Multiple sequence alignment - TraesCS6B01G265500

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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 TraesCS6B01G265500 chr6B 100.000 3904 0 0 1 3904 477785033 477788936 0.000000e+00 7210
1 TraesCS6B01G265500 chr6B 76.106 452 95 9 377 817 186956624 186957073 1.410000e-54 224
2 TraesCS6B01G265500 chr6A 94.924 2029 63 14 1900 3904 446725221 446727233 0.000000e+00 3140
3 TraesCS6B01G265500 chr6A 86.834 1633 161 31 278 1899 446723510 446725099 0.000000e+00 1775
4 TraesCS6B01G265500 chr6D 91.471 1747 106 21 1965 3703 309950148 309951859 0.000000e+00 2361
5 TraesCS6B01G265500 chr6D 92.891 1069 41 9 910 1966 309949030 309950075 0.000000e+00 1520
6 TraesCS6B01G265500 chr6D 90.417 720 54 8 77 789 309948072 309948783 0.000000e+00 933
7 TraesCS6B01G265500 chr6D 95.210 167 8 0 3738 3904 309951860 309952026 8.320000e-67 265
8 TraesCS6B01G265500 chr5B 78.016 514 100 9 377 881 69287430 69286921 1.050000e-80 311
9 TraesCS6B01G265500 chr5D 78.864 440 77 8 412 838 338659225 338659661 2.300000e-72 283
10 TraesCS6B01G265500 chr5D 77.559 508 88 19 407 909 446678570 446679056 2.300000e-72 283
11 TraesCS6B01G265500 chr5D 78.109 402 85 3 481 881 548674777 548675176 6.480000e-63 252
12 TraesCS6B01G265500 chr4D 92.000 200 13 3 1971 2169 226631150 226631347 1.070000e-70 278
13 TraesCS6B01G265500 chr4D 86.667 255 22 5 1724 1966 226630820 226631074 4.970000e-69 272
14 TraesCS6B01G265500 chr4D 76.682 446 91 10 385 819 505724493 505724936 6.520000e-58 235
15 TraesCS6B01G265500 chr3D 77.393 491 85 20 398 881 10639876 10639405 6.430000e-68 268
16 TraesCS6B01G265500 chr2A 77.046 501 91 17 411 907 516417599 516417119 2.310000e-67 267
17 TraesCS6B01G265500 chr7D 76.726 507 92 16 407 907 182613156 182613642 3.870000e-65 259
18 TraesCS6B01G265500 chr7D 82.060 301 50 2 594 894 37872673 37872377 1.800000e-63 254
19 TraesCS6B01G265500 chr7A 75.926 486 96 16 375 847 83227816 83228293 3.030000e-56 230
20 TraesCS6B01G265500 chr7A 75.514 486 98 16 375 847 78651860 78651383 6.570000e-53 219
21 TraesCS6B01G265500 chr7B 77.078 397 84 7 488 881 222312389 222311997 5.080000e-54 222


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 TraesCS6B01G265500 chr6B 477785033 477788936 3903 False 7210.00 7210 100.00000 1 3904 1 chr6B.!!$F2 3903
1 TraesCS6B01G265500 chr6A 446723510 446727233 3723 False 2457.50 3140 90.87900 278 3904 2 chr6A.!!$F1 3626
2 TraesCS6B01G265500 chr6D 309948072 309952026 3954 False 1269.75 2361 92.49725 77 3904 4 chr6D.!!$F1 3827
