Multiple sequence alignment - TraesCS4B01G102100

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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 TraesCS4B01G102100 chr4B 100.000 2324 0 0 1 2324 108079124 108081447 0.000000e+00 4292
1 TraesCS4B01G102100 chr4B 87.880 1939 196 24 181 2100 222962737 222964655 0.000000e+00 2242
2 TraesCS4B01G102100 chr4B 90.657 1659 116 15 450 2100 560024528 560022901 0.000000e+00 2169
3 TraesCS4B01G102100 chr4B 94.783 230 11 1 2095 2324 560022768 560022540 7.900000e-95 357
4 TraesCS4B01G102100 chr6B 96.555 2148 70 3 178 2324 648849563 648851707 0.000000e+00 3554
5 TraesCS4B01G102100 chr6B 96.508 2148 71 3 178 2324 648885612 648887756 0.000000e+00 3548
6 TraesCS4B01G102100 chr3B 96.455 2144 73 3 182 2324 21575812 21573671 0.000000e+00 3535
7 TraesCS4B01G102100 chr3B 90.678 1931 128 16 182 2100 436378642 436376752 0.000000e+00 2521
8 TraesCS4B01G102100 chr3B 97.790 181 4 0 1 181 526540321 526540141 1.730000e-81 313
9 TraesCS4B01G102100 chr5B 91.219 1936 149 13 182 2100 49392136 49394067 0.000000e+00 2614
10 TraesCS4B01G102100 chr5B 91.144 1931 128 15 182 2100 10496065 10497964 0.000000e+00 2579
11 TraesCS4B01G102100 chr2B 90.398 1937 141 16 182 2100 311834122 311836031 0.000000e+00 2505
12 TraesCS4B01G102100 chr2B 90.057 1931 134 20 182 2100 22380453 22382337 0.000000e+00 2449
13 TraesCS4B01G102100 chr2B 94.783 230 11 1 2095 2324 22382469 22382697 7.900000e-95 357
14 TraesCS4B01G102100 chr1D 92.888 1392 75 13 712 2100 417758040 417759410 0.000000e+00 2001
15 TraesCS4B01G102100 chr1D 97.238 181 5 0 1 181 355214993 355214813 8.070000e-80 307
16 TraesCS4B01G102100 chr5A 93.837 1217 72 2 884 2100 693881418 693880205 0.000000e+00 1829
17 TraesCS4B01G102100 chr1B 91.293 1160 86 9 182 1329 92853804 92852648 0.000000e+00 1568
18 TraesCS4B01G102100 chr1B 87.539 1284 98 25 182 1435 678498970 678500221 0.000000e+00 1428
19 TraesCS4B01G102100 chr1B 95.217 230 11 0 2095 2324 92852582 92852353 4.720000e-97 364
20 TraesCS4B01G102100 chr1B 97.238 181 5 0 1 181 389264604 389264784 8.070000e-80 307
21 TraesCS4B01G102100 chr2D 95.217 230 11 0 2095 2324 613465808 613466037 4.720000e-97 364
22 TraesCS4B01G102100 chr6D 94.783 230 12 0 2095 2324 55694 55465 2.200000e-95 359
23 TraesCS4B01G102100 chr7B 94.783 230 11 1 2095 2324 101716681 101716909 7.900000e-95 357
24 TraesCS4B01G102100 chr7B 97.790 181 4 0 1 181 653071045 653071225 1.730000e-81 313
25 TraesCS4B01G102100 chrUn 97.790 181 4 0 1 181 317937877 317938057 1.730000e-81 313
26 TraesCS4B01G102100 chr3D 97.790 181 4 0 1 181 298827053 298827233 1.730000e-81 313
27 TraesCS4B01G102100 chr3D 97.238 181 5 0 1 181 484582148 484581968 8.070000e-80 307
28 TraesCS4B01G102100 chr5D 97.238 181 5 0 1 181 190679694 190679874 8.070000e-80 307
29 TraesCS4B01G102100 chr5D 97.238 181 5 0 1 181 296237158 296237338 8.070000e-80 307


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 TraesCS4B01G102100 chr4B 108079124 108081447 2323 False 4292 4292 100.000 1 2324 1 chr4B.!!$F1 2323
