Multiple sequence alignment - TraesCS6A01G011000

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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 TraesCS6A01G011000 chr6A 100.000 3077 0 0 1 3077 5136833 5133757 0.000000e+00 5683.0
1 TraesCS6A01G011000 chr6A 89.992 1299 126 2 944 2242 4855252 4856546 0.000000e+00 1676.0
2 TraesCS6A01G011000 chr6A 83.051 531 50 16 2289 2782 4856617 4857144 2.180000e-121 446.0
3 TraesCS6A01G011000 chr6A 91.250 160 11 3 2792 2949 4857338 4857496 6.680000e-52 215.0
4 TraesCS6A01G011000 chr6D 93.595 1655 95 6 944 2591 5830417 5828767 0.000000e+00 2459.0
5 TraesCS6A01G011000 chr6D 92.444 450 34 0 1275 1724 13863554 13864003 0.000000e+00 643.0
6 TraesCS6A01G011000 chr6D 84.305 446 52 1 1797 2242 13864006 13864433 1.320000e-113 420.0
7 TraesCS6A01G011000 chr6D 81.970 538 53 17 2289 2785 13864505 13865039 1.710000e-112 416.0
8 TraesCS6A01G011000 chr6D 89.735 302 12 10 2792 3075 5828519 5828219 4.850000e-98 368.0
9 TraesCS6A01G011000 chr6D 78.887 521 77 14 280 791 5831068 5830572 3.830000e-84 322.0
10 TraesCS6A01G011000 chr6D 96.212 132 5 0 2658 2789 5828749 5828618 1.860000e-52 217.0
11 TraesCS6A01G011000 chr6D 82.569 218 29 8 216 430 387789464 387789675 1.880000e-42 183.0
12 TraesCS6A01G011000 chr6D 81.132 212 33 5 221 430 399041615 399041409 2.460000e-36 163.0
13 TraesCS6A01G011000 chr6D 85.030 167 15 5 2792 2949 13865213 13865378 8.830000e-36 161.0
14 TraesCS6A01G011000 chrUn 92.683 1599 104 6 790 2381 76006774 76008366 0.000000e+00 2292.0
15 TraesCS6A01G011000 chrUn 91.358 567 37 5 215 778 76005936 76006493 0.000000e+00 765.0
16 TraesCS6A01G011000 chrUn 94.037 218 13 0 1 218 76005422 76005639 6.360000e-87 331.0
17 TraesCS6A01G011000 chrUn 85.449 323 23 7 2365 2682 76008463 76008766 6.400000e-82 315.0
18 TraesCS6A01G011000 chrUn 82.178 202 26 8 229 425 34141245 34141049 6.830000e-37 165.0
19 TraesCS6A01G011000 chrUn 82.178 202 26 8 229 425 34207341 34207537 6.830000e-37 165.0
20 TraesCS6A01G011000 chr1D 81.132 212 35 4 221 430 110656357 110656149 6.830000e-37 165.0
21 TraesCS6A01G011000 chr5B 80.645 217 35 6 218 431 616650747 616650535 8.830000e-36 161.0
22 TraesCS6A01G011000 chr4D 80.841 214 30 10 221 430 419305030 419304824 1.140000e-34 158.0
23 TraesCS6A01G011000 chr7D 80.093 216 36 6 218 430 105926879 105927090 1.480000e-33 154.0
24 TraesCS6A01G011000 chr5D 92.157 51 0 4 2677 2725 530793864 530793816 5.510000e-08 69.4
25 TraesCS6A01G011000 chr7B 85.246 61 5 2 2677 2737 713379110 713379054 3.310000e-05 60.2


