Multiple sequence alignment - TraesCS2A01G170400

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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 TraesCS2A01G170400 chr2A 100.000 2468 0 0 1 2468 125606953 125609420 0.000000e+00 4558
1 TraesCS2A01G170400 chr2D 86.593 1984 142 53 523 2468 121360008 121361905 0.000000e+00 2076
2 TraesCS2A01G170400 chr2D 85.341 498 36 16 7 498 121359558 121360024 4.770000e-132 481
3 TraesCS2A01G170400 chr2B 89.537 1166 40 28 523 1659 174780373 174781485 0.000000e+00 1402
4 TraesCS2A01G170400 chr2B 84.876 767 48 28 1712 2468 174786786 174787494 0.000000e+00 712
5 TraesCS2A01G170400 chr2B 87.026 501 33 13 1 498 174779918 174780389 1.000000e-148 536


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 TraesCS2A01G170400 chr2A 125606953 125609420 2467 False 4558.0 4558 100.0000 1 2468 1 chr2A.!!$F1 2467
1 TraesCS2A01G170400 chr2D 121359558 121361905 2347 False 1278.5 2076 85.9670 7 2468 2 chr2D.!!$F1 2461
2 TraesCS2A01G170400 chr2B 174779918 174781485 1567 False 969.0 1402 88.2815 1 1659 2 chr2B.!!$F2 1658
3 TraesCS2A01G170400 chr2B 174786786 174787494 708 False 712.0 712 84.8760 1712 2468 1 chr2B.!!$F1 756

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
914 928 0.237498 CACGAACGGGGCTTTTCTTC 59.763 55.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2405 0.53065 CAGTGACAGACGTGGTTGCT 60.531 55.0 0.0 0.0 0.0 3.91 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
134 135 1.228429 GCAGGGGCCAGTTGTAACA 60.228 57.895 4.39 0.00 0.00 2.41
209 217 1.639298 CTTCAGCAAGCGCCCTACAC 61.639 60.000 2.29 0.00 39.83 2.90
225 233 0.865769 ACACGTTCCACGAGAATTGC 59.134 50.000 2.75 0.00 46.05 3.56
227 235 2.288579 ACACGTTCCACGAGAATTGCTA 60.289 45.455 2.75 0.00 46.05 3.49
228 236 2.734606 CACGTTCCACGAGAATTGCTAA 59.265 45.455 2.75 0.00 46.05 3.09
229 237 2.993899 ACGTTCCACGAGAATTGCTAAG 59.006 45.455 2.75 0.00 46.05 2.18
249 257 1.811679 GTCTGCCTCGCCAAGTAGC 60.812 63.158 0.00 0.00 0.00 3.58
384 392 6.037098 AGAATCTATCTACACACAAACTCGC 58.963 40.000 0.00 0.00 36.32 5.03
385 393 4.106029 TCTATCTACACACAAACTCGCC 57.894 45.455 0.00 0.00 0.00 5.54
386 394 3.762288 TCTATCTACACACAAACTCGCCT 59.238 43.478 0.00 0.00 0.00 5.52
387 395 4.945543 TCTATCTACACACAAACTCGCCTA 59.054 41.667 0.00 0.00 0.00 3.93
388 396 3.570926 TCTACACACAAACTCGCCTAG 57.429 47.619 0.00 0.00 0.00 3.02
445 453 0.795698 TCATCAAACACGACGCCATG 59.204 50.000 0.00 0.00 0.00 3.66
471 480 4.761975 TCGTACCAGTTTATTCACCATCC 58.238 43.478 0.00 0.00 0.00 3.51
472 481 4.223255 TCGTACCAGTTTATTCACCATCCA 59.777 41.667 0.00 0.00 0.00 3.41
