Multiple sequence alignment - TraesCS2A01G316200

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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 TraesCS2A01G316200 chr2A 100.000 2339 0 0 1 2339 541848494 541846156 0.000000e+00 4320
1 TraesCS2A01G316200 chr2A 99.451 182 1 0 1 182 612465684 612465503 4.820000e-87 331
2 TraesCS2A01G316200 chr2A 96.392 194 6 1 1 193 187149075 187148882 3.750000e-83 318
3 TraesCS2A01G316200 chr3A 96.213 1241 47 0 178 1418 169838646 169839886 0.000000e+00 2032
4 TraesCS2A01G316200 chr3A 98.913 184 2 0 1 184 345803414 345803231 1.730000e-86 329
5 TraesCS2A01G316200 chr3A 98.913 184 2 0 1 184 557888997 557888814 1.730000e-86 329
6 TraesCS2A01G316200 chr5A 96.067 1246 47 2 178 1423 85661381 85660138 0.000000e+00 2028
7 TraesCS2A01G316200 chr5A 79.575 1224 201 22 182 1391 581576126 581574938 0.000000e+00 830
8 TraesCS2A01G316200 chr5A 98.907 183 2 0 1 183 247057041 247057223 6.230000e-86 327
9 TraesCS2A01G316200 chr5A 98.907 183 2 0 1 183 589887190 589887372 6.230000e-86 327
10 TraesCS2A01G316200 chr1A 95.476 1260 50 3 178 1435 451737070 451738324 0.000000e+00 2004
11 TraesCS2A01G316200 chr1A 96.256 1015 35 2 178 1192 327012054 327013065 0.000000e+00 1661
12 TraesCS2A01G316200 chr1A 79.681 1255 208 29 184 1431 559406899 559405685 0.000000e+00 861
13 TraesCS2A01G316200 chr1A 98.684 304 3 1 1115 1418 327013065 327013367 2.640000e-149 538
14 TraesCS2A01G316200 chr2B 89.331 956 40 16 1414 2339 477611177 477610254 0.000000e+00 1144
15 TraesCS2A01G316200 chr2D 93.741 687 18 5 1667 2339 403508319 403507644 0.000000e+00 1007
16 TraesCS2A01G316200 chr2D 88.417 259 14 8 1414 1664 403508600 403508350 4.890000e-77 298
17 TraesCS2A01G316200 chr7D 79.841 1255 207 26 184 1422 612341747 612342971 0.000000e+00 874
18 TraesCS2A01G316200 chr7D 80.905 199 34 4 534 731 385818037 385817842 1.120000e-33 154
19 TraesCS2A01G316200 chr6B 79.542 1178 205 22 184 1348 479872842 479871688 0.000000e+00 808
20 TraesCS2A01G316200 chr6B 79.960 499 91 4 752 1242 231369997 231370494 2.210000e-95 359
21 TraesCS2A01G316200 chr7A 97.872 188 4 0 1 188 522202647 522202460 2.240000e-85 326
22 TraesCS2A01G316200 chr6A 98.901 182 2 0 1 182 230624291 230624472 2.240000e-85 326
23 TraesCS2A01G316200 chr6A 98.901 182 2 0 1 182 306142445 306142626 2.240000e-85 326


