Multiple sequence alignment - TraesCS1A01G389500

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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 TraesCS1A01G389500 chr1A 100.000 4168 0 0 1 4168 557487984 557492151 0.000000e+00 7697.0
1 TraesCS1A01G389500 chr1D 94.815 2835 99 10 459 3275 465128083 465130887 0.000000e+00 4377.0
2 TraesCS1A01G389500 chr1D 91.981 636 28 10 3464 4080 465131273 465131904 0.000000e+00 870.0
3 TraesCS1A01G389500 chr1D 91.045 268 23 1 120 386 465127795 465128062 1.100000e-95 361.0
4 TraesCS1A01G389500 chr1D 92.063 126 9 1 3279 3404 465131138 465131262 4.280000e-40 176.0
5 TraesCS1A01G389500 chr1D 94.505 91 3 2 4079 4168 465131936 465132025 5.620000e-29 139.0
6 TraesCS1A01G389500 chr7B 91.208 2832 184 26 460 3275 504188172 504190954 0.000000e+00 3790.0
7 TraesCS1A01G389500 chr7B 86.493 807 33 23 3407 4168 504191637 504192412 0.000000e+00 817.0
8 TraesCS1A01G389500 chr7B 87.530 417 41 6 10 422 504187762 504188171 4.880000e-129 472.0
9 TraesCS1A01G389500 chr7B 89.552 134 8 2 3271 3404 504191215 504191342 9.270000e-37 165.0
10 TraesCS1A01G389500 chr7B 93.269 104 5 1 2418 2521 632337770 632337871 7.220000e-33 152.0
11 TraesCS1A01G389500 chr2B 90.980 2827 196 23 457 3275 87924709 87921934 0.000000e+00 3753.0
12 TraesCS1A01G389500 chr2B 88.980 735 35 9 3479 4168 87921126 87920393 0.000000e+00 867.0
13 TraesCS1A01G389500 chr2B 94.488 127 6 1 3274 3400 87921675 87921550 1.180000e-45 195.0
14 TraesCS1A01G389500 chr2B 97.917 48 0 1 3408 3455 87921175 87921129 9.600000e-12 82.4
15 TraesCS1A01G389500 chr2B 83.117 77 10 2 459 532 333863584 333863508 2.690000e-07 67.6
16 TraesCS1A01G389500 chr4B 95.190 1767 57 16 433 2193 112035182 112036926 0.000000e+00 2767.0
17 TraesCS1A01G389500 chr4B 96.044 1087 37 3 2192 3275 112037030 112038113 0.000000e+00 1764.0
18 TraesCS1A01G389500 chr4B 91.367 834 38 11 3274 4080 112038772 112039598 0.000000e+00 1110.0
19 TraesCS1A01G389500 chr4B 91.899 395 26 4 14 404 112034825 112035217 7.880000e-152 547.0
20 TraesCS1A01G389500 chr4B 91.176 102 7 1 2421 2522 27929283 27929184 2.020000e-28 137.0
21 TraesCS1A01G389500 chr4B 93.333 90 5 1 4079 4168 112039626 112039714 9.400000e-27 132.0
22 TraesCS1A01G389500 chr3A 86.998 946 42 21 3274 4168 22206537 22205622 0.000000e+00 990.0
23 TraesCS1A01G389500 chr3A 86.047 946 51 22 3274 4168 22222002 22221087 0.000000e+00 941.0
24 TraesCS1A01G389500 chr3A 88.101 832 44 19 3274 4080 22219473 22218672 0.000000e+00 937.0
25 TraesCS1A01G389500 chr3A 91.935 372 26 3 2905 3275 22220085 22219717 6.180000e-143 518.0
