Multiple sequence alignment - TraesCS6D01G195300

Loading Multiple Alignment...

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 TraesCS6D01G195300 chr6D 100.000 5112 0 0 1 5112 271004235 271009346 0.000000e+00 9441.0
1 TraesCS6D01G195300 chr6D 94.872 78 3 1 2192 2269 456669734 456669658 2.500000e-23 121.0
2 TraesCS6D01G195300 chr6B 96.893 2221 49 10 1 2209 431698883 431701095 0.000000e+00 3701.0
3 TraesCS6D01G195300 chr6B 96.976 1422 34 6 2483 3901 431701442 431702857 0.000000e+00 2379.0
4 TraesCS6D01G195300 chr6B 97.279 735 15 5 4380 5112 431703380 431704111 0.000000e+00 1242.0
5 TraesCS6D01G195300 chr6B 95.316 491 20 2 3893 4380 431702799 431703289 0.000000e+00 776.0
6 TraesCS6D01G195300 chr6B 83.271 269 7 6 2193 2452 431701135 431701374 4.010000e-51 213.0
7 TraesCS6D01G195300 chr6A 96.951 1902 46 11 2483 4380 384968464 384966571 0.000000e+00 3181.0
8 TraesCS6D01G195300 chr6A 91.537 1548 77 19 670 2184 384970148 384968622 0.000000e+00 2084.0
9 TraesCS6D01G195300 chr6A 95.576 746 17 9 4380 5112 384966512 384965770 0.000000e+00 1181.0
10 TraesCS6D01G195300 chr6A 95.036 685 30 2 1 681 384972732 384972048 0.000000e+00 1074.0
11 TraesCS6D01G195300 chr6A 89.362 141 9 1 2273 2413 384968631 384968497 6.800000e-39 172.0
12 TraesCS6D01G195300 chr6A 93.827 81 3 2 2193 2272 189546114 189546035 2.500000e-23 121.0
13 TraesCS6D01G195300 chr6A 93.590 78 4 1 2193 2270 603354565 603354489 1.160000e-21 115.0
14 TraesCS6D01G195300 chr2B 76.511 877 145 43 2668 3507 514866841 514867693 6.120000e-114 422.0
15 TraesCS6D01G195300 chr2B 90.608 181 15 2 3601 3780 514867811 514867990 6.610000e-59 239.0
16 TraesCS6D01G195300 chr2B 95.745 94 4 0 1 94 337473635 337473728 8.870000e-33 152.0
17 TraesCS6D01G195300 chr2B 92.593 81 4 2 2193 2272 132404476 132404397 1.160000e-21 115.0
18 TraesCS6D01G195300 chr2A 75.922 868 150 39 2674 3507 550537793 550536951 1.730000e-104 390.0
19 TraesCS6D01G195300 chr2A 90.110 182 16 2 3600 3780 550536836 550536656 8.560000e-58 235.0
20 TraesCS6D01G195300 chr2A 96.774 31 1 0 2425 2455 38313647 38313617 9.000000e-03 52.8
21 TraesCS6D01G195300 chr2D 75.963 857 149 45 2684 3507 436367837 436367005 6.210000e-104 388.0
22 TraesCS6D01G195300 chr2D 89.011 182 18 2 3600 3780 436366889 436366709 1.850000e-54 224.0
23 TraesCS6D01G195300 chr2D 86.364 176 24 0 3936 4111 436366612 436366437 5.220000e-45 193.0
24 TraesCS6D01G195300 chr5D 98.876 89 1 0 1 89 489290679 489290591 5.300000e-35 159.0
25 TraesCS6D01G195300 chr5D 98.851 87 1 0 1 87 352301619 352301705 6.850000e-34 156.0