473 482 4.331717 CGTACCAGTTTATTCACCATCCAC 59.668 45.833 0.00 0.00 0.00 4.02
474 483 3.343617 ACCAGTTTATTCACCATCCACG 58.656 45.455 0.00 0.00 0.00 4.94
475 484 3.244770 ACCAGTTTATTCACCATCCACGT 60.245 43.478 0.00 0.00 0.00 4.49
498 510 1.370657 CGAGATAACGAGGCGCTCC 60.371 63.158 7.64 0.00 35.09 4.70
500 512 2.029221 GATAACGAGGCGCTCCCC 59.971 66.667 7.64 0.00 0.00 4.81
501 513 3.843117 GATAACGAGGCGCTCCCCG 62.843 68.421 7.64 8.51 40.75 5.73
531 543 7.931578 AAAAAGAGAGAGAGAGAGATAACGA 57.068 36.000 0.00 0.00 0.00 3.85
532 544 7.553881 AAAAGAGAGAGAGAGAGATAACGAG 57.446 40.000 0.00 0.00 0.00 4.18
533 545 5.215252 AGAGAGAGAGAGAGATAACGAGG 57.785 47.826 0.00 0.00 0.00 4.63
534 546 3.740115 AGAGAGAGAGAGATAACGAGGC 58.260 50.000 0.00 0.00 0.00 4.70
535 547 2.478894 GAGAGAGAGAGATAACGAGGCG 59.521 54.545 0.00 0.00 0.00 5.52
536 548 0.948678 AGAGAGAGATAACGAGGCGC 59.051 55.000 0.00 0.00 0.00 6.53
537 549 0.948678 GAGAGAGATAACGAGGCGCT 59.051 55.000 7.64 0.00 0.00 5.92
538 550 0.948678 AGAGAGATAACGAGGCGCTC 59.051 55.000 7.64 1.63 0.00 5.03
539 551 0.663688 GAGAGATAACGAGGCGCTCA 59.336 55.000 7.64 0.00 0.00 4.26
540 552 0.382515 AGAGATAACGAGGCGCTCAC 59.617 55.000 7.64 0.00 0.00 3.51
541 553 0.382515 GAGATAACGAGGCGCTCACT 59.617 55.000 7.64 0.00 0.00 3.41
639 652 4.729918 GGGACAGCACAGGCAGGG 62.730 72.222 0.00 0.00 44.61 4.45
680 693 2.260869 CCCAGACCACAAGCAACGG 61.261 63.158 0.00 0.00 0.00 4.44
899 913 4.617486 ACGCGCTCACGAACACGA 62.617 61.111 5.73 0.00 43.93 4.35
900 914 3.391631 CGCGCTCACGAACACGAA 61.392 61.111 5.56 0.00 43.93 3.85
901 915 2.167918 GCGCTCACGAACACGAAC 59.832 61.111 0.00 0.00 43.93 3.95
902 916 2.459904 CGCTCACGAACACGAACG 59.540 61.111 0.00 0.00 43.93 3.95
914 928 0.237498 CACGAACGGGGCTTTTCTTC 59.763 55.000 0.00 0.00 0.00 2.87
944 970 2.584261 ATCGTCGGAGCAGCAGCAAT 62.584 55.000 3.17 0.00 45.49 3.56
953 979 4.704833 AGCAGCAATCACCGGCGT 62.705 61.111 6.01 0.00 34.54 5.68
954 980 3.737172 GCAGCAATCACCGGCGTT 61.737 61.111 6.01 0.00 34.54 4.84
1038 1084 3.522731 CGCGAGGAGGTGGAGGAG 61.523 72.222 0.00 0.00 0.00 3.69
1489 1547 2.626780 GCGTCCAAGAGGCCCAAAC 61.627 63.158 0.00 0.00 37.46 2.93
1514 1572 1.621317 GCCTCCCCGGAAAATCAAAAA 59.379 47.619 0.73 0.00 33.16 1.94
1543 1601 7.176589 ACCTGATGGTAGTCTCTTCTTTTAG 57.823 40.000 0.00 0.00 46.43 1.85
1544 1602 6.726764 ACCTGATGGTAGTCTCTTCTTTTAGT 59.273 38.462 0.00 0.00 46.43 2.24
1545 1603 7.235812 ACCTGATGGTAGTCTCTTCTTTTAGTT 59.764 37.037 0.00 0.00 46.43 2.24
1595 1659 6.376299 CCTCTGTAAATATGCATGCCATGTAT 59.624 38.462 16.68 12.91 39.05 2.29
