Multiple sequence alignment - TraesCS2D01G370300

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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 TraesCS2D01G370300 chr2D 100.000 4490 0 0 1 4490 474734194 474738683 0.000000e+00 8292.0
1 TraesCS2D01G370300 chr2D 77.070 157 32 4 624 777 37528728 37528883 2.220000e-13 87.9
2 TraesCS2D01G370300 chrUn 94.793 2362 68 29 611 2956 22046189 22048511 0.000000e+00 3629.0
3 TraesCS2D01G370300 chrUn 96.533 548 18 1 2953 3499 22050838 22051385 0.000000e+00 905.0
4 TraesCS2D01G370300 chrUn 95.860 314 11 2 3583 3895 22051384 22051696 1.440000e-139 507.0
5 TraesCS2D01G370300 chrUn 87.755 49 6 0 724 772 94272320 94272368 1.740000e-04 58.4
6 TraesCS2D01G370300 chrUn 96.875 32 0 1 745 776 94302392 94302422 8.000000e-03 52.8
7 TraesCS2D01G370300 chr2A 91.326 2444 140 36 871 3294 617175422 617177813 0.000000e+00 3273.0
8 TraesCS2D01G370300 chr2A 96.141 596 19 3 3882 4475 101562867 101562274 0.000000e+00 970.0
9 TraesCS2D01G370300 chr2A 95.638 596 21 4 3882 4475 197912882 197913474 0.000000e+00 952.0
10 TraesCS2D01G370300 chr2A 96.335 191 7 0 3309 3499 617177799 617177989 9.380000e-82 315.0
11 TraesCS2D01G370300 chr2A 92.969 128 9 0 3583 3710 617177988 617178115 2.130000e-43 187.0
12 TraesCS2D01G370300 chr2A 96.203 79 3 0 3812 3890 617178189 617178267 3.650000e-26 130.0
13 TraesCS2D01G370300 chr4D 98.200 611 7 2 3882 4490 214998083 214998691 0.000000e+00 1064.0
14 TraesCS2D01G370300 chr4D 98.574 491 4 2 3881 4369 215003901 215003412 0.000000e+00 865.0
15 TraesCS2D01G370300 chr6A 96.147 597 19 3 3881 4475 368607937 368607343 0.000000e+00 972.0
16 TraesCS2D01G370300 chr6A 92.857 98 5 1 3487 3584 557970143 557970048 1.680000e-29 141.0
17 TraesCS2D01G370300 chr2B 94.966 596 24 4 3881 4474 168773888 168773297 0.000000e+00 929.0
18 TraesCS2D01G370300 chr2B 80.889 450 67 18 9 448 438881750 438881310 2.000000e-88 337.0
19 TraesCS2D01G370300 chr7B 95.978 547 19 2 3876 4420 705867214 705867759 0.000000e+00 885.0
20 TraesCS2D01G370300 chr7B 95.161 62 3 0 4414 4475 705885378 705885439 1.030000e-16 99.0
21 TraesCS2D01G370300 chr5A 92.545 617 20 11 3882 4475 37514014 37513401 0.000000e+00 861.0
22 TraesCS2D01G370300 chr7D 93.189 602 14 8 3876 4475 157394882 157395458 0.000000e+00 859.0
23 TraesCS2D01G370300 chr7D 81.628 430 63 15 1 421 602796821 602797243 4.300000e-90 342.0
24 TraesCS2D01G370300 chr7D 80.426 470 71 17 1 458 72769688 72769228 5.560000e-89 339.0
25 TraesCS2D01G370300 chr7D 93.069 101 3 3 3488 3588 5068178 5068082 1.300000e-30 145.0
26 TraesCS2D01G370300 chr7D 92.233 103 6 1 3495 3597 22964344 22964244 1.300000e-30 145.0
27 TraesCS2D01G370300 chr7D 75.949 158 35 3 623 777 433884262 433884419 1.340000e-10 78.7
28 TraesCS2D01G370300 chr5D 81.703 552 77 19 2 540 80816175 80815635 5.330000e-119 438.0
