Multiple sequence alignment - TraesCS5B01G466000

Loading Multiple Alignment...

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 TraesCS5B01G466000 chr5B 100.000 2381 0 0 1 2381 640266700 640269080 0.000000e+00 4397
1 TraesCS5B01G466000 chr5A 90.452 1791 92 30 639 2381 636921002 636922761 0.000000e+00 2287
2 TraesCS5B01G466000 chr5D 90.281 1245 62 30 639 1853 509540438 509541653 0.000000e+00 1574
3 TraesCS5B01G466000 chr5D 77.000 300 49 14 1899 2193 509541665 509541949 1.140000e-33 154
4 TraesCS5B01G466000 chrUn 89.933 596 59 1 4 598 38956912 38956317 0.000000e+00 767
5 TraesCS5B01G466000 chr4B 88.255 596 66 4 5 598 29693263 29693856 0.000000e+00 710
6 TraesCS5B01G466000 chr4B 76.215 391 81 12 193 577 639223734 639224118 1.870000e-46 196
7 TraesCS5B01G466000 chr3A 86.144 599 78 5 1 596 693105344 693104748 2.000000e-180 641
8 TraesCS5B01G466000 chr7B 92.644 435 31 1 165 598 741547542 741547976 2.010000e-175 625
9 TraesCS5B01G466000 chr2B 77.211 588 123 11 1 582 764406107 764406689 1.360000e-87 333


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 TraesCS5B01G466000 chr5B 640266700 640269080 2380 False 4397 4397 100.0000 1 2381 1 chr5B.!!$F1 2380
1 TraesCS5B01G466000 chr5A 636921002 636922761 1759 False 2287 2287 90.4520 639 2381 1 chr5A.!!$F1 1742
2 TraesCS5B01G466000 chr5D 509540438 509541949 1511 False 864 1574 83.6405 639 2193 2 chr5D.!!$F1 1554
3 TraesCS5B01G466000 chrUn 38956317 38956912 595 True 767 767 89.9330 4 598 1 chrUn.!!$R1 594
4 TraesCS5B01G466000 chr4B 29693263 29693856 593 False 710 710 88.2550 5 598 1 chr4B.!!$F1 593
5 TraesCS5B01G466000 chr3A 693104748 693105344 596 True 641 641 86.1440 1 596 1 chr3A.!!$R1 595
6 TraesCS5B01G466000 chr2B 764406107 764406689 582 False 333 333 77.2110 1 582 1 chr2B.!!$F1 581

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
993 1001 0.544697 GTCAGAAGGCCGGGGATTTA 59.455 55.0 2.18 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2275 0.106708 TCTTTTGACCGAGCTGCAGT 59.893 50.0 16.64 1.59 0.0 4.4 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
55 56 4.286447 GGGCTGAAACCCCAAACA 57.714 55.556 0.00 0.00 45.00 2.83
57 58 1.055849 GGGCTGAAACCCCAAACATT 58.944 50.000 0.00 0.00 45.00 2.71
61 62 2.368548 GCTGAAACCCCAAACATTCCTT 59.631 45.455 0.00 0.00 0.00 3.36
70 71 1.342819 CAAACATTCCTTCCCGGCAAA 59.657 47.619 0.00 0.00 0.00 3.68
178 182 2.659897 GGCAGTAGCGCGAGATGG 60.660 66.667 12.10 0.00 43.41 3.51
191 195 3.406764 GCGAGATGGCAAAGGAGAATAT 58.593 45.455 0.00 0.00 0.00 1.28
201 205 5.047519 GGCAAAGGAGAATATATTGCAGCAT 60.048 40.000 1.78 0.00 46.12 3.79
