Multiple sequence alignment - TraesCS3A01G225600

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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 TraesCS3A01G225600 chr3A 100.000 2656 0 0 1 2656 423128565 423131220 0.000000e+00 4905.0
1 TraesCS3A01G225600 chr3A 85.526 76 10 1 2258 2333 725162408 725162334 7.880000e-11 78.7
2 TraesCS3A01G225600 chr3A 85.526 76 10 1 2258 2333 725177801 725177727 7.880000e-11 78.7
3 TraesCS3A01G225600 chr3B 91.803 1830 111 14 1 1810 411451168 411452978 0.000000e+00 2512.0
4 TraesCS3A01G225600 chr3B 94.853 136 6 1 1846 1981 411453071 411453205 7.450000e-51 211.0
5 TraesCS3A01G225600 chr3B 76.068 234 49 6 2427 2656 758622476 758622246 6.010000e-22 115.0
6 TraesCS3A01G225600 chr3B 85.714 105 15 0 2552 2656 679528368 679528264 7.770000e-21 111.0
7 TraesCS3A01G225600 chr3D 91.502 1824 98 13 1 1810 309774583 309772803 0.000000e+00 2457.0
8 TraesCS3A01G225600 chr3D 84.770 847 87 23 1831 2656 309772625 309771800 0.000000e+00 811.0
9 TraesCS3A01G225600 chr3D 84.615 286 41 3 265 549 5769211 5768928 5.600000e-72 281.0
10 TraesCS3A01G225600 chr3D 91.935 62 5 0 2267 2328 490847034 490846973 1.310000e-13 87.9
11 TraesCS3A01G225600 chr5D 83.818 550 86 3 1 549 504022804 504022257 1.090000e-143 520.0
12 TraesCS3A01G225600 chr5D 78.912 147 28 3 2512 2656 565787392 565787247 2.180000e-16 97.1
13 TraesCS3A01G225600 chr4D 81.509 530 94 4 1 530 421890355 421890880 1.460000e-117 433.0
14 TraesCS3A01G225600 chr4D 81.098 492 91 2 56 547 59085763 59086252 2.480000e-105 392.0
15 TraesCS3A01G225600 chr5A 78.881 554 90 19 1 549 29187580 29188111 1.510000e-92 350.0
16 TraesCS3A01G225600 chr5A 82.317 164 27 1 2492 2653 671440722 671440885 9.910000e-30 141.0
17 TraesCS3A01G225600 chr5A 73.765 324 47 15 2206 2491 661218381 661218058 2.820000e-15 93.5
18 TraesCS3A01G225600 chr5A 86.111 72 10 0 2418 2489 563357834 563357905 7.880000e-11 78.7
19 TraesCS3A01G225600 chr4A 81.728 405 66 4 1 405 706425935 706426331 5.480000e-87 331.0
20 TraesCS3A01G225600 chr2B 77.679 560 103 16 1 548 443268000 443267451 3.300000e-84 322.0
21 TraesCS3A01G225600 chr2B 85.870 92 7 4 2234 2319 263825985 263825894 2.820000e-15 93.5
22 TraesCS3A01G225600 chr7D 83.784 333 48 5 217 549 263837178 263837504 7.140000e-81 311.0
23 TraesCS3A01G225600 chr7D 72.545 499 89 21 1 493 571235237 571234781 4.640000e-23 119.0
24 TraesCS3A01G225600 chr7D 88.608 79 9 0 2410 2488 524308250 524308328 2.180000e-16 97.1
25 TraesCS3A01G225600 chr4B 84.713 314 39 8 242 549 23672933 23672623 3.320000e-79 305.0
26 TraesCS3A01G225600 chr6B 80.288 416 63 9 1 416 531788285 531787889 2.000000e-76 296.0
27 TraesCS3A01G225600 chr6B 89.535 86 7 2 2407 2490 8599922 8599837 1.010000e-19 108.0
28 TraesCS3A01G225600 chr6B 91.935 62 5 0 2427 2488 492019419 492019358 1.310000e-13 87.9
