Multiple sequence alignment - TraesCS4D01G341400

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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 TraesCS4D01G341400 chr4D 100.000 3633 0 0 1 3633 498064279 498060647 0.000000e+00 6709.0
1 TraesCS4D01G341400 chr5A 94.951 2060 63 13 642 2679 678584283 678582243 0.000000e+00 3190.0
2 TraesCS4D01G341400 chr5A 86.865 571 40 10 2699 3252 678582257 678581705 1.120000e-169 606.0
3 TraesCS4D01G341400 chr5A 94.560 386 16 4 75 459 678585602 678585221 3.120000e-165 592.0
4 TraesCS4D01G341400 chr5A 94.828 290 14 1 3345 3633 678581361 678581072 5.530000e-123 451.0
5 TraesCS4D01G341400 chr4B 94.505 2002 73 14 703 2668 640027691 640025691 0.000000e+00 3053.0
6 TraesCS4D01G341400 chr4B 92.737 537 19 8 2817 3353 640025630 640025114 0.000000e+00 758.0
7 TraesCS4D01G341400 chr4B 94.076 422 18 4 65 482 640028433 640028015 5.120000e-178 634.0
8 TraesCS4D01G341400 chr4B 92.096 291 21 1 3345 3633 640025074 640024784 3.380000e-110 409.0
9 TraesCS4D01G341400 chr2A 76.969 508 89 21 1052 1548 575685951 575686441 7.730000e-67 265.0
10 TraesCS4D01G341400 chr2A 86.170 94 11 2 1052 1144 578117839 578117931 2.310000e-17 100.0
11 TraesCS4D01G341400 chr2B 80.909 330 55 6 1223 1548 483463701 483464026 1.670000e-63 254.0
12 TraesCS4D01G341400 chr2B 77.871 357 77 2 2223 2578 483469444 483469799 1.700000e-53 220.0
13 TraesCS4D01G341400 chr2B 86.170 94 11 2 1052 1144 484591421 484591513 2.310000e-17 100.0
14 TraesCS4D01G341400 chr7D 89.855 69 5 2 494 562 382117466 382117532 1.800000e-13 87.9
15 TraesCS4D01G341400 chr7D 93.182 44 3 0 1101 1144 309913835 309913792 8.420000e-07 65.8
16 TraesCS4D01G341400 chr7B 96.154 52 2 0 511 562 376350606 376350657 6.460000e-13 86.1
17 TraesCS4D01G341400 chr7B 86.441 59 8 0 1086 1144 304523878 304523936 8.420000e-07 65.8
18 TraesCS4D01G341400 chr7B 87.719 57 6 1 511 566 327274548 327274604 8.420000e-07 65.8
19 TraesCS4D01G341400 chr7B 100.000 31 0 0 13 43 144071095 144071065 1.410000e-04 58.4
20 TraesCS4D01G341400 chr6B 94.545 55 3 0 511 565 217157796 217157850 6.460000e-13 86.1
21 TraesCS4D01G341400 chr1A 90.476 63 4 2 511 573 399497086 399497146 8.360000e-12 82.4
22 TraesCS4D01G341400 chr6D 92.727 55 4 0 511 565 123151053 123151107 3.010000e-11 80.5
23 TraesCS4D01G341400 chr6D 94.118 51 2 1 513 563 158225471 158225520 3.890000e-10 76.8
24 TraesCS4D01G341400 chr4A 94.340 53 2 1 511 563 336064394 336064343 3.010000e-11 80.5
25 TraesCS4D01G341400 chr7A 94.231 52 2 1 512 562 429736117 429736168 1.080000e-10 78.7
