Multiple sequence alignment - TraesCS1D01G279900

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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 TraesCS1D01G279900 chr1D 100.000 3768 0 0 1 3768 377948192 377951959 0.000000e+00 6959.0
1 TraesCS1D01G279900 chr1D 81.651 109 15 5 434 539 109810900 109810794 6.710000e-13 86.1
2 TraesCS1D01G279900 chr1B 92.700 3589 195 34 220 3768 505608904 505612465 0.000000e+00 5114.0
3 TraesCS1D01G279900 chr1B 90.393 229 20 2 1 227 505600802 505601030 2.200000e-77 300.0
4 TraesCS1D01G279900 chr1B 77.473 546 89 27 15 541 583093736 583094266 2.850000e-76 296.0
5 TraesCS1D01G279900 chr1A 96.473 1531 39 7 2246 3768 478537320 478538843 0.000000e+00 2514.0
6 TraesCS1D01G279900 chr1A 91.528 1558 77 21 670 2197 478535469 478537001 0.000000e+00 2095.0
7 TraesCS1D01G279900 chr1A 92.079 303 23 1 1 302 478534875 478535177 3.480000e-115 425.0
8 TraesCS1D01G279900 chr1A 84.899 298 42 3 327 622 478535171 478535467 7.910000e-77 298.0
9 TraesCS1D01G279900 chr3B 89.529 850 68 10 2285 3119 54286122 54286965 0.000000e+00 1057.0
10 TraesCS1D01G279900 chr3B 88.757 507 42 4 2630 3122 600749357 600748852 1.160000e-169 606.0
11 TraesCS1D01G279900 chr3B 87.968 507 46 5 2630 3122 600667813 600667308 5.420000e-163 584.0
12 TraesCS1D01G279900 chr3B 87.968 507 46 5 2630 3122 600702506 600702001 5.420000e-163 584.0
13 TraesCS1D01G279900 chr3B 95.152 165 7 1 2285 2449 600813348 600813185 3.730000e-65 259.0
14 TraesCS1D01G279900 chr3B 94.545 165 8 1 2285 2449 600726728 600726565 1.740000e-63 254.0
15 TraesCS1D01G279900 chr3B 92.500 160 11 1 2290 2449 600688487 600688329 1.050000e-55 228.0
16 TraesCS1D01G279900 chr3B 87.097 155 19 1 2444 2598 600667966 600667813 1.390000e-39 174.0
17 TraesCS1D01G279900 chr3B 85.897 156 18 4 2444 2598 600715640 600715488 3.010000e-36 163.0
18 TraesCS1D01G279900 chr3B 88.496 113 13 0 2486 2598 600749469 600749357 1.830000e-28 137.0
19 TraesCS1D01G279900 chr7B 88.498 852 79 9 2285 3122 81304534 81303688 0.000000e+00 1013.0
20 TraesCS1D01G279900 chr7B 80.970 268 47 4 1 267 489641802 489642066 3.810000e-50 209.0
21 TraesCS1D01G279900 chr2A 88.277 853 79 10 2285 3123 226114381 226115226 0.000000e+00 1002.0
22 TraesCS1D01G279900 chr3D 87.835 559 52 10 2574 3118 224776874 224777430 3.170000e-180 641.0
23 TraesCS1D01G279900 chr3D 84.133 271 39 4 1 269 612304362 612304630 3.730000e-65 259.0
24 TraesCS1D01G279900 chr7D 84.252 254 38 2 15 266 412685335 412685082 2.910000e-61 246.0
25 TraesCS1D01G279900 chr7D 78.182 110 18 6 434 539 629822362 629822469 8.740000e-07 65.8
26 TraesCS1D01G279900 chr4D 84.783 230 32 3 44 270 426542644 426542873 1.050000e-55 228.0
27 TraesCS1D01G279900 chr6B 82.143 252 43 2 15 264 667227688 667227437 8.200000e-52 215.0
28 TraesCS1D01G279900 chr6B 80.769 104 14 5 434 533 643415504 643415605 4.040000e-10 76.8
29 TraesCS1D01G279900 chr7A 80.515 272 50 3 1 270 228269694 228269424 4.930000e-49 206.0
30 TraesCS1D01G279900 chr2D 87.179 78 7 3 463 539 600315861 600315786 6.710000e-13 86.1
