Multiple sequence alignment - TraesCS4A01G481900

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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 TraesCS4A01G481900 chr4A 100.000 2723 0 0 1 2723 737441822 737444544 0.000000e+00 5029
1 TraesCS4A01G481900 chr4A 90.000 110 9 2 2381 2489 83741374 83741266 1.020000e-29 141
2 TraesCS4A01G481900 chr4A 86.792 106 14 0 2381 2486 626395569 626395464 4.760000e-23 119
3 TraesCS4A01G481900 chr7A 91.634 2020 118 24 1 2009 6352342 6350363 0.000000e+00 2747
4 TraesCS4A01G481900 chr7A 89.007 282 23 4 2016 2293 6350106 6349829 2.600000e-90 342
5 TraesCS4A01G481900 chr7A 91.870 123 9 1 2480 2601 6349680 6349558 1.300000e-38 171
6 TraesCS4A01G481900 chr7A 93.204 103 7 0 2191 2293 680258159 680258057 4.700000e-33 152
7 TraesCS4A01G481900 chr7A 87.850 107 11 2 2381 2486 6061711 6061816 1.020000e-24 124
8 TraesCS4A01G481900 chr7D 92.033 1318 64 14 1 1311 5125528 5124245 0.000000e+00 1814
9 TraesCS4A01G481900 chr7D 90.874 778 39 13 1253 2009 5124246 5123480 0.000000e+00 1014
10 TraesCS4A01G481900 chr7D 89.404 302 23 4 2309 2601 5123140 5122839 3.310000e-99 372
11 TraesCS4A01G481900 chr7D 91.503 153 12 1 2018 2170 5123283 5123132 2.750000e-50 209
12 TraesCS4A01G481900 chr7D 95.041 121 5 1 2604 2723 5122805 5122685 3.580000e-44 189
13 TraesCS4A01G481900 chr7D 86.792 106 14 0 2381 2486 29073370 29073475 4.760000e-23 119
14 TraesCS4A01G481900 chr1A 93.333 105 7 0 2382 2486 431430080 431429976 3.630000e-34 156
15 TraesCS4A01G481900 chr3B 87.037 108 12 1 2381 2486 96817202 96817309 1.320000e-23 121
16 TraesCS4A01G481900 chr4B 86.916 107 13 1 2381 2486 546376892 546376786 4.760000e-23 119
17 TraesCS4A01G481900 chr2D 86.916 107 13 1 2381 2486 95175818 95175924 4.760000e-23 119


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 TraesCS4A01G481900 chr4A 737441822 737444544 2722 False 5029.000000 5029 100.000 1 2723 1 chr4A.!!$F1 2722
1 TraesCS4A01G481900 chr7A 6349558 6352342 2784 True 1086.666667 2747 90.837 1 2601 3 chr7A.!!$R2 2600
2 TraesCS4A01G481900 chr7D 5122685 5125528 2843 True 719.600000 1814 91.771 1 2723 5 chr7D.!!$R1 2722

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
490 498 1.273327 GTGAGCATTTTTGGGTCCCAG 59.727 52.381 11.40 0.0 33.81 4.45 F
1312 1380 0.179150 CTCTAGTGACTCACTGGCGC 60.179 60.000 20.19 0.0 45.01 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1685 0.041833 CCTCTTCCTCCACCTCCTCA 59.958 60.0 0.00 0.0 0.00 3.86 R
