Multiple sequence alignment - TraesCS3D01G151700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G151700 chr3D 100.000 2609 0 0 1 2609 116051325 116053933 0 4819
1 TraesCS3D01G151700 chr3D 95.314 1003 37 4 1609 2609 99742790 99741796 0 1583
2 TraesCS3D01G151700 chr5D 94.789 1401 62 9 210 1604 21547027 21545632 0 2172
3 TraesCS3D01G151700 chr5D 95.613 1003 34 4 1607 2609 399105386 399106378 0 1600
4 TraesCS3D01G151700 chr5D 95.314 1003 40 2 1607 2609 267149600 267150595 0 1585
5 TraesCS3D01G151700 chr2D 93.424 1399 83 7 210 1604 476786428 476787821 0 2065
6 TraesCS3D01G151700 chr2D 90.948 1392 80 14 223 1604 78330484 78329129 0 1831
7 TraesCS3D01G151700 chr2D 95.319 1004 39 2 1606 2609 446164945 446163950 0 1587
8 TraesCS3D01G151700 chr7D 93.196 1411 70 10 211 1604 72149235 72150636 0 2050
9 TraesCS3D01G151700 chr7D 91.770 1373 98 11 238 1604 593734280 593735643 0 1895
10 TraesCS3D01G151700 chr7D 95.518 1004 40 3 1606 2609 226567229 226566231 0 1600
11 TraesCS3D01G151700 chr7D 95.314 1003 43 3 1607 2609 283036410 283037408 0 1589
12 TraesCS3D01G151700 chr2B 88.445 1428 116 20 210 1604 465668076 465666665 0 1677
13 TraesCS3D01G151700 chr2B 93.122 1134 65 10 479 1604 71646102 71644974 0 1650
14 TraesCS3D01G151700 chr2B 89.727 1207 79 20 209 1372 53302836 53304040 0 1500
15 TraesCS3D01G151700 chr5A 88.301 1436 113 22 209 1604 599226414 599227834 0 1670
16 TraesCS3D01G151700 chr6D 95.920 1005 37 3 1607 2609 291508930 291507928 0 1626
17 TraesCS3D01G151700 chr1D 96.088 997 35 3 610 1604 198494911 198495905 0 1622
18 TraesCS3D01G151700 chr1D 95.124 1005 46 2 1605 2609 462571820 462570819 0 1581
19 TraesCS3D01G151700 chr1D 94.950 1010 43 6 1604 2609 329177974 329178979 0 1576


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 TraesCS3D01G151700 chr3D 116051325 116053933 2608 False 4819 4819 100.000 1 2609 1 chr3D.!!$F1 2608
1 TraesCS3D01G151700 chr3D 99741796 99742790 994 True 1583 1583 95.314 1609 2609 1 chr3D.!!$R1 1000
2 TraesCS3D01G151700 chr5D 21545632 21547027 1395 True 2172 2172 94.789 210 1604 1 chr5D.!!$R1 1394
3 TraesCS3D01G151700 chr5D 399105386 399106378 992 False 1600 1600 95.613 1607 2609 1 chr5D.!!$F2 1002
4 TraesCS3D01G151700 chr5D 267149600 267150595 995 False 1585 1585 95.314 1607 2609 1 chr5D.!!$F1 1002
5 TraesCS3D01G151700 chr2D 476786428 476787821 1393 False 2065 2065 93.424 210 1604 1 chr2D.!!$F1 1394
6 TraesCS3D01G151700 chr2D 78329129 78330484 1355 True 1831 1831 90.948 223 1604 1 chr2D.!!$R1 1381
7 TraesCS3D01G151700 chr2D 446163950 446164945 995 True 1587 1587 95.319 1606 2609 1 chr2D.!!$R2 1003
8 TraesCS3D01G151700 chr7D 72149235 72150636 1401 False 2050 2050 93.196 211 1604 1 chr7D.!!$F1 1393
9 TraesCS3D01G151700 chr7D 593734280 593735643 1363 False 1895 1895 91.770 238 1604 1 chr7D.!!$F3 1366
