Multiple sequence alignment - TraesCS5D01G315200

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 TraesCS5D01G315200 chr5D 100.000 2549 0 0 1 2549 409453528 409456076 0.000000e+00 4708.0
1 TraesCS5D01G315200 chr5D 83.162 778 95 27 845 1607 409575445 409576201 0.000000e+00 678.0
2 TraesCS5D01G315200 chr5D 82.353 799 95 32 827 1612 409523104 409523869 0.000000e+00 652.0
3 TraesCS5D01G315200 chr5D 84.000 675 72 18 1057 1703 409542360 409543026 1.300000e-172 616.0
4 TraesCS5D01G315200 chr5A 86.222 1800 180 40 553 2329 520680327 520682081 0.000000e+00 1888.0
5 TraesCS5D01G315200 chr5A 82.683 820 83 27 965 1750 520705875 520706669 0.000000e+00 673.0
6 TraesCS5D01G315200 chr5A 88.441 571 46 17 1 560 520678719 520679280 0.000000e+00 671.0
7 TraesCS5D01G315200 chr5A 82.013 795 104 25 827 1606 520729367 520730137 7.690000e-180 640.0
8 TraesCS5D01G315200 chr5A 81.496 789 101 28 839 1612 520697320 520698078 7.800000e-170 606.0
9 TraesCS5D01G315200 chr5A 88.152 211 23 1 2335 2545 520682127 520682335 1.510000e-62 250.0
10 TraesCS5D01G315200 chr5B 89.430 1334 86 32 561 1854 491245500 491246818 0.000000e+00 1631.0
11 TraesCS5D01G315200 chr5B 85.648 648 70 14 969 1612 491272681 491273309 0.000000e+00 660.0
12 TraesCS5D01G315200 chr5B 82.301 791 98 28 840 1612 491370035 491370801 0.000000e+00 647.0
13 TraesCS5D01G315200 chr5B 90.777 206 13 5 376 577 491244416 491244619 1.160000e-68 270.0
14 TraesCS5D01G315200 chr5B 86.283 226 18 8 154 369 491243544 491243766 1.520000e-57 233.0
15 TraesCS5D01G315200 chr5B 89.441 161 17 0 1 161 491243289 491243449 1.200000e-48 204.0
16 TraesCS5D01G315200 chr5B 78.161 87 19 0 1927 2013 491246869 491246955 3.540000e-04 56.5
17 TraesCS5D01G315200 chr4A 76.503 183 39 4 1927 2107 617939083 617938903 2.090000e-16 97.1
18 TraesCS5D01G315200 chr7A 75.862 203 39 10 1939 2137 12071447 12071643 7.510000e-16 95.3


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 TraesCS5D01G315200 chr5D 409453528 409456076 2548 False 4708.000000 4708 100.0000 1 2549 1 chr5D.!!$F1 2548
1 TraesCS5D01G315200 chr5D 409575445 409576201 756 False 678.000000 678 83.1620 845 1607 1 chr5D.!!$F4 762
2 TraesCS5D01G315200 chr5D 409523104 409523869 765 False 652.000000 652 82.3530 827 1612 1 chr5D.!!$F2 785
3 TraesCS5D01G315200 chr5D 409542360 409543026 666 False 616.000000 616 84.0000 1057 1703 1 chr5D.!!$F3 646
4 TraesCS5D01G315200 chr5A 520678719 520682335 3616 False 936.333333 1888 87.6050 1 2545 3 chr5A.!!$F4 2544
5 TraesCS5D01G315200 chr5A 520705875 520706669 794 False 673.000000 673 82.6830 965 1750 1 chr5A.!!$F2 785
6 TraesCS5D01G315200 chr5A 520729367 520730137 770 False 640.000000 640 82.0130 827 1606 1 chr5A.!!$F3 779
