Multiple sequence alignment - TraesCS1B01G130700

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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 TraesCS1B01G130700 chr1B 100.000 5664 0 0 1 5664 162349218 162343555 0 10460
1 TraesCS1B01G130700 chr1D 94.697 3036 127 20 1689 4716 103501456 103504465 0 4684
2 TraesCS1B01G130700 chr1D 96.964 1153 30 3 557 1705 103500272 103501423 0 1930
3 TraesCS1B01G130700 chr1D 94.731 949 48 2 4715 5662 103504629 103505576 0 1474
4 TraesCS1B01G130700 chr1D 90.714 560 40 5 3 562 103497991 103498538 0 736
5 TraesCS1B01G130700 chr1A 94.466 3036 144 12 1689 4716 100917915 100914896 0 4654
6 TraesCS1B01G130700 chr1A 95.837 1153 43 3 557 1705 100919099 100917948 0 1858
7 TraesCS1B01G130700 chr1A 93.586 951 59 2 4715 5664 100914738 100913789 0 1417
8 TraesCS1B01G130700 chr1A 92.143 560 37 6 3 560 101082536 101081982 0 784


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 TraesCS1B01G130700 chr1B 162343555 162349218 5663 True 10460 10460 100.000000 1 5664 1 chr1B.!!$R1 5663
1 TraesCS1B01G130700 chr1D 103497991 103505576 7585 False 2206 4684 94.276500 3 5662 4 chr1D.!!$F1 5659
2 TraesCS1B01G130700 chr1A 100913789 100919099 5310 True 2643 4654 94.629667 557 5664 3 chr1A.!!$R2 5107
3 TraesCS1B01G130700 chr1A 101081982 101082536 554 True 784 784 92.143000 3 560 1 chr1A.!!$R1 557

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
110 111 0.750249 TTCCTGTGTTGAGACGCTCA 59.250 50.000 5.59 5.59 38.87 4.26 F
217 224 1.202973 CGATGTTCGAGCTGTAGGCG 61.203 60.000 0.00 0.00 43.74 5.52 F
1423 3176 2.997897 ACTCCTCGAGGTGGTGCC 60.998 66.667 31.17 0.00 33.35 5.01 F
1943 3748 0.795698 CGCATCGATGTGAACACCAA 59.204 50.000 30.54 0.00 40.61 3.67 F
3551 5361 2.047061 CCAGTTTCAGATATCCGGGGA 58.953 52.381 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 3266 3.754965 TGGTTTTCCATCTCCTCTGTTG 58.245 45.455 0.00 0.0 46.22 3.33 R
1701 3454 4.377635 GGCGAGAAAGTTTACATACGCAAA 60.378 41.667 18.32 0.0 45.17 3.68 R
2617 4422 1.838077 ACCACCACAATAGGTAGCCTC 59.162 52.381 0.00 0.0 40.77 4.70 R
3758 5569 1.507141 GAGTTCACAGGGTTGGTGCG 61.507 60.000 0.00 0.0 36.22 5.34 R
5042 7020 0.317479 GGTGGTGTTCGCTACTCACT 59.683 55.000 0.00 0.0 34.43 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
24 25 2.373169 ACTCTCAAAGGGTTGATGCTCA 59.627 45.455 0.00 0.00 42.85 4.26
39 40 6.469782 TGATGCTCACAACTCATATGTAGA 57.530 37.500 1.90 0.00 0.00 2.59
71 72 1.004398 CGACAACGCACACTGCTAAAA 60.004 47.619 0.00 0.00 42.25 1.52
82 83 8.079809 ACGCACACTGCTAAAATTTAATTTACT 58.920 29.630 3.17 0.00 42.25 2.24
