Multiple sequence alignment - TraesCS1B01G022900

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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 TraesCS1B01G022900 chr1B 100.000 3597 0 0 1 3597 10206763 10203167 0.000000e+00 6643
1 TraesCS1B01G022900 chr1D 92.025 3586 202 42 65 3597 7950199 7946645 0.000000e+00 4961
2 TraesCS1B01G022900 chr1D 87.857 280 27 4 702 980 42657848 42657575 4.480000e-84 322
3 TraesCS1B01G022900 chr1D 88.889 270 16 7 152 413 42658443 42658180 1.610000e-83 320
4 TraesCS1B01G022900 chr1A 91.802 3574 218 29 62 3597 9644953 9641417 0.000000e+00 4907
5 TraesCS1B01G022900 chr3A 82.566 608 92 10 393 995 740265724 740265126 1.140000e-144 523
6 TraesCS1B01G022900 chr3B 88.406 414 36 6 573 980 13893699 13893292 4.170000e-134 488
7 TraesCS1B01G022900 chr3B 90.253 277 21 1 152 422 13894574 13894298 1.230000e-94 357
8 TraesCS1B01G022900 chr2D 90.217 276 21 1 153 422 409388905 409389180 4.420000e-94 355
9 TraesCS1B01G022900 chr2D 86.786 280 30 4 702 980 409389515 409389788 4.510000e-79 305
10 TraesCS1B01G022900 chr2D 91.111 135 9 1 430 561 582684528 582684394 2.850000e-41 180
11 TraesCS1B01G022900 chr7D 89.818 275 22 1 154 422 8126197 8125923 7.390000e-92 348
12 TraesCS1B01G022900 chr7D 89.170 277 24 2 152 422 459489076 459489352 1.240000e-89 340
13 TraesCS1B01G022900 chr7D 88.809 277 25 1 152 422 229527642 229527366 5.750000e-88 335
14 TraesCS1B01G022900 chr7D 88.571 280 25 5 702 980 459489687 459489960 2.070000e-87 333
15 TraesCS1B01G022900 chr7D 88.192 271 26 1 152 416 487042915 487042645 5.800000e-83 318
16 TraesCS1B01G022900 chr7D 87.500 280 26 5 702 980 229527031 229526760 7.500000e-82 315
17 TraesCS1B01G022900 chr7D 91.111 135 9 1 430 561 8125554 8125420 2.850000e-41 180
18 TraesCS1B01G022900 chr5D 89.179 268 23 2 153 414 426898207 426898474 2.680000e-86 329
19 TraesCS1B01G022900 chr4D 87.455 279 28 4 702 979 411280644 411280372 7.500000e-82 315


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 TraesCS1B01G022900 chr1B 10203167 10206763 3596 True 6643.0 6643 100.0000 1 3597 1 chr1B.!!$R1 3596
1 TraesCS1B01G022900 chr1D 7946645 7950199 3554 True 4961.0 4961 92.0250 65 3597 1 chr1D.!!$R1 3532
2 TraesCS1B01G022900 chr1D 42657575 42658443 868 True 321.0 322 88.3730 152 980 2 chr1D.!!$R2 828
3 TraesCS1B01G022900 chr1A 9641417 9644953 3536 True 4907.0 4907 91.8020 62 3597 1 chr1A.!!$R1 3535
4 TraesCS1B01G022900 chr3A 740265126 740265724 598 True 523.0 523 82.5660 393 995 1 chr3A.!!$R1 602
