Multiple sequence alignment - TraesCS1B01G394500

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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 TraesCS1B01G394500 chr1B 100.000 2291 0 0 1 2291 626600013 626602303 0.000000e+00 4231
1 TraesCS1B01G394500 chr1B 86.742 445 37 15 872 1313 626507401 626506976 2.060000e-130 475
2 TraesCS1B01G394500 chr1B 87.442 430 33 11 873 1298 626594970 626595382 2.060000e-130 475
3 TraesCS1B01G394500 chr1B 79.032 248 42 7 1041 1282 626649159 626649402 6.550000e-36 161
4 TraesCS1B01G394500 chr1D 88.113 1918 129 42 269 2123 456199029 456200910 0.000000e+00 2187
5 TraesCS1B01G394500 chr1D 86.792 424 41 9 869 1291 456132344 456132753 2.070000e-125 459
6 TraesCS1B01G394500 chr1D 94.815 135 6 1 107 240 456197536 456197670 2.310000e-50 209
7 TraesCS1B01G394500 chr1D 77.966 236 47 5 1051 1282 456203187 456203421 2.370000e-30 143
8 TraesCS1B01G394500 chr1D 76.829 246 51 6 1041 1282 456251773 456252016 1.430000e-27 134
9 TraesCS1B01G394500 chr1A 89.911 1457 86 27 1 1442 549665527 549666937 0.000000e+00 1820
10 TraesCS1B01G394500 chr1A 87.150 428 35 10 874 1298 549637852 549638262 3.450000e-128 468
11 TraesCS1B01G394500 chr1A 87.279 283 28 4 1487 1765 549666936 549667214 1.320000e-82 316
12 TraesCS1B01G394500 chr2B 90.909 176 10 6 2118 2291 232453394 232453565 4.920000e-57 231
13 TraesCS1B01G394500 chr5B 90.286 175 15 2 2118 2291 83466769 83466596 6.370000e-56 228
14 TraesCS1B01G394500 chr5B 86.782 174 20 3 2120 2291 561716289 561716117 8.350000e-45 191
15 TraesCS1B01G394500 chr7B 89.266 177 16 3 2117 2291 740715121 740715296 3.830000e-53 219
16 TraesCS1B01G394500 chr3A 88.068 176 14 6 2120 2291 747039361 747039533 3.860000e-48 202
17 TraesCS1B01G394500 chr2D 87.571 177 18 4 2117 2291 602576530 602576356 3.860000e-48 202
18 TraesCS1B01G394500 chr2D 85.542 166 20 3 2118 2280 645604987 645604823 1.090000e-38 171
19 TraesCS1B01G394500 chr4A 86.188 181 20 5 2114 2291 597327729 597327551 8.350000e-45 191
20 TraesCS1B01G394500 chr2A 82.386 176 26 5 2120 2291 772367766 772367592 5.100000e-32 148


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 TraesCS1B01G394500 chr1B 626600013 626602303 2290 False 4231.000000 4231 100.000000 1 2291 1 chr1B.!!$F2 2290
1 TraesCS1B01G394500 chr1D 456197536 456203421 5885 False 846.333333 2187 86.964667 107 2123 3 chr1D.!!$F3 2016
2 TraesCS1B01G394500 chr1A 549665527 549667214 1687 False 1068.000000 1820 88.595000 1 1765 2 chr1A.!!$F2 1764

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
806 2179 0.034756 AGGCACATCGTTGCACACTA 59.965 50.0 8.32 0.0 44.94 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 3633 0.241481 TTCATAAAAACGTGGGCGCC 59.759 50.0 21.18 21.18 42.83 6.53 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
58 59 1.087501 GAACCGAGGAAGTGCCATTC 58.912 55.000 0.00 0.00 40.02 2.67
88 89 2.739913 CGAAAGGTCGTTGGCTTAATGA 59.260 45.455 0.00 0.00 42.53 2.57
102 103 4.812626 GGCTTAATGAAATGGAGCAATTGG 59.187 41.667 7.72 0.00 36.95 3.16
184 185 1.518903 GAAAGGACACACTGGGCAGC 61.519 60.000 0.00 0.00 0.00 5.25
247 1587 5.362263 GTCTTAAAGGTGGCATAATACCGA 58.638 41.667 0.00 0.00 41.85 4.69
