Multiple sequence alignment - TraesCS2A01G360300

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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 TraesCS2A01G360300 chr2A 100.000 5471 0 0 1 5471 604755064 604749594 0.000000e+00 10104
1 TraesCS2A01G360300 chr2B 94.439 4909 198 34 1 4886 542763916 542759060 0.000000e+00 7483
2 TraesCS2A01G360300 chr2B 95.037 544 12 8 4928 5471 542758356 542757828 0.000000e+00 841
3 TraesCS2A01G360300 chr2B 86.279 430 46 10 630 1054 134859272 134859693 6.460000e-124 455
4 TraesCS2A01G360300 chr2B 86.183 427 46 9 630 1051 652706609 652707027 3.010000e-122 449
5 TraesCS2A01G360300 chr2D 94.037 4880 185 58 1 4855 460988985 460984187 0.000000e+00 7302
6 TraesCS2A01G360300 chr2D 96.344 547 16 4 4925 5471 460983644 460983102 0.000000e+00 896
7 TraesCS2A01G360300 chr4A 81.014 1085 106 50 1 1054 619802856 619801841 0.000000e+00 771
8 TraesCS2A01G360300 chr3D 84.470 528 65 9 4054 4578 598947296 598947809 6.320000e-139 505
9 TraesCS2A01G360300 chr6B 84.280 528 59 12 4054 4577 92344897 92344390 1.370000e-135 494
10 TraesCS2A01G360300 chr5B 84.091 528 60 12 4054 4577 101898772 101898265 6.370000e-134 488
11 TraesCS2A01G360300 chr7A 83.712 528 67 13 4054 4577 33836168 33836680 1.070000e-131 481
12 TraesCS2A01G360300 chr1B 80.568 458 51 17 4054 4499 641635755 641636186 8.840000e-83 318
13 TraesCS2A01G360300 chr3B 86.207 232 30 1 4054 4285 777692744 777692515 3.270000e-62 250


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 TraesCS2A01G360300 chr2A 604749594 604755064 5470 True 10104 10104 100.0000 1 5471 1 chr2A.!!$R1 5470
1 TraesCS2A01G360300 chr2B 542757828 542763916 6088 True 4162 7483 94.7380 1 5471 2 chr2B.!!$R1 5470
2 TraesCS2A01G360300 chr2D 460983102 460988985 5883 True 4099 7302 95.1905 1 5471 2 chr2D.!!$R1 5470
3 TraesCS2A01G360300 chr4A 619801841 619802856 1015 True 771 771 81.0140 1 1054 1 chr4A.!!$R1 1053
4 TraesCS2A01G360300 chr3D 598947296 598947809 513 False 505 505 84.4700 4054 4578 1 chr3D.!!$F1 524
5 TraesCS2A01G360300 chr6B 92344390 92344897 507 True 494 494 84.2800 4054 4577 1 chr6B.!!$R1 523
6 TraesCS2A01G360300 chr5B 101898265 101898772 507 True 488 488 84.0910 4054 4577 1 chr5B.!!$R1 523
7 TraesCS2A01G360300 chr7A 33836168 33836680 512 False 481 481 83.7120 4054 4577 1 chr7A.!!$F1 523

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
589 641 0.103937 CTGGTCCGAGCCTGAGAATC 59.896 60.000 0.00 0.0 0.00 2.52 F
1602 1677 0.036022 AGCTCAAGCACCTCAAGACC 59.964 55.000 4.59 0.0 45.16 3.85 F
1959 2034 2.624838 TGGGAAGCTTTCTTTTGCAGAG 59.375 45.455 4.35 0.0 31.12 3.35 F
2877 2952 1.410224 GGAATACCAAAGGAGCTGGGG 60.410 57.143 0.00 0.0 38.36 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2085 0.251608 ACAACCCTGGTATGTTGCCC 60.252 55.0 12.41 0.00 44.38 5.36 R
2679 2754 0.174389 TCTGGCTGAGATCAAGACGC 59.826 55.0 0.00 0.00 0.00 5.19 R
3459 3534 1.145803 GGACGGCTTTGTACACAGTC 58.854 55.0 10.59 7.21 0.00 3.51 R