1596 1660 7.094075 CCTCTGTAAATATGCATGCCATGTATT 60.094 37.037 16.68 11.32 36.90 1.89
1597 1661 7.595604 TCTGTAAATATGCATGCCATGTATTG 58.404 34.615 16.68 5.59 36.90 1.90
1601 1665 5.847111 ATATGCATGCCATGTATTGATCC 57.153 39.130 16.68 0.00 36.90 3.36
1659 1723 7.174946 AGGAATAAAACCAATGTGTACAGAGTG 59.825 37.037 13.03 13.03 0.00 3.51
1660 1724 7.174253 GGAATAAAACCAATGTGTACAGAGTGA 59.826 37.037 20.60 1.89 0.00 3.41
1670 1734 8.648097 CAATGTGTACAGAGTGAATACAGTAAC 58.352 37.037 14.65 0.00 29.67 2.50
1673 1737 8.198778 TGTGTACAGAGTGAATACAGTAACAAA 58.801 33.333 0.00 0.00 29.67 2.83
1697 1766 7.552050 AAAATATGACCAAATGGAAGTGGAA 57.448 32.000 6.42 0.00 38.36 3.53
1724 1793 9.071276 GTAATTCCATGTGTTTATCATCATCCT 57.929 33.333 0.00 0.00 0.00 3.24
1743 1812 9.661954 ATCATCCTAGTGGTTTCTATTTCTCTA 57.338 33.333 0.00 0.00 34.23 2.43
1744 1813 8.915036 TCATCCTAGTGGTTTCTATTTCTCTAC 58.085 37.037 0.00 0.00 34.23 2.59
1776 1845 2.163815 GCTTCTGCTCAAGTTCATGCAT 59.836 45.455 0.00 0.00 34.79 3.96
1779 1848 2.417586 TCTGCTCAAGTTCATGCATTCG 59.582 45.455 0.00 0.00 34.79 3.34
1783 1852 1.739466 TCAAGTTCATGCATTCGCCTC 59.261 47.619 0.00 0.00 37.32 4.70
1801 1870 3.188254 GCCTCTTCTTCAAACAGCTTCTC 59.812 47.826 0.00 0.00 0.00 2.87
1802 1871 4.640364 CCTCTTCTTCAAACAGCTTCTCT 58.360 43.478 0.00 0.00 0.00 3.10
1804 1873 6.405538 CCTCTTCTTCAAACAGCTTCTCTAT 58.594 40.000 0.00 0.00 0.00 1.98
1805 1874 7.551585 CCTCTTCTTCAAACAGCTTCTCTATA 58.448 38.462 0.00 0.00 0.00 1.31
1806 1875 7.706179 CCTCTTCTTCAAACAGCTTCTCTATAG 59.294 40.741 0.00 0.00 0.00 1.31
1811 1880 6.286240 TCAAACAGCTTCTCTATAGCAGAA 57.714 37.500 11.64 11.64 41.11 3.02
1821 1890 6.541934 TCTCTATAGCAGAAGCATATGCAT 57.458 37.500 28.62 18.24 45.01 3.96
1822 1891 7.651027 TCTCTATAGCAGAAGCATATGCATA 57.349 36.000 28.62 9.27 45.01 3.14
1823 1892 8.247666 TCTCTATAGCAGAAGCATATGCATAT 57.752 34.615 28.62 13.63 45.01 1.78
1824 1893 8.702819 TCTCTATAGCAGAAGCATATGCATATT 58.297 33.333 28.62 14.91 45.01 1.28
1825 1894 8.658499 TCTATAGCAGAAGCATATGCATATTG 57.342 34.615 28.62 20.02 45.01 1.90
1826 1895 4.436242 AGCAGAAGCATATGCATATTGC 57.564 40.909 28.62 26.90 45.01 3.56
1972 2045 2.913590 CGGTGATGATCAGATCGATTCG 59.086 50.000 0.00 0.00 33.17 3.34
1999 2083 7.666063 TTCGATATGGATGAGGATACATCAT 57.334 36.000 0.00 0.00 45.68 2.45
2004 2088 9.676861 GATATGGATGAGGATACATCATTTTCA 57.323 33.333 0.00 0.00 45.68 2.69
2015 2105 9.903682 GGATACATCATTTTCATGGATAAACTG 57.096 33.333 0.00 0.00 0.00 3.16
2019 2109 9.028284 ACATCATTTTCATGGATAAACTGAAGT 57.972 29.630 0.00 0.00 31.79 3.01
