Multiple sequence alignment - TraesCS2B01G582300

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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 TraesCS2B01G582300 chr2B 100.000 2642 0 0 1 2642 769948444 769951085 0.000000e+00 4879.0
1 TraesCS2B01G582300 chr2A 86.182 2721 181 90 1 2640 758101610 758104216 0.000000e+00 2761.0
2 TraesCS2B01G582300 chr2D 88.929 1391 82 34 1281 2642 627583191 627584538 0.000000e+00 1650.0
3 TraesCS2B01G582300 chr2D 87.447 1179 50 32 124 1242 627582052 627583192 0.000000e+00 1267.0
4 TraesCS2B01G582300 chr2D 84.146 82 3 3 116 187 627581826 627581907 1.310000e-08 71.3
5 TraesCS2B01G582300 chr6D 80.872 298 47 7 1338 1632 470633251 470632961 2.650000e-55 226.0
6 TraesCS2B01G582300 chr6B 81.404 285 44 6 1351 1632 720502426 720502704 9.520000e-55 224.0


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 TraesCS2B01G582300 chr2B 769948444 769951085 2641 False 4879.0 4879 100.000000 1 2642 1 chr2B.!!$F1 2641
1 TraesCS2B01G582300 chr2A 758101610 758104216 2606 False 2761.0 2761 86.182000 1 2640 1 chr2A.!!$F1 2639
2 TraesCS2B01G582300 chr2D 627581826 627584538 2712 False 996.1 1650 86.840667 116 2642 3 chr2D.!!$F1 2526

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
242 454 0.109086 AAGAGATCGCGTGTGAGGTG 60.109 55.0 5.77 0.0 0.0 4.00 F
862 1132 0.249280 CCCCGCATTTATTTTCCGCC 60.249 55.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1601 0.103208 ACAACGAGGATGGATCGAGC 59.897 55.0 1.94 0.0 42.76 5.03 R
2100 2438 0.326143 TAGGGGCAGGCAGACACATA 60.326 55.0 0.00 0.0 0.00 2.29 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 19 2.429930 CCGCCTGTGTTGGAAGGA 59.570 61.111 0.00 0.00 35.40 3.36
88 90 2.184836 GTGCGTACATGGCCCGTA 59.815 61.111 0.00 0.00 0.00 4.02
207 419 3.650950 GGCTGGGCTGGGAGTGAA 61.651 66.667 0.00 0.00 0.00 3.18
208 420 2.436109 GCTGGGCTGGGAGTGAAA 59.564 61.111 0.00 0.00 0.00 2.69
240 452 0.526524 GGAAGAGATCGCGTGTGAGG 60.527 60.000 5.77 0.00 0.00 3.86
241 453 0.171455 GAAGAGATCGCGTGTGAGGT 59.829 55.000 5.77 0.00 0.00 3.85
242 454 0.109086 AAGAGATCGCGTGTGAGGTG 60.109 55.000 5.77 0.00 0.00 4.00
243 455 0.960861 AGAGATCGCGTGTGAGGTGA 60.961 55.000 5.77 0.00 0.00 4.02
244 456 0.524392 GAGATCGCGTGTGAGGTGAG 60.524 60.000 5.77 0.00 0.00 3.51
270 482 1.228337 ACCAGCAGCTGTGATGCAA 60.228 52.632 21.26 0.00 46.31 4.08
278 490 0.747283 GCTGTGATGCAAGAGGAGGG 60.747 60.000 0.00 0.00 0.00 4.30
279 491 0.617413 CTGTGATGCAAGAGGAGGGT 59.383 55.000 0.00 0.00 0.00 4.34
282 494 1.225704 GATGCAAGAGGAGGGTGGG 59.774 63.158 0.00 0.00 0.00 4.61
283 495 1.229951 ATGCAAGAGGAGGGTGGGA 60.230 57.895 0.00 0.00 0.00 4.37
323 546 0.250553 TTCCACGCACGGAAGGAAAT 60.251 50.000 10.18 0.00 40.20 2.17
335 558 3.649073 GGAAGGAAATCAAACCAAACCG 58.351 45.455 0.00 0.00 0.00 4.44
336 559 2.812358 AGGAAATCAAACCAAACCGC 57.188 45.000 0.00 0.00 0.00 5.68
