Multiple sequence alignment - TraesCS4D01G182000

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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 TraesCS4D01G182000 chr4D 100.000 7085 0 0 1 7085 317948517 317955601 0.000000e+00 13084
1 TraesCS4D01G182000 chr4D 86.441 118 4 8 483 594 317948939 317949050 1.250000e-22 119
2 TraesCS4D01G182000 chr4D 86.441 118 4 8 423 534 317948999 317949110 1.250000e-22 119
3 TraesCS4D01G182000 chr4A 96.132 6748 175 34 223 6929 156804155 156797453 0.000000e+00 10936
4 TraesCS4D01G182000 chr4A 97.156 211 4 2 1 209 156804349 156804139 8.740000e-94 355
5 TraesCS4D01G182000 chr4A 91.579 95 6 1 6928 7020 156797358 156797264 5.770000e-26 130
6 TraesCS4D01G182000 chr4B 94.732 3512 111 27 223 3714 395245186 395248643 0.000000e+00 5393
7 TraesCS4D01G182000 chr4B 95.038 3406 118 29 3700 7085 395248697 395252071 0.000000e+00 5306
8 TraesCS4D01G182000 chr4B 92.381 210 15 1 1 209 395244993 395245202 1.490000e-76 298
9 TraesCS4D01G182000 chr4B 87.719 114 7 6 483 591 395245389 395245500 7.460000e-25 126


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 TraesCS4D01G182000 chr4D 317948517 317955601 7084 False 13084.00 13084 100.000000 1 7085 1 chr4D.!!$F1 7084
1 TraesCS4D01G182000 chr4A 156797264 156804349 7085 True 3807.00 10936 94.955667 1 7020 3 chr4A.!!$R1 7019
2 TraesCS4D01G182000 chr4B 395244993 395252071 7078 False 2780.75 5393 92.467500 1 7085 4 chr4B.!!$F1 7084

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
382 389 0.318614 AAAGTGGCGCGAAAATGTGG 60.319 50.000 12.10 0.00 0.00 4.17 F
836 851 1.266178 CCACCCATTCCCCTCAAAAC 58.734 55.000 0.00 0.00 0.00 2.43 F
837 852 1.266178 CACCCATTCCCCTCAAAACC 58.734 55.000 0.00 0.00 0.00 3.27 F
1475 1495 1.276989 CTTGCAATGTGGGCTGGAATT 59.723 47.619 0.00 0.00 0.00 2.17 F
2848 2880 1.855295 TGGTCCTTGCATTGCATCAT 58.145 45.000 12.95 0.00 38.76 2.45 F
4065 4175 0.388659 TTGTTTGTCTGGCATGCACC 59.611 50.000 21.36 3.15 0.00 5.01 F
4802 4915 1.544759 GGTATGCCCCAATACCTTCCG 60.545 57.143 6.19 0.00 45.91 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1495 1.067425 CACAACCGGATTACAGGTCGA 60.067 52.381 9.46 0.0 43.29 4.20 R
1650 1670 3.392285 TCAGCCTAGCATCACACCATTAT 59.608 43.478 0.00 0.0 0.00 1.28 R
1787 1810 4.565166 TGTTTGAGCACTTACCGAATATCG 59.435 41.667 0.00 0.0 40.07 2.92 R
2899 2931 1.108776 CCTCATGGGGTGATTGCAAG 58.891 55.000 2.32 0.0 35.97 4.01 R
4363 4475 0.679321 TGCGGCAAACATATGCTCCA 60.679 50.000 0.00 0.0 45.68 3.86 R
5518 5638 1.191425 GAAACGGCGCAAAAATCCAAC 59.809 47.619 10.83 0.0 0.00 3.77 R
