Multiple sequence alignment - TraesCS6A01G070600

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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 TraesCS6A01G070600 chr6A 100.000 4373 0 0 1 4373 38471367 38475739 0.000000e+00 8076
1 TraesCS6A01G070600 chr6D 91.956 2275 107 38 655 2866 34342984 34345245 0.000000e+00 3118
2 TraesCS6A01G070600 chr6D 96.429 1092 31 5 3082 4172 34345510 34346594 0.000000e+00 1794
3 TraesCS6A01G070600 chr6D 92.788 208 13 2 2 209 34342715 34342920 2.560000e-77 300
4 TraesCS6A01G070600 chr6D 98.305 118 2 0 4256 4373 34346593 34346710 1.590000e-49 207
5 TraesCS6A01G070600 chr6D 92.366 131 8 2 2858 2987 34345267 34345396 7.470000e-43 185
6 TraesCS6A01G070600 chr6B 91.325 1487 90 27 449 1908 71039293 71040767 0.000000e+00 1995
7 TraesCS6A01G070600 chr6B 94.449 1207 44 14 2978 4172 71042014 71043209 0.000000e+00 1836
8 TraesCS6A01G070600 chr6B 97.368 950 18 5 1921 2866 71040853 71041799 0.000000e+00 1609
9 TraesCS6A01G070600 chr6B 90.361 249 21 2 102 347 71038884 71039132 1.520000e-84 324
10 TraesCS6A01G070600 chr6B 95.082 122 5 1 4253 4373 71043207 71043328 1.610000e-44 191
11 TraesCS6A01G070600 chr6B 89.855 138 11 2 2858 2993 71041821 71041957 1.620000e-39 174
12 TraesCS6A01G070600 chr6B 82.677 127 15 5 330 455 71039147 71039267 5.980000e-19 106
13 TraesCS6A01G070600 chr4B 94.565 92 5 0 4165 4256 491017635 491017726 4.560000e-30 143
14 TraesCS6A01G070600 chr4B 92.632 95 7 0 4164 4258 104337421 104337327 2.120000e-28 137
15 TraesCS6A01G070600 chr4B 91.837 98 7 1 4158 4255 82163366 82163462 7.630000e-28 135
16 TraesCS6A01G070600 chr2A 93.750 96 4 2 4171 4264 498099527 498099432 4.560000e-30 143
17 TraesCS6A01G070600 chr3D 93.617 94 4 2 4162 4255 107462628 107462719 5.900000e-29 139
18 TraesCS6A01G070600 chr1D 92.784 97 6 1 4163 4258 47644735 47644831 5.900000e-29 139
19 TraesCS6A01G070600 chr7A 94.382 89 5 0 4167 4255 126927404 126927316 2.120000e-28 137
20 TraesCS6A01G070600 chr4A 91.837 98 6 2 4166 4262 579847369 579847273 7.630000e-28 135
21 TraesCS6A01G070600 chr4A 90.196 102 8 2 4154 4255 597739981 597739882 9.870000e-27 132


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 TraesCS6A01G070600 chr6A 38471367 38475739 4372 False 8076.000000 8076 100.000000 1 4373 1 chr6A.!!$F1 4372
1 TraesCS6A01G070600 chr6D 34342715 34346710 3995 False 1120.800000 3118 94.368800 2 4373 5 chr6D.!!$F1 4371
2 TraesCS6A01G070600 chr6B 71038884 71043328 4444 False 890.714286 1995 91.588143 102 4373 7 chr6B.!!$F1 4271

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
650 721 0.179134 CACGCTCCCCTACTCTTTCG 60.179 60.000 0.00 0.00 0.0 3.46 F
988 1103 1.830408 CAGCTCCGGGGTCCTAGAG 60.830 68.421 1.62 0.00 0.0 2.43 F
1680 1818 0.402121 GGAACAAGAAGAGGGCCTGT 59.598 55.000 12.95 2.79 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1815 0.102300 TGATACCGACCGCATCACAG 59.898 55.0 0.00 0.00 0.0 3.66 R
2957 3222 0.981277 GAGTTTGATCCCGGGGAGGA 60.981 60.0 23.50 7.34 45.0 3.71 R
3527 3938 0.035739 GGTACAGTTTGAAGCCGGGA 59.964 55.0 2.18 0.00 0.0 5.14 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
32 33 4.634012 TGAACTAAGGCCACACACTTAT 57.366 40.909 5.01 0.00 0.00 1.73
