Multiple sequence alignment - TraesCS2A01G104100

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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 TraesCS2A01G104100 chr2A 100.000 4305 0 0 1 4305 57546247 57550551 0.000000e+00 7950.0
1 TraesCS2A01G104100 chr2A 89.080 174 12 4 1 173 775685945 775685778 4.360000e-50 209.0
2 TraesCS2A01G104100 chr2A 87.283 173 13 2 1 173 775736703 775736866 5.680000e-44 189.0
3 TraesCS2A01G104100 chr2A 94.444 54 1 2 355 407 775685784 775685732 9.920000e-12 82.4
4 TraesCS2A01G104100 chr2A 94.444 54 1 2 355 407 775736860 775736912 9.920000e-12 82.4
5 TraesCS2A01G104100 chr2B 94.249 3617 141 32 1 3573 88838235 88841828 0.000000e+00 5465.0
6 TraesCS2A01G104100 chr2B 88.089 403 44 4 3575 3975 88842689 88843089 3.900000e-130 475.0
7 TraesCS2A01G104100 chr2D 95.600 2932 104 15 660 3579 56104466 56107384 0.000000e+00 4676.0
8 TraesCS2A01G104100 chr2D 94.225 658 15 6 1 641 56103822 56104473 0.000000e+00 983.0
9 TraesCS2A01G104100 chr2D 85.300 517 64 8 3707 4220 56108130 56108637 1.370000e-144 523.0
10 TraesCS2A01G104100 chr2D 88.194 144 16 1 3572 3714 56107689 56107832 2.060000e-38 171.0
11 TraesCS2A01G104100 chr2D 89.474 57 5 1 3981 4036 403177389 403177333 2.150000e-08 71.3
12 TraesCS2A01G104100 chr4B 75.825 1303 265 34 1008 2288 375139456 375138182 2.200000e-172 616.0
13 TraesCS2A01G104100 chr4D 75.902 1220 255 25 1087 2288 301301373 301300175 4.800000e-164 588.0
14 TraesCS2A01G104100 chr4D 97.222 36 1 0 3699 3734 324249196 324249161 1.290000e-05 62.1
15 TraesCS2A01G104100 chr4A 75.296 1267 272 26 1041 2288 180396031 180397275 6.250000e-158 568.0
16 TraesCS2A01G104100 chr4A 95.122 41 2 0 3989 4029 668284150 668284190 9.990000e-07 65.8
17 TraesCS2A01G104100 chr4A 88.636 44 5 0 3981 4024 544775556 544775599 2.000000e-03 54.7
18 TraesCS2A01G104100 chr5B 91.379 174 8 3 1 173 21726291 21726124 9.310000e-57 231.0
19 TraesCS2A01G104100 chr5B 90.230 174 10 3 1 173 508017169 508017336 2.020000e-53 220.0
20 TraesCS2A01G104100 chr5B 77.005 187 37 4 3044 3227 243361518 243361701 7.620000e-18 102.0
21 TraesCS2A01G104100 chr5B 94.444 54 1 2 355 407 508017330 508017382 9.920000e-12 82.4
22 TraesCS2A01G104100 chr5B 92.593 54 1 3 355 407 21726130 21726079 1.660000e-09 75.0
23 TraesCS2A01G104100 chr5B 87.755 49 6 0 3981 4029 652961269 652961221 1.670000e-04 58.4
