Multiple sequence alignment - TraesCS5D01G178000

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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 TraesCS5D01G178000 chr5D 100.000 2865 0 0 1 2865 277634049 277631185 0.000000e+00 5291.0
1 TraesCS5D01G178000 chr5A 88.744 2221 136 43 694 2865 366761997 366759842 0.000000e+00 2612.0
2 TraesCS5D01G178000 chr5A 95.222 293 11 2 173 462 366762437 366762145 7.230000e-126 460.0
3 TraesCS5D01G178000 chr5A 95.489 133 4 2 2 132 366762562 366762430 8.040000e-51 211.0
4 TraesCS5D01G178000 chr5B 92.984 1468 66 14 555 2005 315834936 315833489 0.000000e+00 2106.0
5 TraesCS5D01G178000 chr5B 90.888 845 45 8 2025 2864 315833106 315832289 0.000000e+00 1105.0
6 TraesCS5D01G178000 chr5B 94.635 466 19 3 2 462 315835655 315835191 0.000000e+00 717.0
7 TraesCS5D01G178000 chr5B 95.098 102 1 4 473 571 315835210 315835110 1.060000e-34 158.0
8 TraesCS5D01G178000 chr7D 84.000 350 41 11 2519 2864 596112225 596112563 3.560000e-84 322.0
9 TraesCS5D01G178000 chr7D 89.831 59 3 3 727 783 378168993 378169050 3.960000e-09 73.1
10 TraesCS5D01G178000 chr2B 84.314 255 25 8 2611 2864 564431682 564431442 4.770000e-58 235.0
11 TraesCS5D01G178000 chr2B 88.660 97 11 0 2517 2613 172875385 172875481 5.010000e-23 119.0
12 TraesCS5D01G178000 chr2B 91.228 57 3 2 730 786 416184019 416184073 3.060000e-10 76.8
13 TraesCS5D01G178000 chr4D 86.667 120 14 2 2625 2744 507667084 507667201 6.440000e-27 132.0
14 TraesCS5D01G178000 chr1A 93.878 49 1 2 730 777 567927197 567927150 3.960000e-09 73.1
15 TraesCS5D01G178000 chr2D 83.333 78 11 2 2786 2862 624029156 624029232 1.420000e-08 71.3
16 TraesCS5D01G178000 chrUn 92.000 50 2 2 730 778 10263823 10263775 5.120000e-08 69.4
17 TraesCS5D01G178000 chr3D 100.000 36 0 0 2826 2861 26610223 26610188 1.840000e-07 67.6
18 TraesCS5D01G178000 chr7B 89.091 55 2 4 730 782 607617969 607618021 6.630000e-07 65.8
19 TraesCS5D01G178000 chr7A 87.931 58 3 4 730 786 425783249 425783303 6.630000e-07 65.8
20 TraesCS5D01G178000 chr1D 90.000 50 3 2 730 778 419720520 419720472 2.380000e-06 63.9


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 TraesCS5D01G178000 chr5D 277631185 277634049 2864 True 5291.000000 5291 100.000000 1 2865 1 chr5D.!!$R1 2864
1 TraesCS5D01G178000 chr5A 366759842 366762562 2720 True 1094.333333 2612 93.151667 2 2865 3 chr5A.!!$R1 2863
