Multiple sequence alignment - TraesCS4A01G101000

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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 TraesCS4A01G101000 chr4A 100.000 2549 0 0 1 2549 113506951 113504403 0.000000e+00 4708.0
1 TraesCS4A01G101000 chr4A 81.178 781 82 29 840 1572 113580110 113579347 3.680000e-158 568.0
2 TraesCS4A01G101000 chr4D 91.994 2598 110 45 1 2549 351736137 351738685 0.000000e+00 3555.0
3 TraesCS4A01G101000 chr4B 92.768 1120 51 17 840 1941 434713753 434714860 0.000000e+00 1592.0
4 TraesCS4A01G101000 chr4B 92.317 846 47 15 1 841 434712891 434713723 0.000000e+00 1186.0
5 TraesCS4A01G101000 chr4B 88.817 465 38 9 1977 2429 434722058 434722520 2.220000e-155 558.0
6 TraesCS4A01G101000 chr1D 84.000 225 23 9 1140 1361 20061991 20062205 1.200000e-48 204.0
7 TraesCS4A01G101000 chr3B 86.239 109 13 1 1244 1352 612104015 612103909 1.600000e-22 117.0
8 TraesCS4A01G101000 chr3B 85.321 109 14 1 1244 1352 612360005 612359899 7.450000e-21 111.0
9 TraesCS4A01G101000 chr3A 86.239 109 13 1 1244 1352 603895557 603895451 1.600000e-22 117.0
10 TraesCS4A01G101000 chr3A 83.740 123 16 3 1232 1352 603813806 603813686 2.070000e-21 113.0
11 TraesCS4A01G101000 chr3D 83.740 123 16 3 1232 1352 461313437 461313317 2.070000e-21 113.0
12 TraesCS4A01G101000 chr2A 86.047 86 12 0 1151 1236 1365033 1364948 2.700000e-15 93.5
13 TraesCS4A01G101000 chr5A 83.544 79 11 2 1145 1222 651528234 651528157 3.520000e-09 73.1


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 TraesCS4A01G101000 chr4A 113504403 113506951 2548 True 4708 4708 100.0000 1 2549 1 chr4A.!!$R1 2548
1 TraesCS4A01G101000 chr4A 113579347 113580110 763 True 568 568 81.1780 840 1572 1 chr4A.!!$R2 732
2 TraesCS4A01G101000 chr4D 351736137 351738685 2548 False 3555 3555 91.9940 1 2549 1 chr4D.!!$F1 2548
3 TraesCS4A01G101000 chr4B 434712891 434714860 1969 False 1389 1592 92.5425 1 1941 2 chr4B.!!$F2 1940

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
267 283 0.437295 CGACGAACGGGACACAAATC 59.563 55.0 0.0 0.0 38.46 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2391 0.318869 TTTGGCATGCGAGCAAACAG 60.319 50.0 12.44 0.0 35.83 3.16 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
63 64 5.334105 GCCAATTATGCATACCACGTCTAAG 60.334 44.000 5.74 0.00 0.00 2.18
64 65 5.989168 CCAATTATGCATACCACGTCTAAGA 59.011 40.000 5.74 0.00 0.00 2.10
65 66 6.481976 CCAATTATGCATACCACGTCTAAGAA 59.518 38.462 5.74 0.00 0.00 2.52
66 67 7.307396 CCAATTATGCATACCACGTCTAAGAAG 60.307 40.741 5.74 0.00 0.00 2.85