26 TraesCS4D01G341400 chr5B 90.000 60 6 0 1088 1147 764811 764752 1.080000e-10 78.7
27 TraesCS4D01G341400 chr5D 86.441 59 8 0 1086 1144 1887253 1887195 8.420000e-07 65.8


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 TraesCS4D01G341400 chr4D 498060647 498064279 3632 True 6709.00 6709 100.0000 1 3633 1 chr4D.!!$R1 3632
1 TraesCS4D01G341400 chr5A 678581072 678585602 4530 True 1209.75 3190 92.8010 75 3633 4 chr5A.!!$R1 3558
2 TraesCS4D01G341400 chr4B 640024784 640028433 3649 True 1213.50 3053 93.3535 65 3633 4 chr4B.!!$R1 3568

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
473 756 0.620556 GGACTCTCCCATTGCTCCAA 59.379 55.000 0.0 0.0 0.0 3.53 F
1366 2395 1.065928 CTCGTCCCTGTACATCGCC 59.934 63.158 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 2398 2.100603 GCGAAGGACGAGACGAGG 59.899 66.667 0.0 0.0 45.77 4.63 R
2692 3727 0.738389 CACGGCACACCAAGTTTTCT 59.262 50.000 0.0 0.0 34.57 2.52 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
51 52 7.695074 ACTACTTAGTGATCTAGGGAGTACT 57.305 40.000 0.00 0.00 42.93 2.73
52 53 7.738847 ACTACTTAGTGATCTAGGGAGTACTC 58.261 42.308 14.87 14.87 42.93 2.59
53 54 6.835029 ACTTAGTGATCTAGGGAGTACTCT 57.165 41.667 21.88 6.36 0.00 3.24
54 55 6.834107 ACTTAGTGATCTAGGGAGTACTCTC 58.166 44.000 21.88 18.89 39.76 3.20
55 56 6.618196 ACTTAGTGATCTAGGGAGTACTCTCT 59.382 42.308 27.89 27.89 44.00 3.10
56 57 7.790798 ACTTAGTGATCTAGGGAGTACTCTCTA 59.209 40.741 27.17 27.17 41.46 2.43
57 58 8.564364 TTAGTGATCTAGGGAGTACTCTCTAA 57.436 38.462 28.31 20.29 41.72 2.10
58 59 7.074653 AGTGATCTAGGGAGTACTCTCTAAG 57.925 44.000 28.31 21.96 41.72 2.18
59 60 5.704053 GTGATCTAGGGAGTACTCTCTAAGC 59.296 48.000 28.31 21.72 41.72 3.09
60 61 5.369993 TGATCTAGGGAGTACTCTCTAAGCA 59.630 44.000 28.31 23.50 41.72 3.91
61 62 5.712084 TCTAGGGAGTACTCTCTAAGCAA 57.288 43.478 28.31 12.14 41.72 3.91
62 63 6.075949 TCTAGGGAGTACTCTCTAAGCAAA 57.924 41.667 28.31 11.47 41.72 3.68
63 64 6.674573 TCTAGGGAGTACTCTCTAAGCAAAT 58.325 40.000 28.31 7.87 41.72 2.32
69 70 6.419413 GGAGTACTCTCTAAGCAAATGAATCG 59.581 42.308 21.88 0.00 40.29 3.34
165 166 3.428862 CGATCTGGGTTACAAAAATGCCC 60.429 47.826 0.00 0.00 39.73 5.36
280 281 2.091588 CCCGTCAAACAATACGACTTCG 59.908 50.000 0.00 0.00 41.55 3.79
331 334 4.963318 AGTGAAGATTCAAGGACAGTGA 57.037 40.909 0.00 0.00 39.21 3.41
332 335 5.495926 AGTGAAGATTCAAGGACAGTGAT 57.504 39.130 0.00 0.00 39.21 3.06
450 455 3.057315 GGTTGTTGTAGCTTGTCATGCAT 60.057 43.478 12.76 0.00 0.00 3.96
458 741 3.960571 AGCTTGTCATGCATTAAGGACT 58.039 40.909 14.02 3.98 0.00 3.85