3 TraesCS6B01G265500 chr5B 69286921 69287430 509 True 311.00 311 78.01600 377 881 1 chr5B.!!$R1 504
4 TraesCS6B01G265500 chr4D 226630820 226631347 527 False 275.00 278 89.33350 1724 2169 2 chr4D.!!$F2 445

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
667 684 0.388659 TCAATGGCAGTGGTTGTTGC 59.611 50.0 15.62 0.0 39.56 4.17 F
1698 1849 0.031178 GTTGCTGAACTGGTGCAAGG 59.969 55.0 0.00 0.0 45.55 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2517 1.066908 ACAAACACAAACAGATGGGCG 59.933 47.619 0.0 0.0 0.0 6.13 R
3299 3667 1.349026 TCTGCCAAGAGACCCAAGAAG 59.651 52.381 0.0 0.0 0.0 2.85 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
19 20 2.417339 TTCCAACGAAGACTGAGACG 57.583 50.000 0.00 0.00 0.00 4.18
20 21 1.601166 TCCAACGAAGACTGAGACGA 58.399 50.000 0.00 0.00 0.00 4.20
21 22 1.951602 TCCAACGAAGACTGAGACGAA 59.048 47.619 0.00 0.00 0.00 3.85
22 23 2.031069 TCCAACGAAGACTGAGACGAAG 60.031 50.000 0.00 0.00 0.00 3.79
60 61 9.052759 AGTTGTAGTAGTAGTTTGAATGTTTGG 57.947 33.333 0.00 0.00 0.00 3.28
61 62 9.048446 GTTGTAGTAGTAGTTTGAATGTTTGGA 57.952 33.333 0.00 0.00 0.00 3.53
62 63 9.787435 TTGTAGTAGTAGTTTGAATGTTTGGAT 57.213 29.630 0.00 0.00 0.00 3.41
63 64 9.214957 TGTAGTAGTAGTTTGAATGTTTGGATG 57.785 33.333 0.00 0.00 0.00 3.51
64 65 9.216117 GTAGTAGTAGTTTGAATGTTTGGATGT 57.784 33.333 0.00 0.00 0.00 3.06
65 66 8.691661 AGTAGTAGTTTGAATGTTTGGATGTT 57.308 30.769 0.00 0.00 0.00 2.71
66 67 9.131791 AGTAGTAGTTTGAATGTTTGGATGTTT 57.868 29.630 0.00 0.00 0.00 2.83
67 68 9.180678 GTAGTAGTTTGAATGTTTGGATGTTTG 57.819 33.333 0.00 0.00 0.00 2.93
68 69 7.781056 AGTAGTTTGAATGTTTGGATGTTTGT 58.219 30.769 0.00 0.00 0.00 2.83
69 70 8.908903 AGTAGTTTGAATGTTTGGATGTTTGTA 58.091 29.630 0.00 0.00 0.00 2.41
70 71 9.180678 GTAGTTTGAATGTTTGGATGTTTGTAG 57.819 33.333 0.00 0.00 0.00 2.74
71 72 7.781056 AGTTTGAATGTTTGGATGTTTGTAGT 58.219 30.769 0.00 0.00 0.00 2.73
72 73 8.908903 AGTTTGAATGTTTGGATGTTTGTAGTA 58.091 29.630 0.00 0.00 0.00 1.82
73 74 9.180678 GTTTGAATGTTTGGATGTTTGTAGTAG 57.819 33.333 0.00 0.00 0.00 2.57
74 75 8.458573 TTGAATGTTTGGATGTTTGTAGTAGT 57.541 30.769 0.00 0.00 0.00 2.73
75 76 8.458573 TGAATGTTTGGATGTTTGTAGTAGTT 57.541 30.769 0.00 0.00 0.00 2.24
107 108 9.828852 TGAATGTTTTGGTATTCGTATGTTTAC 57.171 29.630 0.00 0.00 36.36 2.01
110 111 8.380743 TGTTTTGGTATTCGTATGTTTACACT 57.619 30.769 0.00 0.00 0.00 3.55
220 225 8.617290 AGAAGTCACCGTTTTCTACAAAATAT 57.383 30.769 0.00 0.00 33.98 1.28
