Multiple sequence alignment - TraesCS1A01G057500

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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 TraesCS1A01G057500 chr1A 100.000 2195 0 0 1 2195 37509298 37511492 0.000000e+00 4054
1 TraesCS1A01G057500 chr1A 83.568 1704 244 28 394 2070 37502680 37504374 0.000000e+00 1563
2 TraesCS1A01G057500 chr1A 84.903 1497 220 6 594 2088 36615621 36614129 0.000000e+00 1507
3 TraesCS1A01G057500 chr1A 84.834 1477 222 2 594 2069 36607280 36605805 0.000000e+00 1485
4 TraesCS1A01G057500 chr1A 81.926 1693 273 22 387 2070 36638179 36636511 0.000000e+00 1400
5 TraesCS1A01G057500 chr1B 90.318 1291 122 3 782 2070 58114374 58115663 0.000000e+00 1688
6 TraesCS1A01G057500 chr1B 85.188 1492 212 7 591 2078 56499362 56500848 0.000000e+00 1522
7 TraesCS1A01G057500 chr1B 83.446 1631 249 14 469 2080 58326099 58327727 0.000000e+00 1496
8 TraesCS1A01G057500 chr1B 80.531 1695 295 28 387 2069 57222907 57221236 0.000000e+00 1269
9 TraesCS1A01G057500 chr1B 90.993 433 21 2 378 794 58087281 58087711 3.160000e-158 568
10 TraesCS1A01G057500 chr1B 90.762 433 22 2 378 794 58048347 58048777 1.470000e-156 562
11 TraesCS1A01G057500 chr1B 90.531 433 23 2 378 794 58113926 58114356 6.850000e-155 556
12 TraesCS1A01G057500 chr1B 79.497 795 141 16 387 1174 57108299 57107520 1.480000e-151 545
13 TraesCS1A01G057500 chr1B 89.254 335 30 4 49 380 58086780 58087111 4.360000e-112 414
14 TraesCS1A01G057500 chr1B 89.254 335 30 4 49 380 58113425 58113756 4.360000e-112 414
15 TraesCS1A01G057500 chr1B 86.992 123 16 0 2073 2195 58115771 58115893 2.940000e-29 139
16 TraesCS1A01G057500 chr1B 87.619 105 12 1 387 490 57139691 57139587 1.060000e-23 121
17 TraesCS1A01G057500 chr1D 83.784 1702 244 25 394 2070 38557647 38559341 0.000000e+00 1585
18 TraesCS1A01G057500 chr1D 85.223 1482 215 4 591 2070 38365588 38367067 0.000000e+00 1520
19 TraesCS1A01G057500 chr1D 84.641 1491 220 9 595 2080 38257248 38258734 0.000000e+00 1476
20 TraesCS1A01G057500 chr1D 95.213 376 18 0 1 376 38587366 38587741 1.450000e-166 595
21 TraesCS1A01G057500 chr1D 88.462 130 15 0 2066 2195 36623747 36623876 8.110000e-35 158
22 TraesCS1A01G057500 chr1D 90.179 112 11 0 2078 2189 37963935 37964046 1.760000e-31 147
23 TraesCS1A01G057500 chr1D 87.705 122 15 0 2074 2195 38367176 38367297 2.270000e-30 143
