Multiple sequence alignment - TraesCS2A01G252900

Loading Multiple Alignment...

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 TraesCS2A01G252900 chr2A 100.000 5941 0 0 1 5941 384876944 384882884 0.000000e+00 10972
1 TraesCS2A01G252900 chr2A 96.129 620 19 2 5326 5941 744724398 744723780 0.000000e+00 1007
2 TraesCS2A01G252900 chr2A 95.106 613 23 4 5329 5936 571462228 571462838 0.000000e+00 959
3 TraesCS2A01G252900 chr2B 94.572 4348 152 23 794 5102 373989693 373993995 0.000000e+00 6645
4 TraesCS2A01G252900 chr2B 81.863 612 69 29 98 698 373989039 373989619 1.500000e-130 477
5 TraesCS2A01G252900 chr2B 93.985 133 8 0 5196 5328 373993994 373994126 1.010000e-47 202
6 TraesCS2A01G252900 chr2D 93.608 3817 126 49 22 3790 305903765 305907511 0.000000e+00 5589
7 TraesCS2A01G252900 chr2D 97.431 1557 30 4 3782 5328 305908483 305910039 0.000000e+00 2645
8 TraesCS2A01G252900 chr2D 93.103 116 6 2 5099 5214 389094928 389095041 1.020000e-37 169
9 TraesCS2A01G252900 chr3A 97.097 620 10 8 5325 5941 629034114 629034728 0.000000e+00 1038
10 TraesCS2A01G252900 chr4A 96.921 617 13 5 5326 5939 554842289 554842902 0.000000e+00 1029
11 TraesCS2A01G252900 chr4A 96.580 614 16 4 5329 5940 559939669 559940279 0.000000e+00 1013
12 TraesCS2A01G252900 chr7A 95.948 617 15 7 5329 5941 653531606 653530996 0.000000e+00 992
13 TraesCS2A01G252900 chr7A 95.638 619 19 5 5328 5941 270195398 270196013 0.000000e+00 987
14 TraesCS2A01G252900 chr7A 95.261 612 24 4 5329 5937 312304459 312303850 0.000000e+00 965
15 TraesCS2A01G252900 chr7A 94.935 612 26 4 5329 5937 312358170 312357561 0.000000e+00 953
16 TraesCS2A01G252900 chr1D 96.970 99 3 0 5100 5198 490538115 490538213 3.680000e-37 167
17 TraesCS2A01G252900 chr7D 96.040 101 4 0 5098 5198 51550737 51550637 1.320000e-36 165
18 TraesCS2A01G252900 chr7D 91.228 114 10 0 5084 5197 190163102 190163215 7.970000e-34 156
19 TraesCS2A01G252900 chr5D 96.000 100 4 0 5099 5198 65990489 65990588 4.760000e-36 163
20 TraesCS2A01G252900 chr5D 95.146 103 5 0 5100 5202 558970434 558970536 4.760000e-36 163
21 TraesCS2A01G252900 chr3D 95.146 103 5 0 5100 5202 138076337 138076235 4.760000e-36 163
22 TraesCS2A01G252900 chr5A 88.710 124 12 2 5091 5214 258060685 258060806 3.710000e-32 150


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 TraesCS2A01G252900 chr2A 384876944 384882884 5940 False 10972.000000 10972 100.0000 1 5941 1 chr2A.!!$F1 5940
1 TraesCS2A01G252900 chr2A 744723780 744724398 618 True 1007.000000 1007 96.1290 5326 5941 1 chr2A.!!$R1 615
