Multiple sequence alignment - TraesCS1D01G093100

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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 TraesCS1D01G093100 chr1D 100.000 3557 0 0 1 3557 79093236 79096792 0.000000e+00 6569
1 TraesCS1D01G093100 chr1A 91.388 3321 213 30 256 3540 96362890 96359607 0.000000e+00 4481
2 TraesCS1D01G093100 chr1B 91.837 2597 153 15 982 3557 130000921 130003479 0.000000e+00 3567
3 TraesCS1D01G093100 chr6B 81.633 588 102 6 41 625 713873891 713874475 1.920000e-132 483
4 TraesCS1D01G093100 chr5D 80.134 599 111 7 40 637 305849157 305849748 1.170000e-119 440
5 TraesCS1D01G093100 chr5D 77.928 666 137 8 51 711 480971533 480970873 1.190000e-109 407
6 TraesCS1D01G093100 chr5D 82.857 280 41 6 438 714 454020411 454020686 9.860000e-61 244
7 TraesCS1D01G093100 chr3B 76.651 651 132 18 51 689 665477740 665477098 3.400000e-90 342
8 TraesCS1D01G093100 chrUn 75.740 676 149 15 46 717 396395327 396395991 3.420000e-85 326
9 TraesCS1D01G093100 chr3A 75.740 676 149 15 46 717 738427335 738427999 3.420000e-85 326
10 TraesCS1D01G093100 chr3A 75.740 676 149 15 46 717 738613401 738614065 3.420000e-85 326
11 TraesCS1D01G093100 chr7B 75.873 315 67 5 51 363 102668880 102668573 6.150000e-33 152
12 TraesCS1D01G093100 chr6A 83.036 112 19 0 51 162 97722067 97721956 6.280000e-18 102


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 TraesCS1D01G093100 chr1D 79093236 79096792 3556 False 6569 6569 100.000 1 3557 1 chr1D.!!$F1 3556
1 TraesCS1D01G093100 chr1A 96359607 96362890 3283 True 4481 4481 91.388 256 3540 1 chr1A.!!$R1 3284
2 TraesCS1D01G093100 chr1B 130000921 130003479 2558 False 3567 3567 91.837 982 3557 1 chr1B.!!$F1 2575
3 TraesCS1D01G093100 chr6B 713873891 713874475 584 False 483 483 81.633 41 625 1 chr6B.!!$F1 584
4 TraesCS1D01G093100 chr5D 305849157 305849748 591 False 440 440 80.134 40 637 1 chr5D.!!$F1 597
5 TraesCS1D01G093100 chr5D 480970873 480971533 660 True 407 407 77.928 51 711 1 chr5D.!!$R1 660
6 TraesCS1D01G093100 chr3B 665477098 665477740 642 True 342 342 76.651 51 689 1 chr3B.!!$R1 638
7 TraesCS1D01G093100 chrUn 396395327 396395991 664 False 326 326 75.740 46 717 1 chrUn.!!$F1 671
8 TraesCS1D01G093100 chr3A 738427335 738427999 664 False 326 326 75.740 46 717 1 chr3A.!!$F1 671
9 TraesCS1D01G093100 chr3A 738613401 738614065 664 False 326 326 75.740 46 717 1 chr3A.!!$F2 671

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
40 41 0.034337 GTCCTGAACCCGTACAAGCA 59.966 55.0 0.0 0.0 0.0 3.91 F
285 289 0.251519 ACTAGGACCCGGTTTCGACT 60.252 55.0 0.0 0.0 39.0 4.18 F
786 800 0.034337 CTTTGGGGAGGTCGTTCGAA 59.966 55.0 0.0 0.0 0.0 3.71 F
2130 2159 0.035056 ACAGCATAGTTGGTCTGGGC 60.035 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1718 0.171455 ACGAGACGACATTCCTCTGC 59.829 55.000 0.00 0.00 0.00 4.26 R
1866 1895 1.068610 GCGAAACCATGCACTTGCTTA 60.069 47.619 2.33 0.00 42.66 3.09 R
2305 2334 0.266152 ACACTAGGGCCTGGCTCTAT 59.734 55.000 27.68 15.27 41.11 1.98 R
3534 3584 0.970427 AAAGGTTTATGCCCTGGCGG 60.970 55.000 3.32 0.00 45.51 6.13 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
22 23 4.081322 AGATCACCAAACGGTACAAAGT 57.919 40.909 0.00 0.00 33.92 2.66
23 24 4.062991 AGATCACCAAACGGTACAAAGTC 58.937 43.478 0.00 0.00 33.92 3.01