1 TraesCS4B01G102100 chr4B 222962737 222964655 1918 False 2242 2242 87.880 181 2100 1 chr4B.!!$F2 1919
2 TraesCS4B01G102100 chr4B 560022540 560024528 1988 True 1263 2169 92.720 450 2324 2 chr4B.!!$R1 1874
3 TraesCS4B01G102100 chr6B 648849563 648851707 2144 False 3554 3554 96.555 178 2324 1 chr6B.!!$F1 2146
4 TraesCS4B01G102100 chr6B 648885612 648887756 2144 False 3548 3548 96.508 178 2324 1 chr6B.!!$F2 2146
5 TraesCS4B01G102100 chr3B 21573671 21575812 2141 True 3535 3535 96.455 182 2324 1 chr3B.!!$R1 2142
6 TraesCS4B01G102100 chr3B 436376752 436378642 1890 True 2521 2521 90.678 182 2100 1 chr3B.!!$R2 1918
7 TraesCS4B01G102100 chr5B 49392136 49394067 1931 False 2614 2614 91.219 182 2100 1 chr5B.!!$F2 1918
8 TraesCS4B01G102100 chr5B 10496065 10497964 1899 False 2579 2579 91.144 182 2100 1 chr5B.!!$F1 1918
9 TraesCS4B01G102100 chr2B 311834122 311836031 1909 False 2505 2505 90.398 182 2100 1 chr2B.!!$F1 1918
10 TraesCS4B01G102100 chr2B 22380453 22382697 2244 False 1403 2449 92.420 182 2324 2 chr2B.!!$F2 2142
11 TraesCS4B01G102100 chr1D 417758040 417759410 1370 False 2001 2001 92.888 712 2100 1 chr1D.!!$F1 1388
12 TraesCS4B01G102100 chr5A 693880205 693881418 1213 True 1829 1829 93.837 884 2100 1 chr5A.!!$R1 1216
13 TraesCS4B01G102100 chr1B 678498970 678500221 1251 False 1428 1428 87.539 182 1435 1 chr1B.!!$F2 1253
14 TraesCS4B01G102100 chr1B 92852353 92853804 1451 True 966 1568 93.255 182 2324 2 chr1B.!!$R1 2142

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
84 85 0.035739 GGAGGTGACCAAACGGCTTA 59.964 55.0 3.63 0.0 0.0 3.09 F
647 710 0.249398 CCCTAACCCGTGTCTCCTTG 59.751 60.0 0.00 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1206 0.415429 AGGCGGAGGAGGGATATGAT 59.585 55.0 0.0 0.0 0.00 2.45 R
1671 1757 1.495584 GACGAAACTCTGCGTTGCCA 61.496 55.0 0.0 0.0 41.34 4.92 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
17 18 2.125912 CGGACTTCGGGAGCACAG 60.126 66.667 0.00 0.00 34.75 3.66
18 19 2.636412 CGGACTTCGGGAGCACAGA 61.636 63.158 0.00 0.00 34.75 3.41
19 20 1.671742 GGACTTCGGGAGCACAGAA 59.328 57.895 0.00 0.00 0.00 3.02
20 21 0.250513 GGACTTCGGGAGCACAGAAT 59.749 55.000 0.00 0.00 0.00 2.40
21 22 1.646189 GACTTCGGGAGCACAGAATC 58.354 55.000 0.00 0.00 0.00 2.52
22 23 0.250513 ACTTCGGGAGCACAGAATCC 59.749 55.000 0.00 0.00 34.64 3.01
23 24 0.250234 CTTCGGGAGCACAGAATCCA 59.750 55.000 0.00 0.00 37.33 3.41
24 25 0.911769 TTCGGGAGCACAGAATCCAT 59.088 50.000 0.00 0.00 37.33 3.41
25 26 1.788229 TCGGGAGCACAGAATCCATA 58.212 50.000 0.00 0.00 37.33 2.74
26 27 2.115427 TCGGGAGCACAGAATCCATAA 58.885 47.619 0.00 0.00 37.33 1.90
27 28 2.103094 TCGGGAGCACAGAATCCATAAG 59.897 50.000 0.00 0.00 37.33 1.73
28 29 2.808202 CGGGAGCACAGAATCCATAAGG 60.808 54.545 0.00 0.00 37.33 2.69
47 48 9.892130 CCATAAGGAACAACTTCTAGAATAAGT 57.108 33.333 5.44 0.00 36.44 2.24
51 52 9.442047 AAGGAACAACTTCTAGAATAAGTCATG 57.558 33.333 5.44 0.00 36.17 3.07
52 53 7.550906 AGGAACAACTTCTAGAATAAGTCATGC 59.449 37.037 5.44 0.00 36.17 4.06
53 54 6.893958 ACAACTTCTAGAATAAGTCATGCG 57.106 37.500 5.44 0.00 36.17 4.73
54 55 6.631016 ACAACTTCTAGAATAAGTCATGCGA 58.369 36.000 5.44 0.00 36.17 5.10