209 213 7.336176 GGAGAATATATTGCAGCATCATCTTGA 59.664 37.037 1.78 0.00 0.00 3.02
276 280 3.904800 TTCGTAATGGCCTGATCTTGA 57.095 42.857 3.32 0.00 0.00 3.02
372 376 2.618709 GGTTACTTAGGCCATGATGTGC 59.381 50.000 5.01 0.00 0.00 4.57
377 381 3.036577 GGCCATGATGTGCCGATG 58.963 61.111 8.76 0.00 38.00 3.84
465 469 3.947834 GGCTAATGGTGTTGCTGATACTT 59.052 43.478 0.00 0.00 0.00 2.24
524 529 2.186903 GACGATGTGGTGCCCGAT 59.813 61.111 0.00 0.00 0.00 4.18
525 530 1.883084 GACGATGTGGTGCCCGATC 60.883 63.158 0.00 0.00 0.00 3.69
626 631 3.761897 CCTGACAAAGGTGGGTATTTCA 58.238 45.455 0.00 0.00 41.74 2.69
627 632 4.344104 CCTGACAAAGGTGGGTATTTCAT 58.656 43.478 0.00 0.00 41.74 2.57
628 633 4.158394 CCTGACAAAGGTGGGTATTTCATG 59.842 45.833 0.00 0.00 41.74 3.07
629 634 4.735369 TGACAAAGGTGGGTATTTCATGT 58.265 39.130 0.00 0.00 0.00 3.21
630 635 5.144100 TGACAAAGGTGGGTATTTCATGTT 58.856 37.500 0.00 0.00 0.00 2.71
631 636 5.242838 TGACAAAGGTGGGTATTTCATGTTC 59.757 40.000 0.00 0.00 0.00 3.18
632 637 5.393866 ACAAAGGTGGGTATTTCATGTTCT 58.606 37.500 0.00 0.00 0.00 3.01
633 638 6.548321 ACAAAGGTGGGTATTTCATGTTCTA 58.452 36.000 0.00 0.00 0.00 2.10
634 639 7.007723 ACAAAGGTGGGTATTTCATGTTCTAA 58.992 34.615 0.00 0.00 0.00 2.10
635 640 7.507616 ACAAAGGTGGGTATTTCATGTTCTAAA 59.492 33.333 0.00 0.00 0.00 1.85
636 641 7.703058 AAGGTGGGTATTTCATGTTCTAAAG 57.297 36.000 0.00 0.00 0.00 1.85
637 642 7.027874 AGGTGGGTATTTCATGTTCTAAAGA 57.972 36.000 0.00 0.00 0.00 2.52
655 660 5.468540 AAAGAAAAGGTGGGTATTTCAGC 57.531 39.130 0.00 0.00 35.91 4.26
694 699 2.606213 TGTGGGCTCCATCCGTCA 60.606 61.111 0.00 0.00 35.28 4.35
993 1001 0.544697 GTCAGAAGGCCGGGGATTTA 59.455 55.000 2.18 0.00 0.00 1.40
1276 1287 2.999063 CGTACTCCCCCACCCGTT 60.999 66.667 0.00 0.00 0.00 4.44
1277 1288 2.984623 GTACTCCCCCACCCGTTC 59.015 66.667 0.00 0.00 0.00 3.95
1278 1289 2.284847 TACTCCCCCACCCGTTCC 60.285 66.667 0.00 0.00 0.00 3.62
1279 1290 2.872250 TACTCCCCCACCCGTTCCT 61.872 63.158 0.00 0.00 0.00 3.36
1280 1291 2.810488 TACTCCCCCACCCGTTCCTC 62.810 65.000 0.00 0.00 0.00 3.71
1285 1296 2.284699 CCACCCGTTCCTCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
1299 1310 0.998945 CCTCCTCCTCCTCCTCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1305 1334 2.177669 CTCCTCCTCCTCCTCTTCATCT 59.822 54.545 0.00 0.00 0.00 2.90
1412 1441 3.216800 TGCTCATTCACTGCTTTTGAGT 58.783 40.909 0.00 0.00 36.91 3.41
1425 1454 4.039488 TGCTTTTGAGTTCATGCCTGATTT 59.961 37.500 0.00 0.00 0.00 2.17
1428 1457 5.633830 TTTGAGTTCATGCCTGATTTCTC 57.366 39.130 0.00 3.14 0.00 2.87
1434 1463 1.944709 CATGCCTGATTTCTCATCGCA 59.055 47.619 0.00 0.00 39.49 5.10
