Multiple sequence alignment - TraesCS7A01G316700

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 TraesCS7A01G316700 chr7A 100.000 4926 0 0 1 4926 452748754 452753679 0.000000e+00 9097.0
1 TraesCS7A01G316700 chr7A 99.029 309 3 0 2387 2695 486173322 486173014 5.570000e-154 555.0
2 TraesCS7A01G316700 chr7A 98.611 288 4 0 2404 2691 486175731 486175444 1.220000e-140 510.0
3 TraesCS7A01G316700 chr7A 76.941 425 80 12 333 754 63473858 63473449 4.960000e-55 226.0
4 TraesCS7A01G316700 chr7B 96.470 1388 42 5 2692 4074 400929625 400928240 0.000000e+00 2285.0
5 TraesCS7A01G316700 chr7B 92.857 1260 60 16 544 1789 400937078 400935835 0.000000e+00 1801.0
6 TraesCS7A01G316700 chr7B 92.739 303 20 2 1851 2152 400935834 400935533 2.110000e-118 436.0
7 TraesCS7A01G316700 chr7B 88.980 245 17 3 2153 2388 400929865 400929622 1.340000e-75 294.0
8 TraesCS7A01G316700 chr7B 76.552 435 78 20 193 611 106594944 106595370 2.990000e-52 217.0
9 TraesCS7A01G316700 chr7D 94.468 1410 44 10 2692 4097 397199692 397198313 0.000000e+00 2141.0
10 TraesCS7A01G316700 chr7D 86.463 1832 138 55 1 1789 397201991 397200227 0.000000e+00 1908.0
11 TraesCS7A01G316700 chr7D 93.161 541 31 6 1851 2388 397200226 397199689 0.000000e+00 789.0
12 TraesCS7A01G316700 chr5A 97.222 828 22 1 4099 4926 13095013 13094187 0.000000e+00 1400.0
13 TraesCS7A01G316700 chr5A 94.210 829 41 4 4102 4926 638077642 638076817 0.000000e+00 1258.0
14 TraesCS7A01G316700 chr5A 93.381 831 44 6 4100 4926 568897204 568896381 0.000000e+00 1219.0
15 TraesCS7A01G316700 chr5A 97.049 305 3 1 2388 2692 505014965 505015263 4.400000e-140 508.0
16 TraesCS7A01G316700 chr1A 97.219 827 22 1 4100 4926 588945719 588946544 0.000000e+00 1399.0
17 TraesCS7A01G316700 chr3A 96.981 828 23 2 4099 4926 456384409 456383584 0.000000e+00 1389.0
18 TraesCS7A01G316700 chr2A 96.493 827 27 2 4100 4926 686199691 686198867 0.000000e+00 1365.0
19 TraesCS7A01G316700 chr1D 95.187 831 34 4 4100 4926 433412322 433411494 0.000000e+00 1308.0
20 TraesCS7A01G316700 chr1D 94.620 316 16 1 2382 2696 433461615 433461930 5.730000e-134 488.0
21 TraesCS7A01G316700 chr1D 77.273 418 74 15 341 754 22441607 22441207 4.960000e-55 226.0
22 TraesCS7A01G316700 chr5D 94.224 831 42 4 4100 4926 493683013 493682185 0.000000e+00 1264.0
23 TraesCS7A01G316700 chr5D 76.199 563 94 26 210 754 455810084 455809544 1.360000e-65 261.0
24 TraesCS7A01G316700 chr5B 93.269 832 50 4 4100 4926 339092814 339091984 0.000000e+00 1221.0
25 TraesCS7A01G316700 chr5B 98.392 311 5 0 2384 2694 602935491 602935801 9.320000e-152 547.0
26 TraesCS7A01G316700 chr3B 97.386 306 8 0 2387 2692 664891776 664891471 5.650000e-144 521.0
27 TraesCS7A01G316700 chr3B 94.231 312 18 0 2384 2695 739335237 739335548 1.240000e-130 477.0
28 TraesCS7A01G316700 chr3B 75.524 429 85 15 196 611 458285939 458286360 5.030000e-45 193.0
29 TraesCS7A01G316700 chr6D 94.569 313 16 1 2381 2693 98871778 98871467 2.670000e-132 483.0
