Multiple sequence alignment - TraesCS5B01G385000

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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 TraesCS5B01G385000 chr5B 100.000 1888 0 0 930 2817 563605624 563607511 0.000000e+00 3487.0
1 TraesCS5B01G385000 chr5B 100.000 537 0 0 1 537 563604695 563605231 0.000000e+00 992.0
2 TraesCS5B01G385000 chr5B 88.333 240 21 4 2064 2297 563606693 563606931 5.940000e-72 281.0
3 TraesCS5B01G385000 chr5B 88.333 240 21 4 1999 2237 563606758 563606991 5.940000e-72 281.0
4 TraesCS5B01G385000 chr5B 72.554 368 86 15 1140 1501 619855210 619854852 3.840000e-19 106.0
5 TraesCS5B01G385000 chr5A 94.486 1324 49 14 930 2237 578955912 578957227 0.000000e+00 2019.0
6 TraesCS5B01G385000 chr5A 85.636 550 30 17 2064 2594 578956976 578957495 1.490000e-147 532.0
7 TraesCS5B01G385000 chr5A 94.273 227 10 2 2593 2816 578958077 578958303 7.470000e-91 344.0
8 TraesCS5B01G385000 chr5A 86.268 284 16 9 254 537 578955539 578955799 1.280000e-73 287.0
9 TraesCS5B01G385000 chr5A 73.260 273 60 12 1165 1432 623493378 623493114 1.390000e-13 87.9
10 TraesCS5B01G385000 chr5D 91.977 1371 84 16 930 2297 459339883 459341230 0.000000e+00 1899.0
11 TraesCS5B01G385000 chr5D 85.992 514 48 16 1659 2149 459341458 459341970 1.920000e-146 529.0
12 TraesCS5B01G385000 chr5D 87.857 420 37 2 2061 2479 459341053 459341459 5.460000e-132 481.0
13 TraesCS5B01G385000 chr5D 84.112 535 43 18 2 533 459338999 459339494 1.960000e-131 479.0
14 TraesCS5B01G385000 chr5D 87.083 240 25 3 1999 2237 459341056 459341290 1.660000e-67 267.0
15 TraesCS5B01G385000 chr5D 83.088 136 11 5 2644 2768 215301994 215302128 2.290000e-21 113.0
16 TraesCS5B01G385000 chr5D 72.951 366 80 18 1140 1497 499226597 499226243 2.970000e-20 110.0
17 TraesCS5B01G385000 chr1D 94.649 1084 45 7 994 2074 208819886 208818813 0.000000e+00 1668.0
18 TraesCS5B01G385000 chr1D 96.512 86 3 0 994 1079 208818688 208818773 2.930000e-30 143.0
19 TraesCS5B01G385000 chr6A 88.119 101 11 1 2677 2777 411770306 411770405 4.930000e-23 119.0
20 TraesCS5B01G385000 chr6B 86.667 105 13 1 2677 2781 530129063 530128960 6.380000e-22 115.0
21 TraesCS5B01G385000 chr4A 81.646 158 12 7 2633 2777 565304093 565304246 6.380000e-22 115.0
22 TraesCS5B01G385000 chrUn 88.889 90 9 1 2677 2766 126680577 126680489 2.970000e-20 110.0
23 TraesCS5B01G385000 chr1A 84.404 109 16 1 2677 2785 395177548 395177441 3.840000e-19 106.0
