Multiple sequence alignment - TraesCS4B01G274900

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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 TraesCS4B01G274900 chr4B 100.000 5722 0 0 1 5722 552834462 552828741 0.000000e+00 10567.0
1 TraesCS4B01G274900 chr4A 92.746 5776 289 50 1 5722 24222972 24228671 0.000000e+00 8226.0
2 TraesCS4B01G274900 chr4D 93.737 5461 216 38 325 5722 443514653 443509256 0.000000e+00 8074.0
3 TraesCS4B01G274900 chr4D 91.908 173 14 0 2 174 443515743 443515571 5.730000e-60 243.0
4 TraesCS4B01G274900 chr5B 72.800 250 59 8 2532 2778 379335819 379335576 6.150000e-10 76.8
5 TraesCS4B01G274900 chr5D 76.190 147 30 4 2633 2778 326735831 326735689 7.950000e-09 73.1
6 TraesCS4B01G274900 chr6B 89.362 47 4 1 2644 2689 184363823 184363777 2.230000e-04 58.4


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 TraesCS4B01G274900 chr4B 552828741 552834462 5721 True 10567.0 10567 100.0000 1 5722 1 chr4B.!!$R1 5721
1 TraesCS4B01G274900 chr4A 24222972 24228671 5699 False 8226.0 8226 92.7460 1 5722 1 chr4A.!!$F1 5721
2 TraesCS4B01G274900 chr4D 443509256 443515743 6487 True 4158.5 8074 92.8225 2 5722 2 chr4D.!!$R1 5720

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
983 1771 0.037303 CTCTGCCACTCCACCATTGT 59.963 55.000 0.00 0.00 0.00 2.71 F
1797 2602 2.222886 CACCACATTGTCGGGTAACAA 58.777 47.619 0.00 0.00 42.92 2.83 F
1904 2709 0.405585 ACTGACAAGGAACCCCATGG 59.594 55.000 4.14 4.14 35.55 3.66 F
3108 3916 0.868406 CTTCGTGGTGAGTTCTTGGC 59.132 55.000 0.00 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 2613 1.006281 TGACTACTATGTCCACGGGGT 59.994 52.381 2.12 0.00 36.21 4.95 R
3127 3935 1.022982 ACAGTCCACAGATGCATGCG 61.023 55.000 14.09 0.35 0.00 4.73 R
3646 4471 1.215117 GCAGTCAGAGAAGAGCGCT 59.785 57.895 11.27 11.27 0.00 5.92 R
5022 5872 0.190069 TAGTCACACTCCCCACTGGT 59.810 55.000 0.00 0.00 34.77 4.00 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
29 30 4.734398 AAGAACAAGTGGTTGAATGCAA 57.266 36.364 0.00 0.00 40.63 4.08
49 50 1.019805 GTAAAGTGGAGCGTGAGGGC 61.020 60.000 0.00 0.00 0.00 5.19
178 179 1.298859 GCACGCAGTCCTTAAGTGGG 61.299 60.000 0.97 4.57 41.61 4.61
200 201 4.537015 GAACATGTGCAGTAAACTCCAAC 58.463 43.478 0.00 0.00 0.00 3.77
233 234 6.768078 ACACTATGTTTATCGTTTTTAGGCG 58.232 36.000 0.00 0.00 0.00 5.52
236 237 8.120465 CACTATGTTTATCGTTTTTAGGCGATT 58.880 33.333 4.80 0.00 44.17 3.34
237 238 8.671028 ACTATGTTTATCGTTTTTAGGCGATTT 58.329 29.630 4.80 0.00 44.17 2.17
383 1151 6.216569 TCACAGACTCAAAGTACTTTGCTAG 58.783 40.000 33.93 28.98 46.92 3.42
384 1152 5.986135 CACAGACTCAAAGTACTTTGCTAGT 59.014 40.000 33.93 31.28 46.92 2.57
385 1153 5.986135 ACAGACTCAAAGTACTTTGCTAGTG 59.014 40.000 31.71 27.70 46.92 2.74
386 1154 6.183360 ACAGACTCAAAGTACTTTGCTAGTGA 60.183 38.462 31.71 20.23 46.92 3.41
