Multiple sequence alignment - TraesCS5D01G230200

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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 TraesCS5D01G230200 chr5D 100.000 5290 0 0 1 5290 337296315 337301604 0.000000e+00 9769.0
1 TraesCS5D01G230200 chr5D 96.774 31 1 0 5001 5031 535200790 535200760 1.000000e-02 52.8
2 TraesCS5D01G230200 chr5B 96.647 4951 131 20 59 4990 395916479 395921413 0.000000e+00 8191.0
3 TraesCS5D01G230200 chr5B 90.775 271 16 3 5021 5290 395921397 395921659 2.340000e-93 353.0
4 TraesCS5D01G230200 chr5B 93.548 62 1 1 1 62 395916397 395916455 7.300000e-14 89.8
5 TraesCS5D01G230200 chr5A 95.468 4810 178 20 59 4846 438466470 438471261 0.000000e+00 7638.0
6 TraesCS5D01G230200 chr5A 88.679 212 19 1 5084 5290 438471506 438471717 2.450000e-63 254.0
7 TraesCS5D01G230200 chr7B 96.774 31 1 0 5001 5031 618520558 618520528 1.000000e-02 52.8
8 TraesCS5D01G230200 chr7B 96.774 31 1 0 5001 5031 708149057 708149027 1.000000e-02 52.8
9 TraesCS5D01G230200 chr6B 96.774 31 1 0 5001 5031 391580815 391580785 1.000000e-02 52.8
10 TraesCS5D01G230200 chr6A 96.774 31 1 0 5001 5031 439517529 439517499 1.000000e-02 52.8
11 TraesCS5D01G230200 chr4A 100.000 28 0 0 5001 5028 411853557 411853584 1.000000e-02 52.8
12 TraesCS5D01G230200 chr3D 100.000 28 0 0 5001 5028 216612309 216612336 1.000000e-02 52.8
13 TraesCS5D01G230200 chr1B 100.000 28 0 0 5001 5028 4616564 4616591 1.000000e-02 52.8
14 TraesCS5D01G230200 chr1A 96.774 31 1 0 5001 5031 45537446 45537416 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 TraesCS5D01G230200 chr5D 337296315 337301604 5289 False 9769.000000 9769 100.000000 1 5290 1 chr5D.!!$F1 5289
1 TraesCS5D01G230200 chr5B 395916397 395921659 5262 False 2877.933333 8191 93.656667 1 5290 3 chr5B.!!$F1 5289
2 TraesCS5D01G230200 chr5A 438466470 438471717 5247 False 3946.000000 7638 92.073500 59 5290 2 chr5A.!!$F1 5231

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
690 718 1.203313 AGAGGGTTGAGGGAACAGCTA 60.203 52.381 0.00 0.0 36.12 3.32 F
1483 1511 1.044611 GGTGGTCTCTAGCCCATCTC 58.955 60.000 0.00 0.0 32.32 2.75 F
1734 1762 1.550976 ACTTCTAGAGGGCTTTCACCG 59.449 52.381 6.82 0.0 0.00 4.94 F
3618 3659 1.068541 GTTCCCTCGCAAAATGGTGAC 60.069 52.381 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1626 0.315251 GTTTTGCTCAGTTGCCCTCC 59.685 55.000 0.0 0.0 0.00 4.30 R
