Multiple sequence alignment - TraesCS4D01G265300

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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 TraesCS4D01G265300 chr4D 100.000 3860 0 0 1 3860 435420973 435417114 0.000000e+00 7129.0
1 TraesCS4D01G265300 chr4D 100.000 239 0 0 4216 4454 435416758 435416520 4.090000e-120 442.0
2 TraesCS4D01G265300 chr4D 92.683 164 11 1 3698 3860 435412268 435412105 7.450000e-58 235.0
3 TraesCS4D01G265300 chr4D 84.571 175 25 2 4281 4454 324011979 324012152 5.920000e-39 172.0
4 TraesCS4D01G265300 chr4D 95.918 49 2 0 4216 4264 435416679 435416631 3.690000e-11 80.5
5 TraesCS4D01G265300 chr4A 87.268 2851 230 71 875 3694 36798908 36796160 0.000000e+00 3131.0
6 TraesCS4D01G265300 chr4A 86.266 699 37 22 244 885 36799619 36798923 0.000000e+00 704.0
7 TraesCS4D01G265300 chr4A 96.218 238 9 0 8 245 36799980 36799743 1.500000e-104 390.0
8 TraesCS4D01G265300 chr4A 85.549 173 23 2 4281 4452 555803635 555803464 3.540000e-41 180.0
9 TraesCS4D01G265300 chr4B 90.538 1395 89 25 806 2194 536579715 536578358 0.000000e+00 1805.0
10 TraesCS4D01G265300 chr4B 97.051 712 17 2 3149 3860 536577361 536576654 0.000000e+00 1195.0
11 TraesCS4D01G265300 chr4B 88.260 724 59 13 8 720 536704602 536705310 0.000000e+00 843.0
12 TraesCS4D01G265300 chr4B 97.490 239 6 0 4216 4454 536429107 536428869 4.150000e-110 409.0
13 TraesCS4D01G265300 chr4B 97.838 185 4 0 3676 3860 536430180 536429996 2.000000e-83 320.0
14 TraesCS4D01G265300 chr4B 94.444 72 3 1 3698 3768 536420067 536419996 4.710000e-20 110.0
15 TraesCS4D01G265300 chr4B 95.833 48 2 0 4217 4264 536429027 536428980 1.330000e-10 78.7
16 TraesCS4D01G265300 chr7B 86.705 173 21 2 4281 4452 729541160 729540989 1.640000e-44 191.0
17 TraesCS4D01G265300 chr3D 86.364 176 20 3 4281 4454 592819954 592820127 5.880000e-44 189.0
18 TraesCS4D01G265300 chr7A 86.207 174 22 2 4282 4454 20121483 20121655 2.120000e-43 187.0
19 TraesCS4D01G265300 chr6B 85.549 173 23 2 4281 4452 716331333 716331504 3.540000e-41 180.0
20 TraesCS4D01G265300 chr6A 85.143 175 24 2 4281 4454 615639806 615639633 1.270000e-40 178.0
21 TraesCS4D01G265300 chr2B 85.143 175 24 2 4281 4454 610015297 610015124 1.270000e-40 178.0


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 TraesCS4D01G265300 chr4D 435416520 435420973 4453 True 2550.500000 7129 98.639333 1 4454 3 chr4D.!!$R2 4453
1 TraesCS4D01G265300 chr4A 36796160 36799980 3820 True 1408.333333 3131 89.917333 8 3694 3 chr4A.!!$R2 3686
2 TraesCS4D01G265300 chr4B 536576654 536579715 3061 True 1500.000000 1805 93.794500 806 3860 2 chr4B.!!$R3 3054
3 TraesCS4D01G265300 chr4B 536704602 536705310 708 False 843.000000 843 88.260000 8 720 1 chr4B.!!$F1 712
