Multiple sequence alignment - TraesCS4B01G175100

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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 TraesCS4B01G175100 chr4B 100.000 3953 0 0 1 3953 384293988 384290036 0.000000e+00 7300
1 TraesCS4B01G175100 chr4D 95.531 2797 81 25 892 3665 308371803 308369028 0.000000e+00 4433
2 TraesCS4B01G175100 chr4D 91.778 827 35 14 51 867 308372602 308371799 0.000000e+00 1120
3 TraesCS4B01G175100 chr4D 89.274 317 18 4 3651 3953 308361732 308361418 2.230000e-102 383
4 TraesCS4B01G175100 chr4A 95.422 2490 64 19 892 3354 168791983 168794449 0.000000e+00 3921
5 TraesCS4B01G175100 chr4A 90.217 828 36 26 51 859 168791177 168791978 0.000000e+00 1038
6 TraesCS4B01G175100 chr4A 89.548 641 33 13 3334 3953 168794466 168795093 0.000000e+00 782
7 TraesCS4B01G175100 chr2D 83.575 828 112 22 1201 2010 51192947 51192126 0.000000e+00 754
8 TraesCS4B01G175100 chr2A 81.633 931 141 25 1201 2113 52665880 52664962 0.000000e+00 745
9 TraesCS4B01G175100 chr2B 82.503 863 118 29 1202 2043 80122435 80121585 0.000000e+00 726


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 TraesCS4B01G175100 chr4B 384290036 384293988 3952 True 7300.000000 7300 100.0000 1 3953 1 chr4B.!!$R1 3952
1 TraesCS4B01G175100 chr4D 308369028 308372602 3574 True 2776.500000 4433 93.6545 51 3665 2 chr4D.!!$R2 3614
2 TraesCS4B01G175100 chr4A 168791177 168795093 3916 False 1913.666667 3921 91.7290 51 3953 3 chr4A.!!$F1 3902
3 TraesCS4B01G175100 chr2D 51192126 51192947 821 True 754.000000 754 83.5750 1201 2010 1 chr2D.!!$R1 809
4 TraesCS4B01G175100 chr2A 52664962 52665880 918 True 745.000000 745 81.6330 1201 2113 1 chr2A.!!$R1 912
5 TraesCS4B01G175100 chr2B 80121585 80122435 850 True 726.000000 726 82.5030 1202 2043 1 chr2B.!!$R1 841

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
884 923 0.046397 ATCCCCTCCTGGCCTTAAGT 59.954 55.0 3.32 0.0 0.0 2.24 F
2384 2448 0.247814 CTTGATCGGAATGCACGCAC 60.248 55.0 0.00 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 2556 0.240945 GTTGTTGAGCCCATGGTTCG 59.759 55.0 11.73 0.0 35.65 3.95 R
3780 3921 0.033109 AATAAAGGGGCTGGTGGCTC 60.033 55.0 0.00 0.0 41.61 4.70 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
21 22 3.750371 TCCAACTGTCCATACCTGTTTG 58.250 45.455 0.00 0.00 0.00 2.93
22 23 2.819608 CCAACTGTCCATACCTGTTTGG 59.180 50.000 0.82 0.82 42.93 3.28
23 24 2.200373 ACTGTCCATACCTGTTTGGC 57.800 50.000 2.28 0.00 40.22 4.52
24 25 1.705186 ACTGTCCATACCTGTTTGGCT 59.295 47.619 2.28 0.00 40.22 4.75
25 26 2.910319 ACTGTCCATACCTGTTTGGCTA 59.090 45.455 2.28 0.00 40.22 3.93
26 27 3.055094 ACTGTCCATACCTGTTTGGCTAG 60.055 47.826 2.28 5.58 40.22 3.42
27 28 2.238646 TGTCCATACCTGTTTGGCTAGG 59.761 50.000 2.28 0.00 40.22 3.02
33 34 3.418684 ACCTGTTTGGCTAGGTACAAG 57.581 47.619 0.00 0.00 45.20 3.16
34 35 2.709397 ACCTGTTTGGCTAGGTACAAGT 59.291 45.455 0.00 0.00 45.20 3.16
35 36 3.905591 ACCTGTTTGGCTAGGTACAAGTA 59.094 43.478 0.00 0.00 45.20 2.24
36 37 4.348754 ACCTGTTTGGCTAGGTACAAGTAA 59.651 41.667 0.00 0.00 45.20 2.24
37 38 5.163174 ACCTGTTTGGCTAGGTACAAGTAAA 60.163 40.000 0.00 0.00 45.20 2.01
38 39 5.944007 CCTGTTTGGCTAGGTACAAGTAAAT 59.056 40.000 0.00 0.00 0.00 1.40
