Multiple sequence alignment - TraesCS3A01G096500

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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 TraesCS3A01G096500 chr3A 100.000 5470 0 0 1 5470 61449881 61444412 0.000000e+00 10102
1 TraesCS3A01G096500 chr3A 85.616 146 18 3 4645 4789 61349655 61349512 3.410000e-32 150
2 TraesCS3A01G096500 chr3D 93.146 5019 178 69 560 5470 48963061 48958101 0.000000e+00 7210
3 TraesCS3A01G096500 chr3D 85.940 569 45 10 1 566 48964226 48963690 4.750000e-160 575
4 TraesCS3A01G096500 chr3B 93.946 3221 145 26 2265 5470 78548315 78545130 0.000000e+00 4822
5 TraesCS3A01G096500 chr3B 92.718 1744 79 19 560 2279 78551238 78549519 0.000000e+00 2473
6 TraesCS3A01G096500 chr3B 81.435 474 59 16 96 566 78567648 78567201 1.450000e-95 361


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 TraesCS3A01G096500 chr3A 61444412 61449881 5469 True 10102.0 10102 100.000 1 5470 1 chr3A.!!$R2 5469
1 TraesCS3A01G096500 chr3D 48958101 48964226 6125 True 3892.5 7210 89.543 1 5470 2 chr3D.!!$R1 5469
2 TraesCS3A01G096500 chr3B 78545130 78551238 6108 True 3647.5 4822 93.332 560 5470 2 chr3B.!!$R2 4910

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
136 140 0.174845 TCCCAATCATCGTCGGTGTC 59.825 55.000 5.22 0.0 0.00 3.67 F
408 412 0.250553 TGGTTTGTAGAGGCGGTTGG 60.251 55.000 0.00 0.0 0.00 3.77 F
409 413 0.250597 GGTTTGTAGAGGCGGTTGGT 60.251 55.000 0.00 0.0 0.00 3.67 F
413 417 0.470766 TGTAGAGGCGGTTGGTTTGT 59.529 50.000 0.00 0.0 0.00 2.83 F
812 1458 0.901580 CCAAATCCTGCAGCCCAACT 60.902 55.000 8.66 0.0 0.00 3.16 F
2363 4288 1.203052 CAATGCGCAGGAAAGAATGGT 59.797 47.619 18.32 0.0 0.00 3.55 F
2969 4912 0.254178 TGAATGGCCCAGAGAGCTTC 59.746 55.000 0.00 0.0 0.00 3.86 F
3726 5676 0.107508 AATGGACACAGCGGGATCTG 60.108 55.000 0.00 0.0 39.86 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1978 1.553690 GGTAGCACTTGGGGAGCAGA 61.554 60.000 0.00 0.0 0.00 4.26 R
2363 4288 2.040545 ACCCACCAATATCCAAACGACA 59.959 45.455 0.00 0.0 0.00 4.35 R
2438 4363 5.428184 TCTTTCTCCTCAGAATTCCCTTC 57.572 43.478 0.65 0.0 38.50 3.46 R
2643 4575 9.211485 CTGGATCAAAATAATTTGTTGCTTTCT 57.789 29.630 3.27 0.0 45.02 2.52 R
2662 4594 3.030291 ACCAAGTTTGTTTGCTGGATCA 58.970 40.909 0.00 0.0 0.00 2.92 R
3633 5583 0.390078 CGTGTGGCAATACCGTACCA 60.390 55.000 0.00 0.0 43.94 3.25 R
4417 6399 0.681733 TGACACTGAAGGACCAGAGC 59.318 55.000 0.00 0.0 37.59 4.09 R
4982 6968 0.821711 TTTCTCACCTTTGTGCCGGG 60.822 55.000 2.18 0.0 42.46 5.73 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
46 48 2.834574 TTATTATGTTGGCGCAACGG 57.165 45.000 10.83 0.00 46.13 4.44
91 95 2.876219 GACCTCCTCCACGTCGTC 59.124 66.667 0.00 0.00 0.00 4.20