5 TraesCS1B01G022900 chr3B 13893292 13894574 1282 True 422.5 488 89.3295 152 980 2 chr3B.!!$R1 828
6 TraesCS1B01G022900 chr2D 409388905 409389788 883 False 330.0 355 88.5015 153 980 2 chr2D.!!$F1 827
7 TraesCS1B01G022900 chr7D 459489076 459489960 884 False 336.5 340 88.8705 152 980 2 chr7D.!!$F1 828
8 TraesCS1B01G022900 chr7D 229526760 229527642 882 True 325.0 335 88.1545 152 980 2 chr7D.!!$R3 828
9 TraesCS1B01G022900 chr7D 8125420 8126197 777 True 264.0 348 90.4645 154 561 2 chr7D.!!$R2 407

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
797 1700 0.669318 TGATTTCCGACACGAGGCAC 60.669 55.0 0.0 0.0 0.00 5.01 F
2111 3035 0.034767 TTCTGGGGATGCTTCTGCTG 60.035 55.0 0.0 0.0 40.48 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 3187 0.398318 GACTGCCTTCCTTCACACCT 59.602 55.0 0.0 0.0 0.00 4.0 R
3471 4411 0.250467 AAGCAATGGTCACTCGCTGT 60.250 50.0 0.0 0.0 32.14 4.4 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
19 20 2.736144 GGAGTCCGTGTATGTGTTGA 57.264 50.000 0.00 0.00 0.00 3.18
20 21 3.034721 GGAGTCCGTGTATGTGTTGAA 57.965 47.619 0.00 0.00 0.00 2.69
21 22 3.395639 GGAGTCCGTGTATGTGTTGAAA 58.604 45.455 0.00 0.00 0.00 2.69
22 23 4.000988 GGAGTCCGTGTATGTGTTGAAAT 58.999 43.478 0.00 0.00 0.00 2.17
23 24 5.172934 GGAGTCCGTGTATGTGTTGAAATA 58.827 41.667 0.00 0.00 0.00 1.40
24 25 5.640357 GGAGTCCGTGTATGTGTTGAAATAA 59.360 40.000 0.00 0.00 0.00 1.40
25 26 6.148150 GGAGTCCGTGTATGTGTTGAAATAAA 59.852 38.462 0.00 0.00 0.00 1.40
26 27 7.129109 AGTCCGTGTATGTGTTGAAATAAAG 57.871 36.000 0.00 0.00 0.00 1.85
27 28 6.708949 AGTCCGTGTATGTGTTGAAATAAAGT 59.291 34.615 0.00 0.00 0.00 2.66
28 29 7.227910 AGTCCGTGTATGTGTTGAAATAAAGTT 59.772 33.333 0.00 0.00 0.00 2.66
29 30 7.858879 GTCCGTGTATGTGTTGAAATAAAGTTT 59.141 33.333 0.00 0.00 0.00 2.66
30 31 7.858382 TCCGTGTATGTGTTGAAATAAAGTTTG 59.142 33.333 0.00 0.00 0.00 2.93
31 32 7.858382 CCGTGTATGTGTTGAAATAAAGTTTGA 59.142 33.333 0.00 0.00 0.00 2.69
32 33 9.227490 CGTGTATGTGTTGAAATAAAGTTTGAA 57.773 29.630 0.00 0.00 0.00 2.69
120 121 1.128692 GATTGACCAAAACGAGCTCGG 59.871 52.381 36.93 22.27 44.95 4.63
121 122 1.503818 TTGACCAAAACGAGCTCGGC 61.504 55.000 36.93 17.87 44.95 5.54
144 145 2.068213 CCCCCGTATCGTTCCCCTT 61.068 63.158 0.00 0.00 0.00 3.95
309 332 4.545076 CATCCCCATGCCCCCACC 62.545 72.222 0.00 0.00 0.00 4.61
382 413 1.739562 GCTACTGCTGCTTCGTGCT 60.740 57.895 0.00 0.00 43.37 4.40
469 1105 2.746362 CAGTCTCAGGCCTGATGAAAAC 59.254 50.000 35.11 24.58 39.13 2.43
552 1454 1.227380 CGCCAGCTCTACCATCCAC 60.227 63.158 0.00 0.00 0.00 4.02
