Multiple sequence alignment - TraesCS1D01G110900

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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 TraesCS1D01G110900 chr1D 100.000 4529 0 0 1 4529 106234295 106238823 0 8364
1 TraesCS1D01G110900 chr1A 95.966 3917 93 23 1 3902 107111063 107107197 0 6298
2 TraesCS1D01G110900 chr1A 91.457 597 18 12 3938 4529 107106962 107106394 0 789
3 TraesCS1D01G110900 chr1B 95.923 3802 94 20 1 3768 161213530 161209756 0 6106
4 TraesCS1D01G110900 chr1B 91.585 713 37 12 3828 4529 161209755 161209055 0 963


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 TraesCS1D01G110900 chr1D 106234295 106238823 4528 False 8364.0 8364 100.0000 1 4529 1 chr1D.!!$F1 4528
1 TraesCS1D01G110900 chr1A 107106394 107111063 4669 True 3543.5 6298 93.7115 1 4529 2 chr1A.!!$R1 4528
2 TraesCS1D01G110900 chr1B 161209055 161213530 4475 True 3534.5 6106 93.7540 1 4529 2 chr1B.!!$R1 4528

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
500 519 0.176680 GAGGCAAGAGGCGATTCAGA 59.823 55.000 0.00 0.00 46.16 3.27 F
1209 1233 0.107993 CATCACATCACAGCGTCCCT 60.108 55.000 0.00 0.00 0.00 4.20 F
1629 1653 0.613260 AGTATCTCGGCCTTGCAACA 59.387 50.000 0.00 0.00 0.00 3.33 F
2141 2165 1.338973 CAGCTTGAACAATGTGGCACT 59.661 47.619 19.83 1.19 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1443 0.672401 TCGGCGGAGTGAAATTGTCC 60.672 55.000 7.21 0.0 0.00 4.02 R
2141 2165 1.475034 GGCCGTTCAAGATGCCATCTA 60.475 52.381 7.81 0.0 43.46 1.98 R
3372 3396 4.059511 CAGAGATCTGATTCATGCTGTCC 58.940 47.826 0.00 0.0 46.59 4.02 R
3814 3862 0.036732 GTGTTCCTGCACCTCCATGA 59.963 55.000 0.00 0.0 33.53 3.07 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
46 48 3.440127 TCATCTTCCCACCAAATTTCCC 58.560 45.455 0.00 0.00 0.00 3.97
83 86 1.112916 CCGCCCCCAATTAATGACCC 61.113 60.000 0.00 0.00 0.00 4.46
94 97 0.761702 TAATGACCCGCTCCTACCCC 60.762 60.000 0.00 0.00 0.00 4.95
95 98 2.833151 AATGACCCGCTCCTACCCCA 62.833 60.000 0.00 0.00 0.00 4.96
96 99 3.155167 GACCCGCTCCTACCCCAG 61.155 72.222 0.00 0.00 0.00 4.45
176 180 1.192146 TCCCGGACCCAAGAAGACTG 61.192 60.000 0.73 0.00 0.00 3.51
193 197 1.159285 CTGTGCTCAAAATCTCGCCA 58.841 50.000 0.00 0.00 0.00 5.69
194 198 1.536766 CTGTGCTCAAAATCTCGCCAA 59.463 47.619 0.00 0.00 0.00 4.52
195 199 1.266718 TGTGCTCAAAATCTCGCCAAC 59.733 47.619 0.00 0.00 0.00 3.77
