Multiple sequence alignment - TraesCS4B01G276600

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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 TraesCS4B01G276600 chr4B 100.000 4711 0 0 1 4711 557456786 557452076 0.000000e+00 8700.0
1 TraesCS4B01G276600 chr4B 80.645 93 9 4 24 107 472078207 472078299 3.940000e-06 63.9
2 TraesCS4B01G276600 chr4D 94.856 4763 118 43 1 4711 445712395 445707708 0.000000e+00 7321.0
3 TraesCS4B01G276600 chr4A 93.315 4368 165 41 396 4711 21453081 21457373 0.000000e+00 6331.0
4 TraesCS4B01G276600 chr4A 90.047 211 8 5 142 343 21452543 21452749 1.300000e-65 261.0
5 TraesCS4B01G276600 chr6A 79.837 491 86 9 3232 3709 424800176 424800666 3.490000e-91 346.0
6 TraesCS4B01G276600 chr6A 87.805 82 7 2 1319 1397 424798442 424798523 5.020000e-15 93.5
7 TraesCS4B01G276600 chr6B 95.122 41 2 0 24 64 590397025 590397065 1.090000e-06 65.8
8 TraesCS4B01G276600 chr1B 95.122 41 2 0 24 64 402352176 402352136 1.090000e-06 65.8
9 TraesCS4B01G276600 chr7D 100.000 28 0 0 25 52 367370499 367370526 9.000000e-03 52.8


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 TraesCS4B01G276600 chr4B 557452076 557456786 4710 True 8700.00 8700 100.000 1 4711 1 chr4B.!!$R1 4710
1 TraesCS4B01G276600 chr4D 445707708 445712395 4687 True 7321.00 7321 94.856 1 4711 1 chr4D.!!$R1 4710
2 TraesCS4B01G276600 chr4A 21452543 21457373 4830 False 3296.00 6331 91.681 142 4711 2 chr4A.!!$F1 4569
3 TraesCS4B01G276600 chr6A 424798442 424800666 2224 False 219.75 346 83.821 1319 3709 2 chr6A.!!$F1 2390

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
25 26 0.036388 CAGCTTTAGGACCGCCTTCA 60.036 55.0 0.00 0.0 43.90 3.02 F
31 32 0.036388 TAGGACCGCCTTCAGCTTTG 60.036 55.0 0.00 0.0 43.90 2.77 F
855 1170 0.108138 GTGGCCGCATTGTCTCTACT 60.108 55.0 12.58 0.0 0.00 2.57 F
1468 1813 0.321122 CCTGTCCTCTGTGGTCTTGC 60.321 60.0 0.00 0.0 37.07 4.01 F
2677 3064 0.392998 GGCAGAAGGAAGGCGATGAA 60.393 55.0 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1468 0.107410 TGTTGAACCACTTCCGCACT 60.107 50.0 0.00 0.0 0.0 4.40 R
1648 1999 0.810648 GCATCGAAATTGTCAGCCCA 59.189 50.0 0.00 0.0 0.0 5.36 R
2677 3064 1.091771 CATCTGAGTTCCGCCGCATT 61.092 55.0 0.00 0.0 0.0 3.56 R
3341 3763 0.178876 TCTGGTTCATGTCCTCCCCA 60.179 55.0 10.06 0.0 0.0 4.96 R
4620 5064 0.327867 TCATTCATGGCCCCCTCTCT 60.328 55.0 0.00 0.0 0.0 3.10 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
