Multiple sequence alignment - TraesCS1D01G194100

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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 TraesCS1D01G194100 chr1D 100.000 4241 0 0 1 4241 270024932 270020692 0.000000e+00 7832.0
1 TraesCS1D01G194100 chr1D 88.519 270 29 2 268 537 430320481 430320214 4.090000e-85 326.0
2 TraesCS1D01G194100 chr1B 93.765 2422 112 17 919 3316 343664820 343662414 0.000000e+00 3600.0
3 TraesCS1D01G194100 chr1B 97.300 926 25 0 3315 4240 343662375 343661450 0.000000e+00 1572.0
4 TraesCS1D01G194100 chr1B 88.423 691 59 13 29 708 343665937 343665257 0.000000e+00 813.0
5 TraesCS1D01G194100 chr1A 94.662 1686 56 16 913 2575 343621845 343620171 0.000000e+00 2584.0
6 TraesCS1D01G194100 chr1A 98.384 928 13 2 3315 4241 343618367 343617441 0.000000e+00 1629.0
7 TraesCS1D01G194100 chr1A 96.774 744 22 1 2575 3316 343619141 343618398 0.000000e+00 1240.0
8 TraesCS1D01G194100 chr1A 86.935 819 77 14 10 818 343622633 343621835 0.000000e+00 893.0
9 TraesCS1D01G194100 chr5D 94.804 789 35 5 2330 3116 325957147 325956363 0.000000e+00 1225.0
10 TraesCS1D01G194100 chr5D 84.848 462 33 13 919 1365 325958926 325959365 8.420000e-117 431.0
11 TraesCS1D01G194100 chr5D 85.385 260 29 8 10 268 325958401 325958652 1.170000e-65 261.0
12 TraesCS1D01G194100 chr7B 93.426 791 40 5 2330 3116 5917895 5917113 0.000000e+00 1162.0
13 TraesCS1D01G194100 chr5A 94.993 719 35 1 2398 3116 430641801 430642518 0.000000e+00 1127.0
14 TraesCS1D01G194100 chr5A 93.151 73 3 1 2330 2400 430641463 430641535 5.800000e-19 106.0
15 TraesCS1D01G194100 chr5A 86.765 68 8 1 10 77 430640386 430640320 1.640000e-09 75.0
16 TraesCS1D01G194100 chr6A 87.085 271 33 2 268 537 540151486 540151755 5.330000e-79 305.0
17 TraesCS1D01G194100 chr6D 87.037 270 34 1 268 537 7532101 7532369 1.920000e-78 303.0
18 TraesCS1D01G194100 chr3D 85.915 284 38 2 265 547 29810479 29810197 6.890000e-78 302.0
19 TraesCS1D01G194100 chr3D 86.667 270 36 0 268 537 463681773 463681504 2.480000e-77 300.0
20 TraesCS1D01G194100 chr3A 86.891 267 35 0 268 534 134257418 134257684 2.480000e-77 300.0
21 TraesCS1D01G194100 chr3B 85.766 274 39 0 268 541 62389533 62389260 1.490000e-74 291.0
22 TraesCS1D01G194100 chr4B 87.671 73 8 1 810 881 429609416 429609488 2.720000e-12 84.2
23 TraesCS1D01G194100 chr5B 84.615 78 9 3 807 882 634998838 634998914 1.640000e-09 75.0
24 TraesCS1D01G194100 chrUn 83.824 68 9 2 817 882 60297710 60297777 3.540000e-06 63.9
25 TraesCS1D01G194100 chrUn 87.500 56 5 2 829 882 375799868 375799923 3.540000e-06 63.9
26 TraesCS1D01G194100 chrUn 87.500 56 5 2 829 882 391468901 391468846 3.540000e-06 63.9
27 TraesCS1D01G194100 chrUn 100.000 29 0 0 854 882 365985217 365985189 2.000000e-03 54.7


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 TraesCS1D01G194100 chr1D 270020692 270024932 4240 True 7832.0 7832 100.000000 1 4241 1 chr1D.!!$R1 4240
1 TraesCS1D01G194100 chr1B 343661450 343665937 4487 True 1995.0 3600 93.162667 29 4240 3 chr1B.!!$R1 4211
