Multiple sequence alignment - TraesCS5A01G090300

Loading Multiple Alignment...

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 TraesCS5A01G090300 chr5A 100.000 2845 0 0 1 2845 121721790 121718946 0.000000e+00 5254.0
1 TraesCS5A01G090300 chr5A 95.652 1932 60 12 932 2845 80511326 80509401 0.000000e+00 3081.0
2 TraesCS5A01G090300 chr5A 90.738 1749 106 19 944 2649 35195324 35193589 0.000000e+00 2281.0
3 TraesCS5A01G090300 chr5A 96.688 936 24 6 1 933 80512169 80511238 0.000000e+00 1550.0
4 TraesCS5A01G090300 chr5A 87.295 488 30 11 465 933 35195724 35195250 1.940000e-146 529.0
5 TraesCS5A01G090300 chr5A 100.000 89 0 0 845 933 121720859 121720771 6.310000e-37 165.0
6 TraesCS5A01G090300 chr5D 96.639 1934 36 9 932 2845 87541410 87539486 0.000000e+00 3184.0
7 TraesCS5A01G090300 chr5D 95.478 1946 40 18 932 2845 122060982 122059053 0.000000e+00 3062.0
8 TraesCS5A01G090300 chr5D 90.482 1765 105 24 934 2649 44700937 44699187 0.000000e+00 2270.0
9 TraesCS5A01G090300 chr5D 97.439 937 18 5 1 933 122061828 122060894 0.000000e+00 1592.0
10 TraesCS5A01G090300 chr5D 96.371 937 17 6 1 933 87542245 87541322 0.000000e+00 1526.0
11 TraesCS5A01G090300 chr5D 92.017 476 24 13 1 471 118204299 118203833 0.000000e+00 656.0
12 TraesCS5A01G090300 chr5D 84.505 626 57 17 2029 2635 44633233 44632629 1.470000e-162 582.0
13 TraesCS5A01G090300 chr5D 87.470 415 41 8 520 933 44701256 44700852 4.290000e-128 468.0
14 TraesCS5A01G090300 chr5D 85.714 210 16 10 2648 2845 118203834 118203627 2.870000e-50 209.0
15 TraesCS5A01G090300 chr7B 90.487 1766 104 26 932 2650 726155588 726153840 0.000000e+00 2272.0
16 TraesCS5A01G090300 chr7B 94.086 186 8 2 748 933 726155683 726155501 2.160000e-71 279.0
17 TraesCS5A01G090300 chr5B 90.018 1653 107 21 934 2542 44467102 44465464 0.000000e+00 2085.0
18 TraesCS5A01G090300 chr5B 90.966 476 27 10 1 471 117252629 117253093 6.690000e-176 627.0
19 TraesCS5A01G090300 chr5B 87.440 414 46 5 520 933 44467424 44467017 3.320000e-129 472.0
20 TraesCS5A01G090300 chr5B 90.341 352 23 5 122 471 128675070 128675412 4.320000e-123 451.0
21 TraesCS5A01G090300 chr5B 92.568 296 15 4 178 471 93473138 93472848 4.380000e-113 418.0
22 TraesCS5A01G090300 chr5B 87.324 213 12 4 2648 2845 128675411 128675623 2.200000e-56 230.0
23 TraesCS5A01G090300 chr5B 94.521 146 8 0 2700 2845 93472826 93472681 2.850000e-55 226.0
24 TraesCS5A01G090300 chr5B 86.256 211 16 6 2648 2845 117253092 117253302 1.720000e-52 217.0
25 TraesCS5A01G090300 chr5B 93.000 100 3 3 1 97 93473239 93473141 2.950000e-30 143.0
26 TraesCS5A01G090300 chr7A 91.729 1330 62 13 932 2219 721920401 721919078 0.000000e+00 1803.0
