Multiple sequence alignment - TraesCS3D01G131200

Loading Multiple Alignment...

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 TraesCS3D01G131200 chr3D 100.000 3968 0 0 1 3968 91227048 91223081 0.000000e+00 7328.0
1 TraesCS3D01G131200 chr3A 89.469 3124 166 51 447 3492 107405632 107402594 0.000000e+00 3795.0
2 TraesCS3D01G131200 chr3A 97.751 489 10 1 3480 3968 107402572 107402085 0.000000e+00 841.0
3 TraesCS3D01G131200 chr3A 90.708 226 9 5 127 351 107407371 107407157 1.390000e-74 291.0
4 TraesCS3D01G131200 chr3B 89.097 2614 138 56 637 3199 140858126 140855609 0.000000e+00 3112.0
5 TraesCS3D01G131200 chr3B 95.732 492 17 3 3480 3968 140855068 140854578 0.000000e+00 789.0
6 TraesCS3D01G131200 chr3B 88.556 568 31 18 1 555 140858725 140858179 0.000000e+00 658.0
7 TraesCS3D01G131200 chr1D 92.553 94 5 2 1261 1353 112462198 112462290 2.490000e-27 134.0
8 TraesCS3D01G131200 chr1A 91.000 100 6 3 1256 1353 119704058 119704156 8.950000e-27 132.0
9 TraesCS3D01G131200 chr1B 91.489 94 6 2 1261 1353 172001786 172001878 1.160000e-25 128.0
10 TraesCS3D01G131200 chr5D 84.536 97 10 5 1259 1353 283356049 283355956 1.520000e-14 91.6
11 TraesCS3D01G131200 chr5B 86.842 76 8 2 1279 1353 321559473 321559399 2.540000e-12 84.2
12 TraesCS3D01G131200 chr5A 86.842 76 8 2 1279 1353 375573077 375573003 2.540000e-12 84.2


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 TraesCS3D01G131200 chr3D 91223081 91227048 3967 True 7328.000000 7328 100.000000 1 3968 1 chr3D.!!$R1 3967
1 TraesCS3D01G131200 chr3A 107402085 107407371 5286 True 1642.333333 3795 92.642667 127 3968 3 chr3A.!!$R1 3841
2 TraesCS3D01G131200 chr3B 140854578 140858725 4147 True 1519.666667 3112 91.128333 1 3968 3 chr3B.!!$R1 3967

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
452 1900 0.472471 ACCCTGAGCTTTTCAACGGA 59.528 50.000 0.00 0.0 34.81 4.69 F
459 1907 1.070758 AGCTTTTCAACGGAGAGAGCA 59.929 47.619 14.43 0.0 33.56 4.26 F
1964 3472 0.035458 GTCCTCTAATCATGGCCCGG 59.965 60.000 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 3145 0.321671 CAGAGGCTTCAGTTTCCGGA 59.678 55.0 0.00 0.00 0.00 5.14 R
1982 3490 0.386838 GATTATTCGGGGTCGACGGT 59.613 55.0 9.92 0.00 45.92 4.83 R
3377 5184 1.186917 TCCATTTGGTTGGCTGCCAG 61.187 55.0 22.17 8.16 37.31 4.85 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
