Multiple sequence alignment - TraesCS5B01G107600

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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 TraesCS5B01G107600 chr5B 100.000 4264 0 0 1 4264 146363867 146368130 0.000000e+00 7875
1 TraesCS5B01G107600 chr5B 85.970 727 91 8 4 725 535390333 535389613 0.000000e+00 767
2 TraesCS5B01G107600 chr5A 94.812 2313 75 14 1966 4264 159533418 159535699 0.000000e+00 3565
3 TraesCS5B01G107600 chr5A 94.574 645 23 7 810 1443 159532767 159533410 0.000000e+00 987
4 TraesCS5B01G107600 chr5D 94.202 2018 52 26 1712 3727 134916325 134918279 0.000000e+00 3018
5 TraesCS5B01G107600 chr5D 95.597 954 19 7 732 1673 134915380 134916322 0.000000e+00 1507
6 TraesCS5B01G107600 chr5D 91.168 736 50 3 1 721 134914595 134915330 0.000000e+00 985
7 TraesCS5B01G107600 chr5D 90.761 552 14 4 3721 4264 134918639 134919161 0.000000e+00 702
8 TraesCS5B01G107600 chr5D 95.062 81 4 0 1886 1966 264494525 264494445 1.240000e-25 128
9 TraesCS5B01G107600 chr6D 88.195 737 78 7 3 732 61102994 61103728 0.000000e+00 870
10 TraesCS5B01G107600 chr6D 88.179 736 76 9 1 731 462687564 462688293 0.000000e+00 867
11 TraesCS5B01G107600 chr6D 94.253 87 5 0 1881 1967 122992191 122992105 2.670000e-27 134
12 TraesCS5B01G107600 chr1D 85.849 742 74 11 1 732 223469375 223468655 0.000000e+00 760
13 TraesCS5B01G107600 chr1D 91.860 86 7 0 1881 1966 198901720 198901805 2.080000e-23 121
14 TraesCS5B01G107600 chr3D 84.421 751 90 16 1 731 281081236 281081979 0.000000e+00 713
15 TraesCS5B01G107600 chr3D 81.472 761 88 22 1 721 85024372 85023625 3.700000e-160 575
16 TraesCS5B01G107600 chr3D 79.377 771 97 35 1 732 284990300 284991047 1.780000e-133 486
17 TraesCS5B01G107600 chr3D 91.489 94 8 0 1873 1966 326697048 326696955 3.460000e-26 130
18 TraesCS5B01G107600 chr7D 83.134 753 91 15 1 732 424489645 424488908 0.000000e+00 654
19 TraesCS5B01G107600 chr4B 82.638 743 102 21 1 732 381711352 381710626 2.160000e-177 632
20 TraesCS5B01G107600 chr2D 82.550 745 100 22 1 732 483071246 483070519 2.800000e-176 628
21 TraesCS5B01G107600 chr2A 88.220 382 43 2 1 382 637695349 637694970 5.030000e-124 455
22 TraesCS5B01G107600 chr2A 93.182 88 6 0 1879 1966 385002702 385002789 3.460000e-26 130
23 TraesCS5B01G107600 chr2A 90.323 93 8 1 1876 1967 705588380 705588288 2.080000e-23 121
24 TraesCS5B01G107600 chr6A 94.186 86 5 0 1881 1966 548408060 548408145 9.620000e-27 132
25 TraesCS5B01G107600 chr4A 92.308 91 5 2 1876 1966 625404773 625404861 1.240000e-25 128


