Multiple sequence alignment - TraesCS3A01G271600

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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 TraesCS3A01G271600 chr3A 100.000 5085 0 0 1 5085 500973145 500978229 0.000000e+00 9391.0
1 TraesCS3A01G271600 chr3A 83.333 78 9 4 3570 3647 690193524 690193451 9.140000e-08 69.4
2 TraesCS3A01G271600 chr3B 93.079 3670 155 44 1 3619 490594420 490598041 0.000000e+00 5278.0
3 TraesCS3A01G271600 chr3B 90.415 1158 57 23 3926 5064 490598431 490599553 0.000000e+00 1474.0
4 TraesCS3A01G271600 chr3B 93.930 313 11 1 3622 3926 490598071 490598383 2.770000e-127 466.0
5 TraesCS3A01G271600 chr3B 88.722 133 14 1 628 759 675582022 675582154 1.470000e-35 161.0
6 TraesCS3A01G271600 chr3D 93.075 2888 87 28 795 3619 376162198 376165035 0.000000e+00 4120.0
7 TraesCS3A01G271600 chr3D 91.734 871 44 13 3926 4780 376165298 376166156 0.000000e+00 1184.0
8 TraesCS3A01G271600 chr3D 88.571 630 39 19 1 618 376161563 376162171 0.000000e+00 734.0
9 TraesCS3A01G271600 chr3D 95.567 203 9 0 3726 3928 376165050 376165252 4.910000e-85 326.0
10 TraesCS3A01G271600 chr3D 86.411 287 19 7 4779 5064 376169107 376169374 3.850000e-76 296.0
11 TraesCS3A01G271600 chr3D 97.500 40 1 0 3625 3664 376165055 376165016 9.140000e-08 69.4
12 TraesCS3A01G271600 chr1A 90.769 130 12 0 629 758 335028424 335028295 1.880000e-39 174.0
13 TraesCS3A01G271600 chr4A 87.970 133 13 1 630 759 690884003 690884135 2.450000e-33 154.0
14 TraesCS3A01G271600 chr4A 95.238 42 2 0 3619 3660 569867928 569867887 3.290000e-07 67.6
15 TraesCS3A01G271600 chr4A 91.304 46 4 0 3619 3664 596077824 596077869 4.250000e-06 63.9
16 TraesCS3A01G271600 chr5B 95.349 43 2 0 3619 3661 580101461 580101419 9.140000e-08 69.4
17 TraesCS3A01G271600 chr4B 95.238 42 2 0 3619 3660 47623437 47623478 3.290000e-07 67.6
18 TraesCS3A01G271600 chr6B 91.304 46 4 0 3619 3664 545202836 545202881 4.250000e-06 63.9
19 TraesCS3A01G271600 chr1D 93.023 43 3 0 3619 3661 422838332 422838290 4.250000e-06 63.9


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 TraesCS3A01G271600 chr3A 500973145 500978229 5084 False 9391 9391 100.000000 1 5085 1 chr3A.!!$F1 5084
1 TraesCS3A01G271600 chr3B 490594420 490599553 5133 False 2406 5278 92.474667 1 5064 3 chr3B.!!$F2 5063
2 TraesCS3A01G271600 chr3D 376161563 376169374 7811 False 1332 4120 91.071600 1 5064 5 chr3D.!!$F1 5063

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
788 807 0.523072 CAAGCACATCCCCGTTCTTG 59.477 55.0 0.00 0.0 34.61 3.02 F
1494 1542 0.252479 TCGTCTTAGTCCCGCTCTCT 59.748 55.0 0.00 0.0 0.00 3.10 F
1641 1700 0.042431 ACCTCACCTCATCTGCTCCT 59.958 55.0 0.00 0.0 0.00 3.69 F
