Multiple sequence alignment - TraesCS1D01G236400

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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 TraesCS1D01G236400 chr1D 100.000 7853 0 0 1 7853 325692238 325684386 0.000000e+00 14502.0
1 TraesCS1D01G236400 chr1D 94.737 38 2 0 7183 7220 484866323 484866360 8.510000e-05 60.2
2 TraesCS1D01G236400 chr1B 93.325 7491 337 70 1 7392 438710040 438702614 0.000000e+00 10912.0
3 TraesCS1D01G236400 chr1B 92.537 469 27 4 7390 7853 438702458 438701993 0.000000e+00 665.0
4 TraesCS1D01G236400 chr1B 77.852 149 21 10 7185 7327 556968141 556968283 1.820000e-11 82.4
5 TraesCS1D01G236400 chr1A 95.675 4879 160 31 1 4864 418033044 418037886 0.000000e+00 7793.0
6 TraesCS1D01G236400 chr1A 93.360 2741 111 30 4863 7542 418038145 418040875 0.000000e+00 3988.0
7 TraesCS1D01G236400 chr1A 76.623 308 43 20 7224 7504 76485772 76485467 8.210000e-30 143.0
8 TraesCS1D01G236400 chr4D 89.354 263 27 1 3337 3599 208560168 208560429 5.870000e-86 329.0
9 TraesCS1D01G236400 chr4D 79.618 157 25 5 7353 7505 481380265 481380112 1.080000e-18 106.0
10 TraesCS1D01G236400 chr7B 88.462 260 29 1 3342 3601 107925850 107925592 5.920000e-81 313.0
11 TraesCS1D01G236400 chr7B 83.212 137 18 5 7327 7459 103998570 103998705 3.850000e-23 121.0
12 TraesCS1D01G236400 chr7B 78.531 177 25 10 7337 7504 424059362 424059534 3.880000e-18 104.0
13 TraesCS1D01G236400 chr6D 88.168 262 31 0 3342 3603 103962485 103962224 5.920000e-81 313.0
14 TraesCS1D01G236400 chr7D 88.077 260 30 1 3342 3601 145766955 145766697 2.750000e-79 307.0
15 TraesCS1D01G236400 chr7D 74.859 354 50 28 7183 7504 409510878 409511224 2.980000e-24 124.0
16 TraesCS1D01G236400 chr5B 87.891 256 31 0 3342 3597 324708382 324708127 1.280000e-77 302.0
17 TraesCS1D01G236400 chr5B 86.923 260 31 3 3338 3597 317855564 317855820 9.970000e-74 289.0
18 TraesCS1D01G236400 chr5B 86.822 258 33 1 3341 3597 594870753 594870496 3.590000e-73 287.0
19 TraesCS1D01G236400 chr5A 75.575 348 48 24 7186 7505 661988751 661988413 3.820000e-28 137.0
20 TraesCS1D01G236400 chr7A 74.438 356 52 29 7183 7504 470595226 470595576 4.980000e-22 117.0
21 TraesCS1D01G236400 chr2D 76.860 121 22 5 7183 7298 20920421 20920302 6.580000e-06 63.9
22 TraesCS1D01G236400 chr4A 94.595 37 1 1 7191 7226 624290033 624289997 1.000000e-03 56.5


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 TraesCS1D01G236400 chr1D 325684386 325692238 7852 True 14502.0 14502 100.0000 1 7853 1 chr1D.!!$R1 7852
1 TraesCS1D01G236400 chr1B 438701993 438710040 8047 True 5788.5 10912 92.9310 1 7853 2 chr1B.!!$R1 7852
2 TraesCS1D01G236400 chr1A 418033044 418040875 7831 False 5890.5 7793 94.5175 1 7542 2 chr1A.!!$F1 7541

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
836 839 0.238289 GGACAACACTTGTGGCATCG 59.762 55.000 5.72 0.00 45.52 3.84 F
1733 1754 1.000233 TGCCAGCCCAAATTCGGAT 60.000 52.632 0.00 0.00 0.00 4.18 F
3363 3392 1.269012 CATGTTTGGTTGGCCTCCAT 58.731 50.000 18.17 3.89 34.75 3.41 F
