Multiple sequence alignment - TraesCS5D01G177700

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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 TraesCS5D01G177700 chr5D 100.000 5498 0 0 1 5498 277554963 277560460 0.000000e+00 10154.0
1 TraesCS5D01G177700 chr5B 92.916 5548 250 57 6 5498 315609126 315614585 0.000000e+00 7936.0
2 TraesCS5D01G177700 chr5A 96.145 3632 110 18 1881 5498 366630720 366634335 0.000000e+00 5904.0
3 TraesCS5D01G177700 chr5A 87.070 1454 111 34 354 1796 366629291 366630678 0.000000e+00 1572.0
4 TraesCS5D01G177700 chr5A 87.688 333 37 3 2 332 366628971 366629301 8.640000e-103 385.0
5 TraesCS5D01G177700 chr2A 79.048 315 54 9 1508 1820 451806891 451807195 7.220000e-49 206.0
6 TraesCS5D01G177700 chr2B 77.778 315 61 7 1511 1821 600953307 600952998 9.400000e-43 185.0
7 TraesCS5D01G177700 chr3A 75.962 104 24 1 437 540 378309015 378309117 1.000000e-02 52.8


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 TraesCS5D01G177700 chr5D 277554963 277560460 5497 False 10154.000000 10154 100.000 1 5498 1 chr5D.!!$F1 5497
1 TraesCS5D01G177700 chr5B 315609126 315614585 5459 False 7936.000000 7936 92.916 6 5498 1 chr5B.!!$F1 5492
2 TraesCS5D01G177700 chr5A 366628971 366634335 5364 False 2620.333333 5904 90.301 2 5498 3 chr5A.!!$F1 5496

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
327 330 0.035534 ACGCATGTCTGGTGGCATTA 60.036 50.000 0.00 0.0 0.00 1.90 F
1258 1322 0.037303 TAGGACCCTCTGACGAACGT 59.963 55.000 0.00 0.0 0.00 3.99 F
1823 1903 0.611896 ATGAACCAAAGAAGGCCCGG 60.612 55.000 0.00 0.0 0.00 5.73 F
1839 1919 1.341156 CCGGATCCTCTTCAAGCCCT 61.341 60.000 10.75 0.0 0.00 5.19 F
2540 2626 1.684983 GCCTTGGCAGATTATGTGCAT 59.315 47.619 16.01 0.0 43.12 3.96 F
3402 3489 2.491693 CCTGAATACCACGGCAAATTGT 59.508 45.455 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2163 0.467474 ATCCACCATGGCATCAGCTG 60.467 55.000 13.04 7.63 41.70 4.24 R
3153 3239 0.109723 CGAACCCTCCCTTTTGGTCA 59.890 55.000 0.00 0.00 38.10 4.02 R
3402 3489 2.316867 CGTTGTCCGTCATGCTGCA 61.317 57.895 4.13 4.13 0.00 4.41 R
3800 3892 3.198635 CAGAGGAGCCTAGTTGAATCCAA 59.801 47.826 0.00 0.00 32.21 3.53 R
3851 3943 1.075374 TGATGTCCTTGGTTTCAGGGG 59.925 52.381 0.00 0.00 40.22 4.79 R
5195 5299 0.744874 TCCGAACTCTAAGGGCATCG 59.255 55.000 0.00 0.00 0.00 3.84 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
82 83 0.539051 CAAGGAAGATCCAGAGCCGT 59.461 55.000 0.00 0.00 39.61 5.68
85 86 0.250513 GGAAGATCCAGAGCCGTTGT 59.749 55.000 0.00 0.00 36.28 3.32
87 88 0.976641 AAGATCCAGAGCCGTTGTCA 59.023 50.000 0.00 0.00 0.00 3.58
109 110 3.121030 CTGCCGGCAAGGAGAACG 61.121 66.667 32.09 12.49 45.00 3.95
