Multiple sequence alignment - TraesCS5D01G160700

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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 TraesCS5D01G160700 chr5D 100.000 5245 0 0 1 5245 250415016 250420260 0.000000e+00 9686.0
1 TraesCS5D01G160700 chr5A 95.176 4726 160 30 68 4732 333738522 333743240 0.000000e+00 7402.0
2 TraesCS5D01G160700 chr5A 91.098 528 25 7 4721 5245 333743937 333744445 0.000000e+00 695.0
3 TraesCS5D01G160700 chr5A 88.276 145 15 2 5103 5245 584527364 584527220 6.980000e-39 172.0
4 TraesCS5D01G160700 chr5A 90.000 80 4 2 1 78 333738428 333738505 3.340000e-17 100.0
5 TraesCS5D01G160700 chr5B 94.717 4278 132 33 135 4361 283233878 283238112 0.000000e+00 6562.0
6 TraesCS5D01G160700 chr5B 87.075 147 17 1 5101 5245 547491849 547491995 1.170000e-36 165.0
7 TraesCS5D01G160700 chr5B 85.841 113 10 4 1 112 283233783 283233890 1.190000e-21 115.0
8 TraesCS5D01G160700 chr5B 93.151 73 4 1 4441 4513 283238109 283238180 7.180000e-19 106.0
9 TraesCS5D01G160700 chr2B 85.923 1641 182 23 1282 2876 210669441 210667804 0.000000e+00 1705.0
10 TraesCS5D01G160700 chr2B 87.838 148 14 4 5101 5245 739729675 739729821 2.510000e-38 171.0
11 TraesCS5D01G160700 chr2A 88.922 1345 144 5 1527 2867 148851264 148852607 0.000000e+00 1653.0
12 TraesCS5D01G160700 chr2A 87.755 147 16 2 5101 5245 192003383 192003237 2.510000e-38 171.0
13 TraesCS5D01G160700 chr2A 87.671 146 16 2 5102 5245 89175425 89175280 9.030000e-38 169.0
14 TraesCS5D01G160700 chr2D 88.544 1353 151 4 1527 2876 152664377 152663026 0.000000e+00 1637.0
15 TraesCS5D01G160700 chr2D 89.286 84 9 0 4360 4443 572683042 572682959 7.180000e-19 106.0
16 TraesCS5D01G160700 chr2D 85.870 92 13 0 4356 4447 23305956 23306047 1.200000e-16 99.0
17 TraesCS5D01G160700 chr7D 87.671 146 14 4 5103 5245 127501406 127501550 3.250000e-37 167.0
18 TraesCS5D01G160700 chr7B 87.075 147 17 2 5101 5245 64391799 64391945 1.170000e-36 165.0
19 TraesCS5D01G160700 chr7B 85.000 120 9 4 4158 4277 749409571 749409681 4.290000e-21 113.0
20 TraesCS5D01G160700 chr1B 87.075 147 17 2 5101 5245 482481736 482481590 1.170000e-36 165.0
21 TraesCS5D01G160700 chr1B 87.097 93 12 0 4358 4450 480972933 480973025 7.180000e-19 106.0
22 TraesCS5D01G160700 chr1B 100.000 32 0 0 85 116 665792696 665792727 5.670000e-05 60.2
