Multiple sequence alignment - TraesCS2B01G344900

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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 TraesCS2B01G344900 chr2B 100.000 4102 0 0 1 4102 491714715 491710614 0.000000e+00 7576.0
1 TraesCS2B01G344900 chr2A 91.840 4142 210 55 1 4102 570605951 570610004 0.000000e+00 5659.0
2 TraesCS2B01G344900 chr2A 98.182 55 1 0 3670 3724 570609602 570609656 3.380000e-16 97.1
3 TraesCS2B01G344900 chr2D 93.900 3295 123 32 251 3528 419367248 419364015 0.000000e+00 4900.0
4 TraesCS2B01G344900 chr2D 91.897 543 18 11 3560 4102 419364015 419363499 0.000000e+00 736.0
5 TraesCS2B01G344900 chr7A 77.030 505 82 24 2485 2967 178296378 178295886 4.070000e-65 259.0
6 TraesCS2B01G344900 chr7B 75.697 502 88 24 2488 2967 141864944 141864455 1.920000e-53 220.0
7 TraesCS2B01G344900 chr6B 90.244 41 4 0 2711 2751 475662720 475662680 2.000000e-03 54.7


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 TraesCS2B01G344900 chr2B 491710614 491714715 4101 True 7576.00 7576 100.0000 1 4102 1 chr2B.!!$R1 4101
1 TraesCS2B01G344900 chr2A 570605951 570610004 4053 False 2878.05 5659 95.0110 1 4102 2 chr2A.!!$F1 4101
2 TraesCS2B01G344900 chr2D 419363499 419367248 3749 True 2818.00 4900 92.8985 251 4102 2 chr2D.!!$R1 3851

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
557 558 0.039618 ATGGCCAGGGATTCGTGTTT 59.960 50.0 13.05 0.0 0.0 2.83 F
878 895 0.321996 GTCTTCTTCCCCTTGTCGCT 59.678 55.0 0.00 0.0 0.0 4.93 F
957 976 0.494095 ACCTCTCCTCTTCCAACCCT 59.506 55.0 0.00 0.0 0.0 4.34 F
1950 1975 1.041437 GCCCGAATAGCTACACTCCT 58.959 55.0 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 2372 0.320771 ACCGGACATGAACACTGAGC 60.321 55.0 9.46 0.00 0.00 4.26 R
2383 2411 0.323629 ATTCGGAGCAGGGTTTCGAA 59.676 50.0 0.00 0.00 42.63 3.71 R
2741 2769 1.326213 CCGTCAGCATCTCCAGGAGT 61.326 60.0 16.65 1.00 0.00 3.85 R
3900 3973 0.034476 TGCATGATCTCCGATCTGCC 59.966 55.0 17.41 4.66 0.00 4.85 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
29 30 5.812642 ACTCTCGTCATAATACTTTGCCAAG 59.187 40.000 0.00 0.00 35.92 3.61
33 34 7.985184 TCTCGTCATAATACTTTGCCAAGTAAT 59.015 33.333 13.80 8.71 46.45 1.89
49 50 6.659824 CCAAGTAATAGAGGAGCCCTTTTTA 58.340 40.000 0.00 0.00 31.76 1.52
50 51 7.116736 CCAAGTAATAGAGGAGCCCTTTTTAA 58.883 38.462 0.00 0.00 31.76 1.52
62 63 6.039270 GGAGCCCTTTTTAAAAGTTTGCATTT 59.961 34.615 15.19 1.68 0.00 2.32
63 64 7.026631 AGCCCTTTTTAAAAGTTTGCATTTC 57.973 32.000 15.19 0.00 0.00 2.17
64 65 6.601217 AGCCCTTTTTAAAAGTTTGCATTTCA 59.399 30.769 15.19 0.00 0.00 2.69
65 66 7.121907 AGCCCTTTTTAAAAGTTTGCATTTCAA 59.878 29.630 15.19 0.00 0.00 2.69
66 67 7.219917 GCCCTTTTTAAAAGTTTGCATTTCAAC 59.780 33.333 15.19 0.00 33.73 3.18