117 118 2.762745 GGCAAGGAGAACGACAACTTA 58.237 47.619 0.00 0.00 0.00 2.24
142 143 1.354368 TGGTTTGGATGGGGAGAAGAC 59.646 52.381 0.00 0.00 0.00 3.01
151 152 1.268066 GGGGAGAAGACGAGGAGTTT 58.732 55.000 0.00 0.00 0.00 2.66
161 162 1.340248 ACGAGGAGTTTGAAGAAGCGA 59.660 47.619 0.00 0.00 0.00 4.93
219 220 1.825474 ACAGATTATATAGGCGCGGCT 59.175 47.619 37.69 37.69 0.00 5.52
222 223 2.623889 AGATTATATAGGCGCGGCTAGG 59.376 50.000 39.38 0.00 0.00 3.02
264 267 1.621107 CTTCAATGCGACACAATGGC 58.379 50.000 0.00 0.00 29.54 4.40
281 284 1.214175 TGGCCAGAGTTGGTTTCTTGA 59.786 47.619 0.00 0.00 46.80 3.02
321 324 3.434319 GGCCACGCATGTCTGGTG 61.434 66.667 0.00 6.91 0.00 4.17
323 326 3.434319 CCACGCATGTCTGGTGGC 61.434 66.667 12.24 0.00 44.09 5.01
324 327 2.669229 CACGCATGTCTGGTGGCA 60.669 61.111 0.00 0.00 0.00 4.92
325 328 2.042259 CACGCATGTCTGGTGGCAT 61.042 57.895 0.00 0.00 0.00 4.40
326 329 1.303561 ACGCATGTCTGGTGGCATT 60.304 52.632 0.00 0.00 0.00 3.56
327 330 0.035534 ACGCATGTCTGGTGGCATTA 60.036 50.000 0.00 0.00 0.00 1.90
328 331 1.093972 CGCATGTCTGGTGGCATTAA 58.906 50.000 0.00 0.00 0.00 1.40
329 332 1.677576 CGCATGTCTGGTGGCATTAAT 59.322 47.619 0.00 0.00 0.00 1.40
330 333 2.542205 CGCATGTCTGGTGGCATTAATG 60.542 50.000 11.27 11.27 0.00 1.90
341 344 3.924238 CATTAATGCCGACCACTGC 57.076 52.632 1.74 0.00 0.00 4.40
342 345 1.093972 CATTAATGCCGACCACTGCA 58.906 50.000 1.74 0.00 40.18 4.41
343 346 1.064505 CATTAATGCCGACCACTGCAG 59.935 52.381 13.48 13.48 39.36 4.41
344 347 1.305219 TTAATGCCGACCACTGCAGC 61.305 55.000 15.27 0.00 39.36 5.25
345 348 2.184020 TAATGCCGACCACTGCAGCT 62.184 55.000 15.27 0.00 39.36 4.24
346 349 3.965539 ATGCCGACCACTGCAGCTC 62.966 63.158 15.27 5.07 39.36 4.09
347 350 4.385405 GCCGACCACTGCAGCTCT 62.385 66.667 15.27 0.00 0.00 4.09
348 351 2.433838 CCGACCACTGCAGCTCTG 60.434 66.667 15.27 4.53 0.00 3.35
349 352 2.433838 CGACCACTGCAGCTCTGG 60.434 66.667 15.27 16.84 0.00 3.86
350 353 2.046507 GACCACTGCAGCTCTGGG 60.047 66.667 22.03 14.70 0.00 4.45
351 354 4.341783 ACCACTGCAGCTCTGGGC 62.342 66.667 22.03 0.00 42.19 5.36
410 446 2.037208 AGGATTTTGGGTGGGCCG 59.963 61.111 0.00 0.00 34.97 6.13
440 478 4.033776 CCGCAAAGCCCCCTCTGA 62.034 66.667 0.00 0.00 0.00 3.27
467 515 0.947660 GAAAACAGACGTCCGGACCC 60.948 60.000 28.52 19.78 0.00 4.46
484 532 1.449423 CCATTCACGGACGGATGCA 60.449 57.895 0.00 0.00 0.00 3.96
487 535 2.593468 ATTCACGGACGGATGCAGGG 62.593 60.000 0.00 0.00 0.00 4.45
506 554 2.159057 GGGCTATGTTGGATGGCAAAAG 60.159 50.000 0.00 0.00 0.00 2.27
538 586 2.943680 ATGCGCTCGAGACGGATGTG 62.944 60.000 25.97 5.34 40.23 3.21
