Multiple sequence alignment - TraesCS6A01G210400

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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 TraesCS6A01G210400 chr6A 100.000 2754 0 0 1 2754 381115318 381112565 0.000000e+00 5086
1 TraesCS6A01G210400 chr6A 92.612 1367 77 6 1407 2754 587646795 587645434 0.000000e+00 1943
2 TraesCS6A01G210400 chr6A 95.041 121 5 1 1 121 471601604 471601723 3.620000e-44 189
3 TraesCS6A01G210400 chr6A 86.250 160 18 4 1 158 377406730 377406573 1.310000e-38 171
4 TraesCS6A01G210400 chr3D 94.374 2666 120 8 111 2754 542834182 542836839 0.000000e+00 4065
5 TraesCS6A01G210400 chr3D 92.908 2665 161 10 111 2754 543498843 543501500 0.000000e+00 3849
6 TraesCS6A01G210400 chr7D 93.448 2671 136 12 111 2754 116647692 116650350 0.000000e+00 3927
7 TraesCS6A01G210400 chr2D 93.224 2671 148 13 111 2754 634063573 634060909 0.000000e+00 3899
8 TraesCS6A01G210400 chr2D 92.266 1293 76 5 1486 2754 417207936 417209228 0.000000e+00 1812
9 TraesCS6A01G210400 chr1A 93.184 2670 148 11 111 2754 254400727 254403388 0.000000e+00 3892
10 TraesCS6A01G210400 chr1A 92.900 2676 149 10 111 2754 47184590 47181924 0.000000e+00 3851
11 TraesCS6A01G210400 chr1A 95.161 124 5 1 1 123 549962839 549962962 7.780000e-46 195
12 TraesCS6A01G210400 chr5D 93.074 2671 145 11 111 2754 238121663 238124320 0.000000e+00 3871
13 TraesCS6A01G210400 chr4D 92.940 2663 154 8 111 2754 130443444 130440797 0.000000e+00 3845
14 TraesCS6A01G210400 chr4D 91.067 2653 190 22 111 2731 65098852 65096215 0.000000e+00 3542
15 TraesCS6A01G210400 chr2B 91.030 2631 186 24 111 2731 72759318 72761908 0.000000e+00 3506
16 TraesCS6A01G210400 chr4A 93.407 1623 84 6 1151 2754 136913863 136915481 0.000000e+00 2383
17 TraesCS6A01G210400 chrUn 89.977 858 63 14 1909 2754 24700679 24699833 0.000000e+00 1086
18 TraesCS6A01G210400 chr3B 88.671 865 79 9 1896 2754 476390919 476391770 0.000000e+00 1037
19 TraesCS6A01G210400 chr3A 96.610 118 4 0 1 118 507391292 507391175 2.160000e-46 196
20 TraesCS6A01G210400 chr7A 95.798 119 5 0 1 119 395154706 395154824 2.800000e-45 193
21 TraesCS6A01G210400 chr7A 93.548 124 8 0 1 124 386366918 386367041 4.680000e-43 185
22 TraesCS6A01G210400 chr5A 94.400 125 6 1 1 124 130329450 130329326 1.010000e-44 191
23 TraesCS6A01G210400 chr5A 90.071 141 12 2 1 140 82365063 82364924 6.060000e-42 182
24 TraesCS6A01G210400 chr2A 89.928 139 13 1 1 138 204733818 204733680 7.840000e-41 178


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 TraesCS6A01G210400 chr6A 381112565 381115318 2753 True 5086 5086 100.000 1 2754 1 chr6A.!!$R2 2753
1 TraesCS6A01G210400 chr6A 587645434 587646795 1361 True 1943 1943 92.612 1407 2754 1 chr6A.!!$R3 1347
2 TraesCS6A01G210400 chr3D 542834182 542836839 2657 False 4065 4065 94.374 111 2754 1 chr3D.!!$F1 2643
3 TraesCS6A01G210400 chr3D 543498843 543501500 2657 False 3849 3849 92.908 111 2754 1 chr3D.!!$F2 2643
