Multiple sequence alignment - TraesCS3A01G225900

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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 TraesCS3A01G225900 chr3A 100.000 2761 0 0 1 2761 423547599 423544839 0.000000e+00 5099
1 TraesCS3A01G225900 chr3A 85.859 1280 170 10 875 2146 614566207 614567483 0.000000e+00 1351
2 TraesCS3A01G225900 chr3A 77.906 1127 228 18 1019 2134 711261837 711262953 0.000000e+00 682
3 TraesCS3A01G225900 chr2B 86.571 1750 219 14 1019 2759 141164301 141162559 0.000000e+00 1916
4 TraesCS3A01G225900 chr2B 77.364 698 143 9 2074 2760 547054085 547053392 1.540000e-107 399
5 TraesCS3A01G225900 chr2D 87.395 1309 129 14 1019 2316 529019617 529020900 0.000000e+00 1471
6 TraesCS3A01G225900 chr2D 87.402 635 68 6 2129 2754 529021109 529021740 0.000000e+00 719
7 TraesCS3A01G225900 chr2D 79.696 724 140 6 2040 2758 586952253 586952974 1.470000e-142 516
8 TraesCS3A01G225900 chr2D 77.641 729 146 13 2041 2760 71928566 71927846 7.070000e-116 427
9 TraesCS3A01G225900 chr2D 86.286 175 22 2 842 1016 529019413 529019585 3.630000e-44 189
10 TraesCS3A01G225900 chr6B 87.547 1068 128 5 1017 2081 567615120 567616185 0.000000e+00 1230
11 TraesCS3A01G225900 chr6B 79.370 635 122 6 2078 2705 616930684 616930052 3.260000e-119 438
12 TraesCS3A01G225900 chr6B 74.874 593 134 8 1902 2481 649733390 649733980 3.530000e-64 255
13 TraesCS3A01G225900 chr6B 84.916 179 25 2 838 1016 567614913 567615089 2.180000e-41 180
14 TraesCS3A01G225900 chr5D 88.396 879 91 9 1015 1889 317450287 317449416 0.000000e+00 1048
15 TraesCS3A01G225900 chr5D 84.416 154 21 3 865 1016 317450470 317450318 6.160000e-32 148
16 TraesCS3A01G225900 chr3B 90.988 577 40 7 259 831 416264171 416264739 0.000000e+00 767
17 TraesCS3A01G225900 chr3B 77.864 646 131 8 2041 2679 125581384 125582024 9.270000e-105 390
18 TraesCS3A01G225900 chr3B 92.578 256 15 2 3 257 416263253 416263505 5.620000e-97 364
19 TraesCS3A01G225900 chr4A 81.374 655 120 2 1019 1673 162439020 162438368 1.460000e-147 532
20 TraesCS3A01G225900 chr1A 81.193 654 121 2 1020 1673 573906329 573906980 2.440000e-145 525
21 TraesCS3A01G225900 chr1A 77.905 611 120 12 2078 2679 321857500 321858104 1.560000e-97 366
22 TraesCS3A01G225900 chr7B 79.417 617 120 5 2070 2681 64625020 64625634 1.960000e-116 429
23 TraesCS3A01G225900 chr3D 84.494 445 35 11 259 699 305567372 305566958 2.560000e-110 409
24 TraesCS3A01G225900 chr3D 94.444 144 4 2 695 835 305493512 305493370 4.630000e-53 219
25 TraesCS3A01G225900 chr3D 92.208 154 10 2 17 169 305567830 305567678 1.670000e-52 217