387 1155 6.870965 CAGACTCAAAGTACTTTGCTAGTGAT 59.129 38.462 31.71 22.25 46.92 3.06
388 1156 6.870965 AGACTCAAAGTACTTTGCTAGTGATG 59.129 38.462 31.71 20.22 46.92 3.07
390 1158 5.865085 TCAAAGTACTTTGCTAGTGATGGT 58.135 37.500 33.93 2.90 46.92 3.55
391 1159 6.999950 TCAAAGTACTTTGCTAGTGATGGTA 58.000 36.000 33.93 15.91 46.92 3.25
399 1178 1.342819 GCTAGTGATGGTAGGGCAGAG 59.657 57.143 0.00 0.00 0.00 3.35
434 1213 9.507329 TTGTCATTAAACTAGATCTTGAAAGCT 57.493 29.630 11.29 0.00 0.00 3.74
458 1237 7.703621 GCTTAATGATTTGAGCACACATGTTAT 59.296 33.333 0.00 0.00 42.42 1.89
473 1252 7.765819 CACACATGTTATCTTCATAACTCCAGA 59.234 37.037 0.00 0.00 43.46 3.86
741 1523 3.085952 ACTCTCTTCAGCAGCTAGACT 57.914 47.619 0.00 0.00 0.00 3.24
785 1567 1.040646 TCATCTCACCCGCCATCTAC 58.959 55.000 0.00 0.00 0.00 2.59
806 1588 7.156000 TCTACGGACTAGATCACTAGATGAAG 58.844 42.308 10.60 0.00 46.34 3.02
816 1598 3.198635 TCACTAGATGAAGAAGGCAAGGG 59.801 47.826 0.00 0.00 33.02 3.95
875 1657 1.156736 GCTTCGCAAGGCTTGTCTTA 58.843 50.000 26.71 10.42 38.47 2.10
909 1691 3.254024 ATGGCACGGACGCTTTCCT 62.254 57.895 0.00 0.00 43.25 3.36
911 1693 2.048127 GCACGGACGCTTTCCTCT 60.048 61.111 0.21 0.00 43.25 3.69
930 1712 4.213694 CCTCTGCAGAATCATATCTTGTGC 59.786 45.833 18.85 8.85 41.73 4.57
945 1727 2.435372 TGTGCCCTTTTGTCTGTCTT 57.565 45.000 0.00 0.00 0.00 3.01
948 1730 2.687935 GTGCCCTTTTGTCTGTCTTTGA 59.312 45.455 0.00 0.00 0.00 2.69
980 1768 0.837691 TGTCTCTGCCACTCCACCAT 60.838 55.000 0.00 0.00 0.00 3.55
983 1771 0.037303 CTCTGCCACTCCACCATTGT 59.963 55.000 0.00 0.00 0.00 2.71
1186 1987 3.052455 TCGCAGGTTCACATTGTGTAT 57.948 42.857 16.06 0.00 34.79 2.29
1192 1993 3.831911 AGGTTCACATTGTGTATTTGGGG 59.168 43.478 16.06 0.00 34.79 4.96
1304 2107 6.437477 ACTTTCTGAGCTAAAATTAAAGGGGG 59.563 38.462 0.00 0.00 0.00 5.40
1310 2113 6.323739 TGAGCTAAAATTAAAGGGGGCAATAG 59.676 38.462 0.00 0.00 0.00 1.73
1325 2128 5.221322 GGGGCAATAGAAGACCATTGAATTC 60.221 44.000 0.00 0.00 34.69 2.17
1328 2131 6.097412 GGCAATAGAAGACCATTGAATTCCTT 59.903 38.462 2.27 0.00 34.69 3.36
1382 2185 2.880268 GCACAGCACCATCTAATGCATA 59.120 45.455 0.00 0.00 44.59 3.14
1390 2193 8.393366 CAGCACCATCTAATGCATATATAACAC 58.607 37.037 0.00 0.00 44.59 3.32
1504 2307 5.979993 TCGTTTGTACTCCTTATGCCATAA 58.020 37.500 0.00 0.00 0.00 1.90
1586 2390 6.647334 TGAAGCAATTCAACCATTTGTCTA 57.353 33.333 0.00 0.00 34.02 2.59
1588 2392 8.347004 TGAAGCAATTCAACCATTTGTCTATA 57.653 30.769 0.00 0.00 34.02 1.31
1617 2421 5.803020 AAAACCACGCATCTTAGAGAATC 57.197 39.130 0.00 0.00 0.00 2.52
1664 2469 5.757808 GCAAGAAAAATGTGGCTAAAAGGAA 59.242 36.000 0.00 0.00 0.00 3.36
1797 2602 2.222886 CACCACATTGTCGGGTAACAA 58.777 47.619 0.00 0.00 42.92 2.83
1801 2606 4.456566 ACCACATTGTCGGGTAACAATTAC 59.543 41.667 0.00 0.00 45.29 1.89