85 86 8.647226 CACACTGCTAAAATTTAATTTACTGGC 58.353 33.333 3.17 3.82 0.00 4.85
86 87 8.585018 ACACTGCTAAAATTTAATTTACTGGCT 58.415 29.630 3.17 0.00 0.00 4.75
110 111 0.750249 TTCCTGTGTTGAGACGCTCA 59.250 50.000 5.59 5.59 38.87 4.26
136 137 2.526304 TATATGGACGACAAGGCTGC 57.474 50.000 0.00 0.00 0.00 5.25
142 143 2.167398 GACGACAAGGCTGCAGGGTA 62.167 60.000 17.12 0.00 0.00 3.69
144 145 1.374947 GACAAGGCTGCAGGGTACA 59.625 57.895 17.12 0.00 0.00 2.90
175 176 9.502091 ACTAGCAGTGTTTGATAAATCTAAACA 57.498 29.630 12.54 12.54 40.73 2.83
197 198 5.126869 ACATTGTCAGTACCTCAGATCTCAG 59.873 44.000 0.00 0.00 0.00 3.35
205 206 2.100584 ACCTCAGATCTCAGCGATGTTC 59.899 50.000 0.00 0.00 30.84 3.18
214 221 3.631714 AGCGATGTTCGAGCTGTAG 57.368 52.632 0.00 0.00 43.74 2.74
217 224 1.202973 CGATGTTCGAGCTGTAGGCG 61.203 60.000 0.00 0.00 43.74 5.52
218 225 3.515170 CGATGTTCGAGCTGTAGGCGA 62.515 57.143 0.00 0.00 43.74 5.54
219 226 4.941534 CGATGTTCGAGCTGTAGGCGAA 62.942 54.545 3.32 3.32 43.74 4.70
235 242 4.890088 AGGCGAACACAGTTGATAGTTTA 58.110 39.130 0.00 0.00 0.00 2.01
238 245 5.062308 GGCGAACACAGTTGATAGTTTAGAG 59.938 44.000 0.00 0.00 0.00 2.43
275 283 5.387649 CGCGTTCTATTTTTCTGACACGTAA 60.388 40.000 0.00 0.00 0.00 3.18
332 341 9.469097 CTACTAGTGATAGGAGTAATATGGCTT 57.531 37.037 5.39 0.00 0.00 4.35
425 434 4.245660 TGCACATGAGCAACTAGTAGTTC 58.754 43.478 15.81 8.18 42.46 3.01
528 537 9.567848 AAATACATGCAAACGTATCCTTTAAAG 57.432 29.630 8.32 8.32 0.00 1.85
552 561 7.331791 AGTAAGTTCTAAATGCCCTCAGTTAG 58.668 38.462 6.26 6.26 46.50 2.34
823 2576 5.515270 TGAATGAACTCATTTACTCGCTACG 59.485 40.000 6.40 0.00 45.72 3.51
940 2693 6.786122 TGCTTTACACTATTTAAAGAGGGGT 58.214 36.000 16.11 13.87 38.36 4.95
943 2696 7.498239 GCTTTACACTATTTAAAGAGGGGTAGG 59.502 40.741 16.11 12.61 38.36 3.18
1064 2817 7.707035 ACTTCTCGCTAATGTAATTACAGGAAG 59.293 37.037 22.03 21.76 39.92 3.46
1266 3019 6.945435 TCCATACTAGTGAAAATTTTGCCTCA 59.055 34.615 8.47 0.00 0.00 3.86
1423 3176 2.997897 ACTCCTCGAGGTGGTGCC 60.998 66.667 31.17 0.00 33.35 5.01
1469 3222 9.236006 AGGCTACAATTGATGTATATGGATTTC 57.764 33.333 13.59 0.00 43.42 2.17
1511 3264 3.700538 AGTGCAGCTGGAATTTGGATTA 58.299 40.909 17.12 0.00 0.00 1.75
1513 3266 4.340381 AGTGCAGCTGGAATTTGGATTATC 59.660 41.667 17.12 0.00 0.00 1.75
1518 3271 6.270815 CAGCTGGAATTTGGATTATCAACAG 58.729 40.000 5.57 0.00 0.00 3.16
1701 3454 7.235399 ACTCCACAGAACCCAATCAATAATTTT 59.765 33.333 0.00 0.00 0.00 1.82
1864 3669 4.200838 TGCGACTTCAAATAGACATGGA 57.799 40.909 0.00 0.00 0.00 3.41
1930 3735 3.494626 AGACTACCATATTTTGCGCATCG 59.505 43.478 12.75 0.00 0.00 3.84
