Multiple sequence alignment - TraesCS6B01G066200

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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 TraesCS6B01G066200 chr6B 100.000 5577 0 0 1 5577 44099332 44104908 0.000000e+00 10299
1 TraesCS6B01G066200 chr6B 87.598 2435 276 22 705 3130 43281515 43283932 0.000000e+00 2800
2 TraesCS6B01G066200 chr6B 86.171 2625 305 32 665 3238 43348134 43350751 0.000000e+00 2784
3 TraesCS6B01G066200 chr6B 86.787 2437 290 18 811 3231 43498549 43500969 0.000000e+00 2687
4 TraesCS6B01G066200 chr6B 84.020 1189 175 14 3299 4485 43284279 43285454 0.000000e+00 1129
5 TraesCS6B01G066200 chr6B 82.589 1321 184 33 3299 4596 43350861 43352158 0.000000e+00 1123
6 TraesCS6B01G066200 chr6B 81.176 1275 184 29 3338 4596 43501165 43502399 0.000000e+00 974
7 TraesCS6B01G066200 chrUn 96.446 3095 98 6 1 3085 94817185 94820277 0.000000e+00 5096
8 TraesCS6B01G066200 chrUn 87.454 2455 282 21 705 3147 94047292 94049732 0.000000e+00 2804
9 TraesCS6B01G066200 chrUn 86.418 2599 301 28 665 3220 94179272 94181861 0.000000e+00 2796
10 TraesCS6B01G066200 chrUn 85.659 2587 330 26 665 3231 94220638 94223203 0.000000e+00 2684
11 TraesCS6B01G066200 chrUn 88.358 1529 94 31 4034 5544 94821198 94822660 0.000000e+00 1760
12 TraesCS6B01G066200 chrUn 93.242 873 39 10 3174 4035 94820294 94821157 0.000000e+00 1267
13 TraesCS6B01G066200 chrUn 82.213 1383 189 37 3248 4596 94182032 94183391 0.000000e+00 1138
14 TraesCS6B01G066200 chrUn 88.489 695 69 10 3299 3991 94049935 94050620 0.000000e+00 830
15 TraesCS6B01G066200 chrUn 79.719 498 83 10 4114 4596 94224298 94224792 1.490000e-90 344
16 TraesCS6B01G066200 chr6A 96.391 2189 73 2 902 3085 25631471 25633658 0.000000e+00 3600
17 TraesCS6B01G066200 chr6A 86.506 2616 299 26 665 3238 24853461 24856064 0.000000e+00 2826
18 TraesCS6B01G066200 chr6A 87.393 2451 281 17 705 3147 24838501 24840931 0.000000e+00 2789
19 TraesCS6B01G066200 chr6A 85.819 2588 325 25 665 3231 25017653 25020219 0.000000e+00 2708
20 TraesCS6B01G066200 chr6A 89.340 985 69 15 4032 5003 25634577 25635538 0.000000e+00 1205
21 TraesCS6B01G066200 chr6A 84.255 1194 171 17 3295 4485 24841115 24842294 0.000000e+00 1147
22 TraesCS6B01G066200 chr6A 82.174 1380 194 34 3248 4596 24856113 24857471 0.000000e+00 1138
23 TraesCS6B01G066200 chr6A 89.827 865 51 15 3174 4035 25633667 25634497 0.000000e+00 1075
24 TraesCS6B01G066200 chr6A 82.195 1157 162 30 3338 4488 25020455 25021573 0.000000e+00 955
25 TraesCS6B01G066200 chr6A 89.851 739 45 10 1 733 25630757 25631471 0.000000e+00 922
