Multiple sequence alignment - TraesCS2D01G012700

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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 TraesCS2D01G012700 chr2D 100.000 2746 0 0 1 2746 5923140 5925885 0.000000e+00 5072.0
1 TraesCS2D01G012700 chr2A 87.438 2842 194 75 9 2746 4616007 4618789 0.000000e+00 3120.0
2 TraesCS2D01G012700 chr2A 82.546 1249 114 42 9 1195 4595215 4596421 0.000000e+00 1003.0
3 TraesCS2D01G012700 chr2A 82.126 1242 115 43 9 1195 4527645 4528834 0.000000e+00 965.0
4 TraesCS2D01G012700 chr2A 79.104 134 22 6 6 135 94293152 94293021 1.350000e-13 87.9
5 TraesCS2D01G012700 chr2A 80.180 111 21 1 550 660 16854771 16854662 6.300000e-12 82.4
6 TraesCS2D01G012700 chr2B 86.513 2825 229 75 6 2746 5478316 5481072 0.000000e+00 2966.0
7 TraesCS2D01G012700 chr2B 93.541 418 24 1 2255 2669 5542277 5542694 1.080000e-173 619.0
8 TraesCS2D01G012700 chr2B 94.048 252 13 1 1899 2148 84047545 84047796 5.550000e-102 381.0
9 TraesCS2D01G012700 chr2B 87.402 254 10 6 2182 2413 84047785 84048038 3.480000e-69 272.0
10 TraesCS2D01G012700 chr2B 92.771 83 6 0 2664 2746 5542856 5542938 1.340000e-23 121.0
11 TraesCS2D01G012700 chrUn 81.517 1147 110 42 9 1100 176237446 176236347 0.000000e+00 850.0
12 TraesCS2D01G012700 chr3B 95.635 252 9 1 1899 2148 797654706 797654957 1.180000e-108 403.0
13 TraesCS2D01G012700 chr3B 91.827 208 17 0 1013 1220 754354951 754354744 9.620000e-75 291.0
14 TraesCS2D01G012700 chr3B 88.189 254 8 5 2182 2413 797654946 797655199 1.610000e-72 283.0
15 TraesCS2D01G012700 chr4A 94.841 252 11 1 1899 2148 733543430 733543681 2.560000e-105 392.0
16 TraesCS2D01G012700 chr4A 88.189 254 8 7 2182 2413 733543670 733543923 1.610000e-72 283.0
17 TraesCS2D01G012700 chr4B 91.827 208 17 0 1013 1220 27847619 27847412 9.620000e-75 291.0
18 TraesCS2D01G012700 chr4B 92.118 203 14 2 1013 1214 620640228 620640429 4.480000e-73 285.0
19 TraesCS2D01G012700 chr7B 92.537 201 15 0 1013 1213 686328791 686328991 3.460000e-74 289.0
20 TraesCS2D01G012700 chr1B 92.079 202 16 0 1013 1214 657390952 657391153 4.480000e-73 285.0
21 TraesCS2D01G012700 chr6B 82.353 119 17 4 5 119 156411610 156411728 1.740000e-17 100.0
22 TraesCS2D01G012700 chr5D 82.979 94 9 6 14 102 277259680 277259771 8.150000e-11 78.7
23 TraesCS2D01G012700 chr5D 85.246 61 9 0 82 142 317229119 317229179 2.280000e-06 63.9
24 TraesCS2D01G012700 chr4D 86.207 58 7 1 14 70 63227465 63227408 8.210000e-06 62.1