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 TraesCS2A01G316200 chr2A 541846156 541848494 2338 True 4320.0 4320 100.000 1 2339 1 chr2A.!!$R2 2338
1 TraesCS2A01G316200 chr3A 169838646 169839886 1240 False 2032.0 2032 96.213 178 1418 1 chr3A.!!$F1 1240
2 TraesCS2A01G316200 chr5A 85660138 85661381 1243 True 2028.0 2028 96.067 178 1423 1 chr5A.!!$R1 1245
3 TraesCS2A01G316200 chr5A 581574938 581576126 1188 True 830.0 830 79.575 182 1391 1 chr5A.!!$R2 1209
4 TraesCS2A01G316200 chr1A 451737070 451738324 1254 False 2004.0 2004 95.476 178 1435 1 chr1A.!!$F1 1257
5 TraesCS2A01G316200 chr1A 327012054 327013367 1313 False 1099.5 1661 97.470 178 1418 2 chr1A.!!$F2 1240
6 TraesCS2A01G316200 chr1A 559405685 559406899 1214 True 861.0 861 79.681 184 1431 1 chr1A.!!$R1 1247
7 TraesCS2A01G316200 chr2B 477610254 477611177 923 True 1144.0 1144 89.331 1414 2339 1 chr2B.!!$R1 925
8 TraesCS2A01G316200 chr2D 403507644 403508600 956 True 652.5 1007 91.079 1414 2339 2 chr2D.!!$R1 925
9 TraesCS2A01G316200 chr7D 612341747 612342971 1224 False 874.0 874 79.841 184 1422 1 chr7D.!!$F1 1238
10 TraesCS2A01G316200 chr6B 479871688 479872842 1154 True 808.0 808 79.542 184 1348 1 chr6B.!!$R1 1164

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
85 86 0.605319 TCCGTGGGTCATTGAGTTGC 60.605 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1899 1.065928 GACTCGTAGGATGGGTGCG 59.934 63.158 0.0 0.0 0.0 5.34 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
64 65 7.979444 TGAAAATAACGAAATCTCCAACTCT 57.021 32.000 0.00 0.00 0.00 3.24
65 66 8.029642 TGAAAATAACGAAATCTCCAACTCTC 57.970 34.615 0.00 0.00 0.00 3.20
66 67 7.878127 TGAAAATAACGAAATCTCCAACTCTCT 59.122 33.333 0.00 0.00 0.00 3.10
67 68 7.835634 AAATAACGAAATCTCCAACTCTCTC 57.164 36.000 0.00 0.00 0.00 3.20
68 69 3.878160 ACGAAATCTCCAACTCTCTCC 57.122 47.619 0.00 0.00 0.00 3.71
69 70 2.164624 ACGAAATCTCCAACTCTCTCCG 59.835 50.000 0.00 0.00 0.00 4.63
70 71 2.164624 CGAAATCTCCAACTCTCTCCGT 59.835 50.000 0.00 0.00 0.00 4.69
71 72 3.516615 GAAATCTCCAACTCTCTCCGTG 58.483 50.000 0.00 0.00 0.00 4.94
72 73 1.479709 ATCTCCAACTCTCTCCGTGG 58.520 55.000 0.00 0.00 0.00 4.94
73 74 0.612174 TCTCCAACTCTCTCCGTGGG 60.612 60.000 0.00 0.00 0.00 4.61
74 75 0.900647 CTCCAACTCTCTCCGTGGGT 60.901 60.000 0.00 0.00 0.00 4.51
75 76 0.898789 TCCAACTCTCTCCGTGGGTC 60.899 60.000 0.00 0.00 0.00 4.46
76 77 1.185618 CCAACTCTCTCCGTGGGTCA 61.186 60.000 0.00 0.00 0.00 4.02
77 78 0.898320 CAACTCTCTCCGTGGGTCAT 59.102 55.000 0.00 0.00 0.00 3.06
