Multiple sequence alignment - TraesCS3A01G201300

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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 TraesCS3A01G201300 chr3A 100.000 3382 0 0 1 3382 335997104 335993723 0.000000e+00 6246
1 TraesCS3A01G201300 chr3D 97.783 2706 57 3 675 3379 253617284 253619987 0.000000e+00 4662
2 TraesCS3A01G201300 chr3D 95.858 169 4 2 488 653 253617121 253617289 1.550000e-68 270
3 TraesCS3A01G201300 chr3D 84.579 214 21 4 256 458 611202809 611202597 5.720000e-48 202
4 TraesCS3A01G201300 chr3B 92.608 2611 122 25 678 3258 308394437 308391868 0.000000e+00 3687
5 TraesCS3A01G201300 chr3B 86.916 214 16 4 256 457 166126070 166126283 2.620000e-56 230
6 TraesCS3A01G201300 chr3B 93.913 115 6 1 573 687 308403983 308403870 4.490000e-39 172
7 TraesCS3A01G201300 chrUn 97.665 257 6 0 1 257 73445685 73445941 3.100000e-120 442
8 TraesCS3A01G201300 chrUn 87.054 224 17 4 246 457 231014248 231014025 3.370000e-60 243
9 TraesCS3A01G201300 chrUn 87.558 217 15 4 253 457 214071185 214070969 1.210000e-59 241
10 TraesCS3A01G201300 chrUn 86.222 225 17 4 246 457 204477900 204477677 7.300000e-57 231
11 TraesCS3A01G201300 chr5A 97.276 257 7 0 1 257 32946701 32946445 1.440000e-118 436
12 TraesCS3A01G201300 chr6B 96.887 257 7 1 1 257 151888075 151888330 2.410000e-116 429
13 TraesCS3A01G201300 chr6B 96.124 258 9 1 1 258 80813551 80813807 1.450000e-113 420
14 TraesCS3A01G201300 chr6B 85.930 199 25 3 259 456 80688730 80688534 3.420000e-50 209
15 TraesCS3A01G201300 chr2B 96.887 257 7 1 1 257 657478426 657478171 2.410000e-116 429
16 TraesCS3A01G201300 chr5B 96.124 258 9 1 1 258 535097072 535096816 1.450000e-113 420
17 TraesCS3A01G201300 chr5B 94.139 273 14 2 1 272 52323397 52323668 6.750000e-112 414
18 TraesCS3A01G201300 chr2A 96.124 258 9 1 1 258 441107416 441107672 1.450000e-113 420
19 TraesCS3A01G201300 chr2A 85.377 212 21 5 259 460 124163979 124163768 9.510000e-51 211
20 TraesCS3A01G201300 chr4D 94.981 259 13 0 1 259 273977296 273977038 1.130000e-109 407
21 TraesCS3A01G201300 chr4D 87.963 216 15 4 253 457 439770543 439770758 9.370000e-61 244
22 TraesCS3A01G201300 chr6A 87.907 215 15 4 256 459 436534178 436533964 3.370000e-60 243
23 TraesCS3A01G201300 chr6D 87.383 214 14 8 256 458 461412797 461413008 2.030000e-57 233
24 TraesCS3A01G201300 chr6D 86.792 212 17 4 256 456 105813611 105813400 3.400000e-55 226
25 TraesCS3A01G201300 chr6D 86.792 212 17 4 256 456 105814513 105814302 3.400000e-55 226
26 TraesCS3A01G201300 chr7B 86.916 214 17 4 256 458 378382689 378382476 2.620000e-56 230
27 TraesCS3A01G201300 chr7D 86.449 214 17 4 255 457 373582466 373582254 1.220000e-54 224
28 TraesCS3A01G201300 chr1B 85.849 212 18 3 256 456 642430788 642430998 7.350000e-52 215


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 TraesCS3A01G201300 chr3A 335993723 335997104 3381 True 6246 6246 100.0000 1 3382 1 chr3A.!!$R1 3381
1 TraesCS3A01G201300 chr3D 253617121 253619987 2866 False 2466 4662 96.8205 488 3379 2 chr3D.!!$F1 2891
