Multiple sequence alignment - TraesCS6A01G127900

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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 TraesCS6A01G127900 chr6A 100.000 2111 0 0 1 2111 100671309 100673419 0.000000e+00 3899
1 TraesCS6A01G127900 chr6A 79.390 1213 139 66 38 1161 100643796 100642606 0.000000e+00 752
2 TraesCS6A01G127900 chr6A 89.665 358 22 11 923 1279 100648206 100647863 1.920000e-120 442
3 TraesCS6A01G127900 chr6A 86.024 415 46 10 923 1331 100588445 100588037 3.220000e-118 435
4 TraesCS6A01G127900 chr6A 81.638 354 36 19 873 1204 100373345 100372999 1.240000e-67 267
5 TraesCS6A01G127900 chr6A 82.530 166 15 4 868 1019 63106269 63106434 1.310000e-27 134
6 TraesCS6A01G127900 chr3A 96.464 707 24 1 1405 2111 647791650 647790945 0.000000e+00 1166
7 TraesCS6A01G127900 chr1A 93.927 708 40 3 1405 2111 17871828 17872533 0.000000e+00 1066
8 TraesCS6A01G127900 chr5B 93.362 708 45 2 1405 2111 660154404 660155110 0.000000e+00 1046
9 TraesCS6A01G127900 chr5B 93.079 708 47 2 1405 2111 583610753 583611459 0.000000e+00 1035
10 TraesCS6A01G127900 chr6B 92.938 708 48 2 1405 2111 132652578 132653284 0.000000e+00 1029
11 TraesCS6A01G127900 chr6B 87.608 581 35 15 760 1333 159177977 159178527 6.350000e-180 640
12 TraesCS6A01G127900 chr6B 81.416 791 69 28 30 771 159177201 159177962 1.820000e-160 575
13 TraesCS6A01G127900 chr6B 85.833 480 48 8 872 1334 159059651 159059175 1.880000e-135 492
14 TraesCS6A01G127900 chr6B 79.718 355 42 22 872 1204 158196269 158195923 1.630000e-56 230
15 TraesCS6A01G127900 chr7B 92.797 708 49 2 1405 2111 580155056 580154350 0.000000e+00 1024
16 TraesCS6A01G127900 chr7B 88.333 480 39 9 873 1337 453125469 453124992 5.090000e-156 560
17 TraesCS6A01G127900 chr4A 92.525 709 50 3 1404 2111 673183147 673183853 0.000000e+00 1013
18 TraesCS6A01G127900 chr7D 91.236 696 59 2 1407 2102 47188910 47189603 0.000000e+00 946
19 TraesCS6A01G127900 chr7D 91.707 410 29 4 929 1337 436493815 436493410 3.930000e-157 564
20 TraesCS6A01G127900 chr6D 90.523 707 66 1 1405 2111 281870151 281869446 0.000000e+00 933
21 TraesCS6A01G127900 chr6D 88.203 551 40 11 795 1327 83443380 83443923 2.950000e-178 634
22 TraesCS6A01G127900 chr6D 86.183 427 28 15 868 1279 83429694 83430104 1.160000e-117 433
23 TraesCS6A01G127900 chr6D 85.437 412 50 8 923 1328 83257309 83256902 9.010000e-114 420
24 TraesCS6A01G127900 chr6D 79.782 643 64 24 1 591 83442311 83442939 7.010000e-110 407
25 TraesCS6A01G127900 chr6D 87.387 111 10 3 605 714 83276300 83276193 7.910000e-25 124
26 TraesCS6A01G127900 chr6D 87.368 95 9 1 621 715 83442938 83443029 2.860000e-19 106
27 TraesCS6A01G127900 chr7A 91.885 419 29 3 920 1337 486175782 486176196 3.900000e-162 580