26 TraesCS1A01G389500 chr3A 92.371 367 23 4 2911 3275 22222609 22222246 6.180000e-143 518.0
27 TraesCS1A01G389500 chr3A 90.657 289 19 4 2987 3275 22207061 22206781 1.090000e-100 377.0
28 TraesCS1A01G389500 chr3A 84.564 149 16 5 121 264 723563485 723563339 1.560000e-29 141.0
29 TraesCS1A01G389500 chr5B 94.000 100 4 1 2422 2521 166379183 166379086 2.600000e-32 150.0
30 TraesCS1A01G389500 chr5D 92.233 103 6 1 2419 2521 139440912 139441012 1.210000e-30 145.0
31 TraesCS1A01G389500 chr5A 91.089 101 7 1 2422 2522 580464416 580464514 7.270000e-28 135.0


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 TraesCS1A01G389500 chr1A 557487984 557492151 4167 False 7697.00 7697 100.00000 1 4168 1 chr1A.!!$F1 4167
1 TraesCS1A01G389500 chr1D 465127795 465132025 4230 False 1184.60 4377 92.88180 120 4168 5 chr1D.!!$F1 4048
2 TraesCS1A01G389500 chr7B 504187762 504192412 4650 False 1311.00 3790 88.69575 10 4168 4 chr7B.!!$F2 4158
3 TraesCS1A01G389500 chr2B 87920393 87924709 4316 True 1224.35 3753 93.09125 457 4168 4 chr2B.!!$R2 3711
4 TraesCS1A01G389500 chr4B 112034825 112039714 4889 False 1264.00 2767 93.56660 14 4168 5 chr4B.!!$F1 4154
5 TraesCS1A01G389500 chr3A 22218672 22222609 3937 True 728.50 941 89.61350 2905 4168 4 chr3A.!!$R3 1263
6 TraesCS1A01G389500 chr3A 22205622 22207061 1439 True 683.50 990 88.82750 2987 4168 2 chr3A.!!$R2 1181

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
424 433 0.035534 TGCCATGTCGGTATGTTGCT 60.036 50.000 0.00 0.00 36.97 3.91 F
432 441 0.381801 CGGTATGTTGCTTCCATGCC 59.618 55.000 7.52 7.52 40.47 4.40 F
450 459 0.395311 CCTGAAGATGGGCTGCACAT 60.395 55.000 18.85 18.85 0.00 3.21 F
506 515 0.397941 AGTAGGTCAGCAGCAGCAAA 59.602 50.000 3.17 0.00 45.49 3.68 F
1580 1604 1.164411 GCACGGATGATGGTTCAACA 58.836 50.000 0.00 0.00 34.96 3.33 F
2182 2219 1.442769 AAGCTCATGTTGCTACGGTG 58.557 50.000 14.26 0.00 40.22 4.94 F
2863 3025 1.539372 TGGGTATCCACAACCGGGT 60.539 57.895 6.32 0.00 38.32 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 1757 0.954452 CTGAAAAGCTCGGTTGCCTT 59.046 50.000 0.00 0.0 0.00 4.35 R
2166 2203 1.002366 GAGCACCGTAGCAACATGAG 58.998 55.000 0.00 0.0 36.85 2.90 R
2353 2497 1.388547 TGCTTCTGTCACACCAAACC 58.611 50.000 0.00 0.0 0.00 3.27 R
2471 2617 3.242936 GCAGCGTTGAACTAAGGTTGAAA 60.243 43.478 2.38 0.0 37.50 2.69 R
2863 3025 0.038166 GTCCTGCCATTTGGTCCAGA 59.962 55.000 5.97 0.0 37.57 3.86 R
2997 3159 1.065126 GTAGCATTGTTCTCCTGGCCT 60.065 52.381 3.32 0.0 0.00 5.19 R
4133 5406 1.269958 GCTCCAAATTTCAGGGCCTT 58.730 50.000 1.32 0.0 0.00 4.35 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