25 26 0.036388 CAGCTTTAGGACCGCCTTCA 60.036 55.000 0.00 0.00 43.90 3.02
27 28 1.369839 GCTTTAGGACCGCCTTCAGC 61.370 60.000 0.00 0.00 43.90 4.26
28 29 0.250513 CTTTAGGACCGCCTTCAGCT 59.749 55.000 0.00 0.00 43.90 4.24
29 30 0.690762 TTTAGGACCGCCTTCAGCTT 59.309 50.000 0.00 0.00 43.90 3.74
31 32 0.036388 TAGGACCGCCTTCAGCTTTG 60.036 55.000 0.00 0.00 43.90 2.77
32 33 2.563427 GACCGCCTTCAGCTTTGC 59.437 61.111 0.00 0.00 40.39 3.68
64 76 1.986882 ATCTGGATTCGGGCCATTTC 58.013 50.000 4.39 0.00 34.33 2.17
72 84 1.153588 CGGGCCATTTCCAATGCAC 60.154 57.895 4.39 0.00 0.00 4.57
73 85 1.153588 GGGCCATTTCCAATGCACG 60.154 57.895 4.39 0.00 0.00 5.34
75 87 0.458370 GGCCATTTCCAATGCACGTC 60.458 55.000 0.00 0.00 0.00 4.34
76 88 0.243365 GCCATTTCCAATGCACGTCA 59.757 50.000 0.00 0.00 0.00 4.35
110 130 1.452651 CGGTGGCAAGCTGATCCAT 60.453 57.895 5.32 0.00 31.83 3.41
128 148 0.394352 ATGGGTGATTCGGAGCCAAC 60.394 55.000 0.00 0.00 43.96 3.77
208 228 1.680735 CAATCTCCCTCTCTGTCTCCG 59.319 57.143 0.00 0.00 0.00 4.63
229 249 3.445450 CGAAATGGAAGTCCTCTCTCTCA 59.555 47.826 0.00 0.00 36.82 3.27
282 311 1.545651 GCAGCAGTAACACTTTCCCCT 60.546 52.381 0.00 0.00 0.00 4.79
287 316 3.326747 CAGTAACACTTTCCCCTCGAAG 58.673 50.000 0.00 0.00 0.00 3.79
288 317 2.302157 AGTAACACTTTCCCCTCGAAGG 59.698 50.000 0.00 0.00 33.84 3.46
350 379 0.178873 TCCTTGGGTCTTGCTAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
364 393 0.611200 TAGGGTAGCGAGCAAAAGCA 59.389 50.000 0.00 0.00 35.48 3.91
365 394 0.674895 AGGGTAGCGAGCAAAAGCAG 60.675 55.000 0.00 0.00 35.48 4.24
366 395 0.673644 GGGTAGCGAGCAAAAGCAGA 60.674 55.000 0.00 0.00 35.48 4.26
367 396 0.723981 GGTAGCGAGCAAAAGCAGAG 59.276 55.000 0.00 0.00 35.48 3.35
392 421 3.051803 AGAGAGGGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
394 702 3.051803 AGAGGGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
397 705 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
423 732 2.366916 ACCATCCTAAGATTCCTCTGCG 59.633 50.000 0.00 0.00 0.00 5.18
484 793 0.875908 GCTCGCTCACTCACACACAA 60.876 55.000 0.00 0.00 0.00 3.33
485 794 0.855349 CTCGCTCACTCACACACAAC 59.145 55.000 0.00 0.00 0.00 3.32
486 795 0.174617 TCGCTCACTCACACACAACA 59.825 50.000 0.00 0.00 0.00 3.33
487 796 0.301687 CGCTCACTCACACACAACAC 59.698 55.000 0.00 0.00 0.00 3.32