7 TraesCS5D01G315200 chr5A 520697320 520698078 758 False 606.000000 606 81.4960 839 1612 1 chr5A.!!$F1 773
8 TraesCS5D01G315200 chr5B 491272681 491273309 628 False 660.000000 660 85.6480 969 1612 1 chr5B.!!$F1 643
9 TraesCS5D01G315200 chr5B 491370035 491370801 766 False 647.000000 647 82.3010 840 1612 1 chr5B.!!$F2 772
10 TraesCS5D01G315200 chr5B 491243289 491246955 3666 False 478.900000 1631 86.8184 1 2013 5 chr5B.!!$F3 2012

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
748 3466 0.03254 CACTTTGCCCAAACTCAGCC 59.967 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 5385 0.032403 CGTTTGTCGGGTGGTAGTCA 59.968 55.0 0.0 0.0 35.71 3.41 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 5.694910 AGTACACACCATACAAAACGAGAAG 59.305 40.000 0.00 0.00 0.00 2.85
44 45 5.587043 ACACACCATACAAAACGAGAAGAAA 59.413 36.000 0.00 0.00 0.00 2.52
51 52 8.726988 CCATACAAAACGAGAAGAAAGGAAATA 58.273 33.333 0.00 0.00 0.00 1.40
102 103 7.158021 TCATTTGGACAAAGACAACAAGTTTT 58.842 30.769 3.71 0.00 33.32 2.43
110 111 7.489160 ACAAAGACAACAAGTTTTATTCCCTC 58.511 34.615 0.00 0.00 0.00 4.30
121 122 7.639113 AGTTTTATTCCCTCGCAAATTATCA 57.361 32.000 0.00 0.00 0.00 2.15
132 133 3.468770 GCAAATTATCATGCATGGCCAA 58.531 40.909 25.97 16.82 42.12 4.52
134 135 4.024387 GCAAATTATCATGCATGGCCAAAG 60.024 41.667 25.97 6.90 42.12 2.77
152 153 0.822121 AGTCCCTTCAAAACGTGGCC 60.822 55.000 0.00 0.00 0.00 5.36
169 272 3.389983 GTGGCCTCTGGTACATATTACCA 59.610 47.826 3.32 13.03 44.62 3.25
188 291 5.913137 ACCACTCTTTGTTGTTTGAATGA 57.087 34.783 0.00 0.00 0.00 2.57
311 425 5.222079 GGGTTAAAAAGCCTTTCATTCCA 57.778 39.130 0.68 0.00 45.51 3.53
321 435 6.117975 AGCCTTTCATTCCATTTTGACATT 57.882 33.333 0.00 0.00 0.00 2.71
322 436 5.935789 AGCCTTTCATTCCATTTTGACATTG 59.064 36.000 0.00 0.00 0.00 2.82
323 437 5.933463 GCCTTTCATTCCATTTTGACATTGA 59.067 36.000 0.00 0.00 0.00 2.57
364 478 8.470002 GTCAAGAGCTACCCAAATATTGATTTT 58.530 33.333 0.00 0.00 32.73 1.82
374 488 9.382275 ACCCAAATATTGATTTTACTCAATTGC 57.618 29.630 0.00 0.00 41.89 3.56
383 1140 7.592938 TGATTTTACTCAATTGCAGGTACTTG 58.407 34.615 0.00 0.00 34.60 3.16
484 1241 8.188139 GCTAGGGAAATAAATTCACGATCAAAA 58.812 33.333 0.00 0.00 46.60 2.44
498 1255 7.585867 TCACGATCAAAATTCAAAAATACCGA 58.414 30.769 0.00 0.00 0.00 4.69
582 3295 6.362283 TGCTTATGCTTTCGCTTCTTTTTAAC 59.638 34.615 1.96 0.00 40.48 2.01
588 3301 1.533731 TCGCTTCTTTTTAACAGGGCG 59.466 47.619 10.90 10.90 42.19 6.13
606 3319 4.208686 CTCCGGCAGTAGGGACGC 62.209 72.222 0.00 0.00 38.19 5.19
618 3331 0.313672 AGGGACGCGTACAACGTAAA 59.686 50.000 25.30 0.00 45.24 2.01
619 3332 1.067635 AGGGACGCGTACAACGTAAAT 60.068 47.619 25.30 0.00 45.24 1.40
