Multiple sequence alignment - TraesCS4D01G224000

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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 TraesCS4D01G224000 chr4D 100.000 3449 0 0 1 3449 380798260 380794812 0.000000e+00 6370
1 TraesCS4D01G224000 chr4B 93.553 3366 114 45 72 3392 468052792 468049485 0.000000e+00 4918
2 TraesCS4D01G224000 chr4A 94.935 2784 62 31 439 3159 82846325 82849092 0.000000e+00 4287
3 TraesCS4D01G224000 chr4A 84.759 374 30 10 73 445 82845944 82846291 1.970000e-92 350
4 TraesCS4D01G224000 chr4A 93.137 204 11 1 3189 3392 82849269 82849469 2.600000e-76 296
5 TraesCS4D01G224000 chr4A 95.876 97 4 0 3096 3192 82849093 82849189 1.280000e-34 158


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 TraesCS4D01G224000 chr4D 380794812 380798260 3448 True 6370.00 6370 100.00000 1 3449 1 chr4D.!!$R1 3448
1 TraesCS4D01G224000 chr4B 468049485 468052792 3307 True 4918.00 4918 93.55300 72 3392 1 chr4B.!!$R1 3320
2 TraesCS4D01G224000 chr4A 82845944 82849469 3525 False 1272.75 4287 92.17675 73 3392 4 chr4A.!!$F1 3319

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
340 344 0.107831 ACACCGGCTACTTTTGCAGA 59.892 50.000 0.0 0.0 0.0 4.26 F
341 345 1.271379 ACACCGGCTACTTTTGCAGAT 60.271 47.619 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2255 2.825836 GTCCTGAATGGCGCTGGG 60.826 66.667 7.64 0.9 35.26 4.45 R
2834 2980 5.878406 ATCAGTAAGATGTAGGGTTCAGG 57.122 43.478 0.00 0.0 35.06 3.86 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
19 20 0.665298 GTACGTAGGACCATCGACCC 59.335 60.000 13.73 0.00 0.00 4.46
20 21 0.466189 TACGTAGGACCATCGACCCC 60.466 60.000 13.73 0.00 0.00 4.95
21 22 1.755395 CGTAGGACCATCGACCCCA 60.755 63.158 0.00 0.00 0.00 4.96
22 23 1.821258 GTAGGACCATCGACCCCAC 59.179 63.158 0.00 0.00 0.00 4.61
23 24 0.686769 GTAGGACCATCGACCCCACT 60.687 60.000 0.00 0.00 0.00 4.00
24 25 0.686441 TAGGACCATCGACCCCACTG 60.686 60.000 0.00 0.00 0.00 3.66
25 26 2.584608 GACCATCGACCCCACTGG 59.415 66.667 0.00 0.00 41.37 4.00
26 27 3.682292 GACCATCGACCCCACTGGC 62.682 68.421 0.34 0.00 37.83 4.85
27 28 4.489771 CCATCGACCCCACTGGCC 62.490 72.222 0.00 0.00 37.83 5.36
28 29 3.716195 CATCGACCCCACTGGCCA 61.716 66.667 4.71 4.71 37.83 5.36
29 30 3.717294 ATCGACCCCACTGGCCAC 61.717 66.667 0.00 0.00 37.83 5.01
30 31 4.954118 TCGACCCCACTGGCCACT 62.954 66.667 0.00 0.00 37.83 4.00
31 32 4.394712 CGACCCCACTGGCCACTC 62.395 72.222 0.00 0.00 37.83 3.51
32 33 2.930562 GACCCCACTGGCCACTCT 60.931 66.667 0.00 0.00 37.83 3.24