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 TraesCS6A01G011000 chr6A 5133757 5136833 3076 True 5683.00 5683 100.000000 1 3077 1 chr6A.!!$R1 3076
1 TraesCS6A01G011000 chr6A 4855252 4857496 2244 False 779.00 1676 88.097667 944 2949 3 chr6A.!!$F1 2005
2 TraesCS6A01G011000 chr6D 5828219 5831068 2849 True 841.50 2459 89.607250 280 3075 4 chr6D.!!$R2 2795
3 TraesCS6A01G011000 chr6D 13863554 13865378 1824 False 410.00 643 85.937250 1275 2949 4 chr6D.!!$F2 1674
4 TraesCS6A01G011000 chrUn 76005422 76008766 3344 False 925.75 2292 90.881750 1 2682 4 chrUn.!!$F2 2681

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
303 604 0.034896 GCTCTCCCGACTTGGTGAAA 59.965 55.0 0.00 0.0 35.15 2.69 F
587 895 0.621609 GTGGGCCCAACCATGTAGTA 59.378 55.0 30.64 0.0 43.59 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1169 1834 0.468400 GGTGTAGGCGAGGAGGATCT 60.468 60.0 0.0 0.0 33.73 2.75 R
2127 2793 0.965866 GCAAGGAGGGGTTTAGGTGC 60.966 60.0 0.0 0.0 0.00 5.01 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
25 26 7.155328 TGAAGAGATCTTGACTAAACTTGTCC 58.845 38.462 0.00 0.00 36.11 4.02
36 37 6.426937 TGACTAAACTTGTCCTGCATTAACTC 59.573 38.462 0.00 0.00 33.83 3.01
47 48 8.049117 TGTCCTGCATTAACTCAGAATTTCTAT 58.951 33.333 0.00 0.00 32.26 1.98
51 52 6.772716 TGCATTAACTCAGAATTTCTATCCCC 59.227 38.462 0.00 0.00 0.00 4.81
135 136 8.553459 TTTGTTTCAGCAAAGTTATTTTTGGA 57.447 26.923 1.28 0.00 38.25 3.53
163 164 5.003804 ACAACACATCTCTCCAAACCATAC 58.996 41.667 0.00 0.00 0.00 2.39
172 173 5.302059 TCTCTCCAAACCATACGAATAGAGG 59.698 44.000 0.00 0.00 31.13 3.69
184 185 2.446435 GAATAGAGGGGTTGCTTGCAA 58.554 47.619 3.70 3.70 0.00 4.08
210 211 3.974719 TGCTTGGGTATGCATAGGAAAA 58.025 40.909 6.67 0.00 32.67 2.29
240 541 9.824216 TTATACATATACCTCTTCTAAGCCACT 57.176 33.333 0.00 0.00 0.00 4.00
241 542 6.412362 ACATATACCTCTTCTAAGCCACTG 57.588 41.667 0.00 0.00 0.00 3.66
248 549 0.037326 TTCTAAGCCACTGCACGAGG 60.037 55.000 0.00 0.00 41.13 4.63
253 554 1.185618 AGCCACTGCACGAGGTAAGA 61.186 55.000 0.00 0.00 41.13 2.10
270 571 7.096436 CGAGGTAAGATGATCAGTTGTAAATCG 60.096 40.741 0.09 1.65 0.00 3.34
277 578 2.063266 TCAGTTGTAAATCGCCGACAC 58.937 47.619 0.00 0.00 0.00 3.67
278 579 1.795872 CAGTTGTAAATCGCCGACACA 59.204 47.619 0.00 0.00 0.00 3.72
284 585 3.615056 TGTAAATCGCCGACACATGTAAG 59.385 43.478 0.00 0.00 0.00 2.34
297 598 2.093973 ACATGTAAGCTCTCCCGACTTG 60.094 50.000 0.00 0.00 0.00 3.16
303 604 0.034896 GCTCTCCCGACTTGGTGAAA 59.965 55.000 0.00 0.00 35.15 2.69
