Multiple sequence alignment - TraesCS7A01G097500

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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 TraesCS7A01G097500 chr7A 100.000 2705 0 0 1 2705 60082945 60085649 0.000000e+00 4996
1 TraesCS7A01G097500 chr7A 99.248 2528 17 2 180 2705 60170581 60168054 0.000000e+00 4562
2 TraesCS7A01G097500 chr5A 99.328 2531 15 2 177 2705 16542737 16545267 0.000000e+00 4578
3 TraesCS7A01G097500 chr5A 99.131 2531 19 3 177 2705 420183886 420186415 0.000000e+00 4549
4 TraesCS7A01G097500 chr7B 99.328 2528 15 2 180 2705 742950552 742948025 0.000000e+00 4573
5 TraesCS7A01G097500 chr7B 98.894 2532 25 3 177 2705 716782789 716785320 0.000000e+00 4518
6 TraesCS7A01G097500 chr2A 99.013 2532 22 3 177 2705 755478731 755481262 0.000000e+00 4534
7 TraesCS7A01G097500 chr1B 98.774 2528 28 3 180 2705 583563362 583560836 0.000000e+00 4494
8 TraesCS7A01G097500 chr6A 98.657 2531 32 2 177 2705 155855482 155858012 0.000000e+00 4484
9 TraesCS7A01G097500 chr4D 98.617 2531 32 3 177 2705 123348305 123350834 0.000000e+00 4477
10 TraesCS7A01G097500 chrUn 99.415 171 1 0 13 183 45083738 45083908 7.270000e-81 311
11 TraesCS7A01G097500 chrUn 99.415 171 1 0 13 183 182432623 182432453 7.270000e-81 311
12 TraesCS7A01G097500 chrUn 99.415 171 1 0 13 183 391698984 391699154 7.270000e-81 311
13 TraesCS7A01G097500 chr7D 99.415 171 1 0 13 183 381956293 381956463 7.270000e-81 311
14 TraesCS7A01G097500 chr7D 99.415 171 1 0 13 183 382046016 382045846 7.270000e-81 311
15 TraesCS7A01G097500 chr5B 99.415 171 1 0 13 183 130593632 130593802 7.270000e-81 311
16 TraesCS7A01G097500 chr5B 99.415 171 1 0 13 183 130645024 130644854 7.270000e-81 311
17 TraesCS7A01G097500 chr3A 99.415 171 1 0 13 183 122219228 122219398 7.270000e-81 311
18 TraesCS7A01G097500 chr3A 99.415 171 1 0 13 183 681271270 681271100 7.270000e-81 311


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 TraesCS7A01G097500 chr7A 60082945 60085649 2704 False 4996 4996 100.000 1 2705 1 chr7A.!!$F1 2704
1 TraesCS7A01G097500 chr7A 60168054 60170581 2527 True 4562 4562 99.248 180 2705 1 chr7A.!!$R1 2525
2 TraesCS7A01G097500 chr5A 16542737 16545267 2530 False 4578 4578 99.328 177 2705 1 chr5A.!!$F1 2528
3 TraesCS7A01G097500 chr5A 420183886 420186415 2529 False 4549 4549 99.131 177 2705 1 chr5A.!!$F2 2528
4 TraesCS7A01G097500 chr7B 742948025 742950552 2527 True 4573 4573 99.328 180 2705 1 chr7B.!!$R1 2525
5 TraesCS7A01G097500 chr7B 716782789 716785320 2531 False 4518 4518 98.894 177 2705 1 chr7B.!!$F1 2528
6 TraesCS7A01G097500 chr2A 755478731 755481262 2531 False 4534 4534 99.013 177 2705 1 chr2A.!!$F1 2528
7 TraesCS7A01G097500 chr1B 583560836 583563362 2526 True 4494 4494 98.774 180 2705 1 chr1B.!!$R1 2525
8 TraesCS7A01G097500 chr6A 155855482 155858012 2530 False 4484 4484 98.657 177 2705 1 chr6A.!!$F1 2528
9 TraesCS7A01G097500 chr4D 123348305 123350834 2529 False 4477 4477 98.617 177 2705 1 chr4D.!!$F1 2528

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