92 96 1.674980 GACCTCCTCCACGTCGTCT 60.675 63.158 0.00 0.00 0.00 4.18
93 97 1.924320 GACCTCCTCCACGTCGTCTG 61.924 65.000 0.00 0.00 0.00 3.51
94 98 2.701780 CCTCCTCCACGTCGTCTGG 61.702 68.421 0.00 0.00 0.00 3.86
95 99 3.343788 CTCCTCCACGTCGTCTGGC 62.344 68.421 0.00 0.00 0.00 4.85
96 100 3.374402 CCTCCACGTCGTCTGGCT 61.374 66.667 0.00 0.00 0.00 4.75
97 101 2.179517 CTCCACGTCGTCTGGCTC 59.820 66.667 0.00 0.00 0.00 4.70
98 102 3.343788 CTCCACGTCGTCTGGCTCC 62.344 68.421 0.00 0.00 0.00 4.70
99 103 3.680786 CCACGTCGTCTGGCTCCA 61.681 66.667 0.00 0.00 0.00 3.86
100 104 2.573869 CACGTCGTCTGGCTCCAT 59.426 61.111 0.00 0.00 0.00 3.41
101 105 1.807165 CACGTCGTCTGGCTCCATG 60.807 63.158 0.00 0.00 0.00 3.66
102 106 2.276116 ACGTCGTCTGGCTCCATGT 61.276 57.895 0.00 0.00 0.00 3.21
103 107 1.517257 CGTCGTCTGGCTCCATGTC 60.517 63.158 0.00 0.00 0.00 3.06
104 108 1.591703 GTCGTCTGGCTCCATGTCA 59.408 57.895 0.00 0.00 0.00 3.58
105 109 0.176680 GTCGTCTGGCTCCATGTCAT 59.823 55.000 0.00 0.00 0.00 3.06
110 114 0.393944 CTGGCTCCATGTCATGCAGT 60.394 55.000 7.35 0.00 0.00 4.40
125 129 2.113860 GCAGTAGCAACTCCCAATCA 57.886 50.000 0.00 0.00 41.58 2.57
132 136 1.290203 CAACTCCCAATCATCGTCGG 58.710 55.000 0.00 0.00 0.00 4.79
136 140 0.174845 TCCCAATCATCGTCGGTGTC 59.825 55.000 5.22 0.00 0.00 3.67
144 148 2.573341 ATCGTCGGTGTCGTACGCTG 62.573 60.000 11.24 1.82 38.64 5.18
150 154 1.200839 GTGTCGTACGCTGTGTTGC 59.799 57.895 11.24 0.00 0.00 4.17
151 155 1.952133 TGTCGTACGCTGTGTTGCC 60.952 57.895 11.24 0.00 0.00 4.52
157 161 2.957484 TACGCTGTGTTGCCGTCGTT 62.957 55.000 0.00 0.00 0.00 3.85
158 162 2.052237 GCTGTGTTGCCGTCGTTG 60.052 61.111 0.00 0.00 0.00 4.10
173 177 0.447406 CGTTGCTTGCCATTGATCGA 59.553 50.000 0.00 0.00 0.00 3.59
176 180 2.919229 GTTGCTTGCCATTGATCGAAAG 59.081 45.455 0.00 0.00 0.00 2.62
183 187 1.490490 CCATTGATCGAAAGGGGAGGA 59.510 52.381 0.00 0.00 0.00 3.71
204 208 1.268899 GACGGTGAAAGGAGAAGACGA 59.731 52.381 0.00 0.00 0.00 4.20
263 267 1.762957 AGTTCGTATGGAGTGGGGATG 59.237 52.381 0.00 0.00 0.00 3.51
271 275 1.274126 TGGAGTGGGGATGTATGTGGA 60.274 52.381 0.00 0.00 0.00 4.02
274 278 1.213296 GTGGGGATGTATGTGGAGGT 58.787 55.000 0.00 0.00 0.00 3.85
305 309 4.487412 GTAGGCCGGTCCGACGTG 62.487 72.222 14.39 0.00 40.77 4.49
368 372 2.860817 TAGGCTAGGCTTGAAGGGTA 57.139 50.000 25.37 0.00 0.00 3.69
383 387 1.803289 GGTACCAGTCCGTACGTCC 59.197 63.158 15.21 3.83 39.65 4.79
384 388 0.960364 GGTACCAGTCCGTACGTCCA 60.960 60.000 15.21 0.00 39.65 4.02
385 389 1.098050 GTACCAGTCCGTACGTCCAT 58.902 55.000 15.21 0.00 30.03 3.41
405 409 1.003718 GCTGGTTTGTAGAGGCGGT 60.004 57.895 0.00 0.00 0.00 5.68
