Multiple sequence alignment - TraesCS5B01G393600

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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 TraesCS5B01G393600 chr5B 100.000 3848 0 0 1 3848 571633810 571637657 0.000000e+00 7107.0
1 TraesCS5B01G393600 chr5D 92.911 3047 147 29 776 3797 464664053 464661051 0.000000e+00 4366.0
2 TraesCS5B01G393600 chr2B 94.859 778 34 4 1 775 262902764 262903538 0.000000e+00 1210.0
3 TraesCS5B01G393600 chr2B 93.893 786 43 4 1 781 694690016 694689231 0.000000e+00 1181.0
4 TraesCS5B01G393600 chr7D 94.852 777 34 5 1 773 114468051 114467277 0.000000e+00 1208.0
5 TraesCS5B01G393600 chr7D 94.416 788 35 7 1 784 151540847 151540065 0.000000e+00 1203.0
6 TraesCS5B01G393600 chr3D 94.629 782 37 5 1 779 214959441 214958662 0.000000e+00 1206.0
7 TraesCS5B01G393600 chr7B 94.615 780 36 4 1 777 94806893 94806117 0.000000e+00 1203.0
8 TraesCS5B01G393600 chr7B 94.602 778 39 2 1 776 154684634 154683858 0.000000e+00 1201.0
9 TraesCS5B01G393600 chr5A 94.615 780 36 4 1 777 504755041 504754265 0.000000e+00 1203.0
10 TraesCS5B01G393600 chr5A 93.854 781 48 0 926 1706 585086696 585085916 0.000000e+00 1177.0
11 TraesCS5B01G393600 chr5A 95.000 720 31 3 1701 2415 585080841 585080122 0.000000e+00 1125.0
12 TraesCS5B01G393600 chr5A 91.338 785 48 10 3022 3797 585080118 585079345 0.000000e+00 1055.0
13 TraesCS5B01G393600 chr1B 94.615 780 35 5 1 777 358032004 358031229 0.000000e+00 1201.0
14 TraesCS5B01G393600 chr7A 73.674 1527 314 60 997 2489 91301355 91299883 2.650000e-141 512.0
15 TraesCS5B01G393600 chrUn 74.686 557 122 17 1951 2498 91331193 91331739 2.990000e-56 230.0
16 TraesCS5B01G393600 chr3B 94.872 39 2 0 1436 1474 771623308 771623270 1.150000e-05 62.1
17 TraesCS5B01G393600 chr3B 94.872 39 2 0 1436 1474 771633985 771633947 1.150000e-05 62.1
18 TraesCS5B01G393600 chr6B 97.143 35 1 0 2309 2343 80839819 80839785 4.150000e-05 60.2
19 TraesCS5B01G393600 chr4A 97.143 35 1 0 2309 2343 647321264 647321298 4.150000e-05 60.2


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 TraesCS5B01G393600 chr5B 571633810 571637657 3847 False 7107 7107 100.000 1 3848 1 chr5B.!!$F1 3847
1 TraesCS5B01G393600 chr5D 464661051 464664053 3002 True 4366 4366 92.911 776 3797 1 chr5D.!!$R1 3021
2 TraesCS5B01G393600 chr2B 262902764 262903538 774 False 1210 1210 94.859 1 775 1 chr2B.!!$F1 774
3 TraesCS5B01G393600 chr2B 694689231 694690016 785 True 1181 1181 93.893 1 781 1 chr2B.!!$R1 780
4 TraesCS5B01G393600 chr7D 114467277 114468051 774 True 1208 1208 94.852 1 773 1 chr7D.!!$R1 772
5 TraesCS5B01G393600 chr7D 151540065 151540847 782 True 1203 1203 94.416 1 784 1 chr7D.!!$R2 783
6 TraesCS5B01G393600 chr3D 214958662 214959441 779 True 1206 1206 94.629 1 779 1 chr3D.!!$R1 778
