Multiple sequence alignment - TraesCS3D01G207500

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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 TraesCS3D01G207500 chr3D 100.000 6450 0 0 1 6450 273461985 273468434 0.000000e+00 11912.0
1 TraesCS3D01G207500 chr3D 93.750 48 3 0 4399 4446 219571979 219572026 8.970000e-09 73.1
2 TraesCS3D01G207500 chr3A 97.796 2768 47 10 3251 6008 357064457 357067220 0.000000e+00 4761.0
3 TraesCS3D01G207500 chr3A 97.770 2421 48 3 840 3255 357061917 357064336 0.000000e+00 4167.0
4 TraesCS3D01G207500 chr3A 91.923 260 11 5 6004 6261 357077796 357078047 7.950000e-94 355.0
5 TraesCS3D01G207500 chr3A 93.229 192 12 1 6260 6450 357078296 357078487 1.370000e-71 281.0
6 TraesCS3D01G207500 chr3B 97.559 2294 41 7 2729 5019 360112167 360109886 0.000000e+00 3912.0
7 TraesCS3D01G207500 chr3B 97.540 1829 39 6 793 2620 360114489 360112666 0.000000e+00 3123.0
8 TraesCS3D01G207500 chr3B 97.971 1232 23 2 5011 6241 360109811 360108581 0.000000e+00 2135.0
9 TraesCS3D01G207500 chr3B 83.709 755 111 5 2 744 252665487 252666241 0.000000e+00 702.0
10 TraesCS3D01G207500 chr3B 98.438 192 3 0 6259 6450 360108217 360108026 8.010000e-89 339.0
11 TraesCS3D01G207500 chr3B 97.391 115 2 1 2616 2730 360112362 360112249 1.830000e-45 195.0
12 TraesCS3D01G207500 chr3B 87.805 82 8 2 292 372 72097785 72097865 1.910000e-15 95.3
13 TraesCS3D01G207500 chr3B 84.615 78 10 2 293 369 176427299 176427375 6.930000e-10 76.8
14 TraesCS3D01G207500 chr1D 80.132 760 134 13 2 747 302270926 302270170 9.450000e-153 551.0
15 TraesCS3D01G207500 chr1D 97.619 42 1 0 4405 4446 95867019 95866978 8.970000e-09 73.1
16 TraesCS3D01G207500 chr7D 92.287 376 24 4 3298 3668 162224143 162223768 4.430000e-146 529.0
17 TraesCS3D01G207500 chr5A 79.524 757 142 8 3 747 277344647 277343892 1.590000e-145 527.0
18 TraesCS3D01G207500 chr2D 83.603 494 81 0 86 579 304273847 304274340 1.270000e-126 464.0
19 TraesCS3D01G207500 chr5D 100.000 41 0 0 4406 4446 256458083 256458043 6.930000e-10 76.8
20 TraesCS3D01G207500 chr1B 97.674 43 1 0 4404 4446 156852523 156852565 2.490000e-09 75.0
21 TraesCS3D01G207500 chr5B 91.071 56 2 3 4391 4446 290386302 290386250 8.970000e-09 73.1
22 TraesCS3D01G207500 chr2B 97.619 42 1 0 4405 4446 69342457 69342498 8.970000e-09 73.1
23 TraesCS3D01G207500 chr2B 83.544 79 11 2 292 369 512931005 512931082 8.970000e-09 73.1
24 TraesCS3D01G207500 chrUn 95.455 44 2 0 4409 4452 176717930 176717887 3.230000e-08 71.3


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 TraesCS3D01G207500 chr3D 273461985 273468434 6449 False 11912.0 11912 100.0000 1 6450 1 chr3D.!!$F2 6449
1 TraesCS3D01G207500 chr3A 357061917 357067220 5303 False 4464.0 4761 97.7830 840 6008 2 chr3A.!!$F1 5168