23 TraesCS5D01G160700 chr1A 95.294 85 4 0 4359 4443 587861395 587861311 9.160000e-28 135.0
24 TraesCS5D01G160700 chrUn 90.909 88 6 2 4357 4443 31863633 31863547 3.320000e-22 117.0
25 TraesCS5D01G160700 chr7A 91.250 80 7 0 4364 4443 252187681 252187602 5.550000e-20 110.0
26 TraesCS5D01G160700 chr1D 89.535 86 9 0 4358 4443 358222639 358222554 5.550000e-20 110.0
27 TraesCS5D01G160700 chr3B 89.535 86 7 2 4359 4443 135685003 135685087 2.000000e-19 108.0


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 TraesCS5D01G160700 chr5D 250415016 250420260 5244 False 9686.000000 9686 100.000000 1 5245 1 chr5D.!!$F1 5244
1 TraesCS5D01G160700 chr5A 333738428 333744445 6017 False 2732.333333 7402 92.091333 1 5245 3 chr5A.!!$F1 5244
2 TraesCS5D01G160700 chr5B 283233783 283238180 4397 False 2261.000000 6562 91.236333 1 4513 3 chr5B.!!$F2 4512
3 TraesCS5D01G160700 chr2B 210667804 210669441 1637 True 1705.000000 1705 85.923000 1282 2876 1 chr2B.!!$R1 1594
4 TraesCS5D01G160700 chr2A 148851264 148852607 1343 False 1653.000000 1653 88.922000 1527 2867 1 chr2A.!!$F1 1340
5 TraesCS5D01G160700 chr2D 152663026 152664377 1351 True 1637.000000 1637 88.544000 1527 2876 1 chr2D.!!$R1 1349

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
790 837 0.531974 TTGTTGCGTTTCTCGGAGCT 60.532 50.000 0.00 0.00 41.02 4.09 F
932 1002 0.731417 CAGGGAGCGAGCAATTGAAG 59.269 55.000 10.34 0.04 0.00 3.02 F
953 1023 1.329292 CCAAAACGTCACTCTTTCGCA 59.671 47.619 0.00 0.00 0.00 5.10 F
970 1040 1.418373 GCACCGATTTGTTTGCTTCC 58.582 50.000 0.00 0.00 32.00 3.46 F
2110 2235 2.372264 TCTTCCTTCATGCTGAATGCC 58.628 47.619 0.00 0.00 42.00 4.40 F
3971 4102 0.662619 CGCTTTGGTGTGTGACATGT 59.337 50.000 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 2655 2.168496 GTCAGGGAGTACACTGCACTA 58.832 52.381 3.21 0.0 46.15 2.74 R
2907 3032 6.660521 TCAAACCTGCATCTACTGATTGATTT 59.339 34.615 0.00 0.0 0.00 2.17 R
2970 3095 4.777366 TGTTGAGATAGTGAGACCAATGGA 59.223 41.667 6.16 0.0 0.00 3.41 R
2971 3096 4.872691 GTGTTGAGATAGTGAGACCAATGG 59.127 45.833 0.00 0.0 0.00 3.16 R
3999 4130 1.180456 TGAACCATGGCCTGCAAGTG 61.180 55.000 13.04 0.0 0.00 3.16 R
4949 5800 0.669619 TGTTTGCACGACTCTACGGA 59.330 50.000 0.00 0.0 37.61 4.69 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
20 21 0.767375 CCACCCATAGATCCACCTGG 59.233 60.000 0.00 0.00 0.00 4.45