620 3333 2.163412 AGGGACGCGTACAACGTAAATA 59.837 45.455 25.30 0.00 45.24 1.40
621 3334 2.278875 GGGACGCGTACAACGTAAATAC 59.721 50.000 25.30 0.00 45.24 1.89
748 3466 0.032540 CACTTTGCCCAAACTCAGCC 59.967 55.000 0.00 0.00 0.00 4.85
768 3486 1.071128 CCTAGCAGCAGATCAGGGC 59.929 63.158 0.00 0.00 0.00 5.19
811 3531 4.319261 CCCTTTTACAAAGTACACTCGCAC 60.319 45.833 0.00 0.00 0.00 5.34
861 3588 3.573695 CCCTCCTATATATACCCCACGG 58.426 54.545 0.00 0.00 0.00 4.94
884 3611 2.094803 CAGAGCAGAGAACGACAGACAT 60.095 50.000 0.00 0.00 0.00 3.06
926 3679 4.213482 GCCACCAATCCAGTTCGAATATAC 59.787 45.833 0.00 0.00 0.00 1.47
927 3680 5.611374 CCACCAATCCAGTTCGAATATACT 58.389 41.667 0.00 0.00 0.00 2.12
928 3681 5.696724 CCACCAATCCAGTTCGAATATACTC 59.303 44.000 0.00 0.00 0.00 2.59
948 3713 3.288092 TCCTACTAGCTTGAAGCATCGA 58.712 45.455 20.45 2.88 45.56 3.59
952 3720 0.815095 TAGCTTGAAGCATCGACCGA 59.185 50.000 20.45 0.00 45.56 4.69
953 3721 0.176680 AGCTTGAAGCATCGACCGAT 59.823 50.000 20.45 0.00 45.56 4.18
954 3722 0.579156 GCTTGAAGCATCGACCGATC 59.421 55.000 13.09 0.00 41.89 3.69
1401 4193 3.482783 GAGAAGGTGCGCGTGCTC 61.483 66.667 23.16 18.61 43.34 4.26
1437 4229 1.731613 CTTCCACGTTCGCTGCGTA 60.732 57.895 22.48 10.01 40.90 4.42
1441 4233 1.728074 CACGTTCGCTGCGTAGACA 60.728 57.895 22.48 0.00 40.90 3.41
1545 4361 2.173669 CATCACCGTGGTCATCGCC 61.174 63.158 0.00 0.00 0.00 5.54
1557 4381 2.484417 GGTCATCGCCTGAGTTCATCAT 60.484 50.000 0.00 0.00 37.28 2.45
1625 4453 1.068610 CAAGCTCCGGCGAATTTTCAA 60.069 47.619 9.30 0.00 44.37 2.69
1650 4481 5.119279 GCGCTGATTACTAGTGGAATGTATG 59.881 44.000 5.39 0.00 0.00 2.39
1688 4524 8.132995 TGCTCAATTGCTCATGTAAATATTCAG 58.867 33.333 0.00 0.00 0.00 3.02
1699 4535 1.094785 AATATTCAGCGGCGCAAAGT 58.905 45.000 35.02 19.53 0.00 2.66
1712 4548 1.065401 CGCAAAGTGCTTTCCTGACAA 59.935 47.619 0.00 0.00 42.25 3.18
1787 4630 1.445582 CCGTCGACAAGTAGGGTGC 60.446 63.158 17.16 0.00 0.00 5.01
1790 4633 2.125673 CGACAAGTAGGGTGCCCG 60.126 66.667 0.98 0.00 41.95 6.13
1827 4673 2.361119 CGATGGATGGAGGACGACTAAA 59.639 50.000 0.00 0.00 0.00 1.85
1828 4674 3.181479 CGATGGATGGAGGACGACTAAAA 60.181 47.826 0.00 0.00 0.00 1.52
1829 4675 3.604875 TGGATGGAGGACGACTAAAAC 57.395 47.619 0.00 0.00 0.00 2.43
1830 4676 2.901192 TGGATGGAGGACGACTAAAACA 59.099 45.455 0.00 0.00 0.00 2.83
1849 4698 3.876341 ACAGTTCAACCGACCACTTTTA 58.124 40.909 0.00 0.00 0.00 1.52
1850 4699 4.457466 ACAGTTCAACCGACCACTTTTAT 58.543 39.130 0.00 0.00 0.00 1.40
1851 4700 4.274950 ACAGTTCAACCGACCACTTTTATG 59.725 41.667 0.00 0.00 0.00 1.90
1852 4701 3.252458 AGTTCAACCGACCACTTTTATGC 59.748 43.478 0.00 0.00 0.00 3.14
1853 4702 3.134574 TCAACCGACCACTTTTATGCT 57.865 42.857 0.00 0.00 0.00 3.79