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 TraesCS6A01G127900 chr6A 100671309 100673419 2110 False 3899.000000 3899 100.000000 1 2111 1 chr6A.!!$F2 2110
1 TraesCS6A01G127900 chr6A 100642606 100643796 1190 True 752.000000 752 79.390000 38 1161 1 chr6A.!!$R3 1123
2 TraesCS6A01G127900 chr3A 647790945 647791650 705 True 1166.000000 1166 96.464000 1405 2111 1 chr3A.!!$R1 706
3 TraesCS6A01G127900 chr1A 17871828 17872533 705 False 1066.000000 1066 93.927000 1405 2111 1 chr1A.!!$F1 706
4 TraesCS6A01G127900 chr5B 660154404 660155110 706 False 1046.000000 1046 93.362000 1405 2111 1 chr5B.!!$F2 706
5 TraesCS6A01G127900 chr5B 583610753 583611459 706 False 1035.000000 1035 93.079000 1405 2111 1 chr5B.!!$F1 706
6 TraesCS6A01G127900 chr6B 132652578 132653284 706 False 1029.000000 1029 92.938000 1405 2111 1 chr6B.!!$F1 706
7 TraesCS6A01G127900 chr6B 159177201 159178527 1326 False 607.500000 640 84.512000 30 1333 2 chr6B.!!$F2 1303
8 TraesCS6A01G127900 chr7B 580154350 580155056 706 True 1024.000000 1024 92.797000 1405 2111 1 chr7B.!!$R2 706
9 TraesCS6A01G127900 chr4A 673183147 673183853 706 False 1013.000000 1013 92.525000 1404 2111 1 chr4A.!!$F1 707
10 TraesCS6A01G127900 chr7D 47188910 47189603 693 False 946.000000 946 91.236000 1407 2102 1 chr7D.!!$F1 695
11 TraesCS6A01G127900 chr6D 281869446 281870151 705 True 933.000000 933 90.523000 1405 2111 1 chr6D.!!$R3 706
12 TraesCS6A01G127900 chr6D 83442311 83443923 1612 False 382.333333 634 85.117667 1 1327 3 chr6D.!!$F2 1326

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
99 105 0.163788 CCGCGTCAACACAACATCTC 59.836 55.0 4.92 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2401 0.625849 TTGCCCTCCTTCATCTTCCC 59.374 55.0 0.0 0.0 0.0 3.97 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
27 28 3.762407 TTCCTTGATCTGAACCGAACA 57.238 42.857 0.00 0.00 0.00 3.18
34 35 5.147330 TGATCTGAACCGAACAACTGTAT 57.853 39.130 0.00 0.00 0.00 2.29
45 46 5.523552 CCGAACAACTGTATGCTGATGAATA 59.476 40.000 5.12 0.00 0.00 1.75
54 60 8.213679 ACTGTATGCTGATGAATACCTATGTTT 58.786 33.333 0.00 0.00 34.49 2.83
70 76 8.122472 ACCTATGTTTAACTGGGAAGAAATTG 57.878 34.615 0.00 0.00 0.00 2.32
77 83 2.554032 ACTGGGAAGAAATTGAAGTGCG 59.446 45.455 0.00 0.00 0.00 5.34
99 105 0.163788 CCGCGTCAACACAACATCTC 59.836 55.000 4.92 0.00 0.00 2.75
142 148 1.508088 CCCGCAGAAATGCAACTCC 59.492 57.895 0.00 0.00 34.41 3.85
182 204 5.281693 TGTTCATTGTATTGAGACAAGCG 57.718 39.130 0.00 0.00 42.38 4.68
249 271 3.706698 CAAGTTCTCAGTTCTCACACGA 58.293 45.455 0.00 0.00 0.00 4.35
254 276 2.159558 TCTCAGTTCTCACACGATACGC 60.160 50.000 0.00 0.00 0.00 4.42
291 331 1.322442 AACTGCACTTCTTCTTGCCC 58.678 50.000 0.00 0.00 38.00 5.36
