Multiple sequence alignment - TraesCS6A01G309400

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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 TraesCS6A01G309400 chr6A 100.000 4218 0 0 1 4218 545321797 545317580 0.000000e+00 7790.0
1 TraesCS6A01G309400 chr6A 75.996 904 189 26 2047 2939 71066981 71067867 3.870000e-120 442.0
2 TraesCS6A01G309400 chr6D 92.292 3866 167 48 408 4218 399221351 399217562 0.000000e+00 5367.0
3 TraesCS6A01G309400 chr6D 89.421 397 34 5 1 397 399221834 399221446 1.050000e-135 494.0
4 TraesCS6A01G309400 chr6D 76.053 902 192 23 2047 2939 56552223 56553109 8.320000e-122 448.0
5 TraesCS6A01G309400 chr6B 90.367 3436 155 75 843 4218 597558790 597555471 0.000000e+00 4349.0
6 TraesCS6A01G309400 chr6B 84.507 852 75 16 1 805 597559632 597558791 0.000000e+00 789.0
7 TraesCS6A01G309400 chr6B 75.388 902 198 23 2047 2939 127040030 127040916 8.440000e-112 414.0
8 TraesCS6A01G309400 chr7D 83.088 1153 174 14 1804 2939 198501231 198502379 0.000000e+00 1029.0
9 TraesCS6A01G309400 chr7A 82.738 1147 177 14 1811 2939 207547417 207548560 0.000000e+00 1002.0
10 TraesCS6A01G309400 chr7B 81.873 1153 188 14 1811 2945 162924203 162923054 0.000000e+00 952.0
11 TraesCS6A01G309400 chr7B 84.270 89 11 2 3644 3730 8516942 8516855 2.700000e-12 84.2
12 TraesCS6A01G309400 chr1D 71.698 318 69 21 2588 2896 15049043 15048738 7.570000e-08 69.4
13 TraesCS6A01G309400 chr1D 94.118 34 2 0 128 161 427600074 427600107 8.000000e-03 52.8
14 TraesCS6A01G309400 chr4A 97.297 37 1 0 325 361 674620797 674620833 3.520000e-06 63.9


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 TraesCS6A01G309400 chr6A 545317580 545321797 4217 True 7790.0 7790 100.0000 1 4218 1 chr6A.!!$R1 4217
1 TraesCS6A01G309400 chr6A 71066981 71067867 886 False 442.0 442 75.9960 2047 2939 1 chr6A.!!$F1 892
2 TraesCS6A01G309400 chr6D 399217562 399221834 4272 True 2930.5 5367 90.8565 1 4218 2 chr6D.!!$R1 4217
3 TraesCS6A01G309400 chr6D 56552223 56553109 886 False 448.0 448 76.0530 2047 2939 1 chr6D.!!$F1 892
4 TraesCS6A01G309400 chr6B 597555471 597559632 4161 True 2569.0 4349 87.4370 1 4218 2 chr6B.!!$R1 4217
5 TraesCS6A01G309400 chr6B 127040030 127040916 886 False 414.0 414 75.3880 2047 2939 1 chr6B.!!$F1 892
6 TraesCS6A01G309400 chr7D 198501231 198502379 1148 False 1029.0 1029 83.0880 1804 2939 1 chr7D.!!$F1 1135
7 TraesCS6A01G309400 chr7A 207547417 207548560 1143 False 1002.0 1002 82.7380 1811 2939 1 chr7A.!!$F1 1128
8 TraesCS6A01G309400 chr7B 162923054 162924203 1149 True 952.0 952 81.8730 1811 2945 1 chr7B.!!$R2 1134

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
898 1037 0.528017 CTAGCTTGTCTCTGTCCGCA 59.472 55.0 0.00 0.00 0.00 5.69 F
1086 1227 0.033208 AGGCACCCAGAGAGAGAGAG 60.033 60.0 0.00 0.00 0.00 3.20 F
1604 1772 0.178990 GTTCCTGGCCATATGGGGAC 60.179 60.0 23.30 4.88 37.04 4.46 F
