Multiple sequence alignment - TraesCS7A01G305700

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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 TraesCS7A01G305700 chr7A 100.000 5306 0 0 1 5306 430566675 430561370 0.000000e+00 9799.0
1 TraesCS7A01G305700 chr7A 92.958 71 5 0 3942 4012 712180956 712181026 2.610000e-18 104.0
2 TraesCS7A01G305700 chr7B 95.870 3898 140 7 834 4721 376937702 376933816 0.000000e+00 6287.0
3 TraesCS7A01G305700 chr7B 92.536 844 48 6 1 832 376938570 376937730 0.000000e+00 1195.0
4 TraesCS7A01G305700 chr7B 91.218 501 37 4 4808 5306 376933495 376933000 0.000000e+00 675.0
5 TraesCS7A01G305700 chr7B 79.412 136 21 6 4546 4677 402824680 402824812 7.320000e-14 89.8
6 TraesCS7A01G305700 chr7B 94.000 50 3 0 831 880 376937660 376937611 5.700000e-10 76.8
7 TraesCS7A01G305700 chr7D 95.062 3868 152 21 834 4678 382527025 382523174 0.000000e+00 6048.0
8 TraesCS7A01G305700 chr7D 93.060 634 34 3 1 625 382532149 382531517 0.000000e+00 918.0
9 TraesCS7A01G305700 chr7D 88.034 468 50 3 4831 5297 382522880 382522418 2.790000e-152 549.0
10 TraesCS7A01G305700 chr7D 91.045 134 10 2 623 755 382527345 382527213 4.220000e-41 180.0
11 TraesCS7A01G305700 chr7D 90.141 71 7 0 3942 4012 618489480 618489550 5.660000e-15 93.5
12 TraesCS7A01G305700 chr7D 92.000 50 4 0 831 880 382526983 382526934 2.650000e-08 71.3
13 TraesCS7A01G305700 chr1D 90.510 843 65 7 3 834 54021449 54020611 0.000000e+00 1099.0
14 TraesCS7A01G305700 chr1D 80.741 135 21 4 4545 4676 454768609 454768741 3.380000e-17 100.0
15 TraesCS7A01G305700 chr1D 79.856 139 18 9 4546 4678 252487517 252487383 5.660000e-15 93.5
16 TraesCS7A01G305700 chr2D 90.920 815 61 5 1 806 517078329 517079139 0.000000e+00 1083.0
17 TraesCS7A01G305700 chr2D 84.524 84 10 3 4544 4624 575375824 575375907 4.410000e-11 80.5
18 TraesCS7A01G305700 chr6A 86.972 852 73 16 1 832 579378026 579378859 0.000000e+00 924.0
19 TraesCS7A01G305700 chr1A 89.474 684 60 5 1 675 53486836 53486156 0.000000e+00 854.0
20 TraesCS7A01G305700 chr1A 87.379 618 57 11 1 606 551172441 551173049 0.000000e+00 689.0
21 TraesCS7A01G305700 chr1A 90.196 153 12 2 682 832 53474526 53474375 4.190000e-46 196.0
22 TraesCS7A01G305700 chr5A 85.664 844 78 22 1 832 53579558 53580370 0.000000e+00 848.0
23 TraesCS7A01G305700 chr6D 87.410 556 54 8 289 832 19995364 19995915 4.510000e-175 625.0
24 TraesCS7A01G305700 chr6D 92.308 130 9 1 114 242 19995227 19995356 3.260000e-42 183.0
25 TraesCS7A01G305700 chr6D 82.609 92 10 4 4546 4636 310527567 310527653 5.700000e-10 76.8
26 TraesCS7A01G305700 chr2A 91.632 239 20 0 1240 1478 3515363 3515601 1.100000e-86 331.0
27 TraesCS7A01G305700 chr2A 84.706 85 10 3 4555 4638 778790444 778790526 1.220000e-11 82.4