10 TraesCS3D01G151700 chr7D 226566231 226567229 998 True 1600 1600 95.518 1606 2609 1 chr7D.!!$R1 1003
11 TraesCS3D01G151700 chr7D 283036410 283037408 998 False 1589 1589 95.314 1607 2609 1 chr7D.!!$F2 1002
12 TraesCS3D01G151700 chr2B 465666665 465668076 1411 True 1677 1677 88.445 210 1604 1 chr2B.!!$R2 1394
13 TraesCS3D01G151700 chr2B 71644974 71646102 1128 True 1650 1650 93.122 479 1604 1 chr2B.!!$R1 1125
14 TraesCS3D01G151700 chr2B 53302836 53304040 1204 False 1500 1500 89.727 209 1372 1 chr2B.!!$F1 1163
15 TraesCS3D01G151700 chr5A 599226414 599227834 1420 False 1670 1670 88.301 209 1604 1 chr5A.!!$F1 1395
16 TraesCS3D01G151700 chr6D 291507928 291508930 1002 True 1626 1626 95.920 1607 2609 1 chr6D.!!$R1 1002
17 TraesCS3D01G151700 chr1D 198494911 198495905 994 False 1622 1622 96.088 610 1604 1 chr1D.!!$F1 994
18 TraesCS3D01G151700 chr1D 462570819 462571820 1001 True 1581 1581 95.124 1605 2609 1 chr1D.!!$R1 1004
19 TraesCS3D01G151700 chr1D 329177974 329178979 1005 False 1576 1576 94.950 1604 2609 1 chr1D.!!$F2 1005

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
171 172 0.037605 AAGTTTACTCGGCTGGGTCG 60.038 55.0 0.0 0.0 0.00 4.79 F
359 360 0.178915 ATGGGCTATGGCGGTAGGTA 60.179 55.0 0.0 0.0 39.81 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1478 1.183030 TGGGGATATACACCTCGGCG 61.183 60.0 0.0 0.0 43.74 6.46 R
2264 2399 2.507471 AGGGGGAGAAGCAACATAAGAG 59.493 50.0 0.0 0.0 0.00 2.85 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
33 34 2.492090 CGAAGGGCTCGGACTCAG 59.508 66.667 0.00 0.00 44.20 3.35
34 35 2.896443 GAAGGGCTCGGACTCAGG 59.104 66.667 0.00 0.00 0.00 3.86
35 36 1.985116 GAAGGGCTCGGACTCAGGT 60.985 63.158 0.00 0.00 0.00 4.00
36 37 0.683504 GAAGGGCTCGGACTCAGGTA 60.684 60.000 0.00 0.00 0.00 3.08
37 38 0.252103 AAGGGCTCGGACTCAGGTAA 60.252 55.000 0.00 0.00 0.00 2.85
38 39 0.252103 AGGGCTCGGACTCAGGTAAA 60.252 55.000 0.00 0.00 0.00 2.01
39 40 0.611714 GGGCTCGGACTCAGGTAAAA 59.388 55.000 0.00 0.00 0.00 1.52
40 41 1.405661 GGGCTCGGACTCAGGTAAAAG 60.406 57.143 0.00 0.00 0.00 2.27
41 42 1.405661 GGCTCGGACTCAGGTAAAAGG 60.406 57.143 0.00 0.00 0.00 3.11
42 43 1.405661 GCTCGGACTCAGGTAAAAGGG 60.406 57.143 0.00 0.00 0.00 3.95
43 44 0.611714 TCGGACTCAGGTAAAAGGGC 59.388 55.000 0.00 0.00 0.00 5.19
44 45 0.739813 CGGACTCAGGTAAAAGGGCG 60.740 60.000 0.00 0.00 0.00 6.13
45 46 0.392595 GGACTCAGGTAAAAGGGCGG 60.393 60.000 0.00 0.00 0.00 6.13
46 47 0.392595 GACTCAGGTAAAAGGGCGGG 60.393 60.000 0.00 0.00 0.00 6.13
47 48 1.077716 CTCAGGTAAAAGGGCGGGG 60.078 63.158 0.00 0.00 0.00 5.73
48 49 1.539372 TCAGGTAAAAGGGCGGGGA 60.539 57.895 0.00 0.00 0.00 4.81
49 50 0.917333 TCAGGTAAAAGGGCGGGGAT 60.917 55.000 0.00 0.00 0.00 3.85
50 51 0.751643 CAGGTAAAAGGGCGGGGATG 60.752 60.000 0.00 0.00 0.00 3.51
51 52 1.455032 GGTAAAAGGGCGGGGATGG 60.455 63.158 0.00 0.00 0.00 3.51
52 53 2.125326 GTAAAAGGGCGGGGATGGC 61.125 63.158 0.00 0.00 0.00 4.40
