Multiple sequence alignment - TraesCS4A01G075300

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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 TraesCS4A01G075300 chr4A 100.000 2516 0 0 1 2516 74594408 74596923 0.000000e+00 4647
1 TraesCS4A01G075300 chr2D 94.424 1614 59 12 1 1605 608401511 608403102 0.000000e+00 2453
2 TraesCS4A01G075300 chr2D 86.327 373 37 10 20 385 537421350 537420985 6.520000e-106 394
3 TraesCS4A01G075300 chr2D 92.958 71 4 1 442 512 537420994 537420925 4.430000e-18 102
4 TraesCS4A01G075300 chr4B 93.640 1132 57 7 499 1624 50445506 50444384 0.000000e+00 1677
5 TraesCS4A01G075300 chr4B 91.478 575 47 2 1930 2503 482981514 482982087 0.000000e+00 789
6 TraesCS4A01G075300 chr4B 94.821 502 23 3 1 502 50446085 50445587 0.000000e+00 780
7 TraesCS4A01G075300 chr3A 92.033 979 67 5 645 1623 358337898 358338865 0.000000e+00 1365
8 TraesCS4A01G075300 chr3A 95.274 402 18 1 17 418 358326447 358326847 9.820000e-179 636
9 TraesCS4A01G075300 chr3A 95.417 240 10 1 414 653 358329840 358330078 5.080000e-102 381
10 TraesCS4A01G075300 chr2A 93.309 822 32 4 501 1321 766420121 766420920 0.000000e+00 1192
11 TraesCS4A01G075300 chr2A 95.678 509 16 6 1 508 766419583 766420086 0.000000e+00 813
12 TraesCS4A01G075300 chr2A 95.527 313 11 1 1311 1623 766437202 766437511 4.830000e-137 497
13 TraesCS4A01G075300 chr4D 91.601 631 51 2 1887 2516 393245501 393246130 0.000000e+00 870
14 TraesCS4A01G075300 chr4D 91.083 628 55 1 1890 2516 393649162 393648535 0.000000e+00 848
15 TraesCS4A01G075300 chr4D 89.855 207 18 3 1656 1862 393649358 393649155 1.920000e-66 263
16 TraesCS4A01G075300 chr4D 89.372 207 19 3 1656 1862 393245308 393245511 8.930000e-65 257
17 TraesCS4A01G075300 chr3B 91.333 450 34 5 33 481 757978857 757978412 5.950000e-171 610
18 TraesCS4A01G075300 chr1A 88.462 468 40 3 478 945 567487672 567488125 1.020000e-153 553
19 TraesCS4A01G075300 chr1A 84.454 476 52 14 1029 1492 567502419 567502884 1.370000e-122 449
20 TraesCS4A01G075300 chr1A 94.372 231 9 4 253 481 567487400 567487628 3.980000e-93 351
21 TraesCS4A01G075300 chr1A 90.647 139 13 0 1484 1622 567516962 567517100 4.270000e-43 185
22 TraesCS4A01G075300 chr1D 84.264 394 44 13 1 383 478709051 478709437 3.950000e-98 368
23 TraesCS4A01G075300 chr1D 90.244 123 6 2 1 117 39677418 39677540 3.350000e-34 156
24 TraesCS4A01G075300 chr1D 87.023 131 11 2 255 385 454427337 454427461 2.610000e-30 143
25 TraesCS4A01G075300 chr1D 94.366 71 2 2 442 512 454427452 454427520 9.520000e-20 108
26 TraesCS4A01G075300 chr7A 96.970 66 2 0 447 512 119967259 119967194 7.360000e-21 111


