Multiple sequence alignment - TraesCS1B01G313800

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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 TraesCS1B01G313800 chr1B 100.000 3405 0 0 1 3405 537770501 537773905 0.000000e+00 6288.0
1 TraesCS1B01G313800 chr1B 86.154 1430 155 23 1029 2428 60109090 60107674 0.000000e+00 1504.0
2 TraesCS1B01G313800 chr1B 88.537 916 103 2 1509 2423 60473811 60474725 0.000000e+00 1109.0
3 TraesCS1B01G313800 chr1B 88.571 280 23 9 2542 2818 563706004 563706277 7.040000e-87 331.0
4 TraesCS1B01G313800 chr1B 93.500 200 13 0 1222 1421 60473294 60473493 7.140000e-77 298.0
5 TraesCS1B01G313800 chr1B 90.972 144 8 5 1000 1141 60456804 60456944 4.490000e-44 189.0
6 TraesCS1B01G313800 chr1D 93.768 3434 161 20 1 3405 400791442 400794851 0.000000e+00 5107.0
7 TraesCS1B01G313800 chr1D 89.400 934 99 0 1490 2423 40597990 40598923 0.000000e+00 1177.0
8 TraesCS1B01G313800 chr1D 88.910 532 58 1 2814 3344 72631757 72631226 0.000000e+00 654.0
9 TraesCS1B01G313800 chr1D 87.828 419 40 11 1007 1421 40597375 40597786 6.610000e-132 481.0
10 TraesCS1B01G313800 chr1A 95.572 1897 61 6 656 2542 497082964 497084847 0.000000e+00 3016.0
11 TraesCS1B01G313800 chr1A 84.939 1640 186 37 833 2435 39872318 39870703 0.000000e+00 1604.0
12 TraesCS1B01G313800 chr7A 86.466 1692 160 34 791 2436 130400947 130399279 0.000000e+00 1792.0
13 TraesCS1B01G313800 chr7A 89.850 532 53 1 2814 3344 39235970 39235439 0.000000e+00 682.0
14 TraesCS1B01G313800 chr7A 91.304 46 4 0 542 587 511032480 511032435 2.840000e-06 63.9
15 TraesCS1B01G313800 chr7B 87.378 1537 157 26 925 2436 93068060 93066536 0.000000e+00 1729.0
16 TraesCS1B01G313800 chr7B 88.929 280 22 9 2542 2818 641787930 641788203 1.510000e-88 337.0
17 TraesCS1B01G313800 chr7D 87.333 1500 147 27 968 2436 131652322 131650835 0.000000e+00 1677.0
18 TraesCS1B01G313800 chr7D 89.239 539 53 4 2809 3344 163220931 163221467 0.000000e+00 669.0
19 TraesCS1B01G313800 chr7D 88.889 279 21 10 2543 2818 163220097 163220368 5.440000e-88 335.0
20 TraesCS1B01G313800 chr3D 90.414 532 49 2 2814 3344 110308024 110307494 0.000000e+00 699.0
21 TraesCS1B01G313800 chr3D 87.857 280 20 11 2542 2818 110308862 110308594 1.970000e-82 316.0
22 TraesCS1B01G313800 chr6A 90.226 532 51 1 2814 3344 53087635 53087104 0.000000e+00 693.0
23 TraesCS1B01G313800 chr6A 87.857 280 22 11 2542 2818 53088475 53088205 5.480000e-83 318.0
24 TraesCS1B01G313800 chr5D 89.610 539 53 2 2809 3344 550507618 550507080 0.000000e+00 682.0
