Multiple sequence alignment - TraesCS2A01G197200

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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 TraesCS2A01G197200 chr2A 100.000 2973 0 0 1 2973 166831134 166828162 0.000000e+00 5491.0
1 TraesCS2A01G197200 chr2B 89.222 2069 115 57 959 2973 214535212 214533198 0.000000e+00 2486.0
2 TraesCS2A01G197200 chr2B 94.340 636 22 7 257 886 214536000 214535373 0.000000e+00 963.0
3 TraesCS2A01G197200 chr2B 92.857 238 8 2 1 229 214536232 214535995 1.320000e-88 337.0
4 TraesCS2A01G197200 chr2B 100.000 34 0 0 890 923 214535312 214535279 2.470000e-06 63.9
5 TraesCS2A01G197200 chr2D 86.498 1622 105 50 570 2123 157019804 157018229 0.000000e+00 1677.0
6 TraesCS2A01G197200 chr2D 96.257 855 25 5 2122 2973 157018154 157017304 0.000000e+00 1395.0
7 TraesCS2A01G197200 chr2D 91.429 175 6 3 434 608 157019969 157019804 6.410000e-57 231.0
8 TraesCS2A01G197200 chr2D 92.857 70 5 0 1131 1200 157036296 157036227 5.240000e-18 102.0


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 TraesCS2A01G197200 chr2A 166828162 166831134 2972 True 5491.000 5491 100.000000 1 2973 1 chr2A.!!$R1 2972
1 TraesCS2A01G197200 chr2B 214533198 214536232 3034 True 962.475 2486 94.104750 1 2973 4 chr2B.!!$R1 2972
2 TraesCS2A01G197200 chr2D 157017304 157019969 2665 True 1101.000 1677 91.394667 434 2973 3 chr2D.!!$R2 2539

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
924 1043 0.107831 TTAGCCAACAGGTTGCTCGT 59.892 50.0 6.64 0.0 39.16 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2553 2835 1.973281 CATGACCCTTTGCCAGCGT 60.973 57.895 0.0 0.0 0.0 5.07 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
71 76 3.511540 GCTGCCTCCCAAAAAGAATTACT 59.488 43.478 0.00 0.00 0.00 2.24
82 87 9.692749 CCCAAAAAGAATTACTAGAAACTTTCC 57.307 33.333 0.00 0.00 0.00 3.13
128 133 2.639883 TTTGCGCTGCATTTGTGGCA 62.640 50.000 9.73 0.00 38.76 4.92
140 145 2.123248 TTGTGGCATCTCCTTCGGCA 62.123 55.000 0.00 0.00 35.26 5.69
208 218 1.001020 TGCCAACATACCTGCCCAG 60.001 57.895 0.00 0.00 0.00 4.45
246 256 6.959639 TTTTTCTTCCTGTTTACTGCAGAT 57.040 33.333 23.35 7.41 36.12 2.90
247 257 5.947228 TTTCTTCCTGTTTACTGCAGATG 57.053 39.130 23.35 0.00 36.12 2.90
248 258 4.890158 TCTTCCTGTTTACTGCAGATGA 57.110 40.909 23.35 1.69 36.12 2.92
249 259 5.426689 TCTTCCTGTTTACTGCAGATGAT 57.573 39.130 23.35 0.00 36.12 2.45
250 260 5.423015 TCTTCCTGTTTACTGCAGATGATC 58.577 41.667 23.35 7.18 36.12 2.92
251 261 4.824479 TCCTGTTTACTGCAGATGATCA 57.176 40.909 23.35 11.31 36.12 2.92