4 TraesCS6A01G210400 chr7D 116647692 116650350 2658 False 3927 3927 93.448 111 2754 1 chr7D.!!$F1 2643
5 TraesCS6A01G210400 chr2D 634060909 634063573 2664 True 3899 3899 93.224 111 2754 1 chr2D.!!$R1 2643
6 TraesCS6A01G210400 chr2D 417207936 417209228 1292 False 1812 1812 92.266 1486 2754 1 chr2D.!!$F1 1268
7 TraesCS6A01G210400 chr1A 254400727 254403388 2661 False 3892 3892 93.184 111 2754 1 chr1A.!!$F1 2643
8 TraesCS6A01G210400 chr1A 47181924 47184590 2666 True 3851 3851 92.900 111 2754 1 chr1A.!!$R1 2643
9 TraesCS6A01G210400 chr5D 238121663 238124320 2657 False 3871 3871 93.074 111 2754 1 chr5D.!!$F1 2643
10 TraesCS6A01G210400 chr4D 130440797 130443444 2647 True 3845 3845 92.940 111 2754 1 chr4D.!!$R2 2643
11 TraesCS6A01G210400 chr4D 65096215 65098852 2637 True 3542 3542 91.067 111 2731 1 chr4D.!!$R1 2620
12 TraesCS6A01G210400 chr2B 72759318 72761908 2590 False 3506 3506 91.030 111 2731 1 chr2B.!!$F1 2620
13 TraesCS6A01G210400 chr4A 136913863 136915481 1618 False 2383 2383 93.407 1151 2754 1 chr4A.!!$F1 1603
14 TraesCS6A01G210400 chrUn 24699833 24700679 846 True 1086 1086 89.977 1909 2754 1 chrUn.!!$R1 845
15 TraesCS6A01G210400 chr3B 476390919 476391770 851 False 1037 1037 88.671 1896 2754 1 chr3B.!!$F1 858

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
172 173 0.037232 CCTCCGTTCGAGCTTTCCTT 60.037 55.0 0.00 0.0 37.27 3.36 F
810 817 0.393077 CCCTTGTCTTGTCCGACAGT 59.607 55.0 0.64 0.0 44.02 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1410 0.034896 GGAACTCAGCGTCCCTTGAA 59.965 55.0 0.0 0.0 0.00 2.69 R
2062 2118 0.040646 AGGGTGTCGTCCTACCATCA 59.959 55.0 0.0 0.0 38.74 3.07 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 5.705609 ACATGGGTTGTTGTGAAGATTAC 57.294 39.130 0.00 0.00 33.74 1.89
24 25 4.522789 ACATGGGTTGTTGTGAAGATTACC 59.477 41.667 0.00 0.00 33.74 2.85
25 26 4.447138 TGGGTTGTTGTGAAGATTACCT 57.553 40.909 0.00 0.00 0.00 3.08
26 27 4.394729 TGGGTTGTTGTGAAGATTACCTC 58.605 43.478 0.00 0.00 0.00 3.85
27 28 3.756963 GGGTTGTTGTGAAGATTACCTCC 59.243 47.826 0.00 0.00 0.00 4.30
28 29 3.756963 GGTTGTTGTGAAGATTACCTCCC 59.243 47.826 0.00 0.00 0.00 4.30
29 30 4.506802 GGTTGTTGTGAAGATTACCTCCCT 60.507 45.833 0.00 0.00 0.00 4.20
30 31 4.993705 TGTTGTGAAGATTACCTCCCTT 57.006 40.909 0.00 0.00 0.00 3.95
31 32 4.651778 TGTTGTGAAGATTACCTCCCTTG 58.348 43.478 0.00 0.00 0.00 3.61
32 33 3.350219 TGTGAAGATTACCTCCCTTGC 57.650 47.619 0.00 0.00 0.00 4.01
33 34 2.280628 GTGAAGATTACCTCCCTTGCG 58.719 52.381 0.00 0.00 0.00 4.85
34 35 2.093658 GTGAAGATTACCTCCCTTGCGA 60.094 50.000 0.00 0.00 0.00 5.10
35 36 2.093658 TGAAGATTACCTCCCTTGCGAC 60.094 50.000 0.00 0.00 0.00 5.19
36 37 1.568504 AGATTACCTCCCTTGCGACA 58.431 50.000 0.00 0.00 0.00 4.35
37 38 2.119495 AGATTACCTCCCTTGCGACAT 58.881 47.619 0.00 0.00 0.00 3.06
38 39 2.505819 AGATTACCTCCCTTGCGACATT 59.494 45.455 0.00 0.00 0.00 2.71