567 1469 4.971282 ACCATCCACTCTCCTATGAATCAA 59.029 41.667 0.00 0.00 0.00 2.57
582 1484 5.982890 TGAATCAAAACTTCCCAATCCTC 57.017 39.130 0.00 0.00 0.00 3.71
628 1530 3.956199 AGAGCATTGGGGATGTTATGTTG 59.044 43.478 0.00 0.00 38.07 3.33
629 1531 2.431782 AGCATTGGGGATGTTATGTTGC 59.568 45.455 0.00 0.00 38.07 4.17
649 1551 3.005554 GCTGCTGCATCTTCTTCAGTTA 58.994 45.455 11.11 0.00 39.41 2.24
661 1563 9.273016 CATCTTCTTCAGTTAAAAGAGGTACAA 57.727 33.333 0.00 0.00 34.42 2.41
666 1568 4.661709 TCAGTTAAAAGAGGTACAAGGGGT 59.338 41.667 0.00 0.00 0.00 4.95
700 1602 8.890718 CCATCTGTTTAGGCATATATCATCAAG 58.109 37.037 0.00 0.00 0.00 3.02
725 1627 8.850156 AGAGCAAATGAAAGTAGTGTGTTTAAT 58.150 29.630 0.00 0.00 0.00 1.40
766 1668 4.475381 TCCAACACCTAGCCCAATATTACA 59.525 41.667 0.00 0.00 0.00 2.41
797 1700 0.669318 TGATTTCCGACACGAGGCAC 60.669 55.000 0.00 0.00 0.00 5.01
870 1773 5.185056 AGTTTGTTTGCTGGTACTGACTTTT 59.815 36.000 0.00 0.00 0.00 2.27
901 1804 1.483415 CCATTTGGGGATTCTTGCAGG 59.517 52.381 0.00 0.00 0.00 4.85
910 1813 3.055094 GGGATTCTTGCAGGACTTGAGTA 60.055 47.826 0.00 0.00 0.00 2.59
911 1814 3.935828 GGATTCTTGCAGGACTTGAGTAC 59.064 47.826 0.00 0.00 0.00 2.73
912 1815 4.563580 GGATTCTTGCAGGACTTGAGTACA 60.564 45.833 0.00 0.00 0.00 2.90
913 1816 3.667497 TCTTGCAGGACTTGAGTACAG 57.333 47.619 0.00 0.00 0.00 2.74
1331 2237 2.121948 TGAGGTGATGAAGGATGGGAG 58.878 52.381 0.00 0.00 0.00 4.30
1487 2393 1.004044 AGAGACCTGCCTGATGTTTGG 59.996 52.381 0.00 0.00 0.00 3.28
1501 2407 0.100503 GTTTGGTGCACTTGCGTTCT 59.899 50.000 17.98 0.00 45.83 3.01
1536 2442 8.791355 ACGAGTTTATGTTTTTGATGGTTAAC 57.209 30.769 0.00 0.00 0.00 2.01
1567 2491 8.865590 TTCTTTTTAGCAACCTGAATGTTAAC 57.134 30.769 0.00 0.00 0.00 2.01
1568 2492 8.232913 TCTTTTTAGCAACCTGAATGTTAACT 57.767 30.769 7.22 0.00 0.00 2.24
1570 2494 6.952773 TTTAGCAACCTGAATGTTAACTGT 57.047 33.333 7.22 0.00 0.00 3.55
1571 2495 4.836125 AGCAACCTGAATGTTAACTGTG 57.164 40.909 7.22 0.00 0.00 3.66
1572 2496 3.004734 AGCAACCTGAATGTTAACTGTGC 59.995 43.478 7.22 5.05 0.00 4.57
1573 2497 3.004734 GCAACCTGAATGTTAACTGTGCT 59.995 43.478 7.22 0.00 0.00 4.40
1574 2498 4.215399 GCAACCTGAATGTTAACTGTGCTA 59.785 41.667 7.22 0.00 0.00 3.49
1575 2499 5.106157 GCAACCTGAATGTTAACTGTGCTAT 60.106 40.000 7.22 0.00 0.00 2.97
1576 2500 6.546395 CAACCTGAATGTTAACTGTGCTATC 58.454 40.000 7.22 0.00 0.00 2.08
1577 2501 5.804639 ACCTGAATGTTAACTGTGCTATCA 58.195 37.500 7.22 0.88 0.00 2.15
1578 2502 6.237901 ACCTGAATGTTAACTGTGCTATCAA 58.762 36.000 7.22 0.00 0.00 2.57
1579 2503 6.714810 ACCTGAATGTTAACTGTGCTATCAAA 59.285 34.615 7.22 0.00 0.00 2.69
