Multiple sequence alignment - TraesCS5B01G068600

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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 TraesCS5B01G068600 chr5B 100.000 3353 0 0 1 3353 78222233 78218881 0.000000e+00 6192
1 TraesCS5B01G068600 chr5D 92.597 2715 120 30 1 2682 74144076 74146742 0.000000e+00 3825
2 TraesCS5B01G068600 chr5D 88.819 635 30 8 2733 3353 74146739 74147346 0.000000e+00 741
3 TraesCS5B01G068600 chr5A 90.209 2676 129 55 1 2605 69139699 69142312 0.000000e+00 3367
4 TraesCS5B01G068600 chr5A 89.218 371 27 6 2996 3353 69142628 69142998 5.100000e-123 451
5 TraesCS5B01G068600 chr5A 90.228 307 23 3 834 1139 69222864 69222564 8.720000e-106 394
6 TraesCS5B01G068600 chr5A 92.784 194 9 2 1 192 69148798 69148608 3.300000e-70 276
7 TraesCS5B01G068600 chr5A 88.068 176 12 2 2753 2920 69142365 69142539 2.040000e-47 200
8 TraesCS5B01G068600 chr4A 78.661 1120 197 31 1150 2254 552832916 552831824 0.000000e+00 706
9 TraesCS5B01G068600 chr4A 78.424 1117 200 28 1150 2253 552817054 552818142 0.000000e+00 689
10 TraesCS5B01G068600 chr4D 78.540 1123 191 33 1150 2253 46187188 46186097 0.000000e+00 693
11 TraesCS5B01G068600 chr4B 77.916 1123 200 35 1150 2254 67095230 67096322 0.000000e+00 656
12 TraesCS5B01G068600 chr4B 77.887 1117 206 27 1150 2253 67543626 67542538 0.000000e+00 656
13 TraesCS5B01G068600 chr4B 77.151 1116 216 28 1150 2253 67354025 67352937 2.210000e-171 612
14 TraesCS5B01G068600 chr4B 76.209 1034 211 27 1231 2251 67484854 67483843 6.420000e-142 514
15 TraesCS5B01G068600 chr7B 90.991 222 18 2 2119 2339 449873727 449873507 7.030000e-77 298


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 TraesCS5B01G068600 chr5B 78218881 78222233 3352 True 6192.000000 6192 100.000 1 3353 1 chr5B.!!$R1 3352
1 TraesCS5B01G068600 chr5D 74144076 74147346 3270 False 2283.000000 3825 90.708 1 3353 2 chr5D.!!$F1 3352
2 TraesCS5B01G068600 chr5A 69139699 69142998 3299 False 1339.333333 3367 89.165 1 3353 3 chr5A.!!$F1 3352
3 TraesCS5B01G068600 chr4A 552831824 552832916 1092 True 706.000000 706 78.661 1150 2254 1 chr4A.!!$R1 1104
4 TraesCS5B01G068600 chr4A 552817054 552818142 1088 False 689.000000 689 78.424 1150 2253 1 chr4A.!!$F1 1103
5 TraesCS5B01G068600 chr4D 46186097 46187188 1091 True 693.000000 693 78.540 1150 2253 1 chr4D.!!$R1 1103
6 TraesCS5B01G068600 chr4B 67095230 67096322 1092 False 656.000000 656 77.916 1150 2254 1 chr4B.!!$F1 1104
7 TraesCS5B01G068600 chr4B 67542538 67543626 1088 True 656.000000 656 77.887 1150 2253 1 chr4B.!!$R3 1103
