Multiple sequence alignment - TraesCS5A01G426700

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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 TraesCS5A01G426700 chr5A 100.000 5684 0 0 1 5684 611633100 611638783 0.000000e+00 10497.0
1 TraesCS5A01G426700 chr5A 84.421 475 48 18 2468 2931 589355645 589355186 1.450000e-120 444.0
2 TraesCS5A01G426700 chr5A 96.875 32 1 0 2398 2429 589355709 589355678 3.000000e-03 54.7
3 TraesCS5A01G426700 chr5D 92.757 5771 228 79 1 5670 490007056 490012737 0.000000e+00 8167.0
4 TraesCS5A01G426700 chr5B 94.232 4386 177 32 1324 5670 604145649 604149997 0.000000e+00 6628.0
5 TraesCS5A01G426700 chr5B 86.656 1304 75 30 44 1274 604144380 604145657 0.000000e+00 1352.0
6 TraesCS5A01G426700 chr1A 84.728 478 52 15 2465 2931 7280334 7280801 5.190000e-125 459.0
7 TraesCS5A01G426700 chr1A 100.000 29 0 0 2398 2426 7280273 7280301 3.000000e-03 54.7
8 TraesCS5A01G426700 chr2A 84.167 480 46 22 2465 2931 118246143 118246605 6.760000e-119 438.0
9 TraesCS5A01G426700 chr2A 83.857 477 47 22 2468 2931 118233946 118233487 1.460000e-115 427.0
10 TraesCS5A01G426700 chr2B 80.384 469 53 25 2398 2849 37296850 37297296 2.560000e-83 320.0
11 TraesCS5A01G426700 chr2B 86.792 159 20 1 2773 2931 37308066 37308223 5.850000e-40 176.0
12 TraesCS5A01G426700 chr2B 86.335 161 20 2 2771 2931 37308270 37308428 2.110000e-39 174.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G426700 chr5A 611633100 611638783 5683 False 10497.00 10497 100.000 1 5684 1 chr5A.!!$F1 5683
1 TraesCS5A01G426700 chr5A 589355186 589355709 523 True 249.35 444 90.648 2398 2931 2 chr5A.!!$R1 533
2 TraesCS5A01G426700 chr5D 490007056 490012737 5681 False 8167.00 8167 92.757 1 5670 1 chr5D.!!$F1 5669
3 TraesCS5A01G426700 chr5B 604144380 604149997 5617 False 3990.00 6628 90.444 44 5670 2 chr5B.!!$F1 5626
4 TraesCS5A01G426700 chr1A 7280273 7280801 528 False 256.85 459 92.364 2398 2931 2 chr1A.!!$F1 533

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
691 741 0.391661 TTGTTCTGCTCCGATGCTCC 60.392 55.000 0.0 0.0 0.00 4.70 F
793 843 0.874390 TGATTCTGTGGTTTCTGCGC 59.126 50.000 0.0 0.0 0.00 6.09 F
1349 1433 1.347817 GCTCGGCTCAAAGTCTCACG 61.348 60.000 0.0 0.0 0.00 4.35 F
1355 1439 1.531578 GCTCAAAGTCTCACGTTTCCC 59.468 52.381 0.0 0.0 0.00 3.97 F
1900 1987 2.031157 GTGAAATCCACAAACTCCACCG 60.031 50.000 0.0 0.0 45.03 4.94 F
3498 3619 3.904339 ACGCCTAGATGTATTGATTCCCT 59.096 43.478 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1815 6.531021 TGTGATCAGACTCAATCATATGCAT 58.469 36.000 3.79 3.79 34.60 3.96 R
