Multiple sequence alignment - TraesCS4B01G309300

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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 TraesCS4B01G309300 chr4B 100.000 5105 0 0 1 5105 599888164 599883060 0.000000e+00 9428.0
1 TraesCS4B01G309300 chr4D 95.255 4489 135 30 1 4453 475180108 475175662 0.000000e+00 7038.0
2 TraesCS4B01G309300 chr4D 91.574 451 33 2 4651 5096 475172723 475172273 7.260000e-173 617.0
3 TraesCS4B01G309300 chr4D 92.208 231 14 3 4197 4426 475175534 475175307 1.770000e-84 324.0
4 TraesCS4B01G309300 chr4D 90.698 129 11 1 4412 4539 475175293 475175165 2.440000e-38 171.0
5 TraesCS4B01G309300 chr4D 87.654 81 10 0 3503 3583 88142352 88142272 1.510000e-15 95.3
6 TraesCS4B01G309300 chr4A 94.668 4295 145 27 280 4519 681921371 681917106 0.000000e+00 6586.0
7 TraesCS4B01G309300 chr4A 87.901 934 76 17 4197 5096 681917081 681916151 0.000000e+00 1064.0
8 TraesCS4B01G309300 chr4A 85.566 769 97 8 1040 1795 629294194 629293427 0.000000e+00 793.0
9 TraesCS4B01G309300 chr4A 80.145 690 105 20 2479 3161 629293438 629292774 2.140000e-133 486.0
10 TraesCS4B01G309300 chr4A 81.818 275 22 9 1 264 681921750 681921493 6.700000e-49 206.0
11 TraesCS4B01G309300 chr4A 87.654 81 10 0 3503 3583 501124396 501124316 1.510000e-15 95.3
12 TraesCS4B01G309300 chr5B 84.833 2156 294 21 1021 3161 680993561 680995698 0.000000e+00 2139.0
13 TraesCS4B01G309300 chr5D 84.406 2129 283 23 1057 3159 539453810 539455915 0.000000e+00 2047.0
14 TraesCS4B01G309300 chr6B 78.230 983 166 35 3072 4036 25924608 25923656 2.050000e-163 586.0
15 TraesCS4B01G309300 chr6A 78.270 971 163 37 3072 4024 15438442 15439382 9.530000e-162 580.0
16 TraesCS4B01G309300 chr6A 73.585 1431 334 36 1463 2871 15436848 15438256 4.560000e-140 508.0
17 TraesCS4B01G309300 chr6D 77.732 970 170 35 3072 4024 14077688 14078628 2.080000e-153 553.0
18 TraesCS4B01G309300 chr1A 96.970 33 1 0 1885 1917 22869071 22869103 7.140000e-04 56.5
19 TraesCS4B01G309300 chr7B 96.875 32 1 0 2684 2715 57680410 57680379 3.000000e-03 54.7


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 TraesCS4B01G309300 chr4B 599883060 599888164 5104 True 9428.000000 9428 100.00000 1 5105 1 chr4B.!!$R1 5104
1 TraesCS4B01G309300 chr4D 475172273 475180108 7835 True 2037.500000 7038 92.43375 1 5096 4 chr4D.!!$R2 5095