33 34 2.930562 ACCCCACTGGCCACTCTC 60.931 66.667 0.00 0.00 37.83 3.20
34 35 3.721706 CCCCACTGGCCACTCTCC 61.722 72.222 0.00 0.00 0.00 3.71
35 36 2.930019 CCCACTGGCCACTCTCCA 60.930 66.667 0.00 0.00 0.00 3.86
40 41 4.894719 TGGCCACTCTCCAGATGA 57.105 55.556 0.00 0.00 0.00 2.92
41 42 2.290847 TGGCCACTCTCCAGATGAC 58.709 57.895 0.00 0.00 0.00 3.06
42 43 0.545071 TGGCCACTCTCCAGATGACA 60.545 55.000 0.00 0.00 0.00 3.58
43 44 0.177604 GGCCACTCTCCAGATGACAG 59.822 60.000 0.00 0.00 0.00 3.51
44 45 0.901124 GCCACTCTCCAGATGACAGT 59.099 55.000 0.00 0.00 0.00 3.55
45 46 2.103373 GCCACTCTCCAGATGACAGTA 58.897 52.381 0.00 0.00 0.00 2.74
46 47 2.497675 GCCACTCTCCAGATGACAGTAA 59.502 50.000 0.00 0.00 0.00 2.24
47 48 3.677424 GCCACTCTCCAGATGACAGTAAC 60.677 52.174 0.00 0.00 0.00 2.50
48 49 3.428180 CCACTCTCCAGATGACAGTAACG 60.428 52.174 0.00 0.00 0.00 3.18
49 50 3.440522 CACTCTCCAGATGACAGTAACGA 59.559 47.826 0.00 0.00 0.00 3.85
50 51 4.097135 CACTCTCCAGATGACAGTAACGAT 59.903 45.833 0.00 0.00 0.00 3.73
51 52 4.707448 ACTCTCCAGATGACAGTAACGATT 59.293 41.667 0.00 0.00 0.00 3.34
52 53 5.886474 ACTCTCCAGATGACAGTAACGATTA 59.114 40.000 0.00 0.00 0.00 1.75
53 54 6.038825 ACTCTCCAGATGACAGTAACGATTAG 59.961 42.308 0.00 0.00 0.00 1.73
54 55 4.933330 TCCAGATGACAGTAACGATTAGC 58.067 43.478 0.00 0.00 0.00 3.09
56 57 4.497507 CCAGATGACAGTAACGATTAGCGA 60.498 45.833 0.00 0.00 44.57 4.93
57 58 5.215903 CAGATGACAGTAACGATTAGCGAT 58.784 41.667 0.00 0.00 44.57 4.58
58 59 5.116225 CAGATGACAGTAACGATTAGCGATG 59.884 44.000 0.00 0.00 44.57 3.84
59 60 4.625972 TGACAGTAACGATTAGCGATGA 57.374 40.909 0.00 0.00 44.57 2.92
60 61 5.183014 TGACAGTAACGATTAGCGATGAT 57.817 39.130 0.00 0.00 44.57 2.45
61 62 4.976116 TGACAGTAACGATTAGCGATGATG 59.024 41.667 0.00 0.00 44.57 3.07
62 63 4.299155 ACAGTAACGATTAGCGATGATGG 58.701 43.478 0.00 0.00 44.57 3.51
63 64 4.202121 ACAGTAACGATTAGCGATGATGGT 60.202 41.667 0.00 0.00 44.57 3.55
64 65 4.148871 CAGTAACGATTAGCGATGATGGTG 59.851 45.833 0.00 0.00 44.57 4.17
65 66 3.452755 AACGATTAGCGATGATGGTGA 57.547 42.857 0.00 0.00 44.57 4.02
66 67 3.667497 ACGATTAGCGATGATGGTGAT 57.333 42.857 0.00 0.00 44.57 3.06
67 68 3.579709 ACGATTAGCGATGATGGTGATC 58.420 45.455 0.00 0.00 44.57 2.92
68 69 2.595977 CGATTAGCGATGATGGTGATCG 59.404 50.000 5.88 5.88 45.04 3.69
69 70 3.579709 GATTAGCGATGATGGTGATCGT 58.420 45.455 0.00 0.00 43.74 3.73
70 71 2.422276 TAGCGATGATGGTGATCGTG 57.578 50.000 0.00 0.00 43.74 4.35
80 81 3.165058 TGGTGATCGTGAGCACTAATC 57.835 47.619 16.73 2.35 46.10 1.75
