Multiple sequence alignment - TraesCS5A01G467300

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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 TraesCS5A01G467300 chr5A 100.000 4057 0 0 1 4057 645142093 645138037 0.000000e+00 7492.0
1 TraesCS5A01G467300 chr5B 90.150 2731 130 47 1 2661 650355243 650352582 0.000000e+00 3424.0
2 TraesCS5A01G467300 chr5B 91.634 1291 64 14 2792 4057 650352529 650351258 0.000000e+00 1746.0
3 TraesCS5A01G467300 chr5B 94.118 51 3 0 2716 2766 650352583 650352533 1.210000e-10 78.7
4 TraesCS5A01G467300 chr5D 93.304 2016 88 21 1 1994 517768342 517766352 0.000000e+00 2931.0
5 TraesCS5A01G467300 chr5D 93.910 1330 58 9 2744 4057 517765197 517763875 0.000000e+00 1986.0
6 TraesCS5A01G467300 chr5D 92.019 426 22 9 2017 2435 517766152 517765732 4.520000e-164 588.0
7 TraesCS5A01G467300 chr2B 91.367 417 23 6 1403 1810 33465204 33465616 3.540000e-155 558.0
8 TraesCS5A01G467300 chr2B 91.127 417 24 6 1403 1810 33414306 33414718 1.650000e-153 553.0
9 TraesCS5A01G467300 chr2B 89.928 417 29 5 1403 1810 98122176 98121764 3.590000e-145 525.0
10 TraesCS5A01G467300 chr2B 89.688 417 31 6 1403 1810 687327438 687327851 4.650000e-144 521.0
11 TraesCS5A01G467300 chr2B 80.890 607 94 19 3466 4057 790870493 790869894 3.700000e-125 459.0
12 TraesCS5A01G467300 chr7B 89.928 417 30 4 1403 1810 723521823 723521410 9.990000e-146 527.0
13 TraesCS5A01G467300 chr7B 80.816 245 39 7 5 244 710374897 710374656 6.920000e-43 185.0
14 TraesCS5A01G467300 chr4B 89.688 417 31 7 1403 1810 600318725 600318312 4.650000e-144 521.0
15 TraesCS5A01G467300 chr3B 89.448 417 32 4 1403 1810 189601713 189602126 2.160000e-142 516.0
16 TraesCS5A01G467300 chr6B 81.353 606 94 16 3466 4057 132127848 132128448 3.670000e-130 475.0
17 TraesCS5A01G467300 chr6B 81.054 607 94 18 3466 4057 132122683 132123283 7.940000e-127 464.0
18 TraesCS5A01G467300 chr1A 81.250 608 93 20 3466 4057 561685544 561684942 4.750000e-129 472.0
19 TraesCS5A01G467300 chr1A 80.738 244 39 7 5 244 36534364 36534125 2.490000e-42 183.0
20 TraesCS5A01G467300 chr1A 94.737 57 3 0 2650 2706 371079099 371079043 5.590000e-14 89.8
21 TraesCS5A01G467300 chr6A 81.054 607 92 20 3466 4057 24186477 24185879 2.860000e-126 462.0
22 TraesCS5A01G467300 chr6A 100.000 50 0 0 2657 2706 157958132 157958181 4.320000e-15 93.5
23 TraesCS5A01G467300 chr2D 80.467 599 94 20 3466 4048 35308451 35307860 1.730000e-118 436.0
24 TraesCS5A01G467300 chr2D 81.148 244 38 7 5 244 143239689 143239450 5.350000e-44 189.0
25 TraesCS5A01G467300 chr3D 80.233 602 97 18 3466 4052 610803763 610803169 2.240000e-117 433.0
26 TraesCS5A01G467300 chr3D 80.738 244 39 7 5 244 398729180 398729419 2.490000e-42 183.0
