Multiple sequence alignment - TraesCS4A01G037600

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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 TraesCS4A01G037600 chr4A 100.000 2384 0 0 1 2384 29789459 29791842 0.000000e+00 4403.0
1 TraesCS4A01G037600 chr4A 99.105 2235 20 0 150 2384 617053471 617055705 0.000000e+00 4017.0
2 TraesCS4A01G037600 chr4A 94.079 152 8 1 1 151 29784259 29784410 1.840000e-56 230.0
3 TraesCS4A01G037600 chr4B 87.726 554 37 17 1358 1882 525419927 525419376 3.370000e-173 617.0
4 TraesCS4A01G037600 chr4B 89.357 498 38 7 1896 2384 525419225 525418734 1.570000e-171 612.0
5 TraesCS4A01G037600 chr4B 85.086 523 47 16 595 1110 525420857 525420359 2.730000e-139 505.0
6 TraesCS4A01G037600 chr4B 85.404 507 43 16 595 1094 525284249 525283767 4.580000e-137 497.0
7 TraesCS4A01G037600 chr4B 91.781 219 15 3 1358 1574 525282051 525281834 3.850000e-78 302.0
8 TraesCS4A01G037600 chr4B 82.609 92 16 0 2290 2381 442201617 442201708 5.460000e-12 82.4
9 TraesCS4A01G037600 chr1D 89.178 499 37 9 1896 2384 411428477 411427986 7.290000e-170 606.0
10 TraesCS4A01G037600 chr1D 87.161 553 41 16 1358 1882 411429174 411428624 3.390000e-168 601.0
11 TraesCS4A01G037600 chr1D 85.660 523 44 16 595 1110 411430104 411429606 2.720000e-144 521.0
12 TraesCS4A01G037600 chr1D 85.085 295 27 12 328 607 411430412 411430120 3.880000e-73 285.0
13 TraesCS4A01G037600 chr1D 92.357 157 11 1 1 157 20727887 20727732 3.080000e-54 222.0
14 TraesCS4A01G037600 chr1D 93.793 145 7 2 1 144 20722746 20722603 1.430000e-52 217.0
15 TraesCS4A01G037600 chr7D 80.223 627 106 15 1770 2384 87439138 87438518 2.790000e-124 455.0
16 TraesCS4A01G037600 chr7D 83.459 133 20 2 1598 1730 87439354 87439224 3.220000e-24 122.0
17 TraesCS4A01G037600 chr6A 95.333 150 5 2 1 149 435548041 435548189 1.100000e-58 237.0
18 TraesCS4A01G037600 chr6A 94.483 145 7 1 1 144 81102857 81102713 3.080000e-54 222.0
19 TraesCS4A01G037600 chr6A 92.810 153 11 0 2 154 532800244 532800092 3.080000e-54 222.0
20 TraesCS4A01G037600 chr6A 92.763 152 10 1 1 151 435541629 435541780 3.990000e-53 219.0
21 TraesCS4A01G037600 chr7A 94.040 151 9 0 1 151 33869751 33869901 1.840000e-56 230.0
22 TraesCS4A01G037600 chr7A 81.818 187 29 3 1588 1774 88964420 88964239 4.100000e-33 152.0
23 TraesCS4A01G037600 chr5D 94.483 145 7 1 1 144 423009590 423009446 3.080000e-54 222.0
24 TraesCS4A01G037600 chr3A 74.163 627 100 37 340 944 661987424 661986838 1.120000e-48 204.0
25 TraesCS4A01G037600 chr2A 74.121 626 102 38 340 944 547805781 547805195 1.120000e-48 204.0
26 TraesCS4A01G037600 chr7B 82.558 172 22 5 1603 1774 36440415 36440252 6.870000e-31 145.0


