Multiple sequence alignment - TraesCS6A01G203300

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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 TraesCS6A01G203300 chr6A 100.000 4865 0 0 1 4865 346570502 346575366 0.000000e+00 8985
1 TraesCS6A01G203300 chr6D 97.721 2721 36 4 1737 4440 249994772 249992061 0.000000e+00 4658
2 TraesCS6A01G203300 chr6D 94.352 1735 39 23 18 1740 249996551 249994864 0.000000e+00 2606
3 TraesCS6A01G203300 chr6D 98.345 423 7 0 4439 4861 249992097 249991675 0.000000e+00 743
4 TraesCS6A01G203300 chr6B 94.459 1498 44 15 1484 2954 338014949 338013464 0.000000e+00 2270
5 TraesCS6A01G203300 chr6B 95.405 1001 21 6 2959 3934 338013364 338012364 0.000000e+00 1570
6 TraesCS6A01G203300 chr6B 92.151 930 15 15 357 1253 338016053 338015149 0.000000e+00 1260
7 TraesCS6A01G203300 chr6B 94.323 458 17 4 3981 4436 338012361 338011911 0.000000e+00 693
8 TraesCS6A01G203300 chr6B 94.389 303 13 2 4559 4861 337943299 337943001 3.430000e-126 462
9 TraesCS6A01G203300 chr6B 88.776 294 22 6 17 304 338016510 338016222 2.790000e-92 350
10 TraesCS6A01G203300 chr6B 85.235 149 7 5 1315 1459 338015159 338015022 6.570000e-29 139
11 TraesCS6A01G203300 chr2D 87.055 309 40 0 1052 1360 406950440 406950748 2.790000e-92 350
12 TraesCS6A01G203300 chr2A 87.055 309 40 0 1052 1360 574971094 574971402 2.790000e-92 350
13 TraesCS6A01G203300 chr2B 86.731 309 41 0 1052 1360 482731107 482731415 1.300000e-90 344


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 TraesCS6A01G203300 chr6A 346570502 346575366 4864 False 8985 8985 100.000000 1 4865 1 chr6A.!!$F1 4864
1 TraesCS6A01G203300 chr6D 249991675 249996551 4876 True 2669 4658 96.806000 18 4861 3 chr6D.!!$R1 4843
2 TraesCS6A01G203300 chr6B 338011911 338016510 4599 True 1047 2270 91.724833 17 4436 6 chr6B.!!$R2 4419

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
412 556 0.249322 AGACACACGTACCAGCACAC 60.249 55.0 0.00 0.0 0.00 3.82 F
2081 2519 0.534203 TTCACGCCCTTCTGGAACAC 60.534 55.0 0.00 0.0 35.39 3.32 F
3390 3944 0.980754 TGGACCGTGCCACTATCCAT 60.981 55.0 11.66 0.0 34.50 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2676 0.251354 ATGAGCAGCACCTCGACAAT 59.749 50.0 0.00 0.0 34.56 2.71 R
3584 4138 1.813513 GTTGTATCTGGCAGCAGTGT 58.186 50.0 10.34 0.0 0.00 3.55 R