6481 6603 1.002033 CAGCAAAACAGCTCTGACCAC 60.002 52.381 3.60 0.0 44.54 4.16 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
165 169 1.485397 TTACGACTAAAACGCGTGCA 58.515 45.000 14.98 0.00 38.84 4.57
216 220 8.748380 AAACTTGCTCATATAGTTTTTCTTGC 57.252 30.769 0.00 0.00 38.56 4.01
217 221 6.546395 ACTTGCTCATATAGTTTTTCTTGCG 58.454 36.000 0.00 0.00 0.00 4.85
218 222 5.484173 TGCTCATATAGTTTTTCTTGCGG 57.516 39.130 0.00 0.00 0.00 5.69
219 223 4.335315 TGCTCATATAGTTTTTCTTGCGGG 59.665 41.667 0.00 0.00 0.00 6.13
220 224 4.261197 GCTCATATAGTTTTTCTTGCGGGG 60.261 45.833 0.00 0.00 0.00 5.73
221 225 4.850680 TCATATAGTTTTTCTTGCGGGGT 58.149 39.130 0.00 0.00 0.00 4.95
222 226 5.991861 TCATATAGTTTTTCTTGCGGGGTA 58.008 37.500 0.00 0.00 0.00 3.69
223 227 6.416415 TCATATAGTTTTTCTTGCGGGGTAA 58.584 36.000 0.00 0.00 0.00 2.85
224 228 6.316890 TCATATAGTTTTTCTTGCGGGGTAAC 59.683 38.462 0.00 0.00 0.00 2.50
225 229 2.940158 AGTTTTTCTTGCGGGGTAACT 58.060 42.857 0.00 0.00 0.00 2.24
226 230 3.293337 AGTTTTTCTTGCGGGGTAACTT 58.707 40.909 0.00 0.00 0.00 2.66
227 231 3.067601 AGTTTTTCTTGCGGGGTAACTTG 59.932 43.478 0.00 0.00 0.00 3.16
228 232 0.955905 TTTCTTGCGGGGTAACTTGC 59.044 50.000 0.00 0.00 37.23 4.01
282 287 8.162878 AGATATGACGTAGAAGATCGGTAAAA 57.837 34.615 0.00 0.00 0.00 1.52
328 333 6.339587 TGTGGCGTGAGATATATGACATAA 57.660 37.500 0.00 0.00 0.00 1.90
339 344 2.939460 ATGACATAAAAGGCAACGGC 57.061 45.000 0.00 0.00 46.39 5.68
357 363 2.673368 CGGCAAACCTCTCACATACTTC 59.327 50.000 0.00 0.00 0.00 3.01
382 389 0.318614 AAAGTGGCGCGAAAATGTGG 60.319 50.000 12.10 0.00 0.00 4.17
415 422 1.739067 GGCAAAGCCTCTCGTATGTT 58.261 50.000 0.00 0.00 46.69 2.71
420 427 5.163652 GGCAAAGCCTCTCGTATGTTTAAAT 60.164 40.000 0.00 0.00 46.69 1.40
473 480 6.327104 AGTCTAGATCTCATCCTCATTTGCTT 59.673 38.462 0.00 0.00 0.00 3.91
683 697 6.920758 GCATGTTTGACATAAACAGGTTGTTA 59.079 34.615 15.54 0.00 42.05 2.41
836 851 1.266178 CCACCCATTCCCCTCAAAAC 58.734 55.000 0.00 0.00 0.00 2.43
837 852 1.266178 CACCCATTCCCCTCAAAACC 58.734 55.000 0.00 0.00 0.00 3.27
1310 1328 4.481930 TCTTGTTGTTTCGTGCCTAATG 57.518 40.909 0.00 0.00 0.00 1.90
1322 1340 3.504520 CGTGCCTAATGTTGGGTAACTTT 59.495 43.478 0.00 0.00 37.68 2.66
1475 1495 1.276989 CTTGCAATGTGGGCTGGAATT 59.723 47.619 0.00 0.00 0.00 2.17
1787 1810 9.341899 CTAGCATTGTTACCTAAAAATGTCAAC 57.658 33.333 8.94 0.00 41.05 3.18
1816 1839 4.024387 TCGGTAAGTGCTCAAACATTTCAC 60.024 41.667 0.00 0.00 0.00 3.18
2077 2103 8.651588 GCAGTACTATTGCACTATTGATATGAC 58.348 37.037 0.00 0.00 41.17 3.06
2544 2576 3.008485 AGGTGGAAGGAATCAGTGAAGTC 59.992 47.826 0.00 0.00 0.00 3.01