3212 3246 3.086733 GCATACCCTTGCTCCTGAC 57.913 57.895 0.0 0.0 39.57 3.51 R
3652 3693 0.106708 TTCATGCCAGTCCGATAGCC 59.893 55.000 0.0 0.0 0.00 3.93 R
4736 4791 2.024273 TGGGGTTGGTTAAGGTGACAAA 60.024 45.455 0.0 0.0 0.00 2.83 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
139 167 7.345691 TCAAGAATTATCCAATGTAGAGCCAA 58.654 34.615 0.00 0.00 0.00 4.52
169 197 5.135508 AGCAACGTGTCATACTTCTTACT 57.864 39.130 0.00 0.00 0.00 2.24
171 199 6.323266 AGCAACGTGTCATACTTCTTACTAG 58.677 40.000 0.00 0.00 0.00 2.57
191 219 2.100584 AGGCTTCATCAGTCAGTCGATC 59.899 50.000 0.00 0.00 0.00 3.69
228 256 2.230992 CCCGGCAATTTCAAGTGAATCA 59.769 45.455 0.00 0.00 33.54 2.57
267 295 4.463879 CCCTGTCCTGCGGCTCTG 62.464 72.222 0.00 0.00 0.00 3.35
283 311 3.181500 GGCTCTGTTTTTCTGTCGTTTGT 60.181 43.478 0.00 0.00 0.00 2.83
375 403 1.454479 AATGCCGCTTCTGATGGGG 60.454 57.895 18.66 18.66 40.05 4.96
384 412 2.360165 GCTTCTGATGGGGCATTGTTAG 59.640 50.000 0.00 0.00 0.00 2.34
436 464 3.243636 GCATGTGATGATGTGGATTTCCC 60.244 47.826 0.00 0.00 34.29 3.97
690 718 1.203313 AGAGGGTTGAGGGAACAGCTA 60.203 52.381 0.00 0.00 36.12 3.32
712 740 2.604614 CCGCAAGTTTTGTACTGGAAGC 60.605 50.000 0.00 0.00 37.60 3.86
726 754 2.800544 CTGGAAGCGGGTATGTTATTCG 59.199 50.000 0.00 0.00 0.00 3.34
752 780 1.396301 CTGCAGTTTCAGGATCGCTTC 59.604 52.381 5.25 0.00 0.00 3.86
768 796 3.747010 TCGCTTCGGTACATTGCTTAAAA 59.253 39.130 0.00 0.00 0.00 1.52
769 797 4.393680 TCGCTTCGGTACATTGCTTAAAAT 59.606 37.500 0.00 0.00 0.00 1.82
776 804 7.476667 TCGGTACATTGCTTAAAATATGTTGG 58.523 34.615 0.00 0.00 33.58 3.77
778 806 6.198216 GGTACATTGCTTAAAATATGTTGGCG 59.802 38.462 0.00 0.00 33.58 5.69
817 845 4.829064 TTTGTGTGTCTGGATAGTTTGC 57.171 40.909 0.00 0.00 0.00 3.68
889 917 5.936686 AGTCTGATTGTTTGATGTCTGTG 57.063 39.130 0.00 0.00 0.00 3.66
892 920 4.023792 TCTGATTGTTTGATGTCTGTGTGC 60.024 41.667 0.00 0.00 0.00 4.57
936 964 1.326852 CTGAAGCATTGCAGTAGAGCG 59.673 52.381 11.91 0.00 37.31 5.03
963 991 4.718774 AGGGAGCTAATTTCATGAGAGACA 59.281 41.667 0.00 0.00 0.00 3.41
964 992 4.813697 GGGAGCTAATTTCATGAGAGACAC 59.186 45.833 0.00 0.00 0.00 3.67
994 1022 9.444600 GATGTGGTTGGTTCTAGAAATTACTAA 57.555 33.333 6.78 0.00 0.00 2.24
1298 1326 1.228552 CAACACCCTCCACCCCAAG 60.229 63.158 0.00 0.00 0.00 3.61
1422 1450 1.411787 CGGAACCTGTCTCCCTCCTAT 60.412 57.143 0.00 0.00 0.00 2.57
1425 1453 3.375699 GAACCTGTCTCCCTCCTATCAA 58.624 50.000 0.00 0.00 0.00 2.57
