Multiple sequence alignment - TraesCS6A01G088000

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 TraesCS6A01G088000 chr6A 100.000 3156 0 0 1 3156 56133126 56136281 0.000000e+00 5829.0
1 TraesCS6A01G088000 chr6A 86.458 192 26 0 1481 1672 491027848 491028039 8.870000e-51 211.0
2 TraesCS6A01G088000 chr6A 81.159 138 21 4 2481 2615 60973950 60973815 4.310000e-19 106.0
3 TraesCS6A01G088000 chr6A 81.132 106 18 2 1374 1478 491027053 491027157 2.020000e-12 84.2
4 TraesCS6A01G088000 chr6B 90.374 2836 156 55 25 2798 92696308 92699088 0.000000e+00 3616.0
5 TraesCS6A01G088000 chr6B 85.938 192 27 0 1481 1672 527043570 527043761 4.130000e-49 206.0
6 TraesCS6A01G088000 chr6B 96.078 51 2 0 2800 2850 92699148 92699198 2.020000e-12 84.2
7 TraesCS6A01G088000 chrUn 92.087 2262 93 38 560 2798 20366393 20368591 0.000000e+00 3107.0
8 TraesCS6A01G088000 chrUn 91.971 274 8 4 2894 3156 20368796 20369066 3.840000e-99 372.0
9 TraesCS6A01G088000 chr2B 86.275 255 24 5 103 355 94652960 94652715 1.870000e-67 267.0
10 TraesCS6A01G088000 chr1D 84.586 266 27 7 93 355 438211207 438210953 5.230000e-63 252.0
11 TraesCS6A01G088000 chr1D 83.521 267 29 7 92 355 64729772 64729518 5.260000e-58 235.0
12 TraesCS6A01G088000 chr1D 83.333 114 13 5 2467 2575 52118687 52118799 2.000000e-17 100.0
13 TraesCS6A01G088000 chr3B 84.328 268 28 7 92 355 821290092 821289835 1.880000e-62 250.0
14 TraesCS6A01G088000 chr3B 84.328 268 28 8 92 355 821439513 821439256 1.880000e-62 250.0
15 TraesCS6A01G088000 chr2A 87.558 217 23 2 143 355 677158070 677157854 6.760000e-62 248.0
16 TraesCS6A01G088000 chr7B 89.175 194 21 0 162 355 116491757 116491564 3.140000e-60 243.0
17 TraesCS6A01G088000 chr7D 88.205 195 22 1 161 355 636339833 636339640 6.810000e-57 231.0
18 TraesCS6A01G088000 chr7D 79.688 128 24 2 2480 2605 585666012 585665885 1.210000e-14 91.6
19 TraesCS6A01G088000 chr7D 78.676 136 21 6 2480 2609 626901484 626901617 2.020000e-12 84.2
20 TraesCS6A01G088000 chr1B 82.900 269 31 7 92 355 179513810 179514068 8.810000e-56 228.0
21 TraesCS6A01G088000 chr1B 82.772 267 18 17 103 355 317201042 317200790 2.470000e-51 213.0
22 TraesCS6A01G088000 chr3A 82.500 280 21 16 92 355 423678836 423678569 1.470000e-53 220.0
23 TraesCS6A01G088000 chr5D 83.770 191 29 2 1481 1670 317453030 317452841 2.500000e-41 180.0
24 TraesCS6A01G088000 chr5D 83.582 134 17 3 2478 2606 513534141 513534274 1.540000e-23 121.0
25 TraesCS6A01G088000 chr5D 77.931 145 25 5 2477 2615 462454803 462454660 2.020000e-12 84.2
26 TraesCS6A01G088000 chr5B 83.770 191 29 2 1481 1670 367212629 367212440 2.500000e-41 180.0
27 TraesCS6A01G088000 chr5B 78.676 272 27 16 103 355 14411536 14411795 5.450000e-33 152.0
