Multiple sequence alignment - TraesCS6A01G322100

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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 TraesCS6A01G322100 chr6A 100.000 3479 0 0 1 3479 556039296 556035818 0.000000e+00 6425
1 TraesCS6A01G322100 chr6A 89.346 1605 166 5 816 2419 592458962 592457362 0.000000e+00 2012
2 TraesCS6A01G322100 chr6A 86.819 1487 195 1 932 2418 592613354 592611869 0.000000e+00 1659
3 TraesCS6A01G322100 chr6A 84.025 1615 240 13 816 2419 592599470 592601077 0.000000e+00 1537
4 TraesCS6A01G322100 chr6A 94.756 553 27 1 2431 2983 505772321 505771771 0.000000e+00 859
5 TraesCS6A01G322100 chr6D 97.329 1610 43 0 821 2430 411470965 411469356 0.000000e+00 2736
6 TraesCS6A01G322100 chr6D 88.979 1606 166 8 821 2420 445788958 445787358 0.000000e+00 1975
7 TraesCS6A01G322100 chr6D 90.200 500 30 13 2981 3477 411469363 411468880 4.900000e-178 634
8 TraesCS6A01G322100 chr6D 80.282 710 83 31 110 788 445779685 445779002 1.880000e-132 483
9 TraesCS6A01G322100 chr6D 84.351 262 21 8 549 790 411471203 411470942 4.490000e-59 239
10 TraesCS6A01G322100 chr6D 95.181 83 4 0 406 488 411471306 411471224 7.840000e-27 132
11 TraesCS6A01G322100 chr6D 97.674 43 1 0 21 63 411471563 411471521 1.340000e-09 75
12 TraesCS6A01G322100 chr6B 96.471 1615 53 2 816 2430 618670270 618668660 0.000000e+00 2663
13 TraesCS6A01G322100 chr6B 88.818 1404 148 8 816 2216 672457699 672456302 0.000000e+00 1714
14 TraesCS6A01G322100 chr6B 89.083 1374 150 0 1047 2420 672462674 672461301 0.000000e+00 1707
15 TraesCS6A01G322100 chr6B 85.384 1512 212 7 912 2419 673764288 673765794 0.000000e+00 1559
16 TraesCS6A01G322100 chr6B 86.565 588 37 21 228 792 618670808 618670240 8.260000e-171 610
17 TraesCS6A01G322100 chr6B 88.889 504 35 10 2981 3477 618668667 618668178 4.970000e-168 601
18 TraesCS6A01G322100 chr3A 95.479 553 23 1 2430 2982 49308496 49309046 0.000000e+00 881
19 TraesCS6A01G322100 chr3B 95.109 552 25 1 2430 2981 212054798 212054249 0.000000e+00 869
20 TraesCS6A01G322100 chr3B 94.727 550 27 1 2431 2980 444327780 444327233 0.000000e+00 854
21 TraesCS6A01G322100 chr5B 94.909 550 26 1 2431 2980 439543211 439543758 0.000000e+00 859
22 TraesCS6A01G322100 chr3D 94.909 550 26 2 2431 2980 316464787 316465334 0.000000e+00 859
23 TraesCS6A01G322100 chr1A 94.756 553 25 3 2431 2981 394291706 394292256 0.000000e+00 857
24 TraesCS6A01G322100 chr7B 94.424 556 29 1 2429 2984 278852082 278851529 0.000000e+00 854
25 TraesCS6A01G322100 chr5A 94.575 553 26 3 2430 2981 237500596 237501145 0.000000e+00 852