2121 2499 0.366534 GCAAATTTAAGCTTGGCGCG 59.633 50.0 9.86 0.0 45.59 6.86 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
27 28 8.801882 ACTCTAGCCTCTGATAATATGTACTC 57.198 38.462 0.00 0.00 0.00 2.59
28 29 8.611257 ACTCTAGCCTCTGATAATATGTACTCT 58.389 37.037 0.00 0.00 0.00 3.24
79 80 1.694696 CCTCTAACCTGCATAGACCCC 59.305 57.143 0.00 0.00 0.00 4.95
100 101 7.304479 ACCCCATATACATCAATTCATCCAAA 58.696 34.615 0.00 0.00 0.00 3.28
122 123 9.178758 CCAAAGTTGTAATTATCTAAAGCCTCT 57.821 33.333 0.00 0.00 0.00 3.69
177 178 8.758715 ACTACAACGTTTATGAAAGTACTTCAC 58.241 33.333 8.95 7.16 46.80 3.18
183 184 6.145534 CGTTTATGAAAGTACTTCACTGCTCA 59.854 38.462 8.95 8.18 46.80 4.26
189 190 7.771183 TGAAAGTACTTCACTGCTCAAAATTT 58.229 30.769 8.95 0.00 39.20 1.82
236 238 6.524101 TTGGGTAGGTTTCATATTTTCAGC 57.476 37.500 0.00 0.00 0.00 4.26
312 318 7.394359 TGAAGGCAAAATGACTAGCTTTAGAAT 59.606 33.333 0.00 0.00 31.94 2.40
338 344 2.748461 TTGAAAAGTTTGAGTCGCCG 57.252 45.000 0.00 0.00 0.00 6.46
388 394 2.999063 GCATTTGGGCAGGCCACT 60.999 61.111 17.12 2.94 37.98 4.00
397 403 1.376553 GCAGGCCACTCTCCAAGTC 60.377 63.158 5.01 0.00 35.45 3.01
412 418 7.124298 ACTCTCCAAGTCTATGTAATAGTGCAA 59.876 37.037 0.00 0.00 46.98 4.08
475 483 5.838531 AGTACATACTAAGGTGAGTGAGC 57.161 43.478 0.00 0.00 34.13 4.26
487 495 2.029918 GTGAGTGAGCATTTTTGGGTCC 60.030 50.000 0.00 0.00 31.96 4.46
490 498 1.273327 GTGAGCATTTTTGGGTCCCAG 59.727 52.381 11.40 0.00 33.81 4.45
495 503 2.417243 GCATTTTTGGGTCCCAGATTCG 60.417 50.000 11.40 2.59 33.81 3.34
514 522 4.487714 TCGTTTGAGCTTGGGATCTAAT 57.512 40.909 0.00 0.00 0.00 1.73
534 542 8.925161 TCTAATTTTCTTGAAAACCACACTTG 57.075 30.769 10.24 0.00 0.00 3.16
535 543 6.421377 AATTTTCTTGAAAACCACACTTGC 57.579 33.333 10.24 0.00 0.00 4.01
539 547 4.887748 TCTTGAAAACCACACTTGCAAAA 58.112 34.783 0.00 0.00 0.00 2.44
549 557 5.651576 ACCACACTTGCAAAATTGGAAATTT 59.348 32.000 21.09 0.00 38.05 1.82
588 598 9.127277 ACAAGTAAATACTTTGTAAAGCTTCCA 57.873 29.630 0.00 0.00 43.57 3.53
594 604 7.759489 ATACTTTGTAAAGCTTCCATTGACA 57.241 32.000 0.00 0.00 39.63 3.58
595 605 6.463995 ACTTTGTAAAGCTTCCATTGACAA 57.536 33.333 0.00 1.48 39.63 3.18
596 606 6.872920 ACTTTGTAAAGCTTCCATTGACAAA 58.127 32.000 0.00 8.99 39.63 2.83
618 628 8.547894 ACAAACTTTCACTGAAAAACTTTCAAC 58.452 29.630 5.72 0.00 30.84 3.18
