Multiple sequence alignment - TraesCS2A01G334400

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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 TraesCS2A01G334400 chr2A 100.000 2231 0 0 1 2231 568300076 568302306 0.000000e+00 4120.0
1 TraesCS2A01G334400 chr2A 78.395 162 33 2 1906 2067 502630643 502630484 1.090000e-18 104.0
2 TraesCS2A01G334400 chr2B 87.308 1631 126 31 148 1733 494277835 494279429 0.000000e+00 1790.0
3 TraesCS2A01G334400 chr2B 87.685 406 43 5 1718 2122 494279445 494279844 1.210000e-127 466.0
4 TraesCS2A01G334400 chr2D 85.642 1588 128 37 7 1535 421813844 421815390 0.000000e+00 1578.0
5 TraesCS2A01G334400 chr2D 89.183 453 46 3 1781 2231 421815462 421815913 1.500000e-156 562.0
6 TraesCS2A01G334400 chr2D 81.818 165 28 2 1903 2067 627240776 627240614 1.070000e-28 137.0
7 TraesCS2A01G334400 chr2D 81.061 132 22 3 1879 2007 619373269 619373400 3.920000e-18 102.0
8 TraesCS2A01G334400 chr7B 79.227 207 27 12 1016 1214 700541779 700541977 1.800000e-26 130.0
9 TraesCS2A01G334400 chr7A 78.261 207 29 12 1016 1214 701369767 701369965 3.890000e-23 119.0
10 TraesCS2A01G334400 chr5D 79.235 183 29 8 1883 2063 515797115 515796940 3.890000e-23 119.0
11 TraesCS2A01G334400 chr1A 78.378 185 33 4 1881 2063 552276362 552276183 1.810000e-21 113.0
12 TraesCS2A01G334400 chrUn 79.710 138 27 1 1882 2019 30087758 30087894 5.070000e-17 99.0
13 TraesCS2A01G334400 chr3D 75.393 191 43 4 1879 2067 275908461 275908649 3.050000e-14 89.8


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 TraesCS2A01G334400 chr2A 568300076 568302306 2230 False 4120 4120 100.0000 1 2231 1 chr2A.!!$F1 2230
1 TraesCS2A01G334400 chr2B 494277835 494279844 2009 False 1128 1790 87.4965 148 2122 2 chr2B.!!$F1 1974
2 TraesCS2A01G334400 chr2D 421813844 421815913 2069 False 1070 1578 87.4125 7 2231 2 chr2D.!!$F2 2224

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
350 373 0.03601 ACTCCAAACAGAGGCGGATG 60.036 55.0 0.0 0.0 38.26 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 1706 0.037975 CATGCAAGGGCTTGTCCAAC 60.038 55.0 0.0 0.0 42.31 3.77 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
17 18 3.751342 TCGCTAGATCCTCCGCTG 58.249 61.111 0.00 0.00 0.00 5.18
27 28 4.845580 CTCCGCTGCCGCCATCTT 62.846 66.667 0.00 0.00 0.00 2.40
75 76 3.353836 GCGGCTGCGAAACAAGGA 61.354 61.111 0.00 0.00 0.00 3.36
76 77 2.863153 CGGCTGCGAAACAAGGAG 59.137 61.111 0.00 0.00 0.00 3.69
90 91 0.780090 AAGGAGGGAATTGGGGTGGT 60.780 55.000 0.00 0.00 0.00 4.16
95 96 1.076549 GGAATTGGGGTGGTGAGCA 59.923 57.895 0.00 0.00 0.00 4.26
116 117 1.467678 CGGCATGGTAGAGGAGAGGG 61.468 65.000 0.00 0.00 0.00 4.30
125 126 4.034410 GGTAGAGGAGAGGGTTGAGAAAT 58.966 47.826 0.00 0.00 0.00 2.17
155 174 1.647084 GCGAAAACAGTGCGGTCTT 59.353 52.632 0.00 0.00 0.00 3.01
173 192 4.760047 CGCCTCGGTTCTGGGTGG 62.760 72.222 0.00 0.00 0.00 4.61