1900 1987 6.708285 TGAGACCCAATAAAAGTTAGTCTCC 58.292 40.000 13.09 0.00 45.13 3.71 R
3295 3416 4.697352 AGTGCTCACATTATTGAACAGACC 59.303 41.667 2.63 0.00 0.00 3.85 R
3296 3417 5.409520 TCAGTGCTCACATTATTGAACAGAC 59.590 40.000 2.63 0.00 0.00 3.51 R
3568 3689 1.476891 TCTTCGAATCTCAGGGAACGG 59.523 52.381 0.00 0.00 0.00 4.44 R
5401 5537 0.609406 TGAGAGGTCCAGTCCGACTG 60.609 60.000 19.97 19.97 45.53 3.51 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
25 26 4.167307 TCTTCCCCCTCTTTTGTTTAGTGT 59.833 41.667 0.00 0.00 0.00 3.55
26 27 4.094830 TCCCCCTCTTTTGTTTAGTGTC 57.905 45.455 0.00 0.00 0.00 3.67
27 28 3.720002 TCCCCCTCTTTTGTTTAGTGTCT 59.280 43.478 0.00 0.00 0.00 3.41
28 29 4.909088 TCCCCCTCTTTTGTTTAGTGTCTA 59.091 41.667 0.00 0.00 0.00 2.59
29 30 5.012768 TCCCCCTCTTTTGTTTAGTGTCTAG 59.987 44.000 0.00 0.00 0.00 2.43
30 31 5.012768 CCCCCTCTTTTGTTTAGTGTCTAGA 59.987 44.000 0.00 0.00 0.00 2.43
31 32 6.166982 CCCCTCTTTTGTTTAGTGTCTAGAG 58.833 44.000 0.00 0.00 0.00 2.43
42 43 7.822334 TGTTTAGTGTCTAGAGAGAGAGAGAAG 59.178 40.741 0.00 0.00 30.20 2.85
119 121 3.992943 AACCGAAGAGAGAGAGAGAGA 57.007 47.619 0.00 0.00 0.00 3.10
120 122 3.543680 ACCGAAGAGAGAGAGAGAGAG 57.456 52.381 0.00 0.00 0.00 3.20
121 123 3.104512 ACCGAAGAGAGAGAGAGAGAGA 58.895 50.000 0.00 0.00 0.00 3.10
221 235 3.911698 TCAGTCGGTGTGCGCTGT 61.912 61.111 9.73 0.00 0.00 4.40
263 277 0.666374 CACAACCCAAGGTTCGGTTC 59.334 55.000 0.00 0.00 43.05 3.62
264 278 0.816421 ACAACCCAAGGTTCGGTTCG 60.816 55.000 0.00 0.00 43.05 3.95
265 279 1.228033 AACCCAAGGTTCGGTTCGG 60.228 57.895 0.00 0.00 43.05 4.30
266 280 1.986632 AACCCAAGGTTCGGTTCGGT 61.987 55.000 0.00 0.00 43.05 4.69
267 281 1.228033 CCCAAGGTTCGGTTCGGTT 60.228 57.895 0.00 0.00 0.00 4.44
295 309 4.728102 CGTAAGCGGTCCGTGCCA 62.728 66.667 13.94 0.00 0.00 4.92
333 347 2.030412 CGCAACTTTTTGGGCCCC 59.970 61.111 22.27 0.85 38.67 5.80
335 349 2.503382 GCAACTTTTTGGGCCCCGA 61.503 57.895 22.27 4.75 32.81 5.14
346 379 4.436998 GCCCCGACGTGAGGTCTG 62.437 72.222 0.00 0.00 43.79 3.51
530 563 0.898326 AAAACAACCTCCGGCCATCC 60.898 55.000 2.24 0.00 0.00 3.51
688 737 1.396301 CTTCTTGTTCTGCTCCGATGC 59.604 52.381 0.00 0.00 0.00 3.91
691 741 0.391661 TTGTTCTGCTCCGATGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
725 775 4.814234 TCCTCGTAATAATGCATTGTGGAC 59.186 41.667 22.27 15.01 0.00 4.02
727 777 3.001838 TCGTAATAATGCATTGTGGACGC 59.998 43.478 25.89 10.85 0.00 5.19
793 843 0.874390 TGATTCTGTGGTTTCTGCGC 59.126 50.000 0.00 0.00 0.00 6.09
814 864 2.420466 TTTCAGGGAGGGGTTTCGGC 62.420 60.000 0.00 0.00 0.00 5.54