26 TraesCS6B01G066200 chr6A 90.521 211 10 3 5340 5550 25635965 25636165 2.560000e-68 270
27 TraesCS6B01G066200 chr7B 91.241 685 37 11 4667 5345 225821326 225821993 0.000000e+00 911
28 TraesCS6B01G066200 chr2D 91.228 684 39 8 4667 5345 583715294 583714627 0.000000e+00 911


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 TraesCS6B01G066200 chr6B 44099332 44104908 5576 False 10299.000000 10299 100.0000 1 5577 1 chr6B.!!$F1 5576
1 TraesCS6B01G066200 chr6B 43281515 43285454 3939 False 1964.500000 2800 85.8090 705 4485 2 chr6B.!!$F2 3780
2 TraesCS6B01G066200 chr6B 43348134 43352158 4024 False 1953.500000 2784 84.3800 665 4596 2 chr6B.!!$F3 3931
3 TraesCS6B01G066200 chr6B 43498549 43502399 3850 False 1830.500000 2687 83.9815 811 4596 2 chr6B.!!$F4 3785
4 TraesCS6B01G066200 chrUn 94817185 94822660 5475 False 2707.666667 5096 92.6820 1 5544 3 chrUn.!!$F4 5543
5 TraesCS6B01G066200 chrUn 94179272 94183391 4119 False 1967.000000 2796 84.3155 665 4596 2 chrUn.!!$F2 3931
6 TraesCS6B01G066200 chrUn 94047292 94050620 3328 False 1817.000000 2804 87.9715 705 3991 2 chrUn.!!$F1 3286
7 TraesCS6B01G066200 chrUn 94220638 94224792 4154 False 1514.000000 2684 82.6890 665 4596 2 chrUn.!!$F3 3931
8 TraesCS6B01G066200 chr6A 24853461 24857471 4010 False 1982.000000 2826 84.3400 665 4596 2 chr6A.!!$F2 3931
9 TraesCS6B01G066200 chr6A 24838501 24842294 3793 False 1968.000000 2789 85.8240 705 4485 2 chr6A.!!$F1 3780
10 TraesCS6B01G066200 chr6A 25017653 25021573 3920 False 1831.500000 2708 84.0070 665 4488 2 chr6A.!!$F3 3823
11 TraesCS6B01G066200 chr6A 25630757 25636165 5408 False 1414.400000 3600 91.1860 1 5550 5 chr6A.!!$F4 5549
12 TraesCS6B01G066200 chr7B 225821326 225821993 667 False 911.000000 911 91.2410 4667 5345 1 chr7B.!!$F1 678
13 TraesCS6B01G066200 chr2D 583714627 583715294 667 True 911.000000 911 91.2280 4667 5345 1 chr2D.!!$R1 678

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
68 69 0.758734 CTGATCTCCCGGTATTGGCA 59.241 55.000 0.00 0.00 0.00 4.92 F
1004 1038 0.893727 ACCGTTTGAGGGACAATGGC 60.894 55.000 0.00 0.00 37.68 4.40 F
1036 1070 2.082231 CCATGCTGTTGGTTCTCTCTG 58.918 52.381 0.00 0.00 31.74 3.35 F
2257 2302 1.659794 GTCTGGGCACGTGCAATTT 59.340 52.632 38.60 0.00 44.36 1.82 F
3211 3298 0.813184 CACACCCACATGAAGCATCC 59.187 55.000 0.00 0.00 0.00 3.51 F
3896 4268 0.901827 TAGCCGGCTCAGATTTCACA 59.098 50.000 36.73 8.49 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1036 1070 1.475213 GCCATTAGGGTACAGGAGCAC 60.475 57.143 0.00 0.0 39.65 4.40 R
2257 2302 1.351076 TGAGGTCACCTGAAGCATCA 58.649 50.000 0.00 0.0 31.76 3.07 R
2355 2400 1.374758 GGAGGGACAGTTGACAGCG 60.375 63.158 0.00 0.0 0.00 5.18 R
