Multiple sequence alignment - TraesCS3B01G304700

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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 TraesCS3B01G304700 chr3B 100.000 2350 0 0 1 2350 489359573 489357224 0.000000e+00 4340.0
1 TraesCS3B01G304700 chr3B 100.000 29 0 0 108 136 384264949 384264921 1.000000e-03 54.7
2 TraesCS3B01G304700 chr3D 90.549 910 42 16 32 910 375204602 375203706 0.000000e+00 1164.0
3 TraesCS3B01G304700 chr3D 92.185 627 29 5 1727 2350 375198734 375198125 0.000000e+00 869.0
4 TraesCS3B01G304700 chr3D 90.291 618 22 10 911 1521 375203662 375203076 0.000000e+00 774.0
5 TraesCS3B01G304700 chr3D 96.970 33 1 0 1515 1547 375199014 375198982 3.260000e-04 56.5
6 TraesCS3B01G304700 chr3D 100.000 28 0 0 243 270 210316168 210316141 4.000000e-03 52.8
7 TraesCS3B01G304700 chr3A 94.089 626 26 3 1727 2350 498236223 498235607 0.000000e+00 941.0
8 TraesCS3B01G304700 chr3A 84.954 864 54 26 911 1725 498237145 498236309 0.000000e+00 806.0
9 TraesCS3B01G304700 chr3A 84.877 324 12 8 493 810 498243331 498243039 2.280000e-75 292.0
10 TraesCS3B01G304700 chr3A 83.383 337 15 14 168 478 498243634 498243313 8.270000e-70 274.0
11 TraesCS3B01G304700 chr3A 97.170 106 3 0 805 910 498237288 498237183 1.860000e-41 180.0
12 TraesCS3B01G304700 chr3A 85.276 163 12 6 3 153 498245098 498244936 8.690000e-35 158.0
13 TraesCS3B01G304700 chr3A 87.037 54 5 2 101 153 617479034 617478982 2.520000e-05 60.2
14 TraesCS3B01G304700 chr7D 96.970 33 1 0 104 136 70360609 70360577 3.260000e-04 56.5
15 TraesCS3B01G304700 chr7D 94.444 36 2 0 101 136 384986370 384986335 3.260000e-04 56.5
16 TraesCS3B01G304700 chr5A 100.000 30 0 0 245 274 687946653 687946624 3.260000e-04 56.5
17 TraesCS3B01G304700 chr7B 92.308 39 1 2 103 140 600840716 600840753 1.000000e-03 54.7
18 TraesCS3B01G304700 chr4B 100.000 29 0 0 110 138 119848533 119848505 1.000000e-03 54.7
19 TraesCS3B01G304700 chr2D 96.970 33 0 1 109 140 618986370 618986338 1.000000e-03 54.7
20 TraesCS3B01G304700 chr7A 94.286 35 0 2 103 136 640545931 640545964 4.000000e-03 52.8
21 TraesCS3B01G304700 chr1B 85.714 49 7 0 109 157 268287951 268287903 4.000000e-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 TraesCS3B01G304700 chr3B 489357224 489359573 2349 True 4340.000000 4340 100.0000 1 2350 1 chr3B.!!$R2 2349
1 TraesCS3B01G304700 chr3D 375203076 375204602 1526 True 969.000000 1164 90.4200 32 1521 2 chr3D.!!$R3 1489