37 38 1.460766 GTAGTCGTTTAGCTACGCCG 58.539 55.000 4.11 2.22 41.16 6.46
45 46 0.527600 TTAGCTACGCCGCACTGATG 60.528 55.000 0.00 0.00 0.00 3.07
95 98 7.613411 GGGATATAGCAATTTCTAGAAAGCCAT 59.387 37.037 21.75 16.56 33.32 4.40
98 101 7.992754 ATAGCAATTTCTAGAAAGCCATAGG 57.007 36.000 21.75 8.13 33.32 2.57
119 122 3.255149 GGGCGATACGGGGAGTATATATG 59.745 52.174 0.00 0.00 45.47 1.78
120 123 4.139786 GGCGATACGGGGAGTATATATGA 58.860 47.826 0.00 0.00 45.47 2.15
167 172 7.698836 ATAAAAACAGAATAATTGGATGCGC 57.301 32.000 0.00 0.00 0.00 6.09
242 248 7.275183 AGTCTTTAATGACGGAATGATCATCA 58.725 34.615 9.06 3.33 41.47 3.07
297 303 3.158676 AGAATGAGCCCGTAGAGGATAC 58.841 50.000 0.00 0.00 45.00 2.24
331 337 1.197430 ACCAGCCCCAGTCTCTTCAG 61.197 60.000 0.00 0.00 0.00 3.02
341 347 4.499183 CCAGTCTCTTCAGTATCAACACC 58.501 47.826 0.00 0.00 0.00 4.16
360 369 8.522003 TCAACACCGATACTGTTGTTTATACTA 58.478 33.333 10.27 0.00 45.84 1.82
422 431 2.288729 CAGATGCCATGTCGGTATGTTG 59.711 50.000 0.00 0.00 40.75 3.33
423 432 1.002468 GATGCCATGTCGGTATGTTGC 60.002 52.381 0.00 0.00 40.75 4.17
424 433 0.035534 TGCCATGTCGGTATGTTGCT 60.036 50.000 0.00 0.00 36.97 3.91
425 434 1.094785 GCCATGTCGGTATGTTGCTT 58.905 50.000 0.00 0.00 36.97 3.91
426 435 1.064060 GCCATGTCGGTATGTTGCTTC 59.936 52.381 0.00 0.00 36.97 3.86
427 436 1.670811 CCATGTCGGTATGTTGCTTCC 59.329 52.381 0.00 0.00 0.00 3.46
428 437 2.355197 CATGTCGGTATGTTGCTTCCA 58.645 47.619 0.00 0.00 0.00 3.53
429 438 2.779755 TGTCGGTATGTTGCTTCCAT 57.220 45.000 0.00 0.00 0.00 3.41
430 439 2.355197 TGTCGGTATGTTGCTTCCATG 58.645 47.619 0.00 0.00 0.00 3.66
431 440 1.064060 GTCGGTATGTTGCTTCCATGC 59.936 52.381 0.00 0.00 0.00 4.06
432 441 0.381801 CGGTATGTTGCTTCCATGCC 59.618 55.000 7.52 7.52 40.47 4.40
433 442 1.767759 GGTATGTTGCTTCCATGCCT 58.232 50.000 9.49 0.00 40.64 4.75
434 443 1.406539 GGTATGTTGCTTCCATGCCTG 59.593 52.381 9.49 0.00 40.64 4.85
435 444 2.368439 GTATGTTGCTTCCATGCCTGA 58.632 47.619 0.00 0.00 0.00 3.86
436 445 1.927487 ATGTTGCTTCCATGCCTGAA 58.073 45.000 0.00 0.00 0.00 3.02
437 446 1.250328 TGTTGCTTCCATGCCTGAAG 58.750 50.000 5.99 5.99 41.70 3.02
438 447 1.202915 TGTTGCTTCCATGCCTGAAGA 60.203 47.619 12.69 0.00 41.38 2.87
439 448 2.097825 GTTGCTTCCATGCCTGAAGAT 58.902 47.619 12.69 0.00 41.38 2.40
440 449 1.758936 TGCTTCCATGCCTGAAGATG 58.241 50.000 12.69 0.00 41.38 2.90
441 450 1.030457 GCTTCCATGCCTGAAGATGG 58.970 55.000 12.69 2.17 41.38 3.51
442 451 1.688772 CTTCCATGCCTGAAGATGGG 58.311 55.000 4.66 0.00 41.38 4.00
447 456 2.044650 GCCTGAAGATGGGCTGCA 60.045 61.111 0.50 0.00 44.48 4.41