25 TraesCS1B01G313800 chr5B 89.239 539 54 4 2809 3344 275024529 275025066 0.000000e+00 671.0
26 TraesCS1B01G313800 chr4D 89.493 533 53 3 2814 3344 35598964 35598433 0.000000e+00 671.0
27 TraesCS1B01G313800 chr4D 88.968 281 21 9 2542 2818 35599809 35599535 4.210000e-89 339.0
28 TraesCS1B01G313800 chr3A 87.857 280 23 10 2542 2818 435780245 435780516 5.480000e-83 318.0
29 TraesCS1B01G313800 chr2A 87.770 278 25 9 2542 2818 213401868 213401599 1.970000e-82 316.0
30 TraesCS1B01G313800 chr5A 84.615 65 3 7 526 587 611118478 611118538 1.320000e-04 58.4
31 TraesCS1B01G313800 chr3B 100.000 31 0 0 557 587 712757368 712757398 1.320000e-04 58.4
32 TraesCS1B01G313800 chr2D 78.182 110 11 7 558 655 558072826 558072934 1.320000e-04 58.4
33 TraesCS1B01G313800 chrUn 90.244 41 4 0 541 581 358098995 358099035 2.000000e-03 54.7
34 TraesCS1B01G313800 chrUn 74.638 138 27 5 447 581 358101027 358101159 2.000000e-03 54.7
35 TraesCS1B01G313800 chr4A 90.244 41 4 0 541 581 719305741 719305701 2.000000e-03 54.7
36 TraesCS1B01G313800 chr4A 90.244 41 4 0 541 581 719530103 719530063 2.000000e-03 54.7


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 TraesCS1B01G313800 chr1B 537770501 537773905 3404 False 6288.0 6288 100.0000 1 3405 1 chr1B.!!$F2 3404
1 TraesCS1B01G313800 chr1B 60107674 60109090 1416 True 1504.0 1504 86.1540 1029 2428 1 chr1B.!!$R1 1399
2 TraesCS1B01G313800 chr1B 60473294 60474725 1431 False 703.5 1109 91.0185 1222 2423 2 chr1B.!!$F4 1201
3 TraesCS1B01G313800 chr1D 400791442 400794851 3409 False 5107.0 5107 93.7680 1 3405 1 chr1D.!!$F1 3404
4 TraesCS1B01G313800 chr1D 40597375 40598923 1548 False 829.0 1177 88.6140 1007 2423 2 chr1D.!!$F2 1416
5 TraesCS1B01G313800 chr1D 72631226 72631757 531 True 654.0 654 88.9100 2814 3344 1 chr1D.!!$R1 530
6 TraesCS1B01G313800 chr1A 497082964 497084847 1883 False 3016.0 3016 95.5720 656 2542 1 chr1A.!!$F1 1886
7 TraesCS1B01G313800 chr1A 39870703 39872318 1615 True 1604.0 1604 84.9390 833 2435 1 chr1A.!!$R1 1602
8 TraesCS1B01G313800 chr7A 130399279 130400947 1668 True 1792.0 1792 86.4660 791 2436 1 chr7A.!!$R2 1645
9 TraesCS1B01G313800 chr7A 39235439 39235970 531 True 682.0 682 89.8500 2814 3344 1 chr7A.!!$R1 530
10 TraesCS1B01G313800 chr7B 93066536 93068060 1524 True 1729.0 1729 87.3780 925 2436 1 chr7B.!!$R1 1511
11 TraesCS1B01G313800 chr7D 131650835 131652322 1487 True 1677.0 1677 87.3330 968 2436 1 chr7D.!!$R1 1468
12 TraesCS1B01G313800 chr7D 163220097 163221467 1370 False 502.0 669 89.0640 2543 3344 2 chr7D.!!$F1 801
