Multiple sequence alignment - TraesCS3D01G002700

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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 TraesCS3D01G002700 chr3D 100.000 4465 0 0 736 5200 1256723 1252259 0.000000e+00 8246.0
1 TraesCS3D01G002700 chr3D 100.000 472 0 0 1 472 1257458 1256987 0.000000e+00 872.0
2 TraesCS3D01G002700 chr3A 96.714 4352 110 11 761 5091 7948592 7952931 0.000000e+00 7214.0
3 TraesCS3D01G002700 chr3A 94.722 360 14 3 4841 5200 7958472 7958826 5.880000e-154 555.0
4 TraesCS3D01G002700 chr3A 98.225 169 3 0 164 332 7947933 7948101 3.940000e-76 296.0
5 TraesCS3D01G002700 chr3A 95.152 165 7 1 1 164 7947378 7947542 5.170000e-65 259.0
6 TraesCS3D01G002700 chr3A 92.661 109 3 2 5092 5200 7953834 7953937 9.020000e-33 152.0
7 TraesCS3D01G002700 chr3A 94.915 59 3 0 413 471 7948139 7948197 5.540000e-15 93.5
8 TraesCS3D01G002700 chrUn 92.844 1677 57 25 2676 4320 34304610 34302965 0.000000e+00 2374.0
9 TraesCS3D01G002700 chrUn 96.085 1175 27 8 739 1900 429471014 429469846 0.000000e+00 1897.0
10 TraesCS3D01G002700 chrUn 94.845 776 22 3 1902 2674 467335986 467335226 0.000000e+00 1195.0
11 TraesCS3D01G002700 chrUn 94.239 486 10 4 1 471 333460841 333461323 0.000000e+00 726.0
12 TraesCS3D01G002700 chrUn 92.045 88 3 3 4718 4801 34302481 34302394 2.540000e-23 121.0
13 TraesCS3D01G002700 chrUn 78.771 179 18 6 4352 4510 34302970 34302792 9.210000e-18 102.0
14 TraesCS3D01G002700 chr7A 90.099 101 9 1 4701 4801 597322622 597322721 4.230000e-26 130.0
15 TraesCS3D01G002700 chr7A 97.561 41 1 0 5140 5180 597322740 597322780 2.600000e-08 71.3
16 TraesCS3D01G002700 chr5B 92.105 38 2 1 4902 4938 429415366 429415403 9.000000e-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 TraesCS3D01G002700 chr3D 1252259 1257458 5199 True 4559.000000 8246 100.000000 1 5200 2 chr3D.!!$R1 5199
1 TraesCS3D01G002700 chr3A 7947378 7953937 6559 False 1602.900000 7214 95.533400 1 5200 5 chr3A.!!$F2 5199
2 TraesCS3D01G002700 chrUn 429469846 429471014 1168 True 1897.000000 1897 96.085000 739 1900 1 chrUn.!!$R1 1161
3 TraesCS3D01G002700 chrUn 467335226 467335986 760 True 1195.000000 1195 94.845000 1902 2674 1 chrUn.!!$R2 772
4 TraesCS3D01G002700 chrUn 34302394 34304610 2216 True 865.666667 2374 87.886667 2676 4801 3 chrUn.!!$R3 2125

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
370 763 0.104120 TCGCCGAGAGAGAGAGAGAG 59.896 60.000 0.0 0.0 0.00 3.20 F
371 764 0.104120 CGCCGAGAGAGAGAGAGAGA 59.896 60.000 0.0 0.0 0.00 3.10 F
1067 1589 1.078426 GGACCGCTGCACAAGGTAT 60.078 57.895 0.0 0.0 38.57 2.73 F
