Multiple sequence alignment - TraesCS6A01G288100

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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 TraesCS6A01G288100 chr6A 100.000 4538 0 0 1 4538 520543987 520539450 0.000000e+00 8381
1 TraesCS6A01G288100 chr6D 92.311 4656 189 65 17 4538 380443400 380448020 0.000000e+00 6458
2 TraesCS6A01G288100 chr6B 94.909 2534 101 14 2011 4538 565420790 565418279 0.000000e+00 3940
3 TraesCS6A01G288100 chr6B 92.818 738 30 10 510 1242 565422395 565421676 0.000000e+00 1048
4 TraesCS6A01G288100 chr6B 84.211 551 52 23 1258 1775 565421632 565421084 1.880000e-138 503
5 TraesCS6A01G288100 chr6B 84.843 508 15 26 20 476 565422894 565422398 5.350000e-124 455
6 TraesCS6A01G288100 chr6B 96.739 184 6 0 1795 1978 565420971 565420788 1.590000e-79 307


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 TraesCS6A01G288100 chr6A 520539450 520543987 4537 True 8381.0 8381 100.000 1 4538 1 chr6A.!!$R1 4537
1 TraesCS6A01G288100 chr6D 380443400 380448020 4620 False 6458.0 6458 92.311 17 4538 1 chr6D.!!$F1 4521
2 TraesCS6A01G288100 chr6B 565418279 565422894 4615 True 1250.6 3940 90.704 20 4538 5 chr6B.!!$R1 4518

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
441 499 0.252197 TAGCTCCCTTTCCTTTCGCC 59.748 55.0 0.0 0.0 0.00 5.54 F
1636 1816 0.036388 TTTCGGTGTCTCATGGCTCC 60.036 55.0 0.0 0.0 0.00 4.70 F
3125 3434 0.178873 TTACTCCCAAGGGTCAGCCT 60.179 55.0 4.8 0.0 36.47 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2415 0.323178 AGCCTGAAACAGAGCATGGG 60.323 55.0 0.00 0.0 32.75 4.00 R
3236 3545 0.255318 GGTCTACTCCCGACCTCTGA 59.745 60.0 2.11 0.0 45.87 3.27 R
4076 4387 2.230994 GAGCGCCAGGTGATGTGAGA 62.231 60.0 2.29 0.0 0.00 3.27 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
68 73 2.940410 TGTTTTGACGGTTTCTGAGACC 59.060 45.455 7.29 7.29 0.00 3.85
167 194 2.610694 GCATCCATCATGGCGACGG 61.611 63.158 0.00 0.00 37.47 4.79
309 352 2.429494 GCTGCCTAGCCTCCATCC 59.571 66.667 0.00 0.00 44.33 3.51
377 420 1.228245 CACCCACCTCCACCACAAG 60.228 63.158 0.00 0.00 0.00 3.16
385 428 2.046892 CCACCACAAGGCCTCTCG 60.047 66.667 5.23 0.00 39.06 4.04
441 499 0.252197 TAGCTCCCTTTCCTTTCGCC 59.748 55.000 0.00 0.00 0.00 5.54
442 500 1.002011 GCTCCCTTTCCTTTCGCCT 60.002 57.895 0.00 0.00 0.00 5.52
