Multiple sequence alignment - TraesCS1D01G341600

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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 TraesCS1D01G341600 chr1D 100.000 4398 0 0 1 4398 431703054 431707451 0.000000e+00 8122.0
1 TraesCS1D01G341600 chr1D 100.000 66 0 0 4618 4683 431707671 431707736 6.360000e-24 122.0
2 TraesCS1D01G341600 chr1A 93.666 3647 164 24 283 3886 530170451 530174073 0.000000e+00 5393.0
3 TraesCS1D01G341600 chr1A 87.209 344 22 6 4062 4398 530174682 530175010 5.720000e-99 372.0
4 TraesCS1D01G341600 chr1A 87.838 296 16 5 13 293 530169680 530169970 3.490000e-86 329.0
5 TraesCS1D01G341600 chr1A 90.164 122 6 2 173 293 530170205 530170321 2.260000e-33 154.0
6 TraesCS1D01G341600 chr1A 97.561 41 1 0 3911 3951 530174315 530174355 2.340000e-08 71.3
7 TraesCS1D01G341600 chr1B 92.757 2292 115 22 1 2284 582903917 582906165 0.000000e+00 3265.0
8 TraesCS1D01G341600 chr1B 92.085 1693 77 21 2331 4011 582906243 582907890 0.000000e+00 2331.0
9 TraesCS1D01G341600 chr1B 90.208 337 21 8 4062 4390 582908041 582908373 3.350000e-116 429.0
10 TraesCS1D01G341600 chr1B 93.023 43 3 0 4618 4660 582908681 582908723 3.910000e-06 63.9


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 TraesCS1D01G341600 chr1D 431703054 431707736 4682 False 4122.000 8122 100.00000 1 4683 2 chr1D.!!$F1 4682
1 TraesCS1D01G341600 chr1A 530169680 530175010 5330 False 1263.860 5393 91.28760 13 4398 5 chr1A.!!$F1 4385
2 TraesCS1D01G341600 chr1B 582903917 582908723 4806 False 1522.225 3265 92.01825 1 4660 4 chr1B.!!$F1 4659


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
450 973 0.251341 CCTTTCCTTCCCACCCTGTG 60.251 60.0 0.00 0.00 0.00 3.66 F
1330 1883 0.510359 GTCGATGATGCAAGATCGGC 59.490 55.0 23.12 20.02 41.46 5.54 F
1731 2284 0.393077 ATGATAGTCCCCCTTTCGCG 59.607 55.0 0.00 0.00 0.00 5.87 F
3316 3922 0.319125 TTCCAATTTGTTTCCGCCGC 60.319 50.0 0.00 0.00 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 2005 0.037447 ACCTCAAGCTTTGCTCCTCC 59.963 55.0 0.00 0.0 38.25 4.30 R
3093 3699 0.256752 TGCCTGGGTCATCTTCCATG 59.743 55.0 0.00 0.0 31.95 3.66 R
3415 4021 0.603975 GGCAGCTCGAAGGAACAACT 60.604 55.0 0.00 0.0 0.00 3.16 R
4661 5816 0.304705 CTCATATCAACGCGGCAACC 59.695 55.0 12.47 0.0 0.00 3.77 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
52 59 2.023788 GCTCCTCTCCTGTCTCCTCTG 61.024 61.905 0.00 0.00 0.00 3.35
237 610 4.697756 CCTCCGGCGGCTGTTTCA 62.698 66.667 23.83 0.00 0.00 2.69
259 633 1.222387 CATTCCCTTTCGCCGGGTA 59.778 57.895 2.18 0.00 42.56 3.69