39 40 2.107950 TTACCTCCCTTGCGACATTG 57.892 50.000 0.00 0.00 0.00 2.82
40 41 0.392461 TACCTCCCTTGCGACATTGC 60.392 55.000 0.00 0.00 0.00 3.56
41 42 1.377725 CCTCCCTTGCGACATTGCT 60.378 57.895 0.00 0.00 35.36 3.91
42 43 0.962356 CCTCCCTTGCGACATTGCTT 60.962 55.000 0.00 0.00 35.36 3.91
43 44 0.883833 CTCCCTTGCGACATTGCTTT 59.116 50.000 0.00 0.00 35.36 3.51
44 45 0.881118 TCCCTTGCGACATTGCTTTC 59.119 50.000 0.00 0.00 35.36 2.62
45 46 0.597568 CCCTTGCGACATTGCTTTCA 59.402 50.000 0.00 0.00 35.36 2.69
46 47 1.000385 CCCTTGCGACATTGCTTTCAA 60.000 47.619 0.00 0.00 36.51 2.69
47 48 2.353011 CCCTTGCGACATTGCTTTCAAT 60.353 45.455 0.00 0.00 43.31 2.57
58 59 3.591196 TGCTTTCAATGTGGTTATGCC 57.409 42.857 0.00 0.00 37.90 4.40
59 60 3.164268 TGCTTTCAATGTGGTTATGCCT 58.836 40.909 0.00 0.00 38.35 4.75
60 61 3.193267 TGCTTTCAATGTGGTTATGCCTC 59.807 43.478 0.00 0.00 38.35 4.70
61 62 3.445096 GCTTTCAATGTGGTTATGCCTCT 59.555 43.478 0.00 0.00 38.35 3.69
62 63 4.676196 GCTTTCAATGTGGTTATGCCTCTG 60.676 45.833 0.00 0.00 38.35 3.35
63 64 3.998913 TCAATGTGGTTATGCCTCTGA 57.001 42.857 0.00 0.00 38.35 3.27
64 65 3.877559 TCAATGTGGTTATGCCTCTGAG 58.122 45.455 0.00 0.00 38.35 3.35
65 66 3.264193 TCAATGTGGTTATGCCTCTGAGT 59.736 43.478 3.66 0.00 38.35 3.41
66 67 3.550437 ATGTGGTTATGCCTCTGAGTC 57.450 47.619 3.66 0.00 38.35 3.36
67 68 1.204704 TGTGGTTATGCCTCTGAGTCG 59.795 52.381 3.66 0.00 38.35 4.18
68 69 1.204941 GTGGTTATGCCTCTGAGTCGT 59.795 52.381 3.66 0.00 38.35 4.34
69 70 1.204704 TGGTTATGCCTCTGAGTCGTG 59.795 52.381 3.66 0.00 38.35 4.35
70 71 1.281899 GTTATGCCTCTGAGTCGTGC 58.718 55.000 3.66 0.38 0.00 5.34
71 72 1.134965 GTTATGCCTCTGAGTCGTGCT 60.135 52.381 3.66 0.00 0.00 4.40
72 73 1.186200 TATGCCTCTGAGTCGTGCTT 58.814 50.000 3.66 1.26 0.00 3.91
73 74 0.108424 ATGCCTCTGAGTCGTGCTTC 60.108 55.000 3.66 0.00 0.00 3.86
74 75 1.803519 GCCTCTGAGTCGTGCTTCG 60.804 63.158 3.66 0.00 41.41 3.79
75 76 1.876664 CCTCTGAGTCGTGCTTCGA 59.123 57.895 3.66 0.92 46.83 3.71
82 83 4.260194 TCGTGCTTCGACATGTGG 57.740 55.556 1.15 0.87 44.01 4.17
83 84 1.374125 TCGTGCTTCGACATGTGGG 60.374 57.895 1.15 0.00 44.01 4.61
84 85 1.374125 CGTGCTTCGACATGTGGGA 60.374 57.895 1.15 0.00 42.86 4.37
85 86 1.354337 CGTGCTTCGACATGTGGGAG 61.354 60.000 11.64 11.64 42.86 4.30
86 87 0.037326 GTGCTTCGACATGTGGGAGA 60.037 55.000 19.53 3.33 0.00 3.71
87 88 0.904649 TGCTTCGACATGTGGGAGAT 59.095 50.000 19.53 0.00 0.00 2.75
88 89 2.107366 TGCTTCGACATGTGGGAGATA 58.893 47.619 19.53 5.05 0.00 1.98
89 90 2.700371 TGCTTCGACATGTGGGAGATAT 59.300 45.455 19.53 0.00 0.00 1.63
90 91 3.895041 TGCTTCGACATGTGGGAGATATA 59.105 43.478 19.53 0.29 0.00 0.86
91 92 4.021981 TGCTTCGACATGTGGGAGATATAG 60.022 45.833 19.53 4.48 0.00 1.31
92 93 4.489810 CTTCGACATGTGGGAGATATAGC 58.510 47.826 10.53 0.00 0.00 2.97
93 94 2.826128 TCGACATGTGGGAGATATAGCC 59.174 50.000 1.15 0.00 0.00 3.93
