Multiple sequence alignment - TraesCS7D01G419000

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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 TraesCS7D01G419000 chr7D 100.000 2336 0 0 1 2336 538585971 538588306 0.000000e+00 4314.0
1 TraesCS7D01G419000 chr7D 86.538 1352 122 43 18 1345 538141071 538139756 0.000000e+00 1434.0
2 TraesCS7D01G419000 chr7D 85.357 1359 141 41 21 1345 538661827 538663161 0.000000e+00 1354.0
3 TraesCS7D01G419000 chr7D 84.127 1386 146 40 13 1373 538594537 538595873 0.000000e+00 1273.0
4 TraesCS7D01G419000 chr7D 84.078 1388 150 37 21 1373 538602418 538603769 0.000000e+00 1273.0
5 TraesCS7D01G419000 chr7D 89.326 965 80 13 402 1345 538333165 538332203 0.000000e+00 1190.0
6 TraesCS7D01G419000 chr7D 85.780 1090 117 17 265 1342 538212130 538211067 0.000000e+00 1120.0
7 TraesCS7D01G419000 chr7D 86.757 370 18 11 24 363 538333524 538333156 1.310000e-102 383.0
8 TraesCS7D01G419000 chr7D 99.346 153 1 0 1628 1780 538596294 538596446 6.360000e-71 278.0
9 TraesCS7D01G419000 chr7D 92.432 185 13 1 2150 2334 538630089 538630272 1.780000e-66 263.0
10 TraesCS7D01G419000 chr7D 89.506 162 8 5 1628 1780 538604943 538605104 1.830000e-46 196.0
11 TraesCS7D01G419000 chr7D 91.339 127 8 3 93 217 538240074 538239949 1.110000e-38 171.0
12 TraesCS7D01G419000 chr7D 86.957 115 15 0 1982 2096 538606008 538606122 1.880000e-26 130.0
13 TraesCS7D01G419000 chr7D 98.077 52 1 0 1525 1576 538596171 538596222 8.890000e-15 91.6
14 TraesCS7D01G419000 chr7B 84.764 1608 155 40 17 1590 581313550 581315101 0.000000e+00 1530.0
15 TraesCS7D01G419000 chr7B 87.127 1375 115 30 17 1345 580970584 580969226 0.000000e+00 1502.0
16 TraesCS7D01G419000 chr7B 86.863 1355 130 30 13 1345 581333190 581334518 0.000000e+00 1472.0
17 TraesCS7D01G419000 chr7B 86.130 1341 126 32 18 1340 580885904 580884606 0.000000e+00 1391.0
18 TraesCS7D01G419000 chr7B 89.796 245 19 2 2095 2334 581315809 581316052 2.250000e-80 309.0
19 TraesCS7D01G419000 chr7B 90.741 162 6 5 1628 1780 581315181 581315342 8.460000e-50 207.0
20 TraesCS7D01G419000 chr7A 86.687 1337 116 44 24 1345 619167196 619165907 0.000000e+00 1426.0
21 TraesCS7D01G419000 chr7A 85.725 1345 139 35 26 1345 620171357 620172673 0.000000e+00 1371.0
22 TraesCS7D01G419000 chr7A 85.524 1354 148 31 13 1345 620201246 620202572 0.000000e+00 1371.0
23 TraesCS7D01G419000 chr7A 91.608 846 58 8 1 835 619634312 619633469 0.000000e+00 1157.0
