Multiple sequence alignment - TraesCS7D01G218000

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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 TraesCS7D01G218000 chr7D 100.000 4202 0 0 1 4202 178612227 178608026 0.000000e+00 7760.0
1 TraesCS7D01G218000 chr7A 92.871 4250 204 46 1 4202 182619318 182615120 0.000000e+00 6078.0
2 TraesCS7D01G218000 chr7B 93.107 3714 186 37 1 3675 144664719 144661037 0.000000e+00 5376.0
3 TraesCS7D01G218000 chr7B 90.355 394 31 7 3815 4202 144660953 144660561 1.040000e-140 510.0
4 TraesCS7D01G218000 chr7B 91.892 74 5 1 3700 3772 144661041 144660968 7.430000e-18 102.0
5 TraesCS7D01G218000 chr2D 96.774 31 1 0 1713 1743 335132017 335131987 8.000000e-03 52.8
6 TraesCS7D01G218000 chr2B 96.774 31 1 0 1713 1743 403106517 403106487 8.000000e-03 52.8
7 TraesCS7D01G218000 chr2A 96.774 31 1 0 1713 1743 445758739 445758709 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 TraesCS7D01G218000 chr7D 178608026 178612227 4201 True 7760 7760 100.000000 1 4202 1 chr7D.!!$R1 4201
1 TraesCS7D01G218000 chr7A 182615120 182619318 4198 True 6078 6078 92.871000 1 4202 1 chr7A.!!$R1 4201
2 TraesCS7D01G218000 chr7B 144660561 144664719 4158 True 1996 5376 91.784667 1 4202 3 chr7B.!!$R1 4201

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
229 240 0.452784 ATCAAAAGACGAAAGCGCGC 60.453 50.0 26.66 26.66 42.48 6.86 F
705 724 1.102154 CCTGTTGTGGCTTGTGACAA 58.898 50.0 0.00 0.00 29.94 3.18 F
2676 2726 0.818040 AAGTTGTCAACCAGGTCCGC 60.818 55.0 12.17 0.00 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1536 0.389757 GCCAAGGATCCCGTCTCTAC 59.610 60.0 8.55 0.0 0.00 2.59 R
2685 2735 0.833287 TAGGTTCTGCCATGAGCTCC 59.167 55.0 12.15 0.0 44.23 4.70 R
3798 3856 0.191064 ACTGGACAGAGGAACAGGGA 59.809 55.0 6.29 0.0 35.34 4.20 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
76 77 1.333636 CCCCTGCTTCGATCTCTGGT 61.334 60.000 0.00 0.00 0.00 4.00
81 82 1.478510 TGCTTCGATCTCTGGTTCTCC 59.521 52.381 0.00 0.00 0.00 3.71
229 240 0.452784 ATCAAAAGACGAAAGCGCGC 60.453 50.000 26.66 26.66 42.48 6.86
249 261 2.677875 CACCCCCTGCCTGCTTTC 60.678 66.667 0.00 0.00 0.00 2.62
250 262 4.351054 ACCCCCTGCCTGCTTTCG 62.351 66.667 0.00 0.00 0.00 3.46
258 270 2.815647 CCTGCTTTCGCCGGTCTC 60.816 66.667 1.90 0.00 35.96 3.36
291 305 3.796844 GCTTTCCCTCAGTTTTCTGCAAC 60.797 47.826 0.00 0.00 46.59 4.17
400 418 2.373540 TCGTAGTAAAATGCGCCTGT 57.626 45.000 4.18 0.00 0.00 4.00
500 519 4.320567 GGAAAGAAAGAAAGAAAGAGGGCG 60.321 45.833 0.00 0.00 0.00 6.13
518 537 3.049080 GCCCCTCTTTGCGGATCCT 62.049 63.158 10.75 0.00 0.00 3.24
