Multiple sequence alignment - TraesCS6A01G301900

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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 TraesCS6A01G301900 chr6A 100.000 2987 0 0 1 2987 535404885 535401899 0.000000e+00 5517
1 TraesCS6A01G301900 chr6B 89.653 2967 151 59 1 2863 581869351 581866437 0.000000e+00 3635
2 TraesCS6A01G301900 chr6D 90.665 2646 101 38 2 2553 388952965 388950372 0.000000e+00 3384
3 TraesCS6A01G301900 chr6D 87.888 322 27 10 2553 2872 388950302 388949991 4.700000e-98 368
4 TraesCS6A01G301900 chr6D 93.277 119 5 2 2870 2987 388949961 388949845 3.960000e-39 172
5 TraesCS6A01G301900 chr7A 87.227 321 38 3 1517 1834 135689646 135689326 2.190000e-96 363
6 TraesCS6A01G301900 chr7D 90.146 274 25 2 1517 1789 136204684 136204412 3.660000e-94 355
7 TraesCS6A01G301900 chr7B 88.889 270 30 0 1517 1786 99089374 99089105 1.720000e-87 333
8 TraesCS6A01G301900 chr4D 83.582 268 40 4 1502 1768 438153340 438153604 6.390000e-62 248
9 TraesCS6A01G301900 chr4A 84.314 255 38 2 1515 1768 27589625 27589878 6.390000e-62 248
10 TraesCS6A01G301900 chr5A 89.205 176 19 0 1517 1692 393917978 393918153 1.390000e-53 220
11 TraesCS6A01G301900 chr5D 88.636 176 20 0 1517 1692 304163177 304163002 6.480000e-52 215


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 TraesCS6A01G301900 chr6A 535401899 535404885 2986 True 5517 5517 100.000 1 2987 1 chr6A.!!$R1 2986
1 TraesCS6A01G301900 chr6B 581866437 581869351 2914 True 3635 3635 89.653 1 2863 1 chr6B.!!$R1 2862
2 TraesCS6A01G301900 chr6D 388949845 388952965 3120 True 1308 3384 90.610 2 2987 3 chr6D.!!$R1 2985

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
695 752 0.105778 CCTCTTGCTCGGGATTCTCC 59.894 60.0 0.0 0.0 35.23 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 2480 0.527113 CAGGGATGCACGCATGAAAA 59.473 50.0 9.7 0.0 36.7 2.29 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
42 45 2.753452 GTCCTTACTTTAAGCAAGGGGC 59.247 50.000 20.31 11.94 38.90 5.80
73 76 2.590291 TGCAACGCAGAAGCCGAA 60.590 55.556 0.00 0.00 37.52 4.30
77 80 0.798776 CAACGCAGAAGCCGAATTCT 59.201 50.000 3.52 0.00 40.17 2.40
122 125 3.731136 GCACACGCTGAGGTCAAA 58.269 55.556 0.00 0.00 34.30 2.69
149 152 3.430862 CACCACCCAATGACGCGG 61.431 66.667 12.47 0.00 0.00 6.46
299 302 5.949233 AAGCAACGTCTCATTTTCAAAAC 57.051 34.783 0.00 0.00 0.00 2.43