196 200 0.881118 TGCTCAAAATCTCGCCAACC 59.119 50.000 0.00 0.00 0.00 3.77
197 201 1.168714 GCTCAAAATCTCGCCAACCT 58.831 50.000 0.00 0.00 0.00 3.50
252 256 1.758862 CTTCCAAAATCCCCATCCAGC 59.241 52.381 0.00 0.00 0.00 4.85
261 265 1.895707 CCCATCCAGCCGAGCATTC 60.896 63.158 0.00 0.00 0.00 2.67
306 310 1.006825 GCCCAAAAGTTAAAGCGGCG 61.007 55.000 0.51 0.51 0.00 6.46
307 311 0.388006 CCCAAAAGTTAAAGCGGCGG 60.388 55.000 9.78 0.00 0.00 6.13
308 312 1.006825 CCAAAAGTTAAAGCGGCGGC 61.007 55.000 9.78 8.43 40.37 6.53
358 362 1.003355 CGTTCCACCTGTGCTCCAT 60.003 57.895 0.00 0.00 0.00 3.41
397 401 1.270826 GGCTGGCTTCAAGAAAAGACC 59.729 52.381 0.00 0.00 32.97 3.85
500 519 0.176680 GAGGCAAGAGGCGATTCAGA 59.823 55.000 0.00 0.00 46.16 3.27
501 520 0.615331 AGGCAAGAGGCGATTCAGAA 59.385 50.000 0.00 0.00 46.16 3.02
502 521 1.211457 AGGCAAGAGGCGATTCAGAAT 59.789 47.619 0.00 0.00 46.16 2.40
503 522 2.019984 GGCAAGAGGCGATTCAGAATT 58.980 47.619 0.00 0.00 46.16 2.17
504 523 2.424956 GGCAAGAGGCGATTCAGAATTT 59.575 45.455 0.00 0.00 46.16 1.82
505 524 3.488216 GGCAAGAGGCGATTCAGAATTTC 60.488 47.826 0.00 0.00 46.16 2.17
506 525 3.127548 GCAAGAGGCGATTCAGAATTTCA 59.872 43.478 0.00 0.00 0.00 2.69
507 526 4.730035 GCAAGAGGCGATTCAGAATTTCAG 60.730 45.833 0.00 0.00 0.00 3.02
508 527 2.941720 AGAGGCGATTCAGAATTTCAGC 59.058 45.455 0.00 1.79 0.00 4.26
509 528 2.941720 GAGGCGATTCAGAATTTCAGCT 59.058 45.455 0.00 0.00 0.00 4.24
510 529 2.681848 AGGCGATTCAGAATTTCAGCTG 59.318 45.455 7.63 7.63 0.00 4.24
511 530 2.448219 GCGATTCAGAATTTCAGCTGC 58.552 47.619 9.47 0.00 32.27 5.25
512 531 2.097142 GCGATTCAGAATTTCAGCTGCT 59.903 45.455 9.47 0.00 32.27 4.24
513 532 3.681855 CGATTCAGAATTTCAGCTGCTG 58.318 45.455 23.31 23.31 32.27 4.41
514 533 3.487042 CGATTCAGAATTTCAGCTGCTGG 60.487 47.826 27.79 11.18 31.51 4.85
515 534 1.830279 TCAGAATTTCAGCTGCTGGG 58.170 50.000 27.79 5.18 31.51 4.45
516 535 1.352017 TCAGAATTTCAGCTGCTGGGA 59.648 47.619 27.79 17.30 31.51 4.37
551 573 0.250553 TGCAAAGGTAACCCCTCGTG 60.251 55.000 0.00 0.00 45.47 4.35
738 760 4.218417 TGCCTGATAAGCAAGGTTTCTTTC 59.782 41.667 0.00 0.00 37.28 2.62
739 761 4.460731 GCCTGATAAGCAAGGTTTCTTTCT 59.539 41.667 0.00 0.00 0.00 2.52
745 767 1.269778 GCAAGGTTTCTTTCTGGTGGC 60.270 52.381 0.00 0.00 0.00 5.01
853 875 4.583871 AGATGACATCAGTTTTGAGGGAC 58.416 43.478 17.57 0.00 39.36 4.46
875 897 1.747709 CATGCCTTGGACTCTGGAAG 58.252 55.000 0.00 0.00 0.00 3.46