566 585 2.300437 GGGAGTGCTACATCTACATCCC 59.700 54.545 0.00 0.00 38.51 3.85
633 652 2.614779 CTCTCGCCAGTGCCATATATG 58.385 52.381 5.68 5.68 0.00 1.78
688 707 8.429641 TCTCAAGTGATAACTTTGTTAAGTCCT 58.570 33.333 0.00 0.00 43.74 3.85
705 724 1.102154 CCTGTTGTGGCTTGTGACAA 58.898 50.000 0.00 0.00 29.94 3.18
725 744 4.278170 ACAAGTCTCACTTCTCTCTCACTG 59.722 45.833 0.00 0.00 36.03 3.66
730 749 4.075682 CTCACTTCTCTCTCACTGTGGTA 58.924 47.826 8.11 0.00 0.00 3.25
794 813 6.373005 TCTTGATCTTGTTTGGGACTGATA 57.627 37.500 0.00 0.00 0.00 2.15
798 817 6.542821 TGATCTTGTTTGGGACTGATAGTTT 58.457 36.000 0.00 0.00 0.00 2.66
821 840 5.876612 ACTGTTGATGATCTTTTGCTCTC 57.123 39.130 0.00 0.00 0.00 3.20
1019 1038 3.057033 GCAATGACTTCCAAGACAATGCT 60.057 43.478 18.57 0.00 46.53 3.79
1046 1065 2.469952 CATCCCAACAATCCCCAACAT 58.530 47.619 0.00 0.00 0.00 2.71
1065 1084 4.614946 ACATTGAAGAAAAGAAGCAGTGC 58.385 39.130 7.13 7.13 0.00 4.40
1171 1190 3.678529 GCCAAGCAGTCCAAACAAAGAAA 60.679 43.478 0.00 0.00 0.00 2.52
1181 1200 4.584325 TCCAAACAAAGAAATCCAGTCCAG 59.416 41.667 0.00 0.00 0.00 3.86
1206 1225 2.486982 CCAGAAACCATCTCACAAGCTG 59.513 50.000 0.00 0.00 35.73 4.24
1517 1536 2.372504 AGGCAATCCAGATGATCAGGAG 59.627 50.000 12.25 1.26 35.45 3.69
1530 1549 2.642154 TCAGGAGTAGAGACGGGATC 57.358 55.000 0.00 0.00 0.00 3.36
1581 1600 3.521126 AGAAGCTAGGATGTGGTGACATT 59.479 43.478 0.00 0.00 43.22 2.71
1602 1621 4.350368 TGGCAGTGTGTATCTTTCAGAA 57.650 40.909 0.00 0.00 0.00 3.02
1656 1675 3.010584 AGGTTATGGACAAGGCATCACTT 59.989 43.478 0.00 0.00 0.00 3.16
1711 1730 4.579869 TGAGAAGGAAATCTTACAGTGCC 58.420 43.478 0.00 0.00 35.50 5.01
1773 1792 5.275067 AGACTGATAAGTTCTCATGCCTC 57.725 43.478 0.00 0.00 0.00 4.70
1883 1902 4.081697 TGTCTGATCCATCTTTTACGCTGA 60.082 41.667 0.00 0.00 0.00 4.26
1884 1903 4.505922 GTCTGATCCATCTTTTACGCTGAG 59.494 45.833 0.00 0.00 0.00 3.35
1906 1925 9.953697 CTGAGCGTAATATACTTTACTCTCTTT 57.046 33.333 13.47 0.00 41.34 2.52
1931 1950 8.592105 TTTGACTTTTAGGATTCAGCATTTTG 57.408 30.769 0.00 0.00 0.00 2.44
1935 1954 9.129209 GACTTTTAGGATTCAGCATTTTGTTAC 57.871 33.333 0.00 0.00 0.00 2.50
1942 1961 9.860898 AGGATTCAGCATTTTGTTACTATTTTC 57.139 29.630 0.00 0.00 0.00 2.29
1970 1989 8.806146 ACACAATAGCTTTTATCCAATTCTGTT 58.194 29.630 0.00 0.00 0.00 3.16
1983 2002 5.835819 TCCAATTCTGTTTGTTCCCATGTAA 59.164 36.000 0.00 0.00 0.00 2.41
2023 2042 8.208224 TGAAGAATAGCGGAAAGTTATTATCCA 58.792 33.333 0.00 0.00 36.56 3.41
2028 2047 6.300354 AGCGGAAAGTTATTATCCATTTCG 57.700 37.500 0.00 0.00 32.58 3.46
2061 2080 8.715191 TGAATGTATGGAAAATTGCCATTAAC 57.285 30.769 11.35 4.90 43.42 2.01
