Multiple sequence alignment - TraesCS5B01G500000

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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 TraesCS5B01G500000 chr5B 100.000 2282 0 0 1 2282 666197102 666194821 0.000000e+00 4215.0
1 TraesCS5B01G500000 chr5B 97.260 73 2 0 1 73 443263900 443263828 8.560000e-25 124.0
2 TraesCS5B01G500000 chr5D 89.909 2190 127 36 123 2282 528972803 528970678 0.000000e+00 2734.0
3 TraesCS5B01G500000 chr5A 92.083 1301 86 7 993 2282 657199162 657197868 0.000000e+00 1816.0
4 TraesCS5B01G500000 chr5A 78.571 532 40 34 187 710 657200046 657199581 1.330000e-72 283.0
5 TraesCS5B01G500000 chr1B 87.708 1562 115 33 750 2282 452565357 452566870 0.000000e+00 1749.0
6 TraesCS5B01G500000 chr1B 80.603 531 66 17 133 645 452512624 452513135 2.140000e-100 375.0
7 TraesCS5B01G500000 chr1D 90.051 1186 81 12 750 1928 337211154 337212309 0.000000e+00 1502.0
8 TraesCS5B01G500000 chr1D 92.226 283 17 1 2000 2282 337212570 337212847 1.640000e-106 396.0
9 TraesCS5B01G500000 chr1A 90.920 859 65 8 750 1606 435375908 435376755 0.000000e+00 1142.0
10 TraesCS5B01G500000 chr1A 89.073 604 34 13 1632 2211 435376750 435377345 0.000000e+00 721.0
11 TraesCS5B01G500000 chr1A 96.203 79 3 0 2204 2282 435377422 435377500 1.840000e-26 130.0
12 TraesCS5B01G500000 chr3A 79.048 315 41 18 644 949 744055514 744055812 2.310000e-45 193.0
13 TraesCS5B01G500000 chr7B 98.684 76 1 0 1 76 637866790 637866865 3.950000e-28 135.0
14 TraesCS5B01G500000 chr7B 84.000 75 7 4 878 947 8926795 8926721 1.460000e-07 67.6
15 TraesCS5B01G500000 chr2A 98.667 75 1 0 1 75 24902076 24902002 1.420000e-27 134.0
16 TraesCS5B01G500000 chr7A 86.316 95 8 4 771 864 696502211 696502301 5.190000e-17 99.0
17 TraesCS5B01G500000 chr7D 91.429 70 6 0 3 72 6721516 6721585 1.870000e-16 97.1
18 TraesCS5B01G500000 chr2B 77.931 145 22 8 812 952 426777278 426777416 5.220000e-12 82.4
19 TraesCS5B01G500000 chr6A 82.558 86 7 6 782 865 390114389 390114468 4.070000e-08 69.4


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 TraesCS5B01G500000 chr5B 666194821 666197102 2281 True 4215.000000 4215 100.000000 1 2282 1 chr5B.!!$R2 2281
1 TraesCS5B01G500000 chr5D 528970678 528972803 2125 True 2734.000000 2734 89.909000 123 2282 1 chr5D.!!$R1 2159
2 TraesCS5B01G500000 chr5A 657197868 657200046 2178 True 1049.500000 1816 85.327000 187 2282 2 chr5A.!!$R1 2095
3 TraesCS5B01G500000 chr1B 452565357 452566870 1513 False 1749.000000 1749 87.708000 750 2282 1 chr1B.!!$F2 1532
4 TraesCS5B01G500000 chr1B 452512624 452513135 511 False 375.000000 375 80.603000 133 645 1 chr1B.!!$F1 512
5 TraesCS5B01G500000 chr1D 337211154 337212847 1693 False 949.000000 1502 91.138500 750 2282 2 chr1D.!!$F1 1532
6 TraesCS5B01G500000 chr1A 435375908 435377500 1592 False 664.333333 1142 92.065333 750 2282 3 chr1A.!!$F1 1532

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
74 75 0.249489 GCCATGGCGACGAGTAGATT 60.249 55.0 23.48 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 1725 1.347707 ACACCAGGAAGCGATTTCAGA 59.652 47.619 0.0 0.0 37.54 3.27 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