1580 2504 7.394359 ACCTGAATGTTAACTGTGCTATCAAAT 59.606 33.333 7.22 0.00 0.00 2.32
1581 2505 7.912250 CCTGAATGTTAACTGTGCTATCAAATC 59.088 37.037 7.22 0.00 0.00 2.17
1582 2506 8.334263 TGAATGTTAACTGTGCTATCAAATCA 57.666 30.769 7.22 0.00 0.00 2.57
1583 2507 8.791675 TGAATGTTAACTGTGCTATCAAATCAA 58.208 29.630 7.22 0.00 0.00 2.57
1584 2508 9.624697 GAATGTTAACTGTGCTATCAAATCAAA 57.375 29.630 7.22 0.00 0.00 2.69
1618 2542 7.429636 TTTTCTTAACTCAATAGACAACGGG 57.570 36.000 0.00 0.00 0.00 5.28
1677 2601 7.772292 TGCTATTGATCTTTTAGACATGCTTCT 59.228 33.333 0.00 0.00 0.00 2.85
1684 2608 8.804912 ATCTTTTAGACATGCTTCTTTCAGAT 57.195 30.769 0.00 0.00 0.00 2.90
1990 2914 0.798776 CAGATGTGAGTTTGCCGTCC 59.201 55.000 0.00 0.00 0.00 4.79
2111 3035 0.034767 TTCTGGGGATGCTTCTGCTG 60.035 55.000 0.00 0.00 40.48 4.41
2112 3036 1.203441 TCTGGGGATGCTTCTGCTGT 61.203 55.000 0.00 0.00 40.48 4.40
2154 3084 5.012328 GTCGGTAGACCATCAAAGAGAAT 57.988 43.478 0.00 0.00 41.41 2.40
2194 3124 4.080356 TCATTTAGAGATCAGGTTGGTGGG 60.080 45.833 0.00 0.00 0.00 4.61
2257 3187 1.073284 GAAACTGAACCAGGCCCAGTA 59.927 52.381 11.42 0.00 39.93 2.74
2360 3290 1.067295 ATCAAAGGACAGTGCCTCCA 58.933 50.000 6.58 0.00 37.26 3.86
2466 3396 1.609072 GGACTCTGTTCCAGCAAAACC 59.391 52.381 0.00 0.00 35.49 3.27
2545 3475 5.190528 TGATGAAAAGAAGTCTAGCAGGGAT 59.809 40.000 0.00 0.00 0.00 3.85
2550 3480 2.111384 GAAGTCTAGCAGGGATGTGGA 58.889 52.381 0.00 0.00 0.00 4.02
2551 3481 1.490574 AGTCTAGCAGGGATGTGGAC 58.509 55.000 0.00 0.00 0.00 4.02
2560 3490 1.714899 GGGATGTGGACGCAAATCCG 61.715 60.000 6.25 0.00 42.24 4.18
2628 3558 6.704493 TGTCACATTTCCAGTTAGTAGTGAAC 59.296 38.462 0.00 0.00 36.63 3.18
2648 3578 4.568152 ACTGCCTTGATTACAAACACAC 57.432 40.909 0.00 0.00 35.49 3.82
2727 3657 5.692115 TCCTGCTGTGAATCAAGGTAATA 57.308 39.130 0.00 0.00 0.00 0.98
2735 3665 9.294030 GCTGTGAATCAAGGTAATATCTTTTTG 57.706 33.333 0.00 0.00 0.00 2.44
2776 3706 2.801063 CATGCTTTCTTATGGTTGCGG 58.199 47.619 0.00 0.00 0.00 5.69
2789 3719 2.051518 TTGCGGTCATGGGGATTGC 61.052 57.895 0.00 0.00 0.00 3.56
2835 3765 2.346766 TTCTGTCATTGTGTGGTGCT 57.653 45.000 0.00 0.00 0.00 4.40
2847 3777 4.771903 TGTGTGGTGCTGTTAACTCTTTA 58.228 39.130 7.22 0.00 0.00 1.85
2922 3852 7.071069 TGATGCACTATCTTATTGGACATCT 57.929 36.000 0.00 0.00 36.71 2.90
2923 3853 7.157347 TGATGCACTATCTTATTGGACATCTC 58.843 38.462 0.00 0.00 36.71 2.75
2924 3854 6.484364 TGCACTATCTTATTGGACATCTCA 57.516 37.500 0.00 0.00 0.00 3.27
2925 3855 7.071069 TGCACTATCTTATTGGACATCTCAT 57.929 36.000 0.00 0.00 0.00 2.90