1802 2607 4.698304 CCACATTGTCGGGTAACAATTACT 59.302 41.667 0.00 0.00 45.29 2.24
1804 2609 4.939439 ACATTGTCGGGTAACAATTACTCC 59.061 41.667 0.00 0.00 45.29 3.85
1805 2610 4.895668 TTGTCGGGTAACAATTACTCCT 57.104 40.909 0.00 0.00 34.31 3.69
1807 2612 6.549433 TTGTCGGGTAACAATTACTCCTAT 57.451 37.500 0.00 0.00 34.31 2.57
1808 2613 7.658525 TTGTCGGGTAACAATTACTCCTATA 57.341 36.000 0.00 0.00 34.31 1.31
1809 2614 7.042797 TGTCGGGTAACAATTACTCCTATAC 57.957 40.000 0.00 0.00 32.90 1.47
1811 2616 5.539955 TCGGGTAACAATTACTCCTATACCC 59.460 44.000 7.83 7.83 44.85 3.69
1812 2617 5.279657 CGGGTAACAATTACTCCTATACCCC 60.280 48.000 11.43 0.00 45.29 4.95
1813 2618 5.279657 GGGTAACAATTACTCCTATACCCCG 60.280 48.000 6.81 0.00 43.32 5.73
1814 2619 5.305386 GGTAACAATTACTCCTATACCCCGT 59.695 44.000 0.00 0.00 36.39 5.28
1816 2621 3.644738 ACAATTACTCCTATACCCCGTGG 59.355 47.826 0.00 0.00 37.80 4.94
1817 2622 3.899360 CAATTACTCCTATACCCCGTGGA 59.101 47.826 0.00 0.00 34.81 4.02
1819 2624 0.632835 ACTCCTATACCCCGTGGACA 59.367 55.000 0.00 0.00 34.81 4.02
1821 2626 2.448194 ACTCCTATACCCCGTGGACATA 59.552 50.000 0.00 0.00 34.81 2.29
1822 2627 3.090037 CTCCTATACCCCGTGGACATAG 58.910 54.545 0.00 0.00 33.57 2.23
1824 2629 3.657239 TCCTATACCCCGTGGACATAGTA 59.343 47.826 0.00 0.00 32.71 1.82
1825 2630 4.015084 CCTATACCCCGTGGACATAGTAG 58.985 52.174 0.00 0.00 32.71 2.57
1826 2631 3.607490 ATACCCCGTGGACATAGTAGT 57.393 47.619 0.00 0.00 34.81 2.73
1828 2633 1.006281 ACCCCGTGGACATAGTAGTCA 59.994 52.381 0.00 0.00 40.29 3.41
1868 2673 8.792830 ATCTGTACATACTTAGTTTTGTGCAT 57.207 30.769 15.04 4.12 34.86 3.96
1873 2678 9.672086 GTACATACTTAGTTTTGTGCATTTGAA 57.328 29.630 9.82 0.00 0.00 2.69
1904 2709 0.405585 ACTGACAAGGAACCCCATGG 59.594 55.000 4.14 4.14 35.55 3.66
2143 2951 1.532868 CACTGTCCTGTACTTGCTTGC 59.467 52.381 0.00 0.00 0.00 4.01
2232 3040 4.684134 ACCCACAGGCATGGCACC 62.684 66.667 22.64 0.17 38.55 5.01
2300 3108 6.474140 AATCATTTCTTGAATGCAGGCATA 57.526 33.333 7.26 0.00 43.93 3.14
2302 3110 4.098349 TCATTTCTTGAATGCAGGCATACC 59.902 41.667 7.26 3.67 43.93 2.73
2339 3147 5.385509 ACTTAACAATTTTGTAGCGGCAT 57.614 34.783 1.45 0.00 41.31 4.40
2385 3193 1.202770 GGTTACAGTGCTGTGGTCCTT 60.203 52.381 14.44 0.00 44.63 3.36
2570 3378 4.253257 GCGCGCTACTACCTCGCT 62.253 66.667 26.67 0.00 45.87 4.93
2591 3399 2.282958 TTCGAGGCTGAGACCGGT 60.283 61.111 6.92 6.92 33.69 5.28
2592 3400 2.549611 CTTCGAGGCTGAGACCGGTG 62.550 65.000 14.63 0.00 33.69 4.94
2966 3774 1.658673 GGTGTCGACGGTGTTCTCT 59.341 57.895 11.62 0.00 0.00 3.10
3108 3916 0.868406 CTTCGTGGTGAGTTCTTGGC 59.132 55.000 0.00 0.00 0.00 4.52
3127 3935 1.316651 CCCTACTAGTGGCCGACTAC 58.683 60.000 5.39 0.00 35.96 2.73
3294 4105 5.344743 TGGGTAATCTCTCTCACACAATC 57.655 43.478 0.00 0.00 0.00 2.67
3314 4125 5.782677 ATCCCTACCGAGTATCTATCTGT 57.217 43.478 0.00 0.00 0.00 3.41