1941 3746 1.060937 GCGCATCGATGTGAACACC 59.939 57.895 36.40 18.16 40.61 4.16
1943 3748 0.795698 CGCATCGATGTGAACACCAA 59.204 50.000 30.54 0.00 40.61 3.67
2048 3853 9.793252 TTCCGTGAACTCTTTAATGTATAGTAC 57.207 33.333 0.00 0.00 0.00 2.73
2104 3909 7.361286 GGAGTGATTACCTCAAAGTGTTCATTC 60.361 40.741 0.00 0.00 35.07 2.67
2183 3988 7.573968 ATGGGCTATCTTGTCATTAGTTTTC 57.426 36.000 0.00 0.00 0.00 2.29
2189 3994 8.391106 GCTATCTTGTCATTAGTTTTCGTGATT 58.609 33.333 0.00 0.00 0.00 2.57
2216 4021 2.320681 AGCAAGGTGTGTAGTAGGGA 57.679 50.000 0.00 0.00 0.00 4.20
2316 4121 2.811431 CCCAACTTAATCTCGTGTTGCA 59.189 45.455 0.00 0.00 38.60 4.08
2419 4224 2.076863 CTTGATTGGTGACTCGGTTCC 58.923 52.381 0.00 0.00 0.00 3.62
2460 4265 5.184892 AGCTCCCTACACTCAAAATGATT 57.815 39.130 0.00 0.00 0.00 2.57
2553 4358 2.480416 CCCTAAGCTCTAGTGAAGTGCG 60.480 54.545 0.00 0.00 46.93 5.34
2555 4360 2.821991 AAGCTCTAGTGAAGTGCGTT 57.178 45.000 0.00 0.00 46.93 4.84
2576 4381 3.431673 TGGATGGTTACATGCTTCACA 57.568 42.857 0.00 0.00 44.78 3.58
2591 4396 3.807209 GCTTCACAGAGGGCTTACAAAGA 60.807 47.826 0.00 0.00 0.00 2.52
2606 4411 4.046286 ACAAAGATTATGGGTGGCTGAA 57.954 40.909 0.00 0.00 0.00 3.02
2660 4465 6.888632 GGTCGATAGGTAGAAGGGATACAATA 59.111 42.308 0.00 0.00 39.74 1.90
2707 4513 3.118519 GGTAAAATAGGGAAGAGGCGTGA 60.119 47.826 0.00 0.00 0.00 4.35
2719 4525 2.093973 AGAGGCGTGAAGTATGTTCCAG 60.094 50.000 0.00 0.00 0.00 3.86
2761 4567 3.412386 CCTCCACTTAAAGGTTCCACTG 58.588 50.000 0.00 0.00 0.00 3.66
2791 4598 9.295825 TGGCTCTTCACATTAGAATTTTTCTTA 57.704 29.630 0.00 0.00 41.14 2.10
2836 4643 6.007076 TGATTTGTTGGCCATGACTAGTTTA 58.993 36.000 6.09 0.00 0.00 2.01
2886 4693 7.594351 TCAAAAATTAGCCATGCATACCATA 57.406 32.000 0.00 0.00 31.47 2.74
2928 4735 9.256228 CCCATAAGTAGGATTAGCTATTCTGTA 57.744 37.037 13.77 5.32 0.00 2.74
2953 4760 7.944729 AACAATATGTATGCCTCTTTCACTT 57.055 32.000 0.00 0.00 0.00 3.16
3003 4810 8.040132 TGATCTTTGTCACATCCAAAAACTTTT 58.960 29.630 0.00 0.00 31.86 2.27
3042 4849 6.790232 TTTGGCCCTGAAATATTAGGAAAG 57.210 37.500 0.00 0.00 36.11 2.62
3163 4970 6.459670 AGGACAAAATGAACGGTTTAAAGT 57.540 33.333 0.00 0.00 0.00 2.66
3193 5000 8.621073 ACTTAACCTTAAGGACAATTAGGGATT 58.379 33.333 28.52 9.40 43.38 3.01
3320 5130 7.667635 TCATAAATGTTACACCATCTGTTCCAA 59.332 33.333 0.00 0.00 33.91 3.53
3322 5132 5.964958 ATGTTACACCATCTGTTCCAAAG 57.035 39.130 0.00 0.00 33.91 2.77
3325 5135 5.995282 TGTTACACCATCTGTTCCAAAGTAG 59.005 40.000 0.00 0.00 33.91 2.57
3329 5139 5.995897 ACACCATCTGTTCCAAAGTAGTTAC 59.004 40.000 0.00 0.00 0.00 2.50
3551 5361 2.047061 CCAGTTTCAGATATCCGGGGA 58.953 52.381 0.00 0.00 0.00 4.81
