Multiple sequence alignment - TraesCS7D01G017900

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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 TraesCS7D01G017900 chr7D 100.000 3122 0 0 1 3122 7923403 7926524 0.000000e+00 5766
1 TraesCS7D01G017900 chr7D 92.877 2864 171 11 268 3122 8256697 8253858 0.000000e+00 4128
2 TraesCS7D01G017900 chr7D 87.276 2232 259 13 910 3122 8052766 8054991 0.000000e+00 2525
3 TraesCS7D01G017900 chr7D 86.646 2224 270 22 917 3122 7561054 7563268 0.000000e+00 2436
4 TraesCS7D01G017900 chr7D 84.887 794 117 2 2326 3119 8224728 8225518 0.000000e+00 798
5 TraesCS7D01G017900 chr7D 85.106 376 43 10 269 638 8232876 8233244 3.800000e-99 372
6 TraesCS7D01G017900 chr7D 78.555 429 68 20 268 680 8037888 8038308 8.590000e-66 261
7 TraesCS7D01G017900 chr7D 84.459 148 13 4 473 617 7749519 7749659 1.510000e-28 137
8 TraesCS7D01G017900 chr7A 92.286 2865 183 17 270 3122 8695723 8692885 0.000000e+00 4032
9 TraesCS7D01G017900 chr7A 87.281 456 47 10 451 896 8589261 8589715 7.720000e-141 510
10 TraesCS7D01G017900 chr3B 86.488 2235 269 26 910 3122 741463140 741465363 0.000000e+00 2423
11 TraesCS7D01G017900 chr3B 79.275 193 30 10 303 487 741456991 741457181 3.270000e-25 126
12 TraesCS7D01G017900 chr4A 86.215 2227 281 20 910 3122 731616869 731614655 0.000000e+00 2388
13 TraesCS7D01G017900 chr4A 85.554 2229 300 13 908 3122 731664158 731661938 0.000000e+00 2313
14 TraesCS7D01G017900 chr4A 83.661 2442 351 31 268 2684 732057925 732060343 0.000000e+00 2255
15 TraesCS7D01G017900 chr4A 84.924 2169 298 18 954 3103 731861781 731859623 0.000000e+00 2167
16 TraesCS7D01G017900 chr4A 82.374 1946 251 48 563 2442 732354415 732356334 0.000000e+00 1609
17 TraesCS7D01G017900 chr4A 89.108 964 102 3 2160 3122 731502153 731501192 0.000000e+00 1195
18 TraesCS7D01G017900 chr4A 83.659 410 39 11 364 769 732362001 732362386 8.230000e-96 361
19 TraesCS7D01G017900 chr5B 85.393 534 50 13 268 795 37481024 37481535 2.130000e-146 529
20 TraesCS7D01G017900 chr5B 90.123 243 24 0 1 243 547014089 547013847 1.810000e-82 316
21 TraesCS7D01G017900 chr5B 89.388 245 26 0 1 245 263950778 263950534 3.020000e-80 309
22 TraesCS7D01G017900 chr5B 89.583 240 25 0 1 240 665956286 665956047 3.910000e-79 305
23 TraesCS7D01G017900 chr5B 83.478 115 14 4 269 383 37479800 37479909 5.510000e-18 102