335 849 0.456995 GAGAAAGAGGCGTGAGACCG 60.457 60.000 0.00 0.00 43.69 4.79
369 891 2.294791 TCCCGCCACAAAAACAATACTG 59.705 45.455 0.00 0.00 0.00 2.74
434 956 2.955881 CGTCGCTTTCCCTCCCCTT 61.956 63.158 0.00 0.00 0.00 3.95
435 958 1.379146 GTCGCTTTCCCTCCCCTTT 59.621 57.895 0.00 0.00 0.00 3.11
437 960 1.378646 CGCTTTCCCTCCCCTTTCC 60.379 63.158 0.00 0.00 0.00 3.13
449 972 1.435346 CCCTTTCCTTCCCACCCTGT 61.435 60.000 0.00 0.00 0.00 4.00
450 973 0.251341 CCTTTCCTTCCCACCCTGTG 60.251 60.000 0.00 0.00 0.00 3.66
451 974 0.771127 CTTTCCTTCCCACCCTGTGA 59.229 55.000 0.00 0.00 35.23 3.58
452 975 0.771127 TTTCCTTCCCACCCTGTGAG 59.229 55.000 0.00 0.00 35.23 3.51
470 1005 4.406173 CGAGCGAGCGGTGTGTCT 62.406 66.667 0.00 0.00 0.00 3.41
498 1033 4.161295 CCGCGCTCCCCTCATTCA 62.161 66.667 5.56 0.00 0.00 2.57
590 1125 4.203076 CCCGCCCTCGTTCGGTAG 62.203 72.222 0.00 0.00 43.87 3.18
591 1126 3.136123 CCGCCCTCGTTCGGTAGA 61.136 66.667 0.00 0.00 40.72 2.59
592 1127 2.487532 CCGCCCTCGTTCGGTAGAT 61.488 63.158 0.00 0.00 40.72 1.98
593 1128 1.436336 CGCCCTCGTTCGGTAGATT 59.564 57.895 0.00 0.00 0.00 2.40
656 1197 1.146263 GAATCTGGTAGTGCCCCCG 59.854 63.158 0.00 0.00 36.04 5.73
657 1198 2.942648 GAATCTGGTAGTGCCCCCGC 62.943 65.000 0.00 0.00 36.04 6.13
675 1216 2.203015 CCCCGATACGCACAAGGG 60.203 66.667 0.00 0.00 41.68 3.95
677 1218 2.125310 CCGATACGCACAAGGGCA 60.125 61.111 0.00 0.00 0.00 5.36
688 1229 2.297033 GCACAAGGGCAGATTTTTCTCA 59.703 45.455 0.00 0.00 0.00 3.27
758 1299 0.693049 AACTGATTCAGGTTCGGGCT 59.307 50.000 17.66 0.00 35.51 5.19
763 1304 0.743345 ATTCAGGTTCGGGCTAACGC 60.743 55.000 0.00 0.00 0.00 4.84
799 1343 1.133025 GATTGGCGGTTGAATCTGGTG 59.867 52.381 0.00 0.00 0.00 4.17
936 1480 3.582208 AGTTCTCTGATCCAGTTCTTGCT 59.418 43.478 0.00 0.00 32.61 3.91
1215 1759 3.825611 CCCAGGGCAAAATCGGCG 61.826 66.667 0.00 0.00 0.00 6.46
1326 1879 3.525537 AGAAACGTCGATGATGCAAGAT 58.474 40.909 12.58 0.00 0.00 2.40
1327 1880 3.553511 AGAAACGTCGATGATGCAAGATC 59.446 43.478 12.58 0.00 0.00 2.75
1328 1881 1.481240 ACGTCGATGATGCAAGATCG 58.519 50.000 19.53 19.53 42.29 3.69
1329 1882 0.780596 CGTCGATGATGCAAGATCGG 59.219 55.000 23.12 10.22 41.46 4.18
1330 1883 0.510359 GTCGATGATGCAAGATCGGC 59.490 55.000 23.12 20.02 41.46 5.54
1331 1884 0.940991 TCGATGATGCAAGATCGGCG 60.941 55.000 23.12 0.00 41.46 6.46
1332 1885 1.206072 GATGATGCAAGATCGGCGC 59.794 57.895 0.00 0.00 0.00 6.53
1333 1886 2.490262 GATGATGCAAGATCGGCGCG 62.490 60.000 0.00 0.00 0.00 6.86
1334 1887 2.961721 GATGCAAGATCGGCGCGA 60.962 61.111 12.10 2.30 41.13 5.87