26 TraesCS6D01G195300 chr4A 98.851 87 1 0 1 87 42296317 42296403 6.850000e-34 156.0
27 TraesCS6D01G195300 chr7D 96.739 92 3 0 1 92 422063124 422063033 2.460000e-33 154.0
28 TraesCS6D01G195300 chr7D 94.845 97 5 0 1 97 274676609 274676705 8.870000e-33 152.0
29 TraesCS6D01G195300 chr3D 94.845 97 5 0 1 97 402828944 402828848 8.870000e-33 152.0
30 TraesCS6D01G195300 chr4D 92.308 91 5 2 2184 2272 139042996 139042906 1.490000e-25 128.0
31 TraesCS6D01G195300 chr3A 94.048 84 3 2 2192 2274 700234149 700234231 5.370000e-25 126.0
32 TraesCS6D01G195300 chr1B 95.000 80 1 3 2194 2272 451737829 451737752 6.950000e-24 122.0
33 TraesCS6D01G195300 chr1B 96.970 33 1 0 2423 2455 584135439 584135407 7.150000e-04 56.5
34 TraesCS6D01G195300 chr1A 94.805 77 3 1 2193 2269 57303706 57303781 8.990000e-23 119.0


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 TraesCS6D01G195300 chr6D 271004235 271009346 5111 False 9441.000000 9441 100.000000 1 5112 1 chr6D.!!$F1 5111
1 TraesCS6D01G195300 chr6B 431698883 431704111 5228 False 1662.200000 3701 93.947000 1 5112 5 chr6B.!!$F1 5111
2 TraesCS6D01G195300 chr6A 384965770 384972732 6962 True 1538.400000 3181 93.692400 1 5112 5 chr6A.!!$R3 5111
3 TraesCS6D01G195300 chr2B 514866841 514867990 1149 False 330.500000 422 83.559500 2668 3780 2 chr2B.!!$F2 1112
4 TraesCS6D01G195300 chr2A 550536656 550537793 1137 True 312.500000 390 83.016000 2674 3780 2 chr2A.!!$R2 1106
5 TraesCS6D01G195300 chr2D 436366437 436367837 1400 True 268.333333 388 83.779333 2684 4111 3 chr2D.!!$R1 1427

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
43 44 1.001268 CGTGAGATGGGGTAGTCATCG 60.001 57.143 0.0 0.0 44.04 3.84 F
635 640 1.239347 GCGCTCTCCTGTTCCTTTTT 58.761 50.000 0.0 0.0 0.00 1.94 F
1636 3590 0.455410 TGTGCCTGTTTGTGTTCTGC 59.545 50.000 0.0 0.0 0.00 4.26 F
2035 3995 1.032014 GTGTTCTGCTCCAGCCAAAA 58.968 50.000 0.0 0.0 41.18 2.44 F
3852 5967 0.941542 TCCCGTTTTCGTTTCTGCTG 59.058 50.000 0.0 0.0 42.35 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 3103 1.375551 GTGCGGTACCATCGGATTTT 58.624 50.000 13.54 0.0 0.00 1.82 R
2089 4049 0.320421 CGATGGACACCGTGGTCTTT 60.320 55.000 3.03 0.0 37.91 2.52 R
2514 4575 3.317711 ACCAACGTGCTTTTCATGATTCA 59.682 39.130 0.00 0.0 35.66 2.57 R
3886 6001 0.759346 ACGACAGCAGAAACTTCCCT 59.241 50.000 0.00 0.0 0.00 4.20 R
4669 6930 2.230660 GTAGCACACCTGAGGCTTTTT 58.769 47.619 0.00 0.0 39.01 1.94 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
43 44 1.001268 CGTGAGATGGGGTAGTCATCG 60.001 57.143 0.00 0.00 44.04 3.84