20 21 3.022607 AGGTACGAGAAAACTCAACGG 57.977 47.619 0.00 0.00 0.00 4.44
21 22 1.458445 GGTACGAGAAAACTCAACGGC 59.542 52.381 0.00 0.00 0.00 5.68
22 23 1.123756 GTACGAGAAAACTCAACGGCG 59.876 52.381 4.80 4.80 0.00 6.46
23 24 1.219522 ACGAGAAAACTCAACGGCGG 61.220 55.000 13.24 0.00 0.00 6.13
24 25 1.206831 GAGAAAACTCAACGGCGGC 59.793 57.895 13.24 0.00 0.00 6.53
25 26 1.503818 GAGAAAACTCAACGGCGGCA 61.504 55.000 13.24 0.00 0.00 5.69
26 27 1.082104 GAAAACTCAACGGCGGCAG 60.082 57.895 13.24 6.13 0.00 4.85
27 28 3.194272 AAAACTCAACGGCGGCAGC 62.194 57.895 13.24 0.00 44.18 5.25
44 45 4.124351 CGCCGCCGGAGTACTGAA 62.124 66.667 7.68 0.00 0.00 3.02
45 46 2.263540 GCCGCCGGAGTACTGAAA 59.736 61.111 7.68 0.00 0.00 2.69
46 47 1.375013 GCCGCCGGAGTACTGAAAA 60.375 57.895 7.68 0.00 0.00 2.29
47 48 1.632948 GCCGCCGGAGTACTGAAAAC 61.633 60.000 7.68 0.00 0.00 2.43
48 49 1.017701 CCGCCGGAGTACTGAAAACC 61.018 60.000 5.05 0.00 0.00 3.27
49 50 1.017701 CGCCGGAGTACTGAAAACCC 61.018 60.000 5.05 0.00 0.00 4.11
50 51 0.323957 GCCGGAGTACTGAAAACCCT 59.676 55.000 5.05 0.00 0.00 4.34
51 52 1.551883 GCCGGAGTACTGAAAACCCTA 59.448 52.381 5.05 0.00 0.00 3.53
52 53 2.418334 GCCGGAGTACTGAAAACCCTAG 60.418 54.545 5.05 0.00 0.00 3.02
53 54 2.830321 CCGGAGTACTGAAAACCCTAGT 59.170 50.000 0.00 0.00 0.00 2.57
54 55 3.119209 CCGGAGTACTGAAAACCCTAGTC 60.119 52.174 0.00 0.00 0.00 2.59
55 56 3.427233 CGGAGTACTGAAAACCCTAGTCG 60.427 52.174 0.00 0.00 0.00 4.18
56 57 3.509740 GAGTACTGAAAACCCTAGTCGC 58.490 50.000 0.00 0.00 0.00 5.19
57 58 2.233186 AGTACTGAAAACCCTAGTCGCC 59.767 50.000 0.00 0.00 0.00 5.54
58 59 1.053424 ACTGAAAACCCTAGTCGCCA 58.947 50.000 0.00 0.00 0.00 5.69
59 60 1.628846 ACTGAAAACCCTAGTCGCCAT 59.371 47.619 0.00 0.00 0.00 4.40
60 61 2.009774 CTGAAAACCCTAGTCGCCATG 58.990 52.381 0.00 0.00 0.00 3.66
61 62 1.339631 TGAAAACCCTAGTCGCCATGG 60.340 52.381 7.63 7.63 0.00 3.66
62 63 0.679960 AAAACCCTAGTCGCCATGGC 60.680 55.000 27.67 27.67 37.85 4.40
72 73 2.805546 GCCATGGCGACGAGTAGA 59.194 61.111 23.48 0.00 0.00 2.59
73 74 1.364171 GCCATGGCGACGAGTAGAT 59.636 57.895 23.48 0.00 0.00 1.98
74 75 0.249489 GCCATGGCGACGAGTAGATT 60.249 55.000 23.48 0.00 0.00 2.40
75 76 1.491670 CCATGGCGACGAGTAGATTG 58.508 55.000 0.00 0.00 0.00 2.67
76 77 1.202417 CCATGGCGACGAGTAGATTGT 60.202 52.381 0.00 0.00 0.00 2.71
77 78 2.120232 CATGGCGACGAGTAGATTGTC 58.880 52.381 0.00 0.00 38.76 3.18
78 79 1.460504 TGGCGACGAGTAGATTGTCT 58.539 50.000 0.00 0.00 39.84 3.41
79 80 1.132453 TGGCGACGAGTAGATTGTCTG 59.868 52.381 0.00 0.00 39.84 3.51
80 81 1.400846 GGCGACGAGTAGATTGTCTGA 59.599 52.381 0.00 0.00 39.84 3.27
81 82 2.159421 GGCGACGAGTAGATTGTCTGAA 60.159 50.000 0.00 0.00 39.84 3.02
82 83 3.499048 GCGACGAGTAGATTGTCTGAAA 58.501 45.455 0.00 0.00 39.84 2.69
83 84 3.918591 GCGACGAGTAGATTGTCTGAAAA 59.081 43.478 0.00 0.00 39.84 2.29
84 85 4.563184 GCGACGAGTAGATTGTCTGAAAAT 59.437 41.667 0.00 0.00 39.84 1.82
85 86 5.062308 GCGACGAGTAGATTGTCTGAAAATT 59.938 40.000 0.00 0.00 39.84 1.82
86 87 6.687655 CGACGAGTAGATTGTCTGAAAATTC 58.312 40.000 0.00 0.00 39.84 2.17