1452 2005 2.928731 GCTGGAGTTCTCTTTCCACTCG 60.929 54.545 0.00 0.00 38.53 4.18
1728 2281 2.224646 GCTGGATGATAGTCCCCCTTTC 60.225 54.545 0.00 0.00 37.48 2.62
1731 2284 0.393077 ATGATAGTCCCCCTTTCGCG 59.607 55.000 0.00 0.00 0.00 5.87
1754 2307 1.788258 TCTTCGACAAGAGCAGCAAG 58.212 50.000 0.00 0.00 33.38 4.01
2035 2588 4.643463 TGTCGAAGTTACCATTTTGGCTA 58.357 39.130 0.00 0.00 42.67 3.93
2121 2674 2.839486 TTCTAGCTATCCATTGCCCG 57.161 50.000 0.00 0.00 0.00 6.13
2179 2732 5.106157 GCAGTAACCACTATGTCATTTTGCT 60.106 40.000 0.00 0.00 32.21 3.91
2251 2804 2.224257 TGTTGAGTCAGTATGCAGCACA 60.224 45.455 0.00 0.00 34.76 4.57
2252 2805 2.375173 TGAGTCAGTATGCAGCACAG 57.625 50.000 0.00 0.00 34.76 3.66
2264 2817 2.259618 GCAGCACAGCTCAAATCATTG 58.740 47.619 0.00 0.00 36.40 2.82
2266 2819 3.613193 GCAGCACAGCTCAAATCATTGAA 60.613 43.478 0.00 0.00 44.64 2.69
2269 2822 3.367025 GCACAGCTCAAATCATTGAAAGC 59.633 43.478 0.00 0.00 44.64 3.51
2275 2828 4.143179 GCTCAAATCATTGAAAGCTGCAAC 60.143 41.667 1.02 0.00 44.64 4.17
2277 2830 4.746115 TCAAATCATTGAAAGCTGCAACAC 59.254 37.500 1.02 0.00 42.47 3.32
2487 3086 2.567169 CCCTGGAGATGACAAGTACACA 59.433 50.000 0.00 0.00 0.00 3.72
2565 3170 4.024893 CCGTACCATCAGTGTAATCAATGC 60.025 45.833 0.00 0.00 39.17 3.56
2598 3204 3.008375 TCAAGCTCATAGCCTGTTTCACT 59.992 43.478 0.00 0.00 43.77 3.41
2648 3254 4.523173 TCGCTTGATATTAGACTACCTGGG 59.477 45.833 0.00 0.00 0.00 4.45
2709 3315 4.020218 ACAGCACTGGTAGCATAAGAAAGA 60.020 41.667 2.21 0.00 34.19 2.52
2716 3322 7.766278 CACTGGTAGCATAAGAAAGACAGTATT 59.234 37.037 0.00 0.00 35.17 1.89
2748 3354 7.026631 TGTAGCTACATTTTATCATGTTGGC 57.973 36.000 22.67 0.00 38.40 4.52
2934 3540 4.331108 AGCAACTTCCTTTGGAGAAGATC 58.669 43.478 7.47 0.00 42.80 2.75
2956 3562 0.609131 CTCCGTTGCCCTGGACATTT 60.609 55.000 0.00 0.00 0.00 2.32
2988 3594 2.031683 GGAATACGTTCATTCGCAAGGG 59.968 50.000 0.00 0.00 36.04 3.95
3093 3699 2.610374 TGAAGACGTTTACTGCAACACC 59.390 45.455 0.00 0.00 0.00 4.16
3117 3723 2.565841 GAAGATGACCCAGGCACATAC 58.434 52.381 0.00 0.00 0.00 2.39
3216 3822 1.071071 TGGGAACTGGTTAGTGGTTCG 59.929 52.381 0.00 0.00 39.86 3.95
3279 3885 5.065474 TGCAGTTGTTAATAAGGTATTCGCC 59.935 40.000 0.00 0.00 0.00 5.54
3282 3888 6.317893 CAGTTGTTAATAAGGTATTCGCCCTT 59.682 38.462 0.00 0.00 44.43 3.95
3316 3922 0.319125 TTCCAATTTGTTTCCGCCGC 60.319 50.000 0.00 0.00 0.00 6.53
3379 3985 2.984471 CACAATTCTGCACATGAACTGC 59.016 45.455 0.00 0.00 35.03 4.40
3415 4021 8.924511 AATTCTAATTTCAGAACTTGAGACCA 57.075 30.769 0.00 0.00 37.37 4.02
3481 4087 2.129555 AATGCTGGTCCGCTCAACCT 62.130 55.000 7.14 0.00 37.69 3.50
