Multiple sequence alignment - TraesCS1D01G271800

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 TraesCS1D01G271800 chr1D 100.000 2896 0 0 1 2896 366017729 366020624 0.000000e+00 5349.0
1 TraesCS1D01G271800 chr1D 75.354 848 121 54 972 1758 366005839 366006659 7.740000e-86 327.0
2 TraesCS1D01G271800 chr1D 80.939 362 59 8 996 1352 365905956 365906312 7.900000e-71 278.0
3 TraesCS1D01G271800 chr1D 80.939 362 59 8 996 1352 365996726 365997082 7.900000e-71 278.0
4 TraesCS1D01G271800 chr1B 89.147 2884 161 38 1 2818 489992278 489995075 0.000000e+00 3452.0
5 TraesCS1D01G271800 chr1B 81.513 357 59 5 996 1349 489820534 489820886 1.310000e-73 287.0
6 TraesCS1D01G271800 chr1B 74.533 856 125 57 972 1758 489919898 489920729 1.310000e-73 287.0
7 TraesCS1D01G271800 chr1A 88.595 2569 164 58 414 2896 465281530 465284055 0.000000e+00 3001.0
8 TraesCS1D01G271800 chr1A 85.479 668 59 17 2254 2896 465301555 465302209 0.000000e+00 662.0
9 TraesCS1D01G271800 chr1A 83.658 257 15 13 1 235 465281154 465281405 1.750000e-52 217.0
10 TraesCS1D01G271800 chr1A 77.246 334 54 15 1433 1755 465139925 465140247 2.970000e-40 176.0
11 TraesCS1D01G271800 chr1A 93.043 115 6 2 222 336 465281424 465281536 1.780000e-37 167.0
12 TraesCS1D01G271800 chr1A 77.099 262 38 8 2254 2510 465301308 465301552 6.510000e-27 132.0
13 TraesCS1D01G271800 chr1A 100.000 32 0 0 2334 2365 465295191 465295222 3.120000e-05 60.2
14 TraesCS1D01G271800 chr7A 100.000 28 0 0 1644 1671 254384970 254384943 5.000000e-03 52.8


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 TraesCS1D01G271800 chr1D 366017729 366020624 2895 False 5349.000000 5349 100.000 1 2896 1 chr1D.!!$F4 2895
1 TraesCS1D01G271800 chr1D 366005839 366006659 820 False 327.000000 327 75.354 972 1758 1 chr1D.!!$F3 786
2 TraesCS1D01G271800 chr1B 489992278 489995075 2797 False 3452.000000 3452 89.147 1 2818 1 chr1B.!!$F3 2817
3 TraesCS1D01G271800 chr1B 489919898 489920729 831 False 287.000000 287 74.533 972 1758 1 chr1B.!!$F2 786
4 TraesCS1D01G271800 chr1A 465281154 465284055 2901 False 1128.333333 3001 88.432 1 2896 3 chr1A.!!$F3 2895
5 TraesCS1D01G271800 chr1A 465301308 465302209 901 False 397.000000 662 81.289 2254 2896 2 chr1A.!!$F4 642

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
