Multiple sequence alignment - TraesCS1B01G401200

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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 TraesCS1B01G401200 chr1B 100.000 5007 0 0 1 5007 631714235 631719241 0.000000e+00 9247.0
1 TraesCS1B01G401200 chr1B 81.853 2083 291 55 1990 4010 637952595 637954652 0.000000e+00 1672.0
2 TraesCS1B01G401200 chr1B 92.000 175 14 0 3836 4010 632721361 632721187 3.870000e-61 246.0
3 TraesCS1B01G401200 chr1A 91.671 4250 132 49 894 5001 551530279 551534448 0.000000e+00 5683.0
4 TraesCS1B01G401200 chr1A 85.388 2060 218 47 2017 4011 551788380 551786339 0.000000e+00 2060.0
5 TraesCS1B01G401200 chr1A 82.081 2076 291 44 1982 4010 554880292 554882333 0.000000e+00 1698.0
6 TraesCS1B01G401200 chr1A 88.517 836 73 17 1 833 551529454 551530269 0.000000e+00 990.0
7 TraesCS1B01G401200 chr1A 79.067 750 141 12 2341 3080 552892057 552891314 7.480000e-138 501.0
8 TraesCS1B01G401200 chr1D 93.669 3301 103 32 1759 5002 459520969 459524220 0.000000e+00 4841.0
9 TraesCS1B01G401200 chr1D 88.824 2890 192 49 2190 5002 459626678 459623843 0.000000e+00 3426.0
10 TraesCS1B01G401200 chr1D 87.929 1516 92 38 1 1487 459518160 459519613 0.000000e+00 1701.0
11 TraesCS1B01G401200 chr1D 81.722 2079 286 53 1982 4010 463007220 463009254 0.000000e+00 1648.0
12 TraesCS1B01G401200 chr1D 86.560 811 79 12 2047 2830 460196797 460195990 0.000000e+00 867.0
13 TraesCS1B01G401200 chr1D 79.228 751 138 14 2341 3080 461398261 461397518 1.610000e-139 507.0
14 TraesCS1B01G401200 chr1D 97.748 222 3 2 1557 1777 459519931 459520151 1.020000e-101 381.0
15 TraesCS1B01G401200 chr1D 74.745 392 63 19 323 696 441066414 441066787 5.230000e-30 143.0
16 TraesCS1B01G401200 chr3D 75.759 1712 348 44 2331 3993 575598226 575596533 0.000000e+00 800.0
17 TraesCS1B01G401200 chr3D 88.298 94 11 0 3 96 35725350 35725443 4.100000e-21 113.0
18 TraesCS1B01G401200 chr3A 74.914 1738 359 53 2331 4017 711079648 711077937 0.000000e+00 723.0
19 TraesCS1B01G401200 chr3B 74.971 1710 353 45 2331 3996 766377660 766379338 0.000000e+00 717.0
20 TraesCS1B01G401200 chr5D 76.438 713 119 25 3 692 267757752 267758438 1.730000e-89 340.0
21 TraesCS1B01G401200 chr2A 74.967 747 163 17 2348 3084 759577438 759576706 6.250000e-84 322.0
22 TraesCS1B01G401200 chr2B 73.641 736 171 17 2363 3087 775763672 775762949 3.840000e-66 263.0
23 TraesCS1B01G401200 chr5A 74.474 713 125 24 3 691 355019649 355020328 6.430000e-64 255.0
24 TraesCS1B01G401200 chr5B 86.826 167 20 2 3 169 302749627 302749791 8.560000e-43 185.0
25 TraesCS1B01G401200 chr6D 85.030 167 24 1 3 169 462684973 462684808 8.620000e-38 169.0