42 43 6.245408 AGGCCACACACTTATTTTAGAATGA 58.755 36.000 5.01 0.00 0.00 2.57
51 52 9.668497 ACACTTATTTTAGAATGAAGGGAGTAC 57.332 33.333 0.00 0.00 0.00 2.73
111 112 8.500773 AGATGCAACTTTTATTTTTGCTTCATG 58.499 29.630 18.12 0.00 45.74 3.07
216 218 7.148171 GGCCAATCAAGATCCTATTATTGTAGC 60.148 40.741 0.00 0.00 0.00 3.58
261 263 1.380771 GTTATTGCACGAAAAACGCCG 59.619 47.619 0.00 0.00 46.94 6.46
270 272 3.300066 CACGAAAAACGCCGTTTGTTTTA 59.700 39.130 16.86 0.00 45.89 1.52
283 285 5.431309 CGTTTGTTTTAGGCAGCATTTTTC 58.569 37.500 0.00 0.00 0.00 2.29
290 292 6.616774 TTTAGGCAGCATTTTTCCTTTTTG 57.383 33.333 0.00 0.00 0.00 2.44
291 293 2.880268 AGGCAGCATTTTTCCTTTTTGC 59.120 40.909 0.00 0.00 0.00 3.68
296 300 4.448395 CAGCATTTTTCCTTTTTGCGATGA 59.552 37.500 0.00 0.00 38.32 2.92
298 302 5.050159 AGCATTTTTCCTTTTTGCGATGAAC 60.050 36.000 0.00 0.00 38.32 3.18
305 309 5.415221 TCCTTTTTGCGATGAACTGTTTTT 58.585 33.333 0.00 0.00 0.00 1.94
307 311 5.462034 TTTTTGCGATGAACTGTTTTTGG 57.538 34.783 0.00 0.00 0.00 3.28
310 314 2.159184 TGCGATGAACTGTTTTTGGCAA 60.159 40.909 0.00 0.00 0.00 4.52
314 318 2.600731 TGAACTGTTTTTGGCAACGTG 58.399 42.857 0.00 0.00 42.51 4.49
317 321 0.529555 CTGTTTTTGGCAACGTGGGG 60.530 55.000 0.00 0.00 42.51 4.96
328 332 2.751436 CGTGGGGAGCATGGTTGG 60.751 66.667 0.00 0.00 0.00 3.77
363 399 4.744795 AACCAGAGCTAGATTCAATCGT 57.255 40.909 0.00 0.00 0.00 3.73
368 404 4.505922 CAGAGCTAGATTCAATCGTGAACC 59.494 45.833 0.00 0.00 46.40 3.62
379 415 3.173240 GTGAACCGAGCGCGTCTC 61.173 66.667 17.12 17.12 38.47 3.36
388 424 4.789075 GCGCGTCTCGGCTGGTTA 62.789 66.667 8.43 0.00 38.94 2.85
398 434 1.418637 TCGGCTGGTTAGGTTTCTTGT 59.581 47.619 0.00 0.00 0.00 3.16
402 438 2.956333 GCTGGTTAGGTTTCTTGTTGGT 59.044 45.455 0.00 0.00 0.00 3.67
403 439 3.243401 GCTGGTTAGGTTTCTTGTTGGTG 60.243 47.826 0.00 0.00 0.00 4.17
404 440 3.292460 TGGTTAGGTTTCTTGTTGGTGG 58.708 45.455 0.00 0.00 0.00 4.61
405 441 3.053544 TGGTTAGGTTTCTTGTTGGTGGA 60.054 43.478 0.00 0.00 0.00 4.02
407 443 4.202080 GGTTAGGTTTCTTGTTGGTGGAAC 60.202 45.833 0.00 0.00 34.84 3.62
436 472 2.561419 CCAGGTTCAAGTTCTAGACCGA 59.439 50.000 0.00 0.00 0.00 4.69
439 475 5.450688 CCAGGTTCAAGTTCTAGACCGATAG 60.451 48.000 0.00 0.00 0.00 2.08
464 532 3.531538 CAGGGTGTGCATTTATACGAGT 58.468 45.455 0.00 0.00 0.00 4.18
468 536 4.155280 GGGTGTGCATTTATACGAGTGTTT 59.845 41.667 0.00 0.00 0.00 2.83
473 541 4.626172 TGCATTTATACGAGTGTTTGCGTA 59.374 37.500 0.00 0.00 45.57 4.42
480 548 4.835199 ACGAGTGTTTGCGTATGTATTC 57.165 40.909 0.00 0.00 39.21 1.75
482 550 4.927425 ACGAGTGTTTGCGTATGTATTCTT 59.073 37.500 0.00 0.00 39.21 2.52
484 552 6.587226 ACGAGTGTTTGCGTATGTATTCTTTA 59.413 34.615 0.00 0.00 39.21 1.85
521 591 6.942576 AGATTCATATGGAAAAACCCCGATAG 59.057 38.462 2.13 0.00 39.39 2.08
548 618 6.609616 ACTCACATTTGGAAAGAACCCTAAAA 59.390 34.615 0.00 0.00 0.00 1.52
589 659 4.855298 AGGAACAAGATTCCGGGAATTA 57.145 40.909 22.53 0.00 43.23 1.40
593 663 4.918810 ACAAGATTCCGGGAATTAATGC 57.081 40.909 22.53 10.08 31.89 3.56
595 665 4.580580 ACAAGATTCCGGGAATTAATGCTC 59.419 41.667 22.53 9.62 31.89 4.26
635 706 5.232610 AGTAGACAAGTACTATCACACGC 57.767 43.478 0.00 0.00 31.14 5.34
650 721 0.179134 CACGCTCCCCTACTCTTTCG 60.179 60.000 0.00 0.00 0.00 3.46
