Multiple sequence alignment - TraesCS4A01G109000

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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 TraesCS4A01G109000 chr4A 100.000 5406 0 0 1 5406 129085595 129091000 0.000000e+00 9984.0
1 TraesCS4A01G109000 chr4D 95.709 4568 140 18 865 5406 340090679 340086142 0.000000e+00 7299.0
2 TraesCS4A01G109000 chr4D 88.509 818 74 10 1 799 340095936 340095120 0.000000e+00 972.0
3 TraesCS4A01G109000 chr4D 90.566 53 4 1 1582 1633 497681528 497681580 9.720000e-08 69.4
4 TraesCS4A01G109000 chr4B 95.786 4532 124 21 909 5406 420201571 420197073 0.000000e+00 7249.0
5 TraesCS4A01G109000 chr1A 88.073 218 23 3 2059 2276 147913353 147913139 6.950000e-64 255.0
6 TraesCS4A01G109000 chr7D 86.784 227 26 4 2059 2285 423419358 423419136 3.230000e-62 250.0
7 TraesCS4A01G109000 chr3B 87.156 218 25 3 2059 2276 30335333 30335119 1.500000e-60 244.0
8 TraesCS4A01G109000 chr2D 75.815 368 74 11 2406 2758 35260570 35260937 7.200000e-39 172.0
9 TraesCS4A01G109000 chr2A 76.540 341 64 14 2434 2758 38537348 38537008 7.200000e-39 172.0
10 TraesCS4A01G109000 chr2B 75.281 356 72 14 2419 2758 58322355 58322710 7.250000e-34 156.0
11 TraesCS4A01G109000 chr3A 92.222 90 7 0 2192 2281 7207639 7207728 1.580000e-25 128.0


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 TraesCS4A01G109000 chr4A 129085595 129091000 5405 False 9984 9984 100.000 1 5406 1 chr4A.!!$F1 5405
1 TraesCS4A01G109000 chr4D 340086142 340090679 4537 True 7299 7299 95.709 865 5406 1 chr4D.!!$R1 4541
2 TraesCS4A01G109000 chr4D 340095120 340095936 816 True 972 972 88.509 1 799 1 chr4D.!!$R2 798
3 TraesCS4A01G109000 chr4B 420197073 420201571 4498 True 7249 7249 95.786 909 5406 1 chr4B.!!$R1 4497

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 0.320421 ACCTTTCGGTGGACATGACG 60.320 55.000 0.00 0.0 43.51 4.35 F
896 915 0.461961 CTTAACCGCTCCTCCTCCTG 59.538 60.000 0.00 0.0 0.00 3.86 F
980 1000 0.881118 GCCCTCAAAACTCGCAATGA 59.119 50.000 0.00 0.0 0.00 2.57 F
2008 2035 1.262683 GATTAGCATGACAAGCTCCGC 59.737 52.381 8.73 0.0 42.32 5.54 F
3090 3120 2.210116 TCTCTTGTTGACGCCTTGAAC 58.790 47.619 0.00 0.0 0.00 3.18 F
3102 3132 0.320771 CCTTGAACAGTGACCCGGAG 60.321 60.000 0.73 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1421 0.992695 TGAGGTCCTCGGAGAAGAGA 59.007 55.000 14.34 0.00 40.57 3.10 R
2079 2106 1.134007 TCATGTCATGATGGACCTGGC 60.134 52.381 11.62 0.00 36.97 4.85 R
2969 2999 4.720649 TCTTCATCTACACCTCTTTCGG 57.279 45.455 0.00 0.00 0.00 4.30 R
3102 3132 1.809684 AACTGAGGCGCCTAACTTTC 58.190 50.000 32.97 17.17 0.00 2.62 R
4261 4311 0.168348 AGTCGTCCTCGTTCACATCG 59.832 55.000 0.00 0.00 38.33 3.84 R
