Multiple sequence alignment - TraesCS6D01G204100

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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 TraesCS6D01G204100 chr6D 100.000 3005 0 0 1 3005 289220836 289217832 0.000000e+00 5550.0
1 TraesCS6D01G204100 chr6A 93.964 1756 67 15 954 2685 435772517 435774257 0.000000e+00 2619.0
2 TraesCS6D01G204100 chr6A 89.369 602 28 20 46 616 435760112 435760708 0.000000e+00 725.0
3 TraesCS6D01G204100 chr6A 95.082 183 9 0 735 917 435772268 435772450 3.790000e-74 289.0
4 TraesCS6D01G204100 chr6A 93.714 175 2 2 2831 3005 435774440 435774605 1.380000e-63 254.0
5 TraesCS6D01G204100 chr6A 97.143 105 3 0 2696 2800 435774339 435774443 8.560000e-41 178.0
6 TraesCS6D01G204100 chr6B 96.042 1137 36 3 954 2084 449772829 449771696 0.000000e+00 1842.0
7 TraesCS6D01G204100 chr6B 92.138 318 21 3 299 616 449774729 449774416 2.130000e-121 446.0
8 TraesCS6D01G204100 chr6B 91.373 255 19 3 665 917 449773158 449772905 2.220000e-91 346.0
9 TraesCS6D01G204100 chr6B 86.349 315 10 16 2696 3005 449771305 449771019 2.250000e-81 313.0
10 TraesCS6D01G204100 chr6B 90.604 149 4 8 46 187 449774936 449774791 3.950000e-44 189.0
11 TraesCS6D01G204100 chr6B 96.154 52 2 0 225 276 449774779 449774728 5.340000e-13 86.1
12 TraesCS6D01G204100 chr6B 97.368 38 1 0 629 666 449774432 449774395 6.950000e-07 65.8
13 TraesCS6D01G204100 chr2D 81.494 308 37 8 2182 2474 630766663 630766361 5.010000e-58 235.0
14 TraesCS6D01G204100 chr2D 81.884 276 36 10 2213 2474 32759302 32759027 1.400000e-53 220.0
15 TraesCS6D01G204100 chr7D 81.433 307 38 7 2182 2474 477836950 477837251 1.800000e-57 233.0
16 TraesCS6D01G204100 chr7D 81.169 308 37 11 2182 2474 579248220 579247919 8.380000e-56 228.0
17 TraesCS6D01G204100 chr7D 80.797 276 38 7 2213 2474 430931441 430931715 5.080000e-48 202.0
18 TraesCS6D01G204100 chr4A 81.169 308 30 12 2185 2474 89954608 89954311 3.900000e-54 222.0
19 TraesCS6D01G204100 chr3B 81.356 295 35 7 2182 2462 765840067 765839779 3.900000e-54 222.0
20 TraesCS6D01G204100 chr3D 81.250 304 25 19 2181 2463 428958387 428958679 1.810000e-52 217.0
21 TraesCS6D01G204100 chr3D 80.323 310 37 7 2182 2474 497822765 497823067 2.350000e-51 213.0
22 TraesCS6D01G204100 chr7B 81.609 261 32 9 2213 2463 672769725 672769979 5.080000e-48 202.0
23 TraesCS6D01G204100 chr5A 72.196 633 140 32 1381 1995 33153116 33153730 8.620000e-36 161.0
24 TraesCS6D01G204100 chr3A 88.550 131 5 3 2273 2393 19289943 19289813 1.870000e-32 150.0
25 TraesCS6D01G204100 chr3A 79.006 181 18 8 2213 2374 618161840 618161661 4.100000e-19 106.0
26 TraesCS6D01G204100 chr5B 83.871 93 10 3 2503 2592 586824892 586824982 1.920000e-12 84.2


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 TraesCS6D01G204100 chr6D 289217832 289220836 3004 True 5550.0 5550 100.000000 1 3005 1 chr6D.!!$R1 3004
1 TraesCS6D01G204100 chr6A 435772268 435774605 2337 False 835.0 2619 94.975750 735 3005 4 chr6A.!!$F2 2270
2 TraesCS6D01G204100 chr6A 435760112 435760708 596 False 725.0 725 89.369000 46 616 1 chr6A.!!$F1 570
3 TraesCS6D01G204100 chr6B 449771019 449774936 3917 True 469.7 1842 92.861143 46 3005 7 chr6B.!!$R1 2959