31 TraesCS1D01G279900 chr2D 78.899 109 17 5 434 539 592506351 592506246 6.750000e-08 69.4
32 TraesCS1D01G279900 chr5D 84.211 76 8 4 466 539 545924060 545923987 1.880000e-08 71.3
33 TraesCS1D01G279900 chr5A 79.048 105 15 7 437 539 384217618 384217519 8.740000e-07 65.8


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 TraesCS1D01G279900 chr1D 377948192 377951959 3767 False 6959.0 6959 100.00000 1 3768 1 chr1D.!!$F1 3767
1 TraesCS1D01G279900 chr1B 505608904 505612465 3561 False 5114.0 5114 92.70000 220 3768 1 chr1B.!!$F2 3548
2 TraesCS1D01G279900 chr1B 583093736 583094266 530 False 296.0 296 77.47300 15 541 1 chr1B.!!$F3 526
3 TraesCS1D01G279900 chr1A 478534875 478538843 3968 False 1333.0 2514 91.24475 1 3768 4 chr1A.!!$F1 3767
4 TraesCS1D01G279900 chr3B 54286122 54286965 843 False 1057.0 1057 89.52900 2285 3119 1 chr3B.!!$F1 834
5 TraesCS1D01G279900 chr3B 600702001 600702506 505 True 584.0 584 87.96800 2630 3122 1 chr3B.!!$R2 492
6 TraesCS1D01G279900 chr3B 600667308 600667966 658 True 379.0 584 87.53250 2444 3122 2 chr3B.!!$R6 678
7 TraesCS1D01G279900 chr3B 600748852 600749469 617 True 371.5 606 88.62650 2486 3122 2 chr3B.!!$R7 636
8 TraesCS1D01G279900 chr7B 81303688 81304534 846 True 1013.0 1013 88.49800 2285 3122 1 chr7B.!!$R1 837
9 TraesCS1D01G279900 chr2A 226114381 226115226 845 False 1002.0 1002 88.27700 2285 3123 1 chr2A.!!$F1 838
10 TraesCS1D01G279900 chr3D 224776874 224777430 556 False 641.0 641 87.83500 2574 3118 1 chr3D.!!$F1 544

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
575 641 0.099259 CACATCCGCGTTGATGCAAT 59.901 50.0 20.74 3.85 44.84 3.56 F
1334 1440 0.755686 GCTCCGGATCTCCAGACAAT 59.244 55.0 3.57 0.00 35.14 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1534 0.031178 CTTTGTGCAGTTCAGGTGCC 59.969 55.0 0.0 0.0 40.43 5.01 R
3044 3451 0.108186 TATTCCACCAGACAGCAGCG 60.108 55.0 0.0 0.0 0.00 5.18 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
97 98 1.266178 TCTCCTCATCGCCTGACAAA 58.734 50.000 0.00 0.00 0.00 2.83
103 104 2.270923 TCATCGCCTGACAAAGAATCG 58.729 47.619 0.00 0.00 0.00 3.34
150 151 5.810587 TGAAAAAGTACTCATCGCCACTATC 59.189 40.000 0.00 0.00 0.00 2.08
154 155 3.508012 AGTACTCATCGCCACTATCCATC 59.492 47.826 0.00 0.00 0.00 3.51
163 164 2.965831 GCCACTATCCATCTGTACCTGA 59.034 50.000 0.00 0.00 0.00 3.86
175 176 1.764134 TGTACCTGAGGGTGAAACGTT 59.236 47.619 2.38 0.00 46.75 3.99
186 187 2.162809 GGTGAAACGTTGAACACCTTGT 59.837 45.455 28.86 3.92 46.14 3.16
203 205 2.281484 TGGCACGGTGGAAGAAGC 60.281 61.111 10.60 0.00 0.00 3.86
271 277 3.717294 GGCATGGAGGTGACCGGT 61.717 66.667 6.92 6.92 0.00 5.28
305 366 4.677151 GAGGTGAGGGGGTGGGGT 62.677 72.222 0.00 0.00 0.00 4.95
309 370 4.542627 TGAGGGGGTGGGGTGGTT 62.543 66.667 0.00 0.00 0.00 3.67
310 371 3.979497 GAGGGGGTGGGGTGGTTG 61.979 72.222 0.00 0.00 0.00 3.77
311 372 4.875301 AGGGGGTGGGGTGGTTGT 62.875 66.667 0.00 0.00 0.00 3.32
312 373 4.614036 GGGGGTGGGGTGGTTGTG 62.614 72.222 0.00 0.00 0.00 3.33
