Multiple sequence alignment - TraesCS1D01G268900

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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 TraesCS1D01G268900 chr1D 100.000 3019 0 0 1 3019 364626334 364623316 0.000000e+00 5576.0
1 TraesCS1D01G268900 chr1D 94.054 185 10 1 2768 2952 364600685 364600502 2.290000e-71 279.0
2 TraesCS1D01G268900 chr1D 91.346 104 5 3 2336 2438 364602933 364602833 4.060000e-29 139.0
3 TraesCS1D01G268900 chr1B 93.858 1449 65 7 1059 2488 487951486 487950043 0.000000e+00 2161.0
4 TraesCS1D01G268900 chr1B 84.815 1080 95 31 1 1044 487952587 487951541 0.000000e+00 1022.0
5 TraesCS1D01G268900 chr1B 94.757 267 7 2 2489 2755 487948576 487948317 2.800000e-110 409.0
6 TraesCS1D01G268900 chr1B 92.531 241 18 0 2768 3008 487948254 487948014 2.230000e-91 346.0
7 TraesCS1D01G268900 chr1B 90.385 104 6 3 2336 2438 487821356 487821256 1.890000e-27 134.0
8 TraesCS1D01G268900 chr1B 77.727 220 25 18 157 372 286799575 286799774 2.460000e-21 113.0
9 TraesCS1D01G268900 chr1B 80.380 158 21 5 224 372 505985510 505985666 8.850000e-21 111.0
10 TraesCS1D01G268900 chr1B 88.889 72 8 0 2881 2952 487820130 487820059 4.150000e-14 89.8
11 TraesCS1D01G268900 chr1B 94.737 57 3 0 2827 2883 487820299 487820243 4.150000e-14 89.8
12 TraesCS1D01G268900 chr1A 90.843 1507 88 24 548 2022 463462221 463460733 0.000000e+00 1973.0
13 TraesCS1D01G268900 chr1A 94.551 312 12 4 2064 2371 463460652 463460342 7.570000e-131 477.0
14 TraesCS1D01G268900 chr1A 80.556 504 53 28 2550 3019 463460188 463459696 2.230000e-91 346.0
15 TraesCS1D01G268900 chr1A 86.802 197 19 4 2768 2962 463450635 463450444 2.360000e-51 213.0
16 TraesCS1D01G268900 chr1A 80.952 273 32 11 2503 2771 463451033 463450777 6.600000e-47 198.0
17 TraesCS1D01G268900 chr1A 91.262 103 8 1 2336 2437 463451143 463451041 4.060000e-29 139.0
18 TraesCS1D01G268900 chr1A 97.297 37 1 0 2274 2310 463460346 463460310 2.510000e-06 63.9
19 TraesCS1D01G268900 chr3D 84.280 528 52 23 1058 1563 492131419 492131937 1.260000e-133 486.0
20 TraesCS1D01G268900 chr3D 87.500 80 6 2 411 487 19065709 19065631 4.150000e-14 89.8
21 TraesCS1D01G268900 chr3A 93.407 273 16 2 1059 1330 633922097 633922368 1.300000e-108 403.0
22 TraesCS1D01G268900 chr3A 89.706 136 13 1 1412 1546 633922470 633922605 4.000000e-39 172.0
23 TraesCS1D01G268900 chr3A 82.812 192 20 6 303 485 230540152 230539965 3.120000e-35 159.0
24 TraesCS1D01G268900 chr3A 83.212 137 15 7 218 349 724518794 724518661 5.290000e-23 119.0