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 TraesCS4A01G075300 chr4A 74594408 74596923 2515 False 4647.0 4647 100.0000 1 2516 1 chr4A.!!$F1 2515
1 TraesCS4A01G075300 chr2D 608401511 608403102 1591 False 2453.0 2453 94.4240 1 1605 1 chr2D.!!$F1 1604
2 TraesCS4A01G075300 chr4B 50444384 50446085 1701 True 1228.5 1677 94.2305 1 1624 2 chr4B.!!$R1 1623
3 TraesCS4A01G075300 chr4B 482981514 482982087 573 False 789.0 789 91.4780 1930 2503 1 chr4B.!!$F1 573
4 TraesCS4A01G075300 chr3A 358337898 358338865 967 False 1365.0 1365 92.0330 645 1623 1 chr3A.!!$F1 978
5 TraesCS4A01G075300 chr3A 358326447 358330078 3631 False 508.5 636 95.3455 17 653 2 chr3A.!!$F2 636
6 TraesCS4A01G075300 chr2A 766419583 766420920 1337 False 1002.5 1192 94.4935 1 1321 2 chr2A.!!$F2 1320
7 TraesCS4A01G075300 chr4D 393245308 393246130 822 False 563.5 870 90.4865 1656 2516 2 chr4D.!!$F1 860
8 TraesCS4A01G075300 chr4D 393648535 393649358 823 True 555.5 848 90.4690 1656 2516 2 chr4D.!!$R1 860
9 TraesCS4A01G075300 chr1A 567487400 567488125 725 False 452.0 553 91.4170 253 945 2 chr1A.!!$F3 692

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
930 4066 1.59813 GCGAGGAACAAGCTGTGGT 60.598 57.895 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 5362 1.069596 GCAGCACAAAACTTGGGGG 59.93 57.895 0.0 0.0 33.68 5.4 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
31 32 9.528489 AACAAAACAACTACTTCCCATATACAT 57.472 29.630 0.00 0.00 0.00 2.29
84 85 7.148656 CCAACAAAGTGTGACCAAACTAAAAAG 60.149 37.037 0.00 0.00 0.00 2.27
145 146 7.820872 ACTTAAATTGCCATCCTTCATTGAAAG 59.179 33.333 0.01 0.00 0.00 2.62
330 331 9.651913 AAAAAGAAACAAGAGTCTGCAAAATTA 57.348 25.926 0.00 0.00 0.00 1.40
350 352 9.643693 AAAATTACCATGATGAAAGAACACATC 57.356 29.630 0.00 0.00 41.94 3.06
439 3438 7.931407 ACTATCACATATCATCTACGGCAAAAA 59.069 33.333 0.00 0.00 0.00 1.94
930 4066 1.598130 GCGAGGAACAAGCTGTGGT 60.598 57.895 0.00 0.00 0.00 4.16
1094 4230 4.363990 CCACGCACGGAGCAGAGT 62.364 66.667 3.06 0.00 46.13 3.24
1101 4237 1.025113 CACGGAGCAGAGTCGTCCTA 61.025 60.000 7.41 0.00 34.73 2.94
1108 4244 4.253257 GAGTCGTCCTAGCCGCCG 62.253 72.222 0.00 0.00 0.00 6.46
1184 4325 4.478203 CATGTAGATGAGGAAGGAGGAGA 58.522 47.826 0.00 0.00 0.00 3.71
1415 4556 3.058160 GCGTGGTTGCAGGCATCT 61.058 61.111 0.00 0.00 36.16 2.90
1536 4677 0.598065 GTGGCGATTTTTGGTGCTCT 59.402 50.000 0.00 0.00 0.00 4.09
1562 4703 0.506506 CGTGCCAAAAATCAAACGGC 59.493 50.000 0.00 0.00 43.28 5.68
1624 4765 3.340034 TCGGCACTTATTGATTCCGTTT 58.660 40.909 0.00 0.00 38.18 3.60
1625 4766 3.754323 TCGGCACTTATTGATTCCGTTTT 59.246 39.130 0.00 0.00 38.18 2.43