176 195 3.322466 CTCGGTTCTGGGTGGGCT 61.322 66.667 0.00 0.00 0.00 5.19
177 196 1.987855 CTCGGTTCTGGGTGGGCTA 60.988 63.158 0.00 0.00 0.00 3.93
184 204 2.933287 TGGGTGGGCTAGGGTGTG 60.933 66.667 0.00 0.00 0.00 3.82
194 216 0.613777 CTAGGGTGTGGGAGTCCAAC 59.386 60.000 10.08 10.08 46.04 3.77
198 220 1.444250 GTGTGGGAGTCCAACGTGA 59.556 57.895 12.26 0.00 46.04 4.35
208 230 1.597027 CCAACGTGACTGGTGTCCC 60.597 63.158 0.00 0.00 42.28 4.46
209 231 1.145156 CAACGTGACTGGTGTCCCA 59.855 57.895 0.00 0.00 42.28 4.37
213 235 0.880278 CGTGACTGGTGTCCCAACTG 60.880 60.000 0.00 0.00 41.27 3.16
217 239 4.947147 TGGTGTCCCAACTGCCGC 62.947 66.667 0.00 0.00 37.98 6.53
221 243 1.754621 TGTCCCAACTGCCGCAAAA 60.755 52.632 0.00 0.00 0.00 2.44
224 246 2.790791 CCCAACTGCCGCAAAACCA 61.791 57.895 0.00 0.00 0.00 3.67
270 293 0.991920 AATGGACACCCGGACTGATT 59.008 50.000 0.73 0.00 34.29 2.57
272 295 1.221021 GGACACCCGGACTGATTCC 59.779 63.158 0.73 0.00 41.75 3.01
275 298 1.131303 ACACCCGGACTGATTCCCAA 61.131 55.000 0.73 0.00 42.27 4.12
276 299 0.392998 CACCCGGACTGATTCCCAAG 60.393 60.000 0.73 0.00 42.27 3.61
313 336 1.602323 GGATGGTTTGTGGCGTCCA 60.602 57.895 0.00 0.00 0.00 4.02
327 350 1.444250 GTCCACACAGTTCGGTCCA 59.556 57.895 0.00 0.00 0.00 4.02
330 353 0.319900 CCACACAGTTCGGTCCAGAG 60.320 60.000 0.00 0.00 0.00 3.35
332 355 0.674534 ACACAGTTCGGTCCAGAGAC 59.325 55.000 0.00 0.00 42.73 3.36
333 356 0.962489 CACAGTTCGGTCCAGAGACT 59.038 55.000 0.00 0.00 43.05 3.24
334 357 1.068194 CACAGTTCGGTCCAGAGACTC 60.068 57.143 0.00 0.00 43.05 3.36
335 358 0.528470 CAGTTCGGTCCAGAGACTCC 59.472 60.000 0.00 0.00 43.05 3.85
336 359 0.112606 AGTTCGGTCCAGAGACTCCA 59.887 55.000 0.00 0.00 43.05 3.86
337 360 0.966920 GTTCGGTCCAGAGACTCCAA 59.033 55.000 0.00 0.00 43.05 3.53
338 361 1.343465 GTTCGGTCCAGAGACTCCAAA 59.657 52.381 0.00 0.00 43.05 3.28
339 362 0.966920 TCGGTCCAGAGACTCCAAAC 59.033 55.000 0.00 0.00 43.05 2.93
340 363 0.679505 CGGTCCAGAGACTCCAAACA 59.320 55.000 0.00 0.00 43.05 2.83
341 364 1.337260 CGGTCCAGAGACTCCAAACAG 60.337 57.143 0.00 0.00 43.05 3.16
343 366 2.028567 GGTCCAGAGACTCCAAACAGAG 60.029 54.545 0.00 0.00 43.05 3.35
344 367 2.028567 GTCCAGAGACTCCAAACAGAGG 60.029 54.545 0.00 0.00 40.10 3.69
345 368 1.338579 CCAGAGACTCCAAACAGAGGC 60.339 57.143 0.00 0.00 42.77 4.70
347 370 4.285851 GACTCCAAACAGAGGCGG 57.714 61.111 0.00 0.00 38.26 6.13
348 371 1.671742 GACTCCAAACAGAGGCGGA 59.328 57.895 0.00 0.00 38.26 5.54
349 372 0.250513 GACTCCAAACAGAGGCGGAT 59.749 55.000 0.00 0.00 38.26 4.18
350 373 0.036010 ACTCCAAACAGAGGCGGATG 60.036 55.000 0.00 0.00 38.26 3.51
351 374 0.745845 CTCCAAACAGAGGCGGATGG 60.746 60.000 0.00 0.00 0.00 3.51
355 378 1.613437 CAAACAGAGGCGGATGGTTTT 59.387 47.619 0.00 0.00 29.89 2.43
360 383 1.304134 AGGCGGATGGTTTTGGGTC 60.304 57.895 0.00 0.00 0.00 4.46
366 389 1.918868 GATGGTTTTGGGTCGGCGTC 61.919 60.000 6.85 0.00 0.00 5.19