28 TraesCS6A01G088000 chr5A 83.770 191 29 2 1481 1670 412104193 412104004 2.500000e-41 180.0
29 TraesCS6A01G088000 chr4B 82.812 192 29 4 1481 1670 480590895 480591084 5.410000e-38 169.0
30 TraesCS6A01G088000 chr4A 82.812 192 29 4 1481 1670 72294418 72294607 5.410000e-38 169.0
31 TraesCS6A01G088000 chr6D 78.509 228 25 13 103 317 8556881 8556665 9.190000e-26 128.0
32 TraesCS6A01G088000 chr6D 87.234 94 7 3 2478 2569 403051641 403051551 5.570000e-18 102.0
33 TraesCS6A01G088000 chr6D 82.075 106 17 2 1374 1478 351971318 351971214 4.340000e-14 89.8


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 TraesCS6A01G088000 chr6A 56133126 56136281 3155 False 5829.0 5829 100.000 1 3156 1 chr6A.!!$F1 3155
1 TraesCS6A01G088000 chr6B 92696308 92699198 2890 False 1850.1 3616 93.226 25 2850 2 chr6B.!!$F2 2825
2 TraesCS6A01G088000 chrUn 20366393 20369066 2673 False 1739.5 3107 92.029 560 3156 2 chrUn.!!$F1 2596

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
68 69 0.179189 CCTCGTTCAGCAATTTCCGC 60.179 55.0 0.0 0.0 0.00 5.54 F
484 506 0.392461 TGCCAGGATTTACCGTGCTC 60.392 55.0 0.0 0.0 44.74 4.26 F
1233 1259 0.322975 GGTCATCCATCCATCCTCCG 59.677 60.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1244 0.192064 AGGACGGAGGATGGATGGAT 59.808 55.0 0.00 0.0 0.00 3.41 R
1826 1863 0.974525 AAGGGCCCGTAGTGGTAGTC 60.975 60.0 18.44 0.0 35.15 2.59 R
2582 2657 0.800683 ATTCGTTCGATCTTGCGCGA 60.801 50.0 12.10 0.0 34.32 5.87 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
52 53 1.817209 CCTGAAGAGCGGTACCCTC 59.183 63.158 17.92 17.92 0.00 4.30
67 68 0.447801 CCCTCGTTCAGCAATTTCCG 59.552 55.000 0.00 0.00 0.00 4.30
68 69 0.179189 CCTCGTTCAGCAATTTCCGC 60.179 55.000 0.00 0.00 0.00 5.54
69 70 0.516877 CTCGTTCAGCAATTTCCGCA 59.483 50.000 0.00 0.00 0.00 5.69
70 71 0.516877 TCGTTCAGCAATTTCCGCAG 59.483 50.000 0.00 0.00 0.00 5.18
71 72 1.067199 CGTTCAGCAATTTCCGCAGC 61.067 55.000 0.00 0.00 0.00 5.25
80 84 1.298859 ATTTCCGCAGCAACGACCTC 61.299 55.000 0.00 0.00 34.06 3.85
93 97 1.518774 GACCTCGCCGTTCCCATTA 59.481 57.895 0.00 0.00 0.00 1.90
112 118 2.761786 AGGGAATGCATGGTGCTATT 57.238 45.000 0.00 2.16 45.31 1.73
142 148 5.132648 AGTGCCACCTAGGATAAATGATGAA 59.867 40.000 17.98 0.00 41.22 2.57
143 149 5.827797 GTGCCACCTAGGATAAATGATGAAA 59.172 40.000 17.98 0.00 41.22 2.69
144 150 6.321181 GTGCCACCTAGGATAAATGATGAAAA 59.679 38.462 17.98 0.00 41.22 2.29
145 151 7.014615 GTGCCACCTAGGATAAATGATGAAAAT 59.985 37.037 17.98 0.00 41.22 1.82
146 152 8.224025 TGCCACCTAGGATAAATGATGAAAATA 58.776 33.333 17.98 0.00 41.22 1.40
147 153 9.077885 GCCACCTAGGATAAATGATGAAAATAA 57.922 33.333 17.98 0.00 41.22 1.40
