Multiple sequence alignment - TraesCS6A01G080300

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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 TraesCS6A01G080300 chr6A 100.000 2222 0 0 1 2222 49127268 49129489 0.000000e+00 4104.0
1 TraesCS6A01G080300 chr6B 87.939 1451 102 25 1 1408 88352191 88353611 0.000000e+00 1642.0
2 TraesCS6A01G080300 chr6B 89.404 755 59 12 1471 2222 88411917 88412653 0.000000e+00 931.0
3 TraesCS6A01G080300 chr6B 90.282 710 50 11 1516 2222 88353649 88354342 0.000000e+00 911.0
4 TraesCS6A01G080300 chr6B 89.661 619 26 9 834 1415 88411316 88411933 0.000000e+00 754.0
5 TraesCS6A01G080300 chr6B 84.776 670 66 15 1 663 88396346 88396986 6.690000e-180 640.0
6 TraesCS6A01G080300 chr6B 94.643 56 2 1 1416 1471 465459166 465459112 3.930000e-13 86.1
7 TraesCS6A01G080300 chr6D 90.841 797 34 10 469 1229 37708686 37709479 0.000000e+00 1031.0
8 TraesCS6A01G080300 chr6D 86.308 409 31 13 1471 1871 37709812 37710203 2.640000e-114 422.0
9 TraesCS6A01G080300 chr6D 90.863 197 9 3 1227 1415 37709633 37709828 2.830000e-64 255.0
10 TraesCS6A01G080300 chr6D 94.643 56 2 1 1416 1471 379113047 379112993 3.930000e-13 86.1
11 TraesCS6A01G080300 chrUn 88.999 709 53 10 154 855 469476527 469475837 0.000000e+00 854.0
12 TraesCS6A01G080300 chr2B 83.459 266 37 5 1788 2048 42929734 42929997 7.930000e-60 241.0
13 TraesCS6A01G080300 chr7A 81.818 231 36 4 1823 2048 57099550 57099321 2.910000e-44 189.0
14 TraesCS6A01G080300 chr2A 98.214 56 0 1 1416 1471 168449939 168449885 1.820000e-16 97.1
15 TraesCS6A01G080300 chr7D 96.552 58 1 1 1415 1471 593190677 593190620 6.530000e-16 95.3
16 TraesCS6A01G080300 chr7B 96.491 57 2 0 1416 1472 471362749 471362693 6.530000e-16 95.3
17 TraesCS6A01G080300 chr1A 96.429 56 1 1 1416 1471 317499271 317499325 8.450000e-15 91.6
18 TraesCS6A01G080300 chr3D 94.643 56 3 0 1416 1471 521604202 521604147 1.090000e-13 87.9
19 TraesCS6A01G080300 chr3D 94.643 56 2 1 1416 1471 38096502 38096556 3.930000e-13 86.1
20 TraesCS6A01G080300 chr3D 94.643 56 2 1 1416 1471 353340292 353340346 3.930000e-13 86.1


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 TraesCS6A01G080300 chr6A 49127268 49129489 2221 False 4104.000000 4104 100.000000 1 2222 1 chr6A.!!$F1 2221
1 TraesCS6A01G080300 chr6B 88352191 88354342 2151 False 1276.500000 1642 89.110500 1 2222 2 chr6B.!!$F2 2221
2 TraesCS6A01G080300 chr6B 88411316 88412653 1337 False 842.500000 931 89.532500 834 2222 2 chr6B.!!$F3 1388