368 391 3.719144 GTTTTGGGTCGGCGTCGG 61.719 66.667 10.62 0.00 36.95 4.79
385 408 2.065993 CGGAGATGCCCGTATTACAG 57.934 55.000 0.00 0.00 44.23 2.74
397 421 4.098044 CCCGTATTACAGCCGATATGATCT 59.902 45.833 0.00 0.00 0.00 2.75
425 460 4.085357 AGTTCTAACTTGTGGTGCATGA 57.915 40.909 0.00 0.00 35.21 3.07
437 472 8.139350 ACTTGTGGTGCATGATAATGATAATTG 58.861 33.333 0.00 0.00 0.00 2.32
457 492 1.137872 GACGAAGAGACATGGGCAGAT 59.862 52.381 0.00 0.00 0.00 2.90
459 494 2.766263 ACGAAGAGACATGGGCAGATTA 59.234 45.455 0.00 0.00 0.00 1.75
460 495 3.389329 ACGAAGAGACATGGGCAGATTAT 59.611 43.478 0.00 0.00 0.00 1.28
461 496 4.588951 ACGAAGAGACATGGGCAGATTATA 59.411 41.667 0.00 0.00 0.00 0.98
463 498 5.991606 CGAAGAGACATGGGCAGATTATAAA 59.008 40.000 0.00 0.00 0.00 1.40
464 499 6.146837 CGAAGAGACATGGGCAGATTATAAAG 59.853 42.308 0.00 0.00 0.00 1.85
465 500 6.753913 AGAGACATGGGCAGATTATAAAGA 57.246 37.500 0.00 0.00 0.00 2.52
466 501 7.141758 AGAGACATGGGCAGATTATAAAGAA 57.858 36.000 0.00 0.00 0.00 2.52
468 503 8.055181 AGAGACATGGGCAGATTATAAAGAAAA 58.945 33.333 0.00 0.00 0.00 2.29
539 592 6.432936 TCGAGCGATACGTATATTTTCTGTT 58.567 36.000 8.34 0.00 0.00 3.16
551 604 3.780804 TTTTCTGTTTCGGAGGGATCA 57.219 42.857 0.00 0.00 0.00 2.92
572 625 8.239998 GGATCAAACTCAAATCTACTTTTCCTG 58.760 37.037 0.00 0.00 0.00 3.86
590 643 1.374758 GGCAAGGACGGTCTCAGTG 60.375 63.158 8.23 2.83 0.00 3.66
626 679 0.676184 ATCGTGCGCTACAGATGGAT 59.324 50.000 9.73 0.73 0.00 3.41
663 716 4.158394 GCTTTAGCATCTTTTCACATCCCA 59.842 41.667 0.00 0.00 41.59 4.37
709 762 3.049912 CTCAATCGTATCGCGGAAATCA 58.950 45.455 6.13 0.00 41.72 2.57
720 773 2.582436 GAAATCAGGGCCGTCCGA 59.418 61.111 0.00 0.00 41.52 4.55
740 793 0.827925 CCTCAATCTCCCCGATCGGA 60.828 60.000 35.42 16.09 37.50 4.55
811 864 0.036577 GCTCTCTCCTGCACACACAT 60.037 55.000 0.00 0.00 0.00 3.21
928 986 0.107456 CACACAGCCACTCTCCAACT 59.893 55.000 0.00 0.00 0.00 3.16
1304 1370 0.176449 GGGCGTACGTCCAGGTTATT 59.824 55.000 33.03 0.00 40.19 1.40
1305 1371 1.408702 GGGCGTACGTCCAGGTTATTA 59.591 52.381 33.03 0.00 40.19 0.98
1364 1431 2.570181 GTACGTACGTGCCTGGCT 59.430 61.111 30.25 3.43 0.00 4.75
1445 1537 1.656652 ATGTATCTTCGGTGTGCAGC 58.343 50.000 0.00 0.00 0.00 5.25
1446 1538 0.608130 TGTATCTTCGGTGTGCAGCT 59.392 50.000 0.00 0.00 0.00 4.24
1472 1564 4.270102 GTGCGTGAGTACTATCTACGTTC 58.730 47.826 17.19 10.30 43.79 3.95
1473 1565 3.000623 TGCGTGAGTACTATCTACGTTCG 59.999 47.826 17.19 0.00 37.12 3.95
1474 1566 3.000724 GCGTGAGTACTATCTACGTTCGT 59.999 47.826 17.19 2.91 37.12 3.85
1475 1567 4.207224 GCGTGAGTACTATCTACGTTCGTA 59.793 45.833 17.19 5.02 37.12 3.43
1498 1590 5.940192 AAGTGTTCTGTCGAATAATGCAA 57.060 34.783 0.00 0.00 0.00 4.08
1503 1595 2.348362 TCTGTCGAATAATGCAACGCAG 59.652 45.455 0.00 4.95 43.65 5.18
1511 1603 2.048444 AATGCAACGCAGGAGATGAT 57.952 45.000 0.00 0.00 43.65 2.45
1517 1609 1.051812 ACGCAGGAGATGATAAGGGG 58.948 55.000 0.00 0.00 0.00 4.79