28 TraesCS7A01G305700 chr4A 91.213 239 21 0 1240 1478 23595868 23596106 5.120000e-85 326.0
29 TraesCS7A01G305700 chr4A 83.178 107 17 1 3932 4037 532796834 532796940 4.370000e-16 97.1
30 TraesCS7A01G305700 chr3B 91.200 125 11 0 1210 1334 805395910 805396034 2.540000e-38 171.0
31 TraesCS7A01G305700 chr4D 80.282 142 24 3 3937 4078 397094315 397094178 2.610000e-18 104.0
32 TraesCS7A01G305700 chr4D 86.420 81 11 0 3932 4012 63585457 63585377 7.320000e-14 89.8
33 TraesCS7A01G305700 chr5B 79.412 136 23 4 4547 4678 673048510 673048376 2.040000e-14 91.6
34 TraesCS7A01G305700 chr4B 83.168 101 16 1 3937 4037 489088139 489088040 2.040000e-14 91.6
35 TraesCS7A01G305700 chr4B 82.418 91 12 4 4549 4636 115882868 115882779 5.700000e-10 76.8
36 TraesCS7A01G305700 chr1B 88.732 71 8 0 3942 4012 687276774 687276704 2.630000e-13 87.9


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 TraesCS7A01G305700 chr7A 430561370 430566675 5305 True 9799.000 9799 100.00000 1 5306 1 chr7A.!!$R1 5305
1 TraesCS7A01G305700 chr7B 376933000 376938570 5570 True 2058.450 6287 93.40600 1 5306 4 chr7B.!!$R1 5305
2 TraesCS7A01G305700 chr7D 382522418 382527345 4927 True 1712.075 6048 91.53525 623 5297 4 chr7D.!!$R2 4674
3 TraesCS7A01G305700 chr7D 382531517 382532149 632 True 918.000 918 93.06000 1 625 1 chr7D.!!$R1 624
4 TraesCS7A01G305700 chr1D 54020611 54021449 838 True 1099.000 1099 90.51000 3 834 1 chr1D.!!$R1 831
5 TraesCS7A01G305700 chr2D 517078329 517079139 810 False 1083.000 1083 90.92000 1 806 1 chr2D.!!$F1 805
6 TraesCS7A01G305700 chr6A 579378026 579378859 833 False 924.000 924 86.97200 1 832 1 chr6A.!!$F1 831
7 TraesCS7A01G305700 chr1A 53486156 53486836 680 True 854.000 854 89.47400 1 675 1 chr1A.!!$R2 674
8 TraesCS7A01G305700 chr1A 551172441 551173049 608 False 689.000 689 87.37900 1 606 1 chr1A.!!$F1 605
9 TraesCS7A01G305700 chr5A 53579558 53580370 812 False 848.000 848 85.66400 1 832 1 chr5A.!!$F1 831
10 TraesCS7A01G305700 chr6D 19995227 19995915 688 False 404.000 625 89.85900 114 832 2 chr6D.!!$F2 718

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
155 156 1.071699 TGGCCAACCAGTGAACTACTC 59.928 52.381 0.61 0.0 42.67 2.59 F
1076 1233 0.191064 TCCACTCCACTCTCCCTGTT 59.809 55.000 0.00 0.0 0.00 3.16 F
1314 1474 0.744771 TGCTCGCGCTTCTCTCTCTA 60.745 55.000 5.56 0.0 36.97 2.43 F
1958 2118 0.891904 GCGGAGTTTGGTGGGCTAAA 60.892 55.000 0.00 0.0 0.00 1.85 F
3375 3535 0.815095 TCATCGCCGTGAAGAAGCTA 59.185 50.000 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 2090 0.392998 CCAAACTCCGCTGGTATGCT 60.393 55.000 0.00 0.00 0.00 3.79 R
2677 2837 0.110010 GCCAAGACTTGAAGCTTCGC 60.110 55.000 21.11 11.84 0.00 4.70 R
3240 3400 0.391395 CTGTGAAGCTCAGCCTCTGG 60.391 60.000 0.00 0.00 31.51 3.86 R