4487 5069 0.312102 GGTGAGGCTTGTGCAGTTTC 59.688 55.0 0.00 0.0 41.91 2.78 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
71 72 6.212791 TGCAAGTTACCCAAATAGAGACTACT 59.787 38.462 0.00 0.00 0.00 2.57
79 80 7.612677 ACCCAAATAGAGACTACTAAACACAG 58.387 38.462 0.00 0.00 0.00 3.66
81 82 7.545965 CCCAAATAGAGACTACTAAACACAGTG 59.454 40.741 0.00 0.00 0.00 3.66
86 87 6.062749 AGAGACTACTAAACACAGTGTGAGA 58.937 40.000 29.58 12.46 36.96 3.27
142 144 5.852738 AAATCTCAACTTGACATGTCTCG 57.147 39.130 25.55 17.95 0.00 4.04
155 157 3.258372 ACATGTCTCGACACATACAAGGT 59.742 43.478 5.97 0.00 45.05 3.50
184 186 6.394809 CAAGGGGTTGTTTGATTACCAATAC 58.605 40.000 0.00 0.00 34.23 1.89
185 187 5.899278 AGGGGTTGTTTGATTACCAATACT 58.101 37.500 0.00 0.00 34.23 2.12
186 188 7.034967 AGGGGTTGTTTGATTACCAATACTA 57.965 36.000 0.00 0.00 34.23 1.82
203 205 7.504911 ACCAATACTAGCGATTTCTAGAGGTTA 59.495 37.037 4.97 0.00 38.61 2.85
274 281 4.744137 CGTGCATTGAGAAAACAATTTCCA 59.256 37.500 0.00 0.00 44.96 3.53
275 282 5.107760 CGTGCATTGAGAAAACAATTTCCAG 60.108 40.000 0.00 0.00 44.96 3.86
304 311 2.911484 TGGTTACATGCATGCATCGTA 58.089 42.857 30.07 27.38 33.90 3.43
306 313 3.064682 TGGTTACATGCATGCATCGTAAC 59.935 43.478 38.53 38.53 42.20 2.50
307 314 3.064682 GGTTACATGCATGCATCGTAACA 59.935 43.478 41.25 27.98 43.14 2.41
308 315 4.438065 GGTTACATGCATGCATCGTAACAA 60.438 41.667 41.25 28.48 43.14 2.83
309 316 3.135414 ACATGCATGCATCGTAACAAC 57.865 42.857 30.07 0.00 33.90 3.32
310 317 2.749076 ACATGCATGCATCGTAACAACT 59.251 40.909 30.07 3.48 33.90 3.16
312 319 4.201812 ACATGCATGCATCGTAACAACTAC 60.202 41.667 30.07 0.00 33.90 2.73
315 322 3.370978 GCATGCATCGTAACAACTACTGT 59.629 43.478 14.21 0.00 41.27 3.55
319 326 4.919168 TGCATCGTAACAACTACTGTACAC 59.081 41.667 0.00 0.00 37.23 2.90
320 327 4.919168 GCATCGTAACAACTACTGTACACA 59.081 41.667 0.00 0.00 37.23 3.72
330 474 4.077108 ACTACTGTACACATGAACGGAGA 58.923 43.478 0.00 0.00 0.00 3.71
335 479 1.933021 ACACATGAACGGAGAGGGTA 58.067 50.000 0.00 0.00 0.00 3.69
336 480 1.549170 ACACATGAACGGAGAGGGTAC 59.451 52.381 0.00 0.00 0.00 3.34
337 481 1.548719 CACATGAACGGAGAGGGTACA 59.451 52.381 0.00 0.00 0.00 2.90
338 482 1.825474 ACATGAACGGAGAGGGTACAG 59.175 52.381 0.00 0.00 0.00 2.74
339 483 1.825474 CATGAACGGAGAGGGTACAGT 59.175 52.381 0.00 0.00 0.00 3.55
