Multiple sequence alignment - TraesCS3D01G513300

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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 TraesCS3D01G513300 chr3D 100.000 2252 0 0 1 2252 597420302 597422553 0.000000e+00 4159
1 TraesCS3D01G513300 chr3D 83.943 984 67 30 717 1650 597546746 597547688 0.000000e+00 857
2 TraesCS3D01G513300 chr3D 82.593 270 19 11 14 257 597546186 597546453 1.750000e-51 213
3 TraesCS3D01G513300 chr3A 94.108 1222 51 7 435 1650 727478059 727479265 0.000000e+00 1838
4 TraesCS3D01G513300 chr3A 88.519 270 12 6 1 255 727477599 727477864 2.170000e-80 309
5 TraesCS3D01G513300 chr3A 87.421 159 11 3 271 427 727477848 727477999 8.270000e-40 174
6 TraesCS3D01G513300 chr3A 87.603 121 12 3 1643 1762 155416281 155416399 1.080000e-28 137
7 TraesCS3D01G513300 chr3B 91.680 1226 67 14 435 1650 804248096 804249296 0.000000e+00 1666
8 TraesCS3D01G513300 chr3B 90.566 318 28 2 1888 2205 804249461 804249776 9.620000e-114 420
9 TraesCS3D01G513300 chr3B 86.989 269 16 6 2 255 804247629 804247893 3.660000e-73 285
10 TraesCS3D01G513300 chr3B 88.750 160 15 2 271 427 804247877 804248036 2.280000e-45 193
11 TraesCS3D01G513300 chr3B 89.381 113 11 1 1651 1762 201343570 201343458 8.390000e-30 141
12 TraesCS3D01G513300 chr2A 94.634 1025 46 5 439 1458 605116270 605115250 0.000000e+00 1580
13 TraesCS3D01G513300 chr2A 87.778 270 14 6 1 255 605120340 605120075 4.700000e-77 298
14 TraesCS3D01G513300 chr2A 87.421 159 11 3 271 427 605120091 605119940 8.270000e-40 174
15 TraesCS3D01G513300 chr6B 91.150 113 9 1 1651 1762 542588717 542588605 3.870000e-33 152
16 TraesCS3D01G513300 chr6B 89.256 121 9 4 1643 1762 365555 365672 5.010000e-32 148
17 TraesCS3D01G513300 chr4A 89.381 113 11 1 1651 1762 148043395 148043283 8.390000e-30 141
18 TraesCS3D01G513300 chr1B 89.286 112 11 1 1652 1762 173971082 173970971 3.020000e-29 139
19 TraesCS3D01G513300 chr7D 87.603 121 11 4 1643 1762 33478452 33478569 1.080000e-28 137
20 TraesCS3D01G513300 chr4B 87.500 120 12 3 1644 1762 562355663 562355780 3.900000e-28 135
21 TraesCS3D01G513300 chr2D 81.818 154 21 7 1638 1789 476030974 476031122 3.040000e-24 122


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 TraesCS3D01G513300 chr3D 597420302 597422553 2251 False 4159.000000 4159 100.000000 1 2252 1 chr3D.!!$F1 2251
1 TraesCS3D01G513300 chr3D 597546186 597547688 1502 False 535.000000 857 83.268000 14 1650 2 chr3D.!!$F2 1636
2 TraesCS3D01G513300 chr3A 727477599 727479265 1666 False 773.666667 1838 90.016000 1 1650 3 chr3A.!!$F2 1649
3 TraesCS3D01G513300 chr3B 804247629 804249776 2147 False 641.000000 1666 89.496250 2 2205 4 chr3B.!!$F1 2203
4 TraesCS3D01G513300 chr2A 605115250 605120340 5090 True 684.000000 1580 89.944333 1 1458 3 chr2A.!!$R1 1457

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
368 396 0.108281 GCTCGAAACTACTCCCACCC 60.108 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 5502 0.035725 TGCTACTCTCTCCGTCCGAA 60.036 55.0 0.0 0.0 0.0 4.3 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
