Multiple sequence alignment - TraesCS1B01G227600

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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 TraesCS1B01G227600 chr1B 100.000 6744 0 0 1 6744 409251966 409245223 0.000000e+00 12454.0
1 TraesCS1B01G227600 chr1A 95.483 6310 201 46 307 6576 377020875 377014610 0.000000e+00 9997.0
2 TraesCS1B01G227600 chr1A 88.202 178 21 0 114 291 377021101 377020924 5.300000e-51 213.0
3 TraesCS1B01G227600 chr1D 97.849 4927 69 8 1399 6300 302382443 302377529 0.000000e+00 8477.0
4 TraesCS1B01G227600 chr1D 87.255 1428 108 34 7 1382 302383932 302382527 0.000000e+00 1561.0
5 TraesCS1B01G227600 chr1D 88.675 415 27 5 6330 6744 302377530 302377136 7.860000e-134 488.0
6 TraesCS1B01G227600 chr6B 92.851 1203 79 4 1395 2597 346733574 346732379 0.000000e+00 1738.0
7 TraesCS1B01G227600 chr6B 92.192 333 19 5 2593 2921 346711766 346711437 1.320000e-126 464.0
8 TraesCS1B01G227600 chr6B 92.038 314 24 1 2949 3262 346626891 346626579 2.230000e-119 440.0
9 TraesCS1B01G227600 chr6B 94.681 188 10 0 3293 3480 346625971 346625784 6.620000e-75 292.0
10 TraesCS1B01G227600 chr6B 92.958 71 4 1 4317 4386 346625406 346625336 1.200000e-17 102.0
11 TraesCS1B01G227600 chr7A 88.918 379 42 0 1924 2302 529327642 529328020 1.020000e-127 468.0
12 TraesCS1B01G227600 chr7A 89.767 215 22 0 989 1203 529325848 529326062 6.660000e-70 276.0
13 TraesCS1B01G227600 chr7A 81.022 274 43 6 2423 2693 529328578 529328845 6.850000e-50 209.0
14 TraesCS1B01G227600 chr7D 89.431 369 35 4 1936 2302 469841752 469841386 4.760000e-126 462.0
15 TraesCS1B01G227600 chr7D 84.588 279 36 7 926 1203 469843697 469843425 3.100000e-68 270.0
16 TraesCS1B01G227600 chr7B 89.101 367 40 0 1936 2302 493525205 493524839 2.220000e-124 457.0
17 TraesCS1B01G227600 chr7B 84.946 279 35 7 926 1203 493527140 493526868 6.660000e-70 276.0
18 TraesCS1B01G227600 chr7B 81.752 274 41 6 2423 2693 493524241 493523974 3.170000e-53 220.0
19 TraesCS1B01G227600 chr6D 90.698 43 4 0 2972 3014 23637214 23637256 2.630000e-04 58.4
20 TraesCS1B01G227600 chr5B 94.444 36 1 1 6291 6326 424365824 424365858 3.000000e-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 TraesCS1B01G227600 chr1B 409245223 409251966 6743 True 12454.000000 12454 100.000000 1 6744 1 chr1B.!!$R1 6743
1 TraesCS1B01G227600 chr1A 377014610 377021101 6491 True 5105.000000 9997 91.842500 114 6576 2 chr1A.!!$R1 6462
2 TraesCS1B01G227600 chr1D 302377136 302383932 6796 True 3508.666667 8477 91.259667 7 6744 3 chr1D.!!$R1 6737
