Multiple sequence alignment - TraesCS5B01G483400

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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 TraesCS5B01G483400 chr5B 100.000 3618 0 0 1 3618 655211559 655207942 0.000000e+00 6682.0
1 TraesCS5B01G483400 chr5B 87.789 909 74 16 25 899 333191570 333192475 0.000000e+00 1029.0
2 TraesCS5B01G483400 chr5B 86.294 912 81 23 25 902 425181888 425180987 0.000000e+00 952.0
3 TraesCS5B01G483400 chr5B 91.603 393 31 2 511 903 87139442 87139052 3.180000e-150 542.0
4 TraesCS5B01G483400 chr5A 90.771 2102 147 21 945 3034 647487952 647485886 0.000000e+00 2763.0
5 TraesCS5B01G483400 chr5A 80.743 888 101 45 64 902 543566029 543565163 2.370000e-176 628.0
6 TraesCS5B01G483400 chr5A 81.663 409 45 11 3220 3618 647485711 647485323 2.710000e-81 313.0
7 TraesCS5B01G483400 chr5D 91.473 1935 89 23 903 2795 520201186 520199286 0.000000e+00 2590.0
8 TraesCS5B01G483400 chr5D 90.465 409 22 8 3218 3618 520198901 520198502 1.150000e-144 523.0
9 TraesCS5B01G483400 chr5D 91.943 211 16 1 2825 3034 520199287 520199077 9.820000e-76 294.0
10 TraesCS5B01G483400 chr5D 90.476 105 9 1 3051 3154 520199009 520198905 1.750000e-28 137.0
11 TraesCS5B01G483400 chr3A 89.450 1782 133 19 940 2702 170977275 170979020 0.000000e+00 2198.0
12 TraesCS5B01G483400 chr3A 92.961 412 21 3 3215 3618 170980382 170980793 8.650000e-166 593.0
13 TraesCS5B01G483400 chr3A 91.469 211 17 1 2825 3034 170980000 170980210 4.570000e-74 289.0
14 TraesCS5B01G483400 chr3A 90.476 105 7 3 3051 3153 170980277 170980380 6.300000e-28 135.0
15 TraesCS5B01G483400 chr4B 96.389 914 21 6 1 903 440918100 440919012 0.000000e+00 1495.0
16 TraesCS5B01G483400 chr2B 88.222 883 63 16 25 903 649945435 649944590 0.000000e+00 1016.0
17 TraesCS5B01G483400 chr6B 85.339 914 80 32 26 902 6667224 6668120 0.000000e+00 896.0
18 TraesCS5B01G483400 chr6B 84.759 912 93 23 25 902 6613329 6612430 0.000000e+00 872.0
19 TraesCS5B01G483400 chr6B 82.308 260 32 6 645 904 589049652 589049407 2.830000e-51 213.0
20 TraesCS5B01G483400 chr1B 89.002 591 57 8 25 610 534740274 534740861 0.000000e+00 725.0
21 TraesCS5B01G483400 chr1B 86.922 627 70 11 25 645 25433672 25434292 0.000000e+00 693.0
22 TraesCS5B01G483400 chr1B 82.983 476 45 16 424 867 539601251 539600780 7.280000e-107 398.0
23 TraesCS5B01G483400 chr6A 78.833 737 92 33 211 908 615623683 615622972 4.290000e-119 438.0
24 TraesCS5B01G483400 chr6D 87.209 258 30 3 647 902 83282573 83282829 1.270000e-74 291.0
25 TraesCS5B01G483400 chr3D 87.251 251 29 3 647 896 515024078 515023830 2.130000e-72 283.0
26 TraesCS5B01G483400 chr7A 94.231 52 2 1 857 908 62532962 62532912 1.080000e-10 78.7


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 TraesCS5B01G483400 chr5B 655207942 655211559 3617 True 6682.00 6682 100.00000 1 3618 1 chr5B.!!$R3 3617
1 TraesCS5B01G483400 chr5B 333191570 333192475 905 False 1029.00 1029 87.78900 25 899 1 chr5B.!!$F1 874
2 TraesCS5B01G483400 chr5B 425180987 425181888 901 True 952.00 952 86.29400 25 902 1 chr5B.!!$R2 877