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
694 1973 0.107993 AGTGGCGGTGATGACTGATG 60.108 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 3834 0.107643 TCATCTCACCGGTTGCAACA 59.892 50.0 29.55 8.91 0.0 3.33 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
23 24 3.859443 TGGCACAATGACAAATATTGGC 58.141 40.909 0.00 0.00 39.30 4.52
32 33 3.523547 GACAAATATTGGCAATGCAGCA 58.476 40.909 22.57 0.00 38.99 4.41
33 34 3.933955 GACAAATATTGGCAATGCAGCAA 59.066 39.130 22.57 3.24 38.99 3.91
34 35 4.325119 ACAAATATTGGCAATGCAGCAAA 58.675 34.783 22.57 0.74 35.83 3.68
35 36 4.154556 ACAAATATTGGCAATGCAGCAAAC 59.845 37.500 22.57 0.00 35.83 2.93
36 37 2.383368 TATTGGCAATGCAGCAAACC 57.617 45.000 22.57 1.48 35.83 3.27
37 38 0.397187 ATTGGCAATGCAGCAAACCA 59.603 45.000 12.82 4.57 35.83 3.67
38 39 0.179702 TTGGCAATGCAGCAAACCAA 59.820 45.000 18.49 18.49 34.91 3.67
39 40 0.397187 TGGCAATGCAGCAAACCAAT 59.603 45.000 7.79 0.00 35.83 3.16
40 41 1.202782 TGGCAATGCAGCAAACCAATT 60.203 42.857 7.79 0.00 35.83 2.32
41 42 2.038164 TGGCAATGCAGCAAACCAATTA 59.962 40.909 7.79 0.00 35.83 1.40
42 43 3.272581 GGCAATGCAGCAAACCAATTAT 58.727 40.909 7.79 0.00 35.83 1.28
43 44 3.064271 GGCAATGCAGCAAACCAATTATG 59.936 43.478 7.79 0.00 35.83 1.90
44 45 3.486209 GCAATGCAGCAAACCAATTATGC 60.486 43.478 0.00 0.00 40.34 3.14
58 59 4.514441 CCAATTATGCTCTTACTCTGCCAG 59.486 45.833 0.00 0.00 0.00 4.85
90 94 2.675423 AGGCGGCAGTAGACACGA 60.675 61.111 13.08 0.00 0.00 4.35
91 95 2.005960 GAGGCGGCAGTAGACACGAT 62.006 60.000 13.08 0.00 0.00 3.73
92 96 1.153628 GGCGGCAGTAGACACGATT 60.154 57.895 3.07 0.00 0.00 3.34
93 97 1.146358 GGCGGCAGTAGACACGATTC 61.146 60.000 3.07 0.00 0.00 2.52
94 98 0.457853 GCGGCAGTAGACACGATTCA 60.458 55.000 0.00 0.00 0.00 2.57
95 99 1.802880 GCGGCAGTAGACACGATTCAT 60.803 52.381 0.00 0.00 0.00 2.57
98 102 3.731216 CGGCAGTAGACACGATTCATTAG 59.269 47.826 0.00 0.00 0.00 1.73
140 145 1.078709 CGCGAGCTCTGGATTCAAAA 58.921 50.000 12.85 0.00 0.00 2.44
187 195 4.977741 TTTACCGAGTCAAACGTGATTC 57.022 40.909 0.00 0.00 37.20 2.52
188 196 2.519377 ACCGAGTCAAACGTGATTCA 57.481 45.000 0.00 0.00 39.78 2.57
189 197 3.040147 ACCGAGTCAAACGTGATTCAT 57.960 42.857 0.00 0.00 39.78 2.57
190 198 3.399330 ACCGAGTCAAACGTGATTCATT 58.601 40.909 0.00 0.00 39.78 2.57
191 199 4.562082 ACCGAGTCAAACGTGATTCATTA 58.438 39.130 0.00 0.00 39.78 1.90
192 200 4.625742 ACCGAGTCAAACGTGATTCATTAG 59.374 41.667 0.00 0.00 39.78 1.73
193 201 4.492570 CCGAGTCAAACGTGATTCATTAGC 60.493 45.833 0.00 0.00 39.78 3.09
194 202 4.492570 CGAGTCAAACGTGATTCATTAGCC 60.493 45.833 0.00 0.00 39.78 3.93
195 203 4.579869 AGTCAAACGTGATTCATTAGCCT 58.420 39.130 0.00 0.00 35.80 4.58
440 480 2.293627 CCGCTTATCGCCTTCGTCG 61.294 63.158 0.00 0.00 36.73 5.12
574 614 2.982130 GAGCCCCAGAAAGCGAGA 59.018 61.111 0.00 0.00 0.00 4.04
615 655 4.019174 CAGGCCATCAACAAGAAGGTAAT 58.981 43.478 5.01 0.00 37.43 1.89
616 656 5.045213 TCAGGCCATCAACAAGAAGGTAATA 60.045 40.000 5.01 0.00 37.43 0.98
617 657 5.829924 CAGGCCATCAACAAGAAGGTAATAT 59.170 40.000 5.01 0.00 37.43 1.28
