Multiple sequence alignment - TraesCS4A01G139000

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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 TraesCS4A01G139000 chr4A 100.000 5987 0 0 1 5987 207983285 207977299 0.000000e+00 11057.0
1 TraesCS4A01G139000 chr4A 100.000 28 0 0 4612 4639 207978554 207978527 1.100000e-02 52.8
2 TraesCS4A01G139000 chr4A 100.000 28 0 0 4732 4759 207978674 207978647 1.100000e-02 52.8
3 TraesCS4A01G139000 chr4D 93.925 6074 159 54 1 5979 286397951 286391993 0.000000e+00 8979.0
4 TraesCS4A01G139000 chr4D 100.000 28 0 0 4612 4639 286393282 286393255 1.100000e-02 52.8
5 TraesCS4A01G139000 chr4D 100.000 28 0 0 4732 4759 286393402 286393375 1.100000e-02 52.8
6 TraesCS4A01G139000 chr4B 94.782 2913 71 15 3138 5979 276962349 276965251 0.000000e+00 4462.0
7 TraesCS4A01G139000 chr4B 93.269 1857 35 19 284 2114 276958131 276959923 0.000000e+00 2654.0
8 TraesCS4A01G139000 chr4B 97.154 984 25 1 2101 3081 276961366 276962349 0.000000e+00 1659.0
9 TraesCS4A01G139000 chr4B 93.407 182 12 0 64 245 276957811 276957992 2.750000e-68 270.0
10 TraesCS4A01G139000 chr4B 100.000 28 0 0 4732 4759 276963844 276963871 1.100000e-02 52.8
11 TraesCS4A01G139000 chr7A 85.927 739 86 8 3076 3810 613776524 613777248 0.000000e+00 773.0
12 TraesCS4A01G139000 chr7A 84.097 742 105 10 3076 3815 614595490 614596220 0.000000e+00 704.0
13 TraesCS4A01G139000 chr7A 83.693 742 106 11 3076 3815 614442207 614442935 0.000000e+00 686.0
14 TraesCS4A01G139000 chr7A 83.311 749 107 12 3076 3816 613778343 613779081 0.000000e+00 675.0
15 TraesCS4A01G139000 chr7D 84.501 742 97 12 3076 3815 534072083 534072808 0.000000e+00 717.0
16 TraesCS4A01G139000 chr7D 84.189 740 104 9 3076 3814 534171382 534172109 0.000000e+00 706.0
17 TraesCS4A01G139000 chr7D 83.962 742 103 11 3076 3814 534192068 534192796 0.000000e+00 697.0
18 TraesCS4A01G139000 chr5D 100.000 29 0 0 5772 5800 264633061 264633089 3.000000e-03 54.7
19 TraesCS4A01G139000 chr1B 100.000 28 0 0 5772 5799 498685753 498685780 1.100000e-02 52.8


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 TraesCS4A01G139000 chr4A 207977299 207983285 5986 True 11057.00 11057 100.0000 1 5987 1 chr4A.!!$R1 5986
1 TraesCS4A01G139000 chr4D 286391993 286397951 5958 True 8979.00 8979 93.9250 1 5979 1 chr4D.!!$R1 5978
2 TraesCS4A01G139000 chr4B 276957811 276965251 7440 False 1819.56 4462 95.7224 64 5979 5 chr4B.!!$F1 5915