764 828 0.733729 GACTAGGCGTGATCGTCAGT 59.266 55.0 0.0 0.0 44.74 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2317 0.583438 CATCATCGGCGAATCACACC 59.417 55.0 15.93 0.0 0.0 4.16 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
151 166 1.447140 GCCGTGGTACATTCTGCGA 60.447 57.895 0.00 0.00 44.52 5.10
162 193 2.942376 ACATTCTGCGAACTGTTTGACA 59.058 40.909 11.94 8.04 0.00 3.58
173 204 2.165167 CTGTTTGACACCATCCAGCAT 58.835 47.619 0.00 0.00 0.00 3.79
174 205 3.244875 ACTGTTTGACACCATCCAGCATA 60.245 43.478 0.00 0.00 0.00 3.14
175 206 3.346315 TGTTTGACACCATCCAGCATAG 58.654 45.455 0.00 0.00 0.00 2.23
176 207 3.008923 TGTTTGACACCATCCAGCATAGA 59.991 43.478 0.00 0.00 0.00 1.98
177 208 3.548745 TTGACACCATCCAGCATAGAG 57.451 47.619 0.00 0.00 0.00 2.43
178 209 1.139654 TGACACCATCCAGCATAGAGC 59.860 52.381 0.00 0.00 46.19 4.09
220 251 2.515523 GCCGCCTGCTCATCATGT 60.516 61.111 0.00 0.00 36.87 3.21
331 392 3.138884 TGCTAGTTGACTTTGCCATCA 57.861 42.857 0.00 0.00 0.00 3.07
332 393 3.076621 TGCTAGTTGACTTTGCCATCAG 58.923 45.455 0.00 0.00 0.00 2.90
333 394 2.159462 GCTAGTTGACTTTGCCATCAGC 60.159 50.000 0.00 0.00 44.14 4.26
334 395 2.283145 AGTTGACTTTGCCATCAGCT 57.717 45.000 0.00 0.00 44.23 4.24
335 396 3.423539 AGTTGACTTTGCCATCAGCTA 57.576 42.857 0.00 0.00 44.23 3.32
336 397 3.341823 AGTTGACTTTGCCATCAGCTAG 58.658 45.455 0.00 0.00 44.23 3.42
337 398 3.077359 GTTGACTTTGCCATCAGCTAGT 58.923 45.455 0.00 0.00 44.23 2.57
356 417 1.136500 GTAGCCTAGTAGGTGCACCAC 59.864 57.143 36.39 28.79 37.80 4.16
451 512 9.103582 TCAGGTAAAGTTAGGTGTCCTTTTATA 57.896 33.333 0.00 0.00 34.61 0.98
490 553 2.083774 TGGCGTCCTTTGATTAAGCAG 58.916 47.619 0.00 0.00 32.19 4.24
658 722 1.837051 TGTCCCCTATGCTAGCCGG 60.837 63.158 13.29 9.93 0.00 6.13
672 736 3.177600 CCGGTCAAGTTGGCATCG 58.822 61.111 10.13 4.48 0.00 3.84
692 756 4.624015 TCGAAGTAACCACGTCATTTTCT 58.376 39.130 0.00 0.00 33.27 2.52
701 765 5.547465 ACCACGTCATTTTCTTCACTGATA 58.453 37.500 0.00 0.00 0.00 2.15
750 814 4.224715 TGATCTTTCCGCATACGACTAG 57.775 45.455 0.00 0.00 43.93 2.57
764 828 0.733729 GACTAGGCGTGATCGTCAGT 59.266 55.000 0.00 0.00 44.74 3.41
883 947 1.468914 CTTGACGAGACGACCTCATCA 59.531 52.381 4.75 4.75 41.76 3.07
907 971 2.630580 GTCCTCTACCTAAGGCATCAGG 59.369 54.545 0.00 0.00 37.97 3.86
939 1010 2.723273 TGATCACGCCTCTCAAGTCTA 58.277 47.619 0.00 0.00 0.00 2.59
