Multiple sequence alignment - TraesCS7D01G244300

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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 TraesCS7D01G244300 chr7D 100.000 3933 0 0 1 3933 212204545 212208477 0.000000e+00 7263.0
1 TraesCS7D01G244300 chr7B 91.316 3593 133 68 1 3488 189499506 189495988 0.000000e+00 4741.0
2 TraesCS7D01G244300 chr7B 97.516 161 2 1 3664 3824 189494737 189494579 1.390000e-69 274.0
3 TraesCS7D01G244300 chr7B 92.228 193 8 2 3489 3681 189495936 189495751 2.330000e-67 267.0
4 TraesCS7D01G244300 chr7A 87.982 3528 173 110 483 3885 224035565 224038966 0.000000e+00 3934.0
5 TraesCS7D01G244300 chr7A 88.381 3305 155 109 1 3205 224035127 224038302 0.000000e+00 3764.0
6 TraesCS7D01G244300 chr5D 90.265 113 11 0 2103 2215 375678426 375678538 8.810000e-32 148.0
7 TraesCS7D01G244300 chr5A 89.381 113 12 0 2103 2215 476837049 476837161 4.100000e-30 143.0
8 TraesCS7D01G244300 chr5B 93.590 78 5 0 2536 2613 448467080 448467157 2.480000e-22 117.0
9 TraesCS7D01G244300 chr4B 100.000 28 0 0 1391 1418 27796766 27796739 7.000000e-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 TraesCS7D01G244300 chr7D 212204545 212208477 3932 False 7263.000000 7263 100.000000 1 3933 1 chr7D.!!$F1 3932
1 TraesCS7D01G244300 chr7B 189494579 189499506 4927 True 1760.666667 4741 93.686667 1 3824 3 chr7B.!!$R1 3823
2 TraesCS7D01G244300 chr7A 224035127 224038966 3839 False 3849.000000 3934 88.181500 1 3885 2 chr7A.!!$F1 3884

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
412 451 0.040351 TCTCTCTCCCTCACTGTGGG 59.96 60.0 9.63 9.63 45.9 4.61 F
1510 1608 0.340208 CCACTCCTACTCCCCTCCTT 59.66 60.0 0.00 0.00 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 2431 0.464013 GATCAGCAGCACATCAGCCT 60.464 55.0 0.0 0.0 34.23 4.58 R
3312 3526 0.030235 GGTTTTTGGACTGTGACCGC 59.970 55.0 0.0 0.0 0.00 5.68 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
27 28 2.045926 ATCCCACTCGTTGCCAGC 60.046 61.111 0.00 0.00 0.00 4.85
35 36 1.203994 ACTCGTTGCCAGCGTAATACT 59.796 47.619 0.00 0.00 0.00 2.12
122 125 0.890542 AGAATTCAGCGCCACTTGCA 60.891 50.000 2.29 0.00 41.33 4.08
123 126 0.455633 GAATTCAGCGCCACTTGCAG 60.456 55.000 2.29 0.00 41.33 4.41
185 188 4.309950 ACCCGCCACCGTCTTGTC 62.310 66.667 0.00 0.00 0.00 3.18