87 88 6.504954 CGACGAGTAGATTGTCTGAAAATTCG 60.505 42.308 9.64 9.64 39.84 3.34
88 89 5.062308 ACGAGTAGATTGTCTGAAAATTCGC 59.938 40.000 10.68 1.02 0.00 4.70
89 90 5.062183 CGAGTAGATTGTCTGAAAATTCGCA 59.938 40.000 0.00 0.00 0.00 5.10
90 91 6.170675 AGTAGATTGTCTGAAAATTCGCAC 57.829 37.500 0.00 0.00 0.00 5.34
91 92 5.934625 AGTAGATTGTCTGAAAATTCGCACT 59.065 36.000 0.00 0.00 0.00 4.40
92 93 7.097192 AGTAGATTGTCTGAAAATTCGCACTA 58.903 34.615 0.00 0.00 0.00 2.74
93 94 6.414408 AGATTGTCTGAAAATTCGCACTAG 57.586 37.500 0.00 0.00 0.00 2.57
94 95 5.934625 AGATTGTCTGAAAATTCGCACTAGT 59.065 36.000 0.00 0.00 0.00 2.57
95 96 7.097192 AGATTGTCTGAAAATTCGCACTAGTA 58.903 34.615 0.00 0.00 0.00 1.82
96 97 6.462073 TTGTCTGAAAATTCGCACTAGTAC 57.538 37.500 0.00 0.00 0.00 2.73
97 98 5.779922 TGTCTGAAAATTCGCACTAGTACT 58.220 37.500 0.00 0.00 0.00 2.73
98 99 6.220930 TGTCTGAAAATTCGCACTAGTACTT 58.779 36.000 0.00 0.00 0.00 2.24
99 100 6.145534 TGTCTGAAAATTCGCACTAGTACTTG 59.854 38.462 0.00 0.59 0.00 3.16
100 101 5.120208 TCTGAAAATTCGCACTAGTACTTGC 59.880 40.000 9.15 9.15 35.26 4.01
101 102 4.153475 TGAAAATTCGCACTAGTACTTGCC 59.847 41.667 12.78 0.75 35.14 4.52
102 103 3.611766 AATTCGCACTAGTACTTGCCT 57.388 42.857 12.78 0.00 35.14 4.75
103 104 2.649331 TTCGCACTAGTACTTGCCTC 57.351 50.000 12.78 0.00 35.14 4.70
104 105 0.815734 TCGCACTAGTACTTGCCTCC 59.184 55.000 12.78 0.00 35.14 4.30
105 106 0.818296 CGCACTAGTACTTGCCTCCT 59.182 55.000 12.78 0.00 35.14 3.69
106 107 1.202313 CGCACTAGTACTTGCCTCCTC 60.202 57.143 12.78 0.00 35.14 3.71
107 108 2.104170 GCACTAGTACTTGCCTCCTCT 58.896 52.381 8.14 0.00 32.21 3.69
108 109 2.159170 GCACTAGTACTTGCCTCCTCTG 60.159 54.545 8.14 0.00 32.21 3.35
109 110 3.093057 CACTAGTACTTGCCTCCTCTGT 58.907 50.000 0.00 0.00 0.00 3.41
110 111 3.511934 CACTAGTACTTGCCTCCTCTGTT 59.488 47.826 0.00 0.00 0.00 3.16
111 112 4.021016 CACTAGTACTTGCCTCCTCTGTTT 60.021 45.833 0.00 0.00 0.00 2.83
112 113 3.686916 AGTACTTGCCTCCTCTGTTTC 57.313 47.619 0.00 0.00 0.00 2.78
113 114 3.243724 AGTACTTGCCTCCTCTGTTTCT 58.756 45.455 0.00 0.00 0.00 2.52
114 115 2.557920 ACTTGCCTCCTCTGTTTCTG 57.442 50.000 0.00 0.00 0.00 3.02
115 116 1.771255 ACTTGCCTCCTCTGTTTCTGT 59.229 47.619 0.00 0.00 0.00 3.41
116 117 2.149578 CTTGCCTCCTCTGTTTCTGTG 58.850 52.381 0.00 0.00 0.00 3.66
117 118 1.131638 TGCCTCCTCTGTTTCTGTGT 58.868 50.000 0.00 0.00 0.00 3.72
118 119 2.325484 TGCCTCCTCTGTTTCTGTGTA 58.675 47.619 0.00 0.00 0.00 2.90
119 120 2.906389 TGCCTCCTCTGTTTCTGTGTAT 59.094 45.455 0.00 0.00 0.00 2.29
120 121 3.265791 GCCTCCTCTGTTTCTGTGTATG 58.734 50.000 0.00 0.00 0.00 2.39
121 122 3.265791 CCTCCTCTGTTTCTGTGTATGC 58.734 50.000 0.00 0.00 0.00 3.14
125 126 3.935203 CCTCTGTTTCTGTGTATGCGATT 59.065 43.478 0.00 0.00 0.00 3.34
130 131 5.483811 TGTTTCTGTGTATGCGATTTCCTA 58.516 37.500 0.00 0.00 0.00 2.94
140 141 2.268298 GCGATTTCCTAGCTGAAACGA 58.732 47.619 17.41 0.00 37.08 3.85
148 149 2.417719 CTAGCTGAAACGAGGCTTTGT 58.582 47.619 0.00 0.00 37.50 2.83
201 212 2.021262 CCATAGAGGAGATGGGCTGA 57.979 55.000 0.00 0.00 40.29 4.26
487 515 4.754667 GGTCCTGTTCGGCGGTCC 62.755 72.222 7.21 0.00 0.00 4.46
