Multiple sequence alignment - TraesCS6B01G310000

Loading Multiple Alignment...

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 TraesCS6B01G310000 chr6B 100.000 2492 0 0 1 2492 555340081 555342572 0.000000e+00 4602.0
1 TraesCS6B01G310000 chr6B 100.000 30 0 0 1939 1968 460906305 460906276 3.460000e-04 56.5
2 TraesCS6B01G310000 chr6A 95.785 1115 20 5 848 1946 511038310 511039413 0.000000e+00 1773.0
3 TraesCS6B01G310000 chr6A 87.316 544 40 11 333 849 511037810 511038351 1.650000e-166 595.0
4 TraesCS6B01G310000 chr6A 95.572 271 12 0 2191 2461 511040138 511040408 3.810000e-118 435.0
5 TraesCS6B01G310000 chr6A 94.093 237 7 2 1966 2195 511039668 511039904 1.100000e-93 353.0
6 TraesCS6B01G310000 chr6A 96.970 33 0 1 1936 1967 26954896 26954864 1.000000e-03 54.7
7 TraesCS6B01G310000 chr6D 95.300 1085 27 9 877 1946 370041369 370042444 0.000000e+00 1700.0
8 TraesCS6B01G310000 chr6D 93.528 309 12 4 2191 2492 370043095 370043402 1.050000e-123 453.0
9 TraesCS6B01G310000 chr6D 96.444 225 8 0 1966 2190 370042699 370042923 3.030000e-99 372.0
10 TraesCS6B01G310000 chr6D 87.793 213 24 2 65 276 370040518 370040729 5.320000e-62 248.0
11 TraesCS6B01G310000 chr5B 83.099 497 70 7 2 495 65280500 65280015 8.180000e-120 440.0
12 TraesCS6B01G310000 chr1B 81.431 517 65 19 2 499 544730918 544730414 6.460000e-106 394.0
13 TraesCS6B01G310000 chr7A 81.073 354 51 10 118 469 286515157 286515496 4.090000e-68 268.0
14 TraesCS6B01G310000 chr2A 91.228 171 11 4 1747 1916 451810542 451810375 1.930000e-56 230.0
15 TraesCS6B01G310000 chr2A 90.244 41 4 0 1927 1967 39407386 39407426 1.000000e-03 54.7
16 TraesCS6B01G310000 chr3B 87.255 204 20 5 297 497 651601499 651601699 6.930000e-56 228.0
17 TraesCS6B01G310000 chr2D 90.286 175 13 3 1743 1916 342099803 342099632 2.490000e-55 226.0
18 TraesCS6B01G310000 chr2D 89.143 175 15 4 1743 1916 147232648 147232819 5.400000e-52 215.0
19 TraesCS6B01G310000 chr2B 90.286 175 13 3 1743 1916 407236346 407236175 2.490000e-55 226.0
20 TraesCS6B01G310000 chr2B 89.714 175 14 4 1743 1916 206754375 206754546 1.160000e-53 220.0
21 TraesCS6B01G310000 chr2B 78.351 291 44 12 2 285 676029156 676028878 1.190000e-38 171.0
22 TraesCS6B01G310000 chr2B 100.000 30 0 0 326 355 148195542 148195513 3.460000e-04 56.5
23 TraesCS6B01G310000 chr2B 100.000 30 0 0 1939 1968 464021304 464021333 3.460000e-04 56.5
24 TraesCS6B01G310000 chr3D 79.202 351 52 13 120 469 510317160 510316830 8.970000e-55 224.0
25 TraesCS6B01G310000 chr3D 86.607 112 13 2 387 497 61173537 61173647 3.370000e-24 122.0