406 410 0.605589 GCTGGTTTGTAGAGGCGGTT 60.606 55.000 0.00 0.00 0.00 4.44
407 411 1.156736 CTGGTTTGTAGAGGCGGTTG 58.843 55.000 0.00 0.00 0.00 3.77
408 412 0.250553 TGGTTTGTAGAGGCGGTTGG 60.251 55.000 0.00 0.00 0.00 3.77
409 413 0.250597 GGTTTGTAGAGGCGGTTGGT 60.251 55.000 0.00 0.00 0.00 3.67
410 414 1.601166 GTTTGTAGAGGCGGTTGGTT 58.399 50.000 0.00 0.00 0.00 3.67
411 415 1.951602 GTTTGTAGAGGCGGTTGGTTT 59.048 47.619 0.00 0.00 0.00 3.27
412 416 1.600023 TTGTAGAGGCGGTTGGTTTG 58.400 50.000 0.00 0.00 0.00 2.93
413 417 0.470766 TGTAGAGGCGGTTGGTTTGT 59.529 50.000 0.00 0.00 0.00 2.83
414 418 1.693062 TGTAGAGGCGGTTGGTTTGTA 59.307 47.619 0.00 0.00 0.00 2.41
415 419 2.104451 TGTAGAGGCGGTTGGTTTGTAA 59.896 45.455 0.00 0.00 0.00 2.41
416 420 2.351706 AGAGGCGGTTGGTTTGTAAA 57.648 45.000 0.00 0.00 0.00 2.01
417 421 2.227194 AGAGGCGGTTGGTTTGTAAAG 58.773 47.619 0.00 0.00 0.00 1.85
418 422 2.158726 AGAGGCGGTTGGTTTGTAAAGA 60.159 45.455 0.00 0.00 0.00 2.52
425 429 3.702548 GGTTGGTTTGTAAAGACTGGGTT 59.297 43.478 0.00 0.00 0.00 4.11
463 467 3.036783 CTGACCGAGTCGTCCGTCC 62.037 68.421 12.31 0.00 34.95 4.79
469 473 1.773054 CGAGTCGTCCGTCCGATCAT 61.773 60.000 3.82 0.00 39.34 2.45
475 479 1.588404 CGTCCGTCCGATCATTTTGAG 59.412 52.381 0.00 0.00 0.00 3.02
492 496 1.214673 TGAGGAGTATGGCCGTAGAGT 59.785 52.381 4.44 0.00 0.00 3.24
517 521 6.537301 TCGGTGAATTACATAAGATGGTTGAC 59.463 38.462 0.00 0.00 33.60 3.18
529 533 1.254026 TGGTTGACGTAGAGGTGGAG 58.746 55.000 0.00 0.00 0.00 3.86
801 1447 2.075355 TTGCCCGGTGTCCAAATCCT 62.075 55.000 0.00 0.00 0.00 3.24
812 1458 0.901580 CCAAATCCTGCAGCCCAACT 60.902 55.000 8.66 0.00 0.00 3.16
873 1521 1.377333 CCGCCTCCTCCACCTTTTC 60.377 63.158 0.00 0.00 0.00 2.29
939 1587 2.282039 CGGATTGCCCAGCCCAAAA 61.282 57.895 0.00 0.00 34.14 2.44
982 1634 4.322385 GTTCCCACCGCAACACGC 62.322 66.667 0.00 0.00 41.76 5.34
1152 1807 3.138798 GTCTCCGGCTCCGTGCTA 61.139 66.667 7.59 0.00 42.39 3.49
1877 2554 5.903923 AGGGGAATTTGACTATTTTCACCT 58.096 37.500 0.00 0.00 45.10 4.00
1889 2566 6.342111 ACTATTTTCACCTAACAGCTAGCTC 58.658 40.000 16.15 0.00 0.00 4.09
1897 2574 3.830679 ACAGCTAGCTCTGTTCTGC 57.169 52.632 16.15 0.00 44.26 4.26
1996 2675 2.101640 ATGCCCAAACCCAAAGAGTT 57.898 45.000 0.00 0.00 0.00 3.01
1999 2678 2.312390 GCCCAAACCCAAAGAGTTGTA 58.688 47.619 0.00 0.00 32.40 2.41
2004 2683 5.595133 CCCAAACCCAAAGAGTTGTACTTTA 59.405 40.000 0.00 0.00 36.09 1.85
2025 2704 4.729227 ATCGTTTGGGTTGTCAAAAACT 57.271 36.364 8.84 0.00 38.21 2.66
2072 2751 3.237268 ACTTTTGACCCAGCATTGGTA 57.763 42.857 0.00 0.00 43.40 3.25
2092 2771 9.825109 ATTGGTAACTTCTTCTCTAGCTATTTC 57.175 33.333 0.00 0.00 37.61 2.17