24 TraesCS5B01G385000 chr6D 84.615 104 14 2 2679 2781 289027578 289027680 4.960000e-18 102.0
25 TraesCS5B01G385000 chr2B 83.810 105 15 2 2677 2780 403097799 403097902 6.420000e-17 99.0
26 TraesCS5B01G385000 chr4B 83.099 71 11 1 61 131 16812785 16812716 2.340000e-06 63.9


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 TraesCS5B01G385000 chr5B 563604695 563607511 2816 False 1260.25 3487 94.16650 1 2817 4 chr5B.!!$F1 2816
1 TraesCS5B01G385000 chr5A 578955539 578958303 2764 False 795.50 2019 90.16575 254 2816 4 chr5A.!!$F1 2562
2 TraesCS5B01G385000 chr5D 459338999 459341970 2971 False 731.00 1899 87.40420 2 2479 5 chr5D.!!$F2 2477
3 TraesCS5B01G385000 chr1D 208818813 208819886 1073 True 1668.00 1668 94.64900 994 2074 1 chr1D.!!$R1 1080

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
188 191 0.107897 TCGTGGAAACAGCACACAGT 60.108 50.0 0.0 0.0 44.46 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2176 0.599558 CAGGATTGCTGTGTTGGTGG 59.4 55.0 0.0 0.0 0.0 4.61 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
22 23 1.470098 CCTGCTCCGGATCAAAACAAG 59.530 52.381 3.57 0.00 0.00 3.16
23 24 2.154462 CTGCTCCGGATCAAAACAAGT 58.846 47.619 3.57 0.00 0.00 3.16
27 28 3.146066 CTCCGGATCAAAACAAGTTGGA 58.854 45.455 3.57 0.00 0.00 3.53
28 29 3.146066 TCCGGATCAAAACAAGTTGGAG 58.854 45.455 0.00 0.00 0.00 3.86
29 30 3.146066 CCGGATCAAAACAAGTTGGAGA 58.854 45.455 7.96 0.00 0.00 3.71
35 36 7.326063 CGGATCAAAACAAGTTGGAGAATTTAC 59.674 37.037 7.96 0.00 0.00 2.01
45 46 5.838521 AGTTGGAGAATTTACCACAACCATT 59.161 36.000 0.00 0.00 39.06 3.16
46 47 7.007723 AGTTGGAGAATTTACCACAACCATTA 58.992 34.615 0.00 0.00 39.06 1.90
47 48 6.827586 TGGAGAATTTACCACAACCATTAC 57.172 37.500 1.26 0.00 0.00 1.89
51 52 8.456471 GGAGAATTTACCACAACCATTACTAAC 58.544 37.037 0.00 0.00 0.00 2.34
94 95 6.542574 TCAGTTAATTAACGAAAAGCCGAA 57.457 33.333 19.92 0.00 40.96 4.30
95 96 7.136289 TCAGTTAATTAACGAAAAGCCGAAT 57.864 32.000 19.92 0.00 40.96 3.34
96 97 7.018826 TCAGTTAATTAACGAAAAGCCGAATG 58.981 34.615 19.92 10.05 40.96 2.67
107 108 3.575965 AAGCCGAATGAAAACCATCAC 57.424 42.857 0.00 0.00 33.53 3.06
108 109 2.513753 AGCCGAATGAAAACCATCACA 58.486 42.857 0.00 0.00 33.53 3.58
110 111 3.320541 AGCCGAATGAAAACCATCACAAA 59.679 39.130 0.00 0.00 33.53 2.83
112 113 4.509600 GCCGAATGAAAACCATCACAAAAA 59.490 37.500 0.00 0.00 33.53 1.94
131 134 4.131376 GCTGAGCGGCACACATAT 57.869 55.556 1.45 0.00 0.00 1.78