1854 4703 3.071479 TCAACCGACCACTTTTATGCTC 58.929 45.455 0.00 0.00 0.00 4.26
1855 4704 3.074412 CAACCGACCACTTTTATGCTCT 58.926 45.455 0.00 0.00 0.00 4.09
1856 4705 3.418684 ACCGACCACTTTTATGCTCTT 57.581 42.857 0.00 0.00 0.00 2.85
1857 4706 4.546829 ACCGACCACTTTTATGCTCTTA 57.453 40.909 0.00 0.00 0.00 2.10
1858 4707 5.099042 ACCGACCACTTTTATGCTCTTAT 57.901 39.130 0.00 0.00 0.00 1.73
1859 4708 5.497474 ACCGACCACTTTTATGCTCTTATT 58.503 37.500 0.00 0.00 0.00 1.40
1860 4709 5.944007 ACCGACCACTTTTATGCTCTTATTT 59.056 36.000 0.00 0.00 0.00 1.40
1861 4710 6.433093 ACCGACCACTTTTATGCTCTTATTTT 59.567 34.615 0.00 0.00 0.00 1.82
1862 4711 7.039993 ACCGACCACTTTTATGCTCTTATTTTT 60.040 33.333 0.00 0.00 0.00 1.94
1900 4749 2.457598 TGCTACTCTCTCCGTTCCATT 58.542 47.619 0.00 0.00 0.00 3.16
1905 4754 5.241064 GCTACTCTCTCCGTTCCATTATGTA 59.759 44.000 0.00 0.00 0.00 2.29
1906 4755 6.238953 GCTACTCTCTCCGTTCCATTATGTAA 60.239 42.308 0.00 0.00 0.00 2.41
1907 4756 6.732896 ACTCTCTCCGTTCCATTATGTAAT 57.267 37.500 0.00 0.00 0.00 1.89
1914 4763 8.536175 TCTCCGTTCCATTATGTAATGCATATA 58.464 33.333 0.00 0.00 41.23 0.86
2017 4876 9.031537 TGAAAGTAGGTCTTGTGATGTATCTAA 57.968 33.333 0.00 0.00 36.40 2.10
2031 4890 9.999009 GTGATGTATCTAATGATATGCATTTGG 57.001 33.333 3.54 0.00 44.68 3.28
2074 4933 9.956640 ATCTTCTTCTCTACAAACTTGATCAAT 57.043 29.630 8.96 0.00 0.00 2.57
2143 5002 4.527427 GTGGAACAAAGGGAGTAGTACTCT 59.473 45.833 25.70 8.09 42.67 3.24
2158 5017 0.331954 ACTCTCAGCTTAGGACCGGA 59.668 55.000 9.46 0.00 0.00 5.14
2169 5028 2.572284 GACCGGAGACCCTTCACG 59.428 66.667 9.46 0.00 0.00 4.35
2170 5029 2.995574 ACCGGAGACCCTTCACGG 60.996 66.667 9.46 0.00 45.21 4.94
2188 5047 2.224426 ACGGAAGTGCCTTGTATTGACA 60.224 45.455 0.00 0.00 46.97 3.58
2193 5052 3.002791 AGTGCCTTGTATTGACATCACG 58.997 45.455 0.00 0.00 36.55 4.35
2197 5056 3.198068 CCTTGTATTGACATCACGGAGG 58.802 50.000 0.00 0.00 34.86 4.30
2198 5057 2.309528 TGTATTGACATCACGGAGGC 57.690 50.000 0.00 0.00 0.00 4.70
2224 5083 4.501714 GCGGTATGGTCGCGGTCA 62.502 66.667 6.13 5.40 43.71 4.02
2227 5086 0.242825 CGGTATGGTCGCGGTCATAT 59.757 55.000 19.46 9.57 0.00 1.78
2228 5087 1.469703 CGGTATGGTCGCGGTCATATA 59.530 52.381 19.46 8.85 0.00 0.86
2244 5103 6.517605 GGTCATATAGTTGGTCCTCTTCTTC 58.482 44.000 0.00 0.00 0.00 2.87
2245 5104 6.463190 GGTCATATAGTTGGTCCTCTTCTTCC 60.463 46.154 0.00 0.00 0.00 3.46
2246 5105 6.325286 GTCATATAGTTGGTCCTCTTCTTCCT 59.675 42.308 0.00 0.00 0.00 3.36
2259 5118 7.445707 GTCCTCTTCTTCCTTGTTAACTTCATT 59.554 37.037 7.22 0.00 0.00 2.57
2261 5120 7.445402 CCTCTTCTTCCTTGTTAACTTCATTGA 59.555 37.037 7.22 0.00 0.00 2.57
2277 5136 5.651387 TCATTGACGCCCAATTTTGAATA 57.349 34.783 1.40 0.00 42.55 1.75
