Multiple sequence alignment - TraesCS1A01G217000

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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 TraesCS1A01G217000 chr1A 100.000 3332 0 0 1 3332 384777183 384773852 0.000000e+00 6154
1 TraesCS1A01G217000 chr1B 91.319 2304 104 39 962 3218 413205855 413203601 0.000000e+00 3059
2 TraesCS1A01G217000 chr1D 92.447 1827 79 24 802 2586 305769910 305768101 0.000000e+00 2555
3 TraesCS1A01G217000 chr1D 90.330 424 23 3 2657 3079 305768075 305767669 1.050000e-149 540
4 TraesCS1A01G217000 chr1D 94.767 172 9 0 3161 3332 305767615 305767444 5.480000e-68 268
5 TraesCS1A01G217000 chr5B 98.753 802 10 0 1 802 709380199 709379398 0.000000e+00 1426
6 TraesCS1A01G217000 chr5B 92.020 802 55 4 1 801 416127048 416127841 0.000000e+00 1118
7 TraesCS1A01G217000 chr6B 93.250 800 47 4 2 801 299734197 299734989 0.000000e+00 1171
8 TraesCS1A01G217000 chr6B 91.760 801 60 5 2 801 633694724 633693929 0.000000e+00 1109
9 TraesCS1A01G217000 chr6B 85.625 160 21 2 2021 2179 509259636 509259794 2.060000e-37 167
10 TraesCS1A01G217000 chr3B 92.625 800 53 5 2 801 452509068 452509861 0.000000e+00 1146
11 TraesCS1A01G217000 chr2B 92.375 800 55 5 2 801 528914954 528915747 0.000000e+00 1134
12 TraesCS1A01G217000 chr2B 91.895 802 58 6 2 802 462859112 462859907 0.000000e+00 1114
13 TraesCS1A01G217000 chr2B 91.885 801 59 5 2 801 731135228 731134433 0.000000e+00 1114
14 TraesCS1A01G217000 chr7B 89.677 804 70 9 2 798 699157096 699157893 0.000000e+00 1013
15 TraesCS1A01G217000 chr6D 85.535 159 21 2 2022 2179 315817043 315816886 7.400000e-37 165
16 TraesCS1A01G217000 chr2D 83.019 159 25 2 2022 2179 496637761 496637604 3.470000e-30 143


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 TraesCS1A01G217000 chr1A 384773852 384777183 3331 True 6154 6154 100.000000 1 3332 1 chr1A.!!$R1 3331
1 TraesCS1A01G217000 chr1B 413203601 413205855 2254 True 3059 3059 91.319000 962 3218 1 chr1B.!!$R1 2256
2 TraesCS1A01G217000 chr1D 305767444 305769910 2466 True 1121 2555 92.514667 802 3332 3 chr1D.!!$R1 2530
3 TraesCS1A01G217000 chr5B 709379398 709380199 801 True 1426 1426 98.753000 1 802 1 chr5B.!!$R1 801
4 TraesCS1A01G217000 chr5B 416127048 416127841 793 False 1118 1118 92.020000 1 801 1 chr5B.!!$F1 800
5 TraesCS1A01G217000 chr6B 299734197 299734989 792 False 1171 1171 93.250000 2 801 1 chr6B.!!$F1 799
6 TraesCS1A01G217000 chr6B 633693929 633694724 795 True 1109 1109 91.760000 2 801 1 chr6B.!!$R1 799
7 TraesCS1A01G217000 chr3B 452509068 452509861 793 False 1146 1146 92.625000 2 801 1 chr3B.!!$F1 799
8 TraesCS1A01G217000 chr2B 528914954 528915747 793 False 1134 1134 92.375000 2 801 1 chr2B.!!$F2 799
