Multiple sequence alignment - TraesCS3D01G030700

Loading Multiple Alignment...

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 TraesCS3D01G030700 chr3D 100.000 3561 0 0 1 3561 11360454 11364014 0.000000e+00 6577.0
1 TraesCS3D01G030700 chr3D 85.104 1497 193 14 1032 2501 11772884 11771391 0.000000e+00 1502.0
2 TraesCS3D01G030700 chr3D 83.244 1486 228 8 1044 2513 11393252 11394732 0.000000e+00 1345.0
3 TraesCS3D01G030700 chr3D 83.028 1473 223 13 1053 2501 11370268 11371737 0.000000e+00 1310.0
4 TraesCS3D01G030700 chr3D 97.561 41 1 0 1 41 11281576 11281616 1.770000e-08 71.3
5 TraesCS3D01G030700 chr3B 95.591 3130 96 12 453 3559 16035280 16038390 0.000000e+00 4977.0
6 TraesCS3D01G030700 chr3B 96.254 2723 83 6 604 3325 25282123 25279419 0.000000e+00 4446.0
7 TraesCS3D01G030700 chr3B 83.645 1498 220 9 1034 2507 16049123 16050619 0.000000e+00 1386.0
8 TraesCS3D01G030700 chr3B 84.115 661 96 3 1053 1704 25259762 25259102 6.490000e-177 630.0
9 TraesCS3D01G030700 chr3B 84.977 426 45 6 609 1033 25283705 25283298 7.110000e-112 414.0
10 TraesCS3D01G030700 chr3B 94.595 259 11 2 3304 3559 25276577 25276319 7.160000e-107 398.0
11 TraesCS3D01G030700 chr3B 87.660 235 26 2 222 455 16035021 16035253 1.630000e-68 270.0
12 TraesCS3D01G030700 chr3A 95.715 2357 92 7 604 2958 25912038 25909689 0.000000e+00 3784.0
13 TraesCS3D01G030700 chr3A 95.681 602 19 6 2965 3561 25909651 25909052 0.000000e+00 961.0
14 TraesCS3D01G030700 chr3A 88.946 389 22 5 217 587 25913026 25912641 9.010000e-126 460.0


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 TraesCS3D01G030700 chr3D 11360454 11364014 3560 False 6577.000000 6577 100.000000 1 3561 1 chr3D.!!$F2 3560
1 TraesCS3D01G030700 chr3D 11771391 11772884 1493 True 1502.000000 1502 85.104000 1032 2501 1 chr3D.!!$R1 1469
2 TraesCS3D01G030700 chr3D 11393252 11394732 1480 False 1345.000000 1345 83.244000 1044 2513 1 chr3D.!!$F4 1469
3 TraesCS3D01G030700 chr3D 11370268 11371737 1469 False 1310.000000 1310 83.028000 1053 2501 1 chr3D.!!$F3 1448
4 TraesCS3D01G030700 chr3B 16035021 16038390 3369 False 2623.500000 4977 91.625500 222 3559 2 chr3B.!!$F2 3337
5 TraesCS3D01G030700 chr3B 25276319 25283705 7386 True 1752.666667 4446 91.942000 604 3559 3 chr3B.!!$R2 2955
6 TraesCS3D01G030700 chr3B 16049123 16050619 1496 False 1386.000000 1386 83.645000 1034 2507 1 chr3B.!!$F1 1473
7 TraesCS3D01G030700 chr3B 25259102 25259762 660 True 630.000000 630 84.115000 1053 1704 1 chr3B.!!$R1 651
8 TraesCS3D01G030700 chr3A 25909052 25913026 3974 True 1735.000000 3784 93.447333 217 3561 3 chr3A.!!$R1 3344

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
211 212 0.034337 TACGAGACTGTTGCAACCCC 59.966 55.000 26.14 14.71 0.0 4.95 F
832 1819 0.037232 GTGTGCACTACCTCCACCTC 60.037 60.000 19.41 0.00 0.0 3.85 F
1802 2801 1.679977 CACAGGGAGGGCATTGGTG 60.680 63.158 0.00 0.00 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 2130 0.177604 CTCTCGGCATGCTTCTCCTT 59.822 55.0 18.92 0.0 0.0 3.36 R
2279 3279 0.832135 TGGCTTCAGTTCGAGGAGGT 60.832 55.0 0.00 0.0 0.0 3.85 R