25 TraesCS1D01G268900 chr3A 82.667 75 8 5 1657 1727 633922730 633922803 9.040000e-06 62.1
26 TraesCS1D01G268900 chr3B 92.674 273 18 2 1059 1330 653152047 653152318 2.820000e-105 392.0
27 TraesCS1D01G268900 chr5D 90.406 271 24 2 1063 1332 425077485 425077216 3.700000e-94 355.0
28 TraesCS1D01G268900 chr5D 90.769 130 12 0 1413 1542 200501538 200501667 1.110000e-39 174.0
29 TraesCS1D01G268900 chr5B 90.037 271 25 2 1063 1332 514279627 514279358 1.720000e-92 350.0
30 TraesCS1D01G268900 chr5B 90.769 130 12 0 1413 1542 211146509 211146638 1.110000e-39 174.0
31 TraesCS1D01G268900 chr5B 88.430 121 9 4 217 334 13266199 13266317 1.130000e-29 141.0
32 TraesCS1D01G268900 chr5A 89.630 270 26 2 1063 1331 539093485 539093217 2.880000e-90 342.0
33 TraesCS1D01G268900 chr5A 90.769 130 12 0 1413 1542 214166889 214167018 1.110000e-39 174.0
34 TraesCS1D01G268900 chr5A 83.200 125 16 5 225 346 546987895 546988017 3.180000e-20 110.0
35 TraesCS1D01G268900 chr6D 79.781 366 36 18 157 487 14079324 14078962 6.510000e-57 231.0
36 TraesCS1D01G268900 chr4A 80.586 273 48 4 1063 1331 724400260 724399989 3.950000e-49 206.0
37 TraesCS1D01G268900 chr4A 92.000 125 10 0 1416 1540 517884848 517884972 3.090000e-40 176.0
38 TraesCS1D01G268900 chr4B 89.116 147 14 2 1416 1561 100576910 100577055 6.650000e-42 182.0
39 TraesCS1D01G268900 chr7D 79.787 188 23 11 161 346 611464736 611464562 4.090000e-24 122.0
40 TraesCS1D01G268900 chr7B 81.690 142 10 10 244 372 393460652 393460790 1.480000e-18 104.0
41 TraesCS1D01G268900 chr7A 97.059 34 1 0 339 372 335380032 335380065 1.170000e-04 58.4


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 TraesCS1D01G268900 chr1D 364623316 364626334 3018 True 5576.000000 5576 100.000000 1 3019 1 chr1D.!!$R1 3018
1 TraesCS1D01G268900 chr1D 364600502 364602933 2431 True 209.000000 279 92.700000 2336 2952 2 chr1D.!!$R2 616
2 TraesCS1D01G268900 chr1B 487948014 487952587 4573 True 984.500000 2161 91.490250 1 3008 4 chr1B.!!$R2 3007
3 TraesCS1D01G268900 chr1A 463459696 463462221 2525 True 714.975000 1973 90.811750 548 3019 4 chr1A.!!$R2 2471
4 TraesCS1D01G268900 chr3D 492131419 492131937 518 False 486.000000 486 84.280000 1058 1563 1 chr3D.!!$F1 505
5 TraesCS1D01G268900 chr3A 633922097 633922803 706 False 212.366667 403 88.593333 1059 1727 3 chr3A.!!$F1 668

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
