Multiple sequence alignment - TraesCS5D01G087900

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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 TraesCS5D01G087900 chr5D 100.000 3578 0 0 1 3578 93863957 93860380 0.000000e+00 6608
1 TraesCS5D01G087900 chr5D 85.742 1564 214 4 1012 2566 3660820 3659257 0.000000e+00 1644
2 TraesCS5D01G087900 chr5D 82.812 320 46 3 2848 3158 3638275 3638594 9.780000e-71 278
3 TraesCS5D01G087900 chr5A 94.590 3124 114 16 477 3578 87418314 87415224 0.000000e+00 4782
4 TraesCS5D01G087900 chr5B 97.320 1679 40 2 990 2664 98846277 98844600 0.000000e+00 2846
5 TraesCS5D01G087900 chr5B 84.460 1731 233 17 945 2666 5067285 5065582 0.000000e+00 1674
6 TraesCS5D01G087900 chr5B 85.385 1560 222 4 1013 2566 5072940 5071381 0.000000e+00 1613
7 TraesCS5D01G087900 chr5B 84.749 1036 64 32 1 994 98849566 98848583 0.000000e+00 952
8 TraesCS5D01G087900 chr5B 92.793 222 10 5 2657 2872 98843770 98843549 2.070000e-82 316
9 TraesCS5D01G087900 chr5B 82.812 320 46 3 2848 3158 5064614 5064295 9.780000e-71 278
10 TraesCS5D01G087900 chr5B 94.521 73 4 0 3506 3578 536480815 536480887 2.920000e-21 113
11 TraesCS5D01G087900 chr7A 85.279 1576 223 6 991 2566 700300301 700301867 0.000000e+00 1616
12 TraesCS5D01G087900 chr7A 85.216 1576 224 6 991 2566 700338119 700339685 0.000000e+00 1611
13 TraesCS5D01G087900 chr7A 83.117 154 26 0 3005 3158 700390004 700390157 1.340000e-29 141
14 TraesCS5D01G087900 chr7D 85.968 1518 204 1 991 2508 610421509 610420001 0.000000e+00 1615
15 TraesCS5D01G087900 chr7D 85.987 157 19 1 3005 3158 514989075 514989231 7.950000e-37 165
16 TraesCS5D01G087900 chr7D 81.875 160 21 3 3005 3156 610715666 610715825 1.040000e-25 128
17 TraesCS5D01G087900 chr7B 84.987 1552 224 2 993 2544 698682805 698684347 0.000000e+00 1567
18 TraesCS5D01G087900 chr7B 89.175 388 33 7 3148 3529 286563283 286563667 3.230000e-130 475
19 TraesCS5D01G087900 chr7B 79.605 152 29 2 3005 3156 693710649 693710798 1.360000e-19 108
20 TraesCS5D01G087900 chr2D 94.824 425 20 2 3156 3578 30405003 30404579 0.000000e+00 662
21 TraesCS5D01G087900 chr3B 92.350 366 26 2 3156 3519 225178361 225178726 1.470000e-143 520
22 TraesCS5D01G087900 chr1A 91.375 371 31 1 3150 3519 242688200 242688570 1.150000e-139 507
23 TraesCS5D01G087900 chrUn 90.984 366 31 2 3156 3519 287847625 287847260 3.210000e-135 492
24 TraesCS5D01G087900 chrUn 90.984 366 31 2 3156 3519 295169057 295168692 3.210000e-135 492
25 TraesCS5D01G087900 chrUn 90.984 366 31 2 3156 3519 347971746 347971381 3.210000e-135 492
26 TraesCS5D01G087900 chrUn 83.117 154 26 0 3005 3158 83461799 83461646 1.340000e-29 141
27 TraesCS5D01G087900 chr4A 89.737 380 29 8 3156 3529 249772757 249772382 8.990000e-131 477
28 TraesCS5D01G087900 chr4A 83.439 157 23 1 3005 3158 661981250 661981094 3.720000e-30 143


