Multiple sequence alignment - TraesCS4B01G067100

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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 TraesCS4B01G067100 chr4B 100.000 2492 0 0 1 2492 60025833 60028324 0.000000e+00 4602
1 TraesCS4B01G067100 chr4B 95.338 1566 50 9 234 1787 60073729 60075283 0.000000e+00 2466
2 TraesCS4B01G067100 chr4B 79.921 508 90 11 1972 2471 400701395 400701898 1.820000e-96 363
3 TraesCS4B01G067100 chr4B 82.796 186 16 9 1541 1726 60076800 60076969 4.290000e-33 152
4 TraesCS4B01G067100 chr4D 95.545 1661 53 10 149 1793 40842896 40844551 0.000000e+00 2638
5 TraesCS4B01G067100 chr4A 94.408 1663 62 12 149 1793 558656761 558655112 0.000000e+00 2527
6 TraesCS4B01G067100 chr3B 95.928 663 26 1 1831 2492 764815802 764815140 0.000000e+00 1074
7 TraesCS4B01G067100 chr3B 94.272 611 34 1 1031 1640 487556644 487556034 0.000000e+00 933
8 TraesCS4B01G067100 chrUn 92.433 674 44 4 1823 2492 46187833 46187163 0.000000e+00 955
9 TraesCS4B01G067100 chr2B 94.272 611 34 1 1031 1640 746165653 746165043 0.000000e+00 933
10 TraesCS4B01G067100 chr2B 84.656 189 18 4 1537 1725 202914731 202914908 7.080000e-41 178
11 TraesCS4B01G067100 chr2B 83.333 138 12 7 1569 1703 202914038 202914167 1.570000e-22 117
12 TraesCS4B01G067100 chr1D 80.871 528 93 5 1971 2492 347407766 347408291 2.310000e-110 409
13 TraesCS4B01G067100 chr6D 80.226 531 93 10 1970 2492 337846682 337847208 3.010000e-104 388
14 TraesCS4B01G067100 chr3A 79.882 507 92 8 1991 2492 523759891 523760392 1.820000e-96 363
15 TraesCS4B01G067100 chr2D 79.722 503 93 6 1974 2471 317879239 317878741 3.050000e-94 355
16 TraesCS4B01G067100 chr5B 79.487 507 95 8 1989 2490 512940305 512940807 3.940000e-93 351
17 TraesCS4B01G067100 chr7D 79.482 502 85 14 1974 2465 635668820 635669313 8.540000e-90 340
18 TraesCS4B01G067100 chr7A 85.185 189 17 4 1537 1725 22837349 22837172 1.520000e-42 183
19 TraesCS4B01G067100 chr6B 94.937 79 4 0 57 135 667888620 667888542 9.360000e-25 124
20 TraesCS4B01G067100 chr1A 94.937 79 3 1 53 131 400114132 400114209 3.370000e-24 122
21 TraesCS4B01G067100 chr1B 93.333 75 5 0 57 131 616085691 616085617 7.290000e-21 111
22 TraesCS4B01G067100 chr7B 91.139 79 7 0 57 135 333395994 333396072 9.420000e-20 108
23 TraesCS4B01G067100 chr6A 89.873 79 7 1 53 131 503978222 503978145 1.580000e-17 100


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 TraesCS4B01G067100 chr4B 60025833 60028324 2491 False 4602 4602 100.000 1 2492 1 chr4B.!!$F1 2491
1 TraesCS4B01G067100 chr4B 60073729 60076969 3240 False 1309 2466 89.067 234 1787 2 chr4B.!!$F3 1553
2 TraesCS4B01G067100 chr4B 400701395 400701898 503 False 363 363 79.921 1972 2471 1 chr4B.!!$F2 499
3 TraesCS4B01G067100 chr4D 40842896 40844551 1655 False 2638 2638 95.545 149 1793 1 chr4D.!!$F1 1644
4 TraesCS4B01G067100 chr4A 558655112 558656761 1649 True 2527 2527 94.408 149 1793 1 chr4A.!!$R1 1644
5 TraesCS4B01G067100 chr3B 764815140 764815802 662 True 1074 1074 95.928 1831 2492 1 chr3B.!!$R2 661
6 TraesCS4B01G067100 chr3B 487556034 487556644 610 True 933 933 94.272 1031 1640 1 chr3B.!!$R1 609
7 TraesCS4B01G067100 chrUn 46187163 46187833 670 True 955 955 92.433 1823 2492 1 chrUn.!!$R1 669