24 TraesCS2A01G104100 chr7A 90.805 174 9 3 1 173 709847507 709847674 4.330000e-55 226.0
25 TraesCS2A01G104100 chr7A 94.444 54 1 2 355 407 709847668 709847720 9.920000e-12 82.4
26 TraesCS2A01G104100 chr5A 90.805 174 9 3 1 173 633001487 633001654 4.330000e-55 226.0
27 TraesCS2A01G104100 chr5A 92.593 54 2 2 355 407 633001648 633001700 4.620000e-10 76.8
28 TraesCS2A01G104100 chr3B 77.551 343 68 5 2905 3241 587568015 587568354 9.440000e-47 198.0
29 TraesCS2A01G104100 chr3B 95.349 43 2 0 3985 4027 638957289 638957247 7.720000e-08 69.4
30 TraesCS2A01G104100 chr3B 97.297 37 1 0 3698 3734 106643556 106643520 3.590000e-06 63.9
31 TraesCS2A01G104100 chr5D 77.540 187 36 4 3044 3227 220462830 220463013 1.640000e-19 108.0
32 TraesCS2A01G104100 chr1D 94.118 51 3 0 3974 4024 393399293 393399343 1.280000e-10 78.7
33 TraesCS2A01G104100 chr3D 85.135 74 11 0 3041 3114 506715245 506715318 4.620000e-10 76.8
34 TraesCS2A01G104100 chr3A 85.135 74 11 0 3041 3114 644940124 644940197 4.620000e-10 76.8
35 TraesCS2A01G104100 chr3A 97.500 40 1 0 3985 4024 711201890 711201929 7.720000e-08 69.4
36 TraesCS2A01G104100 chr1B 88.889 54 6 0 3974 4027 529541149 529541096 2.780000e-07 67.6


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 TraesCS2A01G104100 chr2A 57546247 57550551 4304 False 7950.00 7950 100.00000 1 4305 1 chr2A.!!$F1 4304
1 TraesCS2A01G104100 chr2B 88838235 88843089 4854 False 2970.00 5465 91.16900 1 3975 2 chr2B.!!$F1 3974
2 TraesCS2A01G104100 chr2D 56103822 56108637 4815 False 1588.25 4676 90.82975 1 4220 4 chr2D.!!$F1 4219
3 TraesCS2A01G104100 chr4B 375138182 375139456 1274 True 616.00 616 75.82500 1008 2288 1 chr4B.!!$R1 1280
4 TraesCS2A01G104100 chr4D 301300175 301301373 1198 True 588.00 588 75.90200 1087 2288 1 chr4D.!!$R1 1201
5 TraesCS2A01G104100 chr4A 180396031 180397275 1244 False 568.00 568 75.29600 1041 2288 1 chr4A.!!$F1 1247

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
422 440 1.200020 CCTCGGACTTGTTTTCATGCC 59.800 52.381 0.0 0.0 0.0 4.40 F
724 743 2.422832 GCTGGAAAAGAGAGCTGATTGG 59.577 50.000 0.0 0.0 0.0 3.16 F
2205 2250 0.245539 CAAACCTAGTCCCGCTTCGA 59.754 55.000 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2160 0.036388 TCCCTGCCACGACATCTTTC 60.036 55.0 0.00 0.0 0.00 2.62 R
2425 2487 2.175878 ATCAGGCTTCGCATGGATAC 57.824 50.0 0.49 0.0 40.91 2.24 R
3949 5186 0.030908 CGTCCTCTCTCGCATAACCC 59.969 60.0 0.00 0.0 0.00 4.11 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