2 TraesCS3D01G207500 chr3A 357077796 357078487 691 False 318.0 355 92.5760 6004 6450 2 chr3A.!!$F2 446
3 TraesCS3D01G207500 chr3B 360108026 360114489 6463 True 1940.8 3912 97.7798 793 6450 5 chr3B.!!$R1 5657
4 TraesCS3D01G207500 chr3B 252665487 252666241 754 False 702.0 702 83.7090 2 744 1 chr3B.!!$F3 742
5 TraesCS3D01G207500 chr1D 302270170 302270926 756 True 551.0 551 80.1320 2 747 1 chr1D.!!$R2 745
6 TraesCS3D01G207500 chr5A 277343892 277344647 755 True 527.0 527 79.5240 3 747 1 chr5A.!!$R1 744

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
604 606 0.040514 CCGTGCGCTTTGATGTTCAA 60.041 50.000 9.73 0.0 34.03 2.69 F
1650 1663 0.241481 GACCAGTCGACCAGAGTCAC 59.759 60.000 13.01 0.0 43.73 3.67 F
2302 2315 0.179045 AAGCTTGCCGTGTTGAGTCT 60.179 50.000 0.00 0.0 0.00 3.24 F
2357 2370 1.025812 TTGGACGATTGGTTTGCGTT 58.974 45.000 0.00 0.0 38.51 4.84 F
3144 3550 2.288702 CGGGTCCAACATCATTTTTGCA 60.289 45.455 0.00 0.0 0.00 4.08 F
4376 4914 1.880027 ACGAAAGGCCATCAACTGAAC 59.120 47.619 5.01 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2272 2.015456 ATGAGACTGACAGGACCACA 57.985 50.000 7.51 1.38 0.00 4.17 R
3133 3539 1.402720 CGGCTTCCGTGCAAAAATGAT 60.403 47.619 0.00 0.00 42.73 2.45 R
4094 4632 1.202371 TCACGATAACCACCTCGATGC 60.202 52.381 0.00 0.00 38.24 3.91 R
4376 4914 7.414098 CCAAGATACAAGAACCAAAATACCTCG 60.414 40.741 0.00 0.00 0.00 4.63 R
4617 5155 3.495806 GCTTCTCCTAGCTGCACCATTAT 60.496 47.826 1.02 0.00 38.15 1.28 R
5727 6350 2.325484 TCCCAGTTGCAGTTCTAGTGA 58.675 47.619 0.00 0.00 0.00 3.41 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
21 22 3.937814 TGCCATGATGTCGTCTTTAAGT 58.062 40.909 0.00 0.00 0.00 2.24
35 36 2.356665 TTAAGTGTTTGCCAGCAGGA 57.643 45.000 0.00 0.00 36.89 3.86
36 37 1.604604 TAAGTGTTTGCCAGCAGGAC 58.395 50.000 0.00 0.00 36.89 3.85
39 40 0.250727 GTGTTTGCCAGCAGGACCTA 60.251 55.000 0.00 0.00 36.89 3.08
69 70 2.066999 GGAGAAGCCATCCGGTCCT 61.067 63.158 0.00 0.00 36.34 3.85
72 73 2.285368 AAGCCATCCGGTCCTGGA 60.285 61.111 20.00 5.13 43.58 3.86
116 117 2.229543 TGATTGCTTGCCACACTTCATC 59.770 45.455 0.00 0.00 0.00 2.92
169 170 2.203252 CCCTGGGCATGTCGATGG 60.203 66.667 0.00 0.00 0.00 3.51
172 173 1.524002 CTGGGCATGTCGATGGAGT 59.476 57.895 0.00 0.00 0.00 3.85
187 188 3.981071 TGGAGTTCCAATCTACTGTGG 57.019 47.619 0.00 0.00 44.35 4.17
192 193 0.618458 TCCAATCTACTGTGGTGGCC 59.382 55.000 0.00 0.00 36.23 5.36
213 214 2.289072 CCGGCCATGTACAGATCCTAAG 60.289 54.545 2.24 0.00 0.00 2.18
239 240 3.699038 CGGTGGAAATGGTTGTGGATTAT 59.301 43.478 0.00 0.00 0.00 1.28
249 250 5.500234 TGGTTGTGGATTATCTCCTCTTTG 58.500 41.667 0.00 0.00 45.21 2.77
