Multiple sequence alignment - TraesCS6A01G219900

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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 TraesCS6A01G219900 chr6A 100.000 4066 0 0 1 4066 408045235 408041170 0.000000e+00 7509.0
1 TraesCS6A01G219900 chr6A 85.224 1631 177 31 245 1822 408054825 408053206 0.000000e+00 1618.0
2 TraesCS6A01G219900 chr6A 88.054 745 61 16 1815 2556 408052905 408052186 0.000000e+00 857.0
3 TraesCS6A01G219900 chr6A 93.224 487 28 3 3058 3544 408051564 408051083 0.000000e+00 712.0
4 TraesCS6A01G219900 chr6A 86.875 480 47 7 2550 3020 408052032 408051560 1.410000e-144 523.0
5 TraesCS6A01G219900 chr6A 100.000 30 0 0 4384 4413 408040852 408040823 6.170000e-04 56.5
6 TraesCS6A01G219900 chr6A 100.000 29 0 0 3546 3574 408050920 408050892 2.000000e-03 54.7
7 TraesCS6A01G219900 chr6D 88.636 3916 289 77 185 4063 286633799 286630003 0.000000e+00 4623.0
8 TraesCS6A01G219900 chr6B 93.788 2640 107 23 1429 4059 447117376 447114785 0.000000e+00 3914.0
9 TraesCS6A01G219900 chr6B 91.142 1287 74 11 76 1357 447118627 447117376 0.000000e+00 1709.0
10 TraesCS6A01G219900 chr6B 100.000 33 0 0 128 160 472393035 472393067 1.330000e-05 62.1
11 TraesCS6A01G219900 chrUn 90.226 133 11 2 327 458 86488333 86488202 5.870000e-39 172.0
12 TraesCS6A01G219900 chrUn 90.226 133 11 2 327 458 223701429 223701298 5.870000e-39 172.0
13 TraesCS6A01G219900 chrUn 90.226 133 11 2 327 458 270841715 270841846 5.870000e-39 172.0
14 TraesCS6A01G219900 chrUn 90.226 133 11 2 327 458 447073503 447073372 5.870000e-39 172.0
15 TraesCS6A01G219900 chr1A 90.226 133 11 2 327 458 94529183 94529052 5.870000e-39 172.0
16 TraesCS6A01G219900 chr1A 90.226 133 11 2 327 458 94602315 94602184 5.870000e-39 172.0
17 TraesCS6A01G219900 chr4B 88.372 86 9 1 505 590 547043005 547042921 7.810000e-18 102.0
18 TraesCS6A01G219900 chr4B 77.297 185 24 15 3822 3990 19742315 19742497 4.700000e-15 93.5
19 TraesCS6A01G219900 chr7B 100.000 33 0 0 128 160 631599404 631599372 1.330000e-05 62.1
20 TraesCS6A01G219900 chr2B 100.000 33 0 0 128 160 583847083 583847051 1.330000e-05 62.1
21 TraesCS6A01G219900 chr1B 100.000 32 0 0 128 159 152678206 152678237 4.770000e-05 60.2


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 TraesCS6A01G219900 chr6A 408040823 408045235 4412 True 3782.75 7509 100.0000 1 4413 2 chr6A.!!$R1 4412
1 TraesCS6A01G219900 chr6A 408050892 408054825 3933 True 752.94 1618 90.6754 245 3574 5 chr6A.!!$R2 3329
2 TraesCS6A01G219900 chr6D 286630003 286633799 3796 True 4623.00 4623 88.6360 185 4063 1 chr6D.!!$R1 3878
3 TraesCS6A01G219900 chr6B 447114785 447118627 3842 True 2811.50 3914 92.4650 76 4059 2 chr6B.!!$R1 3983

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
267 269 0.175073 GTGGCCTATCCGAAGACGTT 59.825 55.0 3.32 0.00 37.80 3.99 F
629 651 0.731417 GTCTGGATCAGCATGTGCAC 59.269 55.0 10.75 10.75 45.16 4.57 F