24 TraesCS7D01G419000 chr7A 91.608 846 58 8 1 835 619906886 619907729 0.000000e+00 1157.0
25 TraesCS7D01G419000 chr7A 86.477 843 77 23 24 845 619576909 619576083 0.000000e+00 891.0
26 TraesCS7D01G419000 chr7A 91.039 491 42 1 885 1373 619907740 619908230 0.000000e+00 662.0
27 TraesCS7D01G419000 chr7A 92.130 432 33 1 915 1346 619576033 619575603 1.980000e-170 608.0
28 TraesCS7D01G419000 chr7A 92.593 162 3 1 1628 1780 619908503 619908664 8.400000e-55 224.0
29 TraesCS7D01G419000 chr7A 88.889 162 18 0 1781 1942 730603085 730603246 1.420000e-47 200.0
30 TraesCS7D01G419000 chr7A 98.276 58 1 0 1628 1685 620197883 620197940 4.110000e-18 102.0
31 TraesCS7D01G419000 chr7A 94.118 51 3 0 2284 2334 619911866 619911916 6.920000e-11 78.7
32 TraesCS7D01G419000 chr6A 89.506 162 17 0 1781 1942 503245897 503245736 3.040000e-49 206.0
33 TraesCS7D01G419000 chr6A 88.889 162 18 0 1781 1942 615711037 615711198 1.420000e-47 200.0
34 TraesCS7D01G419000 chr1A 89.506 162 17 0 1781 1942 329013773 329013934 3.040000e-49 206.0
35 TraesCS7D01G419000 chr3A 90.728 151 14 0 1789 1939 653920765 653920915 3.940000e-48 202.0
36 TraesCS7D01G419000 chr6D 88.344 163 18 1 1781 1942 254904020 254904182 6.590000e-46 195.0
37 TraesCS7D01G419000 chr4D 88.679 159 18 0 1781 1939 100317692 100317850 6.590000e-46 195.0
38 TraesCS7D01G419000 chr2A 88.272 162 19 0 1781 1942 575349187 575349026 6.590000e-46 195.0
39 TraesCS7D01G419000 chr2A 88.272 162 19 0 1781 1942 608600891 608601052 6.590000e-46 195.0


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 TraesCS7D01G419000 chr7D 538585971 538588306 2335 False 4314.000000 4314 100.000000 1 2336 1 chr7D.!!$F1 2335
1 TraesCS7D01G419000 chr7D 538139756 538141071 1315 True 1434.000000 1434 86.538000 18 1345 1 chr7D.!!$R1 1327
2 TraesCS7D01G419000 chr7D 538661827 538663161 1334 False 1354.000000 1354 85.357000 21 1345 1 chr7D.!!$F3 1324
3 TraesCS7D01G419000 chr7D 538211067 538212130 1063 True 1120.000000 1120 85.780000 265 1342 1 chr7D.!!$R2 1077
4 TraesCS7D01G419000 chr7D 538332203 538333524 1321 True 786.500000 1190 88.041500 24 1345 2 chr7D.!!$R4 1321
5 TraesCS7D01G419000 chr7D 538594537 538596446 1909 False 547.533333 1273 93.850000 13 1780 3 chr7D.!!$F4 1767
6 TraesCS7D01G419000 chr7D 538602418 538606122 3704 False 533.000000 1273 86.847000 21 2096 3 chr7D.!!$F5 2075
7 TraesCS7D01G419000 chr7B 580969226 580970584 1358 True 1502.000000 1502 87.127000 17 1345 1 chr7B.!!$R2 1328
