Multiple sequence alignment - TraesCS6D01G198500

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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 TraesCS6D01G198500 chr6D 100.000 2702 0 0 1 2702 276681568 276684269 0.000000e+00 4990.0
1 TraesCS6D01G198500 chr6D 100.000 29 0 0 2146 2174 77709278 77709306 1.000000e-03 54.7
2 TraesCS6D01G198500 chr6A 88.861 2783 204 37 1 2695 399700446 399697682 0.000000e+00 3325.0
3 TraesCS6D01G198500 chr6B 90.996 1255 71 13 565 1810 438406292 438407513 0.000000e+00 1653.0
4 TraesCS6D01G198500 chr6B 94.805 308 8 4 1809 2112 438407701 438408004 8.760000e-130 473.0
5 TraesCS6D01G198500 chr7A 78.947 418 63 11 2290 2689 667982746 667982336 7.420000e-66 261.0
6 TraesCS6D01G198500 chr7A 82.593 270 30 12 2448 2702 578979755 578979488 3.500000e-54 222.0
7 TraesCS6D01G198500 chr3A 78.774 424 65 14 2284 2690 366872306 366872721 7.420000e-66 261.0
8 TraesCS6D01G198500 chr3A 81.557 244 31 6 2461 2690 328928369 328928126 3.550000e-44 189.0
9 TraesCS6D01G198500 chr3A 74.306 144 33 2 572 712 377139231 377139373 1.040000e-04 58.4
10 TraesCS6D01G198500 chr3A 100.000 29 0 0 2146 2174 366872173 366872201 1.000000e-03 54.7
11 TraesCS6D01G198500 chr5A 78.302 424 68 12 2284 2690 43242983 43243399 4.470000e-63 252.0
12 TraesCS6D01G198500 chr5A 75.658 152 34 2 563 712 708833070 708832920 3.730000e-09 73.1
13 TraesCS6D01G198500 chr1A 78.066 424 69 10 2284 2690 49337587 49338003 2.080000e-61 246.0
14 TraesCS6D01G198500 chr2A 81.579 304 41 6 2402 2690 690349706 690349403 1.250000e-58 237.0
15 TraesCS6D01G198500 chr2A 76.866 134 22 4 648 773 266870640 266870508 1.740000e-07 67.6
16 TraesCS6D01G198500 chr2D 75.000 568 101 18 2146 2690 343678843 343679392 9.740000e-55 224.0
17 TraesCS6D01G198500 chr2D 94.286 35 1 1 8 42 402720047 402720080 5.000000e-03 52.8
18 TraesCS6D01G198500 chr7B 79.297 256 42 6 2448 2702 536654635 536654390 4.630000e-38 169.0
19 TraesCS6D01G198500 chr4A 77.686 121 18 6 648 760 627997556 627997675 6.240000e-07 65.8
20 TraesCS6D01G198500 chr5B 75.385 130 28 4 586 712 710671260 710671132 2.910000e-05 60.2
21 TraesCS6D01G198500 chr3D 96.875 32 1 0 2144 2175 582795795 582795826 1.000000e-03 54.7


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 TraesCS6D01G198500 chr6D 276681568 276684269 2701 False 4990 4990 100.0000 1 2702 1 chr6D.!!$F2 2701
1 TraesCS6D01G198500 chr6A 399697682 399700446 2764 True 3325 3325 88.8610 1 2695 1 chr6A.!!$R1 2694
