Multiple sequence alignment - TraesCS2D01G532800

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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 TraesCS2D01G532800 chr2D 100.000 4049 0 0 1 4049 617898036 617893988 0.000000e+00 7478
1 TraesCS2D01G532800 chr2B 94.349 2672 82 25 1411 4047 753799430 753802067 0.000000e+00 4034
2 TraesCS2D01G532800 chr2B 85.144 1252 63 49 253 1414 753798176 753799394 0.000000e+00 1168
3 TraesCS2D01G532800 chr2B 85.652 230 17 7 39 252 753797822 753798051 1.130000e-55 228
4 TraesCS2D01G532800 chr2A 93.972 2306 62 19 1762 4047 748446187 748443939 0.000000e+00 3417
5 TraesCS2D01G532800 chr2A 86.342 1501 67 71 311 1708 748447668 748446203 0.000000e+00 1509
6 TraesCS2D01G532800 chr2A 85.455 330 28 9 1 313 748449118 748448792 3.900000e-85 326
7 TraesCS2D01G532800 chr7B 90.278 1296 118 7 1762 3050 745143454 745144748 0.000000e+00 1688
8 TraesCS2D01G532800 chr7B 94.825 657 21 5 3111 3764 382087448 382088094 0.000000e+00 1013
9 TraesCS2D01G532800 chr1A 90.078 1290 114 8 1762 3050 6423490 6422214 0.000000e+00 1661
10 TraesCS2D01G532800 chr1A 83.828 303 34 9 1005 1305 6424451 6424162 1.430000e-69 274
11 TraesCS2D01G532800 chr7D 89.946 1293 116 7 1762 3050 632162715 632163997 0.000000e+00 1655
12 TraesCS2D01G532800 chr7D 82.099 324 45 7 983 1305 632161857 632162168 8.630000e-67 265
13 TraesCS2D01G532800 chr6A 95.129 657 19 5 3111 3764 477476219 477475573 0.000000e+00 1024
14 TraesCS2D01G532800 chr6A 94.673 657 23 6 3111 3764 239255946 239256593 0.000000e+00 1009
15 TraesCS2D01G532800 chr6B 94.825 657 21 5 3111 3764 714157088 714156442 0.000000e+00 1013
16 TraesCS2D01G532800 chr6B 94.521 657 23 5 3111 3764 40509770 40510416 0.000000e+00 1002
17 TraesCS2D01G532800 chr4A 94.673 657 22 5 3111 3764 29478863 29478217 0.000000e+00 1007
18 TraesCS2D01G532800 chr4A 94.521 657 23 5 3111 3764 51046127 51046773 0.000000e+00 1002
19 TraesCS2D01G532800 chr1B 94.673 657 22 5 3111 3764 82988234 82987588 0.000000e+00 1007
20 TraesCS2D01G532800 chr3B 73.091 550 118 25 2268 2802 779528868 779528334 6.960000e-38 169
21 TraesCS2D01G532800 chr3D 72.747 455 96 23 2362 2802 582054310 582054750 1.180000e-25 128


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 TraesCS2D01G532800 chr2D 617893988 617898036 4048 True 7478.000000 7478 100.000000 1 4049 1 chr2D.!!$R1 4048
