Multiple sequence alignment - TraesCS4A01G177400

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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 TraesCS4A01G177400 chr4A 100.000 3715 0 0 1 3715 449121891 449118177 0.000000e+00 6861.0
1 TraesCS4A01G177400 chr4B 92.908 3539 116 53 260 3713 184860970 184864458 0.000000e+00 5020.0
2 TraesCS4A01G177400 chr4B 94.737 38 2 0 2170 2207 516959251 516959288 4.010000e-05 60.2
3 TraesCS4A01G177400 chr4D 94.027 1825 70 19 1901 3713 121968556 121970353 0.000000e+00 2730.0
4 TraesCS4A01G177400 chr4D 90.798 1315 68 15 32 1310 121966657 121967954 0.000000e+00 1709.0
5 TraesCS4A01G177400 chr4D 84.651 430 29 19 1440 1852 121968131 121968540 9.670000e-106 394.0
6 TraesCS4A01G177400 chr7D 91.228 57 0 4 2154 2207 495871977 495871923 5.150000e-09 73.1
7 TraesCS4A01G177400 chr7B 92.308 52 0 3 2158 2207 524244352 524244303 1.850000e-08 71.3
8 TraesCS4A01G177400 chrUn 94.737 38 2 0 2170 2207 153391845 153391882 4.010000e-05 60.2
9 TraesCS4A01G177400 chrUn 92.500 40 3 0 2168 2207 331177812 331177851 1.440000e-04 58.4
10 TraesCS4A01G177400 chr6A 94.737 38 2 0 2170 2207 48088988 48089025 4.010000e-05 60.2
11 TraesCS4A01G177400 chr6D 87.755 49 5 1 2159 2207 443269338 443269385 5.180000e-04 56.5
12 TraesCS4A01G177400 chr5A 87.755 49 5 1 2159 2207 335267150 335267197 5.180000e-04 56.5


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 TraesCS4A01G177400 chr4A 449118177 449121891 3714 True 6861 6861 100.000000 1 3715 1 chr4A.!!$R1 3714
1 TraesCS4A01G177400 chr4B 184860970 184864458 3488 False 5020 5020 92.908000 260 3713 1 chr4B.!!$F1 3453
2 TraesCS4A01G177400 chr4D 121966657 121970353 3696 False 1611 2730 89.825333 32 3713 3 chr4D.!!$F1 3681

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
597 619 0.037447 TGGGTTCATGCGTTCCATCA 59.963 50.000 0.00 0.00 29.71 3.07 F
1785 1928 1.197721 ACAGGTACGTACGTGCACTAC 59.802 52.381 35.74 21.22 43.67 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2290 0.179026 CAGTACCGGAGAGGGATCGA 60.179 60.000 9.46 0.0 46.96 3.59 R
3662 3854 1.685224 CTGGCTACTCCCCTGCAAA 59.315 57.895 0.00 0.0 0.00 3.68 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
23 24 4.453819 GGCAACTGATAAGGACATGATAGC 59.546 45.833 0.00 0.00 0.00 2.97
24 25 4.453819 GCAACTGATAAGGACATGATAGCC 59.546 45.833 0.00 0.00 0.00 3.93
25 26 5.744300 GCAACTGATAAGGACATGATAGCCT 60.744 44.000 0.00 0.00 0.00 4.58
26 27 5.736951 ACTGATAAGGACATGATAGCCTC 57.263 43.478 0.00 0.00 0.00 4.70
