Multiple sequence alignment - TraesCS4D01G203800

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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 TraesCS4D01G203800 chr4D 100.000 2738 0 0 1 2738 350832913 350830176 0.000000e+00 5057.0
1 TraesCS4D01G203800 chr4D 88.462 52 5 1 2456 2506 6828236 6828185 8.190000e-06 62.1
2 TraesCS4D01G203800 chr4D 86.207 58 5 3 2456 2511 96149134 96149078 2.940000e-05 60.2
3 TraesCS4D01G203800 chr4B 89.738 2329 121 43 466 2738 434195018 434192752 0.000000e+00 2868.0
4 TraesCS4D01G203800 chr4B 89.234 418 26 9 10 426 434195419 434195020 3.150000e-139 505.0
5 TraesCS4D01G203800 chr4A 91.348 1803 73 28 111 1873 114141106 114142865 0.000000e+00 2388.0
6 TraesCS4D01G203800 chr4A 86.384 683 41 26 2061 2726 114143049 114143696 0.000000e+00 699.0
7 TraesCS4D01G203800 chr4A 93.750 160 9 1 2566 2724 114152543 114152702 3.520000e-59 239.0
8 TraesCS4D01G203800 chr6A 91.935 62 4 1 2444 2504 49461717 49461656 4.860000e-13 86.1
9 TraesCS4D01G203800 chr1D 100.000 44 0 0 1625 1668 384147318 384147275 6.280000e-12 82.4
10 TraesCS4D01G203800 chr1D 78.070 114 21 4 1432 1543 384147787 384147676 4.890000e-08 69.4
11 TraesCS4D01G203800 chr1B 100.000 44 0 0 1625 1668 515455137 515455094 6.280000e-12 82.4
12 TraesCS4D01G203800 chr1B 78.070 114 21 4 1432 1543 515455604 515455493 4.890000e-08 69.4
13 TraesCS4D01G203800 chr1B 100.000 30 0 0 1117 1146 227927792 227927763 3.810000e-04 56.5
14 TraesCS4D01G203800 chr1A 100.000 44 0 0 1625 1668 483928222 483928179 6.280000e-12 82.4
15 TraesCS4D01G203800 chr7D 92.683 41 3 0 2571 2611 69153992 69154032 2.940000e-05 60.2


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 TraesCS4D01G203800 chr4D 350830176 350832913 2737 True 5057.0 5057 100.000 1 2738 1 chr4D.!!$R3 2737
1 TraesCS4D01G203800 chr4B 434192752 434195419 2667 True 1686.5 2868 89.486 10 2738 2 chr4B.!!$R1 2728
2 TraesCS4D01G203800 chr4A 114141106 114143696 2590 False 1543.5 2388 88.866 111 2726 2 chr4A.!!$F2 2615

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
102 103 0.032615 TCTCTCTCTCTCCCCCAAGC 60.033 60.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1990 0.457443 GCTGGCTTTTGATACCTGCC 59.543 55.0 0.0 0.0 41.17 4.85 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
36 37 5.760253 TCTCTAGTGCAAGAAAAAGACTTGG 59.240 40.000 0.00 0.00 43.12 3.61
48 49 2.310779 AGACTTGGAGCAGTAGACCA 57.689 50.000 0.00 0.00 0.00 4.02
52 53 1.895798 CTTGGAGCAGTAGACCACAGA 59.104 52.381 0.00 0.00 33.20 3.41
56 57 1.215647 GCAGTAGACCACAGACGGG 59.784 63.158 0.00 0.00 0.00 5.28