1 TraesCS2D01G532800 chr2B 753797822 753802067 4245 False 1810.000000 4034 88.381667 39 4047 3 chr2B.!!$F1 4008
2 TraesCS2D01G532800 chr2A 748443939 748449118 5179 True 1750.666667 3417 88.589667 1 4047 3 chr2A.!!$R1 4046
3 TraesCS2D01G532800 chr7B 745143454 745144748 1294 False 1688.000000 1688 90.278000 1762 3050 1 chr7B.!!$F2 1288
4 TraesCS2D01G532800 chr7B 382087448 382088094 646 False 1013.000000 1013 94.825000 3111 3764 1 chr7B.!!$F1 653
5 TraesCS2D01G532800 chr1A 6422214 6424451 2237 True 967.500000 1661 86.953000 1005 3050 2 chr1A.!!$R1 2045
6 TraesCS2D01G532800 chr7D 632161857 632163997 2140 False 960.000000 1655 86.022500 983 3050 2 chr7D.!!$F1 2067
7 TraesCS2D01G532800 chr6A 477475573 477476219 646 True 1024.000000 1024 95.129000 3111 3764 1 chr6A.!!$R1 653
8 TraesCS2D01G532800 chr6A 239255946 239256593 647 False 1009.000000 1009 94.673000 3111 3764 1 chr6A.!!$F1 653
9 TraesCS2D01G532800 chr6B 714156442 714157088 646 True 1013.000000 1013 94.825000 3111 3764 1 chr6B.!!$R1 653
10 TraesCS2D01G532800 chr6B 40509770 40510416 646 False 1002.000000 1002 94.521000 3111 3764 1 chr6B.!!$F1 653
11 TraesCS2D01G532800 chr4A 29478217 29478863 646 True 1007.000000 1007 94.673000 3111 3764 1 chr4A.!!$R1 653
12 TraesCS2D01G532800 chr4A 51046127 51046773 646 False 1002.000000 1002 94.521000 3111 3764 1 chr4A.!!$F1 653
13 TraesCS2D01G532800 chr1B 82987588 82988234 646 True 1007.000000 1007 94.673000 3111 3764 1 chr1B.!!$R1 653

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
183 203 0.466739 TAGATGCCTGCTGCCATTGG 60.467 55.000 0.00 0.0 40.16 3.16 F
514 1807 2.290367 CGAAGCACACTTGATTCACCAA 59.710 45.455 3.78 0.0 46.61 3.67 F
1379 2798 1.085091 CACTCTGATGGCTGTTGCTC 58.915 55.000 0.00 0.0 39.59 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 2660 0.044702 ACATGGGGATCTGGACCAGA 59.955 55.0 26.28 26.28 44.99 3.86 R
1409 2833 0.108615 CAGCTAGCGTTACCAGCAGT 60.109 55.0 9.55 0.00 37.78 4.40 R
3075 4940 0.039527 GCCAGCAGGTACGGTTTTTG 60.040 55.0 0.00 0.00 37.19 2.44 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
128 130 1.566231 CTCCCTCCAAATAAGGCAGGT 59.434 52.381 0.00 0.00 32.15 4.00
134 136 4.324254 CCTCCAAATAAGGCAGGTAGTGAA 60.324 45.833 0.00 0.00 0.00 3.18
183 203 0.466739 TAGATGCCTGCTGCCATTGG 60.467 55.000 0.00 0.00 40.16 3.16