13 TraesCS1B01G313800 chr3D 110307494 110308862 1368 True 507.5 699 89.1355 2542 3344 2 chr3D.!!$R1 802
14 TraesCS1B01G313800 chr6A 53087104 53088475 1371 True 505.5 693 89.0415 2542 3344 2 chr6A.!!$R1 802
15 TraesCS1B01G313800 chr5D 550507080 550507618 538 True 682.0 682 89.6100 2809 3344 1 chr5D.!!$R1 535
16 TraesCS1B01G313800 chr5B 275024529 275025066 537 False 671.0 671 89.2390 2809 3344 1 chr5B.!!$F1 535
17 TraesCS1B01G313800 chr4D 35598433 35599809 1376 True 505.0 671 89.2305 2542 3344 2 chr4D.!!$R1 802

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
863 882 0.035317 CCAGCTTAGCCACTGACACA 59.965 55.0 0.0 0.0 35.9 3.72 F
1463 1684 0.314935 CCACGCACTGAAATTTGGCT 59.685 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2510 0.108851 CGTGGATGTCGACCATGTCA 60.109 55.0 14.12 1.7 39.69 3.58 R
2666 3095 0.742990 CGGGCGCACAGAAATTAGGA 60.743 55.0 11.77 0.0 0.00 2.94 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
28 29 2.814336 CCTCAACTTGTCCCAGTTAAGC 59.186 50.000 0.00 0.00 35.10 3.09
40 41 3.084039 CCAGTTAAGCCAGAGATGCAAA 58.916 45.455 0.00 0.00 0.00 3.68
42 43 3.128242 CAGTTAAGCCAGAGATGCAAAGG 59.872 47.826 0.00 0.00 0.00 3.11
43 44 3.009473 AGTTAAGCCAGAGATGCAAAGGA 59.991 43.478 0.00 0.00 0.00 3.36
44 45 2.822707 AAGCCAGAGATGCAAAGGAT 57.177 45.000 0.00 0.00 0.00 3.24
45 46 2.054232 AGCCAGAGATGCAAAGGATG 57.946 50.000 0.00 0.00 0.00 3.51
74 75 0.670162 ATGCAGAGCACCAAACACAC 59.330 50.000 0.00 0.00 43.04 3.82
108 110 6.009589 TGAGGCCTTCAACATAGAATTTCAA 58.990 36.000 6.77 0.00 31.34 2.69
153 155 1.686052 ACCATTGTTCCATGCAACGTT 59.314 42.857 0.00 0.00 0.00 3.99
155 157 2.545532 CCATTGTTCCATGCAACGTTGT 60.546 45.455 27.78 7.89 0.00 3.32
180 182 2.100846 CATCTGAATGGGTGCCACG 58.899 57.895 0.00 0.00 35.80 4.94
219 221 3.709141 ACCAAAACATGCAAAACTAGGGT 59.291 39.130 0.00 0.00 0.00 4.34
220 222 4.163268 ACCAAAACATGCAAAACTAGGGTT 59.837 37.500 0.00 0.00 37.24 4.11
298 300 1.687493 GGGAGGAGGTGGAGGTCTG 60.687 68.421 0.00 0.00 0.00 3.51
299 301 1.687493 GGAGGAGGTGGAGGTCTGG 60.687 68.421 0.00 0.00 0.00 3.86
325 327 3.077695 GAGGAGGGATCTGGGAGGTAATA 59.922 52.174 0.00 0.00 0.00 0.98
334 336 4.037927 TCTGGGAGGTAATAGGGTGAAAG 58.962 47.826 0.00 0.00 0.00 2.62
373 375 7.234355 AGAAAATCAGAACTACCAAGGATTGT 58.766 34.615 0.00 0.00 46.99 2.71
409 417 8.281194 ACATAGTACATACGCTCATATATACGC 58.719 37.037 0.00 0.03 0.00 4.42
424 432 1.016627 TACGCGCGTACACTTATCCT 58.983 50.000 36.55 12.49 0.00 3.24
