Multiple sequence alignment - TraesCS6D01G230000

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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 TraesCS6D01G230000 chr6D 100.000 4777 0 0 1 4777 322574362 322569586 0.000000e+00 8822
1 TraesCS6D01G230000 chr6D 91.809 1636 100 16 2065 3693 322586997 322585389 0.000000e+00 2248
2 TraesCS6D01G230000 chr6D 82.047 557 85 13 184 733 341997519 341998067 1.210000e-125 460
3 TraesCS6D01G230000 chr6A 94.455 3589 141 22 42 3602 459880459 459876901 0.000000e+00 5472
4 TraesCS6D01G230000 chr6A 90.983 1730 113 25 2065 3785 460006423 460004728 0.000000e+00 2290
5 TraesCS6D01G230000 chr6A 85.678 1173 82 44 3603 4717 459876863 459875719 0.000000e+00 1157
6 TraesCS6D01G230000 chr6B 92.796 3609 149 42 43 3602 501060655 501064201 0.000000e+00 5121
7 TraesCS6D01G230000 chr6B 90.473 1732 121 23 2065 3785 500894209 500895907 0.000000e+00 2244
8 TraesCS6D01G230000 chr6B 94.625 707 28 7 3842 4543 501064442 501065143 0.000000e+00 1086
9 TraesCS6D01G230000 chr6B 83.026 542 80 9 194 732 671719753 671720285 9.300000e-132 481
10 TraesCS6D01G230000 chr6B 95.814 215 8 1 3600 3813 501064236 501064450 3.540000e-91 346
11 TraesCS6D01G230000 chr6B 96.528 144 5 0 4578 4721 501065135 501065278 6.180000e-59 239
12 TraesCS6D01G230000 chr6B 98.333 60 1 0 4718 4777 501065303 501065362 6.540000e-19 106
13 TraesCS6D01G230000 chr2D 89.457 1233 110 15 2114 3334 15133806 15135030 0.000000e+00 1539
14 TraesCS6D01G230000 chr3D 87.731 1190 144 2 2115 3303 213996918 213998106 0.000000e+00 1387
15 TraesCS6D01G230000 chr3A 87.594 1193 146 2 2118 3309 279436891 279435700 0.000000e+00 1382
16 TraesCS6D01G230000 chr3A 83.026 542 80 8 194 732 584028616 584028084 9.300000e-132 481
17 TraesCS6D01G230000 chr3B 87.510 1193 147 2 2118 3309 330800921 330799730 0.000000e+00 1376
18 TraesCS6D01G230000 chr1A 83.179 541 78 9 194 732 592323477 592322948 2.590000e-132 483
19 TraesCS6D01G230000 chr1D 82.841 542 77 11 194 732 439108327 439108855 5.600000e-129 472
20 TraesCS6D01G230000 chr2B 82.752 545 77 13 194 732 690213668 690213135 2.010000e-128 470
21 TraesCS6D01G230000 chr1B 82.320 543 84 9 194 733 679233815 679234348 1.210000e-125 460
22 TraesCS6D01G230000 chr4B 87.123 365 32 9 4365 4721 558582176 558582533 2.680000e-107 399
23 TraesCS6D01G230000 chr4A 85.989 364 27 13 4373 4720 21061544 21061189 7.550000e-98 368
24 TraesCS6D01G230000 chr4D 86.121 281 23 11 4450 4721 446431949 446432222 6.050000e-74 289
