Multiple sequence alignment - TraesCS1B01G066800

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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 TraesCS1B01G066800 chr1B 100.000 3375 0 0 495 3869 51000344 50996970 0.000000e+00 6233.0
1 TraesCS1B01G066800 chr1B 73.748 1577 334 61 598 2131 118138822 118140361 2.630000e-151 545.0
2 TraesCS1B01G066800 chr1B 100.000 129 0 0 1 129 51000838 51000710 5.000000e-59 239.0
3 TraesCS1B01G066800 chr4D 86.851 3407 397 30 495 3869 504140650 504137263 0.000000e+00 3762.0
4 TraesCS1B01G066800 chr2D 92.739 1749 124 3 2120 3866 16869790 16871537 0.000000e+00 2523.0
5 TraesCS1B01G066800 chr2B 95.235 1343 62 2 2527 3868 60973661 60972320 0.000000e+00 2124.0
6 TraesCS1B01G066800 chr2B 93.926 1317 61 2 1110 2408 60973660 60974975 0.000000e+00 1971.0
7 TraesCS1B01G066800 chrUn 86.399 1272 170 3 2594 3864 205363445 205362176 0.000000e+00 1387.0
8 TraesCS1B01G066800 chrUn 86.321 1272 171 3 2594 3864 168675770 168674501 0.000000e+00 1382.0
9 TraesCS1B01G066800 chrUn 85.955 890 123 2 2976 3864 313311698 313310810 0.000000e+00 950.0
10 TraesCS1B01G066800 chrUn 85.955 890 123 2 2976 3864 313315477 313314589 0.000000e+00 950.0
11 TraesCS1B01G066800 chrUn 86.207 551 76 0 2594 3144 168625053 168624503 7.150000e-167 597.0
12 TraesCS1B01G066800 chrUn 92.233 412 32 0 2609 3020 459264297 459264708 5.570000e-163 584.0
13 TraesCS1B01G066800 chr3B 86.118 1275 170 5 2594 3864 34560824 34559553 0.000000e+00 1367.0
14 TraesCS1B01G066800 chr3B 85.928 1272 178 1 2594 3864 34506451 34505180 0.000000e+00 1356.0
15 TraesCS1B01G066800 chr3B 79.833 600 99 7 1315 1894 4506210 4506807 5.980000e-113 418.0
16 TraesCS1B01G066800 chr7A 73.073 2232 482 84 612 2779 96097381 96099557 0.000000e+00 682.0
17 TraesCS1B01G066800 chr7D 83.333 60 8 2 793 851 277728277 277728335 2.000000e-03 54.7
18 TraesCS1B01G066800 chr6B 94.286 35 2 0 792 826 674117323 674117289 2.000000e-03 54.7


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 TraesCS1B01G066800 chr1B 50996970 51000838 3868 True 3236 6233 100.000 1 3869 2 chr1B.!!$R1 3868
1 TraesCS1B01G066800 chr1B 118138822 118140361 1539 False 545 545 73.748 598 2131 1 chr1B.!!$F1 1533
2 TraesCS1B01G066800 chr4D 504137263 504140650 3387 True 3762 3762 86.851 495 3869 1 chr4D.!!$R1 3374
3 TraesCS1B01G066800 chr2D 16869790 16871537 1747 False 2523 2523 92.739 2120 3866 1 chr2D.!!$F1 1746
4 TraesCS1B01G066800 chr2B 60972320 60973661 1341 True 2124 2124 95.235 2527 3868 1 chr2B.!!$R1 1341
5 TraesCS1B01G066800 chr2B 60973660 60974975 1315 False 1971 1971 93.926 1110 2408 1 chr2B.!!$F1 1298
