Multiple sequence alignment - TraesCS1A01G164300

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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 TraesCS1A01G164300 chr1A 100.000 7847 0 0 1 7847 296203792 296211638 0.000000e+00 14491.0
1 TraesCS1A01G164300 chr1D 95.850 6289 150 33 747 7003 228293918 228300127 0.000000e+00 10065.0
2 TraesCS1A01G164300 chr1D 97.822 2525 40 7 2362 4877 208853084 208850566 0.000000e+00 4344.0
3 TraesCS1A01G164300 chr1D 97.067 2148 49 5 4869 7003 208835764 208833618 0.000000e+00 3605.0
4 TraesCS1A01G164300 chr1D 93.657 1545 75 15 1 1532 208857287 208855753 0.000000e+00 2289.0
5 TraesCS1A01G164300 chr1D 97.379 763 20 0 1567 2329 208855753 208854991 0.000000e+00 1299.0
6 TraesCS1A01G164300 chr1D 89.151 848 55 17 7004 7835 228300189 228301015 0.000000e+00 1022.0
7 TraesCS1A01G164300 chr1D 91.200 750 50 10 1 745 228292770 228293508 0.000000e+00 1005.0
8 TraesCS1A01G164300 chr1D 85.847 537 47 12 7286 7819 208824487 208823977 1.930000e-150 544.0
9 TraesCS1A01G164300 chr1D 94.218 294 12 3 7002 7292 208833553 208833262 2.010000e-120 444.0
10 TraesCS1A01G164300 chr1D 87.879 165 17 3 7683 7845 483523905 483524068 2.890000e-44 191.0
11 TraesCS1A01G164300 chr1B 95.960 4901 126 24 2139 7003 327835805 327840669 0.000000e+00 7888.0
12 TraesCS1A01G164300 chr1B 94.586 2161 89 14 1 2144 327830601 327832750 0.000000e+00 3317.0
13 TraesCS1A01G164300 chr1B 88.388 887 52 27 7004 7847 327840733 327841611 0.000000e+00 1020.0
14 TraesCS1A01G164300 chr1B 76.578 713 75 44 2567 3248 212661873 212661222 2.750000e-79 307.0
15 TraesCS1A01G164300 chr1B 87.730 163 17 3 7684 7845 673751736 673751896 3.740000e-43 187.0
16 TraesCS1A01G164300 chr4A 84.492 374 40 12 2992 3351 374356147 374356516 3.480000e-93 353.0
17 TraesCS1A01G164300 chr4A 83.690 374 43 13 2992 3351 377580450 377580081 3.510000e-88 337.0
18 TraesCS1A01G164300 chr4A 84.158 202 24 8 7648 7845 577541092 577540895 1.040000e-43 189.0
19 TraesCS1A01G164300 chr4A 84.158 202 21 10 7649 7845 622182127 622182322 1.340000e-42 185.0
20 TraesCS1A01G164300 chr4A 84.158 202 21 11 7649 7845 622197860 622198055 1.340000e-42 185.0
21 TraesCS1A01G164300 chr7D 78.456 557 83 21 2889 3422 11125999 11125457 5.870000e-86 329.0
22 TraesCS1A01G164300 chr7D 83.886 211 17 11 6242 6437 41051665 41051873 1.340000e-42 185.0
23 TraesCS1A01G164300 chr7D 83.544 79 9 2 363 437 446197669 446197747 3.930000e-08 71.3
24 TraesCS1A01G164300 chrUn 82.933 375 46 12 2992 3351 355066347 355065976 9.820000e-84 322.0
25 TraesCS1A01G164300 chr3A 83.832 334 36 10 3036 3351 692317546 692317879 1.280000e-77 302.0
26 TraesCS1A01G164300 chr3A 88.496 113 12 1 2558 2670 136526592 136526481 1.370000e-27 135.0