8 TraesCS5B01G068600 chr4B 67352937 67354025 1088 True 612.000000 612 77.151 1150 2253 1 chr4B.!!$R1 1103
9 TraesCS5B01G068600 chr4B 67483843 67484854 1011 True 514.000000 514 76.209 1231 2251 1 chr4B.!!$R2 1020

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
905 985 0.179137 GAGTAATTTTGGCAGCCGGC 60.179 55.0 21.89 21.89 43.74 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2588 2702 0.250553 GGACCACCGACCAAATCACA 60.251 55.0 0.0 0.0 0.0 3.58 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
66 68 2.668212 ATTCCACACCACACGGCG 60.668 61.111 4.80 4.80 34.57 6.46
67 69 3.171828 ATTCCACACCACACGGCGA 62.172 57.895 16.62 0.00 34.57 5.54
80 82 2.028337 GGCGAGGAAGGATCGAGC 59.972 66.667 0.00 0.00 42.76 5.03
114 119 1.407437 GGAGCCGAATCAACATGGACT 60.407 52.381 0.00 0.00 0.00 3.85
117 122 4.130118 GAGCCGAATCAACATGGACTAAT 58.870 43.478 0.00 0.00 0.00 1.73
118 123 3.879295 AGCCGAATCAACATGGACTAATG 59.121 43.478 0.00 0.00 0.00 1.90
119 124 3.548818 GCCGAATCAACATGGACTAATGC 60.549 47.826 0.00 0.00 0.00 3.56
120 125 3.303329 CCGAATCAACATGGACTAATGCG 60.303 47.826 0.00 0.00 0.00 4.73
121 126 3.621794 GAATCAACATGGACTAATGCGC 58.378 45.455 0.00 0.00 0.00 6.09
123 128 2.279741 TCAACATGGACTAATGCGCTC 58.720 47.619 9.73 0.00 0.00 5.03
124 129 1.331756 CAACATGGACTAATGCGCTCC 59.668 52.381 9.73 7.41 0.00 4.70
126 131 1.065491 ACATGGACTAATGCGCTCCAA 60.065 47.619 17.98 3.81 37.62 3.53
127 132 1.600957 CATGGACTAATGCGCTCCAAG 59.399 52.381 17.98 10.87 37.62 3.61
128 133 0.613260 TGGACTAATGCGCTCCAAGT 59.387 50.000 12.49 8.67 30.81 3.16
129 134 1.003118 TGGACTAATGCGCTCCAAGTT 59.997 47.619 12.49 0.00 30.81 2.66
130 135 1.666189 GGACTAATGCGCTCCAAGTTC 59.334 52.381 9.73 1.98 0.00 3.01
131 136 2.346803 GACTAATGCGCTCCAAGTTCA 58.653 47.619 9.73 0.00 0.00 3.18
132 137 2.939103 GACTAATGCGCTCCAAGTTCAT 59.061 45.455 9.73 0.00 0.00 2.57
133 138 3.347216 ACTAATGCGCTCCAAGTTCATT 58.653 40.909 9.73 0.00 0.00 2.57
144 149 6.914215 CGCTCCAAGTTCATTACGTAGTATAA 59.086 38.462 0.00 0.00 45.21 0.98
192 199 1.026718 GGGCAAAGTGCTGCGTCTAT 61.027 55.000 0.00 0.00 44.28 1.98
193 200 1.651987 GGCAAAGTGCTGCGTCTATA 58.348 50.000 0.00 0.00 44.28 1.31
194 201 2.213499 GGCAAAGTGCTGCGTCTATAT 58.787 47.619 0.00 0.00 44.28 0.86
195 202 3.390135 GGCAAAGTGCTGCGTCTATATA 58.610 45.455 0.00 0.00 44.28 0.86
347 371 1.821332 CCTGGAGATTTCGCTGCCC 60.821 63.158 0.00 0.00 0.00 5.36
357 384 0.811219 TTCGCTGCCCAATCGATCTG 60.811 55.000 0.00 0.00 31.96 2.90
368 395 4.752101 CCCAATCGATCTGTTTCCATCTAC 59.248 45.833 0.00 0.00 0.00 2.59
369 396 5.359756 CCAATCGATCTGTTTCCATCTACA 58.640 41.667 0.00 0.00 0.00 2.74