29 TraesCS3A01G225600 chr7A 78.838 241 42 8 2419 2656 491983610 491983844 1.270000e-33 154.0
30 TraesCS3A01G225600 chr7A 88.889 54 6 0 2396 2449 547715221 547715168 1.710000e-07 67.6
31 TraesCS3A01G225600 chr1A 87.121 132 14 2 2524 2653 132123199 132123069 2.130000e-31 147.0
32 TraesCS3A01G225600 chr1A 83.465 127 21 0 2520 2646 57745124 57745250 4.640000e-23 119.0
33 TraesCS3A01G225600 chr7B 93.939 66 4 0 2258 2323 663687510 663687575 1.680000e-17 100.0
34 TraesCS3A01G225600 chr7B 92.308 65 5 0 2259 2323 663655293 663655357 2.820000e-15 93.5
35 TraesCS3A01G225600 chr7B 92.308 65 5 0 2259 2323 663709762 663709826 2.820000e-15 93.5
36 TraesCS3A01G225600 chr7B 80.531 113 16 6 2207 2317 664090297 664090405 6.090000e-12 82.4
37 TraesCS3A01G225600 chr7B 84.746 59 9 0 2354 2412 747619709 747619651 2.860000e-05 60.2
38 TraesCS3A01G225600 chr2A 77.922 154 26 5 2345 2490 694338784 694338631 3.640000e-14 89.8
39 TraesCS3A01G225600 chr5B 87.671 73 9 0 2419 2491 707065267 707065195 4.710000e-13 86.1
40 TraesCS3A01G225600 chr6A 90.476 63 6 0 2427 2489 548240435 548240497 1.690000e-12 84.2
41 TraesCS3A01G225600 chrUn 85.526 76 10 1 2258 2333 455757595 455757521 7.880000e-11 78.7
42 TraesCS3A01G225600 chr1B 83.721 86 8 4 2234 2313 50361684 50361599 2.840000e-10 76.8


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 TraesCS3A01G225600 chr3A 423128565 423131220 2655 False 4905.0 4905 100.000 1 2656 1 chr3A.!!$F1 2655
1 TraesCS3A01G225600 chr3B 411451168 411453205 2037 False 1361.5 2512 93.328 1 1981 2 chr3B.!!$F1 1980
2 TraesCS3A01G225600 chr3D 309771800 309774583 2783 True 1634.0 2457 88.136 1 2656 2 chr3D.!!$R3 2655
3 TraesCS3A01G225600 chr5D 504022257 504022804 547 True 520.0 520 83.818 1 549 1 chr5D.!!$R1 548
4 TraesCS3A01G225600 chr4D 421890355 421890880 525 False 433.0 433 81.509 1 530 1 chr4D.!!$F2 529
5 TraesCS3A01G225600 chr5A 29187580 29188111 531 False 350.0 350 78.881 1 549 1 chr5A.!!$F1 548
6 TraesCS3A01G225600 chr2B 443267451 443268000 549 True 322.0 322 77.679 1 548 1 chr2B.!!$R2 547

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
636 671 0.107703 TTTGGAGCGGCTGTAGATGG 60.108 55.0 7.5 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2675 0.030638 GCCTCTCGTGCAAGCAAAAA 59.969 50.0 0.0 0.0 0.0 1.94 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
68 73 1.586154 CGCCGAAAGAATGCCAAGGT 61.586 55.000 0.00 0.00 0.00 3.50
80 85 1.985159 TGCCAAGGTACTCCAGATTGT 59.015 47.619 0.00 0.00 38.49 2.71
90 95 4.025040 ACTCCAGATTGTCATTGAGCAA 57.975 40.909 4.80 4.80 0.00 3.91
149 166 1.150827 CTCAAGACGCAGCATGACAA 58.849 50.000 0.00 0.00 39.69 3.18
170 187 4.043168 CGTCTGGCGGTTGAAAGT 57.957 55.556 0.00 0.00 36.85 2.66
174 191 0.394938 TCTGGCGGTTGAAAGTGCTA 59.605 50.000 0.00 0.00 0.00 3.49
193 210 1.700042 AATCATCCTCTCCGGCACCC 61.700 60.000 0.00 0.00 0.00 4.61
207 227 2.362120 ACCCCCGACGACGAAGAT 60.362 61.111 9.28 0.00 42.66 2.40
