Multiple sequence alignment - TraesCS5B01G119100

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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 TraesCS5B01G119100 chr5B 100.000 2324 0 0 1 2324 210168905 210166582 0.000000e+00 4292.0
1 TraesCS5B01G119100 chr5B 96.907 97 3 0 12 108 466687173 466687269 1.850000e-36 163.0
2 TraesCS5B01G119100 chr5B 95.960 99 3 1 12 109 43067481 43067383 2.390000e-35 159.0
3 TraesCS5B01G119100 chr5A 91.660 1295 37 20 720 1990 216961549 216960302 0.000000e+00 1727.0
4 TraesCS5B01G119100 chr5A 94.156 308 10 4 2019 2324 216960303 216960002 1.630000e-126 462.0
5 TraesCS5B01G119100 chr5A 86.280 328 36 5 340 660 216968420 216968095 4.750000e-92 348.0
6 TraesCS5B01G119100 chr5D 89.961 1275 44 20 661 1878 199723849 199722602 0.000000e+00 1568.0
7 TraesCS5B01G119100 chr5D 93.253 415 20 3 1870 2282 199722274 199721866 2.550000e-169 604.0
8 TraesCS5B01G119100 chr5D 90.604 298 24 2 172 469 199724396 199724103 2.160000e-105 392.0
9 TraesCS5B01G119100 chr5D 95.192 208 9 1 453 660 199724087 199723881 6.190000e-86 327.0
10 TraesCS5B01G119100 chr5D 100.000 29 0 0 2296 2324 199721865 199721837 1.000000e-03 54.7
11 TraesCS5B01G119100 chr7B 96.970 99 3 0 12 110 7204664 7204762 1.430000e-37 167.0
12 TraesCS5B01G119100 chr3B 95.918 98 4 0 12 109 367490741 367490644 2.390000e-35 159.0
13 TraesCS5B01G119100 chr2A 96.875 96 2 1 15 109 743327585 743327490 2.390000e-35 159.0
14 TraesCS5B01G119100 chr2A 88.430 121 11 3 15 133 108260369 108260250 2.410000e-30 143.0
15 TraesCS5B01G119100 chr1B 91.964 112 5 4 3 113 49015900 49015792 1.110000e-33 154.0
16 TraesCS5B01G119100 chr4D 91.071 112 9 1 12 122 20141533 20141644 1.440000e-32 150.0
17 TraesCS5B01G119100 chr2B 91.071 112 8 2 15 125 798707353 798707243 1.440000e-32 150.0


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 TraesCS5B01G119100 chr5B 210166582 210168905 2323 True 4292.00 4292 100.000 1 2324 1 chr5B.!!$R2 2323
1 TraesCS5B01G119100 chr5A 216960002 216961549 1547 True 1094.50 1727 92.908 720 2324 2 chr5A.!!$R2 1604
2 TraesCS5B01G119100 chr5D 199721837 199724396 2559 True 589.14 1568 93.802 172 2324 5 chr5D.!!$R1 2152

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
764 831 0.105039 AAAGGCGATCGATGACTCCC 59.895 55.0 21.57 8.52 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2427 0.182775 TCGTCGGGGAGATGAGATGA 59.817 55.0 0.0 0.0 39.8 2.92 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
25 26 7.247929 GGGAACGTCTCTAAAATAAATCCAG 57.752 40.000 0.00 0.00 0.00 3.86
26 27 6.260271 GGGAACGTCTCTAAAATAAATCCAGG 59.740 42.308 0.00 0.00 0.00 4.45
27 28 7.046033 GGAACGTCTCTAAAATAAATCCAGGA 58.954 38.462 0.00 0.00 0.00 3.86
28 29 7.551617 GGAACGTCTCTAAAATAAATCCAGGAA 59.448 37.037 0.00 0.00 0.00 3.36