2253 2316 0.835941 AGGCCAGAGAGCAATACCTG 59.164 55.0 5.01 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1670 0.104934 AGGTGAGGTGAGGTGAGGTT 60.105 55.000 0.00 0.0 0.00 3.50 R
3123 3208 0.038251 GGCTAGGCAAACTTTGGTGC 60.038 55.000 12.16 0.0 40.14 5.01 R
3211 3296 2.087646 GAATGGAAGGACCTGAACTGC 58.912 52.381 0.00 0.0 39.86 4.40 R
4179 4350 0.104487 CCTCAGCGTGCATCTCATCT 59.896 55.000 0.00 0.0 0.00 2.90 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
119 120 1.596752 CCGTACCAACTGCAGCACA 60.597 57.895 15.27 0.00 0.00 4.57
162 163 6.096141 TGAAAAATAGATTAGGCGCCATTTCA 59.904 34.615 31.54 22.81 32.50 2.69
163 164 6.463995 AAAATAGATTAGGCGCCATTTCAA 57.536 33.333 31.54 14.22 0.00 2.69
166 167 2.097466 AGATTAGGCGCCATTTCAAACG 59.903 45.455 31.54 0.00 0.00 3.60
314 328 1.298157 CGAGAAACAGGGCATCGCAA 61.298 55.000 0.00 0.00 0.00 4.85
368 383 3.973305 TGCAGGGGAGATGTGTGATATAA 59.027 43.478 0.00 0.00 0.00 0.98
371 386 4.347876 CAGGGGAGATGTGTGATATAACCA 59.652 45.833 0.00 0.00 0.00 3.67
434 449 4.711846 GGGGATGAAAGGTTTATTCTGCTT 59.288 41.667 0.00 0.00 0.00 3.91
500 516 8.585881 AGTGCTATTATCGTTGTTATATCTGGT 58.414 33.333 0.00 0.00 0.00 4.00
585 602 2.083774 CTGGCAACCATAAGCTCGAAA 58.916 47.619 0.00 0.00 30.82 3.46
595 612 7.073342 ACCATAAGCTCGAAACAGTAAATTC 57.927 36.000 0.00 0.00 0.00 2.17
629 646 1.953686 GTTACTTTGCACCTGCCAAGA 59.046 47.619 15.91 0.33 43.91 3.02
639 656 1.812571 ACCTGCCAAGAGTAAATTGCG 59.187 47.619 0.00 0.00 0.00 4.85
645 662 4.742659 TGCCAAGAGTAAATTGCGAAAAAC 59.257 37.500 0.00 0.00 0.00 2.43
655 674 6.616774 AAATTGCGAAAAACCATCACAATT 57.383 29.167 0.00 0.00 39.78 2.32
678 697 3.938963 GGGTCGAAGTTATCAATGCTTCA 59.061 43.478 0.00 0.00 38.70 3.02
713 732 6.311935 CACTAGAAAACATGCATTTTGATGGG 59.688 38.462 0.00 0.00 31.90 4.00
733 752 3.068024 GGGTGTTTGATGACTTTTGCTCA 59.932 43.478 0.00 0.00 0.00 4.26
737 756 6.292488 GGTGTTTGATGACTTTTGCTCAATTG 60.292 38.462 0.00 0.00 0.00 2.32
740 759 5.771153 TGATGACTTTTGCTCAATTGTGA 57.229 34.783 11.59 0.00 0.00 3.58
744 763 3.656559 ACTTTTGCTCAATTGTGATGGC 58.343 40.909 11.59 7.26 31.85 4.40
747 766 1.466856 TGCTCAATTGTGATGGCCTC 58.533 50.000 11.59 0.00 31.85 4.70
759 778 2.760092 TGATGGCCTCTTGCAATTTACC 59.240 45.455 3.32 0.32 43.89 2.85
788 807 0.523072 CAAGCACATCCCCGTTCTTG 59.477 55.000 0.00 0.00 34.61 3.02
845 864 5.826643 AGGCAATGGAGGTGAAAATTACTA 58.173 37.500 0.00 0.00 0.00 1.82
870 889 6.041637 ACTCCTATGCAACTCGGAAATGTATA 59.958 38.462 0.00 2.25 0.00 1.47
871 890 6.220930 TCCTATGCAACTCGGAAATGTATAC 58.779 40.000 0.00 0.00 0.00 1.47
895 914 2.599578 CCAAGCTGGCAAGTGGCT 60.600 61.111 6.41 0.00 44.01 4.75
922 942 8.763601 ACTAGAGTAGATATTTTCCAGCAGTTT 58.236 33.333 0.00 0.00 0.00 2.66
937 957 2.076100 CAGTTTTGCAGGCTCGATACA 58.924 47.619 0.00 0.00 0.00 2.29