2 TraesCS6D01G198500 chr6B 438406292 438408004 1712 False 1063 1653 92.9005 565 2112 2 chr6B.!!$F1 1547
3 TraesCS6D01G198500 chr2D 343678843 343679392 549 False 224 224 75.0000 2146 2690 1 chr2D.!!$F1 544


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
227 234 0.028902 CCAGCATGCGACATGTGATG 59.971 55.0 13.01 3.86 31.97 3.07 F
379 387 0.036952 CTACCCTATGCCTCATGCCG 60.037 60.0 0.00 0.00 40.16 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1373 0.106708 TTCCGTTGCAGCTCTGAAGT 59.893 50.0 0.29 0.0 0.0 3.01 R
2116 2353 0.318784 GCTAGGTTATGCCGGTCTCG 60.319 60.0 1.90 0.0 43.7 4.04 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
26 27 4.657075 GCAAATTTTGTGCTTCTCATGG 57.343 40.909 10.65 0.00 39.00 3.66
42 43 6.500684 TCTCATGGAAGCACATACTTTTTC 57.499 37.500 0.00 0.00 0.00 2.29
49 50 6.928492 TGGAAGCACATACTTTTTCCATTTTC 59.072 34.615 0.39 0.00 41.60 2.29
50 51 6.928492 GGAAGCACATACTTTTTCCATTTTCA 59.072 34.615 0.00 0.00 37.75 2.69
60 61 6.536224 ACTTTTTCCATTTTCAAGAAGCACAG 59.464 34.615 0.00 0.00 0.00 3.66
62 63 3.225104 TCCATTTTCAAGAAGCACAGCT 58.775 40.909 0.00 0.00 42.56 4.24
126 131 2.859165 TGTCTGCTCCAAAACCTAGG 57.141 50.000 7.41 7.41 0.00 3.02
131 136 4.023107 GTCTGCTCCAAAACCTAGGAAAAC 60.023 45.833 17.98 0.00 32.57 2.43
133 138 2.561419 GCTCCAAAACCTAGGAAAACCC 59.439 50.000 17.98 0.00 32.57 4.11
137 142 4.107311 TCCAAAACCTAGGAAAACCCAGAT 59.893 41.667 17.98 0.00 37.41 2.90
141 148 7.015779 CCAAAACCTAGGAAAACCCAGATAAAA 59.984 37.037 17.98 0.00 37.41 1.52
142 149 7.534723 AAACCTAGGAAAACCCAGATAAAAC 57.465 36.000 17.98 0.00 37.41 2.43
170 177 6.788598 AAAAAGCCATCAAAAACCCAAAAT 57.211 29.167 0.00 0.00 0.00 1.82
172 179 4.019792 AGCCATCAAAAACCCAAAATCC 57.980 40.909 0.00 0.00 0.00 3.01
173 180 2.741517 GCCATCAAAAACCCAAAATCCG 59.258 45.455 0.00 0.00 0.00 4.18
174 181 3.805457 GCCATCAAAAACCCAAAATCCGT 60.805 43.478 0.00 0.00 0.00 4.69
178 185 6.978080 CCATCAAAAACCCAAAATCCGTATAG 59.022 38.462 0.00 0.00 0.00 1.31
180 187 7.762588 TCAAAAACCCAAAATCCGTATAGAA 57.237 32.000 0.00 0.00 0.00 2.10
183 190 8.705134 CAAAAACCCAAAATCCGTATAGAAAAC 58.295 33.333 0.00 0.00 0.00 2.43
186 193 7.712204 ACCCAAAATCCGTATAGAAAACAAT 57.288 32.000 0.00 0.00 0.00 2.71
209 216 8.086843 AATTTTAAAATTAGGAGGGAGCGCCC 62.087 42.308 21.77 19.43 44.48 6.13
227 234 0.028902 CCAGCATGCGACATGTGATG 59.971 55.000 13.01 3.86 31.97 3.07
230 237 1.995646 GCATGCGACATGTGATGGCA 61.996 55.000 1.15 8.03 38.56 4.92