2020 2110 9.297586 CATCATTTTCATGGATAAACTGAAGTG 57.702 33.333 0.00 0.00 31.79 3.16
2021 2111 7.315142 TCATTTTCATGGATAAACTGAAGTGC 58.685 34.615 0.00 0.00 31.11 4.40
2022 2112 6.647334 TTTTCATGGATAAACTGAAGTGCA 57.353 33.333 0.00 0.00 31.11 4.57
2023 2113 6.647334 TTTCATGGATAAACTGAAGTGCAA 57.353 33.333 0.00 0.00 31.11 4.08
2024 2114 6.839124 TTCATGGATAAACTGAAGTGCAAT 57.161 33.333 0.00 0.00 0.00 3.56
2025 2115 7.936496 TTCATGGATAAACTGAAGTGCAATA 57.064 32.000 0.00 0.00 0.00 1.90
2026 2116 7.320443 TCATGGATAAACTGAAGTGCAATAC 57.680 36.000 0.00 0.00 0.00 1.89
2027 2117 6.318648 TCATGGATAAACTGAAGTGCAATACC 59.681 38.462 0.00 0.00 0.00 2.73
2028 2118 5.565509 TGGATAAACTGAAGTGCAATACCA 58.434 37.500 0.00 0.00 0.00 3.25
2171 2266 1.436600 GCCTGCTCCATGATACGATG 58.563 55.000 0.00 0.00 0.00 3.84
2205 2300 1.167851 TTCAAAGCCTCGCAATCAGG 58.832 50.000 0.00 0.00 0.00 3.86
2214 2309 0.108472 TCGCAATCAGGCAGACAGAG 60.108 55.000 0.00 0.00 0.00 3.35
2217 2312 2.275318 GCAATCAGGCAGACAGAGTAC 58.725 52.381 0.00 0.00 0.00 2.73
2218 2313 2.534298 CAATCAGGCAGACAGAGTACG 58.466 52.381 0.00 0.00 0.00 3.67
2219 2314 1.840737 ATCAGGCAGACAGAGTACGT 58.159 50.000 0.00 0.00 0.00 3.57
2220 2315 2.484742 TCAGGCAGACAGAGTACGTA 57.515 50.000 0.00 0.00 0.00 3.57
2221 2316 2.082231 TCAGGCAGACAGAGTACGTAC 58.918 52.381 18.10 18.10 0.00 3.67
2263 2358 1.588932 TGCCATCTCGATCGTTCGC 60.589 57.895 15.94 11.06 45.10 4.70
2324 2420 0.532862 CCAGAAGCAACCACGTCTGT 60.533 55.000 6.70 0.00 42.44 3.41
2325 2421 0.861837 CAGAAGCAACCACGTCTGTC 59.138 55.000 0.00 0.00 40.12 3.51
2399 2495 4.327357 CGCGAGACCAGCCATATAATTAAG 59.673 45.833 0.00 0.00 0.00 1.85
2401 2497 5.178797 CGAGACCAGCCATATAATTAAGGG 58.821 45.833 0.00 0.00 0.00 3.95
2421 2522 2.531206 GAAGTGCGGACAGACAGATAC 58.469 52.381 10.52 0.00 0.00 2.24
2434 2535 1.825474 ACAGATACCGTCTTCACCCAG 59.175 52.381 0.00 0.00 34.00 4.45
2436 2537 1.825474 AGATACCGTCTTCACCCAGTG 59.175 52.381 0.00 0.00 31.47 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.654220 GTTCACATTGGCAGTGCGT 59.346 52.632 10.18 0.00 36.93 5.24
42 43 1.440850 CGTTCACATTGGCAGTGCG 60.441 57.895 10.18 0.15 36.93 5.34
44 45 0.110688 CGTCGTTCACATTGGCAGTG 60.111 55.000 8.60 8.60 38.32 3.66
45 46 0.249699 TCGTCGTTCACATTGGCAGT 60.250 50.000 0.00 0.00 0.00 4.40
46 47 0.163788 GTCGTCGTTCACATTGGCAG 59.836 55.000 0.00 0.00 0.00 4.85
47 48 1.553195 CGTCGTCGTTCACATTGGCA 61.553 55.000 0.00 0.00 0.00 4.92
48 49 1.129809 CGTCGTCGTTCACATTGGC 59.870 57.895 0.00 0.00 0.00 4.52
49 50 0.433492 GTCGTCGTCGTTCACATTGG 59.567 55.000 1.33 0.00 38.33 3.16