29 30 9.110502 GAACGTCTCTAAAATAAATCCAGGAAT 57.889 33.333 0.00 0.00 0.00 3.01
39 40 4.574599 AAATCCAGGAATAAATGCGAGC 57.425 40.909 0.00 0.00 0.00 5.03
40 41 2.708216 TCCAGGAATAAATGCGAGCA 57.292 45.000 0.00 0.00 0.00 4.26
41 42 2.288666 TCCAGGAATAAATGCGAGCAC 58.711 47.619 0.00 0.00 0.00 4.40
42 43 1.334869 CCAGGAATAAATGCGAGCACC 59.665 52.381 0.00 0.00 0.00 5.01
43 44 2.016318 CAGGAATAAATGCGAGCACCA 58.984 47.619 0.00 0.00 0.00 4.17
44 45 2.032550 CAGGAATAAATGCGAGCACCAG 59.967 50.000 0.00 0.00 0.00 4.00
45 46 2.017049 GGAATAAATGCGAGCACCAGT 58.983 47.619 0.00 0.00 0.00 4.00
46 47 3.118408 AGGAATAAATGCGAGCACCAGTA 60.118 43.478 0.00 0.00 0.00 2.74
47 48 3.815401 GGAATAAATGCGAGCACCAGTAT 59.185 43.478 0.00 0.00 0.00 2.12
48 49 4.275936 GGAATAAATGCGAGCACCAGTATT 59.724 41.667 0.00 2.50 0.00 1.89
49 50 5.221048 GGAATAAATGCGAGCACCAGTATTT 60.221 40.000 0.00 0.00 36.77 1.40
50 51 3.492421 AAATGCGAGCACCAGTATTTG 57.508 42.857 0.00 0.00 32.83 2.32
51 52 2.401583 ATGCGAGCACCAGTATTTGA 57.598 45.000 0.00 0.00 0.00 2.69
52 53 2.177394 TGCGAGCACCAGTATTTGAA 57.823 45.000 0.00 0.00 0.00 2.69
53 54 1.804151 TGCGAGCACCAGTATTTGAAC 59.196 47.619 0.00 0.00 0.00 3.18
54 55 1.130561 GCGAGCACCAGTATTTGAACC 59.869 52.381 0.00 0.00 0.00 3.62
55 56 1.737793 CGAGCACCAGTATTTGAACCC 59.262 52.381 0.00 0.00 0.00 4.11
56 57 2.615493 CGAGCACCAGTATTTGAACCCT 60.615 50.000 0.00 0.00 0.00 4.34
57 58 2.749621 GAGCACCAGTATTTGAACCCTG 59.250 50.000 0.00 0.00 0.00 4.45
61 62 2.446435 CCAGTATTTGAACCCTGGTGG 58.554 52.381 0.00 0.00 39.70 4.61
71 72 2.919043 CCTGGTGGGCTGGGATAC 59.081 66.667 0.00 0.00 0.00 2.24
87 88 4.353383 GGATACCACAATCCCTCTAACC 57.647 50.000 0.00 0.00 39.74 2.85
88 89 3.714798 GGATACCACAATCCCTCTAACCA 59.285 47.826 0.00 0.00 39.74 3.67
89 90 4.351111 GGATACCACAATCCCTCTAACCAT 59.649 45.833 0.00 0.00 39.74 3.55
90 91 3.933861 ACCACAATCCCTCTAACCATC 57.066 47.619 0.00 0.00 0.00 3.51
91 92 2.509964 ACCACAATCCCTCTAACCATCC 59.490 50.000 0.00 0.00 0.00 3.51
92 93 2.509548 CCACAATCCCTCTAACCATCCA 59.490 50.000 0.00 0.00 0.00 3.41
93 94 3.053693 CCACAATCCCTCTAACCATCCAA 60.054 47.826 0.00 0.00 0.00 3.53
94 95 3.947834 CACAATCCCTCTAACCATCCAAC 59.052 47.826 0.00 0.00 0.00 3.77
95 96 3.053619 ACAATCCCTCTAACCATCCAACC 60.054 47.826 0.00 0.00 0.00 3.77
96 97 2.352561 TCCCTCTAACCATCCAACCA 57.647 50.000 0.00 0.00 0.00 3.67
97 98 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
98 99 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
99 100 2.242196 CCCTCTAACCATCCAACCACAT 59.758 50.000 0.00 0.00 0.00 3.21
100 101 3.282021 CCTCTAACCATCCAACCACATG 58.718 50.000 0.00 0.00 0.00 3.21
101 102 3.308402 CCTCTAACCATCCAACCACATGT 60.308 47.826 0.00 0.00 0.00 3.21
102 103 4.335416 CTCTAACCATCCAACCACATGTT 58.665 43.478 0.00 0.00 37.80 2.71