649 690 2.905736 ACATTCCCCAATTTTCCCAGTG 59.094 45.455 0.00 0.00 0.00 3.66
666 707 4.003648 CCAGTGTCTGATTCAAACCCTAC 58.996 47.826 0.00 0.00 32.44 3.18
687 728 7.134815 CCTACATGTTGATCGATTCATTTTCC 58.865 38.462 2.30 0.00 33.34 3.13
695 737 3.334691 TCGATTCATTTTCCGCTGTTCT 58.665 40.909 0.00 0.00 0.00 3.01
710 752 5.050091 CCGCTGTTCTGTTATGATTCATACC 60.050 44.000 5.86 0.13 0.00 2.73
711 753 5.332581 CGCTGTTCTGTTATGATTCATACCG 60.333 44.000 5.86 0.00 0.00 4.02
716 763 7.491372 TGTTCTGTTATGATTCATACCGAAGAC 59.509 37.037 5.86 2.12 36.95 3.01
720 767 7.203218 TGTTATGATTCATACCGAAGACTGAG 58.797 38.462 5.86 0.00 36.95 3.35
723 770 4.339530 TGATTCATACCGAAGACTGAGAGG 59.660 45.833 0.00 0.00 36.95 3.69
729 776 3.018149 ACCGAAGACTGAGAGGATGTAC 58.982 50.000 0.00 0.00 0.00 2.90
734 815 5.354513 CGAAGACTGAGAGGATGTACTGTAA 59.645 44.000 0.00 0.00 0.00 2.41
771 854 9.877178 ATACTAGAATTGTTGAAGAACTGGTAG 57.123 33.333 0.00 0.00 32.79 3.18
775 858 7.690256 AGAATTGTTGAAGAACTGGTAGGTAT 58.310 34.615 0.00 0.00 32.79 2.73
776 859 7.607991 AGAATTGTTGAAGAACTGGTAGGTATG 59.392 37.037 0.00 0.00 32.79 2.39
777 860 5.818678 TGTTGAAGAACTGGTAGGTATGT 57.181 39.130 0.00 0.00 32.79 2.29
778 861 6.921486 TGTTGAAGAACTGGTAGGTATGTA 57.079 37.500 0.00 0.00 32.79 2.29
779 862 6.694447 TGTTGAAGAACTGGTAGGTATGTAC 58.306 40.000 0.00 0.00 32.79 2.90
780 863 6.495872 TGTTGAAGAACTGGTAGGTATGTACT 59.504 38.462 0.00 0.00 32.79 2.73
781 864 7.670979 TGTTGAAGAACTGGTAGGTATGTACTA 59.329 37.037 0.00 0.00 32.79 1.82
855 939 4.917415 GTGTGTTTGCAAGACCATATTGAC 59.083 41.667 0.00 0.00 0.00 3.18
866 950 8.531982 GCAAGACCATATTGACCTATATCTACA 58.468 37.037 0.00 0.00 0.00 2.74
915 1090 6.855403 CGTTCACATGTCATATTTGTTGTCAA 59.145 34.615 0.00 0.00 0.00 3.18
920 1095 9.800299 CACATGTCATATTTGTTGTCAATTTTG 57.200 29.630 0.00 0.00 33.32 2.44
952 1133 6.268158 TGGACCACCCTTTTTAAAATTCCTAC 59.732 38.462 0.55 0.00 35.38 3.18
953 1134 6.495872 GGACCACCCTTTTTAAAATTCCTACT 59.504 38.462 0.55 0.00 0.00 2.57
954 1135 7.015877 GGACCACCCTTTTTAAAATTCCTACTT 59.984 37.037 0.55 0.00 0.00 2.24
955 1136 9.081204 GACCACCCTTTTTAAAATTCCTACTTA 57.919 33.333 0.55 0.00 0.00 2.24
980 1161 2.806237 CTACCGGAGAGCGGAACC 59.194 66.667 9.46 0.00 0.00 3.62
986 1169 4.070552 GAGAGCGGAACCGTGCCT 62.071 66.667 14.63 9.01 42.09 4.75
1077 1277 2.094100 TCCAGATGTCCCAGATCCTC 57.906 55.000 0.00 0.00 0.00 3.71
1353 1556 1.421485 CGCTTGTCACTTGATCGCC 59.579 57.895 0.00 0.00 0.00 5.54
1359 1564 2.683968 TGTCACTTGATCGCCTTGTAC 58.316 47.619 0.00 0.00 0.00 2.90
1368 1573 2.943653 GCCTTGTACGTGTGCACC 59.056 61.111 15.69 4.74 0.00 5.01
1381 1586 0.464554 GTGCACCTAGGCCTTCCATC 60.465 60.000 12.58 0.00 33.74 3.51
1424 1661 8.950210 GTTCCTGATTTGTATTCTCAAGATTGA 58.050 33.333 0.00 0.00 35.57 2.57
1453 1691 1.270893 GGGGGTCTGTGTCAAACTCTC 60.271 57.143 0.00 0.00 0.00 3.20
1486 1724 9.071276 TCTAGCAAATGATTTTCTCTTCTGTTT 57.929 29.630 0.00 0.00 0.00 2.83
1487 1725 9.688592 CTAGCAAATGATTTTCTCTTCTGTTTT 57.311 29.630 0.00 0.00 0.00 2.43
1506 1744 2.099141 TCTGAAATCGCTTCCTGGTG 57.901 50.000 0.00 0.00 32.53 4.17