159 165 9.880157 AAATGATGAAAATAATGAGGTGGAAAG 57.120 29.630 0.00 0.00 0.00 2.62
163 169 6.789268 TGAAAATAATGAGGTGGAAAGGAGA 58.211 36.000 0.00 0.00 0.00 3.71
164 170 6.886459 TGAAAATAATGAGGTGGAAAGGAGAG 59.114 38.462 0.00 0.00 0.00 3.20
167 173 6.642733 ATAATGAGGTGGAAAGGAGAGAAA 57.357 37.500 0.00 0.00 0.00 2.52
170 176 6.642733 ATGAGGTGGAAAGGAGAGAAATTA 57.357 37.500 0.00 0.00 0.00 1.40
171 177 6.642733 TGAGGTGGAAAGGAGAGAAATTAT 57.357 37.500 0.00 0.00 0.00 1.28
174 180 8.611257 TGAGGTGGAAAGGAGAGAAATTATAAA 58.389 33.333 0.00 0.00 0.00 1.40
291 297 9.396022 ACTAAAAGATAACCCATTGTAGACATG 57.604 33.333 0.00 0.00 0.00 3.21
364 379 5.725551 ATCAACCATTGTATAAGACCCCA 57.274 39.130 0.00 0.00 0.00 4.96
366 381 3.945640 ACCATTGTATAAGACCCCACC 57.054 47.619 0.00 0.00 0.00 4.61
373 388 3.275497 TGTATAAGACCCCACCCTCCTTA 59.725 47.826 0.00 0.00 0.00 2.69
383 398 0.690077 ACCCTCCTTATCCCGTGTCC 60.690 60.000 0.00 0.00 0.00 4.02
385 400 1.041447 CCTCCTTATCCCGTGTCCGT 61.041 60.000 0.00 0.00 0.00 4.69
388 403 2.026641 TCCTTATCCCGTGTCCGTAAG 58.973 52.381 0.00 0.00 0.00 2.34
404 419 3.581755 CGTAAGGAAAGATTGGTCGACA 58.418 45.455 18.91 0.00 0.00 4.35
423 442 7.254084 GGTCGACATTGATTTTGATTATTTGGC 60.254 37.037 18.91 0.00 0.00 4.52
426 445 8.605746 CGACATTGATTTTGATTATTTGGCAAT 58.394 29.630 0.00 0.00 0.00 3.56
438 457 3.648339 TTTGGCAATTCTCTTGAGCAC 57.352 42.857 0.00 0.00 0.00 4.40
445 464 2.010145 TTCTCTTGAGCACGGCATAC 57.990 50.000 0.00 0.00 0.00 2.39
484 506 0.392461 TGCCAGGATTTACCGTGCTC 60.392 55.000 0.00 0.00 44.74 4.26
499 521 2.159599 CGTGCTCTGAGAAGGAATTTGC 60.160 50.000 9.28 0.00 0.00 3.68
502 524 3.022406 GCTCTGAGAAGGAATTTGCCAT 58.978 45.455 9.28 0.00 0.00 4.40
521 543 4.576463 GCCATCCTCGAGACAATGTAAATT 59.424 41.667 15.71 0.00 0.00 1.82
523 545 6.292919 GCCATCCTCGAGACAATGTAAATTAC 60.293 42.308 15.71 0.00 0.00 1.89
527 549 6.312918 TCCTCGAGACAATGTAAATTACAAGC 59.687 38.462 15.71 0.69 42.76 4.01
530 552 6.034577 TCGAGACAATGTAAATTACAAGCTCG 59.965 38.462 25.80 25.80 42.76 5.03
531 553 5.869350 AGACAATGTAAATTACAAGCTCGC 58.131 37.500 10.09 0.00 42.76 5.03
537 559 6.984740 TGTAAATTACAAGCTCGCAAAAAG 57.015 33.333 2.97 0.00 35.38 2.27
538 560 6.730175 TGTAAATTACAAGCTCGCAAAAAGA 58.270 32.000 2.97 0.00 35.38 2.52
539 561 7.197017 TGTAAATTACAAGCTCGCAAAAAGAA 58.803 30.769 2.97 0.00 35.38 2.52
540 562 7.702772 TGTAAATTACAAGCTCGCAAAAAGAAA 59.297 29.630 2.97 0.00 35.38 2.52
541 563 7.532682 AAATTACAAGCTCGCAAAAAGAAAA 57.467 28.000 0.00 0.00 0.00 2.29
542 564 7.713764 AATTACAAGCTCGCAAAAAGAAAAT 57.286 28.000 0.00 0.00 0.00 1.82
601 623 1.507141 CCCAGGAACGTCAGCACAAC 61.507 60.000 0.00 0.00 0.00 3.32