936 989 5.499139 AACAACAATAGTTCAGTGTGGTG 57.501 39.130 0.00 0.00 38.43 4.17
937 990 3.882888 ACAACAATAGTTCAGTGTGGTGG 59.117 43.478 0.04 0.00 37.97 4.61
938 991 3.857157 ACAATAGTTCAGTGTGGTGGT 57.143 42.857 0.00 0.00 33.30 4.16
996 1051 4.759096 CTTTTTCCTGCGGCCGCG 62.759 66.667 41.73 33.91 45.51 6.46
1047 1126 1.524849 GCTCGGGAGGAAGATTGGC 60.525 63.158 0.00 0.00 0.00 4.52
1098 1177 8.951787 TTGGTATGTTTCATATTAGCTTACGT 57.048 30.769 0.00 0.00 0.00 3.57
1117 1196 2.096811 CGTGCAAAATGGTTGTCATTGC 60.097 45.455 0.00 2.07 44.68 3.56
1122 1201 4.143347 GCAAAATGGTTGTCATTGCGTTAG 60.143 41.667 0.00 0.00 44.68 2.34
1124 1203 4.846779 AATGGTTGTCATTGCGTTAGTT 57.153 36.364 0.00 0.00 43.85 2.24
1125 1204 5.950758 AATGGTTGTCATTGCGTTAGTTA 57.049 34.783 0.00 0.00 43.85 2.24
1126 1205 5.950758 ATGGTTGTCATTGCGTTAGTTAA 57.049 34.783 0.00 0.00 30.55 2.01
1128 1207 4.023878 TGGTTGTCATTGCGTTAGTTAACC 60.024 41.667 0.88 0.00 36.48 2.85
1129 1208 4.214758 GGTTGTCATTGCGTTAGTTAACCT 59.785 41.667 0.88 0.00 33.93 3.50
1130 1209 5.144359 GTTGTCATTGCGTTAGTTAACCTG 58.856 41.667 0.88 0.00 32.69 4.00
1131 1210 3.187637 TGTCATTGCGTTAGTTAACCTGC 59.812 43.478 0.88 2.15 32.69 4.85
1151 1232 9.723601 AACCTGCAAATATCAATGTTTATGTTT 57.276 25.926 0.00 0.00 0.00 2.83
1160 1241 7.684062 ATCAATGTTTATGTTTTCTATGCGC 57.316 32.000 0.00 0.00 0.00 6.09
1161 1242 6.033341 TCAATGTTTATGTTTTCTATGCGCC 58.967 36.000 4.18 0.00 0.00 6.53
1163 1244 5.637006 TGTTTATGTTTTCTATGCGCCTT 57.363 34.783 4.18 0.00 0.00 4.35
1166 1247 6.584563 TGTTTATGTTTTCTATGCGCCTTTTC 59.415 34.615 4.18 0.00 0.00 2.29
1207 1291 1.912043 CAGAATGGAGAGGAAGTGGGT 59.088 52.381 0.00 0.00 0.00 4.51
1226 1310 6.214005 AGTGGGTATAAAGTTGGTAAGTGCTA 59.786 38.462 0.00 0.00 0.00 3.49
1228 1312 7.555195 GTGGGTATAAAGTTGGTAAGTGCTAAT 59.445 37.037 0.00 0.00 0.00 1.73
1274 1358 9.639563 TTTGGAGGATCTATAATTTGTAATGCA 57.360 29.630 0.00 0.00 33.73 3.96
1293 1377 3.003585 TGCACATATATCAGCGGCTTTTG 59.996 43.478 0.00 0.00 0.00 2.44
1307 1391 3.602390 GCTTTTGCACTTCGACACTTA 57.398 42.857 0.00 0.00 46.58 2.24
1308 1392 4.147219 GCTTTTGCACTTCGACACTTAT 57.853 40.909 0.00 0.00 46.58 1.73
1318 1402 1.475280 TCGACACTTATCCCACCTTCG 59.525 52.381 0.00 0.00 0.00 3.79
1349 1433 1.347817 GCTCGGCTCAAAGTCTCACG 61.348 60.000 0.00 0.00 0.00 4.35
1355 1439 1.531578 GCTCAAAGTCTCACGTTTCCC 59.468 52.381 0.00 0.00 0.00 3.97
1358 1442 2.432874 TCAAAGTCTCACGTTTCCCTCA 59.567 45.455 0.00 0.00 0.00 3.86
1372 1456 6.316390 ACGTTTCCCTCAATCTGATTTGTATC 59.684 38.462 0.00 0.00 0.00 2.24
1401 1485 2.542020 TGAAGTCGAAGCATCCACAA 57.458 45.000 0.00 0.00 0.00 3.33