25 TraesCS6D01G230000 chr7A 75.492 559 94 18 235 777 163385445 163384914 2.870000e-57 233


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 TraesCS6D01G230000 chr6D 322569586 322574362 4776 True 8822.0 8822 100.0000 1 4777 1 chr6D.!!$R1 4776
1 TraesCS6D01G230000 chr6D 322585389 322586997 1608 True 2248.0 2248 91.8090 2065 3693 1 chr6D.!!$R2 1628
2 TraesCS6D01G230000 chr6D 341997519 341998067 548 False 460.0 460 82.0470 184 733 1 chr6D.!!$F1 549
3 TraesCS6D01G230000 chr6A 459875719 459880459 4740 True 3314.5 5472 90.0665 42 4717 2 chr6A.!!$R2 4675
4 TraesCS6D01G230000 chr6A 460004728 460006423 1695 True 2290.0 2290 90.9830 2065 3785 1 chr6A.!!$R1 1720
5 TraesCS6D01G230000 chr6B 500894209 500895907 1698 False 2244.0 2244 90.4730 2065 3785 1 chr6B.!!$F1 1720
6 TraesCS6D01G230000 chr6B 501060655 501065362 4707 False 1379.6 5121 95.6192 43 4777 5 chr6B.!!$F3 4734
7 TraesCS6D01G230000 chr6B 671719753 671720285 532 False 481.0 481 83.0260 194 732 1 chr6B.!!$F2 538
8 TraesCS6D01G230000 chr2D 15133806 15135030 1224 False 1539.0 1539 89.4570 2114 3334 1 chr2D.!!$F1 1220
9 TraesCS6D01G230000 chr3D 213996918 213998106 1188 False 1387.0 1387 87.7310 2115 3303 1 chr3D.!!$F1 1188
10 TraesCS6D01G230000 chr3A 279435700 279436891 1191 True 1382.0 1382 87.5940 2118 3309 1 chr3A.!!$R1 1191
11 TraesCS6D01G230000 chr3A 584028084 584028616 532 True 481.0 481 83.0260 194 732 1 chr3A.!!$R2 538
12 TraesCS6D01G230000 chr3B 330799730 330800921 1191 True 1376.0 1376 87.5100 2118 3309 1 chr3B.!!$R1 1191
13 TraesCS6D01G230000 chr1A 592322948 592323477 529 True 483.0 483 83.1790 194 732 1 chr1A.!!$R1 538
14 TraesCS6D01G230000 chr1D 439108327 439108855 528 False 472.0 472 82.8410 194 732 1 chr1D.!!$F1 538
15 TraesCS6D01G230000 chr2B 690213135 690213668 533 True 470.0 470 82.7520 194 732 1 chr2B.!!$R1 538
16 TraesCS6D01G230000 chr1B 679233815 679234348 533 False 460.0 460 82.3200 194 733 1 chr1B.!!$F1 539
17 TraesCS6D01G230000 chr7A 163384914 163385445 531 True 233.0 233 75.4920 235 777 1 chr7A.!!$R1 542

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
652 664 0.040058 TCCAGTCCAATTGCAGCCAT 59.960 50.0 0.00 0.0 0.00 4.40 F
1144 1196 0.107831 TCCTATAAATTGCGCGGCCT 59.892 50.0 8.83 0.0 0.00 5.19 F
1937 2013 0.404040 CCTCAGGGGCCTGTTTGTTA 59.596 55.0 0.84 0.0 43.96 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2038 0.107410 ACGTCCAGGCACAACAAGAA 60.107 50.000 0.00 0.00 0.00 2.52 R
2967 3047 1.153249 GGCAATGTAGGCGCCACTA 60.153 57.895 31.54 14.49 45.52 2.74 R