8 TraesCS7D01G419000 chr7B 581333190 581334518 1328 False 1472.000000 1472 86.863000 13 1345 1 chr7B.!!$F1 1332
9 TraesCS7D01G419000 chr7B 580884606 580885904 1298 True 1391.000000 1391 86.130000 18 1340 1 chr7B.!!$R1 1322
10 TraesCS7D01G419000 chr7B 581313550 581316052 2502 False 682.000000 1530 88.433667 17 2334 3 chr7B.!!$F2 2317
11 TraesCS7D01G419000 chr7A 619165907 619167196 1289 True 1426.000000 1426 86.687000 24 1345 1 chr7A.!!$R1 1321
12 TraesCS7D01G419000 chr7A 620171357 620172673 1316 False 1371.000000 1371 85.725000 26 1345 1 chr7A.!!$F1 1319
13 TraesCS7D01G419000 chr7A 619633469 619634312 843 True 1157.000000 1157 91.608000 1 835 1 chr7A.!!$R2 834
14 TraesCS7D01G419000 chr7A 619575603 619576909 1306 True 749.500000 891 89.303500 24 1346 2 chr7A.!!$R3 1322
15 TraesCS7D01G419000 chr7A 620197883 620202572 4689 False 736.500000 1371 91.900000 13 1685 2 chr7A.!!$F4 1672
16 TraesCS7D01G419000 chr7A 619906886 619911916 5030 False 530.425000 1157 92.339500 1 2334 4 chr7A.!!$F3 2333

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
769 4255 0.252057 TCCTCTGGTTCGATCCCACA 60.252 55.0 10.02 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 10449 0.323087 AGAATTACCCACAACCGCCC 60.323 55.0 0.0 0.0 0.0 6.13 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
74 3431 2.298158 AATACACCGGAGCTGGCGAG 62.298 60.000 9.46 0.00 0.00 5.03
281 3725 4.783621 ACGCATGGCTCGCATGGT 62.784 61.111 0.00 0.00 0.00 3.55
314 3764 1.930100 CGATCCTGCTCGCATGTTC 59.070 57.895 0.00 0.00 0.00 3.18
324 3774 2.644418 GCATGTTCTGCCGTTGCA 59.356 55.556 0.00 0.00 45.66 4.08
354 3804 0.664761 TCGACAAGGAGTTCGACGTT 59.335 50.000 0.00 0.00 0.00 3.99
498 3948 4.421479 CTCAAGCTCGTCGCCGGT 62.421 66.667 1.90 0.00 40.39 5.28
501 3951 1.518572 CAAGCTCGTCGCCGGTAAT 60.519 57.895 1.90 0.00 40.39 1.89
577 4036 2.309528 TTTCGGTCTTGATCGGATGG 57.690 50.000 3.37 0.00 0.00 3.51
585 4044 0.742990 TTGATCGGATGGCACGGTTC 60.743 55.000 0.00 0.00 0.00 3.62
586 4045 2.202878 ATCGGATGGCACGGTTCG 60.203 61.111 0.00 0.00 0.00 3.95
678 4164 1.503818 TTCGAGTTCCTTGGCAACGC 61.504 55.000 0.00 0.00 42.51 4.84
703 4189 2.187946 GAGCCCTACACGCTGCAT 59.812 61.111 0.00 0.00 36.48 3.96
769 4255 0.252057 TCCTCTGGTTCGATCCCACA 60.252 55.000 10.02 0.00 0.00 4.17
818 4304 5.775513 CTGGAACCCAAAGCACATCATGC 62.776 52.174 0.00 0.00 43.99 4.06
851 4337 2.033194 CCGTCGCCCAACCTTCTTC 61.033 63.158 0.00 0.00 0.00 2.87