78 79 1.276421 CAACTCTCTCCGTGGGTCATT 59.724 52.381 0.00 0.00 0.00 2.57
79 80 0.898320 ACTCTCTCCGTGGGTCATTG 59.102 55.000 0.00 0.00 0.00 2.82
80 81 1.186200 CTCTCTCCGTGGGTCATTGA 58.814 55.000 0.00 0.00 0.00 2.57
81 82 1.135915 CTCTCTCCGTGGGTCATTGAG 59.864 57.143 0.00 0.00 0.00 3.02
82 83 0.898320 CTCTCCGTGGGTCATTGAGT 59.102 55.000 0.00 0.00 0.00 3.41
83 84 1.276421 CTCTCCGTGGGTCATTGAGTT 59.724 52.381 0.00 0.00 0.00 3.01
84 85 1.001974 TCTCCGTGGGTCATTGAGTTG 59.998 52.381 0.00 0.00 0.00 3.16
85 86 0.605319 TCCGTGGGTCATTGAGTTGC 60.605 55.000 0.00 0.00 0.00 4.17
86 87 1.497278 CGTGGGTCATTGAGTTGCG 59.503 57.895 0.00 0.00 0.00 4.85
87 88 1.227999 CGTGGGTCATTGAGTTGCGT 61.228 55.000 0.00 0.00 0.00 5.24
88 89 1.803334 GTGGGTCATTGAGTTGCGTA 58.197 50.000 0.00 0.00 0.00 4.42
89 90 1.732259 GTGGGTCATTGAGTTGCGTAG 59.268 52.381 0.00 0.00 0.00 3.51
90 91 1.621317 TGGGTCATTGAGTTGCGTAGA 59.379 47.619 0.00 0.00 0.00 2.59
91 92 2.037902 TGGGTCATTGAGTTGCGTAGAA 59.962 45.455 0.00 0.00 0.00 2.10
92 93 3.270877 GGGTCATTGAGTTGCGTAGAAT 58.729 45.455 0.00 0.00 0.00 2.40
93 94 3.689649 GGGTCATTGAGTTGCGTAGAATT 59.310 43.478 0.00 0.00 0.00 2.17
94 95 4.156008 GGGTCATTGAGTTGCGTAGAATTT 59.844 41.667 0.00 0.00 0.00 1.82
95 96 5.324697 GGTCATTGAGTTGCGTAGAATTTC 58.675 41.667 0.00 0.00 0.00 2.17
96 97 5.122396 GGTCATTGAGTTGCGTAGAATTTCT 59.878 40.000 4.03 4.03 0.00 2.52
97 98 6.312918 GGTCATTGAGTTGCGTAGAATTTCTA 59.687 38.462 1.90 1.90 0.00 2.10
98 99 7.394872 GTCATTGAGTTGCGTAGAATTTCTAG 58.605 38.462 6.37 3.18 28.01 2.43
99 100 6.535150 TCATTGAGTTGCGTAGAATTTCTAGG 59.465 38.462 17.73 17.73 37.76 3.02
100 101 5.654603 TGAGTTGCGTAGAATTTCTAGGA 57.345 39.130 23.59 10.26 37.10 2.94
101 102 6.222038 TGAGTTGCGTAGAATTTCTAGGAT 57.778 37.500 23.59 10.22 37.10 3.24
102 103 6.273825 TGAGTTGCGTAGAATTTCTAGGATC 58.726 40.000 23.59 16.26 37.10 3.36
103 104 6.127451 TGAGTTGCGTAGAATTTCTAGGATCA 60.127 38.462 23.59 17.90 37.10 2.92
104 105 6.640518 AGTTGCGTAGAATTTCTAGGATCAA 58.359 36.000 23.59 17.13 37.10 2.57
105 106 6.535508 AGTTGCGTAGAATTTCTAGGATCAAC 59.464 38.462 23.59 23.86 37.68 3.18
106 107 5.357257 TGCGTAGAATTTCTAGGATCAACC 58.643 41.667 23.59 9.87 37.10 3.77
107 108 5.105106 TGCGTAGAATTTCTAGGATCAACCA 60.105 40.000 23.59 11.77 37.10 3.67
108 109 5.815740 GCGTAGAATTTCTAGGATCAACCAA 59.184 40.000 23.59 0.00 37.10 3.67
