648 0.586748 CACGAGCTAGCGACACGTAG 60.587 60.000 22.97 16.44 35.78 3.51
327 649 1.011019 CGAGCTAGCGACACGTAGG 60.011 63.158 9.55 0.00 0.00 3.18
328 650 1.703438 CGAGCTAGCGACACGTAGGT 61.703 60.000 9.55 0.00 0.00 3.08
329 651 0.027848 GAGCTAGCGACACGTAGGTC 59.972 60.000 9.55 0.00 36.81 3.85
330 652 0.392729 AGCTAGCGACACGTAGGTCT 60.393 55.000 9.55 0.00 35.63 3.85
331 653 0.450983 GCTAGCGACACGTAGGTCTT 59.549 55.000 0.00 0.00 35.63 3.01
332 654 1.794437 GCTAGCGACACGTAGGTCTTG 60.794 57.143 0.00 0.00 35.63 3.02
333 655 0.169672 TAGCGACACGTAGGTCTTGC 59.830 55.000 4.72 2.09 35.63 4.01
334 656 1.080705 GCGACACGTAGGTCTTGCT 60.081 57.895 4.72 0.00 35.63 3.91
335 657 0.666577 GCGACACGTAGGTCTTGCTT 60.667 55.000 4.72 0.00 35.63 3.91
336 658 1.779569 CGACACGTAGGTCTTGCTTT 58.220 50.000 4.72 0.00 35.63 3.51
337 659 2.132762 CGACACGTAGGTCTTGCTTTT 58.867 47.619 4.72 0.00 35.63 2.27
338 660 2.542595 CGACACGTAGGTCTTGCTTTTT 59.457 45.455 4.72 0.00 35.63 1.94
376 698 6.760161 ACGTCTTGCTTAGTTACAAGTTAC 57.240 37.500 0.00 0.00 43.05 2.50
523 848 6.650807 TCTTCGACTAGTTTCCGTTTCTACTA 59.349 38.462 0.00 0.00 0.00 1.82
540 871 2.776312 CTAGAAATCTAGCCGCGTGA 57.224 50.000 4.92 0.00 39.43 4.35
684 1064 1.471684 GAGAACGCGTAAGAGGAAGGA 59.528 52.381 14.46 0.00 43.56 3.36
697 1081 1.135315 GAAGGAGCGCACGTACGTA 59.865 57.895 22.34 0.00 34.88 3.57
747 1146 7.475137 ACACAGATCCTCCTATATAAAGAGC 57.525 40.000 4.56 0.00 0.00 4.09
788 1191 5.241285 TCAAGCACATATCACAAACACACAT 59.759 36.000 0.00 0.00 0.00 3.21
789 1192 6.429385 TCAAGCACATATCACAAACACACATA 59.571 34.615 0.00 0.00 0.00 2.29
790 1193 6.182039 AGCACATATCACAAACACACATAC 57.818 37.500 0.00 0.00 0.00 2.39
791 1194 5.704978 AGCACATATCACAAACACACATACA 59.295 36.000 0.00 0.00 0.00 2.29
792 1195 6.023435 GCACATATCACAAACACACATACAG 58.977 40.000 0.00 0.00 0.00 2.74
793 1196 6.348458 GCACATATCACAAACACACATACAGT 60.348 38.462 0.00 0.00 0.00 3.55
794 1197 7.236474 CACATATCACAAACACACATACAGTC 58.764 38.462 0.00 0.00 0.00 3.51
795 1198 6.934083 ACATATCACAAACACACATACAGTCA 59.066 34.615 0.00 0.00 0.00 3.41
796 1199 7.607607 ACATATCACAAACACACATACAGTCAT 59.392 33.333 0.00 0.00 0.00 3.06
797 1200 9.097257 CATATCACAAACACACATACAGTCATA 57.903 33.333 0.00 0.00 0.00 2.15
798 1201 6.779115 TCACAAACACACATACAGTCATAC 57.221 37.500 0.00 0.00 0.00 2.39
799 1202 6.284459 TCACAAACACACATACAGTCATACA 58.716 36.000 0.00 0.00 0.00 2.29
800 1203 6.201997 TCACAAACACACATACAGTCATACAC 59.798 38.462 0.00 0.00 0.00 2.90
801 1204 5.176774 ACAAACACACATACAGTCATACACG 59.823 40.000 0.00 0.00 0.00 4.49
802 1205 3.845178 ACACACATACAGTCATACACGG 58.155 45.455 0.00 0.00 0.00 4.94
803 1206 3.508402 ACACACATACAGTCATACACGGA 59.492 43.478 0.00 0.00 0.00 4.69
804 1207 4.159693 ACACACATACAGTCATACACGGAT 59.840 41.667 0.00 0.00 0.00 4.18
805 1208 4.740205 CACACATACAGTCATACACGGATC 59.260 45.833 0.00 0.00 0.00 3.36
806 1209 4.202121 ACACATACAGTCATACACGGATCC 60.202 45.833 0.00 0.00 0.00 3.36
807 1210 4.038042 CACATACAGTCATACACGGATCCT 59.962 45.833 10.75 0.00 0.00 3.24
808 1211 4.278669 ACATACAGTCATACACGGATCCTC 59.721 45.833 10.75 0.00 0.00 3.71
809 1212 2.735151 ACAGTCATACACGGATCCTCA 58.265 47.619 10.75 0.00 0.00 3.86
810 1213 3.300388 ACAGTCATACACGGATCCTCAT 58.700 45.455 10.75 0.00 0.00 2.90
811 1214 3.319405 ACAGTCATACACGGATCCTCATC 59.681 47.826 10.75 0.00 0.00 2.92
812 1215 2.894126 AGTCATACACGGATCCTCATCC 59.106 50.000 10.75 0.00 45.04 3.51
813 1216 2.894126 GTCATACACGGATCCTCATCCT 59.106 50.000 10.75 0.00 46.20 3.24
814 1217 3.057174 GTCATACACGGATCCTCATCCTC 60.057 52.174 10.75 0.00 46.20 3.71
815 1218 3.161067 CATACACGGATCCTCATCCTCT 58.839 50.000 10.75 0.00 46.20 3.69
816 1219 4.042934 TCATACACGGATCCTCATCCTCTA 59.957 45.833 10.75 0.00 46.20 2.43
817 1220 3.534357 ACACGGATCCTCATCCTCTAT 57.466 47.619 10.75 0.00 46.20 1.98
818 1221 3.850752 ACACGGATCCTCATCCTCTATT 58.149 45.455 10.75 0.00 46.20 1.73
819 1222 3.829601 ACACGGATCCTCATCCTCTATTC 59.170 47.826 10.75 0.00 46.20 1.75
820 1223 3.194542 CACGGATCCTCATCCTCTATTCC 59.805 52.174 10.75 0.00 46.20 3.01