2 TraesCS1D01G194100 chr1A 343617441 343622633 5192 True 1586.5 2584 94.188750 10 4241 4 chr1A.!!$R1 4231
3 TraesCS1D01G194100 chr5D 325956363 325957147 784 True 1225.0 1225 94.804000 2330 3116 1 chr5D.!!$R1 786
4 TraesCS1D01G194100 chr5D 325958401 325959365 964 False 346.0 431 85.116500 10 1365 2 chr5D.!!$F1 1355
5 TraesCS1D01G194100 chr7B 5917113 5917895 782 True 1162.0 1162 93.426000 2330 3116 1 chr7B.!!$R1 786
6 TraesCS1D01G194100 chr5A 430641463 430642518 1055 False 616.5 1127 94.072000 2330 3116 2 chr5A.!!$F1 786

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
940 1324 0.249911 GCCCACGCGATAATCCTTCT 60.250 55.0 15.93 0.0 0.0 2.85 F
943 1327 0.861837 CACGCGATAATCCTTCTGGC 59.138 55.0 15.93 0.0 0.0 4.85 F
1411 1814 0.953960 GATTCACGAACCCCACGCTT 60.954 55.0 0.00 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2281 2700 2.190325 GCAATCAGCATGCTTGAGTC 57.810 50.000 19.98 3.78 44.46 3.36 R
2322 2741 2.951642 CAGAGACAAGAGGGTGCAAAAA 59.048 45.455 0.00 0.00 0.00 1.94 R
3250 4973 2.289694 CCTTCTCTGACCCGTGTTTCAT 60.290 50.000 0.00 0.00 0.00 2.57 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
18 19 2.854522 GTGTGTTTCCTGGGGATCG 58.145 57.895 0.00 0.00 0.00 3.69
19 20 0.323629 GTGTGTTTCCTGGGGATCGA 59.676 55.000 0.00 0.00 0.00 3.59
20 21 1.065418 GTGTGTTTCCTGGGGATCGAT 60.065 52.381 0.00 0.00 0.00 3.59
21 22 1.633432 TGTGTTTCCTGGGGATCGATT 59.367 47.619 0.00 0.00 0.00 3.34
61 62 5.757320 CCAAAAGCAGGTATAGAGTGATCTG 59.243 44.000 0.00 0.00 0.00 2.90
81 82 6.037786 TCTGATACCGACAGTTCTTGAATT 57.962 37.500 0.00 0.00 36.81 2.17
116 117 1.196766 AGCATGGCTCTCTCACACCA 61.197 55.000 0.00 0.00 30.62 4.17
182 183 7.742767 TGATCACTCTCCACATCATATTCAAT 58.257 34.615 0.00 0.00 0.00 2.57
270 271 7.901874 TTTTTGTGAGAACAAAGTATAACGC 57.098 32.000 4.42 0.00 40.20 4.84
283 284 4.785417 AGTATAACGCTACTCTTCATCGC 58.215 43.478 0.00 0.00 0.00 4.58
288 289 1.437573 CTACTCTTCATCGCCGGCA 59.562 57.895 28.98 14.46 0.00 5.69
301 302 1.724582 GCCGGCAGTTGTTGTTCTGT 61.725 55.000 24.80 0.00 34.57 3.41
308 309 3.181501 GCAGTTGTTGTTCTGTTGTGCTA 60.182 43.478 0.00 0.00 34.57 3.49
320 321 6.782082 TCTGTTGTGCTAGTTCTATGAGAT 57.218 37.500 0.00 0.00 0.00 2.75
375 376 5.238650 ACAACAAGTTTTGTCCGATTCTAGG 59.761 40.000 0.00 0.00 44.59 3.02
379 380 4.094476 AGTTTTGTCCGATTCTAGGGAGA 58.906 43.478 0.00 0.00 31.73 3.71
380 381 4.160626 AGTTTTGTCCGATTCTAGGGAGAG 59.839 45.833 0.00 0.00 31.77 3.20
384 385 2.136863 TCCGATTCTAGGGAGAGAGGT 58.863 52.381 0.00 0.00 31.77 3.85
454 455 4.072839 CGCTAGGTGGTCTATGTATCTGA 58.927 47.826 0.00 0.00 0.00 3.27
703 1059 6.748658 GGGGTGTATAATGCGTTAAGTTTTTC 59.251 38.462 1.76 0.00 0.00 2.29
758 1142 1.080705 AGACAGTCTAACCGCGCAC 60.081 57.895 8.75 0.00 0.00 5.34
774 1158 1.234615 GCACGTGGCCTTGAAAGCTA 61.235 55.000 18.88 0.00 36.11 3.32
775 1159 1.234821 CACGTGGCCTTGAAAGCTAA 58.765 50.000 7.95 0.00 0.00 3.09
811 1195 2.039613 AGTTCAGCCTAGAAAAGCAGCT 59.960 45.455 0.00 0.00 0.00 4.24
814 1198 2.238144 TCAGCCTAGAAAAGCAGCTCAT 59.762 45.455 0.00 0.00 0.00 2.90