59 60 4.440829 GCGGGGATGGCCAAAGGA 62.441 66.667 10.96 0.00 35.15 3.36
60 61 2.124151 CGGGGATGGCCAAAGGAG 60.124 66.667 10.96 0.00 35.15 3.69
61 62 2.280079 GGGGATGGCCAAAGGAGG 59.720 66.667 10.96 0.00 35.15 4.30
69 70 2.437359 CCAAAGGAGGCTGCGAGG 60.437 66.667 0.00 0.00 0.00 4.63
70 71 2.348998 CAAAGGAGGCTGCGAGGT 59.651 61.111 0.00 0.00 0.00 3.85
71 72 1.596934 CAAAGGAGGCTGCGAGGTA 59.403 57.895 0.00 0.00 0.00 3.08
72 73 0.460987 CAAAGGAGGCTGCGAGGTAG 60.461 60.000 0.00 0.00 0.00 3.18
73 74 2.245438 AAAGGAGGCTGCGAGGTAGC 62.245 60.000 0.00 0.00 40.44 3.58
74 75 4.577246 GGAGGCTGCGAGGTAGCG 62.577 72.222 0.00 0.00 42.02 4.26
75 76 4.577246 GAGGCTGCGAGGTAGCGG 62.577 72.222 0.00 0.00 42.02 5.52
95 96 4.139234 GGGGCGGTAGACGGTCAC 62.139 72.222 11.27 6.55 44.51 3.67
96 97 4.139234 GGGCGGTAGACGGTCACC 62.139 72.222 11.27 13.85 44.51 4.02
126 127 4.814294 GGCGACGTAGCAGTGGGG 62.814 72.222 22.25 0.00 39.27 4.96
127 128 4.814294 GCGACGTAGCAGTGGGGG 62.814 72.222 16.21 0.00 37.05 5.40
128 129 3.379445 CGACGTAGCAGTGGGGGT 61.379 66.667 0.00 0.00 0.00 4.95
129 130 2.264794 GACGTAGCAGTGGGGGTG 59.735 66.667 0.00 0.00 0.00 4.61
130 131 3.310860 GACGTAGCAGTGGGGGTGG 62.311 68.421 0.00 0.00 0.00 4.61
131 132 4.096003 CGTAGCAGTGGGGGTGGG 62.096 72.222 0.00 0.00 0.00 4.61
132 133 3.728373 GTAGCAGTGGGGGTGGGG 61.728 72.222 0.00 0.00 0.00 4.96
133 134 3.948360 TAGCAGTGGGGGTGGGGA 61.948 66.667 0.00 0.00 0.00 4.81
134 135 3.943137 TAGCAGTGGGGGTGGGGAG 62.943 68.421 0.00 0.00 0.00 4.30
140 141 4.358181 GGGGGTGGGGAGGTGGTA 62.358 72.222 0.00 0.00 0.00 3.25
141 142 2.204182 GGGGTGGGGAGGTGGTAA 60.204 66.667 0.00 0.00 0.00 2.85
142 143 1.853565 GGGGTGGGGAGGTGGTAAA 60.854 63.158 0.00 0.00 0.00 2.01
143 144 1.689412 GGGTGGGGAGGTGGTAAAG 59.311 63.158 0.00 0.00 0.00 1.85
144 145 1.138228 GGGTGGGGAGGTGGTAAAGT 61.138 60.000 0.00 0.00 0.00 2.66
145 146 0.037734 GGTGGGGAGGTGGTAAAGTG 59.962 60.000 0.00 0.00 0.00 3.16
146 147 0.037734 GTGGGGAGGTGGTAAAGTGG 59.962 60.000 0.00 0.00 0.00 4.00
147 148 1.001269 GGGGAGGTGGTAAAGTGGC 60.001 63.158 0.00 0.00 0.00 5.01
148 149 1.001269 GGGAGGTGGTAAAGTGGCC 60.001 63.158 0.00 0.00 0.00 5.36
149 150 1.376812 GGAGGTGGTAAAGTGGCCG 60.377 63.158 0.00 0.00 0.00 6.13
150 151 1.373812 GAGGTGGTAAAGTGGCCGT 59.626 57.895 0.00 0.00 0.00 5.68
151 152 0.609662 GAGGTGGTAAAGTGGCCGTA 59.390 55.000 0.00 0.00 0.00 4.02
152 153 1.002315 GAGGTGGTAAAGTGGCCGTAA 59.998 52.381 0.00 0.00 0.00 3.18
153 154 1.420891 AGGTGGTAAAGTGGCCGTAAA 59.579 47.619 0.00 0.00 0.00 2.01
154 155 1.808343 GGTGGTAAAGTGGCCGTAAAG 59.192 52.381 0.00 0.00 0.00 1.85
155 156 2.497138 GTGGTAAAGTGGCCGTAAAGT 58.503 47.619 0.00 0.00 0.00 2.66
156 157 2.880268 GTGGTAAAGTGGCCGTAAAGTT 59.120 45.455 0.00 0.00 0.00 2.66
157 158 3.316029 GTGGTAAAGTGGCCGTAAAGTTT 59.684 43.478 0.00 0.00 0.00 2.66
