Multiple sequence alignment - TraesCS1B01G190300

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 TraesCS1B01G190300 chr1B 100.000 3122 0 0 1 3122 341127590 341130711 0.000000e+00 5766.0
1 TraesCS1B01G190300 chr1B 94.177 1185 66 3 975 2157 340992845 340994028 0.000000e+00 1803.0
2 TraesCS1B01G190300 chr1B 91.018 668 55 5 9 674 417428542 417427878 0.000000e+00 896.0
3 TraesCS1B01G190300 chr1B 87.578 161 18 2 2268 2427 340994388 340994547 5.320000e-43 185.0
4 TraesCS1B01G190300 chr1D 95.301 1213 55 2 975 2185 235669718 235670930 0.000000e+00 1923.0
5 TraesCS1B01G190300 chr1D 89.354 263 22 2 2170 2432 235670956 235671212 3.000000e-85 326.0
6 TraesCS1B01G190300 chr1A 92.561 1156 82 3 998 2152 311059506 311060658 0.000000e+00 1655.0
7 TraesCS1B01G190300 chr1A 94.352 1027 35 4 998 2001 310258636 310257610 0.000000e+00 1554.0
8 TraesCS1B01G190300 chr1A 87.308 717 45 11 2431 3122 209531682 209532377 0.000000e+00 778.0
9 TraesCS1B01G190300 chr1A 94.033 419 25 0 998 1416 311058322 311058740 1.220000e-178 636.0
10 TraesCS1B01G190300 chr1A 91.885 419 33 1 998 1416 311057139 311057556 4.490000e-163 584.0
11 TraesCS1B01G190300 chr1A 89.623 424 38 3 996 1413 311055947 311056370 4.580000e-148 534.0
12 TraesCS1B01G190300 chr1A 88.281 256 20 6 1990 2243 310257259 310257012 6.550000e-77 298.0
13 TraesCS1B01G190300 chr1A 88.889 99 3 2 2342 2432 310256923 310256825 7.080000e-22 115.0
14 TraesCS1B01G190300 chr1A 82.353 119 9 6 810 927 311056931 311057038 3.320000e-15 93.5
15 TraesCS1B01G190300 chr1A 82.353 119 9 6 810 927 311059298 311059405 3.320000e-15 93.5
16 TraesCS1B01G190300 chr1A 96.226 53 2 0 875 927 310258789 310258737 1.540000e-13 87.9
17 TraesCS1B01G190300 chr1A 81.513 119 10 4 810 927 311058114 311058221 1.540000e-13 87.9
18 TraesCS1B01G190300 chr1A 97.436 39 1 0 2390 2428 430009171 430009209 2.010000e-07 67.6
19 TraesCS1B01G190300 chr2B 93.481 675 36 4 9 682 608939810 608940477 0.000000e+00 996.0
20 TraesCS1B01G190300 chr2B 84.344 709 67 20 2426 3108 754349600 754350290 0.000000e+00 654.0
21 TraesCS1B01G190300 chr2B 83.310 719 71 22 2431 3122 486954034 486954730 4.420000e-173 617.0
22 TraesCS1B01G190300 chr2B 83.380 710 73 12 2426 3108 754521749 754522440 1.590000e-172 616.0
23 TraesCS1B01G190300 chr6B 93.215 678 41 5 1 676 229545074 229545748 0.000000e+00 992.0
24 TraesCS1B01G190300 chr6B 93.027 674 37 6 9 679 670215794 670215128 0.000000e+00 976.0
25 TraesCS1B01G190300 chr6B 91.121 687 49 7 1 678 607090852 607091535 0.000000e+00 920.0
26 TraesCS1B01G190300 chr7B 92.353 680 43 5 1 678 220084627 220083955 0.000000e+00 959.0
27 TraesCS1B01G190300 chr5B 92.206 680 44 9 1 674 69058087 69057411 0.000000e+00 953.0
28 TraesCS1B01G190300 chr5B 91.716 676 48 4 1 674 468005042 468004373 0.000000e+00 931.0
29 TraesCS1B01G190300 chr4B 90.882 680 53 6 1 678 573225677 573225005 0.000000e+00 904.0
30 TraesCS1B01G190300 chr3A 90.125 719 35 4 2431 3122 50793184 50792475 0.000000e+00 902.0