308 609 4.975631 TCTCCCGACTTGGTGAAAATTTA 58.024 39.130 0.00 0.00 35.15 1.40
312 613 4.517453 CCCGACTTGGTGAAAATTTACTGA 59.483 41.667 0.00 0.00 35.15 3.41
380 681 5.981315 CACGTTAAAACTTGTGTCTCCTCTA 59.019 40.000 0.00 0.00 0.00 2.43
418 719 1.265635 CGTCTTTTCATTTGCCCGTCA 59.734 47.619 0.00 0.00 0.00 4.35
430 731 6.545666 TCATTTGCCCGTCATATCTTTAACAT 59.454 34.615 0.00 0.00 0.00 2.71
491 795 7.448161 CCTCATGCCATACACCTATATTTTTCA 59.552 37.037 0.00 0.00 0.00 2.69
560 864 7.693969 AATTTCTTTGACCAAGGAGTATCTG 57.306 36.000 0.00 0.00 32.64 2.90
587 895 0.621609 GTGGGCCCAACCATGTAGTA 59.378 55.000 30.64 0.00 43.59 1.82
631 939 3.387699 TGCAATTCCCACGATCATCTCTA 59.612 43.478 0.00 0.00 0.00 2.43
634 942 5.471456 GCAATTCCCACGATCATCTCTAAAT 59.529 40.000 0.00 0.00 0.00 1.40
635 943 6.016777 GCAATTCCCACGATCATCTCTAAATT 60.017 38.462 0.00 0.00 0.00 1.82
636 944 7.173218 GCAATTCCCACGATCATCTCTAAATTA 59.827 37.037 0.00 0.00 0.00 1.40
637 945 8.499162 CAATTCCCACGATCATCTCTAAATTAC 58.501 37.037 0.00 0.00 0.00 1.89
638 946 5.769367 TCCCACGATCATCTCTAAATTACG 58.231 41.667 0.00 0.00 0.00 3.18
639 947 4.923871 CCCACGATCATCTCTAAATTACGG 59.076 45.833 0.00 0.00 0.00 4.02
640 948 5.278808 CCCACGATCATCTCTAAATTACGGA 60.279 44.000 0.00 0.00 0.00 4.69
641 949 5.859114 CCACGATCATCTCTAAATTACGGAG 59.141 44.000 0.00 0.00 0.00 4.63
672 980 2.737359 GCGATGTCTGTTGACCGGATTA 60.737 50.000 9.46 0.00 42.28 1.75
696 1004 4.025396 GGAGATGATTGAGTACGTTGCATG 60.025 45.833 0.00 0.00 0.00 4.06
709 1017 6.708502 AGTACGTTGCATGGCATATAATAACA 59.291 34.615 0.00 0.00 38.76 2.41
780 1088 7.596995 CCGTTGAAACCTTTAATTTGCAATCTA 59.403 33.333 0.00 0.00 0.00 1.98
781 1089 8.973378 CGTTGAAACCTTTAATTTGCAATCTAA 58.027 29.630 0.00 0.00 0.00 2.10
823 1400 4.510167 AGGTGATAAGCTTGCATTACCT 57.490 40.909 16.30 16.30 36.58 3.08
880 1457 4.018506 TGCTCCCAAAAGATACTGATCCAA 60.019 41.667 0.00 0.00 31.81 3.53
886 1544 6.709846 CCCAAAAGATACTGATCCAAGATCTC 59.290 42.308 0.00 0.00 31.81 2.75
894 1552 5.599732 ACTGATCCAAGATCTCTTCATTCG 58.400 41.667 0.00 0.00 33.11 3.34
896 1554 2.814269 TCCAAGATCTCTTCATTCGCG 58.186 47.619 0.00 0.00 33.11 5.87
897 1555 1.863454 CCAAGATCTCTTCATTCGCGG 59.137 52.381 6.13 0.00 33.11 6.46
909 1567 2.933906 TCATTCGCGGAACTGAATAACC 59.066 45.455 6.13 0.00 33.23 2.85
911 1569 1.717194 TCGCGGAACTGAATAACCAC 58.283 50.000 6.13 0.00 0.00 4.16
919 1577 5.365619 GGAACTGAATAACCACCGTCATAT 58.634 41.667 0.00 0.00 0.00 1.78