4687 4767 0.608640 AACCCTGGCTGAACTACTCG 59.391 55.0 0.00 0.00 0.00 4.18 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
31 32 2.187946 CATCACACCGCCTCCTCC 59.812 66.667 0.00 0.00 0.00 4.30
82 94 1.212688 TCTCCATCGCCCATTCATTGT 59.787 47.619 0.00 0.00 0.00 2.71
115 127 2.505118 GGCAGTGAGTCGACGCTC 60.505 66.667 20.11 16.28 36.12 5.03
116 128 2.563942 GCAGTGAGTCGACGCTCT 59.436 61.111 20.11 18.28 36.51 4.09
118 130 0.168348 GCAGTGAGTCGACGCTCTAA 59.832 55.000 20.78 0.00 36.51 2.10
187 204 1.370051 GAAAACGCGGTGAGTTGGC 60.370 57.895 12.47 0.00 31.43 4.52
188 205 2.054140 GAAAACGCGGTGAGTTGGCA 62.054 55.000 12.47 0.00 31.43 4.92
189 206 2.058829 AAAACGCGGTGAGTTGGCAG 62.059 55.000 12.47 0.00 31.43 4.85
190 207 4.988598 ACGCGGTGAGTTGGCAGG 62.989 66.667 12.47 0.00 0.00 4.85
260 289 4.379243 CGCGGTGCTGTTCCCTCT 62.379 66.667 0.00 0.00 0.00 3.69
261 290 2.032681 GCGGTGCTGTTCCCTCTT 59.967 61.111 0.00 0.00 0.00 2.85
262 291 2.328099 GCGGTGCTGTTCCCTCTTG 61.328 63.158 0.00 0.00 0.00 3.02
263 292 1.071471 CGGTGCTGTTCCCTCTTGT 59.929 57.895 0.00 0.00 0.00 3.16
264 293 1.230635 CGGTGCTGTTCCCTCTTGTG 61.231 60.000 0.00 0.00 0.00 3.33
265 294 0.108585 GGTGCTGTTCCCTCTTGTGA 59.891 55.000 0.00 0.00 0.00 3.58
267 296 1.808945 GTGCTGTTCCCTCTTGTGATG 59.191 52.381 0.00 0.00 0.00 3.07
268 297 0.807496 GCTGTTCCCTCTTGTGATGC 59.193 55.000 0.00 0.00 0.00 3.91
269 298 1.612726 GCTGTTCCCTCTTGTGATGCT 60.613 52.381 0.00 0.00 0.00 3.79
270 299 2.082231 CTGTTCCCTCTTGTGATGCTG 58.918 52.381 0.00 0.00 0.00 4.41
271 300 0.807496 GTTCCCTCTTGTGATGCTGC 59.193 55.000 0.00 0.00 0.00 5.25
274 303 1.654954 CCCTCTTGTGATGCTGCTGC 61.655 60.000 8.89 8.89 40.20 5.25
275 304 0.677098 CCTCTTGTGATGCTGCTGCT 60.677 55.000 17.00 2.26 40.48 4.24
277 306 1.154016 CTTGTGATGCTGCTGCTGC 60.154 57.895 22.51 22.51 40.48 5.25
295 324 4.892965 TGCTGCCGCCTTGTGGTT 62.893 61.111 0.00 0.00 35.34 3.67
296 325 4.347453 GCTGCCGCCTTGTGGTTG 62.347 66.667 0.00 0.00 35.34 3.77
297 326 2.906897 CTGCCGCCTTGTGGTTGT 60.907 61.111 0.00 0.00 35.34 3.32
298 327 3.198236 CTGCCGCCTTGTGGTTGTG 62.198 63.158 0.00 0.00 35.34 3.33
299 328 2.904866 GCCGCCTTGTGGTTGTGA 60.905 61.111 0.00 0.00 35.34 3.58
300 329 2.908073 GCCGCCTTGTGGTTGTGAG 61.908 63.158 0.00 0.00 35.34 3.51
369 398 2.665603 GAGTGAAAGGCCCGCTCT 59.334 61.111 12.31 3.17 37.96 4.09
421 450 4.988598 CACGGCGGTGCTGTTCCT 62.989 66.667 13.24 0.00 46.97 3.36
422 451 4.988598 ACGGCGGTGCTGTTCCTG 62.989 66.667 13.24 0.00 46.97 3.86
474 519 2.890474 CGCGATTTGAGGGGGTCG 60.890 66.667 0.00 0.00 37.17 4.79
537 589 2.121786 CTGCAAATATGGTGCGATTGC 58.878 47.619 0.00 0.00 45.27 3.56
542 594 2.549064 ATATGGTGCGATTGCTAGCA 57.451 45.000 14.93 14.93 43.34 3.49
570 622 2.263852 GTTCCGGGTTCCCTCGAC 59.736 66.667 0.00 0.00 0.00 4.20
577 629 2.572284 GTTCCCTCGACTGGTCCG 59.428 66.667 0.00 0.00 0.00 4.79
582 634 2.752238 CTCGACTGGTCCGAGCCT 60.752 66.667 0.00 0.00 45.37 4.58
583 635 3.057547 CTCGACTGGTCCGAGCCTG 62.058 68.421 0.00 0.00 45.37 4.85