2 TraesCS4B01G309300 chr4A 681916151 681921750 5599 True 2618.666667 6586 88.12900 1 5096 3 chr4A.!!$R3 5095
3 TraesCS4B01G309300 chr4A 629292774 629294194 1420 True 639.500000 793 82.85550 1040 3161 2 chr4A.!!$R2 2121
4 TraesCS4B01G309300 chr5B 680993561 680995698 2137 False 2139.000000 2139 84.83300 1021 3161 1 chr5B.!!$F1 2140
5 TraesCS4B01G309300 chr5D 539453810 539455915 2105 False 2047.000000 2047 84.40600 1057 3159 1 chr5D.!!$F1 2102
6 TraesCS4B01G309300 chr6B 25923656 25924608 952 True 586.000000 586 78.23000 3072 4036 1 chr6B.!!$R1 964
7 TraesCS4B01G309300 chr6A 15436848 15439382 2534 False 544.000000 580 75.92750 1463 4024 2 chr6A.!!$F1 2561
8 TraesCS4B01G309300 chr6D 14077688 14078628 940 False 553.000000 553 77.73200 3072 4024 1 chr6D.!!$F1 952

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
267 278 0.033796 CATCCAATGCAGGACAGGGT 60.034 55.0 0.0 0.0 41.30 4.34 F
268 279 0.033796 ATCCAATGCAGGACAGGGTG 60.034 55.0 0.0 0.0 41.30 4.61 F
270 281 0.251297 CCAATGCAGGACAGGGTGAA 60.251 55.0 0.0 0.0 0.00 3.18 F
278 395 0.320697 GGACAGGGTGAACGCTAAGT 59.679 55.0 0.0 0.0 37.38 2.24 F
2394 2547 0.309302 CGTCGCTCTCCTTCATCGAT 59.691 55.0 0.0 0.0 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1458 1.173913 TGCTCTGAAGGACGATCGAA 58.826 50.000 24.34 0.00 0.00 3.71 R
2211 2364 2.345244 CACTTGGTGAGGCTCGCT 59.655 61.111 25.73 4.87 35.23 4.93 R
2394 2547 1.005748 CAGCTGGTTGTGCGAGAGA 60.006 57.895 5.57 0.00 35.28 3.10 R
2787 2940 1.528309 CCTCAACAACCCCGTTGCT 60.528 57.895 4.46 0.00 46.20 3.91 R
4240 4432 1.001633 GCTCGTCTCCCCAACTAAACA 59.998 52.381 0.00 0.00 0.00 2.83 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
96 97 1.527311 GTTCAGAACGGCACTCAAGAC 59.473 52.381 0.00 0.00 0.00 3.01
98 99 1.006102 AGAACGGCACTCAAGACGG 60.006 57.895 0.00 0.00 0.00 4.79
107 108 0.620556 ACTCAAGACGGCAATCCCAT 59.379 50.000 0.00 0.00 0.00 4.00
109 110 2.238646 ACTCAAGACGGCAATCCCATAA 59.761 45.455 0.00 0.00 0.00 1.90
115 116 2.812011 GACGGCAATCCCATAATGTACC 59.188 50.000 0.00 0.00 0.00 3.34
151 152 6.127814 TGAGCTCAAGATTGTTCATGATTTCC 60.128 38.462 15.67 0.00 29.84 3.13
155 156 7.601508 GCTCAAGATTGTTCATGATTTCCTTTT 59.398 33.333 0.00 0.00 29.84 2.27
159 160 8.186709 AGATTGTTCATGATTTCCTTTTCAGT 57.813 30.769 0.00 0.00 0.00 3.41
174 175 7.681679 TCCTTTTCAGTTTGTAAAACCCTTTT 58.318 30.769 0.00 0.00 36.67 2.27
180 181 8.766000 TCAGTTTGTAAAACCCTTTTTCTTTC 57.234 30.769 0.00 0.00 36.32 2.62