7 TraesCS5B01G393600 chr7B 94806117 94806893 776 True 1203 1203 94.615 1 777 1 chr7B.!!$R1 776
8 TraesCS5B01G393600 chr7B 154683858 154684634 776 True 1201 1201 94.602 1 776 1 chr7B.!!$R2 775
9 TraesCS5B01G393600 chr5A 504754265 504755041 776 True 1203 1203 94.615 1 777 1 chr5A.!!$R1 776
10 TraesCS5B01G393600 chr5A 585085916 585086696 780 True 1177 1177 93.854 926 1706 1 chr5A.!!$R2 780
11 TraesCS5B01G393600 chr5A 585079345 585080841 1496 True 1090 1125 93.169 1701 3797 2 chr5A.!!$R3 2096
12 TraesCS5B01G393600 chr1B 358031229 358032004 775 True 1201 1201 94.615 1 777 1 chr1B.!!$R1 776
13 TraesCS5B01G393600 chr7A 91299883 91301355 1472 True 512 512 73.674 997 2489 1 chr7A.!!$R1 1492
14 TraesCS5B01G393600 chrUn 91331193 91331739 546 False 230 230 74.686 1951 2498 1 chrUn.!!$F1 547

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
832 840 0.034089 GTAGCTGGTGCCCAATCCTT 60.034 55.000 0.00 0.00 40.80 3.36 F
876 884 0.181114 CGGCCATCCAATCTTCCAGA 59.819 55.000 2.24 0.00 0.00 3.86 F
1298 1315 0.591659 CCGATCATGGATTGCTGCAG 59.408 55.000 10.11 10.11 0.00 4.41 F
1716 1742 1.153449 CGCCTATTGGAAGGACGCA 60.153 57.895 0.00 0.00 39.15 5.24 F
2199 2260 1.738350 CTTCAGCCTGCAGATGACAAG 59.262 52.381 17.39 10.23 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1790 0.251077 GCCTAAGATGGGGGCAGATG 60.251 60.000 0.00 0.0 44.69 2.90 R
2214 2275 1.351017 TCCCAGTCAAAATCGCCTTCT 59.649 47.619 0.00 0.0 0.00 2.85 R
2521 2582 1.474077 CTGGAACTACAGGGCATTTGC 59.526 52.381 0.00 0.0 41.14 3.68 R
2759 2820 1.492319 GAGCGCACCACAAACGTGTA 61.492 55.000 11.47 0.0 35.72 2.90 R
3101 3174 3.128589 GCATTGTGGCGATTCTCCTTTTA 59.871 43.478 0.00 0.0 0.00 1.52 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
51 52 1.070914 TGCCATGTCGGACAACTACAA 59.929 47.619 15.72 0.00 36.56 2.41
155 156 1.047801 TGTGGTCTGCTCTACTGCAA 58.952 50.000 0.00 0.00 42.83 4.08
269 273 4.982999 TCGGATAAAAGAGAGAGTTGTCG 58.017 43.478 0.00 0.00 0.00 4.35
271 275 5.645067 TCGGATAAAAGAGAGAGTTGTCGTA 59.355 40.000 0.00 0.00 0.00 3.43
472 479 0.743688 ACAAAACGCATGGCAACTGA 59.256 45.000 0.00 0.00 37.61 3.41
542 549 1.454104 CCACACACCAGCCCTTGTA 59.546 57.895 0.00 0.00 0.00 2.41
546 553 0.534203 CACACCAGCCCTTGTACGTT 60.534 55.000 0.00 0.00 0.00 3.99
552 560 2.607187 CAGCCCTTGTACGTTACTGAG 58.393 52.381 0.00 0.00 0.00 3.35
587 595 1.503818 AACTGCTAAACGCCCACACG 61.504 55.000 0.00 0.00 38.05 4.49
607 615 1.686325 CCGACCCCTCCATGTGGTAG 61.686 65.000 0.00 0.00 36.34 3.18
620 628 1.964933 TGTGGTAGAACGGATGTGTGA 59.035 47.619 0.00 0.00 0.00 3.58
625 633 0.532573 AGAACGGATGTGTGAGCGAT 59.467 50.000 0.00 0.00 0.00 4.58
699 707 1.808411 ATTCGTGCCAAGATTCGTGT 58.192 45.000 0.00 0.00 0.00 4.49
814 822 8.814038 AATTAAATGTTTGGAGATCTGCTAGT 57.186 30.769 15.82 0.00 0.00 2.57