3 TraesCS5B01G483400 chr5A 647485323 647487952 2629 True 1538.00 2763 86.21700 945 3618 2 chr5A.!!$R2 2673
4 TraesCS5B01G483400 chr5A 543565163 543566029 866 True 628.00 628 80.74300 64 902 1 chr5A.!!$R1 838
5 TraesCS5B01G483400 chr5D 520198502 520201186 2684 True 886.00 2590 91.08925 903 3618 4 chr5D.!!$R1 2715
6 TraesCS5B01G483400 chr3A 170977275 170980793 3518 False 803.75 2198 91.08900 940 3618 4 chr3A.!!$F1 2678
7 TraesCS5B01G483400 chr4B 440918100 440919012 912 False 1495.00 1495 96.38900 1 903 1 chr4B.!!$F1 902
8 TraesCS5B01G483400 chr2B 649944590 649945435 845 True 1016.00 1016 88.22200 25 903 1 chr2B.!!$R1 878
9 TraesCS5B01G483400 chr6B 6667224 6668120 896 False 896.00 896 85.33900 26 902 1 chr6B.!!$F1 876
10 TraesCS5B01G483400 chr6B 6612430 6613329 899 True 872.00 872 84.75900 25 902 1 chr6B.!!$R1 877
11 TraesCS5B01G483400 chr1B 534740274 534740861 587 False 725.00 725 89.00200 25 610 1 chr1B.!!$F2 585
12 TraesCS5B01G483400 chr1B 25433672 25434292 620 False 693.00 693 86.92200 25 645 1 chr1B.!!$F1 620
13 TraesCS5B01G483400 chr6A 615622972 615623683 711 True 438.00 438 78.83300 211 908 1 chr6A.!!$R1 697

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
717 790 0.173708 GGCAGCAGTAGTCGTTAGCT 59.826 55.0 0.0 0.0 35.63 3.32 F
1882 2001 0.259647 TCATTGAGGCATTGGGGAGG 59.740 55.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 2050 1.067582 GGACCGTATCCCTCTTGCG 59.932 63.158 0.0 0.0 42.46 4.85 R
3216 4312 0.878416 GTAGAATGTGCCCGTTTGCA 59.122 50.000 0.0 0.0 39.37 4.08 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
58 68 5.583495 TGTTCGGGAGTTTAACAAATGTTG 58.417 37.500 8.99 0.00 38.90 3.33
209 230 4.920376 ACAAATTTTGGTCAGAACGTGAG 58.080 39.130 13.42 0.00 35.13 3.51
353 379 7.631750 CGCGATTTCAATTATTTGTTCCAATTG 59.368 33.333 0.00 0.00 34.32 2.32
717 790 0.173708 GGCAGCAGTAGTCGTTAGCT 59.826 55.000 0.00 0.00 35.63 3.32
778 867 1.080093 TTCGATTCTTGGTCGCGCT 60.080 52.632 5.56 0.00 38.88 5.92
938 1032 1.257743 TCACCCTCTGACTTTCCTCG 58.742 55.000 0.00 0.00 0.00 4.63
997 1101 0.736325 CCAAACTCCGGTGAGCGTAG 60.736 60.000 11.17 0.00 42.74 3.51
1114 1221 2.361771 CCAAATCAGCCCCAGCCT 59.638 61.111 0.00 0.00 41.25 4.58
1127 1234 4.406763 AGCCTCCGCTCCCCTTCT 62.407 66.667 0.00 0.00 43.95 2.85
1142 1249 1.215423 CCTTCTCCCCATTAACCCCAG 59.785 57.143 0.00 0.00 0.00 4.45
1481 1600 3.691575 TGGAGGTAATGCGGAAAAATGA 58.308 40.909 0.00 0.00 0.00 2.57
1503 1622 1.719529 TCTTTCCGGACCTAACCACA 58.280 50.000 1.83 0.00 0.00 4.17
1513 1632 1.066858 ACCTAACCACACTGCAGATCG 60.067 52.381 23.35 10.83 0.00 3.69
1533 1652 2.159043 CGTCATGGATACTCTGGTTGCT 60.159 50.000 0.00 0.00 37.61 3.91
1686 1805 2.580867 GCCAGCTCGCTCGTACAG 60.581 66.667 0.00 0.00 0.00 2.74
1687 1806 2.103143 CCAGCTCGCTCGTACAGG 59.897 66.667 0.00 0.00 0.00 4.00
1688 1807 2.701780 CCAGCTCGCTCGTACAGGT 61.702 63.158 0.00 0.00 0.00 4.00
1689 1808 1.213013 CAGCTCGCTCGTACAGGTT 59.787 57.895 0.00 0.00 0.00 3.50