26 TraesCS6B01G310000 chr4A 89.714 175 11 6 1743 1914 580298875 580299045 1.500000e-52 217.0
27 TraesCS6B01G310000 chr4A 96.970 33 1 0 1934 1966 155289579 155289611 3.460000e-04 56.5
28 TraesCS6B01G310000 chr4A 96.875 32 1 0 1936 1967 274958947 274958978 1.000000e-03 54.7
29 TraesCS6B01G310000 chr1D 89.080 174 15 4 1743 1915 250738613 250738443 1.940000e-51 213.0
30 TraesCS6B01G310000 chr5A 77.368 380 68 12 120 496 480039258 480039622 2.510000e-50 209.0
31 TraesCS6B01G310000 chr5A 97.059 34 0 1 1935 1967 612917353 612917386 3.460000e-04 56.5
32 TraesCS6B01G310000 chr7B 77.183 355 59 11 111 458 573103184 573102845 1.180000e-43 187.0
33 TraesCS6B01G310000 chr7B 74.728 368 71 17 138 500 43211336 43211686 7.180000e-31 145.0
34 TraesCS6B01G310000 chr1A 76.724 348 59 9 122 469 454039544 454039869 9.160000e-40 174.0
35 TraesCS6B01G310000 chr1A 94.286 35 2 0 1933 1967 54005338 54005304 1.000000e-03 54.7
36 TraesCS6B01G310000 chr4B 81.548 168 31 0 302 469 605281339 605281172 3.340000e-29 139.0
37 TraesCS6B01G310000 chr4B 87.324 71 8 1 330 400 96266320 96266389 2.050000e-11 80.5
38 TraesCS6B01G310000 chr4B 100.000 32 0 0 1936 1967 207152940 207152971 2.680000e-05 60.2


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 TraesCS6B01G310000 chr6B 555340081 555342572 2491 False 4602.00 4602 100.00000 1 2492 1 chr6B.!!$F1 2491
1 TraesCS6B01G310000 chr6A 511037810 511040408 2598 False 789.00 1773 93.19150 333 2461 4 chr6A.!!$F1 2128
2 TraesCS6B01G310000 chr6D 370040518 370043402 2884 False 693.25 1700 93.26625 65 2492 4 chr6D.!!$F1 2427
3 TraesCS6B01G310000 chr1B 544730414 544730918 504 True 394.00 394 81.43100 2 499 1 chr1B.!!$R1 497

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
19 20 0.107897 ATGTTGCTTACCGGCATCGA 60.108 50.0 0.00 0.00 42.09 3.59 F
818 862 0.165727 CTGCACGTGCTTTAATCGCA 59.834 50.0 37.59 15.93 42.66 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1107 0.742990 CTAGGCGGCGGATTTTGACA 60.743 55.0 9.78 0.0 0.00 3.58 R
2322 2892 0.923358 TCAAACTGTGGTTGGGTCCT 59.077 50.0 0.00 0.0 35.63 3.85 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
18 19 2.393557 ATGTTGCTTACCGGCATCG 58.606 52.632 0.00 0.00 42.09 3.84
19 20 0.107897 ATGTTGCTTACCGGCATCGA 60.108 50.000 0.00 0.00 42.09 3.59
21 22 0.373716 GTTGCTTACCGGCATCGAAG 59.626 55.000 0.00 0.00 42.09 3.79
24 25 1.480219 GCTTACCGGCATCGAAGACG 61.480 60.000 9.34 9.34 42.51 4.18
70 72 4.790861 GAAGGACGACCGGGCGAC 62.791 72.222 41.17 32.38 41.83 5.19
114 116 1.474143 GCTCCTACTGTTGGATCTGCC 60.474 57.143 11.32 0.00 32.56 4.85
