Multiple sequence alignment - TraesCS2A01G261500

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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 TraesCS2A01G261500 chr2A 100.000 2681 0 0 1 2681 412431421 412434101 0.000000e+00 4951.0
1 TraesCS2A01G261500 chr2A 94.318 704 40 0 1978 2681 412439029 412439732 0.000000e+00 1079.0
2 TraesCS2A01G261500 chr2A 94.774 574 28 2 207 779 412426069 412426641 0.000000e+00 893.0
3 TraesCS2A01G261500 chr2A 100.000 178 0 0 1 178 453526522 453526699 1.990000e-86 329.0
4 TraesCS2A01G261500 chr2D 93.207 1369 65 11 590 1939 318584201 318582842 0.000000e+00 1988.0
5 TraesCS2A01G261500 chr2D 94.643 280 13 1 316 593 318585245 318584966 1.470000e-117 433.0
6 TraesCS2A01G261500 chr2D 92.763 152 10 1 179 329 318587095 318586944 4.490000e-53 219.0
7 TraesCS2A01G261500 chr2B 91.626 1433 71 27 586 1979 387122865 387121443 0.000000e+00 1936.0
8 TraesCS2A01G261500 chr1D 94.595 703 38 0 1979 2681 188336812 188336110 0.000000e+00 1088.0
9 TraesCS2A01G261500 chr1D 94.318 704 40 0 1978 2681 188331193 188330490 0.000000e+00 1079.0
10 TraesCS2A01G261500 chr1D 94.176 704 41 0 1978 2681 188325572 188324869 0.000000e+00 1074.0
11 TraesCS2A01G261500 chr1D 94.034 704 42 0 1978 2681 410645475 410644772 0.000000e+00 1068.0
12 TraesCS2A01G261500 chr1D 86.885 122 11 3 474 593 362318712 362318830 6.020000e-27 132.0
13 TraesCS2A01G261500 chr1D 89.655 87 7 1 273 357 362318619 362318705 2.820000e-20 110.0
14 TraesCS2A01G261500 chr7D 94.176 704 40 1 1978 2681 523429912 523430614 0.000000e+00 1072.0
15 TraesCS2A01G261500 chr7D 93.803 710 42 2 1972 2680 139853311 139854019 0.000000e+00 1066.0
16 TraesCS2A01G261500 chr7A 94.176 704 40 1 1978 2681 127154403 127155105 0.000000e+00 1072.0
17 TraesCS2A01G261500 chr7A 98.343 181 3 0 1 181 221846298 221846478 4.310000e-83 318.0
18 TraesCS2A01G261500 chr7A 98.876 178 2 0 1 178 648489066 648488889 4.310000e-83 318.0
19 TraesCS2A01G261500 chr7A 95.812 191 6 2 1 191 152059359 152059171 9.320000e-80 307.0
20 TraesCS2A01G261500 chr5A 94.034 704 42 0 1978 2681 482938458 482939161 0.000000e+00 1068.0
21 TraesCS2A01G261500 chr5A 98.876 178 2 0 1 178 375268979 375268802 4.310000e-83 318.0
22 TraesCS2A01G261500 chr4A 98.883 179 2 0 1 179 474894604 474894426 1.200000e-83 320.0
23 TraesCS2A01G261500 chr4A 98.876 178 2 0 1 178 137637025 137637202 4.310000e-83 318.0
24 TraesCS2A01G261500 chr6A 97.814 183 3 1 1 183 138233565 138233746 5.570000e-82 315.0
25 TraesCS2A01G261500 chr1A 97.802 182 4 0 1 182 327266912 327267093 5.570000e-82 315.0
26 TraesCS2A01G261500 chr1A 88.506 87 8 1 273 357 461770868 461770954 1.310000e-18 104.0
27 TraesCS2A01G261500 chr1B 89.552 67 7 0 273 339 484884736 484884802 4.760000e-13 86.1


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 TraesCS2A01G261500 chr2A 412431421 412434101 2680 False 4951 4951 100.000000 1 2681 1 chr2A.!!$F2 2680
1 TraesCS2A01G261500 chr2A 412439029 412439732 703 False 1079 1079 94.318000 1978 2681 1 chr2A.!!$F3 703
2 TraesCS2A01G261500 chr2A 412426069 412426641 572 False 893 893 94.774000 207 779 1 chr2A.!!$F1 572