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 TraesCS5D01G087900 chr5D 93860380 93863957 3577 True 6608.000000 6608 100.000000 1 3578 1 chr5D.!!$R2 3577
1 TraesCS5D01G087900 chr5D 3659257 3660820 1563 True 1644.000000 1644 85.742000 1012 2566 1 chr5D.!!$R1 1554
2 TraesCS5D01G087900 chr5A 87415224 87418314 3090 True 4782.000000 4782 94.590000 477 3578 1 chr5A.!!$R1 3101
3 TraesCS5D01G087900 chr5B 5071381 5072940 1559 True 1613.000000 1613 85.385000 1013 2566 1 chr5B.!!$R1 1553
4 TraesCS5D01G087900 chr5B 98843549 98849566 6017 True 1371.333333 2846 91.620667 1 2872 3 chr5B.!!$R3 2871
5 TraesCS5D01G087900 chr5B 5064295 5067285 2990 True 976.000000 1674 83.636000 945 3158 2 chr5B.!!$R2 2213
6 TraesCS5D01G087900 chr7A 700300301 700301867 1566 False 1616.000000 1616 85.279000 991 2566 1 chr7A.!!$F1 1575
7 TraesCS5D01G087900 chr7A 700338119 700339685 1566 False 1611.000000 1611 85.216000 991 2566 1 chr7A.!!$F2 1575
8 TraesCS5D01G087900 chr7D 610420001 610421509 1508 True 1615.000000 1615 85.968000 991 2508 1 chr7D.!!$R1 1517
9 TraesCS5D01G087900 chr7B 698682805 698684347 1542 False 1567.000000 1567 84.987000 993 2544 1 chr7B.!!$F3 1551

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
163 165 0.252239 GCCCTTTCCCCCACTGAATT 60.252 55.0 0.0 0.0 0.0 2.17 F
238 240 0.473755 ACCTGGCTTGATGTGTGTCA 59.526 50.0 0.0 0.0 0.0 3.58 F
1645 4021 0.321564 CTTCGACACCCTTGCCATGA 60.322 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 3844 2.032620 AGGCAGGTAAGAATCGACGAT 58.967 47.619 4.05 4.05 0.0 3.73 R
1649 4025 2.036387 TGACGTCCTCCTTCTGTTTCA 58.964 47.619 14.12 0.00 0.0 2.69 R
3458 7514 0.319297 GCTGGGAAAAACTGCTGCTG 60.319 55.000 4.89 4.89 0.0 4.41 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
40 41 3.880490 TCAAGTAAATCACCACACCACAC 59.120 43.478 0.00 0.00 0.00 3.82
47 48 1.768275 TCACCACACCACACAGATCTT 59.232 47.619 0.00 0.00 0.00 2.40
49 50 3.389656 TCACCACACCACACAGATCTTTA 59.610 43.478 0.00 0.00 0.00 1.85
50 51 3.748048 CACCACACCACACAGATCTTTAG 59.252 47.826 0.00 0.00 0.00 1.85
73 74 5.188751 AGGATTAGATCAACCTAGCCTATGC 59.811 44.000 0.00 0.00 37.95 3.14
110 112 7.982354 CCGTTAGATCTTGAGGAGACTAAATTT 59.018 37.037 0.00 0.00 44.43 1.82
117 119 7.450074 TCTTGAGGAGACTAAATTTGCAGTTA 58.550 34.615 0.00 0.00 44.43 2.24
118 120 8.103305 TCTTGAGGAGACTAAATTTGCAGTTAT 58.897 33.333 0.00 0.00 44.43 1.89
123 125 9.914131 AGGAGACTAAATTTGCAGTTATTTTTC 57.086 29.630 0.00 6.55 40.61 2.29
139 141 2.708216 TTTCACTTCTGTGGAGCACA 57.292 45.000 0.00 0.00 43.94 4.57
153 155 2.574018 GCACAACAGGCCCTTTCCC 61.574 63.158 0.00 0.00 0.00 3.97
154 156 1.908299 CACAACAGGCCCTTTCCCC 60.908 63.158 0.00 0.00 0.00 4.81
156 158 2.785389 AACAGGCCCTTTCCCCCA 60.785 61.111 0.00 0.00 0.00 4.96
157 159 3.160478 AACAGGCCCTTTCCCCCAC 62.160 63.158 0.00 0.00 0.00 4.61
159 161 3.268032 AGGCCCTTTCCCCCACTG 61.268 66.667 0.00 0.00 0.00 3.66
161 163 2.851045 GCCCTTTCCCCCACTGAA 59.149 61.111 0.00 0.00 0.00 3.02