188 191 1.290955 CCGCCACCGTCTTGTCTTA 59.709 57.895 0.00 0.00 0.00 2.10
192 195 2.093783 CGCCACCGTCTTGTCTTATTTC 59.906 50.000 0.00 0.00 0.00 2.17
206 210 6.403049 TGTCTTATTTCTGCTCCGTTTCATA 58.597 36.000 0.00 0.00 0.00 2.15
214 218 4.507756 TCTGCTCCGTTTCATAATGATTCG 59.492 41.667 0.00 0.00 0.00 3.34
285 311 0.746659 AAAACACACCCAAGCTCAGC 59.253 50.000 0.00 0.00 0.00 4.26
397 436 2.224378 CGGCATCTCTCTCTCTCTCTCT 60.224 54.545 0.00 0.00 0.00 3.10
408 447 2.505407 TCTCTCTCTCTCTCCCTCACTG 59.495 54.545 0.00 0.00 0.00 3.66
409 448 2.239654 CTCTCTCTCTCTCCCTCACTGT 59.760 54.545 0.00 0.00 0.00 3.55
410 449 2.026356 TCTCTCTCTCTCCCTCACTGTG 60.026 54.545 0.17 0.17 0.00 3.66
411 450 1.005332 TCTCTCTCTCCCTCACTGTGG 59.995 57.143 8.11 0.00 0.00 4.17
412 451 0.040351 TCTCTCTCCCTCACTGTGGG 59.960 60.000 9.63 9.63 45.90 4.61
413 452 1.610673 TCTCTCCCTCACTGTGGGC 60.611 63.158 10.92 0.00 44.23 5.36
501 558 2.280797 CTCCCACACCCACACACG 60.281 66.667 0.00 0.00 0.00 4.49
634 702 1.768275 TGCTCGATCTCCTCTCTCTCT 59.232 52.381 0.00 0.00 0.00 3.10
751 819 2.122167 GGTGCGGAGGAGATCGAGT 61.122 63.158 0.00 0.00 0.00 4.18
759 827 1.230497 GGAGATCGAGTGGAGGGGA 59.770 63.158 0.00 0.00 0.00 4.81
760 828 0.397254 GGAGATCGAGTGGAGGGGAA 60.397 60.000 0.00 0.00 0.00 3.97
761 829 1.486211 GAGATCGAGTGGAGGGGAAA 58.514 55.000 0.00 0.00 0.00 3.13
762 830 1.410882 GAGATCGAGTGGAGGGGAAAG 59.589 57.143 0.00 0.00 0.00 2.62
763 831 1.007238 AGATCGAGTGGAGGGGAAAGA 59.993 52.381 0.00 0.00 0.00 2.52
809 881 2.666098 GCTCCCCGGCTGGAAAGTA 61.666 63.158 15.09 0.00 37.49 2.24
972 1052 5.010708 AGAATTATTGGTGTTTGGGAGGT 57.989 39.130 0.00 0.00 0.00 3.85
983 1063 2.190904 TTGGGAGGTAGGAGGGGTCC 62.191 65.000 0.00 0.00 0.00 4.46
1317 1406 0.770499 TGATGTTCCACTCCCAGCAA 59.230 50.000 0.00 0.00 0.00 3.91
1487 1585 2.333688 TTGAACATGGACAACGGTCA 57.666 45.000 0.00 0.00 46.17 4.02
1509 1607 0.856311 ACCACTCCTACTCCCCTCCT 60.856 60.000 0.00 0.00 0.00 3.69
1510 1608 0.340208 CCACTCCTACTCCCCTCCTT 59.660 60.000 0.00 0.00 0.00 3.36
1511 1609 1.689892 CCACTCCTACTCCCCTCCTTC 60.690 61.905 0.00 0.00 0.00 3.46
1512 1610 0.637743 ACTCCTACTCCCCTCCTTCC 59.362 60.000 0.00 0.00 0.00 3.46
1513 1611 0.938192 CTCCTACTCCCCTCCTTCCT 59.062 60.000 0.00 0.00 0.00 3.36