59 60 0.535335 ACACCAGTAGCCATGTACGG 59.465 55.000 0.00 0.00 0.00 4.02
199 200 1.057851 TCCCCACGAACCTCCTTTGT 61.058 55.000 0.00 0.00 0.00 2.83
224 225 0.679505 TCCCGATCATGATCCGGTTC 59.320 55.000 30.29 11.23 37.44 3.62
237 238 2.113774 GGTTCCCGTCCCCGTTTT 59.886 61.111 0.00 0.00 0.00 2.43
296 300 3.764237 TCTTATTCTTATCCCACGGCC 57.236 47.619 0.00 0.00 0.00 6.13
336 340 0.866906 CCGTCGGCGTCGCTAAAATA 60.867 55.000 20.44 0.00 36.15 1.40
351 355 6.070481 TCGCTAAAATACCCATATGCATCCTA 60.070 38.462 0.19 0.00 0.00 2.94
352 356 6.767902 CGCTAAAATACCCATATGCATCCTAT 59.232 38.462 0.19 0.00 0.00 2.57
353 357 7.283127 CGCTAAAATACCCATATGCATCCTATT 59.717 37.037 0.19 0.00 0.00 1.73
355 359 7.722949 AAAATACCCATATGCATCCTATTGG 57.277 36.000 0.19 4.08 0.00 3.16
356 360 3.091633 ACCCATATGCATCCTATTGGC 57.908 47.619 0.19 0.00 0.00 4.52
357 361 2.379567 ACCCATATGCATCCTATTGGCA 59.620 45.455 0.19 0.00 42.43 4.92
362 366 2.955342 TGCATCCTATTGGCATAGCA 57.045 45.000 0.00 0.00 32.17 3.49
379 422 0.664761 GCAGCAGCAACAACAGAGAA 59.335 50.000 0.00 0.00 41.58 2.87
397 440 3.265791 AGAAGATGGCACGAGTTTCATC 58.734 45.455 0.00 0.00 37.02 2.92
398 441 2.768253 AGATGGCACGAGTTTCATCA 57.232 45.000 13.94 0.00 38.64 3.07
419 1867 5.457140 TCATCAGAAAATAAAACCACGCAC 58.543 37.500 0.00 0.00 0.00 5.34
425 1873 3.915437 AATAAAACCACGCACCAGAAG 57.085 42.857 0.00 0.00 0.00 2.85
426 1874 1.600023 TAAAACCACGCACCAGAAGG 58.400 50.000 0.00 0.00 42.21 3.46
430 1878 2.738521 CACGCACCAGAAGGACCG 60.739 66.667 0.00 0.00 38.69 4.79
436 1884 0.605589 CACCAGAAGGACCGAAACCC 60.606 60.000 0.00 0.00 38.69 4.11
447 1895 1.133915 ACCGAAACCCTGAGCTTTTCA 60.134 47.619 8.21 0.00 30.91 2.69
449 1897 2.287608 CCGAAACCCTGAGCTTTTCAAC 60.288 50.000 8.21 0.00 34.81 3.18
450 1898 2.602217 CGAAACCCTGAGCTTTTCAACG 60.602 50.000 8.21 0.00 34.81 4.10
452 1900 0.472471 ACCCTGAGCTTTTCAACGGA 59.528 50.000 0.00 0.00 34.81 4.69
453 1901 1.160137 CCCTGAGCTTTTCAACGGAG 58.840 55.000 0.00 0.00 34.81 4.63
454 1902 1.270839 CCCTGAGCTTTTCAACGGAGA 60.271 52.381 0.00 0.00 34.81 3.71
455 1903 2.072298 CCTGAGCTTTTCAACGGAGAG 58.928 52.381 0.00 0.00 34.81 3.20
456 1904 2.289072 CCTGAGCTTTTCAACGGAGAGA 60.289 50.000 0.00 0.00 34.81 3.10
457 1905 2.992543 CTGAGCTTTTCAACGGAGAGAG 59.007 50.000 0.00 0.00 34.81 3.20
458 1906 1.729517 GAGCTTTTCAACGGAGAGAGC 59.270 52.381 0.00 7.99 0.00 4.09