301 304 3.179599 GCAACGTCTCATTTTCAAAACCG 59.820 43.478 0.00 0.00 0.00 4.44
317 320 3.052082 CGCACTGCCAACTCCCAG 61.052 66.667 0.00 0.00 35.26 4.45
330 334 2.031870 ACTCCCAGCAAACAAGAAACC 58.968 47.619 0.00 0.00 0.00 3.27
352 356 9.716507 AAACCATTAACGAAATTAATCTGATCG 57.283 29.630 9.81 9.81 40.82 3.69
355 359 8.721478 CCATTAACGAAATTAATCTGATCGGAT 58.279 33.333 11.47 11.47 40.82 4.18
380 410 1.901650 GAGTGGTTGCTTCGCTTCGG 61.902 60.000 0.00 0.00 0.00 4.30
490 532 2.595463 AGCAACACGCAGCCACAT 60.595 55.556 0.00 0.00 46.13 3.21
491 533 2.126734 GCAACACGCAGCCACATC 60.127 61.111 0.00 0.00 41.79 3.06
492 534 2.562912 CAACACGCAGCCACATCC 59.437 61.111 0.00 0.00 0.00 3.51
493 535 2.112928 AACACGCAGCCACATCCA 59.887 55.556 0.00 0.00 0.00 3.41
494 536 2.260869 AACACGCAGCCACATCCAC 61.261 57.895 0.00 0.00 0.00 4.02
495 537 3.792047 CACGCAGCCACATCCACG 61.792 66.667 0.00 0.00 0.00 4.94
529 571 1.519455 CGGTGAGGTTGAGCGATCC 60.519 63.158 0.00 0.00 36.43 3.36
552 603 2.669569 GCCCTTCAGCAGCAACGA 60.670 61.111 0.00 0.00 0.00 3.85
564 615 2.830285 GCAACGACGGCAGGTTTGT 61.830 57.895 0.00 0.00 0.00 2.83
618 669 2.624838 CCAGCAGGAACACACAAGAAAT 59.375 45.455 0.00 0.00 36.89 2.17
619 670 3.068590 CCAGCAGGAACACACAAGAAATT 59.931 43.478 0.00 0.00 36.89 1.82
620 671 4.293415 CAGCAGGAACACACAAGAAATTC 58.707 43.478 0.00 0.00 0.00 2.17
695 752 0.105778 CCTCTTGCTCGGGATTCTCC 59.894 60.000 0.00 0.00 35.23 3.71
707 764 3.683847 CGGGATTCTCCTGATTTCTTGCT 60.684 47.826 0.00 0.00 45.95 3.91
716 773 4.287067 TCCTGATTTCTTGCTAACCTCACT 59.713 41.667 0.00 0.00 0.00 3.41
776 833 2.260639 TCTCTCCTGGATTCTTGCCT 57.739 50.000 0.00 0.00 0.00 4.75
850 907 3.187700 CCCTTCTAGTTCGTCCGATTTG 58.812 50.000 0.00 0.00 0.00 2.32
853 910 4.689345 CCTTCTAGTTCGTCCGATTTGTTT 59.311 41.667 0.00 0.00 0.00 2.83
854 911 5.163982 CCTTCTAGTTCGTCCGATTTGTTTC 60.164 44.000 0.00 0.00 0.00 2.78
855 912 4.240096 TCTAGTTCGTCCGATTTGTTTCC 58.760 43.478 0.00 0.00 0.00 3.13
856 913 3.121738 AGTTCGTCCGATTTGTTTCCT 57.878 42.857 0.00 0.00 0.00 3.36
857 914 3.064931 AGTTCGTCCGATTTGTTTCCTC 58.935 45.455 0.00 0.00 0.00 3.71
930 992 3.254166 TCTGATTTTGCACCAGAAAGCTC 59.746 43.478 5.21 0.00 34.38 4.09
932 994 2.071778 TTTTGCACCAGAAAGCTCCT 57.928 45.000 0.00 0.00 0.00 3.69