64 65 2.577059 CACAGACGGGCGGTGTAT 59.423 61.111 5.92 0.00 37.82 2.29
94 95 3.065925 GCTTTCTGCTCTCTCTCTCTCTC 59.934 52.174 0.00 0.00 38.95 3.20
99 100 1.221635 CTCTCTCTCTCTCTCCCCCA 58.778 60.000 0.00 0.00 0.00 4.96
101 102 1.568597 TCTCTCTCTCTCTCCCCCAAG 59.431 57.143 0.00 0.00 0.00 3.61
102 103 0.032615 TCTCTCTCTCTCCCCCAAGC 60.033 60.000 0.00 0.00 0.00 4.01
103 104 1.380515 TCTCTCTCTCCCCCAAGCG 60.381 63.158 0.00 0.00 0.00 4.68
105 106 4.168291 CTCTCTCCCCCAAGCGGC 62.168 72.222 0.00 0.00 0.00 6.53
107 108 4.033776 CTCTCCCCCAAGCGGCAA 62.034 66.667 1.45 0.00 0.00 4.52
108 109 3.567579 CTCTCCCCCAAGCGGCAAA 62.568 63.158 1.45 0.00 0.00 3.68
158 159 1.140589 CACTAGCAGCCACTCCGAG 59.859 63.158 0.00 0.00 0.00 4.63
254 256 4.894896 CCCGCCATGTAAGCCCCC 62.895 72.222 0.00 0.00 0.00 5.40
259 261 2.120909 CCATGTAAGCCCCCAAGCG 61.121 63.158 0.00 0.00 38.01 4.68
304 306 2.091102 TTGTCTGTCCGGTTCGTCCC 62.091 60.000 0.00 0.00 0.00 4.46
338 340 3.882326 CCCGCTCCATGCCTCCAT 61.882 66.667 0.00 0.00 38.78 3.41
339 341 2.281345 CCGCTCCATGCCTCCATC 60.281 66.667 0.00 0.00 38.78 3.51
340 342 2.281345 CGCTCCATGCCTCCATCC 60.281 66.667 0.00 0.00 38.78 3.51
341 343 2.921435 GCTCCATGCCTCCATCCA 59.079 61.111 0.00 0.00 35.15 3.41
342 344 1.459369 GCTCCATGCCTCCATCCAT 59.541 57.895 0.00 0.00 35.15 3.41
343 345 0.894184 GCTCCATGCCTCCATCCATG 60.894 60.000 0.00 0.00 38.78 3.66
344 346 0.894184 CTCCATGCCTCCATCCATGC 60.894 60.000 0.00 0.00 37.96 4.06
345 347 1.152631 CCATGCCTCCATCCATGCA 60.153 57.895 0.00 0.00 37.96 3.96
346 348 0.757561 CCATGCCTCCATCCATGCAA 60.758 55.000 0.00 0.00 37.96 4.08
347 349 1.338107 CATGCCTCCATCCATGCAAT 58.662 50.000 0.00 0.00 37.27 3.56
348 350 1.000843 CATGCCTCCATCCATGCAATG 59.999 52.381 0.00 0.00 46.21 2.82
415 422 1.373999 GCCTCTAGCGCTAGCCATG 60.374 63.158 34.65 23.15 46.67 3.66
426 433 1.747709 CTAGCCATGACAGCAAGCTT 58.252 50.000 0.00 0.00 38.30 3.74
427 434 1.669779 CTAGCCATGACAGCAAGCTTC 59.330 52.381 0.00 0.00 38.30 3.86
428 435 1.136147 GCCATGACAGCAAGCTTCG 59.864 57.895 0.00 0.00 0.00 3.79
429 436 1.580845 GCCATGACAGCAAGCTTCGT 61.581 55.000 0.00 0.00 0.00 3.85
430 437 0.167470 CCATGACAGCAAGCTTCGTG 59.833 55.000 0.00 14.21 0.00 4.35
431 438 1.150827 CATGACAGCAAGCTTCGTGA 58.849 50.000 10.85 0.00 0.00 4.35
432 439 1.736126 CATGACAGCAAGCTTCGTGAT 59.264 47.619 10.85 0.00 0.00 3.06
433 440 1.150827 TGACAGCAAGCTTCGTGATG 58.849 50.000 10.85 6.13 38.35 3.07
434 441 1.270252 TGACAGCAAGCTTCGTGATGA 60.270 47.619 9.02 0.00 35.93 2.92
450 462 8.446599 TTCGTGATGAGTGAGTAGTATGATTA 57.553 34.615 0.00 0.00 0.00 1.75