67 68 8.239998 CCCTTTTTAAAAGTTTGCATTTCAACA 58.760 29.630 15.19 0.00 33.73 3.33
68 69 9.276397 CCTTTTTAAAAGTTTGCATTTCAACAG 57.724 29.630 15.19 0.00 33.73 3.16
77 78 4.707030 TGCATTTCAACAGATCACCATC 57.293 40.909 0.00 0.00 0.00 3.51
90 91 6.536582 ACAGATCACCATCGAGAAAATACTTG 59.463 38.462 0.00 0.00 33.75 3.16
102 103 9.010029 TCGAGAAAATACTTGGCTCTTAAATTT 57.990 29.630 0.00 0.00 0.00 1.82
105 106 9.208022 AGAAAATACTTGGCTCTTAAATTTTGC 57.792 29.630 0.00 0.00 0.00 3.68
107 108 9.506018 AAAATACTTGGCTCTTAAATTTTGCAT 57.494 25.926 0.00 0.00 0.00 3.96
115 116 4.681744 TCTTAAATTTTGCATCCCATCGC 58.318 39.130 0.00 0.00 0.00 4.58
125 126 2.466846 CATCCCATCGCTTGCAAAATC 58.533 47.619 0.00 0.00 0.00 2.17
132 133 2.076100 TCGCTTGCAAAATCTGTCGAT 58.924 42.857 0.00 0.00 0.00 3.59
156 157 1.078759 GAAGGACGCGATGTGACTGG 61.079 60.000 15.93 0.00 0.00 4.00
173 174 1.296715 GGCTCTGACCACCATTCGT 59.703 57.895 0.00 0.00 0.00 3.85
189 190 4.500887 CCATTCGTTCTCGGCTATTCCTAA 60.501 45.833 0.00 0.00 37.69 2.69
226 227 2.997986 GGCCAATTCAATTCTGCACTTG 59.002 45.455 0.00 0.00 0.00 3.16
228 229 2.664568 CCAATTCAATTCTGCACTTGCG 59.335 45.455 0.00 0.00 45.83 4.85
237 238 1.536766 TCTGCACTTGCGAAGGAAATG 59.463 47.619 0.00 0.00 45.83 2.32
239 240 3.005823 CACTTGCGAAGGAAATGCG 57.994 52.632 0.00 0.00 37.43 4.73
302 303 1.471684 ACGGTAACTGACAGACGATCC 59.528 52.381 10.08 3.56 0.00 3.36
328 329 3.976942 CACACTCGCTCAAATTTTTCCTG 59.023 43.478 0.00 0.00 0.00 3.86
370 371 3.964875 CAGGCCACCACACAACGC 61.965 66.667 5.01 0.00 0.00 4.84
371 372 4.189580 AGGCCACCACACAACGCT 62.190 61.111 5.01 0.00 0.00 5.07
372 373 3.660111 GGCCACCACACAACGCTC 61.660 66.667 0.00 0.00 0.00 5.03
373 374 2.899838 GCCACCACACAACGCTCA 60.900 61.111 0.00 0.00 0.00 4.26
374 375 2.260869 GCCACCACACAACGCTCAT 61.261 57.895 0.00 0.00 0.00 2.90
375 376 0.953471 GCCACCACACAACGCTCATA 60.953 55.000 0.00 0.00 0.00 2.15
376 377 1.518325 CCACCACACAACGCTCATAA 58.482 50.000 0.00 0.00 0.00 1.90
377 378 1.876799 CCACCACACAACGCTCATAAA 59.123 47.619 0.00 0.00 0.00 1.40
378 379 2.350388 CCACCACACAACGCTCATAAAC 60.350 50.000 0.00 0.00 0.00 2.01
480 481 0.741927 CACAGCTCCACGCATCATCA 60.742 55.000 0.00 0.00 42.61 3.07
482 483 0.376152 CAGCTCCACGCATCATCAAC 59.624 55.000 0.00 0.00 42.61 3.18
557 558 0.039618 ATGGCCAGGGATTCGTGTTT 59.960 50.000 13.05 0.00 0.00 2.83
588 596 2.544685 CCTACAAAGCAGTGGATCTCG 58.455 52.381 0.00 0.00 0.00 4.04
590 598 3.181471 CCTACAAAGCAGTGGATCTCGAT 60.181 47.826 0.00 0.00 0.00 3.59
592 600 4.679373 ACAAAGCAGTGGATCTCGATAT 57.321 40.909 0.00 0.00 0.00 1.63
646 655 0.792640 AGCAACTGTTTCGCTGATCG 59.207 50.000 4.75 0.00 33.91 3.69
652 661 2.096909 ACTGTTTCGCTGATCGTTTTCG 60.097 45.455 0.00 0.00 45.64 3.46
694 709 1.874231 GCTCCAGATCATCGTCTCGTA 59.126 52.381 0.00 0.00 0.00 3.43