1146 1211 1.287146 TCCTCTCACTACCCCTACCAC 59.713 57.143 0.00 0.00 0.00 4.16
1155 1220 3.461458 ACTACCCCTACCACTACTACTCC 59.539 52.174 0.00 0.00 0.00 3.85
1179 1244 1.475751 CCCTCCATGACCCAAGATTCG 60.476 57.143 0.00 0.00 0.00 3.34
1205 1270 2.202570 CACCCCATCGTCGTCGTC 60.203 66.667 1.33 0.00 38.33 4.20
1207 1272 3.138798 CCCCATCGTCGTCGTCCT 61.139 66.667 1.33 0.00 38.33 3.85
1208 1273 1.820906 CCCCATCGTCGTCGTCCTA 60.821 63.158 1.33 0.00 38.33 2.94
1209 1274 1.354506 CCCATCGTCGTCGTCCTAC 59.645 63.158 1.33 0.00 38.33 3.18
1210 1275 1.011463 CCATCGTCGTCGTCCTACG 60.011 63.158 1.33 0.00 44.19 3.51
1211 1276 1.650536 CATCGTCGTCGTCCTACGC 60.651 63.158 1.33 0.00 42.21 4.42
1212 1277 2.817423 ATCGTCGTCGTCCTACGCC 61.817 63.158 1.33 0.00 42.21 5.68
1213 1278 3.494336 CGTCGTCGTCCTACGCCT 61.494 66.667 0.00 0.00 42.21 5.52
1269 1337 2.509561 GCCTCGCCGTCTTTCTCC 60.510 66.667 0.00 0.00 0.00 3.71
1384 1464 1.669115 TTCTTCGTCCAGCAGCAGC 60.669 57.895 0.00 0.00 42.56 5.25
1385 1465 2.357881 CTTCGTCCAGCAGCAGCA 60.358 61.111 3.17 0.00 45.49 4.41
1386 1466 2.357881 TTCGTCCAGCAGCAGCAG 60.358 61.111 3.17 0.00 45.49 4.24
1422 1502 2.270527 GCTGGTGGCTCCTTCCTC 59.729 66.667 7.19 0.00 38.06 3.71
1425 1505 4.475135 GGTGGCTCCTTCCTCGGC 62.475 72.222 0.00 0.00 0.00 5.54
1590 1670 2.359975 CTCCCCAAGAACCGCACC 60.360 66.667 0.00 0.00 0.00 5.01
1987 2088 0.457851 GGACTCCATCCTGTCGTGAG 59.542 60.000 0.00 0.00 45.22 3.51
2170 2275 7.858498 AGTAATTAGCCAGTGGTGTTTAGTAT 58.142 34.615 11.74 0.00 0.00 2.12
2183 2298 4.501921 GTGTTTAGTATGCTACTACGTGGC 59.498 45.833 0.00 0.00 40.74 5.01
2201 2316 2.238646 TGGCGTAATTGATCTCCTGGTT 59.761 45.455 0.00 0.00 0.00 3.67
2262 2378 5.186215 TCGAGAGGTGTAATCATGTTTACCA 59.814 40.000 19.29 8.62 32.24 3.25
2264 2380 5.186198 AGAGGTGTAATCATGTTTACCAGC 58.814 41.667 19.29 16.33 32.24 4.85
2292 2408 8.567285 AAAGAATTGCACTAGCTTATGTAACT 57.433 30.769 0.00 0.00 42.74 2.24
2318 2435 0.890542 TGCATGTCTCTTGGTGCACC 60.891 55.000 29.67 29.67 42.13 5.01
2332 2449 1.884926 GCACCGCTACTGATCCAGC 60.885 63.158 0.00 0.00 34.37 4.85
2362 2479 0.946221 GTGTGCTCTTGCTGTAGCGT 60.946 55.000 0.00 0.00 45.83 5.07
2363 2480 0.249868 TGTGCTCTTGCTGTAGCGTT 60.250 50.000 0.00 0.00 45.83 4.84
2368 2485 2.032030 GCTCTTGCTGTAGCGTTTTTCA 60.032 45.455 0.00 0.00 45.83 2.69
2426 2543 2.742053 TCGTAGTGCCTTTTCTGATTGC 59.258 45.455 0.00 0.00 0.00 3.56
