Multiple sequence alignment - TraesCS1B01G305700

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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 TraesCS1B01G305700 chr1B 100.000 5967 0 0 1 5967 529213114 529207148 0.000000e+00 11020.0
1 TraesCS1B01G305700 chr1B 93.750 48 3 0 761 808 529212321 529212274 8.300000e-09 73.1
2 TraesCS1B01G305700 chr1B 93.750 48 3 0 794 841 529212354 529212307 8.300000e-09 73.1
3 TraesCS1B01G305700 chr1D 98.604 3726 46 4 1767 5486 393771363 393775088 0.000000e+00 6588.0
4 TraesCS1B01G305700 chr1D 95.333 857 30 3 794 1643 393770509 393771362 0.000000e+00 1352.0
5 TraesCS1B01G305700 chr1D 90.730 507 30 11 29 528 393769732 393770228 0.000000e+00 660.0
6 TraesCS1B01G305700 chr1D 91.329 346 11 8 474 810 393770223 393770558 7.050000e-124 455.0
7 TraesCS1B01G305700 chr1A 96.045 2478 95 3 3492 5967 491987511 491985035 0.000000e+00 4030.0
8 TraesCS1B01G305700 chr1A 89.908 2933 185 55 2227 5101 491649779 491646900 0.000000e+00 3674.0
9 TraesCS1B01G305700 chr1A 96.195 2260 55 9 909 3154 491990902 491988660 0.000000e+00 3668.0
10 TraesCS1B01G305700 chr1A 88.913 1362 81 20 893 2194 491651705 491650354 0.000000e+00 1615.0
11 TraesCS1B01G305700 chr1A 85.632 696 59 23 64 727 491991765 491991079 0.000000e+00 693.0
12 TraesCS1B01G305700 chr1A 97.826 368 8 0 3139 3506 491988645 491988278 2.350000e-178 636.0
13 TraesCS1B01G305700 chr1A 91.045 201 13 2 5142 5337 491646815 491646615 3.550000e-67 267.0
14 TraesCS1B01G305700 chr1A 80.531 113 21 1 5434 5545 359893385 359893497 1.070000e-12 86.1
15 TraesCS1B01G305700 chr1A 80.612 98 13 4 3533 3627 29994267 29994361 2.980000e-08 71.3
16 TraesCS1B01G305700 chr3B 89.579 1401 111 17 2737 4118 785505904 785504520 0.000000e+00 1746.0
17 TraesCS1B01G305700 chr3B 93.528 309 18 2 4213 4519 785504494 785504186 5.450000e-125 459.0
18 TraesCS1B01G305700 chr3B 93.727 271 14 3 4251 4519 785505895 785506164 2.590000e-108 403.0
19 TraesCS1B01G305700 chr3B 78.661 239 39 10 169 398 753873166 753873401 1.340000e-31 148.0
20 TraesCS1B01G305700 chr2D 79.372 223 31 10 174 389 353348708 353348494 6.230000e-30 143.0
21 TraesCS1B01G305700 chr2D 81.429 140 23 3 304 441 2766513 2766375 1.760000e-20 111.0
22 TraesCS1B01G305700 chr5B 82.456 171 20 8 289 456 563123486 563123649 2.240000e-29 141.0
23 TraesCS1B01G305700 chr4D 80.702 171 23 6 284 453 499388303 499388142 2.260000e-24 124.0
24 TraesCS1B01G305700 chr5D 89.474 95 7 1 280 374 459067729 459067820 3.780000e-22 117.0
25 TraesCS1B01G305700 chr6A 80.769 156 22 8 303 453 48171710 48171558 1.360000e-21 115.0
26 TraesCS1B01G305700 chr6A 79.825 114 20 3 5434 5545 616096433 616096545 4.960000e-11 80.5