618 658 6.322201 CAGGCCATCAACAAGAAGGTAATATT 59.678 38.462 5.01 0.00 37.43 1.28
619 659 6.897413 AGGCCATCAACAAGAAGGTAATATTT 59.103 34.615 5.01 0.00 37.43 1.40
620 660 7.400052 AGGCCATCAACAAGAAGGTAATATTTT 59.600 33.333 5.01 0.00 37.43 1.82
621 661 8.040727 GGCCATCAACAAGAAGGTAATATTTTT 58.959 33.333 0.00 0.00 37.43 1.94
641 681 5.975693 TTTTTGCGGATCAATAAGAAGGT 57.024 34.783 0.00 0.00 34.12 3.50
643 683 7.455641 TTTTTGCGGATCAATAAGAAGGTAA 57.544 32.000 0.00 0.00 34.12 2.85
689 1968 1.076533 CGTGTAGTGGCGGTGATGAC 61.077 60.000 0.00 0.00 0.00 3.06
691 1970 0.246360 TGTAGTGGCGGTGATGACTG 59.754 55.000 0.00 0.00 0.00 3.51
692 1971 0.530744 GTAGTGGCGGTGATGACTGA 59.469 55.000 0.00 0.00 0.00 3.41
694 1973 0.107993 AGTGGCGGTGATGACTGATG 60.108 55.000 0.00 0.00 0.00 3.07
695 1974 0.108186 GTGGCGGTGATGACTGATGA 60.108 55.000 0.00 0.00 0.00 2.92
696 1975 0.612744 TGGCGGTGATGACTGATGAA 59.387 50.000 0.00 0.00 0.00 2.57
697 1976 1.210234 TGGCGGTGATGACTGATGAAT 59.790 47.619 0.00 0.00 0.00 2.57
699 1978 2.032550 GGCGGTGATGACTGATGAATTG 59.967 50.000 0.00 0.00 0.00 2.32
700 1979 2.540361 GCGGTGATGACTGATGAATTGC 60.540 50.000 0.00 0.00 0.00 3.56
701 1980 2.941064 CGGTGATGACTGATGAATTGCT 59.059 45.455 0.00 0.00 0.00 3.91
702 1981 3.002042 CGGTGATGACTGATGAATTGCTC 59.998 47.826 0.00 0.00 0.00 4.26
703 1982 3.002042 GGTGATGACTGATGAATTGCTCG 59.998 47.826 0.00 0.00 0.00 5.03
704 1983 2.610833 TGATGACTGATGAATTGCTCGC 59.389 45.455 0.00 0.00 0.00 5.03
705 1984 1.372582 TGACTGATGAATTGCTCGCC 58.627 50.000 0.00 0.00 0.00 5.54
706 1985 1.338960 TGACTGATGAATTGCTCGCCA 60.339 47.619 0.00 0.00 0.00 5.69
707 1986 1.329906 GACTGATGAATTGCTCGCCAG 59.670 52.381 0.00 0.00 34.23 4.85
716 1995 2.731374 GCTCGCCAGCTAGGTAGG 59.269 66.667 0.00 0.00 43.09 3.18
717 1996 2.862223 GCTCGCCAGCTAGGTAGGG 61.862 68.421 0.00 5.51 43.09 3.53
724 2003 1.342076 CCAGCTAGGTAGGGTCTGACA 60.342 57.143 10.38 0.00 0.00 3.58
741 2020 6.482308 GGTCTGACATTGCGTTTATATAGGTT 59.518 38.462 10.38 0.00 0.00 3.50
821 2100 3.893763 CGCGCTCAGGGACGAGAT 61.894 66.667 5.56 0.00 34.79 2.75
895 2174 3.261951 CCATCTACCGCAACGCCG 61.262 66.667 0.00 0.00 0.00 6.46
896 2175 3.925238 CATCTACCGCAACGCCGC 61.925 66.667 0.00 0.00 0.00 6.53
917 2196 1.870055 GCCTTCCACAGGTACGTCGA 61.870 60.000 0.00 0.00 46.07 4.20
918 2197 0.109412 CCTTCCACAGGTACGTCGAC 60.109 60.000 5.18 5.18 37.99 4.20
919 2198 0.594602 CTTCCACAGGTACGTCGACA 59.405 55.000 17.16 0.00 0.00 4.35
920 2199 1.001048 CTTCCACAGGTACGTCGACAA 60.001 52.381 17.16 0.00 0.00 3.18
936 2255 3.559530 GACAATGATGATGTGTCGTCG 57.440 47.619 0.00 0.00 42.22 5.12
939 2258 3.367932 ACAATGATGATGTGTCGTCGTTC 59.632 43.478 2.90 0.00 44.10 3.95
940 2259 3.510388 ATGATGATGTGTCGTCGTTCT 57.490 42.857 0.00 0.00 42.22 3.01
941 2260 2.595386 TGATGATGTGTCGTCGTTCTG 58.405 47.619 0.00 0.00 42.22 3.02
942 2261 2.030274 TGATGATGTGTCGTCGTTCTGT 60.030 45.455 0.00 0.00 42.22 3.41
943 2262 2.502213 TGATGTGTCGTCGTTCTGTT 57.498 45.000 0.00 0.00 0.00 3.16
944 2263 2.816689 TGATGTGTCGTCGTTCTGTTT 58.183 42.857 0.00 0.00 0.00 2.83
945 2264 3.191669 TGATGTGTCGTCGTTCTGTTTT 58.808 40.909 0.00 0.00 0.00 2.43