112 113 3.322514 CCACATGTTGGTTCGTCCT 57.677 52.632 0.00 0.00 41.10 3.85
113 114 2.465860 CCACATGTTGGTTCGTCCTA 57.534 50.000 0.00 0.00 41.10 2.94
114 115 2.985896 CCACATGTTGGTTCGTCCTAT 58.014 47.619 0.00 0.00 41.10 2.57
115 116 3.343617 CCACATGTTGGTTCGTCCTATT 58.656 45.455 0.00 0.00 41.10 1.73
116 117 3.756434 CCACATGTTGGTTCGTCCTATTT 59.244 43.478 0.00 0.00 41.10 1.40
117 118 4.217550 CCACATGTTGGTTCGTCCTATTTT 59.782 41.667 0.00 0.00 41.10 1.82
118 119 5.278758 CCACATGTTGGTTCGTCCTATTTTT 60.279 40.000 0.00 0.00 41.10 1.94
159 160 8.397575 AGATATAGATAGACAAGTTGAAGCGA 57.602 34.615 10.54 0.00 0.00 4.93
160 161 9.019656 AGATATAGATAGACAAGTTGAAGCGAT 57.980 33.333 10.54 2.39 0.00 4.58
183 184 8.061857 CGATAAGCGCAGAAAATATCAAGTTTA 58.938 33.333 11.47 0.00 0.00 2.01
213 214 6.777580 AGGGAAAGTATGAATATTCGGCAAAT 59.222 34.615 10.80 1.26 0.00 2.32
256 257 5.752650 AGGGGTAAAGTTATAAAGGCTGTC 58.247 41.667 0.00 0.00 0.00 3.51
270 271 1.138266 GGCTGTCTATGGCGAACCTAA 59.862 52.381 0.00 0.00 36.63 2.69
291 292 7.656137 ACCTAAGTTTACACACAACATCTACAG 59.344 37.037 0.00 0.00 0.00 2.74
293 294 7.478520 AAGTTTACACACAACATCTACAGTC 57.521 36.000 0.00 0.00 0.00 3.51
295 296 6.924060 AGTTTACACACAACATCTACAGTCTC 59.076 38.462 0.00 0.00 0.00 3.36
314 315 7.119846 ACAGTCTCCAAAACATTATAGAAGCAC 59.880 37.037 0.00 0.00 0.00 4.40
317 318 7.550906 GTCTCCAAAACATTATAGAAGCACTCT 59.449 37.037 0.00 0.00 38.28 3.24
324 325 7.840342 ACATTATAGAAGCACTCTGAAACAG 57.160 36.000 0.00 0.00 35.41 3.16
330 331 4.943705 AGAAGCACTCTGAAACAGTTTTGA 59.056 37.500 0.00 1.72 31.12 2.69
350 351 3.895041 TGATTGCTACGGATCTACCATGA 59.105 43.478 0.00 0.00 38.90 3.07
369 370 2.224992 TGATTGTTGTGGCATGTACCCT 60.225 45.455 0.00 0.00 0.00 4.34
384 385 0.261696 ACCCTGCACACCCTTTTCTT 59.738 50.000 0.00 0.00 0.00 2.52
387 388 2.962421 CCCTGCACACCCTTTTCTTTAA 59.038 45.455 0.00 0.00 0.00 1.52
389 390 4.501400 CCCTGCACACCCTTTTCTTTAAAG 60.501 45.833 9.04 9.04 42.41 1.85
396 397 9.569167 GCACACCCTTTTCTTTAAAGAATATAC 57.431 33.333 26.90 9.73 45.00 1.47
419 420 6.507023 ACAAAAATCTGGCGATGGAATATTC 58.493 36.000 6.93 6.93 0.00 1.75
426 427 6.950842 TCTGGCGATGGAATATTCTTATCAT 58.049 36.000 21.88 14.94 0.00 2.45
485 518 7.518161 GTCATTCTCGTGACAACATAATTTGA 58.482 34.615 2.40 0.00 46.04 2.69
487 520 7.602265 TCATTCTCGTGACAACATAATTTGAGA 59.398 33.333 0.00 0.00 0.00 3.27
518 551 8.382030 AGGTTTGATTTGCTAAAGAAAATTGG 57.618 30.769 0.00 0.00 33.55 3.16
678 742 1.008361 CGTGGGGCGCAAAAAGAATG 61.008 55.000 10.83 0.00 0.00 2.67
764 831 0.105039 AAAGGCGATCGATGACTCCC 59.895 55.000 21.57 8.52 0.00 4.30
884 962 1.661112 GCTTTGCTCTCACGGATACAC 59.339 52.381 0.00 0.00 0.00 2.90
885 963 2.930887 GCTTTGCTCTCACGGATACACA 60.931 50.000 0.00 0.00 0.00 3.72
886 964 3.525537 CTTTGCTCTCACGGATACACAT 58.474 45.455 0.00 0.00 0.00 3.21