116 118 0.179073 CCTACTGTTGGATCTGCCGG 60.179 60.000 1.81 0.00 40.66 6.13
118 120 1.549243 TACTGTTGGATCTGCCGGCA 61.549 55.000 30.59 30.59 40.66 5.69
279 298 3.740128 CTTCCGCCATCCCCACTCG 62.740 68.421 0.00 0.00 0.00 4.18
284 303 1.678970 GCCATCCCCACTCGCTTTT 60.679 57.895 0.00 0.00 0.00 2.27
285 304 0.393808 GCCATCCCCACTCGCTTTTA 60.394 55.000 0.00 0.00 0.00 1.52
286 305 1.668419 CCATCCCCACTCGCTTTTAG 58.332 55.000 0.00 0.00 0.00 1.85
290 309 1.026718 CCCCACTCGCTTTTAGCCTG 61.027 60.000 0.00 0.00 38.18 4.85
293 312 0.955428 CACTCGCTTTTAGCCTGCCA 60.955 55.000 0.00 0.00 38.18 4.92
296 315 2.700773 CGCTTTTAGCCTGCCACCC 61.701 63.158 0.00 0.00 38.18 4.61
297 316 2.351244 GCTTTTAGCCTGCCACCCC 61.351 63.158 0.00 0.00 34.48 4.95
300 319 2.150014 TTTTAGCCTGCCACCCCCTC 62.150 60.000 0.00 0.00 0.00 4.30
371 390 2.382519 CGATTCGGTAACTTCTAGCGG 58.617 52.381 0.00 0.00 38.74 5.52
394 413 2.678580 GCCGGGGGCTGCTTTAAA 60.679 61.111 2.18 0.00 46.69 1.52
447 466 1.565305 GCAACCAAACGCACATTTCA 58.435 45.000 0.00 0.00 0.00 2.69
450 469 3.122297 CAACCAAACGCACATTTCATGT 58.878 40.909 0.00 0.00 46.22 3.21
452 471 2.622942 ACCAAACGCACATTTCATGTCT 59.377 40.909 0.00 0.00 42.70 3.41
458 477 3.565482 ACGCACATTTCATGTCTCAACTT 59.435 39.130 0.00 0.00 42.70 2.66
461 480 4.801891 CACATTTCATGTCTCAACTTGGG 58.198 43.478 0.00 0.00 42.70 4.12
517 536 7.521585 CGCCCTAAGGTATGATTATTTGTTTCC 60.522 40.741 0.00 0.00 34.57 3.13
533 552 3.181448 TGTTTCCCCCTACACAACTTCTC 60.181 47.826 0.00 0.00 0.00 2.87
548 567 6.263168 CACAACTTCTCCTCCTACATTTGTTT 59.737 38.462 0.00 0.00 0.00 2.83
568 587 4.630644 TTTCATGACAGCCTCTCTCTTT 57.369 40.909 0.00 0.00 0.00 2.52
591 610 1.225704 GGAGCCTCAACCCTCCATG 59.774 63.158 0.00 0.00 45.55 3.66
619 638 4.519906 TGTTCCAGGTCCTTTTCTTCTT 57.480 40.909 0.00 0.00 0.00 2.52
627 646 5.360999 CAGGTCCTTTTCTTCTTCCTTTTGT 59.639 40.000 0.00 0.00 0.00 2.83
666 685 4.157849 TGTTCAACCCTTACACACATCA 57.842 40.909 0.00 0.00 0.00 3.07
671 690 4.022416 TCAACCCTTACACACATCATTTGC 60.022 41.667 0.00 0.00 0.00 3.68
674 693 4.218417 ACCCTTACACACATCATTTGCTTC 59.782 41.667 0.00 0.00 0.00 3.86
698 718 1.188871 CCCCCTCTATCCCTCTTCGC 61.189 65.000 0.00 0.00 0.00 4.70
718 738 2.165234 GCCTTTCTCAATTGCCCTTCTC 59.835 50.000 0.00 0.00 0.00 2.87
722 742 5.011431 CCTTTCTCAATTGCCCTTCTCTTTT 59.989 40.000 0.00 0.00 0.00 2.27
765 785 3.614092 AGTCATTGTCAGGCGAATGATT 58.386 40.909 0.00 0.00 39.97 2.57
766 786 3.624861 AGTCATTGTCAGGCGAATGATTC 59.375 43.478 0.00 0.00 39.97 2.52
783 827 3.751175 TGATTCCAACTAAGCTTGAACCG 59.249 43.478 9.86 0.00 0.00 4.44
807 851 1.071605 GACTTCTAAGCCTGCACGTG 58.928 55.000 12.28 12.28 0.00 4.49