235 242 1.215244 CGACATGTGATGGCAGCTAG 58.785 55.000 1.15 0.00 38.56 3.42
236 243 1.590932 GACATGTGATGGCAGCTAGG 58.409 55.000 1.15 0.00 38.49 3.02
247 254 3.636231 AGCTAGGCGTGCCCACAA 61.636 61.111 7.39 0.00 36.58 3.33
278 285 0.536460 TGACCTTTGAAAGTCCCCGC 60.536 55.000 4.02 0.00 0.00 6.13
302 309 6.718294 CAGGGGATAACCTTTAGTTAGTTGT 58.282 40.000 0.00 0.00 44.07 3.32
307 314 8.098912 GGGATAACCTTTAGTTAGTTGTTCTCA 58.901 37.037 0.00 0.00 44.07 3.27
311 318 8.434733 AACCTTTAGTTAGTTGTTCTCACTTC 57.565 34.615 0.00 0.00 36.74 3.01
313 320 8.044908 ACCTTTAGTTAGTTGTTCTCACTTCAA 58.955 33.333 0.00 0.00 33.35 2.69
326 333 1.059913 ACTTCAAGGAGGTGGTCAGG 58.940 55.000 0.00 0.00 0.00 3.86
330 337 0.322975 CAAGGAGGTGGTCAGGTCAG 59.677 60.000 0.00 0.00 0.00 3.51
340 347 1.340248 GGTCAGGTCAGACAAGTTCGA 59.660 52.381 2.17 0.00 40.29 3.71
362 369 2.107378 TCAGGCATCCAACCAAACACTA 59.893 45.455 0.00 0.00 0.00 2.74
368 375 4.855340 CATCCAACCAAACACTACCCTAT 58.145 43.478 0.00 0.00 0.00 2.57
376 383 3.845781 AACACTACCCTATGCCTCATG 57.154 47.619 0.00 0.00 0.00 3.07
379 387 0.036952 CTACCCTATGCCTCATGCCG 60.037 60.000 0.00 0.00 40.16 5.69
382 390 0.886490 CCCTATGCCTCATGCCGTTC 60.886 60.000 0.00 0.00 40.16 3.95
406 414 1.672356 ACAGTGACCATGCGAAGGC 60.672 57.895 0.00 0.00 40.52 4.35
409 417 0.957395 AGTGACCATGCGAAGGCTTG 60.957 55.000 3.46 0.00 42.32 4.01
416 424 0.905357 ATGCGAAGGCTTGGAGTAGT 59.095 50.000 13.81 0.00 40.82 2.73
422 430 3.736433 CGAAGGCTTGGAGTAGTGATCAG 60.736 52.174 3.46 0.00 0.00 2.90
434 442 5.503927 AGTAGTGATCAGCCATGACAAAAT 58.496 37.500 0.00 0.00 38.57 1.82
438 446 5.587844 AGTGATCAGCCATGACAAAATAGAC 59.412 40.000 0.00 0.00 38.57 2.59
444 452 7.147312 TCAGCCATGACAAAATAGACAAAAAG 58.853 34.615 0.00 0.00 0.00 2.27
449 457 9.533253 CCATGACAAAATAGACAAAAAGTTTCT 57.467 29.630 0.00 0.00 0.00 2.52
458 466 5.622180 AGACAAAAAGTTTCTAGGACTCCC 58.378 41.667 0.00 0.00 0.00 4.30
466 474 1.076632 CTAGGACTCCCGTGGCTCT 60.077 63.158 0.00 0.00 37.58 4.09
489 497 0.243095 GAAGGCTTCAAGCAGCTTGG 59.757 55.000 30.71 18.76 44.75 3.61
500 508 4.100529 CAAGCAGCTTGGAAATGTATTCG 58.899 43.478 25.40 0.00 37.77 3.34
515 523 7.935338 AATGTATTCGATGCATCCATTTTTC 57.065 32.000 20.87 6.57 34.39 2.29
520 528 2.159212 CGATGCATCCATTTTTCTGGCA 60.159 45.455 20.87 0.00 36.16 4.92
605 630 8.005466 CCAATGTTGTCAGAAAATTTCAAATCG 58.995 33.333 8.55 0.00 0.00 3.34
831 859 1.337354 TGCTACGGAAGTTCGATGCAA 60.337 47.619 0.00 0.00 46.40 4.08
844 872 2.170260 GATGCAACGGTGACACCACG 62.170 60.000 24.18 13.41 44.09 4.94
