Multiple sequence alignment - TraesCS3A01G294200

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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 TraesCS3A01G294200 chr3A 100.000 4338 0 0 1 4338 527842069 527837732 0.000000e+00 8011
1 TraesCS3A01G294200 chr3B 92.249 3019 135 44 754 3712 531213640 531210661 0.000000e+00 4187
2 TraesCS3A01G294200 chr3B 85.737 624 63 10 1 607 531214248 531213634 1.700000e-178 636
3 TraesCS3A01G294200 chr3B 90.939 309 28 0 4030 4338 531210188 531209880 2.410000e-112 416
4 TraesCS3A01G294200 chr3B 93.277 119 7 1 3876 3994 531210306 531210189 1.600000e-39 174
5 TraesCS3A01G294200 chr3B 83.146 178 14 6 3705 3881 531210635 531210473 9.720000e-32 148
6 TraesCS3A01G294200 chr3D 92.901 2606 100 32 1774 4337 405310315 405307753 0.000000e+00 3709
7 TraesCS3A01G294200 chr3D 90.261 1612 98 21 197 1769 405313509 405311918 0.000000e+00 2052
8 TraesCS3A01G294200 chr1A 83.692 325 53 0 2044 2368 462796271 462795947 1.520000e-79 307
9 TraesCS3A01G294200 chr1D 83.283 329 53 2 2037 2364 363725699 363725372 7.050000e-78 302
10 TraesCS3A01G294200 chr1B 82.154 325 58 0 2044 2368 486971810 486971486 3.300000e-71 279
11 TraesCS3A01G294200 chr2A 79.233 313 61 4 2045 2355 550702033 550701723 9.450000e-52 215
12 TraesCS3A01G294200 chr2D 79.114 316 56 7 2045 2355 437948152 437948462 4.400000e-50 209
13 TraesCS3A01G294200 chrUn 79.153 307 54 7 2054 2355 276463194 276462893 2.050000e-48 204
14 TraesCS3A01G294200 chrUn 78.797 316 57 7 2045 2355 276527303 276527613 2.050000e-48 204


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 TraesCS3A01G294200 chr3A 527837732 527842069 4337 True 8011.0 8011 100.0000 1 4338 1 chr3A.!!$R1 4337
1 TraesCS3A01G294200 chr3B 531209880 531214248 4368 True 1112.2 4187 89.0696 1 4338 5 chr3B.!!$R1 4337
2 TraesCS3A01G294200 chr3D 405307753 405313509 5756 True 2880.5 3709 91.5810 197 4337 2 chr3D.!!$R1 4140

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
437 440 0.033366 ACGGAAATTGGCCAACTTGC 59.967 50.0 23.27 21.31 0.0 4.01 F
980 1012 0.115349 AGCAGTCCACCTCCAGTAGT 59.885 55.0 0.00 0.00 0.0 2.73 F
2390 4055 0.468226 TATGCATCCCGTTCCACTCC 59.532 55.0 0.19 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1582 0.533951 TGCATGCGTGTCTGAGAGAT 59.466 50.0 14.09 0.00 0.0 2.75 R
2400 4065 0.747255 CAGTGGTACGAGGCTAGCAT 59.253 55.0 18.24 10.08 0.0 3.79 R
4202 6105 0.670546 AGTCCAATGCAAGTCGTCCG 60.671 55.0 0.00 0.00 0.0 4.79 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
30 31 7.039644 CCAGAAGACTATAACTGTACCCTATGG 60.040 44.444 0.00 0.00 37.80 2.74
31 32 6.494146 AGAAGACTATAACTGTACCCTATGGC 59.506 42.308 0.00 0.00 33.59 4.40
32 33 5.712752 AGACTATAACTGTACCCTATGGCA 58.287 41.667 0.00 0.00 33.59 4.92
35 36 7.292591 AGACTATAACTGTACCCTATGGCATTT 59.707 37.037 4.78 0.00 33.59 2.32
36 37 7.224297 ACTATAACTGTACCCTATGGCATTTG 58.776 38.462 4.78 0.00 33.59 2.32
37 38 2.654863 ACTGTACCCTATGGCATTTGC 58.345 47.619 4.78 0.00 41.14 3.68
38 39 2.025416 ACTGTACCCTATGGCATTTGCA 60.025 45.455 4.78 0.00 44.36 4.08