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 TraesCS5B01G107600 chr5B 146363867 146368130 4263 False 7875 7875 100.000 1 4264 1 chr5B.!!$F1 4263
1 TraesCS5B01G107600 chr5B 535389613 535390333 720 True 767 767 85.970 4 725 1 chr5B.!!$R1 721
2 TraesCS5B01G107600 chr5A 159532767 159535699 2932 False 2276 3565 94.693 810 4264 2 chr5A.!!$F1 3454
3 TraesCS5B01G107600 chr5D 134914595 134919161 4566 False 1553 3018 92.932 1 4264 4 chr5D.!!$F1 4263
4 TraesCS5B01G107600 chr6D 61102994 61103728 734 False 870 870 88.195 3 732 1 chr6D.!!$F1 729
5 TraesCS5B01G107600 chr6D 462687564 462688293 729 False 867 867 88.179 1 731 1 chr6D.!!$F2 730
6 TraesCS5B01G107600 chr1D 223468655 223469375 720 True 760 760 85.849 1 732 1 chr1D.!!$R1 731
7 TraesCS5B01G107600 chr3D 281081236 281081979 743 False 713 713 84.421 1 731 1 chr3D.!!$F1 730
8 TraesCS5B01G107600 chr3D 85023625 85024372 747 True 575 575 81.472 1 721 1 chr3D.!!$R1 720
9 TraesCS5B01G107600 chr3D 284990300 284991047 747 False 486 486 79.377 1 732 1 chr3D.!!$F2 731
10 TraesCS5B01G107600 chr7D 424488908 424489645 737 True 654 654 83.134 1 732 1 chr7D.!!$R1 731
11 TraesCS5B01G107600 chr4B 381710626 381711352 726 True 632 632 82.638 1 732 1 chr4B.!!$R1 731
12 TraesCS5B01G107600 chr2D 483070519 483071246 727 True 628 628 82.550 1 732 1 chr2D.!!$R1 731

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
842 989 0.840288 TGACTTGCAGGCCCTCCTAA 60.840 55.0 0.00 0.00 41.93 2.69 F
1477 1635 0.248296 GGCGTGCTCTCTTCTACTCG 60.248 60.0 0.00 0.00 0.00 4.18 F
1679 1844 0.329261 ACTGCATGGCCATGTACACT 59.671 50.0 39.08 19.71 40.80 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1932 1.023513 AGCATCGCAAAGACAGAGGC 61.024 55.000 0.0 0.0 41.34 4.70 R
2640 2808 1.878953 AATGACTCGAAAGCAACCGT 58.121 45.000 0.0 0.0 0.00 4.83 R
3277 3448 1.898574 ACGCTGAAGGTTGCAAGGG 60.899 57.895 0.0 0.0 0.00 3.95 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
33 34 2.679336 CTCCATGAACATGCACGATGAA 59.321 45.455 9.03 0.00 37.49 2.57
52 53 2.440980 GTCAATGGGAGGGCCTGC 60.441 66.667 17.94 17.94 0.00 4.85
263 300 1.826024 GGTCACCGGAGCATGAGAT 59.174 57.895 9.46 0.00 41.19 2.75
266 303 0.904649 TCACCGGAGCATGAGATGTT 59.095 50.000 9.46 0.00 0.00 2.71
382 437 1.592400 CCTTACTGGCGACGAGGACA 61.592 60.000 0.00 0.00 0.00 4.02
625 732 3.767630 GATATGGGGTGCGGCCGTT 62.768 63.158 28.70 5.69 38.44 4.44
644 751 2.358247 ATTGGACGCACCGACACC 60.358 61.111 0.00 0.00 42.61 4.16
645 752 3.171828 ATTGGACGCACCGACACCA 62.172 57.895 0.00 0.00 42.61 4.17