3422 3582 1.333308 CGTCTTGTGTGTCCATTTGCA 59.667 47.619 0.00 0.00 0.00 4.08 R
4801 5012 0.033894 ACGGGCCGGTATGGAAATTT 60.034 50.000 31.78 0.20 42.00 1.82 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
155 156 1.071699 TGGCCAACCAGTGAACTACTC 59.928 52.381 0.61 0.00 42.67 2.59
321 338 3.388024 ACACTACACTGTCAGGATGTGTT 59.612 43.478 4.53 0.00 43.53 3.32
370 387 4.636206 GGCATTTGTTCTACTAGAAGGTGG 59.364 45.833 0.00 0.00 34.42 4.61
504 529 9.788960 GTGAATCTTATGTATTCCAAAGAAACC 57.211 33.333 0.00 0.00 35.09 3.27
536 563 7.581213 TTGACAACAATTGGTGAGTTAGAAT 57.419 32.000 29.74 4.47 35.97 2.40
556 583 7.881775 AGAATTAAAAGGGACCATACATCAC 57.118 36.000 0.00 0.00 0.00 3.06
585 613 7.144722 TCATTTGTAACTCTGTTATGCAAGG 57.855 36.000 0.00 0.00 0.00 3.61
652 682 7.898014 AGTCCTCACATTATGATACAGTACA 57.102 36.000 0.00 0.00 36.48 2.90
655 685 9.547753 GTCCTCACATTATGATACAGTACAAAT 57.452 33.333 0.00 0.00 36.48 2.32
755 785 4.212716 ACATGGCTCACTGAATGCATAAT 58.787 39.130 0.00 0.00 0.00 1.28
772 802 6.776744 TGCATAATCAAGCTAAGATCAGGAT 58.223 36.000 0.00 0.00 0.00 3.24
778 808 4.474651 TCAAGCTAAGATCAGGATCCCAAA 59.525 41.667 8.55 0.00 38.58 3.28
793 824 3.766545 TCCCAAATAGCCATCCTAATGC 58.233 45.455 0.00 0.00 0.00 3.56
795 826 3.149196 CCAAATAGCCATCCTAATGCGT 58.851 45.455 0.00 0.00 0.00 5.24
893 1050 2.729882 CGCGGCATAGTAACCATAAGAC 59.270 50.000 0.00 0.00 0.00 3.01
1076 1233 0.191064 TCCACTCCACTCTCCCTGTT 59.809 55.000 0.00 0.00 0.00 3.16
1208 1368 4.082523 CGCCGACACCTCCACCAT 62.083 66.667 0.00 0.00 0.00 3.55
1218 1378 4.854924 TCCACCATCATGGCCGCG 62.855 66.667 2.52 0.00 42.67 6.46
1314 1474 0.744771 TGCTCGCGCTTCTCTCTCTA 60.745 55.000 5.56 0.00 36.97 2.43
1814 1974 2.747855 CGAGGTTGGGCAGCTTCC 60.748 66.667 0.00 0.00 31.44 3.46
1878 2038 3.710722 CTGCCGAGGGAGCTTGGT 61.711 66.667 0.00 0.00 0.00 3.67
1930 2090 4.839550 TCGGGTATAATGGCTACAATGGTA 59.160 41.667 0.00 0.00 0.00 3.25
1947 2107 2.311124 GTAGCATACCAGCGGAGTTT 57.689 50.000 1.50 0.00 40.15 2.66
1958 2118 0.891904 GCGGAGTTTGGTGGGCTAAA 60.892 55.000 0.00 0.00 0.00 1.85
1992 2152 4.811761 GACATCGCCGCGGCAAAC 62.812 66.667 45.26 27.76 42.06 2.93
2052 2212 2.726066 GCGGCTCGAATTTCTGTTTCTG 60.726 50.000 0.00 0.00 0.00 3.02
2082 2242 3.671411 CTAGCCGGCGCGATACCT 61.671 66.667 23.20 2.71 41.18 3.08
2083 2243 3.208884 CTAGCCGGCGCGATACCTT 62.209 63.158 23.20 1.83 41.18 3.50
2154 2314 2.912542 CTCGCCGGAGCTATCCCA 60.913 66.667 5.05 0.00 43.39 4.37
2163 2323 2.737830 GCTATCCCAGCCGGTCTC 59.262 66.667 1.90 0.00 45.23 3.36
2393 2553 2.524394 ACTCTGCACCGGTCACCT 60.524 61.111 2.59 0.00 0.00 4.00
2613 2773 1.153147 GGTCATTTCCCCGAGCCTC 60.153 63.158 0.00 0.00 0.00 4.70
2677 2837 2.916502 TAGCAATACGTGGCGGGCAG 62.917 60.000 3.75 1.88 34.54 4.85