948 971 0.828762 TGGCTGGCTGCATCTTTGTT 60.829 50.000 18.32 0.00 45.15 2.83
959 982 3.896888 TGCATCTTTGTTCAATTCAGGGT 59.103 39.130 0.00 0.00 0.00 4.34
970 994 2.558359 CAATTCAGGGTTCTTGTGTCCC 59.442 50.000 0.00 0.00 41.36 4.46
1025 1049 0.250597 ACCACTACCGGGCAAAAGAC 60.251 55.000 6.32 0.00 0.00 3.01
1048 1072 1.201429 TCTGCTCCTTCTTGGGACCC 61.201 60.000 2.45 2.45 36.20 4.46
1125 1149 1.672030 CATCAACTGCGGCTCCACA 60.672 57.895 0.00 0.00 0.00 4.17
1209 1233 0.107993 CATCACATCACAGCGTCCCT 60.108 55.000 0.00 0.00 0.00 4.20
1419 1443 2.030893 CACCCAGCATGTTGTGTTACTG 60.031 50.000 8.84 0.00 33.75 2.74
1494 1518 6.459710 CGCTGAATATTACCGAGGATATGCTA 60.460 42.308 0.00 0.00 0.00 3.49
1569 1593 8.948631 TTGAAGTAATATCTGTTCCTGATGAC 57.051 34.615 0.00 0.00 0.00 3.06
1629 1653 0.613260 AGTATCTCGGCCTTGCAACA 59.387 50.000 0.00 0.00 0.00 3.33
1772 1796 2.863809 ACTGTTTGCTTACCAAGGGAG 58.136 47.619 0.00 0.00 34.34 4.30
2141 2165 1.338973 CAGCTTGAACAATGTGGCACT 59.661 47.619 19.83 1.19 0.00 4.40
2478 2502 5.847111 ACAGTGATGTAAGCTACCGAATA 57.153 39.130 0.00 0.00 0.00 1.75
2653 2677 2.060050 ATTCCGGACAGAGATCGAGT 57.940 50.000 1.83 0.00 0.00 4.18
2751 2775 5.104900 GGTGTATGAGTACATGGAGAAAGGT 60.105 44.000 0.00 0.00 42.43 3.50
3372 3396 1.097547 GCCCGGACATCTCCAATGTG 61.098 60.000 0.73 0.00 36.12 3.21
3586 3628 3.639094 TGGTAAAAACATGTTGACCTGGG 59.361 43.478 26.00 0.00 0.00 4.45
3759 3806 7.392113 TGTTAACTACCTATTTGGAACACATGG 59.608 37.037 7.22 0.00 39.29 3.66
3788 3836 6.866010 ATTTTCAGCCAAAAACAATTCCTC 57.134 33.333 0.00 0.00 37.52 3.71
3791 3839 3.052036 CAGCCAAAAACAATTCCTCACG 58.948 45.455 0.00 0.00 0.00 4.35
3794 3842 4.039124 AGCCAAAAACAATTCCTCACGAAT 59.961 37.500 0.00 0.00 43.34 3.34
3808 3856 6.437928 TCCTCACGAATTTGACAGAAAATTG 58.562 36.000 0.00 0.00 39.31 2.32
3809 3857 6.262049 TCCTCACGAATTTGACAGAAAATTGA 59.738 34.615 0.00 0.00 39.31 2.57
3810 3858 6.360681 CCTCACGAATTTGACAGAAAATTGAC 59.639 38.462 0.00 0.00 39.31 3.18
3811 3859 6.205784 TCACGAATTTGACAGAAAATTGACC 58.794 36.000 0.00 0.00 39.31 4.02
3812 3860 5.976534 CACGAATTTGACAGAAAATTGACCA 59.023 36.000 0.00 0.00 39.31 4.02
3813 3861 6.642131 CACGAATTTGACAGAAAATTGACCAT 59.358 34.615 0.00 0.00 39.31 3.55
3814 3862 7.169645 CACGAATTTGACAGAAAATTGACCATT 59.830 33.333 0.00 0.00 39.31 3.16
3815 3863 7.382218 ACGAATTTGACAGAAAATTGACCATTC 59.618 33.333 0.00 0.00 39.31 2.67