3 TraesCS6A01G080300 chr6B 88396346 88396986 640 False 640.000000 640 84.776000 1 663 1 chr6B.!!$F1 662
4 TraesCS6A01G080300 chr6D 37708686 37710203 1517 False 569.333333 1031 89.337333 469 1871 3 chr6D.!!$F1 1402
5 TraesCS6A01G080300 chrUn 469475837 469476527 690 True 854.000000 854 88.999000 154 855 1 chrUn.!!$R1 701

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
21 22 0.798776 CTCTGGCTAGCCAACAAACG 59.201 55.0 35.07 22.79 46.63 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1516 0.037697 ACTAGGCGTTGCGACATTGA 60.038 50.0 4.64 0.0 37.34 2.57 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
18 19 1.002134 GCCTCTGGCTAGCCAACAA 60.002 57.895 35.07 22.28 46.69 2.83
21 22 0.798776 CTCTGGCTAGCCAACAAACG 59.201 55.000 35.07 22.79 46.63 3.60
29 30 4.038080 CCAACAAACGGCGAGGCC 62.038 66.667 16.62 0.00 46.75 5.19
77 78 2.764547 GGGACGGAGAAGGGGGAG 60.765 72.222 0.00 0.00 0.00 4.30
79 80 3.471806 GACGGAGAAGGGGGAGGC 61.472 72.222 0.00 0.00 0.00 4.70
80 81 3.986116 GACGGAGAAGGGGGAGGCT 62.986 68.421 0.00 0.00 0.00 4.58
81 82 2.689034 CGGAGAAGGGGGAGGCTT 60.689 66.667 0.00 0.00 0.00 4.35
82 83 3.002371 GGAGAAGGGGGAGGCTTG 58.998 66.667 0.00 0.00 0.00 4.01
83 84 2.684499 GGAGAAGGGGGAGGCTTGG 61.684 68.421 0.00 0.00 0.00 3.61
84 85 1.616628 GAGAAGGGGGAGGCTTGGA 60.617 63.158 0.00 0.00 0.00 3.53
85 86 1.916206 GAGAAGGGGGAGGCTTGGAC 61.916 65.000 0.00 0.00 0.00 4.02
86 87 3.330720 AAGGGGGAGGCTTGGACG 61.331 66.667 0.00 0.00 0.00 4.79
94 95 3.647771 GGCTTGGACGGGGGAAGT 61.648 66.667 0.00 0.00 0.00 3.01
100 101 2.762875 GACGGGGGAAGTCGGGAT 60.763 66.667 0.00 0.00 0.00 3.85
105 106 2.444256 GGGGAAGTCGGGATGGAGG 61.444 68.421 0.00 0.00 0.00 4.30
179 180 3.444916 GAACGACGAGGAAGATGCAATA 58.555 45.455 0.00 0.00 0.00 1.90
208 209 2.071778 AAAAGTGTGTGGCCAGTGAT 57.928 45.000 5.11 0.00 0.00 3.06
211 212 1.055849 AGTGTGTGGCCAGTGATACA 58.944 50.000 5.11 3.98 0.00 2.29
219 220 1.765314 GGCCAGTGATACATGAGTCCT 59.235 52.381 0.00 0.00 0.00 3.85
237 238 9.959721 ATGAGTCCTACATGTTTTATTTACAGT 57.040 29.630 2.30 0.00 0.00 3.55
241 242 9.931210 GTCCTACATGTTTTATTTACAGTATGC 57.069 33.333 2.30 0.00 42.53 3.14
242 243 9.899661 TCCTACATGTTTTATTTACAGTATGCT 57.100 29.630 2.30 0.00 42.53 3.79
322 324 8.718734 GGTAATACCTTATATTCCTTTTGCTCG 58.281 37.037 1.41 0.00 34.73 5.03
333 335 2.348591 CCTTTTGCTCGACGTGTTTCTC 60.349 50.000 0.00 0.00 0.00 2.87
335 337 0.937699 TTGCTCGACGTGTTTCTCCG 60.938 55.000 0.00 0.00 0.00 4.63
353 355 1.255882 CGGGATCTGCTAGAGATGCT 58.744 55.000 16.99 0.00 46.30 3.79