3087 3247 2.562912 GCTGCAATGTGGGTGTCG 59.437 61.111 0.00 0.00 0.00 4.35
3240 3400 1.810030 GTGGAGGATGACCGCGTTC 60.810 63.158 4.92 0.00 41.83 3.95
3375 3535 0.815095 TCATCGCCGTGAAGAAGCTA 59.185 50.000 0.00 0.00 0.00 3.32
3384 3544 1.403323 GTGAAGAAGCTATGGCAAGCC 59.597 52.381 15.03 3.61 43.86 4.35
3495 3655 2.202987 GAGATGCTCGGCCACCTG 60.203 66.667 2.24 0.00 0.00 4.00
3567 3727 2.222886 ACGATGCTGCTCTACGAGTAT 58.777 47.619 0.00 0.00 31.39 2.12
3597 3757 2.361865 AGCCTCGACGAGCTCCTT 60.362 61.111 19.55 0.00 32.71 3.36
3867 4032 1.672030 CATCGCACCAGGTGAGCAA 60.672 57.895 24.96 5.40 39.86 3.91
3881 4046 2.099062 GCAAAGACTCGCGCATGG 59.901 61.111 8.75 0.00 0.00 3.66
4096 4263 4.467084 GATCCAAGGTCGCCGGCA 62.467 66.667 28.98 11.20 0.00 5.69
4320 4503 0.034059 CGTAGATGGTGATGGGCTCC 59.966 60.000 0.00 0.00 0.00 4.70
4321 4504 0.034059 GTAGATGGTGATGGGCTCCG 59.966 60.000 0.00 0.00 32.74 4.63
4365 4550 2.636768 GGTGTACCGCGTAGTTAACT 57.363 50.000 13.68 13.68 0.00 2.24
4366 4551 2.519963 GGTGTACCGCGTAGTTAACTC 58.480 52.381 12.39 3.31 0.00 3.01
4413 4598 6.004574 TGCATTTTGTGTACCATACTACCAA 58.995 36.000 0.00 0.00 0.00 3.67
4415 4600 6.972328 GCATTTTGTGTACCATACTACCAATG 59.028 38.462 0.00 0.00 0.00 2.82
4527 4719 8.402472 GGTTTATGTGCAATGCTAGTAATGTTA 58.598 33.333 6.82 0.00 0.00 2.41
4528 4720 9.781834 GTTTATGTGCAATGCTAGTAATGTTAA 57.218 29.630 6.82 0.00 0.00 2.01
4532 4724 9.950680 ATGTGCAATGCTAGTAATGTTAATTAC 57.049 29.630 6.82 1.22 45.80 1.89
4554 4746 2.490168 GGGTTTGATGTAAGGGTGTGGT 60.490 50.000 0.00 0.00 0.00 4.16
4558 4750 4.986054 TTGATGTAAGGGTGTGGTTAGT 57.014 40.909 0.00 0.00 0.00 2.24
4564 4756 4.595781 TGTAAGGGTGTGGTTAGTTCTCAT 59.404 41.667 0.00 0.00 0.00 2.90
4689 4900 7.840931 TCAAGAATATAGCAAAGTCTCAGTCA 58.159 34.615 0.00 0.00 0.00 3.41
4695 4906 4.689612 AGCAAAGTCTCAGTCACCTAAA 57.310 40.909 0.00 0.00 0.00 1.85
4716 4927 6.885735 AAAATTTAGCAATCATGTTACCGC 57.114 33.333 0.00 0.00 0.00 5.68
4732 4943 1.606668 ACCGCAATGACAAACGTGAAT 59.393 42.857 0.00 0.00 0.00 2.57
4739 4950 5.175491 GCAATGACAAACGTGAATGATTGTT 59.825 36.000 2.83 0.00 35.35 2.83
4744 4955 6.860539 TGACAAACGTGAATGATTGTTAATGG 59.139 34.615 2.83 0.00 35.35 3.16
4760 4971 3.012153 TGGAGACATGGGGAGGAAG 57.988 57.895 0.00 0.00 33.40 3.46
4761 4972 0.621571 TGGAGACATGGGGAGGAAGG 60.622 60.000 0.00 0.00 33.40 3.46
4762 4973 1.348775 GGAGACATGGGGAGGAAGGG 61.349 65.000 0.00 0.00 0.00 3.95
4763 4974 1.308216 AGACATGGGGAGGAAGGGG 60.308 63.158 0.00 0.00 0.00 4.79
4764 4975 3.023735 ACATGGGGAGGAAGGGGC 61.024 66.667 0.00 0.00 0.00 5.80
4765 4976 3.825623 CATGGGGAGGAAGGGGCC 61.826 72.222 0.00 0.00 0.00 5.80
4779 4990 4.559148 GGCCCACCCCTCAAAATT 57.441 55.556 0.00 0.00 0.00 1.82
4780 4991 1.982430 GGCCCACCCCTCAAAATTG 59.018 57.895 0.00 0.00 0.00 2.32