645 655 4.142469 ACGCCCTGTGTGAAAAATATTAGC 60.142 41.667 0.00 0.00 0.00 3.09
906 916 2.036256 GCTCCCACTTGCACCCAT 59.964 61.111 0.00 0.00 0.00 4.00
1021 1032 4.730949 ATGACGTTCGGAGGAATCTTTA 57.269 40.909 0.00 0.00 34.05 1.85
1251 1262 2.613730 CTCGTTCGAGCAACTCAGTA 57.386 50.000 9.23 0.00 32.09 2.74
1279 1347 3.271014 GTGGGTACGAGCGACAGA 58.729 61.111 0.00 0.00 0.00 3.41
1312 1380 0.179150 CTCTAGTGACTCACTGGCGC 60.179 60.000 20.19 0.00 45.01 6.53
1315 1383 1.923227 TAGTGACTCACTGGCGCTCG 61.923 60.000 20.19 0.30 41.47 5.03
1339 1407 1.287730 CTCGAGCAACTCACTGGCAC 61.288 60.000 0.00 0.00 0.00 5.01
1349 1417 2.524394 ACTGGCACTCCCTCGTGT 60.524 61.111 0.00 0.00 37.24 4.49
1408 1476 2.598565 ACTCTAGTGACTCACTGGCAA 58.401 47.619 20.19 3.33 45.01 4.52
1442 1510 0.616111 AACTCATCGGCAGTCCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
1475 1543 3.624861 CCACAGGATGCACATAAGTTCTC 59.375 47.826 0.00 0.00 42.53 2.87
1476 1544 3.624861 CACAGGATGCACATAAGTTCTCC 59.375 47.826 0.00 0.00 42.53 3.71
1477 1545 3.521126 ACAGGATGCACATAAGTTCTCCT 59.479 43.478 0.00 0.00 42.53 3.69
1478 1546 4.125703 CAGGATGCACATAAGTTCTCCTC 58.874 47.826 0.00 0.00 29.39 3.71
1481 1549 3.334583 TGCACATAAGTTCTCCTCACC 57.665 47.619 0.00 0.00 0.00 4.02
1487 1555 1.122019 AAGTTCTCCTCACCGGCAGT 61.122 55.000 0.00 0.00 0.00 4.40
1490 1558 3.775654 CTCCTCACCGGCAGTCCC 61.776 72.222 0.00 0.00 0.00 4.46
1518 1586 0.406361 ACGAGGAGGAGGACTTCAGT 59.594 55.000 0.00 0.00 0.00 3.41
1560 1631 1.063616 GACGAGGACGACGATGATGAA 59.936 52.381 0.00 0.00 42.66 2.57
1609 1680 1.678627 ACGAGGACGAAGATGATGAGG 59.321 52.381 0.00 0.00 42.66 3.86
1614 1685 4.158786 AGGACGAAGATGATGAGGATGAT 58.841 43.478 0.00 0.00 0.00 2.45
1631 1702 1.362584 TGATGAGGAGGTGGAGGAAGA 59.637 52.381 0.00 0.00 0.00 2.87
1717 1791 3.404773 GGGGGAGACTTGAGTGGG 58.595 66.667 0.00 0.00 0.00 4.61
1719 1793 1.679898 GGGGAGACTTGAGTGGGTG 59.320 63.158 0.00 0.00 0.00 4.61
1797 1871 0.107017 AAACAGCAGTGCAGGAGTGT 60.107 50.000 19.20 9.60 0.00 3.55
1813 1887 5.236047 CAGGAGTGTCACTACCTATACGTAC 59.764 48.000 11.86 0.00 25.63 3.67
1861 1936 2.875485 GCTGTCTGCATGCAGGTG 59.125 61.111 39.72 29.90 43.75 4.00
1862 1937 1.673337 GCTGTCTGCATGCAGGTGA 60.673 57.895 39.72 23.51 43.75 4.02
1863 1938 1.645704 GCTGTCTGCATGCAGGTGAG 61.646 60.000 39.72 31.48 43.75 3.51
1864 1939 1.002990 TGTCTGCATGCAGGTGAGG 60.003 57.895 39.72 20.20 43.75 3.86