31 TraesCS1B01G190300 chr2A 92.037 540 28 5 2430 2965 638054999 638054471 0.000000e+00 745.0
32 TraesCS1B01G190300 chr5A 88.783 419 43 3 2431 2846 675409296 675408879 7.720000e-141 510.0
33 TraesCS1B01G190300 chr5A 79.701 335 31 13 2752 3064 675408321 675408002 1.130000e-49 207.0
34 TraesCS1B01G190300 chr7A 91.304 46 4 0 2426 2471 256225868 256225913 2.600000e-06 63.9
35 TraesCS1B01G190300 chr6A 84.375 64 10 0 2580 2643 519768273 519768336 2.600000e-06 63.9


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 TraesCS1B01G190300 chr1B 341127590 341130711 3121 False 5766.000000 5766 100.000000 1 3122 1 chr1B.!!$F1 3121
1 TraesCS1B01G190300 chr1B 340992845 340994547 1702 False 994.000000 1803 90.877500 975 2427 2 chr1B.!!$F2 1452
2 TraesCS1B01G190300 chr1B 417427878 417428542 664 True 896.000000 896 91.018000 9 674 1 chr1B.!!$R1 665
3 TraesCS1B01G190300 chr1D 235669718 235671212 1494 False 1124.500000 1923 92.327500 975 2432 2 chr1D.!!$F1 1457
4 TraesCS1B01G190300 chr1A 209531682 209532377 695 False 778.000000 778 87.308000 2431 3122 1 chr1A.!!$F1 691
5 TraesCS1B01G190300 chr1A 311055947 311060658 4711 False 526.271429 1655 87.760143 810 2152 7 chr1A.!!$F3 1342
6 TraesCS1B01G190300 chr1A 310256825 310258789 1964 True 513.725000 1554 91.937000 875 2432 4 chr1A.!!$R1 1557
7 TraesCS1B01G190300 chr2B 608939810 608940477 667 False 996.000000 996 93.481000 9 682 1 chr2B.!!$F2 673
8 TraesCS1B01G190300 chr2B 754349600 754350290 690 False 654.000000 654 84.344000 2426 3108 1 chr2B.!!$F3 682
9 TraesCS1B01G190300 chr2B 486954034 486954730 696 False 617.000000 617 83.310000 2431 3122 1 chr2B.!!$F1 691
10 TraesCS1B01G190300 chr2B 754521749 754522440 691 False 616.000000 616 83.380000 2426 3108 1 chr2B.!!$F4 682
11 TraesCS1B01G190300 chr6B 229545074 229545748 674 False 992.000000 992 93.215000 1 676 1 chr6B.!!$F1 675
12 TraesCS1B01G190300 chr6B 670215128 670215794 666 True 976.000000 976 93.027000 9 679 1 chr6B.!!$R1 670
13 TraesCS1B01G190300 chr6B 607090852 607091535 683 False 920.000000 920 91.121000 1 678 1 chr6B.!!$F2 677
14 TraesCS1B01G190300 chr7B 220083955 220084627 672 True 959.000000 959 92.353000 1 678 1 chr7B.!!$R1 677
15 TraesCS1B01G190300 chr5B 69057411 69058087 676 True 953.000000 953 92.206000 1 674 1 chr5B.!!$R1 673
16 TraesCS1B01G190300 chr5B 468004373 468005042 669 True 931.000000 931 91.716000 1 674 1 chr5B.!!$R2 673
17 TraesCS1B01G190300 chr4B 573225005 573225677 672 True 904.000000 904 90.882000 1 678 1 chr4B.!!$R1 677
18 TraesCS1B01G190300 chr3A 50792475 50793184 709 True 902.000000 902 90.125000 2431 3122 1 chr3A.!!$R1 691
19 TraesCS1B01G190300 chr2A 638054471 638054999 528 True 745.000000 745 92.037000 2430 2965 1 chr2A.!!$R1 535
20 TraesCS1B01G190300 chr5A 675408002 675409296 1294 True 358.500000 510 84.242000 2431 3064 2 chr5A.!!$R1 633

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
