Multiple sequence alignment - TraesCS7B01G220100

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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 TraesCS7B01G220100 chr7B 100.000 3899 0 0 1 3899 411489873 411493771 0.000000e+00 7201.0
1 TraesCS7B01G220100 chr7B 82.021 584 80 18 41 619 25671072 25671635 1.270000e-129 473.0
2 TraesCS7B01G220100 chr7B 88.048 251 23 5 1147 1396 738788074 738787830 1.370000e-74 291.0
3 TraesCS7B01G220100 chr7B 83.571 140 7 6 1483 1621 728163527 728163651 2.460000e-22 117.0
4 TraesCS7B01G220100 chr7A 96.879 2467 61 11 970 3424 459623647 459626109 0.000000e+00 4115.0
5 TraesCS7B01G220100 chr7A 96.458 480 13 1 3424 3899 459626146 459626625 0.000000e+00 789.0
6 TraesCS7B01G220100 chr7A 88.689 389 38 3 1679 2066 378494676 378495059 1.640000e-128 470.0
7 TraesCS7B01G220100 chr7A 91.304 322 16 6 660 977 459623299 459623612 2.780000e-116 429.0
8 TraesCS7B01G220100 chr7D 94.264 2580 70 15 857 3424 401834089 401836602 0.000000e+00 3873.0
9 TraesCS7B01G220100 chr7D 96.653 478 14 1 3424 3899 401836639 401837116 0.000000e+00 793.0
10 TraesCS7B01G220100 chr7D 89.822 393 34 3 1679 2070 37621767 37622154 2.090000e-137 499.0
11 TraesCS7B01G220100 chr7D 92.925 212 12 3 661 869 401823424 401823635 4.890000e-79 305.0
12 TraesCS7B01G220100 chr2B 88.674 671 35 9 1 635 18166987 18167652 0.000000e+00 780.0
13 TraesCS7B01G220100 chr2B 87.669 665 60 9 1408 2070 12856886 12856242 0.000000e+00 754.0
14 TraesCS7B01G220100 chr2B 84.299 656 72 24 1 635 710051312 710051957 2.580000e-171 612.0
15 TraesCS7B01G220100 chr2B 81.889 646 73 30 1 635 706175979 706176591 4.500000e-139 505.0
16 TraesCS7B01G220100 chr2B 91.566 83 7 0 2105 2187 12856241 12856159 8.850000e-22 115.0
17 TraesCS7B01G220100 chr3B 84.569 661 61 15 1 635 156922377 156923022 5.530000e-173 617.0
18 TraesCS7B01G220100 chr4B 83.981 643 77 19 1 635 592694265 592693641 9.330000e-166 593.0
19 TraesCS7B01G220100 chr6A 81.861 634 78 26 16 635 15300010 15299400 2.090000e-137 499.0
20 TraesCS7B01G220100 chr6A 82.131 610 70 27 41 635 15088836 15088251 1.630000e-133 486.0
21 TraesCS7B01G220100 chr6A 94.083 169 10 0 1902 2070 217043850 217043682 1.390000e-64 257.0
22 TraesCS7B01G220100 chr5B 82.196 601 74 23 43 635 699563628 699563053 1.630000e-133 486.0
23 TraesCS7B01G220100 chr6B 87.678 211 15 4 1408 1617 87325068 87325268 6.510000e-58 235.0