288 308 3.637273 GCCGGTGACAGGAAGGGT 61.637 66.667 5.79 0.00 0.00 4.34
341 361 3.793559 CCGTCTCCGTCTTTAATTCCAT 58.206 45.455 0.00 0.00 0.00 3.41
409 429 3.066203 ACGTGAACTTTGGCGATCTTTTT 59.934 39.130 0.00 0.00 0.00 1.94
434 454 5.989477 AGATCCGTTGGTGATCTTTTGATA 58.011 37.500 0.00 0.00 45.07 2.15
438 458 6.414732 TCCGTTGGTGATCTTTTGATAATCT 58.585 36.000 0.00 0.00 39.67 2.40
552 582 4.698780 CCGGATATAAGATACACGGACAGA 59.301 45.833 0.00 0.00 42.19 3.41
563 593 3.964909 ACACGGACAGAATTTGAAAAGC 58.035 40.909 0.00 0.00 0.00 3.51
565 595 2.616842 ACGGACAGAATTTGAAAAGCGT 59.383 40.909 0.00 0.00 0.00 5.07
567 597 3.058914 CGGACAGAATTTGAAAAGCGTCT 60.059 43.478 0.00 0.00 0.00 4.18
621 656 0.811281 GTTTGAGGGCTCGGATTTGG 59.189 55.000 0.00 0.00 0.00 3.28
636 671 0.107703 TTTGGAGCGGCTGTAGATGG 60.108 55.000 7.50 0.00 0.00 3.51
660 695 6.961554 GGTGTAACAATCAGATCATTCGAAAC 59.038 38.462 0.00 0.00 39.98 2.78
677 712 1.475403 AACACTCGATGGACCGATCT 58.525 50.000 0.00 0.00 37.96 2.75
730 765 1.133025 GCATTGCACATGGTACCACTC 59.867 52.381 19.09 7.14 0.00 3.51
790 825 2.574929 GCCCCATGCACACACATG 59.425 61.111 0.00 0.00 45.74 3.21
991 1031 1.106285 GTTGATTCCATCCAGCCACC 58.894 55.000 0.00 0.00 0.00 4.61
992 1032 0.703488 TTGATTCCATCCAGCCACCA 59.297 50.000 0.00 0.00 0.00 4.17
993 1033 0.703488 TGATTCCATCCAGCCACCAA 59.297 50.000 0.00 0.00 0.00 3.67
994 1034 1.341285 TGATTCCATCCAGCCACCAAG 60.341 52.381 0.00 0.00 0.00 3.61
1084 1124 3.151022 GGGACGCAGGAGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
1085 1125 3.151022 GGACGCAGGAGGAGGAGG 61.151 72.222 0.00 0.00 0.00 4.30
1086 1126 2.043852 GACGCAGGAGGAGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
1087 1127 2.043450 ACGCAGGAGGAGGAGGAG 60.043 66.667 0.00 0.00 0.00 3.69
1088 1128 2.837291 CGCAGGAGGAGGAGGAGG 60.837 72.222 0.00 0.00 0.00 4.30
1089 1129 2.693017 GCAGGAGGAGGAGGAGGA 59.307 66.667 0.00 0.00 0.00 3.71
1206 1246 1.134367 CGGGTCTCGTTCAAGAGCATA 59.866 52.381 5.58 0.00 43.89 3.14
1240 1280 4.363990 CGCTCCACAGCCACGTCT 62.364 66.667 0.00 0.00 43.56 4.18
1323 1363 0.387750 ACGGAAAGTTCGTACGCTCC 60.388 55.000 11.24 9.78 39.22 4.70
1652 1692 2.785713 CCACGTTTCGGGATTTGTTT 57.214 45.000 0.00 0.00 28.17 2.83
1658 1698 4.142337 ACGTTTCGGGATTTGTTTTGAACT 60.142 37.500 0.00 0.00 0.00 3.01
1695 1735 0.766131 TTTGCCCGACCTTACCTTCA 59.234 50.000 0.00 0.00 0.00 3.02
1696 1736 0.988832 TTGCCCGACCTTACCTTCAT 59.011 50.000 0.00 0.00 0.00 2.57
1704 1748 1.271926 ACCTTACCTTCATGTGGGTGC 60.272 52.381 17.90 0.00 37.07 5.01
1708 1752 1.331214 ACCTTCATGTGGGTGCAAAG 58.669 50.000 10.57 0.00 34.16 2.77
1794 1838 4.142730 ACTCTCGCATTCTTTTCTGCATTC 60.143 41.667 0.00 0.00 38.30 2.67
1812 1856 7.571080 TGCATTCTCTGAACATATGCATTAA 57.429 32.000 3.54 0.00 44.59 1.40
1813 1857 7.420002 TGCATTCTCTGAACATATGCATTAAC 58.580 34.615 3.54 0.00 44.59 2.01