3 TraesCS4A01G139000 chr7A 613776524 613779081 2557 False 724.00 773 84.6190 3076 3816 2 chr7A.!!$F3 740
4 TraesCS4A01G139000 chr7A 614595490 614596220 730 False 704.00 704 84.0970 3076 3815 1 chr7A.!!$F2 739
5 TraesCS4A01G139000 chr7A 614442207 614442935 728 False 686.00 686 83.6930 3076 3815 1 chr7A.!!$F1 739
6 TraesCS4A01G139000 chr7D 534072083 534072808 725 False 717.00 717 84.5010 3076 3815 1 chr7D.!!$F1 739
7 TraesCS4A01G139000 chr7D 534171382 534172109 727 False 706.00 706 84.1890 3076 3814 1 chr7D.!!$F2 738
8 TraesCS4A01G139000 chr7D 534192068 534192796 728 False 697.00 697 83.9620 3076 3814 1 chr7D.!!$F3 738

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
945 1076 1.424493 CCAGCCAAGAGAATCGTCGC 61.424 60.000 0.0 0.0 42.67 5.19 F
1361 1496 0.034059 GTCCTACCTGATGGGATGCG 59.966 60.000 0.0 0.0 40.69 4.73 F
2602 4218 0.464735 CCGGTTCAGTGTTTCACCCA 60.465 55.000 0.0 0.0 34.49 4.51 F
2640 4256 2.849942 TCACTGACAAGACAATGGTGG 58.150 47.619 0.0 0.0 0.00 4.61 F
4283 5904 1.490069 TGGCCATTCTTCCGATGATCA 59.510 47.619 0.0 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 4218 1.416401 TGAAGAGGTCACGGCTTTCTT 59.584 47.619 0.0 0.0 0.00 2.52 R
2962 4578 4.002906 ACCTCAACTAACGAAGCATGAA 57.997 40.909 0.0 0.0 0.00 2.57 R
3543 5164 0.106469 TGCCTTTAGGTGTGTTGGCA 60.106 50.000 0.0 0.0 46.59 4.92 R
4569 6211 0.172803 CGTTGGTAGTAGGCTTCGCT 59.827 55.000 0.0 0.0 0.00 4.93 R
5148 6800 0.106217 CCACCACCTGAAAACCCTGT 60.106 55.000 0.0 0.0 0.00 4.00 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
21 22 1.747355 CAATGGATCTTGGCACCACTC 59.253 52.381 0.00 0.00 36.49 3.51
30 31 2.047179 GCACCACTCTCGAACCCC 60.047 66.667 0.00 0.00 0.00 4.95
49 50 1.957877 CCCCTCTTCTACCTCGTGATC 59.042 57.143 0.00 0.00 0.00 2.92
61 62 4.832248 ACCTCGTGATCAATACAACATGT 58.168 39.130 0.00 0.00 0.00 3.21
62 63 4.631377 ACCTCGTGATCAATACAACATGTG 59.369 41.667 0.00 0.00 0.00 3.21
120 121 3.733337 GATTGTCCGATAAGCAGTGGAT 58.267 45.455 0.00 0.00 32.18 3.41
164 165 6.094048 CGACAAACATCCATCCTTTTACATCT 59.906 38.462 0.00 0.00 0.00 2.90
245 246 5.736207 GCAAAAGACACTACTTTTTCAGGGG 60.736 44.000 0.00 0.00 44.33 4.79
246 247 4.790718 AAGACACTACTTTTTCAGGGGT 57.209 40.909 0.00 0.00 0.00 4.95
247 248 4.086706 AGACACTACTTTTTCAGGGGTG 57.913 45.455 0.00 0.00 36.07 4.61
248 249 3.458487 AGACACTACTTTTTCAGGGGTGT 59.542 43.478 0.00 0.00 41.77 4.16