109 110 6.315393 GCGTAGAATTTCTAGGATCAACCAAA 59.685 38.462 23.59 0.00 37.10 3.28
110 111 7.148306 GCGTAGAATTTCTAGGATCAACCAAAA 60.148 37.037 23.59 0.00 37.10 2.44
111 112 8.893727 CGTAGAATTTCTAGGATCAACCAAAAT 58.106 33.333 17.32 0.00 37.10 1.82
113 114 7.550712 AGAATTTCTAGGATCAACCAAAATGC 58.449 34.615 0.00 0.00 42.04 3.56
114 115 6.855763 ATTTCTAGGATCAACCAAAATGCA 57.144 33.333 0.00 0.00 42.04 3.96
115 116 6.662865 TTTCTAGGATCAACCAAAATGCAA 57.337 33.333 0.00 0.00 42.04 4.08
116 117 6.662865 TTCTAGGATCAACCAAAATGCAAA 57.337 33.333 0.00 0.00 42.04 3.68
117 118 6.662865 TCTAGGATCAACCAAAATGCAAAA 57.337 33.333 0.00 0.00 42.04 2.44
118 119 7.243604 TCTAGGATCAACCAAAATGCAAAAT 57.756 32.000 0.00 0.00 42.04 1.82
119 120 8.359875 TCTAGGATCAACCAAAATGCAAAATA 57.640 30.769 0.00 0.00 42.04 1.40
120 121 8.811017 TCTAGGATCAACCAAAATGCAAAATAA 58.189 29.630 0.00 0.00 42.04 1.40
121 122 9.434420 CTAGGATCAACCAAAATGCAAAATAAA 57.566 29.630 0.00 0.00 42.04 1.40
122 123 8.688747 AGGATCAACCAAAATGCAAAATAAAA 57.311 26.923 0.00 0.00 42.04 1.52
123 124 9.299465 AGGATCAACCAAAATGCAAAATAAAAT 57.701 25.926 0.00 0.00 42.04 1.82
396 398 4.617067 CGACGCCTAGAGAGCATAATCAAT 60.617 45.833 0.00 0.00 0.00 2.57
412 414 2.166829 TCAATGCTTGGTTTATGCCGT 58.833 42.857 0.00 0.00 0.00 5.68
440 446 0.966875 TAGTTCTTAGCCCGCGTGGA 60.967 55.000 18.79 0.00 37.49 4.02
511 517 3.118408 TCTGCTATACGTTCCTGCCAAAT 60.118 43.478 0.00 0.00 0.00 2.32
540 546 8.561536 TTTATCCTAGTCACCCTAAATCATCA 57.438 34.615 0.00 0.00 0.00 3.07
546 552 2.158957 TCACCCTAAATCATCAGCGACC 60.159 50.000 0.00 0.00 0.00 4.79
593 599 1.173444 ACTATCGCCGCCTCGATCTT 61.173 55.000 10.49 0.00 44.97 2.40
679 685 1.354368 ACCGACCCATCAATTTGGAGT 59.646 47.619 0.00 0.00 39.25 3.85
1113 1128 3.506455 CAGAGTTGAAGAGGGTAACGAGA 59.494 47.826 0.00 0.00 37.60 4.04
1412 1507 7.906199 TTTTCTTCAAGGGAGTAAAATGGAA 57.094 32.000 0.00 0.00 0.00 3.53
1448 1543 7.652909 TCTTTTTCAAACATAAGCAGGAATGTG 59.347 33.333 0.00 0.00 36.47 3.21
1455 1550 5.195940 ACATAAGCAGGAATGTGTTGCTAT 58.804 37.500 0.00 0.00 46.72 2.97
1468 1563 2.107378 TGTTGCTATTGTCCTTGGTCCA 59.893 45.455 0.00 0.00 0.00 4.02
1574 1678 8.488651 AGACCTAAACAAATTCGTATTACAGG 57.511 34.615 0.00 0.00 0.00 4.00
1664 1768 4.797349 GCACAGGTGATACTAACGAAGTAC 59.203 45.833 3.10 0.00 45.00 2.73
1665 1769 5.392811 GCACAGGTGATACTAACGAAGTACT 60.393 44.000 3.10 0.00 45.00 2.73
1741 1873 2.158755 CCAGCCCAGGGTCTAATTACTG 60.159 54.545 7.55 2.85 0.00 2.74
