Multiple sequence alignment - TraesCS4A01G248200

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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 TraesCS4A01G248200 chr4A 100.000 4969 0 0 1 4969 559043696 559048664 0.000000e+00 9177
1 TraesCS4A01G248200 chr4D 94.069 4991 182 46 1 4969 40657839 40652941 0.000000e+00 7472
2 TraesCS4A01G248200 chr4B 93.656 5028 211 61 1 4969 59595617 59590639 0.000000e+00 7419
3 TraesCS4A01G248200 chr2A 76.744 301 56 10 1105 1403 593443486 593443774 6.660000e-34 156
4 TraesCS4A01G248200 chr2D 77.305 282 51 9 1105 1384 449556344 449556074 2.400000e-33 154
5 TraesCS4A01G248200 chr2B 76.868 281 54 7 1105 1384 528829625 528829895 1.110000e-31 148


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 TraesCS4A01G248200 chr4A 559043696 559048664 4968 False 9177 9177 100.000 1 4969 1 chr4A.!!$F1 4968
1 TraesCS4A01G248200 chr4D 40652941 40657839 4898 True 7472 7472 94.069 1 4969 1 chr4D.!!$R1 4968
2 TraesCS4A01G248200 chr4B 59590639 59595617 4978 True 7419 7419 93.656 1 4969 1 chr4B.!!$R1 4968

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
355 364 0.254462 GGAGGAGGAGGAGGCAAAAG 59.746 60.0 0.0 0.0 0.00 2.27 F
1388 1429 0.169009 GCCCAGCGATGTGAGTTTTC 59.831 55.0 0.0 0.0 0.00 2.29 F
2173 2240 0.040425 GCCGATTTGCTTTGTCGTGT 60.040 50.0 0.0 0.0 33.77 4.49 F
3208 3279 0.038618 AGTACGTCGTCAATGCAGCA 60.039 50.0 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2221 0.040425 ACACGACAAAGCAAATCGGC 60.040 50.0 0.0 0.0 40.16 5.54 R
2648 2715 0.107654 GGCTACCAATCCAGAACGCT 60.108 55.0 0.0 0.0 0.00 5.07 R
3490 3562 0.107508 ATGCCCCTCTGTGATGAACG 60.108 55.0 0.0 0.0 0.00 3.95 R
4645 4724 0.758123 AGCCCAAAACACCACCAATG 59.242 50.0 0.0 0.0 0.00 2.82 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
29 31 3.395639 AGAAAAACGGCGTACATTCAGA 58.604 40.909 24.44 0.00 0.00 3.27
66 68 3.892918 ATATGCTAGACGTACGTGGTC 57.107 47.619 28.16 11.83 34.62 4.02
119 121 1.597461 CCGTCTTCTTCCCCTCCAC 59.403 63.158 0.00 0.00 0.00 4.02
141 143 3.713826 TCAAGTATCCAACCAACCCTC 57.286 47.619 0.00 0.00 0.00 4.30
161 163 0.921896 TCCCCCACGTAGCTACTACT 59.078 55.000 21.20 1.26 35.06 2.57
164 166 1.316651 CCCACGTAGCTACTACTCCC 58.683 60.000 21.20 0.00 35.06 4.30
206 210 2.334946 GCAGGCACGCAGAATGGAA 61.335 57.895 0.00 0.00 35.86 3.53
207 211 1.865788 GCAGGCACGCAGAATGGAAA 61.866 55.000 0.00 0.00 35.86 3.13
347 356 0.836400 AAAGCAACGGAGGAGGAGGA 60.836 55.000 0.00 0.00 0.00 3.71
348 357 1.261238 AAGCAACGGAGGAGGAGGAG 61.261 60.000 0.00 0.00 0.00 3.69