41 42 3.939740 ACAAGTAGGACATGGATGCAT 57.060 42.857 0.00 0.00 0.00 3.96
85 86 9.330063 GATTCTCTAAACATACAACCATGATGA 57.670 33.333 0.00 0.00 0.00 2.92
144 156 8.394822 ACATGGTAGGATCTGATATACAGTACT 58.605 37.037 12.13 0.00 45.86 2.73
216 243 3.629398 GCTTAGGGATGTCCACATTTGAG 59.371 47.826 0.86 0.00 36.57 3.02
284 311 8.980143 TTTTTCCGGAGAATTAATTAAGCAAG 57.020 30.769 8.44 0.00 0.00 4.01
285 312 7.696992 TTTCCGGAGAATTAATTAAGCAAGT 57.303 32.000 3.34 0.00 0.00 3.16
286 313 6.920569 TCCGGAGAATTAATTAAGCAAGTC 57.079 37.500 0.00 0.00 0.00 3.01
287 314 6.411376 TCCGGAGAATTAATTAAGCAAGTCA 58.589 36.000 0.00 0.00 0.00 3.41
288 315 6.538742 TCCGGAGAATTAATTAAGCAAGTCAG 59.461 38.462 0.00 0.00 0.00 3.51
289 316 6.195165 CGGAGAATTAATTAAGCAAGTCAGC 58.805 40.000 0.00 0.00 0.00 4.26
290 317 6.499172 GGAGAATTAATTAAGCAAGTCAGCC 58.501 40.000 0.00 0.00 34.23 4.85
295 322 8.900983 AATTAATTAAGCAAGTCAGCCAAAAA 57.099 26.923 0.00 0.00 34.23 1.94
365 393 1.272490 CTGTGCTCGAAACTACTCCCA 59.728 52.381 0.00 0.00 0.00 4.37
368 396 0.108281 GCTCGAAACTACTCCCACCC 60.108 60.000 0.00 0.00 0.00 4.61
474 4166 8.506437 TCATATCATTTTTGTGTCACTTGACTC 58.494 33.333 10.63 7.59 44.99 3.36
524 4216 4.173036 ACATAATTTTCTGTTGCCGTGG 57.827 40.909 0.00 0.00 0.00 4.94
670 4367 5.360714 CCCCAACATGCTTACTGTGATTAAT 59.639 40.000 0.00 0.00 0.00 1.40
672 4369 7.322664 CCCAACATGCTTACTGTGATTAATTT 58.677 34.615 0.00 0.00 0.00 1.82
866 4568 1.500512 GCCGTCTAAAACACACGCCA 61.501 55.000 0.00 0.00 32.03 5.69
882 4584 1.067669 CGCCACAAGCTAGCTAGATCA 59.932 52.381 25.15 0.00 40.39 2.92
912 4623 0.804989 CAACGCTAGGCTTCCAAAGG 59.195 55.000 0.00 0.00 0.00 3.11
927 4638 6.092396 GCTTCCAAAGGAAACTAACTAGCTAC 59.908 42.308 0.00 0.00 41.54 3.58
1036 4747 3.490759 CGATCCACGTGGTGCTGC 61.491 66.667 32.74 17.22 37.22 5.25
1176 4908 2.352032 CCCGACTCAGGTGGTCTCC 61.352 68.421 0.00 0.00 0.00 3.71
1268 5006 2.025155 CTAGTCACCGGTGAGCTACAT 58.975 52.381 37.04 19.77 40.75 2.29
1272 5010 2.417516 CCGGTGAGCTACATCCCG 59.582 66.667 0.00 0.00 0.00 5.14
1377 5119 6.037500 ACACATGTGCACTGTATATTAAGCAG 59.962 38.462 25.68 6.49 36.41 4.24
1463 5206 7.738437 AATGGTGGTGATTAATTGGATCTTT 57.262 32.000 0.00 0.00 0.00 2.52
1569 5323 5.655893 TTGCTAGCTCATTTTTGTTTTGC 57.344 34.783 17.23 0.00 0.00 3.68
1651 5408 8.867097 TCTCCAGTGGTTTATAGAATACATACC 58.133 37.037 9.54 0.00 0.00 2.73
1652 5409 7.970102 TCCAGTGGTTTATAGAATACATACCC 58.030 38.462 9.54 0.00 0.00 3.69
1653 5410 7.792736 TCCAGTGGTTTATAGAATACATACCCT 59.207 37.037 9.54 0.00 0.00 4.34
1654 5411 8.095169 CCAGTGGTTTATAGAATACATACCCTC 58.905 40.741 0.00 0.00 0.00 4.30
1655 5412 8.095169 CAGTGGTTTATAGAATACATACCCTCC 58.905 40.741 0.00 0.00 0.00 4.30
1656 5413 7.039223 AGTGGTTTATAGAATACATACCCTCCG 60.039 40.741 0.00 0.00 0.00 4.63
1657 5414 6.783977 TGGTTTATAGAATACATACCCTCCGT 59.216 38.462 0.00 0.00 0.00 4.69
1658 5415 7.290714 TGGTTTATAGAATACATACCCTCCGTT 59.709 37.037 0.00 0.00 0.00 4.44
1659 5416 7.816513 GGTTTATAGAATACATACCCTCCGTTC 59.183 40.741 0.00 0.00 0.00 3.95