2588 2775 1.704628 TGCTTTTCATGGGACCTGAGA 59.295 47.619 0.00 0.00 0.00 3.27
2626 2830 6.700960 CAGAGTTCTAGCTTCCAGTTCATATG 59.299 42.308 0.00 0.00 0.00 1.78
2627 2831 5.923204 AGTTCTAGCTTCCAGTTCATATGG 58.077 41.667 2.13 0.00 39.33 2.74
2629 2833 6.611642 AGTTCTAGCTTCCAGTTCATATGGTA 59.388 38.462 2.13 0.00 39.01 3.25
2631 2835 6.136857 TCTAGCTTCCAGTTCATATGGTACT 58.863 40.000 2.13 4.36 39.01 2.73
2636 2840 6.620877 TTCCAGTTCATATGGTACTCAAGT 57.379 37.500 2.13 0.00 39.01 3.16
2637 2841 6.222038 TCCAGTTCATATGGTACTCAAGTC 57.778 41.667 2.13 0.00 39.01 3.01
2638 2842 5.719563 TCCAGTTCATATGGTACTCAAGTCA 59.280 40.000 2.13 0.00 39.01 3.41
2639 2843 6.212589 TCCAGTTCATATGGTACTCAAGTCAA 59.787 38.462 2.13 0.00 39.01 3.18
2641 2845 7.099764 CAGTTCATATGGTACTCAAGTCAAGT 58.900 38.462 2.13 0.00 0.00 3.16
2643 2847 6.850752 TCATATGGTACTCAAGTCAAGTCA 57.149 37.500 2.13 0.00 0.00 3.41
2644 2848 7.239763 TCATATGGTACTCAAGTCAAGTCAA 57.760 36.000 2.13 0.00 0.00 3.18
2645 2849 7.097192 TCATATGGTACTCAAGTCAAGTCAAC 58.903 38.462 2.13 0.00 0.00 3.18
2646 2850 4.746535 TGGTACTCAAGTCAAGTCAACA 57.253 40.909 0.00 0.00 0.00 3.33
2647 2851 4.439057 TGGTACTCAAGTCAAGTCAACAC 58.561 43.478 0.00 0.00 0.00 3.32
2648 2852 4.081365 TGGTACTCAAGTCAAGTCAACACA 60.081 41.667 0.00 0.00 0.00 3.72
2649 2853 5.057149 GGTACTCAAGTCAAGTCAACACAT 58.943 41.667 0.00 0.00 0.00 3.21
2650 2854 5.177696 GGTACTCAAGTCAAGTCAACACATC 59.822 44.000 0.00 0.00 0.00 3.06
2651 2855 4.769688 ACTCAAGTCAAGTCAACACATCA 58.230 39.130 0.00 0.00 0.00 3.07
2693 2897 2.532715 AGGCCTGCCAAGGGAAGA 60.533 61.111 3.11 0.00 44.67 2.87
2772 2979 4.213482 GGTTGCCTATGTCGATTGGTATTC 59.787 45.833 0.00 0.00 0.00 1.75
2783 2990 3.244249 CGATTGGTATTCCCTCTTCTCCC 60.244 52.174 0.00 0.00 0.00 4.30
2795 3002 5.079643 CCCTCTTCTCCCAAAATGAAAAGA 58.920 41.667 0.00 0.00 0.00 2.52
2819 3026 4.885325 ACCAAGTTTCTACGGATGTGTTTT 59.115 37.500 0.00 0.00 0.00 2.43
2851 3058 1.443828 CGCCCTCTTTCTAGCCTCC 59.556 63.158 0.00 0.00 0.00 4.30
2866 3073 2.007608 GCCTCCGCCTAACTAAAACTG 58.992 52.381 0.00 0.00 0.00 3.16
2867 3074 2.614734 GCCTCCGCCTAACTAAAACTGT 60.615 50.000 0.00 0.00 0.00 3.55
2868 3075 3.000727 CCTCCGCCTAACTAAAACTGTG 58.999 50.000 0.00 0.00 0.00 3.66
2916 3156 3.344515 GTTGTATCCAACTTCCAGTCCC 58.655 50.000 0.00 0.00 46.07 4.46
