Multiple sequence alignment - TraesCS6D01G254100

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 TraesCS6D01G254100 chr6D 100.000 4489 0 0 1 4489 358320095 358324583 0.000000e+00 8290.0
1 TraesCS6D01G254100 chr6D 84.304 790 112 9 134 919 323448806 323448025 0.000000e+00 761.0
2 TraesCS6D01G254100 chr6B 95.490 3437 133 12 1063 4489 539721171 539724595 0.000000e+00 5469.0
3 TraesCS6D01G254100 chr6B 75.309 405 54 25 1 387 193182435 193182811 7.780000e-33 152.0
4 TraesCS6D01G254100 chr6B 98.361 61 1 0 979 1039 539721112 539721172 1.710000e-19 108.0
5 TraesCS6D01G254100 chr6A 94.598 3517 148 24 993 4489 500077930 500081424 0.000000e+00 5404.0
6 TraesCS6D01G254100 chr2D 82.711 937 136 17 1 919 414286202 414285274 0.000000e+00 809.0
7 TraesCS6D01G254100 chr2D 81.243 933 156 10 1 919 337309749 337310676 0.000000e+00 736.0
8 TraesCS6D01G254100 chr1D 82.623 938 138 19 1 919 143946607 143945676 0.000000e+00 806.0
9 TraesCS6D01G254100 chr3D 82.585 936 133 20 1 918 316460617 316461540 0.000000e+00 798.0
10 TraesCS6D01G254100 chr3A 81.390 935 139 19 1 907 543025881 543026808 0.000000e+00 730.0
11 TraesCS6D01G254100 chr3A 79.521 918 158 25 1 907 745884853 745885751 1.060000e-175 627.0
12 TraesCS6D01G254100 chr1B 84.765 722 102 8 125 841 680820849 680821567 0.000000e+00 717.0
13 TraesCS6D01G254100 chr1B 76.496 234 39 10 15 237 129216050 129215822 3.670000e-21 113.0
14 TraesCS6D01G254100 chr5B 82.614 811 122 17 100 905 499954200 499954996 0.000000e+00 699.0
15 TraesCS6D01G254100 chr7B 77.311 238 38 12 12 238 277425086 277425318 4.710000e-25 126.0
16 TraesCS6D01G254100 chr7B 77.215 237 38 13 12 237 28083381 28083612 1.700000e-24 124.0
17 TraesCS6D01G254100 chr7A 100.000 28 0 0 4380 4407 82204193 82204220 8.000000e-03 52.8


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 TraesCS6D01G254100 chr6D 358320095 358324583 4488 False 8290.0 8290 100.0000 1 4489 1 chr6D.!!$F1 4488
1 TraesCS6D01G254100 chr6D 323448025 323448806 781 True 761.0 761 84.3040 134 919 1 chr6D.!!$R1 785
2 TraesCS6D01G254100 chr6B 539721112 539724595 3483 False 2788.5 5469 96.9255 979 4489 2 chr6B.!!$F2 3510
3 TraesCS6D01G254100 chr6A 500077930 500081424 3494 False 5404.0 5404 94.5980 993 4489 1 chr6A.!!$F1 3496
4 TraesCS6D01G254100 chr2D 414285274 414286202 928 True 809.0 809 82.7110 1 919 1 chr2D.!!$R1 918
5 TraesCS6D01G254100 chr2D 337309749 337310676 927 False 736.0 736 81.2430 1 919 1 chr2D.!!$F1 918