2565 3094 3.614092 TCAGGTGAGATCCTTTGCATTC 58.386 45.455 0.0 0.0 35.37 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1898 1.546029 CTGATCAGGGTCGTCTTCACA 59.454 52.381 15.38 0.00 0.00 3.58 R
1421 1943 2.015736 AATACTCTTCGCAGTGCCAG 57.984 50.000 10.11 6.06 0.00 4.85 R
2816 3348 0.179113 AAGCAAACACGCCAACTTGG 60.179 50.000 3.10 3.10 41.55 3.61 R
4419 4985 0.110238 CAGACGCAAACAATGTCGGG 60.110 55.000 0.00 0.00 37.69 5.14 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
38 39 2.372690 CGTTCGGAGGTGCTTCGTG 61.373 63.158 0.00 0.00 33.64 4.35
77 78 1.414919 ACCTACAAACGTGCTTCTCCA 59.585 47.619 0.00 0.00 0.00 3.86
91 92 7.064253 ACGTGCTTCTCCACTTTATGTATAAAC 59.936 37.037 0.00 0.00 33.60 2.01
92 93 7.064134 CGTGCTTCTCCACTTTATGTATAAACA 59.936 37.037 0.00 0.00 35.32 2.83
240 633 0.179081 GGGGTCGTATGTGAGAAGCC 60.179 60.000 0.00 0.00 0.00 4.35
253 646 4.013050 GTGAGAAGCCAGAAATTAAGCCT 58.987 43.478 0.00 0.00 0.00 4.58
292 685 2.247311 CGAGGCATCGTTTCCTTTTG 57.753 50.000 13.51 0.00 44.09 2.44
332 725 1.152902 GCACAGCATGGCTCCCATA 60.153 57.895 0.00 0.00 43.15 2.74
333 726 1.170919 GCACAGCATGGCTCCCATAG 61.171 60.000 0.00 0.00 43.15 2.23
334 727 0.182061 CACAGCATGGCTCCCATAGT 59.818 55.000 0.00 0.00 43.15 2.12
335 728 0.921896 ACAGCATGGCTCCCATAGTT 59.078 50.000 0.00 0.00 43.15 2.24
337 730 0.475906 AGCATGGCTCCCATAGTTCC 59.524 55.000 0.00 0.00 43.15 3.62
339 732 1.816961 GCATGGCTCCCATAGTTCCAG 60.817 57.143 0.00 0.00 43.15 3.86
340 733 0.475906 ATGGCTCCCATAGTTCCAGC 59.524 55.000 0.00 0.00 43.19 4.85
341 734 1.149401 GGCTCCCATAGTTCCAGCC 59.851 63.158 0.00 0.00 42.87 4.85
342 735 1.348775 GGCTCCCATAGTTCCAGCCT 61.349 60.000 0.84 0.00 45.40 4.58
343 736 1.424638 GCTCCCATAGTTCCAGCCTA 58.575 55.000 0.00 0.00 0.00 3.93
344 737 1.346068 GCTCCCATAGTTCCAGCCTAG 59.654 57.143 0.00 0.00 0.00 3.02
345 738 2.683768 CTCCCATAGTTCCAGCCTAGT 58.316 52.381 0.00 0.00 0.00 2.57
346 739 3.041946 CTCCCATAGTTCCAGCCTAGTT 58.958 50.000 0.00 0.00 0.00 2.24
347 740 3.456277 CTCCCATAGTTCCAGCCTAGTTT 59.544 47.826 0.00 0.00 0.00 2.66
348 741 3.454812 TCCCATAGTTCCAGCCTAGTTTC 59.545 47.826 0.00 0.00 0.00 2.78
349 742 3.199946 CCCATAGTTCCAGCCTAGTTTCA 59.800 47.826 0.00 0.00 0.00 2.69
350 743 4.141390 CCCATAGTTCCAGCCTAGTTTCAT 60.141 45.833 0.00 0.00 0.00 2.57
351 744 5.440610 CCATAGTTCCAGCCTAGTTTCATT 58.559 41.667 0.00 0.00 0.00 2.57
352 745 5.529060 CCATAGTTCCAGCCTAGTTTCATTC 59.471 44.000 0.00 0.00 0.00 2.67
353 746 3.600388 AGTTCCAGCCTAGTTTCATTCG 58.400 45.455 0.00 0.00 0.00 3.34
354 747 2.024176 TCCAGCCTAGTTTCATTCGC 57.976 50.000 0.00 0.00 0.00 4.70
355 748 1.017387 CCAGCCTAGTTTCATTCGCC 58.983 55.000 0.00 0.00 0.00 5.54
356 749 0.652592 CAGCCTAGTTTCATTCGCCG 59.347 55.000 0.00 0.00 0.00 6.46