3552 5362 2.639839 CCAGTTTCAGATATCCGGGGAT 59.360 50.000 0.00 5.40 38.54 3.85
3634 5444 8.193438 GCTAGATTATTTGTCCTCTTGCATTTT 58.807 33.333 0.00 0.00 36.77 1.82
3739 5550 9.422681 ACTAGAACTAGCTGGAATCAAACTATA 57.577 33.333 3.17 0.00 36.66 1.31
3758 5569 6.407202 ACTATAGTGAACATTGTTGAGTCCC 58.593 40.000 6.80 0.00 0.00 4.46
3846 5657 6.098552 TGTTGGACCGACCTATAATGACATAA 59.901 38.462 9.52 0.00 39.86 1.90
3849 5660 7.741785 TGGACCGACCTATAATGACATAAAAT 58.258 34.615 0.00 0.00 39.86 1.82
3889 5701 0.618458 TGGCTCATGTTGGTAGGGTC 59.382 55.000 0.00 0.00 0.00 4.46
3897 5709 0.462047 GTTGGTAGGGTCGGATGCAG 60.462 60.000 0.00 0.00 0.00 4.41
3915 5727 4.435425 TGCAGCATATTTTTGGAGAATGC 58.565 39.130 0.00 0.00 42.52 3.56
3963 5775 0.941463 CCTGACTGCGACTCACACAC 60.941 60.000 0.00 0.00 0.00 3.82
3965 5777 0.527600 TGACTGCGACTCACACACAC 60.528 55.000 0.00 0.00 0.00 3.82
3970 5782 3.059884 CTGCGACTCACACACACTTTAT 58.940 45.455 0.00 0.00 0.00 1.40
4011 5823 0.392998 AAATCCACTACGGCTGGCAG 60.393 55.000 10.94 10.94 33.14 4.85
4031 5843 3.877508 CAGTGCACTACTTAATTAGCCCC 59.122 47.826 21.20 0.00 37.60 5.80
4043 5855 0.698238 TTAGCCCCTGTGACAGCAAT 59.302 50.000 7.16 0.00 0.00 3.56
4108 5920 2.667470 CTTACAGCTAGGCCCAGTCTA 58.333 52.381 0.00 0.00 0.00 2.59
4410 6222 2.790433 TGAGATTAGTTTTGGCGGCTT 58.210 42.857 11.43 0.00 0.00 4.35
4435 6247 1.110442 CTCACCAAAAGCCACAACCA 58.890 50.000 0.00 0.00 0.00 3.67
4507 6319 7.640240 GCGTCCTTCAACAATATCAAACTAATC 59.360 37.037 0.00 0.00 0.00 1.75
4623 6435 2.014857 GTTCTTTTACGGGGGATCTGC 58.985 52.381 0.00 0.00 0.00 4.26
4765 6742 6.951198 ACAAGTGGTTGGATATTTAATGGTCA 59.049 34.615 0.00 0.00 38.07 4.02
4772 6749 5.392995 TGGATATTTAATGGTCATGGTGGG 58.607 41.667 0.00 0.00 0.00 4.61
4789 6766 3.372675 GGTGGGTGAATTAGGCAACCTAT 60.373 47.826 0.00 0.00 43.61 2.57
4791 6768 5.442391 GTGGGTGAATTAGGCAACCTATTA 58.558 41.667 0.00 0.00 43.61 0.98
4986 6963 3.123959 GCATGCAAATTGTGTGCCTTAAG 59.876 43.478 14.21 0.00 41.49 1.85
4992 6969 6.989169 TGCAAATTGTGTGCCTTAAGTTTATT 59.011 30.769 0.97 0.00 41.49 1.40
4998 6975 7.341445 TGTGTGCCTTAAGTTTATTGAAGTT 57.659 32.000 0.97 0.00 35.18 2.66
5002 6979 8.999431 TGTGCCTTAAGTTTATTGAAGTTAGAG 58.001 33.333 0.97 0.00 35.24 2.43
5005 6982 7.067129 GCCTTAAGTTTATTGAAGTTAGAGGGG 59.933 40.741 0.97 0.00 35.24 4.79
5042 7020 3.517901 CAGTAGGTTCCCACAATAGGTCA 59.482 47.826 0.00 0.00 0.00 4.02
5085 7063 0.531974 GGCGAGACACAGACAACCAA 60.532 55.000 0.00 0.00 0.00 3.67
5112 7090 3.448934 AGTCATCATCTTGGAGTCACCT 58.551 45.455 0.00 0.00 39.86 4.00
5201 7179 0.102481 GGATGTCATCACGCGTAGGT 59.898 55.000 13.44 0.00 0.00 3.08