6 TraesCS6D01G254100 chr1D 143945676 143946607 931 True 806.0 806 82.6230 1 919 1 chr1D.!!$R1 918
7 TraesCS6D01G254100 chr3D 316460617 316461540 923 False 798.0 798 82.5850 1 918 1 chr3D.!!$F1 917
8 TraesCS6D01G254100 chr3A 543025881 543026808 927 False 730.0 730 81.3900 1 907 1 chr3A.!!$F1 906
9 TraesCS6D01G254100 chr3A 745884853 745885751 898 False 627.0 627 79.5210 1 907 1 chr3A.!!$F2 906
10 TraesCS6D01G254100 chr1B 680820849 680821567 718 False 717.0 717 84.7650 125 841 1 chr1B.!!$F1 716
11 TraesCS6D01G254100 chr5B 499954200 499954996 796 False 699.0 699 82.6140 100 905 1 chr5B.!!$F1 805

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
334 365 0.026285 CAAGACTATTTTCGGCGCCG 59.974 55.000 42.13 42.13 41.35 6.46 F
447 483 0.106819 GCCAAGATCATGCCCTCTGT 60.107 55.000 0.00 0.00 0.00 3.41 F
1759 1804 1.065600 GCAGCGGCACAGTTGAAAA 59.934 52.632 3.18 0.00 40.72 2.29 F
1830 1875 2.079925 GAGCATGACTTGGTTCTGGTC 58.920 52.381 0.00 0.00 35.82 4.02 F
2506 2551 4.062293 TGTCAGGGTATTTGAAAGTGACG 58.938 43.478 0.00 0.00 36.46 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1686 1.003355 CTGTGCCATCCCGTTCTGT 60.003 57.895 0.00 0.00 0.00 3.41 R
2426 2471 0.032952 AAGTGCAGCTGCCACAAATG 59.967 50.000 34.64 0.00 41.18 2.32 R
2640 2685 1.010797 GCTGCATGCCGATAACACG 60.011 57.895 16.68 0.00 35.15 4.49 R
2731 2776 1.114627 ATGGCACTACGATGCTCTGA 58.885 50.000 10.09 0.00 45.38 3.27 R
4122 4181 0.175531 ATAAAACAATGCGGCCAGGC 59.824 50.000 1.26 1.26 0.00 4.85 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
94 105 4.124851 ACTACTACTCTTCCAATTGCCG 57.875 45.455 0.00 0.00 0.00 5.69
114 125 4.381566 GCCGCAAAACTGTTGTTACTATTG 59.618 41.667 0.00 0.00 34.96 1.90
127 155 9.309516 TGTTGTTACTATTGCTAATACTGCTAC 57.690 33.333 0.00 0.00 0.00 3.58
129 157 7.143340 TGTTACTATTGCTAATACTGCTACCG 58.857 38.462 0.00 0.00 0.00 4.02
151 179 4.143326 CGTTGCTATCATATTACCGTGCTG 60.143 45.833 0.00 0.00 0.00 4.41
266 295 6.638610 TGTGCCGAATCAATAAATTTGGATT 58.361 32.000 0.00 7.49 41.14 3.01
328 359 4.935205 TGTGGGTCATCAAGACTATTTTCG 59.065 41.667 0.00 0.00 46.72 3.46
330 361 3.312697 GGGTCATCAAGACTATTTTCGGC 59.687 47.826 0.00 0.00 46.72 5.54
331 362 3.001330 GGTCATCAAGACTATTTTCGGCG 59.999 47.826 0.00 0.00 46.72 6.46
332 363 2.607635 TCATCAAGACTATTTTCGGCGC 59.392 45.455 0.00 0.00 0.00 6.53
334 365 0.026285 CAAGACTATTTTCGGCGCCG 59.974 55.000 42.13 42.13 41.35 6.46
335 366 0.390735 AAGACTATTTTCGGCGCCGT 60.391 50.000 44.16 29.68 40.74 5.68