6 TraesCS1B01G066800 chrUn 205362176 205363445 1269 True 1387 1387 86.399 2594 3864 1 chrUn.!!$R3 1270
7 TraesCS1B01G066800 chrUn 168674501 168675770 1269 True 1382 1382 86.321 2594 3864 1 chrUn.!!$R2 1270
8 TraesCS1B01G066800 chrUn 313310810 313315477 4667 True 950 950 85.955 2976 3864 2 chrUn.!!$R4 888
9 TraesCS1B01G066800 chrUn 168624503 168625053 550 True 597 597 86.207 2594 3144 1 chrUn.!!$R1 550
10 TraesCS1B01G066800 chr3B 34559553 34560824 1271 True 1367 1367 86.118 2594 3864 1 chr3B.!!$R2 1270
11 TraesCS1B01G066800 chr3B 34505180 34506451 1271 True 1356 1356 85.928 2594 3864 1 chr3B.!!$R1 1270
12 TraesCS1B01G066800 chr3B 4506210 4506807 597 False 418 418 79.833 1315 1894 1 chr3B.!!$F1 579
13 TraesCS1B01G066800 chr7A 96097381 96099557 2176 False 682 682 73.073 612 2779 1 chr7A.!!$F1 2167

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
790 791 0.037734 TCTCTCCGCCTCTACACACA 59.962 55.0 0.00 0.0 0.00 3.72 F
2349 2382 0.039437 CGTTCTGCCAGTACGACAGT 60.039 55.0 17.59 0.0 40.71 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2429 2462 0.399806 GGAGGGAGGAGAAGGCTGAT 60.400 60.0 0.00 0.0 0.0 2.90 R
3803 4610 0.802494 ATCTAAAGTGGCGCGGTTTG 59.198 50.0 8.83 0.0 0.0 2.93 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 3.854669 CCTCCGCCCAGGTAGCTG 61.855 72.222 15.13 15.13 41.99 4.24
23 24 4.537433 CTCCGCCCAGGTAGCTGC 62.537 72.222 16.62 5.29 41.99 5.25
25 26 4.537433 CCGCCCAGGTAGCTGCTC 62.537 72.222 16.62 8.72 34.51 4.26
28 29 2.185350 CCCAGGTAGCTGCTCACG 59.815 66.667 16.62 2.40 0.00 4.35
29 30 2.650116 CCCAGGTAGCTGCTCACGT 61.650 63.158 16.62 2.15 0.00 4.49
30 31 1.293498 CCAGGTAGCTGCTCACGTT 59.707 57.895 16.62 0.00 0.00 3.99
31 32 0.737715 CCAGGTAGCTGCTCACGTTC 60.738 60.000 16.62 0.00 0.00 3.95
32 33 0.038251 CAGGTAGCTGCTCACGTTCA 60.038 55.000 4.91 0.00 0.00 3.18
34 35 0.790814 GGTAGCTGCTCACGTTCAAC 59.209 55.000 4.91 0.00 0.00 3.18
35 36 1.497991 GTAGCTGCTCACGTTCAACA 58.502 50.000 4.91 0.00 0.00 3.33
36 37 1.864711 GTAGCTGCTCACGTTCAACAA 59.135 47.619 4.91 0.00 0.00 2.83
37 38 0.657840 AGCTGCTCACGTTCAACAAC 59.342 50.000 0.00 0.00 0.00 3.32
38 39 0.317020 GCTGCTCACGTTCAACAACC 60.317 55.000 0.00 0.00 0.00 3.77
39 40 0.307760 CTGCTCACGTTCAACAACCC 59.692 55.000 0.00 0.00 0.00 4.11
40 41 1.098712 TGCTCACGTTCAACAACCCC 61.099 55.000 0.00 0.00 0.00 4.95
41 42 1.098712 GCTCACGTTCAACAACCCCA 61.099 55.000 0.00 0.00 0.00 4.96
42 43 0.944386 CTCACGTTCAACAACCCCAG 59.056 55.000 0.00 0.00 0.00 4.45
43 44 1.098712 TCACGTTCAACAACCCCAGC 61.099 55.000 0.00 0.00 0.00 4.85
46 47 2.203422 TTCAACAACCCCAGCCCG 60.203 61.111 0.00 0.00 0.00 6.13
48 49 3.294493 CAACAACCCCAGCCCGTG 61.294 66.667 0.00 0.00 0.00 4.94