4781 4992 1.552799 GGCCCACCCCTCAAAATTGG 61.553 60.000 0.00 0.00 0.00 3.16
4782 4993 2.682631 CCCACCCCTCAAAATTGGG 58.317 57.895 0.00 0.00 45.34 4.12
4800 5011 1.743589 GGGGGAGGGGATTAGTTAGG 58.256 60.000 0.00 0.00 0.00 2.69
4801 5012 1.224905 GGGGGAGGGGATTAGTTAGGA 59.775 57.143 0.00 0.00 0.00 2.94
4802 5013 2.362159 GGGGGAGGGGATTAGTTAGGAA 60.362 54.545 0.00 0.00 0.00 3.36
4803 5014 3.400419 GGGGAGGGGATTAGTTAGGAAA 58.600 50.000 0.00 0.00 0.00 3.13
4804 5015 3.988186 GGGGAGGGGATTAGTTAGGAAAT 59.012 47.826 0.00 0.00 0.00 2.17
4805 5016 4.419200 GGGGAGGGGATTAGTTAGGAAATT 59.581 45.833 0.00 0.00 0.00 1.82
4806 5017 5.103215 GGGGAGGGGATTAGTTAGGAAATTT 60.103 44.000 0.00 0.00 0.00 1.82
4807 5018 6.069331 GGGAGGGGATTAGTTAGGAAATTTC 58.931 44.000 9.83 9.83 0.00 2.17
4821 5266 0.750182 AATTTCCATACCGGCCCGTG 60.750 55.000 0.00 0.00 33.14 4.94
4854 5323 7.175641 GGGATATTGCATAAAGTGATACAAGCT 59.824 37.037 0.00 0.00 0.00 3.74
4855 5324 8.571336 GGATATTGCATAAAGTGATACAAGCTT 58.429 33.333 0.00 0.00 0.00 3.74
4856 5325 9.604626 GATATTGCATAAAGTGATACAAGCTTC 57.395 33.333 0.00 0.00 0.00 3.86
4857 5326 5.818136 TGCATAAAGTGATACAAGCTTCC 57.182 39.130 0.00 0.00 0.00 3.46
4881 5350 6.036844 CCATCTAATGATACGCATCCAATCTG 59.963 42.308 0.00 0.00 35.78 2.90
4903 5372 1.934589 CATACGTCCATTGCTTCCGA 58.065 50.000 0.00 0.00 0.00 4.55
5014 5483 3.953712 TGAATTCTAGTCTGGCGTTGA 57.046 42.857 7.05 0.00 0.00 3.18
5031 5501 9.862371 CTGGCGTTGATTTCTATCTAATACTAT 57.138 33.333 0.00 0.00 0.00 2.12
5076 5546 5.126545 AGTGTCAATGTATAAGCCGAGTGTA 59.873 40.000 0.00 0.00 0.00 2.90
5088 5558 2.097541 GCCGAGTGTATTTTATCGCGTC 60.098 50.000 5.77 0.00 33.94 5.19
5109 5579 2.767960 CCTCGCCTTAGGTTAGGGTAAA 59.232 50.000 11.65 0.00 35.74 2.01
5149 5619 2.550707 CGCACGAGAGAAAAGAAAACG 58.449 47.619 0.00 0.00 0.00 3.60
5152 5622 2.217847 CACGAGAGAAAAGAAAACGCGA 59.782 45.455 15.93 0.00 0.00 5.87
5164 5634 4.053295 AGAAAACGCGACTTAGCTAACAA 58.947 39.130 15.93 0.00 34.40 2.83
5191 5661 2.477525 CGAGTAGGGCTCTAAACGACAC 60.478 54.545 13.26 0.00 41.98 3.67
5220 5690 8.037758 AGCTTACATATGCTCCTTGACATATAC 58.962 37.037 1.58 0.00 37.37 1.47
5223 5693 3.685139 ATGCTCCTTGACATATACCCG 57.315 47.619 0.00 0.00 0.00 5.28
5233 5703 3.640029 TGACATATACCCGAGAAAGACCC 59.360 47.826 0.00 0.00 0.00 4.46
5256 5726 5.582665 CCCAGCTTACAGAAAGACTCATTAC 59.417 44.000 0.00 0.00 37.38 1.89
5269 5739 5.281314 AGACTCATTACAGTTCCCTACCAT 58.719 41.667 0.00 0.00 0.00 3.55
5297 5767 1.069765 ACAGAGGTGGTTGACTGCG 59.930 57.895 0.00 0.00 34.25 5.18
5303 5773 1.369091 GGTGGTTGACTGCGCTATGG 61.369 60.000 9.73 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.238439 CCCACACAGCTAACAAGGTG 58.762 55.000 3.20 3.20 42.40 4.00
52 53 0.843984 ACCCACACAGCTAACAAGGT 59.156 50.000 0.00 0.00 0.00 3.50
