Multiple sequence alignment - TraesCS2A01G390000

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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 TraesCS2A01G390000 chr2A 100.000 5914 0 0 1 5914 638784120 638778207 0.000000e+00 10922.0
1 TraesCS2A01G390000 chr2D 95.097 4895 117 38 533 5394 495036877 495041681 0.000000e+00 7596.0
2 TraesCS2A01G390000 chr2D 89.011 546 36 11 1 535 495036315 495036847 0.000000e+00 654.0
3 TraesCS2A01G390000 chr2D 86.908 359 27 11 5393 5736 495041757 495042110 9.300000e-103 385.0
4 TraesCS2A01G390000 chr2D 91.729 133 7 2 5785 5914 495043821 495043952 1.310000e-41 182.0
5 TraesCS2A01G390000 chr2B 93.996 4047 124 43 926 4962 582644958 582648895 0.000000e+00 6017.0
6 TraesCS2A01G390000 chr2B 92.818 543 21 10 1 535 582643926 582644458 0.000000e+00 771.0
7 TraesCS2A01G390000 chr2B 89.750 400 25 11 533 927 582644488 582644876 1.140000e-136 497.0
8 TraesCS2A01G390000 chr2B 86.352 381 34 10 5544 5914 582687497 582687869 3.320000e-107 399.0
9 TraesCS2A01G390000 chr2B 92.308 130 10 0 4983 5112 582686204 582686333 1.010000e-42 185.0
10 TraesCS2A01G390000 chr4A 79.630 108 16 6 4215 4319 680452884 680452988 8.220000e-09 73.1
11 TraesCS2A01G390000 chr4B 82.143 84 13 2 4237 4319 596775795 596775877 2.960000e-08 71.3


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 TraesCS2A01G390000 chr2A 638778207 638784120 5913 True 10922.000000 10922 100.00000 1 5914 1 chr2A.!!$R1 5913
1 TraesCS2A01G390000 chr2D 495036315 495043952 7637 False 2204.250000 7596 90.68625 1 5914 4 chr2D.!!$F1 5913
2 TraesCS2A01G390000 chr2B 582643926 582648895 4969 False 2428.333333 6017 92.18800 1 4962 3 chr2B.!!$F1 4961
3 TraesCS2A01G390000 chr2B 582686204 582687869 1665 False 292.000000 399 89.33000 4983 5914 2 chr2B.!!$F2 931

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
509 529 0.563173 TGTGATTTGGGTTTGGGGGA 59.437 50.000 0.00 0.0 0.00 4.81 F
1452 1590 1.410882 GGCGAGGAAGCTCAGAAGTAT 59.589 52.381 0.00 0.0 37.29 2.12 F
2185 2325 0.888619 GGCTTAAACTGGTTGCCTCC 59.111 55.000 0.00 0.0 40.36 4.30 F
2724 2864 0.240945 CGACCGCAGCTGGAAATTTT 59.759 50.000 17.12 0.0 0.00 1.82 F
3180 3321 1.079543 CACCAAGGCTGGAGTCTCG 60.080 63.158 9.53 0.0 46.92 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2134 0.249826 TGATGCTGTGTTGCTCGTCA 60.250 50.000 0.00 0.0 0.00 4.35 R
2703 2843 0.392998 AATTTCCAGCTGCGGTCGAT 60.393 50.000 8.66 0.0 0.00 3.59 R
3180 3321 1.363807 GCCCACTGCTTGAACAACC 59.636 57.895 0.00 0.0 36.87 3.77 R
3785 3926 2.566724 TGCACTCACCATCATGTCTACA 59.433 45.455 0.00 0.0 0.00 2.74 R
5072 5218 0.249398 ACGACCGATGGGGAAGAAAG 59.751 55.000 0.00 0.0 39.97 2.62 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