478 495 1.018226 GTTGCGATGCTCACTGCTCT 61.018 55.000 0.00 0.00 43.37 4.09
479 496 0.532115 TTGCGATGCTCACTGCTCTA 59.468 50.000 0.00 0.00 43.37 2.43
480 497 0.749049 TGCGATGCTCACTGCTCTAT 59.251 50.000 0.00 0.00 43.37 1.98
481 498 1.138337 GCGATGCTCACTGCTCTATG 58.862 55.000 0.00 0.00 43.37 2.23
482 499 1.780806 CGATGCTCACTGCTCTATGG 58.219 55.000 0.00 0.00 43.37 2.74
598 615 4.400251 CCACACTATTTGCCAGTGATTGAT 59.600 41.667 9.33 0.00 45.10 2.57
608 625 3.691118 GCCAGTGATTGATTCTGCACTTA 59.309 43.478 0.00 0.00 39.40 2.24
614 631 6.888632 AGTGATTGATTCTGCACTTAAGGATT 59.111 34.615 7.53 0.00 38.34 3.01
644 666 2.954611 GGCGAAGGAAACAGCACC 59.045 61.111 0.00 0.00 0.00 5.01
651 673 4.966787 GAAACAGCACCGGGGCCA 62.967 66.667 28.92 0.00 0.00 5.36
652 674 4.974721 AAACAGCACCGGGGCCAG 62.975 66.667 28.92 21.93 0.00 4.85
674 699 7.205297 CCAGAAAGAATGAAAGAAAAAGAGCA 58.795 34.615 0.00 0.00 0.00 4.26
819 848 1.021390 CATGGACGACCTGGAAGCAC 61.021 60.000 0.00 0.00 37.04 4.40
1170 1208 5.681982 CAGTTCCTCAGATTACGATTACGAC 59.318 44.000 0.00 0.00 42.66 4.34
1199 1237 3.966665 AGAGGAAGAGCAAGAGGAATAGG 59.033 47.826 0.00 0.00 0.00 2.57
1211 1249 6.268847 GCAAGAGGAATAGGAGGAAGAAGATA 59.731 42.308 0.00 0.00 0.00 1.98
1212 1250 7.038373 GCAAGAGGAATAGGAGGAAGAAGATAT 60.038 40.741 0.00 0.00 0.00 1.63
1287 1326 1.131883 ACTACAATCGTCGTCTTCCCG 59.868 52.381 0.00 0.00 0.00 5.14
1302 1343 1.696063 TCCCGTCCCCTAATTCGTAG 58.304 55.000 0.00 0.00 0.00 3.51
1407 1483 4.625742 ACGTCGACATCAGAATTGGTTAAG 59.374 41.667 17.16 0.00 0.00 1.85
1409 1485 5.444613 CGTCGACATCAGAATTGGTTAAGTG 60.445 44.000 17.16 0.00 0.00 3.16
1421 1497 3.692690 TGGTTAAGTGATTAAGGTGGGC 58.307 45.455 0.00 0.00 0.00 5.36
1467 1545 2.820059 AGAGAAGTGCATGACGTTCA 57.180 45.000 0.00 0.00 0.00 3.18
1548 1626 3.470888 CCTCCACAGGTAGGCCGG 61.471 72.222 0.00 0.00 40.50 6.13
1593 1671 6.788598 TCCTCTGATCAGCAGGAATATATC 57.211 41.667 27.76 0.00 44.98 1.63
1614 1692 2.929531 ATCTGTACTGACGCTGAGTG 57.070 50.000 4.39 0.00 0.00 3.51
1671 1749 2.156343 ACAAGGAGTTCTTCGACAGC 57.844 50.000 0.00 0.00 32.41 4.40
1712 1799 4.648626 AGGCCGAAGCAGCAGCAA 62.649 61.111 3.17 0.00 45.49 3.91
1780 1867 1.293924 CTTGCTCTAGATGTTGGCCG 58.706 55.000 0.00 0.00 0.00 6.13
1817 1904 9.881529 AGTAGAACGAATAATTAGAAGATCGAC 57.118 33.333 11.71 6.75 34.62 4.20
1873 1982 0.960364 GTGGTGGTGCATGTACAGGG 60.960 60.000 16.11 1.13 0.00 4.45
1874 1983 1.378762 GGTGGTGCATGTACAGGGT 59.621 57.895 16.11 0.00 0.00 4.34
1875 1984 0.676782 GGTGGTGCATGTACAGGGTC 60.677 60.000 16.11 0.00 0.00 4.46