26 TraesCS1B01G401200 chrUn 89.474 95 9 1 3 96 39264681 39264587 8.810000e-23 119.0
27 TraesCS1B01G401200 chr6A 94.595 37 1 1 4035 4071 527525981 527526016 7.000000e-04 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 TraesCS1B01G401200 chr1B 631714235 631719241 5006 False 9247.000000 9247 100.000000 1 5007 1 chr1B.!!$F1 5006
1 TraesCS1B01G401200 chr1B 637952595 637954652 2057 False 1672.000000 1672 81.853000 1990 4010 1 chr1B.!!$F2 2020
2 TraesCS1B01G401200 chr1A 551529454 551534448 4994 False 3336.500000 5683 90.094000 1 5001 2 chr1A.!!$F2 5000
3 TraesCS1B01G401200 chr1A 551786339 551788380 2041 True 2060.000000 2060 85.388000 2017 4011 1 chr1A.!!$R1 1994
4 TraesCS1B01G401200 chr1A 554880292 554882333 2041 False 1698.000000 1698 82.081000 1982 4010 1 chr1A.!!$F1 2028
5 TraesCS1B01G401200 chr1A 552891314 552892057 743 True 501.000000 501 79.067000 2341 3080 1 chr1A.!!$R2 739
6 TraesCS1B01G401200 chr1D 459623843 459626678 2835 True 3426.000000 3426 88.824000 2190 5002 1 chr1D.!!$R1 2812
7 TraesCS1B01G401200 chr1D 459518160 459524220 6060 False 2307.666667 4841 93.115333 1 5002 3 chr1D.!!$F3 5001
8 TraesCS1B01G401200 chr1D 463007220 463009254 2034 False 1648.000000 1648 81.722000 1982 4010 1 chr1D.!!$F2 2028
9 TraesCS1B01G401200 chr1D 460195990 460196797 807 True 867.000000 867 86.560000 2047 2830 1 chr1D.!!$R2 783
10 TraesCS1B01G401200 chr1D 461397518 461398261 743 True 507.000000 507 79.228000 2341 3080 1 chr1D.!!$R3 739
11 TraesCS1B01G401200 chr3D 575596533 575598226 1693 True 800.000000 800 75.759000 2331 3993 1 chr3D.!!$R1 1662
12 TraesCS1B01G401200 chr3A 711077937 711079648 1711 True 723.000000 723 74.914000 2331 4017 1 chr3A.!!$R1 1686
13 TraesCS1B01G401200 chr3B 766377660 766379338 1678 False 717.000000 717 74.971000 2331 3996 1 chr3B.!!$F1 1665
14 TraesCS1B01G401200 chr5D 267757752 267758438 686 False 340.000000 340 76.438000 3 692 1 chr5D.!!$F1 689
15 TraesCS1B01G401200 chr2A 759576706 759577438 732 True 322.000000 322 74.967000 2348 3084 1 chr2A.!!$R1 736
16 TraesCS1B01G401200 chr2B 775762949 775763672 723 True 263.000000 263 73.641000 2363 3087 1 chr2B.!!$R1 724
17 TraesCS1B01G401200 chr5A 355019649 355020328 679 False 255.000000 255 74.474000 3 691 1 chr5A.!!$F1 688

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
366 376 0.526662 CCTCGTCAGCGGTTCTAGTT 59.473 55.0 0.00 0.0 38.89 2.24 F
1110 1157 0.392193 ATCGGCTGCTGAAACCTCTG 60.392 55.0 16.13 0.0 0.00 3.35 F
1547 1915 0.535335 GGTCGAGCCCACAACATCTA 59.465 55.0 2.39 0.0 0.00 1.98 F