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 TraesCS3A01G225900 chr3A 423544839 423547599 2760 True 5099.0 5099 100.000000 1 2761 1 chr3A.!!$R1 2760
1 TraesCS3A01G225900 chr3A 614566207 614567483 1276 False 1351.0 1351 85.859000 875 2146 1 chr3A.!!$F1 1271
2 TraesCS3A01G225900 chr3A 711261837 711262953 1116 False 682.0 682 77.906000 1019 2134 1 chr3A.!!$F2 1115
3 TraesCS3A01G225900 chr2B 141162559 141164301 1742 True 1916.0 1916 86.571000 1019 2759 1 chr2B.!!$R1 1740
4 TraesCS3A01G225900 chr2B 547053392 547054085 693 True 399.0 399 77.364000 2074 2760 1 chr2B.!!$R2 686
5 TraesCS3A01G225900 chr2D 529019413 529021740 2327 False 793.0 1471 87.027667 842 2754 3 chr2D.!!$F2 1912
6 TraesCS3A01G225900 chr2D 586952253 586952974 721 False 516.0 516 79.696000 2040 2758 1 chr2D.!!$F1 718
7 TraesCS3A01G225900 chr2D 71927846 71928566 720 True 427.0 427 77.641000 2041 2760 1 chr2D.!!$R1 719
8 TraesCS3A01G225900 chr6B 567614913 567616185 1272 False 705.0 1230 86.231500 838 2081 2 chr6B.!!$F2 1243
9 TraesCS3A01G225900 chr6B 616930052 616930684 632 True 438.0 438 79.370000 2078 2705 1 chr6B.!!$R1 627
10 TraesCS3A01G225900 chr6B 649733390 649733980 590 False 255.0 255 74.874000 1902 2481 1 chr6B.!!$F1 579
11 TraesCS3A01G225900 chr5D 317449416 317450470 1054 True 598.0 1048 86.406000 865 1889 2 chr5D.!!$R1 1024
12 TraesCS3A01G225900 chr3B 416263253 416264739 1486 False 565.5 767 91.783000 3 831 2 chr3B.!!$F2 828
13 TraesCS3A01G225900 chr3B 125581384 125582024 640 False 390.0 390 77.864000 2041 2679 1 chr3B.!!$F1 638
14 TraesCS3A01G225900 chr4A 162438368 162439020 652 True 532.0 532 81.374000 1019 1673 1 chr4A.!!$R1 654
15 TraesCS3A01G225900 chr1A 573906329 573906980 651 False 525.0 525 81.193000 1020 1673 1 chr1A.!!$F2 653
16 TraesCS3A01G225900 chr1A 321857500 321858104 604 False 366.0 366 77.905000 2078 2679 1 chr1A.!!$F1 601
17 TraesCS3A01G225900 chr7B 64625020 64625634 614 False 429.0 429 79.417000 2070 2681 1 chr7B.!!$F1 611
18 TraesCS3A01G225900 chr3D 305566958 305567830 872 True 313.0 409 88.351000 17 699 2 chr3D.!!$R2 682

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
283 953 0.183492 TGAGGTGGCAGCTTCAACTT 59.817 50.0 21.55 0.0 31.48 2.66 F
1129 1837 0.040067 CAAGGAAAGCGTCTGTTGGC 60.040 55.0 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 2045 0.108992 AAGCATCGCCATGTTTGCAG 60.109 50.0 0.0 0.0 37.56 4.41 R
2007 2750 0.318784 GGCGAGTTGTTCTCACGAGT 60.319 55.0 0.0 0.0 42.88 4.18 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