1690 1809 1.073216 CAGCTCGCTCGTACAGGTTG 61.073 60.000 0.00 0.00 0.00 3.77
1691 1810 2.445438 GCTCGCTCGTACAGGTTGC 61.445 63.158 0.00 0.00 0.00 4.17
1692 1811 1.805945 CTCGCTCGTACAGGTTGCC 60.806 63.158 0.00 0.00 0.00 4.52
1693 1812 2.813908 CGCTCGTACAGGTTGCCC 60.814 66.667 0.00 0.00 0.00 5.36
1694 1813 2.345991 GCTCGTACAGGTTGCCCA 59.654 61.111 0.00 0.00 0.00 5.36
1695 1814 1.741770 GCTCGTACAGGTTGCCCAG 60.742 63.158 0.00 0.00 0.00 4.45
1696 1815 1.741770 CTCGTACAGGTTGCCCAGC 60.742 63.158 0.00 0.00 0.00 4.85
1697 1816 2.172483 CTCGTACAGGTTGCCCAGCT 62.172 60.000 0.00 0.00 0.00 4.24
1698 1817 1.741770 CGTACAGGTTGCCCAGCTC 60.742 63.158 0.00 0.00 0.00 4.09
1699 1818 1.741770 GTACAGGTTGCCCAGCTCG 60.742 63.158 0.00 0.00 0.00 5.03
1700 1819 3.605749 TACAGGTTGCCCAGCTCGC 62.606 63.158 0.00 0.00 0.00 5.03
1701 1820 4.711949 CAGGTTGCCCAGCTCGCT 62.712 66.667 4.06 0.00 0.00 4.93
1702 1821 4.400961 AGGTTGCCCAGCTCGCTC 62.401 66.667 4.06 0.00 0.00 5.03
1705 1824 3.378602 TTGCCCAGCTCGCTCGTA 61.379 61.111 4.06 0.00 0.00 3.43
1706 1825 3.642778 TTGCCCAGCTCGCTCGTAC 62.643 63.158 4.06 0.00 0.00 3.67
1707 1826 4.129737 GCCCAGCTCGCTCGTACA 62.130 66.667 0.00 0.00 0.00 2.90
1711 1830 1.213013 CAGCTCGCTCGTACAGGTT 59.787 57.895 0.00 0.00 0.00 3.50
1821 1940 5.546416 CAGCATTTCTGGGCAATGATGCA 62.546 47.826 8.58 0.00 44.33 3.96
1881 2000 1.213678 TCTCATTGAGGCATTGGGGAG 59.786 52.381 13.59 0.00 0.00 4.30
1882 2001 0.259647 TCATTGAGGCATTGGGGAGG 59.740 55.000 0.00 0.00 0.00 4.30
1883 2002 0.757935 CATTGAGGCATTGGGGAGGG 60.758 60.000 0.00 0.00 0.00 4.30
1884 2003 2.594365 ATTGAGGCATTGGGGAGGGC 62.594 60.000 0.00 0.00 34.40 5.19
1885 2004 3.743017 GAGGCATTGGGGAGGGCA 61.743 66.667 0.00 0.00 37.02 5.36
1926 2050 2.627699 TCAGGGTGTTTGAGAAAATGGC 59.372 45.455 0.00 0.00 0.00 4.40
1939 2063 1.680338 AAATGGCGCAAGAGGGATAC 58.320 50.000 10.83 0.00 43.02 2.24
2031 2155 7.553044 GTCCATTAGGTATTACAAGGATATGGC 59.447 40.741 0.00 0.00 35.89 4.40
2317 2441 1.006220 CAGGTTTGGGAAAAGCGGC 60.006 57.895 0.00 0.00 35.49 6.53
2434 2558 2.283145 AGGTTGATGCTGCTGTTTCT 57.717 45.000 0.00 0.00 0.00 2.52
2497 2621 7.121315 GGGAGAGTTGTTTATAGCAAACTGAAT 59.879 37.037 2.00 0.00 0.00 2.57
2596 2720 3.740044 AATTCACGCAACTATTGTCGG 57.260 42.857 9.16 1.59 35.52 4.79
2612 2736 2.414785 CGGGCTAATGGTTGGCACC 61.415 63.158 0.00 0.00 44.56 5.01
2630 2754 4.158394 GGCACCTGTGATTTGTGAACATAT 59.842 41.667 0.51 0.00 31.66 1.78
2633 2757 7.312154 GCACCTGTGATTTGTGAACATATTTA 58.688 34.615 0.51 0.00 31.66 1.40
2635 2759 7.485913 CACCTGTGATTTGTGAACATATTTAGC 59.514 37.037 0.00 0.00 31.66 3.09
2643 2767 3.374058 GTGAACATATTTAGCTGGCACGT 59.626 43.478 0.00 0.00 0.00 4.49
2663 2787 4.873827 ACGTAACTATTTGGTATGCTGGTG 59.126 41.667 0.00 0.00 0.00 4.17
2738 3736 2.583143 AGTTTGGCTGGTGAAAGGTAC 58.417 47.619 0.00 0.00 0.00 3.34
2801 3844 6.726258 CATGCATACCATGTTATCGTGTAT 57.274 37.500 0.00 0.00 45.05 2.29
2802 3845 7.826260 CATGCATACCATGTTATCGTGTATA 57.174 36.000 0.00 0.00 45.05 1.47
2803 3846 8.424274 CATGCATACCATGTTATCGTGTATAT 57.576 34.615 0.00 0.00 45.05 0.86
