Multiple sequence alignment - TraesCS6A01G219100

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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 TraesCS6A01G219100 chr6A 100.000 5169 0 0 1 5169 405665296 405660128 0.000000e+00 9546.0
1 TraesCS6A01G219100 chr6B 95.523 3596 101 11 1518 5084 446053660 446050096 0.000000e+00 5694.0
2 TraesCS6A01G219100 chr6B 94.194 1550 45 18 1 1533 446055198 446053677 0.000000e+00 2322.0
3 TraesCS6A01G219100 chr6B 87.629 97 12 0 2983 3079 643997863 643997959 4.230000e-21 113.0
4 TraesCS6A01G219100 chr6D 95.318 3353 121 13 1373 4710 285183834 285180503 0.000000e+00 5289.0
5 TraesCS6A01G219100 chr6D 94.205 1346 38 10 1 1346 285185228 285183923 0.000000e+00 2017.0
6 TraesCS6A01G219100 chr6D 94.540 348 19 0 4737 5084 285180511 285180164 5.890000e-149 538.0
7 TraesCS6A01G219100 chr6D 78.827 307 34 13 2810 3087 9961359 9961663 1.480000e-40 178.0
8 TraesCS6A01G219100 chr6D 95.833 96 2 2 5075 5169 148179372 148179466 2.490000e-33 154.0
9 TraesCS6A01G219100 chr6D 81.325 166 22 7 2907 3064 470900457 470900621 5.430000e-25 126.0
10 TraesCS6A01G219100 chr1D 78.930 299 31 14 2810 3079 432549643 432549938 1.910000e-39 174.0
11 TraesCS6A01G219100 chr1D 78.289 304 37 11 2810 3085 246041964 246042266 8.900000e-38 169.0
12 TraesCS6A01G219100 chr1D 78.595 299 33 13 2810 3079 397635579 397635875 8.900000e-38 169.0
13 TraesCS6A01G219100 chr1D 78.105 306 34 14 2810 3086 393760268 393759967 4.140000e-36 163.0
14 TraesCS6A01G219100 chr1D 94.949 99 5 0 5071 5169 237138982 237138884 6.930000e-34 156.0
15 TraesCS6A01G219100 chr1D 94.792 96 5 0 5074 5169 211384238 211384143 3.220000e-32 150.0
16 TraesCS6A01G219100 chr7A 80.723 249 25 18 2831 3067 39008500 39008737 6.880000e-39 172.0
17 TraesCS6A01G219100 chr1B 79.021 286 30 17 2828 3087 26466587 26466306 8.900000e-38 169.0
18 TraesCS6A01G219100 chr1B 77.043 257 36 13 2842 3078 580611120 580610867 5.430000e-25 126.0
19 TraesCS6A01G219100 chr5D 96.875 96 3 0 5074 5169 532662099 532662194 1.490000e-35 161.0
20 TraesCS6A01G219100 chr2D 94.898 98 4 1 5072 5169 42937095 42936999 8.960000e-33 152.0
21 TraesCS6A01G219100 chr2D 92.308 104 6 2 5067 5169 591382881 591382779 4.170000e-31 147.0
22 TraesCS6A01G219100 chr1A 95.745 94 4 0 5076 5169 334961023 334960930 8.960000e-33 152.0
23 TraesCS6A01G219100 chr5A 93.204 103 6 1 5067 5169 496752720 496752821 3.220000e-32 150.0
24 TraesCS6A01G219100 chr5A 100.000 30 0 0 4367 4396 519009723 519009694 7.230000e-04 56.5