253 254 5.982356 TGTGGATTATCTCCTCTTTGTCAG 58.018 41.667 0.00 0.00 45.21 3.51
260 261 1.136147 CCTCTTTGTCAGCATGCGC 59.864 57.895 13.01 0.00 34.76 6.09
261 262 1.136147 CTCTTTGTCAGCATGCGCC 59.864 57.895 13.01 4.66 39.83 6.53
262 263 1.579964 CTCTTTGTCAGCATGCGCCA 61.580 55.000 13.01 7.47 39.83 5.69
285 286 2.147387 AACTCCAGCCGGTCCTTGT 61.147 57.895 1.90 0.00 0.00 3.16
300 301 2.166459 TCCTTGTAGCGAGTGGATGAAG 59.834 50.000 0.00 0.00 0.00 3.02
309 310 3.253432 GCGAGTGGATGAAGTTTTTCCTT 59.747 43.478 6.59 0.00 32.09 3.36
312 313 4.461198 AGTGGATGAAGTTTTTCCTTCGT 58.539 39.130 6.59 0.00 43.06 3.85
317 318 4.145365 TGAAGTTTTTCCTTCGTCTGGA 57.855 40.909 0.00 0.00 43.06 3.86
375 376 1.369091 CCGCTCGCAGCCAAGTTATT 61.369 55.000 3.09 0.00 38.18 1.40
382 383 3.194755 TCGCAGCCAAGTTATTCTAGACA 59.805 43.478 0.00 0.00 0.00 3.41
384 385 3.307242 GCAGCCAAGTTATTCTAGACACG 59.693 47.826 0.00 0.00 0.00 4.49
386 387 5.647589 CAGCCAAGTTATTCTAGACACGTA 58.352 41.667 0.00 0.00 0.00 3.57
396 397 1.300971 TAGACACGTAGCGCTTCCGT 61.301 55.000 23.73 23.73 36.67 4.69
417 418 1.738030 GCTTTTTCTACCGCCGCTAGA 60.738 52.381 0.00 0.00 0.00 2.43
429 430 1.610102 GCCGCTAGACCTAGGATACGA 60.610 57.143 17.98 2.12 46.39 3.43
432 433 3.401182 CGCTAGACCTAGGATACGAAGT 58.599 50.000 17.98 0.00 46.39 3.01
441 442 5.044558 CCTAGGATACGAAGTTTCAGAAGC 58.955 45.833 1.05 0.00 37.78 3.86
467 468 2.534042 AGGTGGAATTCTCTCTCGGA 57.466 50.000 5.23 0.00 0.00 4.55
486 487 1.671379 GAGGGTCCGGTGTTCTTGC 60.671 63.158 0.00 0.00 0.00 4.01
487 488 2.112297 GGGTCCGGTGTTCTTGCA 59.888 61.111 0.00 0.00 0.00 4.08
492 493 0.604073 TCCGGTGTTCTTGCACGATA 59.396 50.000 0.00 0.00 40.08 2.92
589 590 3.066342 TCTTAAATCTCTAGCGACCCGTG 59.934 47.826 0.00 0.00 0.00 4.94
590 591 0.179108 AAATCTCTAGCGACCCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
591 592 2.337749 AATCTCTAGCGACCCGTGCG 62.338 60.000 0.00 0.00 37.44 5.34
604 606 0.040514 CCGTGCGCTTTGATGTTCAA 60.041 50.000 9.73 0.00 34.03 2.69
611 613 2.966708 CGCTTTGATGTTCAAACGAGTG 59.033 45.455 14.20 4.01 41.02 3.51
618 620 4.275689 TGATGTTCAAACGAGTGAAAGCAT 59.724 37.500 7.02 7.52 39.18 3.79
620 622 5.940192 TGTTCAAACGAGTGAAAGCATAT 57.060 34.783 7.02 0.00 39.18 1.78
626 628 4.668576 ACGAGTGAAAGCATATGTTGTG 57.331 40.909 4.29 0.00 0.00 3.33
630 632 2.825532 GTGAAAGCATATGTTGTGGGGT 59.174 45.455 4.29 0.00 0.00 4.95
631 633 2.824936 TGAAAGCATATGTTGTGGGGTG 59.175 45.455 4.29 0.00 0.00 4.61
634 636 0.324275 GCATATGTTGTGGGGTGGGT 60.324 55.000 4.29 0.00 0.00 4.51
635 637 1.762708 CATATGTTGTGGGGTGGGTC 58.237 55.000 0.00 0.00 0.00 4.46
636 638 0.254747 ATATGTTGTGGGGTGGGTCG 59.745 55.000 0.00 0.00 0.00 4.79
637 639 1.128809 TATGTTGTGGGGTGGGTCGT 61.129 55.000 0.00 0.00 0.00 4.34