459 1907 1.070758 AGCTTTTCAACGGAGAGAGCA 59.929 47.619 14.43 0.00 33.56 4.26
593 2057 1.537135 GCATGCTCCTTCTCGGTCTAC 60.537 57.143 11.37 0.00 0.00 2.59
607 2071 1.399440 GGTCTACTACATGTCGTCGCA 59.601 52.381 6.25 0.00 0.00 5.10
631 2095 1.195674 GTTGACGGCTGCTCTTTCTTC 59.804 52.381 0.00 0.00 0.00 2.87
689 2160 7.149307 CACATACCAAACCGTCCTTTATTTTT 58.851 34.615 0.00 0.00 0.00 1.94
690 2161 7.327518 CACATACCAAACCGTCCTTTATTTTTC 59.672 37.037 0.00 0.00 0.00 2.29
691 2162 4.862350 ACCAAACCGTCCTTTATTTTTCG 58.138 39.130 0.00 0.00 0.00 3.46
692 2163 4.579753 ACCAAACCGTCCTTTATTTTTCGA 59.420 37.500 0.00 0.00 0.00 3.71
719 2190 1.518056 CGGATGGATTGGGATTGGCG 61.518 60.000 0.00 0.00 0.00 5.69
763 2234 3.702048 ACGTACCGCCCACTGCAT 61.702 61.111 0.00 0.00 41.33 3.96
920 2395 3.028850 CAAGTGTACTTATCTCGGGGGA 58.971 50.000 0.00 0.00 34.28 4.81
921 2396 2.664015 AGTGTACTTATCTCGGGGGAC 58.336 52.381 0.00 0.00 0.00 4.46
922 2397 4.196345 AAGTGTACTTATCTCGGGGGACC 61.196 52.174 0.00 0.00 40.97 4.46
923 2398 6.423801 AAGTGTACTTATCTCGGGGGACCT 62.424 50.000 0.00 0.00 41.32 3.85
1139 2614 1.142748 CTCTCAGAATTCGCGGCCT 59.857 57.895 6.13 0.00 0.00 5.19
1357 2835 1.341852 TCTACAACAAGCAGGTACGCA 59.658 47.619 0.00 0.00 0.00 5.24
1358 2836 1.459592 CTACAACAAGCAGGTACGCAC 59.540 52.381 0.00 0.00 0.00 5.34
1359 2837 1.204062 CAACAAGCAGGTACGCACG 59.796 57.895 0.00 0.00 0.00 5.34
1397 2883 4.148825 CCCTGTTCCTCGCCGGAG 62.149 72.222 5.05 0.00 44.28 4.63
1398 2884 3.382832 CCTGTTCCTCGCCGGAGT 61.383 66.667 5.05 0.00 44.28 3.85
1399 2885 2.657237 CTGTTCCTCGCCGGAGTT 59.343 61.111 5.05 0.00 44.28 3.01
1400 2886 1.446272 CTGTTCCTCGCCGGAGTTC 60.446 63.158 5.05 0.00 44.28 3.01
1401 2887 2.506438 GTTCCTCGCCGGAGTTCG 60.506 66.667 5.05 0.00 44.28 3.95
1402 2888 4.430765 TTCCTCGCCGGAGTTCGC 62.431 66.667 5.05 0.00 44.28 4.70
1609 3109 3.402186 TCAGCCACCTGAACAACAG 57.598 52.632 0.00 0.00 44.79 3.16
1613 3113 2.166254 CAGCCACCTGAACAACAGTTTT 59.834 45.455 0.00 0.00 44.40 2.43
1637 3141 6.377327 TTCGTCTGCTTTTCTCTGAATTTT 57.623 33.333 0.00 0.00 0.00 1.82
1641 3145 6.073331 CGTCTGCTTTTCTCTGAATTTTCTCT 60.073 38.462 0.00 0.00 0.00 3.10
1742 3246 1.380785 CCAACATGAGCCTGGGCAT 60.381 57.895 14.39 0.00 44.88 4.40
1797 3301 1.079057 GGAGCCCTTCTTCACCGTC 60.079 63.158 0.00 0.00 0.00 4.79
1924 3428 0.599558 CAACTGGTTCGTCCCGTCTA 59.400 55.000 0.00 0.00 32.51 2.59