27 TraesCS5A01G090300 chr7A 95.213 188 8 1 746 933 721920500 721920314 2.140000e-76 296.0
28 TraesCS5A01G090300 chr7D 91.579 1330 64 13 932 2219 626378065 626376742 0.000000e+00 1792.0
29 TraesCS5A01G090300 chr7D 88.248 451 37 9 2205 2650 626376726 626376287 2.510000e-145 525.0
30 TraesCS5A01G090300 chr7D 86.469 303 22 8 465 749 626378624 626378323 5.920000e-82 315.0
31 TraesCS5A01G090300 chr7D 95.213 188 8 1 746 933 626378164 626377978 2.140000e-76 296.0
32 TraesCS5A01G090300 chr7D 95.652 46 1 1 2780 2824 104356413 104356368 3.930000e-09 73.1
33 TraesCS5A01G090300 chr4A 89.086 339 33 3 1 335 538715962 538715624 4.380000e-113 418.0
34 TraesCS5A01G090300 chr6A 88.372 258 25 4 80 335 125155340 125155594 3.560000e-79 305.0
35 TraesCS5A01G090300 chr6A 85.047 214 16 10 2648 2845 125155817 125156030 1.340000e-48 204.0
36 TraesCS5A01G090300 chr1D 93.913 115 6 1 357 471 464442189 464442302 3.770000e-39 172.0


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 TraesCS5A01G090300 chr5A 121718946 121721790 2844 True 2709.500000 5254 100.00000 1 2845 2 chr5A.!!$R3 2844
1 TraesCS5A01G090300 chr5A 80509401 80512169 2768 True 2315.500000 3081 96.17000 1 2845 2 chr5A.!!$R2 2844
2 TraesCS5A01G090300 chr5A 35193589 35195724 2135 True 1405.000000 2281 89.01650 465 2649 2 chr5A.!!$R1 2184
3 TraesCS5A01G090300 chr5D 87539486 87542245 2759 True 2355.000000 3184 96.50500 1 2845 2 chr5D.!!$R3 2844
4 TraesCS5A01G090300 chr5D 122059053 122061828 2775 True 2327.000000 3062 96.45850 1 2845 2 chr5D.!!$R5 2844
5 TraesCS5A01G090300 chr5D 44699187 44701256 2069 True 1369.000000 2270 88.97600 520 2649 2 chr5D.!!$R2 2129
6 TraesCS5A01G090300 chr5D 44632629 44633233 604 True 582.000000 582 84.50500 2029 2635 1 chr5D.!!$R1 606
7 TraesCS5A01G090300 chr5D 118203627 118204299 672 True 432.500000 656 88.86550 1 2845 2 chr5D.!!$R4 2844
8 TraesCS5A01G090300 chr7B 726153840 726155683 1843 True 1275.500000 2272 92.28650 748 2650 2 chr7B.!!$R1 1902
9 TraesCS5A01G090300 chr5B 44465464 44467424 1960 True 1278.500000 2085 88.72900 520 2542 2 chr5B.!!$R1 2022
10 TraesCS5A01G090300 chr5B 117252629 117253302 673 False 422.000000 627 88.61100 1 2845 2 chr5B.!!$F1 2844
11 TraesCS5A01G090300 chr5B 128675070 128675623 553 False 340.500000 451 88.83250 122 2845 2 chr5B.!!$F2 2723
12 TraesCS5A01G090300 chr5B 93472681 93473239 558 True 262.333333 418 93.36300 1 2845 3 chr5B.!!$R2 2844
13 TraesCS5A01G090300 chr7A 721919078 721920500 1422 True 1049.500000 1803 93.47100 746 2219 2 chr7A.!!$R1 1473