629 691 0.780002 GCGTCAAATTGCTTGCTGTG 59.220 50.000 0.00 0.00 34.76 3.66
670 732 0.659123 GTTGTTTACGTTGCGCAGGG 60.659 55.000 11.31 9.39 0.00 4.45
690 752 1.663695 GACGTGGAGGAGAGAGAGAG 58.336 60.000 0.00 0.00 0.00 3.20
723 787 6.908284 TGTTGTGCGTATAAACTTTTGAAGAC 59.092 34.615 4.25 0.00 0.00 3.01
724 788 6.606234 TGTGCGTATAAACTTTTGAAGACA 57.394 33.333 0.00 0.00 0.00 3.41
725 789 6.423862 TGTGCGTATAAACTTTTGAAGACAC 58.576 36.000 0.00 0.00 0.00 3.67
726 790 5.558888 GTGCGTATAAACTTTTGAAGACACG 59.441 40.000 0.00 0.00 0.00 4.49
727 791 5.077424 GCGTATAAACTTTTGAAGACACGG 58.923 41.667 0.00 0.00 0.00 4.94
752 819 1.301244 ACAAGCAGACAGACAGGCG 60.301 57.895 0.00 0.00 0.00 5.52
775 842 3.444034 GGCTCCCACTTTGTTAAATCCTC 59.556 47.826 0.00 0.00 0.00 3.71
823 891 1.538204 CCCGACTCTCTCTCTCTCTCG 60.538 61.905 0.00 0.00 0.00 4.04
831 901 1.498865 CTCTCTCTCTCGCTCGCTCC 61.499 65.000 0.00 0.00 0.00 4.70
945 1015 2.045926 ACCGTCATTCCTGCTGCC 60.046 61.111 0.00 0.00 0.00 4.85
1075 1148 3.254892 GTGTCTCTTTTAGCTTCTCCCG 58.745 50.000 0.00 0.00 0.00 5.14
1088 1164 3.165670 CTCCCGTCCGTCGATCGAC 62.166 68.421 33.22 33.22 42.86 4.20
1278 1403 1.376609 CCTTTCCCCGTGTATGCTGC 61.377 60.000 0.00 0.00 0.00 5.25
1291 1416 3.096791 GCTGCATCTCCGTTCAGC 58.903 61.111 0.00 0.00 43.95 4.26
1300 1425 3.353836 CCGTTCAGCCCGGTGTTG 61.354 66.667 0.00 0.02 40.59 3.33
1302 1427 2.604174 CGTTCAGCCCGGTGTTGTC 61.604 63.158 0.00 0.00 0.00 3.18
1303 1428 2.112297 TTCAGCCCGGTGTTGTCC 59.888 61.111 0.00 0.00 0.00 4.02
1352 1484 1.581934 GCTTTGAAAACCAAGTGCCC 58.418 50.000 0.00 0.00 35.94 5.36
1432 1573 1.227999 GCGTGTCAGCTTGCTAACCA 61.228 55.000 0.00 0.00 0.00 3.67
1438 1579 3.253188 TGTCAGCTTGCTAACCAATGAAC 59.747 43.478 0.00 0.00 31.91 3.18
1440 1581 3.888323 TCAGCTTGCTAACCAATGAACAA 59.112 39.130 0.00 0.00 31.91 2.83
1441 1582 4.022935 TCAGCTTGCTAACCAATGAACAAG 60.023 41.667 0.00 0.00 38.00 3.16
1461 1602 3.056313 GACATTTCGCTGCAGGCCC 62.056 63.158 17.12 0.00 37.74 5.80
1482 1623 3.123620 GTCGCTTGAGCCAGCCAG 61.124 66.667 0.00 0.00 36.31 4.85
1600 1780 4.345286 AGGGAGGAGGCTGGCACT 62.345 66.667 3.38 0.55 0.00 4.40
1636 1816 0.036388 TTTCGGTGTCTCATGGCTCC 60.036 55.000 0.00 0.00 0.00 4.70
1657 1837 0.935898 GAATGGAGACTGCGCATGAG 59.064 55.000 12.24 0.87 0.00 2.90
1729 1909 2.094417 GCAAGATTCTAGCACCGACAAC 59.906 50.000 0.00 0.00 0.00 3.32