162 164 1.388133 GCCCTTTCCCCCACTGAAT 59.612 57.895 0.00 0.00 0.00 2.57
163 165 0.252239 GCCCTTTCCCCCACTGAATT 60.252 55.000 0.00 0.00 0.00 2.17
164 166 1.852633 CCCTTTCCCCCACTGAATTC 58.147 55.000 0.00 0.00 0.00 2.17
165 167 1.359130 CCCTTTCCCCCACTGAATTCT 59.641 52.381 7.05 0.00 0.00 2.40
166 168 2.225369 CCCTTTCCCCCACTGAATTCTT 60.225 50.000 7.05 0.00 0.00 2.52
167 169 3.510459 CCTTTCCCCCACTGAATTCTTT 58.490 45.455 7.05 0.00 0.00 2.52
168 170 3.511540 CCTTTCCCCCACTGAATTCTTTC 59.488 47.826 7.05 0.00 0.00 2.62
169 171 3.893753 TTCCCCCACTGAATTCTTTCA 57.106 42.857 7.05 0.00 39.54 2.69
170 172 3.154827 TCCCCCACTGAATTCTTTCAC 57.845 47.619 7.05 0.00 36.94 3.18
171 173 2.445145 TCCCCCACTGAATTCTTTCACA 59.555 45.455 7.05 0.00 36.94 3.58
214 216 4.708177 TCTGACCTTCTTGACCTTTTCAG 58.292 43.478 0.00 0.00 34.94 3.02
215 217 3.214328 TGACCTTCTTGACCTTTTCAGC 58.786 45.455 0.00 0.00 34.94 4.26
228 230 1.108727 TTTCAGCACCACCTGGCTTG 61.109 55.000 0.00 0.00 38.56 4.01
229 231 1.993701 TTCAGCACCACCTGGCTTGA 61.994 55.000 0.00 0.00 38.56 3.02
230 232 1.303888 CAGCACCACCTGGCTTGAT 60.304 57.895 0.00 0.00 38.56 2.57
231 233 1.303888 AGCACCACCTGGCTTGATG 60.304 57.895 0.00 0.00 36.92 3.07
232 234 1.604593 GCACCACCTGGCTTGATGT 60.605 57.895 0.00 0.00 39.32 3.06
233 235 1.870055 GCACCACCTGGCTTGATGTG 61.870 60.000 0.00 0.00 39.32 3.21
234 236 0.538057 CACCACCTGGCTTGATGTGT 60.538 55.000 0.00 0.00 39.32 3.72
235 237 0.538057 ACCACCTGGCTTGATGTGTG 60.538 55.000 0.00 0.00 39.32 3.82
236 238 0.538057 CCACCTGGCTTGATGTGTGT 60.538 55.000 0.00 0.00 0.00 3.72
237 239 0.877071 CACCTGGCTTGATGTGTGTC 59.123 55.000 0.00 0.00 0.00 3.67
238 240 0.473755 ACCTGGCTTGATGTGTGTCA 59.526 50.000 0.00 0.00 0.00 3.58
239 241 1.133823 ACCTGGCTTGATGTGTGTCAA 60.134 47.619 0.00 0.00 36.70 3.18
240 242 1.267806 CCTGGCTTGATGTGTGTCAAC 59.732 52.381 0.00 0.00 34.58 3.18
241 243 1.267806 CTGGCTTGATGTGTGTCAACC 59.732 52.381 0.00 0.00 34.58 3.77
242 244 1.133823 TGGCTTGATGTGTGTCAACCT 60.134 47.619 0.00 0.00 34.58 3.50
296 298 6.721571 TTTCGATTCTACAAACATCAGTCC 57.278 37.500 0.00 0.00 0.00 3.85
297 299 5.661056 TCGATTCTACAAACATCAGTCCT 57.339 39.130 0.00 0.00 0.00 3.85
302 304 7.043125 CGATTCTACAAACATCAGTCCTGTATG 60.043 40.741 0.00 0.80 30.27 2.39
313 315 4.469586 TCAGTCCTGTATGTAAATGGCAGA 59.530 41.667 0.00 0.00 0.00 4.26
347 370 2.906389 AGTCTTGTATGAAGTGGCAGGA 59.094 45.455 0.00 0.00 0.00 3.86
357 380 3.255642 TGAAGTGGCAGGATTTTGTTAGC 59.744 43.478 0.00 0.00 0.00 3.09
372 395 0.874390 TTAGCGCTGAAAACCTGCAG 59.126 50.000 22.90 6.78 39.38 4.41
377 400 1.334869 CGCTGAAAACCTGCAGAAAGT 59.665 47.619 17.39 0.92 39.38 2.66
380 403 4.290969 GCTGAAAACCTGCAGAAAGTTAC 58.709 43.478 17.39 9.33 39.25 2.50
381 404 4.036852 GCTGAAAACCTGCAGAAAGTTACT 59.963 41.667 17.39 2.13 39.25 2.24
382 405 5.751243 TGAAAACCTGCAGAAAGTTACTC 57.249 39.130 17.39 11.29 0.00 2.59
385 408 6.482308 TGAAAACCTGCAGAAAGTTACTCTAC 59.518 38.462 17.39 1.55 0.00 2.59