846 1023 0.104304 GTTGATATCGACGCACCCCT 59.896 55.0 7.35 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2840 6766 0.389948 CGCCTCTCACCAGTAACCAC 60.39 60.0 0.0 0.0 0.0 4.16 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
34 38 2.445525 TCCTACCCCCTATGCCAAATTC 59.554 50.000 0.00 0.00 0.00 2.17
35 39 2.447047 CCTACCCCCTATGCCAAATTCT 59.553 50.000 0.00 0.00 0.00 2.40
36 40 2.755952 ACCCCCTATGCCAAATTCTC 57.244 50.000 0.00 0.00 0.00 2.87
38 42 2.587307 ACCCCCTATGCCAAATTCTCTT 59.413 45.455 0.00 0.00 0.00 2.85
49 53 4.769488 GCCAAATTCTCTTTTTCTCTCCCT 59.231 41.667 0.00 0.00 0.00 4.20
106 111 1.733402 CTTGCACCAAGCCAACCGAA 61.733 55.000 0.00 0.00 44.83 4.30
138 143 4.520179 TCAACTCTAGCGTAGTACATGGA 58.480 43.478 0.00 0.00 0.00 3.41
507 531 3.941188 CTGGGTCGTGTGGGCAGT 61.941 66.667 0.00 0.00 0.00 4.40
608 632 3.948719 TGCGGGCGGGTTCTTCTT 61.949 61.111 0.00 0.00 0.00 2.52
650 674 0.988832 ACAACCACCCGATACACCAT 59.011 50.000 0.00 0.00 0.00 3.55
678 702 1.400494 GCAGTTATCGGCGTCCAAAAT 59.600 47.619 6.85 0.00 0.00 1.82
679 703 2.538939 GCAGTTATCGGCGTCCAAAATC 60.539 50.000 6.85 0.00 0.00 2.17
682 706 3.754323 AGTTATCGGCGTCCAAAATCAAA 59.246 39.130 6.85 0.00 0.00 2.69
684 708 0.594110 TCGGCGTCCAAAATCAAACC 59.406 50.000 6.85 0.00 0.00 3.27
685 709 0.596082 CGGCGTCCAAAATCAAACCT 59.404 50.000 0.00 0.00 0.00 3.50
686 710 1.401018 CGGCGTCCAAAATCAAACCTC 60.401 52.381 0.00 0.00 0.00 3.85
687 711 1.611491 GGCGTCCAAAATCAAACCTCA 59.389 47.619 0.00 0.00 0.00 3.86
688 712 2.607038 GGCGTCCAAAATCAAACCTCAC 60.607 50.000 0.00 0.00 0.00 3.51
689 713 2.034053 GCGTCCAAAATCAAACCTCACA 59.966 45.455 0.00 0.00 0.00 3.58
690 714 3.853307 GCGTCCAAAATCAAACCTCACAG 60.853 47.826 0.00 0.00 0.00 3.66
691 715 3.304659 CGTCCAAAATCAAACCTCACAGG 60.305 47.826 0.00 0.00 42.49 4.00
692 716 3.005791 GTCCAAAATCAAACCTCACAGGG 59.994 47.826 0.00 0.00 40.58 4.45
693 717 3.117322 TCCAAAATCAAACCTCACAGGGA 60.117 43.478 0.00 0.00 40.58 4.20
694 718 3.256631 CCAAAATCAAACCTCACAGGGAG 59.743 47.826 0.00 0.00 40.58 4.30
695 719 2.206576 AATCAAACCTCACAGGGAGC 57.793 50.000 0.00 0.00 42.62 4.70
696 720 1.067295 ATCAAACCTCACAGGGAGCA 58.933 50.000 0.00 0.00 42.62 4.26
697 721 0.108585 TCAAACCTCACAGGGAGCAC 59.891 55.000 0.00 0.00 42.62 4.40
698 722 0.890996 CAAACCTCACAGGGAGCACC 60.891 60.000 0.00 0.00 42.62 5.01
699 723 1.352622 AAACCTCACAGGGAGCACCA 61.353 55.000 1.58 0.00 42.62 4.17
700 724 1.772819 AACCTCACAGGGAGCACCAG 61.773 60.000 1.58 0.00 42.62 4.00
701 725 1.915266 CCTCACAGGGAGCACCAGA 60.915 63.158 1.58 0.00 42.62 3.86
702 726 1.294780 CTCACAGGGAGCACCAGAC 59.705 63.158 1.58 0.00 43.89 3.51
703 727 2.047844 CACAGGGAGCACCAGACG 60.048 66.667 1.58 0.00 43.89 4.18
705 729 1.837051 ACAGGGAGCACCAGACGAA 60.837 57.895 1.58 0.00 43.89 3.85
706 730 1.371183 CAGGGAGCACCAGACGAAA 59.629 57.895 1.58 0.00 43.89 3.46
707 731 0.250295 CAGGGAGCACCAGACGAAAA 60.250 55.000 1.58 0.00 43.89 2.29
708 732 0.472471 AGGGAGCACCAGACGAAAAA 59.528 50.000 1.58 0.00 43.89 1.94
731 755 3.553467 ACGAAAGTGGGGGACGAA 58.447 55.556 0.00 0.00 46.97 3.85