249 250 3.551846 ACACTACTTTTTCAGGGGTGTG 58.448 45.455 0.00 0.00 39.38 3.82
250 251 3.201266 ACACTACTTTTTCAGGGGTGTGA 59.799 43.478 0.00 0.00 39.38 3.58
251 252 3.564225 CACTACTTTTTCAGGGGTGTGAC 59.436 47.826 0.00 0.00 0.00 3.67
252 253 2.067365 ACTTTTTCAGGGGTGTGACC 57.933 50.000 0.00 0.00 37.60 4.02
272 273 4.431131 CACCCCTTCGCTGCCCAT 62.431 66.667 0.00 0.00 0.00 4.00
344 460 9.948964 CAAACCCTGAATGTATATCTCATGATA 57.051 33.333 0.00 0.00 39.25 2.15
363 479 4.277174 TGATAAATGCAGGACGTGTGTTTT 59.723 37.500 0.00 0.00 0.00 2.43
455 582 3.198068 CCTTTGATCCGATGGTGTGTAG 58.802 50.000 0.00 0.00 0.00 2.74
548 679 1.812571 TCCTCAAGGAAATTGCGCTTC 59.187 47.619 9.73 3.82 42.18 3.86
945 1076 1.424493 CCAGCCAAGAGAATCGTCGC 61.424 60.000 0.00 0.00 42.67 5.19
1267 1402 1.536174 AGGGCATGGGGTTTGGTTG 60.536 57.895 0.00 0.00 0.00 3.77
1356 1491 0.178068 CCGTTGTCCTACCTGATGGG 59.822 60.000 0.00 0.00 41.89 4.00
1357 1492 1.191535 CGTTGTCCTACCTGATGGGA 58.808 55.000 0.00 0.00 35.07 4.37
1358 1493 1.762957 CGTTGTCCTACCTGATGGGAT 59.237 52.381 0.00 0.00 40.69 3.85
1359 1494 2.483714 CGTTGTCCTACCTGATGGGATG 60.484 54.545 0.00 0.00 40.69 3.51
1360 1495 1.131638 TGTCCTACCTGATGGGATGC 58.868 55.000 0.00 0.00 40.69 3.91
1361 1496 0.034059 GTCCTACCTGATGGGATGCG 59.966 60.000 0.00 0.00 40.69 4.73
1362 1497 1.302033 CCTACCTGATGGGATGCGC 60.302 63.158 0.00 0.00 38.76 6.09
1363 1498 1.665916 CTACCTGATGGGATGCGCG 60.666 63.158 0.00 0.00 38.76 6.86
1364 1499 3.163832 TACCTGATGGGATGCGCGG 62.164 63.158 8.83 0.00 38.76 6.46
1378 1513 2.597510 GCGGCCCTTGTCCTTGTT 60.598 61.111 0.00 0.00 0.00 2.83
1379 1514 2.919494 GCGGCCCTTGTCCTTGTTG 61.919 63.158 0.00 0.00 0.00 3.33
1441 1576 2.298729 CGATTCATGGGTTTGGTTTGGT 59.701 45.455 0.00 0.00 0.00 3.67
1522 1657 1.264020 GTGCAGTGCTTGTGAATTCGA 59.736 47.619 17.60 0.00 0.00 3.71
1586 1726 4.219033 GTGCAGTGTTTAATTCGGACAAG 58.781 43.478 0.00 0.00 0.00 3.16
1709 1849 3.243301 GCATTGCCTGTCTGATAATGTGG 60.243 47.826 0.00 0.00 32.75 4.17
1753 1893 2.479566 CAGTAACTGCTGGGTGATGT 57.520 50.000 0.00 0.00 33.11 3.06
1754 1894 2.350522 CAGTAACTGCTGGGTGATGTC 58.649 52.381 0.00 0.00 33.11 3.06
1755 1895 1.977854 AGTAACTGCTGGGTGATGTCA 59.022 47.619 0.00 0.00 0.00 3.58
1756 1896 2.027745 AGTAACTGCTGGGTGATGTCAG 60.028 50.000 0.00 0.00 0.00 3.51
1757 1897 0.767375 AACTGCTGGGTGATGTCAGT 59.233 50.000 0.00 0.00 39.42 3.41
1758 1898 0.767375 ACTGCTGGGTGATGTCAGTT 59.233 50.000 0.00 0.00 34.69 3.16