5344 7322 2.698797 GCTGCATAACACCCTACTCCTA 59.301 50.000 0.00 0.00 0.00 2.94
5354 7332 6.947376 ACACCCTACTCCTACTTTTATGTT 57.053 37.500 0.00 0.00 0.00 2.71
5369 7347 6.983890 ACTTTTATGTTGTTGATTTGGTGGAC 59.016 34.615 0.00 0.00 0.00 4.02
5416 7394 2.152016 GGAAAGTGTAGTGTTGCTCCC 58.848 52.381 0.00 0.00 0.00 4.30
5423 7401 4.286032 AGTGTAGTGTTGCTCCCATCTAAA 59.714 41.667 0.00 0.00 0.00 1.85
5450 7428 4.172807 ACCAAGTGTCCAACCTTATCCTA 58.827 43.478 0.00 0.00 0.00 2.94
5470 7448 5.828859 TCCTAAAGTAGATCTGGTCTAGTGC 59.171 44.000 5.18 0.00 41.27 4.40
5494 7472 1.767672 CCCTGCCTCCCATAGCTCA 60.768 63.158 0.00 0.00 0.00 4.26
5518 7496 5.360999 AGTTCTCCTTTTATATTGCAAGGGC 59.639 40.000 4.94 0.00 38.13 5.19
5524 7502 3.326946 TTATATTGCAAGGGCCACCAT 57.673 42.857 6.18 0.00 40.13 3.55
5535 7513 1.065998 GGGCCACCATAGTTGTTACGA 60.066 52.381 4.39 0.00 36.50 3.43
5655 7633 1.555477 CCGCCCAGGGTGTTTACCTA 61.555 60.000 18.40 0.00 46.66 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.160417 GCATCAACCCTTTGAGAGTTCG 59.840 50.000 0.00 0.00 45.07 3.95
1 2 3.416156 AGCATCAACCCTTTGAGAGTTC 58.584 45.455 0.00 0.00 45.07 3.01
18 19 7.733969 AGAATCTACATATGAGTTGTGAGCAT 58.266 34.615 10.38 0.00 0.00 3.79
39 40 2.230508 TGCGTTGTCGGTCTCTAAGAAT 59.769 45.455 0.00 0.00 37.56 2.40
71 72 9.255029 ACAGGAAACATAGCCAGTAAATTAAAT 57.745 29.630 0.00 0.00 0.00 1.40
82 83 3.072330 TCTCAACACAGGAAACATAGCCA 59.928 43.478 0.00 0.00 0.00 4.75
85 86 3.123621 GCGTCTCAACACAGGAAACATAG 59.876 47.826 0.00 0.00 0.00 2.23
86 87 3.064207 GCGTCTCAACACAGGAAACATA 58.936 45.455 0.00 0.00 0.00 2.29
110 111 6.706270 CAGCCTTGTCGTCCATATAACTTTAT 59.294 38.462 0.00 0.00 0.00 1.40
136 137 4.021368 ACACTGCTAGTACTTTGTACCCTG 60.021 45.833 0.00 1.93 0.00 4.45
142 143 8.671384 TTTATCAAACACTGCTAGTACTTTGT 57.329 30.769 0.00 0.00 31.76 2.83
144 145 9.726438 AGATTTATCAAACACTGCTAGTACTTT 57.274 29.630 0.00 0.00 0.00 2.66
175 176 4.099266 GCTGAGATCTGAGGTACTGACAAT 59.901 45.833 11.39 0.00 41.55 2.71
176 177 3.445450 GCTGAGATCTGAGGTACTGACAA 59.555 47.826 11.39 0.00 41.55 3.18
185 186 2.741612 GAACATCGCTGAGATCTGAGG 58.258 52.381 11.39 1.24 37.52 3.86
197 198 1.483424 GCCTACAGCTCGAACATCGC 61.483 60.000 0.00 0.00 40.21 4.58
205 206 1.073216 CTGTGTTCGCCTACAGCTCG 61.073 60.000 0.00 0.00 38.01 5.03
214 221 4.927425 TCTAAACTATCAACTGTGTTCGCC 59.073 41.667 0.00 0.00 0.00 5.54
235 242 9.530633 AATAGAACGCGACTATAATTTTTCTCT 57.469 29.630 15.93 0.00 31.43 3.10
246 253 6.034683 GTGTCAGAAAAATAGAACGCGACTAT 59.965 38.462 15.93 17.87 32.78 2.12
250 258 3.120616 CGTGTCAGAAAAATAGAACGCGA 59.879 43.478 15.93 0.00 32.57 5.87