808 852 0.951040 ACTTCTAAGCCTGCACGTGC 60.951 55.000 33.11 33.11 42.50 5.34
809 853 0.671781 CTTCTAAGCCTGCACGTGCT 60.672 55.000 37.59 21.80 42.66 4.40
811 855 0.250295 TCTAAGCCTGCACGTGCTTT 60.250 50.000 37.59 26.65 45.09 3.51
812 856 1.001520 TCTAAGCCTGCACGTGCTTTA 59.998 47.619 37.59 26.39 45.09 1.85
813 857 1.804151 CTAAGCCTGCACGTGCTTTAA 59.196 47.619 37.59 19.26 45.09 1.52
814 858 1.247567 AAGCCTGCACGTGCTTTAAT 58.752 45.000 37.59 20.20 45.09 1.40
815 859 0.804989 AGCCTGCACGTGCTTTAATC 59.195 50.000 37.59 20.93 42.66 1.75
816 860 0.521242 GCCTGCACGTGCTTTAATCG 60.521 55.000 37.59 18.67 42.66 3.34
817 861 0.521242 CCTGCACGTGCTTTAATCGC 60.521 55.000 37.59 11.87 42.66 4.58
818 862 0.165727 CTGCACGTGCTTTAATCGCA 59.834 50.000 37.59 15.93 42.66 5.10
826 870 3.740044 TGCTTTAATCGCACTTGTAGC 57.260 42.857 0.00 0.00 31.40 3.58
827 871 3.070748 TGCTTTAATCGCACTTGTAGCA 58.929 40.909 0.00 0.00 35.26 3.49
828 872 3.120338 TGCTTTAATCGCACTTGTAGCAC 60.120 43.478 0.00 0.00 32.94 4.40
829 873 3.125316 GCTTTAATCGCACTTGTAGCACT 59.875 43.478 0.00 0.00 0.00 4.40
830 874 4.641954 CTTTAATCGCACTTGTAGCACTG 58.358 43.478 0.00 0.00 0.00 3.66
831 875 2.455674 AATCGCACTTGTAGCACTGA 57.544 45.000 0.00 0.00 0.00 3.41
832 876 2.680312 ATCGCACTTGTAGCACTGAT 57.320 45.000 0.00 0.00 0.00 2.90
833 877 3.801114 ATCGCACTTGTAGCACTGATA 57.199 42.857 0.00 0.00 0.00 2.15
834 878 3.150848 TCGCACTTGTAGCACTGATAG 57.849 47.619 0.00 0.00 0.00 2.08
835 879 1.590238 CGCACTTGTAGCACTGATAGC 59.410 52.381 0.00 0.00 0.00 2.97
836 880 2.621338 GCACTTGTAGCACTGATAGCA 58.379 47.619 0.00 0.00 0.00 3.49
837 881 3.002791 GCACTTGTAGCACTGATAGCAA 58.997 45.455 0.00 0.00 0.00 3.91
838 882 3.436704 GCACTTGTAGCACTGATAGCAAA 59.563 43.478 0.00 0.00 0.00 3.68
839 883 4.095483 GCACTTGTAGCACTGATAGCAAAT 59.905 41.667 0.00 0.00 0.00 2.32
840 884 5.728898 GCACTTGTAGCACTGATAGCAAATC 60.729 44.000 0.00 0.00 0.00 2.17
841 885 4.568359 ACTTGTAGCACTGATAGCAAATCG 59.432 41.667 0.00 0.00 0.00 3.34
842 886 3.457234 TGTAGCACTGATAGCAAATCGG 58.543 45.455 6.40 6.40 0.00 4.18
843 887 1.303309 AGCACTGATAGCAAATCGGC 58.697 50.000 7.59 5.37 0.00 5.54
844 888 1.016627 GCACTGATAGCAAATCGGCA 58.983 50.000 7.59 0.00 35.83 5.69
845 889 1.605710 GCACTGATAGCAAATCGGCAT 59.394 47.619 7.59 0.00 35.83 4.40
846 890 2.603892 GCACTGATAGCAAATCGGCATG 60.604 50.000 7.59 0.00 35.83 4.06
859 903 1.559149 CGGCATGGCTTTGTTTGCAC 61.559 55.000 18.09 0.00 36.82 4.57
865 909 3.876274 TGGCTTTGTTTGCACTTGTAA 57.124 38.095 0.00 0.00 0.00 2.41
888 946 2.224606 CTGATAGCAAATCGGCATGGT 58.775 47.619 0.00 0.00 35.83 3.55