55 56 7.097192 ACAACTTCTAGAATAAGTCATGCGAA 58.903 34.615 5.44 0.00 36.17 4.70
56 57 7.602644 ACAACTTCTAGAATAAGTCATGCGAAA 59.397 33.333 5.44 0.00 36.17 3.46
57 58 8.607459 CAACTTCTAGAATAAGTCATGCGAAAT 58.393 33.333 5.44 0.00 36.17 2.17
58 59 8.359060 ACTTCTAGAATAAGTCATGCGAAATC 57.641 34.615 5.44 0.00 31.56 2.17
59 60 7.439655 ACTTCTAGAATAAGTCATGCGAAATCC 59.560 37.037 5.44 0.00 31.56 3.01
60 61 7.055667 TCTAGAATAAGTCATGCGAAATCCT 57.944 36.000 0.00 0.00 0.00 3.24
61 62 7.148641 TCTAGAATAAGTCATGCGAAATCCTC 58.851 38.462 0.00 0.00 0.00 3.71
62 63 5.674525 AGAATAAGTCATGCGAAATCCTCA 58.325 37.500 0.00 0.00 0.00 3.86
63 64 6.294473 AGAATAAGTCATGCGAAATCCTCAT 58.706 36.000 0.00 0.00 0.00 2.90
64 65 5.936686 ATAAGTCATGCGAAATCCTCATG 57.063 39.130 0.00 0.00 39.02 3.07
65 66 2.569059 AGTCATGCGAAATCCTCATGG 58.431 47.619 0.00 0.00 38.41 3.66
66 67 1.605710 GTCATGCGAAATCCTCATGGG 59.394 52.381 0.00 0.00 38.41 4.00
78 79 1.826385 CTCATGGGAGGTGACCAAAC 58.174 55.000 3.63 0.00 42.17 2.93
79 80 0.036164 TCATGGGAGGTGACCAAACG 59.964 55.000 3.63 0.00 42.17 3.60
80 81 0.960364 CATGGGAGGTGACCAAACGG 60.960 60.000 3.63 0.00 42.17 4.44
81 82 2.671963 GGGAGGTGACCAAACGGC 60.672 66.667 3.63 0.00 0.00 5.68
82 83 2.430367 GGAGGTGACCAAACGGCT 59.570 61.111 3.63 0.00 0.00 5.52
83 84 1.228154 GGAGGTGACCAAACGGCTT 60.228 57.895 3.63 0.00 0.00 4.35
84 85 0.035739 GGAGGTGACCAAACGGCTTA 59.964 55.000 3.63 0.00 0.00 3.09
85 86 1.543871 GGAGGTGACCAAACGGCTTAA 60.544 52.381 3.63 0.00 0.00 1.85
86 87 2.433436 GAGGTGACCAAACGGCTTAAT 58.567 47.619 3.63 0.00 0.00 1.40
87 88 2.418976 GAGGTGACCAAACGGCTTAATC 59.581 50.000 3.63 0.00 0.00 1.75
88 89 2.156098 GGTGACCAAACGGCTTAATCA 58.844 47.619 0.00 0.00 0.00 2.57
89 90 2.554893 GGTGACCAAACGGCTTAATCAA 59.445 45.455 0.00 0.00 0.00 2.57
90 91 3.365969 GGTGACCAAACGGCTTAATCAAG 60.366 47.826 0.00 0.00 34.66 3.02
91 92 3.500680 GTGACCAAACGGCTTAATCAAGA 59.499 43.478 0.00 0.00 33.20 3.02
92 93 4.156008 GTGACCAAACGGCTTAATCAAGAT 59.844 41.667 0.00 0.00 33.20 2.40
93 94 5.353123 GTGACCAAACGGCTTAATCAAGATA 59.647 40.000 0.00 0.00 33.20 1.98
94 95 5.353123 TGACCAAACGGCTTAATCAAGATAC 59.647 40.000 0.00 0.00 33.20 2.24
95 96 5.497474 ACCAAACGGCTTAATCAAGATACT 58.503 37.500 0.00 0.00 33.20 2.12
96 97 6.646267 ACCAAACGGCTTAATCAAGATACTA 58.354 36.000 0.00 0.00 33.20 1.82
97 98 6.537660 ACCAAACGGCTTAATCAAGATACTAC 59.462 38.462 0.00 0.00 33.20 2.73
98 99 6.537301 CCAAACGGCTTAATCAAGATACTACA 59.463 38.462 0.00 0.00 33.20 2.74
99 100 7.065324 CCAAACGGCTTAATCAAGATACTACAA 59.935 37.037 0.00 0.00 33.20 2.41
100 101 8.612619 CAAACGGCTTAATCAAGATACTACAAT 58.387 33.333 0.00 0.00 33.20 2.71
101 102 9.826574 AAACGGCTTAATCAAGATACTACAATA 57.173 29.630 0.00 0.00 33.20 1.90
102 103 9.826574 AACGGCTTAATCAAGATACTACAATAA 57.173 29.630 0.00 0.00 33.20 1.40
103 104 9.998106 ACGGCTTAATCAAGATACTACAATAAT 57.002 29.630 0.00 0.00 33.20 1.28
112 113 9.982651 TCAAGATACTACAATAATAGTGCTTCC 57.017 33.333 0.00 0.00 36.09 3.46
113 114 9.764363 CAAGATACTACAATAATAGTGCTTCCA 57.236 33.333 0.00 0.00 36.09 3.53
114 115 9.988815 AAGATACTACAATAATAGTGCTTCCAG 57.011 33.333 0.00 0.00 36.09 3.86