24 TraesCS1A01G057500 chr1D 87.826 115 14 0 2066 2180 38559442 38559556 3.800000e-28 135
25 TraesCS1A01G057500 chr1D 86.667 120 14 1 2078 2195 49425469 49425588 4.920000e-27 132
26 TraesCS1A01G057500 chr1D 86.441 118 16 0 2078 2195 37424684 37424567 1.770000e-26 130
27 TraesCS1A01G057500 chr1D 86.087 115 16 0 2081 2195 50109454 50109340 8.230000e-25 124


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 TraesCS1A01G057500 chr1A 37509298 37511492 2194 False 4054.00 4054 100.00000 1 2195 1 chr1A.!!$F2 2194
1 TraesCS1A01G057500 chr1A 37502680 37504374 1694 False 1563.00 1563 83.56800 394 2070 1 chr1A.!!$F1 1676
2 TraesCS1A01G057500 chr1A 36614129 36615621 1492 True 1507.00 1507 84.90300 594 2088 1 chr1A.!!$R2 1494
3 TraesCS1A01G057500 chr1A 36605805 36607280 1475 True 1485.00 1485 84.83400 594 2069 1 chr1A.!!$R1 1475
4 TraesCS1A01G057500 chr1A 36636511 36638179 1668 True 1400.00 1400 81.92600 387 2070 1 chr1A.!!$R3 1683
5 TraesCS1A01G057500 chr1B 56499362 56500848 1486 False 1522.00 1522 85.18800 591 2078 1 chr1B.!!$F1 1487
6 TraesCS1A01G057500 chr1B 58326099 58327727 1628 False 1496.00 1496 83.44600 469 2080 1 chr1B.!!$F3 1611
7 TraesCS1A01G057500 chr1B 57221236 57222907 1671 True 1269.00 1269 80.53100 387 2069 1 chr1B.!!$R3 1682
8 TraesCS1A01G057500 chr1B 58113425 58115893 2468 False 699.25 1688 89.27375 49 2195 4 chr1B.!!$F5 2146
9 TraesCS1A01G057500 chr1B 57107520 57108299 779 True 545.00 545 79.49700 387 1174 1 chr1B.!!$R1 787
10 TraesCS1A01G057500 chr1B 58086780 58087711 931 False 491.00 568 90.12350 49 794 2 chr1B.!!$F4 745
11 TraesCS1A01G057500 chr1D 38257248 38258734 1486 False 1476.00 1476 84.64100 595 2080 1 chr1D.!!$F3 1485
12 TraesCS1A01G057500 chr1D 38557647 38559556 1909 False 860.00 1585 85.80500 394 2180 2 chr1D.!!$F7 1786
13 TraesCS1A01G057500 chr1D 38365588 38367297 1709 False 831.50 1520 86.46400 591 2195 2 chr1D.!!$F6 1604

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
291 295 0.035152 TGAACCAATGCGAGGCTGAT 60.035 50.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2286 0.24746 TACTTGCAGCTCGCTCATGT 59.753 50.0 9.12 11.46 43.06 3.21 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
38 39 7.881775 ATTAAACAATGTCTCCTAATCCACC 57.118 36.000 0.00 0.00 0.00 4.61
39 40 3.933861 ACAATGTCTCCTAATCCACCC 57.066 47.619 0.00 0.00 0.00 4.61
40 41 2.509964 ACAATGTCTCCTAATCCACCCC 59.490 50.000 0.00 0.00 0.00 4.95