313 374 4.614036 GGGGTGGGGTGGTTGTGG 62.614 72.222 0.00 0.00 0.00 4.17
314 375 4.614036 GGGTGGGGTGGTTGTGGG 62.614 72.222 0.00 0.00 0.00 4.61
315 376 4.614036 GGTGGGGTGGTTGTGGGG 62.614 72.222 0.00 0.00 0.00 4.96
316 377 4.614036 GTGGGGTGGTTGTGGGGG 62.614 72.222 0.00 0.00 0.00 5.40
318 379 4.614036 GGGGTGGTTGTGGGGGTG 62.614 72.222 0.00 0.00 0.00 4.61
320 381 4.218686 GGTGGTTGTGGGGGTGCT 62.219 66.667 0.00 0.00 0.00 4.40
321 382 2.836187 GGTGGTTGTGGGGGTGCTA 61.836 63.158 0.00 0.00 0.00 3.49
322 383 1.602605 GTGGTTGTGGGGGTGCTAC 60.603 63.158 0.00 0.00 0.00 3.58
323 384 2.359478 GGTTGTGGGGGTGCTACG 60.359 66.667 0.00 0.00 0.00 3.51
324 385 2.359478 GTTGTGGGGGTGCTACGG 60.359 66.667 0.00 0.00 0.00 4.02
325 386 4.338710 TTGTGGGGGTGCTACGGC 62.339 66.667 0.00 0.00 39.26 5.68
352 413 2.360801 CGAAAACAATCCACCAACACCT 59.639 45.455 0.00 0.00 0.00 4.00
407 470 1.303317 GAGGTTTGTGGGTGCGGAT 60.303 57.895 0.00 0.00 0.00 4.18
491 554 2.171448 GGAGTGATGGCTGTTGATAGGT 59.829 50.000 0.00 0.00 0.00 3.08
494 560 3.118482 AGTGATGGCTGTTGATAGGTGAG 60.118 47.826 0.00 0.00 0.00 3.51
541 607 3.155167 CGGGCTAGGGGAGGACAC 61.155 72.222 0.00 0.00 0.00 3.67
542 608 2.040606 GGGCTAGGGGAGGACACA 59.959 66.667 0.00 0.00 0.00 3.72
543 609 2.368011 GGGCTAGGGGAGGACACAC 61.368 68.421 0.00 0.00 0.00 3.82
550 616 3.986006 GGAGGACACACGCGGACA 61.986 66.667 12.47 0.00 0.00 4.02
551 617 2.028484 GAGGACACACGCGGACAA 59.972 61.111 12.47 0.00 0.00 3.18
552 618 1.593209 GAGGACACACGCGGACAAA 60.593 57.895 12.47 0.00 0.00 2.83
553 619 1.153329 AGGACACACGCGGACAAAA 60.153 52.632 12.47 0.00 0.00 2.44
554 620 0.745128 AGGACACACGCGGACAAAAA 60.745 50.000 12.47 0.00 0.00 1.94
575 641 0.099259 CACATCCGCGTTGATGCAAT 59.901 50.000 20.74 3.85 44.84 3.56
580 646 2.460275 CGCGTTGATGCAATCCCGA 61.460 57.895 0.00 0.00 44.73 5.14
601 667 7.616150 TCCCGACCCAAATTTAAATCTGAAATA 59.384 33.333 2.97 0.00 0.00 1.40
606 672 9.320295 ACCCAAATTTAAATCTGAAATAGGTCA 57.680 29.630 2.97 0.00 0.00 4.02
641 709 4.442375 AACAGACACACTTCTATCTCGG 57.558 45.455 0.00 0.00 0.00 4.63
663 738 1.698714 CGTTGGACCGCCGTAATTCC 61.699 60.000 0.00 0.00 36.79 3.01
801 900 3.097114 CAAAAGTTTCCCGCGCGC 61.097 61.111 27.36 23.91 0.00 6.86
1170 1269 1.810532 GGTCTCCTCGATGCGTCTT 59.189 57.895 4.05 0.00 0.00 3.01
1215 1314 2.037251 TCTGGTCTTGTTAGGTGTCTGC 59.963 50.000 0.00 0.00 0.00 4.26
1228 1328 2.476854 GGTGTCTGCATGCGAGAAATTC 60.477 50.000 14.09 5.99 0.00 2.17
1286 1392 6.428159 GGAATTGTTATGTTCTCGCATCCTAT 59.572 38.462 0.00 0.00 0.00 2.57
1299 1405 3.585748 CATCCTATGCGGTTTGTTACG 57.414 47.619 0.00 0.00 0.00 3.18
1300 1406 2.747396 TCCTATGCGGTTTGTTACGT 57.253 45.000 0.00 0.00 0.00 3.57
1301 1407 2.339418 TCCTATGCGGTTTGTTACGTG 58.661 47.619 0.00 0.00 0.00 4.49
1302 1408 2.070783 CCTATGCGGTTTGTTACGTGT 58.929 47.619 0.00 0.00 0.00 4.49
1303 1409 2.481185 CCTATGCGGTTTGTTACGTGTT 59.519 45.455 0.00 0.00 0.00 3.32
1304 1410 2.673976 ATGCGGTTTGTTACGTGTTC 57.326 45.000 0.00 0.00 0.00 3.18
1305 1411 1.366679 TGCGGTTTGTTACGTGTTCA 58.633 45.000 0.00 0.00 0.00 3.18
