Multiple sequence alignment - TraesCS2A01G125200

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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 TraesCS2A01G125200 chr2A 100.000 3810 0 0 1 3810 74107144 74103335 0.000000e+00 7036.0
1 TraesCS2A01G125200 chr2A 91.597 357 12 1 3344 3700 163636031 163635693 9.580000e-131 477.0
2 TraesCS2A01G125200 chr2A 78.261 138 25 5 3575 3711 773302485 773302618 2.440000e-12 84.2
3 TraesCS2A01G125200 chr2D 95.632 2953 94 14 1 2936 74937360 74934426 0.000000e+00 4706.0
4 TraesCS2A01G125200 chr2D 77.225 764 121 33 2075 2817 79401780 79401049 7.670000e-107 398.0
5 TraesCS2A01G125200 chr2D 78.280 465 97 4 3239 3702 155123667 155123206 2.880000e-76 296.0
6 TraesCS2A01G125200 chr2B 92.067 1664 108 15 1 1661 114047625 114045983 0.000000e+00 2320.0
7 TraesCS2A01G125200 chr2B 91.932 1066 79 6 1868 2931 114045905 114044845 0.000000e+00 1485.0
8 TraesCS2A01G125200 chr1B 95.652 644 27 1 3062 3704 449385730 449386373 0.000000e+00 1033.0
9 TraesCS2A01G125200 chr1B 82.875 327 33 16 1486 1810 280475689 280475994 4.850000e-69 272.0
10 TraesCS2A01G125200 chr1B 95.455 132 5 1 2934 3064 449385543 449385674 3.860000e-50 209.0
11 TraesCS2A01G125200 chr7A 95.469 640 28 1 3062 3700 191914903 191914264 0.000000e+00 1020.0
12 TraesCS2A01G125200 chr7A 81.953 338 39 16 1475 1810 266940740 266941057 2.260000e-67 267.0
13 TraesCS2A01G125200 chr7A 93.182 132 8 1 2934 3064 191915090 191914959 3.880000e-45 193.0
14 TraesCS2A01G125200 chr5A 95.469 640 26 2 3062 3700 13419911 13419274 0.000000e+00 1018.0
15 TraesCS2A01G125200 chrUn 95.000 640 29 2 3062 3700 32182155 32181518 0.000000e+00 1002.0
16 TraesCS2A01G125200 chrUn 82.249 338 38 15 1475 1810 50448493 50448810 4.850000e-69 272.0
17 TraesCS2A01G125200 chrUn 93.939 132 7 1 2934 3064 32182342 32182211 8.350000e-47 198.0
18 TraesCS2A01G125200 chr4D 96.947 524 15 1 3062 3584 15525426 15525949 0.000000e+00 878.0
19 TraesCS2A01G125200 chr4D 96.212 132 4 1 2934 3064 15525239 15525370 8.290000e-52 215.0
20 TraesCS2A01G125200 chr3A 89.706 612 61 2 3093 3702 170651484 170650873 0.000000e+00 780.0
21 TraesCS2A01G125200 chr7D 80.372 591 103 11 3117 3700 167575871 167576455 1.630000e-118 436.0
22 TraesCS2A01G125200 chr7B 85.347 389 40 10 2161 2540 15807897 15807517 1.660000e-103 387.0
23 TraesCS2A01G125200 chr7B 81.852 270 42 4 1864 2128 15808162 15807895 1.780000e-53 220.0
24 TraesCS2A01G125200 chr1D 75.617 648 146 9 3063 3706 8309207 8309846 1.030000e-80 311.0
25 TraesCS2A01G125200 chr1D 85.714 140 15 1 772 906 459048046 459047907 3.970000e-30 143.0
26 TraesCS2A01G125200 chr4A 83.180 327 33 15 1486 1810 428994811 428995117 2.900000e-71 279.0
27 TraesCS2A01G125200 chr4A 82.875 327 34 15 1486 1810 29364949 29364643 1.350000e-69 274.0