357 750 0.535335 AGCCTAGTTTCATTCGCCGA 59.465 50.000 0.00 0.00 0.00 5.54
358 751 0.931005 GCCTAGTTTCATTCGCCGAG 59.069 55.000 0.00 0.00 0.00 4.63
359 752 1.470979 GCCTAGTTTCATTCGCCGAGA 60.471 52.381 0.00 0.00 0.00 4.04
360 753 2.464865 CCTAGTTTCATTCGCCGAGAG 58.535 52.381 0.00 0.00 0.00 3.20
361 754 2.099263 CCTAGTTTCATTCGCCGAGAGA 59.901 50.000 0.00 0.00 0.00 3.10
362 755 2.285827 AGTTTCATTCGCCGAGAGAG 57.714 50.000 0.00 0.00 0.00 3.20
363 756 1.819288 AGTTTCATTCGCCGAGAGAGA 59.181 47.619 0.00 0.00 0.00 3.10
364 757 2.159310 AGTTTCATTCGCCGAGAGAGAG 60.159 50.000 0.00 0.00 0.00 3.20
365 758 1.751437 TTCATTCGCCGAGAGAGAGA 58.249 50.000 0.00 0.00 0.00 3.10
366 759 1.304254 TCATTCGCCGAGAGAGAGAG 58.696 55.000 0.00 0.00 0.00 3.20
367 760 1.134371 TCATTCGCCGAGAGAGAGAGA 60.134 52.381 0.00 0.00 0.00 3.10
368 761 1.264020 CATTCGCCGAGAGAGAGAGAG 59.736 57.143 0.00 0.00 0.00 3.20
369 762 0.537653 TTCGCCGAGAGAGAGAGAGA 59.462 55.000 0.00 0.00 0.00 3.10
370 763 0.104120 TCGCCGAGAGAGAGAGAGAG 59.896 60.000 0.00 0.00 0.00 3.20
371 764 0.104120 CGCCGAGAGAGAGAGAGAGA 59.896 60.000 0.00 0.00 0.00 3.10
372 765 1.869754 CGCCGAGAGAGAGAGAGAGAG 60.870 61.905 0.00 0.00 0.00 3.20
373 766 1.412710 GCCGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
374 767 2.546795 GCCGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
375 768 2.959030 CCGAGAGAGAGAGAGAGAGAGA 59.041 54.545 0.00 0.00 0.00 3.10
376 769 3.005261 CCGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
377 770 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
378 771 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
379 772 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
380 773 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
381 774 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
382 775 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
383 776 4.877773 AGAGAGAGAGAGAGAGAGAGACT 58.122 47.826 0.00 0.00 0.00 3.24
384 777 6.019656 AGAGAGAGAGAGAGAGAGAGACTA 57.980 45.833 0.00 0.00 0.00 2.59
385 778 6.068010 AGAGAGAGAGAGAGAGAGAGACTAG 58.932 48.000 0.00 0.00 0.00 2.57
386 779 6.019656 AGAGAGAGAGAGAGAGAGACTAGA 57.980 45.833 0.00 0.00 0.00 2.43
387 780 6.068010 AGAGAGAGAGAGAGAGAGACTAGAG 58.932 48.000 0.00 0.00 0.00 2.43
388 781 6.019656 AGAGAGAGAGAGAGAGACTAGAGA 57.980 45.833 0.00 0.00 0.00 3.10
389 782 6.068010 AGAGAGAGAGAGAGAGACTAGAGAG 58.932 48.000 0.00 0.00 0.00 3.20
390 783 6.019656 AGAGAGAGAGAGAGACTAGAGAGA 57.980 45.833 0.00 0.00 0.00 3.10
391 784 6.619464 AGAGAGAGAGAGAGACTAGAGAGAT 58.381 44.000 0.00 0.00 0.00 2.75
392 785 6.719370 AGAGAGAGAGAGAGACTAGAGAGATC 59.281 46.154 0.00 0.00 0.00 2.75