41 42 2.509548 CAATGTCTCCTAATCCACCCCA 59.490 50.000 0.00 0.00 0.00 4.96
42 43 2.352561 TGTCTCCTAATCCACCCCAA 57.647 50.000 0.00 0.00 0.00 4.12
43 44 2.858644 TGTCTCCTAATCCACCCCAAT 58.141 47.619 0.00 0.00 0.00 3.16
44 45 3.197983 TGTCTCCTAATCCACCCCAATT 58.802 45.455 0.00 0.00 0.00 2.32
45 46 3.202151 TGTCTCCTAATCCACCCCAATTC 59.798 47.826 0.00 0.00 0.00 2.17
46 47 2.783510 TCTCCTAATCCACCCCAATTCC 59.216 50.000 0.00 0.00 0.00 3.01
47 48 2.785857 CTCCTAATCCACCCCAATTCCT 59.214 50.000 0.00 0.00 0.00 3.36
62 63 6.929049 CCCCAATTCCTTAAAAAGTCAGTTTC 59.071 38.462 0.00 0.00 0.00 2.78
66 67 9.546428 CAATTCCTTAAAAAGTCAGTTTCCATT 57.454 29.630 0.00 0.00 0.00 3.16
81 82 2.229792 TCCATTCAAGCACACTGTTCC 58.770 47.619 0.00 0.00 0.00 3.62
87 88 3.554934 TCAAGCACACTGTTCCTCAAAT 58.445 40.909 0.00 0.00 0.00 2.32
105 106 6.732531 TCAAATAGTGAGCAAGAACATGAG 57.267 37.500 0.00 0.00 0.00 2.90
107 108 6.936335 TCAAATAGTGAGCAAGAACATGAGAA 59.064 34.615 0.00 0.00 0.00 2.87
109 110 4.613925 AGTGAGCAAGAACATGAGAAGA 57.386 40.909 0.00 0.00 0.00 2.87
110 111 4.567971 AGTGAGCAAGAACATGAGAAGAG 58.432 43.478 0.00 0.00 0.00 2.85
111 112 4.040217 AGTGAGCAAGAACATGAGAAGAGT 59.960 41.667 0.00 0.00 0.00 3.24
179 180 5.949735 TGATATTTGAAAAAGCGGAAGACC 58.050 37.500 0.00 0.00 0.00 3.85
222 226 2.950309 GGCACTCATTACTCGAGGTAGA 59.050 50.000 18.41 8.05 34.66 2.59
223 227 3.243134 GGCACTCATTACTCGAGGTAGAC 60.243 52.174 18.41 4.69 34.66 2.59
242 246 3.138304 GACCTTGTTGTGCATCTGTGTA 58.862 45.455 0.00 0.00 0.00 2.90
245 249 4.695455 ACCTTGTTGTGCATCTGTGTATAC 59.305 41.667 0.00 0.00 0.00 1.47
280 284 3.320826 GGTGTAAAGCAAGGTGAACCAAT 59.679 43.478 1.62 0.00 38.89 3.16
291 295 0.035152 TGAACCAATGCGAGGCTGAT 60.035 50.000 0.00 0.00 0.00 2.90
297 301 2.547640 AATGCGAGGCTGATGGCAGT 62.548 55.000 0.00 0.00 44.17 4.40
314 318 3.274288 GCAGTTCTCCTCCCAAACATAG 58.726 50.000 0.00 0.00 0.00 2.23
332 336 1.376543 AGCATCAGCAACCTCAATCG 58.623 50.000 0.00 0.00 45.49 3.34
338 342 2.002586 CAGCAACCTCAATCGTCGATT 58.997 47.619 14.69 14.69 31.86 3.34
357 361 1.075601 TCTTCCAGGACCCATTTGCT 58.924 50.000 0.00 0.00 0.00 3.91
358 362 1.428912 TCTTCCAGGACCCATTTGCTT 59.571 47.619 0.00 0.00 0.00 3.91
359 363 2.158325 TCTTCCAGGACCCATTTGCTTT 60.158 45.455 0.00 0.00 0.00 3.51
362 366 1.273327 CCAGGACCCATTTGCTTTGAC 59.727 52.381 0.00 0.00 0.00 3.18