24 TraesCS7B01G220100 chr6B 93.878 98 5 1 1970 2066 87325266 87325363 3.140000e-31 147.0
25 TraesCS7B01G220100 chr5D 88.144 194 6 4 1483 1675 366924977 366925154 8.480000e-52 215.0
26 TraesCS7B01G220100 chr5D 87.629 194 7 4 1483 1675 28572604 28572781 3.950000e-50 209.0
27 TraesCS7B01G220100 chrUn 87.629 194 7 4 1483 1675 154748864 154749041 3.950000e-50 209.0
28 TraesCS7B01G220100 chrUn 95.876 97 4 0 1970 2066 17285315 17285411 1.450000e-34 158.0
29 TraesCS7B01G220100 chr6D 88.889 180 4 2 1497 1675 42385172 42385008 1.420000e-49 207.0
30 TraesCS7B01G220100 chr6D 86.598 194 9 4 1483 1675 396278689 396278866 8.550000e-47 198.0
31 TraesCS7B01G220100 chr1D 87.500 192 7 7 1483 1673 79840469 79840294 5.110000e-49 206.0
32 TraesCS7B01G220100 chr1D 87.113 194 8 4 1483 1675 41783212 41783389 1.840000e-48 204.0
33 TraesCS7B01G220100 chr1D 100.000 32 0 0 1312 1343 20517632 20517601 4.210000e-05 60.2
34 TraesCS7B01G220100 chr5A 97.059 102 3 0 1970 2071 486768847 486768746 5.180000e-39 172.0
35 TraesCS7B01G220100 chr5A 84.524 168 10 5 1483 1649 502848505 502848657 6.750000e-33 152.0
36 TraesCS7B01G220100 chr4A 89.474 95 10 0 1408 1502 427078543 427078449 1.900000e-23 121.0
37 TraesCS7B01G220100 chr4A 95.652 69 3 0 2001 2069 427078438 427078370 1.150000e-20 111.0


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 TraesCS7B01G220100 chr7B 411489873 411493771 3898 False 7201.000000 7201 100.000000 1 3899 1 chr7B.!!$F2 3898
1 TraesCS7B01G220100 chr7B 25671072 25671635 563 False 473.000000 473 82.021000 41 619 1 chr7B.!!$F1 578
2 TraesCS7B01G220100 chr7A 459623299 459626625 3326 False 1777.666667 4115 94.880333 660 3899 3 chr7A.!!$F2 3239
3 TraesCS7B01G220100 chr7D 401834089 401837116 3027 False 2333.000000 3873 95.458500 857 3899 2 chr7D.!!$F3 3042
4 TraesCS7B01G220100 chr2B 18166987 18167652 665 False 780.000000 780 88.674000 1 635 1 chr2B.!!$F1 634
5 TraesCS7B01G220100 chr2B 710051312 710051957 645 False 612.000000 612 84.299000 1 635 1 chr2B.!!$F3 634
6 TraesCS7B01G220100 chr2B 706175979 706176591 612 False 505.000000 505 81.889000 1 635 1 chr2B.!!$F2 634
7 TraesCS7B01G220100 chr2B 12856159 12856886 727 True 434.500000 754 89.617500 1408 2187 2 chr2B.!!$R1 779
8 TraesCS7B01G220100 chr3B 156922377 156923022 645 False 617.000000 617 84.569000 1 635 1 chr3B.!!$F1 634
9 TraesCS7B01G220100 chr4B 592693641 592694265 624 True 593.000000 593 83.981000 1 635 1 chr4B.!!$R1 634