2856 4154 0.034186 TCAATCCTTGGGCGCTTGAT 60.034 50.0 7.64 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1923 0.112995 AGCACAGCTGGAATCCCAAA 59.887 50.000 19.93 0.0 42.98 3.28 R
2842 4140 1.972872 ATCTTATCAAGCGCCCAAGG 58.027 50.000 2.29 0.0 0.00 3.61 R
3346 4711 4.037923 GGAGTGTTGGCATTCTGAAAAAGA 59.962 41.667 0.00 0.0 32.70 2.52 R
4511 5987 0.533032 AAGCTTCACCCGTCTAGAGC 59.467 55.000 0.00 0.0 0.00 4.09 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
158 159 1.336755 ACGGTGGTTGCTTCACATTTC 59.663 47.619 6.89 0.00 36.90 2.17
170 171 2.766313 TCACATTTCTGTTGTCTCCGG 58.234 47.619 0.00 0.00 31.62 5.14
171 172 2.104111 TCACATTTCTGTTGTCTCCGGT 59.896 45.455 0.00 0.00 31.62 5.28
220 221 1.597027 GCAGTAGTTGGCGGTGTGT 60.597 57.895 0.00 0.00 0.00 3.72
252 253 4.007457 ACGAAGTAGTAGCCGCCA 57.993 55.556 0.00 0.00 41.94 5.69
339 349 3.030652 GTGGTTTGGTCACGGCTG 58.969 61.111 0.00 0.00 0.00 4.85
354 364 1.293498 GCTGCCTTCTTCCTCGTCA 59.707 57.895 0.00 0.00 0.00 4.35
362 372 0.894184 TCTTCCTCGTCAGCGGTTCT 60.894 55.000 0.00 0.00 38.89 3.01
366 376 0.526662 CCTCGTCAGCGGTTCTAGTT 59.473 55.000 0.00 0.00 38.89 2.24
367 377 1.067776 CCTCGTCAGCGGTTCTAGTTT 60.068 52.381 0.00 0.00 38.89 2.66
371 381 0.669318 TCAGCGGTTCTAGTTTGCCG 60.669 55.000 10.82 10.82 46.17 5.69
373 383 3.035576 GCGGTTCTAGTTTGCCGGC 62.036 63.158 22.73 22.73 43.90 6.13
400 410 2.044946 ACGAGGGGCTGCAAATCC 60.045 61.111 0.50 0.00 0.00 3.01
401 411 2.045045 CGAGGGGCTGCAAATCCA 60.045 61.111 0.50 0.00 0.00 3.41
406 416 2.283821 GGCTGCAAATCCACCCCA 60.284 61.111 0.50 0.00 0.00 4.96
480 490 4.096003 AGCTGTATTGGCGGCCGT 62.096 61.111 28.70 9.45 41.44 5.68
721 731 5.627499 TTTTAGAGCACACCAACATCATC 57.373 39.130 0.00 0.00 0.00 2.92
722 732 4.558226 TTAGAGCACACCAACATCATCT 57.442 40.909 0.00 0.00 0.00 2.90
723 733 5.675684 TTAGAGCACACCAACATCATCTA 57.324 39.130 0.00 0.00 0.00 1.98
724 734 4.558226 AGAGCACACCAACATCATCTAA 57.442 40.909 0.00 0.00 0.00 2.10
725 735 5.108187 AGAGCACACCAACATCATCTAAT 57.892 39.130 0.00 0.00 0.00 1.73
757 767 2.214376 TGGATCATCGTTTTTGGGCT 57.786 45.000 0.00 0.00 0.00 5.19
768 778 2.301577 TTTTGGGCTTTCGTGGTTTG 57.698 45.000 0.00 0.00 0.00 2.93
772 782 1.135333 TGGGCTTTCGTGGTTTGAAAC 59.865 47.619 0.00 0.00 32.29 2.78
861 871 6.291743 CGATCCGCTAGTCGTCTTCTATATAC 60.292 46.154 5.97 0.00 36.19 1.47
866 876 6.089283 CGCTAGTCGTCTTCTATATACGAGTT 59.911 42.308 9.84 0.67 44.50 3.01
867 877 7.359097 CGCTAGTCGTCTTCTATATACGAGTTT 60.359 40.741 9.84 0.00 44.50 2.66
868 878 8.281893 GCTAGTCGTCTTCTATATACGAGTTTT 58.718 37.037 9.84 0.00 44.50 2.43
871 881 9.323985 AGTCGTCTTCTATATACGAGTTTTACT 57.676 33.333 0.00 0.00 44.50 2.24