1527 1619 7.229506 CAGGAGATGATAAGGGGTTTAATGAAC 59.770 40.741 0.00 0.00 37.53 3.18
1530 1622 6.992715 AGATGATAAGGGGTTTAATGAACTCG 59.007 38.462 0.00 0.00 39.78 4.18
1535 1627 5.431179 AGGGGTTTAATGAACTCGTGTAT 57.569 39.130 0.00 0.00 39.78 2.29
1600 1699 1.133823 TGCAGATGTGGTTCAGTTGGT 60.134 47.619 0.00 0.00 0.00 3.67
1601 1700 1.956477 GCAGATGTGGTTCAGTTGGTT 59.044 47.619 0.00 0.00 0.00 3.67
1602 1701 2.287788 GCAGATGTGGTTCAGTTGGTTG 60.288 50.000 0.00 0.00 0.00 3.77
1603 1702 1.956477 AGATGTGGTTCAGTTGGTTGC 59.044 47.619 0.00 0.00 0.00 4.17
1604 1703 1.956477 GATGTGGTTCAGTTGGTTGCT 59.044 47.619 0.00 0.00 0.00 3.91
1605 1704 1.846007 TGTGGTTCAGTTGGTTGCTT 58.154 45.000 0.00 0.00 0.00 3.91
1606 1705 1.476085 TGTGGTTCAGTTGGTTGCTTG 59.524 47.619 0.00 0.00 0.00 4.01
1607 1706 1.110442 TGGTTCAGTTGGTTGCTTGG 58.890 50.000 0.00 0.00 0.00 3.61
1608 1707 1.111277 GGTTCAGTTGGTTGCTTGGT 58.889 50.000 0.00 0.00 0.00 3.67
1609 1708 1.480545 GGTTCAGTTGGTTGCTTGGTT 59.519 47.619 0.00 0.00 0.00 3.67
1610 1709 2.539476 GTTCAGTTGGTTGCTTGGTTG 58.461 47.619 0.00 0.00 0.00 3.77
1611 1710 1.110442 TCAGTTGGTTGCTTGGTTGG 58.890 50.000 0.00 0.00 0.00 3.77
1633 1732 1.820519 CAAGCCCTTGCATGTATGTGT 59.179 47.619 0.00 0.00 41.13 3.72
1666 1765 2.027073 GAACTGCATGCGTCCACGA 61.027 57.895 14.09 0.00 43.02 4.35
1669 1768 1.154413 CTGCATGCGTCCACGAAAC 60.154 57.895 14.09 0.00 43.02 2.78
1733 1863 7.803189 GGTGTGTAATTTGTAGATTTGTCACTG 59.197 37.037 0.00 0.00 0.00 3.66
1743 1873 3.319972 AGATTTGTCACTGCAAGCATGTT 59.680 39.130 0.00 0.00 37.60 2.71
1747 1877 2.293122 TGTCACTGCAAGCATGTTAACC 59.707 45.455 2.48 0.00 37.60 2.85
1752 1882 1.339610 TGCAAGCATGTTAACCACACC 59.660 47.619 2.48 0.00 38.61 4.16
1758 1888 3.640967 AGCATGTTAACCACACCAATTGT 59.359 39.130 4.43 0.00 38.61 2.71
1766 1896 5.612725 AACCACACCAATTGTCATCTTTT 57.387 34.783 4.43 0.00 35.67 2.27
1849 1979 2.095461 TCTGTGATCAACCGGAGAGAG 58.905 52.381 9.46 1.42 0.00 3.20
1857 1987 4.128925 TCAACCGGAGAGAGATGAATTG 57.871 45.455 9.46 0.00 0.00 2.32
1937 2070 3.134574 TCACCGGAAGTACAAAGCATT 57.865 42.857 9.46 0.00 0.00 3.56
1965 2098 8.803799 CAAACATAATAAAAATTACACCGAGGC 58.196 33.333 0.00 0.00 0.00 4.70
1988 2121 2.732094 GACCACCGAACGACCACG 60.732 66.667 0.00 0.00 45.75 4.94
2007 2140 4.749310 CTGCCGCCAGAACGAGCT 62.749 66.667 0.00 0.00 41.77 4.09
2015 2148 1.372251 CAGAACGAGCTGCTGACGT 60.372 57.895 7.01 8.96 41.97 4.34
2022 2155 2.048222 GCTGCTGACGTGCCACTA 60.048 61.111 0.00 0.00 0.00 2.74
2027 2160 1.139734 CTGACGTGCCACTATCGCT 59.860 57.895 0.00 0.00 0.00 4.93
2038 2171 2.226330 CACTATCGCTGCTCCTCTACT 58.774 52.381 0.00 0.00 0.00 2.57
2040 2173 2.158740 ACTATCGCTGCTCCTCTACTGA 60.159 50.000 0.00 0.00 0.00 3.41
2056 2189 0.036388 CTGAAGCCGGCTTGACCTTA 60.036 55.000 44.71 21.31 36.26 2.69