252 1592 6.538945 AAAGGTGGCATAATACCGAAAAAT 57.461 33.333 0.00 0.00 41.85 1.82
254 1594 4.340950 AGGTGGCATAATACCGAAAAATGG 59.659 41.667 0.00 0.00 41.85 3.16
256 1596 5.163499 GGTGGCATAATACCGAAAAATGGAA 60.163 40.000 0.00 0.00 0.00 3.53
257 1597 5.977129 GTGGCATAATACCGAAAAATGGAAG 59.023 40.000 0.00 0.00 0.00 3.46
272 1612 0.036306 GGAAGGGGGTGTGTAGTGTG 59.964 60.000 0.00 0.00 0.00 3.82
273 1613 0.763035 GAAGGGGGTGTGTAGTGTGT 59.237 55.000 0.00 0.00 0.00 3.72
274 1614 1.972795 GAAGGGGGTGTGTAGTGTGTA 59.027 52.381 0.00 0.00 0.00 2.90
275 1615 1.345063 AGGGGGTGTGTAGTGTGTAC 58.655 55.000 0.00 0.00 0.00 2.90
326 1666 2.143925 GTCGAAGGTCTGTTTTCAGGG 58.856 52.381 0.00 0.00 46.94 4.45
375 1715 8.998277 ATACTGAACTAGACATACAGGTGTAT 57.002 34.615 0.00 0.00 41.58 2.29
383 1723 5.918608 AGACATACAGGTGTATCATTCCAC 58.081 41.667 0.00 0.00 39.06 4.02
400 1765 6.775142 TCATTCCACTCAAAAACCTGAATACA 59.225 34.615 0.00 0.00 0.00 2.29
488 1856 8.381387 CAATAAACTAGTTAAGCTCGACCTTTC 58.619 37.037 8.92 0.00 0.00 2.62
567 1939 1.907807 GGGCATGCAGTCCACCAAA 60.908 57.895 21.36 0.00 43.39 3.28
578 1950 2.430694 AGTCCACCAAACCTGCTTTTTC 59.569 45.455 0.00 0.00 0.00 2.29
695 2068 2.787994 CCAATCCTCTGCACTTTCAGT 58.212 47.619 0.00 0.00 35.63 3.41
735 2108 2.479560 GCGTGGACCATTAATTTCTGCC 60.480 50.000 0.00 0.00 0.00 4.85
772 2145 4.332543 GTCTTCCATGAACGCAATGTGATA 59.667 41.667 0.00 0.00 0.00 2.15
777 2150 1.675483 TGAACGCAATGTGATATGCCC 59.325 47.619 0.00 0.00 39.39 5.36
806 2179 0.034756 AGGCACATCGTTGCACACTA 59.965 50.000 8.32 0.00 44.94 2.74
845 2223 0.523072 CATTTGGCCCGTGTCTGAAG 59.477 55.000 0.00 0.00 0.00 3.02
859 2237 5.049336 CGTGTCTGAAGTCTGAACTCTCTTA 60.049 44.000 0.00 0.00 33.48 2.10
863 2241 7.231519 TGTCTGAAGTCTGAACTCTCTTAATCA 59.768 37.037 0.00 0.00 33.48 2.57
870 2248 9.784531 AGTCTGAACTCTCTTAATCAAAATTCA 57.215 29.630 0.00 0.00 0.00 2.57
897 2275 7.805083 AGCCTATAAATACCACTGATCTCAT 57.195 36.000 0.00 0.00 0.00 2.90
977 2355 5.650703 TCACTACCAGTCGATCTACATTTCA 59.349 40.000 0.00 0.00 0.00 2.69
1065 2443 1.378911 GGTGGTGCTGATGATGGCA 60.379 57.895 0.00 0.00 36.01 4.92
1071 2449 3.274586 CTGATGATGGCACCGGCG 61.275 66.667 0.00 0.00 42.47 6.46
1284 2662 4.740822 AAGGTGCCCGTGCCATCC 62.741 66.667 0.00 0.00 36.33 3.51
1305 2683 4.337274 TCCTGCTAAATCGACGTCTATGAA 59.663 41.667 14.70 0.00 0.00 2.57
1324 2702 8.544622 TCTATGAACTATGATAGGAGACGAGAT 58.455 37.037 4.27 0.00 0.00 2.75
1332 2710 0.553819 AGGAGACGAGATAGCCCAGT 59.446 55.000 0.00 0.00 0.00 4.00
1344 2722 3.502164 GCCCAGTCAGTGGCATAAT 57.498 52.632 0.00 0.00 46.45 1.28
1345 2723 2.638480 GCCCAGTCAGTGGCATAATA 57.362 50.000 0.00 0.00 46.45 0.98
1346 2724 3.146104 GCCCAGTCAGTGGCATAATAT 57.854 47.619 0.00 0.00 46.45 1.28
1350 2728 4.564406 CCCAGTCAGTGGCATAATATCTCC 60.564 50.000 0.00 0.00 46.45 3.71
1352 2730 4.285517 CAGTCAGTGGCATAATATCTCCCT 59.714 45.833 0.00 0.00 0.00 4.20
1372 2755 1.298157 GCACGCTGCAGGTGTTGATA 61.298 55.000 26.07 0.00 44.26 2.15
1375 2758 0.659427 CGCTGCAGGTGTTGATATGG 59.341 55.000 17.12 0.00 0.00 2.74
1396 2780 1.876263 GTGTTTGGTTGCCGTGTGC 60.876 57.895 0.00 0.00 41.77 4.57