80 108 6.024552 TCTATTACCCAAAAGCAAAAGCTG 57.975 37.500 0.00 0.00 0.00 4.24
204 237 3.319904 GCATATGGTGCGACGGAC 58.680 61.111 11.45 11.45 45.23 4.79
242 278 6.709846 GGAGTAATGATTTGCAGAGCTTCTAT 59.290 38.462 0.00 0.00 0.00 1.98
291 327 0.625849 AAATGGCAGGGTGGTAGAGG 59.374 55.000 0.00 0.00 0.00 3.69
312 349 2.178235 GCGAGATTGTTACCGGGGC 61.178 63.158 6.32 0.00 0.00 5.80
458 495 3.764466 CGGCTCGGCTGTCCTTCT 61.764 66.667 0.00 0.00 0.00 2.85
464 501 1.078848 CGGCTGTCCTTCTCCTTGG 60.079 63.158 0.00 0.00 0.00 3.61
465 502 1.831652 CGGCTGTCCTTCTCCTTGGT 61.832 60.000 0.00 0.00 0.00 3.67
552 594 0.540365 ACCTCCGTCGACCAGGTTAA 60.540 55.000 22.66 0.00 37.21 2.01
755 802 3.423154 GCCGTCCTGTTCTTGCGG 61.423 66.667 0.00 0.00 44.60 5.69
790 837 0.531974 TTGTTGCGTTTCTCGGAGCT 60.532 50.000 0.00 0.00 41.02 4.09
798 845 2.062519 GTTTCTCGGAGCTCTGTGTTC 58.937 52.381 21.88 10.48 0.00 3.18
809 858 2.225255 GCTCTGTGTTCTTTTCTGCTCC 59.775 50.000 0.00 0.00 0.00 4.70
868 917 2.501316 CCTGATTCACCCCCAAAATTCC 59.499 50.000 0.00 0.00 0.00 3.01
932 1002 0.731417 CAGGGAGCGAGCAATTGAAG 59.269 55.000 10.34 0.04 0.00 3.02
953 1023 1.329292 CCAAAACGTCACTCTTTCGCA 59.671 47.619 0.00 0.00 0.00 5.10
970 1040 1.418373 GCACCGATTTGTTTGCTTCC 58.582 50.000 0.00 0.00 32.00 3.46
1113 1186 6.506147 TGCTACCATTTCACATCATTAATGC 58.494 36.000 10.76 0.00 39.12 3.56
1159 1239 9.758651 ATTTCAGGAGTTATTTTTGTTGGTAAC 57.241 29.630 0.00 0.00 0.00 2.50
1370 1455 7.179516 TCAGGTACTCTTAACACATGGATGTTA 59.820 37.037 5.12 5.12 39.51 2.41
2110 2235 2.372264 TCTTCCTTCATGCTGAATGCC 58.628 47.619 0.00 0.00 42.00 4.40
2430 2555 2.762459 TGGTACCCCTAGCCAGCG 60.762 66.667 10.07 0.00 0.00 5.18
2530 2655 3.897505 GGGGGATTATGTTTAGCAATGCT 59.102 43.478 13.92 13.92 43.41 3.79
2563 2688 5.762179 ACTCCCTGACATTTGAAGATGTA 57.238 39.130 0.00 0.00 40.21 2.29
2830 2955 4.051237 GCACAGCAACGATATCATCTACA 58.949 43.478 3.12 0.00 0.00 2.74
2857 2982 7.504926 TCCAAGTAAGCTAAATTTCCTCCTA 57.495 36.000 0.00 0.00 0.00 2.94
2907 3032 7.713734 ACTGCCATAGTAGAACTAACTACAA 57.286 36.000 0.00 0.00 43.38 2.41
3115 3240 4.906060 AGTACTAGGGGTGAAACAGAAAGT 59.094 41.667 0.00 0.00 39.98 2.66
3390 3516 4.388773 TCGTATGCGAATGATGCCTAATTC 59.611 41.667 2.49 0.00 44.92 2.17
3635 3761 3.881688 TCTCCATACGGCTTAGACACTAC 59.118 47.826 0.00 0.00 0.00 2.73
