Multiple sequence alignment - TraesCS3A01G345300

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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 TraesCS3A01G345300 chr3A 100.000 3362 0 0 1 3362 594670737 594667376 0.000000e+00 6209
1 TraesCS3A01G345300 chr3B 91.955 3356 173 46 1 3318 594413790 594410494 0.000000e+00 4612
2 TraesCS3A01G345300 chr3B 87.778 360 33 8 1 359 594419913 594419564 8.680000e-111 411
3 TraesCS3A01G345300 chr3D 94.248 2851 134 12 482 3318 452419802 452416968 0.000000e+00 4329
4 TraesCS3A01G345300 chr3D 88.764 356 30 6 1 355 452425275 452424929 8.620000e-116 427
5 TraesCS3A01G345300 chr3D 85.647 425 26 12 2 413 452420664 452420262 6.710000e-112 414


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 TraesCS3A01G345300 chr3A 594667376 594670737 3361 True 6209.0 6209 100.0000 1 3362 1 chr3A.!!$R1 3361
1 TraesCS3A01G345300 chr3B 594410494 594413790 3296 True 4612.0 4612 91.9550 1 3318 1 chr3B.!!$R1 3317
2 TraesCS3A01G345300 chr3D 452416968 452420664 3696 True 2371.5 4329 89.9475 2 3318 2 chr3D.!!$R2 3316

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
993 1413 0.754472 AAGAAGGTTCGTGGTCGGAA 59.246 50.0 0.0 0.0 37.69 4.30 F
2248 2668 0.179094 TACGCCAGCCAAGGTTATCG 60.179 55.0 0.0 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2700 0.034863 TCTTAAACCCCGGCATGACC 60.035 55.0 0.0 0.0 0.00 4.02 R
3071 3507 1.275666 TGTACACCACTGCTAGGCAT 58.724 50.0 0.0 0.0 38.13 4.40 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
74 80 9.702494 CTCCTTTCAAGAGAAGCAAATAAAAAT 57.298 29.630 0.00 0.00 34.71 1.82
79 85 8.006741 TCAAGAGAAGCAAATAAAAATTTCGC 57.993 30.769 0.00 0.00 0.00 4.70
94 100 8.642908 AAAAATTTCGCTTTTATATAGGGTGC 57.357 30.769 0.00 0.00 0.00 5.01
134 142 4.397420 TGGAGACAGTATGCAAACATTGT 58.603 39.130 0.00 0.00 42.53 2.71
135 143 5.555966 TGGAGACAGTATGCAAACATTGTA 58.444 37.500 0.00 0.00 42.53 2.41
136 144 5.411361 TGGAGACAGTATGCAAACATTGTAC 59.589 40.000 0.00 0.00 42.53 2.90
174 182 4.099266 TGAGATTTCACCAACCAACCAAAG 59.901 41.667 0.00 0.00 0.00 2.77
177 185 4.891992 TTTCACCAACCAACCAAAGAAA 57.108 36.364 0.00 0.00 0.00 2.52
201 209 5.905181 ACTTTTGTTTAATAGCAACGTGACG 59.095 36.000 2.24 2.24 0.00 4.35
202 210 3.443054 TGTTTAATAGCAACGTGACGC 57.557 42.857 4.25 0.00 0.00 5.19
203 211 2.158058 TGTTTAATAGCAACGTGACGCC 59.842 45.455 4.25 0.00 0.00 5.68
231 239 1.565759 TCTGAACATCCCCCTTCCATG 59.434 52.381 0.00 0.00 0.00 3.66
263 271 1.153086 CTGGAATGGAAGGCCGGAG 60.153 63.158 5.05 0.00 36.79 4.63
325 333 2.726760 GACACGAGCAGTTACAGTCTTG 59.273 50.000 0.00 0.00 0.00 3.02
337 352 3.409026 ACAGTCTTGGTCTTAAGCAGG 57.591 47.619 0.00 0.00 33.72 4.85
355 370 1.153349 GGAGCGAGGCTAGGGTTTG 60.153 63.158 0.00 0.00 39.88 2.93
356 371 1.815840 GAGCGAGGCTAGGGTTTGC 60.816 63.158 0.00 0.00 39.88 3.68