4 TraesCS4D01G265300 chr4B 536428869 536430180 1311 True 269.233333 409 97.053667 3676 4454 3 chr4B.!!$R2 778

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
399 531 0.250684 TGGCGCCTGATGTTTTGAGA 60.251 50.0 29.70 0.0 0.00 3.27 F
1187 1396 0.893447 GGTAATATCCTCCGTCCCCG 59.107 60.0 0.00 0.0 0.00 5.73 F
2428 2706 0.179145 GCTGTGCATCCAGTTCATGC 60.179 55.0 6.23 0.0 45.92 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1358 1584 1.196012 GGCTAGCTAGAACTGGGTGT 58.804 55.000 25.15 0.0 0.00 4.16 R
2654 2936 1.061131 CATTAACAAGCGAGACAGGCG 59.939 52.381 0.00 0.0 35.00 5.52 R
4365 5358 0.106819 AGGATCAAGTGGCAGATGGC 60.107 55.000 0.00 0.0 43.74 4.40 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
37 38 7.985634 AAAAACATATTAGCCTATTGCAACG 57.014 32.000 0.00 0.00 44.83 4.10
145 146 1.987080 ACTCCCATTAAGCTCCCCTT 58.013 50.000 0.00 0.00 37.57 3.95
259 386 3.941483 AGAAGCTAATTGTGTGCGCTATT 59.059 39.130 9.73 3.42 0.00 1.73
260 387 4.396166 AGAAGCTAATTGTGTGCGCTATTT 59.604 37.500 9.73 0.00 0.00 1.40
344 476 9.416794 GCGCACAGAGATATATAGCAATAATAT 57.583 33.333 0.30 0.00 0.00 1.28
362 494 4.927267 ATATGAAGAACCCTGTGTTGGA 57.073 40.909 0.00 0.00 37.29 3.53
365 497 3.221771 TGAAGAACCCTGTGTTGGATTG 58.778 45.455 0.00 0.00 37.29 2.67
397 529 1.523154 GGTGGCGCCTGATGTTTTGA 61.523 55.000 29.70 0.00 0.00 2.69
399 531 0.250684 TGGCGCCTGATGTTTTGAGA 60.251 50.000 29.70 0.00 0.00 3.27
500 633 4.143326 GGTATATGCATCGTCAATGACACG 60.143 45.833 14.24 0.90 37.59 4.49
568 703 1.195115 TTGCGGAGTTCAGATAGCCT 58.805 50.000 0.00 0.00 0.00 4.58
578 713 4.721776 AGTTCAGATAGCCTTATGGGTGAA 59.278 41.667 9.50 2.10 44.81 3.18
581 726 5.869579 TCAGATAGCCTTATGGGTGAATTC 58.130 41.667 9.50 0.00 44.81 2.17
610 756 5.189625 GTTTTTGTTGAACGTGCATGATTG 58.810 37.500 14.17 0.00 0.00 2.67
720 883 9.588096 AAAGAGTTTCACAATTTACCCTAGAAT 57.412 29.630 0.00 0.00 0.00 2.40
785 970 1.234821 GGACGATTTGTGCAAGTGGA 58.765 50.000 0.00 0.00 39.04 4.02
790 975 2.095768 CGATTTGTGCAAGTGGACGATT 60.096 45.455 0.00 0.00 39.39 3.34
794 979 3.394674 TGTGCAAGTGGACGATTTCTA 57.605 42.857 0.00 0.00 39.39 2.10
827 1012 6.512741 CGCTACGATTGGGCTTGTTTAATATT 60.513 38.462 0.00 0.00 0.00 1.28
912 1121 3.775654 GGGACCCGCTCACCAGAG 61.776 72.222 0.00 0.00 44.96 3.35
913 1122 2.680352 GGACCCGCTCACCAGAGA 60.680 66.667 0.00 0.00 44.98 3.10
914 1123 2.716017 GGACCCGCTCACCAGAGAG 61.716 68.421 0.00 0.00 44.98 3.20
915 1124 1.679305 GACCCGCTCACCAGAGAGA 60.679 63.158 0.00 0.00 44.98 3.10
1174 1383 9.709387 TCGGATCTATCTTTGGATATGGTAATA 57.291 33.333 0.00 0.00 34.37 0.98
1186 1395 2.019807 TGGTAATATCCTCCGTCCCC 57.980 55.000 0.00 0.00 0.00 4.81
1187 1396 0.893447 GGTAATATCCTCCGTCCCCG 59.107 60.000 0.00 0.00 0.00 5.73
1188 1397 1.625511 GTAATATCCTCCGTCCCCGT 58.374 55.000 0.00 0.00 0.00 5.28