821 1224 3.076785 ACGGATCCTCATCCTCTATTCCT 59.923 47.826 10.75 0.00 46.20 3.36
822 1225 3.699038 CGGATCCTCATCCTCTATTCCTC 59.301 52.174 10.75 0.00 46.20 3.71
823 1226 4.030216 GGATCCTCATCCTCTATTCCTCC 58.970 52.174 3.84 0.00 45.06 4.30
824 1227 4.264804 GGATCCTCATCCTCTATTCCTCCT 60.265 50.000 3.84 0.00 45.06 3.69
825 1228 4.125124 TCCTCATCCTCTATTCCTCCTG 57.875 50.000 0.00 0.00 0.00 3.86
826 1229 3.469006 TCCTCATCCTCTATTCCTCCTGT 59.531 47.826 0.00 0.00 0.00 4.00
827 1230 4.670247 TCCTCATCCTCTATTCCTCCTGTA 59.330 45.833 0.00 0.00 0.00 2.74
828 1231 5.136220 TCCTCATCCTCTATTCCTCCTGTAA 59.864 44.000 0.00 0.00 0.00 2.41
829 1232 5.480073 CCTCATCCTCTATTCCTCCTGTAAG 59.520 48.000 0.00 0.00 0.00 2.34
830 1233 6.031964 TCATCCTCTATTCCTCCTGTAAGT 57.968 41.667 0.00 0.00 0.00 2.24
831 1234 7.162973 TCATCCTCTATTCCTCCTGTAAGTA 57.837 40.000 0.00 0.00 0.00 2.24
832 1235 7.770662 TCATCCTCTATTCCTCCTGTAAGTAT 58.229 38.462 0.00 0.00 0.00 2.12
833 1236 8.901841 TCATCCTCTATTCCTCCTGTAAGTATA 58.098 37.037 0.00 0.00 0.00 1.47
834 1237 8.962679 CATCCTCTATTCCTCCTGTAAGTATAC 58.037 40.741 0.00 0.00 0.00 1.47
835 1238 7.468496 TCCTCTATTCCTCCTGTAAGTATACC 58.532 42.308 0.00 0.00 0.00 2.73
836 1239 6.664384 CCTCTATTCCTCCTGTAAGTATACCC 59.336 46.154 0.00 0.00 0.00 3.69
837 1240 7.170554 TCTATTCCTCCTGTAAGTATACCCA 57.829 40.000 0.00 0.00 0.00 4.51
838 1241 7.776745 TCTATTCCTCCTGTAAGTATACCCAT 58.223 38.462 0.00 0.00 0.00 4.00
839 1242 6.936968 ATTCCTCCTGTAAGTATACCCATC 57.063 41.667 0.00 0.00 0.00 3.51
840 1243 4.404640 TCCTCCTGTAAGTATACCCATCG 58.595 47.826 0.00 0.00 0.00 3.84
841 1244 4.105217 TCCTCCTGTAAGTATACCCATCGA 59.895 45.833 0.00 0.00 0.00 3.59
842 1245 5.017490 CCTCCTGTAAGTATACCCATCGAT 58.983 45.833 0.00 0.00 0.00 3.59
843 1246 5.125739 CCTCCTGTAAGTATACCCATCGATC 59.874 48.000 0.00 0.00 0.00 3.69
844 1247 5.637127 TCCTGTAAGTATACCCATCGATCA 58.363 41.667 0.00 0.00 0.00 2.92
845 1248 5.475909 TCCTGTAAGTATACCCATCGATCAC 59.524 44.000 0.00 0.00 0.00 3.06
846 1249 5.243060 CCTGTAAGTATACCCATCGATCACA 59.757 44.000 0.00 0.00 0.00 3.58
847 1250 6.080648 TGTAAGTATACCCATCGATCACAC 57.919 41.667 0.00 0.00 0.00 3.82
848 1251 5.595133 TGTAAGTATACCCATCGATCACACA 59.405 40.000 0.00 0.00 0.00 3.72
849 1252 5.607939 AAGTATACCCATCGATCACACAA 57.392 39.130 0.00 0.00 0.00 3.33
850 1253 5.201713 AGTATACCCATCGATCACACAAG 57.798 43.478 0.00 0.00 0.00 3.16
851 1254 2.979814 TACCCATCGATCACACAAGG 57.020 50.000 0.00 0.00 0.00 3.61
852 1255 0.392998 ACCCATCGATCACACAAGGC 60.393 55.000 0.00 0.00 0.00 4.35
853 1256 0.392863 CCCATCGATCACACAAGGCA 60.393 55.000 0.00 0.00 0.00 4.75
854 1257 0.729116 CCATCGATCACACAAGGCAC 59.271 55.000 0.00 0.00 0.00 5.01
855 1258 1.441738 CATCGATCACACAAGGCACA 58.558 50.000 0.00 0.00 0.00 4.57
856 1259 1.805943 CATCGATCACACAAGGCACAA 59.194 47.619 0.00 0.00 0.00 3.33
857 1260 1.511850 TCGATCACACAAGGCACAAG 58.488 50.000 0.00 0.00 0.00 3.16
858 1261 1.202639 TCGATCACACAAGGCACAAGT 60.203 47.619 0.00 0.00 0.00 3.16
859 1262 2.036604 TCGATCACACAAGGCACAAGTA 59.963 45.455 0.00 0.00 0.00 2.24
860 1263 2.157668 CGATCACACAAGGCACAAGTAC 59.842 50.000 0.00 0.00 0.00 2.73
861 1264 2.700722 TCACACAAGGCACAAGTACA 57.299 45.000 0.00 0.00 0.00 2.90
862 1265 2.285083 TCACACAAGGCACAAGTACAC 58.715 47.619 0.00 0.00 0.00 2.90
863 1266 2.013400 CACACAAGGCACAAGTACACA 58.987 47.619 0.00 0.00 0.00 3.72
864 1267 2.421775 CACACAAGGCACAAGTACACAA 59.578 45.455 0.00 0.00 0.00 3.33
865 1268 2.682856 ACACAAGGCACAAGTACACAAG 59.317 45.455 0.00 0.00 0.00 3.16
866 1269 2.033299 CACAAGGCACAAGTACACAAGG 59.967 50.000 0.00 0.00 0.00 3.61
879 1282 1.824230 ACACAAGGCACAAACACACAT 59.176 42.857 0.00 0.00 0.00 3.21
880 1283 3.020274 ACACAAGGCACAAACACACATA 58.980 40.909 0.00 0.00 0.00 2.29
881 1284 3.181491 ACACAAGGCACAAACACACATAC 60.181 43.478 0.00 0.00 0.00 2.39
882 1285 3.020274 ACAAGGCACAAACACACATACA 58.980 40.909 0.00 0.00 0.00 2.29
883 1286 3.066621 ACAAGGCACAAACACACATACAG 59.933 43.478 0.00 0.00 0.00 2.74