1469 2853 7.624360 AATTATGTATGTTGTTGGTCATCGT 57.376 32.000 0.00 0.00 0.00 3.73
1470 2854 4.944962 ATGTATGTTGTTGGTCATCGTG 57.055 40.909 0.00 0.00 0.00 4.35
1471 2855 2.482336 TGTATGTTGTTGGTCATCGTGC 59.518 45.455 0.00 0.00 0.00 5.34
1472 2856 0.516877 ATGTTGTTGGTCATCGTGCG 59.483 50.000 0.00 0.00 0.00 5.34
1473 2857 0.812014 TGTTGTTGGTCATCGTGCGT 60.812 50.000 0.00 0.00 0.00 5.24
1474 2858 0.306533 GTTGTTGGTCATCGTGCGTT 59.693 50.000 0.00 0.00 0.00 4.84
1521 2909 1.694696 CCACTAGGTAAGAGATGGGCC 59.305 57.143 0.00 0.00 0.00 5.80
1583 2971 9.793252 GTCATCATATATGGCATATGTTTTTCC 57.207 33.333 26.37 8.85 34.51 3.13
1589 2977 3.157881 TGGCATATGTTTTTCCCGAACA 58.842 40.909 4.29 0.00 40.86 3.18
1606 2994 4.024893 CCGAACAGGCATGTGACATATAAC 60.025 45.833 4.03 0.00 40.39 1.89
1608 2996 5.050769 CGAACAGGCATGTGACATATAACTC 60.051 44.000 4.03 0.00 40.39 3.01
1609 2997 5.357742 ACAGGCATGTGACATATAACTCA 57.642 39.130 1.71 0.00 38.57 3.41
1611 2999 5.761726 ACAGGCATGTGACATATAACTCATG 59.238 40.000 1.71 13.91 38.57 3.07
1613 3001 6.261603 CAGGCATGTGACATATAACTCATGTT 59.738 38.462 0.00 0.00 39.00 2.71
1712 3100 9.778741 ATATCATCATTCGGTACACTACAAAAT 57.221 29.630 0.00 0.00 0.00 1.82
1726 3114 7.748847 ACACTACAAAATTAGATAAAGCCACG 58.251 34.615 0.00 0.00 0.00 4.94
1730 3118 7.209471 ACAAAATTAGATAAAGCCACGAACA 57.791 32.000 0.00 0.00 0.00 3.18
1800 3188 5.358922 CACCATCAAAACTGGTTGAATGTT 58.641 37.500 0.00 0.00 44.67 2.71
1804 3192 6.707161 CCATCAAAACTGGTTGAATGTTTCAT 59.293 34.615 0.98 0.00 40.76 2.57
1807 3195 6.756074 TCAAAACTGGTTGAATGTTTCATGTC 59.244 34.615 0.00 0.00 39.84 3.06
1822 3210 6.599244 TGTTTCATGTCCTACCATCTTTCATC 59.401 38.462 0.00 0.00 0.00 2.92
1833 3221 2.488204 TCTTTCATCGATTGCACCCA 57.512 45.000 0.00 0.00 0.00 4.51
1834 3222 2.789213 TCTTTCATCGATTGCACCCAA 58.211 42.857 0.00 0.00 35.01 4.12
1835 3223 3.355378 TCTTTCATCGATTGCACCCAAT 58.645 40.909 0.00 0.00 44.11 3.16
1836 3224 3.129113 TCTTTCATCGATTGCACCCAATG 59.871 43.478 0.00 0.00 41.60 2.82
1868 3273 1.135489 AGCGCTTTCACATGCTGAATG 60.135 47.619 2.64 12.46 38.74 2.67
1878 3283 4.020307 TCACATGCTGAATGAAGGACTACA 60.020 41.667 1.75 0.00 38.72 2.74
1883 3288 6.048732 TGCTGAATGAAGGACTACATACAA 57.951 37.500 0.00 0.00 0.00 2.41
1888 3293 7.629157 TGAATGAAGGACTACATACAAATCCA 58.371 34.615 0.00 0.00 31.41 3.41
1891 3296 7.194112 TGAAGGACTACATACAAATCCATCA 57.806 36.000 0.00 0.00 35.42 3.07
1897 3302 7.308229 GGACTACATACAAATCCATCATGAAGC 60.308 40.741 0.00 0.00 0.00 3.86
1899 3304 6.630444 ACATACAAATCCATCATGAAGCTC 57.370 37.500 0.00 0.00 0.00 4.09
1960 3365 6.166279 TCTCTCGAATTATTGCAACAGTTCT 58.834 36.000 10.69 0.00 0.00 3.01
1961 3366 7.320399 TCTCTCGAATTATTGCAACAGTTCTA 58.680 34.615 10.69 0.00 0.00 2.10
1962 3367 7.489435 TCTCTCGAATTATTGCAACAGTTCTAG 59.511 37.037 10.69 9.20 0.00 2.43
1963 3368 6.036083 TCTCGAATTATTGCAACAGTTCTAGC 59.964 38.462 10.69 0.00 0.00 3.42
1964 3369 5.874810 TCGAATTATTGCAACAGTTCTAGCT 59.125 36.000 10.69 0.00 0.00 3.32
1971 3376 7.921786 ATTGCAACAGTTCTAGCTTATAACA 57.078 32.000 0.00 0.00 0.00 2.41
1974 3379 6.538742 TGCAACAGTTCTAGCTTATAACATCC 59.461 38.462 0.00 0.00 0.00 3.51