2578 2610 4.311816 CATGAGCTGGAGTTGTTTGTTT 57.688 40.909 0.00 0.00 0.00 2.83
2692 2724 7.237055 AGACTGGGTAAACTTAAGGACTGTAAT 59.763 37.037 7.53 0.00 0.00 1.89
2737 2769 2.435437 GCCCCTGTATCCAATGCATTTT 59.565 45.455 9.83 0.22 0.00 1.82
2848 2880 1.855295 TGGTCCTTGCATTGCATCAT 58.145 45.000 12.95 0.00 38.76 2.45
2899 2931 5.391629 CCGTTTATCTAACAGTTTTGAGCCC 60.392 44.000 0.00 0.00 36.50 5.19
2911 2943 0.899717 TTGAGCCCTTGCAATCACCC 60.900 55.000 0.00 0.00 41.13 4.61
2937 2969 2.884639 AGGTGTCCATGTGTTAACTTGC 59.115 45.455 7.22 0.00 31.65 4.01
3059 3091 6.512091 GCTTTAAATTCAACGGTGTGTCAGTA 60.512 38.462 0.00 0.00 0.00 2.74
3293 3325 6.673583 TCTAGAACTCCTAATGATGTCCTGA 58.326 40.000 0.00 0.00 0.00 3.86
3428 3461 4.035208 GGTGTTATTTCATCTAACCAGGCG 59.965 45.833 0.00 0.00 0.00 5.52
3477 3510 6.075984 GTGACCTAGATATTCTCCCCAAGTA 58.924 44.000 0.00 0.00 0.00 2.24
3485 3518 8.337118 AGATATTCTCCCCAAGTATTTCTCAA 57.663 34.615 0.00 0.00 0.00 3.02
3546 3579 3.059352 ACACGCTTTTAGCCTCTTCAT 57.941 42.857 0.00 0.00 38.18 2.57
3547 3580 2.744202 ACACGCTTTTAGCCTCTTCATG 59.256 45.455 0.00 0.00 38.18 3.07
3549 3582 3.189287 CACGCTTTTAGCCTCTTCATGTT 59.811 43.478 0.00 0.00 38.18 2.71
3550 3583 3.821033 ACGCTTTTAGCCTCTTCATGTTT 59.179 39.130 0.00 0.00 38.18 2.83
3552 3585 5.648092 ACGCTTTTAGCCTCTTCATGTTTAT 59.352 36.000 0.00 0.00 38.18 1.40
3554 3587 6.403636 CGCTTTTAGCCTCTTCATGTTTATGT 60.404 38.462 0.00 0.00 38.18 2.29
3555 3588 7.315890 GCTTTTAGCCTCTTCATGTTTATGTT 58.684 34.615 0.00 0.00 34.48 2.71
3556 3589 7.486232 GCTTTTAGCCTCTTCATGTTTATGTTC 59.514 37.037 0.00 0.00 34.48 3.18
3557 3590 8.635765 TTTTAGCCTCTTCATGTTTATGTTCT 57.364 30.769 0.00 0.00 35.73 3.01
3558 3591 8.635765 TTTAGCCTCTTCATGTTTATGTTCTT 57.364 30.769 0.00 0.00 35.73 2.52
3559 3592 9.733556 TTTAGCCTCTTCATGTTTATGTTCTTA 57.266 29.630 0.00 0.00 35.73 2.10
3560 3593 7.856145 AGCCTCTTCATGTTTATGTTCTTAG 57.144 36.000 0.00 0.00 35.73 2.18
3561 3594 6.317391 AGCCTCTTCATGTTTATGTTCTTAGC 59.683 38.462 0.00 0.00 35.73 3.09
3562 3595 6.458888 GCCTCTTCATGTTTATGTTCTTAGCC 60.459 42.308 0.00 0.00 35.73 3.93
3563 3596 6.599244 CCTCTTCATGTTTATGTTCTTAGCCA 59.401 38.462 0.00 0.00 35.73 4.75
3564 3597 7.377766 TCTTCATGTTTATGTTCTTAGCCAC 57.622 36.000 0.00 0.00 35.73 5.01
3565 3598 6.939730 TCTTCATGTTTATGTTCTTAGCCACA 59.060 34.615 0.00 0.00 35.73 4.17
3566 3599 6.494893 TCATGTTTATGTTCTTAGCCACAC 57.505 37.500 0.00 0.00 35.73 3.82
3567 3600 6.237901 TCATGTTTATGTTCTTAGCCACACT 58.762 36.000 0.00 0.00 35.73 3.55
3568 3601 6.714810 TCATGTTTATGTTCTTAGCCACACTT 59.285 34.615 0.00 0.00 35.73 3.16