370 397 5.235186 CCAATCGATCTGTTTCCATCTACAC 59.765 44.000 0.00 0.00 0.00 2.90
376 403 6.238293 CGATCTGTTTCCATCTACACGTACTA 60.238 42.308 0.00 0.00 0.00 1.82
377 404 6.432607 TCTGTTTCCATCTACACGTACTAG 57.567 41.667 0.00 0.00 0.00 2.57
378 405 5.942236 TCTGTTTCCATCTACACGTACTAGT 59.058 40.000 0.00 0.00 0.00 2.57
379 406 7.105588 TCTGTTTCCATCTACACGTACTAGTA 58.894 38.462 0.00 0.00 0.00 1.82
380 407 7.772292 TCTGTTTCCATCTACACGTACTAGTAT 59.228 37.037 5.75 0.00 0.00 2.12
406 441 4.751767 TTGGGTTTGACTTTTGCTTGAT 57.248 36.364 0.00 0.00 0.00 2.57
441 476 3.185330 CACACACTATGCAGCAGTCTAG 58.815 50.000 0.00 0.14 0.00 2.43
442 477 2.828520 ACACACTATGCAGCAGTCTAGT 59.171 45.455 0.00 0.86 0.00 2.57
443 478 3.259374 ACACACTATGCAGCAGTCTAGTT 59.741 43.478 0.00 0.00 0.00 2.24
449 484 2.964740 TGCAGCAGTCTAGTTAGCTTG 58.035 47.619 0.00 0.00 34.61 4.01
451 486 3.006859 TGCAGCAGTCTAGTTAGCTTGAA 59.993 43.478 0.00 0.00 34.61 2.69
452 497 4.187694 GCAGCAGTCTAGTTAGCTTGAAT 58.812 43.478 0.00 0.00 34.61 2.57
463 508 8.076781 TCTAGTTAGCTTGAATATAGCTTGACG 58.923 37.037 3.86 0.00 46.42 4.35
518 563 2.290367 TCTGACGCCAAGTTGACATTTG 59.710 45.455 3.87 0.00 0.00 2.32
626 694 1.793714 GCAAATCATTGTACCGCACCG 60.794 52.381 0.00 0.00 38.85 4.94
627 695 1.466950 CAAATCATTGTACCGCACCGT 59.533 47.619 0.00 0.00 0.00 4.83
637 705 4.662961 CGCACCGTCTCCACAGCA 62.663 66.667 0.00 0.00 0.00 4.41
638 706 2.046892 GCACCGTCTCCACAGCAT 60.047 61.111 0.00 0.00 0.00 3.79
697 765 2.650778 CAAAGGCCGAAGCAACCC 59.349 61.111 0.00 0.00 42.56 4.11
861 941 0.902531 GACATCCCTCGGTTCCTTCA 59.097 55.000 0.00 0.00 0.00 3.02
872 952 1.363246 GTTCCTTCACCCTTCCCTCT 58.637 55.000 0.00 0.00 0.00 3.69
905 985 0.179137 GAGTAATTTTGGCAGCCGGC 60.179 55.000 21.89 21.89 43.74 6.13
921 1001 2.110006 GCTCGATCCCTCCAAGGC 59.890 66.667 0.00 0.00 32.73 4.35
949 1029 5.048921 AGAGACTCGATACTTTGTTGAACGA 60.049 40.000 0.00 0.00 0.00 3.85
974 1054 1.431440 GCTGGTGTTGCGTTTGTGA 59.569 52.632 0.00 0.00 0.00 3.58
2167 2262 2.818132 CCATGGACGAGGAGGAGC 59.182 66.667 5.56 0.00 0.00 4.70
2404 2506 1.144496 ACGTGTAAACCGTGTGGCT 59.856 52.632 0.00 0.00 39.70 4.75
2507 2621 7.483375 GTGTTGCGTATGCTGATTTGTTATTTA 59.517 33.333 8.69 0.00 43.34 1.40
2511 2625 9.018716 TGCGTATGCTGATTTGTTATTTATTTG 57.981 29.630 8.69 0.00 43.34 2.32
2512 2626 9.019764 GCGTATGCTGATTTGTTATTTATTTGT 57.980 29.630 0.00 0.00 38.39 2.83
2588 2702 0.603707 CGGATGAGTGCTGTGTGGTT 60.604 55.000 0.00 0.00 0.00 3.67
2675 2789 4.421033 TGTACACTCTCGACTAAGCAAG 57.579 45.455 0.00 0.00 0.00 4.01
2678 2792 2.490115 ACACTCTCGACTAAGCAAGAGG 59.510 50.000 3.55 0.00 39.64 3.69
