Multiple sequence alignment - TraesCS3A01G150600

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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 TraesCS3A01G150600 chr3A 100.000 4439 0 0 1 4439 137612895 137608457 0.000000e+00 8198
1 TraesCS3A01G150600 chr3D 94.944 2492 93 11 851 3335 126981807 126979342 0.000000e+00 3873
2 TraesCS3A01G150600 chr3D 93.065 721 44 5 1 719 304905996 304905280 0.000000e+00 1050
3 TraesCS3A01G150600 chr3D 87.034 617 59 13 3837 4439 126978954 126978345 0.000000e+00 676
4 TraesCS3A01G150600 chr3D 79.630 324 35 16 3403 3706 126979317 126979005 2.090000e-48 204
5 TraesCS3A01G150600 chr3B 93.553 1908 88 13 1927 3816 181321032 181319142 0.000000e+00 2809
6 TraesCS3A01G150600 chr3B 91.752 1176 74 16 816 1982 181322183 181321022 0.000000e+00 1613
7 TraesCS3A01G150600 chr3B 89.263 624 36 19 3834 4439 181319160 181318550 0.000000e+00 752
8 TraesCS3A01G150600 chr7D 91.363 822 62 7 1 818 565209137 565209953 0.000000e+00 1116
9 TraesCS3A01G150600 chr7D 93.147 715 38 8 1 712 83806068 83805362 0.000000e+00 1038
10 TraesCS3A01G150600 chr4D 91.230 821 62 5 1 818 476862964 476862151 0.000000e+00 1109
11 TraesCS3A01G150600 chr5D 90.898 824 66 6 1 817 431560230 431559409 0.000000e+00 1098
12 TraesCS3A01G150600 chr2D 89.903 822 78 4 1 817 564075211 564074390 0.000000e+00 1053
13 TraesCS3A01G150600 chr2A 88.983 826 76 12 1 817 507075158 507074339 0.000000e+00 1007
14 TraesCS3A01G150600 chr5A 88.499 826 84 7 1 817 400670322 400669499 0.000000e+00 989
15 TraesCS3A01G150600 chr1A 88.480 816 86 7 1 812 478546784 478547595 0.000000e+00 979
16 TraesCS3A01G150600 chr7A 85.340 191 25 2 629 818 230611072 230610884 1.260000e-45 195


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 TraesCS3A01G150600 chr3A 137608457 137612895 4438 True 8198.000000 8198 100.000000 1 4439 1 chr3A.!!$R1 4438
1 TraesCS3A01G150600 chr3D 126978345 126981807 3462 True 1584.333333 3873 87.202667 851 4439 3 chr3D.!!$R2 3588
2 TraesCS3A01G150600 chr3D 304905280 304905996 716 True 1050.000000 1050 93.065000 1 719 1 chr3D.!!$R1 718
3 TraesCS3A01G150600 chr3B 181318550 181322183 3633 True 1724.666667 2809 91.522667 816 4439 3 chr3B.!!$R1 3623
4 TraesCS3A01G150600 chr7D 565209137 565209953 816 False 1116.000000 1116 91.363000 1 818 1 chr7D.!!$F1 817
5 TraesCS3A01G150600 chr7D 83805362 83806068 706 True 1038.000000 1038 93.147000 1 712 1 chr7D.!!$R1 711
6 TraesCS3A01G150600 chr4D 476862151 476862964 813 True 1109.000000 1109 91.230000 1 818 1 chr4D.!!$R1 817