3139 4202 0.673644 CTTCCGGCCTTGTTGATCGT 60.674 55.0 0.00 0.0 0.0 3.73 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
24 25 7.524294 AAAAATTCACAGCAACTTGTTACTG 57.476 32.000 11.04 11.04 36.22 2.74
25 26 6.449635 AAATTCACAGCAACTTGTTACTGA 57.550 33.333 17.55 0.00 34.25 3.41
26 27 4.875544 TTCACAGCAACTTGTTACTGAC 57.124 40.909 17.55 0.00 34.25 3.51
27 28 4.137116 TCACAGCAACTTGTTACTGACT 57.863 40.909 17.55 0.00 34.25 3.41
28 29 5.270893 TCACAGCAACTTGTTACTGACTA 57.729 39.130 17.55 3.23 34.25 2.59
30 31 5.050490 CACAGCAACTTGTTACTGACTAGT 58.950 41.667 17.55 0.00 44.49 2.57
32 33 6.868864 CACAGCAACTTGTTACTGACTAGTAT 59.131 38.462 17.55 0.00 42.31 2.12
33 34 6.868864 ACAGCAACTTGTTACTGACTAGTATG 59.131 38.462 17.55 0.00 42.31 2.39
34 35 6.868864 CAGCAACTTGTTACTGACTAGTATGT 59.131 38.462 7.72 0.00 42.31 2.29
36 37 6.090898 GCAACTTGTTACTGACTAGTATGTGG 59.909 42.308 0.00 0.00 42.31 4.17
37 38 6.912951 ACTTGTTACTGACTAGTATGTGGT 57.087 37.500 0.00 0.00 41.53 4.16
40 41 7.886970 ACTTGTTACTGACTAGTATGTGGTAGA 59.113 37.037 0.00 0.00 41.53 2.59
41 42 7.860918 TGTTACTGACTAGTATGTGGTAGAG 57.139 40.000 0.00 0.00 39.08 2.43
42 43 7.627311 TGTTACTGACTAGTATGTGGTAGAGA 58.373 38.462 0.00 0.00 39.08 3.10
43 44 8.272889 TGTTACTGACTAGTATGTGGTAGAGAT 58.727 37.037 0.00 0.00 39.08 2.75
47 48 6.071320 TGACTAGTATGTGGTAGAGATGCAT 58.929 40.000 0.00 0.00 0.00 3.96
48 49 6.015940 TGACTAGTATGTGGTAGAGATGCATG 60.016 42.308 2.46 0.00 0.00 4.06
50 51 1.875009 ATGTGGTAGAGATGCATGCG 58.125 50.000 14.09 0.00 0.00 4.73
52 53 1.212616 GTGGTAGAGATGCATGCGTC 58.787 55.000 28.89 28.89 0.00 5.19
53 54 1.114627 TGGTAGAGATGCATGCGTCT 58.885 50.000 36.60 36.60 44.18 4.18
54 55 2.034685 GTGGTAGAGATGCATGCGTCTA 59.965 50.000 36.17 25.53 41.85 2.59
55 56 2.693074 TGGTAGAGATGCATGCGTCTAA 59.307 45.455 36.17 25.84 41.85 2.10
56 57 3.321968 TGGTAGAGATGCATGCGTCTAAT 59.678 43.478 36.17 29.05 41.85 1.73
57 58 4.522789 TGGTAGAGATGCATGCGTCTAATA 59.477 41.667 36.17 28.15 41.85 0.98
59 60 6.102663 GGTAGAGATGCATGCGTCTAATAAT 58.897 40.000 36.17 22.86 41.85 1.28
60 61 6.591834 GGTAGAGATGCATGCGTCTAATAATT 59.408 38.462 36.17 21.04 41.85 1.40
62 63 9.140286 GTAGAGATGCATGCGTCTAATAATTAA 57.860 33.333 36.17 16.02 41.85 1.40
63 64 8.783833 AGAGATGCATGCGTCTAATAATTAAT 57.216 30.769 36.17 15.34 41.85 1.40
85 86 7.790782 AATTAATTTTAGGTGCTTCAAGGGA 57.209 32.000 0.00 0.00 0.00 4.20
86 87 6.584185 TTAATTTTAGGTGCTTCAAGGGAC 57.416 37.500 0.00 0.00 0.00 4.46
87 88 2.178912 TTTAGGTGCTTCAAGGGACG 57.821 50.000 0.00 0.00 0.00 4.79
88 89 1.344065 TTAGGTGCTTCAAGGGACGA 58.656 50.000 0.00 0.00 0.00 4.20
89 90 1.344065 TAGGTGCTTCAAGGGACGAA 58.656 50.000 0.00 0.00 0.00 3.85
90 91 0.250338 AGGTGCTTCAAGGGACGAAC 60.250 55.000 0.00 0.00 0.00 3.95
91 92 0.250338 GGTGCTTCAAGGGACGAACT 60.250 55.000 0.00 0.00 0.00 3.01
92 93 0.868406 GTGCTTCAAGGGACGAACTG 59.132 55.000 0.00 0.00 0.00 3.16
93 94 0.884704 TGCTTCAAGGGACGAACTGC 60.885 55.000 0.00 0.00 0.00 4.40
107 108 1.732941 AACTGCGTGTTCTGTGTGAA 58.267 45.000 0.00 0.00 32.63 3.18
108 109 1.732941 ACTGCGTGTTCTGTGTGAAA 58.267 45.000 0.00 0.00 36.30 2.69