366 370 4.403432 CAGGACCCATTTGCTTTGACATAT 59.597 41.667 0.00 0.00 0.00 1.78
473 650 2.054021 TCTTGTGATCTTGACACCCCA 58.946 47.619 0.00 0.00 37.45 4.96
563 750 2.356125 GCAGGAAGGCCTTATGACAAGA 60.356 50.000 26.78 0.00 43.90 3.02
577 764 8.383619 CCTTATGACAAGAAAATAGTTCGACTG 58.616 37.037 0.00 0.00 0.00 3.51
746 951 5.656416 TCCCATCAACCTTGGACAAATAATC 59.344 40.000 0.00 0.00 36.26 1.75
777 982 2.556622 GGCGATCTCACCTTTTTCCAAA 59.443 45.455 0.00 0.00 0.00 3.28
778 983 3.193479 GGCGATCTCACCTTTTTCCAAAT 59.807 43.478 0.00 0.00 0.00 2.32
780 985 5.067805 GGCGATCTCACCTTTTTCCAAATAT 59.932 40.000 0.00 0.00 0.00 1.28
822 1057 2.028130 AGACGAGAACTGGGAGCTATG 58.972 52.381 0.00 0.00 0.00 2.23
973 1209 9.317936 CAAACAAATCCTTAGCTTCTTCTTTTT 57.682 29.630 0.00 0.00 0.00 1.94
1062 1298 4.019174 CACCTAATTTCTGGAACATGGCT 58.981 43.478 0.00 0.00 38.20 4.75
1073 1309 1.258982 GAACATGGCTATCGCTTCGTG 59.741 52.381 0.00 0.00 36.09 4.35
1080 1316 0.642291 CTATCGCTTCGTGTGCACAG 59.358 55.000 22.40 14.50 0.00 3.66
1105 1341 9.232473 AGTTATTTCTAGAAAGGCCTTTAAGTG 57.768 33.333 30.47 19.31 33.32 3.16
1180 1416 3.791973 ACATTTTCCTTGCAACGACAA 57.208 38.095 0.00 0.00 0.00 3.18
1188 1424 0.871722 TTGCAACGACAATTCTCCCG 59.128 50.000 0.00 0.00 0.00 5.14
1223 1459 6.118170 ACCCATCTAGTATGATGCAATATGC 58.882 40.000 0.00 0.00 45.29 3.14
1244 1480 4.037446 TGCAACAGTGTCAGGTTTTATTCC 59.963 41.667 0.00 0.00 0.00 3.01
1250 1486 6.001460 CAGTGTCAGGTTTTATTCCCTTACA 58.999 40.000 0.00 0.00 33.64 2.41
1268 1504 2.607499 ACATGGCATTTCCCTGAACAA 58.393 42.857 0.00 0.00 34.88 2.83
1275 1511 3.656559 CATTTCCCTGAACAAAGCCAAG 58.343 45.455 0.00 0.00 0.00 3.61
1276 1512 2.452600 TTCCCTGAACAAAGCCAAGT 57.547 45.000 0.00 0.00 0.00 3.16
1284 1520 2.254546 ACAAAGCCAAGTCATCGTCA 57.745 45.000 0.00 0.00 0.00 4.35
1381 1617 6.484364 TCATGGCATCAAGTACTCTGAATA 57.516 37.500 0.00 0.00 0.00 1.75
1419 1655 5.221048 GCCAACTAAGCAATATCCGTCAATT 60.221 40.000 0.00 0.00 0.00 2.32
1463 1699 1.419387 AGGCCTCTCATCTATGGCAAC 59.581 52.381 0.00 0.00 46.53 4.17
1518 1754 4.783227 ACCCTTCCTTCTTTGCATAGACTA 59.217 41.667 6.34 0.00 0.00 2.59
1613 1850 2.446435 AGCTTTAACCGCATCACCATT 58.554 42.857 0.00 0.00 0.00 3.16
1624 1861 5.184096 ACCGCATCACCATTTATACAACAAA 59.816 36.000 0.00 0.00 0.00 2.83
1668 1905 1.071699 GGTCTGTTTGGCTGTACTCCA 59.928 52.381 3.73 3.73 0.00 3.86
1710 1947 0.541392 TGTCAATAGCATCGGCCAGT 59.459 50.000 2.24 0.00 42.56 4.00
