Multiple sequence alignment - TraesCS6B01G412300

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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 TraesCS6B01G412300 chr6B 100.000 4203 0 0 1 4203 685965489 685969691 0.000000e+00 7762
1 TraesCS6B01G412300 chr6D 89.464 4366 129 119 1 4203 451558332 451554135 0.000000e+00 5208
2 TraesCS6B01G412300 chr6D 93.861 619 20 9 3486 4101 341539955 341539352 0.000000e+00 917
3 TraesCS6B01G412300 chr6A 88.469 4336 161 122 10 4203 597339306 597343444 0.000000e+00 4924
4 TraesCS6B01G412300 chrUn 94.184 619 18 9 3486 4101 101283095 101282492 0.000000e+00 928
5 TraesCS6B01G412300 chrUn 94.023 619 17 11 3486 4101 21738571 21737970 0.000000e+00 920
6 TraesCS6B01G412300 chr1D 94.051 622 20 9 3483 4101 409370585 409371192 0.000000e+00 928
7 TraesCS6B01G412300 chr5D 93.730 622 22 9 3483 4101 81017934 81018541 0.000000e+00 917
8 TraesCS6B01G412300 chr4D 93.861 619 20 9 3486 4101 265067903 265067300 0.000000e+00 917
9 TraesCS6B01G412300 chr3D 93.861 619 20 9 3486 4101 409319919 409319316 0.000000e+00 917
10 TraesCS6B01G412300 chr2B 92.147 191 12 3 4012 4201 328869306 328869118 2.490000e-67 267


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 TraesCS6B01G412300 chr6B 685965489 685969691 4202 False 7762 7762 100.000 1 4203 1 chr6B.!!$F1 4202
1 TraesCS6B01G412300 chr6D 451554135 451558332 4197 True 5208 5208 89.464 1 4203 1 chr6D.!!$R2 4202
2 TraesCS6B01G412300 chr6D 341539352 341539955 603 True 917 917 93.861 3486 4101 1 chr6D.!!$R1 615
3 TraesCS6B01G412300 chr6A 597339306 597343444 4138 False 4924 4924 88.469 10 4203 1 chr6A.!!$F1 4193
4 TraesCS6B01G412300 chrUn 101282492 101283095 603 True 928 928 94.184 3486 4101 1 chrUn.!!$R2 615
5 TraesCS6B01G412300 chrUn 21737970 21738571 601 True 920 920 94.023 3486 4101 1 chrUn.!!$R1 615
6 TraesCS6B01G412300 chr1D 409370585 409371192 607 False 928 928 94.051 3483 4101 1 chr1D.!!$F1 618
7 TraesCS6B01G412300 chr5D 81017934 81018541 607 False 917 917 93.730 3483 4101 1 chr5D.!!$F1 618
8 TraesCS6B01G412300 chr4D 265067300 265067903 603 True 917 917 93.861 3486 4101 1 chr4D.!!$R1 615
9 TraesCS6B01G412300 chr3D 409319316 409319919 603 True 917 917 93.861 3486 4101 1 chr3D.!!$R1 615

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
688 738 0.739561 GGAGATCGCGTTCTGGTAGT 59.260 55.0 23.56 0.0 0.0 2.73 F