349 358 2.726351 GCAACGGAGGAGGAGGAGG 61.726 68.421 0.00 0.00 0.00 4.30
350 359 2.364448 AACGGAGGAGGAGGAGGC 60.364 66.667 0.00 0.00 0.00 4.70
352 361 2.364317 CGGAGGAGGAGGAGGCAA 60.364 66.667 0.00 0.00 0.00 4.52
353 362 1.990060 CGGAGGAGGAGGAGGCAAA 60.990 63.158 0.00 0.00 0.00 3.68
354 363 1.553690 CGGAGGAGGAGGAGGCAAAA 61.554 60.000 0.00 0.00 0.00 2.44
355 364 0.254462 GGAGGAGGAGGAGGCAAAAG 59.746 60.000 0.00 0.00 0.00 2.27
356 365 0.988063 GAGGAGGAGGAGGCAAAAGT 59.012 55.000 0.00 0.00 0.00 2.66
357 366 1.352687 GAGGAGGAGGAGGCAAAAGTT 59.647 52.381 0.00 0.00 0.00 2.66
358 367 2.572104 GAGGAGGAGGAGGCAAAAGTTA 59.428 50.000 0.00 0.00 0.00 2.24
359 368 2.573915 AGGAGGAGGAGGCAAAAGTTAG 59.426 50.000 0.00 0.00 0.00 2.34
360 369 2.360844 GAGGAGGAGGCAAAAGTTAGC 58.639 52.381 0.00 0.00 0.00 3.09
361 370 1.988846 AGGAGGAGGCAAAAGTTAGCT 59.011 47.619 0.00 0.00 0.00 3.32
362 371 3.182152 AGGAGGAGGCAAAAGTTAGCTA 58.818 45.455 0.00 0.00 0.00 3.32
363 372 3.198853 AGGAGGAGGCAAAAGTTAGCTAG 59.801 47.826 0.00 0.00 0.00 3.42
364 373 2.939756 GAGGAGGCAAAAGTTAGCTAGC 59.060 50.000 6.62 6.62 0.00 3.42
367 376 2.680339 GAGGCAAAAGTTAGCTAGCCTG 59.320 50.000 22.64 10.97 43.21 4.85
562 580 2.156098 GGCCGGACAGTAACAAAATGA 58.844 47.619 5.05 0.00 0.00 2.57
614 637 4.096003 CGGGGTGCAGGGTACAGG 62.096 72.222 0.00 0.00 0.00 4.00
615 638 3.728373 GGGGTGCAGGGTACAGGG 61.728 72.222 0.00 0.00 0.00 4.45
689 714 1.153549 GCACCTAGAACCAGAGCCG 60.154 63.158 0.00 0.00 0.00 5.52
743 774 3.263941 CGAAAAGACGGGCCAAGG 58.736 61.111 4.39 0.00 0.00 3.61
757 790 3.637273 AAGGGGGCGACGAAAGCT 61.637 61.111 0.00 0.00 34.52 3.74
834 868 4.758251 TGCCATCGCTCACCACCG 62.758 66.667 0.00 0.00 35.36 4.94
862 896 4.319046 GGACGGACATCATTCATTCATTCG 60.319 45.833 0.00 0.00 0.00 3.34
863 897 3.002656 ACGGACATCATTCATTCATTCGC 59.997 43.478 0.00 0.00 0.00 4.70
904 942 3.330720 CCCCCTCTCCACCCACAC 61.331 72.222 0.00 0.00 0.00 3.82
905 943 2.203998 CCCCTCTCCACCCACACT 60.204 66.667 0.00 0.00 0.00 3.55
906 944 2.294078 CCCCTCTCCACCCACACTC 61.294 68.421 0.00 0.00 0.00 3.51
907 945 2.294078 CCCTCTCCACCCACACTCC 61.294 68.421 0.00 0.00 0.00 3.85
926 964 1.821136 CCCTCCAATTGAGAAACAGCC 59.179 52.381 7.12 0.00 44.42 4.85
960 1001 4.811761 GCCATTGCCGTCGCGAAC 62.812 66.667 12.06 3.88 38.08 3.95
963 1004 1.631072 CATTGCCGTCGCGAACTAG 59.369 57.895 12.06 2.39 38.08 2.57
964 1005 0.800683 CATTGCCGTCGCGAACTAGA 60.801 55.000 12.06 0.00 38.08 2.43
1231 1272 2.715046 GCAAGATCTTCATGTGGACCA 58.285 47.619 4.57 0.00 0.00 4.02
