Multiple sequence alignment - TraesCS2A01G380100

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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 TraesCS2A01G380100 chr2A 100.000 2537 0 0 1 2537 623151425 623153961 0.000000e+00 4686.0
1 TraesCS2A01G380100 chr2B 90.162 2043 132 26 1 2026 563678071 563680061 0.000000e+00 2595.0
2 TraesCS2A01G380100 chr2B 84.868 152 9 8 2392 2537 563680469 563680612 9.460000e-30 141.0
3 TraesCS2A01G380100 chr2D 91.407 1478 47 24 668 2106 480573581 480575017 0.000000e+00 1953.0
4 TraesCS2A01G380100 chr2D 84.940 166 10 7 2372 2537 480575485 480575635 1.220000e-33 154.0
5 TraesCS2A01G380100 chr2D 83.333 96 14 2 501 595 480570032 480570126 1.250000e-13 87.9
6 TraesCS2A01G380100 chr2D 92.857 56 1 2 2321 2373 480575380 480575435 7.520000e-11 78.7
7 TraesCS2A01G380100 chr2D 100.000 31 0 0 630 660 480573565 480573595 9.800000e-05 58.4
8 TraesCS2A01G380100 chr6B 75.309 243 31 19 1243 1478 466967425 466967645 3.480000e-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 TraesCS2A01G380100 chr2A 623151425 623153961 2536 False 4686.0 4686 100.0000 1 2537 1 chr2A.!!$F1 2536
1 TraesCS2A01G380100 chr2B 563678071 563680612 2541 False 1368.0 2595 87.5150 1 2537 2 chr2B.!!$F1 2536
2 TraesCS2A01G380100 chr2D 480570032 480575635 5603 False 466.4 1953 90.5074 501 2537 5 chr2D.!!$F1 2036

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
277 278 0.109319 GCAGTGGTTTATGTTGGCCG 60.109 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 5833 0.381089 CGGCGGTGTAGGAGTTAGAG 59.619 60.0 0.0 0.0 0.0 2.43 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
52 53 3.855209 CTCGCAAAACACCGCCACG 62.855 63.158 0.00 0.00 0.00 4.94
107 108 1.858091 TCGGTACTACGAGACGGATC 58.142 55.000 0.00 0.00 38.06 3.36
121 122 1.066143 ACGGATCTGTTTTGGAGCGAT 60.066 47.619 0.00 0.00 0.00 4.58
122 123 2.167693 ACGGATCTGTTTTGGAGCGATA 59.832 45.455 0.00 0.00 0.00 2.92
123 124 2.797156 CGGATCTGTTTTGGAGCGATAG 59.203 50.000 0.00 0.00 0.00 2.08
154 155 4.944317 TGGCACACAATTCCGTAATATTGA 59.056 37.500 0.00 0.00 36.03 2.57
181 182 3.861840 TGAGCTATGTCAAGGTTAGTGC 58.138 45.455 0.00 0.00 0.00 4.40
184 185 3.009033 AGCTATGTCAAGGTTAGTGCCAA 59.991 43.478 0.00 0.00 0.00 4.52
193 194 3.347216 AGGTTAGTGCCAACATGATCAC 58.653 45.455 0.00 1.58 0.00 3.06
200 201 3.441222 GTGCCAACATGATCACTCATTGA 59.559 43.478 0.00 0.00 40.20 2.57
212 213 3.253921 TCACTCATTGACATTGTGCAAGG 59.746 43.478 0.00 1.07 0.00 3.61
262 263 2.594592 GGCGGTGTTTGAGGCAGT 60.595 61.111 0.00 0.00 0.00 4.40
272 273 3.957497 TGTTTGAGGCAGTGGTTTATGTT 59.043 39.130 0.00 0.00 0.00 2.71
277 278 0.109319 GCAGTGGTTTATGTTGGCCG 60.109 55.000 0.00 0.00 0.00 6.13