94 95 2.416027 CGACATGTGGGAGATATAGCCG 60.416 54.545 1.15 0.00 0.00 5.52
95 96 1.276421 ACATGTGGGAGATATAGCCGC 59.724 52.381 0.00 0.00 0.00 6.53
96 97 1.276138 CATGTGGGAGATATAGCCGCA 59.724 52.381 0.00 0.00 0.00 5.69
97 98 1.644509 TGTGGGAGATATAGCCGCAT 58.355 50.000 0.00 0.00 0.00 4.73
98 99 1.550524 TGTGGGAGATATAGCCGCATC 59.449 52.381 0.00 0.00 0.00 3.91
99 100 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
100 101 1.103803 GGGAGATATAGCCGCATCGA 58.896 55.000 0.00 0.00 0.00 3.59
101 102 1.066303 GGGAGATATAGCCGCATCGAG 59.934 57.143 0.00 0.00 0.00 4.04
102 103 1.066303 GGAGATATAGCCGCATCGAGG 59.934 57.143 0.00 0.00 0.00 4.63
103 104 1.066303 GAGATATAGCCGCATCGAGGG 59.934 57.143 0.00 0.00 0.00 4.30
172 173 0.037232 CCTCCGTTCGAGCTTTCCTT 60.037 55.000 0.00 0.00 37.27 3.36
226 227 2.108976 GCATCTTCATCGGCCGGA 59.891 61.111 27.83 14.94 0.00 5.14
278 280 0.669318 GCGTTGATCTTCCACGACCA 60.669 55.000 5.44 0.00 0.00 4.02
312 315 0.682209 CAAGCTACAGCCATGGCCTT 60.682 55.000 33.14 23.94 43.38 4.35
409 414 6.686378 GCATGGTTGATTAGTGGTCTGATCTA 60.686 42.308 0.00 0.00 37.51 1.98
454 459 3.243128 GCGGTTGCAATTTGTGGC 58.757 55.556 0.59 0.00 42.15 5.01
551 556 9.617523 TTGAATCATGCTTAGATCTGTGATTTA 57.382 29.630 5.18 7.50 36.68 1.40
580 587 3.760738 TGGTTGTCCATTTGTAGCATGA 58.239 40.909 0.00 0.00 39.03 3.07
640 647 0.902531 GTCTGCTTGGTAGGGTAGCA 59.097 55.000 0.00 0.00 42.22 3.49
786 793 0.574454 CGCAGACGCAAGATCTTAGC 59.426 55.000 7.86 12.84 43.62 3.09
810 817 0.393077 CCCTTGTCTTGTCCGACAGT 59.607 55.000 0.64 0.00 44.02 3.55
850 857 1.448119 CGAGGACTCGCAGCCTATGA 61.448 60.000 8.93 0.00 46.50 2.15
930 949 2.755650 CTCGTTGAGCCAACAACTACT 58.244 47.619 15.40 0.00 43.70 2.57
931 950 2.476619 CTCGTTGAGCCAACAACTACTG 59.523 50.000 15.40 3.39 43.70 2.74
932 951 2.101750 TCGTTGAGCCAACAACTACTGA 59.898 45.455 15.40 5.17 43.70 3.41
933 952 3.067106 CGTTGAGCCAACAACTACTGAT 58.933 45.455 15.40 0.00 43.70 2.90
934 953 3.120546 CGTTGAGCCAACAACTACTGATG 60.121 47.826 15.40 0.00 43.70 3.07
935 954 3.769739 TGAGCCAACAACTACTGATGT 57.230 42.857 0.00 0.00 0.00 3.06
1035 1060 3.622612 CGTTCATGTCCATGTTCATGCTA 59.377 43.478 17.17 8.90 40.54 3.49
1045 1070 4.802039 CCATGTTCATGCTAAACAAGATGC 59.198 41.667 7.21 0.00 39.84 3.91
1082 1107 1.623811 TGGAGTTAGGACTGACAAGGC 59.376 52.381 0.00 0.00 35.88 4.35
1113 1138 1.308783 TGCACTTGAACACCGTTGCA 61.309 50.000 0.00 0.00 0.00 4.08
1122 1147 1.319614 ACACCGTTGCAAAGCAGGTT 61.320 50.000 0.00 0.00 40.61 3.50
1131 1156 2.165437 TGCAAAGCAGGTTTTCGAGTTT 59.835 40.909 0.00 0.00 33.32 2.66
1144 1169 1.140052 TCGAGTTTTGTGGGCAAGAGA 59.860 47.619 0.00 0.00 35.82 3.10
1356 1382 3.198200 TGCCTACCCTAATCGCAACTAAA 59.802 43.478 0.00 0.00 0.00 1.85
1384 1410 6.207417 CACTTGTGTTTCATTCTTAGGACCAT 59.793 38.462 0.00 0.00 0.00 3.55
1385 1411 6.777580 ACTTGTGTTTCATTCTTAGGACCATT 59.222 34.615 0.00 0.00 0.00 3.16