393 786 6.377080 AGAGAGAGAGAGACTAGAGAGATCA 58.623 44.000 0.00 0.00 0.00 2.92
394 787 7.015680 AGAGAGAGAGAGACTAGAGAGATCAT 58.984 42.308 0.00 0.00 0.00 2.45
395 788 7.002250 AGAGAGAGAGACTAGAGAGATCATG 57.998 44.000 0.00 0.00 0.00 3.07
396 789 6.013898 AGAGAGAGAGACTAGAGAGATCATGG 60.014 46.154 0.00 0.00 0.00 3.66
471 879 1.265635 GCCAGTTTGTGCATCGTTGTA 59.734 47.619 0.00 0.00 0.00 2.41
754 1162 4.962836 GCTGCCGGGGATCATGGG 62.963 72.222 2.18 0.00 0.00 4.00
942 1464 2.244117 GATGCTGCAAGTCCGGGAGA 62.244 60.000 6.36 0.00 35.30 3.71
1067 1589 1.078426 GGACCGCTGCACAAGGTAT 60.078 57.895 0.00 0.00 38.57 2.73
1603 2129 7.914859 TCTCTCATTGTGATATCAAGCCATAT 58.085 34.615 7.07 0.00 0.00 1.78
1626 2155 6.032956 TCCAATACGTACTGATGTTCACTT 57.967 37.500 5.43 0.00 0.00 3.16
2341 2870 6.865205 GTCAGCCGAAGAAAACTTTACTACTA 59.135 38.462 0.00 0.00 0.00 1.82
2413 2942 4.090057 GCCTTGACTGCGGCGAAC 62.090 66.667 12.98 0.00 36.45 3.95
2565 3094 3.614092 TCAGGTGAGATCCTTTGCATTC 58.386 45.455 0.00 0.00 35.37 2.67
2597 3126 4.044571 TGTTGGAAGGATCCCTGATCTTTT 59.955 41.667 8.55 0.00 45.95 2.27
2815 3347 2.871096 ACCAGAATTTAAGGGCACGA 57.129 45.000 0.00 0.00 0.00 4.35
2816 3348 2.433436 ACCAGAATTTAAGGGCACGAC 58.567 47.619 0.00 0.00 0.00 4.34
2825 3357 3.670377 GGGCACGACCAAGTTGGC 61.670 66.667 22.25 13.30 42.67 4.52
3220 3752 1.368374 CCCCCTAAAAGTCCCACAGA 58.632 55.000 0.00 0.00 0.00 3.41
3231 3763 4.550076 AGTCCCACAGAAGATCTCTTTG 57.450 45.455 0.00 0.00 36.11 2.77
3467 3999 5.064962 AGCTTAGTGACTGACTGTACGTATC 59.935 44.000 0.00 0.00 35.96 2.24
3725 4269 2.476619 CTGTGAGCCTACTTCAACAACG 59.523 50.000 0.00 0.00 0.00 4.10
3852 4399 1.137086 GGCCGCTCTCTAATGTGAAGA 59.863 52.381 0.00 0.00 0.00 2.87
3917 4467 1.343789 ACCATGATGATCGAGCAGGAG 59.656 52.381 10.08 0.00 0.00 3.69
3918 4468 1.337917 CCATGATGATCGAGCAGGAGG 60.338 57.143 10.08 4.69 0.00 4.30
3919 4469 1.617357 CATGATGATCGAGCAGGAGGA 59.383 52.381 10.08 0.00 0.00 3.71
3970 4520 4.100084 CTGGTGCAGGGCATCCGA 62.100 66.667 0.00 0.00 39.18 4.55
3973 4523 3.127533 GTGCAGGGCATCCGACAC 61.128 66.667 0.00 0.00 41.91 3.67
4005 4555 0.881118 TTTTGCTCATCTCGCCAACC 59.119 50.000 0.00 0.00 0.00 3.77
4171 4721 1.062294 GCTGCTTGAGAAGATTCAGCG 59.938 52.381 0.00 0.00 37.73 5.18
4214 4764 1.160329 AATGATACGGCGCTTGCTCC 61.160 55.000 6.90 0.00 39.13 4.70
4374 4940 5.957842 TTGATTCCTTACAATGTGTGTCC 57.042 39.130 0.00 0.00 41.98 4.02
4382 4948 1.412710 ACAATGTGTGTCCGTCAGACT 59.587 47.619 0.00 0.00 46.46 3.24
4433 4999 0.885196 TAAGCCCCGACATTGTTTGC 59.115 50.000 0.00 0.00 0.00 3.68
4601 5188 7.712797 TCGCTCATATACATCTGTTTTGTAGA 58.287 34.615 0.00 0.00 33.36 2.59