815 823 9.905713 AATTAAATGTTTGGAGATCTGCTAGTA 57.094 29.630 15.82 1.54 0.00 1.82
816 824 8.948631 TTAAATGTTTGGAGATCTGCTAGTAG 57.051 34.615 15.82 0.63 0.00 2.57
824 832 0.755686 ATCTGCTAGTAGCTGGTGCC 59.244 55.000 23.94 0.00 42.97 5.01
832 840 0.034089 GTAGCTGGTGCCCAATCCTT 60.034 55.000 0.00 0.00 40.80 3.36
833 841 0.704076 TAGCTGGTGCCCAATCCTTT 59.296 50.000 0.00 0.00 40.80 3.11
834 842 0.901580 AGCTGGTGCCCAATCCTTTG 60.902 55.000 0.00 0.00 40.80 2.77
842 850 2.978278 TGCCCAATCCTTTGAACCAATT 59.022 40.909 0.00 0.00 34.60 2.32
876 884 0.181114 CGGCCATCCAATCTTCCAGA 59.819 55.000 2.24 0.00 0.00 3.86
923 931 1.977293 ATCTCGCCTTCCAAGCTCCC 61.977 60.000 0.00 0.00 0.00 4.30
989 997 1.062587 CCGCATGTACTAGCAAGCAAC 59.937 52.381 10.04 0.00 33.25 4.17
1026 1034 3.419580 ATGGATCTGGCGCCCCAA 61.420 61.111 26.77 9.79 41.58 4.12
1161 1169 3.893763 CTCCCGCTCACGCTCGAT 61.894 66.667 0.00 0.00 38.22 3.59
1192 1200 2.295885 ACGAGACCTGTCCCTATAACG 58.704 52.381 0.00 0.00 0.00 3.18
1193 1201 2.092753 ACGAGACCTGTCCCTATAACGA 60.093 50.000 0.00 0.00 0.00 3.85
1298 1315 0.591659 CCGATCATGGATTGCTGCAG 59.408 55.000 10.11 10.11 0.00 4.41
1299 1316 1.306148 CGATCATGGATTGCTGCAGT 58.694 50.000 16.64 0.00 0.00 4.40
1487 1510 4.503714 TGATCCCTAACATTCCCTTCAC 57.496 45.455 0.00 0.00 0.00 3.18
1623 1649 3.194062 CTGGAAGGAAAGATCGCTTCTC 58.806 50.000 9.56 2.49 35.21 2.87
1716 1742 1.153449 CGCCTATTGGAAGGACGCA 60.153 57.895 0.00 0.00 39.15 5.24
1768 1795 9.562408 TTCTTCTGAGGTAGTACTATACATCTG 57.438 37.037 5.75 8.22 37.36 2.90
1790 1819 2.338809 CCCCATCTTAGGCACCAGATA 58.661 52.381 0.00 0.00 28.89 1.98
1810 1842 8.906867 CCAGATACAATTGGATGTTCAGTTTAT 58.093 33.333 8.22 0.00 36.55 1.40
1900 1961 7.155655 TGCAGAATAAACTTGTTGCATGATA 57.844 32.000 0.00 0.00 36.71 2.15
1901 1962 7.028962 TGCAGAATAAACTTGTTGCATGATAC 58.971 34.615 0.00 0.00 36.71 2.24
1902 1963 6.473455 GCAGAATAAACTTGTTGCATGATACC 59.527 38.462 0.00 0.00 0.00 2.73
1903 1964 7.629222 GCAGAATAAACTTGTTGCATGATACCT 60.629 37.037 0.00 0.00 0.00 3.08
1904 1965 8.892723 CAGAATAAACTTGTTGCATGATACCTA 58.107 33.333 0.00 0.00 0.00 3.08
1905 1966 9.632638 AGAATAAACTTGTTGCATGATACCTAT 57.367 29.630 0.00 0.00 0.00 2.57
1906 1967 9.884465 GAATAAACTTGTTGCATGATACCTATC 57.116 33.333 0.00 0.00 0.00 2.08
1907 1968 5.991328 AACTTGTTGCATGATACCTATCG 57.009 39.130 0.00 0.00 35.48 2.92
1908 1969 5.276461 ACTTGTTGCATGATACCTATCGA 57.724 39.130 0.00 0.00 35.48 3.59
1909 1970 5.292765 ACTTGTTGCATGATACCTATCGAG 58.707 41.667 0.00 0.00 35.48 4.04
1910 1971 4.937201 TGTTGCATGATACCTATCGAGT 57.063 40.909 0.00 0.00 35.48 4.18
1911 1972 4.620982 TGTTGCATGATACCTATCGAGTG 58.379 43.478 0.00 0.00 35.48 3.51
1912 1973 4.340950 TGTTGCATGATACCTATCGAGTGA 59.659 41.667 0.00 0.00 35.48 3.41