1565 1663 2.620115 CGCGGTTCCATAGTTCCTACTA 59.380 50.000 0.00 0.00 40.96 1.82
2025 2127 5.633830 ACACTAGCATTTCATTCCTTGTG 57.366 39.130 0.00 0.00 37.18 3.33
2234 2336 1.739067 AAGTAAATCCACGCTGCTCC 58.261 50.000 0.00 0.00 0.00 4.70
2235 2337 0.613260 AGTAAATCCACGCTGCTCCA 59.387 50.000 0.00 0.00 0.00 3.86
2236 2338 0.727398 GTAAATCCACGCTGCTCCAC 59.273 55.000 0.00 0.00 0.00 4.02
2258 2377 3.216147 GCACGATTGCCAGTATTGTTT 57.784 42.857 0.00 0.00 43.66 2.83
2259 2378 2.916716 GCACGATTGCCAGTATTGTTTG 59.083 45.455 0.00 0.00 43.66 2.93
2260 2379 2.916716 CACGATTGCCAGTATTGTTTGC 59.083 45.455 0.00 0.00 0.00 3.68
2261 2380 2.556189 ACGATTGCCAGTATTGTTTGCA 59.444 40.909 0.00 0.00 0.00 4.08
2262 2381 2.916716 CGATTGCCAGTATTGTTTGCAC 59.083 45.455 0.00 0.00 0.00 4.57
2263 2382 3.611293 CGATTGCCAGTATTGTTTGCACA 60.611 43.478 0.00 0.00 0.00 4.57
2277 2400 0.813210 TGCACACACACGATTGCTGA 60.813 50.000 0.00 0.00 35.91 4.26
2465 2598 6.870965 CCAATAGGAGATAGAACAGTGTATGC 59.129 42.308 0.00 0.00 36.89 3.14
2642 2779 9.722317 AAATTATCCTCCCAATTACCATAAACA 57.278 29.630 0.00 0.00 0.00 2.83
2672 2809 5.788533 TCAGAGAGAGGGGTAAAATAAACCA 59.211 40.000 0.00 0.00 38.87 3.67
2746 2883 2.991540 AGGAAGCCGCTTTTGCCC 60.992 61.111 7.16 3.74 43.93 5.36
3008 3177 8.728596 TTTAGAAACAAGATTATTTGGGGGAA 57.271 30.769 0.00 0.00 32.32 3.97
3069 3238 1.134098 TGGGTATAAGCAAGCAGAGGC 60.134 52.381 0.00 0.00 41.61 4.70
3143 3330 1.616628 GGAGAAGGGAGCAAGGGGA 60.617 63.158 0.00 0.00 0.00 4.81
3206 3416 7.549488 AGTTTTTGCTGTAACTTCGCTATATCT 59.451 33.333 0.00 0.00 30.72 1.98
3284 3498 4.251246 CTGCCGTAGCCTCTCTCT 57.749 61.111 0.00 0.00 38.69 3.10
3290 3504 1.140052 CCGTAGCCTCTCTCTCTCTCA 59.860 57.143 0.00 0.00 0.00 3.27
3312 3526 5.867174 TCATTTAACACCATCACTACTCACG 59.133 40.000 0.00 0.00 0.00 4.35
3321 3535 0.729478 CACTACTCACGCGGTCACAG 60.729 60.000 12.47 4.28 0.00 3.66
3326 3540 2.279851 CACGCGGTCACAGTCCAA 60.280 61.111 12.47 0.00 0.00 3.53
3327 3541 1.885388 CACGCGGTCACAGTCCAAA 60.885 57.895 12.47 0.00 0.00 3.28
3330 3544 0.316689 CGCGGTCACAGTCCAAAAAC 60.317 55.000 0.00 0.00 0.00 2.43
3345 3559 7.543868 CAGTCCAAAAACCAATAAAATATCGCA 59.456 33.333 0.00 0.00 0.00 5.10
3347 3561 6.814146 TCCAAAAACCAATAAAATATCGCACC 59.186 34.615 0.00 0.00 0.00 5.01
3376 3591 1.165907 TCTGTGTCTTGCTTTGCGGG 61.166 55.000 0.00 0.00 0.00 6.13