223 224 8.218338 ACAAGATTGTTCATGTAGATTGATCC 57.782 34.615 0.00 0.00 38.47 3.36
224 225 8.051535 ACAAGATTGTTCATGTAGATTGATCCT 58.948 33.333 0.00 0.00 38.47 3.24
225 226 8.900781 CAAGATTGTTCATGTAGATTGATCCTT 58.099 33.333 0.00 0.00 0.00 3.36
239 250 7.455891 AGATTGATCCTTTTTGCTGGAAATTT 58.544 30.769 0.00 0.00 35.81 1.82
254 265 7.395772 TGCTGGAAATTTAGTATGTTCATCCAA 59.604 33.333 0.00 0.00 34.31 3.53
264 275 2.439409 TGTTCATCCAATGCAGGACAG 58.561 47.619 0.00 0.00 41.30 3.51
266 277 0.256752 TCATCCAATGCAGGACAGGG 59.743 55.000 0.00 0.00 41.30 4.45
267 278 0.033796 CATCCAATGCAGGACAGGGT 60.034 55.000 0.00 0.00 41.30 4.34
268 279 0.033796 ATCCAATGCAGGACAGGGTG 60.034 55.000 0.00 0.00 41.30 4.61
269 280 1.133181 TCCAATGCAGGACAGGGTGA 61.133 55.000 0.00 0.00 31.23 4.02
270 281 0.251297 CCAATGCAGGACAGGGTGAA 60.251 55.000 0.00 0.00 0.00 3.18
272 283 0.606401 AATGCAGGACAGGGTGAACG 60.606 55.000 0.00 0.00 0.00 3.95
273 284 3.050275 GCAGGACAGGGTGAACGC 61.050 66.667 0.00 0.00 0.00 4.84
274 285 2.743718 CAGGACAGGGTGAACGCT 59.256 61.111 0.00 0.00 39.95 5.07
275 286 1.972198 CAGGACAGGGTGAACGCTA 59.028 57.895 0.00 0.00 37.38 4.26
278 395 0.320697 GGACAGGGTGAACGCTAAGT 59.679 55.000 0.00 0.00 37.38 2.24
368 502 7.206981 ACAAGTTTGTCCACATAGAAATCAG 57.793 36.000 0.00 0.00 36.50 2.90
392 526 1.959282 GGAATCAACCCCATGCATCTC 59.041 52.381 0.00 0.00 0.00 2.75
413 547 2.800736 GCTTAGGCCGCCATGTTG 59.199 61.111 13.15 0.00 0.00 3.33
439 573 4.164294 GTGTCAAGAAATGATTGCAGCTC 58.836 43.478 0.00 0.00 40.97 4.09
704 839 1.594833 CACCAACGCACCCTAGCTA 59.405 57.895 0.00 0.00 0.00 3.32
709 844 1.749634 CAACGCACCCTAGCTAGTAGT 59.250 52.381 19.31 13.12 0.00 2.73
805 944 8.830915 TGGACCTTAAAATAATGGCTTAATCA 57.169 30.769 0.00 0.00 0.00 2.57
828 967 6.836007 TCACATCCTAATCATAGACACACTCT 59.164 38.462 0.00 0.00 0.00 3.24
897 1036 1.470285 CCAAGGCAATCAATGGAAGCG 60.470 52.381 0.00 0.00 34.82 4.68
899 1038 0.966875 AGGCAATCAATGGAAGCGCA 60.967 50.000 11.47 0.00 0.00 6.09
968 1108 2.726351 GCCGAGGAGTGGAGAAGGG 61.726 68.421 0.00 0.00 0.00 3.95
975 1115 1.229984 AGTGGAGAAGGGGAAGGGG 60.230 63.158 0.00 0.00 0.00 4.79
976 1116 2.127297 TGGAGAAGGGGAAGGGGG 59.873 66.667 0.00 0.00 0.00 5.40
977 1117 2.459710 GGAGAAGGGGAAGGGGGA 59.540 66.667 0.00 0.00 0.00 4.81
978 1118 1.694525 GGAGAAGGGGAAGGGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