25 TraesCS6A01G219100 chr3D 94.898 98 2 3 5074 5169 586278697 586278601 3.220000e-32 150.0
26 TraesCS6A01G219100 chr7B 81.768 181 27 6 2808 2987 36385101 36384926 4.170000e-31 147.0
27 TraesCS6A01G219100 chr7B 95.000 40 2 0 4358 4397 92313816 92313777 4.320000e-06 63.9
28 TraesCS6A01G219100 chr4A 76.952 269 43 12 2830 3079 626395297 626395565 9.030000e-28 135.0
29 TraesCS6A01G219100 chr4B 84.034 119 14 4 2965 3079 171628880 171628997 5.470000e-20 110.0
30 TraesCS6A01G219100 chr2B 85.714 105 12 2 2983 3087 76557531 76557430 1.970000e-19 108.0
31 TraesCS6A01G219100 chr5B 97.826 46 1 0 4357 4402 1418376 1418331 4.290000e-11 80.5
32 TraesCS6A01G219100 chr2A 93.478 46 2 1 4353 4398 627915174 627915218 3.340000e-07 67.6
33 TraesCS6A01G219100 chr3B 100.000 31 0 0 4368 4398 225232781 225232751 2.010000e-04 58.4
34 TraesCS6A01G219100 chr3A 94.444 36 2 0 4358 4393 679645664 679645699 7.230000e-04 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 TraesCS6A01G219100 chr6A 405660128 405665296 5168 True 9546.000000 9546 100.000000 1 5169 1 chr6A.!!$R1 5168
1 TraesCS6A01G219100 chr6B 446050096 446055198 5102 True 4008.000000 5694 94.858500 1 5084 2 chr6B.!!$R1 5083
2 TraesCS6A01G219100 chr6D 285180164 285185228 5064 True 2614.666667 5289 94.687667 1 5084 3 chr6D.!!$R1 5083

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
477 478 0.545548 GGGTCCAACTCCTCCTCACT 60.546 60.000 0.0 0.0 0.0 3.41 F
485 486 0.686112 CTCCTCCTCACTCCCCTCAC 60.686 65.000 0.0 0.0 0.0 3.51 F
1298 1316 0.107831 TTTCCAGTCGGTTGTGGAGG 59.892 55.000 0.0 0.0 43.8 4.30 F
1302 1320 0.179056 CAGTCGGTTGTGGAGGTTGT 60.179 55.000 0.0 0.0 0.0 3.32 F
1768 1895 0.606401 AATGCGTGTGGAGAAGGTGG 60.606 55.000 0.0 0.0 0.0 4.61 F
1774 1901 1.002087 GTGTGGAGAAGGTGGGTGTAG 59.998 57.143 0.0 0.0 0.0 2.74 F
1775 1902 1.132977 TGTGGAGAAGGTGGGTGTAGA 60.133 52.381 0.0 0.0 0.0 2.59 F
3301 3431 1.571460 CAACGCTTCAGTGCTGGAC 59.429 57.895 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1299 1.052124 AACCTCCACAACCGACTGGA 61.052 55.000 0.00 0.00 39.21 3.86 R
1746 1873 1.081892 CCTTCTCCACACGCATTCAG 58.918 55.000 0.00 0.00 0.00 3.02 R
2877 3004 1.589968 GCGATGAAAACAGCGATCGAC 60.590 52.381 21.57 10.46 40.06 4.20 R
2930 3057 4.162131 TCATACAAGACTGAAGCTATGCCA 59.838 41.667 0.00 0.00 0.00 4.92 R
3595 3726 0.473755 ATCCTATCACCGCCAATGCA 59.526 50.000 0.00 0.00 37.32 3.96 R
3638 3769 2.108970 GATACCCTTTCCTGTCCGACT 58.891 52.381 0.00 0.00 0.00 4.18 R
