Multiple sequence alignment - TraesCS2D01G455600

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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 TraesCS2D01G455600 chr2D 100.000 5741 0 0 1 5741 563794404 563800144 0.000000e+00 10602.0
1 TraesCS2D01G455600 chr2D 94.009 434 15 5 5271 5695 33028312 33027881 0.000000e+00 647.0
2 TraesCS2D01G455600 chr2B 94.881 5118 186 25 1 5108 674037209 674042260 0.000000e+00 7930.0
3 TraesCS2D01G455600 chr2B 86.695 233 27 3 2593 2825 19107562 19107334 7.380000e-64 255.0
4 TraesCS2D01G455600 chr2B 91.509 106 9 0 5108 5213 674044410 674044515 4.640000e-31 147.0
5 TraesCS2D01G455600 chr2B 90.000 100 10 0 4302 4401 393185627 393185528 4.670000e-26 130.0
6 TraesCS2D01G455600 chr2A 96.443 3121 95 11 308 3419 703876862 703879975 0.000000e+00 5134.0
7 TraesCS2D01G455600 chr2A 93.920 1694 47 16 3599 5273 703879973 703881629 0.000000e+00 2507.0
8 TraesCS2D01G455600 chr2A 95.473 243 11 0 1 243 703876594 703876836 6.980000e-104 388.0
9 TraesCS2D01G455600 chr2A 86.250 240 26 4 2588 2825 41138587 41138821 2.660000e-63 254.0
10 TraesCS2D01G455600 chr7D 94.266 436 12 5 5271 5695 597915408 597914975 0.000000e+00 654.0
11 TraesCS2D01G455600 chr7D 93.103 435 17 6 5271 5695 602674803 602674372 4.880000e-175 625.0
12 TraesCS2D01G455600 chr7D 87.983 233 24 3 2593 2825 426562446 426562218 7.330000e-69 272.0
13 TraesCS2D01G455600 chr4D 93.995 433 16 3 5273 5695 22021818 22021386 0.000000e+00 647.0
14 TraesCS2D01G455600 chr4D 97.959 49 1 0 5693 5741 503911065 503911113 1.020000e-12 86.1
15 TraesCS2D01G455600 chr3D 93.764 433 16 4 5273 5695 25156300 25156731 1.740000e-179 640.0
16 TraesCS2D01G455600 chr3D 93.318 434 18 4 5273 5695 173703476 173703909 1.050000e-176 630.0
17 TraesCS2D01G455600 chr3D 93.525 417 23 4 5273 5687 26434990 26435404 8.170000e-173 617.0
18 TraesCS2D01G455600 chr3D 97.959 49 1 0 5693 5741 25157324 25157372 1.020000e-12 86.1
19 TraesCS2D01G455600 chr3D 97.959 49 1 0 5693 5741 581987182 581987134 1.020000e-12 86.1
20 TraesCS2D01G455600 chr3D 97.959 49 1 0 5693 5741 614100783 614100831 1.020000e-12 86.1
21 TraesCS2D01G455600 chr5D 93.548 434 17 4 5273 5695 6984737 6985170 2.260000e-178 636.0
22 TraesCS2D01G455600 chr5D 85.957 235 27 4 2593 2825 423337798 423337568 4.440000e-61 246.0
23 TraesCS2D01G455600 chr5A 93.488 430 21 3 5273 5695 524666086 524665657 2.920000e-177 632.0
24 TraesCS2D01G455600 chr5A 97.959 49 1 0 5693 5741 348709020 348708972 1.020000e-12 86.1
25 TraesCS2D01G455600 chr4A 97.959 49 1 0 5693 5741 616715917 616715869 1.020000e-12 86.1
26 TraesCS2D01G455600 chr3A 97.959 49 1 0 5693 5741 341600257 341600209 1.020000e-12 86.1
27 TraesCS2D01G455600 chr1D 97.959 49 1 0 5693 5741 74344357 74344309 1.020000e-12 86.1