4818 4868 0.388659 CCGAGGATGCAGAGGAGAAG 59.611 60.000 0.00 0.00 0.00 2.85 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
42 43 6.672657 ACACAGGAGTACAATATTACCTCCTT 59.327 38.462 19.62 12.41 37.72 3.36
43 44 7.147707 ACACAGGAGTACAATATTACCTCCTTC 60.148 40.741 19.62 0.62 37.72 3.46
46 47 6.264970 AGGAGTACAATATTACCTCCTTCGAC 59.735 42.308 17.72 0.78 36.56 4.20
55 56 4.689549 TCCTTCGACGAGGGCCCA 62.690 66.667 27.56 0.00 37.41 5.36
59 60 3.540367 TTCGACGAGGGCCCAAACC 62.540 63.158 27.56 9.46 0.00 3.27
88 89 5.745312 ATTCCTTGTGTGTACTCTCATCA 57.255 39.130 0.98 0.00 0.00 3.07
101 102 4.759782 ACTCTCATCAATACCTTTCGGTG 58.240 43.478 0.00 0.00 45.18 4.94
110 111 0.320421 ACCTTTCGGTGGACATGACG 60.320 55.000 0.00 0.00 43.51 4.35
126 127 1.278985 TGACGCTCCTCCAATCACAAT 59.721 47.619 0.00 0.00 0.00 2.71
133 134 5.486526 GCTCCTCCAATCACAATCCTATAG 58.513 45.833 0.00 0.00 0.00 1.31
136 137 5.544176 TCCTCCAATCACAATCCTATAGGTC 59.456 44.000 18.51 0.00 36.34 3.85
144 145 5.053145 CACAATCCTATAGGTCTTGTCAGC 58.947 45.833 26.14 0.00 38.83 4.26
151 152 6.493802 TCCTATAGGTCTTGTCAGCGAAATAT 59.506 38.462 18.51 0.00 36.34 1.28
155 156 6.412362 AGGTCTTGTCAGCGAAATATCTAT 57.588 37.500 0.00 0.00 0.00 1.98
158 159 6.144724 GGTCTTGTCAGCGAAATATCTATGAC 59.855 42.308 0.00 0.00 38.32 3.06
161 162 6.149129 TGTCAGCGAAATATCTATGACAGT 57.851 37.500 1.92 0.00 40.64 3.55
167 168 4.745125 CGAAATATCTATGACAGTTGGCGT 59.255 41.667 0.00 0.00 0.00 5.68
178 179 2.120909 GTTGGCGTCCATCATGGGG 61.121 63.158 3.05 0.00 38.32 4.96
186 187 0.685131 TCCATCATGGGGCAAGCTTG 60.685 55.000 22.44 22.44 38.32 4.01
203 204 1.532868 CTTGTATGGAAGCTATGGCGC 59.467 52.381 0.00 0.00 44.37 6.53
217 218 1.375908 GGCGCTGATGGTGTCTTCA 60.376 57.895 7.64 0.00 0.00 3.02
222 223 1.929836 GCTGATGGTGTCTTCATCGTC 59.070 52.381 0.00 0.00 42.73 4.20
230 231 4.202212 TGGTGTCTTCATCGTCTTCTTTCA 60.202 41.667 0.00 0.00 0.00 2.69
245 246 2.223144 TCTTTCAACAACATTCGCTCCG 59.777 45.455 0.00 0.00 0.00 4.63
249 250 0.953960 AACAACATTCGCTCCGGGAC 60.954 55.000 0.00 0.00 0.00 4.46
260 261 2.678934 CCGGGACCCTCGAGTTCA 60.679 66.667 12.31 0.00 0.00 3.18
287 288 1.760613 ACGAGTCAGTGTGGGAAAGAA 59.239 47.619 0.00 0.00 0.00 2.52
291 292 1.420138 GTCAGTGTGGGAAAGAAGGGA 59.580 52.381 0.00 0.00 0.00 4.20
292 293 2.131854 TCAGTGTGGGAAAGAAGGGAA 58.868 47.619 0.00 0.00 0.00 3.97
309 310 2.899900 GGGAAAAAGAAAGGTGGCTCAT 59.100 45.455 0.00 0.00 0.00 2.90
311 312 3.366374 GGAAAAAGAAAGGTGGCTCATCG 60.366 47.826 0.00 0.00 0.00 3.84
313 314 2.859165 AAGAAAGGTGGCTCATCGAA 57.141 45.000 0.00 0.00 0.00 3.71
337 338 0.984961 TCCAATCTGAGCTCAGGGGG 60.985 60.000 36.92 32.17 43.91 5.40