1388 1429 0.169009 GCCCAGCGATGTGAGTTTTC 59.831 55.000 0.00 0.00 0.00 2.29
1392 1433 1.466167 CAGCGATGTGAGTTTTCCCAG 59.534 52.381 0.00 0.00 0.00 4.45
1393 1434 0.169009 GCGATGTGAGTTTTCCCAGC 59.831 55.000 0.00 0.00 0.00 4.85
1394 1435 1.813513 CGATGTGAGTTTTCCCAGCT 58.186 50.000 0.00 0.00 0.00 4.24
1395 1436 1.466167 CGATGTGAGTTTTCCCAGCTG 59.534 52.381 6.78 6.78 0.00 4.24
1396 1437 1.200948 GATGTGAGTTTTCCCAGCTGC 59.799 52.381 8.66 0.00 0.00 5.25
1397 1438 0.183492 TGTGAGTTTTCCCAGCTGCT 59.817 50.000 8.66 0.00 0.00 4.24
1398 1439 1.322442 GTGAGTTTTCCCAGCTGCTT 58.678 50.000 8.66 0.00 0.00 3.91
1399 1440 1.268079 GTGAGTTTTCCCAGCTGCTTC 59.732 52.381 8.66 0.00 0.00 3.86
1400 1441 1.143684 TGAGTTTTCCCAGCTGCTTCT 59.856 47.619 8.66 0.02 0.00 2.85
1412 1453 3.436359 CAGCTGCTTCTTCTTCTTCTTCC 59.564 47.826 0.00 0.00 0.00 3.46
1462 1517 2.859165 TGCTTCGATTTCCACCTCTT 57.141 45.000 0.00 0.00 0.00 2.85
1530 1595 1.943693 CTTTTGCGTGGTGCCAACG 60.944 57.895 0.00 0.99 45.60 4.10
1577 1642 6.668283 AGTTATTGTAGCTCTTTGTCCTCCTA 59.332 38.462 0.00 0.00 0.00 2.94
1584 1649 2.032620 TCTTTGTCCTCCTATCGCCTC 58.967 52.381 0.00 0.00 0.00 4.70
1599 1664 2.060383 CCTCCTCGCCACCTCATCA 61.060 63.158 0.00 0.00 0.00 3.07
1642 1707 0.326904 TGGGATGGTGAGATCTGGCT 60.327 55.000 0.00 0.00 0.00 4.75
1690 1755 1.880027 CGGAAGAAACTTCACCTTGGG 59.120 52.381 12.46 0.00 0.00 4.12
1780 1847 1.701704 CAAAAATGGAGCGCACCTTC 58.298 50.000 24.52 5.57 0.00 3.46
1795 1862 3.552273 GCACCTTCTGAGTTCTGACGTTA 60.552 47.826 0.00 0.00 0.00 3.18
1951 2018 0.447801 GCGACGCCATCAAGTTCAAT 59.552 50.000 9.14 0.00 0.00 2.57
1993 2060 1.812922 CATGCTCAGCTGGACGGTC 60.813 63.158 15.13 0.00 0.00 4.79
2116 2183 4.732106 GACACCATCGACCGGATC 57.268 61.111 9.46 0.32 31.28 3.36
2132 2199 1.996786 GATCGTCGCCCAGGTTCGTA 61.997 60.000 0.00 0.00 0.00 3.43
2154 2221 1.493950 GGCTGATCATCTCGGTTGCG 61.494 60.000 0.00 0.00 32.34 4.85
2165 2232 2.258286 GGTTGCGCCGATTTGCTT 59.742 55.556 4.18 0.00 0.00 3.91
2166 2233 1.372872 GGTTGCGCCGATTTGCTTT 60.373 52.632 4.18 0.00 0.00 3.51
2167 2234 1.616872 GGTTGCGCCGATTTGCTTTG 61.617 55.000 4.18 0.00 0.00 2.77
2168 2235 0.939106 GTTGCGCCGATTTGCTTTGT 60.939 50.000 4.18 0.00 0.00 2.83
2169 2236 0.662970 TTGCGCCGATTTGCTTTGTC 60.663 50.000 4.18 0.00 0.00 3.18
2172 2239 1.059657 CGCCGATTTGCTTTGTCGTG 61.060 55.000 0.00 0.00 33.77 4.35
2173 2240 0.040425 GCCGATTTGCTTTGTCGTGT 60.040 50.000 0.00 0.00 33.77 4.49
2174 2241 1.673760 CCGATTTGCTTTGTCGTGTG 58.326 50.000 0.00 0.00 33.77 3.82