7 TraesCS3A01G150600 chr5D 431559409 431560230 821 True 1098.000000 1098 90.898000 1 817 1 chr5D.!!$R1 816
8 TraesCS3A01G150600 chr2D 564074390 564075211 821 True 1053.000000 1053 89.903000 1 817 1 chr2D.!!$R1 816
9 TraesCS3A01G150600 chr2A 507074339 507075158 819 True 1007.000000 1007 88.983000 1 817 1 chr2A.!!$R1 816
10 TraesCS3A01G150600 chr5A 400669499 400670322 823 True 989.000000 989 88.499000 1 817 1 chr5A.!!$R1 816
11 TraesCS3A01G150600 chr1A 478546784 478547595 811 False 979.000000 979 88.480000 1 812 1 chr1A.!!$F1 811

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
774 788 0.037447 TGTCCATGCCGATCCAAACA 59.963 50.0 0.0 0.0 0.00 2.83 F
1521 1537 1.051556 TGCTGGTGTGGTAGGTGTGA 61.052 55.0 0.0 0.0 0.00 3.58 F
2975 3048 0.109319 CACCATGCCAAGGTAAACGC 60.109 55.0 0.0 0.0 37.23 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2759 2832 0.245539 GCACAGCATTCAAGTGGCAT 59.754 50.0 0.00 0.0 33.98 4.40 R
3216 3289 0.029035 CCATCTTCTGCAGCGCATTC 59.971 55.0 11.47 0.0 38.13 2.67 R
3897 3996 0.250684 TGCCAAAGGATGCTTGTCGA 60.251 50.0 0.00 0.0 0.00 4.20 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
161 162 0.392998 GTGAGTCGGGCATCACCATT 60.393 55.000 0.00 0.00 39.94 3.16
265 266 4.070552 GAGCGCCTCCCTCGTTGT 62.071 66.667 2.29 0.00 0.00 3.32
322 326 4.162690 GGCCTCATCCCTCGCGTT 62.163 66.667 5.77 0.00 0.00 4.84
405 412 3.215597 TTCTTCGGCTTGGTCGCGA 62.216 57.895 3.71 3.71 0.00 5.87
627 641 0.396001 GCCCGAGAAGAGGAGTAGGT 60.396 60.000 0.00 0.00 0.00 3.08
629 643 0.741915 CCGAGAAGAGGAGTAGGTGC 59.258 60.000 0.00 0.00 0.00 5.01
690 704 3.007831 CAGCTTAAAATTGGGCCTGGAAA 59.992 43.478 4.53 0.00 0.00 3.13
751 765 2.748647 GGCACGTTGGGCCGTTAT 60.749 61.111 0.00 0.00 42.39 1.89
761 775 2.530701 TGGGCCGTTATTTTTGTCCAT 58.469 42.857 0.00 0.00 0.00 3.41
774 788 0.037447 TGTCCATGCCGATCCAAACA 59.963 50.000 0.00 0.00 0.00 2.83
775 789 1.173043 GTCCATGCCGATCCAAACAA 58.827 50.000 0.00 0.00 0.00 2.83
814 829 1.537202 GTCGCTTCATTGGAGTTGCTT 59.463 47.619 0.00 0.00 0.00 3.91
834 849 4.819088 GCTTTAATTTCCCCTTGCAAAACA 59.181 37.500 0.00 0.00 0.00 2.83
838 853 1.859302 TTCCCCTTGCAAAACACAGT 58.141 45.000 0.00 0.00 0.00 3.55
891 907 1.078426 CAGAACCTACCAAGCCCGG 60.078 63.158 0.00 0.00 0.00 5.73
906 922 2.414785 CCGGCCCCCAAAATTCTCG 61.415 63.158 0.00 0.00 0.00 4.04
1185 1201 2.825836 ACCGCCTACGACTACCCG 60.826 66.667 0.00 0.00 43.93 5.28
1449 1465 1.299926 CCGATTCGATCCGGTGGAC 60.300 63.158 15.34 0.00 40.78 4.02
1452 1468 1.268625 CGATTCGATCCGGTGGACATA 59.731 52.381 0.00 0.00 32.98 2.29
1467 1483 6.405286 CGGTGGACATAGAAATTAAATTGCCA 60.405 38.462 0.00 0.00 0.00 4.92