727 742 1.646447 ACTGGACCAGGAGTAGGATCA 59.354 52.381 25.34 0.00 35.51 2.92
728 743 2.044492 ACTGGACCAGGAGTAGGATCAA 59.956 50.000 25.34 0.00 35.51 2.57
729 744 3.310954 ACTGGACCAGGAGTAGGATCAAT 60.311 47.826 25.34 0.00 35.51 2.57
731 746 2.370189 GGACCAGGAGTAGGATCAATGG 59.630 54.545 0.00 0.00 35.04 3.16
837 854 1.950472 CGACATCGTTTTGTGGAAGC 58.050 50.000 0.00 0.00 34.11 3.86
878 895 0.321996 GTCTTCTTCCCCTTGTCGCT 59.678 55.000 0.00 0.00 0.00 4.93
907 926 3.006217 GCCATTTGTGAAGCTTCTTTCCT 59.994 43.478 26.09 6.78 0.00 3.36
953 972 0.547712 CCCCACCTCTCCTCTTCCAA 60.548 60.000 0.00 0.00 0.00 3.53
957 976 0.494095 ACCTCTCCTCTTCCAACCCT 59.506 55.000 0.00 0.00 0.00 4.34
978 997 2.272146 ACATGGTGTGATCGGCCC 59.728 61.111 0.00 0.00 0.00 5.80
1038 1057 3.782244 GCGCTGTCGTTGCTCCTG 61.782 66.667 0.00 0.00 38.14 3.86
1284 1303 2.919856 AGGCTCACCGTGCTGTCT 60.920 61.111 0.00 0.00 42.76 3.41
1824 1849 1.227380 CTTCCTGCTTATCGCCGCT 60.227 57.895 0.00 0.00 38.05 5.52
1834 1859 1.600511 TATCGCCGCTGTTCTGGTCA 61.601 55.000 0.00 0.00 0.00 4.02
1920 1945 2.913578 CTGGCCCTGCACAGCAAA 60.914 61.111 0.00 0.00 38.41 3.68
1950 1975 1.041437 GCCCGAATAGCTACACTCCT 58.959 55.000 0.00 0.00 0.00 3.69
2358 2383 1.069022 GGTACGTACGCTCAGTGTTCA 60.069 52.381 16.72 0.00 0.00 3.18
2363 2388 1.993370 GTACGCTCAGTGTTCATGTCC 59.007 52.381 0.00 0.00 0.00 4.02
2365 2390 1.354337 CGCTCAGTGTTCATGTCCGG 61.354 60.000 0.00 0.00 0.00 5.14
2381 2409 3.060602 GTCCGGTTCTCTCTGTTTTCTG 58.939 50.000 0.00 0.00 0.00 3.02
2383 2411 2.224305 CCGGTTCTCTCTGTTTTCTGGT 60.224 50.000 0.00 0.00 0.00 4.00
2386 2414 3.495001 GGTTCTCTCTGTTTTCTGGTTCG 59.505 47.826 0.00 0.00 0.00 3.95
2432 2460 8.010733 TCAAAATTTCTGAACTGGTGAGAATT 57.989 30.769 0.00 0.00 0.00 2.17
2741 2769 0.901114 TGTACAGCTTCGGGGTGCTA 60.901 55.000 0.00 0.13 46.30 3.49
3050 3078 1.526225 TCGGAGCATCTCGGTCGAT 60.526 57.895 0.00 0.00 43.39 3.59
3163 3191 5.122328 CGTTCGGTAATTTACGGAAGAAG 57.878 43.478 22.51 15.63 44.91 2.85
3384 3419 9.159364 CAGAGTATGTAATTACATCATCATGGG 57.841 37.037 29.68 16.41 45.11 4.00
3431 3466 5.729454 GCGCGTCACCTAATTAACAATCATT 60.729 40.000 8.43 0.00 0.00 2.57
3452 3487 1.172812 ACCCGAAGAAAACAGCTGCC 61.173 55.000 15.27 0.38 0.00 4.85
3460 3495 0.826062 AAAACAGCTGCCTTTGTGCT 59.174 45.000 15.27 0.00 37.56 4.40
3465 3500 2.005451 CAGCTGCCTTTGTGCTACTAG 58.995 52.381 0.00 0.00 35.05 2.57
3468 3503 2.930682 GCTGCCTTTGTGCTACTAGTAC 59.069 50.000 0.00 0.00 0.00 2.73
3469 3504 3.368531 GCTGCCTTTGTGCTACTAGTACT 60.369 47.826 0.00 0.00 31.77 2.73
3470 3505 4.142227 GCTGCCTTTGTGCTACTAGTACTA 60.142 45.833 1.89 1.89 31.77 1.82
3471 3506 5.452077 GCTGCCTTTGTGCTACTAGTACTAT 60.452 44.000 2.33 0.00 31.77 2.12
3472 3507 6.238953 GCTGCCTTTGTGCTACTAGTACTATA 60.239 42.308 2.33 0.00 31.77 1.31