946 2265 3.619483 TGATGTGTCGTCGTTCTGTTTTT 59.381 39.130 0.00 0.00 0.00 1.94
983 2304 2.423185 TGATGATTTGCGTTGGATCACC 59.577 45.455 0.00 0.00 33.08 4.02
1030 2351 4.379603 GGAGGATGAAGATATGGACGTACG 60.380 50.000 15.01 15.01 0.00 3.67
1120 2449 1.202734 TGTACGAGATAGAGGACCCCG 60.203 57.143 0.00 0.00 0.00 5.73
1174 2503 2.943978 AACGTCTTCCTGCTCCCCG 61.944 63.158 0.00 0.00 0.00 5.73
1230 2559 1.072505 CAACACCACCGCCTACCTT 59.927 57.895 0.00 0.00 0.00 3.50
1416 2745 2.124529 TGCAACGCCAACACCTCA 60.125 55.556 0.00 0.00 0.00 3.86
1798 3128 1.375098 GCTGGACTGGAGCAAGATGC 61.375 60.000 0.00 0.00 45.46 3.91
1872 3202 0.680280 TGTCAGAGAGGAGGTACCGC 60.680 60.000 7.18 7.18 44.74 5.68
1890 3220 4.697756 GTGCTGCGTGCCAGGGTA 62.698 66.667 0.00 0.00 42.03 3.69
1899 3229 3.721706 GCCAGGGTACTGCAGGCT 61.722 66.667 19.93 0.00 43.53 4.58
2011 3341 1.027357 GCTACCGTACTGATTCCCGA 58.973 55.000 0.00 0.00 0.00 5.14
2084 3420 3.386768 TTGTCGGTTCAAGAGGAAGAG 57.613 47.619 0.00 0.00 35.82 2.85
2178 3643 4.817318 AAACATGTTTGACAAAGGGTGT 57.183 36.364 22.71 4.16 45.74 4.16
2180 3645 3.096092 ACATGTTTGACAAAGGGTGTGT 58.904 40.909 0.00 0.11 41.96 3.72
2181 3646 3.119173 ACATGTTTGACAAAGGGTGTGTG 60.119 43.478 0.00 0.00 41.96 3.82
2182 3647 1.821753 TGTTTGACAAAGGGTGTGTGG 59.178 47.619 0.00 0.00 41.96 4.17
2197 3662 2.294074 GTGTGGTGTGCCTAAAACTCA 58.706 47.619 0.00 0.00 35.27 3.41
2205 3670 2.731976 GTGCCTAAAACTCAGTCGACAG 59.268 50.000 19.50 10.43 0.00 3.51
2211 3676 6.622549 CCTAAAACTCAGTCGACAGATACTT 58.377 40.000 19.50 10.35 0.00 2.24
2212 3677 7.627939 GCCTAAAACTCAGTCGACAGATACTTA 60.628 40.741 19.50 10.88 0.00 2.24
2213 3678 7.697291 CCTAAAACTCAGTCGACAGATACTTAC 59.303 40.741 19.50 0.00 0.00 2.34
2214 3679 6.821031 AAACTCAGTCGACAGATACTTACT 57.179 37.500 19.50 0.00 0.00 2.24
2215 3680 6.821031 AACTCAGTCGACAGATACTTACTT 57.179 37.500 19.50 0.00 0.00 2.24
2219 3684 6.769076 TCAGTCGACAGATACTTACTTAACG 58.231 40.000 19.50 0.00 0.00 3.18
2238 3703 3.681855 ACGAAGTATCAATCGAGTGACG 58.318 45.455 18.95 18.10 41.94 4.35
2241 3706 3.320733 AGTATCAATCGAGTGACGTCG 57.679 47.619 18.95 0.00 43.13 5.12
2250 3715 1.731424 CGAGTGACGTCGGCATAGTTT 60.731 52.381 2.93 0.00 36.26 2.66
2363 3834 5.353394 TGCTAGAACCGTCAATTAAGGAT 57.647 39.130 0.00 0.00 0.00 3.24
2441 3912 3.135414 CAAGACATATGTTGCAACCGG 57.865 47.619 26.14 14.77 0.00 5.28
2685 4177 1.266989 GTGGAAGTGCACAAAGCTACC 59.733 52.381 21.04 11.06 45.94 3.18
2686 4178 1.133945 TGGAAGTGCACAAAGCTACCA 60.134 47.619 21.04 13.37 45.94 3.25
2689 4181 2.348411 AGTGCACAAAGCTACCACTT 57.652 45.000 21.04 0.00 45.94 3.16
2690 4182 3.485463 AGTGCACAAAGCTACCACTTA 57.515 42.857 21.04 0.00 45.94 2.24
2692 4184 2.484264 GTGCACAAAGCTACCACTTAGG 59.516 50.000 13.17 0.00 45.94 2.69
2694 4186 3.003480 GCACAAAGCTACCACTTAGGAG 58.997 50.000 0.00 0.00 39.24 3.69
2793 4358 6.622427 ATGTTTGTCTAGTAGTAAGCCCTT 57.378 37.500 0.00 0.00 0.00 3.95
2803 4368 0.036294 GTAAGCCCTTGCCGTCTTCT 60.036 55.000 0.00 0.00 38.69 2.85
2817 4382 1.464997 GTCTTCTACCTTGGCAAAGCG 59.535 52.381 0.00 0.00 31.51 4.68
2820 4385 0.107831 TCTACCTTGGCAAAGCGTGT 59.892 50.000 0.00 0.00 31.51 4.49