438 439 1.883084 CCTCCGCAATGGACGTAGC 60.883 63.158 0.00 0.00 43.74 3.58
465 466 1.827969 CGGAGAAGAAGAGGGACATGT 59.172 52.381 0.00 0.00 0.00 3.21
466 467 2.159170 CGGAGAAGAAGAGGGACATGTC 60.159 54.545 17.91 17.91 0.00 3.06
467 468 3.103742 GGAGAAGAAGAGGGACATGTCT 58.896 50.000 24.50 6.55 0.00 3.41
469 470 3.766591 GAGAAGAAGAGGGACATGTCTGA 59.233 47.826 24.50 0.00 0.00 3.27
471 472 2.894731 AGAAGAGGGACATGTCTGACA 58.105 47.619 24.50 13.60 0.00 3.58
478 479 3.490759 CATGTCTGACACGGCGGC 61.491 66.667 13.50 0.00 0.00 6.53
518 521 1.783031 ATGACCCGCGCTAGTAGTCG 61.783 60.000 5.56 8.92 0.00 4.18
522 525 2.024305 CGCGCTAGTAGTCGGTGG 59.976 66.667 5.56 0.00 0.00 4.61
547 565 2.620112 CCTGGCACCTTGAACGCAG 61.620 63.158 0.00 0.00 0.00 5.18
556 574 0.813610 CTTGAACGCAGTGACCCACA 60.814 55.000 0.00 0.00 45.00 4.17
588 606 3.659089 ATGAACCGAACCTCCCGCG 62.659 63.158 0.00 0.00 0.00 6.46
593 611 2.777972 CCGAACCTCCCGCGTCATA 61.778 63.158 4.92 0.00 0.00 2.15
674 692 2.771639 CGAGACATCGCCGAGGGAA 61.772 63.158 3.07 0.00 42.97 3.97
688 706 3.413327 CGAGGGAAAGATAGAGGATCGA 58.587 50.000 0.00 0.00 42.67 3.59
719 737 3.487376 CGGATTGATTGATTGGACGGTTG 60.487 47.826 0.00 0.00 0.00 3.77
730 748 1.339247 TGGACGGTTGGCGTCATATTT 60.339 47.619 0.00 0.00 38.04 1.40
753 771 3.623510 GCTCGGAAATCTTAAGGAACTGG 59.376 47.826 1.85 0.00 40.86 4.00
757 775 4.336280 GGAAATCTTAAGGAACTGGTGCT 58.664 43.478 1.85 0.00 40.86 4.40
777 796 9.075678 TGGTGCTAGTTCTATAGTAGTATTTCC 57.924 37.037 0.00 2.01 33.11 3.13
795 814 9.811995 AGTATTTCCAAAAAGAAAAAGGTGTAC 57.188 29.630 0.00 0.00 39.11 2.90
799 818 9.810545 TTTCCAAAAAGAAAAAGGTGTACTATG 57.189 29.630 0.00 0.00 32.90 2.23
800 819 8.528044 TCCAAAAAGAAAAAGGTGTACTATGT 57.472 30.769 0.00 0.00 0.00 2.29
801 820 8.973182 TCCAAAAAGAAAAAGGTGTACTATGTT 58.027 29.630 0.00 0.00 0.00 2.71
843 862 9.936759 AAAAAGGAAAAGAAAATCTTGTACACA 57.063 25.926 0.00 0.00 36.71 3.72
844 863 9.936759 AAAAGGAAAAGAAAATCTTGTACACAA 57.063 25.926 0.00 0.00 36.71 3.33
858 877 7.589958 CTTGTACACAAGTATAGAGAGGGAT 57.410 40.000 12.93 0.00 46.11 3.85
859 878 7.584122 TTGTACACAAGTATAGAGAGGGATC 57.416 40.000 0.00 0.00 31.84 3.36
860 879 6.669631 TGTACACAAGTATAGAGAGGGATCA 58.330 40.000 0.00 0.00 31.84 2.92
861 880 7.123383 TGTACACAAGTATAGAGAGGGATCAA 58.877 38.462 0.00 0.00 31.84 2.57
862 881 7.618117 TGTACACAAGTATAGAGAGGGATCAAA 59.382 37.037 0.00 0.00 31.84 2.69
863 882 7.118496 ACACAAGTATAGAGAGGGATCAAAG 57.882 40.000 0.00 0.00 0.00 2.77
879 898 3.942829 TCAAAGATGAATGGCGAGACTT 58.057 40.909 0.00 0.00 30.99 3.01
896 915 0.461961 CTTAACCGCTCCTCCTCCTG 59.538 60.000 0.00 0.00 0.00 3.86