1913 1974 5.011023 TGTTGCATGATACCTATCGAGTGAT 59.989 40.000 0.00 0.00 38.67 3.06
1914 1975 5.316327 TGCATGATACCTATCGAGTGATC 57.684 43.478 0.00 0.00 35.99 2.92
1915 1976 4.766891 TGCATGATACCTATCGAGTGATCA 59.233 41.667 0.00 0.00 35.99 2.92
1916 1977 5.243730 TGCATGATACCTATCGAGTGATCAA 59.756 40.000 0.00 0.00 35.99 2.57
1917 1978 5.804473 GCATGATACCTATCGAGTGATCAAG 59.196 44.000 0.00 0.00 35.99 3.02
1918 1979 6.571344 GCATGATACCTATCGAGTGATCAAGT 60.571 42.308 0.00 0.00 35.99 3.16
1919 1980 6.961360 TGATACCTATCGAGTGATCAAGTT 57.039 37.500 0.00 0.00 35.99 2.66
1920 1981 7.348080 TGATACCTATCGAGTGATCAAGTTT 57.652 36.000 0.00 0.00 35.99 2.66
1921 1982 7.426410 TGATACCTATCGAGTGATCAAGTTTC 58.574 38.462 0.00 0.00 35.99 2.78
1922 1983 5.012328 ACCTATCGAGTGATCAAGTTTCC 57.988 43.478 0.00 0.00 35.99 3.13
1923 1984 4.466370 ACCTATCGAGTGATCAAGTTTCCA 59.534 41.667 0.00 0.00 35.99 3.53
1924 1985 5.046529 CCTATCGAGTGATCAAGTTTCCAG 58.953 45.833 0.00 0.00 35.99 3.86
1925 1986 4.808414 ATCGAGTGATCAAGTTTCCAGA 57.192 40.909 0.00 0.00 0.00 3.86
1926 1987 4.808414 TCGAGTGATCAAGTTTCCAGAT 57.192 40.909 0.00 0.00 0.00 2.90
2018 2079 4.377943 CGACCGCAACACATTTCAGATTTA 60.378 41.667 0.00 0.00 0.00 1.40
2199 2260 1.738350 CTTCAGCCTGCAGATGACAAG 59.262 52.381 17.39 10.23 0.00 3.16
2214 2275 3.286353 TGACAAGGACAAAGCAATGACA 58.714 40.909 0.00 0.00 0.00 3.58
2424 2485 5.485353 GGGTGAGATGAGGTATGGATATGAA 59.515 44.000 0.00 0.00 0.00 2.57
2451 2512 4.002906 ACAAGAGTCCTTTTCATACGCA 57.997 40.909 0.00 0.00 0.00 5.24
2461 2522 4.353737 CTTTTCATACGCATCATGTTGGG 58.646 43.478 16.79 16.79 35.79 4.12
2521 2582 9.218440 ACCCTTTGATTATATTTTTGTTTGCAG 57.782 29.630 0.00 0.00 0.00 4.41
2643 2704 9.323985 TGTTATTTGGGAAGACAATTTTTCTTG 57.676 29.630 2.62 0.00 33.30 3.02
2728 2789 5.534278 TCCTTTGCATTGTAGTTCATTCACA 59.466 36.000 0.00 0.00 0.00 3.58
2743 2804 9.220767 AGTTCATTCACAGAATTTAGGTACTTC 57.779 33.333 0.00 0.00 41.75 3.01
2759 2820 6.838382 AGGTACTTCTCATTGTTTGGTTACT 58.162 36.000 0.00 0.00 27.25 2.24
2813 2874 5.351740 GCTGTATTTAGGGATCTTTATCGCC 59.648 44.000 0.00 0.00 44.14 5.54
2825 2886 2.228138 TTATCGCCCGTTATGACCAC 57.772 50.000 0.00 0.00 0.00 4.16
2835 2896 4.101119 CCCGTTATGACCACTTTATCCTCT 59.899 45.833 0.00 0.00 0.00 3.69
2844 2905 4.250464 CCACTTTATCCTCTACGTGCAAA 58.750 43.478 0.00 0.00 0.00 3.68
2845 2906 4.693566 CCACTTTATCCTCTACGTGCAAAA 59.306 41.667 0.00 0.00 0.00 2.44
2846 2907 5.180492 CCACTTTATCCTCTACGTGCAAAAA 59.820 40.000 0.00 0.00 0.00 1.94
2873 2946 7.516198 ACTCTTATTTGAGCACAAGAAATGT 57.484 32.000 0.00 0.00 38.98 2.71
3014 3087 4.142160 ACAAGGCTTCCAAGAAACAAAGAC 60.142 41.667 0.00 0.00 0.00 3.01
3020 3093 5.625311 GCTTCCAAGAAACAAAGACAATACG 59.375 40.000 0.00 0.00 0.00 3.06
3026 3099 5.120399 AGAAACAAAGACAATACGTGTGGA 58.880 37.500 0.00 0.00 41.96 4.02