109 111 1.603455 CCCAACAACCAGGACGCAT 60.603 57.895 0.00 0.00 0.00 4.73
179 181 2.158519 ACCTCCACTGGTTACAAAAGGG 60.159 50.000 0.00 0.00 36.89 3.95
220 222 4.745649 ACGATAGGGAGAAGAAAGAAACG 58.254 43.478 0.00 0.00 43.77 3.60
228 230 1.595794 GAAGAAAGAAACGCACACCGA 59.404 47.619 0.00 0.00 41.02 4.69
245 247 1.542547 CCGACTACTTTGCAACCACCT 60.543 52.381 0.00 0.00 0.00 4.00
340 344 0.107831 ACACCGGCTACTTTTGCAGA 59.892 50.000 0.00 0.00 0.00 4.26
341 345 1.271379 ACACCGGCTACTTTTGCAGAT 60.271 47.619 0.00 0.00 0.00 2.90
367 371 8.511604 TTTTTCTTCTTCTCAAGAACTCATGT 57.488 30.769 0.00 0.00 42.31 3.21
368 372 8.511604 TTTTCTTCTTCTCAAGAACTCATGTT 57.488 30.769 0.00 0.00 42.31 2.71
370 374 9.613428 TTTCTTCTTCTCAAGAACTCATGTTTA 57.387 29.630 0.00 0.00 42.31 2.01
371 375 9.784531 TTCTTCTTCTCAAGAACTCATGTTTAT 57.215 29.630 0.00 0.00 42.31 1.40
440 484 9.997482 ATAGTTATTTGTTTTATTTCGATGCGT 57.003 25.926 0.00 0.00 0.00 5.24
454 498 7.410800 TTTCGATGCGTAGAAGAAAGTAAAA 57.589 32.000 1.64 0.00 0.00 1.52
496 540 4.220533 TCTTAGCGTCCGTAAATCTAGC 57.779 45.455 0.00 0.00 0.00 3.42
502 546 2.202566 GTCCGTAAATCTAGCACCAGC 58.797 52.381 0.00 0.00 42.56 4.85
695 756 5.629435 GCTCCTGGAAAATCTAAAACAAACG 59.371 40.000 0.00 0.00 0.00 3.60
696 757 6.079424 TCCTGGAAAATCTAAAACAAACGG 57.921 37.500 0.00 0.00 0.00 4.44
831 913 3.051081 AGCAAGCAAACAAACAAACCA 57.949 38.095 0.00 0.00 0.00 3.67
862 948 1.946650 GAGAGCACGATACTGCGGC 60.947 63.158 0.00 0.00 42.42 6.53
974 1093 4.292178 CGAGATCCAGCGAGGGCC 62.292 72.222 0.00 0.00 41.24 5.80
975 1094 3.157252 GAGATCCAGCGAGGGCCA 61.157 66.667 6.18 0.00 41.24 5.36
976 1095 3.160047 AGATCCAGCGAGGGCCAG 61.160 66.667 6.18 0.00 41.24 4.85
977 1096 4.925861 GATCCAGCGAGGGCCAGC 62.926 72.222 14.99 14.99 41.24 4.85
1098 1217 3.310860 CTACCACCACCACCGCCTC 62.311 68.421 0.00 0.00 0.00 4.70
2400 2546 1.138247 GCAGCATGGCAGTAGCAAC 59.862 57.895 11.17 0.40 44.61 4.17
2696 2842 9.428097 GCTAGGAAGATTTTTCAATCATTTTGT 57.572 29.630 0.00 0.00 41.37 2.83
2834 2980 7.328249 CGATCAATATTTAGTTCTCTCTGGAGC 59.672 40.741 0.00 0.00 39.31 4.70
2845 2991 0.827368 CTCTGGAGCCTGAACCCTAC 59.173 60.000 0.00 0.00 0.00 3.18
2962 3108 6.121776 TCTAGCTTTTCCTTTGTGGATACA 57.878 37.500 0.00 0.00 45.68 2.29
3060 3207 3.660501 TTCGTGAGTGCTACTGTGATT 57.339 42.857 0.00 0.00 0.00 2.57
3089 3236 7.924412 ACTTTTCTGAGACAGATTAAACGTACA 59.076 33.333 2.30 0.00 40.39 2.90
3144 3355 0.986992 GCAATTGCAACGTGCTCATC 59.013 50.000 25.36 1.55 45.31 2.92