1699 1758 0.323957 GGGAGCCCTAACTTCGTGTT 59.676 55.0 0.00 2.66 42.31 3.32 F
2950 3515 0.176680 ACTCTATGCCCAACTGCTCG 59.823 55.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1434 0.032403 TGTGCGCACGTAAGGTAGTT 59.968 50.000 33.22 0.0 46.39 2.24 R
2539 2934 0.467844 ACATTGCAGCACAGGTTCCA 60.468 50.000 0.00 0.0 0.00 3.53 R
3004 3569 2.158475 ACAACAAGCAATTCTGGAGGGA 60.158 45.455 0.00 0.0 0.00 4.20 R
4388 5126 0.238817 CCCAAAAATCCGCGTCGAAA 59.761 50.000 4.92 0.0 0.00 3.46 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
35 36 5.444122 GCGCTTTGCATATAGAAAAGTAGG 58.556 41.667 0.00 0.00 43.69 3.18
36 37 5.007724 GCGCTTTGCATATAGAAAAGTAGGT 59.992 40.000 0.00 0.00 43.69 3.08
37 38 6.458342 GCGCTTTGCATATAGAAAAGTAGGTT 60.458 38.462 0.00 0.00 43.69 3.50
38 39 7.254658 GCGCTTTGCATATAGAAAAGTAGGTTA 60.255 37.037 0.00 0.00 43.69 2.85
39 40 8.774586 CGCTTTGCATATAGAAAAGTAGGTTAT 58.225 33.333 0.00 0.00 43.69 1.89
70 71 8.555166 AAATGTTTATATAACCGCAATCAACG 57.445 30.769 0.00 0.00 0.00 4.10
81 82 0.387622 CAATCAACGGCCTTGCACAG 60.388 55.000 0.00 0.00 0.00 3.66
101 102 4.396166 ACAGATTAAGCGCAATTAAGCACT 59.604 37.500 11.47 5.50 34.31 4.40
149 151 0.627986 AGAGCCTAGGCATGCCTTTT 59.372 50.000 42.49 25.00 45.70 2.27
232 234 2.127708 GGGACTATGGGAGGATGTGTT 58.872 52.381 0.00 0.00 0.00 3.32
267 269 0.175073 GTGGCCTATCCGAAGACGTT 59.825 55.000 3.32 0.00 37.80 3.99
293 295 6.096673 TGATCACCTAGCGCTATTGATTAA 57.903 37.500 28.86 21.56 0.00 1.40
294 296 5.926542 TGATCACCTAGCGCTATTGATTAAC 59.073 40.000 28.86 21.09 0.00 2.01
295 297 4.295870 TCACCTAGCGCTATTGATTAACG 58.704 43.478 19.19 2.39 0.00 3.18
296 298 4.049186 CACCTAGCGCTATTGATTAACGT 58.951 43.478 19.19 0.58 0.00 3.99
304 309 3.545426 GCTATTGATTAACGTGGGAACGC 60.545 47.826 0.00 0.00 36.44 4.84
306 311 2.102070 TGATTAACGTGGGAACGCAT 57.898 45.000 0.00 0.00 42.37 4.73
309 314 1.579084 TTAACGTGGGAACGCATGCC 61.579 55.000 13.15 0.00 42.37 4.40
313 318 2.672651 TGGGAACGCATGCCACTG 60.673 61.111 13.15 0.00 45.86 3.66
323 328 2.063266 GCATGCCACTGTGAATGTTTG 58.937 47.619 6.36 0.00 0.00 2.93
340 345 4.523083 TGTTTGTGCTAAGGTTTGAGTCT 58.477 39.130 0.00 0.00 0.00 3.24
345 350 2.038557 TGCTAAGGTTTGAGTCTGTCCC 59.961 50.000 0.00 0.00 0.00 4.46
432 443 5.005779 CGAATCCGAATCCTTAGAACAACTG 59.994 44.000 0.00 0.00 38.22 3.16
442 453 5.699458 TCCTTAGAACAACTGGATTTCGTTC 59.301 40.000 0.00 0.00 36.95 3.95
461 477 4.618927 CGTTCATTCACTGCCCATTTTCAT 60.619 41.667 0.00 0.00 0.00 2.57
462 478 5.392919 CGTTCATTCACTGCCCATTTTCATA 60.393 40.000 0.00 0.00 0.00 2.15
463 479 6.576185 GTTCATTCACTGCCCATTTTCATAT 58.424 36.000 0.00 0.00 0.00 1.78
464 480 7.468494 CGTTCATTCACTGCCCATTTTCATATA 60.468 37.037 0.00 0.00 0.00 0.86
626 648 1.376543 GGTGTCTGGATCAGCATGTG 58.623 55.000 0.00 0.00 37.40 3.21
629 651 0.731417 GTCTGGATCAGCATGTGCAC 59.269 55.000 10.75 10.75 45.16 4.57