2 TraesCS5D01G178000 chr5B 315832289 315835655 3366 True 1021.500000 2106 93.401250 2 2864 4 chr5B.!!$R1 2862

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
727 937 0.597568 GCTTGTATGGCTGTGTGCAA 59.402 50.0 0.0 0.0 45.15 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 3068 0.032267 GCCTACAGCTACCGGATCAC 59.968 60.0 9.46 0.0 38.99 3.06 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
39 40 6.344500 CACTGATGATTACTTAAGCACCTCT 58.656 40.000 1.29 0.00 34.11 3.69
48 49 4.093011 ACTTAAGCACCTCTCTCATGACT 58.907 43.478 1.29 0.00 0.00 3.41
231 237 2.550175 TCCTGGATCTGTTGGACATGA 58.450 47.619 0.00 0.00 0.00 3.07
236 242 4.264253 TGGATCTGTTGGACATGATGAAC 58.736 43.478 0.00 0.00 0.00 3.18
363 369 4.202245 GGAATCCCCCAGCTTTTAAAAC 57.798 45.455 0.00 0.00 0.00 2.43
425 434 2.526432 AGGAAAAGCTGTCGAGGACTA 58.474 47.619 0.00 0.00 33.15 2.59
548 557 7.592938 TCAATTGAAATCGAAGTAGCACAAAT 58.407 30.769 5.45 0.00 0.00 2.32
550 559 9.340695 CAATTGAAATCGAAGTAGCACAAATTA 57.659 29.630 0.00 0.00 0.00 1.40
551 560 9.559958 AATTGAAATCGAAGTAGCACAAATTAG 57.440 29.630 0.00 0.00 0.00 1.73
616 821 2.813754 GAGTCATGGCAGTTTTAGCACA 59.186 45.455 0.00 0.00 0.00 4.57
629 834 5.297776 AGTTTTAGCACATAGATGGCATGAC 59.702 40.000 3.81 0.00 0.00 3.06
727 937 0.597568 GCTTGTATGGCTGTGTGCAA 59.402 50.000 0.00 0.00 45.15 4.08
728 938 1.666888 GCTTGTATGGCTGTGTGCAAC 60.667 52.381 0.00 0.00 45.15 4.17
729 939 1.881973 CTTGTATGGCTGTGTGCAACT 59.118 47.619 0.00 0.00 45.15 3.16
730 940 1.237533 TGTATGGCTGTGTGCAACTG 58.762 50.000 0.00 0.00 45.15 3.16
731 941 1.238439 GTATGGCTGTGTGCAACTGT 58.762 50.000 0.00 0.00 45.15 3.55
732 942 1.069022 GTATGGCTGTGTGCAACTGTG 60.069 52.381 0.00 0.00 45.15 3.66
890 1102 4.673061 CGAAGATCACGAAGCTAGACAGTT 60.673 45.833 6.49 0.00 0.00 3.16
1000 1212 2.350868 CGCATACCCAGAGAGTCGTATG 60.351 54.545 9.51 9.51 40.55 2.39
1289 1507 3.691342 CCAAGACCGGCCTCGTCA 61.691 66.667 18.86 0.00 33.95 4.35
1337 1555 0.322906 GACCAAGGCCAGGAAGAAGG 60.323 60.000 20.01 4.95 0.00 3.46
1345 1563 0.405585 CCAGGAAGAAGGGCAAGGAA 59.594 55.000 0.00 0.00 0.00 3.36
1355 1573 2.980233 GCAAGGAACCGTGCTGCT 60.980 61.111 20.72 0.00 45.43 4.24
1414 1632 2.526873 AACCTGCTCCCTGACGGT 60.527 61.111 0.00 0.00 0.00 4.83
1458 1676 4.615815 GCCATCGCCCGCTGAGAT 62.616 66.667 0.00 0.00 33.29 2.75
1470 1688 4.838152 TGAGATTGAGGCCGCCGC 62.838 66.667 6.14 6.14 0.00 6.53
1551 1772 4.910585 GATGATCGCCGGCCGGTT 62.911 66.667 42.53 28.53 37.59 4.44