24 TraesCS7D01G017900 chr1D 90.417 240 23 0 1 240 439741236 439740997 1.810000e-82 316
25 TraesCS7D01G017900 chr2B 89.583 240 25 0 1 240 716285435 716285196 3.910000e-79 305
26 TraesCS7D01G017900 chr1B 89.076 238 26 0 8 245 622985960 622985723 2.350000e-76 296
27 TraesCS7D01G017900 chr1B 88.306 248 26 1 1 245 31226675 31226922 8.470000e-76 294
28 TraesCS7D01G017900 chrUn 88.655 238 27 0 8 245 370563893 370564130 1.100000e-74 291
29 TraesCS7D01G017900 chrUn 88.655 238 27 0 8 245 370566986 370566749 1.100000e-74 291


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 TraesCS7D01G017900 chr7D 7923403 7926524 3121 False 5766.0 5766 100.0000 1 3122 1 chr7D.!!$F3 3121
1 TraesCS7D01G017900 chr7D 8253858 8256697 2839 True 4128.0 4128 92.8770 268 3122 1 chr7D.!!$R1 2854
2 TraesCS7D01G017900 chr7D 8052766 8054991 2225 False 2525.0 2525 87.2760 910 3122 1 chr7D.!!$F5 2212
3 TraesCS7D01G017900 chr7D 7561054 7563268 2214 False 2436.0 2436 86.6460 917 3122 1 chr7D.!!$F1 2205
4 TraesCS7D01G017900 chr7D 8224728 8225518 790 False 798.0 798 84.8870 2326 3119 1 chr7D.!!$F6 793
5 TraesCS7D01G017900 chr7A 8692885 8695723 2838 True 4032.0 4032 92.2860 270 3122 1 chr7A.!!$R1 2852
6 TraesCS7D01G017900 chr3B 741463140 741465363 2223 False 2423.0 2423 86.4880 910 3122 1 chr3B.!!$F2 2212
7 TraesCS7D01G017900 chr4A 731614655 731616869 2214 True 2388.0 2388 86.2150 910 3122 1 chr4A.!!$R2 2212
8 TraesCS7D01G017900 chr4A 731661938 731664158 2220 True 2313.0 2313 85.5540 908 3122 1 chr4A.!!$R3 2214
9 TraesCS7D01G017900 chr4A 732057925 732060343 2418 False 2255.0 2255 83.6610 268 2684 1 chr4A.!!$F1 2416
10 TraesCS7D01G017900 chr4A 731859623 731861781 2158 True 2167.0 2167 84.9240 954 3103 1 chr4A.!!$R4 2149
11 TraesCS7D01G017900 chr4A 732354415 732356334 1919 False 1609.0 1609 82.3740 563 2442 1 chr4A.!!$F2 1879
12 TraesCS7D01G017900 chr4A 731501192 731502153 961 True 1195.0 1195 89.1080 2160 3122 1 chr4A.!!$R1 962
13 TraesCS7D01G017900 chr5B 37479800 37481535 1735 False 315.5 529 84.4355 268 795 2 chr5B.!!$F1 527

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
192 193 0.166814 GCGCTGTCATGGTTCTTCAC 59.833 55.000 0.0 0.0 0.0 3.18 F
639 1606 1.352352 ACAACTCCATAGCAGCCTTGT 59.648 47.619 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 2298 0.390340 CGCAGCGCCTCATATGGTAT 60.390 55.0 2.29 0.0 0.00 2.73 R
