Multiple sequence alignment - TraesCS6A01G079500

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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 TraesCS6A01G079500 chr6A 100.000 2201 0 0 1 2201 48763578 48765778 0.000000e+00 4065.0
1 TraesCS6A01G079500 chr6A 91.626 824 51 8 614 1426 48713013 48713829 0.000000e+00 1123.0
2 TraesCS6A01G079500 chr6A 87.192 203 23 2 1001 1203 35929295 35929096 6.110000e-56 228.0
3 TraesCS6A01G079500 chr6A 97.321 112 2 1 514 625 477910777 477910887 2.880000e-44 189.0
4 TraesCS6A01G079500 chr6A 90.909 132 8 3 487 616 170914072 170914201 8.080000e-40 174.0
5 TraesCS6A01G079500 chr6A 97.436 78 2 0 393 470 48711224 48711301 1.370000e-27 134.0
6 TraesCS6A01G079500 chr6A 100.000 55 0 0 457 511 48712961 48713015 3.870000e-18 102.0
7 TraesCS6A01G079500 chr6D 88.402 1164 76 26 614 1756 37442771 37443896 0.000000e+00 1347.0
8 TraesCS6A01G079500 chr6D 92.218 514 34 4 1 511 37442263 37442773 0.000000e+00 723.0
9 TraesCS6A01G079500 chr6D 90.262 267 25 1 1935 2201 37444262 37444527 4.500000e-92 348.0
10 TraesCS6A01G079500 chr6B 92.559 766 41 9 613 1370 87540843 87541600 0.000000e+00 1085.0
11 TraesCS6A01G079500 chr6B 92.023 514 36 4 1 510 87540327 87540839 0.000000e+00 717.0
12 TraesCS6A01G079500 chr6B 83.747 363 41 8 1405 1758 87541985 87542338 5.860000e-86 327.0
13 TraesCS6A01G079500 chr6B 87.192 203 23 2 1001 1203 66741872 66741673 6.110000e-56 228.0
14 TraesCS6A01G079500 chr6B 93.277 119 8 0 501 619 706650423 706650305 2.250000e-40 176.0
15 TraesCS6A01G079500 chr6B 77.612 268 53 5 1935 2196 44056737 44057003 2.930000e-34 156.0
16 TraesCS6A01G079500 chrUn 87.685 203 22 2 1001 1203 100705664 100705863 1.310000e-57 233.0
17 TraesCS6A01G079500 chrUn 86.700 203 24 2 1001 1203 100575562 100575761 2.840000e-54 222.0
18 TraesCS6A01G079500 chr5D 81.323 257 44 2 1948 2200 256450044 256449788 2.860000e-49 206.0
19 TraesCS6A01G079500 chr3D 97.273 110 2 1 514 622 606889292 606889401 3.730000e-43 185.0
20 TraesCS6A01G079500 chr3D 97.222 108 3 0 508 615 5081630 5081737 1.340000e-42 183.0
21 TraesCS6A01G079500 chr4A 96.429 112 2 2 514 624 381221332 381221442 1.340000e-42 183.0
22 TraesCS6A01G079500 chr1B 80.078 256 44 7 1945 2196 25824391 25824139 1.340000e-42 183.0
23 TraesCS6A01G079500 chr7B 79.688 256 47 4 1945 2196 198543116 198542862 1.740000e-41 180.0
24 TraesCS6A01G079500 chr7B 78.599 257 48 6 1945 2196 572510269 572510523 1.750000e-36 163.0
25 TraesCS6A01G079500 chr4B 79.920 249 44 5 1941 2184 573409075 573409322 6.240000e-41 178.0
26 TraesCS6A01G079500 chr4B 77.823 248 50 4 1940 2183 660316365 660316611 4.900000e-32 148.0
27 TraesCS6A01G079500 chr4B 94.286 35 1 1 139 172 356546319 356546285 4.000000e-03 52.8
28 TraesCS6A01G079500 chr7A 92.126 127 7 2 497 622 32944538 32944414 2.250000e-40 176.0
29 TraesCS6A01G079500 chr5A 92.000 125 10 0 502 626 672030968 672031092 2.250000e-40 176.0
30 TraesCS6A01G079500 chr3A 89.130 138 13 2 490 626 156132874 156133010 1.040000e-38 171.0
31 TraesCS6A01G079500 chr5B 78.277 267 50 6 1935 2196 506756916 506757179 4.860000e-37 165.0


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 TraesCS6A01G079500 chr6A 48763578 48765778 2200 False 4065.000000 4065 100.000 1 2201 1 chr6A.!!$F1 2200