473 756 0.620556 GGACTCTCCCATTGCTCCAA 59.379 55.000 0.00 0.00 0.00 3.53
483 766 3.012518 CCATTGCTCCAACTTGGACTAG 58.987 50.000 6.39 0.00 42.67 2.57
488 771 6.808321 TTGCTCCAACTTGGACTAGTATAT 57.192 37.500 6.39 0.00 42.67 0.86
492 775 7.728532 TGCTCCAACTTGGACTAGTATATCATA 59.271 37.037 6.39 0.00 42.67 2.15
494 777 9.915629 CTCCAACTTGGACTAGTATATCATAAC 57.084 37.037 6.39 0.00 42.67 1.89
495 778 8.573885 TCCAACTTGGACTAGTATATCATAACG 58.426 37.037 6.39 0.00 42.67 3.18
497 780 9.745880 CAACTTGGACTAGTATATCATAACGTT 57.254 33.333 5.88 5.88 0.00 3.99
498 781 9.745880 AACTTGGACTAGTATATCATAACGTTG 57.254 33.333 11.99 0.00 0.00 4.10
499 782 9.128404 ACTTGGACTAGTATATCATAACGTTGA 57.872 33.333 11.99 0.81 0.00 3.18
511 794 5.393124 TCATAACGTTGATACTTCGTTCGT 58.607 37.500 11.99 0.00 44.58 3.85
514 797 7.536964 TCATAACGTTGATACTTCGTTCGTAAA 59.463 33.333 11.99 0.00 44.58 2.01
515 798 5.736040 ACGTTGATACTTCGTTCGTAAAG 57.264 39.130 0.00 0.00 34.07 1.85
516 799 5.451908 ACGTTGATACTTCGTTCGTAAAGA 58.548 37.500 0.00 0.00 34.07 2.52
517 800 5.914635 ACGTTGATACTTCGTTCGTAAAGAA 59.085 36.000 0.00 0.00 34.07 2.52
519 802 7.115378 ACGTTGATACTTCGTTCGTAAAGAAAT 59.885 33.333 0.00 0.00 41.10 2.17
520 803 8.577939 CGTTGATACTTCGTTCGTAAAGAAATA 58.422 33.333 1.76 0.00 41.10 1.40
526 809 8.853469 ACTTCGTTCGTAAAGAAATATAGGAG 57.147 34.615 1.76 0.00 41.10 3.69
527 810 8.465201 ACTTCGTTCGTAAAGAAATATAGGAGT 58.535 33.333 1.76 0.00 41.10 3.85
528 811 8.624701 TTCGTTCGTAAAGAAATATAGGAGTG 57.375 34.615 0.00 0.00 41.10 3.51
530 813 8.246180 TCGTTCGTAAAGAAATATAGGAGTGTT 58.754 33.333 0.00 0.00 41.10 3.32
599 882 9.804758 CGTAAAGATCTAATGGGATAACCTATC 57.195 37.037 0.00 0.00 41.11 2.08
779 1784 7.040478 GCCATATCTAAACATGAATGCCAACTA 60.040 37.037 0.00 0.00 0.00 2.24
828 1840 1.809567 GCCTGCCCAAAGTTGACCAG 61.810 60.000 0.00 0.00 0.00 4.00
866 1878 3.710722 CCGGCCCTTGAGAGCTGT 61.711 66.667 0.00 0.00 33.32 4.40
906 1918 3.385469 CTGCCAGTCAGCTCTCCA 58.615 61.111 0.00 0.00 35.78 3.86
921 1933 4.832266 AGCTCTCCATCTCGATAACTTGAT 59.168 41.667 0.00 0.00 0.00 2.57
933 1945 7.283354 TCTCGATAACTTGATCAGTGACACTAT 59.717 37.037 8.02 2.72 35.12 2.12
941 1953 8.972127 ACTTGATCAGTGACACTATAATACACT 58.028 33.333 8.02 0.00 41.52 3.55
1164 2189 2.906389 TCAGATTCACCCACAGCTTACT 59.094 45.455 0.00 0.00 0.00 2.24
1180 2205 1.497991 TACTTATGATCTTGCGCGGC 58.502 50.000 8.83 0.00 0.00 6.53
1208 2233 3.579709 GTCTCGTTTCTGATCTCTTGCA 58.420 45.455 0.00 0.00 0.00 4.08
1357 2386 1.608717 CCTCCTTCACCTCGTCCCTG 61.609 65.000 0.00 0.00 0.00 4.45