387 410 5.810080 ACCTGCAGAAAGTTACTCTACTT 57.190 39.130 17.39 0.00 39.97 2.24
389 412 5.304614 ACCTGCAGAAAGTTACTCTACTTCA 59.695 40.000 17.39 0.00 37.37 3.02
396 419 7.872993 CAGAAAGTTACTCTACTTCATCAACCA 59.127 37.037 0.00 0.00 37.37 3.67
400 423 8.608844 AGTTACTCTACTTCATCAACCAAAAG 57.391 34.615 0.00 0.00 0.00 2.27
409 432 7.433680 ACTTCATCAACCAAAAGTAAACCATC 58.566 34.615 0.00 0.00 30.47 3.51
410 433 7.287696 ACTTCATCAACCAAAAGTAAACCATCT 59.712 33.333 0.00 0.00 30.47 2.90
417 440 6.238648 ACCAAAAGTAAACCATCTCCTAGTG 58.761 40.000 0.00 0.00 0.00 2.74
442 465 3.001414 CTCACTTCTTGTCCAGCATCAG 58.999 50.000 0.00 0.00 0.00 2.90
444 467 1.093159 CTTCTTGTCCAGCATCAGGC 58.907 55.000 0.00 0.00 45.30 4.85
481 504 3.754965 TGGTTGCTTGCTAGTGAAGAAT 58.245 40.909 7.59 0.00 0.00 2.40
493 535 4.104383 AGTGAAGAATGCCAAGAAGGAA 57.896 40.909 0.00 0.00 41.22 3.36
494 536 4.077822 AGTGAAGAATGCCAAGAAGGAAG 58.922 43.478 0.00 0.00 41.22 3.46
495 537 3.192212 GTGAAGAATGCCAAGAAGGAAGG 59.808 47.826 0.00 0.00 41.22 3.46
499 541 4.397348 GCCAAGAAGGAAGGCGAA 57.603 55.556 0.00 0.00 41.22 4.70
500 542 2.175236 GCCAAGAAGGAAGGCGAAG 58.825 57.895 0.00 0.00 41.22 3.79
518 560 3.607775 CGAAGCAAAGGACACAACATCAG 60.608 47.826 0.00 0.00 0.00 2.90
557 603 2.997980 TGAAGCAAGGTGACAAGTGAA 58.002 42.857 0.00 0.00 0.00 3.18
558 604 2.945008 TGAAGCAAGGTGACAAGTGAAG 59.055 45.455 0.00 0.00 0.00 3.02
614 662 6.480763 TCCCTTGCATAAAAAGATACAGTGA 58.519 36.000 0.00 0.00 0.00 3.41
666 723 8.644318 ATGGATTGAGTACTACAATACGAAAC 57.356 34.615 17.88 8.45 40.32 2.78
669 726 7.758528 GGATTGAGTACTACAATACGAAACACT 59.241 37.037 15.87 0.00 37.96 3.55
678 735 5.060506 ACAATACGAAACACTCCAACATGA 58.939 37.500 0.00 0.00 0.00 3.07
708 770 3.370953 GCTAGACCCAACCATTCACTCAT 60.371 47.826 0.00 0.00 0.00 2.90
827 889 1.235281 CCCGACGATCTGCTCCGATA 61.235 60.000 0.00 0.00 0.00 2.92
829 891 1.663445 CCGACGATCTGCTCCGATAAC 60.663 57.143 0.00 0.00 0.00 1.89
940 1006 4.680237 CGTCCGGTGCAGAGCCAA 62.680 66.667 0.00 0.00 0.00 4.52
984 1050 5.180304 GCAAGAAAAACCCAAGACACAAAAA 59.820 36.000 0.00 0.00 0.00 1.94
985 1051 6.128035 GCAAGAAAAACCCAAGACACAAAAAT 60.128 34.615 0.00 0.00 0.00 1.82
986 1052 7.463544 CAAGAAAAACCCAAGACACAAAAATC 58.536 34.615 0.00 0.00 0.00 2.17
988 1054 7.164803 AGAAAAACCCAAGACACAAAAATCAA 58.835 30.769 0.00 0.00 0.00 2.57
1468 3844 1.174078 TAAGCGACACCACGACCTCA 61.174 55.000 0.00 0.00 35.09 3.86
1554 3930 1.856265 GCCGCCTCTTCACCAACAAG 61.856 60.000 0.00 0.00 0.00 3.16
1645 4021 0.321564 CTTCGACACCCTTGCCATGA 60.322 55.000 0.00 0.00 0.00 3.07
1649 4025 0.251341 GACACCCTTGCCATGAACCT 60.251 55.000 0.00 0.00 0.00 3.50
1650 4026 0.540365 ACACCCTTGCCATGAACCTG 60.540 55.000 0.00 0.00 0.00 4.00
2243 4619 3.204526 AGAACTACCTAGATGTCGTCGG 58.795 50.000 0.00 0.00 0.00 4.79
2434 4819 0.898320 CAAGGCGAAGGAGGAAGAGA 59.102 55.000 0.00 0.00 0.00 3.10