28 TraesCS2A01G125200 chr4A 82.249 338 38 15 1475 1810 708069681 708069998 4.850000e-69 272.0
29 TraesCS2A01G125200 chr4A 82.249 338 38 15 1475 1810 708092336 708092653 4.850000e-69 272.0
30 TraesCS2A01G125200 chr4B 82.263 327 36 15 1486 1810 458278974 458279280 2.920000e-66 263.0


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 TraesCS2A01G125200 chr2A 74103335 74107144 3809 True 7036.0 7036 100.0000 1 3810 1 chr2A.!!$R1 3809
1 TraesCS2A01G125200 chr2D 74934426 74937360 2934 True 4706.0 4706 95.6320 1 2936 1 chr2D.!!$R1 2935
2 TraesCS2A01G125200 chr2D 79401049 79401780 731 True 398.0 398 77.2250 2075 2817 1 chr2D.!!$R2 742
3 TraesCS2A01G125200 chr2B 114044845 114047625 2780 True 1902.5 2320 91.9995 1 2931 2 chr2B.!!$R1 2930
4 TraesCS2A01G125200 chr1B 449385543 449386373 830 False 621.0 1033 95.5535 2934 3704 2 chr1B.!!$F2 770
5 TraesCS2A01G125200 chr7A 191914264 191915090 826 True 606.5 1020 94.3255 2934 3700 2 chr7A.!!$R1 766
6 TraesCS2A01G125200 chr5A 13419274 13419911 637 True 1018.0 1018 95.4690 3062 3700 1 chr5A.!!$R1 638
7 TraesCS2A01G125200 chrUn 32181518 32182342 824 True 600.0 1002 94.4695 2934 3700 2 chrUn.!!$R1 766
8 TraesCS2A01G125200 chr4D 15525239 15525949 710 False 546.5 878 96.5795 2934 3584 2 chr4D.!!$F1 650
9 TraesCS2A01G125200 chr3A 170650873 170651484 611 True 780.0 780 89.7060 3093 3702 1 chr3A.!!$R1 609
10 TraesCS2A01G125200 chr7D 167575871 167576455 584 False 436.0 436 80.3720 3117 3700 1 chr7D.!!$F1 583
11 TraesCS2A01G125200 chr7B 15807517 15808162 645 True 303.5 387 83.5995 1864 2540 2 chr7B.!!$R1 676
12 TraesCS2A01G125200 chr1D 8309207 8309846 639 False 311.0 311 75.6170 3063 3706 1 chr1D.!!$F1 643

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
199 200 0.893727 GCAACCACCCCTAACCACAG 60.894 60.000 0.0 0.0 0.0 3.66 F
1323 1333 0.240678 TGCGGCTGTGTTTGCTTATG 59.759 50.000 0.0 0.0 0.0 1.90 F
2176 2232 1.065926 CAGCATTCACCTAGTCTGGCA 60.066 52.381 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 1991 0.380378 TGCAAGAAGGTCAAACGCAC 59.620 50.0 0.00 0.00 0.00 5.34 R
2415 2489 0.036577 AGCTGCGAGAGTGAAAGCAT 60.037 50.0 0.00 0.00 39.02 3.79 R
3029 3116 0.730840 GCTTTAATGGAACCGGACGG 59.269 55.0 9.46 9.56 42.03 4.79 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
102 103 3.854784 GCAACAAGCAGAGGACATTTCAC 60.855 47.826 0.00 0.00 44.79 3.18
114 115 5.607477 AGGACATTTCACGTTCTCAAGTAA 58.393 37.500 0.00 0.00 0.00 2.24
128 129 8.373992 CGTTCTCAAGTAAGTAGCTAATTCAAC 58.626 37.037 10.14 4.24 0.00 3.18
178 179 6.039941 CACTCCCTAGGTGATTCTAGTACTTG 59.960 46.154 8.29 0.00 36.02 3.16
199 200 0.893727 GCAACCACCCCTAACCACAG 60.894 60.000 0.00 0.00 0.00 3.66
330 331 1.130054 AGCTCCTTGAGGACCAGCAA 61.130 55.000 11.05 0.00 39.78 3.91