3818 4019 2.482336 GTGTGTGTGTGTGTCAAGAACA 59.518 45.455 0.00 0.00 34.78 3.18 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
23 24 5.862924 ATAACGTGTGAATGAGGTTTGAG 57.137 39.130 0.00 0.00 0.00 3.02
24 25 1.873591 ACGTGTGAATGAGGTTTGAGC 59.126 47.619 0.00 0.00 0.00 4.26
25 26 1.872952 CGTGTGAATGAGGTTTGAGCA 59.127 47.619 0.00 0.00 0.00 4.26
26 27 2.096069 CGTGTGAATGAGGTTTGAGCAG 60.096 50.000 0.00 0.00 0.00 4.24
27 28 2.880890 GTGTGAATGAGGTTTGAGCAGT 59.119 45.455 0.00 0.00 0.00 4.40
28 29 4.065088 GTGTGAATGAGGTTTGAGCAGTA 58.935 43.478 0.00 0.00 0.00 2.74
29 30 4.515191 GTGTGAATGAGGTTTGAGCAGTAA 59.485 41.667 0.00 0.00 0.00 2.24
30 31 5.008613 GTGTGAATGAGGTTTGAGCAGTAAA 59.991 40.000 0.00 0.00 0.00 2.01
31 32 5.239306 TGTGAATGAGGTTTGAGCAGTAAAG 59.761 40.000 0.00 0.00 0.00 1.85
32 33 4.761739 TGAATGAGGTTTGAGCAGTAAAGG 59.238 41.667 0.00 0.00 0.00 3.11
33 34 3.140325 TGAGGTTTGAGCAGTAAAGGG 57.860 47.619 0.00 0.00 0.00 3.95
34 35 2.224769 TGAGGTTTGAGCAGTAAAGGGG 60.225 50.000 0.00 0.00 0.00 4.79
35 36 1.075536 AGGTTTGAGCAGTAAAGGGGG 59.924 52.381 0.00 0.00 0.00 5.40
36 37 1.074889 GGTTTGAGCAGTAAAGGGGGA 59.925 52.381 0.00 0.00 0.00 4.81
37 38 2.437413 GTTTGAGCAGTAAAGGGGGAG 58.563 52.381 0.00 0.00 0.00 4.30
38 39 2.038863 TTGAGCAGTAAAGGGGGAGA 57.961 50.000 0.00 0.00 0.00 3.71
39 40 1.573108 TGAGCAGTAAAGGGGGAGAG 58.427 55.000 0.00 0.00 0.00 3.20
40 41 0.833949 GAGCAGTAAAGGGGGAGAGG 59.166 60.000 0.00 0.00 0.00 3.69
77 78 2.554344 GGCCCATGAGTCCTTTGTGTTA 60.554 50.000 0.00 0.00 0.00 2.41
79 80 3.129287 GCCCATGAGTCCTTTGTGTTATG 59.871 47.826 0.00 0.00 0.00 1.90
89 90 6.995686 AGTCCTTTGTGTTATGTGTCATACAA 59.004 34.615 0.00 0.00 43.77 2.41
97 98 5.352846 TGTTATGTGTCATACAATCCCAACG 59.647 40.000 0.00 0.00 43.77 4.10
154 155 1.334160 TTGTCTAGGGCTCGTGAACA 58.666 50.000 0.00 0.00 0.00 3.18
213 214 1.710996 TTTGGTTCCCTCGCCTCCAA 61.711 55.000 0.00 0.00 36.55 3.53
222 223 1.068741 CCTCGCCTCCAACTACCATAC 59.931 57.143 0.00 0.00 0.00 2.39
273 275 6.867662 TCTTCAAGAGTTTCATGTTCTTCC 57.132 37.500 0.00 0.00 0.00 3.46
282 290 1.066858 TCATGTTCTTCCTCAGCGTCC 60.067 52.381 0.00 0.00 0.00 4.79
556 567 7.765695 TCAATTAAGGCTTTTCATCTTCTGT 57.234 32.000 4.45 0.00 0.00 3.41
649 661 1.246056 TGCTCCAGTCCAATTGCAGC 61.246 55.000 0.00 0.95 0.00 5.25
650 662 1.941999 GCTCCAGTCCAATTGCAGCC 61.942 60.000 0.00 0.00 0.00 4.85
651 663 0.609957 CTCCAGTCCAATTGCAGCCA 60.610 55.000 0.00 0.00 0.00 4.75