733 757 0.180878 ACGAAAGTGGGGGACGAAAA 59.819 50.000 0.00 0.00 46.97 2.29
768 792 8.611051 AAGACTATCCTACCAACATTAAGAGT 57.389 34.615 0.00 0.00 0.00 3.24
769 793 9.710818 AAGACTATCCTACCAACATTAAGAGTA 57.289 33.333 0.00 0.00 0.00 2.59
770 794 9.357161 AGACTATCCTACCAACATTAAGAGTAG 57.643 37.037 0.00 0.00 0.00 2.57
773 797 9.575868 CTATCCTACCAACATTAAGAGTAGAGA 57.424 37.037 0.00 0.00 33.75 3.10
776 800 9.931698 TCCTACCAACATTAAGAGTAGAGATAA 57.068 33.333 0.00 0.00 33.75 1.75
789 813 6.430616 AGAGTAGAGATAAGTATAACCGGCAC 59.569 42.308 0.00 0.00 0.00 5.01
802 826 2.811317 GGCACGGAAGCACTCGAG 60.811 66.667 11.84 11.84 35.83 4.04
804 828 2.089349 GCACGGAAGCACTCGAGTC 61.089 63.158 16.96 10.84 0.00 3.36
805 829 1.285950 CACGGAAGCACTCGAGTCA 59.714 57.895 16.96 0.00 0.00 3.41
806 830 1.004277 CACGGAAGCACTCGAGTCAC 61.004 60.000 16.96 11.18 0.00 3.67
808 832 0.455295 CGGAAGCACTCGAGTCACTC 60.455 60.000 16.96 11.57 0.00 3.51
830 1006 6.403333 TCGAGTGGATTTTTATTCGAGTTG 57.597 37.500 0.00 0.00 31.52 3.16
844 1021 1.488527 GAGTTGATATCGACGCACCC 58.511 55.000 18.86 4.90 35.42 4.61
846 1023 0.104304 GTTGATATCGACGCACCCCT 59.896 55.000 7.35 0.00 0.00 4.79
869 1046 5.923733 TTTTTGCCCAAGTAGTGAAAAGA 57.076 34.783 0.00 0.00 0.00 2.52
870 1047 5.923733 TTTTGCCCAAGTAGTGAAAAGAA 57.076 34.783 0.00 0.00 0.00 2.52
871 1048 5.923733 TTTGCCCAAGTAGTGAAAAGAAA 57.076 34.783 0.00 0.00 0.00 2.52
872 1049 5.923733 TTGCCCAAGTAGTGAAAAGAAAA 57.076 34.783 0.00 0.00 0.00 2.29
873 1050 5.514274 TGCCCAAGTAGTGAAAAGAAAAG 57.486 39.130 0.00 0.00 0.00 2.27
886 1063 3.660501 AAGAAAAGGCCGAATCAAACC 57.339 42.857 0.00 0.00 0.00 3.27
889 1066 3.578282 AGAAAAGGCCGAATCAAACCAAT 59.422 39.130 0.00 0.00 0.00 3.16
941 3528 2.159572 CGATAAAACAGCTGGAAACCCG 60.160 50.000 19.93 10.69 0.00 5.28
942 3529 2.642154 TAAAACAGCTGGAAACCCGA 57.358 45.000 19.93 0.00 0.00 5.14
950 3541 4.058817 CAGCTGGAAACCCGATAATAGAC 58.941 47.826 5.57 0.00 0.00 2.59
1040 3631 2.081425 CTCCCCGCCGATCTTCTCAG 62.081 65.000 0.00 0.00 0.00 3.35
1053 3644 1.066908 CTTCTCAGTGAGATCTCGGGC 59.933 57.143 23.23 10.38 38.56 6.13
1556 4170 1.358877 CACAGCGTCGAATTCCATGA 58.641 50.000 0.00 0.00 0.00 3.07
1691 4305 2.273179 CGGAGTCGTTGGAGACCCA 61.273 63.158 0.00 0.00 41.83 4.51
1923 4537 0.472925 TGTCTGCCAAGGAGTACCCA 60.473 55.000 3.60 0.00 37.41 4.51
2037 5012 3.233507 TGTGGACGATATACCTTACCCC 58.766 50.000 0.00 0.00 0.00 4.95
2125 5100 4.997395 TGAAGAAGCAGGTAGTTTAAGCAG 59.003 41.667 0.00 0.00 0.00 4.24
2157 5133 9.971922 ACAGACTTCAAAATTAATCTTTTCCTG 57.028 29.630 0.00 0.00 0.00 3.86
2168 5351 5.644977 AATCTTTTCCTGACGAAATTCCC 57.355 39.130 0.00 0.00 40.18 3.97
2185 5368 7.592164 CGAAATTCCCGTTGTAACTGTTTTAAT 59.408 33.333 0.00 0.00 0.00 1.40
2201 5423 9.659830 ACTGTTTTAATCACAGAATTTCGTTAC 57.340 29.630 17.95 0.00 43.90 2.50
2202 5424 8.702408 TGTTTTAATCACAGAATTTCGTTACG 57.298 30.769 0.00 0.00 0.00 3.18
2294 5564 3.238108 ACTGTTAGAGCACATCTTCCG 57.762 47.619 0.00 0.00 39.64 4.30