340 484 2.885135 TGAACGGAGAGGGTACAGTA 57.115 50.000 0.00 0.00 0.00 2.74
341 485 2.719739 TGAACGGAGAGGGTACAGTAG 58.280 52.381 0.00 0.00 0.00 2.57
342 486 2.040813 TGAACGGAGAGGGTACAGTAGT 59.959 50.000 0.00 0.00 0.00 2.73
343 487 3.264193 TGAACGGAGAGGGTACAGTAGTA 59.736 47.826 0.00 0.00 0.00 1.82
344 488 4.263462 TGAACGGAGAGGGTACAGTAGTAA 60.263 45.833 0.00 0.00 30.67 2.24
412 556 0.249322 AGACACACGTACCAGCACAC 60.249 55.000 0.00 0.00 0.00 3.82
572 717 2.158943 GGGATAAACGGACAAGAGGGAG 60.159 54.545 0.00 0.00 0.00 4.30
950 1109 4.082733 GCTCGTTATCCAGCTTTTTCCTTT 60.083 41.667 0.00 0.00 32.48 3.11
1271 1448 4.736896 GCTGGTCACCCGACGGTC 62.737 72.222 13.94 0.00 42.04 4.79
1272 1449 4.065281 CTGGTCACCCGACGGTCC 62.065 72.222 13.94 10.01 42.04 4.46
1273 1450 4.918278 TGGTCACCCGACGGTCCA 62.918 66.667 13.94 12.43 42.04 4.02
1274 1451 4.368543 GGTCACCCGACGGTCCAC 62.369 72.222 13.94 5.50 42.04 4.02
1275 1452 4.368543 GTCACCCGACGGTCCACC 62.369 72.222 13.94 0.00 42.04 4.61
1432 1689 7.030234 TCTCTGTTACTCCTACTCCTACTTT 57.970 40.000 0.00 0.00 0.00 2.66
1565 1877 3.788227 TCTTTGCATCAACAGTACCCT 57.212 42.857 0.00 0.00 0.00 4.34
1566 1878 3.674997 TCTTTGCATCAACAGTACCCTC 58.325 45.455 0.00 0.00 0.00 4.30
1567 1879 3.327757 TCTTTGCATCAACAGTACCCTCT 59.672 43.478 0.00 0.00 0.00 3.69
1568 1880 3.334583 TTGCATCAACAGTACCCTCTC 57.665 47.619 0.00 0.00 0.00 3.20
1582 1898 1.612395 CCTCTCTCCCTCCTGTGTGC 61.612 65.000 0.00 0.00 0.00 4.57
1607 1923 4.971830 GTGTGTGCCAATCAATCATATTCG 59.028 41.667 0.00 0.00 0.00 3.34
1699 2015 1.887198 ACACTACTCCCTGAACACTCG 59.113 52.381 0.00 0.00 0.00 4.18
1731 2047 3.053544 TCCCAAAAGTTCTTGTACCCACA 60.054 43.478 0.00 0.00 0.00 4.17
1733 2049 4.440940 CCCAAAAGTTCTTGTACCCACAAC 60.441 45.833 0.00 0.00 39.75 3.32
1735 2051 3.945640 AAGTTCTTGTACCCACAACCT 57.054 42.857 0.00 0.00 39.75 3.50
1777 2189 8.818141 AGTCCGGTTTAGTTAAAACTTACTAC 57.182 34.615 0.00 2.26 45.70 2.73
1779 2191 8.916654 GTCCGGTTTAGTTAAAACTTACTACTC 58.083 37.037 0.00 0.00 45.70 2.59
1780 2192 8.088365 TCCGGTTTAGTTAAAACTTACTACTCC 58.912 37.037 0.00 0.00 45.70 3.85
1900 2338 1.975363 GCTCACCAATCGCTGTCTGC 61.975 60.000 0.00 0.00 38.57 4.26
2081 2519 0.534203 TTCACGCCCTTCTGGAACAC 60.534 55.000 0.00 0.00 35.39 3.32