425 433 0.171903 ACGCGCGTACACTTATCCTT 59.828 50.000 37.08 3.77 0.00 3.36
434 442 5.450171 CGTACACTTATCCTTATGGACTCG 58.550 45.833 0.00 0.00 46.51 4.18
492 501 6.210385 ACCGAGCAGACATATTATCTTGAGAT 59.790 38.462 0.00 0.00 38.51 2.75
507 516 1.079503 GAGATTGACGAAGGCACCAC 58.920 55.000 0.00 0.00 0.00 4.16
509 518 1.003580 AGATTGACGAAGGCACCACAT 59.996 47.619 0.00 0.00 0.00 3.21
510 519 1.131126 GATTGACGAAGGCACCACATG 59.869 52.381 0.00 0.00 0.00 3.21
525 534 3.696051 ACCACATGCACCTCATAATTGAC 59.304 43.478 0.00 0.00 33.19 3.18
527 536 2.945008 ACATGCACCTCATAATTGACGG 59.055 45.455 0.00 0.00 33.19 4.79
555 564 5.578776 GTTTCTTTTCACTGAACACGGATT 58.421 37.500 0.00 0.00 0.00 3.01
556 565 4.811555 TCTTTTCACTGAACACGGATTG 57.188 40.909 0.00 0.00 0.00 2.67
557 566 3.003275 TCTTTTCACTGAACACGGATTGC 59.997 43.478 0.00 0.00 0.00 3.56
598 617 8.655935 AAATCCAGGATAAAGAACTTGAACAT 57.344 30.769 1.02 0.00 0.00 2.71
605 624 4.670896 AAAGAACTTGAACATTGGTGGG 57.329 40.909 0.00 0.00 0.00 4.61
611 630 1.984026 GAACATTGGTGGGCTGGGG 60.984 63.158 0.00 0.00 0.00 4.96
614 633 1.759299 CATTGGTGGGCTGGGGATG 60.759 63.158 0.00 0.00 0.00 3.51
644 663 4.473196 TCCTTCTAACCATCCAAGCACATA 59.527 41.667 0.00 0.00 0.00 2.29
647 666 6.238842 CCTTCTAACCATCCAAGCACATATTG 60.239 42.308 0.00 0.00 0.00 1.90
822 841 3.578272 ACGCGCGCACCAAGAAAA 61.578 55.556 32.58 0.00 0.00 2.29
837 856 6.797033 CACCAAGAAAATAAGCGTGAAGTAAG 59.203 38.462 0.00 0.00 0.00 2.34
847 866 4.499183 AGCGTGAAGTAAGAAGATTCCAG 58.501 43.478 0.00 0.00 0.00 3.86
863 882 0.035317 CCAGCTTAGCCACTGACACA 59.965 55.000 0.00 0.00 35.90 3.72
946 999 5.934043 GCTCTTGTTTCAAAATTTAGGCCAT 59.066 36.000 5.01 0.00 0.00 4.40
951 1011 9.353999 CTTGTTTCAAAATTTAGGCCATAGTAC 57.646 33.333 5.01 0.00 0.00 2.73
954 1014 9.181061 GTTTCAAAATTTAGGCCATAGTACCTA 57.819 33.333 5.01 0.00 37.50 3.08
955 1015 8.974060 TTCAAAATTTAGGCCATAGTACCTAG 57.026 34.615 5.01 0.00 39.65 3.02
956 1016 8.326765 TCAAAATTTAGGCCATAGTACCTAGA 57.673 34.615 5.01 0.00 39.65 2.43
957 1017 8.429641 TCAAAATTTAGGCCATAGTACCTAGAG 58.570 37.037 5.01 0.00 39.65 2.43
958 1018 6.361768 AATTTAGGCCATAGTACCTAGAGC 57.638 41.667 5.01 0.00 39.65 4.09
1463 1684 0.314935 CCACGCACTGAAATTTGGCT 59.685 50.000 0.00 0.00 0.00 4.75
1531 1946 3.256960 TTCCTGACCCCAGTGGCC 61.257 66.667 2.61 0.00 38.74 5.36
1633 2048 2.796651 GTCGCCGATACCGTCACT 59.203 61.111 0.00 0.00 0.00 3.41
1777 2192 2.687566 CCCACCTACTTCCCGGCT 60.688 66.667 0.00 0.00 0.00 5.52
2095 2510 1.748122 CTTCTCCCATGCAAGCGCT 60.748 57.895 2.64 2.64 39.64 5.92