1022 1042 1.710816 GATTCCGGATCACTCCCTCT 58.289 55.000 4.15 0.00 38.45 3.69
1034 1057 1.275002 ACTCCCTCTCCTCTCCTCTCT 60.275 57.143 0.00 0.00 0.00 3.10
1046 1069 0.336737 TCCTCTCTTCTCCACTCCCC 59.663 60.000 0.00 0.00 0.00 4.81
1494 1542 0.252479 TCGTCTTAGTCCCGCTCTCT 59.748 55.000 0.00 0.00 0.00 3.10
1527 1586 1.078143 GCAGTGGGGTAAGCTCCTG 60.078 63.158 0.00 0.00 35.83 3.86
1628 1687 2.494073 CTCTAACCTCACCTCACCTCAC 59.506 54.545 0.00 0.00 0.00 3.51
1641 1700 0.042431 ACCTCACCTCATCTGCTCCT 59.958 55.000 0.00 0.00 0.00 3.69
1668 1728 2.125832 TCCCGACATCGTTTCGCC 60.126 61.111 0.00 0.00 37.74 5.54
1669 1729 2.433491 CCCGACATCGTTTCGCCA 60.433 61.111 0.00 0.00 37.74 5.69
1681 1741 2.032426 CGTTTCGCCAGGTTTTGTAACT 59.968 45.455 0.00 0.00 34.59 2.24
1692 1752 3.633065 GGTTTTGTAACTTAGGGTGTGCA 59.367 43.478 0.00 0.00 34.59 4.57
1814 1874 5.354234 AGCGTTGAGGTTATTCGATCAAATT 59.646 36.000 0.00 0.00 33.74 1.82
1825 1885 2.026356 TCGATCAAATTCCTTGCCCTCA 60.026 45.455 0.00 0.00 34.76 3.86
1834 1894 1.210478 TCCTTGCCCTCAGAATGTAGC 59.790 52.381 0.00 0.00 37.40 3.58
1886 1946 3.181449 TGAGTTGGGTTCTTGGAATTCGA 60.181 43.478 0.00 0.00 0.00 3.71
1905 1965 4.933330 TCGAATGTAGGCTGTCAATAGAC 58.067 43.478 0.00 0.00 45.19 2.59
1912 1972 2.116238 GGCTGTCAATAGACCCACCTA 58.884 52.381 0.00 0.00 44.33 3.08
2005 2065 1.685517 TGGCATTGTAAGCTGTTGCAA 59.314 42.857 0.00 0.00 41.74 4.08
2022 2082 6.611381 TGTTGCAATTCTATAACTGACTTGC 58.389 36.000 0.59 10.45 44.71 4.01
2066 2126 2.547299 TGATGTGTGCATGTGAGACA 57.453 45.000 0.00 0.00 35.07 3.41
2253 2316 0.835941 AGGCCAGAGAGCAATACCTG 59.164 55.000 5.01 0.00 0.00 4.00
2459 2522 3.118542 CAGTTGAAAGAAAGGTTGCAGC 58.881 45.455 0.00 0.00 0.00 5.25
2585 2648 5.886960 ATTCACTTTTGATTAGCGCTTCT 57.113 34.783 18.68 2.30 0.00 2.85
2624 2687 9.677567 TTGTTCATTTTGTATCTGAAACTAAGC 57.322 29.630 0.00 0.00 31.21 3.09
2702 2765 4.213270 TCAGGATTAGTTTGCGTCTTGTTG 59.787 41.667 0.00 0.00 0.00 3.33
3009 3073 8.833493 TGATCTCATTTATAACATTGCACTCTG 58.167 33.333 0.00 0.00 0.00 3.35
3123 3208 6.708054 AGACAAACCATTCTAGTCTTGACTTG 59.292 38.462 8.66 7.19 36.21 3.16
3139 3224 2.360801 GACTTGCACCAAAGTTTGCCTA 59.639 45.455 10.25 0.00 40.48 3.93
3211 3296 8.134905 TCATGATTCACGAAGACAAATATGAG 57.865 34.615 0.00 0.00 0.00 2.90
3265 3350 1.213678 TGCTAATCTGCCTTCAGCCAT 59.786 47.619 0.00 0.00 42.71 4.40
3619 3706 8.164070 TCTTTTAAAATACTTCCTCTGCCTCTT 58.836 33.333 0.09 0.00 0.00 2.85
3620 3707 7.687941 TTTAAAATACTTCCTCTGCCTCTTG 57.312 36.000 0.00 0.00 0.00 3.02
3653 3767 8.649973 AAAACGTCTTATATTTAGAGGCAGAG 57.350 34.615 0.00 0.00 32.26 3.35
3655 3769 5.244178 ACGTCTTATATTTAGAGGCAGAGGG 59.756 44.000 6.98 0.00 32.26 4.30