2821 4386 1.345089 TCTACCTTGGCAAAGCGTGTA 59.655 47.619 0.00 0.00 31.51 2.90
2828 4393 2.573369 TGGCAAAGCGTGTAAAAGGTA 58.427 42.857 0.00 0.00 0.00 3.08
2892 4460 1.485066 ACGAGGTTCAAAGTCACAGGT 59.515 47.619 0.00 0.00 0.00 4.00
2893 4461 2.093128 ACGAGGTTCAAAGTCACAGGTT 60.093 45.455 0.00 0.00 0.00 3.50
2894 4462 2.544267 CGAGGTTCAAAGTCACAGGTTC 59.456 50.000 0.00 0.00 0.00 3.62
2895 4463 3.541632 GAGGTTCAAAGTCACAGGTTCA 58.458 45.455 0.00 0.00 0.00 3.18
2896 4464 4.137543 GAGGTTCAAAGTCACAGGTTCAT 58.862 43.478 0.00 0.00 0.00 2.57
2897 4465 5.304686 AGGTTCAAAGTCACAGGTTCATA 57.695 39.130 0.00 0.00 0.00 2.15
2898 4466 5.690865 AGGTTCAAAGTCACAGGTTCATAA 58.309 37.500 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.694509 GCCAATATTTGTCATTGTGCCAAA 59.305 37.500 0.00 0.00 32.55 3.28
1 2 4.252073 GCCAATATTTGTCATTGTGCCAA 58.748 39.130 0.00 0.00 32.55 4.52
2 3 3.260128 TGCCAATATTTGTCATTGTGCCA 59.740 39.130 0.00 0.00 32.87 4.92
3 4 3.859443 TGCCAATATTTGTCATTGTGCC 58.141 40.909 0.00 0.00 32.87 5.01
4 5 5.728344 GCATTGCCAATATTTGTCATTGTGC 60.728 40.000 0.00 0.00 32.55 4.57
5 6 5.351740 TGCATTGCCAATATTTGTCATTGTG 59.648 36.000 6.12 0.00 32.55 3.33
6 7 5.489249 TGCATTGCCAATATTTGTCATTGT 58.511 33.333 6.12 0.00 32.55 2.71
7 8 5.503357 GCTGCATTGCCAATATTTGTCATTG 60.503 40.000 6.12 0.00 33.93 2.82
8 9 4.573201 GCTGCATTGCCAATATTTGTCATT 59.427 37.500 6.12 0.00 0.00 2.57
9 10 4.124238 GCTGCATTGCCAATATTTGTCAT 58.876 39.130 6.12 0.00 0.00 3.06
10 11 3.056035 TGCTGCATTGCCAATATTTGTCA 60.056 39.130 6.12 0.00 0.00 3.58
11 12 3.523547 TGCTGCATTGCCAATATTTGTC 58.476 40.909 6.12 0.00 0.00 3.18
12 13 3.613494 TGCTGCATTGCCAATATTTGT 57.387 38.095 6.12 0.00 0.00 2.83
13 14 4.437659 GGTTTGCTGCATTGCCAATATTTG 60.438 41.667 1.84 0.00 0.00 2.32
14 15 3.690628 GGTTTGCTGCATTGCCAATATTT 59.309 39.130 1.84 0.00 0.00 1.40
15 16 3.272581 GGTTTGCTGCATTGCCAATATT 58.727 40.909 1.84 0.00 0.00 1.28
16 17 2.236644 TGGTTTGCTGCATTGCCAATAT 59.763 40.909 14.88 0.00 0.00 1.28
17 18 1.622312 TGGTTTGCTGCATTGCCAATA 59.378 42.857 14.88 0.00 0.00 1.90
18 19 0.397187 TGGTTTGCTGCATTGCCAAT 59.603 45.000 14.88 0.00 0.00 3.16
19 20 0.179702 TTGGTTTGCTGCATTGCCAA 59.820 45.000 21.07 21.07 34.12 4.52
20 21 0.397187 ATTGGTTTGCTGCATTGCCA 59.603 45.000 1.84 9.59 0.00 4.92
21 22 1.525941 AATTGGTTTGCTGCATTGCC 58.474 45.000 1.84 6.92 0.00 4.52
22 23 3.486209 GCATAATTGGTTTGCTGCATTGC 60.486 43.478 1.84 0.46 33.61 3.56
23 24 3.936453 AGCATAATTGGTTTGCTGCATTG 59.064 39.130 1.84 0.00 44.63 2.82
24 25 4.081309 AGAGCATAATTGGTTTGCTGCATT 60.081 37.500 1.84 0.00 46.21 3.56
25 26 3.449737 AGAGCATAATTGGTTTGCTGCAT 59.550 39.130 1.84 0.00 46.21 3.96
26 27 2.827322 AGAGCATAATTGGTTTGCTGCA 59.173 40.909 0.00 0.00 46.21 4.41
27 28 3.515330 AGAGCATAATTGGTTTGCTGC 57.485 42.857 10.49 0.00 46.21 5.25
28 29 6.094603 AGAGTAAGAGCATAATTGGTTTGCTG 59.905 38.462 10.49 0.00 46.21 4.41
30 31 6.261118 CAGAGTAAGAGCATAATTGGTTTGC 58.739 40.000 0.00 0.00 32.62 3.68
31 32 6.261118 GCAGAGTAAGAGCATAATTGGTTTG 58.739 40.000 0.00 0.00 32.62 2.93
32 33 5.358160 GGCAGAGTAAGAGCATAATTGGTTT 59.642 40.000 0.00 0.00 32.62 3.27
33 34 4.884164 GGCAGAGTAAGAGCATAATTGGTT 59.116 41.667 0.00 0.00 32.62 3.67
