Multiple sequence alignment - TraesCS2A01G051500

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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 TraesCS2A01G051500 chr2A 100.000 3026 0 0 1 3026 20238921 20235896 0.000000e+00 5589.0
1 TraesCS2A01G051500 chr2A 85.294 1598 208 17 443 2015 21006658 21005063 0.000000e+00 1624.0
2 TraesCS2A01G051500 chr2A 84.493 1567 229 11 457 2015 21148247 21149807 0.000000e+00 1535.0
3 TraesCS2A01G051500 chr2A 87.952 83 8 2 2373 2454 715223326 715223245 2.480000e-16 97.1
4 TraesCS2A01G051500 chr2A 77.714 175 26 8 1973 2146 10550279 10550441 8.930000e-16 95.3
5 TraesCS2A01G051500 chr2D 94.890 2681 117 9 351 3026 20183739 20186404 0.000000e+00 4174.0
6 TraesCS2A01G051500 chr2D 85.957 1531 203 9 491 2014 20381148 20382673 0.000000e+00 1626.0
7 TraesCS2A01G051500 chr2D 84.131 1588 235 13 438 2013 20324723 20323141 0.000000e+00 1520.0
8 TraesCS2A01G051500 chr2D 83.724 1493 235 6 529 2015 20188973 20187483 0.000000e+00 1404.0
9 TraesCS2A01G051500 chr2D 100.000 51 0 0 2400 2450 644515387 644515337 8.930000e-16 95.3
10 TraesCS2A01G051500 chr2B 92.468 2018 124 10 44 2056 33534693 33536687 0.000000e+00 2859.0
11 TraesCS2A01G051500 chr2B 85.384 1601 213 14 431 2015 33728345 33729940 0.000000e+00 1640.0
12 TraesCS2A01G051500 chr2B 83.940 1594 231 16 438 2015 33663048 33664632 0.000000e+00 1502.0
13 TraesCS2A01G051500 chr2B 82.692 156 24 3 2249 2401 195165990 195166145 5.260000e-28 135.0
14 TraesCS2A01G051500 chr2B 87.912 91 9 2 112 200 752204983 752204893 4.130000e-19 106.0
15 TraesCS2A01G051500 chr2B 100.000 41 0 0 1 41 726122279 726122239 3.230000e-10 76.8
16 TraesCS2A01G051500 chr2B 86.885 61 5 2 2165 2222 5364465 5364405 7.000000e-07 65.8
17 TraesCS2A01G051500 chr5A 81.818 539 83 10 1492 2015 511963626 511963088 3.580000e-119 438.0
18 TraesCS2A01G051500 chr5A 87.981 208 17 5 2453 2655 607718668 607718464 3.900000e-59 239.0
19 TraesCS2A01G051500 chr5A 92.308 78 6 0 2373 2450 682942114 682942191 8.870000e-21 111.0
20 TraesCS2A01G051500 chr5D 79.111 675 108 20 1503 2157 406350909 406350248 4.630000e-118 435.0
21 TraesCS2A01G051500 chr5D 90.625 192 14 3 2453 2641 491536989 491536799 5.010000e-63 252.0
22 TraesCS2A01G051500 chr5D 84.615 182 17 2 2246 2418 351556202 351556023 1.440000e-38 171.0
23 TraesCS2A01G051500 chr7D 90.625 192 15 2 2453 2641 556776630 556776821 5.010000e-63 252.0
24 TraesCS2A01G051500 chr7D 89.529 191 17 2 2456 2643 203039587 203039777 3.900000e-59 239.0