2 TraesCS3A01G201300 chr3B 308391868 308394437 2569 True 3687 3687 92.6080 678 3258 1 chr3B.!!$R1 2580
3 TraesCS3A01G201300 chr6D 105813400 105814513 1113 True 226 226 86.7920 256 456 2 chr6D.!!$R1 200

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
665 1203 0.040351 CACAGGGGGAGAGAGAGACA 59.960 60.000 0.0 0.0 0.0 3.41 F
670 1208 0.325203 GGGGAGAGAGAGACAGGCTT 60.325 60.000 0.0 0.0 0.0 4.35 F
1375 1917 1.004891 GAAGGATGGGGAGGAGGGT 59.995 63.158 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 2256 1.134818 TCCGGGTCAATGTCATCTTCG 60.135 52.381 0.0 0.0 0.0 3.79 R
1810 2352 1.361204 TCCTGCCAGTCCTGAAATGA 58.639 50.000 0.0 0.0 0.0 2.57 R
2894 3448 0.391130 TGACAGCTTCGTATGGGCAC 60.391 55.000 0.0 0.0 0.0 5.01 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
36 37 9.896645 AAGAATTTCTTAAGTGCATCATCTAGA 57.103 29.630 9.92 0.00 34.42 2.43
82 83 6.351327 GTTTAGATAAAACATCGCTCAGCT 57.649 37.500 0.00 0.00 45.72 4.24
83 84 6.776094 GTTTAGATAAAACATCGCTCAGCTT 58.224 36.000 0.00 0.00 45.72 3.74
84 85 4.871993 AGATAAAACATCGCTCAGCTTG 57.128 40.909 0.00 0.00 0.00 4.01
85 86 4.256920 AGATAAAACATCGCTCAGCTTGT 58.743 39.130 0.00 0.00 0.00 3.16
86 87 4.697352 AGATAAAACATCGCTCAGCTTGTT 59.303 37.500 8.60 8.60 35.29 2.83
87 88 5.874810 AGATAAAACATCGCTCAGCTTGTTA 59.125 36.000 13.45 2.35 33.66 2.41
88 89 3.813529 AAACATCGCTCAGCTTGTTAC 57.186 42.857 13.45 0.00 33.66 2.50
89 90 2.455674 ACATCGCTCAGCTTGTTACA 57.544 45.000 0.00 0.00 0.00 2.41
90 91 2.977914 ACATCGCTCAGCTTGTTACAT 58.022 42.857 0.00 0.00 0.00 2.29
91 92 2.674852 ACATCGCTCAGCTTGTTACATG 59.325 45.455 0.00 0.00 0.00 3.21
92 93 1.725641 TCGCTCAGCTTGTTACATGG 58.274 50.000 0.00 0.00 0.00 3.66
93 94 1.275010 TCGCTCAGCTTGTTACATGGA 59.725 47.619 0.00 0.00 0.00 3.41
94 95 1.394917 CGCTCAGCTTGTTACATGGAC 59.605 52.381 0.00 0.00 0.00 4.02
95 96 2.426522 GCTCAGCTTGTTACATGGACA 58.573 47.619 0.00 0.00 0.00 4.02
96 97 3.012518 GCTCAGCTTGTTACATGGACAT 58.987 45.455 0.00 0.00 0.00 3.06
97 98 3.181503 GCTCAGCTTGTTACATGGACATG 60.182 47.826 10.57 10.57 44.15 3.21
110 111 5.456192 CATGGACATGTCGTTAGTCTTTC 57.544 43.478 19.33 2.39 34.23 2.62
111 112 4.866508 TGGACATGTCGTTAGTCTTTCT 57.133 40.909 19.33 0.00 32.98 2.52
112 113 5.209818 TGGACATGTCGTTAGTCTTTCTT 57.790 39.130 19.33 0.00 32.98 2.52
113 114 5.607477 TGGACATGTCGTTAGTCTTTCTTT 58.393 37.500 19.33 0.00 32.98 2.52
114 115 6.053005 TGGACATGTCGTTAGTCTTTCTTTT 58.947 36.000 19.33 0.00 32.98 2.27
115 116 6.540914 TGGACATGTCGTTAGTCTTTCTTTTT 59.459 34.615 19.33 0.00 32.98 1.94
116 117 6.851330 GGACATGTCGTTAGTCTTTCTTTTTG 59.149 38.462 19.33 0.00 32.98 2.44
117 118 7.316544 ACATGTCGTTAGTCTTTCTTTTTGT 57.683 32.000 0.00 0.00 0.00 2.83
118 119 7.758495 ACATGTCGTTAGTCTTTCTTTTTGTT 58.242 30.769 0.00 0.00 0.00 2.83
119 120 8.885722 ACATGTCGTTAGTCTTTCTTTTTGTTA 58.114 29.630 0.00 0.00 0.00 2.41
120 121 9.878599 CATGTCGTTAGTCTTTCTTTTTGTTAT 57.121 29.630 0.00 0.00 0.00 1.89
122 123 9.100554 TGTCGTTAGTCTTTCTTTTTGTTATCA 57.899 29.630 0.00 0.00 0.00 2.15
123 124 9.925268 GTCGTTAGTCTTTCTTTTTGTTATCAA 57.075 29.630 0.00 0.00 0.00 2.57