943 954 9.067986 CAACCTCTCCCCTCATAATAAATAAAC 57.932 37.037 0.00 0.00 0.00 2.01
1055 1078 2.338620 CCGATTCGCCGCTATCCA 59.661 61.111 0.00 0.00 0.00 3.41
1110 1157 0.392193 ATCGGCTGCTGAAACCTCTG 60.392 55.000 16.13 0.00 0.00 3.35
1203 1250 2.332063 ACTGATCTAATTGCACCCCG 57.668 50.000 0.00 0.00 0.00 5.73
1320 1386 3.787001 CCCCTCCGGCCAACTCTC 61.787 72.222 2.24 0.00 0.00 3.20
1344 1410 4.082408 TCAAATCGTCAGACCGTATTCTGT 60.082 41.667 0.00 0.00 43.19 3.41
1509 1616 1.072965 CCTCTGTCCTCTGCCAGTTTT 59.927 52.381 0.00 0.00 0.00 2.43
1545 1913 3.890674 GGTCGAGCCCACAACATC 58.109 61.111 2.39 0.00 0.00 3.06
1546 1914 1.296715 GGTCGAGCCCACAACATCT 59.703 57.895 2.39 0.00 0.00 2.90
1547 1915 0.535335 GGTCGAGCCCACAACATCTA 59.465 55.000 2.39 0.00 0.00 1.98
1548 1916 1.139058 GGTCGAGCCCACAACATCTAT 59.861 52.381 2.39 0.00 0.00 1.98
1549 1917 2.364324 GGTCGAGCCCACAACATCTATA 59.636 50.000 2.39 0.00 0.00 1.31
1550 1918 3.006967 GGTCGAGCCCACAACATCTATAT 59.993 47.826 2.39 0.00 0.00 0.86
1551 1919 4.219944 GGTCGAGCCCACAACATCTATATA 59.780 45.833 2.39 0.00 0.00 0.86
1552 1920 5.162075 GTCGAGCCCACAACATCTATATAC 58.838 45.833 0.00 0.00 0.00 1.47
1553 1921 4.219944 TCGAGCCCACAACATCTATATACC 59.780 45.833 0.00 0.00 0.00 2.73
1554 1922 4.021456 CGAGCCCACAACATCTATATACCA 60.021 45.833 0.00 0.00 0.00 3.25
1555 1923 5.337571 CGAGCCCACAACATCTATATACCAT 60.338 44.000 0.00 0.00 0.00 3.55
1641 2009 5.121768 CCAACAGTTCCCGTATCAGTAAAAG 59.878 44.000 0.00 0.00 0.00 2.27
1783 2988 0.901827 TGGTGATGCTCTAAGGCGAA 59.098 50.000 0.00 0.00 34.52 4.70
1843 3048 4.322499 GGTACTTGAAGCACAACTAGGCTA 60.322 45.833 0.00 0.00 40.01 3.93
1844 3049 3.931578 ACTTGAAGCACAACTAGGCTAG 58.068 45.455 19.83 19.83 40.01 3.42
1845 3050 3.325135 ACTTGAAGCACAACTAGGCTAGT 59.675 43.478 21.30 21.30 40.01 2.57
1846 3051 4.527038 ACTTGAAGCACAACTAGGCTAGTA 59.473 41.667 26.47 6.52 40.01 1.82
1847 3052 4.720649 TGAAGCACAACTAGGCTAGTAG 57.279 45.455 26.47 19.28 40.01 2.57
1848 3053 3.119101 TGAAGCACAACTAGGCTAGTAGC 60.119 47.826 26.47 26.36 40.01 3.58
1849 3054 7.586390 TTGAAGCACAACTAGGCTAGTAGCC 62.586 48.000 30.63 30.63 46.67 3.93
1985 3195 5.410439 GGTTATTCCAGCTTTCTTTCGTACA 59.590 40.000 0.00 0.00 35.97 2.90
1986 3196 6.093633 GGTTATTCCAGCTTTCTTTCGTACAT 59.906 38.462 0.00 0.00 35.97 2.29
2045 3255 5.220777 CCGTCAGAGTTCATAGTTCTCTCTC 60.221 48.000 0.00 0.00 36.57 3.20
2573 3865 8.613922 AAGGAAAACCCATCTCATTGATAAAT 57.386 30.769 0.00 0.00 37.41 1.40
2842 4140 2.415893 CGCTTTTCACCCCACATCAATC 60.416 50.000 0.00 0.00 0.00 2.67
2856 4154 0.034186 TCAATCCTTGGGCGCTTGAT 60.034 50.000 7.64 0.00 0.00 2.57