1489 1505 1.724582 ATGCCGCCCGTTAGCAATTC 61.725 55.000 0.00 0.00 40.46 2.17
1521 1537 1.051556 TGCTGGTGTGGTAGGTGTGA 61.052 55.000 0.00 0.00 0.00 3.58
1531 1547 2.158682 TGGTAGGTGTGACATGCTTTGT 60.159 45.455 0.00 0.00 42.79 2.83
1544 1560 4.724798 ACATGCTTTGTACTCCCCCTATTA 59.275 41.667 0.00 0.00 36.57 0.98
1567 1583 1.201647 CTCTCCAGTTGCCATTTGCTG 59.798 52.381 0.00 0.00 42.00 4.41
1594 1614 5.355350 GTCAGTAAGGAATTGCTATGCTTGT 59.645 40.000 0.00 0.00 30.65 3.16
1634 1656 2.430248 TGCATGTCCCGTAGAGTAGA 57.570 50.000 0.00 0.00 0.00 2.59
1810 1833 9.102757 GTTGTCACAATGATCTATCTGTATTGT 57.897 33.333 0.00 0.00 41.23 2.71
1931 1955 3.489229 CCAACTCATGAGCATGCTGAATG 60.489 47.826 28.27 25.92 38.65 2.67
1945 2012 4.383173 TGCTGAATGCGATAGACATGAAT 58.617 39.130 0.00 0.00 46.63 2.57
1952 2019 9.305925 TGAATGCGATAGACATGAATATATGAC 57.694 33.333 0.00 0.00 34.07 3.06
1960 2027 7.920908 AGACATGAATATATGACGCATATCG 57.079 36.000 13.32 0.00 38.00 2.92
2035 2105 6.055588 GTGTATAAGAGCTAGGCATTTTGGA 58.944 40.000 0.00 0.00 0.00 3.53
2198 2268 2.291735 TGGAATTGCTGTCATGGGTCAT 60.292 45.455 0.00 0.00 0.00 3.06
2332 2402 3.204306 AGCATGTATCATGACCTGTGG 57.796 47.619 12.98 0.00 0.00 4.17
2373 2443 4.216042 TCCATGTTATTCTGCTTGTGTGTG 59.784 41.667 0.00 0.00 0.00 3.82
2392 2462 1.416030 TGCAGGTTGTAGAGACAGCAA 59.584 47.619 0.00 0.00 38.47 3.91
2397 2467 2.337583 GTTGTAGAGACAGCAATCGCA 58.662 47.619 0.00 0.00 42.27 5.10
2536 2606 4.526970 CAGTGGGCAGGTACAATTATTCT 58.473 43.478 0.00 0.00 0.00 2.40
2555 2625 9.664332 ATTATTCTTCATGCTCTATCCATACAC 57.336 33.333 0.00 0.00 0.00 2.90
2632 2705 9.716531 TTCTATCTATGTAAGCAATTCCTCATG 57.283 33.333 0.00 0.00 0.00 3.07
2726 2799 2.223805 GCACCTTTTCCCTGACAACTTG 60.224 50.000 0.00 0.00 0.00 3.16
2729 2802 3.699538 ACCTTTTCCCTGACAACTTGAAC 59.300 43.478 0.00 0.00 0.00 3.18
2730 2803 3.699038 CCTTTTCCCTGACAACTTGAACA 59.301 43.478 0.00 0.00 0.00 3.18
2732 2805 5.163416 CCTTTTCCCTGACAACTTGAACAAT 60.163 40.000 0.00 0.00 0.00 2.71
2759 2832 5.410439 GTGCCGAAAGAAACCTAGTCAAATA 59.590 40.000 0.00 0.00 0.00 1.40
2775 2848 4.802039 GTCAAATATGCCACTTGAATGCTG 59.198 41.667 0.00 0.00 31.21 4.41
2776 2849 4.463539 TCAAATATGCCACTTGAATGCTGT 59.536 37.500 0.00 0.00 0.00 4.40
2816 2889 6.274579 TGCATATTTTGTTATCACCATGCAG 58.725 36.000 2.03 0.00 41.71 4.41
2819 2892 7.168637 GCATATTTTGTTATCACCATGCAGAAG 59.831 37.037 0.00 0.00 37.92 2.85
2821 2894 3.998913 TGTTATCACCATGCAGAAGGA 57.001 42.857 9.37 0.00 0.00 3.36
2858 2931 6.015519 TGTTTCCATGTATTCCAAAACCAGAG 60.016 38.462 0.00 0.00 0.00 3.35