2456 3520 0.608035 TTGCATTCCCACGGAAGACC 60.608 55.0 0.00 0.0 45.48 3.85 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 4.394712 CCGAAGCCTTCCTGCCGT 62.395 66.667 0.00 0.00 0.00 5.68
18 19 2.815647 CGAAGCCTTCCTGCCGTC 60.816 66.667 0.00 0.00 0.00 4.79
19 20 2.815647 GAAGCCTTCCTGCCGTCG 60.816 66.667 0.00 0.00 0.00 5.12
53 54 3.595758 GCCACTGCGTTGCCACTT 61.596 61.111 0.00 0.00 0.00 3.16
54 55 2.332514 CCACTGCGTTGCCACTTG 59.667 61.111 0.00 0.00 0.00 3.16
55 56 2.332514 CACTGCGTTGCCACTTGG 59.667 61.111 0.00 0.00 38.53 3.61
56 57 2.906897 ACTGCGTTGCCACTTGGG 60.907 61.111 0.00 0.00 40.85 4.12
57 58 3.673484 CTGCGTTGCCACTTGGGG 61.673 66.667 0.00 0.00 37.04 4.96
65 66 2.046314 CCACTTGGGGCCGTAGTG 60.046 66.667 22.72 22.72 39.13 2.74
111 112 3.777925 CCGCGCGTCAACTTCCTG 61.778 66.667 29.95 4.86 0.00 3.86
112 113 3.036084 CGCGCGTCAACTTCCTGT 61.036 61.111 24.19 0.00 0.00 4.00
113 114 1.731613 CGCGCGTCAACTTCCTGTA 60.732 57.895 24.19 0.00 0.00 2.74
114 115 1.674611 CGCGCGTCAACTTCCTGTAG 61.675 60.000 24.19 0.00 0.00 2.74
115 116 0.666577 GCGCGTCAACTTCCTGTAGT 60.667 55.000 8.43 0.00 0.00 2.73
116 117 1.401931 GCGCGTCAACTTCCTGTAGTA 60.402 52.381 8.43 0.00 0.00 1.82
117 118 2.734492 GCGCGTCAACTTCCTGTAGTAT 60.734 50.000 8.43 0.00 0.00 2.12
118 119 2.852413 CGCGTCAACTTCCTGTAGTATG 59.148 50.000 0.00 0.00 0.00 2.39
119 120 2.603560 GCGTCAACTTCCTGTAGTATGC 59.396 50.000 0.00 0.00 0.00 3.14
120 121 2.852413 CGTCAACTTCCTGTAGTATGCG 59.148 50.000 0.00 0.00 0.00 4.73
121 122 3.672511 CGTCAACTTCCTGTAGTATGCGT 60.673 47.826 0.00 0.00 0.00 5.24
122 123 3.858238 GTCAACTTCCTGTAGTATGCGTC 59.142 47.826 0.00 0.00 0.00 5.19
123 124 2.846039 ACTTCCTGTAGTATGCGTCG 57.154 50.000 0.00 0.00 0.00 5.12
124 125 1.202268 ACTTCCTGTAGTATGCGTCGC 60.202 52.381 11.10 11.10 0.00 5.19
125 126 0.248336 TTCCTGTAGTATGCGTCGCG 60.248 55.000 13.38 0.00 0.00 5.87
180 181 3.712881 GGTGTTGGTCGCGCTGTC 61.713 66.667 5.56 0.00 0.00 3.51
185 186 3.529341 TTGGTCGCGCTGTCATGGT 62.529 57.895 5.56 0.00 0.00 3.55
186 187 2.742372 GGTCGCGCTGTCATGGTT 60.742 61.111 5.56 0.00 0.00 3.67
187 188 2.740714 GGTCGCGCTGTCATGGTTC 61.741 63.158 5.56 0.00 0.00 3.62
189 190 1.005037 TCGCGCTGTCATGGTTCTT 60.005 52.632 5.56 0.00 0.00 2.52
190 191 1.014044 TCGCGCTGTCATGGTTCTTC 61.014 55.000 5.56 0.00 0.00 2.87
191 192 1.291184 CGCGCTGTCATGGTTCTTCA 61.291 55.000 5.56 0.00 0.00 3.02