3 TraesCS2A01G261500 chr2D 318582842 318587095 4253 True 880 1988 93.537667 179 1939 3 chr2D.!!$R1 1760
4 TraesCS2A01G261500 chr2B 387121443 387122865 1422 True 1936 1936 91.626000 586 1979 1 chr2B.!!$R1 1393
5 TraesCS2A01G261500 chr1D 188336110 188336812 702 True 1088 1088 94.595000 1979 2681 1 chr1D.!!$R3 702
6 TraesCS2A01G261500 chr1D 188330490 188331193 703 True 1079 1079 94.318000 1978 2681 1 chr1D.!!$R2 703
7 TraesCS2A01G261500 chr1D 188324869 188325572 703 True 1074 1074 94.176000 1978 2681 1 chr1D.!!$R1 703
8 TraesCS2A01G261500 chr1D 410644772 410645475 703 True 1068 1068 94.034000 1978 2681 1 chr1D.!!$R4 703
9 TraesCS2A01G261500 chr7D 523429912 523430614 702 False 1072 1072 94.176000 1978 2681 1 chr7D.!!$F2 703
10 TraesCS2A01G261500 chr7D 139853311 139854019 708 False 1066 1066 93.803000 1972 2680 1 chr7D.!!$F1 708
11 TraesCS2A01G261500 chr7A 127154403 127155105 702 False 1072 1072 94.176000 1978 2681 1 chr7A.!!$F1 703
12 TraesCS2A01G261500 chr5A 482938458 482939161 703 False 1068 1068 94.034000 1978 2681 1 chr5A.!!$F1 703

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
828 3321 0.043183 TGCCCATGAGAAGAGAGGGA 59.957 55.0 0.0 0.0 42.25 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 4985 0.323725 TAGTAGGCCTCCGAAACCGT 60.324 55.0 9.68 0.0 0.0 4.83 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 3.809234 CTCGTCTATGATCGAGCTCTTG 58.191 50.000 12.85 0.00 44.82 3.02
23 24 3.206964 TCGTCTATGATCGAGCTCTTGT 58.793 45.455 12.85 0.00 0.00 3.16
24 25 4.377897 TCGTCTATGATCGAGCTCTTGTA 58.622 43.478 12.85 0.00 0.00 2.41
25 26 4.998033 TCGTCTATGATCGAGCTCTTGTAT 59.002 41.667 12.85 4.09 0.00 2.29
26 27 5.470437 TCGTCTATGATCGAGCTCTTGTATT 59.530 40.000 12.85 0.00 0.00 1.89
27 28 5.792962 CGTCTATGATCGAGCTCTTGTATTC 59.207 44.000 12.85 0.36 0.00 1.75
28 29 5.792962 GTCTATGATCGAGCTCTTGTATTCG 59.207 44.000 12.85 0.00 34.56 3.34
29 30 4.837896 ATGATCGAGCTCTTGTATTCGA 57.162 40.909 12.85 2.20 44.88 3.71
30 31 4.216366 TGATCGAGCTCTTGTATTCGAG 57.784 45.455 12.85 0.00 44.14 4.04
36 37 1.855360 GCTCTTGTATTCGAGCCTTCG 59.145 52.381 0.00 0.00 45.21 3.79
58 59 2.656947 GCCCCTGGCTTGTAATATGA 57.343 50.000 0.00 0.00 46.69 2.15
59 60 3.160679 GCCCCTGGCTTGTAATATGAT 57.839 47.619 0.00 0.00 46.69 2.45
60 61 2.821969 GCCCCTGGCTTGTAATATGATG 59.178 50.000 0.00 0.00 46.69 3.07
61 62 2.821969 CCCCTGGCTTGTAATATGATGC 59.178 50.000 0.00 0.00 0.00 3.91
62 63 3.499202 CCCCTGGCTTGTAATATGATGCT 60.499 47.826 0.00 0.00 0.00 3.79
63 64 4.147321 CCCTGGCTTGTAATATGATGCTT 58.853 43.478 0.00 0.00 0.00 3.91
64 65 4.022589 CCCTGGCTTGTAATATGATGCTTG 60.023 45.833 0.00 0.00 0.00 4.01
65 66 4.581824 CCTGGCTTGTAATATGATGCTTGT 59.418 41.667 0.00 0.00 0.00 3.16
66 67 5.764686 CCTGGCTTGTAATATGATGCTTGTA 59.235 40.000 0.00 0.00 0.00 2.41
67 68 6.432162 CCTGGCTTGTAATATGATGCTTGTAT 59.568 38.462 0.00 0.00 0.00 2.29
68 69 7.205737 TGGCTTGTAATATGATGCTTGTATG 57.794 36.000 0.00 0.00 0.00 2.39
69 70 6.997476 TGGCTTGTAATATGATGCTTGTATGA 59.003 34.615 0.00 0.00 0.00 2.15