67 68 3.520290 TGCATACCACGTCTAAGAAGG 57.480 47.619 0.00 0.00 0.00 3.46
83 92 2.876550 AGAAGGAAAAACGGTGTGCTAC 59.123 45.455 0.00 0.00 0.00 3.58
95 104 2.612221 GGTGTGCTACAGTTGGAGGTAC 60.612 54.545 0.00 0.00 0.00 3.34
105 114 2.185387 GTTGGAGGTACCTGGAGCTTA 58.815 52.381 22.10 0.00 39.86 3.09
106 115 2.570302 GTTGGAGGTACCTGGAGCTTAA 59.430 50.000 22.10 2.15 39.86 1.85
107 116 3.130734 TGGAGGTACCTGGAGCTTAAT 57.869 47.619 22.10 0.00 39.86 1.40
108 117 3.460825 TGGAGGTACCTGGAGCTTAATT 58.539 45.455 22.10 0.00 39.86 1.40
109 118 3.454812 TGGAGGTACCTGGAGCTTAATTC 59.545 47.826 22.10 0.00 39.86 2.17
110 119 3.492829 GGAGGTACCTGGAGCTTAATTCG 60.493 52.174 22.10 0.00 35.41 3.34
111 120 3.371965 AGGTACCTGGAGCTTAATTCGA 58.628 45.455 15.42 0.00 0.00 3.71
170 186 2.898920 TAGCGGAGACTGGTACCGGG 62.899 65.000 24.73 13.79 45.66 5.73
192 208 6.587990 CGGGTCTAGCATTAATCTTACAGATG 59.412 42.308 0.00 0.00 34.65 2.90
196 212 9.190858 GTCTAGCATTAATCTTACAGATGAGTG 57.809 37.037 0.00 0.00 34.65 3.51
197 213 8.918116 TCTAGCATTAATCTTACAGATGAGTGT 58.082 33.333 0.00 0.00 34.65 3.55
222 238 3.330701 AGTGTAGGCCAATGAAAGGAGAA 59.669 43.478 5.01 0.00 0.00 2.87
225 241 2.529632 AGGCCAATGAAAGGAGAAACC 58.470 47.619 5.01 0.00 39.35 3.27
226 242 1.550524 GGCCAATGAAAGGAGAAACCC 59.449 52.381 0.00 0.00 40.05 4.11
227 243 2.529632 GCCAATGAAAGGAGAAACCCT 58.470 47.619 0.00 0.00 40.05 4.34
228 244 3.563479 GGCCAATGAAAGGAGAAACCCTA 60.563 47.826 0.00 0.00 40.05 3.53
229 245 4.281657 GCCAATGAAAGGAGAAACCCTAT 58.718 43.478 0.00 0.00 40.05 2.57
234 250 8.660435 CCAATGAAAGGAGAAACCCTATCTATA 58.340 37.037 0.00 0.00 40.05 1.31
259 275 3.244976 GTTATCTTTTCGACGAACGGGA 58.755 45.455 10.38 9.02 42.82 5.14
267 283 0.437295 CGACGAACGGGACACAAATC 59.563 55.000 0.00 0.00 38.46 2.17
277 293 2.160417 GGGACACAAATCAAAGCTCTCG 59.840 50.000 0.00 0.00 0.00 4.04
382 401 1.068194 CGTCTCTCTCACCGAAAGCTT 60.068 52.381 0.00 0.00 0.00 3.74
383 402 2.608261 CGTCTCTCTCACCGAAAGCTTT 60.608 50.000 12.53 12.53 0.00 3.51
412 431 4.415150 CTGTGGGCGCTCATGGGT 62.415 66.667 15.93 0.00 0.00 4.51
448 468 3.523157 TCAGTGGGCATAGGAATTCAGAA 59.477 43.478 7.93 0.00 0.00 3.02
507 527 4.301072 TGCCAGGGTTTATATCCTATGC 57.699 45.455 0.00 0.81 33.39 3.14
534 554 1.318158 GCCTGCTCACTTGGAATGGG 61.318 60.000 0.00 0.00 0.00 4.00
568 588 0.731417 GCCATCATCACTCAGCACAC 59.269 55.000 0.00 0.00 0.00 3.82
569 589 1.004595 CCATCATCACTCAGCACACG 58.995 55.000 0.00 0.00 0.00 4.49
570 590 1.004595 CATCATCACTCAGCACACGG 58.995 55.000 0.00 0.00 0.00 4.94