605 627 1.083401 GAACGTCAGCACAACAGCG 60.083 57.895 0.00 0.00 40.15 5.18
609 631 1.279840 GTCAGCACAACAGCGTTCC 59.720 57.895 0.00 0.00 40.15 3.62
615 637 1.268352 GCACAACAGCGTTCCCATTTA 59.732 47.619 0.00 0.00 0.00 1.40
617 639 3.613910 GCACAACAGCGTTCCCATTTATT 60.614 43.478 0.00 0.00 0.00 1.40
618 640 4.555262 CACAACAGCGTTCCCATTTATTT 58.445 39.130 0.00 0.00 0.00 1.40
619 641 5.704888 CACAACAGCGTTCCCATTTATTTA 58.295 37.500 0.00 0.00 0.00 1.40
623 645 7.875554 ACAACAGCGTTCCCATTTATTTATTTT 59.124 29.630 0.00 0.00 0.00 1.82
648 670 2.196997 CTGAATCCGTCCCTGGCCAA 62.197 60.000 7.01 0.00 0.00 4.52
652 674 3.953775 CCGTCCCTGGCCAACTGT 61.954 66.667 7.01 0.00 0.00 3.55
653 675 2.113139 CGTCCCTGGCCAACTGTT 59.887 61.111 7.01 0.00 0.00 3.16
688 710 4.199130 CGCGTCCGTTTCCAAAAC 57.801 55.556 0.00 0.00 0.00 2.43
699 721 4.450757 CCGTTTCCAAAACAATTTCCATCC 59.549 41.667 3.72 0.00 0.00 3.51
751 773 1.573108 AGCTAAGCAGACCTAAGCCA 58.427 50.000 0.00 0.00 33.63 4.75
829 851 1.079057 GTTTCTCCACCTCCGCCTC 60.079 63.158 0.00 0.00 0.00 4.70
937 962 8.429641 CCAGGAAATAGCTTTAGTATAGTTCCA 58.570 37.037 17.49 0.00 42.99 3.53
955 981 0.469070 CATCCAAGCAGAGGAGAGGG 59.531 60.000 0.00 0.00 38.83 4.30
1218 1244 1.497278 GTACGTACGAGTGCGGTCA 59.503 57.895 24.41 0.60 42.92 4.02
1233 1259 0.322975 GGTCATCCATCCATCCTCCG 59.677 60.000 0.00 0.00 0.00 4.63
1342 1375 3.657625 GTCTGTTTTTCATGCAACGTACG 59.342 43.478 15.01 15.01 0.00 3.67
1343 1376 3.310227 TCTGTTTTTCATGCAACGTACGT 59.690 39.130 16.72 16.72 0.00 3.57
1345 1378 3.063588 TGTTTTTCATGCAACGTACGTCA 59.936 39.130 23.05 16.68 0.00 4.35
1346 1379 3.513462 TTTTCATGCAACGTACGTCAG 57.487 42.857 23.05 17.97 0.00 3.51
1347 1380 2.143008 TTCATGCAACGTACGTCAGT 57.857 45.000 23.05 2.76 0.00 3.41
1348 1381 2.143008 TCATGCAACGTACGTCAGTT 57.857 45.000 23.05 2.32 0.00 3.16
1349 1382 3.285816 TCATGCAACGTACGTCAGTTA 57.714 42.857 23.05 11.03 0.00 2.24
1406 1443 0.597637 CATCTCGTCGGCCATGTACC 60.598 60.000 2.24 0.00 0.00 3.34
2005 2042 0.608130 AGCGCAACATGGTCTACTCA 59.392 50.000 11.47 0.00 0.00 3.41
2203 2255 6.744112 TCTTCTCTTCTCTTCTCTTGTGTTC 58.256 40.000 0.00 0.00 0.00 3.18
2275 2327 2.300956 TTTGGCAGTAGCATCCCAAA 57.699 45.000 0.00 0.00 43.05 3.28
2331 2383 3.952174 GCACATTGCATGAAAACGTAC 57.048 42.857 0.00 0.00 44.26 3.67
2332 2384 2.338228 GCACATTGCATGAAAACGTACG 59.662 45.455 15.01 15.01 44.26 3.67
2372 2430 1.284313 CCTTCCTTCCTCCTCTGCTT 58.716 55.000 0.00 0.00 0.00 3.91
2434 2501 1.070643 CGTGGGGAAAAACGTACGTTC 60.071 52.381 31.79 20.36 37.35 3.95
2471 2538 4.445452 TGAAAAGCTACGTCGGACTAAT 57.555 40.909 6.57 0.00 0.00 1.73
2493 2560 3.887916 TTTTAAGGGTGTGGCTAGGTT 57.112 42.857 0.00 0.00 0.00 3.50