39 40 7.107542 CCTGTTTGGCTAGGTACAAGTAAATA 58.892 38.462 0.00 0.00 0.00 1.40
40 41 7.773690 CCTGTTTGGCTAGGTACAAGTAAATAT 59.226 37.037 0.00 0.00 0.00 1.28
41 42 9.174166 CTGTTTGGCTAGGTACAAGTAAATATT 57.826 33.333 0.00 0.00 0.00 1.28
42 43 9.523168 TGTTTGGCTAGGTACAAGTAAATATTT 57.477 29.630 5.89 5.89 0.00 1.40
83 84 4.499865 GGCTTTCTTCCCTTGAAAAGTGTC 60.500 45.833 0.00 0.00 44.25 3.67
84 85 4.339530 GCTTTCTTCCCTTGAAAAGTGTCT 59.660 41.667 0.00 0.00 44.25 3.41
121 122 1.045911 TTTTGGCCAACCCCTGTGAC 61.046 55.000 20.35 0.00 33.59 3.67
141 142 5.125097 GTGACTGATTGGATCAAAGCAATCT 59.875 40.000 10.58 0.00 39.11 2.40
172 174 6.324819 AGGACGCTTAAACATGATTCAATTG 58.675 36.000 0.00 0.00 0.00 2.32
177 179 8.825745 ACGCTTAAACATGATTCAATTGTTTTT 58.174 25.926 18.51 4.06 42.07 1.94
240 246 2.025226 TGGTAAAACCCTGTGTGGACAA 60.025 45.455 0.00 0.00 37.50 3.18
241 247 3.227614 GGTAAAACCCTGTGTGGACAAT 58.772 45.455 0.00 0.00 38.35 2.71
242 248 3.254903 GGTAAAACCCTGTGTGGACAATC 59.745 47.826 0.00 0.00 38.35 2.67
275 281 8.036575 TCAATTTTCTGCCTTATTCTTCCATTG 58.963 33.333 0.00 0.00 0.00 2.82
276 282 4.989279 TTCTGCCTTATTCTTCCATTGC 57.011 40.909 0.00 0.00 0.00 3.56
354 377 4.219288 TCCGATATGATCATGTCACAGAGG 59.781 45.833 26.18 19.62 40.28 3.69
458 482 4.022068 GTGAAGGAGAGGATCATAGCAGAG 60.022 50.000 0.00 0.00 37.82 3.35
459 483 3.173953 AGGAGAGGATCATAGCAGAGG 57.826 52.381 0.00 0.00 37.82 3.69
460 484 2.450500 AGGAGAGGATCATAGCAGAGGT 59.549 50.000 0.00 0.00 37.82 3.85
461 485 2.562298 GGAGAGGATCATAGCAGAGGTG 59.438 54.545 0.00 0.00 37.82 4.00
462 486 3.230134 GAGAGGATCATAGCAGAGGTGT 58.770 50.000 0.00 0.00 37.82 4.16
463 487 2.964464 AGAGGATCATAGCAGAGGTGTG 59.036 50.000 0.00 0.00 37.82 3.82
464 488 2.697751 GAGGATCATAGCAGAGGTGTGT 59.302 50.000 0.00 0.00 33.17 3.72
465 489 2.433604 AGGATCATAGCAGAGGTGTGTG 59.566 50.000 0.00 0.00 0.00 3.82
466 490 2.169352 GGATCATAGCAGAGGTGTGTGT 59.831 50.000 0.00 0.00 0.00 3.72
477 510 1.662438 GGTGTGTGTGGTGTGGGTTG 61.662 60.000 0.00 0.00 0.00 3.77
545 578 1.922135 TTCCGGCGCTTGCTTCAATC 61.922 55.000 7.64 0.00 39.13 2.67
623 656 8.598916 TCTGGGATGTTTTGTGAACTAATACTA 58.401 33.333 0.00 0.00 0.00 1.82
624 657 8.556213 TGGGATGTTTTGTGAACTAATACTAC 57.444 34.615 0.00 0.00 0.00 2.73
625 658 8.380099 TGGGATGTTTTGTGAACTAATACTACT 58.620 33.333 0.00 0.00 0.00 2.57
626 659 8.665685 GGGATGTTTTGTGAACTAATACTACTG 58.334 37.037 0.00 0.00 0.00 2.74
627 660 8.175716 GGATGTTTTGTGAACTAATACTACTGC 58.824 37.037 0.00 0.00 0.00 4.40
736 772 8.730680 TCAAAGAAAACTACCTGATTAAGATGC 58.269 33.333 0.00 0.00 0.00 3.91
737 773 8.734386 CAAAGAAAACTACCTGATTAAGATGCT 58.266 33.333 0.00 0.00 0.00 3.79
738 774 8.499403 AAGAAAACTACCTGATTAAGATGCTC 57.501 34.615 0.00 0.00 0.00 4.26
739 775 7.856415 AGAAAACTACCTGATTAAGATGCTCT 58.144 34.615 0.00 0.00 0.00 4.09
740 776 8.982723 AGAAAACTACCTGATTAAGATGCTCTA 58.017 33.333 0.00 0.00 0.00 2.43
741 777 9.255304 GAAAACTACCTGATTAAGATGCTCTAG 57.745 37.037 0.00 0.00 0.00 2.43
742 778 7.906199 AACTACCTGATTAAGATGCTCTAGT 57.094 36.000 0.00 0.00 0.00 2.57
743 779 8.998277 AACTACCTGATTAAGATGCTCTAGTA 57.002 34.615 0.00 0.00 0.00 1.82