517 518 2.801631 GGACCCGAGCTCATCCCAG 61.802 68.421 15.40 0.00 0.00 4.45
718 725 3.141488 GGAGCTCGCCGGAGAAGA 61.141 66.667 9.83 0.00 43.27 2.87
916 923 1.933853 CGGCCGCCAGATATAAATAGC 59.066 52.381 14.67 0.00 0.00 2.97
952 961 1.736586 CATTCCCCTCTCGGTCTCG 59.263 63.158 0.00 0.00 37.82 4.04
953 962 2.128507 ATTCCCCTCTCGGTCTCGC 61.129 63.158 0.00 0.00 36.13 5.03
1160 1169 2.634600 CCTACTCACTCGCTGTACTCT 58.365 52.381 0.00 0.00 0.00 3.24
1221 1230 2.349886 GCTAGGTTTGAACTGATCTGCG 59.650 50.000 0.00 0.00 0.00 5.18
1234 1243 1.794701 GATCTGCGCTGCGATATTTGA 59.205 47.619 28.07 12.98 0.00 2.69
1249 1258 6.144854 CGATATTTGATTGCCTACAACATGG 58.855 40.000 0.00 0.00 38.99 3.66
1268 1277 5.365314 ACATGGGATCTCTTCTCCTTAGTTC 59.635 44.000 0.00 0.00 33.05 3.01
1323 1333 0.240678 TGCGGCTGTGTTTGCTTATG 59.759 50.000 0.00 0.00 0.00 1.90
1327 1337 2.413239 CGGCTGTGTTTGCTTATGAGTG 60.413 50.000 0.00 0.00 0.00 3.51
1330 1340 3.004734 GCTGTGTTTGCTTATGAGTGGTT 59.995 43.478 0.00 0.00 0.00 3.67
1436 1446 4.096003 AACGCTGCCCGCTGGTAT 62.096 61.111 0.00 0.00 41.76 2.73
1679 1689 1.068055 GTTTGCTCCTGCTTGTCCATG 60.068 52.381 0.00 0.00 40.48 3.66
1720 1730 3.499918 ACTTTGAGAGTTTGAGCAATCGG 59.500 43.478 0.00 0.00 33.92 4.18
1970 1991 9.830294 TTCGAATATAATTATTGCTCTGCATTG 57.170 29.630 2.68 0.00 38.76 2.82
2002 2023 2.662006 TCTTGCAGGATGAAGACGAG 57.338 50.000 0.00 0.00 39.69 4.18
2106 2127 7.067494 TGCAAAGAAGAAAGAAAGTAAGCTCTT 59.933 33.333 0.00 0.00 33.25 2.85
2113 2134 6.871492 AGAAAGAAAGTAAGCTCTTCTAGTGC 59.129 38.462 0.00 0.00 35.13 4.40
2117 2138 6.434652 AGAAAGTAAGCTCTTCTAGTGCTGTA 59.565 38.462 4.25 0.00 43.44 2.74
2128 2184 8.792830 TCTTCTAGTGCTGTATGCTTAAATTT 57.207 30.769 0.00 0.00 43.37 1.82
2134 2190 5.003778 GTGCTGTATGCTTAAATTTTCTGCG 59.996 40.000 0.00 0.00 43.37 5.18
2137 2193 5.879237 TGTATGCTTAAATTTTCTGCGGAG 58.121 37.500 0.00 0.00 0.00 4.63
2143 2199 6.205853 TGCTTAAATTTTCTGCGGAGTTCTAA 59.794 34.615 3.10 0.00 0.00 2.10
2152 2208 4.081642 TCTGCGGAGTTCTAAGCAACTATT 60.082 41.667 3.10 0.00 36.71 1.73
2176 2232 1.065926 CAGCATTCACCTAGTCTGGCA 60.066 52.381 0.00 0.00 0.00 4.92
2179 2235 3.134458 GCATTCACCTAGTCTGGCATAC 58.866 50.000 0.00 0.00 0.00 2.39
2183 2239 5.435686 TTCACCTAGTCTGGCATACATTT 57.564 39.130 5.77 0.00 0.00 2.32
2206 2279 4.460263 TCATTGTCCAGTTTGTGCTAACT 58.540 39.130 0.00 0.00 38.87 2.24
2413 2487 6.862209 TGCAACAGTTTGAGAAAGTTAACAT 58.138 32.000 8.61 0.00 34.24 2.71
2415 2489 8.462811 TGCAACAGTTTGAGAAAGTTAACATAA 58.537 29.630 8.61 0.00 34.24 1.90
2491 2574 3.070590 TCCAGATCATGCTGACGATCATT 59.929 43.478 0.00 0.00 40.45 2.57
2540 2623 0.895559 TGAGGAAGTGCTCTGCGAGA 60.896 55.000 9.32 0.00 0.00 4.04
2608 2691 9.559732 TTCAACAAGATCTAGAATCTTTGTTCA 57.440 29.630 17.24 8.35 36.32 3.18