158 159 4.514816 GTGGTAAAGTGGCCGTAAAGTTTA 59.485 41.667 0.00 0.00 0.00 2.01
159 160 4.514816 TGGTAAAGTGGCCGTAAAGTTTAC 59.485 41.667 17.21 17.21 39.70 2.01
160 161 4.756642 GGTAAAGTGGCCGTAAAGTTTACT 59.243 41.667 21.55 6.11 40.05 2.24
161 162 5.106948 GGTAAAGTGGCCGTAAAGTTTACTC 60.107 44.000 21.55 13.06 40.05 2.59
162 163 2.680577 AGTGGCCGTAAAGTTTACTCG 58.319 47.619 20.60 12.80 0.00 4.18
163 164 1.728425 GTGGCCGTAAAGTTTACTCGG 59.272 52.381 20.60 18.43 43.37 4.63
167 168 1.997606 CCGTAAAGTTTACTCGGCTGG 59.002 52.381 20.60 11.18 35.01 4.85
168 169 1.997606 CGTAAAGTTTACTCGGCTGGG 59.002 52.381 20.60 0.00 0.00 4.45
169 170 2.611224 CGTAAAGTTTACTCGGCTGGGT 60.611 50.000 20.60 2.17 0.00 4.51
170 171 2.180432 AAAGTTTACTCGGCTGGGTC 57.820 50.000 0.00 0.00 0.00 4.46
171 172 0.037605 AAGTTTACTCGGCTGGGTCG 60.038 55.000 0.00 0.00 0.00 4.79
172 173 0.896940 AGTTTACTCGGCTGGGTCGA 60.897 55.000 0.00 0.00 37.31 4.20
181 182 4.135153 CTGGGTCGAGGCCGAGTG 62.135 72.222 0.00 0.00 46.52 3.51
182 183 4.671590 TGGGTCGAGGCCGAGTGA 62.672 66.667 0.00 0.00 46.52 3.41
183 184 3.148279 GGGTCGAGGCCGAGTGAT 61.148 66.667 0.00 0.00 46.52 3.06
184 185 2.722201 GGGTCGAGGCCGAGTGATT 61.722 63.158 0.00 0.00 46.52 2.57
185 186 1.218316 GGTCGAGGCCGAGTGATTT 59.782 57.895 0.00 0.00 46.52 2.17
186 187 0.391263 GGTCGAGGCCGAGTGATTTT 60.391 55.000 0.00 0.00 46.52 1.82
187 188 1.134907 GGTCGAGGCCGAGTGATTTTA 60.135 52.381 0.00 0.00 46.52 1.52
188 189 2.194271 GTCGAGGCCGAGTGATTTTAG 58.806 52.381 0.00 0.00 46.52 1.85
189 190 1.822990 TCGAGGCCGAGTGATTTTAGT 59.177 47.619 0.00 0.00 40.30 2.24
190 191 2.159282 TCGAGGCCGAGTGATTTTAGTC 60.159 50.000 0.00 0.00 40.30 2.59
191 192 2.194271 GAGGCCGAGTGATTTTAGTCG 58.806 52.381 0.00 0.00 41.83 4.18
192 193 0.651031 GGCCGAGTGATTTTAGTCGC 59.349 55.000 0.00 0.00 41.07 5.19
193 194 0.651031 GCCGAGTGATTTTAGTCGCC 59.349 55.000 0.00 0.00 41.07 5.54
194 195 1.287425 CCGAGTGATTTTAGTCGCCC 58.713 55.000 0.00 0.00 41.07 6.13
195 196 0.921347 CGAGTGATTTTAGTCGCCCG 59.079 55.000 0.00 0.00 36.80 6.13
196 197 1.734707 CGAGTGATTTTAGTCGCCCGT 60.735 52.381 0.00 0.00 36.80 5.28
197 198 1.925185 GAGTGATTTTAGTCGCCCGTC 59.075 52.381 0.00 0.00 0.00 4.79
198 199 0.643820 GTGATTTTAGTCGCCCGTCG 59.356 55.000 0.00 0.00 40.15 5.12
199 200 0.527113 TGATTTTAGTCGCCCGTCGA 59.473 50.000 0.00 0.00 46.29 4.20
359 360 0.178915 ATGGGCTATGGCGGTAGGTA 60.179 55.000 0.00 0.00 39.81 3.08
361 362 1.288127 GGCTATGGCGGTAGGTACG 59.712 63.158 0.00 0.00 39.81 3.67
371 372 1.210155 GTAGGTACGTTGACGGCGT 59.790 57.895 14.65 14.65 44.95 5.68
424 426 2.281761 GCCTACCGCCATGGGATG 60.282 66.667 15.13 0.00 44.64 3.51
777 829 8.684520 TGTGCATTTATGACACATTTATGATGA 58.315 29.630 12.65 0.00 38.72 2.92
828 880 3.453868 GGGTTAGTGTTAGGGTTAGGGA 58.546 50.000 0.00 0.00 0.00 4.20
866 960 2.645320 TGTTGGGGGTTATGGTTAGGA 58.355 47.619 0.00 0.00 0.00 2.94