293 445 9.068008 ACGGTTTTATTTATTAATTTCTGTGCG 57.932 29.630 0.00 0.00 0.00 5.34
294 446 8.528295 CGGTTTTATTTATTAATTTCTGTGCGG 58.472 33.333 0.00 0.00 0.00 5.69
497 1790 4.629634 TGTTGGTAGTATGTGAATGCGAAG 59.370 41.667 0.00 0.00 0.00 3.79
514 1807 2.290367 CGAAGCACACTTGATTCACCAA 59.710 45.455 3.78 0.00 46.61 3.67
518 1811 3.567164 AGCACACTTGATTCACCAAGAAG 59.433 43.478 10.21 5.35 44.66 2.85
519 1812 3.316308 GCACACTTGATTCACCAAGAAGT 59.684 43.478 10.21 5.88 44.66 3.01
520 1813 4.515191 GCACACTTGATTCACCAAGAAGTA 59.485 41.667 10.21 0.00 44.66 2.24
521 1814 5.334414 GCACACTTGATTCACCAAGAAGTAG 60.334 44.000 10.21 5.47 44.66 2.57
522 1815 4.757149 ACACTTGATTCACCAAGAAGTAGC 59.243 41.667 10.21 0.00 44.66 3.58
523 1816 4.999950 CACTTGATTCACCAAGAAGTAGCT 59.000 41.667 10.21 0.00 44.66 3.32
524 1817 6.166279 CACTTGATTCACCAAGAAGTAGCTA 58.834 40.000 10.21 0.00 44.66 3.32
525 1818 6.312426 CACTTGATTCACCAAGAAGTAGCTAG 59.688 42.308 10.21 0.00 44.66 3.42
526 1819 5.344743 TGATTCACCAAGAAGTAGCTAGG 57.655 43.478 0.00 0.00 40.15 3.02
527 1820 4.777896 TGATTCACCAAGAAGTAGCTAGGT 59.222 41.667 0.00 0.00 40.15 3.08
528 1821 5.955959 TGATTCACCAAGAAGTAGCTAGGTA 59.044 40.000 0.00 0.00 40.15 3.08
529 1822 5.656213 TTCACCAAGAAGTAGCTAGGTAC 57.344 43.478 21.85 21.85 0.00 3.34
530 1823 4.669700 TCACCAAGAAGTAGCTAGGTACA 58.330 43.478 28.68 6.84 0.00 2.90
531 1824 5.269991 TCACCAAGAAGTAGCTAGGTACAT 58.730 41.667 28.68 20.07 0.00 2.29
532 1825 6.429151 TCACCAAGAAGTAGCTAGGTACATA 58.571 40.000 28.68 2.80 0.00 2.29
533 1826 7.067421 TCACCAAGAAGTAGCTAGGTACATAT 58.933 38.462 28.68 15.34 0.00 1.78
537 1830 7.371936 CAAGAAGTAGCTAGGTACATATGGAC 58.628 42.308 28.68 9.83 0.00 4.02
583 1880 8.893727 ACCAATCAATATACTTACAAAGACAGC 58.106 33.333 0.00 0.00 0.00 4.40
866 2224 8.543774 AGTATATAATTAGCCTCCACCAATCTG 58.456 37.037 0.00 0.00 0.00 2.90
904 2267 5.453567 ACCAAGATCAGTTTAGCAAAACC 57.546 39.130 0.00 0.00 45.11 3.27
910 2277 6.485171 AGATCAGTTTAGCAAAACCCTACAT 58.515 36.000 0.00 0.00 45.11 2.29
911 2278 7.630082 AGATCAGTTTAGCAAAACCCTACATA 58.370 34.615 0.00 0.00 45.11 2.29
912 2279 8.275040 AGATCAGTTTAGCAAAACCCTACATAT 58.725 33.333 0.00 0.00 45.11 1.78
913 2280 9.555727 GATCAGTTTAGCAAAACCCTACATATA 57.444 33.333 0.00 0.00 45.11 0.86
979 2358 6.532826 AGTTCAATCTCTTTCTTGCTCTCTT 58.467 36.000 0.00 0.00 0.00 2.85