151 152 9.829507 TTTCATTACAAAATGGACTTCAATTGT 57.170 25.926 5.13 0.00 42.40 2.71
152 153 9.829507 TTCATTACAAAATGGACTTCAATTGTT 57.170 25.926 5.13 0.00 42.40 2.83
153 154 9.474920 TCATTACAAAATGGACTTCAATTGTTC 57.525 29.630 5.13 0.97 42.40 3.18
154 155 9.258826 CATTACAAAATGGACTTCAATTGTTCA 57.741 29.630 5.13 0.00 39.10 3.18
155 156 8.870160 TTACAAAATGGACTTCAATTGTTCAG 57.130 30.769 5.13 3.19 39.03 3.02
156 157 6.877236 ACAAAATGGACTTCAATTGTTCAGT 58.123 32.000 5.13 6.39 36.63 3.41
157 158 8.006298 ACAAAATGGACTTCAATTGTTCAGTA 57.994 30.769 5.13 0.00 36.63 2.74
158 159 8.474025 ACAAAATGGACTTCAATTGTTCAGTAA 58.526 29.630 5.13 0.22 36.63 2.24
159 160 9.480053 CAAAATGGACTTCAATTGTTCAGTAAT 57.520 29.630 5.13 2.30 0.00 1.89
161 162 9.480053 AAATGGACTTCAATTGTTCAGTAATTG 57.520 29.630 5.13 0.00 43.48 2.32
162 163 7.581213 TGGACTTCAATTGTTCAGTAATTGT 57.419 32.000 5.13 0.00 42.94 2.71
163 164 7.424803 TGGACTTCAATTGTTCAGTAATTGTG 58.575 34.615 5.13 7.21 42.94 3.33
164 165 7.068103 TGGACTTCAATTGTTCAGTAATTGTGT 59.932 33.333 5.13 9.51 42.94 3.72
165 166 7.920682 GGACTTCAATTGTTCAGTAATTGTGTT 59.079 33.333 5.13 0.00 42.94 3.32
166 167 9.301153 GACTTCAATTGTTCAGTAATTGTGTTT 57.699 29.630 5.13 0.00 42.94 2.83
167 168 9.086336 ACTTCAATTGTTCAGTAATTGTGTTTG 57.914 29.630 5.13 0.00 42.94 2.93
168 169 8.994429 TTCAATTGTTCAGTAATTGTGTTTGT 57.006 26.923 5.13 0.00 42.94 2.83
169 170 8.404889 TCAATTGTTCAGTAATTGTGTTTGTG 57.595 30.769 5.13 0.00 42.94 3.33
170 171 8.031864 TCAATTGTTCAGTAATTGTGTTTGTGT 58.968 29.630 5.13 0.00 42.94 3.72
171 172 8.655092 CAATTGTTCAGTAATTGTGTTTGTGTT 58.345 29.630 0.00 0.00 39.49 3.32
172 173 9.862371 AATTGTTCAGTAATTGTGTTTGTGTTA 57.138 25.926 0.00 0.00 0.00 2.41
185 186 9.750125 TTGTGTTTGTGTTATATTGTTTATGCA 57.250 25.926 0.00 0.00 0.00 3.96
186 187 9.920133 TGTGTTTGTGTTATATTGTTTATGCAT 57.080 25.926 3.79 3.79 0.00 3.96
188 189 9.920133 TGTTTGTGTTATATTGTTTATGCATGT 57.080 25.926 10.16 0.00 0.00 3.21
229 230 6.084326 TCTTGTAAATTTTGTCAAGAGCCC 57.916 37.500 19.51 0.00 40.46 5.19
230 231 4.497473 TGTAAATTTTGTCAAGAGCCCG 57.503 40.909 0.00 0.00 0.00 6.13
231 232 3.886505 TGTAAATTTTGTCAAGAGCCCGT 59.113 39.130 0.00 0.00 0.00 5.28
232 233 3.369546 AAATTTTGTCAAGAGCCCGTG 57.630 42.857 0.00 0.00 0.00 4.94
233 234 1.247567 ATTTTGTCAAGAGCCCGTGG 58.752 50.000 0.00 0.00 0.00 4.94
248 249 4.972733 TGGCAACGCATGGGCACT 62.973 61.111 10.10 0.00 41.24 4.40
249 250 4.120331 GGCAACGCATGGGCACTC 62.120 66.667 10.10 0.00 41.24 3.51
250 251 3.058160 GCAACGCATGGGCACTCT 61.058 61.111 10.10 0.00 41.24 3.24
251 252 1.745115 GCAACGCATGGGCACTCTA 60.745 57.895 10.10 0.00 41.24 2.43
252 253 1.982073 GCAACGCATGGGCACTCTAC 61.982 60.000 10.10 0.00 41.24 2.59
253 254 0.391661 CAACGCATGGGCACTCTACT 60.392 55.000 10.10 0.00 41.24 2.57
254 255 1.134818 CAACGCATGGGCACTCTACTA 60.135 52.381 10.10 0.00 41.24 1.82
411 423 8.188799 TGAGAGGTAAATCACAATCTAACGTAG 58.811 37.037 0.00 0.00 0.00 3.51
436 448 9.959721 AGTAGAATATTTATATCCCGTTGCAAT 57.040 29.630 0.59 0.00 0.00 3.56
442 454 1.031235 TATCCCGTTGCAATGCATGG 58.969 50.000 9.39 14.18 38.76 3.66
