Multiple sequence alignment - TraesCS1D01G195500

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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 TraesCS1D01G195500 chr1D 100.000 4166 0 0 1 4166 274471565 274467400 0.000000e+00 7694.0
1 TraesCS1D01G195500 chr1D 87.500 112 9 5 2164 2272 274469180 274469071 1.570000e-24 124.0
2 TraesCS1D01G195500 chr1B 92.561 2097 78 32 1678 3768 374019748 374017724 0.000000e+00 2937.0
3 TraesCS1D01G195500 chr1B 97.017 771 22 1 908 1677 374020596 374019826 0.000000e+00 1295.0
4 TraesCS1D01G195500 chr1B 87.905 587 40 14 1 570 374021480 374020908 0.000000e+00 662.0
5 TraesCS1D01G195500 chr1B 88.189 381 21 14 3804 4166 374017735 374017361 2.300000e-117 433.0
6 TraesCS1D01G195500 chr1B 86.087 115 16 0 1743 1857 249625003 249624889 1.570000e-24 124.0
7 TraesCS1D01G195500 chr1B 77.470 253 23 22 2164 2388 374019076 374018830 2.030000e-23 121.0
8 TraesCS1D01G195500 chr1A 92.722 1580 85 13 24 1573 347325300 347323721 0.000000e+00 2254.0
9 TraesCS1D01G195500 chr1A 88.636 1716 94 43 2462 4124 347323113 347321446 0.000000e+00 1995.0
10 TraesCS1D01G195500 chr1A 94.393 107 6 0 2271 2377 347323055 347322949 9.270000e-37 165.0
11 TraesCS1D01G195500 chr1A 86.047 129 12 5 1848 1973 347323479 347323354 2.610000e-27 134.0
12 TraesCS1D01G195500 chr6B 89.720 107 11 0 1744 1850 617173714 617173820 2.020000e-28 137.0
13 TraesCS1D01G195500 chr6B 88.991 109 10 2 1743 1850 281335964 281336071 2.610000e-27 134.0
14 TraesCS1D01G195500 chr7B 91.667 96 8 0 1743 1838 570465363 570465268 2.610000e-27 134.0
15 TraesCS1D01G195500 chr7B 86.607 112 14 1 1743 1853 3144677 3144788 5.660000e-24 122.0
16 TraesCS1D01G195500 chr7B 86.486 111 13 2 1743 1852 463050470 463050361 2.030000e-23 121.0
17 TraesCS1D01G195500 chr7B 90.476 84 8 0 790 873 152786829 152786746 1.220000e-20 111.0
18 TraesCS1D01G195500 chr2B 87.963 108 13 0 1743 1850 161410873 161410766 1.220000e-25 128.0
19 TraesCS1D01G195500 chr2B 85.965 114 14 2 1740 1852 734295902 734296014 2.030000e-23 121.0
20 TraesCS1D01G195500 chr2B 86.207 87 12 0 790 876 429649500 429649414 1.230000e-15 95.3
21 TraesCS1D01G195500 chr4B 91.667 84 7 0 790 873 351614232 351614315 2.630000e-22 117.0
22 TraesCS1D01G195500 chr4A 89.286 84 9 0 790 873 338747766 338747849 5.700000e-19 106.0
23 TraesCS1D01G195500 chr4A 86.170 94 12 1 786 879 593200946 593200854 2.650000e-17 100.0
24 TraesCS1D01G195500 chr2D 89.286 84 9 0 790 873 565934956 565934873 5.700000e-19 106.0
25 TraesCS1D01G195500 chr5B 86.316 95 11 2 790 883 511366066 511365973 7.370000e-18 102.0
26 TraesCS1D01G195500 chr3D 85.567 97 11 3 786 881 50074649 50074555 9.530000e-17 99.0