166 167 1.732259 GTGTTGTCCCGCTATTGAGTG 59.268 52.381 0.00 0.00 0.00 3.51
241 242 4.650972 TTGGTAATAGTCAAAGGGCAGT 57.349 40.909 0.00 0.00 0.00 4.40
485 489 1.814772 CTCGGCCAACCAATTTGCCA 61.815 55.000 2.24 0.00 33.37 4.92
570 575 3.222173 TGCTCTGTGTTTGGTAATGGT 57.778 42.857 0.00 0.00 0.00 3.55
628 633 2.047465 CAGCTGCGCTCTCCTGTT 60.047 61.111 9.73 0.00 36.40 3.16
635 640 1.239347 GCGCTCTCCTGTTCCTTTTT 58.761 50.000 0.00 0.00 0.00 1.94
643 648 1.815817 CTGTTCCTTTTTGGGGCCCG 61.816 60.000 19.83 2.16 36.20 6.13
748 2665 2.639065 CCCGGCTAAAAGAATGTAGCA 58.361 47.619 0.00 0.00 43.76 3.49
793 2710 6.706270 CGGGCTAAAAAGAATCTAGCTAATGA 59.294 38.462 3.17 0.00 38.47 2.57
805 2722 2.057137 GCTAATGAGCCACATCCCAA 57.943 50.000 0.00 0.00 43.49 4.12
819 2736 5.662657 CCACATCCCAAAATCTATCCCTTTT 59.337 40.000 0.00 0.00 0.00 2.27
846 2763 1.978617 CGACAAGCCCAAGCCCAAT 60.979 57.895 0.00 0.00 41.25 3.16
1152 3103 2.821366 GACGTCCTCTCCGCCGTA 60.821 66.667 3.51 0.00 33.03 4.02
1355 3307 1.138883 CGACGAGGAGATCCGCAAA 59.861 57.895 3.47 0.00 42.08 3.68
1636 3590 0.455410 TGTGCCTGTTTGTGTTCTGC 59.545 50.000 0.00 0.00 0.00 4.26
1835 3794 3.345808 CACCCACGGCGACTTGTG 61.346 66.667 16.62 11.39 35.87 3.33
1975 3935 4.400251 CCCTCAGCTTTGATCTTGCAAATA 59.600 41.667 0.00 0.00 37.16 1.40
2035 3995 1.032014 GTGTTCTGCTCCAGCCAAAA 58.968 50.000 0.00 0.00 41.18 2.44
2089 4049 1.603455 CTTTGCGGGGAAGCTTGGA 60.603 57.895 2.10 0.00 38.13 3.53
2220 4235 1.293498 CTAGTCGCAACTGCAGGGT 59.707 57.895 19.93 1.91 42.21 4.34
2223 4238 3.611674 TCGCAACTGCAGGGTCGA 61.612 61.111 19.93 18.82 42.21 4.20
2236 4251 3.368531 GCAGGGTCGACTATTCAAGAGTT 60.369 47.826 16.46 0.00 0.00 3.01
2355 4370 6.266131 TCACTTGGGATTTAGGCTGAATAT 57.734 37.500 4.30 0.00 0.00 1.28
2363 4378 7.564660 TGGGATTTAGGCTGAATATTCAATGTT 59.435 33.333 18.47 7.83 36.64 2.71
2364 4379 9.077885 GGGATTTAGGCTGAATATTCAATGTTA 57.922 33.333 18.47 6.98 36.64 2.41
2368 4383 9.693739 TTTAGGCTGAATATTCAATGTTAAGGA 57.306 29.630 18.47 1.11 36.64 3.36
2398 4413 7.762159 GGAGTAAGTGGAGTTTCTTTGAGATAG 59.238 40.741 0.00 0.00 0.00 2.08
2452 4476 3.173965 ACTCCCTCCGTCCCATAATATG 58.826 50.000 0.00 0.00 0.00 1.78
2455 4479 3.173965 CCCTCCGTCCCATAATATGAGT 58.826 50.000 1.10 0.00 0.00 3.41
2456 4480 4.044952 TCCCTCCGTCCCATAATATGAGTA 59.955 45.833 1.10 0.00 0.00 2.59
2457 4481 4.402793 CCCTCCGTCCCATAATATGAGTAG 59.597 50.000 1.10 0.00 0.00 2.57
2458 4482 5.262009 CCTCCGTCCCATAATATGAGTAGA 58.738 45.833 1.10 0.00 0.00 2.59
2459 4483 5.125739 CCTCCGTCCCATAATATGAGTAGAC 59.874 48.000 1.10 2.95 0.00 2.59