1626 4767 4.095610 CGGCACTTATTGATTCCGTTTTC 58.904 43.478 0.00 0.00 32.93 2.29
1627 4768 4.142687 CGGCACTTATTGATTCCGTTTTCT 60.143 41.667 0.00 0.00 32.93 2.52
1628 4769 5.619086 CGGCACTTATTGATTCCGTTTTCTT 60.619 40.000 0.00 0.00 32.93 2.52
1629 4770 6.156519 GGCACTTATTGATTCCGTTTTCTTT 58.843 36.000 0.00 0.00 0.00 2.52
1630 4771 6.645003 GGCACTTATTGATTCCGTTTTCTTTT 59.355 34.615 0.00 0.00 0.00 2.27
1631 4772 7.359181 GGCACTTATTGATTCCGTTTTCTTTTG 60.359 37.037 0.00 0.00 0.00 2.44
1632 4773 7.501515 CACTTATTGATTCCGTTTTCTTTTGC 58.498 34.615 0.00 0.00 0.00 3.68
1633 4774 6.645003 ACTTATTGATTCCGTTTTCTTTTGCC 59.355 34.615 0.00 0.00 0.00 4.52
1634 4775 3.006659 TGATTCCGTTTTCTTTTGCCG 57.993 42.857 0.00 0.00 0.00 5.69
1635 4776 2.359531 TGATTCCGTTTTCTTTTGCCGT 59.640 40.909 0.00 0.00 0.00 5.68
1636 4777 2.943449 TTCCGTTTTCTTTTGCCGTT 57.057 40.000 0.00 0.00 0.00 4.44
1637 4778 2.196295 TCCGTTTTCTTTTGCCGTTG 57.804 45.000 0.00 0.00 0.00 4.10
1638 4779 1.202313 TCCGTTTTCTTTTGCCGTTGG 60.202 47.619 0.00 0.00 0.00 3.77
1648 4789 2.727544 GCCGTTGGCTGCAAGAAA 59.272 55.556 0.50 0.00 46.69 2.52
1649 4790 1.067250 GCCGTTGGCTGCAAGAAAA 59.933 52.632 0.50 0.00 46.69 2.29
1650 4791 0.940991 GCCGTTGGCTGCAAGAAAAG 60.941 55.000 0.50 0.00 46.69 2.27
1651 4792 0.667993 CCGTTGGCTGCAAGAAAAGA 59.332 50.000 0.50 0.00 34.07 2.52
1652 4793 1.066908 CCGTTGGCTGCAAGAAAAGAA 59.933 47.619 0.50 0.00 34.07 2.52
1653 4794 2.388121 CGTTGGCTGCAAGAAAAGAAG 58.612 47.619 0.50 0.00 34.07 2.85
1654 4795 2.033299 CGTTGGCTGCAAGAAAAGAAGA 59.967 45.455 0.50 0.00 34.07 2.87
1704 4845 0.761187 GGTTTATCTCCCCGTACCCC 59.239 60.000 0.00 0.00 0.00 4.95
1747 4888 6.202188 CGTGGTTAATTTAAGATCCGTGCTAT 59.798 38.462 0.00 0.00 0.00 2.97
1753 4894 9.796120 TTAATTTAAGATCCGTGCTATTTTTGG 57.204 29.630 0.00 0.00 0.00 3.28
1763 4904 2.554893 TGCTATTTTTGGGGTCGTTGTC 59.445 45.455 0.00 0.00 0.00 3.18
1770 4911 4.473477 TTTGGGGTCGTTGTCAAAATTT 57.527 36.364 0.00 0.00 0.00 1.82
1772 4913 5.593679 TTGGGGTCGTTGTCAAAATTTAA 57.406 34.783 0.00 0.00 0.00 1.52
1774 4915 4.401519 TGGGGTCGTTGTCAAAATTTAACA 59.598 37.500 0.00 0.00 0.00 2.41
1811 4952 5.737757 GTCTGTTCGGTTTTTCTCTTGTTTC 59.262 40.000 0.00 0.00 0.00 2.78
1814 4955 6.626302 TGTTCGGTTTTTCTCTTGTTTCAAT 58.374 32.000 0.00 0.00 0.00 2.57
1821 4962 8.968242 GGTTTTTCTCTTGTTTCAATGTGTATC 58.032 33.333 0.00 0.00 0.00 2.24
1835 4976 5.917541 ATGTGTATCGTCGTGTTTTCTTT 57.082 34.783 0.00 0.00 0.00 2.52
1838 4979 5.063691 TGTGTATCGTCGTGTTTTCTTTGTT 59.936 36.000 0.00 0.00 0.00 2.83
1849 4990 6.583050 CGTGTTTTCTTTGTTTACCAGTGAAA 59.417 34.615 0.00 0.00 0.00 2.69
1862 5003 4.831107 ACCAGTGAAAAATGCACTTGTTT 58.169 34.783 0.00 0.00 43.67 2.83