448 457 2.413142 GCCTGAAGATGGGCTGCAC 61.413 63.158 0.50 0.00 44.48 4.57
449 458 1.001764 CCTGAAGATGGGCTGCACA 60.002 57.895 7.21 7.21 0.00 4.57
450 459 0.395311 CCTGAAGATGGGCTGCACAT 60.395 55.000 18.85 18.85 0.00 3.21
451 460 0.738975 CTGAAGATGGGCTGCACATG 59.261 55.000 24.10 3.13 0.00 3.21
452 461 1.317431 TGAAGATGGGCTGCACATGC 61.317 55.000 24.10 13.56 42.50 4.06
476 485 0.400213 CCACTCCCTAACCAGCACAA 59.600 55.000 0.00 0.00 0.00 3.33
506 515 0.397941 AGTAGGTCAGCAGCAGCAAA 59.602 50.000 3.17 0.00 45.49 3.68
527 536 6.567050 CAAACAGGAGCATTATACAGCAAAT 58.433 36.000 0.00 0.00 0.00 2.32
546 555 5.114780 CAAATCATAGTGGTGACTCTGGAG 58.885 45.833 0.00 0.00 35.43 3.86
557 566 4.704103 TCTGGAGGGCAGCGAGGT 62.704 66.667 0.00 0.00 0.00 3.85
621 630 3.618351 CAGTTGCTCCTGATCCAATCTT 58.382 45.455 0.00 0.00 34.23 2.40
769 789 1.182667 CGTGTCACTCTGGGGATACA 58.817 55.000 0.65 0.00 39.74 2.29
804 824 1.737696 CGGCTGCGTATTGTAACAGGA 60.738 52.381 0.00 0.00 0.00 3.86
838 858 2.943033 GCCGTATTGGTGCTTCATAGTT 59.057 45.455 0.00 0.00 41.21 2.24
1178 1202 2.006169 GAAGAGAGCAGTAGCAAAGGC 58.994 52.381 0.00 0.00 45.49 4.35
1580 1604 1.164411 GCACGGATGATGGTTCAACA 58.836 50.000 0.00 0.00 34.96 3.33
1733 1757 4.522789 GCTACAGGTGGATTTCAAGGAAAA 59.477 41.667 0.00 0.00 35.11 2.29
1820 1845 2.094026 AGCATCGAATGTAGTGACTGCA 60.094 45.455 5.71 5.71 0.00 4.41
2136 2173 6.318396 AGGTTAGTTCACCTCGTAATACTCTC 59.682 42.308 0.00 0.00 44.63 3.20
2137 2174 6.318396 GGTTAGTTCACCTCGTAATACTCTCT 59.682 42.308 0.00 0.00 33.50 3.10
2140 2177 6.413052 AGTTCACCTCGTAATACTCTCTACA 58.587 40.000 0.00 0.00 0.00 2.74
2166 2203 9.971922 ATATGTGCAAATAAATAGAGGAAAAGC 57.028 29.630 0.00 0.00 0.00 3.51
2182 2219 1.442769 AAGCTCATGTTGCTACGGTG 58.557 50.000 14.26 0.00 40.22 4.94
2325 2467 2.310779 TTAGTCTGCTGTCCAGTCCT 57.689 50.000 0.00 0.00 42.38 3.85
2353 2497 7.900782 TGTCCTTTTATTAGTTTCTCCTTCG 57.099 36.000 0.00 0.00 0.00 3.79
2448 2592 4.018779 TCCCTCCGATCCAAAATAAGTGTT 60.019 41.667 0.00 0.00 0.00 3.32
2456 2602 6.420604 CGATCCAAAATAAGTGTTGCAGTTTT 59.579 34.615 0.00 0.00 0.00 2.43
2457 2603 7.042791 CGATCCAAAATAAGTGTTGCAGTTTTT 60.043 33.333 0.00 0.00 0.00 1.94
2510 2668 3.494626 CGCTGCGACACTTATTATGGATT 59.505 43.478 18.66 0.00 0.00 3.01
2742 2904 4.518249 CTCTTTTGGAGGATGGTAAGGTC 58.482 47.826 0.00 0.00 38.35 3.85
2745 2907 1.946984 TGGAGGATGGTAAGGTCGTT 58.053 50.000 0.00 0.00 0.00 3.85
2863 3025 1.539372 TGGGTATCCACAACCGGGT 60.539 57.895 6.32 0.00 38.32 5.28
3070 3232 2.825532 GCCTCAGCCCAAAACTAATTCA 59.174 45.455 0.00 0.00 0.00 2.57