1 TraesCS6A01G079500 chr6A 48711224 48713829 2605 False 453.000000 1123 96.354 393 1426 3 chr6A.!!$F4 1033
2 TraesCS6A01G079500 chr6D 37442263 37444527 2264 False 806.000000 1347 90.294 1 2201 3 chr6D.!!$F1 2200
3 TraesCS6A01G079500 chr6B 87540327 87542338 2011 False 709.666667 1085 89.443 1 1758 3 chr6B.!!$F2 1757

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
377 382 0.317436 TCGATTTTGTTGTGGCGCAC 60.317 50.0 10.83 6.37 34.56 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 4455 0.253327 GGTGGTGATGGAGAAGTCCC 59.747 60.0 0.0 0.0 43.15 4.46 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
51 54 3.869623 ATGTGCCCATGAGAGTGAC 57.130 52.632 0.00 0.00 0.00 3.67
90 93 2.416547 CCTATTGCACTCCGAAACACTG 59.583 50.000 0.00 0.00 0.00 3.66
97 100 0.671781 CTCCGAAACACTGCCTCTGG 60.672 60.000 0.00 0.00 0.00 3.86
115 118 6.205658 GCCTCTGGCCTTTAATATAAGACTTG 59.794 42.308 3.32 0.00 44.06 3.16
135 139 8.819974 AGACTTGTTGCAGTTTAATTCAAATTG 58.180 29.630 0.00 0.00 37.02 2.32
182 186 5.826643 TGGAGGGAGTAGCATTTTGTAAAT 58.173 37.500 0.00 0.00 0.00 1.40
183 187 6.964464 TGGAGGGAGTAGCATTTTGTAAATA 58.036 36.000 0.00 0.00 0.00 1.40
194 198 4.442375 TTTTGTAAATACCCATGCACCG 57.558 40.909 0.00 0.00 0.00 4.94
195 199 2.045561 TGTAAATACCCATGCACCGG 57.954 50.000 0.00 0.00 0.00 5.28
377 382 0.317436 TCGATTTTGTTGTGGCGCAC 60.317 50.000 10.83 6.37 34.56 5.34
514 2192 9.639601 CTCCACCAAAAATAAAAATCTAGTTCC 57.360 33.333 0.00 0.00 0.00 3.62
515 2193 9.374711 TCCACCAAAAATAAAAATCTAGTTCCT 57.625 29.630 0.00 0.00 0.00 3.36
516 2194 9.639601 CCACCAAAAATAAAAATCTAGTTCCTC 57.360 33.333 0.00 0.00 0.00 3.71
517 2195 9.639601 CACCAAAAATAAAAATCTAGTTCCTCC 57.360 33.333 0.00 0.00 0.00 4.30
518 2196 8.520351 ACCAAAAATAAAAATCTAGTTCCTCCG 58.480 33.333 0.00 0.00 0.00 4.63
519 2197 8.520351 CCAAAAATAAAAATCTAGTTCCTCCGT 58.480 33.333 0.00 0.00 0.00 4.69
520 2198 9.908152 CAAAAATAAAAATCTAGTTCCTCCGTT 57.092 29.630 0.00 0.00 0.00 4.44
522 2200 7.860918 AATAAAAATCTAGTTCCTCCGTTCC 57.139 36.000 0.00 0.00 0.00 3.62
523 2201 3.521947 AAATCTAGTTCCTCCGTTCCG 57.478 47.619 0.00 0.00 0.00 4.30
524 2202 2.431954 ATCTAGTTCCTCCGTTCCGA 57.568 50.000 0.00 0.00 0.00 4.55
525 2203 2.205022 TCTAGTTCCTCCGTTCCGAA 57.795 50.000 0.00 0.00 0.00 4.30
526 2204 2.731572 TCTAGTTCCTCCGTTCCGAAT 58.268 47.619 0.00 0.00 0.00 3.34
527 2205 3.094572 TCTAGTTCCTCCGTTCCGAATT 58.905 45.455 0.00 0.00 0.00 2.17
528 2206 4.272489 TCTAGTTCCTCCGTTCCGAATTA 58.728 43.478 0.00 0.00 0.00 1.40
529 2207 3.242549 AGTTCCTCCGTTCCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
530 2208 2.830321 AGTTCCTCCGTTCCGAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
531 2209 3.260128 AGTTCCTCCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
532 2210 3.241067 TCCTCCGTTCCGAATTACTTG 57.759 47.619 0.00 0.00 0.00 3.16
533 2211 2.564062 TCCTCCGTTCCGAATTACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
534 2212 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
535 2213 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
536 2214 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
537 2215 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
538 2216 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
539 2217 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