3257 4586 5.237779 CGTAGTGAGGTATGTGTTGGTTTTT 59.762 40.000 0.00 0.00 0.00 1.94
3260 4606 7.833285 AGTGAGGTATGTGTTGGTTTTTAAT 57.167 32.000 0.00 0.00 0.00 1.40
3263 4609 7.381139 GTGAGGTATGTGTTGGTTTTTAATGTG 59.619 37.037 0.00 0.00 0.00 3.21
3346 4711 9.995003 TGTTGAAATAAAGCATGGTTAATCTTT 57.005 25.926 11.15 8.19 33.80 2.52
3427 4802 4.219115 TGGAAATTGCACTCCTTAAACCA 58.781 39.130 9.47 0.00 32.51 3.67
3546 4939 9.201989 TGTACATCTCTCAGAGTGGTATTAATT 57.798 33.333 0.36 0.00 0.00 1.40
3780 5190 1.276415 GAGAGAGCACATTCACTCGC 58.724 55.000 0.00 0.00 37.99 5.03
3822 5241 6.865834 AACCTATGGCTATGATAGGAGAAG 57.134 41.667 13.82 0.00 43.73 2.85
4026 5472 0.933097 GTAGATCATGGCTGTGTGCG 59.067 55.000 0.00 0.00 44.05 5.34
4028 5474 1.022982 AGATCATGGCTGTGTGCGTG 61.023 55.000 0.00 0.00 44.05 5.34
4037 5483 1.227793 TGTGTGCGTGGCTTGATGA 60.228 52.632 0.00 0.00 0.00 2.92
4103 5549 2.309528 TCATTGACGTGGTATGGAGC 57.690 50.000 0.00 0.00 0.00 4.70
4223 5680 8.087750 GGAATGAGTTATCTGTTCCTAGAGATG 58.912 40.741 0.00 0.00 37.66 2.90
4266 5723 8.494016 ACAATATTAAGAGATTATTAGCGGCC 57.506 34.615 0.00 0.00 0.00 6.13
4439 5906 1.606668 CGTGGGCAGTTTAGCTTTTGA 59.393 47.619 0.00 0.00 34.17 2.69
4511 5987 4.135306 TGTAGCTTAGATGGTCTAGGACG 58.865 47.826 0.00 0.00 32.65 4.79
4533 6009 1.187087 CTAGACGGGTGAAGCTTCCT 58.813 55.000 23.42 13.91 0.00 3.36
4600 6091 0.323087 TGCAGCATCAGGTTGAGCAT 60.323 50.000 0.00 0.00 0.00 3.79
4608 6099 2.507484 TCAGGTTGAGCATGGTGAAAG 58.493 47.619 0.00 0.00 0.00 2.62
4609 6100 2.158623 TCAGGTTGAGCATGGTGAAAGT 60.159 45.455 0.00 0.00 0.00 2.66
4610 6101 3.072330 TCAGGTTGAGCATGGTGAAAGTA 59.928 43.478 0.00 0.00 0.00 2.24
4611 6102 3.438087 CAGGTTGAGCATGGTGAAAGTAG 59.562 47.826 0.00 0.00 0.00 2.57
4612 6103 3.073062 AGGTTGAGCATGGTGAAAGTAGT 59.927 43.478 0.00 0.00 0.00 2.73
4613 6104 3.821033 GGTTGAGCATGGTGAAAGTAGTT 59.179 43.478 0.00 0.00 0.00 2.24
4614 6105 4.278419 GGTTGAGCATGGTGAAAGTAGTTT 59.722 41.667 0.00 0.00 0.00 2.66
4615 6106 5.215160 GTTGAGCATGGTGAAAGTAGTTTG 58.785 41.667 0.00 0.00 0.00 2.93
4616 6107 4.460263 TGAGCATGGTGAAAGTAGTTTGT 58.540 39.130 0.00 0.00 0.00 2.83
4632 6132 5.341407 AGTTTGTTTTGTTGTTTGCAGTG 57.659 34.783 0.00 0.00 0.00 3.66
4661 6161 4.394920 TCTGCCAAATTAAAGAGCGTTAGG 59.605 41.667 0.00 0.00 0.00 2.69
4709 6213 6.926313 TGTTATAACAAGGGCACCAAAATAC 58.074 36.000 15.92 0.00 43.06 1.89
4710 6214 6.349445 TGTTATAACAAGGGCACCAAAATACG 60.349 38.462 15.92 0.00 43.06 3.06
4730 6234 5.320549 ACGTATTCAGTCTCGGTAAATGT 57.679 39.130 0.00 0.00 0.00 2.71
4824 6332 0.895100 ATTGTGAACCGGCACTGCAT 60.895 50.000 12.61 1.41 39.49 3.96