27 TraesCS1D01G195500 chr7D 100.000 28 0 0 4134 4161 496167084 496167111 8.000000e-03 52.8


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 TraesCS1D01G195500 chr1D 274467400 274471565 4165 True 3909.0 7694 93.7500 1 4166 2 chr1D.!!$R1 4165
1 TraesCS1D01G195500 chr1B 374017361 374021480 4119 True 1089.6 2937 88.6284 1 4166 5 chr1B.!!$R2 4165
2 TraesCS1D01G195500 chr1A 347321446 347325300 3854 True 1137.0 2254 90.4495 24 4124 4 chr1A.!!$R1 4100

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
788 954 0.177604 CCCAGATCCTGCTCACAGTC 59.822 60.0 0.00 0.0 42.81 3.51 F
1420 1589 0.596083 TTGCACCGTGCCAATTTTCG 60.596 50.0 20.67 0.0 44.23 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2264 0.846015 AGCTATGCACCCTATTGCCA 59.154 50.0 0.00 0.00 42.25 4.92 R
3314 3701 0.961019 TGCCAGTCATTGCAAGGTTC 59.039 50.0 11.36 6.02 33.87 3.62 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
57 59 3.831911 TCCATTTTTCCAATCCAGTCACC 59.168 43.478 0.00 0.00 0.00 4.02
58 60 3.577848 CCATTTTTCCAATCCAGTCACCA 59.422 43.478 0.00 0.00 0.00 4.17
105 107 2.277404 GAGGAGACGGAGAGGCCT 59.723 66.667 3.86 3.86 0.00 5.19
167 169 2.047179 GCCGCCTTCCTCGTTTCT 60.047 61.111 0.00 0.00 0.00 2.52
230 232 3.499737 CCTCGCCGTGGCATTGAC 61.500 66.667 12.06 0.00 42.06 3.18
272 280 4.681978 GTCCCCGTGCTGTTCGCT 62.682 66.667 0.00 0.00 40.11 4.93
315 323 3.785859 GCCCGCTGATCCACTCCA 61.786 66.667 0.00 0.00 0.00 3.86
359 367 4.308458 CCTGCGTCCGTGGTTCCA 62.308 66.667 0.00 0.00 0.00 3.53
380 394 1.248785 TAGGTTCTTCTGGAGCGCGT 61.249 55.000 8.43 0.00 0.00 6.01
394 408 2.711924 GCGTAGTACTCGGTCCGG 59.288 66.667 12.29 0.00 0.00 5.14
427 442 2.221906 GACGGCTTAGTTCTCGGGCA 62.222 60.000 0.00 0.00 0.00 5.36
441 456 1.559682 TCGGGCAGAGGCTTATTTTCT 59.440 47.619 0.00 0.00 40.87 2.52
450 466 8.903820 GGCAGAGGCTTATTTTCTAAGATTTTA 58.096 33.333 0.00 0.00 40.87 1.52
492 513 1.770110 TGCCCCGCCCTGATAGATT 60.770 57.895 0.00 0.00 0.00 2.40
499 520 1.071385 CGCCCTGATAGATTCAAGCCT 59.929 52.381 0.00 0.00 32.53 4.58
610 767 1.454276 TCTGTTTGCGATTCGAACGTC 59.546 47.619 10.88 5.56 41.10 4.34
666 832 6.577103 TGACTTATCAACCTGTGAGATCATC 58.423 40.000 0.00 0.00 40.43 2.92
699 865 8.981724 TCACGCCAATTATTATCTACAGTATC 57.018 34.615 0.00 0.00 0.00 2.24
786 952 1.070445 GATCCCAGATCCTGCTCACAG 59.930 57.143 0.00 0.00 44.05 3.66
788 954 0.177604 CCCAGATCCTGCTCACAGTC 59.822 60.000 0.00 0.00 42.81 3.51
798 964 1.257743 GCTCACAGTCACTCCCTACA 58.742 55.000 0.00 0.00 0.00 2.74
869 1035 0.709397 TGCATTTTGGGATGGAGGGA 59.291 50.000 0.00 0.00 0.00 4.20
1218 1386 2.368878 GGGATGGGGGCTCCTCTT 60.369 66.667 4.32 0.00 36.20 2.85