744 780 8.998277 ACTACCTGATTAAGATGCTCTAGTAA 57.002 34.615 0.00 0.00 0.00 2.24
801 840 8.685838 TTAACTGTAATTGCCTCTTTAACACT 57.314 30.769 0.00 0.00 0.00 3.55
802 841 9.781633 TTAACTGTAATTGCCTCTTTAACACTA 57.218 29.630 0.00 0.00 0.00 2.74
803 842 7.907214 ACTGTAATTGCCTCTTTAACACTAG 57.093 36.000 0.00 0.00 0.00 2.57
841 880 5.285798 TGTTGCCTAGTTATTGCGTTTAC 57.714 39.130 0.00 0.00 0.00 2.01
862 901 3.254166 ACACTCAGCAAGCAATAAGTTGG 59.746 43.478 0.00 0.00 35.83 3.77
864 903 4.455533 CACTCAGCAAGCAATAAGTTGGTA 59.544 41.667 0.00 0.00 44.74 3.25
865 904 5.048782 CACTCAGCAAGCAATAAGTTGGTAA 60.049 40.000 0.00 0.00 44.74 2.85
866 905 5.711976 ACTCAGCAAGCAATAAGTTGGTAAT 59.288 36.000 0.00 0.00 44.74 1.89
867 906 6.127897 ACTCAGCAAGCAATAAGTTGGTAATC 60.128 38.462 0.00 0.00 44.74 1.75
868 907 5.125417 TCAGCAAGCAATAAGTTGGTAATCC 59.875 40.000 0.00 0.00 44.74 3.01
869 908 4.402474 AGCAAGCAATAAGTTGGTAATCCC 59.598 41.667 0.00 0.00 44.74 3.85
870 909 4.441495 GCAAGCAATAAGTTGGTAATCCCC 60.441 45.833 0.00 0.00 44.74 4.81
871 910 4.881157 AGCAATAAGTTGGTAATCCCCT 57.119 40.909 0.00 0.00 43.75 4.79
872 911 4.793201 AGCAATAAGTTGGTAATCCCCTC 58.207 43.478 0.00 0.00 43.75 4.30
873 912 3.889538 GCAATAAGTTGGTAATCCCCTCC 59.110 47.826 0.00 0.00 35.83 4.30
874 913 4.386424 GCAATAAGTTGGTAATCCCCTCCT 60.386 45.833 0.00 0.00 35.83 3.69
875 914 5.133221 CAATAAGTTGGTAATCCCCTCCTG 58.867 45.833 0.00 0.00 0.00 3.86
876 915 1.596496 AGTTGGTAATCCCCTCCTGG 58.404 55.000 0.00 0.00 0.00 4.45
877 916 0.106669 GTTGGTAATCCCCTCCTGGC 60.107 60.000 0.00 0.00 0.00 4.85
878 917 1.286305 TTGGTAATCCCCTCCTGGCC 61.286 60.000 0.00 0.00 0.00 5.36
879 918 1.386057 GGTAATCCCCTCCTGGCCT 60.386 63.158 3.32 0.00 0.00 5.19
880 919 0.994050 GGTAATCCCCTCCTGGCCTT 60.994 60.000 3.32 0.00 0.00 4.35
881 920 1.697945 GGTAATCCCCTCCTGGCCTTA 60.698 57.143 3.32 0.00 0.00 2.69
882 921 2.132686 GTAATCCCCTCCTGGCCTTAA 58.867 52.381 3.32 0.00 0.00 1.85
883 922 1.226311 AATCCCCTCCTGGCCTTAAG 58.774 55.000 3.32 0.00 0.00 1.85
884 923 0.046397 ATCCCCTCCTGGCCTTAAGT 59.954 55.000 3.32 0.00 0.00 2.24
885 924 0.620700 TCCCCTCCTGGCCTTAAGTC 60.621 60.000 3.32 0.00 0.00 3.01
886 925 0.621862 CCCCTCCTGGCCTTAAGTCT 60.622 60.000 3.32 0.00 0.00 3.24
887 926 1.290134 CCCTCCTGGCCTTAAGTCTT 58.710 55.000 3.32 0.00 0.00 3.01
888 927 1.065126 CCCTCCTGGCCTTAAGTCTTG 60.065 57.143 3.32 0.00 0.00 3.02
889 928 1.630878 CCTCCTGGCCTTAAGTCTTGT 59.369 52.381 3.32 0.00 0.00 3.16
890 929 2.838202 CCTCCTGGCCTTAAGTCTTGTA 59.162 50.000 3.32 0.00 0.00 2.41
944 983 1.758592 GGTGAACACCCCAGCTACA 59.241 57.895 12.42 0.00 45.68 2.74
946 985 1.523758 GTGAACACCCCAGCTACAAG 58.476 55.000 0.00 0.00 0.00 3.16
947 986 1.136828 TGAACACCCCAGCTACAAGT 58.863 50.000 0.00 0.00 0.00 3.16
967 1013 7.746703 ACAAGTAGTAGAGGAAGTGGAATTTT 58.253 34.615 0.00 0.00 0.00 1.82
968 1014 8.877195 ACAAGTAGTAGAGGAAGTGGAATTTTA 58.123 33.333 0.00 0.00 0.00 1.52
1833 1897 2.348243 CCGCCCCCGTACAAGAAA 59.652 61.111 0.00 0.00 0.00 2.52
2110 2174 1.589076 GAGTGAGTACGACGTTGACG 58.411 55.000 10.51 0.90 46.33 4.35
2244 2308 0.807667 CCATGAAAGAGGAGACCGCG 60.808 60.000 0.00 0.00 0.00 6.46
2370 2434 1.492764 ACGGGTACGGATTCCTTGAT 58.507 50.000 0.30 0.00 46.48 2.57