110 111 2.422832 CCTCAGTTCCTGTCGGTACTAC 59.577 54.545 0.00 0.00 38.70 2.73
111 112 3.345414 CTCAGTTCCTGTCGGTACTACT 58.655 50.000 0.00 0.00 38.70 2.57
112 113 4.511527 CTCAGTTCCTGTCGGTACTACTA 58.488 47.826 0.00 0.00 38.70 1.82
113 114 4.256920 TCAGTTCCTGTCGGTACTACTAC 58.743 47.826 0.00 0.00 38.70 2.73
114 115 4.005650 CAGTTCCTGTCGGTACTACTACA 58.994 47.826 0.00 0.00 38.70 2.74
115 116 4.456911 CAGTTCCTGTCGGTACTACTACAA 59.543 45.833 0.00 0.00 38.70 2.41
131 132 5.285798 ACTACAATTGCATTGCATTTTGC 57.714 34.783 23.88 9.22 43.98 3.68
137 138 1.338294 TGCATTGCATTTTGCCAGAGG 60.338 47.619 7.38 0.00 44.23 3.69
309 324 3.786048 CGTATCATGCCGCTTTTCTTTTC 59.214 43.478 0.00 0.00 0.00 2.29
360 378 5.371526 TGCAATTTTTAGGCCATGTTTTCA 58.628 33.333 5.01 0.00 0.00 2.69
406 424 1.279271 AGGTGGAATTTCTGTCCCTCG 59.721 52.381 0.00 0.00 33.89 4.63
422 440 1.200020 CCTCGGACTTGTTTTCATGCC 59.800 52.381 0.00 0.00 0.00 4.40
447 465 5.163992 CGACTGCGTGTGTATTCTTACATTT 60.164 40.000 0.00 0.00 40.35 2.32
714 733 3.249559 GTGAGTCACTTGCTGGAAAAGAG 59.750 47.826 16.26 0.00 0.00 2.85
724 743 2.422832 GCTGGAAAAGAGAGCTGATTGG 59.577 50.000 0.00 0.00 0.00 3.16
886 906 6.034044 CAGCTAGACTTTAAAGCTTAGTGTCG 59.966 42.308 15.24 0.00 43.97 4.35
937 964 7.222611 CACTTTTGTTTGATCAGGTTTGGTTAG 59.777 37.037 0.00 0.00 0.00 2.34
1320 1347 2.771763 AAGTTCTGAGCCTGCGGTCG 62.772 60.000 0.00 0.00 39.47 4.79
1468 1495 5.066968 GGAGCTCTCCTATAATTCCTTCG 57.933 47.826 14.64 0.00 46.16 3.79
1503 1530 6.470278 TCCTACAAGCTTAGAAAACCTTACC 58.530 40.000 0.00 0.00 0.00 2.85
1509 1536 5.070685 AGCTTAGAAAACCTTACCCAGTTG 58.929 41.667 0.00 0.00 0.00 3.16
1549 1576 3.196685 AGAAAATTCTCTCTCTGGACCCG 59.803 47.826 0.00 0.00 29.94 5.28
1650 1677 4.513442 TCCAAACATTCCCAGATAGTTCG 58.487 43.478 0.00 0.00 0.00 3.95
1701 1728 3.686726 CGCCCCTAGATAATTGCTCATTC 59.313 47.826 0.00 0.00 0.00 2.67
1704 1731 4.568592 CCCCTAGATAATTGCTCATTCCCC 60.569 50.000 0.00 0.00 0.00 4.81
1792 1828 5.059833 GGAAACTGAGCATAGGGTTCATAG 58.940 45.833 0.00 0.00 36.07 2.23
1846 1882 3.724508 TGCTAATTGTGGTTGTGTTGG 57.275 42.857 0.00 0.00 0.00 3.77
2115 2160 3.270027 TGTTGTGGTTGTCAAGAGACTG 58.730 45.455 0.00 0.00 45.20 3.51
2205 2250 0.245539 CAAACCTAGTCCCGCTTCGA 59.754 55.000 0.00 0.00 0.00 3.71
2371 2416 2.649816 AGAGAACATAACAAAGGGGCCT 59.350 45.455 0.84 0.00 0.00 5.19