27 TraesCS1A01G164300 chr4B 77.008 635 70 36 2558 3177 223387535 223388108 2.140000e-75 294.0
28 TraesCS1A01G164300 chr4B 82.439 205 14 10 6245 6437 545464075 545463881 8.150000e-35 159.0
29 TraesCS1A01G164300 chr3B 77.143 525 65 17 2490 2998 515894366 515894851 3.630000e-63 254.0
30 TraesCS1A01G164300 chr3B 93.382 136 7 2 7712 7845 42628392 42628257 4.800000e-47 200.0
31 TraesCS1A01G164300 chr3B 84.146 82 8 2 357 437 64244373 64244450 3.040000e-09 75.0
32 TraesCS1A01G164300 chr5A 90.123 162 14 2 7683 7843 526384744 526384584 7.980000e-50 209.0
33 TraesCS1A01G164300 chr7A 83.333 210 18 11 6242 6437 112567500 112567706 2.250000e-40 178.0
34 TraesCS1A01G164300 chr7B 82.857 210 19 11 6242 6437 678623335 678623541 1.050000e-38 172.0
35 TraesCS1A01G164300 chr5B 82.979 94 10 3 356 449 1421231 1421318 6.530000e-11 80.5
36 TraesCS1A01G164300 chr6B 90.196 51 4 1 401 450 414343480 414343530 1.830000e-06 65.8
37 TraesCS1A01G164300 chr2D 100.000 30 0 0 1006 1035 634059615 634059586 1.000000e-03 56.5
38 TraesCS1A01G164300 chr2A 100.000 30 0 0 1006 1035 779665999 779666028 1.000000e-03 56.5


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 TraesCS1A01G164300 chr1A 296203792 296211638 7846 False 14491.000000 14491 100.0000 1 7847 1 chr1A.!!$F1 7846
1 TraesCS1A01G164300 chr1D 228292770 228301015 8245 False 4030.666667 10065 92.0670 1 7835 3 chr1D.!!$F2 7834
2 TraesCS1A01G164300 chr1D 208850566 208857287 6721 True 2644.000000 4344 96.2860 1 4877 3 chr1D.!!$R3 4876
3 TraesCS1A01G164300 chr1D 208833262 208835764 2502 True 2024.500000 3605 95.6425 4869 7292 2 chr1D.!!$R2 2423
4 TraesCS1A01G164300 chr1D 208823977 208824487 510 True 544.000000 544 85.8470 7286 7819 1 chr1D.!!$R1 533
5 TraesCS1A01G164300 chr1B 327830601 327841611 11010 False 4075.000000 7888 92.9780 1 7847 3 chr1B.!!$F2 7846
6 TraesCS1A01G164300 chr1B 212661222 212661873 651 True 307.000000 307 76.5780 2567 3248 1 chr1B.!!$R1 681
7 TraesCS1A01G164300 chr7D 11125457 11125999 542 True 329.000000 329 78.4560 2889 3422 1 chr7D.!!$R1 533
8 TraesCS1A01G164300 chr4B 223387535 223388108 573 False 294.000000 294 77.0080 2558 3177 1 chr4B.!!$F1 619

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
909 1327 2.029380 ACGGATCGATTCTGACACACAA 60.029 45.455 0.0 0.0 34.56 3.33 F
1631 2063 1.001406 GGTCTGAACTCCTGACACCTG 59.999 57.143 0.0 0.0 43.15 4.00 F
2639 8005 1.743394 GATGGTCGGTGGATTGTTTCC 59.257 52.381 0.0 0.0 45.69 3.13 F
3879 9307 1.131883 AGCTTCATGCAGAATTGTCGC 59.868 47.619 0.0 0.0 45.94 5.19 F
5397 10842 1.348696 TGGAATCAAGTGAGAGCAGCA 59.651 47.619 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2639 8005 0.179073 CAGAACTATCAGCCCCACCG 60.179 60.000 0.00 0.00 0.00 4.94 R