57 58 5.581085 CAGAACTAATACCCACACAGCTAAC 59.419 44.000 0.00 0.00 0.00 2.34
252 255 1.203376 TCCCCACCTTGGTCATCTACA 60.203 52.381 0.00 0.00 35.17 2.74
297 314 2.563179 ACATCCTGACAGTGTAGTGTCC 59.437 50.000 15.22 1.32 45.42 4.02
299 316 2.965831 ACACATCCTGACAGTGTAGTGT 59.034 45.455 11.90 11.90 44.02 3.55
321 338 1.957668 CCTCATTGGCATCATGACGA 58.042 50.000 0.00 0.00 0.00 4.20
346 363 5.245531 CACCTTCTAGTAGAACAAATGCCA 58.754 41.667 8.59 0.00 29.89 4.92
370 387 2.464157 AAGAGACTGCCTAACTGCAC 57.536 50.000 0.00 0.00 36.04 4.57
414 431 7.520614 GCATTAGACAACAAAAGTAGAAGCAGT 60.521 37.037 0.00 0.00 0.00 4.40
459 476 3.392947 TCACTAACAGGGACATTTGACCA 59.607 43.478 1.70 0.00 0.00 4.02
504 529 7.095271 ACTCACCAATTGTTGTCAAAACAAAAG 60.095 33.333 0.00 0.00 46.56 2.27
536 563 6.381498 TCTGTGATGTATGGTCCCTTTTAA 57.619 37.500 0.00 0.00 0.00 1.52
556 583 8.453320 TGCATAACAGAGTTACAAATGATTCTG 58.547 33.333 0.00 0.00 38.34 3.02
755 785 3.657610 TGGGATCCTGATCTTAGCTTGA 58.342 45.455 12.58 0.00 37.92 3.02
772 802 3.766545 GCATTAGGATGGCTATTTGGGA 58.233 45.455 0.00 0.00 33.72 4.37
778 808 5.483685 TCTAAACGCATTAGGATGGCTAT 57.516 39.130 8.28 0.00 41.22 2.97
795 826 8.443160 CAGTCTTGCGTTTCAATCTTATCTAAA 58.557 33.333 0.00 0.00 33.57 1.85
877 1034 7.660208 GGTTATGGTGGTCTTATGGTTACTATG 59.340 40.741 0.00 0.00 0.00 2.23
893 1050 1.086696 CTTGCGAGTGGTTATGGTGG 58.913 55.000 0.00 0.00 0.00 4.61
953 1110 4.552365 GGAGCAGCAGCCGCCATA 62.552 66.667 0.00 0.00 43.56 2.74
1076 1233 1.229209 GAGGAGGTGGTGGTGGAGA 60.229 63.158 0.00 0.00 0.00 3.71
1137 1297 1.032114 AGGAAAGGTAATGGCTGCGC 61.032 55.000 0.00 0.00 0.00 6.09
1139 1299 1.751351 GGAAGGAAAGGTAATGGCTGC 59.249 52.381 0.00 0.00 0.00 5.25
1141 1301 2.242452 GGAGGAAGGAAAGGTAATGGCT 59.758 50.000 0.00 0.00 0.00 4.75
1314 1474 0.685660 GGTCGTTCAGGGAGGACTTT 59.314 55.000 0.93 0.00 35.40 2.66
1581 1741 2.357517 CGGAGCAAGAACACCGCT 60.358 61.111 0.00 0.00 36.99 5.52
1894 2054 5.687166 TTATACCCGATCTCAAGGTGTTT 57.313 39.130 4.41 0.00 35.02 2.83
1930 2090 0.392998 CCAAACTCCGCTGGTATGCT 60.393 55.000 0.00 0.00 0.00 3.79
1958 2118 1.979155 TCGAGGTACTGCAGCTGCT 60.979 57.895 36.61 21.93 41.55 4.24
1965 2125 1.589196 GGCGATGTCGAGGTACTGC 60.589 63.158 6.60 0.00 41.55 4.40
2052 2212 1.079503 CGGCTAGCCTGTTCTTGAAC 58.920 55.000 30.55 6.56 0.00 3.18
2102 2262 1.227943 TCAAGAACCTGCAGCGCTT 60.228 52.632 7.50 8.11 0.00 4.68
2163 2323 1.369930 GAGATTCGCGAGCTCTCCG 60.370 63.158 27.49 14.14 35.13 4.63
2393 2553 1.215673 AGAGTATGAGGCGGAGGAGAA 59.784 52.381 0.00 0.00 0.00 2.87
2475 2635 1.006571 GTTGGACTCGAGCCGAACA 60.007 57.895 18.98 6.42 34.74 3.18
2677 2837 0.110010 GCCAAGACTTGAAGCTTCGC 60.110 55.000 21.11 11.84 0.00 4.70