3 TraesCS1B01G227600 chr6B 346732379 346733574 1195 True 1738.000000 1738 92.851000 1395 2597 1 chr6B.!!$R2 1202
4 TraesCS1B01G227600 chr6B 346625336 346626891 1555 True 278.000000 440 93.225667 2949 4386 3 chr6B.!!$R3 1437
5 TraesCS1B01G227600 chr7A 529325848 529328845 2997 False 317.666667 468 86.569000 989 2693 3 chr7A.!!$F1 1704
6 TraesCS1B01G227600 chr7D 469841386 469843697 2311 True 366.000000 462 87.009500 926 2302 2 chr7D.!!$R1 1376
7 TraesCS1B01G227600 chr7B 493523974 493527140 3166 True 317.666667 457 85.266333 926 2693 3 chr7B.!!$R1 1767

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
448 511 0.044855 ATACCCAGGCTCAGTTCCCT 59.955 55.000 0.00 0.00 0.00 4.20 F
1613 1962 0.042131 CTACTGGGGTGGTGGTCCTA 59.958 60.000 0.00 0.00 34.23 2.94 F
2258 3314 1.135859 GCGTGGACAAGAGCAGAAATG 60.136 52.381 0.00 0.00 0.00 2.32 F
4160 6583 1.228337 ACCATTGCTGACTGCTGCA 60.228 52.632 0.88 0.88 45.56 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 2028 4.473444 TGGAAGCCATTTCATATCCTTCC 58.527 43.478 9.63 9.63 45.27 3.46 R
3482 5901 3.310501 TGAGATATGCACATGCGAACAAG 59.689 43.478 0.00 0.00 45.83 3.16 R
4199 6622 1.207488 AACAGGTATCAGCCCAGCCA 61.207 55.000 0.00 0.00 0.00 4.75 R
6109 8536 0.598562 CTGCACGAGTACACCTGAGT 59.401 55.000 0.00 0.00 0.00 3.41 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
53 54 2.363680 CGAGCCTGAGTCCATCATAACT 59.636 50.000 0.00 0.00 37.28 2.24
59 60 5.012561 GCCTGAGTCCATCATAACTAGGAAT 59.987 44.000 0.00 0.00 37.28 3.01
66 67 4.262635 CCATCATAACTAGGAATCACCGCT 60.263 45.833 0.00 0.00 44.74 5.52
82 83 3.188786 CTTGGGTCGCGCTGTAGC 61.189 66.667 5.56 0.00 37.78 3.58
124 125 3.497879 GCCATCGGCCACACTAAC 58.502 61.111 2.24 0.00 44.06 2.34
125 126 2.112815 GCCATCGGCCACACTAACC 61.113 63.158 2.24 0.00 44.06 2.85
127 128 1.813753 CATCGGCCACACTAACCCG 60.814 63.158 2.24 0.00 41.97 5.28
128 129 2.288025 ATCGGCCACACTAACCCGT 61.288 57.895 2.24 0.00 41.38 5.28
175 197 1.001487 CAACATTCGCCAGAGCAACAA 60.001 47.619 0.00 0.00 39.83 2.83
179 201 1.896220 TTCGCCAGAGCAACAATCTT 58.104 45.000 0.00 0.00 39.83 2.40
274 296 0.947960 TGCGCGAGAAACAAATCCAA 59.052 45.000 12.10 0.00 0.00 3.53
278 300 4.142491 TGCGCGAGAAACAAATCCAATAAT 60.142 37.500 12.10 0.00 0.00 1.28
279 301 4.437820 GCGCGAGAAACAAATCCAATAATC 59.562 41.667 12.10 0.00 0.00 1.75
291 313 1.740585 CCAATAATCGTCAACCGCCAA 59.259 47.619 0.00 0.00 36.19 4.52
316 371 2.343101 CTTTGCCCAACGACGATTAGA 58.657 47.619 0.00 0.00 0.00 2.10