3685 3811 2.172851 TTGTTTATTCTCCACGCGGT 57.827 45.000 12.47 0.00 0.00 5.68
3798 3929 0.981183 AAACCATGCGTAGGAGTCCA 59.019 50.000 12.86 0.00 0.00 4.02
3971 4102 0.662619 CGCTTTGGTGTGTGACATGT 59.337 50.000 0.00 0.00 0.00 3.21
3999 4130 7.870954 CCTAAACAAAGTTTCCCCTGAATTTAC 59.129 37.037 0.00 0.00 0.00 2.01
4043 4174 0.976641 ATTCGCAGGAAGGTGAGTCA 59.023 50.000 0.00 0.00 35.19 3.41
4302 4438 1.135859 GTGAGATTTGTTGCGCCTCTG 60.136 52.381 4.18 0.00 0.00 3.35
4303 4439 0.179179 GAGATTTGTTGCGCCTCTGC 60.179 55.000 4.18 0.00 0.00 4.26
4314 4450 2.103094 TGCGCCTCTGCTTGTTAGATAT 59.897 45.455 4.18 0.00 35.36 1.63
4362 4501 6.952773 TTATTGAGGTAAATGCCATGTACC 57.047 37.500 15.23 15.23 38.05 3.34
4369 4508 1.308877 AATGCCATGTACCCCCTCTT 58.691 50.000 0.00 0.00 0.00 2.85
4376 4515 4.825634 GCCATGTACCCCCTCTTTAAATAC 59.174 45.833 0.00 0.00 0.00 1.89
4508 4647 5.277974 GCACTAACTTTGAATGTCAAGCTGA 60.278 40.000 0.00 0.00 37.70 4.26
4613 4752 1.961277 GGGTCTGAGTGTTGGCGTG 60.961 63.158 0.00 0.00 0.00 5.34
4622 4761 0.951558 GTGTTGGCGTGAAGGTCAAT 59.048 50.000 0.00 0.00 33.55 2.57
4623 4762 0.950836 TGTTGGCGTGAAGGTCAATG 59.049 50.000 0.00 0.00 33.55 2.82
4674 4813 1.415672 AAAGGCGACAAGGAGACCCA 61.416 55.000 0.00 0.00 33.88 4.51
4676 4815 1.450312 GGCGACAAGGAGACCCATG 60.450 63.158 0.00 0.00 37.19 3.66
4677 4816 1.296715 GCGACAAGGAGACCCATGT 59.703 57.895 0.00 0.00 46.08 3.21
4692 4832 3.823873 ACCCATGTCGCTGATTGTTTTTA 59.176 39.130 0.00 0.00 0.00 1.52
4766 5617 5.163612 GCCAATTTGGAGATCTTGTTCTACC 60.164 44.000 19.76 0.00 40.96 3.18
4803 5654 7.290110 TGGGATATCCATCTTATAGTATGCG 57.710 40.000 23.27 0.00 41.46 4.73
4833 5684 3.324117 CTCGCCTCTGTGGAATATGATG 58.676 50.000 0.00 0.00 38.35 3.07
4834 5685 2.700371 TCGCCTCTGTGGAATATGATGT 59.300 45.455 0.00 0.00 38.35 3.06
4835 5686 2.804527 CGCCTCTGTGGAATATGATGTG 59.195 50.000 0.00 0.00 38.35 3.21
4836 5687 3.742327 CGCCTCTGTGGAATATGATGTGT 60.742 47.826 0.00 0.00 38.35 3.72
4837 5688 4.202441 GCCTCTGTGGAATATGATGTGTT 58.798 43.478 0.00 0.00 38.35 3.32
4838 5689 4.641989 GCCTCTGTGGAATATGATGTGTTT 59.358 41.667 0.00 0.00 38.35 2.83
4839 5690 5.126061 GCCTCTGTGGAATATGATGTGTTTT 59.874 40.000 0.00 0.00 38.35 2.43
4840 5691 6.350445 GCCTCTGTGGAATATGATGTGTTTTT 60.350 38.462 0.00 0.00 38.35 1.94