25 TraesCS2A01G051500 chr7D 98.039 51 1 0 2400 2450 575587010 575586960 4.160000e-14 89.8
26 TraesCS2A01G051500 chr5B 90.155 193 15 3 2453 2642 360867011 360867202 6.480000e-62 248.0
27 TraesCS2A01G051500 chr5B 82.249 169 17 11 2244 2401 534635135 534635301 1.890000e-27 134.0
28 TraesCS2A01G051500 chr5B 98.276 58 1 0 2393 2450 437912014 437911957 5.340000e-18 102.0
29 TraesCS2A01G051500 chr5B 89.831 59 4 2 2406 2462 683521200 683521258 1.160000e-09 75.0
30 TraesCS2A01G051500 chr6B 89.637 193 16 3 2453 2642 640627030 640626839 3.010000e-60 243.0
31 TraesCS2A01G051500 chr6B 87.578 161 16 2 2242 2402 585810846 585811002 1.850000e-42 183.0
32 TraesCS2A01G051500 chr6B 83.140 172 19 7 2249 2410 107162360 107162531 6.760000e-32 148.0
33 TraesCS2A01G051500 chr6B 100.000 41 0 0 1 41 23660313 23660353 3.230000e-10 76.8
34 TraesCS2A01G051500 chr6B 100.000 41 0 0 1 41 177568147 177568107 3.230000e-10 76.8
35 TraesCS2A01G051500 chr6B 100.000 41 0 0 1 41 177568437 177568397 3.230000e-10 76.8
36 TraesCS2A01G051500 chr3A 89.286 196 17 3 2455 2648 706444519 706444712 3.010000e-60 243.0
37 TraesCS2A01G051500 chr3D 89.637 193 15 4 2453 2641 82744978 82745169 1.080000e-59 241.0
38 TraesCS2A01G051500 chr3D 100.000 51 0 0 2400 2450 185496861 185496811 8.930000e-16 95.3
39 TraesCS2A01G051500 chr3D 98.039 51 1 0 2400 2450 590298192 590298142 4.160000e-14 89.8
40 TraesCS2A01G051500 chr3B 87.685 203 19 5 2453 2650 594928296 594928095 6.520000e-57 231.0
41 TraesCS2A01G051500 chr3B 100.000 42 0 0 1 42 443703278 443703319 8.990000e-11 78.7
42 TraesCS2A01G051500 chr3B 100.000 42 0 0 1 42 807053219 807053178 8.990000e-11 78.7
43 TraesCS2A01G051500 chr3B 97.727 44 1 0 1 44 16463547 16463504 3.230000e-10 76.8
44 TraesCS2A01G051500 chr3B 91.489 47 2 2 2610 2654 802299132 802299086 2.520000e-06 63.9
45 TraesCS2A01G051500 chr7A 86.127 173 14 2 2241 2404 691723815 691723644 8.620000e-41 178.0
46 TraesCS2A01G051500 chr7B 86.747 166 11 3 2246 2401 586635022 586635186 1.120000e-39 174.0
47 TraesCS2A01G051500 chr7B 86.735 98 12 1 2154 2250 639511547 639511644 1.150000e-19 108.0
48 TraesCS2A01G051500 chr7B 84.466 103 12 3 2149 2250 84384225 84384324 6.900000e-17 99.0
49 TraesCS2A01G051500 chr7B 100.000 41 0 0 1 41 693305497 693305537 3.230000e-10 76.8
50 TraesCS2A01G051500 chr4D 84.848 165 20 4 2248 2410 116279755 116279916 8.680000e-36 161.0
51 TraesCS2A01G051500 chr1B 84.393 173 18 1 2246 2409 53070121 53070293 8.680000e-36 161.0
52 TraesCS2A01G051500 chr4A 84.118 170 17 7 2241 2401 676876855 676877023 4.040000e-34 156.0