584 636 3.062466 CGACTGGTCCGAGCCTGA 61.062 66.667 8.57 0.00 0.00 3.86
585 637 2.888863 GACTGGTCCGAGCCTGAG 59.111 66.667 8.57 0.00 0.00 3.35
586 638 1.679305 GACTGGTCCGAGCCTGAGA 60.679 63.158 8.57 0.00 0.00 3.27
587 639 1.228894 ACTGGTCCGAGCCTGAGAA 60.229 57.895 8.57 0.00 0.00 2.87
588 640 0.616111 ACTGGTCCGAGCCTGAGAAT 60.616 55.000 8.57 0.00 0.00 2.40
589 641 0.103937 CTGGTCCGAGCCTGAGAATC 59.896 60.000 0.00 0.00 0.00 2.52
628 680 0.105039 AGGCGGGTGATTCGATTCTC 59.895 55.000 8.63 5.07 0.00 2.87
685 737 4.516698 TCTTGATTTGGAGTTGCTCAGTTC 59.483 41.667 0.00 0.00 31.08 3.01
727 798 9.601217 TCTTAGTATAGCTTTCATTCCTGTTTC 57.399 33.333 0.00 0.00 0.00 2.78
730 801 1.541588 AGCTTTCATTCCTGTTTCGGC 59.458 47.619 0.00 0.00 0.00 5.54
738 809 0.878523 TCCTGTTTCGGCTTGTCGTG 60.879 55.000 0.00 0.00 0.00 4.35
739 810 1.157870 CCTGTTTCGGCTTGTCGTGT 61.158 55.000 0.00 0.00 0.00 4.49
740 811 0.655733 CTGTTTCGGCTTGTCGTGTT 59.344 50.000 0.00 0.00 0.00 3.32
741 812 1.862201 CTGTTTCGGCTTGTCGTGTTA 59.138 47.619 0.00 0.00 0.00 2.41
742 813 2.277969 TGTTTCGGCTTGTCGTGTTAA 58.722 42.857 0.00 0.00 0.00 2.01
743 814 2.030701 TGTTTCGGCTTGTCGTGTTAAC 59.969 45.455 0.00 0.00 0.00 2.01
776 847 4.072131 TCCATTTCTCTGAAAACGAAGGG 58.928 43.478 0.00 0.00 0.00 3.95
786 857 2.882927 AAACGAAGGGGAAGCAAAAC 57.117 45.000 0.00 0.00 0.00 2.43
797 868 4.262938 GGGGAAGCAAAACAGAGTACTACT 60.263 45.833 0.00 0.00 0.00 2.57
826 900 6.885952 TCCTGCAGATAGACAGATAGTTAC 57.114 41.667 17.39 0.00 35.90 2.50
876 950 1.896220 TTCTCTTGCGGCATGTTCTT 58.104 45.000 14.53 0.00 0.00 2.52
884 959 2.163412 TGCGGCATGTTCTTACAATTCC 59.837 45.455 0.00 0.00 37.91 3.01
955 1030 8.484641 CAAGATTATAGCACTTGTTCTTCTCA 57.515 34.615 0.00 0.00 37.03 3.27
985 1060 3.005554 CTCTGAGCATTGGTTGATTCGT 58.994 45.455 0.00 0.00 0.00 3.85
1004 1079 2.868583 CGTGAAGTGAAGATAGCATGGG 59.131 50.000 0.00 0.00 0.00 4.00
1136 1211 3.870274 TCAAGAGCCAGATGATTGACAG 58.130 45.455 0.00 0.00 0.00 3.51
1221 1296 2.125229 TCCTCCTCCTCGTCGTCG 60.125 66.667 0.00 0.00 38.55 5.12
1359 1434 4.176752 GGTGCCATCCCTCCGGAC 62.177 72.222 0.00 0.00 42.48 4.79
1362 1437 2.427753 GCCATCCCTCCGGACATC 59.572 66.667 0.00 0.00 42.48 3.06
1602 1677 0.036022 AGCTCAAGCACCTCAAGACC 59.964 55.000 4.59 0.00 45.16 3.85
1818 1893 5.501156 GGGAATTGTACAAATCTCAGGACT 58.499 41.667 20.24 0.00 0.00 3.85
1893 1968 7.011857 GGGAACATTACTTATCTTGAGAAGCTG 59.988 40.741 5.08 3.95 0.00 4.24
1959 2034 2.624838 TGGGAAGCTTTCTTTTGCAGAG 59.375 45.455 4.35 0.00 31.12 3.35
2469 2544 6.128742 GCAATCTGGTGAATTTGACAACAATC 60.129 38.462 0.00 0.00 34.50 2.67
2520 2595 4.775253 CCTATTCCTCCTCAGATAGGGAAC 59.225 50.000 0.00 0.00 46.55 3.62
2607 2682 4.590850 AGGGAAATTGTCAAAGCTTGTC 57.409 40.909 0.00 0.00 0.00 3.18
2679 2754 7.310664 AGATCTTCAATTGTACAACATTGCAG 58.689 34.615 11.22 12.09 0.00 4.41
2853 2928 4.401519 CAGATTGGTGGCAATCAATTCTCT 59.598 41.667 15.42 8.77 42.38 3.10
2877 2952 1.410224 GGAATACCAAAGGAGCTGGGG 60.410 57.143 0.00 0.00 38.36 4.96