1546 1613 0.320374 TTCTTTGTCCCGTCGCATCT 59.680 50.000 0.00 0.00 0.00 2.90
1547 1614 1.179152 TCTTTGTCCCGTCGCATCTA 58.821 50.000 0.00 0.00 0.00 1.98
1548 1615 1.135199 TCTTTGTCCCGTCGCATCTAC 60.135 52.381 0.00 0.00 0.00 2.59
1549 1616 0.604073 TTTGTCCCGTCGCATCTACA 59.396 50.000 0.00 0.00 0.00 2.74
1550 1617 0.172578 TTGTCCCGTCGCATCTACAG 59.827 55.000 0.00 0.00 0.00 2.74
1643 1714 9.468532 GAATGCTATTTATGAATCCCAACTTTC 57.531 33.333 0.00 0.00 0.00 2.62
1789 1870 2.032178 GCATCTCGGTCAGTTAATTGCC 59.968 50.000 0.00 0.00 0.00 4.52
1884 1965 2.688446 CCTACTCAGCACCTGAACGATA 59.312 50.000 0.00 0.00 40.18 2.92
1885 1966 3.319405 CCTACTCAGCACCTGAACGATAT 59.681 47.826 0.00 0.00 40.18 1.63
1947 2028 9.708092 AGTGTAAATCTTGAAAGTTACTACTCC 57.292 33.333 0.00 0.00 31.99 3.85
1948 2029 8.933807 GTGTAAATCTTGAAAGTTACTACTCCC 58.066 37.037 0.00 0.00 31.99 4.30
1952 2033 6.591750 TCTTGAAAGTTACTACTCCCTCTG 57.408 41.667 0.00 0.00 31.99 3.35
1954 2035 6.553852 TCTTGAAAGTTACTACTCCCTCTGTT 59.446 38.462 0.00 0.00 31.99 3.16
1955 2036 6.342338 TGAAAGTTACTACTCCCTCTGTTC 57.658 41.667 0.00 0.00 31.99 3.18
1956 2037 5.836898 TGAAAGTTACTACTCCCTCTGTTCA 59.163 40.000 0.00 0.00 31.99 3.18
1957 2038 5.725325 AAGTTACTACTCCCTCTGTTCAC 57.275 43.478 0.00 0.00 31.99 3.18
1958 2039 5.000570 AGTTACTACTCCCTCTGTTCACT 57.999 43.478 0.00 0.00 0.00 3.41
1959 2040 5.395611 AGTTACTACTCCCTCTGTTCACTT 58.604 41.667 0.00 0.00 0.00 3.16
1960 2041 5.839606 AGTTACTACTCCCTCTGTTCACTTT 59.160 40.000 0.00 0.00 0.00 2.66
1963 2044 6.936968 ACTACTCCCTCTGTTCACTTTTAT 57.063 37.500 0.00 0.00 0.00 1.40
2012 2328 2.289506 ACTTTTGGTACCGAGGCTCTTC 60.290 50.000 13.50 0.12 0.00 2.87
2143 2466 0.904865 CTGGGTGACACTGCTAGGGA 60.905 60.000 5.39 0.00 0.00 4.20
2164 2487 3.375699 ACCTGGAGACGGTATCAAGATT 58.624 45.455 8.73 0.00 35.86 2.40
2225 2794 4.971939 TGGTTGATGATGACTTGTCAGAA 58.028 39.130 9.39 0.83 0.00 3.02
2263 2832 6.350949 GGTTTCTGGAATGCTTATTGGCTTAA 60.351 38.462 0.00 0.00 0.00 1.85
2300 2870 3.808466 TCTGCTGGTGATATGTGACTC 57.192 47.619 0.00 0.00 0.00 3.36
2322 2892 2.172930 AGCGAGTACTATCCTCCACTCA 59.827 50.000 0.00 0.00 37.80 3.41
2342 2918 1.499007 AGGACCCAACCACAGTTTGAT 59.501 47.619 0.00 0.00 32.45 2.57
2363 2939 6.459923 TGATTTTGCTAAATTGGTACCCAAC 58.540 36.000 10.07 0.00 46.95 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.179108 CCTTCCCCGTCATCGTCTTC 60.179 60.000 0.00 0.00 35.01 2.87
19 20 1.614241 CCCTTCCCCGTCATCGTCTT 61.614 60.000 0.00 0.00 35.01 3.01
21 22 2.499685 CCCTTCCCCGTCATCGTC 59.500 66.667 0.00 0.00 35.01 4.20
