Multiple sequence alignment - TraesCS6B01G308600

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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 TraesCS6B01G308600 chr6B 100.000 2438 0 0 1 2438 552497263 552499700 0.000000e+00 4503.0
1 TraesCS6B01G308600 chr6B 90.344 611 51 6 4 609 552409522 552410129 0.000000e+00 795.0
2 TraesCS6B01G308600 chr6B 94.000 50 2 1 2236 2285 336181253 336181205 9.350000e-10 75.0
3 TraesCS6B01G308600 chr6A 91.682 1611 64 22 633 2231 507144949 507146501 0.000000e+00 2169.0
4 TraesCS6B01G308600 chr6A 97.024 168 5 0 2271 2438 507146500 507146667 1.430000e-72 283.0
5 TraesCS6B01G308600 chr6D 92.525 1485 48 21 625 2083 366699659 366701106 0.000000e+00 2069.0
6 TraesCS6B01G308600 chr6D 90.686 612 48 5 4 609 108197729 108197121 0.000000e+00 806.0
7 TraesCS6B01G308600 chr6D 89.362 611 54 7 4 609 108214620 108214016 0.000000e+00 758.0
8 TraesCS6B01G308600 chr6D 97.619 168 4 0 2271 2438 366701373 366701540 3.070000e-74 289.0
9 TraesCS6B01G308600 chr6D 92.903 155 9 1 2081 2233 366701219 366701373 8.770000e-55 224.0
10 TraesCS6B01G308600 chr6D 100.000 40 0 0 2236 2275 401308327 401308366 9.350000e-10 75.0
11 TraesCS6B01G308600 chr6D 92.157 51 4 0 2236 2286 382547355 382547305 3.360000e-09 73.1
12 TraesCS6B01G308600 chr1B 91.326 611 46 3 4 609 346399924 346399316 0.000000e+00 828.0
13 TraesCS6B01G308600 chr7B 90.164 610 54 5 4 608 226154229 226153621 0.000000e+00 789.0
14 TraesCS6B01G308600 chr7B 85.938 64 5 4 2238 2300 705887451 705887511 5.630000e-07 65.8
15 TraesCS6B01G308600 chr1D 90.016 611 55 5 4 609 248329037 248328428 0.000000e+00 785.0
16 TraesCS6B01G308600 chr1D 88.889 612 61 6 4 609 248334718 248334108 0.000000e+00 747.0
17 TraesCS6B01G308600 chr3D 88.581 613 61 7 4 609 417825712 417826322 0.000000e+00 736.0
18 TraesCS6B01G308600 chr3D 88.455 615 58 7 1 609 385640891 385641498 0.000000e+00 730.0
19 TraesCS6B01G308600 chr1A 92.453 53 3 1 2236 2287 474641713 474641661 9.350000e-10 75.0
20 TraesCS6B01G308600 chrUn 93.878 49 2 1 2236 2284 48471417 48471370 3.360000e-09 73.1
21 TraesCS6B01G308600 chrUn 93.878 49 2 1 2236 2284 48498195 48498148 3.360000e-09 73.1
22 TraesCS6B01G308600 chr4B 94.000 50 0 3 2236 2285 517958990 517958944 3.360000e-09 73.1
23 TraesCS6B01G308600 chr3B 89.286 56 5 1 2230 2284 266567659 266567604 4.350000e-08 69.4


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 TraesCS6B01G308600 chr6B 552497263 552499700 2437 False 4503.000000 4503 100.000 1 2438 1 chr6B.!!$F2 2437
1 TraesCS6B01G308600 chr6B 552409522 552410129 607 False 795.000000 795 90.344 4 609 1 chr6B.!!$F1 605
2 TraesCS6B01G308600 chr6A 507144949 507146667 1718 False 1226.000000 2169 94.353 633 2438 2 chr6A.!!$F1 1805