27 TraesCS1B01G305700 chr2B 80.508 118 19 3 339 453 776276812 776276928 2.960000e-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 TraesCS1B01G305700 chr1B 529207148 529213114 5966 True 3722.066667 11020 95.833333 1 5967 3 chr1B.!!$R1 5966
1 TraesCS1B01G305700 chr1D 393769732 393775088 5356 False 2263.750000 6588 93.999000 29 5486 4 chr1D.!!$F1 5457
2 TraesCS1B01G305700 chr1A 491985035 491991765 6730 True 2256.750000 4030 93.924500 64 5967 4 chr1A.!!$R2 5903
3 TraesCS1B01G305700 chr1A 491646615 491651705 5090 True 1852.000000 3674 89.955333 893 5337 3 chr1A.!!$R1 4444
4 TraesCS1B01G305700 chr3B 785504186 785505904 1718 True 1102.500000 1746 91.553500 2737 4519 2 chr3B.!!$R1 1782

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
807 961 0.112412 AAACCTCATGTCGGCCCTTT 59.888 50.000 0.0 0.0 0.00 3.11 F
810 964 0.322456 CCTCATGTCGGCCCTTTTCA 60.322 55.000 0.0 0.0 0.00 2.69 F
2139 2387 1.002430 TGTGGAAGCTTTGCTCGATCT 59.998 47.619 0.0 0.0 38.25 2.75 F
3584 5207 1.447643 GGGATGACCTGGATCACCG 59.552 63.158 0.0 0.0 39.42 4.94 F
4488 6147 0.532573 CAAGCGAGTAAGGGAGAGCA 59.467 55.000 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 3107 0.478072 AGTCAGGTTGGTTCATGGCA 59.522 50.000 0.00 0.0 0.0 4.92 R
2443 3239 5.016031 AGGGGGTATCTATCCTACAATACGT 59.984 44.000 0.00 0.0 0.0 3.57 R
3963 5595 3.763097 TGATGGCAGAAAACATTAGCG 57.237 42.857 0.00 0.0 0.0 4.26 R
4635 6294 0.035317 AGCAGTCGAGGCAATGAACA 59.965 50.000 11.19 0.0 0.0 3.18 R
5932 7673 0.179145 CGTCCAACCTACACTAGCCG 60.179 60.000 0.00 0.0 0.0 5.52 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
17 18 3.883462 CGCGGCATTCCTGTAACA 58.117 55.556 0.00 0.00 0.00 2.41
18 19 2.167161 CGCGGCATTCCTGTAACAA 58.833 52.632 0.00 0.00 0.00 2.83
19 20 0.179200 CGCGGCATTCCTGTAACAAC 60.179 55.000 0.00 0.00 0.00 3.32
20 21 0.878416 GCGGCATTCCTGTAACAACA 59.122 50.000 0.00 0.00 0.00 3.33
21 22 1.268352 GCGGCATTCCTGTAACAACAA 59.732 47.619 0.00 0.00 0.00 2.83
22 23 2.668279 GCGGCATTCCTGTAACAACAAG 60.668 50.000 0.00 0.00 0.00 3.16
23 24 2.095263 CGGCATTCCTGTAACAACAAGG 60.095 50.000 0.00 0.00 0.00 3.61
24 25 3.153919 GGCATTCCTGTAACAACAAGGA 58.846 45.455 0.00 0.00 0.00 3.36
25 26 3.572255 GGCATTCCTGTAACAACAAGGAA 59.428 43.478 5.88 5.88 42.03 3.36
26 27 4.321230 GGCATTCCTGTAACAACAAGGAAG 60.321 45.833 9.10 3.60 41.27 3.46
27 28 4.518970 GCATTCCTGTAACAACAAGGAAGA 59.481 41.667 9.10 0.00 41.27 2.87
72 73 7.760340 ACGAGGTAAAACTCTTCAAGATACATC 59.240 37.037 0.00 1.93 35.33 3.06
106 107 1.686587 TGTCGGAAGTGCTCTTCTCAA 59.313 47.619 23.63 10.10 46.47 3.02
141 142 5.155278 TGAGCTCGGGTGAATAGTAAAAA 57.845 39.130 9.64 0.00 0.00 1.94
222 224 3.308438 CTTGCAAAGTTTCATCAGGGG 57.692 47.619 0.00 0.00 39.70 4.79
297 306 6.418057 TTGAAATAACATTGTTGGAGCCTT 57.582 33.333 12.30 0.00 0.00 4.35