275 283 3.118738 CCTTGTAGGATTTCGCTACTGGT 60.119 47.826 0.00 0.00 37.67 4.00
332 341 9.379770 TCATATTCATGTTATGAGTCTTAGGGA 57.620 33.333 13.56 0.00 40.94 4.20
413 422 9.250624 GCTCCATTGTAATAGAACTACTAGTTG 57.749 37.037 6.17 0.59 38.80 3.16
416 425 9.817809 TTTGCTCCATTGTAATAGAACTACTAG 57.182 33.333 0.00 0.00 34.35 2.57
425 434 8.081633 TGAACAAGTTTTGCTCCATTGTAATAG 58.918 33.333 0.00 0.00 33.17 1.73
528 537 7.328737 TCTAACTGAGGGCATTTAGAACTTAC 58.671 38.462 0.00 0.00 40.88 2.34
794 2543 7.119699 AGCGAGTAAATGAGTTCATTCAATGAA 59.880 33.333 8.85 8.85 45.06 2.57
943 2696 2.269241 CTTTCCACGGAGGCCCTC 59.731 66.667 0.73 0.73 37.29 4.30
952 2705 1.199624 GTGCTTGTTTGCTTTCCACG 58.800 50.000 0.00 0.00 0.00 4.94
1024 2777 3.865745 GCGAGAAGTAGCACATACAACAT 59.134 43.478 0.00 0.00 36.79 2.71
1258 3011 7.523293 TTACTGAATTTTGATCTGAGGCAAA 57.477 32.000 0.00 4.87 32.63 3.68
1423 3176 4.153117 GCCTCAATGCCATAATAGTTCTCG 59.847 45.833 0.00 0.00 0.00 4.04
1469 3222 4.081917 ACTTAATTGGCCGGGTTGTAAATG 60.082 41.667 2.18 0.00 0.00 2.32
1511 3264 4.043310 TGGTTTTCCATCTCCTCTGTTGAT 59.957 41.667 0.00 0.00 46.22 2.57
1513 3266 3.754965 TGGTTTTCCATCTCCTCTGTTG 58.245 45.455 0.00 0.00 46.22 3.33
1701 3454 4.377635 GGCGAGAAAGTTTACATACGCAAA 60.378 41.667 18.32 0.00 45.17 3.68
1705 3458 4.914312 TTGGCGAGAAAGTTTACATACG 57.086 40.909 0.00 0.00 0.00 3.06
1840 3645 6.345298 TCCATGTCTATTTGAAGTCGCATAA 58.655 36.000 0.00 0.00 0.00 1.90
1930 3735 7.331440 TGCATAAAATTCATTGGTGTTCACATC 59.669 33.333 5.32 0.00 0.00 3.06
1941 3746 8.871862 TCGGAAAAATCTGCATAAAATTCATTG 58.128 29.630 0.00 0.00 0.00 2.82
1943 3748 7.707893 CCTCGGAAAAATCTGCATAAAATTCAT 59.292 33.333 0.00 0.00 0.00 2.57
2183 3988 5.851177 CACACCTTGCTAACTTAAAATCACG 59.149 40.000 0.00 0.00 0.00 4.35
2189 3994 7.156673 CCTACTACACACCTTGCTAACTTAAA 58.843 38.462 0.00 0.00 0.00 1.52
2191 3996 5.186409 CCCTACTACACACCTTGCTAACTTA 59.814 44.000 0.00 0.00 0.00 2.24
2316 4121 5.705609 AGACACTTCCGTTTATTGCATTT 57.294 34.783 0.00 0.00 0.00 2.32
2328 4133 4.386867 TTGGCTATTCTAGACACTTCCG 57.613 45.455 0.00 0.00 45.21 4.30
2419 4224 5.393678 GGAGCTTAGAGGTAGACTTGTCTTG 60.394 48.000 8.66 0.00 0.00 3.02
2460 4265 1.893801 GAGGGACCTTGAAAGACTCGA 59.106 52.381 0.00 0.00 0.00 4.04
2553 4358 4.022416 TGTGAAGCATGTAACCATCCAAAC 60.022 41.667 0.00 0.00 0.00 2.93
2555 4360 3.758023 CTGTGAAGCATGTAACCATCCAA 59.242 43.478 0.00 0.00 0.00 3.53
2576 4381 4.478686 ACCCATAATCTTTGTAAGCCCTCT 59.521 41.667 0.00 0.00 0.00 3.69
2591 4396 3.118298 GCCATTTTTCAGCCACCCATAAT 60.118 43.478 0.00 0.00 0.00 1.28