3575 3947 0.317160 TCGCGGTATAGCTGGATTGG 59.683 55.000 6.13 0.0 34.40 3.16 R
4183 4803 0.459237 CTGACAGTGACAGGATCGCC 60.459 60.000 13.93 0.0 38.75 5.54 R
4860 5503 0.994247 TGCTCACATCCATTCAGGGT 59.006 50.000 0.00 0.0 38.24 4.34 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
38 39 1.926426 ATTGACCCCCTACTGGCTGC 61.926 60.000 0.00 0.00 0.00 5.25
63 64 1.063190 TGTGGACTGATCTCCCGGTAT 60.063 52.381 0.00 0.00 0.00 2.73
68 69 0.758734 CTGATCTCCCGGTATTGGCA 59.241 55.000 0.00 0.00 0.00 4.92
121 122 1.897133 TCTTAGCCCGCTCACAAAGTA 59.103 47.619 0.00 0.00 0.00 2.24
124 125 2.200373 AGCCCGCTCACAAAGTATTT 57.800 45.000 0.00 0.00 40.26 1.40
149 150 2.906389 TGATTGCCTCCTTACTGTGTCT 59.094 45.455 0.00 0.00 0.00 3.41
157 158 2.449031 CTTACTGTGTCTGCCGGCCA 62.449 60.000 26.77 12.55 0.00 5.36
187 188 5.050295 CCTTTGAGTTCTTCAGTCCGTTTAC 60.050 44.000 0.00 0.00 37.07 2.01
189 190 3.385433 TGAGTTCTTCAGTCCGTTTACCA 59.615 43.478 0.00 0.00 0.00 3.25
249 250 2.158608 AGCTGGTTTGGTACTTTGCTCT 60.159 45.455 0.00 0.00 0.00 4.09
407 418 4.818534 ATACGCTGCATAATCCAAAGTG 57.181 40.909 0.00 0.00 0.00 3.16
454 465 5.125257 TGTGCAAACTGAAATCTGTTGAGAA 59.875 36.000 6.47 0.00 37.92 2.87
503 514 7.180051 TGGCTTTTAATTCAAGGACCATAATGT 59.820 33.333 0.00 0.00 0.00 2.71
534 545 6.128172 GGTTTTCTTGGATGAGTGTATGTGAG 60.128 42.308 0.00 0.00 0.00 3.51
599 610 6.963083 TCTTCTTCCTAGGAGCAGTATAAC 57.037 41.667 12.26 0.00 0.00 1.89
636 647 2.533942 GCACAAACCGAAATGTTGTGTC 59.466 45.455 15.01 6.18 33.60 3.67
641 652 1.002900 ACCGAAATGTTGTGTCGCTTG 60.003 47.619 0.00 0.00 33.46 4.01
831 855 4.229876 GTTTGTACTGAGGCTTCAAATGC 58.770 43.478 0.00 0.00 31.69 3.56
838 862 2.224744 TGAGGCTTCAAATGCTGGTACA 60.225 45.455 0.00 0.00 0.00 2.90
884 909 8.677148 TTTAGGGAATACAAGAACTATGCATC 57.323 34.615 0.19 0.00 0.00 3.91
885 910 5.625150 AGGGAATACAAGAACTATGCATCC 58.375 41.667 0.19 0.00 0.00 3.51
952 985 7.234355 GGGATCCCAACTCATTAATAATCTGT 58.766 38.462 26.95 0.00 35.81 3.41
1004 1038 0.893727 ACCGTTTGAGGGACAATGGC 60.894 55.000 0.00 0.00 37.68 4.40
1036 1070 2.082231 CCATGCTGTTGGTTCTCTCTG 58.918 52.381 0.00 0.00 31.74 3.35
1831 1876 3.713826 AACCGACTAAACATGATGGGT 57.286 42.857 0.00 0.00 0.00 4.51
1963 2008 5.690097 GCCACATATCCCCAACTCAAAGATA 60.690 44.000 0.00 0.00 0.00 1.98
1966 2011 7.341769 CCACATATCCCCAACTCAAAGATAAAA 59.658 37.037 0.00 0.00 0.00 1.52
2026 2071 6.377429 AGAAGTACAACCATAGTGATCTTCGA 59.623 38.462 0.00 0.00 35.45 3.71
2089 2134 3.859414 GCTCGGGCTCTGGATGCT 61.859 66.667 0.00 0.00 35.22 3.79
2122 2167 2.912956 TGGTGGTAGCATTTCCTTCTCT 59.087 45.455 0.00 0.00 0.00 3.10