2680 2794 3.191581 CACTCTCGACTAAGCAAGAGGAA 59.808 47.826 3.55 0.00 39.64 3.36
2682 2796 4.097286 ACTCTCGACTAAGCAAGAGGAATC 59.903 45.833 3.55 0.00 39.64 2.52
2683 2797 4.017126 TCTCGACTAAGCAAGAGGAATCA 58.983 43.478 0.00 0.00 0.00 2.57
2684 2798 4.462834 TCTCGACTAAGCAAGAGGAATCAA 59.537 41.667 0.00 0.00 0.00 2.57
2685 2799 5.047306 TCTCGACTAAGCAAGAGGAATCAAA 60.047 40.000 0.00 0.00 0.00 2.69
2686 2800 5.547465 TCGACTAAGCAAGAGGAATCAAAA 58.453 37.500 0.00 0.00 0.00 2.44
2687 2801 5.995282 TCGACTAAGCAAGAGGAATCAAAAA 59.005 36.000 0.00 0.00 0.00 1.94
2758 2872 6.937436 TTGTTCTTTCTAGTTGGGACTTTC 57.063 37.500 0.00 0.00 37.33 2.62
2811 2925 3.061271 CGTTTCGTGTTTGAATTGCAAGG 60.061 43.478 4.94 0.00 37.87 3.61
2831 2945 3.256631 AGGCAAGCTGTTCAAATTAGGTG 59.743 43.478 0.00 0.00 0.00 4.00
2840 2962 5.064558 TGTTCAAATTAGGTGCGTAAAGGA 58.935 37.500 0.00 0.00 0.00 3.36
2879 3001 9.607333 AGAAGGGAAAATTAAAGAAGGAAGATT 57.393 29.630 0.00 0.00 0.00 2.40
2932 3057 2.791927 GGCAGGCCGACGAAATTC 59.208 61.111 0.00 0.00 0.00 2.17
2933 3058 2.399611 GCAGGCCGACGAAATTCG 59.600 61.111 14.35 14.35 46.93 3.34
2942 3067 4.326058 CGAAATTCGTCGCTGCAC 57.674 55.556 7.29 0.00 34.72 4.57
2943 3068 1.225745 CGAAATTCGTCGCTGCACC 60.226 57.895 7.29 0.00 34.72 5.01
2944 3069 1.866237 GAAATTCGTCGCTGCACCA 59.134 52.632 0.00 0.00 0.00 4.17
2945 3070 0.179215 GAAATTCGTCGCTGCACCAG 60.179 55.000 0.00 0.00 34.12 4.00
2946 3071 1.577328 AAATTCGTCGCTGCACCAGG 61.577 55.000 0.00 0.00 31.21 4.45
2967 3092 1.003112 TGCCACCGCCGTAGAAAAT 60.003 52.632 0.00 0.00 0.00 1.82
3009 3173 1.160137 GTCAAGACAGCGATGCCTTT 58.840 50.000 0.00 0.00 0.00 3.11
3047 3215 1.185315 CCCGGTTGCTTCATGGAAAT 58.815 50.000 0.00 0.00 0.00 2.17
3069 3237 8.515695 AAATCATCAAGCAAGATATCTGTCAA 57.484 30.769 5.86 0.00 0.00 3.18
3080 3252 7.655328 GCAAGATATCTGTCAATGTAGTTAGCT 59.345 37.037 5.86 0.00 0.00 3.32
3139 3311 5.592104 AAAAGGAAGGTCGTGTTCATTTT 57.408 34.783 11.13 11.13 40.95 1.82
3145 3317 2.948979 AGGTCGTGTTCATTTTTCAGCA 59.051 40.909 0.00 0.00 0.00 4.41
3208 3383 0.941542 CGCCGAAACTGACAAAGGAA 59.058 50.000 0.00 0.00 0.00 3.36
3237 3413 2.737376 GTTGGTGCCTCCGTCGTC 60.737 66.667 0.00 0.00 39.52 4.20
3256 3433 3.154473 TGGAAGAGGGGCCGATCG 61.154 66.667 8.51 8.51 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.120060 GGACGACAGAGACGCTAAGTTAA 60.120 47.826 0.00 0.00 0.00 2.01
66 68 2.541999 CGTGTTAGCTCGATCCTTCCTC 60.542 54.545 0.00 0.00 33.95 3.71
67 69 1.405821 CGTGTTAGCTCGATCCTTCCT 59.594 52.381 0.00 0.00 33.95 3.36
80 82 0.391263 GGCTCCTTGGGACGTGTTAG 60.391 60.000 0.00 0.00 0.00 2.34