109 110 2.288666 ACTGCGTGTTCTGTGTGAAAT 58.711 42.857 0.00 0.00 36.30 2.17
110 111 3.462982 ACTGCGTGTTCTGTGTGAAATA 58.537 40.909 0.00 0.00 36.30 1.40
111 112 3.247648 ACTGCGTGTTCTGTGTGAAATAC 59.752 43.478 0.00 0.00 36.30 1.89
112 113 3.462982 TGCGTGTTCTGTGTGAAATACT 58.537 40.909 0.00 0.00 36.30 2.12
113 114 3.874543 TGCGTGTTCTGTGTGAAATACTT 59.125 39.130 0.00 0.00 36.30 2.24
115 116 4.260620 GCGTGTTCTGTGTGAAATACTTGT 60.261 41.667 0.00 0.00 36.30 3.16
117 118 5.901884 CGTGTTCTGTGTGAAATACTTGTTC 59.098 40.000 0.00 0.00 36.30 3.18
118 119 6.199393 GTGTTCTGTGTGAAATACTTGTTCC 58.801 40.000 0.00 0.00 36.30 3.62
119 120 6.038271 GTGTTCTGTGTGAAATACTTGTTCCT 59.962 38.462 0.00 0.00 36.30 3.36
121 122 5.063204 TCTGTGTGAAATACTTGTTCCTGG 58.937 41.667 0.00 0.00 0.00 4.45
123 124 3.568007 GTGTGAAATACTTGTTCCTGGCA 59.432 43.478 0.00 0.00 0.00 4.92
125 126 3.191371 GTGAAATACTTGTTCCTGGCAGG 59.809 47.826 28.01 28.01 36.46 4.85
126 127 1.839424 AATACTTGTTCCTGGCAGGC 58.161 50.000 29.02 16.17 34.61 4.85
127 128 0.698238 ATACTTGTTCCTGGCAGGCA 59.302 50.000 29.02 16.46 34.61 4.75
129 130 0.178953 ACTTGTTCCTGGCAGGCAAT 60.179 50.000 29.02 13.82 34.61 3.56
130 131 0.245539 CTTGTTCCTGGCAGGCAATG 59.754 55.000 29.02 15.91 34.61 2.82
131 132 0.178967 TTGTTCCTGGCAGGCAATGA 60.179 50.000 29.02 8.37 34.61 2.57
149 150 7.062906 GCAATGAGCATATGATCTAGTGAAG 57.937 40.000 20.84 6.24 44.79 3.02
150 151 6.649973 GCAATGAGCATATGATCTAGTGAAGT 59.350 38.462 20.84 0.00 44.79 3.01
151 152 7.148606 GCAATGAGCATATGATCTAGTGAAGTC 60.149 40.741 20.84 2.72 44.79 3.01
152 153 7.779754 ATGAGCATATGATCTAGTGAAGTCT 57.220 36.000 20.84 0.00 0.00 3.24
153 154 7.594351 TGAGCATATGATCTAGTGAAGTCTT 57.406 36.000 20.84 0.00 0.00 3.01
155 156 8.481314 TGAGCATATGATCTAGTGAAGTCTTTT 58.519 33.333 20.84 0.00 0.00 2.27
156 157 8.885494 AGCATATGATCTAGTGAAGTCTTTTC 57.115 34.615 6.97 0.00 0.00 2.29
157 158 8.703743 AGCATATGATCTAGTGAAGTCTTTTCT 58.296 33.333 6.97 0.00 0.00 2.52
158 159 8.763356 GCATATGATCTAGTGAAGTCTTTTCTG 58.237 37.037 6.97 0.00 0.00 3.02
166 167 9.155975 TCTAGTGAAGTCTTTTCTGATAATTGC 57.844 33.333 0.00 0.00 0.00 3.56
167 168 7.992754 AGTGAAGTCTTTTCTGATAATTGCT 57.007 32.000 0.00 0.00 0.00 3.91
169 170 8.940952 AGTGAAGTCTTTTCTGATAATTGCTAC 58.059 33.333 0.00 0.00 0.00 3.58
170 171 8.940952 GTGAAGTCTTTTCTGATAATTGCTACT 58.059 33.333 0.00 0.00 0.00 2.57
173 174 9.944376 AAGTCTTTTCTGATAATTGCTACTACA 57.056 29.630 0.00 0.00 0.00 2.74
181 182 9.764363 TCTGATAATTGCTACTACATTTACCAG 57.236 33.333 0.00 0.00 32.12 4.00
182 183 8.902540 TGATAATTGCTACTACATTTACCAGG 57.097 34.615 0.00 0.00 0.00 4.45
185 186 9.914834 ATAATTGCTACTACATTTACCAGGAAA 57.085 29.630 0.00 0.00 0.00 3.13
187 188 7.443259 TTGCTACTACATTTACCAGGAAAAC 57.557 36.000 0.00 0.00 0.00 2.43
188 189 6.535540 TGCTACTACATTTACCAGGAAAACA 58.464 36.000 0.00 0.00 0.00 2.83
190 191 6.653740 GCTACTACATTTACCAGGAAAACACT 59.346 38.462 0.00 0.00 0.00 3.55
192 193 6.362248 ACTACATTTACCAGGAAAACACTGT 58.638 36.000 0.00 0.00 34.16 3.55
193 194 7.511268 ACTACATTTACCAGGAAAACACTGTA 58.489 34.615 0.00 0.00 34.16 2.74