1245 1413 0.819259 TTGCAGCCTTCAACGCTCTT 60.819 50.000 0.00 0.00 33.17 2.85
1284 1452 2.694628 CCAGATGGAGACTCTCTTGAGG 59.305 54.545 6.02 0.00 40.12 3.86
1287 1455 2.980246 TGGAGACTCTCTTGAGGTCA 57.020 50.000 15.97 0.00 44.29 4.02
1309 1477 3.781307 CCGGGGCTCCATTGACGA 61.781 66.667 1.96 0.00 0.00 4.20
1374 1542 1.607178 CTTCCTGGCATGCCCAACA 60.607 57.895 33.44 14.41 44.81 3.33
1420 1589 0.596083 TTGCACCGTGCCAATTTTCG 60.596 50.000 20.67 0.00 44.23 3.46
1741 2080 2.142356 CCACTATGGGCCAATGAACA 57.858 50.000 11.89 0.00 32.67 3.18
1754 2093 0.613777 ATGAACAACTCCCTCCGTCC 59.386 55.000 0.00 0.00 0.00 4.79
1760 2099 0.905357 AACTCCCTCCGTCCAGAATG 59.095 55.000 0.00 0.00 0.00 2.67
1788 2127 4.377841 GCCGCAGAAATGAATGTATCTAGC 60.378 45.833 0.00 0.00 0.00 3.42
1844 2183 5.501897 GCGACAAGTAATTCGTGATAAAGGG 60.502 44.000 0.00 0.00 37.56 3.95
1887 2226 2.233431 AGCACCTGACTCTGATCAGTTC 59.767 50.000 21.92 18.46 43.99 3.01
1924 2263 2.201921 TTGGCGCCTGTATAACCAAA 57.798 45.000 29.70 6.16 37.45 3.28
1925 2264 2.428544 TGGCGCCTGTATAACCAAAT 57.571 45.000 29.70 0.00 0.00 2.32
1926 2265 2.020720 TGGCGCCTGTATAACCAAATG 58.979 47.619 29.70 0.00 0.00 2.32
1927 2266 1.336755 GGCGCCTGTATAACCAAATGG 59.663 52.381 22.15 0.00 42.17 3.16
1928 2267 1.269051 GCGCCTGTATAACCAAATGGC 60.269 52.381 0.00 0.00 39.32 4.40
1930 2269 2.425312 CGCCTGTATAACCAAATGGCAA 59.575 45.455 0.00 0.00 38.87 4.52
1931 2270 3.068024 CGCCTGTATAACCAAATGGCAAT 59.932 43.478 0.00 0.00 38.87 3.56
1933 2272 5.562696 CGCCTGTATAACCAAATGGCAATAG 60.563 44.000 0.00 0.00 38.87 1.73
1934 2273 5.278957 GCCTGTATAACCAAATGGCAATAGG 60.279 44.000 0.00 0.00 38.79 2.57
1935 2274 5.243730 CCTGTATAACCAAATGGCAATAGGG 59.756 44.000 0.00 0.00 39.32 3.53
1976 2315 2.570752 ACCGTGTCTCTAGTCAGTAGGA 59.429 50.000 0.00 0.00 0.00 2.94
1977 2316 3.008813 ACCGTGTCTCTAGTCAGTAGGAA 59.991 47.826 0.00 0.00 0.00 3.36
1978 2317 3.623960 CCGTGTCTCTAGTCAGTAGGAAG 59.376 52.174 0.00 0.00 0.00 3.46
1979 2318 4.255301 CGTGTCTCTAGTCAGTAGGAAGT 58.745 47.826 0.00 0.00 0.00 3.01
1980 2319 4.330620 CGTGTCTCTAGTCAGTAGGAAGTC 59.669 50.000 0.00 0.00 0.00 3.01
1981 2320 5.247084 GTGTCTCTAGTCAGTAGGAAGTCA 58.753 45.833 0.00 0.00 0.00 3.41
1982 2321 5.706369 GTGTCTCTAGTCAGTAGGAAGTCAA 59.294 44.000 0.00 0.00 0.00 3.18
1983 2322 6.376018 GTGTCTCTAGTCAGTAGGAAGTCAAT 59.624 42.308 0.00 0.00 0.00 2.57
1984 2323 6.375736 TGTCTCTAGTCAGTAGGAAGTCAATG 59.624 42.308 0.00 0.00 0.00 2.82
1985 2324 6.600032 GTCTCTAGTCAGTAGGAAGTCAATGA 59.400 42.308 0.00 0.00 0.00 2.57
1989 2328 6.672266 AGTCAGTAGGAAGTCAATGAAAGA 57.328 37.500 0.00 0.00 0.00 2.52
2005 2344 3.321682 TGAAAGAAAGTCCCTGGCAATTG 59.678 43.478 0.00 0.00 0.00 2.32