689 796 2.296814 GATCCCATTGCCGCCCAAAC 62.297 60.000 0.00 0.00 36.92 2.93
693 800 1.667510 CATTGCCGCCCAAACCAAC 60.668 57.895 0.00 0.00 36.92 3.77
732 841 2.968156 CCGTTTCGGGTTGTGCGA 60.968 61.111 0.00 0.00 44.15 5.10
733 842 2.549282 CGTTTCGGGTTGTGCGAG 59.451 61.111 0.00 0.00 0.00 5.03
734 843 2.241880 CGTTTCGGGTTGTGCGAGT 61.242 57.895 0.00 0.00 0.00 4.18
735 844 1.768112 CGTTTCGGGTTGTGCGAGTT 61.768 55.000 0.00 0.00 0.00 3.01
750 897 5.121768 TGTGCGAGTTAGCTCTTATTTTTCC 59.878 40.000 4.99 0.00 39.53 3.13
799 946 8.946085 AGTTGCATCGTTCTTATCTGAATAAAA 58.054 29.630 0.00 0.00 0.00 1.52
840 987 2.530151 TGACTTGCAGGCCCTCCT 60.530 61.111 0.00 0.00 45.66 3.69
841 988 1.229496 TGACTTGCAGGCCCTCCTA 60.229 57.895 0.00 0.00 41.93 2.94
842 989 0.840288 TGACTTGCAGGCCCTCCTAA 60.840 55.000 0.00 0.00 41.93 2.69
1373 1530 3.255642 CACCAGGTTGGATCGAAATGTTT 59.744 43.478 1.40 0.00 40.96 2.83
1385 1543 3.634448 TCGAAATGTTTTCCCTGAAGCAA 59.366 39.130 0.00 0.00 0.00 3.91
1425 1583 1.378514 GGCCCCTTCTTGAATCGCA 60.379 57.895 0.00 0.00 0.00 5.10
1476 1634 0.811915 TGGCGTGCTCTCTTCTACTC 59.188 55.000 0.00 0.00 0.00 2.59
1477 1635 0.248296 GGCGTGCTCTCTTCTACTCG 60.248 60.000 0.00 0.00 0.00 4.18
1478 1636 0.448593 GCGTGCTCTCTTCTACTCGT 59.551 55.000 0.00 0.00 0.00 4.18
1553 1718 1.411612 ACGGGTTAGGAATAAGCGGAG 59.588 52.381 10.46 0.32 33.74 4.63
1625 1790 1.065564 AGCTGAATTCCTGCTCTGTCC 60.066 52.381 14.76 0.00 45.33 4.02
1673 1838 2.025898 TGATACAACTGCATGGCCATG 58.974 47.619 36.80 36.80 41.60 3.66
1675 1840 2.797177 TACAACTGCATGGCCATGTA 57.203 45.000 39.08 35.23 40.80 2.29
1676 1841 1.176527 ACAACTGCATGGCCATGTAC 58.823 50.000 39.08 26.95 40.80 2.90
1677 1842 1.175654 CAACTGCATGGCCATGTACA 58.824 50.000 39.08 29.52 40.80 2.90
1678 1843 1.135315 CAACTGCATGGCCATGTACAC 60.135 52.381 39.08 25.97 40.80 2.90
1679 1844 0.329261 ACTGCATGGCCATGTACACT 59.671 50.000 39.08 19.71 40.80 3.55
1680 1845 1.559219 ACTGCATGGCCATGTACACTA 59.441 47.619 39.08 20.87 40.80 2.74
1681 1846 2.173356 ACTGCATGGCCATGTACACTAT 59.827 45.455 39.08 19.54 40.80 2.12
1682 1847 2.810274 CTGCATGGCCATGTACACTATC 59.190 50.000 39.08 23.70 40.80 2.08
1683 1848 2.439135 TGCATGGCCATGTACACTATCT 59.561 45.455 39.08 4.27 40.80 1.98
1684 1849 2.810274 GCATGGCCATGTACACTATCTG 59.190 50.000 39.08 17.56 40.80 2.90
1685 1850 3.405831 CATGGCCATGTACACTATCTGG 58.594 50.000 33.68 7.00 34.23 3.86
1687 1852 2.918712 GCCATGTACACTATCTGGCT 57.081 50.000 24.01 0.00 46.97 4.75