2 TraesCS3B01G304700 chr3D 375198125 375199014 889 True 462.750000 869 94.5775 1515 2350 2 chr3D.!!$R2 835
3 TraesCS3B01G304700 chr3A 498235607 498237288 1681 True 642.333333 941 92.0710 805 2350 3 chr3A.!!$R2 1545
4 TraesCS3B01G304700 chr3A 498243039 498245098 2059 True 241.333333 292 84.5120 3 810 3 chr3A.!!$R3 807

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
793 2161 0.179062 CTCCTGACCCAGCAGCATAC 60.179 60.0 0.0 0.0 34.56 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 3568 0.039437 GAGTCTTGTTGCGTCTCGGA 60.039 55.0 0.0 0.0 0.0 4.55 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
38 39 7.930325 TGACATATATCAGGAGCAAGAAAAGAG 59.070 37.037 0.00 0.00 0.00 2.85
40 43 8.149647 ACATATATCAGGAGCAAGAAAAGAGAG 58.850 37.037 0.00 0.00 0.00 3.20
54 57 3.742433 AAGAGAGAAGACACCACACAG 57.258 47.619 0.00 0.00 0.00 3.66
74 77 2.986290 CCGTGGTGCTCATACCCA 59.014 61.111 0.00 0.00 40.09 4.51
123 142 0.945813 CGATGGTCTACCTCGTCTCC 59.054 60.000 0.02 0.00 34.37 3.71
138 157 2.526432 GTCTCCTGTGGTCTTAGGACA 58.474 52.381 7.35 0.00 43.77 4.02
146 165 1.340017 TGGTCTTAGGACATTGCTGGC 60.340 52.381 7.35 0.00 43.77 4.85
149 168 1.002746 TTAGGACATTGCTGGCGCA 60.003 52.632 10.83 0.00 46.24 6.09
159 178 1.153568 GCTGGCGCAGTGAGTCATA 60.154 57.895 10.83 0.00 33.43 2.15
166 185 2.356382 GCGCAGTGAGTCATAGAGTACT 59.644 50.000 0.30 0.00 0.00 2.73
207 1513 0.593128 CATGCCGGCTATTAGGTTGC 59.407 55.000 29.70 0.00 0.00 4.17
218 1524 5.474825 GCTATTAGGTTGCCTCTAGATGAC 58.525 45.833 0.00 0.00 34.61 3.06
219 1525 5.011125 GCTATTAGGTTGCCTCTAGATGACA 59.989 44.000 0.00 0.00 34.61 3.58
220 1526 6.295575 GCTATTAGGTTGCCTCTAGATGACAT 60.296 42.308 0.00 0.00 34.61 3.06
221 1527 3.834489 AGGTTGCCTCTAGATGACATG 57.166 47.619 0.00 0.00 0.00 3.21
222 1528 2.437281 AGGTTGCCTCTAGATGACATGG 59.563 50.000 0.00 0.00 0.00 3.66
223 1529 2.216898 GTTGCCTCTAGATGACATGGC 58.783 52.381 10.69 10.69 40.62 4.40
224 1530 1.499368 TGCCTCTAGATGACATGGCA 58.501 50.000 15.18 15.18 46.59 4.92
226 1532 2.216898 GCCTCTAGATGACATGGCAAC 58.783 52.381 4.70 1.74 40.04 4.17
227 1533 2.158842 GCCTCTAGATGACATGGCAACT 60.159 50.000 16.39 16.39 40.04 3.16
228 1534 3.726607 CCTCTAGATGACATGGCAACTC 58.273 50.000 15.57 4.06 37.61 3.01
229 1535 3.494048 CCTCTAGATGACATGGCAACTCC 60.494 52.174 15.57 0.00 37.61 3.85
232 1538 4.962362 TCTAGATGACATGGCAACTCCTTA 59.038 41.667 15.57 0.00 35.26 2.69