2175 2242 1.002900 CCGATTTGCTTTGTCGTGTGT 60.003 47.619 0.00 0.00 33.77 3.72
2221 2288 5.762045 TGCTCAATTGAGTAAAGTTTCAGC 58.238 37.500 30.88 16.57 43.85 4.26
2427 2494 4.318332 CATAGTGTTCAAGGACAGCAAGA 58.682 43.478 0.00 0.00 0.00 3.02
2567 2634 1.250840 GGGATGAGTTTGTGTGGGGC 61.251 60.000 0.00 0.00 0.00 5.80
2636 2703 3.790437 ACAGCTCCAGGGATGGCG 61.790 66.667 0.00 0.00 0.00 5.69
2800 2868 5.814705 CACCAAAGGAATAACAAACAAGCAA 59.185 36.000 0.00 0.00 0.00 3.91
2802 2870 7.655328 CACCAAAGGAATAACAAACAAGCAATA 59.345 33.333 0.00 0.00 0.00 1.90
2825 2893 9.491675 AATATGACAGCATCTAAATGAGAAGAG 57.508 33.333 0.00 0.00 37.85 2.85
2900 2971 8.562052 TGATCAATGTTAATGAAGAATGATCCG 58.438 33.333 13.11 0.00 40.57 4.18
3026 3097 2.430465 ACTGACAATGTCATGTGCTCC 58.570 47.619 17.10 0.00 41.94 4.70
3070 3141 7.284074 TCATTCAACTTCACTAAAGGTTGGTA 58.716 34.615 0.00 0.00 39.47 3.25
3088 3159 5.208463 TGGTAATGCCCTTCTTTGTTTTC 57.792 39.130 0.00 0.00 36.04 2.29
3104 3175 4.985538 TGTTTTCCACTGCCTCTCTAAAT 58.014 39.130 0.00 0.00 0.00 1.40
3208 3279 0.038618 AGTACGTCGTCAATGCAGCA 60.039 50.000 0.00 0.00 0.00 4.41
3235 3306 5.220931 CCTTGCCTCTTTGTATGCTGATTAC 60.221 44.000 0.00 0.00 0.00 1.89
3326 3397 3.838244 TTGCAAAGTCACAGGTAGAGT 57.162 42.857 0.00 0.00 0.00 3.24
3424 3496 5.188359 ACCCTTCAATTTGCAGCTTGATTAT 59.812 36.000 12.20 0.00 31.83 1.28
3463 3535 3.428870 CACAAAAGATGAGCTACGTCGTT 59.571 43.478 1.78 0.00 39.31 3.85
3490 3562 0.803117 GAAAGAAGTACCCCAAGCGC 59.197 55.000 0.00 0.00 0.00 5.92
3562 3634 4.283212 TGCAAAGGAGGTTTTAAATGGAGG 59.717 41.667 0.00 0.00 0.00 4.30
3730 3802 6.488344 TGATTTCTCTAGCTGACATCGATACT 59.512 38.462 0.00 0.00 0.00 2.12
3733 3805 4.068599 CTCTAGCTGACATCGATACTGGA 58.931 47.826 0.00 0.00 0.00 3.86
3739 3811 5.048364 AGCTGACATCGATACTGGAAGATAC 60.048 44.000 0.00 0.00 37.43 2.24
3820 3892 1.508088 GCCATCAGCTTGGAAACCG 59.492 57.895 8.71 0.00 39.25 4.44
3984 4056 7.374272 ACGGATCAGTATAAATCATCTGTCAG 58.626 38.462 0.00 0.00 28.73 3.51
3987 4059 6.737720 TCAGTATAAATCATCTGTCAGCCT 57.262 37.500 0.00 0.00 0.00 4.58
3990 4062 6.988580 CAGTATAAATCATCTGTCAGCCTTGA 59.011 38.462 0.00 0.00 0.00 3.02
4022 4094 6.870965 AGTTGTGTGCAATTTGTGAAACTAAA 59.129 30.769 0.00 0.00 34.76 1.85
4058 4131 5.751509 TGTTGTTATCCATATTCCGAGTTCG 59.248 40.000 0.00 0.00 39.44 3.95
4085 4158 7.487829 TGTGTGAAGTTCTTTTTGTAGAAATGC 59.512 33.333 4.17 0.00 36.01 3.56
4152 4225 6.119536 TCACAGTAAAGAATGTGTGACCTTT 58.880 36.000 5.55 0.00 43.33 3.11
4167 4240 6.636850 GTGTGACCTTTATACAGCTTGTTTTG 59.363 38.462 0.00 0.00 0.00 2.44