1508 1593 9.914131 ATGTTTAATTTACTCCTTTGCTTCTTC 57.086 29.630 0.00 0.00 0.00 2.87
1730 1815 7.039853 TGCTGATCCATGAAGTTATGAAACAAA 60.040 33.333 0.00 0.00 38.12 2.83
1760 1845 5.658468 TGATTGAGTCTGATCACAGTCATC 58.342 41.667 9.05 9.22 43.81 2.92
1900 1987 2.031157 GTGAAATCCACAAACTCCACCG 60.031 50.000 0.00 0.00 45.03 4.94
1979 2068 7.095187 CCGATTTACATCTAGGGCACTTATTTC 60.095 40.741 0.00 0.00 0.00 2.17
2068 2157 7.994425 TCTTTGCATGAGGTTTTATACTTCA 57.006 32.000 0.00 0.00 45.57 3.02
2302 2391 8.756486 ATTGTAAACTTTAACAACTACCCAGT 57.244 30.769 0.00 0.00 38.35 4.00
2649 2738 7.155328 CCATTGTAACATATCTACAGAGGGTC 58.845 42.308 6.48 0.00 31.17 4.46
2726 2829 7.609097 AGGATCATGAGTCTATGCTTCTTAA 57.391 36.000 0.09 0.00 0.00 1.85
2811 2917 7.923344 GTCTATCAAATGTGTCTAGTGCTACAT 59.077 37.037 0.00 0.00 35.43 2.29
3069 3177 7.587037 TGCTATCTTTTCCCAAATTATCCTG 57.413 36.000 0.00 0.00 0.00 3.86
3139 3247 9.239551 TGGTGTATTAGTAGCTATGTGGTATAG 57.760 37.037 0.00 0.00 0.00 1.31
3296 3417 8.958119 TTAGTACTTTGTTATCTTGCCTATGG 57.042 34.615 0.00 0.00 0.00 2.74
3471 3592 7.689812 CGATCATGAAGTTTGTCATTCTGTTAC 59.310 37.037 0.00 0.00 36.04 2.50
3498 3619 3.904339 ACGCCTAGATGTATTGATTCCCT 59.096 43.478 0.00 0.00 0.00 4.20
3568 3689 8.388484 AGTTCATCTCATATTTCCACTATTGC 57.612 34.615 0.00 0.00 0.00 3.56
3706 3827 8.657387 TTGTCCATTAATTTATCCACTGGAAA 57.343 30.769 0.66 0.00 34.34 3.13
4158 4279 1.666888 CCATTCGAGGCACAAAAGCAC 60.667 52.381 0.00 0.00 35.83 4.40
4162 4283 1.789078 CGAGGCACAAAAGCACTGCT 61.789 55.000 0.00 0.00 42.56 4.24
4329 4450 4.943705 TGAGATCTGGTGGATTTTGTAAGC 59.056 41.667 0.00 0.00 34.33 3.09
4433 4554 2.747460 GAAGATGGCTGGCACGCA 60.747 61.111 5.88 0.00 0.00 5.24
4573 4694 2.567049 CGGAGAACGGCTCGTCTT 59.433 61.111 0.69 0.00 44.91 3.01
4579 4700 2.430382 GAACGGCTCGTCTTCACCCA 62.430 60.000 0.69 0.00 39.99 4.51
4585 4706 0.102481 CTCGTCTTCACCCATACCCG 59.898 60.000 0.00 0.00 0.00 5.28
4690 4811 2.160205 ACAGAAGGAAGTGATCGACGA 58.840 47.619 0.00 0.00 0.00 4.20
4778 4902 4.214971 AGCAGACATGAACAATGACTTGAC 59.785 41.667 0.00 0.00 38.94 3.18
4779 4903 4.705492 CAGACATGAACAATGACTTGACG 58.295 43.478 0.00 0.00 38.94 4.35
4780 4904 3.748048 AGACATGAACAATGACTTGACGG 59.252 43.478 0.00 0.00 37.95 4.79
4956 5080 4.173043 ACCCCTCTTCTTCCAGTATAGGAT 59.827 45.833 0.00 0.00 37.56 3.24
4989 5113 2.357154 GGGAAGAAGAGGCTGCCAAATA 60.357 50.000 22.65 0.00 35.04 1.40
5075 5204 3.144657 TCCACTCATTTGTGCATGACT 57.855 42.857 0.00 0.00 36.68 3.41
5155 5284 8.416329 ACATTCAAGAGTTTTTCAAGCTTACAT 58.584 29.630 0.00 0.00 0.00 2.29