194 195 6.628919 ACATTTACCAGGAAAACACTGTAC 57.371 37.500 0.00 0.00 34.16 2.90
195 196 5.237779 ACATTTACCAGGAAAACACTGTACG 59.762 40.000 0.00 0.00 34.16 3.67
196 197 4.669206 TTACCAGGAAAACACTGTACGA 57.331 40.909 0.00 0.00 34.16 3.43
199 200 3.057734 CCAGGAAAACACTGTACGAGAC 58.942 50.000 0.00 0.00 34.16 3.36
200 201 3.243771 CCAGGAAAACACTGTACGAGACT 60.244 47.826 0.00 0.00 34.16 3.24
201 202 3.736252 CAGGAAAACACTGTACGAGACTG 59.264 47.826 0.00 0.00 0.00 3.51
202 203 3.383825 AGGAAAACACTGTACGAGACTGT 59.616 43.478 0.00 0.00 40.59 3.55
205 206 2.135664 ACACTGTACGAGACTGTTGC 57.864 50.000 0.00 0.00 38.09 4.17
206 207 1.407618 ACACTGTACGAGACTGTTGCA 59.592 47.619 0.00 0.00 38.09 4.08
207 208 2.159156 ACACTGTACGAGACTGTTGCAA 60.159 45.455 0.00 0.00 38.09 4.08
208 209 2.218759 CACTGTACGAGACTGTTGCAAC 59.781 50.000 22.83 22.83 38.09 4.17
209 210 1.792949 CTGTACGAGACTGTTGCAACC 59.207 52.381 26.14 11.44 0.00 3.77
211 212 0.034337 TACGAGACTGTTGCAACCCC 59.966 55.000 26.14 14.71 0.00 4.95
212 213 2.317609 CGAGACTGTTGCAACCCCG 61.318 63.158 26.14 16.41 0.00 5.73
214 215 0.818040 GAGACTGTTGCAACCCCGTT 60.818 55.000 26.14 8.60 0.00 4.44
275 276 6.424176 TGTAGAGTGATTTCGAGTACAGAG 57.576 41.667 0.00 0.00 0.00 3.35
278 279 6.767524 AGAGTGATTTCGAGTACAGAGAAT 57.232 37.500 0.00 0.00 0.00 2.40
280 281 7.607250 AGAGTGATTTCGAGTACAGAGAATTT 58.393 34.615 0.00 0.00 0.00 1.82
318 319 7.418337 AAGTTTGTGATTTGGAGTACCTTTT 57.582 32.000 0.00 0.00 37.04 2.27
446 448 1.531578 GAGAACTCAAGGGCGACAAAC 59.468 52.381 0.00 0.00 0.00 2.93
516 550 1.496857 TCACCCACCCATGTTCTTTGA 59.503 47.619 0.00 0.00 0.00 2.69
664 1644 1.269012 AAGTCATGCAACCCCAATGG 58.731 50.000 0.00 0.00 41.37 3.16
796 1783 6.477033 CACAACGATTTAGACCTCCTAAGATG 59.523 42.308 0.00 0.00 38.48 2.90
797 1784 5.793030 ACGATTTAGACCTCCTAAGATGG 57.207 43.478 0.00 0.00 38.48 3.51
832 1819 0.037232 GTGTGCACTACCTCCACCTC 60.037 60.000 19.41 0.00 0.00 3.85
1029 2016 3.330701 AGCATTCCCCTTCAGTTCAGTAA 59.669 43.478 0.00 0.00 0.00 2.24
1089 2076 2.662596 CGGCTGCAGGTGACCTTA 59.337 61.111 17.12 0.00 0.00 2.69
1093 2080 2.679639 CGGCTGCAGGTGACCTTATTAA 60.680 50.000 17.12 0.00 0.00 1.40
1134 2121 2.816411 TCGGGAGGTATTCAGAAGTGT 58.184 47.619 0.00 0.00 0.00 3.55
1143 2130 3.599730 ATTCAGAAGTGTCATGCTCGA 57.400 42.857 0.00 0.00 0.00 4.04
1214 2207 4.593864 GTCGAGGAGGCGGATGGC 62.594 72.222 0.00 0.00 42.51 4.40
1802 2801 1.679977 CACAGGGAGGGCATTGGTG 60.680 63.158 0.00 0.00 0.00 4.17
2279 3279 3.371034 TGCTGCTCCACTACACCTTATA 58.629 45.455 0.00 0.00 0.00 0.98
2322 3334 8.151596 CCAGGAAACTACCTAAGATAAGGATTC 58.848 40.741 0.00 0.00 40.21 2.52
2611 3643 8.992073 TCGCTATAAGTACTGATTACGATTGTA 58.008 33.333 11.38 0.00 35.61 2.41
2747 3779 3.703001 AGTAAAGTCATGGTCAGTGGG 57.297 47.619 0.00 0.00 0.00 4.61
3009 4072 8.283291 CCACATAGAGAGTTTTACACTGAAAAC 58.717 37.037 4.04 4.04 45.60 2.43
3139 4202 6.073447 TCATCATTAGTTGGGCCTTCTAAA 57.927 37.500 18.98 8.99 0.00 1.85
3266 4330 5.183713 AGTCTTAGCAATACAGCAAATGCAA 59.816 36.000 8.28 0.00 45.16 4.08
3271 4335 4.815308 AGCAATACAGCAAATGCAACAAAA 59.185 33.333 8.28 0.00 45.16 2.44