27 TraesCS5A01G467300 chr3D 90.323 62 4 2 2647 2706 31871138 31871077 3.360000e-11 80.5
28 TraesCS5A01G467300 chr6D 80.738 244 39 7 5 244 153078397 153078636 2.490000e-42 183.0
29 TraesCS5A01G467300 chr4D 80.579 242 43 4 5 244 151027378 151027617 2.490000e-42 183.0
30 TraesCS5A01G467300 chr4D 80.738 244 39 8 5 244 242430422 242430661 2.490000e-42 183.0
31 TraesCS5A01G467300 chr4D 94.545 55 1 2 2653 2706 175961505 175961558 2.600000e-12 84.2
32 TraesCS5A01G467300 chr7A 96.429 56 2 0 2656 2711 534326763 534326708 4.320000e-15 93.5
33 TraesCS5A01G467300 chr7D 91.803 61 4 1 2647 2706 11409317 11409257 2.600000e-12 84.2
34 TraesCS5A01G467300 chr1D 94.545 55 1 2 2653 2706 136673604 136673551 2.600000e-12 84.2
35 TraesCS5A01G467300 chr1D 94.545 55 1 2 2653 2706 171522508 171522561 2.600000e-12 84.2
36 TraesCS5A01G467300 chr1D 94.545 55 1 2 2653 2706 305479187 305479240 2.600000e-12 84.2


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 TraesCS5A01G467300 chr5A 645138037 645142093 4056 True 7492.000000 7492 100.000000 1 4057 1 chr5A.!!$R1 4056
1 TraesCS5A01G467300 chr5B 650351258 650355243 3985 True 1749.566667 3424 91.967333 1 4057 3 chr5B.!!$R1 4056
2 TraesCS5A01G467300 chr5D 517763875 517768342 4467 True 1835.000000 2931 93.077667 1 4057 3 chr5D.!!$R1 4056
3 TraesCS5A01G467300 chr2B 790869894 790870493 599 True 459.000000 459 80.890000 3466 4057 1 chr2B.!!$R2 591
4 TraesCS5A01G467300 chr6B 132127848 132128448 600 False 475.000000 475 81.353000 3466 4057 1 chr6B.!!$F2 591
5 TraesCS5A01G467300 chr6B 132122683 132123283 600 False 464.000000 464 81.054000 3466 4057 1 chr6B.!!$F1 591
6 TraesCS5A01G467300 chr1A 561684942 561685544 602 True 472.000000 472 81.250000 3466 4057 1 chr1A.!!$R3 591
7 TraesCS5A01G467300 chr6A 24185879 24186477 598 True 462.000000 462 81.054000 3466 4057 1 chr6A.!!$R1 591
8 TraesCS5A01G467300 chr2D 35307860 35308451 591 True 436.000000 436 80.467000 3466 4048 1 chr2D.!!$R1 582
9 TraesCS5A01G467300 chr3D 610803169 610803763 594 True 433.000000 433 80.233000 3466 4052 1 chr3D.!!$R2 586

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
392 396 1.203001 TCACATTTTCCAGGTGTCCCC 60.203 52.381 0.0 0.0 34.27 4.81 F
2000 2070 0.175760 TAATCAGGCACTCCGCACTC 59.824 55.000 0.0 0.0 45.17 3.51 F
2006 2076 0.739813 GGCACTCCGCACTCGTATTT 60.740 55.000 0.0 0.0 45.17 1.40 F
2674 3171 1.422781 ACATATACTCCCTCCGTCCGA 59.577 52.381 0.0 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2446 0.039618 TGGATTTCCAGAAGCCCACC 59.960 55.000 0.0 0.0 42.01 4.61 R
2852 3349 0.667184 GGCGTGCTGGTGGATTTTTG 60.667 55.000 0.0 0.0 0.00 2.44 R
2904 3401 2.354103 CGTGTTCATCACCCTCATCTGT 60.354 50.000 0.0 0.0 43.51 3.41 R