2495 2562 3.887916 TTAAGGGTGTGGCTAGGTTTT 57.112 42.857 0.00 0.00 0.00 2.43
2503 2570 3.501062 GTGTGGCTAGGTTTTAGTTGACC 59.499 47.826 0.00 0.00 36.15 4.02
2505 2572 4.139038 GTGGCTAGGTTTTAGTTGACCAA 58.861 43.478 0.00 0.00 38.42 3.67
2616 2695 9.395707 GATCGAACGAATATAGTATTCACTGTT 57.604 33.333 0.12 6.06 36.14 3.16
2628 2707 7.897575 AGTATTCACTGTTGATTGAGACTTC 57.102 36.000 0.00 0.00 32.25 3.01
2629 2708 5.852738 ATTCACTGTTGATTGAGACTTCG 57.147 39.130 0.00 0.00 0.00 3.79
2632 2711 1.391485 CTGTTGATTGAGACTTCGGCG 59.609 52.381 0.00 0.00 0.00 6.46
2638 2717 4.250464 TGATTGAGACTTCGGCGTAATTT 58.750 39.130 6.85 0.00 0.00 1.82
2691 2770 1.110442 TCAACACTGCTTTTGGGTGG 58.890 50.000 0.00 0.00 35.53 4.61
2773 2855 2.287915 GGCGCGAATATCTGTGTGAATT 59.712 45.455 12.10 0.00 0.00 2.17
2806 2948 5.346551 TGTGACTTCATTGTTATAACCGTCG 59.653 40.000 13.01 0.00 0.00 5.12
2842 2984 4.568072 AAAGTTTTGGAAGCCTGGTTTT 57.432 36.364 0.00 0.00 0.00 2.43
2869 3011 3.756933 AAAGGTCATGCTTGCAAACAT 57.243 38.095 9.53 9.53 0.00 2.71
2889 3031 7.524717 AACATACCACTGCTGAAATAGTTTT 57.475 32.000 0.00 0.00 0.00 2.43
2890 3032 7.524717 ACATACCACTGCTGAAATAGTTTTT 57.475 32.000 0.00 0.00 0.00 1.94
2891 3033 7.593825 ACATACCACTGCTGAAATAGTTTTTC 58.406 34.615 0.00 0.00 0.00 2.29
2892 3034 5.453567 ACCACTGCTGAAATAGTTTTTCC 57.546 39.130 0.00 0.00 0.00 3.13
3034 3230 5.487153 TTACGCTTGTGTTACATGTGTTT 57.513 34.783 9.11 0.23 42.03 2.83
3039 3235 4.970003 GCTTGTGTTACATGTGTTTGACTC 59.030 41.667 9.11 1.70 0.00 3.36
3047 3243 2.799126 TGTGTTTGACTCCAACACCT 57.201 45.000 18.70 0.00 35.45 4.00
3048 3244 2.639065 TGTGTTTGACTCCAACACCTC 58.361 47.619 18.70 1.06 35.45 3.85
3087 3290 9.301153 CAAGTTGTGGCCTTTTACAAATATATC 57.699 33.333 3.32 0.00 38.40 1.63
3095 3298 7.608761 GGCCTTTTACAAATATATCGGATACCA 59.391 37.037 0.00 0.00 0.00 3.25
3129 3332 7.730364 AACTTCATCTTAACGAACATGTCTT 57.270 32.000 0.00 0.00 0.00 3.01
3130 3333 7.730364 ACTTCATCTTAACGAACATGTCTTT 57.270 32.000 0.00 0.00 0.00 2.52
3131 3334 7.576236 ACTTCATCTTAACGAACATGTCTTTG 58.424 34.615 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.491635 GCTCAAACTAAAGCCTATGGAAG 57.508 43.478 0.00 0.00 32.22 3.46
21 22 3.120025 GCTCTTCAGGCTCAAACTAAAGC 60.120 47.826 0.00 0.00 37.80 3.51
22 23 3.124297 CGCTCTTCAGGCTCAAACTAAAG 59.876 47.826 0.00 0.00 0.00 1.85
23 24 3.067106 CGCTCTTCAGGCTCAAACTAAA 58.933 45.455 0.00 0.00 0.00 1.85
31 32 1.142097 GGTACCGCTCTTCAGGCTC 59.858 63.158 0.00 0.00 0.00 4.70
32 33 2.359967 GGGTACCGCTCTTCAGGCT 61.360 63.158 5.65 0.00 40.86 4.58
52 53 1.067199 GCTGCGGAAATTGCTGAACG 61.067 55.000 0.00 0.00 33.64 3.95