642 664 4.690748 AGCATGTGCACCGTGTATATATTC 59.309 41.667 15.69 0.00 45.16 1.75
733 756 2.203015 ACAATCGGCCGATTCCCG 60.203 61.111 42.73 33.91 42.30 5.14
744 768 1.431488 CGATTCCCGTCATGCCACAG 61.431 60.000 0.00 0.00 0.00 3.66
765 789 2.426522 CACATCACCCTCGACAACATT 58.573 47.619 0.00 0.00 0.00 2.71
816 840 9.841295 ACGTACCTTTTGGATTATATACAACAT 57.159 29.630 0.00 0.00 44.07 2.71
876 900 3.391506 TGGCTAATCTCATGTCGGATG 57.608 47.619 0.00 0.00 0.00 3.51
880 904 3.611766 GCTAATCTCATGTCGGATGCGTA 60.612 47.826 6.49 0.00 0.00 4.42
1038 1073 4.568380 GGAGGCAATCAGGGCATATTATCA 60.568 45.833 0.00 0.00 35.46 2.15
1040 1075 5.396485 AGGCAATCAGGGCATATTATCAAA 58.604 37.500 0.00 0.00 35.46 2.69
1041 1076 5.840149 AGGCAATCAGGGCATATTATCAAAA 59.160 36.000 0.00 0.00 35.46 2.44
1232 1273 6.563422 TGGCTTGCACAATATGAGAATTTAC 58.437 36.000 0.00 0.00 0.00 2.01
1245 1286 6.808008 TGAGAATTTACCTTTCAAGCAGAG 57.192 37.500 0.00 0.00 0.00 3.35
1319 1360 6.994421 AATTTTCTGCTTCCCCTTTCTTAA 57.006 33.333 0.00 0.00 0.00 1.85
1367 1408 7.279536 TGCGTAGTCGATCTTACCTATATTAGG 59.720 40.741 0.00 0.00 44.87 2.69
1389 1430 5.047377 AGGAAACAATGTGTCGGCATAAAAT 60.047 36.000 0.00 0.00 0.00 1.82
1390 1431 5.288472 GGAAACAATGTGTCGGCATAAAATC 59.712 40.000 0.00 0.00 0.00 2.17
1391 1432 4.014847 ACAATGTGTCGGCATAAAATCG 57.985 40.909 0.00 0.00 0.00 3.34
1392 1433 2.755836 ATGTGTCGGCATAAAATCGC 57.244 45.000 0.00 0.00 0.00 4.58
1393 1434 1.443802 TGTGTCGGCATAAAATCGCA 58.556 45.000 0.00 0.00 0.00 5.10
1395 1436 2.173964 GTGTCGGCATAAAATCGCAAC 58.826 47.619 0.00 0.00 0.00 4.17
1396 1437 2.080693 TGTCGGCATAAAATCGCAACT 58.919 42.857 0.00 0.00 0.00 3.16
1397 1438 3.062909 GTGTCGGCATAAAATCGCAACTA 59.937 43.478 0.00 0.00 0.00 2.24
1398 1439 3.062909 TGTCGGCATAAAATCGCAACTAC 59.937 43.478 0.00 0.00 0.00 2.73
1399 1440 2.610374 TCGGCATAAAATCGCAACTACC 59.390 45.455 0.00 0.00 0.00 3.18
1400 1441 2.612212 CGGCATAAAATCGCAACTACCT 59.388 45.455 0.00 0.00 0.00 3.08
1402 1443 4.271533 CGGCATAAAATCGCAACTACCTTA 59.728 41.667 0.00 0.00 0.00 2.69
1403 1444 5.507974 GGCATAAAATCGCAACTACCTTAC 58.492 41.667 0.00 0.00 0.00 2.34
1404 1445 5.195379 GCATAAAATCGCAACTACCTTACG 58.805 41.667 0.00 0.00 0.00 3.18
1405 1446 5.220529 GCATAAAATCGCAACTACCTTACGT 60.221 40.000 0.00 0.00 0.00 3.57
1406 1447 4.657075 AAAATCGCAACTACCTTACGTG 57.343 40.909 0.00 0.00 0.00 4.49
1407 1448 1.636988 ATCGCAACTACCTTACGTGC 58.363 50.000 0.00 0.00 0.00 5.34
1408 1449 0.730155 TCGCAACTACCTTACGTGCG 60.730 55.000 9.88 9.88 44.29 5.34
1426 1484 1.727213 GCGCACAATCTGAAGAGTTGC 60.727 52.381 0.30 5.45 0.00 4.17
1551 1610 1.687368 GCAGCATGGGGAAGAAAGGAT 60.687 52.381 0.00 0.00 35.86 3.24
1569 1628 6.627087 AAGGATGAAGGAGAGAACATTGTA 57.373 37.500 0.00 0.00 0.00 2.41
1699 1758 0.323957 GGGAGCCCTAACTTCGTGTT 59.676 55.000 0.00 2.66 42.31 3.32