27 28 4.219507 ACTGATAAGGACATGATAGCCTCG 59.780 45.833 0.00 0.00 0.00 4.63
28 29 4.152647 TGATAAGGACATGATAGCCTCGT 58.847 43.478 0.00 0.00 0.00 4.18
29 30 4.588951 TGATAAGGACATGATAGCCTCGTT 59.411 41.667 0.00 0.00 0.00 3.85
30 31 3.914426 AAGGACATGATAGCCTCGTTT 57.086 42.857 0.00 0.00 0.00 3.60
50 52 3.746792 TGAGAGGGACAGAGATCTTGA 57.253 47.619 0.00 0.00 0.00 3.02
55 57 3.018149 AGGGACAGAGATCTTGACGTAC 58.982 50.000 0.00 0.00 0.00 3.67
60 62 3.255888 ACAGAGATCTTGACGTACTGCAA 59.744 43.478 0.00 0.00 0.00 4.08
61 63 3.856521 CAGAGATCTTGACGTACTGCAAG 59.143 47.826 14.79 14.79 42.10 4.01
86 88 1.417517 AGTTGAGCCACTGACATGTGA 59.582 47.619 1.15 0.00 40.12 3.58
87 89 2.158769 AGTTGAGCCACTGACATGTGAA 60.159 45.455 1.15 0.00 40.12 3.18
90 92 2.815503 TGAGCCACTGACATGTGAATTG 59.184 45.455 1.15 0.00 40.12 2.32
96 98 5.737063 GCCACTGACATGTGAATTGAAAAGT 60.737 40.000 1.15 0.00 40.12 2.66
119 121 1.072331 GTTGGTCCACCTGTCAGTGAT 59.928 52.381 0.00 0.00 40.34 3.06
121 123 0.250513 GGTCCACCTGTCAGTGATCC 59.749 60.000 0.00 1.13 40.34 3.36
126 128 2.751259 CCACCTGTCAGTGATCCAATTG 59.249 50.000 0.00 0.00 40.34 2.32
131 133 3.688235 TGTCAGTGATCCAATTGCATCA 58.312 40.909 8.01 8.01 0.00 3.07
144 146 1.717937 GCATCATGCAGTCCGTCAC 59.282 57.895 4.20 0.00 44.26 3.67
174 176 4.141620 TGAGTCCTTTGAAAGAGAGTGCTT 60.142 41.667 6.49 0.00 0.00 3.91
176 178 4.102367 AGTCCTTTGAAAGAGAGTGCTTCT 59.898 41.667 6.49 0.00 39.43 2.85
189 191 0.179032 TGCTTCTGCCGGTTTCTTGA 60.179 50.000 1.90 0.00 38.71 3.02
317 322 4.611807 GCTGTACCTACTCGATCGATCTTG 60.612 50.000 19.78 16.31 0.00 3.02
318 323 3.813724 TGTACCTACTCGATCGATCTTGG 59.186 47.826 19.78 18.99 0.00 3.61
324 329 2.550606 ACTCGATCGATCTTGGAGCTAC 59.449 50.000 19.78 0.00 0.00 3.58
325 330 2.550180 CTCGATCGATCTTGGAGCTACA 59.450 50.000 19.78 0.00 0.00 2.74
326 331 2.550180 TCGATCGATCTTGGAGCTACAG 59.450 50.000 22.43 3.30 0.00 2.74
327 332 2.671596 GATCGATCTTGGAGCTACAGC 58.328 52.381 18.29 0.00 42.49 4.40
328 333 0.747255 TCGATCTTGGAGCTACAGCC 59.253 55.000 0.00 0.00 43.38 4.85
329 334 0.596083 CGATCTTGGAGCTACAGCCG 60.596 60.000 0.00 0.00 43.38 5.52
365 370 3.199071 AGGTGGACTGTTTACACTGACAA 59.801 43.478 9.82 0.00 35.53 3.18
370 375 6.704493 GTGGACTGTTTACACTGACAAAGATA 59.296 38.462 0.00 0.00 32.58 1.98
371 376 7.387948 GTGGACTGTTTACACTGACAAAGATAT 59.612 37.037 0.00 0.00 32.58 1.63
406 411 3.190849 CTGCCGTGTCAGGATGCG 61.191 66.667 0.00 0.00 34.76 4.73
488 507 2.124903 GCATGCGTATAGCTGTACGTT 58.875 47.619 33.86 23.12 46.74 3.99