3968 4100 3.010420 GGTTGGATCCAGCAAGTAAGAC 58.990 50.000 27.45 13.86 0.00 3.01 R
4723 4872 0.179018 GAGGTGGCCTTGTCACAAGT 60.179 55.000 16.50 0.00 40.26 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
286 287 1.781555 CGTCACGCTGTTGATGGAC 59.218 57.895 0.00 0.00 0.00 4.02
301 302 0.547075 TGGACGTGTTGGGGAAGAAA 59.453 50.000 0.00 0.00 0.00 2.52
470 471 3.322466 CCAGCGGGTCCAACTCCT 61.322 66.667 0.00 0.00 0.00 3.69
472 473 3.003763 AGCGGGTCCAACTCCTCC 61.004 66.667 0.00 0.00 0.00 4.30
476 477 1.889530 CGGGTCCAACTCCTCCTCAC 61.890 65.000 0.00 0.00 0.00 3.51
477 478 0.545548 GGGTCCAACTCCTCCTCACT 60.546 60.000 0.00 0.00 0.00 3.41
479 480 0.899019 GTCCAACTCCTCCTCACTCC 59.101 60.000 0.00 0.00 0.00 3.85
484 485 1.149782 ACTCCTCCTCACTCCCCTCA 61.150 60.000 0.00 0.00 0.00 3.86
485 486 0.686112 CTCCTCCTCACTCCCCTCAC 60.686 65.000 0.00 0.00 0.00 3.51
565 569 2.818132 GAGGAGATGGACCGGCAG 59.182 66.667 0.00 0.00 0.00 4.85
764 777 1.007336 AGAAGCTAACGTTGGTCGCG 61.007 55.000 11.99 0.00 44.19 5.87
859 872 1.073548 GCCCACGTAGGACCCAAAA 59.926 57.895 3.45 0.00 41.22 2.44
1057 1070 4.804420 TCTCCCCGGCTGCTCCAT 62.804 66.667 0.00 0.00 34.01 3.41
1210 1228 3.050166 TTCATGGCCGATTGCGCAC 62.050 57.895 11.12 0.00 42.61 5.34
1229 1247 2.791560 CACTATGTTCATCTCCGCTTCG 59.208 50.000 0.00 0.00 0.00 3.79
1248 1266 2.347490 GCTTCACTGAAGGCCGGA 59.653 61.111 18.53 0.00 39.76 5.14
1296 1314 2.018515 GTTTTTCCAGTCGGTTGTGGA 58.981 47.619 0.00 0.00 41.29 4.02
1297 1315 1.961793 TTTTCCAGTCGGTTGTGGAG 58.038 50.000 0.00 0.00 43.80 3.86
1298 1316 0.107831 TTTCCAGTCGGTTGTGGAGG 59.892 55.000 0.00 0.00 43.80 4.30
1299 1317 1.052124 TTCCAGTCGGTTGTGGAGGT 61.052 55.000 0.00 0.00 43.80 3.85
1300 1318 1.052124 TCCAGTCGGTTGTGGAGGTT 61.052 55.000 0.00 0.00 37.96 3.50
1301 1319 0.884704 CCAGTCGGTTGTGGAGGTTG 60.885 60.000 0.00 0.00 35.67 3.77
1302 1320 0.179056 CAGTCGGTTGTGGAGGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
1303 1321 0.179056 AGTCGGTTGTGGAGGTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
1304 1322 1.147376 TCGGTTGTGGAGGTTGTGG 59.853 57.895 0.00 0.00 0.00 4.17
1349 1367 8.560576 ACAAGAAAATCGTTTTGTGATAAGTG 57.439 30.769 1.33 0.00 32.90 3.16
1350 1368 7.647715 ACAAGAAAATCGTTTTGTGATAAGTGG 59.352 33.333 1.33 0.00 32.90 4.00
1359 1377 6.430451 GTTTTGTGATAAGTGGTTCTCTGTG 58.570 40.000 0.00 0.00 0.00 3.66
1407 1492 7.357532 GCGTGCATTTCGGATGAATTTTTATAG 60.358 37.037 0.00 0.00 33.20 1.31
1559 1676 4.079253 GCCACTTTCCTCTTTTGACCATA 58.921 43.478 0.00 0.00 0.00 2.74