1863 5004 5.244755 ACCAGTGAAAAATGCACTTGTTTT 58.755 33.333 0.00 0.00 43.67 2.43
1864 5005 5.351189 ACCAGTGAAAAATGCACTTGTTTTC 59.649 36.000 14.94 14.94 43.67 2.29
1865 5006 5.581874 CCAGTGAAAAATGCACTTGTTTTCT 59.418 36.000 19.29 3.92 43.67 2.52
1866 5007 6.455913 CCAGTGAAAAATGCACTTGTTTTCTG 60.456 38.462 19.29 12.28 43.67 3.02
1867 5008 6.310956 CAGTGAAAAATGCACTTGTTTTCTGA 59.689 34.615 19.29 5.89 43.67 3.27
1868 5009 6.873076 AGTGAAAAATGCACTTGTTTTCTGAA 59.127 30.769 19.29 0.00 43.67 3.02
1869 5010 6.955407 GTGAAAAATGCACTTGTTTTCTGAAC 59.045 34.615 19.29 11.02 40.37 3.18
1870 5011 6.648310 TGAAAAATGCACTTGTTTTCTGAACA 59.352 30.769 19.29 0.00 40.37 3.18
1871 5012 7.333921 TGAAAAATGCACTTGTTTTCTGAACAT 59.666 29.630 19.29 0.00 40.37 2.71
1872 5013 6.833342 AAATGCACTTGTTTTCTGAACATC 57.167 33.333 0.00 0.00 0.00 3.06
1873 5014 4.979943 TGCACTTGTTTTCTGAACATCA 57.020 36.364 0.00 0.00 0.00 3.07
1874 5015 4.923893 TGCACTTGTTTTCTGAACATCAG 58.076 39.130 0.88 0.88 45.59 2.90
1875 5016 4.398988 TGCACTTGTTTTCTGAACATCAGT 59.601 37.500 7.21 0.00 44.58 3.41
1876 5017 5.588246 TGCACTTGTTTTCTGAACATCAGTA 59.412 36.000 7.21 0.00 44.58 2.74
1877 5018 6.094742 TGCACTTGTTTTCTGAACATCAGTAA 59.905 34.615 7.21 1.76 44.58 2.24
1878 5019 6.972328 GCACTTGTTTTCTGAACATCAGTAAA 59.028 34.615 7.21 7.49 44.58 2.01
1883 5024 6.912203 TTTTCTGAACATCAGTAAACACGA 57.088 33.333 7.21 0.00 44.58 4.35
1884 5025 5.900339 TTCTGAACATCAGTAAACACGAC 57.100 39.130 7.21 0.00 44.58 4.34
1885 5026 3.978855 TCTGAACATCAGTAAACACGACG 59.021 43.478 7.21 0.00 44.58 5.12
1886 5027 3.967401 TGAACATCAGTAAACACGACGA 58.033 40.909 0.00 0.00 0.00 4.20
1887 5028 4.552355 TGAACATCAGTAAACACGACGAT 58.448 39.130 0.00 0.00 0.00 3.73
1888 5029 5.701855 TGAACATCAGTAAACACGACGATA 58.298 37.500 0.00 0.00 0.00 2.92
1889 5030 5.570206 TGAACATCAGTAAACACGACGATAC 59.430 40.000 0.00 0.00 0.00 2.24
1890 5031 5.050644 ACATCAGTAAACACGACGATACA 57.949 39.130 0.00 0.00 0.00 2.29
1891 5032 4.855388 ACATCAGTAAACACGACGATACAC 59.145 41.667 0.00 0.00 0.00 2.90
1892 5033 4.754372 TCAGTAAACACGACGATACACT 57.246 40.909 0.00 0.00 0.00 3.55
1893 5034 5.112220 TCAGTAAACACGACGATACACTT 57.888 39.130 0.00 0.00 0.00 3.16
1894 5035 4.913345 TCAGTAAACACGACGATACACTTG 59.087 41.667 0.00 0.00 0.00 3.16
1895 5036 4.678287 CAGTAAACACGACGATACACTTGT 59.322 41.667 0.00 0.00 0.00 3.16
1896 5037 5.174398 CAGTAAACACGACGATACACTTGTT 59.826 40.000 0.00 0.00 0.00 2.83
1912 5053 2.799126 TGTTATGGATCGGGTTTGCT 57.201 45.000 0.00 0.00 0.00 3.91
1934 5075 9.710900 TTGCTGATACACGATGAAATATAAGAT 57.289 29.630 0.00 0.00 0.00 2.40