3422 3637 3.452474 TGCGCTGTTTAATTTTGTGCTT 58.548 36.364 9.73 0.00 35.49 3.91
3431 3646 6.975197 TGTTTAATTTTGTGCTTGACGATCAA 59.025 30.769 0.00 0.00 34.79 2.57
3432 3647 7.489435 TGTTTAATTTTGTGCTTGACGATCAAA 59.511 29.630 0.00 0.00 35.73 2.69
3468 3683 4.778213 TTCTGCTTGCCCAATATAGTCT 57.222 40.909 0.00 0.00 0.00 3.24
3545 3811 2.178521 CACGACGAAGGAGGTCCG 59.821 66.667 0.00 0.00 42.08 4.79
3581 3847 3.259064 TGAGAATGCGTGGCTACTTTAC 58.741 45.455 0.00 0.00 0.00 2.01
3616 3882 4.262506 GCTGTCTCTCCATCATCATCATCA 60.263 45.833 0.00 0.00 0.00 3.07
3617 3883 5.569832 GCTGTCTCTCCATCATCATCATCAT 60.570 44.000 0.00 0.00 0.00 2.45
3618 3884 6.038997 TGTCTCTCCATCATCATCATCATC 57.961 41.667 0.00 0.00 0.00 2.92
3619 3885 5.542635 TGTCTCTCCATCATCATCATCATCA 59.457 40.000 0.00 0.00 0.00 3.07
3620 3886 6.213600 TGTCTCTCCATCATCATCATCATCAT 59.786 38.462 0.00 0.00 0.00 2.45
3621 3887 6.759356 GTCTCTCCATCATCATCATCATCATC 59.241 42.308 0.00 0.00 0.00 2.92
3783 5091 2.413310 AGTGTTGGTTATTAGGGGCG 57.587 50.000 0.00 0.00 0.00 6.13
3784 5092 1.064979 AGTGTTGGTTATTAGGGGCGG 60.065 52.381 0.00 0.00 0.00 6.13
3871 5182 0.611896 AAAAAGACGGGGATGGCTGG 60.612 55.000 0.00 0.00 0.00 4.85
3885 5196 0.251787 GGCTGGGGAAAAGATGTGGT 60.252 55.000 0.00 0.00 0.00 4.16
3886 5197 0.890683 GCTGGGGAAAAGATGTGGTG 59.109 55.000 0.00 0.00 0.00 4.17
3887 5198 1.549203 CTGGGGAAAAGATGTGGTGG 58.451 55.000 0.00 0.00 0.00 4.61
3888 5199 0.856982 TGGGGAAAAGATGTGGTGGT 59.143 50.000 0.00 0.00 0.00 4.16
3889 5200 1.203001 TGGGGAAAAGATGTGGTGGTC 60.203 52.381 0.00 0.00 0.00 4.02
3890 5201 1.203001 GGGGAAAAGATGTGGTGGTCA 60.203 52.381 0.00 0.00 0.00 4.02
3891 5202 2.162681 GGGAAAAGATGTGGTGGTCAG 58.837 52.381 0.00 0.00 0.00 3.51
3892 5203 2.162681 GGAAAAGATGTGGTGGTCAGG 58.837 52.381 0.00 0.00 0.00 3.86
3893 5204 2.162681 GAAAAGATGTGGTGGTCAGGG 58.837 52.381 0.00 0.00 0.00 4.45
3894 5205 1.444933 AAAGATGTGGTGGTCAGGGA 58.555 50.000 0.00 0.00 0.00 4.20
3895 5206 1.444933 AAGATGTGGTGGTCAGGGAA 58.555 50.000 0.00 0.00 0.00 3.97
3896 5207 1.444933 AGATGTGGTGGTCAGGGAAA 58.555 50.000 0.00 0.00 0.00 3.13
3897 5208 1.352352 AGATGTGGTGGTCAGGGAAAG 59.648 52.381 0.00 0.00 0.00 2.62
3898 5209 1.351017 GATGTGGTGGTCAGGGAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