1514 1752 0.462047 CGCTTCCTGGTGTGTATCCC 60.462 60.000 0.00 0.00 0.00 3.85
1536 1774 6.786461 TCCCCAATATTGATAATGCAATGGAA 59.214 34.615 17.23 0.00 38.80 3.53
1581 1823 5.186215 ACATTCTTGCACATGGATTCATTCA 59.814 36.000 0.00 0.00 0.00 2.57
1593 1835 9.375974 ACATGGATTCATTCATTGGAATTATCT 57.624 29.630 0.00 0.00 41.78 1.98
1735 1981 9.760660 GAGTAGAATTGTTGTTATGTCAATGTC 57.239 33.333 0.00 0.00 33.04 3.06
1746 1992 3.855255 TGTCAATGTCCCTTGTTCTGA 57.145 42.857 0.00 0.00 0.00 3.27
1829 2075 5.355071 TGTTTCAATCGCTGCTAGATTCATT 59.645 36.000 0.00 0.00 36.30 2.57
2034 2482 4.987408 TGGTTGCATCATTATTGTGAGG 57.013 40.909 0.00 0.00 33.32 3.86
2065 2513 5.959618 ACTTTACAAAGTCAACCTATGCC 57.040 39.130 1.47 0.00 45.65 4.40
2066 2514 5.631119 ACTTTACAAAGTCAACCTATGCCT 58.369 37.500 1.47 0.00 45.65 4.75
2137 2587 5.930569 AGTTCGACATTTTAACTACAGGGAC 59.069 40.000 0.00 0.00 31.84 4.46
2163 2613 2.483106 CTCATGAGCAGAGTGGTTGTTG 59.517 50.000 10.38 0.00 0.00 3.33
2200 2650 5.626142 TGTTCTAGACTAGAGGCATCCTAG 58.374 45.833 11.94 0.00 39.49 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.206831 GCCGCCGTTGAGTTTTCTC 59.793 57.895 0.00 0.00 46.33 2.87
7 8 1.507141 CTGCCGCCGTTGAGTTTTCT 61.507 55.000 0.00 0.00 0.00 2.52
8 9 1.082104 CTGCCGCCGTTGAGTTTTC 60.082 57.895 0.00 0.00 0.00 2.29
9 10 3.030652 CTGCCGCCGTTGAGTTTT 58.969 55.556 0.00 0.00 0.00 2.43
10 11 3.660111 GCTGCCGCCGTTGAGTTT 61.660 61.111 0.00 0.00 0.00 2.66
27 28 3.636313 TTTCAGTACTCCGGCGGCG 62.636 63.158 26.12 26.12 0.00 6.46
28 29 1.375013 TTTTCAGTACTCCGGCGGC 60.375 57.895 23.83 7.19 0.00 6.53
29 30 1.017701 GGTTTTCAGTACTCCGGCGG 61.018 60.000 22.51 22.51 0.00 6.13
30 31 1.017701 GGGTTTTCAGTACTCCGGCG 61.018 60.000 0.00 0.00 0.00 6.46
31 32 0.323957 AGGGTTTTCAGTACTCCGGC 59.676 55.000 0.00 0.00 0.00 6.13
32 33 2.830321 ACTAGGGTTTTCAGTACTCCGG 59.170 50.000 0.00 0.00 0.00 5.14
33 34 3.427233 CGACTAGGGTTTTCAGTACTCCG 60.427 52.174 0.00 0.00 0.00 4.63
34 35 3.675502 GCGACTAGGGTTTTCAGTACTCC 60.676 52.174 0.00 0.00 0.00 3.85
35 36 3.509740 GCGACTAGGGTTTTCAGTACTC 58.490 50.000 0.00 0.00 0.00 2.59
36 37 2.233186 GGCGACTAGGGTTTTCAGTACT 59.767 50.000 0.00 0.00 0.00 2.73
37 38 2.028748 TGGCGACTAGGGTTTTCAGTAC 60.029 50.000 0.00 0.00 0.00 2.73
38 39 2.250031 TGGCGACTAGGGTTTTCAGTA 58.750 47.619 0.00 0.00 0.00 2.74
39 40 1.053424 TGGCGACTAGGGTTTTCAGT 58.947 50.000 0.00 0.00 0.00 3.41
40 41 2.009774 CATGGCGACTAGGGTTTTCAG 58.990 52.381 0.00 0.00 0.00 3.02
41 42 1.339631 CCATGGCGACTAGGGTTTTCA 60.340 52.381 0.00 0.00 0.00 2.69
42 43 1.379527 CCATGGCGACTAGGGTTTTC 58.620 55.000 0.00 0.00 0.00 2.29
43 44 0.679960 GCCATGGCGACTAGGGTTTT 60.680 55.000 23.48 0.00 0.00 2.43
44 45 1.077716 GCCATGGCGACTAGGGTTT 60.078 57.895 23.48 0.00 0.00 3.27
45 46 2.590092 GCCATGGCGACTAGGGTT 59.410 61.111 23.48 0.00 0.00 4.11
55 56 0.249489 AATCTACTCGTCGCCATGGC 60.249 55.000 27.67 27.67 37.85 4.40
56 57 1.202417 ACAATCTACTCGTCGCCATGG 60.202 52.381 7.63 7.63 0.00 3.66
57 58 2.120232 GACAATCTACTCGTCGCCATG 58.880 52.381 0.00 0.00 0.00 3.66
58 59 2.025155 AGACAATCTACTCGTCGCCAT 58.975 47.619 0.00 0.00 34.80 4.40