2168 2863 4.261363 GGCTATGCAGAGCAGGAAATAAAC 60.261 45.833 32.34 9.21 43.65 2.01
2183 2883 7.449086 CAGGAAATAAACCCTACAAAGTTACCA 59.551 37.037 0.00 0.00 0.00 3.25
2185 2885 8.248253 GGAAATAAACCCTACAAAGTTACCATG 58.752 37.037 0.00 0.00 0.00 3.66
2280 4199 4.577687 ACACACATTATCGCGTTAACAG 57.422 40.909 11.57 9.93 0.00 3.16
2363 4288 1.203052 CAATGCGCAGGAAAGAATGGT 59.797 47.619 18.32 0.00 0.00 3.55
2378 4303 5.818136 AGAATGGTGTCGTTTGGATATTG 57.182 39.130 0.00 0.00 0.00 1.90
2438 4363 3.672767 ATTGCTTTTCTGGCTTGGAAG 57.327 42.857 0.00 0.00 0.00 3.46
2488 4413 7.120285 ACAGTCAAAATCATTCATAGGTCAGTG 59.880 37.037 0.00 0.00 0.00 3.66
2614 4546 3.323115 TCTCTGTCAGAATTGCACAGTCT 59.677 43.478 3.67 0.00 38.94 3.24
2704 4636 2.032681 GGGAGCAACGGAGCTGTT 59.967 61.111 8.66 0.00 46.75 3.16
2969 4912 0.254178 TGAATGGCCCAGAGAGCTTC 59.746 55.000 0.00 0.00 0.00 3.86
3051 4994 2.916716 GCTTGATGCCACACGTTAAATG 59.083 45.455 0.00 0.00 35.15 2.32
3053 4996 4.545610 CTTGATGCCACACGTTAAATGTT 58.454 39.130 0.00 0.00 0.00 2.71
3060 5003 4.496673 GCCACACGTTAAATGTTCACTTCA 60.497 41.667 0.00 0.00 0.00 3.02
3063 5006 6.255215 CACACGTTAAATGTTCACTTCAACT 58.745 36.000 0.00 0.00 0.00 3.16
3072 5015 8.560576 AAATGTTCACTTCAACTGTATTTTCG 57.439 30.769 0.00 0.00 0.00 3.46
3073 5016 6.055231 TGTTCACTTCAACTGTATTTTCGG 57.945 37.500 0.00 0.00 0.00 4.30
3075 5018 6.094325 TGTTCACTTCAACTGTATTTTCGGTT 59.906 34.615 0.00 0.00 37.39 4.44
3081 5024 9.673454 ACTTCAACTGTATTTTCGGTTATTTTC 57.327 29.630 0.00 0.00 35.48 2.29
3082 5025 9.124807 CTTCAACTGTATTTTCGGTTATTTTCC 57.875 33.333 0.00 0.00 35.48 3.13
3085 5028 8.911662 CAACTGTATTTTCGGTTATTTTCCTTG 58.088 33.333 0.00 0.00 35.48 3.61
3086 5029 8.398878 ACTGTATTTTCGGTTATTTTCCTTGA 57.601 30.769 0.00 0.00 0.00 3.02
3087 5030 9.020731 ACTGTATTTTCGGTTATTTTCCTTGAT 57.979 29.630 0.00 0.00 0.00 2.57
3154 5099 5.178797 CAAGGGTATAGTTGTCTGGTTGAG 58.821 45.833 0.00 0.00 0.00 3.02
3176 5121 4.341806 AGTCTTGTTGAATTTGCATGACCA 59.658 37.500 0.00 0.00 37.75 4.02
3195 5140 9.759473 CATGACCATATTATCCTATCCCTTTTT 57.241 33.333 0.00 0.00 0.00 1.94
3227 5172 8.863872 TTAATATTAAAGCTCTAGAATGGCCC 57.136 34.615 5.41 0.00 0.00 5.80
3243 5188 2.066393 CCCGCCCTTCTCCATCTCA 61.066 63.158 0.00 0.00 0.00 3.27
3244 5189 1.414061 CCCGCCCTTCTCCATCTCAT 61.414 60.000 0.00 0.00 0.00 2.90
3275 5220 4.858850 TGGAATGATTAGGAATGCAGTGT 58.141 39.130 0.00 0.00 0.00 3.55
3612 5557 2.436417 GCTGGAACATTGTAAGCTCCA 58.564 47.619 7.53 7.53 38.20 3.86
3633 5583 9.822185 GCTCCATTTTTCATATTCTTAACCATT 57.178 29.630 0.00 0.00 0.00 3.16
3640 5590 7.795482 TTCATATTCTTAACCATTGGTACGG 57.205 36.000 9.20 2.36 33.12 4.02
3668 5618 0.373716 CACGATTCTTAACCAGCGGC 59.626 55.000 0.00 0.00 0.00 6.53