4841 5692 7.253422 CCTCTGTGGAATATGATGTGTTTTTC 58.747 38.462 0.00 0.00 38.35 2.29
4847 5698 7.489113 GTGGAATATGATGTGTTTTTCATGGAC 59.511 37.037 0.00 0.00 34.52 4.02
4862 5713 8.945481 TTTTCATGGACAAAGCCATTAATATG 57.055 30.769 0.00 0.00 46.29 1.78
4869 5720 8.415553 TGGACAAAGCCATTAATATGAATCTTG 58.584 33.333 0.00 0.00 33.37 3.02
4870 5721 8.416329 GGACAAAGCCATTAATATGAATCTTGT 58.584 33.333 0.00 0.00 33.37 3.16
4908 5759 4.834496 AGCAACTTTCTGGATCCAAAATCA 59.166 37.500 17.00 0.00 0.00 2.57
4910 5761 5.406477 GCAACTTTCTGGATCCAAAATCAAC 59.594 40.000 17.00 6.44 0.00 3.18
4923 5774 9.868389 GATCCAAAATCAACTTTCACAAAAATC 57.132 29.630 0.00 0.00 0.00 2.17
4940 5791 6.318396 ACAAAAATCAGACCATTTGTTTTGGG 59.682 34.615 9.86 0.00 41.75 4.12
4945 5796 6.054860 TCAGACCATTTGTTTTGGGAAAAA 57.945 33.333 0.00 0.00 38.64 1.94
4949 5800 7.714813 CAGACCATTTGTTTTGGGAAAAATAGT 59.285 33.333 0.00 0.00 38.64 2.12
4950 5801 7.931407 AGACCATTTGTTTTGGGAAAAATAGTC 59.069 33.333 0.00 0.00 38.64 2.59
4951 5802 6.995686 ACCATTTGTTTTGGGAAAAATAGTCC 59.004 34.615 0.00 0.00 38.64 3.85
4952 5803 6.147000 CCATTTGTTTTGGGAAAAATAGTCCG 59.853 38.462 0.00 0.00 35.86 4.79
4953 5804 5.855740 TTGTTTTGGGAAAAATAGTCCGT 57.144 34.783 0.00 0.00 35.86 4.69
4954 5805 6.956202 TTGTTTTGGGAAAAATAGTCCGTA 57.044 33.333 0.00 0.00 35.86 4.02
4955 5806 6.563222 TGTTTTGGGAAAAATAGTCCGTAG 57.437 37.500 0.00 0.00 35.86 3.51
4958 5809 5.750352 TTGGGAAAAATAGTCCGTAGAGT 57.250 39.130 0.00 0.00 35.86 3.24
4959 5810 5.334724 TGGGAAAAATAGTCCGTAGAGTC 57.665 43.478 0.00 0.00 35.86 3.36
4960 5811 4.142315 TGGGAAAAATAGTCCGTAGAGTCG 60.142 45.833 0.00 0.00 35.86 4.18
4961 5812 4.142293 GGGAAAAATAGTCCGTAGAGTCGT 60.142 45.833 0.00 0.00 35.86 4.34
4963 5814 3.417690 AAATAGTCCGTAGAGTCGTGC 57.582 47.619 0.00 0.00 0.00 5.34
4988 5840 4.787551 ACAATTGTTTGGGTGTGAGTCTA 58.212 39.130 4.92 0.00 37.15 2.59
4989 5841 4.578928 ACAATTGTTTGGGTGTGAGTCTAC 59.421 41.667 4.92 0.00 37.15 2.59
4993 5845 6.921486 TTGTTTGGGTGTGAGTCTACTATA 57.079 37.500 0.00 0.00 0.00 1.31
5062 5914 8.641498 AAGCTTCTGAATAAAGAATGGAAAGA 57.359 30.769 0.00 0.00 35.67 2.52
5093 5945 9.940166 GAAGACAATTTTTCAAGCAATTGAAAT 57.060 25.926 10.34 2.21 46.47 2.17
5200 6052 4.861102 AAAGGCTTCTCAAACCAATCAG 57.139 40.909 0.00 0.00 0.00 2.90