83 85 3.665190 ACTCCTTCCGTCTGCTAAAAAG 58.335 45.455 0.00 0.00 0.00 2.27
89 94 5.412904 CCTTCCGTCTGCTAAAAAGAGAAAT 59.587 40.000 0.00 0.00 0.00 2.17
189 206 3.008157 TCTCTACTCTCCACTCAAGACGT 59.992 47.826 0.00 0.00 0.00 4.34
212 229 2.189784 GGAAGCCCTAGGAACGGC 59.810 66.667 11.48 4.80 46.09 5.68
338 355 9.504708 TCCCATACGAACTGTTTTATTTTTCTA 57.495 29.630 0.00 0.00 0.00 2.10
367 384 8.906636 TCATAAACGATCTGAACTGTTACTAC 57.093 34.615 0.00 0.00 0.00 2.73
509 529 0.563173 TGTGATTTGGGTTTGGGGGA 59.437 50.000 0.00 0.00 0.00 4.81
545 597 4.338379 AACAGAGTGGTCTAAAGGACAC 57.662 45.455 0.00 0.00 46.16 3.67
559 611 1.448013 GACACGAGTTGCCTAGCCC 60.448 63.158 0.00 0.00 0.00 5.19
560 612 2.509336 CACGAGTTGCCTAGCCCG 60.509 66.667 0.00 0.00 0.00 6.13
561 613 2.678934 ACGAGTTGCCTAGCCCGA 60.679 61.111 0.00 0.00 0.00 5.14
635 687 2.099062 CTCTTGGCGTTGCGATGC 59.901 61.111 9.88 9.88 37.06 3.91
668 720 5.541484 AGCCTTTCTTGAAACCAAATCAGAT 59.459 36.000 0.00 0.00 0.00 2.90
671 723 4.424061 TCTTGAAACCAAATCAGATGCG 57.576 40.909 0.00 0.00 0.00 4.73
683 735 1.550072 TCAGATGCGTGATGTTCCAGA 59.450 47.619 0.00 0.00 0.00 3.86
760 814 9.788960 GAACTTAGAACCCAAACATTTGATATC 57.211 33.333 5.91 0.00 40.55 1.63
762 816 9.178758 ACTTAGAACCCAAACATTTGATATCTC 57.821 33.333 5.91 0.00 40.55 2.75
769 823 6.919662 CCCAAACATTTGATATCTCGATTTGG 59.080 38.462 20.52 20.52 40.55 3.28
775 829 8.739039 ACATTTGATATCTCGATTTGGTTTCAA 58.261 29.630 3.98 0.00 0.00 2.69
785 839 4.676924 CGATTTGGTTTCAAGAAAGACTGC 59.323 41.667 0.00 0.00 33.98 4.40
789 843 4.206375 TGGTTTCAAGAAAGACTGCATCA 58.794 39.130 0.00 0.00 0.00 3.07
849 903 4.969484 AGTTGTTTGGAGATAGGTTCGTT 58.031 39.130 0.00 0.00 0.00 3.85
1074 1212 3.129287 GGCATTTCTTGATGTACCAGGTG 59.871 47.826 0.76 0.00 0.00 4.00
1235 1373 3.367292 GCCATCTCTAGTGCTATGCTCTC 60.367 52.174 0.00 0.00 34.22 3.20
1241 1379 5.299028 TCTCTAGTGCTATGCTCTCTTCTTG 59.701 44.000 0.00 0.00 34.22 3.02
1259 1397 6.942576 TCTTCTTGCTTTACTGAGCCTAAATT 59.057 34.615 0.00 0.00 42.01 1.82
1297 1435 7.381789 TGTATCTGCCAAGGTTTATATGGTA 57.618 36.000 0.00 0.00 36.57 3.25
1452 1590 1.410882 GGCGAGGAAGCTCAGAAGTAT 59.589 52.381 0.00 0.00 37.29 2.12
1606 1744 6.073331 GCTCTTTCTAGCCTATAAAGTGCATG 60.073 42.308 21.76 0.00 43.74 4.06
1742 1881 9.496710 TCAGTAGTATTTCCAGGGTAGAAATAA 57.503 33.333 7.35 0.00 43.94 1.40
1774 1913 6.694447 ACGTACATACAACAATAACACTCCT 58.306 36.000 0.00 0.00 0.00 3.69
1775 1914 6.810182 ACGTACATACAACAATAACACTCCTC 59.190 38.462 0.00 0.00 0.00 3.71
1995 2134 5.833131 ACATGAGTCCAAAAGTTTACATGGT 59.167 36.000 0.00 0.00 38.35 3.55
2064 2203 1.511850 TGTTCTGAACCTGACATGCG 58.488 50.000 17.26 0.00 0.00 4.73
2114 2253 9.565213 CTATCTTTTTGCAGGTTATTCTTTCTG 57.435 33.333 0.00 0.00 0.00 3.02