25 TraesCS2D01G012700 chr1D 86.792 53 7 0 93 145 483975439 483975387 2.950000e-05 60.2


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 TraesCS2D01G012700 chr2D 5923140 5925885 2745 False 5072 5072 100.000 1 2746 1 chr2D.!!$F1 2745
1 TraesCS2D01G012700 chr2A 4616007 4618789 2782 False 3120 3120 87.438 9 2746 1 chr2A.!!$F3 2737
2 TraesCS2D01G012700 chr2A 4595215 4596421 1206 False 1003 1003 82.546 9 1195 1 chr2A.!!$F2 1186
3 TraesCS2D01G012700 chr2A 4527645 4528834 1189 False 965 965 82.126 9 1195 1 chr2A.!!$F1 1186
4 TraesCS2D01G012700 chr2B 5478316 5481072 2756 False 2966 2966 86.513 6 2746 1 chr2B.!!$F1 2740
5 TraesCS2D01G012700 chr2B 5542277 5542938 661 False 370 619 93.156 2255 2746 2 chr2B.!!$F2 491
6 TraesCS2D01G012700 chrUn 176236347 176237446 1099 True 850 850 81.517 9 1100 1 chrUn.!!$R1 1091

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
249 251 0.113580 TAAAACCAACCCTCAGCCCC 59.886 55.0 0.0 0.0 0.00 5.80 F
264 266 0.179936 GCCCCAGACAGGAGAGATTG 59.820 60.0 0.0 0.0 41.22 2.67 F
578 624 0.378962 TTTTTGCCACGACTTCCACG 59.621 50.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1607 0.169009 GAGCAGCAAAAGCGGTTAGG 59.831 55.000 0.0 0.0 37.01 2.69 R
1509 1613 1.126079 CAACAAGAGCAGCAAAAGCG 58.874 50.000 0.0 0.0 37.01 4.68 R
2456 2603 1.004679 CCAACAATGTGCCTTGCCC 60.005 57.895 0.0 0.0 0.00 5.36 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
30 31 1.139853 CTCCTCCCACTAAGGCACATC 59.860 57.143 0.00 0.00 35.39 3.06
67 68 6.811170 TGAAATAAATCAAGGAAAATGCGACC 59.189 34.615 0.00 0.00 0.00 4.79
69 70 3.575965 AATCAAGGAAAATGCGACCAC 57.424 42.857 0.00 0.00 0.00 4.16
70 71 1.974265 TCAAGGAAAATGCGACCACA 58.026 45.000 0.00 0.00 0.00 4.17
71 72 1.879380 TCAAGGAAAATGCGACCACAG 59.121 47.619 0.00 0.00 0.00 3.66
72 73 1.608590 CAAGGAAAATGCGACCACAGT 59.391 47.619 0.00 0.00 0.00 3.55
79 80 2.831685 ATGCGACCACAGTTAAGTCA 57.168 45.000 0.00 0.00 0.00 3.41
102 103 1.073284 GACTTGAAACCTGGTGGGCTA 59.927 52.381 0.00 0.00 39.10 3.93
103 104 1.497286 ACTTGAAACCTGGTGGGCTAA 59.503 47.619 0.00 0.00 39.10 3.09
110 111 0.393077 CCTGGTGGGCTAAGGATACG 59.607 60.000 0.00 0.00 46.39 3.06
113 114 0.391966 GGTGGGCTAAGGATACGACC 59.608 60.000 0.00 0.00 46.39 4.79
132 133 2.027469 ACCGTCCTTCTAACCATCCAAC 60.027 50.000 0.00 0.00 0.00 3.77
135 136 3.370527 CGTCCTTCTAACCATCCAACCAT 60.371 47.826 0.00 0.00 0.00 3.55