248 285 0.036875 CCCACCTTCTCTGGAACCAC 59.963 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2448 0.968405 AACACACCACATGATTGCCC 59.032 50.0 0.0 0.0 0.0 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
29 30 3.065925 CCTGGAATTCGGAAGATTCTTGC 59.934 47.826 3.03 5.69 41.60 4.01
80 81 1.917872 TTTTGGGTGCGGCTAGAAAT 58.082 45.000 0.00 0.00 0.00 2.17
100 101 2.712057 CAGCCAGCTGAAAATTTCGT 57.288 45.000 17.39 0.00 46.30 3.85
103 104 3.182972 CAGCCAGCTGAAAATTTCGTTTG 59.817 43.478 17.39 0.00 46.30 2.93
104 105 3.068024 AGCCAGCTGAAAATTTCGTTTGA 59.932 39.130 17.39 0.00 0.00 2.69
105 106 3.426525 GCCAGCTGAAAATTTCGTTTGAG 59.573 43.478 17.39 0.00 0.00 3.02
114 132 2.312722 TTTCGTTTGAGGACCGTTGA 57.687 45.000 0.00 0.00 0.00 3.18
134 152 1.416243 ATGCGAAATCAATGGCCCAT 58.584 45.000 0.00 0.00 0.00 4.00
136 154 0.877213 GCGAAATCAATGGCCCATGC 60.877 55.000 0.00 0.00 0.00 4.06
151 169 3.873801 GCCCATGCTCTTTCTTCAACCTA 60.874 47.826 0.00 0.00 33.53 3.08
152 170 4.530875 CCCATGCTCTTTCTTCAACCTAT 58.469 43.478 0.00 0.00 0.00 2.57
158 195 3.508762 TCTTTCTTCAACCTATCGACGC 58.491 45.455 0.00 0.00 0.00 5.19
237 274 3.787001 CCTCGCCTCCCCACCTTC 61.787 72.222 0.00 0.00 0.00 3.46
239 276 2.683933 TCGCCTCCCCACCTTCTC 60.684 66.667 0.00 0.00 0.00 2.87
240 277 2.685380 CGCCTCCCCACCTTCTCT 60.685 66.667 0.00 0.00 0.00 3.10
248 285 0.036875 CCCACCTTCTCTGGAACCAC 59.963 60.000 0.00 0.00 0.00 4.16
249 286 1.059913 CCACCTTCTCTGGAACCACT 58.940 55.000 0.00 0.00 0.00 4.00
252 289 0.615850 CCTTCTCTGGAACCACTCCC 59.384 60.000 0.00 0.00 44.69 4.30
255 292 0.119155 TCTCTGGAACCACTCCCCAT 59.881 55.000 0.00 0.00 44.69 4.00
256 293 0.543749 CTCTGGAACCACTCCCCATC 59.456 60.000 0.00 0.00 44.69 3.51
258 295 2.124695 GGAACCACTCCCCATCGC 60.125 66.667 0.00 0.00 38.44 4.58
289 326 2.925170 CCCCGGCCATCCCTCTAG 60.925 72.222 2.24 0.00 0.00 2.43
290 327 2.925170 CCCGGCCATCCCTCTAGG 60.925 72.222 2.24 0.00 0.00 3.02
318 367 0.606401 CCTGAGCTTTTTCTCCGGCA 60.606 55.000 0.00 0.00 32.14 5.69
330 379 2.282816 CCGGCAAATCCCCACACA 60.283 61.111 0.00 0.00 0.00 3.72
331 380 2.635443 CCGGCAAATCCCCACACAC 61.635 63.158 0.00 0.00 0.00 3.82
333 382 2.635443 GGCAAATCCCCACACACCG 61.635 63.158 0.00 0.00 0.00 4.94
334 383 1.901464 GCAAATCCCCACACACCGT 60.901 57.895 0.00 0.00 0.00 4.83
336 385 1.302192 AAATCCCCACACACCGTCG 60.302 57.895 0.00 0.00 0.00 5.12
337 386 3.894547 AATCCCCACACACCGTCGC 62.895 63.158 0.00 0.00 0.00 5.19
370 419 4.395542 CGAACCCTAAGATAGATACTCGGG 59.604 50.000 0.00 0.00 35.52 5.14
385 434 4.148825 GGGTGATGACGGCGAGCT 62.149 66.667 16.62 0.00 0.00 4.09