2932 3862 8.850007 ATCTTATTGGACATCTCATTCTCATG 57.150 34.615 0.00 0.00 0.00 3.07
2977 3909 4.202050 ACAGTAAAAGCCAGAGTTTGCTTG 60.202 41.667 0.00 0.00 46.58 4.01
3021 3953 3.909430 TCATGTTCGTCTGGTCAAGTAC 58.091 45.455 0.00 0.00 0.00 2.73
3154 4089 1.454201 GGCCTGTTTTGCCTCTACTC 58.546 55.000 0.00 0.00 45.70 2.59
3173 4108 4.421131 ACTCTAGGAGCCCCTAATATGTG 58.579 47.826 0.00 0.00 44.06 3.21
3198 4133 7.341769 TGAGGAGTGATTTTTCTTCCTTTTCAA 59.658 33.333 0.00 0.00 0.00 2.69
3252 4189 0.323629 CGCTTGGTCCCCTGTTTCTA 59.676 55.000 0.00 0.00 0.00 2.10
3266 4203 4.962995 CCTGTTTCTAATAGACTCCCTCCA 59.037 45.833 0.00 0.00 0.00 3.86
3359 4296 4.283212 CCTACTTTTGAATGAAGGCCCAAA 59.717 41.667 0.00 0.00 0.00 3.28
3471 4411 4.963318 AAGCCTAACTAGCATGCATCTA 57.037 40.909 21.98 2.40 0.00 1.98
3476 4416 2.145958 ACTAGCATGCATCTACAGCG 57.854 50.000 21.98 0.00 33.85 5.18
3508 4448 6.647334 TTGCTTGGACTTGATATTTTGACA 57.353 33.333 0.00 0.00 0.00 3.58
3568 4508 1.945580 TGGTATCTGTGCCAGGTACA 58.054 50.000 20.38 10.35 46.46 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.736144 TCAACACATACACGGACTCC 57.264 50.000 0.00 0.00 0.00 3.85
1 2 6.715344 TTATTTCAACACATACACGGACTC 57.285 37.500 0.00 0.00 0.00 3.36
2 3 6.708949 ACTTTATTTCAACACATACACGGACT 59.291 34.615 0.00 0.00 0.00 3.85
3 4 6.894828 ACTTTATTTCAACACATACACGGAC 58.105 36.000 0.00 0.00 0.00 4.79
4 5 7.499321 AACTTTATTTCAACACATACACGGA 57.501 32.000 0.00 0.00 0.00 4.69
5 6 7.858382 TCAAACTTTATTTCAACACATACACGG 59.142 33.333 0.00 0.00 0.00 4.94
6 7 8.775220 TCAAACTTTATTTCAACACATACACG 57.225 30.769 0.00 0.00 0.00 4.49
37 38 8.797674 TCTCCCCATATTTTTCTATACCCTTTT 58.202 33.333 0.00 0.00 0.00 2.27
38 39 8.358082 TCTCCCCATATTTTTCTATACCCTTT 57.642 34.615 0.00 0.00 0.00 3.11
39 40 7.964730 TCTCCCCATATTTTTCTATACCCTT 57.035 36.000 0.00 0.00 0.00 3.95
40 41 7.531269 GCATCTCCCCATATTTTTCTATACCCT 60.531 40.741 0.00 0.00 0.00 4.34
41 42 6.603599 GCATCTCCCCATATTTTTCTATACCC 59.396 42.308 0.00 0.00 0.00 3.69
42 43 6.603599 GGCATCTCCCCATATTTTTCTATACC 59.396 42.308 0.00 0.00 0.00 2.73
43 44 7.631717 GGCATCTCCCCATATTTTTCTATAC 57.368 40.000 0.00 0.00 0.00 1.47
59 60 0.105039 ATTTCGACGAGGGCATCTCC 59.895 55.000 0.00 0.00 39.30 3.71
60 61 1.492720 GATTTCGACGAGGGCATCTC 58.507 55.000 0.00 0.00 39.10 2.75
120 121 2.085042 GAACGATACGGGGGAGAGGC 62.085 65.000 0.00 0.00 0.00 4.70
121 122 1.461911 GGAACGATACGGGGGAGAGG 61.462 65.000 0.00 0.00 0.00 3.69
144 145 0.463654 GAGCGAGAGAGAGCTGGAGA 60.464 60.000 0.00 0.00 44.69 3.71