1976 3381 7.227512 GCAACAGTTCTAGCTTATAACATCCAT 59.772 37.037 0.00 0.00 0.00 3.41
2004 3409 7.602517 AAAGCACAAACTATCACTGAGATAC 57.397 36.000 0.00 0.00 38.19 2.24
2005 3410 5.344066 AGCACAAACTATCACTGAGATACG 58.656 41.667 0.00 0.00 38.19 3.06
2006 3411 4.026475 GCACAAACTATCACTGAGATACGC 60.026 45.833 0.00 0.00 38.19 4.42
2007 3412 4.205181 CACAAACTATCACTGAGATACGCG 59.795 45.833 3.53 3.53 38.19 6.01
2008 3413 2.690173 ACTATCACTGAGATACGCGC 57.310 50.000 5.73 0.00 38.19 6.86
2041 3446 4.083565 GGATTAACCCAACCAAACTAGCA 58.916 43.478 0.00 0.00 0.00 3.49
2046 3451 1.067635 CCCAACCAAACTAGCATGCAC 60.068 52.381 21.98 0.00 0.00 4.57
2048 3453 2.607771 CCAACCAAACTAGCATGCACAC 60.608 50.000 21.98 0.00 0.00 3.82
2052 3457 2.322161 CAAACTAGCATGCACACAAGC 58.678 47.619 21.98 0.00 40.80 4.01
2066 3471 5.124297 TGCACACAAGCTCGTTATACTAGTA 59.876 40.000 4.77 4.77 34.99 1.82
2068 3473 6.200100 CACACAAGCTCGTTATACTAGTAGG 58.800 44.000 8.85 0.00 0.00 3.18
2072 3477 4.396522 AGCTCGTTATACTAGTAGGTGGG 58.603 47.826 8.85 0.00 0.00 4.61
2081 3486 2.293318 ACTAGTAGGTGGGGGCATGTTA 60.293 50.000 1.45 0.00 0.00 2.41
2082 3487 1.907240 AGTAGGTGGGGGCATGTTAT 58.093 50.000 0.00 0.00 0.00 1.89
2103 3515 5.895636 ATATGAATCGCACACCAAAGAAA 57.104 34.783 0.00 0.00 0.00 2.52
2123 3535 2.162681 AGGTGGCAAACATGTAAGAGC 58.837 47.619 0.00 0.71 0.00 4.09
2124 3536 1.885887 GGTGGCAAACATGTAAGAGCA 59.114 47.619 0.00 0.00 0.00 4.26
2125 3537 2.493278 GGTGGCAAACATGTAAGAGCAT 59.507 45.455 0.00 0.00 0.00 3.79
2126 3538 3.428045 GGTGGCAAACATGTAAGAGCATC 60.428 47.826 0.00 0.00 0.00 3.91
2137 3549 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
2146 3558 2.669569 CAGCCGTTGGTCCCACAG 60.670 66.667 0.00 0.00 0.00 3.66
2147 3559 3.953775 AGCCGTTGGTCCCACAGG 61.954 66.667 2.71 2.71 0.00 4.00
2148 3560 3.948719 GCCGTTGGTCCCACAGGA 61.949 66.667 9.69 0.00 41.08 3.86
2149 3561 2.347490 CCGTTGGTCCCACAGGAG 59.653 66.667 1.10 0.00 45.21 3.69
2151 3563 2.034221 GTTGGTCCCACAGGAGGC 59.966 66.667 0.00 0.00 45.21 4.70
2152 3564 3.636231 TTGGTCCCACAGGAGGCG 61.636 66.667 0.00 0.00 45.21 5.52
2155 3567 3.075005 GTCCCACAGGAGGCGCTA 61.075 66.667 7.64 0.00 45.21 4.26
2157 3569 1.916273 TCCCACAGGAGGCGCTAAA 60.916 57.895 7.64 0.00 37.19 1.85
2160 3572 1.463674 CCACAGGAGGCGCTAAAAAT 58.536 50.000 7.64 0.00 0.00 1.82
2162 3574 1.062587 CACAGGAGGCGCTAAAAATCG 59.937 52.381 7.64 0.00 0.00 3.34
2167 3579 2.411701 GCGCTAAAAATCGCCCCC 59.588 61.111 0.00 0.00 45.01 5.40
2168 3580 2.119029 GCGCTAAAAATCGCCCCCT 61.119 57.895 0.00 0.00 45.01 4.79
2169 3581 1.727467 CGCTAAAAATCGCCCCCTG 59.273 57.895 0.00 0.00 0.00 4.45
2170 3582 1.724582 CGCTAAAAATCGCCCCCTGG 61.725 60.000 0.00 0.00 0.00 4.45
2171 3583 0.395173 GCTAAAAATCGCCCCCTGGA 60.395 55.000 0.00 0.00 0.00 3.86
2172 3584 1.680338 CTAAAAATCGCCCCCTGGAG 58.320 55.000 0.00 0.00 0.00 3.86
2173 3585 0.257616 TAAAAATCGCCCCCTGGAGG 59.742 55.000 0.00 0.00 31.33 4.30
2175 3587 2.499303 AAAATCGCCCCCTGGAGGTG 62.499 60.000 0.59 0.59 36.16 4.00
2183 3595 4.704833 CCTGGAGGTGCACCGGTG 62.705 72.222 30.66 30.66 42.08 4.94
2199 3611 3.047280 TGCTAAACCGCACGCTGG 61.047 61.111 0.00 0.00 34.44 4.85