233 1539 4.574674 AGATGACATGGCAACTCCTTAA 57.425 40.909 4.70 0.00 35.26 1.85
234 1540 5.121380 AGATGACATGGCAACTCCTTAAT 57.879 39.130 4.70 0.00 35.26 1.40
312 1624 2.299582 TCGGGTTAAACAATGGACGAGA 59.700 45.455 0.00 0.00 0.00 4.04
313 1625 2.671396 CGGGTTAAACAATGGACGAGAG 59.329 50.000 0.00 0.00 0.00 3.20
314 1626 2.418976 GGGTTAAACAATGGACGAGAGC 59.581 50.000 0.00 0.00 0.00 4.09
315 1627 2.418976 GGTTAAACAATGGACGAGAGCC 59.581 50.000 0.00 0.00 0.00 4.70
316 1628 3.071479 GTTAAACAATGGACGAGAGCCA 58.929 45.455 0.00 0.00 40.55 4.75
317 1629 2.496899 AAACAATGGACGAGAGCCAT 57.503 45.000 0.00 0.00 45.54 4.40
318 1630 1.742761 AACAATGGACGAGAGCCATG 58.257 50.000 0.00 0.00 43.78 3.66
323 1635 2.202987 GACGAGAGCCATGCCCAG 60.203 66.667 0.00 0.00 0.00 4.45
476 1835 4.095185 CGATTTAACAATTAACCCGGCTGA 59.905 41.667 0.00 0.00 0.00 4.26
477 1836 5.220970 CGATTTAACAATTAACCCGGCTGAT 60.221 40.000 0.00 0.00 0.00 2.90
478 1837 5.986501 TTTAACAATTAACCCGGCTGATT 57.013 34.783 0.00 0.00 0.00 2.57
479 1838 5.570234 TTAACAATTAACCCGGCTGATTC 57.430 39.130 0.00 0.00 0.00 2.52
480 1839 3.366052 ACAATTAACCCGGCTGATTCT 57.634 42.857 0.00 0.00 0.00 2.40
481 1840 3.279434 ACAATTAACCCGGCTGATTCTC 58.721 45.455 0.00 0.00 0.00 2.87
482 1841 2.240493 ATTAACCCGGCTGATTCTCG 57.760 50.000 0.00 0.00 0.00 4.04
483 1842 1.187974 TTAACCCGGCTGATTCTCGA 58.812 50.000 0.00 0.00 0.00 4.04
484 1843 1.187974 TAACCCGGCTGATTCTCGAA 58.812 50.000 0.00 0.00 0.00 3.71
485 1844 0.323629 AACCCGGCTGATTCTCGAAA 59.676 50.000 0.00 0.00 0.00 3.46
486 1845 0.323629 ACCCGGCTGATTCTCGAAAA 59.676 50.000 0.00 0.00 0.00 2.29
487 1846 1.271163 ACCCGGCTGATTCTCGAAAAA 60.271 47.619 0.00 0.00 0.00 1.94
507 1866 4.948341 AAAAGAAACAATTAACCCGGCT 57.052 36.364 0.00 0.00 0.00 5.52
508 1867 4.948341 AAAGAAACAATTAACCCGGCTT 57.052 36.364 0.00 0.00 0.00 4.35
602 1961 2.677003 CGTGACATGGTTGCCCGTC 61.677 63.158 0.00 0.00 0.00 4.79
638 1997 1.000731 GAGAGAATCAGGCCGGAGATG 59.999 57.143 12.27 0.00 37.82 2.90
793 2161 0.179062 CTCCTGACCCAGCAGCATAC 60.179 60.000 0.00 0.00 34.56 2.39
817 2185 2.203743 AGGAACGAGGAACCCGGT 60.204 61.111 0.00 0.00 29.95 5.28
888 2256 2.456840 CCTCCCCCAAGTCTCCCT 59.543 66.667 0.00 0.00 0.00 4.20
951 2362 2.900337 CAATAAGCCGGCCGGTCC 60.900 66.667 42.53 28.39 37.65 4.46
1210 2623 6.291377 AGTATAGGTGCACGAAATCATTGAT 58.709 36.000 11.45 0.00 0.00 2.57
1214 2627 3.609373 GGTGCACGAAATCATTGATTGTG 59.391 43.478 18.60 18.60 32.14 3.33