1781 1904 0.672401 GGGAACGGACAATCAAGCGA 60.672 55.0 0.00 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2318 0.027586 AAAGCAAACGTCGACACTGC 59.972 50.0 20.16 20.16 0.0 4.40 R
3246 3428 0.106318 TAGCTAAGGGGGACGAGACC 60.106 60.0 0.00 0.00 0.0 3.85 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
50 53 1.896660 GGGGCAGTGAAAACGCAGA 60.897 57.895 0.00 0.00 0.00 4.26
108 111 2.158841 CCTTTGTTTGATCCGTACGGTG 59.841 50.000 32.16 9.76 36.47 4.94
203 206 4.851179 CCGCTTTACCGAGGGGGC 62.851 72.222 0.44 0.00 43.85 5.80
307 310 2.446036 GGGCCCCGTCACTCCTAT 60.446 66.667 12.23 0.00 0.00 2.57
308 311 1.152398 GGGCCCCGTCACTCCTATA 60.152 63.158 12.23 0.00 0.00 1.31
309 312 0.761702 GGGCCCCGTCACTCCTATAA 60.762 60.000 12.23 0.00 0.00 0.98
310 313 1.349067 GGCCCCGTCACTCCTATAAT 58.651 55.000 0.00 0.00 0.00 1.28
374 390 2.738135 GGACCAAACATGAAACAACCG 58.262 47.619 0.00 0.00 0.00 4.44
472 492 9.691362 TCGGAATAAAGAAAAAGAAAAATGGAG 57.309 29.630 0.00 0.00 0.00 3.86
587 623 3.304057 CGTCACTTTGAAAAAGGAGCCTC 60.304 47.826 4.86 0.00 0.00 4.70
597 633 1.469335 AAGGAGCCTCGTTCCGTTCA 61.469 55.000 0.00 0.00 37.99 3.18
670 720 3.685139 TGTTTTACAGCTCAGAGGAGG 57.315 47.619 0.00 0.00 41.67 4.30
671 721 3.239449 TGTTTTACAGCTCAGAGGAGGA 58.761 45.455 0.00 0.00 41.67 3.71
672 722 3.259374 TGTTTTACAGCTCAGAGGAGGAG 59.741 47.826 0.00 0.00 41.67 3.69
688 738 0.739561 GGAGATCGCGTTCTGGTAGT 59.260 55.000 23.56 0.00 0.00 2.73
693 743 5.105834 AGATCGCGTTCTGGTAGTATTAC 57.894 43.478 18.45 0.00 0.00 1.89
698 748 5.759763 TCGCGTTCTGGTAGTATTACAGATA 59.240 40.000 5.77 0.00 0.00 1.98
699 749 6.073385 TCGCGTTCTGGTAGTATTACAGATAG 60.073 42.308 5.77 0.00 0.00 2.08
700 750 6.073385 CGCGTTCTGGTAGTATTACAGATAGA 60.073 42.308 0.00 0.00 0.00 1.98
701 751 7.361031 CGCGTTCTGGTAGTATTACAGATAGAT 60.361 40.741 0.00 0.00 0.00 1.98
735 794 2.277756 GATTAGCGTCGCGTCCGT 60.278 61.111 12.30 10.41 35.54 4.69
780 860 4.384846 CGTGATATTAGGTGTGTAATCCGC 59.615 45.833 0.00 0.00 0.00 5.54
782 862 4.591498 TGATATTAGGTGTGTAATCCGCCT 59.409 41.667 0.00 0.00 44.72 5.52
809 889 6.210385 TGTCTTAATTTGGTGCCATGTATTGT 59.790 34.615 0.00 0.00 0.00 2.71
810 890 7.394641 TGTCTTAATTTGGTGCCATGTATTGTA 59.605 33.333 0.00 0.00 0.00 2.41
811 891 8.413229 GTCTTAATTTGGTGCCATGTATTGTAT 58.587 33.333 0.00 0.00 0.00 2.29
812 892 8.976353 TCTTAATTTGGTGCCATGTATTGTATT 58.024 29.630 0.00 0.00 0.00 1.89
813 893 8.939201 TTAATTTGGTGCCATGTATTGTATTG 57.061 30.769 0.00 0.00 0.00 1.90