1759 1899 1.271054 ACTGCTGGGTGATGTCAGTTC 60.271 52.381 0.00 0.00 34.69 3.01
1760 1900 1.002888 CTGCTGGGTGATGTCAGTTCT 59.997 52.381 0.00 0.00 33.81 3.01
1761 1901 1.271001 TGCTGGGTGATGTCAGTTCTG 60.271 52.381 0.00 0.00 33.81 3.02
1791 1943 4.136796 GTCAATTGGTCTGGCTATATGCA 58.863 43.478 5.42 0.00 45.15 3.96
1881 2033 0.613777 CGAAGGTTACTCCAGGGCTT 59.386 55.000 0.00 0.00 39.02 4.35
2319 3932 3.052329 TCACCAGTATCCCCATGCATAA 58.948 45.455 0.00 0.00 0.00 1.90
2326 3939 3.959495 ATCCCCATGCATAAGAAGTGT 57.041 42.857 0.00 0.00 0.00 3.55
2436 4049 9.770097 ATGTGTATGATTATCCTAGTGTTTCTG 57.230 33.333 0.00 0.00 0.00 3.02
2486 4102 5.823045 ACCAAGTCAAGTTAACAAGGAAGAG 59.177 40.000 8.61 0.00 0.00 2.85
2491 4107 9.495572 AAGTCAAGTTAACAAGGAAGAGATTAG 57.504 33.333 8.61 0.00 0.00 1.73
2602 4218 0.464735 CCGGTTCAGTGTTTCACCCA 60.465 55.000 0.00 0.00 34.49 4.51
2640 4256 2.849942 TCACTGACAAGACAATGGTGG 58.150 47.619 0.00 0.00 0.00 4.61
2708 4324 3.519510 CCTCCATTTGGACTGGTCTAGAA 59.480 47.826 0.00 0.00 39.78 2.10
2962 4578 8.434589 TTGAAATTGAAAATATCCAAGGAGGT 57.565 30.769 0.00 0.00 39.02 3.85
3012 4628 8.531530 GCATTTTGATACAATACGGATTTCAAC 58.468 33.333 5.62 0.00 0.00 3.18
3056 4672 7.894708 TGAAATGGTGCAAAATGAATCTCTTA 58.105 30.769 0.00 0.00 0.00 2.10
3197 4813 7.587037 AATATGTTGCCTGCTGTAATAACAT 57.413 32.000 0.00 0.00 40.56 2.71
3268 4887 4.034742 TGATTCGCTGATCATGATTGTGTG 59.965 41.667 10.14 9.67 31.35 3.82
3306 4925 3.363341 ACCAAGTGTTGCCAATTAACG 57.637 42.857 0.00 0.00 0.00 3.18
3543 5164 7.881775 AACAAACAAAGGTCTATCTGTTTCT 57.118 32.000 0.00 0.00 39.37 2.52
4052 5673 6.365247 GCTGATGCAAATATTAGCTTTGGATG 59.635 38.462 6.79 0.00 42.41 3.51
4084 5705 9.201127 ATCATTCAGATAATATGTCAAGTGACG 57.799 33.333 6.94 0.00 40.61 4.35
4168 5789 3.324846 AGTGACAGCTCCTGTTAATGACA 59.675 43.478 0.00 0.00 45.44 3.58
4216 5837 2.238646 ACCAAAGAATCGCTGGTGGATA 59.761 45.455 8.23 0.00 41.95 2.59
4231 5852 3.554934 GTGGATATGTTGGAAGCCATGA 58.445 45.455 0.00 0.00 31.53 3.07
4283 5904 1.490069 TGGCCATTCTTCCGATGATCA 59.510 47.619 0.00 0.00 0.00 2.92
4448 6069 6.515272 ACACAGCTTTTATTTACCAGATGG 57.485 37.500 0.00 0.00 42.17 3.51
4803 6445 1.200020 GTTCCTGATGTTTTGGAGGCG 59.800 52.381 0.00 0.00 0.00 5.52
4946 6588 0.678048 GGGGACGCAAGAAGCTTGAT 60.678 55.000 2.10 0.00 42.61 2.57
4990 6635 2.723010 CGCAAGAACGAAGACTGAATGC 60.723 50.000 0.00 0.00 43.02 3.56