488 797 1.368641 GCTCACTCACACACAACACA 58.631 50.000 0.00 0.00 0.00 3.72
570 879 2.168521 TCAGATAAGCTGTGTGGTAGGC 59.831 50.000 0.00 0.00 45.14 3.93
571 880 2.169352 CAGATAAGCTGTGTGGTAGGCT 59.831 50.000 0.00 0.00 39.85 4.58
572 881 3.384789 CAGATAAGCTGTGTGGTAGGCTA 59.615 47.826 0.00 0.00 39.85 3.93
704 1019 3.775654 CCCTGCCCGTCCTCACTC 61.776 72.222 0.00 0.00 0.00 3.51
705 1020 4.135153 CCTGCCCGTCCTCACTCG 62.135 72.222 0.00 0.00 0.00 4.18
855 1170 0.108138 GTGGCCGCATTGTCTCTACT 60.108 55.000 12.58 0.00 0.00 2.57
942 1267 3.672295 CTTCGACCCTGGGCTGCTC 62.672 68.421 14.08 1.29 0.00 4.26
979 1304 4.486503 CCCCTGAGCTGAGCCTGC 62.487 72.222 0.00 0.00 0.00 4.85
1041 1366 2.054799 ACCAAGAAGAGCAAGGTACCA 58.945 47.619 15.94 0.00 0.00 3.25
1051 1376 0.999712 CAAGGTACCACCCTCCCATT 59.000 55.000 15.94 0.00 39.75 3.16
1086 1411 1.981495 CTCCTGGTTCCTCTGTTTCCT 59.019 52.381 0.00 0.00 0.00 3.36
1117 1442 2.594592 GGTTCGGTTGCTGTGGCT 60.595 61.111 0.00 0.00 39.59 4.75
1143 1468 1.272490 CTGTCGTGGTCCAAGAGCTTA 59.728 52.381 7.86 0.00 0.00 3.09
1454 1799 1.470890 CTTCGTCTCCACTCTCCTGTC 59.529 57.143 0.00 0.00 0.00 3.51
1456 1801 0.322997 CGTCTCCACTCTCCTGTCCT 60.323 60.000 0.00 0.00 0.00 3.85
1457 1802 1.470051 GTCTCCACTCTCCTGTCCTC 58.530 60.000 0.00 0.00 0.00 3.71
1458 1803 1.005450 GTCTCCACTCTCCTGTCCTCT 59.995 57.143 0.00 0.00 0.00 3.69
1459 1804 1.005332 TCTCCACTCTCCTGTCCTCTG 59.995 57.143 0.00 0.00 0.00 3.35
1464 1809 1.181786 CTCTCCTGTCCTCTGTGGTC 58.818 60.000 0.00 0.00 37.07 4.02
1466 1811 1.148027 TCTCCTGTCCTCTGTGGTCTT 59.852 52.381 0.00 0.00 37.07 3.01
1468 1813 0.321122 CCTGTCCTCTGTGGTCTTGC 60.321 60.000 0.00 0.00 37.07 4.01
1603 1954 1.872313 GACATCTACGTCCTCGGGTAG 59.128 57.143 0.00 0.00 41.85 3.18
1614 1965 3.145551 CGGGTAGGTGTCTCCGGG 61.146 72.222 0.00 0.00 41.99 5.73
1618 1969 1.560505 GGTAGGTGTCTCCGGGTTTA 58.439 55.000 0.00 0.00 41.99 2.01
1675 2026 1.743623 AATTTCGATGCCGCCGTGA 60.744 52.632 0.00 0.00 35.37 4.35
2142 2502 4.501714 TCGCCCATGTCGTACGGC 62.502 66.667 14.12 14.12 38.07 5.68
2204 2567 1.171308 TCTGGTCACACTAGGTACGC 58.829 55.000 0.00 0.00 0.00 4.42
2209 2572 2.415625 GGTCACACTAGGTACGCTTCAG 60.416 54.545 0.00 0.00 0.00 3.02
2302 2665 1.993370 GACGTGGTGAGTAATCTGTGC 59.007 52.381 0.00 0.00 0.00 4.57
2316 2679 2.300433 TCTGTGCTGCAATCTGTTGTT 58.700 42.857 2.77 0.00 37.65 2.83