50 51 0.089022 CGTCGTCGTCGTTCACATTG 59.911 55.000 3.67 0.00 38.33 2.82
51 52 2.417005 CGTCGTCGTCGTTCACATT 58.583 52.632 3.67 0.00 38.33 2.71
52 53 4.126164 CGTCGTCGTCGTTCACAT 57.874 55.556 3.67 0.00 38.33 3.21
134 135 1.740025 GCTTCGCCTTGTCTATTGCTT 59.260 47.619 0.00 0.00 0.00 3.91
166 167 2.062070 AGCCAAGAGAAACGAGGCT 58.938 52.632 0.00 0.00 44.35 4.58
246 254 1.750399 GTACCTGTCCGGGTCGCTA 60.750 63.158 0.00 0.00 40.48 4.26
249 257 4.487412 GCGTACCTGTCCGGGTCG 62.487 72.222 0.00 6.88 40.48 4.79
252 260 4.789075 CACGCGTACCTGTCCGGG 62.789 72.222 13.44 0.00 42.02 5.73
374 382 2.941453 TCTAGCTAGGCGAGTTTGTG 57.059 50.000 20.58 0.00 33.20 3.33
377 385 3.586892 GTGTTTCTAGCTAGGCGAGTTT 58.413 45.455 20.58 0.00 33.20 2.66
381 389 1.203994 GTGGTGTTTCTAGCTAGGCGA 59.796 52.381 20.58 4.74 0.00 5.54
382 390 1.067142 TGTGGTGTTTCTAGCTAGGCG 60.067 52.381 20.58 0.00 0.00 5.52
383 391 2.347731 GTGTGGTGTTTCTAGCTAGGC 58.652 52.381 20.58 11.52 0.00 3.93
384 392 2.301870 TGGTGTGGTGTTTCTAGCTAGG 59.698 50.000 20.58 2.51 0.00 3.02
385 393 3.244078 TGTGGTGTGGTGTTTCTAGCTAG 60.244 47.826 15.01 15.01 0.00 3.42
386 394 2.701423 TGTGGTGTGGTGTTTCTAGCTA 59.299 45.455 0.00 0.00 0.00 3.32
387 395 1.488812 TGTGGTGTGGTGTTTCTAGCT 59.511 47.619 0.00 0.00 0.00 3.32
388 396 1.602377 GTGTGGTGTGGTGTTTCTAGC 59.398 52.381 0.00 0.00 0.00 3.42
427 435 0.179192 CCATGGCGTCGTGTTTGATG 60.179 55.000 8.67 0.00 0.00 3.07
474 483 1.557651 GCCTCGTTATCTCGTGGAAC 58.442 55.000 10.57 0.00 44.05 3.62
475 484 0.099968 CGCCTCGTTATCTCGTGGAA 59.900 55.000 10.57 0.00 44.05 3.53
507 519 7.067008 CCTCGTTATCTCTCTCTCTCTCTTTTT 59.933 40.741 0.00 0.00 0.00 1.94
508 520 6.542370 CCTCGTTATCTCTCTCTCTCTCTTTT 59.458 42.308 0.00 0.00 0.00 2.27
509 521 6.055588 CCTCGTTATCTCTCTCTCTCTCTTT 58.944 44.000 0.00 0.00 0.00 2.52
510 522 5.611374 CCTCGTTATCTCTCTCTCTCTCTT 58.389 45.833 0.00 0.00 0.00 2.85
511 523 4.503296 GCCTCGTTATCTCTCTCTCTCTCT 60.503 50.000 0.00 0.00 0.00 3.10
512 524 3.746492 GCCTCGTTATCTCTCTCTCTCTC 59.254 52.174 0.00 0.00 0.00 3.20
513 525 3.740115 GCCTCGTTATCTCTCTCTCTCT 58.260 50.000 0.00 0.00 0.00 3.10
514 526 2.478894 CGCCTCGTTATCTCTCTCTCTC 59.521 54.545 0.00 0.00 0.00 3.20
515 527 2.489971 CGCCTCGTTATCTCTCTCTCT 58.510 52.381 0.00 0.00 0.00 3.10
516 528 1.069500 GCGCCTCGTTATCTCTCTCTC 60.069 57.143 0.00 0.00 0.00 3.20
517 529 0.948678 GCGCCTCGTTATCTCTCTCT 59.051 55.000 0.00 0.00 0.00 3.10
518 530 0.948678 AGCGCCTCGTTATCTCTCTC 59.051 55.000 2.29 0.00 0.00 3.20
519 531 0.948678 GAGCGCCTCGTTATCTCTCT 59.051 55.000 2.29 0.00 0.00 3.10
520 532 0.663688 TGAGCGCCTCGTTATCTCTC 59.336 55.000 2.29 0.00 32.35 3.20