10 TraesCS7B01G220100 chr6A 15299400 15300010 610 True 499.000000 499 81.861000 16 635 1 chr6A.!!$R2 619
11 TraesCS7B01G220100 chr6A 15088251 15088836 585 True 486.000000 486 82.131000 41 635 1 chr6A.!!$R1 594
12 TraesCS7B01G220100 chr5B 699563053 699563628 575 True 486.000000 486 82.196000 43 635 1 chr5B.!!$R1 592

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
658 895 0.310854 GCGCCAAATAGGAAATCCCG 59.689 55.000 0.00 0.0 41.22 5.14 F
753 990 0.695462 TCCAGGCTACCAGGCATCAT 60.695 55.000 2.39 0.0 44.19 2.45 F
795 1033 1.145738 AGGCATCAACCAAACAGACCT 59.854 47.619 0.00 0.0 0.00 3.85 F
1265 1557 1.414550 CGATCTTTCCCTTCCTCCTCC 59.585 57.143 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 2117 1.067283 AGCATCAACACCTCTCAGTCG 60.067 52.381 0.00 0.00 0.00 4.18 R
1827 2123 1.561076 TGGCATAGCATCAACACCTCT 59.439 47.619 0.00 0.00 0.00 3.69 R
2143 2439 1.604593 GCAGCCACTTGACCATGGT 60.605 57.895 19.89 19.89 38.34 3.55 R
3007 3305 1.379977 CCAGGCCTCGAGACCTACA 60.380 63.158 20.83 0.00 33.38 2.74 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
102 103 9.893305 GAATTCGAAGAAAGTTTAAAGGATTCA 57.107 29.630 3.35 0.00 45.90 2.57
243 447 6.620678 TCATCGGATTTGGAAAAAGTTCATC 58.379 36.000 0.00 0.00 35.25 2.92
256 460 9.980780 GGAAAAAGTTCATCGAATTTTGAAAAA 57.019 25.926 0.92 0.00 33.12 1.94
500 735 2.118404 CAGGTGTGTTGGCGTGGTT 61.118 57.895 0.00 0.00 0.00 3.67
504 739 0.948678 GTGTGTTGGCGTGGTTGTAT 59.051 50.000 0.00 0.00 0.00 2.29
519 754 3.385755 GGTTGTATCACCCACGGTACTAT 59.614 47.826 0.00 0.00 32.11 2.12
636 873 2.513897 GCTTCAGGCGCCGGTTAT 60.514 61.111 26.04 2.19 0.00 1.89
637 874 1.227438 GCTTCAGGCGCCGGTTATA 60.227 57.895 26.04 3.78 0.00 0.98
638 875 0.602905 GCTTCAGGCGCCGGTTATAT 60.603 55.000 26.04 0.43 0.00 0.86
639 876 1.148310 CTTCAGGCGCCGGTTATATG 58.852 55.000 26.04 14.69 0.00 1.78
640 877 0.882927 TTCAGGCGCCGGTTATATGC 60.883 55.000 26.04 0.00 0.00 3.14
644 881 2.663520 CGCCGGTTATATGCGCCA 60.664 61.111 4.18 0.00 41.95 5.69
645 882 2.248135 CGCCGGTTATATGCGCCAA 61.248 57.895 4.18 0.00 41.95 4.52
646 883 1.777030 CGCCGGTTATATGCGCCAAA 61.777 55.000 4.18 0.00 41.95 3.28
647 884 0.596082 GCCGGTTATATGCGCCAAAT 59.404 50.000 4.18 0.00 0.00 2.32
648 885 1.807742 GCCGGTTATATGCGCCAAATA 59.192 47.619 4.18 0.00 0.00 1.40
649 886 2.159572 GCCGGTTATATGCGCCAAATAG 60.160 50.000 4.18 0.00 0.00 1.73