53 TraesCS2A01G051500 chr1D 83.648 159 20 4 2248 2401 463009271 463009428 8.740000e-31 145.0
54 TraesCS2A01G051500 chr1A 86.316 95 12 1 2157 2250 545477180 545477274 5.340000e-18 102.0
55 TraesCS2A01G051500 chr1A 98.039 51 1 0 2400 2450 60536110 60536160 4.160000e-14 89.8
56 TraesCS2A01G051500 chr4B 100.000 41 0 0 1 41 425366305 425366345 3.230000e-10 76.8


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 TraesCS2A01G051500 chr2A 20235896 20238921 3025 True 5589 5589 100.000 1 3026 1 chr2A.!!$R1 3025
1 TraesCS2A01G051500 chr2A 21005063 21006658 1595 True 1624 1624 85.294 443 2015 1 chr2A.!!$R2 1572
2 TraesCS2A01G051500 chr2A 21148247 21149807 1560 False 1535 1535 84.493 457 2015 1 chr2A.!!$F2 1558
3 TraesCS2A01G051500 chr2D 20183739 20186404 2665 False 4174 4174 94.890 351 3026 1 chr2D.!!$F1 2675
4 TraesCS2A01G051500 chr2D 20381148 20382673 1525 False 1626 1626 85.957 491 2014 1 chr2D.!!$F2 1523
5 TraesCS2A01G051500 chr2D 20323141 20324723 1582 True 1520 1520 84.131 438 2013 1 chr2D.!!$R2 1575
6 TraesCS2A01G051500 chr2D 20187483 20188973 1490 True 1404 1404 83.724 529 2015 1 chr2D.!!$R1 1486
7 TraesCS2A01G051500 chr2B 33534693 33536687 1994 False 2859 2859 92.468 44 2056 1 chr2B.!!$F1 2012
8 TraesCS2A01G051500 chr2B 33728345 33729940 1595 False 1640 1640 85.384 431 2015 1 chr2B.!!$F3 1584
9 TraesCS2A01G051500 chr2B 33663048 33664632 1584 False 1502 1502 83.940 438 2015 1 chr2B.!!$F2 1577
10 TraesCS2A01G051500 chr5A 511963088 511963626 538 True 438 438 81.818 1492 2015 1 chr5A.!!$R1 523
11 TraesCS2A01G051500 chr5D 406350248 406350909 661 True 435 435 79.111 1503 2157 1 chr5D.!!$R2 654

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
310 311 0.403655 TGCATGTAACTGGCCCTTCA 59.596 50.000 0.0 0.0 0.0 3.02 F
311 312 1.202989 TGCATGTAACTGGCCCTTCAA 60.203 47.619 0.0 0.0 0.0 2.69 F
1306 1331 0.887836 AGACCTCAGCGTACGTGTCA 60.888 55.000 17.9 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 1331 0.103208 GCCTGACGATTCTGGACGAT 59.897 55.0 3.50 0.00 42.26 3.73 R
1465 1490 0.179076 GGCTTGTTGTTGCTGGCTTT 60.179 50.0 0.00 0.00 0.00 3.51 R
2548 2596 0.991146 ACCCACCACTACATGCATGA 59.009 50.0 32.75 15.12 0.00 3.07 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
21 22 4.696479 CCTGCTTTATATGAGACCTGGT 57.304 45.455 0.00 0.00 0.00 4.00
22 23 4.636249 CCTGCTTTATATGAGACCTGGTC 58.364 47.826 19.20 19.20 0.00 4.02
23 24 4.346418 CCTGCTTTATATGAGACCTGGTCT 59.654 45.833 28.70 28.70 46.42 3.85