1711 1770 2.095768 ACTTCGTGTTGTGTGCATATGC 60.096 45.455 21.09 21.09 42.50 3.14
1808 1886 1.981256 TGTGCCTTCTTCAACCTTCC 58.019 50.000 0.00 0.00 0.00 3.46
1821 2207 2.678336 CAACCTTCCGCATTCTTAGACC 59.322 50.000 0.00 0.00 0.00 3.85
1822 2208 2.188817 ACCTTCCGCATTCTTAGACCT 58.811 47.619 0.00 0.00 0.00 3.85
1854 2240 2.108362 CTTAAGCGGGGTAGGCGG 59.892 66.667 0.00 0.00 35.00 6.13
1857 2243 1.394266 TTAAGCGGGGTAGGCGGTAG 61.394 60.000 0.00 0.00 35.00 3.18
2075 2469 6.306987 ACCTGACAAGAAGTTTTGTGGATAT 58.693 36.000 7.77 0.00 41.15 1.63
2076 2470 6.207417 ACCTGACAAGAAGTTTTGTGGATATG 59.793 38.462 7.77 0.00 41.15 1.78
2158 2553 2.200081 AGGAACCATACCTCACATGCT 58.800 47.619 0.00 0.00 31.43 3.79
2173 2568 4.067896 CACATGCTATCAATGGGTACTCC 58.932 47.826 0.00 0.00 0.00 3.85
2222 2617 4.307432 GCTCTGTTAGTACAAGAGTTGCA 58.693 43.478 13.22 0.00 34.64 4.08
2255 2650 8.919777 ATAGCGGCTATTTTAGAAACCTATTT 57.080 30.769 16.57 0.00 0.00 1.40
2257 2652 8.379457 AGCGGCTATTTTAGAAACCTATTTAG 57.621 34.615 0.00 0.00 0.00 1.85
2272 2667 7.238486 ACCTATTTAGCACTCAGATATGGAG 57.762 40.000 0.00 0.52 38.36 3.86
2420 2815 9.271828 TGATATCTTAATCTCTTTTTGCGCATA 57.728 29.630 12.75 2.60 0.00 3.14
2539 2934 6.938507 TGGATGGTACGTGTAGTTTCTTTAT 58.061 36.000 0.00 0.00 0.00 1.40
2556 2951 2.512692 TATGGAACCTGTGCTGCAAT 57.487 45.000 2.77 0.00 0.00 3.56
2631 3194 6.348786 CCATGTGAACTGGAGATTTTGTGTAG 60.349 42.308 0.00 0.00 35.70 2.74
2782 3346 7.182749 TCCTATCCTATTATTAGTTGCAGGCAT 59.817 37.037 0.00 0.00 0.00 4.40
2822 3386 8.307483 GGCTCTATCTGTCTATGCATTAAACTA 58.693 37.037 3.54 0.00 0.00 2.24
2823 3387 9.868277 GCTCTATCTGTCTATGCATTAAACTAT 57.132 33.333 3.54 2.72 0.00 2.12
2871 3436 2.023501 AGATGAACTGGGTAGCTCCTCT 60.024 50.000 0.00 0.00 36.25 3.69
2940 3505 4.689612 TTCATGTTCCCTACTCTATGCC 57.310 45.455 0.00 0.00 0.00 4.40
2950 3515 0.176680 ACTCTATGCCCAACTGCTCG 59.823 55.000 0.00 0.00 0.00 5.03
2955 3520 1.903877 ATGCCCAACTGCTCGCTACT 61.904 55.000 0.00 0.00 0.00 2.57
2959 3524 2.271800 CCCAACTGCTCGCTACTAAAG 58.728 52.381 0.00 0.00 0.00 1.85
2969 3534 5.163447 TGCTCGCTACTAAAGTGATGGTTAT 60.163 40.000 0.00 0.00 43.67 1.89
3065 3630 4.657075 ATTCGTTAACTGTTTGCTACCG 57.343 40.909 3.71 0.00 0.00 4.02
3422 3989 3.307059 GGCTCAAAGATAGTGACTGGTGT 60.307 47.826 0.00 0.00 0.00 4.16
3445 4012 3.880490 GTGGTGTTTGGTTCAGTATGTCA 59.120 43.478 0.00 0.00 37.40 3.58
3491 4058 1.274167 TGTGTCCGATTAGTCCACCAC 59.726 52.381 0.00 0.00 0.00 4.16
3607 4335 8.654997 GGCACCCTATATATATGAGATGAACAT 58.345 37.037 5.44 0.00 0.00 2.71
3656 4384 1.531149 CGTCAACGAATGCTTCAGGTT 59.469 47.619 0.00 0.00 43.02 3.50
3759 4487 0.828762 TCAAAGTCGTTCCCCCTCGA 60.829 55.000 0.00 0.00 0.00 4.04
3786 4514 2.229792 TGAACCTGTTGATCCTTGCAC 58.770 47.619 0.00 0.00 0.00 4.57
3812 4540 6.661805 TCCAATTGAAAAATACTGTACTCCCC 59.338 38.462 7.12 0.00 0.00 4.81