2614 2697 5.825593 TCTAGAATCTTTGTTCACCCACT 57.174 39.130 0.00 0.00 0.00 4.00
2645 2728 3.713764 CTGGATTCTTGGTACTGGGATCT 59.286 47.826 0.00 0.00 0.00 2.75
2665 2748 6.708054 GGATCTGTCGATCTGGAAAACATTAT 59.292 38.462 0.00 0.00 44.42 1.28
2841 2926 8.084684 TCTTTGATAACTGTGATAGGATGATCG 58.915 37.037 0.00 0.00 0.00 3.69
2859 2944 7.064609 GGATGATCGAGATGTTCTTGTTTACAA 59.935 37.037 0.00 0.00 0.00 2.41
2873 2960 9.921637 TTCTTGTTTACAATTGTTTCCATATCC 57.078 29.630 17.78 0.00 35.02 2.59
2877 2964 7.608376 TGTTTACAATTGTTTCCATATCCGAGA 59.392 33.333 17.78 0.00 0.00 4.04
2908 2995 4.994852 CGAAACTCAATCTTACCACCAAGA 59.005 41.667 0.00 0.00 38.84 3.02
2920 3007 6.655003 TCTTACCACCAAGAAATAAGAAGCTG 59.345 38.462 0.00 0.00 31.63 4.24
2932 3019 1.811679 GAAGCTGTCGTGCCTAGCC 60.812 63.158 0.00 0.00 38.18 3.93
2933 3020 2.232298 GAAGCTGTCGTGCCTAGCCT 62.232 60.000 0.00 0.00 38.18 4.58
2934 3021 2.510238 GCTGTCGTGCCTAGCCTG 60.510 66.667 0.00 0.00 0.00 4.85
2935 3022 2.973899 CTGTCGTGCCTAGCCTGT 59.026 61.111 0.00 0.00 0.00 4.00
2936 3023 1.446792 CTGTCGTGCCTAGCCTGTG 60.447 63.158 0.00 0.00 0.00 3.66
2937 3024 2.125512 GTCGTGCCTAGCCTGTGG 60.126 66.667 0.00 0.00 0.00 4.17
2951 3038 1.230149 TGTGGGTAGCCTGGGGATT 60.230 57.895 13.11 0.00 0.00 3.01
2994 3081 1.749033 GGGGTGGATCGATCTGGTC 59.251 63.158 23.96 8.74 0.00 4.02
3018 3105 5.050490 CAGCCGTGCTTGAATACTTACTAT 58.950 41.667 0.00 0.00 36.40 2.12
3087 3232 2.610859 ATCCCCACCGCAGTCCTT 60.611 61.111 0.00 0.00 0.00 3.36
3261 3407 1.855213 GCAACGGCAGCAGTCATTCA 61.855 55.000 0.00 0.00 40.72 2.57
3514 3660 3.602483 GTCGCTTATTGGGAAGGTTACA 58.398 45.455 0.00 0.00 39.38 2.41
3534 3681 3.818210 ACATTAAGCATTGTGGTCGTTCA 59.182 39.130 0.00 0.00 0.00 3.18
3726 3874 6.843069 AAATTACACCACAATTGAAGTTGC 57.157 33.333 13.59 0.00 32.32 4.17
3727 3875 2.888834 ACACCACAATTGAAGTTGCC 57.111 45.000 13.59 0.00 32.32 4.52
3728 3876 2.106566 ACACCACAATTGAAGTTGCCA 58.893 42.857 13.59 0.00 32.32 4.92
3729 3877 2.699846 ACACCACAATTGAAGTTGCCAT 59.300 40.909 13.59 0.00 32.32 4.40
3730 3878 3.894427 ACACCACAATTGAAGTTGCCATA 59.106 39.130 13.59 0.00 32.32 2.74
3731 3879 4.343526 ACACCACAATTGAAGTTGCCATAA 59.656 37.500 13.59 0.00 32.32 1.90
3732 3880 5.163364 ACACCACAATTGAAGTTGCCATAAA 60.163 36.000 13.59 0.00 32.32 1.40
3733 3881 5.757320 CACCACAATTGAAGTTGCCATAAAA 59.243 36.000 13.59 0.00 32.32 1.52
3734 3882 6.259608 CACCACAATTGAAGTTGCCATAAAAA 59.740 34.615 13.59 0.00 32.32 1.94
3753 3901 3.540314 AAAAGTTTGAGTTGCCATGCA 57.460 38.095 0.00 0.00 36.47 3.96
3754 3902 3.756933 AAAGTTTGAGTTGCCATGCAT 57.243 38.095 0.00 0.00 38.76 3.96
3755 3903 4.870123 AAAGTTTGAGTTGCCATGCATA 57.130 36.364 0.00 0.00 38.76 3.14
3756 3904 4.870123 AAGTTTGAGTTGCCATGCATAA 57.130 36.364 0.00 0.00 38.76 1.90
3757 3905 4.870123 AGTTTGAGTTGCCATGCATAAA 57.130 36.364 0.00 0.00 38.76 1.40