3899 5210 0.764890 TGTGGTGGTCAGGGAAAGAG 59.235 55.000 0.00 0.00 0.00 2.85
3900 5211 0.606673 GTGGTGGTCAGGGAAAGAGC 60.607 60.000 0.00 0.00 0.00 4.09
3901 5212 0.768221 TGGTGGTCAGGGAAAGAGCT 60.768 55.000 0.00 0.00 34.73 4.09
3902 5213 0.322008 GGTGGTCAGGGAAAGAGCTG 60.322 60.000 0.00 0.00 34.73 4.24
3903 5214 0.957888 GTGGTCAGGGAAAGAGCTGC 60.958 60.000 0.00 0.00 34.73 5.25
3904 5215 1.743252 GGTCAGGGAAAGAGCTGCG 60.743 63.158 0.00 0.00 0.00 5.18
3905 5216 2.046892 TCAGGGAAAGAGCTGCGC 60.047 61.111 0.00 0.00 0.00 6.09
3906 5217 3.130160 CAGGGAAAGAGCTGCGCC 61.130 66.667 4.18 0.00 0.00 6.53
3907 5218 4.767255 AGGGAAAGAGCTGCGCCG 62.767 66.667 4.18 0.00 0.00 6.46
3923 5234 2.897350 CGGGCCGGAGAGAAATGC 60.897 66.667 20.56 0.00 0.00 3.56
3924 5235 2.592308 GGGCCGGAGAGAAATGCT 59.408 61.111 5.05 0.00 0.00 3.79
3925 5236 1.524849 GGGCCGGAGAGAAATGCTC 60.525 63.158 5.05 0.00 44.29 4.26
3932 5243 3.105659 GAGAAATGCTCTGCCCGC 58.894 61.111 0.00 0.00 40.61 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.675510 TGTAGTAGTATTACGCTGGCAAC 58.324 43.478 0.00 0.00 34.88 4.17
35 36 6.805271 GCACGTAGAGAATTGTTTCTGTAGTA 59.195 38.462 0.00 0.00 42.34 1.82
185 188 7.919690 TCATTATGAAACGGAGCAGAAATAAG 58.080 34.615 0.00 0.00 0.00 1.73
188 191 6.949352 ATCATTATGAAACGGAGCAGAAAT 57.051 33.333 0.00 0.00 0.00 2.17
192 195 4.319046 CCGAATCATTATGAAACGGAGCAG 60.319 45.833 26.38 9.12 45.04 4.24
206 210 6.573664 TTTGATTGACTGAACCGAATCATT 57.426 33.333 0.00 0.00 35.35 2.57
214 218 5.234972 CCTTTTGCTTTTGATTGACTGAACC 59.765 40.000 0.00 0.00 0.00 3.62
285 311 1.269778 TGTCGGCTCAACTGAACTGAG 60.270 52.381 0.00 0.00 42.73 3.35
332 358 0.167251 GTGCGTGTTTACCGGAATGG 59.833 55.000 9.46 0.00 46.41 3.16
381 407 3.051803 AGGGAGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
382 408 3.312890 AGGGAGAGAGAGAGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
501 558 3.421888 CGTGGAGCAAATTTTATATGCGC 59.578 43.478 0.00 0.00 44.60 6.09
649 717 3.795924 ATGGAGGGAGGGAGGGGG 61.796 72.222 0.00 0.00 0.00 5.40
650 718 2.122189 GATGGAGGGAGGGAGGGG 60.122 72.222 0.00 0.00 0.00 4.79
725 793 4.135153 CCTCCGCACCCTGACGAG 62.135 72.222 0.00 0.00 0.00 4.18
726 794 4.671590 TCCTCCGCACCCTGACGA 62.672 66.667 0.00 0.00 0.00 4.20