3826 4554 5.444176 TGTACTCCCCCGTTTTTAAAAAGA 58.556 37.500 13.58 6.52 0.00 2.52
3827 4555 5.890419 TGTACTCCCCCGTTTTTAAAAAGAA 59.110 36.000 13.58 0.00 0.00 2.52
3828 4556 5.524971 ACTCCCCCGTTTTTAAAAAGAAG 57.475 39.130 13.58 8.32 0.00 2.85
4064 4802 6.901081 AAAATTGTAGACCTTTTCTGAGGG 57.099 37.500 0.00 0.00 41.31 4.30
4065 4803 5.843019 AATTGTAGACCTTTTCTGAGGGA 57.157 39.130 0.00 0.00 41.31 4.20
4405 5143 4.623122 AAAATTTCGACGCGGATTTTTG 57.377 36.364 12.47 0.00 33.25 2.44
4406 5144 2.256445 ATTTCGACGCGGATTTTTGG 57.744 45.000 12.47 0.00 0.00 3.28
4407 5145 0.238817 TTTCGACGCGGATTTTTGGG 59.761 50.000 12.47 0.00 0.00 4.12
4408 5146 0.603172 TTCGACGCGGATTTTTGGGA 60.603 50.000 12.47 0.00 0.00 4.37
4409 5147 1.133869 CGACGCGGATTTTTGGGAC 59.866 57.895 12.47 0.00 0.00 4.46
4410 5148 1.570347 CGACGCGGATTTTTGGGACA 61.570 55.000 12.47 0.00 0.00 4.02
4411 5149 0.808755 GACGCGGATTTTTGGGACAT 59.191 50.000 12.47 0.00 39.30 3.06
4412 5150 0.525761 ACGCGGATTTTTGGGACATG 59.474 50.000 12.47 0.00 39.30 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.912949 TTTCTATATGCAAAGCGCTTAATTG 57.087 32.000 25.33 19.17 43.06 2.32
6 7 8.190784 ACTTTTCTATATGCAAAGCGCTTAATT 58.809 29.630 25.33 4.74 43.06 1.40
7 8 7.707104 ACTTTTCTATATGCAAAGCGCTTAAT 58.293 30.769 25.33 18.90 43.06 1.40
8 9 7.083875 ACTTTTCTATATGCAAAGCGCTTAA 57.916 32.000 25.33 12.84 43.06 1.85
9 10 6.677781 ACTTTTCTATATGCAAAGCGCTTA 57.322 33.333 25.33 8.57 43.06 3.09
10 11 5.567138 ACTTTTCTATATGCAAAGCGCTT 57.433 34.783 18.98 18.98 43.06 4.68
11 12 5.237344 CCTACTTTTCTATATGCAAAGCGCT 59.763 40.000 2.64 2.64 43.06 5.92
12 13 5.007724 ACCTACTTTTCTATATGCAAAGCGC 59.992 40.000 0.00 0.00 42.89 5.92
13 14 6.604735 ACCTACTTTTCTATATGCAAAGCG 57.395 37.500 0.00 0.00 33.26 4.68
44 45 9.015577 CGTTGATTGCGGTTATATAAACATTTT 57.984 29.630 11.03 0.00 0.00 1.82
45 46 7.646130 CCGTTGATTGCGGTTATATAAACATTT 59.354 33.333 11.03 0.00 43.84 2.32
46 47 7.136119 CCGTTGATTGCGGTTATATAAACATT 58.864 34.615 11.03 1.16 43.84 2.71
47 48 6.664515 CCGTTGATTGCGGTTATATAAACAT 58.335 36.000 11.03 0.00 43.84 2.71
48 49 6.050454 CCGTTGATTGCGGTTATATAAACA 57.950 37.500 11.03 1.33 43.84 2.83
60 61 2.504681 GCAAGGCCGTTGATTGCG 60.505 61.111 16.28 0.00 39.84 4.85
62 63 0.387622 CTGTGCAAGGCCGTTGATTG 60.388 55.000 16.28 8.00 38.60 2.67
63 64 0.537143 TCTGTGCAAGGCCGTTGATT 60.537 50.000 16.28 0.00 38.60 2.57
64 65 0.322816 ATCTGTGCAAGGCCGTTGAT 60.323 50.000 16.28 4.42 38.60 2.57
65 66 0.537143 AATCTGTGCAAGGCCGTTGA 60.537 50.000 16.28 2.43 38.60 3.18
66 67 1.164411 TAATCTGTGCAAGGCCGTTG 58.836 50.000 0.00 3.67 39.41 4.10
67 68 1.812571 CTTAATCTGTGCAAGGCCGTT 59.187 47.619 0.00 0.00 0.00 4.44
68 69 1.453155 CTTAATCTGTGCAAGGCCGT 58.547 50.000 0.00 0.00 0.00 5.68
69 70 0.099436 GCTTAATCTGTGCAAGGCCG 59.901 55.000 0.00 0.00 0.00 6.13
70 71 0.099436 CGCTTAATCTGTGCAAGGCC 59.901 55.000 0.00 0.00 0.00 5.19