639 641 1.343431 TGTTGTGGGGTGGGTCGTTA 61.343 55.000 0.00 0.00 0.00 3.18
653 666 3.002144 GGGTCGTTATCTACAGTCTCGTC 59.998 52.174 0.00 0.00 0.00 4.20
729 742 4.457496 GCTGCTGCTGCCGGTAGA 62.457 66.667 25.04 7.60 38.71 2.59
748 761 2.747460 GCAGCGGGCAGTGATCAA 60.747 61.111 0.00 0.00 43.97 2.57
749 762 2.117156 GCAGCGGGCAGTGATCAAT 61.117 57.895 0.00 0.00 43.97 2.57
750 763 0.815213 GCAGCGGGCAGTGATCAATA 60.815 55.000 0.00 0.00 43.97 1.90
751 764 1.667236 CAGCGGGCAGTGATCAATAA 58.333 50.000 0.00 0.00 0.00 1.40
752 765 1.600957 CAGCGGGCAGTGATCAATAAG 59.399 52.381 0.00 0.00 0.00 1.73
753 766 1.210478 AGCGGGCAGTGATCAATAAGT 59.790 47.619 0.00 0.00 0.00 2.24
754 767 1.599542 GCGGGCAGTGATCAATAAGTC 59.400 52.381 0.00 0.00 0.00 3.01
755 768 1.860950 CGGGCAGTGATCAATAAGTCG 59.139 52.381 0.00 0.00 0.00 4.18
756 769 2.481276 CGGGCAGTGATCAATAAGTCGA 60.481 50.000 0.00 0.00 0.00 4.20
757 770 3.733337 GGGCAGTGATCAATAAGTCGAT 58.267 45.455 0.00 0.00 0.00 3.59
758 771 4.130118 GGGCAGTGATCAATAAGTCGATT 58.870 43.478 0.00 0.00 0.00 3.34
759 772 4.576463 GGGCAGTGATCAATAAGTCGATTT 59.424 41.667 0.00 0.00 0.00 2.17
760 773 5.277538 GGGCAGTGATCAATAAGTCGATTTC 60.278 44.000 0.00 0.00 0.00 2.17
761 774 5.525378 GGCAGTGATCAATAAGTCGATTTCT 59.475 40.000 0.00 0.00 0.00 2.52
762 775 6.417327 GCAGTGATCAATAAGTCGATTTCTG 58.583 40.000 0.00 0.00 0.00 3.02
763 776 6.256539 GCAGTGATCAATAAGTCGATTTCTGA 59.743 38.462 0.00 2.29 30.91 3.27
764 777 7.516470 GCAGTGATCAATAAGTCGATTTCTGAG 60.516 40.741 0.00 0.00 30.91 3.35
765 778 7.704047 CAGTGATCAATAAGTCGATTTCTGAGA 59.296 37.037 0.00 0.00 30.91 3.27
766 779 8.420222 AGTGATCAATAAGTCGATTTCTGAGAT 58.580 33.333 0.00 0.00 0.00 2.75
767 780 9.684448 GTGATCAATAAGTCGATTTCTGAGATA 57.316 33.333 0.00 0.00 0.00 1.98
768 781 9.905171 TGATCAATAAGTCGATTTCTGAGATAG 57.095 33.333 0.00 0.00 0.00 2.08
769 782 8.755696 ATCAATAAGTCGATTTCTGAGATAGC 57.244 34.615 0.00 0.00 0.00 2.97
770 783 6.858478 TCAATAAGTCGATTTCTGAGATAGCG 59.142 38.462 4.22 4.22 0.00 4.26
771 784 4.640789 AAGTCGATTTCTGAGATAGCGT 57.359 40.909 10.07 0.00 0.00 5.07
772 785 4.640789 AGTCGATTTCTGAGATAGCGTT 57.359 40.909 10.07 0.00 0.00 4.84
773 786 5.000012 AGTCGATTTCTGAGATAGCGTTT 58.000 39.130 10.07 0.00 0.00 3.60
774 787 5.411781 AGTCGATTTCTGAGATAGCGTTTT 58.588 37.500 10.07 0.00 0.00 2.43
775 788 5.869888 AGTCGATTTCTGAGATAGCGTTTTT 59.130 36.000 10.07 0.00 0.00 1.94
817 830 4.563140 TTTTAAGGTGTAGTAGCCAGGG 57.437 45.455 0.00 0.00 0.00 4.45
907 920 2.925966 TGGAGCCCATGGAGAAATTT 57.074 45.000 15.22 0.00 0.00 1.82
973 986 1.207085 GCGAACGAGACGACACTCT 59.793 57.895 0.00 0.00 35.06 3.24
1650 1663 0.241481 GACCAGTCGACCAGAGTCAC 59.759 60.000 13.01 0.00 43.73 3.67