357 589 2.035193 CCCGATGATCTCACGAATCACT 59.965 50.000 0.00 0.00 0.00 3.41
377 609 4.637534 CACTGGTGAATCTCCGAAATCAAT 59.362 41.667 0.00 0.00 0.00 2.57
378 610 4.878397 ACTGGTGAATCTCCGAAATCAATC 59.122 41.667 0.00 0.00 0.00 2.67
410 643 0.807667 CCGCTCACCCAAGAAGATCG 60.808 60.000 0.00 0.00 0.00 3.69
428 663 6.521151 AGATCGAATTTTCAAGCAAATCCT 57.479 33.333 0.00 0.00 0.00 3.24
436 671 1.450312 AAGCAAATCCTCGAGCCCG 60.450 57.895 6.99 0.00 37.07 6.13
477 712 0.393267 CCGCCCGGAAAGACCAAATA 60.393 55.000 0.73 0.00 38.90 1.40
484 719 4.142026 CCCGGAAAGACCAAATAAAATCCC 60.142 45.833 0.73 0.00 38.90 3.85
556 822 2.495866 CCCCATGCACGCAAATCC 59.504 61.111 0.00 0.00 0.00 3.01
575 841 1.153289 CATCTCCTCCCCACTTGCG 60.153 63.158 0.00 0.00 0.00 4.85
576 842 1.306141 ATCTCCTCCCCACTTGCGA 60.306 57.895 0.00 0.00 0.00 5.10
577 843 1.617947 ATCTCCTCCCCACTTGCGAC 61.618 60.000 0.00 0.00 0.00 5.19
578 844 2.203788 TCCTCCCCACTTGCGACT 60.204 61.111 0.00 0.00 0.00 4.18
579 845 1.831652 CTCCTCCCCACTTGCGACTT 61.832 60.000 0.00 0.00 0.00 3.01
580 846 1.672356 CCTCCCCACTTGCGACTTG 60.672 63.158 0.00 0.00 0.00 3.16
581 847 1.071471 CTCCCCACTTGCGACTTGT 59.929 57.895 0.00 0.00 0.00 3.16
586 852 0.588252 CCACTTGCGACTTGTCCAAG 59.412 55.000 20.11 20.11 43.79 3.61
589 858 1.412710 ACTTGCGACTTGTCCAAGAGA 59.587 47.619 24.62 0.00 40.79 3.10
607 876 6.239148 CCAAGAGAAGAGAAAAGAAAAAGGGG 60.239 42.308 0.00 0.00 0.00 4.79
629 898 3.004315 GGGAGAAGAGAAGATACGCAGAG 59.996 52.174 0.00 0.00 0.00 3.35
666 935 4.201679 CGCGGGGCATACGAGTGA 62.202 66.667 0.00 0.00 0.00 3.41
667 936 2.585247 GCGGGGCATACGAGTGAC 60.585 66.667 0.00 0.00 0.00 3.67
669 938 2.767445 CGGGGCATACGAGTGACGA 61.767 63.158 0.00 0.00 45.77 4.20
670 939 1.226888 GGGGCATACGAGTGACGAC 60.227 63.158 0.00 0.00 45.77 4.34
671 940 1.585521 GGGCATACGAGTGACGACG 60.586 63.158 0.00 0.00 45.77 5.12
672 941 1.426621 GGCATACGAGTGACGACGA 59.573 57.895 0.00 0.00 45.77 4.20
673 942 0.860618 GGCATACGAGTGACGACGAC 60.861 60.000 0.00 0.00 45.77 4.34
674 943 1.186339 GCATACGAGTGACGACGACG 61.186 60.000 5.58 5.58 45.77 5.12
675 944 0.585764 CATACGAGTGACGACGACGG 60.586 60.000 12.58 0.00 45.77 4.79
676 945 1.699656 ATACGAGTGACGACGACGGG 61.700 60.000 12.58 0.00 45.77 5.28
862 1132 0.249280 CCCCGCATTTATTTTCCGCC 60.249 55.000 0.00 0.00 0.00 6.13
1005 1293 2.736719 CGAGTTTGATCGACTGATGGCT 60.737 50.000 6.31 0.00 45.56 4.75
1248 1548 4.753233 ACAGAGGTGAGAAATCGAATCAG 58.247 43.478 0.00 0.00 0.00 2.90
1252 1552 3.118592 AGGTGAGAAATCGAATCAGTCCC 60.119 47.826 0.00 0.00 0.00 4.46
1253 1553 3.369471 GGTGAGAAATCGAATCAGTCCCA 60.369 47.826 0.00 0.00 0.00 4.37
1254 1554 4.253685 GTGAGAAATCGAATCAGTCCCAA 58.746 43.478 0.00 0.00 0.00 4.12
1255 1555 4.878397 GTGAGAAATCGAATCAGTCCCAAT 59.122 41.667 0.00 0.00 0.00 3.16
1256 1556 5.007136 GTGAGAAATCGAATCAGTCCCAATC 59.993 44.000 0.00 0.00 0.00 2.67