2257 2302 1.659794 GTCTGGGCACGTGCAATTT 59.340 52.632 38.60 0.00 44.36 1.82
2287 2332 1.673168 GTGACCTCATTCATCCTGCC 58.327 55.000 0.00 0.00 0.00 4.85
2308 2353 6.524734 TGCCTATGAGATCATAAACGTCATT 58.475 36.000 4.23 0.00 38.26 2.57
2355 2400 5.705609 TTTTGGTCAAACTATTCTGGCTC 57.294 39.130 0.00 0.00 0.00 4.70
2710 2755 6.624423 ACAGATGGTTGAATCAAATGTAAGC 58.376 36.000 0.00 0.00 0.00 3.09
2713 2758 8.407832 CAGATGGTTGAATCAAATGTAAGCATA 58.592 33.333 0.00 0.00 38.93 3.14
2764 2838 2.519771 TCATACCGTACTGACCAGGT 57.480 50.000 0.00 0.00 40.52 4.00
3085 3164 2.623416 GAGCTTACCTGCACCTTTTGTT 59.377 45.455 0.00 0.00 34.99 2.83
3101 3183 8.237267 CACCTTTTGTTTCATCTTCCTGTATAC 58.763 37.037 0.00 0.00 0.00 1.47
3107 3189 7.458397 TGTTTCATCTTCCTGTATACCAGTTT 58.542 34.615 0.00 0.00 39.74 2.66
3130 3216 8.328146 GTTTTGTTTTCTTAGAAATGTCAAGGC 58.672 33.333 8.31 7.60 0.00 4.35
3132 3218 5.154222 GTTTTCTTAGAAATGTCAAGGCCG 58.846 41.667 8.31 0.00 0.00 6.13
3133 3219 2.985896 TCTTAGAAATGTCAAGGCCGG 58.014 47.619 0.00 0.00 0.00 6.13
3147 3233 0.818040 GGCCGGAACAAGTCTTGTGT 60.818 55.000 18.84 9.18 44.59 3.72
3150 3236 2.032290 GCCGGAACAAGTCTTGTGTAAC 60.032 50.000 18.84 10.48 44.59 2.50
3211 3298 0.813184 CACACCCACATGAAGCATCC 59.187 55.000 0.00 0.00 0.00 3.51
3221 3308 5.278315 CCACATGAAGCATCCAGTGATTATG 60.278 44.000 0.00 0.00 36.38 1.90
3265 3589 8.542080 TGGTGTGAGATATATATGATGCATTGA 58.458 33.333 0.00 0.00 0.00 2.57
3575 3947 5.049167 TGGCTGTTTGTTGTTTTGATCATC 58.951 37.500 0.00 0.00 0.00 2.92
3809 4181 1.071314 TTGGCCCCAAGAAAGGAGGA 61.071 55.000 0.00 0.00 0.00 3.71
3896 4268 0.901827 TAGCCGGCTCAGATTTCACA 59.098 50.000 36.73 8.49 0.00 3.58
3995 4529 7.527084 TTTTGGTGTTAAAAATCCTGAAACG 57.473 32.000 0.00 0.00 0.00 3.60
4036 4652 9.534565 CAATAGTTGTGTATGCTGTCTAGTATT 57.465 33.333 0.00 0.00 31.37 1.89
4040 4656 8.696374 AGTTGTGTATGCTGTCTAGTATTATGT 58.304 33.333 0.00 0.00 31.37 2.29
4041 4657 9.961265 GTTGTGTATGCTGTCTAGTATTATGTA 57.039 33.333 0.00 0.00 31.37 2.29
4089 4708 8.164070 ACTGGTGAAATCTAAAATCTACACCTT 58.836 33.333 0.00 0.00 44.34 3.50
4183 4803 2.022129 GCAAGTGGACCTGTCGACG 61.022 63.158 11.62 5.76 42.14 5.12
4297 4917 1.738099 CAACTCGAACCAGCTCCGG 60.738 63.158 0.00 0.00 0.00 5.14
4388 5008 0.315625 CATCATGCTGCGCAAGTACG 60.316 55.000 13.05 0.00 43.62 3.67
4544 5173 3.751018 TAGAGAGGCCGGCCAGGA 61.751 66.667 45.13 23.49 45.00 3.86
4599 5234 7.484035 AGTTCTTGTGTACAAAAGCTAAGAG 57.516 36.000 19.40 0.00 35.15 2.85
4656 5298 0.901580 TTCTTCGGGTCGGCTTACCT 60.902 55.000 7.76 0.00 39.65 3.08