286 287 1.647346 TATGTTGGCCGTTCGATCAC 58.353 50.000 0.00 0.00 0.00 3.06
304 305 1.220749 CCCATGTCCACCTACACCG 59.779 63.158 0.00 0.00 30.75 4.94
305 306 1.261938 CCCATGTCCACCTACACCGA 61.262 60.000 0.00 0.00 30.75 4.69
306 307 0.611200 CCATGTCCACCTACACCGAA 59.389 55.000 0.00 0.00 30.75 4.30
307 308 1.405526 CCATGTCCACCTACACCGAAG 60.406 57.143 0.00 0.00 30.75 3.79
308 309 0.249398 ATGTCCACCTACACCGAAGC 59.751 55.000 0.00 0.00 30.75 3.86
309 310 1.445582 GTCCACCTACACCGAAGCG 60.446 63.158 0.00 0.00 0.00 4.68
310 311 2.813908 CCACCTACACCGAAGCGC 60.814 66.667 0.00 0.00 0.00 5.92
311 312 2.813908 CACCTACACCGAAGCGCC 60.814 66.667 2.29 0.00 0.00 6.53
312 313 4.078516 ACCTACACCGAAGCGCCC 62.079 66.667 2.29 0.00 0.00 6.13
318 319 4.430765 ACCGAAGCGCCCGTGTAG 62.431 66.667 16.72 5.83 0.00 2.74
349 350 6.070309 CCTTAGCTTCTGCCTCTATATTCCAT 60.070 42.308 0.00 0.00 40.80 3.41
368 369 0.321346 TGTGGCATGTGTCATCGACT 59.679 50.000 0.00 0.00 33.15 4.18
369 370 1.270785 TGTGGCATGTGTCATCGACTT 60.271 47.619 0.00 0.00 33.15 3.01
371 372 1.001860 TGGCATGTGTCATCGACTTGA 59.998 47.619 0.00 0.00 33.15 3.02
428 429 9.337396 TGAGTACATGGTATAATGAAACATTCC 57.663 33.333 0.00 0.00 0.00 3.01
448 449 8.592809 ACATTCCAAATATACCACACAATGTTT 58.407 29.630 0.00 0.00 29.71 2.83
475 476 6.715347 AGTTTTCTAAAATTGCCACACTCT 57.285 33.333 0.00 0.00 0.00 3.24
476 477 6.507023 AGTTTTCTAAAATTGCCACACTCTG 58.493 36.000 0.00 0.00 0.00 3.35
487 489 3.820467 TGCCACACTCTGGTAATTTTCTG 59.180 43.478 0.00 0.00 42.99 3.02
494 496 7.592533 CACACTCTGGTAATTTTCTGAATTGTG 59.407 37.037 0.00 0.00 0.00 3.33
508 510 6.370593 TCTGAATTGTGTTAGTCATTTTCGC 58.629 36.000 0.00 0.00 0.00 4.70
513 515 3.183574 TGTGTTAGTCATTTTCGCGACAG 59.816 43.478 9.15 0.00 34.48 3.51
522 524 4.452795 TCATTTTCGCGACAGGTAATTTGA 59.547 37.500 9.15 4.05 0.00 2.69
525 527 3.520290 TCGCGACAGGTAATTTGAGAT 57.480 42.857 3.71 0.00 0.00 2.75
531 533 4.455606 GACAGGTAATTTGAGATGGAGGG 58.544 47.826 0.00 0.00 0.00 4.30
532 534 4.111577 ACAGGTAATTTGAGATGGAGGGA 58.888 43.478 0.00 0.00 0.00 4.20
538 540 7.235812 AGGTAATTTGAGATGGAGGGAGTATAC 59.764 40.741 0.00 0.00 0.00 1.47
595 1006 8.383318 ACTTTCAATCGGGTCATATTCATTAG 57.617 34.615 0.00 0.00 0.00 1.73
606 1017 8.624776 GGGTCATATTCATTAGGTTTTTCTCAG 58.375 37.037 0.00 0.00 0.00 3.35
623 1034 3.397618 TCTCAGGAAAATCCTCCAAACCA 59.602 43.478 0.00 0.00 45.66 3.67
653 4059 8.522830 CCTTAGAGAAATGCAATTAAAAGGTCA 58.477 33.333 0.00 0.00 33.67 4.02
706 4112 1.199097 GCGGGGAAAATGTGTGTACAG 59.801 52.381 0.00 0.00 40.79 2.74
822 4228 1.480954 GTCTTATCTGCTTCCGGTCCA 59.519 52.381 0.00 0.00 0.00 4.02
