Multiple sequence alignment - TraesCS2D01G368300

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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 TraesCS2D01G368300 chr2D 100.000 3900 0 0 1 3900 472946619 472942720 0.000000e+00 7203.0
1 TraesCS2D01G368300 chr2D 91.228 57 5 0 3156 3212 464519430 464519486 1.160000e-10 78.7
2 TraesCS2D01G368300 chr2B 90.949 1834 117 26 2089 3900 552261606 552259800 0.000000e+00 2422.0
3 TraesCS2D01G368300 chr2B 86.361 1591 116 42 1 1531 552263664 552262115 0.000000e+00 1642.0
4 TraesCS2D01G368300 chr2B 89.860 286 24 3 1590 1872 552262105 552261822 2.860000e-96 363.0
5 TraesCS2D01G368300 chr2B 97.015 201 6 0 1891 2091 552261834 552261634 4.830000e-89 339.0
6 TraesCS2D01G368300 chr2B 91.667 60 3 2 3153 3212 230575161 230575218 8.980000e-12 82.4
7 TraesCS2D01G368300 chr2B 90.164 61 6 0 3152 3212 572788927 572788987 3.230000e-11 80.5
8 TraesCS2D01G368300 chr2A 88.928 1969 110 38 1 1872 614396689 614394732 0.000000e+00 2329.0
9 TraesCS2D01G368300 chr2A 92.371 1088 56 13 2089 3150 614394516 614393430 0.000000e+00 1524.0
10 TraesCS2D01G368300 chr2A 83.179 648 98 7 3258 3900 614393421 614392780 2.020000e-162 582.0
11 TraesCS2D01G368300 chr2A 98.010 201 4 0 1891 2091 614394744 614394544 2.230000e-92 350.0
12 TraesCS2D01G368300 chr7D 90.411 73 6 1 3167 3238 626281069 626281141 1.150000e-15 95.3
13 TraesCS2D01G368300 chr7D 90.476 63 3 1 2570 2632 412016519 412016460 3.230000e-11 80.5
14 TraesCS2D01G368300 chr7B 94.737 57 3 0 3156 3212 351645438 351645494 5.370000e-14 89.8
15 TraesCS2D01G368300 chr3D 88.000 75 9 0 3167 3241 537914058 537914132 5.370000e-14 89.8
16 TraesCS2D01G368300 chr3D 92.857 56 4 0 2581 2636 477910604 477910549 8.980000e-12 82.4
17 TraesCS2D01G368300 chr6D 98.000 50 1 0 2581 2630 317078830 317078781 1.930000e-13 87.9
18 TraesCS2D01G368300 chr6D 97.917 48 1 0 2581 2628 90111211 90111258 2.500000e-12 84.2
19 TraesCS2D01G368300 chr5D 97.959 49 1 0 2581 2629 257131643 257131691 6.940000e-13 86.1
20 TraesCS2D01G368300 chr5A 88.571 70 5 2 2569 2635 55022481 55022412 8.980000e-12 82.4
21 TraesCS2D01G368300 chr4A 92.857 56 3 1 2581 2635 581333669 581333724 3.230000e-11 80.5
22 TraesCS2D01G368300 chr6B 87.143 70 8 1 3156 3225 454560004 454559936 1.160000e-10 78.7
23 TraesCS2D01G368300 chr4B 89.831 59 6 0 3154 3212 642167176 642167118 4.180000e-10 76.8