356 358 2.231964 GGGATCTGCTAGAGATGCTCTG 59.768 54.545 16.99 0.00 46.30 3.35
386 388 4.646572 GCTAGCTAGCCTGGTTGAATATT 58.353 43.478 31.67 0.00 43.39 1.28
405 407 9.107177 TGAATATTTCAAGCTCTTCTCATCTTC 57.893 33.333 0.00 0.00 36.59 2.87
411 413 2.430332 AGCTCTTCTCATCTTCCCTTCG 59.570 50.000 0.00 0.00 0.00 3.79
420 422 5.659525 TCTCATCTTCCCTTCGGTACAAATA 59.340 40.000 0.00 0.00 0.00 1.40
424 426 9.316594 TCATCTTCCCTTCGGTACAAATATATA 57.683 33.333 0.00 0.00 0.00 0.86
453 455 9.896263 AATTTTTATGTGCATGGAAAACATTTC 57.104 25.926 0.00 0.00 37.84 2.17
456 458 9.941325 TTTTATGTGCATGGAAAACATTTCTAT 57.059 25.926 0.00 0.00 37.84 1.98
458 460 6.587206 TGTGCATGGAAAACATTTCTATGA 57.413 33.333 24.40 12.21 39.00 2.15
502 504 5.630680 GGTACTGATGAAAATTGTGTGCAAG 59.369 40.000 0.00 0.00 38.10 4.01
627 634 5.562890 GCTTGATTGACCAACTCAAACTACC 60.563 44.000 0.00 0.00 42.37 3.18
628 635 5.042463 TGATTGACCAACTCAAACTACCA 57.958 39.130 0.00 0.00 42.37 3.25
807 814 9.319143 CTATAAATTCAGTCCAAAACGAGAGAT 57.681 33.333 0.00 0.00 0.00 2.75
817 824 6.201044 GTCCAAAACGAGAGATATACCATGTG 59.799 42.308 0.00 0.00 0.00 3.21
824 831 7.148641 ACGAGAGATATACCATGTGCTAAAAG 58.851 38.462 0.00 0.00 0.00 2.27
869 876 3.982058 CGTAAGAACTTCGAAGAGCTTGT 59.018 43.478 31.08 11.19 37.44 3.16
953 994 2.170397 ACTTATCCGTGCATGGTGATCA 59.830 45.455 24.24 5.24 0.00 2.92
995 1046 6.467677 TGAAGTAGAAATTAACTCAGCTGCT 58.532 36.000 9.47 0.00 0.00 4.24
1229 1280 1.889170 TGTCATCGGATAGCCAGCTAG 59.111 52.381 5.49 0.00 31.45 3.42
1233 1284 2.287977 TCGGATAGCCAGCTAGCTTA 57.712 50.000 16.46 5.71 41.41 3.09
1236 1287 2.094957 CGGATAGCCAGCTAGCTTAGAC 60.095 54.545 16.46 4.67 41.41 2.59
1239 1445 2.054232 AGCCAGCTAGCTTAGACGTA 57.946 50.000 16.46 0.00 41.41 3.57
1261 1467 6.972901 CGTACAGACATAATGAAGCTTCACTA 59.027 38.462 30.66 24.66 40.49 2.74
1288 1494 4.454948 TGGAACAAGTGAGCGTGG 57.545 55.556 0.00 0.00 31.92 4.94
1310 1516 7.307751 CGTGGTGTGTGTTTTCTCTTGTAATAT 60.308 37.037 0.00 0.00 0.00 1.28
1364 1581 9.734620 TGCTTGATCATGTTTTATTGTATAAGC 57.265 29.630 10.05 0.00 35.97 3.09
1410 1627 9.985730 AGGGACGTATCGTTATATTTTTATGAA 57.014 29.630 0.00 0.00 41.37 2.57
1424 1641 6.777526 TTTTTATGAATTTTCACCGCTTGG 57.222 33.333 0.00 0.00 40.49 3.61
1425 1642 5.713792 TTTATGAATTTTCACCGCTTGGA 57.286 34.783 0.00 0.00 40.49 3.53
1426 1643 5.713792 TTATGAATTTTCACCGCTTGGAA 57.286 34.783 0.00 0.00 40.49 3.53
1428 1645 5.913137 ATGAATTTTCACCGCTTGGAATA 57.087 34.783 0.00 0.00 40.49 1.75