650 887 2.418628 CCGGTTATATGCGCCAAATAGG 59.581 50.000 4.18 0.00 41.84 2.57
651 888 3.331150 CGGTTATATGCGCCAAATAGGA 58.669 45.455 4.18 0.00 41.22 2.94
652 889 3.749088 CGGTTATATGCGCCAAATAGGAA 59.251 43.478 4.18 0.00 41.22 3.36
653 890 4.214545 CGGTTATATGCGCCAAATAGGAAA 59.785 41.667 4.18 0.00 41.22 3.13
654 891 5.106317 CGGTTATATGCGCCAAATAGGAAAT 60.106 40.000 4.18 0.00 41.22 2.17
655 892 6.322491 GGTTATATGCGCCAAATAGGAAATC 58.678 40.000 4.18 0.00 41.22 2.17
656 893 6.322491 GTTATATGCGCCAAATAGGAAATCC 58.678 40.000 4.18 0.00 41.22 3.01
657 894 1.398692 TGCGCCAAATAGGAAATCCC 58.601 50.000 4.18 0.00 41.22 3.85
658 895 0.310854 GCGCCAAATAGGAAATCCCG 59.689 55.000 0.00 0.00 41.22 5.14
659 896 1.675552 CGCCAAATAGGAAATCCCGT 58.324 50.000 0.00 0.00 41.22 5.28
660 897 2.841215 CGCCAAATAGGAAATCCCGTA 58.159 47.619 0.00 0.00 41.22 4.02
661 898 3.408634 CGCCAAATAGGAAATCCCGTAT 58.591 45.455 0.00 0.00 41.22 3.06
662 899 3.818773 CGCCAAATAGGAAATCCCGTATT 59.181 43.478 0.00 0.00 41.22 1.89
663 900 4.277423 CGCCAAATAGGAAATCCCGTATTT 59.723 41.667 0.00 0.00 40.59 1.40
664 901 5.528870 GCCAAATAGGAAATCCCGTATTTG 58.471 41.667 18.40 18.40 40.66 2.32
665 902 5.068591 GCCAAATAGGAAATCCCGTATTTGT 59.931 40.000 21.05 0.00 40.15 2.83
666 903 6.503524 CCAAATAGGAAATCCCGTATTTGTG 58.496 40.000 21.05 14.14 40.15 3.33
667 904 6.096282 CCAAATAGGAAATCCCGTATTTGTGT 59.904 38.462 21.05 0.00 40.15 3.72
692 929 1.134175 CAAGGCGTTCAACCAAACAGT 59.866 47.619 0.00 0.00 0.00 3.55
695 932 1.265905 GGCGTTCAACCAAACAGTAGG 59.734 52.381 0.00 0.00 0.00 3.18
697 934 2.286772 GCGTTCAACCAAACAGTAGGTG 60.287 50.000 0.00 0.00 38.37 4.00
702 939 2.622942 CAACCAAACAGTAGGTGCACAT 59.377 45.455 20.43 15.34 38.37 3.21
729 966 3.372025 GCCTGACCAGACATATTTTCCCT 60.372 47.826 0.00 0.00 0.00 4.20
752 989 1.306911 TCCAGGCTACCAGGCATCA 60.307 57.895 2.39 0.00 44.19 3.07
753 990 0.695462 TCCAGGCTACCAGGCATCAT 60.695 55.000 2.39 0.00 44.19 2.45
795 1033 1.145738 AGGCATCAACCAAACAGACCT 59.854 47.619 0.00 0.00 0.00 3.85
811 1049 5.865085 ACAGACCTACAATTTGTAAGCTCA 58.135 37.500 10.32 0.00 31.67 4.26
812 1050 5.934625 ACAGACCTACAATTTGTAAGCTCAG 59.065 40.000 10.32 0.03 31.67 3.35
816 1054 5.221843 ACCTACAATTTGTAAGCTCAGGTGA 60.222 40.000 15.39 0.00 32.38 4.02
854 1092 3.931907 AGTTGCATGTAGGCCATTCTA 57.068 42.857 5.01 0.00 0.00 2.10
923 1163 2.770447 TGTAGACCATTCTGGCCCATA 58.230 47.619 0.00 0.00 42.67 2.74