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 TraesCS4A01G037600 chr4A 29789459 29791842 2383 False 4403.00 4403 100.000000 1 2384 1 chr4A.!!$F2 2383
1 TraesCS4A01G037600 chr4A 617053471 617055705 2234 False 4017.00 4017 99.105000 150 2384 1 chr4A.!!$F3 2234
2 TraesCS4A01G037600 chr4B 525418734 525420857 2123 True 578.00 617 87.389667 595 2384 3 chr4B.!!$R2 1789
3 TraesCS4A01G037600 chr4B 525281834 525284249 2415 True 399.50 497 88.592500 595 1574 2 chr4B.!!$R1 979
4 TraesCS4A01G037600 chr1D 411427986 411430412 2426 True 503.25 606 86.771000 328 2384 4 chr1D.!!$R3 2056
5 TraesCS4A01G037600 chr7D 87438518 87439354 836 True 288.50 455 81.841000 1598 2384 2 chr7D.!!$R1 786
6 TraesCS4A01G037600 chr3A 661986838 661987424 586 True 204.00 204 74.163000 340 944 1 chr3A.!!$R1 604
7 TraesCS4A01G037600 chr2A 547805195 547805781 586 True 204.00 204 74.121000 340 944 1 chr2A.!!$R1 604

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
120 121 0.036306 ACGGAAAAGCGTGGAGGAAT 59.964 50.0 0.0 0.0 0.0 3.01 F
127 128 0.263765 AGCGTGGAGGAATAGGGGTA 59.736 55.0 0.0 0.0 0.0 3.69 F
128 129 0.680061 GCGTGGAGGAATAGGGGTAG 59.320 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 2857 0.321564 CGTCAAAGGCCACCAGATGA 60.322 55.000 5.01 0.00 0.0 2.92 R
1277 2937 2.188994 GATGAGCGGGCTCTTGCT 59.811 61.111 20.27 4.18 45.9 3.91 R
2342 4241 2.780065 TGACTTGCTTGTTGATGTGC 57.220 45.000 0.00 0.00 0.0 4.57 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
34 35 7.216973 CTTATAACTGTATAAGAGGCGGACT 57.783 40.000 7.45 0.00 46.74 3.85
35 36 5.708877 ATAACTGTATAAGAGGCGGACTC 57.291 43.478 1.52 1.52 46.98 3.36
43 44 3.625745 GAGGCGGACTCTTTGGAAA 57.374 52.632 2.86 0.00 43.14 3.13
44 45 1.157585 GAGGCGGACTCTTTGGAAAC 58.842 55.000 2.86 0.00 43.14 2.78
45 46 0.602905 AGGCGGACTCTTTGGAAACG 60.603 55.000 0.00 0.00 0.00 3.60
46 47 1.206831 GCGGACTCTTTGGAAACGC 59.793 57.895 0.00 0.00 38.70 4.84
47 48 1.503818 GCGGACTCTTTGGAAACGCA 61.504 55.000 0.00 0.00 44.32 5.24
48 49 0.512952 CGGACTCTTTGGAAACGCAG 59.487 55.000 0.00 0.00 0.00 5.18
50 51 2.762745 GGACTCTTTGGAAACGCAGTA 58.237 47.619 0.00 0.00 45.00 2.74
51 52 3.335579 GGACTCTTTGGAAACGCAGTAT 58.664 45.455 0.00 0.00 45.00 2.12
52 53 4.501071 GGACTCTTTGGAAACGCAGTATA 58.499 43.478 0.00 0.00 45.00 1.47
53 54 4.933400 GGACTCTTTGGAAACGCAGTATAA 59.067 41.667 0.00 0.00 45.00 0.98
54 55 5.063564 GGACTCTTTGGAAACGCAGTATAAG 59.936 44.000 0.00 0.00 45.00 1.73
55 56 5.790593 ACTCTTTGGAAACGCAGTATAAGA 58.209 37.500 0.00 0.00 45.00 2.10
56 57 6.228258 ACTCTTTGGAAACGCAGTATAAGAA 58.772 36.000 0.00 0.00 45.00 2.52