30 TraesCS7A01G316700 chr2B 93.711 318 19 1 2383 2700 721832612 721832296 4.460000e-130 475.0
31 TraesCS7A01G316700 chr4B 80.979 531 75 12 236 754 400701962 400701446 9.940000e-107 398.0
32 TraesCS7A01G316700 chr4D 77.838 555 96 19 211 754 479414151 479414689 7.960000e-83 318.0
33 TraesCS7A01G316700 chr3D 76.636 428 80 15 196 611 357074778 357075197 8.300000e-53 219.0
34 TraesCS7A01G316700 chr2D 75.683 366 78 9 249 611 296855388 296855031 6.560000e-39 172.0
35 TraesCS7A01G316700 chr4A 87.500 56 6 1 224 278 714182711 714182656 4.120000e-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 TraesCS7A01G316700 chr7A 452748754 452753679 4925 False 9097.000000 9097 100.000 1 4926 1 chr7A.!!$F1 4925
1 TraesCS7A01G316700 chr7A 486173014 486175731 2717 True 532.500000 555 98.820 2387 2695 2 chr7A.!!$R2 308
2 TraesCS7A01G316700 chr7B 400928240 400929865 1625 True 1289.500000 2285 92.725 2153 4074 2 chr7B.!!$R1 1921
3 TraesCS7A01G316700 chr7B 400935533 400937078 1545 True 1118.500000 1801 92.798 544 2152 2 chr7B.!!$R2 1608
4 TraesCS7A01G316700 chr7D 397198313 397201991 3678 True 1612.666667 2141 91.364 1 4097 3 chr7D.!!$R1 4096
5 TraesCS7A01G316700 chr5A 13094187 13095013 826 True 1400.000000 1400 97.222 4099 4926 1 chr5A.!!$R1 827
6 TraesCS7A01G316700 chr5A 638076817 638077642 825 True 1258.000000 1258 94.210 4102 4926 1 chr5A.!!$R3 824
7 TraesCS7A01G316700 chr5A 568896381 568897204 823 True 1219.000000 1219 93.381 4100 4926 1 chr5A.!!$R2 826
8 TraesCS7A01G316700 chr1A 588945719 588946544 825 False 1399.000000 1399 97.219 4100 4926 1 chr1A.!!$F1 826
9 TraesCS7A01G316700 chr3A 456383584 456384409 825 True 1389.000000 1389 96.981 4099 4926 1 chr3A.!!$R1 827
10 TraesCS7A01G316700 chr2A 686198867 686199691 824 True 1365.000000 1365 96.493 4100 4926 1 chr2A.!!$R1 826
11 TraesCS7A01G316700 chr1D 433411494 433412322 828 True 1308.000000 1308 95.187 4100 4926 1 chr1D.!!$R2 826
12 TraesCS7A01G316700 chr5D 493682185 493683013 828 True 1264.000000 1264 94.224 4100 4926 1 chr5D.!!$R2 826
13 TraesCS7A01G316700 chr5D 455809544 455810084 540 True 261.000000 261 76.199 210 754 1 chr5D.!!$R1 544
14 TraesCS7A01G316700 chr5B 339091984 339092814 830 True 1221.000000 1221 93.269 4100 4926 1 chr5B.!!$R1 826
15 TraesCS7A01G316700 chr4B 400701446 400701962 516 True 398.000000 398 80.979 236 754 1 chr4B.!!$R1 518
16 TraesCS7A01G316700 chr4D 479414151 479414689 538 False 318.000000 318 77.838 211 754 1 chr4D.!!$F1 543

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
546 575 1.369625 CAAAATCTACGCCGGAGCTT 58.630 50.0 5.05 0.0 36.60 3.74 F
1717 1770 1.108776 CAATGGCTTGGGACATGGAG 58.891 55.0 0.00 0.0 40.94 3.86 F
1845 1902 0.035343 GGGTTACCTTGCTCTGGTCC 60.035 60.0 0.00 0.0 38.88 4.46 F
2242 2300 0.307760 GTGAACTGAACTTGGTGCCG 59.692 55.0 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 1883 0.035343 GGACCAGAGCAAGGTAACCC 60.035 60.000 0.00 0.00 40.09 4.11 R
