Multiple sequence alignment - TraesCS5A01G187900

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 TraesCS5A01G187900 chr5A 100.000 3623 0 0 1 3623 389712949 389716571 0.000000e+00 6691.0
1 TraesCS5A01G187900 chr5A 85.057 87 12 1 3382 3468 365256974 365256889 1.790000e-13 87.9
2 TraesCS5A01G187900 chr5D 95.764 3187 103 12 444 3615 308230837 308227668 0.000000e+00 5108.0
3 TraesCS5A01G187900 chr5D 89.461 427 32 5 1 414 308231263 308230837 8.910000e-146 527.0
4 TraesCS5A01G187900 chr5D 94.928 138 7 0 2993 3130 529218165 529218302 2.190000e-52 217.0
5 TraesCS5A01G187900 chr5B 94.957 2300 65 16 701 2996 353040836 353038584 0.000000e+00 3557.0
6 TraesCS5A01G187900 chr5B 88.912 487 31 8 3140 3615 353038586 353038112 2.430000e-161 579.0
7 TraesCS5A01G187900 chr2B 96.350 137 5 0 2994 3130 608226725 608226861 3.640000e-55 226.0
8 TraesCS5A01G187900 chr4A 95.620 137 6 0 2994 3130 137966979 137967115 1.690000e-53 220.0
9 TraesCS5A01G187900 chr4A 95.620 137 6 0 2994 3130 137972830 137972694 1.690000e-53 220.0
10 TraesCS5A01G187900 chr3A 95.620 137 6 0 2994 3130 585500349 585500213 1.690000e-53 220.0
11 TraesCS5A01G187900 chr2D 95.620 137 6 0 2994 3130 134301488 134301624 1.690000e-53 220.0
12 TraesCS5A01G187900 chr2D 91.304 69 6 0 3382 3450 598800774 598800706 1.070000e-15 95.3
13 TraesCS5A01G187900 chr2A 93.243 148 9 1 2984 3130 504326610 504326757 2.190000e-52 217.0
14 TraesCS5A01G187900 chr1D 94.891 137 7 0 2994 3130 463470932 463470796 7.880000e-52 215.0
15 TraesCS5A01G187900 chr7D 83.537 164 21 3 3383 3544 102581719 102581560 8.110000e-32 148.0
16 TraesCS5A01G187900 chr7D 82.692 156 20 5 3219 3374 387333756 387333608 8.160000e-27 132.0
17 TraesCS5A01G187900 chr7D 94.231 52 1 2 3258 3308 469530192 469530242 1.080000e-10 78.7
18 TraesCS5A01G187900 chr7A 81.343 134 16 7 3242 3374 437402805 437402680 2.300000e-17 100.0
19 TraesCS5A01G187900 chr6D 92.537 67 5 0 3403 3469 156441819 156441885 2.980000e-16 97.1
20 TraesCS5A01G187900 chr6B 92.537 67 5 0 3403 3469 279034399 279034465 2.980000e-16 97.1


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 TraesCS5A01G187900 chr5A 389712949 389716571 3622 False 6691.0 6691 100.0000 1 3623 1 chr5A.!!$F1 3622
1 TraesCS5A01G187900 chr5D 308227668 308231263 3595 True 2817.5 5108 92.6125 1 3615 2 chr5D.!!$R1 3614
2 TraesCS5A01G187900 chr5B 353038112 353040836 2724 True 2068.0 3557 91.9345 701 3615 2 chr5B.!!$R1 2914

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