1814 1858 6.576313 GCATTCTCTGAACATATGCATTAACG 59.424 38.462 3.54 0.00 40.86 3.18
1815 1859 7.633621 CATTCTCTGAACATATGCATTAACGT 58.366 34.615 3.54 0.00 0.00 3.99
1816 1860 7.609760 TTCTCTGAACATATGCATTAACGTT 57.390 32.000 3.54 5.88 0.00 3.99
1817 1861 8.710835 TTCTCTGAACATATGCATTAACGTTA 57.289 30.769 3.54 3.29 0.00 3.18
1819 1863 7.979537 TCTCTGAACATATGCATTAACGTTACT 59.020 33.333 7.70 0.00 0.00 2.24
1820 1864 8.487313 TCTGAACATATGCATTAACGTTACTT 57.513 30.769 7.70 0.00 0.00 2.24
1821 1865 8.600625 TCTGAACATATGCATTAACGTTACTTC 58.399 33.333 7.70 0.00 0.00 3.01
1824 1868 7.246674 ACATATGCATTAACGTTACTTCCTG 57.753 36.000 7.70 3.19 0.00 3.86
1825 1869 4.616181 ATGCATTAACGTTACTTCCTGC 57.384 40.909 7.70 12.05 0.00 4.85
1826 1870 3.403968 TGCATTAACGTTACTTCCTGCA 58.596 40.909 7.70 14.24 36.15 4.41
1827 1871 3.815962 TGCATTAACGTTACTTCCTGCAA 59.184 39.130 18.45 2.60 35.63 4.08
1828 1872 4.156182 GCATTAACGTTACTTCCTGCAAC 58.844 43.478 7.70 0.00 0.00 4.17
1829 1873 4.319911 GCATTAACGTTACTTCCTGCAACA 60.320 41.667 7.70 0.00 0.00 3.33
1831 1875 6.378582 CATTAACGTTACTTCCTGCAACAAT 58.621 36.000 7.70 0.00 0.00 2.71
1832 1876 4.483476 AACGTTACTTCCTGCAACAATC 57.517 40.909 0.00 0.00 0.00 2.67
1833 1877 3.740115 ACGTTACTTCCTGCAACAATCT 58.260 40.909 0.00 0.00 0.00 2.40
1834 1878 4.890088 ACGTTACTTCCTGCAACAATCTA 58.110 39.130 0.00 0.00 0.00 1.98
1835 1879 4.929808 ACGTTACTTCCTGCAACAATCTAG 59.070 41.667 0.00 0.00 0.00 2.43
1843 2048 8.860088 ACTTCCTGCAACAATCTAGTAATTTTT 58.140 29.630 0.00 0.00 0.00 1.94
1879 2084 3.196254 CCCAGCCATCTAGTTGCAAAATT 59.804 43.478 0.00 0.00 0.00 1.82
1886 2091 5.870978 CCATCTAGTTGCAAAATTTTCCCTG 59.129 40.000 0.00 0.00 0.00 4.45
1981 2187 0.251787 GCCTTTCACTTGGGATGGGT 60.252 55.000 0.00 0.00 0.00 4.51
1985 2191 2.286365 TTCACTTGGGATGGGTTGAC 57.714 50.000 0.00 0.00 0.00 3.18
1987 2193 1.496857 TCACTTGGGATGGGTTGACAA 59.503 47.619 0.00 0.00 0.00 3.18
1990 2196 1.175983 TTGGGATGGGTTGACAACGC 61.176 55.000 24.26 24.26 43.88 4.84
1992 2198 1.964373 GGATGGGTTGACAACGCGT 60.964 57.895 25.17 25.17 46.27 6.01
2021 2227 0.603707 CTCAGTCACCGCCATGTGTT 60.604 55.000 0.00 0.00 37.51 3.32
2026 2232 0.322008 TCACCGCCATGTGTTGCATA 60.322 50.000 0.00 0.00 37.51 3.14
2027 2233 0.099259 CACCGCCATGTGTTGCATAG 59.901 55.000 0.00 0.00 35.74 2.23
2029 2235 1.065782 ACCGCCATGTGTTGCATAGTA 60.066 47.619 0.00 0.00 35.74 1.82
2034 2240 2.279741 CATGTGTTGCATAGTAGGCGT 58.720 47.619 1.88 0.00 35.74 5.68
2042 2248 3.006940 TGCATAGTAGGCGTTTCCTTTG 58.993 45.455 1.88 0.00 44.75 2.77
2114 2321 4.388378 TTCGATTTTTCCGGTTTTTGGT 57.612 36.364 0.00 0.00 0.00 3.67
2150 2357 5.612725 TTCTCAGCTTTTGGACCAATTTT 57.387 34.783 7.99 0.00 0.00 1.82
2151 2358 5.612725 TCTCAGCTTTTGGACCAATTTTT 57.387 34.783 7.99 0.00 0.00 1.94
2199 2406 2.369629 CGTTTTTCCGCGCGAGAGA 61.370 57.895 34.63 18.10 0.00 3.10
2201 2408 1.007336 GTTTTTCCGCGCGAGAGAGA 61.007 55.000 34.63 17.24 0.00 3.10