3569 3602 7.880713 TCATGTTTATGTTCTTAGCCACACTTA 59.119 33.333 0.00 0.00 35.73 2.24
3570 3603 8.511321 CATGTTTATGTTCTTAGCCACACTTAA 58.489 33.333 0.00 0.00 0.00 1.85
3571 3604 8.453238 TGTTTATGTTCTTAGCCACACTTAAA 57.547 30.769 0.00 0.00 0.00 1.52
3572 3605 8.347035 TGTTTATGTTCTTAGCCACACTTAAAC 58.653 33.333 10.47 10.47 38.73 2.01
3573 3606 5.607119 ATGTTCTTAGCCACACTTAAACG 57.393 39.130 0.00 0.00 0.00 3.60
3574 3607 3.810941 TGTTCTTAGCCACACTTAAACGG 59.189 43.478 0.00 0.00 0.00 4.44
3600 3633 9.039870 GGTCAAATGTGATACAATTTGTGAAAA 57.960 29.630 12.30 0.00 35.80 2.29
3894 3995 8.336801 AGTTCCAAATATGAAGGTCTAACAAC 57.663 34.615 0.00 0.00 0.00 3.32
4009 4119 3.264193 TCCCTGTTCATGTGCTGATAGTT 59.736 43.478 0.00 0.00 32.72 2.24
4020 4130 1.129998 GCTGATAGTTGCTGTGCTGTG 59.870 52.381 0.00 0.00 0.00 3.66
4065 4175 0.388659 TTGTTTGTCTGGCATGCACC 59.611 50.000 21.36 3.15 0.00 5.01
4363 4475 2.896685 TGGAATTCATTTGGCGGTTCTT 59.103 40.909 7.93 0.00 0.00 2.52
4474 4586 1.879380 CTTCCGGTGTCTTTGCATGAA 59.121 47.619 0.00 0.00 0.00 2.57
4710 4823 7.044181 TGTTTGCCTGTTTGATATCTCTAGAG 58.956 38.462 13.98 13.98 0.00 2.43
4769 4882 7.768807 ACTAAGTTGTAGAAGAGTCATGAGT 57.231 36.000 1.67 1.67 0.00 3.41
4802 4915 1.544759 GGTATGCCCCAATACCTTCCG 60.545 57.143 6.19 0.00 45.91 4.30
4823 4936 6.551736 TCCGTTTCTATTCTTGCTTTATTGC 58.448 36.000 0.00 0.00 0.00 3.56
4833 4946 4.710865 TCTTGCTTTATTGCCATGATGGAA 59.289 37.500 17.22 0.02 40.96 3.53
4915 5029 6.128849 CGTCAAGGTTTCAAATAAGCAATTGG 60.129 38.462 7.72 0.00 0.00 3.16
4983 5097 3.279434 CTTTTCTATTCCCCTGTTCCCG 58.721 50.000 0.00 0.00 0.00 5.14
5052 5169 2.161609 GCTTCGTTGATCCGTCCAAAAT 59.838 45.455 0.00 0.00 0.00 1.82
5127 5244 4.757799 TGTTCCATATTGTTTCACCACG 57.242 40.909 0.00 0.00 0.00 4.94
5269 5386 3.219281 GGAAGTCCAACTTTAACTGGCA 58.781 45.455 0.00 0.00 38.80 4.92
5371 5490 7.274447 TGATGATGTATGTTGTAAGATCTGCA 58.726 34.615 0.00 0.00 0.00 4.41
5372 5491 7.440255 TGATGATGTATGTTGTAAGATCTGCAG 59.560 37.037 7.63 7.63 0.00 4.41
5428 5547 4.631813 GTCTAAATGATTGCGGACTTCAGT 59.368 41.667 0.00 0.00 0.00 3.41
5446 5565 3.131933 TCAGTTTTAAGGCTTGCTTGCAA 59.868 39.130 10.69 7.83 34.04 4.08
5518 5638 5.759506 AGTAGTGTTGATATCGACTGGAG 57.240 43.478 21.26 0.00 0.00 3.86
5545 5665 0.453793 TTTGCGCCGTTTCCATATGG 59.546 50.000 16.25 16.25 0.00 2.74
5881 6001 7.374272 TCAGATCTGTACAACTTCTCTCAAAG 58.626 38.462 21.92 0.00 0.00 2.77
5998 6118 4.577693 TGCCTAAAAGCATGTCTGATCATC 59.422 41.667 0.00 0.00 38.00 2.92
6276 6397 0.251354 TGGCTGCTGAGAGATGGAAC 59.749 55.000 0.00 0.00 0.00 3.62
6481 6603 3.896648 AAATGTGTAAGTCGCCTTGTG 57.103 42.857 0.00 0.00 31.89 3.33