4061 4232 2.476185 GGCATGCATGAGTTTACACGTC 60.476 50.000 30.64 7.39 0.00 4.34
4104 4275 3.625853 TGTTTAATGCCGATCCCATTCA 58.374 40.909 8.94 1.33 34.87 2.57
4154 4325 7.189079 AGGTTTTAGAAGAGTCTAATCTGGG 57.811 40.000 4.83 0.00 44.12 4.45
4176 4347 2.109181 GGAGATGCCGCCAGGTAC 59.891 66.667 0.00 0.00 40.50 3.34
4177 4348 2.279517 GAGATGCCGCCAGGTACG 60.280 66.667 0.00 0.00 40.50 3.67
4178 4349 3.075005 AGATGCCGCCAGGTACGT 61.075 61.111 0.00 0.00 40.50 3.57
4179 4350 1.731433 GAGATGCCGCCAGGTACGTA 61.731 60.000 0.00 0.00 40.50 3.57
4253 4432 2.546789 CCGCGGAGAAAGTTTACTTTGT 59.453 45.455 24.07 8.52 45.37 2.83
4254 4433 3.002965 CCGCGGAGAAAGTTTACTTTGTT 59.997 43.478 24.07 1.37 45.37 2.83
4255 4434 3.966218 CGCGGAGAAAGTTTACTTTGTTG 59.034 43.478 12.27 6.89 45.37 3.33
4266 4445 9.968870 AAAGTTTACTTTGTTGACTGTACAAAA 57.031 25.926 7.05 0.00 43.87 2.44
4269 4448 5.576447 ACTTTGTTGACTGTACAAAAGGG 57.424 39.130 16.07 0.00 42.87 3.95
4277 4456 1.886542 CTGTACAAAAGGGAGTTGGCC 59.113 52.381 0.00 0.00 0.00 5.36
4337 4516 2.951475 TTTGGTGCACTGACCCCGAC 62.951 60.000 17.98 0.00 34.79 4.79
4358 4537 1.141657 TCCTATGGTTGAGCTGGCATC 59.858 52.381 0.00 0.00 0.00 3.91
4506 4686 0.958091 TTGACCCTGTTCAAATGCCG 59.042 50.000 0.00 0.00 32.42 5.69
4550 4730 5.880887 TGTGTTGTGTGGTGAGTTTAATACA 59.119 36.000 0.00 0.00 0.00 2.29
4551 4731 6.183360 TGTGTTGTGTGGTGAGTTTAATACAC 60.183 38.462 0.00 0.00 38.97 2.90
4598 4781 3.236047 GTGGTGGGGGACTTTTGTTTAT 58.764 45.455 0.00 0.00 0.00 1.40
4656 4839 7.907194 ACGAGAAGAAGAACAAGTAAAGAAAC 58.093 34.615 0.00 0.00 0.00 2.78
4731 4914 2.418609 GCCTGTTTGTTGGGATAATGCC 60.419 50.000 0.00 0.00 0.00 4.40
4733 4916 3.119029 CCTGTTTGTTGGGATAATGCCAG 60.119 47.826 0.00 0.00 39.66 4.85
4760 4946 3.567397 TCAGGTAGTAGATGCCTCCTTC 58.433 50.000 0.00 0.00 43.12 3.46
4765 4951 2.403561 AGTAGATGCCTCCTTCCTTCC 58.596 52.381 0.00 0.00 0.00 3.46
4767 4953 1.211456 AGATGCCTCCTTCCTTCCTG 58.789 55.000 0.00 0.00 0.00 3.86
4768 4954 0.465278 GATGCCTCCTTCCTTCCTGC 60.465 60.000 0.00 0.00 0.00 4.85
4770 4956 0.252696 TGCCTCCTTCCTTCCTGCTA 60.253 55.000 0.00 0.00 0.00 3.49
4771 4957 0.467804 GCCTCCTTCCTTCCTGCTAG 59.532 60.000 0.00 0.00 0.00 3.42
4772 4958 1.967274 GCCTCCTTCCTTCCTGCTAGA 60.967 57.143 0.00 0.00 0.00 2.43
4773 4959 2.688477 CCTCCTTCCTTCCTGCTAGAT 58.312 52.381 0.00 0.00 0.00 1.98
4775 4961 2.368221 CTCCTTCCTTCCTGCTAGATGG 59.632 54.545 0.00 0.00 33.40 3.51
4776 4962 2.122768 CCTTCCTTCCTGCTAGATGGT 58.877 52.381 0.00 0.00 33.75 3.55
4790 7932 4.560513 GCTAGATGGTGTAGATTCCTCTGC 60.561 50.000 0.00 0.00 34.93 4.26
4871 8015 1.132262 CCAACCACGTATGCATTCCAC 59.868 52.381 3.54 0.00 0.00 4.02
4907 8051 5.171476 TCTACAGCAACTCAACTCAATAGC 58.829 41.667 0.00 0.00 0.00 2.97