3 TraesCS6B01G308600 chr6D 366699659 366701540 1881 False 860.666667 2069 94.349 625 2438 3 chr6D.!!$F2 1813
4 TraesCS6B01G308600 chr6D 108197121 108197729 608 True 806.000000 806 90.686 4 609 1 chr6D.!!$R1 605
5 TraesCS6B01G308600 chr6D 108214016 108214620 604 True 758.000000 758 89.362 4 609 1 chr6D.!!$R2 605
6 TraesCS6B01G308600 chr1B 346399316 346399924 608 True 828.000000 828 91.326 4 609 1 chr1B.!!$R1 605
7 TraesCS6B01G308600 chr7B 226153621 226154229 608 True 789.000000 789 90.164 4 608 1 chr7B.!!$R1 604
8 TraesCS6B01G308600 chr1D 248328428 248329037 609 True 785.000000 785 90.016 4 609 1 chr1D.!!$R1 605
9 TraesCS6B01G308600 chr1D 248334108 248334718 610 True 747.000000 747 88.889 4 609 1 chr1D.!!$R2 605
10 TraesCS6B01G308600 chr3D 417825712 417826322 610 False 736.000000 736 88.581 4 609 1 chr3D.!!$F2 605
11 TraesCS6B01G308600 chr3D 385640891 385641498 607 False 730.000000 730 88.455 1 609 1 chr3D.!!$F1 608

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
732 745 0.175073 GGGCCTCTGAATACGACGTT 59.825 55.0 5.5 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 2281 0.037303 AGACACACCCCAAGCATCAG 59.963 55.0 0.0 0.0 0.0 2.9 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
23 24 4.161754 CAGAAACCCTAACCTAACTCGGAT 59.838 45.833 0.00 0.00 0.00 4.18
26 27 4.803329 ACCCTAACCTAACTCGGATAGA 57.197 45.455 0.00 0.00 32.77 1.98
39 40 5.253330 ACTCGGATAGAAATCTTTGGCAAA 58.747 37.500 12.79 12.79 32.29 3.68
83 85 0.534203 GAGTGGTTTGCTTCGGTCCA 60.534 55.000 0.00 0.00 0.00 4.02
111 113 2.410053 GTGAACGATGTCAACTCTCTGC 59.590 50.000 0.00 0.00 0.00 4.26
126 128 5.669477 ACTCTCTGCATCCTTCTGTAATTC 58.331 41.667 0.00 0.00 0.00 2.17
192 194 1.940613 GAGTGAACGTTGCCAACTCTT 59.059 47.619 5.00 0.00 0.00 2.85
238 242 4.245660 GTCTCACCGATCAAATCAACTCA 58.754 43.478 0.00 0.00 0.00 3.41
274 278 1.805345 CTCTGCAGCTTCTGTTTCTGG 59.195 52.381 9.47 0.00 33.43 3.86
294 298 2.297701 GTCTTGTTTTGCCTCCACAGA 58.702 47.619 0.00 0.00 0.00 3.41
356 361 2.542178 TCAACCGTTTTGATGAGACACG 59.458 45.455 0.00 0.00 0.00 4.49
398 408 5.103982 TCCATCAGAGGCCATCTTAATTGAA 60.104 40.000 5.01 0.00 35.47 2.69
436 446 8.773404 TCATAATCTGATGTCAATATGAGCAG 57.227 34.615 5.35 0.00 29.97 4.24
481 491 1.542492 TCCGAGCTCCGTTTTAGACT 58.458 50.000 8.47 0.00 36.31 3.24
511 524 9.910267 TTCATATCCATCTTGATCTTCTCAAAA 57.090 29.630 0.00 0.00 43.20 2.44
577 590 8.524870 AATTTTGACATAGCTTTAAGCAACTG 57.475 30.769 19.63 14.27 45.56 3.16
581 594 7.921786 TGACATAGCTTTAAGCAACTGTTAT 57.078 32.000 19.63 4.19 45.56 1.89
600 613 7.818930 ACTGTTATGATTGTGCCATTTTTAAGG 59.181 33.333 0.00 0.00 0.00 2.69
609 622 3.243569 TGCCATTTTTAAGGGTCAACACG 60.244 43.478 0.00 0.00 34.09 4.49
610 623 3.859252 GCCATTTTTAAGGGTCAACACGG 60.859 47.826 0.00 0.00 34.09 4.94