5240 5369 7.175641 ACCCAGACTCTGATTTTGTTCAATTAG 59.824 37.037 7.69 0.00 32.44 1.73
5252 5381 5.606348 TGTTCAATTAGCACCCAAAGTTT 57.394 34.783 0.00 0.00 0.00 2.66
5287 5416 9.003658 ACTGGTTAAAATACAACTCATCTTCTG 57.996 33.333 0.00 0.00 0.00 3.02
5320 5449 6.218746 GGTTTTGATCTGTTTCAGCTGAAAT 58.781 36.000 37.03 24.88 44.69 2.17
5327 5456 8.077991 TGATCTGTTTCAGCTGAAATTTTACTG 58.922 33.333 37.03 27.84 44.69 2.74
5349 5478 7.586349 ACTGGATTGGTCACTGGATTATTTAT 58.414 34.615 0.00 0.00 0.00 1.40
5351 5481 6.777091 TGGATTGGTCACTGGATTATTTATGG 59.223 38.462 0.00 0.00 0.00 2.74
5364 5494 8.691797 TGGATTATTTATGGCTTACTGGAAAAC 58.308 33.333 0.00 0.00 0.00 2.43
5401 5537 5.582665 TGTGCAGTTTGAATTTAAAACCCAC 59.417 36.000 16.51 16.51 38.91 4.61
5430 5567 3.200825 ACTGGACCTCTCAAACCATATGG 59.799 47.826 20.68 20.68 42.17 2.74
5434 5571 4.016444 GACCTCTCAAACCATATGGCAAA 58.984 43.478 22.18 4.22 39.32 3.68
5467 5604 2.799126 TCACCAAACTGTTCACTGGT 57.201 45.000 9.10 9.10 43.01 4.00
5506 5643 3.855379 GGAACGTTTTCCGATTTTATGGC 59.145 43.478 0.46 0.00 42.20 4.40
5507 5644 3.125698 ACGTTTTCCGATTTTATGGCG 57.874 42.857 0.00 0.00 40.70 5.69
5508 5645 1.843753 CGTTTTCCGATTTTATGGCGC 59.156 47.619 0.00 0.00 39.56 6.53
5509 5646 2.729467 CGTTTTCCGATTTTATGGCGCA 60.729 45.455 10.83 0.00 39.56 6.09
5589 5738 7.500992 TGCCTATTTTGTTGTATTTTTGACCA 58.499 30.769 0.00 0.00 0.00 4.02
5591 5740 8.998377 GCCTATTTTGTTGTATTTTTGACCAAT 58.002 29.630 0.00 0.00 0.00 3.16
5635 5784 9.646522 ATGGCTATTTTCCTACATTAGATTGTT 57.353 29.630 0.00 0.00 0.00 2.83
5675 5824 3.733443 TCTAGAATAGATGCTTGCGCA 57.267 42.857 5.66 5.66 44.15 6.09
5676 5825 3.646946 TCTAGAATAGATGCTTGCGCAG 58.353 45.455 11.31 6.32 44.15 5.18
5677 5826 3.068732 TCTAGAATAGATGCTTGCGCAGT 59.931 43.478 11.31 0.00 44.15 4.40
5678 5827 4.794329 TCTAGAATAGATGCTTGCGCAGTC 60.794 45.833 11.31 7.14 44.15 3.51
5679 5828 7.178096 TCTAGAATAGATGCTTGCGCAGTCA 62.178 44.000 11.31 13.28 44.15 3.41
5680 5829 8.871090 TCTAGAATAGATGCTTGCGCAGTCAG 62.871 46.154 11.31 6.72 44.15 3.51
5683 5832 4.139510 TGCTTGCGCAGTCAGAAA 57.860 50.000 11.31 0.00 42.25 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.777449 TCTCTCCTTCTCTCTCTCTCTAGA 58.223 45.833 0.00 0.00 0.00 2.43
26 27 5.835819 TCTCTCTCCTTCTCTCTCTCTCTAG 59.164 48.000 0.00 0.00 0.00 2.43
27 28 5.777449 TCTCTCTCCTTCTCTCTCTCTCTA 58.223 45.833 0.00 0.00 0.00 2.43
28 29 4.624913 TCTCTCTCCTTCTCTCTCTCTCT 58.375 47.826 0.00 0.00 0.00 3.10
29 30 4.742138 GCTCTCTCTCCTTCTCTCTCTCTC 60.742 54.167 0.00 0.00 0.00 3.20
30 31 3.135530 GCTCTCTCTCCTTCTCTCTCTCT 59.864 52.174 0.00 0.00 0.00 3.10