1298 1507 8.475331 TTTCTATTATCGGTGTTCAGTTCTTC 57.525 34.615 0.00 0.00 0.00 2.87
1299 1508 7.406031 TCTATTATCGGTGTTCAGTTCTTCT 57.594 36.000 0.00 0.00 0.00 2.85
1300 1509 7.837863 TCTATTATCGGTGTTCAGTTCTTCTT 58.162 34.615 0.00 0.00 0.00 2.52
1301 1510 8.963725 TCTATTATCGGTGTTCAGTTCTTCTTA 58.036 33.333 0.00 0.00 0.00 2.10
1302 1511 9.582431 CTATTATCGGTGTTCAGTTCTTCTTAA 57.418 33.333 0.00 0.00 0.00 1.85
1303 1512 8.842358 ATTATCGGTGTTCAGTTCTTCTTAAA 57.158 30.769 0.00 0.00 0.00 1.52
1304 1513 8.842358 TTATCGGTGTTCAGTTCTTCTTAAAT 57.158 30.769 0.00 0.00 0.00 1.40
1305 1514 9.932207 TTATCGGTGTTCAGTTCTTCTTAAATA 57.068 29.630 0.00 0.00 0.00 1.40
1306 1515 7.884816 TCGGTGTTCAGTTCTTCTTAAATAG 57.115 36.000 0.00 0.00 0.00 1.73
1307 1516 7.439381 TCGGTGTTCAGTTCTTCTTAAATAGT 58.561 34.615 0.00 0.00 0.00 2.12
1308 1517 7.384115 TCGGTGTTCAGTTCTTCTTAAATAGTG 59.616 37.037 0.00 0.00 0.00 2.74
1309 1518 7.384115 CGGTGTTCAGTTCTTCTTAAATAGTGA 59.616 37.037 0.00 0.00 0.00 3.41
1310 1519 9.052759 GGTGTTCAGTTCTTCTTAAATAGTGAA 57.947 33.333 0.00 0.00 0.00 3.18
1358 1584 9.902684 TGATTATACGGAATTTGGTAGGTTTTA 57.097 29.630 0.00 0.00 0.00 1.52
1376 1602 4.467198 TTTACACCCAGTTCTAGCTAGC 57.533 45.455 16.35 6.62 0.00 3.42
1568 1824 1.891919 CAACACCTGTGACACCCGG 60.892 63.158 3.94 6.31 0.00 5.73
1597 1853 7.923414 ACTTCCTCACACAAAATCCTTATAC 57.077 36.000 0.00 0.00 0.00 1.47
1646 1902 5.014228 ACAAGGTTTGCTATCTAAGAAGGGT 59.986 40.000 0.00 0.00 0.00 4.34
1700 1956 3.211045 TGCCAAAGTTAGTGTTCACCTC 58.789 45.455 0.00 0.00 0.00 3.85
1730 1986 7.862873 GTGCATATTCTTAACTAGGAAATTGCC 59.137 37.037 0.00 0.00 34.92 4.52
1733 1989 8.571336 CATATTCTTAACTAGGAAATTGCCCTG 58.429 37.037 0.00 0.00 35.30 4.45
1756 2013 7.148689 CCTGTCATTTTCATAAAAAGCTTGCTC 60.149 37.037 0.00 0.00 37.76 4.26
1760 2017 7.332430 TCATTTTCATAAAAAGCTTGCTCATGG 59.668 33.333 0.00 0.00 37.76 3.66
1763 2020 7.408756 TTCATAAAAAGCTTGCTCATGGTAT 57.591 32.000 0.00 0.00 0.00 2.73
1767 2024 9.023967 CATAAAAAGCTTGCTCATGGTATAAAC 57.976 33.333 0.00 0.00 0.00 2.01
1776 2033 5.880332 TGCTCATGGTATAAACTTCTTGGAC 59.120 40.000 0.00 0.00 0.00 4.02
1884 2141 4.776349 TCTGTTCAGTGGTCAGCTTTTTA 58.224 39.130 9.52 0.00 0.00 1.52
2009 2266 4.331968 TCCAGGTACATTCACATTGAACC 58.668 43.478 0.00 0.00 39.45 3.62
2017 2280 5.108517 ACATTCACATTGAACCAACAACAC 58.891 37.500 0.00 0.00 39.45 3.32
2018 2281 3.412981 TCACATTGAACCAACAACACG 57.587 42.857 0.00 0.00 32.50 4.49
2026 2289 1.816074 ACCAACAACACGTTCACAGT 58.184 45.000 0.00 0.00 34.86 3.55
2057 2321 7.744087 ACTATTGTGCTTGACATTGTTTAGA 57.256 32.000 0.00 0.00 33.40 2.10
2095 2359 6.818644 AGTTGTGATGTGATATTCTGTGGTAC 59.181 38.462 0.00 0.00 0.00 3.34
2103 2367 7.508687 TGTGATATTCTGTGGTACTGCATAAT 58.491 34.615 0.00 0.33 0.00 1.28