1760 1892 4.010349 ACTGAATTAGAAAAAGCTCCCCG 58.990 43.478 0.00 0.00 0.00 5.73
1761 1893 2.752903 TGAATTAGAAAAAGCTCCCCGC 59.247 45.455 0.00 0.00 39.57 6.13
1762 1894 2.507407 ATTAGAAAAAGCTCCCCGCA 57.493 45.000 0.00 0.00 42.61 5.69
1763 1895 1.530323 TTAGAAAAAGCTCCCCGCAC 58.470 50.000 0.00 0.00 42.61 5.34
1764 1896 0.672401 TAGAAAAAGCTCCCCGCACG 60.672 55.000 0.00 0.00 42.61 5.34
1765 1897 2.978018 GAAAAAGCTCCCCGCACGG 61.978 63.158 1.02 1.02 42.61 4.94
1813 1945 7.287061 TGTGAAAATTACCAGATATCCCGATT 58.713 34.615 0.00 0.00 0.00 3.34
1822 1954 0.243907 ATATCCCGATTCGTCGCCTG 59.756 55.000 5.20 0.00 0.00 4.85
1853 1985 4.082125 ACCCAATTGCTTCGATTTCTCTT 58.918 39.130 0.00 0.00 0.00 2.85
1854 1986 4.156739 ACCCAATTGCTTCGATTTCTCTTC 59.843 41.667 0.00 0.00 0.00 2.87
1855 1987 4.439289 CCCAATTGCTTCGATTTCTCTTCC 60.439 45.833 0.00 0.00 0.00 3.46
1856 1988 4.439289 CCAATTGCTTCGATTTCTCTTCCC 60.439 45.833 0.00 0.00 0.00 3.97
1857 1989 2.403252 TGCTTCGATTTCTCTTCCCC 57.597 50.000 0.00 0.00 0.00 4.81
1860 1992 2.815478 CTTCGATTTCTCTTCCCCTCG 58.185 52.381 0.00 0.00 0.00 4.63
1914 2051 3.912907 CCGAATCCTCCCCGACGG 61.913 72.222 6.99 6.99 34.77 4.79
2089 2226 5.866633 TCCGTGATGTTTTATTTTTGATGCC 59.133 36.000 0.00 0.00 0.00 4.40
2093 2230 9.729023 CGTGATGTTTTATTTTTGATGCCTATA 57.271 29.630 0.00 0.00 0.00 1.31
2206 2355 4.332819 GTGGTGTGGTACTGATAGCAATTC 59.667 45.833 0.00 0.00 40.40 2.17
2238 2387 1.815421 CGGGGCTCAACTGATTCCG 60.815 63.158 0.00 0.00 0.00 4.30
2267 2420 0.033601 AATCATGCCCGCCCTTAACA 60.034 50.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.667107 AGAGTTGGAGATTTCGTTATTTTCATA 57.333 29.630 0.00 0.00 0.00 2.15
39 40 8.567285 AGAGTTGGAGATTTCGTTATTTTCAT 57.433 30.769 0.00 0.00 0.00 2.57
40 41 7.878127 AGAGAGTTGGAGATTTCGTTATTTTCA 59.122 33.333 0.00 0.00 0.00 2.69
41 42 8.257830 AGAGAGTTGGAGATTTCGTTATTTTC 57.742 34.615 0.00 0.00 0.00 2.29
42 43 7.334671 GGAGAGAGTTGGAGATTTCGTTATTTT 59.665 37.037 0.00 0.00 0.00 1.82
43 44 6.819146 GGAGAGAGTTGGAGATTTCGTTATTT 59.181 38.462 0.00 0.00 0.00 1.40
44 45 6.342111 GGAGAGAGTTGGAGATTTCGTTATT 58.658 40.000 0.00 0.00 0.00 1.40
45 46 5.450688 CGGAGAGAGTTGGAGATTTCGTTAT 60.451 44.000 0.00 0.00 0.00 1.89
46 47 4.142447 CGGAGAGAGTTGGAGATTTCGTTA 60.142 45.833 0.00 0.00 0.00 3.18
47 48 3.367498 CGGAGAGAGTTGGAGATTTCGTT 60.367 47.826 0.00 0.00 0.00 3.85
48 49 2.164624 CGGAGAGAGTTGGAGATTTCGT 59.835 50.000 0.00 0.00 0.00 3.85