4749 5391 3.715628 GGCAACTGGGCAATTGTATAG 57.284 47.619 7.40 5.49 42.77 1.31
4753 5395 4.640201 GCAACTGGGCAATTGTATAGAAGA 59.360 41.667 7.40 0.00 0.00 2.87
4757 5399 5.824624 ACTGGGCAATTGTATAGAAGATGTG 59.175 40.000 7.40 0.00 0.00 3.21
4780 5422 3.118075 TCTTGTCCTTGATGGTGTTGTGA 60.118 43.478 0.00 0.00 37.07 3.58
4820 5463 4.218635 TGTGTTTGTGTGAGTGCCTTTTTA 59.781 37.500 0.00 0.00 0.00 1.52
4840 5483 8.450578 TTTTTATCTTCAGAGTTTCTCTTGCA 57.549 30.769 0.00 0.00 38.99 4.08
4841 5484 8.627208 TTTTATCTTCAGAGTTTCTCTTGCAT 57.373 30.769 0.00 0.00 38.99 3.96
4900 5547 6.841601 AGCAGGCAGGTCTATCATTTAATTA 58.158 36.000 0.00 0.00 0.00 1.40
4902 5549 7.946776 AGCAGGCAGGTCTATCATTTAATTATT 59.053 33.333 0.00 0.00 0.00 1.40
4948 5596 6.455360 TGAACTTCTGCATCCCAATATTTC 57.545 37.500 0.00 0.00 0.00 2.17
4955 5603 7.664552 TCTGCATCCCAATATTTCTTTGATT 57.335 32.000 0.00 0.00 0.00 2.57
5106 5770 5.375956 TCCAGAATAGGAGTATAGGACAGGT 59.624 44.000 0.00 0.00 32.77 4.00
5107 5771 6.565314 TCCAGAATAGGAGTATAGGACAGGTA 59.435 42.308 0.00 0.00 32.77 3.08
5108 5772 6.660094 CCAGAATAGGAGTATAGGACAGGTAC 59.340 46.154 0.00 0.00 0.00 3.34
5126 5790 3.995048 GGTACTAGCTTGTCTTGAACACC 59.005 47.826 3.45 1.17 37.70 4.16
5265 6103 2.588620 AGGGAAAATAAACACCGCACA 58.411 42.857 0.00 0.00 0.00 4.57
5355 6193 9.169592 TGTAACAGGAGTAATAAACAATAAGGC 57.830 33.333 0.00 0.00 0.00 4.35
5383 6221 7.754091 AAATGGGGAAAATGGAATATTCTGT 57.246 32.000 14.95 1.79 0.00 3.41
5475 6313 0.620410 TTCCGACCCACCATCATCCT 60.620 55.000 0.00 0.00 0.00 3.24
5477 6315 0.179045 CCGACCCACCATCATCCTTC 60.179 60.000 0.00 0.00 0.00 3.46
5478 6316 0.179045 CGACCCACCATCATCCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
5479 6317 0.179045 GACCCACCATCATCCTTCCG 60.179 60.000 0.00 0.00 0.00 4.30
5480 6318 1.149174 CCCACCATCATCCTTCCGG 59.851 63.158 0.00 0.00 0.00 5.14
5481 6319 1.526917 CCACCATCATCCTTCCGGC 60.527 63.158 0.00 0.00 0.00 6.13
5544 6382 0.038310 CCTTCCAGAACCTTCCACCC 59.962 60.000 0.00 0.00 0.00 4.61
5568 6406 4.048470 GCCCCACCCTCAACCCTC 62.048 72.222 0.00 0.00 0.00 4.30
5569 6407 3.339093 CCCCACCCTCAACCCTCC 61.339 72.222 0.00 0.00 0.00 4.30
5570 6408 2.204151 CCCACCCTCAACCCTCCT 60.204 66.667 0.00 0.00 0.00 3.69
5571 6409 2.301738 CCCACCCTCAACCCTCCTC 61.302 68.421 0.00 0.00 0.00 3.71
5572 6410 2.301738 CCACCCTCAACCCTCCTCC 61.302 68.421 0.00 0.00 0.00 4.30
5573 6411 2.284699 ACCCTCAACCCTCCTCCG 60.285 66.667 0.00 0.00 0.00 4.63
5574 6412 3.787001 CCCTCAACCCTCCTCCGC 61.787 72.222 0.00 0.00 0.00 5.54
5575 6413 2.685380 CCTCAACCCTCCTCCGCT 60.685 66.667 0.00 0.00 0.00 5.52