887 965 2.871182 TGCTCTCACGGATACACATC 57.129 50.000 0.00 0.00 0.00 3.06
959 1042 2.970974 GCGGCCAGTCTCTTGCAAC 61.971 63.158 2.24 0.00 0.00 4.17
1308 1408 1.444553 CCGCGACCTCAGACAAGAC 60.445 63.158 8.23 0.00 0.00 3.01
1384 1484 3.713288 TGGCTAATGTGATACAGTACGC 58.287 45.455 0.00 0.00 0.00 4.42
1461 1561 8.918961 AAACATCGAGAAATTAGAGACTACTG 57.081 34.615 0.00 0.00 0.00 2.74
1462 1562 7.633193 ACATCGAGAAATTAGAGACTACTGT 57.367 36.000 0.00 0.00 0.00 3.55
1463 1563 8.734218 ACATCGAGAAATTAGAGACTACTGTA 57.266 34.615 0.00 0.00 0.00 2.74
1464 1564 8.614346 ACATCGAGAAATTAGAGACTACTGTAC 58.386 37.037 0.00 0.00 0.00 2.90
1465 1565 8.832521 CATCGAGAAATTAGAGACTACTGTACT 58.167 37.037 0.00 0.00 0.00 2.73
1467 1567 9.311916 TCGAGAAATTAGAGACTACTGTACTAC 57.688 37.037 0.00 0.00 0.00 2.73
1468 1568 9.316730 CGAGAAATTAGAGACTACTGTACTACT 57.683 37.037 0.00 0.00 0.00 2.57
1554 1663 4.383226 GGGAAAGAAAGAGATCGGCTACTT 60.383 45.833 0.00 0.00 0.00 2.24
1559 1668 6.139048 AGAAAGAGATCGGCTACTTAACTC 57.861 41.667 0.00 0.00 0.00 3.01
1582 1716 7.650903 ACTCATGTTCTTTCTTTTGCTGAAATC 59.349 33.333 0.00 0.00 33.65 2.17
1645 1781 3.821841 CTTTGTTAAAATCCGCTCGCTT 58.178 40.909 0.00 0.00 0.00 4.68
1655 1791 1.498865 CCGCTCGCTTGTTGTGTCTT 61.499 55.000 0.00 0.00 0.00 3.01
1656 1792 0.383491 CGCTCGCTTGTTGTGTCTTG 60.383 55.000 0.00 0.00 0.00 3.02
1709 1845 2.069273 CAAGTTGAAGCTACACGGAGG 58.931 52.381 0.00 0.00 0.00 4.30
1802 1938 2.893489 GTTTTCCCCTGAAACAGCTCAT 59.107 45.455 0.00 0.00 40.12 2.90
1874 2010 1.065273 CAAATCGCAGGCAGCATCC 59.935 57.895 1.96 0.00 46.13 3.51
1955 2427 0.035439 CTACCGGTGCCAGGTTTCAT 60.035 55.000 19.93 0.00 42.81 2.57
1956 2428 0.035820 TACCGGTGCCAGGTTTCATC 60.036 55.000 19.93 0.00 42.81 2.92
1957 2429 1.303236 CCGGTGCCAGGTTTCATCA 60.303 57.895 0.00 0.00 0.00 3.07
1958 2430 0.680921 CCGGTGCCAGGTTTCATCAT 60.681 55.000 0.00 0.00 0.00 2.45
1959 2431 0.734889 CGGTGCCAGGTTTCATCATC 59.265 55.000 0.00 0.00 0.00 2.92
2021 2493 1.003003 TGCCGACATGACTGGAATCAA 59.997 47.619 0.00 0.00 30.82 2.57
2062 2534 1.065600 CACAAGCACAAACCACCCG 59.934 57.895 0.00 0.00 0.00 5.28
2175 2649 5.925506 TCAGGATCGTATGACCAACTTTA 57.074 39.130 6.40 0.00 0.00 1.85
2179 2653 6.696148 CAGGATCGTATGACCAACTTTAGTAC 59.304 42.308 6.40 0.00 0.00 2.73
2221 2695 2.742053 ACCACAAAGATGCACGTACATC 59.258 45.455 19.20 19.20 45.62 3.06
2267 2741 9.542462 TTGAACCCTTTATTTATCTCTACATCG 57.458 33.333 0.00 0.00 0.00 3.84
2282 2756 6.150474 TCTCTACATCGTGTCAAAGTCATACA 59.850 38.462 0.00 0.00 0.00 2.29
2283 2757 6.090783 TCTACATCGTGTCAAAGTCATACAC 58.909 40.000 0.00 0.00 40.05 2.90
2285 2759 6.020971 ACATCGTGTCAAAGTCATACACTA 57.979 37.500 0.00 0.00 41.03 2.74
2286 2760 6.631016 ACATCGTGTCAAAGTCATACACTAT 58.369 36.000 0.00 0.00 41.03 2.12