8 TraesCS4B01G067100 chr2B 746165043 746165653 610 True 933 933 94.272 1031 1640 1 chr2B.!!$R1 609
9 TraesCS4B01G067100 chr1D 347407766 347408291 525 False 409 409 80.871 1971 2492 1 chr1D.!!$F1 521
10 TraesCS4B01G067100 chr6D 337846682 337847208 526 False 388 388 80.226 1970 2492 1 chr6D.!!$F1 522
11 TraesCS4B01G067100 chr3A 523759891 523760392 501 False 363 363 79.882 1991 2492 1 chr3A.!!$F1 501
12 TraesCS4B01G067100 chr5B 512940305 512940807 502 False 351 351 79.487 1989 2490 1 chr5B.!!$F1 501

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
51 52 0.036765 TCAACCACGCTGTACCCATC 60.037 55.0 0.00 0.0 0.0 3.51 F
1119 1149 0.105593 AGGTCATCGAGCGCATCATT 59.894 50.0 11.47 0.0 35.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 1339 0.109873 ACGTGGTTCTCGATGTCGTC 60.110 55.000 2.04 0.0 40.8 4.20 R
2015 2961 2.202932 CACAGGGGAGGCGAATCG 60.203 66.667 0.00 0.0 0.0 3.34 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
28 29 2.358737 CCACTTGGCCTGGACGAC 60.359 66.667 3.32 0.00 0.00 4.34
29 30 2.358737 CACTTGGCCTGGACGACC 60.359 66.667 3.32 0.00 0.00 4.79
30 31 4.003788 ACTTGGCCTGGACGACCG 62.004 66.667 3.32 0.00 39.42 4.79
31 32 4.760047 CTTGGCCTGGACGACCGG 62.760 72.222 3.32 5.70 41.93 5.28
40 41 2.732094 GACGACCGGTCAACCACG 60.732 66.667 32.80 21.12 45.36 4.94
41 42 4.955774 ACGACCGGTCAACCACGC 62.956 66.667 32.80 5.45 35.14 5.34
42 43 4.657824 CGACCGGTCAACCACGCT 62.658 66.667 32.80 0.00 35.14 5.07
43 44 3.041940 GACCGGTCAACCACGCTG 61.042 66.667 29.75 0.00 35.14 5.18
44 45 3.802418 GACCGGTCAACCACGCTGT 62.802 63.158 29.75 0.00 35.14 4.40
45 46 2.340809 CCGGTCAACCACGCTGTA 59.659 61.111 0.00 0.00 35.14 2.74
46 47 2.025418 CCGGTCAACCACGCTGTAC 61.025 63.158 0.00 0.00 35.14 2.90
47 48 2.025418 CGGTCAACCACGCTGTACC 61.025 63.158 0.00 0.00 35.14 3.34
48 49 1.670083 GGTCAACCACGCTGTACCC 60.670 63.158 0.00 0.00 35.64 3.69
49 50 1.070105 GTCAACCACGCTGTACCCA 59.930 57.895 0.00 0.00 0.00 4.51
50 51 0.321298 GTCAACCACGCTGTACCCAT 60.321 55.000 0.00 0.00 0.00 4.00
51 52 0.036765 TCAACCACGCTGTACCCATC 60.037 55.000 0.00 0.00 0.00 3.51
52 53 0.321210 CAACCACGCTGTACCCATCA 60.321 55.000 0.00 0.00 0.00 3.07
53 54 0.618458 AACCACGCTGTACCCATCAT 59.382 50.000 0.00 0.00 0.00 2.45
54 55 0.107703 ACCACGCTGTACCCATCATG 60.108 55.000 0.00 0.00 0.00 3.07
55 56 0.107703 CCACGCTGTACCCATCATGT 60.108 55.000 0.00 0.00 0.00 3.21
56 57 1.138069 CCACGCTGTACCCATCATGTA 59.862 52.381 0.00 0.00 0.00 2.29
57 58 2.201732 CACGCTGTACCCATCATGTAC 58.798 52.381 0.00 0.00 39.19 2.90
58 59 1.138266 ACGCTGTACCCATCATGTACC 59.862 52.381 0.00 0.00 38.21 3.34
59 60 1.865865 GCTGTACCCATCATGTACCG 58.134 55.000 0.00 0.00 38.21 4.02
60 61 1.138266 GCTGTACCCATCATGTACCGT 59.862 52.381 0.00 0.00 38.21 4.83
61 62 2.363038 GCTGTACCCATCATGTACCGTA 59.637 50.000 0.00 0.00 38.21 4.02
62 63 3.006537 GCTGTACCCATCATGTACCGTAT 59.993 47.826 0.00 0.00 38.21 3.06
63 64 4.502604 GCTGTACCCATCATGTACCGTATT 60.503 45.833 0.00 0.00 38.21 1.89
64 65 5.607477 CTGTACCCATCATGTACCGTATTT 58.393 41.667 0.00 0.00 38.21 1.40
65 66 5.991861 TGTACCCATCATGTACCGTATTTT 58.008 37.500 0.00 0.00 38.21 1.82