2617 4422 1.838077 ACCACCACAATAGGTAGCCTC 59.162 52.381 0.00 0.00 40.77 4.70
2618 4423 1.838077 GACCACCACAATAGGTAGCCT 59.162 52.381 0.00 0.00 40.77 4.58
2683 4489 3.458487 ACGCCTCTTCCCTATTTTACCAT 59.542 43.478 0.00 0.00 0.00 3.55
2761 4567 7.617041 AAATTCTAATGTGAAGAGCCAGTAC 57.383 36.000 0.00 0.00 0.00 2.73
2807 4614 4.344679 AGTCATGGCCAACAAATCAAAAGA 59.655 37.500 10.96 0.00 0.00 2.52
2836 4643 9.614792 AAGTCAAGTACTCAACAAAAGTCTAAT 57.385 29.630 0.00 0.00 37.50 1.73
2852 4659 7.062255 GCATGGCTAATTTTTGAAGTCAAGTAC 59.938 37.037 0.00 0.00 37.15 2.73
2860 4667 6.339730 TGGTATGCATGGCTAATTTTTGAAG 58.660 36.000 10.16 0.00 0.00 3.02
2871 4678 4.107072 AGTCCTATATGGTATGCATGGCT 58.893 43.478 10.16 0.00 37.07 4.75
2886 4693 3.655972 ATGGGTCCCACATAGTCCTAT 57.344 47.619 14.57 0.00 35.80 2.57
2928 4735 7.944729 AGTGAAAGAGGCATACATATTGTTT 57.055 32.000 0.00 0.00 0.00 2.83
3003 4810 4.383552 GGGCCAAAATAATGCATTGTACCA 60.384 41.667 22.27 1.31 0.00 3.25
3014 4821 9.445973 TTCCTAATATTTCAGGGCCAAAATAAT 57.554 29.630 20.94 17.05 32.67 1.28
3017 4824 7.147497 CCTTTCCTAATATTTCAGGGCCAAAAT 60.147 37.037 17.57 17.57 32.40 1.82
3042 4849 7.440255 TCGCTTTTTAAATATGTAGTAGGAGCC 59.560 37.037 0.00 0.00 0.00 4.70
3083 4890 7.665559 TGCTTTCAACCTTTTAGTGATACTGAT 59.334 33.333 0.00 0.00 0.00 2.90
3090 4897 6.274157 TGTTTGCTTTCAACCTTTTAGTGA 57.726 33.333 0.00 0.00 30.75 3.41
3163 4970 7.881232 CCTAATTGTCCTTAAGGTTAAGTGTGA 59.119 37.037 21.04 0.00 38.73 3.58
3193 5000 5.880332 GGCTACTATGTTTCCAATGAGACAA 59.120 40.000 0.00 0.00 38.88 3.18
3310 5120 6.180472 CCATGGTAACTACTTTGGAACAGAT 58.820 40.000 2.57 0.00 37.19 2.90
3313 5123 5.067273 CACCATGGTAACTACTTTGGAACA 58.933 41.667 19.28 0.00 34.51 3.18
3320 5130 6.938596 GGTTTAGTTCACCATGGTAACTACTT 59.061 38.462 28.21 16.63 35.90 2.24
3322 5132 6.232692 TGGTTTAGTTCACCATGGTAACTAC 58.767 40.000 28.21 23.66 39.53 2.73
3325 5135 6.584185 ATTGGTTTAGTTCACCATGGTAAC 57.416 37.500 19.28 20.18 44.05 2.50
3329 5139 7.461182 TTCTTATTGGTTTAGTTCACCATGG 57.539 36.000 11.19 11.19 44.05 3.66
3482 5292 3.125146 TCGATGATGTCTTTTGAAAGCCG 59.875 43.478 0.00 0.00 35.99 5.52
3578 5388 3.068873 TGGGCAACATGTTTACCTTGAAC 59.931 43.478 22.29 10.17 39.74 3.18
3638 5448 4.465410 TCCCCTTCCCCATCCCCC 62.465 72.222 0.00 0.00 0.00 5.40
3639 5449 2.778717 CTCCCCTTCCCCATCCCC 60.779 72.222 0.00 0.00 0.00 4.81
3725 5536 8.862325 ACAATGTTCACTATAGTTTGATTCCA 57.138 30.769 17.22 6.04 0.00 3.53
3739 5550 2.494059 CGGGACTCAACAATGTTCACT 58.506 47.619 0.00 0.00 0.00 3.41
3758 5569 1.507141 GAGTTCACAGGGTTGGTGCG 61.507 60.000 0.00 0.00 36.22 5.34