1449 1484 7.875316 TCTCATCGCATAGTAAATTAGCTTC 57.125 36.000 0.00 0.00 0.00 3.86
1466 1501 4.404507 GCTTCGAATAGCTTTGTTGTGA 57.595 40.909 0.00 0.00 38.15 3.58
1467 1502 4.783242 GCTTCGAATAGCTTTGTTGTGAA 58.217 39.130 0.00 0.00 38.15 3.18
1469 1504 5.560953 GCTTCGAATAGCTTTGTTGTGAACT 60.561 40.000 0.00 0.00 38.15 3.01
1473 1508 5.396362 CGAATAGCTTTGTTGTGAACTTGTG 59.604 40.000 0.00 0.00 0.00 3.33
1477 1512 3.243643 GCTTTGTTGTGAACTTGTGATGC 59.756 43.478 0.00 0.00 0.00 3.91
1478 1513 4.675510 CTTTGTTGTGAACTTGTGATGCT 58.324 39.130 0.00 0.00 0.00 3.79
1479 1514 5.733091 GCTTTGTTGTGAACTTGTGATGCTA 60.733 40.000 0.00 0.00 0.00 3.49
1480 1515 5.422666 TTGTTGTGAACTTGTGATGCTAG 57.577 39.130 0.00 0.00 0.00 3.42
1481 1516 4.450976 TGTTGTGAACTTGTGATGCTAGT 58.549 39.130 0.00 0.00 34.75 2.57
1482 1517 4.273235 TGTTGTGAACTTGTGATGCTAGTG 59.727 41.667 0.00 0.00 33.63 2.74
1483 1518 4.071961 TGTGAACTTGTGATGCTAGTGT 57.928 40.909 0.00 0.00 33.63 3.55
1484 1519 4.058124 TGTGAACTTGTGATGCTAGTGTC 58.942 43.478 0.00 0.00 33.63 3.67
1503 1538 2.020720 TCGAAATGGTTTGTGCAGTGT 58.979 42.857 0.00 0.00 0.00 3.55
1565 1600 3.509442 TCAAAATTCAGGATGGGCAGTT 58.491 40.909 0.00 0.00 36.16 3.16
1601 1636 2.831526 ACCCGATGGATTTTCTTTTGGG 59.168 45.455 0.00 0.00 40.04 4.12
1677 1718 7.824779 ACATAAAAGTAAGATCTGGTGTCCTTC 59.175 37.037 0.00 0.00 0.00 3.46
1694 1740 6.907748 GTGTCCTTCTCGAAAGAAAGAAAAAG 59.092 38.462 8.37 0.00 40.95 2.27
1774 1823 4.560035 CCGCTGAATTTTAGATGTTGCAAG 59.440 41.667 0.00 0.00 0.00 4.01
1812 1861 5.150715 TGAGGAAGTGGATCATATAGCACT 58.849 41.667 0.00 0.00 0.00 4.40
1820 1869 4.779489 TGGATCATATAGCACTATGCCTGT 59.221 41.667 0.30 0.00 46.52 4.00
1838 1887 4.082571 GCCTGTAATTCTGCTGATGTTTGT 60.083 41.667 0.00 0.00 0.00 2.83
1846 1895 7.876936 ATTCTGCTGATGTTTGTCTGATATT 57.123 32.000 0.00 0.00 0.00 1.28
1847 1896 6.915544 TCTGCTGATGTTTGTCTGATATTC 57.084 37.500 0.00 0.00 0.00 1.75
1860 1909 5.232202 TGTCTGATATTCGAAATCGTTGAGC 59.768 40.000 0.00 4.00 40.80 4.26
1863 1912 2.813779 ATTCGAAATCGTTGAGCTGC 57.186 45.000 0.00 0.00 40.80 5.25
1864 1913 1.507562 TTCGAAATCGTTGAGCTGCA 58.492 45.000 1.02 0.00 40.80 4.41
1940 1990 2.546321 GCGTCACTGAGTTGCACG 59.454 61.111 4.58 4.58 0.00 5.34
1945 1995 2.281070 ACTGAGTTGCACGCCTGG 60.281 61.111 0.00 0.00 0.00 4.45
1949 1999 1.034838 TGAGTTGCACGCCTGGTTTT 61.035 50.000 0.00 0.00 0.00 2.43
2010 2063 5.681639 ACATAGTAGTTTAGTTGCCCATCC 58.318 41.667 0.00 0.00 0.00 3.51
2115 2169 3.380479 TCCAAGGTCGTGAACTTAGTG 57.620 47.619 0.00 0.00 35.91 2.74
2122 2176 4.082679 AGGTCGTGAACTTAGTGATGAGAC 60.083 45.833 0.00 0.00 0.00 3.36