39 40 2.620115 CTGTACCCTATGGCATTTGCAG 59.380 50.000 4.78 3.74 44.36 4.41
40 41 1.956477 GTACCCTATGGCATTTGCAGG 59.044 52.381 4.78 6.14 44.36 4.85
41 42 0.630673 ACCCTATGGCATTTGCAGGA 59.369 50.000 14.33 0.00 44.36 3.86
49 50 1.133790 GGCATTTGCAGGACATCACTC 59.866 52.381 4.74 0.00 44.36 3.51
51 52 1.089920 ATTTGCAGGACATCACTCGC 58.910 50.000 0.00 0.00 0.00 5.03
61 62 0.036952 CATCACTCGCCTCACCAACT 60.037 55.000 0.00 0.00 0.00 3.16
63 64 2.031163 ACTCGCCTCACCAACTGC 59.969 61.111 0.00 0.00 0.00 4.40
98 99 2.401766 GCCTTGACGCATCACCCAG 61.402 63.158 0.00 0.00 33.38 4.45
106 107 2.048603 GCATCACCCAGTCCAAGCC 61.049 63.158 0.00 0.00 0.00 4.35
112 113 4.748144 CCAGTCCAAGCCAGGGCC 62.748 72.222 6.70 0.00 43.17 5.80
135 136 4.962836 CATGCCTCCATCGCCCCC 62.963 72.222 0.00 0.00 0.00 5.40
149 150 1.900545 GCCCCCGCATCCCTCTATAC 61.901 65.000 0.00 0.00 34.03 1.47
150 151 1.265454 CCCCCGCATCCCTCTATACC 61.265 65.000 0.00 0.00 0.00 2.73
171 173 2.485479 CCCCCTACGATCTCCATTGTTG 60.485 54.545 0.00 0.00 0.00 3.33
174 176 2.419990 CCTACGATCTCCATTGTTGGCA 60.420 50.000 0.00 0.00 43.29 4.92
177 179 1.133025 CGATCTCCATTGTTGGCAACC 59.867 52.381 26.31 10.03 43.29 3.77
181 183 0.482446 TCCATTGTTGGCAACCTCCT 59.518 50.000 26.31 6.58 43.29 3.69
209 212 0.698238 CCTGAACCCATCAACCTCCA 59.302 55.000 0.00 0.00 37.67 3.86
225 228 2.928396 CAACTCCCCTCCACCGGT 60.928 66.667 0.00 0.00 0.00 5.28
228 231 2.365635 CTCCCCTCCACCGGTGAT 60.366 66.667 36.07 0.00 0.00 3.06
230 233 1.075525 TCCCCTCCACCGGTGATAG 60.076 63.158 36.07 28.39 0.00 2.08
239 242 1.112113 ACCGGTGATAGCACTACCAG 58.888 55.000 6.12 0.00 44.52 4.00
248 251 0.404426 AGCACTACCAGGTTTTCCCC 59.596 55.000 0.00 0.00 41.86 4.81
312 315 2.029020 CCTCGATGTTGAGTCCTTGTCA 60.029 50.000 0.00 0.00 34.04 3.58
313 316 2.989840 CTCGATGTTGAGTCCTTGTCAC 59.010 50.000 0.00 0.00 0.00 3.67
316 319 0.472471 TGTTGAGTCCTTGTCACCCC 59.528 55.000 0.00 0.00 0.00 4.95
423 426 9.051679 CATTACCTAATATTTGACATGACGGAA 57.948 33.333 0.00 0.00 0.00 4.30
437 440 0.033366 ACGGAAATTGGCCAACTTGC 59.967 50.000 23.27 21.31 0.00 4.01
443 446 3.488778 AATTGGCCAACTTGCAATTCA 57.511 38.095 23.27 0.00 0.00 2.57
496 500 3.264998 AGAAAGCATCTTCTCAGCCTC 57.735 47.619 0.00 0.00 33.39 4.70
498 502 3.200385 AGAAAGCATCTTCTCAGCCTCAT 59.800 43.478 0.00 0.00 33.39 2.90
505 511 5.676584 GCATCTTCTCAGCCTCATCAAAAAG 60.677 44.000 0.00 0.00 0.00 2.27
655 678 4.700448 CCACCATTGGCCAGGGCA 62.700 66.667 21.89 12.83 44.11 5.36
681 704 3.026707 TCTGGGATCGACAAGTCCATA 57.973 47.619 5.21 0.00 36.19 2.74
724 749 2.813908 GCGATCCCAACGCGACTT 60.814 61.111 15.93 0.00 46.05 3.01
728 753 2.253414 GATCCCAACGCGACTTTGGC 62.253 60.000 15.93 0.00 42.06 4.52
738 763 3.936772 GACTTTGGCCGGCCCATCA 62.937 63.158 41.75 22.09 44.89 3.07
835 860 4.473643 CCGTTTTGGTCAGAGCCA 57.526 55.556 0.00 0.00 36.62 4.75
836 861 1.949257 CCGTTTTGGTCAGAGCCAC 59.051 57.895 0.00 0.00 38.42 5.01
848 880 0.665369 AGAGCCACGAAACGTAACGG 60.665 55.000 16.23 2.82 38.32 4.44