927 1168 1.425066 GACCATTCTGGCCCATATGGA 59.575 52.381 24.00 1.76 42.67 3.41
1263 1555 1.501582 CCGATCTTTCCCTTCCTCCT 58.498 55.000 0.00 0.00 0.00 3.69
1265 1557 1.414550 CGATCTTTCCCTTCCTCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
1428 1720 5.355467 TCTCTCGATCGATCTTGATTCTG 57.645 43.478 19.78 2.67 0.00 3.02
1495 1787 1.729881 GGAATTGATCCGTGGCTGC 59.270 57.895 0.00 0.00 38.79 5.25
1687 1980 5.378230 TCTTCTGGCTTCATTCCACATAT 57.622 39.130 0.00 0.00 0.00 1.78
1733 2026 4.277476 TGTGTGACTCAATTCCAAAAGGT 58.723 39.130 0.00 0.00 0.00 3.50
1778 2074 1.885887 TGCCATGCCACTTTGTAAGAC 59.114 47.619 0.00 0.00 0.00 3.01
1801 2097 9.857656 AGACAACATTATGATAGTGATTCCATT 57.142 29.630 0.00 0.00 0.00 3.16
1809 2105 6.823286 TGATAGTGATTCCATTGGTTCCTA 57.177 37.500 1.86 6.03 0.00 2.94
1810 2106 7.392766 TGATAGTGATTCCATTGGTTCCTAT 57.607 36.000 1.86 9.63 0.00 2.57
1811 2107 7.226441 TGATAGTGATTCCATTGGTTCCTATG 58.774 38.462 1.86 6.35 0.00 2.23
1814 2110 4.402155 GTGATTCCATTGGTTCCTATGCAA 59.598 41.667 1.86 0.85 0.00 4.08
1821 2117 5.639082 CCATTGGTTCCTATGCAAAAGTTTC 59.361 40.000 7.55 0.00 0.00 2.78
1827 2123 4.637276 TCCTATGCAAAAGTTTCGACTGA 58.363 39.130 0.00 0.00 0.00 3.41
1833 2129 3.303395 GCAAAAGTTTCGACTGAGAGGTG 60.303 47.826 0.00 0.00 0.00 4.00
1995 2291 4.453819 GCTAGAAGGATATGATGTGGTTGC 59.546 45.833 0.00 0.00 0.00 4.17
2190 2486 4.261867 GCTGCATGCCAATATCTCATTGAA 60.262 41.667 16.68 0.00 35.15 2.69
2451 2748 4.760204 TCTCGAGTAGTGTTGATGTGAAGA 59.240 41.667 13.13 0.00 0.00 2.87
2563 2861 3.181497 GCTAACGCACCATTGTTGATGAT 60.181 43.478 0.00 0.00 35.39 2.45
2687 2985 4.032672 CTGAAGAAGACTTCTGCATAAGCG 59.967 45.833 23.59 10.04 44.23 4.68
2935 3233 7.334171 CACATGACCTGTAAGTATTCAATGACA 59.666 37.037 0.00 0.00 35.91 3.58
2967 3265 1.120530 TCGGGGATGCCTACTTTCTC 58.879 55.000 2.19 0.00 0.00 2.87
2986 3284 3.888930 TCTCCAAAACCATTTCCACTCAC 59.111 43.478 0.00 0.00 0.00 3.51
3007 3305 6.873997 TCACGTTTCCAGTATGAATATGAGT 58.126 36.000 0.00 0.00 39.69 3.41
3016 3314 7.448777 TCCAGTATGAATATGAGTGTAGGTCTC 59.551 40.741 0.00 0.00 39.69 3.36
3097 3397 8.945195 TTATGATTCCAATTGCATAGGAGAAT 57.055 30.769 0.00 1.86 32.11 2.40
3112 3412 3.846588 AGGAGAATTTCTGGAACCAGCTA 59.153 43.478 15.20 6.59 43.31 3.32
3358 3658 5.985530 TGCCTCGTCAAATTATCTGATACTG 59.014 40.000 0.00 0.00 0.00 2.74
3461 3800 6.702716 TGTAAAAACAAGTTACTCAAGGGG 57.297 37.500 0.00 0.00 33.46 4.79