31 32 3.471680 GCTCTCTCTCCTTCTCTCTCTC 58.528 54.545 0.00 0.00 0.00 3.20
42 43 1.157870 CCGTCTCTCGCTCTCTCTCC 61.158 65.000 0.00 0.00 38.35 3.71
119 121 1.569072 GTCTTCCTCCTCCTCCTCTCT 59.431 57.143 0.00 0.00 0.00 3.10
120 122 1.749286 CGTCTTCCTCCTCCTCCTCTC 60.749 61.905 0.00 0.00 0.00 3.20
121 123 0.257616 CGTCTTCCTCCTCCTCCTCT 59.742 60.000 0.00 0.00 0.00 3.69
250 264 1.512156 CCAACCGAACCGAACCTTGG 61.512 60.000 0.00 0.00 0.00 3.61
329 343 4.436998 CAGACCTCACGTCGGGGC 62.437 72.222 8.02 4.83 46.92 5.80
330 344 4.436998 GCAGACCTCACGTCGGGG 62.437 72.222 8.02 5.48 46.92 5.73
331 345 4.436998 GGCAGACCTCACGTCGGG 62.437 72.222 5.48 3.83 46.92 5.14
428 461 2.158355 TCTAGGTCCCCGGGAATAGAAG 60.158 54.545 26.32 12.15 32.70 2.85
475 508 2.448542 GGAGGATGGGGGCAGCTA 60.449 66.667 0.00 0.00 0.00 3.32
688 737 3.686916 ACGAGGAAGGAAAGAAAGGAG 57.313 47.619 0.00 0.00 0.00 3.69
691 741 7.065803 TGCATTATTACGAGGAAGGAAAGAAAG 59.934 37.037 0.00 0.00 0.00 2.62
725 775 2.537560 CCATTGCTAAGGCCGAGCG 61.538 63.158 22.83 11.91 43.19 5.03
727 777 3.425422 GCCATTGCTAAGGCCGAG 58.575 61.111 2.80 0.00 45.18 4.63
746 796 1.714899 CCGCGCCCCTAAAACATCAG 61.715 60.000 0.00 0.00 0.00 2.90
793 843 1.463674 CGAAACCCCTCCCTGAAATG 58.536 55.000 0.00 0.00 0.00 2.32
814 864 3.181507 CCCAGCATGATCAAACAGTAACG 60.182 47.826 0.00 0.00 39.69 3.18
851 902 0.776176 ATCAGCATTCCATCCCCTCC 59.224 55.000 0.00 0.00 0.00 4.30
936 989 4.081420 TGCTCCTCTTCTTCAGATACAACC 60.081 45.833 0.00 0.00 0.00 3.77
937 990 5.078411 TGCTCCTCTTCTTCAGATACAAC 57.922 43.478 0.00 0.00 0.00 3.32
938 991 5.946942 ATGCTCCTCTTCTTCAGATACAA 57.053 39.130 0.00 0.00 0.00 2.41
996 1051 4.002982 TCGCAATAATATGCTCCATGACC 58.997 43.478 0.00 0.00 44.21 4.02
998 1053 3.686241 GCTCGCAATAATATGCTCCATGA 59.314 43.478 0.00 0.00 44.21 3.07
1018 1097 1.339151 CCTCCCGAGCTTAAACTTGCT 60.339 52.381 0.00 0.00 42.82 3.91
1032 1111 0.745845 CACTGCCAATCTTCCTCCCG 60.746 60.000 0.00 0.00 0.00 5.14
1047 1126 1.672356 CTCCCCAAACGAGCCACTG 60.672 63.158 0.00 0.00 0.00 3.66
1098 1177 2.133553 CGCAATGACAACCATTTTGCA 58.866 42.857 9.24 0.00 42.55 4.08
1117 1196 8.181573 ACATTGATATTTGCAGGTTAACTAACG 58.818 33.333 5.42 0.00 37.07 3.18
1125 1204 9.723601 AAACATAAACATTGATATTTGCAGGTT 57.276 25.926 0.00 0.00 0.00 3.50
1126 1205 9.723601 AAAACATAAACATTGATATTTGCAGGT 57.276 25.926 0.00 0.00 0.00 4.00
1151 1232 4.699735 TGAATCAAGAAAAGGCGCATAGAA 59.300 37.500 10.83 0.00 0.00 2.10
1153 1234 4.497006 CCTGAATCAAGAAAAGGCGCATAG 60.497 45.833 10.83 0.00 0.00 2.23
1155 1236 2.165030 CCTGAATCAAGAAAAGGCGCAT 59.835 45.455 10.83 0.00 0.00 4.73