3684 4299 2.393768 CGCCGAAGCTGCTGTGATT 61.394 57.895 1.35 0.00 36.60 2.57
3800 4415 8.293699 AGACACACCTTTCTTTTTCTTTACAT 57.706 30.769 0.00 0.00 0.00 2.29
3801 4416 8.749354 AGACACACCTTTCTTTTTCTTTACATT 58.251 29.630 0.00 0.00 0.00 2.71
3854 4470 7.861630 TCTGTTTTAGAAGAAAAACCATCTCG 58.138 34.615 9.10 0.00 44.89 4.04
3886 4502 9.698309 ATAGACGAAATCTTGATTGTATGGTAG 57.302 33.333 0.00 0.00 39.04 3.18
3887 4503 7.556844 AGACGAAATCTTGATTGTATGGTAGT 58.443 34.615 0.00 0.00 31.62 2.73
3888 4504 8.692710 AGACGAAATCTTGATTGTATGGTAGTA 58.307 33.333 0.00 0.00 31.62 1.82
3909 4745 7.897575 AGTATCAGCTAAAACTTGACTTCTG 57.102 36.000 0.00 0.00 0.00 3.02
3953 4837 6.434028 TGAAATCACAATACAGGAGAAAAGGG 59.566 38.462 0.00 0.00 0.00 3.95
3958 4842 8.153221 TCACAATACAGGAGAAAAGGGTTATA 57.847 34.615 0.00 0.00 0.00 0.98
3959 4843 8.778059 TCACAATACAGGAGAAAAGGGTTATAT 58.222 33.333 0.00 0.00 0.00 0.86
3960 4844 8.840321 CACAATACAGGAGAAAAGGGTTATATG 58.160 37.037 0.00 0.00 0.00 1.78
3961 4845 7.502561 ACAATACAGGAGAAAAGGGTTATATGC 59.497 37.037 0.00 0.00 0.00 3.14
3962 4846 5.717119 ACAGGAGAAAAGGGTTATATGCT 57.283 39.130 0.00 0.00 0.00 3.79
3963 4847 6.824958 ACAGGAGAAAAGGGTTATATGCTA 57.175 37.500 0.00 0.00 0.00 3.49
3964 4848 7.394144 ACAGGAGAAAAGGGTTATATGCTAT 57.606 36.000 0.00 0.00 0.00 2.97
3965 4849 8.506196 ACAGGAGAAAAGGGTTATATGCTATA 57.494 34.615 0.00 0.00 0.00 1.31
3966 4850 8.945193 ACAGGAGAAAAGGGTTATATGCTATAA 58.055 33.333 0.00 0.00 0.00 0.98
4021 4949 1.192534 GTTTGACGACAAGAAGGCTCG 59.807 52.381 0.00 0.00 37.32 5.03
4044 5083 4.732672 ATACTAAGGTTCCCGTCAGTTC 57.267 45.455 0.00 0.00 0.00 3.01
4090 5151 3.132467 AGTGGACCTAGAATCTTAACGCC 59.868 47.826 0.00 0.00 0.00 5.68
4122 5189 7.541783 GCCACGGTTTACATATATCGTGTATAA 59.458 37.037 16.48 1.18 44.07 0.98
4207 5280 5.968528 TGGTTAAAAATCGCCATAGTTGT 57.031 34.783 0.00 0.00 0.00 3.32
4214 5287 9.745880 TTAAAAATCGCCATAGTTGTAACAAAA 57.254 25.926 0.00 0.00 0.00 2.44
4220 5293 5.851177 CGCCATAGTTGTAACAAAAAGTCAG 59.149 40.000 0.00 0.00 0.00 3.51
4265 5338 7.548097 AGATCAGTGGTGTTAAGTACATAGTG 58.452 38.462 0.00 0.00 39.39 2.74
4274 5347 7.224167 GGTGTTAAGTACATAGTGCAGGTTATC 59.776 40.741 0.00 0.00 39.39 1.75
4293 5366 3.825908 TCTTGCAATTTTAGAGGGGGT 57.174 42.857 0.00 0.00 0.00 4.95
4294 5367 3.430453 TCTTGCAATTTTAGAGGGGGTG 58.570 45.455 0.00 0.00 0.00 4.61
4295 5368 1.555967 TGCAATTTTAGAGGGGGTGC 58.444 50.000 0.00 0.00 0.00 5.01
4296 5369 0.824109 GCAATTTTAGAGGGGGTGCC 59.176 55.000 0.00 0.00 0.00 5.01
4297 5370 1.894978 GCAATTTTAGAGGGGGTGCCA 60.895 52.381 0.00 0.00 0.00 4.92