884 1287 2.930950 AGGCACAAACACACATACAGT 58.069 42.857 0.00 0.00 0.00 3.55
885 1288 2.878406 AGGCACAAACACACATACAGTC 59.122 45.455 0.00 0.00 0.00 3.51
886 1289 2.616376 GGCACAAACACACATACAGTCA 59.384 45.455 0.00 0.00 0.00 3.41
924 1329 0.178068 CCATTCCTCCTGTACCCGTG 59.822 60.000 0.00 0.00 0.00 4.94
927 1332 0.901580 TTCCTCCTGTACCCGTGGAC 60.902 60.000 0.00 0.00 0.00 4.02
928 1333 1.305046 CCTCCTGTACCCGTGGACT 60.305 63.158 0.00 0.00 0.00 3.85
1142 1554 0.177141 GGAGCATACGCAAGGGTACA 59.823 55.000 0.00 0.00 46.39 2.90
1160 1572 2.983592 CCCCAAACACCTCACGCC 60.984 66.667 0.00 0.00 0.00 5.68
1163 1575 1.515521 CCCAAACACCTCACGCCTTC 61.516 60.000 0.00 0.00 0.00 3.46
1170 1587 2.009774 CACCTCACGCCTTCCTTATTG 58.990 52.381 0.00 0.00 0.00 1.90
1181 1612 4.451435 GCCTTCCTTATTGCCTACGTAATC 59.549 45.833 0.00 0.00 0.00 1.75
1183 1614 5.927115 CCTTCCTTATTGCCTACGTAATCTC 59.073 44.000 0.00 0.00 0.00 2.75
1185 1616 5.839621 TCCTTATTGCCTACGTAATCTCAC 58.160 41.667 0.00 0.00 0.00 3.51
1200 1648 8.043570 CGTAATCTCACGTAATGGTTAACTAC 57.956 38.462 5.42 0.00 37.16 2.73
1302 1756 2.184322 GAGAAGATCGCCGCCACA 59.816 61.111 0.00 0.00 0.00 4.17
1361 1815 2.157738 CCACAAGAAGAAAGAGGCCAG 58.842 52.381 5.01 0.00 0.00 4.85
1394 1854 4.720902 TGCCCACCGCCACTGATG 62.721 66.667 0.00 0.00 36.24 3.07
1397 1857 2.438975 CCACCGCCACTGATGCAT 60.439 61.111 0.00 0.00 0.00 3.96
1468 1942 2.032030 CGGCCGGTTACATTCATTCATC 60.032 50.000 20.10 0.00 0.00 2.92
1475 1949 5.063438 CGGTTACATTCATTCATCTCGTTGT 59.937 40.000 0.00 0.00 0.00 3.32
1476 1950 6.478588 GGTTACATTCATTCATCTCGTTGTC 58.521 40.000 0.00 0.00 0.00 3.18
1477 1951 6.313905 GGTTACATTCATTCATCTCGTTGTCT 59.686 38.462 0.00 0.00 0.00 3.41
1478 1952 7.148407 GGTTACATTCATTCATCTCGTTGTCTT 60.148 37.037 0.00 0.00 0.00 3.01
1479 1953 6.174451 ACATTCATTCATCTCGTTGTCTTG 57.826 37.500 0.00 0.00 0.00 3.02
1480 1954 5.702670 ACATTCATTCATCTCGTTGTCTTGT 59.297 36.000 0.00 0.00 0.00 3.16
1481 1955 6.205464 ACATTCATTCATCTCGTTGTCTTGTT 59.795 34.615 0.00 0.00 0.00 2.83
1482 1956 5.845985 TCATTCATCTCGTTGTCTTGTTC 57.154 39.130 0.00 0.00 0.00 3.18
1483 1957 4.690748 TCATTCATCTCGTTGTCTTGTTCC 59.309 41.667 0.00 0.00 0.00 3.62
1484 1958 3.744238 TCATCTCGTTGTCTTGTTCCA 57.256 42.857 0.00 0.00 0.00 3.53
1485 1959 4.271696 TCATCTCGTTGTCTTGTTCCAT 57.728 40.909 0.00 0.00 0.00 3.41
1486 1960 5.400066 TCATCTCGTTGTCTTGTTCCATA 57.600 39.130 0.00 0.00 0.00 2.74
1487 1961 5.410924 TCATCTCGTTGTCTTGTTCCATAG 58.589 41.667 0.00 0.00 0.00 2.23
1488 1962 4.866508 TCTCGTTGTCTTGTTCCATAGT 57.133 40.909 0.00 0.00 0.00 2.12
1489 1963 5.970317 TCTCGTTGTCTTGTTCCATAGTA 57.030 39.130 0.00 0.00 0.00 1.82
1490 1964 5.706916 TCTCGTTGTCTTGTTCCATAGTAC 58.293 41.667 0.00 0.00 0.00 2.73
1491 1965 5.475909 TCTCGTTGTCTTGTTCCATAGTACT 59.524 40.000 0.00 0.00 0.00 2.73
1492 1966 6.656270 TCTCGTTGTCTTGTTCCATAGTACTA 59.344 38.462 4.77 4.77 0.00 1.82
1598 2093 1.747355 CATGTTTGGGCACATCTCCTC 59.253 52.381 0.00 0.00 35.03 3.71
1599 2094 1.067295 TGTTTGGGCACATCTCCTCT 58.933 50.000 0.00 0.00 0.00 3.69
1600 2095 2.265367 TGTTTGGGCACATCTCCTCTA 58.735 47.619 0.00 0.00 0.00 2.43
1601 2096 2.642311 TGTTTGGGCACATCTCCTCTAA 59.358 45.455 0.00 0.00 0.00 2.10
1602 2097 3.266772 TGTTTGGGCACATCTCCTCTAAT 59.733 43.478 0.00 0.00 0.00 1.73
1603 2098 4.473196 TGTTTGGGCACATCTCCTCTAATA 59.527 41.667 0.00 0.00 0.00 0.98
1604 2099 5.045213 TGTTTGGGCACATCTCCTCTAATAA 60.045 40.000 0.00 0.00 0.00 1.40
1605 2100 5.912149 TTGGGCACATCTCCTCTAATAAT 57.088 39.130 0.00 0.00 0.00 1.28
1606 2101 5.489792 TGGGCACATCTCCTCTAATAATC 57.510 43.478 0.00 0.00 0.00 1.75
1607 2102 5.158141 TGGGCACATCTCCTCTAATAATCT 58.842 41.667 0.00 0.00 0.00 2.40
1608 2103 6.322931 TGGGCACATCTCCTCTAATAATCTA 58.677 40.000 0.00 0.00 0.00 1.98
1609 2104 6.787458 TGGGCACATCTCCTCTAATAATCTAA 59.213 38.462 0.00 0.00 0.00 2.10
1610 2105 7.292356 TGGGCACATCTCCTCTAATAATCTAAA 59.708 37.037 0.00 0.00 0.00 1.85
1611 2106 8.325046 GGGCACATCTCCTCTAATAATCTAAAT 58.675 37.037 0.00 0.00 0.00 1.40
1612 2107 9.160496 GGCACATCTCCTCTAATAATCTAAATG 57.840 37.037 0.00 0.00 0.00 2.32