1366 2395 1.065928 CTCGTCCCTGTACATCGCC 59.934 63.158 0.00 0.00 0.00 5.54
1369 2398 3.845259 TCCCTGTACATCGCCGGC 61.845 66.667 19.07 19.07 0.00 6.13
1375 2404 3.896133 TACATCGCCGGCCTCGTC 61.896 66.667 23.46 0.00 33.95 4.20
1732 2761 1.819632 GCCGGCCATCGTCATCTTT 60.820 57.895 18.11 0.00 37.11 2.52
1735 2764 0.374758 CGGCCATCGTCATCTTTGTG 59.625 55.000 2.24 0.00 0.00 3.33
2152 3181 1.181098 GCAAGGTGCTGGTCATGGTT 61.181 55.000 0.00 0.00 40.96 3.67
2173 3202 1.065109 CGCGGTGATCATGGTCGTA 59.935 57.895 0.00 0.00 0.00 3.43
2203 3232 2.124736 AACGCGTGGATCATGGGG 60.125 61.111 14.98 0.00 37.58 4.96
2425 3454 2.038975 ACCTTCCTCGCCCTGCTA 59.961 61.111 0.00 0.00 0.00 3.49
2658 3693 2.094575 TGTGTTCGTTTGTCCGTTCAAG 59.905 45.455 0.00 0.00 0.00 3.02
2661 3696 2.536761 TCGTTTGTCCGTTCAAGGAT 57.463 45.000 0.00 0.00 43.04 3.24
2681 3716 6.415573 AGGATAACCTTGATGTACCTGTTTC 58.584 40.000 0.00 0.00 45.36 2.78
2682 3717 6.012858 AGGATAACCTTGATGTACCTGTTTCA 60.013 38.462 0.00 0.00 45.36 2.69
2684 3719 4.706842 ACCTTGATGTACCTGTTTCAGT 57.293 40.909 0.00 0.00 0.00 3.41
2685 3720 5.818678 ACCTTGATGTACCTGTTTCAGTA 57.181 39.130 0.00 0.00 0.00 2.74
2686 3721 6.182507 ACCTTGATGTACCTGTTTCAGTAA 57.817 37.500 0.00 0.00 0.00 2.24
2687 3722 6.597562 ACCTTGATGTACCTGTTTCAGTAAA 58.402 36.000 0.00 0.00 0.00 2.01
2688 3723 6.710744 ACCTTGATGTACCTGTTTCAGTAAAG 59.289 38.462 0.00 0.00 0.00 1.85
2689 3724 6.934645 CCTTGATGTACCTGTTTCAGTAAAGA 59.065 38.462 0.00 0.00 0.00 2.52
2690 3725 7.444183 CCTTGATGTACCTGTTTCAGTAAAGAA 59.556 37.037 0.00 0.00 0.00 2.52
2692 3727 8.740123 TGATGTACCTGTTTCAGTAAAGAAAA 57.260 30.769 0.00 0.00 39.05 2.29
2693 3728 8.836413 TGATGTACCTGTTTCAGTAAAGAAAAG 58.164 33.333 0.00 0.00 39.05 2.27
2694 3729 8.974060 ATGTACCTGTTTCAGTAAAGAAAAGA 57.026 30.769 0.00 0.00 39.05 2.52
2696 3731 9.233649 TGTACCTGTTTCAGTAAAGAAAAGAAA 57.766 29.630 0.00 0.00 39.05 2.52
2699 3734 8.803235 ACCTGTTTCAGTAAAGAAAAGAAAACT 58.197 29.630 0.00 0.00 39.05 2.66
2700 3735 9.639601 CCTGTTTCAGTAAAGAAAAGAAAACTT 57.360 29.630 0.00 0.00 39.05 2.66
2712 3747 0.869880 GAAAACTTGGTGTGCCGTGC 60.870 55.000 0.00 0.00 37.67 5.34
2730 3765 3.586039 CACGCATGCTCGGTTAAAG 57.414 52.632 17.13 0.00 0.00 1.85
2744 3779 6.965500 GCTCGGTTAAAGTTTTATTTAGGAGC 59.035 38.462 0.00 0.84 37.26 4.70
2777 3815 2.260844 TCTTGCTTGGACTTGGAGTG 57.739 50.000 0.00 0.00 0.00 3.51
2791 3831 5.542779 ACTTGGAGTGTCTTGTATTGACTC 58.457 41.667 0.00 0.00 35.63 3.36
2813 3853 2.668279 GCGGATGAATTTGCGAAGTTGT 60.668 45.455 0.00 0.00 31.44 3.32