815 1199 3.015327 CAGCCTAGAAAAGCAGCTCATT 58.985 45.455 0.00 0.00 0.00 2.57
816 1200 4.080919 TCAGCCTAGAAAAGCAGCTCATTA 60.081 41.667 0.00 0.00 0.00 1.90
817 1201 4.272991 CAGCCTAGAAAAGCAGCTCATTAG 59.727 45.833 0.00 0.00 0.00 1.73
818 1202 3.563390 GCCTAGAAAAGCAGCTCATTAGG 59.437 47.826 13.89 13.89 0.00 2.69
819 1203 4.775236 CCTAGAAAAGCAGCTCATTAGGT 58.225 43.478 0.00 0.00 0.00 3.08
820 1204 4.813697 CCTAGAAAAGCAGCTCATTAGGTC 59.186 45.833 0.00 0.00 0.00 3.85
821 1205 4.566426 AGAAAAGCAGCTCATTAGGTCT 57.434 40.909 0.00 0.00 0.00 3.85
822 1206 4.916183 AGAAAAGCAGCTCATTAGGTCTT 58.084 39.130 0.00 0.00 0.00 3.01
823 1207 6.054860 AGAAAAGCAGCTCATTAGGTCTTA 57.945 37.500 0.00 0.00 0.00 2.10
824 1208 6.657875 AGAAAAGCAGCTCATTAGGTCTTAT 58.342 36.000 0.00 0.00 0.00 1.73
825 1209 7.796054 AGAAAAGCAGCTCATTAGGTCTTATA 58.204 34.615 0.00 0.00 0.00 0.98
826 1210 8.435982 AGAAAAGCAGCTCATTAGGTCTTATAT 58.564 33.333 0.00 0.00 0.00 0.86
827 1211 7.976135 AAAGCAGCTCATTAGGTCTTATATG 57.024 36.000 0.00 0.00 0.00 1.78
828 1212 6.924913 AGCAGCTCATTAGGTCTTATATGA 57.075 37.500 0.00 0.00 0.00 2.15
829 1213 7.493499 AGCAGCTCATTAGGTCTTATATGAT 57.507 36.000 0.00 0.00 0.00 2.45
830 1214 7.329499 AGCAGCTCATTAGGTCTTATATGATG 58.671 38.462 0.00 0.00 0.00 3.07
831 1215 6.538021 GCAGCTCATTAGGTCTTATATGATGG 59.462 42.308 0.00 0.00 0.00 3.51
832 1216 7.046652 CAGCTCATTAGGTCTTATATGATGGG 58.953 42.308 0.00 0.00 0.00 4.00
833 1217 6.962311 AGCTCATTAGGTCTTATATGATGGGA 59.038 38.462 0.00 0.00 0.00 4.37
834 1218 7.125507 AGCTCATTAGGTCTTATATGATGGGAG 59.874 40.741 0.00 0.00 0.00 4.30
835 1219 7.634649 GCTCATTAGGTCTTATATGATGGGAGG 60.635 44.444 0.00 0.00 0.00 4.30
836 1220 7.256399 TCATTAGGTCTTATATGATGGGAGGT 58.744 38.462 0.00 0.00 0.00 3.85
837 1221 6.935240 TTAGGTCTTATATGATGGGAGGTG 57.065 41.667 0.00 0.00 0.00 4.00
838 1222 3.584848 AGGTCTTATATGATGGGAGGTGC 59.415 47.826 0.00 0.00 0.00 5.01
839 1223 3.584848 GGTCTTATATGATGGGAGGTGCT 59.415 47.826 0.00 0.00 0.00 4.40
840 1224 4.042187 GGTCTTATATGATGGGAGGTGCTT 59.958 45.833 0.00 0.00 0.00 3.91
841 1225 5.248477 GGTCTTATATGATGGGAGGTGCTTA 59.752 44.000 0.00 0.00 0.00 3.09
842 1226 6.402222 GTCTTATATGATGGGAGGTGCTTAG 58.598 44.000 0.00 0.00 0.00 2.18
843 1227 6.211584 GTCTTATATGATGGGAGGTGCTTAGA 59.788 42.308 0.00 0.00 0.00 2.10
844 1228 6.787458 TCTTATATGATGGGAGGTGCTTAGAA 59.213 38.462 0.00 0.00 0.00 2.10
845 1229 5.912149 ATATGATGGGAGGTGCTTAGAAA 57.088 39.130 0.00 0.00 0.00 2.52
846 1230 3.634397 TGATGGGAGGTGCTTAGAAAG 57.366 47.619 0.00 0.00 0.00 2.62
847 1231 2.239654 TGATGGGAGGTGCTTAGAAAGG 59.760 50.000 0.00 0.00 0.00 3.11
848 1232 1.742308 TGGGAGGTGCTTAGAAAGGT 58.258 50.000 0.00 0.00 0.00 3.50
849 1233 1.351017 TGGGAGGTGCTTAGAAAGGTG 59.649 52.381 0.00 0.00 0.00 4.00
850 1234 1.454201 GGAGGTGCTTAGAAAGGTGC 58.546 55.000 0.00 0.00 0.00 5.01
851 1235 1.003696 GGAGGTGCTTAGAAAGGTGCT 59.996 52.381 0.00 0.00 0.00 4.40
852 1236 2.553247 GGAGGTGCTTAGAAAGGTGCTT 60.553 50.000 0.00 0.00 0.00 3.91