3416 4227 1.374758 CGTCCTGTGCTTCTCCACC 60.375 63.158 0.00 0.00 34.85 4.61
3494 4305 1.934956 CGTGATCTTCGCCGACTCG 60.935 63.158 0.00 0.00 0.00 4.18
3588 4399 1.476891 TCAACTACATCCAGAGCCGTC 59.523 52.381 0.00 0.00 0.00 4.79
3602 4413 1.074889 AGCCGTCCAAGGTAACCAATT 59.925 47.619 0.00 0.00 37.17 2.32
3646 4471 1.801512 CACGCGCGTCTGAGATCAA 60.802 57.895 35.61 0.00 0.00 2.57
3662 4487 1.252175 TCAAGCGCTCTTCTCTGACT 58.748 50.000 12.06 0.00 0.00 3.41
3682 4507 1.815003 CGCATCCATCGTCTGCCAA 60.815 57.895 0.00 0.00 32.24 4.52
3683 4508 1.368345 CGCATCCATCGTCTGCCAAA 61.368 55.000 0.00 0.00 32.24 3.28
3812 4637 6.433847 TCTCCAAACATTCTCAAGGTAGAA 57.566 37.500 0.00 0.00 39.71 2.10
3896 4721 1.211969 GAACTCGCAGCCTGACGTA 59.788 57.895 0.00 0.00 0.00 3.57
4283 5108 3.141488 CTCGGCTACACGGAGGCT 61.141 66.667 0.91 0.00 40.97 4.58
4334 5159 4.731612 CTCGACACCAGCTGCGCT 62.732 66.667 8.66 0.00 40.77 5.92
4370 5195 2.348888 CGCCGACCTCAACTACCCT 61.349 63.158 0.00 0.00 0.00 4.34
4726 5551 5.066246 GTGATACTACTGAGTACTGACCCAC 59.934 48.000 0.00 0.00 41.01 4.61
4727 5552 3.520691 ACTACTGAGTACTGACCCACA 57.479 47.619 0.00 0.00 32.65 4.17
4728 5553 3.840991 ACTACTGAGTACTGACCCACAA 58.159 45.455 0.00 0.00 32.65 3.33
4775 5600 4.555709 AACTTGGCGGTGCACGGA 62.556 61.111 26.71 5.15 44.51 4.69
4790 5615 1.227380 CGGATTCCGGGCTTCAGAG 60.227 63.158 17.53 0.00 44.15 3.35
4791 5616 1.908483 GGATTCCGGGCTTCAGAGT 59.092 57.895 0.00 0.00 0.00 3.24
4792 5617 0.253327 GGATTCCGGGCTTCAGAGTT 59.747 55.000 0.00 0.00 0.00 3.01
4793 5618 1.657822 GATTCCGGGCTTCAGAGTTC 58.342 55.000 0.00 0.00 0.00 3.01
4794 5619 0.984230 ATTCCGGGCTTCAGAGTTCA 59.016 50.000 0.00 0.00 0.00 3.18
4796 5621 0.541998 TCCGGGCTTCAGAGTTCAGA 60.542 55.000 0.00 0.00 0.00 3.27
4797 5622 0.390472 CCGGGCTTCAGAGTTCAGAC 60.390 60.000 0.00 0.00 0.00 3.51
4798 5623 0.390472 CGGGCTTCAGAGTTCAGACC 60.390 60.000 0.00 0.00 31.44 3.85
4799 5624 0.687354 GGGCTTCAGAGTTCAGACCA 59.313 55.000 0.00 0.00 35.50 4.02
4800 5625 1.338579 GGGCTTCAGAGTTCAGACCAG 60.339 57.143 0.00 0.00 35.50 4.00
4801 5626 1.338579 GGCTTCAGAGTTCAGACCAGG 60.339 57.143 0.00 0.00 0.00 4.45
4802 5627 1.620819 GCTTCAGAGTTCAGACCAGGA 59.379 52.381 0.00 0.00 0.00 3.86
4803 5628 2.235898 GCTTCAGAGTTCAGACCAGGAT 59.764 50.000 0.00 0.00 0.00 3.24
4804 5629 3.307339 GCTTCAGAGTTCAGACCAGGATT 60.307 47.826 0.00 0.00 0.00 3.01
4805 5630 4.805609 GCTTCAGAGTTCAGACCAGGATTT 60.806 45.833 0.00 0.00 0.00 2.17
4806 5631 4.543590 TCAGAGTTCAGACCAGGATTTC 57.456 45.455 0.00 0.00 0.00 2.17
4807 5632 3.261897 TCAGAGTTCAGACCAGGATTTCC 59.738 47.826 0.00 0.00 0.00 3.13
4977 5827 5.381174 TCTTGAACATTTGAGATGCCTTG 57.619 39.130 0.00 0.00 0.00 3.61
4978 5828 4.828939 TCTTGAACATTTGAGATGCCTTGT 59.171 37.500 0.00 0.00 0.00 3.16