1865 1940 2.045634 TCTGCATGCAGGTGAGGC 60.046 61.111 39.72 3.23 43.75 4.70
1962 2052 2.984623 TGCTCTGCATCCGCTCTT 59.015 55.556 0.00 0.00 39.64 2.85
1988 2078 3.329520 TGCCTGTATAACACTTCACCCTT 59.670 43.478 0.00 0.00 0.00 3.95
2000 2090 2.825861 TCACCCTTTGTCGAACCTAC 57.174 50.000 0.00 0.00 0.00 3.18
2001 2091 2.040939 TCACCCTTTGTCGAACCTACA 58.959 47.619 0.00 0.00 0.00 2.74
2009 2099 1.271001 TGTCGAACCTACAGACTCCGA 60.271 52.381 0.00 0.00 36.01 4.55
2010 2100 2.015587 GTCGAACCTACAGACTCCGAT 58.984 52.381 0.00 0.00 32.58 4.18
2011 2101 2.422832 GTCGAACCTACAGACTCCGATT 59.577 50.000 0.00 0.00 32.58 3.34
2012 2102 3.087031 TCGAACCTACAGACTCCGATTT 58.913 45.455 0.00 0.00 0.00 2.17
2013 2103 3.119602 TCGAACCTACAGACTCCGATTTG 60.120 47.826 0.00 0.00 0.00 2.32
2014 2104 3.367087 CGAACCTACAGACTCCGATTTGT 60.367 47.826 0.00 0.00 0.00 2.83
2025 2400 0.660005 CCGATTTGTTGCCACGTGTG 60.660 55.000 15.65 7.24 0.00 3.82
2116 2494 7.558444 TCCCGGTAAATAAATTCTGCTTATGTT 59.442 33.333 0.00 0.00 0.00 2.71
2123 2501 2.330231 TTCTGCTTATGTTTGTGCGC 57.670 45.000 0.00 0.00 0.00 6.09
2124 2502 0.165727 TCTGCTTATGTTTGTGCGCG 59.834 50.000 0.00 0.00 0.00 6.86
2182 2560 5.982356 TGATCTAGCTACAGTGAAATGCTT 58.018 37.500 0.00 0.00 35.47 3.91
2199 2577 1.339055 GCTTCACTAGTCCATGTGGCA 60.339 52.381 0.00 0.00 35.15 4.92
2200 2578 2.681976 GCTTCACTAGTCCATGTGGCAT 60.682 50.000 0.00 0.00 35.15 4.40
2219 2597 5.882557 TGGCATGTTTTTCTCCTCTCTAATC 59.117 40.000 0.00 0.00 0.00 1.75
2220 2598 5.882557 GGCATGTTTTTCTCCTCTCTAATCA 59.117 40.000 0.00 0.00 0.00 2.57
2244 2622 7.603404 TCAGTTTTGGCCTTATTTGATCAAATG 59.397 33.333 33.94 22.42 40.83 2.32
2248 2626 6.602410 TGGCCTTATTTGATCAAATGAACA 57.398 33.333 33.94 23.44 40.83 3.18
2265 2643 9.743057 CAAATGAACAAGTTTGTGGACTAAATA 57.257 29.630 0.00 0.00 41.31 1.40
2289 2667 2.783135 TCACTTTCTGAGTTGATGGCC 58.217 47.619 0.00 0.00 36.10 5.36
2293 2671 4.154918 CACTTTCTGAGTTGATGGCCTAAC 59.845 45.833 3.32 7.15 36.10 2.34
2315 2724 1.935873 GCGCATTTCACTCATCTAGCA 59.064 47.619 0.30 0.00 0.00 3.49
2355 2764 1.676006 ACGGGGCGATGAATTGATTTC 59.324 47.619 0.00 0.00 34.72 2.17
2379 2788 1.474077 GCTTCTGCTGGTGTTATTGGG 59.526 52.381 0.00 0.00 36.03 4.12
2401 2810 6.721668 TGGGTTTTTGAAAAAGGGTGAATTTT 59.278 30.769 2.91 0.00 0.00 1.82
2449 2858 8.630278 AGATAATACAAACACGATGAGTACAC 57.370 34.615 0.00 0.00 0.00 2.90
2454 2863 0.242825 ACACGATGAGTACACACCCG 59.757 55.000 12.79 12.79 0.00 5.28