2 TraesCS2A01G252900 chr2A 571462228 571462838 610 False 959.000000 959 95.1060 5329 5936 1 chr2A.!!$F2 607
3 TraesCS2A01G252900 chr2B 373989039 373994126 5087 False 2441.333333 6645 90.1400 98 5328 3 chr2B.!!$F1 5230
4 TraesCS2A01G252900 chr2D 305903765 305910039 6274 False 4117.000000 5589 95.5195 22 5328 2 chr2D.!!$F2 5306
5 TraesCS2A01G252900 chr3A 629034114 629034728 614 False 1038.000000 1038 97.0970 5325 5941 1 chr3A.!!$F1 616
6 TraesCS2A01G252900 chr4A 554842289 554842902 613 False 1029.000000 1029 96.9210 5326 5939 1 chr4A.!!$F1 613
7 TraesCS2A01G252900 chr4A 559939669 559940279 610 False 1013.000000 1013 96.5800 5329 5940 1 chr4A.!!$F2 611
8 TraesCS2A01G252900 chr7A 653530996 653531606 610 True 992.000000 992 95.9480 5329 5941 1 chr7A.!!$R3 612
9 TraesCS2A01G252900 chr7A 270195398 270196013 615 False 987.000000 987 95.6380 5328 5941 1 chr7A.!!$F1 613
10 TraesCS2A01G252900 chr7A 312303850 312304459 609 True 965.000000 965 95.2610 5329 5937 1 chr7A.!!$R1 608
11 TraesCS2A01G252900 chr7A 312357561 312358170 609 True 953.000000 953 94.9350 5329 5937 1 chr7A.!!$R2 608

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
944 1008 0.031616 CTCTCCCAACCCTAGCTCCT 60.032 60.000 0.0 0.0 0.00 3.69 F
1614 1724 0.179045 ACACTAGCCAATCCCGATGC 60.179 55.000 0.0 0.0 0.00 3.91 F
1949 2059 0.845337 TCATGCCCTGTGATATGCCA 59.155 50.000 0.0 0.0 0.00 4.92 F
3091 3201 1.475682 CAGAAAGGGAGAAGGCATTGC 59.524 52.381 0.0 0.0 0.00 3.56 F
3882 4972 1.386533 ATCCTGATTGAAAGGCTGCG 58.613 50.000 0.0 0.0 34.56 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 2567 1.002366 CCTTGAGATGCCGAAAGTCG 58.998 55.000 0.00 0.00 40.07 4.18 R
2997 3107 0.904649 CCATGCTGGTCCTACAGTCA 59.095 55.000 0.00 0.00 40.59 3.41 R
3666 3776 1.514443 GAAGCTCGGACCGTCTTCG 60.514 63.158 24.47 9.48 32.36 3.79 R
3893 4983 2.165319 ACACCCACTAAAGCGTCTTC 57.835 50.000 0.00 0.00 0.00 2.87 R
5272 6376 3.268330 CCACACATTCATCCTGACAGAG 58.732 50.000 3.32 0.00 0.00 3.35 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
64 65 8.159447 TCATTGCTTTATATATTGAGCTGGACT 58.841 33.333 16.37 0.00 36.16 3.85
120 121 2.868504 AAGGAGGGTCAGCCTTTGA 58.131 52.632 0.00 0.00 41.60 2.69
216 217 4.508124 GGACATCCTTACTTTAGTCATGCG 59.492 45.833 0.00 0.00 0.00 4.73
227 229 7.679659 ACTTTAGTCATGCGAAAAGAAAAAC 57.320 32.000 15.82 0.00 33.98 2.43
302 307 7.947890 TGAATCAACCAAGAGTAAAATAACCCT 59.052 33.333 0.00 0.00 0.00 4.34
303 308 9.457436 GAATCAACCAAGAGTAAAATAACCCTA 57.543 33.333 0.00 0.00 0.00 3.53