886 914 2.584608 CCTCTTGGGGCTACGGTG 59.415 66.667 0.00 0.00 0.00 4.94
926 954 1.608590 CCGCTCCAAAACACACAGAAT 59.391 47.619 0.00 0.00 0.00 2.40
927 955 2.350772 CCGCTCCAAAACACACAGAATC 60.351 50.000 0.00 0.00 0.00 2.52
976 1011 2.812591 CACTGATCTTGCAGCTTCAGTT 59.187 45.455 19.06 7.50 44.77 3.16
1062 1097 3.760035 TCGCTCGGCTCCTTGGAC 61.760 66.667 0.00 0.00 0.00 4.02
1244 1279 1.004979 CCCCCTCCAATTTCACGGTAA 59.995 52.381 0.00 0.00 0.00 2.85
1251 1286 3.192422 TCCAATTTCACGGTAAATGCCTG 59.808 43.478 0.00 0.00 0.00 4.85
1291 1331 0.108329 GTCCATTGATCGTGTCCGGT 60.108 55.000 0.00 0.00 33.95 5.28
1461 1501 4.131088 GACGACCTCGGCCACCTC 62.131 72.222 2.24 0.00 42.67 3.85
1539 1579 1.607467 CCTGTTCCCAAGGGCCAAG 60.607 63.158 6.18 0.00 34.68 3.61
1602 1642 3.740397 TCGTACGTCCGCCACCAG 61.740 66.667 16.05 0.00 0.00 4.00
1718 1761 0.539518 TAACAGCGGGATTAGCAGCA 59.460 50.000 0.00 0.00 37.01 4.41
1743 1786 1.825090 CTGGTGTATCAGCTTGGCAA 58.175 50.000 0.00 0.00 32.61 4.52
1784 1827 4.600576 TGTGCCGCTGTCGCTCAA 62.601 61.111 0.00 0.00 0.00 3.02
1785 1828 4.077188 GTGCCGCTGTCGCTCAAC 62.077 66.667 0.00 0.00 0.00 3.18
1814 2047 0.039165 GCCCTGCTTTGCTGTAACAC 60.039 55.000 0.00 0.00 0.00 3.32
1947 2180 1.664873 GATAAGTCCCGGAAACCAGC 58.335 55.000 0.73 0.00 0.00 4.85
1987 2220 0.325602 AAGGTTCGTTGGGCGGATTA 59.674 50.000 0.00 0.00 41.72 1.75
1998 2231 2.202932 CGGATTACGCAGCCAGCT 60.203 61.111 0.00 0.00 42.61 4.24
1999 2232 1.067416 CGGATTACGCAGCCAGCTA 59.933 57.895 0.00 0.00 42.61 3.32
2001 2234 1.224722 GGATTACGCAGCCAGCTAGC 61.225 60.000 6.62 6.62 42.61 3.42
2066 2299 5.629079 AGTTTTGTTCCATTCCGAATCTC 57.371 39.130 0.00 0.00 0.00 2.75
2081 2314 0.173708 ATCTCGAGTGTTCCTTCCGC 59.826 55.000 13.13 0.00 0.00 5.54
2082 2315 1.801913 CTCGAGTGTTCCTTCCGCG 60.802 63.158 3.62 0.00 0.00 6.46
2116 2353 2.087009 GTGACACGCTACGCCACTC 61.087 63.158 0.00 0.00 0.00 3.51
2127 2364 4.148825 GCCACTCGAGACCGGCAT 62.149 66.667 28.27 2.48 44.25 4.40
2136 2373 0.318784 GAGACCGGCATAACCTAGCG 60.319 60.000 0.00 0.00 35.61 4.26
2141 2379 1.148498 GGCATAACCTAGCGCCCTT 59.852 57.895 2.29 0.00 38.67 3.95
2191 2437 4.162812 GTCAGAACTCTTCATCACTCGTC 58.837 47.826 0.00 0.00 0.00 4.20
2273 2522 3.443037 TGAACATGAAAACGCCAAACAG 58.557 40.909 0.00 0.00 0.00 3.16
2292 2541 2.277591 GCCATCAACCAAGCCAGCA 61.278 57.895 0.00 0.00 0.00 4.41
2296 2545 0.248289 ATCAACCAAGCCAGCATTGC 59.752 50.000 0.00 0.00 0.00 3.56