2466 2875 2.297895 ACACCCGGCCTCTGCATAA 61.298 57.895 0.00 0.00 40.13 1.90
2475 2884 3.350833 GGCCTCTGCATAATTAGGATGG 58.649 50.000 0.32 0.00 40.13 3.51
2486 2896 6.127479 GCATAATTAGGATGGACACAACCAAA 60.127 38.462 0.32 0.00 41.68 3.28
2498 2908 0.670162 CAACCAAACTGTCTGCTGGG 59.330 55.000 0.00 0.00 32.94 4.45
2533 2943 5.938125 GGTGTCAAACCTGTCTGTATAACAT 59.062 40.000 0.00 0.00 46.55 2.71
2558 2968 0.105964 CTTGGGTCACGTGTCAAGGA 59.894 55.000 25.87 5.07 34.61 3.36
2601 3018 8.210265 AGATATAAAAGAGGAAGGAAGAAGCAG 58.790 37.037 0.00 0.00 0.00 4.24
2613 3061 0.250234 AGAAGCAGCGCATCTTACCA 59.750 50.000 11.47 0.00 32.50 3.25
2667 3115 2.230660 CCACTCCCTTGTTGTTCTTCC 58.769 52.381 0.00 0.00 0.00 3.46
2681 3129 5.431179 TGTTCTTCCTCTTTACCCCATAC 57.569 43.478 0.00 0.00 0.00 2.39
2686 3134 5.197189 TCTTCCTCTTTACCCCATACCTCTA 59.803 44.000 0.00 0.00 0.00 2.43
2706 3154 7.112779 CCTCTATTTGAAACCTTGTATCCTGT 58.887 38.462 0.00 0.00 0.00 4.00
2715 3163 6.875972 AACCTTGTATCCTGTATCAAGTCT 57.124 37.500 0.00 0.00 36.53 3.24
2716 3164 6.227298 ACCTTGTATCCTGTATCAAGTCTG 57.773 41.667 0.00 0.00 36.53 3.51
2717 3165 5.053145 CCTTGTATCCTGTATCAAGTCTGC 58.947 45.833 0.00 0.00 36.53 4.26
2718 3166 5.163364 CCTTGTATCCTGTATCAAGTCTGCT 60.163 44.000 0.00 0.00 36.53 4.24
2719 3167 5.268118 TGTATCCTGTATCAAGTCTGCTG 57.732 43.478 0.00 0.00 0.00 4.41
2720 3168 4.956075 TGTATCCTGTATCAAGTCTGCTGA 59.044 41.667 0.00 0.00 0.00 4.26
2721 3169 5.600069 TGTATCCTGTATCAAGTCTGCTGAT 59.400 40.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 5.822519 TGCAGGTTAGAGGCAAATATTGTAG 59.177 40.000 0.00 0.00 34.05 2.74
53 54 5.454755 GGTCTATGCAGGTTAGAGGCAAATA 60.455 44.000 0.00 0.00 41.43 1.40
312 318 7.535940 CGGCGACTCAAACTTTTCAAATATTAA 59.464 33.333 0.00 0.00 0.00 1.40
321 327 5.520022 TTATACGGCGACTCAAACTTTTC 57.480 39.130 16.62 0.00 0.00 2.29
332 338 7.864307 AATGTTCTACTAATTATACGGCGAC 57.136 36.000 16.62 0.00 0.00 5.19
388 394 7.124298 ACTTGCACTATTACATAGACTTGGAGA 59.876 37.037 0.00 0.00 36.68 3.71
412 418 4.500499 AATCTCTGCCTTAAGATGCACT 57.500 40.909 3.36 0.00 32.62 4.40
475 483 2.825532 ACGAATCTGGGACCCAAAAATG 59.174 45.455 15.87 7.40 30.80 2.32
487 495 1.470098 CCCAAGCTCAAACGAATCTGG 59.530 52.381 0.00 0.00 0.00 3.86
490 498 3.274288 AGATCCCAAGCTCAAACGAATC 58.726 45.455 0.00 0.00 0.00 2.52
495 503 7.163001 AGAAAATTAGATCCCAAGCTCAAAC 57.837 36.000 0.00 0.00 0.00 2.93