882 4378 0.532862 AACGCCGGCCATCTATTCAG 60.533 55.000 23.46 4.79 0.00 3.02
883 4379 2.320587 CGCCGGCCATCTATTCAGC 61.321 63.158 23.46 0.00 0.00 4.26
890 4399 2.224719 GGCCATCTATTCAGCACAGGAT 60.225 50.000 0.00 0.00 0.00 3.24
994 4519 0.253327 GATCGCCTTCCCCAAGAACT 59.747 55.000 0.00 0.00 0.00 3.01
1210 4753 2.522638 GCGGCCGAAGATTGGTACG 61.523 63.158 33.48 0.00 33.92 3.67
1289 4832 2.165641 TGATCTACAACTACTGCACGGG 59.834 50.000 0.00 0.00 0.00 5.28
1380 4983 2.094854 AGACGACCGGAGATGTGTAAAC 60.095 50.000 9.46 0.00 0.00 2.01
1447 5064 5.235616 CGCCCAACTCGTGTGTAATATATTT 59.764 40.000 2.68 0.00 0.00 1.40
1455 5072 7.506261 ACTCGTGTGTAATATATTTCCTCCTCT 59.494 37.037 2.68 0.00 0.00 3.69
1456 5073 8.929260 TCGTGTGTAATATATTTCCTCCTCTA 57.071 34.615 2.68 0.00 0.00 2.43
1457 5074 9.011095 TCGTGTGTAATATATTTCCTCCTCTAG 57.989 37.037 2.68 0.00 0.00 2.43
1458 5075 8.794553 CGTGTGTAATATATTTCCTCCTCTAGT 58.205 37.037 2.68 0.00 0.00 2.57
1460 5077 9.310449 TGTGTAATATATTTCCTCCTCTAGTCC 57.690 37.037 2.68 0.00 0.00 3.85
1461 5078 9.536510 GTGTAATATATTTCCTCCTCTAGTCCT 57.463 37.037 2.68 0.00 0.00 3.85
1462 5079 9.756571 TGTAATATATTTCCTCCTCTAGTCCTC 57.243 37.037 2.68 0.00 0.00 3.71
1477 5912 1.200716 GTCCTCGTACGTTCATCACCA 59.799 52.381 16.05 0.00 0.00 4.17
1485 5920 4.496840 CGTACGTTCATCACCAGTATGCTA 60.497 45.833 7.22 0.00 31.97 3.49
1501 5936 3.087370 TGCTACTCTCTGCTCACCTTA 57.913 47.619 0.00 0.00 0.00 2.69
1502 5937 3.636679 TGCTACTCTCTGCTCACCTTAT 58.363 45.455 0.00 0.00 0.00 1.73
1503 5938 4.793201 TGCTACTCTCTGCTCACCTTATA 58.207 43.478 0.00 0.00 0.00 0.98
1506 5941 5.278266 GCTACTCTCTGCTCACCTTATACAG 60.278 48.000 0.00 0.00 0.00 2.74
1578 6112 3.627395 TTCTGCTTCGTCCATTGGTAT 57.373 42.857 1.86 0.00 0.00 2.73
1588 6122 1.112950 CCATTGGTATGGTGCATGCA 58.887 50.000 18.46 18.46 45.34 3.96
1589 6123 1.689813 CCATTGGTATGGTGCATGCAT 59.310 47.619 25.64 10.90 45.34 3.96
1780 6370 4.672542 CGTTCGAAATTGATCAGGTTGCAT 60.673 41.667 0.00 0.00 0.00 3.96
1781 6371 5.447144 CGTTCGAAATTGATCAGGTTGCATA 60.447 40.000 0.00 0.00 0.00 3.14
1782 6372 6.498304 GTTCGAAATTGATCAGGTTGCATAT 58.502 36.000 0.00 0.00 0.00 1.78
1783 6373 6.063640 TCGAAATTGATCAGGTTGCATATG 57.936 37.500 0.00 0.00 0.00 1.78
1784 6374 4.678287 CGAAATTGATCAGGTTGCATATGC 59.322 41.667 21.09 21.09 42.50 3.14
1785 6375 4.595762 AATTGATCAGGTTGCATATGCC 57.404 40.909 24.54 10.19 41.18 4.40
1786 6376 2.732844 TGATCAGGTTGCATATGCCA 57.267 45.000 24.54 11.61 41.18 4.92