57 58 6.369065 ACTCTTTGGAAACGCAGTATAAGAAG 59.631 38.462 0.00 0.00 45.00 2.85
58 59 5.642063 TCTTTGGAAACGCAGTATAAGAAGG 59.358 40.000 0.00 0.00 45.00 3.46
59 60 4.546829 TGGAAACGCAGTATAAGAAGGT 57.453 40.909 0.00 0.00 45.00 3.50
60 61 4.501071 TGGAAACGCAGTATAAGAAGGTC 58.499 43.478 0.00 0.00 45.00 3.85
61 62 3.869832 GGAAACGCAGTATAAGAAGGTCC 59.130 47.826 0.00 0.00 45.00 4.46
62 63 3.538634 AACGCAGTATAAGAAGGTCCC 57.461 47.619 0.00 0.00 45.00 4.46
63 64 2.748388 ACGCAGTATAAGAAGGTCCCT 58.252 47.619 0.00 0.00 41.94 4.20
64 65 3.907221 ACGCAGTATAAGAAGGTCCCTA 58.093 45.455 0.00 0.00 41.94 3.53
65 66 3.635836 ACGCAGTATAAGAAGGTCCCTAC 59.364 47.826 0.00 0.00 41.94 3.18
66 67 5.473266 ACGCAGTATAAGAAGGTCCCTACC 61.473 50.000 0.00 0.00 43.57 3.18
74 75 2.122503 GGTCCCTACCCCCTAGCC 60.123 72.222 0.00 0.00 40.21 3.93
75 76 2.723794 GGTCCCTACCCCCTAGCCT 61.724 68.421 0.00 0.00 40.21 4.58
76 77 1.152290 GTCCCTACCCCCTAGCCTC 60.152 68.421 0.00 0.00 0.00 4.70
77 78 2.203655 CCCTACCCCCTAGCCTCG 60.204 72.222 0.00 0.00 0.00 4.63
78 79 2.203655 CCTACCCCCTAGCCTCGG 60.204 72.222 0.00 0.00 0.00 4.63
79 80 2.775741 CCTACCCCCTAGCCTCGGA 61.776 68.421 0.00 0.00 0.00 4.55
80 81 1.228613 CTACCCCCTAGCCTCGGAG 60.229 68.421 0.00 0.00 0.00 4.63
81 82 1.698840 TACCCCCTAGCCTCGGAGA 60.699 63.158 6.58 0.00 0.00 3.71
82 83 1.072505 TACCCCCTAGCCTCGGAGAT 61.073 60.000 6.58 0.00 33.89 2.75
83 84 1.910772 CCCCCTAGCCTCGGAGATG 60.911 68.421 6.58 0.00 33.89 2.90
89 90 3.635204 GCCTCGGAGATGCGATTG 58.365 61.111 6.58 0.00 38.57 2.67
90 91 1.227380 GCCTCGGAGATGCGATTGT 60.227 57.895 6.58 0.00 38.57 2.71
91 92 1.493950 GCCTCGGAGATGCGATTGTG 61.494 60.000 6.58 0.00 38.57 3.33
92 93 0.103026 CCTCGGAGATGCGATTGTGA 59.897 55.000 6.58 0.00 33.89 3.58
93 94 1.485397 CTCGGAGATGCGATTGTGAG 58.515 55.000 0.00 0.00 33.89 3.51
94 95 0.528466 TCGGAGATGCGATTGTGAGC 60.528 55.000 0.00 0.00 0.00 4.26
95 96 1.815212 CGGAGATGCGATTGTGAGCG 61.815 60.000 0.00 0.00 37.81 5.03
96 97 1.493950 GGAGATGCGATTGTGAGCGG 61.494 60.000 0.00 0.00 34.72 5.52
97 98 2.098842 GAGATGCGATTGTGAGCGGC 62.099 60.000 0.00 0.00 34.72 6.53
98 99 2.436469 ATGCGATTGTGAGCGGCA 60.436 55.556 1.45 0.00 34.72 5.69
99 100 1.779025 GATGCGATTGTGAGCGGCAT 61.779 55.000 1.45 0.00 35.36 4.40
100 101 1.779025 ATGCGATTGTGAGCGGCATC 61.779 55.000 1.45 0.00 34.72 3.91
101 102 2.463620 GCGATTGTGAGCGGCATCA 61.464 57.895 1.45 0.05 34.72 3.07
106 107 2.434185 GTGAGCGGCATCACGGAA 60.434 61.111 13.89 0.00 40.18 4.30
107 108 2.032634 GTGAGCGGCATCACGGAAA 61.033 57.895 13.89 0.00 40.18 3.13
108 109 1.302112 TGAGCGGCATCACGGAAAA 60.302 52.632 1.45 0.00 0.00 2.29