2875 2948 3.557595 CCAGAGAATTGGCGTCTATGTTC 59.442 47.826 6.55 0.00 33.41 3.18
2881 2954 5.824624 AGAATTGGCGTCTATGTTCATTCAT 59.175 36.000 0.00 0.00 0.00 2.57
2898 2971 7.395190 TCATTCATGAAACCCTAATGTCAAG 57.605 36.000 13.09 0.00 33.08 3.02
2975 3048 0.109319 CACCATGCCAAGGTAAACGC 60.109 55.000 0.00 0.00 37.23 4.84
3019 3092 6.212388 TGCCCAGAAATTTTACCATGTTATGT 59.788 34.615 0.00 0.00 0.00 2.29
3051 3124 5.294552 GCCGAGCTCAAGTCTATACAATTTT 59.705 40.000 15.40 0.00 0.00 1.82
3177 3250 4.704833 CCTGGCCCCAGTCACACG 62.705 72.222 12.98 0.00 42.15 4.49
3195 3268 0.872388 CGCCCTATAAAATCACCGCC 59.128 55.000 0.00 0.00 0.00 6.13
3204 3277 1.453155 AAATCACCGCCACAGATGTC 58.547 50.000 0.00 0.00 0.00 3.06
3216 3289 0.027194 CAGATGTCGATGGCTTTGCG 59.973 55.000 0.00 0.00 0.00 4.85
3297 3370 5.412594 TGAGAACTCGGAAAATGATGGAAAG 59.587 40.000 0.00 0.00 0.00 2.62
3539 3624 1.518367 TCAAGGGTGAAAGGGACTGT 58.482 50.000 0.00 0.00 40.86 3.55
3624 3715 1.512694 CCTCCGGCAATTTTCTGGC 59.487 57.895 0.00 0.00 38.47 4.85
3714 3812 4.625324 CGACCATTTCAAATACTCCCTCCA 60.625 45.833 0.00 0.00 0.00 3.86
3739 3837 7.789273 TCAGGAAATAAGTGACGTTGTTTTA 57.211 32.000 0.00 0.00 0.00 1.52
3802 3901 4.236527 ACTCAGACCAACAAACTTCCTT 57.763 40.909 0.00 0.00 0.00 3.36
3803 3902 5.367945 ACTCAGACCAACAAACTTCCTTA 57.632 39.130 0.00 0.00 0.00 2.69
3804 3903 5.123936 ACTCAGACCAACAAACTTCCTTAC 58.876 41.667 0.00 0.00 0.00 2.34
3805 3904 5.105567 TCAGACCAACAAACTTCCTTACA 57.894 39.130 0.00 0.00 0.00 2.41
3806 3905 5.123227 TCAGACCAACAAACTTCCTTACAG 58.877 41.667 0.00 0.00 0.00 2.74
3807 3906 4.881850 CAGACCAACAAACTTCCTTACAGT 59.118 41.667 0.00 0.00 0.00 3.55
3808 3907 6.053005 CAGACCAACAAACTTCCTTACAGTA 58.947 40.000 0.00 0.00 0.00 2.74
3809 3908 6.202954 CAGACCAACAAACTTCCTTACAGTAG 59.797 42.308 0.00 0.00 0.00 2.57
3810 3909 5.997843 ACCAACAAACTTCCTTACAGTAGT 58.002 37.500 0.00 0.00 0.00 2.73
3811 3910 6.420638 ACCAACAAACTTCCTTACAGTAGTT 58.579 36.000 0.00 0.00 32.52 2.24
3812 3911 6.888088 ACCAACAAACTTCCTTACAGTAGTTT 59.112 34.615 0.00 0.00 40.42 2.66
3813 3912 7.395206 ACCAACAAACTTCCTTACAGTAGTTTT 59.605 33.333 0.00 0.00 38.41 2.43
3814 3913 8.248253 CCAACAAACTTCCTTACAGTAGTTTTT 58.752 33.333 0.00 0.00 38.41 1.94
3894 3993 7.761651 AGCGCTCAATATACATATACATGTG 57.238 36.000 2.64 0.00 45.17 3.21
3896 3995 6.035975 GCGCTCAATATACATATACATGTGCA 59.964 38.462 9.11 0.00 45.17 4.57
3897 3996 7.254556 GCGCTCAATATACATATACATGTGCAT 60.255 37.037 9.11 0.00 45.17 3.96
3912 4011 1.470098 GTGCATCGACAAGCATCCTTT 59.530 47.619 11.50 0.00 43.44 3.11