2589 4998 2.757868 ACAGGAGTAGAGTGAGCATGTC 59.242 50.000 0.00 0.00 0.00 3.06
2611 5020 1.066858 ACTACATGCTCCGTGACCAAG 60.067 52.381 0.00 0.00 0.00 3.61
2792 6226 8.132362 TGTATTTGTAAATGCAGAACGAAACTT 58.868 29.630 4.36 0.00 36.34 2.66
2808 6243 6.142817 ACGAAACTTAGCTTGTTTGCATAAG 58.857 36.000 18.16 4.30 37.70 1.73
2811 6246 7.268447 CGAAACTTAGCTTGTTTGCATAAGTAC 59.732 37.037 18.16 4.89 37.70 2.73
2873 6920 4.220602 AGAAGTTGAATTTACACATGGCCC 59.779 41.667 0.00 0.00 0.00 5.80
2899 6949 4.141390 ACCACATTCAGGTTCTCTTTGTCT 60.141 41.667 0.00 0.00 35.33 3.41
2905 6955 3.004839 TCAGGTTCTCTTTGTCTGACGAG 59.995 47.826 2.98 4.28 30.58 4.18
2932 6985 2.315781 GACCAGATCCCATGAGCGCA 62.316 60.000 11.47 0.00 30.37 6.09
3002 7058 6.003950 CCAAGTAATCCAGTTCTTTCTTCCA 58.996 40.000 0.00 0.00 0.00 3.53
3006 7062 5.459536 AATCCAGTTCTTTCTTCCAAAGC 57.540 39.130 0.00 0.00 0.00 3.51
3024 7080 1.618837 AGCTGGTTCTTCTCGCTGTTA 59.381 47.619 0.00 0.00 0.00 2.41
3050 7106 1.819288 TCGTCTTCTGAGCCCTTACAG 59.181 52.381 0.00 0.00 35.72 2.74
3086 7142 0.679002 CATGACCAACAGCAGGAGGG 60.679 60.000 0.00 0.00 0.00 4.30
3097 7153 1.518903 GCAGGAGGGTCACAAAGCAC 61.519 60.000 0.00 0.00 0.00 4.40
3162 7218 5.450965 GGATTATGACAACCATCAGGCTTTG 60.451 44.000 0.00 0.00 39.06 2.77
3186 7242 1.490910 GGTAGAAGTGGATTGGGGAGG 59.509 57.143 0.00 0.00 0.00 4.30
3187 7243 2.197465 GTAGAAGTGGATTGGGGAGGT 58.803 52.381 0.00 0.00 0.00 3.85
3188 7244 1.760405 AGAAGTGGATTGGGGAGGTT 58.240 50.000 0.00 0.00 0.00 3.50
3189 7245 2.073776 AGAAGTGGATTGGGGAGGTTT 58.926 47.619 0.00 0.00 0.00 3.27
3190 7246 2.171003 GAAGTGGATTGGGGAGGTTTG 58.829 52.381 0.00 0.00 0.00 2.93
3191 7247 0.409484 AGTGGATTGGGGAGGTTTGG 59.591 55.000 0.00 0.00 0.00 3.28
3192 7248 0.614697 GTGGATTGGGGAGGTTTGGG 60.615 60.000 0.00 0.00 0.00 4.12
3193 7249 1.001631 GGATTGGGGAGGTTTGGGG 59.998 63.158 0.00 0.00 0.00 4.96
3194 7250 1.514864 GGATTGGGGAGGTTTGGGGA 61.515 60.000 0.00 0.00 0.00 4.81
3241 7297 1.615262 CCTTCCCTCCACCCAATCC 59.385 63.158 0.00 0.00 0.00 3.01
3273 7329 0.411848 TTGAATCCCCCAAACCCCTC 59.588 55.000 0.00 0.00 0.00 4.30
3285 7341 1.686236 AACCCCTCCATCCACAATCT 58.314 50.000 0.00 0.00 0.00 2.40
3297 7353 7.885297 TCCATCCACAATCTTCTTTGTTTAAG 58.115 34.615 0.00 0.00 37.73 1.85
3328 7384 5.699097 TTGGTAGGCAAGTTTTGTCATAC 57.301 39.130 0.00 0.00 37.85 2.39
3458 7514 7.547227 ACAAAGTTGCTACATGGGAATAATTC 58.453 34.615 0.13 0.00 0.00 2.17
3482 7538 0.104671 GCAGTTTTTCCCAGCAGCAA 59.895 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.515191 TGTGGTGATTTACTTGACTTGAGC 59.485 41.667 0.00 0.00 0.00 4.26
47 48 7.093289 GCATAGGCTAGGTTGATCTAATCCTAA 60.093 40.741 8.11 0.00 32.91 2.69
49 50 5.188751 GCATAGGCTAGGTTGATCTAATCCT 59.811 44.000 8.11 0.00 36.96 3.24
50 51 5.423886 GCATAGGCTAGGTTGATCTAATCC 58.576 45.833 8.11 0.00 36.96 3.01
73 74 7.094975 CCTCAAGATCTAACGGTCTAGTCATAG 60.095 44.444 0.00 0.00 0.00 2.23