3758 3906 5.212532 AGTTTGAGTTGCCATGCATAAAA 57.787 34.783 0.00 0.00 38.76 1.52
3759 3907 5.797051 AGTTTGAGTTGCCATGCATAAAAT 58.203 33.333 0.00 0.00 38.76 1.82
3760 3908 5.870978 AGTTTGAGTTGCCATGCATAAAATC 59.129 36.000 0.00 4.26 38.76 2.17
3761 3909 4.389890 TGAGTTGCCATGCATAAAATCC 57.610 40.909 0.00 0.00 38.76 3.01
3762 3910 3.181488 TGAGTTGCCATGCATAAAATCCG 60.181 43.478 0.00 0.00 38.76 4.18
3763 3911 3.023119 AGTTGCCATGCATAAAATCCGA 58.977 40.909 0.00 0.00 38.76 4.55
3764 3912 3.115554 GTTGCCATGCATAAAATCCGAC 58.884 45.455 0.00 0.00 38.76 4.79
3765 3913 2.373224 TGCCATGCATAAAATCCGACA 58.627 42.857 0.00 0.00 31.71 4.35
3766 3914 2.757314 TGCCATGCATAAAATCCGACAA 59.243 40.909 0.00 0.00 31.71 3.18
3767 3915 3.194329 TGCCATGCATAAAATCCGACAAA 59.806 39.130 0.00 0.00 31.71 2.83
3768 3916 4.180057 GCCATGCATAAAATCCGACAAAA 58.820 39.130 0.00 0.00 0.00 2.44
3769 3917 4.629200 GCCATGCATAAAATCCGACAAAAA 59.371 37.500 0.00 0.00 0.00 1.94
3793 3941 7.967890 AAAATCATGATTTGTTTCTGGTTCC 57.032 32.000 29.52 0.00 40.57 3.62
3794 3942 6.923199 AATCATGATTTGTTTCTGGTTCCT 57.077 33.333 15.36 0.00 0.00 3.36
3795 3943 6.923199 ATCATGATTTGTTTCTGGTTCCTT 57.077 33.333 1.18 0.00 0.00 3.36
3796 3944 6.331369 TCATGATTTGTTTCTGGTTCCTTC 57.669 37.500 0.00 0.00 0.00 3.46
3797 3945 5.832595 TCATGATTTGTTTCTGGTTCCTTCA 59.167 36.000 0.00 0.00 0.00 3.02
3798 3946 6.323482 TCATGATTTGTTTCTGGTTCCTTCAA 59.677 34.615 0.00 0.00 0.00 2.69
3799 3947 6.729690 TGATTTGTTTCTGGTTCCTTCAAT 57.270 33.333 0.00 0.00 0.00 2.57
3800 3948 6.514947 TGATTTGTTTCTGGTTCCTTCAATG 58.485 36.000 0.00 0.00 0.00 2.82
3801 3949 4.935352 TTGTTTCTGGTTCCTTCAATGG 57.065 40.909 0.00 0.00 0.00 3.16
3802 3950 3.909732 TGTTTCTGGTTCCTTCAATGGT 58.090 40.909 0.00 0.00 0.00 3.55
3803 3951 3.888930 TGTTTCTGGTTCCTTCAATGGTC 59.111 43.478 0.00 0.00 0.00 4.02
3804 3952 2.472695 TCTGGTTCCTTCAATGGTCG 57.527 50.000 0.00 0.00 0.00 4.79
3805 3953 1.003118 TCTGGTTCCTTCAATGGTCGG 59.997 52.381 0.00 0.00 0.00 4.79
3806 3954 1.003118 CTGGTTCCTTCAATGGTCGGA 59.997 52.381 0.00 0.00 0.00 4.55
3807 3955 1.271163 TGGTTCCTTCAATGGTCGGAC 60.271 52.381 0.00 0.00 0.00 4.79
3808 3956 1.271163 GGTTCCTTCAATGGTCGGACA 60.271 52.381 10.76 0.00 0.00 4.02
3809 3957 1.804748 GTTCCTTCAATGGTCGGACAC 59.195 52.381 10.76 0.17 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.128242 CACCATTGCCTGAGTGAGATTTC 59.872 47.826 0.00 0.00 31.46 2.17
102 103 8.373992 GTTGAATTAGCTACTTACTTGAGAACG 58.626 37.037 0.00 0.00 0.00 3.95
114 115 8.970859 ATTATGAAGCAGTTGAATTAGCTACT 57.029 30.769 0.00 0.00 36.07 2.57
178 179 0.608308 GTGGTTAGGGGTGGTTGCTC 60.608 60.000 0.00 0.00 0.00 4.26
199 200 1.081242 CATGGTGCGTTTGCTGGAC 60.081 57.895 0.00 0.00 43.34 4.02