192 193 0.166814 GCGCTGTCATGGTTCTTCAC 59.833 55.000 0.00 0.00 0.00 3.18
203 204 2.608268 GGTTCTTCACCTACTTCGAGC 58.392 52.381 0.00 0.00 43.29 5.03
204 205 2.029290 GGTTCTTCACCTACTTCGAGCA 60.029 50.000 0.00 0.00 43.29 4.26
205 206 3.368531 GGTTCTTCACCTACTTCGAGCAT 60.369 47.826 0.00 0.00 43.29 3.79
206 207 3.784701 TCTTCACCTACTTCGAGCATC 57.215 47.619 0.00 0.00 0.00 3.91
227 228 2.027751 GCCGCGCTCCTAACCTAG 59.972 66.667 5.56 0.00 0.00 3.02
228 229 2.027751 CCGCGCTCCTAACCTAGC 59.972 66.667 5.56 0.00 35.33 3.42
229 230 2.027751 CGCGCTCCTAACCTAGCC 59.972 66.667 5.56 0.00 35.22 3.93
231 232 2.027751 CGCTCCTAACCTAGCCGC 59.972 66.667 0.00 0.00 35.22 6.53
232 233 2.422165 GCTCCTAACCTAGCCGCC 59.578 66.667 0.00 0.00 32.40 6.13
233 234 2.728817 CTCCTAACCTAGCCGCCG 59.271 66.667 0.00 0.00 0.00 6.46
234 235 3.501458 CTCCTAACCTAGCCGCCGC 62.501 68.421 0.00 0.00 0.00 6.53
235 236 4.603946 CCTAACCTAGCCGCCGCC 62.604 72.222 0.00 0.00 34.57 6.13
253 254 2.430367 GCCGTCAGGTGGTCCTTT 59.570 61.111 0.00 0.00 43.07 3.11
255 256 1.515521 GCCGTCAGGTGGTCCTTTTG 61.516 60.000 0.00 0.00 43.07 2.44
301 1259 7.070571 AGACCAAAATGTTTCCTTCCACAATTA 59.929 33.333 0.00 0.00 0.00 1.40
358 1320 9.265901 CTACACTGGATGGTCTTAAGAATATTG 57.734 37.037 6.78 3.10 0.00 1.90
416 1378 5.361427 CCAATGGCAATGCTAAAATGATCA 58.639 37.500 4.82 0.00 0.00 2.92
424 1386 8.505625 GGCAATGCTAAAATGATCAAAAGAAAA 58.494 29.630 4.82 0.00 0.00 2.29
446 1409 9.807649 GAAAATGTTGCATATAGGAAAACAGAT 57.192 29.630 10.50 2.40 34.50 2.90
511 1474 7.744087 TCAATAATAGTGATGTATGGTTGCC 57.256 36.000 0.00 0.00 0.00 4.52
535 1499 1.623542 AATGAGGACCACCGGTAGGC 61.624 60.000 19.28 10.19 42.76 3.93
544 1508 1.689813 CCACCGGTAGGCACATGTATA 59.310 52.381 6.87 0.00 42.76 1.47
549 1513 3.321111 CCGGTAGGCACATGTATAAGTCT 59.679 47.826 0.00 0.00 0.00 3.24
551 1515 4.982916 CGGTAGGCACATGTATAAGTCTTC 59.017 45.833 0.00 0.00 0.00 2.87
552 1516 4.982916 GGTAGGCACATGTATAAGTCTTCG 59.017 45.833 0.00 0.00 0.00 3.79
574 1541 4.623167 CGGTCAATATAGCTCTTGGATTCG 59.377 45.833 0.00 0.00 0.00 3.34
639 1606 1.352352 ACAACTCCATAGCAGCCTTGT 59.648 47.619 0.00 0.00 0.00 3.16
684 1653 2.734673 CGAAGGAACGAGCAGCAGC 61.735 63.158 0.00 0.00 42.56 5.25
778 1764 2.362077 GGCCTTGTTTTGCTCTTCTTCA 59.638 45.455 0.00 0.00 0.00 3.02
881 1896 5.221263 ACAAGAGGGCTATACACGAGTTATG 60.221 44.000 0.00 0.00 0.00 1.90