298 368 2.038295 CACTTCTTCTTGCCCTCAGACT 59.962 50.000 0.00 0.00 0.00 3.24
299 369 2.301583 ACTTCTTCTTGCCCTCAGACTC 59.698 50.000 0.00 0.00 0.00 3.36
314 384 1.967066 AGACTCTTGACACAGTGGAGG 59.033 52.381 5.31 0.00 0.00 4.30
318 388 0.758734 CTTGACACAGTGGAGGTCCA 59.241 55.000 5.31 0.00 45.30 4.02
330 400 3.761897 TGGAGGTCCACACAAAATAAGG 58.238 45.455 0.00 0.00 42.01 2.69
334 404 5.318630 GAGGTCCACACAAAATAAGGGTAA 58.681 41.667 0.00 0.00 0.00 2.85
335 405 5.899278 AGGTCCACACAAAATAAGGGTAAT 58.101 37.500 0.00 0.00 0.00 1.89
336 406 7.034967 AGGTCCACACAAAATAAGGGTAATA 57.965 36.000 0.00 0.00 0.00 0.98
339 409 7.558444 GGTCCACACAAAATAAGGGTAATATGA 59.442 37.037 0.00 0.00 0.00 2.15
340 410 8.403236 GTCCACACAAAATAAGGGTAATATGAC 58.597 37.037 0.00 0.00 0.00 3.06
341 411 7.281324 TCCACACAAAATAAGGGTAATATGACG 59.719 37.037 0.00 0.00 0.00 4.35
342 412 7.414436 CACACAAAATAAGGGTAATATGACGG 58.586 38.462 0.00 0.00 0.00 4.79
343 413 6.038936 ACACAAAATAAGGGTAATATGACGGC 59.961 38.462 0.00 0.00 0.00 5.68
344 414 5.533528 ACAAAATAAGGGTAATATGACGGCC 59.466 40.000 0.00 0.00 0.00 6.13
346 416 6.691255 AAATAAGGGTAATATGACGGCCTA 57.309 37.500 0.00 0.00 0.00 3.93
347 417 6.691255 AATAAGGGTAATATGACGGCCTAA 57.309 37.500 0.00 0.00 0.00 2.69
348 418 4.618920 AAGGGTAATATGACGGCCTAAG 57.381 45.455 0.00 0.00 0.00 2.18
349 419 3.584294 AGGGTAATATGACGGCCTAAGT 58.416 45.455 0.00 0.00 0.00 2.24
350 420 4.744237 AGGGTAATATGACGGCCTAAGTA 58.256 43.478 0.00 0.00 0.00 2.24
351 421 5.339477 AGGGTAATATGACGGCCTAAGTAT 58.661 41.667 0.00 0.00 0.00 2.12
353 423 6.955851 AGGGTAATATGACGGCCTAAGTATTA 59.044 38.462 0.00 2.58 0.00 0.98
354 424 7.622479 AGGGTAATATGACGGCCTAAGTATTAT 59.378 37.037 0.00 0.00 0.00 1.28
355 425 7.709613 GGGTAATATGACGGCCTAAGTATTATG 59.290 40.741 0.00 0.00 0.00 1.90
356 426 8.255905 GGTAATATGACGGCCTAAGTATTATGT 58.744 37.037 0.00 0.00 0.00 2.29
361 431 4.377897 ACGGCCTAAGTATTATGTTGCTC 58.622 43.478 0.00 0.00 0.00 4.26
409 483 7.147776 ACGGCCTAAGTATTATGTTCAAGTACT 60.148 37.037 0.00 0.00 0.00 2.73
410 484 7.709613 CGGCCTAAGTATTATGTTCAAGTACTT 59.290 37.037 1.12 1.12 38.64 2.24
442 516 2.876091 CGGTTCGCTATCTCAGAAACA 58.124 47.619 0.00 0.00 31.53 2.83
444 518 3.865745 CGGTTCGCTATCTCAGAAACAAT 59.134 43.478 0.00 0.00 31.53 2.71
445 519 4.026475 CGGTTCGCTATCTCAGAAACAATC 60.026 45.833 0.00 0.00 31.53 2.67
446 520 4.870426 GGTTCGCTATCTCAGAAACAATCA 59.130 41.667 0.00 0.00 32.29 2.57
448 522 6.244275 GTTCGCTATCTCAGAAACAATCAAC 58.756 40.000 0.00 0.00 0.00 3.18
449 523 5.478407 TCGCTATCTCAGAAACAATCAACA 58.522 37.500 0.00 0.00 0.00 3.33
450 524 5.931724 TCGCTATCTCAGAAACAATCAACAA 59.068 36.000 0.00 0.00 0.00 2.83
520 596 5.537300 TCAGTAAGAACTTCAGAACAGCT 57.463 39.130 0.00 0.00 31.97 4.24