4878 6408 3.517100 AGTTAGGCTGAGCATTCTTCTCA 59.483 43.478 6.82 0.00 38.16 3.27
4978 6515 1.140052 TCAACAAGAGAACGGGAAGCA 59.860 47.619 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 1.370051 GCTTTTTCGCCGGTGTCAC 60.370 57.895 16.01 0.00 0.00 3.67
171 172 0.249953 TAGCTTTTTCGCCGGTGTCA 60.250 50.000 16.01 0.00 0.00 3.58
336 346 0.739112 CTGACGAGGAAGAAGGCAGC 60.739 60.000 0.00 0.00 0.00 5.25
339 349 1.807573 CGCTGACGAGGAAGAAGGC 60.808 63.158 0.00 0.00 43.93 4.35
354 364 1.375523 CCGGCAAACTAGAACCGCT 60.376 57.895 0.00 0.00 44.29 5.52
406 416 0.911769 TGATGCCTCCTCCAAATCGT 59.088 50.000 0.00 0.00 0.00 3.73
461 471 2.190578 GGCCGCCAATACAGCTCT 59.809 61.111 3.91 0.00 0.00 4.09
466 476 4.787286 CCCACGGCCGCCAATACA 62.787 66.667 28.58 0.00 0.00 2.29
480 490 2.920912 ACGCCTTCTTCGACCCCA 60.921 61.111 0.00 0.00 0.00 4.96
518 528 2.591753 CACCCCATGATGTCGCCT 59.408 61.111 0.00 0.00 0.00 5.52
526 536 2.350895 CGCTTGACCACCCCATGA 59.649 61.111 0.00 0.00 0.00 3.07
701 711 4.558226 AGATGATGTTGGTGTGCTCTAA 57.442 40.909 0.00 0.00 0.00 2.10
702 712 5.675684 TTAGATGATGTTGGTGTGCTCTA 57.324 39.130 0.00 0.00 0.00 2.43
703 713 4.558226 TTAGATGATGTTGGTGTGCTCT 57.442 40.909 0.00 0.00 0.00 4.09
704 714 6.316140 TGTTATTAGATGATGTTGGTGTGCTC 59.684 38.462 0.00 0.00 0.00 4.26
705 715 6.179756 TGTTATTAGATGATGTTGGTGTGCT 58.820 36.000 0.00 0.00 0.00 4.40
706 716 6.435430 TGTTATTAGATGATGTTGGTGTGC 57.565 37.500 0.00 0.00 0.00 4.57
707 717 8.212317 TGATGTTATTAGATGATGTTGGTGTG 57.788 34.615 0.00 0.00 0.00 3.82
708 718 8.985315 ATGATGTTATTAGATGATGTTGGTGT 57.015 30.769 0.00 0.00 0.00 4.16
709 719 9.281371 AGATGATGTTATTAGATGATGTTGGTG 57.719 33.333 0.00 0.00 0.00 4.17
723 733 9.730705 AACGATGATCCAATAGATGATGTTATT 57.269 29.630 0.00 0.00 34.42 1.40
724 734 9.730705 AAACGATGATCCAATAGATGATGTTAT 57.269 29.630 0.00 0.00 34.42 1.89
725 735 9.559732 AAAACGATGATCCAATAGATGATGTTA 57.440 29.630 0.00 0.00 34.42 2.41
885 895 9.128404 ACCGATTCCTAGTAAAACTTTCTTTTT 57.872 29.630 0.00 0.00 33.27 1.94
886 896 8.687292 ACCGATTCCTAGTAAAACTTTCTTTT 57.313 30.769 0.00 0.00 0.00 2.27
887 897 9.212641 GTACCGATTCCTAGTAAAACTTTCTTT 57.787 33.333 0.00 0.00 0.00 2.52
888 898 7.543520 CGTACCGATTCCTAGTAAAACTTTCTT 59.456 37.037 0.00 0.00 0.00 2.52
889 899 7.031975 CGTACCGATTCCTAGTAAAACTTTCT 58.968 38.462 0.00 0.00 0.00 2.52
890 900 6.254373 CCGTACCGATTCCTAGTAAAACTTTC 59.746 42.308 0.00 0.00 0.00 2.62
891 901 6.101997 CCGTACCGATTCCTAGTAAAACTTT 58.898 40.000 0.00 0.00 0.00 2.66
892 902 5.394553 CCCGTACCGATTCCTAGTAAAACTT 60.395 44.000 0.00 0.00 0.00 2.66