1592 1813 4.423209 GGGTGGAGGAGGAGGGCT 62.423 72.222 0.00 0.00 0.00 5.19
1612 1833 0.093705 GTTGCAACGAGATCGACAGC 59.906 55.000 14.90 9.78 43.02 4.40
1681 1902 2.650116 GCAGGCGTCCTTCAGGAGA 61.650 63.158 0.00 0.00 46.49 3.71
1734 1955 7.951530 AGGAACTTGTTTTTCTTAATGCATG 57.048 32.000 0.00 0.00 27.25 4.06
1735 1956 7.725251 AGGAACTTGTTTTTCTTAATGCATGA 58.275 30.769 0.00 0.00 27.25 3.07
1799 2023 7.693952 TGTCAAAAACTTAGTAAGAGTTGCTG 58.306 34.615 16.89 10.43 37.41 4.41
1800 2024 6.633234 GTCAAAAACTTAGTAAGAGTTGCTGC 59.367 38.462 16.89 0.00 37.41 5.25
1808 2032 4.508662 AGTAAGAGTTGCTGCCTTGATAC 58.491 43.478 0.00 0.00 0.00 2.24
1851 2075 4.558226 TCAGTGCTTATGGATGTCACTT 57.442 40.909 0.00 0.00 36.01 3.16
1855 2079 5.521735 CAGTGCTTATGGATGTCACTTAGTC 59.478 44.000 0.00 0.00 36.01 2.59
1856 2080 4.811557 GTGCTTATGGATGTCACTTAGTCC 59.188 45.833 0.00 0.00 0.00 3.85
1857 2081 4.716784 TGCTTATGGATGTCACTTAGTCCT 59.283 41.667 0.00 0.00 0.00 3.85
1858 2082 5.189736 TGCTTATGGATGTCACTTAGTCCTT 59.810 40.000 0.00 0.00 0.00 3.36
1859 2083 6.382859 TGCTTATGGATGTCACTTAGTCCTTA 59.617 38.462 0.00 0.00 0.00 2.69
1981 2210 1.486726 GCAGTACCTAGCCCACAATCT 59.513 52.381 0.00 0.00 0.00 2.40
1989 2218 5.086621 ACCTAGCCCACAATCTTTTTCAAT 58.913 37.500 0.00 0.00 0.00 2.57
2013 2242 8.593945 ATGTTTCAACATTATAATCCCACAGT 57.406 30.769 0.00 0.00 46.95 3.55
2014 2243 9.693739 ATGTTTCAACATTATAATCCCACAGTA 57.306 29.630 0.00 0.00 46.95 2.74
2015 2244 8.952278 TGTTTCAACATTATAATCCCACAGTAC 58.048 33.333 0.00 0.00 33.17 2.73
2016 2245 7.780008 TTCAACATTATAATCCCACAGTACG 57.220 36.000 0.00 0.00 0.00 3.67
2018 2247 8.009622 TCAACATTATAATCCCACAGTACGTA 57.990 34.615 0.00 0.00 0.00 3.57
2020 2249 6.752168 ACATTATAATCCCACAGTACGTACC 58.248 40.000 21.80 4.66 0.00 3.34
2021 2250 6.552350 ACATTATAATCCCACAGTACGTACCT 59.448 38.462 21.80 6.95 0.00 3.08
2022 2251 7.725397 ACATTATAATCCCACAGTACGTACCTA 59.275 37.037 21.80 2.28 0.00 3.08
2023 2252 8.746530 CATTATAATCCCACAGTACGTACCTAT 58.253 37.037 21.80 5.15 0.00 2.57
2027 2624 6.645790 ATCCCACAGTACGTACCTATTTAG 57.354 41.667 21.80 5.86 0.00 1.85
2038 2635 4.738740 CGTACCTATTTAGTCCTGCTTTCG 59.261 45.833 0.00 0.00 0.00 3.46
2110 2712 0.251073 GTACCTTTTGAGGCCGCCTA 59.749 55.000 13.29 0.00 31.76 3.93
2135 2750 4.410492 AGTTCACAAATCATTCGACTGC 57.590 40.909 0.00 0.00 0.00 4.40