29 TraesCS2D01G370300 chr5D 78.808 604 85 29 2 578 537172745 537172158 2.550000e-97 366.0
30 TraesCS2D01G370300 chr7A 78.898 635 94 24 2 604 44353832 44353206 1.170000e-105 394.0
31 TraesCS2D01G370300 chr4A 78.550 662 93 35 2 629 56511951 56511305 1.510000e-104 390.0
32 TraesCS2D01G370300 chr4A 95.556 90 2 1 3498 3587 69329939 69329852 4.680000e-30 143.0
33 TraesCS2D01G370300 chr4A 80.892 157 26 4 623 776 464771929 464771774 2.190000e-23 121.0
34 TraesCS2D01G370300 chr1A 82.127 442 63 15 11 444 353654970 353654537 9.180000e-97 364.0
35 TraesCS2D01G370300 chr6B 80.752 452 72 14 2 444 42431993 42431548 5.560000e-89 339.0
36 TraesCS2D01G370300 chr3D 94.845 97 4 1 3494 3589 516197364 516197268 2.800000e-32 150.0
37 TraesCS2D01G370300 chr4B 96.667 90 1 1 3495 3584 106975855 106975942 1.010000e-31 148.0
38 TraesCS2D01G370300 chr5B 93.000 100 4 2 3489 3588 103464769 103464865 4.680000e-30 143.0
39 TraesCS2D01G370300 chr5B 93.000 100 4 2 3489 3588 105695937 105696033 4.680000e-30 143.0
40 TraesCS2D01G370300 chr3B 91.589 107 3 4 3479 3585 265853257 265853357 4.680000e-30 143.0
41 TraesCS2D01G370300 chr3A 76.712 146 31 3 629 771 667130696 667130551 1.340000e-10 78.7


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 TraesCS2D01G370300 chr2D 474734194 474738683 4489 False 8292.000000 8292 100.000000 1 4490 1 chr2D.!!$F2 4489
1 TraesCS2D01G370300 chrUn 22046189 22051696 5507 False 1680.333333 3629 95.728667 611 3895 3 chrUn.!!$F3 3284
2 TraesCS2D01G370300 chr2A 617175422 617178267 2845 False 976.250000 3273 94.208250 871 3890 4 chr2A.!!$F2 3019
3 TraesCS2D01G370300 chr2A 101562274 101562867 593 True 970.000000 970 96.141000 3882 4475 1 chr2A.!!$R1 593
4 TraesCS2D01G370300 chr2A 197912882 197913474 592 False 952.000000 952 95.638000 3882 4475 1 chr2A.!!$F1 593
5 TraesCS2D01G370300 chr4D 214998083 214998691 608 False 1064.000000 1064 98.200000 3882 4490 1 chr4D.!!$F1 608
6 TraesCS2D01G370300 chr6A 368607343 368607937 594 True 972.000000 972 96.147000 3881 4475 1 chr6A.!!$R1 594
7 TraesCS2D01G370300 chr2B 168773297 168773888 591 True 929.000000 929 94.966000 3881 4474 1 chr2B.!!$R1 593
8 TraesCS2D01G370300 chr7B 705867214 705867759 545 False 885.000000 885 95.978000 3876 4420 1 chr7B.!!$F1 544
9 TraesCS2D01G370300 chr5A 37513401 37514014 613 True 861.000000 861 92.545000 3882 4475 1 chr5A.!!$R1 593
10 TraesCS2D01G370300 chr7D 157394882 157395458 576 False 859.000000 859 93.189000 3876 4475 1 chr7D.!!$F1 599
11 TraesCS2D01G370300 chr5D 80815635 80816175 540 True 438.000000 438 81.703000 2 540 1 chr5D.!!$R1 538
12 TraesCS2D01G370300 chr5D 537172158 537172745 587 True 366.000000 366 78.808000 2 578 1 chr5D.!!$R2 576
13 TraesCS2D01G370300 chr7A 44353206 44353832 626 True 394.000000 394 78.898000 2 604 1 chr7A.!!$R1 602