1876 1985 0.036164 GTGGTGCATGTACAGGGTCA 59.964 55.000 16.11 1.10 0.00 4.02
1877 1986 0.324614 TGGTGCATGTACAGGGTCAG 59.675 55.000 16.11 0.00 0.00 3.51
1878 1987 0.392998 GGTGCATGTACAGGGTCAGG 60.393 60.000 16.11 0.00 0.00 3.86
1879 1988 0.324943 GTGCATGTACAGGGTCAGGT 59.675 55.000 9.91 0.00 0.00 4.00
1880 1989 1.064003 TGCATGTACAGGGTCAGGTT 58.936 50.000 9.91 0.00 0.00 3.50
1881 1990 1.271325 TGCATGTACAGGGTCAGGTTG 60.271 52.381 9.91 0.00 0.00 3.77
1882 1991 1.950484 GCATGTACAGGGTCAGGTTGG 60.950 57.143 9.91 0.00 0.00 3.77
1883 1992 0.328258 ATGTACAGGGTCAGGTTGGC 59.672 55.000 0.33 0.00 0.00 4.52
1884 1993 1.057275 TGTACAGGGTCAGGTTGGCA 61.057 55.000 0.00 0.00 0.00 4.92
1885 1994 0.321653 GTACAGGGTCAGGTTGGCAG 60.322 60.000 0.00 0.00 0.00 4.85
1886 1995 1.488705 TACAGGGTCAGGTTGGCAGG 61.489 60.000 0.00 0.00 0.00 4.85
1887 1996 2.450502 AGGGTCAGGTTGGCAGGT 60.451 61.111 0.00 0.00 0.00 4.00
1928 2037 4.813161 ACTGTTGCGATATTCTTCAGATGG 59.187 41.667 0.00 0.00 0.00 3.51
1929 2038 5.022282 TGTTGCGATATTCTTCAGATGGA 57.978 39.130 0.00 0.00 0.00 3.41
1930 2039 5.052481 TGTTGCGATATTCTTCAGATGGAG 58.948 41.667 0.00 0.00 0.00 3.86
1931 2040 4.944619 TGCGATATTCTTCAGATGGAGT 57.055 40.909 0.00 0.00 0.00 3.85
1932 2041 6.183360 TGTTGCGATATTCTTCAGATGGAGTA 60.183 38.462 0.00 0.00 0.00 2.59
1933 2042 5.773575 TGCGATATTCTTCAGATGGAGTAC 58.226 41.667 0.00 0.00 0.00 2.73
1934 2043 4.854291 GCGATATTCTTCAGATGGAGTACG 59.146 45.833 0.00 0.00 0.00 3.67
1961 2070 4.842531 ATTGTACTCATCATGTGTCCCA 57.157 40.909 0.00 0.00 0.00 4.37
2004 2159 0.878416 TGGTCCAAGCAACGCATTAC 59.122 50.000 0.00 0.00 0.00 1.89
2045 2200 2.809665 GCTCCTGCAATCGGATTCTCAT 60.810 50.000 0.00 0.00 39.41 2.90
2079 2234 7.169140 CCCCTCATAACGAACAAAAAGAAAAAG 59.831 37.037 0.00 0.00 0.00 2.27
2091 2246 0.672711 AGAAAAAGCGCGGTAGTCCC 60.673 55.000 12.91 0.00 0.00 4.46
2168 2324 5.296035 CGGGAAAATGGAGGAAACATACTAC 59.704 44.000 0.00 0.00 0.00 2.73
2169 2325 6.424032 GGGAAAATGGAGGAAACATACTACT 58.576 40.000 0.00 0.00 0.00 2.57
2170 2326 6.318900 GGGAAAATGGAGGAAACATACTACTG 59.681 42.308 0.00 0.00 0.00 2.74
2171 2327 6.884836 GGAAAATGGAGGAAACATACTACTGT 59.115 38.462 0.00 0.00 0.00 3.55
2172 2328 7.393515 GGAAAATGGAGGAAACATACTACTGTT 59.606 37.037 0.00 0.00 41.01 3.16
2422 2586 4.522405 GGCAAAATGGGCAAAAATAACCTT 59.478 37.500 0.00 0.00 0.00 3.50
2475 2650 3.586470 TTTCACCAGCTGACCCTTTTA 57.414 42.857 17.39 0.00 0.00 1.52
2483 2658 2.236395 AGCTGACCCTTTTATGTAGCGT 59.764 45.455 0.00 0.00 35.04 5.07
2484 2659 2.608090 GCTGACCCTTTTATGTAGCGTC 59.392 50.000 0.00 0.00 0.00 5.19