2317 2680 2.689471 TCTGTGCTGCAATCTGTTGTTT 59.311 40.909 2.77 0.00 37.65 2.83
2483 2867 3.067106 GGTCACTGTTCGAATGATGTGT 58.933 45.455 0.00 0.00 0.00 3.72
2506 2893 7.901377 GTGTTTATCATGATTTTTGCAATGCTC 59.099 33.333 14.65 0.00 0.00 4.26
2674 3061 2.592308 GGGCAGAAGGAAGGCGAT 59.408 61.111 0.00 0.00 0.00 4.58
2677 3064 0.392998 GGCAGAAGGAAGGCGATGAA 60.393 55.000 0.00 0.00 0.00 2.57
2919 3341 3.651562 AATTACCGAATCGCACTTTCG 57.348 42.857 0.00 5.87 44.17 3.46
3047 3469 0.545787 TGTGTACCGTTGGGATCCCT 60.546 55.000 31.05 13.49 36.97 4.20
3341 3763 3.270877 GACCAATTCCGACAAGTATGCT 58.729 45.455 0.00 0.00 0.00 3.79
3497 3934 1.227383 GTGGTATGGAAGGGGCCTG 59.773 63.158 0.84 0.00 0.00 4.85
3524 3961 2.615447 ACTATCATACGTTCGAGGCGAA 59.385 45.455 16.38 0.00 43.75 4.70
3723 4160 5.779241 TTTCTACTGAAAGGGTCCATGAT 57.221 39.130 0.00 0.00 39.30 2.45
3913 4351 4.593597 TTTCTGATAAATCGGTGAACGC 57.406 40.909 0.00 0.00 43.86 4.84
3962 4403 3.063510 TGCTAAGCACAAAGAGCTGAT 57.936 42.857 0.00 0.00 42.53 2.90
3965 4406 3.190118 GCTAAGCACAAAGAGCTGATTGT 59.810 43.478 7.69 7.69 42.53 2.71
4010 4451 6.182627 TGCACATTGGATACTTTCAGAGAAT 58.817 36.000 0.00 0.00 37.61 2.40
4042 4483 4.326826 CTTGGCTAGTTTCACAGGATTCA 58.673 43.478 0.00 0.00 0.00 2.57
4109 4551 6.799925 CAGTTTTTATGGTGAACAATACGTCC 59.200 38.462 0.00 0.00 0.00 4.79
4215 4659 2.233271 CAAGCCAGTGACCACAAAGAT 58.767 47.619 2.78 0.00 0.00 2.40
4461 4905 6.653020 TGTATAGCAACATTGTTGATCCTCT 58.347 36.000 29.04 18.79 0.00 3.69
4462 4906 6.763135 TGTATAGCAACATTGTTGATCCTCTC 59.237 38.462 29.04 12.08 0.00 3.20
4463 4907 4.298103 AGCAACATTGTTGATCCTCTCT 57.702 40.909 29.04 13.92 0.00 3.10
4464 4908 4.260170 AGCAACATTGTTGATCCTCTCTC 58.740 43.478 29.04 10.82 0.00 3.20
4465 4909 4.019501 AGCAACATTGTTGATCCTCTCTCT 60.020 41.667 29.04 12.67 0.00 3.10
4499 4943 5.362143 TCTCTCTCTCTCTCTCTCTCTCTTG 59.638 48.000 0.00 0.00 0.00 3.02
4500 4944 5.272402 TCTCTCTCTCTCTCTCTCTCTTGA 58.728 45.833 0.00 0.00 0.00 3.02
4501 4945 5.901853 TCTCTCTCTCTCTCTCTCTCTTGAT 59.098 44.000 0.00 0.00 0.00 2.57
4512 4956 5.684704 TCTCTCTCTTGATTCTCTCTCTCC 58.315 45.833 0.00 0.00 0.00 3.71
4572 5016 3.134804 AGTCCTTTGCACAGTCTACACTT 59.865 43.478 0.00 0.00 0.00 3.16
4612 5056 5.692115 AAAAGCTTGGGGAAGAAAGAAAA 57.308 34.783 0.00 0.00 0.00 2.29
4620 5064 7.489239 TTGGGGAAGAAAGAAAAGAAAGAAA 57.511 32.000 0.00 0.00 0.00 2.52