24 25 2.563702 TCACCAAACGGTACAAAGTCC 58.436 47.619 0.00 0.00 33.92 3.85
25 26 2.171027 TCACCAAACGGTACAAAGTCCT 59.829 45.455 0.00 0.00 33.92 3.85
26 27 2.289547 CACCAAACGGTACAAAGTCCTG 59.710 50.000 0.00 0.00 33.92 3.86
27 28 2.171027 ACCAAACGGTACAAAGTCCTGA 59.829 45.455 0.00 0.00 33.92 3.86
28 29 3.207778 CCAAACGGTACAAAGTCCTGAA 58.792 45.455 0.00 0.00 0.00 3.02
29 30 3.002965 CCAAACGGTACAAAGTCCTGAAC 59.997 47.826 0.00 0.00 0.00 3.18
30 31 2.538512 ACGGTACAAAGTCCTGAACC 57.461 50.000 0.00 0.00 0.00 3.62
31 32 1.071228 ACGGTACAAAGTCCTGAACCC 59.929 52.381 0.00 0.00 0.00 4.11
32 33 1.804601 GGTACAAAGTCCTGAACCCG 58.195 55.000 0.00 0.00 0.00 5.28
33 34 1.071228 GGTACAAAGTCCTGAACCCGT 59.929 52.381 0.00 0.00 0.00 5.28
34 35 2.299867 GGTACAAAGTCCTGAACCCGTA 59.700 50.000 0.00 0.00 0.00 4.02
35 36 2.538512 ACAAAGTCCTGAACCCGTAC 57.461 50.000 0.00 0.00 0.00 3.67
36 37 1.764134 ACAAAGTCCTGAACCCGTACA 59.236 47.619 0.00 0.00 0.00 2.90
37 38 2.171027 ACAAAGTCCTGAACCCGTACAA 59.829 45.455 0.00 0.00 0.00 2.41
38 39 2.806244 CAAAGTCCTGAACCCGTACAAG 59.194 50.000 0.00 0.00 0.00 3.16
39 40 0.320697 AGTCCTGAACCCGTACAAGC 59.679 55.000 0.00 0.00 0.00 4.01
40 41 0.034337 GTCCTGAACCCGTACAAGCA 59.966 55.000 0.00 0.00 0.00 3.91
41 42 0.034337 TCCTGAACCCGTACAAGCAC 59.966 55.000 0.00 0.00 0.00 4.40
42 43 0.953960 CCTGAACCCGTACAAGCACC 60.954 60.000 0.00 0.00 0.00 5.01
43 44 0.953960 CTGAACCCGTACAAGCACCC 60.954 60.000 0.00 0.00 0.00 4.61
44 45 1.071814 GAACCCGTACAAGCACCCA 59.928 57.895 0.00 0.00 0.00 4.51
45 46 1.228033 AACCCGTACAAGCACCCAC 60.228 57.895 0.00 0.00 0.00 4.61
46 47 1.702022 AACCCGTACAAGCACCCACT 61.702 55.000 0.00 0.00 0.00 4.00
47 48 0.832983 ACCCGTACAAGCACCCACTA 60.833 55.000 0.00 0.00 0.00 2.74
48 49 0.322322 CCCGTACAAGCACCCACTAA 59.678 55.000 0.00 0.00 0.00 2.24
49 50 1.674817 CCCGTACAAGCACCCACTAAG 60.675 57.143 0.00 0.00 0.00 2.18
64 66 4.202367 CCCACTAAGACCTTGTGAAAGACT 60.202 45.833 11.28 0.00 33.95 3.24
66 68 4.681942 CACTAAGACCTTGTGAAAGACTCG 59.318 45.833 6.53 0.00 33.95 4.18
70 72 0.868406 CCTTGTGAAAGACTCGTGCC 59.132 55.000 0.00 0.00 0.00 5.01
85 88 2.290367 TCGTGCCACAAAAGAATCTGTG 59.710 45.455 0.00 0.00 42.14 3.66
131 134 3.220674 TCAACCACAACATCATCACCA 57.779 42.857 0.00 0.00 0.00 4.17
142 145 1.347062 TCATCACCACCACACTGCTA 58.653 50.000 0.00 0.00 0.00 3.49
145 148 1.055849 TCACCACCACACTGCTACAT 58.944 50.000 0.00 0.00 0.00 2.29
162 165 2.863809 ACATCTTTTCTTTGCTCCGGT 58.136 42.857 0.00 0.00 0.00 5.28
184 187 2.654863 CCAAAAGGACAAGGACACACT 58.345 47.619 0.00 0.00 0.00 3.55
186 189 4.204012 CCAAAAGGACAAGGACACACTTA 58.796 43.478 0.00 0.00 0.00 2.24
251 254 1.019278 GTATCGCCATATGTGCCCCG 61.019 60.000 1.24 0.00 0.00 5.73
273 277 4.678309 CGTTGGATGGAAGAGAACTAGGAC 60.678 50.000 0.00 0.00 0.00 3.85
285 289 0.251519 ACTAGGACCCGGTTTCGACT 60.252 55.000 0.00 0.00 39.00 4.18
331 337 1.366319 AAGCAGGACATCCCTTCAGT 58.634 50.000 0.00 0.00 44.85 3.41
349 358 5.772825 TCAGTAGCAGCACAAAGAAAAAT 57.227 34.783 0.00 0.00 0.00 1.82
355 364 3.985925 GCAGCACAAAGAAAAATGAGGAG 59.014 43.478 0.00 0.00 0.00 3.69
363 372 4.590850 AGAAAAATGAGGAGCAACAACC 57.409 40.909 0.00 0.00 0.00 3.77
379 388 1.067974 CAACCGTAGATCATACCGGCA 59.932 52.381 0.00 0.00 44.14 5.69