57 58 1.141881 CCGTCCCTCCAGATGAACG 59.858 63.158 0.00 0.00 0.00 3.95
83 84 7.488150 GGGCTTCTATTTTTCAGATTTTAACCG 59.512 37.037 0.00 0.00 0.00 4.44
90 91 8.757164 ATTTTTCAGATTTTAACCGCTTAAGG 57.243 30.769 4.29 0.00 37.30 2.69
123 124 4.243270 CCGAGTCAATATAATTCGGTCCC 58.757 47.826 11.58 0.00 44.23 4.46
134 135 4.794278 AATTCGGTCCCACCAAATTAAC 57.206 40.909 0.00 0.00 38.47 2.01
136 137 1.347050 TCGGTCCCACCAAATTAACGA 59.653 47.619 0.00 0.00 38.47 3.85
140 141 3.404899 GTCCCACCAAATTAACGACTCA 58.595 45.455 0.00 0.00 0.00 3.41
148 149 9.418045 CCACCAAATTAACGACTCATAATTTTT 57.582 29.630 0.00 0.00 38.82 1.94
177 178 3.536570 GTGAGATTTTCTAGGGAGTGCC 58.463 50.000 0.00 0.00 0.00 5.01
184 185 4.402056 TTTCTAGGGAGTGCCGAATTAG 57.598 45.455 0.00 0.00 33.83 1.73
190 191 4.737578 AGGGAGTGCCGAATTAGTATAGA 58.262 43.478 0.00 0.00 33.83 1.98
237 238 7.820648 ACATTTGCATTAACTTCCTACTTGAG 58.179 34.615 0.00 0.00 0.00 3.02
250 251 2.103153 ACTTGAGTTGGGGAGAGACA 57.897 50.000 0.00 0.00 0.00 3.41
258 259 5.003096 AGTTGGGGAGAGACAAATCAAAT 57.997 39.130 0.00 0.00 0.00 2.32
259 260 5.012893 AGTTGGGGAGAGACAAATCAAATC 58.987 41.667 0.00 0.00 0.00 2.17
267 268 5.021458 AGAGACAAATCAAATCTTGGCCAT 58.979 37.500 6.09 0.00 30.25 4.40
309 310 1.767759 ATGCATGTAACTGGCCCTTC 58.232 50.000 0.00 0.00 0.00 3.46
310 311 0.403655 TGCATGTAACTGGCCCTTCA 59.596 50.000 0.00 0.00 0.00 3.02
311 312 1.202989 TGCATGTAACTGGCCCTTCAA 60.203 47.619 0.00 0.00 0.00 2.69
312 313 1.474077 GCATGTAACTGGCCCTTCAAG 59.526 52.381 0.00 0.00 0.00 3.02
313 314 2.879756 GCATGTAACTGGCCCTTCAAGA 60.880 50.000 0.00 0.00 0.00 3.02
314 315 3.624777 CATGTAACTGGCCCTTCAAGAT 58.375 45.455 0.00 0.00 0.00 2.40
315 316 4.780815 CATGTAACTGGCCCTTCAAGATA 58.219 43.478 0.00 0.00 0.00 1.98
316 317 4.919774 TGTAACTGGCCCTTCAAGATAA 57.080 40.909 0.00 0.00 0.00 1.75
317 318 4.843728 TGTAACTGGCCCTTCAAGATAAG 58.156 43.478 0.00 0.00 0.00 1.73
318 319 3.372440 AACTGGCCCTTCAAGATAAGG 57.628 47.619 0.00 0.00 44.87 2.69
341 342 7.978925 AGGATGACCATATAGGAGTAAAAAGG 58.021 38.462 0.00 0.00 41.22 3.11
343 344 8.218488 GGATGACCATATAGGAGTAAAAAGGTT 58.782 37.037 0.00 0.00 41.22 3.50
347 348 9.557061 GACCATATAGGAGTAAAAAGGTTTAGG 57.443 37.037 0.00 0.00 41.22 2.69
348 349 7.997223 ACCATATAGGAGTAAAAAGGTTTAGGC 59.003 37.037 0.00 0.00 41.22 3.93
349 350 7.996644 CCATATAGGAGTAAAAAGGTTTAGGCA 59.003 37.037 0.00 0.00 41.22 4.75
350 351 9.574516 CATATAGGAGTAAAAAGGTTTAGGCAT 57.425 33.333 0.00 0.00 29.74 4.40
419 423 3.553095 AAGAACCTCAGCACCGGGC 62.553 63.158 6.32 6.61 45.30 6.13