824 4236 2.103094 TCTTATCTGCTTCCGGTCCATG 59.897 50.000 0.00 0.00 0.00 3.66
829 4241 1.519455 GCTTCCGGTCCATGTCTCG 60.519 63.158 0.00 0.00 0.00 4.04
834 4246 2.887568 GGTCCATGTCTCGCTGCG 60.888 66.667 17.25 17.25 0.00 5.18
934 4347 2.847234 TCCTCACAACCCCGCACT 60.847 61.111 0.00 0.00 0.00 4.40
978 4398 1.812686 TTGAGGCGTCACGGTAAGCT 61.813 55.000 8.96 0.00 30.10 3.74
1278 4709 2.507452 CTGCCGATGAGCATCCCA 59.493 61.111 4.98 2.49 43.09 4.37
1313 4744 2.762875 GGGGGTCGAGTACAGGGG 60.763 72.222 0.00 0.00 0.00 4.79
1538 4969 2.344203 CCGGCTTCGAGGACTGACT 61.344 63.158 0.00 0.00 35.61 3.41
1540 4971 1.587043 CGGCTTCGAGGACTGACTGA 61.587 60.000 0.00 0.00 35.61 3.41
1541 4972 0.109039 GGCTTCGAGGACTGACTGAC 60.109 60.000 0.00 0.00 0.00 3.51
1542 4973 0.109039 GCTTCGAGGACTGACTGACC 60.109 60.000 0.00 0.00 0.00 4.02
1543 4974 0.169230 CTTCGAGGACTGACTGACCG 59.831 60.000 0.00 0.00 35.66 4.79
1544 4975 1.241990 TTCGAGGACTGACTGACCGG 61.242 60.000 0.00 0.00 35.66 5.28
1545 4976 1.674651 CGAGGACTGACTGACCGGA 60.675 63.158 9.46 0.00 35.66 5.14
1546 4977 1.649390 CGAGGACTGACTGACCGGAG 61.649 65.000 9.46 0.00 35.66 4.63
1547 4978 0.322636 GAGGACTGACTGACCGGAGA 60.323 60.000 9.46 0.00 35.66 3.71
1548 4979 0.609681 AGGACTGACTGACCGGAGAC 60.610 60.000 9.46 0.00 35.66 3.36
1614 5049 0.388649 AGTATGCGCCGCAGTATAGC 60.389 55.000 19.64 3.66 43.65 2.97
1726 5161 2.032860 ATGCGATCCTGACGGAAGGG 62.033 60.000 5.88 0.00 44.02 3.95
1746 5189 3.351416 GCGGGTGGGTGTTCGTTC 61.351 66.667 0.00 0.00 0.00 3.95
1747 5190 3.039588 CGGGTGGGTGTTCGTTCG 61.040 66.667 0.00 0.00 0.00 3.95
1748 5191 2.109593 GGGTGGGTGTTCGTTCGT 59.890 61.111 0.00 0.00 0.00 3.85
1749 5192 1.524393 GGGTGGGTGTTCGTTCGTT 60.524 57.895 0.00 0.00 0.00 3.85
1750 5193 1.501337 GGGTGGGTGTTCGTTCGTTC 61.501 60.000 0.00 0.00 0.00 3.95
1751 5194 1.561250 GTGGGTGTTCGTTCGTTCG 59.439 57.895 0.00 0.00 0.00 3.95
1752 5195 1.141449 TGGGTGTTCGTTCGTTCGT 59.859 52.632 2.67 0.00 0.00 3.85
1753 5196 0.459934 TGGGTGTTCGTTCGTTCGTT 60.460 50.000 2.67 0.00 0.00 3.85
1792 5235 4.423231 GGCACCTGGAGGAAAAGG 57.577 61.111 0.00 0.00 39.65 3.11
1793 5236 1.979155 GGCACCTGGAGGAAAAGGC 60.979 63.158 0.00 0.00 37.03 4.35
1794 5237 1.075659 GCACCTGGAGGAAAAGGCT 59.924 57.895 0.00 0.00 37.03 4.58
1795 5238 0.328258 GCACCTGGAGGAAAAGGCTA 59.672 55.000 0.00 0.00 37.03 3.93
1873 5321 3.068165 GTCTTAAGCTTTTTGCAGTGGGT 59.932 43.478 3.20 0.00 45.94 4.51
1919 5367 2.816087 TGCTGAACAGAGAAGAAATGCC 59.184 45.455 5.97 0.00 0.00 4.40
1922 5370 4.070716 CTGAACAGAGAAGAAATGCCTGT 58.929 43.478 0.00 0.00 39.49 4.00
1931 5383 2.318908 AGAAATGCCTGTCTTTGCCAA 58.681 42.857 0.00 0.00 0.00 4.52