381 390 1.758280 ACCGTAGATCATACCGGCAAA 59.242 47.619 0.00 0.00 44.14 3.68
403 412 2.771372 GAGGAGGAAGAAGCTCCATCTT 59.229 50.000 0.00 0.00 39.76 2.40
424 433 2.382882 TGCAAAATCACCAACCACTCA 58.617 42.857 0.00 0.00 0.00 3.41
426 435 3.196469 TGCAAAATCACCAACCACTCAAA 59.804 39.130 0.00 0.00 0.00 2.69
450 459 3.625897 CCCAGCCAGTGTCGGTCA 61.626 66.667 0.00 0.00 0.00 4.02
460 469 0.608640 GTGTCGGTCAACCTCCAGAT 59.391 55.000 0.00 0.00 0.00 2.90
468 478 3.967987 GGTCAACCTCCAGATACCATAGT 59.032 47.826 0.00 0.00 0.00 2.12
482 492 0.172578 CATAGTCCGCGACCTCAACA 59.827 55.000 8.23 0.00 32.18 3.33
483 493 1.112113 ATAGTCCGCGACCTCAACAT 58.888 50.000 8.23 0.00 32.18 2.71
490 500 1.589630 CGACCTCAACATGACCCGA 59.410 57.895 0.00 0.00 0.00 5.14
567 578 3.203716 ACGAAGCCCGAGGAAATTTATC 58.796 45.455 2.99 0.00 41.76 1.75
580 591 2.961526 ATTTATCCAGACGCGACACT 57.038 45.000 15.93 6.23 0.00 3.55
584 595 1.313091 ATCCAGACGCGACACTGCTA 61.313 55.000 15.93 10.16 33.40 3.49
631 643 0.179119 CCCTAACCCTACTGCGAACG 60.179 60.000 0.00 0.00 0.00 3.95
735 747 0.594796 GCACAACACAAAAGGAGCCG 60.595 55.000 0.00 0.00 0.00 5.52
755 767 1.671379 GGTCGCCTCTTTTCGCCTT 60.671 57.895 0.00 0.00 0.00 4.35
763 777 3.009723 CCTCTTTTCGCCTTGCTAATCA 58.990 45.455 0.00 0.00 0.00 2.57
781 795 1.536662 AGCTCTTTGGGGAGGTCGT 60.537 57.895 0.00 0.00 39.48 4.34
785 799 0.828762 TCTTTGGGGAGGTCGTTCGA 60.829 55.000 0.00 0.00 0.00 3.71
786 800 0.034337 CTTTGGGGAGGTCGTTCGAA 59.966 55.000 0.00 0.00 0.00 3.71
787 801 0.469070 TTTGGGGAGGTCGTTCGAAA 59.531 50.000 0.00 0.00 0.00 3.46
791 819 1.338389 GGGGAGGTCGTTCGAAATTCA 60.338 52.381 0.00 0.00 0.00 2.57
838 866 9.905713 TTTGGAAGAATTAATCTAGTGTATGCT 57.094 29.630 0.00 0.00 37.42 3.79
839 867 9.547753 TTGGAAGAATTAATCTAGTGTATGCTC 57.452 33.333 0.00 0.00 37.42 4.26
840 868 8.928448 TGGAAGAATTAATCTAGTGTATGCTCT 58.072 33.333 0.00 0.00 37.42 4.09
841 869 9.418045 GGAAGAATTAATCTAGTGTATGCTCTC 57.582 37.037 0.00 0.00 37.42 3.20
842 870 9.418045 GAAGAATTAATCTAGTGTATGCTCTCC 57.582 37.037 0.00 0.00 37.42 3.71
843 871 8.719645 AGAATTAATCTAGTGTATGCTCTCCT 57.280 34.615 0.00 0.00 36.32 3.69
846 874 9.594936 AATTAATCTAGTGTATGCTCTCCTAGT 57.405 33.333 0.00 0.00 0.00 2.57
849 877 5.369833 TCTAGTGTATGCTCTCCTAGTGAC 58.630 45.833 0.00 0.00 0.00 3.67
851 879 4.605183 AGTGTATGCTCTCCTAGTGACTT 58.395 43.478 0.00 0.00 0.00 3.01
852 880 4.400884 AGTGTATGCTCTCCTAGTGACTTG 59.599 45.833 0.00 0.00 0.00 3.16
853 881 2.977772 ATGCTCTCCTAGTGACTTGC 57.022 50.000 0.00 0.00 0.00 4.01
854 882 1.632589 TGCTCTCCTAGTGACTTGCA 58.367 50.000 0.00 0.00 0.00 4.08
855 883 2.182827 TGCTCTCCTAGTGACTTGCAT 58.817 47.619 0.00 0.00 0.00 3.96
856 884 2.568956 TGCTCTCCTAGTGACTTGCATT 59.431 45.455 0.00 0.00 0.00 3.56
857 885 3.769300 TGCTCTCCTAGTGACTTGCATTA 59.231 43.478 0.00 0.00 0.00 1.90
858 886 4.222810 TGCTCTCCTAGTGACTTGCATTAA 59.777 41.667 0.00 0.00 0.00 1.40
859 887 5.104776 TGCTCTCCTAGTGACTTGCATTAAT 60.105 40.000 0.00 0.00 0.00 1.40
860 888 5.819901 GCTCTCCTAGTGACTTGCATTAATT 59.180 40.000 0.00 0.00 0.00 1.40
861 889 6.317391 GCTCTCCTAGTGACTTGCATTAATTT 59.683 38.462 0.00 0.00 0.00 1.82
862 890 7.495934 GCTCTCCTAGTGACTTGCATTAATTTA 59.504 37.037 0.00 0.00 0.00 1.40
863 891 8.948631 TCTCCTAGTGACTTGCATTAATTTAG 57.051 34.615 0.00 0.00 0.00 1.85