611 624 3.305744 CCATTTTTAAGGGTCAACACGGG 60.306 47.826 0.00 0.00 0.00 5.28
612 625 2.732844 TTTTAAGGGTCAACACGGGT 57.267 45.000 0.00 0.00 0.00 5.28
613 626 2.732844 TTTAAGGGTCAACACGGGTT 57.267 45.000 0.00 0.00 37.87 4.11
614 627 2.259266 TTAAGGGTCAACACGGGTTC 57.741 50.000 0.00 0.00 34.21 3.62
615 628 1.426751 TAAGGGTCAACACGGGTTCT 58.573 50.000 0.00 0.00 34.21 3.01
616 629 1.426751 AAGGGTCAACACGGGTTCTA 58.573 50.000 0.00 0.00 34.21 2.10
617 630 1.426751 AGGGTCAACACGGGTTCTAA 58.573 50.000 0.00 0.00 34.21 2.10
618 631 1.982958 AGGGTCAACACGGGTTCTAAT 59.017 47.619 0.00 0.00 34.21 1.73
619 632 3.175594 AGGGTCAACACGGGTTCTAATA 58.824 45.455 0.00 0.00 34.21 0.98
620 633 3.583966 AGGGTCAACACGGGTTCTAATAA 59.416 43.478 0.00 0.00 34.21 1.40
621 634 4.226620 AGGGTCAACACGGGTTCTAATAAT 59.773 41.667 0.00 0.00 34.21 1.28
622 635 4.945543 GGGTCAACACGGGTTCTAATAATT 59.054 41.667 0.00 0.00 34.21 1.40
623 636 5.416639 GGGTCAACACGGGTTCTAATAATTT 59.583 40.000 0.00 0.00 34.21 1.82
652 665 3.686726 CCTTTCTTCTGAAATGGACTCCG 59.313 47.826 0.00 0.00 40.85 4.63
671 684 1.583404 CGCCGAATTGCAAAACATAGC 59.417 47.619 1.71 1.22 0.00 2.97
702 715 1.758440 TAATAGCAGGCCAGCTCCCG 61.758 60.000 27.70 0.00 45.26 5.14
732 745 0.175073 GGGCCTCTGAATACGACGTT 59.825 55.000 5.50 0.00 0.00 3.99
739 752 5.004535 GCCTCTGAATACGACGTTTTAGAAG 59.995 44.000 5.50 7.24 0.00 2.85
1212 1252 2.182030 GAGGAGGACAAGTCGCCG 59.818 66.667 5.47 0.00 32.27 6.46
1270 1322 3.148279 CCGAGGAGAAGGACCCCG 61.148 72.222 0.00 0.00 0.00 5.73
1271 1323 2.044252 CGAGGAGAAGGACCCCGA 60.044 66.667 0.00 0.00 0.00 5.14
1272 1324 2.416432 CGAGGAGAAGGACCCCGAC 61.416 68.421 0.00 0.00 0.00 4.79
1273 1325 2.362632 AGGAGAAGGACCCCGACG 60.363 66.667 0.00 0.00 0.00 5.12
1274 1326 2.679287 GGAGAAGGACCCCGACGT 60.679 66.667 0.00 0.00 0.00 4.34
1275 1327 2.708865 GGAGAAGGACCCCGACGTC 61.709 68.421 5.18 5.18 0.00 4.34
1276 1328 3.048941 GAGAAGGACCCCGACGTCG 62.049 68.421 30.33 30.33 39.44 5.12
1277 1329 4.790861 GAAGGACCCCGACGTCGC 62.791 72.222 31.73 17.84 38.18 5.19
1293 1345 4.856607 GCCGTCGCCGAGGAGAAG 62.857 72.222 8.59 0.00 35.63 2.85
1294 1346 3.132139 CCGTCGCCGAGGAGAAGA 61.132 66.667 8.59 0.00 35.63 2.87
1295 1347 2.697761 CCGTCGCCGAGGAGAAGAA 61.698 63.158 8.59 0.00 35.63 2.52
1296 1348 1.514443 CGTCGCCGAGGAGAAGAAC 60.514 63.158 0.00 0.00 35.63 3.01
1297 1349 1.153804 GTCGCCGAGGAGAAGAACC 60.154 63.158 0.00 0.00 0.00 3.62
1298 1350 2.184579 CGCCGAGGAGAAGAACCC 59.815 66.667 0.00 0.00 0.00 4.11
1299 1351 2.585153 GCCGAGGAGAAGAACCCC 59.415 66.667 0.00 0.00 0.00 4.95
1300 1352 2.893398 CCGAGGAGAAGAACCCCG 59.107 66.667 0.00 0.00 0.00 5.73
1301 1353 1.681327 CCGAGGAGAAGAACCCCGA 60.681 63.158 0.00 0.00 0.00 5.14
1302 1354 1.511768 CGAGGAGAAGAACCCCGAC 59.488 63.158 0.00 0.00 0.00 4.79