132 135 3.289128 GCTGAGCGGCACACATATA 57.711 52.632 1.45 0.00 0.00 0.86
133 136 1.581934 GCTGAGCGGCACACATATAA 58.418 50.000 1.45 0.00 0.00 0.98
134 137 2.146342 GCTGAGCGGCACACATATAAT 58.854 47.619 1.45 0.00 0.00 1.28
135 138 3.325870 GCTGAGCGGCACACATATAATA 58.674 45.455 1.45 0.00 0.00 0.98
145 148 7.644551 GCGGCACACATATAATAGTAGTATCTC 59.355 40.741 0.00 0.00 0.00 2.75
146 149 8.674607 CGGCACACATATAATAGTAGTATCTCA 58.325 37.037 0.00 0.00 0.00 3.27
159 162 7.304497 AGTAGTATCTCACAAACACCTTTCT 57.696 36.000 0.00 0.00 0.00 2.52
163 166 5.757850 ATCTCACAAACACCTTTCTCAAC 57.242 39.130 0.00 0.00 0.00 3.18
173 176 1.151668 CTTTCTCAACAGGCCTCGTG 58.848 55.000 0.00 3.59 0.00 4.35
176 179 1.118965 TCTCAACAGGCCTCGTGGAA 61.119 55.000 0.00 0.00 34.57 3.53
186 189 0.813610 CCTCGTGGAAACAGCACACA 60.814 55.000 0.00 0.00 44.46 3.72
188 191 0.107897 TCGTGGAAACAGCACACAGT 60.108 50.000 0.00 0.00 44.46 3.55
199 202 1.151668 GCACACAGTCTTCATCGCTT 58.848 50.000 0.00 0.00 0.00 4.68
227 230 2.057137 TGGAGCAAACTTCAGCAAGT 57.943 45.000 0.00 0.00 45.43 3.16
229 232 2.878406 TGGAGCAAACTTCAGCAAGTAC 59.122 45.455 0.00 0.00 42.45 2.73
230 233 2.226674 GGAGCAAACTTCAGCAAGTACC 59.773 50.000 0.00 0.00 42.45 3.34
231 234 2.226674 GAGCAAACTTCAGCAAGTACCC 59.773 50.000 0.00 0.00 42.45 3.69
232 235 1.953686 GCAAACTTCAGCAAGTACCCA 59.046 47.619 0.00 0.00 42.45 4.51
233 236 2.030805 GCAAACTTCAGCAAGTACCCAG 60.031 50.000 0.00 0.00 42.45 4.45
234 237 1.897560 AACTTCAGCAAGTACCCAGC 58.102 50.000 0.00 0.00 42.45 4.85
235 238 0.764890 ACTTCAGCAAGTACCCAGCA 59.235 50.000 4.85 0.00 41.39 4.41
236 239 1.142870 ACTTCAGCAAGTACCCAGCAA 59.857 47.619 4.85 0.00 41.39 3.91
238 241 0.764890 TCAGCAAGTACCCAGCAAGT 59.235 50.000 4.85 0.00 0.00 3.16
239 242 1.974957 TCAGCAAGTACCCAGCAAGTA 59.025 47.619 4.85 0.00 0.00 2.24
240 243 2.571653 TCAGCAAGTACCCAGCAAGTAT 59.428 45.455 4.85 0.00 0.00 2.12
241 244 3.772572 TCAGCAAGTACCCAGCAAGTATA 59.227 43.478 4.85 0.00 0.00 1.47
242 245 3.871594 CAGCAAGTACCCAGCAAGTATAC 59.128 47.826 0.00 0.00 0.00 1.47
250 253 4.840271 ACCCAGCAAGTATACTACAAACC 58.160 43.478 5.65 0.00 0.00 3.27
251 254 4.287585 ACCCAGCAAGTATACTACAAACCA 59.712 41.667 5.65 0.00 0.00 3.67
273 276 3.943691 AGTTTGCCCGGCCGTGTA 61.944 61.111 26.12 10.04 0.00 2.90
297 305 4.460731 TGTCAACACGATCTCTTCTCATCT 59.539 41.667 0.00 0.00 0.00 2.90
298 306 5.034152 GTCAACACGATCTCTTCTCATCTC 58.966 45.833 0.00 0.00 0.00 2.75
299 307 4.702131 TCAACACGATCTCTTCTCATCTCA 59.298 41.667 0.00 0.00 0.00 3.27