1925 3429 1.000060 CAACTGGTTCGTCCCGTCTAA 60.000 52.381 0.00 0.00 32.51 2.10
1928 3436 2.086869 CTGGTTCGTCCCGTCTAACTA 58.913 52.381 0.00 0.00 34.77 2.24
1964 3472 0.035458 GTCCTCTAATCATGGCCCGG 59.965 60.000 0.00 0.00 0.00 5.73
1982 3490 5.318630 GCCCGGTGATTATATTCCCTTTTA 58.681 41.667 0.00 0.00 0.00 1.52
2034 3542 1.298859 ATCCCGTTGCTTTCTCACGC 61.299 55.000 0.00 0.00 0.00 5.34
2035 3543 2.556287 CCGTTGCTTTCTCACGCC 59.444 61.111 0.00 0.00 0.00 5.68
2185 3694 5.544176 TCTCCTTCTTCAGTTCACCAGTAAT 59.456 40.000 0.00 0.00 0.00 1.89
2188 3697 7.159372 TCCTTCTTCAGTTCACCAGTAATAAC 58.841 38.462 0.00 0.00 0.00 1.89
2189 3698 6.934645 CCTTCTTCAGTTCACCAGTAATAACA 59.065 38.462 0.00 0.00 0.00 2.41
2190 3699 7.444183 CCTTCTTCAGTTCACCAGTAATAACAA 59.556 37.037 0.00 0.00 0.00 2.83
2191 3700 8.918202 TTCTTCAGTTCACCAGTAATAACAAT 57.082 30.769 0.00 0.00 0.00 2.71
2192 3701 8.918202 TCTTCAGTTCACCAGTAATAACAATT 57.082 30.769 0.00 0.00 0.00 2.32
2196 3710 7.023575 CAGTTCACCAGTAATAACAATTCAGC 58.976 38.462 0.00 0.00 0.00 4.26
2223 3737 7.605449 TCTCATGATTCTTTCCAAATTCCAAC 58.395 34.615 0.00 0.00 0.00 3.77
2233 3747 4.081406 TCCAAATTCCAACCACTGATGAG 58.919 43.478 0.00 0.00 0.00 2.90
2244 3758 3.254166 ACCACTGATGAGTTTGTTCATGC 59.746 43.478 0.00 0.00 37.90 4.06
2250 3764 2.663808 TGAGTTTGTTCATGCAATGCG 58.336 42.857 0.00 0.00 46.21 4.73
2251 3765 2.034432 TGAGTTTGTTCATGCAATGCGT 59.966 40.909 0.00 0.00 46.21 5.24
2299 3813 2.223803 ACCTCTTCTCGGTGATCACT 57.776 50.000 24.50 0.00 32.41 3.41
2314 3828 0.394192 TCACTGTGCTGTCCTTCCTG 59.606 55.000 2.12 0.00 0.00 3.86
2317 3831 0.954449 CTGTGCTGTCCTTCCTGCTG 60.954 60.000 0.00 0.00 0.00 4.41
2326 3840 1.676967 CTTCCTGCTGTCCTTGCCC 60.677 63.158 0.00 0.00 0.00 5.36
2347 3861 3.618351 CCTGATGATCTTTGCAGAAGGT 58.382 45.455 8.23 2.40 30.76 3.50
2362 3876 1.831652 AAGGTGTCAGCTTCTCCCCG 61.832 60.000 11.52 0.00 28.30 5.73
2416 3930 2.318908 AGCCTGCAAAATCCAGACAAA 58.681 42.857 0.00 0.00 32.03 2.83
2441 3955 6.822667 TGAACTGTTGCATCATCATAACTT 57.177 33.333 0.00 0.00 0.00 2.66
2444 3958 7.175467 TGAACTGTTGCATCATCATAACTTCTT 59.825 33.333 0.00 0.00 0.00 2.52
2445 3959 7.458409 ACTGTTGCATCATCATAACTTCTTT 57.542 32.000 0.00 0.00 0.00 2.52
2447 3961 8.362639 ACTGTTGCATCATCATAACTTCTTTTT 58.637 29.630 0.00 0.00 0.00 1.94
2534 4048 4.687215 GAGCTGTGCGTGAGGGCA 62.687 66.667 0.00 0.00 41.45 5.36