1654 1823 0.676736 GGGATCGGACCAGATCTGAC 59.323 60.0 24.62 16.25 45.82 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2813 3000 2.038813 TGGATGGAGAGCGGGTCA 59.961 61.111 10.15 0.0 0.00 4.02 R
2987 3174 3.996921 ACATCCATGATCAGATAGGGC 57.003 47.619 0.09 0.0 0.00 5.19 R
3142 3341 0.035630 ACAGACAGGATGCAGGCTTC 60.036 55.000 0.00 0.0 42.53 3.86 R
3623 3859 0.539669 AGAAAGTTGGGGGAAAGGCG 60.540 55.000 0.00 0.0 0.00 5.52 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
40 41 9.571804 GAAAATCAATCTTCACAATTTTTGACG 57.428 29.630 0.00 0.00 31.58 4.35
142 143 8.860517 ATGCTATCCATTGGGTATTCTAGATA 57.139 34.615 2.09 0.00 34.93 1.98
192 193 7.473027 TCAAAGGTCGTAAAGTTTGACTTAG 57.527 36.000 0.00 0.00 37.47 2.18
232 233 6.509523 TTATATTTTAGGACTGGGGGAGTG 57.490 41.667 0.00 0.00 33.83 3.51
248 249 8.982471 TGGGGGAGTGTGATATTAGATTAATA 57.018 34.615 0.00 0.00 35.32 0.98
297 298 7.606839 GGATGGCACTATCTTTACCTATAAACC 59.393 40.741 0.00 0.00 0.00 3.27
304 305 5.987019 TCTTTACCTATAAACCTGGCCAT 57.013 39.130 5.51 0.00 0.00 4.40
356 357 7.275888 ACTAACATGCTCAACATTTGAAAGA 57.724 32.000 0.00 0.00 39.58 2.52
362 364 4.079253 GCTCAACATTTGAAAGAGGGGTA 58.921 43.478 0.00 0.00 39.58 3.69
365 367 4.522789 TCAACATTTGAAAGAGGGGTAAGC 59.477 41.667 0.00 0.00 36.59 3.09
372 374 4.479158 TGAAAGAGGGGTAAGCATGTTTT 58.521 39.130 0.00 0.00 0.00 2.43
381 383 4.157656 GGGTAAGCATGTTTTGATAGTGCA 59.842 41.667 0.00 0.00 38.23 4.57
385 387 4.740268 AGCATGTTTTGATAGTGCACATG 58.260 39.130 21.04 11.38 45.03 3.21
398 400 8.156165 TGATAGTGCACATGTCCATAATAATCA 58.844 33.333 21.04 0.00 0.00 2.57
400 402 7.828508 AGTGCACATGTCCATAATAATCAAT 57.171 32.000 21.04 0.00 0.00 2.57
403 405 7.752239 GTGCACATGTCCATAATAATCAATAGC 59.248 37.037 13.17 0.00 0.00 2.97
405 407 8.298854 GCACATGTCCATAATAATCAATAGCAA 58.701 33.333 0.00 0.00 0.00 3.91
464 550 9.705290 ACTGCCTTAATTTTTAAGGTTAACATG 57.295 29.630 21.24 0.00 44.46 3.21
520 632 1.583477 GAAGTGCTTGCTTCAGCCC 59.417 57.895 10.03 0.00 43.10 5.19
725 861 3.607661 GGAGATCGACGGAGCCCC 61.608 72.222 0.00 0.00 0.00 5.80
750 886 4.664677 GTCACTGACGGCGGCAGT 62.665 66.667 40.67 40.67 46.86 4.40
753 889 3.923864 ACTGACGGCGGCAGTTGA 61.924 61.111 40.67 5.95 43.67 3.18
754 890 2.434884 CTGACGGCGGCAGTTGAT 60.435 61.111 33.78 0.00 0.00 2.57
755 891 1.153647 CTGACGGCGGCAGTTGATA 60.154 57.895 33.78 0.00 0.00 2.15
756 892 1.421410 CTGACGGCGGCAGTTGATAC 61.421 60.000 33.78 1.31 0.00 2.24
792 928 1.739562 CTGCTGCCGGAGTCACTTC 60.740 63.158 5.05 0.00 0.00 3.01
866 1002 1.592400 CTCGCCTCCACGTCTACCAA 61.592 60.000 0.00 0.00 0.00 3.67
876 1012 1.063951 CGTCTACCAAGTCGCGTCAC 61.064 60.000 5.77 0.00 0.00 3.67
898 1037 0.528017 CTAGCTTGTCTCTGTCCGCA 59.472 55.000 0.00 0.00 0.00 5.69
940 1080 0.765510 AACGAGGGTGAGAAGCCTTT 59.234 50.000 0.00 0.00 0.00 3.11
