Multiple sequence alignment - TraesCS2D01G203800

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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 TraesCS2D01G203800 chr2D 100.000 2456 0 0 1 2456 155557454 155554999 0.000000e+00 4536.0
1 TraesCS2D01G203800 chr2D 90.646 449 19 2 146 571 155563143 155562695 2.120000e-160 575.0
2 TraesCS2D01G203800 chr2D 96.154 156 5 1 1 155 205683362 205683207 1.130000e-63 254.0
3 TraesCS2D01G203800 chr2B 94.762 1680 62 12 792 2456 212944543 212942875 0.000000e+00 2591.0
4 TraesCS2D01G203800 chr2A 93.321 1123 44 16 802 1903 144608805 144609917 0.000000e+00 1629.0
5 TraesCS2D01G203800 chr2A 89.621 607 45 17 146 743 319015411 319014814 0.000000e+00 756.0
6 TraesCS2D01G203800 chr2A 92.308 65 5 0 2377 2441 144610216 144610280 2.600000e-15 93.5
7 TraesCS2D01G203800 chr4A 91.680 613 39 11 146 751 170814385 170814992 0.000000e+00 839.0
8 TraesCS2D01G203800 chr4D 91.475 610 42 10 146 751 465967720 465967117 0.000000e+00 830.0
9 TraesCS2D01G203800 chr4D 96.774 155 4 1 1 154 241766231 241766077 8.710000e-65 257.0
10 TraesCS2D01G203800 chr1A 89.465 617 44 19 146 751 265535001 265534395 0.000000e+00 760.0
11 TraesCS2D01G203800 chr5D 83.762 622 74 22 146 751 496080360 496080970 4.580000e-157 564.0
12 TraesCS2D01G203800 chr5D 97.931 145 3 0 1 145 456060053 456060197 4.050000e-63 252.0
13 TraesCS2D01G203800 chr5A 83.013 624 76 25 146 751 448576540 448575929 2.780000e-149 538.0
14 TraesCS2D01G203800 chr5A 82.616 558 67 25 146 686 673794401 673794945 1.330000e-127 466.0
15 TraesCS2D01G203800 chr5A 79.407 573 93 24 146 705 85169981 85170541 4.960000e-102 381.0
16 TraesCS2D01G203800 chr3A 80.906 618 78 25 146 751 632624415 632623826 3.720000e-123 451.0
17 TraesCS2D01G203800 chr3A 97.183 71 2 0 681 751 714640515 714640585 1.190000e-23 121.0
18 TraesCS2D01G203800 chr7A 77.352 627 96 29 146 751 15637280 15637881 1.820000e-86 329.0
19 TraesCS2D01G203800 chr7D 95.152 165 5 3 1 163 494829402 494829565 8.710000e-65 257.0
20 TraesCS2D01G203800 chr7D 96.753 154 4 1 1 153 175314287 175314440 3.130000e-64 255.0
21 TraesCS2D01G203800 chr7D 96.753 154 4 1 1 153 175321847 175322000 3.130000e-64 255.0
22 TraesCS2D01G203800 chr7D 96.753 154 4 1 1 153 175330235 175330388 3.130000e-64 255.0
23 TraesCS2D01G203800 chr7D 96.753 154 4 1 1 153 299381631 299381784 3.130000e-64 255.0
24 TraesCS2D01G203800 chr1D 95.597 159 6 1 1 159 177073064 177073221 1.130000e-63 254.0


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 TraesCS2D01G203800 chr2D 155554999 155557454 2455 True 4536.00 4536 100.0000 1 2456 1 chr2D.!!$R1 2455
1 TraesCS2D01G203800 chr2B 212942875 212944543 1668 True 2591.00 2591 94.7620 792 2456 1 chr2B.!!$R1 1664