9 TraesCS1A01G217000 chr2B 462859112 462859907 795 False 1114 1114 91.895000 2 802 1 chr2B.!!$F1 800
10 TraesCS1A01G217000 chr2B 731134433 731135228 795 True 1114 1114 91.885000 2 801 1 chr2B.!!$R1 799
11 TraesCS1A01G217000 chr7B 699157096 699157893 797 False 1013 1013 89.677000 2 798 1 chr7B.!!$F1 796

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
980 1001 0.320771 GAGCTCGGCCAAGAAACTGA 60.321 55.0 2.24 0.0 0.0 3.41 F
1872 1928 0.387878 CACGAGGACAGCTCACAGAC 60.388 60.0 0.00 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 1992 0.443869 ATCGACGCATCAACAGCAAC 59.556 50.0 0.0 0.0 0.0 4.17 R
3197 3349 0.302288 TTGTCGGTGTTCTTTTCGCG 59.698 50.0 0.0 0.0 0.0 5.87 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 1.348036 GGTCCAAGGAGTAGCACAGTT 59.652 52.381 0.00 0.00 0.00 3.16
368 370 8.005192 TCTCCATAGAGATGCATGATATACAC 57.995 38.462 2.46 0.00 44.42 2.90
872 889 4.311208 TCCCTCCAACCCTTTATATCCT 57.689 45.455 0.00 0.00 0.00 3.24
888 905 3.330720 CTCCACCACCTCCCACCC 61.331 72.222 0.00 0.00 0.00 4.61
919 936 4.845705 GCTCGCTCGCGCTCTCTT 62.846 66.667 5.56 0.00 39.59 2.85
931 952 2.094234 GCGCTCTCTTTCTCTCTTTCCT 60.094 50.000 0.00 0.00 0.00 3.36
934 955 4.321601 CGCTCTCTTTCTCTCTTTCCTTCA 60.322 45.833 0.00 0.00 0.00 3.02
946 967 1.544825 TTCCTTCACCTCCAGCTCCG 61.545 60.000 0.00 0.00 0.00 4.63
949 970 2.570582 CTTCACCTCCAGCTCCGAGC 62.571 65.000 12.80 12.80 42.84 5.03
950 971 3.385384 CACCTCCAGCTCCGAGCA 61.385 66.667 22.29 0.86 45.56 4.26
951 972 2.604686 ACCTCCAGCTCCGAGCAA 60.605 61.111 22.29 6.57 45.56 3.91
952 973 2.186384 CCTCCAGCTCCGAGCAAG 59.814 66.667 22.29 14.95 45.56 4.01
959 980 2.970576 GCTCCGAGCAAGCTAAGAG 58.029 57.895 15.78 13.61 41.89 2.85
960 981 1.151172 GCTCCGAGCAAGCTAAGAGC 61.151 60.000 22.23 22.23 41.89 4.09
980 1001 0.320771 GAGCTCGGCCAAGAAACTGA 60.321 55.000 2.24 0.00 0.00 3.41
994 1015 1.949847 AACTGAGGGAGCGATCGGTG 61.950 60.000 26.49 11.52 35.24 4.94
1188 1218 4.808238 GAGACGACGACGACGGCC 62.808 72.222 21.33 13.00 45.81 6.13
1419 1449 1.800315 CGCCGTCAAGTTCGTCGAT 60.800 57.895 0.00 0.00 31.56 3.59
1428 1458 4.798907 GTCAAGTTCGTCGATGACATGTAT 59.201 41.667 18.18 0.00 41.35 2.29
1441 1471 5.628797 TGACATGTATGTATCCACACCAT 57.371 39.130 0.00 0.00 41.95 3.55
1442 1472 5.610398 TGACATGTATGTATCCACACCATC 58.390 41.667 0.00 0.00 41.95 3.51
1443 1473 5.130145 TGACATGTATGTATCCACACCATCA 59.870 40.000 0.00 0.00 41.95 3.07
1444 1474 6.183361 TGACATGTATGTATCCACACCATCAT 60.183 38.462 0.00 0.00 41.95 2.45
1445 1475 6.233434 ACATGTATGTATCCACACCATCATC 58.767 40.000 0.00 0.00 39.68 2.92
1452 1507 2.137702 TCCACACCATCATCCATCCAT 58.862 47.619 0.00 0.00 0.00 3.41