249 254 2.007547 GCCCTAGAACTTGCTTCGACC 61.008 57.143 0.00 0.00 33.60 4.79
250 255 1.550976 CCCTAGAACTTGCTTCGACCT 59.449 52.381 0.00 0.00 33.60 3.85
255 260 2.103263 AGAACTTGCTTCGACCTCTTGT 59.897 45.455 0.00 0.00 33.60 3.16
260 265 2.210116 TGCTTCGACCTCTTGTTGTTC 58.790 47.619 0.00 0.00 0.00 3.18
276 281 6.801539 TGTTGTTCTAAAATAGAGCAGGTG 57.198 37.500 4.51 0.00 44.85 4.00
306 311 6.825213 AGATGCTCTTATTGCAGTGAATGTTA 59.175 34.615 0.00 0.00 44.04 2.41
309 314 6.092670 TGCTCTTATTGCAGTGAATGTTACTC 59.907 38.462 0.00 0.00 35.31 2.59
310 315 6.092670 GCTCTTATTGCAGTGAATGTTACTCA 59.907 38.462 0.00 0.00 0.00 3.41
344 352 1.569708 AAAACAGTTTGCATGCCACG 58.430 45.000 16.68 10.54 0.00 4.94
369 377 4.351874 AGTCGAGAAGAGGATAGGAGAG 57.648 50.000 0.00 0.00 0.00 3.20
438 446 1.202891 TGTGTCCTGTTCGGAGAGAGA 60.203 52.381 0.00 0.00 44.20 3.10
503 512 2.978824 CCCTCGTTCCGATGGTGT 59.021 61.111 0.51 0.00 37.01 4.16
506 515 1.066716 CCCTCGTTCCGATGGTGTTTA 60.067 52.381 0.51 0.00 37.01 2.01
533 542 4.767255 CAGAGGGTGTGCGGAGGC 62.767 72.222 0.00 0.00 40.52 4.70
640 657 5.046591 ACAAGTTGGATCCTTTCGATCTACA 60.047 40.000 14.23 0.00 45.90 2.74
667 684 0.388659 TCAATGGCAGTGGTTGTTGC 59.611 50.000 15.62 0.00 39.56 4.17
689 706 1.889170 CTGATGCGCTGGTCCTATAGA 59.111 52.381 9.73 0.00 0.00 1.98
702 809 1.268352 CCTATAGAGCCTCAGCACGAC 59.732 57.143 0.00 0.00 43.56 4.34
726 833 6.985645 ACGACTTCTCGACTGTCTACTATAAT 59.014 38.462 6.21 0.00 43.06 1.28
745 852 6.944234 ATAATAAGTTTTGCCCAGCTCTAC 57.056 37.500 0.00 0.00 0.00 2.59
761 868 1.497716 TCTACTGAAGGAGGGGCGATA 59.502 52.381 0.00 0.00 0.00 2.92
792 899 1.373497 CTTCGGCTCGCTTCAGTGT 60.373 57.895 0.00 0.00 0.00 3.55
808 915 3.189910 TCAGTGTTTGTAGTCGTCGCTAT 59.810 43.478 0.00 0.00 0.00 2.97
821 928 2.717530 GTCGCTATGTGGTCTACGAAG 58.282 52.381 0.00 0.00 0.00 3.79
832 939 3.512329 TGGTCTACGAAGCTGGATGTAAA 59.488 43.478 0.00 0.00 0.00 2.01
840 947 7.027778 ACGAAGCTGGATGTAAATTTTATCC 57.972 36.000 19.62 19.62 40.59 2.59
847 954 8.686334 GCTGGATGTAAATTTTATCCTTTCTGA 58.314 33.333 23.63 10.26 40.77 3.27
850 957 9.788960 GGATGTAAATTTTATCCTTTCTGACAC 57.211 33.333 19.35 0.67 37.86 3.67
856 963 8.842358 AATTTTATCCTTTCTGACACTCGTTA 57.158 30.769 0.00 0.00 0.00 3.18
973 1123 3.150458 TCTACAACCACGAGGAAGAGA 57.850 47.619 5.68 0.00 38.69 3.10
1411 1561 3.196469 TCATCAGTTCCTGGAGTCATGAC 59.804 47.826 18.47 18.47 31.51 3.06
1513 1663 5.123979 GGAGGATTACATCAAGGTTTGTCAC 59.876 44.000 0.00 0.00 0.00 3.67
1523 1673 0.668535 GGTTTGTCACTGTCTTGCCC 59.331 55.000 0.00 0.00 0.00 5.36