1041 1113 0.528924 TGTCCGTCGTGGTAGGATTG 59.471 55.000 0.00 0.00 39.52 2.67
1042 1114 0.804933 GTCCGTCGTGGTAGGATTGC 60.805 60.000 0.00 0.00 39.52 3.56
1044 1116 0.527817 CCGTCGTGGTAGGATTGCTC 60.528 60.000 0.00 0.00 0.00 4.26
1123 1226 0.460284 ACGCTCGTGTTCATCCATCC 60.460 55.000 0.00 0.00 0.00 3.51
1125 1228 1.807755 CGCTCGTGTTCATCCATCCAT 60.808 52.381 0.00 0.00 0.00 3.41
1126 1229 1.869767 GCTCGTGTTCATCCATCCATC 59.130 52.381 0.00 0.00 0.00 3.51
1127 1230 2.487934 CTCGTGTTCATCCATCCATCC 58.512 52.381 0.00 0.00 0.00 3.51
1128 1231 1.202521 TCGTGTTCATCCATCCATCCG 60.203 52.381 0.00 0.00 0.00 4.18
1192 1295 2.622629 CGCAGCGGAATGACATCG 59.377 61.111 7.00 0.00 0.00 3.84
1193 1296 2.874694 CGCAGCGGAATGACATCGG 61.875 63.158 7.00 0.00 0.00 4.18
1195 1298 1.889105 CAGCGGAATGACATCGGGG 60.889 63.158 0.00 0.00 0.00 5.73
1202 1308 0.695924 AATGACATCGGGGTGTCCAA 59.304 50.000 9.43 0.00 46.17 3.53
1223 1329 4.789075 CGAGTGCGTGTACCCCGG 62.789 72.222 0.00 0.00 0.00 5.73
1393 1520 0.102120 CGTCCTCTCATGGTGAGCTC 59.898 60.000 6.82 6.82 43.95 4.09
1394 1521 1.189752 GTCCTCTCATGGTGAGCTCA 58.810 55.000 13.74 13.74 43.95 4.26
1395 1522 1.136695 GTCCTCTCATGGTGAGCTCAG 59.863 57.143 18.89 5.39 43.95 3.35
1396 1523 0.179078 CCTCTCATGGTGAGCTCAGC 60.179 60.000 33.67 33.67 43.95 4.26
1398 1525 1.207570 CTCTCATGGTGAGCTCAGCTT 59.792 52.381 37.50 30.98 43.95 3.74
1400 1527 0.251354 TCATGGTGAGCTCAGCTTCC 59.749 55.000 37.50 25.91 44.12 3.46
1401 1528 0.252479 CATGGTGAGCTCAGCTTCCT 59.748 55.000 37.50 21.27 44.12 3.36
1426 1567 3.872728 CGATCCAGGCGACGACGA 61.873 66.667 12.29 0.00 42.66 4.20
1448 1610 2.219445 CGACCGATGAATATGCTGTGTG 59.781 50.000 0.00 0.00 0.00 3.82
1452 1614 3.001634 CCGATGAATATGCTGTGTGTGTC 59.998 47.826 0.00 0.00 0.00 3.67
1626 1794 3.292460 CTCGGGATCAAGTCCTACTTCT 58.708 50.000 0.00 0.00 46.91 2.85
1745 1922 3.912907 GACGGGATCGCGATGGGT 61.913 66.667 35.09 20.17 40.63 4.51
1895 2075 2.598099 TACGGGCACGGACACTGA 60.598 61.111 15.46 0.00 46.48 3.41
1901 2081 1.021390 GGCACGGACACTGATTCCAG 61.021 60.000 0.00 0.00 45.76 3.86
1998 2205 7.281324 GTGCTATGTTCTTCTGTCTCTAGTAGA 59.719 40.741 0.00 0.00 0.00 2.59
2008 2215 5.067153 TCTGTCTCTAGTAGAATTCTGCTGC 59.933 44.000 29.70 16.86 39.29 5.25
2078 2285 2.591571 TGATGATCGTCTCTGCTTGG 57.408 50.000 15.81 0.00 0.00 3.61