2384 2448 0.247814 CTTGATCGGAATGCACGCAC 60.248 55.000 0.00 0.00 0.00 5.34
2387 2451 1.643868 GATCGGAATGCACGCACCAA 61.644 55.000 0.00 0.00 0.00 3.67
2492 2556 2.751837 GGCAGCCTACAACCAGCC 60.752 66.667 3.29 0.00 34.71 4.85
2559 2623 2.123854 AGGTCCATCGCCGAGCTA 60.124 61.111 0.00 0.00 36.35 3.32
2586 2650 3.384532 TACGACACCGCCTTCCCC 61.385 66.667 0.00 0.00 39.95 4.81
2656 2720 0.395036 CAATGCCATCACCCCGGTAA 60.395 55.000 0.00 0.00 0.00 2.85
2901 2983 0.807496 GCTCTGGCTTCAACATGTCC 59.193 55.000 0.00 0.00 35.22 4.02
2937 3019 2.342279 CAGAAGAACGACGGCCCA 59.658 61.111 0.00 0.00 0.00 5.36
2953 3035 3.692690 GGCCCAAATTGGTACTACTGAA 58.307 45.455 11.52 0.00 35.17 3.02
2954 3036 4.278310 GGCCCAAATTGGTACTACTGAAT 58.722 43.478 11.52 0.00 35.17 2.57
2955 3037 4.097892 GGCCCAAATTGGTACTACTGAATG 59.902 45.833 11.52 0.00 35.17 2.67
2977 3059 8.930846 AATGATGAAGAATAAACTCATAGGGG 57.069 34.615 0.00 0.00 0.00 4.79
2978 3060 6.841601 TGATGAAGAATAAACTCATAGGGGG 58.158 40.000 0.00 0.00 0.00 5.40
3046 3133 3.745803 GGGGAAGCGTCGTCGTCT 61.746 66.667 3.66 0.00 39.49 4.18
3236 3330 5.297776 GCTAAATGCTGTTCATATGACTGGT 59.702 40.000 4.48 0.00 38.95 4.00
3317 3411 4.040339 TGAACTGGTGCTCTCTTATGTGAA 59.960 41.667 0.00 0.00 0.00 3.18
3390 3526 0.108233 CCATGCCGGGGAATTTTGTG 60.108 55.000 2.18 0.00 0.00 3.33
3398 3534 4.676986 GCCGGGGAATTTTGTGAAATAGTC 60.677 45.833 2.18 0.00 34.44 2.59
3436 3572 0.037046 GCCAGGCTGGTGGAAATTTG 60.037 55.000 32.80 5.57 40.44 2.32
3469 3606 3.133362 GGTTCACCTGGATGTCGGTATAA 59.867 47.826 0.00 0.00 30.91 0.98
3473 3610 5.424757 TCACCTGGATGTCGGTATAAAAAG 58.575 41.667 0.00 0.00 30.91 2.27
3510 3647 4.099419 TCTTTTTCTTGCCCTGAACTTTCC 59.901 41.667 0.00 0.00 0.00 3.13
3528 3668 9.849166 GAACTTTCCGGTAAAATAAATTCATCA 57.151 29.630 0.00 0.00 0.00 3.07
3589 3729 3.059884 TGACTTTCACATCAAGACGCTC 58.940 45.455 0.00 0.00 0.00 5.03
3704 3845 0.383949 TTTGGTGCTCGCCAGAAAAC 59.616 50.000 2.18 0.00 40.01 2.43
3706 3847 0.749818 TGGTGCTCGCCAGAAAACAA 60.750 50.000 0.00 0.00 33.97 2.83
3714 3855 2.360483 TCGCCAGAAAACAATCTTTGCA 59.640 40.909 0.00 0.00 0.00 4.08
3719 3860 5.782047 CCAGAAAACAATCTTTGCATGGTA 58.218 37.500 0.00 0.00 0.00 3.25
3748 3889 6.648879 AAAAAGAAAGAAACATGGATCCGA 57.351 33.333 7.39 0.00 0.00 4.55
3775 3916 1.134401 TGGATGGTCCTCGCTTTGATC 60.134 52.381 0.00 0.00 37.46 2.92
3776 3917 1.134401 GGATGGTCCTCGCTTTGATCA 60.134 52.381 0.00 0.00 32.53 2.92
3777 3918 1.936547 GATGGTCCTCGCTTTGATCAC 59.063 52.381 0.00 0.00 0.00 3.06
3778 3919 0.684535 TGGTCCTCGCTTTGATCACA 59.315 50.000 0.00 0.00 0.00 3.58
3779 3920 1.071542 TGGTCCTCGCTTTGATCACAA 59.928 47.619 0.00 0.00 0.00 3.33
3780 3921 1.734465 GGTCCTCGCTTTGATCACAAG 59.266 52.381 0.00 4.18 37.32 3.16
3781 3922 2.612972 GGTCCTCGCTTTGATCACAAGA 60.613 50.000 16.82 5.78 37.32 3.02
3782 3923 2.670414 GTCCTCGCTTTGATCACAAGAG 59.330 50.000 16.82 14.37 37.32 2.85
3783 3924 1.396301 CCTCGCTTTGATCACAAGAGC 59.604 52.381 16.82 12.89 37.32 4.09
3784 3925 1.396301 CTCGCTTTGATCACAAGAGCC 59.604 52.381 16.82 4.05 37.12 4.70
3789 3930 2.189594 TTGATCACAAGAGCCACCAG 57.810 50.000 0.00 0.00 0.00 4.00
3812 3953 1.617850 CCTTTATTGCTTGGTGGCACA 59.382 47.619 20.82 2.61 42.27 4.57