1772 1952 7.434013 AGACGATTGGTTCAAAATGTTTTGTAC 59.566 33.333 15.51 15.43 45.77 2.90
1775 1955 9.405587 CGATTGGTTCAAAATGTTTTGTACTAT 57.594 29.630 20.00 15.51 45.77 2.12
1959 2232 4.572389 AGATAAATGACAGGCAAGCTAACG 59.428 41.667 0.00 0.00 0.00 3.18
2004 2277 3.837213 GCATTGTGCAGAGTACACATT 57.163 42.857 0.00 0.00 46.72 2.71
2005 2278 4.944962 GCATTGTGCAGAGTACACATTA 57.055 40.909 0.00 0.00 46.72 1.90
2006 2279 4.901814 GCATTGTGCAGAGTACACATTAG 58.098 43.478 0.00 0.00 46.72 1.73
2007 2280 4.728882 GCATTGTGCAGAGTACACATTAGC 60.729 45.833 0.00 0.00 46.72 3.09
2008 2281 3.676291 TGTGCAGAGTACACATTAGCA 57.324 42.857 0.00 0.00 42.88 3.49
2009 2282 3.588955 TGTGCAGAGTACACATTAGCAG 58.411 45.455 0.00 0.00 42.88 4.24
2016 2313 6.035112 GCAGAGTACACATTAGCAGTAGAAAC 59.965 42.308 0.00 0.00 0.00 2.78
2118 2415 7.138692 TCGTAACCTTCTAAGAAGTGTCTAC 57.861 40.000 0.00 0.00 32.16 2.59
2128 2425 2.499289 AGAAGTGTCTACCCATGCTCTG 59.501 50.000 0.00 0.00 29.93 3.35
2142 2439 0.514691 GCTCTGTTTCAGGCTTGACG 59.485 55.000 0.00 0.00 31.71 4.35
2150 2447 1.805945 CAGGCTTGACGTACTCCGC 60.806 63.158 0.00 0.00 41.42 5.54
2202 2499 4.097135 GGGATAAAGCTTCTTTCCTTCTGC 59.903 45.833 17.13 2.66 0.00 4.26
2247 2544 1.748122 GGCACATCAGTCAGCAGGG 60.748 63.158 0.00 0.00 0.00 4.45
2279 2577 5.638596 AAATTCTCACCCCGTAAACATTC 57.361 39.130 0.00 0.00 0.00 2.67
2348 2646 5.127519 CCAAAAATATGAGTCAGGCATTCCA 59.872 40.000 0.00 0.00 33.74 3.53
2413 2718 8.515473 TGTATAGACATTGTACAATATGCGTC 57.485 34.615 20.39 20.70 31.38 5.19
2469 2774 8.202461 TGATTCTAACCTTACTTTCTCCTTCA 57.798 34.615 0.00 0.00 0.00 3.02
2524 2829 1.068474 GATCACGTTGGAGGAACACG 58.932 55.000 0.00 0.00 33.73 4.49
2581 2886 5.233225 CAGATGACAGAGAGCACAAAGTTA 58.767 41.667 0.00 0.00 0.00 2.24
2716 3025 2.224161 GGAGGCTTATCAGCTACCACAG 60.224 54.545 0.00 0.00 46.44 3.66
2717 3026 2.695666 GAGGCTTATCAGCTACCACAGA 59.304 50.000 0.00 0.00 46.44 3.41
2718 3027 2.697751 AGGCTTATCAGCTACCACAGAG 59.302 50.000 0.00 0.00 46.44 3.35
2821 3130 1.304381 GAAATCAGCACAGCCCCCA 60.304 57.895 0.00 0.00 0.00 4.96
2854 3163 4.399303 AGAACATAGCAGGTATTTGGCAAC 59.601 41.667 0.00 0.00 0.00 4.17
2858 3167 5.590259 ACATAGCAGGTATTTGGCAACTTAG 59.410 40.000 0.00 0.00 37.61 2.18
2892 3201 7.433425 GCTTTTATGTTCACCTTCTGCATTATC 59.567 37.037 0.00 0.00 0.00 1.75