14 TraesCS5A01G090300 chr7D 626376287 626378624 2337 True 732.000000 1792 90.37725 465 2650 4 chr7D.!!$R2 2185
15 TraesCS5A01G090300 chr6A 125155340 125156030 690 False 254.500000 305 86.70950 80 2845 2 chr6A.!!$F1 2765

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
950 1245 0.174162 GGCATGGGTTCTTGATGTGC 59.826 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 3032 1.134491 GCGAAGGTTATACAGGGTGCT 60.134 52.381 0.0 0.0 0.0 4.4 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
98 102 4.602995 TGGTTTTACTTTTGTGCGTGATC 58.397 39.130 0.00 0.00 0.00 2.92
254 270 4.244066 TGTTTGCCATGTATCATGTTTGC 58.756 39.130 8.57 5.95 0.00 3.68
271 287 6.154203 TGTTTGCATATCAGTTTGTTTGGA 57.846 33.333 0.00 0.00 0.00 3.53
339 355 5.438761 TTTTTCTTCTGCTGCCTAAAGTC 57.561 39.130 0.00 0.00 0.00 3.01
340 356 2.770164 TCTTCTGCTGCCTAAAGTCC 57.230 50.000 0.00 0.00 0.00 3.85
341 357 2.260822 TCTTCTGCTGCCTAAAGTCCT 58.739 47.619 0.00 0.00 0.00 3.85
342 358 2.639839 TCTTCTGCTGCCTAAAGTCCTT 59.360 45.455 0.00 0.00 0.00 3.36
343 359 3.838317 TCTTCTGCTGCCTAAAGTCCTTA 59.162 43.478 0.00 0.00 0.00 2.69
344 360 4.286032 TCTTCTGCTGCCTAAAGTCCTTAA 59.714 41.667 0.00 0.00 0.00 1.85
397 508 8.324191 TCCAAGTCACTCTGAATATATTCCTT 57.676 34.615 20.29 12.23 35.97 3.36
441 552 3.784701 TCTGGTCGATCTGTTCTAAGC 57.215 47.619 0.00 0.00 0.00 3.09
686 819 7.606456 CCTACTTTTGATACCTTAAGCTCACAA 59.394 37.037 0.00 0.00 0.00 3.33
727 860 7.229106 CCAAAATTTCCTCATGTGGACATTTTT 59.771 33.333 31.89 24.39 46.08 1.94
892 1187 6.713762 TCTCCAAATTGCCTTGGTTATATG 57.286 37.500 8.65 0.00 45.29 1.78
893 1188 5.068987 TCTCCAAATTGCCTTGGTTATATGC 59.931 40.000 8.65 0.00 45.29 3.14
894 1189 4.713814 TCCAAATTGCCTTGGTTATATGCA 59.286 37.500 8.65 0.00 45.29 3.96
895 1190 5.188555 TCCAAATTGCCTTGGTTATATGCAA 59.811 36.000 8.65 0.00 45.29 4.08
898 1193 3.731652 TGCCTTGGTTATATGCAATGC 57.268 42.857 0.00 0.00 0.00 3.56
899 1194 3.298619 TGCCTTGGTTATATGCAATGCT 58.701 40.909 6.82 0.00 0.00 3.79
900 1195 3.068448 TGCCTTGGTTATATGCAATGCTG 59.932 43.478 6.82 0.00 0.00 4.41
901 1196 3.553508 GCCTTGGTTATATGCAATGCTGG 60.554 47.826 6.82 0.00 0.00 4.85
902 1197 3.638160 CCTTGGTTATATGCAATGCTGGT 59.362 43.478 6.82 0.00 0.00 4.00
903 1198 4.826733 CCTTGGTTATATGCAATGCTGGTA 59.173 41.667 6.82 0.00 0.00 3.25
904 1199 5.301551 CCTTGGTTATATGCAATGCTGGTAA 59.698 40.000 6.82 0.00 0.00 2.85
905 1200 6.015180 CCTTGGTTATATGCAATGCTGGTAAT 60.015 38.462 6.82 0.00 0.00 1.89
906 1201 6.573664 TGGTTATATGCAATGCTGGTAATC 57.426 37.500 6.82 3.90 0.00 1.75
907 1202 5.476599 TGGTTATATGCAATGCTGGTAATCC 59.523 40.000 6.82 7.46 0.00 3.01