5039 6684 4.373156 ACCCATATATTTGGAGGCTGAC 57.627 45.455 13.30 0.00 39.25 3.51
5042 6687 3.402110 CATATATTTGGAGGCTGACGCA 58.598 45.455 0.00 0.00 38.10 5.24
5065 6710 2.026542 AGGATGAGCAGATTGTCTTGCA 60.027 45.455 0.00 0.00 0.00 4.08
5071 6716 1.203994 GCAGATTGTCTTGCATGGCTT 59.796 47.619 5.73 0.00 0.00 4.35
5185 6837 3.181497 GGTGGATTTCACAATCGACATGG 60.181 47.826 10.91 0.00 45.41 3.66
5192 6844 0.548031 ACAATCGACATGGGCCATCT 59.452 50.000 18.16 4.55 0.00 2.90
5280 6954 5.413309 TGCTCTCCCTTTCTTTCTAGAAG 57.587 43.478 5.12 0.80 41.25 2.85
5353 7027 8.736244 TGTTTAGTTTATAGAAGGGTTTCATGC 58.264 33.333 0.00 0.00 35.70 4.06
5554 7228 7.120873 TGCATTCGAGAGTTAAGTTAGACTAGT 59.879 37.037 0.00 0.00 0.00 2.57
5557 7231 9.889128 ATTCGAGAGTTAAGTTAGACTAGTACT 57.111 33.333 0.00 0.00 0.00 2.73
5682 7356 7.658525 TTGGATTTGTAACATGGCTATCAAT 57.341 32.000 0.00 0.00 0.00 2.57
5686 7360 8.362639 GGATTTGTAACATGGCTATCAATGAAT 58.637 33.333 0.00 0.00 0.00 2.57
5724 7398 4.335400 AGTAATGCCAACAAAAACTGGG 57.665 40.909 0.00 0.00 32.95 4.45
5725 7399 3.964031 AGTAATGCCAACAAAAACTGGGA 59.036 39.130 0.00 0.00 37.46 4.37
5751 7425 9.917887 ATACTGTATAATAGTATTACCTCCGCT 57.082 33.333 4.71 0.00 37.95 5.52
5753 7427 8.108364 ACTGTATAATAGTATTACCTCCGCTCT 58.892 37.037 4.71 0.00 0.00 4.09
5794 7468 4.210331 CAAGTAATTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 32.95 4.30
5850 8360 2.231716 GGTTACCCCCAGCTTTCATT 57.768 50.000 0.00 0.00 0.00 2.57
5898 8629 3.878778 CACTCTATTTTGGAGGGACAGG 58.121 50.000 0.00 0.00 36.41 4.00
5901 8634 3.115390 TCTATTTTGGAGGGACAGGGAG 58.885 50.000 0.00 0.00 0.00 4.30
5979 8713 6.855836 TGCACAAAATTGGAGTAGATGATTC 58.144 36.000 0.00 0.00 0.00 2.52
5981 8715 6.971184 GCACAAAATTGGAGTAGATGATTCTG 59.029 38.462 0.00 0.00 33.17 3.02
5983 8717 8.517878 CACAAAATTGGAGTAGATGATTCTGTT 58.482 33.333 0.00 0.00 33.17 3.16
5984 8718 9.082313 ACAAAATTGGAGTAGATGATTCTGTTT 57.918 29.630 0.00 0.00 33.17 2.83
5985 8719 9.918630 CAAAATTGGAGTAGATGATTCTGTTTT 57.081 29.630 0.00 0.00 33.17 2.43
5986 8720 9.918630 AAAATTGGAGTAGATGATTCTGTTTTG 57.081 29.630 0.00 0.00 33.17 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.656002 TGATCACGAGGTAGAAGAGGG 58.344 52.381 0.00 0.00 0.00 4.30
32 33 6.378710 TGTATTGATCACGAGGTAGAAGAG 57.621 41.667 0.00 0.00 0.00 2.85
101 102 2.499693 TCATCCACTGCTTATCGGACAA 59.500 45.455 0.00 0.00 0.00 3.18
120 121 0.960364 GCACCCGCAAGAAAGGATCA 60.960 55.000 0.00 0.00 43.02 2.92