2 TraesCS2D01G203800 chr2A 144608805 144610280 1475 False 861.25 1629 92.8145 802 2441 2 chr2A.!!$F1 1639
3 TraesCS2D01G203800 chr2A 319014814 319015411 597 True 756.00 756 89.6210 146 743 1 chr2A.!!$R1 597
4 TraesCS2D01G203800 chr4A 170814385 170814992 607 False 839.00 839 91.6800 146 751 1 chr4A.!!$F1 605
5 TraesCS2D01G203800 chr4D 465967117 465967720 603 True 830.00 830 91.4750 146 751 1 chr4D.!!$R2 605
6 TraesCS2D01G203800 chr1A 265534395 265535001 606 True 760.00 760 89.4650 146 751 1 chr1A.!!$R1 605
7 TraesCS2D01G203800 chr5D 496080360 496080970 610 False 564.00 564 83.7620 146 751 1 chr5D.!!$F2 605
8 TraesCS2D01G203800 chr5A 448575929 448576540 611 True 538.00 538 83.0130 146 751 1 chr5A.!!$R1 605
9 TraesCS2D01G203800 chr5A 673794401 673794945 544 False 466.00 466 82.6160 146 686 1 chr5A.!!$F2 540
10 TraesCS2D01G203800 chr5A 85169981 85170541 560 False 381.00 381 79.4070 146 705 1 chr5A.!!$F1 559
11 TraesCS2D01G203800 chr3A 632623826 632624415 589 True 451.00 451 80.9060 146 751 1 chr3A.!!$R1 605
12 TraesCS2D01G203800 chr7A 15637280 15637881 601 False 329.00 329 77.3520 146 751 1 chr7A.!!$F1 605

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
770 936 0.102481 GAGCTCCCGATGTCGCTTAA 59.898 55.0 0.87 0.0 38.18 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 2743 0.108186 TGCCTACACAGGAAGCATCG 60.108 55.0 0.0 0.0 45.91 3.84 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
22 23 1.324736 GCGATTGTAAGCCAACTCTCG 59.675 52.381 0.00 0.00 35.44 4.04
25 26 4.171005 CGATTGTAAGCCAACTCTCGTTA 58.829 43.478 0.00 0.00 35.44 3.18
26 27 4.804139 CGATTGTAAGCCAACTCTCGTTAT 59.196 41.667 0.00 0.00 35.44 1.89
27 28 5.051641 CGATTGTAAGCCAACTCTCGTTATC 60.052 44.000 0.00 0.00 35.44 1.75
28 29 4.119442 TGTAAGCCAACTCTCGTTATCC 57.881 45.455 0.00 0.00 0.00 2.59
29 30 2.693267 AAGCCAACTCTCGTTATCCC 57.307 50.000 0.00 0.00 0.00 3.85
30 31 1.568504 AGCCAACTCTCGTTATCCCA 58.431 50.000 0.00 0.00 0.00 4.37
32 33 2.505819 AGCCAACTCTCGTTATCCCATT 59.494 45.455 0.00 0.00 0.00 3.16
33 34 2.872858 GCCAACTCTCGTTATCCCATTC 59.127 50.000 0.00 0.00 0.00 2.67
35 36 4.770795 CCAACTCTCGTTATCCCATTCTT 58.229 43.478 0.00 0.00 0.00 2.52
36 37 4.572389 CCAACTCTCGTTATCCCATTCTTG 59.428 45.833 0.00 0.00 0.00 3.02
37 38 5.178797 CAACTCTCGTTATCCCATTCTTGT 58.821 41.667 0.00 0.00 0.00 3.16
38 39 5.422214 ACTCTCGTTATCCCATTCTTGTT 57.578 39.130 0.00 0.00 0.00 2.83
40 41 5.046591 ACTCTCGTTATCCCATTCTTGTTCA 60.047 40.000 0.00 0.00 0.00 3.18
43 44 7.561251 TCTCGTTATCCCATTCTTGTTCATTA 58.439 34.615 0.00 0.00 0.00 1.90
44 45 7.494625 TCTCGTTATCCCATTCTTGTTCATTAC 59.505 37.037 0.00 0.00 0.00 1.89
45 46 7.106890 TCGTTATCCCATTCTTGTTCATTACA 58.893 34.615 0.00 0.00 34.12 2.41