1360 1415 4.463879 CTGCCGAGGCTGTGGAGG 62.464 72.222 15.75 0.00 42.51 4.30
1368 1423 4.459089 GCTGTGGAGGGCGAGGAC 62.459 72.222 0.00 0.00 0.00 3.85
1376 1431 2.683933 GGGCGAGGACAAGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
1382 1437 1.645710 GAGGACAAGGGAGAGGACAA 58.354 55.000 0.00 0.00 0.00 3.18
1398 1453 0.471211 ACAAGGAGGTCGAACTGGGA 60.471 55.000 8.28 0.00 0.00 4.37
1405 1460 1.203075 AGGTCGAACTGGGAGAGAAGT 60.203 52.381 0.00 0.00 0.00 3.01
1596 1653 2.891191 TTAAGGCTTACCCTGGGTTG 57.109 50.000 26.00 17.94 45.62 3.77
1661 1720 5.305128 ACATCTGTGTGGATGGTTTCATTTT 59.695 36.000 8.91 0.00 45.11 1.82
1694 1753 2.012673 CTTGCTTATCCTGTGGACAGC 58.987 52.381 10.91 10.91 42.47 4.40
1761 1820 7.581213 TGTGGTTCAGTCATTTTAATCAGTT 57.419 32.000 0.00 0.00 0.00 3.16
1822 1881 1.583477 GCTGTCTTTCCTGCTTGGC 59.417 57.895 0.00 0.00 35.26 4.52
1936 1995 8.682936 ACATCTGTTGTTCTACTTCTTCAAAT 57.317 30.769 0.00 0.00 33.74 2.32
1967 2026 4.992688 TGCAAGGTTGTTCAGTTGTTTAG 58.007 39.130 0.00 0.00 0.00 1.85
1979 2038 7.776030 TGTTCAGTTGTTTAGGTATTTCTTGGA 59.224 33.333 0.00 0.00 0.00 3.53
1981 2040 6.713450 TCAGTTGTTTAGGTATTTCTTGGACC 59.287 38.462 0.00 0.00 0.00 4.46
2139 2313 1.198637 GTGTGTCTTTGATGCTGCCTC 59.801 52.381 0.00 0.00 0.00 4.70
2209 2383 4.467198 ACTTAGCAGCGTGGTTACTTAT 57.533 40.909 0.00 0.00 0.00 1.73
2240 2416 8.480133 ACATCAGTATTTACTACTCCCTAAGG 57.520 38.462 0.00 0.00 38.68 2.69
2241 2417 8.066247 ACATCAGTATTTACTACTCCCTAAGGT 58.934 37.037 0.00 0.00 38.68 3.50
2242 2418 8.925338 CATCAGTATTTACTACTCCCTAAGGTT 58.075 37.037 0.00 0.00 38.68 3.50
2244 2420 9.995594 TCAGTATTTACTACTCCCTAAGGTTAA 57.004 33.333 0.00 0.00 38.68 2.01
2248 2424 8.906238 ATTTACTACTCCCTAAGGTTAAGACA 57.094 34.615 0.00 0.00 0.00 3.41
2249 2425 7.709149 TTACTACTCCCTAAGGTTAAGACAC 57.291 40.000 0.00 0.00 0.00 3.67
2250 2426 5.901598 ACTACTCCCTAAGGTTAAGACACT 58.098 41.667 0.00 0.00 0.00 3.55
2251 2427 6.321321 ACTACTCCCTAAGGTTAAGACACTT 58.679 40.000 0.00 0.00 0.00 3.16
2252 2428 7.473593 ACTACTCCCTAAGGTTAAGACACTTA 58.526 38.462 0.00 0.00 0.00 2.24
2253 2429 8.121185 ACTACTCCCTAAGGTTAAGACACTTAT 58.879 37.037 0.00 0.00 0.00 1.73
2254 2430 7.809880 ACTCCCTAAGGTTAAGACACTTATT 57.190 36.000 0.00 0.00 0.00 1.40
2255 2431 8.215954 ACTCCCTAAGGTTAAGACACTTATTT 57.784 34.615 0.00 0.00 0.00 1.40
2256 2432 8.666821 ACTCCCTAAGGTTAAGACACTTATTTT 58.333 33.333 0.00 0.00 0.00 1.82
2257 2433 8.857694 TCCCTAAGGTTAAGACACTTATTTTG 57.142 34.615 0.00 0.00 0.00 2.44
2258 2434 7.886446 TCCCTAAGGTTAAGACACTTATTTTGG 59.114 37.037 0.00 0.00 0.00 3.28
2259 2435 7.122204 CCCTAAGGTTAAGACACTTATTTTGGG 59.878 40.741 0.00 0.00 0.00 4.12
2260 2436 7.886446 CCTAAGGTTAAGACACTTATTTTGGGA 59.114 37.037 0.00 0.00 0.00 4.37
2261 2437 7.520451 AAGGTTAAGACACTTATTTTGGGAC 57.480 36.000 0.00 0.00 0.00 4.46