6800 6926 6.712095 TGATAGTGATCTTGTTCAGCTTTGTT 59.288 34.615 0.00 0.00 32.79 2.83
6801 6927 5.179045 AGTGATCTTGTTCAGCTTTGTTG 57.821 39.130 0.00 0.00 0.00 3.33
6803 6929 3.953612 TGATCTTGTTCAGCTTTGTTGGT 59.046 39.130 0.00 0.00 0.00 3.67
6805 6931 4.370364 TCTTGTTCAGCTTTGTTGGTTC 57.630 40.909 0.00 0.00 0.00 3.62
6809 6936 3.128589 TGTTCAGCTTTGTTGGTTCTGTC 59.871 43.478 0.00 0.00 0.00 3.51
6847 6974 2.717639 CGGAGGAAGATTGGACCAAT 57.282 50.000 19.92 19.92 36.72 3.16
6995 7220 7.041721 GGATAACAAGATATGCCATATCGTCA 58.958 38.462 16.87 4.44 44.92 4.35
6998 7223 3.895232 AGATATGCCATATCGTCACCC 57.105 47.619 16.87 0.00 44.92 4.61
7030 7261 4.885325 GTGTTTGGTTTGAGGAACTAGGAA 59.115 41.667 0.00 0.00 41.55 3.36
7032 7263 3.396260 TGGTTTGAGGAACTAGGAACG 57.604 47.619 0.00 0.00 41.55 3.95
7065 7296 4.568152 AAATGTTCCTGGTTTGACTTCG 57.432 40.909 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 204 6.317893 AGTTACCCCGCAAGAAAAACTATATG 59.682 38.462 0.00 0.00 43.02 1.78
201 205 6.420638 AGTTACCCCGCAAGAAAAACTATAT 58.579 36.000 0.00 0.00 43.02 0.86
202 206 5.807909 AGTTACCCCGCAAGAAAAACTATA 58.192 37.500 0.00 0.00 43.02 1.31
203 207 4.659115 AGTTACCCCGCAAGAAAAACTAT 58.341 39.130 0.00 0.00 43.02 2.12
204 208 4.089408 AGTTACCCCGCAAGAAAAACTA 57.911 40.909 0.00 0.00 43.02 2.24
205 209 2.940158 AGTTACCCCGCAAGAAAAACT 58.060 42.857 0.00 0.00 43.02 2.66
206 210 3.377439 CAAGTTACCCCGCAAGAAAAAC 58.623 45.455 0.00 0.00 43.02 2.43
207 211 2.223852 GCAAGTTACCCCGCAAGAAAAA 60.224 45.455 0.00 0.00 43.02 1.94
208 212 1.338655 GCAAGTTACCCCGCAAGAAAA 59.661 47.619 0.00 0.00 43.02 2.29
209 213 0.955905 GCAAGTTACCCCGCAAGAAA 59.044 50.000 0.00 0.00 43.02 2.52
210 214 0.109723 AGCAAGTTACCCCGCAAGAA 59.890 50.000 0.00 0.00 43.02 2.52
211 215 0.321298 GAGCAAGTTACCCCGCAAGA 60.321 55.000 0.00 0.00 43.02 3.02
212 216 0.605319 TGAGCAAGTTACCCCGCAAG 60.605 55.000 0.00 0.00 0.00 4.01
213 217 0.037590 ATGAGCAAGTTACCCCGCAA 59.962 50.000 0.00 0.00 0.00 4.85
214 218 0.906066 TATGAGCAAGTTACCCCGCA 59.094 50.000 0.00 0.00 0.00 5.69
215 219 2.256117 ATATGAGCAAGTTACCCCGC 57.744 50.000 0.00 0.00 0.00 6.13
216 220 4.602340 ACTATATGAGCAAGTTACCCCG 57.398 45.455 0.00 0.00 0.00 5.73
223 227 9.534565 CACTTATGTGTAACTATATGAGCAAGT 57.465 33.333 0.62 0.00 39.24 3.16
224 228 8.982685 CCACTTATGTGTAACTATATGAGCAAG 58.017 37.037 7.86 0.00 42.34 4.01
225 229 7.441157 GCCACTTATGTGTAACTATATGAGCAA 59.559 37.037 7.86 0.00 42.34 3.91
226 230 6.929049 GCCACTTATGTGTAACTATATGAGCA 59.071 38.462 7.86 0.00 42.34 4.26
227 231 6.089551 CGCCACTTATGTGTAACTATATGAGC 59.910 42.308 7.86 0.00 42.34 4.26