2118 2251 4.154195 GTGTACATTTTCTACACAGGGCAG 59.846 45.833 0.00 0.00 42.42 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.049618 GCAGCGGAGGATCTAGCG 60.050 66.667 0.00 0.00 41.89 4.26
2 3 2.341911 GGCAGCGGAGGATCTAGC 59.658 66.667 0.00 0.00 38.57 3.42
3 4 2.647875 CGGCAGCGGAGGATCTAG 59.352 66.667 0.00 0.00 33.73 2.43
4 5 3.606662 GCGGCAGCGGAGGATCTA 61.607 66.667 3.69 0.00 33.73 1.98
23 24 2.000447 GTACGAAAAGCTGCCGAAGAT 59.000 47.619 9.22 0.00 0.00 2.40
27 28 1.735198 CCGTACGAAAAGCTGCCGA 60.735 57.895 18.76 0.00 0.00 5.54
29 30 1.632948 GACCCGTACGAAAAGCTGCC 61.633 60.000 18.76 0.00 0.00 4.85
33 34 0.725117 CATGGACCCGTACGAAAAGC 59.275 55.000 18.76 0.93 0.00 3.51
63 64 1.885887 CAATTCCCTCCTTGTTTCGCA 59.114 47.619 0.00 0.00 0.00 5.10
70 71 0.324645 CCACCCCAATTCCCTCCTTG 60.325 60.000 0.00 0.00 0.00 3.61
72 73 1.151361 ACCACCCCAATTCCCTCCT 60.151 57.895 0.00 0.00 0.00 3.69
75 76 2.087248 CTCACCACCCCAATTCCCT 58.913 57.895 0.00 0.00 0.00 4.20
76 77 1.682344 GCTCACCACCCCAATTCCC 60.682 63.158 0.00 0.00 0.00 3.97
90 91 2.187685 CTACCATGCCGCTGCTCA 59.812 61.111 0.70 0.00 38.71 4.26
95 96 1.075970 TCTCCTCTACCATGCCGCT 60.076 57.895 0.00 0.00 0.00 5.52
100 101 2.697751 CTCAACCCTCTCCTCTACCATG 59.302 54.545 0.00 0.00 0.00 3.66
116 117 2.766313 GGCAAAACCCCATTTCTCAAC 58.234 47.619 0.00 0.00 0.00 3.18
125 126 2.423898 TTTTCGCGGCAAAACCCCA 61.424 52.632 6.13 0.00 33.26 4.96
138 139 0.111266 CGAAGACCGCACTGTTTTCG 60.111 55.000 8.55 8.55 43.37 3.46
150 169 1.446272 CAGAACCGAGGCGAAGACC 60.446 63.158 0.00 0.00 31.70 3.85
152 171 2.646175 CCCAGAACCGAGGCGAAGA 61.646 63.158 0.00 0.00 0.00 2.87
155 174 3.691342 CACCCAGAACCGAGGCGA 61.691 66.667 0.00 0.00 0.00 5.54
162 181 2.680370 CCCTAGCCCACCCAGAACC 61.680 68.421 0.00 0.00 0.00 3.62
173 192 2.368011 GGACTCCCACACCCTAGCC 61.368 68.421 0.00 0.00 0.00 3.93
176 195 1.189524 CGTTGGACTCCCACACCCTA 61.190 60.000 0.47 0.00 43.41 3.53
177 196 2.516888 CGTTGGACTCCCACACCCT 61.517 63.158 0.47 0.00 43.41 4.34
184 204 1.004918 CCAGTCACGTTGGACTCCC 60.005 63.158 5.62 0.00 46.05 4.30
208 230 1.591327 GGTGGTTTTGCGGCAGTTG 60.591 57.895 1.67 0.00 0.00 3.16
209 231 1.756561 AGGTGGTTTTGCGGCAGTT 60.757 52.632 1.67 0.00 0.00 3.16
224 246 0.396556 AAACCGGAAGCAAACCAGGT 60.397 50.000 9.46 0.00 36.47 4.00
253 276 1.550130 GGAATCAGTCCGGGTGTCCA 61.550 60.000 0.00 0.00 36.40 4.02
270 293 0.250945 TGTACCGCATTTGCTTGGGA 60.251 50.000 0.51 0.00 39.32 4.37
272 295 0.109319 GGTGTACCGCATTTGCTTGG 60.109 55.000 0.51 0.00 39.32 3.61
275 298 1.202114 CAATGGTGTACCGCATTTGCT 59.798 47.619 0.51 0.00 39.43 3.91
276 299 1.627879 CAATGGTGTACCGCATTTGC 58.372 50.000 0.00 0.00 39.43 3.68
313 336 0.674534 GTCTCTGGACCGAACTGTGT 59.325 55.000 0.00 0.00 36.53 3.72
314 337 0.962489 AGTCTCTGGACCGAACTGTG 59.038 55.000 0.00 0.00 43.05 3.66
321 344 0.679505 TGTTTGGAGTCTCTGGACCG 59.320 55.000 0.00 0.00 43.05 4.79
327 350 0.605589 CGCCTCTGTTTGGAGTCTCT 59.394 55.000 0.00 0.00 0.00 3.10