3101 3174 7.486407 AATATCTCAAGCTTGGATGGTTTTT 57.514 32.000 27.19 15.90 0.00 1.94
3210 3283 5.369110 AGAAATAGGGATTCACAGCTGAGAT 59.631 40.000 23.35 10.75 0.00 2.75
3364 3438 6.615088 AGATGTTGTTGATTGAATACAGTGC 58.385 36.000 0.00 0.00 0.00 4.40
3408 3482 4.816392 TGTCTGTTCATGCGTACTAATGT 58.184 39.130 5.00 0.00 0.00 2.71
3409 3483 5.234752 TGTCTGTTCATGCGTACTAATGTT 58.765 37.500 5.00 0.00 0.00 2.71
3492 3566 4.576463 GGGATATGGTCTGATGTTGTCAAC 59.424 45.833 8.86 8.86 36.14 3.18
3494 3568 2.613026 TGGTCTGATGTTGTCAACGT 57.387 45.000 10.25 10.25 36.14 3.99
3565 3639 1.272212 GGTGCCCTGGTTTGTTGTATG 59.728 52.381 0.00 0.00 0.00 2.39
3566 3640 1.272212 GTGCCCTGGTTTGTTGTATGG 59.728 52.381 0.00 0.00 0.00 2.74
3568 3642 1.544246 GCCCTGGTTTGTTGTATGGTC 59.456 52.381 0.00 0.00 0.00 4.02
3569 3643 2.167662 CCCTGGTTTGTTGTATGGTCC 58.832 52.381 0.00 0.00 0.00 4.46
3570 3644 1.810151 CCTGGTTTGTTGTATGGTCCG 59.190 52.381 0.00 0.00 0.00 4.79
3574 3648 3.244596 TGGTTTGTTGTATGGTCCGATGA 60.245 43.478 0.00 0.00 0.00 2.92
3575 3649 3.945285 GGTTTGTTGTATGGTCCGATGAT 59.055 43.478 0.00 0.00 0.00 2.45
3576 3650 5.120399 GGTTTGTTGTATGGTCCGATGATA 58.880 41.667 0.00 0.00 0.00 2.15
3577 3651 5.763204 GGTTTGTTGTATGGTCCGATGATAT 59.237 40.000 0.00 0.00 0.00 1.63
3578 3652 6.262273 GGTTTGTTGTATGGTCCGATGATATT 59.738 38.462 0.00 0.00 0.00 1.28
3579 3653 7.442969 GGTTTGTTGTATGGTCCGATGATATTA 59.557 37.037 0.00 0.00 0.00 0.98
3580 3654 8.832521 GTTTGTTGTATGGTCCGATGATATTAA 58.167 33.333 0.00 0.00 0.00 1.40
3581 3655 9.567776 TTTGTTGTATGGTCCGATGATATTAAT 57.432 29.630 0.00 0.00 0.00 1.40
3582 3656 9.567776 TTGTTGTATGGTCCGATGATATTAATT 57.432 29.630 0.00 0.00 0.00 1.40
3583 3657 9.567776 TGTTGTATGGTCCGATGATATTAATTT 57.432 29.630 0.00 0.00 0.00 1.82
3612 3686 9.342308 CTACTATGGTTTGTATTGTTGGATGAT 57.658 33.333 0.00 0.00 0.00 2.45
3646 3720 9.349713 ACTTTTATTCTTATGTTGGTGAGTCAA 57.650 29.630 0.00 0.00 0.00 3.18
3662 3736 5.049474 GTGAGTCAAGTACATGCATGTTTCA 60.049 40.000 35.45 22.10 41.97 2.69
3690 3765 2.262915 GACACCCTGTCAGCGGAG 59.737 66.667 12.72 8.28 46.22 4.63
3704 3779 5.112686 GTCAGCGGAGATTCAAGAAGTAAT 58.887 41.667 0.00 0.00 0.00 1.89
3706 3781 4.272018 CAGCGGAGATTCAAGAAGTAATGG 59.728 45.833 0.00 0.00 0.00 3.16
3839 3920 6.928979 TTTTGGAGAGAAAAACACGTATGA 57.071 33.333 0.00 0.00 0.00 2.15
3840 3921 6.539649 TTTGGAGAGAAAAACACGTATGAG 57.460 37.500 0.00 0.00 0.00 2.90
3841 3922 5.209818 TGGAGAGAAAAACACGTATGAGT 57.790 39.130 0.00 0.00 0.00 3.41
3842 3923 5.607477 TGGAGAGAAAAACACGTATGAGTT 58.393 37.500 0.00 0.00 0.00 3.01
3843 3924 6.053005 TGGAGAGAAAAACACGTATGAGTTT 58.947 36.000 4.84 4.84 40.03 2.66
3844 3925 6.018262 TGGAGAGAAAAACACGTATGAGTTTG 60.018 38.462 10.68 0.00 38.61 2.93
3845 3926 6.202188 GGAGAGAAAAACACGTATGAGTTTGA 59.798 38.462 10.68 0.00 38.61 2.69