3816 3864 7.381948 CGAATTTGACAGAAAATTGACCATTCA 59.618 33.333 0.00 0.00 39.31 2.57
3817 3865 9.211485 GAATTTGACAGAAAATTGACCATTCAT 57.789 29.630 0.00 0.00 39.31 2.57
3818 3866 7.949903 TTTGACAGAAAATTGACCATTCATG 57.050 32.000 0.00 0.00 0.00 3.07
3835 3883 1.278985 CATGGAGGTGCAGGAACACTA 59.721 52.381 0.00 0.00 40.52 2.74
3838 3886 1.834263 GGAGGTGCAGGAACACTAGAT 59.166 52.381 0.00 0.00 40.52 1.98
3894 3943 4.497473 TTTGAACGATGCCTAAAAGGTG 57.503 40.909 0.00 0.00 37.80 4.00
3911 3960 1.760875 TGCTCCCTCCGTCCCATAC 60.761 63.158 0.00 0.00 0.00 2.39
3913 3962 0.178970 GCTCCCTCCGTCCCATACTA 60.179 60.000 0.00 0.00 0.00 1.82
3914 3963 1.912417 CTCCCTCCGTCCCATACTAG 58.088 60.000 0.00 0.00 0.00 2.57
3915 3964 1.145325 CTCCCTCCGTCCCATACTAGT 59.855 57.143 0.00 0.00 0.00 2.57
3926 4176 5.180868 CGTCCCATACTAGTAACGCTCTTAT 59.819 44.000 6.70 0.00 0.00 1.73
3930 4180 9.964354 TCCCATACTAGTAACGCTCTTATATTA 57.036 33.333 6.70 0.00 0.00 0.98
4027 4277 2.158842 ACTGATCATGCTAGCCAAGTCC 60.159 50.000 13.29 0.00 0.00 3.85
4034 4284 4.349048 TCATGCTAGCCAAGTCCAGATAAT 59.651 41.667 13.29 0.00 0.00 1.28
4035 4285 4.342862 TGCTAGCCAAGTCCAGATAATC 57.657 45.455 13.29 0.00 0.00 1.75
4036 4286 3.243873 TGCTAGCCAAGTCCAGATAATCG 60.244 47.826 13.29 0.00 0.00 3.34
4037 4287 2.246719 AGCCAAGTCCAGATAATCGC 57.753 50.000 0.00 0.00 0.00 4.58
4038 4288 1.486310 AGCCAAGTCCAGATAATCGCA 59.514 47.619 0.00 0.00 0.00 5.10
4039 4289 2.092968 AGCCAAGTCCAGATAATCGCAA 60.093 45.455 0.00 0.00 0.00 4.85
4041 4291 3.535561 CCAAGTCCAGATAATCGCAACT 58.464 45.455 0.00 0.00 0.00 3.16
4042 4292 3.310774 CCAAGTCCAGATAATCGCAACTG 59.689 47.826 0.00 0.00 0.00 3.16
4043 4293 2.555199 AGTCCAGATAATCGCAACTGC 58.445 47.619 0.00 0.00 37.78 4.40
4049 4303 4.560035 CCAGATAATCGCAACTGCAAAAAG 59.440 41.667 2.12 0.00 42.21 2.27
4114 4368 9.771915 AACATTTGTCAAACATGAAAAATTCAC 57.228 25.926 0.00 0.00 43.48 3.18
4144 4398 2.806244 CAGGTTTGACAGGTTTAGACGG 59.194 50.000 0.00 0.00 0.00 4.79
4165 4419 0.874607 GAGGCATAACGCGAACCGAT 60.875 55.000 15.93 0.00 43.84 4.18
4190 4444 8.234887 TGTTCGACAAACATACTAACATAGTG 57.765 34.615 0.37 0.00 42.95 2.74
4230 4484 2.086869 CCCAAGAGACGATGCAACAAT 58.913 47.619 0.00 0.00 0.00 2.71
4460 4714 2.312390 CTCCTCCTAGGGCTGTAACTC 58.688 57.143 9.46 0.00 35.59 3.01