330 353 0.250513 ATCCGCCTCTGTTTGGAGTC 59.749 55.000 0.00 0.00 33.21 3.36
332 355 0.745845 CCATCCGCCTCTGTTTGGAG 60.746 60.000 0.00 0.00 33.21 3.86
333 356 1.299648 CCATCCGCCTCTGTTTGGA 59.700 57.895 0.00 0.00 34.45 3.53
334 357 0.609131 AACCATCCGCCTCTGTTTGG 60.609 55.000 0.00 0.00 0.00 3.28
335 358 1.247567 AAACCATCCGCCTCTGTTTG 58.752 50.000 0.00 0.00 0.00 2.93
336 359 1.613437 CAAAACCATCCGCCTCTGTTT 59.387 47.619 0.00 0.00 0.00 2.83
337 360 1.247567 CAAAACCATCCGCCTCTGTT 58.752 50.000 0.00 0.00 0.00 3.16
338 361 0.609131 CCAAAACCATCCGCCTCTGT 60.609 55.000 0.00 0.00 0.00 3.41
339 362 1.315257 CCCAAAACCATCCGCCTCTG 61.315 60.000 0.00 0.00 0.00 3.35
340 363 1.000896 CCCAAAACCATCCGCCTCT 60.001 57.895 0.00 0.00 0.00 3.69
341 364 1.304134 ACCCAAAACCATCCGCCTC 60.304 57.895 0.00 0.00 0.00 4.70
343 366 2.696759 CGACCCAAAACCATCCGCC 61.697 63.158 0.00 0.00 0.00 6.13
344 367 2.696759 CCGACCCAAAACCATCCGC 61.697 63.158 0.00 0.00 0.00 5.54
345 368 2.696759 GCCGACCCAAAACCATCCG 61.697 63.158 0.00 0.00 0.00 4.18
346 369 2.696759 CGCCGACCCAAAACCATCC 61.697 63.158 0.00 0.00 0.00 3.51
347 370 1.918868 GACGCCGACCCAAAACCATC 61.919 60.000 0.00 0.00 0.00 3.51
348 371 1.969589 GACGCCGACCCAAAACCAT 60.970 57.895 0.00 0.00 0.00 3.55
349 372 2.592287 GACGCCGACCCAAAACCA 60.592 61.111 0.00 0.00 0.00 3.67
350 373 3.719144 CGACGCCGACCCAAAACC 61.719 66.667 0.00 0.00 38.22 3.27
351 374 3.719144 CCGACGCCGACCCAAAAC 61.719 66.667 0.00 0.00 38.22 2.43
382 405 1.898472 CTCCCAGATCATATCGGCTGT 59.102 52.381 0.00 0.00 0.00 4.40
383 406 1.898472 ACTCCCAGATCATATCGGCTG 59.102 52.381 0.00 0.00 0.00 4.85
384 407 2.317371 ACTCCCAGATCATATCGGCT 57.683 50.000 0.00 0.00 0.00 5.52
385 408 3.093057 ACTACTCCCAGATCATATCGGC 58.907 50.000 0.00 0.00 0.00 5.54
397 421 4.039973 CACCACAAGTTAGAACTACTCCCA 59.960 45.833 0.00 0.00 38.57 4.37
425 460 9.212641 CCATGTCTCTTCGTCAATTATCATTAT 57.787 33.333 0.00 0.00 0.00 1.28
437 472 0.532573 TCTGCCCATGTCTCTTCGTC 59.467 55.000 0.00 0.00 0.00 4.20
459 494 9.981460 ATCTCTCCCTGTAAACATTTTCTTTAT 57.019 29.630 0.00 0.00 0.00 1.40
460 495 9.807921 AATCTCTCCCTGTAAACATTTTCTTTA 57.192 29.630 0.00 0.00 0.00 1.85
461 496 8.712228 AATCTCTCCCTGTAAACATTTTCTTT 57.288 30.769 0.00 0.00 0.00 2.52
463 498 6.887002 GGAATCTCTCCCTGTAAACATTTTCT 59.113 38.462 0.00 0.00 38.44 2.52
464 499 6.183360 CGGAATCTCTCCCTGTAAACATTTTC 60.183 42.308 0.00 0.00 41.87 2.29
465 500 5.648092 CGGAATCTCTCCCTGTAAACATTTT 59.352 40.000 0.00 0.00 41.87 1.82
466 501 5.045869 TCGGAATCTCTCCCTGTAAACATTT 60.046 40.000 0.00 0.00 41.87 2.32
468 503 4.030913 TCGGAATCTCTCCCTGTAAACAT 58.969 43.478 0.00 0.00 41.87 2.71
477 526 1.337387 CGTACCTTCGGAATCTCTCCC 59.663 57.143 0.00 0.00 41.87 4.30
478 527 2.022934 ACGTACCTTCGGAATCTCTCC 58.977 52.381 0.00 0.00 41.40 3.71
479 528 3.250521 CCTACGTACCTTCGGAATCTCTC 59.749 52.174 0.00 0.00 34.94 3.20