3920 4019 0.529378 CAAGCATCCTTTGGCAGACC 59.471 55.000 0.00 0.00 0.00 3.85
4024 4124 2.299582 CTGTCAAAACCATGGGCAATCA 59.700 45.455 18.09 7.11 0.00 2.57
4026 4126 3.327172 TGTCAAAACCATGGGCAATCAAT 59.673 39.130 18.09 0.00 0.00 2.57
4027 4127 3.685756 GTCAAAACCATGGGCAATCAATG 59.314 43.478 18.09 3.67 0.00 2.82
4042 4148 5.412640 CAATCAATGCTTGCATCACCTAAA 58.587 37.500 8.64 0.00 0.00 1.85
4096 4202 0.451383 TTTGCAGCGCCATATGACAC 59.549 50.000 2.29 0.00 0.00 3.67
4101 4207 1.114627 AGCGCCATATGACACTCTGA 58.885 50.000 2.29 0.00 0.00 3.27
4117 4224 8.988934 TGACACTCTGAAGTTAAATATTGACAC 58.011 33.333 0.00 0.00 31.71 3.67
4132 4239 8.673626 AATATTGACACGTTCAGCTAATTTTG 57.326 30.769 0.00 0.00 34.94 2.44
4134 4254 4.843147 TGACACGTTCAGCTAATTTTGTG 58.157 39.130 0.00 0.00 0.00 3.33
4151 4271 4.926860 TTGTGAAGACATCAAGTATGCG 57.073 40.909 0.00 0.00 40.50 4.73
4174 4300 2.030363 CAGGATCGACTGGATGAGTAGC 60.030 54.545 0.00 0.00 34.82 3.58
4260 4386 7.881142 TGAATCTCGTGTACCAAAAATGAATT 58.119 30.769 0.00 0.00 0.00 2.17
4331 4457 3.679389 ACAAACAGCGGATCTTTCTCAT 58.321 40.909 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 1.138883 CTCGTCGGCATTTCCTCGA 59.861 57.895 0.00 0.00 37.33 4.04
195 196 4.473520 CCTCCAAGCCGCCATCGT 62.474 66.667 0.00 0.00 0.00 3.73
505 512 1.202734 CCATGAAGGATGCCATCGACT 60.203 52.381 0.00 0.00 41.22 4.18
515 522 1.496429 CCCCAACTAGCCATGAAGGAT 59.504 52.381 0.00 0.00 41.22 3.24
549 558 4.050934 CAAAAACGCTCCCGCCCC 62.051 66.667 0.00 0.00 38.22 5.80
567 576 4.225717 CCACCATCATTTTCCCATTTTCCT 59.774 41.667 0.00 0.00 0.00 3.36
613 625 1.178276 CGTGCACCTACTCCTCTTCT 58.822 55.000 12.15 0.00 0.00 2.85
658 672 5.997129 CCCAATTTTAAGCTGGATTTGTGTT 59.003 36.000 0.00 0.00 31.38 3.32
749 763 3.625853 TGGATCGGCATGGACAAAAATA 58.374 40.909 0.00 0.00 0.00 1.40
751 765 1.916506 TGGATCGGCATGGACAAAAA 58.083 45.000 0.00 0.00 0.00 1.94
761 775 0.309302 CGTGTTTGTTTGGATCGGCA 59.691 50.000 0.00 0.00 0.00 5.69
774 788 0.863144 CATTTCGTCCGTCCGTGTTT 59.137 50.000 0.00 0.00 0.00 2.83
775 789 0.947180 CCATTTCGTCCGTCCGTGTT 60.947 55.000 0.00 0.00 0.00 3.32
799 814 6.463360 GGGAAATTAAAGCAACTCCAATGAA 58.537 36.000 0.00 0.00 0.00 2.57
800 815 5.046663 GGGGAAATTAAAGCAACTCCAATGA 60.047 40.000 0.00 0.00 0.00 2.57
814 829 5.104735 ACTGTGTTTTGCAAGGGGAAATTAA 60.105 36.000 0.00 0.00 34.15 1.40
838 853 1.662876 GGTTTGCGTCGTACAGTCGTA 60.663 52.381 0.00 0.00 34.03 3.43
875 891 2.437895 GCCGGGCTTGGTAGGTTC 60.438 66.667 12.87 0.00 0.00 3.62
891 907 1.472878 GAGAACGAGAATTTTGGGGGC 59.527 52.381 0.00 0.00 0.00 5.80