2115 2254 7.581213 TCTTTTTGCAGGTTATTCTTTCTGA 57.419 32.000 0.00 0.00 0.00 3.27
2116 2255 8.006298 TCTTTTTGCAGGTTATTCTTTCTGAA 57.994 30.769 0.00 0.00 39.24 3.02
2117 2256 8.641541 TCTTTTTGCAGGTTATTCTTTCTGAAT 58.358 29.630 0.00 0.00 46.22 2.57
2118 2257 9.264719 CTTTTTGCAGGTTATTCTTTCTGAATT 57.735 29.630 0.00 0.00 42.28 2.17
2119 2258 9.612066 TTTTTGCAGGTTATTCTTTCTGAATTT 57.388 25.926 0.00 0.00 42.28 1.82
2120 2259 8.816640 TTTGCAGGTTATTCTTTCTGAATTTC 57.183 30.769 0.00 0.00 42.28 2.17
2121 2260 7.765695 TGCAGGTTATTCTTTCTGAATTTCT 57.234 32.000 0.00 0.00 42.28 2.52
2122 2261 7.820648 TGCAGGTTATTCTTTCTGAATTTCTC 58.179 34.615 0.00 0.00 42.28 2.87
2123 2262 7.448161 TGCAGGTTATTCTTTCTGAATTTCTCA 59.552 33.333 0.00 0.00 42.28 3.27
2124 2263 8.465201 GCAGGTTATTCTTTCTGAATTTCTCAT 58.535 33.333 0.00 0.00 42.28 2.90
2126 2265 9.972106 AGGTTATTCTTTCTGAATTTCTCATCT 57.028 29.630 0.00 0.00 42.28 2.90
2185 2325 0.888619 GGCTTAAACTGGTTGCCTCC 59.111 55.000 0.00 0.00 40.36 4.30
2568 2708 6.182627 TGGAGAGTTCAATGCTACAATTCAT 58.817 36.000 0.00 0.00 0.00 2.57
2703 2843 2.903350 CTGCACAGCCACACAGCA 60.903 61.111 0.00 0.00 34.23 4.41
2724 2864 0.240945 CGACCGCAGCTGGAAATTTT 59.759 50.000 17.12 0.00 0.00 1.82
2800 2940 2.339728 CGGAGCTCGGTGAGAATATC 57.660 55.000 12.89 0.00 34.75 1.63
3027 3168 9.813080 GAAAGCTACTAGTTTGATTTGTAAGTG 57.187 33.333 13.82 0.00 0.00 3.16
3030 3171 9.209175 AGCTACTAGTTTGATTTGTAAGTGAAG 57.791 33.333 0.00 0.00 0.00 3.02
3066 3207 5.298347 ACTTGTTTGTAGGCAGTAGAAGAC 58.702 41.667 0.00 0.00 0.00 3.01
3072 3213 1.339097 AGGCAGTAGAAGACGGTGTT 58.661 50.000 0.00 0.00 0.00 3.32
3180 3321 1.079543 CACCAAGGCTGGAGTCTCG 60.080 63.158 9.53 0.00 46.92 4.04
3429 3570 7.646130 CGTACTATCTGTTTCAGATCTTCCTTC 59.354 40.741 14.31 2.52 46.83 3.46
3785 3926 2.282180 GCCATGGTTGTGGACGGT 60.282 61.111 14.67 0.00 42.02 4.83
4715 4859 2.804090 GACGAGTTCACCGTCGCC 60.804 66.667 0.00 0.00 45.23 5.54
4966 5112 2.243810 CTGTATACAGAGGGAGGAGCC 58.756 57.143 25.83 0.00 46.59 4.70
4969 5115 0.937441 ATACAGAGGGAGGAGCCTCA 59.063 55.000 17.68 0.00 44.40 3.86
4981 5127 2.087646 GGAGCCTCACAAAATCTGGAC 58.912 52.381 0.00 0.00 0.00 4.02
5072 5218 0.394352 ATTTCAGGCCACGTCATCCC 60.394 55.000 5.01 0.00 0.00 3.85
5178 5377 2.064723 CTCGCCATCTCCGTCGATGT 62.065 60.000 3.52 0.00 39.26 3.06
5185 5384 2.047002 TCTCCGTCGATGTATCACCA 57.953 50.000 3.52 0.00 0.00 4.17
5186 5385 1.947456 TCTCCGTCGATGTATCACCAG 59.053 52.381 3.52 0.00 0.00 4.00
5187 5386 1.676529 CTCCGTCGATGTATCACCAGT 59.323 52.381 3.52 0.00 0.00 4.00
5206 5431 2.526120 GGCGAGATTGTAGCACGGC 61.526 63.158 0.00 0.00 41.48 5.68
5208 5433 2.230940 CGAGATTGTAGCACGGCCG 61.231 63.158 26.86 26.86 0.00 6.13
5223 5448 2.584608 CCGCCAGTGGGTTCCTAG 59.415 66.667 12.15 0.00 36.17 3.02