2200 3612 4.460873 GCTAAACCGCACGCTGGC 62.461 66.667 0.74 0.00 0.00 4.85
2220 3632 4.082523 CGTGATGCCCCCAGTCGT 62.083 66.667 0.00 0.00 0.00 4.34
2221 3633 2.436646 GTGATGCCCCCAGTCGTG 60.437 66.667 0.00 0.00 0.00 4.35
2222 3634 3.716195 TGATGCCCCCAGTCGTGG 61.716 66.667 0.00 0.00 44.56 4.94
2236 5146 3.032339 GTGGCGCCCACGTTTTTA 58.968 55.556 26.77 0.00 44.95 1.52
2238 5148 0.731174 GTGGCGCCCACGTTTTTATG 60.731 55.000 26.77 0.00 44.95 1.90
2242 5152 2.395654 GCGCCCACGTTTTTATGAAAA 58.604 42.857 0.00 0.00 42.83 2.29
2246 5156 5.118817 GCGCCCACGTTTTTATGAAAATTTA 59.881 36.000 0.00 0.00 42.83 1.40
2264 5706 7.772332 AAATTTAAATTACGCCACAAACACA 57.228 28.000 13.68 0.00 0.00 3.72
2269 5711 4.249020 CGCCACAAACACAGCGCA 62.249 61.111 11.47 0.00 42.31 6.09
2271 5713 1.518133 GCCACAAACACAGCGCAAA 60.518 52.632 11.47 0.00 0.00 3.68
2272 5714 0.875474 GCCACAAACACAGCGCAAAT 60.875 50.000 11.47 0.00 0.00 2.32
2273 5715 1.569708 CCACAAACACAGCGCAAATT 58.430 45.000 11.47 0.00 0.00 1.82
2276 5718 2.602211 CACAAACACAGCGCAAATTCAA 59.398 40.909 11.47 0.00 0.00 2.69
2278 5720 1.851658 AACACAGCGCAAATTCAACC 58.148 45.000 11.47 0.00 0.00 3.77
2279 5721 0.743688 ACACAGCGCAAATTCAACCA 59.256 45.000 11.47 0.00 0.00 3.67
2280 5722 1.135915 ACACAGCGCAAATTCAACCAA 59.864 42.857 11.47 0.00 0.00 3.67
2284 5726 2.865551 CAGCGCAAATTCAACCAAACTT 59.134 40.909 11.47 0.00 0.00 2.66
2286 5728 2.097444 GCGCAAATTCAACCAAACTTCG 60.097 45.455 0.30 0.00 0.00 3.79
2287 5729 2.470999 CGCAAATTCAACCAAACTTCGG 59.529 45.455 0.00 0.00 0.00 4.30
2289 5731 2.415697 AATTCAACCAAACTTCGGCG 57.584 45.000 0.00 0.00 0.00 6.46
2290 5732 1.600023 ATTCAACCAAACTTCGGCGA 58.400 45.000 4.99 4.99 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.408127 CCCACGCATCACATTTAGGGA 60.408 52.381 0.00 0.00 37.22 4.20
8 9 2.093181 AGCTACCCACGCATCACATTTA 60.093 45.455 0.00 0.00 0.00 1.40
58 59 1.270465 AACGACCTTTCGGTTAGTGGG 60.270 52.381 0.00 0.00 45.19 4.61
83 84 7.560991 ACATAGACCAATTGCTCCATTTCATTA 59.439 33.333 0.00 0.00 0.00 1.90
88 89 4.336433 CGACATAGACCAATTGCTCCATTT 59.664 41.667 0.00 0.00 0.00 2.32
102 103 3.521947 AGTGTAAAGGGCGACATAGAC 57.478 47.619 0.00 0.00 0.00 2.59
184 185 3.314331 ACCCTCACTGACGGGCTG 61.314 66.667 11.53 0.00 44.63 4.85
193 194 4.083565 GAGAAACTCTACTCACCCTCACT 58.916 47.826 0.00 0.00 33.86 3.41
247 1587 2.487746 ACACACCCCCTTCCATTTTT 57.512 45.000 0.00 0.00 0.00 1.94
252 1592 0.400815 ACACTACACACCCCCTTCCA 60.401 55.000 0.00 0.00 0.00 3.53
254 1594 0.763035 ACACACTACACACCCCCTTC 59.237 55.000 0.00 0.00 0.00 3.46
256 1596 1.345063 GTACACACTACACACCCCCT 58.655 55.000 0.00 0.00 0.00 4.79
257 1597 1.001633 CTGTACACACTACACACCCCC 59.998 57.143 0.00 0.00 0.00 5.40
326 1666 2.430465 TCTTCAGAGCATTTGGTCAGC 58.570 47.619 11.89 0.00 44.42 4.26
375 1715 6.775142 TGTATTCAGGTTTTTGAGTGGAATGA 59.225 34.615 0.00 0.00 0.00 2.57
460 1825 8.059798 AGGTCGAGCTTAACTAGTTTATTGTA 57.940 34.615 14.49 0.00 0.00 2.41
462 1827 7.829378 AAGGTCGAGCTTAACTAGTTTATTG 57.171 36.000 27.36 3.27 0.00 1.90
465 1832 6.393171 GGAAAGGTCGAGCTTAACTAGTTTA 58.607 40.000 28.51 3.46 0.00 2.01