1562 1713 7.117812 CGATTTCTGGTAGCAGAGACTTAAAAA 59.882 37.037 22.75 13.07 32.21 1.94
1600 1751 4.745620 GCTAGTAATGAGGTCGATTTGGTC 59.254 45.833 0.00 0.00 0.00 4.02
1614 1765 4.202080 CGATTTGGTCGGGTAACTAGATCA 60.202 45.833 0.00 0.00 46.47 2.92
1635 1786 1.989165 GCGTGTTGCTTTTGTTTGTCA 59.011 42.857 0.00 0.00 41.73 3.58
1636 1787 2.602660 GCGTGTTGCTTTTGTTTGTCAT 59.397 40.909 0.00 0.00 41.73 3.06
1656 1807 2.949177 TTTGTGTGGTCCTGTATGCT 57.051 45.000 0.00 0.00 0.00 3.79
1657 1808 2.949177 TTGTGTGGTCCTGTATGCTT 57.051 45.000 0.00 0.00 0.00 3.91
1658 1809 2.183478 TGTGTGGTCCTGTATGCTTG 57.817 50.000 0.00 0.00 0.00 4.01
1663 1814 1.985159 TGGTCCTGTATGCTTGGAAGT 59.015 47.619 0.00 0.00 0.00 3.01
1667 1818 4.564821 GGTCCTGTATGCTTGGAAGTTGTA 60.565 45.833 0.00 0.00 0.00 2.41
1698 1849 0.031178 GTTGCTGAACTGGTGCAAGG 59.969 55.000 0.00 0.00 45.55 3.61
1699 1850 0.395586 TTGCTGAACTGGTGCAAGGT 60.396 50.000 0.00 0.00 41.06 3.50
1700 1851 0.472044 TGCTGAACTGGTGCAAGGTA 59.528 50.000 0.00 0.00 33.48 3.08
1706 1857 0.606604 ACTGGTGCAAGGTAGTACCG 59.393 55.000 13.76 1.80 45.93 4.02
1717 1868 6.051074 GCAAGGTAGTACCGGTAATTATTGT 58.949 40.000 21.06 0.00 44.90 2.71
1744 1895 1.003118 TGGTCCGAGGAGTGGAAATTG 59.997 52.381 0.00 0.00 37.23 2.32
1838 1989 8.721478 GTGAGCATTTAGAATTTCAGTAGTGAA 58.279 33.333 8.98 8.98 41.13 3.18
1874 2026 2.034558 AGTTTTGTGGCATTTGAGGACG 59.965 45.455 0.00 0.00 0.00 4.79
1883 2035 3.065371 GGCATTTGAGGACGGACTTATTG 59.935 47.826 0.00 0.00 0.00 1.90
1969 2315 5.936956 AGAGCTCTTCCTTGTTGTCTATTTG 59.063 40.000 11.45 0.00 0.00 2.32
2178 2525 7.758076 AGCTATTAAAAAGTAAAAACGCCCATC 59.242 33.333 0.00 0.00 0.00 3.51
2186 2533 2.507339 AAAACGCCCATCTGTTTGTG 57.493 45.000 0.00 0.00 38.26 3.33
2187 2534 1.398692 AAACGCCCATCTGTTTGTGT 58.601 45.000 0.00 0.00 36.96 3.72
2190 2537 1.066908 ACGCCCATCTGTTTGTGTTTG 59.933 47.619 0.00 0.00 0.00 2.93
2191 2538 1.066908 CGCCCATCTGTTTGTGTTTGT 59.933 47.619 0.00 0.00 0.00 2.83
2198 2552 5.691305 CCATCTGTTTGTGTTTGTACCATTG 59.309 40.000 0.00 0.00 0.00 2.82
2356 2710 7.315247 TGTCAGGTATGTACATTTGCATTAC 57.685 36.000 14.77 3.88 29.75 1.89
2428 2787 4.553547 GCATGCGATCTTACCAAAAGCTAG 60.554 45.833 0.00 0.00 0.00 3.42
2537 2896 5.939883 TGGACTTGAAAGTATGATGTTCCAG 59.060 40.000 0.00 0.00 39.88 3.86
2597 2956 1.081641 CTTTGCTTGCTGTGCCTCG 60.082 57.895 0.00 0.00 0.00 4.63
2620 2980 9.225201 CTCGTTGATGTGGAAATGTTATTTATG 57.775 33.333 0.00 0.00 0.00 1.90
2622 2982 9.009327 CGTTGATGTGGAAATGTTATTTATGTC 57.991 33.333 0.00 0.00 0.00 3.06