386 435 2.125512 GGTGATGACGGCGAGCTT 60.126 61.111 16.62 2.99 0.00 3.74
390 439 0.458543 TGATGACGGCGAGCTTCTTC 60.459 55.000 16.62 8.98 0.00 2.87
402 451 0.176910 GCTTCTTCCTTCTCTCCGGG 59.823 60.000 0.00 0.00 0.00 5.73
419 468 3.412408 GGAGGCCCTCCCTTGTCC 61.412 72.222 19.95 0.00 46.60 4.02
443 492 6.072508 CCTTCCTTCATTCAAAAATCGACTGA 60.073 38.462 0.00 0.00 0.00 3.41
444 493 6.241207 TCCTTCATTCAAAAATCGACTGAC 57.759 37.500 0.00 0.00 0.00 3.51
456 505 1.586564 GACTGACGCCGAATCCGAG 60.587 63.158 0.00 0.00 38.22 4.63
476 525 4.573900 GAGAATCACCTGACTGATGTGTT 58.426 43.478 0.00 0.00 30.92 3.32
483 532 3.815401 ACCTGACTGATGTGTTGCTAAAC 59.185 43.478 0.00 0.00 36.78 2.01
506 555 6.386654 ACTGTATTTCTTTTGCATTTACGGG 58.613 36.000 0.00 0.00 0.00 5.28
525 574 2.223479 GGGTGTGTTTGTTGTGCTGTAG 60.223 50.000 0.00 0.00 0.00 2.74
527 576 3.242739 GGTGTGTTTGTTGTGCTGTAGAG 60.243 47.826 0.00 0.00 0.00 2.43
574 623 2.093711 TGTATGTATGCCACTGTTCGCT 60.094 45.455 0.00 0.00 0.00 4.93
659 714 7.609056 CACCAACTTCTACTAAACCTAGCTAA 58.391 38.462 0.00 0.00 0.00 3.09
685 740 2.568623 AAGGCGAACATCTTCCAACT 57.431 45.000 0.00 0.00 0.00 3.16
713 768 2.356313 CCTGCAGCGACGTCTGTT 60.356 61.111 14.70 2.43 36.49 3.16
761 818 4.164843 ACTCTGCCTACCAAACTCAAAA 57.835 40.909 0.00 0.00 0.00 2.44
944 1003 4.419939 GGGCAGCGAAAAAGGGCG 62.420 66.667 0.00 0.00 0.00 6.13
1009 1069 4.410400 CTCTCCCCGCCCCAACAC 62.410 72.222 0.00 0.00 0.00 3.32
1044 1106 2.888111 CCGCACTGCTCTGCTCTA 59.112 61.111 0.00 0.00 34.77 2.43
1045 1107 1.226916 CCGCACTGCTCTGCTCTAG 60.227 63.158 0.00 0.00 34.77 2.43
1153 1255 1.043816 CTGATCGCCTACATCAGGGT 58.956 55.000 3.69 0.00 45.66 4.34
1247 1349 0.105039 GCTGGATGAACTACCTCCGG 59.895 60.000 0.00 0.00 40.90 5.14
1366 1493 4.394078 TCGTCGACGTGCCTTCGG 62.394 66.667 34.40 6.41 40.80 4.30
1410 1540 1.970917 GACAACGGGAATGCTCGCTG 61.971 60.000 0.00 0.00 43.33 5.18
1585 1718 4.838152 CGCCCGGCACACATAGCT 62.838 66.667 10.77 0.00 0.00 3.32
1623 1756 4.404098 ACCCACGATGTTCGCCCC 62.404 66.667 0.00 0.00 45.12 5.80
1729 1883 0.469331 ACCTGAACCTCGACCTGTCA 60.469 55.000 0.00 0.00 0.00 3.58
1906 2060 3.315470 GCCAGTACATATGAGACGAGACA 59.685 47.826 10.38 0.00 0.00 3.41
2076 2279 0.168128 GTATCGTTGGTTGGTGCTGC 59.832 55.000 0.00 0.00 0.00 5.25
2078 2281 1.518056 ATCGTTGGTTGGTGCTGCTG 61.518 55.000 0.00 0.00 0.00 4.41
2080 2283 1.066257 GTTGGTTGGTGCTGCTGTG 59.934 57.895 0.00 0.00 0.00 3.66
2081 2284 2.784356 TTGGTTGGTGCTGCTGTGC 61.784 57.895 0.00 0.00 0.00 4.57