2284 5143 6.071672 TGACGCCCAATTTTGAATAGAATCAA 60.072 34.615 0.00 0.00 37.53 2.57
2285 5144 6.696411 ACGCCCAATTTTGAATAGAATCAAA 58.304 32.000 0.00 0.00 45.07 2.69
2313 5172 5.790593 TCCTCGGGTACTTTTCATATATGC 58.209 41.667 7.92 0.00 0.00 3.14
2318 5177 6.017440 TCGGGTACTTTTCATATATGCTTTGC 60.017 38.462 7.92 0.00 0.00 3.68
2329 5188 8.518430 TCATATATGCTTTGCTTTCTACCAAA 57.482 30.769 7.92 0.00 0.00 3.28
2331 5190 9.585099 CATATATGCTTTGCTTTCTACCAAAAA 57.415 29.630 0.00 0.00 31.29 1.94
2332 5191 7.889589 ATATGCTTTGCTTTCTACCAAAAAC 57.110 32.000 0.00 0.00 31.29 2.43
2333 5192 4.438148 TGCTTTGCTTTCTACCAAAAACC 58.562 39.130 0.00 0.00 31.29 3.27
2336 5235 5.050159 GCTTTGCTTTCTACCAAAAACCATG 60.050 40.000 0.00 0.00 31.29 3.66
2446 5345 1.135083 TCAAGAAGGAATCGACGCTCC 60.135 52.381 7.52 7.52 0.00 4.70
2452 5351 4.814294 AATCGACGCTCCCACGCC 62.814 66.667 0.00 0.00 36.19 5.68
2471 5370 3.202906 GCCGATGCTAGTTGGTCAAATA 58.797 45.455 0.00 0.00 33.53 1.40
2498 5397 0.902531 AGACCAATGACTACCACCCG 59.097 55.000 0.00 0.00 0.00 5.28
2499 5398 0.899720 GACCAATGACTACCACCCGA 59.100 55.000 0.00 0.00 0.00 5.14
2500 5399 0.611714 ACCAATGACTACCACCCGAC 59.388 55.000 0.00 0.00 0.00 4.79
2504 5403 2.467566 ATGACTACCACCCGACAAAC 57.532 50.000 0.00 0.00 0.00 2.93
2528 5427 0.032952 TCTCGAACCAACACCTTCCG 59.967 55.000 0.00 0.00 0.00 4.30
2534 5433 0.818040 ACCAACACCTTCCGCAAGAC 60.818 55.000 0.00 0.00 43.02 3.01
2539 5438 1.021202 CACCTTCCGCAAGACAACAA 58.979 50.000 0.00 0.00 43.02 2.83
2545 5444 3.188159 TCCGCAAGACAACAACTTACT 57.812 42.857 0.00 0.00 43.02 2.24
2546 5445 2.869801 TCCGCAAGACAACAACTTACTG 59.130 45.455 0.00 0.00 43.02 2.74
2547 5446 2.612212 CCGCAAGACAACAACTTACTGT 59.388 45.455 0.00 0.00 43.02 3.55
2548 5447 3.546020 CCGCAAGACAACAACTTACTGTG 60.546 47.826 0.00 0.00 43.02 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.468746 TCCTTTCTTCTCGTTTTGTATGGTG 59.531 40.000 0.00 0.00 0.00 4.17
33 34 8.846211 TGTTTTCATATTTCCTTTCTTCTCGTT 58.154 29.630 0.00 0.00 0.00 3.85
41 42 8.593492 AAGCACTTGTTTTCATATTTCCTTTC 57.407 30.769 0.00 0.00 0.00 2.62
91 92 3.886505 TGCGAGGGAATAAAACTTGTTGT 59.113 39.130 0.00 0.00 0.00 3.32
92 93 4.497473 TGCGAGGGAATAAAACTTGTTG 57.503 40.909 0.00 0.00 0.00 3.33
102 103 5.069318 TGCATGATAATTTGCGAGGGAATA 58.931 37.500 0.00 0.00 41.80 1.75
110 111 2.063266 GGCCATGCATGATAATTTGCG 58.937 47.619 28.31 8.75 41.80 4.85
121 122 1.389327 AGGGACTTTGGCCATGCAT 59.611 52.632 6.09 0.00 27.25 3.96
134 135 0.822121 AGGCCACGTTTTGAAGGGAC 60.822 55.000 5.01 0.00 0.00 4.46
223 328 5.043762 TCCATTTTTGGGAGGTCTAGGTAT 58.956 41.667 0.00 0.00 0.00 2.73
229 334 3.903530 ACTTCCATTTTTGGGAGGTCT 57.096 42.857 5.34 0.00 40.33 3.85
230 335 4.918588 TCTACTTCCATTTTTGGGAGGTC 58.081 43.478 5.34 0.00 42.96 3.85