2460 4484 5.888901 TCCGTCCCATAATATGAGTAGACT 58.111 41.667 1.10 0.00 0.00 3.24
2461 4485 7.024345 TCCGTCCCATAATATGAGTAGACTA 57.976 40.000 1.10 0.00 0.00 2.59
2464 4488 8.407064 CCGTCCCATAATATGAGTAGACTATTC 58.593 40.741 1.10 0.00 0.00 1.75
2467 4491 8.972127 TCCCATAATATGAGTAGACTATTCAGC 58.028 37.037 12.58 0.00 0.00 4.26
2475 4499 7.291411 TGAGTAGACTATTCAGCCTAAATCC 57.709 40.000 3.69 0.00 0.00 3.01
2476 4500 6.267928 TGAGTAGACTATTCAGCCTAAATCCC 59.732 42.308 3.69 0.00 0.00 3.85
2477 4501 6.143915 AGTAGACTATTCAGCCTAAATCCCA 58.856 40.000 0.00 0.00 0.00 4.37
2478 4502 5.975988 AGACTATTCAGCCTAAATCCCAA 57.024 39.130 0.00 0.00 0.00 4.12
2479 4503 5.934781 AGACTATTCAGCCTAAATCCCAAG 58.065 41.667 0.00 0.00 0.00 3.61
2481 4505 5.440610 ACTATTCAGCCTAAATCCCAAGTG 58.559 41.667 0.00 0.00 0.00 3.16
2538 4600 3.077229 TCATGAAAAGCACGTTGGTTG 57.923 42.857 0.00 0.00 38.20 3.77
2551 4613 3.756434 ACGTTGGTTGAGTGGAATTATGG 59.244 43.478 0.00 0.00 0.00 2.74
2562 4624 8.106247 TGAGTGGAATTATGGTTGTTTCTTAC 57.894 34.615 0.00 0.00 0.00 2.34
2563 4625 7.942341 TGAGTGGAATTATGGTTGTTTCTTACT 59.058 33.333 0.00 0.00 0.00 2.24
2564 4626 8.706322 AGTGGAATTATGGTTGTTTCTTACTT 57.294 30.769 0.00 0.00 0.00 2.24
2565 4627 9.802039 AGTGGAATTATGGTTGTTTCTTACTTA 57.198 29.630 0.00 0.00 0.00 2.24
2584 4646 9.941325 CTTACTTATTATCCATGATGCTCTTCT 57.059 33.333 0.00 0.00 0.00 2.85
2733 4795 2.042831 GCGTGAAGCCCATCTTGCT 61.043 57.895 0.00 0.00 41.89 3.91
2770 4832 2.943036 AAAGGTTGGCGAGAAGGTAA 57.057 45.000 0.00 0.00 0.00 2.85
3806 5920 5.715070 TGGAAACAACCGCCTAATTTTATG 58.285 37.500 0.00 0.00 37.44 1.90
3822 5937 6.906157 ATTTTATGTCCCATTCCTATGCAG 57.094 37.500 0.00 0.00 0.00 4.41
3843 5958 3.807622 AGCATACATACATCCCGTTTTCG 59.192 43.478 0.00 0.00 43.67 3.46
3845 5960 4.034742 GCATACATACATCCCGTTTTCGTT 59.965 41.667 0.00 0.00 42.35 3.85
3846 5961 5.448089 GCATACATACATCCCGTTTTCGTTT 60.448 40.000 0.00 0.00 42.35 3.60
3847 5962 4.673534 ACATACATCCCGTTTTCGTTTC 57.326 40.909 0.00 0.00 42.35 2.78
3848 5963 4.320870 ACATACATCCCGTTTTCGTTTCT 58.679 39.130 0.00 0.00 42.35 2.52
3849 5964 4.153475 ACATACATCCCGTTTTCGTTTCTG 59.847 41.667 0.00 0.00 42.35 3.02
3850 5965 1.265905 ACATCCCGTTTTCGTTTCTGC 59.734 47.619 0.00 0.00 42.35 4.26
3851 5966 1.535462 CATCCCGTTTTCGTTTCTGCT 59.465 47.619 0.00 0.00 42.35 4.24
3852 5967 0.941542 TCCCGTTTTCGTTTCTGCTG 59.058 50.000 0.00 0.00 42.35 4.41
3854 5969 1.333791 CCCGTTTTCGTTTCTGCTGTC 60.334 52.381 0.00 0.00 42.35 3.51
3856 5971 2.032030 CCGTTTTCGTTTCTGCTGTCAT 60.032 45.455 0.00 0.00 42.35 3.06