300 308 5.359292 TCAACACGATCTCTTCTCATCTCAT 59.641 40.000 0.00 0.00 0.00 2.90
301 309 5.437289 ACACGATCTCTTCTCATCTCATC 57.563 43.478 0.00 0.00 0.00 2.92
314 322 3.317430 TCATCTCATCATCTGACGACCAG 59.683 47.826 0.00 0.00 44.27 4.00
321 329 1.949847 ATCTGACGACCAGCGGAAGG 61.950 60.000 1.50 0.00 46.49 3.46
337 345 1.761500 AAGGGCGGACACGGTACTTT 61.761 55.000 0.00 0.00 41.36 2.66
342 350 1.562575 CGGACACGGTACTTTGCCAC 61.563 60.000 0.00 0.00 36.18 5.01
343 351 1.232621 GGACACGGTACTTTGCCACC 61.233 60.000 0.00 0.00 0.00 4.61
357 365 1.067250 CCACCAAGCAAAACCCACG 59.933 57.895 0.00 0.00 0.00 4.94
378 386 4.658786 ACGGCACCTTCCTCCCCT 62.659 66.667 0.00 0.00 0.00 4.79
380 388 3.412408 GGCACCTTCCTCCCCTCC 61.412 72.222 0.00 0.00 0.00 4.30
381 389 3.412408 GCACCTTCCTCCCCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
382 390 2.692741 CACCTTCCTCCCCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
383 391 2.882143 ACCTTCCTCCCCTCCCCT 60.882 66.667 0.00 0.00 0.00 4.79
384 392 2.040359 CCTTCCTCCCCTCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
385 393 2.040359 CTTCCTCCCCTCCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
386 394 3.707189 TTCCTCCCCTCCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
389 397 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
453 461 2.047830 ACCCCACCTCGATTCCTATTC 58.952 52.381 0.00 0.00 0.00 1.75
454 462 1.348036 CCCCACCTCGATTCCTATTCC 59.652 57.143 0.00 0.00 0.00 3.01
455 463 2.330216 CCCACCTCGATTCCTATTCCT 58.670 52.381 0.00 0.00 0.00 3.36
456 464 2.300437 CCCACCTCGATTCCTATTCCTC 59.700 54.545 0.00 0.00 0.00 3.71
457 465 2.300437 CCACCTCGATTCCTATTCCTCC 59.700 54.545 0.00 0.00 0.00 4.30
458 466 3.235200 CACCTCGATTCCTATTCCTCCT 58.765 50.000 0.00 0.00 0.00 3.69
459 467 3.257127 CACCTCGATTCCTATTCCTCCTC 59.743 52.174 0.00 0.00 0.00 3.71
460 468 3.141272 ACCTCGATTCCTATTCCTCCTCT 59.859 47.826 0.00 0.00 0.00 3.69
461 469 3.761752 CCTCGATTCCTATTCCTCCTCTC 59.238 52.174 0.00 0.00 0.00 3.20
462 470 3.761752 CTCGATTCCTATTCCTCCTCTCC 59.238 52.174 0.00 0.00 0.00 3.71
494 510 0.701310 ACCACTTTCCCCCAACCTCT 60.701 55.000 0.00 0.00 0.00 3.69
1140 1159 4.856607 GAGGTCTTCCGCTCGCCG 62.857 72.222 0.00 0.00 39.05 6.46
1617 1636 3.381272 CCTATGTCCGCATTGGTTGATTT 59.619 43.478 0.00 0.00 41.17 2.17
1618 1637 3.959535 ATGTCCGCATTGGTTGATTTT 57.040 38.095 0.00 0.00 39.52 1.82
1729 1749 6.015504 GCAATTCTGTTTCATATATACGGCG 58.984 40.000 4.80 4.80 0.00 6.46
