Multiple sequence alignment - TraesCS3D01G450800

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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 TraesCS3D01G450800 chr3D 100.000 5790 0 0 1 5790 559070945 559076734 0.000000e+00 10693.0
1 TraesCS3D01G450800 chr3D 100.000 2003 0 0 6079 8081 559077023 559079025 0.000000e+00 3699.0
2 TraesCS3D01G450800 chr3A 96.681 5243 115 19 560 5790 695495552 695500747 0.000000e+00 8663.0
3 TraesCS3D01G450800 chr3A 92.049 2025 95 41 6079 8081 695500999 695502979 0.000000e+00 2787.0
4 TraesCS3D01G450800 chr3B 97.166 3564 65 10 2252 5790 741858619 741862171 0.000000e+00 5989.0
5 TraesCS3D01G450800 chr3B 94.243 2258 100 12 1 2244 741856108 741858349 0.000000e+00 3422.0
6 TraesCS3D01G450800 chr3B 92.449 1086 44 15 6079 7155 741862237 741863293 0.000000e+00 1517.0
7 TraesCS3D01G450800 chr3B 89.409 897 66 21 7192 8081 741863480 741864354 0.000000e+00 1103.0
8 TraesCS3D01G450800 chr6D 91.459 562 43 5 1 559 70528731 70529290 0.000000e+00 767.0
9 TraesCS3D01G450800 chr6D 89.343 563 53 6 1 560 16571315 16571873 0.000000e+00 701.0
10 TraesCS3D01G450800 chr4B 90.714 560 51 1 1 560 489267635 489268193 0.000000e+00 745.0
11 TraesCS3D01G450800 chr4B 89.343 563 57 3 1 561 204129858 204130419 0.000000e+00 704.0
12 TraesCS3D01G450800 chrUn 90.536 560 49 4 1 559 296004539 296003983 0.000000e+00 737.0
13 TraesCS3D01G450800 chr1D 90.536 560 49 4 1 559 8412933 8412377 0.000000e+00 737.0
14 TraesCS3D01G450800 chr1D 90.536 560 49 4 1 559 8444428 8443872 0.000000e+00 737.0
15 TraesCS3D01G450800 chr7A 89.680 562 54 4 1 559 585372282 585372842 0.000000e+00 713.0
16 TraesCS3D01G450800 chr7A 94.643 56 3 0 8026 8081 10285195 10285250 4.020000e-13 87.9
17 TraesCS3D01G450800 chr5A 90.380 395 38 0 2252 2646 149229784 149230178 3.340000e-143 520.0
18 TraesCS3D01G450800 chr5A 90.380 395 37 1 2252 2646 110283671 110283278 1.200000e-142 518.0
19 TraesCS3D01G450800 chr7D 93.056 72 5 0 7950 8021 149469404 149469333 1.110000e-18 106.0
20 TraesCS3D01G450800 chr4A 94.643 56 3 0 8026 8081 727050828 727050773 4.020000e-13 87.9
21 TraesCS3D01G450800 chr2A 94.643 56 3 0 8026 8081 691606842 691606787 4.020000e-13 87.9


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 TraesCS3D01G450800 chr3D 559070945 559079025 8080 False 7196.00 10693 100.00000 1 8081 2 chr3D.!!$F1 8080
1 TraesCS3D01G450800 chr3A 695495552 695502979 7427 False 5725.00 8663 94.36500 560 8081 2 chr3A.!!$F1 7521