1986 5438 4.918810 AAGAAATTGCTTTCGGTTGAGT 57.081 36.364 0.00 0.00 44.52 3.41
2002 5454 4.879545 GGTTGAGTGTTACACCTTTCTGAA 59.120 41.667 12.28 0.00 34.49 3.02
2044 5736 9.010029 ACATTTTTCTTCCAATATAACGACACT 57.990 29.630 0.00 0.00 0.00 3.55
2116 5808 8.988546 ATAATATCTATCGGATGTGTCTAGCT 57.011 34.615 0.00 0.00 35.98 3.32
2117 5809 6.935741 ATATCTATCGGATGTGTCTAGCTC 57.064 41.667 0.00 0.00 35.98 4.09
2119 5811 4.320023 TCTATCGGATGTGTCTAGCTCTC 58.680 47.826 0.00 0.00 0.00 3.20
2121 5813 2.937519 TCGGATGTGTCTAGCTCTCAT 58.062 47.619 0.00 0.00 0.00 2.90
2122 5814 2.881513 TCGGATGTGTCTAGCTCTCATC 59.118 50.000 15.12 15.12 36.03 2.92
2123 5815 2.884012 CGGATGTGTCTAGCTCTCATCT 59.116 50.000 19.13 0.00 36.60 2.90
2124 5816 4.068599 CGGATGTGTCTAGCTCTCATCTA 58.931 47.826 19.13 0.00 36.60 1.98
2125 5817 4.699735 CGGATGTGTCTAGCTCTCATCTAT 59.300 45.833 19.13 0.00 36.60 1.98
2126 5818 5.877564 CGGATGTGTCTAGCTCTCATCTATA 59.122 44.000 19.13 0.00 36.60 1.31
2127 5819 6.183360 CGGATGTGTCTAGCTCTCATCTATAC 60.183 46.154 19.13 9.40 36.60 1.47
2128 5820 6.884295 GGATGTGTCTAGCTCTCATCTATACT 59.116 42.308 19.13 0.00 36.60 2.12
2129 5821 8.044309 GGATGTGTCTAGCTCTCATCTATACTA 58.956 40.741 19.13 0.00 36.60 1.82
2130 5822 9.098355 GATGTGTCTAGCTCTCATCTATACTAG 57.902 40.741 15.68 0.00 34.81 2.57
2131 5823 8.196378 TGTGTCTAGCTCTCATCTATACTAGA 57.804 38.462 0.00 0.00 39.50 2.43
2132 5824 8.821817 TGTGTCTAGCTCTCATCTATACTAGAT 58.178 37.037 0.00 0.00 46.06 1.98
2158 5850 3.312146 GTCTACTCTAACTCCTACACCGC 59.688 52.174 0.00 0.00 0.00 5.68
2162 5854 0.813184 CTAACTCCTACACCGCCGAA 59.187 55.000 0.00 0.00 0.00 4.30
2183 6072 3.917329 TTCTACGCGGAGATTCATAGG 57.083 47.619 24.23 0.00 0.00 2.57
2189 6078 3.621715 ACGCGGAGATTCATAGGTTTTTC 59.378 43.478 12.47 0.00 0.00 2.29
2190 6079 3.002348 CGCGGAGATTCATAGGTTTTTCC 59.998 47.826 0.00 0.00 0.00 3.13
2191 6080 3.315470 GCGGAGATTCATAGGTTTTTCCC 59.685 47.826 0.00 0.00 36.75 3.97
2193 6082 4.627741 CGGAGATTCATAGGTTTTTCCCCA 60.628 45.833 0.00 0.00 36.75 4.96
2196 6085 6.183360 GGAGATTCATAGGTTTTTCCCCATTG 60.183 42.308 0.00 0.00 36.75 2.82
2203 6092 4.397420 AGGTTTTTCCCCATTGATTTTGC 58.603 39.130 0.00 0.00 36.75 3.68
2209 6098 2.978278 TCCCCATTGATTTTGCTTGGTT 59.022 40.909 0.00 0.00 0.00 3.67
2230 6119 6.043411 GGTTAATCAGCAGTGTAGGAGTTAG 58.957 44.000 0.00 0.00 0.00 2.34
2232 6121 7.418025 GGTTAATCAGCAGTGTAGGAGTTAGAT 60.418 40.741 0.00 0.00 0.00 1.98
2249 6138 8.081633 GGAGTTAGATGAGACATTGTAGATGAG 58.918 40.741 0.00 0.00 0.00 2.90
2278 6168 9.716507 TTAGCAAATTCGCTATCTGAAAAATAC 57.283 29.630 0.00 0.00 43.77 1.89
2280 6170 7.698130 AGCAAATTCGCTATCTGAAAAATACAC 59.302 33.333 0.00 0.00 41.55 2.90