1085 1226 0.324183 CAGGCACCCAGAGAGAGAGA 60.324 60.000 0.00 0.00 0.00 3.10
1086 1227 0.033208 AGGCACCCAGAGAGAGAGAG 60.033 60.000 0.00 0.00 0.00 3.20
1147 1292 2.825836 GGCAGGCCATGAAGTCGG 60.826 66.667 5.01 0.00 35.81 4.79
1154 1299 1.153289 CCATGAAGTCGGCCAGGAG 60.153 63.158 2.24 0.00 0.00 3.69
1311 1468 1.135603 TGCTGATTGATTCTTGTGCGC 60.136 47.619 0.00 0.00 0.00 6.09
1352 1509 3.786048 GGATTTATCTTTCTTTGCGTGCG 59.214 43.478 0.00 0.00 0.00 5.34
1356 1513 2.349376 CTTTCTTTGCGTGCGTGCG 61.349 57.895 0.00 0.00 37.81 5.34
1372 1529 2.724708 GCGTGCTGCAGAGAAGACG 61.725 63.158 20.43 16.57 45.45 4.18
1402 1559 1.748122 CAAAGCAGAGGAGCGGCAT 60.748 57.895 1.45 0.00 40.40 4.40
1410 1567 2.281345 GGAGCGGCATGGGATGAG 60.281 66.667 1.45 0.00 0.00 2.90
1427 1584 1.301677 GAGCAAGGGAAGCGTCAAGG 61.302 60.000 1.14 0.00 37.01 3.61
1482 1647 1.678101 GGATTCAGCTGGTATGTTGCC 59.322 52.381 15.13 2.14 0.00 4.52
1483 1648 1.331756 GATTCAGCTGGTATGTTGCCG 59.668 52.381 15.13 0.00 0.00 5.69
1484 1649 1.305219 TTCAGCTGGTATGTTGCCGC 61.305 55.000 15.13 0.00 0.00 6.53
1485 1650 2.819595 AGCTGGTATGTTGCCGCG 60.820 61.111 0.00 0.00 33.25 6.46
1486 1651 2.817834 GCTGGTATGTTGCCGCGA 60.818 61.111 8.23 0.00 0.00 5.87
1487 1652 2.813179 GCTGGTATGTTGCCGCGAG 61.813 63.158 8.23 0.00 0.00 5.03
1488 1653 2.813179 CTGGTATGTTGCCGCGAGC 61.813 63.158 8.23 10.56 44.14 5.03
1489 1654 3.573491 GGTATGTTGCCGCGAGCC 61.573 66.667 8.23 0.00 42.71 4.70
1490 1655 3.573491 GTATGTTGCCGCGAGCCC 61.573 66.667 8.23 3.58 42.71 5.19
1545 1710 1.199097 CGTTCTTGGGGATTGTTTCCG 59.801 52.381 0.00 0.00 46.52 4.30
1604 1772 0.178990 GTTCCTGGCCATATGGGGAC 60.179 60.000 23.30 4.88 37.04 4.46
1621 1789 4.105697 TGGGGACTGAATTAATGGGTATCC 59.894 45.833 0.00 0.00 0.00 2.59
1641 1810 1.745087 CAATGGAGTTTGTGGGGATCG 59.255 52.381 0.00 0.00 0.00 3.69
1654 1823 0.676736 GGGATCGGACCAGATCTGAC 59.323 60.000 24.62 16.25 45.82 3.51
1656 1825 1.025812 GATCGGACCAGATCTGACGT 58.974 55.000 24.62 14.09 45.82 4.34
1982 2154 1.954146 GCTGTCGCACGTCAAGGAA 60.954 57.895 0.00 0.00 35.78 3.36
1994 2166 1.452108 CAAGGAATGGACCCTCCGC 60.452 63.158 4.46 0.00 40.17 5.54
3138 3337 7.114247 TGTTCTTTCGTTCAGTTTCTTTGTTTG 59.886 33.333 0.00 0.00 0.00 2.93
3139 3338 6.674066 TCTTTCGTTCAGTTTCTTTGTTTGT 58.326 32.000 0.00 0.00 0.00 2.83
3141 3340 7.650104 TCTTTCGTTCAGTTTCTTTGTTTGTTT 59.350 29.630 0.00 0.00 0.00 2.83
3142 3341 6.683090 TCGTTCAGTTTCTTTGTTTGTTTG 57.317 33.333 0.00 0.00 0.00 2.93
3143 3342 6.439599 TCGTTCAGTTTCTTTGTTTGTTTGA 58.560 32.000 0.00 0.00 0.00 2.69
3144 3343 6.918569 TCGTTCAGTTTCTTTGTTTGTTTGAA 59.081 30.769 0.00 0.00 0.00 2.69
3154 3368 2.224018 TGTTTGTTTGAAGCCTGCATCC 60.224 45.455 0.00 0.00 0.00 3.51
3174 3389 6.628175 GCATCCTGTCTGTATGAAGTCTACAA 60.628 42.308 0.00 0.00 0.00 2.41
3177 3392 6.071896 TCCTGTCTGTATGAAGTCTACAACTG 60.072 42.308 0.00 0.00 38.58 3.16