2262 2438 5.704053 AGGTTAAGACACTTATTTTGGGACG 59.296 40.000 0.00 0.00 0.00 4.79
2263 2439 5.106436 GGTTAAGACACTTATTTTGGGACGG 60.106 44.000 0.00 0.00 0.00 4.79
2264 2440 4.360951 AAGACACTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
2265 2441 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
2266 2442 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2267 2443 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2268 2444 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2269 2445 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2270 2446 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2273 2449 1.200519 TTTGGGACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
2311 2487 0.035534 ATGTTAGTGGCCGTGCATGA 60.036 50.000 7.72 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.750021 ATCCGAGTTAGGTTAGGGTTTC 57.250 45.455 0.00 0.00 0.00 2.78
23 24 6.987386 TCCGAAAATTTGCCAAAGATTTCTA 58.013 32.000 20.04 11.18 32.42 2.10
26 27 6.229733 TGATCCGAAAATTTGCCAAAGATTT 58.770 32.000 0.00 0.00 0.00 2.17
39 40 2.280628 GCTCCGAGTTGATCCGAAAAT 58.719 47.619 0.00 0.00 0.00 1.82
111 113 2.438021 TCCGGGGAATTACAGAAGGATG 59.562 50.000 0.00 0.00 0.00 3.51
192 194 5.106475 CCGAGTTGATCCGAAAAATTACCAA 60.106 40.000 0.00 0.00 0.00 3.67
238 242 1.202582 CAGAGTCATTTCGGACCGACT 59.797 52.381 18.12 10.76 41.32 4.18
274 278 2.297701 TCTGTGGAGGCAAAACAAGAC 58.702 47.619 0.00 0.00 0.00 3.01
294 298 2.910688 AATCCGAGGTCGTATGCAAT 57.089 45.000 0.00 0.00 37.74 3.56
330 335 7.136119 GTGTCTCATCAAAACGGTTGATTTTA 58.864 34.615 12.43 3.37 37.06 1.52
345 350 1.792367 CGAAAGTTGCGTGTCTCATCA 59.208 47.619 0.00 0.00 0.00 3.07
356 361 3.701241 TGGAAAATGACACGAAAGTTGC 58.299 40.909 0.00 0.00 46.40 4.17
398 408 7.289317 ACATCAGATTATGAAATGGCCAGAAAT 59.711 33.333 13.05 4.87 42.53 2.17
436 446 5.626955 GCAAAAGTTATGACAAGTTCAGAGC 59.373 40.000 0.00 0.00 37.77 4.09
555 568 6.633500 ACAGTTGCTTAAAGCTATGTCAAA 57.367 33.333 0.00 0.00 42.97 2.69
600 613 6.319399 CAAATTATTAGAACCCGTGTTGACC 58.681 40.000 0.00 0.00 33.97 4.02
609 622 6.731292 AGGAATGGCAAATTATTAGAACCC 57.269 37.500 0.00 0.00 0.00 4.11
610 623 8.478066 AGAAAGGAATGGCAAATTATTAGAACC 58.522 33.333 0.00 0.00 0.00 3.62
611 624 9.875691 AAGAAAGGAATGGCAAATTATTAGAAC 57.124 29.630 0.00 0.00 0.00 3.01
613 626 9.479549 AGAAGAAAGGAATGGCAAATTATTAGA 57.520 29.630 0.00 0.00 0.00 2.10
614 627 9.525409 CAGAAGAAAGGAATGGCAAATTATTAG 57.475 33.333 0.00 0.00 0.00 1.73
615 628 9.253832 TCAGAAGAAAGGAATGGCAAATTATTA 57.746 29.630 0.00 0.00 0.00 0.98
616 629 8.137745 TCAGAAGAAAGGAATGGCAAATTATT 57.862 30.769 0.00 0.00 0.00 1.40
617 630 7.722949 TCAGAAGAAAGGAATGGCAAATTAT 57.277 32.000 0.00 0.00 0.00 1.28
618 631 7.537596 TTCAGAAGAAAGGAATGGCAAATTA 57.462 32.000 0.00 0.00 0.00 1.40