541 562 5.298527 CCACTTAGTATGGTCACGTGAGATA 59.701 44.000 20.73 15.08 32.08 1.98
574 595 3.131400 TCATCGTCGATCCACCAAACATA 59.869 43.478 4.34 0.00 0.00 2.29
578 599 3.621268 CGTCGATCCACCAAACATATTGT 59.379 43.478 0.00 0.00 0.00 2.71
580 601 3.944650 TCGATCCACCAAACATATTGTGG 59.055 43.478 0.00 0.00 38.46 4.17
581 602 3.066621 CGATCCACCAAACATATTGTGGG 59.933 47.826 7.60 0.00 36.69 4.61
582 603 3.534357 TCCACCAAACATATTGTGGGT 57.466 42.857 7.60 0.00 38.79 4.51
597 619 0.037447 TGGGTTCATGCGTTCCATCA 59.963 50.000 0.00 0.00 29.71 3.07
607 629 2.253603 GCGTTCCATCACTTTGCAATC 58.746 47.619 0.00 0.00 0.00 2.67
612 634 4.771590 TCCATCACTTTGCAATCTTCAC 57.228 40.909 0.00 0.00 0.00 3.18
661 684 3.821421 ACCTGCTGTATGCTAAGTACC 57.179 47.619 0.00 0.00 43.37 3.34
725 762 5.046910 TGAATCAACCTGAAAAAGCGATC 57.953 39.130 0.00 0.00 0.00 3.69
943 990 1.503784 TCCTCCATCCCTACCTAGGTG 59.496 57.143 25.33 13.80 42.03 4.00
1120 1182 4.947147 TTCCACCACCGGCAGCAC 62.947 66.667 0.00 0.00 0.00 4.40
1172 1234 1.380246 TGGTTGATCTGGCCATGGC 60.380 57.895 29.47 29.47 41.06 4.40
1196 1258 4.496336 GGCCAGGGAGCGATGCTT 62.496 66.667 0.00 0.00 39.88 3.91
1276 1338 2.125106 GGGTGTCAAGCGCTAGGG 60.125 66.667 12.05 3.39 0.00 3.53
1381 1516 4.226761 GCATTTCGAATTTCGGTCACTTT 58.773 39.130 18.02 0.00 40.88 2.66
1427 1562 3.656651 CGAGCTAATTCGTTGCATCAA 57.343 42.857 0.00 0.00 35.91 2.57
1428 1563 4.201208 CGAGCTAATTCGTTGCATCAAT 57.799 40.909 0.00 0.00 35.91 2.57
1429 1564 5.328886 CGAGCTAATTCGTTGCATCAATA 57.671 39.130 0.00 0.00 35.91 1.90
1430 1565 5.133264 CGAGCTAATTCGTTGCATCAATAC 58.867 41.667 0.00 0.00 35.91 1.89
1437 1572 9.321590 CTAATTCGTTGCATCAATACATACATG 57.678 33.333 0.00 0.00 0.00 3.21
1554 1689 3.776969 TCTGGTCAGTCCTGCAATTATCT 59.223 43.478 0.00 0.00 37.07 1.98
1593 1735 7.566858 AATTATCTCATGTTTGCGTTTGTTC 57.433 32.000 0.00 0.00 0.00 3.18
1625 1767 8.394121 GGGATTATTTTTGCTCATAGATCGATC 58.606 37.037 17.91 17.91 0.00 3.69
1626 1768 8.113062 GGATTATTTTTGCTCATAGATCGATCG 58.887 37.037 19.33 9.36 0.00 3.69
1627 1769 8.763049 ATTATTTTTGCTCATAGATCGATCGA 57.237 30.769 21.86 21.86 0.00 3.59
1628 1770 8.763049 TTATTTTTGCTCATAGATCGATCGAT 57.237 30.769 29.76 29.76 37.59 3.59
1783 1926 1.466167 CTACAGGTACGTACGTGCACT 59.534 52.381 35.74 24.22 43.67 4.40
1784 1927 1.522668 ACAGGTACGTACGTGCACTA 58.477 50.000 35.74 11.11 43.67 2.74
1785 1928 1.197721 ACAGGTACGTACGTGCACTAC 59.802 52.381 35.74 21.22 43.67 2.73
1788 1931 2.932614 AGGTACGTACGTGCACTACTAG 59.067 50.000 32.30 0.68 32.33 2.57