3649 3718 2.728846 CGTCCATGAAATTCCTGTTGCG 60.729 50.000 0.00 0.00 0.00 4.85 R
3810 3879 1.921230 GTTAGCTACTGAGTTGCGCTC 59.079 52.381 12.96 1.40 44.36 5.03 R
4151 4224 0.834612 CCTGTAATCCTGGCCGGTTA 59.165 55.000 11.58 0.12 0.00 2.85 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
49 50 8.315482 AGTATTTTCTCTTCAACTCTTCTACCC 58.685 37.037 0.00 0.00 0.00 3.69
50 51 6.749036 TTTTCTCTTCAACTCTTCTACCCT 57.251 37.500 0.00 0.00 0.00 4.34
51 52 5.730296 TTCTCTTCAACTCTTCTACCCTG 57.270 43.478 0.00 0.00 0.00 4.45
163 173 9.468532 AAAGAAAAAGATCTGTAATTCAGCAAC 57.531 29.630 0.00 0.00 43.32 4.17
167 177 9.768662 AAAAAGATCTGTAATTCAGCAACAAAT 57.231 25.926 0.00 0.00 43.32 2.32
300 313 7.797121 ACATTGAGATTTTAAGACCCCAAAT 57.203 32.000 0.00 0.00 0.00 2.32
440 463 2.530497 GCCGCAATCGTCGCCATTA 61.530 57.895 0.00 0.00 0.00 1.90
468 495 4.004196 TGCATAGATCTGAAGCATCTGG 57.996 45.455 5.18 0.00 32.61 3.86
487 514 4.638865 TCTGGCATCAAATCTCATCACAAG 59.361 41.667 0.00 0.00 0.00 3.16
488 515 4.591929 TGGCATCAAATCTCATCACAAGA 58.408 39.130 0.00 0.00 0.00 3.02
489 516 5.198207 TGGCATCAAATCTCATCACAAGAT 58.802 37.500 0.00 0.00 34.96 2.40
492 520 7.339976 TGGCATCAAATCTCATCACAAGATAAA 59.660 33.333 0.00 0.00 33.15 1.40
520 548 3.270877 CCTAACCTCATCGTCCCAAAAG 58.729 50.000 0.00 0.00 0.00 2.27
546 575 1.369625 CAAAATCTACGCCGGAGCTT 58.630 50.000 5.05 0.00 36.60 3.74
562 591 3.585862 GAGCTTTGTCGACTACATCCAA 58.414 45.455 17.92 0.00 38.10 3.53
581 610 4.459685 TCCAAACGGACAAACTCAAAAAGA 59.540 37.500 0.00 0.00 0.00 2.52
616 645 3.243301 ACGACAAACTCGAAGAAGTAGCA 60.243 43.478 0.00 0.00 46.14 3.49
637 666 4.280494 CCATCCGCCCGAGTACCG 62.280 72.222 0.00 0.00 38.18 4.02
687 716 2.028385 ACCCTGACCTAAACTGCTAACG 60.028 50.000 0.00 0.00 0.00 3.18
689 718 3.306502 CCCTGACCTAAACTGCTAACGAA 60.307 47.826 0.00 0.00 0.00 3.85
701 730 3.869473 TAACGAAAGCGGCGGCACT 62.869 57.895 19.21 0.15 43.41 4.40
726 755 1.692042 CTCCTCCCCATCACCAGCT 60.692 63.158 0.00 0.00 0.00 4.24
766 796 3.769300 GAGGGGAGGCAACAAATTACATT 59.231 43.478 0.00 0.00 41.41 2.71
774 804 8.416329 GGAGGCAACAAATTACATTAGATTGAT 58.584 33.333 0.00 0.00 41.41 2.57
800 832 4.410555 AGAGATCAAACTAAGATGGACCCC 59.589 45.833 0.00 0.00 0.00 4.95
878 911 7.637709 AGTTTCATTTTTATCGCCACTTTTC 57.362 32.000 0.00 0.00 0.00 2.29
926 962 2.851824 GCAAATTGCATACGTGGCTAAC 59.148 45.455 13.73 0.00 44.26 2.34
1097 1146 3.041211 TCTCAACCCGATCCATTCTCAT 58.959 45.455 0.00 0.00 0.00 2.90
1204 1253 3.702048 CCCCTCTCGTTTCGGCCA 61.702 66.667 2.24 0.00 0.00 5.36
1207 1256 2.125512 CTCTCGTTTCGGCCAGGG 60.126 66.667 2.24 0.00 0.00 4.45
1298 1347 1.713647 ACAGAGGAGGAAGAGGAGACA 59.286 52.381 0.00 0.00 0.00 3.41
1612 1661 3.486108 CGCTGTCGGATTCATAGTGTTAC 59.514 47.826 0.00 0.00 0.00 2.50
1661 1712 1.586154 AAGAAGAATTGCACGGGCCG 61.586 55.000 27.06 27.06 40.13 6.13
1691 1743 4.731853 TGACGCCCCCTGGATGGA 62.732 66.667 6.43 0.00 38.35 3.41
1716 1769 3.286404 CAATGGCTTGGGACATGGA 57.714 52.632 0.00 0.00 40.94 3.41