2486 2661 2.199236 GACCCTTTTATGTAGCGTCCG 58.801 52.381 0.00 0.00 0.00 4.79
2487 2662 1.826720 ACCCTTTTATGTAGCGTCCGA 59.173 47.619 0.00 0.00 0.00 4.55
2488 2663 2.199236 CCCTTTTATGTAGCGTCCGAC 58.801 52.381 0.00 0.00 0.00 4.79
2489 2664 2.417651 CCCTTTTATGTAGCGTCCGACA 60.418 50.000 0.00 0.00 0.00 4.35
2490 2665 2.858344 CCTTTTATGTAGCGTCCGACAG 59.142 50.000 0.00 0.00 30.04 3.51
2491 2666 2.572191 TTTATGTAGCGTCCGACAGG 57.428 50.000 0.00 0.00 39.46 4.00
2492 2667 1.466856 TTATGTAGCGTCCGACAGGT 58.533 50.000 0.00 0.38 39.05 4.00
2493 2668 1.019673 TATGTAGCGTCCGACAGGTC 58.980 55.000 0.00 0.00 39.05 3.85
2506 2681 1.064296 CAGGTCGGCGCTACACTAG 59.936 63.158 7.64 0.00 0.00 2.57
2512 2687 0.450583 CGGCGCTACACTAGACTGAA 59.549 55.000 7.64 0.00 0.00 3.02
2517 2692 3.003897 GCGCTACACTAGACTGAATAGCT 59.996 47.826 0.00 0.00 34.26 3.32
2524 2699 5.830457 ACACTAGACTGAATAGCTGCTGATA 59.170 40.000 13.43 0.00 0.00 2.15
2525 2700 6.148948 CACTAGACTGAATAGCTGCTGATAC 58.851 44.000 13.43 1.94 0.00 2.24
2527 2702 4.942852 AGACTGAATAGCTGCTGATACAC 58.057 43.478 13.43 0.00 0.00 2.90
2528 2703 3.711086 ACTGAATAGCTGCTGATACACG 58.289 45.455 13.43 4.72 0.00 4.49
2529 2704 2.473816 TGAATAGCTGCTGATACACGC 58.526 47.619 13.43 0.00 0.00 5.34
2530 2705 1.795286 GAATAGCTGCTGATACACGCC 59.205 52.381 13.43 0.00 0.00 5.68
2533 2708 1.153568 GCTGCTGATACACGCCTGA 60.154 57.895 0.00 0.00 0.00 3.86
2583 2769 1.276421 CCCACCTCACCTCTAGTTGTG 59.724 57.143 7.73 7.73 0.00 3.33
2586 2772 1.620819 ACCTCACCTCTAGTTGTGCAG 59.379 52.381 8.83 7.63 32.51 4.41
2589 2775 1.374758 ACCTCTAGTTGTGCAGCGC 60.375 57.895 0.00 0.00 0.00 5.92
2613 2799 0.870307 CCGACATGCGCTACACTACC 60.870 60.000 9.73 0.00 39.11 3.18
2616 2802 2.194271 GACATGCGCTACACTACCTTC 58.806 52.381 9.73 0.00 0.00 3.46
2716 2907 3.647590 ACAAACCCCAAGAGCATTTGAAT 59.352 39.130 2.27 0.00 34.93 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.068264 CACTAGAGAACTGTGCGAGCA 60.068 52.381 0.00 0.00 0.00 4.26
1 2 1.623359 CACTAGAGAACTGTGCGAGC 58.377 55.000 0.00 0.00 0.00 5.03
2 3 1.623359 GCACTAGAGAACTGTGCGAG 58.377 55.000 0.00 0.00 45.62 5.03
3 4 3.794690 GCACTAGAGAACTGTGCGA 57.205 52.632 0.00 0.00 45.62 5.10
6 7 5.991328 TTTTCTTGCACTAGAGAACTGTG 57.009 39.130 0.00 0.00 32.01 3.66
7 8 6.258947 GTCTTTTTCTTGCACTAGAGAACTGT 59.741 38.462 0.00 0.00 32.01 3.55
8 9 6.481644 AGTCTTTTTCTTGCACTAGAGAACTG 59.518 38.462 0.00 0.00 32.01 3.16
36 37 0.171455 CCGTCTGTGGTCTACTGCTC 59.829 60.000 0.00 0.00 0.00 4.26
48 49 2.577059 CATACACCGCCCGTCTGT 59.423 61.111 0.00 0.00 0.00 3.41
52 53 3.451004 TACGCATACACCGCCCGT 61.451 61.111 0.00 0.00 36.07 5.28
