Multiple sequence alignment - TraesCS6A01G015000

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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 TraesCS6A01G015000 chr6A 100.000 3248 0 0 1 3248 7187802 7184555 0.000000e+00 5999.0
1 TraesCS6A01G015000 chr6A 88.699 2221 216 25 947 3149 7176019 7173816 0.000000e+00 2678.0
2 TraesCS6A01G015000 chr6A 86.851 2426 273 35 744 3144 7079353 7081757 0.000000e+00 2671.0
3 TraesCS6A01G015000 chr6A 89.196 1157 79 15 2094 3248 7091335 7092447 0.000000e+00 1402.0
4 TraesCS6A01G015000 chr6A 93.204 103 7 0 3146 3248 7081795 7081897 5.610000e-33 152.0
5 TraesCS6A01G015000 chr6B 91.285 2203 172 15 951 3144 12886533 12888724 0.000000e+00 2987.0
6 TraesCS6A01G015000 chr6B 89.057 2184 216 15 979 3149 13653943 13651770 0.000000e+00 2687.0
7 TraesCS6A01G015000 chr6B 89.632 2122 206 12 1032 3144 26861831 26863947 0.000000e+00 2687.0
8 TraesCS6A01G015000 chr6B 86.130 2199 219 33 1 2147 13705866 13703702 0.000000e+00 2292.0
9 TraesCS6A01G015000 chr6B 89.200 250 19 4 640 885 13441772 13441527 4.070000e-79 305.0
10 TraesCS6A01G015000 chr6B 80.000 210 30 6 665 865 13654260 13654054 9.390000e-31 145.0
11 TraesCS6A01G015000 chr6B 79.085 153 19 6 1 140 691030280 691030432 3.450000e-15 93.5
12 TraesCS6A01G015000 chr5B 90.331 2203 195 13 951 3144 432982634 432984827 0.000000e+00 2872.0
13 TraesCS6A01G015000 chrUn 90.500 2179 189 15 973 3144 79937079 79939246 0.000000e+00 2861.0
14 TraesCS6A01G015000 chrUn 88.629 2181 229 15 979 3149 80037161 80034990 0.000000e+00 2636.0
15 TraesCS6A01G015000 chrUn 86.829 1602 195 11 973 2567 79854623 79856215 0.000000e+00 1775.0
16 TraesCS6A01G015000 chrUn 76.526 213 32 13 652 862 79936783 79936979 2.060000e-17 100.0
17 TraesCS6A01G015000 chrUn 75.676 222 36 13 643 862 79854318 79854523 9.590000e-16 95.3
18 TraesCS6A01G015000 chrUn 81.651 109 15 4 760 865 80037370 80037264 5.770000e-13 86.1
19 TraesCS6A01G015000 chr7D 88.990 2207 223 16 954 3149 597677181 597674984 0.000000e+00 2712.0
20 TraesCS6A01G015000 chr7D 84.483 58 9 0 329 386 443428505 443428562 1.260000e-04 58.4
21 TraesCS6A01G015000 chr6D 84.738 1756 250 13 984 2731 22182617 22184362 0.000000e+00 1742.0
22 TraesCS6A01G015000 chr6D 89.286 56 6 0 423 478 266746689 266746634 1.620000e-08 71.3
23 TraesCS6A01G015000 chr7B 82.308 520 79 8 5 518 185285240 185284728 3.850000e-119 438.0
24 TraesCS6A01G015000 chr3B 80.570 386 56 11 5 390 807485611 807485977 2.470000e-71 279.0