4683 5127 9.288576 CCTCATACTATCATCTATCTCATCTCC 57.711 40.741 0.00 0.00 0.00 3.71
4688 5132 7.577303 ACTATCATCTATCTCATCTCCTCTCC 58.423 42.308 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.099592 CAGTTTCACTGGCAAAGCTGAA 59.900 45.455 8.12 1.49 42.35 3.02
25 26 2.057137 TCAGTTTCACTGGCAAAGCT 57.943 45.000 4.09 0.00 45.94 3.74
27 28 4.543692 CAGATTCAGTTTCACTGGCAAAG 58.456 43.478 4.09 0.00 45.94 2.77
28 29 3.318839 CCAGATTCAGTTTCACTGGCAAA 59.681 43.478 4.09 0.00 45.94 3.68
29 30 2.886523 CCAGATTCAGTTTCACTGGCAA 59.113 45.455 4.09 0.00 45.94 4.52
31 32 2.783135 TCCAGATTCAGTTTCACTGGC 58.217 47.619 0.00 0.00 45.94 4.85
32 33 4.093998 CGAATCCAGATTCAGTTTCACTGG 59.906 45.833 18.00 0.00 45.94 4.00
60 72 1.196808 GACGTGACGTGCATTGGAAAT 59.803 47.619 18.09 0.00 41.37 2.17
64 76 0.110688 CTTGACGTGACGTGCATTGG 60.111 55.000 18.09 3.85 41.37 3.16
72 84 2.049228 GAAGTACACCTTGACGTGACG 58.951 52.381 2.24 2.24 37.20 4.35
73 85 2.049228 CGAAGTACACCTTGACGTGAC 58.951 52.381 0.00 0.00 37.20 3.67
75 87 1.269413 ACCGAAGTACACCTTGACGTG 60.269 52.381 0.00 0.00 39.75 4.49
76 88 1.035139 ACCGAAGTACACCTTGACGT 58.965 50.000 0.00 0.00 32.03 4.34
110 130 1.002624 GTTGGCTCCGAATCACCCA 60.003 57.895 0.00 0.00 0.00 4.51
128 148 1.604604 TTCAAACGAAGGCCCTTCAG 58.395 50.000 22.83 16.84 40.17 3.02
192 212 1.840737 TTTCGGAGACAGAGAGGGAG 58.159 55.000 0.00 0.00 34.32 4.30
208 228 4.221703 TGTGAGAGAGAGGACTTCCATTTC 59.778 45.833 0.00 0.00 38.89 2.17
229 249 2.627515 AAGCATGTGACTCTGTGTGT 57.372 45.000 0.00 0.00 0.00 3.72
282 311 1.678635 CCAAGCAATGCCCCTTCGA 60.679 57.895 0.00 0.00 0.00 3.71
287 316 1.329171 TGCATACCAAGCAATGCCCC 61.329 55.000 0.00 0.00 46.34 5.80
288 317 0.754472 ATGCATACCAAGCAATGCCC 59.246 50.000 0.00 0.00 46.34 5.36
364 393 3.051803 TCTCTCTCTCCCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
365 394 3.309296 TCTCTCTCTCCCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
366 395 3.051803 TCTCTCTCTCTCCCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
367 396 3.309296 TCTCTCTCTCTCCCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
392 421 4.871871 TCTTAGGATGGTCAGTCTCTCT 57.128 45.455 0.00 0.00 0.00 3.10
394 702 4.898861 GGAATCTTAGGATGGTCAGTCTCT 59.101 45.833 0.00 0.00 31.75 3.10
397 705 4.898861 AGAGGAATCTTAGGATGGTCAGTC 59.101 45.833 0.00 0.00 31.75 3.51
423 732 1.671328 GTGGAAGGGAATAAAGCGCTC 59.329 52.381 12.06 0.00 0.00 5.03