981 2360 7.501892 AGTTCAATCTCTTTCTTGCTCTCTTTT 59.498 33.333 0.00 0.00 0.00 2.27
1263 2660 2.936032 GAGGACCTGCCCCTGGTT 60.936 66.667 0.00 0.00 35.85 3.67
1309 2724 2.486982 GAGAAGCAGGTCAGTACGTACA 59.513 50.000 26.55 5.02 0.00 2.90
1310 2725 2.889045 AGAAGCAGGTCAGTACGTACAA 59.111 45.455 26.55 12.16 0.00 2.41
1379 2798 1.085091 CACTCTGATGGCTGTTGCTC 58.915 55.000 0.00 0.00 39.59 4.26
1409 2833 4.615912 CGCATGATCCATCACTCGTATACA 60.616 45.833 3.32 0.00 40.03 2.29
1556 3059 5.881637 AACAAATATTGTCGTTGTTGCAC 57.118 34.783 2.42 0.00 44.59 4.57
1558 3061 5.212194 ACAAATATTGTCGTTGTTGCACTC 58.788 37.500 0.00 0.00 40.56 3.51
1559 3062 4.419522 AATATTGTCGTTGTTGCACTCC 57.580 40.909 0.00 0.00 0.00 3.85
1590 3115 4.396166 ACGTCCATCCAAATTCATCAAGAC 59.604 41.667 0.00 0.00 0.00 3.01
1661 3192 5.013007 GAGTCAACTCTCTCCGGTACGTC 62.013 56.522 0.00 0.00 45.01 4.34
1718 3264 7.848491 ACATACTTACGAAAGTTTTGTCTGTC 58.152 34.615 11.88 0.00 43.60 3.51
1721 3476 7.316544 ACTTACGAAAGTTTTGTCTGTCAAT 57.683 32.000 11.88 0.00 43.60 2.57
1729 3484 3.419264 TTTGTCTGTCAATGTGTGTGC 57.581 42.857 0.00 0.00 35.84 4.57
1730 3485 1.308047 TGTCTGTCAATGTGTGTGCC 58.692 50.000 0.00 0.00 0.00 5.01
2873 4738 3.137687 CACCAACAAGGGGGCAAC 58.862 61.111 0.00 0.00 43.89 4.17
2892 4757 3.753294 ACGAAGAAGAAGAAGAGCCAA 57.247 42.857 0.00 0.00 0.00 4.52
3070 4935 2.990514 AGTGACGCCAACAAAACAAAAC 59.009 40.909 0.00 0.00 0.00 2.43
3071 4936 2.731976 GTGACGCCAACAAAACAAAACA 59.268 40.909 0.00 0.00 0.00 2.83
3073 4938 3.807622 TGACGCCAACAAAACAAAACAAA 59.192 34.783 0.00 0.00 0.00 2.83
3074 4939 4.272504 TGACGCCAACAAAACAAAACAAAA 59.727 33.333 0.00 0.00 0.00 2.44
3075 4940 4.528504 ACGCCAACAAAACAAAACAAAAC 58.471 34.783 0.00 0.00 0.00 2.43
3148 5013 6.978343 ACTTAATTTGCATTGCGTACTAGA 57.022 33.333 3.84 0.00 0.00 2.43
3159 5024 7.120726 TGCATTGCGTACTAGATAGATAGCTTA 59.879 37.037 3.84 0.00 0.00 3.09
3179 5044 5.538118 CTTATTGTTTTTCAGGACCAACCC 58.462 41.667 0.00 0.00 40.05 4.11
3429 5296 4.142622 TGTTGCAAGATGAATGATCCGAAC 60.143 41.667 0.00 0.00 0.00 3.95
3430 5297 2.945008 TGCAAGATGAATGATCCGAACC 59.055 45.455 0.00 0.00 0.00 3.62
3743 5618 3.785887 ACAGATACACCCACCCACATAAT 59.214 43.478 0.00 0.00 0.00 1.28
3756 5631 7.382110 CCACCCACATAATTATTCAACACAAA 58.618 34.615 0.00 0.00 0.00 2.83
3998 5892 6.089016 CACTCAAACTGCATCACAAATTCATC 59.911 38.462 0.00 0.00 0.00 2.92