25 TraesCS6A01G015000 chr1D 78.547 289 49 11 105 391 346667249 346666972 9.260000e-41 178.0
26 TraesCS6A01G015000 chr2B 78.000 250 38 5 124 373 2125183 2124951 1.210000e-29 141.0
27 TraesCS6A01G015000 chr3D 82.278 79 14 0 312 390 518319978 518320056 5.810000e-08 69.4
28 TraesCS6A01G015000 chr1B 85.484 62 9 0 325 386 304183241 304183302 7.520000e-07 65.8


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 TraesCS6A01G015000 chr6A 7184555 7187802 3247 True 5999.00 5999 100.0000 1 3248 1 chr6A.!!$R2 3247
1 TraesCS6A01G015000 chr6A 7173816 7176019 2203 True 2678.00 2678 88.6990 947 3149 1 chr6A.!!$R1 2202
2 TraesCS6A01G015000 chr6A 7079353 7081897 2544 False 1411.50 2671 90.0275 744 3248 2 chr6A.!!$F2 2504
3 TraesCS6A01G015000 chr6A 7091335 7092447 1112 False 1402.00 1402 89.1960 2094 3248 1 chr6A.!!$F1 1154
4 TraesCS6A01G015000 chr6B 12886533 12888724 2191 False 2987.00 2987 91.2850 951 3144 1 chr6B.!!$F1 2193
5 TraesCS6A01G015000 chr6B 26861831 26863947 2116 False 2687.00 2687 89.6320 1032 3144 1 chr6B.!!$F2 2112
6 TraesCS6A01G015000 chr6B 13703702 13705866 2164 True 2292.00 2292 86.1300 1 2147 1 chr6B.!!$R2 2146
7 TraesCS6A01G015000 chr6B 13651770 13654260 2490 True 1416.00 2687 84.5285 665 3149 2 chr6B.!!$R3 2484
8 TraesCS6A01G015000 chr5B 432982634 432984827 2193 False 2872.00 2872 90.3310 951 3144 1 chr5B.!!$F1 2193
9 TraesCS6A01G015000 chrUn 79936783 79939246 2463 False 1480.50 2861 83.5130 652 3144 2 chrUn.!!$F2 2492
10 TraesCS6A01G015000 chrUn 80034990 80037370 2380 True 1361.05 2636 85.1400 760 3149 2 chrUn.!!$R1 2389
11 TraesCS6A01G015000 chrUn 79854318 79856215 1897 False 935.15 1775 81.2525 643 2567 2 chrUn.!!$F1 1924
12 TraesCS6A01G015000 chr7D 597674984 597677181 2197 True 2712.00 2712 88.9900 954 3149 1 chr7D.!!$R1 2195
13 TraesCS6A01G015000 chr6D 22182617 22184362 1745 False 1742.00 1742 84.7380 984 2731 1 chr6D.!!$F1 1747
14 TraesCS6A01G015000 chr7B 185284728 185285240 512 True 438.00 438 82.3080 5 518 1 chr7B.!!$R1 513

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
644 671 0.108233 CACCTCTTGAGAGAGCCAGC 60.108 60.0 9.55 0.0 46.64 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 2571 0.543749 AAAGAGATCCTGGGCTTCCG 59.456 55.0 0.0 0.0 0.0 4.3 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
89 90 4.880537 CGCGCGGGAAGAGCTCAT 62.881 66.667 24.84 2.97 43.79 2.90
111 112 2.079326 GGAGCTGAACCTCCCCTTT 58.921 57.895 0.00 0.00 44.60 3.11