864 892 8.540388 TCTCCTAGTGACTTGCATTAATTTAGT 58.460 33.333 0.00 0.00 0.00 2.24
865 893 9.167311 CTCCTAGTGACTTGCATTAATTTAGTT 57.833 33.333 0.00 0.00 0.00 2.24
866 894 8.946085 TCCTAGTGACTTGCATTAATTTAGTTG 58.054 33.333 0.00 0.00 0.00 3.16
867 895 7.698130 CCTAGTGACTTGCATTAATTTAGTTGC 59.302 37.037 0.00 6.52 35.67 4.17
868 896 6.980593 AGTGACTTGCATTAATTTAGTTGCA 58.019 32.000 10.39 10.39 42.90 4.08
876 904 6.654161 TGCATTAATTTAGTTGCAAGCCAAAT 59.346 30.769 0.00 3.21 41.76 2.32
891 919 7.765360 TGCAAGCCAAATGAGAATTTATTTAGG 59.235 33.333 0.00 0.00 0.00 2.69
967 995 1.547372 CCTTTGCAGCCTAGCACATTT 59.453 47.619 0.00 0.00 45.61 2.32
991 1019 1.006102 CCCGTCAGTCAAACTCGCT 60.006 57.895 0.00 0.00 0.00 4.93
1086 1114 1.878656 CGCTCCCCGTCTTCAACTCT 61.879 60.000 0.00 0.00 0.00 3.24
1227 1255 1.690985 CTCCTTCCTCCCCCTCCAC 60.691 68.421 0.00 0.00 0.00 4.02
1228 1256 2.692741 CCTTCCTCCCCCTCCACC 60.693 72.222 0.00 0.00 0.00 4.61
1229 1257 2.692741 CTTCCTCCCCCTCCACCC 60.693 72.222 0.00 0.00 0.00 4.61
1230 1258 4.364686 TTCCTCCCCCTCCACCCC 62.365 72.222 0.00 0.00 0.00 4.95
1232 1260 4.825679 CCTCCCCCTCCACCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
1233 1261 4.825679 CTCCCCCTCCACCCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
1275 1303 3.068691 TCCCTCCACGCCTTCTCG 61.069 66.667 0.00 0.00 0.00 4.04
1566 1595 2.184579 GACGGTAGGGAGCTGCAC 59.815 66.667 7.79 0.00 0.00 4.57
1611 1640 3.861263 GGCGACGGCGATTTCCAC 61.861 66.667 18.90 0.00 41.24 4.02
1689 1718 0.804989 GGGTTTTCGACAGGATGCAG 59.195 55.000 0.00 0.00 42.53 4.41
1784 1813 1.606313 CTTTCCGGGCAATGTGGGT 60.606 57.895 0.00 0.00 0.00 4.51
1830 1859 1.008875 TCGCGTTGATCAGTGTGCTC 61.009 55.000 5.77 0.00 0.00 4.26
1866 1895 0.621571 TCATGGGCTTAGCAGAGGGT 60.622 55.000 6.53 0.00 0.00 4.34
2000 2029 3.342377 TTTCGATGATGGTACTTGGCA 57.658 42.857 0.00 0.00 0.00 4.92
2031 2060 2.512692 TCTCATGGGGTTCAATGGTG 57.487 50.000 0.00 0.00 0.00 4.17
2130 2159 0.035056 ACAGCATAGTTGGTCTGGGC 60.035 55.000 0.00 0.00 0.00 5.36
2175 2204 2.040412 AGGAATGGTGTTGAAGGGACTC 59.960 50.000 0.00 0.00 38.49 3.36
2382 2411 9.013490 CACAGTAACAAAGAAACTCAAGATTTG 57.987 33.333 0.00 0.00 37.00 2.32
2419 2448 6.865834 TTCTTAGATTGGAAGAAGAGAGCT 57.134 37.500 0.00 0.00 37.87 4.09
2635 2666 2.353839 CAGCGCACACAAACTGGC 60.354 61.111 11.47 0.00 0.00 4.85
2665 2696 3.130869 TGGAATCATTGGCATTGTACAGC 59.869 43.478 9.03 0.00 0.00 4.40
2675 2706 2.159476 GCATTGTACAGCACCACATCAG 60.159 50.000 2.40 0.00 0.00 2.90
2690 2721 4.229096 CACATCAGCACAAATTGTACCAC 58.771 43.478 0.00 0.00 0.00 4.16
2728 2759 3.020984 AGAGCTGCTGTACTTCCTCTAC 58.979 50.000 7.01 0.00 0.00 2.59
2729 2760 3.020984 GAGCTGCTGTACTTCCTCTACT 58.979 50.000 7.01 0.00 0.00 2.57
2743 2774 7.347252 ACTTCCTCTACTCTCATACATGTACA 58.653 38.462 7.96 0.00 0.00 2.90
2750 2781 7.998964 TCTACTCTCATACATGTACATTCAGGA 59.001 37.037 7.96 3.28 0.00 3.86
2770 2801 4.076394 GGAGGTGGTTATTACAGCAAACA 58.924 43.478 0.00 0.00 38.72 2.83
2923 2955 6.462347 GGTGCTTCCTTATTTTTCACCAGAAA 60.462 38.462 0.00 0.00 41.40 2.52
2925 2957 7.116805 GTGCTTCCTTATTTTTCACCAGAAATG 59.883 37.037 0.00 0.00 42.90 2.32
2928 2960 5.046663 TCCTTATTTTTCACCAGAAATGGGC 60.047 40.000 0.00 0.00 42.90 5.36