28 TraesCS2D01G455600 chr1D 97.959 49 1 0 5693 5741 391337660 391337612 1.020000e-12 86.1


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 TraesCS2D01G455600 chr2D 563794404 563800144 5740 False 10602.000000 10602 100.000000 1 5741 1 chr2D.!!$F1 5740
1 TraesCS2D01G455600 chr2B 674037209 674044515 7306 False 4038.500000 7930 93.195000 1 5213 2 chr2B.!!$F1 5212
2 TraesCS2D01G455600 chr2A 703876594 703881629 5035 False 2676.333333 5134 95.278667 1 5273 3 chr2A.!!$F2 5272
3 TraesCS2D01G455600 chr3D 25156300 25157372 1072 False 363.050000 640 95.861500 5273 5741 2 chr3D.!!$F4 468

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
266 267 0.103208 CCACCGGAGCTAGCAAGTAG 59.897 60.0 18.83 3.86 0.00 2.57 F
949 958 0.534203 TTCCAGCCTGTCCGTTGTTC 60.534 55.0 0.00 0.00 0.00 3.18 F
1434 1454 0.443478 TTCTGTCATCGCGCATGTTG 59.557 50.0 8.75 0.00 33.66 3.33 F
3299 3324 0.940126 GTGCCATTCTAGATGTGCCG 59.060 55.0 0.00 0.00 0.00 5.69 F
3579 3605 0.396435 TGATCAGTTGAGTGGGCGTT 59.604 50.0 0.00 0.00 0.00 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1408 0.179156 GGCCGATGATTGCAACTGTG 60.179 55.000 0.00 0.0 0.00 3.66 R
1923 1943 0.681175 AGAAAACCCTGCATTGTGCC 59.319 50.000 0.00 0.0 44.23 5.01 R
3376 3401 1.204146 GTCTAATCCCCAGGCTCACA 58.796 55.000 0.00 0.0 0.00 3.58 R
4726 4754 1.005394 CCCTTTAGCACGACGTGGT 60.005 57.895 32.20 32.2 46.27 4.16 R
5306 7498 0.179084 CCTCAGGCGGCGATTTTAGA 60.179 55.000 12.98 0.0 0.00 2.10 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
70 71 9.896645 TCTAGAGAATAAGATTGCATTTTGTCT 57.103 29.630 0.00 0.00 0.00 3.41
114 115 4.737177 AAGCAGCAGCCTGGCTCC 62.737 66.667 20.49 10.69 43.68 4.70
212 213 1.303643 CAGAGGCACCAAACCCCTC 60.304 63.158 0.00 0.00 44.34 4.30
224 225 2.030562 CCCCTCGTGGTGTCACAC 59.969 66.667 0.00 0.00 43.79 3.82
246 247 2.508436 TGACGCTTCACAAGGCCA 59.492 55.556 5.01 0.00 0.00 5.36
247 248 1.891919 TGACGCTTCACAAGGCCAC 60.892 57.895 5.01 0.00 0.00 5.01
248 249 2.594592 ACGCTTCACAAGGCCACC 60.595 61.111 5.01 0.00 0.00 4.61
249 250 2.594303 CGCTTCACAAGGCCACCA 60.594 61.111 5.01 0.00 0.00 4.17
250 251 2.908073 CGCTTCACAAGGCCACCAC 61.908 63.158 5.01 0.00 0.00 4.16
251 252 2.564721 GCTTCACAAGGCCACCACC 61.565 63.158 5.01 0.00 0.00 4.61
252 253 2.203280 TTCACAAGGCCACCACCG 60.203 61.111 5.01 0.00 33.69 4.94
253 254 3.783362 TTCACAAGGCCACCACCGG 62.783 63.158 5.01 0.00 33.69 5.28
254 255 4.263572 CACAAGGCCACCACCGGA 62.264 66.667 9.46 0.00 33.69 5.14
255 256 3.953775 ACAAGGCCACCACCGGAG 61.954 66.667 9.46 0.00 33.69 4.63
258 259 4.715130 AGGCCACCACCGGAGCTA 62.715 66.667 9.46 0.00 33.69 3.32
259 260 4.162690 GGCCACCACCGGAGCTAG 62.163 72.222 9.46 0.00 0.00 3.42
260 261 4.840005 GCCACCACCGGAGCTAGC 62.840 72.222 9.46 6.62 0.00 3.42