2088 2295 2.555757 GTCTCTGCTTGGAAGTGCAAAT 59.444 45.455 0.00 0.00 38.81 2.32
2089 2296 3.005155 GTCTCTGCTTGGAAGTGCAAATT 59.995 43.478 0.00 0.00 38.81 1.82
2110 2317 7.473027 AATTTGAGCTTTGAGATTTTGTGTG 57.527 32.000 0.00 0.00 0.00 3.82
2116 2323 4.439974 GCTTTGAGATTTTGTGTGGTGTGA 60.440 41.667 0.00 0.00 0.00 3.58
2117 2324 5.737063 GCTTTGAGATTTTGTGTGGTGTGAT 60.737 40.000 0.00 0.00 0.00 3.06
2118 2325 5.850557 TTGAGATTTTGTGTGGTGTGATT 57.149 34.783 0.00 0.00 0.00 2.57
2119 2326 5.437289 TGAGATTTTGTGTGGTGTGATTC 57.563 39.130 0.00 0.00 0.00 2.52
2181 2388 7.712264 ACAAACATTTCACCACATTTACATG 57.288 32.000 0.00 0.00 36.34 3.21
2182 2389 6.705381 ACAAACATTTCACCACATTTACATGG 59.295 34.615 0.00 0.00 42.13 3.66
2199 2406 3.726517 GACGCACGGCAGCACAAT 61.727 61.111 0.00 0.00 0.00 2.71
2203 2410 1.854664 GCACGGCAGCACAATTTTG 59.145 52.632 0.00 0.00 0.00 2.44
2207 2414 0.879400 CGGCAGCACAATTTTGGCAA 60.879 50.000 0.00 0.00 37.24 4.52
2272 2480 7.675962 AGTAGTACTACTGTCTTCAGAGTTG 57.324 40.000 30.33 0.00 44.11 3.16
2283 2744 4.009675 TCTTCAGAGTTGAGAGAGAGAGC 58.990 47.826 0.00 0.00 34.15 4.09
2285 2746 3.081061 TCAGAGTTGAGAGAGAGAGCAC 58.919 50.000 0.00 0.00 0.00 4.40
2292 2753 1.408702 GAGAGAGAGAGCACCATCACC 59.591 57.143 0.00 0.00 0.00 4.02
2293 2754 1.006998 AGAGAGAGAGCACCATCACCT 59.993 52.381 0.00 0.00 0.00 4.00
2294 2755 1.408702 GAGAGAGAGCACCATCACCTC 59.591 57.143 0.00 0.00 0.00 3.85
2295 2756 1.006998 AGAGAGAGCACCATCACCTCT 59.993 52.381 0.00 0.00 38.58 3.69
2296 2757 1.136695 GAGAGAGCACCATCACCTCTG 59.863 57.143 0.00 0.00 36.16 3.35
2297 2758 0.901124 GAGAGCACCATCACCTCTGT 59.099 55.000 0.00 0.00 36.16 3.41
2298 2759 2.103373 GAGAGCACCATCACCTCTGTA 58.897 52.381 0.00 0.00 36.16 2.74
2299 2760 2.497675 GAGAGCACCATCACCTCTGTAA 59.502 50.000 0.00 0.00 36.16 2.41
2318 2779 1.254284 ACTCTGTTCCTCTCTGGGCG 61.254 60.000 0.00 0.00 36.20 6.13
2321 2782 2.232298 CTGTTCCTCTCTGGGCGGTC 62.232 65.000 0.00 0.00 36.20 4.79
2375 2843 2.747855 CCGCAGAAGGGGCAGAAC 60.748 66.667 0.00 0.00 41.32 3.01
2387 2855 3.423154 CAGAACCGGAACTGCGGC 61.423 66.667 9.46 0.00 0.00 6.53
2701 3194 2.032675 GCTGCCGATTTCCTCTGAATTC 59.967 50.000 0.00 0.00 0.00 2.17
2718 3211 1.945354 TTCTTCTCGCGCGATCCCTT 61.945 55.000 34.86 0.00 0.00 3.95
2720 3213 4.873129 TCTCGCGCGATCCCTTGC 62.873 66.667 34.86 0.00 0.00 4.01