1689 1854 3.654414 GCCATGTACACTATCTGGCTAC 58.346 50.000 24.01 2.44 46.97 3.58
1690 1855 3.069586 GCCATGTACACTATCTGGCTACA 59.930 47.826 24.01 0.00 46.97 2.74
1691 1856 4.262635 GCCATGTACACTATCTGGCTACAT 60.263 45.833 24.01 0.00 46.97 2.29
1692 1857 5.743130 GCCATGTACACTATCTGGCTACATT 60.743 44.000 24.01 0.00 46.97 2.71
1693 1858 5.928839 CCATGTACACTATCTGGCTACATTC 59.071 44.000 0.00 0.00 0.00 2.67
1694 1859 5.531122 TGTACACTATCTGGCTACATTCC 57.469 43.478 0.00 0.00 0.00 3.01
1695 1860 5.208890 TGTACACTATCTGGCTACATTCCT 58.791 41.667 0.00 0.00 0.00 3.36
1696 1861 5.661312 TGTACACTATCTGGCTACATTCCTT 59.339 40.000 0.00 0.00 0.00 3.36
1697 1862 5.700402 ACACTATCTGGCTACATTCCTTT 57.300 39.130 0.00 0.00 0.00 3.11
1698 1863 6.067217 ACACTATCTGGCTACATTCCTTTT 57.933 37.500 0.00 0.00 0.00 2.27
1699 1864 5.882557 ACACTATCTGGCTACATTCCTTTTG 59.117 40.000 0.00 0.00 0.00 2.44
1700 1865 6.115446 CACTATCTGGCTACATTCCTTTTGA 58.885 40.000 0.00 0.00 0.00 2.69
1701 1866 6.259608 CACTATCTGGCTACATTCCTTTTGAG 59.740 42.308 0.00 0.00 0.00 3.02
1702 1867 4.908601 TCTGGCTACATTCCTTTTGAGA 57.091 40.909 0.00 0.00 0.00 3.27
1703 1868 5.441718 TCTGGCTACATTCCTTTTGAGAT 57.558 39.130 0.00 0.00 0.00 2.75
1704 1869 6.560003 TCTGGCTACATTCCTTTTGAGATA 57.440 37.500 0.00 0.00 0.00 1.98
1705 1870 6.586344 TCTGGCTACATTCCTTTTGAGATAG 58.414 40.000 0.00 0.00 0.00 2.08
1706 1871 5.684704 TGGCTACATTCCTTTTGAGATAGG 58.315 41.667 0.00 0.00 0.00 2.57
1707 1872 4.517075 GGCTACATTCCTTTTGAGATAGGC 59.483 45.833 0.00 0.00 0.00 3.93
1708 1873 4.517075 GCTACATTCCTTTTGAGATAGGCC 59.483 45.833 0.00 0.00 0.00 5.19
1709 1874 3.545703 ACATTCCTTTTGAGATAGGCCG 58.454 45.455 0.00 0.00 0.00 6.13
1710 1875 3.199946 ACATTCCTTTTGAGATAGGCCGA 59.800 43.478 0.00 0.00 0.00 5.54
1767 1932 9.307121 CTATAAAATGTACTCACTGGAACTCTG 57.693 37.037 0.00 0.00 0.00 3.35
1797 1962 6.705825 TGTCTTTGCGATGCTGTATTATGTAT 59.294 34.615 0.00 0.00 0.00 2.29
1811 1976 8.432110 TGTATTATGTATGTAACAACAGCCTG 57.568 34.615 0.00 0.00 42.70 4.85
1844 2009 5.643379 TTCCATTTTCTTGTCCAGTATGC 57.357 39.130 0.00 0.00 31.97 3.14
1873 2038 6.943899 ATCCTAACCTCTCTTTGTTCTCTT 57.056 37.500 0.00 0.00 0.00 2.85
1883 2048 7.486551 CCTCTCTTTGTTCTCTTGTTATCTACG 59.513 40.741 0.00 0.00 0.00 3.51
1902 2067 2.158667 ACGCCCTCCGATCCAAAATAAT 60.159 45.455 0.00 0.00 41.02 1.28
2139 2304 3.266636 CCACATCGGCATGTACACTTAA 58.733 45.455 0.00 0.00 41.69 1.85
2148 2313 5.579119 CGGCATGTACACTTAACAGATTGTA 59.421 40.000 0.00 0.00 0.00 2.41
2247 2412 7.056006 AGCAATTATATGTGTCTGACCATTCA 58.944 34.615 14.17 6.01 0.00 2.57