939 1969 5.063564 GGATTACGAGGTTGTTCATGTTCTC 59.936 44.000 0.00 0.00 0.00 2.87
1659 2718 5.186409 CCAACAGATCCAGAAACATTTCCAT 59.814 40.000 0.68 0.00 37.92 3.41
1929 2989 7.067129 AGCATAATAGTAGTCACAACTCGAAGA 59.933 37.037 0.00 0.00 36.92 2.87
1988 3048 4.081752 CCTCAAGCTAGAATGTCTGAGTGT 60.082 45.833 6.95 0.00 0.00 3.55
2004 3064 5.089970 TGAGTGTACAAGATTCATGGGAG 57.910 43.478 0.00 0.00 0.00 4.30
2090 3153 3.003275 AGGCGTATTGTCAATAAATGCGG 59.997 43.478 6.85 0.00 41.53 5.69
2091 3154 3.296628 GCGTATTGTCAATAAATGCGGG 58.703 45.455 6.85 0.00 41.53 6.13
2324 3387 5.907662 TGAGATGGAGAAGGATAGGTTGATT 59.092 40.000 0.00 0.00 0.00 2.57
2368 3431 6.382608 GCTTTATTCAAGAAGAGGGAACAAC 58.617 40.000 0.00 0.00 33.80 3.32
2381 3444 8.934023 AAGAGGGAACAACAGATTTAATACAA 57.066 30.769 0.00 0.00 0.00 2.41
2420 3484 2.185004 ATGAGTTGGTTTGGAGGTCG 57.815 50.000 0.00 0.00 0.00 4.79
2447 3511 5.045869 CCTCCAAGATAAGAAAGTGGTGGTA 60.046 44.000 0.00 0.00 37.94 3.25
2456 3520 6.391227 AAGAAAGTGGTGGTAAAATCTGTG 57.609 37.500 0.00 0.00 0.00 3.66
2461 3525 4.141251 AGTGGTGGTAAAATCTGTGGTCTT 60.141 41.667 0.00 0.00 0.00 3.01
2462 3526 4.215613 GTGGTGGTAAAATCTGTGGTCTTC 59.784 45.833 0.00 0.00 0.00 2.87
2468 3532 0.324943 AATCTGTGGTCTTCCGTGGG 59.675 55.000 0.00 0.00 36.30 4.61
2471 3535 0.324943 CTGTGGTCTTCCGTGGGAAT 59.675 55.000 0.00 0.00 41.23 3.01
2472 3536 0.036164 TGTGGTCTTCCGTGGGAATG 59.964 55.000 0.00 0.00 41.23 2.67
2482 3546 2.692557 TCCGTGGGAATGCAAAATATGG 59.307 45.455 0.00 0.00 0.00 2.74
2533 3597 6.954487 AATGCATGATCTAGCAAAAGATGA 57.046 33.333 14.89 0.00 44.88 2.92
2601 3665 5.810074 GCATTGTTAAAAGGTGTTTGTCACT 59.190 36.000 0.00 0.00 45.50 3.41
2606 3670 4.470334 AAAAGGTGTTTGTCACTTGCAT 57.530 36.364 0.00 0.00 45.50 3.96
2610 3674 2.098934 GGTGTTTGTCACTTGCATGTGA 59.901 45.455 26.52 26.52 45.50 3.58
2700 3764 5.008811 GCTCCTTCAGAATCATTCAAGGATG 59.991 44.000 16.11 12.31 41.42 3.51
2746 3816 6.873605 TGATACAAGGATGTTACAGAGTTGTG 59.126 38.462 14.99 2.14 41.05 3.33
2779 3849 3.367703 GCACCACTAAGAGCATTGCATTT 60.368 43.478 11.91 7.11 0.00 2.32
2864 3934 2.564504 CTCTGGGTCTGACATTGTGAGA 59.435 50.000 10.38 1.50 0.00 3.27
3021 4091 6.591935 AGTCTCAAAAGTATGTCTCCAAACA 58.408 36.000 0.00 0.00 0.00 2.83
3092 4162 2.057922 GGAGATGGCCTTGGGATAGAA 58.942 52.381 3.32 0.00 0.00 2.10
3103 4173 4.566488 CCTTGGGATAGAACAGCTCAAAGT 60.566 45.833 0.00 0.00 0.00 2.66