4047 5941 9.350357 CTTTTCCACATGAATTTATGTTCTCAG 57.650 33.333 12.81 2.48 39.17 3.35
4048 5942 6.441093 TCCACATGAATTTATGTTCTCAGC 57.559 37.500 12.81 0.00 39.17 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.163818 TCCAGAATCGGACACAACAC 57.836 50.000 0.00 0.00 0.00 3.32
128 130 2.700897 GCTAGCCCTGGATTCTTCACTA 59.299 50.000 2.29 0.00 0.00 2.74
134 136 1.696884 GCTAAGCTAGCCCTGGATTCT 59.303 52.381 12.13 0.00 45.95 2.40
185 205 2.288825 GCTGCATCCATTCCATTCCATG 60.289 50.000 0.00 0.00 0.00 3.66
186 206 1.968493 GCTGCATCCATTCCATTCCAT 59.032 47.619 0.00 0.00 0.00 3.41
187 207 1.342175 TGCTGCATCCATTCCATTCCA 60.342 47.619 0.00 0.00 0.00 3.53
188 208 1.068127 GTGCTGCATCCATTCCATTCC 59.932 52.381 5.27 0.00 0.00 3.01
189 209 1.268896 CGTGCTGCATCCATTCCATTC 60.269 52.381 5.27 0.00 0.00 2.67
190 210 0.742505 CGTGCTGCATCCATTCCATT 59.257 50.000 5.27 0.00 0.00 3.16
289 441 1.636988 ACGCACTAGTAATTCCGCAC 58.363 50.000 0.00 0.00 0.00 5.34
299 451 9.504708 GGAGATATACCATATATACGCACTAGT 57.495 37.037 0.00 0.00 0.00 2.57
301 453 9.503399 CAGGAGATATACCATATATACGCACTA 57.497 37.037 0.00 0.00 0.00 2.74
381 1667 9.941325 TTGTGCATGATTGAACCTTTATTTATT 57.059 25.926 0.00 0.00 29.21 1.40
382 1668 9.369904 GTTGTGCATGATTGAACCTTTATTTAT 57.630 29.630 0.00 0.00 29.21 1.40
383 1669 8.363390 TGTTGTGCATGATTGAACCTTTATTTA 58.637 29.630 0.00 0.00 29.21 1.40
384 1670 7.215789 TGTTGTGCATGATTGAACCTTTATTT 58.784 30.769 0.00 0.00 29.21 1.40
385 1671 6.757237 TGTTGTGCATGATTGAACCTTTATT 58.243 32.000 0.00 0.00 29.21 1.40
386 1672 6.209192 TCTGTTGTGCATGATTGAACCTTTAT 59.791 34.615 0.00 0.00 29.21 1.40
387 1673 5.534278 TCTGTTGTGCATGATTGAACCTTTA 59.466 36.000 0.00 0.00 29.21 1.85
388 1674 4.341806 TCTGTTGTGCATGATTGAACCTTT 59.658 37.500 0.00 0.00 29.21 3.11
389 1675 3.890756 TCTGTTGTGCATGATTGAACCTT 59.109 39.130 0.00 0.00 29.21 3.50
497 1790 3.316308 ACTTCTTGGTGAATCAAGTGTGC 59.684 43.478 3.35 0.00 43.25 4.57
514 1807 6.011481 GGTCCATATGTACCTAGCTACTTCT 58.989 44.000 10.11 0.00 32.72 2.85
518 1811 5.567025 GCAAGGTCCATATGTACCTAGCTAC 60.567 48.000 19.38 5.19 45.51 3.58
519 1812 4.527038 GCAAGGTCCATATGTACCTAGCTA 59.473 45.833 19.38 0.00 45.51 3.32
520 1813 3.325135 GCAAGGTCCATATGTACCTAGCT 59.675 47.826 19.38 2.53 45.51 3.32
521 1814 3.325135 AGCAAGGTCCATATGTACCTAGC 59.675 47.826 19.38 8.10 45.51 3.42