563 639 5.697826 CAAGAGCTTCTGATTTCCTTTGTC 58.302 41.667 0.00 0.00 0.00 3.18
577 653 4.440839 CCTTTGTCTTAAGGAACCATGC 57.559 45.455 1.85 0.00 46.28 4.06
599 675 8.729756 CATGCCATATCATTACGATTAGGAAAA 58.270 33.333 0.00 0.00 35.39 2.29
600 676 8.862325 TGCCATATCATTACGATTAGGAAAAT 57.138 30.769 0.00 0.00 35.39 1.82
603 679 8.677300 CCATATCATTACGATTAGGAAAATGGG 58.323 37.037 0.00 0.00 35.39 4.00
604 680 8.677300 CATATCATTACGATTAGGAAAATGGGG 58.323 37.037 0.00 0.00 35.39 4.96
605 681 5.381757 TCATTACGATTAGGAAAATGGGGG 58.618 41.667 0.00 0.00 0.00 5.40
606 682 4.866327 TTACGATTAGGAAAATGGGGGT 57.134 40.909 0.00 0.00 0.00 4.95
611 702 1.225403 TAGGAAAATGGGGGTGGGGG 61.225 60.000 0.00 0.00 0.00 5.40
622 713 2.599597 GTGGGGGATGCAGCTGAT 59.400 61.111 20.43 8.20 0.00 2.90
626 717 2.203451 GGGATGCAGCTGATGGGG 60.203 66.667 20.43 0.00 0.00 4.96
630 721 1.992519 GATGCAGCTGATGGGGTCCT 61.993 60.000 20.43 0.00 0.00 3.85
645 736 2.419713 GGGTCCTAGAAGGTTTAAGGCG 60.420 54.545 0.00 0.00 36.53 5.52
646 737 2.419713 GGTCCTAGAAGGTTTAAGGCGG 60.420 54.545 0.00 0.00 36.53 6.13
652 743 1.002773 GAAGGTTTAAGGCGGGACAGA 59.997 52.381 0.00 0.00 0.00 3.41
653 744 1.286248 AGGTTTAAGGCGGGACAGAT 58.714 50.000 0.00 0.00 0.00 2.90
654 745 1.065418 AGGTTTAAGGCGGGACAGATG 60.065 52.381 0.00 0.00 0.00 2.90
721 1099 4.160626 ACTCCTCCACAATACTAACAGCTC 59.839 45.833 0.00 0.00 0.00 4.09
737 1118 3.066064 ACAGCTCGTTATGCACAAACAAA 59.934 39.130 12.74 1.65 0.00 2.83
746 1128 6.494842 GTTATGCACAAACAAAGACTTCAGA 58.505 36.000 8.51 0.00 0.00 3.27
832 1240 7.902387 TTTTAAACCTTGTGTTGGGTAAAAC 57.098 32.000 0.00 0.00 37.23 2.43
840 1248 4.759782 TGTGTTGGGTAAAACAATGGTTG 58.240 39.130 0.00 0.00 41.52 3.77
876 1284 7.244886 AGCCAAAGCAATTAGGACTAAAATT 57.755 32.000 0.00 0.00 43.56 1.82
921 1343 4.980702 CCTGCCTGGCCTGTTGCA 62.981 66.667 17.53 8.87 43.89 4.08
938 1360 2.780924 AACACCTGAGGGCCCCAA 60.781 61.111 21.43 5.88 35.63 4.12
1081 1503 2.116238 AGGCCGAGAAAGGTATGCTTA 58.884 47.619 0.00 0.00 0.00 3.09
1212 1636 1.312371 GCGTTTCCCTGCCATTGCTA 61.312 55.000 0.00 0.00 38.71 3.49
1217 1641 0.978667 TCCCTGCCATTGCTACCGTA 60.979 55.000 0.00 0.00 38.71 4.02
1274 1699 1.980772 GCCTCAACAGCCCAGCAAT 60.981 57.895 0.00 0.00 0.00 3.56
1333 1766 6.120220 GGTAGGGCATAATTAGTTGTCAAGT 58.880 40.000 0.00 0.00 0.00 3.16
1334 1767 7.277396 GGTAGGGCATAATTAGTTGTCAAGTA 58.723 38.462 0.00 0.00 0.00 2.24
1335 1768 7.226128 GGTAGGGCATAATTAGTTGTCAAGTAC 59.774 40.741 0.00 0.00 0.00 2.73
1336 1769 6.958767 AGGGCATAATTAGTTGTCAAGTACT 58.041 36.000 0.00 0.00 0.00 2.73
1337 1770 7.048512 AGGGCATAATTAGTTGTCAAGTACTC 58.951 38.462 0.00 0.00 0.00 2.59
1338 1771 6.260271 GGGCATAATTAGTTGTCAAGTACTCC 59.740 42.308 0.00 0.00 0.00 3.85