3846 3927 7.178712 AGAGAAAAACACGTATGAGTTTGAG 57.821 36.000 10.68 0.00 38.61 3.02
3847 3928 5.748592 AGAAAAACACGTATGAGTTTGAGC 58.251 37.500 10.68 4.69 38.61 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 2.868839 GCAGTTGAGCAAACATGGCAAT 60.869 45.455 0.00 0.00 41.61 3.56
145 146 4.913335 AATCATGGCAATTGCAGTAGAG 57.087 40.909 30.32 14.00 44.36 2.43
155 156 7.678837 TCCTAAAGTTTTGAAATCATGGCAAT 58.321 30.769 0.00 0.00 0.00 3.56
251 254 6.868622 AGCATACGACAACTCTCTCTTTTAT 58.131 36.000 0.00 0.00 0.00 1.40
401 408 2.555757 GCAAACAGATGGCAACTCTCTT 59.444 45.455 0.00 0.00 37.61 2.85
418 425 4.085357 ACTGTCCTAGTGTGATTGCAAA 57.915 40.909 1.71 0.00 38.49 3.68
472 479 1.770110 TCTCCCACACCCAAGCTGT 60.770 57.895 0.00 0.00 0.00 4.40
542 549 2.029623 ACACACCAGTCTCAGTAACGT 58.970 47.619 0.00 0.00 0.00 3.99
546 553 1.338107 CCCACACACCAGTCTCAGTA 58.662 55.000 0.00 0.00 0.00 2.74
552 560 2.110213 TTCGCCCACACACCAGTC 59.890 61.111 0.00 0.00 0.00 3.51
587 595 4.489771 CCACATGGAGGGGTCGGC 62.490 72.222 0.00 0.00 35.41 5.54
599 607 2.565391 TCACACATCCGTTCTACCACAT 59.435 45.455 0.00 0.00 0.00 3.21
607 615 0.924090 GATCGCTCACACATCCGTTC 59.076 55.000 0.00 0.00 0.00 3.95
620 628 0.814457 GGTGTGTGAGAGAGATCGCT 59.186 55.000 0.00 0.00 0.00 4.93
625 633 1.409064 GTGTGTGGTGTGTGAGAGAGA 59.591 52.381 0.00 0.00 0.00 3.10
699 707 3.446161 CCATCACCGTCCAGTAACTTCTA 59.554 47.826 0.00 0.00 0.00 2.10
759 767 8.389586 GAAATTAATTCGGAAATGTTAACGCT 57.610 30.769 0.10 0.00 0.00 5.07
786 794 7.769220 AGCAGATCTCCAAACATTTAATTCAG 58.231 34.615 0.00 0.00 0.00 3.02
962 970 1.403647 GCTAGTACATGCGGTGTGTGA 60.404 52.381 4.94 0.00 42.24 3.58
1026 1034 3.264866 GACCTCCGCGACAACGTCT 62.265 63.158 8.23 0.00 41.98 4.18
1161 1169 1.751351 CAGGTCTCGTAGAAGATGCCA 59.249 52.381 0.00 0.00 34.09 4.92
1192 1200 1.203287 GCTGGAGAAAAGCATGGGTTC 59.797 52.381 0.00 0.00 40.52 3.62
1193 1201 1.260544 GCTGGAGAAAAGCATGGGTT 58.739 50.000 0.00 0.00 40.52 4.11
1298 1315 1.028868 GCACATCAGGAGAAGGCCAC 61.029 60.000 5.01 0.00 0.00 5.01
1299 1316 1.203441 AGCACATCAGGAGAAGGCCA 61.203 55.000 5.01 0.00 0.00 5.36
1411 1434 2.717530 GTACACGAGGTAGCGATTCTG 58.282 52.381 0.00 0.00 31.13 3.02
1487 1510 3.515316 ATATGCCCCGTCGGAAGCG 62.515 63.158 14.39 0.00 0.00 4.68
1656 1682 5.488341 ACAGTATCATAAACCGCTTTCACT 58.512 37.500 0.00 0.00 0.00 3.41
1716 1742 3.502920 CTCTTCGCAACGAACATAGAGT 58.497 45.455 0.00 0.00 41.05 3.24
1763 1790 0.251077 GCCTAAGATGGGGGCAGATG 60.251 60.000 0.00 0.00 44.69 2.90
1768 1795 2.195956 GGTGCCTAAGATGGGGGC 59.804 66.667 0.00 0.00 45.45 5.80
1811 1843 3.459710 ACGGATATTGGTGGGGAAAAA 57.540 42.857 0.00 0.00 0.00 1.94
1859 1893 4.681744 TCTGCAAGAACCAAATCAACAAC 58.318 39.130 0.00 0.00 42.31 3.32