2065 2084 7.827701 TGTATGGAAAATTGCCATTAACGTAA 58.172 30.769 11.35 0.00 43.42 3.18
2081 2100 5.707411 AACGTAACTAATTGGCGACATAC 57.293 39.130 0.00 0.00 42.32 2.39
2095 2115 2.606065 CGACATACCGTGTGTCTTGTGA 60.606 50.000 21.69 0.00 42.36 3.58
2128 2151 5.215160 ACGAGAAAGCAACTGCAAATTTAG 58.785 37.500 4.22 0.00 45.16 1.85
2204 2252 7.546778 TGAAGCAAATACAACATATAGCGAA 57.453 32.000 0.00 0.00 0.00 4.70
2295 2345 3.692257 AAAGCTACTGCACACTGATCT 57.308 42.857 0.00 0.00 42.74 2.75
2301 2351 4.685165 GCTACTGCACACTGATCTGATATG 59.315 45.833 6.60 2.94 39.41 1.78
2364 2414 3.455910 TCCTTGCTATGGAGTACTTGCAT 59.544 43.478 0.00 0.78 41.20 3.96
2370 2420 5.245977 TGCTATGGAGTACTTGCATATGCTA 59.754 40.000 27.13 19.39 39.09 3.49
2373 2423 3.244215 TGGAGTACTTGCATATGCTAGGC 60.244 47.826 32.74 25.88 45.76 3.93
2493 2543 3.226777 CCCGACTCTAATCAGGTCATCT 58.773 50.000 0.00 0.00 0.00 2.90
2676 2726 0.818040 AAGTTGTCAACCAGGTCCGC 60.818 55.000 12.17 0.00 0.00 5.54
2712 2762 1.279496 TGGCAGAACCTAGTGATGCT 58.721 50.000 6.47 0.00 40.22 3.79
2739 2789 2.575694 TGTCATTTGTTGGCACACAC 57.424 45.000 0.00 0.00 39.29 3.82
2778 2828 3.464833 AGATTATCAAAGGTGAGGGCCAT 59.535 43.478 6.18 0.00 37.14 4.40
2820 2870 9.177927 TGGTGGACCTTTGGTATATTCTTATAT 57.822 33.333 0.00 0.00 35.25 0.86
2871 2921 0.599204 GTTCAGGAAACCGAGCGACA 60.599 55.000 0.00 0.00 31.20 4.35
2907 2957 4.383602 CAGCCGTTGCGTTTCCCG 62.384 66.667 0.00 0.00 44.33 5.14
3117 3167 3.239861 GCAGACTACAAAGCTGCCT 57.760 52.632 0.00 0.00 42.30 4.75
3263 3316 3.821033 AGAAGTTGTAGGCTTTTCGCATT 59.179 39.130 0.00 0.00 41.67 3.56
3334 3387 8.220755 AGCTATTTTCTGTTTTGTAGTGAACA 57.779 30.769 0.00 0.00 35.88 3.18
3349 3402 7.424803 TGTAGTGAACAAATTGGATGTTTCAG 58.575 34.615 0.00 0.00 40.90 3.02
3383 3436 3.807622 TCCACAAGTTTTGAAGTCGCTAG 59.192 43.478 0.00 0.00 0.00 3.42
3403 3456 6.400515 CGCTAGTCTTTGTGAGTTGAAATCTC 60.401 42.308 0.00 0.00 0.00 2.75
3404 3457 5.914085 AGTCTTTGTGAGTTGAAATCTCG 57.086 39.130 0.00 0.00 34.99 4.04
3405 3458 5.360591 AGTCTTTGTGAGTTGAAATCTCGT 58.639 37.500 0.00 0.00 34.99 4.18
3406 3459 5.235186 AGTCTTTGTGAGTTGAAATCTCGTG 59.765 40.000 0.00 0.00 34.99 4.35
3407 3460 3.878086 TTGTGAGTTGAAATCTCGTGC 57.122 42.857 0.00 0.00 34.99 5.34
3408 3461 1.792367 TGTGAGTTGAAATCTCGTGCG 59.208 47.619 0.00 0.00 34.99 5.34
3409 3462 0.790207 TGAGTTGAAATCTCGTGCGC 59.210 50.000 0.00 0.00 34.99 6.09
3410 3463 0.095417 GAGTTGAAATCTCGTGCGCC 59.905 55.000 4.18 0.00 0.00 6.53
3468 3523 7.042950 TGCTGCCGTGAAATAAGTTATTACTA 58.957 34.615 8.54 0.00 33.17 1.82
3489 3544 0.392998 CAGCAACCGAGGCACCTTAT 60.393 55.000 0.00 0.00 0.00 1.73