330 331 3.322466 CCAAGAGGGCGGACTGGT 61.322 66.667 0.00 0.00 0.00 4.00
349 350 0.776810 TCTGGGTGAAGGCCATGAAA 59.223 50.000 5.01 0.00 0.00 2.69
517 518 2.507324 GAGACGCCGAGGTTCAGC 60.507 66.667 0.00 0.00 0.00 4.26
694 695 3.536917 CGGCGAGCTCCCATGGTA 61.537 66.667 11.73 0.00 0.00 3.25
718 725 3.444805 GCTCAGCTCCCTCGTCGT 61.445 66.667 0.00 0.00 0.00 4.34
817 824 1.745489 CCTGGGAAAGCTACACGGC 60.745 63.158 0.00 0.00 0.00 5.68
952 961 3.132289 GGCTAAAATCCCAAAACCCTAGC 59.868 47.826 0.00 0.00 0.00 3.42
953 962 4.610333 AGGCTAAAATCCCAAAACCCTAG 58.390 43.478 0.00 0.00 0.00 3.02
996 1005 1.982073 GCTTGTCGAATTCGCTGGGG 61.982 60.000 22.90 11.97 39.60 4.96
1160 1169 5.470437 CCACTACGAACTAGCAGATCTGATA 59.530 44.000 27.04 22.84 0.00 2.15
1221 1230 3.250762 TGTAGGCAATCAAATATCGCAGC 59.749 43.478 0.00 0.00 0.00 5.25
1234 1243 3.461085 AGAGATCCCATGTTGTAGGCAAT 59.539 43.478 0.00 0.00 36.92 3.56
1249 1258 4.208746 TCGGAACTAAGGAGAAGAGATCC 58.791 47.826 0.00 0.00 37.07 3.36
1268 1277 3.911868 TCACCAGATTTGCAAAATTCGG 58.088 40.909 17.19 15.84 0.00 4.30
1323 1333 4.293415 CAGAAGCATCACAAAAACCACTC 58.707 43.478 0.00 0.00 0.00 3.51
1461 1471 5.100259 CACATACTACACTTCGTACCTTGG 58.900 45.833 0.00 0.00 0.00 3.61
1679 1689 9.221775 CTCAAAGTAGTAATTGACACAACAAAC 57.778 33.333 0.00 0.00 32.46 2.93
1720 1730 4.452114 CCTTCAAAGGGCAAATAAAAGCAC 59.548 41.667 0.50 0.00 42.66 4.40
1842 1857 2.154462 AGCTTGGCATACACACAGTTC 58.846 47.619 0.00 0.00 0.00 3.01
1970 1991 0.380378 TGCAAGAAGGTCAAACGCAC 59.620 50.000 0.00 0.00 0.00 5.34
2002 2023 4.277672 CCAAACAGATCCATGTCATCATCC 59.722 45.833 5.04 0.00 31.50 3.51
2113 2134 5.879237 TCCGCAGAAAATTTAAGCATACAG 58.121 37.500 9.25 0.00 0.00 2.74
2117 2138 5.183904 AGAACTCCGCAGAAAATTTAAGCAT 59.816 36.000 9.25 0.00 0.00 3.79
2128 2184 2.037251 AGTTGCTTAGAACTCCGCAGAA 59.963 45.455 0.00 0.00 29.85 3.02
2134 2190 5.178797 TGCAGAATAGTTGCTTAGAACTCC 58.821 41.667 0.00 0.00 42.02 3.85
2137 2193 4.393062 TGCTGCAGAATAGTTGCTTAGAAC 59.607 41.667 20.43 0.00 42.02 3.01
2143 2199 3.128242 GTGAATGCTGCAGAATAGTTGCT 59.872 43.478 20.43 0.00 42.02 3.91
2152 2208 2.093816 CAGACTAGGTGAATGCTGCAGA 60.094 50.000 20.43 2.70 0.00 4.26
2176 2232 6.646240 GCACAAACTGGACAATGAAAATGTAT 59.354 34.615 0.00 0.00 0.00 2.29
2179 2235 5.051816 AGCACAAACTGGACAATGAAAATG 58.948 37.500 0.00 0.00 0.00 2.32
2183 2239 4.887071 AGTTAGCACAAACTGGACAATGAA 59.113 37.500 0.00 0.00 38.28 2.57
2206 2279 3.730215 TGCCACCTAAATAAGCTTGGA 57.270 42.857 9.86 0.00 31.33 3.53
2380 2454 2.880268 TCAAACTGTTGCATCAGTGAGG 59.120 45.455 26.80 19.28 46.25 3.86
2402 2476 9.548208 GAGAGTGAAAGCATTATGTTAACTTTC 57.452 33.333 7.22 12.75 44.05 2.62
2413 2487 2.002586 GCTGCGAGAGTGAAAGCATTA 58.997 47.619 0.00 0.00 39.02 1.90
2415 2489 0.036577 AGCTGCGAGAGTGAAAGCAT 60.037 50.000 0.00 0.00 39.02 3.79