1731 1751 3.239254 TCTGTTTCATATATACGGCGCG 58.761 45.455 6.90 0.00 0.00 6.86
1737 1757 3.208594 TCATATATACGGCGCGGTATCT 58.791 45.455 34.90 28.61 34.96 1.98
1766 1786 2.355132 TCGTGTGTTGGCGTGTAAAAAT 59.645 40.909 0.00 0.00 0.00 1.82
1786 1808 7.573968 AAAATACTAGATTGGCTTGTGATCC 57.426 36.000 0.00 0.00 34.43 3.36
1885 1907 8.673711 GTGTAAAGCTGTTATGTTGATAATGGA 58.326 33.333 0.00 0.00 0.00 3.41
1930 1952 7.377928 CACTATAGTTTGCTGCAAATGCTAATC 59.622 37.037 28.21 14.76 42.66 1.75
2026 2050 6.484643 TGTTTCTAGATCTTAGATTGCCATGC 59.515 38.462 0.00 0.00 0.00 4.06
2102 2172 4.839121 AGATTGCCATGACAATGCAAAAT 58.161 34.783 12.33 7.56 40.31 1.82
2118 2188 2.995258 CAAAATATGCCACCAACACAGC 59.005 45.455 0.00 0.00 0.00 4.40
2119 2189 1.921982 AATATGCCACCAACACAGCA 58.078 45.000 0.00 0.00 40.00 4.41
2120 2190 1.921982 ATATGCCACCAACACAGCAA 58.078 45.000 0.00 0.00 38.99 3.91
2123 2194 1.290009 GCCACCAACACAGCAATCC 59.710 57.895 0.00 0.00 0.00 3.01
2138 2209 2.877168 GCAATCCTGTGCTTCTAGATGG 59.123 50.000 7.66 0.00 41.51 3.51
2149 2220 4.061596 GCTTCTAGATGGTAGATTGCCAC 58.938 47.826 7.66 0.00 39.03 5.01
2150 2221 4.443457 GCTTCTAGATGGTAGATTGCCACA 60.443 45.833 7.66 0.00 39.03 4.17
2151 2222 4.944619 TCTAGATGGTAGATTGCCACAG 57.055 45.455 0.00 0.00 39.03 3.66
2209 2280 2.515926 TCTAGATGGCAGATTGCGAC 57.484 50.000 0.00 0.00 46.21 5.19
2225 2296 1.202132 GCGACGGCAATGCAAAAGATA 60.202 47.619 7.79 0.00 39.62 1.98
2260 2336 3.567478 ATCCTGTGTTTCTAGATGGCC 57.433 47.619 0.00 0.00 0.00 5.36
2298 2374 6.343716 TGCAAAAGATACCATCAACACATT 57.656 33.333 0.00 0.00 0.00 2.71
2309 2385 4.853196 CCATCAACACATTTGCTCGTTTAG 59.147 41.667 0.00 0.00 0.00 1.85
2311 2387 5.493133 TCAACACATTTGCTCGTTTAGTT 57.507 34.783 0.00 0.00 0.00 2.24
2317 2393 7.699566 ACACATTTGCTCGTTTAGTTTCTTTA 58.300 30.769 0.00 0.00 0.00 1.85
2408 2484 0.735632 CTTGACTGAGCAGAGACGCC 60.736 60.000 4.21 0.00 0.00 5.68
2414 2490 4.087892 AGCAGAGACGCCGGCAAT 62.088 61.111 28.98 14.60 0.00 3.56
2426 2502 1.648720 CGGCAATGGGCTTATGACG 59.351 57.895 0.00 0.00 44.01 4.35
2459 2535 0.692419 CTCCTGTACCCATCCTGCCT 60.692 60.000 0.00 0.00 0.00 4.75
2521 2597 0.846015 TGATGATACCCAAGGCCCAG 59.154 55.000 0.00 0.00 0.00 4.45
2660 3323 7.316393 TCCCCTGGTTCACTATTATAAGATG 57.684 40.000 0.00 0.00 0.00 2.90
2816 3481 8.590204 TGACCTTCAACTCATAGTAACATGTAA 58.410 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.202879 TGTTTTGATCCGGAGCAGGTT 60.203 47.619 23.31 0.00 0.00 3.50