434 457 5.483937 GGATTACAAAAGAAATCCAACCCCT 59.516 40.000 8.80 0.00 46.95 4.79
435 458 6.013725 GGATTACAAAAGAAATCCAACCCCTT 60.014 38.462 8.80 0.00 46.95 3.95
440 463 3.739401 AGAAATCCAACCCCTTGTAGG 57.261 47.619 0.00 0.00 34.30 3.18
444 467 1.358152 TCCAACCCCTTGTAGGAGTG 58.642 55.000 0.00 0.00 37.67 3.51
558 972 4.101448 ATGCCCTCCACTCACGCC 62.101 66.667 0.00 0.00 0.00 5.68
643 1057 3.251972 CAGGCTTTTCGCTTCTTCTTCTT 59.748 43.478 0.00 0.00 39.13 2.52
644 1058 3.500299 AGGCTTTTCGCTTCTTCTTCTTC 59.500 43.478 0.00 0.00 39.13 2.87
645 1059 3.500299 GGCTTTTCGCTTCTTCTTCTTCT 59.500 43.478 0.00 0.00 39.13 2.85
687 1101 2.342648 GTTCGTGGAGCTTCCGGT 59.657 61.111 0.00 0.00 40.17 5.28
719 1133 5.290400 GCTGAACAAAGGTACCGTACTAATC 59.710 44.000 6.18 1.55 0.00 1.75
729 1143 1.268234 CCGTACTAATCACCGACGACC 60.268 57.143 0.00 0.00 35.59 4.79
760 1174 4.787598 ACATGATCGAGTTCTTGTTTTGC 58.212 39.130 0.00 0.00 31.96 3.68
790 1204 2.071540 TCTGCTTTGCAATCGTCTGAG 58.928 47.619 0.00 0.00 38.41 3.35
950 1367 4.044426 GCATGTTTGTTTGACTTCCTGTC 58.956 43.478 0.00 0.00 45.54 3.51
951 1368 4.202050 GCATGTTTGTTTGACTTCCTGTCT 60.202 41.667 0.00 0.00 45.54 3.41
952 1369 5.514279 CATGTTTGTTTGACTTCCTGTCTC 58.486 41.667 0.00 0.00 45.54 3.36
953 1370 4.584874 TGTTTGTTTGACTTCCTGTCTCA 58.415 39.130 0.00 0.00 45.54 3.27
954 1371 5.007034 TGTTTGTTTGACTTCCTGTCTCAA 58.993 37.500 0.00 0.00 45.54 3.02
955 1372 5.106317 TGTTTGTTTGACTTCCTGTCTCAAC 60.106 40.000 0.00 0.00 45.54 3.18
956 1373 4.487714 TGTTTGACTTCCTGTCTCAACT 57.512 40.909 0.00 0.00 45.54 3.16
966 1383 2.411904 CTGTCTCAACTCTCAACCAGC 58.588 52.381 0.00 0.00 0.00 4.85
971 1391 1.768275 TCAACTCTCAACCAGCCTGAA 59.232 47.619 0.00 0.00 0.00 3.02
974 1394 2.050144 ACTCTCAACCAGCCTGAAGAA 58.950 47.619 0.00 0.00 0.00 2.52
985 1405 2.104963 AGCCTGAAGAAAGAAGGTTCGT 59.895 45.455 0.00 0.00 33.34 3.85
993 1413 0.754472 AAGAAGGTTCGTGGTCGGAA 59.246 50.000 0.00 0.00 37.69 4.30
1215 1635 2.946762 GCGCACCTCAAAGTCCAC 59.053 61.111 0.30 0.00 0.00 4.02
1377 1797 2.410939 CATGTGCCGTATGATCCTGAG 58.589 52.381 0.00 0.00 0.00 3.35
1468 1888 5.022282 TCTGAATATGAACGAATGGAGCA 57.978 39.130 0.00 0.00 0.00 4.26
1469 1889 5.052481 TCTGAATATGAACGAATGGAGCAG 58.948 41.667 0.00 0.00 0.00 4.24
1482 1902 1.663173 GAGCAGCCCGAGGTATCTC 59.337 63.158 0.00 0.00 36.69 2.75
1497 1917 6.260050 CGAGGTATCTCTCTCATATAAGCTCC 59.740 46.154 0.62 0.00 37.86 4.70
1500 1920 6.321181 GGTATCTCTCTCATATAAGCTCCAGG 59.679 46.154 0.00 0.00 0.00 4.45
1638 2058 2.104963 GGAGGAGAAGATTGGCCGTAAT 59.895 50.000 0.00 0.00 0.00 1.89
1666 2086 2.224597 TGCAGAGAAGGATGCTTCACAA 60.225 45.455 26.36 9.43 42.98 3.33
1667 2087 2.161211 GCAGAGAAGGATGCTTCACAAC 59.839 50.000 26.36 13.60 39.38 3.32