469 1105 7.015226 TGTGTTGTTTCAACTGAATCTACTG 57.985 36.000 12.66 0.00 33.66 2.74
552 1454 6.418101 TGGGAAGTTTTGATTCATAGGAGAG 58.582 40.000 0.00 0.00 0.00 3.20
628 1530 1.451067 ACTGAAGAAGATGCAGCAGC 58.549 50.000 4.07 1.15 42.57 5.25
629 1531 5.618056 TTTAACTGAAGAAGATGCAGCAG 57.382 39.130 4.07 0.00 33.03 4.24
649 1551 6.669631 CCATATTACCCCTTGTACCTCTTTT 58.330 40.000 0.00 0.00 0.00 2.27
661 1563 2.718456 ACAGATGGCCATATTACCCCT 58.282 47.619 20.84 6.62 0.00 4.79
666 1568 5.317600 TGCCTAAACAGATGGCCATATTA 57.682 39.130 20.84 14.17 45.56 0.98
690 1592 9.624373 ACTACTTTCATTTGCTCTTGATGATAT 57.376 29.630 0.00 0.00 30.59 1.63
698 1600 6.699575 AACACACTACTTTCATTTGCTCTT 57.300 33.333 0.00 0.00 0.00 2.85
700 1602 9.463443 AATTAAACACACTACTTTCATTTGCTC 57.537 29.630 0.00 0.00 0.00 4.26
725 1627 4.139162 TGGATGATTTCCCCCTTTTGAA 57.861 40.909 0.00 0.00 44.77 2.69
732 1634 1.007118 AGGTGTTGGATGATTTCCCCC 59.993 52.381 0.00 0.00 44.77 5.40
766 1668 4.215399 TGTCGGAAATCAGAAAAAGCGAAT 59.785 37.500 0.00 0.00 0.00 3.34
797 1700 2.614057 GCAGAAATATTCCACTGGTCGG 59.386 50.000 14.56 0.29 0.00 4.79
870 1773 6.439058 AGAATCCCCAAATGGACGAATTAAAA 59.561 34.615 0.00 0.00 37.20 1.52
872 1775 5.515106 AGAATCCCCAAATGGACGAATTAA 58.485 37.500 0.00 0.00 37.20 1.40
883 1786 2.043526 AGTCCTGCAAGAATCCCCAAAT 59.956 45.455 0.00 0.00 34.07 2.32
884 1787 1.428912 AGTCCTGCAAGAATCCCCAAA 59.571 47.619 0.00 0.00 34.07 3.28
886 1789 1.075601 AAGTCCTGCAAGAATCCCCA 58.924 50.000 0.00 0.00 34.07 4.96
901 1804 3.570550 ACAGGACTGTCTGTACTCAAGTC 59.429 47.826 7.85 2.57 45.18 3.01
911 1814 0.035458 GAACCCCACAGGACTGTCTG 59.965 60.000 7.85 6.72 42.83 3.51
912 1815 0.399949 TGAACCCCACAGGACTGTCT 60.400 55.000 7.85 0.00 42.83 3.41
913 1816 0.693049 ATGAACCCCACAGGACTGTC 59.307 55.000 1.21 0.00 42.83 3.51
1038 1944 2.665603 GAGAACGGCTCCAAGGCT 59.334 61.111 0.00 0.00 38.85 4.58
1098 2004 1.024271 GAGCTGGTTGCACTTTCACA 58.976 50.000 0.00 0.00 45.94 3.58
1134 2040 0.615331 TGGGACCAAGATGTGAGCTC 59.385 55.000 6.82 6.82 0.00 4.09
1501 2407 4.241590 ACATAAACTCGTACGTCCAACA 57.758 40.909 16.05 0.00 0.00 3.33
1536 2442 4.750098 TCAGGTTGCTAAAAAGAAGTCTCG 59.250 41.667 0.00 0.00 0.00 4.04
1618 2542 6.035843 CACAATATTCCATTACAGGCACAAC 58.964 40.000 0.00 0.00 0.00 3.32
1677 2601 5.867903 TTCTTGGGCAGAAAAATCTGAAA 57.132 34.783 9.89 0.72 38.68 2.69
1750 2674 4.588899 TGGAGCAACTGTTAGTTATGCAT 58.411 39.130 3.79 3.79 36.03 3.96
1822 2746 2.783828 TTGCAACAAATGTACCGTGG 57.216 45.000 0.00 0.00 0.00 4.94
1825 2749 2.970609 CTCGTTTGCAACAAATGTACCG 59.029 45.455 0.00 3.67 0.00 4.02