3988 4527 3.073678 CCCCTTTTGTATTTTGCAAGCC 58.926 45.455 0.0 0.0 0.00 4.35 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
385 389 8.940768 TTTAAAAAGTTCTCACATTTTCCAGG 57.059 30.769 0.00 0.00 35.80 4.45
390 394 3.140325 TCTCACATTTTCCAGGTGTCC 57.860 47.619 0.00 0.00 34.27 4.02
391 395 2.162681 CTCACATTTTCCAGGTGTCCC 58.837 52.381 0.00 0.00 34.27 4.46
392 396 1.203001 TCACATTTTCCAGGTGTCCCC 60.203 52.381 0.00 0.00 34.27 4.81
396 400 1.822425 TTTTCCAGGTGTCCCCTACA 58.178 50.000 0.00 0.00 43.86 2.74
398 402 2.953093 TTCCAGGTGTCCCCTACATA 57.047 50.000 0.00 0.00 43.86 2.29
399 403 2.953093 TCCAGGTGTCCCCTACATAA 57.047 50.000 0.00 0.00 43.86 1.90
474 480 5.047188 GCCGTGAAAAGAAAAATGGAAAGA 58.953 37.500 0.00 0.00 0.00 2.52
600 613 2.828877 TGACTACAACACCTCGTTTGG 58.171 47.619 0.00 0.00 34.86 3.28
618 631 9.478019 CTCGTTTGGATAATCGCAATATATTTC 57.522 33.333 0.00 0.00 0.00 2.17
619 632 9.214957 TCGTTTGGATAATCGCAATATATTTCT 57.785 29.630 0.00 0.00 0.00 2.52
620 633 9.825972 CGTTTGGATAATCGCAATATATTTCTT 57.174 29.630 0.00 0.00 0.00 2.52
700 713 3.713826 TGCTAATCGGGAGTTTTCCTT 57.286 42.857 0.00 0.00 43.49 3.36
803 821 3.489738 CGCTTTGCCCTAATTCATTCCAG 60.490 47.826 0.00 0.00 0.00 3.86
804 822 3.701040 GCTTTGCCCTAATTCATTCCAGA 59.299 43.478 0.00 0.00 0.00 3.86
922 946 2.211353 AAGCCTTCGATTCGAGCTAC 57.789 50.000 19.28 7.53 36.62 3.58
952 1004 5.907945 ACAAGTTATCGATCGATCTGTTACG 59.092 40.000 32.50 18.04 36.17 3.18
953 1005 5.919272 AGTTATCGATCGATCTGTTACGA 57.081 39.130 32.50 14.53 42.49 3.43
954 1006 6.296365 AGTTATCGATCGATCTGTTACGAA 57.704 37.500 32.50 16.48 41.65 3.85
955 1007 6.134730 AGTTATCGATCGATCTGTTACGAAC 58.865 40.000 32.50 25.39 41.65 3.95
956 1008 4.815040 ATCGATCGATCTGTTACGAACT 57.185 40.909 24.60 0.00 41.65 3.01
957 1009 4.611310 TCGATCGATCTGTTACGAACTT 57.389 40.909 22.43 0.00 41.65 2.66
958 1010 5.723492 TCGATCGATCTGTTACGAACTTA 57.277 39.130 22.43 0.00 41.65 2.24
959 1011 5.496387 TCGATCGATCTGTTACGAACTTAC 58.504 41.667 22.43 0.00 41.65 2.34
960 1012 4.372235 CGATCGATCTGTTACGAACTTACG 59.628 45.833 22.43 0.93 41.65 3.18
977 1029 6.474140 ACTTACGATGGTATGATGGTGTTA 57.526 37.500 7.61 0.00 0.00 2.41
1218 1270 0.800683 TCGACAACGATGACGCCATC 60.801 55.000 12.17 0.99 43.81 3.51
1280 1332 4.373116 GCCGCCTCTGTTGGACGA 62.373 66.667 0.00 0.00 0.00 4.20
1434 1489 6.019762 CCTTTTCGGCGACTCTTATTTTAAC 58.980 40.000 10.16 0.00 0.00 2.01
1445 1500 5.046520 ACTCTTATTTTAACGCCTCCTCACT 60.047 40.000 0.00 0.00 0.00 3.41
1454 1509 4.379243 CTCCTCACTGCCGCCGTT 62.379 66.667 0.00 0.00 0.00 4.44
1556 1614 3.261897 ACCATGGGAGAAACTCAGTACTG 59.738 47.826 18.09 17.17 29.99 2.74
1824 1894 0.555769 AGGAGCAAAAGGTGGTGGAA 59.444 50.000 0.00 0.00 38.34 3.53