1222 2643 8.207252 CACGAAATCATTGATTGTGTACAAAAC 58.793 33.333 12.50 0.00 39.55 2.43
1353 2774 4.253257 CCGCCGACGACTAGGAGC 62.253 72.222 0.00 0.00 43.93 4.70
1474 2901 3.393800 GGTGATAGTATCATGCGCTTGT 58.606 45.455 21.14 12.05 42.04 3.16
1476 2903 4.988540 GGTGATAGTATCATGCGCTTGTTA 59.011 41.667 21.14 15.01 42.04 2.41
1477 2904 5.465390 GGTGATAGTATCATGCGCTTGTTAA 59.535 40.000 21.14 4.52 42.04 2.01
1478 2905 6.346919 GGTGATAGTATCATGCGCTTGTTAAG 60.347 42.308 21.14 0.00 42.04 1.85
1479 2906 5.696270 TGATAGTATCATGCGCTTGTTAAGG 59.304 40.000 21.14 0.00 33.59 2.69
1480 2907 2.614057 AGTATCATGCGCTTGTTAAGGC 59.386 45.455 21.14 7.52 0.00 4.35
1518 2954 4.832248 TGTAGTGATGGAAGAACATGACC 58.168 43.478 0.00 0.00 35.88 4.02
1569 3005 4.336153 CCTGAAGCTTTTTGCCACATTTTT 59.664 37.500 0.00 0.00 44.23 1.94
1574 3023 4.949238 AGCTTTTTGCCACATTTTTCCTTT 59.051 33.333 0.00 0.00 44.23 3.11
1590 3039 2.158325 TCCTTTGATCCCTGCTTGGTTT 60.158 45.455 0.00 0.00 0.00 3.27
1591 3040 2.028748 CCTTTGATCCCTGCTTGGTTTG 60.029 50.000 0.00 0.00 0.00 2.93
1592 3041 2.673775 TTGATCCCTGCTTGGTTTGA 57.326 45.000 0.00 0.00 0.00 2.69
1593 3042 2.205022 TGATCCCTGCTTGGTTTGAG 57.795 50.000 0.00 0.00 0.00 3.02
1594 3043 1.272092 TGATCCCTGCTTGGTTTGAGG 60.272 52.381 0.00 0.00 0.00 3.86
1595 3044 0.040204 ATCCCTGCTTGGTTTGAGGG 59.960 55.000 0.00 0.00 45.97 4.30
1596 3045 1.607467 CCCTGCTTGGTTTGAGGGG 60.607 63.158 0.00 0.00 41.51 4.79
1597 3046 1.153756 CCTGCTTGGTTTGAGGGGT 59.846 57.895 0.00 0.00 0.00 4.95
1598 3047 0.469892 CCTGCTTGGTTTGAGGGGTT 60.470 55.000 0.00 0.00 0.00 4.11
1599 3048 1.413118 CTGCTTGGTTTGAGGGGTTT 58.587 50.000 0.00 0.00 0.00 3.27
1600 3049 1.069049 CTGCTTGGTTTGAGGGGTTTG 59.931 52.381 0.00 0.00 0.00 2.93
1601 3050 1.342474 TGCTTGGTTTGAGGGGTTTGA 60.342 47.619 0.00 0.00 0.00 2.69
1602 3051 1.068588 GCTTGGTTTGAGGGGTTTGAC 59.931 52.381 0.00 0.00 0.00 3.18
1620 3070 3.415237 CTGACTCTCAGGCTCGTTG 57.585 57.895 0.00 0.00 40.71 4.10
1675 3145 2.144833 CTGCCGTTCCAAGCATGCAA 62.145 55.000 21.98 1.65 38.56 4.08
1677 3147 1.959085 CCGTTCCAAGCATGCAAGT 59.041 52.632 21.98 0.94 0.00 3.16
1678 3148 1.164411 CCGTTCCAAGCATGCAAGTA 58.836 50.000 21.98 0.00 0.00 2.24
1679 3149 1.135689 CCGTTCCAAGCATGCAAGTAC 60.136 52.381 21.98 10.45 0.00 2.73
1706 3177 3.055891 TGGATCTCTGAATTGTCGCTTGA 60.056 43.478 0.00 0.00 0.00 3.02
1719 3272 3.129813 TGTCGCTTGATGTACGATTACCT 59.870 43.478 0.00 0.00 38.22 3.08