387 422 6.946340 TCACTTGAGGAGTTAAATATCTGCA 58.054 36.000 0.00 0.00 36.10 4.41
446 482 0.822532 GGCCAAGATCATGCCCTCTG 60.823 60.000 0.00 0.00 39.30 3.35
447 483 0.106819 GCCAAGATCATGCCCTCTGT 60.107 55.000 0.00 0.00 0.00 3.41
503 542 3.326747 ACGCTTGATTCACCTACTGTTC 58.673 45.455 0.00 0.00 0.00 3.18
515 554 6.746120 TCACCTACTGTTCTAAGTCAACTTC 58.254 40.000 0.00 0.00 37.40 3.01
535 574 1.884926 GACGCTGCCACCTGCTATC 60.885 63.158 0.00 0.00 42.00 2.08
546 585 4.573900 CCACCTGCTATCCAATCTGATAC 58.426 47.826 0.00 0.00 0.00 2.24
548 587 3.259374 ACCTGCTATCCAATCTGATACGG 59.741 47.826 0.00 0.00 0.00 4.02
570 609 4.438744 GGCGCAAGTAATAGACATTGCTTT 60.439 41.667 10.83 0.00 42.36 3.51
601 640 7.303634 TGATGATATTCATGATGATGCTTCG 57.696 36.000 0.00 0.00 37.20 3.79
608 647 4.506758 TCATGATGATGCTTCGACTTTGA 58.493 39.130 0.00 0.00 0.00 2.69
618 657 7.763985 TGATGCTTCGACTTTGACTGATAAATA 59.236 33.333 0.00 0.00 0.00 1.40
620 659 8.492673 TGCTTCGACTTTGACTGATAAATATT 57.507 30.769 0.00 0.00 0.00 1.28
669 709 9.559732 TGCTCATATTGCTAAAGCTAAAGAATA 57.440 29.630 3.26 0.00 42.66 1.75
716 756 4.771054 CACCTGTTACACCTAGTACTCCTT 59.229 45.833 0.00 0.00 30.91 3.36
810 851 6.213677 TGGCTTATGATACTCGTAATGACAC 58.786 40.000 0.00 0.00 28.56 3.67
870 911 9.726232 CGTGAACAAAATGATGAAATATGATCT 57.274 29.630 0.00 0.00 0.00 2.75
942 983 9.771534 ATTTTTGATAGAAAAACCGAAAATCCA 57.228 25.926 0.00 0.00 30.81 3.41
943 984 9.771534 TTTTTGATAGAAAAACCGAAAATCCAT 57.228 25.926 0.00 0.00 0.00 3.41
945 986 9.849166 TTTGATAGAAAAACCGAAAATCCATAC 57.151 29.630 0.00 0.00 0.00 2.39
946 987 7.992008 TGATAGAAAAACCGAAAATCCATACC 58.008 34.615 0.00 0.00 0.00 2.73
947 988 5.654603 AGAAAAACCGAAAATCCATACCC 57.345 39.130 0.00 0.00 0.00 3.69
948 989 5.081032 AGAAAAACCGAAAATCCATACCCA 58.919 37.500 0.00 0.00 0.00 4.51
949 990 5.719563 AGAAAAACCGAAAATCCATACCCAT 59.280 36.000 0.00 0.00 0.00 4.00
950 991 5.337578 AAAACCGAAAATCCATACCCATG 57.662 39.130 0.00 0.00 0.00 3.66
958 999 2.113139 CATACCCATGGGACGGCC 59.887 66.667 38.07 0.00 38.96 6.13
959 1000 3.556306 ATACCCATGGGACGGCCG 61.556 66.667 38.07 26.86 38.96 6.13
1039 1083 1.922135 CTTTTGGACCCGATGCCACG 61.922 60.000 0.00 0.00 33.01 4.94
1056 1100 2.339556 CGCGGGGCCATTCAGAAAA 61.340 57.895 4.39 0.00 0.00 2.29
1062 1106 2.643551 GGGCCATTCAGAAAATCTCGA 58.356 47.619 4.39 0.00 0.00 4.04
1063 1107 2.356069 GGGCCATTCAGAAAATCTCGAC 59.644 50.000 4.39 0.00 0.00 4.20
1170 1215 2.363147 GCGGACTCCTCCACTCCT 60.363 66.667 0.00 0.00 36.12 3.69