48 50 1.977544 CCCGGTCGTCCTTCACTCT 60.978 63.158 0.00 0.00 0.00 3.24
53 55 4.790861 GTCGCCCGGTCGTCCTTC 62.791 72.222 4.19 0.00 0.00 3.46
68 70 0.960364 TGCTCTTCCATTTGGCCGTC 60.960 55.000 0.00 0.00 34.44 4.79
70 72 1.805254 CTGCTCTTCCATTTGGCCG 59.195 57.895 0.00 0.00 34.44 6.13
104 106 4.776322 CGGTGCCGGCAGATCCAA 62.776 66.667 33.73 1.60 35.56 3.53
118 120 0.390866 CTCAGATCTGTGCAAGCGGT 60.391 55.000 21.92 0.00 0.00 5.68
160 173 0.984995 ACAACCACTTCCTCTAGCCC 59.015 55.000 0.00 0.00 0.00 5.19
260 279 3.406595 GAGTGGGGATGGCGGAAGG 62.407 68.421 0.00 0.00 0.00 3.46
279 298 2.351244 GGGGTGGCAGGCTAAAAGC 61.351 63.158 0.00 0.00 41.46 3.51
358 377 0.179081 CCTGGCCCGCTAGAAGTTAC 60.179 60.000 0.00 0.00 0.00 2.50
359 378 1.968050 GCCTGGCCCGCTAGAAGTTA 61.968 60.000 7.66 0.00 0.00 2.24
361 380 3.787001 GCCTGGCCCGCTAGAAGT 61.787 66.667 7.66 0.00 0.00 3.01
362 381 4.554036 GGCCTGGCCCGCTAGAAG 62.554 72.222 27.77 0.00 44.06 2.85
379 398 0.526211 GAAGTTTAAAGCAGCCCCCG 59.474 55.000 0.00 0.00 0.00 5.73
381 400 1.068541 CACGAAGTTTAAAGCAGCCCC 60.069 52.381 0.00 0.00 41.61 5.80
447 466 0.773644 ACCAGCCCAAGTTGAGACAT 59.226 50.000 3.87 0.00 0.00 3.06
450 469 0.823356 GCAACCAGCCCAAGTTGAGA 60.823 55.000 3.87 0.00 44.93 3.27
452 471 2.192861 CGCAACCAGCCCAAGTTGA 61.193 57.895 3.87 0.00 44.93 3.18
458 477 2.331893 CGAAATCGCAACCAGCCCA 61.332 57.895 0.00 0.00 41.38 5.36
461 480 1.154225 CCACGAAATCGCAACCAGC 60.154 57.895 2.15 0.00 44.43 4.85
489 508 4.634012 AATAATCATACCTTAGGGCGCA 57.366 40.909 10.83 0.00 35.63 6.09
517 536 1.555533 GGAGGAGAAGTTGTGTAGGGG 59.444 57.143 0.00 0.00 0.00 4.79
533 552 6.573664 TGTCATGAAAACAAATGTAGGAGG 57.426 37.500 0.00 0.00 0.00 4.30
548 567 3.580022 TGAAAGAGAGAGGCTGTCATGAA 59.420 43.478 14.66 0.00 0.00 2.57
568 587 3.319198 GGGTTGAGGCTCCGGTGA 61.319 66.667 12.86 0.00 0.00 4.02
591 610 1.620822 AGGACCTGGAACAACAATGC 58.379 50.000 0.00 0.00 38.70 3.56
619 638 1.384525 CGACAACCACCACAAAAGGA 58.615 50.000 0.00 0.00 0.00 3.36
642 661 3.135225 TGTGTGTAAGGGTTGAACATCG 58.865 45.455 0.00 0.00 0.00 3.84
645 664 4.157849 TGATGTGTGTAAGGGTTGAACA 57.842 40.909 0.00 0.00 0.00 3.18
666 685 1.547495 AGGGGGAGGGGAAGCAAAT 60.547 57.895 0.00 0.00 0.00 2.32
671 690 0.178888 GGATAGAGGGGGAGGGGAAG 60.179 65.000 0.00 0.00 0.00 3.46
674 693 2.107565 AGGGATAGAGGGGGAGGGG 61.108 68.421 0.00 0.00 0.00 4.79
698 718 3.694926 AGAGAAGGGCAATTGAGAAAGG 58.305 45.455 10.34 0.00 0.00 3.11
722 742 1.064505 AGACACGACACGAACGAGAAA 59.935 47.619 0.14 0.00 34.70 2.52
730 750 3.004002 ACAATGACTTAGACACGACACGA 59.996 43.478 0.00 0.00 0.00 4.35