1787 6377 2.300433 TGATCAGGTTGCATATGCCAC 58.700 47.619 24.54 22.52 41.18 5.01
1798 6388 7.642071 GTTGCATATGCCACCAAATTAATAG 57.358 36.000 24.54 0.00 41.18 1.73
1799 6389 5.782047 TGCATATGCCACCAAATTAATAGC 58.218 37.500 24.54 0.00 41.18 2.97
1801 6391 6.014413 TGCATATGCCACCAAATTAATAGCAT 60.014 34.615 24.54 0.00 41.89 3.79
1802 6392 6.875195 GCATATGCCACCAAATTAATAGCATT 59.125 34.615 17.26 0.00 39.89 3.56
1803 6393 8.034215 GCATATGCCACCAAATTAATAGCATTA 58.966 33.333 17.26 0.00 39.89 1.90
1804 6394 9.577110 CATATGCCACCAAATTAATAGCATTAG 57.423 33.333 0.00 0.00 39.89 1.73
1806 6396 7.838079 TGCCACCAAATTAATAGCATTAGAT 57.162 32.000 0.00 0.00 0.00 1.98
1807 6397 8.248904 TGCCACCAAATTAATAGCATTAGATT 57.751 30.769 0.00 0.00 0.00 2.40
1808 6398 8.359642 TGCCACCAAATTAATAGCATTAGATTC 58.640 33.333 0.00 0.00 0.00 2.52
1848 7211 7.527568 TTCATCATATGCCTATTTGATTGCA 57.472 32.000 0.00 0.00 34.18 4.08
1853 7216 6.979817 TCATATGCCTATTTGATTGCACAAAC 59.020 34.615 4.76 0.00 41.49 2.93
1856 7219 5.549347 TGCCTATTTGATTGCACAAACATT 58.451 33.333 4.76 0.00 41.49 2.71
1857 7220 6.695429 TGCCTATTTGATTGCACAAACATTA 58.305 32.000 4.76 0.00 41.49 1.90
1858 7221 7.157347 TGCCTATTTGATTGCACAAACATTAA 58.843 30.769 4.76 0.00 41.49 1.40
1860 7223 9.311916 GCCTATTTGATTGCACAAACATTAATA 57.688 29.630 4.76 0.00 41.49 0.98
1935 9554 7.803279 AAGTTGGAAGTACACTCTTTTAAGG 57.197 36.000 0.00 0.00 0.00 2.69
1936 9555 7.133133 AGTTGGAAGTACACTCTTTTAAGGA 57.867 36.000 0.00 0.00 0.00 3.36
1937 9556 6.990939 AGTTGGAAGTACACTCTTTTAAGGAC 59.009 38.462 0.00 0.00 0.00 3.85
1938 9557 5.535333 TGGAAGTACACTCTTTTAAGGACG 58.465 41.667 0.00 0.00 0.00 4.79
1971 9632 8.647143 AAAAGAAATTCAACACCAGTAATGTG 57.353 30.769 0.00 0.00 39.63 3.21
1983 9645 6.147164 ACACCAGTAATGTGAATAACGACAAG 59.853 38.462 0.00 0.00 37.18 3.16
1993 10340 8.716646 TGTGAATAACGACAAGACATGAATAT 57.283 30.769 0.00 0.00 0.00 1.28
2021 10368 6.262944 TCAAAAAGTGCACTATTCACATCTGT 59.737 34.615 22.01 0.00 36.93 3.41
2023 10370 5.869753 AAGTGCACTATTCACATCTGTTC 57.130 39.130 22.01 0.00 36.93 3.18
2024 10371 4.256920 AGTGCACTATTCACATCTGTTCC 58.743 43.478 20.16 0.00 36.93 3.62
2100 10447 8.812147 AGGTGTTGTATACATATATGTCAACG 57.188 34.615 27.06 4.79 41.97 4.10
2101 10448 8.418662 AGGTGTTGTATACATATATGTCAACGT 58.581 33.333 27.06 18.56 41.97 3.99
2102 10449 8.484799 GGTGTTGTATACATATATGTCAACGTG 58.515 37.037 27.06 4.85 41.97 4.49