2540 2623 0.535335 ACATACTCGTTGATGGGCGT 59.465 50.000 0.00 0.00 0.00 5.68
2608 2691 1.829533 CCAGCAGCAACAAGTGGGT 60.830 57.895 0.00 0.00 0.00 4.51
2614 2697 1.614903 CCAAGAATCCAGCAGCAACAA 59.385 47.619 0.00 0.00 0.00 2.83
2645 2728 6.183360 CGACAATAATGTTTTCCAGATCGACA 60.183 38.462 0.00 0.00 40.74 4.35
2665 2748 3.307621 GGGGTAACTAAATGGGACGACAA 60.308 47.826 0.00 0.00 0.00 3.18
2841 2926 8.968242 GGAAACAATTGTAAACAAGAACATCTC 58.032 33.333 12.39 0.00 39.47 2.75
2877 2964 5.869888 GGTAAGATTGAGTTTCGAGTCACAT 59.130 40.000 0.00 0.00 0.00 3.21
2908 2995 3.059352 AGGCACGACAGCTTCTTATTT 57.941 42.857 0.00 0.00 34.17 1.40
2920 3007 2.125512 CCACAGGCTAGGCACGAC 60.126 66.667 19.70 0.00 0.00 4.34
2932 3019 1.281925 AATCCCCAGGCTACCCACAG 61.282 60.000 0.00 0.00 0.00 3.66
2933 3020 1.230149 AATCCCCAGGCTACCCACA 60.230 57.895 0.00 0.00 0.00 4.17
2934 3021 0.988678 AGAATCCCCAGGCTACCCAC 60.989 60.000 0.00 0.00 0.00 4.61
2935 3022 0.253630 AAGAATCCCCAGGCTACCCA 60.254 55.000 0.00 0.00 0.00 4.51
2936 3023 0.183731 CAAGAATCCCCAGGCTACCC 59.816 60.000 0.00 0.00 0.00 3.69
2937 3024 1.213296 TCAAGAATCCCCAGGCTACC 58.787 55.000 0.00 0.00 0.00 3.18
2951 3038 3.074412 GGCCTCTTCGACAATTTCAAGA 58.926 45.455 0.00 0.00 0.00 3.02
2994 3081 1.453155 AAGTATTCAAGCACGGCTGG 58.547 50.000 0.00 0.00 39.62 4.85
3018 3105 3.451793 CCGGACGGTCATTCATCAA 57.548 52.632 10.76 0.00 0.00 2.57
3029 3116 0.730840 GCTTTAATGGAACCGGACGG 59.269 55.000 9.46 9.56 42.03 4.79
3104 3249 5.473039 GAAGTTGTTTGCAATAGCCAGAAT 58.527 37.500 0.00 0.00 41.13 2.40
3173 3318 3.758554 ACAAATCTCGGATTGGGTTTCAG 59.241 43.478 6.13 0.00 0.00 3.02
3261 3407 7.680730 TGCTAAGAAGTTACCTTTCTCATCTT 58.319 34.615 0.00 0.00 33.92 2.40
3514 3660 4.201812 CGATGAACGACCACAATGCTTAAT 60.202 41.667 0.00 0.00 45.77 1.40
3534 3681 1.339438 ACATGAGCTGCTTGGTTCGAT 60.339 47.619 2.53 0.00 0.00 3.59
3589 3736 3.542648 GAGGCTCATTAACCCAACTACC 58.457 50.000 10.25 0.00 0.00 3.18
3706 3854 3.701542 TGGCAACTTCAATTGTGGTGTAA 59.298 39.130 16.23 6.54 37.61 2.41
3707 3855 3.291584 TGGCAACTTCAATTGTGGTGTA 58.708 40.909 16.23 7.31 37.61 2.90
3708 3856 2.106566 TGGCAACTTCAATTGTGGTGT 58.893 42.857 16.23 5.69 37.61 4.16
3709 3857 2.886862 TGGCAACTTCAATTGTGGTG 57.113 45.000 5.13 9.71 37.61 4.17
3710 3858 5.543507 TTTATGGCAACTTCAATTGTGGT 57.456 34.783 5.13 2.97 37.61 4.16
3711 3859 6.857777 TTTTTATGGCAACTTCAATTGTGG 57.142 33.333 5.13 2.33 37.61 4.17
3732 3880 3.871485 TGCATGGCAACTCAAACTTTTT 58.129 36.364 0.00 0.00 34.76 1.94
3733 3881 3.540314 TGCATGGCAACTCAAACTTTT 57.460 38.095 0.00 0.00 34.76 2.27
3734 3882 3.756933 ATGCATGGCAACTCAAACTTT 57.243 38.095 0.00 0.00 43.62 2.66
3735 3883 4.870123 TTATGCATGGCAACTCAAACTT 57.130 36.364 10.16 0.00 43.62 2.66
3736 3884 4.870123 TTTATGCATGGCAACTCAAACT 57.130 36.364 10.16 0.00 43.62 2.66