1069 1168 3.609853 CTTGGAAATGACGATGAAGGGA 58.390 45.455 0.00 0.00 0.00 4.20
1123 1222 9.897744 CAAGCTTTGATGATCTTGTAGTTAAAA 57.102 29.630 0.00 0.00 33.27 1.52
1182 1282 5.366460 GAGGTTAAGCTTATTGGGAGGTAC 58.634 45.833 8.87 0.00 0.00 3.34
1184 1284 2.327200 AAGCTTATTGGGAGGTACGC 57.673 50.000 0.00 0.00 0.00 4.42
1200 1300 2.398554 CGCCGTTGGATTGGGAGTG 61.399 63.158 0.00 0.00 0.00 3.51
1239 1339 0.413037 TGGCCATCACCTCCCAATTT 59.587 50.000 0.00 0.00 0.00 1.82
1377 1478 4.225942 TCCTCCCCAATACATGATGATAGC 59.774 45.833 0.00 0.00 0.00 2.97
1499 1624 6.765036 GCTATTCCTCATGTTGAAGAAGATGA 59.235 38.462 0.00 0.00 39.04 2.92
1550 1675 1.550524 TGCTCAAGAGGATGCTTACGT 59.449 47.619 0.00 0.00 0.00 3.57
1555 1680 1.115467 AGAGGATGCTTACGTGGAGG 58.885 55.000 0.00 0.00 0.00 4.30
2003 2135 2.361438 ACGATCGGGGAACAGAATAGAC 59.639 50.000 20.98 0.00 38.30 2.59
2064 2196 0.613260 CAATCGGGACCCTGTTCTGA 59.387 55.000 9.41 0.00 30.22 3.27
2077 2209 2.583441 TTCTGACACCCTGCCGGAG 61.583 63.158 5.05 0.00 34.64 4.63
2264 2399 4.511826 ACGAGCTTTGCTATTATAGTTGGC 59.488 41.667 0.94 1.86 39.88 4.52
2443 2578 9.283768 ACTTGATGTATGTTTTAGTGATCAACA 57.716 29.630 0.00 0.00 34.97 3.33
2454 2589 0.037447 TGATCAACATGCGGGTTCCA 59.963 50.000 0.00 0.00 0.00 3.53
2490 2625 1.917872 TAGGGGTTGGCACATGTTTC 58.082 50.000 0.00 0.00 39.30 2.78
2499 2634 1.069227 GGCACATGTTTCCGTCTTGAC 60.069 52.381 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.683504 TACCTGAGTCCGAGCCCTTC 60.684 60.000 0.00 0.00 0.00 3.46
18 19 0.252103 TTACCTGAGTCCGAGCCCTT 60.252 55.000 0.00 0.00 0.00 3.95
19 20 0.252103 TTTACCTGAGTCCGAGCCCT 60.252 55.000 0.00 0.00 0.00 5.19
20 21 0.611714 TTTTACCTGAGTCCGAGCCC 59.388 55.000 0.00 0.00 0.00 5.19
21 22 1.405661 CCTTTTACCTGAGTCCGAGCC 60.406 57.143 0.00 0.00 0.00 4.70
22 23 1.405661 CCCTTTTACCTGAGTCCGAGC 60.406 57.143 0.00 0.00 0.00 5.03
23 24 1.405661 GCCCTTTTACCTGAGTCCGAG 60.406 57.143 0.00 0.00 0.00 4.63
24 25 0.611714 GCCCTTTTACCTGAGTCCGA 59.388 55.000 0.00 0.00 0.00 4.55
25 26 0.739813 CGCCCTTTTACCTGAGTCCG 60.740 60.000 0.00 0.00 0.00 4.79
26 27 0.392595 CCGCCCTTTTACCTGAGTCC 60.393 60.000 0.00 0.00 0.00 3.85
27 28 0.392595 CCCGCCCTTTTACCTGAGTC 60.393 60.000 0.00 0.00 0.00 3.36
28 29 1.683441 CCCGCCCTTTTACCTGAGT 59.317 57.895 0.00 0.00 0.00 3.41
29 30 1.077716 CCCCGCCCTTTTACCTGAG 60.078 63.158 0.00 0.00 0.00 3.35
30 31 0.917333 ATCCCCGCCCTTTTACCTGA 60.917 55.000 0.00 0.00 0.00 3.86
31 32 0.751643 CATCCCCGCCCTTTTACCTG 60.752 60.000 0.00 0.00 0.00 4.00
32 33 1.613061 CATCCCCGCCCTTTTACCT 59.387 57.895 0.00 0.00 0.00 3.08
33 34 1.455032 CCATCCCCGCCCTTTTACC 60.455 63.158 0.00 0.00 0.00 2.85
34 35 2.125326 GCCATCCCCGCCCTTTTAC 61.125 63.158 0.00 0.00 0.00 2.01
35 36 2.277404 GCCATCCCCGCCCTTTTA 59.723 61.111 0.00 0.00 0.00 1.52
36 37 4.777854 GGCCATCCCCGCCCTTTT 62.778 66.667 0.00 0.00 40.78 2.27