74 75 6.711194 CCTCAAGATCTAACGGTCTAGTCATA 59.289 42.308 0.00 0.00 0.00 2.15
75 76 5.533154 CCTCAAGATCTAACGGTCTAGTCAT 59.467 44.000 0.00 0.00 0.00 3.06
76 77 4.882427 CCTCAAGATCTAACGGTCTAGTCA 59.118 45.833 0.00 0.00 0.00 3.41
77 78 5.124645 TCCTCAAGATCTAACGGTCTAGTC 58.875 45.833 0.00 0.00 0.00 2.59
123 125 1.600957 CTGTTGTGCTCCACAGAAGTG 59.399 52.381 13.22 0.00 45.39 3.16
128 130 2.263741 GGCCTGTTGTGCTCCACAG 61.264 63.158 11.88 11.88 45.39 3.66
129 131 2.203337 GGCCTGTTGTGCTCCACA 60.203 61.111 0.00 0.00 43.02 4.17
139 141 2.785389 TGGGGGAAAGGGCCTGTT 60.785 61.111 6.92 3.40 0.00 3.16
153 155 5.520376 AACTTGTGAAAGAATTCAGTGGG 57.480 39.130 8.44 0.00 45.88 4.61
154 156 6.256321 CCAAAACTTGTGAAAGAATTCAGTGG 59.744 38.462 8.44 0.00 45.88 4.00
156 158 6.154363 TCCCAAAACTTGTGAAAGAATTCAGT 59.846 34.615 8.44 0.00 45.88 3.41
157 159 6.572519 TCCCAAAACTTGTGAAAGAATTCAG 58.427 36.000 8.44 0.00 45.88 3.02
159 161 8.337532 CAAATCCCAAAACTTGTGAAAGAATTC 58.662 33.333 0.00 0.00 36.04 2.17
161 163 7.563906 TCAAATCCCAAAACTTGTGAAAGAAT 58.436 30.769 0.00 0.00 0.00 2.40
162 164 6.940739 TCAAATCCCAAAACTTGTGAAAGAA 58.059 32.000 0.00 0.00 0.00 2.52
163 165 6.537453 TCAAATCCCAAAACTTGTGAAAGA 57.463 33.333 0.00 0.00 0.00 2.52
164 166 7.790823 AATCAAATCCCAAAACTTGTGAAAG 57.209 32.000 0.00 0.00 0.00 2.62
165 167 7.826252 TCAAATCAAATCCCAAAACTTGTGAAA 59.174 29.630 0.00 0.00 0.00 2.69
166 168 7.334090 TCAAATCAAATCCCAAAACTTGTGAA 58.666 30.769 0.00 0.00 0.00 3.18
167 169 6.882656 TCAAATCAAATCCCAAAACTTGTGA 58.117 32.000 0.00 0.00 0.00 3.58
168 170 7.658575 AGATCAAATCAAATCCCAAAACTTGTG 59.341 33.333 0.00 0.00 0.00 3.33
169 171 7.658575 CAGATCAAATCAAATCCCAAAACTTGT 59.341 33.333 0.00 0.00 0.00 3.16
170 172 7.874016 TCAGATCAAATCAAATCCCAAAACTTG 59.126 33.333 0.00 0.00 0.00 3.16
171 173 7.874528 GTCAGATCAAATCAAATCCCAAAACTT 59.125 33.333 0.00 0.00 0.00 2.66
214 216 1.604593 ACATCAAGCCAGGTGGTGC 60.605 57.895 0.00 0.00 37.57 5.01
215 217 0.538057 ACACATCAAGCCAGGTGGTG 60.538 55.000 0.00 0.00 37.57 4.17
228 230 5.330455 TGATCTCTAGGTTGACACACATC 57.670 43.478 0.00 0.00 0.00 3.06
229 231 5.337894 CCTTGATCTCTAGGTTGACACACAT 60.338 44.000 0.00 0.00 34.77 3.21
230 232 4.021104 CCTTGATCTCTAGGTTGACACACA 60.021 45.833 0.00 0.00 34.77 3.72
231 233 4.499183 CCTTGATCTCTAGGTTGACACAC 58.501 47.826 0.00 0.00 34.77 3.82
232 234 4.808414 CCTTGATCTCTAGGTTGACACA 57.192 45.455 0.00 0.00 34.77 3.72
240 242 1.799933 AGCCCACCTTGATCTCTAGG 58.200 55.000 6.20 6.20 43.16 3.02
288 290 5.125356 TGCCATTTACATACAGGACTGATG 58.875 41.667 6.29 7.98 0.00 3.07
296 298 7.558161 TCAGAATTCTGCCATTTACATACAG 57.442 36.000 27.45 1.66 43.46 2.74
297 299 7.392953 TGTTCAGAATTCTGCCATTTACATACA 59.607 33.333 27.45 14.83 43.46 2.29
302 304 6.855836 TGATGTTCAGAATTCTGCCATTTAC 58.144 36.000 27.45 18.48 43.46 2.01
347 370 4.298332 CAGGTTTTCAGCGCTAACAAAAT 58.702 39.130 20.03 6.36 0.00 1.82