2922 8301 0.819582 AATTGGGCCTTCATGAAGCG 59.180 50.000 27.01 20.67 37.11 4.68 R
4125 9559 4.390909 CCAAGCTTGAAATGAGGAATTTGC 59.609 41.667 28.05 0.00 38.64 3.68 R
5401 10846 1.463056 CGGAGCACTTACGATTTTGCA 59.537 47.619 0.00 0.00 37.44 4.08 R
7180 12753 0.459585 GAAGATTACCACGCGGCAGA 60.460 55.000 12.47 0.00 34.57 4.26 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
22 23 3.209410 AGAAAATCTCCATCATCGGTGC 58.791 45.455 0.00 0.00 0.00 5.01
37 38 3.482436 TCGGTGCTTGTCCATTAACTTT 58.518 40.909 0.00 0.00 0.00 2.66
93 101 5.779922 AGACTTTGTATCTAAACGTCTGCA 58.220 37.500 0.00 0.00 32.25 4.41
94 102 6.220930 AGACTTTGTATCTAAACGTCTGCAA 58.779 36.000 0.00 0.00 32.25 4.08
95 103 6.145696 AGACTTTGTATCTAAACGTCTGCAAC 59.854 38.462 0.00 0.00 32.25 4.17
303 311 7.016268 TCCAAACTCTACTATTGTTCTTGGTCT 59.984 37.037 0.00 0.00 0.00 3.85
306 314 7.726033 ACTCTACTATTGTTCTTGGTCTCAT 57.274 36.000 0.00 0.00 0.00 2.90
365 373 7.071069 TCTGGACAAAGATGACATATGCTAT 57.929 36.000 1.58 0.00 0.00 2.97
435 443 6.513720 GCCTACCAAAACGTCTTGTATTTTGA 60.514 38.462 0.20 0.00 43.07 2.69
439 447 7.091443 ACCAAAACGTCTTGTATTTTGAAACA 58.909 30.769 0.20 0.00 43.07 2.83
442 450 9.019764 CAAAACGTCTTGTATTTTGAAACAGAT 57.980 29.630 0.00 0.00 43.07 2.90
462 470 6.818644 ACAGATGTAGTAATACAGTGCCTTTG 59.181 38.462 9.15 0.37 32.97 2.77
479 487 6.593382 GTGCCTTTGTAAATTTGCATATCCAA 59.407 34.615 9.89 0.51 0.00 3.53
482 490 7.102346 CCTTTGTAAATTTGCATATCCAACCA 58.898 34.615 9.89 0.00 0.00 3.67
485 493 7.473735 TGTAAATTTGCATATCCAACCAGAA 57.526 32.000 4.71 0.00 0.00 3.02
535 543 4.290155 CAACACCTTCGTCCATTTTGAAG 58.710 43.478 0.00 0.00 39.01 3.02
736 746 8.894731 AGAACAAGAAAAACTCTCTAGAAAACC 58.105 33.333 0.00 0.00 31.02 3.27
748 1166 9.713713 ACTCTCTAGAAAACCAAGAAATAACTC 57.286 33.333 0.00 0.00 0.00 3.01
837 1255 4.767928 TCTCTCCCTCTCACTAGTTTGTTC 59.232 45.833 0.00 0.00 0.00 3.18
889 1307 7.095355 ACCAATCGAGAAACGGCATATAATAAC 60.095 37.037 0.00 0.00 42.82 1.89
906 1324 4.649088 ATAACGGATCGATTCTGACACA 57.351 40.909 0.00 0.00 34.56 3.72
909 1327 2.029380 ACGGATCGATTCTGACACACAA 60.029 45.455 0.00 0.00 34.56 3.33
921 1339 6.618287 TCTGACACACAATTCGAAATCTTT 57.382 33.333 0.00 0.00 0.00 2.52
926 1344 7.026631 ACACACAATTCGAAATCTTTTCTCA 57.973 32.000 0.00 0.00 0.00 3.27
1062 1493 8.589335 TTCTTGCTCCGTGAATAATCTATTAC 57.411 34.615 0.00 0.00 0.00 1.89
1309 1741 2.859538 GTGTGATTTTGCAACTGTGTGG 59.140 45.455 0.00 0.00 0.00 4.17
1468 1900 2.345341 GTGTGCTCAACAGTTTGTTTGC 59.655 45.455 8.72 8.72 38.77 3.68
1472 1904 2.223249 GCTCAACAGTTTGTTTGCGAGA 60.223 45.455 10.27 0.00 38.77 4.04
1585 2017 6.265196 ACCATTGCTTTTGTCACTTCAGATAA 59.735 34.615 0.00 0.00 0.00 1.75
1631 2063 1.001406 GGTCTGAACTCCTGACACCTG 59.999 57.143 0.00 0.00 43.15 4.00