853 1237 3.307480 GGAGGTGCTTAGAAAGGTGCTTA 60.307 47.826 0.00 0.00 0.00 3.09
854 1238 4.324267 GAGGTGCTTAGAAAGGTGCTTAA 58.676 43.478 0.00 0.00 0.00 1.85
855 1239 4.725490 AGGTGCTTAGAAAGGTGCTTAAA 58.275 39.130 0.00 0.00 0.00 1.52
856 1240 5.137551 AGGTGCTTAGAAAGGTGCTTAAAA 58.862 37.500 0.00 0.00 0.00 1.52
857 1241 5.596772 AGGTGCTTAGAAAGGTGCTTAAAAA 59.403 36.000 0.00 0.00 0.00 1.94
897 1281 9.855021 TTCTTAAGCATTATTTTTCTAAGCACC 57.145 29.630 0.00 0.00 0.00 5.01
898 1282 9.243105 TCTTAAGCATTATTTTTCTAAGCACCT 57.757 29.630 0.00 0.00 0.00 4.00
899 1283 9.508567 CTTAAGCATTATTTTTCTAAGCACCTC 57.491 33.333 0.00 0.00 0.00 3.85
900 1284 6.456795 AGCATTATTTTTCTAAGCACCTCC 57.543 37.500 0.00 0.00 0.00 4.30
901 1285 6.190587 AGCATTATTTTTCTAAGCACCTCCT 58.809 36.000 0.00 0.00 0.00 3.69
902 1286 6.319911 AGCATTATTTTTCTAAGCACCTCCTC 59.680 38.462 0.00 0.00 0.00 3.71
903 1287 6.319911 GCATTATTTTTCTAAGCACCTCCTCT 59.680 38.462 0.00 0.00 0.00 3.69
904 1288 7.499232 GCATTATTTTTCTAAGCACCTCCTCTA 59.501 37.037 0.00 0.00 0.00 2.43
905 1289 9.396022 CATTATTTTTCTAAGCACCTCCTCTAA 57.604 33.333 0.00 0.00 0.00 2.10
906 1290 9.620259 ATTATTTTTCTAAGCACCTCCTCTAAG 57.380 33.333 0.00 0.00 0.00 2.18
907 1291 4.473477 TTTCTAAGCACCTCCTCTAAGC 57.527 45.455 0.00 0.00 0.00 3.09
908 1292 2.025155 TCTAAGCACCTCCTCTAAGCG 58.975 52.381 0.00 0.00 0.00 4.68
909 1293 1.751924 CTAAGCACCTCCTCTAAGCGT 59.248 52.381 0.00 0.00 0.00 5.07
910 1294 1.848652 AAGCACCTCCTCTAAGCGTA 58.151 50.000 0.00 0.00 0.00 4.42
911 1295 1.104630 AGCACCTCCTCTAAGCGTAC 58.895 55.000 0.00 0.00 0.00 3.67
912 1296 0.815734 GCACCTCCTCTAAGCGTACA 59.184 55.000 0.00 0.00 0.00 2.90
913 1297 1.203994 GCACCTCCTCTAAGCGTACAA 59.796 52.381 0.00 0.00 0.00 2.41
914 1298 2.735762 GCACCTCCTCTAAGCGTACAAG 60.736 54.545 0.00 0.00 0.00 3.16
915 1299 2.100989 ACCTCCTCTAAGCGTACAAGG 58.899 52.381 0.00 0.00 0.00 3.61
916 1300 1.202428 CCTCCTCTAAGCGTACAAGGC 60.202 57.143 0.00 0.00 0.00 4.35
917 1301 0.822164 TCCTCTAAGCGTACAAGGCC 59.178 55.000 0.00 0.00 0.00 5.19
940 1324 0.249911 GCCCACGCGATAATCCTTCT 60.250 55.000 15.93 0.00 0.00 2.85
941 1325 1.502231 CCCACGCGATAATCCTTCTG 58.498 55.000 15.93 0.00 0.00 3.02
942 1326 1.502231 CCACGCGATAATCCTTCTGG 58.498 55.000 15.93 0.91 0.00 3.86
943 1327 0.861837 CACGCGATAATCCTTCTGGC 59.138 55.000 15.93 0.00 0.00 4.85
977 1361 1.827394 GGCCCACCGCAGTATCTAA 59.173 57.895 0.00 0.00 40.31 2.10
1131 1519 2.686106 GCCCGACTCCCCCTTGTA 60.686 66.667 0.00 0.00 0.00 2.41
1267 1669 1.403687 CGTGGATTCTCCCTCTCCCC 61.404 65.000 0.00 0.00 35.03 4.81
1406 1809 2.289819 GGTAACTGATTCACGAACCCCA 60.290 50.000 0.00 0.00 0.00 4.96
1411 1814 0.953960 GATTCACGAACCCCACGCTT 60.954 55.000 0.00 0.00 0.00 4.68
1440 1843 2.165998 GGAGATTTCAACTGCTTGGCT 58.834 47.619 0.00 0.00 0.00 4.75
1584 2002 4.467769 CAGGGAAAGCATCAATGAGGTAT 58.532 43.478 0.00 0.00 0.00 2.73
1667 2085 7.394359 ACCGGCTAAATTCATGATTATTATGCT 59.606 33.333 0.00 0.00 0.00 3.79
2137 2556 5.742926 GTCTTCTAAGAACATGCGTAGTACC 59.257 44.000 0.00 0.00 36.68 3.34