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 TraesCS2D01G368300 chr2D 472942720 472946619 3899 True 7203.00 7203 100.00000 1 3900 1 chr2D.!!$R1 3899
1 TraesCS2D01G368300 chr2B 552259800 552263664 3864 True 1191.50 2422 91.04625 1 3900 4 chr2B.!!$R1 3899
2 TraesCS2D01G368300 chr2A 614392780 614396689 3909 True 1196.25 2329 90.62200 1 3900 4 chr2A.!!$R1 3899

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
903 999 0.167033 CTCGGATCGGATCTACAGCG 59.833 60.000 16.96 11.61 0.00 5.18 F
1188 1317 0.159763 GCGCAATATTCTCGAGTCGC 59.840 55.000 13.13 12.46 34.61 5.19 F
1204 1333 0.306533 TCGCTTGTGGTTTCGCTTTC 59.693 50.000 0.00 0.00 0.00 2.62 F
1560 1695 1.202463 CCACGTGCTGCTAGAAGCTAT 60.202 52.381 23.50 6.21 42.97 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 2024 0.470766 AGTCAAGTTACACCCCGCAA 59.529 50.000 0.0 0.0 0.0 4.85 R
1998 2140 1.126948 TGCCACCATCACTGTCCAGA 61.127 55.000 0.4 0.0 0.0 3.86 R
2780 3004 2.544721 TGAGATCAGAAGGACCAGCTT 58.455 47.619 0.0 0.0 0.0 3.74 R
3271 3510 1.035385 CCCCCGGCCTTTGTATCAAC 61.035 60.000 0.0 0.0 0.0 3.18 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
362 420 2.359531 CCGGCAAACCAGTAAGAAAACA 59.640 45.455 0.00 0.00 34.57 2.83
408 476 1.612676 AGGAACCTTGTAAAACCGGC 58.387 50.000 0.00 0.00 0.00 6.13
447 515 0.808755 GATTTATAATGGGCCGGCCG 59.191 55.000 38.22 21.04 36.85 6.13
617 689 4.662961 TGACAGACTGGGCGCGTG 62.663 66.667 8.43 0.00 0.00 5.34
638 710 4.824515 CCCGTCCTCTCGCTCCCT 62.825 72.222 0.00 0.00 0.00 4.20
749 826 2.418746 CGCAGTACTTGACCTGCCTTAT 60.419 50.000 6.10 0.00 39.42 1.73
763 840 3.150848 GCCTTATACAAGTTGGCAAGC 57.849 47.619 7.96 0.00 42.79 4.01
787 864 1.618876 TATGCCCTACCACACACCGG 61.619 60.000 0.00 0.00 0.00 5.28
797 893 2.144078 ACACACCGGGTCCATGTGA 61.144 57.895 24.26 0.00 45.34 3.58
798 894 1.299648 CACACCGGGTCCATGTGAT 59.700 57.895 15.17 0.02 45.34 3.06
799 895 1.026182 CACACCGGGTCCATGTGATG 61.026 60.000 15.17 0.00 45.34 3.07
800 896 2.114670 CACCGGGTCCATGTGATGC 61.115 63.158 6.32 0.00 31.66 3.91
801 897 2.896854 CCGGGTCCATGTGATGCG 60.897 66.667 0.00 0.00 0.00 4.73
802 898 2.186644 CGGGTCCATGTGATGCGA 59.813 61.111 0.00 0.00 0.00 5.10
803 899 2.173669 CGGGTCCATGTGATGCGAC 61.174 63.158 0.00 0.00 32.91 5.19
804 900 2.173669 GGGTCCATGTGATGCGACG 61.174 63.158 0.00 0.00 33.83 5.12
805 901 1.447838 GGTCCATGTGATGCGACGT 60.448 57.895 0.00 0.00 33.83 4.34
806 902 1.695893 GGTCCATGTGATGCGACGTG 61.696 60.000 0.00 0.00 33.83 4.49
807 903 3.092403 CCATGTGATGCGACGTGG 58.908 61.111 0.00 7.07 44.63 4.94