1820 2252 2.158769 TCTAATTGATGGCATGACCGCT 60.159 45.455 3.81 0.00 43.94 5.52
1987 2419 2.375174 ACAATGCCCAGAGGAGTTTGTA 59.625 45.455 0.00 0.00 32.48 2.41
2121 2553 6.099701 AGTGCTGTCCTGGTAATGTTATATGA 59.900 38.462 0.00 0.00 0.00 2.15
2179 5671 5.074804 GGTTGGTAGTCATTTAGGTGGTTT 58.925 41.667 0.00 0.00 0.00 3.27
2192 5684 8.686334 CATTTAGGTGGTTTCTTATGCACTTAT 58.314 33.333 0.00 0.00 0.00 1.73
2381 7747 5.182190 TCATAACGCTTGGCTGTATTTGAAA 59.818 36.000 0.00 0.00 0.00 2.69
2394 7760 8.825745 GGCTGTATTTGAAACAAAAAGATCAAA 58.174 29.630 0.00 2.69 43.53 2.69
2639 8005 1.743394 GATGGTCGGTGGATTGTTTCC 59.257 52.381 0.00 0.00 45.69 3.13
2922 8301 4.216257 TGGAAAGCTCTTGCATGACTTTAC 59.784 41.667 20.68 20.68 42.74 2.01
3339 8766 4.337274 TCATTATGCAGTCATCCAGCAAAG 59.663 41.667 0.00 0.00 42.15 2.77
3411 8838 9.023962 TCATACTCTTGGCTTTGATGTAATTTT 57.976 29.630 0.00 0.00 0.00 1.82
3635 9062 2.363306 ACCTGAAATTGTGAGCCACA 57.637 45.000 4.16 4.16 43.02 4.17
3733 9160 8.668353 TCTTGTGTATGCATATTTGAACTCTTC 58.332 33.333 10.16 0.00 0.00 2.87
3771 9198 1.529244 GCCTGATGGTGCATACCCC 60.529 63.158 0.00 0.00 46.96 4.95
3879 9307 1.131883 AGCTTCATGCAGAATTGTCGC 59.868 47.619 0.00 0.00 45.94 5.19
3999 9433 7.717875 TGACCAAATTAAGTAAGTGCTGTAGTT 59.282 33.333 0.00 0.00 0.00 2.24
4065 9499 5.633601 TCGTTCTATGACATTCAACAGTGAC 59.366 40.000 0.00 0.00 31.90 3.67
4427 9863 9.312904 TCCTAAACTTCAGAAATTTGATCCATT 57.687 29.630 0.00 0.00 0.00 3.16
4535 9971 6.594159 GGAAGTTTATCGATTTCCAGAAGACA 59.406 38.462 17.84 0.00 39.09 3.41
4812 10257 3.102972 AGAGCTGAATCTGCACCTCTTA 58.897 45.455 14.35 0.00 28.85 2.10
5232 10677 2.565391 GGGGACATTAACTGTTTTGGGG 59.435 50.000 0.00 0.00 38.54 4.96
5391 10836 3.743521 CAACTGGTGGAATCAAGTGAGA 58.256 45.455 0.00 0.00 0.00 3.27
5392 10837 3.692257 ACTGGTGGAATCAAGTGAGAG 57.308 47.619 0.00 0.00 0.00 3.20
5393 10838 2.289945 ACTGGTGGAATCAAGTGAGAGC 60.290 50.000 0.00 0.00 0.00 4.09
5394 10839 1.699083 TGGTGGAATCAAGTGAGAGCA 59.301 47.619 0.00 0.00 0.00 4.26
5395 10840 2.289882 TGGTGGAATCAAGTGAGAGCAG 60.290 50.000 0.00 0.00 0.00 4.24
5396 10841 1.736681 GTGGAATCAAGTGAGAGCAGC 59.263 52.381 0.00 0.00 0.00 5.25
5397 10842 1.348696 TGGAATCAAGTGAGAGCAGCA 59.651 47.619 0.00 0.00 0.00 4.41
5398 10843 2.026542 TGGAATCAAGTGAGAGCAGCAT 60.027 45.455 0.00 0.00 0.00 3.79
5399 10844 3.198417 TGGAATCAAGTGAGAGCAGCATA 59.802 43.478 0.00 0.00 0.00 3.14
5400 10845 4.194640 GGAATCAAGTGAGAGCAGCATAA 58.805 43.478 0.00 0.00 0.00 1.90
5401 10846 4.820716 GGAATCAAGTGAGAGCAGCATAAT 59.179 41.667 0.00 0.00 0.00 1.28
5402 10847 5.277876 GGAATCAAGTGAGAGCAGCATAATG 60.278 44.000 0.00 0.00 0.00 1.90
5403 10848 2.941064 TCAAGTGAGAGCAGCATAATGC 59.059 45.455 0.00 0.00 46.88 3.56
5572 11045 5.702065 TGGCTTGGTATACATTACTTCCA 57.298 39.130 5.01 0.00 0.00 3.53