2743 3110 5.824624 CCTATGAAGTTGCAAGTGTATGGAT 59.175 40.000 7.73 0.00 0.00 3.41
2753 3120 4.067896 CAAGTGTATGGATCACATAGCCC 58.932 47.826 0.00 0.00 42.50 5.19
2843 3210 7.765695 ATTGAGTTCATCTGCTTTAAGGAAA 57.234 32.000 0.00 0.00 0.00 3.13
2920 3287 6.465084 GTGTTTAGAGAGGAAACATACTGGT 58.535 40.000 4.43 0.00 45.71 4.00
2972 3339 2.349886 GTCCGCTGAAGCTTGTTATCAG 59.650 50.000 2.10 5.75 42.70 2.90
3193 3560 4.632688 AGGTCGTTTGGAATAATGGTAACG 59.367 41.667 0.00 0.00 39.55 3.18
3227 3594 0.601558 GGTGCCTCTTCTGTGACGTA 59.398 55.000 0.00 0.00 0.00 3.57
3299 3667 2.555199 CTCCATTCCGATCCACTGTTC 58.445 52.381 0.00 0.00 0.00 3.18
3410 3778 4.020839 TGCAGTTAAGAGGTACCCACTTAC 60.021 45.833 21.29 17.19 36.66 2.34
3468 3836 8.439971 AGGACCAGTAATTATCTGATGCAAATA 58.560 33.333 13.42 0.00 35.20 1.40
3570 3938 9.643693 AACAAAAGATTAATTGCTTATGTGGAG 57.356 29.630 0.00 0.00 0.00 3.86
3616 3984 9.076596 GTAATATTTGAATGGCAAGTTCAAGAC 57.923 33.333 14.02 7.28 43.90 3.01
3653 4021 4.022762 TCCACAACCATAAATTCACAACCG 60.023 41.667 0.00 0.00 0.00 4.44
3837 4212 3.612860 CCGGACTTAGAAATGAGTTGACG 59.387 47.826 0.00 0.00 0.00 4.35
3876 4251 1.003355 ATGGCCACCTCACAACTCG 60.003 57.895 8.16 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.951602 TCGTCTCAGTCTTCGTTGGAA 59.048 47.619 0.00 0.00 0.00 3.53
1 2 1.601166 TCGTCTCAGTCTTCGTTGGA 58.399 50.000 0.00 0.00 0.00 3.53
2 3 2.287668 ACTTCGTCTCAGTCTTCGTTGG 60.288 50.000 0.00 0.00 0.00 3.77
3 4 3.001395 ACTTCGTCTCAGTCTTCGTTG 57.999 47.619 0.00 0.00 0.00 4.10
5 6 3.401182 ACTACTTCGTCTCAGTCTTCGT 58.599 45.455 0.00 0.00 0.00 3.85
6 7 4.407496 AACTACTTCGTCTCAGTCTTCG 57.593 45.455 0.00 0.00 0.00 3.79
7 8 6.901265 ACTAAACTACTTCGTCTCAGTCTTC 58.099 40.000 0.00 0.00 0.00 2.87
8 9 6.880942 ACTAAACTACTTCGTCTCAGTCTT 57.119 37.500 0.00 0.00 0.00 3.01
9 10 6.880942 AACTAAACTACTTCGTCTCAGTCT 57.119 37.500 0.00 0.00 0.00 3.24
10 11 8.288913 ACTAAACTAAACTACTTCGTCTCAGTC 58.711 37.037 0.00 0.00 0.00 3.51
11 12 8.164058 ACTAAACTAAACTACTTCGTCTCAGT 57.836 34.615 0.00 0.00 0.00 3.41
12 13 8.903723 CAACTAAACTAAACTACTTCGTCTCAG 58.096 37.037 0.00 0.00 0.00 3.35
13 14 8.408601 ACAACTAAACTAAACTACTTCGTCTCA 58.591 33.333 0.00 0.00 0.00 3.27
14 15 8.794308 ACAACTAAACTAAACTACTTCGTCTC 57.206 34.615 0.00 0.00 0.00 3.36
15 16 9.890352 CTACAACTAAACTAAACTACTTCGTCT 57.110 33.333 0.00 0.00 0.00 4.18
16 17 9.670719 ACTACAACTAAACTAAACTACTTCGTC 57.329 33.333 0.00 0.00 0.00 4.20
34 35 9.052759 CCAAACATTCAAACTACTACTACAACT 57.947 33.333 0.00 0.00 0.00 3.16