912 931 2.737252 CTCCTGGAAGTTACAAACTCGC 59.263 50.000 0.00 0.00 41.91 5.03
980 1000 0.881118 GCCCTCAAAACTCGCAATGA 59.119 50.000 0.00 0.00 0.00 2.57
1401 1421 2.199236 GTCGACGACTTCCACAACTTT 58.801 47.619 20.52 0.00 0.00 2.66
1933 1960 5.907207 TGACTAGCTGTATCTGAATGTTCC 58.093 41.667 0.00 0.00 0.00 3.62
2008 2035 1.262683 GATTAGCATGACAAGCTCCGC 59.737 52.381 8.73 0.00 42.32 5.54
2079 2106 5.390885 CCGTTGACTGTAAATCTCATGGTTG 60.391 44.000 0.00 0.00 0.00 3.77
2173 2200 3.689347 TGGCAATCAACTTAGCAGTGAT 58.311 40.909 0.00 0.00 31.60 3.06
2310 2337 6.830873 ATGACAAATCCTTCCTTCAAGAAG 57.169 37.500 2.83 2.83 42.46 2.85
2456 2485 7.949903 TTGAAATGTTTGACATCCATCAAAG 57.050 32.000 1.30 0.00 46.53 2.77
3002 3032 7.070946 AGGTGTAGATGAAGATGATGAACAGAT 59.929 37.037 0.00 0.00 0.00 2.90
3090 3120 2.210116 TCTCTTGTTGACGCCTTGAAC 58.790 47.619 0.00 0.00 0.00 3.18
3102 3132 0.320771 CCTTGAACAGTGACCCGGAG 60.321 60.000 0.73 0.00 0.00 4.63
3154 3184 1.005867 CTTGCAAAAGTGGCGGCAT 60.006 52.632 17.19 0.00 35.98 4.40
3197 3227 9.880157 AGTGAGGTTCGCTTAGTAAATTTATTA 57.120 29.630 0.31 0.00 32.48 0.98
3223 3253 3.591527 TGACCAGGAAACAATGTAGGGAT 59.408 43.478 0.00 0.00 0.00 3.85
3238 3268 9.376075 CAATGTAGGGATACAGTCATATCATTC 57.624 37.037 0.00 0.00 33.83 2.67
3293 3323 6.763610 CCACTTCTCTTTGTCTTACTGAAGTT 59.236 38.462 0.00 0.00 40.06 2.66
3422 3452 1.597797 ATGGTGCTCAAATGGTGGCG 61.598 55.000 0.00 0.00 0.00 5.69
3489 3524 7.733402 TTGTGTTTGGATACCTACTGTTTAC 57.267 36.000 0.00 0.00 0.00 2.01
3602 3637 3.559655 TGTGCTATGTTCGTTATCCATGC 59.440 43.478 0.00 0.00 0.00 4.06
3622 3657 2.663063 GCGCTCTTCAGTTGTTGCTAAC 60.663 50.000 0.00 0.00 0.00 2.34
3652 3687 3.683802 TGCCATTTTATTTTTGCAGGGG 58.316 40.909 0.00 0.00 0.00 4.79
3730 3765 5.415701 TGGCTATGTGAAGAAACCAGATTTC 59.584 40.000 0.00 0.00 46.21 2.17
3787 3822 1.816835 CCGACAGCAGACTTACCTGTA 59.183 52.381 0.00 0.00 39.72 2.74
3831 3866 5.830799 AATGCATTCCTTCCTTTCCTTTT 57.169 34.783 5.99 0.00 0.00 2.27
3832 3867 5.830799 ATGCATTCCTTCCTTTCCTTTTT 57.169 34.783 0.00 0.00 0.00 1.94
3834 3869 4.237724 GCATTCCTTCCTTTCCTTTTTCG 58.762 43.478 0.00 0.00 0.00 3.46
3865 3900 4.601315 GAAACGGGTTTCACGTGC 57.399 55.556 11.67 0.00 46.03 5.34
3979 4014 6.543430 TTTATGCAAAGGTATTGCCAGAAT 57.457 33.333 10.34 0.81 44.32 2.40
3986 4021 3.614092 AGGTATTGCCAGAATCACTGTG 58.386 45.455 0.17 0.17 44.40 3.66
4030 4066 3.077359 AGAATCGGAAAAGAAGTGCCAG 58.923 45.455 0.00 0.00 0.00 4.85
4076 4126 3.743911 TGTATACAAGTGAACGCCAACTG 59.256 43.478 2.20 0.00 0.00 3.16
4261 4311 0.666577 GTGTGGAGGTGCACGAGTAC 60.667 60.000 11.45 8.24 0.00 2.73
4463 4513 2.981805 GCATTGCACATGTGTTGTAGTG 59.018 45.455 26.01 16.69 36.57 2.74