652 664 0.040058 TCCAGTCCAATTGCAGCCAT 59.960 50.000 0.00 0.00 0.00 4.40
688 700 9.890352 CAAAGTCTTTGAAGAATTTCTTCTAGG 57.110 33.333 29.74 24.48 46.62 3.02
799 839 9.715121 TGTATCGAATATGAATAAAACTACCCC 57.285 33.333 0.00 0.00 0.00 4.95
800 840 9.715121 GTATCGAATATGAATAAAACTACCCCA 57.285 33.333 0.00 0.00 0.00 4.96
801 841 8.617290 ATCGAATATGAATAAAACTACCCCAC 57.383 34.615 0.00 0.00 0.00 4.61
802 842 7.566569 TCGAATATGAATAAAACTACCCCACA 58.433 34.615 0.00 0.00 0.00 4.17
803 843 8.047911 TCGAATATGAATAAAACTACCCCACAA 58.952 33.333 0.00 0.00 0.00 3.33
804 844 8.679100 CGAATATGAATAAAACTACCCCACAAA 58.321 33.333 0.00 0.00 0.00 2.83
876 925 6.709397 ACTATACACGCATACTTAGCTACAGA 59.291 38.462 0.00 0.00 0.00 3.41
901 950 3.119029 GCCTACCAAACACGTCCATAGTA 60.119 47.826 0.00 0.00 0.00 1.82
1051 1103 1.743252 CGAGGAGGGCTTCAGCAAC 60.743 63.158 0.30 0.00 44.36 4.17
1144 1196 0.107831 TCCTATAAATTGCGCGGCCT 59.892 50.000 8.83 0.00 0.00 5.19
1472 1532 2.735772 CGGCCAGCCTGGTGTATCT 61.736 63.158 13.35 0.00 40.46 1.98
1474 1534 1.821332 GCCAGCCTGGTGTATCTGC 60.821 63.158 13.35 0.00 40.46 4.26
1538 1598 6.662865 TGCTATGGATCTTTTGTTTTTCCA 57.337 33.333 0.00 0.00 40.54 3.53
1632 1698 1.527034 GCTGGTGTTGCTTCTCATGA 58.473 50.000 0.00 0.00 0.00 3.07
1937 2013 0.404040 CCTCAGGGGCCTGTTTGTTA 59.596 55.000 0.84 0.00 43.96 2.41
2130 2206 2.040544 CACGGAAGAAATGGCGGCT 61.041 57.895 11.43 0.00 0.00 5.52
2967 3047 2.424302 CCAACCAAGGTCGACCGT 59.576 61.111 28.26 23.34 42.08 4.83
3547 3639 2.689471 TGTGCAATTTGCTCTGTCACTT 59.311 40.909 21.19 0.00 45.31 3.16
3596 3692 7.007723 TGTTTTGTGTAGTTTCCCCTCATAAT 58.992 34.615 0.00 0.00 0.00 1.28
3601 3734 4.721776 TGTAGTTTCCCCTCATAATGCTCT 59.278 41.667 0.00 0.00 0.00 4.09
3628 3762 6.715280 TCATAATGCTCTTTCTTCCAGAGTT 58.285 36.000 0.00 0.00 40.13 3.01
3770 3970 1.815408 GCCCAACTCAAGCAGAAGTGA 60.815 52.381 0.00 0.00 0.00 3.41
3798 3999 4.242811 TGGGATCTGGATTTATACTGCCT 58.757 43.478 0.00 0.00 0.00 4.75
3807 4008 5.189736 TGGATTTATACTGCCTCTGTTCACT 59.810 40.000 0.00 0.00 0.00 3.41
3813 4014 2.141517 CTGCCTCTGTTCACTTGACTG 58.858 52.381 0.00 0.00 0.00 3.51
3814 4015 1.762370 TGCCTCTGTTCACTTGACTGA 59.238 47.619 0.00 0.00 0.00 3.41
3815 4016 2.139118 GCCTCTGTTCACTTGACTGAC 58.861 52.381 0.00 0.00 0.00 3.51
3816 4017 2.224161 GCCTCTGTTCACTTGACTGACT 60.224 50.000 0.00 0.00 0.00 3.41
3817 4018 3.648009 CCTCTGTTCACTTGACTGACTC 58.352 50.000 0.00 0.00 0.00 3.36
3818 4019 3.320541 CCTCTGTTCACTTGACTGACTCT 59.679 47.826 0.00 0.00 0.00 3.24