476 1843 2.100879 AACAGCGGAAAGGTCGAGCT 62.101 55.000 12.24 12.24 38.47 4.09
488 1856 4.273969 TGTTAACTGGTTAAAGAACAGCGG 59.726 41.667 7.22 0.00 36.86 5.52
567 1939 0.853530 ACCCAGAGGAAAAAGCAGGT 59.146 50.000 0.00 0.00 36.73 4.00
578 1950 1.134098 ACAAGTGTCACAACCCAGAGG 60.134 52.381 5.62 0.00 40.04 3.69
709 2082 5.296780 CAGAAATTAATGGTCCACGCACTAT 59.703 40.000 0.00 0.00 0.00 2.12
735 2108 4.094830 TGGAAGACATGATGATGATGGG 57.905 45.455 0.00 0.00 33.36 4.00
772 2145 1.000866 GCCTTTTCCTCAGGGGCAT 59.999 57.895 3.88 0.00 42.08 4.40
777 2150 1.089920 CGATGTGCCTTTTCCTCAGG 58.910 55.000 0.00 0.00 34.08 3.86
806 2179 2.047844 CACGGCTGCTGCAGTACT 60.048 61.111 28.50 9.97 45.29 2.73
870 2248 8.494433 TGAGATCAGTGGTATTTATAGGCTTTT 58.506 33.333 0.00 0.00 0.00 2.27
897 2275 1.660019 ATGGTGTGGGTGTTTGGGGA 61.660 55.000 0.00 0.00 0.00 4.81
1218 2596 1.429463 GGGAGTTGACGTACTGCTTG 58.571 55.000 9.47 0.00 36.78 4.01
1284 2662 5.274718 AGTTCATAGACGTCGATTTAGCAG 58.725 41.667 10.46 0.00 0.00 4.24
1305 2683 5.433526 GGCTATCTCGTCTCCTATCATAGT 58.566 45.833 0.00 0.00 0.00 2.12
1332 2710 3.008375 GCAGGGAGATATTATGCCACTGA 59.992 47.826 0.00 0.00 0.00 3.41
1342 2720 0.533755 GCAGCGTGCAGGGAGATATT 60.534 55.000 8.72 0.00 44.26 1.28
1343 2721 1.070445 GCAGCGTGCAGGGAGATAT 59.930 57.895 8.72 0.00 44.26 1.63
1344 2722 2.501128 GCAGCGTGCAGGGAGATA 59.499 61.111 8.72 0.00 44.26 1.98
1363 2746 3.443681 CCAAACACTCCCATATCAACACC 59.556 47.826 0.00 0.00 0.00 4.16
1372 2755 1.178534 CGGCAACCAAACACTCCCAT 61.179 55.000 0.00 0.00 0.00 4.00
1375 2758 1.358759 CACGGCAACCAAACACTCC 59.641 57.895 0.00 0.00 0.00 3.85
1396 2780 5.477291 AGATACAGATACATCGGGGTAACTG 59.523 44.000 16.95 16.95 44.81 3.16
1399 2783 5.637127 TCAGATACAGATACATCGGGGTAA 58.363 41.667 0.00 0.00 0.00 2.85
1448 2832 4.331443 GCACGATGACCAACAACATACATA 59.669 41.667 0.00 0.00 0.00 2.29
1453 2837 0.516877 CGCACGATGACCAACAACAT 59.483 50.000 0.00 0.00 0.00 2.71
1461 2845 1.006391 CGAACATAACGCACGATGACC 60.006 52.381 0.00 0.00 0.00 4.02
1463 2847 1.135344 TCCGAACATAACGCACGATGA 60.135 47.619 0.00 0.00 0.00 2.92
1464 2848 1.273688 TCCGAACATAACGCACGATG 58.726 50.000 0.00 0.00 0.00 3.84
1465 2849 1.858458 CATCCGAACATAACGCACGAT 59.142 47.619 0.00 0.00 0.00 3.73
1466 2850 1.273688 CATCCGAACATAACGCACGA 58.726 50.000 0.00 0.00 0.00 4.35
1467 2851 0.300491 CCATCCGAACATAACGCACG 59.700 55.000 0.00 0.00 0.00 5.34
1468 2852 1.062002 CACCATCCGAACATAACGCAC 59.938 52.381 0.00 0.00 0.00 5.34
1469 2853 1.364721 CACCATCCGAACATAACGCA 58.635 50.000 0.00 0.00 0.00 5.24
1470 2854 0.027586 GCACCATCCGAACATAACGC 59.972 55.000 0.00 0.00 0.00 4.84
1471 2855 1.651987 AGCACCATCCGAACATAACG 58.348 50.000 0.00 0.00 0.00 3.18
1472 2856 2.747446 ACAAGCACCATCCGAACATAAC 59.253 45.455 0.00 0.00 0.00 1.89
1473 2857 2.746904 CACAAGCACCATCCGAACATAA 59.253 45.455 0.00 0.00 0.00 1.90
1474 2858 2.290008 ACACAAGCACCATCCGAACATA 60.290 45.455 0.00 0.00 0.00 2.29
1521 2909 4.153117 CGAACAGTTCTTTCTCCCATCAAG 59.847 45.833 11.60 0.00 0.00 3.02
1583 2971 2.022764 TATGTCACATGCCTGTTCGG 57.977 50.000 0.00 0.00 31.62 4.30
1589 2977 5.933617 ACATGAGTTATATGTCACATGCCT 58.066 37.500 0.00 0.00 38.70 4.75