70 71 7.041167 TGGCTTGTAATATGATGCTTGTATGAC 60.041 37.037 0.00 0.00 0.00 3.06
71 72 7.173907 GGCTTGTAATATGATGCTTGTATGACT 59.826 37.037 0.00 0.00 0.00 3.41
72 73 8.562892 GCTTGTAATATGATGCTTGTATGACTT 58.437 33.333 0.00 0.00 0.00 3.01
104 105 8.902540 TTTGTAGAGTTGTGTTGTGATATCTT 57.097 30.769 3.98 0.00 0.00 2.40
105 106 8.902540 TTGTAGAGTTGTGTTGTGATATCTTT 57.097 30.769 3.98 0.00 0.00 2.52
106 107 8.534333 TGTAGAGTTGTGTTGTGATATCTTTC 57.466 34.615 3.98 0.00 0.00 2.62
107 108 7.602644 TGTAGAGTTGTGTTGTGATATCTTTCC 59.397 37.037 3.98 0.00 0.00 3.13
108 109 5.639506 AGAGTTGTGTTGTGATATCTTTCCG 59.360 40.000 3.98 0.00 0.00 4.30
109 110 5.305585 AGTTGTGTTGTGATATCTTTCCGT 58.694 37.500 3.98 0.00 0.00 4.69
110 111 5.179368 AGTTGTGTTGTGATATCTTTCCGTG 59.821 40.000 3.98 0.00 0.00 4.94
111 112 4.888917 TGTGTTGTGATATCTTTCCGTGA 58.111 39.130 3.98 0.00 0.00 4.35
112 113 4.929211 TGTGTTGTGATATCTTTCCGTGAG 59.071 41.667 3.98 0.00 0.00 3.51
113 114 4.929808 GTGTTGTGATATCTTTCCGTGAGT 59.070 41.667 3.98 0.00 0.00 3.41
114 115 5.062308 GTGTTGTGATATCTTTCCGTGAGTC 59.938 44.000 3.98 0.00 0.00 3.36
115 116 4.386867 TGTGATATCTTTCCGTGAGTCC 57.613 45.455 3.98 0.00 0.00 3.85
116 117 3.132289 TGTGATATCTTTCCGTGAGTCCC 59.868 47.826 3.98 0.00 0.00 4.46
117 118 3.385111 GTGATATCTTTCCGTGAGTCCCT 59.615 47.826 3.98 0.00 0.00 4.20
118 119 3.384789 TGATATCTTTCCGTGAGTCCCTG 59.615 47.826 3.98 0.00 0.00 4.45
119 120 1.938585 ATCTTTCCGTGAGTCCCTGA 58.061 50.000 0.00 0.00 0.00 3.86
120 121 1.938585 TCTTTCCGTGAGTCCCTGAT 58.061 50.000 0.00 0.00 0.00 2.90
121 122 1.825474 TCTTTCCGTGAGTCCCTGATC 59.175 52.381 0.00 0.00 0.00 2.92
122 123 1.827969 CTTTCCGTGAGTCCCTGATCT 59.172 52.381 0.00 0.00 0.00 2.75
123 124 1.938585 TTCCGTGAGTCCCTGATCTT 58.061 50.000 0.00 0.00 0.00 2.40
124 125 1.186200 TCCGTGAGTCCCTGATCTTG 58.814 55.000 0.00 0.00 0.00 3.02
125 126 1.186200 CCGTGAGTCCCTGATCTTGA 58.814 55.000 0.00 0.00 0.00 3.02
126 127 1.759445 CCGTGAGTCCCTGATCTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
127 128 2.223923 CCGTGAGTCCCTGATCTTGATC 60.224 54.545 3.82 3.82 0.00 2.92
128 129 2.542618 CGTGAGTCCCTGATCTTGATCG 60.543 54.545 6.19 2.03 0.00 3.69
129 130 2.428890 GTGAGTCCCTGATCTTGATCGT 59.571 50.000 6.19 0.00 0.00 3.73
130 131 3.632604 GTGAGTCCCTGATCTTGATCGTA 59.367 47.826 6.19 0.00 0.00 3.43
131 132 3.632604 TGAGTCCCTGATCTTGATCGTAC 59.367 47.826 6.19 2.53 0.00 3.67
132 133 3.632333 AGTCCCTGATCTTGATCGTACA 58.368 45.455 6.19 0.00 0.00 2.90
133 134 3.381908 AGTCCCTGATCTTGATCGTACAC 59.618 47.826 6.19 1.73 0.00 2.90
134 135 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
135 136 2.099263 CCCTGATCTTGATCGTACACGT 59.901 50.000 1.19 0.00 40.80 4.49
136 137 3.428999 CCCTGATCTTGATCGTACACGTT 60.429 47.826 1.19 0.00 40.80 3.99
137 138 4.174009 CCTGATCTTGATCGTACACGTTT 58.826 43.478 1.19 0.00 40.80 3.60
138 139 4.031765 CCTGATCTTGATCGTACACGTTTG 59.968 45.833 1.19 0.00 40.80 2.93
139 140 3.366724 TGATCTTGATCGTACACGTTTGC 59.633 43.478 1.19 0.00 40.80 3.68
140 141 1.717113 TCTTGATCGTACACGTTTGCG 59.283 47.619 5.81 5.81 44.93 4.85
154 155 4.123276 CGTTTGCGTGTATGTTTAGTGT 57.877 40.909 0.00 0.00 0.00 3.55