2736 3229 4.070552 GCTGCCTCGGTTCTCGGT 62.071 66.667 0.00 0.00 39.77 4.69
2752 3260 2.289820 CTCGGTTCCGTTCGATCTGATA 59.710 50.000 11.04 0.00 34.77 2.15
2787 3295 1.203758 TGGCTCGGTGTAGTGTATGTG 59.796 52.381 0.00 0.00 0.00 3.21
2801 3309 3.425525 GTGTATGTGTATGGATCGCTTCG 59.574 47.826 0.00 0.00 0.00 3.79
2810 3318 0.179215 GGATCGCTTCGTTGTGCTTG 60.179 55.000 0.00 0.00 0.00 4.01
2812 3320 1.724623 GATCGCTTCGTTGTGCTTGTA 59.275 47.619 0.00 0.00 0.00 2.41
2818 3326 3.589988 CTTCGTTGTGCTTGTAGAGGAT 58.410 45.455 0.00 0.00 0.00 3.24
2837 3345 0.549169 TGGGGGAAACGGGAAGAGAT 60.549 55.000 0.00 0.00 0.00 2.75
2884 3395 3.090532 ACGGGAATCCTGAGCCCC 61.091 66.667 16.23 0.00 38.69 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.127810 TCTAGCAAATCATCATCAACTTGC 57.872 37.500 0.00 0.00 39.50 4.01
11 12 5.682659 AGAGCAACTCTAGCAAATCATCAT 58.317 37.500 0.00 0.00 39.28 2.45
12 13 5.095145 AGAGCAACTCTAGCAAATCATCA 57.905 39.130 0.00 0.00 39.28 3.07
15 16 6.409704 ACATAAGAGCAACTCTAGCAAATCA 58.590 36.000 0.00 0.00 40.28 2.57
151 166 1.956477 GCTGGATGGTGTCAAACAGTT 59.044 47.619 0.00 0.00 34.93 3.16
162 193 4.923516 ATAATGCTCTATGCTGGATGGT 57.076 40.909 0.00 0.00 43.37 3.55
173 204 4.854173 TGCCTTGAACCAATAATGCTCTA 58.146 39.130 0.00 0.00 0.00 2.43
174 205 3.700538 TGCCTTGAACCAATAATGCTCT 58.299 40.909 0.00 0.00 0.00 4.09
175 206 4.614946 GATGCCTTGAACCAATAATGCTC 58.385 43.478 0.00 0.00 0.00 4.26
176 207 3.067180 CGATGCCTTGAACCAATAATGCT 59.933 43.478 0.00 0.00 0.00 3.79
177 208 3.374745 CGATGCCTTGAACCAATAATGC 58.625 45.455 0.00 0.00 0.00 3.56
178 209 3.796504 GCCGATGCCTTGAACCAATAATG 60.797 47.826 0.00 0.00 0.00 1.90
179 210 2.362077 GCCGATGCCTTGAACCAATAAT 59.638 45.455 0.00 0.00 0.00 1.28
213 244 6.963242 GTGTGCACTTTGTATAGAACATGATG 59.037 38.462 19.41 0.00 38.10 3.07
258 319 1.421410 CTGGCCGCTGATTACGACAC 61.421 60.000 0.00 0.00 0.00 3.67
259 320 1.153647 CTGGCCGCTGATTACGACA 60.154 57.895 0.00 0.00 0.00 4.35
264 325 1.227943 GGATGCTGGCCGCTGATTA 60.228 57.895 18.14 0.97 40.11 1.75
333 394 3.687551 TGGTGCACCTACTAGGCTACTAG 60.688 52.174 34.75 0.47 43.46 2.57
334 395 2.242965 TGGTGCACCTACTAGGCTACTA 59.757 50.000 34.75 8.56 39.63 1.82
335 396 1.006758 TGGTGCACCTACTAGGCTACT 59.993 52.381 34.75 0.00 39.63 2.57
336 397 1.136500 GTGGTGCACCTACTAGGCTAC 59.864 57.143 34.75 18.27 39.63 3.58