1339 1772 6.260271 GGCATAATTAGTTGTCAAGTACTCCC 59.740 42.308 0.00 0.00 0.00 4.30
1340 1773 6.821665 GCATAATTAGTTGTCAAGTACTCCCA 59.178 38.462 0.00 0.00 0.00 4.37
1341 1774 7.011482 GCATAATTAGTTGTCAAGTACTCCCAG 59.989 40.741 0.00 0.00 0.00 4.45
1342 1775 4.884668 TTAGTTGTCAAGTACTCCCAGG 57.115 45.455 0.00 0.00 0.00 4.45
1343 1776 2.972348 AGTTGTCAAGTACTCCCAGGA 58.028 47.619 0.00 0.00 0.00 3.86
1344 1777 2.900546 AGTTGTCAAGTACTCCCAGGAG 59.099 50.000 12.29 12.29 46.91 3.69
1357 1790 5.422214 CTCCCAGGAGTAGTAAACATGTT 57.578 43.478 4.92 4.92 37.47 2.71
1358 1791 5.416271 TCCCAGGAGTAGTAAACATGTTC 57.584 43.478 12.39 0.00 0.00 3.18
1359 1792 5.091552 TCCCAGGAGTAGTAAACATGTTCT 58.908 41.667 12.39 8.27 0.00 3.01
1360 1793 5.187186 TCCCAGGAGTAGTAAACATGTTCTC 59.813 44.000 12.39 12.94 0.00 2.87
1361 1794 5.046591 CCCAGGAGTAGTAAACATGTTCTCA 60.047 44.000 19.91 5.32 0.00 3.27
1362 1795 6.464222 CCAGGAGTAGTAAACATGTTCTCAA 58.536 40.000 19.91 3.82 0.00 3.02
1363 1796 6.934645 CCAGGAGTAGTAAACATGTTCTCAAA 59.065 38.462 19.91 2.64 0.00 2.69
1364 1797 7.444183 CCAGGAGTAGTAAACATGTTCTCAAAA 59.556 37.037 19.91 1.76 0.00 2.44
1365 1798 8.836413 CAGGAGTAGTAAACATGTTCTCAAAAA 58.164 33.333 19.91 0.46 0.00 1.94
1389 1822 7.838771 AAAAGTTGTCAAGTAGTAAACGAGT 57.161 32.000 0.00 0.00 0.00 4.18
1390 1823 7.838771 AAAGTTGTCAAGTAGTAAACGAGTT 57.161 32.000 0.00 0.00 0.00 3.01
1391 1824 8.931385 AAAGTTGTCAAGTAGTAAACGAGTTA 57.069 30.769 0.00 0.00 0.00 2.24
1392 1825 8.931385 AAGTTGTCAAGTAGTAAACGAGTTAA 57.069 30.769 0.00 0.00 0.00 2.01
1393 1826 8.345224 AGTTGTCAAGTAGTAAACGAGTTAAC 57.655 34.615 0.00 0.00 0.00 2.01
1394 1827 7.975616 AGTTGTCAAGTAGTAAACGAGTTAACA 59.024 33.333 8.61 0.00 0.00 2.41
1395 1828 7.919313 TGTCAAGTAGTAAACGAGTTAACAG 57.081 36.000 8.61 3.98 0.00 3.16
1396 1829 7.483307 TGTCAAGTAGTAAACGAGTTAACAGT 58.517 34.615 8.61 4.65 0.00 3.55
1397 1830 7.433131 TGTCAAGTAGTAAACGAGTTAACAGTG 59.567 37.037 8.61 0.00 0.00 3.66
1398 1831 6.919662 TCAAGTAGTAAACGAGTTAACAGTGG 59.080 38.462 8.61 0.00 0.00 4.00
1399 1832 6.396829 AGTAGTAAACGAGTTAACAGTGGT 57.603 37.500 8.61 0.00 0.00 4.16
1400 1833 6.809869 AGTAGTAAACGAGTTAACAGTGGTT 58.190 36.000 8.61 4.47 41.06 3.67
1401 1834 7.940850 AGTAGTAAACGAGTTAACAGTGGTTA 58.059 34.615 8.61 3.50 38.45 2.85
1402 1835 8.413229 AGTAGTAAACGAGTTAACAGTGGTTAA 58.587 33.333 8.61 0.00 44.88 2.01
1505 1941 1.718280 AAACCGGAGTCTCCTCAAGT 58.282 50.000 17.00 6.17 39.64 3.16
1896 2333 6.183360 TGCTACGTTTAAGGCACTATCTGTAT 60.183 38.462 0.00 0.00 38.49 2.29
1921 2358 4.897509 TCTTGACAAGTCCATCATCAGT 57.102 40.909 14.75 0.00 0.00 3.41
1964 2401 3.357021 CAAAATCATTGCATCTCGACGG 58.643 45.455 0.00 0.00 0.00 4.79
2077 2514 5.238583 GGAGTGCCATATAGACCACATAAC 58.761 45.833 0.00 0.00 0.00 1.89