908 1203 5.476599 GGTTATATGCAATGCTGGTAATCCA 59.523 40.000 6.82 0.00 42.05 3.41
909 1204 6.153340 GGTTATATGCAATGCTGGTAATCCAT 59.847 38.462 6.82 0.00 43.43 3.41
910 1205 7.339212 GGTTATATGCAATGCTGGTAATCCATA 59.661 37.037 6.82 0.00 43.43 2.74
911 1206 8.739039 GTTATATGCAATGCTGGTAATCCATAA 58.261 33.333 6.82 0.00 43.43 1.90
912 1207 7.966339 ATATGCAATGCTGGTAATCCATAAT 57.034 32.000 6.82 0.00 43.43 1.28
914 1209 7.966339 ATGCAATGCTGGTAATCCATAATAT 57.034 32.000 6.82 0.00 43.43 1.28
915 1210 7.160547 TGCAATGCTGGTAATCCATAATATG 57.839 36.000 6.82 0.00 43.43 1.78
916 1211 6.947158 TGCAATGCTGGTAATCCATAATATGA 59.053 34.615 6.82 0.00 43.43 2.15
917 1212 7.094248 TGCAATGCTGGTAATCCATAATATGAC 60.094 37.037 6.82 0.00 43.43 3.06
918 1213 7.121759 GCAATGCTGGTAATCCATAATATGACT 59.878 37.037 1.10 0.00 43.43 3.41
919 1214 8.671921 CAATGCTGGTAATCCATAATATGACTC 58.328 37.037 1.10 0.00 43.43 3.36
920 1215 7.559335 TGCTGGTAATCCATAATATGACTCT 57.441 36.000 1.10 0.00 43.43 3.24
921 1216 7.977818 TGCTGGTAATCCATAATATGACTCTT 58.022 34.615 1.10 0.00 43.43 2.85
922 1217 8.439971 TGCTGGTAATCCATAATATGACTCTTT 58.560 33.333 1.10 0.00 43.43 2.52
923 1218 8.940952 GCTGGTAATCCATAATATGACTCTTTC 58.059 37.037 1.10 0.00 43.43 2.62
936 1231 6.939132 ATGACTCTTTCTATTTCAGGCATG 57.061 37.500 0.00 0.00 31.27 4.06
937 1232 5.188434 TGACTCTTTCTATTTCAGGCATGG 58.812 41.667 0.00 0.00 0.00 3.66
938 1233 4.530875 ACTCTTTCTATTTCAGGCATGGG 58.469 43.478 0.00 0.00 0.00 4.00
939 1234 4.018050 ACTCTTTCTATTTCAGGCATGGGT 60.018 41.667 0.00 0.00 0.00 4.51
940 1235 4.934356 TCTTTCTATTTCAGGCATGGGTT 58.066 39.130 0.00 0.00 0.00 4.11
941 1236 4.949856 TCTTTCTATTTCAGGCATGGGTTC 59.050 41.667 0.00 0.00 0.00 3.62
942 1237 4.591321 TTCTATTTCAGGCATGGGTTCT 57.409 40.909 0.00 0.00 0.00 3.01
943 1238 4.591321 TCTATTTCAGGCATGGGTTCTT 57.409 40.909 0.00 0.00 0.00 2.52
944 1239 4.272489 TCTATTTCAGGCATGGGTTCTTG 58.728 43.478 0.00 0.00 0.00 3.02
945 1240 2.673775 TTTCAGGCATGGGTTCTTGA 57.326 45.000 0.00 0.00 0.00 3.02
946 1241 2.905415 TTCAGGCATGGGTTCTTGAT 57.095 45.000 0.00 0.00 0.00 2.57
947 1242 2.133281 TCAGGCATGGGTTCTTGATG 57.867 50.000 0.00 0.00 0.00 3.07
948 1243 1.355381 TCAGGCATGGGTTCTTGATGT 59.645 47.619 0.00 0.00 0.00 3.06
949 1244 1.475280 CAGGCATGGGTTCTTGATGTG 59.525 52.381 0.00 0.00 0.00 3.21
950 1245 0.174162 GGCATGGGTTCTTGATGTGC 59.826 55.000 0.00 0.00 0.00 4.57
951 1246 0.889994 GCATGGGTTCTTGATGTGCA 59.110 50.000 0.00 0.00 0.00 4.57
952 1247 1.403249 GCATGGGTTCTTGATGTGCAC 60.403 52.381 10.75 10.75 0.00 4.57
953 1248 1.203052 CATGGGTTCTTGATGTGCACC 59.797 52.381 15.69 0.00 0.00 5.01
954 1249 0.539438 TGGGTTCTTGATGTGCACCC 60.539 55.000 15.69 5.24 46.61 4.61