2282 6172 9.507280 CAAATTCGCTATCTGAAAAATACACAT 57.493 29.630 0.00 0.00 0.00 3.21
2303 6193 8.695456 ACACATATTGAATTATGGGAAGTTTCC 58.305 33.333 2.17 2.17 46.82 3.13
2356 6246 7.767261 AGTTTAGCTTCTGTAGTCTACATCTG 58.233 38.462 13.10 7.36 38.15 2.90
2404 6363 5.363580 AGTTCCAAAAGAAAAGCTGATGGAA 59.636 36.000 0.00 0.00 43.96 3.53
2429 6388 3.865164 CGGCAGCTGGATTTTAAATTTCC 59.135 43.478 17.12 9.67 0.00 3.13
2473 6436 1.658717 CCGCGCAAGAGTAGGATCG 60.659 63.158 8.75 0.00 43.02 3.69
2476 6439 1.197036 CGCGCAAGAGTAGGATCGATA 59.803 52.381 8.75 0.00 43.02 2.92
2508 6471 8.322906 TCAATAATTGATCATCCATCCGTTAC 57.677 34.615 0.00 0.00 34.08 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.062124 CGAGCTAAAACACGCAAACAAAC 60.062 43.478 0.00 0.00 0.00 2.93
20 21 3.448076 GCGAGCTAAAACACGCAAA 57.552 47.368 10.01 0.00 46.77 3.68
24 25 2.710760 TGTTTTGCGAGCTAAAACACG 58.289 42.857 17.89 4.17 46.90 4.49
67 68 2.965147 AGCCAGCAACATTTTGTTAGGT 59.035 40.909 0.00 0.00 38.77 3.08
73 74 0.314935 ACCGAGCCAGCAACATTTTG 59.685 50.000 0.00 0.00 35.62 2.44
79 80 0.801067 CGTAGTACCGAGCCAGCAAC 60.801 60.000 0.00 0.00 0.00 4.17
102 103 1.656652 ATCGCTCCAAAACAGATCCG 58.343 50.000 0.00 0.00 0.00 4.18
103 104 4.060038 TCTATCGCTCCAAAACAGATCC 57.940 45.455 0.00 0.00 0.00 3.36
104 105 5.292765 TGATCTATCGCTCCAAAACAGATC 58.707 41.667 0.00 0.00 38.15 2.75
105 106 5.282055 TGATCTATCGCTCCAAAACAGAT 57.718 39.130 0.00 0.00 0.00 2.90
106 107 4.736126 TGATCTATCGCTCCAAAACAGA 57.264 40.909 0.00 0.00 0.00 3.41
107 108 4.260538 GCTTGATCTATCGCTCCAAAACAG 60.261 45.833 0.00 0.00 0.00 3.16
121 122 2.857186 TTGTGTGCCAGCTTGATCTA 57.143 45.000 0.00 0.00 0.00 1.98
122 123 2.211250 ATTGTGTGCCAGCTTGATCT 57.789 45.000 0.00 0.00 0.00 2.75
123 124 2.416431 GGAATTGTGTGCCAGCTTGATC 60.416 50.000 0.00 0.00 0.00 2.92
127 128 0.823356 ACGGAATTGTGTGCCAGCTT 60.823 50.000 0.00 0.00 0.00 3.74
130 131 5.065859 TCAATATTACGGAATTGTGTGCCAG 59.934 40.000 0.00 0.00 35.16 4.85
154 155 1.473965 CCTTGACATAGCTCATGCCGT 60.474 52.381 0.00 0.00 38.29 5.68
157 158 4.272018 CACTAACCTTGACATAGCTCATGC 59.728 45.833 0.00 0.00 38.29 4.06
160 161 3.369471 GGCACTAACCTTGACATAGCTCA 60.369 47.826 0.00 0.00 0.00 4.26
181 182 5.830000 ATGTCAATGAGTGATCATGTTGG 57.170 39.130 0.00 0.00 38.90 3.77
184 185 5.392703 GCACAATGTCAATGAGTGATCATGT 60.393 40.000 0.00 0.00 38.90 3.21
193 194 3.005050 ACACCTTGCACAATGTCAATGAG 59.995 43.478 0.00 0.00 0.00 2.90
200 201 2.099592 CACTTGACACCTTGCACAATGT 59.900 45.455 0.00 0.00 0.00 2.71
212 213 3.002246 TCAATCTTTGACGCACTTGACAC 59.998 43.478 0.00 0.00 34.08 3.67
241 242 2.983592 CCTCAAACACCGCCCCAC 60.984 66.667 0.00 0.00 0.00 4.61