326 381 3.572584 ACGACGATTAGAGTTTTCGCTT 58.427 40.909 0.00 0.00 36.37 4.68
331 386 4.621886 ACGATTAGAGTTTTCGCTTGAGAC 59.378 41.667 0.00 0.00 36.37 3.36
340 395 2.258591 GCTTGAGACCGACGCAGA 59.741 61.111 0.00 0.00 0.00 4.26
356 411 2.548920 CGCAGAGTCTTCCTTTGTTCCT 60.549 50.000 0.00 0.00 0.00 3.36
427 490 3.436496 GTCTGTGTAGACGCAATAGTCC 58.564 50.000 0.00 0.00 43.49 3.85
428 491 3.086282 TCTGTGTAGACGCAATAGTCCA 58.914 45.455 0.00 0.00 41.83 4.02
448 511 0.044855 ATACCCAGGCTCAGTTCCCT 59.955 55.000 0.00 0.00 0.00 4.20
480 559 5.249420 AGAGGCTCAGTTTGGAGAATAAAC 58.751 41.667 18.26 0.00 37.05 2.01
498 577 8.322091 AGAATAAACCAGGCTACATATATGGTC 58.678 37.037 16.96 1.79 43.36 4.02
499 578 7.814693 ATAAACCAGGCTACATATATGGTCT 57.185 36.000 16.96 4.13 43.36 3.85
500 579 5.489792 AACCAGGCTACATATATGGTCTG 57.510 43.478 16.96 15.06 43.36 3.51
522 604 3.928211 CGGAGCAAGATGTGTAAATTCG 58.072 45.455 0.00 0.00 0.00 3.34
598 681 3.373748 TGTAACACTTATCATGCTTGGCG 59.626 43.478 0.00 0.00 0.00 5.69
635 718 3.872560 AGTTTAGGAAGAAAACACGCG 57.127 42.857 3.53 3.53 38.92 6.01
726 809 4.924924 GACGCGCATATCTCGTCT 57.075 55.556 5.73 0.00 46.18 4.18
765 848 1.900245 TCCTTTTAGCAACGGTTCCC 58.100 50.000 0.00 0.00 0.00 3.97
782 865 1.089112 CCCGGTTTTATTCGTGGGAC 58.911 55.000 0.00 0.00 39.03 4.46
784 867 2.152830 CCGGTTTTATTCGTGGGACAA 58.847 47.619 0.00 0.00 44.16 3.18
819 902 3.252284 CTATCCAGCCCGGCCCAT 61.252 66.667 5.55 0.00 33.14 4.00
828 911 1.002134 CCCGGCCCATACATCCATC 60.002 63.158 0.00 0.00 0.00 3.51
864 947 3.568007 TCCTTTTGGATGTTTCGTGAAGG 59.432 43.478 0.00 0.00 45.19 3.46
1232 1316 1.662438 GCACTCTCTCACTCCCCTCG 61.662 65.000 0.00 0.00 0.00 4.63
1468 1812 6.071560 GGGAAGTTCGGGTTTCTGAATAATTT 60.072 38.462 0.00 0.00 40.08 1.82
1469 1813 7.375834 GGAAGTTCGGGTTTCTGAATAATTTT 58.624 34.615 0.00 0.00 40.08 1.82
1475 1819 5.417580 CGGGTTTCTGAATAATTTTCTCCCA 59.582 40.000 0.00 0.00 0.00 4.37
1613 1962 0.042131 CTACTGGGGTGGTGGTCCTA 59.958 60.000 0.00 0.00 34.23 2.94
1679 2028 4.084013 GGTATTCACCCGATTAGAATTGCG 60.084 45.833 0.00 0.00 39.11 4.85
2258 3314 1.135859 GCGTGGACAAGAGCAGAAATG 60.136 52.381 0.00 0.00 0.00 2.32
3004 4576 5.200454 CAATCCGAATTAATTGACTCAGCG 58.800 41.667 5.17 0.96 35.35 5.18
3480 5899 8.280258 TGTTCCAATGGATAATATCTCTTCCT 57.720 34.615 1.39 0.00 0.00 3.36
3481 5900 8.727149 TGTTCCAATGGATAATATCTCTTCCTT 58.273 33.333 1.39 0.00 0.00 3.36
3482 5901 9.225436 GTTCCAATGGATAATATCTCTTCCTTC 57.775 37.037 1.39 0.00 0.00 3.46
4160 6583 1.228337 ACCATTGCTGACTGCTGCA 60.228 52.632 0.88 0.88 45.56 4.41