1257 1557 4.455606 AGAAATCGAATCAGTCCCAATCC 58.544 43.478 0.00 0.00 0.00 3.01
1300 1600 2.159382 TCTTCAAGAAATTGGACGGCC 58.841 47.619 0.00 0.00 0.00 6.13
1301 1601 0.878416 TTCAAGAAATTGGACGGCCG 59.122 50.000 26.86 26.86 36.79 6.13
1322 1624 2.029828 GCTCGATCCATCCTCGTTGTAT 60.030 50.000 0.00 0.00 37.40 2.29
1340 1642 6.315393 CGTTGTATATGTTCTAACCTGCCTTT 59.685 38.462 0.00 0.00 0.00 3.11
1341 1643 7.465513 CGTTGTATATGTTCTAACCTGCCTTTC 60.466 40.741 0.00 0.00 0.00 2.62
1349 1651 1.322442 AACCTGCCTTTCTTCTGTGC 58.678 50.000 0.00 0.00 0.00 4.57
1359 1661 0.250038 TCTTCTGTGCTGCAGTGACC 60.250 55.000 16.64 0.00 45.23 4.02
1371 1673 1.456892 AGTGACCACCGTGGACTCA 60.457 57.895 24.80 15.01 40.96 3.41
1440 1742 5.292765 GTGAACATGATCATCACCGACTAT 58.707 41.667 14.46 0.00 37.97 2.12
1648 1950 2.190313 GCATCCGGTGATCAGCCA 59.810 61.111 18.81 6.50 0.00 4.75
1649 1951 2.182842 GCATCCGGTGATCAGCCAC 61.183 63.158 18.81 0.00 36.37 5.01
1654 1956 2.668632 GGTGATCAGCCACCGGAA 59.331 61.111 9.46 0.00 46.00 4.30
1658 1960 3.011517 ATCAGCCACCGGAAGCCT 61.012 61.111 9.46 0.00 0.00 4.58
1663 1965 4.796231 CCACCGGAAGCCTCGACG 62.796 72.222 9.46 0.00 0.00 5.12
1748 2061 0.036010 CCATGGACATAGATCCGCCC 60.036 60.000 5.56 0.00 42.24 6.13
1749 2062 0.390340 CATGGACATAGATCCGCCCG 60.390 60.000 0.00 0.00 42.24 6.13
1750 2063 2.048127 GGACATAGATCCGCCCGC 60.048 66.667 0.00 0.00 0.00 6.13
1751 2064 2.574955 GGACATAGATCCGCCCGCT 61.575 63.158 0.00 0.00 0.00 5.52
1752 2065 1.373497 GACATAGATCCGCCCGCTG 60.373 63.158 0.00 0.00 0.00 5.18
1753 2066 2.740055 CATAGATCCGCCCGCTGC 60.740 66.667 0.00 0.00 0.00 5.25
1754 2067 4.008933 ATAGATCCGCCCGCTGCC 62.009 66.667 0.00 0.00 36.24 4.85
1796 2109 4.027437 ACAACAGCTTAACTTTTTGGGGA 58.973 39.130 0.00 0.00 0.00 4.81
1847 2165 2.007608 GATGTTAGTTCGTCCCCTTGC 58.992 52.381 0.00 0.00 0.00 4.01
1881 2199 3.340814 TCAGAGATGCCAAGAAGAACC 57.659 47.619 0.00 0.00 0.00 3.62
1885 2203 4.279169 CAGAGATGCCAAGAAGAACCAAAA 59.721 41.667 0.00 0.00 0.00 2.44
1886 2204 5.047519 CAGAGATGCCAAGAAGAACCAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
1887 2205 5.184671 AGAGATGCCAAGAAGAACCAAAATC 59.815 40.000 0.00 0.00 0.00 2.17
1911 2229 3.535561 ACAGAGTATTCATTCGGCCAAG 58.464 45.455 2.24 0.00 0.00 3.61
1929 2247 4.157472 GCCAAGAGAAAGGAAATCTTCTGG 59.843 45.833 0.00 0.00 33.94 3.86
1936 2254 7.774625 AGAGAAAGGAAATCTTCTGGATGAATC 59.225 37.037 0.00 0.00 33.94 2.52
1946 2264 6.955364 TCTTCTGGATGAATCTTGTTCAGAT 58.045 36.000 0.00 0.00 45.03 2.90
1948 2266 8.712103 TCTTCTGGATGAATCTTGTTCAGATAT 58.288 33.333 0.00 0.00 41.93 1.63
1983 2313 2.613595 GCTACATGTCGAAATGGCATCA 59.386 45.455 19.65 0.00 31.46 3.07
2014 2344 6.208644 AGCAACATGTTGACAGTTTCATAAC 58.791 36.000 36.65 16.91 42.93 1.89
2021 2351 3.674997 TGACAGTTTCATAACCAGAGCC 58.325 45.455 0.00 0.00 34.71 4.70
2047 2385 7.656707 ATCTTTTGCAACAATTAACCATCAC 57.343 32.000 0.00 0.00 0.00 3.06