619 632 6.423776 TTCAGAAGAAAGGAATGGCAAATT 57.576 33.333 0.00 0.00 0.00 1.82
620 633 6.423776 TTTCAGAAGAAAGGAATGGCAAAT 57.576 33.333 0.00 0.00 38.76 2.32
621 634 5.867903 TTTCAGAAGAAAGGAATGGCAAA 57.132 34.783 0.00 0.00 38.76 3.68
622 635 5.279607 CCATTTCAGAAGAAAGGAATGGCAA 60.280 40.000 4.41 0.00 45.67 4.52
623 636 4.221262 CCATTTCAGAAGAAAGGAATGGCA 59.779 41.667 4.41 0.00 45.67 4.92
652 665 2.605030 TGCTATGTTTTGCAATTCGGC 58.395 42.857 0.00 1.45 36.15 5.54
671 684 3.491447 GCCTGCTATTACATGGGCTTTTG 60.491 47.826 0.00 0.00 36.96 2.44
702 715 1.001633 TCAGAGGCCCAAACGTTAGAC 59.998 52.381 0.00 0.00 0.00 2.59
732 745 2.831685 TGCGTCCAGAAGCTTCTAAA 57.168 45.000 28.02 16.19 35.34 1.85
739 752 4.451652 GCGCTTGCGTCCAGAAGC 62.452 66.667 16.38 0.00 41.05 3.86
1279 1331 1.153804 GGTTCTTCTCCTCGGCGAC 60.154 63.158 4.99 0.00 0.00 5.19
1280 1332 2.348888 GGGTTCTTCTCCTCGGCGA 61.349 63.158 10.14 10.14 0.00 5.54
1281 1333 2.184579 GGGTTCTTCTCCTCGGCG 59.815 66.667 0.00 0.00 0.00 6.46
1282 1334 2.585153 GGGGTTCTTCTCCTCGGC 59.415 66.667 0.00 0.00 32.92 5.54
1283 1335 2.893398 CGGGGTTCTTCTCCTCGG 59.107 66.667 0.00 0.00 44.22 4.63
1285 1337 1.249469 ACGTCGGGGTTCTTCTCCTC 61.249 60.000 0.00 0.00 33.68 3.71
1286 1338 1.228800 ACGTCGGGGTTCTTCTCCT 60.229 57.895 0.00 0.00 33.68 3.69
1287 1339 1.214853 GACGTCGGGGTTCTTCTCC 59.785 63.158 0.00 0.00 0.00 3.71
1288 1340 1.154073 CGACGTCGGGGTTCTTCTC 60.154 63.158 29.70 0.00 35.37 2.87
1289 1341 2.960170 CGACGTCGGGGTTCTTCT 59.040 61.111 29.70 0.00 35.37 2.85
1290 1342 2.808321 GCGACGTCGGGGTTCTTC 60.808 66.667 36.13 15.40 40.23 2.87
1291 1343 4.368543 GGCGACGTCGGGGTTCTT 62.369 66.667 36.13 0.00 40.23 2.52
1353 1408 2.525629 TTGTCCTCGCCCTCCACA 60.526 61.111 0.00 0.00 0.00 4.17
1360 1415 2.726351 CCTCTCCCTTGTCCTCGCC 61.726 68.421 0.00 0.00 0.00 5.54
1368 1423 0.908198 CCTCCTTGTCCTCTCCCTTG 59.092 60.000 0.00 0.00 0.00 3.61
1376 1431 0.969894 CAGTTCGACCTCCTTGTCCT 59.030 55.000 0.00 0.00 31.35 3.85
1382 1437 0.323908 CTCTCCCAGTTCGACCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
1398 1453 3.394836 GCCGCCTCCCACTTCTCT 61.395 66.667 0.00 0.00 0.00 3.10
1596 1653 5.291971 ACTGAATGCAAAATGTCAGAAACC 58.708 37.500 16.70 0.00 39.94 3.27
1661 1720 1.999648 AAGCAAGCAGTTTCCATGGA 58.000 45.000 11.44 11.44 0.00 3.41
1694 1753 8.567948 AGAACAACCTATGTGACAATAAGTTTG 58.432 33.333 0.00 0.00 42.99 2.93
1761 1820 0.998928 ACATCACCATTACCCTGGCA 59.001 50.000 0.00 0.00 40.15 4.92
1793 1852 5.127031 GCAGGAAAGACAGCCCAAAATAATA 59.873 40.000 0.00 0.00 0.00 0.98
1822 1881 4.102210 TCTCCCTCAGAGGAAATGCATAAG 59.898 45.833 19.21 0.00 43.44 1.73
1915 1974 7.195646 TGCAATTTGAAGAAGTAGAACAACAG 58.804 34.615 0.00 0.00 0.00 3.16