1972 5113 5.979517 GGAAGGAAAACTCAATGAACACTTG 59.020 40.000 0.00 0.00 0.00 3.16
1989 5130 9.513906 TGAACACTTGGAAACATGATAATTCTA 57.486 29.630 0.00 0.00 42.32 2.10
2063 5205 2.211250 ATGGGATATCCTGTGCATGC 57.789 50.000 21.18 11.82 36.20 4.06
2079 5221 7.362401 CCTGTGCATGCTAGAATTACTTTTCTT 60.362 37.037 20.33 0.00 37.20 2.52
2095 5237 7.830099 ACTTTTCTTCAAGTTCATCTGGATT 57.170 32.000 0.00 0.00 32.81 3.01
2109 5251 1.143838 GGATTTTGGGGCATTCGGC 59.856 57.895 0.00 0.00 43.74 5.54
2110 5252 1.226945 GATTTTGGGGCATTCGGCG 60.227 57.895 0.00 0.00 46.16 6.46
2134 5276 7.537649 GCGCTTTCATTAGGGTAAATATTAAGC 59.462 37.037 0.00 0.00 0.00 3.09
2169 5311 7.238486 TCTGCCATTTACCAACATTTGTTAT 57.762 32.000 0.00 0.00 36.32 1.89
2220 5362 8.834465 ACATTATCAAGTGCAATATGAGAAGAC 58.166 33.333 9.58 0.00 29.02 3.01
2234 5376 2.623416 GAGAAGACCCCCAAGTTTTGTG 59.377 50.000 0.00 0.00 0.00 3.33
2236 5378 0.261696 AGACCCCCAAGTTTTGTGCT 59.738 50.000 0.00 0.00 0.00 4.40
2251 5393 1.759445 TGTGCTGCTTTTGGCCTTTTA 59.241 42.857 3.32 0.00 40.92 1.52
2364 5507 2.642171 TCATGTGGAAGAGGTAGGGT 57.358 50.000 0.00 0.00 0.00 4.34
2424 5567 1.302192 TGGCCGTACTGACTTTGGC 60.302 57.895 0.00 0.00 44.98 4.52
2471 5614 2.301346 GGATTGGTGCCTACATTCCAG 58.699 52.381 0.00 0.00 37.95 3.86
2473 5616 2.969821 TTGGTGCCTACATTCCAGTT 57.030 45.000 0.00 0.00 0.00 3.16
2479 5622 1.614317 GCCTACATTCCAGTTGTGCCT 60.614 52.381 0.00 0.00 0.00 4.75
2492 5635 5.112686 CAGTTGTGCCTAGAATAAGACCTC 58.887 45.833 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.635714 AGATGCATCGCAGATTCACAA 58.364 42.857 20.67 0.00 43.65 3.33
84 85 2.037901 TGAGGCAGAGATGAGATGGAC 58.962 52.381 0.00 0.00 0.00 4.02
350 352 4.644498 ACCCATGGCAATTTTCTCAAAAG 58.356 39.130 6.09 0.00 33.22 2.27
352 354 4.703379 AACCCATGGCAATTTTCTCAAA 57.297 36.364 6.09 0.00 0.00 2.69
439 3438 3.570125 GCAGTAGGCCAGTTTTCTTTCTT 59.430 43.478 5.01 0.00 36.11 2.52
761 3897 4.582701 TTTACCAACAACTGAAGCATGG 57.417 40.909 0.00 0.00 0.00 3.66
1026 4162 3.719883 TTGACCGTCGGCGTTGTGT 62.720 57.895 12.28 0.00 36.15 3.72
1078 4214 2.807045 GACTCTGCTCCGTGCGTG 60.807 66.667 0.00 0.00 46.63 5.34
1079 4215 4.406173 CGACTCTGCTCCGTGCGT 62.406 66.667 0.00 0.00 46.63 5.24
1080 4216 4.406173 ACGACTCTGCTCCGTGCG 62.406 66.667 0.00 0.00 46.63 5.34
1081 4217 2.505118 GACGACTCTGCTCCGTGC 60.505 66.667 0.00 0.00 43.25 5.34
1082 4218 1.025113 TAGGACGACTCTGCTCCGTG 61.025 60.000 0.00 0.00 36.60 4.94
1083 4219 0.745128 CTAGGACGACTCTGCTCCGT 60.745 60.000 0.00 0.00 39.41 4.69
1084 4220 2.018544 CTAGGACGACTCTGCTCCG 58.981 63.158 0.00 0.00 0.00 4.63
1108 4244 4.459089 GCCAGACTCTCCACGCCC 62.459 72.222 0.00 0.00 0.00 6.13