2098 2436 1.230635 ACATGCTCACGGCTGTTCAC 61.231 55.000 0.00 0.00 42.39 3.18
2100 2438 0.321919 ATGCTCACGGCTGTTCACAT 60.322 50.000 0.00 0.00 42.39 3.21
2134 2472 3.026694 GCCCCTAATCATGCTTTGTCTT 58.973 45.455 0.00 0.00 0.00 3.01
2164 2503 6.303970 CGCGATACATTTTCCATGATTGATTC 59.696 38.462 0.00 0.00 0.00 2.52
2180 2519 6.591062 TGATTGATTCTTAACAATTGCTTGCC 59.409 34.615 5.05 0.00 36.94 4.52
2188 2527 0.535335 CAATTGCTTGCCCTGATGCT 59.465 50.000 0.00 0.00 0.00 3.79
2189 2528 1.752498 CAATTGCTTGCCCTGATGCTA 59.248 47.619 0.00 0.00 0.00 3.49
2190 2529 2.364324 CAATTGCTTGCCCTGATGCTAT 59.636 45.455 0.00 0.00 0.00 2.97
2207 2546 2.983136 GCTATTGATGATGTCGACGAGG 59.017 50.000 11.62 0.00 0.00 4.63
2208 2547 1.858091 ATTGATGATGTCGACGAGGC 58.142 50.000 11.62 0.46 0.00 4.70
2210 2549 0.101219 TGATGATGTCGACGAGGCAG 59.899 55.000 11.62 0.00 38.18 4.85
2215 2554 2.946990 TGATGTCGACGAGGCAGTATAA 59.053 45.455 11.62 0.00 38.18 0.98
2219 2558 3.501062 TGTCGACGAGGCAGTATAATAGG 59.499 47.826 11.62 0.00 0.00 2.57
2223 2562 4.142859 CGACGAGGCAGTATAATAGGAGAC 60.143 50.000 0.00 0.00 0.00 3.36
2224 2563 4.726583 ACGAGGCAGTATAATAGGAGACA 58.273 43.478 0.00 0.00 0.00 3.41
2233 2572 7.596995 GCAGTATAATAGGAGACACACAATCTC 59.403 40.741 0.00 0.00 41.68 2.75
2256 2595 1.518515 TCGTACGTGCGTATCTCGTAG 59.481 52.381 24.94 0.00 44.52 3.51
2304 2643 3.466836 TGTCTTAGGTGAGCTGTTGTTG 58.533 45.455 0.00 0.00 0.00 3.33
2344 2683 0.317160 GAAAAAGTCCAAAGGCCGGG 59.683 55.000 2.18 0.00 0.00 5.73
2356 2695 0.547712 AGGCCGGGAGCATATATGGT 60.548 55.000 17.08 17.08 46.50 3.55
2357 2696 1.200519 GGCCGGGAGCATATATGGTA 58.799 55.000 17.08 0.00 46.50 3.25
2410 2762 0.249657 CGGAGATCTGCTTACCTGGC 60.250 60.000 12.78 0.00 0.00 4.85
2447 2799 1.754745 ACAAGGCGATGTGAGGTGT 59.245 52.632 0.00 0.00 30.82 4.16
2450 2802 3.127533 GGCGATGTGAGGTGTGGC 61.128 66.667 0.00 0.00 0.00 5.01
2480 2832 0.403655 TGTATGTGGCCACCATGTGT 59.596 50.000 32.62 13.71 35.28 3.72
2482 2834 0.034574 TATGTGGCCACCATGTGTCC 60.035 55.000 32.62 5.24 35.28 4.02
2484 2836 4.343323 TGGCCACCATGTGTCCGG 62.343 66.667 0.00 0.00 33.91 5.14
2486 2838 4.722700 GCCACCATGTGTCCGGCT 62.723 66.667 0.00 0.00 39.73 5.52
2487 2839 2.747460 CCACCATGTGTCCGGCTG 60.747 66.667 0.00 0.00 0.00 4.85
2488 2840 3.434319 CACCATGTGTCCGGCTGC 61.434 66.667 0.00 0.00 0.00 5.25
2489 2841 4.722700 ACCATGTGTCCGGCTGCC 62.723 66.667 9.11 9.11 0.00 4.85
2536 2888 2.276732 ATAAACATGCGGATCAGGGG 57.723 50.000 0.00 0.00 0.00 4.79
2547 2899 2.637165 GGATCAGGGGGAAGATATGGT 58.363 52.381 0.00 0.00 0.00 3.55
2552 2904 2.307098 CAGGGGGAAGATATGGTGGATC 59.693 54.545 0.00 0.00 0.00 3.36
2573 2926 0.179129 GTGCTGCAGCTGTGTGTTTT 60.179 50.000 36.61 0.00 42.66 2.43
2574 2927 0.179132 TGCTGCAGCTGTGTGTTTTG 60.179 50.000 36.61 0.00 42.66 2.44
2576 2929 1.736696 GCTGCAGCTGTGTGTTTTGTT 60.737 47.619 31.33 0.00 38.21 2.83