852 884 0.785979 CCACGAAACGTAACGGGAAG 59.214 55.000 16.10 5.23 38.32 3.46
854 886 0.945743 ACGAAACGTAACGGGAAGCC 60.946 55.000 16.23 0.00 38.73 4.35
855 887 0.945265 CGAAACGTAACGGGAAGCCA 60.945 55.000 6.44 0.00 0.00 4.75
952 984 2.510238 CGCGCTCTGCCTTTAGCT 60.510 61.111 5.56 0.00 44.23 3.32
955 987 0.460284 GCGCTCTGCCTTTAGCTACA 60.460 55.000 0.00 0.00 44.23 2.74
959 991 2.167487 GCTCTGCCTTTAGCTACAGACT 59.833 50.000 8.52 0.00 44.23 3.24
962 994 5.584253 TCTGCCTTTAGCTACAGACTAAG 57.416 43.478 8.52 1.31 44.23 2.18
980 1012 0.115349 AGCAGTCCACCTCCAGTAGT 59.885 55.000 0.00 0.00 0.00 2.73
1194 1241 3.245315 CGCTACAGGTACGCACGC 61.245 66.667 0.00 0.00 0.00 5.34
1195 1242 2.126228 GCTACAGGTACGCACGCA 60.126 61.111 0.00 0.00 0.00 5.24
1196 1243 2.442188 GCTACAGGTACGCACGCAC 61.442 63.158 0.00 0.00 0.00 5.34
1239 1286 4.792528 AGTCGCGTACTGTTAGATAGAC 57.207 45.455 5.77 0.00 36.93 2.59
1292 1339 1.004918 CAGGGTGTGGGAGACGTTC 60.005 63.158 0.00 0.00 0.00 3.95
1439 1486 2.678190 GCTCACTTTCTTCGTGCCCTAT 60.678 50.000 0.00 0.00 32.54 2.57
1469 1516 2.935481 GGTCTTACCTTGTCGTCGAT 57.065 50.000 0.00 0.00 34.73 3.59
1511 1559 1.078759 GGTGCTGCTGCTACTACGTG 61.079 60.000 17.00 0.00 40.48 4.49
1530 1578 0.963355 GCTCCCTCAGTGTCGAGACT 60.963 60.000 9.83 9.83 34.79 3.24
1534 1582 3.493334 TCCCTCAGTGTCGAGACTTTAA 58.507 45.455 13.32 0.88 34.79 1.52
1552 1603 1.649664 AATCTCTCAGACACGCATGC 58.350 50.000 7.91 7.91 0.00 4.06
1593 1646 4.566488 CCTGTAGATCCTGCCTTGTTTCTT 60.566 45.833 0.00 0.00 0.00 2.52
1668 1721 1.889105 CATTCCGCTCCATCACCCG 60.889 63.158 0.00 0.00 0.00 5.28
1753 1806 2.099431 GCGCAGAGTCAGCTCCTTG 61.099 63.158 0.30 0.00 42.59 3.61
1772 1825 5.532025 CTTGTTTGCAAGGTACTACTAGC 57.468 43.478 0.00 0.00 46.17 3.42
1976 3627 6.459573 CGTCCAGATTCTCTCTTCCTTTCTAG 60.460 46.154 0.00 0.00 29.16 2.43
1991 3642 7.507797 TCCTTTCTAGGAGTACTGTAGTAGT 57.492 40.000 0.00 0.00 45.82 2.73
1998 3655 9.707957 TCTAGGAGTACTGTAGTAGTAGTAGTT 57.292 37.037 0.00 0.00 43.87 2.24
1999 3656 9.965824 CTAGGAGTACTGTAGTAGTAGTAGTTC 57.034 40.741 0.00 0.00 43.87 3.01
2017 3674 1.660167 TCTTCTTCCTCATGCATGCG 58.340 50.000 22.25 16.00 0.00 4.73
2046 3704 0.942252 CACGGATGATGATGCAGGTG 59.058 55.000 0.00 0.00 0.00 4.00
2049 3707 1.602311 GGATGATGATGCAGGTGACC 58.398 55.000 0.00 0.00 0.00 4.02
2380 4039 5.888105 ACTTCGTACGTATATATGCATCCC 58.112 41.667 16.05 0.00 0.00 3.85
2381 4046 4.541085 TCGTACGTATATATGCATCCCG 57.459 45.455 16.05 2.07 0.00 5.14
2387 4052 3.863424 CGTATATATGCATCCCGTTCCAC 59.137 47.826 0.19 0.00 0.00 4.02
2388 4053 4.381612 CGTATATATGCATCCCGTTCCACT 60.382 45.833 0.19 0.00 0.00 4.00
2389 4054 2.550830 ATATGCATCCCGTTCCACTC 57.449 50.000 0.19 0.00 0.00 3.51
2390 4055 0.468226 TATGCATCCCGTTCCACTCC 59.532 55.000 0.19 0.00 0.00 3.85
2391 4056 1.561769 ATGCATCCCGTTCCACTCCA 61.562 55.000 0.00 0.00 0.00 3.86
2392 4057 1.002624 GCATCCCGTTCCACTCCAA 60.003 57.895 0.00 0.00 0.00 3.53
2393 4058 0.608035 GCATCCCGTTCCACTCCAAA 60.608 55.000 0.00 0.00 0.00 3.28
2394 4059 1.165270 CATCCCGTTCCACTCCAAAC 58.835 55.000 0.00 0.00 0.00 2.93