3253 3468 4.262079 GGATTACATACTCCTTCGGTGAGG 60.262 50.000 0.00 0.00 38.20 3.86
3268 3483 2.814336 GGTGAGGAAAGGTGTTGCTAAG 59.186 50.000 0.00 0.00 0.00 2.18
3286 3501 1.656587 AGTGCATAAGGGTGGACAGA 58.343 50.000 0.00 0.00 42.17 3.41
3314 3529 4.099573 GTCCGGTCTCTCATCCATTTCTTA 59.900 45.833 0.00 0.00 0.00 2.10
3347 3562 4.444733 CCCTTTCAAAATGGAGGCAAAAGT 60.445 41.667 0.00 0.00 0.00 2.66
3350 3565 6.765512 CCTTTCAAAATGGAGGCAAAAGTTTA 59.234 34.615 0.00 0.00 0.00 2.01
3351 3566 7.254761 CCTTTCAAAATGGAGGCAAAAGTTTAC 60.255 37.037 0.00 0.00 0.00 2.01
3352 3567 6.227298 TCAAAATGGAGGCAAAAGTTTACA 57.773 33.333 0.00 0.00 0.00 2.41
3353 3568 6.825610 TCAAAATGGAGGCAAAAGTTTACAT 58.174 32.000 0.00 0.00 0.00 2.29
3355 3570 6.418057 AAATGGAGGCAAAAGTTTACATCA 57.582 33.333 5.81 0.00 0.00 3.07
3356 3571 6.610075 AATGGAGGCAAAAGTTTACATCAT 57.390 33.333 5.81 0.00 0.00 2.45
3358 3573 6.024552 TGGAGGCAAAAGTTTACATCATTC 57.975 37.500 5.81 0.00 0.00 2.67
3360 3575 5.047377 GGAGGCAAAAGTTTACATCATTCCA 60.047 40.000 5.81 0.00 0.00 3.53
3361 3576 6.351286 GGAGGCAAAAGTTTACATCATTCCAT 60.351 38.462 5.81 0.00 0.00 3.41
3435 3669 7.338449 ACCAGAGCTAACAAACAAAGACTAAAA 59.662 33.333 0.00 0.00 0.00 1.52
3477 3712 6.669154 TCTCTTGGCAGAATATTTCCCAAATT 59.331 34.615 13.16 0.00 35.36 1.82
3513 3748 1.275657 CACACGTCGTTGCCTCAAC 59.724 57.895 0.00 0.00 40.54 3.18
3515 3750 0.874607 ACACGTCGTTGCCTCAACTC 60.875 55.000 0.00 1.42 41.62 3.01
3520 3755 2.993899 CGTCGTTGCCTCAACTCTAATT 59.006 45.455 7.91 0.00 41.62 1.40
3527 3762 5.726980 TGCCTCAACTCTAATTTTGCATT 57.273 34.783 0.00 0.00 0.00 3.56
3538 3773 6.575267 TCTAATTTTGCATTGGATGATGGTG 58.425 36.000 0.00 0.00 0.00 4.17
3554 3789 4.588106 TGATGGTGGACATTGTCAAAACAT 59.412 37.500 18.09 17.71 40.72 2.71
3605 3841 1.203928 ATCGATCAAGCGAAAGAGCG 58.796 50.000 0.00 3.28 44.22 5.03
3636 3872 4.293671 CCACCGCCTTTCCCCCAA 62.294 66.667 0.00 0.00 0.00 4.12
3645 3881 2.438021 GCCTTTCCCCCAACTTTCTTTT 59.562 45.455 0.00 0.00 0.00 2.27
3686 3922 6.548251 TCAATCTATGCATCAAACATCATGGT 59.452 34.615 0.19 0.00 0.00 3.55
3687 3923 6.971726 ATCTATGCATCAAACATCATGGTT 57.028 33.333 0.19 0.00 0.00 3.67
3735 3973 2.704725 ACAACCGTGTTCATGCATTC 57.295 45.000 0.00 0.00 32.58 2.67
3757 3995 3.699038 CCTTTTTCCTCCTTTCACACACA 59.301 43.478 0.00 0.00 0.00 3.72
3831 4069 1.447314 CGTCGGGTCTTTGGCTACC 60.447 63.158 0.00 0.00 34.85 3.18
3862 4100 1.604604 ATTATCCCAATCCAACGCGG 58.395 50.000 12.47 0.00 0.00 6.46
3864 4102 3.323286 TCCCAATCCAACGCGGGA 61.323 61.111 12.47 9.14 45.66 5.14
3865 4103 2.824041 CCCAATCCAACGCGGGAG 60.824 66.667 12.47 0.00 41.62 4.30
3923 4161 5.839621 AGATTAAATTGACATGCTGATGCC 58.160 37.500 0.00 0.00 38.71 4.40
3946 4184 3.198200 TCCCCGGAAAATAGTGATCGAAA 59.802 43.478 0.73 0.00 0.00 3.46
3947 4185 3.942748 CCCCGGAAAATAGTGATCGAAAA 59.057 43.478 0.73 0.00 0.00 2.29