2204 2274 3.095332 TGCTATTGTTGCATTAAGGCCA 58.905 40.909 9.98 0.00 35.31 5.36
2205 2275 3.513119 TGCTATTGTTGCATTAAGGCCAA 59.487 39.130 9.98 7.88 35.31 4.52
2209 2279 1.000731 TGTTGCATTAAGGCCAACTGC 59.999 47.619 20.07 9.55 40.16 4.40
2214 2285 1.133790 CATTAAGGCCAACTGCAGCTC 59.866 52.381 15.27 0.00 43.89 4.09
2223 2294 0.947244 AACTGCAGCTCGGTCAAAAG 59.053 50.000 15.27 0.00 31.79 2.27
2225 2296 0.514691 CTGCAGCTCGGTCAAAAGAC 59.485 55.000 0.00 0.00 0.00 3.01
2226 2297 0.179059 TGCAGCTCGGTCAAAAGACA 60.179 50.000 0.00 0.00 0.00 3.41
2227 2298 1.160137 GCAGCTCGGTCAAAAGACAT 58.840 50.000 0.00 0.00 0.00 3.06
2230 2301 3.814945 CAGCTCGGTCAAAAGACATTTC 58.185 45.455 0.00 0.00 0.00 2.17
2231 2302 3.250762 CAGCTCGGTCAAAAGACATTTCA 59.749 43.478 0.00 0.00 0.00 2.69
2237 2323 4.148696 CGGTCAAAAGACATTTCATTGCAC 59.851 41.667 0.00 0.00 0.00 4.57
2240 2326 6.203338 GGTCAAAAGACATTTCATTGCACATT 59.797 34.615 0.00 0.00 0.00 2.71
2248 2334 7.544566 AGACATTTCATTGCACATTCTGAATTC 59.455 33.333 0.00 0.00 0.00 2.17
2266 2352 9.300681 TCTGAATTCCTGATGTAAACAGAAAAT 57.699 29.630 2.27 0.00 39.37 1.82
2274 2360 6.081049 TGATGTAAACAGAAAATTAACGCCG 58.919 36.000 0.00 0.00 0.00 6.46
2275 2361 5.670149 TGTAAACAGAAAATTAACGCCGA 57.330 34.783 0.00 0.00 0.00 5.54
2276 2362 6.243811 TGTAAACAGAAAATTAACGCCGAT 57.756 33.333 0.00 0.00 0.00 4.18
2282 2368 5.105917 ACAGAAAATTAACGCCGATGGAATT 60.106 36.000 0.00 0.00 0.00 2.17
2283 2369 5.229887 CAGAAAATTAACGCCGATGGAATTG 59.770 40.000 0.00 0.00 0.00 2.32
2291 2377 2.797156 CGCCGATGGAATTGAAGACTAG 59.203 50.000 0.00 0.00 0.00 2.57
2310 2396 8.430801 AGACTAGCTTGACAATGATATTCAAC 57.569 34.615 1.04 0.00 0.00 3.18
2320 2406 6.938507 ACAATGATATTCAACATGCTGGTTT 58.061 32.000 0.00 0.00 0.00 3.27
2321 2407 6.814644 ACAATGATATTCAACATGCTGGTTTG 59.185 34.615 0.00 0.00 0.00 2.93
2328 2414 3.450457 TCAACATGCTGGTTTGAGGTTTT 59.550 39.130 0.00 0.00 0.00 2.43
2338 2424 5.511363 TGGTTTGAGGTTTTGACTCCTAAA 58.489 37.500 0.00 0.00 33.83 1.85
2346 2432 4.390264 GTTTTGACTCCTAAACTCTGCCT 58.610 43.478 0.00 0.00 35.89 4.75
2348 2434 1.276421 TGACTCCTAAACTCTGCCTGC 59.724 52.381 0.00 0.00 0.00 4.85
2349 2435 1.276421 GACTCCTAAACTCTGCCTGCA 59.724 52.381 0.00 0.00 0.00 4.41
2350 2436 1.277557 ACTCCTAAACTCTGCCTGCAG 59.722 52.381 12.91 12.91 44.86 4.41
2351 2437 0.036010 TCCTAAACTCTGCCTGCAGC 60.036 55.000 14.22 4.57 43.31 5.25
2352 2438 0.035630 CCTAAACTCTGCCTGCAGCT 60.036 55.000 14.22 0.00 43.31 4.24
2353 2439 1.612726 CCTAAACTCTGCCTGCAGCTT 60.613 52.381 14.22 9.54 43.31 3.74
2354 2440 1.467734 CTAAACTCTGCCTGCAGCTTG 59.532 52.381 14.22 9.14 43.31 4.01