1306 1412 1.062294 TGCGGTTTGTTACGTGTTCAC 59.938 47.619 0.00 0.00 0.00 3.18
1308 1414 2.598205 GCGGTTTGTTACGTGTTCACTC 60.598 50.000 0.00 0.00 0.00 3.51
1309 1415 2.033492 CGGTTTGTTACGTGTTCACTCC 60.033 50.000 0.00 0.00 0.00 3.85
1310 1416 3.200483 GGTTTGTTACGTGTTCACTCCT 58.800 45.455 0.00 0.00 0.00 3.69
1311 1417 4.370917 GGTTTGTTACGTGTTCACTCCTA 58.629 43.478 0.00 0.00 0.00 2.94
1312 1418 4.810491 GGTTTGTTACGTGTTCACTCCTAA 59.190 41.667 0.00 0.00 0.00 2.69
1313 1419 5.050567 GGTTTGTTACGTGTTCACTCCTAAG 60.051 44.000 0.00 0.00 0.00 2.18
1314 1420 5.518848 TTGTTACGTGTTCACTCCTAAGA 57.481 39.130 0.00 0.00 0.00 2.10
1315 1421 5.117355 TGTTACGTGTTCACTCCTAAGAG 57.883 43.478 0.00 0.00 46.36 2.85
1316 1422 2.726832 ACGTGTTCACTCCTAAGAGC 57.273 50.000 0.00 0.00 44.65 4.09
1317 1423 2.240279 ACGTGTTCACTCCTAAGAGCT 58.760 47.619 0.00 0.00 44.65 4.09
1318 1424 2.229302 ACGTGTTCACTCCTAAGAGCTC 59.771 50.000 5.27 5.27 44.65 4.09
1319 1425 2.416162 CGTGTTCACTCCTAAGAGCTCC 60.416 54.545 10.93 0.00 44.65 4.70
1329 1435 1.885887 CTAAGAGCTCCGGATCTCCAG 59.114 57.143 27.50 21.24 37.20 3.86
1334 1440 0.755686 GCTCCGGATCTCCAGACAAT 59.244 55.000 3.57 0.00 35.14 2.71
1341 1447 3.639094 CGGATCTCCAGACAATCCTTAGT 59.361 47.826 0.00 0.00 37.42 2.24
1359 1465 5.122396 CCTTAGTGTTCTGCATCCTTGTTAC 59.878 44.000 0.00 0.00 0.00 2.50
1381 1487 6.490566 ACTATGTTAAAGCGGAATTTCGTT 57.509 33.333 8.18 0.00 0.00 3.85
1395 1501 7.490055 CGGAATTTCGTTTAATCTTGTTTGTG 58.510 34.615 0.00 0.00 0.00 3.33
1428 1534 1.155889 TCAGCAACTGTTATGTGCCG 58.844 50.000 0.00 0.00 32.61 5.69
1445 1551 2.186160 CGGCACCTGAACTGCACAA 61.186 57.895 0.00 0.00 36.27 3.33
1452 1558 0.236711 CTGAACTGCACAAAGCCTCG 59.763 55.000 0.00 0.00 44.83 4.63
1467 1573 3.596214 AGCCTCGGTACAATTGTTAGTG 58.404 45.455 17.78 9.09 0.00 2.74
1471 1577 5.123344 GCCTCGGTACAATTGTTAGTGATTT 59.877 40.000 17.78 0.00 0.00 2.17
1475 1581 6.932400 TCGGTACAATTGTTAGTGATTTGTCT 59.068 34.615 17.78 0.00 0.00 3.41
1477 1583 7.305474 GGTACAATTGTTAGTGATTTGTCTGG 58.695 38.462 17.78 0.00 0.00 3.86
1483 1589 0.877071 AGTGATTTGTCTGGCTTGCG 59.123 50.000 0.00 0.00 0.00 4.85
1490 1608 0.884704 TGTCTGGCTTGCGAAGGTTC 60.885 55.000 0.00 0.00 0.00 3.62
1494 1612 2.563427 GCTTGCGAAGGTTCTGGC 59.437 61.111 0.00 0.00 0.00 4.85
1495 1613 2.260869 GCTTGCGAAGGTTCTGGCA 61.261 57.895 0.00 0.00 0.00 4.92
1496 1614 1.576421 CTTGCGAAGGTTCTGGCAC 59.424 57.895 0.00 0.00 34.72 5.01
1497 1615 1.856265 CTTGCGAAGGTTCTGGCACC 61.856 60.000 0.00 0.00 34.72 5.01
1504 1622 2.271944 AGGTTCTGGCACCTGTTAAC 57.728 50.000 0.00 0.00 46.22 2.01
1522 1640 7.095187 CCTGTTAACCAACATCTGTTTACTCTC 60.095 40.741 2.48 0.00 43.58 3.20
1545 1663 1.004440 GCTTCACGCCACTCTTCCT 60.004 57.895 0.00 0.00 0.00 3.36
1548 1666 0.884704 TTCACGCCACTCTTCCTTGC 60.885 55.000 0.00 0.00 0.00 4.01
1575 1693 2.045340 AGCCAACACATACCGGCC 60.045 61.111 0.00 0.00 46.08 6.13
1582 1700 1.241315 ACACATACCGGCCAAACTGC 61.241 55.000 0.00 0.00 0.00 4.40