3167 3331 6.480763 TGCTCTGTTGATTCAAACCCTATTA 58.519 36.000 0.00 0.00 0.00 0.98
3311 4158 2.559668 CAAAATGGTGTGATGGAGCTGT 59.440 45.455 0.00 0.00 0.00 4.40
3348 4195 2.105993 TGATGCAGGCAGAATGATAGCT 59.894 45.455 0.00 0.00 39.69 3.32
3407 4261 9.642312 CAGTCGAACAAATATTTCATCATACAG 57.358 33.333 0.00 0.00 0.00 2.74
3458 4674 4.774779 ACCTGGGGATGTATGTACCATAT 58.225 43.478 0.00 0.00 0.00 1.78
3459 4675 4.536090 ACCTGGGGATGTATGTACCATATG 59.464 45.833 0.00 0.00 0.00 1.78
3472 4688 2.251818 ACCATATGCTCCGTCTGCTAT 58.748 47.619 0.00 0.00 0.00 2.97
3473 4689 2.634940 ACCATATGCTCCGTCTGCTATT 59.365 45.455 0.00 0.00 0.00 1.73
3476 4692 4.083643 CCATATGCTCCGTCTGCTATTTTG 60.084 45.833 0.00 0.00 0.00 2.44
3493 4709 7.095857 TGCTATTTTGAAGTTAAATTTGCACCG 60.096 33.333 0.00 0.00 33.06 4.94
3555 4771 8.856490 AGTTCAACATCAAAGTTTCACATAAC 57.144 30.769 0.00 0.00 0.00 1.89
3613 4829 1.212935 AGGAGGGAAAATGATGGTCCG 59.787 52.381 0.00 0.00 31.73 4.79
3636 4852 3.126000 GCTATCTTTGACAGGTTCAGTGC 59.874 47.826 0.00 0.00 34.94 4.40
3738 4954 1.003118 ACAGGCTCTCGTTTAATGGCA 59.997 47.619 0.00 0.00 0.00 4.92
3823 5039 2.228103 CTGTTTCAGCATCACAGCACAT 59.772 45.455 0.00 0.00 36.85 3.21
3846 5062 2.564062 CAACCAGCATTCAGGTTCCATT 59.436 45.455 0.00 0.00 45.93 3.16
3847 5063 3.737559 ACCAGCATTCAGGTTCCATTA 57.262 42.857 0.00 0.00 33.39 1.90
3848 5064 3.356290 ACCAGCATTCAGGTTCCATTAC 58.644 45.455 0.00 0.00 33.39 1.89
3872 5108 7.007723 ACAATGGGAAATAAGGTTTCAGTGTA 58.992 34.615 0.00 0.00 0.00 2.90
3963 5199 4.205587 TCTTAACCTCTCGGATGTAGGTC 58.794 47.826 7.14 0.00 42.86 3.85
4080 5316 5.514204 GCATTAGTGTTGCTGTGAATGAATC 59.486 40.000 0.00 0.00 37.14 2.52
4102 5374 4.514816 TCAGAAATGTGTCGCATCAGAAAA 59.485 37.500 0.00 0.00 36.67 2.29
4133 5406 0.755698 GATGAGACGTGGGCTAGGGA 60.756 60.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.806868 CCATGTCACCACATCAGTGC 59.193 55.000 0.00 0.00 41.69 4.40
45 46 3.270877 GTCCTTGTATCCATGTCACCAC 58.729 50.000 0.00 0.00 0.00 4.16
95 98 0.700564 ATACTCCCCGTATCGCCCTA 59.299 55.000 0.00 0.00 33.55 3.53
97 100 1.772836 ATATACTCCCCGTATCGCCC 58.227 55.000 0.00 0.00 39.48 6.13
98 101 4.139786 TCATATATACTCCCCGTATCGCC 58.860 47.826 0.00 0.00 39.48 5.54
167 172 3.134458 GGGGCAGTATTTTGATCTCTCG 58.866 50.000 0.00 0.00 0.00 4.04
224 230 6.548622 AGGAAATTGATGATCATTCCGTCATT 59.451 34.615 17.55 2.27 39.39 2.57
230 236 8.179509 AGATTGAGGAAATTGATGATCATTCC 57.820 34.615 16.42 16.42 36.34 3.01
242 248 8.655935 AAAGTACCATGAAGATTGAGGAAATT 57.344 30.769 0.00 0.00 0.00 1.82
297 303 3.629398 GGGCTGGTATTGTCAATCAGAAG 59.371 47.826 15.18 6.00 0.00 2.85