49 50 2.164624 ACGGAGAGAGTTGGAGATTTCG 59.835 50.000 0.00 0.00 0.00 3.46
50 51 3.516615 CACGGAGAGAGTTGGAGATTTC 58.483 50.000 0.00 0.00 0.00 2.17
51 52 2.234908 CCACGGAGAGAGTTGGAGATTT 59.765 50.000 0.00 0.00 0.00 2.17
52 53 1.827969 CCACGGAGAGAGTTGGAGATT 59.172 52.381 0.00 0.00 0.00 2.40
53 54 1.479709 CCACGGAGAGAGTTGGAGAT 58.520 55.000 0.00 0.00 0.00 2.75
54 55 0.612174 CCCACGGAGAGAGTTGGAGA 60.612 60.000 0.00 0.00 0.00 3.71
55 56 0.900647 ACCCACGGAGAGAGTTGGAG 60.901 60.000 0.00 0.00 0.00 3.86
56 57 0.898789 GACCCACGGAGAGAGTTGGA 60.899 60.000 0.00 0.00 0.00 3.53
57 58 1.185618 TGACCCACGGAGAGAGTTGG 61.186 60.000 0.00 0.00 0.00 3.77
58 59 0.898320 ATGACCCACGGAGAGAGTTG 59.102 55.000 0.00 0.00 0.00 3.16
59 60 1.276421 CAATGACCCACGGAGAGAGTT 59.724 52.381 0.00 0.00 0.00 3.01
60 61 0.898320 CAATGACCCACGGAGAGAGT 59.102 55.000 0.00 0.00 0.00 3.24
61 62 1.135915 CTCAATGACCCACGGAGAGAG 59.864 57.143 0.00 0.00 0.00 3.20
62 63 1.186200 CTCAATGACCCACGGAGAGA 58.814 55.000 0.00 0.00 0.00 3.10
63 64 0.898320 ACTCAATGACCCACGGAGAG 59.102 55.000 0.00 0.00 0.00 3.20
64 65 1.001974 CAACTCAATGACCCACGGAGA 59.998 52.381 0.00 0.00 0.00 3.71
65 66 1.442769 CAACTCAATGACCCACGGAG 58.557 55.000 0.00 0.00 0.00 4.63
66 67 0.605319 GCAACTCAATGACCCACGGA 60.605 55.000 0.00 0.00 0.00 4.69
67 68 1.875963 GCAACTCAATGACCCACGG 59.124 57.895 0.00 0.00 0.00 4.94
68 69 1.227999 ACGCAACTCAATGACCCACG 61.228 55.000 0.00 0.00 0.00 4.94
69 70 1.732259 CTACGCAACTCAATGACCCAC 59.268 52.381 0.00 0.00 0.00 4.61
70 71 1.621317 TCTACGCAACTCAATGACCCA 59.379 47.619 0.00 0.00 0.00 4.51
71 72 2.380084 TCTACGCAACTCAATGACCC 57.620 50.000 0.00 0.00 0.00 4.46
72 73 4.946784 AATTCTACGCAACTCAATGACC 57.053 40.909 0.00 0.00 0.00 4.02
73 74 6.170675 AGAAATTCTACGCAACTCAATGAC 57.829 37.500 0.00 0.00 0.00 3.06
74 75 6.535150 CCTAGAAATTCTACGCAACTCAATGA 59.465 38.462 0.00 0.00 0.00 2.57
75 76 6.535150 TCCTAGAAATTCTACGCAACTCAATG 59.465 38.462 0.00 0.00 0.00 2.82
76 77 6.640518 TCCTAGAAATTCTACGCAACTCAAT 58.359 36.000 0.00 0.00 0.00 2.57
77 78 6.032956 TCCTAGAAATTCTACGCAACTCAA 57.967 37.500 0.00 0.00 0.00 3.02
78 79 5.654603 TCCTAGAAATTCTACGCAACTCA 57.345 39.130 0.00 0.00 0.00 3.41
79 80 6.273825 TGATCCTAGAAATTCTACGCAACTC 58.726 40.000 0.00 0.00 0.00 3.01
80 81 6.222038 TGATCCTAGAAATTCTACGCAACT 57.778 37.500 0.00 0.00 0.00 3.16
81 82 6.238130 GGTTGATCCTAGAAATTCTACGCAAC 60.238 42.308 16.04 16.04 0.00 4.17