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 TraesCS6A01G322100 chr6A 556035818 556039296 3478 True 6425.000000 6425 100.000000 1 3479 1 chr6A.!!$R2 3478
1 TraesCS6A01G322100 chr6A 592457362 592458962 1600 True 2012.000000 2012 89.346000 816 2419 1 chr6A.!!$R3 1603
2 TraesCS6A01G322100 chr6A 592611869 592613354 1485 True 1659.000000 1659 86.819000 932 2418 1 chr6A.!!$R4 1486
3 TraesCS6A01G322100 chr6A 592599470 592601077 1607 False 1537.000000 1537 84.025000 816 2419 1 chr6A.!!$F1 1603
4 TraesCS6A01G322100 chr6A 505771771 505772321 550 True 859.000000 859 94.756000 2431 2983 1 chr6A.!!$R1 552
5 TraesCS6A01G322100 chr6D 445787358 445788958 1600 True 1975.000000 1975 88.979000 821 2420 1 chr6D.!!$R2 1599
6 TraesCS6A01G322100 chr6D 411468880 411471563 2683 True 763.200000 2736 92.947000 21 3477 5 chr6D.!!$R3 3456
7 TraesCS6A01G322100 chr6D 445779002 445779685 683 True 483.000000 483 80.282000 110 788 1 chr6D.!!$R1 678
8 TraesCS6A01G322100 chr6B 672456302 672462674 6372 True 1710.500000 1714 88.950500 816 2420 2 chr6B.!!$R2 1604
9 TraesCS6A01G322100 chr6B 673764288 673765794 1506 False 1559.000000 1559 85.384000 912 2419 1 chr6B.!!$F1 1507
10 TraesCS6A01G322100 chr6B 618668178 618670808 2630 True 1291.333333 2663 90.641667 228 3477 3 chr6B.!!$R1 3249
11 TraesCS6A01G322100 chr3A 49308496 49309046 550 False 881.000000 881 95.479000 2430 2982 1 chr3A.!!$F1 552
12 TraesCS6A01G322100 chr3B 212054249 212054798 549 True 869.000000 869 95.109000 2430 2981 1 chr3B.!!$R1 551
13 TraesCS6A01G322100 chr3B 444327233 444327780 547 True 854.000000 854 94.727000 2431 2980 1 chr3B.!!$R2 549
14 TraesCS6A01G322100 chr5B 439543211 439543758 547 False 859.000000 859 94.909000 2431 2980 1 chr5B.!!$F1 549
15 TraesCS6A01G322100 chr3D 316464787 316465334 547 False 859.000000 859 94.909000 2431 2980 1 chr3D.!!$F1 549
16 TraesCS6A01G322100 chr1A 394291706 394292256 550 False 857.000000 857 94.756000 2431 2981 1 chr1A.!!$F1 550
17 TraesCS6A01G322100 chr7B 278851529 278852082 553 True 854.000000 854 94.424000 2429 2984 1 chr7B.!!$R1 555
18 TraesCS6A01G322100 chr5A 237500596 237501145 549 False 852.000000 852 94.575000 2430 2981 1 chr5A.!!$F1 551

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
601 619 0.105593 CAGGAGGTGGATGTCCGATG 59.894 60.0 0.0 0.0 37.97 3.84 F
716 758 0.465460 TGCAGCGTTTTCCTGTTCCT 60.465 50.0 0.0 0.0 32.93 3.36 F