191 192 0.315059 CGAATAACGTGCATGCGGTC 60.315 55.000 14.09 5.26 37.22 4.79 F
506 520 0.465460 TCAAGCGTCACCCTTGCTTT 60.465 50.000 0.00 0.00 46.12 3.51 F
1627 1660 0.820871 CTTCTTCAGAGAGTCGGGGG 59.179 60.000 0.00 0.00 32.44 5.40 F
2391 2424 1.074014 TATCCCACCCTACCAGGCC 60.074 63.158 0.00 0.00 32.73 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1668 0.969149 ACGTCTTGGCTGAGACATCA 59.031 50.000 17.47 0.0 44.98 3.07 R
2460 2493 2.202987 GTGCTCCGCCTCATCCTG 60.203 66.667 0.00 0.0 0.00 3.86 R
2545 2578 0.753262 AGTTCTTGGTCACTGCTCGT 59.247 50.000 0.00 0.0 0.00 4.18 R
3285 3318 1.092549 ACAAATCAATGGGAGGGGGT 58.907 50.000 0.00 0.0 0.00 4.95 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
22 23 2.036414 TCTCCTGGAGCGCAGAGT 59.964 61.111 19.08 0.00 0.00 3.24
32 33 2.571757 CGCAGAGTGGCCGAGTTA 59.428 61.111 0.00 0.00 0.00 2.24
41 42 0.454600 TGGCCGAGTTAGACTAAGCG 59.545 55.000 0.00 9.38 29.73 4.68
58 59 0.733150 GCGTGGGAACAATTCTAGGC 59.267 55.000 0.00 0.00 46.06 3.93
60 61 1.339631 CGTGGGAACAATTCTAGGCCA 60.340 52.381 5.01 0.00 46.06 5.36
102 103 4.659172 CAACCAAGGCCGCCCTGA 62.659 66.667 9.78 0.00 41.90 3.86
141 142 3.507162 TGAAGGAAGCCATGAAGAACA 57.493 42.857 0.00 0.00 0.00 3.18
142 143 3.149196 TGAAGGAAGCCATGAAGAACAC 58.851 45.455 0.00 0.00 0.00 3.32
144 145 1.425066 AGGAAGCCATGAAGAACACCA 59.575 47.619 0.00 0.00 0.00 4.17
145 146 1.815003 GGAAGCCATGAAGAACACCAG 59.185 52.381 0.00 0.00 0.00 4.00
163 164 3.458163 GGAGTCGCCGTCCCATCA 61.458 66.667 0.00 0.00 0.00 3.07
172 173 1.234615 CCGTCCCATCACACACCAAC 61.235 60.000 0.00 0.00 0.00 3.77
176 177 1.073125 TCCCATCACACACCAACGAAT 59.927 47.619 0.00 0.00 0.00 3.34
191 192 0.315059 CGAATAACGTGCATGCGGTC 60.315 55.000 14.09 5.26 37.22 4.79
221 222 1.452108 CGCCAGGATCAAGTTCCCC 60.452 63.158 0.00 0.00 36.35 4.81
241 242 2.227626 CCGCCAAACACACATACAATGA 59.772 45.455 0.00 0.00 0.00 2.57
244 245 4.382457 CGCCAAACACACATACAATGAAAG 59.618 41.667 0.00 0.00 0.00 2.62
254 255 1.156736 ACAATGAAAGGAGCGGTTCG 58.843 50.000 0.00 0.00 0.00 3.95
271 272 1.186200 TCGAGAAGGTCATGGAGTGG 58.814 55.000 0.00 0.00 0.00 4.00
302 304 5.479375 ACGTCAAACTCTTGAGGGTATCTAA 59.521 40.000 11.08 0.00 46.87 2.10
304 306 6.350277 CGTCAAACTCTTGAGGGTATCTAAGT 60.350 42.308 2.55 0.00 42.27 2.24
342 344 4.890088 TGTACTTGCACCGTCTCTAATTT 58.110 39.130 0.00 0.00 0.00 1.82
345 359 4.385825 ACTTGCACCGTCTCTAATTTTCA 58.614 39.130 0.00 0.00 0.00 2.69
357 371 7.857885 CGTCTCTAATTTTCAAGTTCAAAGCTT 59.142 33.333 0.00 0.00 0.00 3.74