115 116 8.091449 AGATACTACAATAATAGTGCTTCCAGC 58.909 37.037 0.00 0.00 42.82 4.85
116 117 6.240549 ACTACAATAATAGTGCTTCCAGCT 57.759 37.500 0.00 0.00 42.97 4.24
117 118 7.361457 ACTACAATAATAGTGCTTCCAGCTA 57.639 36.000 0.00 0.00 42.97 3.32
118 119 7.437748 ACTACAATAATAGTGCTTCCAGCTAG 58.562 38.462 0.00 0.00 42.97 3.42
119 120 5.615289 ACAATAATAGTGCTTCCAGCTAGG 58.385 41.667 0.00 0.00 42.97 3.02
120 121 5.131142 ACAATAATAGTGCTTCCAGCTAGGT 59.869 40.000 0.00 0.00 42.97 3.08
121 122 3.550437 AATAGTGCTTCCAGCTAGGTG 57.450 47.619 15.13 15.13 42.97 4.00
122 123 0.537188 TAGTGCTTCCAGCTAGGTGC 59.463 55.000 16.62 5.73 42.97 5.01
131 132 4.187056 GCTAGGTGCGTCCACTTC 57.813 61.111 0.00 0.00 41.75 3.01
132 133 1.292223 GCTAGGTGCGTCCACTTCA 59.708 57.895 0.00 0.00 41.75 3.02
133 134 1.014564 GCTAGGTGCGTCCACTTCAC 61.015 60.000 0.00 0.00 41.75 3.18
134 135 0.603569 CTAGGTGCGTCCACTTCACT 59.396 55.000 0.75 0.00 41.75 3.41
135 136 0.317160 TAGGTGCGTCCACTTCACTG 59.683 55.000 0.75 0.00 41.75 3.66
136 137 1.961277 GGTGCGTCCACTTCACTGG 60.961 63.158 0.00 0.00 41.75 4.00
137 138 1.069090 GTGCGTCCACTTCACTGGA 59.931 57.895 0.00 0.00 38.93 3.86
138 139 0.531974 GTGCGTCCACTTCACTGGAA 60.532 55.000 0.00 0.00 42.22 3.53
139 140 0.531974 TGCGTCCACTTCACTGGAAC 60.532 55.000 0.00 0.00 42.22 3.62
140 141 1.228657 GCGTCCACTTCACTGGAACC 61.229 60.000 0.00 0.00 42.22 3.62
141 142 0.393077 CGTCCACTTCACTGGAACCT 59.607 55.000 0.00 0.00 42.22 3.50
142 143 1.616865 CGTCCACTTCACTGGAACCTA 59.383 52.381 0.00 0.00 42.22 3.08
143 144 2.233922 CGTCCACTTCACTGGAACCTAT 59.766 50.000 0.00 0.00 42.22 2.57
144 145 3.676324 CGTCCACTTCACTGGAACCTATC 60.676 52.174 0.00 0.00 42.22 2.08
145 146 3.515901 GTCCACTTCACTGGAACCTATCT 59.484 47.826 0.00 0.00 42.22 1.98
146 147 3.769844 TCCACTTCACTGGAACCTATCTC 59.230 47.826 0.00 0.00 37.39 2.75
147 148 3.515502 CCACTTCACTGGAACCTATCTCA 59.484 47.826 0.00 0.00 32.30 3.27
148 149 4.163078 CCACTTCACTGGAACCTATCTCAT 59.837 45.833 0.00 0.00 32.30 2.90
149 150 5.363868 CCACTTCACTGGAACCTATCTCATA 59.636 44.000 0.00 0.00 32.30 2.15
150 151 6.462207 CCACTTCACTGGAACCTATCTCATAG 60.462 46.154 0.00 0.00 32.30 2.23
151 152 6.097554 CACTTCACTGGAACCTATCTCATAGT 59.902 42.308 0.00 0.00 0.00 2.12
152 153 6.670027 ACTTCACTGGAACCTATCTCATAGTT 59.330 38.462 0.00 0.00 0.00 2.24
153 154 6.716934 TCACTGGAACCTATCTCATAGTTC 57.283 41.667 0.00 0.00 0.00 3.01
154 155 6.436027 TCACTGGAACCTATCTCATAGTTCT 58.564 40.000 0.00 0.00 0.00 3.01
155 156 6.897966 TCACTGGAACCTATCTCATAGTTCTT 59.102 38.462 0.00 0.00 0.00 2.52
156 157 6.983307 CACTGGAACCTATCTCATAGTTCTTG 59.017 42.308 0.00 0.00 0.00 3.02
157 158 6.098982 ACTGGAACCTATCTCATAGTTCTTGG 59.901 42.308 0.00 0.00 0.00 3.61
158 159 6.202331 TGGAACCTATCTCATAGTTCTTGGA 58.798 40.000 0.00 0.00 0.00 3.53
159 160 6.672218 TGGAACCTATCTCATAGTTCTTGGAA 59.328 38.462 0.00 0.00 0.00 3.53
160 161 7.147655 TGGAACCTATCTCATAGTTCTTGGAAG 60.148 40.741 0.00 0.00 0.00 3.46
161 162 7.070074 GGAACCTATCTCATAGTTCTTGGAAGA 59.930 40.741 0.00 0.00 0.00 2.87