550 598 3.517901 AGACGGATGTGGATGGTTTAAGA 59.482 43.478 0.00 0.00 0.00 2.10
556 604 5.123979 GGATGTGGATGGTTTAAGAGTCAAC 59.876 44.000 0.00 0.00 0.00 3.18
592 640 7.998964 ACCTAATGTATTTTAACCATCTCCCAG 59.001 37.037 0.00 0.00 0.00 4.45
612 660 0.391597 GTCGGTGGTCAAACTCCTCA 59.608 55.000 0.00 0.00 0.00 3.86
671 719 1.347221 GACCAAAGTTATCGGCGCG 59.653 57.895 0.00 0.00 0.00 6.86
710 759 4.554960 TTCTCTCGGAGTGAAGTAGAGA 57.445 45.455 16.23 2.44 40.60 3.10
730 779 1.370064 GTGCCAGTAGGTCCAACGT 59.630 57.895 0.00 0.00 37.19 3.99
769 818 0.751643 ACCCACAGCAGTCCAAACAC 60.752 55.000 0.00 0.00 0.00 3.32
771 820 0.813610 CCACAGCAGTCCAAACACGA 60.814 55.000 0.00 0.00 0.00 4.35
873 922 0.468214 CCGTGAGATCCCAGGCTCTA 60.468 60.000 0.00 0.00 32.44 2.43
919 968 1.343789 CAGGATGCGTGGAGATGAGAT 59.656 52.381 0.00 0.00 0.00 2.75
1050 1100 1.270907 TCTTCTTCCTCCTGCTGTCC 58.729 55.000 0.00 0.00 0.00 4.02
1127 1177 3.456277 GGGTAATGGATCTGTCACCTCTT 59.544 47.826 0.00 0.00 0.00 2.85
1130 1180 6.049790 GGTAATGGATCTGTCACCTCTTTAC 58.950 44.000 0.00 0.00 0.00 2.01
1132 1182 6.380079 AATGGATCTGTCACCTCTTTACTT 57.620 37.500 0.00 0.00 0.00 2.24
1142 1192 6.866770 TGTCACCTCTTTACTTTATTCAGTCG 59.133 38.462 0.00 0.00 0.00 4.18
1154 1204 6.543100 ACTTTATTCAGTCGGTTTTGGTTGTA 59.457 34.615 0.00 0.00 0.00 2.41
1189 1249 3.763097 TGCTGCGTCCTTTTTATGATG 57.237 42.857 0.00 0.00 0.00 3.07
1190 1250 3.342719 TGCTGCGTCCTTTTTATGATGA 58.657 40.909 0.00 0.00 0.00 2.92
1191 1251 3.947196 TGCTGCGTCCTTTTTATGATGAT 59.053 39.130 0.00 0.00 0.00 2.45
1192 1252 4.035558 TGCTGCGTCCTTTTTATGATGATC 59.964 41.667 0.00 0.00 0.00 2.92
1193 1253 4.555511 GCTGCGTCCTTTTTATGATGATCC 60.556 45.833 0.00 0.00 0.00 3.36
1194 1254 4.780815 TGCGTCCTTTTTATGATGATCCT 58.219 39.130 0.00 0.00 0.00 3.24
1195 1255 4.816385 TGCGTCCTTTTTATGATGATCCTC 59.184 41.667 0.00 0.00 0.00 3.71
1196 1256 5.059833 GCGTCCTTTTTATGATGATCCTCT 58.940 41.667 0.00 0.00 0.00 3.69
1250 1314 5.365021 ACTGATTTGATTAGGACCCTCTG 57.635 43.478 0.00 0.00 0.00 3.35
1253 1317 3.887621 TTTGATTAGGACCCTCTGACG 57.112 47.619 0.00 0.00 0.00 4.35
1254 1318 2.820728 TGATTAGGACCCTCTGACGA 57.179 50.000 0.00 0.00 0.00 4.20
1255 1319 3.095912 TGATTAGGACCCTCTGACGAA 57.904 47.619 0.00 0.00 0.00 3.85
1258 1322 0.037303 TAGGACCCTCTGACGAACGT 59.963 55.000 0.00 0.00 0.00 3.99
1259 1323 0.826672 AGGACCCTCTGACGAACGTT 60.827 55.000 0.00 0.00 0.00 3.99
1291 1363 1.780806 CGGCACATGCAAACAATTCA 58.219 45.000 6.15 0.00 44.36 2.57
1318 1390 5.170748 GCATTTTTAGTTGATGAAGTGGGG 58.829 41.667 0.00 0.00 0.00 4.96
1323 1395 6.884472 TTTAGTTGATGAAGTGGGGAGATA 57.116 37.500 0.00 0.00 0.00 1.98