484 793 0.732571 CTTGAGCCGTTGTGTTGTGT 59.267 50.000 0.00 0.00 0.00 3.72
485 794 0.732571 ACTTGAGCCGTTGTGTTGTG 59.267 50.000 0.00 0.00 0.00 3.33
486 795 1.459450 AACTTGAGCCGTTGTGTTGT 58.541 45.000 0.00 0.00 0.00 3.32
487 796 2.559998 AAACTTGAGCCGTTGTGTTG 57.440 45.000 0.00 0.00 0.00 3.33
488 797 3.192633 AGAAAAACTTGAGCCGTTGTGTT 59.807 39.130 0.00 0.00 0.00 3.32
570 879 4.594062 TCCTCTCCTACTAGTAGCCAGTAG 59.406 50.000 22.39 16.45 43.38 2.57
571 880 4.564799 TCCTCTCCTACTAGTAGCCAGTA 58.435 47.826 22.39 10.16 31.95 2.74
572 881 3.393278 CTCCTCTCCTACTAGTAGCCAGT 59.607 52.174 22.39 0.00 31.95 4.00
705 1020 0.808125 TCTCTTCTCTCTGCGAGTGC 59.192 55.000 5.66 0.00 40.75 4.40
855 1170 1.273896 GGAAGGAAGAAGAGGGAGGGA 60.274 57.143 0.00 0.00 0.00 4.20
979 1304 0.519077 GTTCCTTTCCTTGCTCAGCG 59.481 55.000 0.00 0.00 0.00 5.18
986 1311 5.125097 CCATCTCTCATTGTTCCTTTCCTTG 59.875 44.000 0.00 0.00 0.00 3.61
993 1318 2.683152 GCAGCCATCTCTCATTGTTCCT 60.683 50.000 0.00 0.00 0.00 3.36
1041 1366 0.419459 AGACAGAGGAATGGGAGGGT 59.581 55.000 0.00 0.00 0.00 4.34
1051 1376 2.558575 CCAGGAGGAAGAAGACAGAGGA 60.559 54.545 0.00 0.00 36.89 3.71
1086 1411 1.851021 CGAACCGCATTCAGGCACAA 61.851 55.000 0.00 0.00 37.12 3.33
1117 1442 0.753867 TTGGACCACGACAGCTACAA 59.246 50.000 0.00 0.00 0.00 2.41
1143 1468 0.107410 TGTTGAACCACTTCCGCACT 60.107 50.000 0.00 0.00 0.00 4.40
1232 1557 1.064946 CTCCACTCCTCATCGTCGC 59.935 63.158 0.00 0.00 0.00 5.19
1236 1561 2.801631 GCCCCTCCACTCCTCATCG 61.802 68.421 0.00 0.00 0.00 3.84
1237 1562 1.690633 TGCCCCTCCACTCCTCATC 60.691 63.158 0.00 0.00 0.00 2.92
1238 1563 1.692042 CTGCCCCTCCACTCCTCAT 60.692 63.158 0.00 0.00 0.00 2.90
1430 1770 3.563808 CAGGAGAGTGGAGACGAAGATAG 59.436 52.174 0.00 0.00 0.00 2.08
1431 1771 3.054287 ACAGGAGAGTGGAGACGAAGATA 60.054 47.826 0.00 0.00 0.00 1.98
1454 1799 2.163818 TTAACGCAAGACCACAGAGG 57.836 50.000 0.00 0.00 42.73 3.69
1456 1801 6.621316 TTTTAATTAACGCAAGACCACAGA 57.379 33.333 0.00 0.00 43.62 3.41
1457 1802 7.136119 TCTTTTTAATTAACGCAAGACCACAG 58.864 34.615 0.00 0.00 43.62 3.66
1458 1803 7.028926 TCTTTTTAATTAACGCAAGACCACA 57.971 32.000 0.00 0.00 43.62 4.17
1459 1804 7.917720 TTCTTTTTAATTAACGCAAGACCAC 57.082 32.000 10.95 0.00 43.62 4.16
1466 1811 6.419413 CAGGCAGTTTCTTTTTAATTAACGCA 59.581 34.615 0.00 0.00 0.00 5.24