906 922 4.678309 CGGGAGTCTTTGGATACTGAGAAC 60.678 50.000 0.00 0.00 31.64 3.01
1449 1465 8.649841 CGGCATTATGGCAATTTAATTTCTATG 58.350 33.333 18.57 0.00 43.94 2.23
1452 1468 5.466393 GCGGCATTATGGCAATTTAATTTCT 59.534 36.000 18.57 0.00 43.94 2.52
1467 1483 0.464735 TTGCTAACGGGCGGCATTAT 60.465 50.000 12.47 0.00 35.84 1.28
1489 1505 1.962144 CCAGCAGTGGCAAAGAAGG 59.038 57.895 0.00 0.00 44.61 3.46
1521 1537 1.372501 AGGGGGAGTACAAAGCATGT 58.627 50.000 0.00 0.67 46.36 3.21
1531 1547 3.801317 TGGAGAGGTTAATAGGGGGAGTA 59.199 47.826 0.00 0.00 0.00 2.59
1544 1560 2.242043 CAAATGGCAACTGGAGAGGTT 58.758 47.619 0.00 0.00 37.61 3.50
1567 1583 4.025647 GCATAGCAATTCCTTACTGACGAC 60.026 45.833 0.00 0.00 0.00 4.34
1594 1614 2.157834 AATTAGTGCCGTCACACGAA 57.842 45.000 0.00 0.00 46.05 3.85
1931 1955 5.743872 TGCGTCATATATTCATGTCTATCGC 59.256 40.000 0.00 0.00 38.29 4.58
1960 2027 6.985117 TGATACCGTATTACCATTCCACTAC 58.015 40.000 0.00 0.00 0.00 2.73
1966 2033 6.926826 TGACACATGATACCGTATTACCATTC 59.073 38.462 0.00 0.00 0.00 2.67
2035 2105 9.686683 AAAGGTATATTACATGAAAGCTCAAGT 57.313 29.630 0.00 0.00 37.30 3.16
2332 2402 4.439305 TGGAGCAAAATGTATGTCAAGC 57.561 40.909 0.00 0.00 0.00 4.01
2373 2443 2.169832 TTGCTGTCTCTACAACCTGC 57.830 50.000 0.00 0.00 34.49 4.85
2392 2462 1.381928 CCAGCCTCTTGCAATGCGAT 61.382 55.000 0.00 0.00 44.83 4.58
2397 2467 1.969862 GCAACCAGCCTCTTGCAAT 59.030 52.632 0.00 0.00 44.83 3.56
2536 2606 6.676990 ATCAGTGTATGGATAGAGCATGAA 57.323 37.500 0.00 0.00 0.00 2.57
2612 2685 4.823442 TGCCATGAGGAATTGCTTACATAG 59.177 41.667 0.00 0.00 36.89 2.23
2623 2696 1.038681 TTGCGCATGCCATGAGGAAT 61.039 50.000 12.75 0.00 41.78 3.01
2631 2704 1.655885 GCATAGATTGCGCATGCCA 59.344 52.632 19.61 8.49 42.54 4.92
2632 2705 4.546637 GCATAGATTGCGCATGCC 57.453 55.556 19.61 8.62 42.54 4.40
2726 2799 4.026062 GGTTTCTTTCGGCACAAATTGTTC 60.026 41.667 0.00 0.00 0.00 3.18
2729 2802 3.716601 AGGTTTCTTTCGGCACAAATTG 58.283 40.909 0.00 0.00 0.00 2.32
2730 2803 4.583073 ACTAGGTTTCTTTCGGCACAAATT 59.417 37.500 0.00 0.00 0.00 1.82
2732 2805 3.547746 ACTAGGTTTCTTTCGGCACAAA 58.452 40.909 0.00 0.00 0.00 2.83
2759 2832 0.245539 GCACAGCATTCAAGTGGCAT 59.754 50.000 0.00 0.00 33.98 4.40
2775 2848 0.807496 GCAAGACCAAGAGGATGCAC 59.193 55.000 0.00 0.00 40.05 4.57
2776 2849 0.401356 TGCAAGACCAAGAGGATGCA 59.599 50.000 0.00 0.00 44.15 3.96
2782 2855 8.461222 TGATAACAAAATATGCAAGACCAAGAG 58.539 33.333 0.00 0.00 0.00 2.85
2858 2931 5.484173 TGAATGAACATAGACGCCAATTC 57.516 39.130 0.00 0.00 0.00 2.17
2875 2948 7.094248 TGTCTTGACATTAGGGTTTCATGAATG 60.094 37.037 9.40 5.21 34.40 2.67