337 398 1.272816 TGTGGTGCACCTACTAGGCTA 60.273 52.381 34.75 10.14 39.63 3.93
356 417 8.461222 AGTGATAACAAATGATGTGTGGTATTG 58.539 33.333 0.00 0.00 42.99 1.90
395 456 7.962918 GCTAGCGATAACAAAGATTCTCAAAAA 59.037 33.333 0.00 0.00 0.00 1.94
396 457 7.334421 AGCTAGCGATAACAAAGATTCTCAAAA 59.666 33.333 9.55 0.00 0.00 2.44
397 458 6.818644 AGCTAGCGATAACAAAGATTCTCAAA 59.181 34.615 9.55 0.00 0.00 2.69
398 459 6.341316 AGCTAGCGATAACAAAGATTCTCAA 58.659 36.000 9.55 0.00 0.00 3.02
399 460 5.907207 AGCTAGCGATAACAAAGATTCTCA 58.093 37.500 9.55 0.00 0.00 3.27
400 461 6.256757 ACAAGCTAGCGATAACAAAGATTCTC 59.743 38.462 9.55 0.00 0.00 2.87
416 477 4.870991 CCTAACTTTACCTGACAAGCTAGC 59.129 45.833 6.62 6.62 0.00 3.42
468 529 2.887783 TGCTTAATCAAAGGACGCCAAA 59.112 40.909 0.00 0.00 35.58 3.28
469 530 2.487762 CTGCTTAATCAAAGGACGCCAA 59.512 45.455 0.00 0.00 35.58 4.52
472 533 2.096013 GGACTGCTTAATCAAAGGACGC 59.904 50.000 0.00 0.00 35.58 5.19
473 534 2.348666 CGGACTGCTTAATCAAAGGACG 59.651 50.000 0.00 0.00 35.58 4.79
577 640 2.544694 CGATTCGCAGAGCTGGTAGATT 60.545 50.000 0.00 0.00 38.43 2.40
588 651 2.202610 CGTGCTCCGATTCGCAGA 60.203 61.111 0.06 0.00 39.56 4.26
593 656 1.005975 CGTGAATTCGTGCTCCGATTC 60.006 52.381 0.04 7.05 46.75 2.52
658 722 3.120304 GGTTACTTCGATGCCAACTTGAC 60.120 47.826 12.93 0.00 0.00 3.18
672 736 6.018180 AGTGAAGAAAATGACGTGGTTACTTC 60.018 38.462 0.00 7.44 34.03 3.01
692 756 9.082313 TGTCTGATATCATAGCTTATCAGTGAA 57.918 33.333 23.27 13.02 46.22 3.18
701 765 5.167121 GCGACATGTCTGATATCATAGCTT 58.833 41.667 22.95 0.00 0.00 3.74
718 782 0.370273 GAAAGATCAACGCGCGACAT 59.630 50.000 39.36 23.64 0.00 3.06
750 814 0.101399 AGATCACTGACGATCACGCC 59.899 55.000 12.14 0.00 43.61 5.68
764 828 1.066143 GGGAAAGCGAGGTCAAGATCA 60.066 52.381 0.00 0.00 0.00 2.92
801 865 3.397349 AACCATTGTTACGGGCACCTTC 61.397 50.000 0.00 0.00 38.91 3.46
802 866 1.479757 AACCATTGTTACGGGCACCTT 60.480 47.619 0.00 0.00 38.91 3.50
803 867 0.111639 AACCATTGTTACGGGCACCT 59.888 50.000 0.00 0.00 38.91 4.00
831 895 3.449322 TTCTTCACGCGTATTCTTTGC 57.551 42.857 13.44 0.00 0.00 3.68
883 947 0.033405 TGCCTTAGGTAGAGGACGCT 60.033 55.000 0.00 0.00 36.33 5.07
907 971 1.325338 GCGTGATCAAATGCAAATGGC 59.675 47.619 0.00 0.00 45.13 4.40
915 979 3.005554 ACTTGAGAGGCGTGATCAAATG 58.994 45.455 0.00 0.00 32.87 2.32