1613 2108 9.717942 GCACATCTCCTCTAATAATCTAAATGT 57.282 33.333 0.00 0.00 0.00 2.71
1625 2120 5.819825 AATCTAAATGTCTTCTTTCGGGC 57.180 39.130 0.00 0.00 0.00 6.13
1626 2121 4.280436 TCTAAATGTCTTCTTTCGGGCA 57.720 40.909 0.00 0.00 0.00 5.36
1627 2122 4.000988 TCTAAATGTCTTCTTTCGGGCAC 58.999 43.478 0.00 0.00 0.00 5.01
1628 2123 2.270352 AATGTCTTCTTTCGGGCACA 57.730 45.000 0.00 0.00 0.00 4.57
1629 2124 2.496899 ATGTCTTCTTTCGGGCACAT 57.503 45.000 0.00 0.00 0.00 3.21
1630 2125 1.808411 TGTCTTCTTTCGGGCACATC 58.192 50.000 0.00 0.00 0.00 3.06
1631 2126 1.347707 TGTCTTCTTTCGGGCACATCT 59.652 47.619 0.00 0.00 0.00 2.90
1632 2127 2.003301 GTCTTCTTTCGGGCACATCTC 58.997 52.381 0.00 0.00 0.00 2.75
1633 2128 1.066143 TCTTCTTTCGGGCACATCTCC 60.066 52.381 0.00 0.00 0.00 3.71
1634 2129 0.984230 TTCTTTCGGGCACATCTCCT 59.016 50.000 0.00 0.00 0.00 3.69
1702 2200 5.801350 TTGCGAGTTCAGAAATAGAATGG 57.199 39.130 0.00 0.00 0.00 3.16
1721 2219 3.631250 TGGATCTCCATTGTAAAAGGCC 58.369 45.455 0.00 0.00 42.01 5.19
1722 2220 3.011144 TGGATCTCCATTGTAAAAGGCCA 59.989 43.478 5.01 0.00 42.01 5.36
1723 2221 4.023291 GGATCTCCATTGTAAAAGGCCAA 58.977 43.478 5.01 0.00 33.94 4.52
1727 2225 4.837860 TCTCCATTGTAAAAGGCCAACATT 59.162 37.500 5.01 0.00 33.94 2.71
1741 2239 9.869757 AAAGGCCAACATTATTACAAGATTTAC 57.130 29.630 5.01 0.00 0.00 2.01
1743 2241 9.255029 AGGCCAACATTATTACAAGATTTACTT 57.745 29.630 5.01 0.00 39.70 2.24
1765 2270 8.553459 ACTTAATGTCATGGAGTACTTTCTTG 57.447 34.615 0.00 2.14 0.00 3.02
1788 2293 0.822944 TCACGTCACCACCGTCCTAA 60.823 55.000 0.00 0.00 36.17 2.69
1789 2294 0.245539 CACGTCACCACCGTCCTAAT 59.754 55.000 0.00 0.00 36.17 1.73
1790 2295 0.971386 ACGTCACCACCGTCCTAATT 59.029 50.000 0.00 0.00 31.97 1.40
1791 2296 1.337447 ACGTCACCACCGTCCTAATTG 60.337 52.381 0.00 0.00 31.97 2.32
1792 2297 1.067425 CGTCACCACCGTCCTAATTGA 60.067 52.381 0.00 0.00 0.00 2.57
1793 2298 2.618053 GTCACCACCGTCCTAATTGAG 58.382 52.381 0.00 0.00 0.00 3.02
1794 2299 2.028385 GTCACCACCGTCCTAATTGAGT 60.028 50.000 0.00 0.00 0.00 3.41
1795 2300 2.028476 TCACCACCGTCCTAATTGAGTG 60.028 50.000 0.00 0.00 0.00 3.51
1796 2301 1.975680 ACCACCGTCCTAATTGAGTGT 59.024 47.619 0.00 0.00 0.00 3.55
1797 2302 2.370849 ACCACCGTCCTAATTGAGTGTT 59.629 45.455 0.00 0.00 0.00 3.32
1798 2303 3.181448 ACCACCGTCCTAATTGAGTGTTT 60.181 43.478 0.00 0.00 0.00 2.83
1799 2304 3.188460 CCACCGTCCTAATTGAGTGTTTG 59.812 47.826 0.00 0.00 0.00 2.93
1800 2305 2.812011 ACCGTCCTAATTGAGTGTTTGC 59.188 45.455 0.00 0.00 0.00 3.68
1801 2306 3.074412 CCGTCCTAATTGAGTGTTTGCT 58.926 45.455 0.00 0.00 0.00 3.91
1802 2307 3.502211 CCGTCCTAATTGAGTGTTTGCTT 59.498 43.478 0.00 0.00 0.00 3.91
1803 2308 4.023193 CCGTCCTAATTGAGTGTTTGCTTT 60.023 41.667 0.00 0.00 0.00 3.51
1804 2309 4.911610 CGTCCTAATTGAGTGTTTGCTTTG 59.088 41.667 0.00 0.00 0.00 2.77
1805 2310 4.681483 GTCCTAATTGAGTGTTTGCTTTGC 59.319 41.667 0.00 0.00 0.00 3.68
1806 2311 4.584325 TCCTAATTGAGTGTTTGCTTTGCT 59.416 37.500 0.00 0.00 0.00 3.91
1807 2312 5.767665 TCCTAATTGAGTGTTTGCTTTGCTA 59.232 36.000 0.00 0.00 0.00 3.49
1808 2313 5.858581 CCTAATTGAGTGTTTGCTTTGCTAC 59.141 40.000 0.00 0.00 0.00 3.58
1809 2314 3.708563 TTGAGTGTTTGCTTTGCTACC 57.291 42.857 0.00 0.00 0.00 3.18
1810 2315 1.601903 TGAGTGTTTGCTTTGCTACCG 59.398 47.619 0.00 0.00 0.00 4.02
1811 2316 1.602377 GAGTGTTTGCTTTGCTACCGT 59.398 47.619 0.00 0.00 0.00 4.83
1812 2317 2.803956 GAGTGTTTGCTTTGCTACCGTA 59.196 45.455 0.00 0.00 0.00 4.02
1813 2318 3.207778 AGTGTTTGCTTTGCTACCGTAA 58.792 40.909 0.00 0.00 0.00 3.18
1814 2319 3.002965 AGTGTTTGCTTTGCTACCGTAAC 59.997 43.478 0.00 0.00 0.00 2.50
1815 2320 2.943690 TGTTTGCTTTGCTACCGTAACA 59.056 40.909 0.00 0.00 0.00 2.41
1816 2321 3.566322 TGTTTGCTTTGCTACCGTAACAT 59.434 39.130 0.00 0.00 0.00 2.71
1817 2322 3.822594 TTGCTTTGCTACCGTAACATG 57.177 42.857 0.00 0.00 0.00 3.21
1818 2323 2.773487 TGCTTTGCTACCGTAACATGT 58.227 42.857 0.00 0.00 0.00 3.21
1819 2324 3.142951 TGCTTTGCTACCGTAACATGTT 58.857 40.909 16.68 16.68 0.00 2.71