93 95 4.943705 CCAAACATACTCTAAGGCACATGT 59.056 41.667 0.00 0.00 0.00 3.21
192 194 6.153756 TCTACGAATTTCATGTGTTTCGAGA 58.846 36.000 23.25 18.83 42.55 4.04
259 261 1.001020 TGGTTGGCCCACTGCATAG 60.001 57.895 6.95 0.00 43.89 2.23
274 944 2.366590 TGCATAGTATCTGAGGTGGCAG 59.633 50.000 0.00 0.00 37.24 4.85
283 953 0.183492 TGAGGTGGCAGCTTCAACTT 59.817 50.000 21.55 0.00 31.48 2.66
319 990 1.293924 CGAGGCATGAATCAGACACC 58.706 55.000 0.00 0.00 0.00 4.16
321 992 2.286872 GAGGCATGAATCAGACACCTG 58.713 52.381 0.00 0.00 41.74 4.00
389 1060 7.989416 TTGATGAAATCCCGTTTTTAGTAGT 57.011 32.000 0.00 0.00 44.73 2.73
407 1078 8.574251 TTAGTAGTTCACATATGCCATGTTTT 57.426 30.769 1.58 0.00 0.00 2.43
452 1123 7.093289 CCTTCATCCGAATATAGGGTCTAATGT 60.093 40.741 0.00 0.00 0.00 2.71
456 1127 8.528643 CATCCGAATATAGGGTCTAATGTGTAA 58.471 37.037 0.00 0.00 0.00 2.41
597 1271 7.372060 ACCTAATATATCTGGGTAGAGGGAA 57.628 40.000 8.31 0.00 36.14 3.97
638 1312 4.279169 TCTGTAGCAGTTGTACTTTACGGT 59.721 41.667 0.00 0.00 30.24 4.83
691 1365 7.491048 CACTATTTAAAACTTTTGTGCACAGGT 59.509 33.333 20.59 16.53 0.00 4.00
699 1373 3.605664 GTGCACAGGTTGGTGGCC 61.606 66.667 13.17 0.00 39.19 5.36
721 1395 4.825085 CCACCTAGGAGTGTTTGCTAAAAA 59.175 41.667 17.98 0.00 41.22 1.94
823 1497 9.534565 GCTACATCTAAGATCTTGTAATGTCAA 57.465 33.333 23.93 13.80 0.00 3.18
842 1516 9.715121 AATGTCAATTCATTTGAATAGTTGCTT 57.285 25.926 6.24 0.00 45.71 3.91
843 1517 9.715121 ATGTCAATTCATTTGAATAGTTGCTTT 57.285 25.926 6.24 0.00 45.71 3.51
844 1518 9.545105 TGTCAATTCATTTGAATAGTTGCTTTT 57.455 25.926 6.24 0.00 45.71 2.27
847 1521 9.815936 CAATTCATTTGAATAGTTGCTTTTTCC 57.184 29.630 6.24 0.00 43.41 3.13
848 1522 9.783081 AATTCATTTGAATAGTTGCTTTTTCCT 57.217 25.926 6.24 0.00 43.41 3.36
857 1531 3.329225 AGTTGCTTTTTCCTCCTAGCTCT 59.671 43.478 0.00 0.00 34.77 4.09
949 1624 1.616994 GCATAAGTGTTCCCTGGGCTT 60.617 52.381 8.22 8.19 0.00 4.35
953 1628 1.062488 AGTGTTCCCTGGGCTTCTGT 61.062 55.000 8.22 0.00 0.00 3.41
964 1639 1.081108 GCTTCTGTGTCTCGCTCGT 60.081 57.895 0.00 0.00 0.00 4.18
994 1669 0.976641 TCCTCGGATGCAAACTCAGT 59.023 50.000 0.00 0.00 0.00 3.41
1001 1679 3.935203 CGGATGCAAACTCAGTGACTAAT 59.065 43.478 0.00 0.00 0.00 1.73
1003 1681 4.937620 GGATGCAAACTCAGTGACTAATGA 59.062 41.667 0.00 0.00 0.00 2.57
1123 1831 1.134965 CGGAGATCAAGGAAAGCGTCT 60.135 52.381 0.00 0.00 0.00 4.18
1129 1837 0.040067 CAAGGAAAGCGTCTGTTGGC 60.040 55.000 0.00 0.00 0.00 4.52
1164 1872 4.966168 AGGGTTCATACCAACAAAACCTTT 59.034 37.500 0.00 0.00 46.96 3.11
1238 1946 0.458669 GTTAGATTCTGGCCGGTCGA 59.541 55.000 12.43 0.00 0.00 4.20