158 180 1.976132 GATGGCTGGCTGGCTAGTGA 61.976 60.000 18.27 0.00 42.34 3.41
197 219 0.450983 GAGCAAGCTTGACCAGATGC 59.549 55.000 30.39 12.74 37.22 3.91
201 223 0.254178 AAGCTTGACCAGATGCGGAT 59.746 50.000 0.00 0.00 0.00 4.18
248 270 1.805428 GCCGCCACACACTTCCATTT 61.805 55.000 0.00 0.00 0.00 2.32
264 286 1.807742 CATTTAAAAGGACGGGCACGA 59.192 47.619 19.19 0.00 44.60 4.35
282 304 1.134098 CGAGGCCCTTCCATACATTGT 60.134 52.381 0.00 0.00 37.29 2.71
288 310 1.942657 CCTTCCATACATTGTCAGGCG 59.057 52.381 0.00 0.00 0.00 5.52
380 402 2.445085 ACACCGAGGGGACACACA 60.445 61.111 0.00 0.00 36.97 3.72
395 417 3.445687 ACAGCGCGTCCGTCCATA 61.446 61.111 8.43 0.00 36.67 2.74
401 423 1.138247 GCGTCCGTCCATAAGTCGT 59.862 57.895 0.00 0.00 0.00 4.34
408 430 0.591741 GTCCATAAGTCGTCGCGGAG 60.592 60.000 6.13 0.00 0.00 4.63
409 431 1.028330 TCCATAAGTCGTCGCGGAGT 61.028 55.000 6.13 0.00 0.00 3.85
428 450 1.511887 CGAAGCGGACGCATTTTGG 60.512 57.895 19.48 2.35 44.88 3.28
429 451 1.873165 GAAGCGGACGCATTTTGGA 59.127 52.632 19.48 0.00 44.88 3.53
438 460 1.967066 ACGCATTTTGGATTTGGGTCA 59.033 42.857 0.00 0.00 31.77 4.02
440 462 2.029110 CGCATTTTGGATTTGGGTCAGT 60.029 45.455 0.00 0.00 0.00 3.41
462 484 1.468395 CGTTGGGCAGTCGTTTTTGTT 60.468 47.619 0.00 0.00 0.00 2.83
465 487 0.933047 GGGCAGTCGTTTTTGTTCGC 60.933 55.000 0.00 0.00 0.00 4.70
469 491 3.792719 GTCGTTTTTGTTCGCGACT 57.207 47.368 9.15 0.00 46.74 4.18
478 500 0.600782 TGTTCGCGACTACCCAAACC 60.601 55.000 9.15 0.00 0.00 3.27
479 501 0.320160 GTTCGCGACTACCCAAACCT 60.320 55.000 9.15 0.00 0.00 3.50
480 502 0.320073 TTCGCGACTACCCAAACCTG 60.320 55.000 9.15 0.00 0.00 4.00
481 503 1.740296 CGCGACTACCCAAACCTGG 60.740 63.158 0.00 0.00 43.10 4.45
496 523 1.184970 CCTGGCGGACAAAATGGGTT 61.185 55.000 0.00 0.00 0.00 4.11
498 525 0.757188 TGGCGGACAAAATGGGTTGT 60.757 50.000 0.00 0.00 44.38 3.32
525 552 3.811083 TGAAGTTGCTCGAAGGGTAAAA 58.189 40.909 0.00 0.00 0.00 1.52
527 554 2.501261 AGTTGCTCGAAGGGTAAAACC 58.499 47.619 0.00 0.00 37.60 3.27
534 561 4.309933 CTCGAAGGGTAAAACCGTAAACT 58.690 43.478 0.00 0.00 39.83 2.66
560 587 3.273434 TGCGTAGTAGTACAGGTGTAGG 58.727 50.000 8.43 0.00 0.00 3.18
581 608 2.762327 GGATGCCAAATGGTGTGAAGAT 59.238 45.455 0.71 0.00 37.57 2.40
583 610 2.596346 TGCCAAATGGTGTGAAGATGT 58.404 42.857 0.71 0.00 37.57 3.06
590 617 3.576078 TGGTGTGAAGATGTCCTTTGT 57.424 42.857 0.00 0.00 34.68 2.83
599 626 4.552166 AGATGTCCTTTGTTGTTTCACG 57.448 40.909 0.00 0.00 0.00 4.35
600 627 3.315191 AGATGTCCTTTGTTGTTTCACGG 59.685 43.478 0.00 0.00 0.00 4.94