1994 2064 4.580580 CCAAGGTAATTAATCAGGCACTCC 59.419 45.833 0.00 0.00 34.60 3.85
1995 2065 4.073293 AGGTAATTAATCAGGCACTCCG 57.927 45.455 0.00 0.00 34.60 4.63
1996 2066 2.548480 GGTAATTAATCAGGCACTCCGC 59.452 50.000 0.00 0.00 34.60 5.54
1997 2067 2.418368 AATTAATCAGGCACTCCGCA 57.582 45.000 0.00 0.00 45.17 5.69
1998 2068 1.668419 ATTAATCAGGCACTCCGCAC 58.332 50.000 0.00 0.00 45.17 5.34
2000 2070 0.175760 TAATCAGGCACTCCGCACTC 59.824 55.000 0.00 0.00 45.17 3.51
2001 2071 2.842394 AATCAGGCACTCCGCACTCG 62.842 60.000 0.00 0.00 45.17 4.18
2003 2073 2.675423 AGGCACTCCGCACTCGTA 60.675 61.111 0.00 0.00 45.17 3.43
2005 2075 1.153628 GGCACTCCGCACTCGTATT 60.154 57.895 0.00 0.00 45.17 1.89
2006 2076 0.739813 GGCACTCCGCACTCGTATTT 60.740 55.000 0.00 0.00 45.17 1.40
2008 2078 1.463444 GCACTCCGCACTCGTATTTTT 59.537 47.619 0.00 0.00 41.79 1.94
2049 2296 9.445786 CATGGTTAATTAATTAAGGCTTACACG 57.554 33.333 18.76 3.69 33.31 4.49
2075 2322 9.394477 GAATTGGAGTACAAAAACTTGTGATAC 57.606 33.333 0.00 0.00 43.46 2.24
2089 2336 5.641209 ACTTGTGATACTTCATCAACTCTGC 59.359 40.000 0.00 0.00 45.28 4.26
2116 2363 3.446442 TTACAGAGAAGTACGGGGAGT 57.554 47.619 0.00 0.00 0.00 3.85
2316 2563 2.359975 CAGCCAAAGGGGACGTCC 60.360 66.667 27.04 27.04 40.01 4.79
2400 2647 4.082125 CCATGCTGGTAACCTTTTCTCTT 58.918 43.478 0.00 0.00 31.35 2.85
2429 2683 9.603921 TTTTCTTCTCTTTTGCAATTTGATTCT 57.396 25.926 0.00 0.00 0.00 2.40
2482 2747 9.549509 TTCATAACTAATTTGCGTACAATTCAC 57.450 29.630 0.00 0.00 35.21 3.18
2554 3029 9.203421 ACAAATTTTCGTGATTTTTAATCCTCC 57.797 29.630 0.00 0.00 0.00 4.30
2587 3062 3.932710 TGAGAGACGTGACATTATTTGGC 59.067 43.478 0.00 0.00 0.00 4.52
2645 3142 7.451877 TCCTACTACTAATTCAGATAAGCCCTG 59.548 40.741 0.00 0.00 0.00 4.45
2663 3160 8.910351 AAGCCCTGAGAATTTTACATATACTC 57.090 34.615 0.00 0.00 0.00 2.59
2664 3161 7.454225 AGCCCTGAGAATTTTACATATACTCC 58.546 38.462 0.00 0.00 0.00 3.85
2667 3164 8.097662 CCCTGAGAATTTTACATATACTCCCTC 58.902 40.741 0.00 0.00 0.00 4.30
2668 3165 8.097662 CCTGAGAATTTTACATATACTCCCTCC 58.902 40.741 0.00 0.00 0.00 4.30
2669 3166 7.667557 TGAGAATTTTACATATACTCCCTCCG 58.332 38.462 0.00 0.00 0.00 4.63
2670 3167 7.289317 TGAGAATTTTACATATACTCCCTCCGT 59.711 37.037 0.00 0.00 0.00 4.69
2671 3168 7.668492 AGAATTTTACATATACTCCCTCCGTC 58.332 38.462 0.00 0.00 0.00 4.79
2672 3169 5.796424 TTTTACATATACTCCCTCCGTCC 57.204 43.478 0.00 0.00 0.00 4.79
2673 3170 1.906990 ACATATACTCCCTCCGTCCG 58.093 55.000 0.00 0.00 0.00 4.79
2674 3171 1.422781 ACATATACTCCCTCCGTCCGA 59.577 52.381 0.00 0.00 0.00 4.55
2675 3172 2.158564 ACATATACTCCCTCCGTCCGAA 60.159 50.000 0.00 0.00 0.00 4.30
2676 3173 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