2350 2515 3.013921 TCTGGTTTGTCACAACCTGTTC 58.986 45.455 14.22 0.00 39.74 3.18
2389 2555 6.577103 TGTTTTGTAAAATGATTGTGCTGGA 58.423 32.000 0.00 0.00 0.00 3.86
2487 2654 8.224389 TGGATTATCAGAATTGTGTGGTAATG 57.776 34.615 2.11 0.00 35.13 1.90
2493 2660 4.925054 CAGAATTGTGTGGTAATGCAAAGG 59.075 41.667 0.00 0.00 0.00 3.11
2516 2683 5.181433 GGTTCCATTCTCCTTGTGTACTTTC 59.819 44.000 0.00 0.00 0.00 2.62
2544 2711 4.156556 TGTGAATAAAGTTCAGGATGCAGC 59.843 41.667 0.00 0.00 34.76 5.25
2556 2723 2.434336 AGGATGCAGCCGTCAAGTATAA 59.566 45.455 16.75 0.00 0.00 0.98
2640 2808 3.883830 ATGCTTGTTTGTGTTGGTCAA 57.116 38.095 0.00 0.00 0.00 3.18
2747 2915 7.330262 TCTGTTTAGATCATGCACTTACATCA 58.670 34.615 0.00 0.00 0.00 3.07
2780 2948 6.431234 ACATCTACCAGTTCATTTGGTCTTTC 59.569 38.462 0.00 0.00 45.67 2.62
2792 2960 6.826231 TCATTTGGTCTTTCAGTTTACAGACA 59.174 34.615 0.00 0.00 37.92 3.41
2922 3093 7.095439 GCTTACATCAGATATGTTGGTAAGCTC 60.095 40.741 26.79 13.00 37.13 4.09
2935 3106 2.290323 GGTAAGCTCCAATGGTGTCTGT 60.290 50.000 0.00 0.00 0.00 3.41
3277 3448 3.472652 TGGGGTAAATCATCGTATGTGC 58.527 45.455 0.00 0.00 0.00 4.57
3372 3543 8.151596 TGATTGTGTTATCTGGTAGTGTAAACA 58.848 33.333 0.00 0.00 0.00 2.83
3582 3753 4.927978 ATATGAGGAACAGAAGAGACCG 57.072 45.455 0.00 0.00 0.00 4.79
3597 3768 1.376609 GACCGGCTTCATTTCCGCAT 61.377 55.000 0.00 0.00 44.01 4.73
3699 3870 9.626045 GAAAATTGATGACGGGGATATAATTTC 57.374 33.333 0.00 0.00 0.00 2.17
3865 4401 5.173854 CGGAAGCTTGTTTTCTTTTGATCAC 59.826 40.000 2.10 0.00 0.00 3.06
3904 4440 8.573035 GGTCACCTAACTCATTTGTGATTTTTA 58.427 33.333 0.00 0.00 0.00 1.52
3976 4512 6.006275 AGAGAGTGTATGTATTGCCCAATT 57.994 37.500 0.00 0.00 32.50 2.32
3995 4531 6.293626 CCCAATTTGTCTTCTAGAAGTGTGTG 60.294 42.308 27.59 18.83 39.38 3.82
4040 4576 0.033601 AGTGGTGGTTGTCTGGCAAA 60.034 50.000 0.00 0.00 39.03 3.68
4112 4649 2.489329 CTGCAACTATCCAGTGGGTTTG 59.511 50.000 9.92 5.87 34.36 2.93
4216 4761 6.187682 TGGAAGAAAGGGAAGGATTATTCAC 58.812 40.000 0.00 0.00 32.47 3.18
4231 4776 2.363788 TTCACGTGCAGTAAGCTAGG 57.636 50.000 11.67 0.00 45.94 3.02
4239 4784 4.120589 GTGCAGTAAGCTAGGTACAATCC 58.879 47.826 0.00 0.00 45.94 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.610859 AGGCCCTCCCATTGACGT 60.611 61.111 0.00 0.00 35.39 4.34
52 53 2.422479 CAGAGAAGGCAATCATGGTGTG 59.578 50.000 0.00 0.00 0.00 3.82
176 213 4.640855 CGACCGTGCACGACCAGT 62.641 66.667 39.10 27.51 43.02 4.00
266 303 3.716195 CCATCTCACCCCGTGGCA 61.716 66.667 0.00 0.00 33.87 4.92