82 83 5.815740 GGTTGATCCTAGAAATTCTACGCAA 59.184 40.000 0.00 0.00 0.00 4.85
83 84 5.105106 TGGTTGATCCTAGAAATTCTACGCA 60.105 40.000 0.00 0.00 37.07 5.24
84 85 5.357257 TGGTTGATCCTAGAAATTCTACGC 58.643 41.667 0.00 0.00 37.07 4.42
85 86 7.843490 TTTGGTTGATCCTAGAAATTCTACG 57.157 36.000 0.00 0.00 37.07 3.51
87 88 8.686334 GCATTTTGGTTGATCCTAGAAATTCTA 58.314 33.333 2.44 2.44 37.07 2.10
88 89 7.178983 TGCATTTTGGTTGATCCTAGAAATTCT 59.821 33.333 0.00 0.00 37.07 2.40
89 90 7.322664 TGCATTTTGGTTGATCCTAGAAATTC 58.677 34.615 0.00 0.00 37.07 2.17
90 91 7.243604 TGCATTTTGGTTGATCCTAGAAATT 57.756 32.000 0.00 0.00 37.07 1.82
91 92 6.855763 TGCATTTTGGTTGATCCTAGAAAT 57.144 33.333 0.00 0.00 37.07 2.17
92 93 6.662865 TTGCATTTTGGTTGATCCTAGAAA 57.337 33.333 0.00 0.00 37.07 2.52
93 94 6.662865 TTTGCATTTTGGTTGATCCTAGAA 57.337 33.333 0.00 0.00 37.07 2.10
94 95 6.662865 TTTTGCATTTTGGTTGATCCTAGA 57.337 33.333 0.00 0.00 37.07 2.43
95 96 9.434420 TTTATTTTGCATTTTGGTTGATCCTAG 57.566 29.630 0.00 0.00 37.07 3.02
96 97 9.784531 TTTTATTTTGCATTTTGGTTGATCCTA 57.215 25.926 0.00 0.00 37.07 2.94
97 98 8.688747 TTTTATTTTGCATTTTGGTTGATCCT 57.311 26.923 0.00 0.00 37.07 3.24
157 158 9.270640 TCTGTAACATCCCAAATTTTCAATTTG 57.729 29.630 12.97 12.97 38.39 2.32
158 159 9.844257 TTCTGTAACATCCCAAATTTTCAATTT 57.156 25.926 0.00 0.00 0.00 1.82
159 160 9.844257 TTTCTGTAACATCCCAAATTTTCAATT 57.156 25.926 0.00 0.00 0.00 2.32
160 161 9.844257 TTTTCTGTAACATCCCAAATTTTCAAT 57.156 25.926 0.00 0.00 0.00 2.57
161 162 9.844257 ATTTTCTGTAACATCCCAAATTTTCAA 57.156 25.926 0.00 0.00 0.00 2.69
162 163 9.270640 CATTTTCTGTAACATCCCAAATTTTCA 57.729 29.630 0.00 0.00 0.00 2.69
163 164 8.720562 CCATTTTCTGTAACATCCCAAATTTTC 58.279 33.333 0.00 0.00 0.00 2.29
164 165 7.665145 CCCATTTTCTGTAACATCCCAAATTTT 59.335 33.333 0.00 0.00 0.00 1.82
165 166 7.167535 CCCATTTTCTGTAACATCCCAAATTT 58.832 34.615 0.00 0.00 0.00 1.82
166 167 6.272090 ACCCATTTTCTGTAACATCCCAAATT 59.728 34.615 0.00 0.00 0.00 1.82
167 168 5.784906 ACCCATTTTCTGTAACATCCCAAAT 59.215 36.000 0.00 0.00 0.00 2.32
168 169 5.011533 CACCCATTTTCTGTAACATCCCAAA 59.988 40.000 0.00 0.00 0.00 3.28
169 170 4.526262 CACCCATTTTCTGTAACATCCCAA 59.474 41.667 0.00 0.00 0.00 4.12
170 171 4.085733 CACCCATTTTCTGTAACATCCCA 58.914 43.478 0.00 0.00 0.00 4.37
171 172 3.447229 CCACCCATTTTCTGTAACATCCC 59.553 47.826 0.00 0.00 0.00 3.85