42 43 4.440829 TCCTTTGGCCATCCCCGC 62.441 66.667 6.09 0.00 0.00 6.13
43 44 2.124151 CTCCTTTGGCCATCCCCG 60.124 66.667 6.09 0.00 0.00 5.73
44 45 2.280079 CCTCCTTTGGCCATCCCC 59.720 66.667 6.09 0.00 0.00 4.81
45 46 2.442830 GCCTCCTTTGGCCATCCC 60.443 66.667 6.09 0.00 46.82 3.85
52 53 1.899437 TACCTCGCAGCCTCCTTTGG 61.899 60.000 0.00 0.00 0.00 3.28
53 54 0.460987 CTACCTCGCAGCCTCCTTTG 60.461 60.000 0.00 0.00 0.00 2.77
54 55 1.901085 CTACCTCGCAGCCTCCTTT 59.099 57.895 0.00 0.00 0.00 3.11
55 56 2.726351 GCTACCTCGCAGCCTCCTT 61.726 63.158 0.00 0.00 32.68 3.36
56 57 3.151022 GCTACCTCGCAGCCTCCT 61.151 66.667 0.00 0.00 32.68 3.69
57 58 4.577246 CGCTACCTCGCAGCCTCC 62.577 72.222 0.00 0.00 35.53 4.30
58 59 4.577246 CCGCTACCTCGCAGCCTC 62.577 72.222 0.00 0.00 35.53 4.70
78 79 4.139234 GTGACCGTCTACCGCCCC 62.139 72.222 0.00 0.00 34.38 5.80
79 80 4.139234 GGTGACCGTCTACCGCCC 62.139 72.222 0.00 0.00 34.38 6.13
83 84 2.361610 TCCCGGTGACCGTCTACC 60.362 66.667 23.73 5.27 46.80 3.18
84 85 2.413142 CCTCCCGGTGACCGTCTAC 61.413 68.421 23.73 0.00 46.80 2.59
85 86 2.044650 CCTCCCGGTGACCGTCTA 60.045 66.667 23.73 6.65 46.80 2.59
86 87 4.296729 ACCTCCCGGTGACCGTCT 62.297 66.667 23.73 0.00 46.80 4.18
101 102 4.849329 CTACGTCGCCGGCTCACC 62.849 72.222 26.68 8.16 38.78 4.02
109 110 4.814294 CCCCACTGCTACGTCGCC 62.814 72.222 9.82 0.00 0.00 5.54
110 111 4.814294 CCCCCACTGCTACGTCGC 62.814 72.222 4.90 4.90 0.00 5.19
111 112 3.379445 ACCCCCACTGCTACGTCG 61.379 66.667 0.00 0.00 0.00 5.12
112 113 2.264794 CACCCCCACTGCTACGTC 59.735 66.667 0.00 0.00 0.00 4.34
113 114 3.319198 CCACCCCCACTGCTACGT 61.319 66.667 0.00 0.00 0.00 3.57
114 115 4.096003 CCCACCCCCACTGCTACG 62.096 72.222 0.00 0.00 0.00 3.51
115 116 3.728373 CCCCACCCCCACTGCTAC 61.728 72.222 0.00 0.00 0.00 3.58
116 117 3.943137 CTCCCCACCCCCACTGCTA 62.943 68.421 0.00 0.00 0.00 3.49
123 124 3.895253 TTACCACCTCCCCACCCCC 62.895 68.421 0.00 0.00 0.00 5.40
124 125 1.853565 TTTACCACCTCCCCACCCC 60.854 63.158 0.00 0.00 0.00 4.95
125 126 1.138228 ACTTTACCACCTCCCCACCC 61.138 60.000 0.00 0.00 0.00 4.61
126 127 0.037734 CACTTTACCACCTCCCCACC 59.962 60.000 0.00 0.00 0.00 4.61
127 128 0.037734 CCACTTTACCACCTCCCCAC 59.962 60.000 0.00 0.00 0.00 4.61
128 129 1.785353 GCCACTTTACCACCTCCCCA 61.785 60.000 0.00 0.00 0.00 4.96
129 130 1.001269 GCCACTTTACCACCTCCCC 60.001 63.158 0.00 0.00 0.00 4.81
130 131 1.001269 GGCCACTTTACCACCTCCC 60.001 63.158 0.00 0.00 0.00 4.30
131 132 1.376812 CGGCCACTTTACCACCTCC 60.377 63.158 2.24 0.00 0.00 4.30
132 133 0.609662 TACGGCCACTTTACCACCTC 59.390 55.000 2.24 0.00 0.00 3.85
133 134 1.058284 TTACGGCCACTTTACCACCT 58.942 50.000 2.24 0.00 0.00 4.00
134 135 1.808343 CTTTACGGCCACTTTACCACC 59.192 52.381 2.24 0.00 0.00 4.61
135 136 2.497138 ACTTTACGGCCACTTTACCAC 58.503 47.619 2.24 0.00 0.00 4.16
136 137 2.934886 ACTTTACGGCCACTTTACCA 57.065 45.000 2.24 0.00 0.00 3.25