304 309 9.816787 AATCAACCAAGAGTAAAATAACCCTAA 57.183 29.630 0.00 0.00 0.00 2.69
305 310 9.816787 ATCAACCAAGAGTAAAATAACCCTAAA 57.183 29.630 0.00 0.00 0.00 1.85
306 311 9.643735 TCAACCAAGAGTAAAATAACCCTAAAA 57.356 29.630 0.00 0.00 0.00 1.52
350 355 5.291614 CGCAAATGAAGGGACAAATATTTGG 59.708 40.000 27.43 12.85 42.34 3.28
360 365 5.768333 GACAAATATTTGGCAGCAAAGAC 57.232 39.130 26.03 4.90 45.54 3.01
374 379 4.096984 CAGCAAAGACAAGAGACCAAAAGT 59.903 41.667 0.00 0.00 0.00 2.66
375 380 4.336713 AGCAAAGACAAGAGACCAAAAGTC 59.663 41.667 0.00 0.00 46.71 3.01
432 437 4.988598 AACCAGCTCGCCACACCG 62.989 66.667 0.00 0.00 0.00 4.94
532 559 0.614415 CTCAGCACCCCACTCTCTCT 60.614 60.000 0.00 0.00 0.00 3.10
533 560 0.613292 TCAGCACCCCACTCTCTCTC 60.613 60.000 0.00 0.00 0.00 3.20
534 561 0.614415 CAGCACCCCACTCTCTCTCT 60.614 60.000 0.00 0.00 0.00 3.10
535 562 0.324275 AGCACCCCACTCTCTCTCTC 60.324 60.000 0.00 0.00 0.00 3.20
536 563 0.324275 GCACCCCACTCTCTCTCTCT 60.324 60.000 0.00 0.00 0.00 3.10
537 564 1.762708 CACCCCACTCTCTCTCTCTC 58.237 60.000 0.00 0.00 0.00 3.20
538 565 1.284785 CACCCCACTCTCTCTCTCTCT 59.715 57.143 0.00 0.00 0.00 3.10
539 566 1.564348 ACCCCACTCTCTCTCTCTCTC 59.436 57.143 0.00 0.00 0.00 3.20
540 567 1.846439 CCCCACTCTCTCTCTCTCTCT 59.154 57.143 0.00 0.00 0.00 3.10
541 568 2.158755 CCCCACTCTCTCTCTCTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
542 569 2.774234 CCCACTCTCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
543 570 3.181461 CCCACTCTCTCTCTCTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
558 597 1.230650 TCTCTCTCCCTCTCCCCCA 60.231 63.158 0.00 0.00 0.00 4.96
663 704 3.955543 ATGGGCCCCGCGTTGAAAT 62.956 57.895 22.27 0.00 0.00 2.17
864 924 2.514824 GTCCAATCCTCAGCCCGC 60.515 66.667 0.00 0.00 0.00 6.13
942 1006 0.325765 ACCTCTCCCAACCCTAGCTC 60.326 60.000 0.00 0.00 0.00 4.09
943 1007 1.051556 CCTCTCCCAACCCTAGCTCC 61.052 65.000 0.00 0.00 0.00 4.70
944 1008 0.031616 CTCTCCCAACCCTAGCTCCT 60.032 60.000 0.00 0.00 0.00 3.69
951 1018 0.263468 AACCCTAGCTCCTCTCCTCC 59.737 60.000 0.00 0.00 0.00 4.30
955 1022 0.560688 CTAGCTCCTCTCCTCCCCTT 59.439 60.000 0.00 0.00 0.00 3.95
1037 1110 0.714439 GTAAGTGTTTCTCCGCGCTC 59.286 55.000 5.56 0.00 0.00 5.03
1066 1139 2.287788 CGCTTCCTTTTGCACTGTCAAT 60.288 45.455 0.00 0.00 0.00 2.57
1163 1255 1.333435 GGTTGTAACTGGAAACGCGTG 60.333 52.381 14.98 1.17 0.00 5.34
1164 1256 1.328374 GTTGTAACTGGAAACGCGTGT 59.672 47.619 14.98 7.31 0.00 4.49