2677 3174 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2678 3175 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2679 3176 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2680 3177 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2682 3179 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2683 3180 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2685 3182 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2688 3185 3.763360 TCCGTCCGAAAATACTTGTCCTA 59.237 43.478 0.00 0.00 0.00 2.94
2690 3187 4.142315 CCGTCCGAAAATACTTGTCCTAGA 60.142 45.833 0.00 0.00 0.00 2.43
2691 3188 5.404946 CGTCCGAAAATACTTGTCCTAGAA 58.595 41.667 0.00 0.00 0.00 2.10
2695 3192 6.821665 TCCGAAAATACTTGTCCTAGAAATGG 59.178 38.462 0.00 0.00 0.00 3.16
2696 3193 6.821665 CCGAAAATACTTGTCCTAGAAATGGA 59.178 38.462 0.00 0.00 0.00 3.41
2697 3194 7.499232 CCGAAAATACTTGTCCTAGAAATGGAT 59.501 37.037 0.00 0.00 35.87 3.41
2698 3195 9.542462 CGAAAATACTTGTCCTAGAAATGGATA 57.458 33.333 0.00 0.00 35.87 2.59
2705 3202 8.336235 ACTTGTCCTAGAAATGGATAAAATGGA 58.664 33.333 0.00 0.00 34.98 3.41
2706 3203 9.189156 CTTGTCCTAGAAATGGATAAAATGGAA 57.811 33.333 0.00 0.00 34.98 3.53
2708 3205 9.354673 TGTCCTAGAAATGGATAAAATGGAATC 57.645 33.333 0.00 0.00 35.87 2.52
2709 3206 9.579932 GTCCTAGAAATGGATAAAATGGAATCT 57.420 33.333 0.00 0.00 35.87 2.40
2714 3211 9.804977 AGAAATGGATAAAATGGAATCTAGGAG 57.195 33.333 0.00 0.00 0.00 3.69
2719 3216 9.621239 TGGATAAAATGGAATCTAGGAGTATCT 57.379 33.333 0.00 0.00 33.73 1.98
2766 3263 4.670896 TTAATCCTCATGCACTCGATCA 57.329 40.909 0.00 0.00 0.00 2.92
2769 3266 5.417754 AATCCTCATGCACTCGATCATAT 57.582 39.130 0.00 0.00 0.00 1.78
2770 3267 4.879197 TCCTCATGCACTCGATCATATT 57.121 40.909 0.00 0.00 0.00 1.28
2771 3268 4.814147 TCCTCATGCACTCGATCATATTC 58.186 43.478 0.00 0.00 0.00 1.75
2777 3274 3.006217 TGCACTCGATCATATTCCTCCAG 59.994 47.826 0.00 0.00 0.00 3.86
2782 3279 7.210174 CACTCGATCATATTCCTCCAGTTTAA 58.790 38.462 0.00 0.00 0.00 1.52
2784 3281 7.070074 ACTCGATCATATTCCTCCAGTTTAACT 59.930 37.037 0.00 0.00 0.00 2.24
2785 3282 7.210174 TCGATCATATTCCTCCAGTTTAACTG 58.790 38.462 17.37 17.37 45.53 3.16
2786 3283 6.073548 CGATCATATTCCTCCAGTTTAACTGC 60.074 42.308 18.72 0.78 44.63 4.40
2850 3347 3.438781 GGTGATCTGCAAATTGTTCCGTA 59.561 43.478 0.00 0.00 0.00 4.02
2852 3349 3.438781 TGATCTGCAAATTGTTCCGTACC 59.561 43.478 0.00 0.00 0.00 3.34
2856 3353 4.098044 TCTGCAAATTGTTCCGTACCAAAA 59.902 37.500 0.00 0.00 0.00 2.44
2868 3365 2.351350 CGTACCAAAAATCCACCAGCAC 60.351 50.000 0.00 0.00 0.00 4.40
2904 3401 2.028112 CCTGTTCAGTCGGGAGATCAAA 60.028 50.000 0.00 0.00 43.27 2.69
3062 3559 4.486125 TCCCAAAGATCAATGATCGTCA 57.514 40.909 16.57 0.00 43.17 4.35