1430 1647 5.708948 TGAATTTTCACCGCTTGGAATAAG 58.291 37.500 0.00 0.00 36.26 1.73
1431 1648 3.569250 TTTTCACCGCTTGGAATAAGC 57.431 42.857 1.70 1.70 39.77 3.09
1506 1723 0.314302 GACCTGACGCGTGGCTATAT 59.686 55.000 20.70 0.00 0.00 0.86
1509 1726 2.030185 ACCTGACGCGTGGCTATATTAG 60.030 50.000 20.70 0.00 0.00 1.73
1513 1730 1.605710 ACGCGTGGCTATATTAGTCGT 59.394 47.619 12.93 0.00 31.65 4.34
1514 1731 2.807967 ACGCGTGGCTATATTAGTCGTA 59.192 45.455 12.93 0.00 31.65 3.43
1582 1806 5.633830 AATCATGTTTAGTGCCTTGTCTG 57.366 39.130 0.00 0.00 0.00 3.51
1592 1816 1.133945 TGCCTTGTCTGCACAGGTTTA 60.134 47.619 0.00 0.00 32.71 2.01
1594 1818 2.558359 GCCTTGTCTGCACAGGTTTAAT 59.442 45.455 0.00 0.00 32.71 1.40
1599 1828 3.146066 GTCTGCACAGGTTTAATGTGGA 58.854 45.455 9.19 5.91 46.50 4.02
1624 1853 6.507958 TTGTGATCAACAACTTGACTGAAA 57.492 33.333 0.00 0.00 43.96 2.69
1625 1854 6.507958 TGTGATCAACAACTTGACTGAAAA 57.492 33.333 0.00 0.00 39.28 2.29
1626 1855 6.918626 TGTGATCAACAACTTGACTGAAAAA 58.081 32.000 0.00 0.00 39.28 1.94
1667 1896 4.921515 TCATGTGTAGTCGCTTGAGTAAAC 59.078 41.667 0.00 0.00 36.61 2.01
1671 1901 3.319972 TGTAGTCGCTTGAGTAAACAGGT 59.680 43.478 0.00 0.00 29.49 4.00
1686 1916 0.515564 CAGGTTTAACGTGGCTTCGG 59.484 55.000 9.62 0.00 30.93 4.30
1709 1940 4.448210 GAACTACAACTTGACTGACCCAA 58.552 43.478 0.00 0.00 0.00 4.12
1789 2020 5.499004 AGACATACAAACCTTGCCTAGAA 57.501 39.130 0.00 0.00 0.00 2.10
1822 2053 4.284178 AGGAAGATGCAACATTTATGCCT 58.716 39.130 0.00 0.00 43.16 4.75
1898 2129 0.671796 CAACGAAGGGGTGGGAAAAC 59.328 55.000 0.00 0.00 0.00 2.43
1900 2131 1.437397 ACGAAGGGGTGGGAAAACTA 58.563 50.000 0.00 0.00 0.00 2.24
1903 2134 2.791655 GAAGGGGTGGGAAAACTACAG 58.208 52.381 0.00 0.00 31.13 2.74
1919 2150 9.394477 GAAAACTACAGTAACCTAAAGCAATTG 57.606 33.333 0.00 0.00 0.00 2.32
1930 2161 6.752168 ACCTAAAGCAATTGGATATTCATGC 58.248 36.000 7.72 1.82 0.00 4.06
1964 2195 9.740239 CCTTCAAGTATCCATAATCAAAACATG 57.260 33.333 0.00 0.00 0.00 3.21
1995 2226 4.450419 GCGATGATCTAATGAACCAGAAGG 59.550 45.833 0.00 0.00 42.21 3.46
2008 2239 2.827921 ACCAGAAGGAATCCATTGCAAC 59.172 45.455 0.00 0.00 38.69 4.17
2016 2247 4.460382 AGGAATCCATTGCAACTGTTGTAG 59.540 41.667 20.57 6.64 0.00 2.74
2035 2266 4.515191 TGTAGACAAGCAAACAGATCCAAC 59.485 41.667 0.00 0.00 0.00 3.77
2050 2281 7.675062 ACAGATCCAACATAGAGTATCAATCC 58.325 38.462 0.00 0.00 37.82 3.01
2070 2301 1.543802 CGTTTTGGGCTAGCCATTTCA 59.456 47.619 34.09 20.22 37.98 2.69