14 TraesCS2D01G370300 chr4A 56511305 56511951 646 True 390.000000 390 78.550000 2 629 1 chr4A.!!$R1 627

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
639 774 0.611714 AATAGGGGCTCGAACGTTGT 59.388 50.0 5.0 0.0 0.00 3.32 F
797 932 0.927029 AAGGGAGAAATAGGGGTGCC 59.073 55.0 0.0 0.0 0.00 5.01 F
1805 1959 0.806868 AATTGTGATGCTGGAGTGCG 59.193 50.0 0.0 0.0 35.36 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1941 1.028330 CCGCACTCCAGCATCACAAT 61.028 55.000 0.00 0.0 0.0 2.71 R
2721 2889 2.571653 TGTTGTAGATCTGGAACCTGGG 59.428 50.000 5.18 0.0 0.0 4.45 R
3568 6067 1.784593 TGATATACTCCCTCCGTCCCA 59.215 52.381 0.00 0.0 0.0 4.37 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
588 718 2.124570 CCATCTGGGCTTCCACCG 60.125 66.667 0.00 0.00 36.39 4.94
617 752 2.124278 CCCCGAGGCTTAAAGGGC 60.124 66.667 11.33 0.00 42.47 5.19
634 769 1.158484 GGCGAAATAGGGGCTCGAAC 61.158 60.000 0.00 0.00 34.52 3.95
637 772 1.738030 CGAAATAGGGGCTCGAACGTT 60.738 52.381 0.00 0.00 34.52 3.99
639 774 0.611714 AATAGGGGCTCGAACGTTGT 59.388 50.000 5.00 0.00 0.00 3.32
645 780 3.000080 GCTCGAACGTTGTGGCTCG 62.000 63.158 5.00 1.24 0.00 5.03
682 817 1.745087 GCATGTCCAATGAATGACCGT 59.255 47.619 0.00 0.00 0.00 4.83
760 895 4.276431 ACGGTTGAATAAAAAGCTTCGGAA 59.724 37.500 0.00 0.00 0.00 4.30
765 900 7.170828 GGTTGAATAAAAAGCTTCGGAATTTGT 59.829 33.333 0.00 0.00 0.00 2.83
766 901 7.867445 TGAATAAAAAGCTTCGGAATTTGTC 57.133 32.000 0.00 0.02 0.00 3.18
767 902 7.657336 TGAATAAAAAGCTTCGGAATTTGTCT 58.343 30.769 0.00 0.00 0.00 3.41
768 903 8.788806 TGAATAAAAAGCTTCGGAATTTGTCTA 58.211 29.630 0.00 0.00 0.00 2.59
769 904 9.620660 GAATAAAAAGCTTCGGAATTTGTCTAA 57.379 29.630 0.00 0.00 0.00 2.10
770 905 9.974980 AATAAAAAGCTTCGGAATTTGTCTAAA 57.025 25.926 0.00 0.00 0.00 1.85
771 906 9.974980 ATAAAAAGCTTCGGAATTTGTCTAAAA 57.025 25.926 0.00 0.00 0.00 1.52
796 931 4.455070 AATAAGGGAGAAATAGGGGTGC 57.545 45.455 0.00 0.00 0.00 5.01
797 932 0.927029 AAGGGAGAAATAGGGGTGCC 59.073 55.000 0.00 0.00 0.00 5.01
798 933 0.994050 AGGGAGAAATAGGGGTGCCC 60.994 60.000 0.00 0.00 45.90 5.36
1094 1247 2.193248 CAATTCCCCTCCCTCCGC 59.807 66.667 0.00 0.00 0.00 5.54
1114 1267 1.355796 CGCAATTCGCCGAACACCTA 61.356 55.000 0.00 0.00 37.30 3.08
1632 1785 0.984230 GGTGGGGAGTTCTCACATGA 59.016 55.000 3.20 0.00 33.45 3.07
1659 1812 9.229784 CATTTTCCAGTTTCTTATCATTCATCG 57.770 33.333 0.00 0.00 0.00 3.84
1787 1941 3.444742 CCATGCAACTTCTGATGGCTTAA 59.555 43.478 0.00 0.00 30.76 1.85
1805 1959 0.806868 AATTGTGATGCTGGAGTGCG 59.193 50.000 0.00 0.00 35.36 5.34
1889 2045 2.355716 GGATCCATCCTCCAAACGACAA 60.356 50.000 6.95 0.00 43.73 3.18
2005 2164 3.485877 GCGTCTCATTATTTGGCACTGTC 60.486 47.826 0.00 0.00 0.00 3.51
2062 2221 7.586300 CAGAACCACTCTTAATTTGTTGTAACG 59.414 37.037 0.00 0.00 29.07 3.18
2100 2259 2.575735 TCCATGTTCCAGCAAGATACCA 59.424 45.455 0.00 0.00 0.00 3.25