1820 2325 3.058570 TGCTTTGCTACCGTAACATGTTG 60.059 43.478 21.42 7.09 0.00 3.33
1821 2326 3.669557 GCTTTGCTACCGTAACATGTTGG 60.670 47.826 21.42 16.42 0.00 3.77
1822 2327 2.843401 TGCTACCGTAACATGTTGGT 57.157 45.000 21.42 21.02 38.51 3.67
1823 2328 2.690786 TGCTACCGTAACATGTTGGTC 58.309 47.619 20.59 10.60 35.93 4.02
1824 2329 2.300723 TGCTACCGTAACATGTTGGTCT 59.699 45.455 20.59 4.12 35.93 3.85
1825 2330 3.244284 TGCTACCGTAACATGTTGGTCTT 60.244 43.478 20.59 5.56 35.93 3.01
1846 2351 2.944349 TGTTACCGAAAAAGGCTTTCGT 59.056 40.909 13.76 9.60 46.85 3.85
2174 2698 3.706373 GAGCCGCTCACCCCTGAA 61.706 66.667 15.78 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.949856 TCCATCCATAGAACAAAAAGGAGC 59.050 41.667 0.00 0.00 0.00 4.70
60 61 9.639563 AGTATCATCTACAGTATCCATCCATAG 57.360 37.037 0.00 0.00 0.00 2.23
61 62 9.997172 AAGTATCATCTACAGTATCCATCCATA 57.003 33.333 0.00 0.00 0.00 2.74
68 69 7.768807 ACCTGAAGTATCATCTACAGTATCC 57.231 40.000 0.00 0.00 34.37 2.59
99 100 8.865978 GGAGTAACATTTTTCTTTTCAAAACGT 58.134 29.630 0.00 0.00 0.00 3.99
105 108 9.883142 ACAAATGGAGTAACATTTTTCTTTTCA 57.117 25.926 1.74 0.00 45.94 2.69
226 547 7.214381 GGCCCAAAATAAGTGACTTAAGTTTT 58.786 34.615 10.02 9.53 29.35 2.43
230 551 4.142469 CCGGCCCAAAATAAGTGACTTAAG 60.142 45.833 9.35 0.00 29.35 1.85
233 554 2.167662 CCGGCCCAAAATAAGTGACTT 58.832 47.619 2.37 2.37 0.00 3.01
278 600 5.004156 CGTACGTGCATCTACCTTAAAAGTC 59.996 44.000 7.22 0.00 0.00 3.01
284 606 2.355756 GGACGTACGTGCATCTACCTTA 59.644 50.000 31.41 0.00 36.45 2.69
285 607 1.133790 GGACGTACGTGCATCTACCTT 59.866 52.381 31.41 0.27 36.45 3.50
338 660 2.553086 AGACGTACGTGCTTCCAAAAA 58.447 42.857 28.16 0.00 0.00 1.94
339 661 2.228138 AGACGTACGTGCTTCCAAAA 57.772 45.000 28.16 0.00 0.00 2.44
340 662 1.862201 CAAGACGTACGTGCTTCCAAA 59.138 47.619 28.16 0.00 0.00 3.28
341 663 1.493772 CAAGACGTACGTGCTTCCAA 58.506 50.000 28.16 0.00 0.00 3.53
342 664 3.188773 CAAGACGTACGTGCTTCCA 57.811 52.632 28.16 0.00 0.00 3.53
348 670 4.221342 TGTAACTAAGCAAGACGTACGTG 58.779 43.478 28.16 13.03 0.00 4.49
349 671 4.488126 TGTAACTAAGCAAGACGTACGT 57.512 40.909 23.04 23.04 0.00 3.57
350 672 4.913924 ACTTGTAACTAAGCAAGACGTACG 59.086 41.667 15.01 15.01 43.29 3.67
351 673 6.760161 AACTTGTAACTAAGCAAGACGTAC 57.240 37.500 10.69 0.00 43.29 3.67
352 674 7.651808 AGTAACTTGTAACTAAGCAAGACGTA 58.348 34.615 10.69 0.00 43.29 3.57
353 675 6.510536 AGTAACTTGTAACTAAGCAAGACGT 58.489 36.000 10.69 0.00 43.29 4.34
376 698 2.601763 CGGAATTTTCGACCCGACTAAG 59.398 50.000 0.00 0.00 44.29 2.18
523 848 0.818296 ACTCACGCGGCTAGATTTCT 59.182 50.000 12.47 0.00 0.00 2.52
540 871 9.784531 TTTCTTCTTCAGATAGAAAATGACACT 57.215 29.630 9.73 0.00 35.58 3.55
703 1087 4.487412 GGGCGCAACATGCAGCTC 62.487 66.667 10.83 9.95 45.36 4.09
706 1090 3.124270 TACGGGCGCAACATGCAG 61.124 61.111 10.83 0.00 45.36 4.41
788 1191 3.893521 TGAGGATCCGTGTATGACTGTA 58.106 45.455 5.98 0.00 0.00 2.74
789 1192 2.735151 TGAGGATCCGTGTATGACTGT 58.265 47.619 5.98 0.00 0.00 3.55
790 1193 3.305676 GGATGAGGATCCGTGTATGACTG 60.306 52.174 5.98 0.00 39.04 3.51
791 1194 2.894126 GGATGAGGATCCGTGTATGACT 59.106 50.000 5.98 0.00 39.04 3.41
792 1195 3.305398 GGATGAGGATCCGTGTATGAC 57.695 52.381 5.98 0.00 39.04 3.06
802 1205 4.711355 CAGGAGGAATAGAGGATGAGGATC 59.289 50.000 0.00 0.00 0.00 3.36
803 1206 4.109435 ACAGGAGGAATAGAGGATGAGGAT 59.891 45.833 0.00 0.00 0.00 3.24
804 1207 3.469006 ACAGGAGGAATAGAGGATGAGGA 59.531 47.826 0.00 0.00 0.00 3.71
805 1208 3.855668 ACAGGAGGAATAGAGGATGAGG 58.144 50.000 0.00 0.00 0.00 3.86
806 1209 6.074648 ACTTACAGGAGGAATAGAGGATGAG 58.925 44.000 0.00 0.00 0.00 2.90
807 1210 6.031964 ACTTACAGGAGGAATAGAGGATGA 57.968 41.667 0.00 0.00 0.00 2.92
808 1211 8.962679 GTATACTTACAGGAGGAATAGAGGATG 58.037 40.741 0.00 0.00 0.00 3.51
809 1212 8.117312 GGTATACTTACAGGAGGAATAGAGGAT 58.883 40.741 2.25 0.00 0.00 3.24
810 1213 7.468496 GGTATACTTACAGGAGGAATAGAGGA 58.532 42.308 2.25 0.00 0.00 3.71
811 1214 6.664384 GGGTATACTTACAGGAGGAATAGAGG 59.336 46.154 2.25 0.00 0.00 3.69