4979 5829 4.771590 TGAACATTTGAGATGCCTTGTC 57.228 40.909 0.00 0.00 0.00 3.18
4980 5830 3.507233 TGAACATTTGAGATGCCTTGTCC 59.493 43.478 0.00 0.00 0.00 4.02
4981 5831 3.446442 ACATTTGAGATGCCTTGTCCT 57.554 42.857 0.00 0.00 0.00 3.85
4982 5832 3.087031 ACATTTGAGATGCCTTGTCCTG 58.913 45.455 0.00 0.00 0.00 3.86
4983 5833 3.245016 ACATTTGAGATGCCTTGTCCTGA 60.245 43.478 0.00 0.00 0.00 3.86
4999 5849 2.267324 GAGTCCTGACCAGCTGGC 59.733 66.667 33.06 24.14 39.32 4.85
5021 5871 0.673022 GTGCTGAGCAGTGGAAGAGG 60.673 60.000 7.71 0.00 40.08 3.69
5022 5872 0.833409 TGCTGAGCAGTGGAAGAGGA 60.833 55.000 1.40 0.00 33.32 3.71
5075 5925 2.233186 TGCAGTCATCTCTTCAGACCAG 59.767 50.000 0.00 0.00 32.82 4.00
5078 5928 2.233431 AGTCATCTCTTCAGACCAGTGC 59.767 50.000 0.00 0.00 32.82 4.40
5113 5963 6.201044 CGGGAGTACAATACTTGAAAGCTATG 59.799 42.308 0.00 0.00 39.59 2.23
5139 5989 8.430801 AATAGCTCATGTGAAGTGAAATCTAC 57.569 34.615 0.00 0.00 0.00 2.59
5254 6104 2.998670 CTCCACTCACAAGTACATGCAG 59.001 50.000 0.00 0.00 33.25 4.41
5332 6182 7.073208 TCTAGTCCATATACAACCATTGGAGA 58.927 38.462 10.37 0.00 37.16 3.71
5383 6233 6.166982 CAAATATAGGAGGGAAGATCGTTCC 58.833 44.000 12.85 12.85 37.86 3.62
5493 6344 4.036352 CGAAGATTTCTAGTAGCACCGTC 58.964 47.826 0.00 0.00 0.00 4.79
5670 6528 7.660208 CCACATATATAGTTTAAGCGGGTCTTT 59.340 37.037 0.00 0.00 36.25 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.608640 CCCTCACGCTCCACTTTACT 59.391 55.000 0.00 0.00 0.00 2.24
109 110 6.378280 TGATAATACTGAGCACTCACTCTTCA 59.622 38.462 0.00 0.00 37.58 3.02
178 179 4.036262 TGTTGGAGTTTACTGCACATGTTC 59.964 41.667 3.42 0.00 44.04 3.18
254 299 5.221126 CCTGCAACCTTCTATAGCAAAATCC 60.221 44.000 0.00 0.00 34.45 3.01
292 337 1.160137 CCGCTGAGGAAAAACCAGAG 58.840 55.000 0.00 0.00 45.00 3.35
383 1151 0.983378 ACCCTCTGCCCTACCATCAC 60.983 60.000 0.00 0.00 0.00 3.06
384 1152 0.253160 AACCCTCTGCCCTACCATCA 60.253 55.000 0.00 0.00 0.00 3.07
385 1153 0.919710 AAACCCTCTGCCCTACCATC 59.080 55.000 0.00 0.00 0.00 3.51
386 1154 0.625849 CAAACCCTCTGCCCTACCAT 59.374 55.000 0.00 0.00 0.00 3.55
387 1155 0.770557 ACAAACCCTCTGCCCTACCA 60.771 55.000 0.00 0.00 0.00 3.25
388 1156 0.035343 GACAAACCCTCTGCCCTACC 60.035 60.000 0.00 0.00 0.00 3.18
390 1158 1.351017 CAAGACAAACCCTCTGCCCTA 59.649 52.381 0.00 0.00 0.00 3.53
391 1159 0.111253 CAAGACAAACCCTCTGCCCT 59.889 55.000 0.00 0.00 0.00 5.19
399 1178 7.739498 TCTAGTTTAATGACAAGACAAACCC 57.261 36.000 0.00 0.00 31.06 4.11
434 1213 8.959548 AGATAACATGTGTGCTCAAATCATTAA 58.040 29.630 0.00 0.00 0.00 1.40
458 1237 4.563580 GGCAAGTGTCTGGAGTTATGAAGA 60.564 45.833 0.00 0.00 0.00 2.87
473 1252 4.215109 AGTTCAACCAAATAGGCAAGTGT 58.785 39.130 0.00 0.00 43.14 3.55
643 1422 7.968956 CGTGTGTTAATCATCTGTTCTAGTAGT 59.031 37.037 0.00 0.00 0.00 2.73
644 1423 8.182227 TCGTGTGTTAATCATCTGTTCTAGTAG 58.818 37.037 0.00 0.00 0.00 2.57