1166 1258 1.210870 GTAACTGGAAACGCGTGTCA 58.789 50.000 29.40 18.31 0.00 3.58
1194 1286 7.364200 CGTTTTTGTTTATGGTTCTATGGACA 58.636 34.615 0.00 0.00 0.00 4.02
1195 1287 7.537306 CGTTTTTGTTTATGGTTCTATGGACAG 59.463 37.037 0.00 0.00 0.00 3.51
1253 1349 1.534729 CTGTTGGTTGGCTTCCTACC 58.465 55.000 9.11 9.11 46.81 3.18
1306 1402 2.039084 AGGGAGAACCAACTGCTGTTAG 59.961 50.000 8.79 4.48 43.89 2.34
1313 1409 2.069273 CCAACTGCTGTTAGACTTCCG 58.931 52.381 8.79 0.00 34.60 4.30
1360 1468 2.122413 TGTGGGCTGGACTGGAGT 60.122 61.111 0.00 0.00 0.00 3.85
1393 1502 0.602562 GCTGTTTGCTGCCCATTGTA 59.397 50.000 0.00 0.00 38.95 2.41
1448 1557 1.948834 TCACAATGAGGCAACACTGTG 59.051 47.619 16.00 16.00 45.35 3.66
1449 1558 0.670162 ACAATGAGGCAACACTGTGC 59.330 50.000 7.90 0.00 44.14 4.57
1501 1610 6.456988 CCAAAGCGTAAACATCATCCTAGAAC 60.457 42.308 0.00 0.00 0.00 3.01
1614 1724 0.179045 ACACTAGCCAATCCCGATGC 60.179 55.000 0.00 0.00 0.00 3.91
1812 1922 4.953667 TGGATGCAGATGTAGAGATCAAC 58.046 43.478 0.00 0.00 0.00 3.18
1892 2002 5.011840 TCAAGGAGGATATGATGCTCTTGAG 59.988 44.000 7.75 0.00 45.78 3.02
1899 2009 2.398252 TGATGCTCTTGAGAAGCCAG 57.602 50.000 1.30 0.00 0.00 4.85
1949 2059 0.845337 TCATGCCCTGTGATATGCCA 59.155 50.000 0.00 0.00 0.00 4.92
1982 2092 6.799827 AGCCAATAGTAGAGATAGATGAGGT 58.200 40.000 0.00 0.00 0.00 3.85
1995 2105 4.647564 AGATGAGGTGTTCAATGACCTT 57.352 40.909 0.00 0.00 42.95 3.50
2011 2121 8.198109 TCAATGACCTTAAGCTACTCTTGATAC 58.802 37.037 0.00 0.00 36.25 2.24
2253 2363 5.661056 TCCGTCAAGAGTTGATGTCTATT 57.339 39.130 7.83 0.00 43.53 1.73
2297 2407 4.039730 AGAAGATGAATCACATAGTCCCCG 59.960 45.833 0.00 0.00 39.56 5.73
2457 2567 8.246871 CCCAGAGAAGTAATTTCTGAAAAATCC 58.753 37.037 6.95 0.00 46.12 3.01
2683 2793 4.852134 TCAAGGGTTGACACAATCATTG 57.148 40.909 13.47 13.47 37.11 2.82
2749 2859 4.927425 CACTTGAGGAAAATTGCAGATTGG 59.073 41.667 0.00 0.00 0.00 3.16
2793 2903 3.117663 ACCTTGAAAACCAGCACCTTAGA 60.118 43.478 0.00 0.00 0.00 2.10
2912 3022 4.943705 ACAAATTATGAGACAAGTCGGCAT 59.056 37.500 13.33 13.33 35.11 4.40
2997 3107 7.220683 CGAACTGTGACAAGAAATTTTGTTGAT 59.779 33.333 21.72 9.10 41.15 2.57
3091 3201 1.475682 CAGAAAGGGAGAAGGCATTGC 59.524 52.381 0.00 0.00 0.00 3.56
3118 3228 9.283420 GTTTAGCTAATGAAGAAAATCAGAAGC 57.717 33.333 7.08 5.85 39.49 3.86
3381 3491 4.532834 TGGAATACAATGGGTTTCTAGGC 58.467 43.478 0.00 0.00 0.00 3.93
3549 3659 7.757941 TCCATATTGTTGATTCTCACACAAA 57.242 32.000 8.09 0.00 34.07 2.83
3556 3666 9.630098 ATTGTTGATTCTCACACAAATTGATAC 57.370 29.630 0.00 0.00 34.07 2.24