109 110 1.298157 TGAGCGGCATCACGGAAAAG 61.298 55.000 1.45 0.00 0.00 2.27
110 111 2.202479 GCGGCATCACGGAAAAGC 60.202 61.111 0.00 0.00 0.00 3.51
111 112 2.098298 CGGCATCACGGAAAAGCG 59.902 61.111 0.00 0.00 0.00 4.68
112 113 2.677003 CGGCATCACGGAAAAGCGT 61.677 57.895 0.00 0.00 0.00 5.07
113 114 1.154225 GGCATCACGGAAAAGCGTG 60.154 57.895 0.00 0.00 37.45 5.34
114 115 1.154225 GCATCACGGAAAAGCGTGG 60.154 57.895 0.00 0.00 36.83 4.94
115 116 1.573829 GCATCACGGAAAAGCGTGGA 61.574 55.000 0.00 0.00 36.83 4.02
116 117 0.443869 CATCACGGAAAAGCGTGGAG 59.556 55.000 0.00 0.00 36.83 3.86
117 118 0.673644 ATCACGGAAAAGCGTGGAGG 60.674 55.000 0.00 0.00 36.83 4.30
118 119 1.301401 CACGGAAAAGCGTGGAGGA 60.301 57.895 0.00 0.00 33.05 3.71
119 120 0.882927 CACGGAAAAGCGTGGAGGAA 60.883 55.000 0.00 0.00 33.05 3.36
120 121 0.036306 ACGGAAAAGCGTGGAGGAAT 59.964 50.000 0.00 0.00 0.00 3.01
121 122 1.276989 ACGGAAAAGCGTGGAGGAATA 59.723 47.619 0.00 0.00 0.00 1.75
122 123 1.933853 CGGAAAAGCGTGGAGGAATAG 59.066 52.381 0.00 0.00 0.00 1.73
123 124 2.289565 GGAAAAGCGTGGAGGAATAGG 58.710 52.381 0.00 0.00 0.00 2.57
124 125 2.289565 GAAAAGCGTGGAGGAATAGGG 58.710 52.381 0.00 0.00 0.00 3.53
125 126 0.546598 AAAGCGTGGAGGAATAGGGG 59.453 55.000 0.00 0.00 0.00 4.79
126 127 0.620700 AAGCGTGGAGGAATAGGGGT 60.621 55.000 0.00 0.00 0.00 4.95
127 128 0.263765 AGCGTGGAGGAATAGGGGTA 59.736 55.000 0.00 0.00 0.00 3.69
128 129 0.680061 GCGTGGAGGAATAGGGGTAG 59.320 60.000 0.00 0.00 0.00 3.18
129 130 1.756690 GCGTGGAGGAATAGGGGTAGA 60.757 57.143 0.00 0.00 0.00 2.59
130 131 1.962100 CGTGGAGGAATAGGGGTAGAC 59.038 57.143 0.00 0.00 0.00 2.59
131 132 2.327373 GTGGAGGAATAGGGGTAGACC 58.673 57.143 0.00 0.00 39.11 3.85
132 133 1.941682 TGGAGGAATAGGGGTAGACCA 59.058 52.381 0.21 0.00 42.91 4.02
133 134 2.327373 GGAGGAATAGGGGTAGACCAC 58.673 57.143 0.21 0.00 42.91 4.16
134 135 2.359994 GGAGGAATAGGGGTAGACCACA 60.360 54.545 3.26 0.00 43.57 4.17
135 136 3.381335 GAGGAATAGGGGTAGACCACAA 58.619 50.000 3.26 0.00 43.57 3.33
136 137 3.113043 AGGAATAGGGGTAGACCACAAC 58.887 50.000 3.26 0.00 43.57 3.32
137 138 2.841881 GGAATAGGGGTAGACCACAACA 59.158 50.000 3.26 0.00 43.57 3.33
138 139 3.458487 GGAATAGGGGTAGACCACAACAT 59.542 47.826 3.26 0.00 43.57 2.71
139 140 4.657039 GGAATAGGGGTAGACCACAACATA 59.343 45.833 3.26 0.00 43.57 2.29
140 141 5.309806 GGAATAGGGGTAGACCACAACATAT 59.690 44.000 3.26 0.00 43.57 1.78
141 142 6.183361 GGAATAGGGGTAGACCACAACATATT 60.183 42.308 3.26 0.00 43.57 1.28
142 143 6.841781 ATAGGGGTAGACCACAACATATTT 57.158 37.500 3.26 0.00 43.57 1.40
143 144 5.112129 AGGGGTAGACCACAACATATTTC 57.888 43.478 3.26 0.00 43.57 2.17