35 36 9.048446 TCCAAACATTCAAACTACTACTACAAC 57.952 33.333 0.00 0.00 0.00 3.32
36 37 9.787435 ATCCAAACATTCAAACTACTACTACAA 57.213 29.630 0.00 0.00 0.00 2.41
37 38 9.214957 CATCCAAACATTCAAACTACTACTACA 57.785 33.333 0.00 0.00 0.00 2.74
38 39 9.216117 ACATCCAAACATTCAAACTACTACTAC 57.784 33.333 0.00 0.00 0.00 2.73
39 40 9.787435 AACATCCAAACATTCAAACTACTACTA 57.213 29.630 0.00 0.00 0.00 1.82
40 41 8.691661 AACATCCAAACATTCAAACTACTACT 57.308 30.769 0.00 0.00 0.00 2.57
41 42 9.180678 CAAACATCCAAACATTCAAACTACTAC 57.819 33.333 0.00 0.00 0.00 2.73
42 43 8.908903 ACAAACATCCAAACATTCAAACTACTA 58.091 29.630 0.00 0.00 0.00 1.82
43 44 7.781056 ACAAACATCCAAACATTCAAACTACT 58.219 30.769 0.00 0.00 0.00 2.57
44 45 9.180678 CTACAAACATCCAAACATTCAAACTAC 57.819 33.333 0.00 0.00 0.00 2.73
45 46 8.908903 ACTACAAACATCCAAACATTCAAACTA 58.091 29.630 0.00 0.00 0.00 2.24
46 47 7.781056 ACTACAAACATCCAAACATTCAAACT 58.219 30.769 0.00 0.00 0.00 2.66
47 48 9.180678 CTACTACAAACATCCAAACATTCAAAC 57.819 33.333 0.00 0.00 0.00 2.93
48 49 8.908903 ACTACTACAAACATCCAAACATTCAAA 58.091 29.630 0.00 0.00 0.00 2.69
49 50 8.458573 ACTACTACAAACATCCAAACATTCAA 57.541 30.769 0.00 0.00 0.00 2.69
50 51 8.458573 AACTACTACAAACATCCAAACATTCA 57.541 30.769 0.00 0.00 0.00 2.57
53 54 9.569122 ACTAAACTACTACAAACATCCAAACAT 57.431 29.630 0.00 0.00 0.00 2.71
54 55 8.967664 ACTAAACTACTACAAACATCCAAACA 57.032 30.769 0.00 0.00 0.00 2.83
57 58 9.616156 TCAAACTAAACTACTACAAACATCCAA 57.384 29.630 0.00 0.00 0.00 3.53
58 59 9.616156 TTCAAACTAAACTACTACAAACATCCA 57.384 29.630 0.00 0.00 0.00 3.41
72 73 9.458374 CGAATACCAAAACATTCAAACTAAACT 57.542 29.630 0.00 0.00 31.86 2.66
73 74 9.240159 ACGAATACCAAAACATTCAAACTAAAC 57.760 29.630 0.00 0.00 31.86 2.01
225 230 3.196901 TCGAAGCAAGTTCTAGGGCATAA 59.803 43.478 0.00 0.00 32.33 1.90
235 240 2.484889 ACAAGAGGTCGAAGCAAGTTC 58.515 47.619 0.00 0.00 0.00 3.01
249 254 7.389053 ACCTGCTCTATTTTAGAACAACAAGAG 59.611 37.037 0.00 0.00 31.19 2.85
250 255 7.173218 CACCTGCTCTATTTTAGAACAACAAGA 59.827 37.037 0.00 0.00 31.19 3.02
255 260 6.206634 CCAACACCTGCTCTATTTTAGAACAA 59.793 38.462 0.00 0.00 31.19 2.83
260 265 5.734720 TCTCCAACACCTGCTCTATTTTAG 58.265 41.667 0.00 0.00 0.00 1.85
328 336 0.743688 TTTCGTGGCATGCAAACTGT 59.256 45.000 21.36 0.00 0.00 3.55
344 352 5.591067 TCTCCTATCCTCTTCTCGACTTTTC 59.409 44.000 0.00 0.00 0.00 2.29
364 372 4.359434 ACAAAACCCTTCTTCTCTCTCC 57.641 45.455 0.00 0.00 0.00 3.71
395 403 6.318900 ACAAACCCTAAGAAAAGTCAGAAGTG 59.681 38.462 0.00 0.00 0.00 3.16