2133 2571 1.000396 GCTGCCACCCAAGAGGATT 60.000 57.895 0.00 0.00 39.89 3.01
2202 2645 5.357314 CGAGGAAGAGGAACAATCACTACTA 59.643 44.000 0.00 0.00 0.00 1.82
2517 2962 1.664649 TGGAGCAACGAGAGCAACG 60.665 57.895 0.00 0.00 0.00 4.10
2783 3228 2.223735 TGTCGTCGTCTCAAGCTTCTTT 60.224 45.455 0.00 0.00 0.00 2.52
3068 3616 1.066143 AGGCTACAAGTTCGACCCATG 60.066 52.381 0.00 0.00 0.00 3.66
3390 3944 0.980754 TGGACCGTGCCACTATCCAT 60.981 55.000 11.66 0.00 34.50 3.41
3401 3955 2.300152 CCACTATCCATACACCAGCGAT 59.700 50.000 0.00 0.00 0.00 4.58
3453 4007 2.092699 GCCTAGCATCACCTCTTCCTTT 60.093 50.000 0.00 0.00 0.00 3.11
3454 4008 3.623453 GCCTAGCATCACCTCTTCCTTTT 60.623 47.826 0.00 0.00 0.00 2.27
3483 4037 5.649831 AGCTGAAACAGAAACAGAACTTTCT 59.350 36.000 2.81 0.00 40.47 2.52
3584 4138 1.005037 ATGAAGTTGCCAGCGACGA 60.005 52.632 0.00 0.00 35.57 4.20
4092 4660 4.790766 GCCCAGATGCATGAACGAATTTAG 60.791 45.833 2.46 0.00 0.00 1.85
4387 4969 1.825474 TCGGAAACAAACCTTTGGCAA 59.175 42.857 0.00 0.00 42.34 4.52
4403 4985 6.260936 CCTTTGGCAAAGTGTATACTGATAGG 59.739 42.308 31.68 13.52 37.19 2.57
4404 4986 6.553953 TTGGCAAAGTGTATACTGATAGGA 57.446 37.500 0.00 0.00 37.19 2.94
4405 4987 6.553953 TGGCAAAGTGTATACTGATAGGAA 57.446 37.500 4.17 0.00 37.19 3.36
4406 4988 7.136822 TGGCAAAGTGTATACTGATAGGAAT 57.863 36.000 4.17 0.00 37.19 3.01
4407 4989 6.992123 TGGCAAAGTGTATACTGATAGGAATG 59.008 38.462 4.17 0.00 37.19 2.67
4408 4990 7.147567 TGGCAAAGTGTATACTGATAGGAATGA 60.148 37.037 4.17 0.00 37.19 2.57
4409 4991 7.880195 GGCAAAGTGTATACTGATAGGAATGAT 59.120 37.037 4.17 0.00 37.19 2.45
4410 4992 9.929180 GCAAAGTGTATACTGATAGGAATGATA 57.071 33.333 4.17 0.00 37.19 2.15
4421 5003 9.097946 ACTGATAGGAATGATACAATGATCTGA 57.902 33.333 0.00 0.00 0.00 3.27
4422 5004 9.939802 CTGATAGGAATGATACAATGATCTGAA 57.060 33.333 0.00 0.00 0.00 3.02
4426 5008 8.218338 AGGAATGATACAATGATCTGAAACAC 57.782 34.615 0.00 0.00 0.00 3.32
4427 5009 7.011763 AGGAATGATACAATGATCTGAAACACG 59.988 37.037 0.00 0.00 0.00 4.49
4428 5010 7.011389 GGAATGATACAATGATCTGAAACACGA 59.989 37.037 0.00 0.00 0.00 4.35
4429 5011 7.848223 ATGATACAATGATCTGAAACACGAA 57.152 32.000 0.00 0.00 0.00 3.85
4430 5012 7.060600 TGATACAATGATCTGAAACACGAAC 57.939 36.000 0.00 0.00 0.00 3.95
4431 5013 6.648725 TGATACAATGATCTGAAACACGAACA 59.351 34.615 0.00 0.00 0.00 3.18