979 1119 2.286502 AGAAGGGGAAGGGGGAGC 60.287 66.667 0.00 0.00 0.00 4.70
980 1120 2.614013 GAAGGGGAAGGGGGAGCA 60.614 66.667 0.00 0.00 0.00 4.26
984 1124 3.093172 GGGAAGGGGGAGCAGAGG 61.093 72.222 0.00 0.00 0.00 3.69
1429 1582 4.432741 GGTTCCCTGCTGGCCTCC 62.433 72.222 3.32 2.10 0.00 4.30
1812 1965 2.653115 CTGCAGGAGCTCGACACA 59.347 61.111 5.57 2.47 42.74 3.72
1830 1983 5.236478 CGACACAGTGTTCCTTTACAAGAAT 59.764 40.000 7.86 0.00 0.00 2.40
2394 2547 0.309302 CGTCGCTCTCCTTCATCGAT 59.691 55.000 0.00 0.00 0.00 3.59
2643 2796 1.531739 GCTTCACCGGCCAAATTCCA 61.532 55.000 0.00 0.00 0.00 3.53
2800 2953 4.514585 TGCCAGCAACGGGGTTGT 62.515 61.111 9.90 0.00 44.40 3.32
3603 3786 1.620524 CCCAACATGGAGGCCAAGATT 60.621 52.381 5.01 0.00 40.96 2.40
3921 4104 1.050988 GGGAGGAGATGCTGCTGGTA 61.051 60.000 0.00 0.00 30.82 3.25
4074 4257 0.818040 ACAAGGACAAGCCGGTGTTC 60.818 55.000 1.90 0.00 43.43 3.18
4075 4258 0.535102 CAAGGACAAGCCGGTGTTCT 60.535 55.000 1.90 0.81 39.14 3.01
4076 4259 0.250338 AAGGACAAGCCGGTGTTCTC 60.250 55.000 6.47 0.00 36.25 2.87
4105 4288 1.679944 CGGACTCCGGTTACCTGTAGA 60.680 57.143 9.85 0.00 44.15 2.59
4118 4301 7.489113 CGGTTACCTGTAGATAATTACGTGTTT 59.511 37.037 0.00 0.00 0.00 2.83
4150 4333 0.033504 GGCTCAGAGACGTGACCAAA 59.966 55.000 0.00 0.00 0.00 3.28
4154 4337 3.994392 GCTCAGAGACGTGACCAAAATTA 59.006 43.478 0.00 0.00 0.00 1.40
4164 4347 3.419596 GTGACCAAAATTAAACGACGTGC 59.580 43.478 0.00 0.00 0.00 5.34
4194 4386 6.309712 TGTACGTAGCTCATGTAATCTACC 57.690 41.667 0.00 0.00 30.35 3.18
4197 4389 4.888239 ACGTAGCTCATGTAATCTACCACT 59.112 41.667 0.00 0.00 0.00 4.00
4200 4392 6.017357 CGTAGCTCATGTAATCTACCACTACA 60.017 42.308 0.00 0.00 0.00 2.74
4235 4427 7.662897 TCACATAGTTTTGAATTTGGGGTTAC 58.337 34.615 0.00 0.00 0.00 2.50
4253 4445 5.304871 GGGTTACATTTTGTTTAGTTGGGGA 59.695 40.000 0.00 0.00 0.00 4.81
4255 4447 6.265876 GGTTACATTTTGTTTAGTTGGGGAGA 59.734 38.462 0.00 0.00 0.00 3.71
4256 4448 5.784578 ACATTTTGTTTAGTTGGGGAGAC 57.215 39.130 0.00 0.00 0.00 3.36
4257 4449 4.277423 ACATTTTGTTTAGTTGGGGAGACG 59.723 41.667 0.00 0.00 0.00 4.18
4258 4450 3.842007 TTTGTTTAGTTGGGGAGACGA 57.158 42.857 0.00 0.00 0.00 4.20
4260 4452 1.001633 TGTTTAGTTGGGGAGACGAGC 59.998 52.381 0.00 0.00 0.00 5.03
4261 4453 0.611714 TTTAGTTGGGGAGACGAGCC 59.388 55.000 0.00 0.00 0.00 4.70