3857 5972 3.185594 CCGTTTTCGTTTCTGCTGTCATA 59.814 43.478 0.00 0.00 42.35 2.15
3860 5975 5.504755 CGTTTTCGTTTCTGCTGTCATATTC 59.495 40.000 0.00 0.00 38.65 1.75
3861 5976 6.370593 GTTTTCGTTTCTGCTGTCATATTCA 58.629 36.000 0.00 0.00 0.00 2.57
3863 5978 7.841915 TTTCGTTTCTGCTGTCATATTCATA 57.158 32.000 0.00 0.00 0.00 2.15
3864 5979 8.437360 TTTCGTTTCTGCTGTCATATTCATAT 57.563 30.769 0.00 0.00 0.00 1.78
3866 5981 8.437360 TCGTTTCTGCTGTCATATTCATATTT 57.563 30.769 0.00 0.00 0.00 1.40
3867 5982 8.892723 TCGTTTCTGCTGTCATATTCATATTTT 58.107 29.630 0.00 0.00 0.00 1.82
3868 5983 9.507280 CGTTTCTGCTGTCATATTCATATTTTT 57.493 29.630 0.00 0.00 0.00 1.94
3890 6005 7.411486 TTTTGTCTTTCATTTGTTGTAGGGA 57.589 32.000 0.00 0.00 0.00 4.20
3891 6006 7.411486 TTTGTCTTTCATTTGTTGTAGGGAA 57.589 32.000 0.00 0.00 0.00 3.97
3903 6018 3.402628 TGTAGGGAAGTTTCTGCTGTC 57.597 47.619 0.00 0.00 0.00 3.51
3912 6027 5.446473 GGAAGTTTCTGCTGTCGTATTCATG 60.446 44.000 0.00 0.00 0.00 3.07
4120 6284 7.063426 CGAGTCATTGATCTGTAAAAGTTGCTA 59.937 37.037 0.00 0.00 0.00 3.49
4123 6287 9.282247 GTCATTGATCTGTAAAAGTTGCTATTG 57.718 33.333 0.00 0.00 0.00 1.90
4130 6294 7.990917 TCTGTAAAAGTTGCTATTGTTGTTGA 58.009 30.769 0.00 0.00 0.00 3.18
4277 6446 8.733092 ATGAACTCATATCCCAGAAGATAAGA 57.267 34.615 0.00 0.00 34.26 2.10
4309 6478 4.816385 TGTTTCTTCTGTGATGAACCTGTC 59.184 41.667 0.00 0.00 0.00 3.51
4570 6831 8.757982 AGTACATCAATTGGCTCATTTCTAAT 57.242 30.769 5.42 0.00 0.00 1.73
4669 6930 2.166050 ACATTGTGTGCTGCAAAACTCA 59.834 40.909 2.77 0.00 0.00 3.41
4713 6974 1.807142 GCAGCTCTGGGAAAACTACAC 59.193 52.381 0.00 0.00 0.00 2.90
4778 7040 5.809051 GCTCTGCAGGGATAAAAGAAATTTG 59.191 40.000 20.53 0.00 32.27 2.32
4782 7044 7.450014 TCTGCAGGGATAAAAGAAATTTGTGTA 59.550 33.333 15.13 0.00 32.27 2.90
4828 7090 3.821033 GCTCTGGGAAAACTACATGTGTT 59.179 43.478 9.11 8.15 0.00 3.32
5087 7362 7.355017 TGAGATGAAGAAGAAAAACGATGTTG 58.645 34.615 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 5.551760 ACGAAGAATGATGTGGTCAATTC 57.448 39.130 0.00 0.00 40.97 2.17
241 242 5.970612 CACAAAATCATTCTGTTTGTCGTCA 59.029 36.000 0.00 0.00 42.13 4.35
570 575 1.522258 GTAAAGGCGACAACGAAACGA 59.478 47.619 0.00 0.00 42.66 3.85
628 633 1.717038 TACACGGGCCCCAAAAAGGA 61.717 55.000 18.66 0.00 41.22 3.36
635 640 2.453812 AACAGTTACACGGGCCCCA 61.454 57.895 18.66 0.00 0.00 4.96
643 648 1.173913 GATGGGGCCAACAGTTACAC 58.826 55.000 4.39 0.00 0.00 2.90
793 2710 3.437052 GGGATAGATTTTGGGATGTGGCT 60.437 47.826 0.00 0.00 0.00 4.75