814 894 4.383850 TTGGTGCCATGTATTGTATTGC 57.616 40.909 0.00 0.00 0.00 3.56
832 912 4.166011 CCGCGGCTGCTGCTTTAC 62.166 66.667 28.80 2.50 39.65 2.01
833 913 4.166011 CGCGGCTGCTGCTTTACC 62.166 66.667 28.80 1.76 39.65 2.85
834 914 2.747855 GCGGCTGCTGCTTTACCT 60.748 61.111 25.48 0.00 39.59 3.08
875 955 5.334105 GCGTGCATATCCAAATTTACGATCT 60.334 40.000 9.40 0.00 32.58 2.75
876 956 6.658831 CGTGCATATCCAAATTTACGATCTT 58.341 36.000 0.00 0.00 32.58 2.40
881 961 7.361286 GCATATCCAAATTTACGATCTTCCTCC 60.361 40.741 3.79 0.00 0.00 4.30
883 963 3.883489 CCAAATTTACGATCTTCCTCCCC 59.117 47.826 0.00 0.00 0.00 4.81
1127 1227 4.821589 CAAGGAGGACTCGGCGGC 62.822 72.222 7.21 0.00 0.00 6.53
1705 1828 1.000896 GTGGTCACATGGAAGGGGG 60.001 63.158 0.00 0.00 0.00 5.40
1778 1901 2.868253 GGGGGAACGGACAATCAAG 58.132 57.895 0.00 0.00 0.00 3.02
1779 1902 1.313091 GGGGGAACGGACAATCAAGC 61.313 60.000 0.00 0.00 0.00 4.01
1781 1904 0.672401 GGGAACGGACAATCAAGCGA 60.672 55.000 0.00 0.00 0.00 4.93
1782 1905 1.153353 GGAACGGACAATCAAGCGAA 58.847 50.000 0.00 0.00 0.00 4.70
1783 1906 1.136057 GGAACGGACAATCAAGCGAAC 60.136 52.381 0.00 0.00 0.00 3.95
1785 1908 1.289109 ACGGACAATCAAGCGAACCG 61.289 55.000 0.00 0.00 43.61 4.44
1837 1960 2.754254 GAATGGCCGGGGTGGTTC 60.754 66.667 2.18 0.00 41.21 3.62
1889 2015 3.716195 TGTCGGTGGCATGAGGGG 61.716 66.667 0.00 0.00 0.00 4.79
1910 2036 1.154197 GGCCGTGACCAAAGTTACTC 58.846 55.000 0.00 0.00 30.49 2.59
1912 2038 1.541670 GCCGTGACCAAAGTTACTCCA 60.542 52.381 0.00 0.00 30.49 3.86
1913 2039 2.874457 GCCGTGACCAAAGTTACTCCAT 60.874 50.000 0.00 0.00 30.49 3.41
2177 2315 2.100797 CGTACCGACGCGAATGGA 59.899 61.111 15.93 0.00 43.21 3.41
2178 2316 2.219562 CGTACCGACGCGAATGGAC 61.220 63.158 15.93 5.92 43.21 4.02
2179 2317 1.875364 GTACCGACGCGAATGGACC 60.875 63.158 15.93 3.73 0.00 4.46
2180 2318 3.399797 TACCGACGCGAATGGACCG 62.400 63.158 15.93 4.12 0.00 4.79
2187 2325 3.474806 CGAATGGACCGCAGTGTC 58.525 61.111 0.00 0.00 34.42 3.67
2188 2326 2.444624 CGAATGGACCGCAGTGTCG 61.445 63.158 0.00 0.00 36.07 4.35
2189 2327 1.080093 GAATGGACCGCAGTGTCGA 60.080 57.895 8.27 0.00 36.07 4.20
2258 2412 1.019278 AAGTAATGGCGTCGCAGTGG 61.019 55.000 20.50 0.00 0.00 4.00
2259 2413 2.817834 TAATGGCGTCGCAGTGGC 60.818 61.111 20.50 1.09 0.00 5.01
2270 2424 2.033141 CAGTGGCCTGGGAGTGTG 59.967 66.667 3.32 0.00 34.90 3.82
2271 2425 3.958860 AGTGGCCTGGGAGTGTGC 61.959 66.667 3.32 0.00 0.00 4.57