2144 2563 6.466885 AGAACATGCGTAGTACCTTATCTT 57.533 37.500 0.00 0.00 0.00 2.40
2240 2659 8.598924 CATCATATGAGTTACTTCTGTTCACAC 58.401 37.037 11.78 0.00 0.00 3.82
2281 2700 8.761575 AAATGTCTTTATACAATTGCAACAGG 57.238 30.769 0.00 0.00 32.02 4.00
2322 2741 1.815003 GAAATAGCTGCAGTGCCTGTT 59.185 47.619 16.64 5.81 33.43 3.16
2545 3234 4.828939 TGACAGGTAAAGACTCCTACGAAA 59.171 41.667 0.00 0.00 32.26 3.46
2552 3241 3.528597 AGACTCCTACGAAATTCAGGC 57.471 47.619 0.00 0.00 0.00 4.85
2623 4342 4.340381 CAGGAGCAATTAAGGATTCCTTGG 59.660 45.833 25.26 13.86 44.44 3.61
2994 4716 4.811557 GTGCAGGATTTTATCGTTAGAGCT 59.188 41.667 0.00 0.00 0.00 4.09
3126 4849 5.633830 TCAGGATTTCTGCTGAAACAATC 57.366 39.130 19.47 13.51 45.62 2.67
3142 4865 9.277783 CTGAAACAATCGAGGATAGGAATAAAT 57.722 33.333 0.00 0.00 0.00 1.40
3250 4973 6.881065 GGAAGTAGCTGCATAATCATCCAATA 59.119 38.462 4.12 0.00 0.00 1.90
3305 5030 9.817809 GATACAAATCATTACTTACTGAGTCCA 57.182 33.333 0.00 0.00 34.59 4.02
3530 5296 1.517242 CAGGAGAAACTGTGTGGCTC 58.483 55.000 0.00 0.00 33.81 4.70
3658 5424 7.447238 CAGTTCCTTTACTTCCTCAATAACCAA 59.553 37.037 0.00 0.00 0.00 3.67
3710 5476 0.675633 AAGCAAAAGCAGCGAATGGT 59.324 45.000 0.00 0.00 42.89 3.55
3871 5637 0.036022 GGCAGAGCAGTTCTTGAGGT 59.964 55.000 0.00 0.00 32.41 3.85
3933 5699 1.820519 TGGCAGATCCATGTTTTGAGC 59.179 47.619 0.00 0.00 40.72 4.26
4006 5772 3.064408 GCTTCATGAAGATGATCGCACAA 59.936 43.478 34.43 0.00 40.79 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.323629 TCGATCCCCAGGAAACACAC 59.676 55.000 0.00 0.00 34.34 3.82
3 4 1.633432 ACAATCGATCCCCAGGAAACA 59.367 47.619 0.00 0.00 34.34 2.83
5 6 2.307392 TCAACAATCGATCCCCAGGAAA 59.693 45.455 0.00 0.00 34.34 3.13
8 9 2.645838 ATCAACAATCGATCCCCAGG 57.354 50.000 0.00 0.00 0.00 4.45
9 10 3.324846 TCCTATCAACAATCGATCCCCAG 59.675 47.826 0.00 0.00 0.00 4.45
11 12 4.351874 TTCCTATCAACAATCGATCCCC 57.648 45.455 0.00 0.00 0.00 4.81
12 13 4.938226 GGATTCCTATCAACAATCGATCCC 59.062 45.833 0.00 0.00 32.09 3.85
13 14 4.938226 GGGATTCCTATCAACAATCGATCC 59.062 45.833 0.00 0.00 32.09 3.36
14 15 4.938226 GGGGATTCCTATCAACAATCGATC 59.062 45.833 0.00 0.00 32.09 3.69
15 16 4.263506 GGGGGATTCCTATCAACAATCGAT 60.264 45.833 2.01 0.00 35.33 3.59
16 17 3.072476 GGGGGATTCCTATCAACAATCGA 59.928 47.826 2.01 0.00 35.33 3.59
17 18 3.181445 TGGGGGATTCCTATCAACAATCG 60.181 47.826 2.01 0.00 35.33 3.34
18 19 4.453480 TGGGGGATTCCTATCAACAATC 57.547 45.455 2.01 0.00 35.33 2.67
19 20 4.898014 TTGGGGGATTCCTATCAACAAT 57.102 40.909 2.01 0.00 35.33 2.71
20 21 4.683766 TTTGGGGGATTCCTATCAACAA 57.316 40.909 2.01 0.00 35.33 2.83
21 22 4.609301 CTTTTGGGGGATTCCTATCAACA 58.391 43.478 2.01 0.00 35.33 3.33
61 62 8.025243 TGTAAAATTCAAGAACTGTCGGTATC 57.975 34.615 0.00 0.00 0.00 2.24
81 82 4.157656 GCCATGCTGATTGGTACTTGTAAA 59.842 41.667 0.00 0.00 36.57 2.01
270 271 0.596083 CTGCCGGCGATGAAGAGTAG 60.596 60.000 23.90 5.20 0.00 2.57
283 284 0.738389 AACAGAACAACAACTGCCGG 59.262 50.000 0.00 0.00 37.61 6.13