2104 2368 7.442062 TGTGATATTCTGTGGTACTGCATAATG 59.558 37.037 0.00 0.00 0.00 1.90
2113 2377 6.208402 TGTGGTACTGCATAATGTTGTGAAAT 59.792 34.615 0.00 0.00 0.00 2.17
2136 2401 9.717942 AAATAATTGGTAGTAATTGCAAGCAAA 57.282 25.926 11.89 0.00 39.55 3.68
2163 2428 3.565516 GCTTTGTCTTCAATTTCCGGTC 58.434 45.455 0.00 0.00 33.32 4.79
2165 2430 4.537015 CTTTGTCTTCAATTTCCGGTCAC 58.463 43.478 0.00 0.00 33.32 3.67
2173 2438 3.816523 TCAATTTCCGGTCACCAAGTTAC 59.183 43.478 0.00 0.00 0.00 2.50
2174 2439 3.782656 ATTTCCGGTCACCAAGTTACT 57.217 42.857 0.00 0.00 0.00 2.24
2175 2440 3.564053 TTTCCGGTCACCAAGTTACTT 57.436 42.857 0.00 0.00 0.00 2.24
2176 2441 3.564053 TTCCGGTCACCAAGTTACTTT 57.436 42.857 0.00 0.00 0.00 2.66
2177 2442 2.841215 TCCGGTCACCAAGTTACTTTG 58.159 47.619 0.00 0.00 0.00 2.77
2178 2443 2.171027 TCCGGTCACCAAGTTACTTTGT 59.829 45.455 0.00 0.00 0.00 2.83
2179 2444 3.387374 TCCGGTCACCAAGTTACTTTGTA 59.613 43.478 0.00 0.00 0.00 2.41
2180 2445 4.040706 TCCGGTCACCAAGTTACTTTGTAT 59.959 41.667 0.00 0.00 0.00 2.29
2181 2446 4.758165 CCGGTCACCAAGTTACTTTGTATT 59.242 41.667 1.46 0.00 0.00 1.89
2182 2447 5.334569 CCGGTCACCAAGTTACTTTGTATTG 60.335 44.000 1.46 0.00 0.00 1.90
2183 2448 5.237779 CGGTCACCAAGTTACTTTGTATTGT 59.762 40.000 1.46 0.00 0.00 2.71
2184 2449 6.238538 CGGTCACCAAGTTACTTTGTATTGTT 60.239 38.462 1.46 0.00 0.00 2.83
2185 2450 7.041916 CGGTCACCAAGTTACTTTGTATTGTTA 60.042 37.037 1.46 0.00 0.00 2.41
2186 2451 8.789762 GGTCACCAAGTTACTTTGTATTGTTAT 58.210 33.333 1.46 0.00 0.00 1.89
2218 2483 5.615925 AGGGGACACTCTGTATTGTTATC 57.384 43.478 0.00 0.00 0.00 1.75
2282 2559 5.408299 TGTCATTTCTGTCAATACGAACTGG 59.592 40.000 0.00 0.00 0.00 4.00
2296 2573 2.159099 CGAACTGGTAAGCTCCTATGCA 60.159 50.000 0.00 0.00 34.99 3.96
2375 2652 9.578439 GTTAGTAGTTTATTATCCGACTGTGTT 57.422 33.333 0.00 0.00 0.00 3.32
2395 2672 9.726232 CTGTGTTAATTTATCCATTGAGTGATG 57.274 33.333 0.00 0.00 0.00 3.07
2416 2694 5.512753 TGAAGTTTAATTTCAGCTGTGCA 57.487 34.783 14.67 0.00 31.35 4.57
2428 2706 0.179145 GCTGTGCATCCAGTTCATGC 60.179 55.000 6.23 0.00 45.92 4.06
2430 2708 2.635714 CTGTGCATCCAGTTCATGCTA 58.364 47.619 6.24 0.00 45.90 3.49
2487 2766 3.514645 ACGAACGTACACTGAAGTTTGT 58.485 40.909 0.00 0.00 36.65 2.83
2577 2859 6.897413 AGCCCCATATCACTTGTAAGAAATTT 59.103 34.615 0.00 0.00 0.00 1.82
2628 2910 7.286087 TGCATGATAAAAAGAAGCACCATCTAT 59.714 33.333 0.00 0.00 0.00 1.98
2654 2936 1.235724 AACAGTAAAAGGCGCTCACC 58.764 50.000 7.64 0.00 0.00 4.02
2803 3089 1.535028 CTGGACTGCGCATGTGTTTAA 59.465 47.619 12.24 0.00 0.00 1.52
2868 3154 5.894807 GTGCTAAACACCATCTTATGCATT 58.105 37.500 3.54 0.00 44.02 3.56
2914 3200 3.999001 TGCATCTCTCTGTTGCTTTACTG 59.001 43.478 0.00 0.00 40.86 2.74