252 262 5.164620 TCCTGTTTACTGCAGATGATCAA 57.835 39.130 23.35 1.28 36.12 2.57
253 263 4.937620 TCCTGTTTACTGCAGATGATCAAC 59.062 41.667 23.35 12.89 36.12 3.18
254 264 4.940046 CCTGTTTACTGCAGATGATCAACT 59.060 41.667 23.35 0.00 36.12 3.16
255 265 5.163784 CCTGTTTACTGCAGATGATCAACTG 60.164 44.000 24.46 24.46 36.12 3.16
256 266 5.308014 TGTTTACTGCAGATGATCAACTGT 58.692 37.500 27.62 14.85 36.62 3.55
257 267 5.764686 TGTTTACTGCAGATGATCAACTGTT 59.235 36.000 27.62 17.44 36.62 3.16
258 268 6.262944 TGTTTACTGCAGATGATCAACTGTTT 59.737 34.615 27.62 17.16 36.62 2.83
259 269 6.882610 TTACTGCAGATGATCAACTGTTTT 57.117 33.333 27.62 16.88 36.62 2.43
260 270 5.779529 ACTGCAGATGATCAACTGTTTTT 57.220 34.783 27.62 11.94 36.62 1.94
261 271 5.766222 ACTGCAGATGATCAACTGTTTTTC 58.234 37.500 27.62 14.93 36.62 2.29
343 353 3.389329 AGCACTGGATCGATAACCAAGAT 59.611 43.478 7.21 0.03 35.67 2.40
365 375 7.633789 AGATGTGGAATTATGTACTTGGAAGT 58.366 34.615 0.00 0.00 42.91 3.01
422 432 2.787249 GTTCATCAGCGTGCGCAT 59.213 55.556 15.91 0.00 44.88 4.73
588 598 1.292223 CCCGATTGTCACCGAGTGT 59.708 57.895 4.33 0.00 34.79 3.55
589 599 0.528924 CCCGATTGTCACCGAGTGTA 59.471 55.000 4.33 0.00 34.79 2.90
657 701 2.124193 TGCATGGGCTTGGGATCG 60.124 61.111 0.00 0.00 41.91 3.69
663 707 2.115291 GGGCTTGGGATCGCAGAAC 61.115 63.158 12.66 6.41 43.58 3.01
729 773 3.689161 TGTTGGCCTGATAAGATTGTTCG 59.311 43.478 3.32 0.00 0.00 3.95
756 802 4.241999 CGTACGTACGCCCCTCGG 62.242 72.222 32.36 6.87 43.14 4.63
786 832 1.005394 GAGGTTGCCGTTTCGAGGA 60.005 57.895 0.00 0.00 0.00 3.71
923 1042 1.398390 GATTAGCCAACAGGTTGCTCG 59.602 52.381 6.64 0.00 39.16 5.03
924 1043 0.107831 TTAGCCAACAGGTTGCTCGT 59.892 50.000 6.64 0.00 39.16 4.18
925 1044 0.320421 TAGCCAACAGGTTGCTCGTC 60.320 55.000 6.64 0.00 39.16 4.20
926 1045 2.954753 GCCAACAGGTTGCTCGTCG 61.955 63.158 6.64 0.00 39.16 5.12
929 1048 1.664965 AACAGGTTGCTCGTCGCTC 60.665 57.895 0.00 0.00 40.11 5.03
930 1049 2.811317 CAGGTTGCTCGTCGCTCC 60.811 66.667 0.00 4.35 40.11 4.70
931 1050 3.303135 AGGTTGCTCGTCGCTCCA 61.303 61.111 12.73 0.00 40.11 3.86
932 1051 2.811317 GGTTGCTCGTCGCTCCAG 60.811 66.667 0.00 0.00 40.11 3.86
939 1073 2.356313 CGTCGCTCCAGTGTTGCT 60.356 61.111 3.66 0.00 0.00 3.91
1038 1191 4.200283 CCAGCTCTCGGCCTCGAC 62.200 72.222 0.00 0.00 40.88 4.20
1148 1302 1.403514 GCGCAGAAGCTCACTTAGACT 60.404 52.381 0.30 0.00 35.82 3.24
1152 1306 2.163412 CAGAAGCTCACTTAGACTCGCT 59.837 50.000 0.00 0.00 35.82 4.93
1153 1307 2.163412 AGAAGCTCACTTAGACTCGCTG 59.837 50.000 0.00 0.00 35.82 5.18