3470 3809 8.439964 ACAAGTTACTCAAGGGGTAATAAGTA 57.560 34.615 0.00 0.00 32.78 2.24
3535 3874 9.229784 GTCTTGATTATGTGAAATAGCAACATG 57.770 33.333 0.00 0.00 0.00 3.21
3629 3972 5.222870 CTCCTGAGGGAATATGGCCTATAT 58.777 45.833 3.32 3.00 41.69 0.86
3631 3974 6.385443 TCCTGAGGGAATATGGCCTATATAG 58.615 44.000 3.32 2.46 38.93 1.31
3817 4160 4.956700 TGGGTTAGTGATCTCCTCTAACAG 59.043 45.833 20.41 0.00 46.11 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 237 8.035165 TCGATGAACTTTTTCCGAATTTGATA 57.965 30.769 0.00 0.00 0.00 2.15
230 433 9.980780 TTTTTCAAAATTCGATGAACTTTTTCC 57.019 25.926 0.00 0.00 35.42 3.13
256 460 8.702163 AACTGTTTTCAAAATCGATGAACTTT 57.298 26.923 0.00 0.00 36.57 2.66
424 652 7.924541 ACCTTTTCCCTTTTTACCTTTTTCTT 58.075 30.769 0.00 0.00 0.00 2.52
500 735 3.382227 CACATAGTACCGTGGGTGATACA 59.618 47.826 0.00 0.00 36.19 2.29
504 739 1.927487 ACACATAGTACCGTGGGTGA 58.073 50.000 11.17 0.00 36.19 4.02
519 754 0.908910 AACCACAGACCTCACACACA 59.091 50.000 0.00 0.00 0.00 3.72
635 872 3.763897 GGGATTTCCTATTTGGCGCATAT 59.236 43.478 10.83 1.04 35.95 1.78
636 873 3.153919 GGGATTTCCTATTTGGCGCATA 58.846 45.455 10.83 0.00 35.95 3.14
637 874 1.963515 GGGATTTCCTATTTGGCGCAT 59.036 47.619 10.83 0.00 35.95 4.73
638 875 1.398692 GGGATTTCCTATTTGGCGCA 58.601 50.000 10.83 0.00 35.95 6.09
639 876 0.310854 CGGGATTTCCTATTTGGCGC 59.689 55.000 0.00 0.00 35.95 6.53
640 877 1.675552 ACGGGATTTCCTATTTGGCG 58.324 50.000 0.00 0.00 35.95 5.69
641 878 5.068591 ACAAATACGGGATTTCCTATTTGGC 59.931 40.000 22.49 0.00 42.66 4.52
642 879 6.096282 ACACAAATACGGGATTTCCTATTTGG 59.904 38.462 22.49 17.14 42.66 3.28
643 880 7.095695 ACACAAATACGGGATTTCCTATTTG 57.904 36.000 19.68 19.68 43.18 2.32
644 881 6.887545 TGACACAAATACGGGATTTCCTATTT 59.112 34.615 0.00 0.00 35.45 1.40
645 882 6.419791 TGACACAAATACGGGATTTCCTATT 58.580 36.000 0.00 0.00 35.45 1.73
646 883 5.996644 TGACACAAATACGGGATTTCCTAT 58.003 37.500 0.00 0.00 35.45 2.57
647 884 5.423704 TGACACAAATACGGGATTTCCTA 57.576 39.130 0.00 0.00 35.45 2.94
648 885 4.261801 CTGACACAAATACGGGATTTCCT 58.738 43.478 0.00 0.00 35.45 3.36
649 886 3.377172 CCTGACACAAATACGGGATTTCC 59.623 47.826 0.00 0.00 35.45 3.13
650 887 3.181500 GCCTGACACAAATACGGGATTTC 60.181 47.826 0.00 0.00 35.45 2.17
651 888 2.752903 GCCTGACACAAATACGGGATTT 59.247 45.455 0.00 0.00 38.34 2.17
652 889 2.290641 TGCCTGACACAAATACGGGATT 60.291 45.455 0.00 0.00 32.36 3.01