4432 5014 5.749596 ACAATGATCTGAAACACGAACAA 57.250 34.783 0.00 0.00 0.00 2.83
4433 5015 5.751680 ACAATGATCTGAAACACGAACAAG 58.248 37.500 0.00 0.00 0.00 3.16
4434 5016 3.878086 TGATCTGAAACACGAACAAGC 57.122 42.857 0.00 0.00 0.00 4.01
4435 5017 2.548057 TGATCTGAAACACGAACAAGCC 59.452 45.455 0.00 0.00 0.00 4.35
4436 5018 2.031258 TCTGAAACACGAACAAGCCA 57.969 45.000 0.00 0.00 0.00 4.75
4437 5019 2.360844 TCTGAAACACGAACAAGCCAA 58.639 42.857 0.00 0.00 0.00 4.52
4487 5069 7.512426 CGAACAAGCCAAAAGTAAGTTAAAACG 60.512 37.037 0.00 0.00 0.00 3.60
4570 5152 6.662865 TTCTTCATGGCCTTACAATCAAAA 57.337 33.333 3.32 0.00 0.00 2.44
4571 5153 6.855763 TCTTCATGGCCTTACAATCAAAAT 57.144 33.333 3.32 0.00 0.00 1.82
4611 5193 4.811557 GGGAGCTGCTACAAAATAGTACTG 59.188 45.833 14.92 0.00 0.00 2.74
4775 5357 2.369860 TGACAAGCAACTCATCTGGTCT 59.630 45.455 0.00 0.00 34.98 3.85
4849 5431 3.054655 ACCCTACGTTGCCAGAATACAAT 60.055 43.478 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.549078 TGCCAATACAACATTTCGACTAATATA 57.451 29.630 0.00 0.00 0.00 0.86
4 5 8.342634 GTGCCAATACAACATTTCGACTAATAT 58.657 33.333 0.00 0.00 0.00 1.28
5 6 7.201661 GGTGCCAATACAACATTTCGACTAATA 60.202 37.037 0.00 0.00 0.00 0.98
6 7 6.404293 GGTGCCAATACAACATTTCGACTAAT 60.404 38.462 0.00 0.00 0.00 1.73
7 8 5.106475 GGTGCCAATACAACATTTCGACTAA 60.106 40.000 0.00 0.00 0.00 2.24
8 9 4.393680 GGTGCCAATACAACATTTCGACTA 59.606 41.667 0.00 0.00 0.00 2.59
9 10 3.190535 GGTGCCAATACAACATTTCGACT 59.809 43.478 0.00 0.00 0.00 4.18
10 11 3.498082 GGTGCCAATACAACATTTCGAC 58.502 45.455 0.00 0.00 0.00 4.20
11 12 2.490115 GGGTGCCAATACAACATTTCGA 59.510 45.455 0.00 0.00 0.00 3.71
12 13 2.230025 TGGGTGCCAATACAACATTTCG 59.770 45.455 0.00 0.00 0.00 3.46
13 14 3.951775 TGGGTGCCAATACAACATTTC 57.048 42.857 0.00 0.00 0.00 2.17
14 15 4.696479 TTTGGGTGCCAATACAACATTT 57.304 36.364 0.00 0.00 43.55 2.32
15 16 4.102367 AGTTTTGGGTGCCAATACAACATT 59.898 37.500 0.28 0.00 44.14 2.71
39 40 5.999205 ATTTGGGTAACTTGCATCAATGA 57.001 34.783 0.00 0.00 0.00 2.57
71 72 3.867857 TGCTTGTCTCACACTGTGTTTA 58.132 40.909 11.40 1.57 34.79 2.01
86 87 1.547372 GCATTTGGGAGACATGCTTGT 59.453 47.619 4.68 4.68 40.23 3.16
142 144 4.457949 CCCTTGGTAAACCTTGTATGTGTC 59.542 45.833 0.02 0.00 36.82 3.67
155 157 8.515861 TTGGTAATCAAACAACCCCTTGGTAAA 61.516 37.037 0.00 0.00 36.70 2.01