601 628 2.438411 TGTCCTTTGTTGTTTCACGGT 58.562 42.857 0.00 0.00 0.00 4.83
620 647 1.172180 TACTGCTGTGCTGCAAACCC 61.172 55.000 2.77 0.00 42.83 4.11
621 648 2.441717 TGCTGTGCTGCAAACCCA 60.442 55.556 2.77 0.00 40.29 4.51
622 649 2.028043 GCTGTGCTGCAAACCCAC 59.972 61.111 2.77 0.00 0.00 4.61
623 650 2.492773 GCTGTGCTGCAAACCCACT 61.493 57.895 2.77 0.00 0.00 4.00
624 651 2.019897 GCTGTGCTGCAAACCCACTT 62.020 55.000 2.77 0.00 0.00 3.16
626 653 0.682532 TGTGCTGCAAACCCACTTCA 60.683 50.000 2.77 0.00 0.00 3.02
628 655 1.363807 GCTGCAAACCCACTTCACC 59.636 57.895 0.00 0.00 0.00 4.02
632 659 1.064017 TGCAAACCCACTTCACCTCTT 60.064 47.619 0.00 0.00 0.00 2.85
633 660 1.338020 GCAAACCCACTTCACCTCTTG 59.662 52.381 0.00 0.00 0.00 3.02
634 661 2.930950 CAAACCCACTTCACCTCTTGA 58.069 47.619 0.00 0.00 0.00 3.02
635 662 2.880890 CAAACCCACTTCACCTCTTGAG 59.119 50.000 0.00 0.00 34.94 3.02
636 663 2.103153 ACCCACTTCACCTCTTGAGA 57.897 50.000 0.00 0.00 34.94 3.27
637 664 1.974236 ACCCACTTCACCTCTTGAGAG 59.026 52.381 0.93 0.93 41.71 3.20
638 665 2.251818 CCCACTTCACCTCTTGAGAGA 58.748 52.381 9.55 0.00 44.74 3.10
640 667 2.353605 CCACTTCACCTCTTGAGAGAGC 60.354 54.545 9.55 0.00 46.64 4.09
641 668 1.899142 ACTTCACCTCTTGAGAGAGCC 59.101 52.381 9.55 0.00 46.64 4.70
643 670 1.554836 TCACCTCTTGAGAGAGCCAG 58.445 55.000 9.55 0.00 46.64 4.85
644 671 0.108233 CACCTCTTGAGAGAGCCAGC 60.108 60.000 9.55 0.00 46.64 4.85
647 674 2.904470 CTCTTGAGAGAGCCAGCGGC 62.904 65.000 11.02 11.02 44.74 6.53
742 787 2.185350 CTGGCACCAGCGAGTAGG 59.815 66.667 3.23 0.00 41.15 3.18
768 813 3.141488 CGTCCTCGTCCCCCTCAG 61.141 72.222 0.00 0.00 0.00 3.35
915 982 0.741915 CCGTCCTCCTAACTCTGCTC 59.258 60.000 0.00 0.00 0.00 4.26
929 996 6.472686 AACTCTGCTCTCGTTATTTCCTAT 57.527 37.500 0.00 0.00 0.00 2.57
969 1053 2.203728 TGGTAGGTGGTGAGCGGT 60.204 61.111 0.00 0.00 0.00 5.68
1093 1195 0.884259 CGGACACATTGGCACTCACA 60.884 55.000 0.00 0.00 0.00 3.58
1197 1299 2.693762 CCGTGATTGCCCTGTGCTG 61.694 63.158 0.00 0.00 42.00 4.41
1477 1582 7.775120 ACCAAATATTTTCTCCTACAGCATTG 58.225 34.615 0.00 0.00 0.00 2.82
1634 1742 1.771854 TGAGGTGGACCAAGCTTACAA 59.228 47.619 0.00 0.00 38.89 2.41
1715 1823 0.815734 ATCTCTGGCATGTGCAAAGC 59.184 50.000 7.36 0.00 44.36 3.51
1719 1827 0.315886 CTGGCATGTGCAAAGCTCAA 59.684 50.000 7.36 0.00 44.36 3.02
1720 1828 0.970640 TGGCATGTGCAAAGCTCAAT 59.029 45.000 7.36 0.00 44.36 2.57
1723 1831 2.259618 GCATGTGCAAAGCTCAATCAG 58.740 47.619 0.00 0.00 41.59 2.90