1710 1837 2.584835 AAGCCAAGCACTAACCATCA 57.415 45.000 0.00 0.00 0.00 3.07
1746 1873 6.385649 TTGGTGAGAGTTTATGTTTCAACC 57.614 37.500 0.00 0.00 0.00 3.77
1767 1894 0.798776 GAATGCGTGTGGAGAAGGTG 59.201 55.000 0.00 0.00 0.00 4.00
1768 1895 0.606401 AATGCGTGTGGAGAAGGTGG 60.606 55.000 0.00 0.00 0.00 4.61
1769 1896 2.358737 GCGTGTGGAGAAGGTGGG 60.359 66.667 0.00 0.00 0.00 4.61
1770 1897 3.148084 CGTGTGGAGAAGGTGGGT 58.852 61.111 0.00 0.00 0.00 4.51
1771 1898 1.301716 CGTGTGGAGAAGGTGGGTG 60.302 63.158 0.00 0.00 0.00 4.61
1772 1899 1.837090 GTGTGGAGAAGGTGGGTGT 59.163 57.895 0.00 0.00 0.00 4.16
1773 1900 1.053424 GTGTGGAGAAGGTGGGTGTA 58.947 55.000 0.00 0.00 0.00 2.90
1774 1901 1.002087 GTGTGGAGAAGGTGGGTGTAG 59.998 57.143 0.00 0.00 0.00 2.74
1775 1902 1.132977 TGTGGAGAAGGTGGGTGTAGA 60.133 52.381 0.00 0.00 0.00 2.59
1776 1903 2.188817 GTGGAGAAGGTGGGTGTAGAT 58.811 52.381 0.00 0.00 0.00 1.98
1777 1904 2.572104 GTGGAGAAGGTGGGTGTAGATT 59.428 50.000 0.00 0.00 0.00 2.40
1781 1908 4.099727 GGAGAAGGTGGGTGTAGATTACTC 59.900 50.000 0.00 0.00 0.00 2.59
1905 2032 2.429610 GACCATCCAATGCAAGCAATCT 59.570 45.455 0.00 0.00 0.00 2.40
2093 2220 8.503196 TCACTGTTAACTAAGTGCAACATTATG 58.497 33.333 17.21 0.00 42.88 1.90
2312 2439 1.927895 CTTGGTAGCTAAGAGGTGCG 58.072 55.000 0.00 0.00 0.00 5.34
2472 2599 6.585695 TCGTTACTTCTGTCCTGTAATTCT 57.414 37.500 0.00 0.00 0.00 2.40
2635 2762 6.038271 GTCCACATGTCATAAGTTGTATTCCC 59.962 42.308 0.00 0.00 0.00 3.97
2806 2933 7.434897 GCAACTTGAATCTGTTTCATTGTTACA 59.565 33.333 14.29 0.00 43.73 2.41
2877 3004 4.266976 GGATATGGTCGTTGTTGTACTTCG 59.733 45.833 0.00 0.00 0.00 3.79
2930 3057 6.769134 TTTCTTTTCTTTTTCCTCCGTCTT 57.231 33.333 0.00 0.00 0.00 3.01
3117 3246 3.850752 TCAAAACATGGCTTTCCCCTAA 58.149 40.909 0.00 0.00 0.00 2.69
3301 3431 1.571460 CAACGCTTCAGTGCTGGAC 59.429 57.895 0.00 0.00 0.00 4.02
3351 3481 4.468510 AGTGTCTTATCGTGTTATTGGGGA 59.531 41.667 0.00 0.00 0.00 4.81
3390 3520 2.813061 GCAATTGCATAATCGCTGGTT 58.187 42.857 25.36 0.00 41.59 3.67
3391 3521 3.189285 GCAATTGCATAATCGCTGGTTT 58.811 40.909 25.36 0.00 41.59 3.27
3629 3760 2.502142 AGGATTGACTGCTGCATTGA 57.498 45.000 1.31 0.00 0.00 2.57
3638 3769 4.705991 TGACTGCTGCATTGATATTGGAAA 59.294 37.500 1.31 0.00 0.00 3.13
3696 3827 8.680903 ACATAAGTTGAGCATAAAGAGGAAATG 58.319 33.333 0.00 0.00 0.00 2.32
3968 4100 1.946768 CTCGACCAGGAGAGCTCTAAG 59.053 57.143 18.25 9.35 36.08 2.18
4086 4218 4.829064 TTCCTGGACTGAAAATCAAACG 57.171 40.909 0.00 0.00 0.00 3.60