5227 5452 0.038310 GCCAGTGGGTTCCTAGCTTT 59.962 55.000 12.15 0.00 36.17 3.51
5229 5454 1.351017 CCAGTGGGTTCCTAGCTTTGA 59.649 52.381 0.00 0.00 0.00 2.69
5273 5498 1.191944 CGTTGGATCGTGTGAGATCG 58.808 55.000 1.54 0.00 45.90 3.69
5285 5510 1.732259 GTGAGATCGAACGGTTTGCAT 59.268 47.619 3.11 0.00 0.00 3.96
5305 5530 3.723348 GACCAGCGCACCGTTTCC 61.723 66.667 11.47 0.00 0.00 3.13
5361 5587 0.738762 TGCAAGAGCGAGATCTGTGC 60.739 55.000 0.00 3.88 46.23 4.57
5424 6456 5.359194 TCATTCTGATCCAAAGTACTCCC 57.641 43.478 0.00 0.00 0.00 4.30
5425 6457 5.032846 TCATTCTGATCCAAAGTACTCCCT 58.967 41.667 0.00 0.00 0.00 4.20
5426 6458 5.129485 TCATTCTGATCCAAAGTACTCCCTC 59.871 44.000 0.00 0.00 0.00 4.30
5427 6459 3.375699 TCTGATCCAAAGTACTCCCTCC 58.624 50.000 0.00 0.00 0.00 4.30
5428 6460 2.101582 CTGATCCAAAGTACTCCCTCCG 59.898 54.545 0.00 0.00 0.00 4.63
5429 6461 2.108970 GATCCAAAGTACTCCCTCCGT 58.891 52.381 0.00 0.00 0.00 4.69
5430 6462 1.263356 TCCAAAGTACTCCCTCCGTG 58.737 55.000 0.00 0.00 0.00 4.94
5431 6463 0.249398 CCAAAGTACTCCCTCCGTGG 59.751 60.000 0.00 0.00 0.00 4.94
5432 6464 0.391263 CAAAGTACTCCCTCCGTGGC 60.391 60.000 0.00 0.00 0.00 5.01
5433 6465 1.885163 AAAGTACTCCCTCCGTGGCG 61.885 60.000 0.00 0.00 0.00 5.69
5434 6466 3.066814 GTACTCCCTCCGTGGCGT 61.067 66.667 0.00 0.00 0.00 5.68
5435 6467 2.283388 TACTCCCTCCGTGGCGTT 60.283 61.111 0.00 0.00 0.00 4.84
5437 6469 0.611618 TACTCCCTCCGTGGCGTTTA 60.612 55.000 0.00 0.00 0.00 2.01
5438 6470 1.153628 CTCCCTCCGTGGCGTTTAG 60.154 63.158 0.00 0.00 0.00 1.85
5439 6471 1.601419 CTCCCTCCGTGGCGTTTAGA 61.601 60.000 0.00 0.00 0.00 2.10
5440 6472 0.974010 TCCCTCCGTGGCGTTTAGAT 60.974 55.000 0.00 0.00 0.00 1.98
5441 6473 0.529992 CCCTCCGTGGCGTTTAGATC 60.530 60.000 0.00 0.00 0.00 2.75
5443 6475 1.278238 CTCCGTGGCGTTTAGATCAC 58.722 55.000 0.00 0.00 0.00 3.06
5444 6476 0.892755 TCCGTGGCGTTTAGATCACT 59.107 50.000 0.00 0.00 0.00 3.41
5445 6477 2.093890 TCCGTGGCGTTTAGATCACTA 58.906 47.619 0.00 0.00 0.00 2.74
5446 6478 2.492881 TCCGTGGCGTTTAGATCACTAA 59.507 45.455 0.00 0.00 36.90 2.24
5447 6479 3.056678 TCCGTGGCGTTTAGATCACTAAA 60.057 43.478 0.00 0.00 43.52 1.85
5524 6562 8.911918 ACTAGACGAGATTAGATGTATGAGTT 57.088 34.615 0.00 0.00 0.00 3.01
5547 6585 6.723298 TCTCAAAATTTAAGGGTTGCTCAA 57.277 33.333 0.00 0.00 0.00 3.02
5610 6648 2.399916 AGCTGAAGCCATTGACTCTC 57.600 50.000 0.00 0.00 43.38 3.20
5651 6695 1.824852 TCTAGCTCTGAATGCGACCAA 59.175 47.619 0.00 0.00 35.28 3.67
5699 6743 3.367992 TTACGCAGACACGGTTTAAGA 57.632 42.857 0.00 0.00 37.37 2.10
5707 6780 5.049954 GCAGACACGGTTTAAGAATGTAACA 60.050 40.000 0.00 0.00 0.00 2.41
5720 6793 6.903883 AGAATGTAACAATCATACGTGGTC 57.096 37.500 0.00 0.00 0.00 4.02
5721 6794 6.403049 AGAATGTAACAATCATACGTGGTCA 58.597 36.000 0.00 0.00 0.00 4.02