1735 1843 2.355108 GCTCAATCAGTGGACAAGGCTA 60.355 50.000 0.00 0.00 0.00 3.93
1761 1869 5.049129 GGAGGTTCTTCAACAGATGTTTGAG 60.049 44.000 0.00 0.00 35.83 3.02
1809 1917 8.314751 ACCACATATAATAGTCTGATACAAGGC 58.685 37.037 0.00 0.00 0.00 4.35
1844 1952 0.321564 CGGTGCAAAGAGGTGGATCA 60.322 55.000 0.00 0.00 0.00 2.92
1929 2037 2.945668 GGATTATCTTTGCAAGAGCGGT 59.054 45.455 0.00 0.00 46.23 5.68
1930 2038 3.002759 GGATTATCTTTGCAAGAGCGGTC 59.997 47.826 6.48 6.48 46.23 4.79
1931 2039 2.760634 TATCTTTGCAAGAGCGGTCA 57.239 45.000 18.15 0.00 46.23 4.02
1983 2091 3.683365 ATGATCAGTTTGGGCCAAAAC 57.317 42.857 31.94 25.93 39.80 2.43
1991 2099 3.680786 GGGCCAAAACCCGACTGC 61.681 66.667 4.39 0.00 40.98 4.40
2082 2190 9.252962 CTTATTGATTTGATGGTAGAAAATGGC 57.747 33.333 0.00 0.00 0.00 4.40
2091 2199 4.415596 TGGTAGAAAATGGCATTTCACCT 58.584 39.130 30.70 25.37 40.89 4.00
2127 2235 9.347934 GTCTACAACATACTCATATCTGCATAC 57.652 37.037 0.00 0.00 0.00 2.39
2321 2430 4.351407 TCCTGGTACCATAGTTTTCAACCA 59.649 41.667 16.75 0.00 34.52 3.67
2405 2515 2.106938 GGATCGCGCATCTGTCCA 59.893 61.111 8.75 0.00 0.00 4.02
2461 2571 4.754618 CCTTTGCAAAAATGGAAGGGTTAC 59.245 41.667 13.84 0.00 33.01 2.50
2707 2817 4.142049 TGTTTTCAGGGAAATGTTGGACAC 60.142 41.667 0.00 0.00 31.34 3.67
2713 2823 1.539827 GGAAATGTTGGACACGAAGGG 59.460 52.381 0.00 0.00 0.00 3.95
2720 2830 1.447314 GGACACGAAGGGTAAGCCG 60.447 63.158 0.00 0.00 34.97 5.52
2731 2841 2.431057 AGGGTAAGCCGTCTGTTATCAG 59.569 50.000 0.00 0.00 38.11 2.90
2768 2878 2.632028 TGGTGCATTGCTTAAATGTGGT 59.368 40.909 10.49 0.00 46.37 4.16
2813 2923 3.299503 GTTTGATGGTATCTGGGCCAAT 58.700 45.455 8.04 7.05 38.38 3.16
2908 3018 9.077885 AGAGTCTGATGATCTATTCCTTTCTAC 57.922 37.037 0.00 0.00 0.00 2.59
2941 3051 3.449227 TGCTGCCGACTCCCGTAG 61.449 66.667 0.00 0.00 36.31 3.51
2984 3094 4.538089 AGCTTACTTCAGAAAGGGGAGATT 59.462 41.667 0.00 0.00 36.78 2.40
2987 3097 3.536287 ACTTCAGAAAGGGGAGATTCCT 58.464 45.455 0.00 0.00 36.78 3.36
3080 3190 2.416107 CTGCACTTGCTTCAGGGGGA 62.416 60.000 2.33 0.00 42.66 4.81
3095 3205 1.688311 GGGGGAAAAGGCCAGGAATAC 60.688 57.143 5.01 0.00 0.00 1.89
3151 3297 2.031870 GGAACAGGGCACTTTGAACTT 58.968 47.619 0.00 0.00 0.00 2.66
3160 3306 4.636206 GGGCACTTTGAACTTCTAATCGAT 59.364 41.667 0.00 0.00 0.00 3.59
3207 3353 9.974980 GTTACATCTCCCAACATTTTCTTTTTA 57.025 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 3.706373 GGAGGTTCAGCTCCGGCA 61.706 66.667 9.27 0.00 41.70 5.69