142 143 6.381498 TCTAACCATCCAACCATAGTTTGA 57.619 37.500 0.00 0.00 32.45 2.69
145 146 6.933514 AACCATCCAACCATAGTTTGATTT 57.066 33.333 0.00 0.00 36.49 2.17
165 166 1.004277 TGTGATAGGCCCAACTTGTCC 59.996 52.381 0.00 0.00 0.00 4.02
167 168 1.559682 TGATAGGCCCAACTTGTCCTC 59.440 52.381 0.00 0.00 0.00 3.71
170 171 1.228154 GGCCCAACTTGTCCTCGTT 60.228 57.895 0.00 0.00 0.00 3.85
205 207 8.041323 ACTGAAAATACAATGGAGGTAGTAGTG 58.959 37.037 0.00 0.00 0.00 2.74
221 223 7.037802 AGGTAGTAGTGGTTTGCTAAAGGTAAT 60.038 37.037 0.00 0.00 0.00 1.89
248 250 2.231716 ATAAAACCAACCCTCAGCCC 57.768 50.000 0.00 0.00 0.00 5.19
249 251 0.113580 TAAAACCAACCCTCAGCCCC 59.886 55.000 0.00 0.00 0.00 5.80
264 266 0.179936 GCCCCAGACAGGAGAGATTG 59.820 60.000 0.00 0.00 41.22 2.67
270 273 4.263243 CCCAGACAGGAGAGATTGTTTCTT 60.263 45.833 0.00 0.00 41.22 2.52
276 279 9.579932 AGACAGGAGAGATTGTTTCTTAATTTT 57.420 29.630 0.00 0.00 33.74 1.82
393 427 5.063564 CCTCTTTTAGCTCGGTATGAACAAC 59.936 44.000 0.00 0.00 0.00 3.32
399 433 5.046910 AGCTCGGTATGAACAACAAAATG 57.953 39.130 0.00 0.00 0.00 2.32
400 434 4.759693 AGCTCGGTATGAACAACAAAATGA 59.240 37.500 0.00 0.00 0.00 2.57
401 435 5.240623 AGCTCGGTATGAACAACAAAATGAA 59.759 36.000 0.00 0.00 0.00 2.57
402 436 5.918011 GCTCGGTATGAACAACAAAATGAAA 59.082 36.000 0.00 0.00 0.00 2.69
403 437 6.419413 GCTCGGTATGAACAACAAAATGAAAA 59.581 34.615 0.00 0.00 0.00 2.29
404 438 7.043059 GCTCGGTATGAACAACAAAATGAAAAA 60.043 33.333 0.00 0.00 0.00 1.94
481 515 5.106038 TGCTTGCCAAATTTCATCACTAGAG 60.106 40.000 0.00 0.00 0.00 2.43
486 520 5.163713 GCCAAATTTCATCACTAGAGGACAC 60.164 44.000 0.00 0.00 33.74 3.67
498 532 2.743636 GAGGACACTCGTGGAAATCA 57.256 50.000 1.77 0.00 33.35 2.57
528 565 5.534207 TCAACACTCCAAATGCTTTCAAT 57.466 34.783 0.00 0.00 0.00 2.57
545 582 9.270640 TGCTTTCAATAATAACATTTTTGCAGT 57.729 25.926 0.00 0.00 0.00 4.40
557 594 5.348451 ACATTTTTGCAGTATCGATTTTGCC 59.652 36.000 22.99 11.32 35.75 4.52
558 595 4.782019 TTTTGCAGTATCGATTTTGCCT 57.218 36.364 22.99 4.13 35.75 4.75
578 624 0.378962 TTTTTGCCACGACTTCCACG 59.621 50.000 0.00 0.00 0.00 4.94
591 637 4.921515 CGACTTCCACGAATGTTCTTTCTA 59.078 41.667 0.00 0.00 0.00 2.10
695 741 0.818296 AGATACTCCGCTTCAACGCT 59.182 50.000 0.00 0.00 0.00 5.07
712 759 6.301486 TCAACGCTATTATACTACTCCCTCA 58.699 40.000 0.00 0.00 0.00 3.86
823 899 5.044624 TGGAGAAAGAAATGATGGGTCAGAT 60.045 40.000 0.00 0.00 37.87 2.90
953 1030 2.043801 AGGCTTGTAGGGTCTCTCTCTT 59.956 50.000 0.00 0.00 0.00 2.85