1184 4325 1.803555 GCGCTCTTCTCTTTGCTTCTT 59.196 47.619 0.00 0.00 0.00 2.52
1415 4556 3.173965 CCTACACTCCTTTCTTCTCCCA 58.826 50.000 0.00 0.00 0.00 4.37
1536 4677 5.465935 GTTTGATTTTTGGCACGAATCCTA 58.534 37.500 15.48 5.30 0.00 2.94
1562 4703 2.182030 GTCCGAACGCCTCCTCTG 59.818 66.667 0.00 0.00 0.00 3.35
1632 4773 0.667993 TCTTTTCTTGCAGCCAACGG 59.332 50.000 0.00 0.00 0.00 4.44
1633 4774 2.033299 TCTTCTTTTCTTGCAGCCAACG 59.967 45.455 0.00 0.00 0.00 4.10
1634 4775 3.715628 TCTTCTTTTCTTGCAGCCAAC 57.284 42.857 0.00 0.00 0.00 3.77
1635 4776 4.460382 CCTATCTTCTTTTCTTGCAGCCAA 59.540 41.667 0.00 0.00 0.00 4.52
1636 4777 4.012374 CCTATCTTCTTTTCTTGCAGCCA 58.988 43.478 0.00 0.00 0.00 4.75
1637 4778 4.013050 ACCTATCTTCTTTTCTTGCAGCC 58.987 43.478 0.00 0.00 0.00 4.85
1638 4779 4.697352 TCACCTATCTTCTTTTCTTGCAGC 59.303 41.667 0.00 0.00 0.00 5.25
1639 4780 6.429385 ACTTCACCTATCTTCTTTTCTTGCAG 59.571 38.462 0.00 0.00 0.00 4.41
1640 4781 6.205464 CACTTCACCTATCTTCTTTTCTTGCA 59.795 38.462 0.00 0.00 0.00 4.08
1641 4782 6.348868 CCACTTCACCTATCTTCTTTTCTTGC 60.349 42.308 0.00 0.00 0.00 4.01
1642 4783 6.936900 TCCACTTCACCTATCTTCTTTTCTTG 59.063 38.462 0.00 0.00 0.00 3.02
1643 4784 7.079451 TCCACTTCACCTATCTTCTTTTCTT 57.921 36.000 0.00 0.00 0.00 2.52
1644 4785 6.688073 TCCACTTCACCTATCTTCTTTTCT 57.312 37.500 0.00 0.00 0.00 2.52
1645 4786 6.710744 TGTTCCACTTCACCTATCTTCTTTTC 59.289 38.462 0.00 0.00 0.00 2.29
1646 4787 6.601332 TGTTCCACTTCACCTATCTTCTTTT 58.399 36.000 0.00 0.00 0.00 2.27
1647 4788 6.187727 TGTTCCACTTCACCTATCTTCTTT 57.812 37.500 0.00 0.00 0.00 2.52
1648 4789 5.825593 TGTTCCACTTCACCTATCTTCTT 57.174 39.130 0.00 0.00 0.00 2.52
1649 4790 5.799213 CTTGTTCCACTTCACCTATCTTCT 58.201 41.667 0.00 0.00 0.00 2.85
1650 4791 4.393371 GCTTGTTCCACTTCACCTATCTTC 59.607 45.833 0.00 0.00 0.00 2.87
1651 4792 4.042187 AGCTTGTTCCACTTCACCTATCTT 59.958 41.667 0.00 0.00 0.00 2.40
1652 4793 3.584848 AGCTTGTTCCACTTCACCTATCT 59.415 43.478 0.00 0.00 0.00 1.98
1653 4794 3.935828 GAGCTTGTTCCACTTCACCTATC 59.064 47.826 0.00 0.00 0.00 2.08
1654 4795 3.327757 TGAGCTTGTTCCACTTCACCTAT 59.672 43.478 0.00 0.00 0.00 2.57
1684 4825 0.761187 GGGTACGGGGAGATAAACCC 59.239 60.000 0.00 0.00 46.05 4.11
1704 4845 0.530650 CGGACGGTGGATCCATGAAG 60.531 60.000 19.62 11.95 35.83 3.02
1732 4873 4.642885 CCCCAAAAATAGCACGGATCTTAA 59.357 41.667 0.00 0.00 0.00 1.85
1733 4874 4.204012 CCCCAAAAATAGCACGGATCTTA 58.796 43.478 0.00 0.00 0.00 2.10
1734 4875 3.023832 CCCCAAAAATAGCACGGATCTT 58.976 45.455 0.00 0.00 0.00 2.40
1747 4888 3.955650 TTTTGACAACGACCCCAAAAA 57.044 38.095 0.00 0.00 36.10 1.94