1294 2025 0.830648 GGACTGGGAACGGATCATGA 59.169 55.000 0.00 0.00 41.09 3.07
1295 2026 1.209504 GGACTGGGAACGGATCATGAA 59.790 52.381 0.00 0.00 41.09 2.57
1296 2027 2.355716 GGACTGGGAACGGATCATGAAA 60.356 50.000 0.00 0.00 41.09 2.69
1297 2028 2.678336 GACTGGGAACGGATCATGAAAC 59.322 50.000 0.00 0.00 41.09 2.78
1298 2029 2.039746 ACTGGGAACGGATCATGAAACA 59.960 45.455 0.00 0.00 41.09 2.83
1299 2030 3.081061 CTGGGAACGGATCATGAAACAA 58.919 45.455 0.00 0.00 39.98 2.83
1300 2031 3.081061 TGGGAACGGATCATGAAACAAG 58.919 45.455 0.00 0.00 0.00 3.16
1301 2032 2.423538 GGGAACGGATCATGAAACAAGG 59.576 50.000 0.00 0.00 0.00 3.61
1302 2033 2.159379 GGAACGGATCATGAAACAAGGC 60.159 50.000 0.00 0.00 0.00 4.35
1303 2034 2.198827 ACGGATCATGAAACAAGGCA 57.801 45.000 0.00 0.00 0.00 4.75
1304 2035 1.812571 ACGGATCATGAAACAAGGCAC 59.187 47.619 0.00 0.00 0.00 5.01
1305 2036 1.811965 CGGATCATGAAACAAGGCACA 59.188 47.619 0.00 0.00 0.00 4.57
1306 2037 2.424601 CGGATCATGAAACAAGGCACAT 59.575 45.455 0.00 0.00 0.00 3.21
1307 2038 3.732774 CGGATCATGAAACAAGGCACATG 60.733 47.826 0.00 0.00 40.65 3.21
1308 2039 3.429822 GGATCATGAAACAAGGCACATGG 60.430 47.826 0.00 0.00 40.00 3.66
1309 2040 2.596346 TCATGAAACAAGGCACATGGT 58.404 42.857 0.00 0.00 40.00 3.55
1310 2041 2.964464 TCATGAAACAAGGCACATGGTT 59.036 40.909 0.00 0.00 40.74 3.67
1311 2042 4.148079 TCATGAAACAAGGCACATGGTTA 58.852 39.130 0.00 0.00 36.95 2.85
1312 2043 4.771577 TCATGAAACAAGGCACATGGTTAT 59.228 37.500 0.00 0.00 36.95 1.89
1313 2044 5.245751 TCATGAAACAAGGCACATGGTTATT 59.754 36.000 0.00 0.00 36.95 1.40
1314 2045 5.132897 TGAAACAAGGCACATGGTTATTC 57.867 39.130 0.00 0.00 36.95 1.75
1315 2046 4.832266 TGAAACAAGGCACATGGTTATTCT 59.168 37.500 0.00 0.00 36.95 2.40
1316 2047 4.789012 AACAAGGCACATGGTTATTCTG 57.211 40.909 0.00 0.00 0.00 3.02
1317 2048 2.493278 ACAAGGCACATGGTTATTCTGC 59.507 45.455 0.00 0.00 0.00 4.26
1318 2049 2.492881 CAAGGCACATGGTTATTCTGCA 59.507 45.455 0.00 0.00 0.00 4.41
1328 2059 2.163412 GGTTATTCTGCAAACATGGCGA 59.837 45.455 0.00 0.00 0.00 5.54
1333 2064 0.108992 CTGCAAACATGGCGATGCTT 60.109 50.000 8.81 0.00 39.49 3.91
1364 2095 0.673985 CGATGGATTCAGTCGGGCTA 59.326 55.000 2.97 0.00 0.00 3.93
1416 2147 3.054139 TGGCTTCATATTCACAAGCTCCT 60.054 43.478 3.12 0.00 41.94 3.69
1428 2159 2.293586 ACAAGCTCCTGGACCCCTATTA 60.294 50.000 0.00 0.00 0.00 0.98
1442 2173 6.353255 GGACCCCTATTACAAGGAACACATTA 60.353 42.308 0.00 0.00 39.15 1.90
1471 2202 1.384191 GTTGAAGGGTGCAGGGGAT 59.616 57.895 0.00 0.00 0.00 3.85
1489 2220 3.840666 GGGATATCTTGGAGATGTGGCTA 59.159 47.826 2.05 0.00 35.37 3.93