1717 1770 1.108776 CAATGGCTTGGGACATGGAG 58.891 55.000 0.00 0.00 40.94 3.86
1805 1862 7.778470 CATCCATGGAGTACTTCTTAACTTC 57.222 40.000 21.33 0.00 0.00 3.01
1808 1865 8.660295 TCCATGGAGTACTTCTTAACTTCTTA 57.340 34.615 11.44 0.00 0.00 2.10
1809 1866 9.096823 TCCATGGAGTACTTCTTAACTTCTTAA 57.903 33.333 11.44 0.00 0.00 1.85
1811 1868 8.874816 CATGGAGTACTTCTTAACTTCTTAAGC 58.125 37.037 2.07 0.00 39.12 3.09
1815 1872 9.292846 GAGTACTTCTTAACTTCTTAAGCTAGC 57.707 37.037 6.62 6.62 39.12 3.42
1816 1873 8.804204 AGTACTTCTTAACTTCTTAAGCTAGCA 58.196 33.333 18.83 0.00 39.12 3.49
1817 1874 9.589111 GTACTTCTTAACTTCTTAAGCTAGCAT 57.411 33.333 18.83 7.77 39.12 3.79
1819 1876 7.550906 ACTTCTTAACTTCTTAAGCTAGCATGG 59.449 37.037 18.83 4.13 39.12 3.66
1820 1877 5.817816 TCTTAACTTCTTAAGCTAGCATGGC 59.182 40.000 18.83 0.00 46.31 4.40
1828 1885 1.595382 GCTAGCATGGCACTACGGG 60.595 63.158 10.63 0.00 44.73 5.28
1829 1886 1.823295 CTAGCATGGCACTACGGGT 59.177 57.895 0.00 0.00 0.00 5.28
1830 1887 0.178068 CTAGCATGGCACTACGGGTT 59.822 55.000 0.00 0.00 0.00 4.11
1831 1888 1.411246 CTAGCATGGCACTACGGGTTA 59.589 52.381 0.00 0.00 0.00 2.85
1832 1889 0.107848 AGCATGGCACTACGGGTTAC 60.108 55.000 0.00 0.00 0.00 2.50
1833 1890 1.093496 GCATGGCACTACGGGTTACC 61.093 60.000 0.00 0.00 0.00 2.85
1835 1892 1.065709 CATGGCACTACGGGTTACCTT 60.066 52.381 0.00 0.00 33.28 3.50
1836 1893 0.322322 TGGCACTACGGGTTACCTTG 59.678 55.000 0.00 0.00 33.28 3.61
1837 1894 1.022982 GGCACTACGGGTTACCTTGC 61.023 60.000 0.00 2.97 33.28 4.01
1838 1895 0.036671 GCACTACGGGTTACCTTGCT 60.037 55.000 0.00 0.00 33.28 3.91
1839 1896 2.005560 GCACTACGGGTTACCTTGCTC 61.006 57.143 0.00 0.00 33.28 4.26
1840 1897 1.549170 CACTACGGGTTACCTTGCTCT 59.451 52.381 0.00 0.00 33.28 4.09
1842 1899 0.899720 TACGGGTTACCTTGCTCTGG 59.100 55.000 0.00 0.00 33.28 3.86
1843 1900 1.125711 ACGGGTTACCTTGCTCTGGT 61.126 55.000 0.00 0.00 41.28 4.00
1844 1901 0.391263 CGGGTTACCTTGCTCTGGTC 60.391 60.000 0.00 0.00 38.88 4.02
1845 1902 0.035343 GGGTTACCTTGCTCTGGTCC 60.035 60.000 0.00 0.00 38.88 4.46
1846 1903 0.391263 GGTTACCTTGCTCTGGTCCG 60.391 60.000 0.00 0.00 38.88 4.79
1847 1904 0.320697 GTTACCTTGCTCTGGTCCGT 59.679 55.000 0.00 0.00 38.88 4.69
1848 1905 0.606604 TTACCTTGCTCTGGTCCGTC 59.393 55.000 0.00 0.00 38.88 4.79
1849 1906 1.255667 TACCTTGCTCTGGTCCGTCC 61.256 60.000 0.00 0.00 38.88 4.79
1927 1984 0.837691 TCACCTGCCTCACCATCAGT 60.838 55.000 0.00 0.00 0.00 3.41
2002 2059 5.650543 CAGCAGGTTTGGTATTTTGGATAC 58.349 41.667 0.00 0.00 32.80 2.24
2085 2143 6.985188 TGAATGTTTACAATCTCTACTGGC 57.015 37.500 0.21 0.00 0.00 4.85
2101 2159 2.325857 GCGGCTCTTGCGCTTATG 59.674 61.111 9.73 0.00 40.82 1.90
2167 2225 5.369404 TGGGGTTTATATCAGATGCTTCTCA 59.631 40.000 0.00 0.00 0.00 3.27
2189 2247 7.390440 TCTCATTTTTCATATTTCTCGTGGTGT 59.610 33.333 0.00 0.00 0.00 4.16
2200 2258 5.456548 TTCTCGTGGTGTTGTATTAGTCA 57.543 39.130 0.00 0.00 0.00 3.41
2242 2300 0.307760 GTGAACTGAACTTGGTGCCG 59.692 55.000 0.00 0.00 0.00 5.69