4908 8052 2.738846 ACAGCAACTCAACTCAATAGCG 59.261 45.455 0.00 0.00 0.00 4.26
4909 8053 2.995939 CAGCAACTCAACTCAATAGCGA 59.004 45.455 0.00 0.00 0.00 4.93
4912 8056 3.181526 GCAACTCAACTCAATAGCGAGTG 60.182 47.826 0.00 0.00 45.56 3.51
4913 8057 3.944055 ACTCAACTCAATAGCGAGTGT 57.056 42.857 0.00 0.00 45.56 3.55
4914 8058 3.579709 ACTCAACTCAATAGCGAGTGTG 58.420 45.455 0.00 0.00 45.56 3.82
4915 8059 3.005897 ACTCAACTCAATAGCGAGTGTGT 59.994 43.478 0.00 0.00 45.56 3.72
5017 8161 1.396301 GAATGCTGCAGAGGAGAAACG 59.604 52.381 20.43 0.00 0.00 3.60
5035 8179 4.676951 TGGGGCGGCAAAAGGGAG 62.677 66.667 12.47 0.00 0.00 4.30
5043 8188 1.677217 CGGCAAAAGGGAGGAAGAGAG 60.677 57.143 0.00 0.00 0.00 3.20
5049 8194 5.806079 GCAAAAGGGAGGAAGAGAGAAGATT 60.806 44.000 0.00 0.00 0.00 2.40
5076 8221 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
5077 8222 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
5078 8223 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
5079 8224 9.638176 ATCATCATCATCATCATCATCATCATT 57.362 29.630 0.00 0.00 0.00 2.57
5080 8225 8.896744 TCATCATCATCATCATCATCATCATTG 58.103 33.333 0.00 0.00 0.00 2.82
5081 8226 7.088589 TCATCATCATCATCATCATCATTGC 57.911 36.000 0.00 0.00 0.00 3.56
5082 8227 5.897377 TCATCATCATCATCATCATTGCC 57.103 39.130 0.00 0.00 0.00 4.52
5083 8228 5.321102 TCATCATCATCATCATCATTGCCA 58.679 37.500 0.00 0.00 0.00 4.92
5084 8229 5.183140 TCATCATCATCATCATCATTGCCAC 59.817 40.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 0.454957 CAGGAGCGTTTGAAATGGCG 60.455 55.000 0.00 0.00 0.00 5.69
180 181 3.631145 TTACGAAGTTGTCTACGCACT 57.369 42.857 0.00 0.00 37.78 4.40
196 197 3.296943 GCATTGTGTAACGCAACATTACG 59.703 43.478 0.00 0.00 42.39 3.18
314 328 6.054295 TGCAGCAAAAAGGAACACAATATTT 58.946 32.000 0.00 0.00 0.00 1.40
368 383 3.359033 CCACATGACATGGAAATCTGGT 58.641 45.455 19.39 0.00 39.87 4.00
371 386 2.381911 GCCCACATGACATGGAAATCT 58.618 47.619 19.39 0.00 39.87 2.40
434 449 4.523173 AGAACCGATGAACTACAAGTCTGA 59.477 41.667 0.00 0.00 0.00 3.27
477 493 8.251721 AGGACCAGATATAACAACGATAATAGC 58.748 37.037 0.00 0.00 0.00 2.97
486 502 4.038162 AGCTCGAGGACCAGATATAACAAC 59.962 45.833 15.58 0.00 0.00 3.32
500 516 0.176680 GGATGCTTTCAGCTCGAGGA 59.823 55.000 15.58 0.22 42.97 3.71
595 612 6.140737 GTGCAAAGTAACACGAAATTCTGAAG 59.859 38.462 0.00 0.00 0.00 3.02
629 646 5.837437 TGTGATGGTTTTTCGCAATTTACT 58.163 33.333 0.00 0.00 31.07 2.24
639 656 3.987220 CGACCCAATTGTGATGGTTTTTC 59.013 43.478 4.43 0.00 36.14 2.29
645 662 2.436417 ACTTCGACCCAATTGTGATGG 58.564 47.619 4.43 0.65 37.71 3.51
655 674 3.627395 AGCATTGATAACTTCGACCCA 57.373 42.857 0.00 0.00 0.00 4.51
685 704 5.304101 TCAAAATGCATGTTTTCTAGTGGGT 59.696 36.000 0.00 0.00 0.00 4.51