2083 2286 2.333938 GTTGGTGCTGCTGTGCTG 59.666 61.111 0.00 0.00 0.00 4.41
2084 2287 2.124193 TTGGTGCTGCTGTGCTGT 60.124 55.556 0.00 0.00 0.00 4.40
2086 2289 2.592574 GGTGCTGCTGTGCTGTGA 60.593 61.111 0.00 0.00 0.00 3.58
2242 2448 1.307355 TGTGGATGGATGTTGCGCAG 61.307 55.000 11.31 0.00 0.00 5.18
2265 2471 3.494251 GGCAATCATGTGGTGTGTTTTTC 59.506 43.478 0.00 0.00 0.00 2.29
2266 2472 4.370917 GCAATCATGTGGTGTGTTTTTCT 58.629 39.130 0.00 0.00 0.00 2.52
2483 2689 5.803020 ATGGAAGCATTTCGAAGAACTAC 57.197 39.130 0.00 0.00 45.90 2.73
2678 4384 2.709475 CTGCGCCGATACAAAGCC 59.291 61.111 4.18 0.00 0.00 4.35
2690 4396 0.694771 ACAAAGCCCTCATCAGCAGA 59.305 50.000 0.00 0.00 0.00 4.26
2699 4405 2.200067 CTCATCAGCAGATCGGAACAC 58.800 52.381 0.00 0.00 30.20 3.32
2700 4406 1.827344 TCATCAGCAGATCGGAACACT 59.173 47.619 0.00 0.00 30.20 3.55
2701 4407 1.931841 CATCAGCAGATCGGAACACTG 59.068 52.381 0.00 0.00 30.20 3.66
2702 4408 1.256812 TCAGCAGATCGGAACACTGA 58.743 50.000 12.12 9.54 34.07 3.41
2703 4409 1.827344 TCAGCAGATCGGAACACTGAT 59.173 47.619 12.12 0.00 34.07 2.90
2704 4410 2.159184 TCAGCAGATCGGAACACTGATC 60.159 50.000 10.04 10.04 43.10 2.92
2765 6309 4.687215 TGCTGGCGCTCGCTTCTT 62.687 61.111 19.07 0.00 41.60 2.52
2766 6310 3.858989 GCTGGCGCTCGCTTCTTC 61.859 66.667 7.64 0.00 41.60 2.87
2779 6395 5.052106 GCTCGCTTCTTCTTCTTTTGTTTTG 60.052 40.000 0.00 0.00 0.00 2.44
2789 6405 6.998802 TCTTCTTTTGTTTTGTTTTCTGGGA 58.001 32.000 0.00 0.00 0.00 4.37
2790 6406 7.445945 TCTTCTTTTGTTTTGTTTTCTGGGAA 58.554 30.769 0.00 0.00 0.00 3.97
2802 6418 2.047274 TGGGAAGAAGAAGCGCCG 60.047 61.111 2.29 0.00 0.00 6.46
2890 6509 6.802348 ACGTACATCTGAATATACAATCGAGC 59.198 38.462 0.00 0.00 0.00 5.03
2912 6531 2.863739 CACTTCGACATCGTAGCTGAA 58.136 47.619 7.71 0.00 39.82 3.02
2966 6585 1.339631 TGATCGGGTCAAAGGCGAAAT 60.340 47.619 0.00 0.00 32.78 2.17
2967 6586 1.743394 GATCGGGTCAAAGGCGAAATT 59.257 47.619 0.00 0.00 0.00 1.82
2970 6589 2.362717 TCGGGTCAAAGGCGAAATTTTT 59.637 40.909 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.065925 GGCAAGAATCTTCCGAATTCCAG 59.934 47.826 0.00 0.00 0.00 3.86
29 30 4.796038 AGAATGTCAATTCAAGCCAAGG 57.204 40.909 1.64 0.00 44.05 3.61
61 62 1.816224 GATTTCTAGCCGCACCCAAAA 59.184 47.619 0.00 0.00 0.00 2.44
90 91 4.219143 ACGGTCCTCAAACGAAATTTTC 57.781 40.909 0.00 0.00 0.00 2.29
95 96 2.312722 TCAACGGTCCTCAAACGAAA 57.687 45.000 0.00 0.00 0.00 3.46
98 99 1.399727 GCATTCAACGGTCCTCAAACG 60.400 52.381 0.00 0.00 0.00 3.60