521 533 0.382515 GTGAGCGCCTCGTTATCTCT 59.617 55.000 2.29 0.00 32.35 3.10
522 534 0.382515 AGTGAGCGCCTCGTTATCTC 59.617 55.000 2.29 0.00 32.35 2.75
523 535 0.818296 AAGTGAGCGCCTCGTTATCT 59.182 50.000 2.29 0.00 32.35 1.98
524 536 0.924090 CAAGTGAGCGCCTCGTTATC 59.076 55.000 2.29 0.00 32.35 1.75
525 537 0.530744 TCAAGTGAGCGCCTCGTTAT 59.469 50.000 2.29 0.00 32.35 1.89
526 538 0.530744 ATCAAGTGAGCGCCTCGTTA 59.469 50.000 2.29 0.00 32.35 3.18
527 539 1.016130 CATCAAGTGAGCGCCTCGTT 61.016 55.000 2.29 0.00 32.35 3.85
528 540 1.446792 CATCAAGTGAGCGCCTCGT 60.447 57.895 2.29 0.00 32.35 4.18
529 541 1.446792 ACATCAAGTGAGCGCCTCG 60.447 57.895 2.29 0.00 32.35 4.63
530 542 4.606071 ACATCAAGTGAGCGCCTC 57.394 55.556 2.29 1.22 0.00 4.70
597 609 1.061131 CTGCGACTGATTAACTTGCCG 59.939 52.381 0.00 0.00 0.00 5.69
666 679 4.025401 CCGCCGTTGCTTGTGGTC 62.025 66.667 0.00 0.00 34.43 4.02
784 798 0.179018 ACTGAATTATGAGGCCGGGC 60.179 55.000 22.67 22.67 0.00 6.13
785 799 1.873903 CGACTGAATTATGAGGCCGGG 60.874 57.143 2.18 0.00 0.00 5.73
786 800 1.502231 CGACTGAATTATGAGGCCGG 58.498 55.000 0.00 0.00 0.00 6.13
818 832 4.415150 AGATGCTGGCGTGTGGGG 62.415 66.667 0.00 0.00 0.00 4.96
893 907 0.464916 AGAAAAGCCCCGTTCGTGTT 60.465 50.000 0.00 0.00 0.00 3.32
899 913 0.771755 AGAGGAAGAAAAGCCCCGTT 59.228 50.000 0.00 0.00 0.00 4.44
900 914 0.325272 GAGAGGAAGAAAAGCCCCGT 59.675 55.000 0.00 0.00 0.00 5.28
901 915 0.615850 AGAGAGGAAGAAAAGCCCCG 59.384 55.000 0.00 0.00 0.00 5.73
902 916 1.340502 CCAGAGAGGAAGAAAAGCCCC 60.341 57.143 0.00 0.00 41.22 5.80
914 928 0.748367 TCCGACGATGACCAGAGAGG 60.748 60.000 0.00 0.00 45.67 3.69
944 970 2.342279 CCTTCTCAACGCCGGTGA 59.658 61.111 24.59 4.13 0.00 4.02
1030 1076 1.075600 CCTCCTCCTCCTCCTCCAC 60.076 68.421 0.00 0.00 0.00 4.02
1031 1077 1.230650 TCCTCCTCCTCCTCCTCCA 60.231 63.158 0.00 0.00 0.00 3.86
1032 1078 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1033 1079 1.293683 ACCTCCTCCTCCTCCTCCTC 61.294 65.000 0.00 0.00 0.00 3.71
1034 1080 1.230819 ACCTCCTCCTCCTCCTCCT 60.231 63.158 0.00 0.00 0.00 3.69
1035 1081 1.075600 CACCTCCTCCTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
1036 1082 1.075600 CCACCTCCTCCTCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
1037 1083 3.114390 CCACCTCCTCCTCCTCCT 58.886 66.667 0.00 0.00 0.00 3.69
1038 1084 2.766229 GCCACCTCCTCCTCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
1158 1210 2.187946 CACATCTCCTCGGCCACC 59.812 66.667 2.24 0.00 0.00 4.61
1469 1527 2.748058 TTTGGGCCTCTTGGACGCTC 62.748 60.000 4.53 0.00 44.25 5.03