916 980 3.055530 AGACTTGAGAGGCGTGATCAAAT 60.056 43.478 0.00 0.00 35.43 2.32
939 1010 2.994995 TGTGAGACGGATGGGCGT 60.995 61.111 0.00 0.00 0.00 5.68
1021 1093 0.815734 AATCCTACCACGACGGACAG 59.184 55.000 0.00 0.22 38.63 3.51
1123 1226 4.033817 GCTCAGTTTCTTTGAGATCGGATG 59.966 45.833 6.44 0.00 43.75 3.51
1125 1228 3.259374 AGCTCAGTTTCTTTGAGATCGGA 59.741 43.478 6.44 0.00 43.75 4.55
1126 1229 3.370366 CAGCTCAGTTTCTTTGAGATCGG 59.630 47.826 6.44 0.00 43.75 4.18
1127 1230 4.091220 GTCAGCTCAGTTTCTTTGAGATCG 59.909 45.833 6.44 0.00 43.75 3.69
1128 1231 4.993584 TGTCAGCTCAGTTTCTTTGAGATC 59.006 41.667 6.44 0.00 43.75 2.75
1192 1295 2.214920 ACTCGGTCTTGGACACCCC 61.215 63.158 0.14 0.00 33.68 4.95
1193 1296 1.004918 CACTCGGTCTTGGACACCC 60.005 63.158 0.14 0.00 33.68 4.61
1195 1298 2.022129 CGCACTCGGTCTTGGACAC 61.022 63.158 0.14 0.00 33.68 3.67
1202 1308 2.633509 GGGTACACGCACTCGGTCT 61.634 63.158 0.00 0.00 40.69 3.85
1393 1520 2.131183 GATCGAATCGGAAGGAAGCTG 58.869 52.381 1.76 0.00 0.00 4.24
1394 1521 1.069358 GGATCGAATCGGAAGGAAGCT 59.931 52.381 1.76 0.00 0.00 3.74
1395 1522 1.202533 TGGATCGAATCGGAAGGAAGC 60.203 52.381 1.76 0.00 0.00 3.86
1396 1523 2.546795 CCTGGATCGAATCGGAAGGAAG 60.547 54.545 1.76 0.00 30.75 3.46
1398 1525 1.040646 CCTGGATCGAATCGGAAGGA 58.959 55.000 1.76 0.00 30.75 3.36
1400 1527 0.941463 CGCCTGGATCGAATCGGAAG 60.941 60.000 1.76 0.00 0.00 3.46
1401 1528 1.067416 CGCCTGGATCGAATCGGAA 59.933 57.895 1.76 0.00 0.00 4.30
1426 1567 2.159099 ACACAGCATATTCATCGGTCGT 60.159 45.455 0.00 0.00 0.00 4.34
1430 1571 2.938451 ACACACACAGCATATTCATCGG 59.062 45.455 0.00 0.00 0.00 4.18
1431 1572 3.001634 GGACACACACAGCATATTCATCG 59.998 47.826 0.00 0.00 0.00 3.84
1745 1922 1.663379 CGTACATCGGAGCAGGGTGA 61.663 60.000 0.00 0.00 35.71 4.02
1887 2067 1.450312 CGGGCTGGAATCAGTGTCC 60.450 63.158 0.00 0.00 42.78 4.02
1888 2068 2.109126 GCGGGCTGGAATCAGTGTC 61.109 63.158 0.00 0.00 42.78 3.67
1889 2069 2.045926 GCGGGCTGGAATCAGTGT 60.046 61.111 0.00 0.00 42.78 3.55
1890 2070 2.110967 CAGCGGGCTGGAATCAGTG 61.111 63.158 12.78 0.00 42.78 3.66
1891 2071 2.270205 CAGCGGGCTGGAATCAGT 59.730 61.111 12.78 0.00 42.78 3.41
1892 2072 3.207669 GCAGCGGGCTGGAATCAG 61.208 66.667 21.10 0.00 43.77 2.90
1998 2205 3.081061 TGGTGATTTACGCAGCAGAATT 58.919 40.909 0.00 0.00 38.67 2.17
2030 2237 2.187163 GGGAACAGCCTACGAGCC 59.813 66.667 0.00 0.00 36.66 4.70