228 232 6.089551 GCGCCACTTATGTGTAACTATATGAG 59.910 42.308 0.00 0.00 42.34 2.90
282 287 9.049523 CACATTGCATGTAAGTATATGAGAAGT 57.950 33.333 1.90 0.00 42.70 3.01
312 317 7.387673 CCGTTGCCTTTTATGTCATATATCTCA 59.612 37.037 0.00 0.00 0.00 3.27
328 333 0.755327 AGAGGTTTGCCGTTGCCTTT 60.755 50.000 0.00 0.00 40.50 3.11
357 363 3.733024 TTTTCGCGCCACTTTACATAG 57.267 42.857 0.00 0.00 0.00 2.23
382 389 3.442100 GCTTTGCCATTATCTTCTGCAC 58.558 45.455 0.00 0.00 0.00 4.57
409 416 8.047859 CGCGCCATTTTTCTAATTTAAACATAC 58.952 33.333 0.00 0.00 0.00 2.39
413 420 6.620253 TCGCGCCATTTTTCTAATTTAAAC 57.380 33.333 0.00 0.00 0.00 2.01
415 422 7.639162 TTTTCGCGCCATTTTTCTAATTTAA 57.361 28.000 0.00 0.00 0.00 1.52
420 427 6.306837 CAGTATTTTTCGCGCCATTTTTCTAA 59.693 34.615 0.00 0.00 0.00 2.10
454 461 7.938715 ACAAATAAGCAAATGAGGATGAGATC 58.061 34.615 0.00 0.00 0.00 2.75
473 480 5.700846 TCGCGCCATTTTTCTTAACAAATA 58.299 33.333 0.00 0.00 0.00 1.40
1475 1495 1.067425 CACAACCGGATTACAGGTCGA 60.067 52.381 9.46 0.00 43.29 4.20
1650 1670 3.392285 TCAGCCTAGCATCACACCATTAT 59.608 43.478 0.00 0.00 0.00 1.28
1787 1810 4.565166 TGTTTGAGCACTTACCGAATATCG 59.435 41.667 0.00 0.00 40.07 2.92
1825 1848 4.568359 AGCAACTCACATACGATGATCAAC 59.432 41.667 0.00 0.00 0.00 3.18
1826 1849 4.758688 AGCAACTCACATACGATGATCAA 58.241 39.130 0.00 0.00 0.00 2.57
2077 2103 5.277825 TCACCAGTAATTGTTTCTTTTGCG 58.722 37.500 0.00 0.00 0.00 4.85
2123 2149 7.256286 GTCAACACGATCCTACACTTATACTT 58.744 38.462 0.00 0.00 0.00 2.24
2899 2931 1.108776 CCTCATGGGGTGATTGCAAG 58.891 55.000 2.32 0.00 35.97 4.01
2911 2943 2.205022 AACACATGGACACCTCATGG 57.795 50.000 0.00 0.00 44.42 3.66
2937 2969 3.438087 AGGACAACGAAGAAATGATGCTG 59.562 43.478 0.00 0.00 0.00 4.41
3059 3091 1.212935 AGCTGGGCGTATGGAAAATCT 59.787 47.619 0.00 0.00 0.00 2.40
3229 3261 7.333528 TGTTACAGAAGCTGTTTTGAGAAAT 57.666 32.000 5.31 0.00 42.59 2.17
3410 3443 9.214957 CAAATATACGCCTGGTTAGATGAAATA 57.785 33.333 0.00 0.00 0.00 1.40
3428 3461 8.936864 ACTGTTCACTGCTTTAGTCAAATATAC 58.063 33.333 0.00 0.00 37.60 1.47
3516 3549 7.389607 AGAGGCTAAAAGCGTGTTAAGATAAAA 59.610 33.333 0.00 0.00 43.62 1.52
3546 3579 8.347035 GTTTAAGTGTGGCTAAGAACATAAACA 58.653 33.333 11.40 0.00 34.69 2.83
3547 3580 7.532884 CGTTTAAGTGTGGCTAAGAACATAAAC 59.467 37.037 8.40 8.40 32.99 2.01
3549 3582 6.148150 CCGTTTAAGTGTGGCTAAGAACATAA 59.852 38.462 0.00 0.00 0.00 1.90
3550 3583 5.640357 CCGTTTAAGTGTGGCTAAGAACATA 59.360 40.000 0.00 0.00 0.00 2.29
3552 3585 3.810941 CCGTTTAAGTGTGGCTAAGAACA 59.189 43.478 0.00 0.00 0.00 3.18
3554 3587 3.181452 ACCCGTTTAAGTGTGGCTAAGAA 60.181 43.478 0.00 0.00 0.00 2.52