144 145 4.079958 AGGGGTAGACCACAACATATTTCC 60.080 45.833 3.26 0.00 43.57 3.13
145 146 4.079958 GGGGTAGACCACAACATATTTCCT 60.080 45.833 0.21 0.00 42.91 3.36
146 147 5.131475 GGGGTAGACCACAACATATTTCCTA 59.869 44.000 0.21 0.00 42.91 2.94
147 148 6.053650 GGGTAGACCACAACATATTTCCTAC 58.946 44.000 0.21 0.00 39.85 3.18
148 149 6.352394 GGGTAGACCACAACATATTTCCTACA 60.352 42.308 0.21 0.00 39.85 2.74
213 214 6.226052 TCAGAACGCAGCTGATTCATATATT 58.774 36.000 24.76 7.77 37.46 1.28
1197 2857 4.261614 GCAGGAAACTTCTTGTTCGGAAAT 60.262 41.667 3.83 0.00 40.21 2.17
1277 2937 1.817357 CAGCAGAAGGAGTTGCATCA 58.183 50.000 0.00 0.00 42.67 3.07
2342 4241 0.979709 TGGTGGGAGGAGATGCAGAG 60.980 60.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.216973 AGTCCGCCTCTTATACAGTTATAAG 57.783 40.000 5.42 5.42 44.76 1.73
11 12 7.211966 GAGTCCGCCTCTTATACAGTTATAA 57.788 40.000 0.00 0.00 37.22 0.98
12 13 6.814506 GAGTCCGCCTCTTATACAGTTATA 57.185 41.667 0.00 0.00 37.22 0.98
13 14 5.708877 GAGTCCGCCTCTTATACAGTTAT 57.291 43.478 0.00 0.00 37.22 1.89
25 26 1.157585 GTTTCCAAAGAGTCCGCCTC 58.842 55.000 0.00 0.00 40.80 4.70
26 27 0.602905 CGTTTCCAAAGAGTCCGCCT 60.603 55.000 0.00 0.00 0.00 5.52
27 28 1.866925 CGTTTCCAAAGAGTCCGCC 59.133 57.895 0.00 0.00 0.00 6.13
28 29 1.206831 GCGTTTCCAAAGAGTCCGC 59.793 57.895 0.00 0.00 0.00 5.54
29 30 0.512952 CTGCGTTTCCAAAGAGTCCG 59.487 55.000 0.00 0.00 0.00 4.79
30 31 1.594331 ACTGCGTTTCCAAAGAGTCC 58.406 50.000 0.00 0.00 0.00 3.85
31 32 5.867716 TCTTATACTGCGTTTCCAAAGAGTC 59.132 40.000 0.00 0.00 0.00 3.36
32 33 5.790593 TCTTATACTGCGTTTCCAAAGAGT 58.209 37.500 0.00 0.00 0.00 3.24
33 34 6.183360 CCTTCTTATACTGCGTTTCCAAAGAG 60.183 42.308 0.00 0.00 0.00 2.85
34 35 5.642063 CCTTCTTATACTGCGTTTCCAAAGA 59.358 40.000 0.00 0.00 0.00 2.52
35 36 5.411669 ACCTTCTTATACTGCGTTTCCAAAG 59.588 40.000 0.00 0.00 0.00 2.77
36 37 5.310451 ACCTTCTTATACTGCGTTTCCAAA 58.690 37.500 0.00 0.00 0.00 3.28
37 38 4.901868 ACCTTCTTATACTGCGTTTCCAA 58.098 39.130 0.00 0.00 0.00 3.53
38 39 4.501071 GACCTTCTTATACTGCGTTTCCA 58.499 43.478 0.00 0.00 0.00 3.53
39 40 3.869832 GGACCTTCTTATACTGCGTTTCC 59.130 47.826 0.00 0.00 0.00 3.13
40 41 3.869832 GGGACCTTCTTATACTGCGTTTC 59.130 47.826 0.00 0.00 0.00 2.78
41 42 3.518303 AGGGACCTTCTTATACTGCGTTT 59.482 43.478 0.00 0.00 0.00 3.60
42 43 3.105283 AGGGACCTTCTTATACTGCGTT 58.895 45.455 0.00 0.00 0.00 4.84
43 44 2.748388 AGGGACCTTCTTATACTGCGT 58.252 47.619 0.00 0.00 0.00 5.24
44 45 3.005578 GGTAGGGACCTTCTTATACTGCG 59.994 52.174 0.00 0.00 43.16 5.18
45 46 3.324268 GGGTAGGGACCTTCTTATACTGC 59.676 52.174 0.00 0.00 46.09 4.40