66 67 6.050432 TGTACCCATCATGTACCGTATTTTC 58.950 40.000 0.00 0.00 38.21 2.29
67 68 5.105567 ACCCATCATGTACCGTATTTTCA 57.894 39.130 0.00 0.00 0.00 2.69
68 69 4.879545 ACCCATCATGTACCGTATTTTCAC 59.120 41.667 0.00 0.00 0.00 3.18
69 70 4.025229 CCCATCATGTACCGTATTTTCACG 60.025 45.833 0.00 0.00 41.59 4.35
70 71 4.569162 CCATCATGTACCGTATTTTCACGT 59.431 41.667 0.00 0.00 40.31 4.49
71 72 5.276678 CCATCATGTACCGTATTTTCACGTC 60.277 44.000 0.00 0.00 40.31 4.34
72 73 4.807443 TCATGTACCGTATTTTCACGTCA 58.193 39.130 0.00 0.00 40.31 4.35
73 74 4.622313 TCATGTACCGTATTTTCACGTCAC 59.378 41.667 0.00 0.00 40.31 3.67
74 75 3.974912 TGTACCGTATTTTCACGTCACA 58.025 40.909 0.00 0.00 40.31 3.58
75 76 4.558178 TGTACCGTATTTTCACGTCACAT 58.442 39.130 0.00 0.00 40.31 3.21
76 77 4.622313 TGTACCGTATTTTCACGTCACATC 59.378 41.667 0.00 0.00 40.31 3.06
77 78 3.655486 ACCGTATTTTCACGTCACATCA 58.345 40.909 0.00 0.00 40.31 3.07
78 79 4.250464 ACCGTATTTTCACGTCACATCAT 58.750 39.130 0.00 0.00 40.31 2.45
79 80 5.412640 ACCGTATTTTCACGTCACATCATA 58.587 37.500 0.00 0.00 40.31 2.15
80 81 6.046593 ACCGTATTTTCACGTCACATCATAT 58.953 36.000 0.00 0.00 40.31 1.78
81 82 6.537301 ACCGTATTTTCACGTCACATCATATT 59.463 34.615 0.00 0.00 40.31 1.28
82 83 7.063456 CCGTATTTTCACGTCACATCATATTC 58.937 38.462 0.00 0.00 40.31 1.75
83 84 7.254286 CCGTATTTTCACGTCACATCATATTCA 60.254 37.037 0.00 0.00 40.31 2.57
84 85 8.113675 CGTATTTTCACGTCACATCATATTCAA 58.886 33.333 0.00 0.00 37.16 2.69
85 86 9.935682 GTATTTTCACGTCACATCATATTCAAT 57.064 29.630 0.00 0.00 0.00 2.57
86 87 8.845942 ATTTTCACGTCACATCATATTCAATG 57.154 30.769 0.00 0.00 0.00 2.82
87 88 7.608308 TTTCACGTCACATCATATTCAATGA 57.392 32.000 0.00 0.00 0.00 2.57
88 89 6.588348 TCACGTCACATCATATTCAATGAC 57.412 37.500 0.00 0.00 34.46 3.06
89 90 5.523552 TCACGTCACATCATATTCAATGACC 59.476 40.000 0.00 0.00 34.32 4.02
90 91 4.507756 ACGTCACATCATATTCAATGACCG 59.492 41.667 0.00 0.00 34.32 4.79
91 92 4.507756 CGTCACATCATATTCAATGACCGT 59.492 41.667 0.00 0.00 34.32 4.83
92 93 5.689961 CGTCACATCATATTCAATGACCGTA 59.310 40.000 0.00 0.00 34.32 4.02
93 94 6.366061 CGTCACATCATATTCAATGACCGTAT 59.634 38.462 0.00 0.00 34.32 3.06
94 95 7.410835 CGTCACATCATATTCAATGACCGTATC 60.411 40.741 0.00 0.00 34.32 2.24
95 96 6.586082 TCACATCATATTCAATGACCGTATCG 59.414 38.462 0.00 0.00 0.00 2.92
96 97 6.586082 CACATCATATTCAATGACCGTATCGA 59.414 38.462 0.00 0.00 0.00 3.59
97 98 6.808704 ACATCATATTCAATGACCGTATCGAG 59.191 38.462 0.00 0.00 0.00 4.04
98 99 5.161358 TCATATTCAATGACCGTATCGAGC 58.839 41.667 0.00 0.00 0.00 5.03
99 100 1.835121 TTCAATGACCGTATCGAGCG 58.165 50.000 5.35 5.35 0.00 5.03
100 101 0.736636 TCAATGACCGTATCGAGCGT 59.263 50.000 10.52 0.69 0.00 5.07
101 102 1.941975 TCAATGACCGTATCGAGCGTA 59.058 47.619 10.52 0.00 0.00 4.42
102 103 2.551032 TCAATGACCGTATCGAGCGTAT 59.449 45.455 10.52 0.00 0.00 3.06
103 104 3.004002 TCAATGACCGTATCGAGCGTATT 59.996 43.478 10.52 6.23 0.00 1.89
104 105 2.675767 TGACCGTATCGAGCGTATTC 57.324 50.000 10.52 5.50 0.00 1.75
105 106 2.216046 TGACCGTATCGAGCGTATTCT 58.784 47.619 10.52 0.00 0.00 2.40
106 107 3.392882 TGACCGTATCGAGCGTATTCTA 58.607 45.455 10.52 0.00 0.00 2.10
107 108 3.809279 TGACCGTATCGAGCGTATTCTAA 59.191 43.478 10.52 0.00 0.00 2.10