1154 1308 0.172352 AGCTCACTTAGACTCGCTGC 59.828 55.000 0.00 0.00 0.00 5.25
1156 1310 0.528017 CTCACTTAGACTCGCTGCCA 59.472 55.000 0.00 0.00 0.00 4.92
1265 1419 3.787001 GTGGCTTCTCCCCCTCCG 61.787 72.222 0.00 0.00 0.00 4.63
1298 1452 2.676822 TCCGTCGAGCTGCCTCTT 60.677 61.111 0.00 0.00 35.90 2.85
1308 1462 1.078567 CTGCCTCTTCAGGTCAGCC 60.079 63.158 0.00 0.00 42.74 4.85
1360 1521 3.709653 TCATACAGGGGTAGGACATTGTC 59.290 47.826 8.34 8.34 35.54 3.18
1382 1549 2.248487 GCATGCTTCTTTTCAGCTTCG 58.752 47.619 11.37 0.00 38.19 3.79
1389 1556 4.143221 GCTTCTTTTCAGCTTCGACTGTAG 60.143 45.833 3.27 1.31 38.84 2.74
1390 1557 4.585955 TCTTTTCAGCTTCGACTGTAGT 57.414 40.909 3.27 0.00 38.84 2.73
1392 1559 4.278669 TCTTTTCAGCTTCGACTGTAGTCT 59.721 41.667 10.05 0.00 42.66 3.24
1393 1560 3.560902 TTCAGCTTCGACTGTAGTCTG 57.439 47.619 10.05 4.48 42.66 3.51
1394 1561 2.505405 TCAGCTTCGACTGTAGTCTGT 58.495 47.619 10.05 0.00 42.66 3.41
1396 1563 4.262617 TCAGCTTCGACTGTAGTCTGTAT 58.737 43.478 10.05 0.00 42.66 2.29
1397 1564 5.425630 TCAGCTTCGACTGTAGTCTGTATA 58.574 41.667 10.05 0.00 42.66 1.47
1398 1565 5.293814 TCAGCTTCGACTGTAGTCTGTATAC 59.706 44.000 10.05 0.00 42.66 1.47
1400 1567 4.334759 GCTTCGACTGTAGTCTGTATACCA 59.665 45.833 10.05 0.00 42.66 3.25
1401 1568 5.163683 GCTTCGACTGTAGTCTGTATACCAA 60.164 44.000 10.05 0.00 42.66 3.67
1402 1569 6.624423 GCTTCGACTGTAGTCTGTATACCAAA 60.624 42.308 10.05 0.00 42.66 3.28
1406 1573 6.128090 CGACTGTAGTCTGTATACCAAACTGA 60.128 42.308 10.05 0.00 42.66 3.41
1408 1575 5.946298 TGTAGTCTGTATACCAAACTGACG 58.054 41.667 0.00 0.00 45.29 4.35
1428 1595 2.853542 TGGAACAGGAGCTGGGCA 60.854 61.111 0.00 0.00 35.51 5.36
1491 1661 2.000323 AACGACAACGACGACGACG 61.000 57.895 17.60 17.60 42.66 5.12
1513 1683 0.750182 GAGGGAGAGGTCGTGGAGAG 60.750 65.000 0.00 0.00 0.00 3.20
1586 1756 0.463204 ACCGGCAGACAGATCATGAG 59.537 55.000 0.00 0.00 0.00 2.90
1587 1757 0.879400 CCGGCAGACAGATCATGAGC 60.879 60.000 1.78 1.78 0.00 4.26
1684 1866 3.167921 GCATGCAGCCATAACATTTGA 57.832 42.857 14.21 0.00 37.23 2.69
1688 1870 4.177165 TGCAGCCATAACATTTGACAAG 57.823 40.909 0.00 0.00 0.00 3.16
1695 1877 5.638657 GCCATAACATTTGACAAGCATTTCA 59.361 36.000 0.00 0.00 0.00 2.69
1823 2010 1.270465 ACGGCTGCTAAAAACGTAGGT 60.270 47.619 0.00 0.00 35.85 3.08
1838 2025 4.279145 ACGTAGGTATTCATGTCTCCACT 58.721 43.478 0.00 0.00 0.00 4.00
1842 2029 6.918569 CGTAGGTATTCATGTCTCCACTAAAG 59.081 42.308 0.00 0.00 0.00 1.85
1852 2039 5.123227 TGTCTCCACTAAAGAAACACCTTG 58.877 41.667 0.00 0.00 0.00 3.61