2395 4060 1.064825 ATCCCGTTCCACTCCAAACT 58.935 50.000 0.00 0.00 0.00 2.66
2396 4061 1.719529 TCCCGTTCCACTCCAAACTA 58.280 50.000 0.00 0.00 0.00 2.24
2397 4062 2.262637 TCCCGTTCCACTCCAAACTAT 58.737 47.619 0.00 0.00 0.00 2.12
2398 4063 3.443052 TCCCGTTCCACTCCAAACTATA 58.557 45.455 0.00 0.00 0.00 1.31
2399 4064 3.839490 TCCCGTTCCACTCCAAACTATAA 59.161 43.478 0.00 0.00 0.00 0.98
2400 4065 4.286549 TCCCGTTCCACTCCAAACTATAAA 59.713 41.667 0.00 0.00 0.00 1.40
2401 4066 5.045432 TCCCGTTCCACTCCAAACTATAAAT 60.045 40.000 0.00 0.00 0.00 1.40
2402 4067 5.065988 CCCGTTCCACTCCAAACTATAAATG 59.934 44.000 0.00 0.00 0.00 2.32
2415 4080 5.388408 ACTATAAATGCTAGCCTCGTACC 57.612 43.478 13.29 0.00 0.00 3.34
2422 4087 0.101399 CTAGCCTCGTACCACTGCAG 59.899 60.000 13.48 13.48 0.00 4.41
2429 4094 1.010935 CGTACCACTGCAGTGCTCTG 61.011 60.000 36.38 25.86 44.34 3.35
2436 4101 2.776659 TGCAGTGCTCTGATGCATC 58.223 52.632 20.14 20.14 44.56 3.91
2636 4301 1.072159 CCCCAAGGCGATGAGATCC 59.928 63.158 0.00 0.00 0.00 3.36
2753 4422 1.905637 AAAGCCTTACGGTTGAAGGG 58.094 50.000 10.82 0.00 43.28 3.95
2762 4431 2.836667 ACGGTTGAAGGGGTAGGAATA 58.163 47.619 0.00 0.00 0.00 1.75
2767 4443 3.414759 TGAAGGGGTAGGAATAGCTCA 57.585 47.619 0.00 0.00 0.00 4.26
2774 4450 4.822350 GGGGTAGGAATAGCTCACAAATTC 59.178 45.833 0.00 0.00 0.00 2.17
2823 4502 1.688772 GAGATGGTGGCCGAGTACTA 58.311 55.000 0.00 0.00 0.00 1.82
2830 4509 4.261781 GCCGAGTACTACGCCCCG 62.262 72.222 0.00 0.00 0.00 5.73
2909 4593 4.262079 CCGGAGAAGTGGTATGTAGAATCC 60.262 50.000 0.00 0.00 0.00 3.01
2941 4629 5.862924 ACCACGTTATCTTGAATTCACAG 57.137 39.130 7.89 9.17 0.00 3.66
2947 4635 6.147821 ACGTTATCTTGAATTCACAGACCTTG 59.852 38.462 7.89 8.31 0.00 3.61
2948 4636 6.317857 GTTATCTTGAATTCACAGACCTTGC 58.682 40.000 7.89 2.17 0.00 4.01
2975 4663 8.386264 AGGGCTTGCATATTACTACTAATCAAT 58.614 33.333 0.00 0.00 0.00 2.57
2976 4664 8.669243 GGGCTTGCATATTACTACTAATCAATC 58.331 37.037 0.00 0.00 0.00 2.67
3060 4748 3.067461 CGGGTTCATGACTTGACCAAAAA 59.933 43.478 14.71 0.00 32.84 1.94
3223 4911 1.595929 GCCGTTCACTTTCCGGACA 60.596 57.895 1.83 0.00 44.41 4.02
3224 4912 1.566018 GCCGTTCACTTTCCGGACAG 61.566 60.000 16.17 16.17 44.41 3.51
3238 4926 1.134699 CGGACAGCCAAGCTATCTCAA 60.135 52.381 0.00 0.00 36.40 3.02
3447 5135 5.825532 TGGAAGGATACACCAAAATGATCA 58.174 37.500 0.00 0.00 41.14 2.92
3470 5158 2.749621 GGGACTGTACAAAGGCTGAATG 59.250 50.000 0.00 0.00 0.00 2.67
3617 5305 9.302345 CTGTTGATTGTACTCGAACATAGTTAT 57.698 33.333 0.00 0.00 0.00 1.89
3714 5442 5.095809 ACAAGTATTCACCTTACCACCCTA 58.904 41.667 0.00 0.00 0.00 3.53
3717 5445 3.994931 ATTCACCTTACCACCCTACAC 57.005 47.619 0.00 0.00 0.00 2.90
3722 5450 3.836562 CACCTTACCACCCTACACTACTT 59.163 47.826 0.00 0.00 0.00 2.24
3749 5477 1.081242 CAACCATGCACGGAGTTGC 60.081 57.895 5.45 0.00 41.61 4.17
3758 5486 1.466360 GCACGGAGTTGCAATCACATC 60.466 52.381 0.59 0.00 41.61 3.06
3789 5519 4.329801 TCGACAATTTCATGAATCACTCCG 59.670 41.667 9.40 9.19 0.00 4.63
3793 5523 3.616956 TTTCATGAATCACTCCGCTCT 57.383 42.857 9.40 0.00 0.00 4.09