71 72 0.524180 GCGCTTAATCTGTGCAAGGC 60.524 55.000 0.00 0.00 40.28 4.35
72 73 0.804364 TGCGCTTAATCTGTGCAAGG 59.196 50.000 9.73 0.00 46.07 3.61
101 102 3.680458 GGTTTTGGTCAGAAAAACGCAAA 59.320 39.130 5.88 0.00 44.69 3.68
107 108 2.502130 GGGTGGGTTTTGGTCAGAAAAA 59.498 45.455 0.00 0.00 0.00 1.94
267 269 3.573967 TCAATAGCGCTAGGTGATCATCA 59.426 43.478 23.37 3.79 0.00 3.07
296 298 2.672651 CAGTGGCATGCGTTCCCA 60.673 61.111 12.44 0.00 0.00 4.37
304 309 3.054166 CACAAACATTCACAGTGGCATG 58.946 45.455 0.00 6.42 0.00 4.06
306 311 1.202394 GCACAAACATTCACAGTGGCA 60.202 47.619 0.00 0.00 0.00 4.92
309 314 4.036734 ACCTTAGCACAAACATTCACAGTG 59.963 41.667 0.00 0.00 0.00 3.66
313 318 5.587289 TCAAACCTTAGCACAAACATTCAC 58.413 37.500 0.00 0.00 0.00 3.18
323 328 3.067833 GGACAGACTCAAACCTTAGCAC 58.932 50.000 0.00 0.00 0.00 4.40
432 443 2.159379 GGGCAGTGAATGAACGAAATCC 60.159 50.000 0.00 0.00 0.00 3.01
442 453 7.230108 AGACTATATGAAAATGGGCAGTGAATG 59.770 37.037 0.00 0.00 0.00 2.67
463 479 8.989980 GCTTAGCTACAAAGAAAGAAAAGACTA 58.010 33.333 0.00 0.00 0.00 2.59
464 480 7.499232 TGCTTAGCTACAAAGAAAGAAAAGACT 59.501 33.333 5.60 0.00 0.00 3.24
484 500 9.906660 TTTCTTGTACCAAACATTATTGCTTAG 57.093 29.630 0.00 0.00 38.10 2.18
626 648 6.220930 TCCAAAGAGAATATATACACGGTGC 58.779 40.000 8.30 0.00 0.00 5.01
642 664 3.077359 GTCACCACCAATCTCCAAAGAG 58.923 50.000 0.00 0.00 41.93 2.85
675 697 6.099845 AGTTCCAAGAACTCAGGAAAGAAGTA 59.900 38.462 4.16 0.00 42.59 2.24
744 768 0.602638 TGTTGTCGAGGGTGATGTGC 60.603 55.000 0.00 0.00 0.00 4.57
753 777 5.929697 ATATATGCACAATGTTGTCGAGG 57.070 39.130 0.00 0.00 39.91 4.63
765 789 0.893270 GGGCGGCCAATATATGCACA 60.893 55.000 25.33 0.00 0.00 4.57
816 840 6.017440 GTGAGTATACTTTGTTTCACAAGCCA 60.017 38.462 6.88 0.00 39.53 4.75
876 900 0.373716 GCTATGTTGCACTGGTACGC 59.626 55.000 0.00 0.00 0.00 4.42
880 904 3.981071 TCTAAGCTATGTTGCACTGGT 57.019 42.857 0.00 0.00 34.99 4.00
1041 1076 9.157104 TCTTTTTCTTGCCGAAATTAACTTTTT 57.843 25.926 0.00 0.00 41.04 1.94
1232 1273 3.341823 ACTACATGCTCTGCTTGAAAGG 58.658 45.455 11.46 2.90 37.20 3.11
1245 1286 2.691409 TCCTGGCAGTAACTACATGC 57.309 50.000 14.43 0.00 39.25 4.06
1297 1338 6.314917 TCTTAAGAAAGGGGAAGCAGAAAAT 58.685 36.000 1.68 0.00 33.22 1.82
1300 1341 4.351111 ACTCTTAAGAAAGGGGAAGCAGAA 59.649 41.667 6.63 0.00 37.53 3.02
1305 1346 3.759086 GGCAACTCTTAAGAAAGGGGAAG 59.241 47.826 6.63 0.00 37.53 3.46
1319 1360 3.959293 TCACATTGATGATGGCAACTCT 58.041 40.909 0.00 0.00 40.21 3.24
1367 1408 5.003402 CGATTTTATGCCGACACATTGTTTC 59.997 40.000 0.00 0.00 0.00 2.78
1389 1430 0.730155 CGCACGTAAGGTAGTTGCGA 60.730 55.000 8.51 0.00 46.22 5.10
1391 1432 1.286354 TGCGCACGTAAGGTAGTTGC 61.286 55.000 5.66 0.00 46.39 4.17
1392 1433 0.437295 GTGCGCACGTAAGGTAGTTG 59.563 55.000 26.77 0.00 46.39 3.16
1393 1434 0.032403 TGTGCGCACGTAAGGTAGTT 59.968 50.000 33.22 0.00 46.39 2.24