361 375 9.019764 TCTAATTTTCAAGTTCAAAGCTTTTCG 57.980 29.630 9.53 0.00 0.00 3.46
394 408 1.008938 AGCCCTCCAAGTATGAGAGGT 59.991 52.381 4.69 0.00 40.03 3.85
406 420 9.110502 CCAAGTATGAGAGGTATTCCTTTTTAC 57.889 37.037 0.00 0.00 45.24 2.01
428 442 8.755696 TTACAATCAATAGACACAAAATTGCC 57.244 30.769 0.00 0.00 31.98 4.52
429 443 5.863397 ACAATCAATAGACACAAAATTGCCG 59.137 36.000 0.00 0.00 31.98 5.69
430 444 5.643379 ATCAATAGACACAAAATTGCCGT 57.357 34.783 0.00 0.00 31.98 5.68
431 445 5.041951 TCAATAGACACAAAATTGCCGTC 57.958 39.130 7.77 7.77 35.37 4.79
432 446 4.517075 TCAATAGACACAAAATTGCCGTCA 59.483 37.500 14.85 5.57 36.75 4.35
433 447 5.182950 TCAATAGACACAAAATTGCCGTCAT 59.817 36.000 14.85 7.01 36.75 3.06
434 448 3.287312 AGACACAAAATTGCCGTCATG 57.713 42.857 14.85 0.00 36.75 3.07
435 449 2.884012 AGACACAAAATTGCCGTCATGA 59.116 40.909 14.85 0.00 36.75 3.07
436 450 3.507233 AGACACAAAATTGCCGTCATGAT 59.493 39.130 14.85 0.00 36.75 2.45
437 451 4.699735 AGACACAAAATTGCCGTCATGATA 59.300 37.500 14.85 0.00 36.75 2.15
438 452 5.182950 AGACACAAAATTGCCGTCATGATAA 59.817 36.000 14.85 0.00 36.75 1.75
439 453 5.964758 ACACAAAATTGCCGTCATGATAAT 58.035 33.333 0.00 0.00 0.00 1.28
440 454 7.066887 AGACACAAAATTGCCGTCATGATAATA 59.933 33.333 14.85 0.00 36.75 0.98
441 455 7.715657 ACACAAAATTGCCGTCATGATAATAT 58.284 30.769 0.00 0.00 0.00 1.28
442 456 8.196771 ACACAAAATTGCCGTCATGATAATATT 58.803 29.630 0.00 0.00 0.00 1.28
443 457 9.033481 CACAAAATTGCCGTCATGATAATATTT 57.967 29.630 0.00 0.00 0.00 1.40
464 478 9.914131 ATATTTTCCTTTCAAAGTCTAAAGCAC 57.086 29.630 0.00 0.00 32.48 4.40
465 479 6.767524 TTTCCTTTCAAAGTCTAAAGCACA 57.232 33.333 0.00 0.00 32.48 4.57
506 520 0.465460 TCAAGCGTCACCCTTGCTTT 60.465 50.000 0.00 0.00 46.12 3.51
548 562 5.750352 AGAGTACGAAATCCTTAAACCCA 57.250 39.130 0.00 0.00 0.00 4.51
589 603 5.011982 TCTCTCCCTCTCTTCCTACAAAA 57.988 43.478 0.00 0.00 0.00 2.44
625 640 9.942850 AGAAAAATGTGAAAGGAAAAGAAGAAA 57.057 25.926 0.00 0.00 0.00 2.52
672 687 2.669133 CCGTGGATGGAGCCCTTCA 61.669 63.158 8.64 0.00 30.42 3.02
675 690 1.396653 GTGGATGGAGCCCTTCATTG 58.603 55.000 8.64 0.00 30.42 2.82
685 700 4.692155 GGAGCCCTTCATTGTTCAAAATTG 59.308 41.667 0.00 0.00 0.00 2.32
751 769 1.418342 CCGTCGCCGTATTGTCCTTG 61.418 60.000 0.00 0.00 0.00 3.61
770 788 3.306472 TGTACAAGCCCAAGTTTCCTT 57.694 42.857 0.00 0.00 0.00 3.36
771 789 3.637769 TGTACAAGCCCAAGTTTCCTTT 58.362 40.909 0.00 0.00 0.00 3.11
810 836 1.617839 CAGGCCCTCCTCTCCCTTT 60.618 63.158 0.00 0.00 41.93 3.11
868 894 2.776913 GCGACCTCCTCTTCCTCCG 61.777 68.421 0.00 0.00 0.00 4.63