3529 3558 1.025812 TTGTGGCTGTAACCAAACGG 58.974 50.000 0.00 0.00 42.70 4.44 F
5009 5311 0.036388 TTGGACAGGGAAGCGTGATC 60.036 55.000 0.00 0.00 0.00 2.92 F
6322 6677 0.179045 ATGGGCACTTGCGATCCTAC 60.179 55.000 0.00 0.00 43.26 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1780 1.139058 ACCGGCAAGAATAGCACCTAG 59.861 52.381 0.00 0.00 0.00 3.02 R
3392 3421 0.249405 ACAAAAACTGTGGCATGCCG 60.249 50.000 30.87 19.48 36.69 5.69 R
4599 4638 2.098233 GCGGACGCAGGAATCGAAA 61.098 57.895 12.31 0.00 41.49 3.46 R
5390 5692 0.776810 TGGTGGTGGTGGTGATGATT 59.223 50.000 0.00 0.00 0.00 2.57 R
6783 7151 0.168788 ATTCAAGGCGCAATGTGTCG 59.831 50.000 10.83 0.00 0.00 4.35 R
7161 7533 0.543749 GCCCTACATGGAGCTCAAGT 59.456 55.000 17.19 12.64 38.35 3.16 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
46 47 2.137425 AACGCCGAGTGTCGTCATCA 62.137 55.000 0.00 0.00 38.40 3.07
68 69 0.453793 CGGAACACCTTGCAAACACA 59.546 50.000 0.00 0.00 0.00 3.72
134 136 1.906333 AACACGCCAAATGTCCCCC 60.906 57.895 0.00 0.00 0.00 5.40
192 194 1.304381 GTGGGGAGGCTTGCATCAA 60.304 57.895 9.44 0.00 0.00 2.57
197 199 1.700955 GGAGGCTTGCATCAATCCAT 58.299 50.000 9.44 0.00 32.69 3.41
217 219 1.371389 GCGAACGACGAGTCAACCT 60.371 57.895 0.00 0.00 45.77 3.50
229 231 1.202639 AGTCAACCTGCAACATCGACA 60.203 47.619 0.00 0.00 0.00 4.35
243 245 2.280797 GACACAAGCCGCAGTGGA 60.281 61.111 17.07 0.00 42.00 4.02
251 253 0.613260 AGCCGCAGTGGATGTTCTTA 59.387 50.000 3.39 0.00 42.00 2.10
259 261 3.434641 CAGTGGATGTTCTTACAGCACAG 59.565 47.826 0.00 0.00 42.40 3.66
260 262 3.071602 AGTGGATGTTCTTACAGCACAGT 59.928 43.478 0.00 0.00 42.40 3.55
265 267 4.137116 TGTTCTTACAGCACAGTTGTCT 57.863 40.909 0.00 0.00 0.00 3.41
329 331 6.789268 TGTGGAAGGGATAATGAGAAGAAAA 58.211 36.000 0.00 0.00 0.00 2.29
392 394 2.629050 ATAGCGACGACGGCTTGCAT 62.629 55.000 9.67 0.00 40.15 3.96
395 397 2.434185 GACGACGGCTTGCATCCA 60.434 61.111 0.00 0.00 0.00 3.41
410 412 3.140707 TGCATCCATGGTGATATTCCCTT 59.859 43.478 12.58 0.00 0.00 3.95
449 451 2.965147 GCTTGTGGCGCGTGAATCA 61.965 57.895 8.43 0.00 0.00 2.57
486 489 7.291885 AGTCTAATCATGATGATGAGGGAAAGA 59.708 37.037 17.67 6.49 42.01 2.52
489 492 5.548181 TCATGATGATGAGGGAAAGAGAG 57.452 43.478 0.00 0.00 33.40 3.20
491 494 6.138967 TCATGATGATGAGGGAAAGAGAGTA 58.861 40.000 0.00 0.00 33.40 2.59
494 497 7.443302 TGATGATGAGGGAAAGAGAGTAAAT 57.557 36.000 0.00 0.00 0.00 1.40
540 543 1.831106 CCCAGGTGCTACTGTGATACA 59.169 52.381 7.31 0.00 36.75 2.29
585 588 1.927895 ATCGAACGACATCTGGAAGC 58.072 50.000 0.00 0.00 0.00 3.86
619 622 4.320057 GCTGGATCTATGCTCAATTTTCGG 60.320 45.833 0.00 0.00 0.00 4.30
690 693 0.824109 AATCTGAGAATCCGACGGCA 59.176 50.000 9.66 0.00 28.86 5.69
762 765 2.505819 TCCTAGAAATGAAGGTGGCTCC 59.494 50.000 0.00 0.00 0.00 4.70
774 777 0.465705 GTGGCTCCTGGATGATTCGA 59.534 55.000 0.00 0.00 0.00 3.71
821 824 2.970324 GCGTGGCAAAGACGGACA 60.970 61.111 0.00 0.00 37.30 4.02