728 796 2.022240 GATCTCCTCCGCACCCTGAC 62.022 65.000 0.00 0.00 0.00 3.51
731 799 2.835431 CGATCTCCTCCGCACCCT 60.835 66.667 0.00 0.00 0.00 4.34
737 805 1.169661 CCTCCACTCGATCTCCTCCG 61.170 65.000 0.00 0.00 0.00 4.63
740 808 1.231641 CCCCTCCACTCGATCTCCT 59.768 63.158 0.00 0.00 0.00 3.69
809 881 4.356436 CCAGGGAAAAGAAAAGATGGGAT 58.644 43.478 0.00 0.00 0.00 3.85
972 1052 4.153330 GCTCCCGGACCCCTCCTA 62.153 72.222 0.73 0.00 33.79 2.94
983 1063 0.879400 CATCAGCTAGCTTGCTCCCG 60.879 60.000 20.13 9.51 41.98 5.14
1317 1406 1.674651 CATCTGCTGCTGGTGCTGT 60.675 57.895 6.85 0.00 39.81 4.40
1428 1526 3.768922 GAGCTGCTCTGCCGGAGT 61.769 66.667 21.93 0.00 43.62 3.85
1487 1585 1.570024 GAGGGGAGTAGGAGTGGTACT 59.430 57.143 0.00 0.00 33.25 2.73
1499 1597 0.498685 AAGGAAGGAAGGAGGGGAGT 59.501 55.000 0.00 0.00 0.00 3.85
1509 1607 3.265995 AGAAGGCCGAATTAAGGAAGGAA 59.734 43.478 0.00 0.00 0.00 3.36
1510 1608 2.844348 AGAAGGCCGAATTAAGGAAGGA 59.156 45.455 0.00 0.00 0.00 3.36
1511 1609 3.283259 AGAAGGCCGAATTAAGGAAGG 57.717 47.619 0.00 0.00 0.00 3.46
1512 1610 5.402398 CAAAAGAAGGCCGAATTAAGGAAG 58.598 41.667 0.00 0.00 0.00 3.46
1513 1611 4.219725 CCAAAAGAAGGCCGAATTAAGGAA 59.780 41.667 0.00 0.00 0.00 3.36
1565 1663 1.318576 GGGCTGTAATAATTGCGGCT 58.681 50.000 0.00 0.00 45.49 5.52
1772 1870 1.515952 CGACGAGAAGCTGAGCTGG 60.516 63.158 8.16 0.18 39.62 4.85
1907 2005 3.075641 GACGACTCCTCCCACCCC 61.076 72.222 0.00 0.00 0.00 4.95
2000 2098 7.246311 CACAAGGAATGAAATGCTAGTGTAAG 58.754 38.462 0.00 0.00 0.00 2.34
2203 2305 0.538118 ATTTACTTACCCGCTCGGCA 59.462 50.000 2.18 0.00 33.26 5.69
2258 2377 0.813210 TCAGCAATCGTGTGTGTGCA 60.813 50.000 0.00 0.00 39.50 4.57
2259 2378 0.518636 ATCAGCAATCGTGTGTGTGC 59.481 50.000 0.00 0.00 37.26 4.57
2260 2379 2.071540 AGATCAGCAATCGTGTGTGTG 58.928 47.619 0.00 0.00 39.55 3.82
2261 2380 2.462456 AGATCAGCAATCGTGTGTGT 57.538 45.000 0.00 0.00 39.55 3.72
2262 2381 3.434641 AGAAAGATCAGCAATCGTGTGTG 59.565 43.478 0.00 0.00 39.55 3.82
2263 2382 3.668447 AGAAAGATCAGCAATCGTGTGT 58.332 40.909 0.00 0.00 39.55 3.72
2302 2431 0.464013 GATCAGCAGCACATCAGCCT 60.464 55.000 0.00 0.00 34.23 4.58
2305 2434 2.478031 GCAAAGATCAGCAGCACATCAG 60.478 50.000 0.00 0.00 0.00 2.90
2465 2598 4.398988 TCCTTGCATAGCACATTTGGTAAG 59.601 41.667 0.00 0.00 39.14 2.34