2980 3013 8.744568 ATGATTGAGTTCCTTTTTCTAGGATC 57.255 34.615 0.00 0.00 43.66 3.36
3210 3245 1.135859 CGACTGAAATGAGCTTGCACC 60.136 52.381 0.00 0.00 0.00 5.01
3254 3304 1.268079 GGGCTGAAGACTTGAGTTTGC 59.732 52.381 3.53 0.00 0.00 3.68
3316 3366 9.768662 AGTTTCTCTTGCACATTTATTCATTTT 57.231 25.926 0.00 0.00 0.00 1.82
3322 3372 9.844790 TCTTGCACATTTATTCATTTTGACTAG 57.155 29.630 0.00 0.00 0.00 2.57
3349 3399 4.055360 TGGACGACAACACAAGACATTAG 58.945 43.478 0.00 0.00 0.00 1.73
3384 3434 1.996187 GTTGGTCCCTCCTCCCTCC 60.996 68.421 0.00 0.00 37.07 4.30
3413 3463 2.417586 GGACCGGCTACACAATTGTAAC 59.582 50.000 11.53 0.89 37.77 2.50
3437 3487 8.863872 ACTGTTACCTTAAAACATCATAGCTT 57.136 30.769 0.00 0.00 36.33 3.74
3439 3489 8.050778 TGTTACCTTAAAACATCATAGCTTGG 57.949 34.615 0.00 0.00 32.07 3.61
3444 3494 7.672239 ACCTTAAAACATCATAGCTTGGGTTTA 59.328 33.333 0.00 0.00 34.38 2.01
3497 3547 2.356382 CTCTTAGCCGAGTCGAACTCAT 59.644 50.000 15.64 0.00 45.30 2.90
3503 3553 2.791567 CCGAGTCGAACTCATTGAGAG 58.208 52.381 20.33 10.63 45.30 3.20
3534 3584 3.779759 TCAATGACAAGTGTTTTGGTGC 58.220 40.909 7.70 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.841215 TCAGGACTTTGTACCGTTTGG 58.159 47.619 0.00 0.00 42.84 3.28
8 9 3.002965 GGTTCAGGACTTTGTACCGTTTG 59.997 47.826 0.00 0.00 30.42 2.93
9 10 3.208594 GGTTCAGGACTTTGTACCGTTT 58.791 45.455 0.00 0.00 30.42 3.60
10 11 2.486013 GGGTTCAGGACTTTGTACCGTT 60.486 50.000 0.00 0.00 38.85 4.44
11 12 1.071228 GGGTTCAGGACTTTGTACCGT 59.929 52.381 0.00 0.00 38.85 4.83
12 13 1.804601 GGGTTCAGGACTTTGTACCG 58.195 55.000 0.00 0.00 38.85 4.02
13 14 1.071228 ACGGGTTCAGGACTTTGTACC 59.929 52.381 0.00 0.00 37.67 3.34
14 15 2.538512 ACGGGTTCAGGACTTTGTAC 57.461 50.000 0.00 0.00 0.00 2.90
15 16 2.964464 TGTACGGGTTCAGGACTTTGTA 59.036 45.455 0.00 0.00 0.00 2.41
16 17 1.764134 TGTACGGGTTCAGGACTTTGT 59.236 47.619 0.00 0.00 0.00 2.83
17 18 2.536761 TGTACGGGTTCAGGACTTTG 57.463 50.000 0.00 0.00 0.00 2.77
18 19 2.809299 GCTTGTACGGGTTCAGGACTTT 60.809 50.000 0.00 0.00 0.00 2.66
19 20 1.270678 GCTTGTACGGGTTCAGGACTT 60.271 52.381 0.00 0.00 0.00 3.01
20 21 0.320697 GCTTGTACGGGTTCAGGACT 59.679 55.000 0.00 0.00 0.00 3.85
21 22 0.034337 TGCTTGTACGGGTTCAGGAC 59.966 55.000 0.00 0.00 0.00 3.85
22 23 0.034337 GTGCTTGTACGGGTTCAGGA 59.966 55.000 0.00 0.00 0.00 3.86
23 24 0.953960 GGTGCTTGTACGGGTTCAGG 60.954 60.000 0.00 0.00 0.00 3.86
24 25 0.953960 GGGTGCTTGTACGGGTTCAG 60.954 60.000 0.00 0.00 0.00 3.02
25 26 1.071814 GGGTGCTTGTACGGGTTCA 59.928 57.895 0.00 0.00 0.00 3.18
26 27 1.071814 TGGGTGCTTGTACGGGTTC 59.928 57.895 0.00 0.00 0.00 3.62
27 28 1.228033 GTGGGTGCTTGTACGGGTT 60.228 57.895 0.00 0.00 0.00 4.11
28 29 0.832983 TAGTGGGTGCTTGTACGGGT 60.833 55.000 0.00 0.00 0.00 5.28
29 30 0.322322 TTAGTGGGTGCTTGTACGGG 59.678 55.000 0.00 0.00 0.00 5.28
30 31 1.274167 TCTTAGTGGGTGCTTGTACGG 59.726 52.381 0.00 0.00 0.00 4.02
31 32 2.334838 GTCTTAGTGGGTGCTTGTACG 58.665 52.381 0.00 0.00 0.00 3.67
32 33 2.302157 AGGTCTTAGTGGGTGCTTGTAC 59.698 50.000 0.00 0.00 0.00 2.90
33 34 2.616524 AGGTCTTAGTGGGTGCTTGTA 58.383 47.619 0.00 0.00 0.00 2.41
34 35 1.435256 AGGTCTTAGTGGGTGCTTGT 58.565 50.000 0.00 0.00 0.00 3.16
35 36 2.154462 CAAGGTCTTAGTGGGTGCTTG 58.846 52.381 0.00 0.00 0.00 4.01
36 37 1.774856 ACAAGGTCTTAGTGGGTGCTT 59.225 47.619 0.00 0.00 0.00 3.91