12 13 7.926018 GTGGTAAATTCTCCAACTTGTTTTGAT 59.074 33.333 3.59 0.00 35.38 2.57
22 23 5.722021 ATGGTTGTGGTAAATTCTCCAAC 57.278 39.130 3.59 0.00 35.38 3.77
23 24 7.007723 AGTAATGGTTGTGGTAAATTCTCCAA 58.992 34.615 3.59 0.00 35.38 3.53
72 73 7.018826 TCATTCGGCTTTTCGTTAATTAACTG 58.981 34.615 22.57 16.63 34.12 3.16
74 75 7.784790 TTCATTCGGCTTTTCGTTAATTAAC 57.215 32.000 16.87 16.87 0.00 2.01
77 78 6.144886 GGTTTTCATTCGGCTTTTCGTTAATT 59.855 34.615 0.00 0.00 0.00 1.40
94 95 4.507388 CAGCGTTTTTGTGATGGTTTTCAT 59.493 37.500 0.00 0.00 39.13 2.57
95 96 3.862267 CAGCGTTTTTGTGATGGTTTTCA 59.138 39.130 0.00 0.00 0.00 2.69
96 97 4.109050 TCAGCGTTTTTGTGATGGTTTTC 58.891 39.130 0.00 0.00 0.00 2.29
132 135 9.654663 GAAAGGTGTTTGTGAGATACTACTATT 57.345 33.333 0.00 0.00 0.00 1.73
133 136 9.036980 AGAAAGGTGTTTGTGAGATACTACTAT 57.963 33.333 0.00 0.00 0.00 2.12
134 137 8.418597 AGAAAGGTGTTTGTGAGATACTACTA 57.581 34.615 0.00 0.00 0.00 1.82
135 138 7.015292 TGAGAAAGGTGTTTGTGAGATACTACT 59.985 37.037 0.00 0.00 0.00 2.57
145 148 3.734902 GCCTGTTGAGAAAGGTGTTTGTG 60.735 47.826 0.00 0.00 35.86 3.33
146 149 2.427095 GCCTGTTGAGAAAGGTGTTTGT 59.573 45.455 0.00 0.00 35.86 2.83
159 162 0.534203 GTTTCCACGAGGCCTGTTGA 60.534 55.000 12.00 7.53 33.74 3.18
163 166 2.328099 GCTGTTTCCACGAGGCCTG 61.328 63.158 12.00 5.11 33.74 4.85
173 176 2.288666 TGAAGACTGTGTGCTGTTTCC 58.711 47.619 0.00 0.00 0.00 3.13
176 179 2.138320 CGATGAAGACTGTGTGCTGTT 58.862 47.619 0.00 0.00 0.00 3.16
199 202 1.065600 GTTTGCTCCAAACGCTGCA 59.934 52.632 0.00 0.00 42.97 4.41
221 224 3.775316 AGTATACTTGCTGGGTACTTGCT 59.225 43.478 0.00 0.00 0.00 3.91
227 230 5.484644 TGGTTTGTAGTATACTTGCTGGGTA 59.515 40.000 11.40 0.00 43.54 3.69
229 232 4.839121 TGGTTTGTAGTATACTTGCTGGG 58.161 43.478 11.40 0.00 43.54 4.45
230 233 6.202954 GCTATGGTTTGTAGTATACTTGCTGG 59.797 42.308 11.40 0.00 43.54 4.85
231 234 6.761242 TGCTATGGTTTGTAGTATACTTGCTG 59.239 38.462 11.40 0.00 43.54 4.41
232 235 6.884832 TGCTATGGTTTGTAGTATACTTGCT 58.115 36.000 11.40 0.00 43.54 3.91
233 236 6.761714 ACTGCTATGGTTTGTAGTATACTTGC 59.238 38.462 11.40 5.51 43.54 4.01
234 237 8.718102 AACTGCTATGGTTTGTAGTATACTTG 57.282 34.615 11.40 0.00 43.54 3.16
235 238 9.162764 CAAACTGCTATGGTTTGTAGTATACTT 57.837 33.333 11.40 0.00 44.66 2.24
236 239 8.718102 CAAACTGCTATGGTTTGTAGTATACT 57.282 34.615 10.87 10.87 44.66 2.12
250 253 2.774799 GGCCGGGCAAACTGCTATG 61.775 63.158 25.33 0.00 44.28 2.23