4189 4321 4.439700 CCCATGATTCTGTTTAGCAGCTTG 60.440 45.833 0.00 0.00 44.66 4.01
4233 4365 7.704899 CGGTCATATATATGCCACGATTTTAGA 59.295 37.037 23.99 3.57 32.81 2.10
4320 4454 6.478512 TGTGTATATGATGTTGCTCTGGTA 57.521 37.500 0.00 0.00 0.00 3.25
4338 4472 7.058023 TCTGGTAGTAAAGTTTACTGCTTCA 57.942 36.000 30.51 23.10 32.04 3.02
4428 4562 5.864418 ATAAATGGCATGTGCTTTGATCT 57.136 34.783 0.00 0.00 41.70 2.75
4455 4589 4.204792 ACTCTCCATCAGGATACATGGA 57.795 45.455 0.00 0.84 44.50 3.41
4540 4674 0.394565 AGAGAACTGACCTGTGGTGC 59.605 55.000 0.00 0.00 35.25 5.01
4565 4699 3.710086 TTCCTTTGGGGTTAGGGTTTT 57.290 42.857 0.00 0.00 36.25 2.43
4594 4728 4.725490 GGGGCAACACATATATAGGTTGT 58.275 43.478 20.82 9.97 42.67 3.32
4626 4761 2.566824 CCACATTGGCCTAAAGCGT 58.433 52.632 3.32 0.00 45.17 5.07
4628 4763 0.171007 CACATTGGCCTAAAGCGTGG 59.829 55.000 3.32 0.00 45.17 4.94
4662 4797 3.055530 AGCACAGAGAAGATACAACCCAG 60.056 47.826 0.00 0.00 0.00 4.45
4678 4827 1.492133 CCAGCACTCCCCCTCAAGAA 61.492 60.000 0.00 0.00 0.00 2.52
4746 4895 0.108585 GTGACAAGGCCACCTCTTCA 59.891 55.000 5.01 0.00 30.89 3.02
4764 4913 0.251916 CAACGCCTCCCCTATTGTCA 59.748 55.000 0.00 0.00 0.00 3.58
4849 4998 1.740380 CGTTGTCTTCCGAGATGCCAT 60.740 52.381 0.00 0.00 33.70 4.40
4853 5002 1.153107 CTTCCGAGATGCCATGCCA 60.153 57.895 0.00 0.00 0.00 4.92
4873 5022 3.519579 CATCTCTAACTGCCACTGTGAG 58.480 50.000 9.86 1.95 0.00 3.51
4894 5043 1.788203 CGTGTCGCAACGATGTTGC 60.788 57.895 21.38 21.38 46.49 4.17
4964 5113 1.405526 GGCTGCGTATTCTGGTTCTCA 60.406 52.381 0.00 0.00 0.00 3.27
5022 5171 8.948401 TCTTGATCAGGAGCTATAGTTCTATT 57.052 34.615 15.24 0.85 0.00 1.73
5092 5241 4.792087 GGTCGACCCTGAAGCAAA 57.208 55.556 24.75 0.00 0.00 3.68
5093 5242 3.249687 GGTCGACCCTGAAGCAAAT 57.750 52.632 24.75 0.00 0.00 2.32
5094 5243 2.396590 GGTCGACCCTGAAGCAAATA 57.603 50.000 24.75 0.00 0.00 1.40
5095 5244 2.007608 GGTCGACCCTGAAGCAAATAC 58.992 52.381 24.75 0.00 0.00 1.89
5096 5245 1.659098 GTCGACCCTGAAGCAAATACG 59.341 52.381 3.51 0.00 0.00 3.06
5097 5246 0.373716 CGACCCTGAAGCAAATACGC 59.626 55.000 0.00 0.00 0.00 4.42
5098 5247 0.733150 GACCCTGAAGCAAATACGCC 59.267 55.000 0.00 0.00 0.00 5.68
5099 5248 0.679960 ACCCTGAAGCAAATACGCCC 60.680 55.000 0.00 0.00 0.00 6.13
5100 5249 0.394352 CCCTGAAGCAAATACGCCCT 60.394 55.000 0.00 0.00 0.00 5.19
5101 5250 1.134220 CCCTGAAGCAAATACGCCCTA 60.134 52.381 0.00 0.00 0.00 3.53
5102 5251 2.213499 CCTGAAGCAAATACGCCCTAG 58.787 52.381 0.00 0.00 0.00 3.02