540 2218 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
541 2219 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
542 2220 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
543 2221 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
544 2222 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
545 2223 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
546 2224 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
547 2225 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
548 2226 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
549 2227 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
550 2228 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
551 2229 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
552 2230 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
553 2231 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
554 2232 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
555 2233 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
556 2234 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
557 2235 5.952347 TCGCAGGTATGGATGTATCTAGATT 59.048 40.000 11.25 0.00 0.00 2.40
558 2236 6.437477 TCGCAGGTATGGATGTATCTAGATTT 59.563 38.462 11.25 0.00 0.00 2.17
559 2237 7.614192 TCGCAGGTATGGATGTATCTAGATTTA 59.386 37.037 11.25 0.66 0.00 1.40
560 2238 8.417106 CGCAGGTATGGATGTATCTAGATTTAT 58.583 37.037 11.25 5.86 0.00 1.40
587 2265 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
588 2266 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
589 2267 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
590 2268 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
591 2269 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
592 2270 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
593 2271 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
594 2272 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
595 2273 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
596 2274 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
597 2275 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
598 2276 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
599 2277 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
600 2278 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
601 2279 4.092821 CCATTTCTGCGACGAGTAATTTGA 59.907 41.667 0.00 0.00 0.00 2.69
602 2280 5.390461 CCATTTCTGCGACGAGTAATTTGAA 60.390 40.000 0.00 0.00 0.00 2.69
603 2281 5.660629 TTTCTGCGACGAGTAATTTGAAA 57.339 34.783 0.00 0.00 0.00 2.69
604 2282 4.640805 TCTGCGACGAGTAATTTGAAAC 57.359 40.909 0.00 0.00 0.00 2.78
605 2283 3.120616 TCTGCGACGAGTAATTTGAAACG 59.879 43.478 0.00 0.00 0.00 3.60
606 2284 2.156117 TGCGACGAGTAATTTGAAACGG 59.844 45.455 0.00 0.00 0.00 4.44
607 2285 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
608 2286 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
609 2287 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
610 2288 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
611 2289 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
626 2304 3.304794 CGGAGGGAGTAGATAGAAAAGCG 60.305 52.174 0.00 0.00 0.00 4.68
902 2589 5.583061 CCGCTTACATCAAGTACATAAACCA 59.417 40.000 0.00 0.00 36.55 3.67