4651 5239 7.503902 TGGTTCATCTGATATATATCTCCCTCG 59.496 40.741 20.74 7.41 33.88 4.63
4808 5531 6.347725 GCATCAATAAACCATAGTGATCGGTC 60.348 42.308 0.00 0.00 30.95 4.79
4815 5538 0.818445 ATAGTGATCGGTCGCGAGGT 60.818 55.000 10.24 0.00 39.83 3.85
4817 5540 1.445582 GTGATCGGTCGCGAGGTTT 60.446 57.895 10.24 0.00 0.00 3.27
4818 5541 1.153901 TGATCGGTCGCGAGGTTTC 60.154 57.895 10.24 5.53 0.00 2.78
4822 5545 0.249573 TCGGTCGCGAGGTTTCTTTT 60.250 50.000 10.24 0.00 0.00 2.27
4889 5612 1.708027 CCGAACAGAATTCGACCGC 59.292 57.895 10.46 0.00 43.97 5.68
4891 5614 1.708027 GAACAGAATTCGACCGCGG 59.292 57.895 26.86 26.86 38.28 6.46
4896 5619 0.179134 AGAATTCGACCGCGGAAGAG 60.179 55.000 35.90 19.10 38.28 2.85
4929 5652 0.539669 AAGGGAAACTGGGCCGAAAG 60.540 55.000 0.00 0.00 0.00 2.62
4994 5719 6.383436 AGGTAGGGTTATGAGGTCTAGAAAAC 59.617 42.308 0.00 0.00 0.00 2.43
5040 5769 2.949451 TCTGATCCAGAAACGAGAGC 57.051 50.000 0.00 0.00 37.57 4.09
5061 5790 3.496331 CACCCAAACCCAAAGTCACTAT 58.504 45.455 0.00 0.00 0.00 2.12
5103 6734 0.478072 TGCACAATCACTCCACCCTT 59.522 50.000 0.00 0.00 0.00 3.95
5127 6758 2.457366 AGCTCCTTAGGTTGTGAACG 57.543 50.000 0.00 0.00 0.00 3.95
5137 6768 1.345415 GGTTGTGAACGGAGGGAGTAA 59.655 52.381 0.00 0.00 0.00 2.24
5138 6769 2.224354 GGTTGTGAACGGAGGGAGTAAA 60.224 50.000 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.633769 CTTCCCTCCAGAAGCTGC 57.366 61.111 0.00 0.00 37.08 5.25
113 114 6.637254 GCTTTAGTTTTTGGTGTTTCTCTAGC 59.363 38.462 0.00 0.00 0.00 3.42
119 120 6.237835 GCTTCTGCTTTAGTTTTTGGTGTTTC 60.238 38.462 0.00 0.00 36.03 2.78
240 633 9.173939 CGCATAATCTTTTAGGCTTAATTTCTG 57.826 33.333 0.00 0.00 41.70 3.02
253 646 4.177783 TCGCACTCACGCATAATCTTTTA 58.822 39.130 0.00 0.00 0.00 1.52
332 725 3.600388 CGAATGAAACTAGGCTGGAACT 58.400 45.455 4.33 0.00 0.00 3.01
333 726 2.096013 GCGAATGAAACTAGGCTGGAAC 59.904 50.000 4.33 0.00 0.00 3.62
334 727 2.356135 GCGAATGAAACTAGGCTGGAA 58.644 47.619 4.33 0.00 0.00 3.53
335 728 1.406887 GGCGAATGAAACTAGGCTGGA 60.407 52.381 4.33 0.00 0.00 3.86
337 730 0.652592 CGGCGAATGAAACTAGGCTG 59.347 55.000 0.00 0.00 0.00 4.85
339 732 0.931005 CTCGGCGAATGAAACTAGGC 59.069 55.000 12.13 0.00 0.00 3.93
340 733 2.099263 TCTCTCGGCGAATGAAACTAGG 59.901 50.000 12.13 0.00 0.00 3.02
341 734 3.065510 TCTCTCTCGGCGAATGAAACTAG 59.934 47.826 12.13 0.00 0.00 2.57
342 735 3.014623 TCTCTCTCGGCGAATGAAACTA 58.985 45.455 12.13 0.00 0.00 2.24
343 736 1.819288 TCTCTCTCGGCGAATGAAACT 59.181 47.619 12.13 0.00 0.00 2.66
344 737 2.159366 TCTCTCTCTCGGCGAATGAAAC 60.159 50.000 12.13 0.00 0.00 2.78
345 738 2.092323 TCTCTCTCTCGGCGAATGAAA 58.908 47.619 12.13 0.00 0.00 2.69