1900 1961 4.466370 TGGAAACTTGATCACTCGATAGGT 59.534 41.667 0.00 0.00 29.66 3.08
1901 1962 5.011090 TGGAAACTTGATCACTCGATAGG 57.989 43.478 0.00 0.00 29.66 2.57
1902 1963 5.895928 TCTGGAAACTTGATCACTCGATAG 58.104 41.667 0.00 0.00 29.66 2.08
1903 1964 5.914898 TCTGGAAACTTGATCACTCGATA 57.085 39.130 0.00 0.00 29.66 2.92
1904 1965 4.808414 TCTGGAAACTTGATCACTCGAT 57.192 40.909 0.00 0.00 33.31 3.59
1905 1966 4.498241 CATCTGGAAACTTGATCACTCGA 58.502 43.478 0.00 0.00 0.00 4.04
1906 1967 3.620374 CCATCTGGAAACTTGATCACTCG 59.380 47.826 0.00 0.00 37.39 4.18
1907 1968 4.836825 TCCATCTGGAAACTTGATCACTC 58.163 43.478 0.00 0.00 42.18 3.51
1908 1969 4.916041 TCCATCTGGAAACTTGATCACT 57.084 40.909 0.00 0.00 42.18 3.41
1920 1981 9.170890 ACAGTATATCCTTTATTTCCATCTGGA 57.829 33.333 0.00 0.00 43.73 3.86
1921 1982 9.224267 CACAGTATATCCTTTATTTCCATCTGG 57.776 37.037 0.00 0.00 0.00 3.86
1922 1983 8.725148 GCACAGTATATCCTTTATTTCCATCTG 58.275 37.037 0.00 0.00 0.00 2.90
1923 1984 7.885399 GGCACAGTATATCCTTTATTTCCATCT 59.115 37.037 0.00 0.00 0.00 2.90
1924 1985 7.885399 AGGCACAGTATATCCTTTATTTCCATC 59.115 37.037 0.00 0.00 0.00 3.51
1925 1986 7.759607 AGGCACAGTATATCCTTTATTTCCAT 58.240 34.615 0.00 0.00 0.00 3.41
1926 1987 7.149202 AGGCACAGTATATCCTTTATTTCCA 57.851 36.000 0.00 0.00 0.00 3.53
2018 2079 2.947652 CCATGCGATTCATCAAGGAACT 59.052 45.455 0.00 0.00 33.73 3.01
2122 2183 2.029073 CGACTGCACGACCCAGTT 59.971 61.111 8.31 0.00 43.17 3.16
2199 2260 2.352127 GCCTTCTGTCATTGCTTTGTCC 60.352 50.000 0.00 0.00 0.00 4.02
2214 2275 1.351017 TCCCAGTCAAAATCGCCTTCT 59.649 47.619 0.00 0.00 0.00 2.85
2424 2485 5.753721 ATGAAAAGGACTCTTGTAGCTCT 57.246 39.130 0.00 0.00 32.75 4.09
2451 2512 3.814504 AAGTTCCTCACCCAACATGAT 57.185 42.857 0.00 0.00 0.00 2.45
2461 2522 2.038557 TGCTTCCTGGTAAGTTCCTCAC 59.961 50.000 0.00 0.00 0.00 3.51
2521 2582 1.474077 CTGGAACTACAGGGCATTTGC 59.526 52.381 0.00 0.00 41.14 3.68
2728 2789 9.014297 CCAAACAATGAGAAGTACCTAAATTCT 57.986 33.333 0.00 0.00 36.02 2.40
2743 2804 5.917541 ACGTGTAGTAACCAAACAATGAG 57.082 39.130 0.00 0.00 0.00 2.90
2759 2820 1.492319 GAGCGCACCACAAACGTGTA 61.492 55.000 11.47 0.00 35.72 2.90
2794 2855 3.326880 ACGGGCGATAAAGATCCCTAAAT 59.673 43.478 0.00 0.00 36.61 1.40
2813 2874 5.277857 AGAGGATAAAGTGGTCATAACGG 57.722 43.478 0.00 0.00 0.00 4.44
2845 2906 9.822185 ATTTCTTGTGCTCAAATAAGAGTTTTT 57.178 25.926 2.44 0.00 37.94 1.94
2846 2907 9.252962 CATTTCTTGTGCTCAAATAAGAGTTTT 57.747 29.630 2.44 0.00 37.94 2.43
2847 2908 8.416329 ACATTTCTTGTGCTCAAATAAGAGTTT 58.584 29.630 2.44 0.00 37.11 2.66
2848 2909 7.945134 ACATTTCTTGTGCTCAAATAAGAGTT 58.055 30.769 2.44 0.00 37.11 3.01
2849 2910 7.516198 ACATTTCTTGTGCTCAAATAAGAGT 57.484 32.000 2.44 1.55 37.11 3.24
2850 2911 9.897744 TTAACATTTCTTGTGCTCAAATAAGAG 57.102 29.630 2.44 0.00 38.99 2.85