1903 2323 3.452474 GCAGACAGAGATGACCATACAC 58.548 50.000 0.00 0.00 0.00 2.90
2070 2490 3.755378 ACTTGGATCACAGAGCATTTGTC 59.245 43.478 0.00 0.00 0.00 3.18
2074 2494 2.084610 TCACAGAGCATTTGTCGAGG 57.915 50.000 0.00 0.00 0.00 4.63
2127 2547 3.512724 AGAAATTTGTGAGGATGGCAAGG 59.487 43.478 0.00 0.00 0.00 3.61
2158 2578 0.387367 ACTACTCGCAGTTGCTCGTG 60.387 55.000 2.29 0.00 39.32 4.35
2169 2589 0.321346 TTGCTCGTGCTCTGAATCCA 59.679 50.000 11.19 0.00 40.48 3.41
2195 2615 7.588512 AGAGCTGAAATGTTTTATGTCAAGAC 58.411 34.615 0.00 0.00 0.00 3.01
2217 2637 2.143925 GGTGTTCAGTTTCGGAAGGAG 58.856 52.381 0.00 0.00 0.00 3.69
2232 2652 2.386661 AGGAGCACATGGAAAGTACG 57.613 50.000 0.00 0.00 0.00 3.67
2242 2662 1.305930 GGAAAGTACGCCAGCCAAGG 61.306 60.000 0.00 0.00 0.00 3.61
2248 2668 0.179094 TACGCCAGCCAAGGTTATCG 60.179 55.000 0.00 0.00 0.00 2.92
2257 2677 2.483889 GCCAAGGTTATCGGAGAAGAGG 60.484 54.545 0.00 0.00 43.58 3.69
2258 2678 3.031736 CCAAGGTTATCGGAGAAGAGGA 58.968 50.000 0.00 0.00 43.58 3.71
2259 2679 3.068873 CCAAGGTTATCGGAGAAGAGGAG 59.931 52.174 0.00 0.00 43.58 3.69
2280 2700 3.875134 AGAAGTTCAGTGTTGGGTTTACG 59.125 43.478 5.50 0.00 0.00 3.18
2324 2744 2.413310 TGCACTGTCATCAGATGCAT 57.587 45.000 0.00 0.00 44.74 3.96
2325 2745 2.718563 TGCACTGTCATCAGATGCATT 58.281 42.857 5.41 0.00 44.74 3.56
2335 2755 7.604549 TGTCATCAGATGCATTGTTTATTTGT 58.395 30.769 5.41 0.00 0.00 2.83
2374 2794 6.990341 TGGACTTCTGAACACATCATATTG 57.010 37.500 0.00 0.00 37.44 1.90
2403 2823 7.588512 CCATTAGGTAAGCAGAATCAAATAGC 58.411 38.462 0.00 0.00 0.00 2.97
2405 2825 9.494271 CATTAGGTAAGCAGAATCAAATAGCTA 57.506 33.333 0.00 0.00 34.66 3.32
2477 2897 3.571590 CCTAGGAGTTGAGGAGCACTAT 58.428 50.000 1.05 0.00 34.46 2.12
2584 3004 2.874701 CCATAAATCAGGCCTCTGTTCG 59.125 50.000 0.00 0.00 41.59 3.95
2592 3012 0.108138 GGCCTCTGTTCGTGTGCTAT 60.108 55.000 0.00 0.00 0.00 2.97
2597 3017 3.369147 CCTCTGTTCGTGTGCTATTTGAG 59.631 47.826 0.00 0.00 0.00 3.02
2610 3030 6.128391 TGTGCTATTTGAGATACCAACGAAAC 60.128 38.462 0.00 0.00 0.00 2.78
2631 3051 9.051679 CGAAACTGGATAATGGAATGTGTATAA 57.948 33.333 0.00 0.00 0.00 0.98
2733 3167 7.963532 TCTATTTATCTAACCATGAGTGGGTC 58.036 38.462 0.00 0.00 43.92 4.46
2767 3201 2.564947 AGAAGTTCATCTGCCGAAGAGT 59.435 45.455 5.50 0.00 38.67 3.24
2914 3348 2.268298 CAACCTTCCTCCACGTATTCG 58.732 52.381 0.00 0.00 43.34 3.34
3008 3442 1.751924 CAGAGGAAGGACGGGTAGAAG 59.248 57.143 0.00 0.00 0.00 2.85
3060 3496 9.730705 ATACAACATGAGGTCATATTAATCCTG 57.269 33.333 0.00 0.00 34.26 3.86
3061 3497 7.000472 ACAACATGAGGTCATATTAATCCTGG 59.000 38.462 0.00 0.00 34.26 4.45
3071 3507 9.515226 GGTCATATTAATCCTGGCAGTTTATTA 57.485 33.333 14.43 11.13 0.00 0.98
3074 3510 9.793252 CATATTAATCCTGGCAGTTTATTATGC 57.207 33.333 21.15 0.00 41.80 3.14
3083 3524 5.100751 GCAGTTTATTATGCCTAGCAGTG 57.899 43.478 0.00 0.00 43.65 3.66