691 710 6.164876 CACCCATCAAAATGCATGTTTTCTA 58.835 36.000 0.00 0.00 0.00 2.10
713 732 6.256321 ACAATTGAGCAAAAGTCATCAAACAC 59.744 34.615 13.59 0.00 35.47 3.32
733 752 1.927487 TGCAAGAGGCCATCACAATT 58.073 45.000 5.01 0.00 43.89 2.32
737 756 3.429410 GGTAAATTGCAAGAGGCCATCAC 60.429 47.826 5.01 0.00 43.89 3.06
740 759 2.110578 GGGTAAATTGCAAGAGGCCAT 58.889 47.619 5.01 0.00 43.89 4.40
744 763 2.493278 CAGGTGGGTAAATTGCAAGAGG 59.507 50.000 4.94 0.00 0.00 3.69
747 766 2.610232 GCACAGGTGGGTAAATTGCAAG 60.610 50.000 4.94 0.00 0.00 4.01
845 864 3.055094 ACATTTCCGAGTTGCATAGGAGT 60.055 43.478 0.00 0.00 33.89 3.85
870 889 1.422531 TTGCCAGCTTGGGAAAATGT 58.577 45.000 6.66 0.00 45.09 2.71
895 914 8.998277 ACTGCTGGAAAATATCTACTCTAGTA 57.002 34.615 0.00 0.00 0.00 1.82
922 942 0.894835 TCAGTGTATCGAGCCTGCAA 59.105 50.000 0.00 0.00 0.00 4.08
937 957 1.226603 GCGTCCGCGAGTTATCAGT 60.227 57.895 8.23 0.00 41.33 3.41
1022 1042 2.241176 GAGTGGAGAAGAGAGGAGAGGA 59.759 54.545 0.00 0.00 0.00 3.71
1046 1069 1.853319 GCGTGAAATATCTCGGCGG 59.147 57.895 7.21 0.00 41.54 6.13
1475 1502 0.252479 AGAGAGCGGGACTAAGACGA 59.748 55.000 0.00 0.00 0.00 4.20
1494 1542 3.947196 CCCACTGCAGAACATTTATGCTA 59.053 43.478 23.35 0.00 40.62 3.49
1527 1586 2.287547 TGCTCAAACGAATTGCTTGGTC 60.288 45.455 0.00 0.00 38.98 4.02
1611 1670 0.104934 AGGTGAGGTGAGGTGAGGTT 60.105 55.000 0.00 0.00 0.00 3.50
1612 1671 0.543174 GAGGTGAGGTGAGGTGAGGT 60.543 60.000 0.00 0.00 0.00 3.85
1613 1672 0.542938 TGAGGTGAGGTGAGGTGAGG 60.543 60.000 0.00 0.00 0.00 3.86
1614 1673 1.480137 GATGAGGTGAGGTGAGGTGAG 59.520 57.143 0.00 0.00 0.00 3.51
1615 1674 1.077828 AGATGAGGTGAGGTGAGGTGA 59.922 52.381 0.00 0.00 0.00 4.02
1628 1687 1.134461 CCAAGTGAGGAGCAGATGAGG 60.134 57.143 0.00 0.00 0.00 3.86
1641 1700 0.320374 GATGTCGGGACACCAAGTGA 59.680 55.000 3.22 0.00 45.05 3.41
1668 1728 4.261447 GCACACCCTAAGTTACAAAACCTG 60.261 45.833 0.00 0.00 36.15 4.00
1669 1729 3.887110 GCACACCCTAAGTTACAAAACCT 59.113 43.478 0.00 0.00 36.15 3.50
1681 1741 3.407698 CACACTACAATGCACACCCTAA 58.592 45.455 0.00 0.00 0.00 2.69
1692 1752 6.053632 TCAGATCAACATCCACACTACAAT 57.946 37.500 0.00 0.00 0.00 2.71
1814 1874 1.210478 GCTACATTCTGAGGGCAAGGA 59.790 52.381 0.00 0.00 0.00 3.36
1825 1885 5.131809 AGGCAAGAGAATAAGGCTACATTCT 59.868 40.000 18.96 18.96 42.72 2.40
1834 1894 3.549794 CCCAAGAGGCAAGAGAATAAGG 58.450 50.000 0.00 0.00 0.00 2.69
1859 1919 3.754965 TCCAAGAACCCAACTCATTGAG 58.245 45.455 12.17 12.17 38.15 3.02
1886 1946 3.780294 TGGGTCTATTGACAGCCTACATT 59.220 43.478 9.51 0.00 44.61 2.71
1912 1972 3.006323 CGGAGCTAGCTTCCATCTAATGT 59.994 47.826 20.42 0.00 0.00 2.71
2066 2126 9.313118 GAACATGGTGAAATTTTTGTTAGAAGT 57.687 29.630 0.00 0.00 0.00 3.01