261 262 3.390521 CCACCACCGGAGCTAGCA 61.391 66.667 18.83 0.00 0.00 3.49
262 263 2.662596 CACCACCGGAGCTAGCAA 59.337 61.111 18.83 0.00 0.00 3.91
263 264 1.448540 CACCACCGGAGCTAGCAAG 60.449 63.158 18.83 7.31 0.00 4.01
264 265 1.913762 ACCACCGGAGCTAGCAAGT 60.914 57.895 18.83 5.30 0.00 3.16
265 266 0.613853 ACCACCGGAGCTAGCAAGTA 60.614 55.000 18.83 0.00 0.00 2.24
266 267 0.103208 CCACCGGAGCTAGCAAGTAG 59.897 60.000 18.83 3.86 0.00 2.57
284 285 3.423154 CTCTTGTTCGCACGGGCC 61.423 66.667 2.82 0.00 36.38 5.80
331 332 4.633126 TGTCATCTGATTAGAAGCAACTGC 59.367 41.667 0.00 0.00 36.32 4.40
356 357 0.839853 AGAGCTTCTTCAGGCCCAGT 60.840 55.000 0.00 0.00 0.00 4.00
467 470 0.611896 ACGCTTTTGGATTCCCCCAG 60.612 55.000 0.00 0.00 37.53 4.45
485 488 4.161377 CCCCAGTTGTTTTCCTCAAAAGAA 59.839 41.667 0.00 0.00 33.52 2.52
568 571 1.366366 CCGGTGGTTGAGTTCGTCT 59.634 57.895 0.00 0.00 0.00 4.18
611 617 9.959721 TTTCCTTTCTTATGCTTCTTATACAGT 57.040 29.630 0.00 0.00 0.00 3.55
652 658 9.921637 CATATCTTAAGATGAAGGGTCTCTTAC 57.078 37.037 25.22 0.00 34.44 2.34
678 684 6.305272 TCTGAATCTTCAAAGGTAGCATCT 57.695 37.500 0.00 0.00 36.64 2.90
730 737 3.152341 CCAACATTTCTTGTCAGGAGCT 58.848 45.455 0.00 0.00 37.68 4.09
767 774 2.057137 TGAGCCCCAGTTCATATTGC 57.943 50.000 0.00 0.00 0.00 3.56
915 924 4.381185 GCTTGACATGCATCATCAGGAAAA 60.381 41.667 18.75 2.51 0.00 2.29
949 958 0.534203 TTCCAGCCTGTCCGTTGTTC 60.534 55.000 0.00 0.00 0.00 3.18
974 983 2.092968 TGAAGCATGGACGCCTAAGAAT 60.093 45.455 0.00 0.00 0.00 2.40
1020 1029 3.426695 CCATGAAGTTCGCACTCCATTTC 60.427 47.826 0.00 0.00 30.45 2.17
1035 1044 2.232208 CCATTTCTGGGGTCTTTTCTGC 59.768 50.000 0.00 0.00 39.04 4.26
1050 1059 2.662006 TCTGCTGTCTGTATGCACTC 57.338 50.000 0.00 0.00 32.91 3.51
1078 1087 0.817654 TATCTATGCGAGGCCCGATG 59.182 55.000 16.53 0.00 41.76 3.84
1145 1154 1.626825 AGCTGCCAAGATTGCCATTTT 59.373 42.857 0.00 0.00 0.00 1.82
1211 1220 1.597663 CACAAACCTGGTTGTCGAGAC 59.402 52.381 13.79 0.00 39.73 3.36
1311 1331 8.284693 CGAATCATGCAGATTTATGTTATGACA 58.715 33.333 11.18 0.00 46.76 3.58
1312 1332 9.955208 GAATCATGCAGATTTATGTTATGACAA 57.045 29.630 11.18 0.00 46.76 3.18
1313 1333 9.740239 AATCATGCAGATTTATGTTATGACAAC 57.260 29.630 0.00 0.00 44.48 3.32
1314 1334 8.278729 TCATGCAGATTTATGTTATGACAACA 57.721 30.769 0.00 0.00 39.66 3.33
1315 1335 8.738106 TCATGCAGATTTATGTTATGACAACAA 58.262 29.630 0.00 0.00 39.66 2.83
1316 1336 9.524106 CATGCAGATTTATGTTATGACAACAAT 57.476 29.630 0.00 0.00 39.66 2.71
1388 1408 4.565564 GCATTGCAATTCATGGAGAAAGAC 59.434 41.667 9.83 0.00 40.22 3.01
1412 1432 1.314534 TTGCAATCATCGGCCCACAG 61.315 55.000 0.00 0.00 0.00 3.66
1434 1454 0.443478 TTCTGTCATCGCGCATGTTG 59.557 50.000 8.75 0.00 33.66 3.33