3575 3685 6.805713 TGATACGAGTATTGCTGAATTCAGA 58.194 36.000 34.43 18.02 46.59 3.27
3732 3842 6.825213 TCTTTTCTGGTCATATCTGATGTTGG 59.175 38.462 0.00 0.00 32.98 3.77
3765 3875 3.077391 AGGGACCAATCCTTTCCAATTGA 59.923 43.478 7.12 0.00 45.46 2.57
3882 4972 1.386533 ATCCTGATTGAAAGGCTGCG 58.613 50.000 0.00 0.00 34.56 5.18
4058 5149 6.947733 TCATCCATTTGTCAGATAAACCAGTT 59.052 34.615 0.00 0.00 0.00 3.16
4095 5186 8.451687 TGCATCAAGTGAATTTAATCTTTTCG 57.548 30.769 0.00 0.00 0.00 3.46
4103 5194 6.900299 GTGAATTTAATCTTTTCGGAGCTACG 59.100 38.462 13.63 13.63 0.00 3.51
4127 5218 8.400947 ACGTTCCTGATTTTGATTCATCTATTG 58.599 33.333 0.00 0.00 0.00 1.90
4164 5255 3.101437 TGAGCATCGGAGGGTAAAACTA 58.899 45.455 0.00 0.00 38.61 2.24
4191 5282 8.993121 GTAGATGGTTACATAATCATGTTCCTG 58.007 37.037 2.08 0.00 42.98 3.86
4205 5303 6.199376 TCATGTTCCTGTGTTATAGAGGGTA 58.801 40.000 0.00 0.00 40.23 3.69
4272 5370 6.045318 GCAAGTGAGTCTGCTGATATCTTTA 58.955 40.000 3.98 0.00 0.00 1.85
4472 5570 3.319405 TGACTCTCGAGCATTATTCTCCC 59.681 47.826 7.81 0.00 0.00 4.30
4768 5872 6.712095 AGAAGAATACTTGTTCTGTGCATCAA 59.288 34.615 0.00 0.00 41.19 2.57
4902 6006 1.608590 GCAAGCTTGTTGCAGGTCTAA 59.391 47.619 26.55 0.00 45.94 2.10
5272 6376 4.130286 ACCAGCTAGCAACATTCTCTAC 57.870 45.455 18.83 0.00 0.00 2.59
5296 6400 1.825090 TCAGGATGAATGTGTGGCAC 58.175 50.000 11.55 11.55 45.97 5.01
5318 6422 6.291849 GCACGCTACTGTAGATTCATTTAGTG 60.292 42.308 18.64 12.31 0.00 2.74
5790 6906 4.318332 GCTGAAAAATCGTCTACGCAAAAG 59.682 41.667 0.00 0.00 39.60 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.371136 CAGTTGATACTGTTGAGTATATGTGTT 57.629 33.333 0.00 0.00 44.14 3.32
5 6 8.932945 CAGTTGATACTGTTGAGTATATGTGT 57.067 34.615 0.00 0.00 44.14 3.72
36 37 9.524496 TCCAGCTCAATATATAAAGCAATGATT 57.476 29.630 17.11 0.00 37.22 2.57
88 89 4.223144 ACCCTCCTTTTTATGTGTGCTTT 58.777 39.130 0.00 0.00 0.00 3.51
91 92 3.153919 TGACCCTCCTTTTTATGTGTGC 58.846 45.455 0.00 0.00 0.00 4.57
102 103 2.868504 TCAAAGGCTGACCCTCCTT 58.131 52.632 0.00 0.00 45.62 3.36
103 104 4.668925 TCAAAGGCTGACCCTCCT 57.331 55.556 0.00 0.00 45.62 3.69
216 217 5.786574 TCGCGTATCAATCGTTTTTCTTTTC 59.213 36.000 5.77 0.00 0.00 2.29
227 229 4.675565 ACTCAAGTAATCGCGTATCAATCG 59.324 41.667 5.77 0.00 0.00 3.34
305 310 9.930693 TTTGCGGTTATATTATTCTTGGTTTTT 57.069 25.926 0.00 0.00 0.00 1.94
307 312 9.528018 CATTTGCGGTTATATTATTCTTGGTTT 57.472 29.630 0.00 0.00 0.00 3.27
308 313 8.908903 TCATTTGCGGTTATATTATTCTTGGTT 58.091 29.630 0.00 0.00 0.00 3.67