100 104 3.243201 GCACTCCTAAAATAGCACCATGC 60.243 47.826 0.00 0.00 45.46 4.06
101 105 3.316308 GGCACTCCTAAAATAGCACCATG 59.684 47.826 0.00 0.00 0.00 3.66
142 148 6.642733 TCTCTCCTTTCCACCTCATTATTT 57.357 37.500 0.00 0.00 0.00 1.40
143 149 6.642733 TTCTCTCCTTTCCACCTCATTATT 57.357 37.500 0.00 0.00 0.00 1.40
144 150 6.642733 TTTCTCTCCTTTCCACCTCATTAT 57.357 37.500 0.00 0.00 0.00 1.28
145 151 6.642733 ATTTCTCTCCTTTCCACCTCATTA 57.357 37.500 0.00 0.00 0.00 1.90
146 152 5.527026 ATTTCTCTCCTTTCCACCTCATT 57.473 39.130 0.00 0.00 0.00 2.57
147 153 5.527026 AATTTCTCTCCTTTCCACCTCAT 57.473 39.130 0.00 0.00 0.00 2.90
148 154 6.642733 ATAATTTCTCTCCTTTCCACCTCA 57.357 37.500 0.00 0.00 0.00 3.86
149 155 9.462606 TTTTATAATTTCTCTCCTTTCCACCTC 57.537 33.333 0.00 0.00 0.00 3.85
150 156 9.822727 TTTTTATAATTTCTCTCCTTTCCACCT 57.177 29.630 0.00 0.00 0.00 4.00
263 269 8.822805 TGTCTACAATGGGTTATCTTTTAGTCT 58.177 33.333 0.00 0.00 0.00 3.24
265 271 9.396022 CATGTCTACAATGGGTTATCTTTTAGT 57.604 33.333 0.00 0.00 0.00 2.24
270 276 8.650143 AAAACATGTCTACAATGGGTTATCTT 57.350 30.769 0.00 0.00 0.00 2.40
299 305 8.430801 AGTCTTGCATGTAATTTAGAGATGAC 57.569 34.615 0.00 0.00 0.00 3.06
355 361 2.361070 GGATAAGGAGGGTGGGGTCTTA 60.361 54.545 0.00 0.00 0.00 2.10
357 363 0.029989 GGATAAGGAGGGTGGGGTCT 60.030 60.000 0.00 0.00 0.00 3.85
364 379 0.690077 GGACACGGGATAAGGAGGGT 60.690 60.000 0.00 0.00 0.00 4.34
366 381 1.041447 ACGGACACGGGATAAGGAGG 61.041 60.000 0.00 0.00 46.48 4.30
373 388 1.206371 CTTTCCTTACGGACACGGGAT 59.794 52.381 0.00 0.00 46.48 3.85
383 398 3.581755 TGTCGACCAATCTTTCCTTACG 58.418 45.455 14.12 0.00 0.00 3.18
385 400 5.800296 TCAATGTCGACCAATCTTTCCTTA 58.200 37.500 14.12 0.00 0.00 2.69
388 403 5.567138 AATCAATGTCGACCAATCTTTCC 57.433 39.130 14.12 0.00 0.00 3.13
396 411 7.758980 CCAAATAATCAAAATCAATGTCGACCA 59.241 33.333 14.12 1.26 0.00 4.02
423 442 1.159285 TGCCGTGCTCAAGAGAATTG 58.841 50.000 0.32 0.00 0.00 2.32
426 445 1.405526 GGTATGCCGTGCTCAAGAGAA 60.406 52.381 0.32 0.00 0.00 2.87
428 447 0.811616 GGGTATGCCGTGCTCAAGAG 60.812 60.000 0.00 0.00 34.97 2.85
465 487 0.392461 GAGCACGGTAAATCCTGGCA 60.392 55.000 0.00 0.00 36.04 4.92
476 498 1.270907 ATTCCTTCTCAGAGCACGGT 58.729 50.000 0.00 0.00 0.00 4.83
484 506 3.629087 AGGATGGCAAATTCCTTCTCAG 58.371 45.455 2.22 0.00 39.36 3.35
499 521 6.761242 TGTAATTTACATTGTCTCGAGGATGG 59.239 38.462 13.56 1.64 32.89 3.51
502 524 6.312918 GCTTGTAATTTACATTGTCTCGAGGA 59.687 38.462 13.56 0.00 38.68 3.71
521 543 7.075741 GTCTATTTTCTTTTTGCGAGCTTGTA 58.924 34.615 2.14 0.00 0.00 2.41
523 545 5.914635 TGTCTATTTTCTTTTTGCGAGCTTG 59.085 36.000 0.00 0.00 0.00 4.01
527 549 7.858052 ACATTGTCTATTTTCTTTTTGCGAG 57.142 32.000 0.00 0.00 0.00 5.03