5688 11161 1.580845 GCTGGAGAACGCAGTGCATT 61.581 55.000 16.83 5.87 45.00 3.56
5748 11221 7.461107 CAAAACCATCAAGAATTCATTCATGC 58.539 34.615 8.44 0.00 39.23 4.06
5836 11309 5.724328 TGCTATTATTCGGGAGACATGATC 58.276 41.667 0.00 0.00 39.59 2.92
6269 11749 1.133945 TGCTGTGGTCTTTTACTGCCA 60.134 47.619 0.00 0.00 39.91 4.92
6368 11855 9.654919 ATGGTAATATTTGGGCTTATACAAGTT 57.345 29.630 0.00 0.00 34.00 2.66
6369 11856 8.908903 TGGTAATATTTGGGCTTATACAAGTTG 58.091 33.333 0.00 0.00 34.00 3.16
6373 11860 9.651913 AATATTTGGGCTTATACAAGTTGTTTG 57.348 29.630 14.90 3.64 42.68 2.93
6412 11899 1.754226 ACATTTGAACGTTGCCTTGGT 59.246 42.857 5.00 0.00 0.00 3.67
6483 11970 1.202842 TGTCGTCTACTCCACCAGTCA 60.203 52.381 0.00 0.00 36.43 3.41
6566 12055 6.761242 TGATCCTGCTGTACATACAATGTAAC 59.239 38.462 0.00 0.00 46.36 2.50
6646 12135 5.831702 AGAGCTGGAAAAGATAAATGCAG 57.168 39.130 0.00 0.00 35.84 4.41
6704 12193 6.621316 TCAATTCAAAAACTAGGCGTTACA 57.379 33.333 0.00 0.00 33.90 2.41
6708 12197 4.197750 TCAAAAACTAGGCGTTACAACCA 58.802 39.130 0.00 0.00 33.90 3.67
6922 12417 4.430137 TTAACAGCTACGACGACAGAAT 57.570 40.909 0.00 0.00 0.00 2.40
7026 12591 1.270907 TCTTGCTCCTTGTCTCTCCC 58.729 55.000 0.00 0.00 0.00 4.30
7177 12750 0.249447 TTAGGATGGCTGATCACGCG 60.249 55.000 3.53 3.53 31.91 6.01
7178 12751 2.087462 TAGGATGGCTGATCACGCGG 62.087 60.000 12.47 0.00 31.91 6.46
7180 12753 3.740128 GATGGCTGATCACGCGGGT 62.740 63.158 8.89 0.00 0.00 5.28
7345 12926 3.965379 ACATCGTATGTGGGTGTTACA 57.035 42.857 0.56 0.00 43.01 2.41
7346 12927 3.592059 ACATCGTATGTGGGTGTTACAC 58.408 45.455 6.99 6.99 43.01 2.90
7347 12928 3.259876 ACATCGTATGTGGGTGTTACACT 59.740 43.478 15.44 0.00 43.01 3.55
7348 12929 3.306917 TCGTATGTGGGTGTTACACTG 57.693 47.619 15.44 0.00 39.52 3.66
7349 12930 2.629137 TCGTATGTGGGTGTTACACTGT 59.371 45.455 15.44 0.53 39.52 3.55
7350 12931 3.069872 TCGTATGTGGGTGTTACACTGTT 59.930 43.478 15.44 0.00 39.52 3.16
7351 12932 4.280425 TCGTATGTGGGTGTTACACTGTTA 59.720 41.667 15.44 0.97 39.52 2.41
7352 12933 4.386652 CGTATGTGGGTGTTACACTGTTAC 59.613 45.833 15.44 9.53 39.52 2.50
7364 12945 7.592533 GTGTTACACTGTTACGTGATAGAAAGA 59.407 37.037 11.06 0.00 38.27 2.52
7373 12961 9.387257 TGTTACGTGATAGAAAGAGTATACTGA 57.613 33.333 10.90 0.00 0.00 3.41
7506 13122 2.168728 GAGACGGCTAGAGAAAACCCAT 59.831 50.000 0.00 0.00 0.00 4.00
7544 13160 1.225704 CAGCCACAGAAGATCCCCC 59.774 63.158 0.00 0.00 0.00 5.40
7616 13234 1.451387 ATTGAATCGGACGGCCCAC 60.451 57.895 0.00 0.00 34.14 4.61
7662 13280 1.086696 CCAGCGTTTAGTCCCACATG 58.913 55.000 0.00 0.00 0.00 3.21
7700 13318 2.608090 GCAGACCAGTTTATAAGCCGAC 59.392 50.000 0.00 0.00 0.00 4.79
7702 13320 2.494870 AGACCAGTTTATAAGCCGACGT 59.505 45.455 0.00 0.00 0.00 4.34