3146 4212 8.539544 CCCATTAGAAGGTTTTTAATGTTCCAT 58.460 33.333 9.71 0.00 34.51 3.41
3262 4328 9.201127 GATTTTTCTTCTTCTTTTTCCCTGATG 57.799 33.333 0.00 0.00 0.00 3.07
3293 4359 5.769662 TGATACAACTTGGAGCAAATTGTCT 59.230 36.000 0.00 0.00 39.08 3.41
3334 4616 8.682710 AGTAATAACAACGATGCATTTTATGGT 58.317 29.630 0.00 0.00 0.00 3.55
3406 4740 7.964604 AACAAACCTATGACTAGAGACAAAC 57.035 36.000 0.00 0.00 0.00 2.93
3591 4927 3.834231 AGATTTTGGCCTGCTAACAACAT 59.166 39.130 3.32 0.00 0.00 2.71
3596 4932 1.533625 GCCTGCTAACAACATCCACA 58.466 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.569858 AGAGTACTCCCTAGATCACTAAGTAGT 59.430 40.741 19.38 0.00 36.90 2.73
28 29 7.970102 AGAGTACTCCCTAGATCACTAAGTAG 58.030 42.308 19.38 0.00 0.00 2.57
29 30 7.790798 AGAGAGTACTCCCTAGATCACTAAGTA 59.209 40.741 19.38 0.00 43.53 2.24
30 31 6.618196 AGAGAGTACTCCCTAGATCACTAAGT 59.382 42.308 19.38 0.00 43.53 2.24
31 32 7.074653 AGAGAGTACTCCCTAGATCACTAAG 57.925 44.000 19.38 0.00 43.53 2.18
32 33 8.564364 TTAGAGAGTACTCCCTAGATCACTAA 57.436 38.462 19.38 11.29 43.53 2.24
33 34 7.256404 GCTTAGAGAGTACTCCCTAGATCACTA 60.256 44.444 19.38 0.00 43.53 2.74
34 35 6.465321 GCTTAGAGAGTACTCCCTAGATCACT 60.465 46.154 19.38 7.55 43.53 3.41
35 36 5.704053 GCTTAGAGAGTACTCCCTAGATCAC 59.296 48.000 19.38 3.05 43.53 3.06
36 37 5.369993 TGCTTAGAGAGTACTCCCTAGATCA 59.630 44.000 19.38 12.22 43.53 2.92
37 38 5.871834 TGCTTAGAGAGTACTCCCTAGATC 58.128 45.833 19.38 9.16 43.53 2.75
38 39 5.915744 TGCTTAGAGAGTACTCCCTAGAT 57.084 43.478 19.38 0.00 43.53 1.98
39 40 5.712084 TTGCTTAGAGAGTACTCCCTAGA 57.288 43.478 19.38 7.50 43.53 2.43
40 41 6.547880 TCATTTGCTTAGAGAGTACTCCCTAG 59.452 42.308 19.38 12.26 43.53 3.02
41 42 6.432581 TCATTTGCTTAGAGAGTACTCCCTA 58.567 40.000 19.38 14.50 43.53 3.53
42 43 5.273208 TCATTTGCTTAGAGAGTACTCCCT 58.727 41.667 19.38 15.62 43.53 4.20
43 44 5.599999 TCATTTGCTTAGAGAGTACTCCC 57.400 43.478 19.38 7.90 43.53 4.30
44 45 6.419413 CGATTCATTTGCTTAGAGAGTACTCC 59.581 42.308 19.38 10.83 43.53 3.85
45 46 6.975772 ACGATTCATTTGCTTAGAGAGTACTC 59.024 38.462 15.41 15.41 42.90 2.59
46 47 6.754209 CACGATTCATTTGCTTAGAGAGTACT 59.246 38.462 0.00 0.00 0.00 2.73
47 48 6.531948 ACACGATTCATTTGCTTAGAGAGTAC 59.468 38.462 0.00 0.00 0.00 2.73
48 49 6.631016 ACACGATTCATTTGCTTAGAGAGTA 58.369 36.000 0.00 0.00 0.00 2.59
49 50 5.482908 ACACGATTCATTTGCTTAGAGAGT 58.517 37.500 0.00 0.00 0.00 3.24
50 51 7.706281 ATACACGATTCATTTGCTTAGAGAG 57.294 36.000 0.00 0.00 0.00 3.20
51 52 8.414003 AGTATACACGATTCATTTGCTTAGAGA 58.586 33.333 5.50 0.00 0.00 3.10