1371 1443 8.597662 TCTCGTTTTACAACTAAAACTGCTAT 57.402 30.769 12.10 0.00 45.21 2.97
1372 1444 9.695526 TCTCGTTTTACAACTAAAACTGCTATA 57.304 29.630 12.10 0.00 45.21 1.31
1391 1463 5.163754 GCTATAGCAAAGATGGTTCGTTTGT 60.164 40.000 20.01 0.00 41.59 2.83
1452 1532 2.452505 AGTCTCTTCCTGCAGTAGTCC 58.547 52.381 13.81 2.92 0.00 3.85
1533 1613 3.181445 GGCCTCCTTTGGTTTGGAATTTT 60.181 43.478 0.00 0.00 31.23 1.82
1669 1749 8.243426 TGCACATCTCAGGAAAATAAACATTAC 58.757 33.333 0.00 0.00 0.00 1.89
1687 1767 7.923414 ACATTACCCTAGACTCAATGAAAAC 57.077 36.000 11.06 0.00 32.29 2.43
1706 1786 8.408043 TGAAAACAAATCCTATGATGTGAACT 57.592 30.769 5.28 0.00 38.32 3.01
1723 1803 9.243637 GATGTGAACTAACAGACATCTATCTTC 57.756 37.037 0.00 0.00 40.95 2.87
1781 1861 7.742089 CGACATCTCAATTTCTACAAGTTTCAC 59.258 37.037 0.00 0.00 0.00 3.18
1823 1903 0.611896 ATGAACCAAAGAAGGCCCGG 60.612 55.000 0.00 0.00 0.00 5.73
1839 1919 1.341156 CCGGATCCTCTTCAAGCCCT 61.341 60.000 10.75 0.00 0.00 5.19
2081 2163 6.843069 AAATAAATCACCTTGTGTTTGTGC 57.157 33.333 0.00 0.00 34.79 4.57
2200 2282 4.746611 GCCCTTTTCAACTCTTCATGTTTG 59.253 41.667 0.00 0.00 0.00 2.93
2210 2292 5.634118 ACTCTTCATGTTTGGAAATGAGGA 58.366 37.500 0.00 0.00 36.79 3.71
2212 2294 4.766891 TCTTCATGTTTGGAAATGAGGACC 59.233 41.667 0.00 0.00 34.92 4.46
2233 2315 4.756642 ACCGCAATATTCACAGTGGATATG 59.243 41.667 14.30 9.94 35.66 1.78
2418 2504 4.383948 GCTTTTCAGCTGCAATGTTAGAAC 59.616 41.667 9.47 0.00 43.51 3.01
2457 2543 6.092533 AGGTTTCGTTCAGTCGTTAAAAAGAA 59.907 34.615 0.00 0.00 0.00 2.52
2525 2611 1.688772 CATCAGGAATGAGGGCCTTG 58.311 55.000 7.89 0.00 37.59 3.61
2540 2626 1.684983 GCCTTGGCAGATTATGTGCAT 59.315 47.619 16.01 0.00 43.12 3.96
2634 2720 6.899393 AGCCAGTCAAAATGTTTCTGATAA 57.101 33.333 0.00 0.00 0.00 1.75
2847 2933 9.944663 TCATCTAAAACTTACACATGTCAAAAC 57.055 29.630 0.00 0.00 0.00 2.43
2858 2944 5.043248 CACATGTCAAAACTGGTTTTCCTC 58.957 41.667 8.28 3.97 40.45 3.71
2859 2945 4.202010 ACATGTCAAAACTGGTTTTCCTCG 60.202 41.667 8.28 0.00 40.45 4.63
2860 2946 3.349022 TGTCAAAACTGGTTTTCCTCGT 58.651 40.909 8.28 0.00 40.45 4.18
2861 2947 4.515361 TGTCAAAACTGGTTTTCCTCGTA 58.485 39.130 8.28 0.00 40.45 3.43
2862 2948 4.573201 TGTCAAAACTGGTTTTCCTCGTAG 59.427 41.667 8.28 0.00 40.45 3.51
2957 3043 3.565482 AGTATGACAACTGCAACAACCAG 59.435 43.478 0.00 0.00 36.41 4.00
3019 3105 7.067494 ACAGAACTTAGAAGCTTGTCACATTTT 59.933 33.333 2.10 0.00 0.00 1.82
3029 3115 6.555315 AGCTTGTCACATTTTATCCGAATTC 58.445 36.000 0.00 0.00 0.00 2.17
3031 3117 6.806249 GCTTGTCACATTTTATCCGAATTCAA 59.194 34.615 6.22 0.00 0.00 2.69
3153 3239 6.321181 TGGTAACTGATTCTTGCTTTTCAACT 59.679 34.615 0.00 0.00 37.61 3.16