920 1578 5.236478 GGAACTGAATAACCACCGTCATATG 59.764 44.000 0.00 0.00 0.00 1.78
932 1593 1.002430 CGTCATATGTAGGGCAGGCAT 59.998 52.381 1.90 0.00 0.00 4.40
979 1644 2.725275 AATGGCACCACGAAAACGCG 62.725 55.000 3.53 3.53 37.29 6.01
997 1662 1.202325 GCGAACGGAAAAACAACCCTT 60.202 47.619 0.00 0.00 0.00 3.95
1000 1665 1.187087 ACGGAAAAACAACCCTTGCA 58.813 45.000 0.00 0.00 0.00 4.08
1001 1666 1.760029 ACGGAAAAACAACCCTTGCAT 59.240 42.857 0.00 0.00 0.00 3.96
1004 1669 1.526464 GAAAAACAACCCTTGCATGCG 59.474 47.619 14.09 0.35 0.00 4.73
1007 1672 3.376078 CAACCCTTGCATGCGGCT 61.376 61.111 14.09 0.00 45.15 5.52
1033 1698 3.845259 GGATGCTACCGGCGGACA 61.845 66.667 35.78 26.25 45.43 4.02
1239 1904 1.216710 GCCCTTCGTCTCTCTGGTG 59.783 63.158 0.00 0.00 0.00 4.17
1244 1909 1.476085 CTTCGTCTCTCTGGTGCATCT 59.524 52.381 0.00 0.00 0.00 2.90
1287 1952 3.286751 GCCAACAAGCACCTCGCA 61.287 61.111 0.00 0.00 46.13 5.10
1296 1961 2.432628 CACCTCGCACCCTTCGTC 60.433 66.667 0.00 0.00 0.00 4.20
1344 2009 1.614241 GCCGGTATGACCCTGTGACT 61.614 60.000 1.90 0.00 33.75 3.41
1347 2012 1.548719 CGGTATGACCCTGTGACTTCA 59.451 52.381 0.00 0.00 33.75 3.02
1635 2300 2.970324 GCCGCACTGTCCGACAAA 60.970 61.111 2.19 0.00 0.00 2.83
1675 2341 2.016318 CTGTCACTGAACACTTTGGCA 58.984 47.619 0.00 0.00 0.00 4.92
1711 2377 1.207811 ACCACGATGAGCATGATGACA 59.792 47.619 0.00 0.00 0.00 3.58
1803 2469 1.381928 CGAGGAAGCTAGGCACGGTA 61.382 60.000 0.00 0.00 0.00 4.02
1888 2554 1.593296 GAGGCTACGGTTCCTCGTGT 61.593 60.000 11.63 0.00 43.70 4.49
1935 2601 0.328592 TACAATTACCTGGCGGCCAA 59.671 50.000 23.94 8.54 30.80 4.52
1992 2658 1.034838 AGCTGCGGTTGTTTGAACCA 61.035 50.000 0.00 0.00 40.28 3.67
2074 2740 1.311859 CATGTTGCGGATACATGGCT 58.688 50.000 17.88 0.00 45.72 4.75
2089 2755 2.730672 GGCTAACGCTGTGTGCTCG 61.731 63.158 0.00 0.00 40.11 5.03
2127 2793 4.530875 AGACCAAGGAAATTCATAGGCAG 58.469 43.478 0.00 0.00 0.00 4.85
2190 2856 4.677182 AGAGGTTACAGGGCATGAAAATT 58.323 39.130 5.99 0.00 0.00 1.82
2192 2858 5.047092 AGAGGTTACAGGGCATGAAAATTTG 60.047 40.000 5.99 0.00 0.00 2.32
2507 3351 9.698309 TCTAGTCAAAGTAATTTCAGTCTTGAG 57.302 33.333 0.00 0.00 34.15 3.02
2516 3360 4.487714 TTTCAGTCTTGAGTCACCAAGT 57.512 40.909 0.00 0.00 42.95 3.16
2546 3409 1.444933 TGGAACCAGGAAGTGACCAT 58.555 50.000 0.00 0.00 0.00 3.55
2547 3410 1.780309 TGGAACCAGGAAGTGACCATT 59.220 47.619 0.00 0.00 0.00 3.16
2548 3411 2.983192 TGGAACCAGGAAGTGACCATTA 59.017 45.455 0.00 0.00 0.00 1.90
2738 3608 3.243336 GTGACAGTCTGTTTACTAGCGG 58.757 50.000 7.00 0.00 0.00 5.52