2121 10623 0.323087 GGGCGGTTGTGGGTAATTCT 60.323 55.000 0.00 0.00 0.00 2.40
2133 10635 2.656002 GGTAATTCTTCCCTCCCTTGC 58.344 52.381 0.00 0.00 0.00 4.01
2138 10640 2.034066 TTCCCTCCCTTGCGCTTG 59.966 61.111 9.73 0.33 0.00 4.01
2161 10668 3.716539 ATCGACGTGGGCGGATGTG 62.717 63.158 0.00 0.00 43.45 3.21
2234 10741 1.839598 GCAGATGCGTCATGCTAGGC 61.840 60.000 17.74 4.03 46.63 3.93
2237 10744 1.825285 GATGCGTCATGCTAGGCGTG 61.825 60.000 0.00 5.48 45.79 5.34
2261 10768 4.506802 GGGATCCTATGGTCCAAATGGTAC 60.507 50.000 12.58 0.00 36.19 3.34
2288 10795 7.582667 ATGGATAAGAAATTTCCTTTACGGG 57.417 36.000 14.61 0.00 0.00 5.28
2295 10802 6.007703 AGAAATTTCCTTTACGGGACAATCA 58.992 36.000 14.61 0.00 34.78 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.280552 GGGACAGGACGGTACTGCA 61.281 63.158 20.21 0.00 39.55 4.41
6 7 2.577593 GGGACAGGACGGTACTGC 59.422 66.667 20.21 12.45 39.55 4.40
74 3431 2.028337 GGCGAATCGGAGAGGAGC 59.972 66.667 4.35 0.00 43.63 4.70
262 3705 4.899687 CATGCGAGCCATGCGTGC 62.900 66.667 0.00 0.00 44.34 5.34
324 3774 1.517257 CTTGTCGAAGCTCGCCGAT 60.517 57.895 8.66 0.00 40.21 4.18
498 3948 4.085204 ACGGTGCCGGCGGAATTA 62.085 61.111 33.44 9.52 44.69 1.40
577 4036 1.226030 ACCAAGTTAGCGAACCGTGC 61.226 55.000 6.04 0.00 36.08 5.34
585 4044 1.069500 CCAAACCGAACCAAGTTAGCG 60.069 52.381 0.00 0.00 0.00 4.26
586 4045 1.951602 ACCAAACCGAACCAAGTTAGC 59.048 47.619 0.00 0.00 0.00 3.09
750 4236 0.252057 TGTGGGATCGAACCAGAGGA 60.252 55.000 14.28 0.00 39.00 3.71
769 4255 2.036862 GGAGTAGGTGTGGAAGTCGTTT 59.963 50.000 0.00 0.00 0.00 3.60
818 4304 0.652592 GACGGCGATCAATCCACTTG 59.347 55.000 16.62 0.00 36.09 3.16
823 4309 3.338676 GGCGACGGCGATCAATCC 61.339 66.667 18.90 0.00 41.24 3.01
851 4337 1.663161 GCCGGCGTTCTTGAAAGAAAG 60.663 52.381 12.58 12.58 45.77 2.62
882 4378 2.175878 AGTCACTGAACATCCTGTGC 57.824 50.000 0.00 0.00 36.39 4.57
883 4379 6.808008 AAATTAGTCACTGAACATCCTGTG 57.192 37.500 0.00 0.00 37.35 3.66
902 4415 7.118680 CCATGAAGCTGCATTTACAAGAAAATT 59.881 33.333 3.72 0.00 0.00 1.82
906 4419 4.523943 ACCATGAAGCTGCATTTACAAGAA 59.476 37.500 3.72 0.00 0.00 2.52
908 4421 4.171005 CACCATGAAGCTGCATTTACAAG 58.829 43.478 3.72 0.00 0.00 3.16
1053 4578 1.736645 CCAATCCGTCTTGACGCGT 60.737 57.895 13.85 13.85 0.00 6.01
1317 4860 1.815421 CTACATGGTGCACTCGGCC 60.815 63.158 17.98 0.00 43.89 6.13
1391 5008 2.091541 ACATGAACTGGGCGTAAATGG 58.908 47.619 0.00 0.00 0.00 3.16