1241 1302 0.600057 GGGTCGAAGTCCAGTAACGT 59.400 55.0 0.0 0.0 37.49 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2371 0.938008 GCAGCTTATAACGGTCAGCC 59.062 55.0 0.0 0.0 32.25 4.85 R
2376 2438 0.973632 TTTCAGCCTCCGCAGAGTAA 59.026 50.0 0.0 0.0 38.58 2.24 R
2972 3577 2.025321 CCTTTCCTTTTGGCTAGGGCTA 60.025 50.0 0.0 0.0 40.12 3.93 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
67 68 2.959507 ACCTTTGTTGGTGCTTTGTC 57.040 45.000 0.00 0.00 39.17 3.18
68 69 2.456577 ACCTTTGTTGGTGCTTTGTCT 58.543 42.857 0.00 0.00 39.17 3.41
69 70 2.427095 ACCTTTGTTGGTGCTTTGTCTC 59.573 45.455 0.00 0.00 39.17 3.36
70 71 2.541588 CCTTTGTTGGTGCTTTGTCTCG 60.542 50.000 0.00 0.00 0.00 4.04
71 72 2.031258 TTGTTGGTGCTTTGTCTCGA 57.969 45.000 0.00 0.00 0.00 4.04
72 73 2.031258 TGTTGGTGCTTTGTCTCGAA 57.969 45.000 0.00 0.00 0.00 3.71
73 74 2.360844 TGTTGGTGCTTTGTCTCGAAA 58.639 42.857 0.00 0.00 0.00 3.46
74 75 2.750166 TGTTGGTGCTTTGTCTCGAAAA 59.250 40.909 0.00 0.00 0.00 2.29
75 76 3.191581 TGTTGGTGCTTTGTCTCGAAAAA 59.808 39.130 0.00 0.00 0.00 1.94
103 104 4.641645 TTGGTGCTGTGAGGCCGG 62.642 66.667 0.00 0.00 0.00 6.13
187 191 1.723288 GTTTCCCCACCCATTCCAAA 58.277 50.000 0.00 0.00 0.00 3.28
191 195 1.612146 CCCACCCATTCCAAACCCC 60.612 63.158 0.00 0.00 0.00 4.95
335 343 2.651232 CCGAGGCGACGTCGATTC 60.651 66.667 39.74 30.44 43.02 2.52
343 356 0.801067 CGACGTCGATTCTTCCACCC 60.801 60.000 33.35 0.00 43.02 4.61
347 360 0.806492 GTCGATTCTTCCACCCGAGC 60.806 60.000 0.00 0.00 0.00 5.03
371 384 1.950973 TTGATCCCGTTCCGCGATGA 61.951 55.000 8.23 0.00 44.77 2.92
489 507 9.596308 AGGAAATAGCCCGGTTTATTTATTTAT 57.404 29.630 16.15 0.00 31.50 1.40
526 544 0.393077 AACCCGTTCTGGAGTGTCTG 59.607 55.000 0.00 0.00 42.00 3.51
536 554 1.066858 TGGAGTGTCTGGAAATCGCTC 60.067 52.381 0.00 0.00 37.80 5.03
554 572 5.111989 TCGCTCTCTAAATCTGATTGGTTG 58.888 41.667 3.22 0.00 0.00 3.77
569 587 1.913419 TGGTTGGGTCCTTCCAGATAC 59.087 52.381 0.00 0.00 38.17 2.24
596 614 5.123979 GTGTTAAATTCAGGAGGTGGATGTC 59.876 44.000 0.00 0.00 0.00 3.06
601 619 0.105593 CAGGAGGTGGATGTCCGATG 59.894 60.000 0.00 0.00 37.97 3.84
614 632 2.219458 GTCCGATGATCTCGTGGACTA 58.781 52.381 15.31 0.00 46.18 2.59
635 655 7.331193 GGACTAGTTGTTCTAATTGGTGTACTG 59.669 40.741 0.00 0.00 0.00 2.74
699 741 5.050634 GGTCGTTTGGTTAATTTTTCCTTGC 60.051 40.000 0.00 0.00 0.00 4.01
708 750 4.794248 AATTTTTCCTTGCAGCGTTTTC 57.206 36.364 0.00 0.00 0.00 2.29
716 758 0.465460 TGCAGCGTTTTCCTGTTCCT 60.465 50.000 0.00 0.00 32.93 3.36
724 775 6.967199 CAGCGTTTTCCTGTTCCTTATAAATC 59.033 38.462 0.00 0.00 0.00 2.17
736 787 5.308825 TCCTTATAAATCTTAGCCTGCAGC 58.691 41.667 8.66 3.91 44.25 5.25