540 562 8.665685 GGACGTTTCTCATTTACATTGTCTATT 58.334 33.333 0.00 0.00 0.00 1.73
541 563 7.822334 TGGACGTTTCTCATTTACATTGTCTAT 59.178 33.333 0.00 0.00 0.00 1.98
542 564 7.156000 TGGACGTTTCTCATTTACATTGTCTA 58.844 34.615 0.00 0.00 0.00 2.59
555 577 2.302260 TGGCAAAATGGACGTTTCTCA 58.698 42.857 0.00 0.00 0.00 3.27
601 623 7.435192 GGAGAAAATAAATAAATGGGAACGCTG 59.565 37.037 0.00 0.00 0.00 5.18
605 627 8.204160 CAGGGGAGAAAATAAATAAATGGGAAC 58.796 37.037 0.00 0.00 0.00 3.62
609 631 9.987272 GATTCAGGGGAGAAAATAAATAAATGG 57.013 33.333 0.00 0.00 0.00 3.16
615 637 5.766590 ACGGATTCAGGGGAGAAAATAAAT 58.233 37.500 0.00 0.00 0.00 1.40
617 639 4.384868 GGACGGATTCAGGGGAGAAAATAA 60.385 45.833 0.00 0.00 0.00 1.40
618 640 3.135895 GGACGGATTCAGGGGAGAAAATA 59.864 47.826 0.00 0.00 0.00 1.40
619 641 2.092375 GGACGGATTCAGGGGAGAAAAT 60.092 50.000 0.00 0.00 0.00 1.82
623 645 1.382695 GGGACGGATTCAGGGGAGA 60.383 63.158 0.00 0.00 0.00 3.71
648 670 6.157211 CGTACAAGGAAACTATCTCAACAGT 58.843 40.000 0.00 0.00 42.68 3.55
652 674 4.171005 CGCGTACAAGGAAACTATCTCAA 58.829 43.478 0.00 0.00 42.68 3.02
653 675 3.192001 ACGCGTACAAGGAAACTATCTCA 59.808 43.478 11.67 0.00 42.68 3.27
684 706 1.708822 GCGCGGATGGAAATTGTTTT 58.291 45.000 8.83 0.00 0.00 2.43
688 710 1.297598 GACGCGCGGATGGAAATTG 60.298 57.895 35.22 1.22 0.00 2.32
737 759 3.256281 GCTTTGGCTTAGGTCTGCT 57.744 52.632 0.00 0.00 35.22 4.24
751 773 5.163395 CGGAGAAATAGGAGGAGTTAGCTTT 60.163 44.000 0.00 0.00 0.00 3.51
829 851 2.315176 TCTTGGGTGGGTGACAAATTG 58.685 47.619 0.00 0.00 0.00 2.32
934 959 1.493861 CTCTCCTCTGCTTGGATGGA 58.506 55.000 0.00 0.00 32.56 3.41
937 962 0.693767 CCCCTCTCCTCTGCTTGGAT 60.694 60.000 0.00 0.00 32.56 3.41
955 981 2.601966 ATCGATCCCCTCTCCGCC 60.602 66.667 0.00 0.00 0.00 6.13
1218 1244 0.192064 AGGACGGAGGATGGATGGAT 59.808 55.000 0.00 0.00 0.00 3.41
1292 1320 3.442625 CCCCAGAAATTAACGGAGGAAAC 59.557 47.826 0.00 0.00 0.00 2.78
1349 1382 8.986991 TGCCCATTTTAATTACCATTAACTGAT 58.013 29.630 0.00 0.00 35.05 2.90
1471 1508 1.611592 CGCCGTTGGACGTGTAGAAC 61.612 60.000 0.00 0.00 40.58 3.01
1789 1826 2.840753 GGAGGTGGCCCAGTTGGAA 61.841 63.158 0.00 0.00 37.39 3.53
1825 1862 1.380920 GGGCCCGTAGTGGTAGTCT 60.381 63.158 5.69 0.00 35.15 3.24
1826 1863 0.974525 AAGGGCCCGTAGTGGTAGTC 60.975 60.000 18.44 0.00 35.15 2.59
2203 2255 5.473504 CCCAAATCTCCGTCCCTAATTAATG 59.526 44.000 0.00 0.00 0.00 1.90
2275 2327 1.234615 CGTGTCACCCAAATTCCGCT 61.235 55.000 0.00 0.00 0.00 5.52
2346 2399 1.201429 GGAGGAAGGAAGGGAGCACA 61.201 60.000 0.00 0.00 0.00 4.57
2372 2430 2.592993 CGGTGGGGGAGAAGAGCAA 61.593 63.158 0.00 0.00 0.00 3.91