2272 2338 6.423302 GCTAGTATCTGTTCAATGATGTCCTG 59.577 42.308 0.00 0.00 0.00 3.86
2296 2363 9.099454 CTGGTTTAGGTCTCAATAGAATTACAC 57.901 37.037 0.00 0.00 32.16 2.90
2324 2391 3.130633 TGCTGCCTTAGTTATATGCGTG 58.869 45.455 0.00 0.00 0.00 5.34
2329 2396 5.364778 TGCCTTAGTTATATGCGTGATTGT 58.635 37.500 0.00 0.00 0.00 2.71
2384 2451 7.684529 TGGGTAATATTTTGTTGCTTCCAATT 58.315 30.769 0.00 0.00 32.75 2.32
2385 2452 8.816894 TGGGTAATATTTTGTTGCTTCCAATTA 58.183 29.630 0.00 0.00 32.75 1.40
2386 2453 9.660180 GGGTAATATTTTGTTGCTTCCAATTAA 57.340 29.630 0.00 0.00 32.75 1.40
2389 2456 8.791327 AATATTTTGTTGCTTCCAATTAAGGG 57.209 30.769 0.00 0.00 32.75 3.95
2390 2457 3.676291 TTGTTGCTTCCAATTAAGGGC 57.324 42.857 0.00 0.00 32.75 5.19
2537 2604 5.319043 TGTAAAAAGAGGTTGGAGTGGAT 57.681 39.130 0.00 0.00 0.00 3.41
2717 2784 6.297582 AGATTCTAGAGGCTCATTTTGATGG 58.702 40.000 18.26 0.00 0.00 3.51
2877 2945 6.660521 AGTCATACAATGGCTTCATTTTCTCA 59.339 34.615 0.00 0.00 44.07 3.27
2920 2988 7.028962 TGCATATTGTCTACAAATGAAAGTGC 58.971 34.615 15.77 11.41 39.55 4.40
3154 3222 1.876156 CAACACTTGAGGGAGCACTTC 59.124 52.381 0.00 0.00 0.00 3.01
3235 3303 4.466370 AGTCGTGTCTATGGATTCCTTTCA 59.534 41.667 3.95 0.00 0.00 2.69
3434 3502 9.158233 CATCTCGGGTTAGTTTGTATAAGAAAA 57.842 33.333 0.00 0.00 0.00 2.29
3516 3584 5.186797 GCTTACCAGTAGCTCCATGATATCT 59.813 44.000 3.98 0.00 0.00 1.98
3739 3808 3.394606 AGCCAAACCCTTGAGAGTTAGAA 59.605 43.478 0.00 0.00 34.14 2.10
3741 3810 4.072839 CCAAACCCTTGAGAGTTAGAACC 58.927 47.826 0.00 0.00 34.14 3.62
3766 3835 6.915843 CGGAAGCTACTGTGTTTATTTTTGTT 59.084 34.615 0.00 0.00 0.00 2.83
3769 3838 9.296400 GAAGCTACTGTGTTTATTTTTGTTTGA 57.704 29.630 0.00 0.00 0.00 2.69
3807 3876 2.796593 GTTCATTGTTCAGGCACTTTGC 59.203 45.455 0.00 0.00 44.08 3.68
3962 4032 7.008440 TGAAATCTTGTGAGAGCATTATTCG 57.992 36.000 0.00 0.00 34.85 3.34
3990 4060 6.461648 GGGATCTTGACGATTCATTCTAGTCA 60.462 42.308 0.00 0.00 39.68 3.41
4074 4147 4.327357 GTCTTCCACGAATGTATCACACAG 59.673 45.833 0.00 0.00 41.51 3.66
4078 4151 3.368427 CCACGAATGTATCACACAGGAGT 60.368 47.826 0.00 0.00 41.51 3.85
4092 4165 0.625849 AGGAGTATGTTGCCAAGGGG 59.374 55.000 0.00 0.00 37.18 4.79
4097 4170 0.251564 TATGTTGCCAAGGGGGTGTG 60.252 55.000 0.00 0.00 39.65 3.82
4325 4401 3.657956 CACCACCGTGCATGTTTTT 57.342 47.368 4.96 0.00 32.04 1.94
4599 4675 1.579964 TTGTCGAGACGAAGGCGCTA 61.580 55.000 7.64 0.00 42.48 4.26
4635 4713 2.020694 GCCAAGAGTATGCAGCACCAT 61.021 52.381 0.00 0.00 0.00 3.55
4815 4893 0.109342 CCACCACTTGAGCACTTCCT 59.891 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.525629 CAGGGTAGAAGAGTTGAAGAGAAAA 58.474 40.000 0.00 0.00 0.00 2.29
57 58 2.231478 TGTTCGTGCTTTAGAGGGAGAG 59.769 50.000 0.00 0.00 0.00 3.20
58 59 2.244695 TGTTCGTGCTTTAGAGGGAGA 58.755 47.619 0.00 0.00 0.00 3.71
60 61 4.222145 AGTTATGTTCGTGCTTTAGAGGGA 59.778 41.667 0.00 0.00 0.00 4.20
109 118 8.368668 TCTTTTAGTTTCTTGAAACAAAACCCA 58.631 29.630 22.92 11.52 34.23 4.51