2372 2417 3.076032 AGAGAACATAACAAAGGGGCCTT 59.924 43.478 0.84 0.00 37.98 4.35
2391 2448 4.543692 CCTTCATTGCTCAAGTGTCAAAG 58.456 43.478 0.00 0.00 0.00 2.77
2406 2468 9.233232 CAAGTGTCAAAGTAATTGTTACCTTTC 57.767 33.333 0.00 0.00 40.11 2.62
2407 2469 7.636326 AGTGTCAAAGTAATTGTTACCTTTCG 58.364 34.615 0.00 0.00 40.11 3.46
2435 2497 2.679837 AGAACTTGCTTGTATCCATGCG 59.320 45.455 0.00 0.00 42.91 4.73
2437 2499 2.710377 ACTTGCTTGTATCCATGCGAA 58.290 42.857 0.00 0.00 42.91 4.70
2510 2579 8.189119 ACCTTTATTTTGCAATAGGTCTGAAA 57.811 30.769 0.00 0.00 0.00 2.69
2521 2590 7.882791 TGCAATAGGTCTGAAAATAAGACTTGA 59.117 33.333 0.00 0.00 43.03 3.02
2522 2591 8.394121 GCAATAGGTCTGAAAATAAGACTTGAG 58.606 37.037 0.00 0.00 43.03 3.02
2523 2592 9.442047 CAATAGGTCTGAAAATAAGACTTGAGT 57.558 33.333 0.00 0.00 43.03 3.41
2567 2636 4.387862 CCTGAAGCTGCATTGATTGTTTTC 59.612 41.667 0.00 0.00 0.00 2.29
2713 2782 2.674796 AGACGCCATTAGACTGGAAC 57.325 50.000 0.00 0.00 38.69 3.62
3283 3352 1.507174 CGACGAGAGGTTCAGGGAC 59.493 63.158 0.00 0.00 0.00 4.46
3358 3428 6.016192 AGCAGATCATTGGATTCATTTAGCTG 60.016 38.462 0.00 0.00 32.67 4.24
3412 3482 2.264794 GACATCGGGTGCGACCTT 59.735 61.111 5.48 0.00 38.64 3.50
3434 3504 4.789012 ACTGGATCGAACAATTTGCATT 57.211 36.364 0.00 0.00 0.00 3.56
3454 3524 5.675575 GCATTGAGACTGTAATCTTGGCAAG 60.676 44.000 21.17 21.17 0.00 4.01
3485 3555 3.910568 TTCATTGGGGGATTGAATTGC 57.089 42.857 0.00 0.00 0.00 3.56
3487 3557 4.262891 TCATTGGGGGATTGAATTGCTA 57.737 40.909 0.00 0.00 0.00 3.49
3489 3559 5.963092 TCATTGGGGGATTGAATTGCTATA 58.037 37.500 0.00 0.00 0.00 1.31
3514 3584 3.248266 GTTTCATTGCTGTGCTGAATCC 58.752 45.455 0.00 0.00 0.00 3.01
3517 3587 2.089201 CATTGCTGTGCTGAATCCTCA 58.911 47.619 0.00 0.00 0.00 3.86
3520 3590 1.022735 GCTGTGCTGAATCCTCATGG 58.977 55.000 0.00 0.00 0.00 3.66
3523 3593 1.911357 TGTGCTGAATCCTCATGGAGT 59.089 47.619 0.00 0.00 46.91 3.85
3539 3609 0.890542 GAGTCATGGTGGCAAGTGCA 60.891 55.000 5.52 0.00 44.36 4.57
3576 4505 3.531538 CCTTTCAGGCTAGCAAACGATA 58.468 45.455 18.24 1.47 0.00 2.92
3587 4516 2.452813 AAACGATACAGCAGCCGCG 61.453 57.895 0.00 0.00 45.49 6.46
3611 4542 3.599285 TAGAAGGCGCCGTTGTGGG 62.599 63.158 23.20 0.00 38.63 4.61
3645 4576 1.690633 GGGAGATGGGGTGCTCAGA 60.691 63.158 0.00 0.00 32.83 3.27
3646 4577 1.694133 GGGAGATGGGGTGCTCAGAG 61.694 65.000 0.00 0.00 32.83 3.35