59 60 1.132453 CAGACAATCTACTCGTCGCCA 59.868 52.381 0.00 0.00 34.80 5.69
60 61 1.400846 TCAGACAATCTACTCGTCGCC 59.599 52.381 0.00 0.00 34.80 5.54
61 62 2.826979 TCAGACAATCTACTCGTCGC 57.173 50.000 0.00 0.00 34.80 5.19
62 63 6.504954 CGAATTTTCAGACAATCTACTCGTCG 60.505 42.308 0.00 0.00 34.80 5.12
63 64 6.687655 CGAATTTTCAGACAATCTACTCGTC 58.312 40.000 0.00 0.00 0.00 4.20
64 65 5.062308 GCGAATTTTCAGACAATCTACTCGT 59.938 40.000 0.00 0.00 0.00 4.18
65 66 5.062183 TGCGAATTTTCAGACAATCTACTCG 59.938 40.000 0.00 0.00 0.00 4.18
66 67 6.091441 AGTGCGAATTTTCAGACAATCTACTC 59.909 38.462 0.00 0.00 0.00 2.59
67 68 5.934625 AGTGCGAATTTTCAGACAATCTACT 59.065 36.000 0.00 0.00 0.00 2.57
68 69 6.170675 AGTGCGAATTTTCAGACAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
69 70 7.097192 ACTAGTGCGAATTTTCAGACAATCTA 58.903 34.615 0.00 0.00 0.00 1.98
70 71 5.934625 ACTAGTGCGAATTTTCAGACAATCT 59.065 36.000 0.00 0.00 0.00 2.40
71 72 6.170675 ACTAGTGCGAATTTTCAGACAATC 57.829 37.500 0.00 0.00 0.00 2.67
72 73 6.874134 AGTACTAGTGCGAATTTTCAGACAAT 59.126 34.615 5.39 0.00 0.00 2.71
73 74 6.220930 AGTACTAGTGCGAATTTTCAGACAA 58.779 36.000 5.39 0.00 0.00 3.18
74 75 5.779922 AGTACTAGTGCGAATTTTCAGACA 58.220 37.500 5.39 0.00 0.00 3.41
75 76 6.526222 CAAGTACTAGTGCGAATTTTCAGAC 58.474 40.000 5.39 0.00 0.00 3.51
76 77 5.120208 GCAAGTACTAGTGCGAATTTTCAGA 59.880 40.000 5.39 0.00 0.00 3.27
77 78 5.316770 GCAAGTACTAGTGCGAATTTTCAG 58.683 41.667 5.39 0.00 0.00 3.02
78 79 4.153475 GGCAAGTACTAGTGCGAATTTTCA 59.847 41.667 12.28 0.00 41.85 2.69
79 80 4.392138 AGGCAAGTACTAGTGCGAATTTTC 59.608 41.667 12.28 0.00 41.85 2.29
80 81 4.324267 AGGCAAGTACTAGTGCGAATTTT 58.676 39.130 12.28 0.00 41.85 1.82
81 82 3.933332 GAGGCAAGTACTAGTGCGAATTT 59.067 43.478 12.28 0.00 41.85 1.82
82 83 3.522553 GAGGCAAGTACTAGTGCGAATT 58.477 45.455 12.28 0.00 41.85 2.17
83 84 2.159085 GGAGGCAAGTACTAGTGCGAAT 60.159 50.000 12.28 2.71 41.85 3.34
84 85 1.203994 GGAGGCAAGTACTAGTGCGAA 59.796 52.381 12.28 0.00 41.85 4.70
85 86 0.815734 GGAGGCAAGTACTAGTGCGA 59.184 55.000 12.28 0.00 41.85 5.10
86 87 0.818296 AGGAGGCAAGTACTAGTGCG 59.182 55.000 12.28 0.00 41.85 5.34
87 88 2.104170 AGAGGAGGCAAGTACTAGTGC 58.896 52.381 10.53 10.53 40.14 4.40
88 89 3.093057 ACAGAGGAGGCAAGTACTAGTG 58.907 50.000 5.39 0.00 0.00 2.74
89 90 3.459710 ACAGAGGAGGCAAGTACTAGT 57.540 47.619 0.00 0.00 0.00 2.57
90 91 4.464597 AGAAACAGAGGAGGCAAGTACTAG 59.535 45.833 0.00 0.00 0.00 2.57
91 92 4.220821 CAGAAACAGAGGAGGCAAGTACTA 59.779 45.833 0.00 0.00 0.00 1.82
92 93 3.007398 CAGAAACAGAGGAGGCAAGTACT 59.993 47.826 0.00 0.00 0.00 2.73
93 94 3.244249 ACAGAAACAGAGGAGGCAAGTAC 60.244 47.826 0.00 0.00 0.00 2.73
94 95 2.972713 ACAGAAACAGAGGAGGCAAGTA 59.027 45.455 0.00 0.00 0.00 2.24
95 96 1.771255 ACAGAAACAGAGGAGGCAAGT 59.229 47.619 0.00 0.00 0.00 3.16
96 97 2.149578 CACAGAAACAGAGGAGGCAAG 58.850 52.381 0.00 0.00 0.00 4.01
97 98 1.490490 ACACAGAAACAGAGGAGGCAA 59.510 47.619 0.00 0.00 0.00 4.52
98 99 1.131638 ACACAGAAACAGAGGAGGCA 58.868 50.000 0.00 0.00 0.00 4.75
99 100 3.265791 CATACACAGAAACAGAGGAGGC 58.734 50.000 0.00 0.00 0.00 4.70