108 109 4.273235 TGACCGTATCGAGCGTATTCTAAA 59.727 41.667 10.52 0.00 0.00 1.85
109 110 4.781071 ACCGTATCGAGCGTATTCTAAAG 58.219 43.478 10.52 0.00 0.00 1.85
110 111 3.602915 CCGTATCGAGCGTATTCTAAAGC 59.397 47.826 10.52 0.00 0.00 3.51
111 112 4.465016 CGTATCGAGCGTATTCTAAAGCT 58.535 43.478 4.30 0.00 43.33 3.74
117 118 4.720649 AGCGTATTCTAAAGCTCAGTGA 57.279 40.909 0.00 0.00 34.48 3.41
118 119 4.425520 AGCGTATTCTAAAGCTCAGTGAC 58.574 43.478 0.00 0.00 34.48 3.67
119 120 3.552294 GCGTATTCTAAAGCTCAGTGACC 59.448 47.826 0.00 0.00 0.00 4.02
120 121 3.791887 CGTATTCTAAAGCTCAGTGACCG 59.208 47.826 0.00 0.00 0.00 4.79
121 122 3.963428 ATTCTAAAGCTCAGTGACCGT 57.037 42.857 0.00 0.00 0.00 4.83
122 123 5.448225 CGTATTCTAAAGCTCAGTGACCGTA 60.448 44.000 0.00 0.00 0.00 4.02
123 124 5.599999 ATTCTAAAGCTCAGTGACCGTAT 57.400 39.130 0.00 0.00 0.00 3.06
124 125 4.634184 TCTAAAGCTCAGTGACCGTATC 57.366 45.455 0.00 0.00 0.00 2.24
125 126 2.279582 AAAGCTCAGTGACCGTATCG 57.720 50.000 0.00 0.00 0.00 2.92
126 127 1.174783 AAGCTCAGTGACCGTATCGT 58.825 50.000 0.00 0.00 0.00 3.73
127 128 0.452184 AGCTCAGTGACCGTATCGTG 59.548 55.000 0.00 0.00 0.00 4.35
128 129 1.140407 GCTCAGTGACCGTATCGTGC 61.140 60.000 0.00 0.00 0.00 5.34
129 130 0.452184 CTCAGTGACCGTATCGTGCT 59.548 55.000 0.00 0.00 0.00 4.40
130 131 0.885879 TCAGTGACCGTATCGTGCTT 59.114 50.000 0.00 0.00 0.00 3.91
131 132 0.992072 CAGTGACCGTATCGTGCTTG 59.008 55.000 0.00 0.00 0.00 4.01
132 133 0.885879 AGTGACCGTATCGTGCTTGA 59.114 50.000 0.00 0.00 0.00 3.02
133 134 1.135373 AGTGACCGTATCGTGCTTGAG 60.135 52.381 0.00 0.00 0.00 3.02
134 135 0.885879 TGACCGTATCGTGCTTGAGT 59.114 50.000 0.00 0.00 0.00 3.41
135 136 1.269166 GACCGTATCGTGCTTGAGTG 58.731 55.000 0.00 0.00 0.00 3.51
136 137 0.601558 ACCGTATCGTGCTTGAGTGT 59.398 50.000 0.00 0.00 0.00 3.55
137 138 1.814394 ACCGTATCGTGCTTGAGTGTA 59.186 47.619 0.00 0.00 0.00 2.90
138 139 2.426024 ACCGTATCGTGCTTGAGTGTAT 59.574 45.455 0.00 0.00 0.00 2.29
139 140 3.119245 ACCGTATCGTGCTTGAGTGTATT 60.119 43.478 0.00 0.00 0.00 1.89
140 141 3.863424 CCGTATCGTGCTTGAGTGTATTT 59.137 43.478 0.00 0.00 0.00 1.40
141 142 5.038683 CCGTATCGTGCTTGAGTGTATTTA 58.961 41.667 0.00 0.00 0.00 1.40
142 143 5.690409 CCGTATCGTGCTTGAGTGTATTTAT 59.310 40.000 0.00 0.00 0.00 1.40
143 144 6.129168 CCGTATCGTGCTTGAGTGTATTTATC 60.129 42.308 0.00 0.00 0.00 1.75
144 145 6.637254 CGTATCGTGCTTGAGTGTATTTATCT 59.363 38.462 0.00 0.00 0.00 1.98
145 146 7.149112 CGTATCGTGCTTGAGTGTATTTATCTC 60.149 40.741 0.00 0.00 0.00 2.75
146 147 5.348986 TCGTGCTTGAGTGTATTTATCTCC 58.651 41.667 0.00 0.00 0.00 3.71
147 148 5.105513 TCGTGCTTGAGTGTATTTATCTCCA 60.106 40.000 0.00 0.00 0.00 3.86
212 214 1.354337 CGACCCGTTGCACATCTCTG 61.354 60.000 0.00 0.00 0.00 3.35
317 319 3.461773 CGGGATGCCGTCTCCACT 61.462 66.667 18.74 0.00 34.24 4.00
319 321 2.060980 GGGATGCCGTCTCCACTCT 61.061 63.158 0.00 0.00 34.24 3.24
418 427 1.467190 TTCTCCCCACACCCCCAAT 60.467 57.895 0.00 0.00 0.00 3.16
537 551 2.690452 CGAGAGGGGGAGGAGGAA 59.310 66.667 0.00 0.00 0.00 3.36
586 604 2.447443 AGTCCTTCATGAGCTACGTCA 58.553 47.619 0.00 0.00 0.00 4.35
650 680 2.680352 GACCGAGCTCACCCAGGA 60.680 66.667 15.40 0.00 0.00 3.86