5103 5252 2.158957 CCTGAAGCAAATACGCCCTAGA 60.159 50.000 0.00 0.00 0.00 2.43
5104 5253 3.126831 CTGAAGCAAATACGCCCTAGAG 58.873 50.000 0.00 0.00 0.00 2.43
5105 5254 2.158957 TGAAGCAAATACGCCCTAGAGG 60.159 50.000 0.00 0.00 39.47 3.69
5121 5270 7.881775 CCCTAGAGGCAATAATAAAGTTGTT 57.118 36.000 0.00 0.00 0.00 2.83
5122 5271 8.974060 CCCTAGAGGCAATAATAAAGTTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
5123 5272 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
286 287 1.512156 CCCGTTTCTTCCCCAACACG 61.512 60.000 0.00 0.00 0.00 4.49
301 302 2.915659 TCGCTCCAGTTCACCCGT 60.916 61.111 0.00 0.00 0.00 5.28
462 463 1.268283 GGGGAGTGAGGAGGAGTTGG 61.268 65.000 0.00 0.00 0.00 3.77
463 464 0.252467 AGGGGAGTGAGGAGGAGTTG 60.252 60.000 0.00 0.00 0.00 3.16
464 465 0.041982 GAGGGGAGTGAGGAGGAGTT 59.958 60.000 0.00 0.00 0.00 3.01
465 466 1.149782 TGAGGGGAGTGAGGAGGAGT 61.150 60.000 0.00 0.00 0.00 3.85
466 467 0.686112 GTGAGGGGAGTGAGGAGGAG 60.686 65.000 0.00 0.00 0.00 3.69
467 468 1.149782 AGTGAGGGGAGTGAGGAGGA 61.150 60.000 0.00 0.00 0.00 3.71
470 471 0.333312 GAGAGTGAGGGGAGTGAGGA 59.667 60.000 0.00 0.00 0.00 3.71
472 473 0.334676 AGGAGAGTGAGGGGAGTGAG 59.665 60.000 0.00 0.00 0.00 3.51
476 477 1.454847 CCGAGGAGAGTGAGGGGAG 60.455 68.421 0.00 0.00 0.00 4.30
477 478 2.684104 CCGAGGAGAGTGAGGGGA 59.316 66.667 0.00 0.00 0.00 4.81
479 480 2.043450 AGCCGAGGAGAGTGAGGG 60.043 66.667 0.00 0.00 0.00 4.30
484 485 2.757917 GAGCCAGCCGAGGAGAGT 60.758 66.667 0.00 0.00 0.00 3.24
485 486 3.535962 GGAGCCAGCCGAGGAGAG 61.536 72.222 0.00 0.00 0.00 3.20
546 550 4.593864 GCCGGTCCATCTCCTCGC 62.594 72.222 1.90 0.00 0.00 5.03
764 777 2.743928 CTCACTCAACTGGCGCCC 60.744 66.667 26.77 6.44 0.00 6.13
974 987 3.080121 CTCCTGCGCTCCTTCCCT 61.080 66.667 9.73 0.00 0.00 4.20
976 989 2.498726 CTCTCCTGCGCTCCTTCC 59.501 66.667 9.73 0.00 0.00 3.46
1057 1070 1.304217 AGAAGAGGAAGACGCCCGA 60.304 57.895 0.00 0.00 0.00 5.14
1210 1228 2.791560 CACGAAGCGGAGATGAACATAG 59.208 50.000 0.00 0.00 0.00 2.23
1229 1247 2.328099 CCGGCCTTCAGTGAAGCAC 61.328 63.158 24.85 18.45 38.24 4.40
1248 1266 1.018226 GCGTCATGAAGCAGCTCACT 61.018 55.000 25.91 0.00 35.86 3.41
1281 1299 1.052124 AACCTCCACAACCGACTGGA 61.052 55.000 0.00 0.00 39.21 3.86
1296 1314 2.906897 CCGCAACAGCCACAACCT 60.907 61.111 0.00 0.00 0.00 3.50
1297 1315 3.216292 ACCGCAACAGCCACAACC 61.216 61.111 0.00 0.00 0.00 3.77
1298 1316 2.026014 CACCGCAACAGCCACAAC 59.974 61.111 0.00 0.00 0.00 3.32