2741 3611 0.535797 AGTCTGTTTACTAGCGGCCC 59.464 55.000 0.00 0.00 0.00 5.80
2790 3661 9.606631 ATTATGTTTTTCCTTGTTTTGCTAACA 57.393 25.926 1.54 1.54 0.00 2.41
2820 3875 7.621832 TGAACTTCGTTAATGCAAAGAATTG 57.378 32.000 0.00 0.00 34.69 2.32
2949 4014 3.160679 ACAGCTAGCAAGGAAAATGGT 57.839 42.857 18.83 0.00 0.00 3.55
2956 4021 5.823045 GCTAGCAAGGAAAATGGTAGTGTAT 59.177 40.000 10.63 0.00 45.86 2.29
2989 4055 3.378427 GCAAAGAGAAAGTGGAGTGTGTT 59.622 43.478 0.00 0.00 0.00 3.32
3000 4100 3.055385 GTGGAGTGTGTTAGCATCCCTAA 60.055 47.826 0.00 0.00 33.69 2.69
3014 4114 0.543749 CCCTAACCTGAAGGCTCCAG 59.456 60.000 0.00 0.00 39.32 3.86
3015 4115 0.107459 CCTAACCTGAAGGCTCCAGC 60.107 60.000 0.00 0.00 39.32 4.85
3016 4116 0.908198 CTAACCTGAAGGCTCCAGCT 59.092 55.000 0.00 0.00 41.70 4.24
3017 4117 0.615331 TAACCTGAAGGCTCCAGCTG 59.385 55.000 6.78 6.78 41.70 4.24
3018 4118 2.438075 CCTGAAGGCTCCAGCTGC 60.438 66.667 8.66 0.00 41.70 5.25
3070 4170 1.339055 CGTCCCCAGCATCTGAAGAAA 60.339 52.381 0.00 0.00 32.44 2.52
3075 4175 2.517959 CCAGCATCTGAAGAAACCCAA 58.482 47.619 0.00 0.00 32.44 4.12
3076 4176 2.229784 CCAGCATCTGAAGAAACCCAAC 59.770 50.000 0.00 0.00 32.44 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.716628 AGAAATTCTGAGTTAATGCAGGACAA 59.283 34.615 0.00 0.00 33.05 3.18
25 26 7.040823 GGGGATAGAAATTCTGAGTTAATGCAG 60.041 40.741 5.64 2.16 0.00 4.41
127 128 7.227156 AGAGATGTGTTGTACTCTCCAAAAAT 58.773 34.615 4.43 0.00 35.19 1.82
135 136 5.511545 GGTTTGGAGAGATGTGTTGTACTCT 60.512 44.000 0.00 0.00 41.52 3.24
163 164 1.017387 GCAAGCAACCCCTCTATTCG 58.983 55.000 0.00 0.00 0.00 3.34
228 529 1.354040 CTCGTGCAGTGGCTTAGAAG 58.646 55.000 0.00 0.00 41.91 2.85
231 532 0.530744 TACCTCGTGCAGTGGCTTAG 59.469 55.000 0.00 0.00 41.91 2.18
240 541 2.760650 ACTGATCATCTTACCTCGTGCA 59.239 45.455 0.00 0.00 0.00 4.57
241 542 3.444703 ACTGATCATCTTACCTCGTGC 57.555 47.619 0.00 0.00 0.00 5.34
248 549 6.562270 CGGCGATTTACAACTGATCATCTTAC 60.562 42.308 0.00 0.00 0.00 2.34
253 554 3.555956 GTCGGCGATTTACAACTGATCAT 59.444 43.478 14.79 0.00 0.00 2.45
270 571 1.281899 GAGAGCTTACATGTGTCGGC 58.718 55.000 9.11 7.28 0.00 5.54
277 578 2.544685 CAAGTCGGGAGAGCTTACATG 58.455 52.381 0.00 0.00 41.26 3.21
278 579 1.482593 CCAAGTCGGGAGAGCTTACAT 59.517 52.381 0.00 0.00 41.26 2.29
284 585 0.034896 TTTCACCAAGTCGGGAGAGC 59.965 55.000 0.00 0.00 41.26 4.09
297 598 3.821841 CGCCAGTCAGTAAATTTTCACC 58.178 45.455 0.00 0.00 0.00 4.02
303 604 1.024579 CGGGCGCCAGTCAGTAAATT 61.025 55.000 30.85 0.00 0.00 1.82