2577 2930 2.479389 GCTGCAGCTGTGTGTTTTGTTA 60.479 45.455 31.33 0.00 38.21 2.41
2578 2931 3.796504 GCTGCAGCTGTGTGTTTTGTTAT 60.797 43.478 31.33 0.00 38.21 1.89
2590 2943 6.698329 GTGTGTTTTGTTATTTAGGTTGGGTC 59.302 38.462 0.00 0.00 0.00 4.46
2602 2955 4.251103 AGGTTGGGTCCTGATTTTATCC 57.749 45.455 0.00 0.00 36.35 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.766313 CGTGATCTTCCTTCCAACACA 58.234 47.619 0.00 0.00 0.00 3.72
9 11 0.606096 TCGCGTGATCTTCCTTCCAA 59.394 50.000 5.77 0.00 0.00 3.53
40 42 2.181021 GACCGGTCGCTCGTCATT 59.819 61.111 20.85 0.00 0.00 2.57
41 43 4.175489 CGACCGGTCGCTCGTCAT 62.175 66.667 40.78 0.00 46.50 3.06
71 73 2.169146 GTACGGGCCATGTACGCAC 61.169 63.158 18.33 4.17 33.57 5.34
72 74 2.184836 GTACGGGCCATGTACGCA 59.815 61.111 18.33 0.00 33.57 5.24
111 113 2.857744 ATTCGGATCGGTCGGCCTC 61.858 63.158 3.66 0.00 0.00 4.70
112 114 2.838225 ATTCGGATCGGTCGGCCT 60.838 61.111 3.66 0.00 0.00 5.19
113 115 2.638330 TTCATTCGGATCGGTCGGCC 62.638 60.000 0.00 0.00 0.00 6.13
114 116 0.808453 TTTCATTCGGATCGGTCGGC 60.808 55.000 0.00 0.00 0.00 5.54
115 117 1.792949 GATTTCATTCGGATCGGTCGG 59.207 52.381 0.00 0.00 0.00 4.79
116 118 1.792949 GGATTTCATTCGGATCGGTCG 59.207 52.381 0.00 0.00 0.00 4.79
117 119 1.792949 CGGATTTCATTCGGATCGGTC 59.207 52.381 0.00 0.00 0.00 4.79
118 120 1.540363 CCGGATTTCATTCGGATCGGT 60.540 52.381 0.00 0.00 45.96 4.69
119 121 1.148310 CCGGATTTCATTCGGATCGG 58.852 55.000 0.00 0.00 45.96 4.18
120 122 1.148310 CCCGGATTTCATTCGGATCG 58.852 55.000 0.73 0.00 45.96 3.69
121 123 1.071699 TCCCCGGATTTCATTCGGATC 59.928 52.381 0.73 0.00 45.96 3.36
122 124 1.136828 TCCCCGGATTTCATTCGGAT 58.863 50.000 0.73 0.00 45.96 4.18
123 125 1.071699 GATCCCCGGATTTCATTCGGA 59.928 52.381 0.73 0.00 45.96 4.55
124 126 1.523758 GATCCCCGGATTTCATTCGG 58.476 55.000 0.73 0.00 43.05 4.30
207 419 3.875571 TCTCTTCCTTCCTTCCTTCCTT 58.124 45.455 0.00 0.00 0.00 3.36
208 420 3.569135 TCTCTTCCTTCCTTCCTTCCT 57.431 47.619 0.00 0.00 0.00 3.36
240 452 1.950828 CTGCTGGTGATCCATCTCAC 58.049 55.000 0.00 0.00 43.43 3.51
241 453 0.179702 GCTGCTGGTGATCCATCTCA 59.820 55.000 0.00 0.00 43.43 3.27
242 454 0.469070 AGCTGCTGGTGATCCATCTC 59.531 55.000 0.00 0.00 43.43 2.75
243 455 0.180642 CAGCTGCTGGTGATCCATCT 59.819 55.000 21.71 0.00 43.43 2.90
244 456 0.107312 ACAGCTGCTGGTGATCCATC 60.107 55.000 31.00 0.00 43.43 3.51
256 468 0.675837 TCCTCTTGCATCACAGCTGC 60.676 55.000 15.27 0.00 40.10 5.25
270 482 0.042731 TTCGATTCCCACCCTCCTCT 59.957 55.000 0.00 0.00 0.00 3.69
278 490 1.001393 TTGCCCCTTCGATTCCCAC 60.001 57.895 0.00 0.00 0.00 4.61
279 491 1.302949 CTTGCCCCTTCGATTCCCA 59.697 57.895 0.00 0.00 0.00 4.37
282 494 1.087501 GTCACTTGCCCCTTCGATTC 58.912 55.000 0.00 0.00 0.00 2.52
283 495 0.322546 GGTCACTTGCCCCTTCGATT 60.323 55.000 0.00 0.00 0.00 3.34
323 546 1.228306 ATCGGGCGGTTTGGTTTGA 60.228 52.632 0.00 0.00 0.00 2.69