3948 4186 4.035208 CCCCGGAAAATAGTGATCGAAAAG 59.965 45.833 0.73 0.00 0.00 2.27
3949 4187 4.495844 CCCGGAAAATAGTGATCGAAAAGC 60.496 45.833 0.73 0.00 0.00 3.51
3969 4207 2.999063 GCAAGCAAGCCACCCCAT 60.999 61.111 0.00 0.00 0.00 4.00
3970 4208 3.010413 GCAAGCAAGCCACCCCATC 62.010 63.158 0.00 0.00 0.00 3.51
3971 4209 2.037847 AAGCAAGCCACCCCATCC 59.962 61.111 0.00 0.00 0.00 3.51
3972 4210 2.855770 AAGCAAGCCACCCCATCCA 61.856 57.895 0.00 0.00 0.00 3.41
3973 4211 2.283821 GCAAGCCACCCCATCCAA 60.284 61.111 0.00 0.00 0.00 3.53
3989 4227 3.449746 TCCAACCCCATCTTTTACCTG 57.550 47.619 0.00 0.00 0.00 4.00
4013 4251 0.536460 TTTTCTTGACTGCCCCGGTC 60.536 55.000 0.00 0.00 39.93 4.79
4018 4256 1.534476 TGACTGCCCCGGTCAGTAA 60.534 57.895 21.86 14.72 43.73 2.24
4019 4257 1.079336 GACTGCCCCGGTCAGTAAC 60.079 63.158 21.86 10.52 44.09 2.50
4020 4258 1.535687 ACTGCCCCGGTCAGTAACT 60.536 57.895 20.87 1.40 42.45 2.24
4022 4260 1.534476 TGCCCCGGTCAGTAACTGA 60.534 57.895 0.00 0.00 38.25 3.41
4023 4261 1.218316 GCCCCGGTCAGTAACTGAG 59.782 63.158 0.00 0.00 41.46 3.35
4031 4270 4.498850 CCGGTCAGTAACTGAGATGAGATG 60.499 50.000 0.00 0.00 41.46 2.90
4166 4408 3.726004 TGGATCCACGCACCAGAT 58.274 55.556 11.44 0.00 0.00 2.90
4167 4409 2.909140 TGGATCCACGCACCAGATA 58.091 52.632 11.44 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 161 7.754851 AACTTTACGACCTTTGACCAATAAT 57.245 32.000 0.00 0.00 0.00 1.28
165 166 4.333372 GTCAAACTTTACGACCTTTGACCA 59.667 41.667 9.86 0.00 43.35 4.02
205 206 8.004801 ACTCCCCCAGTCCTAAAATATAATTTG 58.995 37.037 0.00 0.00 0.00 2.32
209 210 5.974370 ACACTCCCCCAGTCCTAAAATATAA 59.026 40.000 0.00 0.00 30.26 0.98
248 249 8.202461 TCCCGATACTGGATATAGACAAATTT 57.798 34.615 0.00 0.00 0.00 1.82
256 257 3.960755 TGCCATCCCGATACTGGATATAG 59.039 47.826 0.00 0.00 40.68 1.31
267 268 3.008049 GGTAAAGATAGTGCCATCCCGAT 59.992 47.826 0.00 0.00 0.00 4.18
271 272 7.606839 GGTTTATAGGTAAAGATAGTGCCATCC 59.393 40.741 0.00 0.00 30.76 3.51
297 298 8.281212 AGTCAAACTTTATAAACTATGGCCAG 57.719 34.615 13.05 0.00 0.00 4.85
316 317 6.972328 GCATGTTAGTTTTGTTCTGAGTCAAA 59.028 34.615 0.00 6.17 32.75 2.69
331 332 7.715657 TCTTTCAAATGTTGAGCATGTTAGTT 58.284 30.769 0.00 0.00 41.38 2.24
356 357 4.949856 CACTATCAAAACATGCTTACCCCT 59.050 41.667 0.00 0.00 0.00 4.79
362 364 4.852134 TGTGCACTATCAAAACATGCTT 57.148 36.364 19.41 0.00 37.20 3.91
372 374 8.156165 TGATTATTATGGACATGTGCACTATCA 58.844 33.333 23.18 20.24 32.58 2.15
421 507 5.381757 AGGCAGTTAAATCAACCACAACTA 58.618 37.500 0.00 0.00 37.93 2.24
422 508 4.215109 AGGCAGTTAAATCAACCACAACT 58.785 39.130 0.00 0.00 37.93 3.16
424 510 6.716934 TTAAGGCAGTTAAATCAACCACAA 57.283 33.333 0.00 0.00 37.93 3.33
464 550 2.483877 TGCAGTCGAATCAACAACATCC 59.516 45.455 0.00 0.00 0.00 3.51
725 861 2.258591 CGTCAGTGACCAGTCCCG 59.741 66.667 17.57 0.00 0.00 5.14
750 886 0.317854 CAGATCGAGCGCGGTATCAA 60.318 55.000 19.82 4.20 38.28 2.57