2079 2516 6.210784 GGAGTGCCATATAGACCACATAACTA 59.789 42.308 0.00 0.00 0.00 2.24
2093 2530 6.658816 ACCACATAACTATTGTGATCTTTGCA 59.341 34.615 5.43 0.00 45.83 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.274950 TGTTCGGTTCAGATCAAGGAAAAC 59.725 41.667 0.00 0.00 0.00 2.43
17 18 2.805671 CAGCATACAGTTGTTCGGTTCA 59.194 45.455 0.00 0.00 0.00 3.18
18 19 3.064207 TCAGCATACAGTTGTTCGGTTC 58.936 45.455 0.00 0.00 0.00 3.62
27 28 7.739825 ACATAGGTATTCATCAGCATACAGTT 58.260 34.615 0.00 0.00 0.00 3.16
34 35 7.498900 CCAGTTAAACATAGGTATTCATCAGCA 59.501 37.037 0.00 0.00 0.00 4.41
45 46 7.947890 TCAATTTCTTCCCAGTTAAACATAGGT 59.052 33.333 0.00 0.00 0.00 3.08
54 60 4.215399 CGCACTTCAATTTCTTCCCAGTTA 59.785 41.667 0.00 0.00 0.00 2.24
77 83 1.503818 ATGTTGTGTTGACGCGGACC 61.504 55.000 12.47 0.00 0.00 4.46
99 105 8.943002 GGGTATATTTCTGTTGTAATATTCCGG 58.057 37.037 0.00 0.00 35.86 5.14
170 176 2.042831 GCTGGCCGCTTGTCTCAAT 61.043 57.895 11.61 0.00 35.14 2.57
171 177 2.669569 GCTGGCCGCTTGTCTCAA 60.670 61.111 11.61 0.00 35.14 3.02
172 178 4.704833 GGCTGGCCGCTTGTCTCA 62.705 66.667 17.07 0.00 39.13 3.27
173 179 4.400961 AGGCTGGCCGCTTGTCTC 62.401 66.667 17.07 2.28 41.95 3.36
174 180 4.711949 CAGGCTGGCCGCTTGTCT 62.712 66.667 18.78 5.11 40.53 3.41
182 204 0.733150 GAAACGTAATCAGGCTGGCC 59.267 55.000 15.73 3.00 0.00 5.36
238 260 1.912110 GACAGCGTATCGTGTGAGAAC 59.088 52.381 0.00 0.00 0.00 3.01
239 261 1.135489 GGACAGCGTATCGTGTGAGAA 60.135 52.381 0.00 0.00 0.00 2.87
240 262 0.450583 GGACAGCGTATCGTGTGAGA 59.549 55.000 0.00 0.00 0.00 3.27
241 263 0.170339 TGGACAGCGTATCGTGTGAG 59.830 55.000 0.00 0.00 0.00 3.51
242 264 0.815095 ATGGACAGCGTATCGTGTGA 59.185 50.000 0.00 0.00 0.00 3.58
243 265 0.923403 CATGGACAGCGTATCGTGTG 59.077 55.000 0.00 0.00 0.00 3.82
244 266 0.815095 TCATGGACAGCGTATCGTGT 59.185 50.000 0.00 0.00 0.00 4.49
249 271 5.339008 TTCTAGTTTCATGGACAGCGTAT 57.661 39.130 0.00 0.00 0.00 3.06
254 276 5.239306 TGCAGTTTTCTAGTTTCATGGACAG 59.761 40.000 0.00 0.00 0.00 3.51
291 331 2.625314 TCCACTGTGTCAAGAGTCTGAG 59.375 50.000 7.08 0.00 0.00 3.35
298 368 1.048601 GGACCTCCACTGTGTCAAGA 58.951 55.000 7.08 0.00 35.64 3.02
299 369 0.758734 TGGACCTCCACTGTGTCAAG 59.241 55.000 7.08 1.51 42.01 3.02
314 384 8.403236 GTCATATTACCCTTATTTTGTGTGGAC 58.597 37.037 0.00 0.00 0.00 4.02
318 388 6.038936 GCCGTCATATTACCCTTATTTTGTGT 59.961 38.462 0.00 0.00 0.00 3.72
330 400 8.255905 ACATAATACTTAGGCCGTCATATTACC 58.744 37.037 12.11 0.00 0.00 2.85
334 404 6.594159 GCAACATAATACTTAGGCCGTCATAT 59.406 38.462 0.00 0.00 0.00 1.78
335 405 5.929992 GCAACATAATACTTAGGCCGTCATA 59.070 40.000 0.00 0.00 0.00 2.15
336 406 4.755123 GCAACATAATACTTAGGCCGTCAT 59.245 41.667 0.00 0.00 0.00 3.06