1660 5417 5.640189 ATAGAATACATACCCTCCGTTCG 57.360 43.478 0.00 0.00 0.00 3.95
1661 5418 2.626743 AGAATACATACCCTCCGTTCGG 59.373 50.000 4.74 4.74 0.00 4.30
1662 5419 2.369983 ATACATACCCTCCGTTCGGA 57.630 50.000 13.34 13.34 0.00 4.55
1663 5420 2.142356 TACATACCCTCCGTTCGGAA 57.858 50.000 14.79 0.81 33.41 4.30
1664 5421 1.492764 ACATACCCTCCGTTCGGAAT 58.507 50.000 14.79 3.18 33.41 3.01
1665 5422 1.835531 ACATACCCTCCGTTCGGAATT 59.164 47.619 14.79 5.06 33.41 2.17
1666 5423 3.033184 ACATACCCTCCGTTCGGAATTA 58.967 45.455 14.79 6.92 33.41 1.40
1667 5424 3.181472 ACATACCCTCCGTTCGGAATTAC 60.181 47.826 14.79 0.00 33.41 1.89
1668 5425 1.565067 ACCCTCCGTTCGGAATTACT 58.435 50.000 14.79 0.00 33.41 2.24
1669 5426 1.904537 ACCCTCCGTTCGGAATTACTT 59.095 47.619 14.79 0.00 33.41 2.24
1670 5427 2.277084 CCCTCCGTTCGGAATTACTTG 58.723 52.381 14.79 1.97 33.41 3.16
1671 5428 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1672 5429 3.332034 CCTCCGTTCGGAATTACTTGTT 58.668 45.455 14.79 0.00 33.41 2.83
1673 5430 3.124636 CCTCCGTTCGGAATTACTTGTTG 59.875 47.826 14.79 0.00 33.41 3.33
1674 5431 2.481185 TCCGTTCGGAATTACTTGTTGC 59.519 45.455 11.66 0.00 0.00 4.17
1675 5432 2.224549 CCGTTCGGAATTACTTGTTGCA 59.775 45.455 5.19 0.00 0.00 4.08
1676 5433 3.119990 CCGTTCGGAATTACTTGTTGCAT 60.120 43.478 5.19 0.00 0.00 3.96
1677 5434 4.093703 CCGTTCGGAATTACTTGTTGCATA 59.906 41.667 5.19 0.00 0.00 3.14
1678 5435 5.391097 CCGTTCGGAATTACTTGTTGCATAA 60.391 40.000 5.19 0.00 0.00 1.90
1679 5436 6.081049 CGTTCGGAATTACTTGTTGCATAAA 58.919 36.000 0.00 0.00 0.00 1.40
1680 5437 6.745450 CGTTCGGAATTACTTGTTGCATAAAT 59.255 34.615 0.00 0.00 0.00 1.40
1681 5438 7.253288 CGTTCGGAATTACTTGTTGCATAAATG 60.253 37.037 0.00 0.00 0.00 2.32
1682 5439 7.384439 TCGGAATTACTTGTTGCATAAATGA 57.616 32.000 0.00 0.00 0.00 2.57
1683 5440 7.821652 TCGGAATTACTTGTTGCATAAATGAA 58.178 30.769 0.00 0.00 0.00 2.57
1684 5441 8.465999 TCGGAATTACTTGTTGCATAAATGAAT 58.534 29.630 0.00 0.00 0.00 2.57
1685 5442 8.533965 CGGAATTACTTGTTGCATAAATGAATG 58.466 33.333 0.00 0.00 0.00 2.67
1686 5443 9.585099 GGAATTACTTGTTGCATAAATGAATGA 57.415 29.630 0.00 0.00 0.00 2.57
1692 5449 9.491675 ACTTGTTGCATAAATGAATGAAAATGA 57.508 25.926 0.00 0.00 0.00 2.57
1735 5492 6.582677 ATGTCTAGATACATCCTTTCTCCG 57.417 41.667 0.00 0.00 35.08 4.63
1736 5493 5.691896 TGTCTAGATACATCCTTTCTCCGA 58.308 41.667 0.00 0.00 0.00 4.55
1737 5494 5.531659 TGTCTAGATACATCCTTTCTCCGAC 59.468 44.000 0.00 0.00 0.00 4.79
1738 5495 5.531659 GTCTAGATACATCCTTTCTCCGACA 59.468 44.000 0.00 0.00 0.00 4.35
1739 5496 6.039493 GTCTAGATACATCCTTTCTCCGACAA 59.961 42.308 0.00 0.00 0.00 3.18
1740 5497 5.269505 AGATACATCCTTTCTCCGACAAG 57.730 43.478 0.00 0.00 0.00 3.16
1741 5498 4.712337 AGATACATCCTTTCTCCGACAAGT 59.288 41.667 0.00 0.00 0.00 3.16
1742 5499 5.892119 AGATACATCCTTTCTCCGACAAGTA 59.108 40.000 0.00 0.00 0.00 2.24
1743 5500 6.551601 AGATACATCCTTTCTCCGACAAGTAT 59.448 38.462 0.00 0.00 0.00 2.12
1744 5501 5.422214 ACATCCTTTCTCCGACAAGTATT 57.578 39.130 0.00 0.00 0.00 1.89