5722 6795 7.047891 AGAATGTAACAATCATACGTGGTCAT 58.952 34.615 0.00 0.00 0.00 3.06
5723 6796 6.603237 ATGTAACAATCATACGTGGTCATG 57.397 37.500 0.00 0.00 0.00 3.07
5724 6797 4.331443 TGTAACAATCATACGTGGTCATGC 59.669 41.667 0.00 0.00 0.00 4.06
5725 6798 3.266510 ACAATCATACGTGGTCATGCT 57.733 42.857 0.00 0.00 0.00 3.79
5726 6799 4.400529 ACAATCATACGTGGTCATGCTA 57.599 40.909 0.00 0.00 0.00 3.49
5727 6800 4.765273 ACAATCATACGTGGTCATGCTAA 58.235 39.130 0.00 0.00 0.00 3.09
5728 6801 4.570772 ACAATCATACGTGGTCATGCTAAC 59.429 41.667 0.00 0.00 0.00 2.34
5729 6802 3.173668 TCATACGTGGTCATGCTAACC 57.826 47.619 0.00 0.00 37.31 2.85
5730 6803 2.764010 TCATACGTGGTCATGCTAACCT 59.236 45.455 0.00 0.00 37.69 3.50
5731 6804 3.955551 TCATACGTGGTCATGCTAACCTA 59.044 43.478 0.00 0.00 37.69 3.08
5732 6805 2.961526 ACGTGGTCATGCTAACCTAG 57.038 50.000 3.91 1.09 37.69 3.02
5733 6806 2.453521 ACGTGGTCATGCTAACCTAGA 58.546 47.619 3.91 0.00 37.69 2.43
5734 6807 2.829720 ACGTGGTCATGCTAACCTAGAA 59.170 45.455 3.91 0.00 37.69 2.10
5735 6808 3.451178 ACGTGGTCATGCTAACCTAGAAT 59.549 43.478 3.91 0.00 37.69 2.40
5736 6809 4.051922 CGTGGTCATGCTAACCTAGAATC 58.948 47.826 3.91 0.00 37.69 2.52
5737 6810 4.381411 GTGGTCATGCTAACCTAGAATCC 58.619 47.826 3.91 0.00 37.69 3.01
5738 6811 4.037222 TGGTCATGCTAACCTAGAATCCA 58.963 43.478 3.91 0.00 37.69 3.41
5739 6812 4.101585 TGGTCATGCTAACCTAGAATCCAG 59.898 45.833 3.91 0.00 37.69 3.86
5740 6813 4.101741 GGTCATGCTAACCTAGAATCCAGT 59.898 45.833 0.00 0.00 33.78 4.00
5741 6814 5.396884 GGTCATGCTAACCTAGAATCCAGTT 60.397 44.000 0.00 0.00 33.78 3.16
5742 6815 6.116126 GTCATGCTAACCTAGAATCCAGTTT 58.884 40.000 0.00 0.00 0.00 2.66
5743 6816 6.258947 GTCATGCTAACCTAGAATCCAGTTTC 59.741 42.308 0.00 0.00 0.00 2.78
5744 6817 5.755409 TGCTAACCTAGAATCCAGTTTCA 57.245 39.130 0.00 0.00 0.00 2.69
5745 6818 6.121776 TGCTAACCTAGAATCCAGTTTCAA 57.878 37.500 0.00 0.00 0.00 2.69
5746 6819 6.539173 TGCTAACCTAGAATCCAGTTTCAAA 58.461 36.000 0.00 0.00 0.00 2.69
5747 6820 7.001674 TGCTAACCTAGAATCCAGTTTCAAAA 58.998 34.615 0.00 0.00 0.00 2.44
5748 6821 7.504238 TGCTAACCTAGAATCCAGTTTCAAAAA 59.496 33.333 0.00 0.00 0.00 1.94
5844 8617 0.888619 GGGCGGAGATGATATGACGA 59.111 55.000 0.00 0.00 0.00 4.20
5849 8622 2.412977 CGGAGATGATATGACGACGACC 60.413 54.545 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 94 2.635915 TGCCGGGTTTCTAAAGAGAAGA 59.364 45.455 2.18 0.00 42.66 2.87
120 132 4.827284 TCCTTTTCAGTTCCATTCTTCCAC 59.173 41.667 0.00 0.00 0.00 4.02
121 133 5.060427 TCCTTTTCAGTTCCATTCTTCCA 57.940 39.130 0.00 0.00 0.00 3.53
122 134 6.393171 CATTCCTTTTCAGTTCCATTCTTCC 58.607 40.000 0.00 0.00 0.00 3.46
123 135 6.393171 CCATTCCTTTTCAGTTCCATTCTTC 58.607 40.000 0.00 0.00 0.00 2.87