836 839 0.238289 GGACAACACTTGTGGCATCG 59.762 55.000 5.72 0.00 45.52 3.84
842 845 1.229428 CACTTGTGGCATCGTCAACT 58.771 50.000 0.00 0.00 0.00 3.16
862 865 7.534239 GTCAACTGATGGATTAGAAACGTTTTC 59.466 37.037 15.89 8.40 0.00 2.29
869 872 9.556030 GATGGATTAGAAACGTTTTCCTTAAAG 57.444 33.333 23.27 0.00 0.00 1.85
1733 1754 1.000233 TGCCAGCCCAAATTCGGAT 60.000 52.632 0.00 0.00 0.00 4.18
1760 1781 9.347240 ACATACGGTATAACACAGTTATCTACT 57.653 33.333 5.74 0.00 36.84 2.57
1955 1976 1.561542 CTAGGGGAGTTTCTGGTGCAT 59.438 52.381 0.00 0.00 0.00 3.96
1964 1986 5.048083 GGAGTTTCTGGTGCATATTTGTGAA 60.048 40.000 0.00 0.00 0.00 3.18
2033 2055 9.716507 CGTGCATTTAGTTATTAATGTTAGCTT 57.283 29.630 0.00 0.00 34.88 3.74
2078 2100 8.208718 TGTGGTGTATTCTCTTATTGTATTGC 57.791 34.615 0.00 0.00 0.00 3.56
2130 2152 8.823220 ATAAACCCATTTTCTTAGTACATGCT 57.177 30.769 0.00 0.00 0.00 3.79
2185 2207 7.400052 TCTGGGTATTGATATATGCTTGAGCTA 59.600 37.037 4.44 0.00 42.66 3.32
2550 2572 3.375299 GTCAATGCTTTGCCGAATAGACT 59.625 43.478 7.44 0.00 32.61 3.24
2815 2839 1.751924 TGCCTTAACAAAAACTGCCGT 59.248 42.857 0.00 0.00 0.00 5.68
2847 2871 5.961272 AGGCGAAAGTTTATAAAATGGTGG 58.039 37.500 0.00 0.00 0.00 4.61
3015 3043 2.623889 AGTGTGAGTTCGCTAGTTCAGT 59.376 45.455 0.00 0.00 0.00 3.41
3016 3044 2.726760 GTGTGAGTTCGCTAGTTCAGTG 59.273 50.000 0.00 0.00 35.99 3.66
3017 3045 2.361119 TGTGAGTTCGCTAGTTCAGTGT 59.639 45.455 0.00 0.00 36.11 3.55
3018 3046 3.566742 TGTGAGTTCGCTAGTTCAGTGTA 59.433 43.478 0.00 0.00 36.11 2.90
3019 3047 4.217767 TGTGAGTTCGCTAGTTCAGTGTAT 59.782 41.667 0.00 0.00 36.11 2.29
3020 3048 4.559251 GTGAGTTCGCTAGTTCAGTGTATG 59.441 45.833 0.00 0.00 36.11 2.39
3021 3049 4.106197 GAGTTCGCTAGTTCAGTGTATGG 58.894 47.826 0.00 0.00 36.11 2.74
3022 3050 2.579207 TCGCTAGTTCAGTGTATGGC 57.421 50.000 0.00 0.00 36.11 4.40
3258 3286 7.333528 AGCTTTGATCACACAAAAGTAGAAA 57.666 32.000 0.00 0.00 38.90 2.52
3363 3392 1.269012 CATGTTTGGTTGGCCTCCAT 58.731 50.000 18.17 3.89 34.75 3.41
3377 3406 4.966168 TGGCCTCCATATTTAGTCACACTA 59.034 41.667 3.32 0.00 0.00 2.74
3392 3421 2.336554 CACTATTGTGCCACAAGTGC 57.663 50.000 16.35 0.00 41.94 4.40
3529 3558 1.025812 TTGTGGCTGTAACCAAACGG 58.974 50.000 0.00 0.00 42.70 4.44
3649 3678 1.078848 ATGTCCGCTCAGTTGAGGC 60.079 57.895 10.88 3.08 42.29 4.70
3704 3733 8.526147 CACTAATGATTCCCATTTTGACTTCTT 58.474 33.333 0.00 0.00 42.55 2.52
3740 3769 5.008019 TGTTGTGATCTTTTCTGTTGAGCTC 59.992 40.000 6.82 6.82 0.00 4.09
3845 3874 4.403453 GCTTTATGCTACAAAAGACGGTG 58.597 43.478 0.00 0.00 35.19 4.94
3938 3967 3.754965 TGTAAGGCAGAAATGCTTCACT 58.245 40.909 0.00 0.00 33.64 3.41
3986 4022 3.525537 TGCGAATCTTCTTCCTGTCATC 58.474 45.455 0.00 0.00 0.00 2.92
3990 4026 5.451242 GCGAATCTTCTTCCTGTCATCTACT 60.451 44.000 0.00 0.00 0.00 2.57
4014 4050 1.875963 CCCCACAATCTGTCAACGC 59.124 57.895 0.00 0.00 0.00 4.84
4551 4587 3.228188 TCTGAAAGGTTGGATGCTTGT 57.772 42.857 0.00 0.00 0.00 3.16
4599 4638 5.979517 GCTTGCTTCTTGTTATTTGTCTTGT 59.020 36.000 0.00 0.00 0.00 3.16