100 101 3.265791 GCATACACAGAAACAGAGGAGG 58.734 50.000 0.00 0.00 0.00 4.30
101 102 2.926200 CGCATACACAGAAACAGAGGAG 59.074 50.000 0.00 0.00 0.00 3.69
102 103 2.560981 TCGCATACACAGAAACAGAGGA 59.439 45.455 0.00 0.00 0.00 3.71
103 104 2.959516 TCGCATACACAGAAACAGAGG 58.040 47.619 0.00 0.00 0.00 3.69
104 105 5.446473 GGAAATCGCATACACAGAAACAGAG 60.446 44.000 0.00 0.00 0.00 3.35
105 106 4.391830 GGAAATCGCATACACAGAAACAGA 59.608 41.667 0.00 0.00 0.00 3.41
106 107 4.393062 AGGAAATCGCATACACAGAAACAG 59.607 41.667 0.00 0.00 0.00 3.16
107 108 4.323417 AGGAAATCGCATACACAGAAACA 58.677 39.130 0.00 0.00 0.00 2.83
108 109 4.946784 AGGAAATCGCATACACAGAAAC 57.053 40.909 0.00 0.00 0.00 2.78
109 110 4.570772 GCTAGGAAATCGCATACACAGAAA 59.429 41.667 0.00 0.00 0.00 2.52
110 111 4.119862 GCTAGGAAATCGCATACACAGAA 58.880 43.478 0.00 0.00 0.00 3.02
111 112 3.384789 AGCTAGGAAATCGCATACACAGA 59.615 43.478 0.00 0.00 0.00 3.41
112 113 3.492383 CAGCTAGGAAATCGCATACACAG 59.508 47.826 0.00 0.00 0.00 3.66
113 114 3.132111 TCAGCTAGGAAATCGCATACACA 59.868 43.478 0.00 0.00 0.00 3.72
114 115 3.717707 TCAGCTAGGAAATCGCATACAC 58.282 45.455 0.00 0.00 0.00 2.90
115 116 4.400529 TTCAGCTAGGAAATCGCATACA 57.599 40.909 0.00 0.00 0.00 2.29
116 117 4.318121 CGTTTCAGCTAGGAAATCGCATAC 60.318 45.833 2.86 0.00 38.86 2.39
117 118 3.802139 CGTTTCAGCTAGGAAATCGCATA 59.198 43.478 2.86 0.00 38.86 3.14
118 119 2.609459 CGTTTCAGCTAGGAAATCGCAT 59.391 45.455 2.86 0.00 38.86 4.73
119 120 1.999735 CGTTTCAGCTAGGAAATCGCA 59.000 47.619 2.86 0.00 38.86 5.10
120 121 2.268298 TCGTTTCAGCTAGGAAATCGC 58.732 47.619 2.86 0.00 38.86 4.58
121 122 2.860735 CCTCGTTTCAGCTAGGAAATCG 59.139 50.000 2.86 8.20 38.86 3.34
125 126 1.267121 AGCCTCGTTTCAGCTAGGAA 58.733 50.000 1.97 0.00 34.38 3.36
130 131 1.680338 AACAAAGCCTCGTTTCAGCT 58.320 45.000 0.00 0.00 38.88 4.24
140 141 0.106015 AGCCCAGTGAAACAAAGCCT 60.106 50.000 0.00 0.00 41.43 4.58
148 149 2.237143 CCTGTAGATCAGCCCAGTGAAA 59.763 50.000 0.00 0.00 42.38 2.69
154 155 0.982852 CCACCCTGTAGATCAGCCCA 60.983 60.000 0.00 0.00 42.38 5.36
220 232 1.609783 GGGAACATAGGCAGCCTGT 59.390 57.895 25.59 15.70 34.61 4.00
583 623 2.208619 TGTTTAGTCGTGGGGCGGA 61.209 57.895 0.00 0.00 41.72 5.54
649 690 5.705441 TCAACATGTAGGGTTTGAATCAGAC 59.295 40.000 0.00 0.00 0.00 3.51
666 707 4.438797 GCGGAAAATGAATCGATCAACATG 59.561 41.667 0.00 0.00 42.54 3.21
687 728 5.332581 CGGTATGAATCATAACAGAACAGCG 60.333 44.000 17.38 7.23 34.02 5.18
695 737 7.068226 TCTCAGTCTTCGGTATGAATCATAACA 59.932 37.037 17.38 3.27 34.02 2.41
710 752 3.692101 ACAGTACATCCTCTCAGTCTTCG 59.308 47.826 0.00 0.00 0.00 3.79
711 753 6.761099 TTACAGTACATCCTCTCAGTCTTC 57.239 41.667 0.00 0.00 0.00 2.87
745 826 9.877178 CTACCAGTTCTTCAACAATTCTAGTAT 57.123 33.333 0.00 0.00 34.60 2.12
746 827 8.311836 CCTACCAGTTCTTCAACAATTCTAGTA 58.688 37.037 0.00 0.00 34.60 1.82
747 828 7.162082 CCTACCAGTTCTTCAACAATTCTAGT 58.838 38.462 0.00 0.00 34.60 2.57
748 829 7.162082 ACCTACCAGTTCTTCAACAATTCTAG 58.838 38.462 0.00 0.00 34.60 2.43
765 846 6.720288 AGCCTACATTAGTACATACCTACCAG 59.280 42.308 0.00 0.00 0.00 4.00