46 47 3.902467 GGGGTAGGGACCTTCTTATACTG 59.098 52.174 0.00 0.00 46.09 2.74
47 48 3.116434 GGGGGTAGGGACCTTCTTATACT 60.116 52.174 0.00 0.00 46.09 2.12
48 49 3.116434 AGGGGGTAGGGACCTTCTTATAC 60.116 52.174 0.00 0.00 46.09 1.47
49 50 3.153292 AGGGGGTAGGGACCTTCTTATA 58.847 50.000 0.00 0.00 46.09 0.98
50 51 1.952659 AGGGGGTAGGGACCTTCTTAT 59.047 52.381 0.00 0.00 46.09 1.73
51 52 1.411741 AGGGGGTAGGGACCTTCTTA 58.588 55.000 0.00 0.00 46.09 2.10
52 53 1.294373 CTAGGGGGTAGGGACCTTCTT 59.706 57.143 0.00 0.00 46.09 2.52
53 54 0.942721 CTAGGGGGTAGGGACCTTCT 59.057 60.000 0.00 0.00 46.09 2.85
54 55 0.763604 GCTAGGGGGTAGGGACCTTC 60.764 65.000 0.00 0.00 46.09 3.46
55 56 1.317321 GCTAGGGGGTAGGGACCTT 59.683 63.158 0.00 0.00 46.09 3.50
56 57 2.723794 GGCTAGGGGGTAGGGACCT 61.724 68.421 0.00 0.00 46.09 3.85
57 58 2.122503 GGCTAGGGGGTAGGGACC 60.123 72.222 0.00 0.00 46.13 4.46
58 59 1.152290 GAGGCTAGGGGGTAGGGAC 60.152 68.421 0.00 0.00 0.00 4.46
59 60 2.775741 CGAGGCTAGGGGGTAGGGA 61.776 68.421 0.00 0.00 0.00 4.20
60 61 2.203655 CGAGGCTAGGGGGTAGGG 60.204 72.222 0.00 0.00 0.00 3.53
61 62 2.203655 CCGAGGCTAGGGGGTAGG 60.204 72.222 5.64 0.00 0.00 3.18
62 63 1.228613 CTCCGAGGCTAGGGGGTAG 60.229 68.421 14.03 0.00 0.00 3.18
63 64 1.072505 ATCTCCGAGGCTAGGGGGTA 61.073 60.000 14.02 0.00 0.00 3.69
64 65 2.404750 ATCTCCGAGGCTAGGGGGT 61.405 63.158 14.02 2.95 0.00 4.95
65 66 1.910772 CATCTCCGAGGCTAGGGGG 60.911 68.421 14.02 5.62 0.00 5.40
66 67 2.578714 GCATCTCCGAGGCTAGGGG 61.579 68.421 14.03 10.86 36.37 4.79
67 68 2.925262 CGCATCTCCGAGGCTAGGG 61.925 68.421 14.03 5.76 37.20 3.53
68 69 1.247419 ATCGCATCTCCGAGGCTAGG 61.247 60.000 7.42 7.42 40.97 3.02
69 70 0.600557 AATCGCATCTCCGAGGCTAG 59.399 55.000 0.00 0.00 40.97 3.42
70 71 0.315251 CAATCGCATCTCCGAGGCTA 59.685 55.000 0.00 0.00 40.97 3.93
71 72 1.068753 CAATCGCATCTCCGAGGCT 59.931 57.895 0.00 0.00 40.97 4.58
72 73 1.227380 ACAATCGCATCTCCGAGGC 60.227 57.895 0.00 0.00 40.97 4.70
73 74 0.103026 TCACAATCGCATCTCCGAGG 59.897 55.000 0.00 0.00 40.97 4.63
74 75 1.485397 CTCACAATCGCATCTCCGAG 58.515 55.000 0.00 0.00 40.97 4.63
75 76 0.528466 GCTCACAATCGCATCTCCGA 60.528 55.000 0.00 0.00 41.98 4.55
76 77 1.815212 CGCTCACAATCGCATCTCCG 61.815 60.000 0.00 0.00 0.00 4.63
77 78 1.493950 CCGCTCACAATCGCATCTCC 61.494 60.000 0.00 0.00 0.00 3.71
78 79 1.930100 CCGCTCACAATCGCATCTC 59.070 57.895 0.00 0.00 0.00 2.75
79 80 2.176273 GCCGCTCACAATCGCATCT 61.176 57.895 0.00 0.00 0.00 2.90
80 81 1.779025 ATGCCGCTCACAATCGCATC 61.779 55.000 0.00 0.00 0.00 3.91
81 82 1.779025 GATGCCGCTCACAATCGCAT 61.779 55.000 0.00 0.00 0.00 4.73
82 83 2.436469 ATGCCGCTCACAATCGCA 60.436 55.556 0.00 0.00 0.00 5.10