3819 4020 4.297510 CTCTGTTCACTTGACTGACTCTG 58.702 47.826 0.00 0.00 0.00 3.35
3820 4021 3.701542 TCTGTTCACTTGACTGACTCTGT 59.298 43.478 0.00 0.00 0.00 3.41
3826 4027 4.402474 TCACTTGACTGACTCTGTTCTTGA 59.598 41.667 0.00 0.00 0.00 3.02
3827 4028 4.505922 CACTTGACTGACTCTGTTCTTGAC 59.494 45.833 0.00 0.00 0.00 3.18
3828 4029 4.160439 ACTTGACTGACTCTGTTCTTGACA 59.840 41.667 0.00 0.00 36.65 3.58
3829 4030 4.046938 TGACTGACTCTGTTCTTGACAC 57.953 45.455 0.00 0.00 33.82 3.67
3830 4031 3.447229 TGACTGACTCTGTTCTTGACACA 59.553 43.478 0.00 0.00 33.82 3.72
3831 4032 3.786635 ACTGACTCTGTTCTTGACACAC 58.213 45.455 0.00 0.00 33.82 3.82
3832 4033 3.195610 ACTGACTCTGTTCTTGACACACA 59.804 43.478 0.00 0.00 33.82 3.72
3833 4034 3.521560 TGACTCTGTTCTTGACACACAC 58.478 45.455 0.00 0.00 33.82 3.82
3834 4035 3.056179 TGACTCTGTTCTTGACACACACA 60.056 43.478 0.00 0.00 33.82 3.72
3835 4036 3.262420 ACTCTGTTCTTGACACACACAC 58.738 45.455 0.00 0.00 33.82 3.82
3838 4039 2.741517 CTGTTCTTGACACACACACACA 59.258 45.455 0.00 0.00 33.82 3.72
3842 4043 1.803555 CTTGACACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
3848 4049 3.194062 CACACACACACACACACTATGA 58.806 45.455 0.00 0.00 0.00 2.15
3893 4094 3.290948 TCAGGTTTGGTGTAAACTGCT 57.709 42.857 0.00 0.00 46.26 4.24
3900 4101 0.865769 GGTGTAAACTGCTGTCCACG 59.134 55.000 0.00 0.00 0.00 4.94
3940 4141 1.615107 CGTCGCCGGTCACTCTTTTC 61.615 60.000 1.90 0.00 0.00 2.29
3941 4142 1.005394 TCGCCGGTCACTCTTTTCC 60.005 57.895 1.90 0.00 0.00 3.13
4028 4232 1.275291 CGGCCTGACACTCTCCTTTTA 59.725 52.381 0.00 0.00 0.00 1.52
4029 4233 2.093447 CGGCCTGACACTCTCCTTTTAT 60.093 50.000 0.00 0.00 0.00 1.40
4030 4234 3.132289 CGGCCTGACACTCTCCTTTTATA 59.868 47.826 0.00 0.00 0.00 0.98
4104 4338 5.018539 TGCTCCTGGTACACATGTATAAC 57.981 43.478 0.00 0.00 32.54 1.89
4116 4350 7.096884 ACACATGTATAACGTACTGACTGAT 57.903 36.000 0.00 0.00 0.00 2.90
4215 4465 6.709145 TCTGTTTATTGAATGTTGCATTGC 57.291 33.333 0.46 0.46 0.00 3.56
4267 4521 9.325150 CATTACAGTAAACCAAGACATTTTACG 57.675 33.333 0.00 0.00 39.60 3.18
4277 4532 6.487331 ACCAAGACATTTTACGTGTATCCAAA 59.513 34.615 0.00 0.00 0.00 3.28
4330 4586 0.549658 TACCACCCGGGGTATTGGTT 60.550 55.000 31.99 18.96 42.42 3.67
4331 4587 1.384975 CCACCCGGGGTATTGGTTT 59.615 57.895 27.92 0.00 32.11 3.27
4345 4601 8.758829 GGGGTATTGGTTTTAGAAAAATCTGAT 58.241 33.333 0.00 0.00 0.00 2.90
4363 4619 8.868522 AATCTGATACTTGGAATGTTTCTTCA 57.131 30.769 0.00 0.00 0.00 3.02
4633 4892 0.743097 GGAACATGATTCCTGCCTGC 59.257 55.000 15.67 0.00 35.73 4.85