329 338 0.174162 GCCATGTCTCCCACAAATGC 59.826 55.000 0.00 0.00 38.97 3.56
334 343 1.106285 GTCTCCCACAAATGCCATCC 58.894 55.000 0.00 0.00 0.00 3.51
375 384 8.068977 GCAAGCAATCAAAACATTTGTCAATAA 58.931 29.630 3.06 0.00 0.00 1.40
535 597 1.732259 AGCTCAAATTAACCGCGTCAG 59.268 47.619 4.92 0.00 0.00 3.51
603 666 5.180117 ACTTTTGTTAGCTACTCATGCACAG 59.820 40.000 0.00 0.00 0.00 3.66
780 934 1.879380 TCATGTCAGCCCGTTTCAAAG 59.121 47.619 0.00 0.00 0.00 2.77
781 935 1.879380 CATGTCAGCCCGTTTCAAAGA 59.121 47.619 0.00 0.00 0.00 2.52
782 936 1.305201 TGTCAGCCCGTTTCAAAGAC 58.695 50.000 0.00 0.00 0.00 3.01
783 937 1.134220 TGTCAGCCCGTTTCAAAGACT 60.134 47.619 0.00 0.00 0.00 3.24
784 938 2.103432 TGTCAGCCCGTTTCAAAGACTA 59.897 45.455 0.00 0.00 0.00 2.59
785 939 3.135994 GTCAGCCCGTTTCAAAGACTAA 58.864 45.455 0.00 0.00 0.00 2.24
786 940 3.562557 GTCAGCCCGTTTCAAAGACTAAA 59.437 43.478 0.00 0.00 0.00 1.85
787 941 3.813166 TCAGCCCGTTTCAAAGACTAAAG 59.187 43.478 0.00 0.00 0.00 1.85
788 942 3.813166 CAGCCCGTTTCAAAGACTAAAGA 59.187 43.478 0.00 0.00 0.00 2.52
789 943 4.274950 CAGCCCGTTTCAAAGACTAAAGAA 59.725 41.667 0.00 0.00 0.00 2.52
790 944 4.885325 AGCCCGTTTCAAAGACTAAAGAAA 59.115 37.500 0.00 0.00 0.00 2.52
791 945 4.974275 GCCCGTTTCAAAGACTAAAGAAAC 59.026 41.667 13.30 13.30 43.76 2.78
792 946 5.516996 CCCGTTTCAAAGACTAAAGAAACC 58.483 41.667 15.76 5.19 44.12 3.27
793 947 5.298527 CCCGTTTCAAAGACTAAAGAAACCT 59.701 40.000 15.76 0.00 44.12 3.50
794 948 6.427974 CCGTTTCAAAGACTAAAGAAACCTC 58.572 40.000 15.76 0.69 44.12 3.85
795 949 6.037830 CCGTTTCAAAGACTAAAGAAACCTCA 59.962 38.462 15.76 0.00 44.12 3.86
796 950 7.255139 CCGTTTCAAAGACTAAAGAAACCTCAT 60.255 37.037 15.76 0.00 44.12 2.90
797 951 7.587757 CGTTTCAAAGACTAAAGAAACCTCATG 59.412 37.037 15.76 0.00 44.12 3.07
798 952 8.406297 GTTTCAAAGACTAAAGAAACCTCATGT 58.594 33.333 12.70 0.00 42.28 3.21
799 953 7.730364 TCAAAGACTAAAGAAACCTCATGTC 57.270 36.000 0.00 0.00 0.00 3.06
800 954 6.423905 TCAAAGACTAAAGAAACCTCATGTCG 59.576 38.462 0.00 0.00 0.00 4.35
801 955 4.822026 AGACTAAAGAAACCTCATGTCGG 58.178 43.478 0.00 0.00 0.00 4.79
802 956 3.335579 ACTAAAGAAACCTCATGTCGGC 58.664 45.455 0.00 0.00 0.00 5.54
803 957 1.534729 AAAGAAACCTCATGTCGGCC 58.465 50.000 0.00 0.00 0.00 6.13
804 958 0.322546 AAGAAACCTCATGTCGGCCC 60.323 55.000 0.00 0.00 0.00 5.80
805 959 1.201429 AGAAACCTCATGTCGGCCCT 61.201 55.000 0.00 0.00 0.00 5.19
806 960 0.322546 GAAACCTCATGTCGGCCCTT 60.323 55.000 0.00 0.00 0.00 3.95
807 961 0.112412 AAACCTCATGTCGGCCCTTT 59.888 50.000 0.00 0.00 0.00 3.11
808 962 0.112412 AACCTCATGTCGGCCCTTTT 59.888 50.000 0.00 0.00 0.00 2.27
809 963 0.322546 ACCTCATGTCGGCCCTTTTC 60.323 55.000 0.00 0.00 0.00 2.29