1483 1511 1.044611 GGTGGTCTCTAGCCCATCTC 58.955 60.000 0.00 0.00 32.32 2.75
1503 1531 7.179872 CCATCTCTAGATCATATCAAGGGACAA 59.820 40.741 0.00 0.00 31.21 3.18
1598 1626 5.369833 TCGACCTTCAGAAGATCTACCTAG 58.630 45.833 12.14 0.00 0.00 3.02
1734 1762 1.550976 ACTTCTAGAGGGCTTTCACCG 59.449 52.381 6.82 0.00 0.00 4.94
3212 3246 3.114616 CTGCGCCTTCCAGTCACG 61.115 66.667 4.18 0.00 0.00 4.35
3512 3550 5.365021 AATCAAGTCTCCAACCATAGAGG 57.635 43.478 0.00 0.00 45.67 3.69
3513 3551 4.061131 TCAAGTCTCCAACCATAGAGGA 57.939 45.455 0.00 0.00 41.22 3.71
3514 3552 4.425772 TCAAGTCTCCAACCATAGAGGAA 58.574 43.478 0.00 0.00 41.22 3.36
3618 3659 1.068541 GTTCCCTCGCAAAATGGTGAC 60.069 52.381 0.00 0.00 0.00 3.67
3646 3687 2.018542 TCCGCCATTTTTCGTAGGAG 57.981 50.000 0.00 0.00 0.00 3.69
3648 3689 1.369625 CGCCATTTTTCGTAGGAGCT 58.630 50.000 0.00 0.00 0.00 4.09
3652 3693 2.348666 CCATTTTTCGTAGGAGCTGTCG 59.651 50.000 0.00 0.00 0.00 4.35
3799 3840 0.104671 CCTTTTGTGCACACCCTTGG 59.895 55.000 21.56 13.44 0.00 3.61
3932 3978 6.474140 TCAGTGACTGTTTTAACTGACCTA 57.526 37.500 12.93 0.00 43.01 3.08
4380 4426 7.603180 TGAGCCTGTGACTATAAGAACATAT 57.397 36.000 0.00 0.00 0.00 1.78
4387 4433 8.424274 TGTGACTATAAGAACATATTGTGCAG 57.576 34.615 0.00 0.00 0.00 4.41
4419 4465 6.505272 AGGAATCCGTAGAGAAGAAATAACG 58.495 40.000 0.00 0.00 0.00 3.18
4482 4529 3.124578 TGCTGTGCAGATAACAACTCA 57.875 42.857 3.02 0.00 33.32 3.41
4487 4534 4.702831 TGTGCAGATAACAACTCAACAGA 58.297 39.130 0.00 0.00 0.00 3.41
4489 4536 4.752101 GTGCAGATAACAACTCAACAGAGT 59.248 41.667 0.00 0.00 44.25 3.24
4563 4610 1.132500 ATAGTGCACTTCTAGCCCCC 58.868 55.000 27.06 0.00 0.00 5.40
4729 4784 3.253188 GTGTTGCCAGATTTTGTAGCTGA 59.747 43.478 0.00 0.00 0.00 4.26
4736 4791 4.382901 CCAGATTTTGTAGCTGAGCTCTCT 60.383 45.833 11.68 13.98 40.44 3.10
4856 4917 4.963276 CACCTGTGTGGGTACATTTATG 57.037 45.455 0.00 0.00 39.39 1.90
4929 5055 8.926715 AGTTTAAAGTCTTTGAATTGTGGAAC 57.073 30.769 8.14 0.00 37.35 3.62
4985 5150 2.601763 GCTGCTGCTGTAATGCAAATTC 59.398 45.455 8.53 0.00 42.83 2.17
4988 5153 3.258872 TGCTGCTGTAATGCAAATTCCTT 59.741 39.130 0.00 0.00 42.83 3.36
4990 5155 4.328169 GCTGCTGTAATGCAAATTCCTTTC 59.672 41.667 0.00 0.00 42.83 2.62
4991 5156 5.717119 CTGCTGTAATGCAAATTCCTTTCT 58.283 37.500 0.00 0.00 42.83 2.52
4992 5157 6.100404 TGCTGTAATGCAAATTCCTTTCTT 57.900 33.333 0.00 0.00 40.29 2.52