56 57 1.082117 AAGCTGTACGCATACACCGC 61.082 55.000 11.30 0.00 42.61 5.68
61 62 2.721129 GCAGAAAGCTGTACGCATAC 57.279 50.000 11.30 0.00 44.17 2.39
74 75 3.620488 GGAGAGAGAGAGAGAGCAGAAA 58.380 50.000 0.00 0.00 0.00 2.52
105 106 4.389576 GCAGTCACGCCCGCTTTG 62.390 66.667 0.00 0.00 0.00 2.77
158 159 4.157656 TCATTCAAATCAATTGGTCCCGAC 59.842 41.667 5.42 0.00 39.62 4.79
343 345 3.613737 GTGTACAACATGCATTCCATTGC 59.386 43.478 0.00 0.00 43.07 3.56
344 346 4.175516 GGTGTACAACATGCATTCCATTG 58.824 43.478 5.89 2.31 29.71 2.82
345 347 3.119531 CGGTGTACAACATGCATTCCATT 60.120 43.478 12.27 0.00 29.71 3.16
346 348 2.423185 CGGTGTACAACATGCATTCCAT 59.577 45.455 12.27 0.00 33.39 3.41
347 349 1.809547 CGGTGTACAACATGCATTCCA 59.190 47.619 12.27 0.00 0.00 3.53
348 350 1.132262 CCGGTGTACAACATGCATTCC 59.868 52.381 12.27 0.00 0.00 3.01
349 351 1.132262 CCCGGTGTACAACATGCATTC 59.868 52.381 12.27 0.00 0.00 2.67
415 422 1.392853 CTCATCACGAAGCTTGCTGTC 59.607 52.381 2.10 0.00 0.00 3.51
426 433 6.944234 AATCATACTACTCACTCATCACGA 57.056 37.500 0.00 0.00 0.00 4.35
427 434 7.866729 AGTAATCATACTACTCACTCATCACG 58.133 38.462 0.00 0.00 40.62 4.35
428 435 9.457110 CAAGTAATCATACTACTCACTCATCAC 57.543 37.037 0.00 0.00 41.57 3.06
429 436 9.408648 TCAAGTAATCATACTACTCACTCATCA 57.591 33.333 0.00 0.00 41.57 3.07
450 462 3.372206 GTGAGCATCGCAACTAATCAAGT 59.628 43.478 0.00 0.00 46.97 3.16
478 495 3.104512 CACTGTGTACTTCCTCCCCATA 58.895 50.000 0.00 0.00 0.00 2.74
479 496 1.909302 CACTGTGTACTTCCTCCCCAT 59.091 52.381 0.00 0.00 0.00 4.00
480 497 1.132977 TCACTGTGTACTTCCTCCCCA 60.133 52.381 7.79 0.00 0.00 4.96
481 498 1.640917 TCACTGTGTACTTCCTCCCC 58.359 55.000 7.79 0.00 0.00 4.81
482 499 2.289506 GGTTCACTGTGTACTTCCTCCC 60.290 54.545 15.61 0.00 0.00 4.30
598 615 4.697352 GCTTGAGAATCCTTAAGTGCAGAA 59.303 41.667 0.97 0.00 38.04 3.02
608 625 0.460987 CGGCTCGCTTGAGAATCCTT 60.461 55.000 0.00 0.00 42.66 3.36
632 654 4.660938 GCCCCGGTGCTGTTTCCT 62.661 66.667 0.00 0.00 0.00 3.36
635 657 4.974721 CTGGCCCCGGTGCTGTTT 62.975 66.667 9.33 0.00 0.00 2.83
644 666 1.474077 CTTTCATTCTTTCTGGCCCCG 59.526 52.381 0.00 0.00 0.00 5.73
651 673 6.922407 GCTGCTCTTTTTCTTTCATTCTTTCT 59.078 34.615 0.00 0.00 0.00 2.52
652 674 6.129247 CGCTGCTCTTTTTCTTTCATTCTTTC 60.129 38.462 0.00 0.00 0.00 2.62
653 675 5.689068 CGCTGCTCTTTTTCTTTCATTCTTT 59.311 36.000 0.00 0.00 0.00 2.52
674 699 1.146263 GGATTCGGGATTCCACGCT 59.854 57.895 4.80 0.00 32.57 5.07
1100 1138 4.400109 GCGTGCAGAGTCGACGGA 62.400 66.667 10.46 0.00 33.68 4.69