3393 3480 7.228314 TCTAATTCCTATCCTGAATACCACG 57.772 40.000 0.00 0.00 32.31 4.94
3402 3489 2.491693 CCTGAATACCACGGCAAATTGT 59.508 45.455 0.00 0.00 0.00 2.71
4213 4305 1.461268 TGTGGAACAGAGGGCCTGA 60.461 57.895 12.95 0.00 45.67 3.86
4315 4407 8.480643 ACAGTAAGCACTTTGTCTAATCATAC 57.519 34.615 0.00 0.00 30.46 2.39
4423 4515 1.740025 GCTTGCAGGATGAGGTTACAC 59.260 52.381 0.00 0.00 39.69 2.90
4449 4541 1.673920 GTGCAAGGAAACCTGACGAAA 59.326 47.619 0.00 0.00 32.13 3.46
4526 4618 8.430828 CAGTATTCTCGACATTGCATATTACTG 58.569 37.037 0.00 0.00 0.00 2.74
4529 4621 7.694388 TTCTCGACATTGCATATTACTGTAC 57.306 36.000 0.00 0.00 0.00 2.90
4594 4687 3.260632 TGGTATGTGTACATGCTGTGTCT 59.739 43.478 11.83 0.00 42.29 3.41
4642 4745 2.941064 CCATGTCACATGTGTCCAGATC 59.059 50.000 24.63 8.80 0.00 2.75
4794 4898 9.077885 ACATGTCACTAAATTTCAGTACCAAAT 57.922 29.630 0.00 0.00 0.00 2.32
5195 5299 2.597713 GCCGGCTTTGTTGCTTTGC 61.598 57.895 22.15 0.00 0.00 3.68
5206 5310 0.810648 TTGCTTTGCGATGCCCTTAG 59.189 50.000 9.22 0.00 0.00 2.18
5419 5523 3.670627 GCTAAGGGTTCAGATTGTTTGCG 60.671 47.826 0.00 0.00 0.00 4.85
5431 5535 4.953579 AGATTGTTTGCGGTAATGGGTAAT 59.046 37.500 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.121030 CGGCCACCAGCTCTTTCG 61.121 66.667 2.24 0.00 43.05 3.46
1 2 1.301677 CTTCGGCCACCAGCTCTTTC 61.302 60.000 2.24 0.00 43.05 2.62
3 4 2.177594 CTCTTCGGCCACCAGCTCTT 62.178 60.000 2.24 0.00 43.05 2.85
4 5 2.604686 TCTTCGGCCACCAGCTCT 60.605 61.111 2.24 0.00 43.05 4.09
5 6 2.125350 CTCTTCGGCCACCAGCTC 60.125 66.667 2.24 0.00 43.05 4.09
6 7 4.400961 GCTCTTCGGCCACCAGCT 62.401 66.667 2.24 0.00 43.05 4.24
56 57 4.385088 GCTCTGGATCTTCCTTGGATCTTT 60.385 45.833 0.00 0.00 39.41 2.52
98 99 2.737252 CCTAAGTTGTCGTTCTCCTTGC 59.263 50.000 0.00 0.00 0.00 4.01
99 100 2.737252 GCCTAAGTTGTCGTTCTCCTTG 59.263 50.000 0.00 0.00 0.00 3.61
100 101 2.367567 TGCCTAAGTTGTCGTTCTCCTT 59.632 45.455 0.00 0.00 0.00 3.36
109 110 3.153919 TCCAAACCATGCCTAAGTTGTC 58.846 45.455 0.00 0.00 0.00 3.18
117 118 1.002017 CCCCATCCAAACCATGCCT 59.998 57.895 0.00 0.00 0.00 4.75
142 143 2.065993 TCGCTTCTTCAAACTCCTCG 57.934 50.000 0.00 0.00 0.00 4.63
161 162 1.825090 TCCACATCTTTGCGCTCATT 58.175 45.000 9.73 0.00 0.00 2.57
174 175 1.447838 GCGACGTCCACATCCACAT 60.448 57.895 10.58 0.00 0.00 3.21
243 246 1.068402 CCATTGTGTCGCATTGAAGCA 60.068 47.619 9.34 0.00 31.96 3.91
307 310 1.588824 AATGCCACCAGACATGCGTG 61.589 55.000 3.82 3.82 0.00 5.34
323 326 1.064505 CTGCAGTGGTCGGCATTAATG 59.935 52.381 11.27 11.27 42.99 1.90
324 327 1.382522 CTGCAGTGGTCGGCATTAAT 58.617 50.000 5.25 0.00 42.99 1.40