572 592 2.046892 ATCACTCAGCACACGGCC 60.047 61.111 0.00 0.00 46.50 6.13
645 667 1.367900 GTACGAGACGAGCTAGCGC 60.368 63.158 9.55 9.06 33.86 5.92
775 797 2.757077 CCCTCTTTTGTCCGCCCT 59.243 61.111 0.00 0.00 0.00 5.19
842 895 2.562912 CGCGCCTTGACAAAGCAT 59.437 55.556 9.37 0.00 31.51 3.79
890 943 3.056821 AGCTATAAATACGCGCCAGATCA 60.057 43.478 5.73 0.00 0.00 2.92
909 962 5.771666 AGATCATCTCTTCCTCTCACTCATC 59.228 44.000 0.00 0.00 0.00 2.92
941 1008 3.951769 AAGCACCTGCCCATCAGCC 62.952 63.158 0.00 0.00 43.38 4.85
981 1048 2.035961 TCTCGGTTGTCTTCTGGTCTTG 59.964 50.000 0.00 0.00 0.00 3.02
1585 1694 4.902443 TTTGCGTCTGAACCATACAAAA 57.098 36.364 0.00 0.00 0.00 2.44
1624 1741 2.159476 ACGTATTTGCATTGAGCTGCTG 60.159 45.455 7.01 0.00 45.94 4.41
1714 1835 3.555966 GCAGGGGCTCTGTATTTACAAT 58.444 45.455 17.19 0.00 45.08 2.71
1745 1866 5.505173 TCTGGCGGTATTTGTAGTACTAC 57.495 43.478 23.58 23.58 36.63 2.73
1746 1867 5.195940 TCTGGCGGTATTTGTAGTACTACT 58.804 41.667 28.56 14.73 37.00 2.57
1747 1868 6.356556 TCTGGCGGTATTTGTAGTACTACTA 58.643 40.000 28.56 20.97 37.00 1.82
1749 1870 6.356556 TGGCGGTATTTGTAGTACTACTAGA 58.643 40.000 28.56 16.91 37.00 2.43
1750 1871 6.260936 TGGCGGTATTTGTAGTACTACTAGAC 59.739 42.308 28.56 22.41 37.00 2.59
1751 1872 6.358762 GCGGTATTTGTAGTACTACTAGACG 58.641 44.000 28.56 23.77 37.00 4.18
1752 1873 6.564873 GCGGTATTTGTAGTACTACTAGACGG 60.565 46.154 28.56 24.62 37.00 4.79
1753 1874 6.480320 CGGTATTTGTAGTACTACTAGACGGT 59.520 42.308 28.56 13.10 37.00 4.83
1754 1875 7.011482 CGGTATTTGTAGTACTACTAGACGGTT 59.989 40.741 28.56 11.04 37.00 4.44
1796 1919 0.841289 TTTCCACGGGGAGTTCAGTT 59.159 50.000 6.46 0.00 46.01 3.16
1799 1922 2.048601 TCCACGGGGAGTTCAGTTTTA 58.951 47.619 0.00 0.00 38.64 1.52
1899 2030 3.214328 CCAGGATTTATTCCCAAGTCGG 58.786 50.000 0.00 0.00 46.81 4.79
1919 2050 1.663379 GCGGGCTATTTGTGGGTTCC 61.663 60.000 0.00 0.00 0.00 3.62
1930 2061 5.683876 TTTGTGGGTTCCTTGAAATCAAA 57.316 34.783 0.00 0.00 35.15 2.69
1965 2096 8.824159 AATCTGTTCTCATGGATAAGAATACG 57.176 34.615 0.00 0.00 34.26 3.06
2022 2153 2.487762 TGAAGCCGCTTGGATTAAACAG 59.512 45.455 11.20 0.00 42.67 3.16
2025 2156 0.802494 CCGCTTGGATTAAACAGCGT 59.198 50.000 13.75 0.00 43.14 5.07
2030 2161 1.434555 TGGATTAAACAGCGTCCACG 58.565 50.000 0.00 0.00 35.91 4.94
2043 2174 0.462047 GTCCACGCTCGAAATGGGAT 60.462 55.000 8.88 0.00 34.03 3.85
2078 2211 1.155390 TCAGGTCCTTGTCGGAGGT 59.845 57.895 0.00 0.00 44.20 3.85
2107 2240 1.441515 CGGTTCGTCGTGATGTCGT 60.442 57.895 0.00 0.00 0.00 4.34