162 163 7.979786 ACCTATCTCATAGTTCTTGGAAGAA 57.020 36.000 0.00 0.00 42.41 2.52
163 164 8.017418 ACCTATCTCATAGTTCTTGGAAGAAG 57.983 38.462 1.96 0.00 45.01 2.85
164 165 7.621683 ACCTATCTCATAGTTCTTGGAAGAAGT 59.378 37.037 12.86 12.86 45.01 3.01
165 166 8.482128 CCTATCTCATAGTTCTTGGAAGAAGTT 58.518 37.037 13.38 3.79 44.17 2.66
166 167 9.528018 CTATCTCATAGTTCTTGGAAGAAGTTC 57.472 37.037 13.38 0.00 44.17 3.01
647 710 0.249398 CCCTAACCCGTGTCTCCTTG 59.751 60.000 0.00 0.00 0.00 3.61
655 718 1.821061 CGTGTCTCCTTGCACCTCCT 61.821 60.000 0.00 0.00 32.40 3.69
678 741 2.010582 GCTCATCTTCTCGTCGGCCT 62.011 60.000 0.00 0.00 0.00 5.19
975 1054 2.399356 TTCGCGTGGTTGTGTGCAA 61.399 52.632 5.77 0.00 0.00 4.08
994 1075 3.839778 CAAACAGTTAAAGGAAGGGGGA 58.160 45.455 0.00 0.00 0.00 4.81
1085 1166 3.382832 CGAGGAGGCACCGAACCT 61.383 66.667 0.00 0.00 44.74 3.50
1120 1201 1.871772 GAAGTGAAGCTGCACGCAT 59.128 52.632 19.38 9.75 43.42 4.73
1125 1206 2.357396 AAGCTGCACGCATCGTCA 60.357 55.556 1.02 0.00 38.32 4.35
1146 1227 0.833834 CATATCCCTCCTCCGCCTGT 60.834 60.000 0.00 0.00 0.00 4.00
1151 1232 1.672356 CCTCCTCCGCCTGTTGTTG 60.672 63.158 0.00 0.00 0.00 3.33
1201 1282 0.039764 ATCCACGAGGTGAGGTCTCA 59.960 55.000 0.00 0.00 35.23 3.27
1206 1287 1.032657 CGAGGTGAGGTCTCATCCGT 61.033 60.000 7.55 0.00 41.52 4.69
1238 1319 2.883574 CTGCTTGTGTTTATGCCCATG 58.116 47.619 0.00 0.00 0.00 3.66
1293 1375 2.158295 CCTACAGCCTCTACCCACCTAT 60.158 54.545 0.00 0.00 0.00 2.57
1383 1465 2.285668 CCAGCAAGAGGGGAGGGA 60.286 66.667 0.00 0.00 0.00 4.20
1435 1517 3.660970 TCCCATATACTTTTGCCTGCA 57.339 42.857 0.00 0.00 0.00 4.41
1451 1533 3.993081 GCCTGCATCAAGTACTAGCATAG 59.007 47.826 11.15 8.21 46.50 2.23
1524 1606 8.506168 TGCTAATCATAGTTTAAGACTTTGGG 57.494 34.615 0.00 0.00 39.86 4.12
1654 1740 2.283101 TTGCATCCACCACCTGCC 60.283 61.111 0.00 0.00 35.02 4.85
1714 1800 6.261603 TCCTGCACTATATTTCTTGCTCAATG 59.738 38.462 0.00 0.00 35.91 2.82
2038 2125 5.243730 CCTTCTCTTTTTGGTTGCCTGAATA 59.756 40.000 0.00 0.00 0.00 1.75
2281 2506 8.044060 TGCTTGAATTATAGTCTTTTGTCTGG 57.956 34.615 0.00 0.00 0.00 3.86
2292 2517 7.195374 AGTCTTTTGTCTGGCCTATGTATAA 57.805 36.000 3.32 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.125912 CTGTGCTCCCGAAGTCCG 60.126 66.667 0.00 0.00 38.18 4.79
1 2 0.250513 ATTCTGTGCTCCCGAAGTCC 59.749 55.000 0.00 0.00 0.00 3.85
2 3 1.646189 GATTCTGTGCTCCCGAAGTC 58.354 55.000 0.00 0.00 0.00 3.01
3 4 0.250513 GGATTCTGTGCTCCCGAAGT 59.749 55.000 0.00 0.00 0.00 3.01
4 5 0.250234 TGGATTCTGTGCTCCCGAAG 59.750 55.000 0.00 0.00 0.00 3.79
5 6 0.911769 ATGGATTCTGTGCTCCCGAA 59.088 50.000 0.00 0.00 0.00 4.30
6 7 1.788229 TATGGATTCTGTGCTCCCGA 58.212 50.000 0.00 0.00 0.00 5.14
7 8 2.487934 CTTATGGATTCTGTGCTCCCG 58.512 52.381 0.00 0.00 0.00 5.14
8 9 2.439507 TCCTTATGGATTCTGTGCTCCC 59.560 50.000 0.00 0.00 37.46 4.30
9 10 3.845781 TCCTTATGGATTCTGTGCTCC 57.154 47.619 0.00 0.00 37.46 4.70
10 11 4.517285 TGTTCCTTATGGATTCTGTGCTC 58.483 43.478 0.00 0.00 42.81 4.26
11 12 4.574674 TGTTCCTTATGGATTCTGTGCT 57.425 40.909 0.00 0.00 42.81 4.40
12 13 4.702131 AGTTGTTCCTTATGGATTCTGTGC 59.298 41.667 0.00 0.00 42.81 4.57