443 455 0.683828 ATCCCGTTGCAATGCATGGA 60.684 50.000 23.25 21.17 38.76 3.41
457 469 6.594788 AATGCATGGACATTGTTCTAGTTT 57.405 33.333 0.00 0.00 38.80 2.66
458 470 6.594788 ATGCATGGACATTGTTCTAGTTTT 57.405 33.333 0.00 0.00 0.00 2.43
459 471 6.403866 TGCATGGACATTGTTCTAGTTTTT 57.596 33.333 0.00 0.00 0.00 1.94
650 1188 2.677003 CCGCGCTAAACCACCACAG 61.677 63.158 5.56 0.00 0.00 3.66
651 1189 2.677003 CGCGCTAAACCACCACAGG 61.677 63.158 5.56 0.00 0.00 4.00
652 1190 2.332654 GCGCTAAACCACCACAGGG 61.333 63.158 0.00 0.00 41.29 4.45
653 1191 1.674322 CGCTAAACCACCACAGGGG 60.674 63.158 0.00 0.00 44.81 4.79
660 1198 3.719121 CACCACAGGGGGAGAGAG 58.281 66.667 0.00 0.00 41.63 3.20
661 1199 1.079256 CACCACAGGGGGAGAGAGA 59.921 63.158 0.00 0.00 41.63 3.10
662 1200 0.975040 CACCACAGGGGGAGAGAGAG 60.975 65.000 0.00 0.00 41.63 3.20
663 1201 1.149782 ACCACAGGGGGAGAGAGAGA 61.150 60.000 0.00 0.00 42.91 3.10
664 1202 0.686112 CCACAGGGGGAGAGAGAGAC 60.686 65.000 0.00 0.00 0.00 3.36
665 1203 0.040351 CACAGGGGGAGAGAGAGACA 59.960 60.000 0.00 0.00 0.00 3.41
666 1204 0.334676 ACAGGGGGAGAGAGAGACAG 59.665 60.000 0.00 0.00 0.00 3.51
667 1205 0.396974 CAGGGGGAGAGAGAGACAGG 60.397 65.000 0.00 0.00 0.00 4.00
668 1206 1.760480 GGGGGAGAGAGAGACAGGC 60.760 68.421 0.00 0.00 0.00 4.85
669 1207 1.309688 GGGGAGAGAGAGACAGGCT 59.690 63.158 0.00 0.00 0.00 4.58
670 1208 0.325203 GGGGAGAGAGAGACAGGCTT 60.325 60.000 0.00 0.00 0.00 4.35
671 1209 1.567357 GGGAGAGAGAGACAGGCTTT 58.433 55.000 0.00 0.00 0.00 3.51
672 1210 1.206849 GGGAGAGAGAGACAGGCTTTG 59.793 57.143 0.00 0.00 0.00 2.77
673 1211 1.206849 GGAGAGAGAGACAGGCTTTGG 59.793 57.143 0.00 0.00 0.00 3.28
674 1212 2.175202 GAGAGAGAGACAGGCTTTGGA 58.825 52.381 0.00 0.00 0.00 3.53
675 1213 1.899142 AGAGAGAGACAGGCTTTGGAC 59.101 52.381 0.00 0.00 0.00 4.02
676 1214 1.899142 GAGAGAGACAGGCTTTGGACT 59.101 52.381 0.00 0.00 0.00 3.85
806 1344 2.482333 CCACCTCTCCTACTCCGCG 61.482 68.421 0.00 0.00 0.00 6.46
1002 1544 2.279120 GATCGGACTCTGCTGGCG 60.279 66.667 0.00 0.00 0.00 5.69
1008 1550 1.032657 GGACTCTGCTGGCGTCTAGA 61.033 60.000 11.50 0.00 0.00 2.43
1030 1572 2.960688 GCTTGAGGAGGGGTCGCTT 61.961 63.158 0.00 0.00 0.00 4.68
1097 1639 3.858868 GACGACGCTGTCAAGGCCA 62.859 63.158 5.01 0.00 38.75 5.36
1195 1737 2.190578 CCCTTGCTCCCCATCGAC 59.809 66.667 0.00 0.00 0.00 4.20
1349 1891 2.338809 TGAGGGAAAGGAAGCAGAAGA 58.661 47.619 0.00 0.00 0.00 2.87
1375 1917 1.004891 GAAGGATGGGGAGGAGGGT 59.995 63.158 0.00 0.00 0.00 4.34
1448 1990 1.081892 CCACCAGATCAAGAAGCACG 58.918 55.000 0.00 0.00 0.00 5.34
1495 2037 1.795286 CTCGAAAAGGACTGCACTGTC 59.205 52.381 0.00 0.00 36.31 3.51
1510 2052 3.033764 GTCGAGGACGTGCGCAAA 61.034 61.111 14.00 0.00 40.69 3.68
1657 2199 4.245660 TCGATCTTGTTGGTTCTGATGAC 58.754 43.478 0.00 0.00 0.00 3.06
1714 2256 3.875134 CCCGTTCATACAATGGGTTCTAC 59.125 47.826 3.71 0.00 40.77 2.59
1753 2295 5.233988 CCGGATGAGATATTCAGGAACTTC 58.766 45.833 0.00 0.00 39.68 3.01
1810 2352 0.684805 TTGGGCAGTTTGGGACGTTT 60.685 50.000 0.00 0.00 0.00 3.60
1826 2368 1.879380 CGTTTCATTTCAGGACTGGCA 59.121 47.619 0.00 0.00 0.00 4.92