808 904 2.463620 CCATGTGATGCGACGTGGG 61.464 63.158 11.88 0.00 45.76 4.61
809 905 2.125147 ATGTGATGCGACGTGGGG 60.125 61.111 0.00 0.00 0.00 4.96
810 906 3.680620 ATGTGATGCGACGTGGGGG 62.681 63.158 0.00 0.00 0.00 5.40
811 907 4.077184 GTGATGCGACGTGGGGGA 62.077 66.667 0.00 0.00 0.00 4.81
812 908 3.770040 TGATGCGACGTGGGGGAG 61.770 66.667 0.00 0.00 0.00 4.30
813 909 4.530857 GATGCGACGTGGGGGAGG 62.531 72.222 0.00 0.00 0.00 4.30
903 999 0.167033 CTCGGATCGGATCTACAGCG 59.833 60.000 16.96 11.61 0.00 5.18
1087 1192 1.112113 TAAGCTACCTTCGGCCTCTG 58.888 55.000 0.00 0.00 32.47 3.35
1088 1193 0.614979 AAGCTACCTTCGGCCTCTGA 60.615 55.000 0.00 0.00 0.00 3.27
1152 1281 1.227380 GTAGCTCGGTGATGGCCTG 60.227 63.158 3.32 0.00 0.00 4.85
1188 1317 0.159763 GCGCAATATTCTCGAGTCGC 59.840 55.000 13.13 12.46 34.61 5.19
1194 1323 2.561733 TATTCTCGAGTCGCTTGTGG 57.438 50.000 13.13 0.00 0.00 4.17
1204 1333 0.306533 TCGCTTGTGGTTTCGCTTTC 59.693 50.000 0.00 0.00 0.00 2.62
1367 1496 9.827411 AAATCTCTTCGTTAGCTTACAAATTTC 57.173 29.630 3.47 0.00 0.00 2.17
1434 1563 5.806286 TCAATTTATCGATCAACGCTTTCC 58.194 37.500 0.00 0.00 42.26 3.13
1451 1580 5.565045 CGCTTTCCTTCACTAGTAGTGTTCT 60.565 44.000 25.83 0.00 46.03 3.01
1458 1587 6.800892 CCTTCACTAGTAGTGTTCTAAACGAC 59.199 42.308 25.83 0.00 46.03 4.34
1466 1598 8.739649 AGTAGTGTTCTAAACGACATCTTAAC 57.260 34.615 0.00 0.00 0.00 2.01
1560 1695 1.202463 CCACGTGCTGCTAGAAGCTAT 60.202 52.381 23.50 6.21 42.97 2.97
1666 1801 7.946655 TCATAATAAGAACGCAGATCGATTT 57.053 32.000 0.00 0.00 41.67 2.17
1712 1851 7.011773 GCTAAAAGCACGTTAAGTAGTTAACC 58.988 38.462 21.95 11.78 41.74 2.85
1730 1869 3.398318 ACCCATCTTATTTTCCCACCC 57.602 47.619 0.00 0.00 0.00 4.61
1742 1881 1.817941 CCCACCCCGTTTGCGATAG 60.818 63.158 0.00 0.00 41.33 2.08
1759 1898 2.862674 TAGGCCGAATCAACCGTGGC 62.863 60.000 0.00 0.00 44.98 5.01
1869 2011 8.035394 TGACTTCCTTATGAGATGTAACTTGAC 58.965 37.037 0.00 0.00 0.00 3.18
1870 2012 8.140112 ACTTCCTTATGAGATGTAACTTGACT 57.860 34.615 0.00 0.00 0.00 3.41
1871 2013 8.598041 ACTTCCTTATGAGATGTAACTTGACTT 58.402 33.333 0.00 0.00 0.00 3.01
1898 2040 2.873133 TTTTTGCGGGGTGTAACTTG 57.127 45.000 0.00 0.00 36.74 3.16
1899 2041 2.054232 TTTTGCGGGGTGTAACTTGA 57.946 45.000 0.00 0.00 36.74 3.02
2153 2355 4.486125 AAAACTGGCTCAAATGTTTGGT 57.514 36.364 5.71 0.00 38.66 3.67
2165 2367 7.517259 GCTCAAATGTTTGGTGAAATCTGTTTC 60.517 37.037 5.71 0.00 40.03 2.78