955 1250 0.251341 GGGTTCTTGATGTGCACCCT 60.251 55.000 15.69 0.70 43.51 4.34
956 1251 1.620822 GGTTCTTGATGTGCACCCTT 58.379 50.000 15.69 0.00 0.00 3.95
957 1252 1.541588 GGTTCTTGATGTGCACCCTTC 59.458 52.381 15.69 9.37 0.00 3.46
958 1253 2.508526 GTTCTTGATGTGCACCCTTCT 58.491 47.619 15.69 0.00 0.00 2.85
959 1254 2.479566 TCTTGATGTGCACCCTTCTC 57.520 50.000 15.69 4.11 0.00 2.87
960 1255 1.003580 TCTTGATGTGCACCCTTCTCC 59.996 52.381 15.69 0.00 0.00 3.71
961 1256 0.770499 TTGATGTGCACCCTTCTCCA 59.230 50.000 15.69 0.00 0.00 3.86
962 1257 0.770499 TGATGTGCACCCTTCTCCAA 59.230 50.000 15.69 0.00 0.00 3.53
963 1258 1.144708 TGATGTGCACCCTTCTCCAAA 59.855 47.619 15.69 0.00 0.00 3.28
964 1259 2.225091 TGATGTGCACCCTTCTCCAAAT 60.225 45.455 15.69 0.00 0.00 2.32
965 1260 2.380064 TGTGCACCCTTCTCCAAATT 57.620 45.000 15.69 0.00 0.00 1.82
966 1261 1.962807 TGTGCACCCTTCTCCAAATTG 59.037 47.619 15.69 0.00 0.00 2.32
967 1262 0.968405 TGCACCCTTCTCCAAATTGC 59.032 50.000 0.00 0.00 0.00 3.56
968 1263 0.247460 GCACCCTTCTCCAAATTGCC 59.753 55.000 0.00 0.00 0.00 4.52
969 1264 1.928868 CACCCTTCTCCAAATTGCCT 58.071 50.000 0.00 0.00 0.00 4.75
970 1265 2.250924 CACCCTTCTCCAAATTGCCTT 58.749 47.619 0.00 0.00 0.00 4.35
971 1266 2.028748 CACCCTTCTCCAAATTGCCTTG 60.029 50.000 0.00 0.00 0.00 3.61
972 1267 1.551883 CCCTTCTCCAAATTGCCTTGG 59.448 52.381 3.49 3.49 46.27 3.61
973 1268 2.250924 CCTTCTCCAAATTGCCTTGGT 58.749 47.619 8.65 0.00 45.29 3.67
974 1269 2.634453 CCTTCTCCAAATTGCCTTGGTT 59.366 45.455 8.65 0.00 45.29 3.67
975 1270 3.831911 CCTTCTCCAAATTGCCTTGGTTA 59.168 43.478 8.65 0.00 45.29 2.85
976 1271 4.467438 CCTTCTCCAAATTGCCTTGGTTAT 59.533 41.667 8.65 0.00 45.29 1.89
977 1272 5.656416 CCTTCTCCAAATTGCCTTGGTTATA 59.344 40.000 8.65 0.00 45.29 0.98
978 1273 6.324770 CCTTCTCCAAATTGCCTTGGTTATAT 59.675 38.462 8.65 0.00 45.29 0.86
1052 1349 4.614535 GCTCACTGGTGCTGTTGATTTAAG 60.615 45.833 0.00 0.00 0.00 1.85
1300 1601 4.104831 ACTGCTCCAGTAGATTTACCCTT 58.895 43.478 0.00 0.00 43.46 3.95
1336 1639 2.102578 GCCATCCCACTTGCTTTATGT 58.897 47.619 0.00 0.00 0.00 2.29
1407 1726 2.306512 ACCTACTATTTCGGGCAAACCA 59.693 45.455 0.00 0.00 40.22 3.67
1430 1749 2.262423 AGTGAGTCCAAGGACAAAGC 57.738 50.000 20.52 8.17 46.76 3.51
1431 1750 1.202818 AGTGAGTCCAAGGACAAAGCC 60.203 52.381 20.52 4.56 46.76 4.35
1510 1831 5.048643 ACATCGACATAAGGATCGGTCTAAG 60.049 44.000 0.00 0.00 38.86 2.18
1545 1871 8.836735 AGGACAAGGATAAGAAAAAGGATAAGA 58.163 33.333 0.00 0.00 0.00 2.10
1546 1872 9.462606 GGACAAGGATAAGAAAAAGGATAAGAA 57.537 33.333 0.00 0.00 0.00 2.52