1478 1498 2.040278 TCAAGTGCCTATGCTGTCCTTT 59.960 45.455 0.00 0.00 38.71 3.11
1759 1779 1.171308 CTGGTCAGGGTTGCATTGAG 58.829 55.000 0.00 0.00 0.00 3.02
1775 1795 1.835494 TGAGGGAATCTCGAGTCGTT 58.165 50.000 13.13 6.26 45.32 3.85
1802 1822 1.404391 CATGCAAATCCTGACTCTGGC 59.596 52.381 0.00 0.00 0.00 4.85
1806 1826 2.356125 GCAAATCCTGACTCTGGCCTTA 60.356 50.000 3.32 0.00 0.00 2.69
1923 1943 2.602456 CGTCTCGACATCGGATTACTGG 60.602 54.545 0.73 0.00 40.29 4.00
1961 1981 1.132436 CACATTACGCCAGCACACG 59.868 57.895 0.00 0.00 0.00 4.49
2097 2117 1.486310 TCTGGATCCTTGCTTATGCGT 59.514 47.619 14.23 0.00 43.34 5.24
2380 2400 1.561542 CTATTCTGGCCTGTCCACCTT 59.438 52.381 3.32 0.00 40.72 3.50
2468 2488 1.399714 TATGGCCAGGTGAGACTACG 58.600 55.000 13.05 0.00 0.00 3.51
2612 2632 5.119931 TCTGTATTGATGTGTTTGTTGCC 57.880 39.130 0.00 0.00 0.00 4.52
2657 2677 5.894393 TCCAGTTCCATTTAAGTTTGTTCCA 59.106 36.000 0.00 0.00 0.00 3.53
2811 2831 5.312120 TCTTTCATGTCTAGGACTTCGAC 57.688 43.478 0.00 0.00 33.15 4.20
2832 2852 2.352814 CGCTGTGGTAGGTGATATAGCC 60.353 54.545 0.00 0.00 0.00 3.93
3112 3132 5.162637 TCCTAGTATACCAATTGGAGCCAT 58.837 41.667 31.22 18.21 38.94 4.40
3179 3200 6.939622 TCATGCATTAAAGAAGAGAGAGTGA 58.060 36.000 0.00 0.00 0.00 3.41
3183 3204 5.816777 GCATTAAAGAAGAGAGAGTGAGCAT 59.183 40.000 0.00 0.00 0.00 3.79
3260 3284 4.959723 ACAAAGCCAGCAAATTATGTTGT 58.040 34.783 0.00 0.00 38.48 3.32
3272 3296 7.763528 AGCAAATTATGTTGTGTCTTTTGTTGA 59.236 29.630 0.00 0.00 0.00 3.18
3299 3324 0.940126 GTGCCATTCTAGATGTGCCG 59.060 55.000 0.00 0.00 0.00 5.69
3322 3347 5.163642 CGATACAAAGTCTAGTGGCTGTAGT 60.164 44.000 0.00 0.00 0.00 2.73
3365 3390 1.969256 GTGCTGTCATTTTAACACGCG 59.031 47.619 3.53 3.53 0.00 6.01
3376 3401 8.697067 GTCATTTTAACACGCGTATGTATAGAT 58.303 33.333 13.44 0.00 30.75 1.98
3384 3409 3.119814 CGCGTATGTATAGATGTGAGCCT 60.120 47.826 0.00 0.00 0.00 4.58
3420 3445 7.338449 ACTTATTTCCCGCACACTTTACATTAT 59.662 33.333 0.00 0.00 0.00 1.28
3524 3549 6.641169 AATCACTTCCCTTCTGAAAAGTTC 57.359 37.500 3.79 0.00 29.78 3.01
3547 3573 9.234384 GTTCTTTTTAGGAAGTTCTACTTTTGC 57.766 33.333 2.25 0.00 38.80 3.68
3548 3574 8.514330 TCTTTTTAGGAAGTTCTACTTTTGCA 57.486 30.769 2.25 0.00 38.80 4.08
3549 3575 8.403236 TCTTTTTAGGAAGTTCTACTTTTGCAC 58.597 33.333 2.25 0.00 38.80 4.57
3579 3605 0.396435 TGATCAGTTGAGTGGGCGTT 59.604 50.000 0.00 0.00 0.00 4.84
3582 3608 3.449377 TGATCAGTTGAGTGGGCGTTATA 59.551 43.478 0.00 0.00 0.00 0.98
3596 3622 5.761234 TGGGCGTTATACCAGAAATTATCAC 59.239 40.000 0.00 0.00 31.92 3.06
3798 3824 7.830739 AGTTCTTGTGCATTTTTATCTTAGGG 58.169 34.615 0.00 0.00 0.00 3.53
3886 3912 2.437359 CCAGCTACACTGCCAGCC 60.437 66.667 0.00 0.00 45.78 4.85
4008 4034 2.289195 TGCGGAAAGTTACCTCGTGAAT 60.289 45.455 0.00 0.00 0.00 2.57