909 935 0.976590 ACTTCCTCGGTAAGCCCCTC 60.977 60.000 0.00 0.00 0.00 4.30
933 960 1.150081 CCCTGCTCCCACATCCATC 59.850 63.158 0.00 0.00 0.00 3.51
1473 1506 1.352156 GGCTGTTCCGTGCTTACTCG 61.352 60.000 0.00 0.00 0.00 4.18
1560 1593 1.377202 GCTGGCCGATTTCCACTCA 60.377 57.895 0.00 0.00 0.00 3.41
1627 1660 0.820871 CTTCTTCAGAGAGTCGGGGG 59.179 60.000 0.00 0.00 32.44 5.40
1635 1668 2.211468 GAGAGTCGGGGGCCCATTTT 62.211 60.000 26.86 6.76 35.37 1.82
1767 1800 1.378882 ATGTGCCTGCCTACAATGCG 61.379 55.000 0.00 0.00 0.00 4.73
1863 1896 1.509923 GCTTGTTCCAGATGCTGCC 59.490 57.895 0.00 0.00 0.00 4.85
2211 2244 8.532977 ACATGTTACTAAAAATGTTGATTGGC 57.467 30.769 0.00 0.00 40.04 4.52
2391 2424 1.074014 TATCCCACCCTACCAGGCC 60.074 63.158 0.00 0.00 32.73 5.19
2460 2493 4.008074 TCAACTTGAGGTCCTCATTGAC 57.992 45.455 24.80 0.72 40.39 3.18
2519 2552 1.261619 GGCAAGTATCATGCGCAGTAC 59.738 52.381 18.32 17.88 44.75 2.73
2545 2578 2.573462 AGGGCTGATGAAACTAGAAGCA 59.427 45.455 0.00 0.00 32.28 3.91
2830 2863 3.159213 TCCTGGTCAAGCAATTGATGT 57.841 42.857 10.34 0.00 33.02 3.06
2955 2988 9.399797 TGTTTCTCATTTGCTGATATGAACTAT 57.600 29.630 0.00 0.00 32.10 2.12
3004 3037 5.516059 TCATACTATCATACTCCCTCCGT 57.484 43.478 0.00 0.00 0.00 4.69
3017 3050 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3135 3168 9.071276 GCATTGGAATATCTAAAAAGATGGAGA 57.929 33.333 0.00 0.00 0.00 3.71
3254 3287 5.238583 AGGAGAGATAGTTGGTTTCGTTTG 58.761 41.667 0.00 0.00 0.00 2.93
3285 3318 1.132849 ACCCCTCCCATCGATACATGA 60.133 52.381 0.00 0.00 0.00 3.07
3296 3329 1.747444 GATACATGACCCCCTCCCAT 58.253 55.000 0.00 0.00 0.00 4.00
3331 3364 2.557317 ACCACGCGATAACCCTAATTG 58.443 47.619 15.93 0.00 0.00 2.32
3335 3368 4.274950 CCACGCGATAACCCTAATTGATTT 59.725 41.667 15.93 0.00 0.00 2.17
3476 3510 9.293404 CAACATATCTCAATCTCAACCCAATAT 57.707 33.333 0.00 0.00 0.00 1.28
3536 3577 1.260561 CATTGCTACGCACGGGTATTC 59.739 52.381 0.00 0.00 38.71 1.75
3553 3594 9.086758 ACGGGTATTCAGCTAGTACTATTTAAT 57.913 33.333 2.33 4.51 0.00 1.40
3615 3659 9.559958 CTGACACATTAGTCATTTAATTTCACC 57.440 33.333 0.00 0.00 46.51 4.02
3616 3660 9.295825 TGACACATTAGTCATTTAATTTCACCT 57.704 29.630 0.00 0.00 43.18 4.00
3617 3661 9.774742 GACACATTAGTCATTTAATTTCACCTC 57.225 33.333 0.00 0.00 38.40 3.85
3618 3662 9.520515 ACACATTAGTCATTTAATTTCACCTCT 57.479 29.630 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.347322 ACTCTGCGCTCCAGGAGAC 61.347 63.158 21.89 11.67 42.05 3.36