49 50 3.494254 AACAACCCCAGCCCGTGA 61.494 61.111 0.00 0.00 0.00 4.35
55 56 3.470888 CCCAGCCCGTGACCCTAG 61.471 72.222 0.00 0.00 0.00 3.02
56 57 3.470888 CCAGCCCGTGACCCTAGG 61.471 72.222 0.06 0.06 0.00 3.02
57 58 4.162690 CAGCCCGTGACCCTAGGC 62.163 72.222 2.05 0.00 46.13 3.93
59 60 4.468689 GCCCGTGACCCTAGGCAC 62.469 72.222 2.05 6.35 45.07 5.01
61 62 3.782443 CCGTGACCCTAGGCACCC 61.782 72.222 2.05 0.00 0.00 4.61
62 63 3.000819 CGTGACCCTAGGCACCCA 61.001 66.667 2.05 0.00 0.00 4.51
64 65 1.224592 GTGACCCTAGGCACCCATG 59.775 63.158 2.05 0.00 0.00 3.66
73 74 4.164258 GCACCCATGCCCATACTC 57.836 61.111 0.00 0.00 46.97 2.59
75 76 1.922057 CACCCATGCCCATACTCCA 59.078 57.895 0.00 0.00 0.00 3.86
76 77 0.466189 CACCCATGCCCATACTCCAC 60.466 60.000 0.00 0.00 0.00 4.02
78 79 1.227943 CCATGCCCATACTCCACCG 60.228 63.158 0.00 0.00 0.00 4.94
79 80 1.893808 CATGCCCATACTCCACCGC 60.894 63.158 0.00 0.00 0.00 5.68
81 82 1.708993 ATGCCCATACTCCACCGCAT 61.709 55.000 0.00 0.00 32.32 4.73
82 83 1.051556 TGCCCATACTCCACCGCATA 61.052 55.000 0.00 0.00 0.00 3.14
83 84 0.107831 GCCCATACTCCACCGCATAA 59.892 55.000 0.00 0.00 0.00 1.90
84 85 1.878102 GCCCATACTCCACCGCATAAG 60.878 57.143 0.00 0.00 0.00 1.73
86 87 1.202639 CCATACTCCACCGCATAAGCA 60.203 52.381 0.00 0.00 42.27 3.91
87 88 1.867233 CATACTCCACCGCATAAGCAC 59.133 52.381 0.00 0.00 42.27 4.40
89 90 0.673644 ACTCCACCGCATAAGCACAC 60.674 55.000 0.00 0.00 42.27 3.82
90 91 1.369091 CTCCACCGCATAAGCACACC 61.369 60.000 0.00 0.00 42.27 4.16
91 92 2.749865 CCACCGCATAAGCACACCG 61.750 63.158 0.00 0.00 42.27 4.94
92 93 3.124921 ACCGCATAAGCACACCGC 61.125 61.111 0.00 0.00 42.27 5.68
93 94 3.876198 CCGCATAAGCACACCGCC 61.876 66.667 0.00 0.00 44.04 6.13
94 95 3.876198 CGCATAAGCACACCGCCC 61.876 66.667 0.00 0.00 44.04 6.13
95 96 3.876198 GCATAAGCACACCGCCCG 61.876 66.667 0.00 0.00 44.04 6.13
109 110 3.204827 CCCGCCTAGTGCATGCAC 61.205 66.667 37.87 37.87 46.50 4.57
118 119 2.281692 TGCATGCACCGCAAGACT 60.282 55.556 18.46 0.00 43.62 3.24
121 122 1.792301 CATGCACCGCAAGACTCTG 59.208 57.895 0.00 0.00 43.62 3.35
125 126 1.011451 GCACCGCAAGACTCTGTCTC 61.011 60.000 0.42 0.00 42.59 3.36
126 127 0.389166 CACCGCAAGACTCTGTCTCC 60.389 60.000 0.42 0.00 42.59 3.71
127 128 1.153939 CCGCAAGACTCTGTCTCCG 60.154 63.158 0.42 7.10 42.59 4.63
128 129 1.803519 CGCAAGACTCTGTCTCCGC 60.804 63.158 0.42 6.39 42.59 5.54
519 520 4.033776 CCCTGACCGCCACACCAT 62.034 66.667 0.00 0.00 0.00 3.55
525 526 0.965363 GACCGCCACACCATTCCAAT 60.965 55.000 0.00 0.00 0.00 3.16
565 566 1.991339 CTGATCCATGCCCTGCCTCA 61.991 60.000 0.00 0.00 0.00 3.86
577 578 1.276138 CCTGCCTCACAGTCACATGTA 59.724 52.381 0.00 0.00 45.68 2.29