155 156 5.253334 CGTTTGCGTGTATGTTTAGTGTA 57.747 39.130 0.00 0.00 0.00 2.90
156 157 5.068256 CGTTTGCGTGTATGTTTAGTGTAC 58.932 41.667 0.00 0.00 0.00 2.90
157 158 4.889519 TTGCGTGTATGTTTAGTGTACG 57.110 40.909 0.00 0.00 0.00 3.67
158 159 3.244156 TGCGTGTATGTTTAGTGTACGG 58.756 45.455 0.00 0.00 0.00 4.02
159 160 3.244976 GCGTGTATGTTTAGTGTACGGT 58.755 45.455 0.00 0.00 0.00 4.83
160 161 3.301642 GCGTGTATGTTTAGTGTACGGTC 59.698 47.826 0.00 0.00 0.00 4.79
161 162 4.475028 CGTGTATGTTTAGTGTACGGTCA 58.525 43.478 0.00 0.00 0.00 4.02
162 163 4.916831 CGTGTATGTTTAGTGTACGGTCAA 59.083 41.667 0.00 0.00 0.00 3.18
163 164 5.401972 CGTGTATGTTTAGTGTACGGTCAAA 59.598 40.000 0.00 0.00 0.00 2.69
164 165 6.584056 GTGTATGTTTAGTGTACGGTCAAAC 58.416 40.000 0.00 5.65 0.00 2.93
165 166 5.695816 TGTATGTTTAGTGTACGGTCAAACC 59.304 40.000 8.69 0.00 34.05 3.27
175 176 4.629523 GTCAAACCGGGGGCGTCA 62.630 66.667 6.32 0.00 0.00 4.35
176 177 4.629523 TCAAACCGGGGGCGTCAC 62.630 66.667 6.32 0.00 0.00 3.67
177 178 4.939368 CAAACCGGGGGCGTCACA 62.939 66.667 6.32 0.00 0.00 3.58
182 183 2.504032 CGGGGGCGTCACACATAT 59.496 61.111 0.00 0.00 0.00 1.78
187 188 0.107410 GGGCGTCACACATATTGGGA 60.107 55.000 0.00 0.00 34.11 4.37
200 201 5.125900 CACATATTGGGAAGTTCTTGCATCA 59.874 40.000 2.25 0.00 0.00 3.07
202 203 6.381994 ACATATTGGGAAGTTCTTGCATCATT 59.618 34.615 2.25 0.00 0.00 2.57
240 241 8.094798 TGTTTTGCTGATTAAGTGTACTAAGG 57.905 34.615 0.00 0.00 0.00 2.69
479 2195 2.893637 AGACTCGCACCATTCACATAC 58.106 47.619 0.00 0.00 0.00 2.39
725 3214 1.754226 ACTGGTTTTGTTTGGACGCAT 59.246 42.857 0.00 0.00 0.00 4.73
828 3321 0.043183 TGCCCATGAGAAGAGAGGGA 59.957 55.000 0.00 0.00 42.25 4.20
867 3360 2.673368 CGCAAGAAGTCGCCTAATTCTT 59.327 45.455 3.95 3.95 42.49 2.52
895 3388 2.291741 GGATTGGATTAGGCGCTTCTTG 59.708 50.000 7.64 0.00 0.00 3.02
902 3395 1.485294 TAGGCGCTTCTTGGTCCCAA 61.485 55.000 7.64 0.00 0.00 4.12
952 3445 7.919313 TTCCTCTGTACGTAAAATAATAGCG 57.081 36.000 0.00 0.00 0.00 4.26
1125 3618 2.347322 GCAGGTGTCCGCTCTCTCT 61.347 63.158 0.00 0.00 0.00 3.10
1129 3622 0.318762 GGTGTCCGCTCTCTCTTTGT 59.681 55.000 0.00 0.00 0.00 2.83
1166 3689 9.770097 CCATGATTCTGTATGACTGTATTACTT 57.230 33.333 0.00 0.00 0.00 2.24
1195 3718 3.208594 GTCCCCGTACTGTTTTCTGTTT 58.791 45.455 0.00 0.00 34.05 2.83
1205 3732 6.567769 ACTGTTTTCTGTTTAAATTGTGCG 57.432 33.333 0.00 0.00 0.00 5.34
1235 3762 1.000283 ACTGAAGACCAGCGTGAAGAG 60.000 52.381 0.00 0.00 46.81 2.85
1272 3799 1.871418 TCTGGCATGAGGAGCTAACT 58.129 50.000 0.00 0.00 0.00 2.24
1318 3845 4.067896 ACCAATCAAGCTTGTGAGTACTG 58.932 43.478 25.19 6.46 0.00 2.74
1339 3866 3.255642 TGCCTACTGTTTTCTTGCAATCC 59.744 43.478 0.00 0.00 0.00 3.01
1384 3911 2.849880 TGAAGAAAACTGTGCTGTGC 57.150 45.000 0.00 0.00 0.00 4.57
1621 4153 1.144716 GACATGATCCTGCGCCTCA 59.855 57.895 4.18 2.97 0.00 3.86
1720 4252 1.376543 GCACATGCATGCAGAGTACT 58.623 50.000 26.69 4.78 45.39 2.73
1748 4280 4.824537 AGTATATCTCGATCCATCCATCCG 59.175 45.833 0.00 0.00 0.00 4.18
1949 4488 6.705863 TTTTACTCCTCTACCTAACCGATC 57.294 41.667 0.00 0.00 0.00 3.69