1759 3316 5.669477 AGACTTCATACCAGATTTCTGCTC 58.331 41.667 1.90 0.00 42.47 4.26
1773 3330 1.753649 TCTGCTCCATCTTTCTCCTCG 59.246 52.381 0.00 0.00 0.00 4.63
1780 3337 1.205655 CATCTTTCTCCTCGGCTGACA 59.794 52.381 0.00 0.00 0.00 3.58
1857 3414 4.647399 CCCTGGGTTTTCACTTCAGTTTTA 59.353 41.667 3.97 0.00 0.00 1.52
1878 3435 6.715344 TTAGGTGAAACTTTATACAGCACG 57.285 37.500 0.00 0.00 36.74 5.34
1882 3439 6.021596 GGTGAAACTTTATACAGCACGATTG 58.978 40.000 0.00 0.00 36.74 2.67
1963 3520 7.331687 TCATGATACAAACATATAGCACATCGG 59.668 37.037 0.00 0.00 0.00 4.18
1971 3528 4.453478 ACATATAGCACATCGGCATCAAAG 59.547 41.667 0.00 0.00 35.83 2.77
1975 3532 2.679837 AGCACATCGGCATCAAAGTAAG 59.320 45.455 0.00 0.00 35.83 2.34
2007 3567 1.636988 AAACGCCGAATTACCGAGAG 58.363 50.000 0.00 0.00 0.00 3.20
2008 3568 0.529378 AACGCCGAATTACCGAGAGT 59.471 50.000 0.00 0.00 0.00 3.24
2009 3569 0.100146 ACGCCGAATTACCGAGAGTC 59.900 55.000 0.00 0.00 0.00 3.36
2010 3570 0.594284 CGCCGAATTACCGAGAGTCC 60.594 60.000 0.00 0.00 0.00 3.85
2011 3571 0.594284 GCCGAATTACCGAGAGTCCG 60.594 60.000 0.00 0.00 0.00 4.79
2012 3572 1.019673 CCGAATTACCGAGAGTCCGA 58.980 55.000 3.00 0.00 0.00 4.55
2013 3573 1.002684 CCGAATTACCGAGAGTCCGAG 60.003 57.143 3.00 0.00 0.00 4.63
2014 3574 1.938577 CGAATTACCGAGAGTCCGAGA 59.061 52.381 3.00 0.00 0.00 4.04
2035 3595 1.355971 GCAACAAGACTCGCGGAATA 58.644 50.000 6.13 0.00 0.00 1.75
2099 3659 4.039730 ACCATATCGCTCTATTCACAAGCT 59.960 41.667 0.00 0.00 33.83 3.74
2153 3713 1.377202 GGCCTGAAATGCCGACAGA 60.377 57.895 0.00 0.00 38.04 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.444629 CTGATATATGTCAGGATTTTGGGTG 57.555 40.000 18.99 0.00 41.49 4.61
38 39 1.606737 GGCTCTGTGTGGTGTCTTCTC 60.607 57.143 0.00 0.00 0.00 2.87
40 43 0.946221 CGGCTCTGTGTGGTGTCTTC 60.946 60.000 0.00 0.00 0.00 2.87
74 77 3.870299 GCAGTAGAAACCCTAGCTTGCTT 60.870 47.826 0.00 0.00 32.28 3.91
123 142 3.005554 CAGCAATGTCCTAAGACCACAG 58.994 50.000 0.00 0.00 42.81 3.66
146 165 4.624336 AAGTACTCTATGACTCACTGCG 57.376 45.455 0.00 0.00 0.00 5.18
166 185 9.291664 GCATGTGCGGTAGTAAATTTTTAATAA 57.708 29.630 0.00 0.00 0.00 1.40
184 1490 1.568612 CCTAATAGCCGGCATGTGCG 61.569 60.000 31.54 11.87 43.26 5.34
186 1492 1.603802 CAACCTAATAGCCGGCATGTG 59.396 52.381 31.54 14.01 0.00 3.21
207 1513 3.494048 GGAGTTGCCATGTCATCTAGAGG 60.494 52.174 0.00 0.00 36.34 3.69
219 1525 9.866655 TGATTATAAGAATTAAGGAGTTGCCAT 57.133 29.630 0.00 0.00 32.89 4.40