2165 2780 4.384940 TGTCGATTTCACCACAAAGATCA 58.615 39.130 0.00 0.00 0.00 2.92
2183 2801 5.363101 AGATCAATGCACACATAGTACCTG 58.637 41.667 0.00 0.00 34.62 4.00
2190 2808 5.612351 TGCACACATAGTACCTGTAAAACA 58.388 37.500 0.00 0.00 0.00 2.83
2294 2912 1.066430 TCCTGTCTTGGCGTCCATAAC 60.066 52.381 0.00 2.77 31.53 1.89
2352 2971 3.343617 TCGAAAGGGGCATAAACTTCAG 58.656 45.455 0.00 0.00 0.00 3.02
2430 3057 1.678728 CCCAGTTCAGTGTGTGTGTGT 60.679 52.381 0.00 0.00 0.00 3.72
2431 3058 1.398041 CCAGTTCAGTGTGTGTGTGTG 59.602 52.381 0.00 0.00 0.00 3.82
2432 3059 2.076100 CAGTTCAGTGTGTGTGTGTGT 58.924 47.619 0.00 0.00 0.00 3.72
2433 3060 2.076100 AGTTCAGTGTGTGTGTGTGTG 58.924 47.619 0.00 0.00 0.00 3.82
2434 3061 1.804151 GTTCAGTGTGTGTGTGTGTGT 59.196 47.619 0.00 0.00 0.00 3.72
2435 3062 1.437625 TCAGTGTGTGTGTGTGTGTG 58.562 50.000 0.00 0.00 0.00 3.82
2436 3063 1.155889 CAGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
2437 3064 1.136000 CAGTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
2438 3065 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2439 3066 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2440 3067 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2441 3068 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2442 3069 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2443 3070 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2449 3076 0.531753 TGTGTGTGTGTGTGATCCGG 60.532 55.000 0.00 0.00 0.00 5.14
2456 3083 0.246635 GTGTGTGATCCGGTAGCTGT 59.753 55.000 0.00 0.00 0.00 4.40
2460 3087 0.032267 GTGATCCGGTAGCTGTAGGC 59.968 60.000 0.00 0.00 42.19 3.93
2504 3131 3.658725 TCTAATCCTGGGAAGCTAGCTT 58.341 45.455 29.71 29.71 39.23 3.74
2563 3190 4.555116 GCTACTTAGCGGTAGATCTCACAC 60.555 50.000 0.00 0.00 40.98 3.82
2598 3225 0.826715 AGATGCGTGTGAGCTATGGT 59.173 50.000 0.00 0.00 38.13 3.55
2603 3230 0.532573 CGTGTGAGCTATGGTCCACT 59.467 55.000 0.00 0.00 32.96 4.00
2645 3272 4.213270 CACCTTTTACGCATTTCAGAGTCA 59.787 41.667 0.00 0.00 0.00 3.41
2659 3286 1.344438 AGAGTCAAATCACTGTGCGGA 59.656 47.619 2.12 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.312895 CCTCTAGCTAGCTAAGTCATGAGA 58.687 45.833 26.29 18.53 0.00 3.27
48 49 0.477204 TCCCGCCTCTAGCTAGCTAA 59.523 55.000 24.20 14.31 40.39 3.09
231 237 6.294397 GGACAAAAGAAGCTTCTCATGTTCAT 60.294 38.462 31.49 18.49 36.65 2.57
236 242 3.192212 GGGGACAAAAGAAGCTTCTCATG 59.808 47.826 28.58 27.79 36.28 3.07