1170 1208 0.898320 TTGCTCTTCCTCTTCCTCGG 59.102 55.000 0.00 0.00 0.00 4.63
1199 1237 7.278875 CAGGGCCATATTATATCTTCTTCCTC 58.721 42.308 6.18 0.00 0.00 3.71
1211 1249 1.909302 CGTCTCCCAGGGCCATATTAT 59.091 52.381 6.18 0.00 0.00 1.28
1212 1250 1.132977 TCGTCTCCCAGGGCCATATTA 60.133 52.381 6.18 0.00 0.00 0.98
1287 1326 3.814005 TCAAGCTACGAATTAGGGGAC 57.186 47.619 0.00 0.00 0.00 4.46
1316 1357 2.743510 GCTAGCTAGAAGAACCAAGGGC 60.744 54.545 25.15 0.75 0.00 5.19
1407 1483 5.580691 GCAAATTAAAGCCCACCTTAATCAC 59.419 40.000 0.00 0.00 32.20 3.06
1409 1485 5.729510 TGCAAATTAAAGCCCACCTTAATC 58.270 37.500 0.00 0.00 32.20 1.75
1467 1545 1.129917 CACTCCTCCATGCTCATCCT 58.870 55.000 0.00 0.00 0.00 3.24
1542 1620 2.125106 GATTTGAGACGCCGGCCT 60.125 61.111 23.46 13.78 0.00 5.19
1548 1626 4.606457 AGCAGTAATTGATTTGAGACGC 57.394 40.909 0.00 0.00 0.00 5.19
1593 1671 3.242903 CCACTCAGCGTCAGTACAGATAG 60.243 52.174 0.00 0.00 0.00 2.08
1614 1692 4.332637 CACACTGCAAGCACGCCC 62.333 66.667 0.00 0.00 37.60 6.13
1712 1799 4.614112 TGCTGTCGCTGCTGCTGT 62.614 61.111 14.03 0.00 36.97 4.40
1780 1867 7.807687 TTATTCGTTCTACTAAGTGCAGAAC 57.192 36.000 6.61 6.61 42.67 3.01
1873 1982 2.489938 TTGATACCTGCCAACCTGAC 57.510 50.000 0.00 0.00 0.00 3.51
1874 1983 3.420893 CTTTTGATACCTGCCAACCTGA 58.579 45.455 0.00 0.00 0.00 3.86
1875 1984 2.094545 GCTTTTGATACCTGCCAACCTG 60.095 50.000 0.00 0.00 0.00 4.00
1876 1985 2.171003 GCTTTTGATACCTGCCAACCT 58.829 47.619 0.00 0.00 0.00 3.50
1877 1986 1.204704 GGCTTTTGATACCTGCCAACC 59.795 52.381 0.00 0.00 42.79 3.77
1878 1987 2.654749 GGCTTTTGATACCTGCCAAC 57.345 50.000 0.00 0.00 42.79 3.77
1881 1990 0.457443 GCTGGCTTTTGATACCTGCC 59.543 55.000 0.00 0.00 41.17 4.85
1882 1991 1.403323 GAGCTGGCTTTTGATACCTGC 59.597 52.381 0.00 0.00 45.69 4.85
1883 1992 1.667724 CGAGCTGGCTTTTGATACCTG 59.332 52.381 0.00 0.00 0.00 4.00
1884 1993 1.279271 ACGAGCTGGCTTTTGATACCT 59.721 47.619 0.00 0.00 0.00 3.08
1885 1994 1.739067 ACGAGCTGGCTTTTGATACC 58.261 50.000 0.00 0.00 0.00 2.73
1886 1995 3.307242 CAGTACGAGCTGGCTTTTGATAC 59.693 47.826 0.00 0.00 33.11 2.24
1887 1996 3.056107 ACAGTACGAGCTGGCTTTTGATA 60.056 43.478 13.53 0.00 40.59 2.15
1961 2070 1.277557 GCACACAGTGGGAGAGAAGAT 59.722 52.381 7.11 0.00 33.64 2.40
2054 2209 7.306574 GCTTTTTCTTTTTGTTCGTTATGAGGG 60.307 37.037 0.00 0.00 0.00 4.30
2091 2246 2.205074 AGAACAGTGTTTCTCTGTGCG 58.795 47.619 10.45 0.00 43.89 5.34
2168 2324 3.257393 ACTTCTCGCTGAGCATAAACAG 58.743 45.455 4.88 0.00 0.00 3.16
2169 2325 3.319137 ACTTCTCGCTGAGCATAAACA 57.681 42.857 4.88 0.00 0.00 2.83