2804 3847 9.528018 CATGCATACCATGTTATCGTGTATATA 57.472 33.333 0.00 0.00 45.05 0.86
2874 3917 6.073327 TGATGAGTAGTGGATTAAGTAGCG 57.927 41.667 0.00 0.00 0.00 4.26
2892 3935 3.764885 GCGGAAAGCTACATGAAACAT 57.235 42.857 0.00 0.00 44.04 2.71
2902 3945 6.672147 AGCTACATGAAACATTGAGACAAAC 58.328 36.000 0.00 0.00 0.00 2.93
2911 3955 8.819015 TGAAACATTGAGACAAACAATCAAATG 58.181 29.630 0.00 0.00 36.59 2.32
2919 3963 6.981722 AGACAAACAATCAAATGGGTAGAAC 58.018 36.000 0.00 0.00 0.00 3.01
2928 3972 5.253330 TCAAATGGGTAGAACAGAATGGAC 58.747 41.667 0.00 0.00 43.62 4.02
2945 3989 5.947228 ATGGACAGACATGTACTGTTTTG 57.053 39.130 23.09 7.92 46.57 2.44
2967 4011 1.963515 TGTGTACTTCTGCTGCTCTGA 59.036 47.619 0.00 0.00 0.00 3.27
3039 4123 2.555227 GGGGAAATGCAGAGAACTTGGA 60.555 50.000 0.00 0.00 0.00 3.53
3078 4173 6.904626 AGCCTGATGTATCCTTGAATAACTT 58.095 36.000 0.00 0.00 0.00 2.66
3154 4250 7.116948 CCGATCCTTAGCTGAACTTGTTATATG 59.883 40.741 0.00 0.00 0.00 1.78
3155 4251 7.867909 CGATCCTTAGCTGAACTTGTTATATGA 59.132 37.037 0.00 0.00 0.00 2.15
3156 4252 9.717942 GATCCTTAGCTGAACTTGTTATATGAT 57.282 33.333 0.00 0.00 0.00 2.45
3157 4253 8.893219 TCCTTAGCTGAACTTGTTATATGATG 57.107 34.615 0.00 0.00 0.00 3.07
3158 4254 7.442364 TCCTTAGCTGAACTTGTTATATGATGC 59.558 37.037 0.00 0.00 0.00 3.91
3159 4255 7.308229 CCTTAGCTGAACTTGTTATATGATGCC 60.308 40.741 0.00 0.00 0.00 4.40
3160 4256 5.439721 AGCTGAACTTGTTATATGATGCCA 58.560 37.500 0.00 0.00 0.00 4.92
3161 4257 5.530171 AGCTGAACTTGTTATATGATGCCAG 59.470 40.000 0.00 0.00 0.00 4.85
3162 4258 5.297776 GCTGAACTTGTTATATGATGCCAGT 59.702 40.000 0.00 0.00 0.00 4.00
3163 4259 6.183360 GCTGAACTTGTTATATGATGCCAGTT 60.183 38.462 0.00 0.00 0.00 3.16
3164 4260 7.012327 GCTGAACTTGTTATATGATGCCAGTTA 59.988 37.037 0.00 0.00 0.00 2.24
3165 4261 8.978874 TGAACTTGTTATATGATGCCAGTTAT 57.021 30.769 0.00 0.00 0.00 1.89
3166 4262 9.056005 TGAACTTGTTATATGATGCCAGTTATC 57.944 33.333 0.00 0.00 0.00 1.75
3167 4263 8.978874 AACTTGTTATATGATGCCAGTTATCA 57.021 30.769 0.00 0.00 38.76 2.15
3168 4264 9.578576 AACTTGTTATATGATGCCAGTTATCAT 57.421 29.630 0.00 0.00 44.86 2.45
3178 4274 9.970553 ATGATGCCAGTTATCATATATGAAGTT 57.029 29.630 19.03 6.07 41.99 2.66
3179 4275 9.440773 TGATGCCAGTTATCATATATGAAGTTC 57.559 33.333 19.03 10.06 40.69 3.01
3180 4276 9.440773 GATGCCAGTTATCATATATGAAGTTCA 57.559 33.333 19.03 8.27 40.69 3.18
3181 4277 9.797642 ATGCCAGTTATCATATATGAAGTTCAA 57.202 29.630 19.03 6.31 40.69 2.69
3182 4278 9.797642 TGCCAGTTATCATATATGAAGTTCAAT 57.202 29.630 19.03 7.57 40.69 2.57
3191 4287 8.685427 TCATATATGAAGTTCAATTGTTGTGGG 58.315 33.333 13.12 0.00 33.08 4.61
3192 4288 6.916360 ATATGAAGTTCAATTGTTGTGGGT 57.084 33.333 10.14 0.00 0.00 4.51
3193 4289 5.612725 ATGAAGTTCAATTGTTGTGGGTT 57.387 34.783 10.14 0.00 0.00 4.11
3194 4290 6.723298 ATGAAGTTCAATTGTTGTGGGTTA 57.277 33.333 10.14 0.00 0.00 2.85
3195 4291 6.723298 TGAAGTTCAATTGTTGTGGGTTAT 57.277 33.333 2.20 0.00 0.00 1.89