1952 4491 2.108601 CTCCTCTACCTAACCGATCCCT 59.891 54.545 0.00 0.00 0.00 4.20
1957 4496 5.887035 CCTCTACCTAACCGATCCCTAATAG 59.113 48.000 0.00 0.00 0.00 1.73
1959 4498 7.281366 TCTACCTAACCGATCCCTAATAGAT 57.719 40.000 0.00 0.00 0.00 1.98
1960 4499 7.344913 TCTACCTAACCGATCCCTAATAGATC 58.655 42.308 0.00 0.00 37.39 2.75
1964 4503 4.744795 ACCGATCCCTAATAGATCATGC 57.255 45.455 0.00 0.00 40.17 4.06
1976 4515 8.997323 CCTAATAGATCATGCTGGAGTAAAAAG 58.003 37.037 0.00 0.00 0.00 2.27
2001 4540 7.397192 AGTGTTGGAAATATGAGCAATTTACCT 59.603 33.333 0.00 0.00 0.00 3.08
2227 4766 6.588204 TGTAGCAAAACCTCTAACAGAAAGA 58.412 36.000 0.00 0.00 0.00 2.52
2254 4793 2.048597 CGTACGGGACAGCAGCAA 60.049 61.111 7.57 0.00 0.00 3.91
2301 4840 1.153309 CTCGCCTGCCATGTCATCA 60.153 57.895 0.00 0.00 0.00 3.07
2446 4985 2.564062 CCCGTACAGGACTCAAAAGGTA 59.436 50.000 5.46 0.00 45.00 3.08
2465 5004 0.323725 ACGGTTTCGGAGGCCTACTA 60.324 55.000 14.69 0.00 41.39 1.82
2470 5009 0.559205 TTCGGAGGCCTACTATCCCA 59.441 55.000 14.69 0.00 0.00 4.37
2476 5015 0.828677 GGCCTACTATCCCAACGTGT 59.171 55.000 0.00 0.00 0.00 4.49
2507 5046 1.767759 CAAGCCGGGATGAGGAAAAT 58.232 50.000 2.18 0.00 0.00 1.82
2516 5055 4.273318 GGGATGAGGAAAATAACAGCAGT 58.727 43.478 0.00 0.00 0.00 4.40
2556 5096 2.041350 ACGAGGGAAGGAGTAGTTCTGA 59.959 50.000 0.00 0.00 0.00 3.27
2572 5112 2.037901 TCTGATGCATCTCTCTGGGAC 58.962 52.381 26.32 0.00 0.00 4.46
2646 5186 0.602905 AGGCGAAACAAAGAGACGGG 60.603 55.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.206964 ACAAGAGCTCGATCATAGACGA 58.793 45.455 8.37 0.00 37.03 4.20
3 4 3.617540 ACAAGAGCTCGATCATAGACG 57.382 47.619 8.37 0.00 0.00 4.18
4 5 5.792962 CGAATACAAGAGCTCGATCATAGAC 59.207 44.000 8.37 0.00 33.13 2.59
5 6 5.701290 TCGAATACAAGAGCTCGATCATAGA 59.299 40.000 8.37 0.82 35.52 1.98
6 7 5.932661 TCGAATACAAGAGCTCGATCATAG 58.067 41.667 8.37 0.00 35.52 2.23
7 8 5.932661 CTCGAATACAAGAGCTCGATCATA 58.067 41.667 8.37 0.00 39.39 2.15
8 9 4.793071 CTCGAATACAAGAGCTCGATCAT 58.207 43.478 8.37 0.00 39.39 2.45
9 10 4.216366 CTCGAATACAAGAGCTCGATCA 57.784 45.455 8.37 0.00 39.39 2.92
40 41 2.821969 GCATCATATTACAAGCCAGGGG 59.178 50.000 0.00 0.00 0.00 4.79
41 42 3.759581 AGCATCATATTACAAGCCAGGG 58.240 45.455 0.00 0.00 0.00 4.45
42 43 4.581824 ACAAGCATCATATTACAAGCCAGG 59.418 41.667 0.00 0.00 0.00 4.45
43 44 5.762825 ACAAGCATCATATTACAAGCCAG 57.237 39.130 0.00 0.00 0.00 4.85
44 45 6.997476 TCATACAAGCATCATATTACAAGCCA 59.003 34.615 0.00 0.00 0.00 4.75
45 46 7.173907 AGTCATACAAGCATCATATTACAAGCC 59.826 37.037 0.00 0.00 0.00 4.35
46 47 8.092521 AGTCATACAAGCATCATATTACAAGC 57.907 34.615 0.00 0.00 0.00 4.01
78 79 9.507329 AAGATATCACAACACAACTCTACAAAT 57.493 29.630 5.32 0.00 0.00 2.32
79 80 8.902540 AAGATATCACAACACAACTCTACAAA 57.097 30.769 5.32 0.00 0.00 2.83
80 81 8.902540 AAAGATATCACAACACAACTCTACAA 57.097 30.769 5.32 0.00 0.00 2.41
81 82 7.602644 GGAAAGATATCACAACACAACTCTACA 59.397 37.037 5.32 0.00 0.00 2.74
82 83 7.201444 CGGAAAGATATCACAACACAACTCTAC 60.201 40.741 5.32 0.00 0.00 2.59
83 84 6.811665 CGGAAAGATATCACAACACAACTCTA 59.188 38.462 5.32 0.00 0.00 2.43