2528 2703 2.028778 GCGCCAACAATGCCAACA 59.971 55.556 0.00 0.00 0.00 3.33
2587 2765 3.753070 GACGTCCTCATCGGCGTCC 62.753 68.421 6.85 0.00 46.81 4.79
3209 3391 4.496336 GCCGGGATTGAGCCTGCT 62.496 66.667 2.18 0.00 32.72 4.24
3210 3392 2.203126 CCGGGATTGAGCCTGCTC 60.203 66.667 12.18 12.18 43.01 4.26
3212 3394 2.194326 GGGATTGAGCCTGCTCCC 59.806 66.667 16.06 10.00 42.09 4.30
3213 3395 2.203126 GGATTGAGCCTGCTCCCG 60.203 66.667 16.06 0.00 42.09 5.14
3214 3396 2.899339 GATTGAGCCTGCTCCCGC 60.899 66.667 16.06 2.12 42.09 6.13
3215 3397 4.845580 ATTGAGCCTGCTCCCGCG 62.846 66.667 16.06 0.00 42.09 6.46
3355 3566 2.173669 CCGTCGTCATGCATCCACC 61.174 63.158 0.00 0.00 0.00 4.61
3356 3567 2.173669 CGTCGTCATGCATCCACCC 61.174 63.158 0.00 0.00 0.00 4.61
3357 3568 1.078497 GTCGTCATGCATCCACCCA 60.078 57.895 0.00 0.00 0.00 4.51
3406 3617 2.160205 GTCAGCATCCATCCATCCATG 58.840 52.381 0.00 0.00 0.00 3.66
3438 3649 2.869503 ATCCTGGCCGGCGTTAGTTG 62.870 60.000 22.54 7.08 0.00 3.16
3563 3774 3.247162 AGGAGGGCAGGAGAAATAGATC 58.753 50.000 0.00 0.00 0.00 2.75
3564 3775 2.304470 GGAGGGCAGGAGAAATAGATCC 59.696 54.545 0.00 0.00 35.71 3.36
3714 3932 1.604278 GGAAAGTTGGTGTGTGCTCTC 59.396 52.381 0.00 0.00 0.00 3.20
3731 3949 4.728917 CTCTCAAGCAAGAGTGTTGAAG 57.271 45.455 3.80 0.00 38.38 3.02
3732 3950 4.125703 CTCTCAAGCAAGAGTGTTGAAGT 58.874 43.478 3.80 0.00 38.38 3.01
3734 3952 3.872696 TCAAGCAAGAGTGTTGAAGTGA 58.127 40.909 3.80 0.85 0.00 3.41
3735 3953 4.260985 TCAAGCAAGAGTGTTGAAGTGAA 58.739 39.130 3.80 0.00 0.00 3.18
3736 3954 4.333649 TCAAGCAAGAGTGTTGAAGTGAAG 59.666 41.667 3.80 0.00 0.00 3.02
3737 3955 3.209410 AGCAAGAGTGTTGAAGTGAAGG 58.791 45.455 3.80 0.00 0.00 3.46
3738 3956 3.118261 AGCAAGAGTGTTGAAGTGAAGGA 60.118 43.478 3.80 0.00 0.00 3.36
3739 3957 3.817647 GCAAGAGTGTTGAAGTGAAGGAT 59.182 43.478 3.80 0.00 0.00 3.24
3740 3958 4.083590 GCAAGAGTGTTGAAGTGAAGGATC 60.084 45.833 3.80 0.00 0.00 3.36
3967 4202 9.668497 ACCTTTCTTTTTACTAGTAGCCATTAG 57.332 33.333 2.23 0.00 0.00 1.73
4059 4295 8.374743 AGGAATTATAATCCTTCAGCTCTTCTC 58.625 37.037 0.00 0.00 45.06 2.87
4105 4345 3.273434 TGCCTCTATGCAACTTGTGATC 58.727 45.455 0.00 0.00 38.56 2.92
4107 4347 3.064545 GCCTCTATGCAACTTGTGATCAC 59.935 47.826 19.27 19.27 0.00 3.06
4114 4354 2.094545 GCAACTTGTGATCACCCAATCC 60.095 50.000 22.85 4.34 0.00 3.01
4166 4422 0.108898 AAATGCTAATGCGCCGCAAA 60.109 45.000 18.69 6.59 43.62 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 53 2.592308 GCAAGGAATCTCCCGGCT 59.408 61.111 0.00 0.00 37.19 5.52