1203 1248 3.322466 CTCCACGCCCACCTCCTT 61.322 66.667 0.00 0.00 0.00 3.36
1431 1476 1.376466 GCTGTCCCTCCTGCTCAAA 59.624 57.895 0.00 0.00 0.00 2.69
1641 1686 1.661480 CGTGGTGACTGGGTACGAA 59.339 57.895 0.00 0.00 36.94 3.85
1749 1794 4.819761 GTGATCTCGGCAGCGGCA 62.820 66.667 11.88 0.00 43.71 5.69
1757 1802 3.286751 GGCAGCGGCACAGTTGAA 61.287 61.111 11.88 0.00 43.71 2.69
1758 1803 2.721231 GCAGCGGCACAGTTGAAA 59.279 55.556 3.18 0.00 40.72 2.69
1759 1804 1.065600 GCAGCGGCACAGTTGAAAA 59.934 52.632 3.18 0.00 40.72 2.29
1813 1858 3.006247 GTTCTCAGGAATGACTTGGAGC 58.994 50.000 0.00 0.00 33.71 4.70
1830 1875 2.079925 GAGCATGACTTGGTTCTGGTC 58.920 52.381 0.00 0.00 35.82 4.02
2426 2471 7.307811 GGTTAACACTGGTTTCTGTGATAAGAC 60.308 40.741 8.10 3.03 42.95 3.01
2427 2472 5.290493 ACACTGGTTTCTGTGATAAGACA 57.710 39.130 9.71 0.00 42.95 3.41
2459 2504 5.009631 AGCTGCACTTGTGGATTTGTATTA 58.990 37.500 1.02 0.00 0.00 0.98
2504 2549 4.072131 GCTGTCAGGGTATTTGAAAGTGA 58.928 43.478 1.14 0.00 33.33 3.41
2506 2551 4.062293 TGTCAGGGTATTTGAAAGTGACG 58.938 43.478 0.00 0.00 36.46 4.35
2554 2599 5.310068 AGCTCAATGATCTCAGGTTATGGAT 59.690 40.000 0.00 0.00 0.00 3.41
2640 2685 6.534634 ACCTAATAGCCTGACATTTGTATCC 58.465 40.000 0.00 0.00 0.00 2.59
2731 2776 5.240183 CGAGTCTATGGAATCATGCCAAATT 59.760 40.000 7.32 0.00 39.21 1.82
2820 2865 0.698238 TCCATGAAACAGGTGGGAGG 59.302 55.000 0.00 0.00 33.78 4.30
3011 3056 9.042450 TGTAAAAGAGACTAGGGACATTATCAA 57.958 33.333 0.00 0.00 0.00 2.57
3048 3093 4.332637 GTGCCAGGTTGCAGTGCG 62.333 66.667 11.20 0.00 43.02 5.34
3143 3188 0.836606 TTGCTCTGGGAGTTGTCACA 59.163 50.000 0.00 0.00 33.90 3.58
3154 3199 4.201920 GGGAGTTGTCACAAAAGTTGAGAC 60.202 45.833 10.46 10.46 46.88 3.36
3189 3234 2.234300 TTCAGTTGGACCGTCACTTC 57.766 50.000 0.00 0.00 0.00 3.01
3230 3275 4.717877 TCTTCTCCAAGCTGAAACATGAA 58.282 39.130 0.00 0.00 0.00 2.57
3256 3301 5.554437 TCAATACACTTCACTTGGTGGTA 57.446 39.130 0.00 0.00 37.72 3.25
3269 3314 4.286291 ACTTGGTGGTAAGTTCCTAGAAGG 59.714 45.833 0.00 0.00 37.62 3.46
3286 3331 8.031277 TCCTAGAAGGAAGTAACGACAAAATAC 58.969 37.037 0.00 0.00 42.51 1.89
3366 3411 9.729023 TTGCACTAATTGTAACATTGTATATGC 57.271 29.630 0.00 0.00 0.00 3.14
3471 3517 3.287867 AACTTATGGTCAGAGCATGGG 57.712 47.619 22.95 16.89 36.89 4.00
3480 3526 4.079253 GGTCAGAGCATGGGAAACTTTTA 58.921 43.478 0.00 0.00 0.00 1.52
3481 3527 4.706962 GGTCAGAGCATGGGAAACTTTTAT 59.293 41.667 0.00 0.00 0.00 1.40
3482 3528 5.885912 GGTCAGAGCATGGGAAACTTTTATA 59.114 40.000 0.00 0.00 0.00 0.98