1107 1200 2.765807 CCATCACCTCCTCCGCCT 60.766 66.667 0.00 0.00 0.00 5.52
1295 1390 3.249799 TGTAATTTCTGCCTGTGTTGACG 59.750 43.478 0.00 0.00 0.00 4.35
1314 1409 1.590147 GGACGTCGAACCCAGATGT 59.410 57.895 9.92 0.00 40.22 3.06
1398 1493 1.206072 GCTCTGCGTGCAGTTCTTG 59.794 57.895 20.33 8.81 43.96 3.02
1399 1494 1.224069 GCTCTGCGTGCAGTTCTTGA 61.224 55.000 20.33 0.71 43.96 3.02
1400 1495 1.436600 CTCTGCGTGCAGTTCTTGAT 58.563 50.000 20.33 0.00 43.96 2.57
1401 1496 1.392853 CTCTGCGTGCAGTTCTTGATC 59.607 52.381 20.33 0.00 43.96 2.92
1402 1497 1.001293 TCTGCGTGCAGTTCTTGATCT 59.999 47.619 20.33 0.00 43.96 2.75
1403 1498 1.392853 CTGCGTGCAGTTCTTGATCTC 59.607 52.381 13.62 0.00 39.10 2.75
1503 1607 3.803162 GGAGAAGAGGGGCCAGGC 61.803 72.222 4.39 1.26 0.00 4.85
1563 1670 2.334977 TGGAGAAGGCTACCAAGAACA 58.665 47.619 5.70 0.00 0.00 3.18
1667 1774 2.372690 CGTCTCGTGCACTTTCCCG 61.373 63.158 16.19 6.83 0.00 5.14
1740 1847 2.542907 GGTGTGTGCCGGTTGACAG 61.543 63.158 1.90 0.00 0.00 3.51
1850 1957 2.435372 TGTTTCAAGGGCAGACTGTT 57.565 45.000 3.99 0.00 0.00 3.16
1858 1965 2.699954 AGGGCAGACTGTTGAATTACG 58.300 47.619 3.99 0.00 0.00 3.18
1863 1970 3.370061 GCAGACTGTTGAATTACGTACCC 59.630 47.826 3.99 0.00 0.00 3.69
1875 1982 7.431249 TGAATTACGTACCCAGATTCTGATAC 58.569 38.462 15.36 14.41 32.44 2.24
1889 1996 5.362556 TTCTGATACTTGCTCACAAAAGC 57.637 39.130 0.00 0.00 42.82 3.51
1916 2036 4.929479 TGGTTTGACCATGCTAAATAGGT 58.071 39.130 0.00 0.00 44.79 3.08
1920 2040 8.275758 TGGTTTGACCATGCTAAATAGGTATTA 58.724 33.333 0.00 0.00 44.79 0.98
1929 2049 9.561069 CATGCTAAATAGGTATTAAGGTTGAGT 57.439 33.333 0.00 0.00 0.00 3.41
2083 2204 2.743664 TGAATGAAGCGTGATTGGACTG 59.256 45.455 0.00 0.00 0.00 3.51
2085 2206 3.610040 ATGAAGCGTGATTGGACTGTA 57.390 42.857 0.00 0.00 0.00 2.74
2109 2230 5.887598 AGGCTATGCATTTGATAGTGACAAA 59.112 36.000 3.54 0.00 40.62 2.83
2149 2275 8.237267 CAGTAAACTGTCATATTGGAGGAAAAC 58.763 37.037 1.81 0.00 39.09 2.43
2159 2285 2.712709 TGGAGGAAAACACAACAACGA 58.287 42.857 0.00 0.00 0.00 3.85
2321 2467 2.622436 AGTGGTCTTCTTAATGAGCGC 58.378 47.619 0.00 0.00 40.25 5.92
2446 2593 5.016051 ACTGAATATGAGTGGCACTACAG 57.984 43.478 22.11 21.39 0.00 2.74
2456 2603 0.460987 GGCACTACAGGCTACAGCAG 60.461 60.000 3.24 0.00 44.36 4.24
2496 2646 4.941263 GGCATTATACCATGAAGCCGATAA 59.059 41.667 0.00 0.00 0.00 1.75
2543 2693 2.606378 ACTCGTCCCTTGGGTATATCC 58.394 52.381 5.51 0.00 0.00 2.59