1468 1523 0.458669 CCATCCCAGCTCATGCAAAC 59.541 55.000 0.00 0.00 42.74 2.93
1476 1531 3.924686 CCAGCTCATGCAAACTCAAAATC 59.075 43.478 0.00 0.00 42.74 2.17
1479 1534 4.521639 AGCTCATGCAAACTCAAAATCTCA 59.478 37.500 0.00 0.00 42.74 3.27
1481 1536 4.801891 TCATGCAAACTCAAAATCTCAGC 58.198 39.130 0.00 0.00 0.00 4.26
1501 1556 4.878397 CAGCCCCAAATTAACAACAAACAA 59.122 37.500 0.00 0.00 0.00 2.83
1505 1560 6.183360 GCCCCAAATTAACAACAAACAAACAT 60.183 34.615 0.00 0.00 0.00 2.71
1533 1588 2.559668 ACACCATCTGCATTCCTGTTTG 59.440 45.455 0.00 0.00 0.00 2.93
1534 1589 2.094390 CACCATCTGCATTCCTGTTTGG 60.094 50.000 0.00 0.00 37.10 3.28
1595 1650 4.935808 ACTGAACCATAATTGAGGTCGTTC 59.064 41.667 4.36 0.00 37.07 3.95
1872 1928 0.387878 CACGAGGACAGCTCACAGAC 60.388 60.000 0.00 0.00 0.00 3.51
2009 2065 6.747280 AGAGAAAACTTGACGAATGTTTGTTG 59.253 34.615 0.00 0.00 34.63 3.33
2010 2066 6.386654 AGAAAACTTGACGAATGTTTGTTGT 58.613 32.000 0.00 0.00 34.63 3.32
2011 2067 6.307800 AGAAAACTTGACGAATGTTTGTTGTG 59.692 34.615 0.00 0.00 34.63 3.33
2012 2068 4.955925 ACTTGACGAATGTTTGTTGTGA 57.044 36.364 0.00 0.00 0.00 3.58
2013 2069 5.303747 ACTTGACGAATGTTTGTTGTGAA 57.696 34.783 0.00 0.00 0.00 3.18
2058 2114 3.072468 TACTTCGCGAGGGTGGGG 61.072 66.667 22.87 4.82 0.00 4.96
2181 2237 2.202987 CTGCAGACCGAGATGGCC 60.203 66.667 8.42 0.00 43.94 5.36
2220 2276 3.872728 TCCATCGACGCCGTCTCG 61.873 66.667 16.07 3.61 37.05 4.04
2337 2402 0.383590 AGCTCACCGTCTGATCGATG 59.616 55.000 0.54 0.00 0.00 3.84
2348 2413 1.000731 CTGATCGATGGAGCTCTTCCC 59.999 57.143 14.64 0.00 46.19 3.97
2350 2415 1.124477 ATCGATGGAGCTCTTCCCCC 61.124 60.000 14.64 0.00 46.19 5.40
2448 2519 4.210724 TGGTACATAGGTGTTGGTTAGC 57.789 45.455 0.00 0.00 39.77 3.09
2497 2572 5.549347 AGGATCGATCATGAATGGAAGAAG 58.451 41.667 25.93 0.00 0.00 2.85
2519 2594 0.940126 ATCGGATTGAGATTGTGCGC 59.060 50.000 0.00 0.00 0.00 6.09
2613 2694 1.597742 TGCTTTGCTTGTCTCCTGTC 58.402 50.000 0.00 0.00 0.00 3.51
2643 2724 6.261826 TCTTTTCCTCTGCTCTTCTTTTTCTG 59.738 38.462 0.00 0.00 0.00 3.02
2744 2826 1.072965 GGATGGCGGAGATTGGAGAAT 59.927 52.381 0.00 0.00 0.00 2.40
2758 2840 3.278574 TGGAGAATAAGCGGGTTTGATG 58.721 45.455 0.00 0.00 0.00 3.07
2804 2886 2.253154 CGCTGCATGGTGTGTGTG 59.747 61.111 0.00 0.00 0.00 3.82
2806 2888 1.008194 GCTGCATGGTGTGTGTGTG 60.008 57.895 0.00 0.00 0.00 3.82
2807 2889 1.727511 GCTGCATGGTGTGTGTGTGT 61.728 55.000 0.00 0.00 0.00 3.72
2808 2890 0.029700 CTGCATGGTGTGTGTGTGTG 59.970 55.000 0.00 0.00 0.00 3.82
2809 2891 0.679321 TGCATGGTGTGTGTGTGTGT 60.679 50.000 0.00 0.00 0.00 3.72
2810 2892 0.248580 GCATGGTGTGTGTGTGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