251 254 2.440247 GGCCGGGCAAACTGCTAT 60.440 61.111 25.33 0.00 44.28 2.97
273 276 4.790765 TGAGAAGAGATCGTGTTGACAT 57.209 40.909 0.00 0.00 0.00 3.06
297 305 0.101219 CGCTGGTCGTCAGATGATGA 59.899 55.000 11.52 0.54 46.18 2.92
298 306 0.873312 CCGCTGGTCGTCAGATGATG 60.873 60.000 11.52 0.00 46.18 3.07
299 307 1.037579 TCCGCTGGTCGTCAGATGAT 61.038 55.000 11.52 0.00 46.18 2.45
300 308 1.248101 TTCCGCTGGTCGTCAGATGA 61.248 55.000 11.52 0.00 46.18 2.92
301 309 0.803768 CTTCCGCTGGTCGTCAGATG 60.804 60.000 11.52 4.30 46.18 2.90
321 329 2.674084 GCAAAGTACCGTGTCCGCC 61.674 63.158 0.00 0.00 0.00 6.13
337 345 1.687146 TGGGTTTTGCTTGGTGGCA 60.687 52.632 0.00 0.00 40.74 4.92
342 350 1.008995 CGACGTGGGTTTTGCTTGG 60.009 57.895 0.00 0.00 0.00 3.61
343 351 0.316689 GTCGACGTGGGTTTTGCTTG 60.317 55.000 0.00 0.00 0.00 4.01
357 365 2.126031 GAGGAAGGTGCCGTCGAC 60.126 66.667 5.18 5.18 0.00 4.20
378 386 2.446337 ATTTGTGGGAGGGGAGGGGA 62.446 60.000 0.00 0.00 0.00 4.81
380 388 0.846693 CTATTTGTGGGAGGGGAGGG 59.153 60.000 0.00 0.00 0.00 4.30
381 389 0.183731 GCTATTTGTGGGAGGGGAGG 59.816 60.000 0.00 0.00 0.00 4.30
382 390 0.183731 GGCTATTTGTGGGAGGGGAG 59.816 60.000 0.00 0.00 0.00 4.30
383 391 1.632018 CGGCTATTTGTGGGAGGGGA 61.632 60.000 0.00 0.00 0.00 4.81
384 392 1.152963 CGGCTATTTGTGGGAGGGG 60.153 63.158 0.00 0.00 0.00 4.79
385 393 1.152963 CCGGCTATTTGTGGGAGGG 60.153 63.158 0.00 0.00 0.00 4.30
386 394 0.463833 GTCCGGCTATTTGTGGGAGG 60.464 60.000 0.00 0.00 0.00 4.30
387 395 0.810031 CGTCCGGCTATTTGTGGGAG 60.810 60.000 0.00 0.00 0.00 4.30
388 396 1.219664 CGTCCGGCTATTTGTGGGA 59.780 57.895 0.00 0.00 0.00 4.37
389 397 1.817941 CCGTCCGGCTATTTGTGGG 60.818 63.158 0.00 0.00 0.00 4.61
453 461 1.074850 GGGAGGAAGGGAGAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
454 462 1.074850 GGGGAGGAAGGGAGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
455 463 2.647949 GGGGGAGGAAGGGAGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
456 464 2.040359 GGGGGAGGAAGGGAGAGG 60.040 72.222 0.00 0.00 0.00 3.69
494 510 2.308722 GGTGGAATCTGGCTGGGGA 61.309 63.158 0.00 0.00 0.00 4.81
1518 1537 1.216710 CTCCTGCTCGGTGAGGAAC 59.783 63.158 0.00 0.00 37.93 3.62
1617 1636 2.186160 CACCACGCCAGACTGCAAA 61.186 57.895 0.00 0.00 0.00 3.68
1618 1637 2.591429 CACCACGCCAGACTGCAA 60.591 61.111 0.00 0.00 0.00 4.08
1729 1749 3.000925 CACACGAACCAATAAGATACCGC 59.999 47.826 0.00 0.00 0.00 5.68