158 180 0.170561 CCTCGTCGTCGACCAGAAAT 59.829 55.000 19.88 0.00 41.35 2.17
197 219 1.475751 CCACTTTCATCTCCCCATCCG 60.476 57.143 0.00 0.00 0.00 4.18
201 223 2.507058 CTCATCCACTTTCATCTCCCCA 59.493 50.000 0.00 0.00 0.00 4.96
235 257 4.277423 CCGTCCTTTTAAATGGAAGTGTGT 59.723 41.667 24.42 0.00 34.45 3.72
248 270 1.294138 CCTCGTGCCCGTCCTTTTA 59.706 57.895 0.00 0.00 35.01 1.52
264 286 1.922447 TGACAATGTATGGAAGGGCCT 59.078 47.619 0.00 0.00 37.63 5.19
282 304 4.435970 TACCTCGAGCCCGCCTGA 62.436 66.667 6.99 0.00 35.37 3.86
288 310 4.862823 AGCCCCTACCTCGAGCCC 62.863 72.222 6.99 0.00 0.00 5.19
362 384 2.342648 GTGTGTCCCCTCGGTGTC 59.657 66.667 0.00 0.00 0.00 3.67
380 402 2.104331 CTTATGGACGGACGCGCT 59.896 61.111 5.73 0.00 0.00 5.92
395 417 2.510190 CTTCGACTCCGCGACGACTT 62.510 60.000 8.23 0.00 39.36 3.01
408 430 0.789383 CAAAATGCGTCCGCTTCGAC 60.789 55.000 13.31 0.00 42.51 4.20
409 431 1.495509 CAAAATGCGTCCGCTTCGA 59.504 52.632 13.31 0.00 42.51 3.71
416 438 1.275010 ACCCAAATCCAAAATGCGTCC 59.725 47.619 0.00 0.00 0.00 4.79
420 442 3.328505 CACTGACCCAAATCCAAAATGC 58.671 45.455 0.00 0.00 0.00 3.56
428 450 0.240945 CCAACGCACTGACCCAAATC 59.759 55.000 0.00 0.00 0.00 2.17
429 451 1.178534 CCCAACGCACTGACCCAAAT 61.179 55.000 0.00 0.00 0.00 2.32
438 460 3.750373 AACGACTGCCCAACGCACT 62.750 57.895 0.00 0.00 44.64 4.40
452 474 1.522258 GGTAGTCGCGAACAAAAACGA 59.478 47.619 12.06 0.00 0.00 3.85
462 484 1.290955 CAGGTTTGGGTAGTCGCGA 59.709 57.895 3.71 3.71 0.00 5.87
465 487 1.740296 CGCCAGGTTTGGGTAGTCG 60.740 63.158 0.00 0.00 45.16 4.18
469 491 1.706995 TTGTCCGCCAGGTTTGGGTA 61.707 55.000 0.00 0.00 45.16 3.69
478 500 0.038343 CAACCCATTTTGTCCGCCAG 60.038 55.000 0.00 0.00 0.00 4.85
479 501 0.757188 ACAACCCATTTTGTCCGCCA 60.757 50.000 0.00 0.00 34.48 5.69
480 502 0.038618 GACAACCCATTTTGTCCGCC 60.039 55.000 4.91 0.00 46.60 6.13
481 503 3.489813 GACAACCCATTTTGTCCGC 57.510 52.632 4.91 0.00 46.60 5.54
496 523 0.878523 CGAGCAACTTCAACGGGACA 60.879 55.000 0.00 0.00 0.00 4.02
498 525 0.105224 TTCGAGCAACTTCAACGGGA 59.895 50.000 0.00 0.00 0.00 5.14
525 552 2.053627 CTACGCAAACGAGTTTACGGT 58.946 47.619 20.77 12.40 41.98 4.83
527 554 3.908382 ACTACTACGCAAACGAGTTTACG 59.092 43.478 16.79 16.79 42.98 3.18
534 561 2.813754 ACCTGTACTACTACGCAAACGA 59.186 45.455 0.00 0.00 43.93 3.85
542 569 4.277921 GCATCCCTACACCTGTACTACTAC 59.722 50.000 0.00 0.00 0.00 2.73
543 570 4.467769 GCATCCCTACACCTGTACTACTA 58.532 47.826 0.00 0.00 0.00 1.82