3737 3885 5.063817 GGATTTTATGCATGGCAACTCAAAC 59.936 40.000 10.16 0.00 43.62 2.93
3738 3886 5.177326 GGATTTTATGCATGGCAACTCAAA 58.823 37.500 10.16 0.00 43.62 2.69
3739 3887 4.677514 CGGATTTTATGCATGGCAACTCAA 60.678 41.667 10.16 0.00 43.62 3.02
3740 3888 3.181488 CGGATTTTATGCATGGCAACTCA 60.181 43.478 10.16 0.00 43.62 3.41
3741 3889 3.066621 TCGGATTTTATGCATGGCAACTC 59.933 43.478 10.16 3.52 43.62 3.01
3742 3890 3.023119 TCGGATTTTATGCATGGCAACT 58.977 40.909 10.16 0.00 43.62 3.16
3743 3891 3.115554 GTCGGATTTTATGCATGGCAAC 58.884 45.455 10.16 0.00 43.62 4.17
3744 3892 2.757314 TGTCGGATTTTATGCATGGCAA 59.243 40.909 10.16 0.00 43.62 4.52
3745 3893 2.373224 TGTCGGATTTTATGCATGGCA 58.627 42.857 10.16 0.00 44.86 4.92
3746 3894 3.435105 TTGTCGGATTTTATGCATGGC 57.565 42.857 10.16 0.00 0.00 4.40
3768 3916 8.212995 AGGAACCAGAAACAAATCATGATTTTT 58.787 29.630 27.30 20.72 38.84 1.94
3769 3917 7.738847 AGGAACCAGAAACAAATCATGATTTT 58.261 30.769 27.30 15.75 38.84 1.82
3770 3918 7.307131 AGGAACCAGAAACAAATCATGATTT 57.693 32.000 24.83 24.83 41.33 2.17
3771 3919 6.923199 AGGAACCAGAAACAAATCATGATT 57.077 33.333 15.36 15.36 0.00 2.57
3772 3920 6.494491 TGAAGGAACCAGAAACAAATCATGAT 59.506 34.615 1.18 1.18 0.00 2.45
3773 3921 5.832595 TGAAGGAACCAGAAACAAATCATGA 59.167 36.000 0.00 0.00 0.00 3.07
3774 3922 6.088016 TGAAGGAACCAGAAACAAATCATG 57.912 37.500 0.00 0.00 0.00 3.07
3775 3923 6.729690 TTGAAGGAACCAGAAACAAATCAT 57.270 33.333 0.00 0.00 0.00 2.45
3776 3924 6.462768 CCATTGAAGGAACCAGAAACAAATCA 60.463 38.462 0.00 0.00 0.00 2.57
3777 3925 5.928264 CCATTGAAGGAACCAGAAACAAATC 59.072 40.000 0.00 0.00 0.00 2.17
3778 3926 5.366477 ACCATTGAAGGAACCAGAAACAAAT 59.634 36.000 0.00 0.00 0.00 2.32
3779 3927 4.714308 ACCATTGAAGGAACCAGAAACAAA 59.286 37.500 0.00 0.00 0.00 2.83
3780 3928 4.285863 ACCATTGAAGGAACCAGAAACAA 58.714 39.130 0.00 0.00 0.00 2.83
3781 3929 3.888930 GACCATTGAAGGAACCAGAAACA 59.111 43.478 0.00 0.00 0.00 2.83
3782 3930 3.058224 CGACCATTGAAGGAACCAGAAAC 60.058 47.826 0.00 0.00 0.00 2.78
3783 3931 3.146066 CGACCATTGAAGGAACCAGAAA 58.854 45.455 0.00 0.00 0.00 2.52
3784 3932 2.552155 CCGACCATTGAAGGAACCAGAA 60.552 50.000 0.00 0.00 0.00 3.02
3785 3933 1.003118 CCGACCATTGAAGGAACCAGA 59.997 52.381 0.00 0.00 0.00 3.86
3786 3934 1.003118 TCCGACCATTGAAGGAACCAG 59.997 52.381 0.00 0.00 0.00 4.00
3787 3935 1.060729 TCCGACCATTGAAGGAACCA 58.939 50.000 0.00 0.00 0.00 3.67
3788 3936 1.271163 TGTCCGACCATTGAAGGAACC 60.271 52.381 0.00 0.00 34.17 3.62
3789 3937 1.804748 GTGTCCGACCATTGAAGGAAC 59.195 52.381 0.00 0.00 34.17 3.62
3790 3938 2.178912 GTGTCCGACCATTGAAGGAA 57.821 50.000 0.00 0.00 34.17 3.36
3791 3939 3.927555 GTGTCCGACCATTGAAGGA 57.072 52.632 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.