810 964 0.322456 CCTCATGTCGGCCCTTTTCA 60.322 55.000 0.00 0.00 0.00 2.69
811 965 1.533625 CTCATGTCGGCCCTTTTCAA 58.466 50.000 0.00 0.00 0.00 2.69
812 966 1.885887 CTCATGTCGGCCCTTTTCAAA 59.114 47.619 0.00 0.00 0.00 2.69
817 971 2.105134 TGTCGGCCCTTTTCAAAGACTA 59.895 45.455 0.00 0.00 38.28 2.59
841 995 2.511600 CCTCATGTCGGCCCGTTC 60.512 66.667 1.63 0.00 0.00 3.95
865 1019 4.322567 GGATTTATGGACCTCTCATCAGC 58.677 47.826 0.00 0.00 0.00 4.26
876 1030 5.788450 ACCTCTCATCAGCCTAAATAATCG 58.212 41.667 0.00 0.00 0.00 3.34
879 1033 6.405278 TCTCATCAGCCTAAATAATCGTCA 57.595 37.500 0.00 0.00 0.00 4.35
939 1122 1.271656 CGAACGTACCCAGAGGAGTTT 59.728 52.381 0.00 0.00 36.73 2.66
986 1169 4.819761 GCAGGACGATCAGCCGCA 62.820 66.667 0.00 0.00 0.00 5.69
988 1171 3.071206 AGGACGATCAGCCGCACT 61.071 61.111 0.00 0.00 0.00 4.40
1077 1285 1.746220 AGGAGAACGTCGAGGAAGATG 59.254 52.381 12.85 0.00 0.00 2.90
1267 1478 2.037847 ATTTGGCCAGGGAGGTGC 59.962 61.111 5.11 0.00 40.61 5.01
1338 1549 6.248569 AGACTGGAGTTGGAGAAAACTAAA 57.751 37.500 0.00 0.00 40.48 1.85
1632 1853 5.824904 AGTATTGCAGGCAGTTATTTCTG 57.175 39.130 0.00 0.00 38.35 3.02
1698 1943 2.945447 TGCATGTGAATTAAGCTGCC 57.055 45.000 0.00 0.00 0.00 4.85
1843 2088 7.692291 GTCAAATCCACATTGTTACTTATCACG 59.308 37.037 0.00 0.00 0.00 4.35
1938 2186 3.318839 CCCTGTCAGTTTGATTTTCAGCA 59.681 43.478 0.00 0.00 0.00 4.41
2139 2387 1.002430 TGTGGAAGCTTTGCTCGATCT 59.998 47.619 0.00 0.00 38.25 2.75
2315 3107 7.571025 CCCTGGTACACCTAACTACATTATTT 58.429 38.462 0.00 0.00 36.82 1.40
2443 3239 7.301868 TGCATAAGTGTGATAGTATCATCCA 57.698 36.000 15.77 7.62 42.04 3.41
2927 3729 7.820648 AGCTTAGACAATCCAGTTTGTATTTG 58.179 34.615 0.00 0.00 39.85 2.32
3196 4033 6.796552 TCATGTCGAAATTCGTTTGATCTTTG 59.203 34.615 15.34 2.64 41.35 2.77
3584 5207 1.447643 GGGATGACCTGGATCACCG 59.552 63.158 0.00 0.00 39.42 4.94
3741 5364 7.784037 AGTGTTTCCGTATTGTATGTACCATA 58.216 34.615 0.00 0.00 0.00 2.74
3963 5595 7.935804 TTTTATGTTACGCTAACGCATTTAC 57.064 32.000 0.00 0.00 45.53 2.01
4033 5669 4.051922 CTCTATGCATGGTAACGTTCTCC 58.948 47.826 10.16 9.81 42.51 3.71
4039 5675 3.309954 GCATGGTAACGTTCTCCTGATTC 59.690 47.826 18.71 2.10 42.51 2.52
4157 5813 3.431673 TGGCATTGTGTTCACTATCCA 57.568 42.857 4.59 8.66 0.00 3.41
4253 5911 4.279169 TGATCAGCTGTCCCTTTTCTTTTG 59.721 41.667 14.67 0.00 0.00 2.44
4257 5915 2.546584 GCTGTCCCTTTTCTTTTGCCAG 60.547 50.000 0.00 0.00 0.00 4.85
4346 6005 2.363925 GTCCTACCCGTGCTCCCT 60.364 66.667 0.00 0.00 0.00 4.20
4488 6147 0.532573 CAAGCGAGTAAGGGAGAGCA 59.467 55.000 0.00 0.00 0.00 4.26
4635 6294 1.147824 CAGATGGATTCAGCGGGCT 59.852 57.895 0.00 0.00 33.94 5.19
4911 6570 0.872388 GAAGTTACCGTTGGCTGGTG 59.128 55.000 6.86 0.00 40.73 4.17