3149 3360 1.150827 TGCAACGTGCTCATCTTCAG 58.849 50.000 10.54 0.00 45.31 3.02
3197 3491 9.418045 GCTTTCTCATTATGAACTACTAGATCC 57.582 37.037 0.00 0.00 0.00 3.36
3281 3575 6.953520 TGGGAATCACCAATTGTCTAGAAAAT 59.046 34.615 1.97 1.97 41.20 1.82
3339 3633 4.305769 CGATGGGAAGATCTGATCACTTC 58.694 47.826 19.12 13.96 39.16 3.01
3340 3634 4.039004 CGATGGGAAGATCTGATCACTTCT 59.961 45.833 19.12 9.71 39.61 2.85
3341 3635 5.453057 CGATGGGAAGATCTGATCACTTCTT 60.453 44.000 19.12 15.94 39.61 2.52
3411 3705 9.521841 TTTTTGTATTGTATTGTACCAGGATGA 57.478 29.630 0.00 0.00 39.69 2.92
3412 3706 8.731275 TTTGTATTGTATTGTACCAGGATGAG 57.269 34.615 0.00 0.00 39.69 2.90
3413 3707 7.669089 TGTATTGTATTGTACCAGGATGAGA 57.331 36.000 0.00 0.00 39.69 3.27
3414 3708 8.084985 TGTATTGTATTGTACCAGGATGAGAA 57.915 34.615 0.00 0.00 39.69 2.87
3415 3709 8.713971 TGTATTGTATTGTACCAGGATGAGAAT 58.286 33.333 0.00 0.00 39.69 2.40
3416 3710 8.993121 GTATTGTATTGTACCAGGATGAGAATG 58.007 37.037 0.00 0.00 39.69 2.67
3417 3711 5.928976 TGTATTGTACCAGGATGAGAATGG 58.071 41.667 0.00 0.00 39.69 3.16
3419 3713 4.927267 TTGTACCAGGATGAGAATGGTT 57.073 40.909 0.83 0.00 44.98 3.67
3420 3714 4.927267 TGTACCAGGATGAGAATGGTTT 57.073 40.909 0.83 0.00 44.98 3.27
3421 3715 5.255397 TGTACCAGGATGAGAATGGTTTT 57.745 39.130 0.83 0.00 44.98 2.43
3422 3716 5.009631 TGTACCAGGATGAGAATGGTTTTG 58.990 41.667 0.83 0.00 44.98 2.44
3423 3717 4.118168 ACCAGGATGAGAATGGTTTTGT 57.882 40.909 0.00 0.00 44.98 2.83
3424 3718 3.828451 ACCAGGATGAGAATGGTTTTGTG 59.172 43.478 0.00 0.00 44.98 3.33
3425 3719 3.828451 CCAGGATGAGAATGGTTTTGTGT 59.172 43.478 0.00 0.00 39.69 3.72
3426 3720 4.321452 CCAGGATGAGAATGGTTTTGTGTG 60.321 45.833 0.00 0.00 39.69 3.82
3427 3721 4.279169 CAGGATGAGAATGGTTTTGTGTGT 59.721 41.667 0.00 0.00 39.69 3.72
3428 3722 5.473162 CAGGATGAGAATGGTTTTGTGTGTA 59.527 40.000 0.00 0.00 39.69 2.90
3429 3723 6.016360 CAGGATGAGAATGGTTTTGTGTGTAA 60.016 38.462 0.00 0.00 39.69 2.41
3430 3724 6.549364 AGGATGAGAATGGTTTTGTGTGTAAA 59.451 34.615 0.00 0.00 0.00 2.01
3431 3725 7.069331 AGGATGAGAATGGTTTTGTGTGTAAAA 59.931 33.333 0.00 0.00 0.00 1.52
3432 3726 7.708752 GGATGAGAATGGTTTTGTGTGTAAAAA 59.291 33.333 0.00 0.00 31.92 1.94
3433 3727 9.260002 GATGAGAATGGTTTTGTGTGTAAAAAT 57.740 29.630 0.00 0.00 31.92 1.82
3434 3728 9.612066 ATGAGAATGGTTTTGTGTGTAAAAATT 57.388 25.926 0.00 0.00 31.92 1.82
3435 3729 9.442047 TGAGAATGGTTTTGTGTGTAAAAATTT 57.558 25.926 0.00 0.00 31.92 1.82
3436 3730 9.914923 GAGAATGGTTTTGTGTGTAAAAATTTC 57.085 29.630 0.00 0.00 31.92 2.17