522 1815 5.163301 ACAAGCAAGGTCCATATGTACCTAG 60.163 44.000 19.38 10.22 45.51 3.02
523 1816 4.719773 ACAAGCAAGGTCCATATGTACCTA 59.280 41.667 19.38 0.00 45.51 3.08
525 1818 3.886123 ACAAGCAAGGTCCATATGTACC 58.114 45.455 9.39 9.39 35.91 3.34
526 1819 5.183140 ACAAACAAGCAAGGTCCATATGTAC 59.817 40.000 1.24 0.00 0.00 2.90
527 1820 5.321102 ACAAACAAGCAAGGTCCATATGTA 58.679 37.500 1.24 0.00 0.00 2.29
528 1821 4.151883 ACAAACAAGCAAGGTCCATATGT 58.848 39.130 1.24 0.00 0.00 2.29
529 1822 4.789012 ACAAACAAGCAAGGTCCATATG 57.211 40.909 0.00 0.00 0.00 1.78
530 1823 5.539955 AGAAACAAACAAGCAAGGTCCATAT 59.460 36.000 0.00 0.00 0.00 1.78
531 1824 4.892934 AGAAACAAACAAGCAAGGTCCATA 59.107 37.500 0.00 0.00 0.00 2.74
532 1825 3.706086 AGAAACAAACAAGCAAGGTCCAT 59.294 39.130 0.00 0.00 0.00 3.41
533 1826 3.096092 AGAAACAAACAAGCAAGGTCCA 58.904 40.909 0.00 0.00 0.00 4.02
537 1830 3.865164 GGTGAAGAAACAAACAAGCAAGG 59.135 43.478 0.00 0.00 0.00 3.61
672 1987 6.040504 TGCTATCTGTACTAATACACTGGGTG 59.959 42.308 0.00 0.00 36.34 4.61
673 1988 6.134055 TGCTATCTGTACTAATACACTGGGT 58.866 40.000 0.00 0.00 36.34 4.51
675 1990 6.642950 GCTTGCTATCTGTACTAATACACTGG 59.357 42.308 0.00 0.00 36.34 4.00
678 1993 7.203910 AGTGCTTGCTATCTGTACTAATACAC 58.796 38.462 0.00 0.00 36.34 2.90
713 2050 2.421424 CACAGTTGAGGGCAAGATTAGC 59.579 50.000 0.00 0.00 34.01 3.09
807 2148 1.430369 ATTGGGGGCCAGGCTAGATC 61.430 60.000 12.43 0.00 33.81 2.75
841 2182 8.322091 ACAGATTGGTGGAGGCTAATTATATAC 58.678 37.037 0.00 0.00 0.00 1.47
844 2185 6.558775 AGACAGATTGGTGGAGGCTAATTATA 59.441 38.462 0.00 0.00 0.00 0.98
845 2186 5.370880 AGACAGATTGGTGGAGGCTAATTAT 59.629 40.000 0.00 0.00 0.00 1.28
866 2224 5.954296 TCTTGGTAGGTGCGTATATAGAC 57.046 43.478 0.00 0.00 0.00 2.59
967 2346 3.244700 CCTCCTCCAAAAGAGAGCAAGAA 60.245 47.826 0.00 0.00 46.50 2.52
979 2358 3.598264 TCCTTCTTCTTCCTCCTCCAAA 58.402 45.455 0.00 0.00 0.00 3.28
981 2360 3.110705 CATCCTTCTTCTTCCTCCTCCA 58.889 50.000 0.00 0.00 0.00 3.86
1193 2581 2.278330 CCCTTGTTCCTGCTTGGGC 61.278 63.158 0.00 0.00 36.20 5.36
1263 2660 0.044702 ACATGGGGATCTGGACCAGA 59.955 55.000 26.28 26.28 44.99 3.86
1409 2833 0.108615 CAGCTAGCGTTACCAGCAGT 60.109 55.000 9.55 0.00 37.78 4.40
1495 2998 7.273712 TGCATGCATATGTTGTGGAAATTAAT 58.726 30.769 18.46 0.00 36.65 1.40