1993 2535 6.041979 ACCCTTATGAGCACAAATTTCAAACT 59.958 34.615 0.00 0.00 0.00 2.66
2116 2658 9.139734 AGGGATTACTACTCGATAATAACACAA 57.860 33.333 0.00 0.00 0.00 3.33
2264 2806 4.708421 ACTCTCCATGCACATTATTTTGCT 59.292 37.500 0.00 0.00 39.62 3.91
2268 2810 5.649557 TCCATGCACATTATTTTGCTGTAC 58.350 37.500 0.00 0.00 39.62 2.90
2353 2895 8.405531 TGCCTTGTATCTTGATATTTTTACTGC 58.594 33.333 0.00 0.00 0.00 4.40
2440 2982 0.110056 CACACATGGCAAGCGAGTTC 60.110 55.000 0.00 0.00 0.00 3.01
2604 3146 6.994221 AGCTACACAACTGAGTAACTGTAAT 58.006 36.000 0.00 0.00 0.00 1.89
2608 3150 7.859325 ACACAACTGAGTAACTGTAATTTGT 57.141 32.000 0.00 0.00 0.00 2.83
3090 3647 0.738412 CGTAACCCCAACACTAGGCG 60.738 60.000 0.00 0.00 0.00 5.52
3168 3731 4.100963 TGGTGTATACATGCCTCGATTCTT 59.899 41.667 9.18 0.00 0.00 2.52
3170 3733 5.527582 GGTGTATACATGCCTCGATTCTTTT 59.472 40.000 9.18 0.00 0.00 2.27
3309 3877 6.049790 GCGAGAGGTTAATAACTCCTTGAAT 58.950 40.000 2.96 0.00 34.27 2.57
3372 3940 6.461092 GGTTTTGTAGCCTTTTTCAGTAAGCT 60.461 38.462 0.00 0.00 0.00 3.74
3375 3943 1.889170 AGCCTTTTTCAGTAAGCTGGC 59.111 47.619 0.00 0.00 42.78 4.85
3379 3947 3.057946 CCTTTTTCAGTAAGCTGGCTGAC 60.058 47.826 17.00 1.98 40.91 3.51
3380 3948 1.795768 TTTCAGTAAGCTGGCTGACG 58.204 50.000 17.00 1.21 40.91 4.35
3381 3949 0.037326 TTCAGTAAGCTGGCTGACGG 60.037 55.000 17.00 4.42 40.91 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.896645 TCTAGATGATGCACTTAAGAAATTCTT 57.103 29.630 13.20 13.20 40.35 2.52
59 60 6.351327 AGCTGAGCGATGTTTTATCTAAAC 57.649 37.500 0.00 0.00 45.17 2.01
60 61 6.371548 ACAAGCTGAGCGATGTTTTATCTAAA 59.628 34.615 12.11 0.00 31.66 1.85
61 62 5.874810 ACAAGCTGAGCGATGTTTTATCTAA 59.125 36.000 12.11 0.00 31.66 2.10
62 63 5.419542 ACAAGCTGAGCGATGTTTTATCTA 58.580 37.500 12.11 0.00 31.66 1.98
63 64 4.256920 ACAAGCTGAGCGATGTTTTATCT 58.743 39.130 12.11 0.00 31.66 1.98
64 65 4.606457 ACAAGCTGAGCGATGTTTTATC 57.394 40.909 12.11 0.00 31.66 1.75
65 66 5.411361 TGTAACAAGCTGAGCGATGTTTTAT 59.589 36.000 27.49 12.84 41.17 1.40
66 67 4.752604 TGTAACAAGCTGAGCGATGTTTTA 59.247 37.500 27.49 17.82 41.17 1.52
67 68 3.563808 TGTAACAAGCTGAGCGATGTTTT 59.436 39.130 27.49 13.68 41.17 2.43
68 69 3.138304 TGTAACAAGCTGAGCGATGTTT 58.862 40.909 27.49 16.30 41.17 2.83
69 70 2.766313 TGTAACAAGCTGAGCGATGTT 58.234 42.857 26.24 26.24 42.53 2.71
70 71 2.455674 TGTAACAAGCTGAGCGATGT 57.544 45.000 12.11 12.11 35.67 3.06
71 72 2.031314 CCATGTAACAAGCTGAGCGATG 59.969 50.000 10.93 10.93 0.00 3.84
72 73 2.093500 TCCATGTAACAAGCTGAGCGAT 60.093 45.455 0.00 0.00 0.00 4.58
73 74 1.275010 TCCATGTAACAAGCTGAGCGA 59.725 47.619 0.00 0.00 0.00 4.93
74 75 1.394917 GTCCATGTAACAAGCTGAGCG 59.605 52.381 0.00 0.00 0.00 5.03
75 76 2.426522 TGTCCATGTAACAAGCTGAGC 58.573 47.619 0.00 0.00 0.00 4.26
76 77 4.611310 CATGTCCATGTAACAAGCTGAG 57.389 45.455 2.65 0.00 34.23 3.35
88 89 5.171476 AGAAAGACTAACGACATGTCCATG 58.829 41.667 20.03 8.85 44.15 3.66
89 90 5.407407 AGAAAGACTAACGACATGTCCAT 57.593 39.130 20.03 11.31 0.00 3.41
90 91 4.866508 AGAAAGACTAACGACATGTCCA 57.133 40.909 20.03 4.89 0.00 4.02