592 593 0.691078 ATGTACCCTCACCGCCTGAT 60.691 55.000 0.00 0.00 0.00 2.90
604 605 1.144057 GCCTGATCCCTGTACCACG 59.856 63.158 0.00 0.00 0.00 4.94
605 606 1.144057 CCTGATCCCTGTACCACGC 59.856 63.158 0.00 0.00 0.00 5.34
609 610 3.935456 ATCCCTGTACCACGCCCCA 62.935 63.158 0.00 0.00 0.00 4.96
655 656 1.665916 CATGGATAGGCCGCTGACG 60.666 63.158 0.00 0.00 40.66 4.35
676 677 0.304098 CCAGGTCGTATCGAGACGTC 59.696 60.000 29.24 24.06 43.39 4.34
692 693 1.220750 ACGTCCTTATCTCCCCTCCAT 59.779 52.381 0.00 0.00 0.00 3.41
748 749 1.581727 ATAACGCATGCACCGCACAA 61.582 50.000 19.57 0.00 43.04 3.33
751 752 2.126734 GCATGCACCGCACAACTC 60.127 61.111 14.21 0.00 43.04 3.01
755 756 2.594592 GCACCGCACAACTCCCTT 60.595 61.111 0.00 0.00 0.00 3.95
757 758 1.966451 CACCGCACAACTCCCTTCC 60.966 63.158 0.00 0.00 0.00 3.46
758 759 2.147387 ACCGCACAACTCCCTTCCT 61.147 57.895 0.00 0.00 0.00 3.36
762 763 0.398318 GCACAACTCCCTTCCTCAGT 59.602 55.000 0.00 0.00 0.00 3.41
781 782 3.764466 CACCGCTTCTCTCCGCCT 61.764 66.667 0.00 0.00 0.00 5.52
784 785 1.824329 CCGCTTCTCTCCGCCTCTA 60.824 63.158 0.00 0.00 0.00 2.43
790 791 0.037734 TCTCTCCGCCTCTACACACA 59.962 55.000 0.00 0.00 0.00 3.72
868 872 2.114670 CATTAGGTGTGCCCGCTGG 61.115 63.158 0.00 0.00 38.74 4.85
947 952 1.303643 CTCTCCCAGCAAACCCCAC 60.304 63.158 0.00 0.00 0.00 4.61
966 971 0.394352 CCGCCTCTAACCCAGCATTT 60.394 55.000 0.00 0.00 0.00 2.32
982 987 1.618343 CATTTCACCTCCAACCCAACC 59.382 52.381 0.00 0.00 0.00 3.77
1018 1023 4.536526 TGGCCAACCCAGCTGCAA 62.537 61.111 8.66 0.00 39.18 4.08
1027 1032 2.032528 CAGCTGCAACTTCCCCGA 59.967 61.111 0.00 0.00 0.00 5.14
1100 1105 2.455565 CCCCCTTCATCGGCATCCT 61.456 63.158 0.00 0.00 0.00 3.24
1260 1265 1.302033 CCCGTCTCCTATGCATGCC 60.302 63.158 16.68 0.00 0.00 4.40
1299 1304 2.315443 CCATTCTGGCCCTCCTCTT 58.685 57.895 0.00 0.00 0.00 2.85
1300 1305 0.182299 CCATTCTGGCCCTCCTCTTC 59.818 60.000 0.00 0.00 0.00 2.87
1320 1325 2.981560 GCACGCACCCCTCATTGTG 61.982 63.158 0.00 0.00 35.58 3.33
1669 1693 0.902984 TCTTAGCCGCCTTGGAGACA 60.903 55.000 0.00 0.00 42.00 3.41
1777 1801 1.566298 GGACTCCCTGCCAATCCAGT 61.566 60.000 0.00 0.00 0.00 4.00
1896 1926 3.873883 GACTCGGACGCGGACGAT 61.874 66.667 23.72 15.39 43.93 3.73
1913 1943 1.604438 CGATCACCACTTCAACCACGA 60.604 52.381 0.00 0.00 0.00 4.35
1956 1986 1.153369 GGGCAATGCTGACGAGCTA 60.153 57.895 4.82 0.00 46.39 3.32
2019 2049 2.095978 CTCCTCCCAACAACGTCGGT 62.096 60.000 0.00 0.00 0.00 4.69
2349 2382 0.039437 CGTTCTGCCAGTACGACAGT 60.039 55.000 17.59 0.00 40.71 3.55
2380 2413 2.033675 TCAAACTTCGACAGTGACGCTA 59.966 45.455 10.19 0.39 35.12 4.26