702 732 1.136329 AGGGCTTCTTCAAGGAGGCA 61.136 55.000 20.61 0.00 39.59 4.75
1080 1110 1.801332 CCGCTACTACACGCTCACT 59.199 57.895 0.00 0.00 0.00 3.41
1119 1149 0.105593 AGGTCATCGAGCGCATCATT 59.894 50.000 11.47 0.00 35.00 2.57
1309 1339 2.127869 TCGCAGGGGGAGAAGATCG 61.128 63.158 0.00 0.00 0.00 3.69
1453 1483 0.757512 GCTGCTCCTCATCCTCATCA 59.242 55.000 0.00 0.00 0.00 3.07
1459 1489 3.261137 GCTCCTCATCCTCATCATCATCA 59.739 47.826 0.00 0.00 0.00 3.07
1468 1498 3.265995 CCTCATCATCATCATCCCCATCA 59.734 47.826 0.00 0.00 0.00 3.07
1602 1635 2.859165 TTCGTTGATTTCTGCTCCCT 57.141 45.000 0.00 0.00 0.00 4.20
1615 1649 1.063942 TGCTCCCTCCGAATGTCTCTA 60.064 52.381 0.00 0.00 0.00 2.43
1618 1652 1.964223 TCCCTCCGAATGTCTCTATGC 59.036 52.381 0.00 0.00 0.00 3.14
1696 1731 4.741342 CAACCCTGAAAAATCTGCTGATC 58.259 43.478 6.55 0.00 31.51 2.92
1809 1879 3.523564 ACCCTGTACACAAGATAGGCAAT 59.476 43.478 0.00 0.00 0.00 3.56
1810 1880 4.719773 ACCCTGTACACAAGATAGGCAATA 59.280 41.667 0.00 0.00 0.00 1.90
1842 1988 7.039363 GGCTTCCTATCATCACTAGTAGAATGT 60.039 40.741 3.59 2.18 0.00 2.71
1853 1999 1.000506 AGTAGAATGTCCGTGCGTTGT 59.999 47.619 0.00 0.00 0.00 3.32
2125 3076 4.797743 AGGGATTTCTATTCCTTGAAGGC 58.202 43.478 6.30 0.00 36.20 4.35
2227 3179 2.695359 GTAGTCAATGGAGTTTCGGCA 58.305 47.619 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.358737 GTCGTCCAGGCCAAGTGG 60.359 66.667 5.01 3.84 36.28 4.00
12 13 2.358737 GGTCGTCCAGGCCAAGTG 60.359 66.667 5.01 0.00 46.14 3.16
18 19 3.998672 TTGACCGGTCGTCCAGGC 61.999 66.667 28.70 4.29 41.18 4.85
19 20 2.048503 GTTGACCGGTCGTCCAGG 60.049 66.667 28.70 3.96 41.18 4.45
20 21 2.048503 GGTTGACCGGTCGTCCAG 60.049 66.667 30.35 0.00 41.18 3.86
21 22 2.838693 TGGTTGACCGGTCGTCCA 60.839 61.111 32.61 32.61 41.18 4.02
22 23 2.356673 GTGGTTGACCGGTCGTCC 60.357 66.667 29.33 29.33 41.18 4.79
23 24 2.732094 CGTGGTTGACCGGTCGTC 60.732 66.667 28.70 22.26 42.33 4.20
24 25 4.955774 GCGTGGTTGACCGGTCGT 62.956 66.667 28.70 0.00 39.43 4.34
25 26 4.657824 AGCGTGGTTGACCGGTCG 62.658 66.667 28.70 17.72 39.43 4.79
26 27 2.424705 TACAGCGTGGTTGACCGGTC 62.425 60.000 28.17 28.17 39.43 4.79
27 28 2.500714 TACAGCGTGGTTGACCGGT 61.501 57.895 6.92 6.92 39.43 5.28
28 29 2.025418 GTACAGCGTGGTTGACCGG 61.025 63.158 0.00 0.00 39.43 5.28
29 30 2.025418 GGTACAGCGTGGTTGACCG 61.025 63.158 0.00 0.00 39.43 4.79
30 31 1.670083 GGGTACAGCGTGGTTGACC 60.670 63.158 0.00 0.00 0.00 4.02
31 32 0.321298 ATGGGTACAGCGTGGTTGAC 60.321 55.000 0.00 0.00 0.00 3.18
32 33 0.036765 GATGGGTACAGCGTGGTTGA 60.037 55.000 0.00 0.00 0.00 3.18
33 34 0.321210 TGATGGGTACAGCGTGGTTG 60.321 55.000 0.00 0.00 35.27 3.77
34 35 0.618458 ATGATGGGTACAGCGTGGTT 59.382 50.000 0.00 0.00 35.27 3.67
35 36 0.107703 CATGATGGGTACAGCGTGGT 60.108 55.000 0.00 0.00 44.21 4.16
36 37 2.694065 CATGATGGGTACAGCGTGG 58.306 57.895 0.00 0.00 44.21 4.94
38 39 1.138266 GGTACATGATGGGTACAGCGT 59.862 52.381 0.00 0.00 42.21 5.07
39 40 1.865865 GGTACATGATGGGTACAGCG 58.134 55.000 0.00 0.00 42.21 5.18
40 41 1.138266 ACGGTACATGATGGGTACAGC 59.862 52.381 0.00 0.00 42.21 4.40
41 42 4.866508 ATACGGTACATGATGGGTACAG 57.133 45.455 0.00 0.00 42.21 2.74