2085 2424 3.435566 CATGTGATTCATTGCTGCAGTC 58.564 45.455 16.64 8.39 34.09 3.51
2099 2438 0.880278 GCAGTCCGTTGCTTCTGTCA 60.880 55.000 0.00 0.00 40.89 3.58
2568 2948 3.104602 CTGGCGCGCATCCAAAGAG 62.105 63.158 34.42 10.47 32.41 2.85
2580 2960 6.697892 GCGCATCCAAAGAGTATATATAGTCC 59.302 42.308 19.70 6.48 34.05 3.85
2770 3151 3.002583 TCATGAGGGACGCTGGCA 61.003 61.111 0.00 0.00 0.00 4.92
2871 3252 0.391661 CCGTCAAGCAGTACATGGCT 60.392 55.000 0.00 0.00 43.46 4.75
2874 3255 0.692476 TCAAGCAGTACATGGCTGGT 59.308 50.000 15.42 15.42 45.23 4.00
2886 3267 3.626924 GCTGGTGGTCGGGACACT 61.627 66.667 0.75 0.00 38.83 3.55
2916 3297 1.757423 GCCAGGGCTCTCTCATCCTC 61.757 65.000 2.30 0.00 38.26 3.71
3178 3559 2.674380 GCTGACTGGCCCAAGGTG 60.674 66.667 0.00 0.00 0.00 4.00
3266 3653 1.070601 AGGACCATGGCAAACAAAAGC 59.929 47.619 13.04 0.00 0.00 3.51
3269 3656 2.941720 GACCATGGCAAACAAAAGCAAA 59.058 40.909 13.04 0.00 0.00 3.68
3273 3660 4.096081 CCATGGCAAACAAAAGCAAAGAAA 59.904 37.500 0.00 0.00 0.00 2.52
3274 3661 4.943142 TGGCAAACAAAAGCAAAGAAAG 57.057 36.364 0.00 0.00 0.00 2.62
3275 3662 3.688673 TGGCAAACAAAAGCAAAGAAAGG 59.311 39.130 0.00 0.00 0.00 3.11
3301 3688 0.883833 ACCATTCTTCTTTGCTGCGG 59.116 50.000 0.00 0.00 0.00 5.69
3324 3711 2.045561 TGTTTCCGAGAACCTTGCAA 57.954 45.000 0.00 0.00 0.00 4.08
3325 3712 2.582052 TGTTTCCGAGAACCTTGCAAT 58.418 42.857 0.00 0.00 0.00 3.56
3348 3735 0.612453 TGGCAGCAATGGCAGAATCA 60.612 50.000 0.00 0.00 44.61 2.57
3376 3763 7.885922 TGGTGATAATAAAGGTTGAGCTTTACA 59.114 33.333 15.26 8.06 0.00 2.41
3387 3774 1.536766 GAGCTTTACATGTGCTGTGCA 59.463 47.619 13.39 0.00 38.92 4.57
3395 3782 1.034356 ATGTGCTGTGCATGTGTGTT 58.966 45.000 0.00 0.00 41.91 3.32
3411 3798 1.726791 GTGTTATGTGTGGAGTGAGCG 59.273 52.381 0.00 0.00 0.00 5.03
3484 3871 2.355126 CATCCGACGGCGATCCAG 60.355 66.667 15.16 0.00 40.82 3.86
3538 3926 0.459237 TGCGCCTTTGTGGTTTGTTG 60.459 50.000 4.18 0.00 38.35 3.33
3666 4054 5.178438 GTGGTGTGTTCTCTTCTCATCTTTC 59.822 44.000 0.00 0.00 0.00 2.62
3671 4059 7.440856 GTGTGTTCTCTTCTCATCTTTCTTCTT 59.559 37.037 0.00 0.00 0.00 2.52
3672 4060 7.989741 TGTGTTCTCTTCTCATCTTTCTTCTTT 59.010 33.333 0.00 0.00 0.00 2.52
3678 4066 6.933521 TCTTCTCATCTTTCTTCTTTGTGGAG 59.066 38.462 0.00 0.00 0.00 3.86
3692 4080 2.190578 GGAGGGGCGGATTGAGTG 59.809 66.667 0.00 0.00 0.00 3.51
3718 4106 1.438651 CATTTCGCCTCGGAGTCAAA 58.561 50.000 4.02 0.55 0.00 2.69
3733 4121 4.870991 GGAGTCAAAGGTAATTCTCTTCCG 59.129 45.833 0.00 0.00 0.00 4.30
3737 4125 6.771267 AGTCAAAGGTAATTCTCTTCCGTTTT 59.229 34.615 0.00 0.00 0.00 2.43
3760 4148 0.674581 CTGTGAATGCCCGCTCTTCA 60.675 55.000 2.45 2.45 0.00 3.02