2345 2594 1.431440 GTTGCAAACTGACGTGGCA 59.569 52.632 0.00 0.00 45.32 4.92
2348 2597 2.639286 CAAACTGACGTGGCAGGC 59.361 61.111 7.77 1.00 40.20 4.85
2364 2613 2.049156 GCTTGAAACGCCAAGGCC 60.049 61.111 5.34 0.00 42.73 5.19
2412 2661 2.017752 GCCTATGGCGTTTCTGCTC 58.982 57.895 0.00 0.00 39.62 4.26
2415 2664 2.548920 GCCTATGGCGTTTCTGCTCTAT 60.549 50.000 0.00 0.00 39.62 1.98
2427 2677 9.193133 GCGTTTCTGCTCTATATATTTAAGTGA 57.807 33.333 0.00 0.00 0.00 3.41
2440 2690 0.824109 TAAGTGATCGTGGGGCTCTG 59.176 55.000 0.00 0.00 0.00 3.35
2444 2694 2.039624 ATCGTGGGGCTCTGACCT 59.960 61.111 0.00 0.00 0.00 3.85
2446 2696 0.105453 ATCGTGGGGCTCTGACCTAT 60.105 55.000 0.00 0.00 0.00 2.57
2459 2709 2.092323 TGACCTATCACTCACCACTCG 58.908 52.381 0.00 0.00 0.00 4.18
2474 2724 1.380515 CTCGCTCTCTTCTCCCCCA 60.381 63.158 0.00 0.00 0.00 4.96
2482 2732 1.076485 CTTCTCCCCCATTGGCCTG 60.076 63.158 3.32 0.00 0.00 4.85
2492 2742 0.323178 CATTGGCCTGTCTCCAGCTT 60.323 55.000 3.32 0.00 37.38 3.74
2510 2760 3.133691 GCTTTTGCCCTTTTCTCCTTTG 58.866 45.455 0.00 0.00 40.15 2.77
2511 2761 3.432186 GCTTTTGCCCTTTTCTCCTTTGT 60.432 43.478 0.00 0.00 40.15 2.83
2512 2762 4.371786 CTTTTGCCCTTTTCTCCTTTGTC 58.628 43.478 0.00 0.00 0.00 3.18
2513 2763 3.312736 TTGCCCTTTTCTCCTTTGTCT 57.687 42.857 0.00 0.00 0.00 3.41
2514 2764 2.863809 TGCCCTTTTCTCCTTTGTCTC 58.136 47.619 0.00 0.00 0.00 3.36
2516 2766 2.224892 GCCCTTTTCTCCTTTGTCTCCT 60.225 50.000 0.00 0.00 0.00 3.69
2534 2785 5.046231 GTCTCCTTCACTTAAACCCTCTCAT 60.046 44.000 0.00 0.00 0.00 2.90
2538 2789 5.986135 CCTTCACTTAAACCCTCTCATATCG 59.014 44.000 0.00 0.00 0.00 2.92
2677 2942 4.022329 CCCTAGTTTTGAACATGGTTCCAC 60.022 45.833 6.64 1.95 0.00 4.02
2695 2960 7.094420 TGGTTCCACATTATGATGTTTGTAGTG 60.094 37.037 0.00 0.00 43.92 2.74
2696 2961 7.094377 GGTTCCACATTATGATGTTTGTAGTGT 60.094 37.037 0.00 0.00 43.92 3.55
2697 2962 7.994425 TCCACATTATGATGTTTGTAGTGTT 57.006 32.000 0.00 0.00 43.92 3.32
2698 2963 8.402798 TCCACATTATGATGTTTGTAGTGTTT 57.597 30.769 0.00 0.00 43.92 2.83
2699 2964 9.508642 TCCACATTATGATGTTTGTAGTGTTTA 57.491 29.630 0.00 0.00 43.92 2.01
2700 2965 9.554724 CCACATTATGATGTTTGTAGTGTTTAC 57.445 33.333 0.00 0.00 43.92 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.945033 TGAAAATGGAAAAAGTATGTGCTTC 57.055 32.000 0.00 0.00 0.00 3.86
36 37 6.510638 GCTGTGCTTCTTGAAAATGGAAAAAG 60.511 38.462 0.00 0.00 0.00 2.27
42 43 3.572584 GAGCTGTGCTTCTTGAAAATGG 58.427 45.455 0.00 0.00 39.88 3.16
112 117 2.561419 GGGTTTTCCTAGGTTTTGGAGC 59.439 50.000 9.08 0.44 40.46 4.70