684 755 8.646004 TGTGAATTTCCATCAGTCCAAATTTTA 58.354 29.630 0.00 0.00 30.35 1.52
696 767 9.094578 TCAGTCCAAATTTTATTTCATACCCAA 57.905 29.630 0.00 0.00 0.00 4.12
894 1006 4.771127 GTGCCCACGACTTTCTCA 57.229 55.556 0.00 0.00 0.00 3.27
988 1103 1.830408 CAGCTCCGGGGTCCTAGAG 60.830 68.421 1.62 0.00 0.00 2.43
1340 1457 4.489306 AAGCACAACCTTAGATAGTCCC 57.511 45.455 0.00 0.00 0.00 4.46
1341 1458 2.772515 AGCACAACCTTAGATAGTCCCC 59.227 50.000 0.00 0.00 0.00 4.81
1387 1506 4.481368 TGTAGCAACGGATGAATTACCT 57.519 40.909 0.00 0.00 0.00 3.08
1412 1549 5.351740 GGAGAGGCTTGTTAGTTGTTACATC 59.648 44.000 0.00 0.00 0.00 3.06
1432 1570 2.138320 CCGCATAGCTGTAATCCTGTG 58.862 52.381 0.00 0.00 0.00 3.66
1435 1573 2.547211 GCATAGCTGTAATCCTGTGCTG 59.453 50.000 0.00 0.00 41.27 4.41
1466 1604 5.866335 TGTTCCGGTGTTATAATTGTGTC 57.134 39.130 0.00 0.00 0.00 3.67
1471 1609 4.806775 CCGGTGTTATAATTGTGTCGATGA 59.193 41.667 0.00 0.00 0.00 2.92
1480 1618 3.913548 TTGTGTCGATGAATGGGTTTG 57.086 42.857 0.00 0.00 0.00 2.93
1534 1672 2.893637 CAAAGATCATCGACGGGAAGT 58.106 47.619 0.00 0.00 0.00 3.01
1673 1811 1.986378 CTACGTGCGGAACAAGAAGAG 59.014 52.381 0.00 0.00 0.00 2.85
1677 1815 2.041115 GCGGAACAAGAAGAGGGCC 61.041 63.158 0.00 0.00 0.00 5.80
1680 1818 0.402121 GGAACAAGAAGAGGGCCTGT 59.598 55.000 12.95 2.79 0.00 4.00
1831 1969 2.097629 CCTCGCGTGAGTTCTCAATAGA 59.902 50.000 23.55 3.82 40.85 1.98
1832 1970 3.358775 CTCGCGTGAGTTCTCAATAGAG 58.641 50.000 17.90 8.96 39.10 2.43
1833 1971 3.064134 CTCGCGTGAGTTCTCAATAGAGA 59.936 47.826 17.90 12.03 41.71 3.10
1980 2200 8.362639 CAGGCATAATAAATCTGTTAAGGCATT 58.637 33.333 0.00 0.00 28.80 3.56
2028 2248 7.041107 CCTACACCAAACATTCCCATTTATTG 58.959 38.462 0.00 0.00 0.00 1.90
2086 2306 3.891049 AGAAGCCATCTGGTTACATTCC 58.109 45.455 0.00 0.00 36.88 3.01
2331 2561 3.623848 TCCAGTGAACATTGGACGG 57.376 52.632 13.59 0.00 41.50 4.79
2466 2696 1.922447 AGGAGCAATATTGTGGGGACA 59.078 47.619 16.61 0.00 38.70 4.02
2636 2866 5.389935 CGAGGAAATAACAAGACAAGCAGAC 60.390 44.000 0.00 0.00 0.00 3.51
2767 2997 7.977293 CCTACTCTCTTTTAGCTAGAACCTTTC 59.023 40.741 0.00 0.00 0.00 2.62
2769 2999 6.270231 ACTCTCTTTTAGCTAGAACCTTTCCA 59.730 38.462 0.00 0.00 0.00 3.53
2851 3085 4.947645 TGTTTCTCAATGGAAAAGCTTGG 58.052 39.130 0.00 0.00 37.02 3.61
2864 3127 8.410673 TGGAAAAGCTTGGTAATGTTTGTATA 57.589 30.769 0.00 0.00 0.00 1.47
2899 3164 7.424227 TCAGAATGCAAAATTTTGACAATCC 57.576 32.000 30.40 18.90 39.84 3.01
2924 3189 1.595311 TATGGGGAGTTCTGCATGGT 58.405 50.000 0.00 0.00 0.00 3.55
2953 3218 3.000727 GGGGAGTATGTGTTTGTCTTCG 58.999 50.000 0.00 0.00 0.00 3.79
2957 3222 4.062991 GAGTATGTGTTTGTCTTCGGGTT 58.937 43.478 0.00 0.00 0.00 4.11
2988 3253 3.117888 GGATCAAACTCTATGAAGCCCCA 60.118 47.826 0.00 0.00 0.00 4.96
3002 3409 0.108041 GCCCCATGCTTGGAACATTG 60.108 55.000 19.85 2.05 46.92 2.82
3021 3428 8.458573 AACATTGTGGTGAATTTGTAGACTTA 57.541 30.769 0.00 0.00 0.00 2.24
3042 3449 7.902087 ACTTATTATTTTAAGTTTGGGCAGCA 58.098 30.769 0.00 0.00 38.90 4.41
3048 3455 0.395586 AAGTTTGGGCAGCACAGTGA 60.396 50.000 4.15 0.00 0.00 3.41
3052 3459 0.607217 TTGGGCAGCACAGTGATCAG 60.607 55.000 4.15 0.00 0.00 2.90