2287 2761 7.097192 ACATCGTGTCAAAGTCATACACTATT 58.903 34.615 0.00 0.00 41.03 1.73
2288 2762 8.248253 ACATCGTGTCAAAGTCATACACTATTA 58.752 33.333 0.00 0.00 41.03 0.98
2289 2763 8.532341 CATCGTGTCAAAGTCATACACTATTAC 58.468 37.037 0.00 0.00 41.03 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.813672 TGGATTTATTTTAGAGACGTTCCCG 59.186 40.000 0.00 0.00 40.83 5.14
1 2 6.260271 CCTGGATTTATTTTAGAGACGTTCCC 59.740 42.308 0.00 0.00 0.00 3.97
2 3 7.046033 TCCTGGATTTATTTTAGAGACGTTCC 58.954 38.462 0.00 0.00 0.00 3.62
3 4 8.488651 TTCCTGGATTTATTTTAGAGACGTTC 57.511 34.615 0.00 0.00 0.00 3.95
13 14 7.653311 GCTCGCATTTATTCCTGGATTTATTTT 59.347 33.333 0.00 0.00 0.00 1.82
14 15 7.147976 GCTCGCATTTATTCCTGGATTTATTT 58.852 34.615 0.00 0.00 0.00 1.40
15 16 6.265196 TGCTCGCATTTATTCCTGGATTTATT 59.735 34.615 0.00 0.00 0.00 1.40
16 17 5.769662 TGCTCGCATTTATTCCTGGATTTAT 59.230 36.000 0.00 0.00 0.00 1.40
17 18 5.008613 GTGCTCGCATTTATTCCTGGATTTA 59.991 40.000 0.00 0.00 0.00 1.40
18 19 3.953612 TGCTCGCATTTATTCCTGGATTT 59.046 39.130 0.00 0.00 0.00 2.17
19 20 3.316308 GTGCTCGCATTTATTCCTGGATT 59.684 43.478 0.00 0.00 0.00 3.01
20 21 2.880890 GTGCTCGCATTTATTCCTGGAT 59.119 45.455 0.00 0.00 0.00 3.41
21 22 2.288666 GTGCTCGCATTTATTCCTGGA 58.711 47.619 0.00 0.00 0.00 3.86
22 23 1.334869 GGTGCTCGCATTTATTCCTGG 59.665 52.381 0.00 0.00 0.00 4.45
23 24 2.016318 TGGTGCTCGCATTTATTCCTG 58.984 47.619 0.00 0.00 0.00 3.86
24 25 2.292267 CTGGTGCTCGCATTTATTCCT 58.708 47.619 0.00 0.00 0.00 3.36
25 26 2.017049 ACTGGTGCTCGCATTTATTCC 58.983 47.619 0.00 0.00 0.00 3.01
26 27 5.424121 AATACTGGTGCTCGCATTTATTC 57.576 39.130 0.00 0.00 0.00 1.75
27 28 5.356751 TCAAATACTGGTGCTCGCATTTATT 59.643 36.000 0.00 0.00 0.00 1.40
28 29 4.881273 TCAAATACTGGTGCTCGCATTTAT 59.119 37.500 0.00 0.00 0.00 1.40
29 30 4.257731 TCAAATACTGGTGCTCGCATTTA 58.742 39.130 0.00 0.00 0.00 1.40
30 31 3.081061 TCAAATACTGGTGCTCGCATTT 58.919 40.909 0.00 0.00 0.00 2.32
31 32 2.710377 TCAAATACTGGTGCTCGCATT 58.290 42.857 0.00 0.00 0.00 3.56
32 33 2.401583 TCAAATACTGGTGCTCGCAT 57.598 45.000 0.00 0.00 0.00 4.73
33 34 1.804151 GTTCAAATACTGGTGCTCGCA 59.196 47.619 0.00 0.00 0.00 5.10
34 35 1.130561 GGTTCAAATACTGGTGCTCGC 59.869 52.381 0.00 0.00 0.00 5.03
35 36 1.737793 GGGTTCAAATACTGGTGCTCG 59.262 52.381 0.00 0.00 0.00 5.03
36 37 2.749621 CAGGGTTCAAATACTGGTGCTC 59.250 50.000 0.00 0.00 0.00 4.26
37 38 2.555227 CCAGGGTTCAAATACTGGTGCT 60.555 50.000 0.00 0.00 44.21 4.40
38 39 1.818674 CCAGGGTTCAAATACTGGTGC 59.181 52.381 0.00 0.00 44.21 5.01
54 55 2.757124 GGTATCCCAGCCCACCAGG 61.757 68.421 0.00 0.00 39.47 4.45
55 56 2.000701 TGGTATCCCAGCCCACCAG 61.001 63.158 0.00 0.00 36.15 4.00
56 57 2.126142 TGGTATCCCAGCCCACCA 59.874 61.111 0.00 0.00 38.72 4.17
57 58 1.858739 TTGTGGTATCCCAGCCCACC 61.859 60.000 5.66 0.00 46.49 4.61