1593 1711 1.606224 GCCAAACTGCAAGGTTCATGG 60.606 52.381 5.56 5.56 43.11 3.66
1643 1761 5.991328 AGTATTCATTACTTGTGCGGATG 57.009 39.130 0.00 0.00 37.96 3.51
1644 1762 4.816385 AGTATTCATTACTTGTGCGGATGG 59.184 41.667 0.00 0.00 37.96 3.51
1659 1777 2.286833 CGGATGGTAAATTGTACTGCCG 59.713 50.000 0.00 0.00 0.00 5.69
1662 1783 2.428491 TGGTAAATTGTACTGCCGTGG 58.572 47.619 0.00 0.00 0.00 4.94
1757 1878 6.614694 TCATGGTAGCTACAGTTCCTTTTA 57.385 37.500 24.75 0.00 0.00 1.52
1787 1908 3.386768 TTATGCTGATCCCTAACTCGC 57.613 47.619 0.00 0.00 0.00 5.03
1879 2000 3.281727 TTCAGGCATTGATCAGGTACC 57.718 47.619 2.73 2.73 35.27 3.34
1933 2054 2.812591 TCTCGACCTGTGAGTAACTGAC 59.187 50.000 0.00 0.00 34.99 3.51
1952 2073 8.641498 AACTGACTAATTTCACCATTTCATCT 57.359 30.769 0.00 0.00 0.00 2.90
1959 2080 6.790285 ATTTCACCATTTCATCTGCAAAAC 57.210 33.333 0.00 0.00 0.00 2.43
1964 2085 4.507388 ACCATTTCATCTGCAAAACAAACG 59.493 37.500 0.00 0.00 0.00 3.60
2217 2338 1.474855 GCTCTCTCTCCCCTTCAATGC 60.475 57.143 0.00 0.00 0.00 3.56
2244 2365 8.748412 TGATTATACATGCTTAACCTGCTTTTT 58.252 29.630 0.00 0.00 0.00 1.94
2709 3109 2.879103 TCCCACTCTGAATGTTTCCC 57.121 50.000 0.00 0.00 0.00 3.97
2866 3267 3.052455 ACGCAATACATTGACCAGTGA 57.948 42.857 6.13 0.00 40.14 3.41
3044 3451 1.339929 ACCCACAACATTTTCTTCGCC 59.660 47.619 0.00 0.00 0.00 5.54
3161 3574 1.051812 AGGGACTGTGAACTGTGGAG 58.948 55.000 0.00 0.00 37.18 3.86
3183 3596 3.851098 CTCCAGCCTAGTTGTTAGTGAC 58.149 50.000 0.00 0.00 0.00 3.67
3400 3813 3.388676 TGTTCTCTCCCGTGTTCCTTTTA 59.611 43.478 0.00 0.00 0.00 1.52
3401 3814 3.955650 TCTCTCCCGTGTTCCTTTTAG 57.044 47.619 0.00 0.00 0.00 1.85
3469 3882 2.435805 TCAGAGGCAACAACTCAGACTT 59.564 45.455 0.00 0.00 37.43 3.01
3470 3883 2.547211 CAGAGGCAACAACTCAGACTTG 59.453 50.000 0.00 0.00 37.43 3.16
3515 3928 3.565307 TCTTTTCATCACTTTGCCAGGT 58.435 40.909 0.00 0.00 0.00 4.00
3602 4015 3.685139 AGGTGTACTGGACATCACTTG 57.315 47.619 5.98 0.00 42.18 3.16
3700 4114 3.016031 TGAGTGCAGTGTCATGTTGTTT 58.984 40.909 0.00 0.00 0.00 2.83
3714 4128 4.433186 TGTTGTTTCTGGCATAATTCCG 57.567 40.909 0.00 0.00 0.00 4.30
3719 4133 2.818751 TCTGGCATAATTCCGGGTTT 57.181 45.000 0.00 0.00 0.00 3.27
3727 4141 4.336993 GCATAATTCCGGGTTTCACATGTA 59.663 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.493278 CGATGTTCAGGGGCTCAATTTT 59.507 45.455 0.00 0.00 0.00 1.82
13 14 2.989639 CCGATGTTCAGGGGCTCA 59.010 61.111 0.00 0.00 0.00 4.26
35 36 2.355197 TCATGACCACATTGCTAACCG 58.645 47.619 0.00 0.00 34.15 4.44
163 164 1.385528 GGTGTTCAACGTTTCACCCT 58.614 50.000 24.57 0.00 42.90 4.34
167 168 2.162608 CCACAAGGTGTTCAACGTTTCA 59.837 45.455 0.00 0.00 34.69 2.69
175 176 1.821759 CCGTGCCACAAGGTGTTCA 60.822 57.895 0.00 0.00 37.19 3.18
186 187 2.281484 GCTTCTTCCACCGTGCCA 60.281 61.111 0.00 0.00 0.00 4.92
249 251 1.221840 GTCACCTCCATGCCGACAT 59.778 57.895 0.00 0.00 36.79 3.06
292 322 4.542627 AACCACCCCACCCCCTCA 62.543 66.667 0.00 0.00 0.00 3.86
303 364 2.836187 TAGCACCCCCACAACCACC 61.836 63.158 0.00 0.00 0.00 4.61