161 164 2.863132 TATAATTAACGCCCCGCCAT 57.137 45.000 0.00 0.00 0.00 4.40
162 165 2.634815 TTATAATTAACGCCCCGCCA 57.365 45.000 0.00 0.00 0.00 5.69
290 293 0.761702 TTATAGGAGTGACGGGGCCC 60.762 60.000 15.76 15.76 0.00 5.80
291 294 1.349067 ATTATAGGAGTGACGGGGCC 58.651 55.000 0.00 0.00 0.00 5.80
292 295 2.367567 TCAATTATAGGAGTGACGGGGC 59.632 50.000 0.00 0.00 0.00 5.80
293 296 3.386726 TGTCAATTATAGGAGTGACGGGG 59.613 47.826 1.77 0.00 44.96 5.73
294 297 4.665833 TGTCAATTATAGGAGTGACGGG 57.334 45.455 1.77 0.00 44.96 5.28
295 298 7.254795 GGAATTTGTCAATTATAGGAGTGACGG 60.255 40.741 1.77 0.00 44.96 4.79
296 299 7.495934 AGGAATTTGTCAATTATAGGAGTGACG 59.504 37.037 1.77 0.00 44.96 4.35
297 300 8.738645 AGGAATTTGTCAATTATAGGAGTGAC 57.261 34.615 0.00 0.00 43.01 3.67
298 301 9.177608 CAAGGAATTTGTCAATTATAGGAGTGA 57.822 33.333 0.00 0.00 32.35 3.41
406 426 1.578915 GTGGCGTACGTACATACAACG 59.421 52.381 24.50 13.01 45.64 4.10
407 427 1.919918 GGTGGCGTACGTACATACAAC 59.080 52.381 24.50 17.58 0.00 3.32
409 429 1.132834 CAGGTGGCGTACGTACATACA 59.867 52.381 24.50 16.29 0.00 2.29
410 430 1.133025 ACAGGTGGCGTACGTACATAC 59.867 52.381 24.50 17.95 0.00 2.39
412 432 1.462616 TACAGGTGGCGTACGTACAT 58.537 50.000 24.50 11.30 0.00 2.29
413 433 1.132834 CATACAGGTGGCGTACGTACA 59.867 52.381 24.50 13.54 0.00 2.90
414 434 1.534595 CCATACAGGTGGCGTACGTAC 60.535 57.143 17.90 15.90 31.43 3.67
415 435 0.740149 CCATACAGGTGGCGTACGTA 59.260 55.000 17.90 3.55 31.43 3.57
416 436 1.514087 CCATACAGGTGGCGTACGT 59.486 57.895 17.90 0.00 31.43 3.57
417 437 1.227147 CCCATACAGGTGGCGTACG 60.227 63.158 11.84 11.84 37.96 3.67
472 492 4.147322 CATGTGACGCGCGGGTTC 62.147 66.667 35.22 22.78 0.00 3.62
587 623 7.485277 GGATATATATCTTCTGTGAACGGAACG 59.515 40.741 19.72 0.00 44.81 3.95
670 720 3.900388 ATACTACCAGAACGCGATCTC 57.100 47.619 16.69 7.68 0.00 2.75
671 721 4.577693 TGTAATACTACCAGAACGCGATCT 59.422 41.667 15.93 14.66 0.00 2.75
672 722 4.852138 TGTAATACTACCAGAACGCGATC 58.148 43.478 15.93 11.81 0.00 3.69
693 743 8.544622 TCGGGCCTATCTATCTATATCTATCTG 58.455 40.741 0.84 0.00 0.00 2.90
698 748 7.832187 GCTAATCGGGCCTATCTATCTATATCT 59.168 40.741 0.84 0.00 0.00 1.98
699 749 7.201661 CGCTAATCGGGCCTATCTATCTATATC 60.202 44.444 0.84 0.00 33.78 1.63
700 750 6.600032 CGCTAATCGGGCCTATCTATCTATAT 59.400 42.308 0.84 0.00 33.78 0.86
701 751 5.938710 CGCTAATCGGGCCTATCTATCTATA 59.061 44.000 0.84 0.00 33.78 1.31