5576 6414 2.726351 CCTCAACCCTCCTCCGCTC 61.726 68.421 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.142748 GAGATCAGTCCACAGGCCG 59.857 63.158 0.00 0.00 0.00 6.13
49 50 0.758734 TGCCAATACCGGGAGATCAG 59.241 55.000 6.32 0.00 0.00 2.90
63 64 2.132996 CAACAACCAGGGCTGCCAA 61.133 57.895 22.05 0.00 0.00 4.52
68 69 0.540365 CCATCACAACAACCAGGGCT 60.540 55.000 0.00 0.00 0.00 5.19
109 110 2.483877 TCAGCCAAATACTTTGTGAGCG 59.516 45.455 0.00 0.00 38.98 5.03
157 158 3.970640 ACTGAAGAACTCAAAGGAGACCT 59.029 43.478 0.00 0.00 44.26 3.85
187 188 7.254319 GCATTTCATTCATTTAGCAACTGATGG 60.254 37.037 0.00 0.00 0.00 3.51
189 190 7.491372 CAGCATTTCATTCATTTAGCAACTGAT 59.509 33.333 0.00 0.00 0.00 2.90
249 250 0.393402 CACTGCCTAAGATGCCAGCA 60.393 55.000 0.00 0.00 0.00 4.41
391 402 4.380867 GGGAACACACTTTGGATTATGCAG 60.381 45.833 0.00 0.00 0.00 4.41
407 418 3.313526 CACTATTGCTATGCAGGGAACAC 59.686 47.826 0.00 0.00 40.61 3.32
526 537 4.439305 TCCAGCATTTTTGCTCACATAC 57.561 40.909 0.00 0.00 44.30 2.39
570 581 4.219115 TGCTCCTAGGAAGAAGATACAGG 58.781 47.826 13.77 0.00 0.00 4.00
599 610 2.296792 TGTGCCATTGATGTTATCCGG 58.703 47.619 0.00 0.00 0.00 5.14
636 647 3.492421 ACAATCCATTTGTAGCAAGCG 57.508 42.857 0.00 0.00 46.75 4.68
814 837 2.040278 ACCAGCATTTGAAGCCTCAGTA 59.960 45.455 0.00 0.00 31.69 2.74
831 855 5.185249 ACATAGTTGGTGTAGACTGTACCAG 59.815 44.000 11.15 4.54 44.56 4.00
838 862 8.529476 CCTAAAGTAACATAGTTGGTGTAGACT 58.471 37.037 0.00 0.00 31.14 3.24
884 909 5.176406 CAGAGCAGATGTTATTGTGATACGG 59.824 44.000 0.00 0.00 0.00 4.02
885 910 5.750547 ACAGAGCAGATGTTATTGTGATACG 59.249 40.000 0.00 0.00 0.00 3.06
952 985 5.680619 ACTGGATGGTTATTCGCATCTTAA 58.319 37.500 0.00 0.00 0.00 1.85
967 1001 1.098050 GTGCAAAGGCTACTGGATGG 58.902 55.000 0.00 0.00 41.91 3.51
1004 1038 2.292267 ACAGCATGGGAAAAGCTATCG 58.708 47.619 0.00 0.00 43.62 2.92
1036 1070 1.475213 GCCATTAGGGTACAGGAGCAC 60.475 57.143 0.00 0.00 39.65 4.40
1315 1358 6.313658 CGATATCATTGTCACAACTCCAGAAA 59.686 38.462 3.12 0.00 0.00 2.52
1831 1876 5.476599 GGTTGCAATCCATACATAGCCATTA 59.523 40.000 0.59 0.00 0.00 1.90
1963 2008 8.477419 TCCACTTGGAGATCAAATTACTTTTT 57.523 30.769 0.00 0.00 39.78 1.94
2089 2134 3.055458 TGCTACCACCATCATCGAAGAAA 60.055 43.478 0.00 0.00 43.58 2.52
2257 2302 1.351076 TGAGGTCACCTGAAGCATCA 58.649 50.000 0.00 0.00 31.76 3.07
2287 2332 8.593492 TTCCAATGACGTTTATGATCTCATAG 57.407 34.615 0.00 0.00 39.69 2.23
2308 2353 2.051518 GGTCCGCATGCCATTTCCA 61.052 57.895 13.15 0.00 0.00 3.53
2355 2400 1.374758 GGAGGGACAGTTGACAGCG 60.375 63.158 0.00 0.00 0.00 5.18
2383 2428 6.260663 AGAAGTATTTGGGGGCTTTGAATAA 58.739 36.000 0.00 0.00 0.00 1.40