2 TraesCS3D01G450800 chr3B 741856108 741864354 8246 False 3007.75 5989 93.31675 1 8081 4 chr3B.!!$F1 8080
3 TraesCS3D01G450800 chr6D 70528731 70529290 559 False 767.00 767 91.45900 1 559 1 chr6D.!!$F2 558
4 TraesCS3D01G450800 chr6D 16571315 16571873 558 False 701.00 701 89.34300 1 560 1 chr6D.!!$F1 559
5 TraesCS3D01G450800 chr4B 489267635 489268193 558 False 745.00 745 90.71400 1 560 1 chr4B.!!$F2 559
6 TraesCS3D01G450800 chr4B 204129858 204130419 561 False 704.00 704 89.34300 1 561 1 chr4B.!!$F1 560
7 TraesCS3D01G450800 chrUn 296003983 296004539 556 True 737.00 737 90.53600 1 559 1 chrUn.!!$R1 558
8 TraesCS3D01G450800 chr1D 8412377 8412933 556 True 737.00 737 90.53600 1 559 1 chr1D.!!$R1 558
9 TraesCS3D01G450800 chr1D 8443872 8444428 556 True 737.00 737 90.53600 1 559 1 chr1D.!!$R2 558
10 TraesCS3D01G450800 chr7A 585372282 585372842 560 False 713.00 713 89.68000 1 559 1 chr7A.!!$F2 558

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
195 198 0.397675 ATCAGATGACGGAGCCCAGA 60.398 55.000 0.00 0.0 0.00 3.86 F
740 752 1.464395 TCCCTAGGCCAACCCAACA 60.464 57.895 5.01 0.0 36.11 3.33 F
1624 1649 1.065126 GCCTCTGTGGGTTAGCAATCT 60.065 52.381 0.00 0.0 36.00 2.40 F
2564 2856 2.195922 CGTGTCGATGCATGATTCTGA 58.804 47.619 2.46 0.0 0.00 3.27 F
3906 4223 3.935203 CGCCTGGATAATACTAATGCCTG 59.065 47.826 0.00 0.0 0.00 4.85 F
4185 4502 3.965026 CTCCCTCACCTCCGCTCCA 62.965 68.421 0.00 0.0 0.00 3.86 F
5358 5675 0.392193 CCACGAGGAGCAGCAAATCT 60.392 55.000 0.00 0.0 36.89 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1339 0.109342 GCGGAATCCCTGATCCACAT 59.891 55.000 0.00 0.0 0.00 3.21 R
2600 2892 0.877743 GACTGCAAGGAAAGGAGCAC 59.122 55.000 0.00 0.0 39.30 4.40 R
2909 3202 5.428253 TGTATATTTGAAGAGACAGCCACC 58.572 41.667 0.00 0.0 0.00 4.61 R
4168 4485 3.317436 ATGGAGCGGAGGTGAGGGA 62.317 63.158 0.00 0.0 39.88 4.20 R
5358 5675 0.671781 GCAAGCTTCGAAGGCTCTCA 60.672 55.000 25.77 0.0 39.30 3.27 R
6111 6428 3.769844 GACAGATGAAACTAGTGGAGGGA 59.230 47.826 0.00 0.0 0.00 4.20 R
7148 7488 1.267806 ACTTGAGGCTTTGATTGCACG 59.732 47.619 0.00 0.0 0.00 5.34 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
63 64 4.647564 AGTCCAAAGATATAGCCCCATG 57.352 45.455 0.00 0.00 0.00 3.66
195 198 0.397675 ATCAGATGACGGAGCCCAGA 60.398 55.000 0.00 0.00 0.00 3.86
205 208 1.606531 GAGCCCAGAAGCCAGATGT 59.393 57.895 0.00 0.00 0.00 3.06