4635 4894 1.033746 AACATGATTCCTGCCTGCCG 61.034 55.000 0.00 0.00 0.00 5.69
4739 5027 7.559533 TGCAAAGTGGAGGCTATTCATATTTTA 59.440 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.154195 GCTCAAACCTCATTCACACGTTAT 59.846 41.667 0.00 0.00 0.00 1.89
2 3 3.496884 GCTCAAACCTCATTCACACGTTA 59.503 43.478 0.00 0.00 0.00 3.18
5 6 1.872952 TGCTCAAACCTCATTCACACG 59.127 47.619 0.00 0.00 0.00 4.49
6 7 2.880890 ACTGCTCAAACCTCATTCACAC 59.119 45.455 0.00 0.00 0.00 3.82
7 8 3.213206 ACTGCTCAAACCTCATTCACA 57.787 42.857 0.00 0.00 0.00 3.58
8 9 5.335191 CCTTTACTGCTCAAACCTCATTCAC 60.335 44.000 0.00 0.00 0.00 3.18
9 10 4.761739 CCTTTACTGCTCAAACCTCATTCA 59.238 41.667 0.00 0.00 0.00 2.57
10 11 4.156739 CCCTTTACTGCTCAAACCTCATTC 59.843 45.833 0.00 0.00 0.00 2.67
11 12 4.082125 CCCTTTACTGCTCAAACCTCATT 58.918 43.478 0.00 0.00 0.00 2.57
12 13 3.562176 CCCCTTTACTGCTCAAACCTCAT 60.562 47.826 0.00 0.00 0.00 2.90
13 14 2.224769 CCCCTTTACTGCTCAAACCTCA 60.225 50.000 0.00 0.00 0.00 3.86
14 15 2.437413 CCCCTTTACTGCTCAAACCTC 58.563 52.381 0.00 0.00 0.00 3.85
15 16 1.075536 CCCCCTTTACTGCTCAAACCT 59.924 52.381 0.00 0.00 0.00 3.50
16 17 1.074889 TCCCCCTTTACTGCTCAAACC 59.925 52.381 0.00 0.00 0.00 3.27
17 18 2.039879 TCTCCCCCTTTACTGCTCAAAC 59.960 50.000 0.00 0.00 0.00 2.93
18 19 2.305927 CTCTCCCCCTTTACTGCTCAAA 59.694 50.000 0.00 0.00 0.00 2.69
19 20 1.909302 CTCTCCCCCTTTACTGCTCAA 59.091 52.381 0.00 0.00 0.00 3.02
20 21 1.573108 CTCTCCCCCTTTACTGCTCA 58.427 55.000 0.00 0.00 0.00 4.26
21 22 0.833949 CCTCTCCCCCTTTACTGCTC 59.166 60.000 0.00 0.00 0.00 4.26
22 23 0.621862 CCCTCTCCCCCTTTACTGCT 60.622 60.000 0.00 0.00 0.00 4.24
23 24 0.914902 ACCCTCTCCCCCTTTACTGC 60.915 60.000 0.00 0.00 0.00 4.40
24 25 1.560146 GAACCCTCTCCCCCTTTACTG 59.440 57.143 0.00 0.00 0.00 2.74
25 26 1.557426 GGAACCCTCTCCCCCTTTACT 60.557 57.143 0.00 0.00 0.00 2.24
26 27 0.917533 GGAACCCTCTCCCCCTTTAC 59.082 60.000 0.00 0.00 0.00 2.01
27 28 0.804255 AGGAACCCTCTCCCCCTTTA 59.196 55.000 0.00 0.00 35.95 1.85
28 29 0.550393 GAGGAACCCTCTCCCCCTTT 60.550 60.000 5.78 0.00 46.41 3.11
29 30 1.083141 GAGGAACCCTCTCCCCCTT 59.917 63.158 5.78 0.00 46.41 3.95
30 31 2.788589 GAGGAACCCTCTCCCCCT 59.211 66.667 5.78 0.00 46.41 4.79
38 39 1.614824 CTGCCTGAGGAGGAACCCT 60.615 63.158 0.65 0.00 42.93 4.34
39 40 2.674220 CCTGCCTGAGGAGGAACCC 61.674 68.421 0.65 0.00 46.33 4.11
40 41 2.993853 CCTGCCTGAGGAGGAACC 59.006 66.667 0.65 0.00 46.33 3.62
77 78 3.054728 TCCGTTGGGATTGTATGACACAT 60.055 43.478 0.00 0.00 37.43 3.21