2811 2893 1.093972 CATGGTGTGTGTGTGTGTGT 58.906 50.000 0.00 0.00 0.00 3.72
2812 2894 1.093972 ATGGTGTGTGTGTGTGTGTG 58.906 50.000 0.00 0.00 0.00 3.82
2813 2895 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
2814 2896 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
2815 2897 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2816 2898 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2817 2899 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2818 2900 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2819 2901 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2820 2902 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2821 2903 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2822 2904 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2823 2905 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2824 2906 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2828 2910 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2885 2970 2.958576 GCGGAAAATGACGGCCAA 59.041 55.556 2.24 0.00 0.00 4.52
3116 3225 2.223203 CCATCAATGCTTCTTCAGACGC 60.223 50.000 0.00 0.00 39.44 5.19
3117 3226 1.442769 TCAATGCTTCTTCAGACGCC 58.557 50.000 3.07 0.00 38.39 5.68
3118 3227 1.002430 TCAATGCTTCTTCAGACGCCT 59.998 47.619 3.07 0.00 38.39 5.52
3119 3228 1.808945 CAATGCTTCTTCAGACGCCTT 59.191 47.619 3.07 0.00 38.39 4.35
3120 3229 2.191128 ATGCTTCTTCAGACGCCTTT 57.809 45.000 3.07 0.00 38.39 3.11
3121 3230 1.967319 TGCTTCTTCAGACGCCTTTT 58.033 45.000 3.07 0.00 38.39 2.27
3122 3231 3.120321 TGCTTCTTCAGACGCCTTTTA 57.880 42.857 3.07 0.00 38.39 1.52
3123 3232 3.674997 TGCTTCTTCAGACGCCTTTTAT 58.325 40.909 3.07 0.00 38.39 1.40
3124 3233 4.827692 TGCTTCTTCAGACGCCTTTTATA 58.172 39.130 3.07 0.00 38.39 0.98
3125 3234 4.630069 TGCTTCTTCAGACGCCTTTTATAC 59.370 41.667 3.07 0.00 38.39 1.47
3126 3235 4.870991 GCTTCTTCAGACGCCTTTTATACT 59.129 41.667 0.00 0.00 33.76 2.12
3127 3236 5.220491 GCTTCTTCAGACGCCTTTTATACTG 60.220 44.000 0.00 0.00 33.76 2.74
3128 3237 5.654603 TCTTCAGACGCCTTTTATACTGA 57.345 39.130 0.00 0.00 33.53 3.41
3129 3238 6.032956 TCTTCAGACGCCTTTTATACTGAA 57.967 37.500 0.00 0.00 40.44 3.02
3130 3239 6.640518 TCTTCAGACGCCTTTTATACTGAAT 58.359 36.000 0.00 0.00 41.33 2.57
3131 3240 7.103641 TCTTCAGACGCCTTTTATACTGAATT 58.896 34.615 0.00 0.00 41.33 2.17
3132 3241 7.606456 TCTTCAGACGCCTTTTATACTGAATTT 59.394 33.333 0.00 0.00 41.33 1.82
3133 3242 7.681939 TCAGACGCCTTTTATACTGAATTTT 57.318 32.000 0.00 0.00 32.66 1.82
3134 3243 8.780846 TCAGACGCCTTTTATACTGAATTTTA 57.219 30.769 0.00 0.00 32.66 1.52
3135 3244 9.221933 TCAGACGCCTTTTATACTGAATTTTAA 57.778 29.630 0.00 0.00 32.66 1.52