2355 2441 0.179009 AAACTCTGCCTGCAGCTTGA 60.179 50.000 14.22 4.44 43.31 3.02
2358 2447 0.107606 CTCTGCCTGCAGCTTGAGAT 60.108 55.000 14.22 0.00 41.83 2.75
2361 2450 2.172082 TCTGCCTGCAGCTTGAGATAAT 59.828 45.455 14.22 0.00 43.31 1.28
2368 2457 6.623114 GCCTGCAGCTTGAGATAATGATTATG 60.623 42.308 8.66 0.00 38.99 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.404040 TCACTTTGCCGGGAAGGAAT 59.596 50.000 24.53 0.00 45.00 3.01
57 58 0.035439 GATCACTTTGCCGGGAAGGA 60.035 55.000 24.53 15.82 45.00 3.36
61 62 0.327924 ATGTGATCACTTTGCCGGGA 59.672 50.000 25.55 0.00 0.00 5.14
107 108 8.404000 AGAAAGCTGCATCAACATTTATCTTAG 58.596 33.333 1.02 0.00 0.00 2.18
178 182 5.443185 TGCTGCAATATATTCTCCTTTGC 57.557 39.130 0.00 0.00 42.23 3.68
191 195 8.733458 GGTATAAATCAAGATGATGCTGCAATA 58.267 33.333 6.36 0.00 37.15 1.90
201 205 7.095229 GCTAACATGCGGTATAAATCAAGATGA 60.095 37.037 0.00 0.00 0.00 2.92
209 213 5.611374 ACTGAGCTAACATGCGGTATAAAT 58.389 37.500 0.00 0.00 38.13 1.40
276 280 4.142093 GGAGTTGCATCCAATATTTGCTGT 60.142 41.667 10.98 0.00 39.34 4.40
372 376 2.738846 GCTTGCACTCCATATACATCGG 59.261 50.000 0.00 0.00 0.00 4.18
377 381 4.261741 CCCAAATGCTTGCACTCCATATAC 60.262 45.833 0.00 0.00 0.00 1.47
436 440 3.713764 AGCAACACCATTAGCCTCTCTAT 59.286 43.478 0.00 0.00 0.00 1.98
494 499 1.819288 ACATCGTCCCACACACTAGAG 59.181 52.381 0.00 0.00 0.00 2.43
524 529 9.058174 TCGTTTACAATTTGGTGAGAAATAAGA 57.942 29.630 0.78 0.00 0.00 2.10
525 530 9.840427 ATCGTTTACAATTTGGTGAGAAATAAG 57.160 29.630 0.78 0.00 0.00 1.73
606 611 4.766891 ACATGAAATACCCACCTTTGTCAG 59.233 41.667 0.00 0.00 0.00 3.51
607 612 4.735369 ACATGAAATACCCACCTTTGTCA 58.265 39.130 0.00 0.00 0.00 3.58
608 613 5.476945 AGAACATGAAATACCCACCTTTGTC 59.523 40.000 0.00 0.00 0.00 3.18
609 614 5.393866 AGAACATGAAATACCCACCTTTGT 58.606 37.500 0.00 0.00 0.00 2.83
610 615 5.982890 AGAACATGAAATACCCACCTTTG 57.017 39.130 0.00 0.00 0.00 2.77
611 616 7.947890 TCTTTAGAACATGAAATACCCACCTTT 59.052 33.333 0.00 0.00 0.00 3.11
612 617 7.466804 TCTTTAGAACATGAAATACCCACCTT 58.533 34.615 0.00 0.00 0.00 3.50
613 618 7.027874 TCTTTAGAACATGAAATACCCACCT 57.972 36.000 0.00 0.00 0.00 4.00
614 619 7.696992 TTCTTTAGAACATGAAATACCCACC 57.303 36.000 0.00 0.00 0.00 4.61
615 620 9.626045 CTTTTCTTTAGAACATGAAATACCCAC 57.374 33.333 0.00 0.00 33.13 4.61
616 621 8.802267 CCTTTTCTTTAGAACATGAAATACCCA 58.198 33.333 0.00 0.00 33.13 4.51
617 622 8.803235 ACCTTTTCTTTAGAACATGAAATACCC 58.197 33.333 0.00 0.00 33.13 3.69
618 623 9.626045 CACCTTTTCTTTAGAACATGAAATACC 57.374 33.333 0.00 0.00 33.13 2.73
619 624 9.626045 CCACCTTTTCTTTAGAACATGAAATAC 57.374 33.333 0.00 0.00 33.13 1.89