1484 1542 4.426313 GGGGAGGCCTCGGTTTGG 62.426 72.222 26.36 0.00 0.00 3.28
1568 1628 4.136796 TGGCATGCATATTTACAGAGGAC 58.863 43.478 21.36 0.00 0.00 3.85
1569 1633 4.436113 TGGCATGCATATTTACAGAGGA 57.564 40.909 21.36 0.00 0.00 3.71
1595 1659 4.028131 TCCTAAGCTAGAAACGGGATCAA 58.972 43.478 0.00 0.00 0.00 2.57
1596 1660 3.638860 TCCTAAGCTAGAAACGGGATCA 58.361 45.455 0.00 0.00 0.00 2.92
1597 1661 4.281182 TCATCCTAAGCTAGAAACGGGATC 59.719 45.833 0.00 0.00 30.77 3.36
1601 1665 3.743396 GCATCATCCTAAGCTAGAAACGG 59.257 47.826 0.00 0.00 0.00 4.44
1673 1737 7.235399 ACTTCCACTTCCATTTGGTCATATTTT 59.765 33.333 0.00 0.00 34.19 1.82
1676 1740 5.831103 ACTTCCACTTCCATTTGGTCATAT 58.169 37.500 0.00 0.00 34.19 1.78
1677 1741 5.255397 ACTTCCACTTCCATTTGGTCATA 57.745 39.130 0.00 0.00 34.19 2.15
1679 1743 3.593442 ACTTCCACTTCCATTTGGTCA 57.407 42.857 0.00 0.00 34.19 4.02
1680 1744 6.590234 AATTACTTCCACTTCCATTTGGTC 57.410 37.500 0.00 0.00 34.19 4.02
1697 1766 9.071276 GGATGATGATAAACACATGGAATTACT 57.929 33.333 0.00 0.00 0.00 2.24
1724 1793 6.810182 GCAACGTAGAGAAATAGAAACCACTA 59.190 38.462 0.00 0.00 0.00 2.74
1776 1845 1.873591 GCTGTTTGAAGAAGAGGCGAA 59.126 47.619 0.00 0.00 0.00 4.70
1779 1848 3.145286 AGAAGCTGTTTGAAGAAGAGGC 58.855 45.455 0.00 0.00 0.00 4.70
1783 1852 6.815641 TGCTATAGAGAAGCTGTTTGAAGAAG 59.184 38.462 3.21 0.00 40.73 2.85
1801 1870 7.353497 GCAATATGCATATGCTTCTGCTATAG 58.647 38.462 27.13 8.84 44.26 1.31
1802 1871 7.255491 GCAATATGCATATGCTTCTGCTATA 57.745 36.000 27.13 15.07 44.26 1.31
1804 1873 5.556355 GCAATATGCATATGCTTCTGCTA 57.444 39.130 27.13 6.67 44.26 3.49
1805 1874 4.436242 GCAATATGCATATGCTTCTGCT 57.564 40.909 27.13 8.55 44.26 4.24
1826 1895 5.163764 TGCTACGAAAAAGTGCATTCCTATG 60.164 40.000 0.00 0.00 34.76 2.23
1827 1896 4.941263 TGCTACGAAAAAGTGCATTCCTAT 59.059 37.500 0.00 0.00 0.00 2.57
1828 1897 4.320023 TGCTACGAAAAAGTGCATTCCTA 58.680 39.130 0.00 0.00 0.00 2.94
1829 1898 3.146066 TGCTACGAAAAAGTGCATTCCT 58.854 40.909 0.00 0.00 0.00 3.36
1830 1899 3.552604 TGCTACGAAAAAGTGCATTCC 57.447 42.857 0.00 0.00 0.00 3.01
1878 1948 4.694982 TCTCATCGAGATCAGATGCTCTAC 59.305 45.833 20.03 0.00 43.68 2.59
1879 1949 4.904241 TCTCATCGAGATCAGATGCTCTA 58.096 43.478 20.03 7.72 43.68 2.43
1881 1951 4.022935 ACTTCTCATCGAGATCAGATGCTC 60.023 45.833 20.03 0.00 43.68 4.26
1895 1965 3.188667 GGTTCGGTTTCCAACTTCTCATC 59.811 47.826 0.00 0.00 0.00 2.92
1897 1967 2.092861 TGGTTCGGTTTCCAACTTCTCA 60.093 45.455 0.00 0.00 0.00 3.27
1972 2045 6.471233 TGTATCCTCATCCATATCGAATCC 57.529 41.667 0.00 0.00 0.00 3.01