4831 4873 8.811994 TCCTTTCCATTTTCCTATTTTTGTAGG 58.188 33.333 0.00 0.00 42.19 3.18
5006 5308 0.606401 ATGTTGGACAGGGAAGCGTG 60.606 55.000 0.00 0.00 0.00 5.34
5009 5311 0.036388 TTGGACAGGGAAGCGTGATC 60.036 55.000 0.00 0.00 0.00 2.92
5389 5691 1.971505 ATCATCGCCGTCACCACCAT 61.972 55.000 0.00 0.00 0.00 3.55
5390 5692 1.142965 CATCGCCGTCACCACCATA 59.857 57.895 0.00 0.00 0.00 2.74
5654 5974 3.515104 TCATGCAGTGTCACCATCTTCTA 59.485 43.478 0.00 0.00 0.00 2.10
5773 6093 0.720027 CAGTGTCTCTTGCTCATGCG 59.280 55.000 0.00 0.00 43.34 4.73
5838 6158 5.988561 ACACATGTGAGTCTTTTCTCTCTTC 59.011 40.000 31.94 0.00 35.68 2.87
5849 6169 6.310224 GTCTTTTCTCTCTTCTCTCATTTCCG 59.690 42.308 0.00 0.00 0.00 4.30
5876 6196 5.048224 GCTGCCAGACATTGCTAATATCAAT 60.048 40.000 0.00 0.00 34.74 2.57
5959 6283 3.070018 CAGACCTCAGCGATCAGTTTTT 58.930 45.455 0.00 0.00 0.00 1.94
5976 6300 5.519566 CAGTTTTTATGCTTGTCACTGCAAA 59.480 36.000 4.12 0.00 42.74 3.68
6018 6350 5.744171 TGATTTGGTGTACTGTGATGCTAT 58.256 37.500 0.00 0.00 0.00 2.97
6049 6381 4.001618 TGTAAACTGCACTGCTATGTCA 57.998 40.909 1.98 0.00 0.00 3.58
6129 6480 9.342308 AGTATCATCTTTGTTCTCTGTTTCAAA 57.658 29.630 0.00 0.00 0.00 2.69
6226 6578 6.097839 TCCTGATACCTACCTGTCATGTAAAC 59.902 42.308 0.00 0.00 0.00 2.01
6322 6677 0.179045 ATGGGCACTTGCGATCCTAC 60.179 55.000 0.00 0.00 43.26 3.18
6327 6682 1.002366 CACTTGCGATCCTACTGTGC 58.998 55.000 0.00 0.00 0.00 4.57
6356 6711 1.137872 GGGTCTACCATGACAGAGCTG 59.862 57.143 18.89 0.00 38.90 4.24
6386 6742 4.725790 GCTGAAGGCAGTCCAAAATAAT 57.274 40.909 0.00 0.00 44.17 1.28
6678 7042 1.067582 GCGTATAGCGGTTGCCTCT 59.932 57.895 0.00 0.00 44.31 3.69
6699 7063 3.496331 TGGTTCAAATTCTCAGGGGTTC 58.504 45.455 0.00 0.00 0.00 3.62
6700 7064 3.117322 TGGTTCAAATTCTCAGGGGTTCA 60.117 43.478 0.00 0.00 0.00 3.18
6734 7098 5.944007 TGGACCGATAGATTCTCGATGATTA 59.056 40.000 0.00 0.00 38.38 1.75
6758 7122 4.163458 TCCCGAATAGTAAACCTGAGCATT 59.837 41.667 0.00 0.00 0.00 3.56
6765 7129 5.763876 AGTAAACCTGAGCATTAGAAGGT 57.236 39.130 0.00 0.00 45.01 3.50
6783 7151 4.836125 AGGTGTGATGATGTGTTTTGAC 57.164 40.909 0.00 0.00 0.00 3.18
6806 7174 1.727880 CACATTGCGCCTTGAATTTGG 59.272 47.619 4.18 0.00 0.00 3.28
6856 7225 1.078347 TTCCAAACCCCTGATGGCC 59.922 57.895 0.00 0.00 34.13 5.36
6871 7240 2.710902 GGCCGTTGCAGGGATTTCC 61.711 63.158 9.86 0.00 40.13 3.13
7014 7384 0.381801 GCATATGGTCGGTGCAAAGG 59.618 55.000 4.56 0.00 38.68 3.11
7022 7392 2.250939 CGGTGCAAAGGAGCGTGAA 61.251 57.895 1.98 0.00 37.31 3.18
7144 7515 1.599542 GATGTAAATGACTCGCAGCCC 59.400 52.381 0.00 0.00 0.00 5.19
7147 7518 0.459585 TAAATGACTCGCAGCCCGAC 60.460 55.000 0.00 0.00 41.89 4.79
7161 7533 1.748493 GCCCGACAATGCTAAATGGAA 59.252 47.619 0.00 0.00 0.00 3.53
7183 7555 0.975556 TGAGCTCCATGTAGGGCGAA 60.976 55.000 12.15 0.00 38.25 4.70
7245 7631 7.910584 TCACATATGCCAGAGACATAATGTAT 58.089 34.615 1.58 0.00 33.89 2.29