304 365 1.602605 GTAGCACCCCCACAACCAC 60.603 63.158 0.00 0.00 0.00 4.16
305 366 2.840576 GTAGCACCCCCACAACCA 59.159 61.111 0.00 0.00 0.00 3.67
306 367 2.359478 CGTAGCACCCCCACAACC 60.359 66.667 0.00 0.00 0.00 3.77
307 368 2.359478 CCGTAGCACCCCCACAAC 60.359 66.667 0.00 0.00 0.00 3.32
308 369 4.338710 GCCGTAGCACCCCCACAA 62.339 66.667 0.00 0.00 39.53 3.33
323 384 4.413800 ATTGTTTTCGCCGCCGCC 62.414 61.111 0.00 0.00 0.00 6.13
324 385 2.874315 GATTGTTTTCGCCGCCGC 60.874 61.111 0.00 0.00 0.00 6.53
325 386 2.202427 GGATTGTTTTCGCCGCCG 60.202 61.111 0.00 0.00 0.00 6.46
326 387 1.443702 GTGGATTGTTTTCGCCGCC 60.444 57.895 0.00 0.00 0.00 6.13
327 388 1.443702 GGTGGATTGTTTTCGCCGC 60.444 57.895 0.00 0.00 0.00 6.53
328 389 0.312416 TTGGTGGATTGTTTTCGCCG 59.688 50.000 0.00 0.00 34.06 6.46
329 390 1.067821 TGTTGGTGGATTGTTTTCGCC 59.932 47.619 0.00 0.00 0.00 5.54
330 391 2.124122 GTGTTGGTGGATTGTTTTCGC 58.876 47.619 0.00 0.00 0.00 4.70
331 392 2.360801 AGGTGTTGGTGGATTGTTTTCG 59.639 45.455 0.00 0.00 0.00 3.46
332 393 3.716601 CAGGTGTTGGTGGATTGTTTTC 58.283 45.455 0.00 0.00 0.00 2.29
352 413 4.717629 CCGACGACCGCTCTTGCA 62.718 66.667 0.00 0.00 39.64 4.08
385 448 2.200337 GCACCCACAAACCTCCCAC 61.200 63.158 0.00 0.00 0.00 4.61
449 512 4.082523 CCACCACGCCCTCGACAT 62.083 66.667 0.00 0.00 39.41 3.06
476 539 1.492176 CCCTCACCTATCAACAGCCAT 59.508 52.381 0.00 0.00 0.00 4.40
529 595 3.066190 CGCGTGTGTCCTCCCCTA 61.066 66.667 0.00 0.00 0.00 3.53
534 600 1.155424 TTTTGTCCGCGTGTGTCCTC 61.155 55.000 4.92 0.00 0.00 3.71
551 617 2.660490 CATCAACGCGGATGTGTTTTT 58.340 42.857 12.47 0.00 46.24 1.94
552 618 1.665735 GCATCAACGCGGATGTGTTTT 60.666 47.619 21.28 0.00 46.24 2.43
553 619 0.109781 GCATCAACGCGGATGTGTTT 60.110 50.000 21.28 0.00 46.24 2.83
555 621 1.233950 TTGCATCAACGCGGATGTGT 61.234 50.000 21.28 7.72 45.11 3.72
559 625 1.447317 GGGATTGCATCAACGCGGAT 61.447 55.000 12.47 0.58 33.35 4.18
567 633 0.038890 TTTGGGTCGGGATTGCATCA 59.961 50.000 0.00 0.00 0.00 3.07
575 641 4.924625 TCAGATTTAAATTTGGGTCGGGA 58.075 39.130 16.31 0.02 0.00 5.14
580 646 9.320295 TGACCTATTTCAGATTTAAATTTGGGT 57.680 29.630 16.31 14.56 31.48 4.51
601 667 0.745128 TTTTTGTCCGCGTGTGACCT 60.745 50.000 4.92 0.00 31.60 3.85
622 688 2.792890 CGCCGAGATAGAAGTGTGTCTG 60.793 54.545 0.00 0.00 0.00 3.51
624 690 1.828832 CGCCGAGATAGAAGTGTGTC 58.171 55.000 0.00 0.00 0.00 3.67
626 692 1.202973 CGCGCCGAGATAGAAGTGTG 61.203 60.000 0.00 0.00 0.00 3.82
631 699 1.226859 CCAACGCGCCGAGATAGAA 60.227 57.895 5.73 0.00 0.00 2.10
663 738 2.574222 GCGCCGTCCGTTTAGATCG 61.574 63.158 0.00 0.00 39.71 3.69
801 900 1.604147 GAAGGGGAATTTGGCGTGGG 61.604 60.000 0.00 0.00 0.00 4.61
985 1084 1.043116 TACATCCTGCCACTCCTCCG 61.043 60.000 0.00 0.00 0.00 4.63
993 1092 2.494445 CTCGCGTACATCCTGCCA 59.506 61.111 5.77 0.00 0.00 4.92
1066 1165 5.411669 AGAGGCGAAGAATTACGTTGAAAAT 59.588 36.000 0.00 0.00 0.00 1.82
1170 1269 3.147553 GGCAAAATTGGGCCCTAAAAA 57.852 42.857 25.70 9.39 44.53 1.94
1241 1341 5.825593 TCCCATAGGGCTGTAAAATAGAG 57.174 43.478 0.00 0.00 43.94 2.43