220 1526 9.693739 TTGATTATAAGAATTAAGGAGTTGCCA 57.306 29.630 0.00 0.00 32.89 4.92
485 1844 5.284861 AGCCGGGTTAATTGTTTCTTTTT 57.715 34.783 0.00 0.00 0.00 1.94
486 1845 4.948341 AGCCGGGTTAATTGTTTCTTTT 57.052 36.364 0.00 0.00 0.00 2.27
487 1846 4.948341 AAGCCGGGTTAATTGTTTCTTT 57.052 36.364 19.23 0.00 0.00 2.52
488 1847 5.712917 TGATAAGCCGGGTTAATTGTTTCTT 59.287 36.000 28.35 9.95 0.00 2.52
489 1848 5.258051 TGATAAGCCGGGTTAATTGTTTCT 58.742 37.500 28.35 10.68 0.00 2.52
490 1849 5.570234 TGATAAGCCGGGTTAATTGTTTC 57.430 39.130 28.35 19.86 0.00 2.78
491 1850 5.986501 TTGATAAGCCGGGTTAATTGTTT 57.013 34.783 28.35 12.16 0.00 2.83
492 1851 5.654650 TGATTGATAAGCCGGGTTAATTGTT 59.345 36.000 28.35 12.90 0.00 2.83
493 1852 5.197451 TGATTGATAAGCCGGGTTAATTGT 58.803 37.500 28.35 13.29 0.00 2.71
494 1853 5.530915 TCTGATTGATAAGCCGGGTTAATTG 59.469 40.000 28.35 15.74 0.00 2.32
495 1854 5.690865 TCTGATTGATAAGCCGGGTTAATT 58.309 37.500 28.35 14.41 0.00 1.40
496 1855 5.304686 TCTGATTGATAAGCCGGGTTAAT 57.695 39.130 28.35 19.63 0.00 1.40
497 1856 4.764050 TCTGATTGATAAGCCGGGTTAA 57.236 40.909 28.35 15.72 0.00 2.01
498 1857 4.974645 ATCTGATTGATAAGCCGGGTTA 57.025 40.909 27.02 27.02 32.79 2.85
499 1858 3.864789 ATCTGATTGATAAGCCGGGTT 57.135 42.857 24.22 24.22 32.79 4.11
500 1859 3.480470 CAATCTGATTGATAAGCCGGGT 58.520 45.455 22.75 0.00 42.83 5.28
501 1860 2.227388 GCAATCTGATTGATAAGCCGGG 59.773 50.000 29.34 4.00 42.83 5.73
502 1861 2.880268 TGCAATCTGATTGATAAGCCGG 59.120 45.455 29.34 0.00 42.83 6.13
503 1862 3.811497 TCTGCAATCTGATTGATAAGCCG 59.189 43.478 29.34 12.92 42.83 5.52
504 1863 5.762825 TTCTGCAATCTGATTGATAAGCC 57.237 39.130 29.34 13.67 42.83 4.35
505 1864 5.680229 CGTTTCTGCAATCTGATTGATAAGC 59.320 40.000 29.34 19.35 42.83 3.09
506 1865 6.037500 TCCGTTTCTGCAATCTGATTGATAAG 59.962 38.462 29.34 21.77 42.83 1.73
507 1866 5.879777 TCCGTTTCTGCAATCTGATTGATAA 59.120 36.000 29.34 17.57 42.83 1.75
508 1867 5.427378 TCCGTTTCTGCAATCTGATTGATA 58.573 37.500 29.34 17.56 42.83 2.15
638 1997 1.138266 ACATAGTGTGTACCCGCATCC 59.862 52.381 0.00 0.00 39.91 3.51
777 2136 1.065926 TCAAGTATGCTGCTGGGTCAG 60.066 52.381 0.00 0.00 37.15 3.51
793 2161 1.608283 GGTTCCTCGTTCCTGGTCAAG 60.608 57.143 0.00 0.00 0.00 3.02
817 2185 1.000171 CGATGATTCATGGAGCTCGGA 60.000 52.381 7.83 2.28 0.00 4.55
888 2256 2.756025 CCGGCCTTTTATTCGCGCA 61.756 57.895 8.75 0.00 0.00 6.09