3928 5830 7.138736 CGAAAAACAAGGAATTGTACATCAGT 58.861 34.615 0.00 0.00 34.24 3.41
3991 5894 1.604604 TGGCTTGCGCTTTTTAGAGT 58.395 45.000 9.73 0.00 36.09 3.24
4018 5921 4.394300 GCTGAATTTTAGAGAGCAGAGCAA 59.606 41.667 0.00 0.00 0.00 3.91
4021 5924 6.413052 TGAATTTTAGAGAGCAGAGCAATCT 58.587 36.000 0.00 0.00 32.14 2.40
4042 5945 4.753107 TCTCAAACAAGCCCTAAGTTTACG 59.247 41.667 0.00 0.00 34.03 3.18
4128 6031 2.483876 CAGTTGGATGTGAACACGTCT 58.516 47.619 21.24 4.55 44.57 4.18
4140 6043 6.231951 TGTGAACACGTCTTAAAATGGGATA 58.768 36.000 0.00 0.00 0.00 2.59
4202 6105 3.883489 GCCTCCCATAACAATTAGTGACC 59.117 47.826 0.00 0.00 0.00 4.02
4279 6182 7.367285 TGTAGATTTTGTGCCTTGATAACAAC 58.633 34.615 0.00 0.00 33.73 3.32
4282 6185 1.598882 TGTGCCTTGATAACAACGCA 58.401 45.000 5.51 5.51 42.38 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.267014 TGCCATAGGGTACAGTTATAGTCTTC 59.733 42.308 0.00 0.00 36.17 2.87
11 12 7.224297 CAAATGCCATAGGGTACAGTTATAGT 58.776 38.462 0.00 0.00 36.17 2.12
15 16 4.204012 GCAAATGCCATAGGGTACAGTTA 58.796 43.478 0.00 0.00 36.17 2.24
17 18 2.025416 TGCAAATGCCATAGGGTACAGT 60.025 45.455 2.46 0.00 41.18 3.55
30 31 1.202110 CGAGTGATGTCCTGCAAATGC 60.202 52.381 0.00 0.00 42.50 3.56
31 32 1.202110 GCGAGTGATGTCCTGCAAATG 60.202 52.381 0.00 0.00 0.00 2.32
32 33 1.089920 GCGAGTGATGTCCTGCAAAT 58.910 50.000 0.00 0.00 0.00 2.32
35 36 2.230994 GAGGCGAGTGATGTCCTGCA 62.231 60.000 0.00 0.00 0.00 4.41
36 37 1.520342 GAGGCGAGTGATGTCCTGC 60.520 63.158 0.00 0.00 0.00 4.85
37 38 0.459237 GTGAGGCGAGTGATGTCCTG 60.459 60.000 0.00 0.00 0.00 3.86
38 39 1.608717 GGTGAGGCGAGTGATGTCCT 61.609 60.000 0.00 0.00 0.00 3.85
39 40 1.153549 GGTGAGGCGAGTGATGTCC 60.154 63.158 0.00 0.00 0.00 4.02
40 41 0.037326 TTGGTGAGGCGAGTGATGTC 60.037 55.000 0.00 0.00 0.00 3.06
41 42 0.320771 GTTGGTGAGGCGAGTGATGT 60.321 55.000 0.00 0.00 0.00 3.06
51 52 2.360350 ATGGCGCAGTTGGTGAGG 60.360 61.111 10.83 0.00 0.00 3.86
86 87 1.003355 CTTGGACTGGGTGATGCGT 60.003 57.895 0.00 0.00 0.00 5.24
87 88 2.401766 GCTTGGACTGGGTGATGCG 61.402 63.158 0.00 0.00 0.00 4.73
98 99 4.432741 GGAGGCCCTGGCTTGGAC 62.433 72.222 8.29 0.00 38.98 4.02
112 113 2.281345 GATGGAGGCATGGCGGAG 60.281 66.667 14.30 0.00 0.00 4.63
131 132 1.265454 GGTATAGAGGGATGCGGGGG 61.265 65.000 0.00 0.00 0.00 5.40
135 136 2.287829 GGGGGTATAGAGGGATGCG 58.712 63.158 0.00 0.00 0.00 4.73
150 151 1.424638 ACAATGGAGATCGTAGGGGG 58.575 55.000 0.00 0.00 0.00 5.40
174 176 0.689623 CAGGAGAGTGCAAGGAGGTT 59.310 55.000 0.00 0.00 0.00 3.50
177 179 1.338579 GGTTCAGGAGAGTGCAAGGAG 60.339 57.143 0.00 0.00 0.00 3.69
181 183 1.003580 GATGGGTTCAGGAGAGTGCAA 59.996 52.381 0.00 0.00 0.00 4.08
190 193 0.698238 TGGAGGTTGATGGGTTCAGG 59.302 55.000 0.00 0.00 35.27 3.86
209 212 2.928396 CACCGGTGGAGGGGAGTT 60.928 66.667 27.57 0.00 36.61 3.01
225 228 3.054655 GGGAAAACCTGGTAGTGCTATCA 60.055 47.826 0.00 0.00 35.85 2.15
228 231 1.631898 GGGGAAAACCTGGTAGTGCTA 59.368 52.381 0.00 0.00 40.03 3.49
230 233 0.958876 CGGGGAAAACCTGGTAGTGC 60.959 60.000 0.00 0.00 42.34 4.40