2101 2260 2.684881 CCATGTTCCAGCAAGATACCAC 59.315 50.000 0.00 0.00 0.00 4.16
2102 2261 3.346315 CATGTTCCAGCAAGATACCACA 58.654 45.455 0.00 0.00 0.00 4.17
2103 2262 2.778299 TGTTCCAGCAAGATACCACAC 58.222 47.619 0.00 0.00 0.00 3.82
2104 2263 2.105649 TGTTCCAGCAAGATACCACACA 59.894 45.455 0.00 0.00 0.00 3.72
2110 2276 5.589855 TCCAGCAAGATACCACACAAATATG 59.410 40.000 0.00 0.00 0.00 1.78
2552 2720 1.674221 CCAGAGGTCTGTACTGCTTGC 60.674 57.143 6.25 0.00 42.27 4.01
2568 2736 3.737774 TGCTTGCGATCTTGAAGATATCG 59.262 43.478 7.82 10.52 44.04 2.92
2622 2790 9.674824 TTATTTTACTGCTATTAGCGAGTACTC 57.325 33.333 13.18 13.18 46.26 2.59
2721 2889 2.399916 ATCTTTCTGCAGACTCTGGC 57.600 50.000 18.03 1.47 31.21 4.85
2962 5460 4.565564 CCTTAAATTCCGAAGTAGGTGTCG 59.434 45.833 0.00 0.00 37.01 4.35
3297 5795 8.925161 TTCTGTAAACCTGTTGAAAAATCTTG 57.075 30.769 0.00 0.00 0.00 3.02
3305 5804 5.816777 CCTGTTGAAAAATCTTGGCAAAAGA 59.183 36.000 0.00 3.80 0.00 2.52
3307 5806 7.071014 TGTTGAAAAATCTTGGCAAAAGAAC 57.929 32.000 0.00 0.00 0.00 3.01
3497 5996 3.412386 CTGGCACCAGCTAAAGTAAACT 58.588 45.455 3.23 0.00 41.70 2.66
3498 5997 4.564821 CCTGGCACCAGCTAAAGTAAACTA 60.565 45.833 11.39 0.00 42.35 2.24
3499 5998 4.320870 TGGCACCAGCTAAAGTAAACTAC 58.679 43.478 0.00 0.00 41.70 2.73
3500 5999 4.041198 TGGCACCAGCTAAAGTAAACTACT 59.959 41.667 0.00 0.00 40.05 2.57
3501 6000 4.630505 GGCACCAGCTAAAGTAAACTACTC 59.369 45.833 0.00 0.00 38.41 2.59
3502 6001 4.630505 GCACCAGCTAAAGTAAACTACTCC 59.369 45.833 0.00 0.00 36.40 3.85
3503 6002 5.176592 CACCAGCTAAAGTAAACTACTCCC 58.823 45.833 0.00 0.00 38.26 4.30
3504 6003 5.046520 CACCAGCTAAAGTAAACTACTCCCT 60.047 44.000 0.00 0.00 38.26 4.20
3505 6004 5.187381 ACCAGCTAAAGTAAACTACTCCCTC 59.813 44.000 0.00 0.00 38.26 4.30
3506 6005 5.395435 CCAGCTAAAGTAAACTACTCCCTCC 60.395 48.000 0.00 0.00 38.26 4.30
3507 6006 4.401837 AGCTAAAGTAAACTACTCCCTCCG 59.598 45.833 0.00 0.00 38.26 4.63
3508 6007 4.159321 GCTAAAGTAAACTACTCCCTCCGT 59.841 45.833 0.00 0.00 38.26 4.69
3509 6008 4.797800 AAAGTAAACTACTCCCTCCGTC 57.202 45.455 0.00 0.00 38.26 4.79
3510 6009 2.732763 AGTAAACTACTCCCTCCGTCC 58.267 52.381 0.00 0.00 32.47 4.79
3511 6010 1.753649 GTAAACTACTCCCTCCGTCCC 59.246 57.143 0.00 0.00 0.00 4.46
3512 6011 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
3513 6012 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3514 6013 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3515 6014 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3516 6015 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3517 6016 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3518 6017 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3519 6018 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3520 6019 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3521 6020 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3522 6021 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3523 6022 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3524 6023 5.015924 TCCCTCCGTCCCATAATATAAGAGA 59.984 44.000 0.00 0.00 0.00 3.10