609 628 3.130160 CCTTCAAGCCGCTCCTGC 61.130 66.667 0.00 0.00 0.00 4.85
1068 1093 2.124570 GCCACCATGGTCGATGCT 60.125 61.111 16.53 0.00 40.46 3.79
1306 1331 0.887836 AGACCTCAGCGTACGTGTCA 60.888 55.000 17.90 0.00 0.00 3.58
1317 1342 2.477357 CGTACGTGTCATCGTCCAGAAT 60.477 50.000 7.22 0.00 43.12 2.40
1465 1490 2.607631 GGCGTACCTATACTTTGGCA 57.392 50.000 0.00 0.00 0.00 4.92
1467 1492 3.272581 GGCGTACCTATACTTTGGCAAA 58.727 45.455 12.79 12.79 0.00 3.68
1551 1579 4.866508 TGTCAAGAACAAGTCCGACTAT 57.133 40.909 0.26 0.00 34.03 2.12
1570 1598 1.002011 GTCAAGAAGGCCCTCACCC 60.002 63.158 3.68 0.00 0.00 4.61
1824 1868 2.040606 AGCCCGAGGGGTGTGTAT 59.959 61.111 12.67 0.00 46.51 2.29
1868 1912 2.935955 CGTGAACAAGGTGGTCGC 59.064 61.111 0.00 0.00 40.95 5.19
1872 1916 1.227853 GAACAAGGTGGTCGCTGGT 60.228 57.895 0.00 0.00 0.00 4.00
2068 2112 6.697019 GTGTAACTGGCCAAGCAATATATTTG 59.303 38.462 7.01 0.00 0.00 2.32
2074 2118 6.945218 TGGCCAAGCAATATATTTGAAAACT 58.055 32.000 0.61 0.00 0.00 2.66
2204 2250 6.092748 GCGGGAATCGATTGCAATATATTTT 58.907 36.000 27.71 2.28 42.43 1.82
2206 2252 7.753132 GCGGGAATCGATTGCAATATATTTTAA 59.247 33.333 27.71 0.00 42.43 1.52
2233 2279 4.408993 TGATTGTGTGAAGCTTTCATCG 57.591 40.909 0.00 0.00 42.47 3.84
2258 2304 9.084164 CGTTGAATTAATAATATAGTCCCTCCG 57.916 37.037 0.00 0.00 0.00 4.63
2274 2320 7.724287 AGTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2342 2388 9.830186 AGGGAATCTACAGTGTCTATATACATT 57.170 33.333 0.00 0.00 0.00 2.71
2569 2617 1.065199 CATGCATGTAGTGGTGGGTCT 60.065 52.381 18.91 0.00 0.00 3.85
2573 2621 2.552155 GCATGTAGTGGTGGGTCTTTGA 60.552 50.000 0.00 0.00 0.00 2.69
2587 2635 5.249622 TGGGTCTTTGATAAGGTGACATGTA 59.750 40.000 0.00 0.00 32.02 2.29
2593 2641 8.210265 TCTTTGATAAGGTGACATGTATGCATA 58.790 33.333 1.16 1.16 31.28 3.14
2625 2673 9.965902 ATAAATATGATAGTGGGGATCAACTTC 57.034 33.333 0.00 0.00 36.90 3.01
2630 2678 6.830912 TGATAGTGGGGATCAACTTCTTATG 58.169 40.000 0.00 0.00 30.35 1.90
2665 2713 8.948853 TTCGTGAACATAAAATGATCAGTTTC 57.051 30.769 23.16 10.49 41.77 2.78
2666 2714 8.322906 TCGTGAACATAAAATGATCAGTTTCT 57.677 30.769 23.16 12.12 41.77 2.52
2873 2921 5.591643 GAAGTTTTGACTACTTCGCATCA 57.408 39.130 0.00 0.00 41.28 3.07
2874 2922 6.170675 GAAGTTTTGACTACTTCGCATCAT 57.829 37.500 0.00 0.00 41.28 2.45
2897 2945 1.002576 CATGTTTGTTGCGTGCTCTGA 60.003 47.619 0.00 0.00 0.00 3.27
2955 3003 6.149633 GGCAAAGATATCGTTGTTGAGTTTT 58.850 36.000 25.62 3.93 37.59 2.43