262 265 1.152567 AGGCGAGGCTGAGCTAGAT 60.153 57.895 3.72 0.00 0.00 1.98
263 266 2.124060 CAGGCGAGGCTGAGCTAGA 61.124 63.158 20.16 0.00 0.00 2.43
288 291 0.898320 AGGACTCAACATCGAGGTGG 59.102 55.000 2.27 0.00 37.34 4.61
289 292 2.289072 ACAAGGACTCAACATCGAGGTG 60.289 50.000 2.27 0.00 37.34 4.00
290 293 1.971357 ACAAGGACTCAACATCGAGGT 59.029 47.619 0.00 0.00 37.34 3.85
323 326 0.603065 GGTCAATTTTGCCCGAAGCT 59.397 50.000 0.00 0.00 44.23 3.74
415 418 1.923356 AGTTGGCCAATTTCCGTCAT 58.077 45.000 23.66 0.00 0.00 3.06
423 426 3.488778 TGAATTGCAAGTTGGCCAATT 57.511 38.095 23.66 15.80 31.74 2.32
443 446 5.347620 ACAAATAATGCCATGCAAGACAT 57.652 34.783 0.00 0.00 43.62 3.06
496 500 9.276397 GAAATTTGTTGTTTGTCCTTTTTGATG 57.724 29.630 0.00 0.00 0.00 3.07
498 502 8.383318 TGAAATTTGTTGTTTGTCCTTTTTGA 57.617 26.923 0.00 0.00 0.00 2.69
505 511 5.050159 GCCTCATGAAATTTGTTGTTTGTCC 60.050 40.000 0.00 0.00 0.00 4.02
650 673 2.615227 GATCCCAGATTGCGTGCCCT 62.615 60.000 0.00 0.00 0.00 5.19
654 677 0.460109 TGTCGATCCCAGATTGCGTG 60.460 55.000 0.00 0.00 0.00 5.34
655 678 0.249120 TTGTCGATCCCAGATTGCGT 59.751 50.000 0.00 0.00 0.00 5.24
728 753 2.903855 GACATGCTGATGGGCCGG 60.904 66.667 0.00 0.00 33.39 6.13
738 763 4.479993 GGGCAGCCGAGACATGCT 62.480 66.667 5.00 0.00 39.88 3.79
789 814 2.853235 ACGGGAACACCTTTAGGAAG 57.147 50.000 2.06 0.00 38.94 3.46
790 815 2.224597 GGAACGGGAACACCTTTAGGAA 60.225 50.000 2.06 0.00 38.94 3.36
831 856 1.665599 CCCGTTACGTTTCGTGGCT 60.666 57.895 3.52 0.00 41.39 4.75
832 857 1.220817 TTCCCGTTACGTTTCGTGGC 61.221 55.000 3.52 0.00 41.39 5.01
834 859 0.162294 GCTTCCCGTTACGTTTCGTG 59.838 55.000 3.52 0.00 41.39 4.35
835 860 0.945743 GGCTTCCCGTTACGTTTCGT 60.946 55.000 3.52 0.00 44.35 3.85
836 861 0.945265 TGGCTTCCCGTTACGTTTCG 60.945 55.000 3.52 0.00 0.00 3.46
952 984 3.090037 GAGGTGGACTGCTTAGTCTGTA 58.910 50.000 7.31 0.00 38.74 2.74
955 987 1.203187 TGGAGGTGGACTGCTTAGTCT 60.203 52.381 7.31 0.00 38.54 3.24
959 991 2.225293 ACTACTGGAGGTGGACTGCTTA 60.225 50.000 0.00 0.00 38.54 3.09
962 994 0.247736 CACTACTGGAGGTGGACTGC 59.752 60.000 0.00 0.00 38.16 4.40
970 1002 1.435515 GCTCGCTCACTACTGGAGG 59.564 63.158 0.00 0.00 32.96 4.30
1144 1182 1.303888 AGACGAGGTACTTGCCGGA 60.304 57.895 5.05 0.00 45.68 5.14
1239 1286 2.511600 GATCACCTTCACCGCCCG 60.512 66.667 0.00 0.00 0.00 6.13
1292 1339 1.077930 CACCACCAGCAGGATCAGG 60.078 63.158 0.35 0.61 38.69 3.86
1469 1516 1.751351 AGTGCGATCTTCTTCGGATCA 59.249 47.619 0.00 0.00 41.52 2.92
1511 1559 0.963355 AGTCTCGACACTGAGGGAGC 60.963 60.000 0.00 0.00 36.61 4.70
1530 1578 3.618594 GCATGCGTGTCTGAGAGATTAAA 59.381 43.478 0.00 0.00 0.00 1.52
1534 1582 0.533951 TGCATGCGTGTCTGAGAGAT 59.466 50.000 14.09 0.00 0.00 2.75
1552 1603 7.489160 TCTACAGGTAAATACAGTAGTGCATG 58.511 38.462 15.75 0.00 37.49 4.06
1593 1646 3.252215 CGACAGATACCTGCAAACCAAAA 59.748 43.478 0.00 0.00 44.16 2.44
1753 1806 4.312443 TGTGCTAGTAGTACCTTGCAAAC 58.688 43.478 14.86 0.00 43.08 2.93
1772 1825 7.328005 CAGTGCTTATCTACATATGCTACTGTG 59.672 40.741 1.58 0.00 38.30 3.66