231 336 4.811063 GCTCTACTTCCATTTTTGGGAGGT 60.811 45.833 5.34 2.69 45.50 3.85
274 386 1.606903 AACCCCGCATAAACGTTGAA 58.393 45.000 0.00 0.00 0.00 2.69
276 388 3.555917 TTTAACCCCGCATAAACGTTG 57.444 42.857 0.00 0.00 0.00 4.10
277 389 4.548494 CTTTTTAACCCCGCATAAACGTT 58.452 39.130 0.00 0.00 0.00 3.99
280 392 3.056393 AGGCTTTTTAACCCCGCATAAAC 60.056 43.478 0.00 0.00 0.00 2.01
286 398 1.341852 TGAAAGGCTTTTTAACCCCGC 59.658 47.619 14.66 0.00 0.00 6.13
331 445 3.628008 TGGGTAGCTCTTGACGAAGATA 58.372 45.455 0.00 0.00 37.58 1.98
334 448 2.743636 TTGGGTAGCTCTTGACGAAG 57.256 50.000 0.00 0.00 0.00 3.79
343 457 9.120538 TGAGTAAAATCAATATTTGGGTAGCTC 57.879 33.333 0.00 0.00 35.46 4.09
364 478 4.002982 CAGCAAGTACCTGCAATTGAGTA 58.997 43.478 18.37 4.53 45.18 2.59
374 488 5.237815 TCAATTGTCTACAGCAAGTACCTG 58.762 41.667 5.13 0.00 36.41 4.00
380 1137 7.063426 TCGATTTACTCAATTGTCTACAGCAAG 59.937 37.037 5.13 0.00 0.00 4.01
383 1140 6.310467 TGTCGATTTACTCAATTGTCTACAGC 59.690 38.462 5.13 0.00 0.00 4.40
512 1269 9.487442 AAGGGATAGATAGAAATACTCCATCTC 57.513 37.037 0.00 0.00 29.81 2.75
513 1270 9.487442 GAAGGGATAGATAGAAATACTCCATCT 57.513 37.037 0.00 0.00 31.38 2.90
514 1271 8.700973 GGAAGGGATAGATAGAAATACTCCATC 58.299 40.741 0.00 0.00 0.00 3.51
527 1286 3.238788 TGCTCACGGAAGGGATAGATA 57.761 47.619 0.00 0.00 46.45 1.98
588 3301 4.208686 CGTCCCTACTGCCGGAGC 62.209 72.222 5.05 0.00 40.48 4.70
596 3309 1.503542 CGTTGTACGCGTCCCTACT 59.496 57.895 18.63 0.00 33.65 2.57
630 3343 7.801104 TCCTTGTCAAAAGTGCATATATAGGA 58.199 34.615 0.00 0.00 0.00 2.94
632 3345 8.554528 CACTCCTTGTCAAAAGTGCATATATAG 58.445 37.037 12.42 0.00 33.42 1.31
636 3349 4.460382 CCACTCCTTGTCAAAAGTGCATAT 59.540 41.667 16.88 0.00 38.21 1.78
748 3466 1.300775 CCTGATCTGCTGCTAGGCG 60.301 63.158 0.00 0.00 34.52 5.52
768 3486 3.058160 CTCCCCAGCCAAGTTGCG 61.058 66.667 0.00 0.00 36.02 4.85
811 3531 1.966762 GTGCCCACCATTGTTCTGG 59.033 57.895 0.00 0.00 42.35 3.86
861 3588 1.537638 TCTGTCGTTCTCTGCTCTGTC 59.462 52.381 0.00 0.00 0.00 3.51
884 3611 2.035961 GGCTGTGTTGTCTGTCTCTGTA 59.964 50.000 0.00 0.00 0.00 2.74
926 3679 3.316588 TCGATGCTTCAAGCTAGTAGGAG 59.683 47.826 11.57 0.00 42.97 3.69
927 3680 3.066900 GTCGATGCTTCAAGCTAGTAGGA 59.933 47.826 11.57 0.00 42.97 2.94
928 3681 3.376540 GTCGATGCTTCAAGCTAGTAGG 58.623 50.000 11.57 0.00 42.97 3.18
958 3726 2.125106 GAGATGTCCACCCGGCAC 60.125 66.667 0.00 0.00 0.00 5.01
962 3745 0.833287 ATCCAAGAGATGTCCACCCG 59.167 55.000 0.00 0.00 32.41 5.28
1132 3924 2.742372 GAAGAAGAGCGCGGCCAA 60.742 61.111 8.83 0.00 0.00 4.52
1513 4306 0.732880 GTGATGACCGTGTCCGTCTG 60.733 60.000 2.23 0.00 0.00 3.51
1545 4361 3.727079 GCTTCGTTGCATGATGAACTCAG 60.727 47.826 0.00 0.00 37.28 3.35