3086 3527 5.008019 CAGTTTATTATGCCTAGCAGTGGTG 59.992 44.000 4.76 0.00 43.65 4.17
3098 3539 4.701956 AGCAGTGGTGTACAAATATTGC 57.298 40.909 0.00 5.93 0.00 3.56
3102 3543 5.123186 GCAGTGGTGTACAAATATTGCACTA 59.877 40.000 13.96 0.00 31.04 2.74
3245 3686 2.032550 CGAAGGGCTGCATACTGAATTG 59.967 50.000 0.50 0.00 0.00 2.32
3246 3687 3.282021 GAAGGGCTGCATACTGAATTGA 58.718 45.455 0.50 0.00 0.00 2.57
3249 3690 3.445096 AGGGCTGCATACTGAATTGAAAC 59.555 43.478 0.50 0.00 0.00 2.78
3261 3703 5.163519 ACTGAATTGAAACACCAACCAGAAG 60.164 40.000 0.00 0.00 35.49 2.85
3288 3730 3.507233 TCAGCATAAGGAAAACTTGCAGG 59.493 43.478 0.00 0.00 40.37 4.85
3323 3765 8.983307 AAAAATTGTTCAAAATTGTTGTGCAT 57.017 23.077 0.00 0.00 27.99 3.96
3324 3766 8.983307 AAAATTGTTCAAAATTGTTGTGCATT 57.017 23.077 0.00 0.00 30.21 3.56
3325 3767 8.983307 AAATTGTTCAAAATTGTTGTGCATTT 57.017 23.077 0.00 0.00 30.21 2.32
3326 3768 8.983307 AATTGTTCAAAATTGTTGTGCATTTT 57.017 23.077 0.00 0.00 33.58 1.82
3327 3769 7.792383 TTGTTCAAAATTGTTGTGCATTTTG 57.208 28.000 12.59 12.59 42.25 2.44
3328 3770 6.906659 TGTTCAAAATTGTTGTGCATTTTGT 58.093 28.000 16.43 0.00 41.84 2.83
3329 3771 6.800408 TGTTCAAAATTGTTGTGCATTTTGTG 59.200 30.769 16.43 0.00 41.84 3.33
3330 3772 6.732531 TCAAAATTGTTGTGCATTTTGTGA 57.267 29.167 16.43 1.27 41.84 3.58
3331 3773 7.317842 TCAAAATTGTTGTGCATTTTGTGAT 57.682 28.000 16.43 0.00 41.84 3.06
3332 3774 7.408123 TCAAAATTGTTGTGCATTTTGTGATC 58.592 30.769 16.43 0.00 41.84 2.92
3333 3775 5.579384 AATTGTTGTGCATTTTGTGATCG 57.421 34.783 0.00 0.00 0.00 3.69
3334 3776 3.978718 TGTTGTGCATTTTGTGATCGA 57.021 38.095 0.00 0.00 0.00 3.59
3335 3777 4.502171 TGTTGTGCATTTTGTGATCGAT 57.498 36.364 0.00 0.00 0.00 3.59
3336 3778 4.869215 TGTTGTGCATTTTGTGATCGATT 58.131 34.783 0.00 0.00 0.00 3.34
3337 3779 6.006759 TGTTGTGCATTTTGTGATCGATTA 57.993 33.333 0.00 0.00 0.00 1.75
3338 3780 6.619744 TGTTGTGCATTTTGTGATCGATTAT 58.380 32.000 0.00 0.00 0.00 1.28
3339 3781 7.756558 TGTTGTGCATTTTGTGATCGATTATA 58.243 30.769 0.00 0.00 0.00 0.98
3340 3782 8.404765 TGTTGTGCATTTTGTGATCGATTATAT 58.595 29.630 0.00 0.00 0.00 0.86
3341 3783 8.684655 GTTGTGCATTTTGTGATCGATTATATG 58.315 33.333 0.00 0.43 0.00 1.78
3342 3784 7.929159 TGTGCATTTTGTGATCGATTATATGT 58.071 30.769 0.00 0.00 0.00 2.29
3343 3785 9.050601 TGTGCATTTTGTGATCGATTATATGTA 57.949 29.630 0.00 0.00 0.00 2.29
3344 3786 9.318041 GTGCATTTTGTGATCGATTATATGTAC 57.682 33.333 0.00 5.02 0.00 2.90
3345 3787 8.503196 TGCATTTTGTGATCGATTATATGTACC 58.497 33.333 0.00 0.00 0.00 3.34
3346 3788 8.721478 GCATTTTGTGATCGATTATATGTACCT 58.279 33.333 0.00 0.00 0.00 3.08
3348 3790 9.778741 ATTTTGTGATCGATTATATGTACCTGT 57.221 29.630 0.00 0.00 0.00 4.00
3349 3791 9.607988 TTTTGTGATCGATTATATGTACCTGTT 57.392 29.630 0.00 0.00 0.00 3.16