3009 3057 7.484959 GCTGAACTATTTTATTTTTCTCACCCG 59.515 37.037 0.00 0.00 0.00 5.28
3020 3068 6.591750 TTTTTCTCACCCGGCAAATATTTA 57.408 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.346418 AGACCAGGTCTCATATAAAGCAGG 59.654 45.833 17.31 0.00 38.71 4.85
1 2 5.543507 AGACCAGGTCTCATATAAAGCAG 57.456 43.478 17.31 0.00 38.71 4.24
33 34 1.004277 CATCTGGAGGGACGGGAAAAA 59.996 52.381 0.00 0.00 0.00 1.94
34 35 0.618458 CATCTGGAGGGACGGGAAAA 59.382 55.000 0.00 0.00 0.00 2.29
35 36 0.252513 TCATCTGGAGGGACGGGAAA 60.253 55.000 0.00 0.00 0.00 3.13
36 37 0.252513 TTCATCTGGAGGGACGGGAA 60.253 55.000 0.00 0.00 0.00 3.97
37 38 0.976073 GTTCATCTGGAGGGACGGGA 60.976 60.000 0.00 0.00 0.00 5.14
38 39 1.522569 GTTCATCTGGAGGGACGGG 59.477 63.158 0.00 0.00 0.00 5.28
39 40 1.141881 CGTTCATCTGGAGGGACGG 59.858 63.158 8.02 0.00 0.00 4.79
40 41 1.141881 CCGTTCATCTGGAGGGACG 59.858 63.158 8.82 8.82 0.00 4.79
41 42 1.522569 CCCGTTCATCTGGAGGGAC 59.477 63.158 0.00 0.00 44.70 4.46
42 43 2.367202 GCCCGTTCATCTGGAGGGA 61.367 63.158 2.59 0.00 44.70 4.20
46 47 1.860641 TAGAAGCCCGTTCATCTGGA 58.139 50.000 0.00 0.00 37.67 3.86
49 50 5.253330 TGAAAAATAGAAGCCCGTTCATCT 58.747 37.500 0.00 0.00 37.67 2.90
57 58 7.488150 CGGTTAAAATCTGAAAAATAGAAGCCC 59.512 37.037 0.00 0.00 0.00 5.19
90 91 3.790089 ATTGACTCGGATTATTCCCCC 57.210 47.619 0.00 0.00 39.01 5.40
103 104 4.995487 GGTGGGACCGAATTATATTGACTC 59.005 45.833 0.00 0.00 0.00 3.36
122 123 8.980143 AAAATTATGAGTCGTTAATTTGGTGG 57.020 30.769 17.56 0.00 37.80 4.61
148 149 8.755977 ACTCCCTAGAAAATCTCACGTTAATTA 58.244 33.333 0.00 0.00 0.00 1.40
217 218 5.705441 CCAACTCAAGTAGGAAGTTAATGCA 59.295 40.000 0.00 0.00 0.00 3.96
223 224 3.323775 TCCCCAACTCAAGTAGGAAGTT 58.676 45.455 1.65 0.00 0.00 2.66
237 238 5.012893 AGATTTGATTTGTCTCTCCCCAAC 58.987 41.667 0.00 0.00 0.00 3.77
250 251 5.493809 CCTTTCATGGCCAAGATTTGATTT 58.506 37.500 10.96 0.00 0.00 2.17
267 268 1.378514 GGAATCTGCCCGCCTTTCA 60.379 57.895 0.00 0.00 0.00 2.69
309 310 8.372877 ACTCCTATATGGTCATCCTTATCTTG 57.627 38.462 0.00 0.00 36.14 3.02
315 316 8.440771 CCTTTTTACTCCTATATGGTCATCCTT 58.559 37.037 0.00 0.00 37.07 3.36
316 317 7.572861 ACCTTTTTACTCCTATATGGTCATCCT 59.427 37.037 0.00 0.00 37.07 3.24
317 318 7.746703 ACCTTTTTACTCCTATATGGTCATCC 58.253 38.462 0.00 0.00 37.07 3.51
318 319 9.628500 AAACCTTTTTACTCCTATATGGTCATC 57.372 33.333 0.00 0.00 37.07 2.92
419 423 3.767230 CTGCCGCGTGTTCTCGTG 61.767 66.667 4.92 1.69 40.38 4.35
426 430 1.019278 ATTTTCGATCTGCCGCGTGT 61.019 50.000 4.92 0.00 0.00 4.49