3437 3731 8.888716 AGAATGGTTTTGTGTGTAAAAATTTCC 58.111 29.630 0.00 0.00 31.92 3.13
3438 3732 6.648725 TGGTTTTGTGTGTAAAAATTTCCG 57.351 33.333 0.00 0.00 31.92 4.30
3439 3733 6.164176 TGGTTTTGTGTGTAAAAATTTCCGT 58.836 32.000 0.00 0.00 31.92 4.69
3440 3734 6.649557 TGGTTTTGTGTGTAAAAATTTCCGTT 59.350 30.769 0.00 0.00 31.92 4.44
3441 3735 6.956520 GGTTTTGTGTGTAAAAATTTCCGTTG 59.043 34.615 0.00 0.00 31.92 4.10
3442 3736 7.360185 GGTTTTGTGTGTAAAAATTTCCGTTGT 60.360 33.333 0.00 0.00 31.92 3.32
3443 3737 6.633668 TTGTGTGTAAAAATTTCCGTTGTG 57.366 33.333 0.00 0.00 0.00 3.33
3444 3738 5.710984 TGTGTGTAAAAATTTCCGTTGTGT 58.289 33.333 0.00 0.00 0.00 3.72
3445 3739 5.800941 TGTGTGTAAAAATTTCCGTTGTGTC 59.199 36.000 0.00 0.00 0.00 3.67
3446 3740 5.800941 GTGTGTAAAAATTTCCGTTGTGTCA 59.199 36.000 0.00 0.00 0.00 3.58
3447 3741 6.474102 GTGTGTAAAAATTTCCGTTGTGTCAT 59.526 34.615 0.00 0.00 0.00 3.06
3448 3742 6.473778 TGTGTAAAAATTTCCGTTGTGTCATG 59.526 34.615 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.665298 GGGTCGATGGTCCTACGTAC 59.335 60.000 0.00 0.00 0.00 3.67
1 2 0.466189 GGGGTCGATGGTCCTACGTA 60.466 60.000 0.00 0.00 0.00 3.57
2 3 1.755783 GGGGTCGATGGTCCTACGT 60.756 63.158 0.00 0.00 0.00 3.57
3 4 1.755395 TGGGGTCGATGGTCCTACG 60.755 63.158 0.00 0.00 0.00 3.51
4 5 0.686769 AGTGGGGTCGATGGTCCTAC 60.687 60.000 0.00 0.00 33.04 3.18
5 6 0.686441 CAGTGGGGTCGATGGTCCTA 60.686 60.000 0.00 0.00 0.00 2.94
6 7 1.990060 CAGTGGGGTCGATGGTCCT 60.990 63.158 0.00 0.00 0.00 3.85
7 8 2.584608 CAGTGGGGTCGATGGTCC 59.415 66.667 0.00 0.00 0.00 4.46
8 9 2.584608 CCAGTGGGGTCGATGGTC 59.415 66.667 0.00 0.00 0.00 4.02
9 10 3.717294 GCCAGTGGGGTCGATGGT 61.717 66.667 12.15 0.00 39.65 3.55
10 11 4.489771 GGCCAGTGGGGTCGATGG 62.490 72.222 12.15 0.00 39.65 3.51
15 16 2.930562 AGAGTGGCCAGTGGGGTC 60.931 66.667 20.47 2.44 43.63 4.46
16 17 2.930562 GAGAGTGGCCAGTGGGGT 60.931 66.667 20.47 0.00 39.65 4.95
17 18 3.721706 GGAGAGTGGCCAGTGGGG 61.722 72.222 20.47 0.00 40.85 4.96
18 19 2.930019 TGGAGAGTGGCCAGTGGG 60.930 66.667 20.47 0.00 37.18 4.61
19 20 2.667418 CTGGAGAGTGGCCAGTGG 59.333 66.667 20.47 4.20 46.19 4.00
23 24 0.545071 TGTCATCTGGAGAGTGGCCA 60.545 55.000 0.00 0.00 0.00 5.36
24 25 0.177604 CTGTCATCTGGAGAGTGGCC 59.822 60.000 0.00 0.00 32.40 5.36
25 26 3.756739 CTGTCATCTGGAGAGTGGC 57.243 57.895 0.00 0.00 32.40 5.01
29 30 4.909696 ATCGTTACTGTCATCTGGAGAG 57.090 45.455 0.00 0.00 42.44 3.20
30 31 5.221067 GCTAATCGTTACTGTCATCTGGAGA 60.221 44.000 0.00 0.00 0.00 3.71