396 404 6.318900 CACAAACCCTAAGAAAAGTCAGAAGT 59.681 38.462 0.00 0.00 0.00 3.01
397 405 6.318900 ACACAAACCCTAAGAAAAGTCAGAAG 59.681 38.462 0.00 0.00 0.00 2.85
438 446 1.248785 TAGAGAGTTGTCGCCGCCTT 61.249 55.000 0.00 0.00 0.00 4.35
503 512 2.098607 CACCCTCTGACGACGCTATAAA 59.901 50.000 0.00 0.00 0.00 1.40
506 515 0.680280 ACACCCTCTGACGACGCTAT 60.680 55.000 0.00 0.00 0.00 2.97
537 546 1.523258 CTGCAAGATCCGCCAGAGG 60.523 63.158 2.49 0.00 34.07 3.69
595 605 2.587956 CGACACACGAATAAAGACCGA 58.412 47.619 0.00 0.00 45.77 4.69
640 657 2.107204 ACCACTGCCATTGAAGAGAAGT 59.893 45.455 0.00 0.00 0.00 3.01
667 684 0.678395 ATAGGACCAGCGCATCAGAG 59.322 55.000 11.47 0.00 0.00 3.35
689 706 2.479412 GAAGTCGTCGTGCTGAGGCT 62.479 60.000 0.00 0.00 39.59 4.58
726 833 3.326588 TCAGTAGAGCTGGGCAAAACTTA 59.673 43.478 0.00 0.00 45.08 2.24
745 852 0.830648 TGTTATCGCCCCTCCTTCAG 59.169 55.000 0.00 0.00 0.00 3.02
761 868 3.118454 CGAAGGCACGCCGATGTT 61.118 61.111 1.61 0.00 41.95 2.71
782 889 2.124903 ACGACTACAAACACTGAAGCG 58.875 47.619 0.00 0.00 0.00 4.68
792 899 2.229543 ACCACATAGCGACGACTACAAA 59.770 45.455 0.00 0.00 0.00 2.83
808 915 1.204704 CATCCAGCTTCGTAGACCACA 59.795 52.381 0.00 0.00 34.32 4.17
821 928 8.686334 TCAGAAAGGATAAAATTTACATCCAGC 58.314 33.333 23.73 15.85 40.67 4.85
840 947 9.175060 CATGATAGTATAACGAGTGTCAGAAAG 57.825 37.037 0.00 0.00 0.00 2.62
847 954 9.631452 CATCAATCATGATAGTATAACGAGTGT 57.369 33.333 9.04 0.00 44.53 3.55
916 1063 7.443575 GGATTGACTCATACATGTGCTTAGATT 59.556 37.037 9.11 0.00 0.00 2.40
973 1123 5.506730 TTTCTTGTTGTTTTCCCCCTTTT 57.493 34.783 0.00 0.00 0.00 2.27
1086 1236 1.457831 GCCTCCTAGGACCACGGAT 60.458 63.158 17.06 0.00 37.67 4.18
1367 1517 5.365025 TGAACATGGGTGGAAAATCAAAAGA 59.635 36.000 0.00 0.00 0.00 2.52
1411 1561 1.070577 CAAGAACACGACCAAGAAGCG 60.071 52.381 0.00 0.00 0.00 4.68
1513 1663 1.341209 GAAAACAAGGGGGCAAGACAG 59.659 52.381 0.00 0.00 0.00 3.51
1523 1673 3.568538 CAGAAATCGCAGAAAACAAGGG 58.431 45.455 0.00 0.00 43.58 3.95
1562 1713 2.260822 ACTAGCTATCCGCCCAATCAT 58.739 47.619 0.00 0.00 40.39 2.45
1600 1751 1.404391 ACACGCTGATCTAGTTACCCG 59.596 52.381 0.00 0.00 0.00 5.28
1633 1784 3.505680 GCATACAGGACCACACAAAATGA 59.494 43.478 0.00 0.00 0.00 2.57
1635 1786 3.766545 AGCATACAGGACCACACAAAAT 58.233 40.909 0.00 0.00 0.00 1.82
1636 1787 3.222173 AGCATACAGGACCACACAAAA 57.778 42.857 0.00 0.00 0.00 2.44
1656 1807 8.739039 CAACCAAATCATATCTACAACTTCCAA 58.261 33.333 0.00 0.00 0.00 3.53
1657 1808 7.148086 GCAACCAAATCATATCTACAACTTCCA 60.148 37.037 0.00 0.00 0.00 3.53
