Multiple sequence alignment - TraesCS1D01G078300

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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 TraesCS1D01G078300 chr1D 100.000 2387 0 0 1 2387 60184867 60187253 0.000000e+00 4409.0
1 TraesCS1D01G078300 chr1D 98.462 130 1 1 1763 1892 60186586 60186714 6.640000e-56 228.0
2 TraesCS1D01G078300 chr1D 98.462 130 1 1 1720 1848 60186629 60186758 6.640000e-56 228.0
3 TraesCS1D01G078300 chr1D 97.701 87 1 1 1806 1892 60186586 60186671 5.320000e-32 148.0
4 TraesCS1D01G078300 chr1D 97.701 87 1 1 1720 1805 60186672 60186758 5.320000e-32 148.0
5 TraesCS1D01G078300 chr1D 87.356 87 3 2 757 835 60185577 60185663 2.530000e-15 93.5
6 TraesCS1D01G078300 chr1D 87.356 87 3 2 711 797 60185623 60185701 2.530000e-15 93.5
7 TraesCS1D01G078300 chr1D 97.674 43 1 0 1850 1892 60186586 60186628 9.150000e-10 75.0
8 TraesCS1D01G078300 chr1D 97.674 43 1 0 1720 1762 60186716 60186758 9.150000e-10 75.0
9 TraesCS1D01G078300 chr1A 96.057 837 25 2 801 1629 58860060 58860896 0.000000e+00 1356.0
10 TraesCS1D01G078300 chr1A 90.420 762 62 6 1 760 58859351 58860103 0.000000e+00 992.0
11 TraesCS1D01G078300 chr1A 100.000 41 0 0 757 797 58860054 58860094 2.540000e-10 76.8
12 TraesCS1D01G078300 chr1A 82.609 69 12 0 512 580 462135945 462135877 7.120000e-06 62.1
13 TraesCS1D01G078300 chr1B 95.191 811 29 3 801 1602 96313915 96314724 0.000000e+00 1273.0
14 TraesCS1D01G078300 chr1B 91.093 494 40 3 1806 2298 96314938 96315428 0.000000e+00 665.0
15 TraesCS1D01G078300 chr1B 98.204 167 3 0 1639 1805 96314857 96315023 2.320000e-75 292.0
16 TraesCS1D01G078300 chr1B 98.837 86 1 0 1763 1848 96314938 96315023 1.140000e-33 154.0
17 TraesCS1D01G078300 chr1B 89.623 106 11 0 280 385 96313669 96313774 4.140000e-28 135.0
18 TraesCS1D01G078300 chr1B 100.000 43 0 0 1720 1762 96314981 96315023 1.970000e-11 80.5
19 TraesCS1D01G078300 chr1B 97.674 43 0 1 756 798 96313909 96313950 3.290000e-09 73.1
20 TraesCS1D01G078300 chr2B 86.992 861 59 21 805 1616 62418516 62417660 0.000000e+00 920.0
21 TraesCS1D01G078300 chr2A 90.075 534 42 7 990 1513 3755152 3754620 0.000000e+00 682.0
22 TraesCS1D01G078300 chr2D 94.005 417 24 1 987 1403 5174619 5175034 4.330000e-177 630.0
23 TraesCS1D01G078300 chr2D 81.618 544 87 12 1850 2387 322851021 322851557 2.820000e-119 438.0
24 TraesCS1D01G078300 chr3B 79.602 402 67 14 1996 2387 564106960 564106564 8.410000e-70 274.0
25 TraesCS1D01G078300 chr4A 80.233 344 58 10 2049 2387 176781304 176780966 1.420000e-62 250.0
26 TraesCS1D01G078300 chr4A 77.841 352 66 10 2042 2386 454758360 454758014 8.650000e-50 207.0
27 TraesCS1D01G078300 chr7D 81.579 266 42 7 2126 2387 127138438 127138176 1.860000e-51 213.0
28 TraesCS1D01G078300 chr3A 79.514 288 44 12 2108 2387 161467861 161467581 8.710000e-45 191.0
29 TraesCS1D01G078300 chr5A 74.498 498 98 24 1905 2387 645875525 645876008 3.130000e-44 189.0
30 TraesCS1D01G078300 chr5A 74.424 434 88 19 1965 2387 377416633 377416212 5.280000e-37 165.0
31 TraesCS1D01G078300 chr5B 82.323 198 30 5 2181 2377 549676936 549676743 1.470000e-37 167.0