544 571 3.297736 GCATCCCTACACCTGTACTACT 58.702 50.000 0.00 0.00 0.00 2.57
560 587 2.170166 TCTTCACACCATTTGGCATCC 58.830 47.619 0.00 0.00 39.32 3.51
581 608 2.438411 ACCGTGAAACAACAAAGGACA 58.562 42.857 0.00 0.00 35.74 4.02
583 610 3.623960 CAGTACCGTGAAACAACAAAGGA 59.376 43.478 0.00 0.00 35.74 3.36
590 617 1.937223 CACAGCAGTACCGTGAAACAA 59.063 47.619 0.00 0.00 35.74 2.83
599 626 0.040067 GTTTGCAGCACAGCAGTACC 60.040 55.000 0.00 0.00 46.54 3.34
600 627 0.040067 GGTTTGCAGCACAGCAGTAC 60.040 55.000 5.86 0.00 46.54 2.73
601 628 1.172180 GGGTTTGCAGCACAGCAGTA 61.172 55.000 12.62 0.00 46.54 2.74
730 775 0.468400 GATCTCCCCTACTCGCTGGT 60.468 60.000 0.00 0.00 0.00 4.00
731 776 0.178975 AGATCTCCCCTACTCGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
732 777 1.243902 GAGATCTCCCCTACTCGCTG 58.756 60.000 12.00 0.00 0.00 5.18
733 778 0.250553 CGAGATCTCCCCTACTCGCT 60.251 60.000 17.13 0.00 43.71 4.93
734 779 2.249692 CGAGATCTCCCCTACTCGC 58.750 63.158 17.13 0.00 43.71 5.03
736 781 1.422402 AGGACGAGATCTCCCCTACTC 59.578 57.143 22.93 7.68 30.55 2.59
737 782 1.422402 GAGGACGAGATCTCCCCTACT 59.578 57.143 23.78 11.40 31.88 2.57
738 783 1.878948 CGAGGACGAGATCTCCCCTAC 60.879 61.905 23.78 17.61 42.66 3.18
739 784 0.397187 CGAGGACGAGATCTCCCCTA 59.603 60.000 23.78 0.00 42.66 3.53
740 785 1.149627 CGAGGACGAGATCTCCCCT 59.850 63.158 23.91 23.91 42.66 4.79
741 786 1.152922 ACGAGGACGAGATCTCCCC 60.153 63.158 17.13 17.05 42.66 4.81
742 787 1.167781 GGACGAGGACGAGATCTCCC 61.168 65.000 17.13 12.95 42.66 4.30
885 937 3.011517 AGGACGGGCTTGCTCCAT 61.012 61.111 2.92 0.00 0.00 3.41
943 1022 0.686769 ACCACCTACCAGACCGGATC 60.687 60.000 9.46 1.42 38.63 3.36
944 1023 0.976073 CACCACCTACCAGACCGGAT 60.976 60.000 9.46 0.00 38.63 4.18
952 1031 2.203728 ACCGCTCACCACCTACCA 60.204 61.111 0.00 0.00 0.00 3.25
969 1053 1.741401 CCTGAAGAATGCGTCGCCA 60.741 57.895 15.88 2.97 0.00 5.69
975 1075 1.377725 ACCTGGCCTGAAGAATGCG 60.378 57.895 11.88 0.00 0.00 4.73
977 1077 0.329261 TCCACCTGGCCTGAAGAATG 59.671 55.000 11.88 0.00 34.44 2.67
1093 1195 0.179094 TCGAACAGGTTGAGTGCGTT 60.179 50.000 0.00 0.00 39.08 4.84
1291 1393 1.227823 CGTGTCCAAGGTCCAAGCA 60.228 57.895 0.00 0.00 0.00 3.91
1326 1428 6.900194 AGCTTCTGTAAATCCCAGCTTAATA 58.100 36.000 0.00 0.00 33.79 0.98
1333 1435 4.950050 ACGATAGCTTCTGTAAATCCCAG 58.050 43.478 0.00 0.00 42.67 4.45
1477 1582 2.287009 CGTTGCAGAGACCCTTGAAAAC 60.287 50.000 0.00 0.00 0.00 2.43
1634 1742 3.758554 ACGCAGCATTTCAGAAAATAGGT 59.241 39.130 0.00 0.00 33.27 3.08