4168 4241 6.544197 TGTGACCTTTATACAGCTTGTTTTGA 59.456 34.615 0.00 0.00 0.00 2.69
4172 4245 7.425606 ACCTTTATACAGCTTGTTTTGACTTG 58.574 34.615 0.00 0.00 0.00 3.16
4181 4254 5.577945 AGCTTGTTTTGACTTGTTTGACATG 59.422 36.000 0.00 0.00 0.00 3.21
4184 4257 5.417811 TGTTTTGACTTGTTTGACATGCAT 58.582 33.333 0.00 0.00 0.00 3.96
4200 4273 4.576053 ACATGCATTATACACTTCATGCGT 59.424 37.500 0.00 0.00 44.22 5.24
4201 4274 4.534794 TGCATTATACACTTCATGCGTG 57.465 40.909 11.82 11.82 44.22 5.34
4332 4410 6.450545 TGAACAGAAAACACACAATTTCACA 58.549 32.000 0.00 0.00 37.87 3.58
4566 4644 8.190122 GCAATTATTCCCGCATCAATTATGATA 58.810 33.333 0.00 0.00 44.53 2.15
4572 4650 4.633126 CCCGCATCAATTATGATAGTGAGG 59.367 45.833 0.00 0.00 44.53 3.86
4645 4724 4.887748 TCAGAACAATCCTGTGAGTTCTC 58.112 43.478 0.00 0.00 45.35 2.87
4724 4803 6.244552 TCATCATCTACTCTCAAAGGCAAT 57.755 37.500 0.00 0.00 0.00 3.56
4808 4887 1.779221 CATTAGCATGCCCCTTGGAA 58.221 50.000 15.66 0.00 0.00 3.53
4809 4888 2.322658 CATTAGCATGCCCCTTGGAAT 58.677 47.619 15.66 0.28 0.00 3.01
4901 4980 4.142609 TCCTGATTATCTTGTCACTGGC 57.857 45.455 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 0.727398 GCCCGTTGCTCTGAATGTAC 59.273 55.000 0.00 0.00 36.87 2.90
29 31 3.617531 GCATATAGTAGATGCCCGTTGCT 60.618 47.826 17.24 0.00 43.24 3.91
42 44 5.541845 ACCACGTACGTCTAGCATATAGTA 58.458 41.667 19.94 0.00 0.00 1.82
43 45 4.384056 ACCACGTACGTCTAGCATATAGT 58.616 43.478 19.94 0.63 0.00 2.12
44 46 4.433936 CGACCACGTACGTCTAGCATATAG 60.434 50.000 19.94 2.85 34.56 1.31
45 47 3.429881 CGACCACGTACGTCTAGCATATA 59.570 47.826 19.94 0.00 34.56 0.86
46 48 2.222678 CGACCACGTACGTCTAGCATAT 59.777 50.000 19.94 0.00 34.56 1.78
66 68 2.580815 GGGACGGGGAAAGGTACG 59.419 66.667 0.00 0.00 0.00 3.67
119 121 4.010349 GAGGGTTGGTTGGATACTTGAAG 58.990 47.826 0.00 0.00 37.61 3.02
141 143 1.133853 AGTAGTAGCTACGTGGGGGAG 60.134 57.143 17.99 0.00 41.37 4.30
161 163 6.159575 TCTGTGGAATGGATAATAGTTTGGGA 59.840 38.462 0.00 0.00 0.00 4.37
164 166 6.016777 GCCTCTGTGGAATGGATAATAGTTTG 60.017 42.308 0.00 0.00 38.35 2.93
207 211 7.548097 GTCTTTCTTTGAGTTTCTCCCTTTTT 58.452 34.615 0.00 0.00 0.00 1.94
212 216 3.058846 GCGTCTTTCTTTGAGTTTCTCCC 60.059 47.826 0.00 0.00 0.00 4.30
214 218 4.795970 TGCGTCTTTCTTTGAGTTTCTC 57.204 40.909 0.00 0.00 0.00 2.87
347 356 2.619074 CCAGGCTAGCTAACTTTTGCCT 60.619 50.000 15.72 14.49 42.65 4.75
348 357 1.745653 CCAGGCTAGCTAACTTTTGCC 59.254 52.381 15.72 10.65 36.45 4.52
349 358 1.133216 GCCAGGCTAGCTAACTTTTGC 59.867 52.381 15.72 2.63 0.00 3.68