147 148 5.698104 TGCATCAGATGTAAAAGGATGGAT 58.302 37.500 12.18 0.00 36.68 3.41
164 165 2.203470 TGCCAAGATCTGTTGCATCA 57.797 45.000 9.33 0.00 0.00 3.07
230 231 3.434596 GGTCACACCCCTGAAAAAGTAGT 60.435 47.826 0.00 0.00 30.04 2.73
247 248 4.029809 CGAAGGGGTGGGGGTCAC 62.030 72.222 0.00 0.00 45.34 3.67
255 256 4.431131 ATGGGCAGCGAAGGGGTG 62.431 66.667 0.00 0.00 46.88 4.61
256 257 4.115199 GATGGGCAGCGAAGGGGT 62.115 66.667 0.00 0.00 0.00 4.95
257 258 4.883354 GGATGGGCAGCGAAGGGG 62.883 72.222 0.00 0.00 0.00 4.79
258 259 3.426309 ATGGATGGGCAGCGAAGGG 62.426 63.158 0.00 0.00 0.00 3.95
259 260 1.895707 GATGGATGGGCAGCGAAGG 60.896 63.158 0.00 0.00 0.00 3.46
260 261 0.465097 AAGATGGATGGGCAGCGAAG 60.465 55.000 0.00 0.00 0.00 3.79
266 267 4.464008 GAAGTATGAAAGATGGATGGGCA 58.536 43.478 0.00 0.00 0.00 5.36
272 273 6.233905 TGAATCGGAAGTATGAAAGATGGA 57.766 37.500 0.00 0.00 0.00 3.41
300 416 3.414549 TTGAGACCGCTGAAACAAAAC 57.585 42.857 0.00 0.00 0.00 2.43
344 460 3.518634 AAAAACACACGTCCTGCATTT 57.481 38.095 0.00 0.00 0.00 2.32
455 582 2.027073 TTCATCTCACGTGCGTGCC 61.027 57.895 18.54 0.00 45.04 5.01
725 856 1.082756 GGTTTGTTCGCTCGCAGTG 60.083 57.895 0.00 0.00 0.00 3.66
791 922 3.933900 GAAGGCATGTGCGTGCGTG 62.934 63.158 11.57 0.00 45.97 5.34
792 923 3.726517 GAAGGCATGTGCGTGCGT 61.727 61.111 9.87 7.88 45.97 5.24
793 924 4.465512 GGAAGGCATGTGCGTGCG 62.466 66.667 9.87 0.00 45.97 5.34
794 925 3.044059 GAGGAAGGCATGTGCGTGC 62.044 63.158 7.78 7.78 44.31 5.34
795 926 2.401766 GGAGGAAGGCATGTGCGTG 61.402 63.158 0.51 0.00 43.26 5.34
796 927 2.045926 GGAGGAAGGCATGTGCGT 60.046 61.111 0.00 0.00 43.26 5.24
797 928 3.197790 CGGAGGAAGGCATGTGCG 61.198 66.667 0.00 0.00 43.26 5.34
798 929 3.512516 GCGGAGGAAGGCATGTGC 61.513 66.667 0.00 0.00 41.14 4.57
799 930 2.110967 CAGCGGAGGAAGGCATGTG 61.111 63.158 0.00 0.00 0.00 3.21
800 931 2.270205 CAGCGGAGGAAGGCATGT 59.730 61.111 0.00 0.00 0.00 3.21
807 938 3.760035 GGACGAGCAGCGGAGGAA 61.760 66.667 4.06 0.00 46.49 3.36
987 1118 3.790437 CCCATGCAGGAGAGCCGT 61.790 66.667 0.00 0.00 41.22 5.68
1091 1225 4.191485 CGACGCGCATCACCGAAC 62.191 66.667 5.73 0.00 0.00 3.95
1341 1476 1.131638 GCATCCCATCAGGTAGGACA 58.868 55.000 0.00 0.00 36.75 4.02
1361 1496 2.597510 AACAAGGACAAGGGCCGC 60.598 61.111 0.00 0.00 0.00 6.53
1362 1497 2.268076 CCAACAAGGACAAGGGCCG 61.268 63.158 0.00 0.00 41.22 6.13