309 314 8.458573 TCATTTGCGGTTATATTATTCTTGGT 57.541 30.769 0.00 0.00 0.00 3.67
310 315 9.398170 CTTCATTTGCGGTTATATTATTCTTGG 57.602 33.333 0.00 0.00 0.00 3.61
311 316 9.398170 CCTTCATTTGCGGTTATATTATTCTTG 57.602 33.333 0.00 0.00 0.00 3.02
312 317 8.576442 CCCTTCATTTGCGGTTATATTATTCTT 58.424 33.333 0.00 0.00 0.00 2.52
313 318 7.942341 TCCCTTCATTTGCGGTTATATTATTCT 59.058 33.333 0.00 0.00 0.00 2.40
314 319 8.021396 GTCCCTTCATTTGCGGTTATATTATTC 58.979 37.037 0.00 0.00 0.00 1.75
315 320 7.504238 TGTCCCTTCATTTGCGGTTATATTATT 59.496 33.333 0.00 0.00 0.00 1.40
316 321 7.001674 TGTCCCTTCATTTGCGGTTATATTAT 58.998 34.615 0.00 0.00 0.00 1.28
317 322 6.358178 TGTCCCTTCATTTGCGGTTATATTA 58.642 36.000 0.00 0.00 0.00 0.98
318 323 5.197451 TGTCCCTTCATTTGCGGTTATATT 58.803 37.500 0.00 0.00 0.00 1.28
319 324 4.787551 TGTCCCTTCATTTGCGGTTATAT 58.212 39.130 0.00 0.00 0.00 0.86
320 325 4.223556 TGTCCCTTCATTTGCGGTTATA 57.776 40.909 0.00 0.00 0.00 0.98
321 326 3.080300 TGTCCCTTCATTTGCGGTTAT 57.920 42.857 0.00 0.00 0.00 1.89
322 327 2.570415 TGTCCCTTCATTTGCGGTTA 57.430 45.000 0.00 0.00 0.00 2.85
323 328 1.698506 TTGTCCCTTCATTTGCGGTT 58.301 45.000 0.00 0.00 0.00 4.44
324 329 1.698506 TTTGTCCCTTCATTTGCGGT 58.301 45.000 0.00 0.00 0.00 5.68
325 330 4.654091 ATATTTGTCCCTTCATTTGCGG 57.346 40.909 0.00 0.00 0.00 5.69
326 331 5.291614 CCAAATATTTGTCCCTTCATTTGCG 59.708 40.000 23.24 2.95 36.45 4.85
327 332 5.065090 GCCAAATATTTGTCCCTTCATTTGC 59.935 40.000 23.24 12.74 36.45 3.68
350 355 1.597742 TGGTCTCTTGTCTTTGCTGC 58.402 50.000 0.00 0.00 0.00 5.25
360 365 5.835113 TTTCCTTGACTTTTGGTCTCTTG 57.165 39.130 0.00 0.00 44.74 3.02
374 379 1.715785 CCCTTGGGCTTTTTCCTTGA 58.284 50.000 0.00 0.00 0.00 3.02
375 380 0.035317 GCCCTTGGGCTTTTTCCTTG 59.965 55.000 22.47 0.00 0.00 3.61
395 400 3.698765 CCGCTCCCATGGCTTTTT 58.301 55.556 6.09 0.00 0.00 1.94
532 559 3.309296 GAGAGGGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
533 560 2.370189 GGAGAGGGAGAGAGAGAGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
534 561 2.408565 GGAGAGGGAGAGAGAGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
535 562 1.421646 GGGAGAGGGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
536 563 1.518367 GGGAGAGGGAGAGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
537 564 0.478507 GGGGAGAGGGAGAGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
538 565 0.996762 GGGGGAGAGGGAGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
539 566 1.292941 TGGGGGAGAGGGAGAGAGAG 61.293 65.000 0.00 0.00 0.00 3.20