4336 5410 0.686441 TGACACCCCCACTAGATCCG 60.686 60.000 0.00 0.00 0.00 4.18
4660 5815 6.263168 GGTGGAATATGCTTTGTTGCTACTAT 59.737 38.462 0.00 0.00 0.00 2.12
4661 5816 7.134815 GTGGAATATGCTTTGTTGCTACTATG 58.865 38.462 0.00 0.00 0.00 2.23
4662 5817 6.262944 TGGAATATGCTTTGTTGCTACTATGG 59.737 38.462 0.00 0.00 0.00 2.74
4663 5818 6.263168 GGAATATGCTTTGTTGCTACTATGGT 59.737 38.462 0.00 0.00 0.00 3.55
4664 5819 7.201821 GGAATATGCTTTGTTGCTACTATGGTT 60.202 37.037 0.00 0.00 0.00 3.67
4665 5820 4.764679 TGCTTTGTTGCTACTATGGTTG 57.235 40.909 0.00 0.00 0.00 3.77
4666 5821 3.057596 TGCTTTGTTGCTACTATGGTTGC 60.058 43.478 8.63 8.63 42.75 4.17
4667 5822 3.673323 GCTTTGTTGCTACTATGGTTGCC 60.673 47.826 12.62 0.00 42.00 4.52
4668 5823 1.732941 TGTTGCTACTATGGTTGCCG 58.267 50.000 12.62 0.00 42.00 5.69
4669 5824 0.377203 GTTGCTACTATGGTTGCCGC 59.623 55.000 12.62 2.62 42.00 6.53
4670 5825 1.087202 TTGCTACTATGGTTGCCGCG 61.087 55.000 12.62 0.00 42.00 6.46
4671 5826 1.520787 GCTACTATGGTTGCCGCGT 60.521 57.895 4.92 0.00 38.03 6.01
4672 5827 1.087771 GCTACTATGGTTGCCGCGTT 61.088 55.000 4.92 0.00 38.03 4.84
4673 5828 0.650512 CTACTATGGTTGCCGCGTTG 59.349 55.000 4.92 0.00 0.00 4.10
4674 5829 0.246910 TACTATGGTTGCCGCGTTGA 59.753 50.000 4.92 0.00 0.00 3.18
4675 5830 0.392461 ACTATGGTTGCCGCGTTGAT 60.392 50.000 4.92 0.00 0.00 2.57
4676 5831 1.134640 ACTATGGTTGCCGCGTTGATA 60.135 47.619 4.92 0.00 0.00 2.15
4677 5832 2.143122 CTATGGTTGCCGCGTTGATAT 58.857 47.619 4.92 0.00 0.00 1.63
4678 5833 0.662619 ATGGTTGCCGCGTTGATATG 59.337 50.000 4.92 0.00 0.00 1.78
4679 5834 0.391793 TGGTTGCCGCGTTGATATGA 60.392 50.000 4.92 0.00 0.00 2.15
4680 5835 0.304705 GGTTGCCGCGTTGATATGAG 59.695 55.000 4.92 0.00 0.00 2.90
4681 5836 0.304705 GTTGCCGCGTTGATATGAGG 59.695 55.000 4.92 0.00 33.73 3.86
4682 5837 0.813610 TTGCCGCGTTGATATGAGGG 60.814 55.000 4.92 0.00 31.47 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 59 3.384399 CGAGCGCGTACCGTATGC 61.384 66.667 8.43 12.07 39.71 3.14
155 176 4.410400 AGCGGAGGAAAAGCGGGG 62.410 66.667 0.00 0.00 35.78 5.73
233 606 2.495669 GGCGAAAGGGAATGGAATGAAA 59.504 45.455 0.00 0.00 0.00 2.69
237 610 0.751643 CCGGCGAAAGGGAATGGAAT 60.752 55.000 9.30 0.00 0.00 3.01
259 633 1.592669 CGCGCCCAGATCGAATCTT 60.593 57.895 0.00 0.00 37.58 2.40
335 849 2.761195 GCGGGATTCAAAGGCCGTC 61.761 63.158 0.00 0.00 0.00 4.79
369 891 0.664224 GCGAGTGGAGTAGGAGTAGC 59.336 60.000 0.00 0.00 0.00 3.58
434 956 1.779061 GCTCACAGGGTGGGAAGGAA 61.779 60.000 0.00 0.00 35.82 3.36