83 84 2.325857 GATGCCGCTCACAATCGC 59.674 61.111 0.00 0.00 0.00 4.58
84 85 1.349627 GTGATGCCGCTCACAATCG 59.650 57.895 14.40 0.00 44.03 3.34
85 86 1.349627 CGTGATGCCGCTCACAATC 59.650 57.895 17.51 3.18 44.69 2.67
86 87 2.108514 CCGTGATGCCGCTCACAAT 61.109 57.895 17.51 0.00 44.69 2.71
87 88 2.723586 TTCCGTGATGCCGCTCACAA 62.724 55.000 17.51 7.32 44.69 3.33
88 89 2.723586 TTTCCGTGATGCCGCTCACA 62.724 55.000 17.51 3.25 44.69 3.58
89 90 1.573829 TTTTCCGTGATGCCGCTCAC 61.574 55.000 10.99 10.99 41.73 3.51
90 91 1.298157 CTTTTCCGTGATGCCGCTCA 61.298 55.000 0.00 0.00 0.00 4.26
91 92 1.425428 CTTTTCCGTGATGCCGCTC 59.575 57.895 0.00 0.00 0.00 5.03
92 93 2.690778 GCTTTTCCGTGATGCCGCT 61.691 57.895 0.00 0.00 0.00 5.52
93 94 2.202479 GCTTTTCCGTGATGCCGC 60.202 61.111 0.00 0.00 0.00 6.53
94 95 2.098298 CGCTTTTCCGTGATGCCG 59.902 61.111 0.00 0.00 0.00 5.69
95 96 3.263941 ACGCTTTTCCGTGATGCC 58.736 55.556 0.00 0.00 40.40 4.40
101 102 0.036306 ATTCCTCCACGCTTTTCCGT 59.964 50.000 0.00 0.00 43.11 4.69
102 103 1.933853 CTATTCCTCCACGCTTTTCCG 59.066 52.381 0.00 0.00 0.00 4.30
103 104 2.289565 CCTATTCCTCCACGCTTTTCC 58.710 52.381 0.00 0.00 0.00 3.13
104 105 2.289565 CCCTATTCCTCCACGCTTTTC 58.710 52.381 0.00 0.00 0.00 2.29
105 106 1.064685 CCCCTATTCCTCCACGCTTTT 60.065 52.381 0.00 0.00 0.00 2.27
106 107 0.546598 CCCCTATTCCTCCACGCTTT 59.453 55.000 0.00 0.00 0.00 3.51
107 108 0.620700 ACCCCTATTCCTCCACGCTT 60.621 55.000 0.00 0.00 0.00 4.68
108 109 0.263765 TACCCCTATTCCTCCACGCT 59.736 55.000 0.00 0.00 0.00 5.07
109 110 0.680061 CTACCCCTATTCCTCCACGC 59.320 60.000 0.00 0.00 0.00 5.34
110 111 1.962100 GTCTACCCCTATTCCTCCACG 59.038 57.143 0.00 0.00 0.00 4.94
111 112 2.327373 GGTCTACCCCTATTCCTCCAC 58.673 57.143 0.00 0.00 0.00 4.02
112 113 1.941682 TGGTCTACCCCTATTCCTCCA 59.058 52.381 0.00 0.00 34.29 3.86
113 114 2.327373 GTGGTCTACCCCTATTCCTCC 58.673 57.143 0.00 0.00 34.29 4.30
114 115 3.042059 TGTGGTCTACCCCTATTCCTC 57.958 52.381 0.00 0.00 34.29 3.71
115 116 3.113043 GTTGTGGTCTACCCCTATTCCT 58.887 50.000 0.00 0.00 34.29 3.36
116 117 2.841881 TGTTGTGGTCTACCCCTATTCC 59.158 50.000 0.00 0.00 34.29 3.01
117 118 4.772886 ATGTTGTGGTCTACCCCTATTC 57.227 45.455 0.00 0.00 34.29 1.75
118 119 6.841781 AATATGTTGTGGTCTACCCCTATT 57.158 37.500 0.00 0.00 34.29 1.73
119 120 6.183361 GGAAATATGTTGTGGTCTACCCCTAT 60.183 42.308 0.00 0.00 34.29 2.57
120 121 5.131475 GGAAATATGTTGTGGTCTACCCCTA 59.869 44.000 0.00 0.00 34.29 3.53
121 122 4.079958 GGAAATATGTTGTGGTCTACCCCT 60.080 45.833 0.00 0.00 34.29 4.79
122 123 4.079958 AGGAAATATGTTGTGGTCTACCCC 60.080 45.833 0.00 0.00 34.29 4.95