2202 2404 2.009051 TGCATTTCGATTGATGTCGCT 58.991 42.857 0.37 0.00 41.22 4.93
2221 2423 4.382728 CATCGCGGGATGCAAAAC 57.617 55.556 26.79 0.00 46.97 2.43
2253 2455 3.250280 GCAGATTGCATCATCCACTACAG 59.750 47.826 0.00 0.00 44.26 2.74
2459 2663 2.034685 CGTGTCCTCTGTTTCTCTGTGA 59.965 50.000 0.00 0.00 0.00 3.58
2469 2673 8.091449 CCTCTGTTTCTCTGTGACTAACTAAAT 58.909 37.037 0.00 0.00 0.00 1.40
2608 2820 3.034721 TCCGTTTGAGCGACAAGTAAT 57.965 42.857 0.00 0.00 39.77 1.89
2639 2851 4.452825 GAGGAAGTACCATCTTTTAGCCC 58.547 47.826 0.00 0.00 42.04 5.19
2651 2863 6.830838 CCATCTTTTAGCCCTTCAACTTCTAT 59.169 38.462 0.00 0.00 0.00 1.98
2653 2865 7.923414 TCTTTTAGCCCTTCAACTTCTATTC 57.077 36.000 0.00 0.00 0.00 1.75
2654 2866 7.458397 TCTTTTAGCCCTTCAACTTCTATTCA 58.542 34.615 0.00 0.00 0.00 2.57
2655 2867 7.942341 TCTTTTAGCCCTTCAACTTCTATTCAA 59.058 33.333 0.00 0.00 0.00 2.69
2656 2868 7.448748 TTTAGCCCTTCAACTTCTATTCAAC 57.551 36.000 0.00 0.00 0.00 3.18
2657 2869 5.248380 AGCCCTTCAACTTCTATTCAACT 57.752 39.130 0.00 0.00 0.00 3.16
2658 2870 5.635120 AGCCCTTCAACTTCTATTCAACTT 58.365 37.500 0.00 0.00 0.00 2.66
2659 2871 5.707764 AGCCCTTCAACTTCTATTCAACTTC 59.292 40.000 0.00 0.00 0.00 3.01
2660 2872 5.707764 GCCCTTCAACTTCTATTCAACTTCT 59.292 40.000 0.00 0.00 0.00 2.85
2661 2873 6.879458 GCCCTTCAACTTCTATTCAACTTCTA 59.121 38.462 0.00 0.00 0.00 2.10
2662 2874 7.065204 GCCCTTCAACTTCTATTCAACTTCTAG 59.935 40.741 0.00 0.00 0.00 2.43
2663 2875 8.097662 CCCTTCAACTTCTATTCAACTTCTAGT 58.902 37.037 0.00 0.00 0.00 2.57
2673 2888 9.909644 TCTATTCAACTTCTAGTTTGTGTAGAC 57.090 33.333 0.00 0.00 36.03 2.59
2675 2890 8.819643 ATTCAACTTCTAGTTTGTGTAGACTC 57.180 34.615 0.00 0.00 36.03 3.36
2680 2895 4.476297 TCTAGTTTGTGTAGACTCACCCA 58.524 43.478 0.00 0.00 37.51 4.51
2701 2917 5.248640 CCAGTCTTCTTTTATGCTCCTTCA 58.751 41.667 0.00 0.00 0.00 3.02
2780 3004 8.366401 TGCTTTCCATTTTTATGAAGATGAACA 58.634 29.630 2.65 0.00 30.93 3.18
2960 3187 3.256136 AGTCGTGTGCTAGAACTAAAGCT 59.744 43.478 1.64 0.00 39.53 3.74
2999 3226 4.625742 AGACTGTATTTGTCGTTGATTCCG 59.374 41.667 0.00 0.00 39.24 4.30
3102 3329 5.431765 CACTTGTATGAAGTATGAGCCCTT 58.568 41.667 0.00 0.00 0.00 3.95
3164 3392 8.210946 CCCCATTTCTTATGTAATACTCACTCA 58.789 37.037 0.00 0.00 0.00 3.41
3165 3393 9.613428 CCCATTTCTTATGTAATACTCACTCAA 57.387 33.333 0.00 0.00 0.00 3.02
3191 3419 8.335532 TCCCAAAATAAGTGTCTCAACATTAG 57.664 34.615 0.00 0.00 37.81 1.73