3527 7459 1.072806 GCACCATGATGCCATCTCCTA 59.927 52.381 0.00 0.00 39.86 2.94
3533 7465 2.981921 TGATGCCATCTCCTATCCTGT 58.018 47.619 6.21 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.524294 CAGTAACAAGTTGCTGTGAATTTTT 57.476 32.000 18.88 0.00 44.63 1.94
10 11 6.868864 CACATACTAGTCAGTAACAAGTTGCT 59.131 38.462 0.00 0.00 40.61 3.91
11 12 6.090898 CCACATACTAGTCAGTAACAAGTTGC 59.909 42.308 0.00 0.00 40.61 4.17
12 13 7.152645 ACCACATACTAGTCAGTAACAAGTTG 58.847 38.462 0.00 0.00 40.61 3.16
13 14 7.299246 ACCACATACTAGTCAGTAACAAGTT 57.701 36.000 0.00 0.00 40.61 2.66
15 16 8.277490 TCTACCACATACTAGTCAGTAACAAG 57.723 38.462 0.00 0.00 40.61 3.16
16 17 8.105197 TCTCTACCACATACTAGTCAGTAACAA 58.895 37.037 0.00 0.00 40.61 2.83
18 19 8.561212 CATCTCTACCACATACTAGTCAGTAAC 58.439 40.741 0.00 0.00 40.61 2.50
19 20 7.228906 GCATCTCTACCACATACTAGTCAGTAA 59.771 40.741 0.00 0.00 40.61 2.24
20 21 6.711194 GCATCTCTACCACATACTAGTCAGTA 59.289 42.308 0.00 0.00 41.47 2.74
21 22 5.533154 GCATCTCTACCACATACTAGTCAGT 59.467 44.000 0.00 0.00 38.91 3.41
23 24 5.445964 TGCATCTCTACCACATACTAGTCA 58.554 41.667 0.00 0.00 0.00 3.41
24 25 6.385843 CATGCATCTCTACCACATACTAGTC 58.614 44.000 0.00 0.00 0.00 2.59
25 26 5.279206 GCATGCATCTCTACCACATACTAGT 60.279 44.000 14.21 0.00 0.00 2.57
26 27 5.167121 GCATGCATCTCTACCACATACTAG 58.833 45.833 14.21 0.00 0.00 2.57
27 28 4.321230 CGCATGCATCTCTACCACATACTA 60.321 45.833 19.57 0.00 0.00 1.82
28 29 3.553715 CGCATGCATCTCTACCACATACT 60.554 47.826 19.57 0.00 0.00 2.12
30 31 2.365293 ACGCATGCATCTCTACCACATA 59.635 45.455 19.57 0.00 0.00 2.29
32 33 0.536724 ACGCATGCATCTCTACCACA 59.463 50.000 19.57 0.00 0.00 4.17
33 34 1.202463 AGACGCATGCATCTCTACCAC 60.202 52.381 19.57 0.00 0.00 4.16
34 35 1.114627 AGACGCATGCATCTCTACCA 58.885 50.000 19.57 0.00 0.00 3.25
36 37 7.588143 AATTATTAGACGCATGCATCTCTAC 57.412 36.000 21.16 0.79 0.00 2.59
37 38 9.875691 ATTAATTATTAGACGCATGCATCTCTA 57.124 29.630 21.16 15.06 0.00 2.43
59 60 9.315363 TCCCTTGAAGCACCTAAAATTAATTAA 57.685 29.630 0.01 0.00 0.00 1.40
60 61 8.745590 GTCCCTTGAAGCACCTAAAATTAATTA 58.254 33.333 0.01 0.00 0.00 1.40
62 63 6.127730 CGTCCCTTGAAGCACCTAAAATTAAT 60.128 38.462 0.00 0.00 0.00 1.40
63 64 5.182380 CGTCCCTTGAAGCACCTAAAATTAA 59.818 40.000 0.00 0.00 0.00 1.40
65 66 3.506067 CGTCCCTTGAAGCACCTAAAATT 59.494 43.478 0.00 0.00 0.00 1.82
66 67 3.081804 CGTCCCTTGAAGCACCTAAAAT 58.918 45.455 0.00 0.00 0.00 1.82
67 68 2.105134 TCGTCCCTTGAAGCACCTAAAA 59.895 45.455 0.00 0.00 0.00 1.52
68 69 1.695242 TCGTCCCTTGAAGCACCTAAA 59.305 47.619 0.00 0.00 0.00 1.85
70 71 1.001633 GTTCGTCCCTTGAAGCACCTA 59.998 52.381 0.00 0.00 0.00 3.08
72 73 0.250338 AGTTCGTCCCTTGAAGCACC 60.250 55.000 0.00 0.00 0.00 5.01
73 74 0.868406 CAGTTCGTCCCTTGAAGCAC 59.132 55.000 0.00 0.00 0.00 4.40
74 75 0.884704 GCAGTTCGTCCCTTGAAGCA 60.885 55.000 0.00 0.00 0.00 3.91
77 78 4.354155 CGCAGTTCGTCCCTTGAA 57.646 55.556 0.00 0.00 0.00 2.69
88 89 1.732941 TTCACACAGAACACGCAGTT 58.267 45.000 0.00 0.00 41.61 3.16
90 91 3.494626 AGTATTTCACACAGAACACGCAG 59.505 43.478 0.00 0.00 35.56 5.18