335 558 1.269778 TGATTCGTGAGATCATCGGGC 60.270 52.381 0.00 0.00 41.60 6.13
336 559 2.035193 AGTGATTCGTGAGATCATCGGG 59.965 50.000 0.00 0.00 41.60 5.14
357 589 4.199310 GGATTGATTTCGGAGATTCACCA 58.801 43.478 0.97 0.00 35.04 4.17
403 635 7.031975 AGGATTTGCTTGAAAATTCGATCTTC 58.968 34.615 0.00 0.00 31.35 2.87
410 643 4.560427 GCTCGAGGATTTGCTTGAAAATTC 59.440 41.667 15.58 0.00 29.89 2.17
477 712 2.362889 CCGGCTGGCTGGGATTTT 60.363 61.111 12.31 0.00 38.78 1.82
556 822 1.225704 GCAAGTGGGGAGGAGATGG 59.774 63.158 0.00 0.00 0.00 3.51
575 841 6.284459 TCTTTTCTCTTCTCTTGGACAAGTC 58.716 40.000 11.44 0.00 39.38 3.01
576 842 6.240549 TCTTTTCTCTTCTCTTGGACAAGT 57.759 37.500 11.44 0.00 39.38 3.16
577 843 7.559590 TTTCTTTTCTCTTCTCTTGGACAAG 57.440 36.000 5.72 5.72 39.71 3.16
578 844 7.938140 TTTTCTTTTCTCTTCTCTTGGACAA 57.062 32.000 0.00 0.00 0.00 3.18
579 845 7.067494 CCTTTTTCTTTTCTCTTCTCTTGGACA 59.933 37.037 0.00 0.00 0.00 4.02
580 846 7.421599 CCTTTTTCTTTTCTCTTCTCTTGGAC 58.578 38.462 0.00 0.00 0.00 4.02
581 847 6.547510 CCCTTTTTCTTTTCTCTTCTCTTGGA 59.452 38.462 0.00 0.00 0.00 3.53
586 852 5.713792 CCCCCTTTTTCTTTTCTCTTCTC 57.286 43.478 0.00 0.00 0.00 2.87
607 876 2.952978 TCTGCGTATCTTCTCTTCTCCC 59.047 50.000 0.00 0.00 0.00 4.30
610 879 3.315191 GCTCTCTGCGTATCTTCTCTTCT 59.685 47.826 0.00 0.00 0.00 2.85
611 880 3.066064 TGCTCTCTGCGTATCTTCTCTTC 59.934 47.826 0.00 0.00 46.63 2.87
612 881 3.020274 TGCTCTCTGCGTATCTTCTCTT 58.980 45.455 0.00 0.00 46.63 2.85
651 920 2.278596 CGTCACTCGTATGCCCCG 60.279 66.667 0.00 0.00 34.52 5.73
652 921 1.226888 GTCGTCACTCGTATGCCCC 60.227 63.158 0.00 0.00 40.80 5.80
655 924 1.186339 CGTCGTCGTCACTCGTATGC 61.186 60.000 0.00 0.00 40.80 3.14
656 925 0.585764 CCGTCGTCGTCACTCGTATG 60.586 60.000 0.71 0.00 40.80 2.39
657 926 1.699656 CCCGTCGTCGTCACTCGTAT 61.700 60.000 0.71 0.00 40.80 3.06
658 927 2.382746 CCCGTCGTCGTCACTCGTA 61.383 63.158 0.71 0.00 40.80 3.43
659 928 3.720193 CCCGTCGTCGTCACTCGT 61.720 66.667 0.71 0.00 40.80 4.18
871 1142 1.537562 GCGGCGGTATATATACAGGGC 60.538 57.143 21.56 21.00 34.98 5.19
958 1245 3.886505 GAGCAGCAGGAGTAGTAGTATGT 59.113 47.826 0.00 0.00 0.00 2.29
1102 1402 2.579787 GTCGGCGTCGGTCATCAG 60.580 66.667 10.62 0.00 36.95 2.90
1248 1548 0.740737 CGGCTTGATTGGATTGGGAC 59.259 55.000 0.00 0.00 0.00 4.46
1252 1552 1.587088 GCGCGGCTTGATTGGATTG 60.587 57.895 8.83 0.00 0.00 2.67
1253 1553 1.718757 GAGCGCGGCTTGATTGGATT 61.719 55.000 8.83 0.00 39.88 3.01
1254 1554 2.124570 AGCGCGGCTTGATTGGAT 60.125 55.556 8.83 0.00 33.89 3.41
1255 1555 2.819595 GAGCGCGGCTTGATTGGA 60.820 61.111 8.83 0.00 39.88 3.53
1256 1556 3.880846 GGAGCGCGGCTTGATTGG 61.881 66.667 8.83 0.00 39.88 3.16
1257 1557 4.228097 CGGAGCGCGGCTTGATTG 62.228 66.667 8.83 0.00 39.88 2.67
1277 1577 4.415735 GCCGTCCAATTTCTTGAAGAATC 58.584 43.478 8.64 0.00 33.67 2.52
1300 1600 0.936764 CAACGAGGATGGATCGAGCG 60.937 60.000 1.94 0.00 42.76 5.03