1658 1671 3.252701 GTCGACCAGAGTCACTGTTTCTA 59.747 47.826 3.51 0.00 43.73 2.10
2076 2089 5.832060 AGAAATTGAAGGATGAAGGCCATAG 59.168 40.000 5.01 0.00 35.17 2.23
2259 2272 3.007723 TGCTTTCTGATCTGCTGAAGTCT 59.992 43.478 0.00 0.00 36.10 3.24
2263 2276 2.233186 TCTGATCTGCTGAAGTCTGTGG 59.767 50.000 0.00 0.00 0.00 4.17
2302 2315 0.179045 AAGCTTGCCGTGTTGAGTCT 60.179 50.000 0.00 0.00 0.00 3.24
2344 2357 3.198068 CATCCCTATGACAAGTTGGACG 58.802 50.000 7.96 0.00 34.84 4.79
2357 2370 1.025812 TTGGACGATTGGTTTGCGTT 58.974 45.000 0.00 0.00 38.51 4.84
2447 2460 5.453567 ACTTCTATGCAACTTGGGTTTTC 57.546 39.130 0.00 0.00 32.73 2.29
2448 2461 4.023193 ACTTCTATGCAACTTGGGTTTTCG 60.023 41.667 0.00 0.00 32.73 3.46
2549 2563 5.410924 TCAGTGAATAGTGTTTCTCCATCG 58.589 41.667 0.00 0.00 0.00 3.84
3043 3449 9.871238 GAGTTGATCTAGTGGTATTTACTTCAA 57.129 33.333 0.00 0.00 0.00 2.69
3123 3529 8.036273 TCTGATTTTACGGGAACTAAAACATC 57.964 34.615 0.00 0.00 30.93 3.06
3133 3539 3.495434 ACTAAAACATCGGGTCCAACA 57.505 42.857 0.00 0.00 0.00 3.33
3144 3550 2.288702 CGGGTCCAACATCATTTTTGCA 60.289 45.455 0.00 0.00 0.00 4.08
3260 3795 7.710907 GTGTTCCTGTAATGATAGCATCACTTA 59.289 37.037 0.00 0.00 43.01 2.24
3358 3896 9.313118 GTCCAAAATAACAGATTTTTGTGAACT 57.687 29.630 7.20 0.00 39.86 3.01
3515 4053 7.961326 AATTTCCTTTGCAGGTTATACTGAT 57.039 32.000 0.00 0.00 41.69 2.90
3789 4327 8.606040 ACAATGGTGTTTAATGAAATGAAAGG 57.394 30.769 0.00 0.00 32.58 3.11
4014 4552 5.968676 AGTGGGGTGCTATTACTATTTGA 57.031 39.130 0.00 0.00 0.00 2.69
4094 4632 8.912658 GCATTTAGTATCATGATTTCAGCATTG 58.087 33.333 14.65 4.51 0.00 2.82
4376 4914 1.880027 ACGAAAGGCCATCAACTGAAC 59.120 47.619 5.01 0.00 0.00 3.18
4617 5155 2.037772 GTCCAGGAGCTTTGTTCTGAGA 59.962 50.000 0.00 0.00 0.00 3.27
5112 5735 1.063417 AGGGGGATGCTCCAAAATCAG 60.063 52.381 5.68 0.00 38.64 2.90
5323 5946 3.135530 GGATGACTGGTCAAGGCTATTCT 59.864 47.826 7.53 0.00 43.58 2.40
5596 6219 3.295973 TCCAGGCTACAAGCAAAACTTT 58.704 40.909 0.78 0.00 44.75 2.66
5727 6350 2.839486 TTCAATTCAGCGAGGTCACT 57.161 45.000 0.00 0.00 0.00 3.41
6042 6665 5.867716 AGGCAGTAAATGTAAGACGTGTTAG 59.132 40.000 5.25 0.00 0.00 2.34
6126 6749 8.579850 TGAGAAATCATGGCAACTAATTACTT 57.420 30.769 0.00 0.00 37.61 2.24
6142 6765 8.910944 ACTAATTACTTAGAGGAAGTCGCAATA 58.089 33.333 6.84 0.00 45.81 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.550842 CCTGCTGGCAAACACTTAAAGAC 60.551 47.826 0.00 0.00 0.00 3.01
13 14 2.622942 CCTGCTGGCAAACACTTAAAGA 59.377 45.455 0.00 0.00 0.00 2.52
18 19 1.109323 GGTCCTGCTGGCAAACACTT 61.109 55.000 4.42 0.00 0.00 3.16
21 22 0.476338 TTAGGTCCTGCTGGCAAACA 59.524 50.000 4.42 0.00 0.00 2.83
35 36 0.531200 CTCCGGCGTCTTCTTTAGGT 59.469 55.000 6.01 0.00 0.00 3.08