2586 2736 6.811253 AGAAACGTGGAAATGTAGCATTAA 57.189 33.333 0.00 0.00 0.00 1.40
2660 2810 2.708216 ATGGTATGACGCCATGAACA 57.292 45.000 0.00 0.00 44.36 3.18
2662 2812 3.828875 TGGTATGACGCCATGAACATA 57.171 42.857 0.00 0.00 34.31 2.29
2694 3011 3.243002 GCTGGATAGCTTTGAATGCTGTC 60.243 47.826 17.49 17.49 46.57 3.51
2713 3030 3.512329 TGTCGGTATGTGACTATTGTGGT 59.488 43.478 0.00 0.00 37.26 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.663734 CCTTAGTGGGAGGAGACATTTTAAT 58.336 40.000 0.00 0.00 36.33 1.40
1 2 5.572885 GCCTTAGTGGGAGGAGACATTTTAA 60.573 44.000 0.00 0.00 36.33 1.52
2 3 4.080526 GCCTTAGTGGGAGGAGACATTTTA 60.081 45.833 0.00 0.00 36.33 1.52
3 4 3.308473 GCCTTAGTGGGAGGAGACATTTT 60.308 47.826 0.00 0.00 36.33 1.82
4 5 2.239907 GCCTTAGTGGGAGGAGACATTT 59.760 50.000 0.00 0.00 36.33 2.32
7 8 0.116342 TGCCTTAGTGGGAGGAGACA 59.884 55.000 0.00 0.00 36.33 3.41
35 36 8.776376 TTTTCCTTGATTTATTTCAGGCATTC 57.224 30.769 0.00 0.00 0.00 2.67
38 39 6.594937 GCATTTTCCTTGATTTATTTCAGGCA 59.405 34.615 0.00 0.00 0.00 4.75
79 80 1.133482 CCCACCAGGTTTCAAGTCCTT 60.133 52.381 0.00 0.00 30.91 3.36
90 91 1.508256 GTATCCTTAGCCCACCAGGT 58.492 55.000 0.00 0.00 38.26 4.00
95 96 0.031721 CGGTCGTATCCTTAGCCCAC 59.968 60.000 0.00 0.00 0.00 4.61
110 111 1.829222 TGGATGGTTAGAAGGACGGTC 59.171 52.381 0.00 0.00 0.00 4.79
113 114 2.027561 TGGTTGGATGGTTAGAAGGACG 60.028 50.000 0.00 0.00 0.00 4.79
119 120 6.381498 TCAAACTATGGTTGGATGGTTAGA 57.619 37.500 0.00 0.00 35.63 2.10
132 133 5.010012 GGGCCTATCACAAATCAAACTATGG 59.990 44.000 0.84 0.00 0.00 2.74
135 136 5.186256 TGGGCCTATCACAAATCAAACTA 57.814 39.130 4.53 0.00 0.00 2.24
142 143 3.763897 GACAAGTTGGGCCTATCACAAAT 59.236 43.478 4.53 0.00 0.00 2.32
145 146 1.004277 GGACAAGTTGGGCCTATCACA 59.996 52.381 4.53 0.00 0.00 3.58
191 193 3.182152 AGCAAACCACTACTACCTCCAT 58.818 45.455 0.00 0.00 0.00 3.41
196 198 4.903054 ACCTTTAGCAAACCACTACTACC 58.097 43.478 0.00 0.00 0.00 3.18
197 199 9.657419 TTATTACCTTTAGCAAACCACTACTAC 57.343 33.333 0.00 0.00 0.00 2.73
221 223 8.315482 GGCTGAGGGTTGGTTTTATTAATTTTA 58.685 33.333 0.00 0.00 0.00 1.52
237 239 2.121963 TGTCTGGGGCTGAGGGTT 60.122 61.111 0.00 0.00 0.00 4.11
245 247 0.179936 CAATCTCTCCTGTCTGGGGC 59.820 60.000 0.00 0.00 35.85 5.80
248 250 4.550076 AGAAACAATCTCTCCTGTCTGG 57.450 45.455 0.00 0.00 30.46 3.86
249 251 8.558973 AATTAAGAAACAATCTCTCCTGTCTG 57.441 34.615 0.00 0.00 37.42 3.51