137 138 4.756642 AGTAAACTTTACGGCCACTTTACC 59.243 41.667 2.24 0.00 0.00 2.85
138 139 5.388786 CGAGTAAACTTTACGGCCACTTTAC 60.389 44.000 2.24 4.89 0.00 2.01
139 140 4.685628 CGAGTAAACTTTACGGCCACTTTA 59.314 41.667 2.24 0.00 0.00 1.85
140 141 3.495753 CGAGTAAACTTTACGGCCACTTT 59.504 43.478 2.24 0.00 0.00 2.66
141 142 3.062042 CGAGTAAACTTTACGGCCACTT 58.938 45.455 2.24 0.00 0.00 3.16
142 143 2.611224 CCGAGTAAACTTTACGGCCACT 60.611 50.000 2.24 0.00 37.32 4.00
143 144 1.728425 CCGAGTAAACTTTACGGCCAC 59.272 52.381 2.24 0.00 37.32 5.01
144 145 2.083167 CCGAGTAAACTTTACGGCCA 57.917 50.000 2.24 0.00 37.32 5.36
147 148 1.997606 CCAGCCGAGTAAACTTTACGG 59.002 52.381 0.00 0.00 45.26 4.02
148 149 1.997606 CCCAGCCGAGTAAACTTTACG 59.002 52.381 6.11 0.00 0.00 3.18
149 150 2.998670 GACCCAGCCGAGTAAACTTTAC 59.001 50.000 3.77 3.77 0.00 2.01
150 151 2.353011 CGACCCAGCCGAGTAAACTTTA 60.353 50.000 0.00 0.00 0.00 1.85
151 152 1.607251 CGACCCAGCCGAGTAAACTTT 60.607 52.381 0.00 0.00 0.00 2.66
152 153 0.037605 CGACCCAGCCGAGTAAACTT 60.038 55.000 0.00 0.00 0.00 2.66
153 154 0.896940 TCGACCCAGCCGAGTAAACT 60.897 55.000 0.00 0.00 0.00 2.66
154 155 0.458025 CTCGACCCAGCCGAGTAAAC 60.458 60.000 0.00 0.00 45.89 2.01
155 156 1.888018 CTCGACCCAGCCGAGTAAA 59.112 57.895 0.00 0.00 45.89 2.01
156 157 3.599584 CTCGACCCAGCCGAGTAA 58.400 61.111 0.00 0.00 45.89 2.24
164 165 4.135153 CACTCGGCCTCGACCCAG 62.135 72.222 0.00 0.00 40.88 4.45
165 166 3.957435 ATCACTCGGCCTCGACCCA 62.957 63.158 0.00 0.00 40.88 4.51
166 167 2.240162 AAATCACTCGGCCTCGACCC 62.240 60.000 0.00 0.00 40.88 4.46
167 168 0.391263 AAAATCACTCGGCCTCGACC 60.391 55.000 0.00 0.00 40.88 4.79
168 169 2.194271 CTAAAATCACTCGGCCTCGAC 58.806 52.381 0.00 0.00 40.88 4.20
169 170 1.822990 ACTAAAATCACTCGGCCTCGA 59.177 47.619 0.00 0.00 43.86 4.04
170 171 2.194271 GACTAAAATCACTCGGCCTCG 58.806 52.381 0.00 0.00 37.82 4.63
171 172 2.194271 CGACTAAAATCACTCGGCCTC 58.806 52.381 0.00 0.00 0.00 4.70
172 173 1.739371 GCGACTAAAATCACTCGGCCT 60.739 52.381 0.00 0.00 0.00 5.19
173 174 0.651031 GCGACTAAAATCACTCGGCC 59.349 55.000 0.00 0.00 0.00 6.13
174 175 0.651031 GGCGACTAAAATCACTCGGC 59.349 55.000 0.00 0.00 43.25 5.54
175 176 1.287425 GGGCGACTAAAATCACTCGG 58.713 55.000 0.00 0.00 0.00 4.63
176 177 0.921347 CGGGCGACTAAAATCACTCG 59.079 55.000 0.00 0.00 0.00 4.18
177 178 1.925185 GACGGGCGACTAAAATCACTC 59.075 52.381 0.00 0.00 0.00 3.51
178 179 1.734707 CGACGGGCGACTAAAATCACT 60.735 52.381 0.00 0.00 44.57 3.41
179 180 0.643820 CGACGGGCGACTAAAATCAC 59.356 55.000 0.00 0.00 44.57 3.06
180 181 0.527113 TCGACGGGCGACTAAAATCA 59.473 50.000 0.00 0.00 45.59 2.57
181 182 1.197910 CTCGACGGGCGACTAAAATC 58.802 55.000 0.00 0.00 45.59 2.17
182 183 0.804933 GCTCGACGGGCGACTAAAAT 60.805 55.000 2.80 0.00 45.59 1.82
183 184 1.444895 GCTCGACGGGCGACTAAAA 60.445 57.895 2.80 0.00 45.59 1.52