3223 3462 9.220767 CTTTGTACTAAAGTTGAGGCTCTTATT 57.779 33.333 16.72 8.14 0.00 1.40
3225 3464 8.773404 TGTACTAAAGTTGAGGCTCTTATTTC 57.227 34.615 16.72 0.00 0.00 2.17
3226 3465 8.594550 TGTACTAAAGTTGAGGCTCTTATTTCT 58.405 33.333 16.72 2.47 0.00 2.52
3228 3467 7.680730 ACTAAAGTTGAGGCTCTTATTTCTGA 58.319 34.615 16.72 0.00 0.00 3.27
3271 3510 1.200716 GGTGATGGTTGTGTGCATCAG 59.799 52.381 0.00 0.00 35.11 2.90
3286 3525 2.223340 GCATCAGTTGATACAAAGGCCG 60.223 50.000 0.00 0.00 32.63 6.13
3287 3526 2.107950 TCAGTTGATACAAAGGCCGG 57.892 50.000 0.00 0.00 0.00 6.13
3352 3593 1.741706 TCTGTTACCTCGTCGATGGTC 59.258 52.381 16.42 7.34 37.74 4.02
3549 3791 3.379688 GGGCTCTGACATCCTTGATTTTC 59.620 47.826 0.00 0.00 0.00 2.29
3554 3796 6.349944 GCTCTGACATCCTTGATTTTCACAAT 60.350 38.462 0.00 0.00 0.00 2.71
3563 3805 8.592105 TCCTTGATTTTCACAATTTTGATCAC 57.408 30.769 0.00 0.00 0.00 3.06
3582 3824 0.992802 CGCTTTTCGTCTCTAGTGGC 59.007 55.000 0.00 0.00 0.00 5.01
3593 3835 4.620803 CGTCTCTAGTGGCAGTGGTTTTAT 60.621 45.833 4.76 0.00 0.00 1.40
3639 3881 3.554731 GCTTCAATAGTGGTACTAACGGC 59.445 47.826 0.00 0.00 33.89 5.68
3717 3962 1.977293 TTTGGGGTTGCCCTTGTTGC 61.977 55.000 4.02 0.00 44.66 4.17
3722 3967 1.227234 GTTGCCCTTGTTGCGCTTT 60.227 52.632 9.73 0.00 0.00 3.51
3736 3981 1.660333 GCGCTTTGAAAGTCGGAACTG 60.660 52.381 18.19 0.00 35.36 3.16
3752 3997 1.338107 ACTGTCGGGTTCTCATGTCA 58.662 50.000 0.00 0.00 0.00 3.58
3760 4005 1.677217 GGTTCTCATGTCAGTGCCTCC 60.677 57.143 0.00 0.00 0.00 4.30
3762 4007 0.611896 TCTCATGTCAGTGCCTCCGA 60.612 55.000 0.00 0.00 0.00 4.55
3787 4032 4.574892 AGCCTTTCTCTTCTTAGTTGCTC 58.425 43.478 0.00 0.00 0.00 4.26
3792 4037 6.412362 TTTCTCTTCTTAGTTGCTCAGTCT 57.588 37.500 0.00 0.00 0.00 3.24
3799 4044 0.605589 AGTTGCTCAGTCTAGCGCTT 59.394 50.000 18.68 0.00 45.85 4.68
3810 4055 0.372679 CTAGCGCTTCGTCGACACTA 59.627 55.000 18.68 5.92 0.00 2.74
3811 4056 0.095935 TAGCGCTTCGTCGACACTAC 59.904 55.000 18.68 0.85 0.00 2.73
3841 4086 2.324860 GTTTGGTATTGCCGACTTTGC 58.675 47.619 0.00 0.00 41.21 3.68
3878 4123 4.454728 TTGTTGACTGCTTGCTTTTTCT 57.545 36.364 0.00 0.00 0.00 2.52
3889 4134 5.081394 GCTTGCTTTTTCTGTTTTTGTGTG 58.919 37.500 0.00 0.00 0.00 3.82
3890 4135 5.334028 GCTTGCTTTTTCTGTTTTTGTGTGT 60.334 36.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
379 447 2.501261 ACAAGGTTCCTAAGCGGTTTC 58.499 47.619 4.64 0.00 0.00 2.78
408 476 1.301677 GAGCGAGAAAACTGCCAGGG 61.302 60.000 0.00 0.00 0.00 4.45