3688 5638 1.730121 CGTTGCAGTTGCCACATGATC 60.730 52.381 0.00 0.00 41.18 2.92
3724 5674 1.154205 CGAATGGACACAGCGGGATC 61.154 60.000 0.00 0.00 0.00 3.36
3726 5676 0.107508 AATGGACACAGCGGGATCTG 60.108 55.000 0.00 0.00 39.86 2.90
4255 6237 0.321387 CAGATCGGGCTGCTATGCAT 60.321 55.000 3.79 3.79 38.13 3.96
4488 6470 9.232473 GAAGATAACCCTAAACATCTGTTTTCT 57.768 33.333 13.06 6.00 45.07 2.52
4534 6517 4.613850 GCGAAGAATCTGTGTTTTTCCTCC 60.614 45.833 0.00 0.00 0.00 4.30
4740 6726 2.830104 TCATGTCAGCATCAGGATTCG 58.170 47.619 0.00 0.00 31.99 3.34
4821 6807 3.120095 GCATTTAAAACGGTCTTACGGCT 60.120 43.478 0.00 0.00 38.39 5.52
4864 6850 5.310409 AGAGGAAGGAAATGACACAGAAA 57.690 39.130 0.00 0.00 0.00 2.52
4885 6871 0.546267 AAAGAGAGGGCAGAGGAGCA 60.546 55.000 0.00 0.00 35.83 4.26
4946 6932 2.136298 TTCCACCAGCACAAGAAACA 57.864 45.000 0.00 0.00 0.00 2.83
5011 6997 4.334481 ACAAAGGTGAGAAACAGGTTAACG 59.666 41.667 0.00 0.00 0.00 3.18
5063 7049 3.661648 AGGGCCGCACTGGGAATT 61.662 61.111 0.00 0.00 38.63 2.17
5122 7108 0.546122 TGAGAAGGCGGGTATTGCAT 59.454 50.000 0.00 0.00 0.00 3.96
5182 7168 4.461431 AGGAAAATACCTTAAACTTGGCCG 59.539 41.667 0.00 0.00 36.86 6.13
5347 7336 3.806949 AGCTTAATTTGGGGAGACACA 57.193 42.857 0.00 0.00 46.89 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 95 2.405143 CTGCATGACATGGAGCCAG 58.595 57.895 22.00 13.64 41.79 4.85
92 96 4.649845 CTGCATGACATGGAGCCA 57.350 55.556 22.00 8.38 41.79 4.75
110 114 2.481276 CGACGATGATTGGGAGTTGCTA 60.481 50.000 0.00 0.00 0.00 3.49
121 125 1.530441 CGTACGACACCGACGATGATT 60.530 52.381 10.44 0.00 39.67 2.57
125 129 2.099062 GCGTACGACACCGACGAT 59.901 61.111 21.65 0.00 39.67 3.73
132 136 1.200839 GCAACACAGCGTACGACAC 59.799 57.895 21.65 0.54 0.00 3.67
136 140 2.995450 GACGGCAACACAGCGTACG 61.995 63.158 11.84 11.84 34.64 3.67
144 148 1.654137 CAAGCAACGACGGCAACAC 60.654 57.895 0.00 0.00 0.00 3.32
150 154 1.442520 CAATGGCAAGCAACGACGG 60.443 57.895 0.00 0.00 0.00 4.79
151 155 0.168788 ATCAATGGCAAGCAACGACG 59.831 50.000 0.00 0.00 0.00 5.12
157 161 1.473677 CCTTTCGATCAATGGCAAGCA 59.526 47.619 0.00 0.00 0.00 3.91
158 162 1.202336 CCCTTTCGATCAATGGCAAGC 60.202 52.381 0.00 0.00 0.00 4.01
173 177 0.473117 TTCACCGTCTCCTCCCCTTT 60.473 55.000 0.00 0.00 0.00 3.11
176 180 1.597461 CTTTCACCGTCTCCTCCCC 59.403 63.158 0.00 0.00 0.00 4.81
183 187 1.269998 CGTCTTCTCCTTTCACCGTCT 59.730 52.381 0.00 0.00 0.00 4.18
204 208 2.896685 CTCACTCCACTCCACTTCTCTT 59.103 50.000 0.00 0.00 0.00 2.85
263 267 0.541863 CCCACCTCACCTCCACATAC 59.458 60.000 0.00 0.00 0.00 2.39
274 278 2.285368 CTACCCTGGCCCACCTCA 60.285 66.667 0.00 0.00 36.63 3.86
333 337 5.189934 CCTAGCCTAAATCTAGGTATTGGGG 59.810 48.000 7.69 0.00 45.96 4.96