37 38 1.072331 CACAAGGTCTTAGTGGGTGCT 59.928 52.381 0.00 0.00 0.00 4.40
38 39 1.071699 TCACAAGGTCTTAGTGGGTGC 59.928 52.381 10.81 0.00 34.17 5.01
39 40 3.485463 TTCACAAGGTCTTAGTGGGTG 57.515 47.619 10.81 0.00 34.17 4.61
40 41 3.714798 TCTTTCACAAGGTCTTAGTGGGT 59.285 43.478 10.81 0.00 34.17 4.51
41 42 4.065789 GTCTTTCACAAGGTCTTAGTGGG 58.934 47.826 10.81 0.00 34.17 4.61
42 43 4.962155 AGTCTTTCACAAGGTCTTAGTGG 58.038 43.478 10.81 0.00 34.17 4.00
43 44 4.681942 CGAGTCTTTCACAAGGTCTTAGTG 59.318 45.833 0.00 0.00 34.67 2.74
44 45 4.341520 ACGAGTCTTTCACAAGGTCTTAGT 59.658 41.667 0.00 0.00 0.00 2.24
45 46 4.681942 CACGAGTCTTTCACAAGGTCTTAG 59.318 45.833 0.00 0.00 0.00 2.18
46 47 4.617959 CACGAGTCTTTCACAAGGTCTTA 58.382 43.478 0.00 0.00 0.00 2.10
47 48 3.458189 CACGAGTCTTTCACAAGGTCTT 58.542 45.455 0.00 0.00 0.00 3.01
48 49 2.803492 GCACGAGTCTTTCACAAGGTCT 60.803 50.000 0.00 0.00 0.00 3.85
49 50 1.527311 GCACGAGTCTTTCACAAGGTC 59.473 52.381 0.00 0.00 0.00 3.85
64 66 2.290367 CACAGATTCTTTTGTGGCACGA 59.710 45.455 13.77 8.59 40.69 4.35
66 68 3.632189 GTCACAGATTCTTTTGTGGCAC 58.368 45.455 11.55 11.55 46.35 5.01
85 88 0.108585 TGTCTTGCTTGGGTCTGGTC 59.891 55.000 0.00 0.00 0.00 4.02
131 134 4.357918 AGAAAAGATGTAGCAGTGTGGT 57.642 40.909 0.00 0.00 0.00 4.16
142 145 2.554032 CACCGGAGCAAAGAAAAGATGT 59.446 45.455 9.46 0.00 0.00 3.06
145 148 0.951558 GCACCGGAGCAAAGAAAAGA 59.048 50.000 19.70 0.00 0.00 2.52
162 165 1.341482 TGTGTCCTTGTCCTTTTGGCA 60.341 47.619 0.00 0.00 40.12 4.92
184 187 1.477700 GCAGGCTTGTTGGATGCATAA 59.522 47.619 0.00 0.00 36.88 1.90
186 189 1.895238 GCAGGCTTGTTGGATGCAT 59.105 52.632 0.00 0.00 36.88 3.96
251 254 4.383226 GGTCCTAGTTCTCTTCCATCCAAC 60.383 50.000 0.00 0.00 0.00 3.77
331 337 4.826733 TCCTCATTTTTCTTTGTGCTGCTA 59.173 37.500 0.00 0.00 0.00 3.49
349 358 1.334160 TCTACGGTTGTTGCTCCTCA 58.666 50.000 0.00 0.00 0.00 3.86
355 364 2.538449 CGGTATGATCTACGGTTGTTGC 59.462 50.000 0.00 0.00 0.00 4.17
363 372 3.309388 CTCTTTGCCGGTATGATCTACG 58.691 50.000 1.90 0.00 0.00 3.51
403 412 2.762887 TGAGTGGTTGGTGATTTTGCAA 59.237 40.909 0.00 0.00 0.00 4.08
450 459 3.231818 CGGACTATGGTATCTGGAGGTT 58.768 50.000 0.00 0.00 0.00 3.50
460 469 0.107066 TGAGGTCGCGGACTATGGTA 60.107 55.000 6.13 0.00 32.47 3.25
468 478 1.080093 GTCATGTTGAGGTCGCGGA 60.080 57.895 6.13 0.00 0.00 5.54
482 492 1.004230 TTGGGGATCCTCGGGTCAT 59.996 57.895 12.58 0.00 0.00 3.06
483 493 1.993391 GTTGGGGATCCTCGGGTCA 60.993 63.158 12.58 0.00 0.00 4.02
490 500 4.760220 AGCGGGGTTGGGGATCCT 62.760 66.667 12.58 0.00 0.00 3.24
567 578 1.801913 GTAGCAGTGTCGCGTCTGG 60.802 63.158 21.81 7.61 36.85 3.86
580 591 2.671619 GCCAAGGCCGTTGTAGCA 60.672 61.111 0.00 0.00 33.87 3.49
598 609 2.810274 GGTTAGGGTTGAGGAAAACGTC 59.190 50.000 0.00 0.00 0.00 4.34
603 614 3.585732 CAGTAGGGTTAGGGTTGAGGAAA 59.414 47.826 0.00 0.00 0.00 3.13
631 643 1.067142 TCGGATCTGTGTGTAGGTTGC 60.067 52.381 0.42 0.00 0.00 4.17
637 649 1.822990 GGAACCTCGGATCTGTGTGTA 59.177 52.381 0.42 0.00 0.00 2.90
719 731 1.370414 CGCGGCTCCTTTTGTGTTG 60.370 57.895 0.00 0.00 0.00 3.33
735 747 4.148645 GCGAAAAGAGGCGACCGC 62.149 66.667 5.75 5.75 41.06 5.68
742 754 3.009723 TGATTAGCAAGGCGAAAAGAGG 58.990 45.455 0.00 0.00 0.00 3.69