540 567 1.230650 TGGGGGAGAGGGAGAGAGA 60.231 63.158 0.00 0.00 0.00 3.10
541 568 1.075600 GTGGGGGAGAGGGAGAGAG 60.076 68.421 0.00 0.00 0.00 3.20
542 569 2.637640 GGTGGGGGAGAGGGAGAGA 61.638 68.421 0.00 0.00 0.00 3.10
543 570 2.041405 GGTGGGGGAGAGGGAGAG 60.041 72.222 0.00 0.00 0.00 3.20
663 704 4.988716 AGCTGACGTCGGGGTCCA 62.989 66.667 25.20 0.00 36.07 4.02
788 843 1.202486 GGAAGACGACACACCAGACAA 60.202 52.381 0.00 0.00 0.00 3.18
840 900 2.190578 GAGGATTGGACCAGGCGG 59.809 66.667 0.00 0.00 38.77 6.13
864 924 1.219393 GAGGAGGGAGCGGTGAAAG 59.781 63.158 0.00 0.00 0.00 2.62
1163 1255 3.972403 ACCATAAACAAAAACGGCTGAC 58.028 40.909 0.00 0.00 0.00 3.51
1164 1256 4.339814 AGAACCATAAACAAAAACGGCTGA 59.660 37.500 0.00 0.00 0.00 4.26
1166 1258 4.929819 AGAACCATAAACAAAAACGGCT 57.070 36.364 0.00 0.00 0.00 5.52
1214 1307 1.436600 CAGAGCGCACAGTTGATTCT 58.563 50.000 11.47 0.00 0.00 2.40
1253 1349 8.656806 TCTTATCCCTACCATTACCAAATACTG 58.343 37.037 0.00 0.00 0.00 2.74
1254 1350 8.808240 TCTTATCCCTACCATTACCAAATACT 57.192 34.615 0.00 0.00 0.00 2.12
1255 1351 9.503399 CTTCTTATCCCTACCATTACCAAATAC 57.497 37.037 0.00 0.00 0.00 1.89
1256 1352 9.455144 TCTTCTTATCCCTACCATTACCAAATA 57.545 33.333 0.00 0.00 0.00 1.40
1257 1353 8.344939 TCTTCTTATCCCTACCATTACCAAAT 57.655 34.615 0.00 0.00 0.00 2.32
1258 1354 7.637301 GCTCTTCTTATCCCTACCATTACCAAA 60.637 40.741 0.00 0.00 0.00 3.28
1313 1409 2.058057 CCAGTTGCGGTAAAAATGCAC 58.942 47.619 0.00 0.00 38.55 4.57
1393 1502 2.043980 CACTTAACGGCCGGCCATT 61.044 57.895 42.78 37.48 35.37 3.16
1403 1512 4.647291 ACAATTCGCTTCTCACTTAACG 57.353 40.909 0.00 0.00 0.00 3.18
1448 1557 1.291184 GAAAAATGTGCAAGCGGGGC 61.291 55.000 0.00 0.00 0.00 5.80
1449 1558 0.318120 AGAAAAATGTGCAAGCGGGG 59.682 50.000 0.00 0.00 0.00 5.73
1821 1931 9.442047 ACTTCCAGTTTCATCAAATCTAAGTAG 57.558 33.333 0.00 0.00 0.00 2.57
1892 2002 4.036734 TGTCATGAACAAAGTTCTGGCTTC 59.963 41.667 10.79 0.00 34.03 3.86
1899 2009 4.913924 GCATCACTGTCATGAACAAAGTTC 59.086 41.667 0.00 3.05 37.45 3.01
1949 2059 6.753913 TCTCTACTATTGGCTTTCCATGAT 57.246 37.500 0.00 0.00 43.05 2.45
1982 2092 6.360370 AGAGTAGCTTAAGGTCATTGAACA 57.640 37.500 11.11 0.00 0.00 3.18
1995 2105 6.127423 GGAACACCAGTATCAAGAGTAGCTTA 60.127 42.308 0.00 0.00 34.31 3.09
2011 2121 2.094752 CCTTAATTTGCCGGAACACCAG 60.095 50.000 5.05 0.00 0.00 4.00
2181 2291 4.355549 TCCGGTTCTCCCTTAGATTGTTA 58.644 43.478 0.00 0.00 33.05 2.41
2253 2363 4.404394 TCTGAAGGTAACAGCATATCCGAA 59.596 41.667 0.00 0.00 41.41 4.30