1546 2277 6.084326 AGGGTGAATCACAACATTAAACAC 57.916 37.500 15.86 0.00 38.06 3.32
1588 2319 2.753009 ATTGTGCGAGCAAGGGAGCA 62.753 55.000 0.00 0.00 36.85 4.26
1641 2372 2.223386 GCTCGTTTTTGCAAGGTGTGTA 60.223 45.455 0.00 0.00 0.00 2.90
1650 2381 2.304470 TGCAAGGTGTGTAGGCTGATAA 59.696 45.455 0.00 0.00 0.00 1.75
1851 2586 0.402887 ACAAACCCGGAAACCCTAGG 59.597 55.000 0.73 0.06 0.00 3.02
1855 2590 2.598787 CCCGGAAACCCTAGGCACA 61.599 63.158 0.73 0.00 0.00 4.57
1856 2591 1.377229 CCGGAAACCCTAGGCACAA 59.623 57.895 2.05 0.00 0.00 3.33
1946 2683 2.597510 GCTGTTGAGGCGGGGTTT 60.598 61.111 0.00 0.00 0.00 3.27
1969 2712 4.172232 TGCCCCGGGAGCTCCTAT 62.172 66.667 31.36 0.00 35.95 2.57
1989 2732 3.540211 GCTTTGCTAGCTCTCACCA 57.460 52.632 17.23 0.00 46.77 4.17
2007 2750 1.191535 CAACGGGAGTGGAGTGGATA 58.808 55.000 0.00 0.00 46.69 2.59
2048 2791 1.069022 GCGAGCAGTGATTCAAGCAAA 60.069 47.619 13.01 0.00 0.00 3.68
2096 2840 5.928264 CAGTGACAATAATGAGATATCGGCA 59.072 40.000 0.00 0.39 0.00 5.69
2135 2879 1.660052 CGCCGGACGCAATGAATATTG 60.660 52.381 5.05 0.00 45.17 1.90
2139 2883 3.312421 CCGGACGCAATGAATATTGTCTT 59.688 43.478 0.00 0.00 44.41 3.01
2146 2892 6.597672 ACGCAATGAATATTGTCTTGGAACTA 59.402 34.615 0.00 0.00 44.41 2.24
2176 2941 2.649034 GCCGGACAGTTCGTGAGA 59.351 61.111 5.05 0.00 39.20 3.27
2201 2966 0.600057 GCCCTCTCAAAAGCCAACAG 59.400 55.000 0.00 0.00 0.00 3.16
2253 3018 2.158696 GCAGGATTCAGCTAAGGTGGAT 60.159 50.000 0.00 0.00 31.30 3.41
2266 3031 6.012771 AGCTAAGGTGGATAAGTTAAAGTGGT 60.013 38.462 0.00 0.00 0.00 4.16
2394 3562 2.607187 AGGTTCATCGATGTTCGTGTC 58.393 47.619 24.09 8.85 41.35 3.67
2421 3589 3.609853 TGGTGGTTCTGATGTTCTATGC 58.390 45.455 0.00 0.00 0.00 3.14
2491 3659 1.383109 TGGGATCATCTCTGCCGGT 60.383 57.895 1.90 0.00 0.00 5.28
2494 3662 0.179000 GGATCATCTCTGCCGGTTGT 59.821 55.000 1.90 0.00 0.00 3.32
2496 3664 0.745845 ATCATCTCTGCCGGTTGTGC 60.746 55.000 1.90 0.00 0.00 4.57
2506 3674 0.738389 CCGGTTGTGCTCAGTTTTGT 59.262 50.000 0.00 0.00 0.00 2.83
2511 3679 3.242870 GGTTGTGCTCAGTTTTGTGAGAG 60.243 47.826 5.05 0.00 46.02 3.20
2559 3727 0.034380 AAGCACTCTGGCAGCATGAT 60.034 50.000 18.49 11.39 39.69 2.45
2697 3865 1.614903 CAGGCCGGGTATCGTAATGTA 59.385 52.381 2.18 0.00 37.11 2.29
2722 3890 4.973168 AGTTCACCTTGATCAAGCTGTTA 58.027 39.130 27.01 14.54 37.11 2.41
2727 3895 4.701651 CACCTTGATCAAGCTGTTATGGAA 59.298 41.667 27.01 0.00 37.11 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.746721 GTGTGGCAAAATTTCTTAGTTTCGT 59.253 36.000 0.00 0.00 0.00 3.85