980 1003 1.630369 TGGTGAAAGAGATCCCCTGTG 59.370 52.381 0.00 0.00 0.00 3.66
981 1004 2.044793 TGGTGAAAGAGATCCCCTGT 57.955 50.000 0.00 0.00 0.00 4.00
1320 1386 4.500837 CAGAATACGGTCTGACGATTTGAG 59.499 45.833 7.11 0.00 46.76 3.02
1344 1410 1.200519 CAGTCCAGGTCCCCGAAATA 58.799 55.000 0.00 0.00 0.00 1.40
1540 1647 8.677871 TGGAATCCCAAATGGTATATAGATGTT 58.322 33.333 0.00 0.00 40.09 2.71
1543 1911 7.185304 AGCTGGAATCCCAAATGGTATATAGAT 59.815 37.037 0.00 0.00 42.98 1.98
1544 1912 6.505344 AGCTGGAATCCCAAATGGTATATAGA 59.495 38.462 0.00 0.00 42.98 1.98
1545 1913 6.600822 CAGCTGGAATCCCAAATGGTATATAG 59.399 42.308 5.57 0.00 42.98 1.31
1546 1914 6.045459 ACAGCTGGAATCCCAAATGGTATATA 59.955 38.462 19.93 0.00 42.98 0.86
1547 1915 5.162947 ACAGCTGGAATCCCAAATGGTATAT 60.163 40.000 19.93 0.00 42.98 0.86
1548 1916 4.167892 ACAGCTGGAATCCCAAATGGTATA 59.832 41.667 19.93 0.00 42.98 1.47
1549 1917 3.052642 ACAGCTGGAATCCCAAATGGTAT 60.053 43.478 19.93 0.00 42.98 2.73
1550 1918 2.311542 ACAGCTGGAATCCCAAATGGTA 59.688 45.455 19.93 0.00 42.98 3.25
1551 1919 1.077663 ACAGCTGGAATCCCAAATGGT 59.922 47.619 19.93 0.00 42.98 3.55
1552 1920 1.479323 CACAGCTGGAATCCCAAATGG 59.521 52.381 19.93 0.00 42.98 3.16
1553 1921 1.134907 GCACAGCTGGAATCCCAAATG 60.135 52.381 19.93 3.90 42.98 2.32
1554 1922 1.188863 GCACAGCTGGAATCCCAAAT 58.811 50.000 19.93 0.00 42.98 2.32
1555 1923 0.112995 AGCACAGCTGGAATCCCAAA 59.887 50.000 19.93 0.00 42.98 3.28
1641 2009 3.774734 ACTTCCCCTAACCCACAATTTC 58.225 45.455 0.00 0.00 0.00 2.17
1783 2988 8.050316 ACCTGAACTGATATCTCCCATATTTT 57.950 34.615 3.98 0.00 0.00 1.82
1843 3048 6.089808 AGTTCCCTTTAGTACTAGGCTACT 57.910 41.667 6.21 8.15 0.00 2.57
1844 3049 5.301551 GGAGTTCCCTTTAGTACTAGGCTAC 59.698 48.000 6.21 6.33 0.00 3.58
1845 3050 5.195349 AGGAGTTCCCTTTAGTACTAGGCTA 59.805 44.000 6.21 0.00 44.85 3.93
1846 3051 4.016386 AGGAGTTCCCTTTAGTACTAGGCT 60.016 45.833 6.21 0.00 44.85 4.58
1847 3052 4.288398 AGGAGTTCCCTTTAGTACTAGGC 58.712 47.826 6.21 0.00 44.85 3.93
1985 3195 9.428097 GCCTGAACAAGAAAAGATAAAAATGAT 57.572 29.630 0.00 0.00 0.00 2.45
1986 3196 8.420222 TGCCTGAACAAGAAAAGATAAAAATGA 58.580 29.630 0.00 0.00 0.00 2.57
2045 3255 4.445052 TGCTCATGAAACTCAAATTTTGCG 59.555 37.500 4.19 0.87 0.00 4.85
2842 4140 1.972872 ATCTTATCAAGCGCCCAAGG 58.027 50.000 2.29 0.00 0.00 3.61
2856 4154 8.296713 GGCACAGATGTAAACTTTTCAATCTTA 58.703 33.333 0.00 0.00 0.00 2.10
3260 4606 8.554835 TCCTTATAATTTGAATCGTTGACACA 57.445 30.769 0.00 0.00 0.00 3.72
3263 4609 7.693952 TGCTCCTTATAATTTGAATCGTTGAC 58.306 34.615 0.00 0.00 0.00 3.18
3346 4711 4.037923 GGAGTGTTGGCATTCTGAAAAAGA 59.962 41.667 0.00 0.00 32.70 2.52