31 32 4.979197 GCTAATCGTTACTGTCATCTGGAG 59.021 45.833 0.00 0.00 0.00 3.86
32 33 4.497507 CGCTAATCGTTACTGTCATCTGGA 60.498 45.833 0.00 0.00 0.00 3.86
33 34 3.731216 CGCTAATCGTTACTGTCATCTGG 59.269 47.826 0.00 0.00 0.00 3.86
34 35 4.598062 TCGCTAATCGTTACTGTCATCTG 58.402 43.478 0.00 0.00 39.67 2.90
35 36 4.895224 TCGCTAATCGTTACTGTCATCT 57.105 40.909 0.00 0.00 39.67 2.90
36 37 5.212934 TCATCGCTAATCGTTACTGTCATC 58.787 41.667 0.00 0.00 39.67 2.92
37 38 5.183014 TCATCGCTAATCGTTACTGTCAT 57.817 39.130 0.00 0.00 39.67 3.06
38 39 4.625972 TCATCGCTAATCGTTACTGTCA 57.374 40.909 0.00 0.00 39.67 3.58
39 40 4.383052 CCATCATCGCTAATCGTTACTGTC 59.617 45.833 0.00 0.00 39.67 3.51
40 41 4.202121 ACCATCATCGCTAATCGTTACTGT 60.202 41.667 0.00 0.00 39.67 3.55
41 42 4.148871 CACCATCATCGCTAATCGTTACTG 59.851 45.833 0.00 0.00 39.67 2.74
42 43 4.037565 TCACCATCATCGCTAATCGTTACT 59.962 41.667 0.00 0.00 39.67 2.24
43 44 4.295870 TCACCATCATCGCTAATCGTTAC 58.704 43.478 0.00 0.00 39.67 2.50
44 45 4.577834 TCACCATCATCGCTAATCGTTA 57.422 40.909 0.00 0.00 39.67 3.18
45 46 3.452755 TCACCATCATCGCTAATCGTT 57.547 42.857 0.00 0.00 39.67 3.85
46 47 3.579709 GATCACCATCATCGCTAATCGT 58.420 45.455 0.00 0.00 39.67 3.73
47 48 2.595977 CGATCACCATCATCGCTAATCG 59.404 50.000 0.00 0.00 36.98 3.34
48 49 3.366121 CACGATCACCATCATCGCTAATC 59.634 47.826 2.07 0.00 45.83 1.75
49 50 3.005791 TCACGATCACCATCATCGCTAAT 59.994 43.478 2.07 0.00 45.83 1.73
50 51 2.360801 TCACGATCACCATCATCGCTAA 59.639 45.455 2.07 0.00 45.83 3.09
51 52 1.953686 TCACGATCACCATCATCGCTA 59.046 47.619 2.07 0.00 45.83 4.26
52 53 0.746659 TCACGATCACCATCATCGCT 59.253 50.000 2.07 0.00 45.83 4.93
53 54 1.135046 CTCACGATCACCATCATCGC 58.865 55.000 2.07 0.00 45.83 4.58
55 56 1.863454 GTGCTCACGATCACCATCATC 59.137 52.381 0.00 0.00 0.00 2.92
56 57 1.483827 AGTGCTCACGATCACCATCAT 59.516 47.619 0.00 0.00 36.20 2.45
57 58 0.897621 AGTGCTCACGATCACCATCA 59.102 50.000 0.00 0.00 36.20 3.07
58 59 2.871182 TAGTGCTCACGATCACCATC 57.129 50.000 0.00 0.00 36.20 3.51
59 60 3.386078 AGATTAGTGCTCACGATCACCAT 59.614 43.478 16.06 0.00 33.90 3.55
60 61 2.760650 AGATTAGTGCTCACGATCACCA 59.239 45.455 16.06 0.00 33.90 4.17
61 62 3.119291 CAGATTAGTGCTCACGATCACC 58.881 50.000 16.06 0.02 33.90 4.02
62 63 4.033990 TCAGATTAGTGCTCACGATCAC 57.966 45.455 16.06 0.00 33.90 3.06
63 64 3.947834 TCTCAGATTAGTGCTCACGATCA 59.052 43.478 16.06 2.88 33.90 2.92
64 65 4.536065 CTCTCAGATTAGTGCTCACGATC 58.464 47.826 0.00 9.73 36.20 3.69
65 66 3.317711 CCTCTCAGATTAGTGCTCACGAT 59.682 47.826 0.00 0.00 36.20 3.73