325 328 1.305219 GCTGCAGTGGTCGGCATTAA 61.305 55.000 16.64 0.00 42.99 1.40
326 329 1.745115 GCTGCAGTGGTCGGCATTA 60.745 57.895 16.64 0.00 42.99 1.90
327 330 3.058160 GCTGCAGTGGTCGGCATT 61.058 61.111 16.64 0.00 42.99 3.56
328 331 3.965539 GAGCTGCAGTGGTCGGCAT 62.966 63.158 16.64 0.00 42.99 4.40
329 332 4.687215 GAGCTGCAGTGGTCGGCA 62.687 66.667 16.64 0.00 41.89 5.69
330 333 4.385405 AGAGCTGCAGTGGTCGGC 62.385 66.667 16.64 0.00 39.21 5.54
331 334 2.433838 CAGAGCTGCAGTGGTCGG 60.434 66.667 16.64 7.06 39.21 4.79
332 335 2.433838 CCAGAGCTGCAGTGGTCG 60.434 66.667 16.64 6.65 39.21 4.79
333 336 2.046507 CCCAGAGCTGCAGTGGTC 60.047 66.667 16.64 9.98 34.96 4.02
334 337 4.341783 GCCCAGAGCTGCAGTGGT 62.342 66.667 16.64 0.00 38.99 4.16
343 346 4.802051 TTCATGCCGGCCCAGAGC 62.802 66.667 26.77 0.00 42.60 4.09
344 347 2.191513 CATTCATGCCGGCCCAGAG 61.192 63.158 26.77 9.23 0.00 3.35
345 348 2.124193 CATTCATGCCGGCCCAGA 60.124 61.111 26.77 16.42 0.00 3.86
396 432 3.922364 ACCCGGCCCACCCAAAAT 61.922 61.111 0.00 0.00 0.00 1.82
423 459 2.843912 AATCAGAGGGGGCTTTGCGG 62.844 60.000 0.00 0.00 0.00 5.69
425 461 0.533951 CAAATCAGAGGGGGCTTTGC 59.466 55.000 0.00 0.00 0.00 3.68
440 478 1.265905 GACGTCTGTTTTCCCGCAAAT 59.734 47.619 8.70 0.00 0.00 2.32
467 515 1.431488 CCTGCATCCGTCCGTGAATG 61.431 60.000 0.00 0.00 0.00 2.67
484 532 0.630673 TTGCCATCCAACATAGCCCT 59.369 50.000 0.00 0.00 0.00 5.19
487 535 4.176271 GTTCTTTTGCCATCCAACATAGC 58.824 43.478 0.00 0.00 31.97 2.97
488 536 4.082787 ACGTTCTTTTGCCATCCAACATAG 60.083 41.667 0.00 0.00 31.97 2.23
506 554 2.776072 CGCATGGTTCGGACGTTC 59.224 61.111 0.00 0.00 0.00 3.95
538 586 4.083484 CCAACGTTGACTCTTAAACCATCC 60.083 45.833 29.35 0.00 0.00 3.51
550 598 5.187186 ACATTAGGTATCTCCAACGTTGACT 59.813 40.000 29.35 15.71 39.02 3.41
592 640 0.320508 GAGGAGTTTGACCACCGACC 60.321 60.000 0.00 0.00 0.00 4.79
682 731 0.807667 CACTCCGAGAGAAATGCGGG 60.808 60.000 1.33 0.00 44.87 6.13
710 759 1.370064 GTTGGACCTACTGGCACGT 59.630 57.895 0.00 0.00 36.63 4.49
730 779 1.144708 TGAGCCATCCAGAAACAACCA 59.855 47.619 0.00 0.00 0.00 3.67
769 818 6.426980 TTTGAAATGGTCATCTGAGAATCG 57.573 37.500 0.00 0.00 34.68 3.34
800 849 2.641559 GCAGCTGTGTGCAGAACC 59.358 61.111 16.64 0.00 45.28 3.62
919 968 2.946564 CGAGTGATCCGCTTATATGCA 58.053 47.619 10.84 0.00 0.00 3.96
987 1037 2.459086 GGCCATGGCAGAGGATCCT 61.459 63.158 36.56 16.13 44.11 3.24
1127 1177 7.067251 ACAACCAAAACCGACTGAATAAAGTAA 59.933 33.333 0.00 0.00 0.00 2.24
1130 1180 5.827666 ACAACCAAAACCGACTGAATAAAG 58.172 37.500 0.00 0.00 0.00 1.85
1132 1182 6.939132 TTACAACCAAAACCGACTGAATAA 57.061 33.333 0.00 0.00 0.00 1.40