218 229 5.181245 TGTTGAACTTTGCTAATAGACCTGC 59.819 40.000 0.00 0.00 0.00 4.85
300 313 5.912892 TCATTCTGACGGCAATAGTGATTA 58.087 37.500 0.00 0.00 0.00 1.75
303 316 3.785486 CTCATTCTGACGGCAATAGTGA 58.215 45.455 0.00 0.00 0.00 3.41
309 322 1.741401 CGGCTCATTCTGACGGCAA 60.741 57.895 0.00 0.00 0.00 4.52
377 399 1.986378 CGTGCACGAAGACTTCCTAAG 59.014 52.381 34.93 0.00 43.02 2.18
437 460 6.264067 GCTTCAGATCTATGCAAGGGTTTAAT 59.736 38.462 0.00 0.00 0.00 1.40
440 463 3.950395 GCTTCAGATCTATGCAAGGGTTT 59.050 43.478 0.00 0.00 0.00 3.27
468 495 9.577110 TTTTTATCTTGTGATGAGATTTGATGC 57.423 29.630 0.00 0.00 35.56 3.91
520 548 0.651031 GGCGTAGATTTTGCCGTCTC 59.349 55.000 0.00 0.00 39.30 3.36
546 575 2.296752 TCCGTTTGGATGTAGTCGACAA 59.703 45.455 19.50 2.94 42.78 3.18
562 591 5.065474 TCGATTCTTTTTGAGTTTGTCCGTT 59.935 36.000 0.00 0.00 0.00 4.44
616 645 3.968837 TACTCGGGCGGATGGTGGT 62.969 63.158 0.00 0.00 0.00 4.16
687 716 1.090052 ATTCTAGTGCCGCCGCTTTC 61.090 55.000 0.00 0.00 35.36 2.62
689 718 1.078426 AATTCTAGTGCCGCCGCTT 60.078 52.632 0.00 0.00 35.36 4.68
695 724 1.069358 GGGAGGAGAATTCTAGTGCCG 59.931 57.143 8.25 0.00 0.00 5.69
701 730 3.311327 TGGTGATGGGGAGGAGAATTCTA 60.311 47.826 8.25 0.00 0.00 2.10
774 804 6.352222 GGGTCCATCTTAGTTTGATCTCTTCA 60.352 42.308 0.00 0.00 0.00 3.02
778 809 4.164221 TGGGGTCCATCTTAGTTTGATCTC 59.836 45.833 0.00 0.00 0.00 2.75
780 811 4.503714 TGGGGTCCATCTTAGTTTGATC 57.496 45.455 0.00 0.00 0.00 2.92
835 868 2.169352 ACTAGAGGCAGCGATGTCAAAT 59.831 45.455 8.46 0.00 0.00 2.32
926 962 3.873026 GAGATGAGCGGCCCGATGG 62.873 68.421 7.68 0.00 0.00 3.51
1185 1234 3.387947 GCCGAAACGAGAGGGGGA 61.388 66.667 0.00 0.00 0.00 4.81
1590 1639 2.209838 ACACTATGAATCCGACAGCG 57.790 50.000 0.00 0.00 37.24 5.18
1606 1655 4.399303 ACACCGTGTAGGGTATAGTAACAC 59.601 45.833 1.18 0.00 46.96 3.32
1612 1661 6.395426 TGATAAACACCGTGTAGGGTATAG 57.605 41.667 4.17 0.00 46.96 1.31
1671 1723 3.402681 ATCCAGGGGGCGTCACTG 61.403 66.667 4.19 4.19 0.00 3.66
1716 1769 1.650528 GCCATGCCTATCTCCTACCT 58.349 55.000 0.00 0.00 0.00 3.08
1717 1770 0.615850 GGCCATGCCTATCTCCTACC 59.384 60.000 0.00 0.00 46.69 3.18
1789 1846 9.292846 GCTAGCTTAAGAAGTTAAGAAGTACTC 57.707 37.037 7.70 0.00 45.67 2.59
1790 1847 8.804204 TGCTAGCTTAAGAAGTTAAGAAGTACT 58.196 33.333 17.23 0.00 45.67 2.73
1793 1850 7.550906 CCATGCTAGCTTAAGAAGTTAAGAAGT 59.449 37.037 17.23 0.00 45.67 3.01
1794 1851 7.466590 GCCATGCTAGCTTAAGAAGTTAAGAAG 60.467 40.741 17.23 6.32 45.67 2.85
1795 1852 6.316390 GCCATGCTAGCTTAAGAAGTTAAGAA 59.684 38.462 17.23 0.00 45.67 2.52
1796 1853 5.817816 GCCATGCTAGCTTAAGAAGTTAAGA 59.182 40.000 17.23 0.00 45.67 2.10
1798 1855 5.354234 GTGCCATGCTAGCTTAAGAAGTTAA 59.646 40.000 17.23 0.00 0.00 2.01
1800 1857 3.691609 GTGCCATGCTAGCTTAAGAAGTT 59.308 43.478 17.23 0.00 0.00 2.66
1801 1858 3.054802 AGTGCCATGCTAGCTTAAGAAGT 60.055 43.478 17.23 0.00 0.00 3.01
1803 1860 3.634397 AGTGCCATGCTAGCTTAAGAA 57.366 42.857 17.23 0.00 0.00 2.52