1286 1392 1.062294 GTGAACACGTAACAAACCGCA 59.938 47.619 0.00 0.00 0.00 5.69
1296 1402 3.418995 AGCTCTTAGGAGTGAACACGTA 58.581 45.455 3.55 0.00 41.38 3.57
1297 1403 2.229302 GAGCTCTTAGGAGTGAACACGT 59.771 50.000 6.43 0.00 41.38 4.49
1298 1404 2.416162 GGAGCTCTTAGGAGTGAACACG 60.416 54.545 14.64 0.00 41.38 4.49
1299 1405 2.416162 CGGAGCTCTTAGGAGTGAACAC 60.416 54.545 14.64 0.00 41.38 3.32
1300 1406 1.819288 CGGAGCTCTTAGGAGTGAACA 59.181 52.381 14.64 0.00 41.38 3.18
1301 1407 1.135333 CCGGAGCTCTTAGGAGTGAAC 59.865 57.143 14.64 0.00 41.38 3.18
1302 1408 1.005569 TCCGGAGCTCTTAGGAGTGAA 59.994 52.381 14.64 0.00 41.38 3.18
1303 1409 0.624254 TCCGGAGCTCTTAGGAGTGA 59.376 55.000 14.64 0.00 41.38 3.41
1304 1410 1.611491 GATCCGGAGCTCTTAGGAGTG 59.389 57.143 23.10 3.69 41.38 3.51
1305 1411 1.497286 AGATCCGGAGCTCTTAGGAGT 59.503 52.381 18.52 14.44 41.38 3.85
1306 1412 2.159382 GAGATCCGGAGCTCTTAGGAG 58.841 57.143 36.46 0.00 40.46 3.69
1308 1414 1.253100 GGAGATCCGGAGCTCTTAGG 58.747 60.000 39.90 14.52 42.99 2.69
1309 1415 1.885887 CTGGAGATCCGGAGCTCTTAG 59.114 57.143 39.90 33.02 45.36 2.18
1310 1416 1.495148 TCTGGAGATCCGGAGCTCTTA 59.505 52.381 39.90 29.55 46.04 2.10
1311 1417 0.260230 TCTGGAGATCCGGAGCTCTT 59.740 55.000 39.90 14.76 46.04 2.85
1312 1418 1.926657 TCTGGAGATCCGGAGCTCT 59.073 57.895 39.90 25.99 46.04 4.09
1313 1419 4.589046 TCTGGAGATCCGGAGCTC 57.411 61.111 36.24 36.24 46.04 4.09
1318 1424 1.418334 AGGATTGTCTGGAGATCCGG 58.582 55.000 0.00 0.00 43.25 5.14
1319 1425 3.639094 ACTAAGGATTGTCTGGAGATCCG 59.361 47.826 0.00 0.00 43.25 4.18
1329 1435 4.333926 GGATGCAGAACACTAAGGATTGTC 59.666 45.833 0.00 0.00 0.00 3.18
1334 1440 3.327757 ACAAGGATGCAGAACACTAAGGA 59.672 43.478 0.00 0.00 0.00 3.36
1341 1447 5.804639 ACATAGTAACAAGGATGCAGAACA 58.195 37.500 0.00 0.00 0.00 3.18
1359 1465 8.883789 TTAAACGAAATTCCGCTTTAACATAG 57.116 30.769 0.00 0.00 0.00 2.23
1428 1534 0.031178 CTTTGTGCAGTTCAGGTGCC 59.969 55.000 0.00 0.00 40.43 5.01
1445 1551 4.000988 CACTAACAATTGTACCGAGGCTT 58.999 43.478 12.39 0.00 0.00 4.35
1452 1558 7.305474 CCAGACAAATCACTAACAATTGTACC 58.695 38.462 12.39 0.00 34.59 3.34
1467 1573 1.135575 CCTTCGCAAGCCAGACAAATC 60.136 52.381 0.00 0.00 37.18 2.17
1471 1577 0.884704 GAACCTTCGCAAGCCAGACA 60.885 55.000 0.00 0.00 37.18 3.41
1475 1581 1.600636 CCAGAACCTTCGCAAGCCA 60.601 57.895 0.00 0.00 37.18 4.75
1477 1583 2.260869 TGCCAGAACCTTCGCAAGC 61.261 57.895 0.00 0.00 37.18 4.01
1490 1608 1.686355 TGTTGGTTAACAGGTGCCAG 58.314 50.000 8.10 0.00 41.66 4.85
1499 1617 7.724305 TGAGAGTAAACAGATGTTGGTTAAC 57.276 36.000 0.00 0.00 40.52 2.01
1500 1618 7.990886 ACTTGAGAGTAAACAGATGTTGGTTAA 59.009 33.333 0.00 0.00 40.52 2.01
1501 1619 7.441157 CACTTGAGAGTAAACAGATGTTGGTTA 59.559 37.037 0.00 0.00 37.93 2.85
1502 1620 6.260936 CACTTGAGAGTAAACAGATGTTGGTT 59.739 38.462 0.00 0.00 40.59 3.67
1503 1621 5.760253 CACTTGAGAGTAAACAGATGTTGGT 59.240 40.000 0.00 0.00 34.27 3.67
1504 1622 5.334414 GCACTTGAGAGTAAACAGATGTTGG 60.334 44.000 0.00 0.00 34.27 3.77