919 2608 8.909923 ACATAAACCATATAAACACCTTAAGGC 58.090 33.333 21.92 0.00 39.32 4.35
920 2609 6.785337 AAACCATATAAACACCTTAAGGCC 57.215 37.500 21.92 0.00 39.32 5.19
924 2613 2.188062 TAAACACCTTAAGGCCACCG 57.812 50.000 21.92 7.58 39.32 4.94
934 2631 2.045340 GGCCACCGCTTACACCAT 60.045 61.111 0.00 0.00 34.44 3.55
965 2662 1.005512 AATACACAGGCGCACGTCA 60.006 52.632 10.83 0.00 0.00 4.35
1427 3500 6.405278 TCGATTGATGCTTATAGAGGTTGA 57.595 37.500 0.00 0.00 0.00 3.18
1428 3501 6.816136 TCGATTGATGCTTATAGAGGTTGAA 58.184 36.000 0.00 0.00 0.00 2.69
1431 3504 7.867909 CGATTGATGCTTATAGAGGTTGAAGTA 59.132 37.037 0.00 0.00 0.00 2.24
1502 3586 4.214310 AGATCACACCCAAATTTGACACA 58.786 39.130 19.86 0.00 0.00 3.72
1504 3588 6.009589 AGATCACACCCAAATTTGACACATA 58.990 36.000 19.86 1.62 0.00 2.29
1507 3593 5.538053 TCACACCCAAATTTGACACATATGT 59.462 36.000 19.86 1.41 43.71 2.29
1538 3624 6.049955 AGACGGAATATTCTTCAGTTGGAA 57.950 37.500 14.95 0.00 0.00 3.53
1540 3626 7.112779 AGACGGAATATTCTTCAGTTGGAAAT 58.887 34.615 14.95 0.00 34.44 2.17
1543 3629 7.557719 ACGGAATATTCTTCAGTTGGAAATGAT 59.442 33.333 14.95 0.00 34.44 2.45
1556 3642 7.987458 CAGTTGGAAATGATGTACTATAGGTGT 59.013 37.037 4.43 0.00 0.00 4.16
1558 3644 7.669089 TGGAAATGATGTACTATAGGTGTCA 57.331 36.000 4.43 3.61 0.00 3.58
1583 3669 6.915544 TGATGACTTTGTCAATCTATCTGC 57.084 37.500 4.46 0.00 45.96 4.26
1618 3704 5.047590 TCTCGAATGTGCTTGTAAAGGTAGA 60.048 40.000 0.00 0.00 46.35 2.59
1632 3718 2.724454 AGGTAGAGTATGCGTGACTGT 58.276 47.619 0.00 0.00 0.00 3.55
1640 3726 4.816392 AGTATGCGTGACTGTGTTCATAA 58.184 39.130 0.00 0.00 0.00 1.90
1660 3746 4.386867 AAGGGATGAGTGTATGTACGTG 57.613 45.455 0.00 0.00 0.00 4.49
1663 3749 4.337555 AGGGATGAGTGTATGTACGTGTAC 59.662 45.833 0.00 3.21 36.63 2.90
1664 3750 4.277258 GGATGAGTGTATGTACGTGTACG 58.723 47.826 0.00 2.43 46.33 3.67
1707 3793 6.079763 CCGTGTCTCTCAAAAATACAATGTG 58.920 40.000 0.00 0.00 0.00 3.21
1799 3936 8.901472 ATATAAGATAGACTAGGATGTTGGCA 57.099 34.615 0.00 0.00 0.00 4.92
1803 3940 6.998802 AGATAGACTAGGATGTTGGCATTAC 58.001 40.000 0.00 0.00 35.07 1.89
1818 3955 5.381757 TGGCATTACCTTGTCTTGTACTTT 58.618 37.500 0.00 0.00 40.22 2.66
1869 4006 6.389091 TGTCCATGATGCTCAAACAATAAAC 58.611 36.000 0.00 0.00 0.00 2.01
1878 4015 9.362539 GATGCTCAAACAATAAACAATGATTCT 57.637 29.630 0.00 0.00 0.00 2.40
1932 4069 7.613585 TGTTATCAACCTAACCGATTCTAACA 58.386 34.615 0.00 0.00 31.83 2.41
1933 4070 8.095792 TGTTATCAACCTAACCGATTCTAACAA 58.904 33.333 0.00 0.00 31.83 2.83
1958 4234 1.813786 CCGGAGTTTTCTCTCTCTCGT 59.186 52.381 0.00 0.00 45.52 4.18
2054 4330 1.749638 CCGCACCTCTAGTCCGACT 60.750 63.158 6.25 6.25 0.00 4.18
2084 4360 0.673644 CAACCGGCCACTTCTTCGAT 60.674 55.000 0.00 0.00 0.00 3.59
2134 4410 2.280592 GGTCGTTGTCCGTGCCTT 60.281 61.111 0.00 0.00 37.94 4.35
2175 4451 1.901948 CTATCGCCGCCCTACTCCA 60.902 63.158 0.00 0.00 0.00 3.86
2179 4455 4.832608 GCCGCCCTACTCCAACCG 62.833 72.222 0.00 0.00 0.00 4.44
2184 4460 1.305887 CCCTACTCCAACCGGGACT 60.306 63.158 6.32 0.00 42.15 3.85
2190 4466 1.152204 TCCAACCGGGACTTCTCCA 60.152 57.895 6.32 0.00 42.15 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 11 4.067896 ACACAAAATCACTGACCTAGCTG 58.932 43.478 0.00 0.00 0.00 4.24
51 54 4.402528 TTGATGGTGTCCGGGCCG 62.403 66.667 21.46 21.46 0.00 6.13