4993 5158 6.523840 TGCTGTAATGCAAATTCCTTTCTTT 58.476 32.000 0.00 0.00 40.29 2.52
4994 5159 6.991531 TGCTGTAATGCAAATTCCTTTCTTTT 59.008 30.769 0.00 0.00 40.29 2.27
4995 5160 7.498570 TGCTGTAATGCAAATTCCTTTCTTTTT 59.501 29.630 0.00 0.00 40.29 1.94
4996 5161 8.011673 GCTGTAATGCAAATTCCTTTCTTTTTC 58.988 33.333 0.00 0.00 0.00 2.29
4997 5162 8.071122 TGTAATGCAAATTCCTTTCTTTTTCG 57.929 30.769 0.00 0.00 0.00 3.46
4998 5163 7.923344 TGTAATGCAAATTCCTTTCTTTTTCGA 59.077 29.630 0.00 0.00 0.00 3.71
4999 5164 7.784633 AATGCAAATTCCTTTCTTTTTCGAA 57.215 28.000 0.00 0.00 0.00 3.71
5000 5165 6.582437 TGCAAATTCCTTTCTTTTTCGAAC 57.418 33.333 0.00 0.00 0.00 3.95
5001 5166 5.231147 TGCAAATTCCTTTCTTTTTCGAACG 59.769 36.000 0.00 0.00 0.00 3.95
5002 5167 5.457473 GCAAATTCCTTTCTTTTTCGAACGA 59.543 36.000 0.00 0.00 0.00 3.85
5003 5168 6.143919 GCAAATTCCTTTCTTTTTCGAACGAT 59.856 34.615 0.00 0.00 0.00 3.73
5004 5169 7.306574 GCAAATTCCTTTCTTTTTCGAACGATT 60.307 33.333 0.00 0.00 0.00 3.34
5005 5170 8.539674 CAAATTCCTTTCTTTTTCGAACGATTT 58.460 29.630 0.00 0.00 0.00 2.17
5006 5171 8.642908 AATTCCTTTCTTTTTCGAACGATTTT 57.357 26.923 0.00 0.00 0.00 1.82
5007 5172 7.673810 TTCCTTTCTTTTTCGAACGATTTTC 57.326 32.000 0.00 0.00 0.00 2.29
5008 5173 7.023197 TCCTTTCTTTTTCGAACGATTTTCT 57.977 32.000 0.00 0.00 0.00 2.52
5009 5174 7.477494 TCCTTTCTTTTTCGAACGATTTTCTT 58.523 30.769 0.00 0.00 0.00 2.52
5010 5175 7.642586 TCCTTTCTTTTTCGAACGATTTTCTTC 59.357 33.333 0.00 0.00 0.00 2.87
5011 5176 7.431084 CCTTTCTTTTTCGAACGATTTTCTTCA 59.569 33.333 0.00 0.00 0.00 3.02
5012 5177 8.850454 TTTCTTTTTCGAACGATTTTCTTCAT 57.150 26.923 0.00 0.00 0.00 2.57
5013 5178 8.488979 TTCTTTTTCGAACGATTTTCTTCATC 57.511 30.769 0.00 0.00 0.00 2.92
5014 5179 7.635423 TCTTTTTCGAACGATTTTCTTCATCA 58.365 30.769 0.00 0.00 0.00 3.07
5015 5180 7.586300 TCTTTTTCGAACGATTTTCTTCATCAC 59.414 33.333 0.00 0.00 0.00 3.06
5016 5181 4.921470 TCGAACGATTTTCTTCATCACC 57.079 40.909 0.00 0.00 0.00 4.02
5017 5182 3.682858 TCGAACGATTTTCTTCATCACCC 59.317 43.478 0.00 0.00 0.00 4.61
5018 5183 3.435327 CGAACGATTTTCTTCATCACCCA 59.565 43.478 0.00 0.00 0.00 4.51
5019 5184 4.436050 CGAACGATTTTCTTCATCACCCAG 60.436 45.833 0.00 0.00 0.00 4.45
5020 5185 3.347216 ACGATTTTCTTCATCACCCAGG 58.653 45.455 0.00 0.00 0.00 4.45
5021 5186 3.244911 ACGATTTTCTTCATCACCCAGGT 60.245 43.478 0.00 0.00 0.00 4.00
5022 5187 4.019681 ACGATTTTCTTCATCACCCAGGTA 60.020 41.667 0.00 0.00 0.00 3.08