1789 3440 0.883833 GCCAAGTGCACAGTGCTTAT 59.116 50.000 25.83 9.30 45.31 1.73
1828 3479 0.959553 CACGTACTGACCAGTGACCT 59.040 55.000 12.54 0.00 42.52 3.85
1976 3627 9.313118 GAAGAACTACTACTACTACAGTACTCC 57.687 40.741 0.00 0.00 38.80 3.85
1980 3631 9.883142 GGAAGAAGAACTACTACTACTACAGTA 57.117 37.037 0.00 0.00 38.80 2.74
1981 3632 8.605065 AGGAAGAAGAACTACTACTACTACAGT 58.395 37.037 0.00 0.00 41.62 3.55
1982 3633 9.101655 GAGGAAGAAGAACTACTACTACTACAG 57.898 40.741 0.00 0.00 0.00 2.74
1983 3634 8.600668 TGAGGAAGAAGAACTACTACTACTACA 58.399 37.037 0.00 0.00 0.00 2.74
1984 3635 9.617523 ATGAGGAAGAAGAACTACTACTACTAC 57.382 37.037 0.00 0.00 0.00 2.73
1985 3636 9.616156 CATGAGGAAGAAGAACTACTACTACTA 57.384 37.037 0.00 0.00 0.00 1.82
1986 3637 7.067737 GCATGAGGAAGAAGAACTACTACTACT 59.932 40.741 0.00 0.00 0.00 2.57
1987 3638 7.148052 TGCATGAGGAAGAAGAACTACTACTAC 60.148 40.741 0.00 0.00 0.00 2.73
1988 3639 6.890268 TGCATGAGGAAGAAGAACTACTACTA 59.110 38.462 0.00 0.00 0.00 1.82
1989 3640 5.717178 TGCATGAGGAAGAAGAACTACTACT 59.283 40.000 0.00 0.00 0.00 2.57
1990 3641 5.967088 TGCATGAGGAAGAAGAACTACTAC 58.033 41.667 0.00 0.00 0.00 2.73
1991 3642 6.577103 CATGCATGAGGAAGAAGAACTACTA 58.423 40.000 22.59 0.00 0.00 1.82
1998 3655 1.065926 ACGCATGCATGAGGAAGAAGA 60.066 47.619 30.64 0.00 31.50 2.87
1999 3656 1.063616 CACGCATGCATGAGGAAGAAG 59.936 52.381 30.64 10.23 31.50 2.85
2017 3674 4.541482 CATCCGTGGCGCATGCAC 62.541 66.667 19.57 8.05 45.35 4.57
2046 3704 4.980805 TGCACCGCGAACAGGGTC 62.981 66.667 8.23 0.00 33.23 4.46
2049 3707 3.716006 CAGTGCACCGCGAACAGG 61.716 66.667 14.63 0.00 0.00 4.00
2380 4039 5.354234 AGCATTTATAGTTTGGAGTGGAACG 59.646 40.000 0.00 0.00 45.86 3.95
2381 4046 6.759497 AGCATTTATAGTTTGGAGTGGAAC 57.241 37.500 0.00 0.00 0.00 3.62
2387 4052 5.406780 CGAGGCTAGCATTTATAGTTTGGAG 59.593 44.000 18.24 0.00 0.00 3.86
2388 4053 5.163343 ACGAGGCTAGCATTTATAGTTTGGA 60.163 40.000 18.24 0.00 0.00 3.53
2389 4054 5.057149 ACGAGGCTAGCATTTATAGTTTGG 58.943 41.667 18.24 0.00 0.00 3.28
2390 4055 6.145696 GGTACGAGGCTAGCATTTATAGTTTG 59.854 42.308 18.24 0.00 0.00 2.93
2391 4056 6.183360 TGGTACGAGGCTAGCATTTATAGTTT 60.183 38.462 18.24 0.00 0.00 2.66
2392 4057 5.303589 TGGTACGAGGCTAGCATTTATAGTT 59.696 40.000 18.24 0.00 0.00 2.24
2393 4058 4.831155 TGGTACGAGGCTAGCATTTATAGT 59.169 41.667 18.24 8.56 0.00 2.12
2394 4059 5.047943 AGTGGTACGAGGCTAGCATTTATAG 60.048 44.000 18.24 2.87 0.00 1.31
2395 4060 4.831155 AGTGGTACGAGGCTAGCATTTATA 59.169 41.667 18.24 0.50 0.00 0.98
2396 4061 3.641906 AGTGGTACGAGGCTAGCATTTAT 59.358 43.478 18.24 1.53 0.00 1.40
2397 4062 3.028850 AGTGGTACGAGGCTAGCATTTA 58.971 45.455 18.24 2.17 0.00 1.40
2398 4063 1.831736 AGTGGTACGAGGCTAGCATTT 59.168 47.619 18.24 3.23 0.00 2.32
2399 4064 1.137086 CAGTGGTACGAGGCTAGCATT 59.863 52.381 18.24 3.52 0.00 3.56
2400 4065 0.747255 CAGTGGTACGAGGCTAGCAT 59.253 55.000 18.24 10.08 0.00 3.79
2401 4066 1.945354 GCAGTGGTACGAGGCTAGCA 61.945 60.000 18.24 0.00 0.00 3.49