2903 3212 9.888878 CACCTTCTGCATTATCTAATTACATTG 57.111 33.333 0.00 0.00 0.00 2.82
2943 3252 9.547753 TCTTTGTAAATGGTGAGAGCTATATTC 57.452 33.333 0.00 0.00 0.00 1.75
3031 3340 3.123050 GTCAACCATGAACCAAAACTGC 58.877 45.455 0.00 0.00 37.30 4.40
3100 3409 2.902486 AGATGACAGCCAGAGTCTTTCA 59.098 45.455 0.00 0.00 36.94 2.69
3125 3434 0.178873 TTACTCCCAAGGGTCAGCCT 60.179 55.000 4.80 0.00 36.47 4.58
3236 3545 8.677148 TGTTACATAAACTGAAAGAAGCTCTT 57.323 30.769 0.00 0.00 37.36 2.85
3241 3550 7.387397 ACATAAACTGAAAGAAGCTCTTCAGAG 59.613 37.037 27.23 17.46 41.84 3.35
3359 3668 3.141398 ACAATGATGCATCGATGTACCC 58.859 45.455 26.57 16.73 0.00 3.69
3360 3669 2.084610 ATGATGCATCGATGTACCCG 57.915 50.000 25.47 0.30 0.00 5.28
3376 3685 1.802365 ACCCGCGTTTACTGATCAAAC 59.198 47.619 4.92 0.00 33.47 2.93
3421 3731 9.846248 AAGTTTCTAAATCATGTTATGACTTGC 57.154 29.630 0.00 0.00 43.01 4.01
3425 3735 8.201554 TCTAAATCATGTTATGACTTGCTCAC 57.798 34.615 0.00 0.00 43.01 3.51
3426 3736 6.822667 AAATCATGTTATGACTTGCTCACA 57.177 33.333 0.00 0.00 43.01 3.58
3431 3741 4.960938 TGTTATGACTTGCTCACAGTTCT 58.039 39.130 0.00 0.00 0.00 3.01
3432 3742 6.096673 TGTTATGACTTGCTCACAGTTCTA 57.903 37.500 0.00 0.00 0.00 2.10
3603 3913 0.236711 CAGACAAGGACTTTGCAGCG 59.763 55.000 0.00 0.00 40.59 5.18
3606 3916 3.357079 AAGGACTTTGCAGCGGCG 61.357 61.111 0.51 0.51 45.35 6.46
3707 4017 1.528824 TGCTATTGGGAGAGCAGCC 59.471 57.895 0.00 0.00 44.61 4.85
3775 4085 5.049474 TCAGATTCTTGTACAATGTGTGTGC 60.049 40.000 9.13 0.00 41.89 4.57
3799 4109 6.319658 GCATTTCTCCCTCATTCAACTCAATA 59.680 38.462 0.00 0.00 0.00 1.90
3845 4155 3.556004 GGTCCTAGGATGCAGCTTGTATC 60.556 52.174 16.27 0.00 38.52 2.24
3846 4156 2.297315 TCCTAGGATGCAGCTTGTATCG 59.703 50.000 7.62 0.00 39.86 2.92
3847 4157 2.297315 CCTAGGATGCAGCTTGTATCGA 59.703 50.000 1.05 0.00 39.86 3.59
3848 4158 2.988010 AGGATGCAGCTTGTATCGAA 57.012 45.000 0.22 0.00 39.86 3.71
4050 4360 3.203716 GTGTATCAGATTCCGTTTCCCC 58.796 50.000 0.00 0.00 0.00 4.81
4076 4387 2.290960 GGTGGGTAAGATTGGAGCAAGT 60.291 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.528743 CGGGAGATCATGCGTGTGC 61.529 63.158 5.68 0.00 43.20 4.57
11 12 1.884464 CCGGGAGATCATGCGTGTG 60.884 63.158 5.68 0.00 0.00 3.82
12 13 2.501128 CCGGGAGATCATGCGTGT 59.499 61.111 5.68 0.00 0.00 4.49