350 359 2.716217 AGCCAGGCTAGCTAACTTTTG 58.284 47.619 14.18 2.46 39.29 2.44
361 370 1.007238 ACAGTTCTCCTAGCCAGGCTA 59.993 52.381 20.66 20.66 42.30 3.93
362 371 0.252467 ACAGTTCTCCTAGCCAGGCT 60.252 55.000 20.63 20.63 42.30 4.58
363 372 0.176910 GACAGTTCTCCTAGCCAGGC 59.823 60.000 1.84 1.84 42.30 4.85
364 373 0.457851 CGACAGTTCTCCTAGCCAGG 59.542 60.000 0.00 0.00 44.17 4.45
367 376 1.142097 GGCGACAGTTCTCCTAGCC 59.858 63.158 0.00 0.00 36.08 3.93
498 510 0.037790 GCAGTAGATCTGGGATCGCC 60.038 60.000 5.18 0.12 43.78 5.54
614 637 0.889306 ACTTCACTCGCCTCTGTACC 59.111 55.000 0.00 0.00 0.00 3.34
615 638 1.402984 CCACTTCACTCGCCTCTGTAC 60.403 57.143 0.00 0.00 0.00 2.90
689 714 0.035458 CTATCGGATGGGTTGGCTCC 59.965 60.000 0.00 0.00 0.00 4.70
742 773 2.510918 GTAGCTTTCGTCGCCCCC 60.511 66.667 0.00 0.00 0.00 5.40
743 774 2.884207 CGTAGCTTTCGTCGCCCC 60.884 66.667 0.00 0.00 0.00 5.80
757 790 3.956314 GGTGGTGGTTGGGGCGTA 61.956 66.667 0.00 0.00 0.00 4.42
834 868 3.400599 AATGATGTCCGTCCGGGGC 62.401 63.158 0.00 0.00 42.42 5.80
835 869 1.227556 GAATGATGTCCGTCCGGGG 60.228 63.158 0.00 0.00 36.01 5.73
836 870 0.106708 ATGAATGATGTCCGTCCGGG 59.893 55.000 0.00 0.00 35.59 5.73
862 896 0.605589 GAAGGTGGTGGTGGTACTGC 60.606 60.000 0.00 0.00 0.00 4.40
863 897 0.320421 CGAAGGTGGTGGTGGTACTG 60.320 60.000 0.00 0.00 0.00 2.74
904 942 2.751806 GCTGTTTCTCAATTGGAGGGAG 59.248 50.000 5.42 0.00 44.19 4.30
905 943 2.555227 GGCTGTTTCTCAATTGGAGGGA 60.555 50.000 5.42 0.00 44.19 4.20
906 944 1.821136 GGCTGTTTCTCAATTGGAGGG 59.179 52.381 5.42 0.00 44.19 4.30
907 945 1.821136 GGGCTGTTTCTCAATTGGAGG 59.179 52.381 5.42 0.00 44.19 4.30
960 1001 1.142748 CCGCCTCCTTGCTGTCTAG 59.857 63.158 0.00 0.00 0.00 2.43
1388 1429 2.083002 GAAGAAGAAGAAGCAGCTGGG 58.917 52.381 17.12 0.00 0.00 4.45
1392 1433 3.673902 AGGAAGAAGAAGAAGAAGCAGC 58.326 45.455 0.00 0.00 0.00 5.25
1393 1434 6.631971 AAAAGGAAGAAGAAGAAGAAGCAG 57.368 37.500 0.00 0.00 0.00 4.24
1435 1490 3.751698 GTGGAAATCGAAGCAAAGGTAGT 59.248 43.478 0.00 0.00 0.00 2.73
1436 1491 3.127030 GGTGGAAATCGAAGCAAAGGTAG 59.873 47.826 0.00 0.00 0.00 3.18
1462 1517 0.974383 GGAGAGGAAAGGGACGAACA 59.026 55.000 0.00 0.00 0.00 3.18
1584 1649 0.531532 GACATGATGAGGTGGCGAGG 60.532 60.000 0.00 0.00 0.00 4.63
1599 1664 5.367937 AGACATGCTAAATGTAGGAGGACAT 59.632 40.000 2.83 0.00 41.92 3.06
1780 1847 3.604198 CACGACATAACGTCAGAACTCAG 59.396 47.826 0.00 0.00 45.70 3.35
1795 1862 3.738982 TGACAATTTCAGACCACGACAT 58.261 40.909 0.00 0.00 0.00 3.06