1800 1955 4.072839 TGCACTACTAGATCCGATCGATT 58.927 43.478 18.66 2.60 0.00 3.34
1818 1973 6.376056 TCGATTGCTTTATATTCGATCACG 57.624 37.500 0.00 0.00 34.24 4.35
1837 1992 2.688958 ACGAGCTCCCTGTGATTAGTAC 59.311 50.000 8.47 0.00 0.00 2.73
1871 2030 2.282701 ACCATGCATGCAAATTCGAC 57.717 45.000 26.68 0.00 0.00 4.20
2070 2236 1.526455 CTACCTCGACCTCCTCCCG 60.526 68.421 0.00 0.00 0.00 5.14
2121 2290 2.300967 TTGCATCCGCCTCCTCCTT 61.301 57.895 0.00 0.00 37.32 3.36
2142 2311 1.033574 GATCCCTCTCCGGTACTGTG 58.966 60.000 0.00 0.00 0.00 3.66
2558 2739 2.961062 AGCACTTGAAACAAGCTTGGAT 59.039 40.909 29.18 17.69 29.98 3.41
2639 2820 1.718396 TTGCATTCGAGAGCACTGAG 58.282 50.000 12.61 0.00 41.05 3.35
2790 2971 6.907212 CACACAAGAGTAACAACTGATCAAAC 59.093 38.462 0.00 0.00 0.00 2.93
2805 2986 9.944376 AACTGATCAAACTAGTTAAGCTCATTA 57.056 29.630 8.92 0.00 33.22 1.90
3101 3287 7.167968 CAGTTGTTGTGTTGAACCATAATCTTG 59.832 37.037 0.00 0.00 0.00 3.02
3162 3348 0.449786 AGCGACAGTGAGATCGACTG 59.550 55.000 20.36 20.36 45.39 3.51
3180 3366 3.938109 GGAAGAGTCCGCCTTTCTT 57.062 52.632 0.00 0.00 33.05 2.52
3185 3371 4.333095 GGAAGAGTCCGCCTTTCTTATTTC 59.667 45.833 0.00 0.00 33.05 2.17
3191 3377 4.153655 GTCCGCCTTTCTTATTTCGAAAGT 59.846 41.667 16.80 7.31 43.54 2.66
3196 3382 6.237861 CGCCTTTCTTATTTCGAAAGTAGGAG 60.238 42.308 16.80 12.50 43.54 3.69
3256 3442 7.707464 TGTGATGAATCAAATTGATATGTTGCC 59.293 33.333 9.09 0.00 35.76 4.52
3446 3638 5.482163 GGAATAGATCCTGAGGGAAGAAG 57.518 47.826 0.00 0.00 45.78 2.85
3447 3639 5.151454 GGAATAGATCCTGAGGGAAGAAGA 58.849 45.833 0.00 0.00 45.78 2.87
3448 3640 5.604650 GGAATAGATCCTGAGGGAAGAAGAA 59.395 44.000 0.00 0.00 45.78 2.52
3540 3732 1.960689 GTCTGCTCTATCTCCCTGACC 59.039 57.143 0.00 0.00 0.00 4.02
3598 3790 2.027192 GGTAGCCCACTCACTGATGAAA 60.027 50.000 0.00 0.00 33.30 2.69
3603 3795 4.946157 AGCCCACTCACTGATGAAATTAAG 59.054 41.667 0.00 0.00 33.30 1.85
3607 3799 6.259608 CCCACTCACTGATGAAATTAAGCTAG 59.740 42.308 0.00 0.00 33.30 3.42
3630 3822 4.706035 CAGCTAGCCTGAAGAATTGATCT 58.294 43.478 12.13 0.00 44.64 2.75
3662 3854 7.011482 GTCTAATTCTTAATCTCCATTGCACGT 59.989 37.037 0.00 0.00 0.00 4.49
3682 3880 3.402681 GCAGGGGAGTAGCCAGCA 61.403 66.667 0.00 0.00 38.95 4.41
3713 3911 7.659652 AGTTTCAGTTCAGATAACTAACTGC 57.340 36.000 9.08 0.00 46.18 4.40
3714 3912 7.217200 AGTTTCAGTTCAGATAACTAACTGCA 58.783 34.615 9.08 0.00 46.18 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.453819 GCTATCATGTCCTTATCAGTTGCC 59.546 45.833 0.00 0.00 0.00 4.52