3473 3508 7.273320 TGCCTTTGTGCTACTAGTACTATAG 57.727 40.000 2.33 8.59 31.77 1.31
3513 3549 5.986004 AACGGTAAAGAGAAAGTGTTCTG 57.014 39.130 0.00 0.00 44.42 3.02
3529 3565 5.929992 AGTGTTCTGAATTTGCCATGAAATG 59.070 36.000 0.00 0.00 46.21 2.32
3555 3591 2.474359 GGAATCACGAGCATGATCTTCG 59.526 50.000 9.64 8.37 38.40 3.79
3557 3593 0.103026 TCACGAGCATGATCTTCGGG 59.897 55.000 9.64 7.26 0.00 5.14
3558 3594 1.227380 ACGAGCATGATCTTCGGGC 60.227 57.895 9.64 0.00 0.00 6.13
3559 3595 1.227350 CGAGCATGATCTTCGGGCA 60.227 57.895 9.64 0.00 0.00 5.36
3560 3596 1.220169 CGAGCATGATCTTCGGGCAG 61.220 60.000 9.64 0.00 0.00 4.85
3561 3597 0.179062 GAGCATGATCTTCGGGCAGT 60.179 55.000 3.07 0.00 0.00 4.40
3562 3598 1.069204 GAGCATGATCTTCGGGCAGTA 59.931 52.381 3.07 0.00 0.00 2.74
3563 3599 1.486310 AGCATGATCTTCGGGCAGTAA 59.514 47.619 0.00 0.00 0.00 2.24
3578 3614 0.250727 AGTAACACGCATTGGCCACT 60.251 50.000 3.88 0.00 36.38 4.00
3618 3654 1.202440 TCACGTCAGTTTGTTACGCCT 60.202 47.619 0.00 0.00 40.18 5.52
3637 3673 2.546373 CCTTGGTACGACTTTTCCACGA 60.546 50.000 0.00 0.00 0.00 4.35
3646 3682 2.781646 GACTTTTCCACGACGCAAAAAG 59.218 45.455 19.80 19.80 41.96 2.27
3647 3683 2.420722 ACTTTTCCACGACGCAAAAAGA 59.579 40.909 24.61 2.26 39.80 2.52
3673 3709 3.065371 AGAGTTTTCTGTGAAAGCAACGG 59.935 43.478 8.97 0.00 30.72 4.44
3727 3800 3.411517 CCCGGCCAAGATCCTGGT 61.412 66.667 12.03 0.00 38.86 4.00
3728 3801 2.677228 CCGGCCAAGATCCTGGTT 59.323 61.111 12.03 0.00 38.86 3.67
3729 3802 1.750399 CCGGCCAAGATCCTGGTTG 60.750 63.158 12.03 4.84 38.86 3.77
3730 3803 2.409870 CGGCCAAGATCCTGGTTGC 61.410 63.158 12.03 0.00 38.86 4.17
3731 3804 1.304381 GGCCAAGATCCTGGTTGCA 60.304 57.895 12.03 0.00 38.86 4.08
3732 3805 1.318158 GGCCAAGATCCTGGTTGCAG 61.318 60.000 12.03 0.00 38.86 4.41
3733 3806 1.941999 GCCAAGATCCTGGTTGCAGC 61.942 60.000 12.03 0.00 38.86 5.25
3734 3807 0.323178 CCAAGATCCTGGTTGCAGCT 60.323 55.000 1.78 0.00 0.00 4.24
3735 3808 0.809385 CAAGATCCTGGTTGCAGCTG 59.191 55.000 10.11 10.11 0.00 4.24
3736 3809 0.964358 AAGATCCTGGTTGCAGCTGC 60.964 55.000 31.89 31.89 42.50 5.25
3773 3846 1.109323 CCCCCAAATCCCAGCGAATC 61.109 60.000 0.00 0.00 0.00 2.52
3844 3917 0.595310 GCCGAGCATAACTCTCCGAC 60.595 60.000 0.00 0.00 43.85 4.79
3900 3973 1.713937 TTGCAGTTGGACACACAGCG 61.714 55.000 0.00 0.00 0.00 5.18
3903 3976 2.899838 GTTGGACACACAGCGGCA 60.900 61.111 1.45 0.00 0.00 5.69
3904 3977 2.591429 TTGGACACACAGCGGCAG 60.591 61.111 1.45 0.00 0.00 4.85
3905 3978 3.100503 TTGGACACACAGCGGCAGA 62.101 57.895 1.45 0.00 0.00 4.26
3906 3979 2.046892 GGACACACAGCGGCAGAT 60.047 61.111 1.45 0.00 0.00 2.90
3907 3980 2.103042 GGACACACAGCGGCAGATC 61.103 63.158 1.45 0.00 0.00 2.75
3908 3981 2.433145 ACACACAGCGGCAGATCG 60.433 61.111 1.45 0.00 0.00 3.69