3350 3792 8.812147 TTGTGATCGATTATATGTACCTGTTC 57.188 34.615 0.00 0.00 0.00 3.18
3351 3793 7.375834 TGTGATCGATTATATGTACCTGTTCC 58.624 38.462 0.00 0.00 0.00 3.62
3352 3794 6.812160 GTGATCGATTATATGTACCTGTTCCC 59.188 42.308 0.00 0.00 0.00 3.97
3353 3795 6.724441 TGATCGATTATATGTACCTGTTCCCT 59.276 38.462 0.00 0.00 0.00 4.20
3354 3796 6.989155 TCGATTATATGTACCTGTTCCCTT 57.011 37.500 0.00 0.00 0.00 3.95
3355 3797 6.755206 TCGATTATATGTACCTGTTCCCTTG 58.245 40.000 0.00 0.00 0.00 3.61
3356 3798 6.325545 TCGATTATATGTACCTGTTCCCTTGT 59.674 38.462 0.00 0.00 0.00 3.16
3357 3799 6.645415 CGATTATATGTACCTGTTCCCTTGTC 59.355 42.308 0.00 0.00 0.00 3.18
3358 3800 6.877668 TTATATGTACCTGTTCCCTTGTCA 57.122 37.500 0.00 0.00 0.00 3.58
3359 3801 5.975988 ATATGTACCTGTTCCCTTGTCAT 57.024 39.130 0.00 0.00 0.00 3.06
3360 3802 3.695830 TGTACCTGTTCCCTTGTCATC 57.304 47.619 0.00 0.00 0.00 2.92
3361 3803 2.304761 TGTACCTGTTCCCTTGTCATCC 59.695 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.276678 CCACAGGACACAGCCATATATTTG 59.723 45.833 0.00 0.00 0.00 2.32
12 13 4.079787 ACCACAGGACACAGCCATATATTT 60.080 41.667 0.00 0.00 0.00 1.40
22 26 1.227943 CCACCACCACAGGACACAG 60.228 63.158 0.00 0.00 0.00 3.66
70 74 7.147811 TGGCACCCTATATAAAAGCGAAATTTT 60.148 33.333 0.00 0.00 36.40 1.82
74 80 4.783055 TGGCACCCTATATAAAAGCGAAA 58.217 39.130 0.00 0.00 0.00 3.46
77 83 6.811253 TTAATGGCACCCTATATAAAAGCG 57.189 37.500 0.00 0.00 0.00 4.68
79 85 9.520515 ACTCATTAATGGCACCCTATATAAAAG 57.479 33.333 15.36 2.43 0.00 2.27
94 100 4.406972 TCTCCAGTCCTCACTCATTAATGG 59.593 45.833 15.36 8.69 0.00 3.16
134 142 7.182026 TGAAATCTCATTTTGGGAGAGGTAGTA 59.818 37.037 0.00 0.00 44.04 1.82
135 143 6.012508 TGAAATCTCATTTTGGGAGAGGTAGT 60.013 38.462 0.00 0.00 44.04 2.73
136 144 6.317391 GTGAAATCTCATTTTGGGAGAGGTAG 59.683 42.308 0.00 0.00 44.04 3.18
174 182 8.257166 GTCACGTTGCTATTAAACAAAAGTTTC 58.743 33.333 0.00 0.00 0.00 2.78
177 185 5.905181 CGTCACGTTGCTATTAAACAAAAGT 59.095 36.000 0.00 0.00 0.00 2.66
202 210 4.473520 ATGTTCAGAGCGGGCGGG 62.474 66.667 0.00 0.00 0.00 6.13
203 211 2.892425 GATGTTCAGAGCGGGCGG 60.892 66.667 0.00 0.00 0.00 6.13
217 225 2.199535 GGGCATGGAAGGGGGATG 59.800 66.667 0.00 0.00 0.00 3.51
231 239 0.539986 TTCCAGATCTTACCACGGGC 59.460 55.000 0.00 0.00 0.00 6.13
263 271 1.476891 TCTGTAACCGCAGATCTGACC 59.523 52.381 27.04 8.57 40.23 4.02
325 333 0.179097 CTCGCTCCCTGCTTAAGACC 60.179 60.000 6.67 0.00 40.11 3.85
337 352 1.153349 CAAACCCTAGCCTCGCTCC 60.153 63.158 0.00 0.00 40.44 4.70
434 457 2.901839 GGAACCACTACCACTCCTACAA 59.098 50.000 0.00 0.00 0.00 2.41
435 458 2.532843 GGAACCACTACCACTCCTACA 58.467 52.381 0.00 0.00 0.00 2.74
463 489 1.152839 GAGACGAGGAGGGAGGGAG 60.153 68.421 0.00 0.00 0.00 4.30
471 497 2.634777 GCGGATCGAGACGAGGAG 59.365 66.667 14.69 0.00 39.91 3.69