148 155 5.301551 GGATTTTGGGTTTTTGATGGCTTTT 59.698 36.000 0.00 0.00 0.00 2.27
156 163 7.762588 TTCTATACGGATTTTGGGTTTTTGA 57.237 32.000 0.00 0.00 0.00 2.69
158 165 8.422566 TGTTTTCTATACGGATTTTGGGTTTTT 58.577 29.630 0.00 0.00 0.00 1.94
180 187 7.817478 CGCTCCCTCCTAATTTTAAAATTGTTT 59.183 33.333 28.45 11.79 38.90 2.83
183 190 5.748630 GCGCTCCCTCCTAATTTTAAAATTG 59.251 40.000 28.45 19.71 38.90 2.32
186 193 3.697542 GGCGCTCCCTCCTAATTTTAAAA 59.302 43.478 7.64 2.51 0.00 1.52
209 216 0.028902 CCATCACATGTCGCATGCTG 59.971 55.000 17.13 9.68 0.00 4.41
214 221 2.400962 GCTGCCATCACATGTCGCA 61.401 57.895 0.00 0.60 0.00 5.10
230 237 3.612247 CTTGTGGGCACGCCTAGCT 62.612 63.158 8.20 0.00 36.10 3.32
254 261 4.202212 CGGGGACTTTCAAAGGTCATTTTT 60.202 41.667 1.31 0.00 34.49 1.94
278 285 6.718294 ACAACTAACTAAAGGTTATCCCCTG 58.282 40.000 0.00 0.00 39.36 4.45
302 309 2.368875 GACCACCTCCTTGAAGTGAGAA 59.631 50.000 10.86 0.00 33.21 2.87
307 314 1.059913 CCTGACCACCTCCTTGAAGT 58.940 55.000 0.00 0.00 0.00 3.01
311 318 0.322975 CTGACCTGACCACCTCCTTG 59.677 60.000 0.00 0.00 0.00 3.61
313 320 0.543174 GTCTGACCTGACCACCTCCT 60.543 60.000 0.00 0.00 0.00 3.69
326 333 1.996191 GCCTGATCGAACTTGTCTGAC 59.004 52.381 0.00 0.00 0.00 3.51
330 337 1.936547 GGATGCCTGATCGAACTTGTC 59.063 52.381 0.00 0.00 30.87 3.18
340 347 1.895131 GTGTTTGGTTGGATGCCTGAT 59.105 47.619 0.00 0.00 0.00 2.90
379 387 2.668550 GGTCACTGTGGGCCGAAC 60.669 66.667 8.11 0.00 0.00 3.95
382 390 2.747460 CATGGTCACTGTGGGCCG 60.747 66.667 8.11 0.00 0.00 6.13
385 393 1.300971 CTTCGCATGGTCACTGTGGG 61.301 60.000 8.11 0.00 0.00 4.61
406 414 3.133542 TCATGGCTGATCACTACTCCAAG 59.866 47.826 0.00 0.00 0.00 3.61
409 417 2.432146 TGTCATGGCTGATCACTACTCC 59.568 50.000 0.00 0.00 32.98 3.85
416 424 5.499313 TGTCTATTTTGTCATGGCTGATCA 58.501 37.500 0.00 0.00 32.98 2.92
422 430 7.713764 AACTTTTTGTCTATTTTGTCATGGC 57.286 32.000 0.00 0.00 0.00 4.40
434 442 6.517864 CGGGAGTCCTAGAAACTTTTTGTCTA 60.518 42.308 9.58 0.00 0.00 2.59
438 446 4.213482 CACGGGAGTCCTAGAAACTTTTTG 59.787 45.833 9.58 0.00 44.67 2.44
444 452 0.108281 GCCACGGGAGTCCTAGAAAC 60.108 60.000 9.58 0.00 44.67 2.78
449 457 1.379977 CAGAGCCACGGGAGTCCTA 60.380 63.158 9.58 0.00 44.67 2.94
489 497 7.935338 AAAATGGATGCATCGAATACATTTC 57.065 32.000 26.86 11.39 44.29 2.17
500 508 3.118884 AGTGCCAGAAAAATGGATGCATC 60.119 43.478 18.81 18.81 43.57 3.91
535 543 8.066000 AGCTATTAACGTTTTAAAGTGTGTCAC 58.934 33.333 5.91 0.00 30.86 3.67