2295 5565 2.563179 ACTGTTAGAGCACATCTTCCGT 59.437 45.455 0.00 0.00 39.64 4.69
2322 5592 2.198827 TTGACCGTTGGATCAGCATT 57.801 45.000 0.00 0.00 0.00 3.56
2371 5641 5.607939 TTGTCTCCAAATAATAGGCTCGA 57.392 39.130 0.00 0.00 0.00 4.04
2392 5670 4.201881 CGATGAAAGCTGATTTGCTGATCA 60.202 41.667 0.00 0.00 43.24 2.92
2396 5674 6.460781 TGAAAGCTGATTTGCTGATCAAAAT 58.539 32.000 5.27 5.27 46.60 1.82
2626 5904 3.821421 ATCCACGATCTCCTGTTAACC 57.179 47.619 2.48 0.00 0.00 2.85
2633 5911 1.078426 CTCCTGTTAACCGGGCCTG 60.078 63.158 15.22 3.88 39.73 4.85
2653 5931 3.733960 GGGCCTTCGGTTTGTCGC 61.734 66.667 0.84 0.00 0.00 5.19
2689 5969 1.028905 CACAACTTTGGAAGGGCGAA 58.971 50.000 0.00 0.00 0.00 4.70
2693 5974 3.123050 CAACTTTGGAAGGGCGAAAAAG 58.877 45.455 0.00 0.00 34.70 2.27
2705 5986 2.474032 GGCGAAAAAGAAATCGTCGAGG 60.474 50.000 0.00 0.00 41.01 4.63
2712 5993 0.669318 GAAATCGTCGAGGGCACACA 60.669 55.000 5.12 0.00 0.00 3.72
2798 6172 1.470890 CGAGAGGAGTTGAGACAGTCC 59.529 57.143 0.00 0.00 0.00 3.85
2833 6301 1.194772 GGAAAAAGAAGTGAGTCGCGG 59.805 52.381 6.13 0.00 0.00 6.46
2866 6792 0.888619 CTGGTGAGAGGCGAGTGTTA 59.111 55.000 0.00 0.00 0.00 2.41
2873 6799 0.179134 GAGGCGAGTGTTAGCGATGT 60.179 55.000 0.00 0.00 0.00 3.06
2923 6849 4.101790 CATGCGGCCGTGTTGGTC 62.102 66.667 28.70 8.52 41.21 4.02
3026 6977 6.248433 AGGAGGCAATGAATTTTCAGTTCTA 58.752 36.000 0.00 0.00 41.08 2.10
3027 6978 6.376581 AGGAGGCAATGAATTTTCAGTTCTAG 59.623 38.462 0.00 0.00 41.08 2.43
3028 6979 6.405176 GGAGGCAATGAATTTTCAGTTCTAGG 60.405 42.308 0.00 0.00 41.08 3.02
3029 6980 5.420104 AGGCAATGAATTTTCAGTTCTAGGG 59.580 40.000 0.00 0.00 41.08 3.53
3030 6981 5.418840 GGCAATGAATTTTCAGTTCTAGGGA 59.581 40.000 0.00 0.00 41.08 4.20
3031 6982 6.405176 GGCAATGAATTTTCAGTTCTAGGGAG 60.405 42.308 0.00 0.00 41.08 4.30
3032 6983 6.151817 GCAATGAATTTTCAGTTCTAGGGAGT 59.848 38.462 0.00 0.00 41.08 3.85
3093 7044 1.090052 GCGACTAATGGAGGTGTGCC 61.090 60.000 0.00 0.00 0.00 5.01
3110 7061 1.218196 TGCCTTTTCCCCAACCTACAA 59.782 47.619 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.273618 TGGCATAGGGGGTAGGAAAAATT 59.726 43.478 0.00 0.00 0.00 1.82
106 111 3.258622 ACGCTAGAGTTGAGCTAAGGTTT 59.741 43.478 0.00 0.00 37.81 3.27
138 143 0.833287 ACCAGCATACGCCAGATCTT 59.167 50.000 0.00 0.00 39.83 2.40
254 259 0.321671 CTCGTCCTTCTTCTGGCCAA 59.678 55.000 7.01 0.00 0.00 4.52
350 373 0.035343 GCCTTCCCACCTCTAACCAC 60.035 60.000 0.00 0.00 0.00 4.16
358 381 2.746375 CCATAGCGCCTTCCCACCT 61.746 63.158 2.29 0.00 0.00 4.00
460 483 0.103208 CTCCTTTCGATCCCCTGTCG 59.897 60.000 0.00 0.00 40.30 4.35
608 632 3.047735 ACGTCTCGTGTGGCATGA 58.952 55.556 0.00 0.00 39.18 3.07
650 674 1.804746 CGCCGATAACTGCCACATGTA 60.805 52.381 0.00 0.00 0.00 2.29
678 702 0.108585 GTGCTCCCTGTGAGGTTTGA 59.891 55.000 0.00 0.00 41.73 2.69
679 703 0.890996 GGTGCTCCCTGTGAGGTTTG 60.891 60.000 0.00 0.00 41.73 2.93
682 706 2.122413 TGGTGCTCCCTGTGAGGT 60.122 61.111 1.59 0.00 41.73 3.85
684 708 1.294780 GTCTGGTGCTCCCTGTGAG 59.705 63.158 1.59 0.00 44.47 3.51