339 409 4.101119 AGAGCAACATAATACTTAGGCCGT 59.899 41.667 0.00 0.00 0.00 5.68
340 410 4.632153 AGAGCAACATAATACTTAGGCCG 58.368 43.478 0.00 0.00 0.00 6.13
341 411 5.611374 TGAGAGCAACATAATACTTAGGCC 58.389 41.667 0.00 0.00 0.00 5.19
342 412 8.472683 CTATGAGAGCAACATAATACTTAGGC 57.527 38.462 0.00 0.00 31.26 3.93
361 431 5.569441 CGTTCGGTCATATTACTGCTATGAG 59.431 44.000 0.00 0.00 36.53 2.90
380 454 5.045215 TGAACATAATACTTAGGCCGTTCG 58.955 41.667 0.00 0.00 35.43 3.95
409 483 1.298157 CGAACCGCTCATGCCAAGAA 61.298 55.000 0.00 0.00 35.36 2.52
410 484 1.741401 CGAACCGCTCATGCCAAGA 60.741 57.895 0.00 0.00 35.36 3.02
466 542 7.642194 TGAATAGTCGCTTTTGTGTTTAACTTG 59.358 33.333 0.00 0.00 0.00 3.16
478 554 5.527582 ACTGAACACTTGAATAGTCGCTTTT 59.472 36.000 0.00 0.00 33.85 2.27
520 596 2.304470 TGCAGGCAGTGTATACTTTGGA 59.696 45.455 4.17 0.00 34.07 3.53
563 639 6.906157 AATGATATGGCATGGTTCCTTAAG 57.094 37.500 10.98 0.00 0.00 1.85
577 653 8.677300 CCCATTTTCCTAATCGTAATGATATGG 58.323 37.037 0.00 0.00 35.84 2.74
603 679 4.828296 CAGCTGCATCCCCCACCC 62.828 72.222 0.00 0.00 0.00 4.61
604 680 3.065787 ATCAGCTGCATCCCCCACC 62.066 63.158 9.47 0.00 0.00 4.61
605 681 1.826921 CATCAGCTGCATCCCCCAC 60.827 63.158 9.47 0.00 0.00 4.61
606 682 2.599032 CATCAGCTGCATCCCCCA 59.401 61.111 9.47 0.00 0.00 4.96
611 702 1.527844 GGACCCCATCAGCTGCATC 60.528 63.158 9.47 0.00 0.00 3.91
619 710 2.661176 AACCTTCTAGGACCCCATCA 57.339 50.000 0.00 0.00 37.67 3.07
622 713 3.187112 CCTTAAACCTTCTAGGACCCCA 58.813 50.000 0.00 0.00 37.67 4.96
626 717 2.419713 CCCGCCTTAAACCTTCTAGGAC 60.420 54.545 0.00 0.00 37.67 3.85
630 721 2.235402 CTGTCCCGCCTTAAACCTTCTA 59.765 50.000 0.00 0.00 0.00 2.10
645 736 3.703001 TTCTTCTTGACCATCTGTCCC 57.297 47.619 0.00 0.00 43.78 4.46
646 737 6.581171 ATTTTTCTTCTTGACCATCTGTCC 57.419 37.500 0.00 0.00 43.78 4.02
652 743 7.288810 TGTAGCAATTTTTCTTCTTGACCAT 57.711 32.000 0.00 0.00 0.00 3.55
653 744 6.707440 TGTAGCAATTTTTCTTCTTGACCA 57.293 33.333 0.00 0.00 0.00 4.02
654 745 6.524586 CGATGTAGCAATTTTTCTTCTTGACC 59.475 38.462 0.00 0.00 0.00 4.02
721 1099 5.270083 TGAAGTCTTTGTTTGTGCATAACG 58.730 37.500 0.00 0.00 0.00 3.18
737 1118 8.808092 ACTGCTATTTTACTAGTTCTGAAGTCT 58.192 33.333 0.00 0.00 0.00 3.24
832 1240 4.097892 GGCTAACCCTGTAATCAACCATTG 59.902 45.833 0.00 0.00 0.00 2.82
840 1248 3.352648 TGCTTTGGCTAACCCTGTAATC 58.647 45.455 0.00 0.00 39.59 1.75
876 1284 5.661759 ACCCCAACCAATACAAAGTAAACAA 59.338 36.000 0.00 0.00 0.00 2.83
913 1322 1.174712 CCCTCAGGTGTTGCAACAGG 61.175 60.000 31.81 26.12 40.05 4.00
918 1327 4.284550 GGGCCCTCAGGTGTTGCA 62.285 66.667 17.04 0.00 34.57 4.08
921 1343 2.169810 ATTGGGGCCCTCAGGTGTT 61.170 57.895 25.93 0.00 34.57 3.32
938 1360 1.904865 CACCACAGTGGCTTGCCAT 60.905 57.895 20.48 4.37 42.67 4.40