5205 6057 5.541484 AGGCTTCTCAAACCAATCAGAAATT 59.459 36.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.947652 CACTTTGCCAGGTGGATCTATG 59.052 50.000 0.00 0.00 37.39 2.23
9 10 1.067295 TCACTTTGCCAGGTGGATCT 58.933 50.000 0.00 0.00 37.39 2.75
20 21 0.038892 CCCTGCACATGTCACTTTGC 60.039 55.000 0.00 0.00 35.45 3.68
128 156 2.478200 CGGCCGTGTTTACACTGTTTTT 60.478 45.455 19.50 0.00 44.34 1.94
129 157 1.064357 CGGCCGTGTTTACACTGTTTT 59.936 47.619 19.50 0.00 44.34 2.43
130 158 0.658897 CGGCCGTGTTTACACTGTTT 59.341 50.000 19.50 0.00 44.34 2.83
131 159 0.462403 ACGGCCGTGTTTACACTGTT 60.462 50.000 33.75 0.00 44.34 3.16
132 160 0.388659 TACGGCCGTGTTTACACTGT 59.611 50.000 40.02 11.62 44.34 3.55
133 161 1.458064 CTTACGGCCGTGTTTACACTG 59.542 52.381 40.02 14.55 44.34 3.66
242 278 1.599667 GCGTGACACTTGTTCTCGAGA 60.600 52.381 12.08 12.08 0.00 4.04
291 327 0.529992 CCCGGTAACAATCTCGCTCC 60.530 60.000 0.00 0.00 0.00 4.70
405 442 2.596851 GCAGAGGGACTTGGAGGCA 61.597 63.158 0.00 0.00 41.55 4.75
445 482 1.544825 CCAAGGAGAAGGACAGCCGA 61.545 60.000 0.00 0.00 39.96 5.54
450 487 0.178944 TCGGACCAAGGAGAAGGACA 60.179 55.000 0.00 0.00 0.00 4.02
452 489 1.258445 GCTCGGACCAAGGAGAAGGA 61.258 60.000 0.00 0.00 31.90 3.36
454 491 0.174617 GAGCTCGGACCAAGGAGAAG 59.825 60.000 0.00 0.00 31.90 2.85
455 492 1.258445 GGAGCTCGGACCAAGGAGAA 61.258 60.000 7.83 0.00 31.90 2.87
456 493 1.682684 GGAGCTCGGACCAAGGAGA 60.683 63.158 7.83 0.00 31.90 3.71
458 495 2.119611 TGGAGCTCGGACCAAGGA 59.880 61.111 7.83 0.00 32.93 3.36
755 802 1.081242 CAAGTGGCGGCATCACAAC 60.081 57.895 17.19 0.00 37.58 3.32
790 837 3.845781 AGGAGCAGAAAAGAACACAGA 57.154 42.857 0.00 0.00 0.00 3.41
798 845 3.722728 AGCAACAAAGGAGCAGAAAAG 57.277 42.857 0.00 0.00 0.00 2.27
809 858 3.217626 AGAGGAGGAACAAGCAACAAAG 58.782 45.455 0.00 0.00 0.00 2.77
868 917 1.765904 GAGCTAAAGGGAGAAGAGGGG 59.234 57.143 0.00 0.00 0.00 4.79
932 1002 1.920272 GCGAAAGAGTGACGTTTTGGC 60.920 52.381 1.75 1.75 0.00 4.52
953 1023 2.545742 GCAAGGAAGCAAACAAATCGGT 60.546 45.455 0.00 0.00 0.00 4.69
970 1040 0.392998 ATTGGACTAGTGGGCGCAAG 60.393 55.000 10.83 2.52 43.44 4.01
1113 1186 5.964958 AATGCGAATGTATATTGGGGAAG 57.035 39.130 0.00 0.00 0.00 3.46
1159 1239 8.292448 ACTCAACAAGAACATAAACAGCTAATG 58.708 33.333 0.00 0.00 0.00 1.90
1165 1245 7.011389 TCAGTCACTCAACAAGAACATAAACAG 59.989 37.037 0.00 0.00 0.00 3.16
2110 2235 3.069016 TCACATAGCCATAGTACGGTTGG 59.931 47.826 7.24 7.24 0.00 3.77