1715 1952 2.002505 ATAGCATCGGCCAGTCTACT 57.997 50.000 2.24 0.00 42.56 2.57
1717 1954 1.299468 GCATCGGCCAGTCTACTCG 60.299 63.158 2.24 0.00 0.00 4.18
1721 1958 1.226323 CGGCCAGTCTACTCGTTCG 60.226 63.158 2.24 0.00 0.00 3.95
1723 1960 0.524862 GGCCAGTCTACTCGTTCGAA 59.475 55.000 0.00 0.00 0.00 3.71
1730 1967 4.974275 CAGTCTACTCGTTCGAAAAAGTGA 59.026 41.667 18.96 13.03 0.00 3.41
1806 2044 7.025963 GCATTTCAGTAAATATGAGCATAGCC 58.974 38.462 0.00 0.00 33.45 3.93
1870 2108 4.494484 GTTGAAAACTTGACAAGTGGCTT 58.506 39.130 21.24 14.35 45.32 4.35
1919 2157 7.964604 TGAAGAGATCAATCATATCAGCAAG 57.035 36.000 0.00 0.00 34.30 4.01
1998 2236 4.651867 CCCTTGGCAGTCATGGAG 57.348 61.111 8.55 0.00 41.70 3.86
2048 2286 1.203038 TCCATGCTTGCAAAGGGAAGA 60.203 47.619 14.46 0.00 46.35 2.87
2054 2292 2.094854 GCTTGCAAAGGGAAGACATGAG 60.095 50.000 0.00 0.00 46.35 2.90
2080 2423 3.127030 GCTGCAAGTAACTGTATTGGGTC 59.873 47.826 0.00 0.00 35.30 4.46
2161 2504 2.261037 GCACAACGCAGCAATAATCA 57.739 45.000 0.00 0.00 41.79 2.57
2174 2517 8.232513 CGCAGCAATAATCAAGTTATATGTCAT 58.767 33.333 0.00 0.00 32.70 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.403583 GGTGGATTAGGAGACATTGTTTAATTA 57.596 33.333 0.00 0.00 0.00 1.40
13 14 7.342026 GGGTGGATTAGGAGACATTGTTTAATT 59.658 37.037 0.00 0.00 0.00 1.40
14 15 6.833933 GGGTGGATTAGGAGACATTGTTTAAT 59.166 38.462 0.00 0.00 0.00 1.40
15 16 6.184789 GGGTGGATTAGGAGACATTGTTTAA 58.815 40.000 0.00 0.00 0.00 1.52
16 17 5.339695 GGGGTGGATTAGGAGACATTGTTTA 60.340 44.000 0.00 0.00 0.00 2.01
17 18 4.569865 GGGGTGGATTAGGAGACATTGTTT 60.570 45.833 0.00 0.00 0.00 2.83
18 19 3.053619 GGGGTGGATTAGGAGACATTGTT 60.054 47.826 0.00 0.00 0.00 2.83
19 20 2.509964 GGGGTGGATTAGGAGACATTGT 59.490 50.000 0.00 0.00 0.00 2.71
20 21 2.509548 TGGGGTGGATTAGGAGACATTG 59.490 50.000 0.00 0.00 0.00 2.82
21 22 2.858644 TGGGGTGGATTAGGAGACATT 58.141 47.619 0.00 0.00 0.00 2.71
22 23 2.587060 TGGGGTGGATTAGGAGACAT 57.413 50.000 0.00 0.00 0.00 3.06
23 24 2.352561 TTGGGGTGGATTAGGAGACA 57.647 50.000 0.00 0.00 0.00 3.41
24 25 3.435169 GGAATTGGGGTGGATTAGGAGAC 60.435 52.174 0.00 0.00 0.00 3.36
25 26 2.783510 GGAATTGGGGTGGATTAGGAGA 59.216 50.000 0.00 0.00 0.00 3.71
26 27 2.785857 AGGAATTGGGGTGGATTAGGAG 59.214 50.000 0.00 0.00 0.00 3.69
27 28 2.871796 AGGAATTGGGGTGGATTAGGA 58.128 47.619 0.00 0.00 0.00 2.94