3554 3610 1.009675 CGTTGCTGTTGCTCACACC 60.010 57.895 0.00 0.00 40.48 4.16
3560 3616 0.603707 CTGTTGCTCACACCGATGGT 60.604 55.000 0.00 0.00 35.62 3.55
3601 3657 2.470983 TGAATCACATTCAGGCGACA 57.529 45.000 0.00 0.00 43.84 4.35
3605 3661 2.542020 TCACATTCAGGCGACAAAGA 57.458 45.000 0.00 0.00 0.00 2.52
3607 3663 1.197721 CACATTCAGGCGACAAAGACC 59.802 52.381 0.00 0.00 0.00 3.85
3634 3690 8.289618 TGCTGAAATAGTGTTTGATTGAAGTAC 58.710 33.333 0.00 0.00 0.00 2.73
3712 3770 2.383368 AGTTGCTGAGCTCACTGATC 57.617 50.000 13.74 2.83 0.00 2.92
3749 3807 4.275196 CACAGATGCTCCCTATCAACAATG 59.725 45.833 0.00 0.00 0.00 2.82
3752 3810 5.768662 CAGATGCTCCCTATCAACAATGATT 59.231 40.000 0.00 0.00 43.89 2.57
3777 3835 9.653287 TTCTACTAATTGATTGTCTACACCTTG 57.347 33.333 0.00 0.00 0.00 3.61
3779 3837 7.672983 ACTAATTGATTGTCTACACCTTGTG 57.327 36.000 0.00 0.00 39.75 3.33
3784 3842 5.237815 TGATTGTCTACACCTTGTGCTTAG 58.762 41.667 0.00 0.00 36.98 2.18
3789 3847 1.538047 ACACCTTGTGCTTAGCCATG 58.462 50.000 0.29 2.08 36.98 3.66
3793 3851 1.474077 CCTTGTGCTTAGCCATGTTCC 59.526 52.381 0.29 0.00 0.00 3.62
3794 3852 1.474077 CTTGTGCTTAGCCATGTTCCC 59.526 52.381 0.29 0.00 0.00 3.97
3795 3853 0.698238 TGTGCTTAGCCATGTTCCCT 59.302 50.000 0.29 0.00 0.00 4.20
3796 3854 1.340017 TGTGCTTAGCCATGTTCCCTC 60.340 52.381 0.29 0.00 0.00 4.30
3797 3855 1.065126 GTGCTTAGCCATGTTCCCTCT 60.065 52.381 0.29 0.00 0.00 3.69
3798 3856 1.635487 TGCTTAGCCATGTTCCCTCTT 59.365 47.619 0.29 0.00 0.00 2.85
3799 3857 2.293170 GCTTAGCCATGTTCCCTCTTC 58.707 52.381 0.00 0.00 0.00 2.87
3800 3858 2.924421 CTTAGCCATGTTCCCTCTTCC 58.076 52.381 0.00 0.00 0.00 3.46
3801 3859 1.213296 TAGCCATGTTCCCTCTTCCC 58.787 55.000 0.00 0.00 0.00 3.97
3802 3860 0.551131 AGCCATGTTCCCTCTTCCCT 60.551 55.000 0.00 0.00 0.00 4.20
3803 3861 0.394899 GCCATGTTCCCTCTTCCCTG 60.395 60.000 0.00 0.00 0.00 4.45
3804 3862 0.995024 CCATGTTCCCTCTTCCCTGT 59.005 55.000 0.00 0.00 0.00 4.00
3805 3863 1.355720 CCATGTTCCCTCTTCCCTGTT 59.644 52.381 0.00 0.00 0.00 3.16
3806 3864 2.619074 CCATGTTCCCTCTTCCCTGTTC 60.619 54.545 0.00 0.00 0.00 3.18
3807 3865 1.064825 TGTTCCCTCTTCCCTGTTCC 58.935 55.000 0.00 0.00 0.00 3.62
3823 3881 2.271800 GTTCCTCTGTCCAGTTATGCG 58.728 52.381 0.00 0.00 0.00 4.73
3832 3890 0.452618 CCAGTTATGCGTGTTGTGCG 60.453 55.000 0.00 0.00 34.24 5.34
3877 3935 1.869774 TGCGTGCATCTGTATCATCC 58.130 50.000 0.00 0.00 0.00 3.51
3887 3945 5.928839 GCATCTGTATCATCCGTATGTTTCT 59.071 40.000 0.00 0.00 34.50 2.52
3900 3958 5.231991 CCGTATGTTTCTAATTGCAATTGCC 59.768 40.000 30.43 15.29 41.18 4.52