3909 3982 3.190849 CACACAGCGGCAGATCGG 61.191 66.667 1.45 0.00 0.00 4.18
3928 4018 0.393402 GAGATCATGCACTGCACCCA 60.393 55.000 5.67 0.00 43.04 4.51
3929 4019 0.679002 AGATCATGCACTGCACCCAC 60.679 55.000 5.67 0.00 43.04 4.61
4065 4157 4.206477 TGGTCGATGTGAGTGAATGAAT 57.794 40.909 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.008986 ACTTGGCAAAGTATTATGACGAGAGTT 61.009 37.037 4.12 0.00 45.14 3.01
9 10 9.256477 CTATTACTTGGCAAAGTATTATGACGA 57.744 33.333 14.52 0.00 45.93 4.20
12 13 9.778741 CCTCTATTACTTGGCAAAGTATTATGA 57.221 33.333 14.52 12.16 45.93 2.15
18 19 5.396436 GGCTCCTCTATTACTTGGCAAAGTA 60.396 44.000 9.77 9.77 45.01 2.24
29 30 8.577048 ACTTTTAAAAAGGGCTCCTCTATTAC 57.423 34.615 1.66 0.00 30.89 1.89
33 34 6.239204 GCAAACTTTTAAAAAGGGCTCCTCTA 60.239 38.462 1.66 0.00 30.89 2.43
49 50 6.258507 GGTGATCTGTTGAAATGCAAACTTTT 59.741 34.615 0.00 0.00 38.44 2.27
50 51 5.754890 GGTGATCTGTTGAAATGCAAACTTT 59.245 36.000 0.00 0.00 38.44 2.66
62 63 4.535526 TTTCTCGATGGTGATCTGTTGA 57.464 40.909 0.00 0.00 0.00 3.18
63 64 5.808042 ATTTTCTCGATGGTGATCTGTTG 57.192 39.130 0.00 0.00 0.00 3.33
64 65 6.644347 AGTATTTTCTCGATGGTGATCTGTT 58.356 36.000 0.00 0.00 0.00 3.16
65 66 6.227298 AGTATTTTCTCGATGGTGATCTGT 57.773 37.500 0.00 0.00 0.00 3.41
66 67 6.018425 CCAAGTATTTTCTCGATGGTGATCTG 60.018 42.308 0.00 0.00 0.00 2.90
67 68 6.051717 CCAAGTATTTTCTCGATGGTGATCT 58.948 40.000 0.00 0.00 0.00 2.75
68 69 5.277538 GCCAAGTATTTTCTCGATGGTGATC 60.278 44.000 0.00 0.00 0.00 2.92
69 70 4.576463 GCCAAGTATTTTCTCGATGGTGAT 59.424 41.667 0.00 0.00 0.00 3.06
70 71 3.938963 GCCAAGTATTTTCTCGATGGTGA 59.061 43.478 0.00 0.00 0.00 4.02
77 78 9.626045 AAAATTTAAGAGCCAAGTATTTTCTCG 57.374 29.630 0.00 0.00 0.00 4.04
90 91 4.470334 TGGGATGCAAAATTTAAGAGCC 57.530 40.909 0.00 0.00 0.00 4.70
102 103 1.678300 TGCAAGCGATGGGATGCAA 60.678 52.632 0.00 0.00 45.04 4.08
105 106 2.100252 AGATTTTGCAAGCGATGGGATG 59.900 45.455 0.00 0.00 0.00 3.51
107 108 1.473677 CAGATTTTGCAAGCGATGGGA 59.526 47.619 0.00 0.00 0.00 4.37
115 116 5.617609 TCGTTTATCGACAGATTTTGCAAG 58.382 37.500 0.00 0.00 44.01 4.01
132 133 1.068402 TCACATCGCGTCCTTCGTTTA 60.068 47.619 5.77 0.00 42.13 2.01
141 142 2.125912 AGCCAGTCACATCGCGTC 60.126 61.111 5.77 0.00 0.00 5.19
156 157 1.079503 GAACGAATGGTGGTCAGAGC 58.920 55.000 0.00 0.00 0.00 4.09
173 174 6.094881 CCAAAACAATTAGGAATAGCCGAGAA 59.905 38.462 0.00 0.00 43.43 2.87
189 190 2.999356 GCCAAACGGCCAAAACAAT 58.001 47.368 2.24 0.00 44.46 2.71
216 217 1.674359 TTTCCTTCGCAAGTGCAGAA 58.326 45.000 3.87 7.14 42.21 3.02
226 227 1.863446 GAACGCGCATTTCCTTCGC 60.863 57.895 5.73 0.00 44.76 4.70
228 229 4.765611 GGAACGCGCATTTCCTTC 57.234 55.556 24.17 7.19 39.68 3.46