812 1215 7.239438 TGGGTATACTTACAGGAGGAATAGAG 58.761 42.308 2.25 0.00 0.00 2.43
813 1216 7.170554 TGGGTATACTTACAGGAGGAATAGA 57.829 40.000 2.25 0.00 0.00 1.98
814 1217 7.148052 CGATGGGTATACTTACAGGAGGAATAG 60.148 44.444 2.25 0.00 0.00 1.73
815 1218 6.662234 CGATGGGTATACTTACAGGAGGAATA 59.338 42.308 2.25 0.00 0.00 1.75
816 1219 5.480772 CGATGGGTATACTTACAGGAGGAAT 59.519 44.000 2.25 0.00 0.00 3.01
817 1220 4.831155 CGATGGGTATACTTACAGGAGGAA 59.169 45.833 2.25 0.00 0.00 3.36
818 1221 4.105217 TCGATGGGTATACTTACAGGAGGA 59.895 45.833 2.25 0.00 0.00 3.71
819 1222 4.404640 TCGATGGGTATACTTACAGGAGG 58.595 47.826 2.25 0.00 0.00 4.30
820 1223 5.710567 TGATCGATGGGTATACTTACAGGAG 59.289 44.000 0.54 0.00 0.00 3.69
821 1224 5.475909 GTGATCGATGGGTATACTTACAGGA 59.524 44.000 0.54 3.19 0.00 3.86
822 1225 5.243060 TGTGATCGATGGGTATACTTACAGG 59.757 44.000 0.54 0.00 0.00 4.00
823 1226 6.150318 GTGTGATCGATGGGTATACTTACAG 58.850 44.000 0.54 0.00 0.00 2.74
824 1227 5.595133 TGTGTGATCGATGGGTATACTTACA 59.405 40.000 0.54 0.65 0.00 2.41
825 1228 6.080648 TGTGTGATCGATGGGTATACTTAC 57.919 41.667 0.54 0.00 0.00 2.34
826 1229 6.239204 CCTTGTGTGATCGATGGGTATACTTA 60.239 42.308 0.54 0.00 0.00 2.24
827 1230 5.453339 CCTTGTGTGATCGATGGGTATACTT 60.453 44.000 0.54 0.00 0.00 2.24
828 1231 4.039245 CCTTGTGTGATCGATGGGTATACT 59.961 45.833 0.54 0.00 0.00 2.12
829 1232 4.307432 CCTTGTGTGATCGATGGGTATAC 58.693 47.826 0.54 0.00 0.00 1.47
830 1233 3.244078 GCCTTGTGTGATCGATGGGTATA 60.244 47.826 0.54 0.00 0.00 1.47
831 1234 2.485479 GCCTTGTGTGATCGATGGGTAT 60.485 50.000 0.54 0.00 0.00 2.73
832 1235 1.134521 GCCTTGTGTGATCGATGGGTA 60.135 52.381 0.54 0.00 0.00 3.69
833 1236 0.392998 GCCTTGTGTGATCGATGGGT 60.393 55.000 0.54 0.00 0.00 4.51
834 1237 0.392863 TGCCTTGTGTGATCGATGGG 60.393 55.000 0.54 0.00 0.00 4.00
835 1238 0.729116 GTGCCTTGTGTGATCGATGG 59.271 55.000 0.54 0.00 0.00 3.51
836 1239 1.441738 TGTGCCTTGTGTGATCGATG 58.558 50.000 0.54 0.00 0.00 3.84
837 1240 2.079158 CTTGTGCCTTGTGTGATCGAT 58.921 47.619 0.00 0.00 0.00 3.59
838 1241 1.202639 ACTTGTGCCTTGTGTGATCGA 60.203 47.619 0.00 0.00 0.00 3.59
839 1242 1.229428 ACTTGTGCCTTGTGTGATCG 58.771 50.000 0.00 0.00 0.00 3.69
840 1243 3.058914 GTGTACTTGTGCCTTGTGTGATC 60.059 47.826 0.00 0.00 0.00 2.92
841 1244 2.878406 GTGTACTTGTGCCTTGTGTGAT 59.122 45.455 0.00 0.00 0.00 3.06
842 1245 2.285083 GTGTACTTGTGCCTTGTGTGA 58.715 47.619 0.00 0.00 0.00 3.58
843 1246 2.013400 TGTGTACTTGTGCCTTGTGTG 58.987 47.619 0.00 0.00 0.00 3.82
844 1247 2.411628 TGTGTACTTGTGCCTTGTGT 57.588 45.000 0.00 0.00 0.00 3.72
845 1248 2.033299 CCTTGTGTACTTGTGCCTTGTG 59.967 50.000 0.00 0.00 0.00 3.33
846 1249 2.297701 CCTTGTGTACTTGTGCCTTGT 58.702 47.619 0.00 0.00 0.00 3.16
847 1250 1.001378 GCCTTGTGTACTTGTGCCTTG 60.001 52.381 0.00 0.00 0.00 3.61
848 1251 1.318576 GCCTTGTGTACTTGTGCCTT 58.681 50.000 0.00 0.00 0.00 4.35
849 1252 0.182537 TGCCTTGTGTACTTGTGCCT 59.817 50.000 0.00 0.00 0.00 4.75
850 1253 0.310854 GTGCCTTGTGTACTTGTGCC 59.689 55.000 0.00 0.00 0.00 5.01
851 1254 1.021202 TGTGCCTTGTGTACTTGTGC 58.979 50.000 0.00 0.00 0.00 4.57
852 1255 3.119673 TGTTTGTGCCTTGTGTACTTGTG 60.120 43.478 0.00 0.00 0.00 3.33
853 1256 3.085533 TGTTTGTGCCTTGTGTACTTGT 58.914 40.909 0.00 0.00 0.00 3.16
854 1257 3.119673 TGTGTTTGTGCCTTGTGTACTTG 60.120 43.478 0.00 0.00 0.00 3.16
855 1258 3.085533 TGTGTTTGTGCCTTGTGTACTT 58.914 40.909 0.00 0.00 0.00 2.24
856 1259 2.422127 GTGTGTTTGTGCCTTGTGTACT 59.578 45.455 0.00 0.00 0.00 2.73
857 1260 2.162608 TGTGTGTTTGTGCCTTGTGTAC 59.837 45.455 0.00 0.00 0.00 2.90
858 1261 2.437413 TGTGTGTTTGTGCCTTGTGTA 58.563 42.857 0.00 0.00 0.00 2.90
859 1262 1.252175 TGTGTGTTTGTGCCTTGTGT 58.748 45.000 0.00 0.00 0.00 3.72
860 1263 2.582728 ATGTGTGTTTGTGCCTTGTG 57.417 45.000 0.00 0.00 0.00 3.33
861 1264 3.020274 TGTATGTGTGTTTGTGCCTTGT 58.980 40.909 0.00 0.00 0.00 3.16
862 1265 3.066621 ACTGTATGTGTGTTTGTGCCTTG 59.933 43.478 0.00 0.00 0.00 3.61
863 1266 3.287222 ACTGTATGTGTGTTTGTGCCTT 58.713 40.909 0.00 0.00 0.00 4.35