1951 2875 1.296715 CGGGAGACTTTGAGTGGGG 59.703 63.158 0.00 0.00 0.00 4.96
1990 2914 0.743688 CATCGTCAGAGTCTGGAGGG 59.256 60.000 19.99 7.21 31.51 4.30
2111 3035 3.758554 ACTGCCTGGTTGTCATCATTAAC 59.241 43.478 0.00 0.00 0.00 2.01
2112 3036 4.009675 GACTGCCTGGTTGTCATCATTAA 58.990 43.478 13.56 0.00 0.00 1.40
2143 3073 4.836825 TCCGCTTTCTGATTCTCTTTGAT 58.163 39.130 0.00 0.00 0.00 2.57
2154 3084 1.328279 TGACACTCTCCGCTTTCTGA 58.672 50.000 0.00 0.00 0.00 3.27
2194 3124 2.369394 CCAACCACCTGAATAAGCTCC 58.631 52.381 0.00 0.00 0.00 4.70
2257 3187 0.398318 GACTGCCTTCCTTCACACCT 59.602 55.000 0.00 0.00 0.00 4.00
2360 3290 3.587506 AGCTTATCTGTTACCCCACTGTT 59.412 43.478 0.00 0.00 0.00 3.16
2466 3396 2.454832 ATACGCCCATGATGAGCCCG 62.455 60.000 0.00 0.00 0.00 6.13
2482 3412 3.754965 TGGCTGGCCATCTGATTTATAC 58.245 45.455 5.51 0.00 41.89 1.47
2545 3475 3.053291 GCCGGATTTGCGTCCACA 61.053 61.111 5.05 0.00 38.21 4.17
2550 3480 0.464373 ATCATCAGCCGGATTTGCGT 60.464 50.000 5.05 0.00 32.57 5.24
2551 3481 1.462283 CTATCATCAGCCGGATTTGCG 59.538 52.381 5.05 0.00 32.57 4.85
2560 3490 5.149973 AGTCATCATCACTATCATCAGCC 57.850 43.478 0.00 0.00 0.00 4.85
2628 3558 3.554524 CGTGTGTTTGTAATCAAGGCAG 58.445 45.455 0.00 0.00 34.88 4.85
2648 3578 3.492421 AACATAACATTTCTGCTGCCG 57.508 42.857 0.00 0.00 0.00 5.69
2735 3665 7.337942 AGCATGCTCTAACATTAATATTAGGCC 59.662 37.037 16.30 0.00 0.00 5.19
2776 3706 1.014352 GTACGTGCAATCCCCATGAC 58.986 55.000 0.00 0.00 0.00 3.06
2789 3719 0.679640 ATGGGGCAACATGGTACGTG 60.680 55.000 0.00 0.00 39.74 4.49
2912 3842 7.713734 AAAACATGAGAATGAGATGTCCAAT 57.286 32.000 0.00 0.00 0.00 3.16
2977 3909 1.376037 AGCAGCGGTTCAAGCTACC 60.376 57.895 0.00 0.00 44.06 3.18
3021 3953 9.277565 GGAGCATATGCAATAAAATTATGTACG 57.722 33.333 28.62 0.00 45.16 3.67
3154 4089 3.772025 CCTCACATATTAGGGGCTCCTAG 59.228 52.174 13.33 3.55 45.60 3.02
3173 4108 7.277174 TGAAAAGGAAGAAAAATCACTCCTC 57.723 36.000 0.00 0.00 0.00 3.71
3252 4189 3.198853 GCTTGAACTGGAGGGAGTCTATT 59.801 47.826 0.00 0.00 0.00 1.73
3266 4203 0.250640 CAGACAGCAGGGCTTGAACT 60.251 55.000 0.00 0.00 36.40 3.01
3471 4411 0.250467 AAGCAATGGTCACTCGCTGT 60.250 50.000 0.00 0.00 32.14 4.40
3498 4438 7.760794 TCGTACGTCCAAACTATGTCAAAATAT 59.239 33.333 16.05 0.00 0.00 1.28
3508 4448 3.350833 AGACCTCGTACGTCCAAACTAT 58.649 45.455 16.05 0.00 0.00 2.12
3568 4508 2.581709 ACCCACTGCTAGAGTACCTAGT 59.418 50.000 15.52 1.71 45.26 2.57


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

AutoCloner maintained by Alex Coulton.