4940 6599 3.120792 CCGTTATGTTATCCCACTGACG 58.879 50.000 0.00 0.00 0.00 4.35
5169 6907 5.695816 TGTTGCTTCTGAAATGGCATTTTAC 59.304 36.000 25.02 14.52 34.59 2.01
5453 7194 4.824479 ATGCTTGTAAATGGAAAAGGGG 57.176 40.909 0.00 0.00 0.00 4.79
5502 7243 7.823745 AATGTCATGATAATTAAGGGGTCAC 57.176 36.000 0.00 0.00 0.00 3.67
5545 7286 4.828939 TGAAGACAATCTTGAAAGTGGCAT 59.171 37.500 0.00 0.00 36.73 4.40
5547 7288 4.147321 AGACAATCTTGAAAGTGGCATGT 58.853 39.130 0.00 0.00 0.00 3.21
5566 7307 6.421801 GGCATGTATTCAAAGTGGCAAATATC 59.578 38.462 0.00 0.00 35.67 1.63
5577 7318 7.486407 AAGTGGCAAATATCCAATTTTCTCT 57.514 32.000 0.00 0.00 38.58 3.10
5578 7319 6.870769 AGTGGCAAATATCCAATTTTCTCTG 58.129 36.000 0.00 0.00 35.01 3.35
5592 7333 4.659111 TTTCTCTGAACCACAACTACGA 57.341 40.909 0.00 0.00 0.00 3.43
5609 7350 5.638133 ACTACGAGAGGGCTATTATTGGTA 58.362 41.667 0.00 0.00 0.00 3.25
5650 7391 3.150335 CCTAGCTCTGGCGGCTCA 61.150 66.667 11.43 0.00 44.37 4.26
5674 7415 2.093075 GGAAACCTAACCTCCTGTAGCC 60.093 54.545 0.00 0.00 0.00 3.93
5687 7428 4.835456 TAGCCGGCCCTCCCCATT 62.835 66.667 26.15 2.97 0.00 3.16
5693 7434 2.597903 GCCCTCCCCATTGACTCC 59.402 66.667 0.00 0.00 0.00 3.85
5695 7436 1.988982 GCCCTCCCCATTGACTCCTC 61.989 65.000 0.00 0.00 0.00 3.71
5697 7438 1.348775 CCTCCCCATTGACTCCTCCC 61.349 65.000 0.00 0.00 0.00 4.30
5702 7443 0.108138 CCATTGACTCCTCCCGTCAC 60.108 60.000 0.00 0.00 40.78 3.67
5709 7450 4.436998 CCTCCCGTCACCGCTGTC 62.437 72.222 0.00 0.00 0.00 3.51
5720 7461 3.826754 CGCTGTCGCTGGCTCCTA 61.827 66.667 0.00 0.00 0.00 2.94
5725 7466 3.449227 TCGCTGGCTCCTACCACG 61.449 66.667 0.00 0.00 35.33 4.94
5766 7507 3.721087 TGAAAGAGGGTGGGAATCTTC 57.279 47.619 0.00 0.00 32.21 2.87
5772 7513 1.814169 GGTGGGAATCTTCGGTCGC 60.814 63.158 0.00 0.00 0.00 5.19
5821 7562 3.305516 CAACTTGGTGCTGGGGGC 61.306 66.667 0.00 0.00 42.22 5.80
5868 7609 4.394712 GCCTGGGTGTGGACCTCG 62.395 72.222 0.00 0.00 42.66 4.63
5874 7615 3.036084 GTGTGGACCTCGTGTGCG 61.036 66.667 0.00 0.00 38.31 5.34
5932 7673 4.586235 ACAGCTGGGTGTGGTGGC 62.586 66.667 19.93 0.00 37.25 5.01
5941 7682 3.238497 TGTGGTGGCGGCTAGTGT 61.238 61.111 11.43 0.00 0.00 3.55
5949 7690 1.610554 GGCGGCTAGTGTAGGTTGGA 61.611 60.000 0.00 0.00 0.00 3.53
5959 7700 2.981560 TAGGTTGGACGCGACGACC 61.982 63.158 26.62 26.62 41.80 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179200 GTTGTTACAGGAATGCCGCG 60.179 55.000 0.00 0.00 39.96 6.46
2 3 2.095263 CCTTGTTGTTACAGGAATGCCG 60.095 50.000 0.00 0.00 39.96 5.69
5 6 5.765182 ACTCTTCCTTGTTGTTACAGGAATG 59.235 40.000 4.61 4.38 39.08 2.67
6 7 5.941788 ACTCTTCCTTGTTGTTACAGGAAT 58.058 37.500 4.61 0.00 39.08 3.01
7 8 5.104693 TGACTCTTCCTTGTTGTTACAGGAA 60.105 40.000 4.19 4.19 38.30 3.36
8 9 4.407621 TGACTCTTCCTTGTTGTTACAGGA 59.592 41.667 0.00 0.00 33.45 3.86