2071 2302 2.415893 CGTTTTGGGCTAGCCATTTCAG 60.416 50.000 34.09 17.15 37.98 3.02
2072 2303 2.825532 GTTTTGGGCTAGCCATTTCAGA 59.174 45.455 34.09 15.63 37.98 3.27
2077 2308 2.284190 GGCTAGCCATTTCAGAGTCAC 58.716 52.381 29.33 0.00 35.81 3.67
2105 2336 4.835615 ACAGCTAGTCTTCTTTGAGGAAGA 59.164 41.667 1.87 1.87 46.22 2.87
2150 2381 6.992123 TGAATAGTAGGTTGCATATTGTCCTG 59.008 38.462 0.00 0.00 0.00 3.86
2159 2390 2.292569 GCATATTGTCCTGATGTGGCTG 59.707 50.000 0.00 0.00 0.00 4.85
2165 2396 2.105649 TGTCCTGATGTGGCTGTTGTTA 59.894 45.455 0.00 0.00 0.00 2.41
2170 2401 4.320494 CCTGATGTGGCTGTTGTTACTTTC 60.320 45.833 0.00 0.00 0.00 2.62
2177 2408 6.544197 TGTGGCTGTTGTTACTTTCAAGAATA 59.456 34.615 0.00 0.00 0.00 1.75
2205 2436 7.601508 TCCTAAGAATACGAAGTTGGTTTCTTC 59.398 37.037 20.36 12.03 37.78 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.764547 CTCCCCCTTCTCCGTCCC 60.765 72.222 0.00 0.00 0.00 4.46
63 64 3.564347 AAGCCTCCCCCTTCTCCGT 62.564 63.158 0.00 0.00 0.00 4.69
64 65 2.689034 AAGCCTCCCCCTTCTCCG 60.689 66.667 0.00 0.00 0.00 4.63
65 66 2.684499 CCAAGCCTCCCCCTTCTCC 61.684 68.421 0.00 0.00 0.00 3.71
67 68 1.925972 GTCCAAGCCTCCCCCTTCT 60.926 63.158 0.00 0.00 0.00 2.85
68 69 2.677848 GTCCAAGCCTCCCCCTTC 59.322 66.667 0.00 0.00 0.00 3.46
69 70 3.330720 CGTCCAAGCCTCCCCCTT 61.331 66.667 0.00 0.00 0.00 3.95
75 76 3.327404 TTCCCCCGTCCAAGCCTC 61.327 66.667 0.00 0.00 0.00 4.70
76 77 3.330720 CTTCCCCCGTCCAAGCCT 61.331 66.667 0.00 0.00 0.00 4.58
77 78 3.623703 GACTTCCCCCGTCCAAGCC 62.624 68.421 0.00 0.00 0.00 4.35
79 80 2.264794 CGACTTCCCCCGTCCAAG 59.735 66.667 0.00 0.00 0.00 3.61
80 81 3.315949 CCGACTTCCCCCGTCCAA 61.316 66.667 0.00 0.00 0.00 3.53
83 84 2.762875 ATCCCGACTTCCCCCGTC 60.763 66.667 0.00 0.00 0.00 4.79
84 85 3.081409 CATCCCGACTTCCCCCGT 61.081 66.667 0.00 0.00 0.00 5.28
85 86 3.861797 CCATCCCGACTTCCCCCG 61.862 72.222 0.00 0.00 0.00 5.73
86 87 2.366435 TCCATCCCGACTTCCCCC 60.366 66.667 0.00 0.00 0.00 5.40
87 88 2.444256 CCTCCATCCCGACTTCCCC 61.444 68.421 0.00 0.00 0.00 4.81
88 89 3.108288 GCCTCCATCCCGACTTCCC 62.108 68.421 0.00 0.00 0.00 3.97
91 92 4.162690 GCGCCTCCATCCCGACTT 62.163 66.667 0.00 0.00 0.00 3.01
111 112 2.991540 GCCTTTGTCCTGGCCCAC 60.992 66.667 0.00 0.00 43.11 4.61
120 121 3.508840 CCGCCCATCGCCTTTGTC 61.509 66.667 0.00 0.00 36.73 3.18
211 212 9.959721 ACTGTAAATAAAACATGTAGGACTCAT 57.040 29.630 0.00 0.00 0.00 2.90
239 240 9.814899 TCTTCAAAAGAAATGTCATAAAAAGCA 57.185 25.926 0.00 0.00 33.83 3.91
254 255 9.901172 AGTAAAGAGTAGGTTTCTTCAAAAGAA 57.099 29.630 0.00 0.00 45.30 2.52