28 29 3.688049 AAGGAATTGGGGTGGATTAGG 57.312 47.619 0.00 0.00 0.00 2.69
29 30 7.180229 ACTTTTTAAGGAATTGGGGTGGATTAG 59.820 37.037 0.00 0.00 0.00 1.73
30 31 7.020009 ACTTTTTAAGGAATTGGGGTGGATTA 58.980 34.615 0.00 0.00 0.00 1.75
31 32 5.849475 ACTTTTTAAGGAATTGGGGTGGATT 59.151 36.000 0.00 0.00 0.00 3.01
32 33 5.411493 ACTTTTTAAGGAATTGGGGTGGAT 58.589 37.500 0.00 0.00 0.00 3.41
33 34 4.821940 ACTTTTTAAGGAATTGGGGTGGA 58.178 39.130 0.00 0.00 0.00 4.02
34 35 4.591072 TGACTTTTTAAGGAATTGGGGTGG 59.409 41.667 0.00 0.00 0.00 4.61
35 36 5.304357 ACTGACTTTTTAAGGAATTGGGGTG 59.696 40.000 0.00 0.00 0.00 4.61
36 37 5.464069 ACTGACTTTTTAAGGAATTGGGGT 58.536 37.500 0.00 0.00 0.00 4.95
37 38 6.419484 AACTGACTTTTTAAGGAATTGGGG 57.581 37.500 0.00 0.00 0.00 4.96
38 39 6.929049 GGAAACTGACTTTTTAAGGAATTGGG 59.071 38.462 0.00 0.00 0.00 4.12
39 40 7.496747 TGGAAACTGACTTTTTAAGGAATTGG 58.503 34.615 0.00 0.00 0.00 3.16
40 41 9.546428 AATGGAAACTGACTTTTTAAGGAATTG 57.454 29.630 0.00 0.00 0.00 2.32
41 42 9.764363 GAATGGAAACTGACTTTTTAAGGAATT 57.236 29.630 0.00 0.00 0.00 2.17
42 43 8.923270 TGAATGGAAACTGACTTTTTAAGGAAT 58.077 29.630 0.00 0.00 0.00 3.01
43 44 8.299990 TGAATGGAAACTGACTTTTTAAGGAA 57.700 30.769 0.00 0.00 0.00 3.36
44 45 7.889873 TGAATGGAAACTGACTTTTTAAGGA 57.110 32.000 0.00 0.00 0.00 3.36
45 46 7.169813 GCTTGAATGGAAACTGACTTTTTAAGG 59.830 37.037 0.00 0.00 0.00 2.69
46 47 7.706179 TGCTTGAATGGAAACTGACTTTTTAAG 59.294 33.333 0.00 0.00 0.00 1.85
47 48 7.491048 GTGCTTGAATGGAAACTGACTTTTTAA 59.509 33.333 0.00 0.00 0.00 1.52
62 63 2.227388 GAGGAACAGTGTGCTTGAATGG 59.773 50.000 0.06 0.00 0.00 3.16
66 67 2.708216 TTGAGGAACAGTGTGCTTGA 57.292 45.000 0.06 0.00 0.00 3.02
87 88 5.244851 ACTCTTCTCATGTTCTTGCTCACTA 59.755 40.000 0.00 0.00 0.00 2.74
130 131 3.791953 TTTTTACCTCACGGAATCCCA 57.208 42.857 0.00 0.00 0.00 4.37
163 164 3.732471 CGTTTTGGTCTTCCGCTTTTTCA 60.732 43.478 0.00 0.00 36.30 2.69
179 180 1.816224 CCACCATACCCTTCCGTTTTG 59.184 52.381 0.00 0.00 0.00 2.44
222 226 2.057137 ACACAGATGCACAACAAGGT 57.943 45.000 0.00 0.00 0.00 3.50
223 227 4.094887 GGTATACACAGATGCACAACAAGG 59.905 45.833 5.01 0.00 0.00 3.61
227 231 4.503910 TCAGGTATACACAGATGCACAAC 58.496 43.478 5.01 0.00 0.00 3.32
230 234 4.568359 CACTTCAGGTATACACAGATGCAC 59.432 45.833 5.01 0.00 0.00 4.57
232 236 4.122776 CCACTTCAGGTATACACAGATGC 58.877 47.826 5.01 0.00 0.00 3.91