1531 1559 2.204090 GACTTCCCTGGGACCCCA 60.204 66.667 16.85 7.67 45.02 4.96
1618 1646 4.352001 CCCATCCATGATAGGAAGAGGAAA 59.648 45.833 0.00 0.00 41.92 3.13
1755 1783 1.257743 GGCGCTATCATGACCTAGGA 58.742 55.000 17.98 0.00 0.00 2.94
1791 1819 0.107800 GCTCTCATGGCAGCTCTCAA 60.108 55.000 8.99 0.00 32.48 3.02
1852 1881 3.695606 ATGGCCGACGCTCACAGT 61.696 61.111 0.00 0.00 34.44 3.55
1853 1882 2.348104 ATGGCCGACGCTCACAGTA 61.348 57.895 0.00 0.00 34.44 2.74
1894 1923 3.887621 CTGGGCAAGCACTACTACTAA 57.112 47.619 0.00 0.00 0.00 2.24
2062 2118 3.079578 CTCATGCTGATGGTGAACTTGT 58.920 45.455 0.00 0.00 0.00 3.16
2140 2196 3.682718 GCTAGGAAGAACTTGCTATGCCA 60.683 47.826 14.20 0.00 41.52 4.92
2325 2405 1.287815 CCAGTGCACAAGTGGCATG 59.712 57.895 21.04 5.51 42.56 4.06
2392 2479 1.629043 ACAAGCTTACTCCGACTGGA 58.371 50.000 0.00 0.00 43.88 3.86
2437 2547 0.668535 GCAAGGTTGGAGGTGTCAAC 59.331 55.000 0.00 0.00 42.53 3.18
2441 2551 0.179067 GGTTGGAGGTGTCAACGTGA 60.179 55.000 0.00 0.00 43.75 4.35
2461 2571 1.523758 ATCGTCAGTTTGGGCTGAAC 58.476 50.000 0.00 0.00 45.75 3.18
2551 2661 2.185387 GGGTAAGCTCACCAACTAGGA 58.815 52.381 8.72 0.00 40.65 2.94
2553 2663 3.432326 GGGTAAGCTCACCAACTAGGATG 60.432 52.174 8.72 0.00 40.65 3.51
2568 2678 3.091633 AGGATGCAAGGTAAGCACAAT 57.908 42.857 0.00 0.00 45.95 2.71
2593 2703 1.870383 GCCGTATGCAACCAAACGA 59.130 52.632 0.00 0.00 40.77 3.85
2678 2788 0.826715 GCAGGGACACTAGATGCAGA 59.173 55.000 0.00 0.00 36.88 4.26
2709 2820 2.039418 ACTGGCAGATGGCGTATTAGA 58.961 47.619 23.66 0.00 46.16 2.10
2721 2832 5.302360 TGGCGTATTAGAGTCTGTTTTTGT 58.698 37.500 1.86 0.00 0.00 2.83
2731 2842 4.086457 AGTCTGTTTTTGTTCAACCAGGT 58.914 39.130 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.708230 GGTAATCTTCACAACAACCCATGTA 59.292 40.000 0.00 0.00 42.99 2.29
1 2 4.522789 GGTAATCTTCACAACAACCCATGT 59.477 41.667 0.00 0.00 46.82 3.21
2 3 4.766891 AGGTAATCTTCACAACAACCCATG 59.233 41.667 0.00 0.00 0.00 3.66
3 4 4.998051 AGGTAATCTTCACAACAACCCAT 58.002 39.130 0.00 0.00 0.00 4.00
4 5 4.394729 GAGGTAATCTTCACAACAACCCA 58.605 43.478 0.00 0.00 0.00 4.51
5 6 3.756963 GGAGGTAATCTTCACAACAACCC 59.243 47.826 0.00 0.00 0.00 4.11
6 7 3.756963 GGGAGGTAATCTTCACAACAACC 59.243 47.826 0.00 0.00 0.00 3.77
7 8 4.652822 AGGGAGGTAATCTTCACAACAAC 58.347 43.478 0.00 0.00 0.00 3.32
8 9 4.993705 AGGGAGGTAATCTTCACAACAA 57.006 40.909 0.00 0.00 0.00 2.83
9 10 4.651778 CAAGGGAGGTAATCTTCACAACA 58.348 43.478 0.00 0.00 0.00 3.33
10 11 3.440522 GCAAGGGAGGTAATCTTCACAAC 59.559 47.826 0.00 0.00 0.00 3.32
11 12 3.686016 GCAAGGGAGGTAATCTTCACAA 58.314 45.455 0.00 0.00 0.00 3.33
12 13 2.354704 CGCAAGGGAGGTAATCTTCACA 60.355 50.000 0.00 0.00 0.00 3.58
13 14 2.093658 TCGCAAGGGAGGTAATCTTCAC 60.094 50.000 0.00 0.00 38.47 3.18
14 15 2.093658 GTCGCAAGGGAGGTAATCTTCA 60.094 50.000 0.00 0.00 38.47 3.02
15 16 2.093658 TGTCGCAAGGGAGGTAATCTTC 60.094 50.000 0.00 0.00 38.47 2.87