1658 1809 7.067494 AGCAACCAAATCATATCTACAACTTCC 59.933 37.037 0.00 0.00 0.00 3.46
1663 1814 7.611467 AGTTCAGCAACCAAATCATATCTACAA 59.389 33.333 0.00 0.00 32.22 2.41
1667 1818 5.359009 CCAGTTCAGCAACCAAATCATATCT 59.641 40.000 0.00 0.00 32.22 1.98
1700 1851 8.083462 CCAAAACAAACAATAATTACCGGTACT 58.917 33.333 15.53 6.15 0.00 2.73
1706 1857 7.146648 TCGGACCAAAACAAACAATAATTACC 58.853 34.615 0.00 0.00 0.00 2.85
1717 1868 2.294074 CACTCCTCGGACCAAAACAAA 58.706 47.619 0.00 0.00 0.00 2.83
1744 1895 6.246420 ACTAAATTCTCAACATGACTGCAC 57.754 37.500 0.00 0.00 0.00 4.57
1838 1989 6.258507 GCCACAAAACTTCATTTCAAAGTCAT 59.741 34.615 0.00 0.00 35.96 3.06
1874 2026 4.320057 GCATGCACAGATAGCAATAAGTCC 60.320 45.833 14.21 0.00 46.27 3.85
1883 2035 4.514441 AGAACATTAGCATGCACAGATAGC 59.486 41.667 21.98 2.68 33.05 2.97
1932 2205 5.961421 AGGAAGAGCTCTTTAGTACAAGGAT 59.039 40.000 29.02 2.68 36.11 3.24
2158 2504 6.394025 ACAGATGGGCGTTTTTACTTTTTA 57.606 33.333 0.00 0.00 0.00 1.52
2171 2517 1.066908 ACAAACACAAACAGATGGGCG 59.933 47.619 0.00 0.00 0.00 6.13
2190 2537 7.894847 GCTTTTGCAATATGTTACAATGGTAC 58.105 34.615 0.00 0.00 46.58 3.34
2356 2710 5.125100 TCAACTAAATGCCAGAAAAGCTG 57.875 39.130 0.00 0.00 44.49 4.24
2402 2761 4.261155 GCTTTTGGTAAGATCGCATGCATA 60.261 41.667 19.57 5.21 0.00 3.14
2537 2896 3.019564 GCATGATTAGGATGGCCCATAC 58.980 50.000 0.00 0.00 37.41 2.39
2620 2980 5.945191 ACCACTTAGTGTCTCCTTACTAGAC 59.055 44.000 11.68 0.00 43.04 2.59
2622 2982 5.125739 CCACCACTTAGTGTCTCCTTACTAG 59.874 48.000 11.68 0.00 35.93 2.57
2743 3110 3.548745 CTCATCAGTTGGGCTATGTGA 57.451 47.619 0.00 0.00 0.00 3.58
2753 3120 3.427638 CCTGCAATGAAGCTCATCAGTTG 60.428 47.826 0.00 0.00 35.76 3.16
2843 3210 3.755434 GCTTGTGCAGCCTCAAGT 58.245 55.556 20.95 0.00 43.65 3.16
2920 3287 8.370182 TCAGATTTATGTATGCAGCTCAAGATA 58.630 33.333 0.00 0.00 0.00 1.98
3017 3384 3.872560 GTCGACGTTTGAAGACCATTT 57.127 42.857 0.00 0.00 0.00 2.32
3193 3560 6.272822 AGAGGCACCAAATTCATTTAGTTC 57.727 37.500 0.00 0.00 0.00 3.01
3299 3667 1.349026 TCTGCCAAGAGACCCAAGAAG 59.651 52.381 0.00 0.00 0.00 2.85
3567 3935 6.534634 ACACCTTATTTGCTGGATATACTCC 58.465 40.000 0.00 0.00 45.19 3.85
3653 4021 2.988010 TCTACTGATGTGGACATGGC 57.012 50.000 0.00 0.00 36.57 4.40
3837 4212 2.155279 GGAGACAAGTTCTTGGCCTTC 58.845 52.381 13.91 6.89 33.22 3.46
3876 4251 0.250234 TCACATACCAGTGCTCCTGC 59.750 55.000 0.00 0.00 40.06 4.85


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

AutoCloner maintained by Alex Coulton.