3196 4292 6.744112 TGAAGTTCAATTGTTGTGGGTTATC 58.256 36.000 2.20 0.00 0.00 1.75
3197 4293 6.322456 TGAAGTTCAATTGTTGTGGGTTATCA 59.678 34.615 2.20 0.00 0.00 2.15
3198 4294 6.916360 AGTTCAATTGTTGTGGGTTATCAT 57.084 33.333 5.13 0.00 0.00 2.45
3199 4295 8.415950 AAGTTCAATTGTTGTGGGTTATCATA 57.584 30.769 5.13 0.00 0.00 2.15
3200 4296 8.593945 AGTTCAATTGTTGTGGGTTATCATAT 57.406 30.769 5.13 0.00 0.00 1.78
3201 4297 9.693739 AGTTCAATTGTTGTGGGTTATCATATA 57.306 29.630 5.13 0.00 0.00 0.86
3204 4300 9.467796 TCAATTGTTGTGGGTTATCATATAACA 57.532 29.630 5.13 0.00 0.00 2.41
3207 4303 8.871629 TTGTTGTGGGTTATCATATAACAAGT 57.128 30.769 10.92 0.00 33.44 3.16
3208 4304 8.871629 TGTTGTGGGTTATCATATAACAAGTT 57.128 30.769 10.92 0.00 0.00 2.66
3209 4305 9.961264 TGTTGTGGGTTATCATATAACAAGTTA 57.039 29.630 10.92 0.00 0.00 2.24
3424 4522 3.625764 GGTGTTACTCTTTGTTCTGCACA 59.374 43.478 0.00 0.00 0.00 4.57
3425 4523 4.495844 GGTGTTACTCTTTGTTCTGCACAC 60.496 45.833 0.00 0.00 33.98 3.82
3481 4580 8.367911 TCTGTAACTACCTATGCCATTATCTTG 58.632 37.037 0.00 0.00 0.00 3.02
3495 4594 2.604046 ATCTTGACACGATGTAGGCC 57.396 50.000 0.00 0.00 0.00 5.19
3500 4599 1.079405 ACACGATGTAGGCCGTTGG 60.079 57.895 0.00 0.00 36.83 3.77
3501 4600 1.813753 CACGATGTAGGCCGTTGGG 60.814 63.158 0.00 0.00 36.83 4.12
3520 4625 2.491693 GGGTTTTCATGAAGATGCGGAA 59.508 45.455 8.41 0.00 0.00 4.30
3524 4629 5.401550 GTTTTCATGAAGATGCGGAATCAA 58.598 37.500 8.41 0.00 37.81 2.57
3534 4639 7.500227 TGAAGATGCGGAATCAAGAGATAATTT 59.500 33.333 0.00 0.00 37.81 1.82
3556 4661 2.012673 CCAGAACAGTTGCTATCAGGC 58.987 52.381 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.674471 AAACTCCCGAACAAAATTTCAAAAA 57.326 28.000 0.00 0.00 0.00 1.94
58 68 8.903570 AATTTCGAACAAAATTTGAAAAACCC 57.096 26.923 13.19 0.00 35.78 4.11
209 230 7.449934 ACATTTTCTGAAACGTGAACATTTC 57.550 32.000 16.91 0.00 35.73 2.17
353 379 6.317789 TGAAAAGTGGAGACATTTCATGAC 57.682 37.500 0.00 0.00 41.79 3.06
717 790 1.472878 CAAGCACTACTAGCCACTCGA 59.527 52.381 0.00 0.00 0.00 4.04
997 1101 2.517166 GAGGAGGCGGGCCATTTC 60.517 66.667 12.97 0.48 38.92 2.17
1089 1196 1.543944 GGGCTGATTTGGTGGGGTTG 61.544 60.000 0.00 0.00 0.00 3.77
1114 1221 4.798682 GGGGAGAAGGGGAGCGGA 62.799 72.222 0.00 0.00 0.00 5.54
1127 1234 0.922243 GGGACTGGGGTTAATGGGGA 60.922 60.000 0.00 0.00 0.00 4.81
1383 1502 3.267483 GTTGCAGGTATGTACGGAATGT 58.733 45.455 0.00 0.00 0.00 2.71
1385 1504 3.620427 TGTTGCAGGTATGTACGGAAT 57.380 42.857 0.00 0.00 0.00 3.01
1446 1565 4.704103 TCCAGGGCAGGCTCGACT 62.704 66.667 0.00 0.00 0.00 4.18
1481 1600 2.027469 GTGGTTAGGTCCGGAAAGATGT 60.027 50.000 5.23 0.00 0.00 3.06
1503 1622 2.961741 AGTATCCATGACGATCTGCAGT 59.038 45.455 14.67 0.42 0.00 4.40
1513 1632 3.201290 CAGCAACCAGAGTATCCATGAC 58.799 50.000 0.00 0.00 33.66 3.06
1533 1652 1.529010 CTTGTTGACCTGCCTGGCA 60.529 57.895 21.96 21.96 40.22 4.92
1687 1806 3.642778 TACGAGCGAGCTGGGCAAC 62.643 63.158 11.55 2.33 0.00 4.17
1688 1807 3.378602 TACGAGCGAGCTGGGCAA 61.379 61.111 11.55 0.00 0.00 4.52