184 186 6.153067 CCATGTAACCTCTAGAAATCGCTAG 58.847 44.000 0.00 0.00 39.35 3.42
185 187 5.010719 CCCATGTAACCTCTAGAAATCGCTA 59.989 44.000 0.00 0.00 0.00 4.26
186 188 4.202264 CCCATGTAACCTCTAGAAATCGCT 60.202 45.833 0.00 0.00 0.00 4.93
203 205 1.576577 TGCATCTCACTCTCCCATGT 58.423 50.000 0.00 0.00 0.00 3.21
274 281 1.877443 GCATGTAACCAAACACCGACT 59.123 47.619 0.00 0.00 30.75 4.18
275 282 1.604755 TGCATGTAACCAAACACCGAC 59.395 47.619 0.00 0.00 30.75 4.79
304 311 4.748102 CCGTTCATGTGTACAGTAGTTGTT 59.252 41.667 0.00 0.00 41.29 2.83
306 313 4.552355 TCCGTTCATGTGTACAGTAGTTG 58.448 43.478 0.00 0.00 0.00 3.16
307 314 4.521639 TCTCCGTTCATGTGTACAGTAGTT 59.478 41.667 0.00 0.00 0.00 2.24
308 315 4.077108 TCTCCGTTCATGTGTACAGTAGT 58.923 43.478 0.00 0.00 0.00 2.73
309 316 4.438880 CCTCTCCGTTCATGTGTACAGTAG 60.439 50.000 0.00 0.00 0.00 2.57
310 317 3.442625 CCTCTCCGTTCATGTGTACAGTA 59.557 47.826 0.00 0.00 0.00 2.74
312 319 2.417379 CCCTCTCCGTTCATGTGTACAG 60.417 54.545 0.00 0.00 0.00 2.74
315 322 1.933021 ACCCTCTCCGTTCATGTGTA 58.067 50.000 0.00 0.00 0.00 2.90
319 326 1.825474 ACTGTACCCTCTCCGTTCATG 59.175 52.381 0.00 0.00 0.00 3.07
320 327 2.233305 ACTGTACCCTCTCCGTTCAT 57.767 50.000 0.00 0.00 0.00 2.57
340 484 8.971321 CACGTGTGTAGTTTATTACTGTTTACT 58.029 33.333 7.58 0.00 37.73 2.24
341 485 8.967218 TCACGTGTGTAGTTTATTACTGTTTAC 58.033 33.333 16.51 0.00 37.73 2.01
342 486 8.967218 GTCACGTGTGTAGTTTATTACTGTTTA 58.033 33.333 16.51 0.00 37.73 2.01
343 487 7.492020 TGTCACGTGTGTAGTTTATTACTGTTT 59.508 33.333 16.51 0.00 37.73 2.83
344 488 6.979817 TGTCACGTGTGTAGTTTATTACTGTT 59.020 34.615 16.51 0.00 37.73 3.16
412 556 2.358125 TTCATGCGGACGTGTGGG 60.358 61.111 0.00 0.00 34.22 4.61
572 717 3.366781 GGCTTGGATTTGTTCTCAGCTTC 60.367 47.826 0.00 0.00 32.80 3.86
692 842 0.883833 GGATGGTGGTGTTCTTGCAG 59.116 55.000 0.00 0.00 0.00 4.41
693 843 0.539438 GGGATGGTGGTGTTCTTGCA 60.539 55.000 0.00 0.00 0.00 4.08
694 844 0.539438 TGGGATGGTGGTGTTCTTGC 60.539 55.000 0.00 0.00 0.00 4.01
695 845 1.247567 GTGGGATGGTGGTGTTCTTG 58.752 55.000 0.00 0.00 0.00 3.02
696 846 0.112412 GGTGGGATGGTGGTGTTCTT 59.888 55.000 0.00 0.00 0.00 2.52
1565 1877 0.902048 CAGCACACAGGAGGGAGAGA 60.902 60.000 0.00 0.00 0.00 3.10