91 92 3.462982 AGTATTTCACACAGAACACGCA 58.537 40.909 0.00 0.00 35.56 5.24
92 93 4.211389 CAAGTATTTCACACAGAACACGC 58.789 43.478 0.00 0.00 35.56 5.34
93 94 5.403897 ACAAGTATTTCACACAGAACACG 57.596 39.130 0.00 0.00 35.56 4.49
94 95 6.038271 AGGAACAAGTATTTCACACAGAACAC 59.962 38.462 0.00 0.00 35.56 3.32
95 96 6.038161 CAGGAACAAGTATTTCACACAGAACA 59.962 38.462 0.00 0.00 35.56 3.18
96 97 6.430451 CAGGAACAAGTATTTCACACAGAAC 58.570 40.000 0.00 0.00 35.56 3.01
97 98 5.530915 CCAGGAACAAGTATTTCACACAGAA 59.469 40.000 0.00 0.00 0.00 3.02
98 99 5.063204 CCAGGAACAAGTATTTCACACAGA 58.937 41.667 0.00 0.00 0.00 3.41
99 100 4.320494 GCCAGGAACAAGTATTTCACACAG 60.320 45.833 0.00 0.00 0.00 3.66
100 101 3.568007 GCCAGGAACAAGTATTTCACACA 59.432 43.478 0.00 0.00 0.00 3.72
101 102 3.568007 TGCCAGGAACAAGTATTTCACAC 59.432 43.478 0.00 0.00 0.00 3.82
102 103 3.820467 CTGCCAGGAACAAGTATTTCACA 59.180 43.478 0.00 0.00 0.00 3.58
103 104 3.191371 CCTGCCAGGAACAAGTATTTCAC 59.809 47.826 4.15 0.00 37.67 3.18
104 105 3.420893 CCTGCCAGGAACAAGTATTTCA 58.579 45.455 4.15 0.00 37.67 2.69
105 106 2.164422 GCCTGCCAGGAACAAGTATTTC 59.836 50.000 16.85 0.00 37.67 2.17
107 108 1.075374 TGCCTGCCAGGAACAAGTATT 59.925 47.619 16.85 0.00 37.67 1.89
108 109 0.698238 TGCCTGCCAGGAACAAGTAT 59.302 50.000 16.85 0.00 37.67 2.12
109 110 0.476338 TTGCCTGCCAGGAACAAGTA 59.524 50.000 16.85 0.00 37.67 2.24
110 111 0.178953 ATTGCCTGCCAGGAACAAGT 60.179 50.000 16.85 0.00 37.67 3.16
111 112 0.245539 CATTGCCTGCCAGGAACAAG 59.754 55.000 16.85 1.20 37.67 3.16
112 113 0.178967 TCATTGCCTGCCAGGAACAA 60.179 50.000 16.85 10.68 37.67 2.83
113 114 0.609957 CTCATTGCCTGCCAGGAACA 60.610 55.000 16.85 0.00 37.67 3.18
115 116 1.679977 GCTCATTGCCTGCCAGGAA 60.680 57.895 16.85 0.00 37.67 3.36
117 118 0.466739 TATGCTCATTGCCTGCCAGG 60.467 55.000 6.32 6.32 42.00 4.45
118 119 1.269723 CATATGCTCATTGCCTGCCAG 59.730 52.381 0.00 0.00 42.00 4.85
119 120 1.133730 TCATATGCTCATTGCCTGCCA 60.134 47.619 0.00 0.00 42.00 4.92
121 122 3.082548 AGATCATATGCTCATTGCCTGC 58.917 45.455 9.13 0.00 42.00 4.85
123 124 5.247792 TCACTAGATCATATGCTCATTGCCT 59.752 40.000 9.13 0.00 42.00 4.75
125 126 6.649973 ACTTCACTAGATCATATGCTCATTGC 59.350 38.462 9.13 0.00 43.25 3.56
126 127 8.089597 AGACTTCACTAGATCATATGCTCATTG 58.910 37.037 9.13 3.28 0.00 2.82
127 128 8.192743 AGACTTCACTAGATCATATGCTCATT 57.807 34.615 9.13 0.00 0.00 2.57
129 130 7.594351 AAGACTTCACTAGATCATATGCTCA 57.406 36.000 9.13 0.00 0.00 4.26
130 131 8.885494 AAAAGACTTCACTAGATCATATGCTC 57.115 34.615 0.00 0.00 0.00 4.26
131 132 8.703743 AGAAAAGACTTCACTAGATCATATGCT 58.296 33.333 0.00 0.00 0.00 3.79
140 141 9.155975 GCAATTATCAGAAAAGACTTCACTAGA 57.844 33.333 0.00 0.00 0.00 2.43
141 142 9.160496 AGCAATTATCAGAAAAGACTTCACTAG 57.840 33.333 0.00 0.00 0.00 2.57
144 145 8.940952 AGTAGCAATTATCAGAAAAGACTTCAC 58.059 33.333 0.00 0.00 0.00 3.18
155 156 9.764363 CTGGTAAATGTAGTAGCAATTATCAGA 57.236 33.333 7.88 0.00 41.75 3.27
156 157 8.993121 CCTGGTAAATGTAGTAGCAATTATCAG 58.007 37.037 7.01 7.01 40.22 2.90
157 158 8.710239 TCCTGGTAAATGTAGTAGCAATTATCA 58.290 33.333 0.00 0.00 0.00 2.15