620 625 8.802267 CCCACCTTTTCTTTAGAACATGAAATA 58.198 33.333 0.00 0.00 33.13 1.40
621 626 7.290014 ACCCACCTTTTCTTTAGAACATGAAAT 59.710 33.333 0.00 0.00 33.13 2.17
622 627 6.609616 ACCCACCTTTTCTTTAGAACATGAAA 59.390 34.615 0.00 0.00 33.13 2.69
623 628 6.133356 ACCCACCTTTTCTTTAGAACATGAA 58.867 36.000 0.00 0.00 33.13 2.57
624 629 5.701224 ACCCACCTTTTCTTTAGAACATGA 58.299 37.500 0.00 0.00 33.13 3.07
625 630 7.703058 ATACCCACCTTTTCTTTAGAACATG 57.297 36.000 0.00 0.00 33.13 3.21
626 631 8.721133 AAATACCCACCTTTTCTTTAGAACAT 57.279 30.769 0.00 0.00 33.13 2.71
627 632 7.780745 TGAAATACCCACCTTTTCTTTAGAACA 59.219 33.333 0.00 0.00 33.13 3.18
628 633 8.173542 TGAAATACCCACCTTTTCTTTAGAAC 57.826 34.615 0.00 0.00 33.13 3.01
629 634 7.039993 GCTGAAATACCCACCTTTTCTTTAGAA 60.040 37.037 0.00 0.00 32.02 2.10
630 635 6.433093 GCTGAAATACCCACCTTTTCTTTAGA 59.567 38.462 0.00 0.00 32.02 2.10
631 636 6.350194 GGCTGAAATACCCACCTTTTCTTTAG 60.350 42.308 0.00 0.00 32.02 1.85
632 637 5.479027 GGCTGAAATACCCACCTTTTCTTTA 59.521 40.000 0.00 0.00 32.02 1.85
633 638 4.283467 GGCTGAAATACCCACCTTTTCTTT 59.717 41.667 0.00 0.00 32.02 2.52
634 639 3.832490 GGCTGAAATACCCACCTTTTCTT 59.168 43.478 0.00 0.00 32.02 2.52
635 640 3.181423 TGGCTGAAATACCCACCTTTTCT 60.181 43.478 0.00 0.00 32.02 2.52
636 641 3.161866 TGGCTGAAATACCCACCTTTTC 58.838 45.455 0.00 0.00 0.00 2.29
637 642 3.252554 TGGCTGAAATACCCACCTTTT 57.747 42.857 0.00 0.00 0.00 2.27
978 986 0.549469 TCCTTAAATCCCCGGCCTTC 59.451 55.000 0.00 0.00 0.00 3.46
993 1001 2.635443 CCGCACCGCCATTTTCCTT 61.635 57.895 0.00 0.00 0.00 3.36
1248 1259 3.138798 GAGTACGGGGCGAGCAGA 61.139 66.667 0.00 0.00 0.00 4.26
1270 1281 2.039137 GGAGGAGGAGGAACGGGT 59.961 66.667 0.00 0.00 0.00 5.28
1271 1282 1.758906 GAGGAGGAGGAGGAACGGG 60.759 68.421 0.00 0.00 0.00 5.28
1272 1283 1.758906 GGAGGAGGAGGAGGAACGG 60.759 68.421 0.00 0.00 0.00 4.44
1273 1284 0.753848 GAGGAGGAGGAGGAGGAACG 60.754 65.000 0.00 0.00 0.00 3.95
1274 1285 0.397957 GGAGGAGGAGGAGGAGGAAC 60.398 65.000 0.00 0.00 0.00 3.62
1275 1286 0.556380 AGGAGGAGGAGGAGGAGGAA 60.556 60.000 0.00 0.00 0.00 3.36
1276 1287 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1277 1288 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1278 1289 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1279 1290 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1280 1291 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
1281 1292 0.933700 AAGAGGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
1285 1296 2.222271 AGATGAAGAGGAGGAGGAGGA 58.778 52.381 0.00 0.00 0.00 3.71
1343 1372 1.601419 GATGTCGTCCCCGTCCTCAA 61.601 60.000 0.00 0.00 35.01 3.02