2128 2261 1.306654 ATGAACGAGGGGCTGGGTA 60.307 57.895 0.00 0.00 0.00 3.69
2134 2267 0.760945 CGAGGGGCTGGGTAGAGAAT 60.761 60.000 0.00 0.00 0.00 2.40
2135 2268 1.052617 GAGGGGCTGGGTAGAGAATC 58.947 60.000 0.00 0.00 0.00 2.52
2136 2269 0.760945 AGGGGCTGGGTAGAGAATCG 60.761 60.000 0.00 0.00 42.67 3.34
2137 2270 1.069935 GGGCTGGGTAGAGAATCGC 59.930 63.158 0.00 0.00 42.67 4.58
2138 2271 1.300233 GGCTGGGTAGAGAATCGCG 60.300 63.158 0.00 0.00 42.67 5.87
2142 2285 2.735237 GGTAGAGAATCGCGGGGG 59.265 66.667 6.13 0.00 42.67 5.40
2170 2313 3.318313 TGGTTGGAAGAGGAAGAAGAGT 58.682 45.455 0.00 0.00 0.00 3.24
2179 2322 2.810852 GAGGAAGAAGAGTTGTTGGCTG 59.189 50.000 0.00 0.00 0.00 4.85
2188 2331 4.218312 AGAGTTGTTGGCTGGAAAAATCT 58.782 39.130 0.00 0.00 0.00 2.40
2191 2334 5.140454 AGTTGTTGGCTGGAAAAATCTACT 58.860 37.500 0.00 0.00 0.00 2.57
2195 2338 3.334691 TGGCTGGAAAAATCTACTGACG 58.665 45.455 0.00 0.00 0.00 4.35
2202 2345 4.844522 GGAAAAATCTACTGACGCGAAAAC 59.155 41.667 15.93 1.38 0.00 2.43
2210 2353 5.921976 TCTACTGACGCGAAAACTTTTATCA 59.078 36.000 15.93 0.00 0.00 2.15
2214 2357 6.146510 ACTGACGCGAAAACTTTTATCATACA 59.853 34.615 15.93 0.00 0.00 2.29
2234 2377 8.739039 TCATACAACTTACAAAATCAATCCCTG 58.261 33.333 0.00 0.00 0.00 4.45
2272 2415 1.734117 GCTCGCATGCCAAAACACC 60.734 57.895 13.15 0.00 0.00 4.16
2294 2437 7.044798 CACCAGATTGTCCTTTTTGGTTTAAA 58.955 34.615 0.00 0.00 36.83 1.52
2328 2471 1.153958 CGATGCTCGTCTGCAGACA 60.154 57.895 38.31 26.28 46.71 3.41
2348 2491 2.052237 AAGTTGTCGCGCGCTTTG 60.052 55.556 30.48 14.31 0.00 2.77
2371 2514 1.130373 GCGCCATTCTTCGTTCATTCA 59.870 47.619 0.00 0.00 0.00 2.57
2372 2515 2.414029 GCGCCATTCTTCGTTCATTCAA 60.414 45.455 0.00 0.00 0.00 2.69
2414 2557 3.273434 TCATTGCTGATCACTAGGTTGC 58.727 45.455 0.00 0.00 0.00 4.17
2419 2562 2.930887 GCTGATCACTAGGTTGCGAACA 60.931 50.000 0.00 0.00 0.00 3.18
2428 2571 6.366877 TCACTAGGTTGCGAACATTAGTTAAC 59.633 38.462 0.00 0.00 38.30 2.01
2433 2576 4.010667 TGCGAACATTAGTTAACCTGGT 57.989 40.909 0.88 0.00 38.30 4.00
2435 2578 3.373130 GCGAACATTAGTTAACCTGGTCC 59.627 47.826 0.00 0.00 38.30 4.46
2438 2581 2.237893 ACATTAGTTAACCTGGTCCCGG 59.762 50.000 0.00 0.00 0.00 5.73
2439 2582 2.028561 TTAGTTAACCTGGTCCCGGT 57.971 50.000 0.00 0.00 35.97 5.28
2440 2583 1.269012 TAGTTAACCTGGTCCCGGTG 58.731 55.000 5.63 0.00 34.33 4.94
2441 2584 0.765519 AGTTAACCTGGTCCCGGTGT 60.766 55.000 5.63 0.00 34.33 4.16
2455 2598 1.268335 CCGGTGTTTTTCCTTGTGACG 60.268 52.381 0.00 0.00 0.00 4.35