4527 4577 5.530519 TTGATTTGTCGCAGATGTAAGAC 57.469 39.130 0.00 0.00 40.67 3.01
4556 4606 1.804748 GGCTGGTAGAACCGTGAAAAG 59.195 52.381 0.00 0.00 42.58 2.27
4622 4672 1.860950 CGTGCGATCAGGAATGTAAGG 59.139 52.381 0.00 0.00 0.00 2.69
4656 4706 2.695359 GACGGTGCTGATTGAACCTAA 58.305 47.619 0.00 0.00 42.49 2.69
4728 4778 4.016706 AAGGGCAAGGGGACGACG 62.017 66.667 0.00 0.00 0.00 5.12
4827 4877 3.780173 GCCGCCTGCTTCTCCTCT 61.780 66.667 0.00 0.00 36.87 3.69
4836 4886 0.249405 GCTTCTCCTCTGCATCCTCG 60.249 60.000 0.00 0.00 0.00 4.63
4845 4895 4.148825 GCATCCTCGGGCGTGTCT 62.149 66.667 0.00 0.00 0.00 3.41
4959 5018 2.300967 GGTGGAGGTCATGGGCTCA 61.301 63.158 0.00 0.00 0.00 4.26
5239 5298 7.997915 AGGCCTCAGGTAATTAGTAGACTATA 58.002 38.462 0.00 0.00 0.00 1.31
5240 5299 8.625571 AGGCCTCAGGTAATTAGTAGACTATAT 58.374 37.037 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.069085 GGAGGTAATATTGTACTCCTGTGTGTA 59.931 40.741 19.52 0.00 0.00 2.90
19 20 6.040616 CGAAGGAGGTAATATTGTACTCCTGT 59.959 42.308 25.44 18.84 39.49 4.00
42 43 4.011517 GGTTTGGGCCCTCGTCGA 62.012 66.667 25.70 0.00 0.00 4.20
43 44 4.016706 AGGTTTGGGCCCTCGTCG 62.017 66.667 25.70 0.00 0.00 5.12
46 47 0.034477 AATACAGGTTTGGGCCCTCG 60.034 55.000 25.70 7.23 0.00 4.63
55 56 8.161425 AGTACACACAAGGAATAATACAGGTTT 58.839 33.333 0.00 0.00 0.00 3.27
59 60 8.251026 TGAGAGTACACACAAGGAATAATACAG 58.749 37.037 0.00 0.00 0.00 2.74
101 102 0.179000 ATTGGAGGAGCGTCATGTCC 59.821 55.000 0.00 0.00 0.00 4.02
110 111 2.725221 AGGATTGTGATTGGAGGAGC 57.275 50.000 0.00 0.00 0.00 4.70
126 127 3.292492 TCGCTGACAAGACCTATAGGA 57.708 47.619 26.01 0.00 38.94 2.94
133 134 6.144724 GTCATAGATATTTCGCTGACAAGACC 59.855 42.308 12.70 0.00 37.74 3.85
136 137 6.699204 ACTGTCATAGATATTTCGCTGACAAG 59.301 38.462 17.57 14.83 42.40 3.16
144 145 4.745125 ACGCCAACTGTCATAGATATTTCG 59.255 41.667 0.00 0.00 0.00 3.46
151 152 1.262417 TGGACGCCAACTGTCATAGA 58.738 50.000 0.00 0.00 38.10 1.98
155 156 0.324614 ATGATGGACGCCAACTGTCA 59.675 50.000 2.68 3.15 36.95 3.58
158 159 1.378882 CCCATGATGGACGCCAACTG 61.379 60.000 14.26 0.00 40.96 3.16
161 162 2.275089 CCCCATGATGGACGCCAA 59.725 61.111 14.26 0.00 40.96 4.52
167 168 0.685131 CAAGCTTGCCCCATGATGGA 60.685 55.000 14.26 0.00 40.96 3.41
186 187 1.151668 CAGCGCCATAGCTTCCATAC 58.848 55.000 2.29 0.00 46.80 2.39
201 202 0.926155 CGATGAAGACACCATCAGCG 59.074 55.000 0.00 0.00 46.87 5.18
203 204 3.516981 AGACGATGAAGACACCATCAG 57.483 47.619 0.00 0.00 40.17 2.90
217 218 5.679906 CGAATGTTGTTGAAAGAAGACGAT 58.320 37.500 0.00 0.00 0.00 3.73
222 223 4.222114 GGAGCGAATGTTGTTGAAAGAAG 58.778 43.478 0.00 0.00 0.00 2.85