1862 2050 3.411446 AGAAACACCTTGCGATCATTGA 58.589 40.909 0.00 0.00 0.00 2.57
1896 2084 4.909696 TTTTCATCCAAAGCTTCGTTCA 57.090 36.364 0.00 0.00 0.00 3.18
1903 2091 3.436704 TCCAAAGCTTCGTTCATGTGATC 59.563 43.478 0.00 0.00 0.00 2.92
1927 2115 9.874205 ATCTGGAAATTATAATTGGTTGTTGTG 57.126 29.630 11.42 0.00 0.00 3.33
2060 2248 5.303971 CAAGTGAGACAGTGAATCCTCTTT 58.696 41.667 0.00 0.00 0.00 2.52
2099 2292 3.873952 CCTCTGTTAATAGCCAAGTCTGC 59.126 47.826 0.00 0.00 0.00 4.26
2109 2302 1.939255 GCCAAGTCTGCTCTATTCTGC 59.061 52.381 0.00 0.00 0.00 4.26
2123 2316 7.087639 GCTCTATTCTGCGAGAACATAACTAT 58.912 38.462 1.44 0.00 37.00 2.12
2127 2397 5.836821 TCTGCGAGAACATAACTATGAGT 57.163 39.130 3.73 0.00 37.15 3.41
2156 2428 6.210584 CCCACCTGATTAAAAGTATGGTTTGT 59.789 38.462 0.00 0.00 0.00 2.83
2176 2448 2.019337 AACACCTTCGTTGAACGGC 58.981 52.632 18.32 0.00 42.81 5.68
2177 2449 0.745128 AACACCTTCGTTGAACGGCA 60.745 50.000 18.32 4.16 42.81 5.69
2185 2457 1.227999 CGTTGAACGGCACAGGATGT 61.228 55.000 10.31 0.00 45.18 3.06
2215 2492 7.706159 TGCAATTATAAGCTGATTTCGTGAAT 58.294 30.769 0.00 0.00 0.00 2.57
2288 2566 9.023967 GCAATTTTGACTAACATACATGATTCC 57.976 33.333 0.00 0.00 0.00 3.01
2294 2572 7.492524 TGACTAACATACATGATTCCTCTGTC 58.507 38.462 0.00 0.00 0.00 3.51
2300 2578 2.567169 ACATGATTCCTCTGTCGTTCCA 59.433 45.455 0.00 0.00 0.00 3.53
2320 2598 4.513692 TCCACGTCAGTACAAAAATGGAAG 59.486 41.667 5.89 0.00 32.13 3.46
2372 2652 5.535030 AGATTACACAAAGACCCCAAACTTC 59.465 40.000 0.00 0.00 0.00 3.01
2373 2653 3.382083 ACACAAAGACCCCAAACTTCT 57.618 42.857 0.00 0.00 0.00 2.85
2374 2654 4.513406 ACACAAAGACCCCAAACTTCTA 57.487 40.909 0.00 0.00 0.00 2.10
2510 2792 0.482446 AGGTCACTCCCATTTGCCAA 59.518 50.000 0.00 0.00 36.75 4.52
2553 2835 0.687757 AGGGCAGAGCAGGATAACGA 60.688 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 76 6.859112 AGAGATGCTACAGGAAAGTTTCTA 57.141 37.500 15.05 0.00 0.00 2.10
113 118 4.082192 GATGCCACAAATGCAGCG 57.918 55.556 0.00 0.00 42.92 5.18
118 123 2.838386 CGAAGGAGATGCCACAAATG 57.162 50.000 0.00 0.00 40.02 2.32
140 145 6.051717 GCCAGTTCTCATACTGTCATACAAT 58.948 40.000 0.00 0.00 43.17 2.71
164 169 3.730761 GCCAGTCTGCCAAGTGCG 61.731 66.667 0.00 0.00 45.60 5.34
229 239 5.164620 TGATCATCTGCAGTAAACAGGAA 57.835 39.130 14.67 0.00 35.78 3.36
230 240 4.824479 TGATCATCTGCAGTAAACAGGA 57.176 40.909 14.67 0.86 35.78 3.86
231 241 4.940046 AGTTGATCATCTGCAGTAAACAGG 59.060 41.667 14.67 0.00 35.78 4.00
232 242 5.410746 ACAGTTGATCATCTGCAGTAAACAG 59.589 40.000 26.61 3.55 35.37 3.16