2685 2845 2.048222 CTCGCCGCCAAGACTTGA 60.048 61.111 16.99 0.00 0.00 3.02
3240 3400 0.391395 CTGTGAAGCTCAGCCTCTGG 60.391 60.000 0.00 0.00 31.51 3.86
3384 3544 3.431725 GTCTCCTTTTGCGCCGGG 61.432 66.667 4.18 1.38 0.00 5.73
3422 3582 1.333308 CGTCTTGTGTGTCCATTTGCA 59.667 47.619 0.00 0.00 0.00 4.08
3526 3686 3.276091 CTCGCCGTTTGTGCACCA 61.276 61.111 15.69 0.00 0.00 4.17
3527 3687 2.970324 TCTCGCCGTTTGTGCACC 60.970 61.111 15.69 0.00 0.00 5.01
3867 4032 2.094659 CGAACCATGCGCGAGTCTT 61.095 57.895 12.10 0.00 0.00 3.01
4365 4550 1.087202 ACACGAGCGCTGTTTTGTGA 61.087 50.000 18.48 0.00 33.75 3.58
4366 4551 0.654472 GACACGAGCGCTGTTTTGTG 60.654 55.000 18.48 17.33 35.31 3.33
4413 4598 2.619074 GGTTAAAGCTCACTCAGGGCAT 60.619 50.000 0.00 0.00 0.00 4.40
4415 4600 1.454201 GGTTAAAGCTCACTCAGGGC 58.546 55.000 0.00 0.00 0.00 5.19
4527 4719 4.703093 CACCCTTACATCAAACCCGTAATT 59.297 41.667 0.00 0.00 0.00 1.40
4528 4720 4.263594 ACACCCTTACATCAAACCCGTAAT 60.264 41.667 0.00 0.00 0.00 1.89
4529 4721 3.072768 ACACCCTTACATCAAACCCGTAA 59.927 43.478 0.00 0.00 0.00 3.18
4530 4722 2.638855 ACACCCTTACATCAAACCCGTA 59.361 45.455 0.00 0.00 0.00 4.02
4531 4723 1.422402 ACACCCTTACATCAAACCCGT 59.578 47.619 0.00 0.00 0.00 5.28
4532 4724 1.810151 CACACCCTTACATCAAACCCG 59.190 52.381 0.00 0.00 0.00 5.28
4533 4725 2.167662 CCACACCCTTACATCAAACCC 58.832 52.381 0.00 0.00 0.00 4.11
4534 4726 2.871453 ACCACACCCTTACATCAAACC 58.129 47.619 0.00 0.00 0.00 3.27
4535 4727 5.067954 ACTAACCACACCCTTACATCAAAC 58.932 41.667 0.00 0.00 0.00 2.93
4536 4728 5.313280 ACTAACCACACCCTTACATCAAA 57.687 39.130 0.00 0.00 0.00 2.69
4539 4731 5.161943 AGAACTAACCACACCCTTACATC 57.838 43.478 0.00 0.00 0.00 3.06
4564 4756 4.931661 ACTTGGTTAAGTCTCAGTCGAA 57.068 40.909 0.00 0.00 43.53 3.71
4689 4900 8.188139 CGGTAACATGATTGCTAAATTTTAGGT 58.812 33.333 16.02 3.13 0.00 3.08
4695 4906 5.574891 TGCGGTAACATGATTGCTAAATT 57.425 34.783 0.00 0.00 0.00 1.82
4716 4927 6.752335 AACAATCATTCACGTTTGTCATTG 57.248 33.333 1.81 3.74 31.42 2.82
4732 4943 4.229353 TCCCCATGTCTCCATTAACAATCA 59.771 41.667 0.00 0.00 0.00 2.57
4739 4950 2.887454 TCCTCCCCATGTCTCCATTA 57.113 50.000 0.00 0.00 0.00 1.90
4744 4955 1.348775 CCCCTTCCTCCCCATGTCTC 61.349 65.000 0.00 0.00 0.00 3.36
4762 4973 1.552799 CCAATTTTGAGGGGTGGGCC 61.553 60.000 0.00 0.00 0.00 5.80
4763 4974 1.552799 CCCAATTTTGAGGGGTGGGC 61.553 60.000 0.00 0.00 42.44 5.36
4764 4975 2.682631 CCCAATTTTGAGGGGTGGG 58.317 57.895 0.00 0.00 42.94 4.61
4781 4992 1.224905 TCCTAACTAATCCCCTCCCCC 59.775 57.143 0.00 0.00 0.00 5.40
4782 4993 2.809309 TCCTAACTAATCCCCTCCCC 57.191 55.000 0.00 0.00 0.00 4.81
4783 4994 5.664815 AATTTCCTAACTAATCCCCTCCC 57.335 43.478 0.00 0.00 0.00 4.30
4784 4995 6.069331 GGAAATTTCCTAACTAATCCCCTCC 58.931 44.000 26.94 0.00 44.11 4.30