492 541 4.147321 TCCATTCTACCATCCTACGTACC 58.853 47.826 0.00 0.00 0.00 3.34
502 555 2.239400 TCGCTCGATCCATTCTACCAT 58.761 47.619 0.00 0.00 0.00 3.55
503 556 1.687563 TCGCTCGATCCATTCTACCA 58.312 50.000 0.00 0.00 0.00 3.25
539 592 3.780804 TTTGAGTTTGATCCCTCCGAA 57.219 42.857 0.00 0.00 0.00 4.30
551 604 5.833131 TGCCAGGAAAAGTAGATTTGAGTTT 59.167 36.000 0.00 0.00 0.00 2.66
572 625 1.374758 CACTGAGACCGTCCTTGCC 60.375 63.158 0.00 0.00 0.00 4.52
581 634 1.947456 GGTTGGTGAAACACTGAGACC 59.053 52.381 0.00 0.00 40.86 3.85
590 643 3.078837 ACGATATGGTGGTTGGTGAAAC 58.921 45.455 0.00 0.00 38.12 2.78
626 679 0.246910 TAAAGCACGGCCGTACATGA 59.753 50.000 33.70 9.01 0.00 3.07
663 716 0.179119 GATCGAACGGTCCGGATTGT 60.179 55.000 17.28 6.57 0.00 2.71
696 749 1.070786 GGCCCTGATTTCCGCGATA 59.929 57.895 8.23 0.00 0.00 2.92
697 750 2.203209 GGCCCTGATTTCCGCGAT 60.203 61.111 8.23 0.00 0.00 4.58
720 773 1.115930 CCGATCGGGGAGATTGAGGT 61.116 60.000 26.95 0.00 42.22 3.85
725 778 2.857744 GCGTCCGATCGGGGAGATT 61.858 63.158 32.79 0.00 40.26 2.40
811 864 0.655208 CTTGTGTGCGTGCTTGTGTA 59.345 50.000 0.00 0.00 0.00 2.90
878 936 1.219393 GGAAGGTGAGAAGAGGCCG 59.781 63.158 0.00 0.00 0.00 6.13
911 969 1.338200 GGTAGTTGGAGAGTGGCTGTG 60.338 57.143 0.00 0.00 0.00 3.66
928 986 2.957006 GCTAGCTAGCTAACCAGTGGTA 59.043 50.000 33.71 3.26 45.62 3.25
1252 1318 1.034356 ACGTACATGTATAGGCGGCA 58.966 50.000 13.08 0.00 0.00 5.69
1277 1343 2.044650 ACGTACGCCCTAGCTGGA 60.045 61.111 16.72 0.00 38.35 3.86
1305 1371 8.266473 AGATCGATCTTATTCCCTATACGTAGT 58.734 37.037 22.32 0.00 38.23 2.73
1347 1414 0.248377 CTAGCCAGGCACGTACGTAC 60.248 60.000 22.34 16.05 0.00 3.67
1361 1428 1.301322 GCTCATCGGGAAGCTAGCC 60.301 63.158 12.13 0.00 0.00 3.93
1364 1431 2.366640 ACTAGCTCATCGGGAAGCTA 57.633 50.000 11.34 11.34 38.66 3.32
1404 1471 7.854534 ACATAACATATGATCACATCAACACG 58.145 34.615 10.38 0.00 43.50 4.49
1445 1537 2.352034 AGATAGTACTCACGCACACGAG 59.648 50.000 0.00 0.00 43.93 4.18
1446 1538 2.353323 AGATAGTACTCACGCACACGA 58.647 47.619 0.00 0.00 43.93 4.35
1468 1560 3.038017 TCGACAGAACACTTTACGAACG 58.962 45.455 0.00 0.00 0.00 3.95
1472 1564 5.952064 GCATTATTCGACAGAACACTTTACG 59.048 40.000 0.00 0.00 39.48 3.18
1473 1565 6.827641 TGCATTATTCGACAGAACACTTTAC 58.172 36.000 0.00 0.00 39.48 2.01
1474 1566 7.295201 GTTGCATTATTCGACAGAACACTTTA 58.705 34.615 0.00 0.00 39.48 1.85
1475 1567 5.940192 TGCATTATTCGACAGAACACTTT 57.060 34.783 0.00 0.00 39.48 2.66
1498 1590 1.051812 CCCCTTATCATCTCCTGCGT 58.948 55.000 0.00 0.00 0.00 5.24
1503 1595 7.290813 AGTTCATTAAACCCCTTATCATCTCC 58.709 38.462 0.00 0.00 38.76 3.71
1511 1603 5.231702 ACACGAGTTCATTAAACCCCTTA 57.768 39.130 0.00 0.00 38.76 2.69
1559 1651 9.056005 TCTGCATTTCAAGTTGTCCATATATAC 57.944 33.333 2.11 0.00 0.00 1.47
1573 1672 4.022589 ACTGAACCACATCTGCATTTCAAG 60.023 41.667 0.00 0.00 0.00 3.02