91 92 6.541111 AAAAGAAAGACTAACGACATGTCC 57.459 37.500 20.03 4.89 0.00 4.02
92 93 7.407337 ACAAAAAGAAAGACTAACGACATGTC 58.593 34.615 16.21 16.21 0.00 3.06
93 94 7.316544 ACAAAAAGAAAGACTAACGACATGT 57.683 32.000 0.00 0.00 0.00 3.21
94 95 9.878599 ATAACAAAAAGAAAGACTAACGACATG 57.121 29.630 0.00 0.00 0.00 3.21
96 97 9.100554 TGATAACAAAAAGAAAGACTAACGACA 57.899 29.630 0.00 0.00 0.00 4.35
97 98 9.925268 TTGATAACAAAAAGAAAGACTAACGAC 57.075 29.630 0.00 0.00 32.73 4.34
125 126 9.829507 ACAATTGAAGTCCATTTTGTAATGAAA 57.170 25.926 13.59 0.00 43.12 2.69
126 127 9.829507 AACAATTGAAGTCCATTTTGTAATGAA 57.170 25.926 13.59 0.00 43.12 2.57
127 128 9.474920 GAACAATTGAAGTCCATTTTGTAATGA 57.525 29.630 13.59 0.00 43.12 2.57
128 129 9.258826 TGAACAATTGAAGTCCATTTTGTAATG 57.741 29.630 13.59 0.00 40.70 1.90
129 130 9.480053 CTGAACAATTGAAGTCCATTTTGTAAT 57.520 29.630 13.59 0.00 33.22 1.89
130 131 8.474025 ACTGAACAATTGAAGTCCATTTTGTAA 58.526 29.630 13.59 0.00 33.22 2.41
131 132 8.006298 ACTGAACAATTGAAGTCCATTTTGTA 57.994 30.769 13.59 0.00 33.22 2.41
132 133 6.877236 ACTGAACAATTGAAGTCCATTTTGT 58.123 32.000 13.59 0.00 34.76 2.83
133 134 8.870160 TTACTGAACAATTGAAGTCCATTTTG 57.130 30.769 13.59 0.00 0.00 2.44
135 136 9.480053 CAATTACTGAACAATTGAAGTCCATTT 57.520 29.630 13.59 0.00 43.14 2.32
136 137 8.641541 ACAATTACTGAACAATTGAAGTCCATT 58.358 29.630 13.59 10.83 43.14 3.16
137 138 8.084073 CACAATTACTGAACAATTGAAGTCCAT 58.916 33.333 13.59 6.09 43.14 3.41
138 139 7.068103 ACACAATTACTGAACAATTGAAGTCCA 59.932 33.333 13.59 4.19 43.14 4.02
139 140 7.425606 ACACAATTACTGAACAATTGAAGTCC 58.574 34.615 13.59 0.00 43.14 3.85
140 141 8.856490 AACACAATTACTGAACAATTGAAGTC 57.144 30.769 13.59 6.99 43.14 3.01
141 142 9.086336 CAAACACAATTACTGAACAATTGAAGT 57.914 29.630 13.59 14.14 43.14 3.01
142 143 9.086336 ACAAACACAATTACTGAACAATTGAAG 57.914 29.630 13.59 9.01 43.14 3.02
143 144 8.867935 CACAAACACAATTACTGAACAATTGAA 58.132 29.630 13.59 0.00 43.14 2.69
144 145 8.031864 ACACAAACACAATTACTGAACAATTGA 58.968 29.630 13.59 0.00 43.14 2.57
145 146 8.183830 ACACAAACACAATTACTGAACAATTG 57.816 30.769 3.24 3.24 45.01 2.32
146 147 8.770438 AACACAAACACAATTACTGAACAATT 57.230 26.923 0.00 0.00 0.00 2.32
159 160 9.750125 TGCATAAACAATATAACACAAACACAA 57.250 25.926 0.00 0.00 0.00 3.33
160 161 9.920133 ATGCATAAACAATATAACACAAACACA 57.080 25.926 0.00 0.00 0.00 3.72
162 163 9.920133 ACATGCATAAACAATATAACACAAACA 57.080 25.926 0.00 0.00 0.00 2.83
206 207 5.278266 CGGGCTCTTGACAAAATTTACAAGA 60.278 40.000 22.16 22.16 43.79 3.02
207 208 4.917415 CGGGCTCTTGACAAAATTTACAAG 59.083 41.667 18.32 18.32 40.37 3.16
208 209 4.339814 ACGGGCTCTTGACAAAATTTACAA 59.660 37.500 0.00 0.00 0.00 2.41
209 210 3.886505 ACGGGCTCTTGACAAAATTTACA 59.113 39.130 0.00 0.00 0.00 2.41
210 211 4.226761 CACGGGCTCTTGACAAAATTTAC 58.773 43.478 0.00 0.00 0.00 2.01
211 212 3.254657 CCACGGGCTCTTGACAAAATTTA 59.745 43.478 0.00 0.00 0.00 1.40
212 213 2.035832 CCACGGGCTCTTGACAAAATTT 59.964 45.455 0.00 0.00 0.00 1.82
213 214 1.613437 CCACGGGCTCTTGACAAAATT 59.387 47.619 0.00 0.00 0.00 1.82