13 14 6.656693 AGAAGTTGTTCCTTATGGATTCTGTG 59.343 38.462 8.80 0.00 42.81 3.66
14 15 6.784031 AGAAGTTGTTCCTTATGGATTCTGT 58.216 36.000 8.80 0.00 42.81 3.41
15 16 8.260818 TCTAGAAGTTGTTCCTTATGGATTCTG 58.739 37.037 15.65 9.14 42.81 3.02
16 17 8.380742 TCTAGAAGTTGTTCCTTATGGATTCT 57.619 34.615 12.54 12.54 42.81 2.40
17 18 9.620259 ATTCTAGAAGTTGTTCCTTATGGATTC 57.380 33.333 11.53 0.00 42.81 2.52
21 22 9.892130 ACTTATTCTAGAAGTTGTTCCTTATGG 57.108 33.333 11.53 0.00 33.25 2.74
25 26 9.442047 CATGACTTATTCTAGAAGTTGTTCCTT 57.558 33.333 11.53 0.00 37.27 3.36
26 27 7.550906 GCATGACTTATTCTAGAAGTTGTTCCT 59.449 37.037 11.53 0.00 37.27 3.36
27 28 7.464710 CGCATGACTTATTCTAGAAGTTGTTCC 60.465 40.741 11.53 0.25 37.27 3.62
28 29 7.275779 TCGCATGACTTATTCTAGAAGTTGTTC 59.724 37.037 11.53 4.48 37.27 3.18
29 30 7.097192 TCGCATGACTTATTCTAGAAGTTGTT 58.903 34.615 11.53 0.00 37.27 2.83
30 31 6.631016 TCGCATGACTTATTCTAGAAGTTGT 58.369 36.000 11.53 8.74 37.27 3.32
31 32 7.525688 TTCGCATGACTTATTCTAGAAGTTG 57.474 36.000 11.53 5.70 37.27 3.16
32 33 8.723942 ATTTCGCATGACTTATTCTAGAAGTT 57.276 30.769 11.53 0.00 37.27 2.66
33 34 7.439655 GGATTTCGCATGACTTATTCTAGAAGT 59.560 37.037 11.53 3.15 39.85 3.01
34 35 7.655328 AGGATTTCGCATGACTTATTCTAGAAG 59.345 37.037 11.53 0.00 0.00 2.85
35 36 7.500992 AGGATTTCGCATGACTTATTCTAGAA 58.499 34.615 7.82 7.82 0.00 2.10
36 37 7.055667 AGGATTTCGCATGACTTATTCTAGA 57.944 36.000 0.00 0.00 0.00 2.43
37 38 6.925718 TGAGGATTTCGCATGACTTATTCTAG 59.074 38.462 0.00 0.00 0.00 2.43
38 39 6.816136 TGAGGATTTCGCATGACTTATTCTA 58.184 36.000 0.00 0.00 0.00 2.10
39 40 5.674525 TGAGGATTTCGCATGACTTATTCT 58.325 37.500 0.00 0.00 0.00 2.40
40 41 5.991328 TGAGGATTTCGCATGACTTATTC 57.009 39.130 0.00 0.00 0.00 1.75
48 49 1.878088 CTCCCATGAGGATTTCGCATG 59.122 52.381 1.89 1.89 46.33 4.06
49 50 2.267174 CTCCCATGAGGATTTCGCAT 57.733 50.000 0.00 0.00 46.33 4.73
50 51 3.786656 CTCCCATGAGGATTTCGCA 57.213 52.632 0.00 0.00 46.33 5.10
59 60 1.826385 GTTTGGTCACCTCCCATGAG 58.174 55.000 0.00 0.00 38.42 2.90
60 61 0.036164 CGTTTGGTCACCTCCCATGA 59.964 55.000 0.00 0.00 0.00 3.07
61 62 0.960364 CCGTTTGGTCACCTCCCATG 60.960 60.000 0.00 0.00 0.00 3.66
62 63 1.378762 CCGTTTGGTCACCTCCCAT 59.621 57.895 0.00 0.00 0.00 4.00
63 64 2.833227 CCGTTTGGTCACCTCCCA 59.167 61.111 0.00 0.00 0.00 4.37
64 65 2.671963 GCCGTTTGGTCACCTCCC 60.672 66.667 0.00 0.00 37.67 4.30
65 66 0.035739 TAAGCCGTTTGGTCACCTCC 59.964 55.000 0.00 0.00 37.67 4.30
66 67 1.886886 TTAAGCCGTTTGGTCACCTC 58.113 50.000 0.00 0.00 37.67 3.85
67 68 2.224670 TGATTAAGCCGTTTGGTCACCT 60.225 45.455 0.00 0.00 37.67 4.00
68 69 2.156098 TGATTAAGCCGTTTGGTCACC 58.844 47.619 0.00 0.00 37.67 4.02
69 70 3.500680 TCTTGATTAAGCCGTTTGGTCAC 59.499 43.478 0.00 0.00 37.67 3.67
70 71 3.745799 TCTTGATTAAGCCGTTTGGTCA 58.254 40.909 0.00 0.00 37.67 4.02
71 72 4.965119 ATCTTGATTAAGCCGTTTGGTC 57.035 40.909 0.00 0.00 37.67 4.02
72 73 5.497474 AGTATCTTGATTAAGCCGTTTGGT 58.503 37.500 0.00 0.00 37.67 3.67
73 74 6.537301 TGTAGTATCTTGATTAAGCCGTTTGG 59.463 38.462 0.00 0.00 33.82 3.28
74 75 7.534085 TGTAGTATCTTGATTAAGCCGTTTG 57.466 36.000 0.00 0.00 33.82 2.93