1745 5502 5.805728 ACATCCTTTCTCCGACAAGTATTT 58.194 37.500 0.00 0.00 0.00 1.40
1746 5503 6.238648 ACATCCTTTCTCCGACAAGTATTTT 58.761 36.000 0.00 0.00 0.00 1.82
1747 5504 6.371825 ACATCCTTTCTCCGACAAGTATTTTC 59.628 38.462 0.00 0.00 0.00 2.29
1748 5505 4.927425 TCCTTTCTCCGACAAGTATTTTCG 59.073 41.667 0.00 0.00 0.00 3.46
1754 5511 2.598589 CGACAAGTATTTTCGGACGGA 58.401 47.619 0.00 0.00 0.00 4.69
1755 5512 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1756 5513 3.671433 CGACAAGTATTTTCGGACGGAGA 60.671 47.826 0.00 0.00 0.00 3.71
1757 5514 3.846360 ACAAGTATTTTCGGACGGAGAG 58.154 45.455 0.00 0.00 0.00 3.20
1758 5515 3.508793 ACAAGTATTTTCGGACGGAGAGA 59.491 43.478 0.00 0.00 0.00 3.10
1759 5516 4.106197 CAAGTATTTTCGGACGGAGAGAG 58.894 47.826 0.00 0.00 0.00 3.20
1762 5519 4.575645 AGTATTTTCGGACGGAGAGAGTAG 59.424 45.833 0.00 0.00 0.00 2.57
1777 5534 7.498900 CGGAGAGAGTAGCAGATATGAGATATT 59.501 40.741 0.00 0.00 0.00 1.28
1814 5571 7.338196 TCGAGAGAGATCAGACAAGAATTAGTT 59.662 37.037 0.00 0.00 34.84 2.24
1831 5588 9.517609 AGAATTAGTTACTTTGAGTATAGCACG 57.482 33.333 0.00 0.00 29.64 5.34
1833 5590 8.853469 ATTAGTTACTTTGAGTATAGCACGAC 57.147 34.615 0.00 0.00 29.64 4.34
1863 5620 4.284746 CCCTACATAGGTGGATCTTCTTCC 59.715 50.000 4.26 0.00 42.03 3.46
1867 5624 2.797177 AGGTGGATCTTCTTCCTTGC 57.203 50.000 0.00 0.00 36.68 4.01
1873 5630 3.520721 TGGATCTTCTTCCTTGCTGATGA 59.479 43.478 0.00 0.00 36.68 2.92
1874 5631 4.128643 GGATCTTCTTCCTTGCTGATGAG 58.871 47.826 0.00 0.00 32.68 2.90
1929 5723 5.854010 TGCTCCTAGTAGTCCAACTAATG 57.146 43.478 0.00 0.00 31.62 1.90
1938 5732 7.778185 AGTAGTCCAACTAATGTAGTTCACT 57.222 36.000 11.40 11.40 45.38 3.41
1939 5733 8.874744 AGTAGTCCAACTAATGTAGTTCACTA 57.125 34.615 10.09 10.09 45.38 2.74
1982 5776 8.458573 TCTTGGTGTGTTGTTTCTGTATATTT 57.541 30.769 0.00 0.00 0.00 1.40
1986 5780 7.858382 TGGTGTGTTGTTTCTGTATATTTTTCG 59.142 33.333 0.00 0.00 0.00 3.46
1988 5782 6.858993 TGTGTTGTTTCTGTATATTTTTCGCC 59.141 34.615 0.00 0.00 0.00 5.54
1991 5785 6.964741 TGTTTCTGTATATTTTTCGCCGTA 57.035 33.333 0.00 0.00 0.00 4.02
1993 5787 5.624715 TTCTGTATATTTTTCGCCGTACG 57.375 39.130 8.69 8.69 45.62 3.67
1998 5792 1.219646 ATTTTTCGCCGTACGTGTGT 58.780 45.000 15.21 0.00 44.19 3.72
2004 5798 0.578211 CGCCGTACGTGTGTTTTCTT 59.422 50.000 15.21 0.00 36.87 2.52
2007 5801 3.302350 CGCCGTACGTGTGTTTTCTTAAA 60.302 43.478 15.21 0.00 36.87 1.52
2035 5829 9.331282 GTTTGATCTACTAGCCTGTAATCAAAT 57.669 33.333 21.63 4.39 39.09 2.32
2079 5873 5.968387 ATAAGGAAATCGTGTAGAAAGCG 57.032 39.130 0.00 0.00 0.00 4.68
2128 5922 7.709613 CAGTAACCATACCACTTAGGATTGTAC 59.290 40.741 0.00 0.00 41.22 2.90
2129 5923 6.886178 AACCATACCACTTAGGATTGTACT 57.114 37.500 0.00 0.00 41.22 2.73
2177 5971 2.293122 CTCTCTATGACGAGGCTTCCAG 59.707 54.545 0.00 0.00 0.00 3.86
2187 5981 2.180276 GAGGCTTCCAGAACTAGGTCA 58.820 52.381 11.14 0.00 0.00 4.02
2207 6001 8.525290 AGGTCATTTAATTGGTTTCTCTATGG 57.475 34.615 0.00 0.00 0.00 2.74
2208 6002 7.068716 AGGTCATTTAATTGGTTTCTCTATGGC 59.931 37.037 0.00 0.00 0.00 4.40