2456 2599 1.399089 CGGTGTTTTTCCTTGTGACGT 59.601 47.619 0.00 0.00 0.00 4.34
2461 2604 3.095738 GTTTTTCCTTGTGACGTTGTCG 58.904 45.455 0.00 0.00 43.34 4.35
2482 2625 5.585047 GTCGTCCTTAGCTTTTATTGGATGT 59.415 40.000 0.00 0.00 33.65 3.06
2484 2627 5.584649 CGTCCTTAGCTTTTATTGGATGTGA 59.415 40.000 0.00 0.00 0.00 3.58
2489 2632 8.689972 CCTTAGCTTTTATTGGATGTGAGATTT 58.310 33.333 0.00 0.00 0.00 2.17
2490 2633 9.512435 CTTAGCTTTTATTGGATGTGAGATTTG 57.488 33.333 0.00 0.00 0.00 2.32
2508 2651 5.779771 AGATTTGGACATAAAGGAAAAGGCA 59.220 36.000 0.00 0.00 0.00 4.75
2518 2661 7.396055 ACATAAAGGAAAAGGCAGTGCTTATTA 59.604 33.333 16.11 4.46 0.00 0.98
2533 2676 7.928706 CAGTGCTTATTACTGAGTAAATAGGCT 59.071 37.037 9.35 0.00 46.52 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.818060 TGCATAATTGGCAGTGGTGTC 59.182 47.619 2.84 0.00 36.11 3.67
31 32 1.921982 TGCATAATTGGCAGTGGTGT 58.078 45.000 2.84 0.00 36.11 4.16
32 33 3.243501 GGTATGCATAATTGGCAGTGGTG 60.244 47.826 8.28 0.00 45.68 4.17
63 64 2.614983 TGTAGCACACCGTTTTTCCTTC 59.385 45.455 0.00 0.00 0.00 3.46
64 65 2.616842 CTGTAGCACACCGTTTTTCCTT 59.383 45.455 0.00 0.00 0.00 3.36
65 66 2.218603 CTGTAGCACACCGTTTTTCCT 58.781 47.619 0.00 0.00 0.00 3.36
66 67 1.944709 ACTGTAGCACACCGTTTTTCC 59.055 47.619 0.00 0.00 0.00 3.13
67 68 3.359654 CAACTGTAGCACACCGTTTTTC 58.640 45.455 0.00 0.00 32.85 2.29
83 92 0.250513 GCTCCAGGTACCTCCAACTG 59.749 60.000 12.84 0.00 39.02 3.16
95 104 9.023967 CAAAAATTATTCGAATTAAGCTCCAGG 57.976 33.333 17.19 0.00 0.00 4.45
105 114 6.934083 ACCCTGCAACAAAAATTATTCGAATT 59.066 30.769 17.19 0.00 0.00 2.17
106 115 6.463360 ACCCTGCAACAAAAATTATTCGAAT 58.537 32.000 16.15 16.15 0.00 3.34
107 116 5.848406 ACCCTGCAACAAAAATTATTCGAA 58.152 33.333 0.00 0.00 0.00 3.71
108 117 5.461032 ACCCTGCAACAAAAATTATTCGA 57.539 34.783 0.00 0.00 0.00 3.71
109 118 6.526674 GTCTACCCTGCAACAAAAATTATTCG 59.473 38.462 0.00 0.00 0.00 3.34
110 119 7.542130 CAGTCTACCCTGCAACAAAAATTATTC 59.458 37.037 0.00 0.00 0.00 1.75
111 120 7.378181 CAGTCTACCCTGCAACAAAAATTATT 58.622 34.615 0.00 0.00 0.00 1.40
192 208 3.056107 TCATTGGCCTACACTACACACTC 60.056 47.826 3.32 0.00 0.00 3.51
196 212 3.689649 CCTTTCATTGGCCTACACTACAC 59.310 47.826 3.32 0.00 0.00 2.90
197 213 3.585289 TCCTTTCATTGGCCTACACTACA 59.415 43.478 3.32 0.00 0.00 2.74
228 244 9.888878 TTCGTCGAAAAGATAACGAATATAGAT 57.111 29.630 4.91 0.00 45.87 1.98
251 267 2.916111 CTTTGATTTGTGTCCCGTTCG 58.084 47.619 0.00 0.00 0.00 3.95
252 268 2.293399 AGCTTTGATTTGTGTCCCGTTC 59.707 45.455 0.00 0.00 0.00 3.95