3136 3245 9.834628 CAGACGCCTTTTATACTGAATTTTAAA 57.165 29.630 0.00 0.00 0.00 1.52
3158 3267 5.956068 AAAAATCTTCAGAGCTCAGTTCC 57.044 39.130 17.77 0.00 0.00 3.62
3159 3268 3.625649 AATCTTCAGAGCTCAGTTCCC 57.374 47.619 17.77 0.00 0.00 3.97
3197 3349 2.678336 GCAGTTACCATACACAGCTTCC 59.322 50.000 0.00 0.00 0.00 3.46
3225 3377 1.191647 GAACACCGACAAGTTACTGCG 59.808 52.381 0.00 0.00 0.00 5.18
3230 3382 1.779683 GACAAGTTACTGCGGTCGC 59.220 57.895 0.00 8.54 42.35 5.19
3242 3394 1.014352 GCGGTCGCTCCATGTTTATT 58.986 50.000 8.20 0.00 38.26 1.40
3253 3405 7.441157 TCGCTCCATGTTTATTTCGATCTAAAT 59.559 33.333 9.83 9.83 33.69 1.40
3290 3442 4.075963 AGCAAAAGTCCAATGCACAAAT 57.924 36.364 0.00 0.00 42.45 2.32
3326 3478 0.383231 GAAATGGGGCGAGCATCTTG 59.617 55.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.068519 CGTCTCAAATGTAGTGCTGCA 58.931 47.619 0.00 0.00 0.00 4.41
872 889 4.995058 GGGGTGGGAGGTGGTGGA 62.995 72.222 0.00 0.00 0.00 4.02
919 936 3.580458 CTGGAGGTGAAGGAAAGAGAGAA 59.420 47.826 0.00 0.00 0.00 2.87
931 952 2.650116 GCTCGGAGCTGGAGGTGAA 61.650 63.158 22.32 0.00 38.45 3.18
934 955 2.604686 TTGCTCGGAGCTGGAGGT 60.605 61.111 28.42 0.00 42.97 3.85
946 967 2.296658 GCTCGCTCTTAGCTTGCTC 58.703 57.895 0.00 0.00 39.60 4.26
952 973 2.656973 GCCGAGCTCGCTCTTAGC 60.657 66.667 30.49 22.15 40.69 3.09
954 975 2.284798 CTTGGCCGAGCTCGCTCTTA 62.285 60.000 30.49 12.52 40.69 2.10
956 977 4.140599 CTTGGCCGAGCTCGCTCT 62.141 66.667 30.49 0.00 40.69 4.09
957 978 3.649277 TTCTTGGCCGAGCTCGCTC 62.649 63.158 30.49 22.53 39.55 5.03
959 980 2.742372 TTTCTTGGCCGAGCTCGC 60.742 61.111 30.49 23.62 38.18 5.03
960 981 1.374758 AGTTTCTTGGCCGAGCTCG 60.375 57.895 29.06 29.06 39.44 5.03
967 988 0.962855 GCTCCCTCAGTTTCTTGGCC 60.963 60.000 0.00 0.00 0.00 5.36
994 1015 1.669115 CCATCGTCATCATCGGCCC 60.669 63.158 0.00 0.00 0.00 5.80
1188 1218 1.801178 GACACCGCCTTCTTCTTCTTG 59.199 52.381 0.00 0.00 0.00 3.02
1251 1281 0.394565 GGAAGATGCGCTCCAGGTAT 59.605 55.000 9.73 0.00 0.00 2.73
1441 1471 1.062364 GAGCTGGGATGGATGGATGA 58.938 55.000 0.00 0.00 0.00 2.92
1442 1472 0.769247 TGAGCTGGGATGGATGGATG 59.231 55.000 0.00 0.00 0.00 3.51
1443 1473 1.354705 CATGAGCTGGGATGGATGGAT 59.645 52.381 0.00 0.00 0.00 3.41
1444 1474 0.769247 CATGAGCTGGGATGGATGGA 59.231 55.000 0.00 0.00 0.00 3.41
1445 1475 0.894184 GCATGAGCTGGGATGGATGG 60.894 60.000 0.00 0.00 37.91 3.51
1452 1507 0.401356 TGAGTTTGCATGAGCTGGGA 59.599 50.000 0.00 0.00 42.74 4.37
1468 1523 4.813750 AATTTGGGGCTGAGATTTTGAG 57.186 40.909 0.00 0.00 0.00 3.02
1476 1531 4.599047 TTGTTGTTAATTTGGGGCTGAG 57.401 40.909 0.00 0.00 0.00 3.35
1479 1534 4.762289 TGTTTGTTGTTAATTTGGGGCT 57.238 36.364 0.00 0.00 0.00 5.19