59 60 0.550914 GATTGTGGTATCCCAGCCCA 59.449 55.000 0.00 0.00 42.94 5.36
60 61 0.178990 GGATTGTGGTATCCCAGCCC 60.179 60.000 0.00 0.00 42.94 5.19
61 62 3.421567 GGATTGTGGTATCCCAGCC 57.578 57.895 0.00 0.00 42.94 4.85
66 67 3.714798 TGGTTAGAGGGATTGTGGTATCC 59.285 47.826 0.00 0.00 42.84 2.59
67 68 5.513267 GGATGGTTAGAGGGATTGTGGTATC 60.513 48.000 0.00 0.00 0.00 2.24
68 69 4.351111 GGATGGTTAGAGGGATTGTGGTAT 59.649 45.833 0.00 0.00 0.00 2.73
69 70 3.714798 GGATGGTTAGAGGGATTGTGGTA 59.285 47.826 0.00 0.00 0.00 3.25
70 71 2.509964 GGATGGTTAGAGGGATTGTGGT 59.490 50.000 0.00 0.00 0.00 4.16
71 72 2.509548 TGGATGGTTAGAGGGATTGTGG 59.490 50.000 0.00 0.00 0.00 4.17
72 73 3.931907 TGGATGGTTAGAGGGATTGTG 57.068 47.619 0.00 0.00 0.00 3.33
73 74 3.053619 GGTTGGATGGTTAGAGGGATTGT 60.054 47.826 0.00 0.00 0.00 2.71
74 75 3.053693 TGGTTGGATGGTTAGAGGGATTG 60.054 47.826 0.00 0.00 0.00 2.67
75 76 3.053619 GTGGTTGGATGGTTAGAGGGATT 60.054 47.826 0.00 0.00 0.00 3.01
76 77 2.509964 GTGGTTGGATGGTTAGAGGGAT 59.490 50.000 0.00 0.00 0.00 3.85
77 78 1.913419 GTGGTTGGATGGTTAGAGGGA 59.087 52.381 0.00 0.00 0.00 4.20
78 79 1.633432 TGTGGTTGGATGGTTAGAGGG 59.367 52.381 0.00 0.00 0.00 4.30
79 80 3.282021 CATGTGGTTGGATGGTTAGAGG 58.718 50.000 0.00 0.00 0.00 3.69
80 81 3.955471 ACATGTGGTTGGATGGTTAGAG 58.045 45.455 0.00 0.00 0.00 2.43
81 82 4.380843 AACATGTGGTTGGATGGTTAGA 57.619 40.909 0.00 0.00 38.60 2.10
95 96 5.371115 AAAATAGGACGAACCAACATGTG 57.629 39.130 0.00 0.00 42.04 3.21
133 134 9.503399 TCGCTTCAACTTGTCTATCTATATCTA 57.497 33.333 0.00 0.00 0.00 1.98
134 135 8.397575 TCGCTTCAACTTGTCTATCTATATCT 57.602 34.615 0.00 0.00 0.00 1.98
138 139 7.596995 GCTTATCGCTTCAACTTGTCTATCTAT 59.403 37.037 0.00 0.00 35.14 1.98
139 140 6.918569 GCTTATCGCTTCAACTTGTCTATCTA 59.081 38.462 0.00 0.00 35.14 1.98
140 141 5.751028 GCTTATCGCTTCAACTTGTCTATCT 59.249 40.000 0.00 0.00 35.14 1.98
141 142 5.331905 CGCTTATCGCTTCAACTTGTCTATC 60.332 44.000 0.00 0.00 36.13 2.08
142 143 4.504461 CGCTTATCGCTTCAACTTGTCTAT 59.496 41.667 0.00 0.00 36.13 1.98
143 144 3.857665 CGCTTATCGCTTCAACTTGTCTA 59.142 43.478 0.00 0.00 36.13 2.59
144 145 2.668457 CGCTTATCGCTTCAACTTGTCT 59.332 45.455 0.00 0.00 36.13 3.41
145 146 3.026557 CGCTTATCGCTTCAACTTGTC 57.973 47.619 0.00 0.00 36.13 3.18
157 158 5.978878 ACTTGATATTTTCTGCGCTTATCG 58.021 37.500 9.73 0.00 42.12 2.92
158 159 9.716507 TTAAACTTGATATTTTCTGCGCTTATC 57.283 29.630 9.73 6.54 0.00 1.75
160 161 9.337091 GTTTAAACTTGATATTTTCTGCGCTTA 57.663 29.630 9.73 0.00 0.00 3.09
161 162 7.060633 CGTTTAAACTTGATATTTTCTGCGCTT 59.939 33.333 16.01 0.00 0.00 4.68
162 163 6.523201 CGTTTAAACTTGATATTTTCTGCGCT 59.477 34.615 16.01 0.00 0.00 5.92
163 164 6.521821 TCGTTTAAACTTGATATTTTCTGCGC 59.478 34.615 16.01 0.00 0.00 6.09
164 165 7.216317 CCTCGTTTAAACTTGATATTTTCTGCG 59.784 37.037 16.01 0.00 0.00 5.18