1299 1317 3.215568 CCACCGCAACAGCCACAA 61.216 61.111 0.00 0.00 0.00 3.33
1300 1318 2.610532 TAACCACCGCAACAGCCACA 62.611 55.000 0.00 0.00 0.00 4.17
1301 1319 1.852067 CTAACCACCGCAACAGCCAC 61.852 60.000 0.00 0.00 0.00 5.01
1302 1320 1.599518 CTAACCACCGCAACAGCCA 60.600 57.895 0.00 0.00 0.00 4.75
1303 1321 2.978018 GCTAACCACCGCAACAGCC 61.978 63.158 0.00 0.00 0.00 4.85
1304 1322 2.561373 GCTAACCACCGCAACAGC 59.439 61.111 0.00 0.00 0.00 4.40
1346 1364 4.417437 ACATACTACCACAGAGAACCACT 58.583 43.478 0.00 0.00 0.00 4.00
1347 1365 4.803098 ACATACTACCACAGAGAACCAC 57.197 45.455 0.00 0.00 0.00 4.16
1348 1366 4.222145 GGAACATACTACCACAGAGAACCA 59.778 45.833 0.00 0.00 0.00 3.67
1349 1367 4.222145 TGGAACATACTACCACAGAGAACC 59.778 45.833 0.00 0.00 0.00 3.62
1350 1368 5.401531 TGGAACATACTACCACAGAGAAC 57.598 43.478 0.00 0.00 0.00 3.01
1359 1377 4.184629 CAGAGCACTTGGAACATACTACC 58.815 47.826 0.00 0.00 39.30 3.18
1569 1686 7.257003 CAAGGCATTAATACAACATGCTGTAA 58.743 34.615 12.70 0.00 42.55 2.41
1710 1837 5.934781 ACTCTCACCAAATCAGAACTTTCT 58.065 37.500 0.00 0.00 38.25 2.52
1746 1873 1.081892 CCTTCTCCACACGCATTCAG 58.918 55.000 0.00 0.00 0.00 3.02
1767 1894 7.108841 TGATACAGTTGAGTAATCTACACCC 57.891 40.000 7.47 0.00 0.00 4.61
1768 1895 7.702772 CACTGATACAGTTGAGTAATCTACACC 59.297 40.741 7.47 0.00 42.59 4.16
1769 1896 8.244802 ACACTGATACAGTTGAGTAATCTACAC 58.755 37.037 7.47 0.00 42.59 2.90
1770 1897 8.349568 ACACTGATACAGTTGAGTAATCTACA 57.650 34.615 7.47 0.00 42.59 2.74
1771 1898 9.291664 GAACACTGATACAGTTGAGTAATCTAC 57.708 37.037 1.46 0.00 42.59 2.59
1772 1899 8.467598 GGAACACTGATACAGTTGAGTAATCTA 58.532 37.037 1.46 0.00 42.59 1.98
1773 1900 7.039011 TGGAACACTGATACAGTTGAGTAATCT 60.039 37.037 1.46 0.00 42.59 2.40
1774 1901 7.097192 TGGAACACTGATACAGTTGAGTAATC 58.903 38.462 1.46 0.00 42.59 1.75
1775 1902 7.004555 TGGAACACTGATACAGTTGAGTAAT 57.995 36.000 1.46 0.00 42.59 1.89
1776 1903 6.413783 TGGAACACTGATACAGTTGAGTAA 57.586 37.500 1.46 0.00 42.59 2.24
1777 1904 6.413783 TTGGAACACTGATACAGTTGAGTA 57.586 37.500 1.46 0.00 42.59 2.59
1905 2032 7.168219 GGCTTCTTCCATACAATATATGTCCA 58.832 38.462 0.00 0.00 42.70 4.02
2246 2373 9.937175 CAGCTACAACTATAATAAAAAGAAGCC 57.063 33.333 0.00 0.00 0.00 4.35
2312 2439 3.119352 GCCTGGTTCATTTGATGAGTTCC 60.119 47.826 0.00 0.00 40.94 3.62
2472 2599 7.762588 CCTTCGGAGGAGAGATTAATTAGTA 57.237 40.000 2.45 0.00 46.74 1.82
2877 3004 1.589968 GCGATGAAAACAGCGATCGAC 60.590 52.381 21.57 10.46 40.06 4.20