5023 5188 4.941263 CGATTTTCTTCATCACCCAGGTAA 59.059 41.667 0.00 0.00 0.00 2.85
5024 5189 5.590259 CGATTTTCTTCATCACCCAGGTAAT 59.410 40.000 0.00 0.00 0.00 1.89
5025 5190 6.458751 CGATTTTCTTCATCACCCAGGTAATG 60.459 42.308 0.00 0.00 0.00 1.90
5026 5191 3.281727 TCTTCATCACCCAGGTAATGC 57.718 47.619 0.00 0.00 0.00 3.56
5027 5192 2.575735 TCTTCATCACCCAGGTAATGCA 59.424 45.455 0.00 0.00 0.00 3.96
5028 5193 3.010027 TCTTCATCACCCAGGTAATGCAA 59.990 43.478 0.00 0.00 0.00 4.08
5029 5194 3.448093 TCATCACCCAGGTAATGCAAA 57.552 42.857 0.00 0.00 0.00 3.68
5030 5195 3.979911 TCATCACCCAGGTAATGCAAAT 58.020 40.909 0.00 0.00 0.00 2.32
5071 5236 8.469200 CATTTATGATGGTTTGGTGAATACTGT 58.531 33.333 0.00 0.00 0.00 3.55
5072 5237 9.693739 ATTTATGATGGTTTGGTGAATACTGTA 57.306 29.630 0.00 0.00 0.00 2.74
5073 5238 9.693739 TTTATGATGGTTTGGTGAATACTGTAT 57.306 29.630 0.00 0.00 0.00 2.29
5074 5239 9.693739 TTATGATGGTTTGGTGAATACTGTATT 57.306 29.630 12.62 12.62 0.00 1.89
5075 5240 7.389803 TGATGGTTTGGTGAATACTGTATTG 57.610 36.000 17.21 0.00 0.00 1.90
5076 5241 6.945435 TGATGGTTTGGTGAATACTGTATTGT 59.055 34.615 17.21 0.00 0.00 2.71
5077 5242 6.567687 TGGTTTGGTGAATACTGTATTGTG 57.432 37.500 17.21 0.00 0.00 3.33
5082 5247 8.736244 GTTTGGTGAATACTGTATTGTGGTATT 58.264 33.333 17.21 0.00 38.39 1.89
5131 5296 9.151752 GCTACTCTTAAACTTTACGTTCAAAAC 57.848 33.333 0.00 0.00 33.90 2.43
5140 5305 9.628746 AAACTTTACGTTCAAAACACAAGTAAT 57.371 25.926 0.00 0.00 33.90 1.89
5178 5343 8.213518 TCTTAGCTACATTAGGCTTTGATTTG 57.786 34.615 0.00 0.00 39.65 2.32
5219 5385 2.676839 CCACAAGAGCAATCACAGCTAG 59.323 50.000 0.00 0.00 43.58 3.42
5258 5429 5.988310 TCATTCTTGCTTGACATCCAAAT 57.012 34.783 0.00 0.00 33.76 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.393402 TGTGGCTGGATTGCTGCTAG 60.393 55.000 0.00 0.00 0.00 3.42
35 36 0.677731 GTGTGGCTGGATTGCTGCTA 60.678 55.000 0.00 0.00 0.00 3.49
36 37 1.975407 GTGTGGCTGGATTGCTGCT 60.975 57.895 0.00 0.00 0.00 4.24
139 167 3.988379 ATGACACGTTGCTTTCATTGT 57.012 38.095 0.00 0.00 0.00 2.71
169 197 2.723273 TCGACTGACTGATGAAGCCTA 58.277 47.619 0.00 0.00 0.00 3.93
171 199 2.468831 GATCGACTGACTGATGAAGCC 58.531 52.381 0.00 0.00 0.00 4.35
191 219 1.369625 CGGGAATTTTCCTCGACTGG 58.630 55.000 9.13 0.00 46.72 4.00
228 256 4.392940 GCACATGCCTATAGAACCAATCT 58.607 43.478 0.00 0.00 37.33 2.40
265 293 5.969741 TCGATACAAACGACAGAAAAACAG 58.030 37.500 0.00 0.00 34.85 3.16