753 889 2.049985 GCAGATCGAGCGCGGTAT 60.050 61.111 12.41 0.75 38.28 2.73
754 890 3.182472 GAGCAGATCGAGCGCGGTA 62.182 63.158 12.41 0.00 38.28 4.02
755 891 4.560856 GAGCAGATCGAGCGCGGT 62.561 66.667 12.23 12.23 38.28 5.68
756 892 4.263209 AGAGCAGATCGAGCGCGG 62.263 66.667 10.69 0.00 36.87 6.46
792 928 2.674220 GCAGGGGAGACTTGGGGAG 61.674 68.421 0.00 0.00 0.00 4.30
795 931 3.732849 GGGCAGGGGAGACTTGGG 61.733 72.222 0.00 0.00 0.00 4.12
876 1012 0.179124 GGACAGAGACAAGCTAGCGG 60.179 60.000 9.55 8.52 0.00 5.52
940 1080 2.280524 CTGTCGTTGAACGGGGCA 60.281 61.111 18.32 12.93 42.81 5.36
1085 1226 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1086 1227 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1154 1299 3.827898 CGTCCCCTCTCGACAGGC 61.828 72.222 0.32 0.00 31.23 4.85
1277 1434 4.406173 AGCACGAGTCTGTCCGCG 62.406 66.667 0.00 0.00 0.00 6.46
1278 1435 2.549611 ATCAGCACGAGTCTGTCCGC 62.550 60.000 0.00 0.00 33.48 5.54
1279 1436 0.109086 AATCAGCACGAGTCTGTCCG 60.109 55.000 0.00 0.00 33.48 4.79
1280 1437 1.067565 TCAATCAGCACGAGTCTGTCC 60.068 52.381 0.00 0.00 33.48 4.02
1281 1438 2.354109 TCAATCAGCACGAGTCTGTC 57.646 50.000 0.00 0.00 33.48 3.51
1282 1439 3.056250 AGAATCAATCAGCACGAGTCTGT 60.056 43.478 0.00 0.00 33.21 3.41
1283 1440 3.519579 AGAATCAATCAGCACGAGTCTG 58.480 45.455 0.00 0.00 33.21 3.51
1284 1441 3.883830 AGAATCAATCAGCACGAGTCT 57.116 42.857 0.00 0.00 29.78 3.24
1285 1442 3.681897 ACAAGAATCAATCAGCACGAGTC 59.318 43.478 0.00 0.00 0.00 3.36
1286 1443 3.434641 CACAAGAATCAATCAGCACGAGT 59.565 43.478 0.00 0.00 0.00 4.18
1287 1444 3.727079 GCACAAGAATCAATCAGCACGAG 60.727 47.826 0.00 0.00 0.00 4.18
1288 1445 2.160219 GCACAAGAATCAATCAGCACGA 59.840 45.455 0.00 0.00 0.00 4.35
1289 1446 2.512885 GCACAAGAATCAATCAGCACG 58.487 47.619 0.00 0.00 0.00 5.34
1290 1447 2.512885 CGCACAAGAATCAATCAGCAC 58.487 47.619 0.00 0.00 0.00 4.40
1291 1448 1.135603 GCGCACAAGAATCAATCAGCA 60.136 47.619 0.30 0.00 0.00 4.41
1292 1449 1.131883 AGCGCACAAGAATCAATCAGC 59.868 47.619 11.47 0.00 0.00 4.26
1293 1450 3.168963 CAAGCGCACAAGAATCAATCAG 58.831 45.455 11.47 0.00 0.00 2.90
1311 1468 2.134789 CCCCCTCATTCAGAACCAAG 57.865 55.000 0.00 0.00 0.00 3.61
1356 1513 1.739562 CCCGTCTTCTCTGCAGCAC 60.740 63.158 9.47 0.00 0.00 4.40
1372 1529 3.140814 GCTTTGATGGCGTCCCCC 61.141 66.667 3.88 0.00 0.00 5.40
1402 1559 1.304282 GCTTCCCTTGCTCATCCCA 59.696 57.895 0.00 0.00 0.00 4.37
1410 1567 1.600916 ACCTTGACGCTTCCCTTGC 60.601 57.895 0.00 0.00 0.00 4.01
1489 1654 3.901797 AAGGAAGCAAGGGACGCGG 62.902 63.158 12.47 0.00 0.00 6.46
1490 1655 2.358737 AAGGAAGCAAGGGACGCG 60.359 61.111 3.53 3.53 0.00 6.01
1491 1656 2.041115 GGAAGGAAGCAAGGGACGC 61.041 63.158 0.00 0.00 0.00 5.19
1492 1657 0.674895 CAGGAAGGAAGCAAGGGACG 60.675 60.000 0.00 0.00 0.00 4.79