3109 4179 5.048434 GGATAGAACAGCTCAAAGTTTTGCT 60.048 40.000 6.96 6.96 38.05 3.91
3114 4184 6.486657 AGAACAGCTCAAAGTTTTGCTATACA 59.513 34.615 11.21 0.00 38.05 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.394712 ACGGCAGGAAGGCTTCGG 62.395 66.667 20.26 15.66 41.46 4.30
1 2 2.815647 GACGGCAGGAAGGCTTCG 60.816 66.667 20.26 11.98 41.46 3.79
2 3 2.815647 CGACGGCAGGAAGGCTTC 60.816 66.667 18.98 18.98 41.46 3.86
48 49 2.046314 CACTACGGCCCCAAGTGG 60.046 66.667 15.70 4.88 37.55 4.00
49 50 2.746277 GCACTACGGCCCCAAGTG 60.746 66.667 18.12 18.12 42.80 3.16
94 95 3.777925 CAGGAAGTTGACGCGCGG 61.778 66.667 35.22 16.31 0.00 6.46
95 96 1.674611 CTACAGGAAGTTGACGCGCG 61.675 60.000 30.96 30.96 0.00 6.86
97 98 2.624316 TACTACAGGAAGTTGACGCG 57.376 50.000 3.53 3.53 0.00 6.01
98 99 2.603560 GCATACTACAGGAAGTTGACGC 59.396 50.000 0.00 0.00 0.00 5.19
99 100 2.852413 CGCATACTACAGGAAGTTGACG 59.148 50.000 0.00 0.00 0.00 4.35
100 101 3.846360 ACGCATACTACAGGAAGTTGAC 58.154 45.455 0.00 0.00 0.00 3.18
102 103 2.852413 CGACGCATACTACAGGAAGTTG 59.148 50.000 0.00 0.00 0.00 3.16
103 104 2.734492 GCGACGCATACTACAGGAAGTT 60.734 50.000 16.42 0.00 0.00 2.66
164 165 2.317609 ATGACAGCGCGACCAACAC 61.318 57.895 12.10 0.00 0.00 3.32
165 166 2.030412 ATGACAGCGCGACCAACA 59.970 55.556 12.10 2.76 0.00 3.33
166 167 2.476051 CATGACAGCGCGACCAAC 59.524 61.111 12.10 0.00 0.00 3.77
167 168 2.741985 CCATGACAGCGCGACCAA 60.742 61.111 12.10 0.00 0.00 3.67
169 170 2.740714 GAACCATGACAGCGCGACC 61.741 63.158 12.10 0.00 0.00 4.79
170 171 1.291877 AAGAACCATGACAGCGCGAC 61.292 55.000 12.10 0.04 0.00 5.19
171 172 1.005037 AAGAACCATGACAGCGCGA 60.005 52.632 12.10 0.00 0.00 5.87
172 173 1.291184 TGAAGAACCATGACAGCGCG 61.291 55.000 0.00 0.00 0.00 6.86
173 174 0.166814 GTGAAGAACCATGACAGCGC 59.833 55.000 0.00 0.00 0.00 5.92
185 186 3.427638 CGATGCTCGAAGTAGGTGAAGAA 60.428 47.826 0.00 0.00 43.74 2.52
186 187 2.097629 CGATGCTCGAAGTAGGTGAAGA 59.902 50.000 0.00 0.00 43.74 2.87
187 188 2.455032 CGATGCTCGAAGTAGGTGAAG 58.545 52.381 0.00 0.00 43.74 3.02
189 190 0.100682 GCGATGCTCGAAGTAGGTGA 59.899 55.000 9.32 0.00 43.74 4.02
190 191 0.872021 GGCGATGCTCGAAGTAGGTG 60.872 60.000 9.32 0.00 43.74 4.00
191 192 1.437986 GGCGATGCTCGAAGTAGGT 59.562 57.895 9.32 0.00 43.74 3.08
192 193 1.658717 CGGCGATGCTCGAAGTAGG 60.659 63.158 0.00 0.00 43.74 3.18