3579 3625 2.948979 TGTTGGAGAATGCGTTTGTTCT 59.051 40.909 0.00 0.00 37.39 3.01
3624 3672 5.196341 TGTGAACAGTTAGTGATCTCGTT 57.804 39.130 0.00 0.00 0.00 3.85
3661 3709 6.690194 ATGCATTTGTTCTCTGGAGATAAC 57.310 37.500 0.00 0.00 37.29 1.89
3759 3807 5.862860 TGACCGGTTTTAAAAGTTGTTTCAC 59.137 36.000 9.42 0.00 0.00 3.18
3811 3859 7.113437 TGCTTTGTGTAGGGCAATATACTTAA 58.887 34.615 0.00 0.00 0.00 1.85
3907 3957 3.062042 CAGGTACACCGAAACCAGTTAC 58.938 50.000 0.00 0.00 42.08 2.50
3912 3962 1.796459 CACCGAAACCAGTTACGAAGG 59.204 52.381 0.00 0.00 0.00 3.46
3913 3963 0.794473 CCGAAACCAGTTACGAAGGC 59.206 55.000 0.00 0.00 0.00 4.35
4033 4092 5.276820 GCCTTGCATTTGTTGTCTTTTGTAC 60.277 40.000 0.00 0.00 0.00 2.90
4035 4094 7.199766 CCTTGCATTTGTTGTCTTTTGTACTA 58.800 34.615 0.00 0.00 0.00 1.82
4036 4095 7.379529 CCTTGCATTTGTTGTCTTTTGTACTAG 59.620 37.037 0.00 0.00 0.00 2.57
4037 4096 6.205784 TGCATTTGTTGTCTTTTGTACTAGC 58.794 36.000 0.00 0.00 0.00 3.42
4068 4127 1.364626 CGCTCTGAACACCTGGATGC 61.365 60.000 0.00 0.00 0.00 3.91
4113 4172 4.022416 GGTGGAACTATCACAATGTTTGCA 60.022 41.667 0.00 0.00 36.90 4.08
4122 4181 8.192774 ACTATCACAATGTTTGCATCTAATTGG 58.807 33.333 13.29 0.00 33.50 3.16
4180 4239 1.050204 ACCGGTTAGTTACCTGCACA 58.950 50.000 0.00 0.00 45.40 4.57
4260 4320 0.536233 TGCGGCCAAAGAAGCTTACA 60.536 50.000 2.24 0.00 0.00 2.41
4266 4326 3.877508 GGCCAAAGAAGCTTACATATCGT 59.122 43.478 0.00 0.00 0.00 3.73
4320 4380 3.730061 GCAGCATTATCAGTCAGTTGCAC 60.730 47.826 0.00 0.00 36.60 4.57
4366 4426 7.607991 ACACATACTCCCTCAATTTGAACTAAG 59.392 37.037 0.01 0.00 0.00 2.18
4394 4454 4.324267 GACAATAATTATGGGACGGAGGG 58.676 47.826 4.84 0.00 0.00 4.30
4399 4459 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
4473 4534 0.819259 TGTCAAGAGCCACACAAGCC 60.819 55.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.276201 CGTAGGCATTGGATCAACGAA 58.724 47.619 0.00 0.00 0.00 3.85
82 91 1.794116 CAGTTTTGCGGCAATTGGAAG 59.206 47.619 17.19 1.45 0.00 3.46
94 105 8.742554 ATTAGCAATAGTAACAACAGTTTTGC 57.257 30.769 8.08 8.08 36.35 3.68
114 125 2.822764 AGCAACGGTAGCAGTATTAGC 58.177 47.619 0.00 0.00 0.00 3.09
127 155 3.122948 GCACGGTAATATGATAGCAACGG 59.877 47.826 0.00 0.00 0.00 4.44
129 157 4.377431 GCAGCACGGTAATATGATAGCAAC 60.377 45.833 0.00 0.00 0.00 4.17
151 179 5.654497 ACTTCCTTGCAGCAAATTATTAGC 58.346 37.500 9.65 0.00 0.00 3.09
238 266 5.913137 AATTTATTGATTCGGCACAAGGA 57.087 34.783 0.00 0.00 0.00 3.36