1993 2060 0.537188 ACTTGGCCCTGTACTCGATG 59.463 55.000 0.00 0.00 0.00 3.84
2116 2183 2.202570 CTACGAACCTGGGCGACG 60.203 66.667 16.34 9.64 0.00 5.12
2132 2199 1.411977 CAACCGAGATGATCAGCCTCT 59.588 52.381 19.49 10.67 0.00 3.69
2154 2221 0.040425 ACACGACAAAGCAAATCGGC 60.040 50.000 0.00 0.00 40.16 5.54
2161 2228 1.885388 CCGGACACACGACAAAGCA 60.885 57.895 0.00 0.00 35.47 3.91
2162 2229 2.604174 CCCGGACACACGACAAAGC 61.604 63.158 0.73 0.00 35.47 3.51
2163 2230 0.531090 TTCCCGGACACACGACAAAG 60.531 55.000 0.73 0.00 35.47 2.77
2165 2232 0.107081 ATTTCCCGGACACACGACAA 59.893 50.000 0.73 0.00 35.47 3.18
2166 2233 0.107081 AATTTCCCGGACACACGACA 59.893 50.000 0.73 0.00 35.47 4.35
2167 2234 0.515564 CAATTTCCCGGACACACGAC 59.484 55.000 0.73 0.00 35.47 4.34
2168 2235 0.604243 CCAATTTCCCGGACACACGA 60.604 55.000 0.73 0.00 35.47 4.35
2169 2236 1.582610 CCCAATTTCCCGGACACACG 61.583 60.000 0.73 0.00 0.00 4.49
2172 2239 1.605165 TGCCCAATTTCCCGGACAC 60.605 57.895 0.73 0.00 0.00 3.67
2173 2240 1.605165 GTGCCCAATTTCCCGGACA 60.605 57.895 0.73 0.00 0.00 4.02
2174 2241 2.348104 GGTGCCCAATTTCCCGGAC 61.348 63.158 0.73 0.00 0.00 4.79
2175 2242 2.036572 GGTGCCCAATTTCCCGGA 59.963 61.111 0.73 0.00 0.00 5.14
2198 2265 5.532406 AGCTGAAACTTTACTCAATTGAGCA 59.468 36.000 30.95 19.03 45.79 4.26
2199 2266 6.006759 AGCTGAAACTTTACTCAATTGAGC 57.993 37.500 30.95 15.75 45.79 4.26
2221 2288 7.548427 ACAAGAAGTTCATATGACATCAGTGAG 59.452 37.037 4.48 0.00 0.00 3.51
2393 2460 1.450134 CACTATGGAAGCTGCGGCA 60.450 57.895 21.93 1.29 41.70 5.69
2399 2466 3.327757 TGTCCTTGAACACTATGGAAGCT 59.672 43.478 0.00 0.00 0.00 3.74
2427 2494 1.197264 GACGAGCTTGTCAGAGTACGT 59.803 52.381 26.35 9.27 38.75 3.57
2567 2634 1.410737 CGAAGTACATCCACGCACCG 61.411 60.000 0.00 0.00 0.00 4.94
2645 2712 0.539986 TACCAATCCAGAACGCTCCC 59.460 55.000 0.00 0.00 0.00 4.30
2648 2715 0.107654 GGCTACCAATCCAGAACGCT 60.108 55.000 0.00 0.00 0.00 5.07
2768 2836 5.719173 TGTTATTCCTTTGGTGCTAAATGC 58.281 37.500 0.00 0.00 43.25 3.56
2800 2868 8.868103 TCTCTTCTCATTTAGATGCTGTCATAT 58.132 33.333 0.00 0.00 33.05 1.78
2802 2870 7.122138 TCTCTTCTCATTTAGATGCTGTCAT 57.878 36.000 0.00 0.00 33.05 3.06
3070 3141 3.711190 AGTGGAAAACAAAGAAGGGCATT 59.289 39.130 0.00 0.00 0.00 3.56
3088 3159 2.503356 AGTGGATTTAGAGAGGCAGTGG 59.497 50.000 0.00 0.00 0.00 4.00
3124 3195 5.708230 TCCTGCAAAACATTCGGTTACTTAT 59.292 36.000 0.00 0.00 39.29 1.73
3208 3279 3.698040 CAGCATACAAAGAGGCAAGGAAT 59.302 43.478 0.00 0.00 0.00 3.01
3235 3306 1.406069 GGTGTATCTGCAGTGTCCAGG 60.406 57.143 14.67 0.00 0.00 4.45