13 14 2.280389 CCCGGGAGATCATGCGTG 60.280 66.667 18.48 0.00 0.00 5.34
14 15 2.764128 ACCCGGGAGATCATGCGT 60.764 61.111 32.02 0.00 0.00 5.24
15 16 2.029666 GACCCGGGAGATCATGCG 59.970 66.667 32.02 0.00 0.00 4.73
16 17 2.427753 GGACCCGGGAGATCATGC 59.572 66.667 32.02 4.48 0.00 4.06
17 18 2.872388 CGGGACCCGGGAGATCATG 61.872 68.421 32.02 6.70 44.15 3.07
18 19 2.524394 CGGGACCCGGGAGATCAT 60.524 66.667 32.02 1.84 44.15 2.45
68 73 0.251077 ATCTACCTACCTACCGGCCG 60.251 60.000 21.04 21.04 0.00 6.13
75 80 3.556633 CGCGGAGAAGATCTACCTACCTA 60.557 52.174 0.00 0.00 0.00 3.08
76 81 2.811136 CGCGGAGAAGATCTACCTACCT 60.811 54.545 0.00 0.00 0.00 3.08
318 361 3.775654 CCCTCTGTCTCCACCGCC 61.776 72.222 0.00 0.00 0.00 6.13
404 447 1.261089 CTAGCTAGGTCGCGTAGTCAC 59.739 57.143 13.32 0.00 34.40 3.67
608 670 1.057636 CAGCAAGCAATTTGACGCAG 58.942 50.000 0.00 0.00 39.21 5.18
670 732 0.253610 TCTCTCTCTCCTCCACGTCC 59.746 60.000 0.00 0.00 0.00 4.79
690 752 1.586154 ATACGCACAACAGCAAGGGC 61.586 55.000 0.00 0.00 41.61 5.19
723 787 1.260561 GTCTGCTTGTGTTGTACCGTG 59.739 52.381 0.00 0.00 0.00 4.94
724 788 1.134640 TGTCTGCTTGTGTTGTACCGT 60.135 47.619 0.00 0.00 0.00 4.83
725 789 1.526887 CTGTCTGCTTGTGTTGTACCG 59.473 52.381 0.00 0.00 0.00 4.02
726 790 2.544267 GTCTGTCTGCTTGTGTTGTACC 59.456 50.000 0.00 0.00 0.00 3.34
727 791 3.194861 TGTCTGTCTGCTTGTGTTGTAC 58.805 45.455 0.00 0.00 0.00 2.90
752 819 2.496070 GGATTTAACAAAGTGGGAGCCC 59.504 50.000 0.00 0.00 0.00 5.19
775 842 2.107141 GAGGCGAGGGGATTGACG 59.893 66.667 0.00 0.00 0.00 4.35
831 901 2.917971 GCAGAGCTTATTATAGTCGGCG 59.082 50.000 0.00 0.00 0.00 6.46
992 1065 3.350031 AAGAGCTCCATTGCCGGGG 62.350 63.158 10.93 0.00 0.00 5.73
1101 1177 2.077155 CGAATTACGCATGCACTCAC 57.923 50.000 19.57 3.25 34.51 3.51
1291 1416 1.599797 GGACAAGGACAACACCGGG 60.600 63.158 6.32 0.00 34.73 5.73
1300 1425 3.753797 GAGAATTGAAGGTGGACAAGGAC 59.246 47.826 0.00 0.00 0.00 3.85
1302 1427 3.084786 GGAGAATTGAAGGTGGACAAGG 58.915 50.000 0.00 0.00 0.00 3.61
1303 1428 3.755378 CAGGAGAATTGAAGGTGGACAAG 59.245 47.826 0.00 0.00 0.00 3.16
1432 1573 4.539870 CAGCGAAATGTCACTTGTTCATT 58.460 39.130 0.00 0.00 33.94 2.57
1438 1579 1.400629 CCTGCAGCGAAATGTCACTTG 60.401 52.381 8.66 0.00 0.00 3.16
1440 1581 1.580845 GCCTGCAGCGAAATGTCACT 61.581 55.000 8.66 0.00 0.00 3.41