97 100 7.762382 ACTGCAACAAGTCTTATATTAAAGGC 58.238 34.615 0.00 0.00 0.00 4.35
135 139 9.696917 CCATCCCTTAATATAAGACATTTTTGC 57.303 33.333 0.00 0.00 0.00 3.68
159 163 4.919774 TTACAAAATGCTACTCCCTCCA 57.080 40.909 0.00 0.00 0.00 3.86
194 198 4.023980 AGAAGGCTAAATAAAAGGGTGCC 58.976 43.478 0.00 0.00 39.19 5.01
195 199 5.886474 ACTAGAAGGCTAAATAAAAGGGTGC 59.114 40.000 0.00 0.00 0.00 5.01
518 2196 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
519 2197 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
520 2198 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
521 2199 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
522 2200 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
523 2201 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
524 2202 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
525 2203 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
526 2204 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
527 2205 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
528 2206 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
529 2207 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
530 2208 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
531 2209 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
532 2210 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
533 2211 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
534 2212 5.843673 ATCTAGATACATCCATACCTGCG 57.156 43.478 2.53 0.00 0.00 5.18
561 2239 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
562 2240 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
563 2241 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
564 2242 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
565 2243 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
566 2244 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
567 2245 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
568 2246 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
569 2247 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
570 2248 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
571 2249 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
572 2250 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
573 2251 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
574 2252 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
575 2253 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
576 2254 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
577 2255 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
578 2256 4.092821 TCAAATTACTCGTCGCAGAAATGG 59.907 41.667 0.00 0.00 39.69 3.16
579 2257 5.203358 TCAAATTACTCGTCGCAGAAATG 57.797 39.130 0.00 0.00 39.69 2.32
580 2258 5.856126 TTCAAATTACTCGTCGCAGAAAT 57.144 34.783 0.00 0.00 39.69 2.17
581 2259 5.437263 GTTTCAAATTACTCGTCGCAGAAA 58.563 37.500 0.00 0.00 39.69 2.52
582 2260 4.375606 CGTTTCAAATTACTCGTCGCAGAA 60.376 41.667 0.00 0.00 39.69 3.02
583 2261 3.120616 CGTTTCAAATTACTCGTCGCAGA 59.879 43.478 0.00 0.00 0.00 4.26
584 2262 3.395671 CGTTTCAAATTACTCGTCGCAG 58.604 45.455 0.00 0.00 0.00 5.18
585 2263 2.156117 CCGTTTCAAATTACTCGTCGCA 59.844 45.455 0.00 0.00 0.00 5.10
586 2264 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