242 243 4.966787 GCCTCAAACACCGCCCCA 62.967 66.667 0.00 0.00 0.00 4.96
262 263 0.875728 CGAACGGCCAACATAAACCA 59.124 50.000 2.24 0.00 0.00 3.67
272 273 2.665089 ATGGGTGATCGAACGGCCA 61.665 57.895 2.24 0.00 0.00 5.36
277 278 1.369625 GTGGACATGGGTGATCGAAC 58.630 55.000 0.00 0.00 0.00 3.95
286 287 1.220749 CGGTGTAGGTGGACATGGG 59.779 63.158 0.00 0.00 0.00 4.00
304 305 2.508663 GACCTACACGGGCGCTTC 60.509 66.667 7.64 0.00 36.97 3.86
305 306 4.078516 GGACCTACACGGGCGCTT 62.079 66.667 7.64 0.00 44.30 4.68
318 319 1.815840 GCAGAAGCTAAGGCGGACC 60.816 63.158 0.00 0.00 44.37 4.46
349 350 0.321346 AGTCGATGACACATGCCACA 59.679 50.000 0.00 0.00 34.60 4.17
418 419 7.767250 TGTGTGGTATATTTGGAATGTTTCA 57.233 32.000 0.00 0.00 0.00 2.69
428 429 9.906660 ACTTGTAAACATTGTGTGGTATATTTG 57.093 29.630 0.00 0.00 0.00 2.32
448 449 7.777095 AGTGTGGCAATTTTAGAAAACTTGTA 58.223 30.769 0.00 0.00 0.00 2.41
475 476 9.126151 TGACTAACACAATTCAGAAAATTACCA 57.874 29.630 0.00 0.00 0.00 3.25
487 489 5.280678 GTCGCGAAAATGACTAACACAATTC 59.719 40.000 12.06 0.00 32.37 2.17
494 496 2.735134 ACCTGTCGCGAAAATGACTAAC 59.265 45.455 12.06 0.00 36.10 2.34
505 507 3.186909 CATCTCAAATTACCTGTCGCGA 58.813 45.455 3.71 3.71 0.00 5.87
508 510 4.122776 CCTCCATCTCAAATTACCTGTCG 58.877 47.826 0.00 0.00 0.00 4.35
513 515 4.779993 ACTCCCTCCATCTCAAATTACC 57.220 45.455 0.00 0.00 0.00 2.85
522 524 3.896272 GGAAACGTATACTCCCTCCATCT 59.104 47.826 0.56 0.00 0.00 2.90
525 527 3.393426 AGGAAACGTATACTCCCTCCA 57.607 47.619 6.12 0.00 0.00 3.86
531 533 9.916397 CATTTGATTTGTAGGAAACGTATACTC 57.084 33.333 0.56 0.00 0.00 2.59
532 534 8.395633 GCATTTGATTTGTAGGAAACGTATACT 58.604 33.333 0.56 0.00 0.00 2.12
538 540 9.897744 ATATATGCATTTGATTTGTAGGAAACG 57.102 29.630 3.54 0.00 0.00 3.60
576 578 8.533569 AAAAACCTAATGAATATGACCCGATT 57.466 30.769 0.00 0.00 0.00 3.34
577 579 7.998964 AGAAAAACCTAATGAATATGACCCGAT 59.001 33.333 0.00 0.00 0.00 4.18
579 581 7.282224 TGAGAAAAACCTAATGAATATGACCCG 59.718 37.037 0.00 0.00 0.00 5.28
606 1017 2.028112 GCCTTGGTTTGGAGGATTTTCC 60.028 50.000 0.00 0.00 34.91 3.13
623 1034 7.480760 TTTAATTGCATTTCTCTAAGGCCTT 57.519 32.000 24.18 24.18 42.69 4.35
683 4089 1.115467 ACACACATTTTCCCCGCAAA 58.885 45.000 0.00 0.00 0.00 3.68
706 4112 1.750399 ACTTGTCCGGCATGATGGC 60.750 57.895 9.17 9.17 39.85 4.40
838 4250 1.817572 TAGCCTAGTGGGTGGGTCCA 61.818 60.000 0.00 0.00 44.81 4.02
934 4347 1.677552 GTCTTTGGCGGAGGGAAGA 59.322 57.895 0.00 0.00 0.00 2.87
978 4398 2.691771 GCTCTCGTCTGTGCCTCGA 61.692 63.158 0.00 0.00 0.00 4.04
1278 4709 1.202330 CCAGGATCTTCTGCCAGTCT 58.798 55.000 0.00 0.00 33.64 3.24
1350 4781 1.862147 CTTGCCGTAGTCGTCGTCG 60.862 63.158 0.00 0.00 38.55 5.12