158 159 9.555727 TTCCTGGTAAATGTAGTAGCAATTATC 57.444 33.333 0.00 0.00 0.00 1.75
159 160 9.914834 TTTCCTGGTAAATGTAGTAGCAATTAT 57.085 29.630 0.00 0.00 0.00 1.28
160 161 9.742144 TTTTCCTGGTAAATGTAGTAGCAATTA 57.258 29.630 0.00 0.00 0.00 1.40
161 162 8.520351 GTTTTCCTGGTAAATGTAGTAGCAATT 58.480 33.333 1.70 0.00 0.00 2.32
162 163 7.668052 TGTTTTCCTGGTAAATGTAGTAGCAAT 59.332 33.333 1.70 0.00 0.00 3.56
163 164 6.999272 TGTTTTCCTGGTAAATGTAGTAGCAA 59.001 34.615 1.70 0.00 0.00 3.91
164 165 6.428771 GTGTTTTCCTGGTAAATGTAGTAGCA 59.571 38.462 1.70 0.00 0.00 3.49
165 166 6.653740 AGTGTTTTCCTGGTAAATGTAGTAGC 59.346 38.462 1.70 0.00 0.00 3.58
166 167 7.660208 ACAGTGTTTTCCTGGTAAATGTAGTAG 59.340 37.037 1.70 0.00 34.16 2.57
167 168 7.511268 ACAGTGTTTTCCTGGTAAATGTAGTA 58.489 34.615 1.70 0.00 34.16 1.82
168 169 6.362248 ACAGTGTTTTCCTGGTAAATGTAGT 58.638 36.000 1.70 0.00 34.16 2.73
169 170 6.877611 ACAGTGTTTTCCTGGTAAATGTAG 57.122 37.500 1.70 0.00 34.16 2.74
170 171 6.424509 CGTACAGTGTTTTCCTGGTAAATGTA 59.575 38.462 0.00 4.64 34.16 2.29
171 172 5.237779 CGTACAGTGTTTTCCTGGTAAATGT 59.762 40.000 0.00 5.50 34.16 2.71
172 173 5.467399 TCGTACAGTGTTTTCCTGGTAAATG 59.533 40.000 0.00 0.00 34.16 2.32
173 174 5.613329 TCGTACAGTGTTTTCCTGGTAAAT 58.387 37.500 0.00 0.00 34.16 1.40
174 175 5.021033 TCGTACAGTGTTTTCCTGGTAAA 57.979 39.130 0.00 0.00 34.16 2.01
175 176 4.341806 TCTCGTACAGTGTTTTCCTGGTAA 59.658 41.667 0.00 0.00 34.16 2.85
176 177 3.890756 TCTCGTACAGTGTTTTCCTGGTA 59.109 43.478 0.00 0.00 34.16 3.25
177 178 2.696707 TCTCGTACAGTGTTTTCCTGGT 59.303 45.455 0.00 0.00 34.16 4.00
179 180 3.736252 CAGTCTCGTACAGTGTTTTCCTG 59.264 47.826 0.00 0.00 36.01 3.86
180 181 3.383825 ACAGTCTCGTACAGTGTTTTCCT 59.616 43.478 0.00 0.00 0.00 3.36
181 182 3.714391 ACAGTCTCGTACAGTGTTTTCC 58.286 45.455 0.00 0.00 0.00 3.13
182 183 4.550255 GCAACAGTCTCGTACAGTGTTTTC 60.550 45.833 0.00 0.00 27.19 2.29
185 186 2.159156 TGCAACAGTCTCGTACAGTGTT 60.159 45.455 0.00 0.00 29.16 3.32
187 188 2.134201 TGCAACAGTCTCGTACAGTG 57.866 50.000 0.00 0.00 0.00 3.66
188 189 2.470821 GTTGCAACAGTCTCGTACAGT 58.529 47.619 24.52 0.00 0.00 3.55
190 191 1.539496 GGGTTGCAACAGTCTCGTACA 60.539 52.381 29.55 0.00 0.00 2.90
192 193 0.034337 GGGGTTGCAACAGTCTCGTA 59.966 55.000 29.55 0.00 0.00 3.43
193 194 1.227853 GGGGTTGCAACAGTCTCGT 60.228 57.895 29.55 0.00 0.00 4.18
194 195 2.317609 CGGGGTTGCAACAGTCTCG 61.318 63.158 29.55 20.13 0.00 4.04
195 196 0.818040 AACGGGGTTGCAACAGTCTC 60.818 55.000 29.55 12.57 0.00 3.36
196 197 0.818040 GAACGGGGTTGCAACAGTCT 60.818 55.000 29.55 15.73 0.00 3.24
199 200 1.654220 CTGAACGGGGTTGCAACAG 59.346 57.895 29.55 21.33 0.00 3.16
200 201 1.826054 CCTGAACGGGGTTGCAACA 60.826 57.895 29.55 7.66 0.00 3.33
201 202 0.893727 ATCCTGAACGGGGTTGCAAC 60.894 55.000 21.59 21.59 0.00 4.17
202 203 0.893270 CATCCTGAACGGGGTTGCAA 60.893 55.000 0.00 0.00 0.00 4.08
205 206 1.382522 CATCATCCTGAACGGGGTTG 58.617 55.000 0.00 0.00 0.00 3.77
206 207 0.255890 CCATCATCCTGAACGGGGTT 59.744 55.000 0.00 0.00 0.00 4.11
207 208 0.914417 ACCATCATCCTGAACGGGGT 60.914 55.000 0.00 0.00 29.94 4.95