357 380 1.334869 ACTTTCTGCAGGTTTTCAGCG 59.665 47.619 15.13 0.00 0.00 5.18
372 395 8.603242 TTGGTTGATGAAGTAGAGTAACTTTC 57.397 34.615 0.00 0.00 39.78 2.62
380 403 8.290325 GGTTTACTTTTGGTTGATGAAGTAGAG 58.710 37.037 0.00 0.00 36.35 2.43
381 404 7.776030 TGGTTTACTTTTGGTTGATGAAGTAGA 59.224 33.333 0.00 0.00 36.35 2.59
382 405 7.936584 TGGTTTACTTTTGGTTGATGAAGTAG 58.063 34.615 0.00 0.00 36.35 2.57
385 408 7.661040 AGATGGTTTACTTTTGGTTGATGAAG 58.339 34.615 0.00 0.00 0.00 3.02
387 410 6.208599 GGAGATGGTTTACTTTTGGTTGATGA 59.791 38.462 0.00 0.00 0.00 2.92
389 412 6.314917 AGGAGATGGTTTACTTTTGGTTGAT 58.685 36.000 0.00 0.00 0.00 2.57
396 419 8.606830 AGAATCACTAGGAGATGGTTTACTTTT 58.393 33.333 0.00 0.00 0.00 2.27
400 423 7.113658 TGAGAATCACTAGGAGATGGTTTAC 57.886 40.000 0.00 0.00 42.56 2.01
417 440 3.668447 TGCTGGACAAGAAGTGAGAATC 58.332 45.455 0.00 0.00 0.00 2.52
427 450 0.401356 TTGCCTGATGCTGGACAAGA 59.599 50.000 0.00 0.00 42.00 3.02
432 455 1.001764 CCACTTGCCTGATGCTGGA 60.002 57.895 0.00 0.00 42.00 3.86
435 458 1.677966 CTGCCACTTGCCTGATGCT 60.678 57.895 0.00 0.00 42.00 3.79
442 465 2.575461 GCAATCCTGCCACTTGCC 59.425 61.111 0.00 0.00 43.26 4.52
481 504 0.606401 CTTCGCCTTCCTTCTTGGCA 60.606 55.000 0.00 0.00 46.39 4.92
493 535 0.465460 TTGTGTCCTTTGCTTCGCCT 60.465 50.000 0.00 0.00 0.00 5.52
494 536 0.317854 GTTGTGTCCTTTGCTTCGCC 60.318 55.000 0.00 0.00 0.00 5.54
495 537 0.380378 TGTTGTGTCCTTTGCTTCGC 59.620 50.000 0.00 0.00 0.00 4.70
496 538 2.290367 TGATGTTGTGTCCTTTGCTTCG 59.710 45.455 0.00 0.00 0.00 3.79
497 539 3.565482 TCTGATGTTGTGTCCTTTGCTTC 59.435 43.478 0.00 0.00 0.00 3.86
498 540 3.554934 TCTGATGTTGTGTCCTTTGCTT 58.445 40.909 0.00 0.00 0.00 3.91
499 541 3.144506 CTCTGATGTTGTGTCCTTTGCT 58.855 45.455 0.00 0.00 0.00 3.91
500 542 2.227388 CCTCTGATGTTGTGTCCTTTGC 59.773 50.000 0.00 0.00 0.00 3.68
501 543 3.743521 TCCTCTGATGTTGTGTCCTTTG 58.256 45.455 0.00 0.00 0.00 2.77
502 544 4.392940 CTTCCTCTGATGTTGTGTCCTTT 58.607 43.478 0.00 0.00 0.00 3.11
503 545 3.808618 GCTTCCTCTGATGTTGTGTCCTT 60.809 47.826 0.00 0.00 0.00 3.36
504 546 2.289945 GCTTCCTCTGATGTTGTGTCCT 60.290 50.000 0.00 0.00 0.00 3.85
505 547 2.079925 GCTTCCTCTGATGTTGTGTCC 58.920 52.381 0.00 0.00 0.00 4.02
506 548 2.079925 GGCTTCCTCTGATGTTGTGTC 58.920 52.381 0.00 0.00 0.00 3.67
507 549 1.421268 TGGCTTCCTCTGATGTTGTGT 59.579 47.619 0.00 0.00 0.00 3.72
508 550 2.189594 TGGCTTCCTCTGATGTTGTG 57.810 50.000 0.00 0.00 0.00 3.33
509 551 2.957402 TTGGCTTCCTCTGATGTTGT 57.043 45.000 0.00 0.00 0.00 3.32
510 552 2.426024 CCATTGGCTTCCTCTGATGTTG 59.574 50.000 0.00 0.00 0.00 3.33
511 553 2.309755 TCCATTGGCTTCCTCTGATGTT 59.690 45.455 0.00 0.00 0.00 2.71
518 560 2.092753 TCATGTCTCCATTGGCTTCCTC 60.093 50.000 0.00 0.00 0.00 3.71
538 580 2.945668 ACTTCACTTGTCACCTTGCTTC 59.054 45.455 0.00 0.00 0.00 3.86
546 588 3.932710 TGTCACTTCACTTCACTTGTCAC 59.067 43.478 0.00 0.00 0.00 3.67
557 603 1.617850 CTCTGCTCCTGTCACTTCACT 59.382 52.381 0.00 0.00 0.00 3.41