1481 1536 6.743575 TGTTTGTTTGTTGTTAATTTGGGG 57.256 33.333 0.00 0.00 0.00 4.96
1501 1556 4.260985 TGCAGATGGTGTAATTCGATGTT 58.739 39.130 0.00 0.00 0.00 2.71
1505 1560 3.876914 GGAATGCAGATGGTGTAATTCGA 59.123 43.478 0.00 0.00 34.55 3.71
1533 1588 1.140252 TCGCTTTAATCCTACTGGCCC 59.860 52.381 0.00 0.00 0.00 5.80
1534 1589 2.614829 TCGCTTTAATCCTACTGGCC 57.385 50.000 0.00 0.00 0.00 5.36
1595 1650 5.034797 CAGTTAAATGATCATGCTGCACTG 58.965 41.667 9.46 12.77 0.00 3.66
1894 1950 0.737019 CAATGGTGAATTGCGGTGGC 60.737 55.000 0.00 0.00 39.36 5.01
1935 1991 0.878086 TCGACGCATCAACAGCAACA 60.878 50.000 0.00 0.00 0.00 3.33
1936 1992 0.443869 ATCGACGCATCAACAGCAAC 59.556 50.000 0.00 0.00 0.00 4.17
1937 1993 0.721154 GATCGACGCATCAACAGCAA 59.279 50.000 0.00 0.00 0.00 3.91
1992 2048 5.743398 ACATTCACAACAAACATTCGTCAAG 59.257 36.000 0.00 0.00 0.00 3.02
2009 2065 3.777465 AGCATCTGCATTCACATTCAC 57.223 42.857 4.79 0.00 45.16 3.18
2010 2066 4.263435 TGTAGCATCTGCATTCACATTCA 58.737 39.130 4.79 0.00 45.16 2.57
2011 2067 4.888038 TGTAGCATCTGCATTCACATTC 57.112 40.909 4.79 0.00 45.16 2.67
2012 2068 4.460034 TGTTGTAGCATCTGCATTCACATT 59.540 37.500 4.79 0.00 45.16 2.71
2013 2069 4.011698 TGTTGTAGCATCTGCATTCACAT 58.988 39.130 4.79 0.00 45.16 3.21
2058 2114 2.692368 TCCATGAGGCTGACCCCC 60.692 66.667 0.00 0.00 36.11 5.40
2062 2118 2.170187 AGTTCATCTCCATGAGGCTGAC 59.830 50.000 0.00 0.00 40.28 3.51
2070 2126 3.070734 CCTCCAGGTAGTTCATCTCCATG 59.929 52.174 0.00 0.00 0.00 3.66
2181 2237 4.208686 GGCGGGTGCTCGAGGTAG 62.209 72.222 15.58 0.00 42.25 3.18
2415 2486 6.110707 CACCTATGTACCAAGAACGGTAAAT 58.889 40.000 0.00 0.00 43.14 1.40
2448 2519 3.480470 ACAATGGCGAAATCCATCCTAG 58.520 45.455 0.00 0.00 45.64 3.02
2497 2572 1.876156 GCACAATCTCAATCCGATCCC 59.124 52.381 0.00 0.00 0.00 3.85
2519 2594 0.802494 AGCTCGTTAAACAATGGGCG 59.198 50.000 0.00 0.00 40.05 6.13
2605 2686 4.656112 AGAGGAAAAGAAACAGACAGGAGA 59.344 41.667 0.00 0.00 0.00 3.71
2613 2694 5.062528 AGAAGAGCAGAGGAAAAGAAACAG 58.937 41.667 0.00 0.00 0.00 3.16
2643 2724 0.960861 CTCCAGAAAGCGGGGGAAAC 60.961 60.000 0.00 0.00 30.39 2.78
2744 2826 3.946604 TGAGCATCAAACCCGCTTA 57.053 47.368 0.00 0.00 45.97 3.09
2804 2886 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2806 2888 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2807 2889 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2808 2890 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2809 2891 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2810 2892 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2811 2893 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
2812 2894 2.538737 GCATACACACACACACACACAC 60.539 50.000 0.00 0.00 0.00 3.82