256 257 9.110502 ACAGTAAAGAGTAGGTTTCTTCAAAAG 57.889 33.333 0.00 0.00 33.92 2.27
307 309 3.596214 ACACGTCGAGCAAAAGGAATAT 58.404 40.909 0.00 0.00 0.00 1.28
313 315 2.348591 GGAGAAACACGTCGAGCAAAAG 60.349 50.000 0.00 0.00 0.00 2.27
322 324 0.531200 AGATCCCGGAGAAACACGTC 59.469 55.000 0.73 0.00 0.00 4.34
333 335 0.246086 GCATCTCTAGCAGATCCCGG 59.754 60.000 0.00 0.00 40.20 5.73
377 379 8.891720 AGATGAGAAGAGCTTGAAATATTCAAC 58.108 33.333 1.57 0.82 44.21 3.18
378 380 9.458727 AAGATGAGAAGAGCTTGAAATATTCAA 57.541 29.630 5.50 5.50 46.68 2.69
386 388 3.843027 AGGGAAGATGAGAAGAGCTTGAA 59.157 43.478 0.00 0.00 0.00 2.69
429 431 8.674263 AGAAATGTTTTCCATGCACATAAAAA 57.326 26.923 0.00 0.00 32.82 1.94
439 441 9.480053 AAGTTTGTCATAGAAATGTTTTCCATG 57.520 29.630 3.08 3.08 32.82 3.66
442 444 9.528018 TTCAAGTTTGTCATAGAAATGTTTTCC 57.472 29.630 0.00 0.00 34.50 3.13
453 455 7.482743 CCGAATCAATGTTCAAGTTTGTCATAG 59.517 37.037 0.00 0.00 0.00 2.23
456 458 5.067153 ACCGAATCAATGTTCAAGTTTGTCA 59.933 36.000 0.00 0.00 0.00 3.58
458 460 5.514274 ACCGAATCAATGTTCAAGTTTGT 57.486 34.783 0.00 0.00 0.00 2.83
502 504 8.431593 TGCGCATCTTAATTTTGAAACATAAAC 58.568 29.630 5.66 0.00 0.00 2.01
627 634 9.661187 CTAGCTAACTGATGATTTGCTATTTTG 57.339 33.333 0.00 0.00 38.88 2.44
628 635 9.401058 ACTAGCTAACTGATGATTTGCTATTTT 57.599 29.630 0.00 0.00 38.88 1.82
807 814 5.110814 AGCCACTTTTAGCACATGGTATA 57.889 39.130 0.00 0.00 32.71 1.47
817 824 5.795441 CGATTAACTGAAAGCCACTTTTAGC 59.205 40.000 10.69 0.00 39.60 3.09
824 831 4.473199 GTTTCCGATTAACTGAAAGCCAC 58.527 43.478 0.00 0.00 37.60 5.01
966 1012 9.160496 AGCTGAGTTAATTTCTACTTCAATCAG 57.840 33.333 0.00 0.00 0.00 2.90
1229 1280 6.074782 GCTTCATTATGTCTGTACGTCTAAGC 60.075 42.308 0.00 0.00 0.00 3.09
1233 1284 5.584253 AGCTTCATTATGTCTGTACGTCT 57.416 39.130 0.00 0.00 0.00 4.18
1236 1287 5.807520 AGTGAAGCTTCATTATGTCTGTACG 59.192 40.000 30.65 0.00 39.73 3.67
1239 1445 6.989169 GGATAGTGAAGCTTCATTATGTCTGT 59.011 38.462 35.56 23.58 39.33 3.41
1261 1467 2.569853 TCACTTGTTCCATACGTGGGAT 59.430 45.455 11.05 0.00 46.06 3.85
1310 1516 0.037697 ACTAGGCGTTGCGACATTGA 60.038 50.000 4.64 0.00 37.34 2.57
1360 1577 3.947196 CACATGATTAAGGGCTGTGCTTA 59.053 43.478 0.00 0.00 31.81 3.09
1364 1581 2.947652 CTCCACATGATTAAGGGCTGTG 59.052 50.000 0.00 0.00 37.53 3.66
1368 1585 1.494721 TCCCTCCACATGATTAAGGGC 59.505 52.381 17.10 0.00 45.35 5.19
1410 1627 4.110036 GCTTATTCCAAGCGGTGAAAAT 57.890 40.909 0.00 0.00 33.20 1.82