4186 6609 5.708230 GTCCTTATTTGTGGTATGGTGTGAA 59.292 40.000 0.00 0.00 0.00 3.18
4199 6622 0.657840 GTGTGAAGCAGTTTCGCTGT 59.342 50.000 11.36 0.00 46.64 4.40
4231 6654 6.929049 GCTGATACCTGTTATTGCTATGTGTA 59.071 38.462 0.00 0.00 0.00 2.90
4278 6701 1.418097 TTTCTCTCCTGTGCTGGGCA 61.418 55.000 0.00 0.00 35.60 5.36
4304 6727 2.045045 CCCATTCAGCCTTGCCGA 60.045 61.111 0.00 0.00 0.00 5.54
4739 7165 7.669089 TTTTCCTTGAAGAATTGTAGGGTTT 57.331 32.000 0.00 0.00 0.00 3.27
4756 7182 7.675195 TGTAGGGTTTTAAGACCTCATACTGTA 59.325 37.037 14.38 0.00 39.71 2.74
4757 7183 7.184067 AGGGTTTTAAGACCTCATACTGTAG 57.816 40.000 14.38 0.00 39.71 2.74
4758 7184 5.816258 GGGTTTTAAGACCTCATACTGTAGC 59.184 44.000 14.38 0.00 39.71 3.58
4904 7330 3.244630 ACCATGCAGGCAACAAAATGATT 60.245 39.130 0.00 0.00 43.14 2.57
5253 7679 8.757982 AATCTCAGCAAATTCAGGTATTATGT 57.242 30.769 0.00 0.00 0.00 2.29
5344 7770 4.924305 ACGTCACTTGTCCTTGTACTTA 57.076 40.909 0.00 0.00 0.00 2.24
5456 7882 3.193267 TGCTTGCACAATCCTACCAATTC 59.807 43.478 0.00 0.00 0.00 2.17
5465 7891 7.013274 GCACAATCCTACCAATTCTATTGCTTA 59.987 37.037 0.00 0.00 0.00 3.09
5848 8275 0.598065 GGCCACTTGCTTGTACCTTG 59.402 55.000 0.00 0.00 40.92 3.61
6160 8587 7.310361 CCTCCATTTAAAAGGCCATGAAAAGTA 60.310 37.037 5.01 0.00 0.00 2.24
6427 8902 9.431887 ACACAATAACTCGTATGTTTAACTCAT 57.568 29.630 0.00 0.00 0.00 2.90
6457 8932 8.706322 TGTATACAGCCTCTCATATGAGTTAA 57.294 34.615 27.80 11.67 42.60 2.01
6458 8933 9.143155 TGTATACAGCCTCTCATATGAGTTAAA 57.857 33.333 27.80 11.34 42.60 1.52
6459 8934 9.413048 GTATACAGCCTCTCATATGAGTTAAAC 57.587 37.037 27.80 15.87 42.60 2.01
6460 8935 6.299805 ACAGCCTCTCATATGAGTTAAACA 57.700 37.500 27.80 10.35 42.60 2.83
6461 8936 6.893583 ACAGCCTCTCATATGAGTTAAACAT 58.106 36.000 27.80 10.36 42.60 2.71
6462 8937 8.023021 ACAGCCTCTCATATGAGTTAAACATA 57.977 34.615 27.80 9.03 42.60 2.29
6463 8938 8.147058 ACAGCCTCTCATATGAGTTAAACATAG 58.853 37.037 27.80 16.71 42.60 2.23
6464 8939 7.601886 CAGCCTCTCATATGAGTTAAACATAGG 59.398 40.741 27.80 23.82 42.60 2.57
6465 8940 7.510685 AGCCTCTCATATGAGTTAAACATAGGA 59.489 37.037 27.80 13.59 42.60 2.94
6517 8992 9.740710 AAGGGGAGTATGATTTAGTATATTTGC 57.259 33.333 0.00 0.00 0.00 3.68
6565 9040 7.914427 AGATGTAACTGGTATAACAGGATGA 57.086 36.000 21.65 3.75 42.75 2.92
6586 9061 6.761731 TGAAAAACTTTTTATCGTGCATGG 57.238 33.333 5.98 0.00 0.00 3.66
6610 9085 9.290988 TGGCTACATGTTAGACTTTTTGAATTA 57.709 29.630 2.30 0.00 0.00 1.40