1613 4440 0.109781 TCAGCGCTTGAAAATTCGCC 60.110 50.000 7.50 0.00 44.86 5.54
1625 4453 3.133003 ACATTCCACTAGTAATCAGCGCT 59.867 43.478 2.64 2.64 0.00 5.92
1699 4535 4.973168 ACTCATAGTTTGTCAGGAAAGCA 58.027 39.130 0.00 0.00 0.00 3.91
1827 4673 2.413310 AAGTGGTCGGTTGAACTGTT 57.587 45.000 3.80 0.00 31.14 3.16
1828 4674 2.413310 AAAGTGGTCGGTTGAACTGT 57.587 45.000 3.80 0.00 31.14 3.55
1829 4675 4.783242 CATAAAAGTGGTCGGTTGAACTG 58.217 43.478 0.00 0.00 31.14 3.16
1830 4676 3.252458 GCATAAAAGTGGTCGGTTGAACT 59.748 43.478 0.00 0.00 31.14 3.01
1859 4708 4.796618 GCATAAAAGTGGTACCCGCAAAAA 60.797 41.667 10.07 0.00 36.32 1.94
1860 4709 3.305471 GCATAAAAGTGGTACCCGCAAAA 60.305 43.478 10.07 0.00 36.32 2.44
1861 4710 2.229302 GCATAAAAGTGGTACCCGCAAA 59.771 45.455 10.07 0.00 36.32 3.68
1862 4711 1.813786 GCATAAAAGTGGTACCCGCAA 59.186 47.619 10.07 0.00 36.32 4.85
1863 4712 1.003812 AGCATAAAAGTGGTACCCGCA 59.996 47.619 10.07 0.00 36.32 5.69
1864 4713 1.746470 AGCATAAAAGTGGTACCCGC 58.254 50.000 10.07 2.12 0.00 6.13
1869 4718 5.067413 CGGAGAGAGTAGCATAAAAGTGGTA 59.933 44.000 0.00 0.00 0.00 3.25
1870 4719 4.142138 CGGAGAGAGTAGCATAAAAGTGGT 60.142 45.833 0.00 0.00 0.00 4.16
1871 4720 4.142138 ACGGAGAGAGTAGCATAAAAGTGG 60.142 45.833 0.00 0.00 0.00 4.00
1872 4721 5.000012 ACGGAGAGAGTAGCATAAAAGTG 58.000 43.478 0.00 0.00 0.00 3.16
1873 4722 5.394333 GGAACGGAGAGAGTAGCATAAAAGT 60.394 44.000 0.00 0.00 0.00 2.66
1874 4723 5.044558 GGAACGGAGAGAGTAGCATAAAAG 58.955 45.833 0.00 0.00 0.00 2.27
1875 4724 4.464951 TGGAACGGAGAGAGTAGCATAAAA 59.535 41.667 0.00 0.00 0.00 1.52
1876 4725 4.021229 TGGAACGGAGAGAGTAGCATAAA 58.979 43.478 0.00 0.00 0.00 1.40
1877 4726 3.628008 TGGAACGGAGAGAGTAGCATAA 58.372 45.455 0.00 0.00 0.00 1.90
1878 4727 3.292492 TGGAACGGAGAGAGTAGCATA 57.708 47.619 0.00 0.00 0.00 3.14
1988 4847 6.619801 ACATCACAAGACCTACTTTCAAAC 57.380 37.500 0.00 0.00 36.61 2.93
1989 4848 8.375506 AGATACATCACAAGACCTACTTTCAAA 58.624 33.333 0.00 0.00 36.61 2.69
1999 4858 8.877779 GCATATCATTAGATACATCACAAGACC 58.122 37.037 0.00 0.00 39.43 3.85
2101 4960 8.532819 TGTTCCACAATGTAGTGTGTGTATATA 58.467 33.333 10.96 0.00 46.18 0.86
2104 4963 5.616270 TGTTCCACAATGTAGTGTGTGTAT 58.384 37.500 10.96 0.00 46.18 2.29
2107 4966 4.891627 TTGTTCCACAATGTAGTGTGTG 57.108 40.909 10.96 1.32 46.18 3.82
2116 4975 4.398319 ACTACTCCCTTTGTTCCACAATG 58.602 43.478 0.00 0.00 38.00 2.82
2126 4985 4.020543 AGCTGAGAGTACTACTCCCTTTG 58.979 47.826 11.94 1.66 46.18 2.77
2127 4986 4.325084 AGCTGAGAGTACTACTCCCTTT 57.675 45.455 11.94 0.00 46.18 3.11
2128 4987 4.325084 AAGCTGAGAGTACTACTCCCTT 57.675 45.455 11.94 14.27 46.18 3.95
2130 4989 4.139038 CCTAAGCTGAGAGTACTACTCCC 58.861 52.174 11.94 1.94 46.18 4.30