759 810 4.216411 AGTTGGTTACTGTTCACTGTGT 57.784 40.909 7.79 0.00 35.19 3.72
788 839 7.516198 AAGCACATGAATCTTTCAAACTAGT 57.484 32.000 0.00 0.00 43.95 2.57
789 840 8.621532 AAGCACATGAATCTTTCAAACTAGTA 57.378 30.769 0.00 0.00 43.95 1.82
790 841 8.034058 AGCACATGAATCTTTCAAACTAGTAC 57.966 34.615 0.00 0.00 43.95 2.73
791 842 7.661437 AGCACATGAATCTTTCAAACTAGTACA 59.339 33.333 0.00 0.00 43.95 2.90
792 843 7.959651 GCACATGAATCTTTCAAACTAGTACAG 59.040 37.037 0.00 0.00 43.95 2.74
793 844 7.959651 CACATGAATCTTTCAAACTAGTACAGC 59.040 37.037 0.00 0.00 43.95 4.40
794 845 7.880195 ACATGAATCTTTCAAACTAGTACAGCT 59.120 33.333 0.00 0.00 43.95 4.24
795 846 7.658179 TGAATCTTTCAAACTAGTACAGCTG 57.342 36.000 13.48 13.48 36.59 4.24
796 847 7.217200 TGAATCTTTCAAACTAGTACAGCTGT 58.783 34.615 25.12 25.12 36.59 4.40
797 848 7.715249 TGAATCTTTCAAACTAGTACAGCTGTT 59.285 33.333 27.06 10.85 36.59 3.16
798 849 9.204570 GAATCTTTCAAACTAGTACAGCTGTTA 57.795 33.333 27.06 11.51 0.00 2.41
799 850 9.555727 AATCTTTCAAACTAGTACAGCTGTTAA 57.444 29.630 27.06 4.60 0.00 2.01
800 851 9.726438 ATCTTTCAAACTAGTACAGCTGTTAAT 57.274 29.630 27.06 13.66 0.00 1.40
801 852 9.555727 TCTTTCAAACTAGTACAGCTGTTAATT 57.444 29.630 27.06 5.49 0.00 1.40
802 853 9.599322 CTTTCAAACTAGTACAGCTGTTAATTG 57.401 33.333 27.06 19.48 0.00 2.32
803 854 7.667043 TCAAACTAGTACAGCTGTTAATTGG 57.333 36.000 27.06 9.29 0.00 3.16
804 855 7.221450 TCAAACTAGTACAGCTGTTAATTGGT 58.779 34.615 27.06 9.99 0.00 3.67
805 856 7.717875 TCAAACTAGTACAGCTGTTAATTGGTT 59.282 33.333 27.06 15.48 0.00 3.67
806 857 8.995220 CAAACTAGTACAGCTGTTAATTGGTTA 58.005 33.333 27.06 0.00 0.00 2.85
807 858 9.734984 AAACTAGTACAGCTGTTAATTGGTTAT 57.265 29.630 27.06 7.28 0.00 1.89
808 859 8.943909 ACTAGTACAGCTGTTAATTGGTTATC 57.056 34.615 27.06 0.00 0.00 1.75
809 860 8.759782 ACTAGTACAGCTGTTAATTGGTTATCT 58.240 33.333 27.06 6.30 0.00 1.98
810 861 9.601217 CTAGTACAGCTGTTAATTGGTTATCTT 57.399 33.333 27.06 0.00 0.00 2.40
811 862 8.268850 AGTACAGCTGTTAATTGGTTATCTTG 57.731 34.615 27.06 0.00 0.00 3.02
812 863 7.883311 AGTACAGCTGTTAATTGGTTATCTTGT 59.117 33.333 27.06 0.00 0.00 3.16
813 864 7.524717 ACAGCTGTTAATTGGTTATCTTGTT 57.475 32.000 15.25 0.00 0.00 2.83
814 865 7.951591 ACAGCTGTTAATTGGTTATCTTGTTT 58.048 30.769 15.25 0.00 0.00 2.83
837 888 9.142515 GTTTGATATGCACATGAATCTTTCAAA 57.857 29.630 0.00 5.70 43.95 2.69
838 889 8.692110 TTGATATGCACATGAATCTTTCAAAC 57.308 30.769 0.00 0.00 43.95 2.93
897 957 6.015772 TCCCTTTTACATTTGTTCTTACAGCC 60.016 38.462 0.00 0.00 35.28 4.85