84 85 5.639506 CGGAAAGATATCACAACACAACTCT 59.360 40.000 5.32 0.00 0.00 3.24
85 86 5.408604 ACGGAAAGATATCACAACACAACTC 59.591 40.000 5.32 0.00 0.00 3.01
86 87 5.179368 CACGGAAAGATATCACAACACAACT 59.821 40.000 5.32 0.00 0.00 3.16
87 88 5.178623 TCACGGAAAGATATCACAACACAAC 59.821 40.000 5.32 0.00 0.00 3.32
88 89 5.301555 TCACGGAAAGATATCACAACACAA 58.698 37.500 5.32 0.00 0.00 3.33
89 90 4.888917 TCACGGAAAGATATCACAACACA 58.111 39.130 5.32 0.00 0.00 3.72
90 91 4.929808 ACTCACGGAAAGATATCACAACAC 59.070 41.667 5.32 0.00 0.00 3.32
91 92 5.147330 ACTCACGGAAAGATATCACAACA 57.853 39.130 5.32 0.00 0.00 3.33
92 93 4.567159 GGACTCACGGAAAGATATCACAAC 59.433 45.833 5.32 0.00 0.00 3.32
93 94 4.382685 GGGACTCACGGAAAGATATCACAA 60.383 45.833 5.32 0.00 0.00 3.33
94 95 3.132289 GGGACTCACGGAAAGATATCACA 59.868 47.826 5.32 0.00 0.00 3.58
95 96 3.385111 AGGGACTCACGGAAAGATATCAC 59.615 47.826 5.32 0.00 0.00 3.06
96 97 3.384789 CAGGGACTCACGGAAAGATATCA 59.615 47.826 5.32 0.00 34.60 2.15
97 98 3.637229 TCAGGGACTCACGGAAAGATATC 59.363 47.826 0.00 0.00 34.60 1.63
98 99 3.643237 TCAGGGACTCACGGAAAGATAT 58.357 45.455 0.00 0.00 34.60 1.63
99 100 3.095912 TCAGGGACTCACGGAAAGATA 57.904 47.619 0.00 0.00 34.60 1.98
100 101 1.938585 TCAGGGACTCACGGAAAGAT 58.061 50.000 0.00 0.00 34.60 2.40
101 102 1.825474 GATCAGGGACTCACGGAAAGA 59.175 52.381 0.00 0.00 34.60 2.52
102 103 1.827969 AGATCAGGGACTCACGGAAAG 59.172 52.381 0.00 0.00 34.60 2.62
103 104 1.938585 AGATCAGGGACTCACGGAAA 58.061 50.000 0.00 0.00 34.60 3.13
104 105 1.550524 CAAGATCAGGGACTCACGGAA 59.449 52.381 0.00 0.00 34.60 4.30
105 106 1.186200 CAAGATCAGGGACTCACGGA 58.814 55.000 0.00 0.00 34.60 4.69
106 107 1.186200 TCAAGATCAGGGACTCACGG 58.814 55.000 0.00 0.00 34.60 4.94
107 108 2.542618 CGATCAAGATCAGGGACTCACG 60.543 54.545 10.39 0.00 34.60 4.35
108 109 2.428890 ACGATCAAGATCAGGGACTCAC 59.571 50.000 10.39 0.00 34.60 3.51
109 110 2.739943 ACGATCAAGATCAGGGACTCA 58.260 47.619 10.39 0.00 34.60 3.41
110 111 3.632604 TGTACGATCAAGATCAGGGACTC 59.367 47.826 10.39 0.00 34.60 3.36
111 112 3.381908 GTGTACGATCAAGATCAGGGACT 59.618 47.826 10.39 0.00 43.88 3.85
112 113 3.707793 GTGTACGATCAAGATCAGGGAC 58.292 50.000 10.39 2.84 37.69 4.46
113 114 2.357952 CGTGTACGATCAAGATCAGGGA 59.642 50.000 10.39 0.00 43.02 4.20
114 115 2.099263 ACGTGTACGATCAAGATCAGGG 59.901 50.000 11.79 0.00 43.02 4.45
115 116 3.422417 ACGTGTACGATCAAGATCAGG 57.578 47.619 11.79 0.51 43.02 3.86
116 117 4.490959 GCAAACGTGTACGATCAAGATCAG 60.491 45.833 11.79 5.82 43.02 2.90
117 118 3.366724 GCAAACGTGTACGATCAAGATCA 59.633 43.478 11.79 0.00 43.02 2.92
118 119 3.539592 CGCAAACGTGTACGATCAAGATC 60.540 47.826 11.79 0.00 43.02 2.75
119 120 2.344441 CGCAAACGTGTACGATCAAGAT 59.656 45.455 11.79 0.00 43.02 2.40
120 121 1.717113 CGCAAACGTGTACGATCAAGA 59.283 47.619 11.79 0.00 43.02 3.02
121 122 2.125168 CGCAAACGTGTACGATCAAG 57.875 50.000 11.79 0.00 43.02 3.02
134 135 5.068256 CGTACACTAAACATACACGCAAAC 58.932 41.667 0.00 0.00 0.00 2.93
135 136 4.150274 CCGTACACTAAACATACACGCAAA 59.850 41.667 0.00 0.00 0.00 3.68