253 269 2.293399 GAGCTTTGATTTGTGTCCCGTT 59.707 45.455 0.00 0.00 0.00 4.44
254 270 1.880027 GAGCTTTGATTTGTGTCCCGT 59.120 47.619 0.00 0.00 0.00 5.28
255 271 2.154462 AGAGCTTTGATTTGTGTCCCG 58.846 47.619 0.00 0.00 0.00 5.14
277 293 1.279840 GGTCGTTTGCTGTGACTGC 59.720 57.895 7.56 7.56 33.21 4.40
382 401 0.250124 CCCACAGTTCACGGTGCTAA 60.250 55.000 2.51 0.00 40.04 3.09
383 402 1.369692 CCCACAGTTCACGGTGCTA 59.630 57.895 2.51 0.00 40.04 3.49
412 431 2.366590 CCCACTGATCCTGATCGATCAA 59.633 50.000 27.09 15.24 46.08 2.57
448 468 2.042433 ACTAGCTGAGAAGAGTGAGGGT 59.958 50.000 0.00 0.00 0.00 4.34
534 554 0.879090 ATGGCTTTTTCGTTCGGGTC 59.121 50.000 0.00 0.00 0.00 4.46
645 667 1.429148 GCCGTTCCGCTACTTCCATG 61.429 60.000 0.00 0.00 0.00 3.66
775 797 2.819154 CCGTGACGGCATGCATGA 60.819 61.111 30.64 5.84 41.17 3.07
842 895 0.388659 GTCCACTGTTGCATGCCAAA 59.611 50.000 16.68 0.00 34.68 3.28
890 943 3.221771 CGGATGAGTGAGAGGAAGAGAT 58.778 50.000 0.00 0.00 0.00 2.75
941 1008 4.676723 CGAGACAAAGCTAGGAGAAGGAAG 60.677 50.000 0.00 0.00 0.00 3.46
981 1048 0.108615 TTAGTCCAAGAGCAGAGCGC 60.109 55.000 0.00 0.00 42.91 5.92
1143 1223 1.444553 GCACTCGAACACCCTCTCG 60.445 63.158 0.00 0.00 36.39 4.04
1215 1295 2.434185 CGCGGCTTCTTGTGGCTA 60.434 61.111 0.00 0.00 0.00 3.93
1593 1702 7.584123 GCTCAATGCAAATACGTATTGAACTAG 59.416 37.037 21.00 13.13 44.12 2.57
1624 1741 1.608283 CCAAGGGTCGTTGACTTCTCC 60.608 57.143 5.13 0.00 32.47 3.71
1704 1825 6.523201 CGCCAGAAGTCAAACATTGTAAATAC 59.477 38.462 0.00 0.00 0.00 1.89
1714 1835 2.851263 ATACCGCCAGAAGTCAAACA 57.149 45.000 0.00 0.00 0.00 2.83
1768 1891 3.135027 CCCGTGGAAAAAGGGGAAA 57.865 52.632 0.00 0.00 46.40 3.13
1796 1919 5.268387 TGCCTCCAAGGAGCATAAAATAAA 58.732 37.500 10.68 0.00 37.67 1.40
1799 1922 3.386932 TGCCTCCAAGGAGCATAAAAT 57.613 42.857 10.68 0.00 37.67 1.82
1899 2030 1.663379 GAACCCACAAATAGCCCGCC 61.663 60.000 0.00 0.00 0.00 6.13
1965 2096 3.553095 AACCCTTCCTGTGCGGCTC 62.553 63.158 0.00 0.00 0.00 4.70
2025 2156 0.461870 CATCCCATTTCGAGCGTGGA 60.462 55.000 12.69 6.38 34.94 4.02
2030 2161 2.546494 CGGCCATCCCATTTCGAGC 61.546 63.158 2.24 0.00 0.00 5.03
2107 2240 2.721167 CCAGCCCCTCGTTCATCGA 61.721 63.158 0.00 0.00 46.83 3.59
2128 2261 2.435693 CCTTCCCCCGCGATTCTCT 61.436 63.158 8.23 0.00 0.00 3.10
2136 2269 3.739613 AACCATCCCTTCCCCCGC 61.740 66.667 0.00 0.00 0.00 6.13
2137 2270 2.275418 CAACCATCCCTTCCCCCG 59.725 66.667 0.00 0.00 0.00 5.73
2138 2271 1.514864 TTCCAACCATCCCTTCCCCC 61.515 60.000 0.00 0.00 0.00 5.40
2142 2285 1.916181 TCCTCTTCCAACCATCCCTTC 59.084 52.381 0.00 0.00 0.00 3.46