1715 1823 2.486472 AGCCTTGTCCACTGATTGAG 57.514 50.000 0.00 0.00 0.00 3.02
1719 1827 2.503356 CTCCTTAGCCTTGTCCACTGAT 59.497 50.000 0.00 0.00 0.00 2.90
1720 1828 1.902508 CTCCTTAGCCTTGTCCACTGA 59.097 52.381 0.00 0.00 0.00 3.41
1723 1831 0.984995 ACCTCCTTAGCCTTGTCCAC 59.015 55.000 0.00 0.00 0.00 4.02
1735 1843 4.713792 ACATCTGTTGAAGAACCTCCTT 57.286 40.909 0.00 0.00 38.79 3.36
1761 1869 6.772716 TGGTAATATTTGGCAGAATTCCTCTC 59.227 38.462 0.65 0.00 29.07 3.20
1806 1914 5.794894 CACCGTCCTAATGAATAATAGCCT 58.205 41.667 0.00 0.00 0.00 4.58
1809 1917 7.441157 TCTTTGCACCGTCCTAATGAATAATAG 59.559 37.037 0.00 0.00 0.00 1.73
1929 2037 3.261643 TCTTCCTAGCTTCTGCACATTGA 59.738 43.478 0.00 0.00 42.74 2.57
1930 2038 3.603532 TCTTCCTAGCTTCTGCACATTG 58.396 45.455 0.00 0.00 42.74 2.82
1931 2039 3.988976 TCTTCCTAGCTTCTGCACATT 57.011 42.857 0.00 0.00 42.74 2.71
1983 2091 1.948145 CTGTAGGTAGTAGCAGTCGGG 59.052 57.143 1.58 0.00 0.00 5.14
1991 2099 7.569639 TGAAGCAGAATACTGTAGGTAGTAG 57.430 40.000 0.00 0.00 45.04 2.57
2058 2166 8.303780 TGCCATTTTCTACCATCAAATCAATA 57.696 30.769 0.00 0.00 0.00 1.90
2082 2190 8.667076 TGTAGACATAATGATCAGGTGAAATG 57.333 34.615 0.09 1.45 0.00 2.32
2127 2235 4.215399 TCACCAACCATTTCTTCTTTAGCG 59.785 41.667 0.00 0.00 0.00 4.26
2321 2430 8.626526 CACAAGTACAAAAACCACTAATAAGGT 58.373 33.333 0.00 0.00 40.61 3.50
2461 2571 0.543749 AAAGAGATCCTGGGCTTCCG 59.456 55.000 0.00 0.00 0.00 4.30
2707 2817 0.037605 AACAGACGGCTTACCCTTCG 60.038 55.000 0.00 0.00 36.98 3.79
2713 2823 5.857822 AAAACTGATAACAGACGGCTTAC 57.142 39.130 7.05 0.00 46.03 2.34
2768 2878 5.520748 AATCTTTGGCTTCTTCCTTCCTA 57.479 39.130 0.00 0.00 0.00 2.94
2813 2923 1.340088 TAACGTCAGGCACTAACCCA 58.660 50.000 0.00 0.00 36.02 4.51
2908 3018 1.938577 CAGCACATCCATTCTTCTCCG 59.061 52.381 0.00 0.00 0.00 4.63
2984 3094 1.866943 AGATAAGTCCCAGCCCTAGGA 59.133 52.381 11.48 0.00 0.00 2.94
2987 3097 2.247635 AGACAGATAAGTCCCAGCCCTA 59.752 50.000 0.00 0.00 39.34 3.53
3080 3190 3.076032 ACTCCTTGTATTCCTGGCCTTTT 59.924 43.478 3.32 0.00 0.00 2.27
3144 3254 5.084818 TCAGGCATCGATTAGAAGTTCAA 57.915 39.130 5.50 0.00 0.00 2.69
3151 3297 5.734720 AGAAAAGTTCAGGCATCGATTAGA 58.265 37.500 0.00 0.00 0.00 2.10
3160 3306 2.430332 CCCACAAAGAAAAGTTCAGGCA 59.570 45.455 0.00 0.00 0.00 4.75
3207 3353 7.159372 AGTGACCTTCATTTTAGACGTACAAT 58.841 34.615 0.00 0.00 0.00 2.71
3209 3355 6.092955 AGTGACCTTCATTTTAGACGTACA 57.907 37.500 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.