16 17 1.906574 TGTCGCAAGGGAGGTAATCTT 59.093 47.619 0.00 0.00 38.47 2.40
17 18 1.568504 TGTCGCAAGGGAGGTAATCT 58.431 50.000 0.00 0.00 38.47 2.40
18 19 2.614057 CAATGTCGCAAGGGAGGTAATC 59.386 50.000 0.00 0.00 38.47 1.75
19 20 2.643551 CAATGTCGCAAGGGAGGTAAT 58.356 47.619 0.00 0.00 38.47 1.89
20 21 1.948611 GCAATGTCGCAAGGGAGGTAA 60.949 52.381 0.00 0.00 38.47 2.85
21 22 0.392461 GCAATGTCGCAAGGGAGGTA 60.392 55.000 0.00 0.00 38.47 3.08
22 23 1.675641 GCAATGTCGCAAGGGAGGT 60.676 57.895 0.00 0.00 38.47 3.85
23 24 0.962356 AAGCAATGTCGCAAGGGAGG 60.962 55.000 0.00 0.00 38.47 4.30
24 25 0.883833 AAAGCAATGTCGCAAGGGAG 59.116 50.000 0.00 0.00 38.47 4.30
25 26 0.881118 GAAAGCAATGTCGCAAGGGA 59.119 50.000 0.00 0.00 38.47 4.20
26 27 0.597568 TGAAAGCAATGTCGCAAGGG 59.402 50.000 0.00 0.00 38.47 3.95
27 28 2.420628 TTGAAAGCAATGTCGCAAGG 57.579 45.000 0.00 0.00 38.47 3.61
36 37 4.223477 AGGCATAACCACATTGAAAGCAAT 59.777 37.500 0.00 0.00 42.85 3.56
37 38 3.577848 AGGCATAACCACATTGAAAGCAA 59.422 39.130 0.00 0.00 43.14 3.91
38 39 3.164268 AGGCATAACCACATTGAAAGCA 58.836 40.909 0.00 0.00 43.14 3.91
39 40 3.445096 AGAGGCATAACCACATTGAAAGC 59.555 43.478 0.00 0.00 43.14 3.51
40 41 4.701651 TCAGAGGCATAACCACATTGAAAG 59.298 41.667 0.00 0.00 43.14 2.62
41 42 4.661222 TCAGAGGCATAACCACATTGAAA 58.339 39.130 0.00 0.00 43.14 2.69
42 43 4.263462 ACTCAGAGGCATAACCACATTGAA 60.263 41.667 1.53 0.00 43.14 2.69
43 44 3.264193 ACTCAGAGGCATAACCACATTGA 59.736 43.478 1.53 0.00 43.14 2.57
44 45 3.614092 ACTCAGAGGCATAACCACATTG 58.386 45.455 1.53 0.00 43.14 2.82
45 46 3.679917 CGACTCAGAGGCATAACCACATT 60.680 47.826 3.54 0.00 43.14 2.71
46 47 2.159043 CGACTCAGAGGCATAACCACAT 60.159 50.000 3.54 0.00 43.14 3.21
47 48 1.204704 CGACTCAGAGGCATAACCACA 59.795 52.381 3.54 0.00 43.14 4.17
48 49 1.204941 ACGACTCAGAGGCATAACCAC 59.795 52.381 3.54 0.00 43.14 4.16
49 50 1.204704 CACGACTCAGAGGCATAACCA 59.795 52.381 3.54 0.00 43.14 3.67
50 51 1.927895 CACGACTCAGAGGCATAACC 58.072 55.000 3.54 0.00 39.61 2.85
51 52 1.134965 AGCACGACTCAGAGGCATAAC 60.135 52.381 3.54 0.00 0.00 1.89
52 53 1.186200 AGCACGACTCAGAGGCATAA 58.814 50.000 3.54 0.00 0.00 1.90
53 54 1.135139 GAAGCACGACTCAGAGGCATA 59.865 52.381 3.54 0.00 0.00 3.14
54 55 0.108424 GAAGCACGACTCAGAGGCAT 60.108 55.000 3.54 0.00 0.00 4.40
55 56 1.290324 GAAGCACGACTCAGAGGCA 59.710 57.895 3.54 0.00 0.00 4.75
56 57 1.803519 CGAAGCACGACTCAGAGGC 60.804 63.158 1.53 0.00 45.77 4.70
57 58 1.876664 TCGAAGCACGACTCAGAGG 59.123 57.895 1.53 0.00 46.45 3.69
66 67 1.354337 CTCCCACATGTCGAAGCACG 61.354 60.000 0.00 0.00 44.09 5.34
67 68 0.037326 TCTCCCACATGTCGAAGCAC 60.037 55.000 0.00 0.00 0.00 4.40
68 69 0.904649 ATCTCCCACATGTCGAAGCA 59.095 50.000 0.00 0.00 0.00 3.91
69 70 2.890808 TATCTCCCACATGTCGAAGC 57.109 50.000 0.00 0.00 0.00 3.86
70 71 4.489810 GCTATATCTCCCACATGTCGAAG 58.510 47.826 0.00 0.00 0.00 3.79