32 TraesCS1D01G078300 chr4D 90.769 65 6 0 501 565 416090935 416090999 1.180000e-13 87.9


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 TraesCS1D01G078300 chr1D 60184867 60187253 2386 False 610.888889 4409 95.820667 1 2387 9 chr1D.!!$F1 2386
1 TraesCS1D01G078300 chr1A 58859351 58860896 1545 False 808.266667 1356 95.492333 1 1629 3 chr1A.!!$F1 1628
2 TraesCS1D01G078300 chr1B 96313669 96315428 1759 False 381.800000 1273 95.803143 280 2298 7 chr1B.!!$F1 2018
3 TraesCS1D01G078300 chr2B 62417660 62418516 856 True 920.000000 920 86.992000 805 1616 1 chr2B.!!$R1 811
4 TraesCS1D01G078300 chr2A 3754620 3755152 532 True 682.000000 682 90.075000 990 1513 1 chr2A.!!$R1 523
5 TraesCS1D01G078300 chr2D 322851021 322851557 536 False 438.000000 438 81.618000 1850 2387 1 chr2D.!!$F2 537

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
102 104 0.099968 CTCCAATGCAACTGCCATCG 59.900 55.0 0.0 0.0 41.18 3.84 F
496 498 0.109086 ACAGTGACCTGAATCGCTCG 60.109 55.0 0.0 0.0 41.50 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1407 0.039617 GCGAGCTAGACGATGCAGAT 60.040 55.0 12.59 0.00 0.0 2.90 R
1616 1678 0.107993 TTTCCGAGAGATGCTGCAGG 60.108 55.0 17.12 2.49 0.0 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 0.871057 GAATATCGCCAGAAGCAGCC 59.129 55.000 0.00 0.00 44.04 4.85
44 45 2.433318 AGAAGCAGCCGCGAAGAC 60.433 61.111 8.23 0.00 45.49 3.01
58 60 1.656095 CGAAGACCTTGCGAAGATGAC 59.344 52.381 0.00 0.00 0.00 3.06
62 64 0.389948 ACCTTGCGAAGATGACGGTC 60.390 55.000 0.00 0.00 0.00 4.79
76 78 5.357032 AGATGACGGTCAAAAACAAAGAGTT 59.643 36.000 15.72 0.00 43.89 3.01
83 85 5.289595 GTCAAAAACAAAGAGTTGATCCCC 58.710 41.667 0.00 0.00 41.19 4.81
93 95 1.358787 AGTTGATCCCCTCCAATGCAA 59.641 47.619 0.00 0.00 0.00 4.08
97 99 0.685458 ATCCCCTCCAATGCAACTGC 60.685 55.000 0.00 0.00 42.50 4.40
102 104 0.099968 CTCCAATGCAACTGCCATCG 59.900 55.000 0.00 0.00 41.18 3.84
110 112 1.586422 CAACTGCCATCGGATAGGTG 58.414 55.000 0.00 0.00 0.00 4.00
123 125 3.477530 GGATAGGTGGACAATAGCCAAC 58.522 50.000 0.00 0.00 43.57 3.77
137 139 0.727398 GCCAACAGTATCAGCGAACC 59.273 55.000 0.00 0.00 0.00 3.62
151 153 2.247311 CGAACCGCCAAATGAAGAAG 57.753 50.000 0.00 0.00 0.00 2.85
170 172 3.443045 GCCGCCAACATCACCCTG 61.443 66.667 0.00 0.00 0.00 4.45
208 210 2.223618 GCTCCAGCAAACCGTAACAAAA 60.224 45.455 0.00 0.00 41.59 2.44
210 212 2.099427 TCCAGCAAACCGTAACAAAACC 59.901 45.455 0.00 0.00 0.00 3.27
214 216 3.054166 GCAAACCGTAACAAAACCCATC 58.946 45.455 0.00 0.00 0.00 3.51
240 242 1.619432 GCACATCAAATCCCTCCCCAA 60.619 52.381 0.00 0.00 0.00 4.12
242 244 1.340991 ACATCAAATCCCTCCCCAACG 60.341 52.381 0.00 0.00 0.00 4.10
271 273 2.066999 CCCCTCTGTAGACAGCCCC 61.067 68.421 4.72 0.00 43.46 5.80
272 274 1.306141 CCCTCTGTAGACAGCCCCA 60.306 63.158 4.72 0.00 43.46 4.96
278 280 0.766674 TGTAGACAGCCCCAACTGGT 60.767 55.000 0.00 0.00 42.21 4.00
322 324 3.695606 GCCCTCTCAGTCGCCACA 61.696 66.667 0.00 0.00 0.00 4.17
360 362 1.825474 AGACTTACGGTCCCACTCATG 59.175 52.381 0.00 0.00 45.54 3.07
392 394 2.683859 CCATGCGTCCACACAGCTG 61.684 63.158 13.48 13.48 0.00 4.24