1752 4893 4.741185 GTGTTAAATTTTGACAACGACCCC 59.259 41.667 8.17 0.00 0.00 4.95
1753 4894 4.438471 CGTGTTAAATTTTGACAACGACCC 59.562 41.667 16.41 3.22 0.00 4.46
1770 4911 6.906143 CGAACAGACCATTTTAAAACGTGTTA 59.094 34.615 1.97 0.00 0.00 2.41
1772 4913 5.267776 CGAACAGACCATTTTAAAACGTGT 58.732 37.500 1.97 0.81 0.00 4.49
1774 4915 4.336153 ACCGAACAGACCATTTTAAAACGT 59.664 37.500 1.97 2.50 0.00 3.99
1786 4927 3.626217 ACAAGAGAAAAACCGAACAGACC 59.374 43.478 0.00 0.00 0.00 3.85
1787 4928 4.877323 ACAAGAGAAAAACCGAACAGAC 57.123 40.909 0.00 0.00 0.00 3.51
1789 4930 5.636837 TGAAACAAGAGAAAAACCGAACAG 58.363 37.500 0.00 0.00 0.00 3.16
1811 4952 5.264060 AGAAAACACGACGATACACATTG 57.736 39.130 0.00 0.00 0.00 2.82
1814 4955 4.567558 ACAAAGAAAACACGACGATACACA 59.432 37.500 0.00 0.00 0.00 3.72
1821 4962 4.649977 TGGTAAACAAAGAAAACACGACG 58.350 39.130 0.00 0.00 0.00 5.12
1835 4976 5.590530 AGTGCATTTTTCACTGGTAAACA 57.409 34.783 0.00 0.00 42.63 2.83
1838 4979 5.590530 ACAAGTGCATTTTTCACTGGTAA 57.409 34.783 1.63 0.00 44.49 2.85
1849 4990 6.339730 TGATGTTCAGAAAACAAGTGCATTT 58.660 32.000 0.00 0.00 33.42 2.32
1865 5006 3.967401 TCGTCGTGTTTACTGATGTTCA 58.033 40.909 0.00 0.00 0.00 3.18
1866 5007 5.570206 TGTATCGTCGTGTTTACTGATGTTC 59.430 40.000 0.00 0.00 0.00 3.18
1867 5008 5.344128 GTGTATCGTCGTGTTTACTGATGTT 59.656 40.000 0.00 0.00 0.00 2.71
1868 5009 4.855388 GTGTATCGTCGTGTTTACTGATGT 59.145 41.667 0.00 0.00 0.00 3.06
1869 5010 5.093457 AGTGTATCGTCGTGTTTACTGATG 58.907 41.667 0.00 0.00 0.00 3.07
1870 5011 5.306532 AGTGTATCGTCGTGTTTACTGAT 57.693 39.130 0.00 0.00 0.00 2.90
1871 5012 4.754372 AGTGTATCGTCGTGTTTACTGA 57.246 40.909 0.00 0.00 0.00 3.41
1872 5013 4.678287 ACAAGTGTATCGTCGTGTTTACTG 59.322 41.667 0.00 0.00 0.00 2.74
1873 5014 4.863491 ACAAGTGTATCGTCGTGTTTACT 58.137 39.130 0.00 0.00 0.00 2.24
1874 5015 5.565723 AACAAGTGTATCGTCGTGTTTAC 57.434 39.130 0.00 0.00 33.95 2.01
1875 5016 6.308524 CCATAACAAGTGTATCGTCGTGTTTA 59.691 38.462 1.23 0.00 37.43 2.01
1876 5017 5.119588 CCATAACAAGTGTATCGTCGTGTTT 59.880 40.000 1.23 0.00 37.43 2.83
1877 5018 4.624024 CCATAACAAGTGTATCGTCGTGTT 59.376 41.667 0.00 0.00 38.98 3.32
1878 5019 4.082625 TCCATAACAAGTGTATCGTCGTGT 60.083 41.667 0.00 0.00 0.00 4.49
1879 5020 4.417506 TCCATAACAAGTGTATCGTCGTG 58.582 43.478 0.00 0.00 0.00 4.35
1880 5021 4.707030 TCCATAACAAGTGTATCGTCGT 57.293 40.909 0.00 0.00 0.00 4.34
1881 5022 4.378910 CGATCCATAACAAGTGTATCGTCG 59.621 45.833 5.71 0.00 30.96 5.12
1882 5023 4.680110 CCGATCCATAACAAGTGTATCGTC 59.320 45.833 10.83 0.00 32.62 4.20
1883 5024 4.500887 CCCGATCCATAACAAGTGTATCGT 60.501 45.833 10.83 0.00 32.62 3.73