1 2 5.174943 GGTGTGGCAAAATTTCTTAGTTTCG 59.825 40.000 0.00 0.00 0.00 3.46
19 20 2.306341 TGCAAACAATTGTGGTGTGG 57.694 45.000 12.82 0.00 38.85 4.17
93 95 3.814625 TGTGTCTCCAAAGCAATGTGTA 58.185 40.909 0.00 0.00 0.00 2.90
164 166 6.848800 CGAAACACATGAAATTCGTAGAAACA 59.151 34.615 17.20 0.00 45.90 2.83
172 174 5.058492 GCTTTCTCGAAACACATGAAATTCG 59.942 40.000 18.49 18.49 44.34 3.34
179 181 3.904136 AAGGCTTTCTCGAAACACATG 57.096 42.857 0.00 0.00 0.00 3.21
180 182 5.473504 ACATTAAGGCTTTCTCGAAACACAT 59.526 36.000 4.45 0.00 0.00 3.21
181 183 4.819630 ACATTAAGGCTTTCTCGAAACACA 59.180 37.500 4.45 0.00 0.00 3.72
257 259 2.461300 AGCTGCCACCTCAGATACTA 57.539 50.000 0.00 0.00 36.19 1.82
259 261 1.208052 TGAAGCTGCCACCTCAGATAC 59.792 52.381 0.00 0.00 36.19 2.24
274 944 5.614887 CGCTAGTTGAACCTTAAGTTGAAGC 60.615 44.000 0.97 0.00 39.40 3.86
283 953 0.889994 TCGCCGCTAGTTGAACCTTA 59.110 50.000 0.00 0.00 0.00 2.69
366 1037 7.662258 TGAACTACTAAAAACGGGATTTCATCA 59.338 33.333 0.00 0.00 0.00 3.07
417 1088 8.634444 CCTATATTCGGATGAAGGGAGTATAAG 58.366 40.741 0.00 0.00 37.57 1.73
420 1091 5.900123 CCCTATATTCGGATGAAGGGAGTAT 59.100 44.000 16.82 0.00 37.83 2.12
567 1241 9.702253 CTCTACCCAGATATATTAGGTACATGT 57.298 37.037 2.69 2.69 31.89 3.21
699 1373 6.575162 ATTTTTAGCAAACACTCCTAGGTG 57.425 37.500 9.08 9.22 42.34 4.00
823 1497 9.428097 GAGGAAAAAGCAACTATTCAAATGAAT 57.572 29.630 12.82 12.82 45.77 2.57
831 1505 5.883115 AGCTAGGAGGAAAAAGCAACTATTC 59.117 40.000 0.00 0.00 37.44 1.75
832 1506 5.821097 AGCTAGGAGGAAAAAGCAACTATT 58.179 37.500 0.00 0.00 37.44 1.73
833 1507 5.190726 AGAGCTAGGAGGAAAAAGCAACTAT 59.809 40.000 0.00 0.00 37.44 2.12
834 1508 4.532521 AGAGCTAGGAGGAAAAAGCAACTA 59.467 41.667 0.00 0.00 37.44 2.24
835 1509 3.329225 AGAGCTAGGAGGAAAAAGCAACT 59.671 43.478 0.00 0.00 37.44 3.16
836 1510 3.680490 AGAGCTAGGAGGAAAAAGCAAC 58.320 45.455 0.00 0.00 37.44 4.17
837 1511 3.617531 CGAGAGCTAGGAGGAAAAAGCAA 60.618 47.826 0.00 0.00 37.44 3.91
838 1512 2.093973 CGAGAGCTAGGAGGAAAAAGCA 60.094 50.000 0.00 0.00 37.44 3.91
839 1513 2.545731 CGAGAGCTAGGAGGAAAAAGC 58.454 52.381 0.00 0.00 35.16 3.51
857 1531 1.664321 GAGAGAAACCCTAGCCGCGA 61.664 60.000 8.23 0.00 0.00 5.87
927 1601 0.748005 CCCAGGGAACACTTATGCGG 60.748 60.000 0.00 0.00 0.00 5.69
932 1606 1.351017 CAGAAGCCCAGGGAACACTTA 59.649 52.381 10.89 0.00 0.00 2.24
933 1607 0.111253 CAGAAGCCCAGGGAACACTT 59.889 55.000 10.89 2.06 0.00 3.16
934 1608 1.062488 ACAGAAGCCCAGGGAACACT 61.062 55.000 10.89 0.00 0.00 3.55
949 1624 0.169009 CATCACGAGCGAGACACAGA 59.831 55.000 0.00 0.00 0.00 3.41