267 295 6.642917 TCTTCGATACAAACGACAGAAAAAC 58.357 36.000 0.00 0.00 39.46 2.43
375 403 2.632377 TGCCTAGCAGACTAACAATGC 58.368 47.619 0.00 0.00 40.29 3.56
376 404 4.937620 TCTTTGCCTAGCAGACTAACAATG 59.062 41.667 0.00 0.00 40.61 2.82
384 412 2.863137 CGAATCTCTTTGCCTAGCAGAC 59.137 50.000 0.00 0.00 40.61 3.51
436 464 0.478507 AGGGGTTTTGGGACAGACAG 59.521 55.000 0.00 0.00 42.39 3.51
690 718 2.335316 TCCAGTACAAAACTTGCGGT 57.665 45.000 0.00 0.00 35.76 5.68
712 740 4.053295 CAGGTAACCGAATAACATACCCG 58.947 47.826 0.00 0.00 37.35 5.28
752 780 6.198216 GCCAACATATTTTAAGCAATGTACCG 59.802 38.462 0.00 0.00 32.44 4.02
768 796 5.835113 AGAAAAATACAGCGCCAACATAT 57.165 34.783 2.29 0.00 0.00 1.78
769 797 5.398169 CAAGAAAAATACAGCGCCAACATA 58.602 37.500 2.29 0.00 0.00 2.29
776 804 5.006261 ACAAAAACCAAGAAAAATACAGCGC 59.994 36.000 0.00 0.00 0.00 5.92
778 806 7.148490 ACACACAAAAACCAAGAAAAATACAGC 60.148 33.333 0.00 0.00 0.00 4.40
817 845 5.192327 AGATTCACTTGAAACAAGCAAGG 57.808 39.130 10.78 0.65 45.31 3.61
860 888 3.942829 TCAAACAATCAGACTAGGCCAG 58.057 45.455 5.01 2.64 0.00 4.85
889 917 1.078848 ATCTGCAGAAGGTCCGCAC 60.079 57.895 22.50 0.00 0.00 5.34
892 920 0.179089 CCAGATCTGCAGAAGGTCCG 60.179 60.000 22.50 6.28 36.60 4.79
936 964 3.282021 TCATGAAATTAGCTCCCTGCAC 58.718 45.455 0.00 0.00 45.94 4.57
963 991 2.341846 AGAACCAACCACATCAACGT 57.658 45.000 0.00 0.00 0.00 3.99
964 992 3.659786 TCTAGAACCAACCACATCAACG 58.340 45.455 0.00 0.00 0.00 4.10
994 1022 6.485984 GTGCTCTTATGAACATCCATGAAGAT 59.514 38.462 0.00 0.00 0.00 2.40
1298 1326 4.192317 GACTGGTGTTATGGACCTTGATC 58.808 47.826 0.00 0.00 34.26 2.92
1422 1450 0.674581 CAGCCGCAGACTCCAATTGA 60.675 55.000 7.12 0.00 0.00 2.57
1425 1453 2.437359 GCAGCCGCAGACTCCAAT 60.437 61.111 0.00 0.00 38.36 3.16
1483 1511 5.047731 TCGCTTGTCCCTTGATATGATCTAG 60.048 44.000 0.00 0.00 32.92 2.43
1503 1531 1.539388 CTCTCAGTCAGAACACTCGCT 59.461 52.381 0.00 0.00 0.00 4.93
1598 1626 0.315251 GTTTTGCTCAGTTGCCCTCC 59.685 55.000 0.00 0.00 0.00 4.30
1734 1762 5.351189 GTCTTCAGAAGCAGAAATCTTCCTC 59.649 44.000 5.15 0.00 40.48 3.71
1791 1819 2.231716 TAGCTAGTCTCCTTGCCACA 57.768 50.000 0.00 0.00 39.85 4.17
2307 2335 9.724839 GCTAATTTTATGAGGTGCGTTATAAAA 57.275 29.630 13.13 13.13 38.55 1.52
2315 2343 6.545504 AGTATGCTAATTTTATGAGGTGCG 57.454 37.500 0.00 0.00 0.00 5.34
2751 2783 4.425577 ACTCGAATGGAAAAGAACATGC 57.574 40.909 0.00 0.00 0.00 4.06