1603 1702 0.675633 CAAGGGCTTGTCCAACCAAG 59.324 55.000 0.00 0.00 43.76 3.61
1604 1703 1.398958 GCAAGGGCTTGTCCAACCAA 61.399 55.000 0.00 0.00 42.31 3.67
1605 1704 1.832167 GCAAGGGCTTGTCCAACCA 60.832 57.895 0.00 0.00 42.31 3.67
1606 1705 1.187567 ATGCAAGGGCTTGTCCAACC 61.188 55.000 0.00 0.00 42.31 3.77
1607 1706 0.037975 CATGCAAGGGCTTGTCCAAC 60.038 55.000 0.00 0.00 42.31 3.77
1608 1707 2.353858 CATGCAAGGGCTTGTCCAA 58.646 52.632 0.00 0.00 42.31 3.53
1609 1708 4.100479 CATGCAAGGGCTTGTCCA 57.900 55.556 0.00 0.00 42.31 4.02
1618 1717 4.260497 CGAGATCAACACATACATGCAAGG 60.260 45.833 0.00 0.00 0.00 3.61
1633 1732 5.009854 TGCAGTTCATGTATCGAGATCAA 57.990 39.130 0.00 0.00 0.00 2.57
1661 1760 2.664851 TGCCGCTCTGTTTCGTGG 60.665 61.111 0.00 0.00 0.00 4.94
1666 1765 1.032014 ACAATTGTGCCGCTCTGTTT 58.968 45.000 11.07 0.00 0.00 2.83
1669 1768 0.387622 CCAACAATTGTGCCGCTCTG 60.388 55.000 12.82 4.52 0.00 3.35
1733 1863 1.339610 TGGTGTGGTTAACATGCTTGC 59.660 47.619 8.10 0.00 41.97 4.01
1743 1873 6.322456 TGAAAAGATGACAATTGGTGTGGTTA 59.678 34.615 10.83 0.00 41.96 2.85
1747 1877 5.835257 ACTGAAAAGATGACAATTGGTGTG 58.165 37.500 10.83 0.00 41.96 3.82
1766 1896 7.880713 TGCATTTGGACATTTACTACTAACTGA 59.119 33.333 0.00 0.00 0.00 3.41
1900 2033 9.893305 CTTCCGGTGAACAATTATAATAAATCC 57.107 33.333 0.00 0.00 0.00 3.01
1904 2037 9.887629 TGTACTTCCGGTGAACAATTATAATAA 57.112 29.630 0.00 0.00 0.00 1.40
1960 2093 3.827898 GGTGGTCTCCGAGCCTCG 61.828 72.222 7.25 7.25 40.07 4.63
1976 2109 3.103911 GCAGTCGTGGTCGTTCGG 61.104 66.667 0.00 0.00 38.33 4.30
1988 2121 2.811317 CTCGTTCTGGCGGCAGTC 60.811 66.667 34.57 26.31 0.00 3.51
2007 2140 1.153842 CGATAGTGGCACGTCAGCA 60.154 57.895 20.55 3.12 35.83 4.41
2015 2148 2.021068 GAGGAGCAGCGATAGTGGCA 62.021 60.000 0.00 0.00 39.25 4.92
2019 2152 2.158740 TCAGTAGAGGAGCAGCGATAGT 60.159 50.000 0.00 0.00 39.35 2.12
2022 2155 1.680735 CTTCAGTAGAGGAGCAGCGAT 59.319 52.381 0.00 0.00 0.00 4.58
2027 2160 1.323271 CCGGCTTCAGTAGAGGAGCA 61.323 60.000 0.00 0.00 0.00 4.26
2038 2171 0.618458 ATAAGGTCAAGCCGGCTTCA 59.382 50.000 38.34 26.24 43.70 3.02
2040 2173 0.462047 CGATAAGGTCAAGCCGGCTT 60.462 55.000 35.84 35.84 43.70 4.35
2081 2214 5.523438 AATGTACACCACCGTTTTGAAAT 57.477 34.783 0.00 0.00 0.00 2.17
2087 2220 5.007921 GTGTAGAAAATGTACACCACCGTTT 59.992 40.000 0.00 0.00 43.00 3.60
2088 2221 4.512571 GTGTAGAAAATGTACACCACCGTT 59.487 41.667 0.00 0.00 43.00 4.44
2141 2274 9.494271 CTTATACATGTACATACCATTTGCTCT 57.506 33.333 7.96 0.00 0.00 4.09
2157 2290 8.530311 CATCCTGCTAGATCTTCTTATACATGT 58.470 37.037 0.00 2.69 0.00 3.21
2161 2294 6.071108 TGCCATCCTGCTAGATCTTCTTATAC 60.071 42.308 0.00 0.00 0.00 1.47
2164 2297 4.226384 TGCCATCCTGCTAGATCTTCTTA 58.774 43.478 0.00 0.00 0.00 2.10
2173 2306 2.401967 GCACTTGCCATCCTGCTAG 58.598 57.895 0.00 0.00 39.53 3.42


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

AutoCloner maintained by Alex Coulton.