3555 3588 2.369532 ACCCGTTTAAGTGTGGCTAAGA 59.630 45.455 0.00 0.00 0.00 2.10
3556 3589 2.740447 GACCCGTTTAAGTGTGGCTAAG 59.260 50.000 0.00 0.00 0.00 2.18
3557 3590 2.104451 TGACCCGTTTAAGTGTGGCTAA 59.896 45.455 0.00 0.00 0.00 3.09
3558 3591 1.693062 TGACCCGTTTAAGTGTGGCTA 59.307 47.619 0.00 0.00 0.00 3.93
3559 3592 0.470766 TGACCCGTTTAAGTGTGGCT 59.529 50.000 0.00 0.00 0.00 4.75
3560 3593 1.310904 TTGACCCGTTTAAGTGTGGC 58.689 50.000 0.00 0.00 0.00 5.01
3561 3594 3.316868 ACATTTGACCCGTTTAAGTGTGG 59.683 43.478 0.00 0.00 0.00 4.17
3562 3595 4.035792 TCACATTTGACCCGTTTAAGTGTG 59.964 41.667 0.00 0.00 40.91 3.82
3563 3596 4.200874 TCACATTTGACCCGTTTAAGTGT 58.799 39.130 0.00 0.00 0.00 3.55
3564 3597 4.822036 TCACATTTGACCCGTTTAAGTG 57.178 40.909 0.00 0.00 0.00 3.16
3565 3598 5.998981 TGTATCACATTTGACCCGTTTAAGT 59.001 36.000 0.00 0.00 33.38 2.24
3566 3599 6.489127 TGTATCACATTTGACCCGTTTAAG 57.511 37.500 0.00 0.00 33.38 1.85
3567 3600 6.879276 TTGTATCACATTTGACCCGTTTAA 57.121 33.333 0.00 0.00 33.38 1.52
3568 3601 7.455641 AATTGTATCACATTTGACCCGTTTA 57.544 32.000 0.00 0.00 33.38 2.01
3569 3602 5.975693 ATTGTATCACATTTGACCCGTTT 57.024 34.783 0.00 0.00 33.38 3.60
3570 3603 5.975693 AATTGTATCACATTTGACCCGTT 57.024 34.783 0.00 0.00 33.38 4.44
3571 3604 5.242838 ACAAATTGTATCACATTTGACCCGT 59.757 36.000 10.76 0.00 34.17 5.28
3572 3605 5.572511 CACAAATTGTATCACATTTGACCCG 59.427 40.000 10.76 0.00 34.17 5.28
3573 3606 6.686630 TCACAAATTGTATCACATTTGACCC 58.313 36.000 10.76 0.00 34.17 4.46
3574 3607 8.586570 TTTCACAAATTGTATCACATTTGACC 57.413 30.769 10.76 0.00 34.17 4.02
3600 3633 7.346471 ACCCATAAGAACATAAACATAGCAGT 58.654 34.615 0.00 0.00 0.00 4.40
4009 4119 3.600843 TGCAAACACAGCACAGCA 58.399 50.000 0.00 0.00 37.02 4.41
4065 4175 6.964934 CGAATGACACATATATTCATGCCATG 59.035 38.462 0.00 0.00 31.87 3.66
4071 4181 8.837788 ACACATCGAATGACACATATATTCAT 57.162 30.769 7.02 0.00 31.87 2.57
4075 4185 7.714813 TGGAAACACATCGAATGACACATATAT 59.285 33.333 7.02 0.00 33.40 0.86
4148 4258 7.267128 AGTTGAAATTTCTGCATCAAAACTCA 58.733 30.769 18.64 2.03 33.93 3.41
4295 4405 8.481492 AAATGGCATCATACAATTGAGGATAA 57.519 30.769 13.59 2.45 32.44 1.75
4363 4475 0.679321 TGCGGCAAACATATGCTCCA 60.679 50.000 0.00 0.00 45.68 3.86
4447 4559 1.831652 AAGACACCGGAAGAGGCCAG 61.832 60.000 9.46 0.00 33.69 4.85
4474 4586 2.509964 AGGACTCCAAAGAGGTGTTTGT 59.490 45.455 0.00 0.00 43.87 2.83
4687 4800 7.187824 ACTCTAGAGATATCAAACAGGCAAA 57.812 36.000 26.57 0.00 0.00 3.68
4769 4882 4.156477 GGGGCATACCAGGCATATTAAAA 58.844 43.478 0.00 0.00 42.91 1.52