435 958 2.224159 GCTCACAGGGTGGGAAGGA 61.224 63.158 0.00 0.00 35.82 3.36
437 960 2.046892 CGCTCACAGGGTGGGAAG 60.047 66.667 0.00 0.00 35.82 3.46
535 1070 4.382320 TCGGTTCGGGAAAGGCCG 62.382 66.667 0.00 0.00 43.32 6.13
576 1111 0.458669 TCAATCTACCGAACGAGGGC 59.541 55.000 0.00 0.00 35.02 5.19
590 1125 3.443681 ACCACGGAATCAACCAATCAATC 59.556 43.478 0.00 0.00 0.00 2.67
591 1126 3.193267 CACCACGGAATCAACCAATCAAT 59.807 43.478 0.00 0.00 0.00 2.57
592 1127 2.556189 CACCACGGAATCAACCAATCAA 59.444 45.455 0.00 0.00 0.00 2.57
593 1128 2.158559 CACCACGGAATCAACCAATCA 58.841 47.619 0.00 0.00 0.00 2.57
656 1197 2.895372 CTTGTGCGTATCGGGGGC 60.895 66.667 0.00 0.00 0.00 5.80
657 1198 2.203015 CCTTGTGCGTATCGGGGG 60.203 66.667 0.00 0.00 0.00 5.40
660 1201 2.125310 TGCCCTTGTGCGTATCGG 60.125 61.111 0.00 0.00 0.00 4.18
661 1202 0.530650 ATCTGCCCTTGTGCGTATCG 60.531 55.000 0.00 0.00 0.00 2.92
662 1203 1.668419 AATCTGCCCTTGTGCGTATC 58.332 50.000 0.00 0.00 0.00 2.24
663 1204 2.128771 AAATCTGCCCTTGTGCGTAT 57.871 45.000 0.00 0.00 0.00 3.06
664 1205 1.904287 AAAATCTGCCCTTGTGCGTA 58.096 45.000 0.00 0.00 0.00 4.42
675 1216 8.983307 AATCAAGAAGAATGAGAAAAATCTGC 57.017 30.769 0.00 0.00 0.00 4.26
688 1229 8.897872 AAACAGCAAATCAAATCAAGAAGAAT 57.102 26.923 0.00 0.00 0.00 2.40
758 1299 2.046023 TCCTCCTCGTCGGCGTTA 60.046 61.111 10.18 0.00 39.49 3.18
962 1506 2.100605 AGCAAACCAGATCCGAGAAC 57.899 50.000 0.00 0.00 0.00 3.01
1116 1660 6.713903 TGAGCTCTGAATCAAAATCTTTCTGT 59.286 34.615 16.19 0.00 0.00 3.41
1330 1883 2.809601 CTTCGGTCCAACCTCGCG 60.810 66.667 0.00 0.00 35.66 5.87
1331 1884 2.434359 CCTTCGGTCCAACCTCGC 60.434 66.667 0.00 0.00 35.66 5.03
1332 1885 1.823169 TTCCCTTCGGTCCAACCTCG 61.823 60.000 0.00 0.00 35.66 4.63
1333 1886 0.399075 TTTCCCTTCGGTCCAACCTC 59.601 55.000 0.00 0.00 35.66 3.85
1334 1887 0.109913 GTTTCCCTTCGGTCCAACCT 59.890 55.000 0.00 0.00 35.66 3.50
1344 1897 0.321996 AGCTCAGACCGTTTCCCTTC 59.678 55.000 0.00 0.00 0.00 3.46
1356 1909 4.564782 ATCCAGTGATTTCAAGCTCAGA 57.435 40.909 0.00 0.00 0.00 3.27
1452 2005 0.037447 ACCTCAAGCTTTGCTCCTCC 59.963 55.000 0.00 0.00 38.25 4.30
1554 2107 1.134280 CCATCTCCAGCGACCTTGAAT 60.134 52.381 0.00 0.00 0.00 2.57
1635 2188 3.130160 GCAGCTTTCGCCTCCCTG 61.130 66.667 0.00 0.00 36.60 4.45
1728 2281 3.087638 TCTTGTCGAAGAGAACGCG 57.912 52.632 3.53 3.53 33.85 6.01
1752 2305 5.512404 GGCCCTTTTAGTTACCAATTTGCTT 60.512 40.000 0.00 0.00 0.00 3.91
1754 2307 4.020573 AGGCCCTTTTAGTTACCAATTTGC 60.021 41.667 0.00 0.00 0.00 3.68
1767 2320 0.331616 GCCAGGAAGAGGCCCTTTTA 59.668 55.000 0.00 0.00 46.50 1.52