1097 1158 0.796491 CTCGTGTCGAAGCAGCTCTC 60.796 60.000 0.00 0.00 34.74 3.20
1102 1163 1.908299 TCGAAGCAGCTCTCCACCA 60.908 57.895 0.00 0.00 0.00 4.17
1241 1302 0.600057 GGGTCGAAGTCCAGTAACGT 59.400 55.000 0.00 0.00 37.49 3.99
1420 1481 3.196685 AGCAGTCACTTCTACTGGGATTC 59.803 47.826 5.47 0.00 43.71 2.52
1984 2046 1.134098 GCTGCCCTATGCTTCAGGTTA 60.134 52.381 0.00 0.00 42.00 2.85
2205 2267 6.647067 GGTCTATAACTGATGCTGGTATGAAC 59.353 42.308 0.00 0.00 0.00 3.18
2208 2270 6.932356 ATAACTGATGCTGGTATGAACTTG 57.068 37.500 0.00 0.00 0.00 3.16
2224 2286 5.918608 TGAACTTGATTATACAGGCTCCTC 58.081 41.667 0.00 0.00 0.00 3.71
2309 2371 1.563435 CGTGCACAGAAGCTGGAGTG 61.563 60.000 18.64 7.98 35.51 3.51
2323 2385 2.167693 CTGGAGTGGCTGACCGTTATAA 59.832 50.000 0.00 0.00 39.70 0.98
2376 2438 3.015327 GAGAGCTGCCAAATCAGTTCAT 58.985 45.455 0.00 0.00 43.80 2.57
2526 2588 9.890629 AGCTTGACTCAACTCATTATTATAACA 57.109 29.630 0.00 0.00 0.00 2.41
3087 3700 6.878389 GTCATTTTCTCTTCTGATGAGTTCCT 59.122 38.462 17.10 2.92 33.59 3.36
3138 3751 3.002042 CCGAACATGCTTCTGCTTCTATG 59.998 47.826 0.00 0.00 40.48 2.23
3181 3794 1.276622 TGTAAGGTCTCCTCCTTGCC 58.723 55.000 8.06 0.58 45.27 4.52
3182 3795 0.542333 GTAAGGTCTCCTCCTTGCCC 59.458 60.000 8.06 0.00 45.96 5.36
3183 3796 0.417841 TAAGGTCTCCTCCTTGCCCT 59.582 55.000 8.06 0.00 45.96 5.19
3253 3868 4.021544 TGGGGTTCGGATTTTGAAAGAATG 60.022 41.667 0.00 0.00 0.00 2.67
3259 3874 3.193267 CGGATTTTGAAAGAATGCCAGGA 59.807 43.478 0.00 0.00 0.00 3.86
3283 3898 1.868469 TTGGCTGCTTGAAAATGCAC 58.132 45.000 0.00 0.00 35.20 4.57
3289 3904 3.626977 CTGCTTGAAAATGCACGTGTTA 58.373 40.909 18.38 7.28 35.20 2.41
3372 3987 1.113788 TCTTGGCTGCTGCTTTTGTT 58.886 45.000 15.64 0.00 39.59 2.83
3399 4045 6.055588 CAGAGACTCTTTTGTCCCTTGTTTA 58.944 40.000 0.98 0.00 37.66 2.01
3411 4057 2.299867 CCCTTGTTTATGCTTTGTGCCT 59.700 45.455 0.00 0.00 42.00 4.75
3412 4058 3.509575 CCCTTGTTTATGCTTTGTGCCTA 59.490 43.478 0.00 0.00 42.00 3.93
3413 4059 4.021544 CCCTTGTTTATGCTTTGTGCCTAA 60.022 41.667 0.00 0.00 42.00 2.69
3477 4124 2.031682 CGAAGGTGCCACTGAAAGAAAG 60.032 50.000 0.00 0.00 37.43 2.62
3478 4125 3.214328 GAAGGTGCCACTGAAAGAAAGA 58.786 45.455 0.00 0.00 37.43 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.370593 GTGATAATGTCACGTGATGTTGTTT 58.629 36.000 23.12 11.26 46.99 2.83
3 4 5.530519 GTGATAATGTCACGTGATGTTGT 57.469 39.130 23.12 16.72 46.99 3.32
14 15 2.679639 GCCCGACTTGGTGATAATGTCA 60.680 50.000 0.00 0.00 35.15 3.58
15 16 1.940613 GCCCGACTTGGTGATAATGTC 59.059 52.381 0.00 0.00 35.15 3.06