4802 4915 7.975616 TCATGGCAATAAAGCAAGAATAGAAAC 59.024 33.333 0.00 0.00 35.83 2.78
4955 5069 3.267031 CAGGGGAATAGAAAAGGACCACT 59.733 47.826 0.00 0.00 0.00 4.00
4956 5070 3.010250 ACAGGGGAATAGAAAAGGACCAC 59.990 47.826 0.00 0.00 0.00 4.16
5013 5130 8.914654 CAACGAAGCTATCAAATTTTCAAATGA 58.085 29.630 0.00 0.00 0.00 2.57
5127 5244 2.906354 ACAAGTAACAGATCGATGGGC 58.094 47.619 0.54 0.00 0.00 5.36
5269 5386 6.374417 AACCACCTACACAGAACTAATCAT 57.626 37.500 0.00 0.00 0.00 2.45
5371 5490 8.086522 GGATATATCAATGCATTTTGCTTCACT 58.913 33.333 9.83 0.00 45.31 3.41
5372 5491 7.868922 TGGATATATCAATGCATTTTGCTTCAC 59.131 33.333 9.83 0.00 45.31 3.18
5412 5531 4.215399 CCTTAAAACTGAAGTCCGCAATCA 59.785 41.667 0.00 0.00 0.00 2.57
5428 5547 4.333913 TGATTGCAAGCAAGCCTTAAAA 57.666 36.364 16.30 0.00 41.12 1.52
5446 5565 4.523173 CCATTTCAGCTGCCTATTCATGAT 59.477 41.667 9.47 0.00 0.00 2.45
5508 5628 3.191371 GCAAAAATCCAACTCCAGTCGAT 59.809 43.478 0.00 0.00 0.00 3.59
5518 5638 1.191425 GAAACGGCGCAAAAATCCAAC 59.809 47.619 10.83 0.00 0.00 3.77
5603 5723 1.666209 CCCATCCAACCCAATCACGC 61.666 60.000 0.00 0.00 0.00 5.34
5998 6118 2.618053 CAGTTTCTGTAAGTAGGCCGG 58.382 52.381 0.00 0.00 33.76 6.13
6097 6217 6.373005 TCTGGATATTCACAGGTTTGAGAA 57.627 37.500 0.00 0.00 38.09 2.87
6276 6397 1.688197 TGGAAGCTTCAGGGCAAAAAG 59.312 47.619 27.02 0.00 34.17 2.27
6481 6603 1.002033 CAGCAAAACAGCTCTGACCAC 60.002 52.381 3.60 0.00 44.54 4.16
6646 6769 4.630894 TGCAAGAGTAAACAACAACAGG 57.369 40.909 0.00 0.00 0.00 4.00
6800 6926 5.863965 TCACATATCTTGTTGACAGAACCA 58.136 37.500 0.00 0.00 36.00 3.67
6801 6927 6.621596 GCTTCACATATCTTGTTGACAGAACC 60.622 42.308 0.00 0.00 36.00 3.62
6803 6929 5.412594 GGCTTCACATATCTTGTTGACAGAA 59.587 40.000 0.00 0.00 36.00 3.02
6805 6931 4.095483 GGGCTTCACATATCTTGTTGACAG 59.905 45.833 0.00 0.00 36.00 3.51
6809 6936 2.355756 CCGGGCTTCACATATCTTGTTG 59.644 50.000 0.00 0.00 36.00 3.33
6813 6940 1.417890 CCTCCGGGCTTCACATATCTT 59.582 52.381 0.00 0.00 0.00 2.40
6847 6974 7.564793 TGCTCAAAGATTAAGCTAAGACCATA 58.435 34.615 0.00 0.00 36.96 2.74
6856 6983 7.700022 AGAAGAAATGCTCAAAGATTAAGCT 57.300 32.000 0.00 0.00 36.96 3.74
6995 7220 1.564348 ACCAAACACAAGTCAGAGGGT 59.436 47.619 0.00 0.00 0.00 4.34
6998 7223 4.201950 CCTCAAACCAAACACAAGTCAGAG 60.202 45.833 0.00 0.00 0.00 3.35
7030 7261 3.632145 GGAACATTTTGGGATCATAGCGT 59.368 43.478 0.00 0.00 0.00 5.07
7032 7263 4.038402 CCAGGAACATTTTGGGATCATAGC 59.962 45.833 0.00 0.00 0.00 2.97
7065 7296 2.510664 CCAGGTCTGGCTACTCCTC 58.489 63.158 3.86 0.00 44.73 3.71


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

AutoCloner maintained by Alex Coulton.