4140 4166 3.452627 AGCGTCCCTATGTTGAGATCTTT 59.547 43.478 0.00 0.00 0.00 2.52
4214 4242 2.711542 CTGGGGCTTCGTGAGTTTATT 58.288 47.619 0.00 0.00 0.00 1.40
4215 4243 3.081804 CTGGGGCTTCGTGAGTTTATTT 58.918 45.455 0.00 0.00 0.00 1.40
4216 4244 2.817258 TGGGGCTTCGTGAGTTTATTTG 59.183 45.455 0.00 0.00 0.00 2.32
4217 4245 3.078837 GGGGCTTCGTGAGTTTATTTGA 58.921 45.455 0.00 0.00 0.00 2.69
4218 4246 3.694566 GGGGCTTCGTGAGTTTATTTGAT 59.305 43.478 0.00 0.00 0.00 2.57
4219 4247 4.157840 GGGGCTTCGTGAGTTTATTTGATT 59.842 41.667 0.00 0.00 0.00 2.57
4220 4248 5.355910 GGGGCTTCGTGAGTTTATTTGATTA 59.644 40.000 0.00 0.00 0.00 1.75
4221 4249 6.039382 GGGGCTTCGTGAGTTTATTTGATTAT 59.961 38.462 0.00 0.00 0.00 1.28
4264 4292 8.723942 AAATAATAGCACCTAGTTTCAGTGAG 57.276 34.615 0.00 0.00 33.21 3.51
4354 4382 1.517257 CTGTCGACGTCCATCCTGC 60.517 63.158 10.58 0.00 0.00 4.85
4497 4525 1.817099 GCTGTTCCTCATCTGCGGG 60.817 63.158 0.00 0.00 0.00 6.13
4740 4768 1.300311 CACCACCACGTCGTGCTAA 60.300 57.895 20.01 0.00 32.10 3.09
5079 5121 4.404507 TGAAGATTTTGTAAGCGTGCTC 57.595 40.909 0.00 0.00 0.00 4.26
5323 7515 0.804544 CGTCTAAAATCGCCGCCTGA 60.805 55.000 0.00 0.00 0.00 3.86
5441 7634 0.596082 AAATTTCGGCACAGTTCGGG 59.404 50.000 0.00 0.00 0.00 5.14
5461 7654 2.344025 GGAAGTTCGGCTAAACACGAT 58.656 47.619 0.00 0.00 39.06 3.73
5480 7673 3.127895 CGATAAATTTCGGCCAACTTGGA 59.872 43.478 12.37 0.00 39.92 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.558746 GCCCCATGTCATTATCTGGAGAG 60.559 52.174 0.00 0.00 0.00 3.20
70 71 2.373169 GCCCCATGTCATTATCTGGAGA 59.627 50.000 0.00 0.00 0.00 3.71
114 115 2.061773 CAACGACTGTCTAGCCTGTTG 58.938 52.381 6.21 7.74 31.69 3.33
154 155 5.703592 AGCTCGAGTAGTTATGTCCAGATAG 59.296 44.000 15.13 0.00 0.00 2.08
212 213 4.532490 ACCAAGTGTGACACCACG 57.468 55.556 12.81 2.02 46.06 4.94
243 244 4.840005 GCTAGCTCCGGTGGTGGC 62.840 72.222 24.68 24.68 35.06 5.01
244 245 2.859273 CTTGCTAGCTCCGGTGGTGG 62.859 65.000 17.23 15.90 0.00 4.61
246 247 0.613853 TACTTGCTAGCTCCGGTGGT 60.614 55.000 17.23 13.38 0.00 4.16
247 248 0.103208 CTACTTGCTAGCTCCGGTGG 59.897 60.000 17.23 7.47 0.00 4.61
248 249 0.528684 GCTACTTGCTAGCTCCGGTG 60.529 60.000 17.23 0.00 44.24 4.94
249 250 1.817209 GCTACTTGCTAGCTCCGGT 59.183 57.895 17.23 11.23 44.24 5.28
250 251 4.740235 GCTACTTGCTAGCTCCGG 57.260 61.111 17.23 0.00 44.24 5.14
261 262 1.419374 CGTGCGAACAAGAGCTACTT 58.581 50.000 0.00 0.00 39.70 2.24
262 263 0.388649 CCGTGCGAACAAGAGCTACT 60.389 55.000 0.00 0.00 0.00 2.57
263 264 1.352156 CCCGTGCGAACAAGAGCTAC 61.352 60.000 0.00 0.00 0.00 3.58
264 265 1.080093 CCCGTGCGAACAAGAGCTA 60.080 57.895 0.00 0.00 0.00 3.32
265 266 2.357517 CCCGTGCGAACAAGAGCT 60.358 61.111 0.00 0.00 0.00 4.09