2938 3224 2.014857 CATGTGCTTCTGAGTCATGGG 58.985 52.381 0.00 0.00 35.65 4.00
2939 3225 0.321919 TGTGCTTCTGAGTCATGGGC 60.322 55.000 0.00 0.00 0.00 5.36
2940 3226 1.028868 GTGCTTCTGAGTCATGGGCC 61.029 60.000 0.00 0.00 0.00 5.80
2941 3227 1.203441 TGCTTCTGAGTCATGGGCCT 61.203 55.000 4.53 0.00 0.00 5.19
2942 3228 0.463474 GCTTCTGAGTCATGGGCCTC 60.463 60.000 4.53 0.00 0.00 4.70
2943 3229 0.907486 CTTCTGAGTCATGGGCCTCA 59.093 55.000 4.53 0.00 36.35 3.86
2944 3230 1.489649 CTTCTGAGTCATGGGCCTCAT 59.510 52.381 4.53 1.07 37.11 2.90
2988 3274 9.826574 AACAAGTGTAGTATTCAAGTGTCTTAA 57.173 29.630 0.00 0.00 0.00 1.85
3008 3294 1.226717 GAACTCTAGGCGGCAGTCG 60.227 63.158 13.08 0.00 42.76 4.18
3044 3330 3.312421 CGAAAGAGGAAGTTTGCACTGAA 59.688 43.478 0.00 0.00 31.60 3.02
3045 3331 4.201910 CGAAAGAGGAAGTTTGCACTGAAA 60.202 41.667 0.00 0.00 31.60 2.69
3102 3388 4.436113 TCATATCTGCATTTGCTACCCA 57.564 40.909 3.94 0.00 42.66 4.51
3108 3394 1.005332 TGCATTTGCTACCCAAGGCTA 59.995 47.619 3.94 0.00 42.66 3.93
3339 3791 1.452145 GGAACGCCTTGACCTTTGCA 61.452 55.000 0.00 0.00 0.00 4.08
3648 4107 7.372451 TGTCAAGGATAGATTTTGTTTACCG 57.628 36.000 0.00 0.00 0.00 4.02
3788 4248 2.166870 TGACCGTTTACAGGATGCGTAT 59.833 45.455 0.00 0.00 42.53 3.06
3852 4312 9.639563 TTTTCATCTAGCATCCCATGTATTAAA 57.360 29.630 0.00 0.00 0.00 1.52
4278 5271 6.322712 GCCAAATGGTTAAACACCCATATCTA 59.677 38.462 0.00 0.00 46.68 1.98
4294 5287 7.797617 ACCCATATCTATTAACACCCTCCTTTA 59.202 37.037 0.00 0.00 0.00 1.85
4365 5358 4.307432 TGACCGAAAGAGCTTTAGTGAAG 58.693 43.478 0.00 0.00 38.45 3.02
4407 5400 5.152623 TGGATGGAATGAATCGTATCTCC 57.847 43.478 0.00 0.00 0.00 3.71
4422 5415 4.690748 CGTATCTCCAGTTTCTTTTCTGCA 59.309 41.667 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.991388 GGCTAATATGTTTTTATACGTGTGAAA 57.009 29.630 0.00 0.00 0.00 2.69
2 3 9.386010 AGGCTAATATGTTTTTATACGTGTGAA 57.614 29.630 0.00 0.00 0.00 3.18
3 4 8.951787 AGGCTAATATGTTTTTATACGTGTGA 57.048 30.769 0.00 0.00 0.00 3.58
145 146 3.392947 TGTCACCAACTTCCTATGGTCAA 59.607 43.478 0.00 0.00 46.94 3.18
259 386 9.325198 CAGTACTCATTACATTAAGTATGCCAA 57.675 33.333 0.00 0.00 37.81 4.52
260 387 7.441157 GCAGTACTCATTACATTAAGTATGCCA 59.559 37.037 0.00 0.00 37.81 4.92
344 476 3.221771 CAATCCAACACAGGGTTCTTCA 58.778 45.455 0.00 0.00 37.72 3.02
362 494 1.531423 CACCTCAACTGCTCAGCAAT 58.469 50.000 0.00 0.00 38.41 3.56
365 497 2.331132 GCCACCTCAACTGCTCAGC 61.331 63.158 0.00 0.00 0.00 4.26
397 529 2.032030 CCGAACTTGCAATGTTTCGTCT 60.032 45.455 24.57 3.89 34.00 4.18
399 531 1.673920 ACCGAACTTGCAATGTTTCGT 59.326 42.857 24.57 16.20 34.00 3.85
500 633 2.011222 TCAAACAAAGTGTCCCGTGTC 58.989 47.619 0.00 0.00 0.00 3.67
504 637 1.403679 TGCTTCAAACAAAGTGTCCCG 59.596 47.619 0.00 0.00 0.00 5.14