376 383 9.472361 GACTTGTTTACTTATGTCTGTACTCAA 57.528 33.333 0.00 0.00 0.00 3.02
442 449 3.513912 GCCCCTGGCTTGTAATAAAAAGT 59.486 43.478 0.00 0.00 46.69 2.66
504 513 2.045561 TCCCGTGAGTCTCTGATCTC 57.954 55.000 0.65 3.95 0.00 2.75
617 629 3.698539 CACTGCTCTCTCTTGAGTATGGA 59.301 47.826 0.00 0.00 40.98 3.41
656 668 1.681076 GTACCGGCTTCTTTCCCCA 59.319 57.895 0.00 0.00 0.00 4.96
740 752 1.464395 TCCCTAGGCCAACCCAACA 60.464 57.895 5.01 0.00 36.11 3.33
948 970 2.105993 GGTTCCTATAACGAAGGGGCAT 59.894 50.000 0.00 0.00 34.66 4.40
996 1018 3.470709 ACAATGGAAGCGATCGATGATT 58.529 40.909 21.57 9.38 0.00 2.57
1297 1322 2.044352 GGAATGGTTCCGGGGGTG 60.044 66.667 0.00 0.00 40.59 4.61
1298 1323 2.608550 GGAATGGTTCCGGGGGTGA 61.609 63.158 0.00 0.00 40.59 4.02
1306 1331 4.489771 CCGGGGGTGAGATGTGGC 62.490 72.222 0.00 0.00 0.00 5.01
1309 1334 4.489771 GGGGTGAGATGTGGCGGG 62.490 72.222 0.00 0.00 0.00 6.13
1312 1337 4.101448 GTGAGATGTGGCGGGCCT 62.101 66.667 11.55 0.00 36.94 5.19
1314 1339 3.785859 GAGATGTGGCGGGCCTGA 61.786 66.667 18.31 0.00 36.94 3.86
1315 1340 3.092511 AGATGTGGCGGGCCTGAT 61.093 61.111 18.31 0.00 36.94 2.90
1317 1342 3.704231 GATGTGGCGGGCCTGATGT 62.704 63.158 18.31 0.00 36.94 3.06
1359 1384 5.010213 GCTCCTACGGAAGATCTTATGTCTT 59.990 44.000 8.25 0.00 38.57 3.01
1394 1419 7.452880 TCCATCCATCCATTTCGATTTAATC 57.547 36.000 0.00 0.00 0.00 1.75
1400 1425 7.559533 TCCATCCATTTCGATTTAATCTTTCCA 59.440 33.333 3.34 0.00 0.00 3.53
1484 1509 4.438744 CGACTAGATTTGGGTTTGGCATTC 60.439 45.833 0.00 0.00 0.00 2.67
1554 1579 4.604843 GCAGAAGCAAATTATTTTGGGC 57.395 40.909 11.07 0.00 42.09 5.36
1582 1607 6.500684 TTTGATTCTACAAGTGAGGAATGC 57.499 37.500 7.72 0.00 0.00 3.56
1618 1643 2.094675 CCAAATGCCTCTGTGGGTTAG 58.905 52.381 0.00 0.00 36.00 2.34
1624 1649 1.065126 GCCTCTGTGGGTTAGCAATCT 60.065 52.381 0.00 0.00 36.00 2.40
1735 1761 8.523658 AGGCAGGACATTTATTCTTTTTAAGTC 58.476 33.333 0.00 0.00 0.00 3.01
1756 1782 7.688918 AGTCCCAGATGATAGAAAAGAAGAT 57.311 36.000 0.00 0.00 0.00 2.40
1785 1811 9.881649 ATGATCTCGCATATTGTAGTTATCAAT 57.118 29.630 0.00 0.00 38.72 2.57
1786 1812 9.358872 TGATCTCGCATATTGTAGTTATCAATC 57.641 33.333 0.00 0.00 36.92 2.67
1787 1813 9.358872 GATCTCGCATATTGTAGTTATCAATCA 57.641 33.333 0.00 0.00 36.92 2.57
1788 1814 9.710900 ATCTCGCATATTGTAGTTATCAATCAA 57.289 29.630 0.00 0.00 36.92 2.57
1808 1834 8.775527 CAATCAAGGATAACTCATCTGAATCTG 58.224 37.037 0.00 0.00 33.78 2.90
2545 2837 3.328382 TCATCTGTTGGTTACCTTCCG 57.672 47.619 2.07 0.00 0.00 4.30