864 1267 2.878406 GACTGTATGTGTGTTTGTGCCT 59.122 45.455 0.00 0.00 0.00 4.75
865 1268 2.616376 TGACTGTATGTGTGTTTGTGCC 59.384 45.455 0.00 0.00 0.00 5.01
866 1269 3.961477 TGACTGTATGTGTGTTTGTGC 57.039 42.857 0.00 0.00 0.00 4.57
879 1282 5.536538 GGATGAGGATCTGTGTATGACTGTA 59.463 44.000 0.00 0.00 34.92 2.74
880 1283 4.343526 GGATGAGGATCTGTGTATGACTGT 59.656 45.833 0.00 0.00 34.92 3.55
881 1284 4.588106 AGGATGAGGATCTGTGTATGACTG 59.412 45.833 0.00 0.00 34.92 3.51
882 1285 4.813809 AGGATGAGGATCTGTGTATGACT 58.186 43.478 0.00 0.00 34.92 3.41
883 1286 4.021544 GGAGGATGAGGATCTGTGTATGAC 60.022 50.000 0.00 0.00 34.92 3.06
884 1287 4.155709 GGAGGATGAGGATCTGTGTATGA 58.844 47.826 0.00 0.00 34.92 2.15
885 1288 3.899980 TGGAGGATGAGGATCTGTGTATG 59.100 47.826 0.00 0.00 34.92 2.39
886 1289 4.204792 TGGAGGATGAGGATCTGTGTAT 57.795 45.455 0.00 0.00 34.92 2.29
924 1329 2.380410 CGCGTGCCTTGTGTAGTCC 61.380 63.158 0.00 0.00 0.00 3.85
927 1332 1.372997 ACTCGCGTGCCTTGTGTAG 60.373 57.895 5.77 0.00 0.00 2.74
928 1333 1.663388 CACTCGCGTGCCTTGTGTA 60.663 57.895 5.77 0.00 33.82 2.90
1142 1554 2.203294 GCGTGAGGTGTTTGGGGT 60.203 61.111 0.00 0.00 0.00 4.95
1160 1572 6.421202 GTGAGATTACGTAGGCAATAAGGAAG 59.579 42.308 0.00 0.00 0.00 3.46
1163 1575 4.680110 CGTGAGATTACGTAGGCAATAAGG 59.320 45.833 0.00 0.00 39.13 2.69
1181 1612 6.864685 TCAGTTGTAGTTAACCATTACGTGAG 59.135 38.462 0.88 0.00 0.00 3.51
1183 1614 7.591006 ATCAGTTGTAGTTAACCATTACGTG 57.409 36.000 0.88 0.00 0.00 4.49
1200 1648 9.546428 TGTATACCATGAAGTGATTATCAGTTG 57.454 33.333 18.69 7.89 39.91 3.16
1218 1668 1.822371 TGCTTCTCGTGCTGTATACCA 59.178 47.619 0.00 0.00 0.00 3.25
1361 1815 3.084579 CATGACGAGCGTGCTTCC 58.915 61.111 0.00 0.00 0.00 3.46
1479 1953 8.774586 CCAAACAGCAATATAGTACTATGGAAC 58.225 37.037 23.09 11.38 0.00 3.62
1480 1954 8.491134 ACCAAACAGCAATATAGTACTATGGAA 58.509 33.333 23.09 6.02 0.00 3.53
1481 1955 8.029782 ACCAAACAGCAATATAGTACTATGGA 57.970 34.615 23.09 6.73 0.00 3.41
1482 1956 9.944376 ATACCAAACAGCAATATAGTACTATGG 57.056 33.333 23.09 15.65 0.00 2.74
1486 1960 9.681062 AAACATACCAAACAGCAATATAGTACT 57.319 29.630 0.00 0.00 0.00 2.73
1599 2094 9.052759 GCCCGAAAGAAGACATTTAGATTATTA 57.947 33.333 0.00 0.00 0.00 0.98
1600 2095 7.556275 TGCCCGAAAGAAGACATTTAGATTATT 59.444 33.333 0.00 0.00 0.00 1.40
1601 2096 7.012421 GTGCCCGAAAGAAGACATTTAGATTAT 59.988 37.037 0.00 0.00 0.00 1.28
1602 2097 6.315393 GTGCCCGAAAGAAGACATTTAGATTA 59.685 38.462 0.00 0.00 0.00 1.75
1603 2098 5.123979 GTGCCCGAAAGAAGACATTTAGATT 59.876 40.000 0.00 0.00 0.00 2.40
1604 2099 4.636206 GTGCCCGAAAGAAGACATTTAGAT 59.364 41.667 0.00 0.00 0.00 1.98
1605 2100 4.000988 GTGCCCGAAAGAAGACATTTAGA 58.999 43.478 0.00 0.00 0.00 2.10
1606 2101 3.751175 TGTGCCCGAAAGAAGACATTTAG 59.249 43.478 0.00 0.00 0.00 1.85
1607 2102 3.745799 TGTGCCCGAAAGAAGACATTTA 58.254 40.909 0.00 0.00 0.00 1.40
1608 2103 2.582052 TGTGCCCGAAAGAAGACATTT 58.418 42.857 0.00 0.00 0.00 2.32
1609 2104 2.270352 TGTGCCCGAAAGAAGACATT 57.730 45.000 0.00 0.00 0.00 2.71
1610 2105 2.026822 AGATGTGCCCGAAAGAAGACAT 60.027 45.455 0.00 0.00 0.00 3.06
1611 2106 1.347707 AGATGTGCCCGAAAGAAGACA 59.652 47.619 0.00 0.00 0.00 3.41
1612 2107 2.003301 GAGATGTGCCCGAAAGAAGAC 58.997 52.381 0.00 0.00 0.00 3.01
1613 2108 1.066143 GGAGATGTGCCCGAAAGAAGA 60.066 52.381 0.00 0.00 0.00 2.87
1614 2109 1.065854 AGGAGATGTGCCCGAAAGAAG 60.066 52.381 0.00 0.00 0.00 2.85
1615 2110 0.984230 AGGAGATGTGCCCGAAAGAA 59.016 50.000 0.00 0.00 0.00 2.52
1616 2111 0.537188 GAGGAGATGTGCCCGAAAGA 59.463 55.000 0.00 0.00 0.00 2.52
1617 2112 0.539051 AGAGGAGATGTGCCCGAAAG 59.461 55.000 0.00 0.00 0.00 2.62
1618 2113 1.860641 TAGAGGAGATGTGCCCGAAA 58.139 50.000 0.00 0.00 0.00 3.46
1619 2114 1.860641 TTAGAGGAGATGTGCCCGAA 58.139 50.000 0.00 0.00 0.00 4.30
1620 2115 2.088104 ATTAGAGGAGATGTGCCCGA 57.912 50.000 0.00 0.00 0.00 5.14
1621 2116 4.221703 AGATTATTAGAGGAGATGTGCCCG 59.778 45.833 0.00 0.00 0.00 6.13
1622 2117 5.753721 AGATTATTAGAGGAGATGTGCCC 57.246 43.478 0.00 0.00 0.00 5.36
1623 2118 9.160496 CATTTAGATTATTAGAGGAGATGTGCC 57.840 37.037 0.00 0.00 0.00 5.01