1864 2417 3.181493 GCAAATCTGTGGCCAATGAGTAG 60.181 47.826 7.24 3.83 0.00 2.57
2035 2588 0.833287 ACATTACGATGCTGGAGCCT 59.167 50.000 0.00 0.00 41.18 4.58
2155 2708 5.095490 GCAAAATGACATAGTGGTTACTGC 58.905 41.667 0.00 0.00 37.78 4.40
2179 2732 6.321181 GGGCAGTTCCATGAATACATAGAAAA 59.679 38.462 0.00 0.00 36.33 2.29
2251 2804 3.257375 TGCAGCTTTCAATGATTTGAGCT 59.743 39.130 0.00 0.00 41.49 4.09
2252 2805 3.581755 TGCAGCTTTCAATGATTTGAGC 58.418 40.909 0.00 0.00 42.60 4.26
2275 2828 2.802816 GCCCTACAGAAGATAATGCGTG 59.197 50.000 0.00 0.00 0.00 5.34
2277 2830 2.037772 AGGCCCTACAGAAGATAATGCG 59.962 50.000 0.00 0.00 0.00 4.73
2284 2837 2.327325 AGTTGAGGCCCTACAGAAGA 57.673 50.000 0.00 0.00 0.00 2.87
2290 2843 5.254115 AGAAATACAAAGTTGAGGCCCTAC 58.746 41.667 0.00 0.00 0.00 3.18
2324 2923 5.179368 GTCATGCTTGCAGAAACACTACTAA 59.821 40.000 0.87 0.00 0.00 2.24
2325 2924 4.690748 GTCATGCTTGCAGAAACACTACTA 59.309 41.667 0.87 0.00 0.00 1.82
2565 3170 4.208047 GCTATGAGCTTGACAACTATGACG 59.792 45.833 0.00 0.00 38.45 4.35
2622 3228 7.093902 CCCAGGTAGTCTAATATCAAGCGAATA 60.094 40.741 0.00 0.00 0.00 1.75
2623 3229 6.295349 CCCAGGTAGTCTAATATCAAGCGAAT 60.295 42.308 0.00 0.00 0.00 3.34
2632 3238 3.248888 GGTGGCCCAGGTAGTCTAATAT 58.751 50.000 0.00 0.00 0.00 1.28
2633 3239 2.686119 GGTGGCCCAGGTAGTCTAATA 58.314 52.381 0.00 0.00 0.00 0.98
2648 3254 1.137404 CAAATACAGCTGCGGTGGC 59.863 57.895 15.27 0.00 35.13 5.01
2679 3285 5.982890 ATGCTACCAGTGCTGTTTTAAAT 57.017 34.783 0.00 0.00 0.00 1.40
2683 3289 4.651778 TCTTATGCTACCAGTGCTGTTTT 58.348 39.130 0.00 0.00 0.00 2.43
2727 3333 5.653769 AGTGCCAACATGATAAAATGTAGCT 59.346 36.000 0.00 0.00 39.89 3.32
2934 3540 1.450312 GTCCAGGGCAACGGAGATG 60.450 63.158 0.00 0.00 37.60 2.90
2956 3562 2.529780 ACGTATTCCAAACCACGTGA 57.470 45.000 19.30 0.00 45.14 4.35
2988 3594 2.162754 CACGTCGCGGTGGATTACC 61.163 63.158 6.13 0.00 46.56 2.85
3000 3606 0.318699 TGTTCTCAGGCTTCACGTCG 60.319 55.000 0.00 0.00 0.00 5.12
3093 3699 0.256752 TGCCTGGGTCATCTTCCATG 59.743 55.000 0.00 0.00 31.95 3.66
3117 3723 4.240103 TCCGGCGCCATCCATCTG 62.240 66.667 28.98 7.02 0.00 2.90
3216 3822 5.336372 CGGAGTCATCTCTTCATAAGGGATC 60.336 48.000 0.00 0.00 45.57 3.36
3316 3922 5.789643 TTCTTTGGGAAATTTCCTCACTG 57.210 39.130 31.23 21.05 46.72 3.66
3342 3948 7.118971 GCAGAATTGTGAAGAGAGTAAACTGAT 59.881 37.037 6.80 0.00 0.00 2.90
3354 3960 4.823442 AGTTCATGTGCAGAATTGTGAAGA 59.177 37.500 6.80 0.00 0.00 2.87
3358 3964 2.984471 GCAGTTCATGTGCAGAATTGTG 59.016 45.455 10.14 0.00 40.86 3.33
3415 4021 0.603975 GGCAGCTCGAAGGAACAACT 60.604 55.000 0.00 0.00 0.00 3.16