685 709 2.574018 CGTCTGGTGCTCCCTGTGA 61.574 63.158 1.59 0.00 33.97 3.58
686 710 2.047844 CGTCTGGTGCTCCCTGTG 60.048 66.667 1.59 0.00 33.97 3.66
687 711 1.407656 TTTCGTCTGGTGCTCCCTGT 61.408 55.000 1.59 0.00 33.97 4.00
688 712 0.250295 TTTTCGTCTGGTGCTCCCTG 60.250 55.000 1.59 0.00 0.00 4.45
689 713 0.472471 TTTTTCGTCTGGTGCTCCCT 59.528 50.000 1.59 0.00 0.00 4.20
690 714 3.015516 TTTTTCGTCTGGTGCTCCC 57.984 52.632 1.59 0.00 0.00 4.30
706 730 4.261698 CGTCCCCCACTTTCGTTTATTTTT 60.262 41.667 0.00 0.00 0.00 1.94
707 731 3.253921 CGTCCCCCACTTTCGTTTATTTT 59.746 43.478 0.00 0.00 0.00 1.82
708 732 2.815503 CGTCCCCCACTTTCGTTTATTT 59.184 45.455 0.00 0.00 0.00 1.40
710 734 1.624813 TCGTCCCCCACTTTCGTTTAT 59.375 47.619 0.00 0.00 0.00 1.40
712 736 0.180878 TTCGTCCCCCACTTTCGTTT 59.819 50.000 0.00 0.00 0.00 3.60
713 737 0.180878 TTTCGTCCCCCACTTTCGTT 59.819 50.000 0.00 0.00 0.00 3.85
714 738 0.180878 TTTTCGTCCCCCACTTTCGT 59.819 50.000 0.00 0.00 0.00 3.85
715 739 1.310904 TTTTTCGTCCCCCACTTTCG 58.689 50.000 0.00 0.00 0.00 3.46
743 767 8.611051 ACTCTTAATGTTGGTAGGATAGTCTT 57.389 34.615 0.00 0.00 0.00 3.01
744 768 9.357161 CTACTCTTAATGTTGGTAGGATAGTCT 57.643 37.037 0.00 0.00 0.00 3.24
745 769 9.352191 TCTACTCTTAATGTTGGTAGGATAGTC 57.648 37.037 0.00 0.00 33.06 2.59
746 770 9.357161 CTCTACTCTTAATGTTGGTAGGATAGT 57.643 37.037 0.00 0.00 33.06 2.12
747 771 9.575868 TCTCTACTCTTAATGTTGGTAGGATAG 57.424 37.037 0.00 0.00 33.06 2.08
750 774 9.931698 TTATCTCTACTCTTAATGTTGGTAGGA 57.068 33.333 0.00 0.00 33.06 2.94
761 785 9.007901 GCCGGTTATACTTATCTCTACTCTTAA 57.992 37.037 1.90 0.00 0.00 1.85
763 787 7.002879 TGCCGGTTATACTTATCTCTACTCTT 58.997 38.462 1.90 0.00 0.00 2.85
764 788 6.430616 GTGCCGGTTATACTTATCTCTACTCT 59.569 42.308 1.90 0.00 0.00 3.24
765 789 6.610456 GTGCCGGTTATACTTATCTCTACTC 58.390 44.000 1.90 0.00 0.00 2.59
767 791 5.388944 CGTGCCGGTTATACTTATCTCTAC 58.611 45.833 1.90 0.00 0.00 2.59
768 792 4.456911 CCGTGCCGGTTATACTTATCTCTA 59.543 45.833 1.90 0.00 42.73 2.43
769 793 3.255149 CCGTGCCGGTTATACTTATCTCT 59.745 47.826 1.90 0.00 42.73 3.10
770 794 3.572584 CCGTGCCGGTTATACTTATCTC 58.427 50.000 1.90 0.00 42.73 2.75
784 808 4.717629 TCGAGTGCTTCCGTGCCG 62.718 66.667 0.00 0.00 0.00 5.69
785 809 2.811317 CTCGAGTGCTTCCGTGCC 60.811 66.667 3.62 0.00 0.00 5.01
786 810 2.049063 ACTCGAGTGCTTCCGTGC 60.049 61.111 19.30 0.00 0.00 5.34
789 813 0.455295 GAGTGACTCGAGTGCTTCCG 60.455 60.000 25.58 0.00 0.00 4.30
790 814 3.410098 GAGTGACTCGAGTGCTTCC 57.590 57.895 25.58 8.66 0.00 3.46
804 828 6.025707 CTCGAATAAAAATCCACTCGAGTG 57.974 41.667 33.87 33.87 44.40 3.51
808 832 6.403333 TCAACTCGAATAAAAATCCACTCG 57.597 37.500 0.00 0.00 0.00 4.18
810 834 8.765219 CGATATCAACTCGAATAAAAATCCACT 58.235 33.333 3.12 0.00 38.38 4.00
811 835 8.761497 TCGATATCAACTCGAATAAAAATCCAC 58.239 33.333 3.12 0.00 41.79 4.02
812 836 8.761497 GTCGATATCAACTCGAATAAAAATCCA 58.239 33.333 3.12 0.00 45.75 3.41
813 837 7.945178 CGTCGATATCAACTCGAATAAAAATCC 59.055 37.037 3.12 0.00 45.75 3.01