47 48 7.857389 CGTTATCCCATTCTTGTTCATTACATG 59.143 37.037 0.00 0.00 36.44 3.21
48 49 6.720112 ATCCCATTCTTGTTCATTACATGG 57.280 37.500 0.00 0.00 36.44 3.66
49 50 5.266733 CCCATTCTTGTTCATTACATGGG 57.733 43.478 0.00 0.00 43.44 4.00
51 52 6.720112 CCATTCTTGTTCATTACATGGGAT 57.280 37.500 0.00 0.00 36.44 3.85
53 54 6.982141 CCATTCTTGTTCATTACATGGGATTG 59.018 38.462 0.00 0.00 36.44 2.67
54 55 7.364056 CCATTCTTGTTCATTACATGGGATTGT 60.364 37.037 0.00 0.00 36.44 2.71
60 61 8.224389 TGTTCATTACATGGGATTGTATGAAG 57.776 34.615 0.00 0.00 34.31 3.02
61 62 8.052141 TGTTCATTACATGGGATTGTATGAAGA 58.948 33.333 0.00 0.00 34.31 2.87
62 63 9.071276 GTTCATTACATGGGATTGTATGAAGAT 57.929 33.333 0.00 0.00 34.31 2.40
63 64 8.625786 TCATTACATGGGATTGTATGAAGATG 57.374 34.615 0.00 0.00 32.39 2.90
64 65 8.439172 TCATTACATGGGATTGTATGAAGATGA 58.561 33.333 0.00 0.00 32.39 2.92
65 66 8.509690 CATTACATGGGATTGTATGAAGATGAC 58.490 37.037 0.00 0.00 32.39 3.06
67 68 4.437682 TGGGATTGTATGAAGATGACCC 57.562 45.455 0.00 0.00 35.82 4.46
68 69 4.047166 TGGGATTGTATGAAGATGACCCT 58.953 43.478 0.00 0.00 36.20 4.34
69 70 4.478317 TGGGATTGTATGAAGATGACCCTT 59.522 41.667 0.00 0.00 36.20 3.95
70 71 5.066593 GGGATTGTATGAAGATGACCCTTC 58.933 45.833 0.00 0.00 42.09 3.46
72 73 6.360618 GGATTGTATGAAGATGACCCTTCTT 58.639 40.000 0.00 0.00 42.20 2.52
74 75 4.517285 TGTATGAAGATGACCCTTCTTGC 58.483 43.478 0.00 0.00 42.20 4.01
75 76 2.099141 TGAAGATGACCCTTCTTGCG 57.901 50.000 0.00 0.00 42.20 4.85
76 77 1.623311 TGAAGATGACCCTTCTTGCGA 59.377 47.619 0.00 0.00 42.20 5.10
77 78 2.003301 GAAGATGACCCTTCTTGCGAC 58.997 52.381 0.00 0.00 39.44 5.19
79 80 1.347707 AGATGACCCTTCTTGCGACAA 59.652 47.619 0.00 0.00 0.00 3.18
82 83 2.695359 TGACCCTTCTTGCGACAATAC 58.305 47.619 0.00 0.00 0.00 1.89
83 84 2.007608 GACCCTTCTTGCGACAATACC 58.992 52.381 0.00 0.00 0.00 2.73
85 86 2.835764 ACCCTTCTTGCGACAATACCTA 59.164 45.455 0.00 0.00 0.00 3.08
89 90 4.876107 CCTTCTTGCGACAATACCTACAAT 59.124 41.667 0.00 0.00 0.00 2.71
90 91 5.220662 CCTTCTTGCGACAATACCTACAATG 60.221 44.000 0.00 0.00 0.00 2.82
95 96 2.933906 CGACAATACCTACAATGCGGTT 59.066 45.455 0.18 0.00 34.76 4.44
97 98 4.748102 CGACAATACCTACAATGCGGTTAT 59.252 41.667 0.18 0.00 34.76 1.89
98 99 5.333035 CGACAATACCTACAATGCGGTTATG 60.333 44.000 0.18 3.66 34.76 1.90
99 100 4.274950 ACAATACCTACAATGCGGTTATGC 59.725 41.667 0.18 0.00 34.76 3.14
102 103 1.873591 CCTACAATGCGGTTATGCCTC 59.126 52.381 0.00 0.00 34.25 4.70
104 105 3.244078 CCTACAATGCGGTTATGCCTCTA 60.244 47.826 0.00 0.00 34.25 2.43
105 106 3.275617 ACAATGCGGTTATGCCTCTAA 57.724 42.857 0.00 0.00 34.25 2.10
106 107 3.206150 ACAATGCGGTTATGCCTCTAAG 58.794 45.455 0.00 0.00 34.25 2.18
107 108 3.206150 CAATGCGGTTATGCCTCTAAGT 58.794 45.455 0.00 0.00 34.25 2.24