2917 3157 2.626785 TGTATCCAACTTCCAGTCCCA 58.373 47.619 0.00 0.00 0.00 4.37
2918 3158 3.189606 TGTATCCAACTTCCAGTCCCAT 58.810 45.455 0.00 0.00 0.00 4.00
2922 3162 1.614317 CCAACTTCCAGTCCCATGACC 60.614 57.143 0.00 0.00 42.81 4.02
2932 3172 1.595382 CCCATGACCGCCGATCTTC 60.595 63.158 0.00 0.00 0.00 2.87
2957 3197 1.950909 CTGTTTGGGTTAGGTCGCAAA 59.049 47.619 5.15 5.15 43.99 3.68
2974 3214 2.964768 GCAAACGAAAGCACTCTTAACG 59.035 45.455 0.00 0.00 37.82 3.18
2976 3216 4.201576 CAAACGAAAGCACTCTTAACGTC 58.798 43.478 0.00 0.00 41.11 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.392393 TGCTTAAAGTAAGGACCAAGTAAATCC 59.608 37.037 0.00 0.00 36.31 3.01
42 45 1.962822 TTGCACCAAGAGCTGCGAG 60.963 57.895 0.00 0.00 36.08 5.03
73 76 0.610174 TTGTGCTCTGCTCCGAGAAT 59.390 50.000 0.00 0.00 32.74 2.40
77 80 1.004560 CCTTTGTGCTCTGCTCCGA 60.005 57.895 0.00 0.00 0.00 4.55
111 114 3.016474 GCGCTCGTTTGACCTCAGC 62.016 63.158 0.00 0.00 0.00 4.26
213 216 3.195698 GTCGCGGCCAATGAGGAC 61.196 66.667 6.13 0.00 44.64 3.85
299 302 4.641645 TGGGAGTTGGCAGTGCGG 62.642 66.667 9.45 0.00 0.00 5.69
301 304 3.368571 GCTGGGAGTTGGCAGTGC 61.369 66.667 6.55 6.55 0.00 4.40
317 320 6.576551 TTTCGTTAATGGTTTCTTGTTTGC 57.423 33.333 0.00 0.00 0.00 3.68
330 334 9.746711 GATCCGATCAGATTAATTTCGTTAATG 57.253 33.333 3.33 0.00 41.82 1.90
347 351 1.735973 CACTCAGGCGATCCGATCA 59.264 57.895 9.07 0.00 37.47 2.92
352 356 2.109126 GCAACCACTCAGGCGATCC 61.109 63.158 0.00 0.00 43.14 3.36
355 359 1.301716 GAAGCAACCACTCAGGCGA 60.302 57.895 0.00 0.00 43.14 5.54
490 532 1.550130 GGAGTGGAATGGGACGTGGA 61.550 60.000 0.00 0.00 0.00 4.02
491 533 1.078426 GGAGTGGAATGGGACGTGG 60.078 63.158 0.00 0.00 0.00 4.94
492 534 0.673644 GTGGAGTGGAATGGGACGTG 60.674 60.000 0.00 0.00 0.00 4.49
493 535 1.677552 GTGGAGTGGAATGGGACGT 59.322 57.895 0.00 0.00 0.00 4.34
494 536 1.447838 CGTGGAGTGGAATGGGACG 60.448 63.158 0.00 0.00 0.00 4.79
495 537 1.078426 CCGTGGAGTGGAATGGGAC 60.078 63.158 0.00 0.00 0.00 4.46
529 571 2.507992 CTGCTGAAGGGCTCGTCG 60.508 66.667 0.00 0.00 0.00 5.12
552 603 0.468226 TCAGAGAACAAACCTGCCGT 59.532 50.000 0.00 0.00 0.00 5.68
564 615 5.878406 AAAGACCAGAGAAGTTCAGAGAA 57.122 39.130 5.50 0.00 0.00 2.87
639 694 6.211584 TCCGATCTAATAATCCCAGAAGAAGG 59.788 42.308 0.00 0.00 0.00 3.46
668 725 3.780173 GAGCAAGAGGAGGGCGCT 61.780 66.667 7.64 1.38 35.14 5.92