1 2 4.453819 GGCTATCATGTCCTTATCAGTTGC 59.546 45.833 0.00 0.00 0.00 4.17
2 3 5.862845 AGGCTATCATGTCCTTATCAGTTG 58.137 41.667 0.00 0.00 0.00 3.16
3 4 5.279206 CGAGGCTATCATGTCCTTATCAGTT 60.279 44.000 0.00 0.00 0.00 3.16
4 5 4.219507 CGAGGCTATCATGTCCTTATCAGT 59.780 45.833 0.00 0.00 0.00 3.41
5 6 4.219507 ACGAGGCTATCATGTCCTTATCAG 59.780 45.833 0.00 0.00 0.00 2.90
6 7 4.152647 ACGAGGCTATCATGTCCTTATCA 58.847 43.478 0.00 0.00 0.00 2.15
7 8 4.792521 ACGAGGCTATCATGTCCTTATC 57.207 45.455 0.00 0.00 0.00 1.75
8 9 5.070446 TCAAACGAGGCTATCATGTCCTTAT 59.930 40.000 0.00 0.00 0.00 1.73
9 10 4.404394 TCAAACGAGGCTATCATGTCCTTA 59.596 41.667 0.00 0.00 0.00 2.69
10 11 3.197766 TCAAACGAGGCTATCATGTCCTT 59.802 43.478 0.00 0.00 0.00 3.36
11 12 2.766263 TCAAACGAGGCTATCATGTCCT 59.234 45.455 0.00 0.00 0.00 3.85
12 13 3.126831 CTCAAACGAGGCTATCATGTCC 58.873 50.000 0.00 0.00 0.00 4.02
13 14 4.046938 TCTCAAACGAGGCTATCATGTC 57.953 45.455 0.00 0.00 0.00 3.06
14 15 3.181471 CCTCTCAAACGAGGCTATCATGT 60.181 47.826 0.00 0.00 43.69 3.21
15 16 3.388308 CCTCTCAAACGAGGCTATCATG 58.612 50.000 0.00 0.00 43.69 3.07
16 17 3.742433 CCTCTCAAACGAGGCTATCAT 57.258 47.619 0.00 0.00 43.69 2.45
24 25 2.163509 TCTCTGTCCCTCTCAAACGAG 58.836 52.381 0.00 0.00 0.00 4.18
25 26 2.287977 TCTCTGTCCCTCTCAAACGA 57.712 50.000 0.00 0.00 0.00 3.85
26 27 2.757868 AGATCTCTGTCCCTCTCAAACG 59.242 50.000 0.00 0.00 0.00 3.60
27 28 4.221703 TCAAGATCTCTGTCCCTCTCAAAC 59.778 45.833 0.00 0.00 0.00 2.93
28 29 4.221703 GTCAAGATCTCTGTCCCTCTCAAA 59.778 45.833 0.00 0.00 0.00 2.69
29 30 3.766591 GTCAAGATCTCTGTCCCTCTCAA 59.233 47.826 0.00 0.00 0.00 3.02
30 31 3.360867 GTCAAGATCTCTGTCCCTCTCA 58.639 50.000 0.00 0.00 0.00 3.27
60 62 0.689055 TCAGTGGCTCAACTGCATCT 59.311 50.000 9.11 0.00 45.93 2.90
61 63 0.801251 GTCAGTGGCTCAACTGCATC 59.199 55.000 9.11 1.55 45.93 3.91
64 66 0.520404 CATGTCAGTGGCTCAACTGC 59.480 55.000 0.00 6.22 45.93 4.40
86 88 4.587262 GGTGGACCAACCTACTTTTCAATT 59.413 41.667 0.00 0.00 39.86 2.32
87 89 4.149598 GGTGGACCAACCTACTTTTCAAT 58.850 43.478 0.00 0.00 39.86 2.57
126 128 0.742281 AGTGACGGACTGCATGATGC 60.742 55.000 11.12 11.12 45.29 3.91
138 140 0.038159 GGACTCAACTCCAGTGACGG 60.038 60.000 0.00 0.00 0.00 4.79
139 141 0.962489 AGGACTCAACTCCAGTGACG 59.038 55.000 0.00 0.00 31.94 4.35
144 146 4.708177 TCTTTCAAAGGACTCAACTCCAG 58.292 43.478 0.00 0.00 31.94 3.86
196 198 7.814587 AGAGTTTTTGTTTTTCTTCAGTCAAGG 59.185 33.333 0.00 0.00 32.22 3.61