400 402 2.791158 CGTCCACACAGCTGAACAAAAC 60.791 50.000 23.35 9.93 0.00 2.43
412 414 5.638234 AGCTGAACAAAACGACCTATAGAAC 59.362 40.000 0.00 0.00 0.00 3.01
414 416 6.073440 GCTGAACAAAACGACCTATAGAACAA 60.073 38.462 0.00 0.00 0.00 2.83
431 433 1.071605 CAAGCTAACTCACGCAGTCC 58.928 55.000 0.00 0.00 41.61 3.85
434 436 1.355066 GCTAACTCACGCAGTCCAGC 61.355 60.000 6.13 6.13 41.61 4.85
455 457 1.341852 TCACATTTGGACGACCGAGAA 59.658 47.619 0.00 0.00 39.42 2.87
496 498 0.109086 ACAGTGACCTGAATCGCTCG 60.109 55.000 0.00 0.00 41.50 5.03
498 500 0.109086 AGTGACCTGAATCGCTCGTG 60.109 55.000 0.00 0.00 34.24 4.35
517 519 1.810151 TGGGAGTTTAACGAGCAATGC 59.190 47.619 0.00 0.00 0.00 3.56
522 524 4.435651 GGAGTTTAACGAGCAATGCTACAC 60.436 45.833 8.12 0.00 39.88 2.90
547 549 6.537660 CCTACGAAAGGTTAGGTAAGGAATTG 59.462 42.308 0.00 0.00 40.94 2.32
572 574 7.067737 TGACGTAATTGATGATGTGGAGTACTA 59.932 37.037 0.00 0.00 0.00 1.82
574 576 8.082852 ACGTAATTGATGATGTGGAGTACTATC 58.917 37.037 0.00 0.00 0.00 2.08
580 582 6.554605 TGATGATGTGGAGTACTATCATTGGA 59.445 38.462 16.40 5.47 37.51 3.53
582 584 5.305386 TGATGTGGAGTACTATCATTGGAGG 59.695 44.000 0.00 0.00 0.00 4.30
583 585 3.967326 TGTGGAGTACTATCATTGGAGGG 59.033 47.826 0.00 0.00 0.00 4.30
584 586 3.325135 GTGGAGTACTATCATTGGAGGGG 59.675 52.174 0.00 0.00 0.00 4.79
585 587 2.907042 GGAGTACTATCATTGGAGGGGG 59.093 54.545 0.00 0.00 0.00 5.40
586 588 3.439558 GGAGTACTATCATTGGAGGGGGA 60.440 52.174 0.00 0.00 0.00 4.81
587 589 3.835395 GAGTACTATCATTGGAGGGGGAG 59.165 52.174 0.00 0.00 0.00 4.30
611 613 4.041075 GGGGGCAAAAGAATTAGTTGGAAA 59.959 41.667 0.00 0.00 0.00 3.13
645 648 8.857098 GGTGTCCAGTAGATGTAGTATTATTCA 58.143 37.037 0.00 0.00 0.00 2.57
682 685 7.439108 ACTAGGGTGCTTAGTGATTTAGAAT 57.561 36.000 0.00 0.00 30.46 2.40
711 714 1.135333 GCCCAAACCAAAACTCGTCAA 59.865 47.619 0.00 0.00 0.00 3.18
712 715 2.223947 GCCCAAACCAAAACTCGTCAAT 60.224 45.455 0.00 0.00 0.00 2.57
713 716 3.739830 GCCCAAACCAAAACTCGTCAATT 60.740 43.478 0.00 0.00 0.00 2.32
714 717 4.438148 CCCAAACCAAAACTCGTCAATTT 58.562 39.130 0.00 0.00 0.00 1.82
715 718 4.873259 CCCAAACCAAAACTCGTCAATTTT 59.127 37.500 0.00 0.00 0.00 1.82
716 719 5.352846 CCCAAACCAAAACTCGTCAATTTTT 59.647 36.000 0.00 0.00 0.00 1.94
741 744 9.463902 TTTGTAACTTCTCTATAGTCTAGCAGT 57.536 33.333 0.00 0.00 0.00 4.40
742 745 9.463902 TTGTAACTTCTCTATAGTCTAGCAGTT 57.536 33.333 9.02 9.02 0.00 3.16
745 748 7.739498 ACTTCTCTATAGTCTAGCAGTTAGC 57.261 40.000 0.00 0.00 46.19 3.09
962 975 1.071385 AGTCACAGTGAGGAAAGCAGG 59.929 52.381 2.53 0.00 0.00 4.85
970 983 0.405973 GAGGAAAGCAGGGAAAGGGT 59.594 55.000 0.00 0.00 0.00 4.34
1372 1407 3.989838 ATCGTCCTCGGCGTCTGGA 62.990 63.158 6.85 10.75 37.69 3.86
1522 1583 6.121590 TGTGCCTTTGATGCTGATATTTAGA 58.878 36.000 0.00 0.00 0.00 2.10
1602 1664 6.601613 GGGAACTTGGTAATTGTATCACATGA 59.398 38.462 0.00 0.00 0.00 3.07
1616 1678 2.937591 CACATGATGTGCTGAACAACC 58.062 47.619 13.15 0.00 41.89 3.77
1629 1691 0.403271 AACAACCCTGCAGCATCTCT 59.597 50.000 8.66 0.00 0.00 3.10
1630 1692 0.035630 ACAACCCTGCAGCATCTCTC 60.036 55.000 8.66 0.00 0.00 3.20