242 246 3.191888 ACACCTCTCCACTTCAGGTAT 57.808 47.619 0.00 0.00 38.57 2.73
245 249 3.866449 GCTTTACACCTCTCCACTTCAGG 60.866 52.174 0.00 0.00 0.00 3.86
280 284 3.258228 AACTGCCATCAGCCTCGCA 62.258 57.895 0.00 0.00 44.10 5.10
297 301 3.523157 TGATGCTATGTTTGGGAGGAGAA 59.477 43.478 0.00 0.00 0.00 2.87
314 318 1.063174 GACGATTGAGGTTGCTGATGC 59.937 52.381 0.00 0.00 40.20 3.91
332 336 0.902531 TGGGTCCTGGAAGAATCGAC 59.097 55.000 0.00 0.00 34.07 4.20
338 342 1.075601 AGCAAATGGGTCCTGGAAGA 58.924 50.000 0.00 0.00 34.07 2.87
357 361 7.094592 TGGTTGCGATCTGTTTTATATGTCAAA 60.095 33.333 0.00 0.00 0.00 2.69
358 362 6.372937 TGGTTGCGATCTGTTTTATATGTCAA 59.627 34.615 0.00 0.00 0.00 3.18
359 363 5.877564 TGGTTGCGATCTGTTTTATATGTCA 59.122 36.000 0.00 0.00 0.00 3.58
362 366 7.701924 ACAAATGGTTGCGATCTGTTTTATATG 59.298 33.333 0.00 0.00 38.39 1.78
366 370 5.218885 CACAAATGGTTGCGATCTGTTTTA 58.781 37.500 0.00 0.00 38.39 1.52
376 380 3.896648 AGTCTAACACAAATGGTTGCG 57.103 42.857 0.00 0.00 38.39 4.85
470 647 7.484641 CGTATTTCATTGAGTACATTTTGTGGG 59.515 37.037 0.00 0.00 0.00 4.61
473 650 8.450964 CCTCGTATTTCATTGAGTACATTTTGT 58.549 33.333 0.00 0.00 0.00 2.83
555 742 8.088981 AGTACAGTCGAACTATTTTCTTGTCAT 58.911 33.333 0.00 0.00 0.00 3.06
563 750 7.916450 GCTATCTCAGTACAGTCGAACTATTTT 59.084 37.037 0.00 0.00 0.00 1.82
577 764 4.138290 TGACTAGCTGGCTATCTCAGTAC 58.862 47.826 0.00 0.00 34.89 2.73
642 847 8.097662 AGAAACGGGAAATATCAGGAGAATATC 58.902 37.037 0.00 0.00 0.00 1.63
746 951 1.227497 GAGATCGCCAAGGCTGGAG 60.227 63.158 9.73 4.18 46.92 3.86
822 1057 3.272574 TCATCAATGGAGAAGAGTGGC 57.727 47.619 0.00 0.00 0.00 5.01
909 1145 0.817654 GGTTGGTGCCTAATGCTTCC 59.182 55.000 0.00 0.00 42.00 3.46
973 1209 5.543507 AATGCATTGTACAAGGTTGGAAA 57.456 34.783 20.31 2.13 0.00 3.13
1062 1298 0.038618 ACTGTGCACACGAAGCGATA 60.039 50.000 17.42 0.00 33.85 2.92
1073 1309 5.392057 GGCCTTTCTAGAAATAACTGTGCAC 60.392 44.000 18.02 10.75 0.00 4.57
1080 1316 9.011095 ACACTTAAAGGCCTTTCTAGAAATAAC 57.989 33.333 33.64 10.82 34.23 1.89
1180 1416 1.818674 GTTGTTTCATGCCGGGAGAAT 59.181 47.619 2.18 0.00 0.00 2.40
1188 1424 3.356290 ACTAGATGGGTTGTTTCATGCC 58.644 45.455 0.00 0.00 0.00 4.40
1223 1459 4.827284 AGGGAATAAAACCTGACACTGTTG 59.173 41.667 0.00 0.00 35.30 3.33
1250 1486 2.027837 GCTTTGTTCAGGGAAATGCCAT 60.028 45.455 0.00 0.00 38.95 4.40