4800 5011 0.666374 CGGGCCGGTATGGAAATTTC 59.334 55.000 20.56 9.83 42.00 2.17
4801 5012 0.033894 ACGGGCCGGTATGGAAATTT 60.034 50.000 31.78 0.20 42.00 1.82
4802 5013 0.750182 CACGGGCCGGTATGGAAATT 60.750 55.000 31.78 0.83 42.00 1.82
4803 5014 1.153046 CACGGGCCGGTATGGAAAT 60.153 57.895 31.78 1.72 42.00 2.17
4804 5015 2.269562 CACGGGCCGGTATGGAAA 59.730 61.111 31.78 0.00 42.00 3.13
4805 5016 3.788145 CCACGGGCCGGTATGGAA 61.788 66.667 31.78 0.00 42.00 3.53
4806 5017 4.781616 TCCACGGGCCGGTATGGA 62.782 66.667 31.78 29.20 42.00 3.41
4807 5018 3.556306 ATCCACGGGCCGGTATGG 61.556 66.667 31.78 27.38 42.50 2.74
4808 5019 1.750341 TACATCCACGGGCCGGTATG 61.750 60.000 31.78 28.17 0.00 2.39
4809 5020 1.458020 TACATCCACGGGCCGGTAT 60.458 57.895 31.78 17.07 0.00 2.73
4810 5021 2.043147 TACATCCACGGGCCGGTA 60.043 61.111 31.78 18.74 0.00 4.02
4811 5022 3.467226 CTACATCCACGGGCCGGT 61.467 66.667 31.78 19.85 0.00 5.28
4812 5023 4.235762 CCTACATCCACGGGCCGG 62.236 72.222 31.78 18.68 0.00 6.13
4813 5024 4.235762 CCCTACATCCACGGGCCG 62.236 72.222 27.06 27.06 0.00 6.13
4814 5025 0.834687 TATCCCTACATCCACGGGCC 60.835 60.000 0.00 0.00 37.89 5.80
4821 5266 7.168219 TCACTTTATGCAATATCCCTACATCC 58.832 38.462 0.00 0.00 0.00 3.51
4854 5323 5.482163 TGGATGCGTATCATTAGATGGAA 57.518 39.130 15.61 0.00 35.05 3.53
4855 5324 5.482163 TTGGATGCGTATCATTAGATGGA 57.518 39.130 15.61 0.00 35.05 3.41
4856 5325 6.036844 CAGATTGGATGCGTATCATTAGATGG 59.963 42.308 15.61 0.00 35.05 3.51
4857 5326 6.592994 ACAGATTGGATGCGTATCATTAGATG 59.407 38.462 15.61 8.62 35.05 2.90
4881 5350 1.064060 GGAAGCAATGGACGTATGCAC 59.936 52.381 14.83 9.43 42.45 4.57
4903 5372 7.337942 GTCATCCTGATGTAATCCTTCTTTGTT 59.662 37.037 7.00 0.00 44.73 2.83
4986 5455 5.241662 GCCAGACTAGAATTCAACTGTCTT 58.758 41.667 8.44 0.00 33.21 3.01
4994 5463 3.953712 TCAACGCCAGACTAGAATTCA 57.046 42.857 8.44 0.00 0.00 2.57
5031 5501 3.162202 TGACGACGTGTGTTTTTCCTA 57.838 42.857 4.58 0.00 0.00 2.94
5088 5558 2.077687 TACCCTAACCTAAGGCGAGG 57.922 55.000 6.92 6.92 42.89 4.63
5109 5579 3.427863 GCGCTCTTTAGTTTGTACTCGTT 59.572 43.478 0.00 0.00 35.78 3.85
5149 5619 3.060473 CGGCTTATTGTTAGCTAAGTCGC 60.060 47.826 6.38 4.26 43.43 5.19
5152 5622 5.340439 ACTCGGCTTATTGTTAGCTAAGT 57.660 39.130 6.38 0.00 38.67 2.24
5191 5661 4.749099 GTCAAGGAGCATATGTAAGCTGAG 59.251 45.833 4.29 0.00 42.04 3.35
5220 5690 1.842381 AAGCTGGGGTCTTTCTCGGG 61.842 60.000 0.00 0.00 0.00 5.14
5223 5693 2.567615 TCTGTAAGCTGGGGTCTTTCTC 59.432 50.000 0.00 0.00 0.00 2.87
5233 5703 6.166279 TGTAATGAGTCTTTCTGTAAGCTGG 58.834 40.000 0.00 0.00 33.66 4.85
5256 5726 0.394352 GGCCACATGGTAGGGAACTG 60.394 60.000 0.00 0.00 37.00 3.16


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

AutoCloner maintained by Alex Coulton.