108 109 2.596904 TGCGGTTATGCCTCTAAGTC 57.403 50.000 0.00 0.00 34.25 3.01
109 110 1.202371 TGCGGTTATGCCTCTAAGTCG 60.202 52.381 0.00 0.00 34.25 4.18
111 112 2.460918 CGGTTATGCCTCTAAGTCGTG 58.539 52.381 0.00 0.00 34.25 4.35
114 115 1.776662 TATGCCTCTAAGTCGTGCCT 58.223 50.000 0.00 0.00 0.00 4.75
115 116 0.461961 ATGCCTCTAAGTCGTGCCTC 59.538 55.000 0.00 0.00 0.00 4.70
126 127 3.986006 GTGCCTCGACACGTGGGA 61.986 66.667 21.57 15.34 40.31 4.37
127 128 3.680786 TGCCTCGACACGTGGGAG 61.681 66.667 24.04 24.04 40.31 4.30
129 130 2.711922 GCCTCGACACGTGGGAGAT 61.712 63.158 29.41 7.79 40.31 2.75
132 133 2.501261 CCTCGACACGTGGGAGATATA 58.499 52.381 29.41 5.30 36.95 0.86
134 135 1.878088 TCGACACGTGGGAGATATAGC 59.122 52.381 21.57 0.00 0.00 2.97
135 136 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
137 138 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
139 140 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
140 141 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
141 142 1.827969 GTGGGAGATATAGCCGCATCT 59.172 52.381 0.00 0.00 34.19 2.90
143 144 2.234661 TGGGAGATATAGCCGCATCTTG 59.765 50.000 0.00 0.00 31.63 3.02
144 145 2.419297 GGGAGATATAGCCGCATCTTGG 60.419 54.545 0.00 0.00 31.63 3.61
551 710 8.426489 ACAGATGTACTTTAAATATTCGCCCTA 58.574 33.333 0.00 0.00 0.00 3.53
561 720 0.696501 ATTCGCCCTACCTTGTGGTT 59.303 50.000 0.00 0.00 46.05 3.67
565 724 1.002773 CGCCCTACCTTGTGGTTAGTT 59.997 52.381 0.00 0.00 46.05 2.24
633 792 0.888619 TGCGAGTTCGATCCTCTGTT 59.111 50.000 5.60 0.00 43.02 3.16
682 848 1.929836 CAAACGAGCTCTATCCACTGC 59.070 52.381 12.85 0.00 0.00 4.40
751 917 2.325082 AACTGGCACTAAAGGCGCG 61.325 57.895 0.00 0.00 36.77 6.86
752 918 2.434185 CTGGCACTAAAGGCGCGA 60.434 61.111 12.10 0.00 36.77 5.87
753 919 2.434185 TGGCACTAAAGGCGCGAG 60.434 61.111 12.10 0.00 36.77 5.03
767 933 3.893763 CGAGCTCCCGATGTCGCT 61.894 66.667 8.47 0.00 38.18 4.93
768 934 2.496817 GAGCTCCCGATGTCGCTT 59.503 61.111 0.87 0.00 38.18 4.68
769 935 1.734137 GAGCTCCCGATGTCGCTTA 59.266 57.895 0.87 0.00 38.18 3.09
770 936 0.102481 GAGCTCCCGATGTCGCTTAA 59.898 55.000 0.87 0.00 38.18 1.85
771 937 0.179108 AGCTCCCGATGTCGCTTAAC 60.179 55.000 0.00 0.00 38.18 2.01
772 938 1.480219 GCTCCCGATGTCGCTTAACG 61.480 60.000 0.00 0.00 45.62 3.18
773 939 1.480219 CTCCCGATGTCGCTTAACGC 61.480 60.000 0.00 0.00 43.23 4.84
785 951 1.791204 GCTTAACGCGAAGTATAGGGC 59.209 52.381 15.93 0.31 0.00 5.19
788 954 2.733593 CGCGAAGTATAGGGCGCC 60.734 66.667 21.18 21.18 46.04 6.53
789 955 2.357154 GCGAAGTATAGGGCGCCC 60.357 66.667 39.29 39.29 43.33 6.13
790 956 2.342648 CGAAGTATAGGGCGCCCC 59.657 66.667 41.72 26.23 45.90 5.80
810 976 1.972660 GATGGGTCAACGAGGGGGAG 61.973 65.000 0.00 0.00 0.00 4.30
819 985 2.444256 CGAGGGGGAGATTGGGTCC 61.444 68.421 0.00 0.00 0.00 4.46