75 76 8.732746 ATTGTAGTATCTTGATTAAGCCGTTT 57.267 30.769 0.00 0.00 33.82 3.60
76 77 9.826574 TTATTGTAGTATCTTGATTAAGCCGTT 57.173 29.630 0.00 0.00 33.82 4.44
77 78 9.998106 ATTATTGTAGTATCTTGATTAAGCCGT 57.002 29.630 0.00 0.00 33.82 5.68
86 87 9.982651 GGAAGCACTATTATTGTAGTATCTTGA 57.017 33.333 0.00 0.00 33.29 3.02
87 88 9.764363 TGGAAGCACTATTATTGTAGTATCTTG 57.236 33.333 0.00 0.00 33.29 3.02
88 89 9.988815 CTGGAAGCACTATTATTGTAGTATCTT 57.011 33.333 0.00 0.00 33.29 2.40
108 109 1.153549 GGACGCACCTAGCTGGAAG 60.154 63.158 0.00 0.00 42.61 3.46
109 110 1.911269 TGGACGCACCTAGCTGGAA 60.911 57.895 0.00 0.00 42.61 3.53
110 111 2.283604 TGGACGCACCTAGCTGGA 60.284 61.111 0.00 0.00 42.61 3.86
111 112 2.125512 GTGGACGCACCTAGCTGG 60.126 66.667 0.00 0.00 42.61 4.85
112 113 0.737715 GAAGTGGACGCACCTAGCTG 60.738 60.000 0.00 0.00 42.61 4.24
113 114 1.185618 TGAAGTGGACGCACCTAGCT 61.186 55.000 0.00 0.00 42.61 3.32
114 115 1.014564 GTGAAGTGGACGCACCTAGC 61.015 60.000 1.15 0.00 39.86 3.42
115 116 0.603569 AGTGAAGTGGACGCACCTAG 59.396 55.000 0.00 0.00 39.86 3.02
116 117 0.317160 CAGTGAAGTGGACGCACCTA 59.683 55.000 0.00 0.00 39.86 3.08
117 118 1.069765 CAGTGAAGTGGACGCACCT 59.930 57.895 0.00 0.00 39.86 4.00
118 119 1.961277 CCAGTGAAGTGGACGCACC 60.961 63.158 0.00 0.00 40.44 5.01
119 120 0.531974 TTCCAGTGAAGTGGACGCAC 60.532 55.000 6.36 0.00 46.75 5.34
120 121 0.531974 GTTCCAGTGAAGTGGACGCA 60.532 55.000 6.36 0.00 46.75 5.24
121 122 1.228657 GGTTCCAGTGAAGTGGACGC 61.229 60.000 6.36 3.40 46.75 5.19
122 123 0.393077 AGGTTCCAGTGAAGTGGACG 59.607 55.000 6.36 0.00 46.75 4.79
123 124 3.515901 AGATAGGTTCCAGTGAAGTGGAC 59.484 47.826 6.36 2.97 46.75 4.02
124 125 3.769844 GAGATAGGTTCCAGTGAAGTGGA 59.230 47.826 2.59 2.59 45.37 4.02
125 126 3.515502 TGAGATAGGTTCCAGTGAAGTGG 59.484 47.826 0.00 0.00 39.19 4.00
126 127 4.808414 TGAGATAGGTTCCAGTGAAGTG 57.192 45.455 0.00 0.00 0.00 3.16
127 128 6.198639 ACTATGAGATAGGTTCCAGTGAAGT 58.801 40.000 0.00 0.00 37.18 3.01
128 129 6.723298 ACTATGAGATAGGTTCCAGTGAAG 57.277 41.667 0.00 0.00 37.18 3.02
129 130 6.897966 AGAACTATGAGATAGGTTCCAGTGAA 59.102 38.462 0.00 0.00 37.18 3.18
130 131 6.436027 AGAACTATGAGATAGGTTCCAGTGA 58.564 40.000 0.00 0.00 37.18 3.41
131 132 6.723298 AGAACTATGAGATAGGTTCCAGTG 57.277 41.667 0.00 0.00 37.18 3.66
132 133 6.098982 CCAAGAACTATGAGATAGGTTCCAGT 59.901 42.308 0.00 0.00 37.18 4.00
133 134 6.325028 TCCAAGAACTATGAGATAGGTTCCAG 59.675 42.308 0.00 0.00 37.18 3.86
134 135 6.202331 TCCAAGAACTATGAGATAGGTTCCA 58.798 40.000 0.00 0.00 37.18 3.53
135 136 6.732896 TCCAAGAACTATGAGATAGGTTCC 57.267 41.667 0.00 0.00 37.18 3.62
136 137 8.012957 TCTTCCAAGAACTATGAGATAGGTTC 57.987 38.462 0.00 0.00 37.18 3.62
137 138 7.979786 TCTTCCAAGAACTATGAGATAGGTT 57.020 36.000 0.00 0.00 37.18 3.50
138 139 7.621683 ACTTCTTCCAAGAACTATGAGATAGGT 59.378 37.037 0.00 0.00 39.95 3.08
139 140 8.017418 ACTTCTTCCAAGAACTATGAGATAGG 57.983 38.462 0.00 0.00 39.95 2.57
140 141 9.528018 GAACTTCTTCCAAGAACTATGAGATAG 57.472 37.037 0.00 0.00 39.95 2.08
141 142 8.478877 GGAACTTCTTCCAAGAACTATGAGATA 58.521 37.037 0.00 0.00 45.11 1.98