288 289 4.261801 ACTAGCACAACAGAACAACAACT 58.738 39.130 0.00 0.00 0.00 3.16
301 302 7.068716 TGCTAAGATCTCATAGAACTAGCACAA 59.931 37.037 14.53 0.00 33.51 3.33
308 309 6.488344 TCGTCATGCTAAGATCTCATAGAACT 59.512 38.462 5.74 0.00 0.00 3.01
320 321 1.134367 CGGGAAGTCGTCATGCTAAGA 59.866 52.381 0.00 0.00 0.00 2.10
364 365 2.136863 ACCTCTCTCCCTAGAATCGGA 58.863 52.381 0.00 0.00 0.00 4.55
375 376 0.457851 CCGTCATCACACCTCTCTCC 59.542 60.000 0.00 0.00 0.00 3.71
379 380 2.573869 CGCCGTCATCACACCTCT 59.426 61.111 0.00 0.00 0.00 3.69
380 381 2.509336 CCGCCGTCATCACACCTC 60.509 66.667 0.00 0.00 0.00 3.85
475 476 0.105964 TTGGCAGTACAACGAGCACT 59.894 50.000 0.00 0.00 0.00 4.40
725 1107 4.127171 GACTGTCTGCTTTCCACTTAACA 58.873 43.478 0.00 0.00 0.00 2.41
737 1119 1.213013 CGCGGTTAGACTGTCTGCT 59.787 57.895 20.19 0.00 0.00 4.24
758 1142 1.401539 GCTTTAGCTTTCAAGGCCACG 60.402 52.381 5.01 0.00 38.21 4.94
768 1152 2.489938 TCGTCATGGGCTTTAGCTTT 57.510 45.000 0.00 0.00 41.70 3.51
774 1158 3.941483 CTGAACTTATCGTCATGGGCTTT 59.059 43.478 0.00 0.00 0.00 3.51
775 1159 3.535561 CTGAACTTATCGTCATGGGCTT 58.464 45.455 0.00 0.00 0.00 4.35
811 1195 7.180946 CACCTCCCATCATATAAGACCTAATGA 59.819 40.741 0.00 0.00 33.20 2.57
814 1198 5.248477 GCACCTCCCATCATATAAGACCTAA 59.752 44.000 0.00 0.00 0.00 2.69
815 1199 4.777896 GCACCTCCCATCATATAAGACCTA 59.222 45.833 0.00 0.00 0.00 3.08
816 1200 3.584848 GCACCTCCCATCATATAAGACCT 59.415 47.826 0.00 0.00 0.00 3.85
817 1201 3.584848 AGCACCTCCCATCATATAAGACC 59.415 47.826 0.00 0.00 0.00 3.85
818 1202 4.899352 AGCACCTCCCATCATATAAGAC 57.101 45.455 0.00 0.00 0.00 3.01
819 1203 6.322931 TCTAAGCACCTCCCATCATATAAGA 58.677 40.000 0.00 0.00 0.00 2.10
820 1204 6.611613 TCTAAGCACCTCCCATCATATAAG 57.388 41.667 0.00 0.00 0.00 1.73
821 1205 7.387265 TTTCTAAGCACCTCCCATCATATAA 57.613 36.000 0.00 0.00 0.00 0.98
822 1206 6.013379 CCTTTCTAAGCACCTCCCATCATATA 60.013 42.308 0.00 0.00 0.00 0.86
823 1207 5.222007 CCTTTCTAAGCACCTCCCATCATAT 60.222 44.000 0.00 0.00 0.00 1.78
824 1208 4.103153 CCTTTCTAAGCACCTCCCATCATA 59.897 45.833 0.00 0.00 0.00 2.15
825 1209 3.117738 CCTTTCTAAGCACCTCCCATCAT 60.118 47.826 0.00 0.00 0.00 2.45
826 1210 2.239654 CCTTTCTAAGCACCTCCCATCA 59.760 50.000 0.00 0.00 0.00 3.07
827 1211 2.239907 ACCTTTCTAAGCACCTCCCATC 59.760 50.000 0.00 0.00 0.00 3.51
828 1212 2.025887 CACCTTTCTAAGCACCTCCCAT 60.026 50.000 0.00 0.00 0.00 4.00
829 1213 1.351017 CACCTTTCTAAGCACCTCCCA 59.649 52.381 0.00 0.00 0.00 4.37
830 1214 1.950954 GCACCTTTCTAAGCACCTCCC 60.951 57.143 0.00 0.00 0.00 4.30
831 1215 1.003696 AGCACCTTTCTAAGCACCTCC 59.996 52.381 0.00 0.00 0.00 4.30
832 1216 2.481289 AGCACCTTTCTAAGCACCTC 57.519 50.000 0.00 0.00 0.00 3.85
833 1217 2.959465 AAGCACCTTTCTAAGCACCT 57.041 45.000 0.00 0.00 0.00 4.00
834 1218 5.447624 TTTTAAGCACCTTTCTAAGCACC 57.552 39.130 0.00 0.00 0.00 5.01
871 1255 9.855021 GGTGCTTAGAAAAATAATGCTTAAGAA 57.145 29.630 6.67 0.00 0.00 2.52
872 1256 9.243105 AGGTGCTTAGAAAAATAATGCTTAAGA 57.757 29.630 6.67 0.00 0.00 2.10