3951 4011 7.625828 ACAATTAAGTACAAGGCTCATTACC 57.374 36.000 0.00 0.00 0.00 2.85
3955 4015 8.644374 ATTAAGTACAAGGCTCATTACCAAAA 57.356 30.769 0.00 0.00 0.00 2.44
4003 4067 4.512198 CAGAGATATGCTGAAAAGCTCCAG 59.488 45.833 6.41 6.41 35.39 3.86
4009 4073 1.337823 GCTGAAAAGCTCCAGGTACGA 60.338 52.381 11.21 0.00 0.00 3.43
4050 4114 5.556915 ACACCATGGATCGAGAAGTTTAAA 58.443 37.500 21.47 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 0.340208 GGGAGGAAGAGGGAGGAGAA 59.660 60.000 0.00 0.00 0.00 2.87
81 82 3.157949 GGCGGGAGGAAGAGGGAG 61.158 72.222 0.00 0.00 0.00 4.30
151 158 2.476241 CGTAAAAAGAGTAAACGGCGGT 59.524 45.455 13.24 0.00 0.00 5.68
248 260 0.179084 GGAAATCATGAGACCGGCGA 60.179 55.000 9.30 0.00 0.00 5.54
249 261 1.160329 GGGAAATCATGAGACCGGCG 61.160 60.000 0.00 0.00 0.00 6.46
250 262 1.160329 CGGGAAATCATGAGACCGGC 61.160 60.000 17.39 0.00 37.80 6.13
251 263 1.160329 GCGGGAAATCATGAGACCGG 61.160 60.000 22.96 18.63 41.46 5.28
252 264 0.179073 AGCGGGAAATCATGAGACCG 60.179 55.000 19.61 19.61 43.81 4.79
253 265 2.044123 AAGCGGGAAATCATGAGACC 57.956 50.000 0.09 4.38 0.00 3.85
254 266 2.356069 GGAAAGCGGGAAATCATGAGAC 59.644 50.000 0.09 0.00 0.00 3.36
255 267 2.643551 GGAAAGCGGGAAATCATGAGA 58.356 47.619 0.09 0.00 0.00 3.27
256 268 1.678101 GGGAAAGCGGGAAATCATGAG 59.322 52.381 0.09 0.00 0.00 2.90
257 269 1.284785 AGGGAAAGCGGGAAATCATGA 59.715 47.619 0.00 0.00 0.00 3.07
258 270 1.678101 GAGGGAAAGCGGGAAATCATG 59.322 52.381 0.00 0.00 0.00 3.07
291 305 2.220824 TCACATCGAAACGCAGACTTTG 59.779 45.455 0.00 0.00 0.00 2.77
400 418 2.987125 GACGCCTTTAGCCCCTCA 59.013 61.111 0.00 0.00 38.78 3.86
566 585 7.201556 CCACTAACTGTAATCATGCAACACTAG 60.202 40.741 0.00 0.00 0.00 2.57
633 652 0.252330 GCCCCTCCTATCCTAGTCCC 60.252 65.000 0.00 0.00 0.00 4.46
688 707 1.742831 GACTTGTCACAAGCCACAACA 59.257 47.619 17.93 0.00 0.00 3.33
705 724 3.820467 CACAGTGAGAGAGAAGTGAGACT 59.180 47.826 0.00 0.00 0.00 3.24
725 744 3.456277 AGATCCATCAACCTTCCTACCAC 59.544 47.826 0.00 0.00 0.00 4.16
730 749 3.199508 CACTCAGATCCATCAACCTTCCT 59.800 47.826 0.00 0.00 0.00 3.36
794 813 7.446625 AGAGCAAAAGATCATCAACAGTAAACT 59.553 33.333 0.00 0.00 0.00 2.66
798 817 6.592994 CAGAGAGCAAAAGATCATCAACAGTA 59.407 38.462 0.00 0.00 0.00 2.74
821 840 4.118410 GACTACATGAGCCATCAACTCAG 58.882 47.826 0.00 0.00 46.71 3.35
849 868 7.678947 AAGATAGATACATGCAGGCAATAAC 57.321 36.000 0.00 0.00 0.00 1.89
1019 1038 2.534990 GGATTGTTGGGATGGTTTGGA 58.465 47.619 0.00 0.00 0.00 3.53
1046 1065 4.202441 AGAGCACTGCTTCTTTTCTTCAA 58.798 39.130 4.67 0.00 39.88 2.69
1065 1084 4.894705 TCCAGAGAGGAATCATTCTGAGAG 59.105 45.833 0.00 0.00 45.65 3.20