1358 1387 1.323271 ATCGACGTGAGGGCTGATGT 61.323 55.000 0.00 0.00 0.00 3.06
1412 1441 2.615447 GCGATGAGAAATCAGGCATGAA 59.385 45.455 4.62 0.00 39.39 2.57
1425 1454 6.582672 CGAAGCTAATTTACTATGCGATGAGA 59.417 38.462 0.00 0.00 0.00 3.27
1428 1457 6.690704 TCGAAGCTAATTTACTATGCGATG 57.309 37.500 0.00 0.00 0.00 3.84
1449 1484 5.396362 CACAAGTTCACAACAAAGCTATTCG 59.604 40.000 0.00 0.00 0.00 3.34
1466 1501 3.660501 TCGACACTAGCATCACAAGTT 57.339 42.857 0.00 0.00 0.00 2.66
1467 1502 3.660501 TTCGACACTAGCATCACAAGT 57.339 42.857 0.00 0.00 0.00 3.16
1469 1504 3.684305 CCATTTCGACACTAGCATCACAA 59.316 43.478 0.00 0.00 0.00 3.33
1473 1508 4.154195 ACAAACCATTTCGACACTAGCATC 59.846 41.667 0.00 0.00 0.00 3.91
1477 1512 3.249799 TGCACAAACCATTTCGACACTAG 59.750 43.478 0.00 0.00 0.00 2.57
1478 1513 3.206964 TGCACAAACCATTTCGACACTA 58.793 40.909 0.00 0.00 0.00 2.74
1479 1514 2.020720 TGCACAAACCATTTCGACACT 58.979 42.857 0.00 0.00 0.00 3.55
1480 1515 2.223479 ACTGCACAAACCATTTCGACAC 60.223 45.455 0.00 0.00 0.00 3.67
1481 1516 2.020720 ACTGCACAAACCATTTCGACA 58.979 42.857 0.00 0.00 0.00 4.35
1482 1517 2.223479 ACACTGCACAAACCATTTCGAC 60.223 45.455 0.00 0.00 0.00 4.20
1483 1518 2.020720 ACACTGCACAAACCATTTCGA 58.979 42.857 0.00 0.00 0.00 3.71
1484 1519 2.118683 CACACTGCACAAACCATTTCG 58.881 47.619 0.00 0.00 0.00 3.46
1503 1538 7.987458 GGAGGTACAGATTATTCAGAATTCACA 59.013 37.037 8.44 0.00 0.00 3.58
1565 1600 2.607499 TCGGGTTTGGGTAGTAGTCAA 58.393 47.619 0.00 0.00 0.00 3.18
1601 1636 1.257750 GGTTGAATTCCAGTGGGGGC 61.258 60.000 9.92 0.00 37.22 5.80
1677 1718 6.580416 GGATTGAGCTTTTTCTTTCTTTCGAG 59.420 38.462 0.00 0.00 0.00 4.04
1694 1740 5.931146 CCAGAACTGATACATAGGATTGAGC 59.069 44.000 3.19 0.00 0.00 4.26
1756 1805 3.304293 GCGCCTTGCAACATCTAAAATTC 59.696 43.478 0.00 0.00 45.45 2.17
1774 1823 4.218852 ACTTCCTCAAGATATACTAGCGCC 59.781 45.833 2.29 0.00 33.34 6.53
1812 1861 5.039920 ACATCAGCAGAATTACAGGCATA 57.960 39.130 0.00 0.00 0.00 3.14
1820 1869 8.969260 ATATCAGACAAACATCAGCAGAATTA 57.031 30.769 0.00 0.00 0.00 1.40
1838 1887 5.460091 CAGCTCAACGATTTCGAATATCAGA 59.540 40.000 7.01 3.63 43.02 3.27
1846 1895 1.070821 CTGCAGCTCAACGATTTCGA 58.929 50.000 0.00 0.00 43.02 3.71
1847 1896 0.792640 ACTGCAGCTCAACGATTTCG 59.207 50.000 15.27 0.00 46.33 3.46
1860 1909 4.983538 TGAAAATGCACAATAACACTGCAG 59.016 37.500 13.48 13.48 43.88 4.41
1863 1912 7.410800 ACAATGAAAATGCACAATAACACTG 57.589 32.000 0.00 0.00 0.00 3.66
1864 1913 8.436046 AAACAATGAAAATGCACAATAACACT 57.564 26.923 0.00 0.00 0.00 3.55
1920 1969 3.038417 GCAACTCAGTGACGCGCT 61.038 61.111 5.73 0.00 0.00 5.92