2917 2990 9.853177 CAAAATCTTAATGTTCCTAGATAGGGT 57.147 33.333 6.07 0.00 43.79 4.34
2988 3061 5.514274 TTGTTTCTTGGAAGCCTTGTTAG 57.486 39.130 0.00 0.00 0.00 2.34
3014 3087 6.761242 TCCATTAGAATTCTCCACACGTATTG 59.239 38.462 12.24 0.00 0.00 1.90
3020 3093 5.440610 ACCATCCATTAGAATTCTCCACAC 58.559 41.667 12.24 0.00 0.00 3.82
3026 3099 7.213178 AGTACCAACCATCCATTAGAATTCT 57.787 36.000 13.56 13.56 0.00 2.40
3101 3174 3.128589 GCATTGTGGCGATTCTCCTTTTA 59.871 43.478 0.00 0.00 0.00 1.52
3346 3420 6.230472 ACTACTGCACTGTATTCAATCAACA 58.770 36.000 0.00 0.00 0.00 3.33
3408 3482 4.261994 GCTGCTGGACAACCAAAAAGATAA 60.262 41.667 0.00 0.00 46.32 1.75
3409 3483 3.255642 GCTGCTGGACAACCAAAAAGATA 59.744 43.478 0.00 0.00 46.32 1.98
3492 3566 5.560148 AGCTGCAGTCGAAAATAAAATACG 58.440 37.500 16.64 0.00 0.00 3.06
3494 3568 9.900710 TTAAAAGCTGCAGTCGAAAATAAAATA 57.099 25.926 16.64 0.00 0.00 1.40
3582 3656 9.575868 TCCAACAATACAAACCATAGTAGAAAA 57.424 29.630 0.00 0.00 0.00 2.29
3583 3657 9.747898 ATCCAACAATACAAACCATAGTAGAAA 57.252 29.630 0.00 0.00 0.00 2.52
3584 3658 9.173021 CATCCAACAATACAAACCATAGTAGAA 57.827 33.333 0.00 0.00 0.00 2.10
3596 3670 9.733556 AGTAACTAACATCATCCAACAATACAA 57.266 29.630 0.00 0.00 0.00 2.41
3640 3714 5.611796 TGAAACATGCATGTACTTGACTC 57.388 39.130 31.55 18.06 40.80 3.36
3642 3716 5.941733 TCATGAAACATGCATGTACTTGAC 58.058 37.500 31.55 18.17 42.77 3.18
3646 3720 7.049754 TGATACTCATGAAACATGCATGTACT 58.950 34.615 31.55 21.57 42.77 2.73
3662 3736 4.679373 GACAGGGTGTCATGATACTCAT 57.321 45.455 22.76 11.47 46.22 2.90
3683 3758 4.272018 CCATTACTTCTTGAATCTCCGCTG 59.728 45.833 0.00 0.00 0.00 5.18
3704 3779 6.169557 ACCAGCGAATATGAAAGTATACCA 57.830 37.500 0.00 0.00 0.00 3.25
3706 3781 8.395633 ACAAAACCAGCGAATATGAAAGTATAC 58.604 33.333 0.00 0.00 0.00 1.47
3715 3790 6.949578 AATTGAACAAAACCAGCGAATATG 57.050 33.333 0.00 0.00 0.00 1.78
3815 3896 7.066525 ACTCATACGTGTTTTTCTCTCCAAAAA 59.933 33.333 0.00 0.00 33.72 1.94
3816 3897 6.540914 ACTCATACGTGTTTTTCTCTCCAAAA 59.459 34.615 0.00 0.00 0.00 2.44
3817 3898 6.053005 ACTCATACGTGTTTTTCTCTCCAAA 58.947 36.000 0.00 0.00 0.00 3.28
3818 3899 5.607477 ACTCATACGTGTTTTTCTCTCCAA 58.393 37.500 0.00 0.00 0.00 3.53
3819 3900 5.209818 ACTCATACGTGTTTTTCTCTCCA 57.790 39.130 0.00 0.00 0.00 3.86
3820 3901 6.202188 TCAAACTCATACGTGTTTTTCTCTCC 59.798 38.462 0.00 0.00 36.86 3.71
3821 3902 7.173863 TCAAACTCATACGTGTTTTTCTCTC 57.826 36.000 0.00 0.00 36.86 3.20
3822 3903 6.292919 GCTCAAACTCATACGTGTTTTTCTCT 60.293 38.462 0.00 0.00 36.86 3.10
3823 3904 5.846473 GCTCAAACTCATACGTGTTTTTCTC 59.154 40.000 0.00 0.00 36.86 2.87
3824 3905 5.748592 GCTCAAACTCATACGTGTTTTTCT 58.251 37.500 0.00 0.00 36.86 2.52


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

AutoCloner maintained by Alex Coulton.