472 498 2.900838 GGCGGATCGAGACGAGGA 60.901 66.667 14.69 0.00 39.91 3.71
473 499 3.967335 GGGCGGATCGAGACGAGG 61.967 72.222 14.69 0.00 39.91 4.63
474 500 3.967335 GGGGCGGATCGAGACGAG 61.967 72.222 14.69 0.18 39.91 4.18
558 972 2.897350 GGGGCGGCAGAATCTTCG 60.897 66.667 12.47 0.00 0.00 3.79
604 1018 2.709213 CCTGCAGGAAGAAGAAGAAGG 58.291 52.381 29.88 0.00 37.39 3.46
605 1019 2.083002 GCCTGCAGGAAGAAGAAGAAG 58.917 52.381 37.21 5.10 37.39 2.85
606 1020 1.701847 AGCCTGCAGGAAGAAGAAGAA 59.298 47.619 37.21 0.00 37.39 2.52
643 1057 0.599204 GTTCTTGCACGGACGGAAGA 60.599 55.000 2.39 2.39 41.02 2.87
644 1058 1.860078 GTTCTTGCACGGACGGAAG 59.140 57.895 0.00 0.00 35.80 3.46
645 1059 1.952133 CGTTCTTGCACGGACGGAA 60.952 57.895 15.89 0.00 36.47 4.30
695 1109 3.036075 AGTACGGTACCTTTGTTCAGC 57.964 47.619 14.41 0.00 0.00 4.26
719 1133 2.736343 TAACAGCACGGTCGTCGGTG 62.736 60.000 14.30 14.30 44.45 4.94
729 1143 2.530177 ACTCGATCATGTAACAGCACG 58.470 47.619 0.00 0.00 0.00 5.34
760 1174 2.708051 TGCAAAGCAGAGGAGAAGATG 58.292 47.619 0.00 0.00 33.32 2.90
790 1204 1.523938 GGGCGTATGGGTTCTGAGC 60.524 63.158 0.00 0.00 0.00 4.26
825 1239 3.735591 CAAGAACCTCCGGTTACAAGAA 58.264 45.455 0.00 0.00 46.95 2.52
828 1242 1.141254 TGCAAGAACCTCCGGTTACAA 59.859 47.619 0.00 0.00 46.95 2.41
829 1243 0.759959 TGCAAGAACCTCCGGTTACA 59.240 50.000 0.00 0.00 46.95 2.41
865 1279 7.012421 AGGATTGAGTTCCGTAATAAATTCTGC 59.988 37.037 0.00 0.00 40.94 4.26
950 1367 1.345741 TCAGGCTGGTTGAGAGTTGAG 59.654 52.381 15.73 0.00 0.00 3.02
951 1368 1.423584 TCAGGCTGGTTGAGAGTTGA 58.576 50.000 15.73 0.00 0.00 3.18
952 1369 2.149578 CTTCAGGCTGGTTGAGAGTTG 58.850 52.381 15.73 0.00 0.00 3.16
953 1370 2.050144 TCTTCAGGCTGGTTGAGAGTT 58.950 47.619 15.73 0.00 0.00 3.01
954 1371 1.722034 TCTTCAGGCTGGTTGAGAGT 58.278 50.000 15.73 0.00 0.00 3.24
955 1372 2.847327 TTCTTCAGGCTGGTTGAGAG 57.153 50.000 15.73 3.95 0.00 3.20
956 1373 2.705658 TCTTTCTTCAGGCTGGTTGAGA 59.294 45.455 15.73 10.22 0.00 3.27
966 1383 2.808543 CCACGAACCTTCTTTCTTCAGG 59.191 50.000 0.00 0.00 0.00 3.86
971 1391 1.270147 CCGACCACGAACCTTCTTTCT 60.270 52.381 0.00 0.00 42.66 2.52
974 1394 0.754472 TTCCGACCACGAACCTTCTT 59.246 50.000 0.00 0.00 42.66 2.52
1401 1821 0.164647 CTTCAAGCTCCGACGCAAAG 59.835 55.000 0.00 0.00 0.00 2.77
1468 1888 0.847373 TGAGAGAGATACCTCGGGCT 59.153 55.000 0.00 0.00 44.08 5.19
1469 1889 1.917872 ATGAGAGAGATACCTCGGGC 58.082 55.000 0.00 0.00 44.08 6.13
1482 1902 6.351202 CCTGAATCCTGGAGCTTATATGAGAG 60.351 46.154 1.52 0.00 33.65 3.20
1497 1917 3.323403 GGTCCTGATACTCCTGAATCCTG 59.677 52.174 0.00 0.00 0.00 3.86
1566 1986 3.234630 CTCGGGTCGAAGCCAACCA 62.235 63.158 0.00 0.00 37.28 3.67
1638 2058 1.137675 CATCCTTCTCTGCACGATCCA 59.862 52.381 0.00 0.00 0.00 3.41