1447 5064 1.411977 CGTACGAGGACTAGAGGAGGA 59.588 57.143 10.44 0.00 0.00 3.71
1455 5072 2.679837 GGTGATGAACGTACGAGGACTA 59.320 50.000 24.41 0.94 0.00 2.59
1456 5073 1.471684 GGTGATGAACGTACGAGGACT 59.528 52.381 24.41 1.88 0.00 3.85
1457 5074 1.200716 TGGTGATGAACGTACGAGGAC 59.799 52.381 24.41 10.15 0.00 3.85
1458 5075 1.471287 CTGGTGATGAACGTACGAGGA 59.529 52.381 24.41 4.73 0.00 3.71
1459 5076 1.201647 ACTGGTGATGAACGTACGAGG 59.798 52.381 24.41 0.00 0.00 4.63
1460 5077 2.631418 ACTGGTGATGAACGTACGAG 57.369 50.000 24.41 7.79 0.00 4.18
1461 5078 3.732774 GCATACTGGTGATGAACGTACGA 60.733 47.826 24.41 0.00 0.00 3.43
1462 5079 2.534349 GCATACTGGTGATGAACGTACG 59.466 50.000 15.01 15.01 0.00 3.67
1485 5920 4.861196 TCTGTATAAGGTGAGCAGAGAGT 58.139 43.478 0.00 0.00 33.05 3.24
1501 5936 5.411669 GGAACCGAATGTTTCAGTTCTGTAT 59.588 40.000 13.23 0.00 43.35 2.29
1502 5937 4.753107 GGAACCGAATGTTTCAGTTCTGTA 59.247 41.667 13.23 0.00 43.35 2.74
1503 5938 3.564225 GGAACCGAATGTTTCAGTTCTGT 59.436 43.478 13.23 0.00 43.35 3.41
1506 5941 3.606153 CGTGGAACCGAATGTTTCAGTTC 60.606 47.826 7.50 7.50 43.23 3.01
1578 6112 1.133853 TGTGGCTATATGCATGCACCA 60.134 47.619 25.37 22.12 45.15 4.17
1588 6122 2.547218 CGGCGTTTAGGTGTGGCTATAT 60.547 50.000 0.00 0.00 0.00 0.86
1589 6123 1.202440 CGGCGTTTAGGTGTGGCTATA 60.202 52.381 0.00 0.00 0.00 1.31
1780 6370 8.932434 TCTAATGCTATTAATTTGGTGGCATA 57.068 30.769 0.00 0.00 37.85 3.14
1781 6371 7.838079 TCTAATGCTATTAATTTGGTGGCAT 57.162 32.000 0.00 0.00 40.04 4.40
1782 6372 7.838079 ATCTAATGCTATTAATTTGGTGGCA 57.162 32.000 0.00 0.00 0.00 4.92
1783 6373 8.359642 TGAATCTAATGCTATTAATTTGGTGGC 58.640 33.333 0.00 0.00 0.00 5.01
1824 6414 7.014422 TGTGCAATCAAATAGGCATATGATGAA 59.986 33.333 6.97 0.00 38.68 2.57
1825 6415 6.490721 TGTGCAATCAAATAGGCATATGATGA 59.509 34.615 6.97 8.89 38.68 2.92
1826 6416 6.683715 TGTGCAATCAAATAGGCATATGATG 58.316 36.000 6.97 0.00 38.68 3.07
1827 6417 6.904463 TGTGCAATCAAATAGGCATATGAT 57.096 33.333 6.97 0.00 38.68 2.45
1828 6418 6.712179 TTGTGCAATCAAATAGGCATATGA 57.288 33.333 6.97 0.00 38.68 2.15
1832 7195 5.149973 TGTTTGTGCAATCAAATAGGCAT 57.850 34.783 5.85 0.00 39.09 4.40
1834 7197 7.593875 TTAATGTTTGTGCAATCAAATAGGC 57.406 32.000 5.85 0.00 39.09 3.93
1912 9531 6.990939 GTCCTTAAAAGAGTGTACTTCCAACT 59.009 38.462 0.00 0.00 0.00 3.16
1913 9532 6.073927 CGTCCTTAAAAGAGTGTACTTCCAAC 60.074 42.308 0.00 0.00 0.00 3.77
1914 9533 5.987347 CGTCCTTAAAAGAGTGTACTTCCAA 59.013 40.000 0.00 0.00 0.00 3.53