266 267 4.090057 GCCCGTGCGAACAAGAGC 62.090 66.667 0.00 0.00 0.00 4.09
291 292 0.832135 ACACGAGATGGGTGTGAGGT 60.832 55.000 0.00 0.00 46.22 3.85
331 332 0.108424 CCTGAAGAAGCTCTGGTCGG 60.108 60.000 0.00 0.00 31.52 4.79
397 400 1.557371 CCCTCAACCTCTCTCTTTCCC 59.443 57.143 0.00 0.00 0.00 3.97
485 488 8.023128 CACGAAGTTGACATGGAATTAAATCTT 58.977 33.333 0.00 0.00 41.61 2.40
652 658 6.808008 TGCTACCTTTGAAGATTCAGAAAG 57.192 37.500 0.00 0.00 38.61 2.62
730 737 3.565482 GCTCAACTGAACAGAAATGGACA 59.435 43.478 8.87 0.00 0.00 4.02
767 774 8.046107 GGAAAGAGAGGAGGATAAATCATATGG 58.954 40.741 2.13 0.00 0.00 2.74
915 924 5.585844 CAGGCTGGAAGAACAAAAACAAAAT 59.414 36.000 6.61 0.00 34.07 1.82
949 958 2.758089 GGCGTCCATGCTTCAGCTG 61.758 63.158 7.63 7.63 42.66 4.24
997 1006 0.396435 TGGAGTGCGAACTTCATGGT 59.604 50.000 0.00 0.00 0.00 3.55
1020 1029 1.072965 AGACAGCAGAAAAGACCCCAG 59.927 52.381 0.00 0.00 0.00 4.45
1050 1059 3.370366 GCCTCGCATAGATATTCTTGCTG 59.630 47.826 0.00 0.00 32.35 4.41
1078 1087 2.358003 AGCTCCAACGCTCACTGC 60.358 61.111 0.00 0.00 34.57 4.40
1145 1154 3.062122 TGATCTCATTGACAGCAGCAA 57.938 42.857 0.00 0.00 0.00 3.91
1321 1341 4.659111 TGTAAGTCGTATACCATGTGGG 57.341 45.455 3.77 0.00 44.81 4.61
1352 1372 3.596310 TGCAATGCTAACACATGCAAT 57.404 38.095 6.82 0.00 44.48 3.56
1388 1408 0.179156 GGCCGATGATTGCAACTGTG 60.179 55.000 0.00 0.00 0.00 3.66
1412 1432 0.299895 CATGCGCGATGACAGAAGAC 59.700 55.000 12.10 0.00 33.31 3.01
1434 1454 6.476380 TGAAGTTCATTTGCAACATGAGAAAC 59.524 34.615 17.70 14.83 32.20 2.78
1478 1498 1.421268 AGAGTTGGATCAGTTGCACCA 59.579 47.619 0.00 0.00 0.00 4.17
1759 1779 4.291783 CAGAATAACGACTCGAGATTCCC 58.708 47.826 21.68 1.67 34.63 3.97
1775 1795 4.529897 AGTCAGGATTTGCATGCAGAATA 58.470 39.130 21.50 2.53 0.00 1.75
1802 1822 3.686726 GTGCCAATGAGAGAAGTGTAAGG 59.313 47.826 0.00 0.00 0.00 2.69
1806 1826 1.800805 CGTGCCAATGAGAGAAGTGT 58.199 50.000 0.00 0.00 0.00 3.55
1923 1943 0.681175 AGAAAACCCTGCATTGTGCC 59.319 50.000 0.00 0.00 44.23 5.01
1961 1981 7.554476 AGCATACTCTTCCTTCTTGTATTTTCC 59.446 37.037 0.00 0.00 0.00 3.13
2097 2117 6.057533 CACCTCTACTGAAATATGCATCCAA 58.942 40.000 0.19 0.00 0.00 3.53
2380 2400 4.040339 TCATGTAAAGAGTCTCAGGCAACA 59.960 41.667 1.94 0.00 41.41 3.33
2468 2488 1.451387 CCATCCACGTGGCCTTACC 60.451 63.158 30.25 0.00 39.84 2.85
2612 2632 2.704725 ATTGTAACAAGTTGGCTGCG 57.295 45.000 7.96 0.00 0.00 5.18
2657 2677 4.141158 GGATTCTGACTACCATCCCCAAAT 60.141 45.833 0.00 0.00 30.51 2.32
2811 2831 2.352814 GGCTATATCACCTACCACAGCG 60.353 54.545 0.00 0.00 0.00 5.18
2832 2852 3.366273 CCCTTGTCCGATTTGTGACAATG 60.366 47.826 0.00 3.70 46.89 2.82
3149 3170 5.175673 TCTCTTCTTTAATGCATGATACGCG 59.824 40.000 3.53 3.53 0.00 6.01