822 998 2.447250 GTGCGTCGATATCAACTCGAA 58.553 47.619 3.12 0.00 45.75 3.71
830 1006 1.949465 AAAAGGGGTGCGTCGATATC 58.051 50.000 0.00 0.00 0.00 1.63
851 1028 4.340950 CCTTTTCTTTTCACTACTTGGGCA 59.659 41.667 0.00 0.00 0.00 5.36
852 1029 4.796290 GCCTTTTCTTTTCACTACTTGGGC 60.796 45.833 0.00 0.00 0.00 5.36
855 1032 4.274950 TCGGCCTTTTCTTTTCACTACTTG 59.725 41.667 0.00 0.00 0.00 3.16
857 1034 4.081322 TCGGCCTTTTCTTTTCACTACT 57.919 40.909 0.00 0.00 0.00 2.57
858 1035 4.823790 TTCGGCCTTTTCTTTTCACTAC 57.176 40.909 0.00 0.00 0.00 2.73
859 1036 5.067273 TGATTCGGCCTTTTCTTTTCACTA 58.933 37.500 0.00 0.00 0.00 2.74
860 1037 3.888930 TGATTCGGCCTTTTCTTTTCACT 59.111 39.130 0.00 0.00 0.00 3.41
861 1038 4.237349 TGATTCGGCCTTTTCTTTTCAC 57.763 40.909 0.00 0.00 0.00 3.18
862 1039 4.927978 TTGATTCGGCCTTTTCTTTTCA 57.072 36.364 0.00 0.00 0.00 2.69
863 1040 4.447724 GGTTTGATTCGGCCTTTTCTTTTC 59.552 41.667 0.00 0.00 0.00 2.29
864 1041 4.141824 TGGTTTGATTCGGCCTTTTCTTTT 60.142 37.500 0.00 0.00 0.00 2.27
865 1042 3.386402 TGGTTTGATTCGGCCTTTTCTTT 59.614 39.130 0.00 0.00 0.00 2.52
866 1043 2.962421 TGGTTTGATTCGGCCTTTTCTT 59.038 40.909 0.00 0.00 0.00 2.52
867 1044 2.593026 TGGTTTGATTCGGCCTTTTCT 58.407 42.857 0.00 0.00 0.00 2.52
868 1045 3.378911 TTGGTTTGATTCGGCCTTTTC 57.621 42.857 0.00 0.00 0.00 2.29
869 1046 4.350368 AATTGGTTTGATTCGGCCTTTT 57.650 36.364 0.00 0.00 0.00 2.27
870 1047 4.770010 TCTAATTGGTTTGATTCGGCCTTT 59.230 37.500 0.00 0.00 0.00 3.11
871 1048 4.340617 TCTAATTGGTTTGATTCGGCCTT 58.659 39.130 0.00 0.00 0.00 4.35
872 1049 3.963129 TCTAATTGGTTTGATTCGGCCT 58.037 40.909 0.00 0.00 0.00 5.19
873 1050 4.712122 TTCTAATTGGTTTGATTCGGCC 57.288 40.909 0.00 0.00 0.00 6.13
941 3528 1.797025 GGCGTGCCTGGTCTATTATC 58.203 55.000 2.98 0.00 0.00 1.75
942 3529 0.033504 CGGCGTGCCTGGTCTATTAT 59.966 55.000 9.55 0.00 0.00 1.28
950 3541 4.680237 TCAGTTCGGCGTGCCTGG 62.680 66.667 6.85 0.00 0.00 4.45
972 3563 2.831526 GCCTCTTTCTCTCCTCTTCTGT 59.168 50.000 0.00 0.00 0.00 3.41
973 3564 3.099141 AGCCTCTTTCTCTCCTCTTCTG 58.901 50.000 0.00 0.00 0.00 3.02
974 3565 3.473113 AGCCTCTTTCTCTCCTCTTCT 57.527 47.619 0.00 0.00 0.00 2.85
975 3566 4.252878 CAAAGCCTCTTTCTCTCCTCTTC 58.747 47.826 0.00 0.00 0.00 2.87
977 3568 2.027285 GCAAAGCCTCTTTCTCTCCTCT 60.027 50.000 0.00 0.00 0.00 3.69
978 3569 2.355197 GCAAAGCCTCTTTCTCTCCTC 58.645 52.381 0.00 0.00 0.00 3.71
979 3570 1.338579 CGCAAAGCCTCTTTCTCTCCT 60.339 52.381 0.00 0.00 0.00 3.69
980 3571 1.082690 CGCAAAGCCTCTTTCTCTCC 58.917 55.000 0.00 0.00 0.00 3.71
981 3572 2.086054 TCGCAAAGCCTCTTTCTCTC 57.914 50.000 0.00 0.00 0.00 3.20
982 3573 2.354259 CATCGCAAAGCCTCTTTCTCT 58.646 47.619 0.00 0.00 0.00 3.10
983 3574 1.399791 CCATCGCAAAGCCTCTTTCTC 59.600 52.381 0.00 0.00 0.00 2.87
984 3575 1.457346 CCATCGCAAAGCCTCTTTCT 58.543 50.000 0.00 0.00 0.00 2.52
1040 3631 4.593864 GGCGGCCCGAGATCTCAC 62.594 72.222 22.31 10.70 0.00 3.51
1254 3845 3.449227 CCGCAGCAGTACGGGAGA 61.449 66.667 0.00 0.00 45.74 3.71