953 1628 2.181777 GCCATCACGAGCGAGACA 59.818 61.111 0.00 0.00 0.00 3.41
964 1639 3.147595 CCGAGGAGGACGCCATCA 61.148 66.667 0.00 0.00 45.00 3.07
994 1669 1.001520 CACCACCACCGTCATTAGTCA 59.998 52.381 0.00 0.00 0.00 3.41
1027 1735 5.165961 TGGTCGAAGAAATTCTCCAGATT 57.834 39.130 0.00 0.00 39.69 2.40
1164 1872 3.369471 CCTTGTAGAAGGCCGATGAAGAA 60.369 47.826 5.60 0.00 42.60 2.52
1294 2025 4.561326 GCAGAATAACCATGTGCCTTGTTT 60.561 41.667 0.00 0.00 0.00 2.83
1295 2026 3.056607 GCAGAATAACCATGTGCCTTGTT 60.057 43.478 0.00 0.00 0.00 2.83
1296 2027 2.493278 GCAGAATAACCATGTGCCTTGT 59.507 45.455 0.00 0.00 0.00 3.16
1297 2028 2.492881 TGCAGAATAACCATGTGCCTTG 59.507 45.455 0.39 0.00 32.99 3.61
1298 2029 2.806434 TGCAGAATAACCATGTGCCTT 58.194 42.857 0.39 0.00 32.99 4.35
1299 2030 2.512692 TGCAGAATAACCATGTGCCT 57.487 45.000 0.39 0.00 32.99 4.75
1300 2031 3.253230 GTTTGCAGAATAACCATGTGCC 58.747 45.455 0.39 0.00 32.99 5.01
1301 2032 3.911868 TGTTTGCAGAATAACCATGTGC 58.088 40.909 0.00 0.00 34.62 4.57
1302 2033 4.865925 CCATGTTTGCAGAATAACCATGTG 59.134 41.667 4.70 0.00 0.00 3.21
1303 2034 4.621274 GCCATGTTTGCAGAATAACCATGT 60.621 41.667 4.70 0.00 0.00 3.21
1304 2035 3.866910 GCCATGTTTGCAGAATAACCATG 59.133 43.478 0.00 0.00 0.00 3.66
1305 2036 3.429272 CGCCATGTTTGCAGAATAACCAT 60.429 43.478 0.00 0.00 0.00 3.55
1306 2037 2.094803 CGCCATGTTTGCAGAATAACCA 60.095 45.455 0.00 0.00 0.00 3.67
1307 2038 2.163412 TCGCCATGTTTGCAGAATAACC 59.837 45.455 0.00 0.00 0.00 2.85
1308 2039 3.485947 TCGCCATGTTTGCAGAATAAC 57.514 42.857 0.00 0.00 0.00 1.89
1309 2040 3.734597 GCATCGCCATGTTTGCAGAATAA 60.735 43.478 0.00 0.00 35.22 1.40
1310 2041 2.223548 GCATCGCCATGTTTGCAGAATA 60.224 45.455 0.00 0.00 35.22 1.75
1311 2042 1.470285 GCATCGCCATGTTTGCAGAAT 60.470 47.619 0.00 0.00 35.22 2.40
1312 2043 0.109179 GCATCGCCATGTTTGCAGAA 60.109 50.000 0.00 0.00 35.22 3.02
1313 2044 0.961857 AGCATCGCCATGTTTGCAGA 60.962 50.000 8.49 0.00 37.56 4.26
1314 2045 0.108992 AAGCATCGCCATGTTTGCAG 60.109 50.000 0.00 0.00 37.56 4.41
1315 2046 0.109179 GAAGCATCGCCATGTTTGCA 60.109 50.000 0.00 0.00 33.86 4.08
1316 2047 0.171903 AGAAGCATCGCCATGTTTGC 59.828 50.000 0.00 0.00 33.86 3.68
1317 2048 3.624900 CATAGAAGCATCGCCATGTTTG 58.375 45.455 0.00 0.00 33.86 2.93
1318 2049 2.033801 GCATAGAAGCATCGCCATGTTT 59.966 45.455 0.00 0.00 36.24 2.83
1333 2064 5.011023 ACTGAATCCATCGTACATGCATAGA 59.989 40.000 0.00 0.00 0.00 1.98
1364 2095 5.775686 CATGTGATCAAACACCACATCTTT 58.224 37.500 0.00 0.00 46.23 2.52
1402 2133 1.559682 GGGTCCAGGAGCTTGTGAATA 59.440 52.381 18.34 0.00 0.00 1.75