645 1424 8.047413 TCGTGTGTTAATCATCTGTTCTAGTA 57.953 34.615 0.00 0.00 0.00 1.82
741 1523 7.870509 TTAAGCCTATCGAGTTAAGTACAGA 57.129 36.000 0.00 0.00 0.00 3.41
785 1567 6.072728 CCTTCTTCATCTAGTGATCTAGTCCG 60.073 46.154 0.00 0.00 42.88 4.79
806 1588 1.406903 CATCATTCCCCCTTGCCTTC 58.593 55.000 0.00 0.00 0.00 3.46
816 1598 0.468585 TCCATGGCTGCATCATTCCC 60.469 55.000 6.96 0.00 0.00 3.97
875 1657 0.396139 CCATGCCATAGGGTGCTTGT 60.396 55.000 0.00 0.00 36.17 3.16
909 1691 4.132336 GGCACAAGATATGATTCTGCAGA 58.868 43.478 13.74 13.74 30.95 4.26
911 1693 3.117776 AGGGCACAAGATATGATTCTGCA 60.118 43.478 0.00 0.00 30.95 4.41
930 1712 4.823989 AGACATCAAAGACAGACAAAAGGG 59.176 41.667 0.00 0.00 0.00 3.95
945 1727 9.479549 TGGCAGAGACATATATATAGACATCAA 57.520 33.333 0.00 0.00 0.00 2.57
948 1730 9.130661 GAGTGGCAGAGACATATATATAGACAT 57.869 37.037 0.00 0.00 0.00 3.06
1106 1906 6.931281 TCTGATCTGACAAACAGGTAAAAGAG 59.069 38.462 0.00 0.00 45.76 2.85
1186 1987 1.668101 GACCGTTGTTGTGCCCCAAA 61.668 55.000 0.00 0.00 34.07 3.28
1192 1993 0.582005 GAGTCAGACCGTTGTTGTGC 59.418 55.000 0.00 0.00 0.00 4.57
1284 2087 4.023291 TGCCCCCTTTAATTTTAGCTCAG 58.977 43.478 0.00 0.00 0.00 3.35
1304 2107 6.705863 AGGAATTCAATGGTCTTCTATTGC 57.294 37.500 7.93 0.00 40.66 3.56
1310 2113 6.581171 ACTTCAAGGAATTCAATGGTCTTC 57.419 37.500 7.93 0.00 0.00 2.87
1360 2163 0.383231 GCATTAGATGGTGCTGTGCC 59.617 55.000 0.00 0.00 38.30 5.01
1422 2225 9.787435 AACTTTATGTTGTTTACCTGATAGTCA 57.213 29.630 0.00 0.00 37.52 3.41
1539 2342 6.764308 AGTTAAGCATGCAATACAGATTGT 57.236 33.333 21.98 0.00 43.82 2.71
1586 2390 9.391006 TCTAAGATGCGTGGTTTTATCTTTTAT 57.609 29.630 0.00 0.00 39.71 1.40
1588 2392 7.606456 TCTCTAAGATGCGTGGTTTTATCTTTT 59.394 33.333 0.00 0.00 39.71 2.27
1601 2405 3.701542 TGTCCAGATTCTCTAAGATGCGT 59.298 43.478 0.00 0.00 0.00 5.24
1617 2421 5.224888 CCAAATGAGAACAAACATGTCCAG 58.775 41.667 0.00 0.00 0.00 3.86
1622 2426 5.291178 TCTTGCCAAATGAGAACAAACATG 58.709 37.500 0.00 0.00 0.00 3.21
1664 2469 9.740239 GCAATATTGTGATCATTCATGTAAGTT 57.260 29.630 16.61 0.00 33.56 2.66
1678 2483 1.133823 TCCGGCCTGCAATATTGTGAT 60.134 47.619 16.61 0.00 0.00 3.06
1738 2543 0.883833 CTGCCGCAAAACCAGAGAAT 59.116 50.000 0.00 0.00 0.00 2.40
1797 2602 3.117016 TGTCCACGGGGTATAGGAGTAAT 60.117 47.826 2.12 0.00 34.93 1.89
1801 2606 2.011122 ATGTCCACGGGGTATAGGAG 57.989 55.000 2.12 0.00 34.93 3.69
1802 2607 2.448194 ACTATGTCCACGGGGTATAGGA 59.552 50.000 24.50 0.00 37.05 2.94
1804 2609 4.660168 ACTACTATGTCCACGGGGTATAG 58.340 47.826 21.37 21.37 37.88 1.31
1805 2610 4.104579 TGACTACTATGTCCACGGGGTATA 59.895 45.833 2.12 3.30 36.21 1.47
1807 2612 2.241941 TGACTACTATGTCCACGGGGTA 59.758 50.000 2.12 0.00 36.21 3.69
1808 2613 1.006281 TGACTACTATGTCCACGGGGT 59.994 52.381 2.12 0.00 36.21 4.95