3059 3466 4.082571 GGCAGCACAGTGATCAGTTAATTT 60.083 41.667 4.15 0.00 0.00 1.82
3096 3506 2.704572 CTGGAAGGTTCTACTTGGCTG 58.295 52.381 0.00 0.00 0.00 4.85
3348 3758 1.069978 TCGAACACACTGGATTCAGCA 59.930 47.619 0.00 0.00 44.59 4.41
3527 3938 7.797121 ATTTTGACAGGGGTGAGAAATTTAT 57.203 32.000 0.00 0.00 0.00 1.40
3649 4060 5.933790 TGAACCGTATGTTATGCTTGTTTC 58.066 37.500 0.00 0.00 37.29 2.78
3684 4095 1.382522 CATACATGAGTGGTGGTGGC 58.617 55.000 0.00 0.00 0.00 5.01
3698 4109 2.614969 TGGCCTCCCCTGCTGATT 60.615 61.111 3.32 0.00 0.00 2.57
3728 4139 1.352687 AGGAGAGGGAAGGAAACAAGC 59.647 52.381 0.00 0.00 0.00 4.01
3794 4211 8.700439 TTTTATTAGCTGTCCCAACTAGTTTT 57.300 30.769 5.07 0.00 0.00 2.43
3974 4393 3.611766 TTGCTTCTAAGTGTAGGGAGC 57.388 47.619 0.00 0.00 37.40 4.70
3998 4417 8.472683 GCGGATGCTTGATATCCTATATAATC 57.527 38.462 0.00 0.00 41.57 1.75
3999 4418 8.090831 GCGGATGCTTGATATCCTATATAATCA 58.909 37.037 0.00 0.00 41.57 2.57
4005 4424 9.979578 GCTTGATATCCTATATAATCAGTGGAG 57.020 37.037 0.00 0.00 0.00 3.86
4007 4426 9.720874 TTGATATCCTATATAATCAGTGGAGCT 57.279 33.333 0.00 0.00 0.00 4.09
4028 4447 0.030638 CCAAATAAATGAGGGCCGCG 59.969 55.000 0.00 0.00 0.00 6.46
4139 4558 3.510459 TGACCTGGAACTGAATCAGAGA 58.490 45.455 18.20 0.00 35.18 3.10
4178 4597 9.832445 TTCTGAAATAATAACATGTACTCCCTC 57.168 33.333 0.00 0.00 0.00 4.30
4179 4598 9.213777 TCTGAAATAATAACATGTACTCCCTCT 57.786 33.333 0.00 0.00 0.00 3.69
4180 4599 9.265901 CTGAAATAATAACATGTACTCCCTCTG 57.734 37.037 0.00 0.00 0.00 3.35
4181 4600 8.768397 TGAAATAATAACATGTACTCCCTCTGT 58.232 33.333 0.00 0.00 0.00 3.41
4182 4601 9.262358 GAAATAATAACATGTACTCCCTCTGTC 57.738 37.037 0.00 0.00 0.00 3.51
4183 4602 5.615925 AATAACATGTACTCCCTCTGTCC 57.384 43.478 0.00 0.00 0.00 4.02
4184 4603 1.867363 ACATGTACTCCCTCTGTCCC 58.133 55.000 0.00 0.00 0.00 4.46
4185 4604 1.078823 ACATGTACTCCCTCTGTCCCA 59.921 52.381 0.00 0.00 0.00 4.37
4186 4605 2.293184 ACATGTACTCCCTCTGTCCCAT 60.293 50.000 0.00 0.00 0.00 4.00
4187 4606 3.052109 ACATGTACTCCCTCTGTCCCATA 60.052 47.826 0.00 0.00 0.00 2.74
4188 4607 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
4189 4608 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
4190 4609 5.412617 TGTACTCCCTCTGTCCCATAATA 57.587 43.478 0.00 0.00 0.00 0.98
4191 4610 5.977533 TGTACTCCCTCTGTCCCATAATAT 58.022 41.667 0.00 0.00 0.00 1.28
4192 4611 7.111136 TGTACTCCCTCTGTCCCATAATATA 57.889 40.000 0.00 0.00 0.00 0.86
4193 4612 7.541074 TGTACTCCCTCTGTCCCATAATATAA 58.459 38.462 0.00 0.00 0.00 0.98
4194 4613 7.674348 TGTACTCCCTCTGTCCCATAATATAAG 59.326 40.741 0.00 0.00 0.00 1.73
4195 4614 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
4196 4615 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
4197 4616 6.875469 TCCCTCTGTCCCATAATATAAGAGT 58.125 40.000 0.00 0.00 0.00 3.24
4198 4617 6.726299 TCCCTCTGTCCCATAATATAAGAGTG 59.274 42.308 0.00 0.00 0.00 3.51
4199 4618 6.498651 CCCTCTGTCCCATAATATAAGAGTGT 59.501 42.308 0.00 0.00 0.00 3.55
4200 4619 7.016661 CCCTCTGTCCCATAATATAAGAGTGTT 59.983 40.741 0.00 0.00 0.00 3.32
4201 4620 8.432805 CCTCTGTCCCATAATATAAGAGTGTTT 58.567 37.037 0.00 0.00 0.00 2.83
4202 4621 9.838339 CTCTGTCCCATAATATAAGAGTGTTTT 57.162 33.333 0.00 0.00 0.00 2.43