346 739 1.673400 CTCTCTCTCTCGGCGAATGAA 59.327 52.381 12.13 0.00 0.00 2.57
347 740 1.134371 TCTCTCTCTCTCGGCGAATGA 60.134 52.381 12.13 11.02 0.00 2.57
348 741 1.264020 CTCTCTCTCTCTCGGCGAATG 59.736 57.143 12.13 6.76 0.00 2.67
349 742 1.140052 TCTCTCTCTCTCTCGGCGAAT 59.860 52.381 12.13 0.00 0.00 3.34
350 743 0.537653 TCTCTCTCTCTCTCGGCGAA 59.462 55.000 12.13 1.06 0.00 4.70
351 744 0.104120 CTCTCTCTCTCTCTCGGCGA 59.896 60.000 10.14 10.14 0.00 5.54
352 745 0.104120 TCTCTCTCTCTCTCTCGGCG 59.896 60.000 0.00 0.00 0.00 6.46
353 746 1.412710 TCTCTCTCTCTCTCTCTCGGC 59.587 57.143 0.00 0.00 0.00 5.54
354 747 2.959030 TCTCTCTCTCTCTCTCTCTCGG 59.041 54.545 0.00 0.00 0.00 4.63
355 748 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
356 749 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
357 750 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
358 751 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
359 752 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
360 753 4.892934 AGTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
361 754 4.877773 AGTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
362 755 6.065374 TCTAGTCTCTCTCTCTCTCTCTCTC 58.935 48.000 0.00 0.00 0.00 3.20
363 756 6.019656 TCTAGTCTCTCTCTCTCTCTCTCT 57.980 45.833 0.00 0.00 0.00 3.10
364 757 6.065374 TCTCTAGTCTCTCTCTCTCTCTCTC 58.935 48.000 0.00 0.00 0.00 3.20
365 758 6.019656 TCTCTAGTCTCTCTCTCTCTCTCT 57.980 45.833 0.00 0.00 0.00 3.10
366 759 6.065374 TCTCTCTAGTCTCTCTCTCTCTCTC 58.935 48.000 0.00 0.00 0.00 3.20
367 760 6.019656 TCTCTCTAGTCTCTCTCTCTCTCT 57.980 45.833 0.00 0.00 0.00 3.10
368 761 6.491745 TGATCTCTCTAGTCTCTCTCTCTCTC 59.508 46.154 0.00 0.00 0.00 3.20
369 762 6.377080 TGATCTCTCTAGTCTCTCTCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
370 763 6.656632 TGATCTCTCTAGTCTCTCTCTCTC 57.343 45.833 0.00 0.00 0.00 3.20
371 764 6.013898 CCATGATCTCTCTAGTCTCTCTCTCT 60.014 46.154 0.00 0.00 0.00 3.10
372 765 6.169094 CCATGATCTCTCTAGTCTCTCTCTC 58.831 48.000 0.00 0.00 0.00 3.20
373 766 5.013495 CCCATGATCTCTCTAGTCTCTCTCT 59.987 48.000 0.00 0.00 0.00 3.10
374 767 5.248640 CCCATGATCTCTCTAGTCTCTCTC 58.751 50.000 0.00 0.00 0.00 3.20
375 768 4.043310 CCCCATGATCTCTCTAGTCTCTCT 59.957 50.000 0.00 0.00 0.00 3.10
376 769 4.335416 CCCCATGATCTCTCTAGTCTCTC 58.665 52.174 0.00 0.00 0.00 3.20
377 770 3.075882 CCCCCATGATCTCTCTAGTCTCT 59.924 52.174 0.00 0.00 0.00 3.10
378 771 3.075283 TCCCCCATGATCTCTCTAGTCTC 59.925 52.174 0.00 0.00 0.00 3.36
379 772 3.067470 TCCCCCATGATCTCTCTAGTCT 58.933 50.000 0.00 0.00 0.00 3.24
380 773 3.534357 TCCCCCATGATCTCTCTAGTC 57.466 52.381 0.00 0.00 0.00 2.59
381 774 3.245948 GGATCCCCCATGATCTCTCTAGT 60.246 52.174 0.00 0.00 40.80 2.57