136 137 3.674281 CCGTACACTAAACATACACGCAA 59.326 43.478 0.00 0.00 0.00 4.85
137 138 3.244156 CCGTACACTAAACATACACGCA 58.756 45.455 0.00 0.00 0.00 5.24
138 139 3.244976 ACCGTACACTAAACATACACGC 58.755 45.455 0.00 0.00 0.00 5.34
139 140 4.475028 TGACCGTACACTAAACATACACG 58.525 43.478 0.00 0.00 0.00 4.49
140 141 6.346838 GGTTTGACCGTACACTAAACATACAC 60.347 42.308 11.57 0.00 33.99 2.90
141 142 5.695816 GGTTTGACCGTACACTAAACATACA 59.304 40.000 11.57 0.00 33.99 2.29
142 143 6.156932 GGTTTGACCGTACACTAAACATAC 57.843 41.667 11.57 0.00 33.99 2.39
158 159 4.629523 TGACGCCCCCGGTTTGAC 62.630 66.667 0.00 0.00 39.22 3.18
159 160 4.629523 GTGACGCCCCCGGTTTGA 62.630 66.667 0.00 0.00 39.22 2.69
160 161 4.939368 TGTGACGCCCCCGGTTTG 62.939 66.667 0.00 0.00 39.22 2.93
161 162 4.941309 GTGTGACGCCCCCGGTTT 62.941 66.667 0.00 0.00 39.22 3.27
164 165 2.602746 AATATGTGTGACGCCCCCGG 62.603 60.000 0.00 0.00 39.22 5.73
165 166 1.153249 AATATGTGTGACGCCCCCG 60.153 57.895 0.00 0.00 41.14 5.73
166 167 1.101049 CCAATATGTGTGACGCCCCC 61.101 60.000 0.00 0.00 0.00 5.40
167 168 1.101049 CCCAATATGTGTGACGCCCC 61.101 60.000 0.00 0.00 0.00 5.80
168 169 0.107410 TCCCAATATGTGTGACGCCC 60.107 55.000 0.00 0.00 0.00 6.13
169 170 1.670811 CTTCCCAATATGTGTGACGCC 59.329 52.381 0.00 0.00 0.00 5.68
170 171 2.356135 ACTTCCCAATATGTGTGACGC 58.644 47.619 0.00 0.00 0.00 5.19
171 172 4.253685 AGAACTTCCCAATATGTGTGACG 58.746 43.478 0.00 0.00 0.00 4.35
172 173 5.619981 GCAAGAACTTCCCAATATGTGTGAC 60.620 44.000 0.00 0.00 0.00 3.67
173 174 4.458989 GCAAGAACTTCCCAATATGTGTGA 59.541 41.667 0.00 0.00 0.00 3.58
174 175 4.218200 TGCAAGAACTTCCCAATATGTGTG 59.782 41.667 0.00 0.00 0.00 3.82
175 176 4.406456 TGCAAGAACTTCCCAATATGTGT 58.594 39.130 0.00 0.00 0.00 3.72
176 177 5.125900 TGATGCAAGAACTTCCCAATATGTG 59.874 40.000 0.00 0.00 0.00 3.21
177 178 5.263599 TGATGCAAGAACTTCCCAATATGT 58.736 37.500 0.00 0.00 0.00 2.29
182 183 4.462483 GGTAATGATGCAAGAACTTCCCAA 59.538 41.667 0.00 0.00 0.00 4.12
187 188 6.186957 TGGTATGGTAATGATGCAAGAACTT 58.813 36.000 0.00 0.00 0.00 2.66
200 201 6.606796 TCAGCAAAACATGATGGTATGGTAAT 59.393 34.615 0.00 0.00 45.53 1.89
202 203 5.504853 TCAGCAAAACATGATGGTATGGTA 58.495 37.500 0.00 0.00 45.53 3.25
240 241 7.930217 TCTGCAAGTTGGTTTATATATGCTTC 58.070 34.615 4.75 0.00 33.87 3.86
375 2089 7.352739 CAAGTTCAAATACGAAGTTGCTTACT 58.647 34.615 7.96 0.00 44.81 2.24
388 2102 7.256756 AGCATCATAGCTCAAGTTCAAATAC 57.743 36.000 0.00 0.00 42.18 1.89
479 2195 0.671781 CAGTGGGCTCGAGTGGAAAG 60.672 60.000 15.13 0.00 0.00 2.62
648 3137 3.963383 CGTGAGCAAAAAGTGGTACTT 57.037 42.857 0.00 0.00 40.80 2.24
676 3165 3.648339 TTTTTGGCATCTCTCTTGCAC 57.352 42.857 0.00 0.00 41.95 4.57
705 3194 1.178276 TGCGTCCAAACAAAACCAGT 58.822 45.000 0.00 0.00 0.00 4.00
725 3214 2.439409 CTGACCATTTCTCATGTGCCA 58.561 47.619 0.00 0.00 0.00 4.92
867 3360 3.616560 GCGCCTAATCCAATCCTCGAATA 60.617 47.826 0.00 0.00 0.00 1.75
913 3406 2.332654 GGAATGTGGTCGGTGTGGC 61.333 63.158 0.00 0.00 0.00 5.01
1125 3618 7.068593 ACAGAATCATGGACAAGAAGAAACAAA 59.931 33.333 0.00 0.00 0.00 2.83