341 347 7.259882 TGGTGGTAGTATAAACAACAGTATCG 58.740 38.462 0.00 0.00 0.00 2.92
360 369 1.145738 AGCCAATCTTCAGTTGGTGGT 59.854 47.619 6.74 0.00 46.21 4.16
422 431 1.030457 CCATCTTCAGGCATGGAAGC 58.970 55.000 0.00 0.00 42.11 3.86
423 432 1.688772 CCCATCTTCAGGCATGGAAG 58.311 55.000 0.00 1.58 42.11 3.46
424 433 3.909587 CCCATCTTCAGGCATGGAA 57.090 52.632 0.00 0.00 42.11 3.53
431 440 0.395311 ATGTGCAGCCCATCTTCAGG 60.395 55.000 0.00 0.00 0.00 3.86
432 441 0.738975 CATGTGCAGCCCATCTTCAG 59.261 55.000 0.00 0.00 0.00 3.02
433 442 1.317431 GCATGTGCAGCCCATCTTCA 61.317 55.000 0.00 0.00 41.59 3.02
434 443 1.436336 GCATGTGCAGCCCATCTTC 59.564 57.895 0.00 0.00 41.59 2.87
435 444 2.056223 GGCATGTGCAGCCCATCTT 61.056 57.895 4.10 0.00 46.50 2.40
436 445 2.441532 GGCATGTGCAGCCCATCT 60.442 61.111 4.10 0.00 46.50 2.90
443 452 4.409218 GTGGCGTGGCATGTGCAG 62.409 66.667 8.75 0.00 44.36 4.41
444 453 4.953010 AGTGGCGTGGCATGTGCA 62.953 61.111 8.75 0.00 44.36 4.57
445 454 4.107051 GAGTGGCGTGGCATGTGC 62.107 66.667 8.75 4.69 41.14 4.57
446 455 3.434319 GGAGTGGCGTGGCATGTG 61.434 66.667 8.75 0.00 0.00 3.21
447 456 4.722700 GGGAGTGGCGTGGCATGT 62.723 66.667 8.75 0.00 0.00 3.21
448 457 2.535485 TTAGGGAGTGGCGTGGCATG 62.535 60.000 1.31 1.31 0.00 4.06
449 458 2.297895 TTAGGGAGTGGCGTGGCAT 61.298 57.895 0.00 0.00 0.00 4.40
450 459 2.925706 TTAGGGAGTGGCGTGGCA 60.926 61.111 0.00 0.00 0.00 4.92
451 460 2.436115 GTTAGGGAGTGGCGTGGC 60.436 66.667 0.00 0.00 0.00 5.01
452 461 2.267961 GGTTAGGGAGTGGCGTGG 59.732 66.667 0.00 0.00 0.00 4.94
453 462 1.079127 CTGGTTAGGGAGTGGCGTG 60.079 63.158 0.00 0.00 0.00 5.34
454 463 2.955881 GCTGGTTAGGGAGTGGCGT 61.956 63.158 0.00 0.00 0.00 5.68
455 464 2.125106 GCTGGTTAGGGAGTGGCG 60.125 66.667 0.00 0.00 0.00 5.69
476 485 2.613977 GCTGACCTACTGATGTTGCTGT 60.614 50.000 0.00 0.00 0.00 4.40
506 515 5.439721 TGATTTGCTGTATAATGCTCCTGT 58.560 37.500 0.00 0.00 0.00 4.00
527 536 2.624293 CCCTCCAGAGTCACCACTATGA 60.624 54.545 0.00 0.00 43.51 2.15
546 555 2.514824 GGATTCACCTCGCTGCCC 60.515 66.667 0.00 0.00 35.41 5.36
557 566 4.812476 CGTCGCCGCCTGGATTCA 62.812 66.667 0.00 0.00 37.49 2.57
609 618 2.573369 CAGGGCAGAAGATTGGATCAG 58.427 52.381 0.00 0.00 0.00 2.90
621 630 0.322816 GCTCAATTGACCAGGGCAGA 60.323 55.000 3.38 0.00 0.00 4.26
775 795 2.358193 ATACGCAGCCGATACGCCAA 62.358 55.000 0.00 0.00 38.29 4.52
1178 1202 3.064987 ATCGGGAGGTTGCGAGACG 62.065 63.158 0.00 0.00 0.00 4.18
1580 1604 3.499338 TGCAACATCCTCATTTTCACCT 58.501 40.909 0.00 0.00 0.00 4.00
1733 1757 0.954452 CTGAAAAGCTCGGTTGCCTT 59.046 50.000 0.00 0.00 0.00 4.35