1809 2614 1.681793 CTGACTACTATGTCCACGGGG 59.318 57.143 0.00 0.00 36.21 5.73
1811 2616 4.713824 TTTCTGACTACTATGTCCACGG 57.286 45.455 0.00 0.00 36.21 4.94
1812 2617 5.466819 TGTTTTCTGACTACTATGTCCACG 58.533 41.667 0.00 0.00 36.21 4.94
1813 2618 7.491696 GGTATGTTTTCTGACTACTATGTCCAC 59.508 40.741 0.00 0.00 36.21 4.02
1814 2619 7.399191 AGGTATGTTTTCTGACTACTATGTCCA 59.601 37.037 0.00 0.00 36.21 4.02
1855 2660 7.658982 TGGCAATATTCAAATGCACAAAACTAA 59.341 29.630 0.00 0.00 41.80 2.24
1904 2709 9.606631 ACCTCTTCTGTTTCTGATTATAATGAC 57.393 33.333 1.78 0.00 0.00 3.06
1913 2718 7.125507 ACTGATATGACCTCTTCTGTTTCTGAT 59.874 37.037 0.00 0.00 0.00 2.90
2143 2951 1.155042 GTGTGAAGCCAGAGAAGCTG 58.845 55.000 0.00 0.00 40.49 4.24
2232 3040 4.408993 TGTTCATGTCATTTCTCTTGCG 57.591 40.909 0.00 0.00 0.00 4.85
2300 3108 3.446442 AAGTTCAGATCTTGGCATGGT 57.554 42.857 0.00 0.00 0.00 3.55
2302 3110 5.885230 TGTTAAGTTCAGATCTTGGCATG 57.115 39.130 0.00 0.00 0.00 4.06
2339 3147 4.558226 ACAGGAATGAGTATGAGTGCAA 57.442 40.909 0.00 0.00 0.00 4.08
2385 3193 2.807967 GCAGACACACACTGAAATGCTA 59.192 45.455 0.00 0.00 37.54 3.49
2570 3378 2.650116 GGTCTCAGCCTCGAAGCCA 61.650 63.158 1.47 0.00 0.00 4.75
3108 3916 1.316651 GTAGTCGGCCACTAGTAGGG 58.683 60.000 13.35 0.00 38.35 3.53
3127 3935 1.022982 ACAGTCCACAGATGCATGCG 61.023 55.000 14.09 0.35 0.00 4.73
3294 4105 6.651975 AAAACAGATAGATACTCGGTAGGG 57.348 41.667 0.00 0.00 0.00 3.53
3314 4125 2.356382 ACGCAAATCGGTCAGTCAAAAA 59.644 40.909 0.00 0.00 43.86 1.94
3416 4227 2.192979 CCGGACACCATCCCCATG 59.807 66.667 0.00 0.00 46.04 3.66
3588 4399 4.412843 AGGTGGTTAATTGGTTACCTTGG 58.587 43.478 2.07 0.00 35.09 3.61
3602 4413 2.699768 CGACGGCGGTAGGTGGTTA 61.700 63.158 13.24 0.00 0.00 2.85
3633 4458 1.478622 GAGCGCTTGATCTCAGACGC 61.479 60.000 13.26 16.43 45.82 5.19
3636 4461 2.098614 AGAAGAGCGCTTGATCTCAGA 58.901 47.619 13.26 0.00 37.37 3.27
3646 4471 1.215117 GCAGTCAGAGAAGAGCGCT 59.785 57.895 11.27 11.27 0.00 5.92
3662 4487 2.891936 GCAGACGATGGATGCGCA 60.892 61.111 14.96 14.96 0.00 6.09
3812 4637 2.613977 CCAAGCTCAGGTGATCGTTTCT 60.614 50.000 0.00 0.00 0.00 2.52
3854 4679 3.553511 GCAACAGATCGGTTCAGTCTATG 59.446 47.826 8.37 0.00 0.00 2.23
3857 4682 1.620819 AGCAACAGATCGGTTCAGTCT 59.379 47.619 8.37 1.66 0.00 3.24
3989 4814 1.301637 CATGGACGTGCCTGTGTCA 60.302 57.895 4.04 0.00 36.83 3.58
4074 4899 3.692406 GAGGGCGGACTTGACGGT 61.692 66.667 0.00 0.00 0.00 4.83
4076 4901 1.811266 CATGAGGGCGGACTTGACG 60.811 63.158 0.00 0.00 0.00 4.35
4160 4985 4.052229 CCGGTGTCGAAGGCGTCT 62.052 66.667 0.00 0.00 39.00 4.18
4283 5108 3.321648 ACCATCTGCCGCACCTGA 61.322 61.111 0.00 0.00 0.00 3.86
4349 5174 1.582968 GTAGTTGAGGTCGGCGTCA 59.417 57.895 8.58 8.58 37.68 4.35
4484 5309 3.986006 GGCCACACCTCGACGTGA 61.986 66.667 19.44 0.00 37.20 4.35