1395 1436 1.323534 GATTGTGCGCACGTAAGGTAG 59.676 52.381 33.22 0.00 46.39 3.18
1396 1437 1.067425 AGATTGTGCGCACGTAAGGTA 60.067 47.619 33.22 13.22 46.39 3.08
1397 1438 0.320421 AGATTGTGCGCACGTAAGGT 60.320 50.000 33.22 16.08 46.39 3.50
1398 1439 0.095245 CAGATTGTGCGCACGTAAGG 59.905 55.000 33.22 19.52 46.39 2.69
1400 1441 1.459209 CTTCAGATTGTGCGCACGTAA 59.541 47.619 33.22 23.89 0.00 3.18
1402 1443 0.599991 TCTTCAGATTGTGCGCACGT 60.600 50.000 33.22 24.98 0.00 4.49
1403 1444 0.094216 CTCTTCAGATTGTGCGCACG 59.906 55.000 33.22 19.76 0.00 5.34
1404 1445 1.151668 ACTCTTCAGATTGTGCGCAC 58.848 50.000 33.11 33.11 0.00 5.34
1405 1446 1.532437 CAACTCTTCAGATTGTGCGCA 59.468 47.619 5.66 5.66 0.00 6.09
1406 1447 1.727213 GCAACTCTTCAGATTGTGCGC 60.727 52.381 0.00 0.00 0.00 6.09
1407 1448 1.532437 TGCAACTCTTCAGATTGTGCG 59.468 47.619 0.00 0.00 0.00 5.34
1408 1449 3.631145 TTGCAACTCTTCAGATTGTGC 57.369 42.857 0.00 0.00 0.00 4.57
1426 1484 1.139163 GCACCAAACGATGCCTTTTG 58.861 50.000 0.00 0.00 35.73 2.44
1488 1546 1.938585 TGATTCCTCACGGGAGAAGT 58.061 50.000 18.51 0.00 46.01 3.01
1551 1610 5.939883 CCACAATACAATGTTCTCTCCTTCA 59.060 40.000 0.00 0.00 0.00 3.02
1699 1758 0.718904 GAACGACGCATATGCACACA 59.281 50.000 26.52 0.00 42.21 3.72
1711 1770 2.159707 CCATTAAAGCACCAGAACGACG 60.160 50.000 0.00 0.00 0.00 5.12
1788 1866 2.519013 GGAAGGTTGAAGAAGGCACAT 58.481 47.619 0.00 0.00 0.00 3.21
1808 1886 1.482593 AGGTGGAGGTCTAAGAATGCG 59.517 52.381 0.00 0.00 0.00 4.73
1860 2246 2.190578 GCTGGATGGCCGCTTAGT 59.809 61.111 0.00 0.00 36.79 2.24
2012 2406 0.749649 TGAAGCAAACGCAACCCAAT 59.250 45.000 0.00 0.00 0.00 3.16
2158 2553 5.905331 AGATTGTCTGGAGTACCCATTGATA 59.095 40.000 3.86 0.00 45.57 2.15
2173 2568 8.491152 CAGTACTACAAAAGTGAAGATTGTCTG 58.509 37.037 0.00 0.00 39.39 3.51
2222 2617 9.998106 TTTCTAAAATAGCCGCTATTTCTAGAT 57.002 29.630 29.70 22.05 43.27 1.98
2255 2650 6.798427 AAACTTCTCCATATCTGAGTGCTA 57.202 37.500 0.00 0.00 0.00 3.49
2257 2652 9.547753 TTAATAAACTTCTCCATATCTGAGTGC 57.452 33.333 0.05 0.00 0.00 4.40
2284 2679 8.058847 TGGTTGCTAAATAAGTGGGATAAAGAT 58.941 33.333 0.00 0.00 0.00 2.40
2307 2702 8.623903 CAGTGAACAGCAATGTATATTAATGGT 58.376 33.333 0.00 0.00 37.78 3.55
2324 2719 7.441157 TCTTTGTTAAGATACCACAGTGAACAG 59.559 37.037 0.62 0.00 35.49 3.16
2326 2721 7.724305 TCTTTGTTAAGATACCACAGTGAAC 57.276 36.000 0.62 0.00 35.49 3.18
2354 2749 9.816354 GCTACAACATTACCAATGGATTAATTT 57.184 29.630 6.16 0.00 43.21 1.82
2373 2768 5.098893 TCAACACACACAAATTGCTACAAC 58.901 37.500 0.00 0.00 0.00 3.32
2377 2772 7.686438 AGATATCAACACACACAAATTGCTA 57.314 32.000 5.32 0.00 0.00 3.49
2408 2803 3.792956 CAGCCTACAATATGCGCAAAAAG 59.207 43.478 17.11 8.05 0.00 2.27
2420 2815 1.207488 TGTGCCTCCCAGCCTACAAT 61.207 55.000 0.00 0.00 0.00 2.71
2539 2934 0.467844 ACATTGCAGCACAGGTTCCA 60.468 50.000 0.00 0.00 0.00 3.53