237 238 3.258290 GCTGAGCTAGGAACGCGC 61.258 66.667 5.73 0.00 0.00 6.86
239 240 0.654683 CAATGCTGAGCTAGGAACGC 59.345 55.000 5.83 0.00 0.00 4.84
302 303 3.885484 AAATTTGAGCGAGTGTGTGAG 57.115 42.857 0.00 0.00 0.00 3.51
328 329 1.450134 TCATGATGGCGTCAGGTGC 60.450 57.895 19.58 0.00 40.92 5.01
370 371 5.029014 CGTAACTGTCGAGAGGTTTATGAG 58.971 45.833 14.79 0.00 0.00 2.90
371 372 4.142534 CCGTAACTGTCGAGAGGTTTATGA 60.143 45.833 14.79 0.00 0.00 2.15
372 373 4.103357 CCGTAACTGTCGAGAGGTTTATG 58.897 47.826 14.79 9.33 0.00 1.90
373 374 3.760684 ACCGTAACTGTCGAGAGGTTTAT 59.239 43.478 14.79 0.00 0.00 1.40
374 375 3.149196 ACCGTAACTGTCGAGAGGTTTA 58.851 45.455 14.79 1.65 0.00 2.01
375 376 1.959282 ACCGTAACTGTCGAGAGGTTT 59.041 47.619 14.79 2.65 0.00 3.27
376 377 1.613836 ACCGTAACTGTCGAGAGGTT 58.386 50.000 14.79 8.32 0.00 3.50
377 378 1.538950 GAACCGTAACTGTCGAGAGGT 59.461 52.381 14.79 10.30 0.00 3.85
378 379 1.135460 GGAACCGTAACTGTCGAGAGG 60.135 57.143 14.79 0.00 0.00 3.69
480 481 1.810412 GCTTCGTGGACTGGTTCAGTT 60.810 52.381 1.90 0.00 45.44 3.16
482 483 1.284982 CGCTTCGTGGACTGGTTCAG 61.285 60.000 0.00 0.00 37.52 3.02
557 558 3.947196 CTGCTTTGTAGGCCAATGTGATA 59.053 43.478 5.01 0.00 31.81 2.15
588 596 4.025061 CAGTTGTTGCTAGCTGCTGATATC 60.025 45.833 17.23 0.00 43.37 1.63
590 598 3.055891 TCAGTTGTTGCTAGCTGCTGATA 60.056 43.478 17.23 0.00 43.37 2.15
592 600 1.070601 TCAGTTGTTGCTAGCTGCTGA 59.929 47.619 17.23 16.98 43.37 4.26
646 655 0.027586 ACTCAACAGTGCGCGAAAAC 59.972 50.000 12.10 4.30 0.00 2.43
652 661 0.657840 AACTCAACTCAACAGTGCGC 59.342 50.000 0.00 0.00 31.06 6.09
694 709 2.029073 CCAGTTGACGCTGACGGT 59.971 61.111 0.00 0.00 46.04 4.83
748 763 1.597027 CGTTGGACGGCTGAGGTTT 60.597 57.895 0.00 0.00 38.08 3.27
878 895 3.146066 AGCTTCACAAATGGCTCGTTTA 58.854 40.909 0.00 0.00 0.00 2.01
907 926 6.596497 GGGACGAAACAAGAAAGTGGAATATA 59.404 38.462 0.00 0.00 0.00 0.86
978 997 4.410400 GCGGTGGTCCCTTCCCTG 62.410 72.222 0.00 0.00 0.00 4.45
1027 1046 4.680237 CACGGCCAGGAGCAACGA 62.680 66.667 2.24 0.00 46.50 3.85
1164 1183 4.351938 CAGACGACGCCGGTCCAA 62.352 66.667 1.90 0.00 40.17 3.53
1194 1213 4.640690 AGGTGGAGCCCCGTGACT 62.641 66.667 0.00 0.00 38.26 3.41
1599 1618 3.134127 ATGCCGCCGAAGCCTTTC 61.134 61.111 0.00 0.00 34.57 2.62
1626 1645 0.389948 GTGTCGTGCCGAGGAAAGAT 60.390 55.000 0.00 0.00 36.23 2.40
1824 1849 1.608055 CACAGGCAATGACCAGAACA 58.392 50.000 0.00 0.00 0.00 3.18
1865 1890 0.321653 CTGGCTGCGGTAGGTTCTTT 60.322 55.000 0.00 0.00 0.00 2.52
2345 2370 0.667487 CGGACATGAACACTGAGCGT 60.667 55.000 0.00 0.00 0.00 5.07
2346 2371 1.354337 CCGGACATGAACACTGAGCG 61.354 60.000 0.00 0.00 0.00 5.03
2347 2372 0.320771 ACCGGACATGAACACTGAGC 60.321 55.000 9.46 0.00 0.00 4.26
2348 2373 2.069273 GAACCGGACATGAACACTGAG 58.931 52.381 9.46 0.00 0.00 3.35