514 522 4.887748 TGCAAGTGTGGTTTTCAAGAAAA 58.112 34.783 3.98 3.98 37.90 2.29
534 542 9.518906 AATGTTTTCAGAAATTTCCAATTTTGC 57.481 25.926 14.61 0.41 0.00 3.68
582 592 4.741676 CAGTGAAAGTTTGTCAATGGAAGC 59.258 41.667 0.00 0.00 37.42 3.86
583 593 6.135290 TCAGTGAAAGTTTGTCAATGGAAG 57.865 37.500 5.45 0.00 40.55 3.46
584 594 6.522625 TTCAGTGAAAGTTTGTCAATGGAA 57.477 33.333 2.20 0.00 40.55 3.53
585 595 6.522625 TTTCAGTGAAAGTTTGTCAATGGA 57.477 33.333 14.35 0.00 40.55 3.41
586 596 7.331687 AGTTTTTCAGTGAAAGTTTGTCAATGG 59.668 33.333 17.36 0.00 40.55 3.16
587 597 8.243289 AGTTTTTCAGTGAAAGTTTGTCAATG 57.757 30.769 17.36 0.00 41.30 2.82
588 598 8.831715 AAGTTTTTCAGTGAAAGTTTGTCAAT 57.168 26.923 17.36 0.00 32.93 2.57
589 599 8.655651 AAAGTTTTTCAGTGAAAGTTTGTCAA 57.344 26.923 17.36 5.60 37.90 3.18
590 600 7.923344 TGAAAGTTTTTCAGTGAAAGTTTGTCA 59.077 29.630 17.36 15.60 38.85 3.58
591 601 8.293114 TGAAAGTTTTTCAGTGAAAGTTTGTC 57.707 30.769 17.36 13.62 38.85 3.18
592 602 8.547894 GTTGAAAGTTTTTCAGTGAAAGTTTGT 58.452 29.630 17.36 5.78 38.85 2.83
593 603 8.764287 AGTTGAAAGTTTTTCAGTGAAAGTTTG 58.236 29.630 17.36 0.00 38.85 2.93
594 604 8.887036 AGTTGAAAGTTTTTCAGTGAAAGTTT 57.113 26.923 17.36 16.85 40.46 2.66
595 605 8.887036 AAGTTGAAAGTTTTTCAGTGAAAGTT 57.113 26.923 17.36 10.35 32.93 2.66
596 606 8.887036 AAAGTTGAAAGTTTTTCAGTGAAAGT 57.113 26.923 17.36 5.11 32.93 2.66
618 628 3.701532 TTTTTCACACAGGGCGTAAAG 57.298 42.857 0.00 0.00 0.00 1.85
672 682 2.734755 CCCAGATGTATCTTGGGCAA 57.265 50.000 13.04 0.00 37.95 4.52
906 916 2.671070 GAGTTAGCTGCCCTGCCA 59.329 61.111 0.00 0.00 0.00 4.92
953 963 0.170784 TATGGCTTGTGTGCATTGCG 59.829 50.000 3.84 0.00 34.04 4.85
1021 1032 2.190578 GATGTAGCCGGGCAAGCT 59.809 61.111 23.09 2.24 44.49 3.74
1116 1127 2.097038 CAGCTTTCGCTCCTGTCGG 61.097 63.158 0.00 0.00 45.15 4.79
1119 1130 2.740055 CGCAGCTTTCGCTCCTGT 60.740 61.111 0.00 0.00 45.15 4.00
1197 1208 0.108615 CACTAGAGAACCCCTGCGTG 60.109 60.000 0.00 0.00 0.00 5.34
1279 1347 1.689233 TAGAGAACCCATGCGCCCT 60.689 57.895 4.18 0.00 0.00 5.19
1323 1391 0.952984 GGAGTGCCAGTGAGTTGCTC 60.953 60.000 0.00 0.00 0.00 4.26
1324 1392 1.072159 GGAGTGCCAGTGAGTTGCT 59.928 57.895 0.00 0.00 0.00 3.91
1325 1393 1.968540 GGGAGTGCCAGTGAGTTGC 60.969 63.158 0.00 0.00 35.15 4.17
1388 1456 2.294449 TGCCAGTGAGTCACTAGAGT 57.706 50.000 25.04 0.34 43.43 3.24