3894 4044 0.177604 CCCTCCTCACATGCTCTCAC 59.822 60.000 0.00 0.00 0.00 3.51
3905 4055 2.575805 TGCTCTCACTCTCACTCTCA 57.424 50.000 0.00 0.00 0.00 3.27
3910 4060 1.745087 CTCACTCTCACTCTCAGAGGC 59.255 57.143 6.64 0.00 41.66 4.70
3923 4080 1.692749 AGAGGCGCCCCCTGATTTA 60.693 57.895 26.15 0.00 46.60 1.40
3934 4091 2.358090 CCCCTGATTTACATGGAGGCAA 60.358 50.000 0.00 0.00 36.59 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.497763 CCAAACAGGTATGGACAGTTGGA 60.498 47.826 0.00 0.00 39.12 3.53
1 2 2.819608 CCAAACAGGTATGGACAGTTGG 59.180 50.000 0.00 0.00 39.12 3.77
2 3 2.228822 GCCAAACAGGTATGGACAGTTG 59.771 50.000 0.00 0.00 39.12 3.16
3 4 2.108250 AGCCAAACAGGTATGGACAGTT 59.892 45.455 0.00 0.00 39.12 3.16
4 5 1.705186 AGCCAAACAGGTATGGACAGT 59.295 47.619 0.00 0.00 39.12 3.55
5 6 2.496899 AGCCAAACAGGTATGGACAG 57.503 50.000 0.00 0.00 39.12 3.51
6 7 2.238646 CCTAGCCAAACAGGTATGGACA 59.761 50.000 0.00 0.00 39.12 4.02
7 8 2.238898 ACCTAGCCAAACAGGTATGGAC 59.761 50.000 0.00 0.00 43.48 4.02
8 9 2.557869 ACCTAGCCAAACAGGTATGGA 58.442 47.619 0.00 0.00 43.48 3.41
9 10 3.199071 TGTACCTAGCCAAACAGGTATGG 59.801 47.826 3.94 0.00 46.42 2.74
10 11 4.481368 TGTACCTAGCCAAACAGGTATG 57.519 45.455 3.94 0.00 46.42 2.39
11 12 4.534897 ACTTGTACCTAGCCAAACAGGTAT 59.465 41.667 3.94 0.00 46.42 2.73
12 13 3.905591 ACTTGTACCTAGCCAAACAGGTA 59.094 43.478 0.00 0.00 43.48 3.08
13 14 2.709397 ACTTGTACCTAGCCAAACAGGT 59.291 45.455 0.00 0.00 46.88 4.00
14 15 3.418684 ACTTGTACCTAGCCAAACAGG 57.581 47.619 0.00 0.00 41.84 4.00
15 16 8.732746 ATATTTACTTGTACCTAGCCAAACAG 57.267 34.615 0.00 0.00 0.00 3.16
16 17 9.523168 AAATATTTACTTGTACCTAGCCAAACA 57.477 29.630 0.00 0.00 0.00 2.83
38 39 9.866655 AAGCCATCTTTTATGGAGATGTAAATA 57.133 29.630 8.20 0.00 45.74 1.40
39 40 8.773033 AAGCCATCTTTTATGGAGATGTAAAT 57.227 30.769 8.20 0.00 45.74 1.40
40 41 8.593945 AAAGCCATCTTTTATGGAGATGTAAA 57.406 30.769 8.20 0.00 45.74 2.01
41 42 8.055181 AGAAAGCCATCTTTTATGGAGATGTAA 58.945 33.333 8.20 0.00 45.74 2.41
42 43 7.577303 AGAAAGCCATCTTTTATGGAGATGTA 58.423 34.615 8.20 0.00 45.74 2.29
43 44 6.430007 AGAAAGCCATCTTTTATGGAGATGT 58.570 36.000 8.20 0.00 45.74 3.06
44 45 6.956202 AGAAAGCCATCTTTTATGGAGATG 57.044 37.500 8.20 7.04 46.40 2.90
45 46 6.548993 GGAAGAAAGCCATCTTTTATGGAGAT 59.451 38.462 8.20 0.00 42.24 2.75
46 47 5.888161 GGAAGAAAGCCATCTTTTATGGAGA 59.112 40.000 8.20 0.00 42.24 3.71
47 48 5.068329 GGGAAGAAAGCCATCTTTTATGGAG 59.932 44.000 8.20 0.00 42.24 3.86
48 49 4.956075 GGGAAGAAAGCCATCTTTTATGGA 59.044 41.667 8.20 0.00 42.24 3.41
49 50 4.958581 AGGGAAGAAAGCCATCTTTTATGG 59.041 41.667 3.37 0.00 42.24 2.74
83 84 3.294038 AATGATGAGAAAGCAGGGGAG 57.706 47.619 0.00 0.00 0.00 4.30
84 85 3.744940 AAATGATGAGAAAGCAGGGGA 57.255 42.857 0.00 0.00 0.00 4.81
121 122 6.627243 TGAAAGATTGCTTTGATCCAATCAG 58.373 36.000 18.66 0.00 46.03 2.90
141 142 5.000591 TCATGTTTAAGCGTCCTCATGAAA 58.999 37.500 12.01 0.00 38.68 2.69
172 174 6.759497 ATAATCCTAGCAGGTCACAAAAAC 57.241 37.500 2.68 0.00 36.53 2.43
177 179 5.402630 TCCATATAATCCTAGCAGGTCACA 58.597 41.667 2.68 0.00 36.53 3.58
215 217 8.465322 TTGTCCACACAGGGTTTTACCAAAAC 62.465 42.308 6.06 6.06 41.02 2.43