2930 3057 4.162131 TCATACAAGACTGAAGCTATGCCA 59.838 41.667 0.00 0.00 0.00 4.92
3117 3246 7.826690 AGACAAAACAAAGAACCGCATATAAT 58.173 30.769 0.00 0.00 0.00 1.28
3351 3481 4.497291 TGCATACGGGTCCTAAGATTTT 57.503 40.909 0.00 0.00 0.00 1.82
3390 3520 8.355169 GCAATCATATATGCTCAAGGAAAGAAA 58.645 33.333 7.92 0.00 39.46 2.52
3391 3521 7.879070 GCAATCATATATGCTCAAGGAAAGAA 58.121 34.615 7.92 0.00 39.46 2.52
3595 3726 0.473755 ATCCTATCACCGCCAATGCA 59.526 50.000 0.00 0.00 37.32 3.96
3629 3760 4.837093 TTCCTGTCCGACTTTCCAATAT 57.163 40.909 0.00 0.00 0.00 1.28
3638 3769 2.108970 GATACCCTTTCCTGTCCGACT 58.891 52.381 0.00 0.00 0.00 4.18
3968 4100 3.010420 GGTTGGATCCAGCAAGTAAGAC 58.990 50.000 27.45 13.86 0.00 3.01
4189 4321 1.336125 CCGGTGGATCGAACTACTACC 59.664 57.143 8.98 8.07 33.02 3.18
4233 4365 5.830799 AAAGAAAATTCAAGGGAGCCAAT 57.169 34.783 0.00 0.00 0.00 3.16
4235 4367 4.743348 GCAAAAGAAAATTCAAGGGAGCCA 60.743 41.667 0.00 0.00 0.00 4.75
4320 4454 9.869757 AACAAAAATGAAGCAGTAAACTTTACT 57.130 25.926 8.19 8.19 0.00 2.24
4428 4562 3.037851 ATCCTGATGGAGAGTACTGCA 57.962 47.619 0.00 0.00 46.91 4.41
4540 4674 3.268595 ACCCTAACCCCAAAGGAATACAG 59.731 47.826 0.00 0.00 39.89 2.74
4594 4728 0.411452 ATGTGGCCCATGTAACCCAA 59.589 50.000 0.00 0.00 30.69 4.12
4626 4761 0.251634 TGTGCTTCAGTGTGTGTCCA 59.748 50.000 0.00 0.00 0.00 4.02
4628 4763 1.863454 CTCTGTGCTTCAGTGTGTGTC 59.137 52.381 8.75 0.00 43.97 3.67
4662 4797 1.201429 TCCTTCTTGAGGGGGAGTGC 61.201 60.000 0.00 0.00 46.31 4.40
4687 4836 8.654094 TGTGACAAGATGGACATGATAGATATT 58.346 33.333 0.00 0.00 0.00 1.28
4723 4872 0.179018 GAGGTGGCCTTGTCACAAGT 60.179 55.000 16.50 0.00 40.26 3.16
4746 4895 0.541863 CTGACAATAGGGGAGGCGTT 59.458 55.000 0.00 0.00 0.00 4.84
4789 4938 2.033141 GCCAGCAGCAGAGGAACA 59.967 61.111 0.00 0.00 42.97 3.18
4853 5002 3.435275 TCTCACAGTGGCAGTTAGAGAT 58.565 45.455 15.76 0.00 0.00 2.75
4860 5009 2.341543 CGCTCTCACAGTGGCAGT 59.658 61.111 0.00 0.00 0.00 4.40
4894 5043 4.711949 ACCTGCCTTGCCAGAGCG 62.712 66.667 0.00 0.00 44.31 5.03
4964 5113 2.046507 CGCTCAGGGCAGCTTTCT 60.047 61.111 0.00 0.00 41.91 2.52
5084 5233 2.158957 CCTCTAGGGCGTATTTGCTTCA 60.159 50.000 0.00 0.00 34.52 3.02
5085 5234 2.484889 CCTCTAGGGCGTATTTGCTTC 58.515 52.381 0.00 0.00 34.52 3.86
5086 5235 2.622064 CCTCTAGGGCGTATTTGCTT 57.378 50.000 0.00 0.00 34.52 3.91
5097 5246 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53


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

AutoCloner maintained by Alex Coulton.