1636 3024 0.249447 CGTAATGATGCAGAGGCCGA 60.249 55.000 0.00 0.00 40.13 5.54
1685 3073 8.587952 TTTGTAGTGTACCGAATGATGATATG 57.412 34.615 0.00 0.00 0.00 1.78
1686 3074 9.778741 ATTTTGTAGTGTACCGAATGATGATAT 57.221 29.630 0.00 0.00 0.00 1.63
1698 3086 9.169592 TGGCTTTATCTAATTTTGTAGTGTACC 57.830 33.333 0.00 0.00 0.00 3.34
1712 3100 6.621316 TTTGTTGTTCGTGGCTTTATCTAA 57.379 33.333 0.00 0.00 0.00 2.10
1800 3188 5.128663 TCGATGAAAGATGGTAGGACATGAA 59.871 40.000 0.00 0.00 0.00 2.57
1804 3192 5.359756 CAATCGATGAAAGATGGTAGGACA 58.640 41.667 0.00 0.00 0.00 4.02
1807 3195 4.024556 GTGCAATCGATGAAAGATGGTAGG 60.025 45.833 0.00 0.00 0.00 3.18
1833 3221 1.071385 AGCGCTGGAGCTTATAGCATT 59.929 47.619 10.39 3.17 46.80 3.56
1834 3222 0.683973 AGCGCTGGAGCTTATAGCAT 59.316 50.000 10.39 3.68 46.80 3.79
1835 3223 2.127839 AGCGCTGGAGCTTATAGCA 58.872 52.632 10.39 0.00 46.80 3.49
1857 3262 4.558226 TGTAGTCCTTCATTCAGCATGT 57.442 40.909 0.00 0.00 37.40 3.21
1868 3273 7.933577 TCATGATGGATTTGTATGTAGTCCTTC 59.066 37.037 0.00 0.00 35.10 3.46
1878 3283 6.598503 TCAGAGCTTCATGATGGATTTGTAT 58.401 36.000 10.35 0.00 0.00 2.29
1897 3302 3.441496 TTTTGCAGGTTGCTTTCAGAG 57.559 42.857 2.48 0.00 45.31 3.35
1899 3304 5.488645 AAAATTTTGCAGGTTGCTTTCAG 57.511 34.783 1.75 0.00 45.31 3.02
1941 3346 6.111768 AGCTAGAACTGTTGCAATAATTCG 57.888 37.500 10.99 0.88 0.00 3.34
1950 3355 6.538742 TGGATGTTATAAGCTAGAACTGTTGC 59.461 38.462 0.00 0.00 31.51 4.17
1960 3365 9.706691 GTGCTTTACTATGGATGTTATAAGCTA 57.293 33.333 0.00 0.00 37.10 3.32
1961 3366 8.210946 TGTGCTTTACTATGGATGTTATAAGCT 58.789 33.333 0.00 0.00 37.10 3.74
1962 3367 8.378172 TGTGCTTTACTATGGATGTTATAAGC 57.622 34.615 0.00 0.00 36.81 3.09
1971 3376 8.267894 AGTGATAGTTTGTGCTTTACTATGGAT 58.732 33.333 0.00 0.00 35.74 3.41
1974 3379 8.479313 TCAGTGATAGTTTGTGCTTTACTATG 57.521 34.615 0.00 0.00 35.74 2.23
1976 3381 7.892609 TCTCAGTGATAGTTTGTGCTTTACTA 58.107 34.615 0.00 0.00 0.00 1.82
2004 3409 4.260497 GGTTAATCCTAAAGTTAAGGCGCG 60.260 45.833 0.00 0.00 33.84 6.86
2005 3410 4.036027 GGGTTAATCCTAAAGTTAAGGCGC 59.964 45.833 0.00 0.00 33.84 6.53
2006 3411 5.187687 TGGGTTAATCCTAAAGTTAAGGCG 58.812 41.667 6.28 0.00 33.84 5.52
2007 3412 6.127535 GGTTGGGTTAATCCTAAAGTTAAGGC 60.128 42.308 6.28 0.00 38.38 4.35
2008 3413 6.949463 TGGTTGGGTTAATCCTAAAGTTAAGG 59.051 38.462 6.28 0.00 38.38 2.69
2041 3446 3.861840 AGTATAACGAGCTTGTGTGCAT 58.138 40.909 7.56 2.01 34.99 3.96
2046 3451 6.200100 CACCTACTAGTATAACGAGCTTGTG 58.800 44.000 7.56 0.00 0.00 3.33
2048 3453 5.278364 CCCACCTACTAGTATAACGAGCTTG 60.278 48.000 2.33 0.00 0.00 4.01
2052 3457 4.077822 CCCCCACCTACTAGTATAACGAG 58.922 52.174 2.33 0.00 0.00 4.18
2054 3459 2.560105 GCCCCCACCTACTAGTATAACG 59.440 54.545 2.33 0.00 0.00 3.18
2066 3471 2.427872 TCATATAACATGCCCCCACCT 58.572 47.619 0.00 0.00 0.00 4.00
2068 3473 3.440173 CGATTCATATAACATGCCCCCAC 59.560 47.826 0.00 0.00 0.00 4.61
2072 3477 3.501828 TGTGCGATTCATATAACATGCCC 59.498 43.478 0.00 0.00 0.00 5.36
2081 3486 5.163622 CCTTTCTTTGGTGTGCGATTCATAT 60.164 40.000 0.00 0.00 0.00 1.78
2082 3487 4.155826 CCTTTCTTTGGTGTGCGATTCATA 59.844 41.667 0.00 0.00 0.00 2.15