1493 1658 0.402121 ACAGGAAGGAAGCAAGGGAC 59.598 55.000 0.00 0.00 0.00 4.46
1494 1659 0.401738 CACAGGAAGGAAGCAAGGGA 59.598 55.000 0.00 0.00 0.00 4.20
1557 1722 0.541392 TCCTGCCGTATCATGCAACT 59.459 50.000 0.00 0.00 36.98 3.16
1559 1724 2.121291 TTTCCTGCCGTATCATGCAA 57.879 45.000 0.00 0.00 36.98 4.08
1560 1725 2.346766 ATTTCCTGCCGTATCATGCA 57.653 45.000 0.00 0.00 35.86 3.96
1604 1772 7.006509 ACTCCATTGGATACCCATTAATTCAG 58.993 38.462 5.70 0.00 43.12 3.02
1621 1789 1.745087 CGATCCCCACAAACTCCATTG 59.255 52.381 0.00 0.00 36.37 2.82
1641 1810 1.737363 GCTCAACGTCAGATCTGGTCC 60.737 57.143 22.42 9.90 0.00 4.46
1654 1823 2.473530 TTGCAAAAGTCAGCTCAACG 57.526 45.000 0.00 0.00 0.00 4.10
1656 1825 3.551454 GCAGATTGCAAAAGTCAGCTCAA 60.551 43.478 1.71 0.00 44.26 3.02
1709 1881 4.941309 GTGTCGGCGGGTTTGGGT 62.941 66.667 7.21 0.00 0.00 4.51
2813 3000 2.038813 TGGATGGAGAGCGGGTCA 59.961 61.111 10.15 0.00 0.00 4.02
2987 3174 3.996921 ACATCCATGATCAGATAGGGC 57.003 47.619 0.09 0.00 0.00 5.19
2988 3175 7.191593 TCATTACATCCATGATCAGATAGGG 57.808 40.000 0.09 0.00 0.00 3.53
3138 3337 1.200948 GACAGGATGCAGGCTTCAAAC 59.799 52.381 9.05 0.00 42.53 2.93
3139 3338 1.074405 AGACAGGATGCAGGCTTCAAA 59.926 47.619 9.05 0.00 42.53 2.69
3141 3340 0.035725 CAGACAGGATGCAGGCTTCA 60.036 55.000 9.05 0.00 42.53 3.02
3142 3341 0.035630 ACAGACAGGATGCAGGCTTC 60.036 55.000 0.00 0.00 42.53 3.86
3143 3342 1.279496 TACAGACAGGATGCAGGCTT 58.721 50.000 0.00 0.00 42.53 4.35
3144 3343 1.140452 CATACAGACAGGATGCAGGCT 59.860 52.381 0.00 0.00 42.53 4.58
3154 3368 5.574830 GCAGTTGTAGACTTCATACAGACAG 59.425 44.000 0.00 0.00 36.10 3.51
3174 3389 5.423015 CATCTTACCACTACATTCTGCAGT 58.577 41.667 14.67 0.00 0.00 4.40
3177 3392 5.023533 TCCATCTTACCACTACATTCTGC 57.976 43.478 0.00 0.00 0.00 4.26
3180 3395 6.258947 GCTTCTTCCATCTTACCACTACATTC 59.741 42.308 0.00 0.00 0.00 2.67
3189 3404 3.629398 CCACATGCTTCTTCCATCTTACC 59.371 47.826 0.00 0.00 0.00 2.85
3268 3483 2.292267 CATCTGTCCACCCTTATGCAC 58.708 52.381 0.00 0.00 0.00 4.57
3286 3501 1.698506 GATGAGAGACCGGACTCCAT 58.301 55.000 26.94 26.15 37.60 3.41
3435 3669 4.373156 AGAGAGCAATGTTTACAAGGGT 57.627 40.909 0.00 0.00 0.00 4.34
3477 3712 1.214589 GCTACGGTTGGAGCGAAGA 59.785 57.895 6.53 0.00 42.41 2.87
3513 3748 6.700081 CACCATCATCCAATGCAAAATTAGAG 59.300 38.462 0.00 0.00 0.00 2.43
3515 3750 5.756347 CCACCATCATCCAATGCAAAATTAG 59.244 40.000 0.00 0.00 0.00 1.73
3520 3755 2.496871 GTCCACCATCATCCAATGCAAA 59.503 45.455 0.00 0.00 0.00 3.68
3527 3762 2.308275 TGACAATGTCCACCATCATCCA 59.692 45.455 11.24 0.00 31.75 3.41
3538 3773 6.016777 AGTCTTCAGATGTTTTGACAATGTCC 60.017 38.462 11.24 0.00 0.00 4.02
3574 3810 5.066375 TCGCTTGATCGATTTGAAATGGAAT 59.934 36.000 6.70 0.00 33.02 3.01
3623 3859 0.539669 AGAAAGTTGGGGGAAAGGCG 60.540 55.000 0.00 0.00 0.00 5.52
3645 3881 9.410556 GCATAGATTGAAAGTTTTTCTAGCAAA 57.589 29.630 3.53 0.00 0.00 3.68