1442 1510 3.642503 CCTGTGGCCCGTACCCAA 61.643 66.667 0.00 0.00 33.39 4.12
1475 1543 3.775654 GAGGGACTGCCGGTGAGG 61.776 72.222 1.90 0.00 41.55 3.86
1476 1544 4.135153 CGAGGGACTGCCGGTGAG 62.135 72.222 1.90 1.59 41.55 3.51
1477 1545 4.988716 ACGAGGGACTGCCGGTGA 62.989 66.667 1.90 0.00 41.55 4.02
1478 1546 4.742201 CACGAGGGACTGCCGGTG 62.742 72.222 1.90 0.00 41.55 4.94
1560 1631 1.683385 TCGAAGGCATCATCGTCATCT 59.317 47.619 0.00 0.00 39.91 2.90
1609 1680 2.094100 TCCTCCACCTCCTCATCATC 57.906 55.000 0.00 0.00 0.00 2.92
1614 1685 0.041833 CCTCTTCCTCCACCTCCTCA 59.958 60.000 0.00 0.00 0.00 3.86
1717 1791 1.154338 GCTTGCAGCGTCATCACAC 60.154 57.895 0.00 0.00 0.00 3.82
1719 1793 0.727122 GTTGCTTGCAGCGTCATCAC 60.727 55.000 0.00 0.00 46.26 3.06
1858 1933 2.527951 AATCGCACTCCAGCCTCACC 62.528 60.000 0.00 0.00 0.00 4.02
1860 1935 0.901827 TAAATCGCACTCCAGCCTCA 59.098 50.000 0.00 0.00 0.00 3.86
1861 1936 2.024176 TTAAATCGCACTCCAGCCTC 57.976 50.000 0.00 0.00 0.00 4.70
1862 1937 2.489938 TTTAAATCGCACTCCAGCCT 57.510 45.000 0.00 0.00 0.00 4.58
1863 1938 4.893424 TTATTTAAATCGCACTCCAGCC 57.107 40.909 3.39 0.00 0.00 4.85
1890 1980 6.952358 TGGATTTAGTTACAGACACTAGGAGT 59.048 38.462 0.00 0.00 0.00 3.85
1957 2047 4.455877 AGTGTTATACAGGCACAAAAGAGC 59.544 41.667 0.00 0.00 35.75 4.09
1962 2052 4.517453 GGTGAAGTGTTATACAGGCACAAA 59.483 41.667 0.00 0.00 35.75 2.83
1988 2078 1.538512 CGGAGTCTGTAGGTTCGACAA 59.461 52.381 0.00 0.00 0.00 3.18
2013 2103 0.884704 AGTCCATCACACGTGGCAAC 60.885 55.000 21.57 8.84 36.66 4.17
2014 2104 0.884259 CAGTCCATCACACGTGGCAA 60.884 55.000 21.57 4.78 36.66 4.52
2070 2448 9.205513 ACCGGGAGTAGAATTTACTTCTATTTA 57.794 33.333 6.32 0.00 45.78 1.40
2073 2451 8.773033 TTACCGGGAGTAGAATTTACTTCTAT 57.227 34.615 6.32 0.00 45.78 1.98
2074 2452 8.593945 TTTACCGGGAGTAGAATTTACTTCTA 57.406 34.615 6.32 0.00 42.56 2.10
2075 2453 7.486407 TTTACCGGGAGTAGAATTTACTTCT 57.514 36.000 6.32 0.00 46.16 2.85
2076 2454 9.822185 TTATTTACCGGGAGTAGAATTTACTTC 57.178 33.333 6.32 1.52 30.92 3.01
2086 2464 6.289064 AGCAGAATTTATTTACCGGGAGTAG 58.711 40.000 6.32 0.00 30.92 2.57
2105 2483 0.165727 CGCGCACAAACATAAGCAGA 59.834 50.000 8.75 0.00 0.00 4.26
2116 2494 2.064723 TTTAAGCTTGGCGCGCACAA 62.065 50.000 34.42 29.32 45.59 3.33
2121 2499 0.366534 GCAAATTTAAGCTTGGCGCG 59.633 50.000 9.86 0.00 45.59 6.86
2182 2560 1.908619 ACATGCCACATGGACTAGTGA 59.091 47.619 0.00 0.00 37.97 3.41