230 231 0.953960 GTCCCGGAGCGAATGTTGTT 60.954 55.000 0.73 0.00 0.00 2.83
245 246 1.592223 CTGTGAACTCGAGGGTCCC 59.408 63.158 18.41 0.00 0.00 4.46
249 250 2.125912 CCGCTGTGAACTCGAGGG 60.126 66.667 18.41 1.19 0.00 4.30
260 261 2.194212 ACACTGACTCGTCCGCTGT 61.194 57.895 0.00 0.00 0.00 4.40
287 288 2.091333 TGAGCCACCTTTCTTTTTCCCT 60.091 45.455 0.00 0.00 0.00 4.20
291 292 3.486383 TCGATGAGCCACCTTTCTTTTT 58.514 40.909 0.00 0.00 0.00 1.94
292 293 3.140325 TCGATGAGCCACCTTTCTTTT 57.860 42.857 0.00 0.00 0.00 2.27
337 338 2.266055 CTCAGTTGCCCTCCGGTC 59.734 66.667 0.00 0.00 0.00 4.79
341 342 2.045536 CCAGCTCAGTTGCCCTCC 60.046 66.667 0.00 0.00 0.00 4.30
423 424 1.743623 TTGGCTACGTCCATTGCGG 60.744 57.895 0.00 0.00 35.77 5.69
425 426 1.064060 GATGTTGGCTACGTCCATTGC 59.936 52.381 9.74 0.00 36.89 3.56
428 429 0.179084 CCGATGTTGGCTACGTCCAT 60.179 55.000 14.23 0.00 39.22 3.41
438 439 2.419297 CCCTCTTCTTCTCCGATGTTGG 60.419 54.545 0.00 0.00 0.00 3.77
580 598 3.102515 CGTAATATGACGCGGGAGG 57.897 57.895 12.47 0.00 35.79 4.30
588 606 2.480845 GAGGGTGGTGCGTAATATGAC 58.519 52.381 0.00 0.00 0.00 3.06
593 611 2.125269 GCGAGGGTGGTGCGTAAT 60.125 61.111 0.00 0.00 0.00 1.89
657 675 0.528684 CTTTCCCTCGGCGATGTCTC 60.529 60.000 11.27 0.00 0.00 3.36
666 684 2.490115 CGATCCTCTATCTTTCCCTCGG 59.510 54.545 0.00 0.00 31.87 4.63
719 737 1.295792 TTCCGAGCAAATATGACGCC 58.704 50.000 0.00 0.00 0.00 5.68
730 748 4.253685 CAGTTCCTTAAGATTTCCGAGCA 58.746 43.478 3.36 0.00 0.00 4.26
817 836 9.936759 TGTGTACAAGATTTTCTTTTCCTTTTT 57.063 25.926 0.00 0.00 33.78 1.94
818 837 9.936759 TTGTGTACAAGATTTTCTTTTCCTTTT 57.063 25.926 0.00 0.00 33.78 2.27
835 854 7.123383 TGATCCCTCTCTATACTTGTGTACAA 58.877 38.462 0.00 0.00 0.00 2.41
836 855 6.669631 TGATCCCTCTCTATACTTGTGTACA 58.330 40.000 0.00 0.00 0.00 2.90
837 856 7.584122 TTGATCCCTCTCTATACTTGTGTAC 57.416 40.000 0.00 0.00 0.00 2.90
838 857 8.059461 TCTTTGATCCCTCTCTATACTTGTGTA 58.941 37.037 0.00 0.00 0.00 2.90
839 858 6.897966 TCTTTGATCCCTCTCTATACTTGTGT 59.102 38.462 0.00 0.00 0.00 3.72
840 859 7.353414 TCTTTGATCCCTCTCTATACTTGTG 57.647 40.000 0.00 0.00 0.00 3.33
841 860 7.786943 TCATCTTTGATCCCTCTCTATACTTGT 59.213 37.037 0.00 0.00 0.00 3.16
842 861 8.187913 TCATCTTTGATCCCTCTCTATACTTG 57.812 38.462 0.00 0.00 0.00 3.16
843 862 8.789767 TTCATCTTTGATCCCTCTCTATACTT 57.210 34.615 0.00 0.00 0.00 2.24
844 863 8.814931 CATTCATCTTTGATCCCTCTCTATACT 58.185 37.037 0.00 0.00 0.00 2.12
845 864 8.040132 CCATTCATCTTTGATCCCTCTCTATAC 58.960 40.741 0.00 0.00 0.00 1.47
846 865 7.310921 GCCATTCATCTTTGATCCCTCTCTATA 60.311 40.741 0.00 0.00 0.00 1.31