300 337 2.270527 GCTGGAGGCTCCTGGAAC 59.729 66.667 33.19 18.28 37.46 3.62
353 408 1.674441 CGCCAGTAAGGTCGATGTAGA 59.326 52.381 0.00 0.00 38.60 2.59
382 437 2.663520 TCACGCGTCGCCATTGTT 60.664 55.556 9.86 0.00 0.00 2.83
503 594 4.749245 AATTAAACAGTCTTCACAGGCG 57.251 40.909 0.00 0.00 0.00 5.52
596 700 3.503365 CACCCCATATCATGCAGGATTT 58.497 45.455 20.25 8.98 0.00 2.17
597 701 2.820485 GCACCCCATATCATGCAGGATT 60.820 50.000 20.25 4.75 38.00 3.01
625 732 1.666553 GTGTCGGTGCGTCCAATGA 60.667 57.895 0.00 0.00 35.57 2.57
689 796 3.496884 TCCGTTTTGATCTCTTTCGTTGG 59.503 43.478 0.00 0.00 0.00 3.77
693 800 2.729882 ACGTCCGTTTTGATCTCTTTCG 59.270 45.455 0.00 0.00 0.00 3.46
721 830 1.352156 GAGCTAACTCGCACAACCCG 61.352 60.000 0.00 0.00 32.04 5.28
732 841 8.787852 CAGACTTTGGAAAAATAAGAGCTAACT 58.212 33.333 0.00 0.00 0.00 2.24
733 842 8.568794 ACAGACTTTGGAAAAATAAGAGCTAAC 58.431 33.333 0.00 0.00 0.00 2.34
734 843 8.691661 ACAGACTTTGGAAAAATAAGAGCTAA 57.308 30.769 0.00 0.00 0.00 3.09
735 844 7.936847 TGACAGACTTTGGAAAAATAAGAGCTA 59.063 33.333 0.00 0.00 0.00 3.32
750 897 5.820131 TGCAGTTTAACATGACAGACTTTG 58.180 37.500 0.00 0.00 0.00 2.77
781 928 9.878599 ACAAACAGTTTTATTCAGATAAGAACG 57.121 29.630 0.00 0.00 31.47 3.95
799 946 6.589907 CAGCCTTTCTTTTTAACACAAACAGT 59.410 34.615 0.00 0.00 0.00 3.55
840 987 7.617041 GCTTTTGGAGATTCTAGAAAGCTTA 57.383 36.000 21.57 1.76 43.23 3.09
841 988 6.507958 GCTTTTGGAGATTCTAGAAAGCTT 57.492 37.500 21.57 0.00 43.23 3.74
865 1015 1.189524 TCCGGCGAAAAGGAAGAGGA 61.190 55.000 9.30 0.00 32.86 3.71
965 1119 0.323629 CCTTCGTTGGTCCTTGGCTA 59.676 55.000 0.00 0.00 0.00 3.93
1250 1407 4.148825 AGGGCGACACGGAGCATC 62.149 66.667 0.00 0.00 34.54 3.91
1385 1543 1.846439 ACTCCATCCGGTTCCATGAAT 59.154 47.619 0.00 0.00 0.00 2.57
1425 1583 2.563179 AGAAATGTCTGAGTAGTGCGGT 59.437 45.455 0.00 0.00 30.83 5.68
1452 1610 2.508526 AGAAGAGAGCACGCCATTTTT 58.491 42.857 0.00 0.00 0.00 1.94
1476 1634 5.773239 TCGTCTGGCTCTAAAAATAAACG 57.227 39.130 0.00 0.00 0.00 3.60
1477 1635 7.064728 AGACATCGTCTGGCTCTAAAAATAAAC 59.935 37.037 0.00 0.00 40.02 2.01
1478 1636 7.103641 AGACATCGTCTGGCTCTAAAAATAAA 58.896 34.615 0.00 0.00 40.02 1.40
1519 1684 0.635009 ACCCGTCTATCCTTCCTCCA 59.365 55.000 0.00 0.00 0.00 3.86
1553 1718 2.672195 GCAAATTGTCTTACAGCCTGCC 60.672 50.000 0.00 0.00 0.00 4.85
1605 1770 1.065564 GGACAGAGCAGGAATTCAGCT 60.066 52.381 20.48 20.48 42.17 4.24
1625 1790 5.237815 TGCAGACCAACTAATTCAGTACAG 58.762 41.667 0.00 0.00 36.04 2.74