3166 3672 9.308000 AGTAGAAGTCATAGGATATCCTCTTTG 57.692 37.037 27.86 21.49 44.77 2.77
3297 3814 6.753279 TGTAGTATCAACGTTACCTGCATTAC 59.247 38.462 0.00 0.00 0.00 1.89
3324 3841 7.584108 TGACATTAACTATGCACAACTCAAAG 58.416 34.615 0.00 0.00 37.81 2.77
3355 3872 4.418013 TGAAAAATGTATGAGTGCACCG 57.582 40.909 14.63 0.00 0.00 4.94
3491 4011 1.674359 TCAACACATGTGAGCCGTTT 58.326 45.000 31.94 11.88 0.00 3.60
3565 4087 2.041265 CCCTAGCCACTCCACCCT 59.959 66.667 0.00 0.00 0.00 4.34
3574 4097 1.406887 CCACTCCACCCTTTACGATGG 60.407 57.143 0.00 0.00 0.00 3.51
3714 4249 1.200020 GGTGATTGAAGGCTCAAACGG 59.800 52.381 0.00 0.00 44.64 4.44
3715 4250 1.880027 GTGATTGAAGGCTCAAACGGT 59.120 47.619 0.00 0.00 44.64 4.83
3717 4252 1.880027 GATTGAAGGCTCAAACGGTGT 59.120 47.619 0.00 0.00 44.64 4.16
3937 4475 4.935578 TGAGAGGAATCTCAAGGACTGTA 58.064 43.478 5.50 0.00 43.03 2.74
3941 4479 5.128499 AGAGGAATCTCAAGGACTGTATGTG 59.872 44.000 0.00 0.00 42.34 3.21
3988 4527 2.743636 TGGTTAAGAGTCCAAGAGCG 57.256 50.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.112984 GTCGTTTGTTCCTTCACAATATCAAAC 59.887 37.037 0.00 0.00 36.54 2.93
362 366 7.123547 ACACCTGGAAAATGTGAGAACTTTTTA 59.876 33.333 0.00 0.00 34.18 1.52
368 372 3.253432 GGACACCTGGAAAATGTGAGAAC 59.747 47.826 0.00 0.00 34.18 3.01
487 498 8.380644 TCTTTCGACTGCTTTTATTTTCTATCG 58.619 33.333 0.00 0.00 0.00 2.92
492 503 9.180678 TCATTTCTTTCGACTGCTTTTATTTTC 57.819 29.630 0.00 0.00 0.00 2.29
493 504 9.528018 TTCATTTCTTTCGACTGCTTTTATTTT 57.472 25.926 0.00 0.00 0.00 1.82
494 505 9.528018 TTTCATTTCTTTCGACTGCTTTTATTT 57.472 25.926 0.00 0.00 0.00 1.40
495 506 9.528018 TTTTCATTTCTTTCGACTGCTTTTATT 57.472 25.926 0.00 0.00 0.00 1.40
496 507 9.696917 ATTTTCATTTCTTTCGACTGCTTTTAT 57.303 25.926 0.00 0.00 0.00 1.40
502 513 7.903431 ACGTATATTTTCATTTCTTTCGACTGC 59.097 33.333 0.00 0.00 0.00 4.40
600 613 9.846248 AGGCAAAAGAAATATATTGCGATTATC 57.154 29.630 0.00 0.00 46.88 1.75
700 713 3.974912 AGACGATCGACTGACGTAGATA 58.025 45.455 24.34 0.00 43.13 1.98
820 838 3.932710 TGGAATCAGAATCACGTTGTAGC 59.067 43.478 0.00 0.00 0.00 3.58
887 911 1.466360 GGCTTTACGATGCAGCAACAG 60.466 52.381 1.53 0.00 35.05 3.16
922 946 5.974158 AGATCGATCGATAACTTGTCAACAG 59.026 40.000 29.45 0.00 34.60 3.16
952 1004 5.357257 ACACCATCATACCATCGTAAGTTC 58.643 41.667 0.00 0.00 39.48 3.01
953 1005 5.353394 ACACCATCATACCATCGTAAGTT 57.647 39.130 0.00 0.00 39.48 2.66
954 1006 5.353394 AACACCATCATACCATCGTAAGT 57.647 39.130 0.00 0.00 39.48 2.24
955 1007 6.745116 TCTAACACCATCATACCATCGTAAG 58.255 40.000 0.00 0.00 0.00 2.34
956 1008 6.718522 TCTAACACCATCATACCATCGTAA 57.281 37.500 0.00 0.00 0.00 3.18
957 1009 6.097129 TGTTCTAACACCATCATACCATCGTA 59.903 38.462 0.00 0.00 33.17 3.43