1624 2119 9.717942 ACATTTAGATTATTAGAGGAGATGTGC 57.282 33.333 0.00 0.00 0.00 4.57
1702 2200 4.462483 TGTTGGCCTTTTACAATGGAGATC 59.538 41.667 3.32 0.00 0.00 2.75
1712 2210 9.869757 AATCTTGTAATAATGTTGGCCTTTTAC 57.130 29.630 3.32 0.00 0.00 2.01
1715 2213 9.869757 GTAAATCTTGTAATAATGTTGGCCTTT 57.130 29.630 3.32 0.00 0.00 3.11
1716 2214 9.255029 AGTAAATCTTGTAATAATGTTGGCCTT 57.745 29.630 3.32 0.00 0.00 4.35
1739 2237 9.653287 CAAGAAAGTACTCCATGACATTAAGTA 57.347 33.333 0.00 3.56 0.00 2.24
1740 2238 7.607991 CCAAGAAAGTACTCCATGACATTAAGT 59.392 37.037 0.00 5.15 0.00 2.24
1741 2239 7.066284 CCCAAGAAAGTACTCCATGACATTAAG 59.934 40.741 0.00 0.00 0.00 1.85
1743 2241 6.012858 ACCCAAGAAAGTACTCCATGACATTA 60.013 38.462 0.00 0.00 0.00 1.90
1765 2270 2.663852 CGGTGGTGACGTGAACCC 60.664 66.667 13.16 1.55 36.83 4.11
1788 2293 3.304659 CGGTAGCAAAGCAAACACTCAAT 60.305 43.478 0.00 0.00 0.00 2.57
1789 2294 2.032799 CGGTAGCAAAGCAAACACTCAA 59.967 45.455 0.00 0.00 0.00 3.02
1790 2295 1.601903 CGGTAGCAAAGCAAACACTCA 59.398 47.619 0.00 0.00 0.00 3.41
1791 2296 1.602377 ACGGTAGCAAAGCAAACACTC 59.398 47.619 0.00 0.00 0.00 3.51
1792 2297 1.675552 ACGGTAGCAAAGCAAACACT 58.324 45.000 0.00 0.00 0.00 3.55
1793 2298 3.242804 TGTTACGGTAGCAAAGCAAACAC 60.243 43.478 1.96 0.00 30.45 3.32
1794 2299 2.943690 TGTTACGGTAGCAAAGCAAACA 59.056 40.909 1.96 0.00 32.02 2.83
1795 2300 3.612472 TGTTACGGTAGCAAAGCAAAC 57.388 42.857 1.96 0.00 0.00 2.93
1796 2301 3.566322 ACATGTTACGGTAGCAAAGCAAA 59.434 39.130 8.77 0.00 0.00 3.68
1797 2302 3.142951 ACATGTTACGGTAGCAAAGCAA 58.857 40.909 8.77 0.00 0.00 3.91
1798 2303 2.773487 ACATGTTACGGTAGCAAAGCA 58.227 42.857 8.77 0.00 0.00 3.91
1799 2304 3.488489 CAACATGTTACGGTAGCAAAGC 58.512 45.455 11.53 0.00 0.00 3.51
1800 2305 3.500680 ACCAACATGTTACGGTAGCAAAG 59.499 43.478 16.79 7.38 0.00 2.77
1801 2306 3.478509 ACCAACATGTTACGGTAGCAAA 58.521 40.909 16.79 0.00 0.00 3.68
1802 2307 3.068560 GACCAACATGTTACGGTAGCAA 58.931 45.455 17.96 0.00 0.00 3.91
1803 2308 2.300723 AGACCAACATGTTACGGTAGCA 59.699 45.455 17.96 7.16 0.00 3.49
1804 2309 2.968675 AGACCAACATGTTACGGTAGC 58.031 47.619 17.96 8.94 0.00 3.58
1805 2310 4.312443 ACAAGACCAACATGTTACGGTAG 58.688 43.478 17.96 13.73 0.00 3.18
1806 2311 4.339872 ACAAGACCAACATGTTACGGTA 57.660 40.909 17.96 0.00 0.00 4.02
1807 2312 3.202829 ACAAGACCAACATGTTACGGT 57.797 42.857 17.97 17.97 0.00 4.83
1808 2313 5.025986 GTAACAAGACCAACATGTTACGG 57.974 43.478 11.53 11.97 46.17 4.02
1811 2316 4.958509 TCGGTAACAAGACCAACATGTTA 58.041 39.130 11.53 0.00 40.24 2.41
1812 2317 3.811083 TCGGTAACAAGACCAACATGTT 58.189 40.909 4.92 4.92 42.01 2.71
1813 2318 3.478857 TCGGTAACAAGACCAACATGT 57.521 42.857 0.00 0.00 39.72 3.21
1814 2319 4.822036 TTTCGGTAACAAGACCAACATG 57.178 40.909 0.00 0.00 39.72 3.21
1815 2320 5.221165 CCTTTTTCGGTAACAAGACCAACAT 60.221 40.000 0.00 0.00 39.72 2.71
1816 2321 4.096682 CCTTTTTCGGTAACAAGACCAACA 59.903 41.667 0.00 0.00 39.72 3.33
1817 2322 4.603985 CCTTTTTCGGTAACAAGACCAAC 58.396 43.478 0.00 0.00 39.72 3.77
1818 2323 3.067040 GCCTTTTTCGGTAACAAGACCAA 59.933 43.478 0.00 0.00 39.72 3.67
1819 2324 2.619646 GCCTTTTTCGGTAACAAGACCA 59.380 45.455 0.00 0.00 39.72 4.02
1820 2325 2.882761 AGCCTTTTTCGGTAACAAGACC 59.117 45.455 0.00 0.00 36.00 3.85
1821 2326 4.563337 AAGCCTTTTTCGGTAACAAGAC 57.437 40.909 0.00 0.00 0.00 3.01
1822 2327 4.260866 CGAAAGCCTTTTTCGGTAACAAGA 60.261 41.667 12.72 0.00 45.17 3.02
1823 2328 3.972502 CGAAAGCCTTTTTCGGTAACAAG 59.027 43.478 12.72 0.00 45.17 3.16
1824 2329 3.954999 CGAAAGCCTTTTTCGGTAACAA 58.045 40.909 12.72 0.00 45.17 2.83
1825 2330 3.612472 CGAAAGCCTTTTTCGGTAACA 57.388 42.857 12.72 0.00 45.17 2.41
1999 2518 1.236628 GCCTCATCTCATCATGGCAC 58.763 55.000 0.00 0.00 40.04 5.01
2174 2698 1.610102 GCTTGACCTGCTCATGAGTGT 60.610 52.381 23.38 17.39 0.00 3.55
2313 2838 2.128035 GTCGTCAGTGTTCTTCAGTGG 58.872 52.381 0.00 0.00 44.89 4.00


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

AutoCloner maintained by Alex Coulton.