358 362 0.974383 ACGGACTGGTACCCTTCAAG 59.026 55.000 10.07 1.61 0.00 3.02
368 372 1.601419 CCATGGACGTACGGACTGGT 61.601 60.000 21.06 0.00 0.00 4.00
371 375 1.681327 AGCCATGGACGTACGGACT 60.681 57.895 18.40 0.00 0.00 3.85
383 387 1.098050 GCCTCTACAAACCAGCCATG 58.902 55.000 0.00 0.00 0.00 3.66
384 388 0.392998 CGCCTCTACAAACCAGCCAT 60.393 55.000 0.00 0.00 0.00 4.40
385 389 1.003839 CGCCTCTACAAACCAGCCA 60.004 57.895 0.00 0.00 0.00 4.75
405 409 4.575645 CGTAACCCAGTCTTTACAAACCAA 59.424 41.667 0.00 0.00 0.00 3.67
406 410 4.128643 CGTAACCCAGTCTTTACAAACCA 58.871 43.478 0.00 0.00 0.00 3.67
407 411 3.499537 CCGTAACCCAGTCTTTACAAACC 59.500 47.826 0.00 0.00 0.00 3.27
408 412 4.129380 ACCGTAACCCAGTCTTTACAAAC 58.871 43.478 0.00 0.00 0.00 2.93
409 413 4.420522 ACCGTAACCCAGTCTTTACAAA 57.579 40.909 0.00 0.00 0.00 2.83
410 414 4.420522 AACCGTAACCCAGTCTTTACAA 57.579 40.909 0.00 0.00 0.00 2.41
411 415 4.420522 AAACCGTAACCCAGTCTTTACA 57.579 40.909 0.00 0.00 0.00 2.41
412 416 4.576053 ACAAAACCGTAACCCAGTCTTTAC 59.424 41.667 0.00 0.00 0.00 2.01
413 417 4.575645 CACAAAACCGTAACCCAGTCTTTA 59.424 41.667 0.00 0.00 0.00 1.85
414 418 3.379057 CACAAAACCGTAACCCAGTCTTT 59.621 43.478 0.00 0.00 0.00 2.52
415 419 2.946990 CACAAAACCGTAACCCAGTCTT 59.053 45.455 0.00 0.00 0.00 3.01
416 420 2.171027 TCACAAAACCGTAACCCAGTCT 59.829 45.455 0.00 0.00 0.00 3.24
417 421 2.288729 GTCACAAAACCGTAACCCAGTC 59.711 50.000 0.00 0.00 0.00 3.51
418 422 2.291365 GTCACAAAACCGTAACCCAGT 58.709 47.619 0.00 0.00 0.00 4.00
443 447 2.176055 CGGACGACTCGGTCAGTG 59.824 66.667 2.98 0.00 38.70 3.66
463 467 3.499918 GGCCATACTCCTCAAAATGATCG 59.500 47.826 0.00 0.00 0.00 3.69
469 473 3.101437 TCTACGGCCATACTCCTCAAAA 58.899 45.455 2.24 0.00 0.00 2.44
475 479 0.592148 CGACTCTACGGCCATACTCC 59.408 60.000 2.24 0.00 0.00 3.85
492 496 6.537301 GTCAACCATCTTATGTAATTCACCGA 59.463 38.462 0.00 0.00 0.00 4.69
503 507 5.043903 CACCTCTACGTCAACCATCTTATG 58.956 45.833 0.00 0.00 0.00 1.90
517 521 3.586892 GAAAAAGACCTCCACCTCTACG 58.413 50.000 0.00 0.00 0.00 3.51
556 560 8.945057 CCTTAATCCACCCACATTTTATTTTTG 58.055 33.333 0.00 0.00 0.00 2.44
558 562 7.629157 CCCTTAATCCACCCACATTTTATTTT 58.371 34.615 0.00 0.00 0.00 1.82
560 564 5.130311 GCCCTTAATCCACCCACATTTTATT 59.870 40.000 0.00 0.00 0.00 1.40
778 1424 2.969300 TTTGGACACCGGGCAAGACC 62.969 60.000 6.32 3.16 37.93 3.85
788 1434 1.598701 GGCTGCAGGATTTGGACACC 61.599 60.000 17.12 0.00 0.00 4.16
801 1447 0.251165 GGGAAGTTAGTTGGGCTGCA 60.251 55.000 0.50 0.00 0.00 4.41
812 1458 1.676615 GGCGAATGGAACGGGAAGTTA 60.677 52.381 0.00 0.00 44.35 2.24
873 1521 3.375922 ACGGGTCTAATGTAAATTTGCCG 59.624 43.478 0.00 0.00 0.00 5.69