1516 4130 4.020378 TTTCGCGCAAGGAACCGC 62.020 61.111 8.75 0.00 46.17 5.68
1517 4131 2.127383 GTTTCGCGCAAGGAACCG 60.127 61.111 8.75 0.00 38.28 4.44
1556 4170 4.532521 GGTCTATGCAGTATATGTTCCCCT 59.467 45.833 0.00 0.00 0.00 4.79
1691 4305 2.038557 ACGCAGTCCTTCCAATACTTGT 59.961 45.455 0.00 0.00 29.74 3.16
1923 4537 3.036429 GCAGTTCCCCCTGATCGCT 62.036 63.158 0.00 0.00 34.23 4.93
1995 4609 1.128200 CACCCGTCCCCAGATCATAA 58.872 55.000 0.00 0.00 0.00 1.90
2037 5012 2.031012 TCCTGCTTGTGCACCTCG 59.969 61.111 15.69 3.47 45.31 4.63
2073 5048 3.211045 CCTTCGAGGACAAAACCAAGAA 58.789 45.455 0.00 0.00 37.67 2.52
2113 5088 5.927115 AGTCTGTGCTTACTGCTTAAACTAC 59.073 40.000 0.00 0.00 43.37 2.73
2117 5092 5.364778 TGAAGTCTGTGCTTACTGCTTAAA 58.635 37.500 0.00 0.00 43.37 1.52
2125 5100 9.899226 AAGATTAATTTTGAAGTCTGTGCTTAC 57.101 29.630 0.00 0.00 0.00 2.34
2157 5133 3.495753 ACAGTTACAACGGGAATTTCGTC 59.504 43.478 7.96 0.00 40.18 4.20
2159 5135 4.477302 AACAGTTACAACGGGAATTTCG 57.523 40.909 0.00 1.43 0.00 3.46
2168 5351 9.445786 AATTCTGTGATTAAAACAGTTACAACG 57.554 29.630 16.84 0.00 44.42 4.10
2263 5533 6.288294 TGTGCTCTAACAGTTTTGATACAGT 58.712 36.000 0.00 0.00 0.00 3.55
2264 5534 6.785488 TGTGCTCTAACAGTTTTGATACAG 57.215 37.500 0.00 0.00 0.00 2.74
2265 5535 7.161404 AGATGTGCTCTAACAGTTTTGATACA 58.839 34.615 0.00 0.99 32.52 2.29
2266 5536 7.602517 AGATGTGCTCTAACAGTTTTGATAC 57.397 36.000 0.00 0.00 32.52 2.24
2294 5564 3.719173 TCCAACGGTCAAAAATCCAAC 57.281 42.857 0.00 0.00 0.00 3.77
2295 5565 3.891977 TGATCCAACGGTCAAAAATCCAA 59.108 39.130 0.00 0.00 0.00 3.53
2322 5592 4.512944 GTCAAAGAGCACAAATCTCAGACA 59.487 41.667 0.00 0.00 33.45 3.41
2371 5641 5.654603 TTGATCAGCAAATCAGCTTTCAT 57.345 34.783 0.00 0.00 43.70 2.57
2392 5670 6.093633 GTGCTCGGGATTAGAGTAACAATTTT 59.906 38.462 0.00 0.00 37.99 1.82
2396 5674 3.512329 TGTGCTCGGGATTAGAGTAACAA 59.488 43.478 0.00 0.00 37.99 2.83
2653 5931 1.376683 TGACGGGGGAAAGCGATTG 60.377 57.895 0.00 0.00 0.00 2.67
2689 5969 1.804748 GTGCCCTCGACGATTTCTTTT 59.195 47.619 0.00 0.00 0.00 2.27
2693 5974 0.669318 TGTGTGCCCTCGACGATTTC 60.669 55.000 0.00 0.00 0.00 2.17
2705 5986 0.533032 GGGAGTAGAGAGTGTGTGCC 59.467 60.000 0.00 0.00 0.00 5.01
2712 5993 1.490574 GCCACATGGGAGTAGAGAGT 58.509 55.000 0.00 0.00 40.01 3.24
2798 6172 2.568696 TTTCCTCGAGAGAAGCGATG 57.431 50.000 15.71 0.00 41.32 3.84
2833 6301 2.433664 CCAGTAACCACGCGACCC 60.434 66.667 15.93 0.00 0.00 4.46
2840 6766 0.389948 CGCCTCTCACCAGTAACCAC 60.390 60.000 0.00 0.00 0.00 4.16
2873 6799 1.666553 CCAGTAACTGCGCGAACCA 60.667 57.895 12.10 0.00 0.00 3.67
2881 6807 2.823628 GTCCACGACCAGTAACTGC 58.176 57.895 0.00 0.00 0.00 4.40
3026 6977 1.008938 AGTGAATGCTCCCTACTCCCT 59.991 52.381 0.00 0.00 0.00 4.20
3027 6978 1.139853 CAGTGAATGCTCCCTACTCCC 59.860 57.143 0.00 0.00 0.00 4.30
3028 6979 2.611225 CAGTGAATGCTCCCTACTCC 57.389 55.000 0.00 0.00 0.00 3.85
3093 7044 1.883926 CGGTTGTAGGTTGGGGAAAAG 59.116 52.381 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.