425 434 2.573915 GTCATCTTTCCCACTCTCCCTT 59.426 50.000 0.00 0.00 0.00 3.95
471 480 8.400947 GCATAGCAAGAAAAATCTTCTGTCATA 58.599 33.333 0.00 0.00 0.00 2.15
472 481 7.094075 TGCATAGCAAGAAAAATCTTCTGTCAT 60.094 33.333 0.00 0.00 34.76 3.06
473 482 6.207221 TGCATAGCAAGAAAAATCTTCTGTCA 59.793 34.615 0.00 0.00 34.76 3.58
474 483 6.615088 TGCATAGCAAGAAAAATCTTCTGTC 58.385 36.000 0.00 0.00 34.76 3.51
475 484 6.579666 TGCATAGCAAGAAAAATCTTCTGT 57.420 33.333 0.00 0.00 34.76 3.41
476 485 6.475727 CCATGCATAGCAAGAAAAATCTTCTG 59.524 38.462 0.00 0.00 43.62 3.02
477 486 6.570692 CCATGCATAGCAAGAAAAATCTTCT 58.429 36.000 0.00 0.00 43.62 2.85
478 487 5.233689 GCCATGCATAGCAAGAAAAATCTTC 59.766 40.000 12.50 0.00 43.62 2.87
479 488 5.114081 GCCATGCATAGCAAGAAAAATCTT 58.886 37.500 12.50 0.00 43.62 2.40
480 489 4.160814 TGCCATGCATAGCAAGAAAAATCT 59.839 37.500 17.73 0.00 43.62 2.40
481 490 4.435425 TGCCATGCATAGCAAGAAAAATC 58.565 39.130 17.73 0.00 43.62 2.17
482 491 4.475051 TGCCATGCATAGCAAGAAAAAT 57.525 36.364 17.73 0.00 43.62 1.82
483 492 3.957591 TGCCATGCATAGCAAGAAAAA 57.042 38.095 17.73 0.00 43.62 1.94
629 834 2.815503 TGAGCATCTGTTTCACATGGTG 59.184 45.455 0.00 0.00 34.92 4.17
681 886 8.178964 TGCGTGTCAATAATGTAGGTAAATTTC 58.821 33.333 0.00 0.00 0.00 2.17
683 888 7.618502 TGCGTGTCAATAATGTAGGTAAATT 57.381 32.000 0.00 0.00 0.00 1.82
685 890 5.064198 GCTGCGTGTCAATAATGTAGGTAAA 59.936 40.000 0.00 0.00 0.00 2.01
689 899 3.198068 AGCTGCGTGTCAATAATGTAGG 58.802 45.455 0.00 0.00 0.00 3.18
692 902 2.813754 ACAAGCTGCGTGTCAATAATGT 59.186 40.909 15.41 0.00 0.00 2.71
734 944 1.445095 GGCCTCTGCATCGAGTGAT 59.555 57.895 0.00 0.00 40.13 3.06
890 1102 9.844257 ATTTTCATCAAACATTTTCCCACTTAA 57.156 25.926 0.00 0.00 0.00 1.85
1067 1279 4.694760 TGAGTAGGTGATCCATGGAATG 57.305 45.455 20.67 0.00 46.21 2.67
1068 1280 4.474651 TGTTGAGTAGGTGATCCATGGAAT 59.525 41.667 20.67 7.49 35.89 3.01
1069 1281 3.843619 TGTTGAGTAGGTGATCCATGGAA 59.156 43.478 20.67 0.00 35.89 3.53
1124 1342 2.047179 GAGGTTGTCGGTGGAGGC 60.047 66.667 0.00 0.00 0.00 4.70
1258 1476 1.004560 CTTGGCGTTGAGGAGAGCA 60.005 57.895 0.00 0.00 0.00 4.26
1260 1478 0.390472 GGTCTTGGCGTTGAGGAGAG 60.390 60.000 0.00 0.00 0.00 3.20
1289 1507 0.324285 CTTCTCCTCAGCTTGCTGGT 59.676 55.000 20.62 0.00 0.00 4.00
1337 1555 4.043200 GCAGCACGGTTCCTTGCC 62.043 66.667 15.04 0.00 39.75 4.52
1414 1632 4.980805 GACCACGAAGGCACGGCA 62.981 66.667 8.70 0.00 43.14 5.69