558 604 1.342819 ACTCTGCTCCTGTCACTTCAC 59.657 52.381 0.00 0.00 0.00 3.18
678 735 0.400594 GTTGGGTCTAGCCAACAGGT 59.599 55.000 29.82 0.00 43.77 4.00
708 770 4.416516 TCCCAGTACAGATTGAGACAAGA 58.583 43.478 0.00 0.00 0.00 3.02
788 850 1.562783 GTAGGTGGAGAGGAGCTGTT 58.437 55.000 0.00 0.00 0.00 3.16
827 889 0.383231 AGGTCGTCGTCTTTGTCGTT 59.617 50.000 0.00 0.00 0.00 3.85
829 891 1.002250 CCAGGTCGTCGTCTTTGTCG 61.002 60.000 0.00 0.00 0.00 4.35
940 1006 2.103941 GCTGGAAGGCTGTAGCTCTATT 59.896 50.000 3.63 0.00 41.70 1.73
984 1050 0.549950 CCATGGCTGGACCTCTTGAT 59.450 55.000 0.00 0.00 46.37 2.57
985 1051 0.547471 TCCATGGCTGGACCTCTTGA 60.547 55.000 6.96 0.00 46.95 3.02
986 1052 0.107312 CTCCATGGCTGGACCTCTTG 60.107 60.000 6.96 0.00 46.95 3.02
988 1054 1.692042 CCTCCATGGCTGGACCTCT 60.692 63.158 15.87 0.00 46.95 3.69
1468 3844 2.032620 AGGCAGGTAAGAATCGACGAT 58.967 47.619 4.05 4.05 0.00 3.73
1645 4021 2.224305 CGTCCTCCTTCTGTTTCAGGTT 60.224 50.000 0.00 0.00 31.51 3.50
1649 4025 2.036387 TGACGTCCTCCTTCTGTTTCA 58.964 47.619 14.12 0.00 0.00 2.69
1650 4026 2.814280 TGACGTCCTCCTTCTGTTTC 57.186 50.000 14.12 0.00 0.00 2.78
2243 4619 1.304381 TCCCCAAACAGCTCATGCC 60.304 57.895 0.00 0.00 40.80 4.40
2589 4998 0.460284 GGTCACGGAGCATGTAGTGG 60.460 60.000 0.00 0.00 35.50 4.00
2611 5020 2.771089 TCTGAACCAACACTGCATCTC 58.229 47.619 0.00 0.00 0.00 2.75
2792 6226 3.997681 TGCGTACTTATGCAAACAAGCTA 59.002 39.130 0.47 0.00 44.50 3.32
2808 6243 5.051641 CGTAGAGAAATGAGGAAATGCGTAC 60.052 44.000 0.00 0.00 0.00 3.67
2811 6246 4.112634 TCGTAGAGAAATGAGGAAATGCG 58.887 43.478 0.00 0.00 0.00 4.73
2873 6920 0.798776 GAGAACCTGAATGTGGTGCG 59.201 55.000 0.00 0.00 38.17 5.34
2905 6955 1.500474 TGGGATCTGGTCAGGACATC 58.500 55.000 1.41 0.00 0.00 3.06
2932 6985 1.138661 GAGAATGCCAGCTCTAGCACT 59.861 52.381 4.54 0.00 42.84 4.40
3002 7058 1.202698 ACAGCGAGAAGAACCAGCTTT 60.203 47.619 0.00 0.00 35.82 3.51
3006 7062 1.986378 CGTAACAGCGAGAAGAACCAG 59.014 52.381 0.00 0.00 0.00 4.00
3050 7106 0.539051 ATGTCTCCTGTAGCTGTGGC 59.461 55.000 0.00 0.00 39.06 5.01
3086 7142 1.268234 GCAGAGTGTGTGCTTTGTGAC 60.268 52.381 0.00 0.00 37.96 3.67
3097 7153 1.071987 TTCAGCTGGGCAGAGTGTG 59.928 57.895 15.13 0.00 0.00 3.82
3162 7218 3.089284 CCCCAATCCACTTCTACCAAAC 58.911 50.000 0.00 0.00 0.00 2.93
3229 7285 0.704076 TTTGAGGGGATTGGGTGGAG 59.296 55.000 0.00 0.00 0.00 3.86
3241 7297 2.179427 GGATTCAAGGGGTTTTGAGGG 58.821 52.381 0.00 0.00 38.25 4.30
3273 7329 7.661040 ACTTAAACAAAGAAGATTGTGGATGG 58.339 34.615 0.00 0.00 42.49 3.51
3297 7353 4.649088 ACTTGCCTACCAAACAGAAAAC 57.351 40.909 0.00 0.00 31.94 2.43
3328 7384 7.615582 AATGTTCTACACCATGTTATGTCAG 57.384 36.000 0.00 0.00 0.00 3.51
3458 7514 0.319297 GCTGGGAAAAACTGCTGCTG 60.319 55.000 4.89 4.89 0.00 4.41
3482 7538 9.491675 TTGATTTCAAGTCATGCAAAATTATGT 57.508 25.926 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.