3768 4156 0.379669 GCCCGCTCTTCATGTTCATG 59.620 55.000 6.46 6.46 0.00 3.07
3777 4165 1.441738 TCATGTTCATGTGCAGACCG 58.558 50.000 11.73 0.00 0.00 4.79
3782 4170 0.324614 TTCATGTGCAGACCGTGGAT 59.675 50.000 0.00 0.00 0.00 3.41
3787 4175 1.337728 TGTGCAGACCGTGGATAGTTG 60.338 52.381 0.00 0.00 0.00 3.16
3790 4178 0.902531 CAGACCGTGGATAGTTGGGT 59.097 55.000 0.00 0.00 0.00 4.51
3791 4179 0.902531 AGACCGTGGATAGTTGGGTG 59.097 55.000 0.00 0.00 0.00 4.61
3792 4180 0.107848 GACCGTGGATAGTTGGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
3793 4181 1.223487 CCGTGGATAGTTGGGTGGG 59.777 63.158 0.00 0.00 0.00 4.61
3794 4182 1.223487 CGTGGATAGTTGGGTGGGG 59.777 63.158 0.00 0.00 0.00 4.96
3796 4184 0.702316 GTGGATAGTTGGGTGGGGTT 59.298 55.000 0.00 0.00 0.00 4.11
3797 4185 0.701731 TGGATAGTTGGGTGGGGTTG 59.298 55.000 0.00 0.00 0.00 3.77
3798 4186 0.683179 GGATAGTTGGGTGGGGTTGC 60.683 60.000 0.00 0.00 0.00 4.17
3799 4187 0.039035 GATAGTTGGGTGGGGTTGCA 59.961 55.000 0.00 0.00 0.00 4.08
3801 4189 1.357272 TAGTTGGGTGGGGTTGCAGT 61.357 55.000 0.00 0.00 0.00 4.40
3873 4289 2.486982 CCTTGTGATTCTTGAGGCACAG 59.513 50.000 0.00 0.00 41.63 3.66
3876 4292 2.104622 TGTGATTCTTGAGGCACAGACA 59.895 45.455 0.00 0.00 36.44 3.41
3980 4411 2.477375 TGATACGGTTGAAACTTGTCGC 59.523 45.455 0.00 0.00 0.00 5.19
3989 4420 2.089433 AAACTTGTCGCGCGTCTGTG 62.089 55.000 30.98 18.91 0.00 3.66
4007 4440 7.587629 CGTCTGTGGTTTATATATTCTCGGTA 58.412 38.462 0.00 0.00 0.00 4.02
4109 4547 0.104409 GGGGGACAGGGGATACAGAT 60.104 60.000 0.00 0.00 39.74 2.90
4114 4552 4.450265 GGGGACAGGGGATACAGATAAGTA 60.450 50.000 0.00 0.00 39.74 2.24
4148 4586 7.810658 TCAGTTACTTACACGGAGTAGTTTAG 58.189 38.462 0.00 0.00 41.61 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.698820 GGGGCTGCTGCTTTTGGG 61.699 66.667 15.64 0.00 39.59 4.12
57 59 3.119709 GAGGAGGAGCGAGCGAGTG 62.120 68.421 0.00 0.00 0.00 3.51
58 60 2.826738 GAGGAGGAGCGAGCGAGT 60.827 66.667 0.00 0.00 0.00 4.18
359 367 0.533032 GCGCTCCAGAAGAACCTAGT 59.467 55.000 0.00 0.00 0.00 2.57
380 394 0.327924 TCAACCCGGACCGAGTACTA 59.672 55.000 17.49 0.00 0.00 1.82
394 408 1.222115 GCCGTCGCATAGGATCAACC 61.222 60.000 0.00 0.00 35.11 3.77
427 442 9.634021 CCCTAAAATCTTAGAAAATAAGCCTCT 57.366 33.333 0.00 0.00 37.32 3.69
430 445 7.563924 ACCCCCTAAAATCTTAGAAAATAAGCC 59.436 37.037 0.00 0.00 37.32 4.35
492 513 5.047377 ACAAAACAAAACAGAGAAGGCTTGA 60.047 36.000 3.46 0.00 0.00 3.02
499 520 8.655651 ACTGAAAAACAAAACAAAACAGAGAA 57.344 26.923 0.00 0.00 0.00 2.87
585 742 1.394572 TCGAATCGCAAACAGATGCAG 59.605 47.619 0.00 0.00 46.76 4.41
635 792 3.521126 ACAGGTTGATAAGTCATGGAGCT 59.479 43.478 0.00 0.00 33.56 4.09