587 2265 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
588 2266 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
589 2267 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
590 2268 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
591 2269 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
592 2270 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
593 2271 5.727434 TCTACTCCCTCCGTTTCAAATTAC 58.273 41.667 0.00 0.00 0.00 1.89
594 2272 6.555463 ATCTACTCCCTCCGTTTCAAATTA 57.445 37.500 0.00 0.00 0.00 1.40
595 2273 4.903045 TCTACTCCCTCCGTTTCAAATT 57.097 40.909 0.00 0.00 0.00 1.82
596 2274 5.897824 TCTATCTACTCCCTCCGTTTCAAAT 59.102 40.000 0.00 0.00 0.00 2.32
597 2275 5.266788 TCTATCTACTCCCTCCGTTTCAAA 58.733 41.667 0.00 0.00 0.00 2.69
598 2276 4.863548 TCTATCTACTCCCTCCGTTTCAA 58.136 43.478 0.00 0.00 0.00 2.69
599 2277 4.515028 TCTATCTACTCCCTCCGTTTCA 57.485 45.455 0.00 0.00 0.00 2.69
600 2278 5.848833 TTTCTATCTACTCCCTCCGTTTC 57.151 43.478 0.00 0.00 0.00 2.78
601 2279 5.395435 GCTTTTCTATCTACTCCCTCCGTTT 60.395 44.000 0.00 0.00 0.00 3.60
602 2280 4.099727 GCTTTTCTATCTACTCCCTCCGTT 59.900 45.833 0.00 0.00 0.00 4.44
603 2281 3.637694 GCTTTTCTATCTACTCCCTCCGT 59.362 47.826 0.00 0.00 0.00 4.69
604 2282 3.304794 CGCTTTTCTATCTACTCCCTCCG 60.305 52.174 0.00 0.00 0.00 4.63
605 2283 3.637694 ACGCTTTTCTATCTACTCCCTCC 59.362 47.826 0.00 0.00 0.00 4.30
606 2284 4.922471 ACGCTTTTCTATCTACTCCCTC 57.078 45.455 0.00 0.00 0.00 4.30
607 2285 4.828387 CCTACGCTTTTCTATCTACTCCCT 59.172 45.833 0.00 0.00 0.00 4.20
608 2286 4.583907 ACCTACGCTTTTCTATCTACTCCC 59.416 45.833 0.00 0.00 0.00 4.30
609 2287 5.521544 CACCTACGCTTTTCTATCTACTCC 58.478 45.833 0.00 0.00 0.00 3.85
610 2288 4.977347 GCACCTACGCTTTTCTATCTACTC 59.023 45.833 0.00 0.00 0.00 2.59
611 2289 4.497674 CGCACCTACGCTTTTCTATCTACT 60.498 45.833 0.00 0.00 0.00 2.57
626 2304 1.302192 TTGAAGCCCACGCACCTAC 60.302 57.895 0.00 0.00 37.52 3.18
836 2523 0.386113 GTCTAGGGTGACGATGCTCC 59.614 60.000 0.00 0.00 0.00 4.70
866 2553 0.245539 GTAAGCGGAGGCAGTGTACA 59.754 55.000 0.00 0.00 43.41 2.90
871 2558 0.613260 TTGATGTAAGCGGAGGCAGT 59.387 50.000 0.00 0.00 43.41 4.40
902 2589 4.457466 CGGTGGCCTTAAGGTGTTTATAT 58.543 43.478 22.55 0.00 37.57 0.86
909 2596 0.035820 TAAGCGGTGGCCTTAAGGTG 60.036 55.000 22.55 8.99 41.24 4.00
918 2607 2.461110 CGATGGTGTAAGCGGTGGC 61.461 63.158 0.00 0.00 36.92 5.01
919 2608 1.079405 ACGATGGTGTAAGCGGTGG 60.079 57.895 0.00 0.00 36.92 4.61
920 2609 1.966493 GCACGATGGTGTAAGCGGTG 61.966 60.000 9.74 0.00 46.13 4.94
924 2613 1.078426 AGGGCACGATGGTGTAAGC 60.078 57.895 9.74 0.00 46.13 3.09
934 2631 1.552792 TGTGTATTGATCAGGGCACGA 59.447 47.619 15.72 7.09 0.00 4.35
956 2653 1.351430 TTCTGCTGTATGACGTGCGC 61.351 55.000 0.00 0.00 0.00 6.09
965 2662 3.693085 CCTGTGATTTGCTTCTGCTGTAT 59.307 43.478 0.00 0.00 40.48 2.29
1324 3027 0.400213 TAACCCTGACAGCCACAAGG 59.600 55.000 0.00 0.00 38.23 3.61
1358 3062 8.071177 TCCTGTGATGATCATATATGAACGAT 57.929 34.615 19.03 12.01 40.69 3.73
1427 3500 5.065914 TGCTGAAGAATGTTGCTCTTACTT 58.934 37.500 0.00 0.00 33.24 2.24
1428 3501 4.645535 TGCTGAAGAATGTTGCTCTTACT 58.354 39.130 0.00 0.00 33.24 2.24
1431 3504 3.825014 ACATGCTGAAGAATGTTGCTCTT 59.175 39.130 0.00 0.00 41.43 2.85
1480 3560 4.214310 TGTGTCAAATTTGGGTGTGATCT 58.786 39.130 17.90 0.00 0.00 2.75