926 1574 2.841988 GTGGTTTTGGGCTGGGCA 60.842 61.111 0.00 0.00 0.00 5.36
929 1577 2.123077 TGGGTGGTTTTGGGCTGG 60.123 61.111 0.00 0.00 0.00 4.85
939 1587 0.252558 CTAGGTAGGTGGTGGGTGGT 60.253 60.000 0.00 0.00 0.00 4.16
1149 1804 1.956620 GCACGAAGTTGTCCGCTAGC 61.957 60.000 4.06 4.06 41.61 3.42
1152 1807 2.665185 GGCACGAAGTTGTCCGCT 60.665 61.111 0.00 0.00 41.61 5.52
1323 1978 1.553690 GGTAGCACTTGGGGAGCAGA 61.554 60.000 0.00 0.00 0.00 4.26
1697 2352 3.075005 GGAGGTAGCAGCCGGTGA 61.075 66.667 1.90 0.00 0.00 4.02
1889 2566 3.293311 CCACTGAATTTGGCAGAACAG 57.707 47.619 11.77 11.77 36.86 3.16
1897 2574 3.502237 GCACTGCCACTGAATTTGG 57.498 52.632 0.00 0.00 37.17 3.28
1920 2597 6.810182 CCAGGAGCTGAAAATAGTCAAAATTG 59.190 38.462 0.00 0.00 32.44 2.32
1996 2675 5.366460 TGACAACCCAAACGATAAAGTACA 58.634 37.500 0.00 0.00 0.00 2.90
1999 2678 5.838531 TTTGACAACCCAAACGATAAAGT 57.161 34.783 0.00 0.00 31.73 2.66
2004 2683 4.429108 CAGTTTTTGACAACCCAAACGAT 58.571 39.130 7.85 0.00 35.95 3.73
2025 2704 4.036971 CCGAAACTGGTGAATTTGTAACCA 59.963 41.667 0.00 0.00 41.66 3.67
2072 2751 9.785982 AAAAGTGAAATAGCTAGAGAAGAAGTT 57.214 29.630 0.00 0.00 0.00 2.66
2092 2771 6.222389 TCATAGCCACCATTTTCAAAAAGTG 58.778 36.000 8.71 8.71 0.00 3.16
2131 2818 7.049799 TCTGCATAGCCTAAACAAAAGTTTT 57.950 32.000 0.00 0.00 0.00 2.43
2134 2821 4.156739 GCTCTGCATAGCCTAAACAAAAGT 59.843 41.667 12.87 0.00 36.45 2.66
2147 2834 4.276926 GGGTTTATTTCCTGCTCTGCATAG 59.723 45.833 0.00 0.00 38.13 2.23
2168 2863 4.647611 TCACACATGGTAACTTTGTAGGG 58.352 43.478 0.00 0.00 33.27 3.53
2280 4199 5.860941 TGTATCAGGAGGATTCAGAGAAC 57.139 43.478 0.00 0.00 37.44 3.01
2363 4288 2.040545 ACCCACCAATATCCAAACGACA 59.959 45.455 0.00 0.00 0.00 4.35
2438 4363 5.428184 TCTTTCTCCTCAGAATTCCCTTC 57.572 43.478 0.65 0.00 38.50 3.46
2643 4575 9.211485 CTGGATCAAAATAATTTGTTGCTTTCT 57.789 29.630 3.27 0.00 45.02 2.52
2662 4594 3.030291 ACCAAGTTTGTTTGCTGGATCA 58.970 40.909 0.00 0.00 0.00 2.92
2756 4699 8.708742 TCAACATATTTTCTTTCTCACACTACG 58.291 33.333 0.00 0.00 0.00 3.51
3051 4994 6.056428 ACCGAAAATACAGTTGAAGTGAAC 57.944 37.500 7.07 0.00 0.00 3.18
3053 4996 7.972832 ATAACCGAAAATACAGTTGAAGTGA 57.027 32.000 7.07 0.00 0.00 3.41
3060 5003 8.852135 TCAAGGAAAATAACCGAAAATACAGTT 58.148 29.630 0.00 0.00 0.00 3.16
3090 5033 8.156165 AGAGTTTTCCATTGATAATGCCAAAAA 58.844 29.630 9.37 7.09 37.57 1.94
3091 5034 7.678837 AGAGTTTTCCATTGATAATGCCAAAA 58.321 30.769 0.00 0.00 37.57 2.44
3092 5035 7.243604 AGAGTTTTCCATTGATAATGCCAAA 57.756 32.000 0.00 0.00 37.57 3.28
3093 5036 6.855763 AGAGTTTTCCATTGATAATGCCAA 57.144 33.333 0.00 0.00 37.57 4.52