2186 2564 4.406456 AGAAAAACATGCCACATGGACTA 58.594 39.130 11.91 0.00 37.39 2.59
2199 2577 9.579932 AAAACTGATTAGAGAGGAGAAAAACAT 57.420 29.630 0.00 0.00 0.00 2.71
2200 2578 8.840321 CAAAACTGATTAGAGAGGAGAAAAACA 58.160 33.333 0.00 0.00 0.00 2.83
2219 2597 7.603404 TCATTTGATCAAATAAGGCCAAAACTG 59.397 33.333 28.61 15.73 38.84 3.16
2220 2598 7.678837 TCATTTGATCAAATAAGGCCAAAACT 58.321 30.769 28.61 4.98 38.84 2.66
2244 2622 9.774742 GATCATATTTAGTCCACAAACTTGTTC 57.225 33.333 0.00 0.00 39.91 3.18
2248 2626 9.520515 AAGTGATCATATTTAGTCCACAAACTT 57.479 29.630 0.00 0.00 0.00 2.66
2265 2643 4.639310 GCCATCAACTCAGAAAGTGATCAT 59.361 41.667 0.00 0.00 38.58 2.45
2289 2667 1.075542 TGAGTGAAATGCGCCGTTAG 58.924 50.000 4.18 0.00 0.00 2.34
2293 2671 1.524355 CTAGATGAGTGAAATGCGCCG 59.476 52.381 4.18 0.00 0.00 6.46
2315 2724 5.066505 CCCGTACGTACTTACATCTTACCTT 59.933 44.000 22.55 0.00 0.00 3.50
2355 2764 0.602638 TAACACCAGCAGAAGCCGTG 60.603 55.000 0.00 0.00 43.50 4.94
2425 2834 8.318876 GTGTGTACTCATCGTGTTTGTATTATC 58.681 37.037 0.24 0.00 0.00 1.75
2427 2836 6.587226 GGTGTGTACTCATCGTGTTTGTATTA 59.413 38.462 0.24 0.00 0.00 0.98
2445 2854 3.702048 GCAGAGGCCGGGTGTGTA 61.702 66.667 2.18 0.00 0.00 2.90
2449 2858 0.466189 AATTATGCAGAGGCCGGGTG 60.466 55.000 2.18 0.00 40.13 4.61
2454 2863 3.009473 TCCATCCTAATTATGCAGAGGCC 59.991 47.826 0.00 0.00 40.13 5.19
2466 2875 4.766891 CAGTTTGGTTGTGTCCATCCTAAT 59.233 41.667 0.00 0.00 37.33 1.73
2475 2884 2.017049 AGCAGACAGTTTGGTTGTGTC 58.983 47.619 0.00 0.00 40.82 3.67
2486 2896 1.004745 CCAATAACCCCAGCAGACAGT 59.995 52.381 0.00 0.00 0.00 3.55
2498 2908 3.985008 GGTTTGACACCAACCAATAACC 58.015 45.455 4.46 0.00 46.42 2.85
2533 2943 2.829120 TGACACGTGACCCAAGATGATA 59.171 45.455 25.01 0.00 0.00 2.15
2558 2968 1.002134 CTCCCGCTGAACCACCAAT 60.002 57.895 0.00 0.00 0.00 3.16
2566 2976 4.899457 TCCTCTTTTATATCTCCCGCTGAA 59.101 41.667 0.00 0.00 0.00 3.02
2601 3018 2.742053 TCTTCTGTTTGGTAAGATGCGC 59.258 45.455 0.00 0.00 0.00 6.09
2613 3061 5.647225 GGATGAAGCTGATTCTCTTCTGTTT 59.353 40.000 7.22 0.00 39.41 2.83
2667 3115 7.374975 TCAAATAGAGGTATGGGGTAAAGAG 57.625 40.000 0.00 0.00 0.00 2.85
2681 3129 7.112779 ACAGGATACAAGGTTTCAAATAGAGG 58.887 38.462 0.00 0.00 41.41 3.69
2686 3134 8.877864 TTGATACAGGATACAAGGTTTCAAAT 57.122 30.769 0.00 0.00 34.82 2.32


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

AutoCloner maintained by Alex Coulton.