1301 1601 0.103208 ACAACGAGGATGGATCGAGC 59.897 55.000 1.94 0.00 42.76 5.03
1322 1624 6.173339 CAGAAGAAAGGCAGGTTAGAACATA 58.827 40.000 0.00 0.00 0.00 2.29
1349 1651 2.666190 CCACGGTGGTCACTGCAG 60.666 66.667 19.15 13.48 41.31 4.41
1359 1661 2.430921 GTCGCTGAGTCCACGGTG 60.431 66.667 0.00 0.00 0.00 4.94
1649 1951 4.194720 CTCCGTCGAGGCTTCCGG 62.195 72.222 12.50 12.50 41.75 5.14
1658 1960 0.841961 TAATCCTCCTCCTCCGTCGA 59.158 55.000 0.00 0.00 0.00 4.20
1663 1965 7.381789 ACTTAAGAATTAATCCTCCTCCTCC 57.618 40.000 10.09 0.00 40.24 4.30
1665 1967 9.374711 CTCTACTTAAGAATTAATCCTCCTCCT 57.625 37.037 10.09 0.00 40.24 3.69
1796 2109 9.987726 TCTAATCATCATCATCATCTACTAGGT 57.012 33.333 0.00 0.00 0.00 3.08
1847 2165 3.504021 TCTGAAGAAGCAGAGCACG 57.496 52.632 0.00 0.00 39.84 5.34
1881 2199 7.008628 GCCGAATGAATACTCTGTTTGATTTTG 59.991 37.037 0.00 0.00 0.00 2.44
1885 2203 4.576463 GGCCGAATGAATACTCTGTTTGAT 59.424 41.667 0.00 0.00 0.00 2.57
1886 2204 3.938963 GGCCGAATGAATACTCTGTTTGA 59.061 43.478 0.00 0.00 0.00 2.69
1887 2205 3.689161 TGGCCGAATGAATACTCTGTTTG 59.311 43.478 0.00 0.00 0.00 2.93
1911 2229 7.774625 AGATTCATCCAGAAGATTTCCTTTCTC 59.225 37.037 0.00 0.00 40.15 2.87
1929 2247 8.348507 GGGAAACATATCTGAACAAGATTCATC 58.651 37.037 0.00 0.00 43.52 2.92
1936 2254 5.749462 AGAGGGGAAACATATCTGAACAAG 58.251 41.667 0.00 0.00 0.00 3.16
1946 2264 3.186283 TGTAGCCAAGAGGGGAAACATA 58.814 45.455 0.00 0.00 37.04 2.29
1948 2266 1.440618 TGTAGCCAAGAGGGGAAACA 58.559 50.000 0.00 0.00 37.04 2.83
1983 2313 4.001652 CTGTCAACATGTTGCTCTGATCT 58.998 43.478 29.84 0.00 40.24 2.75
2014 2344 2.036217 TGTTGCAAAAGATTGGCTCTGG 59.964 45.455 0.00 0.00 37.02 3.86
2021 2351 8.011106 GTGATGGTTAATTGTTGCAAAAGATTG 58.989 33.333 0.00 0.00 39.65 2.67
2098 2436 0.820891 GGGGCAGGCAGACACATATG 60.821 60.000 0.00 0.00 0.00 1.78
2100 2438 0.326143 TAGGGGCAGGCAGACACATA 60.326 55.000 0.00 0.00 0.00 2.29
2134 2472 0.730265 GGAAAATGTATCGCGTGGCA 59.270 50.000 5.77 3.69 0.00 4.92
2164 2503 3.940209 TCAGGGCAAGCAATTGTTAAG 57.060 42.857 7.40 0.00 0.00 1.85
2169 2508 0.535335 AGCATCAGGGCAAGCAATTG 59.465 50.000 0.00 0.00 35.83 2.32
2174 2513 1.683943 TCAATAGCATCAGGGCAAGC 58.316 50.000 0.00 0.00 35.83 4.01
2180 2519 4.388165 GTCGACATCATCAATAGCATCAGG 59.612 45.833 11.55 0.00 0.00 3.86
2188 2527 2.360801 TGCCTCGTCGACATCATCAATA 59.639 45.455 17.16 0.00 0.00 1.90
2189 2528 1.136891 TGCCTCGTCGACATCATCAAT 59.863 47.619 17.16 0.00 0.00 2.57
2190 2529 0.530288 TGCCTCGTCGACATCATCAA 59.470 50.000 17.16 0.00 0.00 2.57
2207 2546 7.437748 AGATTGTGTGTCTCCTATTATACTGC 58.562 38.462 0.00 0.00 0.00 4.40
2208 2547 7.805542 CGAGATTGTGTGTCTCCTATTATACTG 59.194 40.741 0.00 0.00 39.10 2.74
2210 2549 7.872881 TCGAGATTGTGTGTCTCCTATTATAC 58.127 38.462 0.00 0.00 39.10 1.47
2215 2554 4.023622 CGATCGAGATTGTGTGTCTCCTAT 60.024 45.833 10.26 0.00 39.10 2.57