36 37 0.815734 TCTCCGGCGTCTTCTTTAGG 59.184 55.000 6.01 0.00 0.00 2.69
39 40 0.670854 GCTTCTCCGGCGTCTTCTTT 60.671 55.000 6.01 0.00 0.00 2.52
66 67 1.340017 CCAGCGGAAAAATCTCCAGGA 60.340 52.381 0.00 0.00 34.91 3.86
69 70 1.305219 CGCCAGCGGAAAAATCTCCA 61.305 55.000 3.61 0.00 34.91 3.86
72 73 1.133025 CAATCGCCAGCGGAAAAATCT 59.867 47.619 12.71 0.00 40.25 2.40
116 117 0.949105 CGACAACCCTTTCACCGAGG 60.949 60.000 0.00 0.00 0.00 4.63
150 151 1.820906 CATCGACATGCCCAGGGTG 60.821 63.158 7.55 0.06 0.00 4.61
156 157 0.815615 GGAACTCCATCGACATGCCC 60.816 60.000 0.00 0.00 35.64 5.36
169 170 3.600388 CCACCACAGTAGATTGGAACTC 58.400 50.000 0.00 0.00 36.28 3.01
172 173 1.004277 GGCCACCACAGTAGATTGGAA 59.996 52.381 0.00 0.00 36.28 3.53
192 193 1.338107 TAGGATCTGTACATGGCCGG 58.662 55.000 0.00 0.00 0.00 6.13
206 207 3.073062 CCATTTCCACCGATCCTTAGGAT 59.927 47.826 14.42 14.42 46.28 3.24
213 214 1.472480 CACAACCATTTCCACCGATCC 59.528 52.381 0.00 0.00 0.00 3.36
239 240 1.673923 CGCATGCTGACAAAGAGGAGA 60.674 52.381 17.13 0.00 0.00 3.71
249 250 4.564116 GCCATGGCGCATGCTGAC 62.564 66.667 23.48 12.19 40.20 3.51
253 254 4.137872 AGTTGCCATGGCGCATGC 62.138 61.111 30.87 17.93 45.51 4.06
285 286 4.000988 GGAAAAACTTCATCCACTCGCTA 58.999 43.478 0.00 0.00 33.30 4.26
300 301 3.875134 TCAACTCCAGACGAAGGAAAAAC 59.125 43.478 0.00 0.00 34.08 2.43
309 310 1.066858 GCCAAGATCAACTCCAGACGA 60.067 52.381 0.00 0.00 0.00 4.20
312 313 1.280133 CAGGCCAAGATCAACTCCAGA 59.720 52.381 5.01 0.00 0.00 3.86
317 318 1.988107 TCTTCCAGGCCAAGATCAACT 59.012 47.619 5.01 0.00 0.00 3.16
369 370 3.626670 AGCGCTACGTGTCTAGAATAACT 59.373 43.478 8.99 0.00 0.00 2.24
375 376 0.731417 GGAAGCGCTACGTGTCTAGA 59.269 55.000 12.05 0.00 0.00 2.43
396 397 0.037139 TAGCGGCGGTAGAAAAAGCA 60.037 50.000 15.64 0.00 0.00 3.91
400 401 0.174162 GGTCTAGCGGCGGTAGAAAA 59.826 55.000 39.97 22.72 42.92 2.29
417 418 5.394333 GCTTCTGAAACTTCGTATCCTAGGT 60.394 44.000 9.08 0.00 0.00 3.08
429 430 3.071167 ACCTACGGAAGCTTCTGAAACTT 59.929 43.478 36.22 19.06 37.03 2.66
432 433 2.289444 CCACCTACGGAAGCTTCTGAAA 60.289 50.000 36.22 23.34 37.03 2.69
467 468 2.058675 CAAGAACACCGGACCCTCT 58.941 57.895 9.46 0.79 0.00 3.69
473 474 0.604073 TATCGTGCAAGAACACCGGA 59.396 50.000 9.46 0.00 37.25 5.14
478 479 3.521560 GTCTGGATATCGTGCAAGAACA 58.478 45.455 6.39 3.29 0.00 3.18
486 487 2.357952 TGTTCTCCGTCTGGATATCGTG 59.642 50.000 0.00 0.00 45.33 4.35
487 488 2.651455 TGTTCTCCGTCTGGATATCGT 58.349 47.619 0.00 0.00 45.33 3.73
492 493 3.491619 CGATGATTGTTCTCCGTCTGGAT 60.492 47.826 0.00 0.00 45.33 3.41
572 573 1.437986 GCACGGGTCGCTAGAGATT 59.562 57.895 0.00 0.00 0.00 2.40
573 574 2.835705 CGCACGGGTCGCTAGAGAT 61.836 63.158 0.00 0.00 0.00 2.75