3347 4712 4.202141 TGGAGTGTTGGCATTCTGAAAAAG 60.202 41.667 0.00 0.00 32.70 2.27
3427 4802 5.133221 GCATCATAGTTTGGGGATAAGTGT 58.867 41.667 0.00 0.00 0.00 3.55
3822 5241 2.577450 GGAATTTGGCGACGTTACAAC 58.423 47.619 0.00 0.00 0.00 3.32
4026 5472 1.034292 GGGCCTCTTCATCAAGCCAC 61.034 60.000 0.84 0.00 45.72 5.01
4028 5474 1.821332 CGGGCCTCTTCATCAAGCC 60.821 63.158 0.84 0.00 43.09 4.35
4037 5483 2.076803 GGATTACCCCGGGCCTCTT 61.077 63.158 17.73 0.00 0.00 2.85
4103 5549 5.447954 CCAGTATCTATTGCTACCGAGATCG 60.448 48.000 0.00 0.00 39.44 3.69
4262 5719 1.094785 ATCTCCAATTCAAACGGCCG 58.905 50.000 26.86 26.86 0.00 6.13
4266 5723 4.728882 GCACTAGCATCTCCAATTCAAACG 60.729 45.833 0.00 0.00 41.58 3.60
4299 5756 5.437289 TGCCATTCAAAACTCTACAACAG 57.563 39.130 0.00 0.00 0.00 3.16
4511 5987 0.533032 AAGCTTCACCCGTCTAGAGC 59.467 55.000 0.00 0.00 0.00 4.09
4533 6009 1.672030 CGTCCCTTGCATGCACAGA 60.672 57.895 22.58 14.52 0.00 3.41
4600 6091 6.750148 ACAACAAAACAAACTACTTTCACCA 58.250 32.000 0.00 0.00 0.00 4.17
4608 6099 6.074034 ACACTGCAAACAACAAAACAAACTAC 60.074 34.615 0.00 0.00 0.00 2.73
4609 6100 5.986135 ACACTGCAAACAACAAAACAAACTA 59.014 32.000 0.00 0.00 0.00 2.24
4610 6101 4.813697 ACACTGCAAACAACAAAACAAACT 59.186 33.333 0.00 0.00 0.00 2.66
4611 6102 5.089396 ACACTGCAAACAACAAAACAAAC 57.911 34.783 0.00 0.00 0.00 2.93
4612 6103 6.128445 CCATACACTGCAAACAACAAAACAAA 60.128 34.615 0.00 0.00 0.00 2.83
4613 6104 5.349817 CCATACACTGCAAACAACAAAACAA 59.650 36.000 0.00 0.00 0.00 2.83
4614 6105 4.867047 CCATACACTGCAAACAACAAAACA 59.133 37.500 0.00 0.00 0.00 2.83
4615 6106 4.867608 ACCATACACTGCAAACAACAAAAC 59.132 37.500 0.00 0.00 0.00 2.43
4616 6107 5.078411 ACCATACACTGCAAACAACAAAA 57.922 34.783 0.00 0.00 0.00 2.44
4652 6152 3.431233 GCCGGTAATAATTCCTAACGCTC 59.569 47.826 1.90 0.00 0.00 5.03
4661 6161 4.764823 TGATGGATTGGCCGGTAATAATTC 59.235 41.667 1.90 0.00 40.66 2.17
4707 6211 6.441093 ACATTTACCGAGACTGAATACGTA 57.559 37.500 0.00 0.00 0.00 3.57
4708 6212 5.320549 ACATTTACCGAGACTGAATACGT 57.679 39.130 0.00 0.00 0.00 3.57
4709 6213 4.738740 GGACATTTACCGAGACTGAATACG 59.261 45.833 0.00 0.00 0.00 3.06
4710 6214 5.903810 AGGACATTTACCGAGACTGAATAC 58.096 41.667 0.00 0.00 0.00 1.89
4730 6234 5.766174 ACTTTAACCTATTTTGTCGCAAGGA 59.234 36.000 0.00 0.00 38.47 3.36
4824 6332 6.627287 CGTCCATTTCTCTCTGGTGTACATTA 60.627 42.308 0.00 0.00 34.03 1.90
4878 6408 9.367444 GCAAATACAGTAGTTGACTTGTATAGT 57.633 33.333 22.08 0.00 40.71 2.12
4978 6515 3.771577 AAATCGAGAGTGGTGGTTCTT 57.228 42.857 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.