4342 4903 7.040478 TCGGTCTCTTCAAATTCAAATCACATT 60.040 33.333 0.00 0.00 0.00 2.71
4343 4904 7.596248 CGGTCTCTTCAAATTCAAATCACATTT 59.404 33.333 0.00 0.00 0.00 2.32
4486 5076 7.560368 AGGAGAGATAGTTGTTCATTGTTAGG 58.440 38.462 0.00 0.00 0.00 2.69
4496 5086 4.956700 TGTTCATTGTTAGGGTTGTTTGGA 59.043 37.500 0.00 0.00 0.00 3.53
4515 5105 2.437413 GACCCTCTTTGCTTTACCCTG 58.563 52.381 0.00 0.00 0.00 4.45
4571 7528 8.380099 TCACTATCACAACTTTAGGGTGTAAAT 58.620 33.333 0.00 0.00 45.20 1.40
4578 7535 8.356657 CACAACTTTAGGGTGTAAATCAATTGA 58.643 33.333 11.26 11.26 45.20 2.57
4584 7541 5.203528 AGGGTGTAAATCAATTGATCCCTG 58.796 41.667 30.31 0.00 40.43 4.45
4604 7561 9.710900 ATCCCTGAAATTGAAATAACAAGTTTC 57.289 29.630 0.00 0.00 38.00 2.78
4624 7581 9.907229 AAGTTTCCTAAAGATCTTATAGGTTGG 57.093 33.333 26.20 15.77 37.91 3.77
4636 7593 7.865530 TCTTATAGGTTGGCATTATAGTGGA 57.134 36.000 0.00 0.00 0.00 4.02
4707 7664 2.408050 GATAGTTGTCCATGGCTAGCG 58.592 52.381 6.96 0.00 0.00 4.26
4722 7679 1.031571 TAGCGCCATTTGAGCCCAAG 61.032 55.000 2.29 0.00 33.23 3.61
4723 7680 2.182537 CGCCATTTGAGCCCAAGC 59.817 61.111 0.00 0.00 40.32 4.01
4733 7690 3.379880 GCCCAAGCTGATTTGCCA 58.620 55.556 0.00 0.00 35.50 4.92
4739 7696 2.223971 CCAAGCTGATTTGCCATCATCC 60.224 50.000 0.00 0.00 0.00 3.51
4915 7876 4.279671 AGGGTAGACTTCTTCATATCGCTG 59.720 45.833 0.00 0.00 0.00 5.18
4942 7903 7.793036 ACCTATTGGTACTTAATCTCTTGGTC 58.207 38.462 0.00 0.00 46.43 4.02
5026 7988 6.827586 ACACGGATTATAACAAACATGGTT 57.172 33.333 0.00 0.00 0.00 3.67
5042 8004 4.165950 ACATGGTTGGCTGATGACCTATAA 59.834 41.667 0.00 0.00 34.52 0.98
5075 8037 1.162698 GGCCTCGAAAAGGGTAACAC 58.837 55.000 0.00 0.00 46.32 3.32
5096 8058 3.008485 ACGCTTTCCCATCTTCTTCTTCT 59.992 43.478 0.00 0.00 0.00 2.85
5097 8059 4.006319 CGCTTTCCCATCTTCTTCTTCTT 58.994 43.478 0.00 0.00 0.00 2.52
5098 8060 4.094146 CGCTTTCCCATCTTCTTCTTCTTC 59.906 45.833 0.00 0.00 0.00 2.87
5099 8061 5.252547 GCTTTCCCATCTTCTTCTTCTTCT 58.747 41.667 0.00 0.00 0.00 2.85
5100 8062 5.709631 GCTTTCCCATCTTCTTCTTCTTCTT 59.290 40.000 0.00 0.00 0.00 2.52
5101 8063 6.128035 GCTTTCCCATCTTCTTCTTCTTCTTC 60.128 42.308 0.00 0.00 0.00 2.87
5102 8064 6.694445 TTCCCATCTTCTTCTTCTTCTTCT 57.306 37.500 0.00 0.00 0.00 2.85
5103 8065 6.694445 TCCCATCTTCTTCTTCTTCTTCTT 57.306 37.500 0.00 0.00 0.00 2.52
5104 8066 6.706295 TCCCATCTTCTTCTTCTTCTTCTTC 58.294 40.000 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 1.970917 GATTGCCGTCTTGAGTGCCG 61.971 60.000 0.00 0.00 0.00 5.69