1142 1192 8.719560 TTTTATGGAAGTTTACAACCAAAACC 57.280 30.769 0.00 0.00 37.51 3.27
1154 1204 4.881920 ACGCAGCATTTTTATGGAAGTTT 58.118 34.783 0.00 0.00 0.00 2.66
1165 1215 5.132897 TCATAAAAAGGACGCAGCATTTT 57.867 34.783 0.00 0.00 0.00 1.82
1189 1249 4.813697 CCAGATTCCGAAAAAGAGAGGATC 59.186 45.833 0.00 0.00 32.19 3.36
1190 1250 4.226168 ACCAGATTCCGAAAAAGAGAGGAT 59.774 41.667 0.00 0.00 32.19 3.24
1191 1251 3.583086 ACCAGATTCCGAAAAAGAGAGGA 59.417 43.478 0.00 0.00 0.00 3.71
1192 1252 3.935828 GACCAGATTCCGAAAAAGAGAGG 59.064 47.826 0.00 0.00 0.00 3.69
1193 1253 3.935828 GGACCAGATTCCGAAAAAGAGAG 59.064 47.826 0.00 0.00 0.00 3.20
1194 1254 3.939066 GGACCAGATTCCGAAAAAGAGA 58.061 45.455 0.00 0.00 0.00 3.10
1253 1317 2.434359 CTCCCCCAGCGAACGTTC 60.434 66.667 18.47 18.47 0.00 3.95
1254 1318 4.016706 CCTCCCCCAGCGAACGTT 62.017 66.667 0.00 0.00 0.00 3.99
1291 1363 6.875195 CCACTTCATCAACTAAAAATGCCATT 59.125 34.615 0.00 0.00 0.00 3.16
1318 1390 7.325660 TCTTGTGAAGAAAATGCCATATCTC 57.674 36.000 0.00 0.00 33.83 2.75
1323 1395 8.302515 AGAATATCTTGTGAAGAAAATGCCAT 57.697 30.769 0.00 0.00 41.63 4.40
1371 1443 4.130857 TGACAAACGAACCATCTTTGCTA 58.869 39.130 0.00 0.00 32.03 3.49
1372 1444 2.948979 TGACAAACGAACCATCTTTGCT 59.051 40.909 0.00 0.00 32.03 3.91
1410 1490 7.865889 AGACTTAATCAAACGAAAATGTTTCCC 59.134 33.333 0.00 0.00 39.94 3.97
1464 1544 2.641305 CTAAAGGCAAGAGCAGAGCAT 58.359 47.619 0.00 0.00 44.61 3.79
1533 1613 9.203163 TCCTTTCCTGTAAAATTCCTACAAAAA 57.797 29.630 2.90 5.44 0.00 1.94
1669 1749 6.660949 AGGATTTGTTTTCATTGAGTCTAGGG 59.339 38.462 0.00 0.00 0.00 3.53
1687 1767 8.607459 GTCTGTTAGTTCACATCATAGGATTTG 58.393 37.037 0.00 0.00 33.44 2.32
1755 1835 7.742089 GTGAAACTTGTAGAAATTGAGATGTCG 59.258 37.037 0.00 0.00 0.00 4.35
1790 1870 8.108378 TCTTTGGTTCATAGGGTTGGAATATA 57.892 34.615 0.00 0.00 0.00 0.86
1796 1876 3.763897 CCTTCTTTGGTTCATAGGGTTGG 59.236 47.826 0.00 0.00 0.00 3.77
1798 1878 3.431415 GCCTTCTTTGGTTCATAGGGTT 58.569 45.455 0.00 0.00 0.00 4.11
1800 1880 2.379005 GGCCTTCTTTGGTTCATAGGG 58.621 52.381 0.00 0.00 0.00 3.53
1823 1903 4.762289 TTAGAAGGGCTTGAAGAGGATC 57.238 45.455 0.00 0.00 0.00 3.36
1839 1919 3.644738 AGTTCTCCCTGTTCGGTTTAGAA 59.355 43.478 0.00 0.00 0.00 2.10
2069 2151 2.390938 CATCAGCTGCACAAACACAAG 58.609 47.619 9.47 0.00 0.00 3.16
2081 2163 0.467474 ATCCACCATGGCATCAGCTG 60.467 55.000 13.04 7.63 41.70 4.24
2200 2282 3.882888 TGAATATTGCGGTCCTCATTTCC 59.117 43.478 0.00 0.00 0.00 3.13
2210 2292 2.779755 TCCACTGTGAATATTGCGGT 57.220 45.000 9.86 0.00 0.00 5.68
2212 2294 5.929697 ACATATCCACTGTGAATATTGCG 57.070 39.130 9.86 0.00 0.00 4.85
2233 2315 4.030195 GTCGTCTGCAGTTTCAAAACAAAC 59.970 41.667 14.67 0.00 41.30 2.93