695 752 6.402222 AGTAGTGAGGTTAGCAAGAAATCAG 58.598 40.000 0.00 0.00 0.00 2.90
707 764 4.412858 CCTCCTAGGAGAGTAGTGAGGTTA 59.587 50.000 36.08 0.00 44.53 2.85
716 773 4.372588 TCTCTGTTCCTCCTAGGAGAGTA 58.627 47.826 36.08 19.82 46.73 2.59
807 864 5.470368 GGTATTGCAAAAGAACCCTTTCTC 58.530 41.667 1.71 0.00 41.56 2.87
808 865 4.283467 GGGTATTGCAAAAGAACCCTTTCT 59.717 41.667 24.55 1.52 44.53 2.52
850 907 1.624312 ACGAGGGGAAGAAGAGGAAAC 59.376 52.381 0.00 0.00 0.00 2.78
853 910 1.900486 GAAACGAGGGGAAGAAGAGGA 59.100 52.381 0.00 0.00 0.00 3.71
854 911 1.903183 AGAAACGAGGGGAAGAAGAGG 59.097 52.381 0.00 0.00 0.00 3.69
855 912 2.829120 AGAGAAACGAGGGGAAGAAGAG 59.171 50.000 0.00 0.00 0.00 2.85
856 913 2.890814 AGAGAAACGAGGGGAAGAAGA 58.109 47.619 0.00 0.00 0.00 2.87
857 914 4.803098 TTAGAGAAACGAGGGGAAGAAG 57.197 45.455 0.00 0.00 0.00 2.85
909 968 3.572584 GAGCTTTCTGGTGCAAAATCAG 58.427 45.455 0.00 0.00 0.00 2.90
910 969 2.297033 GGAGCTTTCTGGTGCAAAATCA 59.703 45.455 0.00 0.00 34.56 2.57
911 970 2.560105 AGGAGCTTTCTGGTGCAAAATC 59.440 45.455 0.00 0.00 36.95 2.17
912 971 2.601905 AGGAGCTTTCTGGTGCAAAAT 58.398 42.857 0.00 0.00 36.95 1.82
914 973 2.071778 AAGGAGCTTTCTGGTGCAAA 57.928 45.000 0.00 0.00 36.95 3.68
947 1009 1.605753 AGAGAAGGCCGAACCAAAAC 58.394 50.000 0.00 0.00 43.14 2.43
1068 1133 1.326328 TCATGAGCTCCTGATCCGAG 58.674 55.000 16.69 3.13 0.00 4.63
1146 1211 3.396276 TCATGGAGGGAGAGGAGTAGTAG 59.604 52.174 0.00 0.00 0.00 2.57
1155 1220 0.835941 CTTGGGTCATGGAGGGAGAG 59.164 60.000 0.00 0.00 0.00 3.20
1179 1244 1.525995 CGATGGGGTGGCCATGTAC 60.526 63.158 9.72 0.00 0.00 2.90
1205 1270 2.408022 CGAACGAGGAGGCGTAGG 59.592 66.667 0.00 0.00 44.86 3.18
1207 1272 3.047718 CTGCGAACGAGGAGGCGTA 62.048 63.158 0.00 0.00 44.86 4.42
1211 1276 3.708220 GAGGCTGCGAACGAGGAGG 62.708 68.421 0.00 0.00 0.00 4.30
1212 1277 2.202676 GAGGCTGCGAACGAGGAG 60.203 66.667 0.00 0.00 0.00 3.69
1213 1278 2.676822 AGAGGCTGCGAACGAGGA 60.677 61.111 0.00 0.00 0.00 3.71
1436 1516 2.125552 CGGACTGCTTCATCGGCA 60.126 61.111 0.00 0.00 38.10 5.69
1542 1622 4.603535 ACCCACTTGCCCCAGTGC 62.604 66.667 2.89 0.00 42.63 4.40
2003 2104 6.660887 AACGAAGACTGTACTAGTAGTAGC 57.339 41.667 10.38 6.62 40.53 3.58
2137 2238 7.284944 ACACCACTGGCTAATTACTACTAGTAG 59.715 40.741 25.30 25.30 39.04 2.57