2392 2454 1.452108 CCTGAAACGGAGCCCATCC 60.452 63.158 0.00 0.00 45.64 3.51
2420 2486 5.333046 TCCAGAATGAACGTACGTTTTTC 57.667 39.130 32.14 31.12 39.69 2.29
2434 2501 7.958053 AGCTTTTCAAAGAAAATCCAGAATG 57.042 32.000 3.35 0.00 38.28 2.67
2476 2543 3.911894 ACTAAAACCTAGCCACACCCTTA 59.088 43.478 0.00 0.00 0.00 2.69
2493 2560 8.528044 ACTTGGTTAAATCTTGGTCAACTAAA 57.472 30.769 0.00 0.00 0.00 1.85
2495 2562 7.514721 AGACTTGGTTAAATCTTGGTCAACTA 58.485 34.615 0.00 0.00 0.00 2.24
2503 2570 7.227512 ACTTGACTGAGACTTGGTTAAATCTTG 59.772 37.037 0.00 0.00 0.00 3.02
2505 2572 6.708054 CACTTGACTGAGACTTGGTTAAATCT 59.292 38.462 0.00 0.00 0.00 2.40
2552 2627 9.934190 TCTTTGCAAAATTTTCATTTTAGCTTC 57.066 25.926 13.84 0.00 40.09 3.86
2562 2637 5.900789 CGCGAAAATCTTTGCAAAATTTTCA 59.099 32.000 34.82 14.63 44.16 2.69
2580 2655 1.004785 TCGTTCGATCTTGCGCGAAA 61.005 50.000 12.10 4.03 46.45 3.46
2582 2657 0.800683 ATTCGTTCGATCTTGCGCGA 60.801 50.000 12.10 0.00 34.32 5.87
2584 2659 3.669122 ACTATATTCGTTCGATCTTGCGC 59.331 43.478 0.00 0.00 0.00 6.09
2616 2695 3.520290 ATTACGCCGAAGTCTCAATCA 57.480 42.857 0.00 0.00 0.00 2.57
2790 2873 5.220529 GGAAACTCCGACGGTTATAACAATG 60.221 44.000 14.79 8.71 0.00 2.82
2798 2881 2.242043 AGAAGGAAACTCCGACGGTTA 58.758 47.619 14.79 0.00 42.75 2.85
2806 2948 7.778083 TCCAAAACTTTTTAGAAGGAAACTCC 58.222 34.615 0.00 0.00 42.68 3.85
2842 2984 7.712639 TGTTTGCAAGCATGACCTTTTAAAATA 59.287 29.630 12.36 0.00 0.00 1.40
2869 3011 5.475564 GGGAAAAACTATTTCAGCAGTGGTA 59.524 40.000 0.00 0.00 0.00 3.25
2889 3031 9.812347 ATCATTATGCTATGTTGATTTAGGGAA 57.188 29.630 0.00 0.00 0.00 3.97
2890 3032 9.234827 CATCATTATGCTATGTTGATTTAGGGA 57.765 33.333 0.00 0.00 30.33 4.20
2950 3146 2.286831 GCTTCAAGATGATGCGATGGTG 60.287 50.000 2.99 0.00 37.70 4.17
3015 3211 3.723764 GTCAAACACATGTAACACAAGCG 59.276 43.478 0.00 0.00 0.00 4.68
3034 3230 3.239449 ACTATGTGAGGTGTTGGAGTCA 58.761 45.455 0.00 0.00 0.00 3.41
3039 3235 5.977635 TGATTAGACTATGTGAGGTGTTGG 58.022 41.667 0.00 0.00 0.00 3.77
3047 3243 5.874810 GCCACAACTTGATTAGACTATGTGA 59.125 40.000 10.37 0.00 39.30 3.58
3048 3244 5.065218 GGCCACAACTTGATTAGACTATGTG 59.935 44.000 0.00 3.99 37.31 3.21
3087 3290 7.328277 TGAAGTTTATTGGAATTGGTATCCG 57.672 36.000 0.00 0.00 39.98 4.18
3127 3330 5.008415 AGCTGACAACTTCAAGATGACAAAG 59.992 40.000 0.93 0.00 32.21 2.77
3129 3332 4.454678 AGCTGACAACTTCAAGATGACAA 58.545 39.130 0.93 0.00 32.21 3.18
3130 3333 4.077300 AGCTGACAACTTCAAGATGACA 57.923 40.909 0.93 0.61 32.21 3.58
3131 3334 5.028428 GAAGCTGACAACTTCAAGATGAC 57.972 43.478 12.68 0.00 42.53 3.06


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

AutoCloner maintained by Alex Coulton.