3540 3615 0.535102 ACAGGGAAGGAAGCAACACG 60.535 55.000 0.00 0.00 0.00 4.49
3558 3633 2.006772 GGATAACAGCTTCCGTGCG 58.993 57.895 0.00 0.00 38.13 5.34
3873 3948 2.712087 TGACTTTGGGTTGGCTAAGGTA 59.288 45.455 0.00 0.00 0.00 3.08
4140 4217 8.200024 AGAAATCTGACATATACAGCTATGGT 57.800 34.615 0.00 0.00 34.11 3.55
4398 4475 5.865552 TGTTGTAGTTATGTTAAGCGAGTCC 59.134 40.000 0.00 0.00 0.00 3.85
4444 4521 0.100682 GTCGTCGCCTGCTTCTGATA 59.899 55.000 0.00 0.00 0.00 2.15
4552 4632 2.026641 CTGTTGCTTATGGTGGGGATG 58.973 52.381 0.00 0.00 0.00 3.51
4664 4744 3.960102 AGCCTCTCTGATGAAGAAGGTAG 59.040 47.826 0.00 0.00 36.41 3.18
4665 4745 3.704061 GCCTCTCTGATGAAGAAGGTAGT 59.296 47.826 0.00 0.00 36.41 2.73
4687 4767 0.531200 CGAGTCCAGACAGTAACCCC 59.469 60.000 0.00 0.00 0.00 4.95
4722 4803 3.319198 TTCCTCCCTGGACGTGGC 61.319 66.667 0.00 0.00 46.14 5.01
4829 4910 4.271291 GTCTTTCTGAACTTGTGACACTCC 59.729 45.833 7.20 0.00 0.00 3.85
4840 4921 0.394192 TGACACTCCCAGCTGAGTTG 59.606 55.000 17.39 9.06 42.92 3.16
4868 4949 3.153919 AGCTTCCTCGGTGCAATTTTTA 58.846 40.909 0.00 0.00 0.00 1.52
4872 4953 5.622233 GCTTCCTCGGTGCAATTTTTATCTT 60.622 40.000 0.00 0.00 0.00 2.40
4881 4962 8.638565 CGGTGCAATTTTTATCTTAACTTTCTG 58.361 33.333 0.00 0.00 0.00 3.02
4882 4963 9.691362 GGTGCAATTTTTATCTTAACTTTCTGA 57.309 29.630 0.00 0.00 0.00 3.27
4899 5678 6.208204 ACTTTCTGAGCTTATGAATGTGCTTT 59.792 34.615 11.86 0.00 35.76 3.51
4901 5680 6.915544 TCTGAGCTTATGAATGTGCTTTAG 57.084 37.500 0.00 0.00 35.76 1.85
4902 5681 5.295292 TCTGAGCTTATGAATGTGCTTTAGC 59.705 40.000 0.00 0.00 42.50 3.09
4903 5682 4.034394 TGAGCTTATGAATGTGCTTTAGCG 59.966 41.667 0.00 0.00 45.83 4.26
4905 5684 3.621794 CTTATGAATGTGCTTTAGCGGC 58.378 45.455 0.00 0.00 45.83 6.53
4906 5685 1.462616 ATGAATGTGCTTTAGCGGCA 58.537 45.000 1.45 0.00 45.83 5.69
4907 5686 0.804364 TGAATGTGCTTTAGCGGCAG 59.196 50.000 1.45 0.00 45.83 4.85
4909 5688 0.523072 AATGTGCTTTAGCGGCAGTG 59.477 50.000 1.45 0.00 45.83 3.66
4910 5689 0.321564 ATGTGCTTTAGCGGCAGTGA 60.322 50.000 1.45 0.00 45.83 3.41
4911 5690 0.533978 TGTGCTTTAGCGGCAGTGAA 60.534 50.000 1.45 0.00 45.83 3.18
4913 5692 0.250295 TGCTTTAGCGGCAGTGAACT 60.250 50.000 1.45 0.00 45.83 3.01
4914 5693 0.875059 GCTTTAGCGGCAGTGAACTT 59.125 50.000 1.45 0.00 0.00 2.66
4915 5694 1.135944 GCTTTAGCGGCAGTGAACTTC 60.136 52.381 1.45 0.00 0.00 3.01
4916 5695 1.464997 CTTTAGCGGCAGTGAACTTCC 59.535 52.381 1.45 0.00 0.00 3.46
4917 5696 0.685097 TTAGCGGCAGTGAACTTCCT 59.315 50.000 1.45 0.00 0.00 3.36
4918 5697 0.246635 TAGCGGCAGTGAACTTCCTC 59.753 55.000 1.45 0.00 0.00 3.71
4919 5698 1.301716 GCGGCAGTGAACTTCCTCA 60.302 57.895 0.00 0.00 0.00 3.86
4920 5699 0.884704 GCGGCAGTGAACTTCCTCAA 60.885 55.000 0.00 0.00 0.00 3.02
4921 5700 1.151668 CGGCAGTGAACTTCCTCAAG 58.848 55.000 0.00 0.00 35.50 3.02
4922 5701 1.528129 GGCAGTGAACTTCCTCAAGG 58.472 55.000 0.00 0.00 33.37 3.61
4923 5702 1.202818 GGCAGTGAACTTCCTCAAGGT 60.203 52.381 0.00 0.00 33.37 3.50
4978 5757 1.606889 ACCCGTCAGAGGTCAGACC 60.607 63.158 12.25 12.25 38.99 3.85