216 218 3.447944 GTCCACACAGGGTTTTACCAAAA 59.552 43.478 0.00 0.00 41.02 2.44
240 246 5.733620 AGGCAGAAAATTGAACACATGAT 57.266 34.783 0.00 0.00 0.00 2.45
241 247 5.534207 AAGGCAGAAAATTGAACACATGA 57.466 34.783 0.00 0.00 0.00 3.07
242 248 7.816031 AGAATAAGGCAGAAAATTGAACACATG 59.184 33.333 0.00 0.00 0.00 3.21
275 281 6.758886 GCATGACCATATAGGAGTAATACAGC 59.241 42.308 0.00 0.00 41.22 4.40
276 282 7.840931 TGCATGACCATATAGGAGTAATACAG 58.159 38.462 0.00 0.00 41.22 2.74
413 437 9.468532 TTCACAATTATAGATCATCAACTCGAG 57.531 33.333 11.84 11.84 0.00 4.04
415 439 8.706936 CCTTCACAATTATAGATCATCAACTCG 58.293 37.037 0.00 0.00 0.00 4.18
458 482 1.379309 AACCCACACCACACACACC 60.379 57.895 0.00 0.00 0.00 4.16
459 483 1.662438 CCAACCCACACCACACACAC 61.662 60.000 0.00 0.00 0.00 3.82
460 484 1.379176 CCAACCCACACCACACACA 60.379 57.895 0.00 0.00 0.00 3.72
461 485 0.467290 ATCCAACCCACACCACACAC 60.467 55.000 0.00 0.00 0.00 3.82
462 486 1.141185 TATCCAACCCACACCACACA 58.859 50.000 0.00 0.00 0.00 3.72
463 487 2.159382 CTTATCCAACCCACACCACAC 58.841 52.381 0.00 0.00 0.00 3.82
464 488 2.058705 TCTTATCCAACCCACACCACA 58.941 47.619 0.00 0.00 0.00 4.17
465 489 2.871096 TCTTATCCAACCCACACCAC 57.129 50.000 0.00 0.00 0.00 4.16
466 490 2.093181 CGATCTTATCCAACCCACACCA 60.093 50.000 0.00 0.00 0.00 4.17
477 510 3.863424 TCAAAACGCACTCGATCTTATCC 59.137 43.478 0.00 0.00 39.41 2.59
623 656 2.355010 AAGAAAACAGCTGGAGCAGT 57.645 45.000 19.93 0.00 45.16 4.40
624 657 4.320788 CCTTAAAGAAAACAGCTGGAGCAG 60.321 45.833 19.93 0.00 45.16 4.24
625 658 3.569701 CCTTAAAGAAAACAGCTGGAGCA 59.430 43.478 19.93 0.00 45.16 4.26
626 659 3.821033 TCCTTAAAGAAAACAGCTGGAGC 59.179 43.478 19.93 4.33 42.49 4.70
627 660 5.308825 TCTCCTTAAAGAAAACAGCTGGAG 58.691 41.667 19.93 10.17 39.69 3.86
672 705 5.287035 GGTAATTAGACGGTGACTTAACACG 59.713 44.000 0.00 0.00 41.12 4.49
841 880 3.254166 ACCAACTTATTGCTTGCTGAGTG 59.746 43.478 0.00 0.00 34.17 3.51
862 901 1.815757 TAAGGCCAGGAGGGGATTAC 58.184 55.000 5.01 0.00 37.04 1.89
863 902 2.294263 ACTTAAGGCCAGGAGGGGATTA 60.294 50.000 5.01 0.00 37.04 1.75
864 903 1.226311 CTTAAGGCCAGGAGGGGATT 58.774 55.000 5.01 0.00 37.04 3.01
865 904 0.046397 ACTTAAGGCCAGGAGGGGAT 59.954 55.000 5.01 0.00 37.04 3.85
866 905 0.620700 GACTTAAGGCCAGGAGGGGA 60.621 60.000 5.01 0.00 37.04 4.81
867 906 0.621862 AGACTTAAGGCCAGGAGGGG 60.622 60.000 5.01 0.00 37.04 4.79
868 907 1.065126 CAAGACTTAAGGCCAGGAGGG 60.065 57.143 5.01 0.00 40.85 4.30
869 908 1.630878 ACAAGACTTAAGGCCAGGAGG 59.369 52.381 5.01 0.00 38.23 4.30
870 909 3.515901 ACTACAAGACTTAAGGCCAGGAG 59.484 47.826 5.01 6.50 0.00 3.69
871 910 3.517612 ACTACAAGACTTAAGGCCAGGA 58.482 45.455 5.01 0.00 0.00 3.86
872 911 3.983044 ACTACAAGACTTAAGGCCAGG 57.017 47.619 5.01 0.00 0.00 4.45
873 912 8.880750 GTTAATTACTACAAGACTTAAGGCCAG 58.119 37.037 5.01 0.00 0.00 4.85
874 913 7.825761 GGTTAATTACTACAAGACTTAAGGCCA 59.174 37.037 5.01 0.00 0.00 5.36
875 914 8.045507 AGGTTAATTACTACAAGACTTAAGGCC 58.954 37.037 4.17 0.00 0.00 5.19
876 915 8.880750 CAGGTTAATTACTACAAGACTTAAGGC 58.119 37.037 7.53 3.14 0.00 4.35
877 916 9.379791 CCAGGTTAATTACTACAAGACTTAAGG 57.620 37.037 7.53 0.00 0.00 2.69