9 10 4.703897 TGACTCTTCCTTGTTGTTACAGG 58.296 43.478 0.00 0.00 35.28 4.00
10 11 5.760253 ACATGACTCTTCCTTGTTGTTACAG 59.240 40.000 0.00 0.00 35.28 2.74
11 12 5.527214 CACATGACTCTTCCTTGTTGTTACA 59.473 40.000 0.00 0.00 0.00 2.41
12 13 5.049405 CCACATGACTCTTCCTTGTTGTTAC 60.049 44.000 0.00 0.00 0.00 2.50
13 14 5.063204 CCACATGACTCTTCCTTGTTGTTA 58.937 41.667 0.00 0.00 0.00 2.41
14 15 3.885297 CCACATGACTCTTCCTTGTTGTT 59.115 43.478 0.00 0.00 0.00 2.83
15 16 3.117888 ACCACATGACTCTTCCTTGTTGT 60.118 43.478 0.00 0.00 0.00 3.32
16 17 3.480470 ACCACATGACTCTTCCTTGTTG 58.520 45.455 0.00 0.00 0.00 3.33
17 18 3.864789 ACCACATGACTCTTCCTTGTT 57.135 42.857 0.00 0.00 0.00 2.83
18 19 3.744660 GAACCACATGACTCTTCCTTGT 58.255 45.455 0.00 0.00 0.00 3.16
19 20 2.738846 CGAACCACATGACTCTTCCTTG 59.261 50.000 0.00 0.00 0.00 3.61
20 21 2.632996 TCGAACCACATGACTCTTCCTT 59.367 45.455 0.00 0.00 0.00 3.36
21 22 2.232452 CTCGAACCACATGACTCTTCCT 59.768 50.000 0.00 0.00 0.00 3.36
22 23 2.231478 TCTCGAACCACATGACTCTTCC 59.769 50.000 0.00 0.00 0.00 3.46
23 24 3.577649 TCTCGAACCACATGACTCTTC 57.422 47.619 0.00 0.00 0.00 2.87
24 25 3.574396 TCTTCTCGAACCACATGACTCTT 59.426 43.478 0.00 0.00 0.00 2.85
25 26 3.057174 GTCTTCTCGAACCACATGACTCT 60.057 47.826 0.00 0.00 0.00 3.24
26 27 3.246619 GTCTTCTCGAACCACATGACTC 58.753 50.000 0.00 0.00 0.00 3.36
27 28 2.351835 CGTCTTCTCGAACCACATGACT 60.352 50.000 0.00 0.00 0.00 3.41
113 114 0.904649 TTCACCCGAGCTCATGTGAT 59.095 50.000 26.75 0.00 37.55 3.06
222 224 7.477144 TTGTCACGTATTCCATGAATATCAC 57.523 36.000 0.00 0.00 36.96 3.06
329 338 6.184242 CTTGCAAAGTTTCATCATCGGATGG 61.184 44.000 17.42 3.23 44.08 3.51
410 420 5.118050 CGAGCTCGTGTGAACAGTAAAATTA 59.882 40.000 27.79 0.00 34.11 1.40
535 597 2.096496 AGAAGAAAGCATGCATGTACGC 59.904 45.455 26.79 13.32 0.00 4.42
692 779 2.396590 TTCCTCGTGCCAGTAAATCC 57.603 50.000 0.00 0.00 0.00 3.01
780 934 3.371285 GCCGACATGAGGTTTCTTTAGTC 59.629 47.826 0.00 0.00 0.00 2.59
781 935 3.335579 GCCGACATGAGGTTTCTTTAGT 58.664 45.455 0.00 0.00 0.00 2.24
782 936 2.678336 GGCCGACATGAGGTTTCTTTAG 59.322 50.000 0.00 0.00 0.00 1.85
783 937 2.617021 GGGCCGACATGAGGTTTCTTTA 60.617 50.000 0.00 0.00 0.00 1.85
784 938 1.534729 GGCCGACATGAGGTTTCTTT 58.465 50.000 0.00 0.00 0.00 2.52
785 939 0.322546 GGGCCGACATGAGGTTTCTT 60.323 55.000 0.00 0.00 0.00 2.52
786 940 1.201429 AGGGCCGACATGAGGTTTCT 61.201 55.000 0.00 0.00 0.00 2.52
787 941 0.322546 AAGGGCCGACATGAGGTTTC 60.323 55.000 0.00 0.00 0.00 2.78
788 942 0.112412 AAAGGGCCGACATGAGGTTT 59.888 50.000 0.00 0.00 0.00 3.27
789 943 0.112412 AAAAGGGCCGACATGAGGTT 59.888 50.000 0.00 0.00 0.00 3.50
790 944 0.322546 GAAAAGGGCCGACATGAGGT 60.323 55.000 0.00 0.00 0.00 3.85