233 243 5.308014 ACAGTTGATCATCTGCAGTAAACA 58.692 37.500 26.61 6.46 35.37 2.83
234 244 5.869753 ACAGTTGATCATCTGCAGTAAAC 57.130 39.130 26.61 3.86 35.37 2.01
235 245 6.882610 AAACAGTTGATCATCTGCAGTAAA 57.117 33.333 26.61 0.06 35.37 2.01
236 246 6.882610 AAAACAGTTGATCATCTGCAGTAA 57.117 33.333 26.61 0.45 35.37 2.24
237 247 6.347644 CGAAAAACAGTTGATCATCTGCAGTA 60.348 38.462 26.61 0.48 35.37 2.74
238 248 5.561532 CGAAAAACAGTTGATCATCTGCAGT 60.562 40.000 26.61 13.91 35.37 4.40
239 249 4.849926 CGAAAAACAGTTGATCATCTGCAG 59.150 41.667 26.61 7.63 35.37 4.41
240 250 4.275689 ACGAAAAACAGTTGATCATCTGCA 59.724 37.500 26.61 0.00 35.37 4.41
241 251 4.614284 CACGAAAAACAGTTGATCATCTGC 59.386 41.667 26.61 13.41 35.37 4.26
242 252 5.989249 TCACGAAAAACAGTTGATCATCTG 58.011 37.500 25.55 25.55 37.65 2.90
243 253 6.260936 ACTTCACGAAAAACAGTTGATCATCT 59.739 34.615 0.00 0.00 0.00 2.90
244 254 6.430451 ACTTCACGAAAAACAGTTGATCATC 58.570 36.000 0.00 0.00 0.00 2.92
245 255 6.377327 ACTTCACGAAAAACAGTTGATCAT 57.623 33.333 0.00 0.00 0.00 2.45
246 256 5.811399 ACTTCACGAAAAACAGTTGATCA 57.189 34.783 0.00 0.00 0.00 2.92
247 257 6.487103 AGAACTTCACGAAAAACAGTTGATC 58.513 36.000 0.00 0.00 0.00 2.92
248 258 6.436843 AGAACTTCACGAAAAACAGTTGAT 57.563 33.333 0.00 0.00 0.00 2.57
249 259 5.873179 AGAACTTCACGAAAAACAGTTGA 57.127 34.783 0.00 0.00 0.00 3.18
250 260 5.856455 ACAAGAACTTCACGAAAAACAGTTG 59.144 36.000 0.00 0.00 0.00 3.16
251 261 6.009115 ACAAGAACTTCACGAAAAACAGTT 57.991 33.333 0.00 0.00 0.00 3.16
252 262 5.622770 ACAAGAACTTCACGAAAAACAGT 57.377 34.783 0.00 0.00 0.00 3.55
253 263 8.442605 TTTTACAAGAACTTCACGAAAAACAG 57.557 30.769 0.00 0.00 0.00 3.16
254 264 8.291032 TCTTTTACAAGAACTTCACGAAAAACA 58.709 29.630 0.00 0.00 35.99 2.83
255 265 8.663771 TCTTTTACAAGAACTTCACGAAAAAC 57.336 30.769 0.00 0.00 35.99 2.43
256 266 9.680315 TTTCTTTTACAAGAACTTCACGAAAAA 57.320 25.926 3.53 0.00 46.71 1.94
257 267 9.337091 CTTTCTTTTACAAGAACTTCACGAAAA 57.663 29.630 3.53 0.00 46.71 2.29
258 268 8.723311 TCTTTCTTTTACAAGAACTTCACGAAA 58.277 29.630 3.53 0.00 46.71 3.46
259 269 8.259049 TCTTTCTTTTACAAGAACTTCACGAA 57.741 30.769 3.53 0.00 46.71 3.85
260 270 7.762615 TCTCTTTCTTTTACAAGAACTTCACGA 59.237 33.333 3.53 0.00 46.71 4.35
261 271 7.906160 TCTCTTTCTTTTACAAGAACTTCACG 58.094 34.615 3.53 0.00 46.71 4.35
398 408 1.738099 ACGCTGATGAACGCCTGAC 60.738 57.895 0.00 0.00 0.00 3.51
422 432 3.846955 GCTCGTTTACTAGCCCCAA 57.153 52.632 0.00 0.00 32.40 4.12
527 537 0.097325 CTACGTGGTCTCAGCGTCTC 59.903 60.000 0.00 0.00 39.64 3.36