42 43 5.617528 AAATACGGTACATGATGGGTACA 57.382 39.130 0.00 0.00 42.21 2.90
43 44 6.018507 GTGAAAATACGGTACATGATGGGTAC 60.019 42.308 0.00 0.00 40.24 3.34
44 45 6.050432 GTGAAAATACGGTACATGATGGGTA 58.950 40.000 0.00 0.00 0.00 3.69
45 46 4.879545 GTGAAAATACGGTACATGATGGGT 59.120 41.667 0.00 0.00 0.00 4.51
46 47 4.025229 CGTGAAAATACGGTACATGATGGG 60.025 45.833 0.00 0.00 40.22 4.00
47 48 5.078153 CGTGAAAATACGGTACATGATGG 57.922 43.478 0.00 0.00 40.22 3.51
50 51 8.779795 GATGTGACGTGAAAATACGGTACATGA 61.780 40.741 19.46 4.66 45.57 3.07
51 52 6.723083 GATGTGACGTGAAAATACGGTACATG 60.723 42.308 19.46 0.00 45.57 3.21
52 53 5.290158 GATGTGACGTGAAAATACGGTACAT 59.710 40.000 16.55 16.55 46.82 2.29
59 60 9.935682 ATTGAATATGATGTGACGTGAAAATAC 57.064 29.630 0.00 0.00 0.00 1.89
60 61 9.934190 CATTGAATATGATGTGACGTGAAAATA 57.066 29.630 0.00 0.00 0.00 1.40
61 62 8.676401 TCATTGAATATGATGTGACGTGAAAAT 58.324 29.630 0.00 0.00 0.00 1.82
62 63 7.962373 GTCATTGAATATGATGTGACGTGAAAA 59.038 33.333 0.00 0.00 0.00 2.29
63 64 7.413988 GGTCATTGAATATGATGTGACGTGAAA 60.414 37.037 0.00 0.00 37.44 2.69
64 65 6.037062 GGTCATTGAATATGATGTGACGTGAA 59.963 38.462 0.00 0.00 37.44 3.18
65 66 5.523552 GGTCATTGAATATGATGTGACGTGA 59.476 40.000 0.00 0.00 37.44 4.35
66 67 5.556947 CGGTCATTGAATATGATGTGACGTG 60.557 44.000 0.00 0.00 37.44 4.49
67 68 4.507756 CGGTCATTGAATATGATGTGACGT 59.492 41.667 0.00 0.00 37.44 4.34
68 69 4.507756 ACGGTCATTGAATATGATGTGACG 59.492 41.667 0.00 0.00 37.44 4.35
69 70 5.991328 ACGGTCATTGAATATGATGTGAC 57.009 39.130 0.00 0.00 36.22 3.67
70 71 6.586082 CGATACGGTCATTGAATATGATGTGA 59.414 38.462 0.00 0.00 0.00 3.58
71 72 6.586082 TCGATACGGTCATTGAATATGATGTG 59.414 38.462 0.00 0.00 0.00 3.21
72 73 6.687604 TCGATACGGTCATTGAATATGATGT 58.312 36.000 0.00 0.00 0.00 3.06
73 74 6.237675 GCTCGATACGGTCATTGAATATGATG 60.238 42.308 0.00 0.00 0.00 3.07
74 75 5.807520 GCTCGATACGGTCATTGAATATGAT 59.192 40.000 0.00 0.00 0.00 2.45
75 76 5.161358 GCTCGATACGGTCATTGAATATGA 58.839 41.667 0.00 0.00 0.00 2.15
76 77 4.030641 CGCTCGATACGGTCATTGAATATG 59.969 45.833 0.31 0.00 0.00 1.78
77 78 4.166523 CGCTCGATACGGTCATTGAATAT 58.833 43.478 0.31 0.00 0.00 1.28
78 79 3.004002 ACGCTCGATACGGTCATTGAATA 59.996 43.478 11.97 0.00 34.00 1.75
79 80 2.223735 ACGCTCGATACGGTCATTGAAT 60.224 45.455 11.97 0.00 34.00 2.57
80 81 1.133598 ACGCTCGATACGGTCATTGAA 59.866 47.619 11.97 0.00 34.00 2.69
81 82 0.736636 ACGCTCGATACGGTCATTGA 59.263 50.000 11.97 0.00 34.00 2.57
82 83 2.394545 TACGCTCGATACGGTCATTG 57.605 50.000 11.97 0.00 34.00 2.82
83 84 3.252701 AGAATACGCTCGATACGGTCATT 59.747 43.478 11.97 8.14 34.00 2.57
84 85 2.812591 AGAATACGCTCGATACGGTCAT 59.187 45.455 11.97 0.98 34.00 3.06
85 86 2.216046 AGAATACGCTCGATACGGTCA 58.784 47.619 11.97 0.00 34.00 4.02
86 87 2.965477 AGAATACGCTCGATACGGTC 57.035 50.000 11.97 6.68 34.00 4.79
87 88 4.781071 CTTTAGAATACGCTCGATACGGT 58.219 43.478 11.97 0.00 34.00 4.83
88 89 3.602915 GCTTTAGAATACGCTCGATACGG 59.397 47.826 11.97 0.00 34.00 4.02
89 90 4.465016 AGCTTTAGAATACGCTCGATACG 58.535 43.478 6.45 6.45 0.00 3.06
90 91 5.450171 TGAGCTTTAGAATACGCTCGATAC 58.550 41.667 0.00 0.00 43.45 2.24