951 2362 2.792290 CTCTTGGATCGCACGCACG 61.792 63.158 0.00 0.00 0.00 5.34
952 2363 0.457853 TACTCTTGGATCGCACGCAC 60.458 55.000 0.00 0.00 0.00 5.34
953 2364 0.459899 ATACTCTTGGATCGCACGCA 59.540 50.000 0.00 0.00 0.00 5.24
954 2365 1.132588 GATACTCTTGGATCGCACGC 58.867 55.000 0.00 0.00 0.00 5.34
1149 2560 6.516718 ACATGTTAGATCGAGGAGGTAATTG 58.483 40.000 0.00 0.00 0.00 2.32
1150 2561 6.551601 AGACATGTTAGATCGAGGAGGTAATT 59.448 38.462 0.00 0.00 0.00 1.40
1151 2562 6.071984 AGACATGTTAGATCGAGGAGGTAAT 58.928 40.000 0.00 0.00 0.00 1.89
1152 2563 5.446860 AGACATGTTAGATCGAGGAGGTAA 58.553 41.667 0.00 0.00 0.00 2.85
1153 2564 5.050126 AGACATGTTAGATCGAGGAGGTA 57.950 43.478 0.00 0.00 0.00 3.08
1154 2565 3.904717 AGACATGTTAGATCGAGGAGGT 58.095 45.455 0.00 0.00 0.00 3.85
1155 2566 4.083003 GCTAGACATGTTAGATCGAGGAGG 60.083 50.000 15.12 0.00 0.00 4.30
1157 2568 4.276183 GTGCTAGACATGTTAGATCGAGGA 59.724 45.833 15.12 1.76 0.00 3.71
1158 2569 4.277174 AGTGCTAGACATGTTAGATCGAGG 59.723 45.833 15.12 0.00 0.00 4.63
1210 2623 1.338337 CATGCCGGGTTTTGTACACAA 59.662 47.619 2.18 0.00 0.00 3.33
1214 2627 0.109319 CTGCATGCCGGGTTTTGTAC 60.109 55.000 16.68 0.00 0.00 2.90
1222 2643 2.593725 CCTCATCTGCATGCCGGG 60.594 66.667 16.68 5.64 0.00 5.73
1369 2792 0.312416 CATCCATCGTCTCTCCGACC 59.688 60.000 0.00 0.00 40.08 4.79
1381 2804 3.205784 AGGCTTCTACTTGCATCCATC 57.794 47.619 0.00 0.00 0.00 3.51
1444 2867 2.223409 TGATACTATCACCGTGCGTGTC 60.223 50.000 0.00 0.39 43.51 3.67
1479 2906 3.501062 ACTACAAGAAAAAGGCCTAACGC 59.499 43.478 5.16 0.00 0.00 4.84
1480 2907 4.753107 TCACTACAAGAAAAAGGCCTAACG 59.247 41.667 5.16 0.00 0.00 3.18
1518 2954 6.042777 ACAACCGTGATTCACTATAGTCATG 58.957 40.000 14.54 3.67 31.34 3.07
1569 3005 1.075601 ACCAAGCAGGGATCAAAGGA 58.924 50.000 0.10 0.00 43.89 3.36
1574 3023 1.272092 CCTCAAACCAAGCAGGGATCA 60.272 52.381 0.10 0.00 43.89 2.92
1590 3039 1.971357 GAGAGTCAGTCAAACCCCTCA 59.029 52.381 0.00 0.00 0.00 3.86
1591 3040 1.971357 TGAGAGTCAGTCAAACCCCTC 59.029 52.381 0.00 0.00 0.00 4.30
1592 3041 1.974236 CTGAGAGTCAGTCAAACCCCT 59.026 52.381 0.00 0.00 39.58 4.79
1593 3042 1.002544 CCTGAGAGTCAGTCAAACCCC 59.997 57.143 3.35 0.00 42.80 4.95
1594 3043 1.609320 GCCTGAGAGTCAGTCAAACCC 60.609 57.143 3.35 0.00 42.80 4.11
1595 3044 1.346068 AGCCTGAGAGTCAGTCAAACC 59.654 52.381 3.35 0.00 42.80 3.27
1596 3045 2.682836 GAGCCTGAGAGTCAGTCAAAC 58.317 52.381 3.35 0.00 42.80 2.93