1666 2086 1.386772 TTGACACCCCCTTCCTGGT 60.387 57.895 0.00 0.00 34.40 4.00
1667 2087 1.074951 GTTGACACCCCCTTCCTGG 59.925 63.158 0.00 0.00 0.00 4.45
1903 2323 1.352352 ACAGTCAACTGAATCCAGGGG 59.648 52.381 16.71 0.00 46.59 4.79
2080 2500 2.215451 AATGGCGTCCTTGGATGGCT 62.215 55.000 27.81 15.48 37.51 4.75
2082 2502 1.185315 AAAATGGCGTCCTTGGATGG 58.815 50.000 10.50 0.00 0.00 3.51
2127 2547 2.035449 TGCGAGTAGTGCCCATGTATAC 59.965 50.000 0.00 0.00 0.00 1.47
2169 2589 8.078596 GTCTTGACATAAAACATTTCAGCTCTT 58.921 33.333 0.00 0.00 0.00 2.85
2217 2637 0.447801 CTGGCGTACTTTCCATGTGC 59.552 55.000 0.00 0.00 0.00 4.57
2232 2652 0.815615 CTCCGATAACCTTGGCTGGC 60.816 60.000 0.00 0.00 0.00 4.85
2242 2662 5.125739 TGAACTTCTCCTCTTCTCCGATAAC 59.874 44.000 0.00 0.00 0.00 1.89
2248 2668 3.576550 ACACTGAACTTCTCCTCTTCTCC 59.423 47.826 0.00 0.00 0.00 3.71
2257 2677 4.025145 CGTAAACCCAACACTGAACTTCTC 60.025 45.833 0.00 0.00 0.00 2.87
2258 2678 3.875134 CGTAAACCCAACACTGAACTTCT 59.125 43.478 0.00 0.00 0.00 2.85
2259 2679 3.002965 CCGTAAACCCAACACTGAACTTC 59.997 47.826 0.00 0.00 0.00 3.01
2280 2700 0.034863 TCTTAAACCCCGGCATGACC 60.035 55.000 0.00 0.00 0.00 4.02
2324 2744 7.611821 GCGTTAAGCTTACACAAATAAACAA 57.388 32.000 5.45 0.00 44.04 2.83
2374 2794 2.332063 TCTGCTTACCTAATGGCTGC 57.668 50.000 0.00 0.00 36.63 5.25
2403 2823 8.634444 ACTTTGGCTGACAGACTTACTATATAG 58.366 37.037 10.32 8.27 0.00 1.31
2405 2825 7.425224 ACTTTGGCTGACAGACTTACTATAT 57.575 36.000 10.32 0.00 0.00 0.86
2421 2841 4.889995 AGAAGCTTAACAGAAACTTTGGCT 59.110 37.500 0.00 0.00 0.00 4.75
2584 3004 4.868171 TCGTTGGTATCTCAAATAGCACAC 59.132 41.667 0.00 0.28 32.52 3.82
2592 3012 4.963373 TCCAGTTTCGTTGGTATCTCAAA 58.037 39.130 0.00 0.00 37.02 2.69
2597 3017 6.053005 TCCATTATCCAGTTTCGTTGGTATC 58.947 40.000 0.00 0.00 37.02 2.24
2610 3030 9.017509 AGCATTTATACACATTCCATTATCCAG 57.982 33.333 0.00 0.00 0.00 3.86
2631 3051 6.289834 TGTGAAATGGTTTTTGATGAGCATT 58.710 32.000 0.00 0.00 43.50 3.56
2733 3167 7.524912 CAGATGAACTTCTTTTGTACCATCAG 58.475 38.462 0.00 0.00 33.80 2.90
2767 3201 6.146347 CGAAACCAACAAACTTCTTTTCCAAA 59.854 34.615 0.00 0.00 0.00 3.28
2914 3348 4.742438 TTCTGAAAATACAGTTGACGGC 57.258 40.909 0.00 0.00 38.79 5.68
3040 3476 5.563592 TGCCAGGATTAATATGACCTCATG 58.436 41.667 0.00 0.00 37.15 3.07
3061 3497 4.023707 CCACTGCTAGGCATAATAAACTGC 60.024 45.833 0.00 0.00 38.13 4.40
3071 3507 1.275666 TGTACACCACTGCTAGGCAT 58.724 50.000 0.00 0.00 38.13 4.40
3073 3509 2.178912 TTTGTACACCACTGCTAGGC 57.821 50.000 0.00 0.00 0.00 3.93
3074 3510 5.220854 GCAATATTTGTACACCACTGCTAGG 60.221 44.000 0.00 0.00 0.00 3.02
3075 3511 5.353956 TGCAATATTTGTACACCACTGCTAG 59.646 40.000 13.92 0.00 0.00 3.42
3076 3512 5.123186 GTGCAATATTTGTACACCACTGCTA 59.877 40.000 13.92 2.86 44.34 3.49