4511 4765 0.033228 CAGCACGATCATCCCTCCTC 59.967 60.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 86 3.854669 CCTGCTGGGGTAGGAGCG 61.855 72.222 0.71 0.00 46.31 5.03
94 97 0.886490 ACGTTTTCTGGCTCCTGCTG 60.886 55.000 0.00 0.00 39.59 4.41
95 98 0.603975 GACGTTTTCTGGCTCCTGCT 60.604 55.000 0.00 0.00 39.59 4.24
96 99 1.578206 GGACGTTTTCTGGCTCCTGC 61.578 60.000 0.00 0.00 38.76 4.85
176 180 1.401539 GGTTGGCGAGATTTTGAGCAC 60.402 52.381 0.00 0.00 0.00 4.40
261 265 1.134946 GGACAAAGGAATGGCAATCCG 59.865 52.381 15.68 4.80 42.03 4.18
358 362 0.914644 CAAGAAGAGGGATGGGCTGA 59.085 55.000 0.00 0.00 0.00 4.26
397 401 2.125350 GAGCCAGAGCCAGAACCG 60.125 66.667 0.00 0.00 41.25 4.44
467 486 2.282462 CCTCCGCCCAAACAAGCT 60.282 61.111 0.00 0.00 0.00 3.74
500 519 1.542492 CAGTCCCAGCAGCTGAAATT 58.458 50.000 24.90 5.12 32.44 1.82
501 520 0.323178 CCAGTCCCAGCAGCTGAAAT 60.323 55.000 24.90 7.92 32.44 2.17
502 521 1.073722 CCAGTCCCAGCAGCTGAAA 59.926 57.895 24.90 8.30 32.44 2.69
503 522 2.752358 CCAGTCCCAGCAGCTGAA 59.248 61.111 24.90 8.69 32.44 3.02
504 523 3.324930 CCCAGTCCCAGCAGCTGA 61.325 66.667 24.90 1.09 32.44 4.26
505 524 3.324930 TCCCAGTCCCAGCAGCTG 61.325 66.667 16.23 16.23 0.00 4.24
506 525 3.007920 CTCCCAGTCCCAGCAGCT 61.008 66.667 0.00 0.00 0.00 4.24
507 526 4.106925 CCTCCCAGTCCCAGCAGC 62.107 72.222 0.00 0.00 0.00 5.25
508 527 4.106925 GCCTCCCAGTCCCAGCAG 62.107 72.222 0.00 0.00 0.00 4.24
511 530 3.406200 CAGGCCTCCCAGTCCCAG 61.406 72.222 0.00 0.00 0.00 4.45
514 533 4.416738 GTGCAGGCCTCCCAGTCC 62.417 72.222 0.00 0.00 0.00 3.85
515 534 3.325753 AGTGCAGGCCTCCCAGTC 61.326 66.667 0.00 0.00 0.00 3.51
516 535 3.644606 CAGTGCAGGCCTCCCAGT 61.645 66.667 0.00 2.89 0.00 4.00
551 573 2.155197 AACCCAATCCCCCAGCTGAC 62.155 60.000 17.39 0.00 0.00 3.51
745 767 3.151022 GGTCGGCAGGAGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
853 875 1.030488 CCAGAGTCCAAGGCATGCAG 61.030 60.000 21.36 8.55 0.00 4.41
918 940 1.183676 AGCCAGCCAGCAAGGAAAAG 61.184 55.000 5.44 0.00 41.22 2.27
948 971 3.486383 GGACACAAGAACCCTGAATTGA 58.514 45.455 0.00 0.00 0.00 2.57
959 982 0.690762 GGGCTACAGGGACACAAGAA 59.309 55.000 0.00 0.00 0.00 2.52
970 994 2.554032 CAAACAGAAACTGGGGCTACAG 59.446 50.000 7.94 7.94 44.03 2.74
1016 1040 0.520847 GAGCAGAGCTGTCTTTTGCC 59.479 55.000 0.00 0.00 39.88 4.52
1025 1049 0.392729 CCCAAGAAGGAGCAGAGCTG 60.393 60.000 0.00 0.00 39.88 4.24