100 101 0.871722 CGCATTCAACGGTCCTCAAA 59.128 50.000 0.00 0.00 0.00 2.69
103 104 1.153353 TTTCGCATTCAACGGTCCTC 58.847 50.000 0.00 0.00 0.00 3.71
104 105 1.737793 GATTTCGCATTCAACGGTCCT 59.262 47.619 0.00 0.00 0.00 3.85
105 106 1.466950 TGATTTCGCATTCAACGGTCC 59.533 47.619 0.00 0.00 0.00 4.46
114 132 1.193323 TGGGCCATTGATTTCGCATT 58.807 45.000 0.00 0.00 0.00 3.56
129 147 1.203287 GGTTGAAGAAAGAGCATGGGC 59.797 52.381 0.00 0.00 41.61 5.36
134 152 4.495422 GTCGATAGGTTGAAGAAAGAGCA 58.505 43.478 0.00 0.00 0.00 4.26
136 154 3.548268 GCGTCGATAGGTTGAAGAAAGAG 59.452 47.826 0.00 0.00 0.00 2.85
151 169 4.760047 GTGGTGGCTGGCGTCGAT 62.760 66.667 0.00 0.00 0.00 3.59
220 257 3.787001 GAAGGTGGGGAGGCGAGG 61.787 72.222 0.00 0.00 0.00 4.63
221 258 2.685380 AGAAGGTGGGGAGGCGAG 60.685 66.667 0.00 0.00 0.00 5.03
222 259 2.683933 GAGAAGGTGGGGAGGCGA 60.684 66.667 0.00 0.00 0.00 5.54
223 260 2.685380 AGAGAAGGTGGGGAGGCG 60.685 66.667 0.00 0.00 0.00 5.52
224 261 2.674220 CCAGAGAAGGTGGGGAGGC 61.674 68.421 0.00 0.00 0.00 4.70
225 262 0.547712 TTCCAGAGAAGGTGGGGAGG 60.548 60.000 0.00 0.00 35.58 4.30
226 263 0.615850 GTTCCAGAGAAGGTGGGGAG 59.384 60.000 0.00 0.00 35.58 4.30
227 264 0.840722 GGTTCCAGAGAAGGTGGGGA 60.841 60.000 0.00 0.00 35.58 4.81
228 265 1.133809 TGGTTCCAGAGAAGGTGGGG 61.134 60.000 0.00 0.00 35.58 4.96
229 266 0.036875 GTGGTTCCAGAGAAGGTGGG 59.963 60.000 0.00 0.00 35.58 4.61
230 267 1.002544 GAGTGGTTCCAGAGAAGGTGG 59.997 57.143 0.00 0.00 36.28 4.61
232 269 1.353091 GGAGTGGTTCCAGAGAAGGT 58.647 55.000 0.00 0.00 46.01 3.50
291 328 1.475169 AAAAAGCTCAGGGCAAGGGC 61.475 55.000 0.00 0.00 44.79 5.19
295 344 1.620822 GGAGAAAAAGCTCAGGGCAA 58.379 50.000 0.00 0.00 44.79 4.52
318 367 1.302192 CGACGGTGTGTGGGGATTT 60.302 57.895 0.00 0.00 0.00 2.17
341 390 1.117142 TATCTTAGGGTTCGGGGCGG 61.117 60.000 0.00 0.00 0.00 6.13
342 391 0.317479 CTATCTTAGGGTTCGGGGCG 59.683 60.000 0.00 0.00 0.00 6.13
346 395 4.395542 CCGAGTATCTATCTTAGGGTTCGG 59.604 50.000 0.00 0.00 38.02 4.30
347 396 4.395542 CCCGAGTATCTATCTTAGGGTTCG 59.604 50.000 0.00 0.00 32.50 3.95
354 403 5.642491 CGTCATCACCCGAGTATCTATCTTA 59.358 44.000 0.00 0.00 0.00 2.10
370 419 0.737715 AAGAAGCTCGCCGTCATCAC 60.738 55.000 0.00 0.00 0.00 3.06
385 434 0.412244 TCCCCGGAGAGAAGGAAGAA 59.588 55.000 0.73 0.00 0.00 2.52
386 435 0.033011 CTCCCCGGAGAGAAGGAAGA 60.033 60.000 7.30 0.00 44.53 2.87
390 439 3.157949 GCCTCCCCGGAGAGAAGG 61.158 72.222 15.66 8.71 44.53 3.46
416 465 6.072452 AGTCGATTTTTGAATGAAGGAAGGAC 60.072 38.462 0.00 0.00 0.00 3.85