123 124 5.112129 AGGAAATATGTTGTGGTCTACCC 57.888 43.478 0.00 0.00 34.29 3.69
124 125 6.646267 TGTAGGAAATATGTTGTGGTCTACC 58.354 40.000 0.00 0.00 0.00 3.18
125 126 8.732746 AATGTAGGAAATATGTTGTGGTCTAC 57.267 34.615 0.00 0.00 0.00 2.59
126 127 7.709182 CGAATGTAGGAAATATGTTGTGGTCTA 59.291 37.037 0.00 0.00 0.00 2.59
127 128 6.538742 CGAATGTAGGAAATATGTTGTGGTCT 59.461 38.462 0.00 0.00 0.00 3.85
128 129 6.315393 ACGAATGTAGGAAATATGTTGTGGTC 59.685 38.462 0.00 0.00 0.00 4.02
129 130 6.177610 ACGAATGTAGGAAATATGTTGTGGT 58.822 36.000 0.00 0.00 0.00 4.16
130 131 6.538742 AGACGAATGTAGGAAATATGTTGTGG 59.461 38.462 0.00 0.00 0.00 4.17
131 132 7.515215 CGAGACGAATGTAGGAAATATGTTGTG 60.515 40.741 0.00 0.00 0.00 3.33
132 133 6.475727 CGAGACGAATGTAGGAAATATGTTGT 59.524 38.462 0.00 0.00 0.00 3.32
133 134 6.074302 CCGAGACGAATGTAGGAAATATGTTG 60.074 42.308 0.00 0.00 0.00 3.33
134 135 5.983720 CCGAGACGAATGTAGGAAATATGTT 59.016 40.000 0.00 0.00 0.00 2.71
135 136 5.529791 CCGAGACGAATGTAGGAAATATGT 58.470 41.667 0.00 0.00 0.00 2.29
136 137 4.386049 GCCGAGACGAATGTAGGAAATATG 59.614 45.833 0.00 0.00 0.00 1.78
137 138 4.557205 GCCGAGACGAATGTAGGAAATAT 58.443 43.478 0.00 0.00 0.00 1.28
138 139 3.549423 CGCCGAGACGAATGTAGGAAATA 60.549 47.826 0.00 0.00 34.06 1.40
139 140 2.798499 CGCCGAGACGAATGTAGGAAAT 60.798 50.000 0.00 0.00 34.06 2.17
140 141 1.468565 CGCCGAGACGAATGTAGGAAA 60.469 52.381 0.00 0.00 34.06 3.13
141 142 0.099968 CGCCGAGACGAATGTAGGAA 59.900 55.000 0.00 0.00 34.06 3.36
142 143 0.745486 TCGCCGAGACGAATGTAGGA 60.745 55.000 0.00 0.00 39.54 2.94
143 144 0.317103 CTCGCCGAGACGAATGTAGG 60.317 60.000 8.82 0.00 42.39 3.18
144 145 0.930742 GCTCGCCGAGACGAATGTAG 60.931 60.000 20.05 0.00 42.39 2.74
145 146 1.063649 GCTCGCCGAGACGAATGTA 59.936 57.895 20.05 0.00 42.39 2.29
146 147 2.202623 GCTCGCCGAGACGAATGT 60.203 61.111 20.05 0.00 42.39 2.71
147 148 2.202610 TGCTCGCCGAGACGAATG 60.203 61.111 20.05 0.00 42.39 2.67
148 149 2.103143 CTGCTCGCCGAGACGAAT 59.897 61.111 20.05 0.00 42.39 3.34
213 214 7.266905 AGTCTAGCTAAATACAGGGGAAAAA 57.733 36.000 0.00 0.00 0.00 1.94
231 232 3.707793 GTTATGGACGGAGCAAGTCTAG 58.292 50.000 6.27 0.00 38.58 2.43
800 868 6.767524 TCCAACACATTTAAGTTGTCACTT 57.232 33.333 0.00 0.00 45.73 3.16
992 1070 2.684881 GCTACATGTTCCATGGGTTGAG 59.315 50.000 13.02 2.33 0.00 3.02
1197 2857 0.321564 CGTCAAAGGCCACCAGATGA 60.322 55.000 5.01 0.00 0.00 2.92
1225 2885 3.193691 TGTCGTTTCATTCTCTCCTCCTC 59.806 47.826 0.00 0.00 0.00 3.71
1277 2937 2.188994 GATGAGCGGGCTCTTGCT 59.811 61.111 20.27 4.18 45.90 3.91
2342 4241 2.780065 TGACTTGCTTGTTGATGTGC 57.220 45.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.