2219 2558 3.138205 ACGATCGAGATTGTGTGTCTC 57.862 47.619 24.34 0.00 38.95 3.36
2223 2562 2.526289 CACGTACGATCGAGATTGTGTG 59.474 50.000 24.34 14.88 36.19 3.82
2224 2563 2.782163 CACGTACGATCGAGATTGTGT 58.218 47.619 24.34 7.06 36.19 3.72
2233 2572 1.578293 GAGATACGCACGTACGATCG 58.422 55.000 24.41 24.08 36.70 3.69
2256 2595 6.969342 CCGGAGCCGTTTGTATATGTACAAC 61.969 48.000 13.92 8.97 41.78 3.32
2272 2611 1.153628 CTAAGACAACCCGGAGCCG 60.154 63.158 0.73 1.06 39.44 5.52
2277 2616 0.391263 GCTCACCTAAGACAACCCGG 60.391 60.000 0.00 0.00 0.00 5.73
2278 2617 0.608640 AGCTCACCTAAGACAACCCG 59.391 55.000 0.00 0.00 0.00 5.28
2344 2683 7.716998 CCCCATTCATTACTACCATATATGCTC 59.283 40.741 7.24 0.00 0.00 4.26
2356 2695 2.849943 ACAGTGCCCCCATTCATTACTA 59.150 45.455 0.00 0.00 0.00 1.82
2357 2696 1.640670 ACAGTGCCCCCATTCATTACT 59.359 47.619 0.00 0.00 0.00 2.24
2410 2762 3.403277 CGGAAGCAGAATCTGGCG 58.597 61.111 12.66 0.00 34.54 5.69
2438 2790 4.248842 CCCACGCCACACCTCACA 62.249 66.667 0.00 0.00 0.00 3.58
2450 2802 2.167219 CACATACAGCGCTCCCACG 61.167 63.158 7.13 0.00 0.00 4.94
2486 2838 3.860605 CATCCATCCGTCCGGGCA 61.861 66.667 6.96 0.00 34.94 5.36
2487 2839 4.626081 CCATCCATCCGTCCGGGC 62.626 72.222 0.00 0.00 34.94 6.13
2488 2840 1.768684 AATCCATCCATCCGTCCGGG 61.769 60.000 0.00 0.00 35.59 5.73
2489 2841 0.973632 TAATCCATCCATCCGTCCGG 59.026 55.000 0.00 0.00 0.00 5.14
2490 2842 2.806244 GTTTAATCCATCCATCCGTCCG 59.194 50.000 0.00 0.00 0.00 4.79
2491 2843 3.815401 CAGTTTAATCCATCCATCCGTCC 59.185 47.826 0.00 0.00 0.00 4.79
2492 2844 3.815401 CCAGTTTAATCCATCCATCCGTC 59.185 47.826 0.00 0.00 0.00 4.79
2493 2845 3.435026 CCCAGTTTAATCCATCCATCCGT 60.435 47.826 0.00 0.00 0.00 4.69
2494 2846 3.149196 CCCAGTTTAATCCATCCATCCG 58.851 50.000 0.00 0.00 0.00 4.18
2495 2847 4.453480 TCCCAGTTTAATCCATCCATCC 57.547 45.455 0.00 0.00 0.00 3.51
2496 2848 8.360390 GTTTATTCCCAGTTTAATCCATCCATC 58.640 37.037 0.00 0.00 0.00 3.51
2497 2849 7.843760 TGTTTATTCCCAGTTTAATCCATCCAT 59.156 33.333 0.00 0.00 0.00 3.41
2536 2888 2.872038 GCACCGATCCACCATATCTTCC 60.872 54.545 0.00 0.00 0.00 3.46
2547 2899 3.709633 AGCTGCAGCACCGATCCA 61.710 61.111 38.24 0.00 45.16 3.41
2552 2904 4.021631 CACACAGCTGCAGCACCG 62.022 66.667 38.24 27.36 45.16 4.94
2573 2926 5.789574 ATCAGGACCCAACCTAAATAACA 57.210 39.130 0.00 0.00 38.32 2.41
2574 2927 7.476540 AAAATCAGGACCCAACCTAAATAAC 57.523 36.000 0.00 0.00 38.32 1.89
2576 2929 8.002459 GGATAAAATCAGGACCCAACCTAAATA 58.998 37.037 0.00 0.00 38.32 1.40
2577 2930 6.839134 GGATAAAATCAGGACCCAACCTAAAT 59.161 38.462 0.00 0.00 38.32 1.40
2578 2931 6.192044 GGATAAAATCAGGACCCAACCTAAA 58.808 40.000 0.00 0.00 38.32 1.85
2590 2943 6.051717 AGACACAGAATCGGATAAAATCAGG 58.948 40.000 0.00 0.00 0.00 3.86
2602 2955 2.658802 CACGAGACAAGACACAGAATCG 59.341 50.000 0.00 0.00 35.21 3.34


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

AutoCloner maintained by Alex Coulton.