2209 6003 6.912591 GTCATTTAATTGGTTTCTCTATGGCG 59.087 38.462 0.00 0.00 0.00 5.69
2210 6004 6.826231 TCATTTAATTGGTTTCTCTATGGCGA 59.174 34.615 0.00 0.00 0.00 5.54
2211 6005 6.677781 TTTAATTGGTTTCTCTATGGCGAG 57.322 37.500 0.00 0.00 0.00 5.03
2212 6006 3.914426 ATTGGTTTCTCTATGGCGAGT 57.086 42.857 0.00 0.00 32.83 4.18
2213 6007 3.695830 TTGGTTTCTCTATGGCGAGTT 57.304 42.857 0.00 0.00 32.83 3.01
2214 6008 2.972625 TGGTTTCTCTATGGCGAGTTG 58.027 47.619 0.00 0.00 32.83 3.16
2215 6009 1.666189 GGTTTCTCTATGGCGAGTTGC 59.334 52.381 0.00 0.00 45.38 4.17
2225 6019 2.153913 GCGAGTTGCCCTATATGCG 58.846 57.895 0.00 0.00 37.76 4.73
2226 6020 1.901650 GCGAGTTGCCCTATATGCGC 61.902 60.000 0.00 0.00 37.76 6.09
2227 6021 0.599991 CGAGTTGCCCTATATGCGCA 60.600 55.000 14.96 14.96 0.00 6.09
2228 6022 1.813513 GAGTTGCCCTATATGCGCAT 58.186 50.000 28.23 28.23 31.44 4.73
2229 6023 2.673893 CGAGTTGCCCTATATGCGCATA 60.674 50.000 30.72 30.72 31.44 3.14
2230 6024 3.334691 GAGTTGCCCTATATGCGCATAA 58.665 45.455 32.02 19.79 31.44 1.90
2231 6025 3.338249 AGTTGCCCTATATGCGCATAAG 58.662 45.455 32.02 26.10 31.44 1.73
2232 6026 2.401583 TGCCCTATATGCGCATAAGG 57.598 50.000 32.02 31.45 0.00 2.69
2233 6027 1.017387 GCCCTATATGCGCATAAGGC 58.983 55.000 34.41 34.41 39.90 4.35
2243 6037 2.153913 GCATAAGGCGTCATAGGCG 58.846 57.895 0.00 0.00 41.99 5.52
2244 6038 0.600255 GCATAAGGCGTCATAGGCGT 60.600 55.000 0.00 0.00 41.99 5.68
2245 6039 1.419374 CATAAGGCGTCATAGGCGTC 58.581 55.000 0.00 0.00 41.99 5.19
2246 6040 1.037493 ATAAGGCGTCATAGGCGTCA 58.963 50.000 0.00 0.00 41.99 4.35
2247 6041 1.037493 TAAGGCGTCATAGGCGTCAT 58.963 50.000 0.00 0.00 41.99 3.06
2248 6042 1.037493 AAGGCGTCATAGGCGTCATA 58.963 50.000 0.00 0.00 41.99 2.15
2249 6043 1.257743 AGGCGTCATAGGCGTCATAT 58.742 50.000 0.00 0.00 41.99 1.78
2250 6044 2.443416 AGGCGTCATAGGCGTCATATA 58.557 47.619 0.00 0.00 41.99 0.86
2251 6045 2.423892 AGGCGTCATAGGCGTCATATAG 59.576 50.000 0.00 0.00 41.99 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.544622 TCCATGTCCTACTTGTACATCAATTAA 58.455 33.333 0.00 0.00 35.35 1.40
15 16 5.684813 GCATCCATGTCCTACTTGTACATCA 60.685 44.000 0.00 0.00 31.60 3.07
16 17 4.752101 GCATCCATGTCCTACTTGTACATC 59.248 45.833 0.00 0.00 31.60 3.06
17 18 4.164030 TGCATCCATGTCCTACTTGTACAT 59.836 41.667 0.00 0.00 34.22 2.29
18 19 3.517500 TGCATCCATGTCCTACTTGTACA 59.482 43.478 0.00 0.00 0.00 2.90
30 31 1.596203 CGCCGAGATGCATCCATGT 60.596 57.895 23.06 4.30 0.00 3.21
41 42 1.892209 TCTCTATATGCACGCCGAGA 58.108 50.000 0.00 0.00 0.00 4.04
85 86 3.776969 TCATCTCAGTTACTCAATGGCCT 59.223 43.478 3.32 0.00 0.00 5.19
144 156 9.769677 ATAACTAGGCATAGTACCATGATCTAA 57.230 33.333 12.08 0.00 41.54 2.10
259 286 8.581578 ACTTGCTTAATTAATTCTCCGGAAAAA 58.418 29.630 5.23 3.12 34.90 1.94
260 287 8.117813 ACTTGCTTAATTAATTCTCCGGAAAA 57.882 30.769 5.23 0.00 34.90 2.29
261 288 7.392113 TGACTTGCTTAATTAATTCTCCGGAAA 59.608 33.333 5.23 3.39 34.90 3.13
262 289 6.882140 TGACTTGCTTAATTAATTCTCCGGAA 59.118 34.615 5.23 0.00 35.78 4.30
263 290 6.411376 TGACTTGCTTAATTAATTCTCCGGA 58.589 36.000 2.93 2.93 0.00 5.14