570 595 5.850557 TCTGACAACATTGGTTCATGTTT 57.149 34.783 0.00 0.00 38.78 2.83
654 682 6.383436 TGGGCTTTGAATTTGATCCATTATCA 59.617 34.615 0.00 0.00 43.03 2.15
805 833 2.991190 TCGAACTTCCGTAGCACATTTC 59.009 45.455 0.00 0.00 0.00 2.17
831 859 3.612681 CCCTCGTGGTGTCACCGT 61.613 66.667 17.27 0.00 42.58 4.83
844 872 3.073062 AGAATATATGTGCACCCACCCTC 59.927 47.826 15.69 4.72 41.35 4.30
886 914 1.147153 GGCTCCAGCATCCACCTAC 59.853 63.158 0.03 0.00 44.36 3.18
926 954 1.016627 GCAAGAAGCTGTGTGTGTGA 58.983 50.000 0.00 0.00 41.15 3.58
927 955 0.316442 CGCAAGAAGCTGTGTGTGTG 60.316 55.000 0.00 0.00 42.61 3.82
1116 1151 1.302033 CAGGAACTTGACGCTGCCT 60.302 57.895 0.00 0.00 34.60 4.75
1225 1260 2.500392 TTACCGTGAAATTGGAGGGG 57.500 50.000 0.00 0.00 0.00 4.79
1244 1279 1.296056 GCGTCGTTGGTACAGGCATT 61.296 55.000 0.00 0.00 42.39 3.56
1251 1286 1.445582 CAGGAGGCGTCGTTGGTAC 60.446 63.158 0.00 0.00 0.00 3.34
1291 1331 1.609501 AGCTGAACTGGGCGGAGTA 60.610 57.895 0.00 0.00 0.00 2.59
1333 1373 0.106708 TTCCGTTGCAGCTCTGAAGT 59.893 50.000 0.29 0.00 0.00 3.01
1461 1501 2.772691 GGCGTCGTACTCCTCCAGG 61.773 68.421 0.00 0.00 0.00 4.45
1585 1625 3.740397 CTGGTGGCGGACGTACGA 61.740 66.667 27.46 0.00 35.47 3.43
1674 1717 4.454948 CAACTGCCGTTGTGGAGA 57.545 55.556 12.39 0.00 44.27 3.71
1718 1761 4.919653 CTGATACACCAGCACGCT 57.080 55.556 0.00 0.00 0.00 5.07
1733 1776 1.329906 GATCTCACGATTGCCAAGCTG 59.670 52.381 0.00 0.00 0.00 4.24
1743 1786 0.676184 CCCATGGACGATCTCACGAT 59.324 55.000 15.22 0.00 37.03 3.73
1784 1827 1.991230 AGCAGGGCTTACAATCCGT 59.009 52.632 0.00 0.00 33.89 4.69
1785 1828 4.963878 AGCAGGGCTTACAATCCG 57.036 55.556 0.00 0.00 33.89 4.18
1807 1850 5.556915 AGCCAAGCTAATAAGTGTGTTACA 58.443 37.500 0.00 0.00 36.99 2.41
1947 2180 2.743928 GCCCTTGCGTCTGTCCTG 60.744 66.667 0.00 0.00 0.00 3.86
1998 2231 2.750166 CAGAAAGAGACGAGACAGGCTA 59.250 50.000 0.00 0.00 0.00 3.93
1999 2232 1.543802 CAGAAAGAGACGAGACAGGCT 59.456 52.381 0.00 0.00 0.00 4.58
2001 2234 2.817258 AGTCAGAAAGAGACGAGACAGG 59.183 50.000 0.00 0.00 40.84 4.00
2066 2299 3.479269 GCGCGGAAGGAACACTCG 61.479 66.667 8.83 0.00 0.00 4.18
2081 2314 1.000274 TCACTCCATCCACATATCGCG 60.000 52.381 0.00 0.00 0.00 5.87
2082 2315 2.224042 TGTCACTCCATCCACATATCGC 60.224 50.000 0.00 0.00 0.00 4.58
2116 2353 0.318784 GCTAGGTTATGCCGGTCTCG 60.319 60.000 1.90 0.00 43.70 4.04
2125 2362 0.468226 TCCAAGGGCGCTAGGTTATG 59.532 55.000 7.64 0.00 0.00 1.90