7753 13371 7.119262 GGACATCCGATAAAATTGGAACGATAT 59.881 37.037 0.00 0.00 45.74 1.63
7772 13390 6.379703 ACGATATAGAGAAGATTAGCATGGCT 59.620 38.462 0.00 0.00 43.41 4.75
7792 13410 1.737735 CTGCGCAAGGATGACACGA 60.738 57.895 13.05 0.00 36.74 4.35
7794 13412 0.673333 TGCGCAAGGATGACACGAAT 60.673 50.000 8.16 0.00 38.28 3.34
7838 13456 4.792528 TTTTCAAGATTTTGCGCTTTGG 57.207 36.364 9.73 0.00 34.21 3.28
7839 13457 3.451141 TTCAAGATTTTGCGCTTTGGT 57.549 38.095 9.73 0.00 34.21 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.092753 ACAAGCACCGATGATGGAGATT 60.093 45.455 0.00 0.00 0.00 2.40
11 12 1.671979 ATGGACAAGCACCGATGATG 58.328 50.000 0.00 0.00 0.00 3.07
16 17 2.851263 AGTTAATGGACAAGCACCGA 57.149 45.000 0.00 0.00 0.00 4.69
17 18 3.004315 ACAAAGTTAATGGACAAGCACCG 59.996 43.478 0.00 0.00 0.00 4.94
22 23 6.293955 CCCTACACACAAAGTTAATGGACAAG 60.294 42.308 0.00 0.00 0.00 3.16
37 38 4.585879 GCCTTTTCTAATCCCTACACACA 58.414 43.478 0.00 0.00 0.00 3.72
93 101 9.751542 TCGTTATGGTAATTTCATGTTTTTGTT 57.248 25.926 0.00 0.00 0.00 2.83
94 102 9.921637 ATCGTTATGGTAATTTCATGTTTTTGT 57.078 25.926 0.00 0.00 0.00 2.83
198 206 4.994852 GCATCATAAGCATGCAAATCCAAT 59.005 37.500 21.98 1.36 45.19 3.16
267 275 4.381411 AGTAGAGTTTGGACTTGCAGAAC 58.619 43.478 0.00 0.00 35.88 3.01
311 319 9.877178 CTTTCATCTAGTAGTGTCATTAAACCT 57.123 33.333 0.00 0.00 0.00 3.50
321 329 6.211584 TCCAGAAAGCTTTCATCTAGTAGTGT 59.788 38.462 34.39 11.80 39.61 3.55
331 339 5.771666 TCATCTTTGTCCAGAAAGCTTTCAT 59.228 36.000 34.39 19.94 39.61 2.57
435 443 6.947464 AGGCACTGTATTACTACATCTGTTT 58.053 36.000 0.00 0.00 37.24 2.83
439 447 6.947464 ACAAAGGCACTGTATTACTACATCT 58.053 36.000 0.00 0.00 40.86 2.90
442 450 9.509956 AATTTACAAAGGCACTGTATTACTACA 57.490 29.630 0.28 0.00 40.86 2.74
452 460 6.256321 GGATATGCAAATTTACAAAGGCACTG 59.744 38.462 0.00 0.00 40.86 3.66
462 470 8.770438 TTTTCTGGTTGGATATGCAAATTTAC 57.230 30.769 11.58 0.00 0.00 2.01
485 493 4.647424 ACCATCACGTTCATGTGTTTTT 57.353 36.364 0.00 0.00 40.74 1.94
678 688 2.424601 CAATGTCCAAGCCGTGATGATT 59.575 45.455 0.00 0.00 0.00 2.57
889 1307 2.278026 TGTGTGTCAGAATCGATCCG 57.722 50.000 0.00 0.00 0.00 4.18
906 1324 5.617751 CGGCTGAGAAAAGATTTCGAATTGT 60.618 40.000 0.00 0.00 0.00 2.71
909 1327 4.003648 ACGGCTGAGAAAAGATTTCGAAT 58.996 39.130 0.00 0.00 0.00 3.34
969 1397 4.381292 GGCAGCAGTCATAAAAAGCTTGAT 60.381 41.667 0.00 0.00 32.35 2.57
1062 1493 3.494048 CCTGATTCGAGATTCCCAGAAGG 60.494 52.174 0.00 0.00 0.00 3.46
1309 1741 3.592059 TCACTAAACTTACACGCCCATC 58.408 45.455 0.00 0.00 0.00 3.51
1468 1900 7.247929 ACAAACTTTCTTTTAAGGAGTCTCG 57.752 36.000 0.00 0.00 0.00 4.04
1585 2017 6.156748 ACAACATGATCATATTTGCTGCAT 57.843 33.333 21.23 6.39 0.00 3.96