2349 2374 1.691976 AGAACCGGACATGAACACTGA 59.308 47.619 9.46 0.00 0.00 3.41
2350 2375 2.069273 GAGAACCGGACATGAACACTG 58.931 52.381 9.46 0.00 0.00 3.66
2351 2376 1.971357 AGAGAACCGGACATGAACACT 59.029 47.619 9.46 0.00 0.00 3.55
2352 2377 2.028930 AGAGAGAACCGGACATGAACAC 60.029 50.000 9.46 0.00 0.00 3.32
2353 2378 2.029020 CAGAGAGAACCGGACATGAACA 60.029 50.000 9.46 0.00 0.00 3.18
2358 2383 3.325135 AGAAAACAGAGAGAACCGGACAT 59.675 43.478 9.46 0.00 0.00 3.06
2363 2388 3.113260 ACCAGAAAACAGAGAGAACCG 57.887 47.619 0.00 0.00 0.00 4.44
2365 2390 4.369182 TCGAACCAGAAAACAGAGAGAAC 58.631 43.478 0.00 0.00 0.00 3.01
2383 2411 0.323629 ATTCGGAGCAGGGTTTCGAA 59.676 50.000 0.00 0.00 42.63 3.71
2386 2414 2.384203 CGATTCGGAGCAGGGTTTC 58.616 57.895 0.00 0.00 0.00 2.78
2705 2733 4.421479 ACGTCGGCCTTCTGCGAG 62.421 66.667 0.00 0.00 42.61 5.03
2717 2745 1.800315 CCCGAAGCTGTACACGTCG 60.800 63.158 18.91 18.91 38.50 5.12
2741 2769 1.326213 CCGTCAGCATCTCCAGGAGT 61.326 60.000 16.65 1.00 0.00 3.85
2828 2856 4.357947 GTCCACTCCTCGCGCACA 62.358 66.667 8.75 0.00 0.00 4.57
3032 3060 1.526225 ATCGACCGAGATGCTCCGA 60.526 57.895 0.00 0.00 0.00 4.55
3112 3140 2.048503 GGGTGACACGAACCGAGG 60.049 66.667 0.00 0.00 38.70 4.63
3113 3141 1.372997 CTGGGTGACACGAACCGAG 60.373 63.158 0.00 0.00 38.70 4.63
3114 3142 2.732016 CTGGGTGACACGAACCGA 59.268 61.111 0.00 0.00 38.70 4.69
3115 3143 3.041940 GCTGGGTGACACGAACCG 61.042 66.667 0.00 0.00 38.70 4.44
3116 3144 1.302511 ATGCTGGGTGACACGAACC 60.303 57.895 0.00 0.00 36.94 3.62
3117 3145 1.577328 CCATGCTGGGTGACACGAAC 61.577 60.000 0.00 0.00 32.67 3.95
3118 3146 1.302431 CCATGCTGGGTGACACGAA 60.302 57.895 0.00 0.00 32.67 3.85
3119 3147 2.347114 CCATGCTGGGTGACACGA 59.653 61.111 0.00 0.00 32.67 4.35
3120 3148 3.434319 GCCATGCTGGGTGACACG 61.434 66.667 0.00 0.00 38.19 4.49
3384 3419 2.656422 CACGATCGCAACAAAATCAACC 59.344 45.455 16.60 0.00 0.00 3.77
3410 3445 8.126700 GGGTAAATGATTGTTAATTAGGTGACG 58.873 37.037 0.00 0.00 0.00 4.35
3431 3466 1.877443 GCAGCTGTTTTCTTCGGGTAA 59.123 47.619 16.64 0.00 0.00 2.85
3465 3500 7.200655 TCCATGCAGGGGAAGTACTATAGTAC 61.201 46.154 28.43 28.43 43.48 2.73
3468 3503 4.160329 TCCATGCAGGGGAAGTACTATAG 58.840 47.826 18.94 0.00 38.24 1.31
3469 3504 4.207698 TCCATGCAGGGGAAGTACTATA 57.792 45.455 18.94 0.00 38.24 1.31
3470 3505 3.060479 TCCATGCAGGGGAAGTACTAT 57.940 47.619 18.94 0.00 38.24 2.12
3471 3506 2.561209 TCCATGCAGGGGAAGTACTA 57.439 50.000 18.94 0.00 38.24 1.82
3472 3507 1.668826 TTCCATGCAGGGGAAGTACT 58.331 50.000 18.94 0.00 39.44 2.73
3473 3508 2.092323 GTTTCCATGCAGGGGAAGTAC 58.908 52.381 18.94 12.34 44.70 2.73
3478 3514 1.202099 TACCGTTTCCATGCAGGGGA 61.202 55.000 18.94 5.69 38.24 4.81
3529 3565 1.134699 TCATGCTCGTGATTCCACTCC 60.135 52.381 0.00 0.00 41.06 3.85