7289 7675 9.844790 TGTTGAAATACATTAAAATGAGAGCTG 57.155 29.630 9.60 0.00 39.67 4.24
7290 7676 8.801913 GTTGAAATACATTAAAATGAGAGCTGC 58.198 33.333 9.60 0.00 39.67 5.25
7291 7677 8.054152 TGAAATACATTAAAATGAGAGCTGCA 57.946 30.769 9.60 0.00 39.67 4.41
7479 8032 7.398618 TGAATTAAAATAACAGGCTCCATGGAA 59.601 33.333 17.00 0.00 0.00 3.53
7555 8108 9.880157 GTAGTAATATGTTCTTGAGGTGGTTTA 57.120 33.333 0.00 0.00 0.00 2.01
7557 8110 8.603304 AGTAATATGTTCTTGAGGTGGTTTAGT 58.397 33.333 0.00 0.00 0.00 2.24
7572 8125 5.408604 GTGGTTTAGTGTGAAATGACGATCT 59.591 40.000 0.00 0.00 0.00 2.75
7579 8132 5.038033 GTGTGAAATGACGATCTACTCCTC 58.962 45.833 0.00 0.00 0.00 3.71
7582 8135 0.869068 ATGACGATCTACTCCTCGCG 59.131 55.000 0.00 0.00 38.42 5.87
7585 8138 1.532007 GACGATCTACTCCTCGCGATT 59.468 52.381 10.36 0.00 38.42 3.34
7586 8139 1.264557 ACGATCTACTCCTCGCGATTG 59.735 52.381 10.36 4.01 38.42 2.67
7592 8145 1.103803 ACTCCTCGCGATTGAGCTAA 58.896 50.000 26.55 0.00 34.56 3.09
7638 8191 7.667043 TCTTGATGTGGTTTAGTGTGAATAC 57.333 36.000 0.00 0.00 0.00 1.89
7645 8198 5.004156 GTGGTTTAGTGTGAATACGACGATC 59.996 44.000 0.00 0.00 0.00 3.69
7646 8199 4.203764 GGTTTAGTGTGAATACGACGATCG 59.796 45.833 14.88 14.88 46.93 3.69
7666 8219 6.292542 CGATCGTGCTTCATCAGAAATGTTAT 60.293 38.462 7.03 0.00 32.35 1.89
7667 8220 7.096065 CGATCGTGCTTCATCAGAAATGTTATA 60.096 37.037 7.03 0.00 32.35 0.98
7687 8240 9.836864 TGTTATAGACATACTGAGAATTGCAAT 57.163 29.630 5.99 5.99 32.00 3.56
7726 8279 1.401148 GCTCTGACAGAGTTTACGCGA 60.401 52.381 28.76 0.00 44.12 5.87
7761 8314 5.811613 CACAAAGACAAACCAACATGATTGT 59.188 36.000 0.00 2.63 38.62 2.71
7780 8333 5.779241 TTGTATCTGGGGAGAAATCACTT 57.221 39.130 0.00 0.00 0.00 3.16
7837 8390 5.667626 TCCTAAAGGAAGGCTCATGATACTT 59.332 40.000 10.73 10.73 42.18 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.977244 CGTTGCAAGGTGTGGGGC 61.977 66.667 10.97 0.00 0.00 5.80
46 47 2.115911 TTTGCAAGGTGTTCCGCGT 61.116 52.632 4.92 0.00 39.05 6.01
68 69 1.687493 GTGTGCTAGGAGCCCCTCT 60.687 63.158 0.00 0.00 43.14 3.69
134 136 1.003718 GGTGTTGGAAGGTCGGAGG 60.004 63.158 0.00 0.00 0.00 4.30
168 170 2.450502 AAGCCTCCCCACCAGTGT 60.451 61.111 0.00 0.00 0.00 3.55
192 194 1.226974 CTCGTCGTTCGCCATGGAT 60.227 57.895 18.40 0.00 39.67 3.41
197 199 1.659335 GTTGACTCGTCGTTCGCCA 60.659 57.895 0.00 0.00 39.67 5.69
217 219 1.840630 CGGCTTGTGTCGATGTTGCA 61.841 55.000 0.00 0.00 45.19 4.08
229 231 1.228245 AACATCCACTGCGGCTTGT 60.228 52.632 0.00 0.00 33.63 3.16
251 253 0.839946 AGGGAAGACAACTGTGCTGT 59.160 50.000 0.00 0.00 0.00 4.40
259 261 3.119566 CCACTACTACGAGGGAAGACAAC 60.120 52.174 0.00 0.00 0.00 3.32
260 262 3.087031 CCACTACTACGAGGGAAGACAA 58.913 50.000 0.00 0.00 0.00 3.18
265 267 1.754803 CATGCCACTACTACGAGGGAA 59.245 52.381 0.00 0.00 0.00 3.97
355 357 5.522460 TCGCTATTCTAATGTTGCAAGTACC 59.478 40.000 0.00 0.00 0.00 3.34
392 394 4.535781 CAACAAGGGAATATCACCATGGA 58.464 43.478 21.47 0.00 0.00 3.41
395 397 2.951642 CGCAACAAGGGAATATCACCAT 59.048 45.455 0.00 0.00 0.00 3.55