958 1010 5.105106 TGTTCTAACACCATCATACCATCGT 60.105 40.000 0.00 0.00 33.17 3.73
959 1011 5.356426 TGTTCTAACACCATCATACCATCG 58.644 41.667 0.00 0.00 33.17 3.84
960 1012 7.807977 AATGTTCTAACACCATCATACCATC 57.192 36.000 0.00 0.00 42.51 3.51
977 1029 6.839124 TTGCCAATCTACATCAAATGTTCT 57.161 33.333 0.00 0.00 41.63 3.01
1218 1270 2.907910 AGCTGAAAACGCTAGCATTG 57.092 45.000 16.45 0.46 39.84 2.82
1224 1276 8.459635 AGATAATCGATATAGCTGAAAACGCTA 58.540 33.333 0.00 0.00 43.42 4.26
1280 1332 3.367907 AAGGGTGCAAACGGGGTGT 62.368 57.895 0.00 0.00 0.00 4.16
1334 1386 1.597195 GTTGCGATGGATAACGATGCA 59.403 47.619 0.00 0.00 37.85 3.96
1422 1477 5.292101 CAGTGAGGAGGCGTTAAAATAAGAG 59.708 44.000 0.00 0.00 0.00 2.85
1423 1478 5.175859 CAGTGAGGAGGCGTTAAAATAAGA 58.824 41.667 0.00 0.00 0.00 2.10
1424 1479 4.201822 GCAGTGAGGAGGCGTTAAAATAAG 60.202 45.833 0.00 0.00 0.00 1.73
1493 1551 2.296692 GATGTAGTGCGGCAGTTGCG 62.297 60.000 16.53 0.00 43.26 4.85
1556 1614 2.278923 GAGCGGCTTCGGAGTAGC 60.279 66.667 2.97 4.66 37.91 3.58
1824 1894 0.526954 GGATGTTCGTGTCCGCGTAT 60.527 55.000 4.92 0.00 0.00 3.06
2049 2296 9.394477 GTATCACAAGTTTTTGTACTCCAATTC 57.606 33.333 0.00 0.00 45.53 2.17
2075 2322 7.587629 TGTAAAAAGATGCAGAGTTGATGAAG 58.412 34.615 0.00 0.00 0.00 3.02
2089 2336 5.581085 CCCCGTACTTCTCTGTAAAAAGATG 59.419 44.000 0.00 0.00 0.00 2.90
2116 2363 0.045008 TACCATACCCCTTCCTGGCA 59.955 55.000 0.00 0.00 31.72 4.92
2199 2446 0.039618 TGGATTTCCAGAAGCCCACC 59.960 55.000 0.00 0.00 42.01 4.61
2316 2563 1.380302 CTTCAACCTCCAGGGGGTG 59.620 63.158 13.63 8.87 44.90 4.61
2500 2765 9.221775 CCGCTGAAAAACATATACTTTTCATAC 57.778 33.333 17.81 13.94 45.58 2.39
2501 2766 7.913297 GCCGCTGAAAAACATATACTTTTCATA 59.087 33.333 17.81 4.23 45.58 2.15
2503 2768 6.090129 GCCGCTGAAAAACATATACTTTTCA 58.910 36.000 17.05 17.05 44.94 2.69
2504 2769 6.033513 GTGCCGCTGAAAAACATATACTTTTC 59.966 38.462 11.76 11.76 40.43 2.29
2554 3029 1.805345 ACGTCTCTCAGTTACGTCCTG 59.195 52.381 8.47 8.47 46.04 3.86
2559 3034 2.963498 TGTCACGTCTCTCAGTTACG 57.037 50.000 0.00 0.00 42.17 3.18
2587 3062 3.490526 CACGACAATGGAAAAGGCAAAAG 59.509 43.478 0.00 0.00 0.00 2.27
2633 3128 7.814264 ATGTAAAATTCTCAGGGCTTATCTG 57.186 36.000 0.00 0.00 0.00 2.90
2645 3142 7.668492 ACGGAGGGAGTATATGTAAAATTCTC 58.332 38.462 0.00 0.00 0.00 2.87
2663 3160 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2664 3161 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2667 3164 2.968675 AGGACAAGTATTTTCGGACGG 58.031 47.619 0.00 0.00 0.00 4.79
2668 3165 4.990257 TCTAGGACAAGTATTTTCGGACG 58.010 43.478 0.00 0.00 0.00 4.79
2669 3166 7.201617 CCATTTCTAGGACAAGTATTTTCGGAC 60.202 40.741 0.00 0.00 0.00 4.79