312 613 4.887190 AAAACCACGGGCGCCAGT 62.887 61.111 30.85 29.04 0.00 4.00
365 666 7.824779 GGAATTAAACATAGAGGAGACACAAGT 59.175 37.037 0.00 0.00 0.00 3.16
418 719 7.497595 TCGGTGTAGCAGAATGTTAAAGATAT 58.502 34.615 0.00 0.00 39.31 1.63
430 731 2.167662 TGATCACTCGGTGTAGCAGAA 58.832 47.619 0.00 0.00 34.79 3.02
539 843 5.544176 AGTCAGATACTCCTTGGTCAAAGAA 59.456 40.000 0.00 0.00 33.28 2.52
560 864 3.276006 TGGTTGGGCCCACTGTAAGTC 62.276 57.143 28.70 8.38 39.04 3.01
587 895 5.445939 GCACGATTCGTACAATTCAGTTGAT 60.446 40.000 11.99 0.00 38.32 2.57
631 939 7.225931 ACATCGCACAATTATACTCCGTAATTT 59.774 33.333 0.00 0.00 31.28 1.82
634 942 5.593968 ACATCGCACAATTATACTCCGTAA 58.406 37.500 0.00 0.00 0.00 3.18
635 943 5.009310 AGACATCGCACAATTATACTCCGTA 59.991 40.000 0.00 0.00 0.00 4.02
636 944 4.049186 GACATCGCACAATTATACTCCGT 58.951 43.478 0.00 0.00 0.00 4.69
637 945 4.148871 CAGACATCGCACAATTATACTCCG 59.851 45.833 0.00 0.00 0.00 4.63
638 946 5.050490 ACAGACATCGCACAATTATACTCC 58.950 41.667 0.00 0.00 0.00 3.85
639 947 6.255670 TCAACAGACATCGCACAATTATACTC 59.744 38.462 0.00 0.00 0.00 2.59
640 948 6.036083 GTCAACAGACATCGCACAATTATACT 59.964 38.462 0.00 0.00 32.50 2.12
641 949 6.185399 GTCAACAGACATCGCACAATTATAC 58.815 40.000 0.00 0.00 32.50 1.47
672 980 3.195610 TGCAACGTACTCAATCATCTCCT 59.804 43.478 0.00 0.00 0.00 3.69
696 1004 7.382110 TCTCTTGAGAGCTGTTATTATATGCC 58.618 38.462 0.00 0.00 41.80 4.40
709 1017 5.221823 GGCCCTAAAATATCTCTTGAGAGCT 60.222 44.000 6.49 0.00 41.80 4.09
781 1089 9.461312 TCACCTTATTTCTTTGTATGCAAGTAT 57.539 29.630 0.00 0.00 35.82 2.12
786 1094 8.405531 GCTTATCACCTTATTTCTTTGTATGCA 58.594 33.333 0.00 0.00 0.00 3.96
787 1095 8.624776 AGCTTATCACCTTATTTCTTTGTATGC 58.375 33.333 0.00 0.00 0.00 3.14
880 1457 2.428890 AGTTCCGCGAATGAAGAGATCT 59.571 45.455 8.23 0.00 0.00 2.75
886 1544 4.494199 GGTTATTCAGTTCCGCGAATGAAG 60.494 45.833 8.23 0.00 35.31 3.02
894 1552 0.725117 CGGTGGTTATTCAGTTCCGC 59.275 55.000 0.00 0.00 0.00 5.54
896 1554 3.048337 TGACGGTGGTTATTCAGTTCC 57.952 47.619 0.00 0.00 0.00 3.62
897 1555 5.815740 ACATATGACGGTGGTTATTCAGTTC 59.184 40.000 10.38 0.00 0.00 3.01
909 1567 1.270305 CCTGCCCTACATATGACGGTG 60.270 57.143 10.38 4.82 0.00 4.94
911 1569 0.320771 GCCTGCCCTACATATGACGG 60.321 60.000 10.38 8.74 0.00 4.79
919 1577 1.371183 GCGATATGCCTGCCCTACA 59.629 57.895 0.00 0.00 37.76 2.74
920 1578 4.285851 GCGATATGCCTGCCCTAC 57.714 61.111 0.00 0.00 37.76 3.18
932 1593 0.032130 GGATCTGCAACCGAGCGATA 59.968 55.000 0.00 0.00 37.31 2.92