3530 3566 2.299993 TCATGCTCGTGATTCCACTC 57.700 50.000 0.00 0.00 41.06 3.51
3541 3577 1.220169 CTGCCCGAAGATCATGCTCG 61.220 60.000 0.00 0.00 0.00 5.03
3547 3583 1.403647 CGTGTTACTGCCCGAAGATCA 60.404 52.381 0.00 0.00 0.00 2.92
3548 3584 1.278238 CGTGTTACTGCCCGAAGATC 58.722 55.000 0.00 0.00 0.00 2.75
3555 3591 1.506262 CCAATGCGTGTTACTGCCC 59.494 57.895 0.00 0.00 0.00 5.36
3557 3593 1.154035 GGCCAATGCGTGTTACTGC 60.154 57.895 0.00 0.00 38.85 4.40
3558 3594 0.109781 GTGGCCAATGCGTGTTACTG 60.110 55.000 7.24 0.00 38.85 2.74
3559 3595 0.250727 AGTGGCCAATGCGTGTTACT 60.251 50.000 7.24 0.00 38.85 2.24
3560 3596 0.109781 CAGTGGCCAATGCGTGTTAC 60.110 55.000 21.78 0.00 38.85 2.50
3561 3597 0.536233 ACAGTGGCCAATGCGTGTTA 60.536 50.000 31.98 0.00 38.85 2.41
3562 3598 0.536233 TACAGTGGCCAATGCGTGTT 60.536 50.000 31.98 15.39 38.85 3.32
3563 3599 0.536233 TTACAGTGGCCAATGCGTGT 60.536 50.000 31.98 19.45 38.85 4.49
3578 3614 5.050431 CGTGACACTTGACATGACATTTACA 60.050 40.000 0.00 0.00 0.00 2.41
3618 3654 2.472816 GTCGTGGAAAAGTCGTACCAA 58.527 47.619 0.00 0.00 34.11 3.67
3637 3673 6.030228 CAGAAAACTCTTCTTCTTTTTGCGT 58.970 36.000 0.00 0.00 29.29 5.24
3646 3682 6.124088 TGCTTTCACAGAAAACTCTTCTTC 57.876 37.500 0.00 0.00 0.00 2.87
3647 3683 6.325596 GTTGCTTTCACAGAAAACTCTTCTT 58.674 36.000 0.00 0.00 0.00 2.52
3673 3709 0.591170 CCAACACACGTCCATGTTCC 59.409 55.000 6.43 0.00 36.92 3.62
3738 3811 4.719369 GGCAGCAACAGCAGCAGC 62.719 66.667 7.14 0.00 41.91 5.25
3739 3812 4.052229 GGGCAGCAACAGCAGCAG 62.052 66.667 7.14 0.00 41.91 4.24
3746 3819 1.912763 GGATTTGGGGGCAGCAACA 60.913 57.895 0.00 0.00 0.00 3.33
3748 3821 2.284552 GGGATTTGGGGGCAGCAA 60.285 61.111 0.00 0.00 0.00 3.91
3773 3846 1.530441 CGCATTGACGCCTTCTTCATG 60.530 52.381 0.00 0.00 0.00 3.07
3805 3878 2.675889 GCAAGTACGCCTGCCTAAGTAA 60.676 50.000 6.41 0.00 0.00 2.24
3844 3917 6.039616 TCTTCCTTTTGTTTTTGTTCCATCG 58.960 36.000 0.00 0.00 0.00 3.84
3900 3973 0.034476 TGCATGATCTCCGATCTGCC 59.966 55.000 17.41 4.66 0.00 4.85
3903 3976 1.270199 GCAGTGCATGATCTCCGATCT 60.270 52.381 11.09 0.00 0.00 2.75
3904 3977 1.146637 GCAGTGCATGATCTCCGATC 58.853 55.000 11.09 0.00 0.00 3.69
3905 3978 0.466963 TGCAGTGCATGATCTCCGAT 59.533 50.000 15.37 0.00 31.71 4.18
3906 3979 0.460811 GTGCAGTGCATGATCTCCGA 60.461 55.000 22.87 0.00 41.91 4.55
3907 3980 1.434622 GGTGCAGTGCATGATCTCCG 61.435 60.000 22.87 0.00 41.91 4.63
3908 3981 1.099879 GGGTGCAGTGCATGATCTCC 61.100 60.000 22.87 16.04 41.91 3.71
3909 3982 0.393402 TGGGTGCAGTGCATGATCTC 60.393 55.000 22.87 8.84 41.91 2.75
3928 4018 3.769739 TGCCAACTAATGACAGACAGT 57.230 42.857 0.00 0.00 0.00 3.55
3929 4019 3.120060 GCTTGCCAACTAATGACAGACAG 60.120 47.826 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.