2670 3167 6.821665 CCATTTCTAGGACAAGTATTTTCGGA 59.178 38.462 0.00 0.00 0.00 4.55
2671 3168 6.821665 TCCATTTCTAGGACAAGTATTTTCGG 59.178 38.462 0.00 0.00 0.00 4.30
2672 3169 7.843490 TCCATTTCTAGGACAAGTATTTTCG 57.157 36.000 0.00 0.00 0.00 3.46
2678 3175 9.627123 CCATTTTATCCATTTCTAGGACAAGTA 57.373 33.333 0.00 0.00 38.13 2.24
2679 3176 8.336235 TCCATTTTATCCATTTCTAGGACAAGT 58.664 33.333 0.00 0.00 38.13 3.16
2680 3177 8.752005 TCCATTTTATCCATTTCTAGGACAAG 57.248 34.615 0.00 0.00 38.13 3.16
2682 3179 9.354673 GATTCCATTTTATCCATTTCTAGGACA 57.645 33.333 0.00 0.00 38.13 4.02
2683 3180 9.579932 AGATTCCATTTTATCCATTTCTAGGAC 57.420 33.333 0.00 0.00 38.13 3.85
2688 3185 9.804977 CTCCTAGATTCCATTTTATCCATTTCT 57.195 33.333 0.00 0.00 0.00 2.52
2734 3231 9.712305 AGTGCATGAGGATTAAATATGTACTAC 57.288 33.333 0.00 0.00 40.97 2.73
2737 3234 7.598869 TCGAGTGCATGAGGATTAAATATGTAC 59.401 37.037 0.00 0.00 35.49 2.90
2766 3263 3.877508 GCGCAGTTAAACTGGAGGAATAT 59.122 43.478 0.30 0.00 46.01 1.28
2769 3266 1.519408 GCGCAGTTAAACTGGAGGAA 58.481 50.000 0.30 0.00 46.01 3.36
2770 3267 0.321298 GGCGCAGTTAAACTGGAGGA 60.321 55.000 10.83 0.00 46.01 3.71
2771 3268 1.635663 CGGCGCAGTTAAACTGGAGG 61.636 60.000 10.83 0.00 46.01 4.30
2777 3274 0.040781 TTTCAGCGGCGCAGTTAAAC 60.041 50.000 35.02 0.96 0.00 2.01
2782 3279 2.186826 AACTTTTCAGCGGCGCAGT 61.187 52.632 35.02 24.36 0.00 4.40
2784 3281 1.999071 AACAACTTTTCAGCGGCGCA 61.999 50.000 35.02 11.99 0.00 6.09
2785 3282 1.268778 GAACAACTTTTCAGCGGCGC 61.269 55.000 26.86 26.86 0.00 6.53
2786 3283 0.991770 CGAACAACTTTTCAGCGGCG 60.992 55.000 0.51 0.51 0.00 6.46
2850 3347 0.673437 CGTGCTGGTGGATTTTTGGT 59.327 50.000 0.00 0.00 0.00 3.67
2852 3349 0.667184 GGCGTGCTGGTGGATTTTTG 60.667 55.000 0.00 0.00 0.00 2.44
2856 3353 2.360350 CTGGCGTGCTGGTGGATT 60.360 61.111 0.00 0.00 0.00 3.01
2904 3401 2.354103 CGTGTTCATCACCCTCATCTGT 60.354 50.000 0.00 0.00 43.51 3.41
3166 3672 4.886579 ACCATGAAATGCAGGAAAAGAAC 58.113 39.130 0.00 0.00 44.97 3.01
3297 3814 7.075674 TGAGTTGTGCATAGTTAATGTCATG 57.924 36.000 0.00 0.00 37.93 3.07
3350 3867 2.474816 CTAGGAATAGCAAGACGGTGC 58.525 52.381 0.18 0.18 45.28 5.01
3355 3872 7.501844 ACAGTTTATCCTAGGAATAGCAAGAC 58.498 38.462 17.30 6.44 0.00 3.01
3565 4087 6.018589 TCAAATTCACAATGCCATCGTAAA 57.981 33.333 0.00 0.00 0.00 2.01
3574 4097 4.380233 CCCACTCTCTCAAATTCACAATGC 60.380 45.833 0.00 0.00 0.00 3.56
3623 4152 3.169099 CTTCTTCTTCCTCCCTCTCACA 58.831 50.000 0.00 0.00 0.00 3.58
3717 4252 3.191078 CCAAGTTTGGTGCCAATCAAA 57.809 42.857 12.79 0.00 43.43 2.69
3988 4527 3.073678 CCCCTTTTGTATTTTGCAAGCC 58.926 45.455 0.00 0.00 0.00 4.35
4018 4557 6.804534 TTTCAGCAAAACAGAATTTACACG 57.195 33.333 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.