2173 2588 0.755698 ACCTACGCATCCAGGACGAT 60.756 55.000 6.47 0.00 35.76 3.73
2194 2609 3.991051 CTCACGGGGCACACGTCT 61.991 66.667 0.00 0.00 43.58 4.18
2433 2862 3.489059 GGAAGATTCGAGAGAGAGCACAG 60.489 52.174 0.00 0.00 43.69 3.66
2435 2864 2.682856 AGATTCGAGAGAGAGCACAGAC 59.317 50.000 0.00 0.00 43.69 3.51
2436 2865 1.897560 TTCGAGAGAGAGCACAGACA 58.102 50.000 0.00 0.00 43.69 3.41
2437 2866 1.447945 TCGAGAGAGAGCACAGACAG 58.552 55.000 0.00 0.00 34.84 3.51
2444 2873 6.425417 CGAGAGAGAGCACAGACAGTATATTA 59.575 42.308 0.00 0.00 0.00 0.98
2531 2960 9.695526 TTTATCAATTCTTGGTTATGCATATGC 57.304 29.630 21.09 21.09 42.50 3.14
2578 3007 6.648725 GGAGGCATAAGATTTGTCTCATCTAC 59.351 42.308 7.50 0.00 45.52 2.59
2579 3008 7.372260 AGGCATAAGATTTGTCTCATCTACT 57.628 36.000 0.00 0.00 30.35 2.57
2580 3009 7.441017 AGGCATAAGATTTGTCTCATCTACTC 58.559 38.462 0.00 0.00 30.35 2.59
2581 3010 6.648725 GGCATAAGATTTGTCTCATCTACTCC 59.351 42.308 0.00 0.00 30.35 3.85
2582 3011 7.441017 GCATAAGATTTGTCTCATCTACTCCT 58.559 38.462 0.00 0.00 30.35 3.69
2583 3012 8.580720 GCATAAGATTTGTCTCATCTACTCCTA 58.419 37.037 0.00 0.00 30.35 2.94
2666 3095 7.382898 ACAATTACTCGCCCACAAAAATATTT 58.617 30.769 0.00 0.00 0.00 1.40
2677 3106 8.882736 GCCCACAAAAATATTTCCTAATTTCTG 58.117 33.333 0.10 0.00 0.00 3.02
2805 3235 1.375908 TCCACGAGACAAGCATGGC 60.376 57.895 0.00 0.00 33.34 4.40
2894 3903 1.573829 GACGTTTTGGCGCCATCTCA 61.574 55.000 33.25 13.29 34.88 3.27
2946 3955 4.853142 TAGTCCTCCGCGGCCCAT 62.853 66.667 23.51 7.64 0.00 4.00
2976 3986 0.102300 GTCCAACCCATAATTGCGGC 59.898 55.000 0.00 0.00 0.00 6.53
3019 4029 1.823470 ACCGAAGCTGCAAAGCACA 60.823 52.632 1.02 0.00 37.25 4.57
3032 4042 4.931601 TGCAAAGCACACACAAATTTGTTA 59.068 33.333 21.10 0.00 34.31 2.41
3035 4045 6.254589 GCAAAGCACACACAAATTTGTTAGTA 59.745 34.615 21.10 0.00 39.91 1.82
3304 4314 3.092301 GTTTTCCAGCTGCCTTATCCTT 58.908 45.455 8.66 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.067364 TGTGTTTGGTGCTCTGCATTG 59.933 47.619 0.00 0.00 41.91 2.82
54 55 1.067516 GTGTGTTTGGTGCTCTGCATT 59.932 47.619 0.00 0.00 41.91 3.56
74 75 3.582998 TGAAGGCCTCAATCATAAGGG 57.417 47.619 5.23 0.00 32.98 3.95
108 110 5.669447 ACCCTGGTCTCAATCTAGATGAAAT 59.331 40.000 5.86 0.00 0.00 2.17
153 155 0.392863 CCATTCAGATGGCGGTGACA 60.393 55.000 0.00 0.00 45.96 3.58
155 157 4.961637 CCATTCAGATGGCGGTGA 57.038 55.556 0.00 0.00 45.96 4.02
174 176 1.144276 TCTTGGTTTCGACGTGGCA 59.856 52.632 0.00 0.00 0.00 4.92