2204 2411 1.654023 TTTCCGCGCGAGAGAGATGA 61.654 55.000 34.63 14.71 0.00 2.92
2217 2424 2.679837 GAGAGATGATTTTGCTTCCGCA 59.320 45.455 0.00 0.00 46.24 5.69
2232 2439 2.685829 CGCAACAAGCACGGCCATA 61.686 57.895 2.24 0.00 46.13 2.74
2245 2452 0.529992 GGCCATACCTCTCGGAAACG 60.530 60.000 0.00 0.00 46.67 3.60
2301 2508 0.951040 AGTTTTGCTTCCGCGAGAGG 60.951 55.000 8.23 4.88 39.65 3.69
2305 2512 4.443266 GCTTCCGCGAGAGGCACT 62.443 66.667 20.89 0.00 46.54 4.40
2306 2513 2.507992 CTTCCGCGAGAGGCACTG 60.508 66.667 8.23 0.00 41.55 3.66
2307 2514 3.288308 CTTCCGCGAGAGGCACTGT 62.288 63.158 8.23 0.00 41.55 3.55
2308 2515 3.282745 TTCCGCGAGAGGCACTGTC 62.283 63.158 8.23 0.00 46.09 3.51
2328 2535 1.157585 GTGCCTCTCGGAAAGGAAAC 58.842 55.000 0.36 0.00 35.83 2.78
2337 2561 6.374333 CCTCTCGGAAAGGAAACATATTTTCA 59.626 38.462 0.00 0.00 35.83 2.69
2341 2565 8.116651 TCGGAAAGGAAACATATTTTCATTCA 57.883 30.769 17.45 6.93 32.18 2.57
2388 2612 0.981183 AGGTATGGTCGTGCCTTTCA 59.019 50.000 0.00 0.00 38.35 2.69
2396 2620 0.105224 TCGTGCCTTTCAGAAACGGA 59.895 50.000 12.94 0.00 35.08 4.69
2430 2657 2.270352 TCGTCAGAGGCATGGTTTTT 57.730 45.000 0.00 0.00 0.00 1.94
2448 2675 1.888436 TTCTTCCGCGAGAGGCATGT 61.888 55.000 8.23 0.00 43.84 3.21
2457 2684 2.322161 CGAGAGGCATGTTTTTGCTTG 58.678 47.619 0.00 0.00 42.38 4.01
2461 2688 0.232816 GGCATGTTTTTGCTTGCACG 59.767 50.000 0.00 0.00 42.38 5.34
2494 2721 0.534203 TGCCTCTCGAAAACGGCTTT 60.534 50.000 13.02 0.00 42.90 3.51
2496 2723 1.508632 CCTCTCGAAAACGGCTTTCA 58.491 50.000 11.39 0.95 43.22 2.69
2497 2724 1.871039 CCTCTCGAAAACGGCTTTCAA 59.129 47.619 11.39 0.00 43.22 2.69
2526 2753 0.182775 AAAGTGCTTCCGGTCTGGTT 59.817 50.000 0.00 0.00 39.52 3.67
2550 2777 6.693315 TTTTCGTCTGGTTCTCTTTGAAAT 57.307 33.333 0.00 0.00 36.30 2.17
2557 2784 8.129211 CGTCTGGTTCTCTTTGAAATAAAAAGT 58.871 33.333 0.00 0.00 36.30 2.66
2576 2803 7.659290 AAAAGTTCGTCAAAACTTATCAACG 57.341 32.000 2.73 0.00 46.17 4.10
2578 2805 5.734311 AGTTCGTCAAAACTTATCAACGTG 58.266 37.500 0.00 0.00 36.02 4.49
2580 2807 4.370049 TCGTCAAAACTTATCAACGTGGA 58.630 39.130 0.00 0.00 0.00 4.02
2594 2821 7.921786 ATCAACGTGGAATCTAGATTTGAAA 57.078 32.000 18.88 3.29 0.00 2.69
2608 2835 1.378531 TTGAAAATCTCGGCCCGATG 58.621 50.000 6.16 0.68 34.61 3.84
2616 2843 0.882042 CTCGGCCCGATGAATCCAAG 60.882 60.000 6.16 0.00 34.61 3.61
2617 2844 1.893808 CGGCCCGATGAATCCAAGG 60.894 63.158 0.00 0.00 0.00 3.61
2618 2845 1.531748 GGCCCGATGAATCCAAGGA 59.468 57.895 0.00 0.00 0.00 3.36
2641 2868 4.069304 TGAAAACGGTTCGAGATTTGGAT 58.931 39.130 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 59 3.330701 TCTGGAGTACCTTGGCATTCTTT 59.669 43.478 0.00 0.00 37.04 2.52
68 73 4.824479 TGCTCAATGACAATCTGGAGTA 57.176 40.909 0.00 0.00 0.00 2.59
80 85 2.028203 TCACACTCGGATTGCTCAATGA 60.028 45.455 0.00 0.00 0.00 2.57
90 95 4.148825 GCCGCCTCACACTCGGAT 62.149 66.667 3.91 0.00 45.53 4.18