582 583 1.852067 AACATCAAAGCGCACGGGTC 61.852 55.000 11.47 0.00 0.00 4.46
589 590 1.971962 CTCGTTTGAACATCAAAGCGC 59.028 47.619 0.00 0.00 45.83 5.92
590 591 2.966708 CACTCGTTTGAACATCAAAGCG 59.033 45.455 5.81 11.68 45.83 4.68
591 592 4.209452 TCACTCGTTTGAACATCAAAGC 57.791 40.909 5.81 1.84 45.83 3.51
592 593 5.172053 GCTTTCACTCGTTTGAACATCAAAG 59.828 40.000 5.81 0.00 45.83 2.77
604 606 4.083324 CCACAACATATGCTTTCACTCGTT 60.083 41.667 1.58 0.00 0.00 3.85
611 613 2.166254 CCACCCCACAACATATGCTTTC 59.834 50.000 1.58 0.00 0.00 2.62
618 620 1.128809 ACGACCCACCCCACAACATA 61.129 55.000 0.00 0.00 0.00 2.29
620 622 1.343431 TAACGACCCACCCCACAACA 61.343 55.000 0.00 0.00 0.00 3.33
626 628 1.411612 CTGTAGATAACGACCCACCCC 59.588 57.143 0.00 0.00 0.00 4.95
630 632 2.941064 CGAGACTGTAGATAACGACCCA 59.059 50.000 0.00 0.00 0.00 4.51
631 633 2.941720 ACGAGACTGTAGATAACGACCC 59.058 50.000 0.00 0.00 0.00 4.46
634 636 5.868043 TTTGACGAGACTGTAGATAACGA 57.132 39.130 0.00 0.00 0.00 3.85
635 637 5.002282 CGTTTTGACGAGACTGTAGATAACG 59.998 44.000 0.00 0.00 34.64 3.18
636 638 5.855395 ACGTTTTGACGAGACTGTAGATAAC 59.145 40.000 5.91 0.00 36.85 1.89
637 639 5.854866 CACGTTTTGACGAGACTGTAGATAA 59.145 40.000 5.91 0.00 36.85 1.75
639 641 4.227538 CACGTTTTGACGAGACTGTAGAT 58.772 43.478 5.91 0.00 36.85 1.98
653 666 1.566404 GCCAAGGTTTCCACGTTTTG 58.434 50.000 0.00 0.00 0.00 2.44
660 673 0.178964 CCTTCTGGCCAAGGTTTCCA 60.179 55.000 14.58 0.00 38.58 3.53
725 738 2.103042 CACTGCCCGCTGCTTCTAC 61.103 63.158 0.00 0.00 42.00 2.59
726 739 1.617018 ATCACTGCCCGCTGCTTCTA 61.617 55.000 0.00 0.00 42.00 2.10
729 742 2.437359 GATCACTGCCCGCTGCTT 60.437 61.111 0.00 0.00 42.00 3.91
747 760 6.740110 ACGCTATCTCAGAAATCGACTTATT 58.260 36.000 0.00 0.00 0.00 1.40
748 761 6.320494 ACGCTATCTCAGAAATCGACTTAT 57.680 37.500 0.00 0.00 0.00 1.73
749 762 5.752892 ACGCTATCTCAGAAATCGACTTA 57.247 39.130 0.00 0.00 0.00 2.24
750 763 4.640789 ACGCTATCTCAGAAATCGACTT 57.359 40.909 0.00 0.00 0.00 3.01
751 764 4.640789 AACGCTATCTCAGAAATCGACT 57.359 40.909 0.00 0.00 0.00 4.18
752 765 5.704217 AAAACGCTATCTCAGAAATCGAC 57.296 39.130 0.00 0.00 0.00 4.20
795 808 4.808324 GCCCTGGCTACTACACCTTAAAAA 60.808 45.833 0.00 0.00 38.26 1.94
796 809 3.307904 GCCCTGGCTACTACACCTTAAAA 60.308 47.826 0.00 0.00 38.26 1.52
797 810 2.237893 GCCCTGGCTACTACACCTTAAA 59.762 50.000 0.00 0.00 38.26 1.52
798 811 1.835531 GCCCTGGCTACTACACCTTAA 59.164 52.381 0.00 0.00 38.26 1.85
799 812 1.492764 GCCCTGGCTACTACACCTTA 58.507 55.000 0.00 0.00 38.26 2.69
800 813 2.297937 GCCCTGGCTACTACACCTT 58.702 57.895 0.00 0.00 38.26 3.50
801 814 4.051932 GCCCTGGCTACTACACCT 57.948 61.111 0.00 0.00 38.26 4.00