96 97 1.804151 CGGTACATTATGGGATTGCCG 59.196 52.381 0.00 0.00 33.83 5.69
98 99 4.759693 TGATTCGGTACATTATGGGATTGC 59.240 41.667 0.00 0.00 0.00 3.56
107 108 8.147704 TGAGCTCATTAATGATTCGGTACATTA 58.852 33.333 18.26 0.00 37.75 1.90
109 110 6.524734 TGAGCTCATTAATGATTCGGTACAT 58.475 36.000 18.26 0.00 36.02 2.29
115 116 7.637229 ACAATCTTGAGCTCATTAATGATTCG 58.363 34.615 19.04 15.94 36.02 3.34
151 152 9.214957 AGAAAAAGGGTTTTACAAACTGAAAAG 57.785 29.630 0.00 0.00 37.07 2.27
155 156 8.368668 TGAAAGAAAAAGGGTTTTACAAACTGA 58.631 29.630 0.00 0.00 37.07 3.41
159 160 9.780186 TTCTTGAAAGAAAAAGGGTTTTACAAA 57.220 25.926 3.00 0.00 41.75 2.83
198 199 8.051535 AGGATCAATCTACATGAACAATCTTGT 58.948 33.333 0.00 3.37 43.85 3.16
199 200 8.447924 AGGATCAATCTACATGAACAATCTTG 57.552 34.615 0.00 0.00 36.91 3.02
203 204 9.865321 CAAAAAGGATCAATCTACATGAACAAT 57.135 29.630 0.00 0.00 0.00 2.71
204 205 7.814107 GCAAAAAGGATCAATCTACATGAACAA 59.186 33.333 0.00 0.00 0.00 2.83
205 206 7.177216 AGCAAAAAGGATCAATCTACATGAACA 59.823 33.333 0.00 0.00 0.00 3.18
207 208 7.363181 CCAGCAAAAAGGATCAATCTACATGAA 60.363 37.037 0.00 0.00 0.00 2.57
212 213 6.515272 TTCCAGCAAAAAGGATCAATCTAC 57.485 37.500 0.00 0.00 33.10 2.59
214 215 6.616237 ATTTCCAGCAAAAAGGATCAATCT 57.384 33.333 0.00 0.00 33.10 2.40
215 216 7.677454 AAATTTCCAGCAAAAAGGATCAATC 57.323 32.000 0.00 0.00 33.10 2.67
216 217 8.377799 ACTAAATTTCCAGCAAAAAGGATCAAT 58.622 29.630 0.00 0.00 33.10 2.57
217 218 7.734942 ACTAAATTTCCAGCAAAAAGGATCAA 58.265 30.769 0.00 0.00 33.10 2.57
220 221 8.815912 ACATACTAAATTTCCAGCAAAAAGGAT 58.184 29.630 0.00 0.00 33.10 3.24
222 223 8.831715 AACATACTAAATTTCCAGCAAAAAGG 57.168 30.769 0.00 0.00 0.00 3.11
223 224 9.474920 TGAACATACTAAATTTCCAGCAAAAAG 57.525 29.630 0.00 0.00 0.00 2.27
224 225 9.995003 ATGAACATACTAAATTTCCAGCAAAAA 57.005 25.926 0.00 0.00 0.00 1.94
225 226 9.638239 GATGAACATACTAAATTTCCAGCAAAA 57.362 29.630 0.00 0.00 0.00 2.44
239 250 5.104569 TGTCCTGCATTGGATGAACATACTA 60.105 40.000 0.00 0.00 38.52 1.82
254 265 1.003355 CGTTCACCCTGTCCTGCAT 60.003 57.895 0.00 0.00 0.00 3.96
264 275 2.031420 GGAAACAACTTAGCGTTCACCC 60.031 50.000 0.00 0.00 32.27 4.61
266 277 3.955771 TGGAAACAACTTAGCGTTCAC 57.044 42.857 0.00 0.00 37.44 3.18
368 502 1.064017 TGCATGGGGTTGATTCCCTAC 60.064 52.381 0.00 0.00 46.27 3.18