1441 1582 1.154150 GCCTGCAGCGAAATGTCAC 60.154 57.895 8.66 0.00 0.00 3.67
1461 1602 2.734673 GCTGGCTCAAGCGACTTCG 61.735 63.158 0.00 0.00 43.26 3.79
1600 1780 1.990160 AAACAGACGGTTCCCTGCCA 61.990 55.000 0.00 0.00 39.29 4.92
1636 1816 0.656259 CATGCGCAGTCTCCATTCTG 59.344 55.000 18.32 0.22 35.12 3.02
1657 1837 1.164041 CCATAATTCCGGACCGTGCC 61.164 60.000 13.94 0.00 0.00 5.01
1700 1880 2.424601 TGCTAGAATCTTGCCACATTGC 59.575 45.455 13.62 0.00 31.70 3.56
1729 1909 4.447290 TCGTCTCACCTCTAGATCTCTTG 58.553 47.826 0.00 0.00 0.00 3.02
1772 1952 3.885297 CCTGGTTTGCCATCTGGTAATAG 59.115 47.826 0.39 1.35 45.05 1.73
1775 1955 1.427368 ACCTGGTTTGCCATCTGGTAA 59.573 47.619 0.00 0.00 45.05 2.85
1784 1974 2.160813 CGTGTAACATACCTGGTTTGCC 59.839 50.000 15.91 6.30 35.74 4.52
1802 2075 1.800586 CAATCAGTGTCTGAACCCGTG 59.199 52.381 3.58 0.00 44.04 4.94
1925 2198 2.872858 GTCATTTATCTTGGTCCTCCGC 59.127 50.000 0.00 0.00 36.30 5.54
1959 2232 6.927294 ATTCACTACGGAATTTTGATCTCC 57.073 37.500 0.00 0.00 33.85 3.71
1998 2271 5.853936 TCACTGTTTCTACTGCTAATGTGT 58.146 37.500 0.00 0.00 0.00 3.72
2003 2276 7.036220 GCTTATCTCACTGTTTCTACTGCTAA 58.964 38.462 0.00 0.00 0.00 3.09
2004 2277 6.152831 TGCTTATCTCACTGTTTCTACTGCTA 59.847 38.462 0.00 0.00 0.00 3.49
2005 2278 5.047021 TGCTTATCTCACTGTTTCTACTGCT 60.047 40.000 0.00 0.00 0.00 4.24
2006 2279 5.171476 TGCTTATCTCACTGTTTCTACTGC 58.829 41.667 0.00 0.00 0.00 4.40
2007 2280 8.932945 TTATGCTTATCTCACTGTTTCTACTG 57.067 34.615 0.00 0.00 0.00 2.74
2016 2313 9.447040 CATGAACAAATTATGCTTATCTCACTG 57.553 33.333 0.00 0.00 0.00 3.66
2118 2415 0.323178 AGCCTGAAACAGAGCATGGG 60.323 55.000 0.00 0.00 32.75 4.00
2128 2425 2.067013 GGAGTACGTCAAGCCTGAAAC 58.933 52.381 0.00 0.00 31.88 2.78
2142 2439 2.799371 CAGGAGGTCGCGGAGTAC 59.201 66.667 6.13 0.00 0.00 2.73
2202 2499 6.741992 TTTACAAGATGCTGTATGAACCTG 57.258 37.500 0.00 0.00 31.96 4.00
2247 2544 5.878669 ACGGGGTGAGAATTTTGAAGTATAC 59.121 40.000 0.00 0.00 0.00 1.47
2348 2646 1.965083 CATCGACGTCGTTCTGTTCT 58.035 50.000 34.40 9.86 40.80 3.01
2412 2717 6.403855 CCTGTCTTTGTTTCTGGTAAAAACGA 60.404 38.462 0.00 0.00 39.04 3.85
2413 2718 5.741982 CCTGTCTTTGTTTCTGGTAAAAACG 59.258 40.000 0.00 0.00 39.04 3.60
2469 2774 4.898861 TGTCCTGCCAAGAATAAAAAGGTT 59.101 37.500 0.00 0.00 0.00 3.50