4685 5510 2.819595 CGGTGCTGATTCGTGGGG 60.820 66.667 0.00 0.00 0.00 4.96
4726 5551 3.924686 CGTAACTAGGTAGCTTGTGGTTG 59.075 47.826 9.75 0.00 0.00 3.77
4727 5552 3.056322 CCGTAACTAGGTAGCTTGTGGTT 60.056 47.826 9.75 8.20 0.00 3.67
4728 5553 2.494870 CCGTAACTAGGTAGCTTGTGGT 59.505 50.000 9.75 0.00 0.00 4.16
4775 5600 0.984230 TGAACTCTGAAGCCCGGAAT 59.016 50.000 0.73 0.00 0.00 3.01
4790 5615 1.003233 ACGGGAAATCCTGGTCTGAAC 59.997 52.381 12.76 0.00 46.75 3.18
4791 5616 1.003118 CACGGGAAATCCTGGTCTGAA 59.997 52.381 12.76 0.00 46.75 3.02
4792 5617 0.613260 CACGGGAAATCCTGGTCTGA 59.387 55.000 12.76 0.00 46.75 3.27
4793 5618 0.324943 ACACGGGAAATCCTGGTCTG 59.675 55.000 12.76 4.79 46.75 3.51
4794 5619 0.324943 CACACGGGAAATCCTGGTCT 59.675 55.000 12.76 0.00 46.75 3.85
4796 5621 1.131303 TCCACACGGGAAATCCTGGT 61.131 55.000 12.76 5.15 44.80 4.00
4797 5622 1.682849 TCCACACGGGAAATCCTGG 59.317 57.895 12.76 6.22 44.80 4.45
4806 5631 1.195900 CGTTACACAAATCCACACGGG 59.804 52.381 0.00 0.00 38.37 5.28
4807 5632 1.868498 ACGTTACACAAATCCACACGG 59.132 47.619 0.00 0.00 0.00 4.94
4977 5827 0.902516 AGCTGGTCAGGACTCAGGAC 60.903 60.000 15.12 0.00 33.29 3.85
4978 5828 0.902048 CAGCTGGTCAGGACTCAGGA 60.902 60.000 5.57 0.00 33.29 3.86
4979 5829 1.595882 CAGCTGGTCAGGACTCAGG 59.404 63.158 5.57 2.19 33.29 3.86
4980 5830 1.595882 CCAGCTGGTCAGGACTCAG 59.404 63.158 25.53 11.29 34.72 3.35
4981 5831 2.587247 GCCAGCTGGTCAGGACTCA 61.587 63.158 32.81 0.00 37.57 3.41
4982 5832 2.267324 GCCAGCTGGTCAGGACTC 59.733 66.667 32.81 10.76 37.57 3.36
4983 5833 3.325753 GGCCAGCTGGTCAGGACT 61.326 66.667 32.45 0.00 40.23 3.85
4999 5849 3.535629 TTCCACTGCTCAGCACCGG 62.536 63.158 0.00 0.00 33.79 5.28
5002 5852 0.673022 CCTCTTCCACTGCTCAGCAC 60.673 60.000 0.00 0.00 33.79 4.40
5008 5858 0.472734 ACTGGTCCTCTTCCACTGCT 60.473 55.000 0.00 0.00 0.00 4.24
5021 5871 1.122019 AGTCACACTCCCCACTGGTC 61.122 60.000 0.00 0.00 34.77 4.02
5022 5872 0.190069 TAGTCACACTCCCCACTGGT 59.810 55.000 0.00 0.00 34.77 4.00
5113 5963 7.551035 AGATTTCACTTCACATGAGCTATTC 57.449 36.000 0.00 0.00 0.00 1.75
5139 5989 5.186797 TGGAGGTATAACCAAAAGCCATTTG 59.813 40.000 5.76 5.76 46.54 2.32
5202 6052 1.270094 CGGCATATAGCTGGAACGGAA 60.270 52.381 0.00 0.00 46.20 4.30
5332 6182 3.820467 TCTTTCATCAAGATGTGCGGTTT 59.180 39.130 9.66 0.00 36.51 3.27
5383 6233 5.123227 AGGACGTTGGGACACATTTATATG 58.877 41.667 0.00 0.00 39.29 1.78
5434 6285 4.079970 TCTCTGTGTGATTTACCTCTCGT 58.920 43.478 0.00 0.00 0.00 4.18
5435 6286 4.703645 TCTCTGTGTGATTTACCTCTCG 57.296 45.455 0.00 0.00 0.00 4.04
5493 6344 1.269621 ACGAGAAACACCAGGAGAACG 60.270 52.381 0.00 0.00 0.00 3.95
5554 6405 1.840650 CGCCTCCTCCATCCTCCAT 60.841 63.158 0.00 0.00 0.00 3.41
5670 6528 7.999450 AGGGTGACGGTTAAACATTATAAAA 57.001 32.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.