2564 2856 2.195922 CGTGTCGATGCATGATTCTGA 58.804 47.619 2.46 0.00 0.00 3.27
2718 3010 5.047872 TGTGAACTCGTAAGGCACAGTATTA 60.048 40.000 0.00 0.00 37.15 0.98
2719 3011 5.515626 GTGAACTCGTAAGGCACAGTATTAG 59.484 44.000 0.00 0.00 34.16 1.73
3426 3720 4.712122 ATACAAGGGGTAAAATTGTGCG 57.288 40.909 0.30 0.00 37.69 5.34
3816 4133 8.578151 AGTTAAGTTCTTTGTTGTGTACCAAAA 58.422 29.630 0.00 0.00 34.07 2.44
3817 4134 9.194271 GTTAAGTTCTTTGTTGTGTACCAAAAA 57.806 29.630 0.00 0.00 34.07 1.94
3906 4223 3.935203 CGCCTGGATAATACTAATGCCTG 59.065 47.826 0.00 0.00 0.00 4.85
3960 4277 5.961398 TTGCTTAAACTATACCTGCCCTA 57.039 39.130 0.00 0.00 0.00 3.53
4168 4485 5.798125 TTGAACTTGTCTCTCACTCATCT 57.202 39.130 0.00 0.00 0.00 2.90
4185 4502 3.965026 CTCCCTCACCTCCGCTCCA 62.965 68.421 0.00 0.00 0.00 3.86
4498 4815 6.765989 TGCCTATGGTAAGCTTGTAATAACAG 59.234 38.462 9.86 0.00 36.83 3.16
4566 4883 8.806429 TTTCCAGCATTCTCATTTACTGATAA 57.194 30.769 0.00 0.00 32.10 1.75
4963 5280 4.624364 TGACTGGTGTGCCTGCCG 62.624 66.667 0.00 0.00 37.23 5.69
5208 5525 4.500375 GCAAGGTTCATTATGATGGAAGCC 60.500 45.833 0.00 0.00 33.93 4.35
5358 5675 0.392193 CCACGAGGAGCAGCAAATCT 60.392 55.000 0.00 0.00 36.89 2.40
5454 5771 2.042831 GCTGCCAAATGAGGACGCT 61.043 57.895 0.00 0.00 0.00 5.07
6111 6428 5.452255 ACATCCTTTATGCCATTGTCATCT 58.548 37.500 0.00 0.00 39.39 2.90
6117 6434 0.548031 TGCCATTGTCATCTCCCTCC 59.452 55.000 0.00 0.00 0.00 4.30
6118 6435 0.548031 GCCATTGTCATCTCCCTCCA 59.452 55.000 0.00 0.00 0.00 3.86
6228 6546 3.255642 TGTTGCTTGGATGAAAAGGTAGC 59.744 43.478 0.00 0.00 0.00 3.58
6278 6597 2.727123 TGAGAAAAAGGTCACCTGCA 57.273 45.000 0.00 0.00 32.13 4.41
6279 6598 2.575532 TGAGAAAAAGGTCACCTGCAG 58.424 47.619 6.78 6.78 32.13 4.41
6281 6600 3.181440 TGAGAAAAAGGTCACCTGCAGAT 60.181 43.478 17.39 0.00 32.13 2.90
6282 6601 3.152341 AGAAAAAGGTCACCTGCAGATG 58.848 45.455 17.39 9.11 32.13 2.90
6477 6808 6.258727 AGGTGCTCAAACAATTATATGTCTCG 59.741 38.462 0.00 0.00 31.81 4.04
6478 6809 6.257849 GGTGCTCAAACAATTATATGTCTCGA 59.742 38.462 0.00 0.00 31.81 4.04
6480 6811 8.978539 GTGCTCAAACAATTATATGTCTCGATA 58.021 33.333 0.00 0.00 31.81 2.92
6558 6891 2.033194 GGTGCCCCTTTTCGACTCG 61.033 63.158 0.00 0.00 0.00 4.18
6588 6921 5.743872 TCGTAGTCAGATGATTGTCATTTCG 59.256 40.000 0.00 0.00 37.20 3.46
6862 7200 3.501062 GCCCTAATAAAACGCCATACTCC 59.499 47.826 0.00 0.00 0.00 3.85