136 137 0.038166 TCAATCCTGTGCCTGTTCCC 59.962 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2019 5.415065 AGATCACATTGGTGGGGATATAGA 58.585 41.667 0.0 0.0 45.32 1.98 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.271250 TTCCATGCAAAGCTCCTCC 57.729 52.632 0.00 0.00 0.00 4.30
19 20 0.323725 TTCCATGCAAAGCTCCTCCC 60.324 55.000 0.00 0.00 0.00 4.30
20 21 1.755783 CCATGCAAAGCTCCTCCCC 60.756 63.158 0.00 0.00 0.00 4.81
21 22 1.305623 CATGCAAAGCTCCTCCCCT 59.694 57.895 0.00 0.00 0.00 4.79
22 23 0.750911 CATGCAAAGCTCCTCCCCTC 60.751 60.000 0.00 0.00 0.00 4.30
23 24 0.918310 ATGCAAAGCTCCTCCCCTCT 60.918 55.000 0.00 0.00 0.00 3.69
24 25 1.136329 TGCAAAGCTCCTCCCCTCTT 61.136 55.000 0.00 0.00 0.00 2.85
25 26 0.679321 GCAAAGCTCCTCCCCTCTTG 60.679 60.000 0.00 0.00 0.00 3.02
26 27 0.987294 CAAAGCTCCTCCCCTCTTGA 59.013 55.000 0.00 0.00 0.00 3.02
27 28 1.563410 CAAAGCTCCTCCCCTCTTGAT 59.437 52.381 0.00 0.00 0.00 2.57
28 29 1.978361 AAGCTCCTCCCCTCTTGATT 58.022 50.000 0.00 0.00 0.00 2.57
29 30 1.506025 AGCTCCTCCCCTCTTGATTC 58.494 55.000 0.00 0.00 0.00 2.52
30 31 0.472044 GCTCCTCCCCTCTTGATTCC 59.528 60.000 0.00 0.00 0.00 3.01
31 32 1.974197 GCTCCTCCCCTCTTGATTCCT 60.974 57.143 0.00 0.00 0.00 3.36
32 33 2.486716 CTCCTCCCCTCTTGATTCCTT 58.513 52.381 0.00 0.00 0.00 3.36
33 34 2.437651 CTCCTCCCCTCTTGATTCCTTC 59.562 54.545 0.00 0.00 0.00 3.46
34 35 1.492599 CCTCCCCTCTTGATTCCTTCC 59.507 57.143 0.00 0.00 0.00 3.46
35 36 2.200081 CTCCCCTCTTGATTCCTTCCA 58.800 52.381 0.00 0.00 0.00 3.53
36 37 2.172293 CTCCCCTCTTGATTCCTTCCAG 59.828 54.545 0.00 0.00 0.00 3.86
37 38 1.409381 CCCCTCTTGATTCCTTCCAGC 60.409 57.143 0.00 0.00 0.00 4.85
38 39 1.283029 CCCTCTTGATTCCTTCCAGCA 59.717 52.381 0.00 0.00 0.00 4.41
39 40 2.363683 CCTCTTGATTCCTTCCAGCAC 58.636 52.381 0.00 0.00 0.00 4.40
40 41 2.363683 CTCTTGATTCCTTCCAGCACC 58.636 52.381 0.00 0.00 0.00 5.01
41 42 1.704628 TCTTGATTCCTTCCAGCACCA 59.295 47.619 0.00 0.00 0.00 4.17
42 43 1.815003 CTTGATTCCTTCCAGCACCAC 59.185 52.381 0.00 0.00 0.00 4.16
43 44 1.067295 TGATTCCTTCCAGCACCACT 58.933 50.000 0.00 0.00 0.00 4.00
44 45 1.425066 TGATTCCTTCCAGCACCACTT 59.575 47.619 0.00 0.00 0.00 3.16
45 46 2.642311 TGATTCCTTCCAGCACCACTTA 59.358 45.455 0.00 0.00 0.00 2.24
46 47 3.073798 TGATTCCTTCCAGCACCACTTAA 59.926 43.478 0.00 0.00 0.00 1.85
47 48 3.586470 TTCCTTCCAGCACCACTTAAA 57.414 42.857 0.00 0.00 0.00 1.52
48 49 2.858745 TCCTTCCAGCACCACTTAAAC 58.141 47.619 0.00 0.00 0.00 2.01
49 50 2.173782 TCCTTCCAGCACCACTTAAACA 59.826 45.455 0.00 0.00 0.00 2.83
50 51 2.293399 CCTTCCAGCACCACTTAAACAC 59.707 50.000 0.00 0.00 0.00 3.32
51 52 3.214328 CTTCCAGCACCACTTAAACACT 58.786 45.455 0.00 0.00 0.00 3.55
52 53 2.571212 TCCAGCACCACTTAAACACTG 58.429 47.619 0.00 0.00 0.00 3.66
53 54 1.001378 CCAGCACCACTTAAACACTGC 60.001 52.381 0.00 0.00 0.00 4.40
54 55 0.944386 AGCACCACTTAAACACTGCG 59.056 50.000 0.00 0.00 0.00 5.18
55 56 0.040425 GCACCACTTAAACACTGCGG 60.040 55.000 0.00 0.00 0.00 5.69
56 57 1.588674 CACCACTTAAACACTGCGGA 58.411 50.000 0.00 0.00 0.00 5.54
57 58 1.944024 CACCACTTAAACACTGCGGAA 59.056 47.619 0.00 0.00 0.00 4.30
58 59 2.356382 CACCACTTAAACACTGCGGAAA 59.644 45.455 0.00 0.00 0.00 3.13
59 60 2.616842 ACCACTTAAACACTGCGGAAAG 59.383 45.455 0.00 0.00 0.00 2.62