1129 3622 8.102676 TCATACAGAATCATGGACAAGAAGAAA 58.897 33.333 0.00 0.00 0.00 2.52
1166 3689 7.334921 CAGAAAACAGTACGGGGACAATTAATA 59.665 37.037 0.00 0.00 0.00 0.98
1176 3699 5.754543 TTTAAACAGAAAACAGTACGGGG 57.245 39.130 0.00 0.00 0.00 5.73
1178 3701 7.305763 GCACAATTTAAACAGAAAACAGTACGG 60.306 37.037 0.00 0.00 0.00 4.02
1195 3718 4.916831 CAGTTTCTGCAATCGCACAATTTA 59.083 37.500 0.00 0.00 45.36 1.40
1205 3732 3.365767 GCTGGTCTTCAGTTTCTGCAATC 60.366 47.826 0.00 0.00 45.08 2.67
1235 3762 1.689273 AGATAGGGTTCACAGATCGCC 59.311 52.381 0.00 0.00 0.00 5.54
1272 3799 0.963225 TCGGGTTCGTGATTGACAGA 59.037 50.000 0.00 0.00 37.69 3.41
1318 3845 3.670627 CGGATTGCAAGAAAACAGTAGGC 60.671 47.826 4.94 0.00 0.00 3.93
1455 3987 0.178068 TAAAGGGCAGCACCTCGATC 59.822 55.000 3.14 0.00 40.87 3.69
1624 4156 2.280823 ATTTCCCCGCTCTCGACGTC 62.281 60.000 5.18 5.18 38.10 4.34
1717 4249 7.769507 GGATGGATCGAGATATACTGTACAGTA 59.230 40.741 32.18 32.18 46.68 2.74
1720 4252 6.481643 TGGATGGATCGAGATATACTGTACA 58.518 40.000 0.00 0.00 0.00 2.90
1748 4280 1.352156 GACATCTGCAACGGACGGAC 61.352 60.000 0.00 0.00 0.00 4.79
1795 4327 3.788145 CGGGGCGGGGTGTAATCA 61.788 66.667 0.00 0.00 0.00 2.57
1855 4387 2.847327 ACAATGTCCTGGACTGTCAG 57.153 50.000 26.03 14.10 33.15 3.51
1949 4488 6.611613 TTACTCCAGCATGATCTATTAGGG 57.388 41.667 0.00 0.00 39.69 3.53
1952 4491 9.330063 CACTTTTTACTCCAGCATGATCTATTA 57.670 33.333 0.00 0.00 39.69 0.98
1957 4496 5.886960 ACACTTTTTACTCCAGCATGATC 57.113 39.130 0.00 0.00 39.69 2.92
1959 4498 4.278170 CCAACACTTTTTACTCCAGCATGA 59.722 41.667 0.00 0.00 39.69 3.07
1960 4499 4.278170 TCCAACACTTTTTACTCCAGCATG 59.722 41.667 0.00 0.00 0.00 4.06
1964 4503 8.792633 TCATATTTCCAACACTTTTTACTCCAG 58.207 33.333 0.00 0.00 0.00 3.86
1976 4515 7.547227 AGGTAAATTGCTCATATTTCCAACAC 58.453 34.615 0.00 0.00 0.00 3.32
2063 4602 4.154737 CCTTCTCTTTGTCAAATCGCATGA 59.845 41.667 0.00 0.00 0.00 3.07
2121 4660 9.389755 CTTGCTATACTGTCTGCTCTAGATATA 57.610 37.037 0.00 0.00 37.83 0.86
2192 4731 8.465273 AGAGGTTTTGCTACAGTTTCTTATTT 57.535 30.769 0.00 0.00 0.00 1.40
2195 4734 7.988599 TGTTAGAGGTTTTGCTACAGTTTCTTA 59.011 33.333 0.00 0.00 0.00 2.10
2210 4749 8.047310 TGTTCTTCTTCTTTCTGTTAGAGGTTT 58.953 33.333 0.00 0.00 0.00 3.27
2227 4766 1.682854 TGTCCCGTACGTGTTCTTCTT 59.317 47.619 15.21 0.00 0.00 2.52
2254 4793 1.302033 CCAAGTCCAGCGCTTCTGT 60.302 57.895 7.50 0.00 41.25 3.41
2301 4840 2.623915 CGACGTCCACGACCTCCTT 61.624 63.158 10.58 0.00 43.02 3.36
2446 4985 0.323725 TAGTAGGCCTCCGAAACCGT 60.324 55.000 9.68 0.00 0.00 4.83
2507 5046 4.563580 GGTTCCATCTCTGAACTGCTGTTA 60.564 45.833 9.14 0.00 41.42 2.41
2516 5055 2.159240 CGTCATCGGTTCCATCTCTGAA 60.159 50.000 0.00 0.00 0.00 3.02
2556 5096 1.039068 CTCGTCCCAGAGAGATGCAT 58.961 55.000 0.00 0.00 40.57 3.96
2572 5112 3.492829 GCCTATAAAAGGGAGGTCACTCG 60.493 52.174 0.00 0.00 46.65 4.18
2624 5164 1.605712 CGTCTCTTTGTTTCGCCTCCT 60.606 52.381 0.00 0.00 0.00 3.69
2646 5186 1.986575 GCTGGCTGTTCGCTTCATCC 61.987 60.000 0.00 0.00 39.13 3.51


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

AutoCloner maintained by Alex Coulton.