3077 3513 4.078537 TGCAATATTTGTACACCACTGCT 58.921 39.130 13.92 0.00 0.00 4.24
3083 3524 5.878116 TCAGGTAGTGCAATATTTGTACACC 59.122 40.000 10.37 13.27 46.85 4.16
3086 3527 7.843490 TTCTCAGGTAGTGCAATATTTGTAC 57.157 36.000 0.00 0.88 45.13 2.90
3098 3539 7.094162 TGTCTACTCTTGATTTCTCAGGTAGTG 60.094 40.741 0.00 0.00 35.17 2.74
3102 3543 6.672266 TTGTCTACTCTTGATTTCTCAGGT 57.328 37.500 0.00 0.00 31.68 4.00
3245 3686 4.338118 TGATGAACTTCTGGTTGGTGTTTC 59.662 41.667 0.00 0.00 38.41 2.78
3246 3687 4.277476 TGATGAACTTCTGGTTGGTGTTT 58.723 39.130 0.00 0.00 38.41 2.83
3249 3690 2.227388 GCTGATGAACTTCTGGTTGGTG 59.773 50.000 0.00 0.00 38.41 4.17
3261 3703 5.574443 GCAAGTTTTCCTTATGCTGATGAAC 59.426 40.000 0.00 0.00 0.00 3.18
3300 3742 8.983307 AAATGCACAACAATTTTGAACAATTT 57.017 23.077 0.00 0.00 0.00 1.82
3302 3744 8.027771 ACAAAATGCACAACAATTTTGAACAAT 58.972 25.926 21.60 2.79 43.04 2.71
3318 3760 9.318041 GTACATATAATCGATCACAAAATGCAC 57.682 33.333 0.00 0.00 0.00 4.57
3319 3761 8.503196 GGTACATATAATCGATCACAAAATGCA 58.497 33.333 0.00 0.00 0.00 3.96
3320 3762 8.721478 AGGTACATATAATCGATCACAAAATGC 58.279 33.333 0.00 0.00 0.00 3.56
3322 3764 9.778741 ACAGGTACATATAATCGATCACAAAAT 57.221 29.630 0.00 0.00 0.00 1.82
3323 3765 9.607988 AACAGGTACATATAATCGATCACAAAA 57.392 29.630 0.00 0.00 0.00 2.44
3324 3766 9.256477 GAACAGGTACATATAATCGATCACAAA 57.744 33.333 0.00 0.00 0.00 2.83
3325 3767 7.870954 GGAACAGGTACATATAATCGATCACAA 59.129 37.037 0.00 0.00 0.00 3.33
3326 3768 7.375834 GGAACAGGTACATATAATCGATCACA 58.624 38.462 0.00 0.00 0.00 3.58
3327 3769 6.812160 GGGAACAGGTACATATAATCGATCAC 59.188 42.308 0.00 0.00 0.00 3.06
3328 3770 6.724441 AGGGAACAGGTACATATAATCGATCA 59.276 38.462 0.00 0.00 0.00 2.92
3329 3771 7.171630 AGGGAACAGGTACATATAATCGATC 57.828 40.000 0.00 0.00 0.00 3.69
3330 3772 7.016268 ACAAGGGAACAGGTACATATAATCGAT 59.984 37.037 0.00 0.00 0.00 3.59
3331 3773 6.325545 ACAAGGGAACAGGTACATATAATCGA 59.674 38.462 0.00 0.00 0.00 3.59
3332 3774 6.522054 ACAAGGGAACAGGTACATATAATCG 58.478 40.000 0.00 0.00 0.00 3.34
3333 3775 7.506114 TGACAAGGGAACAGGTACATATAATC 58.494 38.462 0.00 0.00 0.00 1.75
3334 3776 7.446106 TGACAAGGGAACAGGTACATATAAT 57.554 36.000 0.00 0.00 0.00 1.28
3335 3777 6.877668 TGACAAGGGAACAGGTACATATAA 57.122 37.500 0.00 0.00 0.00 0.98
3336 3778 6.042781 GGATGACAAGGGAACAGGTACATATA 59.957 42.308 0.00 0.00 0.00 0.86
3337 3779 5.163195 GGATGACAAGGGAACAGGTACATAT 60.163 44.000 0.00 0.00 0.00 1.78
3338 3780 4.163458 GGATGACAAGGGAACAGGTACATA 59.837 45.833 0.00 0.00 0.00 2.29
3339 3781 3.054361 GGATGACAAGGGAACAGGTACAT 60.054 47.826 0.00 0.00 0.00 2.29
3340 3782 2.304761 GGATGACAAGGGAACAGGTACA 59.695 50.000 0.00 0.00 0.00 2.90
3341 3783 2.987232 GGATGACAAGGGAACAGGTAC 58.013 52.381 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.