3525 6024 5.361285 CCCTCCGTCCCATAATATAAGAGAG 59.639 48.000 0.00 0.00 0.00 3.20
3526 6025 5.163499 CCTCCGTCCCATAATATAAGAGAGC 60.163 48.000 0.00 0.00 0.00 4.09
3527 6026 5.330233 TCCGTCCCATAATATAAGAGAGCA 58.670 41.667 0.00 0.00 0.00 4.26
3528 6027 5.958380 TCCGTCCCATAATATAAGAGAGCAT 59.042 40.000 0.00 0.00 0.00 3.79
3529 6028 6.440647 TCCGTCCCATAATATAAGAGAGCATT 59.559 38.462 0.00 0.00 0.00 3.56
3530 6029 7.038302 TCCGTCCCATAATATAAGAGAGCATTT 60.038 37.037 0.00 0.00 0.00 2.32
3531 6030 7.607991 CCGTCCCATAATATAAGAGAGCATTTT 59.392 37.037 0.00 0.00 0.00 1.82
3532 6031 9.003658 CGTCCCATAATATAAGAGAGCATTTTT 57.996 33.333 0.00 0.00 0.00 1.94
3541 6040 9.890629 ATATAAGAGAGCATTTTTGACACTACA 57.109 29.630 0.00 0.00 0.00 2.74
3542 6041 5.931441 AGAGAGCATTTTTGACACTACAC 57.069 39.130 0.00 0.00 0.00 2.90
3543 6042 5.615289 AGAGAGCATTTTTGACACTACACT 58.385 37.500 0.00 0.00 0.00 3.55
3544 6043 6.759272 AGAGAGCATTTTTGACACTACACTA 58.241 36.000 0.00 0.00 0.00 2.74
3545 6044 6.870965 AGAGAGCATTTTTGACACTACACTAG 59.129 38.462 0.00 0.00 0.00 2.57
3546 6045 6.525629 AGAGCATTTTTGACACTACACTAGT 58.474 36.000 0.00 0.00 40.28 2.57
3574 6073 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
3575 6074 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
3576 6075 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
3577 6076 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
3578 6077 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
3579 6078 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
3580 6079 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
3581 6080 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3648 6147 4.974399 AGGTTTGGTAGCATTATCTAGCC 58.026 43.478 0.00 0.00 36.50 3.93
3736 6235 6.855836 TGATCTGCTTGTTCATATGGAAAAC 58.144 36.000 2.13 0.90 37.23 2.43
3738 6237 6.839124 TCTGCTTGTTCATATGGAAAACAT 57.161 33.333 8.73 0.00 43.68 2.71
3740 6239 7.669427 TCTGCTTGTTCATATGGAAAACATTT 58.331 30.769 8.73 0.00 41.03 2.32
3813 6337 7.042456 CCTCGATATCACACTGAAAATACTTGG 60.042 40.741 3.12 0.00 0.00 3.61
4056 6582 2.281276 ACGGGGCAAACCTTCGAC 60.281 61.111 0.00 0.00 40.03 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 71 3.430556 TCGGACAATGTTGAACGTGTATG 59.569 43.478 4.69 0.00 34.43 2.39
195 205 8.502161 ACGAGTGCTTAAAAATGTTGAATAAC 57.498 30.769 0.00 0.00 37.32 1.89
211 221 8.349983 AGTATTAAAAATGTTGAACGAGTGCTT 58.650 29.630 0.00 0.00 0.00 3.91
213 223 8.502161 AAGTATTAAAAATGTTGAACGAGTGC 57.498 30.769 0.00 0.00 0.00 4.40