264 291 6.677781 TGACTTGCTTAATTAATTCTCCGG 57.322 37.500 3.39 0.00 0.00 5.14
265 292 6.195165 GCTGACTTGCTTAATTAATTCTCCG 58.805 40.000 3.39 0.00 0.00 4.63
266 293 6.095440 TGGCTGACTTGCTTAATTAATTCTCC 59.905 38.462 3.39 0.00 0.00 3.71
267 294 7.088589 TGGCTGACTTGCTTAATTAATTCTC 57.911 36.000 3.39 0.00 0.00 2.87
268 295 7.466746 TTGGCTGACTTGCTTAATTAATTCT 57.533 32.000 3.39 0.00 0.00 2.40
269 296 8.532977 TTTTGGCTGACTTGCTTAATTAATTC 57.467 30.769 3.39 0.00 0.00 2.17
270 297 8.900983 TTTTTGGCTGACTTGCTTAATTAATT 57.099 26.923 5.89 5.89 0.00 1.40
327 355 3.196469 CACAGAGAAAGGACTGGCTGATA 59.804 47.826 0.00 0.00 38.30 2.15
365 393 2.919602 TGCCTTAGATTCTTGGAAGGGT 59.080 45.455 13.27 0.00 39.14 4.34
368 396 3.949754 TGCATGCCTTAGATTCTTGGAAG 59.050 43.478 16.68 0.00 0.00 3.46
445 4131 8.461222 TCAAGTGACACAAAAATGATATGATCC 58.539 33.333 8.59 0.00 0.00 3.36
524 4216 4.098416 GTCATCTAAAAATGCAAGGCGTC 58.902 43.478 0.00 0.00 0.00 5.19
629 4322 1.397390 GGGCAAGGAGGAATGCATGG 61.397 60.000 0.00 0.00 44.32 3.66
866 4568 5.163509 TGTTCGATTGATCTAGCTAGCTTGT 60.164 40.000 24.88 11.44 0.00 3.16
882 4584 2.066262 CCTAGCGTTGTGTGTTCGATT 58.934 47.619 0.00 0.00 0.00 3.34
912 4623 6.859017 AGCTTCTCTGTAGCTAGTTAGTTTC 58.141 40.000 0.00 0.00 46.66 2.78
927 4638 0.378962 CCGACGACCTAGCTTCTCTG 59.621 60.000 0.00 0.00 0.00 3.35
1036 4747 4.838152 CCTCCGCATGACCACCCG 62.838 72.222 0.00 0.00 0.00 5.28
1176 4908 4.125703 AGTAGTAATAGTGAGTCGACCCG 58.874 47.826 13.01 0.00 0.00 5.28
1334 5076 7.278646 CACATGTGTGTATGTAGCTAATCAAGT 59.721 37.037 18.03 0.00 39.17 3.16
1377 5119 9.573133 TGTCGATATCATGATGAACACATATAC 57.427 33.333 18.72 5.15 0.00 1.47
1463 5206 1.283613 ACAAAAGTGGACACCTGACCA 59.716 47.619 0.00 0.00 37.52 4.02
1650 5407 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1651 5408 2.968675 ACAAGTAATTCCGAACGGAGG 58.031 47.619 15.34 4.52 46.06 4.30
1652 5409 3.424433 GCAACAAGTAATTCCGAACGGAG 60.424 47.826 15.34 5.60 46.06 4.63
1653 5410 2.481185 GCAACAAGTAATTCCGAACGGA 59.519 45.455 12.04 12.04 43.52 4.69
1654 5411 2.224549 TGCAACAAGTAATTCCGAACGG 59.775 45.455 6.94 6.94 0.00 4.44
1655 5412 3.529634 TGCAACAAGTAATTCCGAACG 57.470 42.857 0.00 0.00 0.00 3.95
1656 5413 7.753132 TCATTTATGCAACAAGTAATTCCGAAC 59.247 33.333 0.00 0.00 0.00 3.95
1657 5414 7.821652 TCATTTATGCAACAAGTAATTCCGAA 58.178 30.769 0.00 0.00 0.00 4.30
1658 5415 7.384439 TCATTTATGCAACAAGTAATTCCGA 57.616 32.000 0.00 0.00 0.00 4.55
1659 5416 8.533965 CATTCATTTATGCAACAAGTAATTCCG 58.466 33.333 0.00 0.00 0.00 4.30
1660 5417 9.585099 TCATTCATTTATGCAACAAGTAATTCC 57.415 29.630 0.00 0.00 0.00 3.01
1666 5423 9.491675 TCATTTTCATTCATTTATGCAACAAGT 57.508 25.926 0.00 0.00 0.00 3.16
1709 5466 8.744652 CGGAGAAAGGATGTATCTAGACATATT 58.255 37.037 0.00 0.00 40.18 1.28
1710 5467 8.110271 TCGGAGAAAGGATGTATCTAGACATAT 58.890 37.037 0.00 0.00 40.18 1.78
1711 5468 7.390996 GTCGGAGAAAGGATGTATCTAGACATA 59.609 40.741 0.00 0.00 38.18 2.29
1712 5469 6.207810 GTCGGAGAAAGGATGTATCTAGACAT 59.792 42.308 0.00 0.00 40.04 3.06