1689 1808 4.129737 GTACGAGCGAGCTGGGCA 62.130 66.667 11.55 0.00 0.00 5.36
1690 1809 4.129737 TGTACGAGCGAGCTGGGC 62.130 66.667 11.55 0.00 0.00 5.36
1691 1810 2.103143 CTGTACGAGCGAGCTGGG 59.897 66.667 11.55 2.09 0.00 4.45
1692 1811 2.103143 CCTGTACGAGCGAGCTGG 59.897 66.667 0.84 3.56 0.00 4.85
1693 1812 1.073216 CAACCTGTACGAGCGAGCTG 61.073 60.000 0.84 0.00 0.00 4.24
1694 1813 1.213013 CAACCTGTACGAGCGAGCT 59.787 57.895 0.00 0.00 0.00 4.09
1695 1814 2.445438 GCAACCTGTACGAGCGAGC 61.445 63.158 0.00 0.00 0.00 5.03
1696 1815 1.805945 GGCAACCTGTACGAGCGAG 60.806 63.158 0.00 0.00 0.00 5.03
1697 1816 2.260434 GGCAACCTGTACGAGCGA 59.740 61.111 0.00 0.00 0.00 4.93
1821 1940 3.978164 GCACTAGCCCATCCTCCT 58.022 61.111 0.00 0.00 33.58 3.69
1840 1959 2.093890 TGGCAATGCGAAACATCATCT 58.906 42.857 0.00 0.00 38.34 2.90
1926 2050 1.067582 GGACCGTATCCCTCTTGCG 59.932 63.158 0.00 0.00 42.46 4.85
1939 2063 1.520787 GGCCATCGTAGTTGGACCG 60.521 63.158 0.00 0.00 36.14 4.79
1984 2108 1.075374 CTGTCCAAATCCCCCAGTGAA 59.925 52.381 0.00 0.00 0.00 3.18
2011 2135 5.186409 GTCCGCCATATCCTTGTAATACCTA 59.814 44.000 0.00 0.00 0.00 3.08
2317 2441 3.243501 CCTCCCAAATGTTCAACACTGTG 60.244 47.826 6.19 6.19 0.00 3.66
2434 2558 2.571653 CCTAAGTGATTCCTCCACCACA 59.428 50.000 0.00 0.00 35.23 4.17
2497 2621 1.600638 CATCTCCAGCAGCCTGTCA 59.399 57.895 0.00 0.00 37.38 3.58
2612 2736 7.699391 CCAGCTAAATATGTTCACAAATCACAG 59.301 37.037 0.00 0.00 0.00 3.66
2630 2754 4.393680 CCAAATAGTTACGTGCCAGCTAAA 59.606 41.667 0.00 0.00 0.00 1.85
2633 2757 2.290071 ACCAAATAGTTACGTGCCAGCT 60.290 45.455 0.00 0.00 0.00 4.24
2635 2759 4.260620 GCATACCAAATAGTTACGTGCCAG 60.261 45.833 0.00 0.00 0.00 4.85
2643 2767 6.094881 GCTTTCACCAGCATACCAAATAGTTA 59.905 38.462 0.00 0.00 39.83 2.24
2663 2787 6.524101 TTAAACCCATATGGAACTGCTTTC 57.476 37.500 24.00 0.00 37.39 2.62
2738 3736 7.819415 TGTCAGAAATATGGACAGTCAAGTAAG 59.181 37.037 2.17 0.00 36.69 2.34
2739 3737 7.676004 TGTCAGAAATATGGACAGTCAAGTAA 58.324 34.615 2.17 0.00 36.69 2.24
2740 3738 7.239763 TGTCAGAAATATGGACAGTCAAGTA 57.760 36.000 2.17 0.00 36.69 2.24
2741 3739 6.114187 TGTCAGAAATATGGACAGTCAAGT 57.886 37.500 2.17 0.00 36.69 3.16
2750 3762 5.263599 AGCCAAACATGTCAGAAATATGGA 58.736 37.500 0.00 0.00 31.12 3.41
2755 3767 7.230849 TGAAATAGCCAAACATGTCAGAAAT 57.769 32.000 0.00 0.00 0.00 2.17
2803 3846 8.527810 CCCCATCAAAACTAGCAAGTAAAAATA 58.472 33.333 0.00 0.00 33.75 1.40
2804 3847 7.016170 ACCCCATCAAAACTAGCAAGTAAAAAT 59.984 33.333 0.00 0.00 33.75 1.82
2805 3848 6.325286 ACCCCATCAAAACTAGCAAGTAAAAA 59.675 34.615 0.00 0.00 33.75 1.94
2806 3849 5.836358 ACCCCATCAAAACTAGCAAGTAAAA 59.164 36.000 0.00 0.00 33.75 1.52
2807 3850 5.390387 ACCCCATCAAAACTAGCAAGTAAA 58.610 37.500 0.00 0.00 33.75 2.01
2808 3851 4.993028 ACCCCATCAAAACTAGCAAGTAA 58.007 39.130 0.00 0.00 33.75 2.24
2809 3852 4.650972 ACCCCATCAAAACTAGCAAGTA 57.349 40.909 0.00 0.00 33.75 2.24
2810 3853 3.525800 ACCCCATCAAAACTAGCAAGT 57.474 42.857 0.00 0.00 37.65 3.16
2811 3854 6.378280 AGAATAACCCCATCAAAACTAGCAAG 59.622 38.462 0.00 0.00 0.00 4.01