609 628 1.078759 GCGTTCCTGATGGACGACAG 61.079 60.000 0.00 0.00 43.06 3.51
1068 1093 2.592993 CGCCAGGAGGTTCCCTTCA 61.593 63.158 0.00 0.00 37.19 3.02
1306 1331 0.103208 GCCTGACGATTCTGGACGAT 59.897 55.000 3.50 0.00 42.26 3.73
1465 1490 0.179076 GGCTTGTTGTTGCTGGCTTT 60.179 50.000 0.00 0.00 0.00 3.51
1467 1492 2.848858 CGGCTTGTTGTTGCTGGCT 61.849 57.895 0.00 0.00 32.37 4.75
1551 1579 1.761174 GGTGAGGGCCTTCTTGACA 59.239 57.895 16.82 0.00 0.00 3.58
1570 1598 0.399454 ATCTTCTCCCATGCATCCCG 59.601 55.000 0.00 0.00 0.00 5.14
1704 1733 3.120060 ACTCGACGTACTGGATGTTGTAC 60.120 47.826 0.00 0.00 36.59 2.90
1820 1864 1.826720 GGTCCCGGTAGTTGACATACA 59.173 52.381 0.00 0.00 0.00 2.29
1824 1868 1.246056 CGAGGTCCCGGTAGTTGACA 61.246 60.000 0.00 0.00 0.00 3.58
1868 1912 1.745653 TCTCATAGCTCGTCACACCAG 59.254 52.381 0.00 0.00 0.00 4.00
1872 1916 1.133216 GCAGTCTCATAGCTCGTCACA 59.867 52.381 0.00 0.00 0.00 3.58
2068 2112 6.654793 TGCACAATTTAACAACCAGTTTTC 57.345 33.333 0.00 0.00 41.64 2.29
2074 2118 4.210120 GCGATTTGCACAATTTAACAACCA 59.790 37.500 0.00 0.00 45.45 3.67
2204 2250 8.358895 TGAAAGCTTCACACAATCAAATCATTA 58.641 29.630 0.00 0.00 34.08 1.90
2206 2252 6.751157 TGAAAGCTTCACACAATCAAATCAT 58.249 32.000 0.00 0.00 34.08 2.45
2233 2279 9.939802 ACGGAGGGACTATATTATTAATTCAAC 57.060 33.333 0.00 0.00 41.55 3.18
2250 2296 7.724287 AGACTTATATTTAGAAACGGAGGGAC 58.276 38.462 0.00 0.00 0.00 4.46
2252 2298 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
2303 2349 2.025887 AGATTCCCTCATTTTGCTCCGT 60.026 45.455 0.00 0.00 0.00 4.69
2391 2437 7.735326 TTTAGCTTTAGTTCATACTCCCTCT 57.265 36.000 0.00 0.00 35.78 3.69
2511 2559 8.354426 CCATTATTAATTGATCTCATGCACACA 58.646 33.333 0.00 0.00 0.00 3.72
2544 2592 3.257873 CCCACCACTACATGCATGAAAAA 59.742 43.478 32.75 13.52 0.00 1.94
2548 2596 0.991146 ACCCACCACTACATGCATGA 59.009 50.000 32.75 15.12 0.00 3.07
2569 2617 8.922931 ATATGCATACATGTCACCTTATCAAA 57.077 30.769 8.99 0.00 37.04 2.69
2573 2621 8.377799 TCTCAATATGCATACATGTCACCTTAT 58.622 33.333 8.99 0.00 37.04 1.73
2665 2713 3.750371 TCATCTACCCCACACACAAAAG 58.250 45.455 0.00 0.00 0.00 2.27
2666 2714 3.866703 TCATCTACCCCACACACAAAA 57.133 42.857 0.00 0.00 0.00 2.44
2867 2915 1.580256 CAACAAACATGCGATGATGCG 59.420 47.619 0.00 0.00 37.81 4.73
2868 2916 1.322338 GCAACAAACATGCGATGATGC 59.678 47.619 10.80 10.80 33.57 3.91
2897 2945 4.357918 ACTATGCAACTGACCTCTTTGT 57.642 40.909 0.00 0.00 0.00 2.83
2991 3039 5.476091 TTGCCGGGTGAGAAAAATAAAAT 57.524 34.783 2.18 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.