91 92 5.238868 ACTGAGCTTTAGAATACGCTCGATA 59.761 40.000 6.00 0.00 43.45 2.92
92 93 4.036971 ACTGAGCTTTAGAATACGCTCGAT 59.963 41.667 6.00 0.00 43.45 3.59
93 94 3.377485 ACTGAGCTTTAGAATACGCTCGA 59.623 43.478 6.00 0.00 43.45 4.04
94 95 3.483922 CACTGAGCTTTAGAATACGCTCG 59.516 47.826 6.00 0.00 43.45 5.03
95 96 4.501198 GTCACTGAGCTTTAGAATACGCTC 59.499 45.833 6.00 0.00 41.88 5.03
96 97 4.425520 GTCACTGAGCTTTAGAATACGCT 58.574 43.478 6.00 0.00 31.16 5.07
97 98 3.552294 GGTCACTGAGCTTTAGAATACGC 59.448 47.826 6.00 0.00 0.00 4.42
98 99 3.791887 CGGTCACTGAGCTTTAGAATACG 59.208 47.826 6.67 0.00 0.00 3.06
99 100 4.745649 ACGGTCACTGAGCTTTAGAATAC 58.254 43.478 6.67 1.85 0.00 1.89
100 101 6.512903 CGATACGGTCACTGAGCTTTAGAATA 60.513 42.308 6.67 0.00 0.00 1.75
101 102 3.963428 ACGGTCACTGAGCTTTAGAAT 57.037 42.857 6.67 0.00 0.00 2.40
102 103 4.438336 CGATACGGTCACTGAGCTTTAGAA 60.438 45.833 6.67 0.00 0.00 2.10
103 104 3.064958 CGATACGGTCACTGAGCTTTAGA 59.935 47.826 6.67 0.00 0.00 2.10
104 105 3.181499 ACGATACGGTCACTGAGCTTTAG 60.181 47.826 6.67 0.00 0.00 1.85
105 106 2.751259 ACGATACGGTCACTGAGCTTTA 59.249 45.455 6.67 0.00 0.00 1.85
106 107 1.544691 ACGATACGGTCACTGAGCTTT 59.455 47.619 6.67 0.00 0.00 3.51
107 108 1.135373 CACGATACGGTCACTGAGCTT 60.135 52.381 6.67 0.00 0.00 3.74
108 109 0.452184 CACGATACGGTCACTGAGCT 59.548 55.000 6.67 0.00 0.00 4.09
109 110 1.140407 GCACGATACGGTCACTGAGC 61.140 60.000 0.00 0.00 0.00 4.26
110 111 0.452184 AGCACGATACGGTCACTGAG 59.548 55.000 0.00 0.00 0.00 3.35
111 112 0.885879 AAGCACGATACGGTCACTGA 59.114 50.000 0.00 0.00 0.00 3.41
112 113 0.992072 CAAGCACGATACGGTCACTG 59.008 55.000 0.00 0.00 0.00 3.66
113 114 0.885879 TCAAGCACGATACGGTCACT 59.114 50.000 0.00 0.00 0.00 3.41
114 115 1.269166 CTCAAGCACGATACGGTCAC 58.731 55.000 0.00 0.00 0.00 3.67
115 116 0.885879 ACTCAAGCACGATACGGTCA 59.114 50.000 0.00 0.00 0.00 4.02
116 117 1.269166 CACTCAAGCACGATACGGTC 58.731 55.000 0.00 0.00 0.00 4.79
117 118 0.601558 ACACTCAAGCACGATACGGT 59.398 50.000 0.00 0.00 0.00 4.83
118 119 2.554806 TACACTCAAGCACGATACGG 57.445 50.000 0.00 0.00 0.00 4.02
119 120 6.637254 AGATAAATACACTCAAGCACGATACG 59.363 38.462 0.00 0.00 0.00 3.06
120 121 7.115095 GGAGATAAATACACTCAAGCACGATAC 59.885 40.741 0.00 0.00 33.00 2.24
121 122 7.145985 GGAGATAAATACACTCAAGCACGATA 58.854 38.462 0.00 0.00 33.00 2.92
122 123 5.986135 GGAGATAAATACACTCAAGCACGAT 59.014 40.000 0.00 0.00 33.00 3.73
123 124 5.105513 TGGAGATAAATACACTCAAGCACGA 60.106 40.000 0.00 0.00 33.00 4.35
124 125 5.005779 GTGGAGATAAATACACTCAAGCACG 59.994 44.000 0.00 0.00 33.00 5.34
125 126 5.874810 TGTGGAGATAAATACACTCAAGCAC 59.125 40.000 0.00 0.00 35.02 4.40
126 127 6.048732 TGTGGAGATAAATACACTCAAGCA 57.951 37.500 0.00 0.00 35.02 3.91
127 128 6.341316 TCTGTGGAGATAAATACACTCAAGC 58.659 40.000 0.00 0.00 35.02 4.01
128 129 8.954950 ATTCTGTGGAGATAAATACACTCAAG 57.045 34.615 0.00 0.00 35.02 3.02
129 130 7.987458 GGATTCTGTGGAGATAAATACACTCAA 59.013 37.037 0.00 0.00 35.02 3.02
130 131 7.500992 GGATTCTGTGGAGATAAATACACTCA 58.499 38.462 0.00 0.00 35.02 3.41
131 132 6.642950 CGGATTCTGTGGAGATAAATACACTC 59.357 42.308 0.00 0.00 35.02 3.51
132 133 6.323996 TCGGATTCTGTGGAGATAAATACACT 59.676 38.462 0.00 0.00 35.02 3.55