2469 2502 7.011482 CCCTCCACTAAAAATACTCAAATCTCG 59.989 40.741 0.00 0.00 0.00 4.04
2675 2708 2.970324 AAAAGCCGCGCGTCTCAA 60.970 55.556 29.95 0.00 0.00 3.02
2874 2907 3.285215 GCCCTGCCATGATGCTCG 61.285 66.667 0.00 0.00 0.00 5.03
2940 2973 1.522355 CCCTACCGCGACTCGACTA 60.522 63.158 8.23 0.00 41.67 2.59
2944 2977 0.940126 TACCGCGACTCGACTAATCC 59.060 55.000 8.23 0.00 41.67 3.01
3024 3829 6.846325 ACCGCTTAGTCTATTGCTTATTTC 57.154 37.500 4.55 0.00 0.00 2.17
3034 3839 9.391006 AGTCTATTGCTTATTTCCGTTTCATAA 57.609 29.630 0.00 0.00 0.00 1.90
3036 3841 9.391006 TCTATTGCTTATTTCCGTTTCATAACT 57.609 29.630 0.00 0.00 31.89 2.24
3038 3843 7.441890 TTGCTTATTTCCGTTTCATAACTGA 57.558 32.000 0.00 0.00 31.89 3.41
3049 3854 6.430451 CGTTTCATAACTGAAGCTTGTTCTT 58.570 36.000 2.10 0.00 42.19 2.52
3278 4084 4.515361 TCGACCAAAAAGTGTTTCTACCA 58.485 39.130 0.00 0.00 0.00 3.25
3281 4087 4.020543 ACCAAAAAGTGTTTCTACCAGCA 58.979 39.130 0.00 0.00 0.00 4.41
3284 4090 5.010012 CCAAAAAGTGTTTCTACCAGCAGAT 59.990 40.000 0.00 0.00 0.00 2.90
3327 4133 7.644157 CAGTTTCAGCTTTTAACTCAAACTACC 59.356 37.037 2.69 0.00 32.64 3.18
3375 4181 4.582701 AACTTTGCCACATCGATCAAAA 57.417 36.364 10.20 1.20 0.00 2.44
3389 4195 1.974265 TCAAAATCACGTCCCTTGCA 58.026 45.000 0.00 0.00 0.00 4.08
3660 4467 0.248866 CACTTGGTCCAACAAACGCC 60.249 55.000 0.00 0.00 0.00 5.68
3662 4469 2.082629 CTTGGTCCAACAAACGCCCC 62.083 60.000 0.00 0.00 0.00 5.80
3706 4513 3.935828 GACCGAGCTTTCTTTAATCTGCT 59.064 43.478 0.00 0.00 0.00 4.24
3747 4554 3.703001 ACACAACCTTATCCTCACTGG 57.297 47.619 0.00 0.00 37.10 4.00
3773 4580 0.968393 TCACATCCGATCACGTCCCA 60.968 55.000 0.00 0.00 37.88 4.37
3803 4610 0.319813 GCATTCAAACAGGTGTGCCC 60.320 55.000 0.00 0.00 34.57 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.854669 CAGCTACCTGGGCGGAGG 61.855 72.222 0.00 0.00 39.28 4.30
6 7 4.537433 GCAGCTACCTGGGCGGAG 62.537 72.222 0.00 0.00 39.54 4.63
9 10 3.774528 TGAGCAGCTACCTGGGCG 61.775 66.667 0.00 0.00 39.54 6.13
10 11 2.124942 GTGAGCAGCTACCTGGGC 60.125 66.667 0.00 0.00 39.54 5.36
11 12 2.172483 AACGTGAGCAGCTACCTGGG 62.172 60.000 0.00 0.00 39.54 4.45
12 13 0.737715 GAACGTGAGCAGCTACCTGG 60.738 60.000 0.00 0.00 39.54 4.45
13 14 0.038251 TGAACGTGAGCAGCTACCTG 60.038 55.000 0.00 0.00 42.13 4.00
14 15 0.679505 TTGAACGTGAGCAGCTACCT 59.320 50.000 0.00 0.00 0.00 3.08
15 16 0.790814 GTTGAACGTGAGCAGCTACC 59.209 55.000 0.00 0.00 0.00 3.18
16 17 1.497991 TGTTGAACGTGAGCAGCTAC 58.502 50.000 0.00 0.00 0.00 3.58
17 18 1.864711 GTTGTTGAACGTGAGCAGCTA 59.135 47.619 0.00 0.00 0.00 3.32
18 19 0.657840 GTTGTTGAACGTGAGCAGCT 59.342 50.000 0.00 0.00 0.00 4.24
19 20 0.317020 GGTTGTTGAACGTGAGCAGC 60.317 55.000 0.00 0.00 32.28 5.25