1731 1751 5.163794 CCAACACACGAACCAATAAGATACC 60.164 44.000 0.00 0.00 0.00 2.73
1737 1757 1.264557 CGCCAACACACGAACCAATAA 59.735 47.619 0.00 0.00 0.00 1.40
1766 1786 6.265649 GTCTAGGATCACAAGCCAATCTAGTA 59.734 42.308 0.00 0.00 31.46 1.82
1848 1870 5.220710 ACAGCTTTACACTCAGTTCAGAT 57.779 39.130 0.00 0.00 0.00 2.90
1885 1907 7.893124 ATAGTGAAGAATCAGATGGCAATTT 57.107 32.000 0.00 0.00 35.88 1.82
1896 1918 6.172630 TGCAGCAAACTATAGTGAAGAATCA 58.827 36.000 6.06 0.00 0.00 2.57
1930 1952 3.362831 GCGAATTGCACAAGAACATCAAG 59.637 43.478 0.00 0.00 45.45 3.02
2053 2077 8.948631 TCATCTAGAAACACAGGAAATGTATC 57.051 34.615 0.00 0.00 41.41 2.24
2102 2172 1.818060 GATTGCTGTGTTGGTGGCATA 59.182 47.619 0.00 0.00 34.59 3.14
2106 2176 0.599558 CAGGATTGCTGTGTTGGTGG 59.400 55.000 0.00 0.00 0.00 4.61
2117 2187 2.877168 CCATCTAGAAGCACAGGATTGC 59.123 50.000 0.00 0.00 43.34 3.56
2118 2188 4.148128 ACCATCTAGAAGCACAGGATTG 57.852 45.455 0.00 0.00 0.00 2.67
2119 2189 5.211973 TCTACCATCTAGAAGCACAGGATT 58.788 41.667 0.00 0.00 0.00 3.01
2120 2190 4.809193 TCTACCATCTAGAAGCACAGGAT 58.191 43.478 0.00 0.00 0.00 3.24
2123 2194 4.749099 GCAATCTACCATCTAGAAGCACAG 59.251 45.833 0.00 0.00 32.51 3.66
2128 2199 5.282055 TGTGGCAATCTACCATCTAGAAG 57.718 43.478 0.00 0.00 39.95 2.85
2131 2202 3.181462 TGCTGTGGCAATCTACCATCTAG 60.181 47.826 0.00 0.00 46.36 2.43
2133 2204 1.561076 TGCTGTGGCAATCTACCATCT 59.439 47.619 0.00 0.00 46.36 2.90
2157 2228 2.746269 CTGTGTTGGTGGCATCTTTTG 58.254 47.619 0.00 0.00 0.00 2.44
2209 2280 2.937469 TGGTATCTTTTGCATTGCCG 57.063 45.000 6.12 0.00 0.00 5.69
2225 2296 2.165167 CAGGATTGCTGTGTTGATGGT 58.835 47.619 0.00 0.00 0.00 3.55
2298 2374 9.834628 CCATTAATAAAGAAACTAAACGAGCAA 57.165 29.630 0.00 0.00 0.00 3.91
2317 2393 7.817418 ACAGCGGTCATTATAAACCATTAAT 57.183 32.000 7.05 0.00 35.13 1.40
2408 2484 1.648720 CGTCATAAGCCCATTGCCG 59.351 57.895 0.00 0.00 42.71 5.69
2422 2498 1.218047 GCACTGATACTGGCCGTCA 59.782 57.895 0.00 0.00 0.00 4.35
2426 2502 2.216148 AGGAGCACTGATACTGGCC 58.784 57.895 0.00 0.00 0.00 5.36
2459 2535 7.490079 CACAAATAACCAATACAGACGTAGCTA 59.510 37.037 0.00 0.00 0.00 3.32
2596 3258 4.631813 GCCAACAGACAAACCACTAGATAG 59.368 45.833 0.00 0.00 0.00 2.08
2603 3265 1.102978 ACAGCCAACAGACAAACCAC 58.897 50.000 0.00 0.00 0.00 4.16
2635 3298 7.349859 ACATCTTATAATAGTGAACCAGGGGAA 59.650 37.037 0.00 0.00 0.00 3.97
2771 3436 4.498345 GGTCAGAAGCCAATCTAGTACTCG 60.498 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.