1597 3046 1.270826 CGAGCCTGAGAGTCAGTCAAA 59.729 52.381 3.35 0.00 42.80 2.69
1598 3047 0.884514 CGAGCCTGAGAGTCAGTCAA 59.115 55.000 3.35 0.00 42.80 3.18
1599 3048 0.250945 ACGAGCCTGAGAGTCAGTCA 60.251 55.000 3.35 0.00 42.80 3.41
1600 3049 0.885196 AACGAGCCTGAGAGTCAGTC 59.115 55.000 3.35 0.00 42.80 3.51
1601 3050 0.600557 CAACGAGCCTGAGAGTCAGT 59.399 55.000 3.35 0.00 42.80 3.41
1602 3051 0.735632 GCAACGAGCCTGAGAGTCAG 60.736 60.000 0.00 0.00 43.91 3.51
1620 3070 1.062148 GACGAAGCCATACTTTTCCGC 59.938 52.381 0.00 0.00 39.29 5.54
1675 3145 7.134362 ACAATTCAGAGATCCATCATGTACT 57.866 36.000 0.00 0.00 0.00 2.73
1677 3147 6.218746 CGACAATTCAGAGATCCATCATGTA 58.781 40.000 0.00 0.00 0.00 2.29
1678 3148 5.055144 CGACAATTCAGAGATCCATCATGT 58.945 41.667 0.00 0.00 0.00 3.21
1679 3149 4.083961 GCGACAATTCAGAGATCCATCATG 60.084 45.833 0.00 0.00 0.00 3.07
1706 3177 3.031736 AGGTGCTGAGGTAATCGTACAT 58.968 45.455 0.00 0.00 31.21 2.29
1719 3272 8.635765 ATGAAGTCTTTAATTTAAGGTGCTGA 57.364 30.769 4.48 0.00 0.00 4.26
1755 3312 0.826715 CCGAGGAGAAAGATGGAGCA 59.173 55.000 0.00 0.00 0.00 4.26
1759 3316 0.826715 TCAGCCGAGGAGAAAGATGG 59.173 55.000 0.00 0.00 0.00 3.51
1773 3330 0.179062 CTCCTACCTGCATGTCAGCC 60.179 60.000 0.00 0.00 41.50 4.85
1780 3337 1.406069 CGCACTTTCTCCTACCTGCAT 60.406 52.381 0.00 0.00 0.00 3.96
1857 3414 4.890088 TCGTGCTGTATAAAGTTTCACCT 58.110 39.130 0.00 0.00 0.00 4.00
1878 3435 6.919721 TGTATTTAGTTCCAACAAGGCAATC 58.080 36.000 0.00 0.00 37.29 2.67
1882 3439 6.919721 TGAATGTATTTAGTTCCAACAAGGC 58.080 36.000 0.00 0.00 37.29 4.35
2007 3567 0.318784 AGTCTTGTTGCGTCTCGGAC 60.319 55.000 0.00 0.00 0.00 4.79
2008 3568 0.039437 GAGTCTTGTTGCGTCTCGGA 60.039 55.000 0.00 0.00 0.00 4.55
2009 3569 1.337817 CGAGTCTTGTTGCGTCTCGG 61.338 60.000 0.00 0.00 42.45 4.63
2010 3570 1.935065 GCGAGTCTTGTTGCGTCTCG 61.935 60.000 8.23 8.23 46.76 4.04
2011 3571 1.775962 GCGAGTCTTGTTGCGTCTC 59.224 57.895 0.00 0.00 0.00 3.36
2012 3572 2.016704 CGCGAGTCTTGTTGCGTCT 61.017 57.895 0.00 0.00 44.01 4.18
2013 3573 2.465920 CGCGAGTCTTGTTGCGTC 59.534 61.111 0.00 0.00 44.01 5.19
2035 3595 2.672996 GGTTGGCGCAGTGGATGT 60.673 61.111 10.83 0.00 0.00 3.06
2067 3627 0.961753 AGCGATATGGTGATGCTCGA 59.038 50.000 0.00 0.00 0.00 4.04
2099 3659 1.526575 GCAGCTTTGGCACCAAGCTA 61.527 55.000 22.27 0.38 44.79 3.32
2153 3713 3.944476 GATGGATTATCGGCAGCCT 57.056 52.632 10.54 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.