1940 1990 2.846193 TGTAGACTGACAAAACCAGGC 58.154 47.619 0.00 0.00 39.93 4.85
1945 1995 7.426929 ACTTGATCATGTAGACTGACAAAAC 57.573 36.000 12.27 0.00 31.83 2.43
1949 1999 7.196331 CGATAACTTGATCATGTAGACTGACA 58.804 38.462 14.07 0.00 0.00 3.58
2115 2169 9.467258 CTTCTCTCAAGAATCAATAGTCTCATC 57.533 37.037 0.00 0.00 40.68 2.92
2204 2274 0.947244 CTTTTGACCGAGCTGCAGTT 59.053 50.000 16.64 9.79 0.00 3.16
2205 2275 0.106708 TCTTTTGACCGAGCTGCAGT 59.893 50.000 16.64 1.59 0.00 4.40
2223 2294 7.201496 GGAATTCAGAATGTGCAATGAAATGTC 60.201 37.037 7.93 0.00 35.47 3.06
2225 2296 6.816640 AGGAATTCAGAATGTGCAATGAAATG 59.183 34.615 7.93 0.00 35.47 2.32
2226 2297 6.816640 CAGGAATTCAGAATGTGCAATGAAAT 59.183 34.615 7.93 0.00 35.47 2.17
2227 2298 6.015265 TCAGGAATTCAGAATGTGCAATGAAA 60.015 34.615 7.93 0.00 35.47 2.69
2230 2301 5.319140 TCAGGAATTCAGAATGTGCAATG 57.681 39.130 7.93 0.00 37.40 2.82
2231 2302 5.421056 ACATCAGGAATTCAGAATGTGCAAT 59.579 36.000 7.93 0.00 37.40 3.56
2237 2323 8.272545 TCTGTTTACATCAGGAATTCAGAATG 57.727 34.615 7.93 9.27 34.15 2.67
2240 2326 8.690203 TTTTCTGTTTACATCAGGAATTCAGA 57.310 30.769 7.93 5.05 31.55 3.27
2248 2334 6.526674 GGCGTTAATTTTCTGTTTACATCAGG 59.473 38.462 0.00 0.00 34.15 3.86
2266 2352 3.372822 GTCTTCAATTCCATCGGCGTTAA 59.627 43.478 6.85 0.00 0.00 2.01
2270 2356 1.656652 AGTCTTCAATTCCATCGGCG 58.343 50.000 0.00 0.00 0.00 6.46
2274 2360 5.877012 TGTCAAGCTAGTCTTCAATTCCATC 59.123 40.000 0.00 0.00 31.27 3.51
2275 2361 5.809001 TGTCAAGCTAGTCTTCAATTCCAT 58.191 37.500 0.00 0.00 31.27 3.41
2276 2362 5.227569 TGTCAAGCTAGTCTTCAATTCCA 57.772 39.130 0.00 0.00 31.27 3.53
2282 2368 8.260114 TGAATATCATTGTCAAGCTAGTCTTCA 58.740 33.333 0.00 0.00 31.27 3.02
2283 2369 8.654230 TGAATATCATTGTCAAGCTAGTCTTC 57.346 34.615 0.00 0.00 31.27 2.87
2291 2377 6.198403 CAGCATGTTGAATATCATTGTCAAGC 59.802 38.462 2.97 0.00 32.15 4.01
2310 2396 3.068590 AGTCAAAACCTCAAACCAGCATG 59.931 43.478 0.00 0.00 0.00 4.06
2320 2406 5.611374 CAGAGTTTAGGAGTCAAAACCTCA 58.389 41.667 13.72 0.00 36.46 3.86
2321 2407 4.452795 GCAGAGTTTAGGAGTCAAAACCTC 59.547 45.833 13.72 11.26 36.46 3.85
2328 2414 1.276421 GCAGGCAGAGTTTAGGAGTCA 59.724 52.381 0.00 0.00 0.00 3.41
2338 2424 1.003597 CTCAAGCTGCAGGCAGAGT 60.004 57.895 24.46 8.03 46.30 3.24
2346 2432 6.653740 CCTCATAATCATTATCTCAAGCTGCA 59.346 38.462 1.02 0.00 0.00 4.41
2348 2434 7.876582 TGTCCTCATAATCATTATCTCAAGCTG 59.123 37.037 0.00 0.00 0.00 4.24
2349 2435 7.971201 TGTCCTCATAATCATTATCTCAAGCT 58.029 34.615 0.00 0.00 0.00 3.74
2350 2436 8.613060 TTGTCCTCATAATCATTATCTCAAGC 57.387 34.615 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.