266 295 6.626623 GCAACAGTCTTCGAGGGTAGTATTTA 60.627 42.308 0.00 0.00 0.00 1.40
330 361 2.050895 CTATGCTCCTCGACGGCG 60.051 66.667 2.87 2.87 39.35 6.46
331 362 2.355244 GCTATGCTCCTCGACGGC 60.355 66.667 0.00 0.00 0.00 5.68
332 363 3.437867 AGCTATGCTCCTCGACGG 58.562 61.111 0.00 0.00 30.62 4.79
446 482 2.149973 TCCTTACCTCCCCTCGTTAC 57.850 55.000 0.00 0.00 0.00 2.50
447 483 2.925966 TTCCTTACCTCCCCTCGTTA 57.074 50.000 0.00 0.00 0.00 3.18
535 574 0.583438 CTTGCGCCGTATCAGATTGG 59.417 55.000 4.18 0.00 0.00 3.16
546 585 2.599848 GCAATGTCTATTACTTGCGCCG 60.600 50.000 4.18 0.00 34.68 6.46
548 587 3.951979 AGCAATGTCTATTACTTGCGC 57.048 42.857 0.00 0.00 42.30 6.09
601 640 8.462016 AGTGGCAAATATTTATCAGTCAAAGTC 58.538 33.333 0.00 0.00 0.00 3.01
746 786 8.970859 ATCTCCTCATCAAAAGTATAACCTTG 57.029 34.615 0.00 0.00 0.00 3.61
919 960 9.849166 GTATGGATTTTCGGTTTTTCTATCAAA 57.151 29.630 0.00 0.00 0.00 2.69
920 961 8.463607 GGTATGGATTTTCGGTTTTTCTATCAA 58.536 33.333 0.00 0.00 0.00 2.57
921 962 7.067737 GGGTATGGATTTTCGGTTTTTCTATCA 59.932 37.037 0.00 0.00 0.00 2.15
922 963 7.067737 TGGGTATGGATTTTCGGTTTTTCTATC 59.932 37.037 0.00 0.00 0.00 2.08
923 964 6.893005 TGGGTATGGATTTTCGGTTTTTCTAT 59.107 34.615 0.00 0.00 0.00 1.98
924 965 6.246919 TGGGTATGGATTTTCGGTTTTTCTA 58.753 36.000 0.00 0.00 0.00 2.10
925 966 5.081032 TGGGTATGGATTTTCGGTTTTTCT 58.919 37.500 0.00 0.00 0.00 2.52
926 967 5.394224 TGGGTATGGATTTTCGGTTTTTC 57.606 39.130 0.00 0.00 0.00 2.29
927 968 5.729510 CATGGGTATGGATTTTCGGTTTTT 58.270 37.500 0.00 0.00 0.00 1.94
928 969 5.337578 CATGGGTATGGATTTTCGGTTTT 57.662 39.130 0.00 0.00 0.00 2.43
941 982 2.113139 GGCCGTCCCATGGGTATG 59.887 66.667 30.28 20.24 36.47 2.39
942 983 3.556306 CGGCCGTCCCATGGGTAT 61.556 66.667 30.28 0.00 36.47 2.73
976 1017 1.683365 CCAAACCTGGCCTCATGGG 60.683 63.158 3.32 0.84 35.39 4.00
977 1018 4.023137 CCAAACCTGGCCTCATGG 57.977 61.111 3.32 3.56 35.39 3.66
1039 1083 0.103026 GATTTTCTGAATGGCCCCGC 59.897 55.000 0.00 0.00 0.00 6.13
1040 1084 1.678101 GAGATTTTCTGAATGGCCCCG 59.322 52.381 0.00 0.00 0.00 5.73
1041 1085 1.678101 CGAGATTTTCTGAATGGCCCC 59.322 52.381 0.00 0.00 0.00 5.80
1042 1086 2.356069 GTCGAGATTTTCTGAATGGCCC 59.644 50.000 0.00 0.00 0.00 5.80
1043 1087 3.274288 AGTCGAGATTTTCTGAATGGCC 58.726 45.455 0.00 0.00 0.00 5.36
1044 1088 4.633565 AGAAGTCGAGATTTTCTGAATGGC 59.366 41.667 0.00 0.00 30.41 4.40
1045 1089 7.925483 AGATAGAAGTCGAGATTTTCTGAATGG 59.075 37.037 10.14 0.00 33.51 3.16