208 209 0.464373 CACCATCATCCTGAACGGGG 60.464 60.000 0.00 0.00 29.94 5.73
209 210 1.097547 GCACCATCATCCTGAACGGG 61.098 60.000 0.00 0.00 29.94 5.28
211 212 0.740868 ACGCACCATCATCCTGAACG 60.741 55.000 0.00 0.00 0.00 3.95
212 213 0.729116 CACGCACCATCATCCTGAAC 59.271 55.000 0.00 0.00 0.00 3.18
214 215 1.450134 GCACGCACCATCATCCTGA 60.450 57.895 0.00 0.00 0.00 3.86
223 224 0.179070 TGTAGAACAAGCACGCACCA 60.179 50.000 0.00 0.00 0.00 4.17
284 285 9.748708 CTCCAAATCACAAACTTTCTATTGAAA 57.251 29.630 2.38 2.38 39.59 2.69
318 319 2.183300 GTAGATGCGCGACCACCA 59.817 61.111 12.10 0.00 0.00 4.17
446 448 2.061773 GCGTCATGATGGTAGAATCGG 58.938 52.381 16.59 0.00 0.00 4.18
516 550 3.245016 TGAGTTGGGATGAGTTGCTGAAT 60.245 43.478 0.00 0.00 0.00 2.57
664 1644 1.343465 TCGGTTGACTGAAGGTCTTCC 59.657 52.381 8.09 0.00 44.74 3.46
707 1687 8.696374 ACAGTCTACATAGTACAATATGTTGCT 58.304 33.333 11.69 9.07 42.40 3.91
765 1752 2.930682 GGTCTAAATCGTTGTGGAGCTC 59.069 50.000 4.71 4.71 0.00 4.09
832 1819 5.533528 TGATGAGGAATCAATGGTTAGCATG 59.466 40.000 0.00 0.00 42.49 4.06
913 1900 7.229907 TGTTGTTGAGATAGATGCATGCATTAT 59.770 33.333 32.60 27.12 36.70 1.28
914 1901 6.543100 TGTTGTTGAGATAGATGCATGCATTA 59.457 34.615 32.60 24.29 36.70 1.90
915 1902 5.358725 TGTTGTTGAGATAGATGCATGCATT 59.641 36.000 32.60 23.11 36.70 3.56
952 1939 4.283722 ACCTTGTAGACTTCAGGTTTCGAT 59.716 41.667 0.00 0.00 0.00 3.59
965 1952 5.956642 TGTTTTGGTTTTCACCTTGTAGAC 58.043 37.500 0.00 0.00 44.61 2.59
1029 2016 2.373169 TGAGAACTTTGGGCTGAGTGAT 59.627 45.455 0.00 0.00 0.00 3.06
1093 2080 5.645497 CCGATCAAAAAGGAGAAGAATCTGT 59.355 40.000 0.00 0.00 35.54 3.41
1134 2121 0.897621 TGCTTCTCCTTCGAGCATGA 59.102 50.000 0.00 0.00 41.15 3.07
1143 2130 0.177604 CTCTCGGCATGCTTCTCCTT 59.822 55.000 18.92 0.00 0.00 3.36
1434 2430 3.340814 CAAGGCATCTTGTAGGTCACT 57.659 47.619 0.00 0.00 43.92 3.41
1802 2801 7.262048 TGACCTCTGAAACAAATTTAACAACC 58.738 34.615 0.00 0.00 0.00 3.77
2279 3279 0.832135 TGGCTTCAGTTCGAGGAGGT 60.832 55.000 0.00 0.00 0.00 3.85
2322 3334 4.321899 GGAGGGATTCTCAATGATCTCTCG 60.322 50.000 6.24 0.00 44.19 4.04
2611 3643 6.857956 TGTATGCAACACACACTTTAACTTT 58.142 32.000 0.00 0.00 31.43 2.66
2738 3770 2.363038 GTGTTTTTAACCCCCACTGACC 59.637 50.000 0.00 0.00 0.00 4.02
2747 3779 9.549078 TTGATTGGAATTTAGTGTTTTTAACCC 57.451 29.630 0.00 0.00 0.00 4.11
2792 3824 4.697352 AGTTATCTGGTGTGAACTGCAATC 59.303 41.667 0.00 0.00 31.05 2.67
3009 4072 6.457392 CCACAAACTAGATCATGGAATTGTCG 60.457 42.308 0.00 0.00 0.00 4.35
3012 4075 6.764308 ACCACAAACTAGATCATGGAATTG 57.236 37.500 12.66 0.00 0.00 2.32
3139 4202 0.673644 CTTCCGGCCTTGTTGATCGT 60.674 55.000 0.00 0.00 0.00 3.73
3212 4275 2.098280 CCATTGTTGTCGTTGTTGTGGA 59.902 45.455 0.00 0.00 0.00 4.02
3266 4330 1.550072 AGTTTGCTGCCACACTTTTGT 59.450 42.857 0.00 0.00 35.84 2.83
3271 4335 2.586425 ACATTAGTTTGCTGCCACACT 58.414 42.857 0.00 0.00 36.12 3.55
3533 7465 4.043310 ACATTTCCTGGAGGTGAATCTTCA 59.957 41.667 14.82 0.00 36.34 3.02


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

AutoCloner maintained by Alex Coulton.