1713 5470 5.531659 GTCGGAGAAAGGATGTATCTAGACA 59.468 44.000 0.00 0.00 39.69 3.41
1714 5471 5.531659 TGTCGGAGAAAGGATGTATCTAGAC 59.468 44.000 0.00 0.00 39.69 2.59
1715 5472 5.691896 TGTCGGAGAAAGGATGTATCTAGA 58.308 41.667 0.00 0.00 39.69 2.43
1716 5473 6.039941 ACTTGTCGGAGAAAGGATGTATCTAG 59.960 42.308 5.61 0.00 39.69 2.43
1717 5474 5.892119 ACTTGTCGGAGAAAGGATGTATCTA 59.108 40.000 5.61 0.00 39.69 1.98
1718 5475 4.712337 ACTTGTCGGAGAAAGGATGTATCT 59.288 41.667 5.61 0.00 39.69 1.98
1719 5476 5.012328 ACTTGTCGGAGAAAGGATGTATC 57.988 43.478 5.61 0.00 39.69 2.24
1720 5477 6.732896 ATACTTGTCGGAGAAAGGATGTAT 57.267 37.500 5.61 0.02 39.69 2.29
1721 5478 6.540438 AATACTTGTCGGAGAAAGGATGTA 57.460 37.500 0.09 0.00 39.69 2.29
1722 5479 5.422214 AATACTTGTCGGAGAAAGGATGT 57.578 39.130 0.09 0.00 39.69 3.06
1723 5480 6.455646 CGAAAATACTTGTCGGAGAAAGGATG 60.456 42.308 0.09 0.00 39.69 3.51
1724 5481 5.581085 CGAAAATACTTGTCGGAGAAAGGAT 59.419 40.000 5.61 0.17 39.69 3.24
1725 5482 4.927425 CGAAAATACTTGTCGGAGAAAGGA 59.073 41.667 5.61 0.00 39.69 3.36
1726 5483 5.204673 CGAAAATACTTGTCGGAGAAAGG 57.795 43.478 5.61 0.00 39.69 3.11
1734 5491 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
1735 5492 3.841643 TCTCCGTCCGAAAATACTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
1736 5493 3.508793 TCTCTCCGTCCGAAAATACTTGT 59.491 43.478 0.00 0.00 0.00 3.16
1737 5494 4.106029 TCTCTCCGTCCGAAAATACTTG 57.894 45.455 0.00 0.00 0.00 3.16
1738 5495 3.762823 ACTCTCTCCGTCCGAAAATACTT 59.237 43.478 0.00 0.00 0.00 2.24
1739 5496 3.354467 ACTCTCTCCGTCCGAAAATACT 58.646 45.455 0.00 0.00 0.00 2.12
1740 5497 3.779271 ACTCTCTCCGTCCGAAAATAC 57.221 47.619 0.00 0.00 0.00 1.89
1741 5498 3.314635 GCTACTCTCTCCGTCCGAAAATA 59.685 47.826 0.00 0.00 0.00 1.40
1742 5499 2.099427 GCTACTCTCTCCGTCCGAAAAT 59.901 50.000 0.00 0.00 0.00 1.82
1743 5500 1.471684 GCTACTCTCTCCGTCCGAAAA 59.528 52.381 0.00 0.00 0.00 2.29
1744 5501 1.093159 GCTACTCTCTCCGTCCGAAA 58.907 55.000 0.00 0.00 0.00 3.46
1745 5502 0.035725 TGCTACTCTCTCCGTCCGAA 60.036 55.000 0.00 0.00 0.00 4.30
1746 5503 0.462225 CTGCTACTCTCTCCGTCCGA 60.462 60.000 0.00 0.00 0.00 4.55
1747 5504 0.462225 TCTGCTACTCTCTCCGTCCG 60.462 60.000 0.00 0.00 0.00 4.79
1748 5505 1.975660 ATCTGCTACTCTCTCCGTCC 58.024 55.000 0.00 0.00 0.00 4.79
1749 5506 4.320023 TCATATCTGCTACTCTCTCCGTC 58.680 47.826 0.00 0.00 0.00 4.79
1750 5507 4.041075 TCTCATATCTGCTACTCTCTCCGT 59.959 45.833 0.00 0.00 0.00 4.69
1751 5508 4.574892 TCTCATATCTGCTACTCTCTCCG 58.425 47.826 0.00 0.00 0.00 4.63
1752 5509 8.752005 AATATCTCATATCTGCTACTCTCTCC 57.248 38.462 0.00 0.00 0.00 3.71
1777 5534 7.441157 GTCTGATCTCTCTCGATTCTTCTTCTA 59.559 40.741 0.00 0.00 0.00 2.10
1779 5536 6.038161 TGTCTGATCTCTCTCGATTCTTCTTC 59.962 42.308 0.00 0.00 0.00 2.87
1783 5540 5.885352 TCTTGTCTGATCTCTCTCGATTCTT 59.115 40.000 0.00 0.00 0.00 2.52
1805 5562 9.517609 CGTGCTATACTCAAAGTAACTAATTCT 57.482 33.333 0.00 0.00 33.89 2.40
1811 5568 6.072064 ACTGTCGTGCTATACTCAAAGTAACT 60.072 38.462 0.00 0.00 33.89 2.24