2812 3855 6.152661 CAGAATAACCCCATCAAAACTAGCAA 59.847 38.462 0.00 0.00 0.00 3.91
2813 3856 5.652014 CAGAATAACCCCATCAAAACTAGCA 59.348 40.000 0.00 0.00 0.00 3.49
2814 3857 5.885912 TCAGAATAACCCCATCAAAACTAGC 59.114 40.000 0.00 0.00 0.00 3.42
2815 3858 7.112779 AGTCAGAATAACCCCATCAAAACTAG 58.887 38.462 0.00 0.00 0.00 2.57
2816 3859 7.027874 AGTCAGAATAACCCCATCAAAACTA 57.972 36.000 0.00 0.00 0.00 2.24
2817 3860 5.892348 AGTCAGAATAACCCCATCAAAACT 58.108 37.500 0.00 0.00 0.00 2.66
2818 3861 7.696992 TTAGTCAGAATAACCCCATCAAAAC 57.303 36.000 0.00 0.00 0.00 2.43
2819 3862 8.893563 ATTTAGTCAGAATAACCCCATCAAAA 57.106 30.769 0.00 0.00 0.00 2.44
2820 3863 8.336235 AGATTTAGTCAGAATAACCCCATCAAA 58.664 33.333 0.00 0.00 0.00 2.69
2821 3864 7.872138 AGATTTAGTCAGAATAACCCCATCAA 58.128 34.615 0.00 0.00 0.00 2.57
2822 3865 7.451731 AGATTTAGTCAGAATAACCCCATCA 57.548 36.000 0.00 0.00 0.00 3.07
2823 3866 7.255277 GCAAGATTTAGTCAGAATAACCCCATC 60.255 40.741 0.00 0.00 0.00 3.51
2824 3867 6.547510 GCAAGATTTAGTCAGAATAACCCCAT 59.452 38.462 0.00 0.00 0.00 4.00
2825 3868 5.885912 GCAAGATTTAGTCAGAATAACCCCA 59.114 40.000 0.00 0.00 0.00 4.96
2874 3917 6.072508 TGTCTCAATGTTTCATGTAGCTTTCC 60.073 38.462 0.00 0.00 0.00 3.13
2886 3929 8.277713 CCATTTGATTGTTTGTCTCAATGTTTC 58.722 33.333 0.00 0.00 35.94 2.78
2892 3935 5.867903 ACCCATTTGATTGTTTGTCTCAA 57.132 34.783 0.00 0.00 0.00 3.02
2902 3945 6.377996 TCCATTCTGTTCTACCCATTTGATTG 59.622 38.462 0.00 0.00 0.00 2.67
2911 3955 3.260884 TGTCTGTCCATTCTGTTCTACCC 59.739 47.826 0.00 0.00 0.00 3.69
2919 3963 4.825422 ACAGTACATGTCTGTCCATTCTG 58.175 43.478 19.10 10.56 41.52 3.02
2928 3972 5.879237 ACACAACAAAACAGTACATGTCTG 58.121 37.500 18.12 18.12 43.00 3.51
2945 3989 2.478134 CAGAGCAGCAGAAGTACACAAC 59.522 50.000 0.00 0.00 0.00 3.32
2967 4011 8.105829 AGATTCCATCTGATGTTTGTAGTTCTT 58.894 33.333 15.95 0.00 38.44 2.52
3017 4061 2.517959 CAAGTTCTCTGCATTTCCCCA 58.482 47.619 0.00 0.00 0.00 4.96
3099 4195 7.813645 ACCGGTTCAACTTTCAAGTATTAATC 58.186 34.615 0.00 0.00 38.57 1.75
3101 4197 7.388500 CCTACCGGTTCAACTTTCAAGTATTAA 59.612 37.037 15.04 0.00 38.57 1.40
3132 4228 7.442364 GCATCATATAACAAGTTCAGCTAAGGA 59.558 37.037 0.00 0.00 0.00 3.36
3138 4234 5.297776 ACTGGCATCATATAACAAGTTCAGC 59.702 40.000 0.00 0.00 0.00 4.26
3154 4250 9.440773 TGAACTTCATATATGATAACTGGCATC 57.559 33.333 16.06 6.00 36.56 3.91
3155 4251 9.797642 TTGAACTTCATATATGATAACTGGCAT 57.202 29.630 16.06 0.00 36.56 4.40
3156 4252 9.797642 ATTGAACTTCATATATGATAACTGGCA 57.202 29.630 16.06 6.22 36.56 4.92
3165 4261 8.685427 CCCACAACAATTGAACTTCATATATGA 58.315 33.333 13.59 11.49 34.44 2.15
3166 4262 8.469200 ACCCACAACAATTGAACTTCATATATG 58.531 33.333 13.59 6.36 0.00 1.78
3167 4263 8.593945 ACCCACAACAATTGAACTTCATATAT 57.406 30.769 13.59 0.00 0.00 0.86
3168 4264 8.415950 AACCCACAACAATTGAACTTCATATA 57.584 30.769 13.59 0.00 0.00 0.86
3169 4265 6.916360 ACCCACAACAATTGAACTTCATAT 57.084 33.333 13.59 0.00 0.00 1.78
3170 4266 6.723298 AACCCACAACAATTGAACTTCATA 57.277 33.333 13.59 0.00 0.00 2.15