137 154 4.170062 CGGCCTTGTCATGCTGCG 62.170 66.667 0.00 0.00 0.00 5.18
170 187 0.681733 GCCGGAGAGGATGATTAGCA 59.318 55.000 5.05 0.00 45.00 3.49
174 191 1.700042 GGGTGCCGGAGAGGATGATT 61.700 60.000 5.05 0.00 45.00 2.57
193 210 1.226603 GGTCATCTTCGTCGTCGGG 60.227 63.158 1.55 0.00 37.69 5.14
204 224 0.689080 ACGAGGAGCCATGGTCATCT 60.689 55.000 14.67 0.69 38.46 2.90
207 227 2.359169 GGACGAGGAGCCATGGTCA 61.359 63.158 14.67 0.00 0.00 4.02
288 308 0.777446 ACTTCCTTGCTGGCCCTTTA 59.223 50.000 0.00 0.00 35.26 1.85
374 394 7.540745 GCCAAAGTTCACGTAATTCACATAAAT 59.459 33.333 0.00 0.00 0.00 1.40
388 408 2.969443 AAAGATCGCCAAAGTTCACG 57.031 45.000 0.00 0.00 0.00 4.35
434 454 8.204160 TCGGATGTAGAAATACACATTCAGATT 58.796 33.333 0.00 0.00 35.55 2.40
438 458 8.731275 AAATCGGATGTAGAAATACACATTCA 57.269 30.769 0.00 0.00 35.55 2.57
552 582 5.067283 ACACTAACCAGACGCTTTTCAAATT 59.933 36.000 0.00 0.00 0.00 1.82
563 593 2.325761 CTTCCGAACACTAACCAGACG 58.674 52.381 0.00 0.00 0.00 4.18
565 595 1.001633 GGCTTCCGAACACTAACCAGA 59.998 52.381 0.00 0.00 0.00 3.86
567 597 3.618171 GGCTTCCGAACACTAACCA 57.382 52.632 0.00 0.00 0.00 3.67
589 619 0.935831 CTCAAACGTACACGGACGCA 60.936 55.000 0.71 0.00 46.87 5.24
600 630 0.036306 AAATCCGAGCCCTCAAACGT 59.964 50.000 0.00 0.00 0.00 3.99
621 656 0.744874 TACACCATCTACAGCCGCTC 59.255 55.000 0.00 0.00 0.00 5.03
636 671 7.478667 GTGTTTCGAATGATCTGATTGTTACAC 59.521 37.037 0.00 1.37 0.00 2.90
660 695 2.159639 CGATAGATCGGTCCATCGAGTG 60.160 54.545 19.85 0.00 45.05 3.51
730 765 2.551270 GTGCAACGCCGACTTCAG 59.449 61.111 0.00 0.00 0.00 3.02
784 819 0.033504 GGTGACTCACCGACATGTGT 59.966 55.000 12.59 0.00 44.95 3.72
991 1031 2.126228 CGTGCCCATGCTTGCTTG 60.126 61.111 2.06 2.06 38.71 4.01
992 1032 3.376078 CCGTGCCCATGCTTGCTT 61.376 61.111 0.00 0.00 38.71 3.91
1075 1115 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1076 1116 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1077 1117 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1078 1118 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1079 1119 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1080 1120 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1081 1121 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1082 1122 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1083 1123 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1084 1124 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1085 1125 2.329399 ACCCCTCCTCCTCCTCCTC 61.329 68.421 0.00 0.00 0.00 3.71
1086 1126 2.204705 ACCCCTCCTCCTCCTCCT 60.205 66.667 0.00 0.00 0.00 3.69
1087 1127 1.967343 ATCACCCCTCCTCCTCCTCC 61.967 65.000 0.00 0.00 0.00 4.30
1088 1128 0.762461 CATCACCCCTCCTCCTCCTC 60.762 65.000 0.00 0.00 0.00 3.71
1089 1129 1.316266 CATCACCCCTCCTCCTCCT 59.684 63.158 0.00 0.00 0.00 3.69
1240 1280 1.180029 GAGTAGGGGTTGCTGACGTA 58.820 55.000 0.00 0.00 0.00 3.57