60 61 2.031157 CCACTTAAACACTGCGGAAAGG 60.031 50.000 0.00 0.00 0.00 3.11
61 62 2.031157 CACTTAAACACTGCGGAAAGGG 60.031 50.000 0.00 0.00 0.00 3.95
62 63 2.227194 CTTAAACACTGCGGAAAGGGT 58.773 47.619 0.00 0.00 34.42 4.34
63 64 2.351706 TAAACACTGCGGAAAGGGTT 57.648 45.000 0.00 0.00 45.80 4.11
64 65 1.480789 AAACACTGCGGAAAGGGTTT 58.519 45.000 0.00 0.00 46.53 3.27
65 66 1.480789 AACACTGCGGAAAGGGTTTT 58.519 45.000 0.00 0.00 41.02 2.43
66 67 0.744281 ACACTGCGGAAAGGGTTTTG 59.256 50.000 0.00 0.00 25.41 2.44
67 68 1.028905 CACTGCGGAAAGGGTTTTGA 58.971 50.000 0.00 0.00 0.00 2.69
68 69 1.029681 ACTGCGGAAAGGGTTTTGAC 58.970 50.000 0.00 0.00 0.00 3.18
69 70 0.313987 CTGCGGAAAGGGTTTTGACC 59.686 55.000 0.00 0.00 0.00 4.02
70 71 0.395862 TGCGGAAAGGGTTTTGACCA 60.396 50.000 0.00 0.00 0.00 4.02
71 72 0.313987 GCGGAAAGGGTTTTGACCAG 59.686 55.000 0.00 0.00 0.00 4.00
72 73 0.313987 CGGAAAGGGTTTTGACCAGC 59.686 55.000 0.00 0.00 0.00 4.85
73 74 1.704641 GGAAAGGGTTTTGACCAGCT 58.295 50.000 0.00 0.00 0.00 4.24
74 75 2.812613 CGGAAAGGGTTTTGACCAGCTA 60.813 50.000 0.00 0.00 0.00 3.32
75 76 2.820197 GGAAAGGGTTTTGACCAGCTAG 59.180 50.000 0.00 0.00 0.00 3.42
76 77 3.487372 GAAAGGGTTTTGACCAGCTAGT 58.513 45.455 0.00 0.00 0.00 2.57
77 78 2.861147 AGGGTTTTGACCAGCTAGTC 57.139 50.000 5.23 5.23 37.28 2.59
78 79 2.054799 AGGGTTTTGACCAGCTAGTCA 58.945 47.619 11.17 11.17 44.89 3.41
79 80 2.039084 AGGGTTTTGACCAGCTAGTCAG 59.961 50.000 14.65 0.00 46.90 3.51
80 81 2.038557 GGGTTTTGACCAGCTAGTCAGA 59.961 50.000 14.65 8.22 46.90 3.27
81 82 3.307762 GGGTTTTGACCAGCTAGTCAGAT 60.308 47.826 14.65 0.00 46.90 2.90
82 83 4.327680 GGTTTTGACCAGCTAGTCAGATT 58.672 43.478 14.65 0.00 46.90 2.40
83 84 4.154918 GGTTTTGACCAGCTAGTCAGATTG 59.845 45.833 14.65 0.00 46.90 2.67
84 85 2.680312 TGACCAGCTAGTCAGATTGC 57.320 50.000 11.17 0.00 41.78 3.56
85 86 1.208052 TGACCAGCTAGTCAGATTGCC 59.792 52.381 11.17 0.00 41.78 4.52
86 87 0.543749 ACCAGCTAGTCAGATTGCCC 59.456 55.000 0.00 0.00 0.00 5.36
87 88 0.179034 CCAGCTAGTCAGATTGCCCC 60.179 60.000 0.00 0.00 0.00 5.80
88 89 0.543277 CAGCTAGTCAGATTGCCCCA 59.457 55.000 0.00 0.00 0.00 4.96
89 90 1.142465 CAGCTAGTCAGATTGCCCCAT 59.858 52.381 0.00 0.00 0.00 4.00
90 91 1.849039 AGCTAGTCAGATTGCCCCATT 59.151 47.619 0.00 0.00 0.00 3.16
91 92 3.048600 AGCTAGTCAGATTGCCCCATTA 58.951 45.455 0.00 0.00 0.00 1.90
92 93 3.142174 GCTAGTCAGATTGCCCCATTAC 58.858 50.000 0.00 0.00 0.00 1.89
93 94 2.332063 AGTCAGATTGCCCCATTACG 57.668 50.000 0.00 0.00 0.00 3.18
94 95 1.134098 AGTCAGATTGCCCCATTACGG 60.134 52.381 0.00 0.00 0.00 4.02
105 106 0.722848 CCATTACGGGTGTGTTACGC 59.277 55.000 0.00 0.00 38.76 4.42
115 116 3.249013 GTGTGTTACGCCAGAAAGTTC 57.751 47.619 0.00 0.00 0.00 3.01
116 117 2.032290 GTGTGTTACGCCAGAAAGTTCC 60.032 50.000 0.00 0.00 0.00 3.62
117 118 2.158871 TGTGTTACGCCAGAAAGTTCCT 60.159 45.455 0.00 0.00 0.00 3.36
118 119 2.479275 GTGTTACGCCAGAAAGTTCCTC 59.521 50.000 0.00 0.00 0.00 3.71
119 120 2.103432 TGTTACGCCAGAAAGTTCCTCA 59.897 45.455 0.00 0.00 0.00 3.86
120 121 3.135994 GTTACGCCAGAAAGTTCCTCAA 58.864 45.455 0.00 0.00 0.00 3.02
121 122 2.568623 ACGCCAGAAAGTTCCTCAAT 57.431 45.000 0.00 0.00 0.00 2.57