763 777 1.128188 AACGACCTCCCCAAAGAGCT 61.128 55.000 0.00 0.00 32.17 4.09
765 779 0.389948 CGAACGACCTCCCCAAAGAG 60.390 60.000 0.00 0.00 0.00 2.85
772 786 2.000447 CTGAATTTCGAACGACCTCCC 59.000 52.381 0.00 0.00 0.00 4.30
781 795 7.213216 TCCATCAAAATGTCTGAATTTCGAA 57.787 32.000 0.00 0.00 0.00 3.71
785 799 9.617523 ACTTTTTCCATCAAAATGTCTGAATTT 57.382 25.926 0.00 0.00 37.66 1.82
786 800 9.617523 AACTTTTTCCATCAAAATGTCTGAATT 57.382 25.926 0.00 0.00 40.00 2.17
787 801 9.617523 AAACTTTTTCCATCAAAATGTCTGAAT 57.382 25.926 0.00 0.00 40.00 2.57
791 819 8.046107 TCCAAAACTTTTTCCATCAAAATGTCT 58.954 29.630 0.00 0.00 40.00 3.41
827 855 5.373222 AGTCACTAGGAGAGCATACACTAG 58.627 45.833 0.00 0.00 37.67 2.57
828 856 5.375283 AGTCACTAGGAGAGCATACACTA 57.625 43.478 0.00 0.00 0.00 2.74
833 861 3.365472 TGCAAGTCACTAGGAGAGCATA 58.635 45.455 0.00 0.00 0.00 3.14
838 866 8.540388 ACTAAATTAATGCAAGTCACTAGGAGA 58.460 33.333 0.00 0.00 0.00 3.71
839 867 8.723942 ACTAAATTAATGCAAGTCACTAGGAG 57.276 34.615 0.00 0.00 0.00 3.69
840 868 8.946085 CAACTAAATTAATGCAAGTCACTAGGA 58.054 33.333 0.00 0.00 0.00 2.94
841 869 7.698130 GCAACTAAATTAATGCAAGTCACTAGG 59.302 37.037 0.00 0.00 38.63 3.02
842 870 8.236586 TGCAACTAAATTAATGCAAGTCACTAG 58.763 33.333 9.72 0.00 45.04 2.57
843 871 8.105097 TGCAACTAAATTAATGCAAGTCACTA 57.895 30.769 9.72 0.00 45.04 2.74
851 879 5.144692 TGGCTTGCAACTAAATTAATGCA 57.855 34.783 8.48 8.48 46.21 3.96
852 880 6.479095 TTTGGCTTGCAACTAAATTAATGC 57.521 33.333 0.00 4.17 39.22 3.56
853 881 8.254178 TCATTTGGCTTGCAACTAAATTAATG 57.746 30.769 15.44 10.36 0.00 1.90
854 882 8.313292 TCTCATTTGGCTTGCAACTAAATTAAT 58.687 29.630 15.44 0.00 0.00 1.40
855 883 7.665690 TCTCATTTGGCTTGCAACTAAATTAA 58.334 30.769 15.44 9.49 0.00 1.40
856 884 7.225784 TCTCATTTGGCTTGCAACTAAATTA 57.774 32.000 15.44 10.27 0.00 1.40
857 885 6.100404 TCTCATTTGGCTTGCAACTAAATT 57.900 33.333 15.44 4.89 0.00 1.82
858 886 5.726980 TCTCATTTGGCTTGCAACTAAAT 57.273 34.783 13.54 13.54 0.00 1.40
859 887 5.528043 TTCTCATTTGGCTTGCAACTAAA 57.472 34.783 0.00 4.13 0.00 1.85
860 888 5.726980 ATTCTCATTTGGCTTGCAACTAA 57.273 34.783 0.00 0.00 0.00 2.24
861 889 5.726980 AATTCTCATTTGGCTTGCAACTA 57.273 34.783 0.00 0.00 0.00 2.24
862 890 4.612264 AATTCTCATTTGGCTTGCAACT 57.388 36.364 0.00 0.00 0.00 3.16
863 891 6.973229 ATAAATTCTCATTTGGCTTGCAAC 57.027 33.333 0.00 0.00 34.29 4.17
864 892 7.982761 AAATAAATTCTCATTTGGCTTGCAA 57.017 28.000 0.00 0.00 34.29 4.08
865 893 7.765360 CCTAAATAAATTCTCATTTGGCTTGCA 59.235 33.333 0.00 0.00 34.29 4.08
866 894 7.765819 ACCTAAATAAATTCTCATTTGGCTTGC 59.234 33.333 3.94 0.00 34.29 4.01
867 895 9.305925 GACCTAAATAAATTCTCATTTGGCTTG 57.694 33.333 3.94 0.00 34.29 4.01
868 896 9.259832 AGACCTAAATAAATTCTCATTTGGCTT 57.740 29.630 3.94 0.00 34.29 4.35
869 897 8.829373 AGACCTAAATAAATTCTCATTTGGCT 57.171 30.769 3.94 0.00 34.29 4.75
918 946 8.927721 GGTCTCTAAATTTGTTTGACTCTCTAC 58.072 37.037 0.00 0.00 0.00 2.59
951 979 1.619654 AACAAATGTGCTAGGCTGCA 58.380 45.000 0.50 1.92 41.05 4.41
958 986 1.268352 GACGGGCAAACAAATGTGCTA 59.732 47.619 0.00 0.00 40.70 3.49
967 995 3.176728 TTTGACTGACGGGCAAACA 57.823 47.368 11.44 0.00 46.84 2.83
1086 1114 2.441164 GCGAGGCTGGAGAGGAGA 60.441 66.667 0.00 0.00 0.00 3.71
1551 1580 2.185350 CAGTGCAGCTCCCTACCG 59.815 66.667 0.00 0.00 0.00 4.02