2672 2809 5.239963 CCACCCACAAATTAAACTAGACGTT 59.760 40.000 0.00 0.00 37.47 3.99
2940 3090 3.891366 GGAGCTTCTTCTAGAGATGAGCT 59.109 47.826 16.81 16.81 36.47 4.09
2941 3091 3.636300 TGGAGCTTCTTCTAGAGATGAGC 59.364 47.826 9.95 9.95 33.49 4.26
3008 3177 5.359194 AAGCTACTACCATGCATTACACT 57.641 39.130 0.00 0.00 0.00 3.55
3069 3238 3.136123 CCATTGCGCACCCTCCTG 61.136 66.667 11.12 0.68 0.00 3.86
3143 3330 1.306997 TCCGGCCTCCATCTTCCTT 60.307 57.895 0.00 0.00 0.00 3.36
3206 3416 3.737559 ACTTTCTATGGGAATGCACCA 57.262 42.857 0.00 0.00 43.22 4.17
3269 3483 0.179029 AGAGAGAGAGAGGCTACGGC 60.179 60.000 0.00 0.00 37.82 5.68
3270 3484 1.140052 TGAGAGAGAGAGAGGCTACGG 59.860 57.143 0.00 0.00 0.00 4.02
3271 3485 2.613026 TGAGAGAGAGAGAGGCTACG 57.387 55.000 0.00 0.00 0.00 3.51
3272 3486 6.320164 TGTTAAATGAGAGAGAGAGAGGCTAC 59.680 42.308 0.00 0.00 0.00 3.58
3273 3487 6.320164 GTGTTAAATGAGAGAGAGAGAGGCTA 59.680 42.308 0.00 0.00 0.00 3.93
3274 3488 5.127031 GTGTTAAATGAGAGAGAGAGAGGCT 59.873 44.000 0.00 0.00 0.00 4.58
3275 3489 5.348164 GTGTTAAATGAGAGAGAGAGAGGC 58.652 45.833 0.00 0.00 0.00 4.70
3276 3490 5.420421 TGGTGTTAAATGAGAGAGAGAGAGG 59.580 44.000 0.00 0.00 0.00 3.69
3277 3491 6.522625 TGGTGTTAAATGAGAGAGAGAGAG 57.477 41.667 0.00 0.00 0.00 3.20
3278 3492 6.665248 TGATGGTGTTAAATGAGAGAGAGAGA 59.335 38.462 0.00 0.00 0.00 3.10
3279 3493 6.756074 GTGATGGTGTTAAATGAGAGAGAGAG 59.244 42.308 0.00 0.00 0.00 3.20
3280 3494 6.438741 AGTGATGGTGTTAAATGAGAGAGAGA 59.561 38.462 0.00 0.00 0.00 3.10
3281 3495 6.638610 AGTGATGGTGTTAAATGAGAGAGAG 58.361 40.000 0.00 0.00 0.00 3.20
3282 3496 6.611613 AGTGATGGTGTTAAATGAGAGAGA 57.388 37.500 0.00 0.00 0.00 3.10
3283 3497 7.551585 AGTAGTGATGGTGTTAAATGAGAGAG 58.448 38.462 0.00 0.00 0.00 3.20
3284 3498 7.178451 TGAGTAGTGATGGTGTTAAATGAGAGA 59.822 37.037 0.00 0.00 0.00 3.10
3290 3504 4.630069 GCGTGAGTAGTGATGGTGTTAAAT 59.370 41.667 0.00 0.00 0.00 1.40
3312 3526 0.030235 GGTTTTTGGACTGTGACCGC 59.970 55.000 0.00 0.00 0.00 5.68
3321 3535 7.201487 GGTGCGATATTTTATTGGTTTTTGGAC 60.201 37.037 0.00 0.00 0.00 4.02
3326 3540 5.344884 CCGGTGCGATATTTTATTGGTTTT 58.655 37.500 0.00 0.00 0.00 2.43
3327 3541 4.735283 GCCGGTGCGATATTTTATTGGTTT 60.735 41.667 1.90 0.00 0.00 3.27
3330 3544 2.552315 AGCCGGTGCGATATTTTATTGG 59.448 45.455 1.90 0.00 44.33 3.16