133 134 6.513180 TCGGATTCTGTGGAGATAAATACAC 58.487 40.000 0.00 0.00 0.00 2.90
134 135 6.724893 TCGGATTCTGTGGAGATAAATACA 57.275 37.500 0.00 0.00 0.00 2.29
135 136 6.091441 GCATCGGATTCTGTGGAGATAAATAC 59.909 42.308 0.00 0.00 0.00 1.89
136 137 6.014242 AGCATCGGATTCTGTGGAGATAAATA 60.014 38.462 0.00 0.00 0.00 1.40
137 138 4.999950 GCATCGGATTCTGTGGAGATAAAT 59.000 41.667 0.00 0.00 0.00 1.40
138 139 4.101585 AGCATCGGATTCTGTGGAGATAAA 59.898 41.667 0.00 0.00 0.00 1.40
139 140 3.643320 AGCATCGGATTCTGTGGAGATAA 59.357 43.478 0.00 0.00 0.00 1.75
140 141 3.234353 AGCATCGGATTCTGTGGAGATA 58.766 45.455 0.00 0.00 0.00 1.98
141 142 2.036992 GAGCATCGGATTCTGTGGAGAT 59.963 50.000 0.00 0.00 0.00 2.75
142 143 1.410517 GAGCATCGGATTCTGTGGAGA 59.589 52.381 0.00 0.00 0.00 3.71
143 144 1.137675 TGAGCATCGGATTCTGTGGAG 59.862 52.381 0.00 0.00 38.61 3.86
144 145 1.194218 TGAGCATCGGATTCTGTGGA 58.806 50.000 0.00 0.00 38.61 4.02
145 146 2.028420 TTGAGCATCGGATTCTGTGG 57.972 50.000 0.00 0.00 38.61 4.17
146 147 3.730061 GCTTTTGAGCATCGGATTCTGTG 60.730 47.826 0.00 0.00 38.61 3.66
147 148 2.421424 GCTTTTGAGCATCGGATTCTGT 59.579 45.455 0.00 0.00 38.61 3.41
212 214 1.503542 CAACGGAAGCTGTGATGGC 59.496 57.895 0.00 0.00 0.00 4.40
317 319 1.480954 GAATAGAGCCGTTGGTGGAGA 59.519 52.381 0.00 0.00 0.00 3.71
319 321 0.539986 GGAATAGAGCCGTTGGTGGA 59.460 55.000 0.00 0.00 0.00 4.02
369 374 3.503412 GGGAAGGGAGGGTTTTAATGGTT 60.503 47.826 0.00 0.00 0.00 3.67
418 427 1.318380 GGGGGAGAGAGATGGGGAA 59.682 63.158 0.00 0.00 0.00 3.97
528 542 2.436824 GCGCCAGTTTCCTCCTCC 60.437 66.667 0.00 0.00 0.00 4.30
537 551 2.031919 TCGTTCATGGCGCCAGTT 59.968 55.556 35.36 17.12 0.00 3.16
540 554 3.950794 GAGGTCGTTCATGGCGCCA 62.951 63.158 34.80 34.80 0.00 5.69
586 604 2.034221 GGCCGCCTTCTTCAGGTT 59.966 61.111 0.71 0.00 46.07 3.50
1309 1339 0.109873 ACGTGGTTCTCGATGTCGTC 60.110 55.000 2.04 0.00 40.80 4.20
1453 1483 1.426598 GGTGGTGATGGGGATGATGAT 59.573 52.381 0.00 0.00 0.00 2.45
1459 1489 2.693871 GGCTGGTGGTGATGGGGAT 61.694 63.158 0.00 0.00 0.00 3.85
1468 1498 1.462238 ACCTCTTGAGGCTGGTGGT 60.462 57.895 15.93 0.00 0.00 4.16
1602 1635 1.337071 GACGGCATAGAGACATTCGGA 59.663 52.381 0.00 0.00 0.00 4.55
1615 1649 1.486310 TCAGCTAAATCCTGACGGCAT 59.514 47.619 0.00 0.00 34.59 4.40
1618 1652 3.459232 TCATCAGCTAAATCCTGACGG 57.541 47.619 0.00 0.00 41.68 4.79
1696 1731 3.714391 TCTCATCTCATGCACAGAATCG 58.286 45.455 1.38 0.00 0.00 3.34
1787 1822 2.546899 TGCCTATCTTGTGTACAGGGT 58.453 47.619 0.00 0.00 0.00 4.34
1793 1828 6.039270 GCCACAAATATTGCCTATCTTGTGTA 59.961 38.462 13.62 0.00 37.26 2.90
1809 1879 6.252599 AGTGATGATAGGAAGCCACAAATA 57.747 37.500 0.00 0.00 0.00 1.40
1810 1880 5.121380 AGTGATGATAGGAAGCCACAAAT 57.879 39.130 0.00 0.00 0.00 2.32
1820 1898 6.655425 CGGACATTCTACTAGTGATGATAGGA 59.345 42.308 17.38 0.00 0.00 2.94
1853 1999 4.804108 CAAAATTACTGAAATGCCCGTGA 58.196 39.130 0.00 0.00 0.00 4.35
2015 2961 2.202932 CACAGGGGAGGCGAATCG 60.203 66.667 0.00 0.00 0.00 3.34
2125 3076 4.457496 ATCCGCCTGAGCACCACG 62.457 66.667 0.00 0.00 39.83 4.94
2227 3179 6.128172 CCGCAAAAGAGACAACAAGAATCTAT 60.128 38.462 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.