1496 2999 6.637657 TGCATGCATATGTTGTGGAAATTAA 58.362 32.000 18.46 0.00 36.65 1.40
1497 3000 6.218108 TGCATGCATATGTTGTGGAAATTA 57.782 33.333 18.46 0.00 36.65 1.40
1498 3001 5.087391 TGCATGCATATGTTGTGGAAATT 57.913 34.783 18.46 0.00 36.65 1.82
1525 3028 3.304257 GACAATATTTGTTGTGCGTGCA 58.696 40.909 0.00 0.00 45.52 4.57
1554 3057 0.611062 TGGACGTACAGGAGGGAGTG 60.611 60.000 0.00 0.00 0.00 3.51
1555 3058 0.335361 ATGGACGTACAGGAGGGAGT 59.665 55.000 6.62 0.00 0.00 3.85
1556 3059 1.033574 GATGGACGTACAGGAGGGAG 58.966 60.000 6.62 0.00 0.00 4.30
1558 3061 0.686441 TGGATGGACGTACAGGAGGG 60.686 60.000 6.62 0.00 0.00 4.30
1559 3062 1.191535 TTGGATGGACGTACAGGAGG 58.808 55.000 6.62 0.00 0.00 4.30
1653 3184 3.166657 GCAAAGTAGTACTGACGTACCG 58.833 50.000 5.39 0.00 45.68 4.02
1655 3186 3.505836 GGGCAAAGTAGTACTGACGTAC 58.494 50.000 5.39 0.00 45.04 3.67
1661 3192 2.930040 CACATCGGGCAAAGTAGTACTG 59.070 50.000 5.39 0.00 0.00 2.74
1718 3264 0.538057 ACTCAGGGGCACACACATTG 60.538 55.000 0.00 0.00 0.00 2.82
1721 3476 1.631071 TTCACTCAGGGGCACACACA 61.631 55.000 0.00 0.00 0.00 3.72
1729 3484 4.351874 TTCTACTTGTTTCACTCAGGGG 57.648 45.455 0.00 0.00 0.00 4.79
1730 3485 8.567285 AATAATTCTACTTGTTTCACTCAGGG 57.433 34.615 0.00 0.00 0.00 4.45
2873 4738 3.120373 GCTTTGGCTCTTCTTCTTCTTCG 60.120 47.826 0.00 0.00 35.22 3.79
3070 4935 3.549873 CAGCAGGTACGGTTTTTGTTTTG 59.450 43.478 0.00 0.00 0.00 2.44
3071 4936 3.429684 CCAGCAGGTACGGTTTTTGTTTT 60.430 43.478 0.00 0.00 0.00 2.43
3073 4938 1.679153 CCAGCAGGTACGGTTTTTGTT 59.321 47.619 0.00 0.00 0.00 2.83
3074 4939 1.314730 CCAGCAGGTACGGTTTTTGT 58.685 50.000 0.00 0.00 0.00 2.83
3075 4940 0.039527 GCCAGCAGGTACGGTTTTTG 60.040 55.000 0.00 0.00 37.19 2.44
3148 5013 9.343539 GGTCCTGAAAAACAATAAGCTATCTAT 57.656 33.333 0.00 0.00 0.00 1.98
3159 5024 3.379452 TGGGTTGGTCCTGAAAAACAAT 58.621 40.909 0.00 0.00 36.25 2.71
3205 5072 2.170166 TGGAAATTAAGCTGGTGCCTG 58.830 47.619 0.00 0.00 40.80 4.85
3429 5296 7.597386 GGCTTTAAAGGCTATTGATATCTTGG 58.403 38.462 29.08 0.00 46.98 3.61
3765 5640 5.699839 GACAAGCGTCTGAAATGGTAATTT 58.300 37.500 0.00 0.00 39.22 1.82
3767 5642 4.946784 GACAAGCGTCTGAAATGGTAAT 57.053 40.909 0.00 0.00 39.22 1.89
3998 5892 6.602179 AGATTGTCGTTGTTTACATGTCATG 58.398 36.000 11.41 11.41 0.00 3.07


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

AutoCloner maintained by Alex Coulton.