142 143 7.334858 GGAACTTCTTCCAAGAACTATGAGAT 58.665 38.462 0.00 0.00 45.11 2.75
143 144 6.702329 GGAACTTCTTCCAAGAACTATGAGA 58.298 40.000 0.00 0.00 45.11 3.27
144 145 6.976636 GGAACTTCTTCCAAGAACTATGAG 57.023 41.667 0.00 0.00 45.11 2.90
156 157 6.360618 AGATATGATGGTTGGAACTTCTTCC 58.639 40.000 0.00 0.00 45.89 3.46
157 158 7.011857 GTGAGATATGATGGTTGGAACTTCTTC 59.988 40.741 0.00 0.00 0.00 2.87
158 159 6.825721 GTGAGATATGATGGTTGGAACTTCTT 59.174 38.462 0.00 0.00 0.00 2.52
159 160 6.157645 AGTGAGATATGATGGTTGGAACTTCT 59.842 38.462 0.00 0.00 0.00 2.85
160 161 6.352516 AGTGAGATATGATGGTTGGAACTTC 58.647 40.000 0.00 0.00 0.00 3.01
161 162 6.319048 AGTGAGATATGATGGTTGGAACTT 57.681 37.500 0.00 0.00 0.00 2.66
162 163 5.965033 AGTGAGATATGATGGTTGGAACT 57.035 39.130 0.00 0.00 0.00 3.01
163 164 6.821388 AGTAGTGAGATATGATGGTTGGAAC 58.179 40.000 0.00 0.00 0.00 3.62
164 165 7.233553 CCTAGTAGTGAGATATGATGGTTGGAA 59.766 40.741 0.00 0.00 0.00 3.53
165 166 6.721668 CCTAGTAGTGAGATATGATGGTTGGA 59.278 42.308 0.00 0.00 0.00 3.53
166 167 6.721668 TCCTAGTAGTGAGATATGATGGTTGG 59.278 42.308 0.00 0.00 0.00 3.77
167 168 7.767250 TCCTAGTAGTGAGATATGATGGTTG 57.233 40.000 0.00 0.00 0.00 3.77
168 169 8.783660 TTTCCTAGTAGTGAGATATGATGGTT 57.216 34.615 0.00 0.00 0.00 3.67
169 170 8.783660 TTTTCCTAGTAGTGAGATATGATGGT 57.216 34.615 0.00 0.00 0.00 3.55
170 171 9.703892 CTTTTTCCTAGTAGTGAGATATGATGG 57.296 37.037 0.00 0.00 0.00 3.51
171 172 9.202273 GCTTTTTCCTAGTAGTGAGATATGATG 57.798 37.037 0.00 0.00 0.00 3.07
172 173 9.153479 AGCTTTTTCCTAGTAGTGAGATATGAT 57.847 33.333 0.00 0.00 0.00 2.45
173 174 8.540507 AGCTTTTTCCTAGTAGTGAGATATGA 57.459 34.615 0.00 0.00 0.00 2.15
638 701 1.194781 GGAGGAGGTGCAAGGAGACA 61.195 60.000 0.00 0.00 0.00 3.41
647 710 1.145819 GATGAGCTGGAGGAGGTGC 59.854 63.158 0.00 0.00 30.42 5.01
655 718 0.735471 CGACGAGAAGATGAGCTGGA 59.265 55.000 0.00 0.00 0.00 3.86
975 1054 2.378886 CCTCCCCCTTCCTTTAACTGTT 59.621 50.000 0.00 0.00 0.00 3.16
994 1075 3.004951 CAGCTTCTCCATGGCCCT 58.995 61.111 6.96 0.00 0.00 5.19
1120 1201 2.808919 GGAGGAGGGATATGATGACGA 58.191 52.381 0.00 0.00 0.00 4.20
1125 1206 0.415429 AGGCGGAGGAGGGATATGAT 59.585 55.000 0.00 0.00 0.00 2.45
1151 1232 0.519077 GTACTGCACTTGCTTCCAGC 59.481 55.000 2.33 0.00 42.82 4.85
1238 1319 2.933906 TGTCGGTGAACAGAGAAACAAC 59.066 45.455 0.00 0.00 0.00 3.32
1293 1375 7.446931 TGAGCACTAAACAAACAATGAGGATTA 59.553 33.333 0.00 0.00 0.00 1.75
1383 1465 1.224039 GATGCCCTGCTCTGCTCTT 59.776 57.895 0.00 0.00 0.00 2.85
1524 1606 1.940613 AGTTGTTCTTGACTTGACCGC 59.059 47.619 0.00 0.00 0.00 5.68
1671 1757 1.495584 GACGAAACTCTGCGTTGCCA 61.496 55.000 0.00 0.00 41.34 4.92
1714 1800 5.303165 AGTACAACCTAAGCACTAACAACC 58.697 41.667 0.00 0.00 0.00 3.77
2038 2125 9.758651 GAAAATTACAGTCCAAAACCACTTTAT 57.241 29.630 0.00 0.00 0.00 1.40
2101 2326 3.220110 CATGCATCCCTTCATGTAAGCT 58.780 45.455 0.00 0.00 36.30 3.74
2222 2447 9.314321 GTAGCTTTGCTTAAGAACATGATACTA 57.686 33.333 6.67 0.00 40.44 1.82


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

AutoCloner maintained by Alex Coulton.