560 690 4.415150 CAGATGGGCCGGCACAGT 62.415 66.667 37.68 24.16 30.39 3.55
600 730 2.124278 GCCCTTTAAGCCTCGGGG 60.124 66.667 0.00 0.00 37.17 5.73
604 734 2.879026 CCTATTTCGCCCTTTAAGCCTC 59.121 50.000 0.00 0.00 0.00 4.70
605 735 2.422945 CCCTATTTCGCCCTTTAAGCCT 60.423 50.000 0.00 0.00 0.00 4.58
617 752 0.179119 ACGTTCGAGCCCCTATTTCG 60.179 55.000 0.00 0.00 35.76 3.46
634 769 1.082756 GAGTTTGCGAGCCACAACG 60.083 57.895 0.00 0.00 0.00 4.10
637 772 3.345808 GCGAGTTTGCGAGCCACA 61.346 61.111 0.00 0.00 0.00 4.17
645 780 2.148365 GCATGCTTCGCGAGTTTGC 61.148 57.895 11.37 13.70 0.00 3.68
655 790 3.513680 TTCATTGGACATGCATGCTTC 57.486 42.857 26.53 16.79 0.00 3.86
667 802 3.348647 ACATGACGGTCATTCATTGGA 57.651 42.857 20.52 0.00 34.28 3.53
682 817 2.790433 GGCTGACCTAACCAAACATGA 58.210 47.619 0.00 0.00 0.00 3.07
721 856 6.474140 TCAACCGTCACAAGGTATACATAT 57.526 37.500 5.01 0.00 41.95 1.78
722 857 5.918426 TCAACCGTCACAAGGTATACATA 57.082 39.130 5.01 0.00 41.95 2.29
734 869 4.611366 CGAAGCTTTTTATTCAACCGTCAC 59.389 41.667 0.00 0.00 0.00 3.67
738 873 4.413495 TCCGAAGCTTTTTATTCAACCG 57.587 40.909 0.00 0.00 0.00 4.44
769 904 9.434275 CACCCCTATTTCTCCCTTATTTTATTT 57.566 33.333 0.00 0.00 0.00 1.40
770 905 7.509318 GCACCCCTATTTCTCCCTTATTTTATT 59.491 37.037 0.00 0.00 0.00 1.40
771 906 7.010771 GCACCCCTATTTCTCCCTTATTTTAT 58.989 38.462 0.00 0.00 0.00 1.40
777 912 2.132686 GGCACCCCTATTTCTCCCTTA 58.867 52.381 0.00 0.00 0.00 2.69
794 929 3.697747 CGAGGTTGTACCGGGGCA 61.698 66.667 6.32 0.15 44.90 5.36
796 931 4.462280 GGCGAGGTTGTACCGGGG 62.462 72.222 6.32 0.00 44.90 5.73
797 932 2.053865 TAGGCGAGGTTGTACCGGG 61.054 63.158 6.32 0.00 44.90 5.73
798 933 1.140375 GTAGGCGAGGTTGTACCGG 59.860 63.158 0.00 0.00 44.90 5.28
799 934 1.226491 CGTAGGCGAGGTTGTACCG 60.226 63.158 0.00 0.00 44.90 4.02
800 935 1.517913 GCGTAGGCGAGGTTGTACC 60.518 63.158 0.00 0.00 41.33 3.34
801 936 0.734889 TAGCGTAGGCGAGGTTGTAC 59.265 55.000 1.05 0.00 46.35 2.90
802 937 0.734889 GTAGCGTAGGCGAGGTTGTA 59.265 55.000 1.05 0.00 46.35 2.41
803 938 1.509923 GTAGCGTAGGCGAGGTTGT 59.490 57.895 1.05 0.00 46.35 3.32
804 939 1.585521 CGTAGCGTAGGCGAGGTTG 60.586 63.158 1.05 0.00 46.35 3.77
805 940 2.796651 CGTAGCGTAGGCGAGGTT 59.203 61.111 1.05 0.00 46.35 3.50
833 968 1.745264 TTTTTGGCGCTCCTTTGGG 59.255 52.632 7.64 0.00 0.00 4.12
867 1002 1.217001 GTTTTTGGCGCTCCTTTTGG 58.783 50.000 7.64 0.00 42.21 3.28
868 1003 1.217001 GGTTTTTGGCGCTCCTTTTG 58.783 50.000 7.64 0.00 0.00 2.44
1066 1215 2.115291 GGGAATTGAGGAGTGCGCC 61.115 63.158 4.18 0.00 0.00 6.53
1592 1745 4.722700 GGAAGCTCTTGGGCGGCA 62.723 66.667 12.47 0.00 37.29 5.69
1787 1941 1.028330 CCGCACTCCAGCATCACAAT 61.028 55.000 0.00 0.00 0.00 2.71
1805 1959 8.145122 TGTGAATTGGTACCTAATTTTGTTTCC 58.855 33.333 14.36 4.93 0.00 3.13
1889 2045 2.676748 TCAGGGGCTCAACAAACAAAT 58.323 42.857 0.00 0.00 0.00 2.32