1517 3603 6.884295 TCATTTCCAACTGAAGAATATTCCGT 59.116 34.615 11.92 0.29 33.63 4.69
1534 3620 7.669089 TGACACCTATAGTACATCATTTCCA 57.331 36.000 0.00 0.00 0.00 3.53
1538 3624 9.716531 CATCATTGACACCTATAGTACATCATT 57.283 33.333 0.00 0.00 0.00 2.57
1540 3626 8.477419 TCATCATTGACACCTATAGTACATCA 57.523 34.615 0.00 0.00 0.00 3.07
1556 3642 9.106070 CAGATAGATTGACAAAGTCATCATTGA 57.894 33.333 0.12 0.00 42.40 2.57
1558 3644 7.013083 GGCAGATAGATTGACAAAGTCATCATT 59.987 37.037 0.12 0.00 42.40 2.57
1581 3667 1.545841 TTCGAGAGACTAAGCTGGCA 58.454 50.000 0.00 0.00 41.84 4.92
1583 3669 3.443037 CACATTCGAGAGACTAAGCTGG 58.557 50.000 0.00 0.00 41.84 4.85
1618 3704 2.812358 TGAACACAGTCACGCATACT 57.188 45.000 0.00 0.00 0.00 2.12
1632 3718 6.560003 ACATACACTCATCCCTTATGAACA 57.440 37.500 0.00 0.00 44.05 3.18
1640 3726 3.362706 ACACGTACATACACTCATCCCT 58.637 45.455 0.00 0.00 0.00 4.20
1684 3770 5.565259 GCACATTGTATTTTTGAGAGACACG 59.435 40.000 0.00 0.00 0.00 4.49
1687 3773 5.565259 CACGCACATTGTATTTTTGAGAGAC 59.435 40.000 0.00 0.00 0.00 3.36
1689 3775 4.321745 GCACGCACATTGTATTTTTGAGAG 59.678 41.667 0.00 0.00 0.00 3.20
1703 3789 0.527565 GAATCCCAAAGCACGCACAT 59.472 50.000 0.00 0.00 0.00 3.21
1707 3793 1.019278 TCTCGAATCCCAAAGCACGC 61.019 55.000 0.00 0.00 0.00 5.34
1774 3911 8.901472 TGCCAACATCCTAGTCTATCTTATAT 57.099 34.615 0.00 0.00 0.00 0.86
1793 3930 4.760204 AGTACAAGACAAGGTAATGCCAAC 59.240 41.667 0.00 0.00 40.61 3.77
1795 3932 4.634012 AGTACAAGACAAGGTAATGCCA 57.366 40.909 0.00 0.00 40.61 4.92
1797 3934 9.908152 AATTTAAAGTACAAGACAAGGTAATGC 57.092 29.630 0.00 0.00 0.00 3.56
1852 3989 9.362539 AGAATCATTGTTTATTGTTTGAGCATC 57.637 29.630 0.00 0.00 0.00 3.91
1905 4042 9.754382 GTTAGAATCGGTTAGGTTGATAACATA 57.246 33.333 0.00 0.00 37.38 2.29
1909 4046 9.104965 CATTGTTAGAATCGGTTAGGTTGATAA 57.895 33.333 0.00 0.00 0.00 1.75
1916 4053 5.405571 CGGATCATTGTTAGAATCGGTTAGG 59.594 44.000 0.00 0.00 0.00 2.69
1925 4062 6.472887 AGAAAACTCCGGATCATTGTTAGAA 58.527 36.000 3.57 0.00 0.00 2.10
1926 4063 6.049955 AGAAAACTCCGGATCATTGTTAGA 57.950 37.500 3.57 0.00 0.00 2.10
1928 4065 6.049955 AGAGAAAACTCCGGATCATTGTTA 57.950 37.500 3.57 0.00 0.00 2.41
1930 4067 4.223923 AGAGAGAAAACTCCGGATCATTGT 59.776 41.667 3.57 0.00 37.60 2.71
1932 4069 4.714308 AGAGAGAGAAAACTCCGGATCATT 59.286 41.667 3.57 0.00 37.60 2.57
1933 4070 4.285863 AGAGAGAGAAAACTCCGGATCAT 58.714 43.478 3.57 0.00 37.60 2.45
1958 4234 2.089936 CGCCGATCAAAACGACCGA 61.090 57.895 0.00 0.00 0.00 4.69
1973 4249 4.182339 TGGAAAACCAAAAAGTAAACGCC 58.818 39.130 0.00 0.00 0.00 5.68
2040 4316 4.959399 CGGAGTCGGACTAGAGGT 57.041 61.111 11.27 0.00 0.00 3.85
2066 4342 0.391263 GATCGAAGAAGTGGCCGGTT 60.391 55.000 1.90 0.00 43.58 4.44
2067 4343 1.218316 GATCGAAGAAGTGGCCGGT 59.782 57.895 1.90 0.00 43.58 5.28
2158 4434 1.456145 TTGGAGTAGGGCGGCGATA 60.456 57.895 12.98 0.00 0.00 2.92
2159 4435 2.762459 TTGGAGTAGGGCGGCGAT 60.762 61.111 12.98 0.00 0.00 4.58
2161 4437 4.832608 GGTTGGAGTAGGGCGGCG 62.833 72.222 0.51 0.51 0.00 6.46
2175 4451 0.613777 GTGATGGAGAAGTCCCGGTT 59.386 55.000 0.00 0.00 43.15 4.44
2179 4455 0.253327 GGTGGTGATGGAGAAGTCCC 59.747 60.000 0.00 0.00 43.15 4.46


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

AutoCloner maintained by Alex Coulton.