382 775 3.373830 GGATCCCCCATGATCTCTCTAG 58.626 54.545 0.00 0.00 40.80 2.43
383 776 3.481559 GGATCCCCCATGATCTCTCTA 57.518 52.381 0.00 0.00 40.80 2.43
384 777 2.340721 GGATCCCCCATGATCTCTCT 57.659 55.000 0.00 0.00 40.80 3.10
735 1143 4.193893 CATGATCCCCGGCAGCCA 62.194 66.667 13.30 0.00 0.00 4.75
736 1144 4.962836 CCATGATCCCCGGCAGCC 62.963 72.222 0.00 0.00 0.00 4.85
737 1145 4.962836 CCCATGATCCCCGGCAGC 62.963 72.222 0.00 0.00 0.00 5.25
742 1150 3.081554 GATCCCCCATGATCCCCG 58.918 66.667 0.00 0.00 36.04 5.73
754 1162 1.059006 AGAGCTCACCATGGGATCCC 61.059 60.000 25.22 25.22 32.75 3.85
848 1361 1.083806 CGCTTAGGCTCATTCGCACA 61.084 55.000 0.00 0.00 36.09 4.57
942 1464 1.480954 GTCCTCCATGTCGTACACCAT 59.519 52.381 0.00 0.00 0.00 3.55
1067 1589 2.033141 GTGCTGCTGAGAAGGCCA 59.967 61.111 5.01 0.00 0.00 5.36
1376 1898 1.546029 CTGATCAGGGTCGTCTTCACA 59.454 52.381 15.38 0.00 0.00 3.58
1417 1939 2.164865 CTCTTCGCAGTGCCAGTCCT 62.165 60.000 10.11 0.00 0.00 3.85
1421 1943 2.015736 AATACTCTTCGCAGTGCCAG 57.984 50.000 10.11 6.06 0.00 4.85
1582 2108 6.781943 TGGATATGGCTTGATATCACAATGA 58.218 36.000 4.48 0.00 37.14 2.57
1603 2129 5.654603 AGTGAACATCAGTACGTATTGGA 57.345 39.130 16.90 7.16 0.00 3.53
1867 2396 4.338879 AGCAGCCTATGTTGTTCTGAAAT 58.661 39.130 0.00 0.00 0.00 2.17
2341 2870 3.447229 CCACACTTCAACTTTCCACCTTT 59.553 43.478 0.00 0.00 0.00 3.11
2413 2942 3.550656 GGCGTCACCTTCGTCTTG 58.449 61.111 0.00 0.00 34.51 3.02
2461 2990 2.224548 CCTCCTCCCGACTCTTTTGTTT 60.225 50.000 0.00 0.00 0.00 2.83
2489 3018 3.065925 ACAAACTGAGCTTTCTTCACTGC 59.934 43.478 0.00 0.00 0.00 4.40
2557 3086 2.299582 CAACATCCCCACAGAATGCAAA 59.700 45.455 0.00 0.00 42.53 3.68
2565 3094 0.698238 TCCTTCCAACATCCCCACAG 59.302 55.000 0.00 0.00 0.00 3.66
2597 3126 4.398358 CCCGTACAAGTCTGAAGTGATCTA 59.602 45.833 0.00 0.00 0.00 1.98
2609 3138 2.688958 AGATCTAGCACCCGTACAAGTC 59.311 50.000 0.00 0.00 0.00 3.01
2815 3347 1.140804 GCAAACACGCCAACTTGGT 59.859 52.632 9.63 0.00 40.46 3.67
2816 3348 0.179113 AAGCAAACACGCCAACTTGG 60.179 50.000 3.10 3.10 41.55 3.61
2825 3357 1.522258 GACCATTTGCAAGCAAACACG 59.478 47.619 21.04 13.63 46.80 4.49
3220 3752 4.723309 AGGTCAACAAGCAAAGAGATCTT 58.277 39.130 0.00 0.00 37.91 2.40
3231 3763 2.246719 AGTGAGTGAGGTCAACAAGC 57.753 50.000 0.00 0.00 0.00 4.01
3725 4269 3.119096 GTCTCCGCGGCAGAAACC 61.119 66.667 23.51 8.87 0.00 3.27
3891 4438 2.752121 CTCGATCATCATGGTCCAGTG 58.248 52.381 0.00 0.00 0.00 3.66
3917 4467 0.880278 TCACGAGCAGCTTGTTGTCC 60.880 55.000 13.16 0.00 0.00 4.02
3918 4468 1.151668 ATCACGAGCAGCTTGTTGTC 58.848 50.000 13.16 0.00 0.00 3.18