184 185 2.180017 GCTCGACGGGCGACTAAA 59.820 61.111 2.80 0.00 45.59 1.85
185 186 3.818787 GGCTCGACGGGCGACTAA 61.819 66.667 14.60 0.00 45.59 2.24
191 192 4.933064 CTCATCGGCTCGACGGGC 62.933 72.222 12.38 12.38 39.18 6.13
192 193 4.271816 CCTCATCGGCTCGACGGG 62.272 72.222 0.00 0.00 39.18 5.28
193 194 4.271816 CCCTCATCGGCTCGACGG 62.272 72.222 0.00 2.05 39.18 4.79
194 195 4.933064 GCCCTCATCGGCTCGACG 62.933 72.222 0.00 0.00 46.10 5.12
201 202 1.472480 ACGAAATTTTGCCCTCATCGG 59.528 47.619 5.27 0.00 33.45 4.18
202 203 2.095263 ACACGAAATTTTGCCCTCATCG 60.095 45.455 5.27 0.00 35.16 3.84
203 204 3.575965 ACACGAAATTTTGCCCTCATC 57.424 42.857 5.27 0.00 0.00 2.92
204 205 3.573967 AGAACACGAAATTTTGCCCTCAT 59.426 39.130 5.27 0.00 0.00 2.90
205 206 2.955660 AGAACACGAAATTTTGCCCTCA 59.044 40.909 5.27 0.00 0.00 3.86
206 207 3.004315 TCAGAACACGAAATTTTGCCCTC 59.996 43.478 5.27 0.06 0.00 4.30
207 208 2.955660 TCAGAACACGAAATTTTGCCCT 59.044 40.909 5.27 0.00 0.00 5.19
312 313 3.784412 CGTGCAAACCTACCGCCG 61.784 66.667 0.00 0.00 0.00 6.46
347 348 0.174162 GTCAACGTACCTACCGCCAT 59.826 55.000 0.00 0.00 0.00 4.40
361 362 3.103911 CCGTCAGACGCCGTCAAC 61.104 66.667 20.65 15.35 40.91 3.18
422 424 2.082140 TCAGTATCCTACCGCCACAT 57.918 50.000 0.00 0.00 0.00 3.21
424 426 1.538419 GCTTCAGTATCCTACCGCCAC 60.538 57.143 0.00 0.00 0.00 5.01
466 468 1.236026 TCCACCTCCCAGGACCCTAT 61.236 60.000 0.00 0.00 37.67 2.57
718 728 5.777732 TCAACACCTAGGGTTTGCAATAAAT 59.222 36.000 14.81 0.00 31.02 1.40
777 829 4.346478 ACCCTAACCCTTGCCATAAATT 57.654 40.909 0.00 0.00 0.00 1.82
828 880 6.045106 CCCCAACATAACCACTATAACCCTAT 59.955 42.308 0.00 0.00 0.00 2.57
1069 1168 4.892934 TGTGTCAAAAACCATAGCCTCTTT 59.107 37.500 0.00 0.00 0.00 2.52
1123 1222 7.335422 GTCATTCCAATGTAAGACACTTCTCAT 59.665 37.037 0.00 0.00 37.65 2.90
1131 1231 7.148086 GCATTTAGGTCATTCCAATGTAAGACA 60.148 37.037 0.00 0.00 39.02 3.41
1182 1282 2.046314 ACTCCCAATCCAACGGCG 60.046 61.111 4.80 4.80 0.00 6.46
1184 1284 1.271379 ACTTCACTCCCAATCCAACGG 60.271 52.381 0.00 0.00 0.00 4.44
1200 1300 4.750598 GCCATACTCTTTAATCGGGACTTC 59.249 45.833 0.00 0.00 0.00 3.01
1239 1339 5.497464 TGTCCTTGTACAGATTCCAATGA 57.503 39.130 0.00 0.00 0.00 2.57
1249 1349 3.673809 GCGTCTACTTTGTCCTTGTACAG 59.326 47.826 0.00 0.00 0.00 2.74
1377 1478 1.183030 TGGGGATATACACCTCGGCG 61.183 60.000 0.00 0.00 43.74 6.46
1499 1624 5.472478 GCATCATCATCAACATGACCACTAT 59.528 40.000 0.00 0.00 42.05 2.12
1594 1719 4.500545 GGAGACGTATCACTGCAGAATGAT 60.501 45.833 23.35 21.30 39.69 2.45
2264 2399 2.507471 AGGGGGAGAAGCAACATAAGAG 59.493 50.000 0.00 0.00 0.00 2.85
2454 2589 2.376518 CCCTATGCATAGGTTCATGGGT 59.623 50.000 38.55 2.48 46.84 4.51
2499 2634 2.354805 CCCCAAAGTTTCTACCGGAGAG 60.355 54.545 9.46 4.89 34.93 3.20


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

AutoCloner maintained by Alex Coulton.