1631 1693 1.088340 CAACCCTGCAGCATCTCTCG 61.088 60.000 8.66 0.00 0.00 4.04
1632 1694 2.108566 CCCTGCAGCATCTCTCGG 59.891 66.667 8.66 0.00 0.00 4.63
1633 1695 2.429767 CCCTGCAGCATCTCTCGGA 61.430 63.158 8.66 0.00 0.00 4.55
1635 1697 0.107993 CCTGCAGCATCTCTCGGAAA 60.108 55.000 8.66 0.00 0.00 3.13
1636 1698 1.676916 CCTGCAGCATCTCTCGGAAAA 60.677 52.381 8.66 0.00 0.00 2.29
1680 1844 1.451067 CTCAGAAGGAGCTTGCTTGG 58.549 55.000 0.00 0.00 36.69 3.61
1730 1894 3.084786 CCTCAGGTCCAAAAATGTCCTC 58.915 50.000 0.00 0.00 0.00 3.71
1802 1966 9.878667 ACATGAAAATGATTATGAATGCAAAGA 57.121 25.926 0.00 0.00 0.00 2.52
1834 1998 6.867662 GTCCTCGGACATGAAAATGATTAT 57.132 37.500 11.12 0.00 44.02 1.28
1835 1999 6.662616 GTCCTCGGACATGAAAATGATTATG 58.337 40.000 11.12 0.00 44.02 1.90
1836 2000 6.483307 GTCCTCGGACATGAAAATGATTATGA 59.517 38.462 11.12 0.00 44.02 2.15
1837 2001 7.012327 GTCCTCGGACATGAAAATGATTATGAA 59.988 37.037 11.12 0.00 44.02 2.57
1838 2002 7.720957 TCCTCGGACATGAAAATGATTATGAAT 59.279 33.333 0.00 0.00 0.00 2.57
1839 2003 7.806487 CCTCGGACATGAAAATGATTATGAATG 59.194 37.037 0.00 0.00 0.00 2.67
1840 2004 7.140705 TCGGACATGAAAATGATTATGAATGC 58.859 34.615 0.00 0.00 0.00 3.56
1841 2005 6.919115 CGGACATGAAAATGATTATGAATGCA 59.081 34.615 0.00 0.00 0.00 3.96
1842 2006 7.435784 CGGACATGAAAATGATTATGAATGCAA 59.564 33.333 0.00 0.00 0.00 4.08
1843 2007 9.100554 GGACATGAAAATGATTATGAATGCAAA 57.899 29.630 0.00 0.00 0.00 3.68
1845 2009 9.878667 ACATGAAAATGATTATGAATGCAAAGA 57.121 25.926 0.00 0.00 0.00 2.52
1882 2046 7.720957 TCCTCGGACATGAAAATGATTATGAAT 59.279 33.333 0.00 0.00 0.00 2.57
1883 2047 7.806487 CCTCGGACATGAAAATGATTATGAATG 59.194 37.037 0.00 0.00 0.00 2.67
1886 2050 7.597369 CGGACATGAAAATGATTATGAATGCAT 59.403 33.333 0.00 0.00 38.54 3.96
1887 2051 9.917129 GGACATGAAAATGATTATGAATGCATA 57.083 29.630 0.00 0.00 35.94 3.14
1928 2092 1.135199 CGCCTACGAAGCCAAAGACTA 60.135 52.381 0.00 0.00 43.93 2.59
1946 2110 5.542779 AGACTAAAGATGAAGCAACGACTT 58.457 37.500 0.00 0.00 0.00 3.01
1969 2133 1.112113 GGAGCCGAGTAATGTCCTCA 58.888 55.000 0.00 0.00 0.00 3.86
1981 2145 6.102663 AGTAATGTCCTCAGTTTGAAGATCG 58.897 40.000 0.00 0.00 0.00 3.69
2036 2200 1.041447 ATACTAACTGCGTCGGCCCT 61.041 55.000 0.00 0.00 38.85 5.19
2078 2244 3.053842 ACCCCTAGACGATCAACTAGTGA 60.054 47.826 16.65 0.00 41.67 3.41
2106 2272 1.462035 GCCAGGCCCCATGATGTAT 59.538 57.895 0.00 0.00 0.00 2.29
2139 2305 0.669318 TTCCTAAGACTTGGCGCACG 60.669 55.000 10.83 0.00 0.00 5.34
2150 2316 4.077188 GCGCACGCTCCAAGACAC 62.077 66.667 7.96 0.00 38.26 3.67
2151 2317 3.767230 CGCACGCTCCAAGACACG 61.767 66.667 0.00 0.00 0.00 4.49
2168 2334 1.958579 CACGATGTAATCCTCGGGGTA 59.041 52.381 0.00 0.00 41.39 3.69
2178 2344 1.639628 TCCTCGGGGTATCTATCTCCC 59.360 57.143 0.00 0.00 40.41 4.30
2193 2359 0.822164 CTCCCGATGTAACCGACCTT 59.178 55.000 0.00 0.00 0.00 3.50
2207 2373 2.824341 CCGACCTTGGTGTAACTCTAGT 59.176 50.000 0.00 0.00 36.74 2.57
2208 2374 4.012374 CCGACCTTGGTGTAACTCTAGTA 58.988 47.826 0.00 0.00 36.74 1.82
2212 2379 4.202760 ACCTTGGTGTAACTCTAGTACCCT 60.203 45.833 0.00 0.00 36.74 4.34