640 797 6.343703 TGATCTCACAGGTTGATAAGTCATG 58.656 40.000 0.00 0.00 33.56 3.07
767 933 1.129917 CTGTGAGCAGGATCTGGGAT 58.870 55.000 0.00 0.00 39.01 3.85
786 952 3.713826 TTTTGGGATGTAGGGAGTGAC 57.286 47.619 0.00 0.00 0.00 3.67
788 954 7.745717 TCTTATATTTTGGGATGTAGGGAGTG 58.254 38.462 0.00 0.00 0.00 3.51
862 1028 3.730594 TGTACCAGGATATACTCCCTCCA 59.269 47.826 0.00 0.00 46.27 3.86
879 1045 8.383318 AGTTGCTTGATCATATGTAATGTACC 57.617 34.615 1.90 0.00 0.00 3.34
971 1139 8.537223 GCTGAATACAATGCAATCAAATTACAG 58.463 33.333 0.00 0.00 0.00 2.74
1218 1386 0.108396 TGAAGGCTGCAACAGTAGCA 59.892 50.000 0.50 0.00 41.98 3.49
1245 1413 1.754745 GCCCCTCACAGTGAACAGA 59.245 57.895 4.41 0.00 0.00 3.41
1299 1467 2.938451 CTGCTGCTTTATCGTCAATGGA 59.062 45.455 0.00 0.00 0.00 3.41
1309 1477 1.084370 GCGACGACCTGCTGCTTTAT 61.084 55.000 0.00 0.00 0.00 1.40
1374 1542 0.982704 ACCTGCACTTGATCAGCTCT 59.017 50.000 6.93 0.00 0.00 4.09
1732 2071 1.271379 ACGGAGGGAGTTGTTCATTGG 60.271 52.381 0.00 0.00 0.00 3.16
1733 2072 2.076863 GACGGAGGGAGTTGTTCATTG 58.923 52.381 0.00 0.00 0.00 2.82
1741 2080 0.905357 CATTCTGGACGGAGGGAGTT 59.095 55.000 0.00 0.00 0.00 3.01
1754 2093 1.159285 TTCTGCGGCAAGTCATTCTG 58.841 50.000 3.44 0.00 0.00 3.02
1760 2099 2.095059 ACATTCATTTCTGCGGCAAGTC 60.095 45.455 3.44 0.00 0.00 3.01
1788 2127 9.537192 TGGATGTATCTACAACTAAAAATACGG 57.463 33.333 0.00 0.00 39.99 4.02
1802 2141 5.289595 TGTCGCAGAAATGGATGTATCTAC 58.710 41.667 0.00 0.00 39.69 2.59
1844 2183 7.226918 GTGCTTTCTTTCCATAACCCTATACTC 59.773 40.741 0.00 0.00 0.00 2.59
1887 2226 5.745294 GCGCCAATGCCTATATATGAAATTG 59.255 40.000 0.00 1.32 0.00 2.32
1924 2263 1.426598 AGCTATGCACCCTATTGCCAT 59.573 47.619 0.00 0.00 42.25 4.40
1925 2264 0.846015 AGCTATGCACCCTATTGCCA 59.154 50.000 0.00 0.00 42.25 4.92
1926 2265 1.202806 TCAGCTATGCACCCTATTGCC 60.203 52.381 0.00 0.00 42.25 4.52
1927 2266 2.260844 TCAGCTATGCACCCTATTGC 57.739 50.000 0.00 0.00 43.31 3.56
1928 2267 5.126061 AGTTTTTCAGCTATGCACCCTATTG 59.874 40.000 0.00 0.00 0.00 1.90
1930 2269 4.641989 CAGTTTTTCAGCTATGCACCCTAT 59.358 41.667 0.00 0.00 0.00 2.57
1931 2270 4.009675 CAGTTTTTCAGCTATGCACCCTA 58.990 43.478 0.00 0.00 0.00 3.53
1933 2272 2.819608 TCAGTTTTTCAGCTATGCACCC 59.180 45.455 0.00 0.00 0.00 4.61
1934 2273 4.229876 GTTCAGTTTTTCAGCTATGCACC 58.770 43.478 0.00 0.00 0.00 5.01
1935 2274 4.229876 GGTTCAGTTTTTCAGCTATGCAC 58.770 43.478 0.00 0.00 0.00 4.57
1976 2315 4.829492 CCAGGGACTTTCTTTCATTGACTT 59.171 41.667 0.00 0.00 34.60 3.01
1977 2316 4.401925 CCAGGGACTTTCTTTCATTGACT 58.598 43.478 0.00 0.00 34.60 3.41
1978 2317 3.057245 GCCAGGGACTTTCTTTCATTGAC 60.057 47.826 0.00 0.00 34.60 3.18