16 17 1.408266 GGCCCGACTTGGTGATAATGT 60.408 52.381 0.00 0.00 35.15 2.71
17 18 1.308998 GGCCCGACTTGGTGATAATG 58.691 55.000 0.00 0.00 35.15 1.90
18 19 0.916086 TGGCCCGACTTGGTGATAAT 59.084 50.000 0.00 0.00 35.15 1.28
19 20 0.693622 TTGGCCCGACTTGGTGATAA 59.306 50.000 0.00 0.00 35.15 1.75
76 77 4.244862 CTCACAGCACCAACAAAGTTTTT 58.755 39.130 0.00 0.00 0.00 1.94
77 78 3.368323 CCTCACAGCACCAACAAAGTTTT 60.368 43.478 0.00 0.00 0.00 2.43
78 79 2.166254 CCTCACAGCACCAACAAAGTTT 59.834 45.455 0.00 0.00 0.00 2.66
79 80 1.750778 CCTCACAGCACCAACAAAGTT 59.249 47.619 0.00 0.00 0.00 2.66
80 81 1.392589 CCTCACAGCACCAACAAAGT 58.607 50.000 0.00 0.00 0.00 2.66
81 82 0.031178 GCCTCACAGCACCAACAAAG 59.969 55.000 0.00 0.00 0.00 2.77
82 83 1.391157 GGCCTCACAGCACCAACAAA 61.391 55.000 0.00 0.00 0.00 2.83
83 84 1.827789 GGCCTCACAGCACCAACAA 60.828 57.895 0.00 0.00 0.00 2.83
84 85 2.203337 GGCCTCACAGCACCAACA 60.203 61.111 0.00 0.00 0.00 3.33
85 86 3.357079 CGGCCTCACAGCACCAAC 61.357 66.667 0.00 0.00 0.00 3.77
86 87 4.641645 CCGGCCTCACAGCACCAA 62.642 66.667 0.00 0.00 0.00 3.67
95 96 4.634703 TTTTGAGCGCCGGCCTCA 62.635 61.111 31.51 31.51 41.24 3.86
127 129 0.320421 CGAAACCCTCGCCTTCTTCA 60.320 55.000 0.00 0.00 41.49 3.02
335 343 0.671781 CAACAGAGCTCGGGTGGAAG 60.672 60.000 22.59 0.00 0.00 3.46
343 356 0.108615 AACGGGATCAACAGAGCTCG 60.109 55.000 8.37 6.04 46.41 5.03
489 507 9.473640 GAACGGGTTTTACCACAAATAAATAAA 57.526 29.630 0.00 0.00 41.02 1.40
490 508 8.858094 AGAACGGGTTTTACCACAAATAAATAA 58.142 29.630 0.00 0.00 41.02 1.40
491 509 8.298140 CAGAACGGGTTTTACCACAAATAAATA 58.702 33.333 0.00 0.00 41.02 1.40
492 510 7.149307 CAGAACGGGTTTTACCACAAATAAAT 58.851 34.615 0.00 0.00 41.02 1.40
493 511 6.461231 CCAGAACGGGTTTTACCACAAATAAA 60.461 38.462 0.00 0.00 41.02 1.40
494 512 5.009811 CCAGAACGGGTTTTACCACAAATAA 59.990 40.000 0.00 0.00 41.02 1.40
495 513 4.519730 CCAGAACGGGTTTTACCACAAATA 59.480 41.667 0.00 0.00 41.02 1.40
496 514 3.319689 CCAGAACGGGTTTTACCACAAAT 59.680 43.478 0.00 0.00 41.02 2.32
497 515 2.688958 CCAGAACGGGTTTTACCACAAA 59.311 45.455 0.00 0.00 41.02 2.83
498 516 2.092538 TCCAGAACGGGTTTTACCACAA 60.093 45.455 0.00 0.00 41.02 3.33
499 517 1.489649 TCCAGAACGGGTTTTACCACA 59.510 47.619 0.00 0.00 41.02 4.17
500 518 2.148768 CTCCAGAACGGGTTTTACCAC 58.851 52.381 0.00 0.00 41.02 4.16
526 544 6.073331 CCAATCAGATTTAGAGAGCGATTTCC 60.073 42.308 0.00 0.00 0.00 3.13
536 554 4.884164 GGACCCAACCAATCAGATTTAGAG 59.116 45.833 0.00 0.00 0.00 2.43
554 572 1.134788 CACACGTATCTGGAAGGACCC 60.135 57.143 0.00 0.00 38.00 4.46