203 208 9.724839 CGGTTATAGAGTTTTTGTTTTTCTTCA 57.275 29.630 0.00 0.00 0.00 3.02
240 245 6.484977 GGTCTTCCTGGCTAGATTTAGATTTG 59.515 42.308 0.00 0.00 0.00 2.32
353 358 9.990360 TTGTCAGTATATCTTTGTCAGTGTAAA 57.010 29.630 0.00 0.00 0.00 2.01
365 370 6.379703 AGTCAGTCAGCTTGTCAGTATATCTT 59.620 38.462 0.00 0.00 0.00 2.40
370 375 3.616076 GCAGTCAGTCAGCTTGTCAGTAT 60.616 47.826 0.00 0.00 0.00 2.12
371 376 2.288457 GCAGTCAGTCAGCTTGTCAGTA 60.288 50.000 0.00 0.00 0.00 2.74
406 411 2.759560 ACCCCATTCCAATGCGGC 60.760 61.111 3.30 0.00 37.78 6.53
415 420 3.795877 CACCAATAAATGCACCCCATTC 58.204 45.455 0.00 0.00 43.22 2.67
488 507 6.210784 GGTAGGGAGCATCATACTGTAATGTA 59.789 42.308 0.00 0.00 36.25 2.29
541 562 1.594397 TCGACGATGAAGCGTACGTAT 59.406 47.619 17.90 5.85 45.72 3.06
553 574 1.720805 TGTTTGGTGGATCGACGATG 58.279 50.000 16.49 0.00 0.00 3.84
574 595 0.887933 GGAACGCATGAACCCACAAT 59.112 50.000 0.00 0.00 0.00 2.71
578 599 0.037447 TGATGGAACGCATGAACCCA 59.963 50.000 0.00 0.00 0.00 4.51
580 601 1.453155 AGTGATGGAACGCATGAACC 58.547 50.000 0.00 0.00 0.00 3.62
581 602 3.236816 CAAAGTGATGGAACGCATGAAC 58.763 45.455 0.00 0.00 0.00 3.18
582 603 2.351641 GCAAAGTGATGGAACGCATGAA 60.352 45.455 0.00 0.00 0.00 2.57
597 619 6.865205 GCTGAAATAAGTGAAGATTGCAAAGT 59.135 34.615 1.71 0.00 0.00 2.66
607 629 1.394917 AGCGCGCTGAAATAAGTGAAG 59.605 47.619 36.13 0.00 0.00 3.02
612 634 7.333269 CAAGATATATAGCGCGCTGAAATAAG 58.667 38.462 41.85 19.93 0.00 1.73
661 684 6.591834 CAGGAGACAAATGGAAACTACTGTAG 59.408 42.308 13.13 13.13 35.54 2.74
725 762 2.642254 CCCACTTGCATGCCTGTGG 61.642 63.158 33.98 33.98 46.74 4.17
802 843 0.039074 TTAAAAACCGCACGCCATGG 60.039 50.000 7.63 7.63 0.00 3.66
943 990 5.169295 GTGTAAATATACGATGGAGGAGCC 58.831 45.833 0.00 0.00 34.60 4.70
1128 1190 2.803670 ACATCGTCAACGTCGCCG 60.804 61.111 2.09 0.00 40.80 6.46
1129 1191 2.769617 CACATCGTCAACGTCGCC 59.230 61.111 2.09 0.00 40.80 5.54
1130 1192 2.093983 GCACATCGTCAACGTCGC 59.906 61.111 2.09 0.00 40.80 5.19
1172 1234 2.125106 GCTCCCTGGCCTTGTACG 60.125 66.667 3.32 0.00 0.00 3.67
1213 1275 1.521681 GACGGTGGATGTAGGCAGC 60.522 63.158 0.00 0.00 0.00 5.25
1276 1338 0.676782 ATGTAGTGGACGGCTTTGGC 60.677 55.000 0.00 0.00 37.82 4.52
1451 1586 0.815095 CCAATCCCAACCGGCTAAAC 59.185 55.000 0.00 0.00 0.00 2.01
1495 1630 1.482593 AGAAGCGGTCCAGATAGTTGG 59.517 52.381 0.00 0.00 39.70 3.77
1593 1735 4.280819 TGAGCAAAAATAATCCCCCAGAG 58.719 43.478 0.00 0.00 0.00 3.35
1625 1767 4.263677 GCATGCAACATTTTAGTGACATCG 59.736 41.667 14.21 0.00 0.00 3.84