22 23 0.454600 CGCTTAGTCTAACTCGGCCA 59.545 55.000 2.24 0.00 0.00 5.36
32 33 3.008049 AGAATTGTTCCCACGCTTAGTCT 59.992 43.478 0.00 0.00 0.00 3.24
41 42 2.092323 GTGGCCTAGAATTGTTCCCAC 58.908 52.381 3.32 0.00 33.34 4.61
58 59 0.177604 GATGGTCTCCTGCTCAGTGG 59.822 60.000 0.00 0.00 0.00 4.00
60 61 2.601664 GGATGGTCTCCTGCTCAGT 58.398 57.895 0.00 0.00 41.29 3.41
102 103 4.431131 CTGCCCGCCCTTCATGGT 62.431 66.667 0.00 0.00 0.00 3.55
115 116 1.030457 CATGGCTTCCTTCATCTGCC 58.970 55.000 0.00 0.00 43.49 4.85
144 145 4.779733 ATGGGACGGCGACTCCCT 62.780 66.667 29.01 16.05 43.94 4.20
145 146 4.222847 GATGGGACGGCGACTCCC 62.223 72.222 24.43 24.43 43.89 4.30
172 173 0.315059 GACCGCATGCACGTTATTCG 60.315 55.000 19.57 0.00 46.00 3.34
176 177 2.048970 ACGACCGCATGCACGTTA 60.049 55.556 22.30 0.00 35.47 3.18
221 222 3.550950 TCATTGTATGTGTGTTTGGCG 57.449 42.857 0.00 0.00 0.00 5.69
241 242 0.037232 CCTTCTCGAACCGCTCCTTT 60.037 55.000 0.00 0.00 0.00 3.11
244 245 1.153804 GACCTTCTCGAACCGCTCC 60.154 63.158 0.00 0.00 0.00 4.70
254 255 0.908198 AGCCACTCCATGACCTTCTC 59.092 55.000 0.00 0.00 0.00 2.87
271 272 4.318831 CCTCAAGAGTTTGACGTGTTTAGC 60.319 45.833 0.00 0.00 38.37 3.09
302 304 5.342866 AGTACAAGAGTTTGGGAGGATACT 58.657 41.667 0.00 0.00 44.88 2.12
304 306 5.570844 GCAAGTACAAGAGTTTGGGAGGATA 60.571 44.000 0.00 0.00 38.66 2.59
342 344 4.439563 GGGACGAAAAGCTTTGAACTTGAA 60.440 41.667 13.54 0.00 0.00 2.69
345 359 3.710326 GGGACGAAAAGCTTTGAACTT 57.290 42.857 13.54 0.00 0.00 2.66
361 375 1.275573 GGAGGGCTATTATGTCGGGAC 59.724 57.143 0.00 0.00 0.00 4.46
406 420 5.863397 ACGGCAATTTTGTGTCTATTGATTG 59.137 36.000 0.00 0.00 32.36 2.67
409 423 4.517075 TGACGGCAATTTTGTGTCTATTGA 59.483 37.500 0.00 0.00 36.94 2.57
414 428 2.884012 TCATGACGGCAATTTTGTGTCT 59.116 40.909 0.00 3.56 36.94 3.41
415 429 3.281341 TCATGACGGCAATTTTGTGTC 57.719 42.857 0.00 9.46 36.72 3.67
416 430 3.940209 ATCATGACGGCAATTTTGTGT 57.060 38.095 0.00 0.00 0.00 3.72
417 431 8.578308 AATATTATCATGACGGCAATTTTGTG 57.422 30.769 0.00 0.00 0.00 3.33
418 432 9.598517 AAAATATTATCATGACGGCAATTTTGT 57.401 25.926 0.00 0.00 0.00 2.83
420 434 9.260002 GGAAAATATTATCATGACGGCAATTTT 57.740 29.630 7.16 7.16 0.00 1.82
421 435 8.641541 AGGAAAATATTATCATGACGGCAATTT 58.358 29.630 0.00 0.00 0.00 1.82
422 436 8.181904 AGGAAAATATTATCATGACGGCAATT 57.818 30.769 0.00 0.00 0.00 2.32
423 437 7.765695 AGGAAAATATTATCATGACGGCAAT 57.234 32.000 0.00 0.00 0.00 3.56
424 438 7.581213 AAGGAAAATATTATCATGACGGCAA 57.419 32.000 0.00 0.00 0.00 4.52