2127 2364 1.335132 CCTCCAAGGGCGCTAGGTTA 61.335 60.000 7.64 0.00 0.00 2.85
2141 2379 0.400213 AACAGTGATTTCGGCCTCCA 59.600 50.000 0.00 0.00 0.00 3.86
2229 2478 4.075682 TCTGAAACGCCATGGTTTATGAA 58.924 39.130 14.67 0.00 40.05 2.57
2230 2479 3.680490 TCTGAAACGCCATGGTTTATGA 58.320 40.909 14.67 5.98 40.05 2.15
2233 2482 3.680490 TCATCTGAAACGCCATGGTTTA 58.320 40.909 14.67 0.00 40.05 2.01
2235 2484 2.198827 TCATCTGAAACGCCATGGTT 57.801 45.000 14.67 0.00 0.00 3.67
2236 2485 1.812571 GTTCATCTGAAACGCCATGGT 59.187 47.619 14.67 0.00 35.58 3.55
2239 2488 3.346315 TCATGTTCATCTGAAACGCCAT 58.654 40.909 0.00 0.00 35.58 4.40
2273 2522 3.010413 GCTGGCTTGGTTGATGGCC 62.010 63.158 0.00 0.00 44.31 5.36
2278 2527 0.828762 AGCAATGCTGGCTTGGTTGA 60.829 50.000 7.07 0.00 38.81 3.18
2292 2541 2.999063 GTGGGCCAAGGCAGCAAT 60.999 61.111 8.40 0.00 44.11 3.56
2320 2569 2.117779 TCAGTTTGCAACGCCAGCA 61.118 52.632 0.00 0.00 40.85 4.41
2334 2583 2.281070 CAAGCCTGCCACGTCAGT 60.281 61.111 3.83 0.00 32.32 3.41
2348 2597 1.535204 ATGGGCCTTGGCGTTTCAAG 61.535 55.000 4.53 7.86 42.63 3.02
2371 2620 1.250840 GGCGTTTGAGGCCCAGAAAT 61.251 55.000 0.00 0.00 42.98 2.17
2410 2659 7.707035 GCCCCACGATCACTTAAATATATAGAG 59.293 40.741 0.00 0.00 0.00 2.43
2412 2661 7.556844 AGCCCCACGATCACTTAAATATATAG 58.443 38.462 0.00 0.00 0.00 1.31
2415 2664 5.542635 AGAGCCCCACGATCACTTAAATATA 59.457 40.000 0.00 0.00 0.00 0.86
2427 2677 0.105453 ATAGGTCAGAGCCCCACGAT 60.105 55.000 0.00 0.00 0.00 3.73
2440 2690 1.202313 GCGAGTGGTGAGTGATAGGTC 60.202 57.143 0.00 0.00 0.00 3.85
2444 2694 2.017782 GAGAGCGAGTGGTGAGTGATA 58.982 52.381 0.00 0.00 0.00 2.15
2446 2696 0.250945 AGAGAGCGAGTGGTGAGTGA 60.251 55.000 0.00 0.00 0.00 3.41
2459 2709 0.182299 CCAATGGGGGAGAAGAGAGC 59.818 60.000 0.00 0.00 0.00 4.09
2482 2732 1.332195 AAAGGGCAAAAGCTGGAGAC 58.668 50.000 0.00 0.00 0.00 3.36
2492 2742 3.636764 GAGACAAAGGAGAAAAGGGCAAA 59.363 43.478 0.00 0.00 0.00 3.68
2510 2760 4.283722 TGAGAGGGTTTAAGTGAAGGAGAC 59.716 45.833 0.00 0.00 0.00 3.36
2511 2761 4.489737 TGAGAGGGTTTAAGTGAAGGAGA 58.510 43.478 0.00 0.00 0.00 3.71
2512 2762 4.891992 TGAGAGGGTTTAAGTGAAGGAG 57.108 45.455 0.00 0.00 0.00 3.69
2513 2763 6.183360 CGATATGAGAGGGTTTAAGTGAAGGA 60.183 42.308 0.00 0.00 0.00 3.36
2514 2764 5.986135 CGATATGAGAGGGTTTAAGTGAAGG 59.014 44.000 0.00 0.00 0.00 3.46
2516 2766 6.540438 ACGATATGAGAGGGTTTAAGTGAA 57.460 37.500 0.00 0.00 0.00 3.18



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

AutoCloner maintained by Alex Coulton.