2170 2326 3.799420 CCTACTTCTCGCTGAGCATAAAC 59.201 47.826 4.88 0.00 0.00 2.01
2171 2327 3.447586 ACCTACTTCTCGCTGAGCATAAA 59.552 43.478 4.88 0.00 0.00 1.40
2172 2328 3.024547 ACCTACTTCTCGCTGAGCATAA 58.975 45.455 4.88 0.00 0.00 1.90
2394 2558 2.447586 TTTGCCCATTTTGCCTCGCC 62.448 55.000 0.00 0.00 0.00 5.54
2422 2586 4.320861 CCATTGTGAATTAGTGGCGTTTCA 60.321 41.667 0.00 0.00 0.00 2.69
2475 2650 1.807886 GACCTGTCGGACGCTACAT 59.192 57.895 3.34 0.00 0.00 2.29
2486 2661 1.651240 TAGTGTAGCGCCGACCTGTC 61.651 60.000 2.29 0.00 0.00 3.51
2487 2662 1.654954 CTAGTGTAGCGCCGACCTGT 61.655 60.000 2.29 0.00 0.00 4.00
2488 2663 1.064296 CTAGTGTAGCGCCGACCTG 59.936 63.158 2.29 0.00 0.00 4.00
2489 2664 1.077930 TCTAGTGTAGCGCCGACCT 60.078 57.895 2.29 5.13 0.00 3.85
2490 2665 1.063811 GTCTAGTGTAGCGCCGACC 59.936 63.158 2.29 0.00 0.00 4.79
2491 2666 0.248134 CAGTCTAGTGTAGCGCCGAC 60.248 60.000 2.29 2.81 0.00 4.79
2492 2667 0.392060 TCAGTCTAGTGTAGCGCCGA 60.392 55.000 2.29 0.00 0.00 5.54
2493 2668 0.450583 TTCAGTCTAGTGTAGCGCCG 59.549 55.000 2.29 0.00 0.00 6.46
2494 2669 2.873133 ATTCAGTCTAGTGTAGCGCC 57.127 50.000 2.29 0.00 0.00 6.53
2495 2670 3.003897 AGCTATTCAGTCTAGTGTAGCGC 59.996 47.826 0.00 0.00 39.47 5.92
2496 2671 4.532276 CAGCTATTCAGTCTAGTGTAGCG 58.468 47.826 0.00 0.00 39.47 4.26
2497 2672 4.037446 AGCAGCTATTCAGTCTAGTGTAGC 59.963 45.833 0.00 0.00 35.88 3.58
2506 2681 3.733224 CGTGTATCAGCAGCTATTCAGTC 59.267 47.826 0.00 0.00 0.00 3.51
2512 2687 1.043816 AGGCGTGTATCAGCAGCTAT 58.956 50.000 0.00 0.00 34.54 2.97
2517 2692 1.153842 CGTCAGGCGTGTATCAGCA 60.154 57.895 6.26 0.00 35.54 4.41
2524 2699 4.640855 CGACACCGTCAGGCGTGT 62.641 66.667 6.26 0.00 42.76 4.49
2528 2703 3.188786 GATGCGACACCGTCAGGC 61.189 66.667 0.00 0.00 42.76 4.85
2529 2704 2.509336 GGATGCGACACCGTCAGG 60.509 66.667 0.00 0.00 45.13 3.86
2530 2705 1.807165 CAGGATGCGACACCGTCAG 60.807 63.158 0.00 0.00 38.24 3.51
2533 2708 2.573869 CTCAGGATGCGACACCGT 59.426 61.111 0.00 0.00 38.24 4.83
2544 2730 3.333219 CCTTGCCCAGCCTCAGGA 61.333 66.667 0.00 0.00 0.00 3.86
2583 2769 4.899239 ATGTCGGCTAGGCGCTGC 62.899 66.667 31.86 22.98 44.92 5.25
2589 2775 1.661821 GTAGCGCATGTCGGCTAGG 60.662 63.158 11.47 0.00 38.94 3.02
2613 2799 1.015109 TCGTCTAGGCGCTACAGAAG 58.985 55.000 12.97 9.91 0.00 2.85
2616 2802 1.400846 TCTTTCGTCTAGGCGCTACAG 59.599 52.381 12.97 4.98 0.00 2.74
2685 2876 4.548513 GGGGTTTGTGTGGGGGCA 62.549 66.667 0.00 0.00 0.00 5.36
2716 2907 0.183014 AGGGAATCGCGACTCCTCTA 59.817 55.000 32.79 0.00 31.88 2.43


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

AutoCloner maintained by Alex Coulton.