4205 4624 9.967451 TGTCCCATAATATAAGAGTGTTTTTGA 57.033 29.630 0.00 0.00 0.00 2.69
4207 4626 9.967451 TCCCATAATATAAGAGTGTTTTTGACA 57.033 29.630 0.00 0.00 35.42 3.58
4244 4663 6.594284 AAAAACGCTCTTATATTACGGGAC 57.406 37.500 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.719370 TGTGGCCTTAGTTCAAATGAAGTAAT 59.281 34.615 18.76 1.27 44.35 1.89
4 5 4.278170 TGTGTGGCCTTAGTTCAAATGAAG 59.722 41.667 3.32 0.00 34.27 3.02
20 21 7.029563 CCTTCATTCTAAAATAAGTGTGTGGC 58.970 38.462 0.00 0.00 0.00 5.01
68 69 8.188799 AGTTGCATCTTGAAGATTACATTCATG 58.811 33.333 4.67 0.00 36.60 3.07
111 112 9.632969 CAAATGCTTACACTAACGTATTCATAC 57.367 33.333 0.00 0.00 0.00 2.39
175 177 3.343941 TTGGCCAAGCGAAAGTAGTAT 57.656 42.857 16.05 0.00 0.00 2.12
216 218 9.167311 ACAGTAATTCTCTTGTTATGGCTAAAG 57.833 33.333 0.00 0.00 0.00 1.85
250 252 3.061732 CCTAAAACAAACGGCGTTTTTCG 60.062 43.478 33.04 24.08 42.41 3.46
258 260 0.031449 TGCTGCCTAAAACAAACGGC 59.969 50.000 0.00 0.00 42.78 5.68
261 263 5.527214 AGGAAAAATGCTGCCTAAAACAAAC 59.473 36.000 0.00 0.00 0.00 2.93
270 272 2.880268 GCAAAAAGGAAAAATGCTGCCT 59.120 40.909 0.00 0.00 34.29 4.75
277 279 6.048509 ACAGTTCATCGCAAAAAGGAAAAAT 58.951 32.000 0.00 0.00 0.00 1.82
283 285 5.491973 CAAAAACAGTTCATCGCAAAAAGG 58.508 37.500 0.00 0.00 0.00 3.11
290 292 2.132740 TGCCAAAAACAGTTCATCGC 57.867 45.000 0.00 0.00 0.00 4.58
291 293 2.467305 CGTTGCCAAAAACAGTTCATCG 59.533 45.455 0.00 0.00 0.00 3.84
296 300 1.404851 CCCACGTTGCCAAAAACAGTT 60.405 47.619 0.00 0.00 0.00 3.16
298 302 0.529555 CCCCACGTTGCCAAAAACAG 60.530 55.000 0.00 0.00 0.00 3.16
305 309 3.965258 ATGCTCCCCACGTTGCCA 61.965 61.111 0.00 0.00 0.00 4.92
307 311 3.443045 CCATGCTCCCCACGTTGC 61.443 66.667 0.00 0.00 0.00 4.17
310 314 2.034066 CAACCATGCTCCCCACGT 59.966 61.111 0.00 0.00 0.00 4.49
314 318 2.276740 CTCCCAACCATGCTCCCC 59.723 66.667 0.00 0.00 0.00 4.81
317 321 1.064463 TGAATCCTCCCAACCATGCTC 60.064 52.381 0.00 0.00 0.00 4.26
328 332 6.120507 AGCTCTGGTTTATATGAATCCTCC 57.879 41.667 0.00 0.00 0.00 4.30
374 410 0.037605 AAACCTAACCAGCCGAGACG 60.038 55.000 0.00 0.00 0.00 4.18
375 411 1.275573 AGAAACCTAACCAGCCGAGAC 59.724 52.381 0.00 0.00 0.00 3.36
376 412 1.640917 AGAAACCTAACCAGCCGAGA 58.359 50.000 0.00 0.00 0.00 4.04
379 415 1.892209 ACAAGAAACCTAACCAGCCG 58.108 50.000 0.00 0.00 0.00 5.52
380 416 2.296190 CCAACAAGAAACCTAACCAGCC 59.704 50.000 0.00 0.00 0.00 4.85
381 417 2.956333 ACCAACAAGAAACCTAACCAGC 59.044 45.455 0.00 0.00 0.00 4.85
384 420 3.558033 TCCACCAACAAGAAACCTAACC 58.442 45.455 0.00 0.00 0.00 2.85
388 424 2.024369 AGGTTCCACCAACAAGAAACCT 60.024 45.455 0.00 0.00 41.95 3.50
398 434 2.197324 GTGGGCAGGTTCCACCAA 59.803 61.111 2.07 0.00 46.58 3.67
402 438 3.579302 CCTGGTGGGCAGGTTCCA 61.579 66.667 0.00 0.00 35.19 3.53
407 443 1.604593 CTTGAACCTGGTGGGCAGG 60.605 63.158 0.00 0.00 45.06 4.85
409 445 0.467290 GAACTTGAACCTGGTGGGCA 60.467 55.000 0.00 0.00 39.10 5.36
410 446 0.178990 AGAACTTGAACCTGGTGGGC 60.179 55.000 0.00 0.00 39.10 5.36
411 447 2.637872 TCTAGAACTTGAACCTGGTGGG 59.362 50.000 0.00 0.00 41.89 4.61
412 448 3.557264 GGTCTAGAACTTGAACCTGGTGG 60.557 52.174 0.00 0.00 39.83 4.61
415 451 2.561419 TCGGTCTAGAACTTGAACCTGG 59.439 50.000 6.16 0.00 0.00 4.45