805 2722 7.444487 GTCGTTATAGGCAAAAGGGATAGATTT 59.556 37.037 0.00 0.00 0.00 2.17
819 2736 0.906066 TGGGCTTGTCGTTATAGGCA 59.094 50.000 0.00 0.00 36.29 4.75
1152 3103 1.375551 GTGCGGTACCATCGGATTTT 58.624 50.000 13.54 0.00 0.00 1.82
1231 3183 1.605165 GGCAATCAACCCCACGGAA 60.605 57.895 0.00 0.00 0.00 4.30
1232 3184 2.034999 GGCAATCAACCCCACGGA 59.965 61.111 0.00 0.00 0.00 4.69
1355 3307 1.821753 CCCACTCACTTCTCATCGAGT 59.178 52.381 0.00 0.00 39.26 4.18
1600 3554 4.160252 AGGCACAGTTCTCACACAAAATTT 59.840 37.500 0.00 0.00 0.00 1.82
2035 3995 3.434167 GGTTCTGCTCACCATATGGATGT 60.434 47.826 28.77 2.74 38.94 3.06
2089 4049 0.320421 CGATGGACACCGTGGTCTTT 60.320 55.000 3.03 0.00 37.91 2.52
2103 4063 3.687321 CTGACTGGTGGCCCGATGG 62.687 68.421 0.00 0.00 0.00 3.51
2211 4226 1.557099 TGAATAGTCGACCCTGCAGT 58.443 50.000 13.01 0.00 0.00 4.40
2220 4235 4.142227 GGGTAGCAACTCTTGAATAGTCGA 60.142 45.833 0.00 0.00 0.00 4.20
2223 4238 3.844211 TGGGGTAGCAACTCTTGAATAGT 59.156 43.478 0.00 0.00 0.00 2.12
2236 4251 1.592400 CGAGTCGTTCTGGGGTAGCA 61.592 60.000 3.82 0.00 0.00 3.49
2355 4370 9.667107 CACTTACTCCTTATCCTTAACATTGAA 57.333 33.333 0.00 0.00 0.00 2.69
2363 4378 7.899709 AGAAACTCCACTTACTCCTTATCCTTA 59.100 37.037 0.00 0.00 0.00 2.69
2364 4379 6.731448 AGAAACTCCACTTACTCCTTATCCTT 59.269 38.462 0.00 0.00 0.00 3.36
2365 4380 6.265304 AGAAACTCCACTTACTCCTTATCCT 58.735 40.000 0.00 0.00 0.00 3.24
2366 4381 6.547930 AGAAACTCCACTTACTCCTTATCC 57.452 41.667 0.00 0.00 0.00 2.59
2367 4382 8.095169 TCAAAGAAACTCCACTTACTCCTTATC 58.905 37.037 0.00 0.00 0.00 1.75
2368 4383 7.974504 TCAAAGAAACTCCACTTACTCCTTAT 58.025 34.615 0.00 0.00 0.00 1.73
2398 4413 7.830099 ATAATTTCCTTCATCCAGAACATCC 57.170 36.000 0.00 0.00 31.61 3.51
2452 4476 6.267928 TGGGATTTAGGCTGAATAGTCTACTC 59.732 42.308 4.30 0.00 40.67 2.59
2455 4479 6.615726 ACTTGGGATTTAGGCTGAATAGTCTA 59.384 38.462 4.30 0.00 40.06 2.59
2456 4480 5.430089 ACTTGGGATTTAGGCTGAATAGTCT 59.570 40.000 4.30 0.00 42.66 3.24
2457 4481 5.529060 CACTTGGGATTTAGGCTGAATAGTC 59.471 44.000 4.30 0.00 0.00 2.59
2458 4482 5.044846 ACACTTGGGATTTAGGCTGAATAGT 60.045 40.000 4.30 2.24 0.00 2.12
2459 4483 5.440610 ACACTTGGGATTTAGGCTGAATAG 58.559 41.667 4.30 1.62 0.00 1.73
2460 4484 5.191722 AGACACTTGGGATTTAGGCTGAATA 59.808 40.000 4.30 0.00 0.00 1.75
2461 4485 4.018050 AGACACTTGGGATTTAGGCTGAAT 60.018 41.667 3.92 3.92 0.00 2.57
2464 4488 3.356529 AGACACTTGGGATTTAGGCTG 57.643 47.619 0.00 0.00 0.00 4.85
2466 4490 3.686016 TCAAGACACTTGGGATTTAGGC 58.314 45.455 10.84 0.00 0.00 3.93
2467 4491 6.209391 ACAATTCAAGACACTTGGGATTTAGG 59.791 38.462 10.84 4.73 0.00 2.69