1451 1669 2.899339 GGCGGCCTCAATCTCAGC 60.899 66.667 12.87 0.00 0.00 4.26
1476 1694 1.502163 CGGGTCGTAGTAGTAGGCCG 61.502 65.000 0.00 3.11 0.00 6.13
1551 1772 3.706373 GCTCGGGCCACTCCAGAA 61.706 66.667 4.39 0.00 38.59 3.02
1592 1813 1.418373 CTGTCGATCTCGTTGCAACA 58.582 50.000 28.01 14.60 40.80 3.33
1792 2016 2.233922 AGTACGTATCAAGGCAGCAACT 59.766 45.455 0.00 0.00 0.00 3.16
1799 2023 4.110482 CCAACTACAGTACGTATCAAGGC 58.890 47.826 0.00 0.00 0.00 4.35
1800 2024 4.441079 CCCCAACTACAGTACGTATCAAGG 60.441 50.000 0.00 0.00 0.00 3.61
1808 2032 0.390735 GCCACCCCAACTACAGTACG 60.391 60.000 0.00 0.00 0.00 3.67
1989 2218 8.952278 GTACTGTGGGATTATAATGTTGAAACA 58.048 33.333 1.78 0.00 44.06 2.83
2002 2231 7.779798 ACTAAATAGGTACGTACTGTGGGATTA 59.220 37.037 24.07 13.10 0.00 1.75
2005 2234 5.509498 ACTAAATAGGTACGTACTGTGGGA 58.491 41.667 24.07 6.67 0.00 4.37
2006 2235 5.221126 GGACTAAATAGGTACGTACTGTGGG 60.221 48.000 24.07 11.46 0.00 4.61
2007 2236 5.591877 AGGACTAAATAGGTACGTACTGTGG 59.408 44.000 24.07 5.65 0.00 4.17
2008 2237 6.493116 CAGGACTAAATAGGTACGTACTGTG 58.507 44.000 24.07 10.60 33.05 3.66
2009 2238 5.067023 GCAGGACTAAATAGGTACGTACTGT 59.933 44.000 24.07 14.61 38.49 3.55
2010 2239 5.298777 AGCAGGACTAAATAGGTACGTACTG 59.701 44.000 24.07 11.41 39.09 2.74
2011 2240 5.444176 AGCAGGACTAAATAGGTACGTACT 58.556 41.667 24.07 13.10 0.00 2.73
2012 2241 5.764487 AGCAGGACTAAATAGGTACGTAC 57.236 43.478 17.56 17.56 0.00 3.67
2013 2242 6.458751 CGAAAGCAGGACTAAATAGGTACGTA 60.459 42.308 0.00 0.00 0.00 3.57
2014 2243 5.658468 GAAAGCAGGACTAAATAGGTACGT 58.342 41.667 0.00 0.00 0.00 3.57
2015 2244 4.738740 CGAAAGCAGGACTAAATAGGTACG 59.261 45.833 0.00 0.00 0.00 3.67
2016 2245 5.048507 CCGAAAGCAGGACTAAATAGGTAC 58.951 45.833 0.00 0.00 0.00 3.34
2018 2247 3.773119 TCCGAAAGCAGGACTAAATAGGT 59.227 43.478 0.00 0.00 31.86 3.08
2020 2249 6.238484 CCAAATCCGAAAGCAGGACTAAATAG 60.238 42.308 0.00 0.00 41.10 1.73
2021 2250 5.588648 CCAAATCCGAAAGCAGGACTAAATA 59.411 40.000 0.00 0.00 41.10 1.40
2022 2251 4.399303 CCAAATCCGAAAGCAGGACTAAAT 59.601 41.667 0.00 0.00 41.10 1.40
2023 2252 3.756434 CCAAATCCGAAAGCAGGACTAAA 59.244 43.478 0.00 0.00 41.10 1.85
2027 2624 0.171231 GCCAAATCCGAAAGCAGGAC 59.829 55.000 0.00 0.00 41.10 3.85
2038 2635 3.339253 AAAAGATTGCAGGCCAAATCC 57.661 42.857 17.51 5.29 36.92 3.01
2070 2668 2.807967 CAAAAGACGCAGAATGTCTCCA 59.192 45.455 0.00 0.00 45.62 3.86