885 1051 0.652071 TTGCAACGCGAGCAGATATG 59.348 50.000 24.49 7.90 43.75 1.78
914 1080 0.618968 CTCTGGCAGGGAAGGGTACT 60.619 60.000 9.31 0.00 0.00 2.73
1221 1394 3.567797 GCCAAGATCGTGCGCCTC 61.568 66.667 4.18 0.00 0.00 4.70
1360 1533 1.652012 CTCATCCTCGTCGAGAGCC 59.348 63.158 23.74 0.00 45.54 4.70
1475 1648 1.799544 TTCGGTTAAGCTTCGGTTCC 58.200 50.000 0.00 0.00 0.00 3.62
1496 1669 3.257393 CTTGACGTAATTCTCTGCAGCT 58.743 45.455 9.47 0.00 0.00 4.24
1558 1738 3.899726 TGGGGTTGTAAGCTGTTAAACA 58.100 40.909 0.00 0.00 0.00 2.83
1579 1759 1.595993 ATCAGCTACCGCTCGTGTGT 61.596 55.000 0.00 0.00 45.15 3.72
1580 1760 2.088763 CAGCTACCGCTCGTGTGTG 61.089 63.158 0.00 0.00 45.15 3.82
1736 1918 3.820467 CACAAATCCTGCAGTGGAGTAAA 59.180 43.478 13.81 0.00 39.78 2.01
1794 1976 1.597742 ATTGTTGTTGCGAGCTCACT 58.402 45.000 15.40 0.00 0.00 3.41
1810 1992 1.065926 TCACTGTTGATGCAGGCTAGG 60.066 52.381 0.00 0.00 40.59 3.02
1849 2032 4.202151 GCTGGCTATCAACAAATTAAGGGG 60.202 45.833 0.00 0.00 0.00 4.79
1852 2035 4.584743 GGCTATCAACAAATTAAGGGGGAG 59.415 45.833 0.00 0.00 0.00 4.30
1930 2121 3.557577 TGTGCTTGTGTAATGTGCATC 57.442 42.857 0.00 0.00 36.04 3.91
1938 2129 6.585702 GCTTGTGTAATGTGCATCATTTGTAA 59.414 34.615 16.19 8.77 43.33 2.41
1990 2181 7.446001 TGAGTATACAAACATGAAACATGCA 57.554 32.000 5.50 0.00 0.00 3.96
2044 2235 3.748048 CCGGTAATGATCAACCTGCTATG 59.252 47.826 13.47 0.00 33.34 2.23
2051 2242 5.619132 TGATCAACCTGCTATGAAGATCA 57.381 39.130 0.00 0.00 38.33 2.92
2061 2252 9.584008 ACCTGCTATGAAGATCATAATCAAATT 57.416 29.630 0.00 0.00 38.72 1.82
2105 2296 2.905075 GCTTTTGCAAAACCAGTTCCT 58.095 42.857 20.46 0.00 46.58 3.36
2106 2297 2.866156 GCTTTTGCAAAACCAGTTCCTC 59.134 45.455 20.46 0.00 46.58 3.71
2122 2313 5.372373 AGTTCCTCCTTTTGAACTGAAGAG 58.628 41.667 4.25 0.00 46.97 2.85
2124 2315 3.073062 TCCTCCTTTTGAACTGAAGAGGG 59.927 47.826 0.00 0.00 0.00 4.30
2266 2457 3.819564 TGGACTATTGGACTGGAATCG 57.180 47.619 0.00 0.00 0.00 3.34
2284 2475 3.211803 TCGATGTCCTGTTCTGTTACG 57.788 47.619 0.00 0.00 0.00 3.18
2292 2678 3.057033 TCCTGTTCTGTTACGCTTCCTAC 60.057 47.826 0.00 0.00 0.00 3.18
2298 2684 3.004629 TCTGTTACGCTTCCTACGTTTGA 59.995 43.478 0.00 0.00 41.93 2.69
2334 2720 6.348498 TCAGTTGTTCATACCATGTAGGATG 58.652 40.000 0.00 0.00 41.22 3.51
2361 2747 3.262420 CAGGTAGTTCTTGGTTCCGATG 58.738 50.000 0.00 0.00 0.00 3.84
2375 2761 0.811616 CCGATGCTTCCTGTGTAGGC 60.812 60.000 0.00 0.00 44.22 3.93
2382 2768 3.009033 TGCTTCCTGTGTAGGCAGTAATT 59.991 43.478 0.00 0.00 44.22 1.40
2442 2828 9.590451 ACTAATTTGCCAAAATCACATCATTAG 57.410 29.630 0.00 0.00 34.84 1.73
2450 2836 9.585099 GCCAAAATCACATCATTAGTTCATTAA 57.415 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.666189 GAGAGTTGGCTTACAATCGCC 59.334 52.381 0.00 0.00 46.46 5.54