1363 1498 1.152830 TCCAACAAGGACAAGGGCC 59.847 57.895 0.00 0.00 43.07 5.80
1364 1499 4.920828 TCCAACAAGGACAAGGGC 57.079 55.556 0.00 0.00 43.07 5.19
1372 1507 0.178935 ACCCACCCAATCCAACAAGG 60.179 55.000 0.00 0.00 39.47 3.61
1373 1508 1.256812 GACCCACCCAATCCAACAAG 58.743 55.000 0.00 0.00 0.00 3.16
1374 1509 0.558220 TGACCCACCCAATCCAACAA 59.442 50.000 0.00 0.00 0.00 2.83
1375 1510 0.112218 CTGACCCACCCAATCCAACA 59.888 55.000 0.00 0.00 0.00 3.33
1376 1511 0.611896 CCTGACCCACCCAATCCAAC 60.612 60.000 0.00 0.00 0.00 3.77
1377 1512 1.773635 CCTGACCCACCCAATCCAA 59.226 57.895 0.00 0.00 0.00 3.53
1378 1513 2.237965 CCCTGACCCACCCAATCCA 61.238 63.158 0.00 0.00 0.00 3.41
1379 1514 2.238701 ACCCTGACCCACCCAATCC 61.239 63.158 0.00 0.00 0.00 3.01
1441 1576 5.127845 AGCAAATCGAGTCATTTCCTAGAGA 59.872 40.000 0.00 0.00 0.00 3.10
1660 1800 9.438228 TGGTGATGTTTAAGATTTATCGTGTTA 57.562 29.630 0.00 0.00 0.00 2.41
1750 1890 5.156608 TGACATCACATCAGAACTGACAT 57.843 39.130 6.67 0.00 43.11 3.06
1751 1891 4.605640 TGACATCACATCAGAACTGACA 57.394 40.909 6.67 0.00 43.11 3.58
1752 1892 6.312487 CAATTGACATCACATCAGAACTGAC 58.688 40.000 6.67 0.00 43.11 3.51
1753 1893 5.413523 CCAATTGACATCACATCAGAACTGA 59.586 40.000 7.12 6.98 44.59 3.41
1754 1894 5.182570 ACCAATTGACATCACATCAGAACTG 59.817 40.000 7.12 0.00 0.00 3.16
1755 1895 5.319453 ACCAATTGACATCACATCAGAACT 58.681 37.500 7.12 0.00 0.00 3.01
1756 1896 5.413833 AGACCAATTGACATCACATCAGAAC 59.586 40.000 7.12 0.00 0.00 3.01
1757 1897 5.413523 CAGACCAATTGACATCACATCAGAA 59.586 40.000 7.12 0.00 0.00 3.02
1758 1898 4.939439 CAGACCAATTGACATCACATCAGA 59.061 41.667 7.12 0.00 0.00 3.27
1759 1899 4.095932 CCAGACCAATTGACATCACATCAG 59.904 45.833 7.12 0.00 0.00 2.90
1760 1900 4.011698 CCAGACCAATTGACATCACATCA 58.988 43.478 7.12 0.00 0.00 3.07
1761 1901 3.181493 GCCAGACCAATTGACATCACATC 60.181 47.826 7.12 0.00 0.00 3.06
1791 1943 5.945784 TGAAGTGGCTTATATGTTTTGAGCT 59.054 36.000 0.00 0.00 33.96 4.09
1833 1985 9.577110 GCATCTCTCTCAGATAAGATTGATTAG 57.423 37.037 0.00 0.00 40.20 1.73
1881 2033 5.123820 GCAACTAGGATGAACTGCATTGTAA 59.876 40.000 0.00 0.00 37.34 2.41
2436 4049 2.640184 GCTTCCCCATACAACTGGTAC 58.360 52.381 0.00 0.00 34.07 3.34
2486 4102 4.876679 GCCCAGTTACCTTCACTTCTAATC 59.123 45.833 0.00 0.00 0.00 1.75
2491 4107 2.561478 TGCCCAGTTACCTTCACTTC 57.439 50.000 0.00 0.00 0.00 3.01
2508 4124 3.271729 CAGCATGAGGATCCAGATATGC 58.728 50.000 23.67 23.67 39.69 3.14