3212 3246 3.086733 GCATACCCTTGCTCCTGAC 57.913 57.895 0.00 0.00 39.57 3.51
3274 3309 9.856488 GTAATATCTGTTCACAAGTAGAAGTGA 57.144 33.333 0.00 0.00 42.55 3.41
3512 3550 6.604735 TGTCACAAGTAAAAGAGCTTCTTC 57.395 37.500 0.00 0.00 35.27 2.87
3513 3551 6.016777 CCATGTCACAAGTAAAAGAGCTTCTT 60.017 38.462 0.00 0.00 38.59 2.52
3514 3552 5.471456 CCATGTCACAAGTAAAAGAGCTTCT 59.529 40.000 0.00 0.00 0.00 2.85
3618 3659 0.171007 AAAATGGCGGATGCAGAACG 59.829 50.000 0.00 0.00 45.35 3.95
3646 3687 1.299468 CAGTCCGATAGCCGACAGC 60.299 63.158 2.43 0.00 41.76 4.40
3648 3689 2.782222 GCCAGTCCGATAGCCGACA 61.782 63.158 2.43 0.00 41.76 4.35
3652 3693 0.106708 TTCATGCCAGTCCGATAGCC 59.893 55.000 0.00 0.00 0.00 3.93
3716 3757 9.463443 GCTTTATTCATAGTTTGTTTGTGACTT 57.537 29.630 0.00 0.00 0.00 3.01
3799 3840 6.039616 TGAAGGTCAAACTTAACAATGCAAC 58.960 36.000 0.00 0.00 0.00 4.17
4129 4175 6.127083 ACCACCAATCAGAGAAACACATTTTT 60.127 34.615 0.00 0.00 0.00 1.94
4130 4176 5.363580 ACCACCAATCAGAGAAACACATTTT 59.636 36.000 0.00 0.00 0.00 1.82
4380 4426 2.708216 TTCCTTGTCTGTCTGCACAA 57.292 45.000 0.00 0.00 29.82 3.33
4387 4433 3.695060 TCTCTACGGATTCCTTGTCTGTC 59.305 47.826 0.30 0.00 36.61 3.51
4419 4465 7.336176 AGGGGATGTTTAATACTCTTTCGTTTC 59.664 37.037 0.00 0.00 0.00 2.78
4657 4712 9.413734 CCATATCTTTCAGTATCTTTTTCCCTT 57.586 33.333 0.00 0.00 0.00 3.95
4729 4784 3.391296 TGGTTAAGGTGACAAAGAGAGCT 59.609 43.478 0.00 0.00 0.00 4.09
4736 4791 2.024273 TGGGGTTGGTTAAGGTGACAAA 60.024 45.455 0.00 0.00 0.00 2.83
4856 4917 6.774656 AGAATTCTGATATCCACCAAACCATC 59.225 38.462 7.30 0.00 0.00 3.51
4929 5055 4.792068 TGCTAAGGGGATCCAATAAAGTG 58.208 43.478 15.23 0.00 34.83 3.16
4933 5059 5.200483 CACTTTGCTAAGGGGATCCAATAA 58.800 41.667 15.23 0.00 35.61 1.40
4985 5150 7.431084 TGAAGAAAATCGTTCGAAAAAGAAAGG 59.569 33.333 0.00 0.00 31.97 3.11
4988 5153 8.126074 TGATGAAGAAAATCGTTCGAAAAAGAA 58.874 29.630 0.00 0.00 0.00 2.52
4990 5155 7.149128 GGTGATGAAGAAAATCGTTCGAAAAAG 60.149 37.037 0.00 0.00 0.00 2.27
4991 5156 6.635239 GGTGATGAAGAAAATCGTTCGAAAAA 59.365 34.615 0.00 0.00 0.00 1.94
4992 5157 6.140110 GGTGATGAAGAAAATCGTTCGAAAA 58.860 36.000 0.00 0.00 0.00 2.29
4993 5158 5.334569 GGGTGATGAAGAAAATCGTTCGAAA 60.335 40.000 0.00 0.00 0.00 3.46
4994 5159 4.153475 GGGTGATGAAGAAAATCGTTCGAA 59.847 41.667 0.00 0.00 0.00 3.71
4995 5160 3.682858 GGGTGATGAAGAAAATCGTTCGA 59.317 43.478 0.00 0.00 0.00 3.71