2 3 1.324736 CGAGAGTTGGCTTACAATCGC 59.675 52.381 0.00 0.00 41.95 4.58
3 4 2.607187 ACGAGAGTTGGCTTACAATCG 58.393 47.619 0.00 12.10 46.40 3.34
17 18 5.419542 TGAACAAGAATGGGATAACGAGAG 58.580 41.667 0.00 0.00 0.00 3.20
18 19 5.414789 TGAACAAGAATGGGATAACGAGA 57.585 39.130 0.00 0.00 0.00 4.04
19 20 6.683974 AATGAACAAGAATGGGATAACGAG 57.316 37.500 0.00 0.00 0.00 4.18
21 22 7.315247 TGTAATGAACAAGAATGGGATAACG 57.685 36.000 0.00 0.00 34.29 3.18
40 41 7.667219 GGTCATCTTCATACAATCCCATGTAAT 59.333 37.037 0.00 0.00 39.12 1.89
43 44 5.380043 GGTCATCTTCATACAATCCCATGT 58.620 41.667 0.00 0.00 37.32 3.21
44 45 4.763793 GGGTCATCTTCATACAATCCCATG 59.236 45.833 0.00 0.00 33.33 3.66
45 46 4.666907 AGGGTCATCTTCATACAATCCCAT 59.333 41.667 0.00 0.00 35.31 4.00
47 48 4.713792 AGGGTCATCTTCATACAATCCC 57.286 45.455 0.00 0.00 0.00 3.85
48 49 5.934781 AGAAGGGTCATCTTCATACAATCC 58.065 41.667 7.26 0.00 44.01 3.01
49 50 6.238593 GCAAGAAGGGTCATCTTCATACAATC 60.239 42.308 7.26 0.00 44.01 2.67
51 52 4.943705 GCAAGAAGGGTCATCTTCATACAA 59.056 41.667 7.26 0.00 44.01 2.41
53 54 3.557595 CGCAAGAAGGGTCATCTTCATAC 59.442 47.826 7.26 0.00 44.01 2.39
54 55 3.797039 CGCAAGAAGGGTCATCTTCATA 58.203 45.455 7.26 0.00 44.01 2.15
70 71 3.544048 CGCATTGTAGGTATTGTCGCAAG 60.544 47.826 0.00 0.00 0.00 4.01
72 73 1.930503 CGCATTGTAGGTATTGTCGCA 59.069 47.619 0.00 0.00 0.00 5.10
74 75 2.546778 ACCGCATTGTAGGTATTGTCG 58.453 47.619 4.50 0.00 39.30 4.35
75 76 5.560183 GCATAACCGCATTGTAGGTATTGTC 60.560 44.000 6.42 2.60 40.37 3.18
76 77 4.274950 GCATAACCGCATTGTAGGTATTGT 59.725 41.667 6.42 0.00 40.37 2.71
77 78 4.320202 GGCATAACCGCATTGTAGGTATTG 60.320 45.833 6.42 8.09 40.37 1.90
79 80 3.072476 AGGCATAACCGCATTGTAGGTAT 59.928 43.478 6.42 0.00 46.52 2.73
82 83 1.873591 GAGGCATAACCGCATTGTAGG 59.126 52.381 0.00 0.00 46.52 3.18
83 84 2.838736 AGAGGCATAACCGCATTGTAG 58.161 47.619 0.00 0.00 46.52 2.74
85 86 3.206150 CTTAGAGGCATAACCGCATTGT 58.794 45.455 0.00 0.00 46.52 2.71
89 90 1.202371 CGACTTAGAGGCATAACCGCA 60.202 52.381 0.00 0.00 46.52 5.69
90 91 1.202382 ACGACTTAGAGGCATAACCGC 60.202 52.381 0.00 0.00 46.52 5.68
95 96 1.681793 GAGGCACGACTTAGAGGCATA 59.318 52.381 0.00 0.00 0.00 3.14
97 98 1.890894 GAGGCACGACTTAGAGGCA 59.109 57.895 0.00 0.00 0.00 4.75
98 99 1.226717 CGAGGCACGACTTAGAGGC 60.227 63.158 0.00 0.00 45.77 4.70
99 100 2.478989 TCGAGGCACGACTTAGAGG 58.521 57.895 2.07 0.00 46.45 3.69
109 110 3.916392 CTCCCACGTGTCGAGGCAC 62.916 68.421 15.65 0.00 36.35 5.01
111 112 1.381928 TATCTCCCACGTGTCGAGGC 61.382 60.000 22.62 0.00 36.35 4.70
114 115 1.878088 GCTATATCTCCCACGTGTCGA 59.122 52.381 15.65 8.55 0.00 4.20
115 116 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
118 119 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