873 1257 9.508567 GAGGTGCTTAGAAAAATAATGCTTAAG 57.491 33.333 0.00 0.00 0.00 1.85
874 1258 8.466798 GGAGGTGCTTAGAAAAATAATGCTTAA 58.533 33.333 0.00 0.00 0.00 1.85
875 1259 7.834181 AGGAGGTGCTTAGAAAAATAATGCTTA 59.166 33.333 0.00 0.00 0.00 3.09
876 1260 6.665248 AGGAGGTGCTTAGAAAAATAATGCTT 59.335 34.615 0.00 0.00 0.00 3.91
877 1261 6.190587 AGGAGGTGCTTAGAAAAATAATGCT 58.809 36.000 0.00 0.00 0.00 3.79
878 1262 6.319911 AGAGGAGGTGCTTAGAAAAATAATGC 59.680 38.462 0.00 0.00 0.00 3.56
879 1263 7.872113 AGAGGAGGTGCTTAGAAAAATAATG 57.128 36.000 0.00 0.00 0.00 1.90
880 1264 9.620259 CTTAGAGGAGGTGCTTAGAAAAATAAT 57.380 33.333 0.00 0.00 0.00 1.28
881 1265 7.553044 GCTTAGAGGAGGTGCTTAGAAAAATAA 59.447 37.037 0.00 0.00 0.00 1.40
882 1266 7.048512 GCTTAGAGGAGGTGCTTAGAAAAATA 58.951 38.462 0.00 0.00 0.00 1.40
883 1267 5.883115 GCTTAGAGGAGGTGCTTAGAAAAAT 59.117 40.000 0.00 0.00 0.00 1.82
884 1268 5.246307 GCTTAGAGGAGGTGCTTAGAAAAA 58.754 41.667 0.00 0.00 0.00 1.94
885 1269 4.620803 CGCTTAGAGGAGGTGCTTAGAAAA 60.621 45.833 0.00 0.00 0.00 2.29
886 1270 3.119101 CGCTTAGAGGAGGTGCTTAGAAA 60.119 47.826 0.00 0.00 0.00 2.52
887 1271 2.427453 CGCTTAGAGGAGGTGCTTAGAA 59.573 50.000 0.00 0.00 0.00 2.10
888 1272 2.025155 CGCTTAGAGGAGGTGCTTAGA 58.975 52.381 0.00 0.00 0.00 2.10
889 1273 1.751924 ACGCTTAGAGGAGGTGCTTAG 59.248 52.381 0.00 0.00 0.00 2.18
890 1274 1.848652 ACGCTTAGAGGAGGTGCTTA 58.151 50.000 0.00 0.00 0.00 3.09
891 1275 1.477295 GTACGCTTAGAGGAGGTGCTT 59.523 52.381 0.00 0.00 0.00 3.91
892 1276 1.104630 GTACGCTTAGAGGAGGTGCT 58.895 55.000 0.00 0.00 0.00 4.40
893 1277 0.815734 TGTACGCTTAGAGGAGGTGC 59.184 55.000 0.00 0.00 0.00 5.01
894 1278 2.159226 CCTTGTACGCTTAGAGGAGGTG 60.159 54.545 0.00 0.00 0.00 4.00
895 1279 2.100989 CCTTGTACGCTTAGAGGAGGT 58.899 52.381 0.00 0.00 0.00 3.85
896 1280 1.202428 GCCTTGTACGCTTAGAGGAGG 60.202 57.143 4.31 0.00 0.00 4.30
897 1281 1.202428 GGCCTTGTACGCTTAGAGGAG 60.202 57.143 0.00 0.00 0.00 3.69
898 1282 0.822164 GGCCTTGTACGCTTAGAGGA 59.178 55.000 0.00 0.00 0.00 3.71
899 1283 0.824759 AGGCCTTGTACGCTTAGAGG 59.175 55.000 0.00 0.00 0.00 3.69
900 1284 2.674796 AAGGCCTTGTACGCTTAGAG 57.325 50.000 19.73 0.00 0.00 2.43
901 1285 2.159142 GCTAAGGCCTTGTACGCTTAGA 60.159 50.000 28.77 2.40 0.00 2.10
902 1286 2.202566 GCTAAGGCCTTGTACGCTTAG 58.797 52.381 28.77 15.29 0.00 2.18
903 1287 2.304751 GCTAAGGCCTTGTACGCTTA 57.695 50.000 28.77 4.02 0.00 3.09
904 1288 3.154589 GCTAAGGCCTTGTACGCTT 57.845 52.632 28.77 0.57 0.00 4.68
905 1289 4.934989 GCTAAGGCCTTGTACGCT 57.065 55.556 28.77 1.45 0.00 5.07
915 1299 0.602905 ATTATCGCGTGGGCTAAGGC 60.603 55.000 5.77 0.00 36.88 4.35
916 1300 1.429463 GATTATCGCGTGGGCTAAGG 58.571 55.000 5.77 0.00 36.88 2.69
917 1301 1.000955 AGGATTATCGCGTGGGCTAAG 59.999 52.381 5.77 0.00 36.88 2.18
924 1308 0.861837 GCCAGAAGGATTATCGCGTG 59.138 55.000 5.77 0.00 36.89 5.34
940 1324 1.471119 CGTAGAGTAAGACCCAGCCA 58.529 55.000 0.00 0.00 0.00 4.75
941 1325 0.745468 CCGTAGAGTAAGACCCAGCC 59.255 60.000 0.00 0.00 0.00 4.85