386 520 4.471761 GCCTAAGCCCTGAGATGC 57.528 61.111 0.00 0.00 0.00 3.91
413 547 4.609947 TGCAATCATTTCTTGACACACAC 58.390 39.130 0.00 0.00 37.11 3.82
439 573 7.202016 TGTCTTGATGGTTTAAACTAAGCTG 57.798 36.000 17.50 5.34 0.00 4.24
704 839 5.685075 GCTTGGTAGCATTGGTGATACTACT 60.685 44.000 0.00 0.00 44.54 2.57
805 944 7.066142 AGAGAGTGTGTCTATGATTAGGATGT 58.934 38.462 0.00 0.00 34.71 3.06
828 967 8.030913 GGAAACTCCCAGGAAAGTATATAAGA 57.969 38.462 0.00 0.00 0.00 2.10
897 1036 4.093998 TCACTAGCTACGTACTAGTTGTGC 59.906 45.833 23.56 11.39 46.36 4.57
899 1038 6.111382 TGATCACTAGCTACGTACTAGTTGT 58.889 40.000 23.56 18.08 46.36 3.32
953 1093 1.199615 CTTCCCCTTCTCCACTCCTC 58.800 60.000 0.00 0.00 0.00 3.71
968 1108 2.041265 TCCTCTGCTCCCCCTTCC 59.959 66.667 0.00 0.00 0.00 3.46
975 1115 1.109323 GCTCTCCTCTCCTCTGCTCC 61.109 65.000 0.00 0.00 0.00 4.70
976 1116 1.109323 GGCTCTCCTCTCCTCTGCTC 61.109 65.000 0.00 0.00 0.00 4.26
977 1117 1.076044 GGCTCTCCTCTCCTCTGCT 60.076 63.158 0.00 0.00 0.00 4.24
978 1118 2.489275 CGGCTCTCCTCTCCTCTGC 61.489 68.421 0.00 0.00 0.00 4.26
979 1119 0.819259 CTCGGCTCTCCTCTCCTCTG 60.819 65.000 0.00 0.00 0.00 3.35
980 1120 1.531748 CTCGGCTCTCCTCTCCTCT 59.468 63.158 0.00 0.00 0.00 3.69
984 1124 1.363443 CATGCTCGGCTCTCCTCTC 59.637 63.158 0.00 0.00 0.00 3.20
1305 1458 1.173913 TGCTCTGAAGGACGATCGAA 58.826 50.000 24.34 0.00 0.00 3.71
1812 1965 7.876068 TCGATGTTATTCTTGTAAAGGAACACT 59.124 33.333 0.00 0.00 46.24 3.55
2211 2364 2.345244 CACTTGGTGAGGCTCGCT 59.655 61.111 25.73 4.87 35.23 4.93
2394 2547 1.005748 CAGCTGGTTGTGCGAGAGA 60.006 57.895 5.57 0.00 35.28 3.10
2787 2940 1.528309 CCTCAACAACCCCGTTGCT 60.528 57.895 4.46 0.00 46.20 3.91
2800 2953 3.325425 TCGTCAGGGTTAATTGTCCTCAA 59.675 43.478 0.00 0.00 37.98 3.02
2859 3012 3.939939 TTGGCTGAGCACGCTGGA 61.940 61.111 6.82 0.00 0.00 3.86
2958 3117 1.578206 CCAGGAGCGCGATCGAGATA 61.578 60.000 23.47 0.00 38.10 1.98
3807 3990 1.319614 TGATCCAGCCGACGATGTCA 61.320 55.000 0.00 0.00 32.09 3.58
3972 4155 3.838795 GTCACCACGTCGCGCATC 61.839 66.667 8.75 0.00 0.00 3.91
4136 4319 5.050567 GTCGTTTAATTTTGGTCACGTCTCT 60.051 40.000 0.00 0.00 0.00 3.10
4150 4333 5.038033 ACAAAACATGCACGTCGTTTAATT 58.962 33.333 0.00 0.00 32.73 1.40
4154 4337 2.553079 ACAAAACATGCACGTCGTTT 57.447 40.000 0.00 0.00 34.42 3.60
4164 4347 5.530519 ACATGAGCTACGTACAAAACATG 57.469 39.130 0.00 15.39 39.42 3.21