3670 4601 6.070194 AGCAAGGTACATAGTTCAGGTTACAT 60.070 38.462 0.00 0.00 0.00 2.29
3682 4613 6.149474 AGTTCAGGTTACATGTAAGATTGTGC 59.851 38.462 18.56 12.60 0.00 4.57
3783 5019 0.674581 CTCCTTCGAAGGTGCATGCA 60.675 55.000 36.74 18.46 46.54 3.96
3806 5042 1.527370 GGAGGCGCCAAATAGACCT 59.473 57.895 31.54 3.33 36.34 3.85
3809 5045 0.328258 AGGCGCCAAATAGACCTTGT 59.672 50.000 31.54 0.00 0.00 3.16
3818 5054 4.631813 CCAAATAGACCTTGTCGAAAGAGG 59.368 45.833 8.09 8.09 43.49 3.69
3823 5059 2.498078 GACCTTGTCGAAAGAGGGATCT 59.502 50.000 12.87 0.00 43.49 2.75
3930 5167 4.314440 GAGTGGTGAGCCGGCACA 62.314 66.667 31.54 27.37 40.52 4.57
3949 5186 4.319766 GCACAATGCAAGGATCTTATACCG 60.320 45.833 0.00 0.00 44.26 4.02
3977 5214 4.803426 GAGAGGACGCAGCCCACG 62.803 72.222 0.00 0.00 0.00 4.94
4006 5243 1.418342 CGTATGCGGACGGTTTGAGG 61.418 60.000 0.00 0.00 39.19 3.86
4007 5244 1.087771 GTATGCGGACGGTTTGAGGG 61.088 60.000 0.00 0.00 0.00 4.30
4012 5249 2.739132 GACGGTTTGAGGGTCGGT 59.261 61.111 0.00 0.00 0.00 4.69
4024 5261 1.003839 GGTCGGTGTTGGAGATGCA 60.004 57.895 0.00 0.00 0.00 3.96
4029 5266 1.732259 CGGTGTTGGAGATGCACTAAC 59.268 52.381 0.00 0.00 33.96 2.34
4030 5267 2.084546 GGTGTTGGAGATGCACTAACC 58.915 52.381 0.00 0.00 33.96 2.85
4034 5271 1.656587 TGGAGATGCACTAACCACCT 58.343 50.000 0.00 0.00 0.00 4.00
4035 5272 1.278985 TGGAGATGCACTAACCACCTG 59.721 52.381 0.00 0.00 0.00 4.00
4049 5286 3.636231 CCTGGGTCACCTCGCCAA 61.636 66.667 0.00 0.00 37.76 4.52
4054 5291 1.026718 GGGTCACCTCGCCAATTCTG 61.027 60.000 0.00 0.00 0.00 3.02
4057 5294 2.359900 GTCACCTCGCCAATTCTGATT 58.640 47.619 0.00 0.00 0.00 2.57
4066 5303 3.561725 CGCCAATTCTGATTACTTCTCCC 59.438 47.826 0.00 0.00 0.00 4.30
4152 5390 8.477419 TTCAGGAACCTTTTCAAAATCTGTAT 57.523 30.769 0.00 0.00 32.80 2.29
4203 5441 9.801873 TTTTGGATTTCAGAACTACTTTTGAAG 57.198 29.630 0.00 0.00 31.85 3.02
4204 5442 8.746052 TTGGATTTCAGAACTACTTTTGAAGA 57.254 30.769 0.00 0.00 31.85 2.87
4205 5443 8.924511 TGGATTTCAGAACTACTTTTGAAGAT 57.075 30.769 0.00 0.00 31.85 2.40
4206 5444 8.786898 TGGATTTCAGAACTACTTTTGAAGATG 58.213 33.333 0.00 0.00 31.85 2.90
4207 5445 9.003658 GGATTTCAGAACTACTTTTGAAGATGA 57.996 33.333 0.00 0.00 31.85 2.92
4210 5448 9.559732 TTTCAGAACTACTTTTGAAGATGATGA 57.440 29.630 0.00 0.00 31.85 2.92
4211 5449 9.559732 TTCAGAACTACTTTTGAAGATGATGAA 57.440 29.630 0.00 0.00 0.00 2.57
4212 5450 9.212641 TCAGAACTACTTTTGAAGATGATGAAG 57.787 33.333 0.00 0.00 0.00 3.02