653 890 1.280710 TGCCTGACACAAATACGGGAT 59.719 47.619 0.00 0.00 32.36 3.85
654 891 0.687920 TGCCTGACACAAATACGGGA 59.312 50.000 0.00 0.00 32.36 5.14
655 892 1.468520 CTTGCCTGACACAAATACGGG 59.531 52.381 0.00 0.00 0.00 5.28
656 893 1.468520 CCTTGCCTGACACAAATACGG 59.531 52.381 0.00 0.00 0.00 4.02
657 894 1.135689 GCCTTGCCTGACACAAATACG 60.136 52.381 0.00 0.00 0.00 3.06
658 895 1.135689 CGCCTTGCCTGACACAAATAC 60.136 52.381 0.00 0.00 0.00 1.89
659 896 1.164411 CGCCTTGCCTGACACAAATA 58.836 50.000 0.00 0.00 0.00 1.40
660 897 0.823356 ACGCCTTGCCTGACACAAAT 60.823 50.000 0.00 0.00 0.00 2.32
661 898 1.034838 AACGCCTTGCCTGACACAAA 61.035 50.000 0.00 0.00 0.00 2.83
662 899 1.444119 GAACGCCTTGCCTGACACAA 61.444 55.000 0.00 0.00 0.00 3.33
663 900 1.891919 GAACGCCTTGCCTGACACA 60.892 57.895 0.00 0.00 0.00 3.72
664 901 1.444119 TTGAACGCCTTGCCTGACAC 61.444 55.000 0.00 0.00 0.00 3.67
665 902 1.153066 TTGAACGCCTTGCCTGACA 60.153 52.632 0.00 0.00 0.00 3.58
666 903 1.282875 GTTGAACGCCTTGCCTGAC 59.717 57.895 0.00 0.00 0.00 3.51
667 904 1.896660 GGTTGAACGCCTTGCCTGA 60.897 57.895 0.00 0.00 0.00 3.86
697 934 2.209064 CTGGTCAGGCTTGCATGTGC 62.209 60.000 7.14 0.00 42.50 4.57
702 939 0.983467 TATGTCTGGTCAGGCTTGCA 59.017 50.000 4.16 0.00 33.37 4.08
708 945 4.510167 AGGGAAAATATGTCTGGTCAGG 57.490 45.455 0.00 0.00 0.00 3.86
709 946 6.660949 AGAAAAGGGAAAATATGTCTGGTCAG 59.339 38.462 0.00 0.00 0.00 3.51
710 947 6.552008 AGAAAAGGGAAAATATGTCTGGTCA 58.448 36.000 0.00 0.00 0.00 4.02
711 948 6.095580 GGAGAAAAGGGAAAATATGTCTGGTC 59.904 42.308 0.00 0.00 0.00 4.02
712 949 5.952347 GGAGAAAAGGGAAAATATGTCTGGT 59.048 40.000 0.00 0.00 0.00 4.00
729 966 0.328258 GCCTGGTAGCCTGGAGAAAA 59.672 55.000 14.14 0.00 44.09 2.29
774 1011 1.270550 GGTCTGTTTGGTTGATGCCTG 59.729 52.381 0.00 0.00 0.00 4.85
795 1033 7.575414 TTTTCACCTGAGCTTACAAATTGTA 57.425 32.000 1.08 1.08 0.00 2.41
923 1163 1.453633 ATGGGCTGGCTAAGATCCAT 58.546 50.000 0.00 0.00 36.93 3.41
927 1168 5.012893 GCTAATAAATGGGCTGGCTAAGAT 58.987 41.667 0.00 0.00 0.00 2.40
1687 1980 8.383175 ACAATGAGGATAAACAGAAGGAAGTAA 58.617 33.333 0.00 0.00 0.00 2.24
1778 2074 8.853126 ACCAATGGAATCACTATCATAATGTTG 58.147 33.333 6.16 0.00 0.00 3.33
1801 2097 4.023536 GTCGAAACTTTTGCATAGGAACCA 60.024 41.667 0.00 0.00 0.00 3.67
1809 2105 3.499918 CCTCTCAGTCGAAACTTTTGCAT 59.500 43.478 0.00 0.00 31.71 3.96