2430 2555 8.893727 ACAGGTATGTGCTTACTTGATTATTTC 58.106 33.333 12.07 0.00 38.57 2.17
2530 2655 2.168496 GTCAGGGAGTACACTGCACTA 58.832 52.381 3.21 0.00 46.15 2.74
2830 2955 7.057264 GGAGGAAATTTAGCTTACTTGGATCT 58.943 38.462 0.00 0.00 0.00 2.75
2907 3032 6.660521 TCAAACCTGCATCTACTGATTGATTT 59.339 34.615 0.00 0.00 0.00 2.17
2970 3095 4.777366 TGTTGAGATAGTGAGACCAATGGA 59.223 41.667 6.16 0.00 0.00 3.41
2971 3096 4.872691 GTGTTGAGATAGTGAGACCAATGG 59.127 45.833 0.00 0.00 0.00 3.16
2973 3098 7.482169 TTAGTGTTGAGATAGTGAGACCAAT 57.518 36.000 0.00 0.00 0.00 3.16
3317 3443 7.279536 CAGAATCTTAGAGACAAAGCAGCAATA 59.720 37.037 0.00 0.00 0.00 1.90
3390 3516 5.625311 GTGACTAAAAACAGGAAGATTTGCG 59.375 40.000 0.00 0.00 0.00 4.85
3798 3929 4.205587 GACCAGATCAGATGATTGGCTTT 58.794 43.478 16.99 5.37 36.78 3.51
3864 3995 3.577649 ACTACAAGATGACTGTCACGG 57.422 47.619 13.50 5.56 0.00 4.94
3971 4102 2.962421 CAGGGGAAACTTTGTTTAGGCA 59.038 45.455 0.00 0.00 0.00 4.75
3999 4130 1.180456 TGAACCATGGCCTGCAAGTG 61.180 55.000 13.04 0.00 0.00 3.16
4043 4174 8.514330 TTGAACTTACAAGAACACCAAAGTAT 57.486 30.769 0.00 0.00 0.00 2.12
4302 4438 5.004448 GGGCTCCCTTTATATCTAACAAGC 58.996 45.833 0.00 0.00 0.00 4.01
4303 4439 6.441088 AGGGCTCCCTTTATATCTAACAAG 57.559 41.667 0.54 0.00 45.70 3.16
4314 4450 4.080526 GTGAGACAAATAGGGCTCCCTTTA 60.081 45.833 13.48 0.00 45.70 1.85
4590 4729 2.808933 CGCCAACACTCAGACCCTAAAA 60.809 50.000 0.00 0.00 0.00 1.52
4628 4767 5.169992 TGGCCCAGAGATAATGACATATG 57.830 43.478 0.00 0.00 0.00 1.78
4640 4779 1.703411 CCTTTGTTTTGGCCCAGAGA 58.297 50.000 0.00 0.00 0.00 3.10
4674 4813 7.222611 GGCAATATTAAAAACAATCAGCGACAT 59.777 33.333 0.00 0.00 0.00 3.06
4676 4815 6.291060 CGGCAATATTAAAAACAATCAGCGAC 60.291 38.462 0.00 0.00 0.00 5.19
4677 4816 5.741510 CGGCAATATTAAAAACAATCAGCGA 59.258 36.000 0.00 0.00 0.00 4.93
4678 4817 5.554324 GCGGCAATATTAAAAACAATCAGCG 60.554 40.000 0.00 0.00 0.00 5.18
4692 4832 3.374058 GCTAACATATCCGCGGCAATATT 59.626 43.478 23.51 14.02 0.00 1.28
4766 5617 4.292571 TGGATATCCCACCCTCTACTAGAG 59.707 50.000 19.34 6.14 40.82 2.43
4803 5654 1.043673 ACAGAGGCGAGGTATCACCC 61.044 60.000 0.00 0.00 39.75 4.61
4819 5670 7.490079 CCATGAAAAACACATCATATTCCACAG 59.510 37.037 0.00 0.00 34.61 3.66
4833 5684 3.791245 TGGCTTTGTCCATGAAAAACAC 58.209 40.909 0.00 0.00 0.00 3.32