2078 2285 5.284079 TCTCAAAGCTCAAATTTGCACTTC 58.716 37.500 19.45 6.48 37.52 3.01
2088 2295 5.105392 ACCACACAAAATCTCAAAGCTCAAA 60.105 36.000 0.00 0.00 0.00 2.69
2089 2296 4.402155 ACCACACAAAATCTCAAAGCTCAA 59.598 37.500 0.00 0.00 0.00 3.02
2110 2317 0.583438 CATCATCGGCGAATCACACC 59.417 55.000 15.93 0.00 0.00 4.16
2182 2389 2.731587 AAATTGTGCTGCCGTGCGTC 62.732 55.000 0.00 0.00 35.36 5.19
2214 2421 6.348868 GCAGCAGAGTTATCAGTAAGCTTTTT 60.349 38.462 3.20 0.00 0.00 1.94
2222 2429 4.535526 TTGTGCAGCAGAGTTATCAGTA 57.464 40.909 0.00 0.00 0.00 2.74
2272 2480 1.408702 GGTGATGGTGCTCTCTCTCTC 59.591 57.143 0.00 0.00 0.00 3.20
2283 2744 3.259374 ACAGAGTTACAGAGGTGATGGTG 59.741 47.826 0.00 0.00 0.00 4.17
2285 2746 4.499183 GAACAGAGTTACAGAGGTGATGG 58.501 47.826 0.00 0.00 0.00 3.51
2292 2753 4.157656 CCAGAGAGGAACAGAGTTACAGAG 59.842 50.000 0.00 0.00 41.22 3.35
2293 2754 4.082845 CCAGAGAGGAACAGAGTTACAGA 58.917 47.826 0.00 0.00 41.22 3.41
2294 2755 3.194542 CCCAGAGAGGAACAGAGTTACAG 59.805 52.174 0.00 0.00 41.22 2.74
2295 2756 3.165875 CCCAGAGAGGAACAGAGTTACA 58.834 50.000 0.00 0.00 41.22 2.41
2296 2757 2.093921 GCCCAGAGAGGAACAGAGTTAC 60.094 54.545 0.00 0.00 41.22 2.50
2297 2758 2.180276 GCCCAGAGAGGAACAGAGTTA 58.820 52.381 0.00 0.00 41.22 2.24
2298 2759 0.980423 GCCCAGAGAGGAACAGAGTT 59.020 55.000 0.00 0.00 41.22 3.01
2299 2760 1.254284 CGCCCAGAGAGGAACAGAGT 61.254 60.000 0.00 0.00 41.22 3.24
2701 3194 2.105128 AAGGGATCGCGCGAGAAG 59.895 61.111 36.99 5.65 0.00 2.85
2718 3211 4.069232 CCGAGAACCGAGGCAGCA 62.069 66.667 0.00 0.00 41.76 4.41
2720 3213 1.446272 GAACCGAGAACCGAGGCAG 60.446 63.158 0.00 0.00 41.76 4.85
2736 3229 5.068234 ACACTTTATCAGATCGAACGGAA 57.932 39.130 0.00 0.00 0.00 4.30
2752 3260 2.034558 CGAGCCATCAAACCAACACTTT 59.965 45.455 0.00 0.00 0.00 2.66
2787 3295 1.004927 GCACAACGAAGCGATCCATAC 60.005 52.381 0.00 0.00 0.00 2.39
2801 3309 2.359900 CCCATCCTCTACAAGCACAAC 58.640 52.381 0.00 0.00 0.00 3.32
2810 3318 0.468648 CCGTTTCCCCCATCCTCTAC 59.531 60.000 0.00 0.00 0.00 2.59
2812 3320 2.001269 CCCGTTTCCCCCATCCTCT 61.001 63.158 0.00 0.00 0.00 3.69
2818 3326 0.549169 ATCTCTTCCCGTTTCCCCCA 60.549 55.000 0.00 0.00 0.00 4.96
2837 3345 3.004839 CGATATTCCGAGCTCTCCAGAAA 59.995 47.826 12.85 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.