847 866 6.522114 GCCATTCATCTTTGATCCCTCTCTAT 60.522 42.308 0.00 0.00 0.00 1.98
848 867 5.221803 GCCATTCATCTTTGATCCCTCTCTA 60.222 44.000 0.00 0.00 0.00 2.43
849 868 4.446023 GCCATTCATCTTTGATCCCTCTCT 60.446 45.833 0.00 0.00 0.00 3.10
850 869 3.819902 GCCATTCATCTTTGATCCCTCTC 59.180 47.826 0.00 0.00 0.00 3.20
851 870 3.746751 CGCCATTCATCTTTGATCCCTCT 60.747 47.826 0.00 0.00 0.00 3.69
852 871 2.551459 CGCCATTCATCTTTGATCCCTC 59.449 50.000 0.00 0.00 0.00 4.30
853 872 2.173356 TCGCCATTCATCTTTGATCCCT 59.827 45.455 0.00 0.00 0.00 4.20
854 873 2.551459 CTCGCCATTCATCTTTGATCCC 59.449 50.000 0.00 0.00 0.00 3.85
855 874 3.249559 GTCTCGCCATTCATCTTTGATCC 59.750 47.826 0.00 0.00 0.00 3.36
856 875 4.125703 AGTCTCGCCATTCATCTTTGATC 58.874 43.478 0.00 0.00 0.00 2.92
857 876 4.148128 AGTCTCGCCATTCATCTTTGAT 57.852 40.909 0.00 0.00 0.00 2.57
858 877 3.616956 AGTCTCGCCATTCATCTTTGA 57.383 42.857 0.00 0.00 0.00 2.69
859 878 5.447818 GGTTAAGTCTCGCCATTCATCTTTG 60.448 44.000 0.00 0.00 0.00 2.77
860 879 4.636206 GGTTAAGTCTCGCCATTCATCTTT 59.364 41.667 0.00 0.00 0.00 2.52
861 880 4.192317 GGTTAAGTCTCGCCATTCATCTT 58.808 43.478 0.00 0.00 0.00 2.40
862 881 3.738281 CGGTTAAGTCTCGCCATTCATCT 60.738 47.826 0.00 0.00 0.00 2.90
863 882 2.540101 CGGTTAAGTCTCGCCATTCATC 59.460 50.000 0.00 0.00 0.00 2.92
879 898 1.381327 CCAGGAGGAGGAGCGGTTA 60.381 63.158 0.00 0.00 36.89 2.85
896 915 2.074576 GGAGGCGAGTTTGTAACTTCC 58.925 52.381 0.00 0.00 43.03 3.46
985 1005 4.265073 CTCTCCATTTTGGGATTTCTCGT 58.735 43.478 0.00 0.00 38.32 4.18
1037 1057 2.047179 GGGGAAGGAGACGTGTGC 60.047 66.667 0.00 0.00 0.00 4.57
1050 1070 4.958158 TCGTTTGGTCCCCGGGGA 62.958 66.667 39.67 39.67 42.90 4.81
1260 1280 3.231736 CCGGTGGCGGCTAGGTAT 61.232 66.667 11.43 0.00 0.00 2.73
1383 1403 2.470821 AGAAAGTTGTGGAAGTCGTCG 58.529 47.619 0.00 0.00 0.00 5.12
1386 1406 4.372656 AGAAGAGAAAGTTGTGGAAGTCG 58.627 43.478 0.00 0.00 0.00 4.18
1401 1421 0.992695 TGAGGTCCTCGGAGAAGAGA 59.007 55.000 14.34 0.00 40.57 3.10
1679 1700 5.237344 CAGCATCTAAGTAGTATTTGGCACC 59.763 44.000 0.00 0.00 0.00 5.01
1933 1960 4.836125 ATAAAGCAGATAATGGCCAACG 57.164 40.909 10.96 0.00 0.00 4.10
2079 2106 1.134007 TCATGTCATGATGGACCTGGC 60.134 52.381 11.62 0.00 36.97 4.85
2173 2200 5.628797 TGATTATGGGAGCATCACTACAA 57.371 39.130 0.00 0.00 41.12 2.41
2969 2999 4.720649 TCTTCATCTACACCTCTTTCGG 57.279 45.455 0.00 0.00 0.00 4.30
3090 3120 2.353803 CCTAACTTTCTCCGGGTCACTG 60.354 54.545 0.00 0.00 0.00 3.66
3102 3132 1.809684 AACTGAGGCGCCTAACTTTC 58.190 50.000 32.97 17.17 0.00 2.62
3154 3184 3.361786 TCACTATCTTCGGACCATGACA 58.638 45.455 0.00 0.00 0.00 3.58
3197 3227 5.245977 CCCTACATTGTTTCCTGGTCAATTT 59.754 40.000 0.00 8.03 30.74 1.82