20 21 0.307760 GGGTTGTTGAACGTGAGCAG 59.692 55.000 0.00 0.00 32.28 4.24
21 22 1.098712 GGGGTTGTTGAACGTGAGCA 61.099 55.000 0.00 0.00 32.28 4.26
22 23 1.098712 TGGGGTTGTTGAACGTGAGC 61.099 55.000 0.00 0.00 32.28 4.26
23 24 0.944386 CTGGGGTTGTTGAACGTGAG 59.056 55.000 0.00 0.00 32.28 3.51
24 25 1.098712 GCTGGGGTTGTTGAACGTGA 61.099 55.000 0.00 0.00 32.28 4.35
25 26 1.358759 GCTGGGGTTGTTGAACGTG 59.641 57.895 0.00 0.00 32.28 4.49
28 29 2.561037 CGGGCTGGGGTTGTTGAAC 61.561 63.158 0.00 0.00 0.00 3.18
29 30 2.203422 CGGGCTGGGGTTGTTGAA 60.203 61.111 0.00 0.00 0.00 2.69
30 31 3.494254 ACGGGCTGGGGTTGTTGA 61.494 61.111 0.00 0.00 0.00 3.18
31 32 3.294493 CACGGGCTGGGGTTGTTG 61.294 66.667 0.00 0.00 0.00 3.33
32 33 3.494254 TCACGGGCTGGGGTTGTT 61.494 61.111 0.00 0.00 0.00 2.83
38 39 3.470888 CTAGGGTCACGGGCTGGG 61.471 72.222 0.00 0.00 0.00 4.45
39 40 3.470888 CCTAGGGTCACGGGCTGG 61.471 72.222 0.00 0.00 0.00 4.85
40 41 4.162690 GCCTAGGGTCACGGGCTG 62.163 72.222 11.72 0.00 38.93 4.85
41 42 4.715130 TGCCTAGGGTCACGGGCT 62.715 66.667 11.72 0.00 41.28 5.19
42 43 4.468689 GTGCCTAGGGTCACGGGC 62.469 72.222 11.72 5.36 41.15 6.13
43 44 3.782443 GGTGCCTAGGGTCACGGG 61.782 72.222 11.72 0.00 33.06 5.28
46 47 1.224592 CATGGGTGCCTAGGGTCAC 59.775 63.158 11.72 10.86 0.00 3.67
48 49 2.193248 GCATGGGTGCCTAGGGTC 59.807 66.667 11.72 0.00 45.76 4.46
57 58 0.466189 GTGGAGTATGGGCATGGGTG 60.466 60.000 0.00 0.00 0.00 4.61
59 60 1.151450 GGTGGAGTATGGGCATGGG 59.849 63.158 0.00 0.00 0.00 4.00
61 62 1.893808 GCGGTGGAGTATGGGCATG 60.894 63.158 0.00 0.00 0.00 4.06
62 63 1.708993 ATGCGGTGGAGTATGGGCAT 61.709 55.000 0.00 0.00 36.38 4.40
64 65 0.107831 TTATGCGGTGGAGTATGGGC 59.892 55.000 0.00 0.00 0.00 5.36
65 66 1.878102 GCTTATGCGGTGGAGTATGGG 60.878 57.143 0.00 0.00 0.00 4.00
66 67 1.202639 TGCTTATGCGGTGGAGTATGG 60.203 52.381 0.00 0.00 43.34 2.74
67 68 1.867233 GTGCTTATGCGGTGGAGTATG 59.133 52.381 0.00 0.00 43.34 2.39
68 69 1.484653 TGTGCTTATGCGGTGGAGTAT 59.515 47.619 0.00 0.00 43.34 2.12
69 70 0.899019 TGTGCTTATGCGGTGGAGTA 59.101 50.000 0.00 0.00 43.34 2.59
70 71 0.673644 GTGTGCTTATGCGGTGGAGT 60.674 55.000 0.00 0.00 43.34 3.85
71 72 1.369091 GGTGTGCTTATGCGGTGGAG 61.369 60.000 0.00 0.00 43.34 3.86
72 73 1.376683 GGTGTGCTTATGCGGTGGA 60.377 57.895 0.00 0.00 43.34 4.02
73 74 2.749865 CGGTGTGCTTATGCGGTGG 61.750 63.158 0.00 0.00 43.34 4.61
75 76 3.124921 GCGGTGTGCTTATGCGGT 61.125 61.111 0.00 0.00 43.34 5.68
76 77 3.876198 GGCGGTGTGCTTATGCGG 61.876 66.667 0.00 0.00 45.43 5.69
78 79 3.876198 CGGGCGGTGTGCTTATGC 61.876 66.667 0.00 0.00 45.43 3.14
79 80 3.876198 GCGGGCGGTGTGCTTATG 61.876 66.667 0.00 0.00 45.43 1.90