2243 2410 7.665145 GTCTATATAAGTCGAGGGGTTTAGACT 59.335 40.741 12.01 0.00 44.81 3.24
2301 2468 7.066404 CGAGGTAGATCAGCATGTACTATGTAT 59.934 40.741 0.00 0.00 37.40 2.29
2303 2470 8.112822 AGGTAGATCAGCATGTACTATGTATCT 58.887 37.037 0.00 8.86 37.40 1.98
2304 2471 8.402472 GGTAGATCAGCATGTACTATGTATCTC 58.598 40.741 0.00 10.76 37.40 2.75
2305 2472 7.403312 AGATCAGCATGTACTATGTATCTCC 57.597 40.000 0.00 0.00 37.40 3.71
2306 2473 5.984695 TCAGCATGTACTATGTATCTCCC 57.015 43.478 0.00 0.00 37.40 4.30
2310 2477 4.322801 GCATGTACTATGTATCTCCCCCAC 60.323 50.000 0.00 0.00 0.00 4.61
2322 2489 4.879295 TCTCCCCCACAATCAATACAAT 57.121 40.909 0.00 0.00 0.00 2.71
2324 2491 5.690865 TCTCCCCCACAATCAATACAATAC 58.309 41.667 0.00 0.00 0.00 1.89
2328 2495 5.451798 CCCCCACAATCAATACAATACAAGC 60.452 44.000 0.00 0.00 0.00 4.01
2329 2496 5.273170 CCCACAATCAATACAATACAAGCG 58.727 41.667 0.00 0.00 0.00 4.68
2357 2524 5.915758 CGTAGGATTTTACATCTTCGAGAGG 59.084 44.000 0.00 0.00 31.33 3.69
2361 2528 1.120530 TTACATCTTCGAGAGGGCCC 58.879 55.000 16.46 16.46 28.79 5.80
2363 2530 2.127869 CATCTTCGAGAGGGCCCGA 61.128 63.158 18.44 6.98 0.00 5.14
2366 2533 3.372554 CTTCGAGAGGGCCCGAACC 62.373 68.421 18.44 7.31 39.49 3.62
2377 2544 2.936928 CCCGAACCTGGGTAAACAC 58.063 57.895 0.00 0.00 44.76 3.32
2379 2546 1.624813 CCCGAACCTGGGTAAACACTA 59.375 52.381 0.00 0.00 44.76 2.74
2383 2550 3.930848 CGAACCTGGGTAAACACTATGTC 59.069 47.826 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.656095 CGTCATCTTCGCAAGGTCTTC 59.344 52.381 0.00 0.00 38.47 2.87
44 45 0.389817 TGACCGTCATCTTCGCAAGG 60.390 55.000 0.00 0.00 38.47 3.61
50 51 5.816919 TCTTTGTTTTTGACCGTCATCTTC 58.183 37.500 1.09 0.00 0.00 2.87
58 60 4.976116 GGATCAACTCTTTGTTTTTGACCG 59.024 41.667 0.00 0.00 36.63 4.79
62 64 5.509670 GGAGGGGATCAACTCTTTGTTTTTG 60.510 44.000 13.51 0.00 36.63 2.44
76 78 1.002069 AGTTGCATTGGAGGGGATCA 58.998 50.000 0.00 0.00 0.00 2.92
83 85 0.099968 CGATGGCAGTTGCATTGGAG 59.900 55.000 6.43 0.00 44.36 3.86
93 95 0.398522 TCCACCTATCCGATGGCAGT 60.399 55.000 0.00 0.00 33.20 4.40
97 99 3.617531 GCTATTGTCCACCTATCCGATGG 60.618 52.174 0.00 0.00 34.58 3.51
102 104 3.118038 TGTTGGCTATTGTCCACCTATCC 60.118 47.826 0.00 0.00 32.45 2.59
110 112 3.561725 GCTGATACTGTTGGCTATTGTCC 59.438 47.826 0.00 0.00 0.00 4.02
180 182 4.344865 TTTGCTGGAGCGGGGGTC 62.345 66.667 0.00 0.00 45.83 4.46
208 210 3.338250 ATGTGCGGTGGGATGGGT 61.338 61.111 0.00 0.00 0.00 4.51
210 212 0.964860 TTTGATGTGCGGTGGGATGG 60.965 55.000 0.00 0.00 0.00 3.51
214 216 1.666209 GGGATTTGATGTGCGGTGGG 61.666 60.000 0.00 0.00 0.00 4.61
252 254 1.001760 GGGCTGTCTACAGAGGGGA 59.998 63.158 14.21 0.00 46.59 4.81
254 256 0.909610 TTGGGGCTGTCTACAGAGGG 60.910 60.000 14.21 0.00 46.59 4.30
271 273 1.300620 TCGCTCGGTTGACCAGTTG 60.301 57.895 0.51 0.00 35.14 3.16
272 274 1.300697 GTCGCTCGGTTGACCAGTT 60.301 57.895 0.51 0.00 35.14 3.16
278 280 2.354188 CACGTGTCGCTCGGTTGA 60.354 61.111 7.58 0.00 0.00 3.18
322 324 5.053978 AGTCTTTCTTGGTCAAAGGTGAT 57.946 39.130 0.00 0.00 35.80 3.06
360 362 3.171388 ATGGGGCCCGATCTGTCC 61.171 66.667 19.83 0.00 0.00 4.02