425 439 7.284261 TGAAAGGAAAATATTATCATGACGGCA 59.716 33.333 0.00 0.00 0.00 5.69
426 440 7.648142 TGAAAGGAAAATATTATCATGACGGC 58.352 34.615 0.00 0.00 0.00 5.68
438 452 9.914131 GTGCTTTAGACTTTGAAAGGAAAATAT 57.086 29.630 10.02 0.00 35.19 1.28
439 453 8.908903 TGTGCTTTAGACTTTGAAAGGAAAATA 58.091 29.630 10.02 0.00 35.19 1.40
440 454 7.781056 TGTGCTTTAGACTTTGAAAGGAAAAT 58.219 30.769 10.02 0.00 35.19 1.82
441 455 7.164230 TGTGCTTTAGACTTTGAAAGGAAAA 57.836 32.000 10.02 5.81 35.19 2.29
442 456 6.767524 TGTGCTTTAGACTTTGAAAGGAAA 57.232 33.333 10.02 5.94 35.19 3.13
443 457 6.959639 ATGTGCTTTAGACTTTGAAAGGAA 57.040 33.333 10.02 0.00 35.19 3.36
454 468 3.117046 GGAGTCGCTATGTGCTTTAGAC 58.883 50.000 0.00 0.00 40.11 2.59
459 473 0.460987 GCTGGAGTCGCTATGTGCTT 60.461 55.000 0.00 0.00 40.11 3.91
460 474 1.142748 GCTGGAGTCGCTATGTGCT 59.857 57.895 0.00 0.00 40.11 4.40
461 475 0.460987 AAGCTGGAGTCGCTATGTGC 60.461 55.000 0.00 0.00 36.56 4.57
463 477 5.531122 TTTATAAGCTGGAGTCGCTATGT 57.469 39.130 0.00 0.00 36.56 2.29
464 478 6.646653 TGATTTTATAAGCTGGAGTCGCTATG 59.353 38.462 0.00 0.00 36.56 2.23
465 479 6.759272 TGATTTTATAAGCTGGAGTCGCTAT 58.241 36.000 0.00 0.00 36.56 2.97
470 484 5.294552 ACGCTTGATTTTATAAGCTGGAGTC 59.705 40.000 0.00 0.00 45.34 3.36
477 491 4.335594 AGGGTGACGCTTGATTTTATAAGC 59.664 41.667 0.00 0.00 44.37 3.09
494 508 2.356665 TGTTAGCAAAGCAAGGGTGA 57.643 45.000 0.00 0.00 0.00 4.02
520 534 7.201617 GGTTTAAGGATTTCGTACTCTTCCATG 60.202 40.741 0.00 0.00 0.00 3.66
548 562 1.470098 GAGAAAGCATGTGTCGGCATT 59.530 47.619 0.00 0.00 0.00 3.56
589 603 9.416284 TCCTTTCACATTTTTCTACCTTAAGTT 57.584 29.630 0.97 0.00 0.00 2.66
624 639 1.001974 GGGCCGCTCCAAATTCTTTTT 59.998 47.619 0.00 0.00 36.21 1.94
625 640 0.608130 GGGCCGCTCCAAATTCTTTT 59.392 50.000 0.00 0.00 36.21 2.27
626 641 0.541764 TGGGCCGCTCCAAATTCTTT 60.542 50.000 0.00 0.00 36.21 2.52
627 642 1.076549 TGGGCCGCTCCAAATTCTT 59.923 52.632 0.00 0.00 36.21 2.52
628 643 1.678970 GTGGGCCGCTCCAAATTCT 60.679 57.895 10.52 0.00 38.72 2.40
629 644 0.393808 TAGTGGGCCGCTCCAAATTC 60.394 55.000 25.40 0.00 38.72 2.17
630 645 0.394352 CTAGTGGGCCGCTCCAAATT 60.394 55.000 25.40 0.00 38.72 1.82
631 646 1.224592 CTAGTGGGCCGCTCCAAAT 59.775 57.895 25.40 0.29 38.72 2.32
655 670 0.107017 AATGAAGGGCTCCATCCACG 60.107 55.000 0.00 0.00 0.00 4.94
672 687 8.729805 TTGTAAGGCTTTCAATTTTGAACAAT 57.270 26.923 14.32 0.00 45.99 2.71
675 690 8.419076 TCTTTGTAAGGCTTTCAATTTTGAAC 57.581 30.769 18.17 1.76 45.99 3.18
720 735 2.022129 GCGACGGTGAGACAAGGTG 61.022 63.158 0.00 0.00 0.00 4.00