735 794 4.495019 CGATATCAATTTTCGTCCCGCAAA 60.495 41.667 3.12 0.00 0.00 3.68
747 811 9.778741 ACACACCTAATATCACGATATCAATTT 57.221 29.630 3.12 0.00 33.13 1.82
753 817 8.188799 CGGATTACACACCTAATATCACGATAT 58.811 37.037 0.00 0.00 35.63 1.63
780 860 4.599047 TGGCACCAAATTAAGACAAAGG 57.401 40.909 0.00 0.00 0.00 3.11
782 862 5.543507 ACATGGCACCAAATTAAGACAAA 57.456 34.783 0.00 0.00 0.00 2.83
826 906 1.459450 TCGGCATCCAAAGGTAAAGC 58.541 50.000 0.00 0.00 0.00 3.51
827 907 5.828299 TTAATCGGCATCCAAAGGTAAAG 57.172 39.130 0.00 0.00 0.00 1.85
828 908 5.451242 GCATTAATCGGCATCCAAAGGTAAA 60.451 40.000 0.00 0.00 0.00 2.01
829 909 4.037446 GCATTAATCGGCATCCAAAGGTAA 59.963 41.667 0.00 0.00 0.00 2.85
830 910 3.568007 GCATTAATCGGCATCCAAAGGTA 59.432 43.478 0.00 0.00 0.00 3.08
831 911 2.362077 GCATTAATCGGCATCCAAAGGT 59.638 45.455 0.00 0.00 0.00 3.50
832 912 2.605338 CGCATTAATCGGCATCCAAAGG 60.605 50.000 0.00 0.00 0.00 3.11
833 913 2.033299 ACGCATTAATCGGCATCCAAAG 59.967 45.455 10.58 0.00 0.00 2.77
834 914 2.020720 ACGCATTAATCGGCATCCAAA 58.979 42.857 10.58 0.00 0.00 3.28
875 955 1.499007 GGATTAATGCCAGGGGAGGAA 59.501 52.381 0.00 0.00 0.00 3.36
876 956 1.149101 GGATTAATGCCAGGGGAGGA 58.851 55.000 0.00 0.00 0.00 3.71
881 961 1.903404 GCCGGGATTAATGCCAGGG 60.903 63.158 26.14 20.57 38.32 4.45
883 963 2.260869 CGGCCGGGATTAATGCCAG 61.261 63.158 23.92 15.03 44.22 4.85
901 982 4.989168 CGGGAGAGGCAAGTATAAATACAC 59.011 45.833 3.13 0.00 35.74 2.90
1363 1474 2.355363 CCGCCGACGAACTGAACA 60.355 61.111 0.00 0.00 43.93 3.18
1600 1723 4.032452 TGATTGCCGCCCAGCTGA 62.032 61.111 17.39 0.00 0.00 4.26
1640 1763 0.248458 CGGTGCGTGCTGTTCTTTTT 60.248 50.000 0.00 0.00 0.00 1.94
1641 1764 1.355210 CGGTGCGTGCTGTTCTTTT 59.645 52.632 0.00 0.00 0.00 2.27
1642 1765 3.022287 CGGTGCGTGCTGTTCTTT 58.978 55.556 0.00 0.00 0.00 2.52
1643 1766 3.649986 GCGGTGCGTGCTGTTCTT 61.650 61.111 0.00 0.00 0.00 2.52
1644 1767 4.908687 TGCGGTGCGTGCTGTTCT 62.909 61.111 0.00 0.00 0.00 3.01
1645 1768 4.666532 GTGCGGTGCGTGCTGTTC 62.667 66.667 0.00 0.00 0.00 3.18
1705 1828 1.509004 GAGTCAGAGTCACCTCCGC 59.491 63.158 0.00 0.00 38.58 5.54
1769 1892 0.093026 CGTCGGTTCGCTTGATTGTC 59.907 55.000 0.00 0.00 0.00 3.18
1772 1895 2.388232 GCCGTCGGTTCGCTTGATT 61.388 57.895 13.94 0.00 0.00 2.57
1773 1896 2.813908 GCCGTCGGTTCGCTTGAT 60.814 61.111 13.94 0.00 0.00 2.57
1889 2015 1.154197 GTAACTTTGGTCACGGCCTC 58.846 55.000 0.00 0.00 0.00 4.70