189 206 0.545787 TTCCTAGGGCTTCCGTTGGA 60.546 55.000 9.46 4.97 40.35 3.53
231 248 8.587952 AAAAAGTGGGATTGAAGAAATTTACG 57.412 30.769 0.00 0.00 0.00 3.18
257 274 4.617253 TGGAAGACAATCTCGAAAGGAA 57.383 40.909 0.00 0.00 0.00 3.36
258 275 4.826274 ATGGAAGACAATCTCGAAAGGA 57.174 40.909 0.00 0.00 0.00 3.36
259 276 5.874810 TGTAATGGAAGACAATCTCGAAAGG 59.125 40.000 0.00 0.00 0.00 3.11
260 277 6.456181 GCTGTAATGGAAGACAATCTCGAAAG 60.456 42.308 0.00 0.00 0.00 2.62
338 355 9.088512 GTAACAGTTCAGATCGTTTATGAGAAT 57.911 33.333 0.00 0.00 0.00 2.40
367 384 1.267235 CGCAAGCGAGCATTTGTCTAG 60.267 52.381 9.11 0.00 42.83 2.43
509 529 3.073062 ACTCTGTTTGTTACTCCTGCCAT 59.927 43.478 0.00 0.00 0.00 4.40
559 611 2.874701 CAAGAACTGGCCCAGATAATCG 59.125 50.000 19.90 0.00 35.18 3.34
560 612 3.891049 ACAAGAACTGGCCCAGATAATC 58.109 45.455 19.90 9.84 35.18 1.75
561 613 4.019174 CAACAAGAACTGGCCCAGATAAT 58.981 43.478 19.90 0.00 35.18 1.28
573 625 3.426159 CGCTTTGTGTGACAACAAGAACT 60.426 43.478 8.72 0.00 40.93 3.01
635 687 6.107343 GGTTTCAAGAAAGGCTAGTAGGTAG 58.893 44.000 0.00 0.00 0.00 3.18
668 720 3.885724 TCTATTCTGGAACATCACGCA 57.114 42.857 0.00 0.00 38.20 5.24
671 723 8.908786 TTAATCCATCTATTCTGGAACATCAC 57.091 34.615 0.00 0.00 45.57 3.06
712 764 5.651530 TCTAACTGAAGAATTAGCCTCGTG 58.348 41.667 0.00 0.00 0.00 4.35
713 765 5.916661 TCTAACTGAAGAATTAGCCTCGT 57.083 39.130 0.00 0.00 0.00 4.18
760 814 6.138761 CAGTCTTTCTTGAAACCAAATCGAG 58.861 40.000 0.00 0.00 0.00 4.04
762 816 4.676924 GCAGTCTTTCTTGAAACCAAATCG 59.323 41.667 0.00 0.00 0.00 3.34
769 823 4.225208 GCTGATGCAGTCTTTCTTGAAAC 58.775 43.478 0.00 0.00 39.41 2.78
775 829 2.239150 AGATGGCTGATGCAGTCTTTCT 59.761 45.455 0.00 0.89 36.97 2.52
785 839 1.767088 TCCCTTCAGAGATGGCTGATG 59.233 52.381 0.00 0.00 43.84 3.07
894 948 9.533831 TTGTAGAATCACTCTATGGCATCTATA 57.466 33.333 1.65 0.00 38.91 1.31
895 949 8.427902 TTGTAGAATCACTCTATGGCATCTAT 57.572 34.615 1.65 0.00 38.91 1.98
896 950 7.839680 TTGTAGAATCACTCTATGGCATCTA 57.160 36.000 1.65 0.00 38.91 1.98
897 951 6.737720 TTGTAGAATCACTCTATGGCATCT 57.262 37.500 1.65 0.00 38.91 2.90
898 952 7.976135 ATTTGTAGAATCACTCTATGGCATC 57.024 36.000 1.65 0.00 38.91 3.91
978 1115 0.988063 GACCCTTCTTTGGCTCCTCT 59.012 55.000 0.00 0.00 0.00 3.69
1074 1212 2.505407 AGGGAATTAAAAAGGGCCATGC 59.495 45.455 6.18 0.00 0.00 4.06
1152 1290 4.502087 GCATGAAGCTTTCCAAAACTTCCT 60.502 41.667 0.00 1.51 39.28 3.36
1174 1312 3.519339 GTGGTGTCACTGCACAGTTGC 62.519 57.143 0.00 0.00 40.20 4.17
1235 1373 6.749923 ATTTAGGCTCAGTAAAGCAAGAAG 57.250 37.500 0.00 0.00 44.35 2.85
1241 1379 3.487544 CCGCAATTTAGGCTCAGTAAAGC 60.488 47.826 0.00 0.00 41.73 3.51
1259 1397 2.036346 CAGATACATGAGATGGACCGCA 59.964 50.000 0.00 0.00 33.60 5.69