2418 2504 5.691508 ACGAAACCTATGAAAATACGTCG 57.308 39.130 0.00 0.00 0.00 5.12
2457 2543 4.010667 TGCCCTGTAAAATAACAGTCGT 57.989 40.909 3.56 0.00 44.45 4.34
2525 2611 1.985473 TCCCATGCACATAATCTGCC 58.015 50.000 0.00 0.00 33.36 4.85
2540 2626 0.250727 CGAGTTTGAGCCCTTTCCCA 60.251 55.000 0.00 0.00 0.00 4.37
2634 2720 0.674534 GTCTCACGTGTTCCCAGTCT 59.325 55.000 16.51 0.00 0.00 3.24
2659 2745 0.253044 CCATGTGGACTGGGGTACTG 59.747 60.000 0.00 0.00 37.39 2.74
2680 2766 3.691609 GTGTGATTTAAGCAAGGGAGAGG 59.308 47.826 0.00 0.00 0.00 3.69
2847 2933 2.167900 CCTACCCTACGAGGAAAACCAG 59.832 54.545 0.00 0.00 37.67 4.00
2858 2944 1.208776 CTTTGGAACCCCTACCCTACG 59.791 57.143 0.00 0.00 0.00 3.51
2859 2945 1.562942 CCTTTGGAACCCCTACCCTAC 59.437 57.143 0.00 0.00 0.00 3.18
2860 2946 1.441956 TCCTTTGGAACCCCTACCCTA 59.558 52.381 0.00 0.00 0.00 3.53
2861 2947 0.197661 TCCTTTGGAACCCCTACCCT 59.802 55.000 0.00 0.00 0.00 4.34
2862 2948 0.624254 CTCCTTTGGAACCCCTACCC 59.376 60.000 0.00 0.00 0.00 3.69
2957 3043 2.749621 CCTTGTTAGTGGGCTGATGTTC 59.250 50.000 0.00 0.00 0.00 3.18
3035 3121 9.713740 GCATTTTTGTTGTGAATATGTCAAAAA 57.286 25.926 13.26 13.26 43.57 1.94
3153 3239 0.109723 CGAACCCTCCCTTTTGGTCA 59.890 55.000 0.00 0.00 38.10 4.02
3402 3489 2.316867 CGTTGTCCGTCATGCTGCA 61.317 57.895 4.13 4.13 0.00 4.41
3560 3651 9.491675 TGAATTGTCATCACAAGCATAATTTTT 57.508 25.926 0.00 0.00 45.85 1.94
3561 3652 8.928733 GTGAATTGTCATCACAAGCATAATTTT 58.071 29.630 2.32 0.00 45.85 1.82
3562 3653 8.470040 GTGAATTGTCATCACAAGCATAATTT 57.530 30.769 2.32 0.00 45.85 1.82
3741 3833 5.127031 ACAATGCTGTTCTGTTGGTTTACTT 59.873 36.000 0.00 0.00 28.57 2.24
3800 3892 3.198635 CAGAGGAGCCTAGTTGAATCCAA 59.801 47.826 0.00 0.00 32.21 3.53
3851 3943 1.075374 TGATGTCCTTGGTTTCAGGGG 59.925 52.381 0.00 0.00 40.22 4.79
4374 4466 1.631388 TCATACGCAGAAAAAGGGGGA 59.369 47.619 0.00 0.00 0.00 4.81
4423 4515 1.542915 CAGGTTTCCTTGCACTGATGG 59.457 52.381 0.00 0.00 0.00 3.51
4449 4541 4.021229 TGCAAGCATGAGAATCCATCTTT 58.979 39.130 0.00 0.00 38.96 2.52
4794 4898 4.979197 CGCCAATGCTTTTGTACAAGTTTA 59.021 37.500 8.56 0.00 34.43 2.01
4801 4905 1.976045 CGTTCGCCAATGCTTTTGTAC 59.024 47.619 0.00 0.00 34.43 2.90
4970 5074 3.616219 TGGGTTTTAATGTGCTATCGCT 58.384 40.909 0.00 0.00 36.97 4.93
5195 5299 0.744874 TCCGAACTCTAAGGGCATCG 59.255 55.000 0.00 0.00 0.00 3.84
5419 5523 8.879427 ATTCCATAGCTAAATTACCCATTACC 57.121 34.615 0.00 0.00 0.00 2.85
5431 5535 5.124776 CGGTGTTTCCAATTCCATAGCTAAA 59.875 40.000 0.00 0.00 35.57 1.85


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

AutoCloner maintained by Alex Coulton.