1566 1878 1.190833 ACAGCACACAGGAGGGAGAG 61.191 60.000 0.00 0.00 0.00 3.20
1567 1879 1.152247 ACAGCACACAGGAGGGAGA 60.152 57.895 0.00 0.00 0.00 3.71
1568 1880 1.004080 CACAGCACACAGGAGGGAG 60.004 63.158 0.00 0.00 0.00 4.30
1582 1898 3.861276 ATGATTGATTGGCACACACAG 57.139 42.857 0.00 0.00 39.29 3.66
1624 1940 6.825721 GTGGAGTACAGGTTAAGCTAGTAGTA 59.174 42.308 6.90 2.83 0.00 1.82
1625 1941 5.651576 GTGGAGTACAGGTTAAGCTAGTAGT 59.348 44.000 6.90 13.69 0.00 2.73
1626 1942 5.651139 TGTGGAGTACAGGTTAAGCTAGTAG 59.349 44.000 6.90 0.00 33.42 2.57
1699 2015 7.497595 ACAAGAACTTTTGGGAATTAAAGACC 58.502 34.615 5.62 0.00 32.32 3.85
2081 2519 0.525668 GTCGACCATACAGAGGCACG 60.526 60.000 3.51 0.00 0.00 5.34
2133 2571 2.568956 AGCAGTGCAGAGACCTGAATTA 59.431 45.455 19.20 0.00 43.02 1.40
2173 2616 5.238650 GTGATTGTTCCTCTTCCTCGAAAAA 59.761 40.000 0.00 0.00 0.00 1.94
2202 2645 9.895138 ACCTGTCGTTATTGTTTTATATAGGTT 57.105 29.630 0.00 0.00 0.00 3.50
2212 2655 6.385649 ACAATTCACCTGTCGTTATTGTTT 57.614 33.333 0.00 0.00 35.26 2.83
2231 2676 0.251354 ATGAGCAGCACCTCGACAAT 59.749 50.000 0.00 0.00 34.56 2.71
2783 3228 0.250467 GCAGCTGGAGAACCTTGACA 60.250 55.000 17.12 0.00 37.04 3.58
3027 3575 6.154021 AGCCTTCAAACTGAGAAATGCAATAT 59.846 34.615 0.00 0.00 0.00 1.28
3454 4008 4.769688 TCTGTTTCTGTTTCAGCTCTGAA 58.230 39.130 8.14 8.14 46.72 3.02
3584 4138 1.813513 GTTGTATCTGGCAGCAGTGT 58.186 50.000 10.34 0.00 0.00 3.55
4092 4660 2.633481 ACTCTCCAACTCCCTACACAAC 59.367 50.000 0.00 0.00 0.00 3.32
4403 4985 7.909267 TCGTGTTTCAGATCATTGTATCATTC 58.091 34.615 0.00 0.00 0.00 2.67
4404 4986 7.848223 TCGTGTTTCAGATCATTGTATCATT 57.152 32.000 0.00 0.00 0.00 2.57
4405 4987 7.334171 TGTTCGTGTTTCAGATCATTGTATCAT 59.666 33.333 0.00 0.00 0.00 2.45
4406 4988 6.648725 TGTTCGTGTTTCAGATCATTGTATCA 59.351 34.615 0.00 0.00 0.00 2.15
4407 4989 7.060600 TGTTCGTGTTTCAGATCATTGTATC 57.939 36.000 0.00 0.00 0.00 2.24
4408 4990 7.433708 TTGTTCGTGTTTCAGATCATTGTAT 57.566 32.000 0.00 0.00 0.00 2.29
4409 4991 6.565811 GCTTGTTCGTGTTTCAGATCATTGTA 60.566 38.462 0.00 0.00 0.00 2.41
4410 4992 5.749596 TTGTTCGTGTTTCAGATCATTGT 57.250 34.783 0.00 0.00 0.00 2.71
4411 4993 4.614284 GCTTGTTCGTGTTTCAGATCATTG 59.386 41.667 0.00 0.00 0.00 2.82
4412 4994 4.320494 GGCTTGTTCGTGTTTCAGATCATT 60.320 41.667 0.00 0.00 0.00 2.57