2583 4097 1.668294 CAGAAGGTGAGAGCCACGT 59.332 57.895 0.00 0.00 46.62 4.49
2584 4098 0.668706 CAGAAGGTGAGAGCCACGTG 60.669 60.000 9.08 9.08 46.62 4.49
2588 4102 1.069090 GGTGAGAGCCACGTGACAA 59.931 57.895 19.30 0.00 46.62 3.18
2650 4172 6.536224 CAGAATGCATGATCTGTAACACTGTA 59.464 38.462 16.97 0.00 38.57 2.74
2704 4226 1.067416 TCGTACATGATCCTGGCGC 59.933 57.895 0.00 0.00 0.00 6.53
2827 4349 5.344743 TGCACTGGGTAAAAACAAATTGA 57.655 34.783 0.00 0.00 0.00 2.57
2854 4384 2.771089 TGCAACCTCTTTCTACTGCAG 58.229 47.619 13.48 13.48 35.02 4.41
2961 4504 3.701040 TCAAGAAAGCAAAGCCAAAGAGT 59.299 39.130 0.00 0.00 0.00 3.24
3377 5184 6.715347 AGATACCATAGGCAACCAAAATTC 57.285 37.500 0.00 0.00 37.17 2.17
3397 5204 0.544833 TGGCAGCCAACCAAATGGAT 60.545 50.000 13.33 0.00 43.54 3.41
3411 5218 4.218852 CCAAATGGATGCCAAAATTTTGCT 59.781 37.500 22.90 11.06 36.95 3.91
3537 5394 2.025037 ACATGCCCCTTATGCTTTGAGA 60.025 45.455 0.00 0.00 0.00 3.27
3543 5400 4.485163 CCCCTTATGCTTTGAGAAAAACG 58.515 43.478 0.00 0.00 0.00 3.60
3593 5452 3.054875 TGCAGGATAGTTCAGCAGTTCAT 60.055 43.478 0.00 0.00 32.68 2.57
3762 5621 4.470304 AGGTTCCAGGTTTCATAGAGTACC 59.530 45.833 0.00 0.00 0.00 3.34
3826 5685 4.236935 CCACCACATCAACATAGCAAAAC 58.763 43.478 0.00 0.00 0.00 2.43
3898 5758 9.899661 TGCTTAAACCAACATTACTGATACTAT 57.100 29.630 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 2.401583 TCAACTGACCGATTGGATGG 57.598 50.000 5.81 0.00 39.21 3.51
199 200 3.402110 CGGATCATGATCGGGAAATGAA 58.598 45.455 27.29 0.00 38.69 2.57
336 340 2.379567 TGCCAATAGGATGCATATGGGT 59.620 45.455 0.00 0.00 36.89 4.51
351 355 0.458669 GTTGCTGCTGCTATGCCAAT 59.541 50.000 17.00 0.00 40.48 3.16
352 356 0.894642 TGTTGCTGCTGCTATGCCAA 60.895 50.000 17.00 0.00 40.48 4.52
353 357 0.894642 TTGTTGCTGCTGCTATGCCA 60.895 50.000 17.00 1.21 40.48 4.92
355 359 0.241749 TGTTGTTGCTGCTGCTATGC 59.758 50.000 17.00 3.60 40.48 3.14
356 360 1.808343 TCTGTTGTTGCTGCTGCTATG 59.192 47.619 17.00 0.98 40.48 2.23
357 361 2.082231 CTCTGTTGTTGCTGCTGCTAT 58.918 47.619 17.00 0.00 40.48 2.97
358 362 1.070601 TCTCTGTTGTTGCTGCTGCTA 59.929 47.619 17.00 6.36 40.48 3.49
359 363 0.179037 TCTCTGTTGTTGCTGCTGCT 60.179 50.000 17.00 0.00 40.48 4.24
360 364 0.664761 TTCTCTGTTGTTGCTGCTGC 59.335 50.000 8.89 8.89 40.20 5.25
362 366 2.627515 TCTTCTCTGTTGTTGCTGCT 57.372 45.000 0.00 0.00 0.00 4.24