122 123 2.427506 ACGCCAGAAAGTTCCTCAATC 58.572 47.619 0.00 0.00 0.00 2.67
123 124 1.740025 CGCCAGAAAGTTCCTCAATCC 59.260 52.381 0.00 0.00 0.00 3.01
124 125 2.616510 CGCCAGAAAGTTCCTCAATCCT 60.617 50.000 0.00 0.00 0.00 3.24
125 126 2.751806 GCCAGAAAGTTCCTCAATCCTG 59.248 50.000 0.00 0.00 0.00 3.86
126 127 3.812167 GCCAGAAAGTTCCTCAATCCTGT 60.812 47.826 0.00 0.00 0.00 4.00
127 128 3.755378 CCAGAAAGTTCCTCAATCCTGTG 59.245 47.826 0.00 0.00 0.00 3.66
128 129 3.190118 CAGAAAGTTCCTCAATCCTGTGC 59.810 47.826 0.00 0.00 0.00 4.57
129 130 2.206576 AAGTTCCTCAATCCTGTGCC 57.793 50.000 0.00 0.00 0.00 5.01
130 131 1.366319 AGTTCCTCAATCCTGTGCCT 58.634 50.000 0.00 0.00 0.00 4.75
131 132 1.004044 AGTTCCTCAATCCTGTGCCTG 59.996 52.381 0.00 0.00 0.00 4.85
132 133 1.067295 TTCCTCAATCCTGTGCCTGT 58.933 50.000 0.00 0.00 0.00 4.00
133 134 1.067295 TCCTCAATCCTGTGCCTGTT 58.933 50.000 0.00 0.00 0.00 3.16
134 135 1.003580 TCCTCAATCCTGTGCCTGTTC 59.996 52.381 0.00 0.00 0.00 3.18
135 136 1.457346 CTCAATCCTGTGCCTGTTCC 58.543 55.000 0.00 0.00 0.00 3.62
136 137 0.038166 TCAATCCTGTGCCTGTTCCC 59.962 55.000 0.00 0.00 0.00 3.97
137 138 1.002134 AATCCTGTGCCTGTTCCCG 60.002 57.895 0.00 0.00 0.00 5.14
138 139 1.488705 AATCCTGTGCCTGTTCCCGA 61.489 55.000 0.00 0.00 0.00 5.14
139 140 1.903877 ATCCTGTGCCTGTTCCCGAG 61.904 60.000 0.00 0.00 0.00 4.63
140 141 2.743928 CTGTGCCTGTTCCCGAGC 60.744 66.667 0.00 0.00 0.00 5.03
141 142 4.680237 TGTGCCTGTTCCCGAGCG 62.680 66.667 0.00 0.00 0.00 5.03
142 143 4.373116 GTGCCTGTTCCCGAGCGA 62.373 66.667 0.00 0.00 0.00 4.93
143 144 4.069232 TGCCTGTTCCCGAGCGAG 62.069 66.667 0.00 0.00 0.00 5.03
144 145 4.070552 GCCTGTTCCCGAGCGAGT 62.071 66.667 0.00 0.00 0.00 4.18
145 146 2.182030 CCTGTTCCCGAGCGAGTC 59.818 66.667 0.00 0.00 0.00 3.36
146 147 2.636412 CCTGTTCCCGAGCGAGTCA 61.636 63.158 0.00 0.00 0.00 3.41
147 148 1.153939 CTGTTCCCGAGCGAGTCAG 60.154 63.158 0.00 0.00 0.00 3.51
148 149 1.867919 CTGTTCCCGAGCGAGTCAGT 61.868 60.000 0.00 0.00 0.00 3.41
149 150 1.153997 GTTCCCGAGCGAGTCAGTC 60.154 63.158 0.00 0.00 0.00 3.51
150 151 2.341101 TTCCCGAGCGAGTCAGTCC 61.341 63.158 0.00 0.00 0.00 3.85
151 152 3.827898 CCCGAGCGAGTCAGTCCC 61.828 72.222 0.00 0.00 0.00 4.46
152 153 3.062466 CCGAGCGAGTCAGTCCCA 61.062 66.667 0.00 0.00 0.00 4.37
153 154 2.418910 CCGAGCGAGTCAGTCCCAT 61.419 63.158 0.00 0.00 0.00 4.00
154 155 1.513158 CGAGCGAGTCAGTCCCATT 59.487 57.895 0.00 0.00 0.00 3.16
155 156 0.108615 CGAGCGAGTCAGTCCCATTT 60.109 55.000 0.00 0.00 0.00 2.32
156 157 1.646189 GAGCGAGTCAGTCCCATTTC 58.354 55.000 0.00 0.00 0.00 2.17
157 158 0.108615 AGCGAGTCAGTCCCATTTCG 60.109 55.000 0.00 0.00 0.00 3.46
158 159 0.108804 GCGAGTCAGTCCCATTTCGA 60.109 55.000 0.00 0.00 0.00 3.71
159 160 1.471676 GCGAGTCAGTCCCATTTCGAT 60.472 52.381 0.00 0.00 0.00 3.59
160 161 2.196749 CGAGTCAGTCCCATTTCGATG 58.803 52.381 0.00 0.00 0.00 3.84
161 162 2.159240 CGAGTCAGTCCCATTTCGATGA 60.159 50.000 0.00 0.00 0.00 2.92
162 163 3.190874 GAGTCAGTCCCATTTCGATGAC 58.809 50.000 3.85 3.85 37.82 3.06
163 164 1.927174 GTCAGTCCCATTTCGATGACG 59.073 52.381 0.00 0.00 41.26 4.35
172 173 4.427793 TCGATGACGAACGACACG 57.572 55.556 0.14 7.94 45.74 4.49