416 452 3.936372 TCGGTCTAGAACTTGAACCTG 57.064 47.619 6.16 0.00 0.00 4.00
443 479 3.309682 CACTCGTATAAATGCACACCCTG 59.690 47.826 0.00 0.00 0.00 4.45
460 528 5.450376 AAGAATACATACGCAAACACTCG 57.550 39.130 0.00 0.00 0.00 4.18
496 566 5.124036 TCGGGGTTTTTCCATATGAATCT 57.876 39.130 3.65 0.00 38.11 2.40
503 573 4.042174 AGTCCTATCGGGGTTTTTCCATA 58.958 43.478 0.00 0.00 38.11 2.74
504 574 2.850568 AGTCCTATCGGGGTTTTTCCAT 59.149 45.455 0.00 0.00 38.11 3.41
507 577 3.268330 GTGAGTCCTATCGGGGTTTTTC 58.732 50.000 0.00 0.00 35.33 2.29
521 591 3.255888 GGGTTCTTTCCAAATGTGAGTCC 59.744 47.826 0.00 0.00 0.00 3.85
534 604 8.631480 TCTAAATGACCTTTTAGGGTTCTTTC 57.369 34.615 12.50 0.00 40.58 2.62
537 607 8.615705 AGAATCTAAATGACCTTTTAGGGTTCT 58.384 33.333 17.96 17.96 40.58 3.01
548 618 8.383175 TGTTCCTTTGTAGAATCTAAATGACCT 58.617 33.333 0.00 0.00 0.00 3.85
568 638 3.739401 AATTCCCGGAATCTTGTTCCT 57.261 42.857 13.24 0.00 36.45 3.36
593 663 8.962111 GTCTACTTTTTGAAAGAATGCAAAGAG 58.038 33.333 7.37 0.00 40.21 2.85
595 665 8.633075 TGTCTACTTTTTGAAAGAATGCAAAG 57.367 30.769 7.37 0.00 35.64 2.77
608 678 8.425491 CGTGTGATAGTACTTGTCTACTTTTTG 58.575 37.037 0.00 0.00 0.00 2.44
629 700 0.608640 AAAGAGTAGGGGAGCGTGTG 59.391 55.000 0.00 0.00 0.00 3.82
630 701 0.896226 GAAAGAGTAGGGGAGCGTGT 59.104 55.000 0.00 0.00 0.00 4.49
635 706 0.179134 CGCACGAAAGAGTAGGGGAG 60.179 60.000 0.00 0.00 0.00 4.30
650 721 2.500509 TGGAAATTCACAAACCGCAC 57.499 45.000 0.00 0.00 0.00 5.34
821 931 2.549926 CCCAGGTTTTGCAAGTGAAAC 58.450 47.619 0.00 0.82 35.54 2.78
823 933 0.463620 GCCCAGGTTTTGCAAGTGAA 59.536 50.000 0.00 0.00 0.00 3.18
894 1006 2.032071 CAAAAGGAGCGGTCGGGT 59.968 61.111 8.77 0.00 0.00 5.28
979 1094 2.128507 CCGCTGGGACTCTAGGACC 61.129 68.421 0.00 0.00 34.06 4.46
980 1095 2.787567 GCCGCTGGGACTCTAGGAC 61.788 68.421 0.00 0.00 34.06 3.85
981 1096 2.442272 GCCGCTGGGACTCTAGGA 60.442 66.667 0.00 0.00 34.06 2.94
1351 1468 9.467258 TCCGTTGCTACAATATAACACTATAAC 57.533 33.333 0.00 0.00 0.00 1.89
1353 1470 9.634163 CATCCGTTGCTACAATATAACACTATA 57.366 33.333 0.00 0.00 0.00 1.31
1354 1471 8.364894 TCATCCGTTGCTACAATATAACACTAT 58.635 33.333 0.00 0.00 0.00 2.12
1356 1473 6.578944 TCATCCGTTGCTACAATATAACACT 58.421 36.000 0.00 0.00 0.00 3.55
1357 1474 6.838198 TCATCCGTTGCTACAATATAACAC 57.162 37.500 0.00 0.00 0.00 3.32
1358 1475 8.445275 AATTCATCCGTTGCTACAATATAACA 57.555 30.769 0.00 0.00 0.00 2.41
1359 1476 9.807386 GTAATTCATCCGTTGCTACAATATAAC 57.193 33.333 0.00 0.00 0.00 1.89
1361 1478 8.372459 AGGTAATTCATCCGTTGCTACAATATA 58.628 33.333 0.00 0.00 0.00 0.86
1362 1479 7.173218 CAGGTAATTCATCCGTTGCTACAATAT 59.827 37.037 0.00 0.00 0.00 1.28
1364 1481 5.296780 CAGGTAATTCATCCGTTGCTACAAT 59.703 40.000 0.00 0.00 0.00 2.71
1365 1482 4.634004 CAGGTAATTCATCCGTTGCTACAA 59.366 41.667 0.00 0.00 0.00 2.41
1387 1506 3.857157 AACAACTAACAAGCCTCTCCA 57.143 42.857 0.00 0.00 0.00 3.86
1412 1549 2.138320 CACAGGATTACAGCTATGCGG 58.862 52.381 0.00 0.00 0.00 5.69
1432 1570 0.179156 CCGGAACAACATGATGCAGC 60.179 55.000 0.00 0.00 0.00 5.25
1435 1573 0.881118 ACACCGGAACAACATGATGC 59.119 50.000 9.46 0.00 0.00 3.91
1466 1604 2.598589 CACAAGCAAACCCATTCATCG 58.401 47.619 0.00 0.00 0.00 3.84