765 785 1.271163 CCCGGTTCAAGCTTAGTTGGA 60.271 52.381 0.00 0.00 0.00 3.53
766 786 1.165270 CCCGGTTCAAGCTTAGTTGG 58.835 55.000 0.00 0.00 0.00 3.77
789 833 0.951040 GCACGTGCAGGCTTAGAAGT 60.951 55.000 34.52 0.00 41.59 3.01
807 851 3.125316 AGTGCTACAAGTGCGATTAAAGC 59.875 43.478 0.00 0.00 0.00 3.51
808 852 4.388773 TCAGTGCTACAAGTGCGATTAAAG 59.611 41.667 0.00 0.00 0.00 1.85
809 853 4.311606 TCAGTGCTACAAGTGCGATTAAA 58.688 39.130 0.00 0.00 0.00 1.52
810 854 3.920446 TCAGTGCTACAAGTGCGATTAA 58.080 40.909 0.00 0.00 0.00 1.40
811 855 3.586100 TCAGTGCTACAAGTGCGATTA 57.414 42.857 0.00 0.00 0.00 1.75
812 856 2.455674 TCAGTGCTACAAGTGCGATT 57.544 45.000 0.00 0.00 0.00 3.34
813 857 2.680312 ATCAGTGCTACAAGTGCGAT 57.320 45.000 0.00 0.00 0.00 4.58
814 858 2.735444 GCTATCAGTGCTACAAGTGCGA 60.735 50.000 0.00 0.00 0.00 5.10
815 859 1.590238 GCTATCAGTGCTACAAGTGCG 59.410 52.381 0.00 0.00 0.00 5.34
816 860 2.621338 TGCTATCAGTGCTACAAGTGC 58.379 47.619 0.00 0.00 0.00 4.40
817 861 5.501413 CGATTTGCTATCAGTGCTACAAGTG 60.501 44.000 0.00 0.00 0.00 3.16
818 862 4.568359 CGATTTGCTATCAGTGCTACAAGT 59.432 41.667 0.00 0.00 0.00 3.16
819 863 4.025396 CCGATTTGCTATCAGTGCTACAAG 60.025 45.833 0.00 0.00 0.00 3.16
820 864 3.871006 CCGATTTGCTATCAGTGCTACAA 59.129 43.478 0.00 0.00 0.00 2.41
821 865 3.457234 CCGATTTGCTATCAGTGCTACA 58.543 45.455 0.00 0.00 0.00 2.74
822 866 2.221981 GCCGATTTGCTATCAGTGCTAC 59.778 50.000 0.00 0.00 0.00 3.58
823 867 2.158971 TGCCGATTTGCTATCAGTGCTA 60.159 45.455 0.00 0.00 0.00 3.49
824 868 1.303309 GCCGATTTGCTATCAGTGCT 58.697 50.000 0.00 0.00 0.00 4.40
825 869 1.016627 TGCCGATTTGCTATCAGTGC 58.983 50.000 0.00 0.00 0.00 4.40
826 870 2.031420 CCATGCCGATTTGCTATCAGTG 60.031 50.000 0.00 0.00 0.00 3.66
827 871 2.224606 CCATGCCGATTTGCTATCAGT 58.775 47.619 0.00 0.00 0.00 3.41
828 872 1.068748 GCCATGCCGATTTGCTATCAG 60.069 52.381 0.00 0.00 0.00 2.90
829 873 0.953727 GCCATGCCGATTTGCTATCA 59.046 50.000 0.00 0.00 0.00 2.15
830 874 1.242076 AGCCATGCCGATTTGCTATC 58.758 50.000 0.00 0.00 0.00 2.08
831 875 1.696063 AAGCCATGCCGATTTGCTAT 58.304 45.000 0.00 0.00 0.00 2.97
832 876 1.134753 CAAAGCCATGCCGATTTGCTA 59.865 47.619 0.75 0.00 0.00 3.49
833 877 0.108520 CAAAGCCATGCCGATTTGCT 60.109 50.000 0.75 0.00 0.00 3.91
834 878 0.390209 ACAAAGCCATGCCGATTTGC 60.390 50.000 11.17 0.00 36.36 3.68
835 879 2.083167 AACAAAGCCATGCCGATTTG 57.917 45.000 10.06 10.06 38.35 2.32
836 880 2.415776 CAAACAAAGCCATGCCGATTT 58.584 42.857 0.00 0.00 0.00 2.17
837 881 1.940752 GCAAACAAAGCCATGCCGATT 60.941 47.619 0.00 0.00 32.73 3.34