1149 1168 1.408702 TCTTTGTTTGGACTGCTTGGC 59.591 47.619 0.00 0.00 0.00 4.52
1152 1171 4.405358 TGGATTTCTTTGTTTGGACTGCTT 59.595 37.500 0.00 0.00 0.00 3.91
1171 1190 2.030027 TTCTGGTCACTGGACTGGAT 57.970 50.000 0.00 0.00 43.77 3.41
1181 1200 3.126001 TGTGAGATGGTTTCTGGTCAC 57.874 47.619 0.00 0.00 33.74 3.67
1206 1225 3.000041 TGTAACATCAACGGACTCATGC 59.000 45.455 0.00 0.00 0.00 4.06
1289 1308 1.260206 CGTCGAGTCTGATTTCACGG 58.740 55.000 0.00 0.00 0.00 4.94
1425 1444 2.607892 GCACGCGCTTTCCTCACTT 61.608 57.895 5.73 0.00 34.30 3.16
1517 1536 0.389757 GCCAAGGATCCCGTCTCTAC 59.610 60.000 8.55 0.00 0.00 2.59
1545 1564 8.772705 CATCCTAGCTTCTTCAATAGCTTAAAG 58.227 37.037 1.59 0.00 45.03 1.85
1569 1588 1.250328 CACTGCCAATGTCACCACAT 58.750 50.000 0.00 0.00 45.89 3.21
1581 1600 4.350368 TTCTGAAAGATACACACTGCCA 57.650 40.909 0.00 0.00 46.36 4.92
1602 1621 4.851639 ATAGCTCTTGGTTCCAGTCAAT 57.148 40.909 0.00 0.00 0.00 2.57
1656 1675 1.621814 AGCAACTTCTTACGGCCTGTA 59.378 47.619 0.00 1.81 0.00 2.74
1711 1730 5.012239 TGTTGGAAGAAAAGGATGATCCAG 58.988 41.667 14.90 0.00 39.61 3.86
1773 1792 1.656652 CAGGGCAGAACTCCATAACG 58.343 55.000 0.00 0.00 0.00 3.18
1901 1920 7.651808 TGCTGAATCCTAAAAGTCAAAAAGAG 58.348 34.615 0.00 0.00 0.00 2.85
1906 1925 8.203485 ACAAAATGCTGAATCCTAAAAGTCAAA 58.797 29.630 0.00 0.00 0.00 2.69
1942 1961 9.079833 CAGAATTGGATAAAAGCTATTGTGTTG 57.920 33.333 0.00 0.00 0.00 3.33
1944 1963 8.353423 ACAGAATTGGATAAAAGCTATTGTGT 57.647 30.769 0.00 0.00 0.00 3.72
1945 1964 9.643693 AAACAGAATTGGATAAAAGCTATTGTG 57.356 29.630 0.00 0.00 0.00 3.33
1954 1973 7.366847 TGGGAACAAACAGAATTGGATAAAA 57.633 32.000 0.00 0.00 37.44 1.52
1983 2002 1.745232 TCTTCACTTTGTTGCCACGT 58.255 45.000 0.00 0.00 0.00 4.49
2023 2042 6.582636 TCCATACATTCAGCTAACTCGAAAT 58.417 36.000 0.00 0.00 0.00 2.17
2028 2047 7.433425 GCAATTTTCCATACATTCAGCTAACTC 59.567 37.037 0.00 0.00 0.00 3.01
2057 2076 6.255453 GGTATGTCGCCAATTAGTTACGTTAA 59.745 38.462 0.00 0.00 0.00 2.01
2061 2080 3.180980 CGGTATGTCGCCAATTAGTTACG 59.819 47.826 0.00 0.00 0.00 3.18
2065 2084 2.093869 ACACGGTATGTCGCCAATTAGT 60.094 45.455 0.00 0.00 36.54 2.24
2081 2100 4.027572 ACAATTTTCACAAGACACACGG 57.972 40.909 0.00 0.00 0.00 4.94
2095 2115 5.516339 CAGTTGCTTTCTCGTTGACAATTTT 59.484 36.000 0.00 0.00 0.00 1.82
2128 2151 5.039333 GCATGGATGTAATCTGAAGCAAAC 58.961 41.667 0.00 0.00 44.71 2.93
2278 2328 2.662006 TCAGATCAGTGTGCAGTAGC 57.338 50.000 0.00 0.00 42.57 3.58
2295 2345 8.009622 TGCAATTAAGAAGAAATGCCATATCA 57.990 30.769 0.00 0.00 0.00 2.15
2301 2351 7.263496 AGAATCTGCAATTAAGAAGAAATGCC 58.737 34.615 0.00 0.00 0.00 4.40