392 394 6.147328 AGCTTGTTCTATAGGTCGTTTTGTTC 59.853 38.462 0.00 0.00 0.00 3.18
400 402 5.972382 GTGAGTTAGCTTGTTCTATAGGTCG 59.028 44.000 0.00 0.00 0.00 4.79
412 414 1.071605 GGACTGCGTGAGTTAGCTTG 58.928 55.000 0.00 0.00 33.83 4.01
414 416 0.244994 CTGGACTGCGTGAGTTAGCT 59.755 55.000 0.00 0.00 33.83 3.32
429 431 0.684535 TCGTCCAAATGTGAGCTGGA 59.315 50.000 0.00 0.00 36.89 3.86
431 433 0.798776 GGTCGTCCAAATGTGAGCTG 59.201 55.000 0.00 0.00 0.00 4.24
434 436 1.067846 TCTCGGTCGTCCAAATGTGAG 60.068 52.381 0.00 0.00 0.00 3.51
496 498 2.414161 GCATTGCTCGTTAAACTCCCAC 60.414 50.000 0.16 0.00 0.00 4.61
498 500 2.084546 AGCATTGCTCGTTAAACTCCC 58.915 47.619 5.03 0.00 30.62 4.30
534 536 8.479689 TCATCAATTACGTCAATTCCTTACCTA 58.520 33.333 0.00 0.00 34.49 3.08
535 537 7.335627 TCATCAATTACGTCAATTCCTTACCT 58.664 34.615 0.00 0.00 34.49 3.08
536 538 7.548196 TCATCAATTACGTCAATTCCTTACC 57.452 36.000 0.00 0.00 34.49 2.85
537 539 8.612619 ACATCATCAATTACGTCAATTCCTTAC 58.387 33.333 0.00 0.00 34.49 2.34
538 540 8.611757 CACATCATCAATTACGTCAATTCCTTA 58.388 33.333 0.00 0.00 34.49 2.69
547 549 6.273825 AGTACTCCACATCATCAATTACGTC 58.726 40.000 0.00 0.00 0.00 4.34
572 574 1.387926 CCCCTCCCCCTCCAATGAT 60.388 63.158 0.00 0.00 0.00 2.45
574 576 3.105928 CCCCCTCCCCCTCCAATG 61.106 72.222 0.00 0.00 0.00 2.82
611 613 5.828871 ACATCTACTGGACACCTACTAACT 58.171 41.667 0.00 0.00 0.00 2.24
682 685 6.426646 AGTTTTGGTTTGGGCATGTTAATA 57.573 33.333 0.00 0.00 0.00 0.98
687 690 1.068434 CGAGTTTTGGTTTGGGCATGT 59.932 47.619 0.00 0.00 0.00 3.21
691 694 0.741915 TGACGAGTTTTGGTTTGGGC 59.258 50.000 0.00 0.00 0.00 5.36
715 718 9.463902 ACTGCTAGACTATAGAGAAGTTACAAA 57.536 33.333 6.78 0.00 0.00 2.83
716 719 9.463902 AACTGCTAGACTATAGAGAAGTTACAA 57.536 33.333 6.78 0.00 0.00 2.41
719 722 9.275398 GCTAACTGCTAGACTATAGAGAAGTTA 57.725 37.037 15.12 15.12 38.95 2.24
720 723 7.229907 GGCTAACTGCTAGACTATAGAGAAGTT 59.770 40.741 14.63 14.63 42.39 2.66
721 724 6.713450 GGCTAACTGCTAGACTATAGAGAAGT 59.287 42.308 6.78 0.56 42.39 3.01
722 725 6.712998 TGGCTAACTGCTAGACTATAGAGAAG 59.287 42.308 6.78 0.00 42.39 2.85
723 726 6.602278 TGGCTAACTGCTAGACTATAGAGAA 58.398 40.000 6.78 0.00 42.39 2.87
724 727 6.189036 TGGCTAACTGCTAGACTATAGAGA 57.811 41.667 6.78 0.00 42.39 3.10
725 728 6.885952 TTGGCTAACTGCTAGACTATAGAG 57.114 41.667 6.78 0.00 42.39 2.43
726 729 7.841282 ATTTGGCTAACTGCTAGACTATAGA 57.159 36.000 6.78 0.00 42.39 1.98
727 730 8.894768 AAATTTGGCTAACTGCTAGACTATAG 57.105 34.615 0.00 0.00 42.39 1.31
728 731 9.109393 CAAAATTTGGCTAACTGCTAGACTATA 57.891 33.333 0.00 0.00 42.39 1.31
729 732 7.829211 TCAAAATTTGGCTAACTGCTAGACTAT 59.171 33.333 5.83 0.00 42.39 2.12
730 733 7.165485 TCAAAATTTGGCTAACTGCTAGACTA 58.835 34.615 5.83 0.00 42.39 2.59
731 734 6.003950 TCAAAATTTGGCTAACTGCTAGACT 58.996 36.000 5.83 0.00 42.39 3.24
732 735 6.254281 TCAAAATTTGGCTAACTGCTAGAC 57.746 37.500 5.83 0.00 42.39 2.59
733 736 6.892658 TTCAAAATTTGGCTAACTGCTAGA 57.107 33.333 5.83 0.00 42.39 2.43
734 737 8.538409 AATTTCAAAATTTGGCTAACTGCTAG 57.462 30.769 5.83 0.00 37.28 3.42