1979 2318 3.157087 GCCAGGGACTTTCTTTCATTGA 58.843 45.455 0.00 0.00 34.60 2.57
1980 2319 2.892852 TGCCAGGGACTTTCTTTCATTG 59.107 45.455 0.00 0.00 34.60 2.82
1981 2320 3.243359 TGCCAGGGACTTTCTTTCATT 57.757 42.857 0.00 0.00 34.60 2.57
1982 2321 2.978156 TGCCAGGGACTTTCTTTCAT 57.022 45.000 0.00 0.00 34.60 2.57
1983 2322 2.746279 TTGCCAGGGACTTTCTTTCA 57.254 45.000 0.00 0.00 34.60 2.69
1984 2323 3.573967 TCAATTGCCAGGGACTTTCTTTC 59.426 43.478 0.00 0.00 34.60 2.62
1985 2324 3.321968 GTCAATTGCCAGGGACTTTCTTT 59.678 43.478 0.00 0.00 34.60 2.52
1989 2328 1.247567 CGTCAATTGCCAGGGACTTT 58.752 50.000 0.00 0.00 34.60 2.66
2005 2344 2.928116 GCATACTGTAGACCCAAACGTC 59.072 50.000 0.00 0.00 0.00 4.34
2085 2424 3.372206 CCTAGAATTGACAGAAGCAACGG 59.628 47.826 0.00 0.00 0.00 4.44
2099 2438 6.794534 AGGATTTTTCAGTGACCCTAGAATT 58.205 36.000 0.00 0.00 0.00 2.17
2770 3151 2.158475 TGCCCTTGAACAGACCTTTGAT 60.158 45.455 0.00 0.00 0.00 2.57
2871 3252 1.754380 CTGAAGTGTCCCGACCACCA 61.754 60.000 0.00 0.00 0.00 4.17
2874 3255 2.879233 GCCTGAAGTGTCCCGACCA 61.879 63.158 0.00 0.00 0.00 4.02
2940 3321 1.374252 GTACACCGTGAGCCACAGG 60.374 63.158 5.28 9.29 35.41 4.00
3033 3414 1.475441 CCGCGACGATCTTCTTGAGC 61.475 60.000 8.23 0.00 0.00 4.26
3269 3656 9.987272 CAAAGAAGAATGGTTAATTTCCTTTCT 57.013 29.630 17.03 17.03 45.19 2.52
3273 3660 7.381323 CAGCAAAGAAGAATGGTTAATTTCCT 58.619 34.615 0.00 0.00 0.00 3.36
3274 3661 6.091305 GCAGCAAAGAAGAATGGTTAATTTCC 59.909 38.462 0.00 0.00 0.00 3.13
3275 3662 6.183360 CGCAGCAAAGAAGAATGGTTAATTTC 60.183 38.462 0.00 0.00 0.00 2.17
3301 3688 2.922335 GCAAGGTTCTCGGAAACAATGC 60.922 50.000 12.80 12.80 0.00 3.56
3303 3690 2.582052 TGCAAGGTTCTCGGAAACAAT 58.418 42.857 4.79 0.00 0.00 2.71
3314 3701 0.961019 TGCCAGTCATTGCAAGGTTC 59.039 50.000 11.36 6.02 33.87 3.62
3324 3711 1.304630 TGCCATTGCTGCCAGTCAT 60.305 52.632 0.00 0.00 38.71 3.06
3325 3712 1.974875 CTGCCATTGCTGCCAGTCA 60.975 57.895 0.00 0.00 38.71 3.41
3344 3731 8.416329 GCTCAACCTTTATTATCACCAATGATT 58.584 33.333 0.00 0.00 43.40 2.57
3348 3735 7.961326 AAGCTCAACCTTTATTATCACCAAT 57.039 32.000 0.00 0.00 0.00 3.16
3376 3763 1.034356 AACACACATGCACAGCACAT 58.966 45.000 0.00 0.00 43.04 3.21
3387 3774 4.318332 CTCACTCCACACATAACACACAT 58.682 43.478 0.00 0.00 0.00 3.21
3395 3782 1.202348 CACTCGCTCACTCCACACATA 59.798 52.381 0.00 0.00 0.00 2.29
3411 3798 4.392138 GCCAAATCACCAACTACTACACTC 59.608 45.833 0.00 0.00 0.00 3.51
3484 3871 0.741221 GACAATCGCTCCCTCACCAC 60.741 60.000 0.00 0.00 0.00 4.16
3538 3926 3.357079 CACCAGACGCTGCAACCC 61.357 66.667 0.00 0.00 0.00 4.11
3633 4021 0.107831 GAACACACCACTACCCAGCA 59.892 55.000 0.00 0.00 0.00 4.41