3179 3200 3.866582 GGTGGAGGGCGCTATGCT 61.867 66.667 7.64 0.00 45.43 3.79
3226 3250 3.877559 CTGGCTTTGTACAGGATGATCA 58.122 45.455 0.00 0.00 39.69 2.92
3272 3296 4.408270 ACATCTAGAATGGCACTGAGATGT 59.592 41.667 21.31 21.31 45.33 3.06
3299 3324 6.095720 AGACTACAGCCACTAGACTTTGTATC 59.904 42.308 0.00 1.70 0.00 2.24
3322 3347 4.082517 CAGAAGCAAGTCAGTAGCTACAGA 60.083 45.833 25.28 19.88 37.70 3.41
3339 3364 4.676924 GTGTTAAAATGACAGCACAGAAGC 59.323 41.667 0.00 0.00 0.00 3.86
3365 3390 4.081420 CCCCAGGCTCACATCTATACATAC 60.081 50.000 0.00 0.00 0.00 2.39
3376 3401 1.204146 GTCTAATCCCCAGGCTCACA 58.796 55.000 0.00 0.00 0.00 3.58
3384 3409 3.181448 GCGGGAAATAAGTCTAATCCCCA 60.181 47.826 3.67 0.00 45.77 4.96
3420 3445 4.340097 TCAGGTTCGAAGTCACTTCTAACA 59.660 41.667 27.32 11.58 43.37 2.41
3493 3518 6.369629 TCAGAAGGGAAGTGATTTGGTTAAA 58.630 36.000 0.00 0.00 0.00 1.52
3524 3549 8.406297 AGTGCAAAAGTAGAACTTCCTAAAAAG 58.594 33.333 0.00 0.00 37.47 2.27
3547 3573 6.016693 ACTCAACTGATCATCTATACCGAGTG 60.017 42.308 0.00 0.00 0.00 3.51
3548 3574 6.016693 CACTCAACTGATCATCTATACCGAGT 60.017 42.308 0.00 0.00 0.00 4.18
3549 3575 6.377780 CACTCAACTGATCATCTATACCGAG 58.622 44.000 0.00 0.00 0.00 4.63
3582 3608 9.965902 AGAAACTAGATTGTGATAATTTCTGGT 57.034 29.630 0.00 0.00 34.68 4.00
3596 3622 6.169419 TGCATCGTTCAAGAAACTAGATTG 57.831 37.500 0.00 0.00 35.59 2.67
3798 3824 1.079750 GGTGCTTCTCGTGTCCTCC 60.080 63.158 0.00 0.00 0.00 4.30
3886 3912 1.135139 CACGGTGAGTATGGAGGTCAG 59.865 57.143 0.74 0.00 0.00 3.51
4110 4136 1.450848 ATAGGGACGCTCGTCGACA 60.451 57.895 17.16 1.87 45.41 4.35
4214 4242 6.411376 TCACTAGGCGGAAAGAAATAATCAA 58.589 36.000 0.00 0.00 0.00 2.57
4215 4243 5.984725 TCACTAGGCGGAAAGAAATAATCA 58.015 37.500 0.00 0.00 0.00 2.57
4216 4244 6.920569 TTCACTAGGCGGAAAGAAATAATC 57.079 37.500 0.00 0.00 0.00 1.75
4217 4245 7.696992 TTTTCACTAGGCGGAAAGAAATAAT 57.303 32.000 0.00 0.00 34.77 1.28
4218 4246 7.696992 ATTTTCACTAGGCGGAAAGAAATAA 57.303 32.000 0.00 0.00 34.77 1.40
4219 4247 8.795842 TTATTTTCACTAGGCGGAAAGAAATA 57.204 30.769 0.00 0.00 34.77 1.40
4220 4248 7.696992 TTATTTTCACTAGGCGGAAAGAAAT 57.303 32.000 0.00 0.00 34.77 2.17
4221 4249 7.696992 ATTATTTTCACTAGGCGGAAAGAAA 57.303 32.000 0.00 1.25 34.77 2.52
4230 4258 7.217906 ACTAGGTGCTATTATTTTCACTAGGC 58.782 38.462 0.00 0.00 0.00 3.93
4234 4262 9.167311 CTGAAACTAGGTGCTATTATTTTCACT 57.833 33.333 0.00 0.00 30.63 3.41
4264 4292 3.812053 CAGGTTAGCTCTGCATCATAACC 59.188 47.826 16.59 16.59 43.69 2.85
4354 4382 2.811317 GCCGTTCTCCGACAGCTG 60.811 66.667 13.48 13.48 39.56 4.24
4725 4753 1.289109 CCCTTTAGCACGACGTGGTG 61.289 60.000 35.58 24.42 44.23 4.17
4726 4754 1.005394 CCCTTTAGCACGACGTGGT 60.005 57.895 32.20 32.20 46.27 4.16
4996 5038 3.748568 ACAAACCAAAAGCTTTCGCAAAA 59.251 34.783 13.10 0.00 39.10 2.44