1157 1238 1.541588 ACCTGAATCAAGAAAAGGCGC 59.458 47.619 0.00 0.00 0.00 6.53
1158 1239 5.567138 AATACCTGAATCAAGAAAAGGCG 57.433 39.130 0.00 0.00 0.00 5.52
1248 1332 9.639563 TGCATTACAAATTATAGATCCTCCAAA 57.360 29.630 0.00 0.00 0.00 3.28
1274 1358 3.003689 GTGCAAAAGCCGCTGATATATGT 59.996 43.478 0.00 0.00 0.00 2.29
1284 1368 1.725973 GTCGAAGTGCAAAAGCCGC 60.726 57.895 0.00 0.00 0.00 6.53
1293 1377 2.000447 GTGGGATAAGTGTCGAAGTGC 59.000 52.381 0.00 0.00 0.00 4.40
1299 1383 1.475280 TCGAAGGTGGGATAAGTGTCG 59.525 52.381 0.00 0.00 0.00 4.35
1307 1391 4.310022 TTTTAACCATCGAAGGTGGGAT 57.690 40.909 14.01 0.00 42.25 3.85
1308 1392 3.791953 TTTTAACCATCGAAGGTGGGA 57.208 42.857 14.01 0.00 42.25 4.37
1318 1402 2.682856 TGAGCCGAGCATTTTAACCATC 59.317 45.455 0.00 0.00 0.00 3.51
1349 1433 7.630242 TGATACAAATCAGATTGAGGGAAAC 57.370 36.000 0.00 0.00 37.20 2.78
1372 1456 2.350522 CTTCGACTTCATGGGTTCCTG 58.649 52.381 0.00 0.00 0.00 3.86
1381 1465 2.744202 GTTGTGGATGCTTCGACTTCAT 59.256 45.455 14.35 0.00 32.30 2.57
1401 1485 6.714810 TGTAAACTTTGGATTCATAGTGCAGT 59.285 34.615 0.00 0.00 35.78 4.40
1730 1815 6.531021 TGTGATCAGACTCAATCATATGCAT 58.469 36.000 3.79 3.79 34.60 3.96
1807 1893 8.934023 TTTTCTTCACCAAGTAAGATAACCAT 57.066 30.769 0.00 0.00 32.05 3.55
1900 1987 6.708285 TGAGACCCAATAAAAGTTAGTCTCC 58.292 40.000 13.09 0.00 45.13 3.71
2013 2102 9.846248 GCACAATTCAAATAATCTCAACTAAGT 57.154 29.630 0.00 0.00 0.00 2.24
2247 2336 9.614792 AATGAACTCGCTACTCCTATTAAATTT 57.385 29.630 0.00 0.00 0.00 1.82
2248 2337 9.614792 AAATGAACTCGCTACTCCTATTAAATT 57.385 29.630 0.00 0.00 0.00 1.82
2789 2895 8.040727 TGTAATGTAGCACTAGACACATTTGAT 58.959 33.333 15.66 0.00 40.88 2.57
2798 2904 9.712305 ATATTTGGATGTAATGTAGCACTAGAC 57.288 33.333 0.00 0.00 0.00 2.59
2811 2917 6.482898 AGGCATTGCAATATTTGGATGTAA 57.517 33.333 12.53 0.00 0.00 2.41
3069 3177 5.859205 AAATAATCCAGTGCCTTGATTCC 57.141 39.130 5.25 0.00 30.32 3.01
3295 3416 4.697352 AGTGCTCACATTATTGAACAGACC 59.303 41.667 2.63 0.00 0.00 3.85
3296 3417 5.409520 TCAGTGCTCACATTATTGAACAGAC 59.590 40.000 2.63 0.00 0.00 3.51
3471 3592 4.233123 TCAATACATCTAGGCGTTACCG 57.767 45.455 0.00 0.00 46.52 4.02
3568 3689 1.476891 TCTTCGAATCTCAGGGAACGG 59.523 52.381 0.00 0.00 0.00 4.44
3622 3743 2.623535 TCACGAACAAATACATCCCGG 58.376 47.619 0.00 0.00 0.00 5.73
3706 3827 9.507329 TTTTCTCAACATCAGCTTATAGAAAGT 57.493 29.630 4.56 0.00 34.33 2.66
4038 4159 5.211973 TCTCTTGTCCTACTGGCAGAATAT 58.788 41.667 23.66 0.12 0.00 1.28
4162 4283 7.710044 GCTTCTCTAGATGAACTGAATGAATCA 59.290 37.037 0.00 0.00 36.38 2.57