52 53 8.581057 AGTATACACGATTCATTTGCTTAGAG 57.419 34.615 5.50 0.00 0.00 2.43
56 57 9.325198 TGATTAGTATACACGATTCATTTGCTT 57.675 29.630 5.50 0.00 0.00 3.91
57 58 8.887036 TGATTAGTATACACGATTCATTTGCT 57.113 30.769 5.50 0.00 0.00 3.91
58 59 9.746711 GATGATTAGTATACACGATTCATTTGC 57.253 33.333 5.50 0.00 33.37 3.68
165 166 1.663695 AACTCTTGTCACAACCACGG 58.336 50.000 0.00 0.00 0.00 4.94
280 281 1.739067 AACCTAACTTCCGCTGCATC 58.261 50.000 0.00 0.00 0.00 3.91
326 329 6.682746 ACTAAGCACGATTCCTATATCACTG 58.317 40.000 0.00 0.00 0.00 3.66
331 334 8.349568 TGTGATACTAAGCACGATTCCTATAT 57.650 34.615 0.00 0.00 45.13 0.86
332 335 7.754851 TGTGATACTAAGCACGATTCCTATA 57.245 36.000 0.00 0.00 45.13 1.31
450 455 2.505819 GGAGCAATGGGAGAGTCCTTAA 59.494 50.000 0.00 0.00 36.57 1.85
458 741 1.272092 CCAAGTTGGAGCAATGGGAGA 60.272 52.381 17.60 0.00 40.96 3.71
473 756 9.128404 TCAACGTTATGATATACTAGTCCAAGT 57.872 33.333 0.00 0.00 0.00 3.16
488 771 5.393124 ACGAACGAAGTATCAACGTTATGA 58.607 37.500 0.00 0.00 45.00 2.15
492 775 5.914635 TCTTTACGAACGAAGTATCAACGTT 59.085 36.000 0.00 0.00 45.00 3.99
494 777 5.980324 TCTTTACGAACGAAGTATCAACG 57.020 39.130 0.14 0.00 45.00 4.10
500 783 9.941664 CTCCTATATTTCTTTACGAACGAAGTA 57.058 33.333 0.14 0.00 45.00 2.24
502 785 8.744011 CACTCCTATATTTCTTTACGAACGAAG 58.256 37.037 0.14 0.00 0.00 3.79
505 788 7.982371 ACACTCCTATATTTCTTTACGAACG 57.018 36.000 0.00 0.00 0.00 3.95
570 853 9.322769 AGGTTATCCCATTAGATCTTTACGTAT 57.677 33.333 0.00 0.00 34.66 3.06
571 854 8.716674 AGGTTATCCCATTAGATCTTTACGTA 57.283 34.615 0.00 0.00 34.66 3.57
572 855 7.613551 AGGTTATCCCATTAGATCTTTACGT 57.386 36.000 0.00 0.00 34.66 3.57
573 856 9.804758 GATAGGTTATCCCATTAGATCTTTACG 57.195 37.037 0.00 0.00 34.66 3.18
639 922 6.598064 CCTTCCGGTTTATAGCCCTATATTTG 59.402 42.308 0.00 0.00 0.00 2.32
783 1795 7.254898 CCAGTGTATATCTCGCATTCATGTTTT 60.255 37.037 0.00 0.00 0.00 2.43
793 1805 1.341209 CAGGCCAGTGTATATCTCGCA 59.659 52.381 5.01 0.00 0.00 5.10
828 1840 5.869888 CCGGCATCCTCTTGTATTTATAGAC 59.130 44.000 0.00 0.00 0.00 2.59
866 1878 2.288025 GGTACCGAGGAAGGGTGCA 61.288 63.158 0.00 0.00 41.35 4.57
906 1918 6.096141 AGTGTCACTGATCAAGTTATCGAGAT 59.904 38.462 4.21 0.00 36.83 2.75
933 1945 4.520179 TCTCGTGCTACTCCAGTGTATTA 58.480 43.478 0.00 0.00 0.00 0.98
939 1951 1.272769 GGTTTCTCGTGCTACTCCAGT 59.727 52.381 0.00 0.00 0.00 4.00
941 1953 1.629043 AGGTTTCTCGTGCTACTCCA 58.371 50.000 0.00 0.00 0.00 3.86
942 1954 2.737252 CAAAGGTTTCTCGTGCTACTCC 59.263 50.000 0.00 0.00 0.00 3.85
943 1955 2.157863 GCAAAGGTTTCTCGTGCTACTC 59.842 50.000 0.00 0.00 33.59 2.59