1964 2121 4.897224 ACGCGAATACATGATCAAACTTG 58.103 39.130 15.93 0.00 0.00 3.16
2062 2221 8.355913 GGAACATGGATATCTTGAGGATTTTTC 58.644 37.037 2.05 0.47 35.98 2.29
2100 2259 9.801873 GACTATTGTTAAATGGCATATTTGTGT 57.198 29.630 0.00 0.00 0.00 3.72
2101 2260 9.800433 TGACTATTGTTAAATGGCATATTTGTG 57.200 29.630 0.00 0.00 0.00 3.33
2355 2523 5.360714 TCACATCTTTTCCAGTTTCTTGCTT 59.639 36.000 0.00 0.00 0.00 3.91
2552 2720 6.074623 CCAAGTTGACGATATCTTCAAGATCG 60.075 42.308 21.31 6.00 46.12 3.69
2568 2736 7.672983 TCTTCTAACAATCATCCAAGTTGAC 57.327 36.000 3.87 0.00 0.00 3.18
2623 2791 4.675190 TCTACAACGTCCGCTATATAGC 57.325 45.455 22.56 22.56 45.62 2.97
2624 2792 7.806487 TGAAAATCTACAACGTCCGCTATATAG 59.194 37.037 5.30 5.30 0.00 1.31
2625 2793 7.650890 TGAAAATCTACAACGTCCGCTATATA 58.349 34.615 0.00 0.00 0.00 0.86
2626 2794 6.509656 TGAAAATCTACAACGTCCGCTATAT 58.490 36.000 0.00 0.00 0.00 0.86
2627 2795 5.893687 TGAAAATCTACAACGTCCGCTATA 58.106 37.500 0.00 0.00 0.00 1.31
2628 2796 4.751060 TGAAAATCTACAACGTCCGCTAT 58.249 39.130 0.00 0.00 0.00 2.97
2721 2889 2.571653 TGTTGTAGATCTGGAACCTGGG 59.428 50.000 5.18 0.00 0.00 4.45
3297 5795 3.518634 TCAACAGGTTGTTCTTTTGCC 57.481 42.857 11.55 0.00 38.77 4.52
3497 5996 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
3498 5997 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
3499 5998 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3500 5999 5.015924 TCTCTTATATTATGGGACGGAGGGA 59.984 44.000 0.00 0.00 0.00 4.20
3501 6000 5.269991 TCTCTTATATTATGGGACGGAGGG 58.730 45.833 0.00 0.00 0.00 4.30
3502 6001 5.163499 GCTCTCTTATATTATGGGACGGAGG 60.163 48.000 0.00 0.00 0.00 4.30
3503 6002 5.419155 TGCTCTCTTATATTATGGGACGGAG 59.581 44.000 0.00 0.00 0.00 4.63
3504 6003 5.330233 TGCTCTCTTATATTATGGGACGGA 58.670 41.667 0.00 0.00 0.00 4.69
3505 6004 5.661056 TGCTCTCTTATATTATGGGACGG 57.339 43.478 0.00 0.00 0.00 4.79
3506 6005 8.553459 AAAATGCTCTCTTATATTATGGGACG 57.447 34.615 0.00 0.00 0.00 4.79
3515 6014 9.890629 TGTAGTGTCAAAAATGCTCTCTTATAT 57.109 29.630 0.00 0.00 0.00 0.86
3516 6015 9.151471 GTGTAGTGTCAAAAATGCTCTCTTATA 57.849 33.333 0.00 0.00 0.00 0.98
3517 6016 7.880195 AGTGTAGTGTCAAAAATGCTCTCTTAT 59.120 33.333 0.00 0.00 0.00 1.73
3518 6017 7.217200 AGTGTAGTGTCAAAAATGCTCTCTTA 58.783 34.615 0.00 0.00 0.00 2.10
3519 6018 6.058183 AGTGTAGTGTCAAAAATGCTCTCTT 58.942 36.000 0.00 0.00 0.00 2.85
3520 6019 5.615289 AGTGTAGTGTCAAAAATGCTCTCT 58.385 37.500 0.00 0.00 0.00 3.10
3521 6020 5.931441 AGTGTAGTGTCAAAAATGCTCTC 57.069 39.130 0.00 0.00 0.00 3.20
3522 6021 6.525629 ACTAGTGTAGTGTCAAAAATGCTCT 58.474 36.000 0.00 0.00 37.69 4.09
3523 6022 6.787085 ACTAGTGTAGTGTCAAAAATGCTC 57.213 37.500 0.00 0.00 37.69 4.26
3550 6049 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
3551 6050 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