6865 7203 6.527423 CCCTAATAAAACGCCATACTCCTAA 58.473 40.000 0.00 0.00 0.00 2.69
6884 7222 5.185249 TCCTAACAGTGATCGTAGCTTCTTT 59.815 40.000 0.00 0.00 0.00 2.52
7016 7355 7.013846 CCCCTTAATCTGTATAAATTTTGCCGA 59.986 37.037 0.00 0.00 0.00 5.54
7102 7442 6.370718 ACCATTCACCGTACTGTCTTTTATTC 59.629 38.462 0.00 0.00 0.00 1.75
7103 7443 6.594159 CCATTCACCGTACTGTCTTTTATTCT 59.406 38.462 0.00 0.00 0.00 2.40
7148 7488 4.083565 TGTATACAAAACAAAGCCTCCCC 58.916 43.478 2.20 0.00 0.00 4.81
7155 7495 1.978617 CAAAGCCTCCCCGTGCAAT 60.979 57.895 0.00 0.00 0.00 3.56
7158 7498 2.361104 GCCTCCCCGTGCAATCAA 60.361 61.111 0.00 0.00 0.00 2.57
7160 7500 1.937546 GCCTCCCCGTGCAATCAAAG 61.938 60.000 0.00 0.00 0.00 2.77
7161 7501 1.508088 CTCCCCGTGCAATCAAAGC 59.492 57.895 0.00 0.00 0.00 3.51
7162 7502 1.937546 CTCCCCGTGCAATCAAAGCC 61.938 60.000 0.00 0.00 0.00 4.35
7163 7503 1.978617 CCCCGTGCAATCAAAGCCT 60.979 57.895 0.00 0.00 0.00 4.58
7164 7504 1.508088 CCCGTGCAATCAAAGCCTC 59.492 57.895 0.00 0.00 0.00 4.70
7165 7505 1.243342 CCCGTGCAATCAAAGCCTCA 61.243 55.000 0.00 0.00 0.00 3.86
7166 7506 0.597568 CCGTGCAATCAAAGCCTCAA 59.402 50.000 0.00 0.00 0.00 3.02
7167 7507 1.401931 CCGTGCAATCAAAGCCTCAAG 60.402 52.381 0.00 0.00 0.00 3.02
7168 7508 1.267806 CGTGCAATCAAAGCCTCAAGT 59.732 47.619 0.00 0.00 0.00 3.16
7170 7510 3.721035 GTGCAATCAAAGCCTCAAGTTT 58.279 40.909 0.00 0.00 0.00 2.66
7171 7511 3.492011 GTGCAATCAAAGCCTCAAGTTTG 59.508 43.478 0.00 0.00 35.38 2.93
7172 7512 3.132646 TGCAATCAAAGCCTCAAGTTTGT 59.867 39.130 0.00 0.00 35.54 2.83
7175 7515 5.535333 CAATCAAAGCCTCAAGTTTGTCAT 58.465 37.500 0.00 0.00 35.54 3.06
7176 7516 4.836125 TCAAAGCCTCAAGTTTGTCATC 57.164 40.909 0.00 0.00 35.54 2.92
7177 7517 4.464008 TCAAAGCCTCAAGTTTGTCATCT 58.536 39.130 0.00 0.00 35.54 2.90
7178 7518 4.889409 TCAAAGCCTCAAGTTTGTCATCTT 59.111 37.500 0.00 0.00 35.54 2.40
7180 7520 6.545666 TCAAAGCCTCAAGTTTGTCATCTTTA 59.454 34.615 0.00 0.00 35.54 1.85
7182 7522 7.530426 AAGCCTCAAGTTTGTCATCTTTATT 57.470 32.000 0.00 0.00 0.00 1.40
7184 7524 8.635765 AGCCTCAAGTTTGTCATCTTTATTTA 57.364 30.769 0.00 0.00 0.00 1.40
7185 7525 9.247861 AGCCTCAAGTTTGTCATCTTTATTTAT 57.752 29.630 0.00 0.00 0.00 1.40
7248 7738 1.151668 CTGCCAACTGAAAGGTCTCG 58.848 55.000 0.00 0.00 39.30 4.04
7297 7787 6.093219 ACATGAACTACATAAGCTCTGCAAAG 59.907 38.462 0.00 0.00 37.46 2.77
7321 7811 6.481976 AGATGTAAATGTCGACACAAACTTGA 59.518 34.615 22.71 0.45 35.64 3.02