458 460 5.184671 TCCCTCATCATCATGATTAGACTCG 59.815 44.000 10.03 0.00 38.42 4.18
462 464 7.511714 TCTCTTTCCCTCATCATCATGATTAGA 59.488 37.037 10.03 1.45 38.42 2.10
465 467 6.101442 ACTCTCTTTCCCTCATCATCATGATT 59.899 38.462 5.16 0.00 38.42 2.57
469 471 7.443302 TTTACTCTCTTTCCCTCATCATCAT 57.557 36.000 0.00 0.00 0.00 2.45
486 489 6.599638 GCACCAAACATTCTCCTATTTACTCT 59.400 38.462 0.00 0.00 0.00 3.24
489 492 6.759497 AGCACCAAACATTCTCCTATTTAC 57.241 37.500 0.00 0.00 0.00 2.01
491 494 5.652452 GGTAGCACCAAACATTCTCCTATTT 59.348 40.000 1.01 0.00 38.42 1.40
494 497 3.369052 CGGTAGCACCAAACATTCTCCTA 60.369 47.826 6.21 0.00 38.47 2.94
553 556 3.000971 GTCGTTCGATTTGAGAATCCGAC 60.001 47.826 10.99 10.99 42.00 4.79
585 588 4.689812 GCATAGATCCAGCAGATACAACAG 59.310 45.833 0.00 0.00 34.42 3.16
640 643 6.317789 TCCTAAGAACTCTGCAAACATTTG 57.682 37.500 0.00 0.00 41.03 2.32
641 644 5.048434 GCTCCTAAGAACTCTGCAAACATTT 60.048 40.000 0.00 0.00 0.00 2.32
644 647 3.403038 GCTCCTAAGAACTCTGCAAACA 58.597 45.455 0.00 0.00 0.00 2.83
645 648 2.744741 GGCTCCTAAGAACTCTGCAAAC 59.255 50.000 0.00 0.00 0.00 2.93
646 649 2.371841 TGGCTCCTAAGAACTCTGCAAA 59.628 45.455 0.00 0.00 0.00 3.68
660 663 2.187239 TCTCAGATTGGATGGCTCCT 57.813 50.000 4.92 0.00 42.59 3.69
715 718 3.872431 GGTGCTACCGAGGCCTAT 58.128 61.111 4.42 0.00 0.00 2.57
762 765 1.920051 CACGCGTCGAATCATCCAG 59.080 57.895 9.86 0.00 0.00 3.86
788 791 4.778143 GCGTCCCCGTGCATCCTT 62.778 66.667 0.00 0.00 36.15 3.36
799 802 3.723348 GTCTTTGCCACGCGTCCC 61.723 66.667 9.86 3.25 0.00 4.46
821 824 1.333619 GTTGACGATGCCACAAGTGTT 59.666 47.619 0.00 0.00 0.00 3.32
836 839 6.481954 AACGTTTCTAATCCATCAGTTGAC 57.518 37.500 0.00 0.00 0.00 3.18
842 845 8.624367 TTAAGGAAAACGTTTCTAATCCATCA 57.376 30.769 24.33 7.95 0.00 3.07
919 923 8.458843 ACAGCGTAAATAATTTTAGCTTGTCAT 58.541 29.630 0.00 0.00 33.43 3.06
934 938 3.511699 CAGTCTGCTGACAGCGTAAATA 58.488 45.455 23.61 2.87 46.26 1.40
1280 1296 4.349365 TCTTCTTCTTCCTTCTCCTCCTC 58.651 47.826 0.00 0.00 0.00 3.71
1388 1404 4.704833 GCGGCAGCCAGAACAGGA 62.705 66.667 13.30 0.00 37.42 3.86
1759 1780 1.139058 ACCGGCAAGAATAGCACCTAG 59.861 52.381 0.00 0.00 0.00 3.02
1760 1781 1.200519 ACCGGCAAGAATAGCACCTA 58.799 50.000 0.00 0.00 0.00 3.08
2033 2055 7.976734 CACCACAACTGATTTTAAACCTTTGTA 59.023 33.333 0.00 0.00 0.00 2.41
2078 2100 4.186077 TCCTCCACCATAGTTCTAGAGG 57.814 50.000 0.00 0.00 40.66 3.69
2185 2207 4.514401 CCATTTTTAGTTCTCCTACCGCT 58.486 43.478 0.00 0.00 0.00 5.52
2550 2572 2.525055 GCAGCTTTTTGTCGTGAACAA 58.475 42.857 0.00 0.00 46.11 2.83
2873 2898 6.209391 CCACCATTCCATATATGAAGGGAAAC 59.791 42.308 23.44 0.00 42.26 2.78
2888 2913 6.101150 AGTTCAATATAGCTACCACCATTCCA 59.899 38.462 0.00 0.00 0.00 3.53
3015 3043 7.285172 AGACAAAATTATGCATACAGCCATACA 59.715 33.333 5.74 0.00 44.83 2.29
3016 3044 7.651808 AGACAAAATTATGCATACAGCCATAC 58.348 34.615 5.74 0.00 44.83 2.39
3017 3045 7.822161 AGACAAAATTATGCATACAGCCATA 57.178 32.000 5.74 0.00 44.83 2.74