791 945 0.322456 TGAAAAGGGCCGACATGAGG 60.322 55.000 0.00 3.38 0.00 3.86
792 946 1.533625 TTGAAAAGGGCCGACATGAG 58.466 50.000 0.00 0.00 0.00 2.90
793 947 1.885887 CTTTGAAAAGGGCCGACATGA 59.114 47.619 0.00 0.00 32.40 3.07
794 948 1.885887 TCTTTGAAAAGGGCCGACATG 59.114 47.619 0.00 0.00 36.67 3.21
795 949 1.886542 GTCTTTGAAAAGGGCCGACAT 59.113 47.619 0.00 0.00 36.67 3.06
796 950 1.133915 AGTCTTTGAAAAGGGCCGACA 60.134 47.619 0.00 0.00 36.67 4.35
797 951 1.605753 AGTCTTTGAAAAGGGCCGAC 58.394 50.000 0.00 0.00 36.67 4.79
798 952 3.495434 TTAGTCTTTGAAAAGGGCCGA 57.505 42.857 0.00 0.00 36.67 5.54
799 953 3.818773 TCTTTAGTCTTTGAAAAGGGCCG 59.181 43.478 0.00 0.00 36.67 6.13
800 954 5.784578 TTCTTTAGTCTTTGAAAAGGGCC 57.215 39.130 0.00 0.00 36.67 5.80
801 955 5.983720 GGTTTCTTTAGTCTTTGAAAAGGGC 59.016 40.000 3.08 0.00 36.67 5.19
802 956 7.068226 TGAGGTTTCTTTAGTCTTTGAAAAGGG 59.932 37.037 3.08 0.00 36.67 3.95
803 957 7.996385 TGAGGTTTCTTTAGTCTTTGAAAAGG 58.004 34.615 3.08 0.00 36.67 3.11
804 958 9.455847 CATGAGGTTTCTTTAGTCTTTGAAAAG 57.544 33.333 0.00 0.00 37.36 2.27
805 959 8.966868 ACATGAGGTTTCTTTAGTCTTTGAAAA 58.033 29.630 0.00 0.00 31.47 2.29
806 960 8.519799 ACATGAGGTTTCTTTAGTCTTTGAAA 57.480 30.769 0.00 0.00 0.00 2.69
807 961 7.042051 CGACATGAGGTTTCTTTAGTCTTTGAA 60.042 37.037 0.00 0.00 0.00 2.69
808 962 6.423905 CGACATGAGGTTTCTTTAGTCTTTGA 59.576 38.462 0.00 0.00 0.00 2.69
809 963 6.347725 CCGACATGAGGTTTCTTTAGTCTTTG 60.348 42.308 0.00 0.00 0.00 2.77
810 964 5.701290 CCGACATGAGGTTTCTTTAGTCTTT 59.299 40.000 0.00 0.00 0.00 2.52
811 965 5.238583 CCGACATGAGGTTTCTTTAGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
812 966 4.822026 CCGACATGAGGTTTCTTTAGTCT 58.178 43.478 0.00 0.00 0.00 3.24
817 971 1.534729 GGCCGACATGAGGTTTCTTT 58.465 50.000 0.00 0.00 0.00 2.52
841 995 3.324846 TGATGAGAGGTCCATAAATCCGG 59.675 47.826 0.00 0.00 0.00 5.14
853 1007 5.305644 ACGATTATTTAGGCTGATGAGAGGT 59.694 40.000 0.00 0.00 0.00 3.85
865 1019 4.271687 GCGCAAACTGACGATTATTTAGG 58.728 43.478 0.30 0.00 0.00 2.69
876 1030 0.381801 CCCATATGGCGCAAACTGAC 59.618 55.000 16.97 0.00 0.00 3.51
939 1122 1.479709 GCTCTGCTCCTGACCTAGAA 58.520 55.000 0.00 0.00 0.00 2.10
986 1169 2.249413 CTCCATCTCGGCAAGCCAGT 62.249 60.000 12.19 0.00 35.37 4.00
988 1171 2.586245 CTCCATCTCGGCAAGCCA 59.414 61.111 12.19 0.00 35.37 4.75
1009 1193 2.330372 CCTCCGTCGTCTCCGAACA 61.330 63.158 0.00 0.00 46.26 3.18
1048 1256 0.033306 GACGTTCTCCTACTCCCCCT 60.033 60.000 0.00 0.00 0.00 4.79
1338 1549 1.664321 CGTCGGGATCCTTCTTCGGT 61.664 60.000 12.58 0.00 0.00 4.69
1843 2088 5.351458 ACAACACAAGAGAAATTCAAAGCC 58.649 37.500 0.00 0.00 0.00 4.35
1938 2186 8.907222 AATCACATTTGGAAAGCAAAATTACT 57.093 26.923 0.00 0.00 0.00 2.24