165 166 7.484959 CCCTCGTTTAAACTTGATATTTTCTGC 59.515 37.037 16.01 0.00 0.00 4.26
166 167 8.726988 TCCCTCGTTTAAACTTGATATTTTCTG 58.273 33.333 16.01 0.00 0.00 3.02
167 168 8.857694 TCCCTCGTTTAAACTTGATATTTTCT 57.142 30.769 16.01 0.00 0.00 2.52
168 169 9.902196 TTTCCCTCGTTTAAACTTGATATTTTC 57.098 29.630 16.01 0.00 0.00 2.29
169 170 9.908152 CTTTCCCTCGTTTAAACTTGATATTTT 57.092 29.630 16.01 0.00 0.00 1.82
170 171 9.074576 ACTTTCCCTCGTTTAAACTTGATATTT 57.925 29.630 16.01 0.00 0.00 1.40
183 184 6.482308 CCGAATATTCATACTTTCCCTCGTTT 59.518 38.462 15.57 0.00 0.00 3.60
228 229 8.050930 CAGCCTTTATAACTTTACCCCTCTTTA 58.949 37.037 0.00 0.00 0.00 1.85
229 230 6.890268 CAGCCTTTATAACTTTACCCCTCTTT 59.110 38.462 0.00 0.00 0.00 2.52
230 231 6.011893 ACAGCCTTTATAACTTTACCCCTCTT 60.012 38.462 0.00 0.00 0.00 2.85
231 232 5.491439 ACAGCCTTTATAACTTTACCCCTCT 59.509 40.000 0.00 0.00 0.00 3.69
232 233 5.752650 ACAGCCTTTATAACTTTACCCCTC 58.247 41.667 0.00 0.00 0.00 4.30
233 234 5.491439 AGACAGCCTTTATAACTTTACCCCT 59.509 40.000 0.00 0.00 0.00 4.79
246 247 2.419574 GGTTCGCCATAGACAGCCTTTA 60.420 50.000 0.00 0.00 37.19 1.85
247 248 1.679032 GGTTCGCCATAGACAGCCTTT 60.679 52.381 0.00 0.00 37.19 3.11
256 257 5.063060 GTGTGTAAACTTAGGTTCGCCATAG 59.937 44.000 0.00 0.00 40.60 2.23
270 271 6.817184 AGACTGTAGATGTTGTGTGTAAACT 58.183 36.000 0.00 0.00 0.00 2.66
291 292 7.550906 AGAGTGCTTCTATAATGTTTTGGAGAC 59.449 37.037 0.00 0.00 33.23 3.36
293 294 7.550551 TCAGAGTGCTTCTATAATGTTTTGGAG 59.449 37.037 0.00 0.00 33.83 3.86
295 296 7.615582 TCAGAGTGCTTCTATAATGTTTTGG 57.384 36.000 0.00 0.00 33.83 3.28
314 315 5.848036 CGTAGCAATCAAAACTGTTTCAGAG 59.152 40.000 6.20 0.00 35.18 3.35
317 318 4.576873 TCCGTAGCAATCAAAACTGTTTCA 59.423 37.500 6.20 0.00 0.00 2.69
324 325 4.873827 TGGTAGATCCGTAGCAATCAAAAC 59.126 41.667 0.00 0.00 39.52 2.43
330 331 5.221722 ACAATCATGGTAGATCCGTAGCAAT 60.222 40.000 0.00 0.00 39.52 3.56
350 351 2.170166 CAGGGTACATGCCACAACAAT 58.830 47.619 0.00 0.00 0.00 2.71
369 370 5.923733 TTCTTTAAAGAAAAGGGTGTGCA 57.076 34.783 24.89 1.39 44.10 4.57
387 388 7.502226 TCCATCGCCAGATTTTTGTATATTCTT 59.498 33.333 0.00 0.00 34.23 2.52
389 390 7.202016 TCCATCGCCAGATTTTTGTATATTC 57.798 36.000 0.00 0.00 34.23 1.75
396 397 6.742109 AGAATATTCCATCGCCAGATTTTTG 58.258 36.000 11.92 0.00 34.23 2.44
419 420 8.455903 ACATGTCAAACCCTAATCATGATAAG 57.544 34.615 9.04 0.60 36.95 1.73
426 427 9.575868 TTTAGTAAACATGTCAAACCCTAATCA 57.424 29.630 0.00 0.00 0.00 2.57
480 513 9.783081 AGCAAATCAAACCTTTTTATCTCAAAT 57.217 25.926 0.00 0.00 0.00 2.32
494 527 7.041167 AGCCAATTTTCTTTAGCAAATCAAACC 60.041 33.333 0.00 0.00 0.00 3.27
518 551 3.127895 TGGTAAATTATGTTGTGGCGAGC 59.872 43.478 0.00 0.00 0.00 5.03
552 585 6.703319 ACAATTTTCTGATCATGCCAAATCA 58.297 32.000 0.00 0.00 0.00 2.57