304 308 8.306313 ACAAAATCTTTTATGAGTATTCCCCC 57.694 34.615 0.00 0.00 0.00 5.40
361 368 3.367087 CCGAGCTAAAAGAGGACTTTCGA 60.367 47.826 0.00 0.00 44.32 3.71
458 492 5.314923 TCTAGTGATGAAATTTGGCAAGC 57.685 39.130 0.00 0.00 0.00 4.01
481 515 5.873179 TTTTATGATTTCCACGAGTGTCC 57.127 39.130 2.36 0.00 0.00 4.02
509 546 8.584157 TGTTATTATTGAAAGCATTTGGAGTGT 58.416 29.630 0.00 0.00 39.27 3.55
591 637 5.831702 TTTGTGCTTGCCAAATTTCATTT 57.168 30.435 0.00 0.00 0.00 2.32
652 698 8.859090 TCTCCTGAGCTCAAATGATTTTAAAAA 58.141 29.630 18.85 0.00 0.00 1.94
661 707 4.343526 GGAGTATCTCCTGAGCTCAAATGA 59.656 45.833 18.85 15.08 46.41 2.57
692 738 7.769507 TGATAGTGAGGGAGTAGTATAATAGCG 59.230 40.741 0.00 0.00 0.00 4.26
770 822 9.560860 AGAAAATACCCCCTCTTAATCAAAAAT 57.439 29.630 0.00 0.00 0.00 1.82
842 918 3.047735 CCACGTGGGCCCTTTTTC 58.952 61.111 27.57 7.35 0.00 2.29
925 1002 1.136500 GACCCTACAAGCCTAGTTCCG 59.864 57.143 0.00 0.00 0.00 4.30
964 1041 4.203076 CGACGGCGGGGTAGGAAG 62.203 72.222 13.24 0.00 0.00 3.46
1092 1185 2.444895 GGAGGCGGAGGAGGTGAT 60.445 66.667 0.00 0.00 0.00 3.06
1267 1362 2.025887 ACAGGCAGAAATTACAGGGAGG 60.026 50.000 0.00 0.00 0.00 4.30
1295 1390 1.153628 CATCTGGGTTCGACGTCCC 60.154 63.158 10.58 18.76 43.67 4.46
1302 1397 1.303236 TTGGGCACATCTGGGTTCG 60.303 57.895 0.00 0.00 0.00 3.95
1314 1409 1.340889 GCAAAGTTGTGATCTTGGGCA 59.659 47.619 0.00 0.00 0.00 5.36
1380 1475 1.206072 CAAGAACTGCACGCAGAGC 59.794 57.895 25.09 15.20 46.30 4.09
1381 1476 1.392853 GATCAAGAACTGCACGCAGAG 59.607 52.381 25.09 9.33 46.30 3.35
1382 1477 1.001293 AGATCAAGAACTGCACGCAGA 59.999 47.619 25.09 2.41 46.30 4.26
1385 1480 1.658095 GAGAGATCAAGAACTGCACGC 59.342 52.381 0.00 0.00 0.00 5.34
1386 1481 2.922387 CAGAGAGATCAAGAACTGCACG 59.078 50.000 0.00 0.00 0.00 5.34
1387 1482 3.924144 ACAGAGAGATCAAGAACTGCAC 58.076 45.455 0.00 0.00 0.00 4.57
1388 1483 4.769488 ACTACAGAGAGATCAAGAACTGCA 59.231 41.667 0.00 0.00 0.00 4.41
1390 1485 6.917477 GCATACTACAGAGAGATCAAGAACTG 59.083 42.308 0.00 0.00 0.00 3.16
1391 1486 6.238621 CGCATACTACAGAGAGATCAAGAACT 60.239 42.308 0.00 0.00 0.00 3.01
1392 1487 5.912396 CGCATACTACAGAGAGATCAAGAAC 59.088 44.000 0.00 0.00 0.00 3.01
1394 1489 5.008118 CACGCATACTACAGAGAGATCAAGA 59.992 44.000 0.00 0.00 0.00 3.02
1395 1490 5.211454 CACGCATACTACAGAGAGATCAAG 58.789 45.833 0.00 0.00 0.00 3.02
1398 1493 3.252215 AGCACGCATACTACAGAGAGATC 59.748 47.826 0.00 0.00 0.00 2.75