1631 2063 2.099756 AGCTTCACAACTTCCACAAAGC 59.900 45.455 0.00 0.00 38.67 3.51
1820 2252 6.775629 ACTAAAACCCAGAGCAAAATAGTTGA 59.224 34.615 0.00 0.00 0.00 3.18
2098 2530 6.464322 CCTCATATAACATTACCAGGACAGCA 60.464 42.308 0.00 0.00 0.00 4.41
2121 2553 7.009179 TGACATAGAAAGTGATGAAACTCCT 57.991 36.000 0.00 0.00 0.00 3.69
2639 8005 0.179073 CAGAACTATCAGCCCCACCG 60.179 60.000 0.00 0.00 0.00 4.94
2750 8120 9.466497 CATATATGGCAACTTTATAGGTTGGAT 57.534 33.333 16.81 0.00 42.77 3.41
2922 8301 0.819582 AATTGGGCCTTCATGAAGCG 59.180 50.000 27.01 20.67 37.11 4.68
3033 8413 6.183360 GGAGGAAAATGTTATCTGGGAACATG 60.183 42.308 2.00 0.00 44.75 3.21
3069 8450 5.665459 ACTAACCAAGTCTAGATGATGCAC 58.335 41.667 0.00 0.00 30.33 4.57
3071 8452 6.109359 ACAACTAACCAAGTCTAGATGATGC 58.891 40.000 0.00 0.00 37.50 3.91
3377 8804 6.660521 TCAAAGCCAAGAGTATGATCAAATGT 59.339 34.615 0.00 0.00 0.00 2.71
3520 8947 9.466497 ACTCTGGTTACAAATACATGAAATCAT 57.534 29.630 0.00 0.00 36.96 2.45
3819 9247 6.866480 TCCAGGATGAAAACAAGATAAATGC 58.134 36.000 0.00 0.00 39.69 3.56
3879 9307 5.556355 TCTGTACCGGCATATAGTATTCG 57.444 43.478 0.00 0.00 0.00 3.34
3999 9433 5.190992 TCGGAAGCTTGCGATAAGTATTA 57.809 39.130 34.96 13.25 45.96 0.98
4125 9559 4.390909 CCAAGCTTGAAATGAGGAATTTGC 59.609 41.667 28.05 0.00 38.64 3.68
4812 10257 6.409810 GGCTTCAATCTAACCCTAGGAGAAAT 60.410 42.308 11.48 0.00 0.00 2.17
4839 10284 4.707448 TCTCTTCTGGTGGTCAGTAGAATC 59.293 45.833 4.43 0.00 45.19 2.52
5380 10825 4.036498 GCATTATGCTGCTCTCACTTGATT 59.964 41.667 10.27 0.00 40.96 2.57
5381 10826 3.564644 GCATTATGCTGCTCTCACTTGAT 59.435 43.478 10.27 0.00 40.96 2.57
5382 10827 2.941064 GCATTATGCTGCTCTCACTTGA 59.059 45.455 10.27 0.00 40.96 3.02
5383 10828 2.681344 TGCATTATGCTGCTCTCACTTG 59.319 45.455 18.44 0.00 45.31 3.16
5384 10829 2.995283 TGCATTATGCTGCTCTCACTT 58.005 42.857 18.44 0.00 45.31 3.16
5385 10830 2.704464 TGCATTATGCTGCTCTCACT 57.296 45.000 18.44 0.00 45.31 3.41
5386 10831 3.770263 TTTGCATTATGCTGCTCTCAC 57.230 42.857 18.44 0.00 45.31 3.51
5387 10832 4.496840 CGATTTTGCATTATGCTGCTCTCA 60.497 41.667 18.44 0.00 45.31 3.27
5388 10833 3.973135 CGATTTTGCATTATGCTGCTCTC 59.027 43.478 18.44 7.75 45.31 3.20
5389 10834 3.379372 ACGATTTTGCATTATGCTGCTCT 59.621 39.130 18.44 0.00 45.31 4.09
5390 10835 3.699067 ACGATTTTGCATTATGCTGCTC 58.301 40.909 18.44 8.69 45.31 4.26
5391 10836 3.788333 ACGATTTTGCATTATGCTGCT 57.212 38.095 18.44 0.59 45.31 4.24
5392 10837 5.036737 ACTTACGATTTTGCATTATGCTGC 58.963 37.500 18.44 0.00 45.31 5.25
5393 10838 5.052172 GCACTTACGATTTTGCATTATGCTG 60.052 40.000 18.44 4.70 45.31 4.41
5394 10839 5.036737 GCACTTACGATTTTGCATTATGCT 58.963 37.500 18.44 0.00 45.31 3.79
5395 10840 5.036737 AGCACTTACGATTTTGCATTATGC 58.963 37.500 10.65 10.65 45.29 3.14