79 80 2.980568 TCCGTTGGGATTGTATGACAC 58.019 47.619 0.00 0.00 37.43 3.67
89 90 1.616159 CCTGTGTTTTCCGTTGGGAT 58.384 50.000 0.00 0.00 43.41 3.85
97 98 2.093711 AGTTTGGTTGCCTGTGTTTTCC 60.094 45.455 0.00 0.00 0.00 3.13
171 172 4.388499 CTAGCGGTGGTTGGCGGT 62.388 66.667 0.00 0.00 0.00 5.68
177 178 0.769247 AAAAGTCCCTAGCGGTGGTT 59.231 50.000 0.00 0.00 0.00 3.67
273 275 1.998315 CAAAGATCACTGGACGCTGAG 59.002 52.381 0.00 0.00 0.00 3.35
282 290 9.299963 TGTTTTCACAAAATACAAAGATCACTG 57.700 29.630 0.00 0.00 32.22 3.66
556 567 1.296392 CGCCTTGAGTCACCCATCA 59.704 57.895 0.00 0.00 0.00 3.07
649 661 6.003950 TCAAAGACTTTGGTAAAGAGGATGG 58.996 40.000 24.22 0.00 41.02 3.51
650 662 7.445402 TCTTCAAAGACTTTGGTAAAGAGGATG 59.555 37.037 24.22 7.33 41.02 3.51
651 663 7.518188 TCTTCAAAGACTTTGGTAAAGAGGAT 58.482 34.615 24.22 0.00 41.02 3.24
652 664 6.895782 TCTTCAAAGACTTTGGTAAAGAGGA 58.104 36.000 24.22 9.67 41.02 3.71
688 700 6.697892 CACCTTCTTCGTGGTATTAATCTCTC 59.302 42.308 0.00 0.00 34.79 3.20
876 925 1.903860 TGGACGTGTTTGGTAGGCTAT 59.096 47.619 0.00 0.00 0.00 2.97
901 950 0.036732 TGAGCTGCCTCCGTCAATTT 59.963 50.000 0.00 0.00 37.29 1.82
1085 1137 1.080974 GCATGAGTGTTGCTGGTGC 60.081 57.895 0.00 0.00 37.14 5.01
1144 1196 1.884075 CGGTGTTGTCCGGAGATCCA 61.884 60.000 3.06 0.00 45.88 3.41
1296 1348 0.179084 AAGCGACCCACGTATGATGG 60.179 55.000 0.00 0.00 44.60 3.51
1500 1560 0.587768 TAGCAAAGTGACGACGACGA 59.412 50.000 15.32 0.00 42.66 4.20
1501 1561 1.317611 CATAGCAAAGTGACGACGACG 59.682 52.381 5.58 5.58 45.75 5.12
1502 1562 1.654105 CCATAGCAAAGTGACGACGAC 59.346 52.381 0.00 0.00 0.00 4.34
1503 1563 1.542472 TCCATAGCAAAGTGACGACGA 59.458 47.619 0.00 0.00 0.00 4.20
1762 1836 2.254152 AGGAAGGGCACATCTCACTA 57.746 50.000 0.00 0.00 0.00 2.74
1937 2013 7.531857 AAAAACACCCCAAAACAAGAAAAAT 57.468 28.000 0.00 0.00 0.00 1.82
1962 2038 0.107410 ACGTCCAGGCACAACAAGAA 60.107 50.000 0.00 0.00 0.00 2.52
2035 2111 1.729131 CGTGCCACAAAATCACGGC 60.729 57.895 6.15 0.00 46.68 5.68
2967 3047 1.153249 GGCAATGTAGGCGCCACTA 60.153 57.895 31.54 14.49 45.52 2.74
3547 3639 7.441157 ACAGAATATGAAAAGTGAAAGTGACGA 59.559 33.333 0.00 0.00 0.00 4.20
3596 3692 4.408270 AGAAAGAGCATTATGAGGAGAGCA 59.592 41.667 0.00 0.00 0.00 4.26
3601 3734 5.426509 TCTGGAAGAAAGAGCATTATGAGGA 59.573 40.000 0.00 0.00 42.31 3.71
3628 3762 8.405531 GCAATAGAATTACACATGGCTCTTTAA 58.594 33.333 0.00 0.00 0.00 1.52
3770 3970 7.395489 GCAGTATAAATCCAGATCCCATCAAAT 59.605 37.037 0.00 0.00 0.00 2.32