634 667 3.463127 CGTTTACACGCGGTAAGAAAAG 58.537 45.455 12.47 2.12 42.63 2.27
678 742 7.881775 AGGTTGTGGTTATGATATTTTCTCC 57.118 36.000 0.00 0.00 0.00 3.71
764 831 3.129287 CCCACCTTTTTATGCTGCTACTG 59.871 47.826 0.00 0.00 0.00 2.74
884 962 1.063183 GGATGGGAGGAGAAGGGATG 58.937 60.000 0.00 0.00 0.00 3.51
885 963 0.649992 TGGATGGGAGGAGAAGGGAT 59.350 55.000 0.00 0.00 0.00 3.85
886 964 0.421495 TTGGATGGGAGGAGAAGGGA 59.579 55.000 0.00 0.00 0.00 4.20
887 965 1.298953 TTTGGATGGGAGGAGAAGGG 58.701 55.000 0.00 0.00 0.00 3.95
1141 1241 0.397675 TGCATCATCCTCCTCCTCGT 60.398 55.000 0.00 0.00 0.00 4.18
1308 1408 2.249309 CGTCAACCGCTGCACTTG 59.751 61.111 0.00 0.00 0.00 3.16
1332 1432 5.360999 AGACCTCCAAAAAGAACAAGGAAAG 59.639 40.000 0.00 0.00 0.00 2.62
1384 1484 1.014564 GTCTCGGCCTCTTCCAAACG 61.015 60.000 0.00 0.00 0.00 3.60
1469 1569 8.696410 AGTCTCTAATTTCGCAAAAACAAAAA 57.304 26.923 0.00 0.00 0.00 1.94
1554 1663 7.566760 TCAGCAAAAGAAAGAACATGAGTTA 57.433 32.000 0.00 0.00 38.30 2.24
1559 1668 7.095774 CCAGATTTCAGCAAAAGAAAGAACATG 60.096 37.037 0.00 0.00 38.27 3.21
1582 1716 3.679389 AGAAAGTCAACAGCATACCCAG 58.321 45.455 0.00 0.00 0.00 4.45
1645 1781 3.730362 CGTTTGATGCACAAGACACAACA 60.730 43.478 0.00 0.00 39.77 3.33
1655 1791 1.438651 GGCTAGTCGTTTGATGCACA 58.561 50.000 0.00 0.00 0.00 4.57
1656 1792 0.370273 CGGCTAGTCGTTTGATGCAC 59.630 55.000 9.00 0.00 0.00 4.57
1709 1845 5.574443 GGATCAGCTGTTACAAAAGAAATGC 59.426 40.000 14.67 0.00 0.00 3.56
1802 1938 3.766151 CGTATGTTTAAGCTCGTCCTCA 58.234 45.455 0.00 0.00 0.00 3.86
1874 2010 2.371841 TCCGGAATTACAGGATGGGATG 59.628 50.000 0.00 0.00 43.62 3.51
1955 2427 0.182775 TCGTCGGGGAGATGAGATGA 59.817 55.000 0.00 0.00 39.80 2.92
1956 2428 0.312416 GTCGTCGGGGAGATGAGATG 59.688 60.000 0.00 0.00 44.85 2.90
1957 2429 1.167155 CGTCGTCGGGGAGATGAGAT 61.167 60.000 0.00 0.00 44.85 2.75
1958 2430 1.818363 CGTCGTCGGGGAGATGAGA 60.818 63.158 0.00 0.00 44.85 3.27
1959 2431 2.113433 ACGTCGTCGGGGAGATGAG 61.113 63.158 7.05 0.00 44.85 2.90
2062 2534 1.069935 GCCCTGGTTCTATCCGAGC 59.930 63.158 0.00 0.00 0.00 5.03
2093 2565 2.589492 CGAGCGCATCCATCGGAAC 61.589 63.158 11.47 0.00 34.34 3.62
2158 2630 8.193438 GGTTAGTACTAAAGTTGGTCATACGAT 58.807 37.037 16.82 0.00 0.00 3.73
2179 2653 9.590451 TGTGGTATTTTAGATTCGTTAGGTTAG 57.410 33.333 0.00 0.00 0.00 2.34
2201 2675 3.389687 GATGTACGTGCATCTTTGTGG 57.610 47.619 31.58 0.00 41.35 4.17
2286 2760 9.863845 TGATTTGTCGTCTTTGTGATATAGTAA 57.136 29.630 0.00 0.00 0.00 2.24
2287 2761 9.516314 CTGATTTGTCGTCTTTGTGATATAGTA 57.484 33.333 0.00 0.00 0.00 1.82
2288 2762 7.492669 CCTGATTTGTCGTCTTTGTGATATAGT 59.507 37.037 0.00 0.00 0.00 2.12
2289 2763 7.706607 TCCTGATTTGTCGTCTTTGTGATATAG 59.293 37.037 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.