878 917 8.880750 GCCAGGTTAATTACTACAAGACTTAAG 58.119 37.037 0.00 0.00 0.00 1.85
879 918 7.825761 GGCCAGGTTAATTACTACAAGACTTAA 59.174 37.037 0.00 0.00 0.00 1.85
880 919 7.181485 AGGCCAGGTTAATTACTACAAGACTTA 59.819 37.037 5.01 0.00 0.00 2.24
881 920 6.012771 AGGCCAGGTTAATTACTACAAGACTT 60.013 38.462 5.01 0.00 0.00 3.01
882 921 5.487845 AGGCCAGGTTAATTACTACAAGACT 59.512 40.000 5.01 0.00 0.00 3.24
883 922 5.742063 AGGCCAGGTTAATTACTACAAGAC 58.258 41.667 5.01 0.00 0.00 3.01
884 923 5.724854 AGAGGCCAGGTTAATTACTACAAGA 59.275 40.000 5.01 0.00 0.00 3.02
885 924 5.990668 AGAGGCCAGGTTAATTACTACAAG 58.009 41.667 5.01 0.00 0.00 3.16
886 925 6.382919 AAGAGGCCAGGTTAATTACTACAA 57.617 37.500 5.01 0.00 0.00 2.41
887 926 6.177610 CAAAGAGGCCAGGTTAATTACTACA 58.822 40.000 5.01 0.00 0.00 2.74
888 927 5.066117 GCAAAGAGGCCAGGTTAATTACTAC 59.934 44.000 5.01 0.00 0.00 2.73
889 928 5.045140 AGCAAAGAGGCCAGGTTAATTACTA 60.045 40.000 5.01 0.00 0.00 1.82
890 929 4.017126 GCAAAGAGGCCAGGTTAATTACT 58.983 43.478 5.01 0.00 0.00 2.24
936 975 4.951094 ACTTCCTCTACTACTTGTAGCTGG 59.049 45.833 7.62 5.51 46.15 4.85
938 977 4.951094 CCACTTCCTCTACTACTTGTAGCT 59.049 45.833 7.62 0.00 46.15 3.32
939 978 4.948621 TCCACTTCCTCTACTACTTGTAGC 59.051 45.833 7.62 0.00 46.15 3.58
941 980 8.431910 AAATTCCACTTCCTCTACTACTTGTA 57.568 34.615 0.00 0.00 0.00 2.41
942 981 6.936968 AATTCCACTTCCTCTACTACTTGT 57.063 37.500 0.00 0.00 0.00 3.16
946 985 9.535878 CAGATAAAATTCCACTTCCTCTACTAC 57.464 37.037 0.00 0.00 0.00 2.73
947 986 9.268282 ACAGATAAAATTCCACTTCCTCTACTA 57.732 33.333 0.00 0.00 0.00 1.82
967 1013 4.019860 AGCAGCTCTTTTTCTCCACAGATA 60.020 41.667 0.00 0.00 0.00 1.98
968 1014 3.080319 GCAGCTCTTTTTCTCCACAGAT 58.920 45.455 0.00 0.00 0.00 2.90
970 1016 2.502295 AGCAGCTCTTTTTCTCCACAG 58.498 47.619 0.00 0.00 0.00 3.66
1038 1087 2.664851 TTGTGCACGCCGGAGAAG 60.665 61.111 13.83 5.01 0.00 2.85
1173 1222 2.027625 CGGGAAGTTGTCAGTCGGC 61.028 63.158 0.00 0.00 0.00 5.54
1179 1228 2.029964 GCGTCCGGGAAGTTGTCA 59.970 61.111 11.61 0.00 0.00 3.58
1833 1897 0.995024 CCTTCTTGAGGTCATGGGGT 59.005 55.000 0.00 0.00 40.95 4.95
2370 2434 2.281139 TTGGTGCGTGCATTCCGA 60.281 55.556 0.00 0.00 0.00 4.55
2379 2443 1.227734 GTACTGGTGGTTGGTGCGT 60.228 57.895 0.00 0.00 0.00 5.24
2384 2448 3.322514 CAGGTGTACTGGTGGTTGG 57.677 57.895 0.00 0.00 43.70 3.77
2492 2556 0.240945 GTTGTTGAGCCCATGGTTCG 59.759 55.000 11.73 0.00 35.65 3.95
2559 2623 1.730064 GCGGTGTCGTACATGTTCATT 59.270 47.619 2.30 0.00 38.89 2.57
2586 2650 1.602668 CCCATGTTCTTGTTGTTGGCG 60.603 52.381 0.00 0.00 0.00 5.69
2591 2655 1.066908 CGTTGCCCATGTTCTTGTTGT 59.933 47.619 0.00 0.00 0.00 3.32
2656 2720 1.827399 AAACCCTCGTCCATCTGCGT 61.827 55.000 0.00 0.00 0.00 5.24
2761 2828 3.036577 CTGCTGTGGCTGTTGTGG 58.963 61.111 0.00 0.00 39.59 4.17
2901 2983 4.487412 GGGTAGTCGACGGTGCCG 62.487 72.222 10.46 9.29 46.03 5.69
2937 3019 9.739276 TTCTTCATCATTCAGTAGTACCAATTT 57.261 29.630 0.00 0.00 0.00 1.82
2953 3035 7.074237 ACCCCCTATGAGTTTATTCTTCATCAT 59.926 37.037 0.00 0.00 0.00 2.45
2954 3036 6.389869 ACCCCCTATGAGTTTATTCTTCATCA 59.610 38.462 0.00 0.00 0.00 3.07
2955 3037 6.842676 ACCCCCTATGAGTTTATTCTTCATC 58.157 40.000 0.00 0.00 0.00 2.92