34 35 4.080356 TGGCAGAGTAAGAGCATAATTGGT 60.080 41.667 0.00 0.00 35.95 3.67
35 36 4.454678 TGGCAGAGTAAGAGCATAATTGG 58.545 43.478 0.00 0.00 0.00 3.16
36 37 4.514441 CCTGGCAGAGTAAGAGCATAATTG 59.486 45.833 17.94 0.00 0.00 2.32
37 38 4.410228 TCCTGGCAGAGTAAGAGCATAATT 59.590 41.667 17.94 0.00 0.00 1.40
38 39 3.969976 TCCTGGCAGAGTAAGAGCATAAT 59.030 43.478 17.94 0.00 0.00 1.28
39 40 3.133003 GTCCTGGCAGAGTAAGAGCATAA 59.867 47.826 17.94 0.00 0.00 1.90
40 41 2.695666 GTCCTGGCAGAGTAAGAGCATA 59.304 50.000 17.94 0.00 0.00 3.14
41 42 1.484240 GTCCTGGCAGAGTAAGAGCAT 59.516 52.381 17.94 0.00 0.00 3.79
42 43 0.898320 GTCCTGGCAGAGTAAGAGCA 59.102 55.000 17.94 0.00 0.00 4.26
43 44 0.898320 TGTCCTGGCAGAGTAAGAGC 59.102 55.000 17.94 0.45 0.00 4.09
44 45 1.135257 CGTGTCCTGGCAGAGTAAGAG 60.135 57.143 17.94 0.00 0.00 2.85
90 94 5.295950 CAACTGATCTCGAGGCTAATGAAT 58.704 41.667 13.56 0.00 0.00 2.57
91 95 4.686972 CAACTGATCTCGAGGCTAATGAA 58.313 43.478 13.56 0.00 0.00 2.57
92 96 3.491619 GCAACTGATCTCGAGGCTAATGA 60.492 47.826 13.56 0.00 0.00 2.57
93 97 2.799412 GCAACTGATCTCGAGGCTAATG 59.201 50.000 13.56 6.63 0.00 1.90
94 98 2.544694 CGCAACTGATCTCGAGGCTAAT 60.545 50.000 13.56 0.00 0.00 1.73
95 99 1.202302 CGCAACTGATCTCGAGGCTAA 60.202 52.381 13.56 0.00 0.00 3.09
98 102 2.520904 GCGCAACTGATCTCGAGGC 61.521 63.158 13.56 5.01 0.00 4.70
338 378 2.482333 CGAGAGATCCTTCCGCGGT 61.482 63.158 27.15 4.54 0.00 5.68
574 614 1.375098 GAGTAGTCGCCGGTAGCAGT 61.375 60.000 1.90 0.00 44.04 4.40
619 659 5.975693 ACCTTCTTATTGATCCGCAAAAA 57.024 34.783 0.00 0.00 40.48 1.94
620 660 7.556275 AGATTACCTTCTTATTGATCCGCAAAA 59.444 33.333 0.00 0.00 40.48 2.44
621 661 7.054124 AGATTACCTTCTTATTGATCCGCAAA 58.946 34.615 0.00 0.00 40.48 3.68
622 662 6.591935 AGATTACCTTCTTATTGATCCGCAA 58.408 36.000 0.00 0.00 41.53 4.85
623 663 6.174720 AGATTACCTTCTTATTGATCCGCA 57.825 37.500 0.00 0.00 0.00 5.69
624 664 7.329717 CAGTAGATTACCTTCTTATTGATCCGC 59.670 40.741 0.00 0.00 0.00 5.54
625 665 8.361139 ACAGTAGATTACCTTCTTATTGATCCG 58.639 37.037 0.00 0.00 0.00 4.18
629 669 9.197306 TGCTACAGTAGATTACCTTCTTATTGA 57.803 33.333 12.15 0.00 0.00 2.57
630 670 9.250624 GTGCTACAGTAGATTACCTTCTTATTG 57.749 37.037 12.15 0.00 0.00 1.90
631 671 8.136165 CGTGCTACAGTAGATTACCTTCTTATT 58.864 37.037 12.15 0.00 0.00 1.40
632 672 7.649973 CGTGCTACAGTAGATTACCTTCTTAT 58.350 38.462 12.15 0.00 0.00 1.73
633 673 6.459298 GCGTGCTACAGTAGATTACCTTCTTA 60.459 42.308 12.15 0.00 0.00 2.10
634 674 5.679127 GCGTGCTACAGTAGATTACCTTCTT 60.679 44.000 12.15 0.00 0.00 2.52
635 675 4.202030 GCGTGCTACAGTAGATTACCTTCT 60.202 45.833 12.15 0.00 0.00 2.85
636 676 4.043073 GCGTGCTACAGTAGATTACCTTC 58.957 47.826 12.15 0.00 0.00 3.46
637 677 3.488721 CGCGTGCTACAGTAGATTACCTT 60.489 47.826 12.15 0.00 0.00 3.50
638 678 2.033049 CGCGTGCTACAGTAGATTACCT 59.967 50.000 12.15 0.00 0.00 3.08
639 679 2.223433 ACGCGTGCTACAGTAGATTACC 60.223 50.000 12.93 0.00 0.00 2.85
640 680 2.782192 CACGCGTGCTACAGTAGATTAC 59.218 50.000 28.16 5.98 0.00 1.89
641 681 3.060978 CACGCGTGCTACAGTAGATTA 57.939 47.619 28.16 0.00 0.00 1.75