2471 4495 6.431234 GTCTACAATTCAAGACACTTGGGATT 59.569 38.462 10.84 8.95 41.46 3.01
2472 4496 5.940470 GTCTACAATTCAAGACACTTGGGAT 59.060 40.000 10.84 4.30 41.46 3.85
2473 4497 5.163248 TGTCTACAATTCAAGACACTTGGGA 60.163 40.000 13.09 2.40 45.40 4.37
2474 4498 5.063204 TGTCTACAATTCAAGACACTTGGG 58.937 41.667 13.09 3.01 45.40 4.12
2475 4499 5.180117 CCTGTCTACAATTCAAGACACTTGG 59.820 44.000 13.09 10.40 45.40 3.61
2476 4500 5.180117 CCCTGTCTACAATTCAAGACACTTG 59.820 44.000 13.09 5.29 45.40 3.16
2477 4501 5.163195 ACCCTGTCTACAATTCAAGACACTT 60.163 40.000 13.09 1.73 45.40 3.16
2478 4502 4.348168 ACCCTGTCTACAATTCAAGACACT 59.652 41.667 13.09 0.58 45.40 3.55
2479 4503 4.642429 ACCCTGTCTACAATTCAAGACAC 58.358 43.478 13.09 0.00 45.40 3.67
2481 4505 6.539103 GGAATACCCTGTCTACAATTCAAGAC 59.461 42.308 9.00 9.00 42.04 3.01
2513 4574 3.916172 CCAACGTGCTTTTCATGATTCAG 59.084 43.478 0.00 0.00 35.66 3.02
2514 4575 3.317711 ACCAACGTGCTTTTCATGATTCA 59.682 39.130 0.00 0.00 35.66 2.57
2538 4600 8.336801 AGTAAGAAACAACCATAATTCCACTC 57.663 34.615 0.00 0.00 0.00 3.51
2562 4624 8.095792 ACTGAGAAGAGCATCATGGATAATAAG 58.904 37.037 0.00 0.00 37.82 1.73
2563 4625 7.971201 ACTGAGAAGAGCATCATGGATAATAA 58.029 34.615 0.00 0.00 37.82 1.40
2564 4626 7.550597 ACTGAGAAGAGCATCATGGATAATA 57.449 36.000 0.00 0.00 37.82 0.98
2565 4627 6.436738 ACTGAGAAGAGCATCATGGATAAT 57.563 37.500 0.00 0.00 37.82 1.28
2733 4795 7.499895 CCAACCTTTACAAAGTACAAGGACTTA 59.500 37.037 12.91 0.00 38.75 2.24
3806 5920 2.283145 ATGCTGCATAGGAATGGGAC 57.717 50.000 14.52 0.00 33.38 4.46
3822 5937 3.558418 ACGAAAACGGGATGTATGTATGC 59.442 43.478 0.00 0.00 0.00 3.14
3866 5981 7.411486 TCCCTACAACAAATGAAAGACAAAA 57.589 32.000 0.00 0.00 0.00 2.44
3867 5982 7.123547 ACTTCCCTACAACAAATGAAAGACAAA 59.876 33.333 0.00 0.00 0.00 2.83
3868 5983 6.605594 ACTTCCCTACAACAAATGAAAGACAA 59.394 34.615 0.00 0.00 0.00 3.18
3869 5984 6.126409 ACTTCCCTACAACAAATGAAAGACA 58.874 36.000 0.00 0.00 0.00 3.41
3870 5985 6.635030 ACTTCCCTACAACAAATGAAAGAC 57.365 37.500 0.00 0.00 0.00 3.01
3871 5986 7.559897 AGAAACTTCCCTACAACAAATGAAAGA 59.440 33.333 0.00 0.00 0.00 2.52
3872 5987 7.649306 CAGAAACTTCCCTACAACAAATGAAAG 59.351 37.037 0.00 0.00 0.00 2.62
3873 5988 7.488322 CAGAAACTTCCCTACAACAAATGAAA 58.512 34.615 0.00 0.00 0.00 2.69
3874 5989 6.460953 GCAGAAACTTCCCTACAACAAATGAA 60.461 38.462 0.00 0.00 0.00 2.57
3875 5990 5.009610 GCAGAAACTTCCCTACAACAAATGA 59.990 40.000 0.00 0.00 0.00 2.57
3876 5991 5.010012 AGCAGAAACTTCCCTACAACAAATG 59.990 40.000 0.00 0.00 0.00 2.32