568 703 9.454859 ACAAAAACAAAAAGAATTCACCCATAA 57.545 25.926 8.44 0.00 0.00 1.90
578 713 6.794636 GCACGTTCAACAAAAACAAAAAGAAT 59.205 30.769 0.00 0.00 0.00 2.40
581 726 5.435557 TGCACGTTCAACAAAAACAAAAAG 58.564 33.333 0.00 0.00 0.00 2.27
610 756 9.564041 CGCTTATACAAATCGTTTAGTACATTC 57.436 33.333 0.00 0.00 0.00 2.67
695 858 9.588096 AATTCTAGGGTAAATTGTGAAACTCTT 57.412 29.630 0.00 0.00 38.04 2.85
785 970 1.137086 AGCGCAGGACATAGAAATCGT 59.863 47.619 11.47 0.00 0.00 3.73
790 975 1.385528 TCGTAGCGCAGGACATAGAA 58.614 50.000 11.47 0.00 0.00 2.10
794 979 0.530650 CCAATCGTAGCGCAGGACAT 60.531 55.000 11.47 0.00 0.00 3.06
802 987 0.802494 AAACAAGCCCAATCGTAGCG 59.198 50.000 0.00 0.00 0.00 4.26
827 1012 0.537143 ACAAGCCCAATCGAACAGCA 60.537 50.000 0.00 0.00 0.00 4.41
912 1121 2.363147 ACGGGACTCCAGCCTCTC 60.363 66.667 0.00 0.00 0.00 3.20
913 1122 2.363147 GACGGGACTCCAGCCTCT 60.363 66.667 0.00 0.00 0.00 3.69
914 1123 2.569218 TAGGACGGGACTCCAGCCTC 62.569 65.000 12.28 0.00 31.94 4.70
915 1124 1.950748 ATAGGACGGGACTCCAGCCT 61.951 60.000 13.10 13.10 31.94 4.58
956 1165 4.148696 TCGTTATCGTTTCCTGTTTCGTTC 59.851 41.667 0.00 0.00 38.33 3.95
1197 1406 1.562475 TCCGGAAAAGGATAAGGTGGG 59.438 52.381 0.00 0.00 34.92 4.61
1327 1536 8.899771 CCTACCAAATTCCGTATAATCAAGTTT 58.100 33.333 0.00 0.00 0.00 2.66
1340 1549 5.050644 GGTGTAAAACCTACCAAATTCCG 57.949 43.478 0.00 0.00 46.55 4.30
1358 1584 1.196012 GGCTAGCTAGAACTGGGTGT 58.804 55.000 25.15 0.00 0.00 4.16
1370 1596 7.177744 GGACAATCTTATACTCTTAGGCTAGCT 59.822 40.741 15.72 3.22 0.00 3.32
1376 1602 9.838339 AAATGTGGACAATCTTATACTCTTAGG 57.162 33.333 0.00 0.00 0.00 2.69
1451 1680 6.332976 ACAAGGAATTGGACTATTGGAGAT 57.667 37.500 0.00 0.00 0.00 2.75
1454 1683 7.638444 TGAATACAAGGAATTGGACTATTGGA 58.362 34.615 0.00 0.00 0.00 3.53
1455 1684 7.880160 TGAATACAAGGAATTGGACTATTGG 57.120 36.000 0.00 0.00 0.00 3.16
1568 1824 7.039313 AGGATTTTGTGTGAGGAAGTTAAAC 57.961 36.000 0.00 0.00 0.00 2.01
1597 1853 5.277683 CCTGAAAACAGAATCCGATATGCAG 60.278 44.000 0.00 0.00 0.00 4.41
1646 1902 1.302511 GCCGAGTGAGCCCTTCAAA 60.303 57.895 0.00 0.00 37.61 2.69
1700 1956 8.492673 TTTCCTAGTTAAGAATATGCACACAG 57.507 34.615 0.00 0.00 0.00 3.66
1730 1986 6.647895 AGCAAGCTTTTTATGAAAATGACAGG 59.352 34.615 0.00 0.00 34.45 4.00
1733 1989 7.642071 TGAGCAAGCTTTTTATGAAAATGAC 57.358 32.000 0.00 0.00 34.45 3.06
1756 2013 6.414732 TCTGGTCCAAGAAGTTTATACCATG 58.585 40.000 0.00 0.00 35.16 3.66
1760 2017 7.981102 AAACTCTGGTCCAAGAAGTTTATAC 57.019 36.000 18.40 0.00 31.57 1.47
1763 2020 5.067283 GCAAAACTCTGGTCCAAGAAGTTTA 59.933 40.000 19.44 0.00 32.32 2.01
1767 2024 2.951642 TGCAAAACTCTGGTCCAAGAAG 59.048 45.455 7.74 2.08 0.00 2.85
1776 2033 4.498682 CCAGAAAGAACTGCAAAACTCTGG 60.499 45.833 12.26 12.26 41.90 3.86