114 119 3.308595 CGTAATGAACTTGGAGCGCATTA 59.691 43.478 11.47 0.00 32.13 1.90
117 122 1.075542 CGTAATGAACTTGGAGCGCA 58.924 50.000 11.47 0.00 0.00 6.09
118 123 1.076332 ACGTAATGAACTTGGAGCGC 58.924 50.000 0.00 0.00 0.00 5.92
119 124 3.508762 ACTACGTAATGAACTTGGAGCG 58.491 45.455 0.00 0.00 0.00 5.03
120 125 7.919621 AGTTATACTACGTAATGAACTTGGAGC 59.080 37.037 0.00 0.00 0.00 4.70
121 126 9.798994 AAGTTATACTACGTAATGAACTTGGAG 57.201 33.333 14.33 0.00 33.01 3.86
126 131 9.282247 CGTGAAAGTTATACTACGTAATGAACT 57.718 33.333 0.00 0.00 0.00 3.01
127 132 9.065871 ACGTGAAAGTTATACTACGTAATGAAC 57.934 33.333 0.00 0.00 42.14 3.18
128 133 9.064804 CACGTGAAAGTTATACTACGTAATGAA 57.935 33.333 10.90 0.00 42.06 2.57
129 134 8.450180 TCACGTGAAAGTTATACTACGTAATGA 58.550 33.333 17.62 0.00 42.06 2.57
130 135 8.605354 TCACGTGAAAGTTATACTACGTAATG 57.395 34.615 17.62 0.00 42.06 1.90
131 136 9.443283 GATCACGTGAAAGTTATACTACGTAAT 57.557 33.333 24.13 0.00 42.06 1.89
132 137 7.910162 GGATCACGTGAAAGTTATACTACGTAA 59.090 37.037 24.13 0.00 42.06 3.18
133 138 7.409697 GGATCACGTGAAAGTTATACTACGTA 58.590 38.462 24.13 0.00 42.06 3.57
144 149 1.887198 AGTCTCGGATCACGTGAAAGT 59.113 47.619 24.13 6.01 45.34 2.66
242 249 1.340502 TGACTTGACCTGCAACCACAA 60.341 47.619 0.00 0.00 31.96 3.33
299 314 0.382873 ATCGTATCGGTAGCAACGCA 59.617 50.000 6.59 0.00 35.40 5.24
357 384 7.042456 TCGATACTAGTACGTGTAGATGGAAAC 60.042 40.741 18.11 0.00 0.00 2.78
368 395 5.179045 ACCCAAATCGATACTAGTACGTG 57.821 43.478 18.11 12.24 0.00 4.49
369 396 5.841957 AACCCAAATCGATACTAGTACGT 57.158 39.130 18.11 0.00 0.00 3.57
370 397 6.197842 GTCAAACCCAAATCGATACTAGTACG 59.802 42.308 4.31 11.03 0.00 3.67
376 403 6.677913 CAAAAGTCAAACCCAAATCGATACT 58.322 36.000 0.00 0.00 0.00 2.12
377 404 5.344933 GCAAAAGTCAAACCCAAATCGATAC 59.655 40.000 0.00 0.00 0.00 2.24
378 405 5.242838 AGCAAAAGTCAAACCCAAATCGATA 59.757 36.000 0.00 0.00 0.00 2.92
379 406 4.039124 AGCAAAAGTCAAACCCAAATCGAT 59.961 37.500 0.00 0.00 0.00 3.59
380 407 3.383185 AGCAAAAGTCAAACCCAAATCGA 59.617 39.130 0.00 0.00 0.00 3.59
406 441 4.859304 AGTGTGTGGATACGTTGAGTAA 57.141 40.909 0.00 0.00 39.04 2.24
449 484 3.871594 AGTTGGCACGTCAAGCTATATTC 59.128 43.478 0.00 0.00 0.00 1.75
451 486 3.543680 AGTTGGCACGTCAAGCTATAT 57.456 42.857 0.00 0.00 0.00 0.86
452 497 3.328382 AAGTTGGCACGTCAAGCTATA 57.672 42.857 0.00 0.00 0.00 1.31
458 503 4.355437 CATGTAAAAAGTTGGCACGTCAA 58.645 39.130 0.00 0.00 0.00 3.18
463 508 4.055360 GTTCCCATGTAAAAAGTTGGCAC 58.945 43.478 0.00 0.00 0.00 5.01
518 563 2.799916 GATCGATCGTACGGCGGC 60.800 66.667 23.79 15.74 41.72 6.53