2881 2954 6.549364 ACAAATGTCTTGACATTAGGGTTTCA 59.451 34.615 23.80 0.00 39.18 2.69
2887 2960 6.032094 GCATGACAAATGTCTTGACATTAGG 58.968 40.000 25.07 20.67 46.77 2.69
2890 2963 5.456548 TGCATGACAAATGTCTTGACATT 57.543 34.783 25.07 19.61 46.77 2.71
2891 2964 4.082408 CCTGCATGACAAATGTCTTGACAT 60.082 41.667 25.07 10.15 46.77 3.06
2898 2971 3.366679 CCAAGACCTGCATGACAAATGTC 60.367 47.826 6.60 6.60 44.97 3.06
2975 3048 3.864686 CGCTGAAATGGACGGCCG 61.865 66.667 26.86 26.86 36.42 6.13
3019 3092 1.638388 CTTGAGCTCGGCGCAAATCA 61.638 55.000 10.83 2.56 46.28 2.57
3051 3124 1.838396 TGTCACCTGCAGGCAGAGA 60.838 57.895 33.06 24.69 46.30 3.10
3177 3250 1.607148 GTGGCGGTGATTTTATAGGGC 59.393 52.381 0.00 0.00 0.00 5.19
3180 3253 4.816385 ACATCTGTGGCGGTGATTTTATAG 59.184 41.667 0.00 0.00 0.00 1.31
3195 3268 1.202110 GCAAAGCCATCGACATCTGTG 60.202 52.381 0.00 0.00 0.00 3.66
3204 3277 1.935917 CGCATTCGCAAAGCCATCG 60.936 57.895 0.00 0.00 38.40 3.84
3216 3289 0.029035 CCATCTTCTGCAGCGCATTC 59.971 55.000 11.47 0.00 38.13 2.67
3225 3298 0.890683 CACCCAAACCCATCTTCTGC 59.109 55.000 0.00 0.00 0.00 4.26
3297 3370 2.422276 ATCAACTGTTTTCGCTTGGC 57.578 45.000 0.00 0.00 0.00 4.52
3300 3373 5.248870 ACTGAAATCAACTGTTTTCGCTT 57.751 34.783 8.13 0.00 36.84 4.68
3337 3410 1.002544 GCCCTGCAGTCTTGTACTCTT 59.997 52.381 13.81 0.00 35.76 2.85
3338 3411 0.610687 GCCCTGCAGTCTTGTACTCT 59.389 55.000 13.81 0.00 35.76 3.24
3521 3606 1.956477 CAACAGTCCCTTTCACCCTTG 59.044 52.381 0.00 0.00 0.00 3.61
3539 3624 2.992593 TGTGTAAGGTGCTCACAACAA 58.007 42.857 2.21 0.00 38.80 2.83
3618 3709 5.538053 TGATTTATGTTGTTCTTGGCCAGAA 59.462 36.000 5.11 9.55 39.39 3.02
3624 3715 7.912250 GCTCATACTGATTTATGTTGTTCTTGG 59.088 37.037 0.00 0.00 32.17 3.61
3714 3812 6.877611 AAACAACGTCACTTATTTCCTGAT 57.122 33.333 0.00 0.00 0.00 2.90
3739 3837 9.849166 CGGTGTATTTGTATTTTATTCCAAACT 57.151 29.630 0.00 0.00 30.37 2.66
3767 3866 6.065976 TGGTCTGAGTTGGTCATGAATTAT 57.934 37.500 0.00 0.00 33.51 1.28
3821 3920 2.823154 CTGTAAGGAATCCCCGCAAAAA 59.177 45.455 0.00 0.00 40.87 1.94
3822 3921 2.224917 ACTGTAAGGAATCCCCGCAAAA 60.225 45.455 0.00 0.00 39.30 2.44
3823 3922 1.353022 ACTGTAAGGAATCCCCGCAAA 59.647 47.619 0.00 0.00 39.30 3.68
3824 3923 0.988832 ACTGTAAGGAATCCCCGCAA 59.011 50.000 0.00 0.00 39.30 4.85
3825 3924 1.760613 CTACTGTAAGGAATCCCCGCA 59.239 52.381 0.00 0.00 39.30 5.69
3826 3925 1.761198 ACTACTGTAAGGAATCCCCGC 59.239 52.381 0.00 0.00 39.30 6.13
3827 3926 4.189231 CAAACTACTGTAAGGAATCCCCG 58.811 47.826 0.00 0.00 39.30 5.73