657 701 2.401766 CCCATGTCGGCAGTTCTGC 61.402 63.158 15.41 15.41 0.00 4.26
729 773 1.432270 CGTACGTACGGGAGGGTCTC 61.432 65.000 34.54 0.92 45.30 3.36
763 809 2.593436 AAACGGCAACCTCGTGGG 60.593 61.111 8.63 2.00 40.96 4.61
882 928 6.581388 ATCCAACATTTATCTCCTCTTGGA 57.419 37.500 0.00 0.00 39.89 3.53
923 1042 3.248029 CAGCAACACTGGAGCGAC 58.752 61.111 0.00 0.00 43.19 5.19
931 1050 0.179018 GTGGAAGGGACAGCAACACT 60.179 55.000 0.00 0.00 0.00 3.55
932 1051 1.507141 CGTGGAAGGGACAGCAACAC 61.507 60.000 0.00 0.00 0.00 3.32
1129 1283 2.525055 GAGTCTAAGTGAGCTTCTGCG 58.475 52.381 0.00 0.00 45.42 5.18
1134 1288 1.403514 GCAGCGAGTCTAAGTGAGCTT 60.404 52.381 0.00 0.00 38.66 3.74
1152 1306 3.117812 CTGCACGTACGCATGGCA 61.118 61.111 16.72 18.08 42.06 4.92
1153 1307 3.864686 CCTGCACGTACGCATGGC 61.865 66.667 16.72 14.40 42.06 4.40
1154 1308 2.434185 ACCTGCACGTACGCATGG 60.434 61.111 16.72 14.57 42.06 3.66
1156 1310 1.446099 CTCACCTGCACGTACGCAT 60.446 57.895 16.72 0.00 42.06 4.73
1233 1387 2.179517 CACGCTGACGGAGAGGAC 59.820 66.667 0.00 0.00 46.04 3.85
1308 1462 3.814945 CAAAGCTACTTCGGAAGCAAAG 58.185 45.455 17.37 12.92 41.32 2.77
1316 1474 0.734889 CCCATGCAAAGCTACTTCGG 59.265 55.000 0.00 0.00 0.00 4.30
1318 1476 1.176527 TGCCCATGCAAAGCTACTTC 58.823 50.000 0.00 0.00 46.66 3.01
1360 1521 0.524862 AGCTGAAAAGAAGCATGCGG 59.475 50.000 13.01 0.00 43.37 5.69
1382 1549 7.028361 GTCAGTTTGGTATACAGACTACAGTC 58.972 42.308 5.01 0.91 42.13 3.51
1389 1556 3.056322 ACCCGTCAGTTTGGTATACAGAC 60.056 47.826 5.01 0.11 34.56 3.51
1390 1557 3.056393 CACCCGTCAGTTTGGTATACAGA 60.056 47.826 5.01 0.00 0.00 3.41
1392 1559 2.027929 CCACCCGTCAGTTTGGTATACA 60.028 50.000 5.01 0.00 0.00 2.29
1393 1560 2.234414 TCCACCCGTCAGTTTGGTATAC 59.766 50.000 0.00 0.00 0.00 1.47
1394 1561 2.538222 TCCACCCGTCAGTTTGGTATA 58.462 47.619 0.00 0.00 0.00 1.47
1396 1563 1.129917 TTCCACCCGTCAGTTTGGTA 58.870 50.000 0.00 0.00 0.00 3.25
1397 1564 0.464916 GTTCCACCCGTCAGTTTGGT 60.465 55.000 0.00 0.00 0.00 3.67
1398 1565 0.464735 TGTTCCACCCGTCAGTTTGG 60.465 55.000 0.00 0.00 0.00 3.28
1400 1567 0.179029 CCTGTTCCACCCGTCAGTTT 60.179 55.000 0.00 0.00 0.00 2.66
1401 1568 1.052124 TCCTGTTCCACCCGTCAGTT 61.052 55.000 0.00 0.00 0.00 3.16
1402 1569 1.458777 TCCTGTTCCACCCGTCAGT 60.459 57.895 0.00 0.00 0.00 3.41
1406 1573 2.526873 AGCTCCTGTTCCACCCGT 60.527 61.111 0.00 0.00 0.00 5.28
1408 1575 2.352805 CCAGCTCCTGTTCCACCC 59.647 66.667 0.00 0.00 0.00 4.61
1428 1595 3.506059 CTCTCGGCGGCGGATCAAT 62.506 63.158 31.73 0.00 0.00 2.57