71 72 3.258372 GGCTATATCTCCCACATGTCGAA 59.742 47.826 0.00 0.00 0.00 3.71
72 73 2.826128 GGCTATATCTCCCACATGTCGA 59.174 50.000 0.00 0.00 0.00 4.20
73 74 2.416027 CGGCTATATCTCCCACATGTCG 60.416 54.545 0.00 0.00 0.00 4.35
74 75 2.675317 GCGGCTATATCTCCCACATGTC 60.675 54.545 0.00 0.00 0.00 3.06
75 76 1.276421 GCGGCTATATCTCCCACATGT 59.724 52.381 0.00 0.00 0.00 3.21
76 77 1.276138 TGCGGCTATATCTCCCACATG 59.724 52.381 0.00 0.00 0.00 3.21
77 78 1.644509 TGCGGCTATATCTCCCACAT 58.355 50.000 0.00 0.00 0.00 3.21
78 79 1.550524 GATGCGGCTATATCTCCCACA 59.449 52.381 0.00 0.00 0.00 4.17
79 80 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
80 81 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
81 82 1.066303 CTCGATGCGGCTATATCTCCC 59.934 57.143 0.00 0.00 0.00 4.30
82 83 1.066303 CCTCGATGCGGCTATATCTCC 59.934 57.143 0.00 0.00 0.00 3.71
83 84 1.066303 CCCTCGATGCGGCTATATCTC 59.934 57.143 0.00 0.00 0.00 2.75
84 85 1.107114 CCCTCGATGCGGCTATATCT 58.893 55.000 0.00 0.00 0.00 1.98
85 86 0.528684 GCCCTCGATGCGGCTATATC 60.529 60.000 10.26 0.00 42.21 1.63
86 87 1.517832 GCCCTCGATGCGGCTATAT 59.482 57.895 10.26 0.00 42.21 0.86
87 88 2.970639 GCCCTCGATGCGGCTATA 59.029 61.111 10.26 0.00 42.21 1.31
94 95 1.014352 AAATGTAACGCCCTCGATGC 58.986 50.000 0.00 0.00 39.41 3.91
95 96 2.221055 GCTAAATGTAACGCCCTCGATG 59.779 50.000 0.00 0.00 39.41 3.84
96 97 2.480845 GCTAAATGTAACGCCCTCGAT 58.519 47.619 0.00 0.00 39.41 3.59
97 98 1.472026 GGCTAAATGTAACGCCCTCGA 60.472 52.381 0.00 0.00 39.41 4.04
98 99 0.935196 GGCTAAATGTAACGCCCTCG 59.065 55.000 0.00 0.00 42.43 4.63
102 103 1.306148 GAGGGGCTAAATGTAACGCC 58.694 55.000 0.00 0.00 41.75 5.68
103 104 1.306148 GGAGGGGCTAAATGTAACGC 58.694 55.000 0.00 0.00 0.00 4.84
104 105 1.489230 AGGGAGGGGCTAAATGTAACG 59.511 52.381 0.00 0.00 0.00 3.18
105 106 2.508300 TGAGGGAGGGGCTAAATGTAAC 59.492 50.000 0.00 0.00 0.00 2.50
106 107 2.508300 GTGAGGGAGGGGCTAAATGTAA 59.492 50.000 0.00 0.00 0.00 2.41
107 108 2.124411 GTGAGGGAGGGGCTAAATGTA 58.876 52.381 0.00 0.00 0.00 2.29
108 109 0.919710 GTGAGGGAGGGGCTAAATGT 59.080 55.000 0.00 0.00 0.00 2.71
109 110 0.183731 GGTGAGGGAGGGGCTAAATG 59.816 60.000 0.00 0.00 0.00 2.32
141 142 0.840722 AACGGAGGGAGAATGGTGGT 60.841 55.000 0.00 0.00 0.00 4.16
242 243 3.691342 CCGGTCGGTGAAGGAGCA 61.691 66.667 0.55 0.00 32.38 4.26
255 256 1.375523 GTGGAAGATCAACGCCGGT 60.376 57.895 1.90 0.00 0.00 5.28
256 257 2.452813 CGTGGAAGATCAACGCCGG 61.453 63.158 0.00 0.00 0.00 6.13
312 315 4.104738 AGAGAAAGGGGATTGAACTCACAA 59.895 41.667 0.00 0.00 0.00 3.33
363 368 5.147767 TGCATCTAGATCAAACCCTAGCTA 58.852 41.667 1.03 0.00 34.02 3.32
409 414 4.726583 AGCAATCAACCATATCAGCTCAT 58.273 39.130 0.00 0.00 0.00 2.90
454 459 2.408271 TGCTTGAACATCTAGCCCTG 57.592 50.000 10.46 0.00 43.03 4.45
580 587 7.648142 CAGGAACATACAACTACAACAAACAT 58.352 34.615 0.00 0.00 0.00 2.71
657 664 9.492973 CATGTACATGGTTCATCACTATCATAA 57.507 33.333 25.41 0.00 35.24 1.90