447 515 1.304713 TCACTAGGGACCGTGGACC 60.305 63.158 4.37 0.00 32.27 4.46
617 689 3.418744 GAGCGAGAGGACGGGCTTC 62.419 68.421 0.00 0.00 35.54 3.86
638 710 1.877637 CCGTGCCGATTGGATGATTA 58.122 50.000 1.98 0.00 37.49 1.75
763 840 0.179045 GTGTGGTAGGGCATAGGCAG 60.179 60.000 0.15 0.00 43.71 4.85
787 864 1.447838 ACGTCGCATCACATGGACC 60.448 57.895 0.00 0.00 31.18 4.46
796 892 4.530857 CCTCCCCCACGTCGCATC 62.531 72.222 0.00 0.00 0.00 3.91
808 904 4.516195 GTCTTCCTCGCGCCTCCC 62.516 72.222 0.00 0.00 0.00 4.30
809 905 4.856607 CGTCTTCCTCGCGCCTCC 62.857 72.222 0.00 0.00 0.00 4.30
1043 1148 0.450983 GTAGTCGGTGTTCTCGAGGG 59.549 60.000 13.56 0.00 37.31 4.30
1188 1317 1.758783 GCAGAAAGCGAAACCACAAG 58.241 50.000 0.00 0.00 0.00 3.16
1204 1333 2.224475 CCCATCCATTAGAGACCAGCAG 60.224 54.545 0.00 0.00 0.00 4.24
1451 1580 8.969121 TTTCACTATCGTTAAGATGTCGTTTA 57.031 30.769 0.00 0.00 40.40 2.01
1458 1587 7.169982 GGACCAGATTTCACTATCGTTAAGATG 59.830 40.741 0.00 0.00 40.40 2.90
1466 1598 4.568359 CACAAGGACCAGATTTCACTATCG 59.432 45.833 0.00 0.00 0.00 2.92
1531 1665 1.448540 CAGCACGTGGAAGCTAGGG 60.449 63.158 18.88 0.00 39.50 3.53
1537 1671 1.354040 CTTCTAGCAGCACGTGGAAG 58.646 55.000 18.88 15.47 0.00 3.46
1587 1722 4.083324 AGACATTACTGACATGGCAAAACG 60.083 41.667 1.11 0.00 31.22 3.60
1712 1851 2.306847 CGGGGTGGGAAAATAAGATGG 58.693 52.381 0.00 0.00 0.00 3.51
1730 1869 1.157870 ATTCGGCCTATCGCAAACGG 61.158 55.000 0.00 0.00 40.31 4.44
1742 1881 3.810896 GCCACGGTTGATTCGGCC 61.811 66.667 0.00 0.00 36.73 6.13
1776 1918 9.132521 CTTTTAACATGTCTTGATGAATTCCAC 57.867 33.333 0.00 0.00 0.00 4.02
1879 2021 2.099427 GTCAAGTTACACCCCGCAAAAA 59.901 45.455 0.00 0.00 0.00 1.94
1880 2022 1.677052 GTCAAGTTACACCCCGCAAAA 59.323 47.619 0.00 0.00 0.00 2.44
1881 2023 1.134037 AGTCAAGTTACACCCCGCAAA 60.134 47.619 0.00 0.00 0.00 3.68
1882 2024 0.470766 AGTCAAGTTACACCCCGCAA 59.529 50.000 0.00 0.00 0.00 4.85
1883 2025 0.470766 AAGTCAAGTTACACCCCGCA 59.529 50.000 0.00 0.00 0.00 5.69
1884 2026 1.154197 GAAGTCAAGTTACACCCCGC 58.846 55.000 0.00 0.00 0.00 6.13
1885 2027 2.140717 GTGAAGTCAAGTTACACCCCG 58.859 52.381 0.00 0.00 0.00 5.73
1886 2028 3.400255 GAGTGAAGTCAAGTTACACCCC 58.600 50.000 0.00 0.00 32.76 4.95
1887 2029 3.057734 CGAGTGAAGTCAAGTTACACCC 58.942 50.000 0.00 0.00 32.76 4.61
1888 2030 3.973657 TCGAGTGAAGTCAAGTTACACC 58.026 45.455 0.00 0.00 32.76 4.16
1889 2031 4.143305 GCATCGAGTGAAGTCAAGTTACAC 60.143 45.833 0.00 0.00 0.00 2.90