2317 2367 5.994054 GGATTTCTGCTACATAGAATCTGCA 59.006 40.000 0.00 0.00 34.42 4.41
2370 2420 6.535963 TTCAGATCACGATATATGATGCCT 57.464 37.500 6.67 0.00 36.92 4.75
2373 2423 6.476053 CAGGCTTCAGATCACGATATATGATG 59.524 42.308 6.67 0.00 36.92 3.07
2493 2543 4.690748 CGAAGTGCTTCTGTTTCAGGATTA 59.309 41.667 9.84 0.00 37.44 1.75
2676 2726 3.882326 ATGAGCTCCGGCCATGGG 61.882 66.667 15.13 0.00 39.73 4.00
2685 2735 0.833287 TAGGTTCTGCCATGAGCTCC 59.167 55.000 12.15 0.00 44.23 4.70
2712 2762 3.505293 TGCCAACAAATGACATTGATCGA 59.495 39.130 0.34 0.00 34.38 3.59
2739 2789 0.970937 TCTCAGGGGCCAAGTACTCG 60.971 60.000 4.39 0.00 0.00 4.18
2778 2828 1.526686 CCAGTCAACAGCACTGCCA 60.527 57.895 0.00 0.00 40.10 4.92
2820 2870 1.333619 GTTTTGCCGAACAGAAGCTCA 59.666 47.619 0.00 0.00 0.00 4.26
2859 2909 0.179094 TGAACAGTGTCGCTCGGTTT 60.179 50.000 0.00 0.00 0.00 3.27
2871 2921 3.329386 CTGACCGATGACATTGAACAGT 58.671 45.455 4.07 0.00 0.00 3.55
2907 2957 2.789409 AGCTCACAACTGGGTATTCC 57.211 50.000 0.00 0.00 0.00 3.01
3117 3167 2.899900 ACTAGCCTCAGATGTTGACACA 59.100 45.455 0.00 0.00 37.31 3.72
3221 3271 9.643693 AACTTCTAATTATGCAAACAAATGGAG 57.356 29.630 0.00 0.00 0.00 3.86
3263 3316 4.459337 ACGACTCATCTGTCAGACACATAA 59.541 41.667 4.21 0.00 36.82 1.90
3383 3436 5.435557 CACGAGATTTCAACTCACAAAGAC 58.564 41.667 0.00 0.00 34.47 3.01
3406 3459 1.583709 GCTTAATTCTGCACGGCGC 60.584 57.895 6.90 0.00 42.89 6.53
3407 3460 0.026803 GAGCTTAATTCTGCACGGCG 59.973 55.000 4.80 4.80 0.00 6.46
3408 3461 1.063174 CTGAGCTTAATTCTGCACGGC 59.937 52.381 0.00 0.00 0.00 5.68
3409 3462 2.350522 ACTGAGCTTAATTCTGCACGG 58.649 47.619 0.00 6.40 33.49 4.94
3410 3463 4.410492 AAACTGAGCTTAATTCTGCACG 57.590 40.909 0.00 0.00 0.00 5.34
3448 3503 9.256477 TGCTGATAGTAATAACTTATTTCACGG 57.744 33.333 0.00 0.00 37.15 4.94
3456 3511 7.431249 CCTCGGTTGCTGATAGTAATAACTTA 58.569 38.462 0.00 0.00 37.15 2.24
3468 3523 2.045926 GGTGCCTCGGTTGCTGAT 60.046 61.111 0.00 0.00 0.00 2.90
3477 3532 1.371558 GGCCCTATAAGGTGCCTCG 59.628 63.158 14.62 0.00 43.84 4.63
3489 3544 1.218196 TCCCAACAAAACAAGGCCCTA 59.782 47.619 0.00 0.00 0.00 3.53
3601 3657 5.827797 TCAAACACTATTTCAGCAGGTCTTT 59.172 36.000 0.00 0.00 0.00 2.52
3605 3661 5.769662 TCAATCAAACACTATTTCAGCAGGT 59.230 36.000 0.00 0.00 0.00 4.00
3607 3663 7.365741 ACTTCAATCAAACACTATTTCAGCAG 58.634 34.615 0.00 0.00 0.00 4.24
3634 3690 4.371786 AGCTGACATACACATGATTACCG 58.628 43.478 0.00 0.00 35.96 4.02
3712 3770 5.769967 GCATCTGTGCTATATTTAGGACG 57.230 43.478 9.59 5.69 46.57 4.79
3752 3810 8.812972 ACAAGGTGTAGACAATCAATTAGTAGA 58.187 33.333 0.00 0.00 0.00 2.59