4979 5758 1.606601 CCCGTCAGAGGTCAGACCA 60.607 63.158 22.31 0.00 41.95 4.02
4980 5759 1.587054 CCGTCAGAGGTCAGACCAC 59.413 63.158 22.31 15.68 41.95 4.16
4981 5760 0.896019 CCGTCAGAGGTCAGACCACT 60.896 60.000 22.31 17.86 41.95 4.00
4982 5761 1.613520 CCGTCAGAGGTCAGACCACTA 60.614 57.143 22.31 7.15 41.95 2.74
4983 5762 1.469308 CGTCAGAGGTCAGACCACTAC 59.531 57.143 22.31 16.20 41.95 2.73
4984 5763 1.819903 GTCAGAGGTCAGACCACTACC 59.180 57.143 22.31 10.29 41.95 3.18
4985 5764 1.427753 TCAGAGGTCAGACCACTACCA 59.572 52.381 22.31 5.51 41.95 3.25
4986 5765 2.158370 TCAGAGGTCAGACCACTACCAA 60.158 50.000 22.31 4.70 41.95 3.67
4987 5766 2.834549 CAGAGGTCAGACCACTACCAAT 59.165 50.000 22.31 0.00 41.95 3.16
5016 5795 2.124778 GCAGAGGAAGCAGGGAGC 60.125 66.667 0.00 0.00 46.19 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.548067 GCGGAGTAGAGAGAGAGGAGAG 60.548 59.091 0.00 0.00 0.00 3.20
110 122 4.796231 CGGGCTGCGTTAGAGCGT 62.796 66.667 0.00 0.00 40.67 5.07
187 204 3.080121 AAGAGCGAGGGAGGCCTG 61.080 66.667 12.00 0.00 0.00 4.85
188 205 3.080121 CAAGAGCGAGGGAGGCCT 61.080 66.667 3.86 3.86 0.00 5.19
189 206 2.960688 AACAAGAGCGAGGGAGGCC 61.961 63.158 0.00 0.00 0.00 5.19
190 207 1.743252 CAACAAGAGCGAGGGAGGC 60.743 63.158 0.00 0.00 0.00 4.70
246 275 0.108585 TCACAAGAGGGAACAGCACC 59.891 55.000 0.00 0.00 0.00 5.01
255 284 1.654954 GCAGCAGCATCACAAGAGGG 61.655 60.000 0.00 0.00 41.58 4.30
256 285 0.677098 AGCAGCAGCATCACAAGAGG 60.677 55.000 3.17 0.00 45.49 3.69
257 286 0.448197 CAGCAGCAGCATCACAAGAG 59.552 55.000 3.17 0.00 45.49 2.85
259 288 1.154016 GCAGCAGCAGCATCACAAG 60.154 57.895 4.63 0.00 45.49 3.16
260 289 1.602605 AGCAGCAGCAGCATCACAA 60.603 52.632 12.92 0.00 45.49 3.33
261 290 2.033602 AGCAGCAGCAGCATCACA 59.966 55.556 12.92 0.00 45.49 3.58
262 291 2.485582 CAGCAGCAGCAGCATCAC 59.514 61.111 12.92 0.00 45.49 3.06
281 310 3.215568 CACAACCACAAGGCGGCA 61.216 61.111 13.08 0.00 39.06 5.69
283 312 2.260869 CCTCACAACCACAAGGCGG 61.261 63.158 0.00 0.00 39.06 6.13
284 313 2.260869 CCCTCACAACCACAAGGCG 61.261 63.158 0.00 0.00 39.06 5.52
285 314 1.152756 ACCCTCACAACCACAAGGC 60.153 57.895 0.00 0.00 39.06 4.35
286 315 0.823356 CCACCCTCACAACCACAAGG 60.823 60.000 0.00 0.00 42.21 3.61
287 316 0.823356 CCCACCCTCACAACCACAAG 60.823 60.000 0.00 0.00 0.00 3.16
288 317 1.228793 CCCACCCTCACAACCACAA 59.771 57.895 0.00 0.00 0.00 3.33
289 318 2.762554 CCCCACCCTCACAACCACA 61.763 63.158 0.00 0.00 0.00 4.17
290 319 2.115266 CCCCACCCTCACAACCAC 59.885 66.667 0.00 0.00 0.00 4.16
291 320 3.182263 CCCCCACCCTCACAACCA 61.182 66.667 0.00 0.00 0.00 3.67
292 321 3.182996 ACCCCCACCCTCACAACC 61.183 66.667 0.00 0.00 0.00 3.77
293 322 2.115266 CACCCCCACCCTCACAAC 59.885 66.667 0.00 0.00 0.00 3.32
294 323 2.039298 TCACCCCCACCCTCACAA 60.039 61.111 0.00 0.00 0.00 3.33
295 324 2.852075 GTCACCCCCACCCTCACA 60.852 66.667 0.00 0.00 0.00 3.58
296 325 4.016706 CGTCACCCCCACCCTCAC 62.017 72.222 0.00 0.00 0.00 3.51