1626 1768 5.162794 TGCATGCAACATTTTAGTGACATC 58.837 37.500 20.30 0.00 0.00 3.06
1627 1769 5.136816 TGCATGCAACATTTTAGTGACAT 57.863 34.783 20.30 0.00 0.00 3.06
1628 1770 4.581077 TGCATGCAACATTTTAGTGACA 57.419 36.364 20.30 0.00 0.00 3.58
1712 1855 0.743688 AACTTGCATGCAACCGACAA 59.256 45.000 28.80 7.45 0.00 3.18
1783 1926 5.707242 AAAGCAATCGATCGGATCTAGTA 57.293 39.130 16.41 0.00 33.02 1.82
1784 1927 4.592485 AAAGCAATCGATCGGATCTAGT 57.408 40.909 16.41 1.58 33.02 2.57
1785 1928 8.864069 AATATAAAGCAATCGATCGGATCTAG 57.136 34.615 16.41 1.86 33.02 2.43
1788 1931 6.472486 TCGAATATAAAGCAATCGATCGGATC 59.528 38.462 16.41 7.95 37.59 3.36
1800 1955 4.871513 AGCTCGTGATCGAATATAAAGCA 58.128 39.130 10.38 0.00 45.61 3.91
1818 1973 2.688958 ACGTACTAATCACAGGGAGCTC 59.311 50.000 4.71 4.71 0.00 4.09
1871 2030 9.762933 CCATGAAATACATTAATTAACCTTGGG 57.237 33.333 0.00 0.00 37.07 4.12
2121 2290 0.179026 CAGTACCGGAGAGGGATCGA 60.179 60.000 9.46 0.00 46.96 3.59
2142 2311 6.624352 TTGATTAATCAATCTGCAGGTAGC 57.376 37.500 23.86 0.00 41.51 3.58
2471 2652 2.367030 TAACACGTACGGGGTCAATG 57.633 50.000 23.48 10.29 0.00 2.82
2558 2739 9.750125 GTACTGTACTTGTGATATTGATGATGA 57.250 33.333 10.64 0.00 0.00 2.92
2591 2772 3.005539 GGACTCCCCTGCAGCTGA 61.006 66.667 20.43 5.69 0.00 4.26
2639 2820 2.155155 GCTGTTAACTGTACTGTCACGC 59.845 50.000 13.27 9.79 0.00 5.34
2806 2987 9.748708 GGTACGTACTAACAATCAATGGTATTA 57.251 33.333 24.07 0.00 28.74 0.98
2917 3098 4.730042 CACAAATACATATGTGCGTGCTTC 59.270 41.667 18.81 0.00 40.32 3.86
3162 3348 3.545366 ATAAGAAAGGCGGACTCTTCC 57.455 47.619 0.00 0.00 38.77 3.46
3180 3366 8.114331 TGTTGAGTACTCCTACTTTCGAAATA 57.886 34.615 20.11 5.60 32.96 1.40
3185 3371 7.310664 TGTAATGTTGAGTACTCCTACTTTCG 58.689 38.462 20.11 0.00 32.96 3.46
3256 3442 3.554692 GGAAGTGCGTGCGATCCG 61.555 66.667 0.00 0.00 0.00 4.18
3446 3638 4.582240 CCTTTGGGGATTGCTATCTTCTTC 59.418 45.833 8.06 0.00 37.23 2.87
3447 3639 4.230502 TCCTTTGGGGATTGCTATCTTCTT 59.769 41.667 8.06 0.00 39.58 2.52
3448 3640 3.788142 TCCTTTGGGGATTGCTATCTTCT 59.212 43.478 8.06 0.00 39.58 2.85
3540 3732 5.292765 ACATATCTTGTAGCCGACAATCAG 58.707 41.667 2.48 0.00 46.95 2.90
3607 3799 2.636830 TCAATTCTTCAGGCTAGCTGC 58.363 47.619 15.72 0.00 41.94 5.25
3632 3824 8.772705 GCAATGGAGATTAAGAATTAGACTCTG 58.227 37.037 0.00 0.00 36.01 3.35
3638 3830 7.251704 ACGTGCAATGGAGATTAAGAATTAG 57.748 36.000 0.00 0.00 0.00 1.73
3662 3854 1.685224 CTGGCTACTCCCCTGCAAA 59.315 57.895 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.