2631 3194 5.376537 GCAAATGCAAAACATAAGAGCAAC 58.623 37.500 0.00 0.00 38.34 4.17
2782 3346 8.034313 ACAGATAGAGCCTTAAATATTGACCA 57.966 34.615 0.00 0.00 0.00 4.02
2822 3386 4.537135 TCCTAAAACTCGAGCACTCAAT 57.463 40.909 13.61 0.00 0.00 2.57
2823 3387 4.330944 TTCCTAAAACTCGAGCACTCAA 57.669 40.909 13.61 0.00 0.00 3.02
2871 3436 6.237901 ACTTCTAATTTGATACACTGCCACA 58.762 36.000 0.00 0.00 0.00 4.17
2902 3467 4.520492 ACATGAAACATTGGTCCTTCTCAC 59.480 41.667 0.00 0.00 0.00 3.51
2940 3505 2.668457 CACTTTAGTAGCGAGCAGTTGG 59.332 50.000 0.00 0.00 0.00 3.77
2950 3515 9.712305 ATATGACATAACCATCACTTTAGTAGC 57.288 33.333 0.00 0.00 0.00 3.58
2955 3520 6.426633 CGGCATATGACATAACCATCACTTTA 59.573 38.462 9.77 0.00 0.00 1.85
2959 3524 4.065088 ACGGCATATGACATAACCATCAC 58.935 43.478 9.77 0.00 0.00 3.06
2969 3534 7.851387 TTGTTTTCTATTACGGCATATGACA 57.149 32.000 9.77 0.00 0.00 3.58
3004 3569 2.158475 ACAACAAGCAATTCTGGAGGGA 60.158 45.455 0.00 0.00 0.00 4.20
3005 3570 2.242043 ACAACAAGCAATTCTGGAGGG 58.758 47.619 0.00 0.00 0.00 4.30
3065 3630 2.425143 TCCTGACATTTCCATGGAGC 57.575 50.000 15.53 4.31 34.27 4.70
3228 3795 5.445142 GCAGCGATCTAATAACGATTGATGG 60.445 44.000 7.40 0.00 38.49 3.51
3422 3989 3.880490 GACATACTGAACCAAACACCACA 59.120 43.478 0.00 0.00 0.00 4.17
3445 4012 2.438975 CACATGCCTGCCGGTGAT 60.439 61.111 1.90 0.00 33.16 3.06
3491 4058 7.432869 TCATCATTGTACAAGAAAAACCCTTG 58.567 34.615 14.65 3.51 44.75 3.61
3698 4426 5.772672 TGAACTTAAAGCCTTGCAGGATAAA 59.227 36.000 0.00 0.00 37.67 1.40
3727 4455 4.369182 ACGACTTTGACGTTCTTCTTGAT 58.631 39.130 0.00 0.00 41.18 2.57
3750 4478 1.762957 GTTCATCTTGATCGAGGGGGA 59.237 52.381 10.19 3.03 0.00 4.81
3752 4480 1.765314 AGGTTCATCTTGATCGAGGGG 59.235 52.381 10.19 3.11 0.00 4.79
3759 4487 5.447778 AGGATCAACAGGTTCATCTTGAT 57.552 39.130 0.00 0.00 36.31 2.57
3786 4514 7.148069 GGGGAGTACAGTATTTTTCAATTGGAG 60.148 40.741 5.42 0.00 0.00 3.86
4383 5121 4.084797 CCAAAAATCCGCGTCGAAATTTTT 60.085 37.500 4.92 19.25 39.73 1.94
4384 5122 3.427193 CCAAAAATCCGCGTCGAAATTTT 59.573 39.130 4.92 6.48 35.38 1.82
4385 5123 2.983803 CCAAAAATCCGCGTCGAAATTT 59.016 40.909 4.92 0.00 0.00 1.82
4386 5124 2.591133 CCAAAAATCCGCGTCGAAATT 58.409 42.857 4.92 0.00 0.00 1.82
4387 5125 1.135517 CCCAAAAATCCGCGTCGAAAT 60.136 47.619 4.92 0.00 0.00 2.17
4388 5126 0.238817 CCCAAAAATCCGCGTCGAAA 59.761 50.000 4.92 0.00 0.00 3.46
4389 5127 0.603172 TCCCAAAAATCCGCGTCGAA 60.603 50.000 4.92 0.00 0.00 3.71
4390 5128 1.004799 TCCCAAAAATCCGCGTCGA 60.005 52.632 4.92 0.00 0.00 4.20
4391 5129 1.133869 GTCCCAAAAATCCGCGTCG 59.866 57.895 4.92 0.00 0.00 5.12
4392 5130 0.808755 ATGTCCCAAAAATCCGCGTC 59.191 50.000 4.92 0.00 0.00 5.19
4393 5131 0.525761 CATGTCCCAAAAATCCGCGT 59.474 50.000 4.92 0.00 0.00 6.01
4394 5132 3.327464 CATGTCCCAAAAATCCGCG 57.673 52.632 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.