786 793 1.303643 GGACAAGACAAGGGCCTGG 60.304 63.158 6.92 6.59 0.00 4.45
810 817 2.548057 GACAAACGATGGAGCAAACTGA 59.452 45.455 0.00 0.00 0.00 3.41
850 857 1.922447 TGAATTAGGTGCCATCTGGGT 59.078 47.619 0.00 0.00 39.65 4.51
880 887 2.968574 GCACATAGAGGGAATCAGAGGA 59.031 50.000 0.00 0.00 0.00 3.71
924 931 1.808945 GCAGCAGCAACATCAGTAGTT 59.191 47.619 0.00 0.00 41.58 2.24
930 949 3.740397 GCGGCAGCAGCAACATCA 61.740 61.111 13.20 0.00 44.61 3.07
1035 1060 1.882912 TGAGCTCACGCATCTTGTTT 58.117 45.000 13.74 0.00 39.10 2.83
1045 1070 0.179116 CCACCAGAGATGAGCTCACG 60.179 60.000 20.97 5.28 46.45 4.35
1060 1085 2.028020 CCTTGTCAGTCCTAACTCCACC 60.028 54.545 0.00 0.00 31.71 4.61
1082 1107 1.202806 TCAAGTGCACCTCCTTGAAGG 60.203 52.381 14.63 4.45 42.92 3.46
1113 1138 4.173256 CACAAAACTCGAAAACCTGCTTT 58.827 39.130 0.00 0.00 0.00 3.51
1122 1147 2.357637 CTCTTGCCCACAAAACTCGAAA 59.642 45.455 0.00 0.00 34.74 3.46
1131 1156 1.883638 GCAGACATCTCTTGCCCACAA 60.884 52.381 0.00 0.00 0.00 3.33
1144 1169 2.759114 CACCTGGGTGGCAGACAT 59.241 61.111 11.62 0.00 42.00 3.06
1184 1209 3.132289 GGACACTTGGATCCATCGACTTA 59.868 47.826 17.06 0.00 34.87 2.24
1384 1410 0.034896 GGAACTCAGCGTCCCTTGAA 59.965 55.000 0.00 0.00 0.00 2.69
1385 1411 0.832135 AGGAACTCAGCGTCCCTTGA 60.832 55.000 0.00 0.00 0.00 3.02
1450 1478 1.002624 CCCAGTTGCTAGCCCGAAA 60.003 57.895 13.29 0.00 0.00 3.46
1554 1582 0.957395 CTTCACAGCGGGCTTGTCAT 60.957 55.000 0.00 0.00 0.00 3.06
1618 1646 0.693767 CCTCCATCAGGCCTCCTCTT 60.694 60.000 0.00 0.00 34.56 2.85
1755 1783 0.254178 AGCCTCATCGTTGAAGCCAT 59.746 50.000 12.38 0.00 39.68 4.40
1791 1819 1.392589 CTTGTTGTCAAGCAGGTGGT 58.607 50.000 0.00 0.00 43.34 4.16
1894 1923 1.873903 CGCTCACAGGCAACACTACTT 60.874 52.381 0.00 0.00 41.41 2.24
2062 2118 0.040646 AGGGTGTCGTCCTACCATCA 59.959 55.000 0.00 0.00 38.74 3.07
2140 2196 7.883833 AGAGAAGTAAAGCATGCATGATCATAT 59.116 33.333 30.64 13.37 0.00 1.78
2325 2405 4.752101 CCTCTATGGTGCTGTTGCTATAAC 59.248 45.833 0.00 0.00 40.48 1.89
2392 2479 4.383602 GTTGCCGTGCGTTCGCAT 62.384 61.111 21.98 0.00 43.37 4.73
2408 2498 0.532862 CCAACCTTGCGACTGTCAGT 60.533 55.000 4.81 4.81 0.00 3.41
2441 2551 1.880027 GTTCAGCCCAAACTGACGATT 59.120 47.619 0.00 0.00 46.13 3.34
2461 2571 4.033817 GCGAAGATGATGAAGTTCTTCAGG 59.966 45.833 21.74 12.01 43.50 3.86
2551 2661 5.007626 CGTACATATTGTGCTTACCTTGCAT 59.992 40.000 0.00 0.00 42.69 3.96
2553 2663 4.785341 GCGTACATATTGTGCTTACCTTGC 60.785 45.833 0.00 0.00 30.49 4.01
2593 2703 0.726827 CGAGCGGCACATAAACATGT 59.273 50.000 1.45 0.00 34.64 3.21
2600 2710 1.966901 ATTGACCCGAGCGGCACATA 61.967 55.000 1.45 0.00 33.26 2.29
2678 2788 1.846007 TCTGCCAGTTGTTTGGTTGT 58.154 45.000 0.00 0.00 40.49 3.32
2709 2820 4.086457 ACCTGGTTGAACAAAAACAGACT 58.914 39.130 3.59 0.00 45.95 3.24


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

AutoCloner maintained by Alex Coulton.