1297 1435 3.057626 ACTGGATCATCCTCCATCACT 57.942 47.619 4.96 0.00 44.23 3.41
1452 1590 3.244044 GCTTTGTTGTGGCCATTTCCTTA 60.244 43.478 9.72 0.00 0.00 2.69
1606 1744 9.869757 AACAGATAAAATGCCTAAAACAATACC 57.130 29.630 0.00 0.00 0.00 2.73
1759 1898 5.766150 TTGTTGGAGGAGTGTTATTGTTG 57.234 39.130 0.00 0.00 0.00 3.33
1774 1913 7.838884 TGAATTCAGCATCATTTATTGTTGGA 58.161 30.769 3.38 0.00 0.00 3.53
1775 1914 8.126871 CTGAATTCAGCATCATTTATTGTTGG 57.873 34.615 21.96 0.00 37.15 3.77
1831 1970 8.908903 TCAACTATAGCAAAACTTCCTTCAAAA 58.091 29.630 0.00 0.00 0.00 2.44
1977 2116 4.273969 TCGTCACCATGTAAACTTTTGGAC 59.726 41.667 0.00 0.00 33.36 4.02
1995 2134 0.249826 TGATGCTGTGTTGCTCGTCA 60.250 50.000 0.00 0.00 0.00 4.35
2033 2172 3.853671 GGTTCAGAACAAATGCGCTTATG 59.146 43.478 15.36 7.17 0.00 1.90
2064 2203 6.655425 AGGGCATAAGAACTAAGAAGTTTCAC 59.345 38.462 0.00 0.00 46.09 3.18
2117 2256 9.519191 TCCTATTGTCAAAATTCAGATGAGAAA 57.481 29.630 0.00 0.00 31.31 2.52
2118 2257 9.519191 TTCCTATTGTCAAAATTCAGATGAGAA 57.481 29.630 0.00 0.00 31.96 2.87
2119 2258 9.690913 ATTCCTATTGTCAAAATTCAGATGAGA 57.309 29.630 0.00 0.00 0.00 3.27
2185 2325 6.324819 CCTGTTGCACATATAACAAAAGAGG 58.675 40.000 0.00 0.00 36.47 3.69
2568 2708 3.495983 CCGGGTCATAAGGTGATGCATAA 60.496 47.826 0.00 0.00 39.48 1.90
2703 2843 0.392998 AATTTCCAGCTGCGGTCGAT 60.393 50.000 8.66 0.00 0.00 3.59
2724 2864 4.385199 CCCCTAGAAATTGCTGGTGTATGA 60.385 45.833 0.00 0.00 0.00 2.15
2870 3010 8.519799 ACCAGAAGAGAAAACAAAATGTTAGA 57.480 30.769 0.00 0.00 40.14 2.10
2884 3024 3.206150 GTCAGTGCAAACCAGAAGAGAA 58.794 45.455 0.00 0.00 0.00 2.87
3012 3152 6.669278 GGAGACCTTCACTTACAAATCAAAC 58.331 40.000 0.00 0.00 0.00 2.93
3066 3207 5.163854 GGAAAGACTGATAACATCAACACCG 60.164 44.000 0.00 0.00 39.11 4.94
3072 3213 4.883585 GCCATGGAAAGACTGATAACATCA 59.116 41.667 18.40 0.00 37.76 3.07
3180 3321 1.363807 GCCCACTGCTTGAACAACC 59.636 57.895 0.00 0.00 36.87 3.77
3381 3522 9.185192 GTACGTACTAGTAACTGTGAATGTTTT 57.815 33.333 18.47 0.00 0.00 2.43
3429 3570 7.305474 AGATGGTAGAAACAAATTAAGCAACG 58.695 34.615 0.00 0.00 0.00 4.10
3785 3926 2.566724 TGCACTCACCATCATGTCTACA 59.433 45.455 0.00 0.00 0.00 2.74
3911 4055 5.744345 CGTGTTGTTCTCATAGTACTCCATC 59.256 44.000 0.00 0.00 0.00 3.51
4271 4415 2.610694 CGCCGACATGATCATGGCC 61.611 63.158 33.31 24.12 43.92 5.36
4427 4571 3.712881 GTGGCGTCGAACACCAGC 61.713 66.667 0.00 0.00 29.78 4.85
4937 5081 5.001874 TCCCTCTGTATACAGTAGTATGCG 58.998 45.833 27.83 12.74 43.65 4.73
4938 5082 5.416326 CCTCCCTCTGTATACAGTAGTATGC 59.584 48.000 27.83 0.00 44.12 3.14
4966 5112 0.443869 CGCCGTCCAGATTTTGTGAG 59.556 55.000 0.00 0.00 0.00 3.51
4969 5115 0.953960 GTCCGCCGTCCAGATTTTGT 60.954 55.000 0.00 0.00 0.00 2.83