2764 2838 6.653020 TCAAGCTCCTGCAGAATAAGATAAA 58.347 36.000 17.39 0.00 42.74 1.40
3042 3121 6.823689 GCTCCTCACCAGAAAATAGTTATCAA 59.176 38.462 0.00 0.00 0.00 2.57
3061 3140 4.943822 GGTGCAGGTAAGCTCCTC 57.056 61.111 0.00 0.00 43.11 3.71
3101 3183 8.925161 TGACATTTCTAAGAAAACAAAACTGG 57.075 30.769 0.00 0.00 0.00 4.00
3107 3189 6.512297 GGCCTTGACATTTCTAAGAAAACAA 58.488 36.000 0.00 0.00 0.00 2.83
3130 3216 3.199677 TGTTACACAAGACTTGTTCCGG 58.800 45.455 18.27 9.67 43.23 5.14
3132 3218 5.751243 ACATGTTACACAAGACTTGTTCC 57.249 39.130 18.27 7.13 43.23 3.62
3133 3219 7.247728 TGAAACATGTTACACAAGACTTGTTC 58.752 34.615 18.27 9.72 43.23 3.18
3147 3233 5.335583 GGTGCTTGCTGTATGAAACATGTTA 60.336 40.000 12.39 0.00 37.50 2.41
3150 3236 3.192001 AGGTGCTTGCTGTATGAAACATG 59.808 43.478 0.00 0.00 37.50 3.21
3156 3243 4.253685 GTTCTAAGGTGCTTGCTGTATGA 58.746 43.478 0.00 0.00 0.00 2.15
3462 3828 4.788679 TCATGAGCCATGTGAATCAGAAT 58.211 39.130 12.89 0.00 41.98 2.40
3469 3835 5.655090 AGATGAAAATCATGAGCCATGTGAA 59.345 36.000 0.09 0.00 41.98 3.18
3470 3836 5.067283 CAGATGAAAATCATGAGCCATGTGA 59.933 40.000 15.25 0.00 41.98 3.58
3575 3947 0.317160 TCGCGGTATAGCTGGATTGG 59.683 55.000 6.13 0.00 34.40 3.16
3809 4181 1.206132 TCGTCAACGATGGCCATAACT 59.794 47.619 20.84 2.20 44.22 2.24
3875 4247 1.134670 GTGAAATCTGAGCCGGCTACT 60.135 52.381 32.97 7.99 0.00 2.57
3896 4268 0.324091 CAAAGCCCCATCCTCTGCTT 60.324 55.000 0.00 0.00 45.40 3.91
3985 4519 6.017357 GGAAGTTAAAACTGTCGTTTCAGGAT 60.017 38.462 0.00 0.00 42.28 3.24
3986 4520 5.295045 GGAAGTTAAAACTGTCGTTTCAGGA 59.705 40.000 0.00 0.00 42.28 3.86
3995 4529 8.403236 ACACAACTATTGGAAGTTAAAACTGTC 58.597 33.333 0.00 0.00 37.61 3.51
4036 4652 7.817418 AAGAAGTGCAAGAAAGGTTTACATA 57.183 32.000 0.00 0.00 0.00 2.29
4039 4655 8.188799 AGTAAAAGAAGTGCAAGAAAGGTTTAC 58.811 33.333 0.00 0.00 0.00 2.01
4040 4656 8.188139 CAGTAAAAGAAGTGCAAGAAAGGTTTA 58.812 33.333 0.00 0.00 0.00 2.01
4041 4657 7.035612 CAGTAAAAGAAGTGCAAGAAAGGTTT 58.964 34.615 0.00 0.00 0.00 3.27
4183 4803 0.459237 CTGACAGTGACAGGATCGCC 60.459 60.000 13.93 0.00 38.75 5.54
4548 5177 1.391485 CTATATCAATGACGCTGCCGC 59.609 52.381 0.00 0.00 38.22 6.53
4599 5234 8.325997 GGGTCGAAAACGTGCATATATATAATC 58.674 37.037 0.00 0.00 0.00 1.75
4611 5246 2.664436 CCTCGGGTCGAAAACGTGC 61.664 63.158 0.00 0.00 34.74 5.34
4631 5273 3.479269 CGACCCGAAGAACAGCGC 61.479 66.667 0.00 0.00 0.00 5.92
4636 5278 0.738762 GGTAAGCCGACCCGAAGAAC 60.739 60.000 0.00 0.00 32.88 3.01
4656 5298 5.737318 TCTATTTCCCCCTCCATTAGATCA 58.263 41.667 0.00 0.00 0.00 2.92
4739 5381 8.607459 GGACAAGACACATCTTCTATACAATTG 58.393 37.037 3.24 3.24 43.69 2.32