3666 4054 1.675641 CCGCCCCTCCACAAAGAAG 60.676 63.158 0.00 0.00 0.00 2.85
3671 4059 2.196997 CTCAATCCGCCCCTCCACAA 62.197 60.000 0.00 0.00 0.00 3.33
3672 4060 2.609299 TCAATCCGCCCCTCCACA 60.609 61.111 0.00 0.00 0.00 4.17
3678 4066 2.825836 CTGCACTCAATCCGCCCC 60.826 66.667 0.00 0.00 0.00 5.80
3692 4080 2.817423 CGAGGCGAAATGGAGCTGC 61.817 63.158 0.00 0.00 0.00 5.25
3718 4106 5.001874 GGACAAAACGGAAGAGAATTACCT 58.998 41.667 0.00 0.00 0.00 3.08
3733 4121 1.335872 CGGGCATTCACAGGACAAAAC 60.336 52.381 0.00 0.00 0.00 2.43
3737 4125 2.359850 GCGGGCATTCACAGGACA 60.360 61.111 0.00 0.00 0.00 4.02
3760 4148 1.159285 CACGGTCTGCACATGAACAT 58.841 50.000 0.00 0.00 0.00 2.71
3768 4156 1.359848 CAACTATCCACGGTCTGCAC 58.640 55.000 0.00 0.00 0.00 4.57
3777 4165 0.702316 AACCCCACCCAACTATCCAC 59.298 55.000 0.00 0.00 0.00 4.02
3782 4170 1.357272 ACTGCAACCCCACCCAACTA 61.357 55.000 0.00 0.00 0.00 2.24
3787 4175 1.152546 AAGAACTGCAACCCCACCC 60.153 57.895 0.00 0.00 0.00 4.61
3790 4178 0.843309 TCTGAAGAACTGCAACCCCA 59.157 50.000 0.00 0.00 0.00 4.96
3791 4179 2.206576 ATCTGAAGAACTGCAACCCC 57.793 50.000 0.00 0.00 0.00 4.95
3792 4180 3.149196 TGAATCTGAAGAACTGCAACCC 58.851 45.455 0.00 0.00 0.00 4.11
3793 4181 4.436584 CGATGAATCTGAAGAACTGCAACC 60.437 45.833 0.00 0.00 0.00 3.77
3794 4182 4.436584 CCGATGAATCTGAAGAACTGCAAC 60.437 45.833 0.00 0.00 0.00 4.17
3796 4184 3.055891 TCCGATGAATCTGAAGAACTGCA 60.056 43.478 0.00 0.00 0.00 4.41
3797 4185 3.525537 TCCGATGAATCTGAAGAACTGC 58.474 45.455 0.00 0.00 0.00 4.40
3798 4186 4.025061 GCATCCGATGAATCTGAAGAACTG 60.025 45.833 12.79 0.00 0.00 3.16
3799 4187 4.125703 GCATCCGATGAATCTGAAGAACT 58.874 43.478 12.79 0.00 0.00 3.01
3801 4189 3.126073 CGCATCCGATGAATCTGAAGAA 58.874 45.455 12.79 0.00 36.29 2.52
3980 4411 5.059343 CGAGAATATATAAACCACAGACGCG 59.941 44.000 3.53 3.53 0.00 6.01
4015 4448 4.287067 GGCACTCTCCCCTAATGATCATTA 59.713 45.833 23.46 23.46 32.50 1.90
4023 4456 0.988678 GGTGGGCACTCTCCCCTAAT 60.989 60.000 0.00 0.00 45.97 1.73
4040 4476 6.825610 TGGCACTTTTAAATGAAATTCAGGT 58.174 32.000 8.00 0.00 33.67 4.00
4123 4561 6.639632 AAACTACTCCGTGTAAGTAACTGA 57.360 37.500 0.00 0.00 0.00 3.41
4124 4562 7.536622 CACTAAACTACTCCGTGTAAGTAACTG 59.463 40.741 0.00 0.00 0.00 3.16
4125 4563 7.229506 ACACTAAACTACTCCGTGTAAGTAACT 59.770 37.037 0.00 0.00 37.09 2.24
4126 4564 7.363431 ACACTAAACTACTCCGTGTAAGTAAC 58.637 38.462 0.00 0.00 37.09 2.50
4127 4565 7.510549 ACACTAAACTACTCCGTGTAAGTAA 57.489 36.000 0.00 0.00 37.09 2.24
4128 4566 6.128553 CGACACTAAACTACTCCGTGTAAGTA 60.129 42.308 0.00 0.00 38.77 2.24
4148 4586 4.438346 ACCACAGAAGCACGACAC 57.562 55.556 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.