1468 1813 6.419413 TGCAGGCAGTTTCTTTTTAATTAACG 59.581 34.615 0.00 0.00 0.00 3.18
1644 1995 1.202879 TCGAAATTGTCAGCCCAACCT 60.203 47.619 0.00 0.00 0.00 3.50
1648 1999 0.810648 GCATCGAAATTGTCAGCCCA 59.189 50.000 0.00 0.00 0.00 5.36
1675 2026 2.649531 TGGAACCTTTGGACGAACAT 57.350 45.000 0.00 0.00 0.00 2.71
2013 2373 4.246206 CCGTAGATCGCGCGGTCA 62.246 66.667 40.72 25.42 40.53 4.02
2088 2448 1.147376 CTCCCCGGTGTTGTTGTCA 59.853 57.895 0.00 0.00 0.00 3.58
2316 2679 3.831333 TGCAACCAGGCAATATCTGAAAA 59.169 39.130 0.00 0.00 41.65 2.29
2317 2680 3.429492 TGCAACCAGGCAATATCTGAAA 58.571 40.909 0.00 0.00 41.65 2.69
2483 2867 9.304731 GTAGAGCATTGCAAAAATCATGATAAA 57.695 29.630 9.04 0.00 0.00 1.40
2506 2893 8.720562 TGTTTGTGATCAACTCATACAATGTAG 58.279 33.333 0.00 0.00 35.97 2.74
2519 2906 3.988379 TGCCTCTTGTTTGTGATCAAC 57.012 42.857 0.00 0.00 32.93 3.18
2674 3061 1.298157 CTGAGTTCCGCCGCATTTCA 61.298 55.000 0.00 0.00 0.00 2.69
2677 3064 1.091771 CATCTGAGTTCCGCCGCATT 61.092 55.000 0.00 0.00 0.00 3.56
2919 3341 0.179081 GGGCCTTCACTGACCGATAC 60.179 60.000 0.84 0.00 0.00 2.24
3047 3469 7.865385 GTGACATAACAATTTTACAGCTTTCCA 59.135 33.333 0.00 0.00 0.00 3.53
3341 3763 0.178876 TCTGGTTCATGTCCTCCCCA 60.179 55.000 10.06 0.00 0.00 4.96
3497 3934 4.288531 CTCGAACGTATGATAGTTGACCC 58.711 47.826 0.00 0.00 0.00 4.46
3524 3961 4.021544 GGCCTATGATCTGAGAAACGAGAT 60.022 45.833 0.00 0.00 0.00 2.75
3530 3967 4.293494 AGACTGGCCTATGATCTGAGAAA 58.707 43.478 3.32 0.00 0.00 2.52
3962 4403 6.025749 AGACTCTGATCGTGACAAATACAA 57.974 37.500 0.00 0.00 0.00 2.41
3965 4406 4.864806 GCAAGACTCTGATCGTGACAAATA 59.135 41.667 7.02 0.00 30.51 1.40
4109 4551 6.644347 ACTGGTTAGGATCAGTAGTTCATTG 58.356 40.000 0.00 0.00 41.81 2.82
4461 4905 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4462 4906 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4463 4907 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4464 4908 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
4465 4909 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
4532 4976 2.413453 GACTACTGCTACTGCTTGTTGC 59.587 50.000 9.06 9.06 45.29 4.17
4572 5016 4.142902 GCTTTTATAAACTGCACGCAGAGA 60.143 41.667 25.09 9.92 46.30 3.10
4612 5056 0.995803 GGCCCCCTCTCTTTCTTTCT 59.004 55.000 0.00 0.00 0.00 2.52
4620 5064 0.327867 TCATTCATGGCCCCCTCTCT 60.328 55.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.