735 738 8.900983 AAATTTCAAAATTTGGCTAACTGCTA 57.099 26.923 11.58 0.00 44.46 3.49
736 739 7.806409 AAATTTCAAAATTTGGCTAACTGCT 57.194 28.000 11.58 0.00 44.46 4.24
737 740 8.854979 AAAAATTTCAAAATTTGGCTAACTGC 57.145 26.923 12.78 0.00 45.16 4.40
798 801 8.569641 CCGCTAGACTATAGAGAAGTTACAATT 58.430 37.037 6.78 0.00 0.00 2.32
799 802 7.720515 ACCGCTAGACTATAGAGAAGTTACAAT 59.279 37.037 6.78 0.00 0.00 2.71
800 803 7.052873 ACCGCTAGACTATAGAGAAGTTACAA 58.947 38.462 6.78 0.00 0.00 2.41
801 804 6.590068 ACCGCTAGACTATAGAGAAGTTACA 58.410 40.000 6.78 0.00 0.00 2.41
802 805 7.495135 AACCGCTAGACTATAGAGAAGTTAC 57.505 40.000 6.78 0.00 0.00 2.50
803 806 7.387397 GCTAACCGCTAGACTATAGAGAAGTTA 59.613 40.741 6.78 4.87 35.14 2.24
1208 1243 3.771160 GGAGGCGGAAGAAGGCGA 61.771 66.667 0.00 0.00 39.33 5.54
1372 1407 0.039617 GCGAGCTAGACGATGCAGAT 60.040 55.000 12.59 0.00 0.00 2.90
1522 1583 5.509670 GCTAAAGGCCAAAATGAGAAACAGT 60.510 40.000 5.01 0.00 34.27 3.55
1602 1664 0.467844 TGCAGGGTTGTTCAGCACAT 60.468 50.000 0.00 0.00 34.43 3.21
1616 1678 0.107993 TTTCCGAGAGATGCTGCAGG 60.108 55.000 17.12 2.49 0.00 4.85
1629 1691 0.536460 GCTCCACCCAGTTTTTCCGA 60.536 55.000 0.00 0.00 0.00 4.55
1630 1692 1.524008 GGCTCCACCCAGTTTTTCCG 61.524 60.000 0.00 0.00 0.00 4.30
1631 1693 0.178961 AGGCTCCACCCAGTTTTTCC 60.179 55.000 0.00 0.00 40.58 3.13
1632 1694 2.579410 TAGGCTCCACCCAGTTTTTC 57.421 50.000 0.00 0.00 40.58 2.29
1633 1695 4.668138 TTATAGGCTCCACCCAGTTTTT 57.332 40.909 0.00 0.00 40.58 1.94
1635 1697 3.785887 TCATTATAGGCTCCACCCAGTTT 59.214 43.478 0.00 0.00 40.58 2.66
1636 1698 3.392616 CTCATTATAGGCTCCACCCAGTT 59.607 47.826 0.00 0.00 40.58 3.16
1680 1844 0.462759 CGAATGGGTCCCTTGAGAGC 60.463 60.000 10.00 0.00 0.00 4.09
1690 1854 1.712018 GCCTTTACGCCGAATGGGTC 61.712 60.000 0.00 0.00 41.04 4.46
1730 1894 6.919115 TGCATTCATAATCATTTTCATGTCCG 59.081 34.615 0.00 0.00 0.00 4.79
1811 1975 6.483307 TCATAATCATTTTCATGTCCGAGGAC 59.517 38.462 14.98 14.98 44.77 3.85
1812 1976 6.591001 TCATAATCATTTTCATGTCCGAGGA 58.409 36.000 0.00 0.00 0.00 3.71
1813 1977 6.866010 TCATAATCATTTTCATGTCCGAGG 57.134 37.500 0.00 0.00 0.00 4.63
1814 1978 7.325338 GCATTCATAATCATTTTCATGTCCGAG 59.675 37.037 0.00 0.00 0.00 4.63
1815 1979 7.140705 GCATTCATAATCATTTTCATGTCCGA 58.859 34.615 0.00 0.00 0.00 4.55
1816 1980 6.919115 TGCATTCATAATCATTTTCATGTCCG 59.081 34.615 0.00 0.00 0.00 4.79
1817 1981 8.651391 TTGCATTCATAATCATTTTCATGTCC 57.349 30.769 0.00 0.00 0.00 4.02
1819 1983 9.878667 TCTTTGCATTCATAATCATTTTCATGT 57.121 25.926 0.00 0.00 0.00 3.21
1855 2019 6.483307 TCATAATCATTTTCATGTCCGAGGAC 59.517 38.462 14.98 14.98 44.77 3.85
1861 2025 8.827177 ATGCATTCATAATCATTTTCATGTCC 57.173 30.769 0.00 0.00 0.00 4.02
1870 2034 9.281371 CCCGATATCTATGCATTCATAATCATT 57.719 33.333 3.54 0.00 34.97 2.57
1871 2035 8.435187 ACCCGATATCTATGCATTCATAATCAT 58.565 33.333 3.54 0.00 34.97 2.45
1873 2037 8.668510 AACCCGATATCTATGCATTCATAATC 57.331 34.615 3.54 1.81 34.97 1.75
1875 2039 7.882791 ACAAACCCGATATCTATGCATTCATAA 59.117 33.333 3.54 0.00 34.97 1.90
1877 2041 6.240894 ACAAACCCGATATCTATGCATTCAT 58.759 36.000 3.54 0.00 36.73 2.57