175 177 1.568025 GTCTTGGTTTCGACGTGGC 59.432 57.895 0.00 0.00 0.00 5.01
180 182 3.116079 TGGTTAGGTCTTGGTTTCGAC 57.884 47.619 0.00 0.00 0.00 4.20
219 221 4.014075 TAGCGGGAGGTGGGGGAA 62.014 66.667 0.00 0.00 42.76 3.97
220 222 4.791069 GTAGCGGGAGGTGGGGGA 62.791 72.222 0.00 0.00 42.76 4.81
284 286 1.218196 TCTATCCAGACCTCCACCTCC 59.782 57.143 0.00 0.00 0.00 4.30
298 300 1.719378 TCCCAGATCCCTCCTCTATCC 59.281 57.143 0.00 0.00 0.00 2.59
299 301 2.292192 CCTCCCAGATCCCTCCTCTATC 60.292 59.091 0.00 0.00 0.00 2.08
325 327 3.714798 TCAGAAGTTACACCTTTCACCCT 59.285 43.478 0.00 0.00 0.00 4.34
334 336 7.730364 TCTGATTTTCTTCAGAAGTTACACC 57.270 36.000 10.09 0.00 46.92 4.16
409 417 4.233123 TCCATAAGGATAAGTGTACGCG 57.767 45.455 3.53 3.53 39.61 6.01
424 432 1.831106 AGGATGTGTGCGAGTCCATAA 59.169 47.619 0.00 0.00 33.12 1.90
425 433 1.485124 AGGATGTGTGCGAGTCCATA 58.515 50.000 0.00 0.00 33.12 2.74
434 442 2.548920 GCTCATAGGGTAGGATGTGTGC 60.549 54.545 0.00 0.00 0.00 4.57
492 501 2.627791 CATGTGGTGCCTTCGTCAA 58.372 52.632 0.00 0.00 0.00 3.18
507 516 3.205338 TCCGTCAATTATGAGGTGCATG 58.795 45.455 0.00 0.00 39.30 4.06
509 518 3.342377 TTCCGTCAATTATGAGGTGCA 57.658 42.857 0.00 0.00 39.30 4.57
510 519 3.485216 CGTTTCCGTCAATTATGAGGTGC 60.485 47.826 0.00 0.00 39.30 5.01
525 534 4.267357 TCAGTGAAAAGAAACGTTTCCG 57.733 40.909 31.87 14.53 37.92 4.30
527 536 5.002189 CGTGTTCAGTGAAAAGAAACGTTTC 59.998 40.000 29.36 29.36 37.45 2.78
532 541 4.609691 TCCGTGTTCAGTGAAAAGAAAC 57.390 40.909 7.25 0.00 0.00 2.78
537 546 2.034053 GGCAATCCGTGTTCAGTGAAAA 59.966 45.455 7.25 0.00 0.00 2.29
540 549 0.107643 TGGCAATCCGTGTTCAGTGA 59.892 50.000 0.00 0.00 34.14 3.41
543 552 2.791383 TTTTGGCAATCCGTGTTCAG 57.209 45.000 0.00 0.00 34.14 3.02
545 554 2.993220 GGATTTTTGGCAATCCGTGTTC 59.007 45.455 0.00 0.00 42.27 3.18
555 564 7.013823 TGGATTTATTTCAGGATTTTTGGCA 57.986 32.000 0.00 0.00 0.00 4.92
556 565 7.543947 CTGGATTTATTTCAGGATTTTTGGC 57.456 36.000 0.00 0.00 0.00 4.52
598 617 4.380945 GCATCCCCAGCCCACCAA 62.381 66.667 0.00 0.00 0.00 3.67
605 624 1.073897 GGATAGTGGCATCCCCAGC 59.926 63.158 0.00 0.00 46.54 4.85
611 630 4.689612 TGGTTAGAAGGATAGTGGCATC 57.310 45.455 0.00 0.00 0.00 3.91
614 633 3.391296 TGGATGGTTAGAAGGATAGTGGC 59.609 47.826 0.00 0.00 0.00 5.01
620 639 3.266772 TGTGCTTGGATGGTTAGAAGGAT 59.733 43.478 0.00 0.00 0.00 3.24
644 663 3.627395 TCCTTGGTAGTGCGAATCAAT 57.373 42.857 0.00 0.00 0.00 2.57
647 666 2.128035 CGATCCTTGGTAGTGCGAATC 58.872 52.381 0.00 0.00 0.00 2.52