1419 1636 0.945099 GCTACCCGCTTATTCCAAGC 59.055 55.000 0.00 0.00 39.77 4.01
1469 1686 8.883731 CGTCAGGTCAAAATTCATAGAAGTATT 58.116 33.333 0.00 0.00 0.00 1.89
1470 1687 7.011482 GCGTCAGGTCAAAATTCATAGAAGTAT 59.989 37.037 0.00 0.00 0.00 2.12
1471 1688 6.312918 GCGTCAGGTCAAAATTCATAGAAGTA 59.687 38.462 0.00 0.00 0.00 2.24
1472 1689 5.122396 GCGTCAGGTCAAAATTCATAGAAGT 59.878 40.000 0.00 0.00 0.00 3.01
1473 1690 5.563842 GCGTCAGGTCAAAATTCATAGAAG 58.436 41.667 0.00 0.00 0.00 2.85
1474 1691 4.092821 CGCGTCAGGTCAAAATTCATAGAA 59.907 41.667 0.00 0.00 0.00 2.10
1475 1692 3.616821 CGCGTCAGGTCAAAATTCATAGA 59.383 43.478 0.00 0.00 0.00 1.98
1476 1693 3.370978 ACGCGTCAGGTCAAAATTCATAG 59.629 43.478 5.58 0.00 0.00 2.23
1477 1694 3.124466 CACGCGTCAGGTCAAAATTCATA 59.876 43.478 9.86 0.00 0.00 2.15
1478 1695 2.095768 CACGCGTCAGGTCAAAATTCAT 60.096 45.455 9.86 0.00 0.00 2.57
1479 1696 1.262950 CACGCGTCAGGTCAAAATTCA 59.737 47.619 9.86 0.00 0.00 2.57
1480 1697 1.399727 CCACGCGTCAGGTCAAAATTC 60.400 52.381 9.86 0.00 0.00 2.17
1490 1707 3.235195 GACTAATATAGCCACGCGTCAG 58.765 50.000 9.86 4.81 0.00 3.51
1493 1710 1.605710 ACGACTAATATAGCCACGCGT 59.394 47.619 5.58 5.58 0.00 6.01
1574 1798 3.569701 ACATTAAACCTGTGCAGACAAGG 59.430 43.478 0.02 0.00 0.00 3.61
1582 1806 4.685628 CACAAATCCACATTAAACCTGTGC 59.314 41.667 2.70 0.00 42.10 4.57
1625 1854 7.818930 ACACATGATTTCAGTCAAGTTGTTTTT 59.181 29.630 0.00 0.00 28.44 1.94
1626 1855 7.322664 ACACATGATTTCAGTCAAGTTGTTTT 58.677 30.769 0.00 0.00 28.44 2.43
1627 1856 6.866480 ACACATGATTTCAGTCAAGTTGTTT 58.134 32.000 0.00 0.00 28.44 2.83
1628 1857 6.455360 ACACATGATTTCAGTCAAGTTGTT 57.545 33.333 0.00 0.00 28.44 2.83
1629 1858 6.767902 ACTACACATGATTTCAGTCAAGTTGT 59.232 34.615 0.00 0.00 28.44 3.32
1630 1859 7.194607 ACTACACATGATTTCAGTCAAGTTG 57.805 36.000 0.00 0.00 28.44 3.16
1631 1860 6.146184 CGACTACACATGATTTCAGTCAAGTT 59.854 38.462 0.00 0.00 33.60 2.66
1632 1861 5.635280 CGACTACACATGATTTCAGTCAAGT 59.365 40.000 0.00 0.00 33.60 3.16
1633 1862 5.445142 GCGACTACACATGATTTCAGTCAAG 60.445 44.000 0.00 0.00 33.60 3.02
1634 1863 4.388773 GCGACTACACATGATTTCAGTCAA 59.611 41.667 0.00 0.00 33.60 3.18
1635 1864 3.926527 GCGACTACACATGATTTCAGTCA 59.073 43.478 0.00 0.00 33.60 3.41
1636 1865 4.177026 AGCGACTACACATGATTTCAGTC 58.823 43.478 0.00 3.91 0.00 3.51
1637 1866 4.193826 AGCGACTACACATGATTTCAGT 57.806 40.909 0.00 0.00 0.00 3.41
1638 1867 4.627035 TCAAGCGACTACACATGATTTCAG 59.373 41.667 0.00 0.00 0.00 3.02