1804 1861 3.490933 CGTAGTGCCATGCTAGCTTAAGA 60.491 47.826 17.23 0.00 0.00 2.10
1805 1862 2.797156 CGTAGTGCCATGCTAGCTTAAG 59.203 50.000 17.23 5.91 0.00 1.85
1808 1865 0.179073 CCGTAGTGCCATGCTAGCTT 60.179 55.000 17.23 6.81 0.00 3.74
1809 1866 1.443407 CCGTAGTGCCATGCTAGCT 59.557 57.895 17.23 0.00 0.00 3.32
1811 1868 0.178068 AACCCGTAGTGCCATGCTAG 59.822 55.000 0.00 0.00 0.00 3.42
1815 1872 0.539986 AGGTAACCCGTAGTGCCATG 59.460 55.000 0.00 0.00 35.12 3.66
1816 1873 1.065709 CAAGGTAACCCGTAGTGCCAT 60.066 52.381 0.00 0.00 35.12 4.40
1817 1874 0.322322 CAAGGTAACCCGTAGTGCCA 59.678 55.000 0.00 0.00 35.12 4.92
1819 1876 0.036671 AGCAAGGTAACCCGTAGTGC 60.037 55.000 0.00 0.00 35.12 4.40
1820 1877 1.549170 AGAGCAAGGTAACCCGTAGTG 59.451 52.381 0.00 0.00 35.12 2.74
1821 1878 1.549170 CAGAGCAAGGTAACCCGTAGT 59.451 52.381 0.00 0.00 35.12 2.73
1822 1879 1.134788 CCAGAGCAAGGTAACCCGTAG 60.135 57.143 0.00 0.00 35.12 3.51
1823 1880 0.899720 CCAGAGCAAGGTAACCCGTA 59.100 55.000 0.00 0.00 35.12 4.02
1825 1882 0.391263 GACCAGAGCAAGGTAACCCG 60.391 60.000 0.00 0.00 40.09 5.28
1826 1883 0.035343 GGACCAGAGCAAGGTAACCC 60.035 60.000 0.00 0.00 40.09 4.11
1828 1885 0.320697 ACGGACCAGAGCAAGGTAAC 59.679 55.000 0.00 0.00 40.09 2.50
1829 1886 0.606604 GACGGACCAGAGCAAGGTAA 59.393 55.000 0.00 0.00 40.09 2.85
1830 1887 1.255667 GGACGGACCAGAGCAAGGTA 61.256 60.000 0.00 0.00 40.09 3.08
1831 1888 2.584391 GGACGGACCAGAGCAAGGT 61.584 63.158 0.00 0.00 43.46 3.50
1832 1889 2.266055 GGACGGACCAGAGCAAGG 59.734 66.667 0.00 0.00 38.79 3.61
1833 1890 2.232298 GAGGGACGGACCAGAGCAAG 62.232 65.000 0.00 0.00 41.20 4.01
1835 1892 2.680352 GAGGGACGGACCAGAGCA 60.680 66.667 0.00 0.00 41.20 4.26
1836 1893 3.827898 CGAGGGACGGACCAGAGC 61.828 72.222 0.00 0.00 41.20 4.09
1845 1902 0.669077 CTATGAACTCCCGAGGGACG 59.331 60.000 6.80 6.44 39.76 4.79
1846 1903 2.068834 TCTATGAACTCCCGAGGGAC 57.931 55.000 6.80 0.00 39.76 4.46
1847 1904 2.840640 TTCTATGAACTCCCGAGGGA 57.159 50.000 10.89 10.89 42.90 4.20
1848 1905 5.070580 ACTTAATTCTATGAACTCCCGAGGG 59.929 44.000 0.65 0.65 0.00 4.30
1849 1906 5.986135 CACTTAATTCTATGAACTCCCGAGG 59.014 44.000 0.00 0.00 0.00 4.63
1885 1942 8.921205 GTGAGTTAAACTCTATCTATGGGGTTA 58.079 37.037 0.00 0.00 45.27 2.85
1927 1984 3.780804 TTTGTGGAGTTGCTAGCCTTA 57.219 42.857 13.29 0.00 0.00 2.69
2002 2059 4.443394 GCTGTTTTCTCTGCACAATTGAAG 59.557 41.667 13.59 6.82 33.55 3.02
2064 2122 4.876107 CCGCCAGTAGAGATTGTAAACATT 59.124 41.667 0.00 0.00 0.00 2.71
2085 2143 0.940126 AATCATAAGCGCAAGAGCCG 59.060 50.000 11.47 0.00 43.02 5.52
2101 2159 9.994432 CAGTTTTCAGTAAGATATTGTGGAATC 57.006 33.333 0.00 0.00 0.00 2.52
2167 2225 7.657336 ACAACACCACGAGAAATATGAAAAAT 58.343 30.769 0.00 0.00 0.00 1.82
2176 2234 6.460781 TGACTAATACAACACCACGAGAAAT 58.539 36.000 0.00 0.00 0.00 2.17
2200 2258 5.155278 TGGTGTGTCGGTCAAATATTACT 57.845 39.130 0.00 0.00 0.00 2.24
2209 2267 0.179094 GTTCACTGGTGTGTCGGTCA 60.179 55.000 0.53 0.00 44.14 4.02