173 174 1.861440 TCGATGACGAACGACACGA 59.139 52.632 14.63 14.63 45.74 4.35
174 175 0.445043 TCGATGACGAACGACACGAT 59.555 50.000 14.63 0.00 45.74 3.73
175 176 0.561593 CGATGACGAACGACACGATG 59.438 55.000 0.14 0.00 42.66 3.84
176 177 1.614385 GATGACGAACGACACGATGT 58.386 50.000 0.14 0.00 34.70 3.06
177 178 2.777494 GATGACGAACGACACGATGTA 58.223 47.619 0.14 0.00 34.70 2.29
178 179 2.905959 TGACGAACGACACGATGTAT 57.094 45.000 0.14 0.00 34.70 2.29
324 325 0.177373 GGTAGGTCAAGCCCTTACCG 59.823 60.000 0.00 0.00 38.37 4.02
413 414 8.966868 GTAGGCTGCTATATCTAGAAAGAGAAT 58.033 37.037 0.00 0.00 34.49 2.40
1429 1433 7.221450 CCCAGGGATTATTGAACGTAAATCTA 58.779 38.462 0.00 0.00 0.00 1.98
2014 2019 0.456221 CAAGCTGGAGACGTATCGGT 59.544 55.000 3.77 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.304282 GGGAGGAGCTTTGCATGGA 59.696 57.895 0.00 0.00 0.00 3.41
2 3 1.755783 GGGGAGGAGCTTTGCATGG 60.756 63.158 0.00 0.00 0.00 3.66
3 4 0.750911 GAGGGGAGGAGCTTTGCATG 60.751 60.000 0.00 0.00 0.00 4.06
4 5 0.918310 AGAGGGGAGGAGCTTTGCAT 60.918 55.000 0.00 0.00 0.00 3.96
5 6 1.136329 AAGAGGGGAGGAGCTTTGCA 61.136 55.000 0.00 0.00 0.00 4.08
6 7 0.679321 CAAGAGGGGAGGAGCTTTGC 60.679 60.000 0.00 0.00 0.00 3.68
7 8 0.987294 TCAAGAGGGGAGGAGCTTTG 59.013 55.000 0.00 0.00 0.00 2.77
8 9 1.978361 ATCAAGAGGGGAGGAGCTTT 58.022 50.000 0.00 0.00 0.00 3.51
9 10 1.843206 GAATCAAGAGGGGAGGAGCTT 59.157 52.381 0.00 0.00 0.00 3.74
10 11 1.506025 GAATCAAGAGGGGAGGAGCT 58.494 55.000 0.00 0.00 0.00 4.09
11 12 0.472044 GGAATCAAGAGGGGAGGAGC 59.528 60.000 0.00 0.00 0.00 4.70
12 13 2.188818 AGGAATCAAGAGGGGAGGAG 57.811 55.000 0.00 0.00 0.00 3.69
13 14 2.482494 GAAGGAATCAAGAGGGGAGGA 58.518 52.381 0.00 0.00 0.00 3.71
14 15 1.492599 GGAAGGAATCAAGAGGGGAGG 59.507 57.143 0.00 0.00 0.00 4.30
15 16 2.172293 CTGGAAGGAATCAAGAGGGGAG 59.828 54.545 0.00 0.00 29.56 4.30
16 17 2.200081 CTGGAAGGAATCAAGAGGGGA 58.800 52.381 0.00 0.00 29.56 4.81
17 18 1.409381 GCTGGAAGGAATCAAGAGGGG 60.409 57.143 0.00 0.00 29.56 4.79
18 19 1.283029 TGCTGGAAGGAATCAAGAGGG 59.717 52.381 0.00 0.00 29.56 4.30
19 20 2.363683 GTGCTGGAAGGAATCAAGAGG 58.636 52.381 0.00 0.00 34.45 3.69
20 21 2.290514 TGGTGCTGGAAGGAATCAAGAG 60.291 50.000 0.00 0.00 34.45 2.85
21 22 1.704628 TGGTGCTGGAAGGAATCAAGA 59.295 47.619 0.00 0.00 34.45 3.02
22 23 1.815003 GTGGTGCTGGAAGGAATCAAG 59.185 52.381 0.00 0.00 34.45 3.02
23 24 1.425066 AGTGGTGCTGGAAGGAATCAA 59.575 47.619 0.00 0.00 34.45 2.57
24 25 1.067295 AGTGGTGCTGGAAGGAATCA 58.933 50.000 0.00 0.00 34.45 2.57
25 26 2.206576 AAGTGGTGCTGGAAGGAATC 57.793 50.000 0.00 0.00 34.45 2.52
26 27 3.806949 TTAAGTGGTGCTGGAAGGAAT 57.193 42.857 0.00 0.00 34.45 3.01
27 28 3.219281 GTTTAAGTGGTGCTGGAAGGAA 58.781 45.455 0.00 0.00 34.45 3.36
28 29 2.173782 TGTTTAAGTGGTGCTGGAAGGA 59.826 45.455 0.00 0.00 0.00 3.36
29 30 2.293399 GTGTTTAAGTGGTGCTGGAAGG 59.707 50.000 0.00 0.00 0.00 3.46
30 31 3.003689 CAGTGTTTAAGTGGTGCTGGAAG 59.996 47.826 0.00 0.00 0.00 3.46
31 32 2.948979 CAGTGTTTAAGTGGTGCTGGAA 59.051 45.455 0.00 0.00 0.00 3.53
32 33 2.571212 CAGTGTTTAAGTGGTGCTGGA 58.429 47.619 0.00 0.00 0.00 3.86