1268 1504 2.026822 AGGATTGACGATGACTTGGCTT 60.027 45.455 0.00 0.00 0.00 4.35
1275 1511 4.878397 AGAAATGGAAGGATTGACGATGAC 59.122 41.667 0.00 0.00 0.00 3.06
1276 1512 5.102953 AGAAATGGAAGGATTGACGATGA 57.897 39.130 0.00 0.00 0.00 2.92
1284 1520 6.672593 TGGCTATTGTAGAAATGGAAGGATT 58.327 36.000 0.00 0.00 0.00 3.01
1381 1617 3.914426 AGTTGGCGAGATGGATAAAGT 57.086 42.857 0.00 0.00 0.00 2.66
1463 1699 6.421501 TGCACAAAATATCTTTGACTTGCTTG 59.578 34.615 13.71 4.95 33.12 4.01
1466 1702 6.035327 GGATGCACAAAATATCTTTGACTTGC 59.965 38.462 13.71 12.95 32.78 4.01
1481 1717 3.096092 GGAAGGGTTATGGATGCACAAA 58.904 45.455 0.00 0.00 0.00 2.83
1531 1767 2.096218 GTCCTGACATTGCGTTCTTCAC 60.096 50.000 0.00 0.00 0.00 3.18
1603 1840 6.531240 CAGGTTTGTTGTATAAATGGTGATGC 59.469 38.462 0.00 0.00 0.00 3.91
1604 1841 7.825681 TCAGGTTTGTTGTATAAATGGTGATG 58.174 34.615 0.00 0.00 0.00 3.07
1613 1850 7.612633 GGTCCCTAATTCAGGTTTGTTGTATAA 59.387 37.037 0.00 0.00 43.80 0.98
1624 1861 2.170012 TAGCGGTCCCTAATTCAGGT 57.830 50.000 0.00 0.00 43.80 4.00
1668 1905 6.183360 ACAAATTCGATGAGATGATTGCCATT 60.183 34.615 0.00 0.00 35.17 3.16
1710 1947 5.008415 AGTCTCACTTTTTCGAACGAGTAGA 59.992 40.000 11.13 11.16 0.00 2.59
1715 1952 7.140705 TGTAATAGTCTCACTTTTTCGAACGA 58.859 34.615 0.00 0.00 0.00 3.85
1717 1954 8.295569 ACTGTAATAGTCTCACTTTTTCGAAC 57.704 34.615 0.00 0.00 33.17 3.95
1806 2044 5.533528 TGCTAAATGTGGAATGATGGATGAG 59.466 40.000 0.00 0.00 0.00 2.90
1857 2095 3.826524 TGGTATTGAAGCCACTTGTCAA 58.173 40.909 0.00 0.00 35.83 3.18
1864 2102 5.988561 TGAAAAACAATGGTATTGAAGCCAC 59.011 36.000 8.41 0.00 37.62 5.01
1919 2157 2.157738 GATATGCCACTGAAGGATGCC 58.842 52.381 0.00 0.00 0.00 4.40
1998 2236 6.416514 CAAAGAAGCTGCAGAAATTTTTGAC 58.583 36.000 20.43 4.88 0.00 3.18
2048 2286 0.247460 TACTTGCAGCTCGCTCATGT 59.753 50.000 9.12 11.46 43.06 3.21
2054 2292 1.710013 TACAGTTACTTGCAGCTCGC 58.290 50.000 0.00 1.70 42.89 5.03
2080 2423 3.062099 CAGATGGTTGATAACGGTGTTCG 59.938 47.826 0.00 0.00 45.88 3.95
2088 2431 2.614057 CCTTCGGCAGATGGTTGATAAC 59.386 50.000 10.15 0.00 37.04 1.89
2111 2454 0.694771 AATGGACAAGGCAGAGCTGA 59.305 50.000 0.85 0.00 0.00 4.26
2112 2455 0.809385 CAATGGACAAGGCAGAGCTG 59.191 55.000 0.00 0.00 0.00 4.24
2161 2504 6.039717 GTGCCCAATGTGATGACATATAACTT 59.960 38.462 0.00 0.00 42.30 2.66


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

AutoCloner maintained by Alex Coulton.