3767 3825 1.974957 TGGCTAAGCACAAGGTGTAGA 59.025 47.619 0.00 0.00 35.75 2.59
3773 3831 1.474077 GGAACATGGCTAAGCACAAGG 59.526 52.381 0.00 0.00 0.00 3.61
3777 3835 1.065126 AGAGGGAACATGGCTAAGCAC 60.065 52.381 0.00 0.00 0.00 4.40
3779 3837 2.293170 GAAGAGGGAACATGGCTAAGC 58.707 52.381 0.00 0.00 0.00 3.09
3784 3842 0.394899 CAGGGAAGAGGGAACATGGC 60.395 60.000 0.00 0.00 0.00 4.40
3789 3847 1.279558 GAGGAACAGGGAAGAGGGAAC 59.720 57.143 0.00 0.00 0.00 3.62
3793 3851 1.552792 GACAGAGGAACAGGGAAGAGG 59.447 57.143 0.00 0.00 0.00 3.69
3794 3852 1.552792 GGACAGAGGAACAGGGAAGAG 59.447 57.143 0.00 0.00 0.00 2.85
3795 3853 1.132849 TGGACAGAGGAACAGGGAAGA 60.133 52.381 0.00 0.00 0.00 2.87
3796 3854 1.277557 CTGGACAGAGGAACAGGGAAG 59.722 57.143 0.00 0.00 0.00 3.46
3797 3855 1.352083 CTGGACAGAGGAACAGGGAA 58.648 55.000 0.00 0.00 0.00 3.97
3798 3856 0.191064 ACTGGACAGAGGAACAGGGA 59.809 55.000 6.29 0.00 35.34 4.20
3799 3857 1.059913 AACTGGACAGAGGAACAGGG 58.940 55.000 6.29 0.00 35.34 4.45
3800 3858 3.866651 CATAACTGGACAGAGGAACAGG 58.133 50.000 6.29 0.00 35.34 4.00
3801 3859 3.265791 GCATAACTGGACAGAGGAACAG 58.734 50.000 6.29 0.00 37.01 3.16
3802 3860 2.353704 CGCATAACTGGACAGAGGAACA 60.354 50.000 6.29 0.00 0.00 3.18
3803 3861 2.271800 CGCATAACTGGACAGAGGAAC 58.728 52.381 6.29 0.00 0.00 3.62
3804 3862 1.899814 ACGCATAACTGGACAGAGGAA 59.100 47.619 6.29 0.00 0.00 3.36
3805 3863 1.204704 CACGCATAACTGGACAGAGGA 59.795 52.381 6.29 0.00 0.00 3.71
3806 3864 1.066858 ACACGCATAACTGGACAGAGG 60.067 52.381 6.29 0.00 0.00 3.69
3807 3865 2.370281 ACACGCATAACTGGACAGAG 57.630 50.000 6.29 0.00 0.00 3.35
3823 3881 5.685511 ACTTCATAAACATTTCGCACAACAC 59.314 36.000 0.00 0.00 0.00 3.32
3858 3916 1.869342 CGGATGATACAGATGCACGCA 60.869 52.381 0.00 0.00 0.00 5.24
3859 3917 0.786581 CGGATGATACAGATGCACGC 59.213 55.000 0.00 0.00 0.00 5.34
3860 3918 2.140065 ACGGATGATACAGATGCACG 57.860 50.000 0.00 0.00 0.00 5.34
3869 3927 8.083462 TGCAATTAGAAACATACGGATGATAC 57.917 34.615 16.36 4.67 36.48 2.24
3877 3935 6.035843 AGGCAATTGCAATTAGAAACATACG 58.964 36.000 30.32 9.07 44.36 3.06
3921 3980 4.941873 AGCCTTGTACTTAATTGTAGTGGC 59.058 41.667 10.89 10.89 35.47 5.01
3959 4019 3.716872 TGTGGGGTTCTTTCTCTCTCTTT 59.283 43.478 0.00 0.00 0.00 2.52
3962 4022 2.900546 TCTGTGGGGTTCTTTCTCTCTC 59.099 50.000 0.00 0.00 0.00 3.20
3964 4024 2.900546 TCTCTGTGGGGTTCTTTCTCTC 59.099 50.000 0.00 0.00 0.00 3.20
3966 4026 3.990959 ATCTCTGTGGGGTTCTTTCTC 57.009 47.619 0.00 0.00 0.00 2.87
4090 4154 1.123077 ATGCGCCATCTTCAGGTAGA 58.877 50.000 4.18 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.