1473 1640 2.000323 CGTCGTCGTCGTTGTCGTT 61.000 57.895 3.67 0.00 38.33 3.85
1479 1646 3.730761 CTCCCCGTCGTCGTCGTT 61.731 66.667 10.76 0.00 38.33 3.85
1486 1656 4.444081 CCTCTCCCTCCCCGTCGT 62.444 72.222 0.00 0.00 0.00 4.34
1491 1661 2.760385 CACGACCTCTCCCTCCCC 60.760 72.222 0.00 0.00 0.00 4.81
1513 1683 3.825160 TTGACGGCAGTGGCACTCC 62.825 63.158 19.13 19.59 43.71 3.85
1586 1756 1.542544 CGCTGCAAAAGAAGCATAGC 58.457 50.000 0.00 0.00 41.82 2.97
1587 1757 1.542544 GCGCTGCAAAAGAAGCATAG 58.457 50.000 0.00 0.00 41.82 2.23
1662 1843 3.196039 TCAAATGTTATGGCTGCATGCTT 59.804 39.130 20.33 0.00 42.39 3.91
1663 1844 2.761767 TCAAATGTTATGGCTGCATGCT 59.238 40.909 20.33 0.00 42.39 3.79
1695 1877 1.684248 GCTTCCAATGGCCTCTCACAT 60.684 52.381 3.32 0.00 0.00 3.21
1823 2010 7.606456 GGTGTTTCTTTAGTGGAGACATGAATA 59.394 37.037 0.00 0.00 46.14 1.75
1838 2025 5.471797 TCAATGATCGCAAGGTGTTTCTTTA 59.528 36.000 0.00 0.00 38.47 1.85
1842 2029 3.829886 TCAATGATCGCAAGGTGTTTC 57.170 42.857 0.00 0.00 38.47 2.78
1852 2039 3.047796 GCAAATGGACATCAATGATCGC 58.952 45.455 0.00 0.00 0.00 4.58
1862 2050 5.423704 TGGATGAAAATGCAAATGGACAT 57.576 34.783 0.00 0.00 0.00 3.06
1903 2091 9.874205 ATCACAACAACCAATTATAATTTCCAG 57.126 29.630 8.01 2.67 0.00 3.86
2060 2248 2.039480 AGAGGCAAATCACTCTGCTTGA 59.961 45.455 0.00 0.00 42.20 3.02
2086 2274 4.502950 GCAGAATAGAGCAGACTTGGCTAT 60.503 45.833 0.00 0.00 42.78 2.97
2099 2292 8.293157 TCATAGTTATGTTCTCGCAGAATAGAG 58.707 37.037 2.61 0.00 36.50 2.43
2109 2302 7.222224 GTGGGTTAACTCATAGTTATGTTCTCG 59.778 40.741 12.21 0.00 40.08 4.04
2123 2316 6.607019 ACTTTTAATCAGGTGGGTTAACTCA 58.393 36.000 3.38 3.38 0.00 3.41
2127 2397 7.471890 ACCATACTTTTAATCAGGTGGGTTAA 58.528 34.615 10.84 0.00 0.00 2.01
2176 2448 8.971321 GCTTATAATTGCATAAAACATCCTGTG 58.029 33.333 0.00 0.00 0.00 3.66
2177 2449 8.917088 AGCTTATAATTGCATAAAACATCCTGT 58.083 29.630 0.00 0.00 0.00 4.00
2215 2492 5.485353 ACCAATAGAATTCACTGTCTGAGGA 59.515 40.000 8.44 0.00 0.00 3.71
2300 2578 3.880490 TGCTTCCATTTTTGTACTGACGT 59.120 39.130 0.00 0.00 0.00 4.34
2320 2598 3.698029 ATGCGACATTTCCTGTTATGC 57.302 42.857 0.00 0.00 38.54 3.14
2372 2652 5.233050 CACAAGCTCGGATCACAAATACTAG 59.767 44.000 0.00 0.00 0.00 2.57
2373 2653 5.109210 CACAAGCTCGGATCACAAATACTA 58.891 41.667 0.00 0.00 0.00 1.82
2374 2654 3.935203 CACAAGCTCGGATCACAAATACT 59.065 43.478 0.00 0.00 0.00 2.12
2510 2792 3.498774 AATCAGTGGAGTTCAACAGCT 57.501 42.857 0.00 0.00 0.00 4.24
2553 2835 1.973281 CATGACCCTTTGCCAGCGT 60.973 57.895 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.