2103 3515 2.162681 GCTCTTACATGTTTGCCACCT 58.837 47.619 2.30 0.00 0.00 4.00
2111 3523 3.539604 GCTGGAGATGCTCTTACATGTT 58.460 45.455 2.30 0.00 0.00 2.71
2129 3541 2.669569 CTGTGGGACCAACGGCTG 60.670 66.667 0.00 0.00 0.00 4.85
2131 3543 3.901797 CTCCTGTGGGACCAACGGC 62.902 68.421 1.71 0.00 36.57 5.68
2132 3544 2.347490 CTCCTGTGGGACCAACGG 59.653 66.667 0.04 0.04 36.57 4.44
2133 3545 2.347490 CCTCCTGTGGGACCAACG 59.653 66.667 0.00 0.00 36.57 4.10
2134 3546 2.034221 GCCTCCTGTGGGACCAAC 59.966 66.667 0.00 0.00 36.57 3.77
2135 3547 3.636231 CGCCTCCTGTGGGACCAA 61.636 66.667 0.00 0.00 36.57 3.67
2138 3550 2.180159 TTTAGCGCCTCCTGTGGGAC 62.180 60.000 2.29 0.00 36.57 4.46
2139 3551 1.485294 TTTTAGCGCCTCCTGTGGGA 61.485 55.000 2.29 0.00 39.70 4.37
2140 3552 0.608035 TTTTTAGCGCCTCCTGTGGG 60.608 55.000 2.29 0.00 0.00 4.61
2141 3553 1.401905 GATTTTTAGCGCCTCCTGTGG 59.598 52.381 2.29 0.00 0.00 4.17
2142 3554 1.062587 CGATTTTTAGCGCCTCCTGTG 59.937 52.381 2.29 0.00 0.00 3.66
2143 3555 1.369625 CGATTTTTAGCGCCTCCTGT 58.630 50.000 2.29 0.00 0.00 4.00
2146 3558 4.998294 GCGATTTTTAGCGCCTCC 57.002 55.556 2.29 0.00 46.93 4.30
2151 3563 1.724582 CCAGGGGGCGATTTTTAGCG 61.725 60.000 0.00 0.00 0.00 4.26
2152 3564 0.395173 TCCAGGGGGCGATTTTTAGC 60.395 55.000 0.00 0.00 0.00 3.09
2154 3566 0.257616 CCTCCAGGGGGCGATTTTTA 59.742 55.000 0.00 0.00 0.00 1.52
2155 3567 1.000359 CCTCCAGGGGGCGATTTTT 60.000 57.895 0.00 0.00 0.00 1.94
2157 3569 2.614013 ACCTCCAGGGGGCGATTT 60.614 61.111 4.69 0.00 40.27 2.17
2182 3594 3.047280 CCAGCGTGCGGTTTAGCA 61.047 61.111 0.00 0.00 45.96 3.49
2183 3595 4.460873 GCCAGCGTGCGGTTTAGC 62.461 66.667 0.00 0.00 37.71 3.09
2203 3615 4.082523 ACGACTGGGGGCATCACG 62.083 66.667 0.00 0.00 0.00 4.35
2204 3616 2.436646 CACGACTGGGGGCATCAC 60.437 66.667 0.00 0.00 0.00 3.06
2205 3617 3.716195 CCACGACTGGGGGCATCA 61.716 66.667 0.00 0.00 33.23 3.07
2220 3632 0.889638 TCATAAAAACGTGGGCGCCA 60.890 50.000 30.85 12.04 42.83 5.69
2221 3633 0.241481 TTCATAAAAACGTGGGCGCC 59.759 50.000 21.18 21.18 42.83 6.53
2222 3634 2.053282 TTTCATAAAAACGTGGGCGC 57.947 45.000 0.00 0.00 42.83 6.53
2223 3635 5.583969 AAATTTTCATAAAAACGTGGGCG 57.416 34.783 0.00 0.00 37.20 6.13
2224 3636 9.885934 AATTTAAATTTTCATAAAAACGTGGGC 57.114 25.926 7.64 0.00 37.20 5.36
2236 5146 9.046296 TGTTTGTGGCGTAATTTAAATTTTCAT 57.954 25.926 18.14 0.00 0.00 2.57
2238 5148 8.328864 TGTGTTTGTGGCGTAATTTAAATTTTC 58.671 29.630 18.14 11.04 0.00 2.29
2242 5152 5.404066 GCTGTGTTTGTGGCGTAATTTAAAT 59.596 36.000 0.00 0.00 0.00 1.40
2246 5156 2.738135 GCTGTGTTTGTGGCGTAATTT 58.262 42.857 0.00 0.00 0.00 1.82
2259 5701 1.135915 TGGTTGAATTTGCGCTGTGTT 59.864 42.857 9.73 0.00 0.00 3.32
2264 5706 2.888834 AGTTTGGTTGAATTTGCGCT 57.111 40.000 9.73 0.00 0.00 5.92
2269 5711 2.359531 TCGCCGAAGTTTGGTTGAATTT 59.640 40.909 10.98 0.00 0.00 1.82
2271 5713 1.600023 TCGCCGAAGTTTGGTTGAAT 58.400 45.000 10.98 0.00 0.00 2.57
2272 5714 3.082165 TCGCCGAAGTTTGGTTGAA 57.918 47.368 10.98 0.00 0.00 2.69
2273 5715 4.859400 TCGCCGAAGTTTGGTTGA 57.141 50.000 10.98 6.58 0.00 3.18


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

AutoCloner maintained by Alex Coulton.