1810 2106 2.872245 CCTCTCAGTCGAAACTTTTGCA 59.128 45.455 0.00 0.00 31.71 4.08
1811 2107 2.872858 ACCTCTCAGTCGAAACTTTTGC 59.127 45.455 0.00 0.00 31.71 3.68
1814 2110 3.821421 ACACCTCTCAGTCGAAACTTT 57.179 42.857 0.00 0.00 31.71 2.66
1821 2117 1.067283 AGCATCAACACCTCTCAGTCG 60.067 52.381 0.00 0.00 0.00 4.18
1827 2123 1.561076 TGGCATAGCATCAACACCTCT 59.439 47.619 0.00 0.00 0.00 3.69
1833 2129 3.012518 ACTCAAGTGGCATAGCATCAAC 58.987 45.455 0.00 0.00 0.00 3.18
1995 2291 6.482308 TGAGTATCATCATGCTGAAACTGATG 59.518 38.462 2.91 5.60 42.56 3.07
2143 2439 1.604593 GCAGCCACTTGACCATGGT 60.605 57.895 19.89 19.89 38.34 3.55
2190 2486 9.744468 AGAAAAATAAACAGAAATACGCAAAGT 57.256 25.926 0.00 0.00 0.00 2.66
2232 2528 4.182693 ACAATCACAATGCCAATCACTG 57.817 40.909 0.00 0.00 0.00 3.66
2432 2729 7.704472 CCTAAGATCTTCACATCAACACTACTC 59.296 40.741 12.24 0.00 0.00 2.59
2563 2861 6.934056 ACAAAATACTTTCATGCAGGCAATA 58.066 32.000 0.00 0.00 0.00 1.90
2935 3233 6.790319 AGGCATCCCCGATATTATTTTTACT 58.210 36.000 0.00 0.00 39.21 2.24
2967 3265 2.360801 ACGTGAGTGGAAATGGTTTTGG 59.639 45.455 0.00 0.00 46.97 3.28
2986 3284 7.382488 CCTACACTCATATTCATACTGGAAACG 59.618 40.741 0.00 0.00 0.00 3.60
3007 3305 1.379977 CCAGGCCTCGAGACCTACA 60.380 63.158 20.83 0.00 33.38 2.74
3016 3314 3.332919 CAGATCATAATTCCAGGCCTCG 58.667 50.000 0.00 0.00 0.00 4.63
3047 3347 3.245300 ACTTGCAGTAGGAGAGACCAGTA 60.245 47.826 0.00 0.00 42.04 2.74
3097 3397 3.055094 GTCAGGATAGCTGGTTCCAGAAA 60.055 47.826 21.32 9.11 36.24 2.52
3112 3412 3.055819 ACACGCAGTTATCAAGTCAGGAT 60.056 43.478 0.00 0.00 41.61 3.24
3322 3622 6.827586 TTTGACGAGGCATATTTAAAACCT 57.172 33.333 0.00 0.00 0.00 3.50
3358 3658 3.259123 AGAAACCATGCTGGAAAATCACC 59.741 43.478 8.91 0.00 40.96 4.02
3470 3809 4.673580 GCTTCGAATGTTGAGATGTTGCAT 60.674 41.667 0.00 0.00 0.00 3.96
3535 3874 4.535526 AAAGAACTCTTGAGGAGCTCTC 57.464 45.455 14.64 9.73 44.08 3.20
3580 3919 5.140454 CCCTTAAGGCCTTAAGTATTGCAT 58.860 41.667 42.43 15.73 46.42 3.96
3629 3972 6.896883 TGCTCTGGTACTACTCTGTAATCTA 58.103 40.000 0.00 0.00 0.00 1.98
3631 3974 6.452494 TTGCTCTGGTACTACTCTGTAATC 57.548 41.667 0.00 0.00 0.00 1.75
3720 4063 3.709653 TCCTTCTGATGGTAATAACGCCT 59.290 43.478 9.18 0.00 0.00 5.52
3817 4160 3.014623 GGGCATTTTAGTACAGTCCCAC 58.985 50.000 0.00 0.00 32.89 4.61


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

AutoCloner maintained by Alex Coulton.