1980 2053 9.457436 CATGAAAATGATGTATCCTCATCCATA 57.543 33.333 4.59 0.00 42.24 2.74
1999 2083 6.647334 TGCACTTCAGTTTATCCATGAAAA 57.353 33.333 0.00 0.00 32.87 2.29
2004 2088 6.095440 GTGGTATTGCACTTCAGTTTATCCAT 59.905 38.462 0.00 0.00 0.00 3.41
2005 2089 5.414454 GTGGTATTGCACTTCAGTTTATCCA 59.586 40.000 0.00 0.00 0.00 3.41
2016 2106 4.887071 TGAACAAGAAGTGGTATTGCACTT 59.113 37.500 0.00 0.00 43.47 3.16
2017 2107 4.460263 TGAACAAGAAGTGGTATTGCACT 58.540 39.130 0.00 0.00 0.00 4.40
2018 2108 4.829064 TGAACAAGAAGTGGTATTGCAC 57.171 40.909 0.00 0.00 0.00 4.57
2019 2109 5.048782 GTCATGAACAAGAAGTGGTATTGCA 60.049 40.000 0.00 0.00 0.00 4.08
2020 2110 5.048782 TGTCATGAACAAGAAGTGGTATTGC 60.049 40.000 0.00 0.00 34.03 3.56
2021 2111 6.427853 TCTGTCATGAACAAGAAGTGGTATTG 59.572 38.462 0.00 0.00 37.45 1.90
2022 2112 6.533730 TCTGTCATGAACAAGAAGTGGTATT 58.466 36.000 0.00 0.00 37.45 1.89
2023 2113 6.114187 TCTGTCATGAACAAGAAGTGGTAT 57.886 37.500 0.00 0.00 37.45 2.73
2024 2114 5.545063 TCTGTCATGAACAAGAAGTGGTA 57.455 39.130 0.00 0.00 37.45 3.25
2025 2115 4.422073 TCTGTCATGAACAAGAAGTGGT 57.578 40.909 0.00 0.00 37.45 4.16
2026 2116 5.756195 TTTCTGTCATGAACAAGAAGTGG 57.244 39.130 13.47 0.00 37.45 4.00
2027 2117 9.734620 TTTTATTTCTGTCATGAACAAGAAGTG 57.265 29.630 16.16 0.74 37.45 3.16
2028 2118 9.956720 CTTTTATTTCTGTCATGAACAAGAAGT 57.043 29.630 13.47 13.34 37.45 3.01
2059 2149 2.894387 GGCTGCTTCCTGCGCTAG 60.894 66.667 9.73 4.25 46.63 3.42
2125 2218 1.534028 GTGAACAATGCGCCGTAATG 58.466 50.000 4.18 0.00 0.00 1.90
2131 2224 2.126888 CCACGTGAACAATGCGCC 60.127 61.111 19.30 0.00 0.00 6.53
2171 2266 3.521796 GAAATGCAGGGCCGAGGC 61.522 66.667 5.37 5.37 41.06 4.70
2205 2300 2.082231 TCTGGTACGTACTCTGTCTGC 58.918 52.381 24.07 6.54 0.00 4.26
2208 2303 2.352342 GCTCTCTGGTACGTACTCTGTC 59.648 54.545 24.07 8.64 0.00 3.51
2234 2329 0.531532 GAGATGGCACTGGACGGATG 60.532 60.000 0.00 0.00 0.00 3.51
2263 2358 1.376037 GGTTCGCTGTTGAGGGGAG 60.376 63.158 0.00 0.00 32.93 4.30
2310 2405 0.530650 CAGTGACAGACGTGGTTGCT 60.531 55.000 0.00 0.00 0.00 3.91
2324 2420 1.185618 ACGGCAGGCTCTAACAGTGA 61.186 55.000 0.00 0.00 0.00 3.41
2325 2421 0.530744 TACGGCAGGCTCTAACAGTG 59.469 55.000 0.00 0.00 0.00 3.66
2383 2479 5.183904 GCACTTCCCTTAATTATATGGCTGG 59.816 44.000 0.00 0.00 0.00 4.85
2399 2495 1.374758 CTGTCTGTCCGCACTTCCC 60.375 63.158 0.00 0.00 0.00 3.97
2401 2497 2.531206 GTATCTGTCTGTCCGCACTTC 58.469 52.381 0.00 0.00 0.00 3.01
2421 2522 2.358737 GCCACTGGGTGAAGACGG 60.359 66.667 0.00 0.00 35.23 4.79


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

AutoCloner maintained by Alex Coulton.