3889 5701 3.316029 TCTCCAAAAATATGCTGCATCCG 59.684 43.478 19.90 2.50 0.00 4.18
3897 5709 4.212636 GCATGGCATTCTCCAAAAATATGC 59.787 41.667 0.00 0.00 39.96 3.14
3938 5750 2.164624 GTGAGTCGCAGTCAGGAATAGT 59.835 50.000 0.00 0.00 0.00 2.12
3970 5782 7.867305 TTTGTAACTTTATGGAGTGACAACA 57.133 32.000 10.97 3.64 45.99 3.33
4011 5823 3.877508 CAGGGGCTAATTAAGTAGTGCAC 59.122 47.826 9.40 9.40 0.00 4.57
4031 5843 9.926751 CTAATAGACATAAAATTGCTGTCACAG 57.073 33.333 0.00 0.00 41.34 3.66
4094 5906 1.616374 GTCTGATAGACTGGGCCTAGC 59.384 57.143 17.38 9.22 41.88 3.42
4108 5920 6.058553 TCATTTCAGTTGATGGAGTCTGAT 57.941 37.500 0.00 0.00 36.91 2.90
4410 6222 2.136298 TGGCTTTTGGTGAGACACAA 57.864 45.000 0.00 0.00 35.86 3.33
4435 6247 0.905357 CACTTCCCATCGGAGGACTT 59.095 55.000 0.00 0.00 40.10 3.01
4623 6435 5.311265 ACATCCAGGTATAATCAGCACATG 58.689 41.667 0.00 0.00 0.00 3.21
4636 6448 4.122337 ACATATACGGGACATCCAGGTA 57.878 45.455 3.04 3.69 37.91 3.08
4638 6450 4.087182 AGTACATATACGGGACATCCAGG 58.913 47.826 3.04 0.00 36.33 4.45
4758 6735 2.925966 ATTCACCCACCATGACCATT 57.074 45.000 0.00 0.00 0.00 3.16
4765 6742 2.456577 GTTGCCTAATTCACCCACCAT 58.543 47.619 0.00 0.00 0.00 3.55
4772 6749 9.780186 ACTTCTATAATAGGTTGCCTAATTCAC 57.220 33.333 0.00 0.00 39.77 3.18
4992 6969 8.770010 TTTTTGTATTTTCCCCTCTAACTTCA 57.230 30.769 0.00 0.00 0.00 3.02
5042 7020 0.317479 GGTGGTGTTCGCTACTCACT 59.683 55.000 0.00 0.00 34.43 3.41
5085 7063 5.483231 TGACTCCAAGATGATGACTTTCTCT 59.517 40.000 0.00 0.00 0.00 3.10
5112 7090 1.475280 GGCTCTATGTACACCGTCACA 59.525 52.381 0.00 0.00 0.00 3.58
5201 7179 4.023450 CCTTAGTGTCTCACGTGTGTTCTA 60.023 45.833 16.51 13.30 39.64 2.10
5344 7322 6.983890 GTCCACCAAATCAACAACATAAAAGT 59.016 34.615 0.00 0.00 0.00 2.66
5354 7332 3.743521 CTCTCTGTCCACCAAATCAACA 58.256 45.455 0.00 0.00 0.00 3.33
5369 7347 3.501445 CCAAAAGGACTTGAAGCTCTCTG 59.499 47.826 0.00 0.00 0.00 3.35
5416 7394 7.148239 GGTTGGACACTTGGTAGAATTTAGATG 60.148 40.741 0.00 0.00 0.00 2.90
5423 7401 4.724279 AAGGTTGGACACTTGGTAGAAT 57.276 40.909 0.00 0.00 0.00 2.40
5450 7428 7.014808 GGATAAGCACTAGACCAGATCTACTTT 59.985 40.741 0.00 0.00 39.04 2.66
5470 7448 1.912043 CTATGGGAGGCAGGGGATAAG 59.088 57.143 0.00 0.00 0.00 1.73
5494 7472 5.360999 GCCCTTGCAATATAAAAGGAGAACT 59.639 40.000 0.00 0.00 42.65 3.01
5518 7496 4.181578 CTCCTTCGTAACAACTATGGTGG 58.818 47.826 0.00 0.00 0.00 4.61
5524 7502 2.028748 GTGCCCTCCTTCGTAACAACTA 60.029 50.000 0.00 0.00 0.00 2.24
5535 7513 1.151899 TGTGGTAGGTGCCCTCCTT 60.152 57.895 0.00 0.00 38.86 3.36


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

AutoCloner maintained by Alex Coulton.