2524 2829 8.903820 AGTATTTCTGTTATGGAATTTACCTGC 58.096 33.333 0.00 0.00 0.00 4.85
2591 2896 9.750125 GTTGACTTGAAAAAGGAATTTATCACT 57.250 29.630 0.00 0.00 0.00 3.41
2609 2914 7.310664 GCATTGATATATGATGGGTTGACTTG 58.689 38.462 0.00 0.00 0.00 3.16
2614 2919 6.209986 ACTTGGCATTGATATATGATGGGTTG 59.790 38.462 0.00 0.00 0.00 3.77
2670 2979 2.771089 TGGACTTGACTGATGTTCTGC 58.229 47.619 0.00 0.00 0.00 4.26
2716 3025 3.006247 GCTCTTTGTTCATGTCCTCCTC 58.994 50.000 0.00 0.00 0.00 3.71
2717 3026 2.373169 TGCTCTTTGTTCATGTCCTCCT 59.627 45.455 0.00 0.00 0.00 3.69
2718 3027 2.783135 TGCTCTTTGTTCATGTCCTCC 58.217 47.619 0.00 0.00 0.00 4.30
2821 3130 2.503356 CTGCTATGTTCTGGGAGGAACT 59.497 50.000 8.47 0.00 44.02 3.01
2854 3163 8.345565 GGTGAACATAAAAGCATATGACCTAAG 58.654 37.037 6.97 0.00 36.87 2.18
2858 3167 6.699575 AGGTGAACATAAAAGCATATGACC 57.300 37.500 6.97 0.19 36.87 4.02
2903 3212 8.244113 CCATTTACAAAGAACCCTGACTATTTC 58.756 37.037 0.00 0.00 0.00 2.17
2961 3270 4.338879 AGGCATACTGTTCTCTGCATTTT 58.661 39.130 0.00 0.00 36.34 1.82
3031 3340 1.133253 CAGTCCGTTGCTTGCATCG 59.867 57.895 16.26 16.26 0.00 3.84
3100 3409 1.351350 GACCCTTGGGAGTAAGCACTT 59.649 52.381 13.39 0.00 34.21 3.16
3175 3484 4.210537 GTCAAAGCAGCGTTCAGTTAGTTA 59.789 41.667 0.00 0.00 0.00 2.24
3188 3497 0.664761 TGTCAGCAAGTCAAAGCAGC 59.335 50.000 0.00 0.00 0.00 5.25
3236 3545 0.255318 GGTCTACTCCCGACCTCTGA 59.745 60.000 2.11 0.00 45.87 3.27
3376 3685 3.497262 ACTTTCTTAAGCGAACTTTCCCG 59.503 43.478 0.00 0.00 37.33 5.14
3451 3761 5.708230 TGAAGCGAAAATACTGGGTAAATGT 59.292 36.000 0.00 0.00 0.00 2.71
3525 3835 2.126071 TAGCTTCAGTCGCACCGC 60.126 61.111 0.00 0.00 0.00 5.68
3677 3987 1.135721 CCAATAGCAGCTTTCCTTGGC 59.864 52.381 0.00 0.00 0.00 4.52
3775 4085 6.770746 ATTGAGTTGAATGAGGGAGAAATG 57.229 37.500 0.00 0.00 0.00 2.32
3845 4155 9.697250 TTGAATTGTTATTATAGCTTTCGTTCG 57.303 29.630 0.00 0.00 0.00 3.95
3848 4158 9.988350 CAGTTGAATTGTTATTATAGCTTTCGT 57.012 29.630 0.00 0.00 0.00 3.85
3880 4190 6.312426 GCATTATAGATCACTCCAGTGTATGC 59.688 42.308 6.61 7.83 45.76 3.14
4050 4360 3.347216 CTCCAATCTTACCCACCACAAG 58.653 50.000 0.00 0.00 0.00 3.16
4076 4387 2.230994 GAGCGCCAGGTGATGTGAGA 62.231 60.000 2.29 0.00 0.00 3.27
4393 4704 2.896443 CGCCTCTTCCACTCCTCC 59.104 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.