66 67 2.685388 CCTCTCAGATTAGTGCTCACGA 59.315 50.000 0.00 0.00 36.20 4.35
67 68 2.425312 ACCTCTCAGATTAGTGCTCACG 59.575 50.000 0.00 0.00 36.20 4.35
68 69 4.429108 GAACCTCTCAGATTAGTGCTCAC 58.571 47.826 0.00 0.00 0.00 3.51
69 70 3.449018 GGAACCTCTCAGATTAGTGCTCA 59.551 47.826 0.00 0.00 0.00 4.26
70 71 4.053469 GGAACCTCTCAGATTAGTGCTC 57.947 50.000 0.00 0.00 0.00 4.26
158 160 2.158519 CCCTTTTGTAACCAGTGGAGGT 60.159 50.000 18.40 2.91 45.91 3.85
179 181 2.739292 GTTCGTTTCTTCCTTTTGGGC 58.261 47.619 0.00 0.00 40.87 5.36
220 222 0.941542 TTGCAAAGTAGTCGGTGTGC 59.058 50.000 0.00 0.00 0.00 4.57
228 230 2.172717 ACAGAGGTGGTTGCAAAGTAGT 59.827 45.455 0.00 0.00 0.00 2.73
245 247 8.565896 AAAGCAGAAATACATGTGATTACAGA 57.434 30.769 9.11 0.00 40.79 3.41
417 421 9.480538 TCTACGCATCGAAATAAAACAAATAAC 57.519 29.630 0.00 0.00 0.00 1.89
436 440 6.142798 CGTACAGTTTTACTTTCTTCTACGCA 59.857 38.462 0.00 0.00 0.00 5.24
440 484 5.630680 CGCCGTACAGTTTTACTTTCTTCTA 59.369 40.000 0.00 0.00 0.00 2.10
625 682 1.199327 GCCTGGGCTTTCGTACTTTTC 59.801 52.381 4.12 0.00 38.26 2.29
695 756 0.319405 TTTCTCCTCCGTTCCGTTCC 59.681 55.000 0.00 0.00 0.00 3.62
696 757 1.672145 CCTTTCTCCTCCGTTCCGTTC 60.672 57.143 0.00 0.00 0.00 3.95
831 913 0.391597 TGCTCTCCTCGGTTCGTTTT 59.608 50.000 0.00 0.00 0.00 2.43
862 948 3.716539 TTCGATTCGCCTCGCCTGG 62.717 63.158 0.00 0.00 38.52 4.45
1662 1808 3.020026 CTCAAGCAGCGCAACGAGG 62.020 63.158 11.47 0.00 0.00 4.63
2109 2255 2.825836 GTCCTGAATGGCGCTGGG 60.826 66.667 7.64 0.90 35.26 4.45
2834 2980 5.878406 ATCAGTAAGATGTAGGGTTCAGG 57.122 43.478 0.00 0.00 35.06 3.86
3060 3207 7.494625 ACGTTTAATCTGTCTCAGAAAAGTTGA 59.505 33.333 3.58 0.00 44.04 3.18
3089 3236 0.180406 ACCAGTGACCAAAGAAGCGT 59.820 50.000 0.00 0.00 0.00 5.07
3144 3355 2.093941 CAGACAATTCGAGCAGCTGAAG 59.906 50.000 20.43 7.57 0.00 3.02
3149 3360 3.423571 CAAATCAGACAATTCGAGCAGC 58.576 45.455 0.00 0.00 0.00 5.25
3314 3608 3.070159 GTGATCAGATCTTCCCATCGGAA 59.930 47.826 11.83 0.00 46.38 4.30
3315 3609 2.630098 GTGATCAGATCTTCCCATCGGA 59.370 50.000 11.83 0.00 35.88 4.55
3339 3633 8.723942 AAAGACTGGATTGCTATAGTAACAAG 57.276 34.615 5.32 6.46 0.00 3.16
3340 3634 9.515226 AAAAAGACTGGATTGCTATAGTAACAA 57.485 29.630 5.32 0.00 0.00 2.83
3341 3635 9.162764 GAAAAAGACTGGATTGCTATAGTAACA 57.837 33.333 5.32 0.08 0.00 2.41
3392 3686 7.000472 CCATTCTCATCCTGGTACAATACAAT 59.000 38.462 0.00 0.00 38.70 2.71
3393 3687 6.069673 ACCATTCTCATCCTGGTACAATACAA 60.070 38.462 0.00 0.00 41.43 2.41