4996 5161 3.435327 TGGGTGATGAAGAAAATCGTTCG 59.565 43.478 0.00 0.00 0.00 3.95
4997 5162 4.142600 CCTGGGTGATGAAGAAAATCGTTC 60.143 45.833 0.00 0.00 0.00 3.95
4998 5163 3.758554 CCTGGGTGATGAAGAAAATCGTT 59.241 43.478 0.00 0.00 0.00 3.85
4999 5164 3.244911 ACCTGGGTGATGAAGAAAATCGT 60.245 43.478 0.00 0.00 0.00 3.73
5000 5165 3.347216 ACCTGGGTGATGAAGAAAATCG 58.653 45.455 0.00 0.00 0.00 3.34
5001 5166 6.681368 GCATTACCTGGGTGATGAAGAAAATC 60.681 42.308 22.97 4.45 42.42 2.17
5002 5167 5.127682 GCATTACCTGGGTGATGAAGAAAAT 59.872 40.000 22.97 1.78 42.42 1.82
5003 5168 4.462483 GCATTACCTGGGTGATGAAGAAAA 59.538 41.667 22.97 0.00 42.42 2.29
5004 5169 4.016444 GCATTACCTGGGTGATGAAGAAA 58.984 43.478 22.97 0.22 42.42 2.52
5005 5170 3.010027 TGCATTACCTGGGTGATGAAGAA 59.990 43.478 22.97 6.99 42.42 2.52
5006 5171 2.575735 TGCATTACCTGGGTGATGAAGA 59.424 45.455 22.97 7.61 42.42 2.87
5007 5172 3.003394 TGCATTACCTGGGTGATGAAG 57.997 47.619 22.97 3.20 42.42 3.02
5008 5173 3.448093 TTGCATTACCTGGGTGATGAA 57.552 42.857 22.97 13.41 42.42 2.57
5009 5174 3.448093 TTTGCATTACCTGGGTGATGA 57.552 42.857 22.97 9.50 42.42 2.92
5010 5175 4.441913 GGAATTTGCATTACCTGGGTGATG 60.442 45.833 16.90 16.90 42.61 3.07
5011 5176 3.706086 GGAATTTGCATTACCTGGGTGAT 59.294 43.478 2.07 0.00 0.00 3.06
5012 5177 3.096092 GGAATTTGCATTACCTGGGTGA 58.904 45.455 2.07 0.00 0.00 4.02
5013 5178 3.099141 AGGAATTTGCATTACCTGGGTG 58.901 45.455 2.07 0.00 0.00 4.61
5014 5179 3.473113 AGGAATTTGCATTACCTGGGT 57.527 42.857 0.00 0.00 0.00 4.51
5015 5180 4.222588 TCAAAGGAATTTGCATTACCTGGG 59.777 41.667 0.00 0.00 32.23 4.45
5016 5181 5.404466 TCAAAGGAATTTGCATTACCTGG 57.596 39.130 0.00 0.00 32.23 4.45
5071 5236 5.997746 GCAGGATAAGCAGAATACCACAATA 59.002 40.000 0.00 0.00 0.00 1.90
5072 5237 4.823989 GCAGGATAAGCAGAATACCACAAT 59.176 41.667 0.00 0.00 0.00 2.71
5073 5238 4.199310 GCAGGATAAGCAGAATACCACAA 58.801 43.478 0.00 0.00 0.00 3.33
5074 5239 3.199727 TGCAGGATAAGCAGAATACCACA 59.800 43.478 0.00 0.00 37.02 4.17
5075 5240 3.808728 TGCAGGATAAGCAGAATACCAC 58.191 45.455 0.00 0.00 37.02 4.16
5143 5308 8.889717 GCCTAATGTAGCTAAGAAAAACATGTA 58.110 33.333 0.00 0.00 31.44 2.29
5146 5311 8.581253 AAGCCTAATGTAGCTAAGAAAAACAT 57.419 30.769 0.00 0.00 38.74 2.71
5178 5343 2.747989 GGGTAGCTGGTAAGTTTTGCTC 59.252 50.000 0.00 0.00 35.47 4.26
5258 5429 4.982241 AGAATTGAACAGAGGACCAGAA 57.018 40.909 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.