3552 6051 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
3553 6052 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
3554 6053 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
3555 6054 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
3556 6055 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
3557 6056 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3558 6057 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3559 6058 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3560 6059 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3561 6060 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3562 6061 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3563 6062 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
3564 6063 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3565 6064 4.044952 TGATATACTCCCTCCGTCCCATAA 59.955 45.833 0.00 0.00 0.00 1.90
3566 6065 3.594685 TGATATACTCCCTCCGTCCCATA 59.405 47.826 0.00 0.00 0.00 2.74
3567 6066 2.382305 TGATATACTCCCTCCGTCCCAT 59.618 50.000 0.00 0.00 0.00 4.00
3568 6067 1.784593 TGATATACTCCCTCCGTCCCA 59.215 52.381 0.00 0.00 0.00 4.37
3569 6068 2.169330 GTGATATACTCCCTCCGTCCC 58.831 57.143 0.00 0.00 0.00 4.46
3570 6069 2.820787 CTGTGATATACTCCCTCCGTCC 59.179 54.545 0.00 0.00 0.00 4.79
3571 6070 2.229302 GCTGTGATATACTCCCTCCGTC 59.771 54.545 0.00 0.00 0.00 4.79
3572 6071 2.240279 GCTGTGATATACTCCCTCCGT 58.760 52.381 0.00 0.00 0.00 4.69
3573 6072 2.239400 TGCTGTGATATACTCCCTCCG 58.761 52.381 0.00 0.00 0.00 4.63
3574 6073 3.055530 CCATGCTGTGATATACTCCCTCC 60.056 52.174 0.00 0.00 0.00 4.30
3575 6074 3.580458 ACCATGCTGTGATATACTCCCTC 59.420 47.826 0.00 0.00 0.00 4.30
3576 6075 3.591789 ACCATGCTGTGATATACTCCCT 58.408 45.455 0.00 0.00 0.00 4.20
3577 6076 4.528596 AGTACCATGCTGTGATATACTCCC 59.471 45.833 0.00 0.00 0.00 4.30
3578 6077 5.730296 AGTACCATGCTGTGATATACTCC 57.270 43.478 0.00 0.00 0.00 3.85
3579 6078 5.406780 GCAAGTACCATGCTGTGATATACTC 59.593 44.000 12.66 0.00 40.64 2.59
3580 6079 5.300752 GCAAGTACCATGCTGTGATATACT 58.699 41.667 12.66 0.00 40.64 2.12
3581 6080 5.597813 GCAAGTACCATGCTGTGATATAC 57.402 43.478 12.66 0.00 40.64 1.47
3736 6235 4.121317 ACATTCACAGTTTGCACCAAATG 58.879 39.130 0.00 0.00 35.74 2.32
3738 6237 3.883830 ACATTCACAGTTTGCACCAAA 57.116 38.095 0.00 0.00 0.00 3.28
3740 6239 3.519579 CAAACATTCACAGTTTGCACCA 58.480 40.909 5.94 0.00 46.16 4.17
3798 6297 4.836125 AGCACACCAAGTATTTTCAGTG 57.164 40.909 0.00 0.00 0.00 3.66
3799 6298 5.621193 ACTAGCACACCAAGTATTTTCAGT 58.379 37.500 0.00 0.00 0.00 3.41
3813 6337 4.574828 TCTGGAACAAAGAAACTAGCACAC 59.425 41.667 0.00 0.00 38.70 3.82
4056 6582 1.201414 GGGTTGAACCACATTAAGCCG 59.799 52.381 17.27 0.00 41.02 5.52


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

AutoCloner maintained by Alex Coulton.