1046 1090 8.870160 AGATAGAAGTCGAGATTTTCTGAATG 57.130 34.615 10.14 0.00 33.51 2.67
1047 1091 8.912988 AGAGATAGAAGTCGAGATTTTCTGAAT 58.087 33.333 10.14 0.35 33.51 2.57
1048 1092 8.287439 AGAGATAGAAGTCGAGATTTTCTGAA 57.713 34.615 10.14 0.00 33.51 3.02
1049 1093 7.873719 AGAGATAGAAGTCGAGATTTTCTGA 57.126 36.000 10.14 0.00 33.51 3.27
1050 1094 8.187480 TGAAGAGATAGAAGTCGAGATTTTCTG 58.813 37.037 10.14 0.00 33.51 3.02
1051 1095 8.287439 TGAAGAGATAGAAGTCGAGATTTTCT 57.713 34.615 0.00 0.00 35.49 2.52
1052 1096 9.180678 GATGAAGAGATAGAAGTCGAGATTTTC 57.819 37.037 0.00 0.00 0.00 2.29
1056 1100 7.665145 TGATGATGAAGAGATAGAAGTCGAGAT 59.335 37.037 0.00 0.00 0.00 2.75
1062 1106 7.341512 TGTCACTGATGATGAAGAGATAGAAGT 59.658 37.037 0.00 0.00 37.14 3.01
1063 1107 7.648908 GTGTCACTGATGATGAAGAGATAGAAG 59.351 40.741 0.00 0.00 37.14 2.85
1431 1476 4.575973 GGGAGCATGGCGCAGGAT 62.576 66.667 10.83 0.00 46.13 3.24
1527 1572 1.625759 CGTACATCTGCACAAGCGCA 61.626 55.000 11.47 0.00 46.23 6.09
1641 1686 1.003355 CTGTGCCATCCCGTTCTGT 60.003 57.895 0.00 0.00 0.00 3.41
1749 1794 3.810310 TTTCGGGCATTTTTCAACTGT 57.190 38.095 0.00 0.00 0.00 3.55
1813 1858 3.366679 GCATTGACCAGAACCAAGTCATG 60.367 47.826 0.00 0.00 40.06 3.07
1830 1875 5.581126 TGTAAAGCCCAAGAATAGCATTG 57.419 39.130 0.00 0.00 0.00 2.82
1960 2005 1.023513 ACGCTCAATGCTTCAGAGGC 61.024 55.000 0.00 0.00 40.11 4.70
2093 2138 1.394917 CGCAACCTATCTTGACAGCAC 59.605 52.381 0.00 0.00 0.00 4.40
2426 2471 0.032952 AAGTGCAGCTGCCACAAATG 59.967 50.000 34.64 0.00 41.18 2.32
2427 2472 0.032952 CAAGTGCAGCTGCCACAAAT 59.967 50.000 34.64 13.72 41.18 2.32
2459 2504 4.398044 CGCTACCCAAGTTTCCACATTTAT 59.602 41.667 0.00 0.00 0.00 1.40
2504 2549 2.169352 AGCACAATATCCTTCTCAGCGT 59.831 45.455 0.00 0.00 0.00 5.07
2506 2551 4.694509 CCATAGCACAATATCCTTCTCAGC 59.305 45.833 0.00 0.00 0.00 4.26
2640 2685 1.010797 GCTGCATGCCGATAACACG 60.011 57.895 16.68 0.00 35.15 4.49
2731 2776 1.114627 ATGGCACTACGATGCTCTGA 58.885 50.000 10.09 0.00 45.38 3.27
3048 3093 7.749570 GTGTGCATTGCATTATTGATCTCTATC 59.250 37.037 15.49 0.00 41.91 2.08
3143 3188 4.398319 ACAATCATCCCGTCTCAACTTTT 58.602 39.130 0.00 0.00 0.00 2.27
3154 3199 5.156355 CAACTGAAAGAAACAATCATCCCG 58.844 41.667 0.00 0.00 37.43 5.14
3215 3260 7.648908 TGTATTGAAAGTTCATGTTTCAGCTTG 59.351 33.333 9.21 0.00 43.11 4.01
3216 3261 7.649306 GTGTATTGAAAGTTCATGTTTCAGCTT 59.351 33.333 9.21 3.76 43.11 3.74
3230 3275 5.299279 CCACCAAGTGAAGTGTATTGAAAGT 59.701 40.000 0.00 0.00 35.23 2.66