2170 2313 5.009610 GTCAGTAGATTTTTCCAGCCAACAA 59.990 40.000 0.00 0.00 0.00 2.83
2179 2322 4.657075 TTTCGCGTCAGTAGATTTTTCC 57.343 40.909 5.77 0.00 0.00 3.13
2188 2331 6.715344 ATGATAAAAGTTTTCGCGTCAGTA 57.285 33.333 5.77 0.00 0.00 2.74
2191 2334 6.469139 TGTATGATAAAAGTTTTCGCGTCA 57.531 33.333 5.77 6.19 0.00 4.35
2195 2338 9.601971 TGTAAGTTGTATGATAAAAGTTTTCGC 57.398 29.630 3.60 0.00 0.00 4.70
2210 2353 8.877864 TCAGGGATTGATTTTGTAAGTTGTAT 57.122 30.769 0.00 0.00 0.00 2.29
2214 2357 7.603784 GCAATTCAGGGATTGATTTTGTAAGTT 59.396 33.333 4.47 0.00 38.93 2.66
2248 2391 0.318869 TTTGGCATGCGAGCAAACAG 60.319 50.000 12.44 0.00 35.83 3.16
2272 2415 8.485976 TGTTTTAAACCAAAAAGGACAATCTG 57.514 30.769 5.32 0.00 41.22 2.90
2294 2437 4.194640 AGCATCGCTCAAATCTGTATGTT 58.805 39.130 0.00 0.00 30.62 2.71
2328 2471 1.772063 AAAGCGCGCGACAACTTCTT 61.772 50.000 37.18 21.88 0.00 2.52
2348 2491 3.718480 GAACGAAGAATGGCGCGGC 62.718 63.158 27.61 27.61 0.00 6.53
2352 2495 3.469899 TTGAATGAACGAAGAATGGCG 57.530 42.857 0.00 0.00 0.00 5.69
2356 2499 9.918630 AGAAAATGAATTGAATGAACGAAGAAT 57.081 25.926 0.00 0.00 0.00 2.40
2414 2557 3.937079 GGGACCAGGTTAACTAATGTTCG 59.063 47.826 5.42 0.00 37.59 3.95
2419 2562 2.237893 CACCGGGACCAGGTTAACTAAT 59.762 50.000 14.38 0.00 40.59 1.73
2428 2571 1.176619 GGAAAAACACCGGGACCAGG 61.177 60.000 9.42 9.42 0.00 4.45
2433 2576 1.064611 TCACAAGGAAAAACACCGGGA 60.065 47.619 6.32 0.00 0.00 5.14
2435 2578 1.268335 CGTCACAAGGAAAAACACCGG 60.268 52.381 0.00 0.00 0.00 5.28
2438 2581 3.828786 ACAACGTCACAAGGAAAAACAC 58.171 40.909 0.00 0.00 0.00 3.32
2439 2582 3.425094 CGACAACGTCACAAGGAAAAACA 60.425 43.478 0.00 0.00 32.09 2.83
2440 2583 3.095738 CGACAACGTCACAAGGAAAAAC 58.904 45.455 0.00 0.00 32.09 2.43
2441 2584 3.392769 CGACAACGTCACAAGGAAAAA 57.607 42.857 0.00 0.00 32.09 1.94
2455 2598 5.410439 TCCAATAAAAGCTAAGGACGACAAC 59.590 40.000 0.00 0.00 0.00 3.32
2456 2599 5.553123 TCCAATAAAAGCTAAGGACGACAA 58.447 37.500 0.00 0.00 0.00 3.18
2461 2604 6.823689 TCTCACATCCAATAAAAGCTAAGGAC 59.176 38.462 0.00 0.00 0.00 3.85
2482 2625 6.071391 GCCTTTTCCTTTATGTCCAAATCTCA 60.071 38.462 0.00 0.00 0.00 3.27
2484 2627 5.779771 TGCCTTTTCCTTTATGTCCAAATCT 59.220 36.000 0.00 0.00 0.00 2.40
2489 2632 3.826157 CACTGCCTTTTCCTTTATGTCCA 59.174 43.478 0.00 0.00 0.00 4.02
2490 2633 3.367395 GCACTGCCTTTTCCTTTATGTCC 60.367 47.826 0.00 0.00 0.00 4.02
2508 2651 8.024145 AGCCTATTTACTCAGTAATAAGCACT 57.976 34.615 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.