818 837 9.479278 GAATCTTCTTACTTCACGCTTATTTTC 57.521 33.333 0.00 0.00 0.00 2.29
822 841 6.640518 TGGAATCTTCTTACTTCACGCTTAT 58.359 36.000 0.00 0.00 0.00 1.73
837 856 2.941720 CAGTGGCTAAGCTGGAATCTTC 59.058 50.000 0.00 0.00 0.00 2.87
847 866 3.923017 ATTTTGTGTCAGTGGCTAAGC 57.077 42.857 0.00 0.00 0.00 3.09
863 882 6.599356 ACCGGCTACTTAAATCCAAATTTT 57.401 33.333 0.00 0.00 36.49 1.82
946 999 2.158593 CCCTGCTCTGCTCTAGGTACTA 60.159 54.545 0.00 0.00 41.75 1.82
951 1011 2.030490 CTGCCCTGCTCTGCTCTAGG 62.030 65.000 0.00 0.00 0.00 3.02
954 1014 3.400928 CCTGCCCTGCTCTGCTCT 61.401 66.667 0.00 0.00 0.00 4.09
955 1015 4.486503 CCCTGCCCTGCTCTGCTC 62.487 72.222 0.00 0.00 0.00 4.26
958 1018 4.798344 CTGCCCTGCCCTGCTCTG 62.798 72.222 0.00 0.00 0.00 3.35
981 1044 2.511600 CTTAGCTTCGCACGGGGG 60.512 66.667 0.00 0.00 0.00 5.40
1441 1588 1.335872 CCAAATTTCAGTGCGTGGTCC 60.336 52.381 0.00 0.00 0.00 4.46
1443 1590 0.031994 GCCAAATTTCAGTGCGTGGT 59.968 50.000 0.00 0.00 0.00 4.16
1452 1599 2.656055 GCCGCCAGCCAAATTTCA 59.344 55.556 0.00 0.00 34.35 2.69
1453 1600 2.283472 ATCGCCGCCAGCCAAATTTC 62.283 55.000 0.00 0.00 38.78 2.17
1463 1684 3.507924 GCATCAACATCGCCGCCA 61.508 61.111 0.00 0.00 0.00 5.69
1513 1928 2.352805 GCCACTGGGGTCAGGAAG 59.647 66.667 0.00 0.00 44.99 3.46
1624 2039 2.076100 ACGACGATGTTAGTGACGGTA 58.924 47.619 0.00 0.00 0.00 4.02
1777 2192 1.444250 GTGGGTCGTGAAGTGGTGA 59.556 57.895 0.00 0.00 0.00 4.02
1930 2345 2.264794 CTGTACTCGGCGGGCTTT 59.735 61.111 6.72 0.00 0.00 3.51
2095 2510 0.108851 CGTGGATGTCGACCATGTCA 60.109 55.000 14.12 1.70 39.69 3.58
2173 2588 2.110213 GTGTGCCCCGTGAGTGAA 59.890 61.111 0.00 0.00 0.00 3.18
2666 3095 0.742990 CGGGCGCACAGAAATTAGGA 60.743 55.000 11.77 0.00 0.00 2.94
2805 3235 1.150567 CGCTCATCTTTGGCCTCTCG 61.151 60.000 3.32 0.00 0.00 4.04
2876 3885 1.599518 TGAGATGGCGCCAAAACGT 60.600 52.632 36.33 17.84 34.88 3.99
2894 3903 2.286872 CCTCTACGACTATCACGGTGT 58.713 52.381 8.17 0.00 34.93 4.16
2996 4006 0.955428 CTTTGCAGCTTCGGTGGCTA 60.955 55.000 0.00 0.00 38.03 3.93
3035 4045 1.757699 GGAGGCCTTCGAGTACTCAAT 59.242 52.381 22.37 1.98 0.00 2.57
3132 4142 6.688073 AAACAAGATTGAGAGGGTCTTCTA 57.312 37.500 0.00 0.00 30.19 2.10
3133 4143 5.574970 AAACAAGATTGAGAGGGTCTTCT 57.425 39.130 0.00 0.00 30.19 2.85
3171 4181 1.900351 CCCTCATCGTGCCTCAAGA 59.100 57.895 0.00 0.00 0.00 3.02
3190 4200 2.100631 GCGGTGTTCTCCATCACGG 61.101 63.158 0.00 0.00 37.74 4.94
3281 4291 3.523564 AGGATAAGGCAGCTGGAAAACTA 59.476 43.478 17.12 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.