1890 2032 3.987868 GCATCGAGTGAAGTCAAGTTACA 59.012 43.478 0.00 0.00 0.00 2.41
1891 2033 3.987868 TGCATCGAGTGAAGTCAAGTTAC 59.012 43.478 0.00 0.00 0.00 2.50
1892 2034 4.251543 TGCATCGAGTGAAGTCAAGTTA 57.748 40.909 0.00 0.00 0.00 2.24
1893 2035 3.111853 TGCATCGAGTGAAGTCAAGTT 57.888 42.857 0.00 0.00 0.00 2.66
1894 2036 2.820059 TGCATCGAGTGAAGTCAAGT 57.180 45.000 0.00 0.00 0.00 3.16
1895 2037 2.222976 GCATGCATCGAGTGAAGTCAAG 60.223 50.000 14.21 0.00 0.00 3.02
1896 2038 1.733912 GCATGCATCGAGTGAAGTCAA 59.266 47.619 14.21 0.00 0.00 3.18
1897 2039 1.338011 TGCATGCATCGAGTGAAGTCA 60.338 47.619 18.46 0.00 0.00 3.41
1898 2040 1.326852 CTGCATGCATCGAGTGAAGTC 59.673 52.381 22.97 0.00 0.00 3.01
1899 2041 1.366679 CTGCATGCATCGAGTGAAGT 58.633 50.000 22.97 0.00 0.00 3.01
1998 2140 1.126948 TGCCACCATCACTGTCCAGA 61.127 55.000 0.40 0.00 0.00 3.86
2253 2455 4.637534 TCCTGCAAGAATCAAATACTCAGC 59.362 41.667 0.00 0.00 34.07 4.26
2469 2673 7.496747 TGCATATACAGTTACTAATGCAGACA 58.503 34.615 15.13 0.23 43.32 3.41
2608 2820 3.605726 TGGTACTTCCTCCGATCCATA 57.394 47.619 0.00 0.00 37.07 2.74
2651 2863 7.705325 GTGAGTCTACACAAACTAGAAGTTGAA 59.295 37.037 0.00 0.00 38.66 2.69
2653 2865 6.421202 GGTGAGTCTACACAAACTAGAAGTTG 59.579 42.308 0.00 0.29 41.88 3.16
2654 2866 6.462628 GGGTGAGTCTACACAAACTAGAAGTT 60.463 42.308 0.00 0.00 41.88 2.66
2655 2867 5.010820 GGGTGAGTCTACACAAACTAGAAGT 59.989 44.000 0.00 0.00 41.88 3.01
2656 2868 5.010719 TGGGTGAGTCTACACAAACTAGAAG 59.989 44.000 0.00 0.00 41.88 2.85
2657 2869 4.897076 TGGGTGAGTCTACACAAACTAGAA 59.103 41.667 0.00 0.00 41.88 2.10
2658 2870 4.476297 TGGGTGAGTCTACACAAACTAGA 58.524 43.478 0.00 0.00 41.88 2.43
2659 2871 4.281182 ACTGGGTGAGTCTACACAAACTAG 59.719 45.833 0.00 0.00 41.88 2.57
2660 2872 4.220724 ACTGGGTGAGTCTACACAAACTA 58.779 43.478 0.00 0.00 41.88 2.24
2661 2873 3.039011 ACTGGGTGAGTCTACACAAACT 58.961 45.455 0.00 0.00 41.88 2.66
2662 2874 3.391049 GACTGGGTGAGTCTACACAAAC 58.609 50.000 0.00 0.00 46.85 2.93
2663 2875 3.746045 GACTGGGTGAGTCTACACAAA 57.254 47.619 0.00 0.00 46.85 2.83
2673 2888 4.583871 AGCATAAAAGAAGACTGGGTGAG 58.416 43.478 0.00 0.00 0.00 3.51
2675 2890 3.691609 GGAGCATAAAAGAAGACTGGGTG 59.308 47.826 0.00 0.00 0.00 4.61
2680 2895 6.944862 ACATTGAAGGAGCATAAAAGAAGACT 59.055 34.615 0.00 0.00 0.00 3.24
2780 3004 2.544721 TGAGATCAGAAGGACCAGCTT 58.455 47.619 0.00 0.00 0.00 3.74
3102 3329 7.990917 TGCAACTCAGTTTAGTGACATTAAAA 58.009 30.769 4.86 0.00 0.00 1.52