1416 2147 3.264964 GTGTTCCTTGTAATAGGGGTCCA 59.735 47.826 0.00 0.00 35.90 4.02
1428 2159 4.631813 GCTTCTCGATAATGTGTTCCTTGT 59.368 41.667 0.00 0.00 0.00 3.16
1442 2173 1.625818 ACCCTTCAACAGCTTCTCGAT 59.374 47.619 0.00 0.00 0.00 3.59
1471 2202 4.442893 CCGTTTAGCCACATCTCCAAGATA 60.443 45.833 0.00 0.00 32.12 1.98
1489 2220 0.249741 CACCTCTCGTGTTCCCGTTT 60.250 55.000 0.00 0.00 37.73 3.60
1650 2381 3.181447 CCACACTCCTTATGATCATGGCT 60.181 47.826 18.72 0.00 0.00 4.75
1806 2541 0.543749 CTCCCTTGGAGCCGAAGAAT 59.456 55.000 0.00 0.00 43.29 2.40
1808 2543 3.713650 CTCCCTTGGAGCCGAAGA 58.286 61.111 0.00 0.00 43.29 2.87
1835 2570 1.848895 TGCCTAGGGTTTCCGGGTT 60.849 57.895 11.72 0.00 38.33 4.11
1851 2586 1.598130 AGAGGGCTTGTCGTTGTGC 60.598 57.895 0.00 0.00 0.00 4.57
1855 2590 0.603975 GCTTCAGAGGGCTTGTCGTT 60.604 55.000 0.00 0.00 0.00 3.85
1856 2591 1.004440 GCTTCAGAGGGCTTGTCGT 60.004 57.895 0.00 0.00 0.00 4.34
1946 2683 1.074775 AGCTCCCGGGGCACTATTA 60.075 57.895 28.68 5.47 0.00 0.98
1989 2732 1.192428 GTATCCACTCCACTCCCGTT 58.808 55.000 0.00 0.00 0.00 4.44
2007 2750 0.318784 GGCGAGTTGTTCTCACGAGT 60.319 55.000 0.00 0.00 42.88 4.18
2048 2791 3.308530 CTTCGAAATTTTCAGCCGCTTT 58.691 40.909 9.66 0.00 0.00 3.51
2135 2879 1.600638 CCCCCGGTAGTTCCAAGAC 59.399 63.158 0.00 0.00 35.57 3.01
2176 2941 1.625315 GGCTTTTGAGAGGGCCAAAAT 59.375 47.619 6.18 0.00 41.08 1.82
2201 2966 3.118223 ACATAGAAAGACTAGCTTGGGGC 60.118 47.826 0.00 0.00 36.80 5.80
2253 3018 4.173290 ACCAAGCCACCACTTTAACTTA 57.827 40.909 0.00 0.00 0.00 2.24
2266 3031 2.521126 GTAGCCCTTTAAACCAAGCCA 58.479 47.619 0.00 0.00 0.00 4.75
2319 3487 3.584848 ACTCATCCCAAAACAGAGCTAGT 59.415 43.478 0.00 0.00 0.00 2.57
2394 3562 1.283029 ACATCAGAACCACCATCCTGG 59.717 52.381 0.00 0.00 45.02 4.45
2421 3589 4.020573 TCCCCATATATAAACGTGCCTCTG 60.021 45.833 0.00 0.00 0.00 3.35
2430 3598 3.118371 CCCTCGGCTCCCCATATATAAAC 60.118 52.174 0.00 0.00 0.00 2.01
2434 3602 0.417841 ACCCTCGGCTCCCCATATAT 59.582 55.000 0.00 0.00 0.00 0.86
2496 3664 2.486982 CCATGGCTCTCACAAAACTGAG 59.513 50.000 0.00 0.00 39.35 3.35
2511 3679 1.978617 CCCACAGACAACCCATGGC 60.979 63.158 6.09 0.00 37.30 4.40
2559 3727 1.613925 CTCGTGGTTCTTGAGAGGTGA 59.386 52.381 0.00 0.00 31.31 4.02
2714 3882 2.310052 AGGGCTTCTTCCATAACAGCTT 59.690 45.455 0.00 0.00 0.00 3.74
2715 3883 1.918957 AGGGCTTCTTCCATAACAGCT 59.081 47.619 0.00 0.00 0.00 4.24
2722 3890 1.568504 TCACGTAGGGCTTCTTCCAT 58.431 50.000 0.00 0.00 0.00 3.41
2727 3895 4.039366 GGAAAGATATCACGTAGGGCTTCT 59.961 45.833 5.32 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.