1761 2087 3.871485 ACAACAAATTTCCTTGCAGCAA 58.129 36.364 7.81 7.81 0.00 3.91
1763 2089 4.883006 ACAACAAATTTCCTTGCAGCAAAT 59.117 33.333 9.65 0.00 0.00 2.32
1816 2142 8.049117 TCTATGACAGCATAAGAGTTCCAAAAT 58.951 33.333 0.00 0.00 36.60 1.82
1834 2160 5.455392 CAAAATCGATGAGATGGGTAATGC 58.545 41.667 0.00 0.00 40.02 3.56
1875 2203 9.315525 AGTTTTCTTCTTACTTCTACTGTCAAC 57.684 33.333 0.00 0.00 0.00 3.18
1948 2276 1.268234 GCTGCAGATCAATTGGTACGC 60.268 52.381 20.43 5.25 0.00 4.42
2199 2557 5.297776 CCTGACTTTGCCAATATTAGTCTGG 59.702 44.000 18.94 18.94 43.62 3.86
2241 2631 7.508687 TCTGTACAATATGTGATGTTAGGCAT 58.491 34.615 0.00 0.00 41.24 4.40
2578 2989 5.120830 ACTCGCAGTTTACTCAATGATGTTC 59.879 40.000 0.00 0.00 0.00 3.18
2621 3032 6.101332 GCCATTTGCAACTCTTTAATGATCA 58.899 36.000 0.00 0.00 40.77 2.92
2762 3184 0.099968 CCAGCGTTGGCATGAGATTG 59.900 55.000 4.99 0.00 43.41 2.67
2778 3200 0.620556 ATTGGACATGGGAAGCGTCT 59.379 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 102 4.570930 GTCAGACCTCTCCACCTAAAAAG 58.429 47.826 0.00 0.00 0.00 2.27
254 270 5.818136 ATCGGTCCAAACAAACTGATATG 57.182 39.130 0.00 0.00 39.22 1.78
271 287 2.040412 AGAAGAGCCCAGAAAAATCGGT 59.960 45.455 0.00 0.00 0.00 4.69
335 351 5.615925 AGATCTAACGCCATTAAGGACTT 57.384 39.130 0.00 0.00 41.22 3.01
337 353 5.463724 CAGAAGATCTAACGCCATTAAGGAC 59.536 44.000 0.00 0.00 41.22 3.85
338 354 5.453339 CCAGAAGATCTAACGCCATTAAGGA 60.453 44.000 0.00 0.00 41.22 3.36
339 355 4.752101 CCAGAAGATCTAACGCCATTAAGG 59.248 45.833 0.00 0.00 41.84 2.69
340 356 5.360591 ACCAGAAGATCTAACGCCATTAAG 58.639 41.667 0.00 0.00 0.00 1.85
341 357 5.353394 ACCAGAAGATCTAACGCCATTAA 57.647 39.130 0.00 0.00 0.00 1.40
342 358 4.499188 CGACCAGAAGATCTAACGCCATTA 60.499 45.833 0.00 0.00 0.00 1.90
343 359 3.738281 CGACCAGAAGATCTAACGCCATT 60.738 47.826 0.00 0.00 0.00 3.16
344 360 2.223829 CGACCAGAAGATCTAACGCCAT 60.224 50.000 0.00 0.00 0.00 4.40
397 508 0.464036 CCACCGCCAGAAGTAGCATA 59.536 55.000 0.00 0.00 0.00 3.14
441 552 0.583438 CAGGAACATATTGAGCGGCG 59.417 55.000 0.51 0.51 0.00 6.46
644 777 4.373156 AGTAGGACAAAGATTGGCTGTT 57.627 40.909 0.00 0.00 39.20 3.16
727 860 6.488344 TGTGGTTGCTCAACATATAGACAAAA 59.512 34.615 13.89 0.00 42.85 2.44
910 1205 9.064706 CATGCCTGAAATAGAAAGAGTCATATT 57.935 33.333 0.00 0.00 0.00 1.28
911 1206 7.664731 CCATGCCTGAAATAGAAAGAGTCATAT 59.335 37.037 0.00 0.00 0.00 1.78
912 1207 6.994496 CCATGCCTGAAATAGAAAGAGTCATA 59.006 38.462 0.00 0.00 0.00 2.15
913 1208 5.826737 CCATGCCTGAAATAGAAAGAGTCAT 59.173 40.000 0.00 0.00 0.00 3.06
914 1209 5.188434 CCATGCCTGAAATAGAAAGAGTCA 58.812 41.667 0.00 0.00 0.00 3.41