4997 5039 3.124297 CACAAACCAAAAGCTTTCGCAAA 59.876 39.130 13.10 0.00 39.10 3.68
4998 5040 2.670414 CACAAACCAAAAGCTTTCGCAA 59.330 40.909 13.10 0.00 39.10 4.85
4999 5041 2.266554 CACAAACCAAAAGCTTTCGCA 58.733 42.857 13.10 0.00 39.10 5.10
5000 5042 2.267426 ACACAAACCAAAAGCTTTCGC 58.733 42.857 13.10 0.00 0.00 4.70
5001 5043 2.529894 CGACACAAACCAAAAGCTTTCG 59.470 45.455 13.10 8.37 0.00 3.46
5002 5044 3.507786 ACGACACAAACCAAAAGCTTTC 58.492 40.909 13.10 0.00 0.00 2.62
5003 5045 3.586100 ACGACACAAACCAAAAGCTTT 57.414 38.095 5.69 5.69 0.00 3.51
5004 5046 4.911514 ATACGACACAAACCAAAAGCTT 57.088 36.364 0.00 0.00 0.00 3.74
5005 5047 5.472137 ACATATACGACACAAACCAAAAGCT 59.528 36.000 0.00 0.00 0.00 3.74
5006 5048 5.695818 ACATATACGACACAAACCAAAAGC 58.304 37.500 0.00 0.00 0.00 3.51
5007 5049 8.447833 ACATACATATACGACACAAACCAAAAG 58.552 33.333 0.00 0.00 0.00 2.27
5008 5050 8.325421 ACATACATATACGACACAAACCAAAA 57.675 30.769 0.00 0.00 0.00 2.44
5009 5051 7.908827 ACATACATATACGACACAAACCAAA 57.091 32.000 0.00 0.00 0.00 3.28
5010 5052 9.036671 CATACATACATATACGACACAAACCAA 57.963 33.333 0.00 0.00 0.00 3.67
5011 5053 8.198778 ACATACATACATATACGACACAAACCA 58.801 33.333 0.00 0.00 0.00 3.67
5012 5054 8.583810 ACATACATACATATACGACACAAACC 57.416 34.615 0.00 0.00 0.00 3.27
5013 5055 9.240159 TGACATACATACATATACGACACAAAC 57.760 33.333 0.00 0.00 0.00 2.93
5014 5056 9.458374 CTGACATACATACATATACGACACAAA 57.542 33.333 0.00 0.00 0.00 2.83
5015 5057 8.626526 ACTGACATACATACATATACGACACAA 58.373 33.333 0.00 0.00 0.00 3.33
5019 5061 9.125906 GGAAACTGACATACATACATATACGAC 57.874 37.037 0.00 0.00 0.00 4.34
5021 5063 9.129209 CTGGAAACTGACATACATACATATACG 57.871 37.037 0.00 0.00 0.00 3.06
5197 7389 3.118454 CGCAGCCGAAACCGTCAT 61.118 61.111 0.00 0.00 36.29 3.06
5296 7488 2.607631 CGATTTTAGACGCCCCCTAA 57.392 50.000 0.00 0.00 0.00 2.69
5306 7498 0.179084 CCTCAGGCGGCGATTTTAGA 60.179 55.000 12.98 0.00 0.00 2.10
5307 7499 1.160329 CCCTCAGGCGGCGATTTTAG 61.160 60.000 12.98 0.00 0.00 1.85
5347 7539 2.266055 GACCAACTCGCCCTCAGG 59.734 66.667 0.00 0.00 0.00 3.86
5349 7541 3.319198 GGGACCAACTCGCCCTCA 61.319 66.667 0.00 0.00 38.85 3.86
5441 7634 1.787012 TCGTGTTTAGCCGAACTTCC 58.213 50.000 2.06 0.00 0.00 3.46
5461 7654 3.223435 TGTCCAAGTTGGCCGAAATTTA 58.777 40.909 17.68 0.00 37.47 1.40
5480 7673 4.510340 GGCGAACTTTGTCGGAATATATGT 59.490 41.667 0.00 0.00 41.40 2.29
5489 7682 0.515564 AAATCGGCGAACTTTGTCGG 59.484 50.000 15.93 0.00 41.40 4.79
5550 7743 0.603569 ACTACTCGGTGTTCAGCCAG 59.396 55.000 0.00 0.00 0.00 4.85
5695 7896 3.965539 GTCAGCAGCAGCGGATGGT 62.966 63.158 11.02 0.00 46.35 3.55


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

AutoCloner maintained by Alex Coulton.