569 587 3.188460 CCACCTCCTGAATTTAACACACG 59.812 47.826 0.00 0.00 0.00 4.49
601 619 4.705337 AGAACAACTAGTCCACGAGATC 57.295 45.455 0.00 0.00 0.00 2.75
614 632 8.426489 TCTAACAGTACACCAATTAGAACAACT 58.574 33.333 0.00 0.00 30.79 3.16
635 655 2.640184 CTCGGTGGGGGATTTTCTAAC 58.360 52.381 0.00 0.00 0.00 2.34
660 702 8.154649 ACCAAACGACCTAATCATATGAAATC 57.845 34.615 9.99 2.71 0.00 2.17
699 741 5.873179 TTATAAGGAACAGGAAAACGCTG 57.127 39.130 0.00 0.00 0.00 5.18
708 750 6.205658 GCAGGCTAAGATTTATAAGGAACAGG 59.794 42.308 0.00 0.00 0.00 4.00
716 758 5.047566 TGGCTGCAGGCTAAGATTTATAA 57.952 39.130 36.39 12.73 41.69 0.98
724 775 1.310933 CCAACTGGCTGCAGGCTAAG 61.311 60.000 36.39 28.69 41.69 2.18
759 810 9.453572 AGTTTGAAAGATTCATGTGCTTATCTA 57.546 29.630 0.00 0.00 39.84 1.98
788 839 8.630054 AACAAGATAACCAATTAACAGCTGTA 57.370 30.769 22.01 5.63 0.00 2.74
789 840 7.524717 AACAAGATAACCAATTAACAGCTGT 57.475 32.000 15.25 15.25 0.00 4.40
790 841 8.081633 TCAAACAAGATAACCAATTAACAGCTG 58.918 33.333 13.48 13.48 0.00 4.24
791 842 8.177119 TCAAACAAGATAACCAATTAACAGCT 57.823 30.769 0.00 0.00 0.00 4.24
792 843 8.986477 ATCAAACAAGATAACCAATTAACAGC 57.014 30.769 0.00 0.00 0.00 4.40
798 849 8.530311 TGTGCATATCAAACAAGATAACCAATT 58.470 29.630 0.00 0.00 34.42 2.32
799 850 8.065473 TGTGCATATCAAACAAGATAACCAAT 57.935 30.769 0.00 0.00 34.42 3.16
800 851 7.459795 TGTGCATATCAAACAAGATAACCAA 57.540 32.000 0.00 0.00 34.42 3.67
801 852 7.338957 TCATGTGCATATCAAACAAGATAACCA 59.661 33.333 0.00 0.00 34.42 3.67
802 853 7.706159 TCATGTGCATATCAAACAAGATAACC 58.294 34.615 0.00 0.00 34.42 2.85
803 854 9.740239 ATTCATGTGCATATCAAACAAGATAAC 57.260 29.630 0.00 0.00 34.42 1.89
804 855 9.955208 GATTCATGTGCATATCAAACAAGATAA 57.045 29.630 0.00 0.00 34.42 1.75
805 856 9.346005 AGATTCATGTGCATATCAAACAAGATA 57.654 29.630 0.00 0.00 35.16 1.98
806 857 8.234136 AGATTCATGTGCATATCAAACAAGAT 57.766 30.769 0.00 0.00 0.00 2.40
807 858 7.634671 AGATTCATGTGCATATCAAACAAGA 57.365 32.000 0.00 0.00 0.00 3.02
808 859 8.697846 AAAGATTCATGTGCATATCAAACAAG 57.302 30.769 0.00 0.00 0.00 3.16
809 860 8.305317 TGAAAGATTCATGTGCATATCAAACAA 58.695 29.630 0.00 0.00 34.08 2.83
810 861 7.828712 TGAAAGATTCATGTGCATATCAAACA 58.171 30.769 0.00 0.00 34.08 2.83
811 862 8.692110 TTGAAAGATTCATGTGCATATCAAAC 57.308 30.769 0.00 0.00 39.84 2.93
812 863 9.142515 GTTTGAAAGATTCATGTGCATATCAAA 57.857 29.630 0.00 0.00 39.84 2.69
813 864 8.525316 AGTTTGAAAGATTCATGTGCATATCAA 58.475 29.630 0.00 0.00 39.84 2.57