119 120 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
120 121 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
121 122 1.827969 AGATGCGGCTATATCTCCCAC 59.172 52.381 0.00 0.00 0.00 4.61
123 124 2.419297 CCAAGATGCGGCTATATCTCCC 60.419 54.545 0.00 0.00 32.71 4.30
124 125 2.234908 ACCAAGATGCGGCTATATCTCC 59.765 50.000 0.00 0.00 32.71 3.71
125 126 3.601443 ACCAAGATGCGGCTATATCTC 57.399 47.619 0.00 0.00 32.71 2.75
126 127 4.357918 AAACCAAGATGCGGCTATATCT 57.642 40.909 0.00 0.00 35.25 1.98
127 128 5.008613 TGAAAAACCAAGATGCGGCTATATC 59.991 40.000 0.00 0.00 0.00 1.63
129 130 4.265893 TGAAAAACCAAGATGCGGCTATA 58.734 39.130 0.00 0.00 0.00 1.31
132 133 1.327303 TGAAAAACCAAGATGCGGCT 58.673 45.000 0.00 0.00 0.00 5.52
134 135 4.143347 CGATTTTGAAAAACCAAGATGCGG 60.143 41.667 0.00 0.00 0.00 5.69
135 136 4.679197 TCGATTTTGAAAAACCAAGATGCG 59.321 37.500 0.00 0.00 0.00 4.73
137 138 7.872163 TCATCGATTTTGAAAAACCAAGATG 57.128 32.000 0.00 6.24 33.71 2.90
139 140 7.488322 AGTTCATCGATTTTGAAAAACCAAGA 58.512 30.769 0.00 0.00 35.03 3.02
140 141 7.698836 AGTTCATCGATTTTGAAAAACCAAG 57.301 32.000 0.00 0.00 35.03 3.61
141 142 8.485976 AAAGTTCATCGATTTTGAAAAACCAA 57.514 26.923 0.00 0.00 35.03 3.67
561 720 4.589216 ACTAAACTACACCGCACAACTA 57.411 40.909 0.00 0.00 0.00 2.24
565 724 2.158928 ACCAACTAAACTACACCGCACA 60.159 45.455 0.00 0.00 0.00 4.57
682 848 4.377708 GCCGGCCCAGCAAAAAGG 62.378 66.667 18.11 0.00 0.00 3.11
740 906 2.184579 GGAGCTCGCGCCTTTAGT 59.815 61.111 7.83 0.00 36.60 2.24
751 917 0.102481 TTAAGCGACATCGGGAGCTC 59.898 55.000 4.71 4.71 39.25 4.09
752 918 0.179108 GTTAAGCGACATCGGGAGCT 60.179 55.000 3.08 0.00 42.35 4.09
753 919 1.480219 CGTTAAGCGACATCGGGAGC 61.480 60.000 3.08 0.00 44.77 4.70
754 920 1.480219 GCGTTAAGCGACATCGGGAG 61.480 60.000 3.08 0.00 44.77 4.30
755 921 1.517694 GCGTTAAGCGACATCGGGA 60.518 57.895 3.08 0.00 44.77 5.14
756 922 3.003478 GCGTTAAGCGACATCGGG 58.997 61.111 3.08 0.00 44.77 5.14
765 931 1.791204 GCCCTATACTTCGCGTTAAGC 59.209 52.381 5.77 0.00 43.95 3.09
766 932 2.049228 CGCCCTATACTTCGCGTTAAG 58.951 52.381 5.77 5.93 39.78 1.85
767 933 1.865248 GCGCCCTATACTTCGCGTTAA 60.865 52.381 5.77 0.00 46.09 2.01
768 934 0.318107 GCGCCCTATACTTCGCGTTA 60.318 55.000 5.77 0.00 46.09 3.18
769 935 1.590792 GCGCCCTATACTTCGCGTT 60.591 57.895 5.77 0.00 46.09 4.84
770 936 2.027169 GCGCCCTATACTTCGCGT 59.973 61.111 5.77 0.00 46.09 6.01
772 938 2.357154 GGGCGCCCTATACTTCGC 60.357 66.667 38.76 7.31 45.99 4.70
773 939 2.342648 GGGGCGCCCTATACTTCG 59.657 66.667 42.70 0.00 41.34 3.79
774 940 1.542187 ATCGGGGCGCCCTATACTTC 61.542 60.000 42.70 24.27 42.67 3.01
775 941 1.535687 ATCGGGGCGCCCTATACTT 60.536 57.895 42.70 20.06 42.67 2.24