3171 4267 5.612725 AACCCACAACAATTGAACTTCAT 57.387 34.783 13.59 0.00 0.00 2.57
3172 4268 6.322456 TGATAACCCACAACAATTGAACTTCA 59.678 34.615 13.59 0.00 0.00 3.02
3173 4269 6.744112 TGATAACCCACAACAATTGAACTTC 58.256 36.000 13.59 0.00 0.00 3.01
3174 4270 6.723298 TGATAACCCACAACAATTGAACTT 57.277 33.333 13.59 0.00 0.00 2.66
3175 4271 6.916360 ATGATAACCCACAACAATTGAACT 57.084 33.333 13.59 0.00 0.00 3.01
3178 4274 9.467796 TGTTATATGATAACCCACAACAATTGA 57.532 29.630 13.59 0.00 0.00 2.57
3181 4277 9.474313 ACTTGTTATATGATAACCCACAACAAT 57.526 29.630 6.85 0.00 35.01 2.71
3182 4278 8.871629 ACTTGTTATATGATAACCCACAACAA 57.128 30.769 6.85 0.00 34.51 2.83
3183 4279 8.871629 AACTTGTTATATGATAACCCACAACA 57.128 30.769 6.85 0.00 0.00 3.33
3198 4294 9.828852 CCGTTTGCAATTAGTTAACTTGTTATA 57.171 29.630 14.49 0.00 0.00 0.98
3199 4295 7.810759 CCCGTTTGCAATTAGTTAACTTGTTAT 59.189 33.333 14.49 0.29 0.00 1.89
3200 4296 7.140048 CCCGTTTGCAATTAGTTAACTTGTTA 58.860 34.615 14.49 0.00 0.00 2.41
3201 4297 5.980715 CCCGTTTGCAATTAGTTAACTTGTT 59.019 36.000 14.49 6.40 0.00 2.83
3202 4298 5.525199 CCCGTTTGCAATTAGTTAACTTGT 58.475 37.500 14.49 0.00 0.00 3.16
3203 4299 4.384547 GCCCGTTTGCAATTAGTTAACTTG 59.615 41.667 14.49 7.43 0.00 3.16
3204 4300 4.038162 TGCCCGTTTGCAATTAGTTAACTT 59.962 37.500 14.49 0.00 38.56 2.66
3205 4301 3.570550 TGCCCGTTTGCAATTAGTTAACT 59.429 39.130 13.68 13.68 38.56 2.24
3206 4302 3.671459 GTGCCCGTTTGCAATTAGTTAAC 59.329 43.478 0.00 0.00 44.11 2.01
3207 4303 3.318275 TGTGCCCGTTTGCAATTAGTTAA 59.682 39.130 0.00 0.00 44.11 2.01
3208 4304 2.885266 TGTGCCCGTTTGCAATTAGTTA 59.115 40.909 0.00 0.00 44.11 2.24
3209 4305 1.683917 TGTGCCCGTTTGCAATTAGTT 59.316 42.857 0.00 0.00 44.11 2.24
3210 4306 1.323412 TGTGCCCGTTTGCAATTAGT 58.677 45.000 0.00 0.00 44.11 2.24
3211 4307 2.652941 ATGTGCCCGTTTGCAATTAG 57.347 45.000 0.00 0.00 44.11 1.73
3212 4308 2.560542 AGAATGTGCCCGTTTGCAATTA 59.439 40.909 0.00 0.00 44.11 1.40
3213 4309 1.344114 AGAATGTGCCCGTTTGCAATT 59.656 42.857 0.00 0.00 44.11 2.32
3214 4310 0.968405 AGAATGTGCCCGTTTGCAAT 59.032 45.000 0.00 0.00 44.11 3.56
3215 4311 1.268352 GTAGAATGTGCCCGTTTGCAA 59.732 47.619 0.00 0.00 44.11 4.08
3216 4312 0.878416 GTAGAATGTGCCCGTTTGCA 59.122 50.000 0.00 0.00 39.37 4.08
3481 4580 1.082117 CCAACGGCCTACATCGTGTC 61.082 60.000 0.00 0.00 39.70 3.67
3495 4594 3.244976 GCATCTTCATGAAAACCCAACG 58.755 45.455 9.88 0.00 30.57 4.10
3500 4599 3.848272 TTCCGCATCTTCATGAAAACC 57.152 42.857 9.88 0.00 30.57 3.27
3501 4600 4.985413 TGATTCCGCATCTTCATGAAAAC 58.015 39.130 9.88 0.00 32.34 2.43
3520 4625 7.637511 ACTGTTCTGGGAAATTATCTCTTGAT 58.362 34.615 0.00 0.00 36.74 2.57
3524 4629 5.649831 GCAACTGTTCTGGGAAATTATCTCT 59.350 40.000 0.00 0.00 0.00 3.10
3534 4639 2.237143 CCTGATAGCAACTGTTCTGGGA 59.763 50.000 0.00 0.00 0.00 4.37
3556 4661 6.259550 TCACGTGATATATCAGTCCTCATG 57.740 41.667 15.76 3.15 37.51 3.07


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

AutoCloner maintained by Alex Coulton.