2159 2222 7.844779 ACTCCCTTAGTATGACATCCTAAAAGA 59.155 37.037 2.54 2.10 36.36 2.52
2459 2522 4.335594 GCCACCAATACCTAAAGTAAGCAG 59.664 45.833 0.00 0.00 33.70 4.24
2579 2642 7.854534 TGAACAAACATCATATATGAGAAGCG 58.145 34.615 19.73 10.94 40.64 4.68
2702 2765 3.563390 GGCAGCACTTTGGAGATAGAATC 59.437 47.826 0.00 0.00 0.00 2.52
3005 3069 3.571401 AGCCTTCAATTTTGACCACAGAG 59.429 43.478 0.00 0.00 36.83 3.35
3009 3073 4.692228 TGAAAGCCTTCAATTTTGACCAC 58.308 39.130 0.00 0.00 38.65 4.16
3043 3127 6.098266 TGCTTGCAGGTTTGTCTATCTATCTA 59.902 38.462 0.00 0.00 0.00 1.98
3093 3177 7.939039 TCAAGACTAGAATGGTTTGTCTGAAAT 59.061 33.333 0.00 0.00 37.93 2.17
3123 3208 0.038251 GGCTAGGCAAACTTTGGTGC 60.038 55.000 12.16 0.00 40.14 5.01
3211 3296 2.087646 GAATGGAAGGACCTGAACTGC 58.912 52.381 0.00 0.00 39.86 4.40
3291 3376 9.727627 GATTCAGATGATGACCATTAGTTTTTC 57.272 33.333 0.00 0.00 37.77 2.29
3452 3537 8.752766 TGTATTACAAGCAAGTAGACAAGTAC 57.247 34.615 0.00 0.00 0.00 2.73
3619 3706 9.820229 CTAAATATAAGACGTTTTTGCAGTTCA 57.180 29.630 0.00 0.00 0.00 3.18
3653 3767 9.521503 GAAAATATTTCAGCAGAAAATACTCCC 57.478 33.333 8.45 0.00 46.06 4.30
3655 3769 9.774742 ACGAAAATATTTCAGCAGAAAATACTC 57.225 29.630 8.45 2.16 46.06 2.59
3708 3822 2.412770 GCAAAGGCAAACATGCATGTAC 59.587 45.455 31.55 22.43 39.09 2.90
3750 3872 0.606604 TGAAGCCGTACTCTGGAACC 59.393 55.000 0.00 0.00 0.00 3.62
3860 3982 0.941542 TCAAACTTCGCGGTTTCCAG 59.058 50.000 6.13 0.00 37.32 3.86
4005 4176 3.317430 GCTTAAAGGGAAGGATGAGCATG 59.683 47.826 0.00 0.00 0.00 4.06
4061 4232 9.956720 AAACAGAATCAAGTTACTTCATTTCAG 57.043 29.630 0.00 0.29 0.00 3.02
4130 4301 6.157123 CCCCAGATTAGACTCTTCTAAAACCT 59.843 42.308 0.00 0.00 45.52 3.50
4131 4302 6.350103 CCCCAGATTAGACTCTTCTAAAACC 58.650 44.000 0.00 0.00 45.52 3.27
4176 4347 1.126890 CAGCGTGCATCTCATCTACG 58.873 55.000 0.00 0.00 37.77 3.51
4177 4348 2.392821 CTCAGCGTGCATCTCATCTAC 58.607 52.381 0.00 0.00 0.00 2.59
4178 4349 1.339291 CCTCAGCGTGCATCTCATCTA 59.661 52.381 0.00 0.00 0.00 1.98
4179 4350 0.104487 CCTCAGCGTGCATCTCATCT 59.896 55.000 0.00 0.00 0.00 2.90
4222 4393 0.609151 TTCTCCGCGGAATGTTGGTA 59.391 50.000 30.53 7.20 0.00 3.25
4223 4394 0.250553 TTTCTCCGCGGAATGTTGGT 60.251 50.000 30.53 0.00 0.00 3.67
4224 4395 0.447801 CTTTCTCCGCGGAATGTTGG 59.552 55.000 30.53 16.53 0.00 3.77
4226 4397 1.892209 AACTTTCTCCGCGGAATGTT 58.108 45.000 30.53 24.09 38.14 2.71
4227 4398 1.892209 AAACTTTCTCCGCGGAATGT 58.108 45.000 30.53 19.79 35.88 2.71
4253 4432 4.204012 CCAACTCCCTTTTGTACAGTCAA 58.796 43.478 0.00 0.00 0.00 3.18
4254 4433 3.815809 CCAACTCCCTTTTGTACAGTCA 58.184 45.455 0.00 0.00 0.00 3.41
4255 4434 2.552743 GCCAACTCCCTTTTGTACAGTC 59.447 50.000 0.00 0.00 0.00 3.51