1491 1629 1.285641 CGCATCGGCCAAAACTGTT 59.714 52.632 2.24 0.00 36.38 3.16
1494 1632 1.302511 AGACGCATCGGCCAAAACT 60.303 52.632 2.24 0.00 34.11 2.66
1534 1672 2.487762 CTCTTATTTGCTTCGCCACCAA 59.512 45.455 0.00 0.00 0.00 3.67
1554 1692 2.282958 TCAACGCCGACCTCCTCT 60.283 61.111 0.00 0.00 0.00 3.69
1579 1717 2.011349 CGATCGCGTCCTTCATCCG 61.011 63.158 5.77 0.00 0.00 4.18
1653 1791 1.986378 CTCTTCTTGTTCCGCACGTAG 59.014 52.381 0.00 0.00 0.00 3.51
1677 1815 0.102300 TGATACCGACCGCATCACAG 59.898 55.000 0.00 0.00 0.00 3.66
1680 1818 0.821517 ACTTGATACCGACCGCATCA 59.178 50.000 0.00 0.00 0.00 3.07
1831 1969 7.402054 TGGGTTCAACAATTATATGACAGTCT 58.598 34.615 1.31 0.00 0.00 3.24
1832 1970 7.624360 TGGGTTCAACAATTATATGACAGTC 57.376 36.000 0.00 0.00 0.00 3.51
1833 1971 8.469200 CAATGGGTTCAACAATTATATGACAGT 58.531 33.333 0.00 0.00 0.00 3.55
1836 1974 6.701400 GGCAATGGGTTCAACAATTATATGAC 59.299 38.462 0.00 0.00 0.00 3.06
1837 1975 6.610830 AGGCAATGGGTTCAACAATTATATGA 59.389 34.615 0.00 0.00 0.00 2.15
1838 1976 6.702723 CAGGCAATGGGTTCAACAATTATATG 59.297 38.462 0.00 0.00 0.00 1.78
1839 1977 6.610830 TCAGGCAATGGGTTCAACAATTATAT 59.389 34.615 0.00 0.00 0.00 0.86
1980 2200 4.464008 GTTGAGGGAATCTGCCATTATCA 58.536 43.478 0.00 0.00 0.00 2.15
2292 2522 2.151202 TGAAAGCCATCAACGTCCTTC 58.849 47.619 0.00 0.00 0.00 3.46
2466 2696 4.202367 ACTTGTAAGAGTAAAGCAGCAGGT 60.202 41.667 0.00 0.00 0.00 4.00
2550 2780 8.605746 TGCATTTGCTTTCTAATAATCATTTGC 58.394 29.630 3.94 0.00 42.66 3.68
2636 2866 2.805671 TCCAACAGCCGCGATTATAATG 59.194 45.455 8.23 0.00 0.00 1.90
2767 2997 5.453567 AAGAAAAGAACGGGAAAAGATGG 57.546 39.130 0.00 0.00 0.00 3.51
2769 2999 8.692710 ACTAAAAAGAAAAGAACGGGAAAAGAT 58.307 29.630 0.00 0.00 0.00 2.40
2864 3127 6.998968 TTTTGCATTCTGAACCAAAACATT 57.001 29.167 18.82 0.00 33.66 2.71
2899 3164 2.173356 TGCAGAACTCCCCATATTCTGG 59.827 50.000 13.46 0.00 46.20 3.86
2930 3195 4.394729 GAAGACAAACACATACTCCCCAA 58.605 43.478 0.00 0.00 0.00 4.12
2940 3205 1.210967 AGGAACCCGAAGACAAACACA 59.789 47.619 0.00 0.00 0.00 3.72
2957 3222 0.981277 GAGTTTGATCCCGGGGAGGA 60.981 60.000 23.50 7.34 45.00 3.71
2988 3253 2.596346 TCACCACAATGTTCCAAGCAT 58.404 42.857 0.00 0.00 0.00 3.79
3021 3428 6.107901 TGTGCTGCCCAAACTTAAAATAAT 57.892 33.333 0.00 0.00 0.00 1.28
3059 3466 6.897986 CCTTCCAGGTACTAGTAGAGTTCTA 58.102 44.000 1.87 0.00 39.81 2.10
3093 3503 7.497249 AGAAAATATACACTGGAAGACATCAGC 59.503 37.037 0.00 0.00 37.43 4.26
3096 3506 9.606631 AAGAGAAAATATACACTGGAAGACATC 57.393 33.333 0.00 0.00 37.43 3.06
3348 3758 9.325198 GGTTACTTGAATTTGTGGATTCTTTTT 57.675 29.630 0.00 0.00 37.04 1.94
3527 3938 0.035739 GGTACAGTTTGAAGCCGGGA 59.964 55.000 2.18 0.00 0.00 5.14
3649 4060 2.824936 TGTATGCCCAATCAGTTTGTGG 59.175 45.455 0.00 0.00 33.15 4.17
3684 4095 1.755783 GCCAAATCAGCAGGGGAGG 60.756 63.158 0.00 0.00 0.00 4.30
3698 4109 1.920325 CCCTCTCCTGTCCTGCCAA 60.920 63.158 0.00 0.00 0.00 4.52
3728 4139 4.384056 AGATTAGATTGGACATTGGAGCG 58.616 43.478 0.00 0.00 0.00 5.03
3794 4211 4.221924 AGTGCAGTGTGTGTACCATACATA 59.778 41.667 11.68 0.00 42.49 2.29
3974 4393 9.636879 CTGATTATATAGGATATCAAGCATCCG 57.363 37.037 4.83 0.00 45.64 4.18
3998 4417 3.444742 TCATTTATTTGGCAGCTCCACTG 59.555 43.478 4.59 0.00 46.55 3.66