1542 4973 2.107750 ATGCATGCTCCGTCTCCG 59.892 61.111 20.33 0.00 0.00 4.63
1543 4974 1.890979 CCATGCATGCTCCGTCTCC 60.891 63.158 21.69 0.00 0.00 3.71
1544 4975 2.541120 GCCATGCATGCTCCGTCTC 61.541 63.158 21.69 0.00 0.00 3.36
1545 4976 2.515523 GCCATGCATGCTCCGTCT 60.516 61.111 21.69 0.00 0.00 4.18
1546 4977 2.825387 TGCCATGCATGCTCCGTC 60.825 61.111 21.69 5.01 31.71 4.79
1586 5017 2.897350 GCGCATACTGGACCAGCC 60.897 66.667 21.95 6.69 34.37 4.85
1594 5025 1.340658 CTATACTGCGGCGCATACTG 58.659 55.000 36.35 25.28 38.13 2.74
1636 5071 3.404564 CCGAAACGAGCGAAACAATTAG 58.595 45.455 0.00 0.00 0.00 1.73
1637 5072 2.158058 CCCGAAACGAGCGAAACAATTA 59.842 45.455 0.00 0.00 0.00 1.40
1746 5189 1.129809 GTCACGCCATGAACGAACG 59.870 57.895 13.95 0.00 39.72 3.95
1747 5190 0.584396 TTGTCACGCCATGAACGAAC 59.416 50.000 13.95 11.37 39.72 3.95
1748 5191 1.300481 TTTGTCACGCCATGAACGAA 58.700 45.000 13.95 0.73 39.72 3.85
1749 5192 1.518325 ATTTGTCACGCCATGAACGA 58.482 45.000 13.95 0.00 39.72 3.85
1750 5193 2.330231 AATTTGTCACGCCATGAACG 57.670 45.000 0.00 0.00 39.72 3.95
1751 5194 3.637432 TGAAATTTGTCACGCCATGAAC 58.363 40.909 0.00 0.00 39.72 3.18
1752 5195 3.305267 CCTGAAATTTGTCACGCCATGAA 60.305 43.478 0.00 0.00 39.72 2.57
1753 5196 2.228582 CCTGAAATTTGTCACGCCATGA 59.771 45.455 0.00 0.00 33.79 3.07
1790 5233 0.912486 CCAACCAACCTAGCTAGCCT 59.088 55.000 15.74 0.97 0.00 4.58
1791 5234 0.618981 ACCAACCAACCTAGCTAGCC 59.381 55.000 15.74 0.00 0.00 3.93
1792 5235 1.278127 TGACCAACCAACCTAGCTAGC 59.722 52.381 15.74 6.62 0.00 3.42
1793 5236 2.093447 CCTGACCAACCAACCTAGCTAG 60.093 54.545 14.20 14.20 0.00 3.42
1794 5237 1.906574 CCTGACCAACCAACCTAGCTA 59.093 52.381 0.00 0.00 0.00 3.32
1795 5238 0.693049 CCTGACCAACCAACCTAGCT 59.307 55.000 0.00 0.00 0.00 3.32
1853 5296 3.733443 ACCCACTGCAAAAAGCTTAAG 57.267 42.857 0.00 0.00 45.94 1.85
1873 5321 1.066303 CGCCCAAAAACAGCAGTACAA 59.934 47.619 0.00 0.00 0.00 2.41
1919 5367 0.804989 GATCGGGTTGGCAAAGACAG 59.195 55.000 0.00 0.00 0.00 3.51
1922 5370 0.690192 TGAGATCGGGTTGGCAAAGA 59.310 50.000 0.00 2.38 0.00 2.52
1931 5383 3.161067 CTCCTGTATCATGAGATCGGGT 58.839 50.000 16.67 0.00 35.67 5.28
1986 5438 5.092554 TGTCACTTCAGAAAGGTGTAACA 57.907 39.130 3.20 0.00 39.98 2.41
2002 5454 8.682936 AGAAAAATGTGAGTAATCTTGTCACT 57.317 30.769 3.59 0.00 41.06 3.41
2044 5736 0.396435 CACTGTTCAGTAGGGCCACA 59.604 55.000 6.18 0.00 0.00 4.17
2106 5798 8.196378 TCTAGTATAGATGAGAGCTAGACACA 57.804 38.462 0.00 0.00 44.15 3.72
2129 5821 9.617523 GTGTAGGAGTTAGAGTAGACTTTATCT 57.382 37.037 0.00 0.00 41.95 1.98
2130 5822 8.839343 GGTGTAGGAGTTAGAGTAGACTTTATC 58.161 40.741 0.00 0.00 0.00 1.75