1884 2141 4.675063 ATCCAACTCCCAAGGTGTTAAT 57.325 40.909 1.07 0.00 38.66 1.40
2009 2266 4.965062 AGTAAACTGTGAACGTGTTGTTG 58.035 39.130 0.00 0.00 42.09 3.33
2017 2280 7.007697 GCACAATAGTAAGTAAACTGTGAACG 58.992 38.462 3.61 0.00 0.00 3.95
2018 2281 8.084590 AGCACAATAGTAAGTAAACTGTGAAC 57.915 34.615 3.61 0.00 0.00 3.18
2026 2289 9.062524 ACAATGTCAAGCACAATAGTAAGTAAA 57.937 29.630 0.00 0.00 38.97 2.01
2057 2321 9.896645 ATCACATCACAACTTCTTCATACTATT 57.103 29.630 0.00 0.00 0.00 1.73
2080 2344 7.508687 ACATTATGCAGTACCACAGAATATCA 58.491 34.615 5.55 0.00 0.00 2.15
2095 2359 8.706492 ACCAATTATTTCACAACATTATGCAG 57.294 30.769 0.00 0.00 0.00 4.41
2103 2367 9.632807 GCAATTACTACCAATTATTTCACAACA 57.367 29.630 0.00 0.00 0.00 3.33
2104 2368 9.632807 TGCAATTACTACCAATTATTTCACAAC 57.367 29.630 0.00 0.00 0.00 3.32
2113 2377 9.717942 AAATTTGCTTGCAATTACTACCAATTA 57.282 25.926 8.93 0.00 0.00 1.40
2125 2390 4.098196 ACAAAGCCAAAATTTGCTTGCAAT 59.902 33.333 14.47 0.00 46.58 3.56
2136 2401 5.466393 CGGAAATTGAAGACAAAGCCAAAAT 59.534 36.000 0.00 0.00 39.54 1.82
2145 2410 2.882137 GGTGACCGGAAATTGAAGACAA 59.118 45.455 9.46 0.00 40.42 3.18
2191 2456 6.195600 ACAATACAGAGTGTCCCCTAAAAA 57.804 37.500 0.00 0.00 0.00 1.94
2192 2457 5.836024 ACAATACAGAGTGTCCCCTAAAA 57.164 39.130 0.00 0.00 0.00 1.52
2193 2458 5.836024 AACAATACAGAGTGTCCCCTAAA 57.164 39.130 0.00 0.00 31.24 1.85
2194 2459 6.099269 GGATAACAATACAGAGTGTCCCCTAA 59.901 42.308 0.00 0.00 31.24 2.69
2195 2460 5.601313 GGATAACAATACAGAGTGTCCCCTA 59.399 44.000 0.00 0.00 31.24 3.53
2196 2461 4.409247 GGATAACAATACAGAGTGTCCCCT 59.591 45.833 0.00 0.00 31.24 4.79
2197 2462 4.409247 AGGATAACAATACAGAGTGTCCCC 59.591 45.833 0.00 0.00 31.24 4.81
2198 2463 5.615925 AGGATAACAATACAGAGTGTCCC 57.384 43.478 0.00 0.00 31.24 4.46
2199 2464 6.407202 ACAAGGATAACAATACAGAGTGTCC 58.593 40.000 0.00 0.00 31.24 4.02
2200 2465 7.624344 GCAACAAGGATAACAATACAGAGTGTC 60.624 40.741 0.00 0.00 31.24 3.67
2201 2466 6.149474 GCAACAAGGATAACAATACAGAGTGT 59.851 38.462 0.00 0.00 34.75 3.55
2202 2467 6.372659 AGCAACAAGGATAACAATACAGAGTG 59.627 38.462 0.00 0.00 0.00 3.51
2203 2468 6.372659 CAGCAACAAGGATAACAATACAGAGT 59.627 38.462 0.00 0.00 0.00 3.24
2218 2483 5.975693 TTTTAGGTATTCCAGCAACAAGG 57.024 39.130 0.00 0.00 35.89 3.61
2257 2534 6.092670 CCAGTTCGTATTGACAGAAATGACAT 59.907 38.462 6.46 0.00 40.90 3.06
2275 2552 2.159099 TGCATAGGAGCTTACCAGTTCG 60.159 50.000 0.00 0.00 31.01 3.95
2282 2559 4.694509 CAGAATCCATGCATAGGAGCTTAC 59.305 45.833 18.60 10.44 38.83 2.34
2360 2637 9.793259 ATGGATAAATTAACACAGTCGGATAAT 57.207 29.630 0.00 0.00 0.00 1.28
2367 2644 8.946085 TCACTCAATGGATAAATTAACACAGTC 58.054 33.333 0.00 0.00 0.00 3.51
2395 2672 5.574443 GGATGCACAGCTGAAATTAAACTTC 59.426 40.000 23.35 7.38 0.00 3.01