7397 7890 3.730761 CAGCAGCCACCGTCTTGC 61.731 66.667 0.00 0.00 0.00 4.01
7601 8094 4.023365 GGAGCAATGAAAGATGTATCCTGC 60.023 45.833 0.00 0.00 0.00 4.85
7604 8097 4.577693 GCAATGAAAGATGTATCCTGCTCA 59.422 41.667 0.00 0.00 0.00 4.26
7632 8125 4.034410 TGTATAACAGGGGTGCTATGTCA 58.966 43.478 0.00 0.00 0.00 3.58
7838 8331 7.495934 CCAAGTTCTTTCAGTCTAGTCTCAAAA 59.504 37.037 0.00 0.00 0.00 2.44
7986 8481 6.312399 TGAAACCAAACTACTGCTGTAATG 57.688 37.500 4.91 4.81 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.545298 GCAGAAATGTCAGAATAGAAGGGAAT 59.455 38.462 0.00 0.00 0.00 3.01
63 64 3.403038 AGTATGCATCGGTATCAAAGGC 58.597 45.455 0.19 0.00 0.00 4.35
155 157 1.686325 GCAGCAATCGGGTAGAGGGA 61.686 60.000 0.00 0.00 0.00 4.20
195 198 2.044946 GGCGGGAACATCTGGCTT 60.045 61.111 0.00 0.00 35.91 4.35
205 208 0.527565 GTAGTAGTCGTTGGCGGGAA 59.472 55.000 0.00 0.00 38.89 3.97
300 303 5.593909 TGATAATTGGATCGAAAAGGCACAT 59.406 36.000 0.00 0.00 0.00 3.21
656 668 2.351276 GACCCACGCTGTTCCCAT 59.649 61.111 0.00 0.00 0.00 4.00
740 752 1.285023 CCGAGTCGAAGAACCACGT 59.715 57.895 15.64 0.00 39.69 4.49
905 927 4.881850 CCACCGTATGCTATTTTCCTTCTT 59.118 41.667 0.00 0.00 0.00 2.52
948 970 4.223556 TGCGGGAACAAGATTACCATTA 57.776 40.909 0.00 0.00 0.00 1.90
1258 1283 2.646175 CGCAGGAGAAACCGGGAGA 61.646 63.158 6.32 0.00 44.74 3.71
1297 1322 3.112205 ATCAGGCCCGCCACATCTC 62.112 63.158 8.74 0.00 38.92 2.75
1298 1323 3.092511 ATCAGGCCCGCCACATCT 61.093 61.111 8.74 0.00 38.92 2.90
1306 1331 2.910360 TGATCCACATCAGGCCCG 59.090 61.111 0.00 0.00 33.80 6.13
1312 1337 1.417517 CGGAATCCCTGATCCACATCA 59.582 52.381 0.00 0.00 36.62 3.07
1314 1339 0.109342 GCGGAATCCCTGATCCACAT 59.891 55.000 0.00 0.00 0.00 3.21
1315 1340 1.526887 GCGGAATCCCTGATCCACA 59.473 57.895 0.00 0.00 0.00 4.17
1317 1342 2.807107 CCGCGGAATCCCTGATCCA 61.807 63.158 24.07 0.00 0.00 3.41
1345 1370 6.878317 TGGATGAACGAAGACATAAGATCTT 58.122 36.000 13.56 13.56 39.15 2.40
1359 1384 2.038952 GGATGGATGGATGGATGAACGA 59.961 50.000 0.00 0.00 0.00 3.85
1394 1419 1.004277 TCCAATCGAACCCCTGGAAAG 59.996 52.381 0.00 0.00 35.02 2.62
1400 1425 0.258774 CCCATTCCAATCGAACCCCT 59.741 55.000 0.00 0.00 31.79 4.79
1439 1464 8.062448 AGTCGAGAAAGATTAAAACAAAGAACG 58.938 33.333 0.00 0.00 0.00 3.95
1484 1509 5.524646 ACCATTCATTCACAGCAAAAACAAG 59.475 36.000 0.00 0.00 0.00 3.16
1554 1579 7.912056 TCCTCACTTGTAGAATCAAATCTTG 57.088 36.000 0.00 0.00 0.00 3.02
1582 1607 5.036737 GCATTTGGTTCGTCATAGAAATGG 58.963 41.667 0.00 0.00 33.40 3.16