1014 2039 2.594303 CCAGCCTCAACGCCAACA 60.594 61.111 0.00 0.00 0.00 3.33
1164 2189 1.520564 ACGCCGCGCAAGATCATAA 60.521 52.632 13.88 0.00 43.02 1.90
1180 2205 0.385598 TCAGAAACGAGACGAGCACG 60.386 55.000 0.76 0.76 45.75 5.34
1208 2233 3.490761 CCGCCTGAATTTCACAACAGTTT 60.491 43.478 0.00 0.00 0.00 2.66
1357 2386 4.203076 ACGAGGCCGGCGATGTAC 62.203 66.667 22.54 4.96 40.78 2.90
1366 2395 3.398353 GAAGGACGAGACGAGGCCG 62.398 68.421 0.00 0.00 42.50 6.13
1369 2398 2.100603 GCGAAGGACGAGACGAGG 59.899 66.667 0.00 0.00 45.77 4.63
1732 2761 2.604686 AGGAAGAGAGCGCCCACA 60.605 61.111 2.29 0.00 0.00 4.17
1735 2764 2.185608 GTGAGGAAGAGAGCGCCC 59.814 66.667 2.29 0.00 0.00 6.13
1948 2977 2.264794 GGCACCACGACGGAGAAT 59.735 61.111 0.00 0.00 38.63 2.40
2152 3181 4.094646 ACCATGATCACCGCGCCA 62.095 61.111 0.00 0.00 0.00 5.69
2425 3454 2.511600 GCGTACTTGAGCCGGCAT 60.512 61.111 31.54 14.28 0.00 4.40
2597 3632 0.813821 GGAGATGAAGCTGGTTTGCC 59.186 55.000 0.00 0.00 0.00 4.52
2658 3693 6.177610 TGAAACAGGTACATCAAGGTTATCC 58.822 40.000 0.00 0.00 0.00 2.59
2661 3696 6.182507 ACTGAAACAGGTACATCAAGGTTA 57.817 37.500 0.00 0.00 35.51 2.85
2669 3704 8.974060 TCTTTTCTTTACTGAAACAGGTACAT 57.026 30.769 0.00 0.00 35.91 2.29
2670 3705 8.795842 TTCTTTTCTTTACTGAAACAGGTACA 57.204 30.769 0.00 0.00 35.91 2.90
2673 3708 8.803235 AGTTTTCTTTTCTTTACTGAAACAGGT 58.197 29.630 0.00 0.00 35.91 4.00
2674 3709 9.639601 AAGTTTTCTTTTCTTTACTGAAACAGG 57.360 29.630 0.00 0.00 36.67 4.00
2676 3711 9.418045 CCAAGTTTTCTTTTCTTTACTGAAACA 57.582 29.630 0.00 0.00 38.17 2.83
2677 3712 9.419297 ACCAAGTTTTCTTTTCTTTACTGAAAC 57.581 29.630 0.00 0.00 38.17 2.78
2678 3713 9.418045 CACCAAGTTTTCTTTTCTTTACTGAAA 57.582 29.630 0.00 0.00 38.17 2.69
2679 3714 8.581578 ACACCAAGTTTTCTTTTCTTTACTGAA 58.418 29.630 0.00 0.00 38.17 3.02
2681 3716 7.201435 GCACACCAAGTTTTCTTTTCTTTACTG 60.201 37.037 0.00 0.00 38.17 2.74
2682 3717 6.811665 GCACACCAAGTTTTCTTTTCTTTACT 59.188 34.615 0.00 0.00 38.17 2.24
2684 3719 6.103330 GGCACACCAAGTTTTCTTTTCTTTA 58.897 36.000 0.00 0.00 38.17 1.85
2685 3720 4.935205 GGCACACCAAGTTTTCTTTTCTTT 59.065 37.500 0.00 0.00 38.17 2.52
2686 3721 4.503910 GGCACACCAAGTTTTCTTTTCTT 58.496 39.130 0.00 0.00 38.17 2.52
2687 3722 3.428862 CGGCACACCAAGTTTTCTTTTCT 60.429 43.478 0.00 0.00 38.17 2.52
2688 3723 2.857748 CGGCACACCAAGTTTTCTTTTC 59.142 45.455 0.00 0.00 38.17 2.29
2689 3724 2.232696 ACGGCACACCAAGTTTTCTTTT 59.767 40.909 0.00 0.00 38.17 2.27
2690 3725 1.822371 ACGGCACACCAAGTTTTCTTT 59.178 42.857 0.00 0.00 38.17 2.52