4213 5451 8.997323 CAGAACTACTTTTGAAGATGATGAAGT 58.003 33.333 0.00 0.00 0.00 3.01
4214 5452 9.566432 AGAACTACTTTTGAAGATGATGAAGTT 57.434 29.630 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.254284 ACAGAACTCCGAGCCTCTGG 61.254 60.000 22.84 11.45 39.71 3.86
137 138 1.739562 CAGGCACAGAACTCCGAGC 60.740 63.158 0.00 0.00 0.00 5.03
293 308 2.893489 AGAAGGAAAAGAAAAGCGGCAT 59.107 40.909 1.45 0.00 0.00 4.40
309 324 4.879197 AAGCAATTCAAGGGAAAGAAGG 57.121 40.909 0.00 0.00 36.43 3.46
360 378 4.082949 GCGCCCTTTAAAGTGTAAAGACAT 60.083 41.667 13.55 0.00 38.04 3.06
406 424 1.068541 GTCGGGCATGAAAACAAGTCC 60.069 52.381 0.00 0.00 0.00 3.85
422 440 1.710013 AAGAATACACACGCAGTCGG 58.290 50.000 0.00 0.00 41.61 4.79
447 465 2.039879 GGAGGCCTGGTTTTCTAGTGAA 59.960 50.000 12.00 0.00 0.00 3.18
666 685 2.882137 CAGGAACGCACCCTTTTTAAGA 59.118 45.455 0.00 0.00 0.00 2.10
714 733 1.093159 CAAGTCAGCCCAATCAGCTC 58.907 55.000 0.00 0.00 38.95 4.09
724 743 2.543777 TGACTGTAACCAAGTCAGCC 57.456 50.000 2.24 0.00 37.61 4.85
886 906 5.186198 ACATTTAGTGAGAACCAGCATACC 58.814 41.667 0.00 0.00 0.00 2.73
937 964 5.977129 CCTTCATTTGTTTACACCAGACAAC 59.023 40.000 0.00 0.00 33.42 3.32
1503 1530 7.824289 TCTTGTAAATTCAGGAGATACAACTGG 59.176 37.037 0.00 0.00 34.02 4.00
1549 1576 3.340814 TGGAAGCTTCAGATCAGGAAC 57.659 47.619 27.02 6.91 0.00 3.62
1683 1710 5.006386 GTGGGGAATGAGCAATTATCTAGG 58.994 45.833 0.00 0.00 0.00 3.02
1701 1728 2.115266 GAGGGTGTTGGTGTGGGG 59.885 66.667 0.00 0.00 0.00 4.96
1704 1731 2.115266 GGGGAGGGTGTTGGTGTG 59.885 66.667 0.00 0.00 0.00 3.82
1846 1882 1.338020 CCTCTTTGAAAGGCACACACC 59.662 52.381 4.94 0.00 0.00 4.16
2115 2160 0.036388 TCCCTGCCACGACATCTTTC 60.036 55.000 0.00 0.00 0.00 2.62
2205 2250 7.069986 TCTCATCCTTGGAATAGTAGTAAGCT 58.930 38.462 0.00 0.00 0.00 3.74
2322 2367 3.490526 GCCATTGCACAGTTAACAACTTG 59.509 43.478 8.61 0.00 37.21 3.16
2371 2416 6.691754 TTACTTTGACACTTGAGCAATGAA 57.308 33.333 0.00 0.00 0.00 2.57
2372 2417 6.882610 ATTACTTTGACACTTGAGCAATGA 57.117 33.333 0.00 0.00 0.00 2.57
2391 2448 8.524870 TCTGTACTTCGAAAGGTAACAATTAC 57.475 34.615 0.00 0.00 41.41 1.89
2406 2468 5.062308 GGATACAAGCAAGTTCTGTACTTCG 59.938 44.000 0.00 0.00 45.29 3.79
2407 2469 6.410243 GGATACAAGCAAGTTCTGTACTTC 57.590 41.667 0.00 0.00 45.29 3.01
2425 2487 2.175878 ATCAGGCTTCGCATGGATAC 57.824 50.000 0.49 0.00 40.91 2.24