3094 5037 6.039717 GCTAGAGTTTTCCATTGATAATGCCA 59.960 38.462 0.00 0.00 37.57 4.92
3095 5038 6.264067 AGCTAGAGTTTTCCATTGATAATGCC 59.736 38.462 0.00 0.00 37.57 4.40
3096 5039 7.269477 AGCTAGAGTTTTCCATTGATAATGC 57.731 36.000 0.00 0.00 37.57 3.56
3108 5052 7.023197 TGTACCAACAAAAGCTAGAGTTTTC 57.977 36.000 0.00 0.00 30.91 2.29
3133 5077 4.426704 ACTCAACCAGACAACTATACCCT 58.573 43.478 0.00 0.00 0.00 4.34
3154 5099 4.619973 TGGTCATGCAAATTCAACAAGAC 58.380 39.130 0.00 0.00 0.00 3.01
3200 5145 9.726438 GGCCATTCTAGAGCTTTAATATTAAGA 57.274 33.333 7.91 0.00 0.00 2.10
3201 5146 8.951243 GGGCCATTCTAGAGCTTTAATATTAAG 58.049 37.037 4.39 4.66 0.00 1.85
3204 5149 5.940470 CGGGCCATTCTAGAGCTTTAATATT 59.060 40.000 4.39 0.00 0.00 1.28
3227 5172 1.415659 AGAATGAGATGGAGAAGGGCG 59.584 52.381 0.00 0.00 0.00 6.13
3275 5220 6.590234 TGCACTGATAGAAGAGTTCAAGTA 57.410 37.500 0.00 0.00 0.00 2.24
3456 5401 3.621715 GGTGGATAATCCGTGTTTCTGAC 59.378 47.826 0.00 0.00 40.17 3.51
3633 5583 0.390078 CGTGTGGCAATACCGTACCA 60.390 55.000 0.00 0.00 43.94 3.25
3640 5590 4.393680 TGGTTAAGAATCGTGTGGCAATAC 59.606 41.667 0.00 0.00 0.00 1.89
3688 5638 5.812127 TCCATTCGACATGACAGTGAAATAG 59.188 40.000 0.00 0.00 0.00 1.73
3724 5674 3.922910 TCAGTGAGCTCAAGATCAACAG 58.077 45.455 20.19 0.90 42.53 3.16
3726 5676 6.593382 ACTTATTCAGTGAGCTCAAGATCAAC 59.407 38.462 20.19 3.82 42.53 3.18
3818 5768 5.376625 AGAACAAGAACACCATAGCTGAAA 58.623 37.500 0.00 0.00 0.00 2.69
4255 6237 2.144078 TCACCAGGGTTCGCTTGGA 61.144 57.895 0.00 0.00 35.89 3.53
4417 6399 0.681733 TGACACTGAAGGACCAGAGC 59.318 55.000 0.00 0.00 37.59 4.09
4509 6492 3.975035 GGAAAAACACAGATTCTTCGCAC 59.025 43.478 0.00 0.00 0.00 5.34
4653 6639 2.158623 AGAAACACTGCCACCTTCATCA 60.159 45.455 0.00 0.00 0.00 3.07
4841 6827 4.982241 TCTGTGTCATTTCCTTCCTCTT 57.018 40.909 0.00 0.00 0.00 2.85
4864 6850 1.004161 GCTCCTCTGCCCTCTCTTTTT 59.996 52.381 0.00 0.00 0.00 1.94
4910 6896 1.147473 GAATTTTTGCCTGGTTGCGG 58.853 50.000 0.00 0.00 0.00 5.69
4926 6912 2.362077 GTGTTTCTTGTGCTGGTGGAAT 59.638 45.455 0.00 0.00 0.00 3.01
4927 6913 1.748493 GTGTTTCTTGTGCTGGTGGAA 59.252 47.619 0.00 0.00 0.00 3.53
4946 6932 4.295119 GGTCGACCCTGCGTGTGT 62.295 66.667 24.75 0.00 0.00 3.72
4982 6968 0.821711 TTTCTCACCTTTGTGCCGGG 60.822 55.000 2.18 0.00 42.46 5.73
5003 6989 1.468736 GCCGTTCGATCTCGTTAACCT 60.469 52.381 0.00 0.00 40.80 3.50
5011 6997 1.140407 CTTCACCGCCGTTCGATCTC 61.140 60.000 0.00 0.00 41.67 2.75
5063 7049 0.895100 GCCCCTGCACTGTTCAATCA 60.895 55.000 0.00 0.00 37.47 2.57
5182 7168 4.202151 GGTGGTCATGGATTTCCTAATTGC 60.202 45.833 0.00 0.00 36.82 3.56


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

AutoCloner maintained by Alex Coulton.