1673 1838 5.793030 AGGAATGTAGCCAGATAGTGTAC 57.207 43.478 0.00 0.00 0.00 2.90
1675 1840 5.700402 AAAGGAATGTAGCCAGATAGTGT 57.300 39.130 0.00 0.00 0.00 3.55
1676 1841 6.115446 TCAAAAGGAATGTAGCCAGATAGTG 58.885 40.000 0.00 0.00 0.00 2.74
1677 1842 6.156949 TCTCAAAAGGAATGTAGCCAGATAGT 59.843 38.462 0.00 0.00 0.00 2.12
1678 1843 6.586344 TCTCAAAAGGAATGTAGCCAGATAG 58.414 40.000 0.00 0.00 0.00 2.08
1679 1844 6.560003 TCTCAAAAGGAATGTAGCCAGATA 57.440 37.500 0.00 0.00 0.00 1.98
1680 1845 5.441718 TCTCAAAAGGAATGTAGCCAGAT 57.558 39.130 0.00 0.00 0.00 2.90
1681 1846 4.908601 TCTCAAAAGGAATGTAGCCAGA 57.091 40.909 0.00 0.00 0.00 3.86
1682 1847 5.762218 CCTATCTCAAAAGGAATGTAGCCAG 59.238 44.000 0.00 0.00 34.58 4.85
1683 1848 5.684704 CCTATCTCAAAAGGAATGTAGCCA 58.315 41.667 0.00 0.00 34.58 4.75
1684 1849 4.517075 GCCTATCTCAAAAGGAATGTAGCC 59.483 45.833 0.00 0.00 34.58 3.93
1685 1850 4.517075 GGCCTATCTCAAAAGGAATGTAGC 59.483 45.833 0.00 0.00 34.58 3.58
1686 1851 4.752101 CGGCCTATCTCAAAAGGAATGTAG 59.248 45.833 0.00 0.00 34.58 2.74
1687 1852 4.407621 TCGGCCTATCTCAAAAGGAATGTA 59.592 41.667 0.00 0.00 34.58 2.29
1688 1853 3.199946 TCGGCCTATCTCAAAAGGAATGT 59.800 43.478 0.00 0.00 34.58 2.71
1689 1854 3.808728 TCGGCCTATCTCAAAAGGAATG 58.191 45.455 0.00 0.00 34.58 2.67
1690 1855 4.503714 TTCGGCCTATCTCAAAAGGAAT 57.496 40.909 0.00 0.00 34.58 3.01
1691 1856 3.992943 TTCGGCCTATCTCAAAAGGAA 57.007 42.857 0.00 0.00 34.58 3.36
1692 1857 4.164221 AGAATTCGGCCTATCTCAAAAGGA 59.836 41.667 0.00 0.00 34.58 3.36
1693 1858 4.455606 AGAATTCGGCCTATCTCAAAAGG 58.544 43.478 0.00 0.00 35.86 3.11
1694 1859 6.054035 GAAGAATTCGGCCTATCTCAAAAG 57.946 41.667 0.00 0.00 34.17 2.27
1709 1874 8.302438 CCTAGCATCAATATTTGGGAAGAATTC 58.698 37.037 0.00 0.00 46.67 2.17
1710 1875 7.256083 GCCTAGCATCAATATTTGGGAAGAATT 60.256 37.037 0.00 0.00 0.00 2.17
1767 1932 1.023513 AGCATCGCAAAGACAGAGGC 61.024 55.000 0.00 0.00 41.34 4.70
1797 1962 1.765904 TCCAGACAGGCTGTTGTTACA 59.234 47.619 22.98 1.22 43.33 2.41
1844 2009 6.293004 ACAAAGAGAGGTTAGGATTCTCTG 57.707 41.667 4.20 0.00 45.10 3.35
1873 2038 1.884579 GATCGGAGGGCGTAGATAACA 59.115 52.381 0.00 0.00 0.00 2.41
1883 2048 3.636764 ACAATTATTTTGGATCGGAGGGC 59.363 43.478 0.00 0.00 0.00 5.19
1902 2067 3.380004 ACTCCAGTTCAAAATTGCGACAA 59.620 39.130 0.00 0.00 0.00 3.18
2139 2304 4.199310 ACACTTGTTGCAGTACAATCTGT 58.801 39.130 4.49 6.65 41.27 3.41
2148 2313 3.584834 GTGGAAAAACACTTGTTGCAGT 58.415 40.909 0.00 0.00 38.44 4.40
2247 2412 1.690219 ATCGGAGCGGCTTGGAATCT 61.690 55.000 2.97 0.00 0.00 2.40