1967 2026 5.710099 TCATTTCACTGGTCCAAGAAATACC 59.290 40.000 22.24 0.00 38.30 2.73
1979 2038 3.966979 TGCACCATATCATTTCACTGGT 58.033 40.909 0.00 0.00 40.79 4.00
1981 2040 5.761165 TGATGCACCATATCATTTCACTG 57.239 39.130 0.00 0.00 30.03 3.66
2107 2281 0.037303 AGACACACCCCAAGCATCAG 59.963 55.000 0.00 0.00 0.00 2.90
2163 2337 8.756864 GTTGAGCTGAGTAGTAAAATATACAGC 58.243 37.037 0.00 0.00 46.18 4.40
2233 2409 7.122204 CCCAAAATAAGTGTCTTAACCTTAGGG 59.878 40.741 2.32 0.00 38.88 3.53
2234 2410 7.886446 TCCCAAAATAAGTGTCTTAACCTTAGG 59.114 37.037 0.00 0.00 0.00 2.69
2235 2411 8.727910 GTCCCAAAATAAGTGTCTTAACCTTAG 58.272 37.037 0.00 0.00 0.00 2.18
2236 2412 7.388500 CGTCCCAAAATAAGTGTCTTAACCTTA 59.612 37.037 0.00 0.00 0.00 2.69
2237 2413 6.206048 CGTCCCAAAATAAGTGTCTTAACCTT 59.794 38.462 0.00 0.00 0.00 3.50
2238 2414 5.704053 CGTCCCAAAATAAGTGTCTTAACCT 59.296 40.000 0.00 0.00 0.00 3.50
2239 2415 5.106436 CCGTCCCAAAATAAGTGTCTTAACC 60.106 44.000 0.00 0.00 0.00 2.85
2240 2416 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
2241 2417 5.867330 TCCGTCCCAAAATAAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
2242 2418 5.484715 CTCCGTCCCAAAATAAGTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
2243 2419 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
2244 2420 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2245 2421 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2246 2422 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2247 2423 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2248 2424 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2249 2425 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2250 2426 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2251 2427 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2252 2428 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2253 2429 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
2254 2430 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2255 2431 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2256 2432 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
2257 2433 2.305858 ATACATACTCCCTCCGTCCC 57.694 55.000 0.00 0.00 0.00 4.46
2258 2434 5.479375 TCAATAATACATACTCCCTCCGTCC 59.521 44.000 0.00 0.00 0.00 4.79
2259 2435 6.585695 TCAATAATACATACTCCCTCCGTC 57.414 41.667 0.00 0.00 0.00 4.79
2260 2436 6.497259 ACATCAATAATACATACTCCCTCCGT 59.503 38.462 0.00 0.00 0.00 4.69
2261 2437 6.936279 ACATCAATAATACATACTCCCTCCG 58.064 40.000 0.00 0.00 0.00 4.63
2262 2438 7.824779 GGAACATCAATAATACATACTCCCTCC 59.175 40.741 0.00 0.00 0.00 4.30
2263 2439 8.598041 AGGAACATCAATAATACATACTCCCTC 58.402 37.037 0.00 0.00 0.00 4.30
2264 2440 8.511748 AGGAACATCAATAATACATACTCCCT 57.488 34.615 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.