3345 3559 1.152963 ACACAGAAGCAAAGCCGGT 60.153 52.632 1.90 0.00 0.00 5.28
3347 3561 0.947244 AAGACACAGAAGCAAAGCCG 59.053 50.000 0.00 0.00 0.00 5.52
3403 3618 4.373914 CGTCAAGCACAAAATTAAACAGCG 60.374 41.667 0.00 0.00 0.00 5.18
3408 3623 7.993821 TTTGATCGTCAAGCACAAAATTAAA 57.006 28.000 0.00 0.00 37.70 1.52
3422 3637 5.237048 TGAACACATCTGATTTGATCGTCA 58.763 37.500 10.56 5.75 0.00 4.35
3431 3646 6.387465 CAAGCAGAATTGAACACATCTGATT 58.613 36.000 15.51 13.34 46.12 2.57
3432 3647 5.621555 GCAAGCAGAATTGAACACATCTGAT 60.622 40.000 15.51 9.37 41.38 2.90
3468 3683 1.039856 GCCTTTCACTTTCAAGCCCA 58.960 50.000 0.00 0.00 0.00 5.36
3528 3794 2.178521 CGGACCTCCTTCGTCGTG 59.821 66.667 0.00 0.00 0.00 4.35
3533 3799 1.614241 ATTGGACCGGACCTCCTTCG 61.614 60.000 23.51 0.00 0.00 3.79
3545 3811 0.036388 TCTCAGCCGTTCATTGGACC 60.036 55.000 0.00 0.00 0.00 4.46
3616 3882 5.491982 GGACTATATTTTGGAGCCGATGAT 58.508 41.667 0.00 0.00 0.00 2.45
3617 3883 4.262894 GGGACTATATTTTGGAGCCGATGA 60.263 45.833 0.00 0.00 0.00 2.92
3618 3884 4.003648 GGGACTATATTTTGGAGCCGATG 58.996 47.826 0.00 0.00 0.00 3.84
3619 3885 3.650942 TGGGACTATATTTTGGAGCCGAT 59.349 43.478 0.00 0.00 0.00 4.18
3620 3886 3.042682 TGGGACTATATTTTGGAGCCGA 58.957 45.455 0.00 0.00 0.00 5.54
3621 3887 3.485463 TGGGACTATATTTTGGAGCCG 57.515 47.619 0.00 0.00 0.00 5.52
3783 5091 0.243636 CCATGCGTCAACTTTTCCCC 59.756 55.000 0.00 0.00 0.00 4.81
3784 5092 0.243636 CCCATGCGTCAACTTTTCCC 59.756 55.000 0.00 0.00 0.00 3.97
3869 5180 0.856982 ACCACCACATCTTTTCCCCA 59.143 50.000 0.00 0.00 0.00 4.96
3871 5182 2.162681 CTGACCACCACATCTTTTCCC 58.837 52.381 0.00 0.00 0.00 3.97
3885 5196 1.376466 GCAGCTCTTTCCCTGACCA 59.624 57.895 0.00 0.00 0.00 4.02
3886 5197 1.743252 CGCAGCTCTTTCCCTGACC 60.743 63.158 0.00 0.00 0.00 4.02
3887 5198 3.882025 CGCAGCTCTTTCCCTGAC 58.118 61.111 0.00 0.00 0.00 3.51
3906 5217 2.897350 GCATTTCTCTCCGGCCCG 60.897 66.667 0.00 0.00 0.00 6.13
3907 5218 1.524849 GAGCATTTCTCTCCGGCCC 60.525 63.158 0.00 0.00 38.78 5.80
3908 5219 4.132999 GAGCATTTCTCTCCGGCC 57.867 61.111 0.00 0.00 38.78 6.13
3915 5226 3.105659 GCGGGCAGAGCATTTCTC 58.894 61.111 0.00 0.00 42.21 2.87


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

AutoCloner maintained by Alex Coulton.