95 96 3.880846 GCGGTGCATGCACTAGGC 61.881 66.667 40.86 35.21 45.52 3.93
97 98 1.020861 TCTTGCGGTGCATGCACTAG 61.021 55.000 40.86 34.50 45.52 2.57
98 99 1.003959 TCTTGCGGTGCATGCACTA 60.004 52.632 40.86 27.75 45.52 2.74
99 100 2.281692 TCTTGCGGTGCATGCACT 60.282 55.556 40.86 0.00 45.52 4.40
100 101 2.126734 GTCTTGCGGTGCATGCAC 60.127 61.111 37.29 37.29 43.10 4.57
103 104 0.952497 ACAGAGTCTTGCGGTGCATG 60.952 55.000 0.00 0.00 38.76 4.06
107 108 0.389166 GGAGACAGAGTCTTGCGGTG 60.389 60.000 0.70 0.00 43.53 4.94
108 109 1.867919 CGGAGACAGAGTCTTGCGGT 61.868 60.000 0.70 0.00 43.53 5.68
109 110 1.153939 CGGAGACAGAGTCTTGCGG 60.154 63.158 0.70 0.00 43.53 5.69
110 111 1.803519 GCGGAGACAGAGTCTTGCG 60.804 63.158 0.70 0.33 43.53 4.85
111 112 4.177229 GCGGAGACAGAGTCTTGC 57.823 61.111 0.70 5.52 43.53 4.01
507 508 0.329931 TATTGGAATGGTGTGGCGGT 59.670 50.000 0.00 0.00 0.00 5.68
516 517 0.583438 CGCGAGCAGTATTGGAATGG 59.417 55.000 0.00 0.00 0.00 3.16
519 520 0.245266 TGACGCGAGCAGTATTGGAA 59.755 50.000 15.93 0.00 0.00 3.53
525 526 4.476410 CGGCTGACGCGAGCAGTA 62.476 66.667 25.73 3.03 41.08 2.74
545 546 2.203451 GGCAGGGCATGGATCAGG 60.203 66.667 0.00 0.00 0.00 3.86
565 566 1.623811 GGTGAGGGTACATGTGACTGT 59.376 52.381 9.11 0.00 0.00 3.55
577 578 3.083997 GGATCAGGCGGTGAGGGT 61.084 66.667 0.00 0.00 39.07 4.34
592 593 3.935456 ATGGGGCGTGGTACAGGGA 62.935 63.158 0.00 0.00 45.29 4.20
604 605 0.329596 AGTCAGTCAAAGGATGGGGC 59.670 55.000 0.00 0.00 0.00 5.80
605 606 1.952367 GCAGTCAGTCAAAGGATGGGG 60.952 57.143 0.00 0.00 0.00 4.96
609 610 3.406764 GTTGAGCAGTCAGTCAAAGGAT 58.593 45.455 0.00 0.00 34.52 3.24
655 656 1.359475 GTCTCGATACGACCTGGGC 59.641 63.158 0.00 0.00 0.00 5.36
676 677 2.370189 GTGTGATGGAGGGGAGATAAGG 59.630 54.545 0.00 0.00 0.00 2.69
692 693 2.203126 TGGTGCATGCGTGTGTGA 60.203 55.556 14.09 0.00 0.00 3.58
748 749 0.545548 GGTGGACTGAGGAAGGGAGT 60.546 60.000 0.00 0.00 0.00 3.85
751 752 2.982130 CGGTGGACTGAGGAAGGG 59.018 66.667 0.00 0.00 0.00 3.95
755 756 1.228894 AGAAGCGGTGGACTGAGGA 60.229 57.895 0.00 0.00 0.00 3.71
757 758 0.172352 GAGAGAAGCGGTGGACTGAG 59.828 60.000 0.00 0.00 0.00 3.35
758 759 1.251527 GGAGAGAAGCGGTGGACTGA 61.252 60.000 0.00 0.00 0.00 3.41
762 763 3.760035 GCGGAGAGAAGCGGTGGA 61.760 66.667 0.00 0.00 0.00 4.02
781 782 2.253154 CGGCGTCGTGTGTGTAGA 59.747 61.111 0.00 0.00 0.00 2.59
832 836 3.071206 GGGTCTCGGCAGAGCTGA 61.071 66.667 9.22 0.10 45.19 4.26
868 872 4.966787 TTTGTGGCCGGAGCACCC 62.967 66.667 5.05 0.00 42.56 4.61
947 952 0.394352 AAATGCTGGGTTAGAGGCGG 60.394 55.000 0.00 0.00 0.00 6.13
966 971 2.824880 CGGGTTGGGTTGGAGGTGA 61.825 63.158 0.00 0.00 0.00 4.02