4235 4427 4.517453 TCGTCTCCCCAACTAAACAAAATG 59.483 41.667 0.00 0.00 0.00 2.32
4240 4432 1.001633 GCTCGTCTCCCCAACTAAACA 59.998 52.381 0.00 0.00 0.00 2.83
4253 4445 2.224426 TGTTTACATTGGTGGCTCGTCT 60.224 45.455 0.00 0.00 0.00 4.18
4255 4447 2.264005 TGTTTACATTGGTGGCTCGT 57.736 45.000 0.00 0.00 0.00 4.18
4256 4448 3.057596 ACATTGTTTACATTGGTGGCTCG 60.058 43.478 8.95 0.00 33.04 5.03
4257 4449 4.519540 ACATTGTTTACATTGGTGGCTC 57.480 40.909 8.95 0.00 33.04 4.70
4258 4450 4.953940 AACATTGTTTACATTGGTGGCT 57.046 36.364 0.00 0.00 33.04 4.75
4260 4452 9.921637 AAGTATAAACATTGTTTACATTGGTGG 57.078 29.630 21.07 0.00 33.04 4.61
4317 4878 6.000891 TGTGATTTGAATTTGAAGAGACCG 57.999 37.500 0.00 0.00 0.00 4.79
4361 4922 6.599638 AGAGTTTGCTACATCCATTCCTTTAC 59.400 38.462 0.00 0.00 0.00 2.01
4486 5076 1.068588 GCAAAGAGGGTCCAAACAACC 59.931 52.381 0.00 0.00 35.97 3.77
4496 5086 1.075536 CCAGGGTAAAGCAAAGAGGGT 59.924 52.381 0.00 0.00 0.00 4.34
4515 5105 4.816925 AGAGTTTTAAGTCAAGTGCAGACC 59.183 41.667 1.23 0.00 36.68 3.85
4571 7528 9.874205 GTTATTTCAATTTCAGGGATCAATTGA 57.126 29.630 11.26 11.26 42.48 2.57
4578 7535 9.710900 GAAACTTGTTATTTCAATTTCAGGGAT 57.289 29.630 0.00 0.00 36.31 3.85
4604 7561 9.965902 ATAATGCCAACCTATAAGATCTTTAGG 57.034 33.333 26.04 26.04 38.76 2.69
4620 7577 6.882610 TGATTCATCCACTATAATGCCAAC 57.117 37.500 0.00 0.00 0.00 3.77
4624 7581 8.332996 AGTTCATGATTCATCCACTATAATGC 57.667 34.615 0.00 0.00 0.00 3.56
4680 7637 3.312890 CCATGGACAACTATCCCTCTCT 58.687 50.000 5.56 0.00 38.06 3.10
4722 7679 1.027357 ACGGATGATGGCAAATCAGC 58.973 50.000 13.56 8.03 34.03 4.26
4723 7680 5.008911 TCAAATACGGATGATGGCAAATCAG 59.991 40.000 13.56 12.05 0.00 2.90
4782 7739 4.677182 AGGGACCAATTTCTTTACATGCT 58.323 39.130 0.00 0.00 0.00 3.79
4881 7842 9.326489 TGAAGAAGTCTACCCTATATAATGCAT 57.674 33.333 0.00 0.00 0.00 3.96
4926 7887 7.597743 GTGAAAGAACGACCAAGAGATTAAGTA 59.402 37.037 0.00 0.00 0.00 2.24
4942 7903 5.799936 AGATGTTTTTGTGTGTGAAAGAACG 59.200 36.000 0.00 0.00 0.00 3.95
5026 7988 4.019771 TGTGTTGTTATAGGTCATCAGCCA 60.020 41.667 0.00 0.00 0.00 4.75
5042 8004 3.294493 GGCCGCCATGTGTGTTGT 61.294 61.111 3.91 0.00 0.00 3.32
5075 8037 3.604582 AGAAGAAGAAGATGGGAAAGCG 58.395 45.455 0.00 0.00 0.00 4.68
5081 8043 6.983474 GAAGAAGAAGAAGAAGAAGATGGG 57.017 41.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.