297 326 2.676319 TAACGTCACCCCCACCCTCA 62.676 60.000 0.00 0.00 0.00 3.86
298 327 1.896122 CTAACGTCACCCCCACCCTC 61.896 65.000 0.00 0.00 0.00 4.30
299 328 1.916777 CTAACGTCACCCCCACCCT 60.917 63.158 0.00 0.00 0.00 4.34
300 329 1.771783 AACTAACGTCACCCCCACCC 61.772 60.000 0.00 0.00 0.00 4.61
369 398 3.606846 CGAAACAGATCTGCGAGCAAAAA 60.607 43.478 22.83 0.00 0.00 1.94
405 434 4.988598 CAGGAACAGCACCGCCGT 62.989 66.667 0.00 0.00 0.00 5.68
424 453 4.753662 TCGGACGGAGGGACCCAG 62.754 72.222 14.60 6.20 34.64 4.45
570 622 0.103937 GATTCTCAGGCTCGGACCAG 59.896 60.000 0.00 0.00 0.00 4.00
581 633 8.674263 AAATAATGCTTACTCCTGATTCTCAG 57.326 34.615 0.00 0.00 43.91 3.35
582 634 9.113838 GAAAATAATGCTTACTCCTGATTCTCA 57.886 33.333 0.00 0.00 0.00 3.27
583 635 9.113838 TGAAAATAATGCTTACTCCTGATTCTC 57.886 33.333 0.00 0.00 0.00 2.87
584 636 9.118300 CTGAAAATAATGCTTACTCCTGATTCT 57.882 33.333 0.00 0.00 0.00 2.40
585 637 8.348507 CCTGAAAATAATGCTTACTCCTGATTC 58.651 37.037 0.00 0.00 0.00 2.52
586 638 7.201857 GCCTGAAAATAATGCTTACTCCTGATT 60.202 37.037 0.00 0.00 0.00 2.57
587 639 6.264067 GCCTGAAAATAATGCTTACTCCTGAT 59.736 38.462 0.00 0.00 0.00 2.90
588 640 5.590259 GCCTGAAAATAATGCTTACTCCTGA 59.410 40.000 0.00 0.00 0.00 3.86
589 641 5.504665 CGCCTGAAAATAATGCTTACTCCTG 60.505 44.000 0.00 0.00 0.00 3.86
590 642 4.576463 CGCCTGAAAATAATGCTTACTCCT 59.424 41.667 0.00 0.00 0.00 3.69
591 643 4.261197 CCGCCTGAAAATAATGCTTACTCC 60.261 45.833 0.00 0.00 0.00 3.85
685 737 1.571919 AAGAATCGAATTCGGGAGCG 58.428 50.000 26.47 1.59 43.92 5.03
738 809 6.492254 AGAAATGGACACTGAAAACGTTAAC 58.508 36.000 0.00 0.00 0.00 2.01
739 810 6.540914 AGAGAAATGGACACTGAAAACGTTAA 59.459 34.615 0.00 0.00 0.00 2.01
740 811 6.018262 CAGAGAAATGGACACTGAAAACGTTA 60.018 38.462 0.00 0.00 0.00 3.18
741 812 4.881850 AGAGAAATGGACACTGAAAACGTT 59.118 37.500 0.00 0.00 0.00 3.99
742 813 4.273480 CAGAGAAATGGACACTGAAAACGT 59.727 41.667 0.00 0.00 0.00 3.99
743 814 4.511454 TCAGAGAAATGGACACTGAAAACG 59.489 41.667 0.00 0.00 33.58 3.60
744 815 6.377327 TTCAGAGAAATGGACACTGAAAAC 57.623 37.500 0.00 0.00 40.11 2.43
746 817 6.458206 CGTTTTCAGAGAAATGGACACTGAAA 60.458 38.462 13.93 13.93 45.41 2.69
747 818 5.007626 CGTTTTCAGAGAAATGGACACTGAA 59.992 40.000 0.00 0.00 40.83 3.02
748 819 4.511454 CGTTTTCAGAGAAATGGACACTGA 59.489 41.667 0.00 0.00 34.37 3.41
749 820 4.511454 TCGTTTTCAGAGAAATGGACACTG 59.489 41.667 0.00 0.00 0.00 3.66
776 847 7.153315 ACTAAGTAGTACTCTGTTTTGCTTCC 58.847 38.462 2.58 0.00 34.13 3.46
786 857 6.151312 TCTGCAGGAAACTAAGTAGTACTCTG 59.849 42.308 15.13 5.98 40.21 3.35
797 868 6.798427 ATCTGTCTATCTGCAGGAAACTAA 57.202 37.500 15.13 0.00 40.21 2.24
826 900 6.980978 TCTAATCAGGAAAGATTCTAACAGCG 59.019 38.462 0.00 0.00 38.97 5.18
876 950 3.444742 CAGAATGCAAGCAGGGAATTGTA 59.555 43.478 0.00 0.00 0.00 2.41
884 959 2.352421 CCTGAAACAGAATGCAAGCAGG 60.352 50.000 0.00 0.00 42.53 4.85
951 1026 1.404717 GCTCAGAGCCGAACAATGAGA 60.405 52.381 11.84 0.00 39.80 3.27
955 1030 1.741706 CAATGCTCAGAGCCGAACAAT 59.258 47.619 20.16 2.30 41.51 2.71