2315 3107 0.478072 AGTCAGGTTGGTTCATGGCA 59.522 50.000 0.00 0.00 0.00 4.92
2443 3239 5.016031 AGGGGGTATCTATCCTACAATACGT 59.984 44.000 0.00 0.00 0.00 3.57
2927 3729 2.978018 GCAACTTGCACGTAGGGGC 61.978 63.158 8.97 1.82 44.26 5.80
3196 4033 5.313712 TGTTTAGTCCCTGATGAAAGAACC 58.686 41.667 0.00 0.00 0.00 3.62
3584 5207 4.144555 GCGCTCAAAGATAATATTGCGAC 58.855 43.478 14.41 4.70 44.02 5.19
3741 5364 8.458573 TGTGAAGTAAAAACCATAACAGACAT 57.541 30.769 0.00 0.00 0.00 3.06
3963 5595 3.763097 TGATGGCAGAAAACATTAGCG 57.237 42.857 0.00 0.00 0.00 4.26
4033 5669 5.803967 GGTAAAATTTGAGCAGCAGAATCAG 59.196 40.000 0.00 0.00 0.00 2.90
4039 5675 5.382618 AAGAGGTAAAATTTGAGCAGCAG 57.617 39.130 7.48 0.00 0.00 4.24
4253 5911 6.939163 ACAATGAGAATATCTCCAATACTGGC 59.061 38.462 5.00 0.00 42.73 4.85
4346 6005 2.879756 GCATAGGCCCAAACAGAGTCAA 60.880 50.000 0.00 0.00 0.00 3.18
4488 6147 2.107750 CGCATGATCTGAGGGCGT 59.892 61.111 0.00 0.00 42.51 5.68
4635 6294 0.035317 AGCAGTCGAGGCAATGAACA 59.965 50.000 11.19 0.00 0.00 3.18
4814 6473 1.949465 AAGAACACCTCACGGTCAAC 58.051 50.000 0.00 0.00 43.24 3.18
4911 6570 4.399934 TGGGATAACATAACGGAAAAAGGC 59.600 41.667 0.00 0.00 0.00 4.35
4940 6599 3.954258 CCATTCTTGGGTGAAGGAATACC 59.046 47.826 0.00 0.00 39.56 2.73
5169 6907 7.962373 TCATTAATTAGCACAAAACATGACTCG 59.038 33.333 0.00 0.00 0.00 4.18
5492 7233 1.987855 CCCAGCTCGTGACCCCTTA 60.988 63.158 0.00 0.00 0.00 2.69
5502 7243 0.388907 CAAAATTGCCACCCAGCTCG 60.389 55.000 0.00 0.00 0.00 5.03
5545 7286 7.473735 TTGGATATTTGCCACTTTGAATACA 57.526 32.000 0.00 0.00 34.56 2.29
5547 7288 9.956640 AAAATTGGATATTTGCCACTTTGAATA 57.043 25.926 0.00 0.00 38.02 1.75
5566 7307 5.520376 AGTTGTGGTTCAGAGAAAATTGG 57.480 39.130 0.00 0.00 0.00 3.16
5577 7318 1.616865 CCCTCTCGTAGTTGTGGTTCA 59.383 52.381 0.00 0.00 0.00 3.18
5578 7319 1.672145 GCCCTCTCGTAGTTGTGGTTC 60.672 57.143 0.00 0.00 0.00 3.62
5592 7333 2.028020 GCGCTACCAATAATAGCCCTCT 60.028 50.000 0.00 0.00 41.76 3.69
5674 7415 3.406595 GAGTCAATGGGGAGGGCCG 62.407 68.421 0.00 0.00 33.83 6.13
5709 7450 4.514577 CCGTGGTAGGAGCCAGCG 62.515 72.222 0.00 0.00 39.53 5.18
5735 7476 1.460255 CTCTTTCAAGGGTGGGGCA 59.540 57.895 0.00 0.00 0.00 5.36
5746 7487 2.027192 CGAAGATTCCCACCCTCTTTCA 60.027 50.000 0.00 0.00 29.64 2.69
5803 7544 2.198426 CCCCCAGCACCAAGTTGT 59.802 61.111 1.45 0.00 0.00 3.32
5851 7592 4.394712 CGAGGTCCACACCCAGGC 62.395 72.222 0.00 0.00 45.12 4.85
5922 7663 4.016706 ACTAGCCGCCACCACACC 62.017 66.667 0.00 0.00 0.00 4.16
5932 7673 0.179145 CGTCCAACCTACACTAGCCG 60.179 60.000 0.00 0.00 0.00 5.52
5937 7678 1.288127 GTCGCGTCCAACCTACACT 59.712 57.895 5.77 0.00 0.00 3.55
5941 7682 2.562912 GTCGTCGCGTCCAACCTA 59.437 61.111 5.77 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.