379 422 2.768253 TGATGAAACTCGTGCCATCT 57.232 45.000 12.82 0.00 37.06 2.90
397 440 4.621034 GGTGCGTGGTTTTATTTTCTGATG 59.379 41.667 0.00 0.00 0.00 3.07
398 441 4.279671 TGGTGCGTGGTTTTATTTTCTGAT 59.720 37.500 0.00 0.00 0.00 2.90
419 1867 0.321653 CAGGGTTTCGGTCCTTCTGG 60.322 60.000 0.00 0.00 0.00 3.86
425 1873 0.250770 AAAGCTCAGGGTTTCGGTCC 60.251 55.000 0.00 0.00 38.58 4.46
426 1874 1.535896 GAAAAGCTCAGGGTTTCGGTC 59.464 52.381 0.00 0.00 41.52 4.79
430 1878 2.287608 CCGTTGAAAAGCTCAGGGTTTC 60.288 50.000 1.60 1.60 41.52 2.78
436 1884 2.992543 CTCTCTCCGTTGAAAAGCTCAG 59.007 50.000 0.00 0.00 34.81 3.35
447 1895 0.798776 CGCATTTTGCTCTCTCCGTT 59.201 50.000 0.00 0.00 42.25 4.44
449 1897 0.740868 TCCGCATTTTGCTCTCTCCG 60.741 55.000 0.00 0.00 42.25 4.63
450 1898 1.012841 CTCCGCATTTTGCTCTCTCC 58.987 55.000 0.00 0.00 42.25 3.71
452 1900 0.393537 CCCTCCGCATTTTGCTCTCT 60.394 55.000 0.00 0.00 42.25 3.10
453 1901 1.379642 CCCCTCCGCATTTTGCTCTC 61.380 60.000 0.00 0.00 42.25 3.20
454 1902 1.379044 CCCCTCCGCATTTTGCTCT 60.379 57.895 0.00 0.00 42.25 4.09
455 1903 2.418083 CCCCCTCCGCATTTTGCTC 61.418 63.158 0.00 0.00 42.25 4.26
456 1904 2.362889 CCCCCTCCGCATTTTGCT 60.363 61.111 0.00 0.00 42.25 3.91
457 1905 2.679996 ACCCCCTCCGCATTTTGC 60.680 61.111 0.00 0.00 40.69 3.68
458 1906 1.000896 AGACCCCCTCCGCATTTTG 60.001 57.895 0.00 0.00 0.00 2.44
459 1907 1.303282 GAGACCCCCTCCGCATTTT 59.697 57.895 0.00 0.00 35.87 1.82
505 1953 0.933097 CAGGAATTGCCGATCTGACG 59.067 55.000 0.00 0.00 43.43 4.35
572 2036 1.219124 GACCGAGAAGGAGCATGCA 59.781 57.895 21.98 0.00 45.00 3.96
576 2040 2.026542 TGTAGTAGACCGAGAAGGAGCA 60.027 50.000 0.00 0.00 45.00 4.26
593 2057 0.109272 ACTGGTGCGACGACATGTAG 60.109 55.000 0.00 0.00 0.00 2.74
631 2095 4.582240 ACAGCAGGGAAAGAAAGAAAGAAG 59.418 41.667 0.00 0.00 0.00 2.85
689 2160 0.758734 ATCCATCCGCCTCAAATCGA 59.241 50.000 0.00 0.00 0.00 3.59
690 2161 1.265095 CAATCCATCCGCCTCAAATCG 59.735 52.381 0.00 0.00 0.00 3.34
691 2162 1.610522 CCAATCCATCCGCCTCAAATC 59.389 52.381 0.00 0.00 0.00 2.17
692 2163 1.696063 CCAATCCATCCGCCTCAAAT 58.304 50.000 0.00 0.00 0.00 2.32
719 2190 7.642669 CAGTGGAATGGAATATGTAATGTGTC 58.357 38.462 0.00 0.00 0.00 3.67
763 2234 7.414814 AAACGTTTGCAGAAAAGAAAGAAAA 57.585 28.000 13.81 0.00 0.00 2.29
796 2267 7.941238 GTCATACTCCTATTACCAGTACTACCA 59.059 40.741 0.00 0.00 0.00 3.25