172 173 4.086457 ACCACCCATTTTCTGTAACATCC 58.914 43.478 0.00 0.00 0.00 3.51
173 174 5.619086 CGAACCACCCATTTTCTGTAACATC 60.619 44.000 0.00 0.00 0.00 3.06
174 175 4.217550 CGAACCACCCATTTTCTGTAACAT 59.782 41.667 0.00 0.00 0.00 2.71
175 176 3.566322 CGAACCACCCATTTTCTGTAACA 59.434 43.478 0.00 0.00 0.00 2.41
176 177 3.610821 GCGAACCACCCATTTTCTGTAAC 60.611 47.826 0.00 0.00 0.00 2.50
180 181 0.958091 TGCGAACCACCCATTTTCTG 59.042 50.000 0.00 0.00 0.00 3.02
245 247 4.306600 AGATGATTTTTGAACGGTTTGGC 58.693 39.130 0.00 0.00 0.00 4.52
396 398 1.302383 CCGACGGCATAAACCAAGCA 61.302 55.000 0.00 0.00 0.00 3.91
412 414 1.403249 GGCTAAGAACTACAACGCCGA 60.403 52.381 0.00 0.00 0.00 5.54
440 446 2.531942 GGGAGGGGGAGGTGTTGT 60.532 66.667 0.00 0.00 0.00 3.32
540 546 0.250513 GGGAAGAAGACATGGTCGCT 59.749 55.000 0.00 0.00 37.67 4.93
546 552 0.462759 GAGGCGGGGAAGAAGACATG 60.463 60.000 0.00 0.00 0.00 3.21
593 599 2.592993 CGGGGCTCACCAGAGGAAA 61.593 63.158 0.00 0.00 42.33 3.13
679 685 4.069232 CTCCTCAGGGACGCGCAA 62.069 66.667 5.73 0.00 36.57 4.85
733 739 1.750399 GCAGTGTGCCACCCATAGG 60.750 63.158 0.00 0.00 37.42 2.57
1113 1128 3.282021 CCAAAATGTCGGGATCATCTGT 58.718 45.455 0.00 0.00 0.00 3.41
1448 1543 2.790433 TGGACCAAGGACAATAGCAAC 58.210 47.619 0.00 0.00 0.00 4.17
1630 1734 7.366847 AGTATCACCTGTGCTAATTACATCT 57.633 36.000 0.00 0.00 0.00 2.90
1631 1735 8.979574 GTTAGTATCACCTGTGCTAATTACATC 58.020 37.037 0.00 0.00 0.00 3.06
1685 1817 3.771216 AGTAGTACTTCGTTCCCCTGAA 58.229 45.455 0.00 0.00 0.00 3.02
1686 1818 3.446442 AGTAGTACTTCGTTCCCCTGA 57.554 47.619 0.00 0.00 0.00 3.86
1687 1819 4.521146 TCTAGTAGTACTTCGTTCCCCTG 58.479 47.826 8.40 0.00 0.00 4.45
1702 1834 6.155221 TGGGCTGGATGCTAATTATCTAGTAG 59.845 42.308 0.00 0.00 42.39 2.57
1741 1873 3.422417 GCGGGGAGCTTTTTCTAATTC 57.578 47.619 0.00 0.00 44.04 2.17
1763 1895 4.910585 GTAGGATGGGTGCGGCCG 62.911 72.222 24.05 24.05 38.44 6.13
1764 1896 4.910585 CGTAGGATGGGTGCGGCC 62.911 72.222 0.00 0.00 0.00 6.13
1765 1897 3.792053 CTCGTAGGATGGGTGCGGC 62.792 68.421 0.00 0.00 0.00 6.53
1766 1898 2.351336 GACTCGTAGGATGGGTGCGG 62.351 65.000 0.00 0.00 0.00 5.69
1767 1899 1.065928 GACTCGTAGGATGGGTGCG 59.934 63.158 0.00 0.00 0.00 5.34
1822 1954 3.068064 CAATTGGGTGGGCCGGAC 61.068 66.667 5.05 0.00 34.97 4.79
2238 2387 2.202783 GCATGATTTGGGGCGTGC 60.203 61.111 0.00 0.00 39.51 5.34


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

AutoCloner maintained by Alex Coulton.