3657 3893 8.058667 TGATGTTTGATGCATAGATTGAAAGT 57.941 30.769 0.00 0.00 0.00 2.66
3670 3906 5.058149 TGTACAACCATGATGTTTGATGC 57.942 39.130 9.76 0.45 32.27 3.91
3719 3957 1.909700 AAGGAATGCATGAACACGGT 58.090 45.000 0.00 0.00 0.00 4.83
3735 3973 3.699038 TGTGTGTGAAAGGAGGAAAAAGG 59.301 43.478 0.00 0.00 0.00 3.11
3757 3995 2.162681 CTTCCTTGGGAGCAAATTCGT 58.837 47.619 0.00 0.00 31.21 3.85
3816 4054 1.376812 GGTGGTAGCCAAAGACCCG 60.377 63.158 0.00 0.00 34.18 5.28
3848 4086 2.824041 CTCCCGCGTTGGATTGGG 60.824 66.667 4.92 0.00 42.00 4.12
3852 4090 0.036306 AAAACTCTCCCGCGTTGGAT 59.964 50.000 4.92 0.00 42.00 3.41
3862 4100 8.814235 GGCTGTTTTTAGTTTTTAAAACTCTCC 58.186 33.333 23.96 12.02 42.10 3.71
3864 4102 9.938280 AAGGCTGTTTTTAGTTTTTAAAACTCT 57.062 25.926 23.96 10.63 42.10 3.24
3865 4103 9.967245 CAAGGCTGTTTTTAGTTTTTAAAACTC 57.033 29.630 23.96 11.68 42.10 3.01
3923 4161 2.364324 TCGATCACTATTTTCCGGGGAG 59.636 50.000 0.00 0.00 0.00 4.30
3946 4184 1.068585 GTGGCTTGCTTGCTTGCTT 59.931 52.632 9.28 0.00 0.00 3.91
3947 4185 2.732658 GTGGCTTGCTTGCTTGCT 59.267 55.556 9.28 0.00 0.00 3.91
3948 4186 2.356673 GGTGGCTTGCTTGCTTGC 60.357 61.111 1.96 0.00 0.00 4.01
3949 4187 2.341176 GGGTGGCTTGCTTGCTTG 59.659 61.111 1.96 0.00 0.00 4.01
3969 4207 2.042433 CCAGGTAAAAGATGGGGTTGGA 59.958 50.000 0.00 0.00 0.00 3.53
3970 4208 2.225267 ACCAGGTAAAAGATGGGGTTGG 60.225 50.000 0.00 0.00 38.48 3.77
3971 4209 3.089284 GACCAGGTAAAAGATGGGGTTG 58.911 50.000 0.00 0.00 38.48 3.77
3972 4210 2.042569 GGACCAGGTAAAAGATGGGGTT 59.957 50.000 0.00 0.00 38.48 4.11
3973 4211 1.639108 GGACCAGGTAAAAGATGGGGT 59.361 52.381 0.00 0.00 38.48 4.95
3989 4227 1.248486 GGGCAGTCAAGAAAAGGACC 58.752 55.000 0.00 0.00 34.58 4.46
4013 4251 4.041049 GCGACATCTCATCTCAGTTACTG 58.959 47.826 5.94 5.94 0.00 2.74
4018 4256 0.383590 CGGCGACATCTCATCTCAGT 59.616 55.000 0.00 0.00 0.00 3.41
4019 4257 0.665298 TCGGCGACATCTCATCTCAG 59.335 55.000 4.99 0.00 0.00 3.35
4020 4258 0.382158 GTCGGCGACATCTCATCTCA 59.618 55.000 33.07 0.00 32.09 3.27
4022 4260 1.095807 TCGTCGGCGACATCTCATCT 61.096 55.000 35.62 0.00 42.81 2.90
4023 4261 1.355563 TCGTCGGCGACATCTCATC 59.644 57.895 35.62 10.19 42.81 2.92
4051 4293 3.729698 GCGTAACGTGTTGGGGGC 61.730 66.667 0.00 0.00 0.00 5.80
4085 4327 2.397549 GCAATTTTGACTTGCTTCGCT 58.602 42.857 0.99 0.00 44.36 4.93
4125 4367 2.244651 CGCCGGGCTTTTCTATCCG 61.245 63.158 18.34 0.00 41.90 4.18
4164 4406 6.266558 TGGAGCACTTCTCTATCCTTTCTATC 59.733 42.308 0.00 0.00 41.60 2.08
4165 4407 6.041523 GTGGAGCACTTCTCTATCCTTTCTAT 59.958 42.308 0.00 0.00 41.60 1.98
4166 4408 5.361285 GTGGAGCACTTCTCTATCCTTTCTA 59.639 44.000 0.00 0.00 41.60 2.10
4167 4409 4.161377 GTGGAGCACTTCTCTATCCTTTCT 59.839 45.833 0.00 0.00 41.60 2.52


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

AutoCloner maintained by Alex Coulton.