33 34 1.001378 GCAGTGTTTAAGTGGTGCTGG 60.001 52.381 0.00 0.00 0.00 4.85
34 35 1.334059 CGCAGTGTTTAAGTGGTGCTG 60.334 52.381 0.00 0.00 0.00 4.41
35 36 0.944386 CGCAGTGTTTAAGTGGTGCT 59.056 50.000 0.00 0.00 0.00 4.40
36 37 0.040425 CCGCAGTGTTTAAGTGGTGC 60.040 55.000 0.00 0.00 0.00 5.01
37 38 1.588674 TCCGCAGTGTTTAAGTGGTG 58.411 50.000 0.00 0.00 34.61 4.17
38 39 2.335316 TTCCGCAGTGTTTAAGTGGT 57.665 45.000 0.00 0.00 34.61 4.16
39 40 2.031157 CCTTTCCGCAGTGTTTAAGTGG 60.031 50.000 0.00 0.00 0.00 4.00
40 41 2.031157 CCCTTTCCGCAGTGTTTAAGTG 60.031 50.000 0.00 0.00 0.00 3.16
41 42 2.227194 CCCTTTCCGCAGTGTTTAAGT 58.773 47.619 0.00 0.00 0.00 2.24
42 43 2.227194 ACCCTTTCCGCAGTGTTTAAG 58.773 47.619 0.00 0.00 0.00 1.85
43 44 2.351706 ACCCTTTCCGCAGTGTTTAA 57.648 45.000 0.00 0.00 0.00 1.52
44 45 2.351706 AACCCTTTCCGCAGTGTTTA 57.648 45.000 0.00 0.00 0.00 2.01
45 46 1.480789 AAACCCTTTCCGCAGTGTTT 58.519 45.000 0.00 0.00 0.00 2.83
46 47 1.136110 CAAAACCCTTTCCGCAGTGTT 59.864 47.619 0.00 0.00 0.00 3.32
47 48 0.744281 CAAAACCCTTTCCGCAGTGT 59.256 50.000 0.00 0.00 0.00 3.55
48 49 1.028905 TCAAAACCCTTTCCGCAGTG 58.971 50.000 0.00 0.00 0.00 3.66
49 50 1.029681 GTCAAAACCCTTTCCGCAGT 58.970 50.000 0.00 0.00 0.00 4.40
50 51 0.313987 GGTCAAAACCCTTTCCGCAG 59.686 55.000 0.00 0.00 39.93 5.18
51 52 0.395862 TGGTCAAAACCCTTTCCGCA 60.396 50.000 0.00 0.00 45.83 5.69
52 53 0.313987 CTGGTCAAAACCCTTTCCGC 59.686 55.000 0.00 0.00 45.83 5.54
53 54 0.313987 GCTGGTCAAAACCCTTTCCG 59.686 55.000 0.00 0.00 45.83 4.30
54 55 1.704641 AGCTGGTCAAAACCCTTTCC 58.295 50.000 0.00 0.00 45.83 3.13
55 56 3.487372 ACTAGCTGGTCAAAACCCTTTC 58.513 45.455 0.00 0.00 45.83 2.62
56 57 3.117663 TGACTAGCTGGTCAAAACCCTTT 60.118 43.478 28.42 0.00 45.83 3.11
57 58 2.441750 TGACTAGCTGGTCAAAACCCTT 59.558 45.455 28.42 0.00 45.83 3.95
58 59 2.039084 CTGACTAGCTGGTCAAAACCCT 59.961 50.000 29.68 0.00 45.83 4.34
59 60 2.038557 TCTGACTAGCTGGTCAAAACCC 59.961 50.000 29.68 5.21 45.83 4.11
60 61 3.402628 TCTGACTAGCTGGTCAAAACC 57.597 47.619 29.68 5.92 44.24 3.27
61 62 4.378874 GCAATCTGACTAGCTGGTCAAAAC 60.379 45.833 29.68 15.78 44.24 2.43
62 63 3.753272 GCAATCTGACTAGCTGGTCAAAA 59.247 43.478 29.68 21.76 44.24 2.44
63 64 3.338249 GCAATCTGACTAGCTGGTCAAA 58.662 45.455 29.68 20.51 44.24 2.69
64 65 2.355108 GGCAATCTGACTAGCTGGTCAA 60.355 50.000 29.68 21.19 44.24 3.18
65 66 1.208052 GGCAATCTGACTAGCTGGTCA 59.792 52.381 28.50 28.50 42.96 4.02
66 67 1.474143 GGGCAATCTGACTAGCTGGTC 60.474 57.143 22.31 22.31 36.81 4.02
67 68 0.543749 GGGCAATCTGACTAGCTGGT 59.456 55.000 0.69 0.69 0.00 4.00
68 69 0.179034 GGGGCAATCTGACTAGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
69 70 0.543277 TGGGGCAATCTGACTAGCTG 59.457 55.000 0.00 0.00 0.00 4.24
70 71 1.516110 ATGGGGCAATCTGACTAGCT 58.484 50.000 0.00 0.00 0.00 3.32
71 72 2.355010 AATGGGGCAATCTGACTAGC 57.645 50.000 0.00 0.00 0.00 3.42
72 73 3.393800 CGTAATGGGGCAATCTGACTAG 58.606 50.000 0.00 0.00 0.00 2.57
73 74 2.104111 CCGTAATGGGGCAATCTGACTA 59.896 50.000 0.00 0.00 0.00 2.59
74 75 1.134098 CCGTAATGGGGCAATCTGACT 60.134 52.381 0.00 0.00 0.00 3.41
75 76 1.308998 CCGTAATGGGGCAATCTGAC 58.691 55.000 0.00 0.00 0.00 3.51