2971 3053 7.419203 AGTTTTAAAAGCTTATGACCCCCTAT 58.581 34.615 0.00 0.00 0.00 2.57
2977 3059 8.074370 ACGAAGAAGTTTTAAAAGCTTATGACC 58.926 33.333 0.00 0.00 0.00 4.02
2978 3060 8.892905 CACGAAGAAGTTTTAAAAGCTTATGAC 58.107 33.333 0.00 0.00 0.00 3.06
3046 3133 8.855804 ATAGAGAATTACCCACTTCTTAGGAA 57.144 34.615 0.00 0.00 31.99 3.36
3213 3306 6.932356 ACCAGTCATATGAACAGCATTTAG 57.068 37.500 7.07 0.00 38.44 1.85
3236 3330 2.168106 ACACAAGCAATTTGACAGCCAA 59.832 40.909 0.00 0.00 39.21 4.52
3317 3411 5.752036 TGAAAATCATCACCAGAGAGAGT 57.248 39.130 0.00 0.00 0.00 3.24
3390 3526 5.634020 ACAAACGTAGCTGTCTGACTATTTC 59.366 40.000 9.51 0.00 0.00 2.17
3398 3534 2.602217 GGCAAACAAACGTAGCTGTCTG 60.602 50.000 0.00 0.00 0.00 3.51
3454 3590 4.814771 GTCCCTTTTTATACCGACATCCAG 59.185 45.833 0.00 0.00 0.00 3.86
3469 3606 3.903530 AGATCTTGGTTGGTCCCTTTT 57.096 42.857 0.00 0.00 34.77 2.27
3473 3610 4.152647 AGAAAAAGATCTTGGTTGGTCCC 58.847 43.478 9.17 0.00 34.77 4.46
3497 3634 1.900245 TTTACCGGAAAGTTCAGGGC 58.100 50.000 9.46 0.00 45.30 5.19
3528 3668 8.421002 ACCACATAAAAAGAAGCAACTTAACAT 58.579 29.630 0.00 0.00 0.00 2.71
3533 3673 6.042143 CACACCACATAAAAAGAAGCAACTT 58.958 36.000 0.00 0.00 0.00 2.66
3589 3729 7.112779 AGTGGGGATCAAATACTAACTTTCTG 58.887 38.462 0.00 0.00 0.00 3.02
3673 3813 4.111916 CGAGCACCAAAAACACTTCAAAT 58.888 39.130 0.00 0.00 0.00 2.32
3746 3887 2.498167 GAGGACCATCCAATCCAATCG 58.502 52.381 0.00 0.00 39.61 3.34
3748 3889 1.477558 GCGAGGACCATCCAATCCAAT 60.478 52.381 0.00 0.00 39.61 3.16
3756 3897 1.134401 TGATCAAAGCGAGGACCATCC 60.134 52.381 0.00 0.00 36.58 3.51
3775 3916 2.674380 GGGCTGGTGGCTCTTGTG 60.674 66.667 0.00 0.00 38.65 3.33
3776 3917 3.971702 GGGGCTGGTGGCTCTTGT 61.972 66.667 0.00 0.00 42.10 3.16
3780 3921 0.033109 AATAAAGGGGCTGGTGGCTC 60.033 55.000 0.00 0.00 41.61 4.70
3781 3922 0.324645 CAATAAAGGGGCTGGTGGCT 60.325 55.000 0.00 0.00 41.46 4.75
3782 3923 1.960040 GCAATAAAGGGGCTGGTGGC 61.960 60.000 0.00 0.00 40.90 5.01
3783 3924 0.324645 AGCAATAAAGGGGCTGGTGG 60.325 55.000 0.00 0.00 36.34 4.61
3784 3925 1.205417 CAAGCAATAAAGGGGCTGGTG 59.795 52.381 0.00 0.00 38.04 4.17
3789 3930 0.536724 CCACCAAGCAATAAAGGGGC 59.463 55.000 0.00 0.00 0.00 5.80
3812 3953 4.081420 GGATAAGATGCACGGATGATAGGT 60.081 45.833 0.00 0.00 0.00 3.08
3813 3954 4.437239 GGATAAGATGCACGGATGATAGG 58.563 47.826 0.00 0.00 0.00 2.57
3814 3955 4.161189 AGGGATAAGATGCACGGATGATAG 59.839 45.833 0.00 0.00 0.00 2.08
3816 3957 2.909006 AGGGATAAGATGCACGGATGAT 59.091 45.455 0.00 0.00 0.00 2.45
3817 3958 2.329267 AGGGATAAGATGCACGGATGA 58.671 47.619 0.00 0.00 0.00 2.92
3818 3959 2.810274 CAAGGGATAAGATGCACGGATG 59.190 50.000 0.00 0.00 0.00 3.51
3819 3960 2.224621 CCAAGGGATAAGATGCACGGAT 60.225 50.000 0.00 0.00 0.00 4.18
3820 3961 1.140852 CCAAGGGATAAGATGCACGGA 59.859 52.381 0.00 0.00 0.00 4.69
3894 4044 1.433064 GCGCCTCTGAGAGTGAGAG 59.567 63.158 8.88 0.00 37.33 3.20
3905 4055 1.692749 TAAATCAGGGGGCGCCTCT 60.693 57.895 28.78 21.01 32.39 3.69
3910 4060 0.182537 TCCATGTAAATCAGGGGGCG 59.817 55.000 0.00 0.00 46.65 6.13
3923 4080 1.153369 CGATCCGTTGCCTCCATGT 60.153 57.895 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.