419 468 6.798959 GTCAGTCGATTTTTGAATGAAGGAAG 59.201 38.462 0.00 0.00 41.46 3.46
443 492 0.527817 GTGATTCTCGGATTCGGCGT 60.528 55.000 6.85 0.00 36.95 5.68
444 493 1.215655 GGTGATTCTCGGATTCGGCG 61.216 60.000 0.00 0.00 36.95 6.46
456 505 3.120060 GCAACACATCAGTCAGGTGATTC 60.120 47.826 0.00 0.00 34.81 2.52
476 525 8.885494 AAATGCAAAAGAAATACAGTTTAGCA 57.115 26.923 0.00 0.00 0.00 3.49
483 532 6.307800 CACCCGTAAATGCAAAAGAAATACAG 59.692 38.462 0.00 0.00 0.00 2.74
506 555 3.374058 ACTCTACAGCACAACAAACACAC 59.626 43.478 0.00 0.00 0.00 3.82
574 623 3.009695 AGAAATACGGAACCCATTGACCA 59.990 43.478 0.00 0.00 0.00 4.02
659 714 4.192317 GGAAGATGTTCGCCTTTATGAGT 58.808 43.478 0.00 0.00 32.92 3.41
713 768 5.649557 CTGGGCATTTTTAATCACGAATCA 58.350 37.500 0.00 0.00 0.00 2.57
761 818 1.808531 TTGGCACGTACCGCTACAGT 61.809 55.000 0.00 0.00 0.00 3.55
847 906 3.810188 TTGGGTGGTGGTTGCGGA 61.810 61.111 0.00 0.00 0.00 5.54
944 1003 4.544689 TGTGTGTTGGTTGCGCGC 62.545 61.111 27.26 27.26 0.00 6.86
945 1004 2.650602 GTGTGTGTTGGTTGCGCG 60.651 61.111 0.00 0.00 0.00 6.86
946 1005 1.871789 GTGTGTGTGTTGGTTGCGC 60.872 57.895 0.00 0.00 0.00 6.09
947 1006 1.226547 GGTGTGTGTGTTGGTTGCG 60.227 57.895 0.00 0.00 0.00 4.85
948 1007 1.140804 GGGTGTGTGTGTTGGTTGC 59.859 57.895 0.00 0.00 0.00 4.17
949 1008 1.813192 GGGGTGTGTGTGTTGGTTG 59.187 57.895 0.00 0.00 0.00 3.77
1003 1063 0.248843 GAGCTCTCTCCTGGTGTTGG 59.751 60.000 6.43 0.00 33.19 3.77
1006 1066 2.347322 GCGAGCTCTCTCCTGGTGT 61.347 63.158 12.85 0.00 35.94 4.16
1007 1067 2.051518 AGCGAGCTCTCTCCTGGTG 61.052 63.158 12.85 0.00 35.94 4.17
1009 1069 2.806929 CAGCGAGCTCTCTCCTGG 59.193 66.667 12.85 0.00 35.66 4.45
1031 1093 3.287222 CCTTCTACTAGAGCAGAGCAGT 58.713 50.000 0.00 0.00 0.00 4.40
1036 1098 3.908643 TCGACCTTCTACTAGAGCAGA 57.091 47.619 0.00 0.00 0.00 4.26
1041 1103 2.158856 TGCCGATCGACCTTCTACTAGA 60.159 50.000 18.66 0.00 0.00 2.43
1044 1106 1.338337 CATGCCGATCGACCTTCTACT 59.662 52.381 18.66 0.00 0.00 2.57
1045 1107 1.603172 CCATGCCGATCGACCTTCTAC 60.603 57.143 18.66 0.00 0.00 2.59
1366 1493 8.191446 TCAGCAAAGAAGTCATACTACTGTATC 58.809 37.037 0.00 0.00 37.28 2.24
1410 1540 1.134965 CGATCAGAGACCACCTTCACC 60.135 57.143 0.00 0.00 0.00 4.02
1525 1655 3.755628 GTGAGCGGGCGGTGAGTA 61.756 66.667 0.00 0.00 0.00 2.59
1623 1756 2.811317 GCTGCTTCGTCGTCAGGG 60.811 66.667 11.58 0.00 0.00 4.45
1625 1758 1.803519 GAGGCTGCTTCGTCGTCAG 60.804 63.158 0.00 0.14 0.00 3.51