2813 2895 1.668237 GCATACACACACACACACACA 59.332 47.619 0.00 0.00 0.00 3.72
2814 2896 1.668237 TGCATACACACACACACACAC 59.332 47.619 0.00 0.00 0.00 3.82
2815 2897 1.939255 CTGCATACACACACACACACA 59.061 47.619 0.00 0.00 0.00 3.72
2816 2898 1.939934 ACTGCATACACACACACACAC 59.060 47.619 0.00 0.00 0.00 3.82
2817 2899 1.939255 CACTGCATACACACACACACA 59.061 47.619 0.00 0.00 0.00 3.72
2818 2900 1.939934 ACACTGCATACACACACACAC 59.060 47.619 0.00 0.00 0.00 3.82
2819 2901 2.323968 ACACTGCATACACACACACA 57.676 45.000 0.00 0.00 0.00 3.72
2820 2902 2.286950 CCAACACTGCATACACACACAC 60.287 50.000 0.00 0.00 0.00 3.82
2821 2903 1.946081 CCAACACTGCATACACACACA 59.054 47.619 0.00 0.00 0.00 3.72
2822 2904 1.266718 CCCAACACTGCATACACACAC 59.733 52.381 0.00 0.00 0.00 3.82
2823 2905 1.141858 TCCCAACACTGCATACACACA 59.858 47.619 0.00 0.00 0.00 3.72
2824 2906 1.535462 GTCCCAACACTGCATACACAC 59.465 52.381 0.00 0.00 0.00 3.82
2828 2910 4.485163 GATTTTGTCCCAACACTGCATAC 58.515 43.478 0.00 0.00 34.35 2.39
3095 3204 2.223203 GCGTCTGAAGAAGCATTGATGG 60.223 50.000 12.51 0.00 46.36 3.51
3136 3245 4.764308 GGGAACTGAGCTCTGAAGATTTTT 59.236 41.667 25.49 8.60 0.00 1.94
3137 3246 4.042684 AGGGAACTGAGCTCTGAAGATTTT 59.957 41.667 25.49 9.28 41.13 1.82
3138 3247 3.586618 AGGGAACTGAGCTCTGAAGATTT 59.413 43.478 25.49 9.97 41.13 2.17
3139 3248 3.180507 AGGGAACTGAGCTCTGAAGATT 58.819 45.455 25.49 10.32 41.13 2.40
3140 3249 2.765699 GAGGGAACTGAGCTCTGAAGAT 59.234 50.000 25.49 4.83 44.43 2.40
3141 3250 2.175202 GAGGGAACTGAGCTCTGAAGA 58.825 52.381 25.49 0.00 44.43 2.87
3142 3251 2.178580 AGAGGGAACTGAGCTCTGAAG 58.821 52.381 25.49 12.42 44.43 3.02
3143 3252 2.317371 AGAGGGAACTGAGCTCTGAA 57.683 50.000 25.49 0.00 44.43 3.02
3144 3253 2.301296 CAAAGAGGGAACTGAGCTCTGA 59.699 50.000 25.49 0.11 44.43 3.27
3145 3254 2.697654 CAAAGAGGGAACTGAGCTCTG 58.302 52.381 18.15 18.15 44.43 3.35
3146 3255 1.003003 GCAAAGAGGGAACTGAGCTCT 59.997 52.381 16.19 0.00 44.43 4.09
3147 3256 1.271054 TGCAAAGAGGGAACTGAGCTC 60.271 52.381 6.82 6.82 44.43 4.09
3148 3257 0.767375 TGCAAAGAGGGAACTGAGCT 59.233 50.000 0.00 0.00 44.43 4.09
3149 3258 1.609208 TTGCAAAGAGGGAACTGAGC 58.391 50.000 0.00 0.00 44.43 4.26
3197 3349 0.302288 TTGTCGGTGTTCTTTTCGCG 59.698 50.000 0.00 0.00 0.00 5.87
3225 3377 2.933906 TCGAAATAAACATGGAGCGACC 59.066 45.455 0.00 0.00 39.54 4.79
3242 3394 7.170393 TCTCTTGTGGAGAATTTAGATCGAA 57.830 36.000 0.00 0.00 46.85 3.71
3271 3423 5.697178 TCATCATTTGTGCATTGGACTTTTG 59.303 36.000 9.80 4.63 0.00 2.44
3290 3442 4.080356 CCATTTCCTTGTAGGGTCTCATCA 60.080 45.833 0.00 0.00 35.59 3.07


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

AutoCloner maintained by Alex Coulton.