193 194 2.296480 GCGGCGATGCTCGAAGTAG 61.296 63.158 12.98 0.00 43.74 2.57
194 195 2.278596 GCGGCGATGCTCGAAGTA 60.279 61.111 12.98 0.00 43.74 2.24
209 210 3.825833 CTAGGTTAGGAGCGCGGCG 62.826 68.421 19.62 19.62 0.00 6.46
210 211 2.027751 CTAGGTTAGGAGCGCGGC 59.972 66.667 8.83 0.00 0.00 6.53
211 212 2.027751 GCTAGGTTAGGAGCGCGG 59.972 66.667 8.83 0.00 0.00 6.46
212 213 2.027751 GGCTAGGTTAGGAGCGCG 59.972 66.667 0.00 0.00 39.72 6.86
213 214 2.027751 CGGCTAGGTTAGGAGCGC 59.972 66.667 0.00 0.00 39.72 5.92
214 215 2.027751 GCGGCTAGGTTAGGAGCG 59.972 66.667 0.00 0.00 39.72 5.03
215 216 2.422165 GGCGGCTAGGTTAGGAGC 59.578 66.667 0.00 0.00 38.00 4.70
216 217 2.728817 CGGCGGCTAGGTTAGGAG 59.271 66.667 7.61 0.00 0.00 3.69
218 219 4.603946 GGCGGCGGCTAGGTTAGG 62.604 72.222 27.22 0.00 39.81 2.69
219 220 4.944372 CGGCGGCGGCTAGGTTAG 62.944 72.222 30.65 9.91 39.81 2.34
275 276 4.285863 TGTGGAAGGAAACATTTTGGTCT 58.714 39.130 0.00 0.00 0.00 3.85
383 1345 3.194542 GCATTGCCATTGGGTTAGTACAA 59.805 43.478 4.53 0.00 36.17 2.41
386 1348 3.380471 AGCATTGCCATTGGGTTAGTA 57.620 42.857 4.70 0.00 36.17 1.82
393 1355 5.361427 TGATCATTTTAGCATTGCCATTGG 58.639 37.500 4.70 0.00 0.00 3.16
511 1474 2.999331 ACCGGTGGTCCTCATTTATTG 58.001 47.619 6.12 0.00 0.00 1.90
535 1499 8.818141 ATATTGACCGAAGACTTATACATGTG 57.182 34.615 9.11 0.00 0.00 3.21
544 1508 6.276847 CAAGAGCTATATTGACCGAAGACTT 58.723 40.000 0.00 0.00 28.67 3.01
549 1513 5.808366 ATCCAAGAGCTATATTGACCGAA 57.192 39.130 7.23 0.00 28.67 4.30
551 1515 4.623167 CGAATCCAAGAGCTATATTGACCG 59.377 45.833 7.23 2.75 28.67 4.79
552 1516 5.542779 ACGAATCCAAGAGCTATATTGACC 58.457 41.667 7.23 0.00 28.67 4.02
574 1541 6.319658 TGGAAGCAAATGGAGATAAGATCAAC 59.680 38.462 0.00 0.00 0.00 3.18
639 1606 2.420269 CCTGTGTAGGTCTCTCGCTAGA 60.420 54.545 0.00 0.00 39.39 2.43
684 1653 0.877071 ATTGGTGAAAGAGCAGCGTG 59.123 50.000 0.00 0.00 39.04 5.34
805 1817 0.958822 GTGGGGTTTTGCCTACTGTG 59.041 55.000 0.00 0.00 37.43 3.66
881 1896 3.691609 AGTTCCACAATAGCTTAGCTTGC 59.308 43.478 13.44 0.00 40.44 4.01
939 1969 6.534793 GGAAAGAAGAGAGATTAAGCACTGAG 59.465 42.308 0.00 0.00 0.00 3.35
1246 2298 0.390340 CGCAGCGCCTCATATGGTAT 60.390 55.000 2.29 0.00 0.00 2.73
1248 2300 2.280389 CGCAGCGCCTCATATGGT 60.280 61.111 2.29 0.00 0.00 3.55
1659 2718 2.226330 ACGCAGTGCCACATCTTTAAA 58.774 42.857 10.11 0.00 42.51 1.52