1399 1494 3.218453 AGCACGCATACTACAGAGAGAT 58.782 45.455 0.00 0.00 0.00 2.75
1400 1495 2.614520 GAGCACGCATACTACAGAGAGA 59.385 50.000 0.00 0.00 0.00 3.10
1401 1496 2.616376 AGAGCACGCATACTACAGAGAG 59.384 50.000 0.00 0.00 0.00 3.20
1402 1497 2.644676 AGAGCACGCATACTACAGAGA 58.355 47.619 0.00 0.00 0.00 3.10
1403 1498 3.111838 CAAGAGCACGCATACTACAGAG 58.888 50.000 0.00 0.00 0.00 3.35
1503 1607 0.169009 GAGCAGCAAAAGCGGTTAGG 59.831 55.000 0.00 0.00 37.01 2.69
1509 1613 1.126079 CAACAAGAGCAGCAAAAGCG 58.874 50.000 0.00 0.00 37.01 4.68
1655 1762 2.604174 CGACACCGGGAAAGTGCAC 61.604 63.158 9.40 9.40 38.87 4.57
1765 1872 9.961265 GAATCATGCTTCATTCATTTATGAGAA 57.039 29.630 4.42 0.00 38.19 2.87
1767 1874 9.399403 CTGAATCATGCTTCATTCATTTATGAG 57.601 33.333 12.12 0.00 38.15 2.90
1835 1942 2.957402 ATTCAACAGTCTGCCCTTGA 57.043 45.000 0.00 0.00 0.00 3.02
1850 1957 5.925506 TCAGAATCTGGGTACGTAATTCA 57.074 39.130 10.71 6.64 31.51 2.57
1858 1965 5.163405 TGAGCAAGTATCAGAATCTGGGTAC 60.163 44.000 10.71 13.06 31.51 3.34
1863 1970 6.732531 TTTGTGAGCAAGTATCAGAATCTG 57.267 37.500 3.38 3.38 35.82 2.90
1875 1982 3.254166 ACCATGTAGCTTTTGTGAGCAAG 59.746 43.478 0.00 0.00 45.12 4.01
1916 2036 4.530553 TGAGCACCAGACTCAACCTTAATA 59.469 41.667 0.00 0.00 41.10 0.98
1920 2040 1.131638 TGAGCACCAGACTCAACCTT 58.868 50.000 0.00 0.00 41.10 3.50
1929 2049 1.347378 TGTTGCATAGTGAGCACCAGA 59.653 47.619 0.00 0.00 42.54 3.86
2083 2204 5.991606 TGTCACTATCAAATGCATAGCCTAC 59.008 40.000 0.00 0.00 0.00 3.18
2085 2206 5.039920 TGTCACTATCAAATGCATAGCCT 57.960 39.130 0.00 0.00 0.00 4.58
2132 2255 6.325919 TGTTGTGTTTTCCTCCAATATGAC 57.674 37.500 0.00 0.00 0.00 3.06
2144 2270 2.590712 CGTTGGTCGTTGTTGTGTTTTC 59.409 45.455 0.00 0.00 34.52 2.29
2149 2275 1.298041 GCCGTTGGTCGTTGTTGTG 60.298 57.895 0.00 0.00 37.94 3.33
2159 2285 2.752903 GTTGATCTTTATGGCCGTTGGT 59.247 45.455 0.77 0.00 0.00 3.67
2227 2353 9.737427 CTACATCTGTCCTAAACTGTTATGTAG 57.263 37.037 15.65 15.65 37.76 2.74
2446 2593 2.439156 CCTTGCCCTGCTGTAGCC 60.439 66.667 0.80 0.00 41.18 3.93
2456 2603 1.004679 CCAACAATGTGCCTTGCCC 60.005 57.895 0.00 0.00 0.00 5.36
2519 2669 1.833787 TACCCAAGGGACGAGTTGGC 61.834 60.000 13.15 0.00 41.77 4.52
2543 2693 3.814842 TCTTGCGCAAACCATATATCAGG 59.185 43.478 25.01 7.55 0.00 3.86
2586 2736 0.830444 TTGCGAGGTCCACAGGTAGT 60.830 55.000 0.00 0.00 0.00 2.73
2694 3011 4.500127 TCAACCACAATAGTCACATACCG 58.500 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.