2692 3727 0.738389 CACGGCACACCAAGTTTTCT 59.262 50.000 0.00 0.00 34.57 2.52
2693 3728 0.869880 GCACGGCACACCAAGTTTTC 60.870 55.000 0.00 0.00 34.57 2.29
2694 3729 1.140804 GCACGGCACACCAAGTTTT 59.859 52.632 0.00 0.00 34.57 2.43
2696 3731 2.439338 TGCACGGCACACCAAGTT 60.439 55.556 0.00 0.00 31.71 2.66
2712 3747 0.796312 ACTTTAACCGAGCATGCGTG 59.204 50.000 13.01 8.70 0.00 5.34
2723 3758 7.025365 CCACGCTCCTAAATAAAACTTTAACC 58.975 38.462 0.00 0.00 0.00 2.85
2730 3765 4.632538 ATGCCACGCTCCTAAATAAAAC 57.367 40.909 0.00 0.00 0.00 2.43
2744 3779 1.808945 AGCAAGAAGAAGAATGCCACG 59.191 47.619 0.00 0.00 39.59 4.94
2777 3815 2.273370 TCCGCGAGTCAATACAAGAC 57.727 50.000 8.23 0.00 36.26 3.01
2808 3848 7.776969 AGACATTTAGCATCCATGATAACAACT 59.223 33.333 0.00 0.00 38.25 3.16
2813 3853 8.000709 AGGAAAGACATTTAGCATCCATGATAA 58.999 33.333 0.00 0.00 36.93 1.75
2915 3969 8.514594 TCAGCATCGTTTCATTAGAAAGATTTT 58.485 29.630 0.00 0.00 43.95 1.82
2919 3973 6.818142 TGATCAGCATCGTTTCATTAGAAAGA 59.182 34.615 0.00 0.00 43.95 2.52
2920 3974 6.904011 GTGATCAGCATCGTTTCATTAGAAAG 59.096 38.462 0.00 0.00 43.95 2.62
2921 3975 6.183360 GGTGATCAGCATCGTTTCATTAGAAA 60.183 38.462 19.79 0.00 41.26 2.52
2922 3976 5.294306 GGTGATCAGCATCGTTTCATTAGAA 59.706 40.000 19.79 0.00 0.00 2.10
2923 3977 4.811024 GGTGATCAGCATCGTTTCATTAGA 59.189 41.667 19.79 0.00 0.00 2.10
2924 3978 4.318333 CGGTGATCAGCATCGTTTCATTAG 60.318 45.833 23.68 0.00 45.86 1.73
2925 3979 3.555547 CGGTGATCAGCATCGTTTCATTA 59.444 43.478 23.68 0.00 45.86 1.90
2926 3980 2.352651 CGGTGATCAGCATCGTTTCATT 59.647 45.455 23.68 0.00 45.86 2.57
2927 3981 1.935873 CGGTGATCAGCATCGTTTCAT 59.064 47.619 23.68 0.00 45.86 2.57
2928 3982 1.358877 CGGTGATCAGCATCGTTTCA 58.641 50.000 23.68 0.00 45.86 2.69
2934 3988 4.199432 AGATATTCCGGTGATCAGCATC 57.801 45.455 23.68 17.27 0.00 3.91
2935 3989 4.040829 TGAAGATATTCCGGTGATCAGCAT 59.959 41.667 23.68 12.62 0.00 3.79
3054 4118 3.754955 GACTGTGTGTCATCGACGATAA 58.245 45.455 10.57 0.00 44.73 1.75
3146 4212 8.642935 TGGAACATCACAATAAACCTTTATCA 57.357 30.769 0.00 0.00 32.46 2.15
3254 4320 3.940335 TGTATCAGGATTCCATCAGGGA 58.060 45.455 5.29 0.00 46.61 4.20
3262 4328 3.879892 GCTCCAAGTTGTATCAGGATTCC 59.120 47.826 1.45 0.00 0.00 3.01
3334 4616 2.573369 GACCCTGCGAGAGTCATACTA 58.427 52.381 0.00 0.00 0.00 1.82
3507 4841 7.913674 AAGAAGCTAGACAACTATTTCCAAG 57.086 36.000 0.00 0.00 0.00 3.61
3591 4927 5.394005 GCATGTAAAATTAGGCACATGTGGA 60.394 40.000 26.55 0.00 46.37 4.02


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

AutoCloner maintained by Alex Coulton.