1048 1072 2.907042 AGGTACCAAGAAGAACCCAGAG 59.093 50.000 15.94 0.00 32.10 3.35
1087 1111 0.178903 AGGTAGTTGTCTGCAGGGGA 60.179 55.000 15.13 0.00 0.00 4.81
1125 1149 0.377554 CGTGGAGATTAGCGTCGACT 59.622 55.000 14.70 0.00 0.00 4.18
1419 1443 0.672401 TCGGCGGAGTGAAATTGTCC 60.672 55.000 7.21 0.00 0.00 4.02
1494 1518 4.015084 CCAGAGGCACAAATGAGAGAATT 58.985 43.478 0.00 0.00 0.00 2.17
1629 1653 6.014242 TCCTGTAGAATGTCTGAAATGACTGT 60.014 38.462 0.00 0.00 37.79 3.55
2141 2165 1.475034 GGCCGTTCAAGATGCCATCTA 60.475 52.381 7.81 0.00 43.46 1.98
3372 3396 4.059511 CAGAGATCTGATTCATGCTGTCC 58.940 47.826 0.00 0.00 46.59 4.02
3586 3628 4.276926 ACAAGCAACAGACATCTCTTTTCC 59.723 41.667 0.00 0.00 0.00 3.13
3688 3730 7.479352 ACATCTAACAGATCATCATAGGGAG 57.521 40.000 0.00 0.00 31.32 4.30
3689 3731 7.862274 AACATCTAACAGATCATCATAGGGA 57.138 36.000 0.00 0.00 31.32 4.20
3690 3732 7.935755 ACAAACATCTAACAGATCATCATAGGG 59.064 37.037 0.00 0.00 31.32 3.53
3691 3733 8.899427 ACAAACATCTAACAGATCATCATAGG 57.101 34.615 0.00 0.00 31.32 2.57
3692 3734 9.538508 TGACAAACATCTAACAGATCATCATAG 57.461 33.333 0.00 0.00 31.32 2.23
3759 3806 9.650371 GAATTGTTTTTGGCTGAAAATTAAGTC 57.350 29.630 3.41 6.84 33.46 3.01
3788 3836 5.976534 TGGTCAATTTTCTGTCAAATTCGTG 59.023 36.000 0.00 0.00 34.70 4.35
3791 3839 8.592105 TGAATGGTCAATTTTCTGTCAAATTC 57.408 30.769 0.00 0.00 34.70 2.17
3794 3842 6.930164 CCATGAATGGTCAATTTTCTGTCAAA 59.070 34.615 0.82 0.00 43.05 2.69
3811 3859 1.747355 GTTCCTGCACCTCCATGAATG 59.253 52.381 0.00 0.00 0.00 2.67
3812 3860 1.355381 TGTTCCTGCACCTCCATGAAT 59.645 47.619 0.00 0.00 0.00 2.57
3813 3861 0.770499 TGTTCCTGCACCTCCATGAA 59.230 50.000 0.00 0.00 0.00 2.57
3814 3862 0.036732 GTGTTCCTGCACCTCCATGA 59.963 55.000 0.00 0.00 33.53 3.07
3815 3863 0.037303 AGTGTTCCTGCACCTCCATG 59.963 55.000 0.00 0.00 40.04 3.66
3816 3864 1.556911 CTAGTGTTCCTGCACCTCCAT 59.443 52.381 0.00 0.00 40.04 3.41
3817 3865 0.976641 CTAGTGTTCCTGCACCTCCA 59.023 55.000 0.00 0.00 40.04 3.86
3818 3866 1.267121 TCTAGTGTTCCTGCACCTCC 58.733 55.000 0.00 0.00 40.04 4.30
3819 3867 3.954904 TCTATCTAGTGTTCCTGCACCTC 59.045 47.826 0.00 0.00 40.04 3.85
3820 3868 3.702045 GTCTATCTAGTGTTCCTGCACCT 59.298 47.826 0.00 0.00 40.04 4.00
3821 3869 3.181474 GGTCTATCTAGTGTTCCTGCACC 60.181 52.174 0.00 0.00 40.04 5.01
3824 3872 4.946478 ATGGTCTATCTAGTGTTCCTGC 57.054 45.455 0.00 0.00 0.00 4.85