214 215 1.247567 CCACGGGCTCTTGACAAAAT 58.752 50.000 0.00 0.00 0.00 1.82
215 216 1.452145 GCCACGGGCTCTTGACAAAA 61.452 55.000 7.58 0.00 46.69 2.44
216 217 1.896660 GCCACGGGCTCTTGACAAA 60.897 57.895 7.58 0.00 46.69 2.83
217 218 2.281484 GCCACGGGCTCTTGACAA 60.281 61.111 7.58 0.00 46.69 3.18
230 231 4.722855 GTGCCCATGCGTTGCCAC 62.723 66.667 0.00 0.00 41.78 5.01
231 232 4.972733 AGTGCCCATGCGTTGCCA 62.973 61.111 0.00 0.00 41.78 4.92
232 233 4.120331 GAGTGCCCATGCGTTGCC 62.120 66.667 0.00 0.00 41.78 4.52
233 234 1.745115 TAGAGTGCCCATGCGTTGC 60.745 57.895 0.00 0.00 41.78 4.17
234 235 0.391661 AGTAGAGTGCCCATGCGTTG 60.392 55.000 0.00 0.00 41.78 4.10
235 236 1.137086 CTAGTAGAGTGCCCATGCGTT 59.863 52.381 0.00 0.00 41.78 4.84
236 237 0.747255 CTAGTAGAGTGCCCATGCGT 59.253 55.000 0.00 0.00 41.78 5.24
237 238 0.747255 ACTAGTAGAGTGCCCATGCG 59.253 55.000 3.59 0.00 41.78 4.73
238 239 5.419155 TCATATACTAGTAGAGTGCCCATGC 59.581 44.000 8.85 0.00 39.39 4.06
239 240 7.652524 ATCATATACTAGTAGAGTGCCCATG 57.347 40.000 8.85 0.00 39.39 3.66
240 241 9.944079 ATTATCATATACTAGTAGAGTGCCCAT 57.056 33.333 8.85 0.90 39.39 4.00
241 242 9.409918 GATTATCATATACTAGTAGAGTGCCCA 57.590 37.037 8.85 0.00 39.39 5.36
242 243 9.409918 TGATTATCATATACTAGTAGAGTGCCC 57.590 37.037 8.85 0.00 39.39 5.36
388 400 9.448294 CTACTACGTTAGATTGTGATTTACCTC 57.552 37.037 0.00 0.00 0.00 3.85
411 423 9.988350 CATTGCAACGGGATATAAATATTCTAC 57.012 33.333 0.00 0.00 0.00 2.59
436 448 6.403866 AAAAACTAGAACAATGTCCATGCA 57.596 33.333 0.00 0.00 0.00 3.96
459 471 0.178947 ATGTCCGCCCCCTTCAAAAA 60.179 50.000 0.00 0.00 0.00 1.94
460 472 0.178947 AATGTCCGCCCCCTTCAAAA 60.179 50.000 0.00 0.00 0.00 2.44
461 473 0.897863 CAATGTCCGCCCCCTTCAAA 60.898 55.000 0.00 0.00 0.00 2.69
462 474 1.304052 CAATGTCCGCCCCCTTCAA 60.304 57.895 0.00 0.00 0.00 2.69
463 475 2.075355 AACAATGTCCGCCCCCTTCA 62.075 55.000 0.00 0.00 0.00 3.02
464 476 1.304134 AACAATGTCCGCCCCCTTC 60.304 57.895 0.00 0.00 0.00 3.46
467 479 0.463833 CTAGAACAATGTCCGCCCCC 60.464 60.000 0.00 0.00 0.00 5.40
468 480 0.252197 ACTAGAACAATGTCCGCCCC 59.748 55.000 0.00 0.00 0.00 5.80
470 482 3.521947 AGTACTAGAACAATGTCCGCC 57.478 47.619 0.00 0.00 0.00 6.13
471 483 8.638685 TTTATTAGTACTAGAACAATGTCCGC 57.361 34.615 2.23 0.00 0.00 5.54
650 1188 1.760480 GCCTGTCTCTCTCTCCCCC 60.760 68.421 0.00 0.00 0.00 5.40
651 1189 0.325203 AAGCCTGTCTCTCTCTCCCC 60.325 60.000 0.00 0.00 0.00 4.81
652 1190 1.206849 CAAAGCCTGTCTCTCTCTCCC 59.793 57.143 0.00 0.00 0.00 4.30
653 1191 1.206849 CCAAAGCCTGTCTCTCTCTCC 59.793 57.143 0.00 0.00 0.00 3.71
654 1192 2.094234 GTCCAAAGCCTGTCTCTCTCTC 60.094 54.545 0.00 0.00 0.00 3.20
655 1193 1.899142 GTCCAAAGCCTGTCTCTCTCT 59.101 52.381 0.00 0.00 0.00 3.10
656 1194 1.899142 AGTCCAAAGCCTGTCTCTCTC 59.101 52.381 0.00 0.00 0.00 3.20
657 1195 1.622811 CAGTCCAAAGCCTGTCTCTCT 59.377 52.381 0.00 0.00 0.00 3.10
658 1196 1.338579 CCAGTCCAAAGCCTGTCTCTC 60.339 57.143 0.00 0.00 0.00 3.20
659 1197 0.689623 CCAGTCCAAAGCCTGTCTCT 59.310 55.000 0.00 0.00 0.00 3.10
660 1198 0.322008 CCCAGTCCAAAGCCTGTCTC 60.322 60.000 0.00 0.00 0.00 3.36