817 830 3.344215 CGATGCCATCTCCGCAGC 61.344 66.667 2.75 0.00 40.15 5.25
907 920 4.968812 TCGTCCACAACAATATCGTCTA 57.031 40.909 0.00 0.00 0.00 2.59
1658 1671 4.636206 GCACCCGAGAAGAGAATTACAAAT 59.364 41.667 0.00 0.00 0.00 2.32
1962 1975 3.366396 ACACTATCCATCTGAAGACCGT 58.634 45.455 0.00 0.00 0.00 4.83
2259 2272 2.015456 ATGAGACTGACAGGACCACA 57.985 50.000 7.51 1.38 0.00 4.17
2263 2276 4.867608 GCTTAGAAATGAGACTGACAGGAC 59.132 45.833 7.51 0.62 0.00 3.85
2302 2315 5.681337 TGCGTCATGTCTATTGAAAAACA 57.319 34.783 0.00 0.00 0.00 2.83
2322 2335 2.945668 GTCCAACTTGTCATAGGGATGC 59.054 50.000 0.00 0.00 32.62 3.91
2344 2357 5.879237 TCTCAATATCAACGCAAACCAATC 58.121 37.500 0.00 0.00 0.00 2.67
2357 2370 8.762645 AGTGTCACCTAGAATTTCTCAATATCA 58.237 33.333 1.27 0.00 0.00 2.15
2447 2460 6.803320 ACAAAGAAACATAAATGATGCAGTCG 59.197 34.615 0.00 0.00 39.39 4.18
2448 2461 8.524870 AACAAAGAAACATAAATGATGCAGTC 57.475 30.769 0.00 0.00 39.39 3.51
2549 2563 7.123830 GTCAGTTATGTATTTGTTATCACGCC 58.876 38.462 0.00 0.00 0.00 5.68
2580 2594 5.779529 ATTCAAGAATAGGCATCGCAAAT 57.220 34.783 0.00 0.00 0.00 2.32
2948 3353 3.061848 ATTGCGAACGGGGCCTTG 61.062 61.111 0.84 0.00 0.00 3.61
3043 3449 5.711976 CAGTGTTCATCTGGGTAAATTCCTT 59.288 40.000 0.00 0.00 0.00 3.36
3123 3529 2.288702 TGCAAAAATGATGTTGGACCCG 60.289 45.455 0.00 0.00 0.00 5.28
3133 3539 1.402720 CGGCTTCCGTGCAAAAATGAT 60.403 47.619 0.00 0.00 42.73 2.45
3153 3559 6.169800 GGTATCATTATCTCTCTTTGCCTCC 58.830 44.000 0.00 0.00 0.00 4.30
3237 3647 8.874156 AGATAAGTGATGCTATCATTACAGGAA 58.126 33.333 4.54 0.00 40.47 3.36
3260 3795 7.786030 ACTACAATGACAATACTGTAGCAGAT 58.214 34.615 13.24 0.00 43.25 2.90
3358 3896 7.297588 AGAATTAGATAGTAGGTACTCCCTCCA 59.702 40.741 0.00 0.00 44.81 3.86
3789 4327 3.493503 CGTACCAGACTTGACACCTTTTC 59.506 47.826 0.00 0.00 0.00 2.29
4014 4552 6.397272 GTCATCAGACAAGATCAAGAAGACT 58.603 40.000 0.00 0.00 44.34 3.24
4094 4632 1.202371 TCACGATAACCACCTCGATGC 60.202 52.381 0.00 0.00 38.24 3.91
4376 4914 7.414098 CCAAGATACAAGAACCAAAATACCTCG 60.414 40.741 0.00 0.00 0.00 4.63
4617 5155 3.495806 GCTTCTCCTAGCTGCACCATTAT 60.496 47.826 1.02 0.00 38.15 1.28
4805 5343 8.941977 ACACGCAAAATAAACAATAGAGATACA 58.058 29.630 0.00 0.00 0.00 2.29
4855 5394 3.927142 CGACTCTCCATTGTCCTGTTAAC 59.073 47.826 0.00 0.00 0.00 2.01
5323 5946 3.584406 AGTTCCTTGATGATGAGTCCACA 59.416 43.478 0.00 0.00 0.00 4.17
5596 6219 6.037062 CGCATACCATAATCTGAAACTCAACA 59.963 38.462 0.00 0.00 0.00 3.33
5727 6350 2.325484 TCCCAGTTGCAGTTCTAGTGA 58.675 47.619 0.00 0.00 0.00 3.41
6042 6665 4.525100 AGTCTTCTTCAGAACTGTCCTACC 59.475 45.833 1.73 0.00 31.28 3.18
6159 6782 8.536407 GTTGCGACACATGTTTAGTTTTTAATT 58.464 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.