806 2280 3.838903 CCCCTGGTCATACTCCTATTACC 59.161 52.174 0.00 0.00 29.98 2.85
808 2282 4.141990 CCCCCTGGTCATACTCCTATTA 57.858 50.000 0.00 0.00 0.00 0.98
809 2283 2.991580 CCCCCTGGTCATACTCCTATT 58.008 52.381 0.00 0.00 0.00 1.73
810 2284 2.723530 CCCCCTGGTCATACTCCTAT 57.276 55.000 0.00 0.00 0.00 2.57
877 2352 0.527565 TAACGACGTTACAGGGAGGC 59.472 55.000 16.19 0.00 0.00 4.70
1085 2560 4.475135 GAGGGGAACAGGAGGCGC 62.475 72.222 0.00 0.00 0.00 6.53
1087 2562 4.475135 GCGAGGGGAACAGGAGGC 62.475 72.222 0.00 0.00 0.00 4.70
1088 2563 3.787001 GGCGAGGGGAACAGGAGG 61.787 72.222 0.00 0.00 0.00 4.30
1114 2589 1.554392 CGAATTCTGAGAGGCACGAG 58.446 55.000 3.52 0.00 0.00 4.18
1126 2601 2.187946 CTCCAGGCCGCGAATTCT 59.812 61.111 8.23 0.00 0.00 2.40
1459 2959 2.050350 CAATGGCAGCACCTGGAGG 61.050 63.158 0.00 0.00 40.22 4.30
1613 3113 6.377327 AAATTCAGAGAAAAGCAGACGAAA 57.623 33.333 0.00 0.00 0.00 3.46
1617 3121 7.200778 AGAGAAAATTCAGAGAAAAGCAGAC 57.799 36.000 0.00 0.00 0.00 3.51
1637 3141 0.608640 GGCTTCAGTTTCCGGAGAGA 59.391 55.000 3.34 0.00 0.00 3.10
1641 3145 0.321671 CAGAGGCTTCAGTTTCCGGA 59.678 55.000 0.00 0.00 0.00 5.14
1742 3246 2.525629 TGAAGGAGACGGCCACCA 60.526 61.111 2.24 0.00 0.00 4.17
1776 3280 1.219393 GGTGAAGAAGGGCTCCGAG 59.781 63.158 0.00 0.00 0.00 4.63
1888 3392 1.343465 GTTGAAGGAGACCTCGGTCAA 59.657 52.381 17.68 8.85 46.76 3.18
1924 3428 4.906618 ACAATGTTCTCCGATGGTTAGTT 58.093 39.130 0.00 0.00 0.00 2.24
1925 3429 4.504858 GACAATGTTCTCCGATGGTTAGT 58.495 43.478 0.00 0.00 0.00 2.24
1928 3436 2.305927 AGGACAATGTTCTCCGATGGTT 59.694 45.455 0.00 0.00 0.00 3.67
1964 3472 6.925165 TCGACGGTAAAAGGGAATATAATCAC 59.075 38.462 0.00 0.00 0.00 3.06
1982 3490 0.386838 GATTATTCGGGGTCGACGGT 59.613 55.000 9.92 0.00 45.92 4.83
2001 3509 4.564110 GGATTCTTCCCGGCCCCG 62.564 72.222 0.00 0.00 35.84 5.73
2022 3530 2.401583 ATATGTGGCGTGAGAAAGCA 57.598 45.000 0.00 0.00 34.54 3.91
2160 3668 3.323403 ACTGGTGAACTGAAGAAGGAGAG 59.677 47.826 0.00 0.00 0.00 3.20
2185 3694 8.515695 AAGAATCATGAGATGCTGAATTGTTA 57.484 30.769 0.09 0.00 39.34 2.41
2188 3697 6.918569 GGAAAGAATCATGAGATGCTGAATTG 59.081 38.462 0.09 0.00 39.34 2.32
2189 3698 6.605995 TGGAAAGAATCATGAGATGCTGAATT 59.394 34.615 0.09 0.00 39.34 2.17
2190 3699 6.127101 TGGAAAGAATCATGAGATGCTGAAT 58.873 36.000 0.09 0.00 39.34 2.57