3164 3392 7.781324 ATGTTGAGACACTTATTTTGGGATT 57.219 32.000 0.00 0.00 38.91 3.01
3165 3393 7.781324 AATGTTGAGACACTTATTTTGGGAT 57.219 32.000 0.00 0.00 38.91 3.85
3206 3445 6.207614 GGTTCAGAAATAAGAGCCTCAACTTT 59.792 38.462 0.00 0.00 32.98 2.66
3217 3456 4.094476 ACTCCCTCGGTTCAGAAATAAGA 58.906 43.478 0.00 0.00 0.00 2.10
3223 3462 2.599408 AGTACTCCCTCGGTTCAGAA 57.401 50.000 0.00 0.00 0.00 3.02
3225 3464 3.118334 TCTCTAGTACTCCCTCGGTTCAG 60.118 52.174 0.00 0.00 0.00 3.02
3226 3465 2.842496 TCTCTAGTACTCCCTCGGTTCA 59.158 50.000 0.00 0.00 0.00 3.18
3228 3467 3.266513 AGTTCTCTAGTACTCCCTCGGTT 59.733 47.826 0.00 0.00 0.00 4.44
3271 3510 1.035385 CCCCCGGCCTTTGTATCAAC 61.035 60.000 0.00 0.00 0.00 3.18
3331 3572 2.358267 GACCATCGACGAGGTAACAGAT 59.642 50.000 15.86 0.00 38.50 2.90
3338 3579 1.321074 GGAAGGACCATCGACGAGGT 61.321 60.000 15.83 15.83 41.83 3.85
3339 3580 1.038130 AGGAAGGACCATCGACGAGG 61.038 60.000 3.01 2.39 42.04 4.63
3383 3624 1.118965 TTTCGTCCTCACCTGCTGGA 61.119 55.000 17.64 0.00 37.04 3.86
3398 3639 4.840271 AGGGTTGTTATAAGAGGGTTTCG 58.160 43.478 0.00 0.00 0.00 3.46
3509 3751 1.559065 CCCCCTAACTCTTTCGCCCA 61.559 60.000 0.00 0.00 0.00 5.36
3529 3771 4.456911 TGTGAAAATCAAGGATGTCAGAGC 59.543 41.667 0.00 0.00 0.00 4.09
3549 3791 4.922064 CGAAAAGCGTGATCAAAATTGTG 58.078 39.130 0.00 0.00 34.64 3.33
3582 3824 2.744202 AGCTCGCTCAATAAAACCACTG 59.256 45.455 0.00 0.00 0.00 3.66
3593 3835 1.618837 ACTAGGTTGAAGCTCGCTCAA 59.381 47.619 0.00 0.00 0.00 3.02
3639 3881 8.607459 CATTCTCACAATAGTACCAGCTTTAAG 58.393 37.037 0.00 0.00 0.00 1.85
3655 3897 5.491070 CCAACATAGAGGTCATTCTCACAA 58.509 41.667 0.00 0.00 36.30 3.33
3686 3928 3.682696 CAACCCCAAACTACTAGGTTCC 58.317 50.000 0.00 0.00 38.76 3.62
3717 3962 1.597663 ACAGTTCCGACTTTCAAAGCG 59.402 47.619 0.00 2.10 32.54 4.68
3722 3967 0.032952 CCCGACAGTTCCGACTTTCA 59.967 55.000 0.00 0.00 33.18 2.69
3736 3981 1.714794 CACTGACATGAGAACCCGAC 58.285 55.000 0.00 0.00 0.00 4.79
3787 4032 0.858135 GTCGACGAAGCGCTAGACTG 60.858 60.000 12.05 0.67 0.00 3.51
3792 4037 0.095935 GTAGTGTCGACGAAGCGCTA 59.904 55.000 12.05 1.67 0.00 4.26
3799 4044 3.117794 CAAAACTTGGTAGTGTCGACGA 58.882 45.455 11.62 0.00 34.01 4.20
3841 4086 4.081406 TCAACAAACCCAGATCCAGAATG 58.919 43.478 0.00 0.00 0.00 2.67
3878 4123 2.685897 GGAGCTACCACACACAAAAACA 59.314 45.455 0.00 0.00 38.79 2.83


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

AutoCloner maintained by Alex Coulton.