915 1210 4.578105 CCCATGCCTGAAATAGAAAGAGTC 59.422 45.833 0.00 0.00 0.00 3.36
916 1211 4.018050 ACCCATGCCTGAAATAGAAAGAGT 60.018 41.667 0.00 0.00 0.00 3.24
917 1212 4.530875 ACCCATGCCTGAAATAGAAAGAG 58.469 43.478 0.00 0.00 0.00 2.85
918 1213 4.591321 ACCCATGCCTGAAATAGAAAGA 57.409 40.909 0.00 0.00 0.00 2.52
919 1214 4.952335 AGAACCCATGCCTGAAATAGAAAG 59.048 41.667 0.00 0.00 0.00 2.62
920 1215 4.934356 AGAACCCATGCCTGAAATAGAAA 58.066 39.130 0.00 0.00 0.00 2.52
921 1216 4.591321 AGAACCCATGCCTGAAATAGAA 57.409 40.909 0.00 0.00 0.00 2.10
922 1217 4.018506 TCAAGAACCCATGCCTGAAATAGA 60.019 41.667 0.00 0.00 0.00 1.98
923 1218 4.272489 TCAAGAACCCATGCCTGAAATAG 58.728 43.478 0.00 0.00 0.00 1.73
924 1219 4.314522 TCAAGAACCCATGCCTGAAATA 57.685 40.909 0.00 0.00 0.00 1.40
925 1220 3.173953 TCAAGAACCCATGCCTGAAAT 57.826 42.857 0.00 0.00 0.00 2.17
926 1221 2.673775 TCAAGAACCCATGCCTGAAA 57.326 45.000 0.00 0.00 0.00 2.69
927 1222 2.225091 ACATCAAGAACCCATGCCTGAA 60.225 45.455 0.00 0.00 0.00 3.02
928 1223 1.355381 ACATCAAGAACCCATGCCTGA 59.645 47.619 0.00 0.00 0.00 3.86
929 1224 1.475280 CACATCAAGAACCCATGCCTG 59.525 52.381 0.00 0.00 0.00 4.85
930 1225 1.843368 CACATCAAGAACCCATGCCT 58.157 50.000 0.00 0.00 0.00 4.75
931 1226 0.174162 GCACATCAAGAACCCATGCC 59.826 55.000 0.00 0.00 0.00 4.40
932 1227 0.889994 TGCACATCAAGAACCCATGC 59.110 50.000 0.00 0.00 0.00 4.06
933 1228 1.203052 GGTGCACATCAAGAACCCATG 59.797 52.381 20.43 0.00 0.00 3.66
934 1229 1.549203 GGTGCACATCAAGAACCCAT 58.451 50.000 20.43 0.00 0.00 4.00
935 1230 3.034924 GGTGCACATCAAGAACCCA 57.965 52.632 20.43 0.00 0.00 4.51
936 1231 2.267045 GGGTGCACATCAAGAACCC 58.733 57.895 20.43 2.96 43.56 4.11
937 1232 1.541588 GAAGGGTGCACATCAAGAACC 59.458 52.381 20.43 7.81 0.00 3.62
938 1233 2.485814 GAGAAGGGTGCACATCAAGAAC 59.514 50.000 20.43 0.00 0.00 3.01
939 1234 2.553028 GGAGAAGGGTGCACATCAAGAA 60.553 50.000 20.43 0.00 0.00 2.52
940 1235 1.003580 GGAGAAGGGTGCACATCAAGA 59.996 52.381 20.43 0.00 0.00 3.02
941 1236 1.271543 TGGAGAAGGGTGCACATCAAG 60.272 52.381 20.43 0.00 0.00 3.02
942 1237 0.770499 TGGAGAAGGGTGCACATCAA 59.230 50.000 20.43 0.00 0.00 2.57
943 1238 0.770499 TTGGAGAAGGGTGCACATCA 59.230 50.000 20.43 2.76 0.00 3.07
944 1239 1.909700 TTTGGAGAAGGGTGCACATC 58.090 50.000 20.43 13.35 0.00 3.06
945 1240 2.564062 CAATTTGGAGAAGGGTGCACAT 59.436 45.455 20.43 3.17 0.00 3.21
946 1241 1.962807 CAATTTGGAGAAGGGTGCACA 59.037 47.619 20.43 0.00 0.00 4.57
947 1242 1.337167 GCAATTTGGAGAAGGGTGCAC 60.337 52.381 8.80 8.80 0.00 4.57
948 1243 0.968405 GCAATTTGGAGAAGGGTGCA 59.032 50.000 0.00 0.00 0.00 4.57