6626 9101 4.126437 TGAATTATGAGGTGCACGTATGG 58.874 43.478 12.81 0.00 0.00 2.74
6662 9137 1.045407 GGTTGTTGGGGAGGGAAAAC 58.955 55.000 0.00 0.00 0.00 2.43
6664 9139 0.468400 TTGTTGGGGAGGGAAAACCG 60.468 55.000 0.00 0.00 46.96 4.44
6678 9153 3.307269 GGAAAACCGAGGGTAGTAAAGCT 60.307 47.826 0.00 0.00 33.12 3.74
6716 9191 1.408702 GTGCTCATGAGGTCCTCTCTC 59.591 57.143 23.89 4.67 42.86 3.20
6734 9209 2.839486 TCGCAATGGGGAGATATCAC 57.161 50.000 5.32 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.042093 GGTGATTCCTAGTTATGATGGACTCA 59.958 42.308 0.00 0.00 36.41 3.41
39 40 6.459923 GGTGATTCCTAGTTATGATGGACTC 58.540 44.000 0.00 0.00 0.00 3.36
43 44 3.997021 GCGGTGATTCCTAGTTATGATGG 59.003 47.826 0.00 0.00 0.00 3.51
53 54 2.691663 ACCCAAGCGGTGATTCCTA 58.308 52.632 0.00 0.00 46.09 2.94
66 67 4.752879 GGCTACAGCGCGACCCAA 62.753 66.667 12.10 0.00 43.26 4.12
77 78 0.899019 TATGCTTCGTGGTGGCTACA 59.101 50.000 1.52 0.00 0.00 2.74
82 83 0.462047 GGTCCTATGCTTCGTGGTGG 60.462 60.000 0.00 0.00 0.00 4.61
116 117 1.346365 CGATGTGACGGGTTAGTGTG 58.654 55.000 0.00 0.00 0.00 3.82
117 118 0.389426 GCGATGTGACGGGTTAGTGT 60.389 55.000 0.00 0.00 0.00 3.55
118 119 1.082117 GGCGATGTGACGGGTTAGTG 61.082 60.000 0.00 0.00 0.00 2.74
119 120 1.217244 GGCGATGTGACGGGTTAGT 59.783 57.895 0.00 0.00 0.00 2.24
127 128 3.248171 GACGAGCGGCGATGTGAC 61.248 66.667 12.98 0.00 44.57 3.67
128 129 4.492160 GGACGAGCGGCGATGTGA 62.492 66.667 12.98 0.00 44.57 3.58
175 197 0.325296 TCGTGGGACTGGCCTAAGAT 60.325 55.000 3.32 0.00 31.09 2.40
179 201 3.075005 GCTCGTGGGACTGGCCTA 61.075 66.667 3.32 0.00 36.66 3.93
215 237 0.679505 CCTCTCGGTGGAGTTGTTCA 59.320 55.000 0.00 0.00 41.26 3.18
255 277 0.947960 TTGGATTTGTTTCTCGCGCA 59.052 45.000 8.75 0.00 0.00 6.09
259 281 6.771076 TGACGATTATTGGATTTGTTTCTCG 58.229 36.000 0.00 0.00 0.00 4.04
326 381 3.264947 GACTCTGCGTCGGTCTCA 58.735 61.111 0.00 0.00 32.04 3.27
340 395 6.381133 ACAAAATTGAGGAACAAAGGAAGACT 59.619 34.615 0.00 0.00 42.03 3.24
347 402 6.697019 ACAATCGACAAAATTGAGGAACAAAG 59.303 34.615 2.84 0.00 42.03 2.77
356 411 6.183360 TGTGACTGAACAATCGACAAAATTGA 60.183 34.615 2.84 0.00 37.51 2.57
421 484 2.975489 CTGAGCCTGGGTATTGGACTAT 59.025 50.000 0.00 0.00 0.00 2.12
422 485 2.292918 ACTGAGCCTGGGTATTGGACTA 60.293 50.000 0.00 0.00 0.00 2.59
423 486 1.207791 CTGAGCCTGGGTATTGGACT 58.792 55.000 0.00 0.00 0.00 3.85
424 487 0.912486 ACTGAGCCTGGGTATTGGAC 59.088 55.000 0.00 0.00 0.00 4.02
425 488 1.559682 GAACTGAGCCTGGGTATTGGA 59.440 52.381 0.00 0.00 0.00 3.53