5030 5176 3.457610 AACGGTTACAGAAGGACGAAA 57.542 42.857 0.00 0.00 0.00 3.46
5072 5218 0.249398 ACGACCGATGGGGAAGAAAG 59.751 55.000 0.00 0.00 39.97 2.62
5178 5377 1.831106 ACAATCTCGCCACTGGTGATA 59.169 47.619 11.85 5.50 41.66 2.15
5185 5384 0.458543 CGTGCTACAATCTCGCCACT 60.459 55.000 0.00 0.00 0.00 4.00
5186 5385 1.421410 CCGTGCTACAATCTCGCCAC 61.421 60.000 0.00 0.00 0.00 5.01
5187 5386 1.153647 CCGTGCTACAATCTCGCCA 60.154 57.895 0.00 0.00 0.00 5.69
5206 5431 2.584608 CTAGGAACCCACTGGCGG 59.415 66.667 0.00 0.00 33.59 6.13
5208 5433 0.038310 AAAGCTAGGAACCCACTGGC 59.962 55.000 0.00 0.00 42.05 4.85
5223 5448 1.008538 CCCACGTTGCAGTCAAAGC 60.009 57.895 0.00 0.00 35.51 3.51
5227 5452 2.899838 GTGCCCACGTTGCAGTCA 60.900 61.111 9.64 0.00 39.87 3.41
5229 5454 3.209097 GTGTGCCCACGTTGCAGT 61.209 61.111 9.64 0.00 39.87 4.40
5273 5498 1.442017 GGTCGCATGCAAACCGTTC 60.442 57.895 19.57 0.00 0.00 3.95
5305 5530 0.174162 ATTTACTTCGGTCGGTCGGG 59.826 55.000 0.00 0.00 0.00 5.14
5424 6456 1.135083 AGTGATCTAAACGCCACGGAG 60.135 52.381 0.00 0.00 34.93 4.63
5425 6457 0.892755 AGTGATCTAAACGCCACGGA 59.107 50.000 0.00 0.00 34.93 4.69
5426 6458 2.572191 TAGTGATCTAAACGCCACGG 57.428 50.000 0.00 0.00 34.93 4.94
5427 6459 4.328983 ACATTTAGTGATCTAAACGCCACG 59.671 41.667 0.00 0.00 45.19 4.94
5428 6460 5.796350 ACATTTAGTGATCTAAACGCCAC 57.204 39.130 0.00 0.00 45.19 5.01
5429 6461 6.636705 ACTACATTTAGTGATCTAAACGCCA 58.363 36.000 0.00 0.00 45.19 5.69
5484 6522 5.809001 TCGTCTAGTACTCCCTCTGTAAAA 58.191 41.667 0.00 0.00 0.00 1.52
5524 6562 6.723298 TTGAGCAACCCTTAAATTTTGAGA 57.277 33.333 0.00 0.00 0.00 3.27
5625 6669 2.857152 CGCATTCAGAGCTAGAGTCAAC 59.143 50.000 0.00 0.00 0.00 3.18
5659 6703 9.337396 TGCGTAATCATAGTTGGAAGATAAAAT 57.663 29.630 0.00 0.00 0.00 1.82
5660 6704 8.725405 TGCGTAATCATAGTTGGAAGATAAAA 57.275 30.769 0.00 0.00 0.00 1.52
5682 6726 2.478894 ACATTCTTAAACCGTGTCTGCG 59.521 45.455 0.00 0.00 0.00 5.18
5699 6743 6.458206 GCATGACCACGTATGATTGTTACATT 60.458 38.462 0.00 0.00 0.00 2.71
5707 6780 4.127171 GGTTAGCATGACCACGTATGATT 58.873 43.478 0.00 0.00 37.14 2.57
5720 6793 6.115446 TGAAACTGGATTCTAGGTTAGCATG 58.885 40.000 0.00 0.00 0.00 4.06
5721 6794 6.313519 TGAAACTGGATTCTAGGTTAGCAT 57.686 37.500 0.00 0.00 0.00 3.79
5722 6795 5.755409 TGAAACTGGATTCTAGGTTAGCA 57.245 39.130 0.00 0.00 0.00 3.49
5723 6796 7.448748 TTTTGAAACTGGATTCTAGGTTAGC 57.551 36.000 0.00 0.00 0.00 3.09
5777 6850 6.641161 ATGGATGGACATGGTATAATGCTA 57.359 37.500 0.00 0.00 0.00 3.49
5778 6851 4.999469 TGGATGGACATGGTATAATGCT 57.001 40.909 0.00 0.00 0.00 3.79
5791 8561 6.703607 GGAATCGATATCATGTATGGATGGAC 59.296 42.308 0.00 7.76 0.00 4.02


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

AutoCloner maintained by Alex Coulton.