1212 1636 1.339727 GGCCAAGAAGTCCAATACGGT 60.340 52.381 0.00 0.00 35.57 4.83
1217 1641 1.147817 AGTTGGGCCAAGAAGTCCAAT 59.852 47.619 21.62 0.00 40.77 3.16
1274 1699 6.992123 CCATGACTATGAGTTAAGCCACATAA 59.008 38.462 0.00 0.00 36.36 1.90
1335 1768 5.187967 AGAACATGTTTACTACTCCTGGGAG 59.812 44.000 13.36 14.44 46.91 4.30
1336 1769 5.091552 AGAACATGTTTACTACTCCTGGGA 58.908 41.667 13.36 0.00 0.00 4.37
1337 1770 5.046591 TGAGAACATGTTTACTACTCCTGGG 60.047 44.000 13.36 0.00 0.00 4.45
1338 1771 6.037786 TGAGAACATGTTTACTACTCCTGG 57.962 41.667 13.36 0.00 0.00 4.45
1339 1772 7.962964 TTTGAGAACATGTTTACTACTCCTG 57.037 36.000 13.36 0.00 0.00 3.86
1340 1773 8.974060 TTTTTGAGAACATGTTTACTACTCCT 57.026 30.769 13.36 2.03 0.00 3.69
1364 1797 8.260270 ACTCGTTTACTACTTGACAACTTTTT 57.740 30.769 0.00 0.00 0.00 1.94
1365 1798 7.838771 ACTCGTTTACTACTTGACAACTTTT 57.161 32.000 0.00 0.00 0.00 2.27
1366 1799 7.838771 AACTCGTTTACTACTTGACAACTTT 57.161 32.000 0.00 0.00 0.00 2.66
1367 1800 8.811378 GTTAACTCGTTTACTACTTGACAACTT 58.189 33.333 0.00 0.00 0.00 2.66
1368 1801 7.975616 TGTTAACTCGTTTACTACTTGACAACT 59.024 33.333 7.22 0.00 0.00 3.16
1369 1802 8.118893 TGTTAACTCGTTTACTACTTGACAAC 57.881 34.615 7.22 0.00 0.00 3.32
1370 1803 7.975616 ACTGTTAACTCGTTTACTACTTGACAA 59.024 33.333 7.22 0.00 0.00 3.18
1371 1804 7.433131 CACTGTTAACTCGTTTACTACTTGACA 59.567 37.037 7.22 0.00 0.00 3.58
1372 1805 7.096312 CCACTGTTAACTCGTTTACTACTTGAC 60.096 40.741 7.22 0.00 0.00 3.18
1373 1806 6.919662 CCACTGTTAACTCGTTTACTACTTGA 59.080 38.462 7.22 0.00 0.00 3.02
1374 1807 6.698766 ACCACTGTTAACTCGTTTACTACTTG 59.301 38.462 7.22 0.00 0.00 3.16
1375 1808 6.809869 ACCACTGTTAACTCGTTTACTACTT 58.190 36.000 7.22 0.00 0.00 2.24
1376 1809 6.396829 ACCACTGTTAACTCGTTTACTACT 57.603 37.500 7.22 0.00 0.00 2.57
1377 1810 8.574196 TTAACCACTGTTAACTCGTTTACTAC 57.426 34.615 7.22 0.00 40.98 2.73
1378 1811 9.762933 ATTTAACCACTGTTAACTCGTTTACTA 57.237 29.630 7.22 0.00 44.47 1.82
1379 1812 8.667076 ATTTAACCACTGTTAACTCGTTTACT 57.333 30.769 7.22 0.00 44.47 2.24
1380 1813 9.720667 AAATTTAACCACTGTTAACTCGTTTAC 57.279 29.630 7.22 0.00 44.47 2.01
1382 1815 9.642327 AAAAATTTAACCACTGTTAACTCGTTT 57.358 25.926 7.22 0.15 44.47 3.60
1430 1864 8.423349 CCCAAGAATGCCTTCATATGAATAAAA 58.577 33.333 18.26 5.79 33.56 1.52
1505 1941 3.023832 TCTGAATGTGACCGATAGCTGA 58.976 45.455 0.00 0.00 0.00 4.26
1816 2252 4.082523 CTTCGGCGCTCCTGGGAA 62.083 66.667 7.64 1.10 0.00 3.97
1888 2325 8.078060 TGGACTTGTCAAGATCAATACAGATA 57.922 34.615 19.53 0.00 0.00 1.98
1896 2333 5.807909 TGATGATGGACTTGTCAAGATCAA 58.192 37.500 19.53 7.08 0.00 2.57
1964 2401 0.625849 TTGCCCTCCTTCATCTTCCC 59.374 55.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.