2132 4991 4.818005 GGTCCTAAGCTGAGAGTACTACTC 59.182 50.000 8.02 8.02 45.38 2.59
2143 5002 0.683504 GGTCTCCGGTCCTAAGCTGA 60.684 60.000 0.00 0.00 0.00 4.26
2151 5010 2.979649 GTGAAGGGTCTCCGGTCC 59.020 66.667 0.00 2.73 38.33 4.46
2158 5017 1.371558 GCACTTCCGTGAAGGGTCT 59.628 57.895 14.70 0.00 44.17 3.85
2175 5034 2.609459 CTCCGTGATGTCAATACAAGGC 59.391 50.000 0.00 0.00 39.58 4.35
2180 5039 1.209128 CGCCTCCGTGATGTCAATAC 58.791 55.000 0.00 0.00 0.00 1.89
2182 5041 1.153369 CCGCCTCCGTGATGTCAAT 60.153 57.895 0.00 0.00 0.00 2.57
2188 5047 4.082523 CACCACCGCCTCCGTGAT 62.083 66.667 0.00 0.00 0.00 3.06
2197 5056 3.496131 CATACCGCACACCACCGC 61.496 66.667 0.00 0.00 0.00 5.68
2198 5057 2.817834 CCATACCGCACACCACCG 60.818 66.667 0.00 0.00 0.00 4.94
2224 5083 6.674419 ACAAGGAAGAAGAGGACCAACTATAT 59.326 38.462 0.00 0.00 0.00 0.86
2227 5086 4.232091 ACAAGGAAGAAGAGGACCAACTA 58.768 43.478 0.00 0.00 0.00 2.24
2228 5087 3.049344 ACAAGGAAGAAGAGGACCAACT 58.951 45.455 0.00 0.00 0.00 3.16
2244 5103 3.365969 GGGCGTCAATGAAGTTAACAAGG 60.366 47.826 8.61 0.00 0.00 3.61
2245 5104 3.252215 TGGGCGTCAATGAAGTTAACAAG 59.748 43.478 8.61 0.00 0.00 3.16
2246 5105 3.215151 TGGGCGTCAATGAAGTTAACAA 58.785 40.909 8.61 0.00 0.00 2.83
2259 5118 5.417266 TGATTCTATTCAAAATTGGGCGTCA 59.583 36.000 0.00 0.00 0.00 4.35
2261 5120 5.913137 TGATTCTATTCAAAATTGGGCGT 57.087 34.783 0.00 0.00 0.00 5.68
2277 5136 4.576330 ACCCGAGGAGAATTTTGATTCT 57.424 40.909 1.53 1.53 43.04 2.40
2284 5143 5.237236 TGAAAAGTACCCGAGGAGAATTT 57.763 39.130 0.00 0.00 0.00 1.82
2285 5144 4.903045 TGAAAAGTACCCGAGGAGAATT 57.097 40.909 0.00 0.00 0.00 2.17
2296 5155 9.237846 GAAAGCAAAGCATATATGAAAAGTACC 57.762 33.333 17.10 0.00 0.00 3.34
2371 5270 9.953697 ACTAATTTTTACGCTCATTTAAACACA 57.046 25.926 0.00 0.00 0.00 3.72
2405 5304 5.132502 TGAAGGTGTTGTTGATGAGTTGAT 58.867 37.500 0.00 0.00 0.00 2.57
2406 5305 4.522114 TGAAGGTGTTGTTGATGAGTTGA 58.478 39.130 0.00 0.00 0.00 3.18
2452 5351 6.313905 ACTTCTTATTTGACCAACTAGCATCG 59.686 38.462 0.00 0.00 0.00 3.84
2471 5370 6.465084 GTGGTAGTCATTGGTCTAACTTCTT 58.535 40.000 6.47 0.00 0.00 2.52
2486 5385 0.032403 CGTTTGTCGGGTGGTAGTCA 59.968 55.000 0.00 0.00 35.71 3.41
2487 5386 2.818350 CGTTTGTCGGGTGGTAGTC 58.182 57.895 0.00 0.00 35.71 2.59
2498 5397 2.409975 TGGTTCGAGATTCCGTTTGTC 58.590 47.619 0.00 0.00 0.00 3.18
2499 5398 2.536761 TGGTTCGAGATTCCGTTTGT 57.463 45.000 0.00 0.00 0.00 2.83
2500 5399 2.546368 TGTTGGTTCGAGATTCCGTTTG 59.454 45.455 0.00 0.00 0.00 2.93
2504 5403 1.076332 GGTGTTGGTTCGAGATTCCG 58.924 55.000 0.00 0.00 0.00 4.30
2510 5409 1.566018 GCGGAAGGTGTTGGTTCGAG 61.566 60.000 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.