4413 4995 3.189287 GGCTTGTTCGTGTTTCAGATCAT 59.811 43.478 0.00 0.00 0.00 2.45
4414 4996 2.548057 GGCTTGTTCGTGTTTCAGATCA 59.452 45.455 0.00 0.00 0.00 2.92
4415 4997 2.548057 TGGCTTGTTCGTGTTTCAGATC 59.452 45.455 0.00 0.00 0.00 2.75
4416 4998 2.571212 TGGCTTGTTCGTGTTTCAGAT 58.429 42.857 0.00 0.00 0.00 2.90
4417 4999 2.031258 TGGCTTGTTCGTGTTTCAGA 57.969 45.000 0.00 0.00 0.00 3.27
4418 5000 2.842208 TTGGCTTGTTCGTGTTTCAG 57.158 45.000 0.00 0.00 0.00 3.02
4419 5001 3.577649 TTTTGGCTTGTTCGTGTTTCA 57.422 38.095 0.00 0.00 0.00 2.69
4420 5002 4.564769 TCATTTTTGGCTTGTTCGTGTTTC 59.435 37.500 0.00 0.00 0.00 2.78
4421 5003 4.499183 TCATTTTTGGCTTGTTCGTGTTT 58.501 34.783 0.00 0.00 0.00 2.83
4422 5004 4.116747 TCATTTTTGGCTTGTTCGTGTT 57.883 36.364 0.00 0.00 0.00 3.32
4423 5005 3.791973 TCATTTTTGGCTTGTTCGTGT 57.208 38.095 0.00 0.00 0.00 4.49
4424 5006 5.218885 TGTATCATTTTTGGCTTGTTCGTG 58.781 37.500 0.00 0.00 0.00 4.35
4425 5007 5.446143 TGTATCATTTTTGGCTTGTTCGT 57.554 34.783 0.00 0.00 0.00 3.85
4426 5008 5.164196 CGTTGTATCATTTTTGGCTTGTTCG 60.164 40.000 0.00 0.00 0.00 3.95
4427 5009 5.918011 TCGTTGTATCATTTTTGGCTTGTTC 59.082 36.000 0.00 0.00 0.00 3.18
4428 5010 5.837437 TCGTTGTATCATTTTTGGCTTGTT 58.163 33.333 0.00 0.00 0.00 2.83
4429 5011 5.446143 TCGTTGTATCATTTTTGGCTTGT 57.554 34.783 0.00 0.00 0.00 3.16
4430 5012 6.252015 CAGATCGTTGTATCATTTTTGGCTTG 59.748 38.462 0.00 0.00 0.00 4.01
4431 5013 6.150976 TCAGATCGTTGTATCATTTTTGGCTT 59.849 34.615 0.00 0.00 0.00 4.35
4432 5014 5.647658 TCAGATCGTTGTATCATTTTTGGCT 59.352 36.000 0.00 0.00 0.00 4.75
4433 5015 5.879237 TCAGATCGTTGTATCATTTTTGGC 58.121 37.500 0.00 0.00 0.00 4.52
4434 5016 7.807433 TGTTTCAGATCGTTGTATCATTTTTGG 59.193 33.333 0.00 0.00 0.00 3.28
4435 5017 8.629986 GTGTTTCAGATCGTTGTATCATTTTTG 58.370 33.333 0.00 0.00 0.00 2.44
4436 5018 7.533900 CGTGTTTCAGATCGTTGTATCATTTTT 59.466 33.333 0.00 0.00 0.00 1.94
4437 5019 7.015289 CGTGTTTCAGATCGTTGTATCATTTT 58.985 34.615 0.00 0.00 0.00 1.82
4487 5069 0.312102 GGTGAGGCTTGTGCAGTTTC 59.688 55.000 0.00 0.00 41.91 2.78
4570 5152 1.913419 CCCAGTTACACCACTACCCAT 59.087 52.381 0.00 0.00 0.00 4.00
4571 5153 1.132785 TCCCAGTTACACCACTACCCA 60.133 52.381 0.00 0.00 0.00 4.51
4634 5216 7.397892 TCTGTCCACTTGTGTTAATTTTGAA 57.602 32.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.