3203 3233 4.538490 TGTATCCCTACATTGTTTCCTGGT 59.462 41.667 0.00 0.00 32.88 4.00
3213 3243 8.543774 GGAATGATATGACTGTATCCCTACATT 58.456 37.037 0.00 0.00 37.24 2.71
3223 3253 7.770433 CACAGAAAAGGGAATGATATGACTGTA 59.230 37.037 0.00 0.00 33.46 2.74
3238 3268 5.906073 ACAGTTTTGATTCACAGAAAAGGG 58.094 37.500 0.00 0.00 0.00 3.95
3293 3323 5.735922 GCTGCTTGTAACAAACAGGATGAAA 60.736 40.000 0.00 0.00 39.69 2.69
3489 3524 4.403752 TCACATCCTGTAACTGGAGATCTG 59.596 45.833 0.00 0.00 35.07 2.90
3516 3551 3.377172 ACCATAACGCAACTAATCAAGGC 59.623 43.478 0.00 0.00 0.00 4.35
3602 3637 2.543848 TGTTAGCAACAACTGAAGAGCG 59.456 45.455 0.09 0.00 38.72 5.03
3622 3657 6.458615 GCAAAAATAAAATGGCAGGCCTTATG 60.459 38.462 0.00 0.00 36.94 1.90
3730 3765 4.414852 CATCCGGACAAGTTTGCATTAAG 58.585 43.478 6.12 0.00 0.00 1.85
3811 3846 4.261994 CGAAAAAGGAAAGGAAGGAATGCA 60.262 41.667 0.00 0.00 0.00 3.96
3822 3857 8.406172 TGAATTTCAGAAACGAAAAAGGAAAG 57.594 30.769 0.00 0.00 38.33 2.62
3865 3900 3.325135 ACTTTGACCTGAGAACCAGTAGG 59.675 47.826 0.00 0.00 41.33 3.18
3979 4014 7.274603 TCATTTTGATGATGAAACACAGTGA 57.725 32.000 7.81 0.00 30.96 3.41
4015 4050 4.590850 ATGTTTCTGGCACTTCTTTTCC 57.409 40.909 0.00 0.00 0.00 3.13
4030 4066 2.663119 GCACGCTGATTTCCAATGTTTC 59.337 45.455 0.00 0.00 0.00 2.78
4076 4126 6.347160 GGCATTCAAATTTCAGTTCTTGCTTC 60.347 38.462 0.00 0.00 0.00 3.86
4135 4185 1.030488 TCCTCATCACCGAGTCCGAC 61.030 60.000 0.00 0.00 38.22 4.79
4261 4311 0.168348 AGTCGTCCTCGTTCACATCG 59.832 55.000 0.00 0.00 38.33 3.84
4463 4513 6.038985 AGCTATCATATGACACGCATGATAC 58.961 40.000 7.78 8.57 39.50 2.24
4527 4577 0.608035 TTCTACCAGCCGCCAAAAGG 60.608 55.000 0.00 0.00 0.00 3.11
4550 4600 5.394115 GGGAAGCAACTCAAAAGTCTTTTCA 60.394 40.000 7.62 0.00 33.48 2.69
4556 4606 1.947456 ACGGGAAGCAACTCAAAAGTC 59.053 47.619 0.00 0.00 33.48 3.01
4656 4706 8.428063 CAGGTCTCTTATCCACTATGATTTTCT 58.572 37.037 0.00 0.00 0.00 2.52
4728 4778 2.124983 TGCTCTGGCGATTGGCTC 60.125 61.111 8.17 0.00 42.94 4.70
4731 4781 3.197790 CCGTGCTCTGGCGATTGG 61.198 66.667 0.00 0.00 42.25 3.16
4772 4822 3.815407 ATGGCCATGGATTCCGCCC 62.815 63.158 20.04 5.55 40.87 6.13
4818 4868 0.388659 CCGAGGATGCAGAGGAGAAG 59.611 60.000 0.00 0.00 0.00 2.85
4827 4877 4.451150 GACACGCCCGAGGATGCA 62.451 66.667 0.00 0.00 0.00 3.96
4943 5002 0.979709 CTCTGAGCCCATGACCTCCA 60.980 60.000 0.00 0.00 0.00 3.86
4959 5018 2.204059 AGCAGCTGGAACCCCTCT 60.204 61.111 17.12 0.00 0.00 3.69
5239 5298 3.260475 TGTCACCGCAGCAAAGTATAT 57.740 42.857 0.00 0.00 0.00 0.86
5240 5299 2.753055 TGTCACCGCAGCAAAGTATA 57.247 45.000 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.