2138 2239 7.121382 ACACCACTGGCTAATTACTACTAGTA 58.879 38.462 1.89 1.89 0.00 1.82
2139 2240 5.956563 ACACCACTGGCTAATTACTACTAGT 59.043 40.000 0.00 0.00 0.00 2.57
2140 2241 6.466885 ACACCACTGGCTAATTACTACTAG 57.533 41.667 0.00 0.00 0.00 2.57
2144 2245 7.248743 ACTAAACACCACTGGCTAATTACTA 57.751 36.000 0.00 0.00 0.00 1.82
2150 2251 4.019681 AGCATACTAAACACCACTGGCTAA 60.020 41.667 0.00 0.00 0.00 3.09
2183 2298 3.871594 GGTCAACCAGGAGATCAATTACG 59.128 47.826 0.00 0.00 35.64 3.18
2227 2343 2.829003 CTCTCGACTGGCCGCCTA 60.829 66.667 11.61 0.00 0.00 3.93
2262 2378 3.683802 AGCTAGTGCAATTCTTTCAGCT 58.316 40.909 1.21 1.21 42.74 4.24
2264 2380 7.081526 ACATAAGCTAGTGCAATTCTTTCAG 57.918 36.000 0.00 0.00 42.74 3.02
2292 2408 6.532826 TGCACCAAGAGACATGCATATTATA 58.467 36.000 0.00 0.00 42.92 0.98
2296 2412 3.286329 TGCACCAAGAGACATGCATAT 57.714 42.857 0.00 0.00 42.92 1.78
2297 2413 2.785540 TGCACCAAGAGACATGCATA 57.214 45.000 0.00 0.00 42.92 3.14
2298 2414 3.656457 TGCACCAAGAGACATGCAT 57.344 47.368 0.00 0.00 42.92 3.96
2299 2415 0.890542 GGTGCACCAAGAGACATGCA 60.891 55.000 31.23 0.00 45.45 3.96
2300 2416 1.878775 GGTGCACCAAGAGACATGC 59.121 57.895 31.23 0.00 38.59 4.06
2301 2417 1.915614 GCGGTGCACCAAGAGACATG 61.916 60.000 34.16 16.12 35.14 3.21
2302 2418 1.672356 GCGGTGCACCAAGAGACAT 60.672 57.895 34.16 0.00 35.14 3.06
2332 2449 1.788258 AGAGCACACTTCACACATCG 58.212 50.000 0.00 0.00 0.00 3.84
2362 2479 1.067706 CAGGGATGCACGCATGAAAAA 60.068 47.619 9.70 0.00 36.70 1.94
2363 2480 0.527113 CAGGGATGCACGCATGAAAA 59.473 50.000 9.70 0.00 36.70 2.29
2368 2485 1.028330 CAACTCAGGGATGCACGCAT 61.028 55.000 3.71 3.71 39.69 4.73
2426 2543 5.983118 TCATCATGTATACTGTACTTTGGCG 59.017 40.000 4.17 0.00 0.00 5.69
2583 2770 4.202101 ACTCTGCTCCGTTCATATTCTCAG 60.202 45.833 0.00 0.00 0.00 3.35
2588 2775 4.744795 AGAACTCTGCTCCGTTCATATT 57.255 40.909 12.64 0.00 41.40 1.28
2626 2830 4.439057 TGTGTTGACTTGACTTGAGTACC 58.561 43.478 0.00 0.00 0.00 3.34
2627 2831 5.753438 TGATGTGTTGACTTGACTTGAGTAC 59.247 40.000 0.00 0.00 0.00 2.73
2629 2833 4.572389 GTGATGTGTTGACTTGACTTGAGT 59.428 41.667 0.00 0.00 0.00 3.41
2631 2835 4.512484 TGTGATGTGTTGACTTGACTTGA 58.488 39.130 0.00 0.00 0.00 3.02
2636 2840 5.879777 TCTTCTTTGTGATGTGTTGACTTGA 59.120 36.000 0.00 0.00 0.00 3.02
2637 2841 6.122850 TCTTCTTTGTGATGTGTTGACTTG 57.877 37.500 0.00 0.00 0.00 3.16