1618 1643 7.041508 CCCTCACTATGATTACAAAGAGATTGC 60.042 40.741 0.00 0.00 43.13 3.56
1624 1649 6.667848 TCAGACCCTCACTATGATTACAAAGA 59.332 38.462 0.00 0.00 0.00 2.52
1692 1717 3.282021 TGCCTGAAGATATGGAAACTGC 58.718 45.455 0.00 0.00 0.00 4.40
1785 1811 7.429374 ACAGATTCAGATGAGTTATCCTTGA 57.571 36.000 0.00 0.00 36.40 3.02
1786 1812 8.420222 AGTACAGATTCAGATGAGTTATCCTTG 58.580 37.037 0.00 0.00 36.40 3.61
1787 1813 8.546083 AGTACAGATTCAGATGAGTTATCCTT 57.454 34.615 0.00 0.00 36.40 3.36
1788 1814 8.004215 AGAGTACAGATTCAGATGAGTTATCCT 58.996 37.037 0.00 0.00 36.40 3.24
2249 2279 2.175069 TGGCCCACCTACAAAAGTGTAA 59.825 45.455 0.00 0.00 39.75 2.41
2545 2837 4.808077 AATCAGAATCATGCATCGACAC 57.192 40.909 0.00 0.00 0.00 3.67
2564 2856 7.385205 CGCTAAGCATACACAGAGGTTAATAAT 59.615 37.037 0.00 0.00 0.00 1.28
2600 2892 0.877743 GACTGCAAGGAAAGGAGCAC 59.122 55.000 0.00 0.00 39.30 4.40
2909 3202 5.428253 TGTATATTTGAAGAGACAGCCACC 58.572 41.667 0.00 0.00 0.00 4.61
3547 3864 7.154656 GGGAAGTTTTCACTGCAGAAATTAAT 58.845 34.615 23.35 0.00 37.35 1.40
3816 4133 8.611654 AAAGCATTAGATGAAAGCAACAATTT 57.388 26.923 0.00 0.00 0.00 1.82
3817 4134 8.500773 CAAAAGCATTAGATGAAAGCAACAATT 58.499 29.630 0.00 0.00 0.00 2.32
3818 4135 7.658575 ACAAAAGCATTAGATGAAAGCAACAAT 59.341 29.630 0.00 0.00 0.00 2.71
4168 4485 3.317436 ATGGAGCGGAGGTGAGGGA 62.317 63.158 0.00 0.00 39.88 4.20
4185 4502 9.981460 AAACTTTAATAACATTGGAGAGAGGAT 57.019 29.630 0.00 0.00 0.00 3.24
4347 4664 4.631131 TCGATGTGTGAACAATCTTCACT 58.369 39.130 13.00 0.00 46.53 3.41
4498 4815 7.148573 TGCAAGAAAGATCTTAATCTCGTCAAC 60.149 37.037 8.75 0.00 44.11 3.18
4566 4883 3.713826 AACCATGGACAACGGTTAGAT 57.286 42.857 21.47 0.00 41.22 1.98
4574 4891 7.836842 ACCTGAAATTATAAACCATGGACAAC 58.163 34.615 21.47 0.00 0.00 3.32
4963 5280 7.865707 AGATTAGTGACAAAATGTGTGAAGAC 58.134 34.615 0.00 0.00 41.96 3.01
5358 5675 0.671781 GCAAGCTTCGAAGGCTCTCA 60.672 55.000 25.77 0.00 39.30 3.27
5454 5771 4.409901 TCATCTTTCACCTGCTGATCCATA 59.590 41.667 0.00 0.00 0.00 2.74
6111 6428 3.769844 GACAGATGAAACTAGTGGAGGGA 59.230 47.826 0.00 0.00 0.00 4.20
6117 6434 7.227512 GGGGAATAATGACAGATGAAACTAGTG 59.772 40.741 0.00 0.00 0.00 2.74
6118 6435 7.127955 AGGGGAATAATGACAGATGAAACTAGT 59.872 37.037 0.00 0.00 0.00 2.57
6261 6579 3.152341 CATCTGCAGGTGACCTTTTTCT 58.848 45.455 23.04 0.00 0.00 2.52
6278 6597 6.881065 ACACATGTATAAAGCACTGAACATCT 59.119 34.615 0.00 0.00 0.00 2.90