3256 3301 5.537674 TGTCGTTACTTCCTTCTAGGAACTT 59.462 40.000 4.07 0.00 46.88 2.66
3269 3314 7.690228 TGCATATGGTATTTTGTCGTTACTTC 58.310 34.615 4.56 0.00 0.00 3.01
3286 3331 8.627208 AAGATGACTTATTACCTTGCATATGG 57.373 34.615 4.56 0.00 34.28 2.74
3304 3349 9.851043 GTGCTATTTTTCTCGTTATAAGATGAC 57.149 33.333 0.00 0.00 0.00 3.06
3316 3361 5.786401 ACTAAGCTGTGCTATTTTTCTCG 57.214 39.130 0.00 0.00 38.25 4.04
3324 3369 4.074970 AGTGCAAAACTAAGCTGTGCTAT 58.925 39.130 0.00 0.00 38.25 2.97
3366 3411 3.181461 ACTTCTTGGAAGTGTCTGTCCTG 60.181 47.826 11.46 0.00 34.77 3.86
3481 3527 8.682710 GGTCAATGTGCTTCTTTAATTATGGTA 58.317 33.333 0.00 0.00 0.00 3.25
3482 3528 7.397192 AGGTCAATGTGCTTCTTTAATTATGGT 59.603 33.333 0.00 0.00 0.00 3.55
3579 3625 2.181975 TCATGAGTCATGAGCAGACCA 58.818 47.619 28.18 7.19 44.60 4.02
3607 3653 3.366070 CCGACAACGAGATCACTAACTGT 60.366 47.826 0.00 0.00 42.66 3.55
3624 3672 4.699735 ACAAATGCATAATGACTTCCGACA 59.300 37.500 16.80 0.00 0.00 4.35
3661 3709 2.002586 AGGTTCGATGCATGAAACTCG 58.997 47.619 18.11 10.34 39.06 4.18
3790 3838 7.013846 GGCATTTAAGTATATTGCCCTACACAA 59.986 37.037 0.77 0.00 45.63 3.33
3811 3859 4.734402 GCAATCGTGTCATTATGTGGCATT 60.734 41.667 0.00 0.00 45.63 3.56
3894 3944 0.794473 GCCTTCGTAACTGGTTTCGG 59.206 55.000 11.29 0.00 34.76 4.30
3895 3945 1.193874 GTGCCTTCGTAACTGGTTTCG 59.806 52.381 6.23 6.23 35.21 3.46
3907 3957 1.630244 CCGCAGAAAGAGTGCCTTCG 61.630 60.000 0.00 0.00 37.67 3.79
3912 3962 3.435186 GGCCCGCAGAAAGAGTGC 61.435 66.667 0.00 0.00 37.58 4.40
3913 3963 2.037136 CAGGCCCGCAGAAAGAGTG 61.037 63.158 0.00 0.00 0.00 3.51
4046 4105 1.847328 TCCAGGTGTTCAGAGCGATA 58.153 50.000 0.00 0.00 0.00 2.92
4122 4181 0.175531 ATAAAACAATGCGGCCAGGC 59.824 50.000 1.26 1.26 0.00 4.85
4136 4195 8.350722 GTGAGACCGAGACTATACATCATAAAA 58.649 37.037 0.00 0.00 0.00 1.52
4180 4239 0.741221 GGCTCGAAGAAATCAGCGGT 60.741 55.000 0.00 0.00 34.79 5.68
4260 4320 5.298527 TCCTGATTTCTGTGACGTACGATAT 59.701 40.000 24.41 0.00 0.00 1.63
4266 4326 2.826128 AGCTCCTGATTTCTGTGACGTA 59.174 45.455 0.00 0.00 0.00 3.57
4320 4380 5.647658 TGTGTTTGTAGATTGAATGCTAGGG 59.352 40.000 0.00 0.00 0.00 3.53
4366 4426 4.210537 CGTCCCATAATTATTGTCGTGGTC 59.789 45.833 0.00 0.00 0.00 4.02
4394 4454 5.470437 GGCCATCCTAAATTGCTTAGTACTC 59.530 44.000 0.00 0.00 36.06 2.59
4399 4459 4.500375 GCTTGGCCATCCTAAATTGCTTAG 60.500 45.833 6.09 0.00 37.36 2.18


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

AutoCloner maintained by Alex Coulton.