572 623 2.063541 GAGTGGTGCAGTGTTGGTGC 62.064 60.000 0.00 0.00 41.59 5.01
626 694 3.503363 GCGGCATGCTGTGGAGAC 61.503 66.667 26.79 6.10 41.73 3.36
688 756 1.079057 GGAGACGAGGGGTTGCTTC 60.079 63.158 0.00 0.00 0.00 3.86
697 765 1.215647 CCGAGGTTTGGAGACGAGG 59.784 63.158 0.00 0.00 0.00 4.63
701 769 2.434359 CGGCCGAGGTTTGGAGAC 60.434 66.667 24.07 0.00 0.00 3.36
861 941 0.691332 GAAACCGAAGAGGGAAGGGT 59.309 55.000 0.00 0.00 46.96 4.34
905 985 2.825264 GGCCTTGGAGGGATCGAG 59.175 66.667 0.00 0.00 35.37 4.04
912 992 3.393970 TCTCTGCGGCCTTGGAGG 61.394 66.667 0.00 0.00 38.80 4.30
921 1001 2.159366 ACAAAGTATCGAGTCTCTGCGG 60.159 50.000 0.00 0.00 0.00 5.69
949 1029 2.672996 GCAACACCAGCCACCGAT 60.673 61.111 0.00 0.00 0.00 4.18
1221 1304 0.824595 TGACGAACGACCCAAGGAGA 60.825 55.000 0.14 0.00 0.00 3.71
1332 1415 3.984200 GAACCCGGCGAACTCTCGG 62.984 68.421 9.30 0.49 45.55 4.63
1335 1418 2.920912 TGGAACCCGGCGAACTCT 60.921 61.111 9.30 0.00 0.00 3.24
1677 1766 2.600769 ACCGACTCGAGGCACCTT 60.601 61.111 20.47 0.00 0.00 3.50
1740 1829 3.345808 GTGAAAGCCAGCGCGTCA 61.346 61.111 8.43 0.00 41.18 4.35
2507 2621 7.264373 TGGACAAACAAACAAACAAACAAAT 57.736 28.000 0.00 0.00 0.00 2.32
2511 2625 7.114106 CCAAAATGGACAAACAAACAAACAAAC 59.886 33.333 0.00 0.00 40.96 2.93
2512 2626 7.141363 CCAAAATGGACAAACAAACAAACAAA 58.859 30.769 0.00 0.00 40.96 2.83
2513 2627 6.263168 ACCAAAATGGACAAACAAACAAACAA 59.737 30.769 2.85 0.00 40.96 2.83
2514 2628 5.765182 ACCAAAATGGACAAACAAACAAACA 59.235 32.000 2.85 0.00 40.96 2.83
2515 2629 6.082984 CACCAAAATGGACAAACAAACAAAC 58.917 36.000 2.85 0.00 40.96 2.93
2555 2669 0.392863 CATCCGTCAACATCCCAGCA 60.393 55.000 0.00 0.00 0.00 4.41
2588 2702 0.250553 GGACCACCGACCAAATCACA 60.251 55.000 0.00 0.00 0.00 3.58
2625 2739 2.603473 CAGTCTCACCGGTCCCCA 60.603 66.667 2.59 0.00 0.00 4.96
2626 2740 2.283676 TCAGTCTCACCGGTCCCC 60.284 66.667 2.59 0.00 0.00 4.81
2630 2744 0.609681 GACCTCTCAGTCTCACCGGT 60.610 60.000 0.00 0.00 33.79 5.28
2631 2745 1.649390 CGACCTCTCAGTCTCACCGG 61.649 65.000 0.00 0.00 34.46 5.28
2725 2839 9.971922 CCAACTAGAAAGAACAATTCTGATTTT 57.028 29.630 0.00 0.00 40.59 1.82
2726 2840 8.579863 CCCAACTAGAAAGAACAATTCTGATTT 58.420 33.333 0.00 0.00 40.59 2.17
2727 2841 7.944554 TCCCAACTAGAAAGAACAATTCTGATT 59.055 33.333 0.00 0.00 40.59 2.57
2728 2842 7.391833 GTCCCAACTAGAAAGAACAATTCTGAT 59.608 37.037 0.00 0.00 40.59 2.90
2729 2843 6.710744 GTCCCAACTAGAAAGAACAATTCTGA 59.289 38.462 0.00 0.00 40.59 3.27
2730 2844 6.712547 AGTCCCAACTAGAAAGAACAATTCTG 59.287 38.462 0.00 0.00 37.67 3.02