2638 2842 6.555315 GTTCTTCTTTGTGATGTGTTGACTT 58.445 36.000 0.00 0.00 0.00 3.01
2639 2843 5.220662 CGTTCTTCTTTGTGATGTGTTGACT 60.221 40.000 0.00 0.00 0.00 3.41
2641 2845 4.634004 ACGTTCTTCTTTGTGATGTGTTGA 59.366 37.500 0.00 0.00 0.00 3.18
2643 2847 5.331902 CAACGTTCTTCTTTGTGATGTGTT 58.668 37.500 0.00 0.00 0.00 3.32
2644 2848 4.730613 GCAACGTTCTTCTTTGTGATGTGT 60.731 41.667 0.00 0.00 0.00 3.72
2645 2849 3.725740 GCAACGTTCTTCTTTGTGATGTG 59.274 43.478 0.00 0.00 0.00 3.21
2646 2850 3.243068 GGCAACGTTCTTCTTTGTGATGT 60.243 43.478 0.00 0.00 0.00 3.06
2647 2851 3.243035 TGGCAACGTTCTTCTTTGTGATG 60.243 43.478 0.00 0.00 42.51 3.07
2648 2852 2.948979 TGGCAACGTTCTTCTTTGTGAT 59.051 40.909 0.00 0.00 42.51 3.06
2649 2853 2.096819 GTGGCAACGTTCTTCTTTGTGA 59.903 45.455 0.00 0.00 42.51 3.58
2650 2854 2.159448 TGTGGCAACGTTCTTCTTTGTG 60.159 45.455 0.00 0.00 42.51 3.33
2651 2855 2.088423 TGTGGCAACGTTCTTCTTTGT 58.912 42.857 0.00 0.00 42.51 2.83
2693 2897 3.278574 TGCTGTTAAGTGTCAGTTTGCT 58.721 40.909 0.00 0.00 34.57 3.91
2772 2979 5.079643 TCTTTTCATTTTGGGAGAAGAGGG 58.920 41.667 0.00 0.00 32.49 4.30
2783 2990 8.531530 CGTAGAAACTTGGTTCTTTTCATTTTG 58.468 33.333 6.22 0.00 38.75 2.44
2795 3002 4.081322 ACACATCCGTAGAAACTTGGTT 57.919 40.909 0.00 0.00 0.00 3.67
2819 3026 1.302511 GGGCGGAAGTCAAAGAGCA 60.303 57.895 0.00 0.00 37.54 4.26
2851 3058 2.740447 GGACCACAGTTTTAGTTAGGCG 59.260 50.000 0.00 0.00 0.00 5.52
2866 3073 4.751098 TGTAAATTAACACTGACGGACCAC 59.249 41.667 0.00 0.00 0.00 4.16
2867 3074 4.958509 TGTAAATTAACACTGACGGACCA 58.041 39.130 0.00 0.00 0.00 4.02
2868 3075 5.410439 ACATGTAAATTAACACTGACGGACC 59.590 40.000 0.00 0.00 30.75 4.46
2915 3155 0.877649 CAGAAGATCGGCGGTCATGG 60.878 60.000 23.68 4.83 0.00 3.66
2916 3156 0.103026 TCAGAAGATCGGCGGTCATG 59.897 55.000 23.68 17.06 0.00 3.07
2917 3157 0.387202 CTCAGAAGATCGGCGGTCAT 59.613 55.000 23.68 10.99 0.00 3.06
2918 3158 1.809869 CTCAGAAGATCGGCGGTCA 59.190 57.895 23.68 0.00 0.00 4.02
2922 3162 0.459237 AACAGCTCAGAAGATCGGCG 60.459 55.000 0.00 0.00 0.00 6.46
2932 3172 2.427506 GACCTAACCCAAACAGCTCAG 58.572 52.381 0.00 0.00 0.00 3.35
2957 3197 2.793232 GTGACGTTAAGAGTGCTTTCGT 59.207 45.455 0.00 0.00 41.95 3.85


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

AutoCloner maintained by Alex Coulton.