2163 2301 4.789075 CGGTCCATTCGCGTCGGT 62.789 66.667 5.77 0.00 0.00 4.69
2170 2308 2.444624 CGACACTGCGGTCCATTCG 61.445 63.158 0.00 0.00 34.24 3.34
2171 2309 1.080093 TCGACACTGCGGTCCATTC 60.080 57.895 0.00 0.00 34.24 2.67
2172 2310 1.374252 GTCGACACTGCGGTCCATT 60.374 57.895 11.55 0.00 34.24 3.16
2173 2311 2.261671 GTCGACACTGCGGTCCAT 59.738 61.111 11.55 0.00 34.24 3.41
2174 2312 4.337060 CGTCGACACTGCGGTCCA 62.337 66.667 17.16 0.00 34.24 4.02
2175 2313 3.836176 AACGTCGACACTGCGGTCC 62.836 63.158 17.16 0.00 34.24 4.46
2176 2314 1.947642 AAACGTCGACACTGCGGTC 60.948 57.895 17.16 0.00 34.42 4.79
2177 2315 2.105528 AAACGTCGACACTGCGGT 59.894 55.556 17.16 0.58 0.00 5.68
2178 2316 2.544359 CAAACGTCGACACTGCGG 59.456 61.111 17.16 0.00 0.00 5.69
2179 2317 2.089433 AAGCAAACGTCGACACTGCG 62.089 55.000 21.02 8.91 38.07 5.18
2180 2318 0.027586 AAAGCAAACGTCGACACTGC 59.972 50.000 20.16 20.16 0.00 4.40
2181 2319 2.538449 AGTAAAGCAAACGTCGACACTG 59.462 45.455 17.16 10.03 0.00 3.66
2182 2320 2.538449 CAGTAAAGCAAACGTCGACACT 59.462 45.455 17.16 4.96 0.00 3.55
2183 2321 2.536803 TCAGTAAAGCAAACGTCGACAC 59.463 45.455 17.16 2.46 0.00 3.67
2184 2322 2.811855 TCAGTAAAGCAAACGTCGACA 58.188 42.857 17.16 0.00 0.00 4.35
2185 2323 4.084745 TCAATCAGTAAAGCAAACGTCGAC 60.085 41.667 5.18 5.18 0.00 4.20
2186 2324 4.052608 TCAATCAGTAAAGCAAACGTCGA 58.947 39.130 0.00 0.00 0.00 4.20
2187 2325 4.383774 TCAATCAGTAAAGCAAACGTCG 57.616 40.909 0.00 0.00 0.00 5.12
2188 2326 5.507077 TGTTCAATCAGTAAAGCAAACGTC 58.493 37.500 0.00 0.00 0.00 4.34
2189 2327 5.065988 ACTGTTCAATCAGTAAAGCAAACGT 59.934 36.000 0.00 0.00 45.31 3.99
2258 2412 4.626081 ACACGCACACTCCCAGGC 62.626 66.667 0.00 0.00 0.00 4.85
2259 2413 1.507141 GAAACACGCACACTCCCAGG 61.507 60.000 0.00 0.00 0.00 4.45
2271 2425 4.104776 ACAAAAAGCATGTCAGAAACACG 58.895 39.130 0.00 0.00 41.75 4.49
2311 2486 1.746239 CTGCGCCATGTCCATGTCA 60.746 57.895 4.18 1.52 37.11 3.58
2335 2510 1.001641 GAACAGCCCTGACAGCCAT 60.002 57.895 1.69 0.00 0.00 4.40
2344 2519 2.338984 GTGTCGTCGAACAGCCCT 59.661 61.111 0.00 0.00 0.00 5.19
2515 2690 4.308265 TCATGTTCATGTTGGCATTGTTG 58.692 39.130 11.73 0.00 31.99 3.33
2528 2703 3.550639 CCGCTGTTGTTGTTCATGTTCAT 60.551 43.478 0.00 0.00 0.00 2.57
2575 2753 2.725008 GAGGAGGACGCCGATGAG 59.275 66.667 0.00 0.00 0.00 2.90
3246 3428 0.106318 TAGCTAAGGGGGACGAGACC 60.106 60.000 0.00 0.00 0.00 3.85