1323 1363 3.135994 TCGATGACCATGCAAGATGATG 58.864 45.455 0.00 0.00 0.00 3.07
1584 1624 1.745489 GGATGGTGAAGGTGCCGAC 60.745 63.158 0.00 0.00 0.00 4.79
1652 1692 3.740044 GCGTGCAGCTAAATAGTTCAA 57.260 42.857 0.00 0.00 44.04 2.69
1695 1735 0.709992 ATACCCCTTTGCACCCACAT 59.290 50.000 0.00 0.00 0.00 3.21
1696 1736 0.485099 AATACCCCTTTGCACCCACA 59.515 50.000 0.00 0.00 0.00 4.17
1704 1748 9.586435 GATCAAACAAGAAATAATACCCCTTTG 57.414 33.333 0.00 0.00 0.00 2.77
1708 1752 6.320418 ACGGATCAAACAAGAAATAATACCCC 59.680 38.462 0.00 0.00 0.00 4.95
1772 1816 4.094590 AGAATGCAGAAAAGAATGCGAGAG 59.905 41.667 0.00 0.00 45.54 3.20
1794 1838 8.131455 AGTAACGTTAATGCATATGTTCAGAG 57.869 34.615 10.11 0.00 0.00 3.35
1810 1854 5.302360 AGATTGTTGCAGGAAGTAACGTTA 58.698 37.500 3.29 3.29 44.65 3.18
1811 1855 4.134563 AGATTGTTGCAGGAAGTAACGTT 58.865 39.130 5.88 5.88 44.65 3.99
1812 1856 3.740115 AGATTGTTGCAGGAAGTAACGT 58.260 40.909 0.00 0.00 44.65 3.99
1813 1857 4.929808 ACTAGATTGTTGCAGGAAGTAACG 59.070 41.667 0.00 0.00 44.65 3.18
1814 1858 7.900782 TTACTAGATTGTTGCAGGAAGTAAC 57.099 36.000 0.00 0.00 42.40 2.50
1815 1859 9.515226 AAATTACTAGATTGTTGCAGGAAGTAA 57.485 29.630 0.00 0.00 33.96 2.24
1816 1860 9.515226 AAAATTACTAGATTGTTGCAGGAAGTA 57.485 29.630 0.00 0.00 0.00 2.24
1817 1861 8.409358 AAAATTACTAGATTGTTGCAGGAAGT 57.591 30.769 0.00 0.00 0.00 3.01
1843 2048 1.988015 CTGGGCCCGACTCCTAAAA 59.012 57.895 19.37 0.00 0.00 1.52
1896 2101 3.250744 CGTCGGAGATTTTGCAACTAGA 58.749 45.455 0.00 0.00 40.67 2.43
1897 2102 2.222819 GCGTCGGAGATTTTGCAACTAG 60.223 50.000 0.00 0.00 40.67 2.57
1990 2196 2.356313 ACTGAGCGCCAAGTGACG 60.356 61.111 11.48 0.00 0.00 4.35
1992 2198 1.300931 GTGACTGAGCGCCAAGTGA 60.301 57.895 16.55 6.23 0.00 3.41
1995 2201 3.114616 CGGTGACTGAGCGCCAAG 61.115 66.667 2.29 4.22 39.02 3.61
2013 2219 1.599071 CGCCTACTATGCAACACATGG 59.401 52.381 0.00 0.00 42.68 3.66
2016 2222 2.465860 AACGCCTACTATGCAACACA 57.534 45.000 0.00 0.00 0.00 3.72
2058 2264 6.969828 AAAAGCCAAAAACGTGTATGAAAA 57.030 29.167 0.00 0.00 0.00 2.29
2059 2265 6.969828 AAAAAGCCAAAAACGTGTATGAAA 57.030 29.167 0.00 0.00 0.00 2.69
2060 2266 8.475331 TTTAAAAAGCCAAAAACGTGTATGAA 57.525 26.923 0.00 0.00 0.00 2.57
2061 2267 8.543774 CATTTAAAAAGCCAAAAACGTGTATGA 58.456 29.630 0.00 0.00 0.00 2.15
2062 2268 7.796197 CCATTTAAAAAGCCAAAAACGTGTATG 59.204 33.333 0.00 0.00 0.00 2.39
2063 2269 7.496263 ACCATTTAAAAAGCCAAAAACGTGTAT 59.504 29.630 0.00 0.00 0.00 2.29
2068 2274 8.454293 AAAAACCATTTAAAAAGCCAAAAACG 57.546 26.923 0.00 0.00 0.00 3.60
2095 2301 5.472320 AAAACCAAAAACCGGAAAAATCG 57.528 34.783 9.46 0.00 0.00 3.34
2096 2302 6.743627 GTGAAAAACCAAAAACCGGAAAAATC 59.256 34.615 9.46 0.00 0.00 2.17
2114 2321 4.526970 AGCTGAGAAAGACTGGTGAAAAA 58.473 39.130 0.00 0.00 0.00 1.94
2123 2330 3.117888 TGGTCCAAAAGCTGAGAAAGACT 60.118 43.478 0.00 0.00 0.00 3.24