4741 5383 8.083828 AGGACAAGACACATCTTCTATACAAT 57.916 34.615 0.00 0.00 43.69 2.71
4749 5391 4.394300 CCATCAAGGACAAGACACATCTTC 59.606 45.833 0.00 0.00 40.96 2.87
4753 5395 3.181440 ACACCATCAAGGACAAGACACAT 60.181 43.478 0.00 0.00 41.22 3.21
4757 5399 3.003689 CACAACACCATCAAGGACAAGAC 59.996 47.826 0.00 0.00 41.22 3.01
4780 5422 3.167485 ACACATTCCTGCCATTCACAAT 58.833 40.909 0.00 0.00 0.00 2.71
4820 5463 5.415077 CCAATGCAAGAGAAACTCTGAAGAT 59.585 40.000 1.97 0.00 40.28 2.40
4860 5503 0.994247 TGCTCACATCCATTCAGGGT 59.006 50.000 0.00 0.00 38.24 4.34
4948 5596 5.234972 GCACTTCCAACCAAGAAAATCAAAG 59.765 40.000 0.00 0.00 0.00 2.77
4955 5603 4.751767 AATTGCACTTCCAACCAAGAAA 57.248 36.364 0.00 0.00 0.00 2.52
5004 5665 1.762708 AACAGTGAAGGTGGTGGTTG 58.237 50.000 0.00 0.00 0.00 3.77
5006 5667 1.684869 CCAAACAGTGAAGGTGGTGGT 60.685 52.381 0.00 0.00 0.00 4.16
5106 5770 3.570975 TCGGTGTTCAAGACAAGCTAGTA 59.429 43.478 0.00 0.00 40.65 1.82
5107 5771 2.364324 TCGGTGTTCAAGACAAGCTAGT 59.636 45.455 0.00 0.00 40.65 2.57
5108 5772 3.026630 TCGGTGTTCAAGACAAGCTAG 57.973 47.619 0.00 0.00 40.65 3.42
5137 5801 6.205464 ACAGATTGTGGTATTTGTGACAAGAG 59.795 38.462 0.00 0.00 32.12 2.85
5141 5805 7.994425 AATACAGATTGTGGTATTTGTGACA 57.006 32.000 0.00 0.00 36.98 3.58
5142 5806 9.691362 AAAAATACAGATTGTGGTATTTGTGAC 57.309 29.630 9.69 0.00 44.88 3.67
5265 6103 3.451141 ACAATGTTCGCAAACCACATT 57.549 38.095 0.00 0.00 40.94 2.71
5345 6183 6.882768 TTCCCCATTTTATGCCTTATTGTT 57.117 33.333 0.00 0.00 0.00 2.83
5346 6184 6.882768 TTTCCCCATTTTATGCCTTATTGT 57.117 33.333 0.00 0.00 0.00 2.71
5347 6185 7.229106 CCATTTTCCCCATTTTATGCCTTATTG 59.771 37.037 0.00 0.00 0.00 1.90
5389 6227 2.355310 CCATAAACGGTAGGGTGCAGAA 60.355 50.000 0.00 0.00 0.00 3.02
5390 6228 1.208535 CCATAAACGGTAGGGTGCAGA 59.791 52.381 0.00 0.00 0.00 4.26
5481 6319 3.174265 GAGGAGGAGGCATGGGGG 61.174 72.222 0.00 0.00 0.00 5.40
5551 6389 4.048470 GAGGGTTGAGGGTGGGGC 62.048 72.222 0.00 0.00 0.00 5.80
5552 6390 3.339093 GGAGGGTTGAGGGTGGGG 61.339 72.222 0.00 0.00 0.00 4.96
5553 6391 2.204151 AGGAGGGTTGAGGGTGGG 60.204 66.667 0.00 0.00 0.00 4.61
5554 6392 2.301738 GGAGGAGGGTTGAGGGTGG 61.302 68.421 0.00 0.00 0.00 4.61
5555 6393 2.660064 CGGAGGAGGGTTGAGGGTG 61.660 68.421 0.00 0.00 0.00 4.61
5556 6394 2.284699 CGGAGGAGGGTTGAGGGT 60.285 66.667 0.00 0.00 0.00 4.34
5557 6395 3.787001 GCGGAGGAGGGTTGAGGG 61.787 72.222 0.00 0.00 0.00 4.30
5558 6396 2.685380 AGCGGAGGAGGGTTGAGG 60.685 66.667 0.00 0.00 0.00 3.86
5559 6397 2.896443 GAGCGGAGGAGGGTTGAG 59.104 66.667 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.