3835 3883 3.713764 AGCAAGCTGGTTATGGTCTATCT 59.286 43.478 0.00 0.00 0.00 1.98
3838 3886 2.837591 TCAGCAAGCTGGTTATGGTCTA 59.162 45.455 20.78 0.00 43.75 2.59
3876 3924 2.084546 AGCACCTTTTAGGCATCGTTC 58.915 47.619 0.00 0.00 39.63 3.95
3877 3925 2.084546 GAGCACCTTTTAGGCATCGTT 58.915 47.619 0.00 0.00 39.63 3.85
3894 3943 0.178970 TAGTATGGGACGGAGGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
3911 3960 8.737175 TCCCACATAATATAAGAGCGTTACTAG 58.263 37.037 0.00 0.00 0.00 2.57
3913 3962 7.376615 GTCCCACATAATATAAGAGCGTTACT 58.623 38.462 0.00 0.00 0.00 2.24
3914 3963 6.307318 CGTCCCACATAATATAAGAGCGTTAC 59.693 42.308 0.00 0.00 0.00 2.50
3915 3964 6.384224 CGTCCCACATAATATAAGAGCGTTA 58.616 40.000 0.00 0.00 0.00 3.18
3926 4176 2.090943 ACTCCCTCCGTCCCACATAATA 60.091 50.000 0.00 0.00 0.00 0.98
3930 4180 0.397254 CTACTCCCTCCGTCCCACAT 60.397 60.000 0.00 0.00 0.00 3.21
3931 4181 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
3932 4182 0.324091 TTCTACTCCCTCCGTCCCAC 60.324 60.000 0.00 0.00 0.00 4.61
3933 4183 0.324091 GTTCTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
4027 4277 5.284660 GTCTTTTTGCAGTTGCGATTATCTG 59.715 40.000 0.00 0.00 45.83 2.90
4034 4284 3.502191 AAAGTCTTTTTGCAGTTGCGA 57.498 38.095 0.00 0.00 45.83 5.10
4035 4285 4.091220 TGAAAAAGTCTTTTTGCAGTTGCG 59.909 37.500 24.53 0.00 42.51 4.85
4036 4286 5.529014 TGAAAAAGTCTTTTTGCAGTTGC 57.471 34.783 24.53 10.99 42.51 4.17
4041 4291 5.788450 TGAACCTGAAAAAGTCTTTTTGCA 58.212 33.333 24.53 19.31 42.51 4.08
4042 4292 6.035005 GTCTGAACCTGAAAAAGTCTTTTTGC 59.965 38.462 24.53 16.56 42.51 3.68
4043 4293 7.090173 TGTCTGAACCTGAAAAAGTCTTTTTG 58.910 34.615 24.53 14.31 42.51 2.44
4049 4303 4.498177 GCCTTGTCTGAACCTGAAAAAGTC 60.498 45.833 0.00 0.00 0.00 3.01
4114 4368 2.398498 CTGTCAAACCTGTCTGAGTCG 58.602 52.381 0.00 0.00 0.00 4.18
4144 4398 2.178235 GGTTCGCGTTATGCCTCCC 61.178 63.158 5.77 0.00 42.08 4.30
4165 4419 7.868922 ACACTATGTTAGTATGTTTGTCGAACA 59.131 33.333 8.12 8.12 43.92 3.18
4190 4444 2.934553 GGCCGAACTCTTATGTTGGTAC 59.065 50.000 0.00 0.00 0.00 3.34
4230 4484 5.417580 GCACCACCCTCAACTTGAATTAATA 59.582 40.000 0.00 0.00 0.00 0.98
4460 4714 0.951040 AAAGGCGACCAAGAAGCTCG 60.951 55.000 0.00 0.00 0.00 5.03
4511 4765 2.651361 AGCCGATCGCCTTATCCG 59.349 61.111 10.32 0.00 38.78 4.18


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

AutoCloner maintained by Alex Coulton.