814 865 8.058667 AGTTTGAAAGATTCATGTGCATATCA 57.941 30.769 0.00 0.00 39.84 2.15
819 870 6.882610 ACTAGTTTGAAAGATTCATGTGCA 57.117 33.333 0.00 0.00 39.84 4.57
873 924 6.156519 GGCTGTAAGAACAAATGTAAAAGGG 58.843 40.000 0.00 0.00 34.49 3.95
897 957 9.498307 GGAACATAACAAGATAACCAATTAACG 57.502 33.333 0.00 0.00 0.00 3.18
1102 1163 3.842923 CCTGTGCTCCGCCTCGAT 61.843 66.667 0.00 0.00 0.00 3.59
1121 1182 0.036164 ACAGCCAACACGGATAGCAA 59.964 50.000 0.00 0.00 36.56 3.91
1241 1302 2.374184 CTTGGTTGTTCAACTGGTCCA 58.626 47.619 14.04 0.00 0.00 4.02
1324 1385 3.131223 CCTAGACCAGTGTCATCGATGTT 59.869 47.826 24.09 6.93 44.33 2.71
1420 1481 4.636435 ACCAACCGCCACCCGAAG 62.636 66.667 0.00 0.00 40.02 3.79
1598 1659 5.820423 TCGAACTCAAACTTTTGGAGATTCA 59.180 36.000 1.94 0.00 38.66 2.57
1984 2046 4.560108 GCAAAATGTGAAGGTGAGCTCAAT 60.560 41.667 20.19 7.51 0.00 2.57
2205 2267 3.321497 GCGAGGAGCCTGTATAATCAAG 58.679 50.000 0.00 0.00 40.81 3.02
2309 2371 0.938008 GCAGCTTATAACGGTCAGCC 59.062 55.000 0.00 0.00 32.25 4.85
2376 2438 0.973632 TTTCAGCCTCCGCAGAGTAA 59.026 50.000 0.00 0.00 38.58 2.24
2458 2520 4.484258 GCGAGTCGAGCCGAGCTT 62.484 66.667 18.61 0.00 39.88 3.74
2526 2588 3.438183 AGCCAATCTTGGATTTGAGCTT 58.562 40.909 13.14 0.00 46.48 3.74
2972 3577 2.025321 CCTTTCCTTTTGGCTAGGGCTA 60.025 50.000 0.00 0.00 40.12 3.93
2984 3589 4.327680 GTGTGTCTGCTATCCTTTCCTTT 58.672 43.478 0.00 0.00 0.00 3.11
2985 3590 3.307762 GGTGTGTCTGCTATCCTTTCCTT 60.308 47.826 0.00 0.00 0.00 3.36
2986 3591 2.237392 GGTGTGTCTGCTATCCTTTCCT 59.763 50.000 0.00 0.00 0.00 3.36
2987 3592 2.027192 TGGTGTGTCTGCTATCCTTTCC 60.027 50.000 0.00 0.00 0.00 3.13
3087 3700 4.040829 TCAGAAGAAGAAATCTGGAGTGCA 59.959 41.667 3.23 0.00 42.62 4.57
3181 3794 3.128242 GTGCCATGTTTTGAGATCTCAGG 59.872 47.826 23.92 20.56 41.13 3.86
3182 3795 3.128242 GGTGCCATGTTTTGAGATCTCAG 59.872 47.826 23.92 12.63 41.13 3.35
3183 3796 3.084039 GGTGCCATGTTTTGAGATCTCA 58.916 45.455 21.67 21.67 37.91 3.27
3259 3874 4.160814 TGCATTTTCAAGCAGCCAATAGAT 59.839 37.500 0.00 0.00 35.51 1.98
3283 3898 8.192068 TGACCAGACAATATTACAATAACACG 57.808 34.615 0.00 0.00 0.00 4.49
3289 3904 7.047891 ACGTGATGACCAGACAATATTACAAT 58.952 34.615 0.00 0.00 0.00 2.71
3411 4057 9.199645 TCCAGATTTTTCTGCATTCCATTATTA 57.800 29.630 0.00 0.00 36.46 0.98
3412 4058 8.081517 TCCAGATTTTTCTGCATTCCATTATT 57.918 30.769 0.00 0.00 36.46 1.40
3413 4059 7.664552 TCCAGATTTTTCTGCATTCCATTAT 57.335 32.000 0.00 0.00 36.46 1.28


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

AutoCloner maintained by Alex Coulton.