2131 5823 7.498570 CGGTGTAGGAGTTAGAGTAGACTTTAT 59.501 40.741 0.00 0.00 0.00 1.40
2132 5824 6.820656 CGGTGTAGGAGTTAGAGTAGACTTTA 59.179 42.308 0.00 0.00 0.00 1.85
2133 5825 5.647225 CGGTGTAGGAGTTAGAGTAGACTTT 59.353 44.000 0.00 0.00 0.00 2.66
2134 5826 5.184711 CGGTGTAGGAGTTAGAGTAGACTT 58.815 45.833 0.00 0.00 0.00 3.01
2135 5827 4.768583 CGGTGTAGGAGTTAGAGTAGACT 58.231 47.826 0.00 0.00 0.00 3.24
2136 5828 3.312146 GCGGTGTAGGAGTTAGAGTAGAC 59.688 52.174 0.00 0.00 0.00 2.59
2137 5829 3.539604 GCGGTGTAGGAGTTAGAGTAGA 58.460 50.000 0.00 0.00 0.00 2.59
2138 5830 2.617774 GGCGGTGTAGGAGTTAGAGTAG 59.382 54.545 0.00 0.00 0.00 2.57
2139 5831 2.648059 GGCGGTGTAGGAGTTAGAGTA 58.352 52.381 0.00 0.00 0.00 2.59
2140 5832 1.472188 GGCGGTGTAGGAGTTAGAGT 58.528 55.000 0.00 0.00 0.00 3.24
2141 5833 0.381089 CGGCGGTGTAGGAGTTAGAG 59.619 60.000 0.00 0.00 0.00 2.43
2158 5850 2.052157 GAATCTCCGCGTAGAATTCGG 58.948 52.381 5.20 0.00 44.16 4.30
2162 5854 3.827302 ACCTATGAATCTCCGCGTAGAAT 59.173 43.478 5.20 0.00 0.00 2.40
2183 6072 5.278414 CCAAGCAAAATCAATGGGGAAAAAC 60.278 40.000 0.00 0.00 0.00 2.43
2189 6078 3.421919 AACCAAGCAAAATCAATGGGG 57.578 42.857 0.00 0.00 35.44 4.96
2190 6079 6.171921 TGATTAACCAAGCAAAATCAATGGG 58.828 36.000 0.00 0.00 35.88 4.00
2191 6080 6.183360 GCTGATTAACCAAGCAAAATCAATGG 60.183 38.462 0.00 0.00 37.76 3.16
2193 6082 6.465948 TGCTGATTAACCAAGCAAAATCAAT 58.534 32.000 6.18 0.00 37.76 2.57
2196 6085 5.346822 CACTGCTGATTAACCAAGCAAAATC 59.653 40.000 9.18 0.00 34.96 2.17
2203 6092 4.832248 TCCTACACTGCTGATTAACCAAG 58.168 43.478 0.00 0.00 0.00 3.61
2209 6098 6.833933 TCATCTAACTCCTACACTGCTGATTA 59.166 38.462 0.00 0.00 0.00 1.75
2230 6119 8.924691 GCTAATTCTCATCTACAATGTCTCATC 58.075 37.037 0.00 0.00 0.00 2.92
2232 6121 7.785033 TGCTAATTCTCATCTACAATGTCTCA 58.215 34.615 0.00 0.00 0.00 3.27
2255 6144 7.484641 TGTGTATTTTTCAGATAGCGAATTTGC 59.515 33.333 9.87 9.87 0.00 3.68
2277 6167 8.695456 GGAAACTTCCCATAATTCAATATGTGT 58.305 33.333 0.00 0.00 41.62 3.72
2356 6246 3.888323 GGACCCTACTAGCTAGTGTTACC 59.112 52.174 32.21 23.22 37.10 2.85
2404 6363 1.544724 TTAAAATCCAGCTGCCGCTT 58.455 45.000 8.66 1.39 46.47 4.68
2415 6374 4.814234 GCCCCGATTGGAAATTTAAAATCC 59.186 41.667 13.76 13.76 37.49 3.01
2429 6388 1.750399 CAACCTCCTGCCCCGATTG 60.750 63.158 0.00 0.00 0.00 2.67
2495 6458 8.051901 TGTGATAGTATAGTAACGGATGGATG 57.948 38.462 0.00 0.00 0.00 3.51
2508 6471 7.228507 CCTAGCTAGATGCCTGTGATAGTATAG 59.771 44.444 22.70 0.00 44.23 1.31
2513 6476 3.446873 CCCTAGCTAGATGCCTGTGATAG 59.553 52.174 22.70 0.23 44.23 2.08


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

AutoCloner maintained by Alex Coulton.