1554 1583 1.599047 GAAGCAGTGCAGCTCCCTA 59.401 57.895 19.20 0.00 45.89 3.53
1611 1640 2.954753 GACAAACCCGCTGCTGACG 61.955 63.158 0.00 0.00 0.00 4.35
1689 1718 0.171455 ACGAGACGACATTCCTCTGC 59.829 55.000 0.00 0.00 0.00 4.26
1758 1787 3.431725 GCCCGGAAAGCCTTCACG 61.432 66.667 0.73 0.00 32.75 4.35
1784 1813 1.557371 TCGGCAGAATACCATCAACCA 59.443 47.619 0.00 0.00 0.00 3.67
1866 1895 1.068610 GCGAAACCATGCACTTGCTTA 60.069 47.619 2.33 0.00 42.66 3.09
2000 2029 3.267812 ACCCCATGAGATGACATCTTTGT 59.732 43.478 18.89 5.97 40.38 2.83
2031 2060 1.410153 CCATGAAGGCCATAACCAAGC 59.590 52.381 5.01 0.00 33.31 4.01
2158 2187 1.276421 CTCGAGTCCCTTCAACACCAT 59.724 52.381 3.62 0.00 0.00 3.55
2175 2204 3.889538 TCACCAGGGAGTTGTATATCTCG 59.110 47.826 0.00 0.00 0.00 4.04
2305 2334 0.266152 ACACTAGGGCCTGGCTCTAT 59.734 55.000 27.68 15.27 41.11 1.98
2382 2411 2.234908 TCTAAGAAGAGACCTGCAAGCC 59.765 50.000 0.00 0.00 0.00 4.35
2419 2448 6.471233 AGATACCGAGACAAGATTTGATGA 57.529 37.500 0.00 0.00 0.00 2.92
2627 2658 2.408271 TCCAGAGCATAGCCAGTTTG 57.592 50.000 0.00 0.00 0.00 2.93
2635 2666 3.483421 TGCCAATGATTCCAGAGCATAG 58.517 45.455 0.00 0.00 0.00 2.23
2665 2696 3.374220 ACAATTTGTGCTGATGTGGTG 57.626 42.857 0.15 0.00 0.00 4.17
2675 2706 1.339610 TGCCAGTGGTACAATTTGTGC 59.660 47.619 11.74 10.54 44.16 4.57
2690 2721 2.161211 GCTCTGCTCTTTTAACTGCCAG 59.839 50.000 0.00 0.00 0.00 4.85
2722 2753 8.171164 TGAATGTACATGTATGAGAGTAGAGG 57.829 38.462 9.63 0.00 0.00 3.69
2728 2759 6.041409 ACCTCCTGAATGTACATGTATGAGAG 59.959 42.308 9.63 10.67 0.00 3.20
2729 2760 5.899547 ACCTCCTGAATGTACATGTATGAGA 59.100 40.000 9.63 1.69 0.00 3.27
2743 2774 4.227300 TGCTGTAATAACCACCTCCTGAAT 59.773 41.667 0.00 0.00 0.00 2.57
2750 2781 5.596772 ACTTTGTTTGCTGTAATAACCACCT 59.403 36.000 0.00 0.00 0.00 4.00
2923 2955 5.461032 TGACAAAATAAAGAAACGCCCAT 57.539 34.783 0.00 0.00 0.00 4.00
2925 2957 5.344933 GTGATGACAAAATAAAGAAACGCCC 59.655 40.000 0.00 0.00 0.00 6.13
2928 2960 8.726650 TCATGTGATGACAAAATAAAGAAACG 57.273 30.769 0.00 0.00 35.11 3.60
2980 3013 7.038048 TCATTCATCTAGCAACTCAGTTACTG 58.962 38.462 5.94 5.94 0.00 2.74
3060 3094 4.041691 TCTTGGGAAGTTAGGTTCTTGGAG 59.958 45.833 0.00 0.00 0.00 3.86
3210 3245 5.464722 CCAGCTGCATATAAAGTGAGTACTG 59.535 44.000 8.66 0.00 37.19 2.74
3238 3273 3.118261 AGACCTGCAAACTCAAGTCTTCA 60.118 43.478 0.00 0.00 34.96 3.02
3254 3304 4.963276 TCTGTTGACAAACAAAGACCTG 57.037 40.909 0.00 0.00 45.50 4.00
3316 3366 4.748102 GTGTTGTCGTCCATTTTCTAGTCA 59.252 41.667 0.00 0.00 0.00 3.41
3322 3372 4.201871 TGTCTTGTGTTGTCGTCCATTTTC 60.202 41.667 0.00 0.00 0.00 2.29
3349 3399 5.086104 ACCAACCATGTGTACATAGAGAC 57.914 43.478 0.00 0.00 34.26 3.36
3358 3408 0.988832 GGAGGGACCAACCATGTGTA 59.011 55.000 0.00 0.00 41.20 2.90
3384 3434 1.218316 GTAGCCGGTCCCAAGACAG 59.782 63.158 1.90 0.00 45.48 3.51
3413 3463 8.184192 CCAAGCTATGATGTTTTAAGGTAACAG 58.816 37.037 0.00 0.00 38.74 3.16
3437 3487 8.950007 AATCTACTCCTCAAAAATTAAACCCA 57.050 30.769 0.00 0.00 0.00 4.51
3503 3553 2.551459 ACTTGTCATTGAAGCAGACTGC 59.449 45.455 20.12 20.12 45.46 4.40
3534 3584 0.970427 AAAGGTTTATGCCCTGGCGG 60.970 55.000 3.32 0.00 45.51 6.13


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

AutoCloner maintained by Alex Coulton.