2150 2357 7.428562 TTCGCGTAAAAATGTTTTCGTTAAA 57.571 28.000 5.77 0.05 39.07 1.52
2151 2358 7.428562 TTTCGCGTAAAAATGTTTTCGTTAA 57.571 28.000 5.77 2.08 39.07 2.01
2152 2359 7.428562 TTTTCGCGTAAAAATGTTTTCGTTA 57.571 28.000 8.54 0.00 39.07 3.18
2154 2361 5.928601 TTTTCGCGTAAAAATGTTTTCGT 57.071 30.435 8.54 0.00 39.07 3.85
2187 2394 1.448119 AATCATCTCTCTCGCGCGGA 61.448 55.000 31.69 23.65 0.00 5.54
2189 2396 1.071633 CAAAATCATCTCTCTCGCGCG 60.072 52.381 26.76 26.76 0.00 6.86
2190 2397 1.332728 GCAAAATCATCTCTCTCGCGC 60.333 52.381 0.00 0.00 0.00 6.86
2217 2424 0.676782 GAGGTATGGCCGTGCTTGTT 60.677 55.000 13.16 0.00 43.70 2.83
2218 2425 1.078426 GAGGTATGGCCGTGCTTGT 60.078 57.895 13.16 0.00 43.70 3.16
2219 2426 0.811616 GAGAGGTATGGCCGTGCTTG 60.812 60.000 13.16 0.00 43.70 4.01
2261 2468 5.385198 ACTATGCCTCTTGTGGAAGAAAAA 58.615 37.500 0.00 0.00 37.77 1.94
2266 2473 4.616835 GCAAAACTATGCCTCTTGTGGAAG 60.617 45.833 0.00 0.00 40.49 3.46
2328 2535 8.554528 ACGCTGTCTCTTATGAATGAAAATATG 58.445 33.333 0.00 0.00 0.00 1.78
2337 2561 4.974591 GCAAAACGCTGTCTCTTATGAAT 58.025 39.130 0.00 0.00 37.77 2.57
2366 2590 1.276622 AAGGCACGACCATACCTCTT 58.723 50.000 0.00 0.00 43.14 2.85
2372 2596 3.071479 GTTTCTGAAAGGCACGACCATA 58.929 45.455 2.48 0.00 43.14 2.74
2374 2598 1.305201 GTTTCTGAAAGGCACGACCA 58.695 50.000 2.48 0.00 43.14 4.02
2415 2642 2.095059 CGGAAGAAAAACCATGCCTCTG 60.095 50.000 0.00 0.00 0.00 3.35
2417 2644 1.402852 GCGGAAGAAAAACCATGCCTC 60.403 52.381 0.00 0.00 0.00 4.70
2419 2646 0.732538 CGCGGAAGAAAAACCATGCC 60.733 55.000 0.00 0.00 0.00 4.40
2423 2650 1.508632 CTCTCGCGGAAGAAAAACCA 58.491 50.000 6.13 0.00 0.00 3.67
2430 2657 1.888436 AACATGCCTCTCGCGGAAGA 61.888 55.000 6.13 0.90 42.08 2.87
2448 2675 0.030638 GCCTCTCGTGCAAGCAAAAA 59.969 50.000 0.00 0.00 0.00 1.94
2482 2709 2.538037 CCCTTTTTGAAAGCCGTTTTCG 59.462 45.455 3.61 0.00 46.65 3.46
2484 2711 3.897141 TCCCTTTTTGAAAGCCGTTTT 57.103 38.095 0.00 0.00 0.00 2.43
2510 2737 1.029681 AAAAACCAGACCGGAAGCAC 58.970 50.000 9.46 0.00 38.63 4.40
2526 2753 6.503589 TTTCAAAGAGAACCAGACGAAAAA 57.496 33.333 0.00 0.00 35.56 1.94
2550 2777 9.212687 CGTTGATAAGTTTTGACGAACTTTTTA 57.787 29.630 8.13 0.00 45.05 1.52
2557 2784 4.809958 TCCACGTTGATAAGTTTTGACGAA 59.190 37.500 0.00 0.00 34.85 3.85
2568 2795 9.443323 TTTCAAATCTAGATTCCACGTTGATAA 57.557 29.630 18.19 10.57 0.00 1.75
2594 2821 0.035458 GGATTCATCGGGCCGAGATT 59.965 55.000 33.82 23.66 39.91 2.40
2603 2830 4.496341 CGTTTTCATCCTTGGATTCATCGG 60.496 45.833 0.00 0.00 0.00 4.18
2608 2835 4.671766 CGAACCGTTTTCATCCTTGGATTC 60.672 45.833 0.00 0.00 0.00 2.52
2616 2843 4.403453 CAAATCTCGAACCGTTTTCATCC 58.597 43.478 0.00 0.00 0.00 3.51
2617 2844 4.153475 TCCAAATCTCGAACCGTTTTCATC 59.847 41.667 0.00 0.00 0.00 2.92
2618 2845 4.069304 TCCAAATCTCGAACCGTTTTCAT 58.931 39.130 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.