982 987 2.983592 GGTGGAAGTTGGTGGCGG 60.984 66.667 0.00 0.00 0.00 6.13
1011 1016 2.032681 GTCGGGGAAGTTGCAGCT 59.967 61.111 0.00 0.00 0.00 4.24
1018 1023 3.782443 GCGGATGGTCGGGGAAGT 61.782 66.667 0.00 0.00 0.00 3.01
1100 1105 1.069090 GTGGAGTGGTGAGCGACAA 59.931 57.895 0.00 0.00 0.00 3.18
1299 1304 2.894257 AATGAGGGGTGCGTGCTGA 61.894 57.895 0.00 0.00 0.00 4.26
1300 1305 2.360350 AATGAGGGGTGCGTGCTG 60.360 61.111 0.00 0.00 0.00 4.41
1746 1770 4.699522 GAGTCCGGCAGGCGGTTT 62.700 66.667 32.63 22.25 37.47 3.27
1777 1801 0.546747 ATGTCGTTGGAGGGAGGGAA 60.547 55.000 0.00 0.00 0.00 3.97
1896 1926 0.537653 TGTCGTGGTTGAAGTGGTGA 59.462 50.000 0.00 0.00 0.00 4.02
1913 1943 2.795297 CGTTGCGTGGGTTGTTGT 59.205 55.556 0.00 0.00 0.00 3.32
2349 2382 1.409790 TCGAAGTTTGACGAGGTGGAA 59.590 47.619 0.00 0.00 34.49 3.53
2380 2413 2.657237 CGAGAAGGTGAAGGCGGT 59.343 61.111 0.00 0.00 0.00 5.68
2429 2462 0.399806 GGAGGGAGGAGAAGGCTGAT 60.400 60.000 0.00 0.00 0.00 2.90
2469 2502 2.224185 TGTGGTCACGGATATGGTATGC 60.224 50.000 0.00 0.00 0.00 3.14
2547 2580 2.876879 CGAACGTTTGGCGCAGTGA 61.877 57.895 10.83 0.00 46.11 3.41
2675 2708 0.723414 CTTTGCGACGTCTGATGCAT 59.277 50.000 14.70 0.00 37.17 3.96
2874 2907 1.521681 GGCGTGCATGGAGGAGTAC 60.522 63.158 11.38 0.00 0.00 2.73
2940 2973 1.793902 AGGGGATAGGTAGACCGGATT 59.206 52.381 9.46 0.00 42.08 3.01
2944 2977 1.242665 GCGAGGGGATAGGTAGACCG 61.243 65.000 0.00 0.00 42.08 4.79
3024 3829 4.749245 ACAAGCTTCAGTTATGAAACGG 57.251 40.909 0.00 0.00 44.68 4.44
3034 3839 5.525378 CACTTAGACAAGAACAAGCTTCAGT 59.475 40.000 0.00 0.00 35.60 3.41
3036 3841 5.428253 ACACTTAGACAAGAACAAGCTTCA 58.572 37.500 0.00 0.00 35.60 3.02
3038 3843 5.462398 CGTACACTTAGACAAGAACAAGCTT 59.538 40.000 0.00 0.00 35.60 3.74
3049 3854 5.065914 AGAAGTACACCGTACACTTAGACA 58.934 41.667 7.02 0.00 32.79 3.41
3281 4087 3.790437 CCACCAGCCGAGCCATCT 61.790 66.667 0.00 0.00 0.00 2.90
3284 4090 4.329545 GTTCCACCAGCCGAGCCA 62.330 66.667 0.00 0.00 0.00 4.75
3327 4133 5.163703 GGTGTGTGTGAGAGAGTACTATGAG 60.164 48.000 0.00 0.00 0.00 2.90
3375 4181 1.302511 GGTGTGCAAGGGACGTGAT 60.303 57.895 0.00 0.00 41.23 3.06
3389 4195 0.850100 TGATGAAGGGTTGTGGGTGT 59.150 50.000 0.00 0.00 0.00 4.16
3660 4467 2.046700 TTCTAAGGTTGGCGCGGG 60.047 61.111 8.83 0.00 0.00 6.13
3662 4469 1.735198 TCGTTCTAAGGTTGGCGCG 60.735 57.895 0.00 0.00 0.00 6.86
3706 4513 5.417580 GTGTTAGGGAAGCAATTATTCCACA 59.582 40.000 18.52 13.14 46.77 4.17
3747 4554 1.787155 GTGATCGGATGTGATACGTGC 59.213 52.381 0.00 0.00 37.96 5.34
3803 4610 0.802494 ATCTAAAGTGGCGCGGTTTG 59.198 50.000 8.83 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.