1545 1663 1.479730 TGTTGGCTCACACAATTGCAA 59.520 42.857 5.05 0.00 0.00 4.08
1575 1693 3.305335 GGTACCATGAACCTTGCAGTTTG 60.305 47.826 7.15 0.00 33.97 2.93
1582 1700 3.377172 GGAATTCGGTACCATGAACCTTG 59.623 47.826 13.54 0.00 34.66 3.61
1593 1711 5.470098 ACAGCAATATCATGGAATTCGGTAC 59.530 40.000 0.00 0.00 0.00 3.34
1636 1754 2.680841 GCAGTACAATTTACCATCCGCA 59.319 45.455 0.00 0.00 0.00 5.69
1638 1756 2.286833 CGGCAGTACAATTTACCATCCG 59.713 50.000 0.00 0.00 0.00 4.18
1643 1761 1.131693 GCCACGGCAGTACAATTTACC 59.868 52.381 2.36 0.00 41.49 2.85
1644 1762 2.537639 GCCACGGCAGTACAATTTAC 57.462 50.000 2.36 0.00 41.49 2.01
1659 1777 1.112113 TTCCGTCCTAGAGATGCCAC 58.888 55.000 0.00 0.00 0.00 5.01
1662 1783 2.034053 CAGAGTTCCGTCCTAGAGATGC 59.966 54.545 0.00 0.00 0.00 3.91
1668 1789 1.115467 ATGCCAGAGTTCCGTCCTAG 58.885 55.000 0.00 0.00 0.00 3.02
1735 1856 7.865706 ATTAAAAGGAACTGTAGCTACCATG 57.134 36.000 21.01 13.11 40.86 3.66
1757 1878 5.461327 AGGGATCAGCATAATGGACAAATT 58.539 37.500 0.00 0.00 0.00 1.82
1787 1908 4.495349 CGCTCTGCAAATTCCATAAGACAG 60.495 45.833 0.00 0.00 0.00 3.51
1879 2000 5.278169 GCATCAACATTCTAATAGGGTGCAG 60.278 44.000 0.00 0.00 0.00 4.41
1912 2033 2.812591 GTCAGTTACTCACAGGTCGAGA 59.187 50.000 0.00 0.00 34.47 4.04
1933 2054 8.437742 GTTTTGCAGATGAAATGGTGAAATTAG 58.562 33.333 0.00 0.00 0.00 1.73
1952 2073 2.354109 TGCAGTTCGTTTGTTTTGCA 57.646 40.000 0.00 0.00 39.03 4.08
1959 2080 3.077229 TGGTTCAATGCAGTTCGTTTG 57.923 42.857 0.00 0.00 0.00 2.93
1964 2085 2.223782 TGCTGTTGGTTCAATGCAGTTC 60.224 45.455 0.00 0.00 33.51 3.01
2184 2305 1.269448 GAGAGAGCCCGATGTGAGATC 59.731 57.143 0.00 0.00 0.00 2.75
2217 2338 7.502120 AAGCAGGTTAAGCATGTATAATCAG 57.498 36.000 7.52 0.00 0.00 2.90
2244 2365 4.882842 TGATTTCAGCTAGTGTACACCA 57.117 40.909 22.28 8.29 0.00 4.17
2837 3238 6.819146 TGGTCAATGTATTGCGTTTATACTGA 59.181 34.615 0.00 0.00 37.68 3.41
3044 3451 0.108186 TATTCCACCAGACAGCAGCG 60.108 55.000 0.00 0.00 0.00 5.18
3161 3574 2.233922 TCACTAACAACTAGGCTGGAGC 59.766 50.000 4.33 0.00 41.14 4.70
3375 3788 1.336980 GGAACACGGGAGAGAACAGTC 60.337 57.143 0.00 0.00 0.00 3.51
3400 3813 1.484653 TGTCACAGCTGTGGTTGTACT 59.515 47.619 39.04 4.34 45.65 2.73
3401 3814 1.948104 TGTCACAGCTGTGGTTGTAC 58.052 50.000 39.04 30.15 45.65 2.90
3440 3853 3.877508 AGTTGTTGCCTCTGACTAAACAC 59.122 43.478 0.00 0.00 30.89 3.32
3469 3882 2.852449 TGGGACAGTAATTGAAACGCA 58.148 42.857 0.00 0.00 0.00 5.24
3470 3883 3.252458 ACTTGGGACAGTAATTGAAACGC 59.748 43.478 0.00 0.00 42.39 4.84
3515 3928 4.401519 AGATGTACTGCGTTAGGCTTTCTA 59.598 41.667 0.00 0.00 44.05 2.10
3602 4015 2.777832 AGAAGATGCCAGTCTCAACC 57.222 50.000 0.00 0.00 0.00 3.77
3700 4114 2.025793 TGAAACCCGGAATTATGCCAGA 60.026 45.455 0.73 0.00 0.00 3.86
3714 4128 4.929819 AAAACACCTACATGTGAAACCC 57.070 40.909 9.11 0.00 39.57 4.11
3719 4133 7.011950 CAGAAACACTAAAACACCTACATGTGA 59.988 37.037 9.11 0.00 39.57 3.58
3727 4141 5.185056 ACAAAGCAGAAACACTAAAACACCT 59.815 36.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.