985 1060 2.421952 GGCCCATGCTATCTTCACTTCA 60.422 50.000 0.00 0.00 37.74 3.02
1136 1211 2.616842 CAGTTGTCAAGGTGGTGGTAAC 59.383 50.000 0.00 0.00 0.00 2.50
1221 1296 1.153745 CACCACTGCTAGCCTCGAC 60.154 63.158 13.29 0.00 0.00 4.20
1284 1359 2.469516 GGTAAGACCGCCAATGCCG 61.470 63.158 0.00 0.00 0.00 5.69
1359 1434 3.504863 CAGTTTTGAGCAATTCCCGATG 58.495 45.455 0.00 0.00 0.00 3.84
1362 1437 1.613437 ACCAGTTTTGAGCAATTCCCG 59.387 47.619 0.00 0.00 0.00 5.14
1434 1509 3.664888 AGCATGGCCAGCTTCCCA 61.665 61.111 20.03 4.66 39.87 4.37
1575 1650 2.669569 TGCTTGAGCTTGCCGACC 60.670 61.111 4.44 0.00 42.66 4.79
1602 1677 0.533755 GATTCTGTCCCAGCCGGATG 60.534 60.000 14.18 14.18 44.66 3.51
1662 1737 2.788515 ACCAAACACGGTCAGGTTG 58.211 52.632 0.00 0.00 32.11 3.77
1749 1824 1.064166 AGCTGATTTCCCCACAGGATG 60.064 52.381 0.00 0.00 46.94 3.51
1818 1893 8.393259 ACCAGATCATTATCATAAAGGGCAATA 58.607 33.333 0.00 0.00 34.28 1.90
1861 1936 7.771183 TCAAGATAAGTAATGTTCCCAATTGC 58.229 34.615 0.00 0.00 0.00 3.56
1911 1986 8.463930 TTTCAGATGGAATGGTACCATTTATC 57.536 34.615 34.93 33.71 46.48 1.75
1959 2034 7.890515 AGAAATTCTCTGAAAAATCAACCTCC 58.109 34.615 0.00 0.00 31.12 4.30
2010 2085 0.251608 ACAACCCTGGTATGTTGCCC 60.252 55.000 12.41 0.00 44.38 5.36
2607 2682 6.364706 GCCTGTTAGATGAGATATTGAAGACG 59.635 42.308 0.00 0.00 0.00 4.18
2679 2754 0.174389 TCTGGCTGAGATCAAGACGC 59.826 55.000 0.00 0.00 0.00 5.19
3213 3288 3.250617 TGCTATGATCTTGCCCATAGGA 58.749 45.455 0.00 0.00 41.37 2.94
3459 3534 1.145803 GGACGGCTTTGTACACAGTC 58.854 55.000 10.59 7.21 0.00 3.51
3519 3594 2.031870 GTGTTGCTTCCTTCCCTGTTT 58.968 47.619 0.00 0.00 0.00 2.83
3540 3615 1.429148 CCGCACGGAAGCTGTTATCC 61.429 60.000 2.01 0.00 37.50 2.59
3558 3633 5.350504 TCTTTCCAAGAGTCATGATCTCC 57.649 43.478 16.74 0.00 32.71 3.71
3873 3948 4.147321 ACTTTGAGACTGGCATGTCAATT 58.853 39.130 0.00 0.00 39.27 2.32
4020 4096 7.097192 TCATCGCTTAACTACAGATTCAAGTT 58.903 34.615 0.00 0.00 37.27 2.66
4398 4475 2.203351 GCCCGGGCCCTATCTTTG 60.203 66.667 36.64 1.10 34.56 2.77
4444 4521 6.227298 TGAGCTATCCTTCTTCGAAGAATT 57.773 37.500 34.19 24.63 45.90 2.17
4508 4585 2.514458 AAGGGAGCAACTGGTATTGG 57.486 50.000 0.00 0.00 0.00 3.16
4552 4632 1.133790 GAATGAGTGCATGCTCCCAAC 59.866 52.381 20.33 8.19 34.26 3.77
4628 4708 5.891551 TCAGAGAGGCTAACATACATACACA 59.108 40.000 0.00 0.00 0.00 3.72
4664 4744 2.162008 GGTTACTGTCTGGACTCGAGAC 59.838 54.545 21.68 13.64 40.34 3.36
4665 4745 2.434428 GGTTACTGTCTGGACTCGAGA 58.566 52.381 21.68 0.00 0.00 4.04
4687 4767 0.608640 AACCCTGGCTGAACTACTCG 59.391 55.000 0.00 0.00 0.00 4.18
4768 4849 7.604927 AGCAAAAGCACATTCATATTTCAACAT 59.395 29.630 0.00 0.00 0.00 2.71
4774 4855 6.040209 TCCAGCAAAAGCACATTCATATTT 57.960 33.333 0.00 0.00 0.00 1.40
4829 4910 2.168106 AGCTCAGATACAACTCAGCTGG 59.832 50.000 15.13 7.28 35.88 4.85
4840 4921 1.537135 GCACCGAGGAAGCTCAGATAC 60.537 57.143 0.00 0.00 0.00 2.24
4868 4949 9.678260 ACATTCATAAGCTCAGAAAGTTAAGAT 57.322 29.630 0.00 0.00 0.00 2.40