3481 4087 3.511477 AGTAAACTCAGGCCTCTTCTCA 58.489 45.455 0.00 0.00 0.00 3.27
3684 4299 2.224159 GGGAGGAAGAGGGCACACA 61.224 63.158 0.00 0.00 0.00 3.72
3762 4377 3.118884 AGGTGTGTCTCGTGTAGTTTGTT 60.119 43.478 0.00 0.00 0.00 2.83
3824 4439 6.887545 TGGTTTTTCTTCTAAAACAGAGTCCA 59.112 34.615 12.37 0.30 45.41 4.02
3854 4470 8.202745 ACAATCAAGATTTCGTCTATTCTTCC 57.797 34.615 0.00 0.00 35.67 3.46
3886 4502 6.402658 GGCAGAAGTCAAGTTTTAGCTGATAC 60.403 42.308 0.00 0.00 0.00 2.24
3887 4503 5.643777 GGCAGAAGTCAAGTTTTAGCTGATA 59.356 40.000 0.00 0.00 0.00 2.15
3888 4504 4.457257 GGCAGAAGTCAAGTTTTAGCTGAT 59.543 41.667 0.00 0.00 0.00 2.90
3991 4875 8.557029 CCTTCTTGTCGTCAAACTTACTTAATT 58.443 33.333 0.00 0.00 32.87 1.40
4013 4941 4.869215 GGAACCTTAGTATACGAGCCTTC 58.131 47.826 0.00 4.12 0.00 3.46
4044 5083 1.263217 GCACCTACAAGTGTTTCCACG 59.737 52.381 0.00 0.00 46.56 4.94
4060 5099 1.848652 TCTAGGTCCACTACTGCACC 58.151 55.000 0.00 0.00 0.00 5.01
4090 5151 3.051479 GTAAACCGTGGCACCCCG 61.051 66.667 12.86 0.00 0.00 5.73
4198 5271 9.796120 TTTTCTGACTTTTTGTTACAACTATGG 57.204 29.630 0.00 0.00 0.00 2.74
4214 5287 6.903419 GCAGTTTAGTGCTATTTTCTGACTT 58.097 36.000 2.34 0.00 40.54 3.01
4246 5319 4.630069 CCTGCACTATGTACTTAACACCAC 59.370 45.833 0.00 0.00 42.09 4.16
4265 5338 6.268566 CCTCTAAAATTGCAAGATAACCTGC 58.731 40.000 4.94 0.00 0.00 4.85
4274 5347 2.094026 GCACCCCCTCTAAAATTGCAAG 60.094 50.000 4.94 0.00 0.00 4.01
4280 5353 0.335019 GGTGGCACCCCCTCTAAAAT 59.665 55.000 26.51 0.00 30.04 1.82
4336 5410 2.281484 TGGCACGGGAACAAGAGC 60.281 61.111 0.00 0.00 0.00 4.09
4617 5692 3.454375 CACCGACCATAGTGACCAATAC 58.546 50.000 0.00 0.00 36.01 1.89
4618 5693 2.432874 CCACCGACCATAGTGACCAATA 59.567 50.000 0.00 0.00 36.01 1.90
4619 5694 1.209504 CCACCGACCATAGTGACCAAT 59.790 52.381 0.00 0.00 36.01 3.16
4627 5782 3.685139 AGCATATTCCACCGACCATAG 57.315 47.619 0.00 0.00 0.00 2.23
4629 5784 2.951642 CAAAGCATATTCCACCGACCAT 59.048 45.455 0.00 0.00 0.00 3.55
4660 5815 0.391793 TCATATCAACGCGGCAACCA 60.392 50.000 12.47 0.00 0.00 3.67
4661 5816 0.304705 CTCATATCAACGCGGCAACC 59.695 55.000 12.47 0.00 0.00 3.77
4662 5817 0.304705 CCTCATATCAACGCGGCAAC 59.695 55.000 12.47 0.00 0.00 4.17
4663 5818 0.813610 CCCTCATATCAACGCGGCAA 60.814 55.000 12.47 0.00 0.00 4.52
4664 5819 1.227527 CCCTCATATCAACGCGGCA 60.228 57.895 12.47 0.00 0.00 5.69
4665 5820 3.642755 CCCTCATATCAACGCGGC 58.357 61.111 12.47 0.00 0.00 6.53



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

AutoCloner maintained by Alex Coulton.