2350 2515 9.757227 TTTTACAAAACAATAGGTGATTTCTGG 57.243 29.630 0.00 0.00 30.35 3.86
2389 2555 8.798859 ACATCTTCTGAAATTAGTTGCAGTAT 57.201 30.769 5.90 0.00 0.00 2.12
2487 2654 2.893489 ACAAGGAGAATGGAACCTTTGC 59.107 45.455 0.00 0.00 41.33 3.68
2493 2660 5.998363 AGAAAGTACACAAGGAGAATGGAAC 59.002 40.000 0.00 0.00 0.00 3.62
2516 2683 5.947228 TCCTGAACTTTATTCACAAGCAG 57.053 39.130 0.00 0.00 0.00 4.24
2544 2711 9.490663 GAAATCTTGAACATTTATACTTGACGG 57.509 33.333 0.00 0.00 0.00 4.79
2556 2723 7.795047 AGAAAAACCCAGAAATCTTGAACATT 58.205 30.769 0.00 0.00 0.00 2.71
2618 2785 4.300189 TGACCAACACAAACAAGCATAC 57.700 40.909 0.00 0.00 0.00 2.39
2640 2808 1.878953 AATGACTCGAAAGCAACCGT 58.121 45.000 0.00 0.00 0.00 4.83
2747 2915 8.567948 CAAATGAACTGGTAGATGTTGTTAAGT 58.432 33.333 0.00 0.00 0.00 2.24
2780 2948 9.612620 GTTGGAAAGAAATATGTCTGTAAACTG 57.387 33.333 0.00 0.00 0.00 3.16
2792 2960 7.255242 CCGCACATAGATGTTGGAAAGAAATAT 60.255 37.037 5.18 0.00 39.39 1.28
2892 3063 9.929180 TTACCAACATATCTGATGTAAGCTATC 57.071 33.333 0.00 0.00 0.00 2.08
2922 3093 3.569277 TGATTGACAACAGACACCATTGG 59.431 43.478 0.00 0.00 0.00 3.16
2935 3106 8.918202 AGTTGTAATAGGACTTTGATTGACAA 57.082 30.769 0.00 0.00 36.65 3.18
3165 3336 3.638160 ACTTTAGGTCCAACGTAGACACA 59.362 43.478 17.52 4.71 35.89 3.72
3277 3448 1.898574 ACGCTGAAGGTTGCAAGGG 60.899 57.895 0.00 0.00 0.00 3.95
3372 3543 8.989980 GCTACTTAACAGTACAGTTTTTCATCT 58.010 33.333 9.07 0.00 34.06 2.90
3531 3702 7.013750 GCCCCTTATAAGAAGAAAAGAGATTGG 59.986 40.741 14.28 1.41 0.00 3.16
3582 3753 2.945668 AGAAGTATGCGGAAATGAAGCC 59.054 45.455 0.00 0.00 0.00 4.35
3699 3870 6.747280 AGAAGTCACAATTGAAGTTTTGTTCG 59.253 34.615 13.59 0.00 33.93 3.95
3865 4401 1.154413 GTGACCAAACTGCATCGCG 60.154 57.895 0.00 0.00 0.00 5.87
3904 4440 9.167311 GACTAAAAGGATGTACATTTCACTGAT 57.833 33.333 10.30 2.84 31.11 2.90
3976 4512 3.728845 GCCACACACTTCTAGAAGACAA 58.271 45.455 33.94 0.00 40.79 3.18
3995 4531 6.636044 GTCTATAGAATGTACAGTAACACGCC 59.364 42.308 3.40 0.00 30.75 5.68
4040 4576 8.784043 CAAAGAAGTGTAAGCAAAATACCTACT 58.216 33.333 0.00 0.00 0.00 2.57
4112 4649 0.033504 TCTCCACGACTGGTCTTTGC 59.966 55.000 0.00 0.00 38.90 3.68
4128 4673 6.143438 CACTTTCAATGCAACAAGAACATCTC 59.857 38.462 0.00 0.00 0.00 2.75
4216 4761 2.933495 TGTACCTAGCTTACTGCACG 57.067 50.000 0.00 0.00 45.94 5.34
4231 4776 3.887621 TGCCACTCTACAGGATTGTAC 57.112 47.619 0.00 0.00 38.76 2.90
4239 4784 5.236047 GCTTCAAGATAATGCCACTCTACAG 59.764 44.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.