426 489 1.408822 GGAACTGAGCCTGGGTATTGG 60.409 57.143 0.00 0.00 0.00 3.16
427 490 1.408822 GGGAACTGAGCCTGGGTATTG 60.409 57.143 0.00 0.00 0.00 1.90
428 491 0.919710 GGGAACTGAGCCTGGGTATT 59.080 55.000 0.00 0.00 0.00 1.89
456 525 5.505181 TTATTCTCCAAACTGAGCCTCTT 57.495 39.130 0.00 0.00 32.22 2.85
480 559 3.677148 CGCAGACCATATATGTAGCCTGG 60.677 52.174 11.73 0.00 0.00 4.45
498 577 1.725641 TTACACATCTTGCTCCGCAG 58.274 50.000 0.00 0.00 40.61 5.18
499 578 2.177394 TTTACACATCTTGCTCCGCA 57.823 45.000 0.00 0.00 36.47 5.69
500 579 3.685058 GAATTTACACATCTTGCTCCGC 58.315 45.455 0.00 0.00 0.00 5.54
570 653 4.081642 AGCATGATAAGTGTTACACCGACT 60.082 41.667 12.28 0.00 34.49 4.18
571 654 4.181578 AGCATGATAAGTGTTACACCGAC 58.818 43.478 12.28 2.66 34.49 4.79
572 655 4.465632 AGCATGATAAGTGTTACACCGA 57.534 40.909 12.28 0.36 34.49 4.69
598 681 0.900421 ACTACCCTTGTACCTTCGCC 59.100 55.000 0.00 0.00 0.00 5.54
635 718 4.489771 CCACCTGGCCCGTCATCC 62.490 72.222 0.00 0.00 0.00 3.51
763 846 1.089112 GTCCCACGAATAAAACCGGG 58.911 55.000 6.32 0.00 34.81 5.73
765 848 3.900388 TTTGTCCCACGAATAAAACCG 57.100 42.857 0.00 0.00 0.00 4.44
784 867 5.196695 GGATAGATGGGCTGACTTCTTTTT 58.803 41.667 0.00 0.00 0.00 1.94
790 873 1.419387 GCTGGATAGATGGGCTGACTT 59.581 52.381 0.00 0.00 0.00 3.01
791 874 1.055040 GCTGGATAGATGGGCTGACT 58.945 55.000 0.00 0.00 0.00 3.41
792 875 0.036022 GGCTGGATAGATGGGCTGAC 59.964 60.000 0.00 0.00 0.00 3.51
793 876 1.130054 GGGCTGGATAGATGGGCTGA 61.130 60.000 0.00 0.00 0.00 4.26
828 911 3.254166 CCAAAAGGATATGGGCTTCATCG 59.746 47.826 0.00 0.00 37.30 3.84
1003 1087 3.620300 AATCGTCGAACGCCAGCGA 62.620 57.895 20.32 0.00 42.21 4.93
1679 2028 4.473444 TGGAAGCCATTTCATATCCTTCC 58.527 43.478 9.63 9.63 45.27 3.46
2258 3314 6.401796 GCATTTCTGAACCATTTCATCAAAGC 60.402 38.462 0.00 0.00 41.05 3.51
3480 5899 3.940852 AGATATGCACATGCGAACAAGAA 59.059 39.130 0.00 0.00 45.83 2.52
3481 5900 3.534554 AGATATGCACATGCGAACAAGA 58.465 40.909 0.00 0.00 45.83 3.02
3482 5901 3.310501 TGAGATATGCACATGCGAACAAG 59.689 43.478 0.00 0.00 45.83 3.16
3673 6096 3.264193 ACAGAAGGTACTGATGAATGCCA 59.736 43.478 0.00 0.00 40.86 4.92
4160 6583 4.258543 CACCATACCACAAATAAGGACGT 58.741 43.478 0.00 0.00 0.00 4.34
4199 6622 1.207488 AACAGGTATCAGCCCAGCCA 61.207 55.000 0.00 0.00 0.00 4.75
4231 6654 1.376466 CTAGCCAGCCCACAACACT 59.624 57.895 0.00 0.00 0.00 3.55
4574 6998 5.870706 TCTGATAATGTACCCAACACAACA 58.129 37.500 0.00 0.00 42.09 3.33
4739 7165 4.709886 TGCTGCTACAGTATGAGGTCTTAA 59.290 41.667 0.00 0.00 39.69 1.85