3919 4469 1.265095 CAATCACGAGCAGCTTGTTGT 59.735 47.619 13.16 1.71 0.00 3.32
4005 4555 5.143376 AGAAAAATGGCATCTGGAAACTG 57.857 39.130 0.00 0.00 0.00 3.16
4108 4658 1.471153 GCGTGTCCTTAACCTCTAGCC 60.471 57.143 0.00 0.00 0.00 3.93
4111 4661 2.163010 CGAAGCGTGTCCTTAACCTCTA 59.837 50.000 0.00 0.00 0.00 2.43
4148 4698 3.597255 CTGAATCTTCTCAAGCAGCTCA 58.403 45.455 0.00 0.00 0.00 4.26
4214 4764 0.405585 AAGGATATGAATGCCGGGGG 59.594 55.000 2.18 0.00 0.00 5.40
4344 4910 3.149005 TGTAAGGAATCAAACGGCCTT 57.851 42.857 0.00 0.00 42.91 4.35
4350 4916 6.149633 GGACACACATTGTAAGGAATCAAAC 58.850 40.000 0.00 0.00 39.17 2.93
4374 4940 6.834959 ATTAATCATTACTGCAGTCTGACG 57.165 37.500 25.56 8.92 0.00 4.35
4419 4985 0.110238 CAGACGCAAACAATGTCGGG 60.110 55.000 0.00 0.00 37.69 5.14
4625 5213 7.503902 CGAGGGAGATATATATCAGATGAACCA 59.496 40.741 21.95 0.00 35.17 3.67
4647 5235 3.316588 AGTCTGTACAGATGCATACGAGG 59.683 47.826 27.54 0.00 39.97 4.63
4651 5239 5.011090 TCCAAGTCTGTACAGATGCATAC 57.989 43.478 27.54 14.52 39.97 2.39
4779 5502 7.387673 CGATCACTATGGTTTATTGATGCCTAA 59.612 37.037 0.00 0.00 0.00 2.69
4822 5545 5.974751 GCTAATGGTTGTTTCGTCAAAGAAA 59.025 36.000 0.00 0.00 37.74 2.52
4825 5548 3.906008 CGCTAATGGTTGTTTCGTCAAAG 59.094 43.478 0.00 0.00 0.00 2.77
4889 5612 2.175035 TAAACGGGCCACCTCTTCCG 62.175 60.000 4.39 0.00 46.95 4.30
4891 5614 2.994186 TATAAACGGGCCACCTCTTC 57.006 50.000 4.39 0.00 33.28 2.87
4896 5619 0.547553 TCCCTTATAAACGGGCCACC 59.452 55.000 4.39 0.00 40.41 4.61
4957 5680 2.439104 CCTACCTCCCAGCTCCAGC 61.439 68.421 0.00 0.00 42.49 4.85
4959 5682 2.119847 AACCCTACCTCCCAGCTCCA 62.120 60.000 0.00 0.00 0.00 3.86
4960 5683 0.031414 TAACCCTACCTCCCAGCTCC 60.031 60.000 0.00 0.00 0.00 4.70
4966 5691 2.090663 AGACCTCATAACCCTACCTCCC 60.091 54.545 0.00 0.00 0.00 4.30
5013 5742 5.111989 TCGTTTCTGGATCAGATGATGTTC 58.888 41.667 0.00 0.00 40.39 3.18
5016 5745 4.941657 TCTCGTTTCTGGATCAGATGATG 58.058 43.478 0.00 0.00 40.39 3.07
5040 5769 1.775385 AGTGACTTTGGGTTTGGGTG 58.225 50.000 0.00 0.00 0.00 4.61
5061 5790 4.100963 AGGTCGTATTTGAGATGCACCATA 59.899 41.667 0.00 0.00 0.00 2.74
5103 6734 4.431416 TCACAACCTAAGGAGCTTTTCA 57.569 40.909 0.00 0.00 0.00 2.69
5127 6758 8.389366 TCCAGTACTATATACTTTACTCCCTCC 58.611 40.741 0.00 0.00 0.00 4.30
5158 6789 3.139850 GTCACCATCGACTAGCTAGCTA 58.860 50.000 22.85 22.85 32.92 3.32
5159 6790 1.950909 GTCACCATCGACTAGCTAGCT 59.049 52.381 23.12 23.12 32.92 3.32
5160 6791 1.001158 GGTCACCATCGACTAGCTAGC 60.001 57.143 20.91 6.62 36.12 3.42
5161 6792 1.609555 GGGTCACCATCGACTAGCTAG 59.390 57.143 19.44 19.44 36.12 3.42


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

AutoCloner maintained by Alex Coulton.