2403 2680 2.211250 ACTGGATGCACAGCTGAAAT 57.789 45.000 23.35 10.48 42.21 2.17
2456 2735 3.932710 AGTGTACGTTCGTACTCGGATTA 59.067 43.478 27.38 10.04 40.93 1.75
2577 2859 7.735326 AAGAATAAGGCTCCTGAGTTTAGTA 57.265 36.000 0.00 0.00 0.00 1.82
2584 2866 3.614092 TGCAAAGAATAAGGCTCCTGAG 58.386 45.455 0.00 0.00 0.00 3.35
2628 2910 7.079475 GTGAGCGCCTTTTACTGTTAAAATTA 58.921 34.615 2.29 0.00 36.73 1.40
2654 2936 1.061131 CATTAACAAGCGAGACAGGCG 59.939 52.381 0.00 0.00 35.00 5.52
2659 2941 2.930682 GGACTCCATTAACAAGCGAGAC 59.069 50.000 0.00 0.00 0.00 3.36
2663 2945 1.398390 GCAGGACTCCATTAACAAGCG 59.602 52.381 0.00 0.00 0.00 4.68
2710 2994 3.806949 AGGGCTTGGTCAGTTAAATGA 57.193 42.857 0.56 0.56 0.00 2.57
2741 3025 3.614616 GTGAAGTCCTTAACAGCATCTCG 59.385 47.826 0.00 0.00 0.00 4.04
2752 3038 4.623932 ACTGCAAGATGTGAAGTCCTTA 57.376 40.909 0.00 0.00 43.38 2.69
2792 3078 8.466798 ACTAAATTACCCTGATTAAACACATGC 58.533 33.333 0.00 0.00 0.00 4.06
2803 3089 6.645884 TTACCACCACTAAATTACCCTGAT 57.354 37.500 0.00 0.00 0.00 2.90
2868 3154 4.011698 TGTGAACAGAGTAGGTATGCGTA 58.988 43.478 0.00 0.00 0.00 4.42
2884 3170 3.037431 ACAGAGAGATGCAGTGTGAAC 57.963 47.619 0.00 0.00 0.00 3.18
2943 3229 6.263842 ACTTGTTGAAATGTCATGACTGTCAT 59.736 34.615 25.55 17.24 37.65 3.06
2944 3230 5.589855 ACTTGTTGAAATGTCATGACTGTCA 59.410 36.000 25.55 20.82 32.48 3.58
2945 3231 5.911280 CACTTGTTGAAATGTCATGACTGTC 59.089 40.000 25.55 18.78 32.48 3.51
2946 3232 5.357878 ACACTTGTTGAAATGTCATGACTGT 59.642 36.000 25.55 13.96 32.48 3.55
2955 3241 9.120538 ACTTGAATACTACACTTGTTGAAATGT 57.879 29.630 0.00 0.00 0.00 2.71
2988 3274 1.305381 ACTGCCGCCTAGAGTTCCT 60.305 57.895 0.00 0.00 0.00 3.36
3008 3294 5.287226 TCCTCTTTCGTTAGAACAACTGAC 58.713 41.667 0.00 0.00 35.86 3.51
3044 3330 9.729281 ACAAAATCATGCTTGAAATATCCTTTT 57.271 25.926 6.36 4.54 34.96 2.27
3045 3331 9.729281 AACAAAATCATGCTTGAAATATCCTTT 57.271 25.926 6.36 0.00 34.96 3.11
3120 3406 9.383519 AGTGGTTGATATTAATAATCATAGCCG 57.616 33.333 0.00 0.00 0.00 5.52
3644 4103 3.317149 CACGACATCTTATCTTCCCGGTA 59.683 47.826 0.00 0.00 0.00 4.02
3648 4107 4.402056 TTCCACGACATCTTATCTTCCC 57.598 45.455 0.00 0.00 0.00 3.97
3788 4248 2.751259 AGTCGTACGCTTCCTATGAACA 59.249 45.455 11.24 0.00 0.00 3.18
3828 4288 9.288576 CTTTTAATACATGGGATGCTAGATGAA 57.711 33.333 0.00 0.00 0.00 2.57
4278 5271 7.699878 AGTTGAGATTAAAGGAGGGTGTTAAT 58.300 34.615 0.00 0.00 31.68 1.40
4365 5358 0.106819 AGGATCAAGTGGCAGATGGC 60.107 55.000 0.00 0.00 43.74 4.40
4407 5400 4.391405 AAGGGTTGCAGAAAAGAAACTG 57.609 40.909 0.00 0.00 37.22 3.16
4422 5415 6.320418 ACTTTCATTTTGTACGAGAAAGGGTT 59.680 34.615 19.73 4.69 45.68 4.11


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

AutoCloner maintained by Alex Coulton.