3247 3429 1.998222 ATAGCTAAGGGGGACGAGAC 58.002 55.000 0.00 0.00 0.00 3.36
3248 3430 2.769602 AATAGCTAAGGGGGACGAGA 57.230 50.000 0.00 0.00 0.00 4.04
3249 3431 7.506261 ACATATATAATAGCTAAGGGGGACGAG 59.494 40.741 0.00 0.00 0.00 4.18
3314 3501 2.537931 CGACGATGACTGACTGACTAGC 60.538 54.545 0.00 0.00 0.00 3.42
3355 3566 1.152902 ATGGCGATGATGGTGGTGG 60.153 57.895 0.00 0.00 0.00 4.61
3356 3567 2.027325 CATGGCGATGATGGTGGTG 58.973 57.895 1.91 0.00 0.00 4.17
3357 3568 1.825191 GCATGGCGATGATGGTGGT 60.825 57.895 13.46 0.00 0.00 4.16
3406 3617 2.203209 AGGATGCCCGGCGATTTC 60.203 61.111 9.30 0.00 37.58 2.17
3438 3649 5.483685 AACCCAAAAGAAAAGCCCTATTC 57.516 39.130 0.00 0.00 0.00 1.75
3563 3774 4.127907 CTGACTCTGTGATTGATCCATGG 58.872 47.826 4.97 4.97 0.00 3.66
3564 3775 4.571176 CACTGACTCTGTGATTGATCCATG 59.429 45.833 9.86 0.00 35.76 3.66
3714 3932 4.497006 CCTTCACTTCAACACTCTTGCTTG 60.497 45.833 0.00 0.00 0.00 4.01
3726 3944 6.016024 CCAACAAATCTGATCCTTCACTTCAA 60.016 38.462 0.00 0.00 0.00 2.69
3727 3945 5.474532 CCAACAAATCTGATCCTTCACTTCA 59.525 40.000 0.00 0.00 0.00 3.02
3729 3947 5.388654 ACCAACAAATCTGATCCTTCACTT 58.611 37.500 0.00 0.00 0.00 3.16
3730 3948 4.990526 ACCAACAAATCTGATCCTTCACT 58.009 39.130 0.00 0.00 0.00 3.41
3731 3949 5.712152 AACCAACAAATCTGATCCTTCAC 57.288 39.130 0.00 0.00 0.00 3.18
3732 3950 5.509501 GCAAACCAACAAATCTGATCCTTCA 60.510 40.000 0.00 0.00 0.00 3.02
3734 3952 4.590222 AGCAAACCAACAAATCTGATCCTT 59.410 37.500 0.00 0.00 0.00 3.36
3735 3953 4.154942 AGCAAACCAACAAATCTGATCCT 58.845 39.130 0.00 0.00 0.00 3.24
3736 3954 4.525912 AGCAAACCAACAAATCTGATCC 57.474 40.909 0.00 0.00 0.00 3.36
3737 3955 6.681777 ACTTAGCAAACCAACAAATCTGATC 58.318 36.000 0.00 0.00 0.00 2.92
3738 3956 6.655078 ACTTAGCAAACCAACAAATCTGAT 57.345 33.333 0.00 0.00 0.00 2.90
3739 3957 6.463995 AACTTAGCAAACCAACAAATCTGA 57.536 33.333 0.00 0.00 0.00 3.27
3740 3958 7.648142 TCTAACTTAGCAAACCAACAAATCTG 58.352 34.615 0.00 0.00 0.00 2.90
4049 4285 0.695347 AAACAGGGGGAGAAGAGCTG 59.305 55.000 0.00 0.00 0.00 4.24
4059 4295 0.771127 TTCACAGGAGAAACAGGGGG 59.229 55.000 0.00 0.00 0.00 5.40
4105 4345 0.967380 GTGCTCAAGGGGATTGGGTG 60.967 60.000 0.00 0.00 41.87 4.61
4107 4347 0.682209 CAGTGCTCAAGGGGATTGGG 60.682 60.000 0.00 0.00 42.83 4.12
4114 4354 0.610174 TCAGTAGCAGTGCTCAAGGG 59.390 55.000 23.64 8.31 40.44 3.95


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

AutoCloner maintained by Alex Coulton.