4872 4953 6.881065 AGCACATTCATAAGCTCAGAAAGTTA 59.119 34.615 0.00 0.00 30.05 2.24
4881 4962 4.521943 CGCTAAAGCACATTCATAAGCTC 58.478 43.478 2.44 0.00 42.21 4.09
4882 4963 3.313526 CCGCTAAAGCACATTCATAAGCT 59.686 43.478 2.44 0.00 42.21 3.74
4883 4964 3.621794 CCGCTAAAGCACATTCATAAGC 58.378 45.455 2.44 0.00 42.21 3.09
4888 5667 0.804364 CTGCCGCTAAAGCACATTCA 59.196 50.000 2.44 0.00 42.21 2.57
4899 5678 0.246635 GAGGAAGTTCACTGCCGCTA 59.753 55.000 5.01 0.00 46.84 4.26
4901 5680 0.884704 TTGAGGAAGTTCACTGCCGC 60.885 55.000 5.01 0.69 46.84 6.53
4902 5681 1.151668 CTTGAGGAAGTTCACTGCCG 58.848 55.000 5.01 0.00 46.84 5.69
4903 5682 1.202818 ACCTTGAGGAAGTTCACTGCC 60.203 52.381 5.01 0.00 42.37 4.85
4905 5684 1.876156 GCACCTTGAGGAAGTTCACTG 59.124 52.381 5.01 0.00 38.94 3.66
4906 5685 1.202818 GGCACCTTGAGGAAGTTCACT 60.203 52.381 5.01 0.00 38.94 3.41
4907 5686 1.202818 AGGCACCTTGAGGAAGTTCAC 60.203 52.381 5.01 0.00 38.94 3.18
4909 5688 1.611936 GGAGGCACCTTGAGGAAGTTC 60.612 57.143 3.59 0.00 38.94 3.01
4910 5689 0.402121 GGAGGCACCTTGAGGAAGTT 59.598 55.000 3.59 0.00 38.94 2.66
4911 5690 0.768221 TGGAGGCACCTTGAGGAAGT 60.768 55.000 3.59 0.00 39.86 3.01
4913 5692 1.492133 CCTGGAGGCACCTTGAGGAA 61.492 60.000 3.59 0.00 39.86 3.36
4914 5693 1.920325 CCTGGAGGCACCTTGAGGA 60.920 63.158 3.59 0.00 39.86 3.71
4915 5694 2.673523 CCTGGAGGCACCTTGAGG 59.326 66.667 1.84 0.00 39.86 3.86
4916 5695 2.190488 GACCCTGGAGGCACCTTGAG 62.190 65.000 1.84 0.00 40.58 3.02
4917 5696 2.121963 ACCCTGGAGGCACCTTGA 60.122 61.111 1.84 0.00 40.58 3.02
4918 5697 2.352805 GACCCTGGAGGCACCTTG 59.647 66.667 1.84 0.00 40.58 3.61
4919 5698 2.121963 TGACCCTGGAGGCACCTT 60.122 61.111 1.84 0.00 40.58 3.50
4920 5699 2.930562 GTGACCCTGGAGGCACCT 60.931 66.667 9.31 0.00 40.58 4.00
4921 5700 2.930562 AGTGACCCTGGAGGCACC 60.931 66.667 15.02 0.00 41.13 5.01
4922 5701 0.614979 TAGAGTGACCCTGGAGGCAC 60.615 60.000 11.82 11.82 40.77 5.01
4923 5702 0.614979 GTAGAGTGACCCTGGAGGCA 60.615 60.000 0.00 0.00 40.58 4.75
4978 5757 3.470709 CTGCCATGGTAGATTGGTAGTG 58.529 50.000 24.36 0.00 39.89 2.74
4979 5758 2.158755 GCTGCCATGGTAGATTGGTAGT 60.159 50.000 31.57 0.00 44.70 2.73
4980 5759 2.158769 TGCTGCCATGGTAGATTGGTAG 60.159 50.000 31.57 6.24 45.39 3.18
4981 5760 1.843206 TGCTGCCATGGTAGATTGGTA 59.157 47.619 31.57 3.31 35.34 3.25
4982 5761 0.625316 TGCTGCCATGGTAGATTGGT 59.375 50.000 31.57 0.00 35.34 3.67
4983 5762 1.134007 TCTGCTGCCATGGTAGATTGG 60.134 52.381 31.57 16.98 36.03 3.16
4984 5763 2.219458 CTCTGCTGCCATGGTAGATTG 58.781 52.381 31.57 19.28 0.00 2.67
4985 5764 1.142465 CCTCTGCTGCCATGGTAGATT 59.858 52.381 31.57 0.00 0.00 2.40
4986 5765 0.763652 CCTCTGCTGCCATGGTAGAT 59.236 55.000 31.57 0.00 0.00 1.98
4987 5766 0.325577 TCCTCTGCTGCCATGGTAGA 60.326 55.000 31.57 18.77 0.00 2.59
5020 5799 4.773117 GAGGACGACGTGCGGGTC 62.773 72.222 14.02 2.68 46.49 4.46


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

AutoCloner maintained by Alex Coulton.