1814 5571 5.637809 CACTGTCGTGCTATACTCAAAGTA 58.362 41.667 0.00 0.00 32.87 2.24
1830 5587 1.202417 CCTATGTAGGGTGCACTGTCG 60.202 57.143 17.98 0.00 39.86 4.35
1831 5588 2.604046 CCTATGTAGGGTGCACTGTC 57.396 55.000 17.98 7.02 39.86 3.51
1840 5597 5.933869 AGGAAGAAGATCCACCTATGTAGGG 60.934 48.000 10.66 0.36 41.34 3.53
1877 5634 9.549078 TCCGCAAATTGATAGTAATACAATACA 57.451 29.630 0.00 0.00 34.48 2.29
1883 5640 9.490663 GCAATATCCGCAAATTGATAGTAATAC 57.509 33.333 0.00 0.00 35.53 1.89
1885 5642 8.340618 AGCAATATCCGCAAATTGATAGTAAT 57.659 30.769 0.00 0.00 35.53 1.89
1886 5643 7.094805 GGAGCAATATCCGCAAATTGATAGTAA 60.095 37.037 0.00 0.00 35.53 2.24
1888 5645 5.182001 GGAGCAATATCCGCAAATTGATAGT 59.818 40.000 0.00 0.00 35.53 2.12
1908 5702 5.855740 ACATTAGTTGGACTACTAGGAGC 57.144 43.478 0.36 0.00 32.54 4.70
1938 5732 7.767198 CACCAAGAATCCGGTAATTAGTTCTTA 59.233 37.037 0.00 0.00 35.01 2.10
1939 5733 6.598064 CACCAAGAATCCGGTAATTAGTTCTT 59.402 38.462 0.00 4.95 36.62 2.52
1982 5776 1.005137 GAAAACACACGTACGGCGAAA 60.005 47.619 21.06 0.00 44.77 3.46
1986 5780 3.857923 TTAAGAAAACACACGTACGGC 57.142 42.857 21.06 0.00 0.00 5.68
1988 5782 7.425882 TCAAACATTTAAGAAAACACACGTACG 59.574 33.333 15.01 15.01 0.00 3.67
1991 5785 8.188139 AGATCAAACATTTAAGAAAACACACGT 58.812 29.630 0.00 0.00 0.00 4.49
2007 5801 8.023021 TGATTACAGGCTAGTAGATCAAACAT 57.977 34.615 0.00 0.00 0.00 2.71
2054 5848 7.709613 ACGCTTTCTACACGATTTCCTTATAAT 59.290 33.333 0.00 0.00 0.00 1.28
2062 5856 3.427528 TGTGACGCTTTCTACACGATTTC 59.572 43.478 0.00 0.00 36.25 2.17
2067 5861 2.124903 AGTTGTGACGCTTTCTACACG 58.875 47.619 0.00 0.00 36.25 4.49
2070 5864 4.905269 ACAAAAGTTGTGACGCTTTCTAC 58.095 39.130 0.00 0.00 43.48 2.59
2071 5865 5.554822 AACAAAAGTTGTGACGCTTTCTA 57.445 34.783 0.00 0.00 44.59 2.10
2079 5873 7.968405 ACTGAATCAAGTAACAAAAGTTGTGAC 59.032 33.333 0.00 0.97 44.59 3.67
2108 5902 5.057149 GCAGTACAATCCTAAGTGGTATGG 58.943 45.833 0.00 0.00 37.07 2.74
2109 5903 5.670485 TGCAGTACAATCCTAAGTGGTATG 58.330 41.667 0.00 0.00 37.07 2.39
2153 5947 4.202472 TGGAAGCCTCGTCATAGAGAGATA 60.202 45.833 0.00 0.00 40.57 1.98
2163 5957 1.819288 CTAGTTCTGGAAGCCTCGTCA 59.181 52.381 0.00 0.00 0.00 4.35
2165 5959 1.187087 CCTAGTTCTGGAAGCCTCGT 58.813 55.000 0.00 0.00 0.00 4.18
2177 5971 9.232473 AGAGAAACCAATTAAATGACCTAGTTC 57.768 33.333 0.00 0.00 0.00 3.01
2187 5981 6.828785 ACTCGCCATAGAGAAACCAATTAAAT 59.171 34.615 0.62 0.00 40.57 1.40
2207 6001 2.153913 CGCATATAGGGCAACTCGC 58.846 57.895 0.79 0.00 41.28 5.03
2225 6019 0.600255 ACGCCTATGACGCCTTATGC 60.600 55.000 0.00 0.00 0.00 3.14
2226 6020 1.269569 TGACGCCTATGACGCCTTATG 60.270 52.381 0.00 0.00 0.00 1.90
2227 6021 1.037493 TGACGCCTATGACGCCTTAT 58.963 50.000 0.00 0.00 0.00 1.73
2228 6022 1.037493 ATGACGCCTATGACGCCTTA 58.963 50.000 0.00 0.00 0.00 2.69
2229 6023 1.037493 TATGACGCCTATGACGCCTT 58.963 50.000 0.00 0.00 0.00 4.35
2230 6024 1.257743 ATATGACGCCTATGACGCCT 58.742 50.000 0.00 0.00 0.00 5.52
2231 6025 2.798680 CTATATGACGCCTATGACGCC 58.201 52.381 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.