3326 3397 6.681729 AGTCCAGGAGTATTGAGTACAAAA 57.318 37.500 0.00 0.00 39.54 2.44
3424 3496 4.919774 TTGTGGGTTCTTGCCTAGAATA 57.080 40.909 0.00 0.00 44.39 1.75
3463 3535 3.052793 TGGGGTACTTCTTTCCAAAACCA 60.053 43.478 0.00 0.00 0.00 3.67
3490 3562 0.107508 ATGCCCCTCTGTGATGAACG 60.108 55.000 0.00 0.00 0.00 3.95
3562 3634 4.022413 AGGGTTTGCTTTCTTAGACTCC 57.978 45.455 0.00 0.00 0.00 3.85
3730 3802 9.383519 GTGTTCTTATCAATTGAGTATCTTCCA 57.616 33.333 14.54 1.47 34.92 3.53
3733 3805 9.911788 ATGGTGTTCTTATCAATTGAGTATCTT 57.088 29.630 14.54 0.00 34.92 2.40
3739 3811 8.503458 AGAAGATGGTGTTCTTATCAATTGAG 57.497 34.615 14.54 0.40 36.10 3.02
3802 3874 1.244019 ACGGTTTCCAAGCTGATGGC 61.244 55.000 0.00 0.00 40.46 4.40
3984 4056 2.024414 ACACAACTTCCAGTTCAAGGC 58.976 47.619 0.00 0.00 36.03 4.35
3987 4059 2.441410 TGCACACAACTTCCAGTTCAA 58.559 42.857 0.00 0.00 36.03 2.69
3990 4062 4.183101 CAAATTGCACACAACTTCCAGTT 58.817 39.130 0.00 0.00 39.39 3.16
4022 4094 5.151454 TGGATAACAACAAGGACCCAAAAT 58.849 37.500 0.00 0.00 0.00 1.82
4058 4131 8.798153 CATTTCTACAAAAAGAACTTCACACAC 58.202 33.333 0.00 0.00 35.25 3.82
4152 4225 7.913297 GTCAAACAAGTCAAAACAAGCTGTATA 59.087 33.333 0.00 0.00 0.00 1.47
4167 4240 7.530010 AGTGTATAATGCATGTCAAACAAGTC 58.470 34.615 0.00 0.00 0.00 3.01
4168 4241 7.452880 AGTGTATAATGCATGTCAAACAAGT 57.547 32.000 0.00 0.00 0.00 3.16
4172 4245 7.043854 GCATGAAGTGTATAATGCATGTCAAAC 60.044 37.037 9.32 0.00 43.84 2.93
4332 4410 6.173427 ACCAGAATTGCCAGTAAATTGTTT 57.827 33.333 0.00 0.00 0.00 2.83
4572 4650 7.389053 AGAAGGTAAATGTTGTGTGAGATTCTC 59.611 37.037 6.73 6.73 0.00 2.87
4582 4660 4.566545 TGTGCAGAAGGTAAATGTTGTG 57.433 40.909 0.00 0.00 0.00 3.33
4586 4664 4.832266 TGGATTTGTGCAGAAGGTAAATGT 59.168 37.500 0.00 0.00 0.00 2.71
4645 4724 0.758123 AGCCCAAAACACCACCAATG 59.242 50.000 0.00 0.00 0.00 2.82
4724 4803 4.989279 AGAAAGCTTTGTTGAAAGAGCA 57.011 36.364 18.30 0.00 41.12 4.26
4808 4887 6.002704 ACACAGAAGCTTCTTGATTGAGAAT 58.997 36.000 29.35 12.99 35.27 2.40
4809 4888 5.237996 CACACAGAAGCTTCTTGATTGAGAA 59.762 40.000 29.35 0.00 34.74 2.87
4851 4930 5.590530 TTGAGGTTGTGCAAACTTAACAT 57.409 34.783 3.83 0.49 38.71 2.71
4901 4980 2.350388 GCGTATGAAACCCATAATGCGG 60.350 50.000 0.00 0.00 39.29 5.69
4924 5003 4.518970 TCAAGGAAAGGTTTCAGCATGTAC 59.481 41.667 4.89 0.00 38.92 2.90
4925 5004 4.724399 TCAAGGAAAGGTTTCAGCATGTA 58.276 39.130 4.89 0.00 38.92 2.29


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

AutoCloner maintained by Alex Coulton.