5396 10841 5.682862 GGAGCACTTACGATTTTGCATTATG 59.317 40.000 0.00 0.00 37.44 1.90
5397 10842 5.504010 CGGAGCACTTACGATTTTGCATTAT 60.504 40.000 0.00 0.00 37.44 1.28
5398 10843 4.201773 CGGAGCACTTACGATTTTGCATTA 60.202 41.667 0.00 0.00 37.44 1.90
5399 10844 3.426159 CGGAGCACTTACGATTTTGCATT 60.426 43.478 0.00 0.00 37.44 3.56
5400 10845 2.095853 CGGAGCACTTACGATTTTGCAT 59.904 45.455 0.00 0.00 37.44 3.96
5401 10846 1.463056 CGGAGCACTTACGATTTTGCA 59.537 47.619 0.00 0.00 37.44 4.08
5402 10847 2.159467 CGGAGCACTTACGATTTTGC 57.841 50.000 0.00 0.00 35.08 3.68
5688 11161 6.153510 AGCTATAAGATCGTCATCATTAGCCA 59.846 38.462 0.00 0.00 35.57 4.75
5836 11309 7.692460 ACCATTACTCAATATATGCACCATG 57.308 36.000 0.00 0.00 0.00 3.66
6211 11684 7.156673 TCAGTAAACCTTATCCAGTGTACAAC 58.843 38.462 0.00 0.00 30.39 3.32
6368 11855 1.803334 GGGCGTAGATGACACAAACA 58.197 50.000 0.00 0.00 0.00 2.83
6369 11856 0.719465 CGGGCGTAGATGACACAAAC 59.281 55.000 0.00 0.00 0.00 2.93
6372 11859 2.183300 GCGGGCGTAGATGACACA 59.817 61.111 0.00 0.00 0.00 3.72
6373 11860 1.878522 CTGCGGGCGTAGATGACAC 60.879 63.158 0.00 0.00 0.00 3.67
6412 11899 3.953712 TGACAAGCTTAAGGATCGTCA 57.046 42.857 0.00 3.89 0.00 4.35
6483 11970 2.088423 CTCTGCTTCGAGGTCTACACT 58.912 52.381 0.00 0.00 0.00 3.55
6962 12457 5.461526 TGCGTATCTCTATCGGAAAATGAG 58.538 41.667 0.00 0.00 0.00 2.90
7026 12591 4.758674 AGTTGTTCATTGATCCACAGAGTG 59.241 41.667 0.00 0.00 0.00 3.51
7177 12750 3.675619 ATTACCACGCGGCAGACCC 62.676 63.158 12.47 0.00 34.57 4.46
7178 12751 2.125269 ATTACCACGCGGCAGACC 60.125 61.111 12.47 0.00 34.57 3.85
7180 12753 0.459585 GAAGATTACCACGCGGCAGA 60.460 55.000 12.47 0.00 34.57 4.26
7345 12926 9.393512 AGTATACTCTTTCTATCACGTAACAGT 57.606 33.333 0.00 0.00 0.00 3.55
7346 12927 9.653067 CAGTATACTCTTTCTATCACGTAACAG 57.347 37.037 1.26 0.00 0.00 3.16
7347 12928 9.387257 TCAGTATACTCTTTCTATCACGTAACA 57.613 33.333 1.26 0.00 0.00 2.41
7364 12945 5.070685 TGACCGTGCTCATATCAGTATACT 58.929 41.667 0.00 0.00 0.00 2.12
7373 12961 3.132824 TGTTCATCTGACCGTGCTCATAT 59.867 43.478 0.00 0.00 0.00 1.78
7449 13037 0.310854 GGACTGCCGTGAAAAAGGTG 59.689 55.000 0.00 0.00 0.00 4.00
7531 13147 0.404040 TTTTGCGGGGGATCTTCTGT 59.596 50.000 0.00 0.00 0.00 3.41
7597 13215 1.451207 TGGGCCGTCCGATTCAATG 60.451 57.895 0.00 0.00 38.76 2.82
7700 13318 1.132262 GGAGAAGAGAGCTCTCACACG 59.868 57.143 38.20 0.00 45.21 4.49
7702 13320 1.357420 AGGGAGAAGAGAGCTCTCACA 59.643 52.381 38.20 0.00 45.21 3.58
7753 13371 4.282957 CAGGAGCCATGCTAATCTTCTCTA 59.717 45.833 0.00 0.00 39.88 2.43
7792 13410 9.942850 AAAATTTGGACCATTTCTCGATTTATT 57.057 25.926 0.00 0.00 0.00 1.40
7822 13440 1.000843 GGGACCAAAGCGCAAAATCTT 59.999 47.619 11.47 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.