3999 4418 3.698040 CTCATTTATTTGGCAGCTCCACT 59.302 43.478 4.59 0.00 46.55 4.00
4005 4424 1.202568 GGCCCTCATTTATTTGGCAGC 60.203 52.381 0.00 0.00 43.96 5.25
4007 4426 1.110442 CGGCCCTCATTTATTTGGCA 58.890 50.000 0.00 0.00 43.96 4.92
4028 4447 0.442699 GGAAATTCCAGCACGTCGAC 59.557 55.000 7.23 5.18 36.28 4.20
4116 4535 4.081254 TCTCTGATTCAGTTCCAGGTCATG 60.081 45.833 13.23 0.00 32.61 3.07
4139 4558 9.995003 TTATTATTTCAGAAACCTTTTGCACAT 57.005 25.926 0.00 0.00 0.00 3.21
4181 4600 9.967451 TGTCAAAAACACTCTTATATTATGGGA 57.033 29.630 0.00 0.00 31.20 4.37
4221 4640 5.232838 CGTCCCGTAATATAAGAGCGTTTTT 59.767 40.000 0.00 0.00 0.00 1.94
4222 4641 4.741676 CGTCCCGTAATATAAGAGCGTTTT 59.258 41.667 0.00 0.00 0.00 2.43
4223 4642 4.293415 CGTCCCGTAATATAAGAGCGTTT 58.707 43.478 0.00 0.00 0.00 3.60
4224 4643 3.304928 CCGTCCCGTAATATAAGAGCGTT 60.305 47.826 0.00 0.00 0.00 4.84
4225 4644 2.227388 CCGTCCCGTAATATAAGAGCGT 59.773 50.000 0.00 0.00 0.00 5.07
4226 4645 2.485426 TCCGTCCCGTAATATAAGAGCG 59.515 50.000 0.00 0.00 0.00 5.03
4227 4646 3.119566 CCTCCGTCCCGTAATATAAGAGC 60.120 52.174 0.00 0.00 0.00 4.09
4228 4647 3.442977 CCCTCCGTCCCGTAATATAAGAG 59.557 52.174 0.00 0.00 0.00 2.85
4229 4648 3.074390 TCCCTCCGTCCCGTAATATAAGA 59.926 47.826 0.00 0.00 0.00 2.10
4230 4649 3.424703 TCCCTCCGTCCCGTAATATAAG 58.575 50.000 0.00 0.00 0.00 1.73
4231 4650 3.181429 ACTCCCTCCGTCCCGTAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
4232 4651 2.376518 ACTCCCTCCGTCCCGTAATATA 59.623 50.000 0.00 0.00 0.00 0.86
4233 4652 1.146566 ACTCCCTCCGTCCCGTAATAT 59.853 52.381 0.00 0.00 0.00 1.28
4234 4653 0.552848 ACTCCCTCCGTCCCGTAATA 59.447 55.000 0.00 0.00 0.00 0.98
4235 4654 0.552848 TACTCCCTCCGTCCCGTAAT 59.447 55.000 0.00 0.00 0.00 1.89
4236 4655 0.552848 ATACTCCCTCCGTCCCGTAA 59.447 55.000 0.00 0.00 0.00 3.18
4237 4656 1.434188 TATACTCCCTCCGTCCCGTA 58.566 55.000 0.00 0.00 0.00 4.02
4238 4657 0.776176 ATATACTCCCTCCGTCCCGT 59.224 55.000 0.00 0.00 0.00 5.28
4239 4658 2.290514 TGTATATACTCCCTCCGTCCCG 60.291 54.545 13.89 0.00 0.00 5.14
4240 4659 3.446442 TGTATATACTCCCTCCGTCCC 57.554 52.381 13.89 0.00 0.00 4.46
4241 4660 3.130693 GCATGTATATACTCCCTCCGTCC 59.869 52.174 13.89 0.00 0.00 4.79
4242 4661 3.762288 TGCATGTATATACTCCCTCCGTC 59.238 47.826 13.89 0.00 0.00 4.79
4243 4662 3.510360 GTGCATGTATATACTCCCTCCGT 59.490 47.826 13.89 0.00 0.00 4.69
4244 4663 3.509967 TGTGCATGTATATACTCCCTCCG 59.490 47.826 13.89 0.00 0.00 4.63
4245 4664 5.012148 AGTTGTGCATGTATATACTCCCTCC 59.988 44.000 13.89 0.00 0.00 4.30
4246 4665 5.928839 CAGTTGTGCATGTATATACTCCCTC 59.071 44.000 13.89 3.47 0.00 4.30
4247 4666 5.602561 TCAGTTGTGCATGTATATACTCCCT 59.397 40.000 13.89 0.00 0.00 4.20
4248 4667 5.853936 TCAGTTGTGCATGTATATACTCCC 58.146 41.667 13.89 3.04 0.00 4.30
4249 4668 7.041780 CCTTTCAGTTGTGCATGTATATACTCC 60.042 40.741 13.89 3.36 0.00 3.85
4250 4669 7.710907 TCCTTTCAGTTGTGCATGTATATACTC 59.289 37.037 13.89 4.37 0.00 2.59
4251 4670 7.564793 TCCTTTCAGTTGTGCATGTATATACT 58.435 34.615 13.89 0.00 0.00 2.12
4252 4671 7.786178 TCCTTTCAGTTGTGCATGTATATAC 57.214 36.000 5.89 5.89 0.00 1.47
4254 4673 9.006839 CATATCCTTTCAGTTGTGCATGTATAT 57.993 33.333 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.