4834 5685 4.686191 ATGGCTTTGTCCATGAAAAACA 57.314 36.364 0.00 0.00 44.72 2.83
4835 5686 7.671495 ATTAATGGCTTTGTCCATGAAAAAC 57.329 32.000 0.00 0.00 45.64 2.43
4836 5687 9.381033 CATATTAATGGCTTTGTCCATGAAAAA 57.619 29.630 0.00 0.00 45.64 1.94
4837 5688 8.756927 TCATATTAATGGCTTTGTCCATGAAAA 58.243 29.630 0.00 0.00 45.64 2.29
4838 5689 8.303780 TCATATTAATGGCTTTGTCCATGAAA 57.696 30.769 0.00 0.00 45.64 2.69
4839 5690 7.894753 TCATATTAATGGCTTTGTCCATGAA 57.105 32.000 0.00 0.00 45.64 2.57
4840 5691 7.894753 TTCATATTAATGGCTTTGTCCATGA 57.105 32.000 0.00 0.00 45.64 3.07
4841 5692 8.582437 AGATTCATATTAATGGCTTTGTCCATG 58.418 33.333 0.00 0.00 45.64 3.66
4862 5713 6.363577 TCAAACAGACACAAGACAAGATTC 57.636 37.500 0.00 0.00 0.00 2.52
4869 5720 3.375299 AGTTGCTCAAACAGACACAAGAC 59.625 43.478 0.00 0.00 41.61 3.01
4870 5721 3.609853 AGTTGCTCAAACAGACACAAGA 58.390 40.909 0.00 0.00 41.61 3.02
4908 5759 7.823799 ACAAATGGTCTGATTTTTGTGAAAGTT 59.176 29.630 11.98 0.00 39.94 2.66
4910 5761 7.775397 ACAAATGGTCTGATTTTTGTGAAAG 57.225 32.000 11.98 0.00 39.94 2.62
4923 5774 6.940831 ATTTTTCCCAAAACAAATGGTCTG 57.059 33.333 0.00 0.00 34.63 3.51
4940 5791 4.264849 GCACGACTCTACGGACTATTTTTC 59.735 45.833 0.00 0.00 37.61 2.29
4945 5796 2.034104 TGCACGACTCTACGGACTAT 57.966 50.000 0.00 0.00 37.61 2.12
4949 5800 0.669619 TGTTTGCACGACTCTACGGA 59.330 50.000 0.00 0.00 37.61 4.69
4950 5801 1.493772 TTGTTTGCACGACTCTACGG 58.506 50.000 0.00 0.00 37.61 4.02
4951 5802 3.059868 ACAATTGTTTGCACGACTCTACG 60.060 43.478 4.92 0.00 36.22 3.51
4952 5803 4.468095 ACAATTGTTTGCACGACTCTAC 57.532 40.909 4.92 0.00 36.22 2.59
4953 5804 5.493133 AAACAATTGTTTGCACGACTCTA 57.507 34.783 30.64 0.00 45.55 2.43
4954 5805 4.370364 AAACAATTGTTTGCACGACTCT 57.630 36.364 30.64 7.31 45.55 3.24
4993 5845 7.498570 CCGAGGTACTACTACTTGAATAGAAGT 59.501 40.741 0.00 0.00 41.55 3.01
5004 5856 5.385628 AGGAATTCCGAGGTACTACTACT 57.614 43.478 18.82 0.00 41.55 2.57
5005 5857 7.757941 AATAGGAATTCCGAGGTACTACTAC 57.242 40.000 18.82 0.00 41.55 2.73
5007 5859 8.953223 AATAATAGGAATTCCGAGGTACTACT 57.047 34.615 18.82 0.00 41.55 2.57
5079 5931 4.339872 ACTTGCCATTTCAATTGCTTGA 57.660 36.364 0.00 0.00 39.62 3.02
5080 5932 5.427036 AAACTTGCCATTTCAATTGCTTG 57.573 34.783 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.