771 854 8.959705 AAAAGAAGCCTACATTAGTACATACC 57.040 34.615 0.00 0.00 0.00 2.73
775 858 8.044309 TGCATAAAAGAAGCCTACATTAGTACA 58.956 33.333 0.00 0.00 0.00 2.90
776 859 8.433421 TGCATAAAAGAAGCCTACATTAGTAC 57.567 34.615 0.00 0.00 0.00 2.73
777 860 9.456147 TTTGCATAAAAGAAGCCTACATTAGTA 57.544 29.630 0.00 0.00 0.00 1.82
778 861 7.938140 TTGCATAAAAGAAGCCTACATTAGT 57.062 32.000 0.00 0.00 0.00 2.24
779 862 9.076596 GTTTTGCATAAAAGAAGCCTACATTAG 57.923 33.333 0.00 0.00 36.51 1.73
780 863 8.802267 AGTTTTGCATAAAAGAAGCCTACATTA 58.198 29.630 0.00 0.00 36.51 1.90
781 864 7.599998 CAGTTTTGCATAAAAGAAGCCTACATT 59.400 33.333 0.00 0.00 36.51 2.71
831 915 4.826733 TCAATATGGTCTTGCAAACACACT 59.173 37.500 0.00 0.00 0.00 3.55
866 950 9.609346 ACGTTCTAATAAATTTACCAGTAGCAT 57.391 29.630 0.00 0.00 0.00 3.79
952 1133 2.817258 CTCTCCGGTAGCTGGATCTAAG 59.183 54.545 0.00 0.00 38.36 2.18
953 1134 2.865079 CTCTCCGGTAGCTGGATCTAA 58.135 52.381 0.00 0.00 38.36 2.10
954 1135 1.545875 GCTCTCCGGTAGCTGGATCTA 60.546 57.143 19.95 0.00 38.36 1.98
955 1136 0.825840 GCTCTCCGGTAGCTGGATCT 60.826 60.000 19.95 0.00 38.36 2.75
980 1161 3.136123 CCATCTTGGGCAGGCACG 61.136 66.667 0.00 0.00 32.67 5.34
989 1187 1.849039 ACTCCTCCATTCCCATCTTGG 59.151 52.381 0.00 0.00 37.25 3.61
991 1189 1.765314 CGACTCCTCCATTCCCATCTT 59.235 52.381 0.00 0.00 0.00 2.40
1307 1510 3.756117 TCTGGGAGGAAAAAGAAGAAGC 58.244 45.455 0.00 0.00 0.00 3.86
1353 1556 1.710013 CCTAGGTGCACACGTACAAG 58.290 55.000 20.43 4.45 0.00 3.16
1359 1564 1.741770 GAAGGCCTAGGTGCACACG 60.742 63.158 20.43 5.73 0.00 4.49
1368 1573 2.289945 GCATACAGGATGGAAGGCCTAG 60.290 54.545 5.16 0.00 43.62 3.02
1381 1586 2.749621 GGAACCAGTTTCAGCATACAGG 59.250 50.000 0.00 0.00 35.70 4.00
1453 1691 7.333921 AGAGAAAATCATTTGCTAGAGTGTGAG 59.666 37.037 0.00 0.00 0.00 3.51
1486 1724 2.224523 ACACCAGGAAGCGATTTCAGAA 60.225 45.455 0.00 0.00 37.54 3.02
1487 1725 1.347707 ACACCAGGAAGCGATTTCAGA 59.652 47.619 0.00 0.00 37.54 3.27
1506 1744 7.701539 TGCATTATCAATATTGGGGATACAC 57.298 36.000 15.36 0.53 44.44 2.90
1514 1752 9.366216 CAGATTCCATTGCATTATCAATATTGG 57.634 33.333 15.36 0.21 35.12 3.16
1536 1774 8.585471 AATGTGGATAACAGAATTTGACAGAT 57.415 30.769 0.00 0.00 43.64 2.90
1593 1835 9.996554 ATCTTGAATTGGTGTCATAACGATATA 57.003 29.630 0.00 0.00 0.00 0.86
1613 1857 4.996758 TCAAATTCGTCTCTGCAATCTTGA 59.003 37.500 0.00 0.00 0.00 3.02
1735 1981 1.467920 GGATGCCTTCAGAACAAGGG 58.532 55.000 1.51 0.00 43.08 3.95
1746 1992 3.718956 AGAGCTACTAATTGGGATGCCTT 59.281 43.478 4.35 0.00 0.00 4.35
1919 2166 4.997395 TGTTCAAGGACAATGAGCTAACTC 59.003 41.667 0.00 0.00 43.76 3.01
1949 2366 8.421002 ACTGTGTAAAGTATTTCCATTTGCTTT 58.579 29.630 0.00 0.00 40.09 3.51
2057 2505 2.089925 ACTATTGGGGAGAGGCATAGGT 60.090 50.000 0.00 0.00 0.00 3.08
2065 2513 2.289072 CCGCATACACTATTGGGGAGAG 60.289 54.545 0.08 0.00 36.62 3.20
2066 2514 1.691976 CCGCATACACTATTGGGGAGA 59.308 52.381 0.08 0.00 36.62 3.71
2163 2613 7.484035 AGTCTAGAACAAAGAACATTGACAC 57.516 36.000 0.00 0.00 34.38 3.67
2200 2650 6.651225 ACCAATGACAAAGAAGAGCTACTAAC 59.349 38.462 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.