4756 7182 0.184933 TAGTTGGTTGGGTTGCTGCT 59.815 50.000 0.00 0.00 0.00 4.24
4757 7183 1.067635 CATAGTTGGTTGGGTTGCTGC 60.068 52.381 0.00 0.00 0.00 5.25
4758 7184 1.067635 GCATAGTTGGTTGGGTTGCTG 60.068 52.381 0.00 0.00 0.00 4.41
4904 7330 0.908910 TTCGCTTGGCCTCCTCAATA 59.091 50.000 3.32 0.00 0.00 1.90
5253 7679 1.777878 TGGGGAGTAAGGCAACAGAAA 59.222 47.619 0.00 0.00 41.41 2.52
5344 7770 2.351835 GCGCACATACTCATCCGACTAT 60.352 50.000 0.30 0.00 0.00 2.12
5456 7882 3.976942 GCATTGACGCCATTAAGCAATAG 59.023 43.478 0.00 0.00 0.00 1.73
5465 7891 1.391577 TATGCTGCATTGACGCCATT 58.608 45.000 21.56 0.00 0.00 3.16
5611 8038 3.026707 TCTCTCATATCGTTGGTCCCA 57.973 47.619 0.00 0.00 0.00 4.37
5848 8275 3.243068 CGTCACAAGCAAAATATAGGCCC 60.243 47.826 0.00 0.00 0.00 5.80
6109 8536 0.598562 CTGCACGAGTACACCTGAGT 59.401 55.000 0.00 0.00 0.00 3.41
6427 8902 9.620259 CTCATATGAGAGGCTGTATACATAGTA 57.380 37.037 25.78 0.00 44.74 1.82
6428 8903 8.112822 ACTCATATGAGAGGCTGTATACATAGT 58.887 37.037 34.16 7.93 44.74 2.12
6429 8904 8.518430 ACTCATATGAGAGGCTGTATACATAG 57.482 38.462 34.16 7.32 44.74 2.23
6440 8915 7.671302 TCCTATGTTTAACTCATATGAGAGGC 58.329 38.462 34.16 19.75 44.74 4.70
6472 8947 8.210946 CTCCCCTTGAGAATTGTATATACAACA 58.789 37.037 26.55 18.10 44.89 3.33
6473 8948 8.211629 ACTCCCCTTGAGAATTGTATATACAAC 58.788 37.037 26.55 16.63 44.89 3.32
6474 8949 8.331931 ACTCCCCTTGAGAATTGTATATACAA 57.668 34.615 26.28 26.28 45.52 2.41
6475 8950 7.931015 ACTCCCCTTGAGAATTGTATATACA 57.069 36.000 11.62 11.62 44.42 2.29
6476 8951 9.877178 CATACTCCCCTTGAGAATTGTATATAC 57.123 37.037 5.89 5.89 44.42 1.47
6542 9017 8.958119 TTTCATCCTGTTATACCAGTTACATC 57.042 34.615 0.00 0.00 0.00 3.06
6558 9033 6.640499 TGCACGATAAAAAGTTTTTCATCCTG 59.360 34.615 16.65 15.77 0.00 3.86
6561 9036 7.447430 CCATGCACGATAAAAAGTTTTTCATC 58.553 34.615 16.65 15.14 0.00 2.92
6565 9040 5.296748 AGCCATGCACGATAAAAAGTTTTT 58.703 33.333 17.26 17.26 0.00 1.94
6600 9075 5.446143 ACGTGCACCTCATAATTCAAAAA 57.554 34.783 12.15 0.00 0.00 1.94
6610 9085 1.153168 GGCCATACGTGCACCTCAT 60.153 57.895 12.15 0.00 0.00 2.90
6626 9101 2.231716 ACCAAATAAGTCCCAAGGGC 57.768 50.000 0.00 0.00 34.68 5.19
6662 9137 2.885894 CCTAGAGCTTTACTACCCTCGG 59.114 54.545 0.00 0.00 0.00 4.63
6664 9139 5.051409 TCTCCTAGAGCTTTACTACCCTC 57.949 47.826 0.00 0.00 0.00 4.30
6678 9153 5.423290 TGAGCACATGAAAATCTCTCCTAGA 59.577 40.000 0.00 0.00 39.02 2.43
6716 9191 2.420642 CAGTGATATCTCCCCATTGCG 58.579 52.381 3.98 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.