2297 2407 3.445096 ACCCAGATTTTCATGCTTACTGC 59.555 43.478 0.00 0.00 43.25 4.40
2358 2468 3.072476 CAGAGTGTTCCTCCCCTGTTTTA 59.928 47.826 0.00 0.00 41.47 1.52
2457 2567 1.002366 CCTTGAGATGCCGAAAGTCG 58.998 55.000 0.00 0.00 40.07 4.18
2474 2584 1.529744 TTCTTCCCCAGTTGAACCCT 58.470 50.000 0.00 0.00 0.00 4.34
2769 2879 2.583143 AGGTGCTGGTTTTCAAGGTAC 58.417 47.619 0.00 0.00 0.00 3.34
2793 2903 3.638160 TCATCTTTTCTGCAAGCAAACCT 59.362 39.130 0.00 0.00 0.00 3.50
2912 3022 8.231007 AGAGATCCTCATAGTCTCCTTTAATGA 58.769 37.037 0.00 0.00 39.30 2.57
2997 3107 0.904649 CCATGCTGGTCCTACAGTCA 59.095 55.000 0.00 0.00 40.59 3.41
3091 3201 9.483062 CTTCTGATTTTCTTCATTAGCTAAACG 57.517 33.333 10.85 5.11 0.00 3.60
3201 3311 8.296713 TCGATATCACGAAGTATCATTTCATCA 58.703 33.333 3.12 0.00 41.61 3.07
3204 3314 7.871853 TCTCGATATCACGAAGTATCATTTCA 58.128 34.615 3.12 0.00 41.61 2.69
3549 3659 7.928167 TCTGAATTCAGCAATACTCGTATCAAT 59.072 33.333 27.45 0.00 43.46 2.57
3556 3666 5.981915 TCTGATCTGAATTCAGCAATACTCG 59.018 40.000 27.45 9.98 43.46 4.18
3666 3776 1.514443 GAAGCTCGGACCGTCTTCG 60.514 63.158 24.47 9.48 32.36 3.79
3732 3842 6.169557 AGGATTGGTCCCTTGTTTAAAAAC 57.830 37.500 0.00 0.00 46.34 2.43
3893 4983 2.165319 ACACCCACTAAAGCGTCTTC 57.835 50.000 0.00 0.00 0.00 2.87
4080 5171 7.001695 ACGTAGCTCCGAAAAGATTAAATTC 57.998 36.000 5.42 0.00 0.00 2.17
4095 5186 3.596214 TCAAAATCAGGAACGTAGCTCC 58.404 45.455 0.00 0.00 44.48 4.70
4127 5218 9.515020 TCCGATGCTCAAATAATTGAAAATAAC 57.485 29.630 0.00 0.00 44.64 1.89
4164 5255 8.938883 AGGAACATGATTATGTAACCATCTACT 58.061 33.333 20.52 3.36 46.54 2.57
4189 5280 9.507329 AATAATTGCATACCCTCTATAACACAG 57.493 33.333 0.00 0.00 0.00 3.66
4205 5303 8.789825 TGTTCTTATTTGCCAAATAATTGCAT 57.210 26.923 19.85 0.00 41.18 3.96
4737 5841 9.372369 GCACAGAACAAGTATTCTTCTAACTAT 57.628 33.333 0.00 0.00 36.78 2.12
4768 5872 4.635699 TTATCTCCAGCATCTGCATCAT 57.364 40.909 4.79 0.00 45.16 2.45
4813 5917 6.882768 ATGAGTAAGACTCTTCCCATCTTT 57.117 37.500 8.04 0.00 45.27 2.52
4826 5930 8.947115 ACAAAAGGCATTAAGTATGAGTAAGAC 58.053 33.333 0.00 0.00 36.26 3.01
4902 6006 8.934023 TGTAAGTCATCCTTTTGTTTATTCCT 57.066 30.769 0.00 0.00 34.46 3.36
5272 6376 3.268330 CCACACATTCATCCTGACAGAG 58.732 50.000 3.32 0.00 0.00 3.35
5296 6400 8.079203 AGATCACTAAATGAATCTACAGTAGCG 58.921 37.037 2.26 0.00 41.93 4.26
5849 6967 8.419076 AAATAAAATTCAACAAGCAGTTTCGT 57.581 26.923 0.00 0.00 38.74 3.85


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

AutoCloner maintained by Alex Coulton.