2435 2497 5.207110 TCAGATGCTAACTATCAGGCTTC 57.793 43.478 0.00 0.00 0.00 3.86
2437 2499 5.620738 TTTCAGATGCTAACTATCAGGCT 57.379 39.130 0.00 0.00 0.00 4.58
2482 2551 6.747280 CAGACCTATTGCAAAATAAAGGTTCG 59.253 38.462 16.82 10.44 0.00 3.95
2510 2579 9.890629 TGTGCAGAAATATACTCAAGTCTTATT 57.109 29.630 0.00 0.00 0.00 1.40
2515 2584 8.125448 GGAAATGTGCAGAAATATACTCAAGTC 58.875 37.037 0.00 0.00 0.00 3.01
2521 2590 5.300286 GGCAGGAAATGTGCAGAAATATACT 59.700 40.000 0.00 0.00 43.12 2.12
2522 2591 5.300286 AGGCAGGAAATGTGCAGAAATATAC 59.700 40.000 0.00 0.00 43.12 1.47
2523 2592 5.300034 CAGGCAGGAAATGTGCAGAAATATA 59.700 40.000 0.00 0.00 43.12 0.86
2713 2782 4.039730 CCTAGTATGATCTTCACCCTGGTG 59.960 50.000 10.13 10.13 46.64 4.17
3013 3082 4.373116 TCGTTCCCCTGCGACTGC 62.373 66.667 0.00 0.00 43.20 4.40
3215 3284 2.653702 GAGCCCCTCGATCATCCG 59.346 66.667 0.00 0.00 0.00 4.18
3335 3405 7.506328 TCAGCTAAATGAATCCAATGATCTG 57.494 36.000 0.00 0.00 0.00 2.90
3358 3428 7.396419 GCATGCATGAACTCAAATTACAAATC 58.604 34.615 30.64 1.71 0.00 2.17
3389 3459 2.821366 GCACCCGATGTCAGCCAG 60.821 66.667 0.00 0.00 0.00 4.85
3401 3471 0.179081 GATCCAGTAAGGTCGCACCC 60.179 60.000 2.18 0.00 39.75 4.61
3412 3482 5.414144 TCAATGCAAATTGTTCGATCCAGTA 59.586 36.000 0.00 0.00 33.49 2.74
3434 3504 4.202357 ACACTTGCCAAGATTACAGTCTCA 60.202 41.667 12.25 0.00 0.00 3.27
3454 3524 4.855340 TCCCCCAATGAAAATCTCTACAC 58.145 43.478 0.00 0.00 0.00 2.90
3485 3555 7.252708 TCAGCACAGCAATGAAACAAATATAG 58.747 34.615 0.00 0.00 0.00 1.31
3487 3557 6.028146 TCAGCACAGCAATGAAACAAATAT 57.972 33.333 0.00 0.00 0.00 1.28
3489 3559 4.325028 TCAGCACAGCAATGAAACAAAT 57.675 36.364 0.00 0.00 0.00 2.32
3517 3587 0.700564 ACTTGCCACCATGACTCCAT 59.299 50.000 0.00 0.00 0.00 3.41
3520 3590 0.890542 TGCACTTGCCACCATGACTC 60.891 55.000 0.00 0.00 41.18 3.36
3521 3591 0.892358 CTGCACTTGCCACCATGACT 60.892 55.000 0.00 0.00 41.18 3.41
3523 3593 2.270257 GCTGCACTTGCCACCATGA 61.270 57.895 0.00 0.00 41.18 3.07
3524 3594 2.260434 GCTGCACTTGCCACCATG 59.740 61.111 0.00 0.00 41.18 3.66
3565 3635 1.651987 GGCTGCTGTATCGTTTGCTA 58.348 50.000 0.00 0.00 0.00 3.49
3576 4505 2.543687 CTAGTGTACGCGGCTGCTGT 62.544 60.000 17.03 16.97 39.65 4.40
3587 4516 0.108945 AACGGCGCCTTCTAGTGTAC 60.109 55.000 26.68 0.00 0.00 2.90
3611 4542 0.681733 TCCCTCTGCTCACTTCACAC 59.318 55.000 0.00 0.00 0.00 3.82