1929 2989 5.940617 TGCATTATAGAGGCCACTTTATGT 58.059 37.500 8.39 0.00 0.00 2.29
1988 3048 5.048083 GCAAACAACTCCCATGAATCTTGTA 60.048 40.000 0.00 0.00 0.00 2.41
2004 3064 6.073873 TGCTAAATGCTTTATGTGCAAACAAC 60.074 34.615 0.00 0.00 44.01 3.32
2120 3183 3.571401 CCTTTGAACTCAGCAATCCACTT 59.429 43.478 0.00 0.00 0.00 3.16
2121 3184 3.152341 CCTTTGAACTCAGCAATCCACT 58.848 45.455 0.00 0.00 0.00 4.00
2288 3351 3.912528 TCTCCATCTCATAATCCTTGGGG 59.087 47.826 0.00 0.00 0.00 4.96
2324 3387 2.694628 GCCATTTGCCATCCATAGTTGA 59.305 45.455 0.00 0.00 0.00 3.18
2400 3464 2.158667 ACGACCTCCAAACCAACTCATT 60.159 45.455 0.00 0.00 0.00 2.57
2420 3484 5.412904 CACCACTTTCTTATCTTGGAGGAAC 59.587 44.000 0.00 0.00 0.00 3.62
2447 3511 2.504367 CCACGGAAGACCACAGATTTT 58.496 47.619 0.00 0.00 35.59 1.82
2456 3520 0.608035 TTGCATTCCCACGGAAGACC 60.608 55.000 0.00 0.00 45.48 3.85
2461 3525 2.692557 CCATATTTTGCATTCCCACGGA 59.307 45.455 0.00 0.00 0.00 4.69
2462 3526 2.224018 CCCATATTTTGCATTCCCACGG 60.224 50.000 0.00 0.00 0.00 4.94
2468 3532 5.723295 ACAGTTGTCCCATATTTTGCATTC 58.277 37.500 0.00 0.00 0.00 2.67
2471 3535 5.714333 ACATACAGTTGTCCCATATTTTGCA 59.286 36.000 0.00 0.00 0.00 4.08
2472 3536 6.207691 ACATACAGTTGTCCCATATTTTGC 57.792 37.500 0.00 0.00 0.00 3.68
2482 3546 6.747280 GTCATGCATTTTACATACAGTTGTCC 59.253 38.462 0.00 0.00 0.00 4.02
2533 3597 6.643388 TCTATACTTGCACATTCATCTGTGT 58.357 36.000 6.13 0.00 46.59 3.72
2601 3665 1.689984 TCAGCCTTTGTCACATGCAA 58.310 45.000 0.00 0.00 0.00 4.08
2606 3670 2.942804 TCCAATTCAGCCTTTGTCACA 58.057 42.857 0.00 0.00 0.00 3.58
2610 3674 2.582052 TCGTTCCAATTCAGCCTTTGT 58.418 42.857 0.00 0.00 0.00 2.83
2709 3776 6.772716 ACATCCTTGTATCATCCGCTAAAAAT 59.227 34.615 0.00 0.00 33.16 1.82
2722 3792 6.313905 CCACAACTCTGTAACATCCTTGTATC 59.686 42.308 0.00 0.00 31.72 2.24
2746 3816 0.254747 TAGTGGTGCCAATACCTGCC 59.745 55.000 0.00 0.00 41.43 4.85
2760 3830 4.201990 GGAGAAATGCAATGCTCTTAGTGG 60.202 45.833 9.70 0.00 31.48 4.00
2779 3849 4.934797 ATGACAATTGAAGAAGGGGAGA 57.065 40.909 13.59 0.00 0.00 3.71
2864 3934 6.071221 ACAACACACATATTGAATCTGGCAAT 60.071 34.615 0.00 0.00 39.20 3.56
2897 3967 5.586243 GCAATCTATGAGCCTTAGTGTTTGA 59.414 40.000 0.00 0.00 0.00 2.69
3092 4162 6.824305 ATGTATAGCAAAACTTTGAGCTGT 57.176 33.333 6.37 7.48 40.55 4.40


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

AutoCloner maintained by Alex Coulton.