3798 3999 3.701542 ACAGAGTCAGTCAAGTGAACAGA 59.298 43.478 0.00 0.00 0.00 3.41
3807 4008 4.081697 TGTGTCAAGAACAGAGTCAGTCAA 60.082 41.667 0.00 0.00 38.97 3.18
3813 4014 3.307242 GTGTGTGTGTCAAGAACAGAGTC 59.693 47.826 0.00 0.00 38.97 3.36
3814 4015 3.262420 GTGTGTGTGTCAAGAACAGAGT 58.738 45.455 0.00 0.00 38.97 3.24
3815 4016 3.062639 GTGTGTGTGTGTCAAGAACAGAG 59.937 47.826 0.00 0.00 38.97 3.35
3816 4017 3.000041 GTGTGTGTGTGTCAAGAACAGA 59.000 45.455 0.00 0.00 38.97 3.41
3817 4018 2.741517 TGTGTGTGTGTGTCAAGAACAG 59.258 45.455 0.00 0.00 38.97 3.16
3818 4019 2.482336 GTGTGTGTGTGTGTCAAGAACA 59.518 45.455 0.00 0.00 34.78 3.18
3819 4020 2.482336 TGTGTGTGTGTGTGTCAAGAAC 59.518 45.455 0.00 0.00 0.00 3.01
3820 4021 2.482336 GTGTGTGTGTGTGTGTCAAGAA 59.518 45.455 0.00 0.00 0.00 2.52
3826 4027 2.753055 TAGTGTGTGTGTGTGTGTGT 57.247 45.000 0.00 0.00 0.00 3.72
3827 4028 3.001228 GTCATAGTGTGTGTGTGTGTGTG 59.999 47.826 0.00 0.00 0.00 3.82
3828 4029 3.118775 AGTCATAGTGTGTGTGTGTGTGT 60.119 43.478 0.00 0.00 0.00 3.72
3829 4030 3.457234 AGTCATAGTGTGTGTGTGTGTG 58.543 45.455 0.00 0.00 0.00 3.82
3830 4031 3.384789 AGAGTCATAGTGTGTGTGTGTGT 59.615 43.478 0.00 0.00 0.00 3.72
3831 4032 3.982475 AGAGTCATAGTGTGTGTGTGTG 58.018 45.455 0.00 0.00 0.00 3.82
3832 4033 3.304726 CGAGAGTCATAGTGTGTGTGTGT 60.305 47.826 0.00 0.00 0.00 3.72
3833 4034 3.058224 TCGAGAGTCATAGTGTGTGTGTG 60.058 47.826 0.00 0.00 0.00 3.82
3834 4035 3.146847 TCGAGAGTCATAGTGTGTGTGT 58.853 45.455 0.00 0.00 0.00 3.72
3835 4036 3.831715 TCGAGAGTCATAGTGTGTGTG 57.168 47.619 0.00 0.00 0.00 3.82
3838 4039 5.358160 TGATGATTCGAGAGTCATAGTGTGT 59.642 40.000 10.42 0.00 37.80 3.72
3842 4043 9.454859 TGTATATGATGATTCGAGAGTCATAGT 57.545 33.333 10.42 5.98 37.80 2.12
3848 4049 9.800433 GATCAATGTATATGATGATTCGAGAGT 57.200 33.333 0.00 0.00 37.64 3.24
3940 4141 0.187361 TTCCAACCAAAGTCAGGGGG 59.813 55.000 0.00 0.00 0.00 5.40
3941 4142 2.299867 CAATTCCAACCAAAGTCAGGGG 59.700 50.000 0.00 0.00 0.00 4.79
4104 4338 6.843208 TCTCAGAGTTTTATCAGTCAGTACG 58.157 40.000 0.00 0.00 0.00 3.67
4116 4350 9.935241 GGAATATATCATGCTCTCAGAGTTTTA 57.065 33.333 2.93 0.00 31.39 1.52
4277 4532 6.535150 CACTCACACTCATAATGTAAACCGAT 59.465 38.462 0.00 0.00 0.00 4.18
4345 4601 5.763204 GGTGAGTGAAGAAACATTCCAAGTA 59.237 40.000 0.00 0.00 0.00 2.24
4363 4619 3.265221 ACATTGGTGATGATCAGGTGAGT 59.735 43.478 0.09 0.00 39.15 3.41


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

AutoCloner maintained by Alex Coulton.