1882 2046 7.051623 AGTTTAACAAACCCGATATCTATGCA 58.948 34.615 0.34 0.00 42.34 3.96
1883 2047 7.492352 AGTTTAACAAACCCGATATCTATGC 57.508 36.000 0.34 0.00 42.34 3.14
1886 2050 5.750067 GCGAGTTTAACAAACCCGATATCTA 59.250 40.000 9.45 0.00 44.05 1.98
1887 2051 4.569564 GCGAGTTTAACAAACCCGATATCT 59.430 41.667 9.45 0.00 44.05 1.98
1921 2085 5.992217 AGTCGTTGCTTCATCTTTAGTCTTT 59.008 36.000 0.00 0.00 0.00 2.52
1928 2092 3.476552 TCCAAGTCGTTGCTTCATCTTT 58.523 40.909 0.00 0.00 31.64 2.52
1946 2110 1.112113 GACATTACTCGGCTCCTCCA 58.888 55.000 0.00 0.00 34.01 3.86
1959 2123 5.046591 ACCGATCTTCAAACTGAGGACATTA 60.047 40.000 0.00 0.00 35.26 1.90
1969 2133 3.872630 GCCCCTAAACCGATCTTCAAACT 60.873 47.826 0.00 0.00 0.00 2.66
1981 2145 0.753111 CCATCAGCAGCCCCTAAACC 60.753 60.000 0.00 0.00 0.00 3.27
2026 2190 4.301027 CCATCCTAGGGCCGACGC 62.301 72.222 9.46 0.00 0.00 5.19
2036 2200 1.457643 CTCGACCCAGCCCATCCTA 60.458 63.158 0.00 0.00 0.00 2.94
2061 2227 3.377485 GTGGCTCACTAGTTGATCGTCTA 59.623 47.826 0.00 0.00 32.17 2.59
2123 2289 1.687494 GAGCGTGCGCCAAGTCTTAG 61.687 60.000 13.21 0.00 43.17 2.18
2124 2290 1.736645 GAGCGTGCGCCAAGTCTTA 60.737 57.895 13.21 0.00 43.17 2.10
2139 2305 2.866762 GGATTACATCGTGTCTTGGAGC 59.133 50.000 0.00 0.00 0.00 4.70
2151 2317 6.130569 AGATAGATACCCCGAGGATTACATC 58.869 44.000 0.00 0.00 36.73 3.06
2178 2344 1.337447 ACACCAAGGTCGGTTACATCG 60.337 52.381 0.00 0.00 37.07 3.84
2193 2359 3.614092 CGAGGGTACTAGAGTTACACCA 58.386 50.000 0.00 0.00 0.00 4.17
2207 2373 5.012046 TCGACTTATATAGACACCGAGGGTA 59.988 44.000 0.00 0.00 32.11 3.69
2208 2374 4.070716 CGACTTATATAGACACCGAGGGT 58.929 47.826 0.00 0.00 35.62 4.34
2212 2379 4.321718 CCCTCGACTTATATAGACACCGA 58.678 47.826 0.00 0.00 0.00 4.69
2261 2428 5.205759 TCTACCTCGAGATCGTATGTGTA 57.794 43.478 15.71 3.17 40.80 2.90
2287 2454 3.838317 TGGGGGAGATACATAGTACATGC 59.162 47.826 0.00 0.00 0.00 4.06
2301 2468 4.879295 ATTGTATTGATTGTGGGGGAGA 57.121 40.909 0.00 0.00 0.00 3.71
2303 2470 5.458451 TGTATTGTATTGATTGTGGGGGA 57.542 39.130 0.00 0.00 0.00 4.81
2304 2471 5.451798 GCTTGTATTGTATTGATTGTGGGGG 60.452 44.000 0.00 0.00 0.00 5.40
2305 2472 5.591099 GCTTGTATTGTATTGATTGTGGGG 58.409 41.667 0.00 0.00 0.00 4.96
2306 2473 5.273170 CGCTTGTATTGTATTGATTGTGGG 58.727 41.667 0.00 0.00 0.00 4.61
2310 2477 5.510671 GTCCCGCTTGTATTGTATTGATTG 58.489 41.667 0.00 0.00 0.00 2.67
2322 2489 1.477553 AATCCTACGTCCCGCTTGTA 58.522 50.000 0.00 0.00 0.00 2.41
2324 2491 1.734163 AAAATCCTACGTCCCGCTTG 58.266 50.000 0.00 0.00 0.00 4.01
2328 2495 4.317671 AGATGTAAAATCCTACGTCCCG 57.682 45.455 0.00 0.00 38.19 5.14
2329 2496 4.743644 CGAAGATGTAAAATCCTACGTCCC 59.256 45.833 0.00 0.00 38.19 4.46
2339 2506 3.433740 GGGCCCTCTCGAAGATGTAAAAT 60.434 47.826 17.04 0.00 33.89 1.82
2346 2513 1.381327 TTCGGGCCCTCTCGAAGAT 60.381 57.895 22.43 0.00 39.94 2.40
2361 2528 3.930848 GACATAGTGTTTACCCAGGTTCG 59.069 47.826 0.00 0.00 0.00 3.95
2363 2530 3.009805 GGGACATAGTGTTTACCCAGGTT 59.990 47.826 0.00 0.00 33.45 3.50


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

AutoCloner maintained by Alex Coulton.