6279 6598 7.076842 ACACATGTATAAAGCACTGAACATC 57.923 36.000 0.00 0.00 0.00 3.06
6281 6600 6.875948 AACACATGTATAAAGCACTGAACA 57.124 33.333 0.00 0.00 0.00 3.18
6282 6601 9.840427 AATTAACACATGTATAAAGCACTGAAC 57.160 29.630 0.00 0.00 0.00 3.18
6385 6708 2.448926 AACGCAAATTTAGGGGCAAC 57.551 45.000 0.00 0.00 0.00 4.17
6500 6833 6.093495 TCAGGTACAAGAAACAAAAGTCACAG 59.907 38.462 0.00 0.00 0.00 3.66
6558 6891 6.531594 TGACAATCATCTGACTACGAAATCAC 59.468 38.462 0.00 0.00 0.00 3.06
6588 6921 5.928264 ACTTTCAAAAGCAACAGCAATATCC 59.072 36.000 2.43 0.00 39.63 2.59
6862 7200 6.952935 AAAAGAAGCTACGATCACTGTTAG 57.047 37.500 0.00 0.00 0.00 2.34
6935 7274 6.452494 TTTACTTCACATCGTTCCCAAAAA 57.548 33.333 0.00 0.00 0.00 1.94
7016 7355 3.709653 TCGCAGATAGGTTACAGGGAAAT 59.290 43.478 0.00 0.00 0.00 2.17
7136 7476 2.713531 ATTGCACGGGGAGGCTTTGT 62.714 55.000 0.00 0.00 0.00 2.83
7138 7478 1.678970 GATTGCACGGGGAGGCTTT 60.679 57.895 0.00 0.00 0.00 3.51
7148 7488 1.267806 ACTTGAGGCTTTGATTGCACG 59.732 47.619 0.00 0.00 0.00 5.34
7155 7495 4.464008 AGATGACAAACTTGAGGCTTTGA 58.536 39.130 3.04 0.00 32.63 2.69
7158 7498 7.530426 AATAAAGATGACAAACTTGAGGCTT 57.470 32.000 0.00 0.00 0.00 4.35
7184 7524 9.203163 AGTAAGATACAAGGCTAGACACTTTAT 57.797 33.333 0.00 0.00 0.00 1.40
7185 7525 8.467598 CAGTAAGATACAAGGCTAGACACTTTA 58.532 37.037 0.00 0.00 0.00 1.85
7186 7526 7.324178 CAGTAAGATACAAGGCTAGACACTTT 58.676 38.462 0.00 0.00 0.00 2.66
7187 7527 6.127310 CCAGTAAGATACAAGGCTAGACACTT 60.127 42.308 0.00 0.00 0.00 3.16
7189 7529 5.452077 CCCAGTAAGATACAAGGCTAGACAC 60.452 48.000 0.00 0.00 0.00 3.67
7190 7530 4.649674 CCCAGTAAGATACAAGGCTAGACA 59.350 45.833 0.00 0.00 0.00 3.41
7248 7738 2.541762 GTGCCATATCGACAAAGCTCTC 59.458 50.000 0.00 0.00 0.00 3.20
7297 7787 6.655062 TCAAGTTTGTGTCGACATTTACATC 58.345 36.000 23.12 7.34 30.13 3.06
7321 7811 5.794894 CATGTTACTAACAGTCTGTTCCCT 58.205 41.667 21.40 8.00 45.95 4.20
7601 8094 5.527582 GCACCCCTGTTATACATTTACTGAG 59.472 44.000 0.00 0.00 0.00 3.35
7604 8097 5.710409 AGCACCCCTGTTATACATTTACT 57.290 39.130 0.00 0.00 0.00 2.24
7632 8125 9.733556 TGAACTAAGTGGTTGTATCATATGTTT 57.266 29.630 1.90 0.00 0.00 2.83
7838 8331 0.821711 TTGCTGCTTTGTAGGCGGTT 60.822 50.000 0.00 0.00 38.25 4.44
8006 8502 9.830186 AACATCTCCTGGTATGTACTTATCTAT 57.170 33.333 14.71 0.00 35.30 1.98


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

AutoCloner maintained by Alex Coulton.