3394 3688 5.428457 ACCATTCTCATCCTGGTACAATACA 59.572 40.000 0.00 0.00 41.43 2.29
3395 3689 5.930135 ACCATTCTCATCCTGGTACAATAC 58.070 41.667 0.00 0.00 41.43 1.89
3396 3690 6.575244 AACCATTCTCATCCTGGTACAATA 57.425 37.500 0.00 0.00 42.38 1.90
3397 3691 5.456921 AACCATTCTCATCCTGGTACAAT 57.543 39.130 0.00 0.00 42.38 2.71
3398 3692 4.927267 AACCATTCTCATCCTGGTACAA 57.073 40.909 0.00 0.00 42.38 2.41
3399 3693 4.927267 AAACCATTCTCATCCTGGTACA 57.073 40.909 0.00 0.00 42.38 2.90
3400 3694 5.010282 ACAAAACCATTCTCATCCTGGTAC 58.990 41.667 0.00 0.00 42.38 3.34
3401 3695 5.009631 CACAAAACCATTCTCATCCTGGTA 58.990 41.667 0.00 0.00 42.38 3.25
3402 3696 3.828451 CACAAAACCATTCTCATCCTGGT 59.172 43.478 0.00 0.00 45.08 4.00
3403 3697 3.828451 ACACAAAACCATTCTCATCCTGG 59.172 43.478 0.00 0.00 36.09 4.45
3404 3698 4.279169 ACACACAAAACCATTCTCATCCTG 59.721 41.667 0.00 0.00 0.00 3.86
3405 3699 4.473444 ACACACAAAACCATTCTCATCCT 58.527 39.130 0.00 0.00 0.00 3.24
3406 3700 4.853924 ACACACAAAACCATTCTCATCC 57.146 40.909 0.00 0.00 0.00 3.51
3407 3701 8.641499 TTTTTACACACAAAACCATTCTCATC 57.359 30.769 0.00 0.00 0.00 2.92
3408 3702 9.612066 AATTTTTACACACAAAACCATTCTCAT 57.388 25.926 0.00 0.00 0.00 2.90
3409 3703 9.442047 AAATTTTTACACACAAAACCATTCTCA 57.558 25.926 0.00 0.00 0.00 3.27
3410 3704 9.914923 GAAATTTTTACACACAAAACCATTCTC 57.085 29.630 0.00 0.00 0.00 2.87
3411 3705 8.888716 GGAAATTTTTACACACAAAACCATTCT 58.111 29.630 0.00 0.00 0.00 2.40
3412 3706 7.848539 CGGAAATTTTTACACACAAAACCATTC 59.151 33.333 0.00 0.00 0.00 2.67
3413 3707 7.334671 ACGGAAATTTTTACACACAAAACCATT 59.665 29.630 0.00 0.00 0.00 3.16
3414 3708 6.819146 ACGGAAATTTTTACACACAAAACCAT 59.181 30.769 0.00 0.00 0.00 3.55
3415 3709 6.164176 ACGGAAATTTTTACACACAAAACCA 58.836 32.000 0.00 0.00 0.00 3.67
3416 3710 6.650239 ACGGAAATTTTTACACACAAAACC 57.350 33.333 0.00 0.00 0.00 3.27
3417 3711 7.475874 CACAACGGAAATTTTTACACACAAAAC 59.524 33.333 0.00 0.00 0.00 2.43
3418 3712 7.170998 ACACAACGGAAATTTTTACACACAAAA 59.829 29.630 0.00 0.00 0.00 2.44
3419 3713 6.645415 ACACAACGGAAATTTTTACACACAAA 59.355 30.769 0.00 0.00 0.00 2.83
3420 3714 6.157211 ACACAACGGAAATTTTTACACACAA 58.843 32.000 0.00 0.00 0.00 3.33
3421 3715 5.710984 ACACAACGGAAATTTTTACACACA 58.289 33.333 0.00 0.00 0.00 3.72
3422 3716 5.800941 TGACACAACGGAAATTTTTACACAC 59.199 36.000 0.00 0.00 0.00 3.82
3423 3717 5.950883 TGACACAACGGAAATTTTTACACA 58.049 33.333 0.00 0.00 0.00 3.72
3424 3718 6.862194 CATGACACAACGGAAATTTTTACAC 58.138 36.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.