1820 1845 3.118112 CCTGAGTCTGGCCTTGATATTGT 60.118 47.826 3.32 0.00 0.00 2.71
2140 2177 9.971922 GCTTTTCCTCTATTTATTTGCACATAT 57.028 29.630 0.00 0.00 0.00 1.78
2166 2203 1.002366 GAGCACCGTAGCAACATGAG 58.998 55.000 0.00 0.00 36.85 2.90
2182 2219 9.798885 GAGTCATTTTACGACATATATTTGAGC 57.201 33.333 0.00 0.00 35.77 4.26
2313 2455 2.237392 AGGACATTTAGGACTGGACAGC 59.763 50.000 0.00 0.00 0.00 4.40
2353 2497 1.388547 TGCTTCTGTCACACCAAACC 58.611 50.000 0.00 0.00 0.00 3.27
2471 2617 3.242936 GCAGCGTTGAACTAAGGTTGAAA 60.243 43.478 2.38 0.00 37.50 2.69
2510 2668 1.007118 TGCTCACAGATACTCCCTCCA 59.993 52.381 0.00 0.00 0.00 3.86
2622 2780 6.017934 CGAACAAAAGGTATAGCTGTGCATAT 60.018 38.462 4.96 0.00 0.00 1.78
2624 2782 4.094887 CGAACAAAAGGTATAGCTGTGCAT 59.905 41.667 4.96 0.66 0.00 3.96
2863 3025 0.038166 GTCCTGCCATTTGGTCCAGA 59.962 55.000 5.97 0.00 37.57 3.86
2994 3156 1.915141 CATTGTTCTCCTGGCCTGTT 58.085 50.000 3.32 0.00 0.00 3.16
2997 3159 1.065126 GTAGCATTGTTCTCCTGGCCT 60.065 52.381 3.32 0.00 0.00 5.19
3084 3246 2.553602 CAGCAAGCACACTATGAAACCA 59.446 45.455 0.00 0.00 0.00 3.67
3386 4233 9.125026 ACCTCCTGTATGATGAAATATTTGTTC 57.875 33.333 5.17 2.99 0.00 3.18
3394 4241 7.446625 GCATTTCTACCTCCTGTATGATGAAAT 59.553 37.037 0.00 0.00 33.93 2.17
3458 4674 2.760634 TCAAAATAGCAGACGGAGCA 57.239 45.000 0.00 0.00 0.00 4.26
3459 4675 3.003480 ACTTCAAAATAGCAGACGGAGC 58.997 45.455 0.00 0.00 0.00 4.70
3472 4688 5.869888 ACACGGTGCAAATTTAACTTCAAAA 59.130 32.000 8.30 0.00 0.00 2.44
3473 4689 5.411781 ACACGGTGCAAATTTAACTTCAAA 58.588 33.333 8.30 0.00 0.00 2.69
3476 4692 7.452630 TTTAACACGGTGCAAATTTAACTTC 57.547 32.000 8.30 0.00 0.00 3.01
3555 4771 2.286872 GCACAGGAGATGACATCTTGG 58.713 52.381 18.89 13.27 40.38 3.61
3613 4829 3.686726 CACTGAACCTGTCAAAGATAGCC 59.313 47.826 0.00 0.00 35.22 3.93
3738 4954 1.838077 AGTTAAACCTAGCAGGCGGAT 59.162 47.619 2.50 0.00 39.63 4.18
3846 5062 7.007723 ACACTGAAACCTTATTTCCCATTGTA 58.992 34.615 0.00 0.00 0.00 2.41
3847 5063 5.838521 ACACTGAAACCTTATTTCCCATTGT 59.161 36.000 0.00 0.00 0.00 2.71
3848 5064 6.345096 ACACTGAAACCTTATTTCCCATTG 57.655 37.500 0.00 0.00 0.00 2.82
3872 5108 2.838202 ACTTGTCGTCCTACCATTGGAT 59.162 45.455 10.37 0.00 35.87 3.41
3924 5160 6.168389 GGTTAAGAACCGTTCCTTATTCTCA 58.832 40.000 7.68 0.00 42.62 3.27
4080 5316 4.408993 TTTCTGATGCGACACATTTCTG 57.591 40.909 0.00 0.00 39.84 3.02
4102 5374 1.736126 CGTCTCATCTGCAGCACAAAT 59.264 47.619 9.47 0.00 0.00 2.32
4133 5406 1.269958 GCTCCAAATTTCAGGGCCTT 58.730 50.000 1.32 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.