3018 3046 6.720112 AGACAAAATTATGCATACAGCCAT 57.280 33.333 5.74 0.00 44.83 4.40
3019 3047 6.601217 TGTAGACAAAATTATGCATACAGCCA 59.399 34.615 5.74 0.00 44.83 4.75
3020 3048 7.026631 TGTAGACAAAATTATGCATACAGCC 57.973 36.000 5.74 0.00 44.83 4.85
3021 3049 7.641411 CACTGTAGACAAAATTATGCATACAGC 59.359 37.037 15.41 0.00 41.49 4.40
3022 3050 8.882736 TCACTGTAGACAAAATTATGCATACAG 58.117 33.333 5.74 11.21 42.75 2.74
3258 3286 5.640147 TGTAGAAGGACCATGTTCCATTTT 58.360 37.500 12.37 0.00 38.25 1.82
3377 3406 3.041701 CCGCACTTGTGGCACAAT 58.958 55.556 31.20 18.90 44.16 2.71
3392 3421 0.249405 ACAAAAACTGTGGCATGCCG 60.249 50.000 30.87 19.48 36.69 5.69
3649 3678 9.651718 GTAAACAAGTAAAAGAGACAGACATTG 57.348 33.333 0.00 0.00 0.00 2.82
3704 3733 2.951457 TCACAACACACGAGTTCTCA 57.049 45.000 0.00 0.00 0.00 3.27
3845 3874 9.871238 TTAGGTATACTTTCATTCAACTCTGAC 57.129 33.333 2.25 0.00 0.00 3.51
4014 4050 9.956720 GTACAATCATTTAGGAATCAGGAATTG 57.043 33.333 0.00 0.00 0.00 2.32
4599 4638 2.098233 GCGGACGCAGGAATCGAAA 61.098 57.895 12.31 0.00 41.49 3.46
5006 5308 8.908786 TTCACATATTATGACCTTGGAAGATC 57.091 34.615 10.62 0.00 0.00 2.75
5009 5311 7.770433 TCACTTCACATATTATGACCTTGGAAG 59.230 37.037 10.62 12.89 0.00 3.46
5389 5691 1.988846 TGGTGGTGGTGGTGATGATTA 59.011 47.619 0.00 0.00 0.00 1.75
5390 5692 0.776810 TGGTGGTGGTGGTGATGATT 59.223 50.000 0.00 0.00 0.00 2.57
5654 5974 2.170187 GAGCAGAAGGTGATGGACTGAT 59.830 50.000 0.00 0.00 0.00 2.90
5773 6093 0.381089 GCACTTGAGCAGGATGATGC 59.619 55.000 0.00 0.00 46.88 3.91
5838 6158 1.712977 GGCAGCTGCGGAAATGAGAG 61.713 60.000 31.19 0.00 43.26 3.20
5849 6169 1.028330 TAGCAATGTCTGGCAGCTGC 61.028 55.000 30.88 30.88 39.07 5.25
5876 6196 5.324409 ACTCCAAGCCTTGATAAATGTTGA 58.676 37.500 5.89 0.00 0.00 3.18
5959 6283 4.520111 ACTCAATTTGCAGTGACAAGCATA 59.480 37.500 3.66 0.20 40.94 3.14
6018 6350 3.257375 AGTGCAGTTTACATGGACTCGTA 59.743 43.478 0.00 0.00 44.91 3.43
6049 6381 3.822940 AGCTAGTCTCATAAGTACCGCT 58.177 45.455 0.00 0.00 0.00 5.52
6051 6383 6.091169 GCTACTAGCTAGTCTCATAAGTACCG 59.909 46.154 29.28 0.84 38.45 4.02
6097 6432 9.757227 ACAGAGAACAAAGATGATACTATTAGC 57.243 33.333 0.00 0.00 0.00 3.09
6327 6682 2.125106 GGTAGACCCGCCAGCAAG 60.125 66.667 0.00 0.00 0.00 4.01
6356 6711 3.429925 GCCTTCAGCATGCTAGCC 58.570 61.111 22.19 0.43 42.97 3.93
6386 6742 6.884295 TGCTAGCTCTTGAAGGCTTTTTATTA 59.116 34.615 17.23 0.00 39.65 0.98
6394 6754 1.746516 GCATGCTAGCTCTTGAAGGCT 60.747 52.381 17.23 11.77 41.92 4.58
6654 7018 2.607187 GCAACCGCTATACGCTGATAT 58.393 47.619 0.00 0.00 41.76 1.63
6656 7020 0.600255 GGCAACCGCTATACGCTGAT 60.600 55.000 0.00 0.00 41.76 2.90
6659 7023 1.067582 GAGGCAACCGCTATACGCT 59.932 57.895 0.00 0.00 41.76 5.07
6678 7042 3.117322 TGAACCCCTGAGAATTTGAACCA 60.117 43.478 0.00 0.00 0.00 3.67
6699 7063 2.346099 ATCGGTCCACGCAAAATTTG 57.654 45.000 0.57 0.57 43.86 2.32
6700 7064 3.340034 TCTATCGGTCCACGCAAAATTT 58.660 40.909 0.00 0.00 43.86 1.82