2602 4218 1.416401 TGAAGAGGTCACGGCTTTCTT 59.584 47.619 0.00 0.00 0.00 2.52
2691 4307 6.688073 TTCTTCTTCTAGACCAGTCCAAAT 57.312 37.500 0.00 0.00 0.00 2.32
2962 4578 4.002906 ACCTCAACTAACGAAGCATGAA 57.997 40.909 0.00 0.00 0.00 2.57
3012 4628 4.826274 TCAGTATCCCTTGTGAAAGAGG 57.174 45.455 0.00 0.00 0.00 3.69
3197 4813 5.072741 AGCTGAAATTTGGCTGTTCTCTTA 58.927 37.500 12.62 0.00 34.82 2.10
3306 4925 7.132694 TGTATGAAACAATATGCGATCATCC 57.867 36.000 0.00 0.00 34.29 3.51
3543 5164 0.106469 TGCCTTTAGGTGTGTTGGCA 60.106 50.000 0.00 0.00 46.59 4.92
3993 5614 0.402121 GAGCCCTCACTTTGAAGGGT 59.598 55.000 9.11 1.10 41.05 4.34
4168 5789 7.888021 TGTACTGTAAACTGATCCCATTTCAAT 59.112 33.333 0.00 0.00 0.00 2.57
4216 5837 1.637553 AGTCCTCATGGCTTCCAACAT 59.362 47.619 0.00 0.00 36.95 2.71
4231 5852 0.767375 ACAGATTGTGGTGCAGTCCT 59.233 50.000 0.00 0.00 34.77 3.85
4283 5904 2.355513 CCACTAGAAATGCCTGAGTGCT 60.356 50.000 0.00 0.00 36.92 4.40
4448 6069 6.141369 CAGTTTCTTTTTCTCGAAATCAGCAC 59.859 38.462 0.00 0.00 32.43 4.40
4569 6211 0.172803 CGTTGGTAGTAGGCTTCGCT 59.827 55.000 0.00 0.00 0.00 4.93
4803 6445 3.065371 CAGTTAGATCATGTTTTCCGGCC 59.935 47.826 0.00 0.00 0.00 6.13
4990 6635 1.693627 ACTACTAGTGGAGATGCCCG 58.306 55.000 13.86 0.00 34.97 6.13
5039 6684 0.656259 CAATCTGCTCATCCTGTGCG 59.344 55.000 0.00 0.00 39.51 5.34
5042 6687 3.607741 CAAGACAATCTGCTCATCCTGT 58.392 45.455 0.00 0.00 0.00 4.00
5065 6710 7.779798 ACACTTTATTACACATATCCAAGCCAT 59.220 33.333 0.00 0.00 0.00 4.40
5148 6800 0.106217 CCACCACCTGAAAACCCTGT 60.106 55.000 0.00 0.00 0.00 4.00
5192 6844 0.904865 ATGGACCGAGGACAGCTTCA 60.905 55.000 0.00 0.00 0.00 3.02
5280 6954 0.458543 TCTTTCTCACGCATCCGAGC 60.459 55.000 0.00 0.00 38.29 5.03
5682 7356 4.338118 ACTTGCCTTTTTCTTGTCGATTCA 59.662 37.500 0.00 0.00 0.00 2.57
5686 7360 5.757886 CATTACTTGCCTTTTTCTTGTCGA 58.242 37.500 0.00 0.00 0.00 4.20
5725 7399 9.917887 AGCGGAGGTAATACTATTATACAGTAT 57.082 33.333 0.00 0.00 40.19 2.12
5751 7425 8.450578 ACTTGTGACAAGACAATTAATTCAGA 57.549 30.769 30.03 0.00 35.32 3.27
5832 8342 5.932619 ATAAAATGAAAGCTGGGGGTAAC 57.067 39.130 0.00 0.00 0.00 2.50
5841 8351 6.248433 TGACTCCCTCAATAAAATGAAAGCT 58.752 36.000 0.00 0.00 0.00 3.74
5850 8360 5.534654 CCAGTTTGTTGACTCCCTCAATAAA 59.465 40.000 2.06 2.06 43.74 1.40
5950 8684 7.828717 TCATCTACTCCAATTTTGTGCAGAATA 59.171 33.333 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.