1884 5025 3.987868 CCCGATCCATAACAAGTGTATCG 59.012 47.826 6.58 6.58 33.65 2.92
1885 5026 4.957296 ACCCGATCCATAACAAGTGTATC 58.043 43.478 0.00 0.00 0.00 2.24
1886 5027 5.367945 AACCCGATCCATAACAAGTGTAT 57.632 39.130 0.00 0.00 0.00 2.29
1887 5028 4.829872 AACCCGATCCATAACAAGTGTA 57.170 40.909 0.00 0.00 0.00 2.90
1888 5029 3.713826 AACCCGATCCATAACAAGTGT 57.286 42.857 0.00 0.00 0.00 3.55
1889 5030 3.427503 GCAAACCCGATCCATAACAAGTG 60.428 47.826 0.00 0.00 0.00 3.16
1890 5031 2.752903 GCAAACCCGATCCATAACAAGT 59.247 45.455 0.00 0.00 0.00 3.16
1891 5032 3.016736 AGCAAACCCGATCCATAACAAG 58.983 45.455 0.00 0.00 0.00 3.16
1892 5033 2.752354 CAGCAAACCCGATCCATAACAA 59.248 45.455 0.00 0.00 0.00 2.83
1893 5034 2.026729 TCAGCAAACCCGATCCATAACA 60.027 45.455 0.00 0.00 0.00 2.41
1894 5035 2.639065 TCAGCAAACCCGATCCATAAC 58.361 47.619 0.00 0.00 0.00 1.89
1895 5036 3.576078 ATCAGCAAACCCGATCCATAA 57.424 42.857 0.00 0.00 0.00 1.90
1896 5037 3.389656 TGTATCAGCAAACCCGATCCATA 59.610 43.478 0.00 0.00 0.00 2.74
1906 5047 9.586150 CTTATATTTCATCGTGTATCAGCAAAC 57.414 33.333 0.00 0.00 0.00 2.93
1912 5053 9.285770 GCGTATCTTATATTTCATCGTGTATCA 57.714 33.333 0.00 0.00 0.00 2.15
1934 5075 4.345859 TTCCTTCCTCTTTCAAAGCGTA 57.654 40.909 0.00 0.00 0.00 4.42
1989 5130 8.379457 AGTTTCGTGCTACTTTTTATCTTCTT 57.621 30.769 0.00 0.00 0.00 2.52
1991 5133 7.793902 TGAGTTTCGTGCTACTTTTTATCTTC 58.206 34.615 0.00 0.00 0.00 2.87
1996 5138 6.183360 TGCTTTGAGTTTCGTGCTACTTTTTA 60.183 34.615 0.00 0.00 0.00 1.52
2079 5221 4.088634 CCCCAAAATCCAGATGAACTTGA 58.911 43.478 0.00 0.00 0.00 3.02
2109 5251 7.744715 CGCTTAATATTTACCCTAATGAAAGCG 59.255 37.037 15.11 15.11 40.51 4.68
2110 5252 8.565416 ACGCTTAATATTTACCCTAATGAAAGC 58.435 33.333 0.00 0.00 31.56 3.51
2134 5276 3.770263 AAATGGCAGATTGACATCACG 57.230 42.857 0.00 0.00 44.20 4.35
2169 5311 6.826668 TCTCATTTTCCAGAACTAGACACAA 58.173 36.000 0.00 0.00 0.00 3.33
2220 5362 1.069596 GCAGCACAAAACTTGGGGG 59.930 57.895 0.00 0.00 33.68 5.40
2234 5376 1.338105 CCCTAAAAGGCCAAAAGCAGC 60.338 52.381 5.01 0.00 46.50 5.25
2251 5393 1.073444 CACTCCTCATGCATATGCCCT 59.927 52.381 24.54 9.55 41.18 5.19
2364 5507 7.020009 TGTCACCCCCTCATATATACATGTTA 58.980 38.462 2.30 0.00 0.00 2.41
2424 5567 2.427245 CCCTCTACCTCTGCGTGGG 61.427 68.421 0.00 0.00 0.00 4.61
2471 5614 5.086104 TGAGGTCTTATTCTAGGCACAAC 57.914 43.478 0.00 0.00 0.00 3.32
2473 5616 3.706594 CCTGAGGTCTTATTCTAGGCACA 59.293 47.826 0.00 0.00 0.00 4.57
2479 5622 6.342819 TCTCTTCCCTGAGGTCTTATTCTA 57.657 41.667 0.00 0.00 34.98 2.10
2492 5635 2.015587 GCAAGCTCATTCTCTTCCCTG 58.984 52.381 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.