949 1244 0.247460 GGCAATTTGGAGAAGGGTGC 59.753 55.000 0.00 0.00 0.00 5.01
950 1245 1.928868 AGGCAATTTGGAGAAGGGTG 58.071 50.000 0.00 0.00 0.00 4.61
951 1246 2.250924 CAAGGCAATTTGGAGAAGGGT 58.749 47.619 0.00 0.00 0.00 4.34
964 1259 4.057406 GCATTGCATATAACCAAGGCAA 57.943 40.909 15.86 0.00 45.09 4.52
965 1260 3.731652 GCATTGCATATAACCAAGGCA 57.268 42.857 15.86 0.00 45.09 4.75
966 1261 3.553508 CCAGCATTGCATATAACCAAGGC 60.554 47.826 11.91 13.97 45.81 4.35
967 1262 3.638160 ACCAGCATTGCATATAACCAAGG 59.362 43.478 11.91 0.00 0.00 3.61
968 1263 4.924305 ACCAGCATTGCATATAACCAAG 57.076 40.909 11.91 0.00 0.00 3.61
969 1264 6.015519 GGATTACCAGCATTGCATATAACCAA 60.016 38.462 11.91 0.00 35.97 3.67
970 1265 5.476599 GGATTACCAGCATTGCATATAACCA 59.523 40.000 11.91 0.00 35.97 3.67
971 1266 5.476599 TGGATTACCAGCATTGCATATAACC 59.523 40.000 11.91 6.58 41.77 2.85
972 1267 6.573664 TGGATTACCAGCATTGCATATAAC 57.426 37.500 11.91 0.00 41.77 1.89
1052 1349 3.667960 CGGCTGCAATTTGTACTGACTTC 60.668 47.826 0.50 0.00 0.00 3.01
1158 1455 4.517285 TCATTCCTTCTCCTTTCCGAATG 58.483 43.478 0.00 0.00 38.48 2.67
1300 1601 5.483231 TGGGATGGCAAAAATGATCTTACAA 59.517 36.000 0.00 0.00 0.00 2.41
1407 1726 4.142160 GCTTTGTCCTTGGACTCACTTTTT 60.142 41.667 19.11 0.00 0.00 1.94
1510 1831 4.223032 TCTTATCCTTGTCCTTGTCTGTCC 59.777 45.833 0.00 0.00 0.00 4.02
1545 1871 2.753452 CAGCAACCTTCTCATGATGCTT 59.247 45.455 14.93 1.01 41.82 3.91
1546 1872 2.290768 ACAGCAACCTTCTCATGATGCT 60.291 45.455 12.38 12.38 44.34 3.79
1547 1873 2.089980 ACAGCAACCTTCTCATGATGC 58.910 47.619 8.37 8.37 33.98 3.91
1586 1912 8.294954 TGAGTAAGACTTGGAGATACTTTAGG 57.705 38.462 0.00 0.00 0.00 2.69
1761 2087 8.257306 AGTCATGTTAACAGACCAACAAAAATT 58.743 29.630 23.19 8.09 38.11 1.82
1763 2089 7.164230 AGTCATGTTAACAGACCAACAAAAA 57.836 32.000 23.19 0.00 38.11 1.94
1816 2142 2.700371 AGTGCATTACCCATCTCATCGA 59.300 45.455 0.00 0.00 0.00 3.59
1834 2160 8.819643 AGAAGAAAACTGTAGCTAACTAAGTG 57.180 34.615 0.00 0.00 0.00 3.16
1875 2203 6.878317 TCCTTCTAACAGAATATGACACTGG 58.122 40.000 0.00 0.00 33.13 4.00
1948 2276 5.084722 CAGCAAATAGAAGTTCAAGAAGCG 58.915 41.667 5.50 0.00 0.00 4.68
2199 2557 6.437928 TGTACAGATGCAGACAAAATCAAAC 58.562 36.000 0.00 0.00 0.00 2.93
2578 2989 5.247507 TGGCATACGATGATTTCAAAAGG 57.752 39.130 0.00 0.00 0.00 3.11
2621 3032 1.134491 GCGAAGGTTATACAGGGTGCT 60.134 52.381 0.00 0.00 0.00 4.40
2762 3184 2.622064 ATAAGACGCTTCCCATGTCC 57.378 50.000 0.00 0.00 33.09 4.02
2778 3200 6.183360 GCCAATGGACCGTGGTTAATAAATAA 60.183 38.462 2.05 0.00 37.23 1.40


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

AutoCloner maintained by Alex Coulton.