2402 4067 1.227002 GCAGTGGTACGAGGCTAGC 60.227 63.158 6.04 6.04 0.00 3.42
2429 4094 0.810648 TTCACGGCCAAAGATGCATC 59.189 50.000 19.37 19.37 0.00 3.91
2436 4101 2.223641 CCATGATCATTCACGGCCAAAG 60.224 50.000 5.16 0.00 33.85 2.77
2753 4422 6.349300 TCAGAATTTGTGAGCTATTCCTACC 58.651 40.000 3.10 0.00 0.00 3.18
2774 4450 5.796935 CCTGCATAGTTCGAAACAAATTCAG 59.203 40.000 0.00 1.68 37.96 3.02
2786 4462 2.098607 TCTCCGTTACCTGCATAGTTCG 59.901 50.000 0.00 0.00 0.00 3.95
2830 4509 3.386078 TCTGCAGTATGATGTCCTCCTTC 59.614 47.826 14.67 0.00 39.69 3.46
2921 4605 5.639506 AGGTCTGTGAATTCAAGATAACGTG 59.360 40.000 10.35 0.00 0.00 4.49
2948 4636 7.161404 TGATTAGTAGTAATATGCAAGCCCTG 58.839 38.462 2.71 0.00 0.00 4.45
2963 4651 9.053840 CAATGAAGATGCAGATTGATTAGTAGT 57.946 33.333 0.00 0.00 0.00 2.73
2964 4652 9.269453 TCAATGAAGATGCAGATTGATTAGTAG 57.731 33.333 0.00 0.00 31.44 2.57
2965 4653 9.049523 GTCAATGAAGATGCAGATTGATTAGTA 57.950 33.333 0.00 0.00 37.22 1.82
2967 4655 7.927048 TGTCAATGAAGATGCAGATTGATTAG 58.073 34.615 0.00 2.38 37.22 1.73
2975 4663 3.986996 TCCTGTCAATGAAGATGCAGA 57.013 42.857 0.00 0.00 0.00 4.26
2976 4664 6.262496 ACAATATCCTGTCAATGAAGATGCAG 59.738 38.462 0.00 0.00 0.00 4.41
3033 4721 1.422024 TCAAGTCATGAACCCGGGAAA 59.578 47.619 32.02 12.74 34.30 3.13
3060 4748 2.074547 GCACTCTGCATTGCATGTTT 57.925 45.000 12.53 0.00 44.26 2.83
3151 4839 1.680651 CAGTCCTCCCTCAGTCGCT 60.681 63.158 0.00 0.00 0.00 4.93
3223 4911 5.396213 CCTTAGAACTTGAGATAGCTTGGCT 60.396 44.000 0.00 0.00 43.41 4.75
3224 4912 4.813697 CCTTAGAACTTGAGATAGCTTGGC 59.186 45.833 0.00 0.00 0.00 4.52
3238 4926 3.310193 GGGCCTACTGATCCTTAGAACT 58.690 50.000 0.84 0.00 0.00 3.01
3447 5135 0.693049 CAGCCTTTGTACAGTCCCCT 59.307 55.000 0.00 0.00 0.00 4.79
3560 5248 3.380142 TCGTTACACCCGTTAAAGTCAC 58.620 45.455 0.00 0.00 0.00 3.67
3617 5305 4.000331 CACCCAATTACATGGTGCAAAA 58.000 40.909 0.00 0.00 42.71 2.44
3714 5442 4.456535 TGGTTGTGTGCATTAAGTAGTGT 58.543 39.130 0.00 0.00 0.00 3.55
3717 5445 4.082841 TGCATGGTTGTGTGCATTAAGTAG 60.083 41.667 0.00 0.00 45.60 2.57
3749 5477 3.498018 TGTCGACAACCTTGATGTGATTG 59.502 43.478 17.62 0.00 0.00 2.67
3758 5486 5.107109 TCATGAAATTGTCGACAACCTTG 57.893 39.130 31.87 26.02 38.86 3.61
3789 5519 2.430465 TGGAGCTGATTTTCACAGAGC 58.570 47.619 0.00 0.00 37.54 4.09
3793 5523 5.477637 TGATGAAATGGAGCTGATTTTCACA 59.522 36.000 13.69 11.58 39.94 3.58
3991 5894 6.682611 GCTCTGCTCTCTAAAATTCAGCTCTA 60.683 42.308 0.00 0.00 0.00 2.43
4007 5910 3.413846 TGTTTGAGATTGCTCTGCTCT 57.586 42.857 0.00 0.00 41.84 4.09
4018 5921 5.411669 CGTAAACTTAGGGCTTGTTTGAGAT 59.588 40.000 0.00 0.00 35.77 2.75
4021 5924 4.273969 CACGTAAACTTAGGGCTTGTTTGA 59.726 41.667 0.00 0.00 35.77 2.69
4042 5945 5.740099 GCGAGTTCACTTCTTATCTACTCAC 59.260 44.000 0.00 0.00 32.22 3.51
4128 6031 7.052142 ACCACACGTTTTTATCCCATTTTAA 57.948 32.000 0.00 0.00 0.00 1.52
4140 6043 4.985538 TTCCATGTTACCACACGTTTTT 57.014 36.364 0.00 0.00 35.03 1.94
4202 6105 0.670546 AGTCCAATGCAAGTCGTCCG 60.671 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.