2212 2270 0.104120 TCAGTTCACTGGTGTGTCGG 59.896 55.000 7.11 0.00 43.91 4.79
2227 2285 0.738389 CAAACGGCACCAAGTTCAGT 59.262 50.000 0.00 0.00 0.00 3.41
2242 2300 6.985188 TCATTGAACAGATACTAGCCAAAC 57.015 37.500 0.00 0.00 0.00 2.93
2272 2338 9.315525 GAGTGTAATTCTATTGAGACCTAAACC 57.684 37.037 0.00 0.00 0.00 3.27
2296 2363 7.412346 CGCATATAACTAAGGCAGCAATTAGAG 60.412 40.741 18.75 2.00 33.96 2.43
2324 2391 9.803315 ACACCATCATACGTATCATATACAATC 57.197 33.333 4.74 0.00 0.00 2.67
2329 2396 8.343168 TGTGACACCATCATACGTATCATATA 57.657 34.615 4.74 0.00 40.28 0.86
2384 2451 3.134081 CCTACGAATCAAAGAGGCCCTTA 59.866 47.826 0.00 0.00 34.00 2.69
2385 2452 2.092914 CCTACGAATCAAAGAGGCCCTT 60.093 50.000 0.00 0.00 36.47 3.95
2386 2453 1.486726 CCTACGAATCAAAGAGGCCCT 59.513 52.381 0.00 0.00 0.00 5.19
2387 2454 1.485066 TCCTACGAATCAAAGAGGCCC 59.515 52.381 0.00 0.00 0.00 5.80
2388 2455 2.981859 TCCTACGAATCAAAGAGGCC 57.018 50.000 0.00 0.00 0.00 5.19
2389 2456 5.819825 AAAATCCTACGAATCAAAGAGGC 57.180 39.130 0.00 0.00 0.00 4.70
2537 2604 9.880157 GTACTACATTTCATAGGAAACCTAACA 57.120 33.333 4.42 0.00 45.22 2.41
2592 2659 9.225436 GGTCCTTTGATTCATAGGATTAGATTC 57.775 37.037 23.34 11.96 41.93 2.52
2877 2945 8.725148 CAATATGCAAGTTGAGAAGAAACTACT 58.275 33.333 7.16 0.00 36.87 2.57
2920 2988 7.837202 TTTGTAATTGGATTACTACACGGAG 57.163 36.000 10.98 0.00 44.17 4.63
2961 3029 6.202331 TCCAGGTCCTATAAGAGAAACATCA 58.798 40.000 0.00 0.00 0.00 3.07
2962 3030 6.732896 TCCAGGTCCTATAAGAGAAACATC 57.267 41.667 0.00 0.00 0.00 3.06
3305 3373 4.079958 ACCCGAGGGAATAAGTAGCAAAAT 60.080 41.667 16.26 0.00 38.96 1.82
3473 3541 3.754965 AGCTTCAGGTTATGCAGAAACA 58.245 40.909 12.36 0.00 0.00 2.83
3649 3718 2.728846 CGTCCATGAAATTCCTGTTGCG 60.729 50.000 0.00 0.00 0.00 4.85
3739 3808 3.975168 ATAAACACAGTAGCTTCCGGT 57.025 42.857 0.00 0.00 0.00 5.28
3741 3810 6.435428 ACAAAAATAAACACAGTAGCTTCCG 58.565 36.000 0.00 0.00 0.00 4.30
3766 3835 7.048629 TGAACTCAATTGGCAAATAAGTCAA 57.951 32.000 3.01 0.00 37.53 3.18
3769 3838 7.444299 ACAATGAACTCAATTGGCAAATAAGT 58.556 30.769 3.01 4.97 0.00 2.24
3810 3879 1.921230 GTTAGCTACTGAGTTGCGCTC 59.079 52.381 12.96 1.40 44.36 5.03
3820 3889 7.588123 CGTACATACAGAAGATGTTAGCTACTG 59.412 40.741 0.00 0.00 39.96 2.74
3962 4032 5.303971 AGAATGAATCGTCAAGATCCCATC 58.696 41.667 0.00 0.00 38.98 3.51
3990 4060 3.561725 GGAAATCCGATCGCTTGATTCTT 59.438 43.478 10.32 0.00 30.70 2.52
4004 4074 1.484240 AGAAGAGGCAGAGGAAATCCG 59.516 52.381 0.00 0.00 42.08 4.18
4062 4135 5.118990 GCAACATACTCCTGTGTGATACAT 58.881 41.667 0.25 0.00 38.92 2.29
4151 4224 0.834612 CCTGTAATCCTGGCCGGTTA 59.165 55.000 11.58 0.12 0.00 2.85
4599 4675 1.228769 GGCCTTCTCCGGGGTTTTT 60.229 57.895 0.00 0.00 0.00 1.94
4635 4713 1.688735 CTCCTATCCTTGACCGATGCA 59.311 52.381 0.00 0.00 0.00 3.96
4815 4893 0.319555 CTTCCTGAAGGCGTCGTCAA 60.320 55.000 7.15 0.00 34.87 3.18


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

AutoCloner maintained by Alex Coulton.