770 788 2.297698 TGGGGAAGTGAGACGAGTAA 57.702 50.000 0.00 0.00 0.00 2.24
771 789 2.526888 ATGGGGAAGTGAGACGAGTA 57.473 50.000 0.00 0.00 0.00 2.59
923 950 6.798315 CTAGAAAGCAATAGATGGATGTGG 57.202 41.667 0.00 0.00 0.00 4.17
1129 1156 2.753043 GAGCCCTGGGTCGACGTA 60.753 66.667 15.56 0.00 32.85 3.57
1290 1323 1.443802 CAAAGAGGAAGAACCGGAGC 58.556 55.000 9.46 0.00 44.74 4.70
1443 1476 3.296709 GAACAGCCGCGGGAAGAGA 62.297 63.158 29.38 0.00 0.00 3.10
1473 1506 4.742201 TCTGGGAGAAGCGCACGC 62.742 66.667 11.47 6.99 42.33 5.34
1488 1521 2.345244 GCCCGGATCGCATCATCT 59.655 61.111 0.73 0.00 0.00 2.90
1560 1593 3.659820 TGGCACAAGGCGAATAGCAGT 62.660 52.381 0.00 0.00 46.16 4.40
1627 1660 1.135721 GGCTGAGACATCAAAATGGGC 59.864 52.381 0.00 0.00 37.19 5.36
1635 1668 0.969149 ACGTCTTGGCTGAGACATCA 59.031 50.000 17.47 0.00 44.98 3.07
1653 1686 2.366916 CCCAGAGATCAGGATGGTGTAC 59.633 54.545 0.00 0.00 36.16 2.90
1863 1896 3.623060 CACGAAGGAATGGACCATAAGTG 59.377 47.826 7.59 8.16 0.00 3.16
2211 2244 4.202264 ACAGCCTTATCAATCCTTCCTACG 60.202 45.833 0.00 0.00 0.00 3.51
2391 2424 2.930950 TCCCTCAAAACCTCACAAGTG 58.069 47.619 0.00 0.00 0.00 3.16
2460 2493 2.202987 GTGCTCCGCCTCATCCTG 60.203 66.667 0.00 0.00 0.00 3.86
2519 2552 5.860941 TCTAGTTTCATCAGCCCTCTTAG 57.139 43.478 0.00 0.00 0.00 2.18
2545 2578 0.753262 AGTTCTTGGTCACTGCTCGT 59.247 50.000 0.00 0.00 0.00 4.18
3032 3065 6.971726 ACATCCGTATGTAGTCCTTATTGA 57.028 37.500 0.00 0.00 44.66 2.57
3084 3117 7.115947 GCGGACTATATACGAAGCAAAATAAGT 59.884 37.037 0.00 0.00 0.00 2.24
3087 3120 6.448852 TGCGGACTATATACGAAGCAAAATA 58.551 36.000 0.00 0.00 0.00 1.40
3102 3135 8.918202 TTTTTAGATATTCCAATGCGGACTAT 57.082 30.769 0.00 0.00 46.36 2.12
3119 3152 7.648039 ACGTACTCTCTCCATCTTTTTAGAT 57.352 36.000 0.00 0.00 0.00 1.98
3135 3168 3.657634 TCTTGACAGACGTACGTACTCT 58.342 45.455 22.87 19.30 0.00 3.24
3238 3271 3.987220 GCAATGCAAACGAAACCAACTAT 59.013 39.130 0.00 0.00 0.00 2.12
3240 3273 2.159114 AGCAATGCAAACGAAACCAACT 60.159 40.909 8.35 0.00 0.00 3.16
3254 3287 2.054453 GGAGGGGTGGAAGCAATGC 61.054 63.158 0.00 0.00 34.77 3.56
3285 3318 1.092549 ACAAATCAATGGGAGGGGGT 58.907 50.000 0.00 0.00 0.00 4.95
3335 3368 1.330234 GTAGGGCCGGTTTGGAAAAA 58.670 50.000 1.90 0.00 42.00 1.94
3348 3381 1.340114 CCAGAAACAAGGAGGTAGGGC 60.340 57.143 0.00 0.00 0.00 5.19
3553 3594 8.655901 TCATAATGGGTGAAATATAGCACAGTA 58.344 33.333 9.32 0.00 36.76 2.74


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

AutoCloner maintained by Alex Coulton.