2191 3700 5.503002 TGGAAAGAATCATGAGATGCTGAA 58.497 37.500 0.09 0.00 39.34 3.02
2192 3701 5.106876 TGGAAAGAATCATGAGATGCTGA 57.893 39.130 0.09 0.00 39.34 4.26
2196 3710 7.778083 TGGAATTTGGAAAGAATCATGAGATG 58.222 34.615 0.09 0.00 33.90 2.90
2223 3737 3.253921 TGCATGAACAAACTCATCAGTGG 59.746 43.478 0.00 0.00 33.66 4.00
2233 3747 2.406024 CAGACGCATTGCATGAACAAAC 59.594 45.455 9.69 0.00 32.27 2.93
2250 3764 1.406614 CCATGAACTCCTCCTGCAGAC 60.407 57.143 17.39 0.00 0.00 3.51
2251 3765 0.907486 CCATGAACTCCTCCTGCAGA 59.093 55.000 17.39 0.00 0.00 4.26
2299 3813 1.071987 CAGCAGGAAGGACAGCACA 59.928 57.895 0.00 0.00 0.00 4.57
2314 3828 1.751927 CATCAGGGGCAAGGACAGC 60.752 63.158 0.00 0.00 0.00 4.40
2317 3831 0.842635 AGATCATCAGGGGCAAGGAC 59.157 55.000 0.00 0.00 0.00 3.85
2326 3840 3.377485 CACCTTCTGCAAAGATCATCAGG 59.623 47.826 9.37 1.01 0.00 3.86
2347 3861 3.706373 GCCGGGGAGAAGCTGACA 61.706 66.667 2.18 0.00 0.00 3.58
2398 3912 4.885413 TCAATTTGTCTGGATTTTGCAGG 58.115 39.130 0.00 0.00 36.40 4.85
2416 3930 7.400599 AGTTATGATGATGCAACAGTTCAAT 57.599 32.000 2.25 0.00 0.00 2.57
2583 4097 1.472552 CCAGAACCGTGTGAGTTGTCA 60.473 52.381 0.00 0.00 0.00 3.58
2584 4098 1.217882 CCAGAACCGTGTGAGTTGTC 58.782 55.000 0.00 0.00 0.00 3.18
2588 4102 0.249911 GAAGCCAGAACCGTGTGAGT 60.250 55.000 0.00 0.00 0.00 3.41
2650 4172 1.296715 GCCAGGACCATCGTCAGTT 59.703 57.895 0.00 0.00 41.13 3.16
2827 4349 3.498774 AGAAAGAGGTTGCAGTGTGAT 57.501 42.857 0.00 0.00 0.00 3.06
2854 4384 2.298729 AGTCAGAAGAGCCACAAGAGAC 59.701 50.000 0.00 0.00 0.00 3.36
2937 4480 3.701040 TCTTTGGCTTTGCTTTCTTGAGT 59.299 39.130 0.00 0.00 0.00 3.41
2988 4534 6.843752 TCTATCTCAAAAACCTGTACCCAAA 58.156 36.000 0.00 0.00 0.00 3.28
2993 4539 9.535878 CTAATCCTCTATCTCAAAAACCTGTAC 57.464 37.037 0.00 0.00 0.00 2.90
3250 5031 6.648879 TGGCACAAGCTATCTTTTTAAGTT 57.351 33.333 0.00 0.00 41.70 2.66
3358 5165 3.515104 CCAGAATTTTGGTTGCCTATGGT 59.485 43.478 6.85 0.00 33.38 3.55
3377 5184 1.186917 TCCATTTGGTTGGCTGCCAG 61.187 55.000 22.17 8.16 37.31 4.85
3397 5204 4.215827 CCAATTGCTAGCAAAATTTTGGCA 59.784 37.500 32.22 24.47 36.32 4.92
3593 5452 1.606668 GTTGAACTGAAATGCCCGACA 59.393 47.619 0.00 0.00 0.00 4.35
3762 5621 1.739929 TGTCCGTATGCTGGCGTTG 60.740 57.895 0.00 0.00 0.00 4.10
3826 5685 2.572191 TAGGTTAAGCGTGTCGGATG 57.428 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.