942 1326 0.102663 GCCGTAGAGTAAGACCCAGC 59.897 60.000 0.00 0.00 0.00 4.85
943 1327 0.745468 GGCCGTAGAGTAAGACCCAG 59.255 60.000 0.00 0.00 0.00 4.45
975 1359 2.642254 CGCCGGACCAGGAGTGTTA 61.642 63.158 5.05 0.00 0.00 2.41
1184 1583 0.331954 AGAGGGTAGCGAGAAGGACA 59.668 55.000 0.00 0.00 0.00 4.02
1371 1774 1.966354 AGTTACCTCGGTTTCGGACTT 59.034 47.619 0.00 0.00 36.95 3.01
1372 1775 1.271656 CAGTTACCTCGGTTTCGGACT 59.728 52.381 0.00 0.00 36.95 3.85
1391 1794 1.669760 GCGTGGGGTTCGTGAATCA 60.670 57.895 0.00 0.00 0.00 2.57
1406 1809 4.003788 CTCCCCCGTGTGAAGCGT 62.004 66.667 0.00 0.00 0.00 5.07
1411 1814 1.060729 TTGAAATCTCCCCCGTGTGA 58.939 50.000 0.00 0.00 0.00 3.58
1440 1843 2.039418 ACTTGCGTATATCTGCAGGGA 58.961 47.619 15.13 1.94 41.92 4.20
1464 1882 7.412563 CGGCGATAAATTACAGAGTCAGAAAAA 60.413 37.037 0.00 0.00 0.00 1.94
1468 1886 4.097437 ACGGCGATAAATTACAGAGTCAGA 59.903 41.667 16.62 0.00 0.00 3.27
1469 1887 4.360563 ACGGCGATAAATTACAGAGTCAG 58.639 43.478 16.62 0.00 0.00 3.51
1584 2002 6.154445 CACTAGCACGGTTCTAACTTCTAAA 58.846 40.000 0.00 0.00 0.00 1.85
1636 2054 9.912634 AATAATCATGAATTTAGCCGGTAAATG 57.087 29.630 14.69 5.89 39.95 2.32
1667 2085 7.387265 TGAGCCCCAATTAGATACAAGAATA 57.613 36.000 0.00 0.00 0.00 1.75
1672 2090 6.430864 TGAAATGAGCCCCAATTAGATACAA 58.569 36.000 0.00 0.00 0.00 2.41
1929 2347 6.653320 AGCAATCAAATCACAATCAAAGCAAT 59.347 30.769 0.00 0.00 0.00 3.56
2083 2501 8.511604 AATCATTTTCCTTCATTCGACTGTAT 57.488 30.769 2.44 0.00 0.00 2.29
2281 2700 2.190325 GCAATCAGCATGCTTGAGTC 57.810 50.000 19.98 3.78 44.46 3.36
2322 2741 2.951642 CAGAGACAAGAGGGTGCAAAAA 59.048 45.455 0.00 0.00 0.00 1.94
2332 2751 3.902881 ATTGGGTAGCAGAGACAAGAG 57.097 47.619 0.00 0.00 0.00 2.85
2399 3088 6.486993 ACCAGAAACTTCCTGTTGTTAAGATC 59.513 38.462 0.00 0.00 39.13 2.75
2463 3152 4.883021 AGGAGATAGAACACCAGGAGTA 57.117 45.455 0.00 0.00 0.00 2.59
2545 3234 8.757982 ATATAATGACAAGTGAAAGCCTGAAT 57.242 30.769 0.00 0.00 0.00 2.57
2577 4296 6.417258 TGAAATAGAGGTGCATGAATCAGAA 58.583 36.000 0.00 0.00 0.00 3.02
2623 4342 3.004839 TGCGCAATCTCATACTCCTCTAC 59.995 47.826 8.16 0.00 0.00 2.59
2883 4605 9.485591 GAATTCGATGCTCTTAAAAATCGTTAA 57.514 29.630 4.10 0.00 41.92 2.01
3069 4791 6.204882 GCAAGTGTGTAAACTGGATTTCTACT 59.795 38.462 0.00 0.00 0.00 2.57
3126 4849 4.386049 GCGACACATTTATTCCTATCCTCG 59.614 45.833 0.00 0.00 0.00 4.63
3142 4865 3.723260 TGAGTAATTTGACAGCGACACA 58.277 40.909 0.00 0.00 0.00 3.72
3250 4973 2.289694 CCTTCTCTGACCCGTGTTTCAT 60.290 50.000 0.00 0.00 0.00 2.57
3305 5030 2.613977 CCAGCGATCAGACCTGTTTTCT 60.614 50.000 0.00 0.00 0.00 2.52
3530 5296 2.260844 ATGATGGTGTGCGATTAGGG 57.739 50.000 0.00 0.00 0.00 3.53
3658 5424 4.342359 AGAAATGGTAGTACGACTGGAGT 58.658 43.478 6.07 0.00 0.00 3.85
3710 5476 3.306364 GCCTTGAGTTCTCTGAAGCACTA 60.306 47.826 1.53 0.00 34.41 2.74
3933 5699 1.006832 CAACCACGGCTATTTCTCGG 58.993 55.000 0.00 0.00 0.00 4.63
4006 5772 1.600636 CGTTGTGCCCCTGATGTGT 60.601 57.895 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.