6734 7098 3.709653 TGCTCAGGTTTACTATTCGGGAT 59.290 43.478 0.00 0.00 0.00 3.85
6758 7122 6.204688 GTCAAAACACATCATCACACCTTCTA 59.795 38.462 0.00 0.00 0.00 2.10
6765 7129 3.873952 TGTCGTCAAAACACATCATCACA 59.126 39.130 0.00 0.00 0.00 3.58
6783 7151 0.168788 ATTCAAGGCGCAATGTGTCG 59.831 50.000 10.83 0.00 0.00 4.35
6806 7174 4.077300 TCAGAATGATCATGTAGGGTGC 57.923 45.455 9.46 0.00 42.56 5.01
6856 7225 1.937546 GCCTGGAAATCCCTGCAACG 61.938 60.000 0.00 0.00 34.76 4.10
6890 7259 0.883814 GCTCAGATGAATCCCAGCCG 60.884 60.000 1.28 0.00 0.00 5.52
6970 7339 1.135402 GCCGGTCATGCGAAAGAAATT 60.135 47.619 1.90 0.00 0.00 1.82
6971 7340 0.451783 GCCGGTCATGCGAAAGAAAT 59.548 50.000 1.90 0.00 0.00 2.17
6980 7350 1.522668 TATGCTATTGCCGGTCATGC 58.477 50.000 1.90 7.54 38.71 4.06
6982 7352 2.040278 ACCATATGCTATTGCCGGTCAT 59.960 45.455 1.90 0.00 38.71 3.06
6986 7356 1.078709 CGACCATATGCTATTGCCGG 58.921 55.000 0.00 0.00 38.71 6.13
7014 7384 1.432514 TGAAGCTCACATTCACGCTC 58.567 50.000 0.00 0.00 31.86 5.03
7022 7392 4.025040 TCACCTGAAATGAAGCTCACAT 57.975 40.909 0.00 0.00 0.00 3.21
7109 7479 8.169268 GTCATTTACATCCAGTCGACTTTAAAG 58.831 37.037 17.26 13.76 0.00 1.85
7144 7515 5.295431 TCAAGTTCCATTTAGCATTGTCG 57.705 39.130 0.00 0.00 0.00 4.35
7147 7518 5.320549 AGCTCAAGTTCCATTTAGCATTG 57.679 39.130 0.00 0.00 32.42 2.82
7161 7533 0.543749 GCCCTACATGGAGCTCAAGT 59.456 55.000 17.19 12.64 38.35 3.16
7218 7604 7.229308 ACATTATGTCTCTGGCATATGTGAAT 58.771 34.615 4.29 0.00 0.00 2.57
7228 7614 6.931281 ACACATGTATACATTATGTCTCTGGC 59.069 38.462 19.97 0.00 33.06 4.85
7450 8002 9.434420 CATGGAGCCTGTTATTTTAATTCAAAA 57.566 29.630 0.00 0.00 40.34 2.44
7479 8032 2.281276 GCGTTTTGGAGGACGGGT 60.281 61.111 0.00 0.00 39.52 5.28
7536 8089 5.995282 CACACTAAACCACCTCAAGAACATA 59.005 40.000 0.00 0.00 0.00 2.29
7555 8108 4.707448 AGGAGTAGATCGTCATTTCACACT 59.293 41.667 0.00 0.00 0.00 3.55
7556 8109 5.000012 AGGAGTAGATCGTCATTTCACAC 58.000 43.478 0.00 0.00 0.00 3.82
7557 8110 4.201920 CGAGGAGTAGATCGTCATTTCACA 60.202 45.833 0.00 0.00 41.90 3.58
7572 8125 1.963172 TAGCTCAATCGCGAGGAGTA 58.037 50.000 29.68 21.12 33.36 2.59
7605 8158 9.988350 CACTAAACCACATCAAGAACATATTAC 57.012 33.333 0.00 0.00 0.00 1.89
7638 8191 0.842613 CTGATGAAGCACGATCGTCG 59.157 55.000 19.84 14.88 46.93 5.12
7645 8198 7.010460 TGTCTATAACATTTCTGATGAAGCACG 59.990 37.037 0.00 0.00 30.86 5.34
7646 8199 8.201554 TGTCTATAACATTTCTGATGAAGCAC 57.798 34.615 0.00 0.00 30.86 4.40
7666 8219 7.928167 CCAGTATTGCAATTCTCAGTATGTCTA 59.072 37.037 18.75 0.00 37.40 2.59
7667 8220 6.765036 CCAGTATTGCAATTCTCAGTATGTCT 59.235 38.462 18.75 0.00 37.40 3.41
7687 8240 2.486636 CTTGCGGACGAGTGCCAGTA 62.487 60.000 0.00 0.00 0.00 2.74
7726 8279 6.106003 GGTTTGTCTTTGTGGTTCTTTTGAT 58.894 36.000 0.00 0.00 0.00 2.57
7780 8333 5.706833 TCGTACCTCTTGTATGTGTCACTTA 59.293 40.000 4.27 0.00 37.64 2.24


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

AutoCloner maintained by Alex Coulton.