1639 1868 4.565022 TCAAGCGACTACACATGATTTCA 58.435 39.130 0.00 0.00 0.00 2.69
1640 1869 4.627467 ACTCAAGCGACTACACATGATTTC 59.373 41.667 0.00 0.00 0.00 2.17
1641 1870 4.569943 ACTCAAGCGACTACACATGATTT 58.430 39.130 0.00 0.00 0.00 2.17
1667 1896 0.515564 CCGAAGCCACGTTAAACCTG 59.484 55.000 0.00 0.00 0.00 4.00
1671 1901 1.202675 AGTTCCCGAAGCCACGTTAAA 60.203 47.619 0.00 0.00 0.00 1.52
1686 1916 3.181458 TGGGTCAGTCAAGTTGTAGTTCC 60.181 47.826 2.11 2.28 0.00 3.62
1750 1981 9.891828 TTGTATGTCTTGATTCACATTAAACAC 57.108 29.630 0.00 0.00 34.92 3.32
1817 2048 5.016173 TGAATTAGGTAGCAACAAAGGCAT 58.984 37.500 0.00 0.00 0.00 4.40
1822 2053 9.823647 TTTCATTTTGAATTAGGTAGCAACAAA 57.176 25.926 0.00 0.00 36.11 2.83
1898 2129 7.865706 ATCCAATTGCTTTAGGTTACTGTAG 57.134 36.000 0.00 0.00 0.00 2.74
1900 2131 8.823220 AATATCCAATTGCTTTAGGTTACTGT 57.177 30.769 0.00 0.00 0.00 3.55
1903 2134 9.683069 CATGAATATCCAATTGCTTTAGGTTAC 57.317 33.333 0.00 0.00 0.00 2.50
1919 2150 2.107204 AGGACCACCAGCATGAATATCC 59.893 50.000 0.00 0.00 39.69 2.59
1930 2161 2.571653 TGGATACTTGAAGGACCACCAG 59.428 50.000 0.00 0.00 36.47 4.00
1964 2195 6.090628 GGTTCATTAGATCATCGCATCTCTTC 59.909 42.308 0.00 0.00 34.75 2.87
1995 2226 5.048782 TGTCTACAACAGTTGCAATGGATTC 60.049 40.000 13.56 0.00 32.81 2.52
2008 2239 5.334414 GGATCTGTTTGCTTGTCTACAACAG 60.334 44.000 4.32 4.32 39.58 3.16
2016 2247 3.988379 TGTTGGATCTGTTTGCTTGTC 57.012 42.857 0.00 0.00 0.00 3.18
2035 2266 5.049405 GCCCAAAACGGATTGATACTCTATG 60.049 44.000 4.24 0.00 36.56 2.23
2070 2301 1.003812 ACTAGCTGTCCTCGTGACTCT 59.996 52.381 0.00 8.17 44.75 3.24
2071 2302 1.399089 GACTAGCTGTCCTCGTGACTC 59.601 57.143 0.00 2.53 44.75 3.36
2072 2303 1.003812 AGACTAGCTGTCCTCGTGACT 59.996 52.381 11.24 0.00 46.46 3.41
2077 2308 3.191581 TCAAAGAAGACTAGCTGTCCTCG 59.808 47.826 11.24 0.00 46.46 4.63
2083 2314 5.398603 TCTTCCTCAAAGAAGACTAGCTG 57.601 43.478 0.00 0.00 45.67 4.24
2150 2381 4.829064 TGAAAGTAACAACAGCCACATC 57.171 40.909 0.00 0.00 0.00 3.06
2165 2396 9.804758 CGTATTCTTAGGAGTATTCTTGAAAGT 57.195 33.333 0.00 0.00 0.00 2.66
2170 2401 9.804758 AACTTCGTATTCTTAGGAGTATTCTTG 57.195 33.333 0.00 0.00 0.00 3.02
2177 2408 5.997384 ACCAACTTCGTATTCTTAGGAGT 57.003 39.130 0.00 0.00 0.00 3.85
2184 2415 7.668492 AGTAGAAGAAACCAACTTCGTATTCT 58.332 34.615 0.00 0.00 45.51 2.40
2190 2421 8.675504 TCTAGATAGTAGAAGAAACCAACTTCG 58.324 37.037 0.00 0.00 45.51 3.79


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

AutoCloner maintained by Alex Coulton.