979 1644 2.198406 GCAAGGGTTGTTTTTCCGTTC 58.802 47.619 0.00 0.00 30.83 3.95
1007 1672 2.183300 GTAGCATCCACGACGCCA 59.817 61.111 0.00 0.00 0.00 5.69
1015 1680 3.845259 GTCCGCCGGTAGCATCCA 61.845 66.667 1.63 0.00 44.04 3.41
1169 1834 0.468400 GGTGTAGGCGAGGAGGATCT 60.468 60.000 0.00 0.00 33.73 2.75
1287 1952 4.052229 CTCCGTGCGACGAAGGGT 62.052 66.667 14.13 0.00 46.05 4.34
1635 2300 2.233566 TCCCCAGCTGACATTGCCT 61.234 57.895 17.39 0.00 0.00 4.75
1711 2377 2.939261 CGCCAGGGAGTACAACGGT 61.939 63.158 0.00 0.00 0.00 4.83
1803 2469 3.806667 GGCATGGCTGGGAGCTCT 61.807 66.667 14.64 0.00 41.99 4.09
1821 2487 2.096248 TGGACTGGTTTGTTGTTGGTC 58.904 47.619 0.00 0.00 0.00 4.02
1888 2554 4.529109 TGGTAATCATGAACACGTCAGA 57.471 40.909 0.00 0.00 40.43 3.27
1935 2601 1.920835 GACCTCCTGCTCCCAACCT 60.921 63.158 0.00 0.00 0.00 3.50
1992 2658 3.836562 ACATACTACCAAGAGGGACGTTT 59.163 43.478 0.00 0.00 41.15 3.60
2089 2755 2.158813 TGGTCTCCAAGTCAAGGACAAC 60.159 50.000 0.00 0.00 34.60 3.32
2127 2793 0.965866 GCAAGGAGGGGTTTAGGTGC 60.966 60.000 0.00 0.00 0.00 5.01
2133 2799 3.564352 CCTCAAATAGCAAGGAGGGGTTT 60.564 47.826 0.00 0.00 42.55 3.27
2190 2856 4.162320 CCTGATAGTTCTGCCTAGGAACAA 59.838 45.833 14.75 0.00 43.67 2.83
2192 2858 3.070302 CCCTGATAGTTCTGCCTAGGAAC 59.930 52.174 14.75 8.42 42.15 3.62
2242 2908 4.175516 CACCCAAAATGTTTGATCCATCG 58.824 43.478 2.30 0.00 0.00 3.84
2375 3071 7.630470 TCGCAAATTTTATGAAACGAAACAT 57.370 28.000 0.00 0.00 0.00 2.71
2497 3341 5.808366 ATTACTTGGTGACTCAAGACTGA 57.192 39.130 16.89 4.36 44.98 3.41
2516 3360 4.871871 TCCTGGTTCCATAAGCCAATTA 57.128 40.909 0.00 0.00 31.91 1.40
2655 3518 2.158667 ACTCAGGGGAAACAATTCACGT 60.159 45.455 0.00 0.00 40.04 4.49
2656 3519 2.504367 ACTCAGGGGAAACAATTCACG 58.496 47.619 0.00 0.00 40.04 4.35
2738 3608 2.357952 AGAAGTTTCAGTTTCAACGGGC 59.642 45.455 0.00 0.00 0.00 6.13
2741 3611 5.556470 TCGAAAGAAGTTTCAGTTTCAACG 58.444 37.500 7.12 0.00 42.06 4.10
2775 3645 6.900568 TCAAATTGTGTTAGCAAAACAAGG 57.099 33.333 6.25 2.17 37.24 3.61
2949 4014 5.762711 TCTTTGCAAGCAACAAGATACACTA 59.237 36.000 7.03 0.00 35.46 2.74
2956 4021 4.158394 ACTTTCTCTTTGCAAGCAACAAGA 59.842 37.500 7.03 10.07 35.46 3.02
2989 4055 1.768870 GCCTTCAGGTTAGGGATGCTA 59.231 52.381 0.00 0.00 37.57 3.49
3000 4100 3.076092 CAGCTGGAGCCTTCAGGT 58.924 61.111 5.57 0.00 42.80 4.00
3051 4151 2.087646 GTTTCTTCAGATGCTGGGGAC 58.912 52.381 0.00 0.00 31.51 4.46


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

AutoCloner maintained by Alex Coulton.