1917 9536 5.776744 TCCGTCCTTAAAAGAGTGTACTTC 58.223 41.667 0.00 0.00 0.00 3.01
1918 9537 5.537674 TCTCCGTCCTTAAAAGAGTGTACTT 59.462 40.000 0.00 0.00 0.00 2.24
1919 9538 5.075493 TCTCCGTCCTTAAAAGAGTGTACT 58.925 41.667 0.00 0.00 0.00 2.73
1920 9539 5.382618 TCTCCGTCCTTAAAAGAGTGTAC 57.617 43.478 0.00 0.00 0.00 2.90
1921 9540 6.409524 TTTCTCCGTCCTTAAAAGAGTGTA 57.590 37.500 0.00 0.00 0.00 2.90
1923 9542 6.613755 TTTTTCTCCGTCCTTAAAAGAGTG 57.386 37.500 0.00 0.00 0.00 3.51
1948 9609 7.581213 TCACATTACTGGTGTTGAATTTCTT 57.419 32.000 0.00 0.00 37.52 2.52
1964 9625 7.959733 TCATGTCTTGTCGTTATTCACATTAC 58.040 34.615 0.00 0.00 0.00 1.89
1967 9628 7.615582 ATTCATGTCTTGTCGTTATTCACAT 57.384 32.000 0.00 0.00 0.00 3.21
1971 9632 9.638300 GACAATATTCATGTCTTGTCGTTATTC 57.362 33.333 12.83 0.00 43.03 1.75
1983 9645 7.596248 AGTGCACTTTTTGACAATATTCATGTC 59.404 33.333 15.25 0.00 45.82 3.06
1993 10340 6.201226 TGTGAATAGTGCACTTTTTGACAA 57.799 33.333 27.06 4.09 37.18 3.18
2003 10350 4.093998 CAGGAACAGATGTGAATAGTGCAC 59.906 45.833 9.40 9.40 36.81 4.57
2021 10368 6.210584 ACAAAGAGAAACAAAAAGGACAGGAA 59.789 34.615 0.00 0.00 0.00 3.36
2023 10370 5.807011 CACAAAGAGAAACAAAAAGGACAGG 59.193 40.000 0.00 0.00 0.00 4.00
2024 10371 6.389906 ACACAAAGAGAAACAAAAAGGACAG 58.610 36.000 0.00 0.00 0.00 3.51
2078 10425 7.654116 CCCACGTTGACATATATGTATACAACA 59.346 37.037 29.49 17.95 41.95 3.33
2092 10439 2.112297 AACCGCCCACGTTGACAT 59.888 55.556 0.00 0.00 37.70 3.06
2096 10443 3.959975 CCACAACCGCCCACGTTG 61.960 66.667 0.00 0.00 37.70 4.10
2099 10446 3.828694 TTACCCACAACCGCCCACG 62.829 63.158 0.00 0.00 39.67 4.94
2100 10447 0.896479 AATTACCCACAACCGCCCAC 60.896 55.000 0.00 0.00 0.00 4.61
2101 10448 0.609681 GAATTACCCACAACCGCCCA 60.610 55.000 0.00 0.00 0.00 5.36
2102 10449 0.323087 AGAATTACCCACAACCGCCC 60.323 55.000 0.00 0.00 0.00 6.13
2121 10623 2.034066 CAAGCGCAAGGGAGGGAA 59.966 61.111 11.47 0.00 38.28 3.97
2161 10668 1.495148 CAAGGGAGGGAGGAAATACCC 59.505 57.143 0.00 0.00 45.88 3.69
2218 10725 1.592669 ACGCCTAGCATGACGCATC 60.593 57.895 0.00 0.00 46.13 3.91
2234 10741 0.762842 TGGACCATAGGATCCCCACG 60.763 60.000 8.55 0.00 33.69 4.94
2237 10744 2.225117 CCATTTGGACCATAGGATCCCC 60.225 54.545 8.55 1.32 37.39 4.81
2266 10773 6.600427 TGTCCCGTAAAGGAAATTTCTTATCC 59.400 38.462 17.42 1.47 45.00 2.59
2286 10793 4.082125 AGACCAAAGTGAATGATTGTCCC 58.918 43.478 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.