2731 2845 6.842676 AGTCCCAACTAGAAAGAACAATTCT 58.157 36.000 0.00 0.00 40.18 2.40
2732 2846 7.511959 AAGTCCCAACTAGAAAGAACAATTC 57.488 36.000 0.00 0.00 33.48 2.17
2733 2847 7.255139 CGAAAGTCCCAACTAGAAAGAACAATT 60.255 37.037 0.00 0.00 33.48 2.32
2734 2848 6.204882 CGAAAGTCCCAACTAGAAAGAACAAT 59.795 38.462 0.00 0.00 33.48 2.71
2735 2849 5.526111 CGAAAGTCCCAACTAGAAAGAACAA 59.474 40.000 0.00 0.00 33.48 2.83
2736 2850 5.054477 CGAAAGTCCCAACTAGAAAGAACA 58.946 41.667 0.00 0.00 33.48 3.18
2758 2872 1.289109 AAACGCCGTTCACATCTCCG 61.289 55.000 1.60 0.00 0.00 4.63
2811 2925 2.989166 GCACCTAATTTGAACAGCTTGC 59.011 45.455 0.00 0.00 0.00 4.01
2831 2945 1.985684 GCACAAGCAAATCCTTTACGC 59.014 47.619 0.00 0.00 41.58 4.42
2840 2962 0.883833 CCCTTCTCGCACAAGCAAAT 59.116 50.000 0.00 0.00 42.27 2.32
2879 3001 6.355747 AGAAATGATCCAAAGCAAACCAAAA 58.644 32.000 0.00 0.00 0.00 2.44
2881 3003 5.549742 AGAAATGATCCAAAGCAAACCAA 57.450 34.783 0.00 0.00 0.00 3.67
2882 3004 5.549742 AAGAAATGATCCAAAGCAAACCA 57.450 34.783 0.00 0.00 0.00 3.67
2887 3009 3.614630 CGGCAAAGAAATGATCCAAAGCA 60.615 43.478 0.00 0.00 0.00 3.91
2925 3050 1.225745 GGTGCAGCGACGAATTTCG 60.226 57.895 16.84 16.84 46.93 3.46
2926 3051 0.179215 CTGGTGCAGCGACGAATTTC 60.179 55.000 11.91 0.00 0.00 2.17
2927 3052 1.577328 CCTGGTGCAGCGACGAATTT 61.577 55.000 11.91 0.00 0.00 1.82
2928 3053 2.034879 CCTGGTGCAGCGACGAATT 61.035 57.895 11.91 0.00 0.00 2.17
2929 3054 2.434884 CCTGGTGCAGCGACGAAT 60.435 61.111 11.91 0.00 0.00 3.34
2947 3072 3.599285 TTTCTACGGCGGTGGCAGG 62.599 63.158 13.24 0.00 42.47 4.85
2948 3073 1.024579 ATTTTCTACGGCGGTGGCAG 61.025 55.000 13.24 0.00 42.47 4.85
2949 3074 1.003112 ATTTTCTACGGCGGTGGCA 60.003 52.632 13.24 0.00 42.47 4.92
2950 3075 1.427819 CATTTTCTACGGCGGTGGC 59.572 57.895 13.24 0.00 38.90 5.01
2967 3092 2.136298 TGAAAGTTTCACAGGCACCA 57.864 45.000 14.35 0.00 34.08 4.17
3009 3173 6.364701 ACCGGGAATTAATTCATCTGAATCA 58.635 36.000 25.55 0.00 43.41 2.57
3047 3215 7.052248 ACATTGACAGATATCTTGCTTGATGA 58.948 34.615 1.33 0.00 0.00 2.92
3055 3223 8.976471 CAGCTAACTACATTGACAGATATCTTG 58.024 37.037 1.33 0.95 0.00 3.02
3069 3237 0.981277 ACCCGGCCAGCTAACTACAT 60.981 55.000 2.24 0.00 0.00 2.29
3139 3311 0.587768 CGTTGCATGTCACTGCTGAA 59.412 50.000 0.00 0.00 42.75 3.02
3145 3317 0.588252 GCACTTCGTTGCATGTCACT 59.412 50.000 0.00 0.00 42.49 3.41
3208 3383 0.734889 GCACCAACGATAGCAGCATT 59.265 50.000 0.00 0.00 42.67 3.56
3237 3413 3.447025 GATCGGCCCCTCTTCCACG 62.447 68.421 0.00 0.00 0.00 4.94
3256 3433 1.580704 CGCACGTACGGTACTCATTTC 59.419 52.381 21.06 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.