76 77 3.798794 CCGTAATGGGGCAATCTGA 57.201 52.632 0.00 0.00 0.00 3.27
86 87 0.722848 GCGTAACACACCCGTAATGG 59.277 55.000 0.00 0.00 37.55 3.16
87 88 0.722848 GGCGTAACACACCCGTAATG 59.277 55.000 0.00 0.00 0.00 1.90
88 89 0.321021 TGGCGTAACACACCCGTAAT 59.679 50.000 0.00 0.00 0.00 1.89
89 90 0.319727 CTGGCGTAACACACCCGTAA 60.320 55.000 0.00 0.00 0.00 3.18
90 91 1.177895 TCTGGCGTAACACACCCGTA 61.178 55.000 0.00 0.00 0.00 4.02
91 92 2.029964 CTGGCGTAACACACCCGT 59.970 61.111 0.00 0.00 0.00 5.28
92 93 0.881159 TTTCTGGCGTAACACACCCG 60.881 55.000 0.00 0.00 0.00 5.28
93 94 0.872388 CTTTCTGGCGTAACACACCC 59.128 55.000 0.00 0.00 0.00 4.61
94 95 1.589803 ACTTTCTGGCGTAACACACC 58.410 50.000 0.00 0.00 0.00 4.16
95 96 2.032290 GGAACTTTCTGGCGTAACACAC 60.032 50.000 0.00 0.00 0.00 3.82
96 97 2.158871 AGGAACTTTCTGGCGTAACACA 60.159 45.455 0.00 0.00 27.25 3.72
97 98 2.479275 GAGGAACTTTCTGGCGTAACAC 59.521 50.000 0.00 0.00 41.55 3.32
98 99 2.103432 TGAGGAACTTTCTGGCGTAACA 59.897 45.455 0.00 0.00 41.55 2.41
99 100 2.762745 TGAGGAACTTTCTGGCGTAAC 58.237 47.619 0.00 0.00 41.55 2.50
100 101 3.478857 TTGAGGAACTTTCTGGCGTAA 57.521 42.857 0.00 0.00 41.55 3.18
101 102 3.596214 GATTGAGGAACTTTCTGGCGTA 58.404 45.455 0.00 0.00 41.55 4.42
102 103 2.427506 GATTGAGGAACTTTCTGGCGT 58.572 47.619 0.00 0.00 41.55 5.68
103 104 1.740025 GGATTGAGGAACTTTCTGGCG 59.260 52.381 0.00 0.00 41.55 5.69
104 105 2.751806 CAGGATTGAGGAACTTTCTGGC 59.248 50.000 0.00 0.00 41.55 4.85
105 106 3.755378 CACAGGATTGAGGAACTTTCTGG 59.245 47.826 0.00 0.00 41.55 3.86
106 107 3.190118 GCACAGGATTGAGGAACTTTCTG 59.810 47.826 0.00 0.00 41.55 3.02
107 108 3.416156 GCACAGGATTGAGGAACTTTCT 58.584 45.455 0.00 0.00 41.55 2.52
108 109 2.489722 GGCACAGGATTGAGGAACTTTC 59.510 50.000 0.00 0.00 41.55 2.62
109 110 2.108952 AGGCACAGGATTGAGGAACTTT 59.891 45.455 0.00 0.00 41.55 2.66
110 111 1.707427 AGGCACAGGATTGAGGAACTT 59.293 47.619 0.00 0.00 41.55 2.66
112 113 1.271597 ACAGGCACAGGATTGAGGAAC 60.272 52.381 0.00 0.00 0.00 3.62
113 114 1.067295 ACAGGCACAGGATTGAGGAA 58.933 50.000 0.00 0.00 0.00 3.36
114 115 1.003580 GAACAGGCACAGGATTGAGGA 59.996 52.381 0.00 0.00 0.00 3.71
115 116 1.457346 GAACAGGCACAGGATTGAGG 58.543 55.000 0.00 0.00 0.00 3.86
116 117 1.457346 GGAACAGGCACAGGATTGAG 58.543 55.000 0.00 0.00 0.00 3.02
117 118 0.038166 GGGAACAGGCACAGGATTGA 59.962 55.000 0.00 0.00 0.00 2.57
118 119 1.308069 CGGGAACAGGCACAGGATTG 61.308 60.000 0.00 0.00 0.00 2.67
119 120 1.002134 CGGGAACAGGCACAGGATT 60.002 57.895 0.00 0.00 0.00 3.01
120 121 1.903877 CTCGGGAACAGGCACAGGAT 61.904 60.000 0.00 0.00 0.00 3.24
121 122 2.525629 TCGGGAACAGGCACAGGA 60.526 61.111 0.00 0.00 0.00 3.86
122 123 2.046892 CTCGGGAACAGGCACAGG 60.047 66.667 0.00 0.00 0.00 4.00
123 124 2.743928 GCTCGGGAACAGGCACAG 60.744 66.667 0.00 0.00 0.00 3.66
124 125 4.680237 CGCTCGGGAACAGGCACA 62.680 66.667 0.00 0.00 0.00 4.57
125 126 4.373116 TCGCTCGGGAACAGGCAC 62.373 66.667 0.00 0.00 0.00 5.01
126 127 4.069232 CTCGCTCGGGAACAGGCA 62.069 66.667 0.00 0.00 0.00 4.75
127 128 3.991536 GACTCGCTCGGGAACAGGC 62.992 68.421 0.00 0.00 0.00 4.85
128 129 2.182030 GACTCGCTCGGGAACAGG 59.818 66.667 0.00 0.00 0.00 4.00