3614 4545 1.829849 CATCTCCCTCTGCTCACTTCA 59.170 52.381 0.00 0.00 0.00 3.02
3645 4576 4.910458 AACCTGAACTATGTACCTTGCT 57.090 40.909 0.00 0.00 0.00 3.91
3646 4577 5.484715 TGTAACCTGAACTATGTACCTTGC 58.515 41.667 0.00 0.00 0.00 4.01
3670 4601 1.066430 GGGACTCCGCACAATCTTACA 60.066 52.381 0.00 0.00 0.00 2.41
3716 4952 1.880340 CTCATCAAGGACGAGGCGC 60.880 63.158 0.00 0.00 0.00 6.53
3790 5026 0.328258 ACAAGGTCTATTTGGCGCCT 59.672 50.000 29.70 10.43 0.00 5.52
3806 5042 1.404181 CGCAGATCCCTCTTTCGACAA 60.404 52.381 0.00 0.00 30.53 3.18
3809 5045 0.895530 AACGCAGATCCCTCTTTCGA 59.104 50.000 0.00 0.00 32.34 3.71
3823 5059 2.855514 GCAAAGGGCTTGGAACGCA 61.856 57.895 0.00 0.00 40.25 5.24
3854 5090 1.478510 CTACAGCCATCCAAGACTCGT 59.521 52.381 0.00 0.00 0.00 4.18
3855 5091 1.804372 GCTACAGCCATCCAAGACTCG 60.804 57.143 0.00 0.00 34.31 4.18
3881 5117 2.513897 CCGCCCCATTCTTCGACC 60.514 66.667 0.00 0.00 0.00 4.79
3925 5162 4.022849 GGTATAAGATCCTTGCATTGTGCC 60.023 45.833 0.00 0.00 44.23 5.01
3930 5167 3.394606 ACCCGGTATAAGATCCTTGCATT 59.605 43.478 0.00 0.00 0.00 3.56
3943 5180 3.079578 CTCTCTCGCATAACCCGGTATA 58.920 50.000 0.00 0.00 0.00 1.47
3946 5183 1.392710 CCTCTCTCGCATAACCCGGT 61.393 60.000 0.00 0.00 0.00 5.28
3949 5186 0.030908 CGTCCTCTCTCGCATAACCC 59.969 60.000 0.00 0.00 0.00 4.11
3977 5214 1.878522 CCGCATACGTCCAGACTGC 60.879 63.158 0.00 0.00 37.70 4.40
3979 5216 1.807886 GTCCGCATACGTCCAGACT 59.192 57.895 0.00 0.00 37.70 3.24
3983 5220 2.157305 AAACCGTCCGCATACGTCCA 62.157 55.000 0.00 0.00 41.27 4.02
4006 5243 1.003839 TGCATCTCCAACACCGACC 60.004 57.895 0.00 0.00 0.00 4.79
4007 5244 0.320771 AGTGCATCTCCAACACCGAC 60.321 55.000 0.00 0.00 34.83 4.79
4012 5249 2.552155 GGTGGTTAGTGCATCTCCAACA 60.552 50.000 11.45 0.00 36.10 3.33
4029 5266 4.394712 GCGAGGTGACCCAGGTGG 62.395 72.222 0.00 0.00 41.37 4.61
4030 5267 4.394712 GGCGAGGTGACCCAGGTG 62.395 72.222 0.00 0.00 0.00 4.00
4034 5271 1.002624 GAATTGGCGAGGTGACCCA 60.003 57.895 0.00 0.00 0.00 4.51
4035 5272 1.026718 CAGAATTGGCGAGGTGACCC 61.027 60.000 0.00 0.00 0.00 4.46
4045 5282 4.786425 AGGGAGAAGTAATCAGAATTGGC 58.214 43.478 0.00 0.00 0.00 4.52
4124 5362 8.267183 ACAGATTTTGAAAAGGTTCCTGAAATT 58.733 29.630 0.00 0.00 32.28 1.82
4131 5369 9.764363 AAAAGATACAGATTTTGAAAAGGTTCC 57.236 29.630 0.00 0.00 32.28 3.62
4187 5425 8.997323 ACTTCATCATCTTCAAAAGTAGTTCTG 58.003 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.