642 682 1.909376 CACGCGTGCTACAGTAGATT 58.091 50.000 28.16 0.00 0.00 2.40
643 683 3.624305 CACGCGTGCTACAGTAGAT 57.376 52.632 28.16 0.00 0.00 1.98
666 706 2.028484 ACCGCCACTACACGTGTG 59.972 61.111 30.83 21.35 42.20 3.82
667 707 1.812686 ATCACCGCCACTACACGTGT 61.813 55.000 26.52 26.52 42.20 4.49
668 708 1.080093 ATCACCGCCACTACACGTG 60.080 57.895 15.48 15.48 43.41 4.49
689 1968 0.029035 GCTGGCGAGCAATTCATCAG 59.971 55.000 16.60 0.00 45.46 2.90
699 1978 2.731374 CCTACCTAGCTGGCGAGC 59.269 66.667 13.51 13.51 46.64 5.03
700 1979 1.455959 ACCCTACCTAGCTGGCGAG 60.456 63.158 0.00 0.00 40.22 5.03
701 1980 1.455217 GACCCTACCTAGCTGGCGA 60.455 63.158 0.00 0.00 40.22 5.54
702 1981 1.455959 AGACCCTACCTAGCTGGCG 60.456 63.158 0.00 0.00 40.22 5.69
703 1982 0.397254 TCAGACCCTACCTAGCTGGC 60.397 60.000 0.00 0.00 40.22 4.85
704 1983 1.342076 TGTCAGACCCTACCTAGCTGG 60.342 57.143 0.00 0.00 42.93 4.85
705 1984 2.145397 TGTCAGACCCTACCTAGCTG 57.855 55.000 0.00 0.00 0.00 4.24
706 1985 3.034635 CAATGTCAGACCCTACCTAGCT 58.965 50.000 0.00 0.00 0.00 3.32
707 1986 2.483889 GCAATGTCAGACCCTACCTAGC 60.484 54.545 0.00 0.00 0.00 3.42
716 1995 5.989777 ACCTATATAAACGCAATGTCAGACC 59.010 40.000 0.00 0.00 0.00 3.85
717 1996 7.011109 ACAACCTATATAAACGCAATGTCAGAC 59.989 37.037 0.00 0.00 0.00 3.51
724 2003 5.603596 TCCGACAACCTATATAAACGCAAT 58.396 37.500 0.00 0.00 0.00 3.56
741 2020 2.748647 TCGATCACGCCTCCGACA 60.749 61.111 0.00 0.00 39.58 4.35
917 2196 2.959516 ACGACGACACATCATCATTGT 58.040 42.857 0.00 0.00 0.00 2.71
918 2197 3.614176 AGAACGACGACACATCATCATTG 59.386 43.478 0.00 0.00 0.00 2.82
919 2198 3.614176 CAGAACGACGACACATCATCATT 59.386 43.478 0.00 0.00 0.00 2.57
920 2199 3.182182 CAGAACGACGACACATCATCAT 58.818 45.455 0.00 0.00 0.00 2.45
946 2265 7.201513 GCAAATCATCAGGCGCTTAATTAAAAA 60.202 33.333 7.64 0.00 0.00 1.94
947 2266 6.255453 GCAAATCATCAGGCGCTTAATTAAAA 59.745 34.615 7.64 0.00 0.00 1.52
948 2267 5.748152 GCAAATCATCAGGCGCTTAATTAAA 59.252 36.000 7.64 0.00 0.00 1.52
949 2268 5.280945 GCAAATCATCAGGCGCTTAATTAA 58.719 37.500 7.64 0.00 0.00 1.40
952 2271 2.287188 CGCAAATCATCAGGCGCTTAAT 60.287 45.455 7.64 0.00 43.14 1.40
960 2279 2.684374 TGATCCAACGCAAATCATCAGG 59.316 45.455 0.00 0.00 0.00 3.86
967 2286 1.176527 CTGGGTGATCCAACGCAAAT 58.823 50.000 4.78 0.00 46.51 2.32
974 2293 1.204146 GTAGCTCCTGGGTGATCCAA 58.796 55.000 0.00 0.00 46.51 3.53
983 2304 0.387202 CATCTCCACGTAGCTCCTGG 59.613 60.000 0.00 0.00 0.00 4.45
1174 2503 2.939022 GAGGTTGCACACGCTGAC 59.061 61.111 0.00 0.00 39.64 3.51
1506 2835 1.802337 CGAGTGTGGTCCGGTTCTCA 61.802 60.000 0.00 0.00 0.00 3.27
1701 3031 2.923035 ACGGACTCCACCACCCTG 60.923 66.667 0.00 0.00 0.00 4.45
2011 3341 4.645136 AGATGTACATACAGACACCGACAT 59.355 41.667 8.71 0.00 39.92 3.06
2055 3391 5.160607 TCTTGAACCGACAATTCCTACAT 57.839 39.130 0.00 0.00 0.00 2.29
2084 3420 4.622740 GCAAATAGCACTGTGACCAAAATC 59.377 41.667 12.86 0.00 44.79 2.17
2175 3640 2.021457 AGTTTTAGGCACACCACACAC 58.979 47.619 0.00 0.00 39.06 3.82
2177 3642 2.290641 CTGAGTTTTAGGCACACCACAC 59.709 50.000 0.00 0.00 39.06 3.82
2178 3643 2.092646 ACTGAGTTTTAGGCACACCACA 60.093 45.455 0.00 0.00 39.06 4.17