129 130 1.153939 CTGACTCGCTCGGGAACAG 60.154 63.158 0.00 1.85 0.00 3.16
130 131 1.863662 GACTGACTCGCTCGGGAACA 61.864 60.000 0.00 0.00 0.00 3.18
131 132 1.153997 GACTGACTCGCTCGGGAAC 60.154 63.158 0.00 0.00 0.00 3.62
132 133 2.341101 GGACTGACTCGCTCGGGAA 61.341 63.158 0.00 0.00 0.00 3.97
133 134 2.750637 GGACTGACTCGCTCGGGA 60.751 66.667 0.00 0.00 0.00 5.14
134 135 3.827898 GGGACTGACTCGCTCGGG 61.828 72.222 0.00 0.00 0.00 5.14
135 136 1.949847 AATGGGACTGACTCGCTCGG 61.950 60.000 0.00 0.00 32.88 4.63
136 137 0.108615 AAATGGGACTGACTCGCTCG 60.109 55.000 0.00 0.00 32.88 5.03
137 138 1.646189 GAAATGGGACTGACTCGCTC 58.354 55.000 0.00 0.00 32.88 5.03
138 139 0.108615 CGAAATGGGACTGACTCGCT 60.109 55.000 0.00 0.00 32.88 4.93
139 140 0.108804 TCGAAATGGGACTGACTCGC 60.109 55.000 0.00 0.00 0.00 5.03
140 141 2.159240 TCATCGAAATGGGACTGACTCG 60.159 50.000 0.00 0.00 33.42 4.18
141 142 3.190874 GTCATCGAAATGGGACTGACTC 58.809 50.000 4.66 0.00 33.42 3.36
142 143 2.417379 CGTCATCGAAATGGGACTGACT 60.417 50.000 9.19 0.00 39.71 3.41
143 144 1.927174 CGTCATCGAAATGGGACTGAC 59.073 52.381 0.00 0.00 39.71 3.51
144 145 1.822371 TCGTCATCGAAATGGGACTGA 59.178 47.619 0.00 0.00 43.34 3.41
145 146 2.293677 TCGTCATCGAAATGGGACTG 57.706 50.000 0.00 0.00 43.34 3.51
155 156 0.445043 ATCGTGTCGTTCGTCATCGA 59.555 50.000 14.11 14.11 44.66 3.59
156 157 0.561593 CATCGTGTCGTTCGTCATCG 59.438 55.000 0.00 2.93 38.55 3.84
157 158 1.614385 ACATCGTGTCGTTCGTCATC 58.386 50.000 0.00 0.00 0.00 2.92
158 159 2.905959 TACATCGTGTCGTTCGTCAT 57.094 45.000 0.00 0.00 0.00 3.06
159 160 2.511879 CATACATCGTGTCGTTCGTCA 58.488 47.619 0.00 0.00 0.00 4.35
160 161 1.252015 GCATACATCGTGTCGTTCGTC 59.748 52.381 0.00 0.00 0.00 4.20
161 162 1.265568 GCATACATCGTGTCGTTCGT 58.734 50.000 0.00 0.00 0.00 3.85
162 163 0.570734 GGCATACATCGTGTCGTTCG 59.429 55.000 0.00 0.00 0.00 3.95
163 164 1.588404 CAGGCATACATCGTGTCGTTC 59.412 52.381 0.00 0.00 0.00 3.95
164 165 1.067142 ACAGGCATACATCGTGTCGTT 60.067 47.619 0.00 0.00 0.00 3.85
165 166 0.530744 ACAGGCATACATCGTGTCGT 59.469 50.000 0.00 0.00 0.00 4.34
166 167 0.923403 CACAGGCATACATCGTGTCG 59.077 55.000 0.00 0.00 31.12 4.35
167 168 1.134818 TCCACAGGCATACATCGTGTC 60.135 52.381 0.00 0.00 31.12 3.67
168 169 0.901827 TCCACAGGCATACATCGTGT 59.098 50.000 0.00 0.00 33.42 4.49
169 170 1.869132 CATCCACAGGCATACATCGTG 59.131 52.381 0.00 0.00 0.00 4.35
170 171 1.811558 GCATCCACAGGCATACATCGT 60.812 52.381 0.00 0.00 0.00 3.73
171 172 0.870393 GCATCCACAGGCATACATCG 59.130 55.000 0.00 0.00 0.00 3.84
172 173 0.870393 CGCATCCACAGGCATACATC 59.130 55.000 0.00 0.00 0.00 3.06
173 174 0.535780 CCGCATCCACAGGCATACAT 60.536 55.000 0.00 0.00 0.00 2.29
174 175 1.153188 CCGCATCCACAGGCATACA 60.153 57.895 0.00 0.00 0.00 2.29
175 176 3.736483 CCGCATCCACAGGCATAC 58.264 61.111 0.00 0.00 0.00 2.39
324 325 9.899226 GATAGCCCATTTTGAATAAGTGTTATC 57.101 33.333 0.00 0.00 0.00 1.75
812 816 1.823610 GGTCTCTACCTTGCTTACCGT 59.176 52.381 0.00 0.00 43.08 4.83
2014 2019 5.415065 AGATCACATTGGTGGGGATATAGA 58.585 41.667 0.00 0.00 45.32 1.98


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

AutoCloner maintained by Alex Coulton.