3877 5992 5.010012 CAGCAGAAACTTCCCTACAACAAAT 59.990 40.000 0.00 0.00 0.00 2.32
3878 5993 4.338118 CAGCAGAAACTTCCCTACAACAAA 59.662 41.667 0.00 0.00 0.00 2.83
3879 5994 3.882888 CAGCAGAAACTTCCCTACAACAA 59.117 43.478 0.00 0.00 0.00 2.83
3881 5996 3.477530 ACAGCAGAAACTTCCCTACAAC 58.522 45.455 0.00 0.00 0.00 3.32
3882 5997 3.740115 GACAGCAGAAACTTCCCTACAA 58.260 45.455 0.00 0.00 0.00 2.41
3884 5999 2.288886 ACGACAGCAGAAACTTCCCTAC 60.289 50.000 0.00 0.00 0.00 3.18
3885 6000 1.968493 ACGACAGCAGAAACTTCCCTA 59.032 47.619 0.00 0.00 0.00 3.53
3886 6001 0.759346 ACGACAGCAGAAACTTCCCT 59.241 50.000 0.00 0.00 0.00 4.20
3887 6002 2.450609 TACGACAGCAGAAACTTCCC 57.549 50.000 0.00 0.00 0.00 3.97
3888 6003 3.994392 TGAATACGACAGCAGAAACTTCC 59.006 43.478 0.00 0.00 0.00 3.46
3889 6004 5.120830 ACATGAATACGACAGCAGAAACTTC 59.879 40.000 0.00 0.00 0.00 3.01
3890 6005 4.997395 ACATGAATACGACAGCAGAAACTT 59.003 37.500 0.00 0.00 0.00 2.66
3891 6006 4.389992 CACATGAATACGACAGCAGAAACT 59.610 41.667 0.00 0.00 0.00 2.66
3903 6018 8.506140 AATGAAAGACAAAACACATGAATACG 57.494 30.769 0.00 0.00 0.00 3.06
3912 6027 7.010091 CCCTACAACAAATGAAAGACAAAACAC 59.990 37.037 0.00 0.00 0.00 3.32
4120 6284 1.615392 GGCCAGAGCTTCAACAACAAT 59.385 47.619 0.00 0.00 39.73 2.71
4123 6287 0.823356 TGGGCCAGAGCTTCAACAAC 60.823 55.000 0.00 0.00 39.73 3.32
4130 6294 1.605738 CTTTGCTGGGCCAGAGCTT 60.606 57.895 37.07 0.00 39.73 3.74
4157 6326 2.614481 GCTGAAATAGGTCCGACAACCA 60.614 50.000 0.00 0.00 42.12 3.67
4164 6333 1.689273 AGGCTAGCTGAAATAGGTCCG 59.311 52.381 15.72 0.00 38.31 4.79
4204 6373 1.152963 ACGCTCAACAAAGCCAGGT 60.153 52.632 0.00 0.00 39.17 4.00
4274 6443 5.762218 CACAGAAGAAACATCCTTCAGTCTT 59.238 40.000 0.00 0.00 41.73 3.01
4277 6446 5.296151 TCACAGAAGAAACATCCTTCAGT 57.704 39.130 0.00 0.00 41.73 3.41
4309 6478 7.664731 ACAGATGATAAGGCTTGGAATGAATAG 59.335 37.037 10.69 0.00 0.00 1.73
4460 6720 1.079197 TATAGCGCGCATGGATGGG 60.079 57.895 35.10 0.00 42.88 4.00
4570 6831 0.033991 TTAGGCAGCCCCGCAAAATA 60.034 50.000 8.22 0.00 39.21 1.40
4575 6836 3.697439 GATGTTAGGCAGCCCCGCA 62.697 63.158 8.22 4.73 39.21 5.69
4669 6930 2.230660 GTAGCACACCTGAGGCTTTTT 58.769 47.619 0.00 0.00 39.01 1.94
4782 7044 8.857098 AGCTGCTTTATAATCAAATCATCACAT 58.143 29.630 0.00 0.00 0.00 3.21
4828 7090 6.742559 AGGGTTCAGTAAGTAGAGACAAAA 57.257 37.500 0.00 0.00 0.00 2.44
5087 7362 2.450160 GTGTTGTGCACTAACAGCAAC 58.550 47.619 25.22 17.11 44.64 4.17


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

AutoCloner maintained by Alex Coulton.