1628 1761 4.070552 GGGAGGCTGCTTCGTCGT 62.071 66.667 5.84 0.00 0.00 4.34
1633 1766 1.153005 CTCCATGGGAGGCTGCTTC 60.153 63.158 13.02 2.75 45.43 3.86
1809 1963 4.994471 CCTGACGGCAGCTGCACA 62.994 66.667 37.63 29.47 44.36 4.57
2145 2351 1.032794 CCGCTACCTCACATCAGCTA 58.967 55.000 0.00 0.00 31.74 3.32
2242 2448 0.968405 AACACACCACATGATTGCCC 59.032 50.000 0.00 0.00 0.00 5.36
2265 2471 3.118738 AGACAAGCCGAAATACCTACCAG 60.119 47.826 0.00 0.00 0.00 4.00
2266 2472 2.835764 AGACAAGCCGAAATACCTACCA 59.164 45.455 0.00 0.00 0.00 3.25
2483 2689 4.478206 TGCTTTCAAGACCATCTCCTAG 57.522 45.455 0.00 0.00 0.00 3.02
2678 4384 1.137675 TGTTCCGATCTGCTGATGAGG 59.862 52.381 11.21 13.35 32.19 3.86
2690 4396 2.834549 AGTTCAGGATCAGTGTTCCGAT 59.165 45.455 13.44 0.00 38.36 4.18
2699 4405 2.762887 TCTGCTACCAGTTCAGGATCAG 59.237 50.000 0.00 0.00 40.09 2.90
2700 4406 2.820178 TCTGCTACCAGTTCAGGATCA 58.180 47.619 0.00 0.00 40.09 2.92
2701 4407 3.196685 ACTTCTGCTACCAGTTCAGGATC 59.803 47.826 0.00 0.00 40.09 3.36
2702 4408 3.177228 ACTTCTGCTACCAGTTCAGGAT 58.823 45.455 0.00 0.00 40.09 3.24
2703 4409 2.609747 ACTTCTGCTACCAGTTCAGGA 58.390 47.619 0.00 0.00 40.09 3.86
2704 4410 3.070018 CAACTTCTGCTACCAGTTCAGG 58.930 50.000 0.00 0.00 40.09 3.86
2751 6295 1.738099 GAAGAAGAAGCGAGCGCCA 60.738 57.895 11.66 0.00 43.17 5.69
2753 6297 0.793250 AAAGAAGAAGAAGCGAGCGC 59.207 50.000 6.78 6.78 42.33 5.92
2759 6303 8.712363 AGAAAACAAAACAAAAGAAGAAGAAGC 58.288 29.630 0.00 0.00 0.00 3.86
2763 6307 7.602265 TCCCAGAAAACAAAACAAAAGAAGAAG 59.398 33.333 0.00 0.00 0.00 2.85
2764 6308 7.445945 TCCCAGAAAACAAAACAAAAGAAGAA 58.554 30.769 0.00 0.00 0.00 2.52
2765 6309 6.998802 TCCCAGAAAACAAAACAAAAGAAGA 58.001 32.000 0.00 0.00 0.00 2.87
2766 6310 7.602265 TCTTCCCAGAAAACAAAACAAAAGAAG 59.398 33.333 0.00 0.00 0.00 2.85
2779 6395 2.350868 GCGCTTCTTCTTCCCAGAAAAC 60.351 50.000 0.00 0.00 38.63 2.43
2789 6405 3.959991 GAGGCCGGCGCTTCTTCTT 62.960 63.158 22.54 0.00 38.07 2.52
2790 6406 4.459089 GAGGCCGGCGCTTCTTCT 62.459 66.667 22.54 9.94 38.07 2.85
2802 6418 0.179054 GAATACCAGAACGGGAGGCC 60.179 60.000 0.00 0.00 40.22 5.19
2890 6509 0.523546 AGCTACGATGTCGAAGTGCG 60.524 55.000 9.67 0.00 43.02 5.34
2912 6531 0.395311 CCCATGATTGCAGCTCCTGT 60.395 55.000 0.00 0.00 33.43 4.00
2970 6589 4.289342 TGACTTGTTATTCGAAACGACGA 58.711 39.130 0.00 0.47 40.55 4.20
2976 6595 5.694910 GTCTCCACTGACTTGTTATTCGAAA 59.305 40.000 0.00 0.00 34.39 3.46


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

AutoCloner maintained by Alex Coulton.