2110 2712 6.662616 CAGTCGAATGATTTGTGAACTTTCT 58.337 36.000 7.15 0.00 0.00 2.52
2135 2750 2.017049 GGTGAAATCGACAGGGAATGG 58.983 52.381 0.00 0.00 0.00 3.16
2165 2780 6.712998 TGTTTTACAGGTACTATGTGTGCATT 59.287 34.615 12.65 0.00 36.02 3.56
2294 2912 4.796830 CACCTGATCAATTTTCTTGATGCG 59.203 41.667 5.25 0.00 39.08 4.73
2295 2913 5.957798 TCACCTGATCAATTTTCTTGATGC 58.042 37.500 5.25 0.00 39.08 3.91
2320 2938 1.419922 CCTTTCGAACATCGTGGCG 59.580 57.895 0.00 0.00 41.35 5.69
2352 2971 5.163195 ACACTGGATGGGGATGATTTACTAC 60.163 44.000 0.00 0.00 0.00 2.73
2430 3057 0.531753 CCGGATCACACACACACACA 60.532 55.000 0.00 0.00 0.00 3.72
2431 3058 0.531974 ACCGGATCACACACACACAC 60.532 55.000 9.46 0.00 0.00 3.82
2432 3059 1.000394 CTACCGGATCACACACACACA 60.000 52.381 9.46 0.00 0.00 3.72
2433 3060 1.710013 CTACCGGATCACACACACAC 58.290 55.000 9.46 0.00 0.00 3.82
2434 3061 0.037697 GCTACCGGATCACACACACA 60.038 55.000 9.46 0.00 0.00 3.72
2435 3062 0.246635 AGCTACCGGATCACACACAC 59.753 55.000 9.46 0.00 0.00 3.82
2436 3063 0.246360 CAGCTACCGGATCACACACA 59.754 55.000 9.46 0.00 0.00 3.72
2437 3064 0.246635 ACAGCTACCGGATCACACAC 59.753 55.000 9.46 0.00 0.00 3.82
2438 3065 1.749063 CTACAGCTACCGGATCACACA 59.251 52.381 9.46 0.00 0.00 3.72
2439 3066 1.067212 CCTACAGCTACCGGATCACAC 59.933 57.143 9.46 0.00 0.00 3.82
2440 3067 1.399714 CCTACAGCTACCGGATCACA 58.600 55.000 9.46 0.00 0.00 3.58
2441 3068 0.032267 GCCTACAGCTACCGGATCAC 59.968 60.000 9.46 0.00 38.99 3.06
2442 3069 2.426651 GCCTACAGCTACCGGATCA 58.573 57.895 9.46 0.00 38.99 2.92
2456 3083 4.969359 AGCAGAGGAAAATAACCTAGCCTA 59.031 41.667 0.00 0.00 38.53 3.93
2460 3087 7.278875 AGATGAAGCAGAGGAAAATAACCTAG 58.721 38.462 0.00 0.00 37.93 3.02
2467 3094 6.771749 CAGGATTAGATGAAGCAGAGGAAAAT 59.228 38.462 0.00 0.00 0.00 1.82
2509 3136 7.807907 CCGCTTAAAATGACTTTGTGAAACTAT 59.192 33.333 0.00 0.00 38.04 2.12
2563 3190 4.449068 ACGCATCTCAGAAAATATAAGCGG 59.551 41.667 0.00 0.00 44.94 5.52
2598 3225 3.535280 TGCGCAATACATCTAAGTGGA 57.465 42.857 8.16 0.00 0.00 4.02
2603 3230 4.881273 AGGTGAAATGCGCAATACATCTAA 59.119 37.500 17.11 0.00 0.00 2.10
2645 3272 2.420129 GGTAGGATCCGCACAGTGATTT 60.420 50.000 17.96 0.00 0.00 2.17
2659 3286 7.824779 GTGTTCTTTTTCTGACTATGGTAGGAT 59.175 37.037 0.00 0.00 0.00 3.24
2828 3462 4.943705 TCTTGATGCCAGGAGTTCAAATAC 59.056 41.667 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.