4270 4391 0.673437 TTGCTTTTGCCTCCTTTCCG 59.327 50.000 0.00 0.00 46.87 4.30
4433 4554 3.645268 GAGGTTGGCCGGCTGGATT 62.645 63.158 28.56 9.84 40.50 3.01
4573 4694 3.463585 GGCGACGGGTATGGGTGA 61.464 66.667 0.00 0.00 0.00 4.02
4690 4811 1.274703 ATTGTCATCGCCTCCAGGGT 61.275 55.000 0.00 0.00 37.43 4.34
4778 4902 1.083489 TTCTGCTTAACCATTCGCCG 58.917 50.000 0.00 0.00 0.00 6.46
4779 4903 2.223572 CCATTCTGCTTAACCATTCGCC 60.224 50.000 0.00 0.00 0.00 5.54
4780 4904 2.796032 GCCATTCTGCTTAACCATTCGC 60.796 50.000 0.00 0.00 0.00 4.70
4956 5080 5.888161 GCCTCTTCTTCCCTATGATTCAAAA 59.112 40.000 0.00 0.00 0.00 2.44
5024 5153 9.971922 CTAAAATTTGAGAGAACACCAAGATTT 57.028 29.630 0.00 0.00 0.00 2.17
5155 5284 2.457598 AGACATCTCTTCGCTTGGGTA 58.542 47.619 0.00 0.00 0.00 3.69
5287 5416 7.142680 TGAAACAGATCAAAACCGGTTAATTC 58.857 34.615 22.60 14.83 0.00 2.17
5320 5449 4.715534 TCCAGTGACCAATCCAGTAAAA 57.284 40.909 0.00 0.00 0.00 1.52
5327 5456 6.294731 GCCATAAATAATCCAGTGACCAATCC 60.295 42.308 0.00 0.00 0.00 3.01
5349 5478 6.418057 AAATGATTGTTTTCCAGTAAGCCA 57.582 33.333 0.00 0.00 0.00 4.75
5401 5537 0.609406 TGAGAGGTCCAGTCCGACTG 60.609 60.000 19.97 19.97 45.53 3.51
5411 5548 2.092429 TGCCATATGGTTTGAGAGGTCC 60.092 50.000 22.79 2.37 37.57 4.46
5439 5576 9.097257 CAGTGAACAGTTTGGTGAAAATTTAAT 57.903 29.630 0.00 0.00 0.00 1.40
5442 5579 5.874261 CCAGTGAACAGTTTGGTGAAAATTT 59.126 36.000 0.00 0.00 0.00 1.82
5445 5582 3.829601 ACCAGTGAACAGTTTGGTGAAAA 59.170 39.130 7.26 0.00 42.12 2.29
5456 5593 5.954296 ATCAATTCTCAACCAGTGAACAG 57.046 39.130 0.00 0.00 35.22 3.16
5462 5599 6.542821 TCCAGTTTATCAATTCTCAACCAGT 58.457 36.000 0.00 0.00 0.00 4.00
5467 5604 7.504924 AACGTTCCAGTTTATCAATTCTCAA 57.495 32.000 0.00 0.00 0.00 3.02
5502 5639 1.526575 CCTTGGTTTCACTGCGCCAT 61.527 55.000 4.18 0.00 0.00 4.40
5504 5641 1.734388 AACCTTGGTTTCACTGCGCC 61.734 55.000 4.18 0.00 0.00 6.53
5506 5643 0.738389 ACAACCTTGGTTTCACTGCG 59.262 50.000 1.76 0.00 0.00 5.18
5507 5644 1.802508 GCACAACCTTGGTTTCACTGC 60.803 52.381 1.76 4.34 0.00 4.40
5508 5645 1.750778 AGCACAACCTTGGTTTCACTG 59.249 47.619 1.76 0.00 0.00 3.66
5509 5646 2.143876 AGCACAACCTTGGTTTCACT 57.856 45.000 1.76 0.00 0.00 3.41
5575 5724 6.426328 GTGGCATGAATTGGTCAAAAATACAA 59.574 34.615 0.00 0.00 40.50 2.41
5577 5726 6.165577 AGTGGCATGAATTGGTCAAAAATAC 58.834 36.000 0.00 0.00 40.50 1.89
5589 5738 4.403432 CCATGGAACTAAGTGGCATGAATT 59.597 41.667 5.56 0.00 0.00 2.17
5591 5740 3.355378 CCATGGAACTAAGTGGCATGAA 58.645 45.455 5.56 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.