776 942 2.119832 ATCGGGGCGCCCTATACT 59.880 61.111 42.70 21.33 42.67 2.12
777 943 2.264794 CATCGGGGCGCCCTATAC 59.735 66.667 42.70 26.18 42.67 1.47
778 944 3.000819 CCATCGGGGCGCCCTATA 61.001 66.667 42.70 28.44 42.67 1.31
789 955 2.186903 CCCTCGTTGACCCATCGG 59.813 66.667 0.00 0.00 0.00 4.18
790 956 2.186903 CCCCTCGTTGACCCATCG 59.813 66.667 0.00 0.00 0.00 3.84
800 966 1.689582 GACCCAATCTCCCCCTCGT 60.690 63.158 0.00 0.00 0.00 4.18
810 976 1.301009 GCGAGATCGGGACCCAATC 60.301 63.158 12.15 7.46 40.23 2.67
914 1080 2.022718 AACCTAGCAAAAATGGGGCA 57.977 45.000 0.00 0.00 0.00 5.36
1475 1648 3.257393 AGCTGCAGAGAATTACGTCAAG 58.743 45.455 20.43 0.00 0.00 3.02
1496 1669 5.183522 ACTTAACACAAAACCGAAGTCCAAA 59.816 36.000 0.00 0.00 0.00 3.28
1579 1759 2.565391 TCGAAATACTTCTGTCCAGGCA 59.435 45.455 0.00 0.00 0.00 4.75
1580 1760 3.119101 TCTCGAAATACTTCTGTCCAGGC 60.119 47.826 0.00 0.00 0.00 4.85
1794 1976 2.584835 AAACCTAGCCTGCATCAACA 57.415 45.000 0.00 0.00 0.00 3.33
1873 2064 8.862325 TCATTAGAAAGCCTAAACAAGAATGA 57.138 30.769 0.00 0.00 40.45 2.57
1966 2157 7.304735 GTGCATGTTTCATGTTTGTATACTCA 58.695 34.615 4.17 1.88 0.00 3.41
1989 2180 4.509970 TCATCACTCAAGTTGTTAACGGTG 59.490 41.667 2.11 4.63 36.23 4.94
1990 2181 4.699637 TCATCACTCAAGTTGTTAACGGT 58.300 39.130 2.11 0.00 36.23 4.83
2023 2214 4.631131 TCATAGCAGGTTGATCATTACCG 58.369 43.478 10.30 7.28 39.46 4.02
2061 2252 6.091441 GCGGTGTGATTTTGGCAAATTAATTA 59.909 34.615 14.29 0.00 32.35 1.40
2063 2254 4.391523 GCGGTGTGATTTTGGCAAATTAAT 59.608 37.500 14.29 4.30 32.35 1.40
2103 2294 3.416156 CCCTCTTCAGTTCAAAAGGAGG 58.584 50.000 0.00 0.00 0.00 4.30
2104 2295 3.181439 ACCCCTCTTCAGTTCAAAAGGAG 60.181 47.826 0.00 0.00 0.00 3.69
2105 2296 2.783510 ACCCCTCTTCAGTTCAAAAGGA 59.216 45.455 0.00 0.00 0.00 3.36
2106 2297 2.887152 CACCCCTCTTCAGTTCAAAAGG 59.113 50.000 0.00 0.00 0.00 3.11
2122 2313 1.210538 CTAAGGTTACCCTCCACCCC 58.789 60.000 0.00 0.00 41.56 4.95
2124 2315 1.836166 GACCTAAGGTTACCCTCCACC 59.164 57.143 0.00 0.00 41.56 4.61
2187 2378 7.373493 CAATAGTCCAAGAAGCAAAGAAACAT 58.627 34.615 0.00 0.00 0.00 2.71
2266 2457 2.960819 AGCGTAACAGAACAGGACATC 58.039 47.619 0.00 0.00 0.00 3.06
2284 2475 4.745649 ACTACTGATCAAACGTAGGAAGC 58.254 43.478 19.29 0.00 35.97 3.86
2292 2678 8.018677 ACAACTGATTTACTACTGATCAAACG 57.981 34.615 0.00 0.00 30.13 3.60
2298 2684 9.601217 GGTATGAACAACTGATTTACTACTGAT 57.399 33.333 0.00 0.00 0.00 2.90
2334 2720 3.629142 ACCAAGAACTACCTGGTATGC 57.371 47.619 7.07 0.12 0.00 3.14
2356 2742 0.811616 GCCTACACAGGAAGCATCGG 60.812 60.000 0.00 0.00 45.91 4.18
2357 2743 0.108186 TGCCTACACAGGAAGCATCG 60.108 55.000 0.00 0.00 45.91 3.84
2382 2768 9.860650 ATCAAGGTATTTATTGCAGGTTACATA 57.139 29.630 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.