2180 3645 2.805295 CGACTGAGTTTTAGGCACACCA 60.805 50.000 0.00 0.00 39.06 4.17
2181 3646 1.798813 CGACTGAGTTTTAGGCACACC 59.201 52.381 0.00 0.00 0.00 4.16
2182 3647 2.475487 GTCGACTGAGTTTTAGGCACAC 59.525 50.000 8.70 0.00 0.00 3.82
2197 3662 6.974932 TCGTTAAGTAAGTATCTGTCGACT 57.025 37.500 17.92 0.00 0.00 4.18
2212 3677 8.351888 CGTCACTCGATTGATACTTCGTTAAGT 61.352 40.741 8.84 0.00 44.36 2.24
2213 3678 6.076040 CGTCACTCGATTGATACTTCGTTAAG 60.076 42.308 8.84 0.00 42.86 1.85
2214 3679 5.735892 CGTCACTCGATTGATACTTCGTTAA 59.264 40.000 8.84 0.00 42.86 2.01
2215 3680 5.163824 ACGTCACTCGATTGATACTTCGTTA 60.164 40.000 8.84 0.00 42.86 3.18
2219 3684 3.719840 CGACGTCACTCGATTGATACTTC 59.280 47.826 17.16 0.69 42.86 3.01
2259 3724 0.179121 TGTAGCATCCAACCGCGTAG 60.179 55.000 4.92 0.00 0.00 3.51
2260 3725 0.246910 TTGTAGCATCCAACCGCGTA 59.753 50.000 4.92 0.00 0.00 4.42
2267 3734 1.268352 GTTGCCGTTTGTAGCATCCAA 59.732 47.619 0.00 0.00 39.11 3.53
2295 3762 3.791993 TTGTTGTTATACCGTCGCAAC 57.208 42.857 0.00 0.00 39.62 4.17
2363 3834 0.107643 TCATCTCACCGGTTGCAACA 59.892 50.000 29.55 8.91 0.00 3.33
2427 3898 3.637911 TTCCTACCGGTTGCAACATAT 57.362 42.857 29.55 16.35 0.00 1.78
2428 3899 3.420300 TTTCCTACCGGTTGCAACATA 57.580 42.857 29.55 17.23 0.00 2.29
2451 3922 1.614996 TGTCCCATCGTTTGCAACAT 58.385 45.000 0.00 0.00 0.00 2.71
2609 4087 8.708742 GCATATTAGGTTTTCCAAAAGTCAAAC 58.291 33.333 0.00 0.00 43.73 2.93
2672 4164 2.370519 TCCTAAGTGGTAGCTTTGTGCA 59.629 45.455 0.00 0.00 39.73 4.57
2685 4177 7.463961 TCAGGTTAGAAACTACTCCTAAGTG 57.536 40.000 0.00 0.00 36.92 3.16
2686 4178 7.894364 TCATCAGGTTAGAAACTACTCCTAAGT 59.106 37.037 0.00 0.00 39.66 2.24
2689 4181 6.321690 GCTCATCAGGTTAGAAACTACTCCTA 59.678 42.308 0.00 0.00 0.00 2.94
2690 4182 5.128008 GCTCATCAGGTTAGAAACTACTCCT 59.872 44.000 0.00 0.00 0.00 3.69
2692 4184 5.967088 TGCTCATCAGGTTAGAAACTACTC 58.033 41.667 0.00 0.00 0.00 2.59
2694 4186 5.932303 TGTTGCTCATCAGGTTAGAAACTAC 59.068 40.000 0.00 0.00 31.18 2.73
2793 4358 1.295423 GCCAAGGTAGAAGACGGCA 59.705 57.895 0.00 0.00 39.38 5.69
2803 4368 2.257691 TTACACGCTTTGCCAAGGTA 57.742 45.000 0.00 0.00 0.00 3.08
2817 4382 4.439057 TCTCATGCCGATACCTTTTACAC 58.561 43.478 0.00 0.00 0.00 2.90
2820 4385 4.873827 GTGTTCTCATGCCGATACCTTTTA 59.126 41.667 0.00 0.00 0.00 1.52
2821 4386 3.689649 GTGTTCTCATGCCGATACCTTTT 59.310 43.478 0.00 0.00 0.00 2.27
2828 4393 1.278985 TCCTTGTGTTCTCATGCCGAT 59.721 47.619 0.00 0.00 0.00 4.18
2892 4460 9.904198 TCCTTCACTGATGTAATGAATTATGAA 57.096 29.630 0.00 0.00 32.16 2.57
2893 4461 9.551734 CTCCTTCACTGATGTAATGAATTATGA 57.448 33.333 0.00 0.00 32.16 2.15
2894 4462 9.551734 TCTCCTTCACTGATGTAATGAATTATG 57.448 33.333 0.00 0.00 32.16 1.90
2895 4463 9.775854 CTCTCCTTCACTGATGTAATGAATTAT 57.224 33.333 0.00 0.00 32.16 1.28
2896 4464 8.981659 TCTCTCCTTCACTGATGTAATGAATTA 58.018 33.333 0.00 0.00 32.16 1.40
2897 4465 7.855375 TCTCTCCTTCACTGATGTAATGAATT 58.145 34.615 0.00 0.00 32.16 2.17
2898 4466 7.429374 TCTCTCCTTCACTGATGTAATGAAT 57.571 36.000 0.00 0.00 32.16 2.57


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

AutoCloner maintained by Alex Coulton.