3828 3927 5.175388 ACAAACTACTGTAAGGAATCCCC 57.825 43.478 0.00 0.00 39.30 4.81
3829 3928 6.002082 ACAACAAACTACTGTAAGGAATCCC 58.998 40.000 0.00 0.00 39.30 3.85
3830 3929 6.567891 GCACAACAAACTACTGTAAGGAATCC 60.568 42.308 0.00 0.00 39.30 3.01
3831 3930 6.017440 TGCACAACAAACTACTGTAAGGAATC 60.017 38.462 0.00 0.00 39.30 2.52
3832 3931 5.825679 TGCACAACAAACTACTGTAAGGAAT 59.174 36.000 0.00 0.00 39.30 3.01
3833 3932 5.186942 TGCACAACAAACTACTGTAAGGAA 58.813 37.500 0.00 0.00 39.30 3.36
3834 3933 4.771903 TGCACAACAAACTACTGTAAGGA 58.228 39.130 0.00 0.00 39.30 3.36
3835 3934 5.689383 ATGCACAACAAACTACTGTAAGG 57.311 39.130 0.00 0.00 39.30 2.69
3836 3935 7.184800 TGTATGCACAACAAACTACTGTAAG 57.815 36.000 1.32 0.00 42.29 2.34
3837 3936 7.555306 TTGTATGCACAACAAACTACTGTAA 57.445 32.000 12.73 0.00 39.75 2.41
3878 3977 9.305925 CTTGTCGATGCACATGTATATGTATAT 57.694 33.333 4.64 3.04 45.53 0.86
3879 3978 7.275560 GCTTGTCGATGCACATGTATATGTATA 59.724 37.037 4.64 0.00 45.53 1.47
3880 3979 6.091305 GCTTGTCGATGCACATGTATATGTAT 59.909 38.462 4.64 0.00 45.53 2.29
3881 3980 5.405269 GCTTGTCGATGCACATGTATATGTA 59.595 40.000 4.64 0.00 45.53 2.29
3883 3982 4.211794 TGCTTGTCGATGCACATGTATATG 59.788 41.667 0.00 0.00 40.24 1.78
3884 3983 4.379652 TGCTTGTCGATGCACATGTATAT 58.620 39.130 0.00 0.00 33.94 0.86
3894 3993 1.202222 CCAAAGGATGCTTGTCGATGC 60.202 52.381 0.00 0.00 0.00 3.91
3896 3995 1.098050 GCCAAAGGATGCTTGTCGAT 58.902 50.000 0.00 0.00 0.00 3.59
3897 3996 0.250684 TGCCAAAGGATGCTTGTCGA 60.251 50.000 0.00 0.00 0.00 4.20
3920 4019 6.017934 TCCTTTCTCAGAATTTGACAGAAACG 60.018 38.462 0.00 0.00 30.93 3.60
4096 4202 8.708742 TGAACGTGTCAATATTTAACTTCAGAG 58.291 33.333 0.00 0.00 31.51 3.35
4101 4207 7.435068 AGCTGAACGTGTCAATATTTAACTT 57.565 32.000 0.00 0.00 35.22 2.66
4114 4221 5.295787 TCTTCACAAAATTAGCTGAACGTGT 59.704 36.000 0.00 0.00 0.00 4.49
4117 4224 5.747565 TGTCTTCACAAAATTAGCTGAACG 58.252 37.500 0.00 0.00 0.00 3.95
4132 4239 2.030946 GGCGCATACTTGATGTCTTCAC 59.969 50.000 10.83 0.00 37.90 3.18
4134 4254 2.279741 TGGCGCATACTTGATGTCTTC 58.720 47.619 10.83 0.00 37.90 2.87
4174 4300 5.662456 TCTCATGAAGAGCTTCTGATTCAG 58.338 41.667 7.38 7.38 44.35 3.02
4201 4327 1.635817 AAGTATGAGCACCGCCCCAT 61.636 55.000 0.00 0.00 0.00 4.00
4202 4328 2.297895 AAGTATGAGCACCGCCCCA 61.298 57.895 0.00 0.00 0.00 4.96
4260 4386 7.148474 GGATTACAAAGTTTAGCTCGACATGAA 60.148 37.037 0.00 0.00 0.00 2.57
4331 4457 4.442018 AAAAACGGTCTTCGGCGA 57.558 50.000 4.99 4.99 44.45 5.54


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

AutoCloner maintained by Alex Coulton.