4266 4445 0.032615 TTTGTGTTGGCCAACTCCCT 60.033 50.000 40.40 0.00 41.67 4.20
4269 4448 3.451141 TGAATTTGTGTTGGCCAACTC 57.549 42.857 40.40 36.92 41.67 3.01
4277 4456 4.420168 ACACGGAACTTGAATTTGTGTTG 58.580 39.130 0.00 0.00 35.74 3.33
4337 4516 0.543277 TGCCAGCTCAACCATAGGAG 59.457 55.000 0.00 0.00 0.00 3.69
4358 4537 6.292168 CGACCTCCTTGCGTAAATAATGTTAG 60.292 42.308 0.00 0.00 0.00 2.34
4416 4595 2.911723 GCTAGTATATTGACAGCTCGCG 59.088 50.000 0.00 0.00 0.00 5.87
4420 4599 3.508012 CCCGAGCTAGTATATTGACAGCT 59.492 47.826 0.00 0.00 44.95 4.24
4485 4665 2.029110 CGGCATTTGAACAGGGTCAATT 60.029 45.455 0.00 0.00 37.36 2.32
4506 4686 3.414700 CAGACCGCGTTCCAGTGC 61.415 66.667 4.92 0.00 0.00 4.40
4525 4705 4.688511 TTAAACTCACCACACAACACAC 57.311 40.909 0.00 0.00 0.00 3.82
4584 4767 5.873179 TGTCATCGATAAACAAAAGTCCC 57.127 39.130 9.65 0.00 0.00 4.46
4598 4781 3.005791 AGGCATCGTATTCATGTCATCGA 59.994 43.478 0.00 0.00 0.00 3.59
4632 4815 8.058915 CAGTTTCTTTACTTGTTCTTCTTCTCG 58.941 37.037 0.00 0.00 0.00 4.04
4656 4839 3.798878 CGTTAGTGATGGCATAGTGTCAG 59.201 47.826 0.00 0.00 34.38 3.51
4731 4914 3.243704 GCATCTACTACCTGAGAAGGCTG 60.244 52.174 0.00 0.00 0.00 4.85
4733 4916 2.036604 GGCATCTACTACCTGAGAAGGC 59.963 54.545 0.00 0.00 0.00 4.35
4760 4946 3.300388 TCTACACCATCTAGCAGGAAGG 58.700 50.000 7.22 0.00 0.00 3.46
4765 4951 4.832266 AGAGGAATCTACACCATCTAGCAG 59.168 45.833 0.00 0.00 0.00 4.24
4767 4953 4.560513 GCAGAGGAATCTACACCATCTAGC 60.561 50.000 0.00 0.00 0.00 3.42
4768 4954 4.021544 GGCAGAGGAATCTACACCATCTAG 60.022 50.000 0.00 0.00 0.00 2.43
4770 4956 2.703007 GGCAGAGGAATCTACACCATCT 59.297 50.000 0.00 0.00 0.00 2.90
4771 4957 2.224402 GGGCAGAGGAATCTACACCATC 60.224 54.545 0.00 0.00 0.00 3.51
4772 4958 1.771255 GGGCAGAGGAATCTACACCAT 59.229 52.381 0.00 0.00 0.00 3.55
4773 4959 1.204146 GGGCAGAGGAATCTACACCA 58.796 55.000 0.00 0.00 0.00 4.17
4775 4961 0.470341 GGGGGCAGAGGAATCTACAC 59.530 60.000 0.00 0.00 0.00 2.90
4776 4962 2.930935 GGGGGCAGAGGAATCTACA 58.069 57.895 0.00 0.00 0.00 2.74
4795 7937 4.798288 CCAATGGCATCAACGCAG 57.202 55.556 0.00 0.00 0.00 5.18
4806 7950 2.564062 ACCACTTGAAGAATGCCAATGG 59.436 45.455 0.00 0.00 0.00 3.16
4907 8051 0.645355 GACACACACACACACACTCG 59.355 55.000 0.00 0.00 0.00 4.18
4908 8052 1.720805 TGACACACACACACACACTC 58.279 50.000 0.00 0.00 0.00 3.51
4909 8053 3.925453 TGACACACACACACACACT 57.075 47.368 0.00 0.00 0.00 3.55
5017 8161 4.986708 TCCCTTTTGCCGCCCCAC 62.987 66.667 0.00 0.00 0.00 4.61
5024 8168 1.630878 TCTCTCTTCCTCCCTTTTGCC 59.369 52.381 0.00 0.00 0.00 4.52
5035 8179 9.590451 GATGATGATGATAATCTTCTCTCTTCC 57.410 37.037 7.33 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.