661 1199 1.763770 CCCAGTCCAAAGCCTGTCT 59.236 57.895 0.00 0.00 0.00 3.41
662 1200 1.973812 GCCCAGTCCAAAGCCTGTC 60.974 63.158 0.00 0.00 0.00 3.51
663 1201 2.116125 GCCCAGTCCAAAGCCTGT 59.884 61.111 0.00 0.00 0.00 4.00
664 1202 2.677875 GGCCCAGTCCAAAGCCTG 60.678 66.667 0.00 0.00 42.34 4.85
665 1203 2.777960 TTGGCCCAGTCCAAAGCCT 61.778 57.895 0.00 0.00 45.94 4.58
666 1204 2.203625 TTGGCCCAGTCCAAAGCC 60.204 61.111 0.00 0.00 42.69 4.35
671 1209 1.204146 GACTCTATTGGCCCAGTCCA 58.796 55.000 0.00 0.00 30.82 4.02
672 1210 1.139853 CAGACTCTATTGGCCCAGTCC 59.860 57.143 0.00 0.00 36.68 3.85
673 1211 1.474143 GCAGACTCTATTGGCCCAGTC 60.474 57.143 0.00 4.02 36.32 3.51
674 1212 0.543749 GCAGACTCTATTGGCCCAGT 59.456 55.000 0.00 0.00 0.00 4.00
675 1213 0.543277 TGCAGACTCTATTGGCCCAG 59.457 55.000 0.00 0.00 0.00 4.45
676 1214 0.253044 GTGCAGACTCTATTGGCCCA 59.747 55.000 0.00 0.00 0.00 5.36
1002 1544 2.693074 CCCTCCTCAAGCTTCTCTAGAC 59.307 54.545 0.00 0.00 0.00 2.59
1008 1550 1.261238 CGACCCCTCCTCAAGCTTCT 61.261 60.000 0.00 0.00 0.00 2.85
1039 1581 4.479993 GCGGCAGATCTGTGGCCT 62.480 66.667 23.38 0.00 45.53 5.19
1097 1639 2.793946 GTTCTTGCCGATGCGCAT 59.206 55.556 25.66 25.66 41.78 4.73
1195 1737 2.204151 AGGGGGTTGAGGAGGTGG 60.204 66.667 0.00 0.00 0.00 4.61
1291 1833 0.944788 CTGATGATGCAGCTCGCGAT 60.945 55.000 10.36 0.00 46.97 4.58
1349 1891 1.563410 CTCCCCATCCTTCTTCTTGCT 59.437 52.381 0.00 0.00 0.00 3.91
1375 1917 2.584064 CCAGCAGTATCACCGCCA 59.416 61.111 0.00 0.00 0.00 5.69
1448 1990 5.046950 CCAGGATCTTGTAGTAATCCCTAGC 60.047 48.000 3.93 0.00 39.90 3.42
1495 2037 4.430423 GCTTTGCGCACGTCCTCG 62.430 66.667 11.12 0.00 43.34 4.63
1510 2052 1.671901 GAGAGAGCTTGCGGTAGGCT 61.672 60.000 1.68 1.68 45.49 4.58
1632 2174 4.336889 TCAGAACCAACAAGATCGAAGT 57.663 40.909 0.00 0.00 0.00 3.01
1657 2199 3.202001 CTGTTGTATGCCGGCGGG 61.202 66.667 29.48 9.71 0.00 6.13
1714 2256 1.134818 TCCGGGTCAATGTCATCTTCG 60.135 52.381 0.00 0.00 0.00 3.79
1753 2295 1.467920 GAGCCATCCCACCAAAGAAG 58.532 55.000 0.00 0.00 0.00 2.85
1810 2352 1.361204 TCCTGCCAGTCCTGAAATGA 58.639 50.000 0.00 0.00 0.00 2.57
1993 2535 6.151480 TGACATAGTATGTTACTCCACGTTGA 59.849 38.462 16.80 0.00 45.03 3.18
2116 2658 2.821969 CTGCAGCTCAACCCTACAATTT 59.178 45.455 0.00 0.00 0.00 1.82
2440 2982 5.885230 TGACATTCAGGTGAAAAGCATAG 57.115 39.130 0.00 0.00 37.61 2.23
2604 3146 2.146342 GCTGCTAGCTGTCAGAACAAA 58.854 47.619 21.03 0.00 38.45 2.83
2660 3202 8.653191 TCTAAACCATATAAACCGGATGTGTAT 58.347 33.333 9.46 0.00 32.01 2.29
2894 3448 0.391130 TGACAGCTTCGTATGGGCAC 60.391 55.000 0.00 0.00 0.00 5.01
2952 3509 9.104965 CTTAACAAATATCAAGAACGTATGGGA 57.895 33.333 0.00 0.00 0.00 4.37
3090 3647 9.329913 GTTGAATTCATTAATGACACTACACAC 57.670 33.333 17.76 3.93 36.36 3.82
3170 3733 9.283768 TCAATCACTTCTTAAAACTCAATAGCA 57.716 29.630 0.00 0.00 0.00 3.49
3226 3789 6.624352 TTCATTATTCTGCAATCACTAGCC 57.376 37.500 0.00 0.00 0.00 3.93
3331 3899 4.339814 ACAAAACCGCTTTGAAACATAGGA 59.660 37.500 13.31 0.00 46.35 2.94


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

AutoCloner maintained by Alex Coulton.