838 882 0.390209 GCAAACAAAGCCATGCCGAT 60.390 50.000 0.00 0.00 32.73 4.18
839 883 1.006337 GCAAACAAAGCCATGCCGA 60.006 52.632 0.00 0.00 32.73 5.54
840 884 1.300775 TGCAAACAAAGCCATGCCG 60.301 52.632 0.00 0.00 38.00 5.69
841 885 0.249996 AGTGCAAACAAAGCCATGCC 60.250 50.000 0.00 0.00 38.00 4.40
842 886 1.262151 CAAGTGCAAACAAAGCCATGC 59.738 47.619 0.00 0.00 39.22 4.06
843 887 2.553086 ACAAGTGCAAACAAAGCCATG 58.447 42.857 0.00 0.00 0.00 3.66
844 888 2.985957 ACAAGTGCAAACAAAGCCAT 57.014 40.000 0.00 0.00 0.00 4.40
845 889 3.056536 TGTTACAAGTGCAAACAAAGCCA 60.057 39.130 0.00 0.00 30.54 4.75
846 890 3.305897 GTGTTACAAGTGCAAACAAAGCC 59.694 43.478 2.58 0.00 35.08 4.35
859 903 5.727791 GCCGATTTGCTATCAGTGTTACAAG 60.728 44.000 0.00 0.00 0.00 3.16
865 909 2.401583 TGCCGATTTGCTATCAGTGT 57.598 45.000 0.00 0.00 0.00 3.55
888 946 1.089481 GCATCAACGCCCTCGATTGA 61.089 55.000 1.18 1.18 38.77 2.57
1047 1107 0.742990 CTAGGCGGCGGATTTTGACA 60.743 55.000 9.78 0.00 0.00 3.58
1546 1613 3.055385 GCCACAGACAAAGGGATACTGTA 60.055 47.826 0.00 0.00 39.33 2.74
1547 1614 2.290323 GCCACAGACAAAGGGATACTGT 60.290 50.000 0.00 0.00 41.52 3.55
1548 1615 2.290260 TGCCACAGACAAAGGGATACTG 60.290 50.000 0.00 0.00 35.14 2.74
1549 1616 1.985159 TGCCACAGACAAAGGGATACT 59.015 47.619 0.00 0.00 0.00 2.12
1550 1617 2.489938 TGCCACAGACAAAGGGATAC 57.510 50.000 0.00 0.00 0.00 2.24
1643 1714 2.048444 AAGCCATACAGCCACATCAG 57.952 50.000 0.00 0.00 0.00 2.90
1739 1820 4.787551 ACTGGCCGATATTTGGAACATTA 58.212 39.130 0.00 0.00 39.30 1.90
1740 1821 3.631250 ACTGGCCGATATTTGGAACATT 58.369 40.909 0.00 0.00 39.30 2.71
1957 2038 9.329913 GCAACAATCACTGTACACTTATAAAAG 57.670 33.333 0.00 0.00 37.23 2.27
1958 2039 9.062524 AGCAACAATCACTGTACACTTATAAAA 57.937 29.630 0.00 0.00 37.23 1.52
1959 2040 8.503196 CAGCAACAATCACTGTACACTTATAAA 58.497 33.333 0.00 0.00 37.23 1.40
1960 2041 7.875554 TCAGCAACAATCACTGTACACTTATAA 59.124 33.333 0.00 0.00 37.23 0.98
1963 2044 5.606505 TCAGCAACAATCACTGTACACTTA 58.393 37.500 0.00 0.00 37.23 2.24
2012 2328 5.335976 GGCCAATCTCTAAAAGTGAAACCTG 60.336 44.000 0.00 0.00 37.80 4.00
2143 2466 2.526888 TCTTGATACCGTCTCCAGGT 57.473 50.000 0.00 0.00 45.28 4.00
2225 2794 4.810345 TCCAGAAACCAAACCCATAAGTT 58.190 39.130 0.00 0.00 0.00 2.66
2263 2832 5.993441 CCAGCAGAAAATGGAAGTGAAAATT 59.007 36.000 0.00 0.00 39.02 1.82
2300 2870 2.550606 GAGTGGAGGATAGTACTCGCTG 59.449 54.545 0.00 0.00 35.82 5.18
2322 2892 0.923358 TCAAACTGTGGTTGGGTCCT 59.077 50.000 0.00 0.00 35.63 3.85
2363 2939 5.689383 ACTGGCTTGTAAGTTGTAATGTG 57.311 39.130 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.