Multiple sequence alignment - TraesCS3D01G146800

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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 TraesCS3D01G146800 chr3D 100.000 4675 0 0 1 4675 110513975 110518649 0.000000e+00 8634.0
1 TraesCS3D01G146800 chr3B 97.943 2723 42 7 646 3357 161772824 161775543 0.000000e+00 4706.0
2 TraesCS3D01G146800 chr3B 94.070 1366 36 13 3354 4675 161775747 161777111 0.000000e+00 2032.0
3 TraesCS3D01G146800 chr3B 89.437 284 30 0 1847 2130 635232192 635232475 4.450000e-95 359.0
4 TraesCS3D01G146800 chr3B 93.714 175 11 0 4501 4675 28176171 28175997 3.590000e-66 263.0
5 TraesCS3D01G146800 chr3A 85.583 1845 145 48 721 2504 119473452 119471668 0.000000e+00 1821.0
6 TraesCS3D01G146800 chr3A 94.633 354 17 2 3385 3737 119470687 119470335 8.840000e-152 547.0
7 TraesCS3D01G146800 chr3A 88.215 297 24 10 2515 2804 119471599 119471307 1.250000e-90 344.0
8 TraesCS3D01G146800 chr2D 93.423 593 36 3 2 592 127831603 127832194 0.000000e+00 876.0
9 TraesCS3D01G146800 chr2D 91.987 599 44 4 1 595 217114789 217114191 0.000000e+00 837.0
10 TraesCS3D01G146800 chr2D 91.549 284 24 0 1847 2130 161360649 161360366 4.390000e-105 392.0
11 TraesCS3D01G146800 chr5D 92.761 594 40 3 2 592 527930235 527929642 0.000000e+00 856.0
12 TraesCS3D01G146800 chr5D 92.424 594 43 2 2 593 273637000 273637593 0.000000e+00 846.0
13 TraesCS3D01G146800 chr5D 97.059 34 1 0 4630 4663 387661756 387661723 1.820000e-04 58.4
14 TraesCS3D01G146800 chrUn 92.593 594 41 3 2 592 290618172 290617579 0.000000e+00 850.0
15 TraesCS3D01G146800 chr6D 92.699 589 39 3 8 593 300464358 300463771 0.000000e+00 846.0
16 TraesCS3D01G146800 chr6D 92.517 588 42 2 7 592 382335518 382336105 0.000000e+00 841.0
17 TraesCS3D01G146800 chr6D 89.510 286 28 2 1847 2131 414117203 414116919 1.240000e-95 361.0
18 TraesCS3D01G146800 chr1D 92.687 588 41 2 7 592 363612972 363613559 0.000000e+00 846.0
19 TraesCS3D01G146800 chr1D 92.650 585 41 2 8 590 343482621 343483205 0.000000e+00 841.0
20 TraesCS3D01G146800 chr1B 89.085 284 31 0 1847 2130 234797901 234798184 2.070000e-93 353.0
21 TraesCS3D01G146800 chr6B 86.254 291 33 4 1847 2130 309683238 309683528 4.540000e-80 309.0
22 TraesCS3D01G146800 chr7B 93.143 175 12 0 4501 4675 90793738 90793912 1.670000e-64 257.0
23 TraesCS3D01G146800 chr7A 84.579 214 20 5 1255 1468 155293550 155293750 2.850000e-47 200.0
24 TraesCS3D01G146800 chr5B 90.000 150 7 1 4526 4675 526950882 526950741 2.220000e-43 187.0
25 TraesCS3D01G146800 chr5B 90.000 150 7 4 4526 4675 527000536 527000395 2.220000e-43 187.0
26 TraesCS3D01G146800 chr4A 89.535 86 8 1 1105 1190 713359329 713359413 1.780000e-19 108.0


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 TraesCS3D01G146800 chr3D 110513975 110518649 4674 False 8634 8634 100.0000 1 4675 1 chr3D.!!$F1 4674
1 TraesCS3D01G146800 chr3B 161772824 161777111 4287 False 3369 4706 96.0065 646 4675 2 chr3B.!!$F2 4029
2 TraesCS3D01G146800 chr3A 119470335 119473452 3117 True 904 1821 89.4770 721 3737 3 chr3A.!!$R1 3016
3 TraesCS3D01G146800 chr2D 127831603 127832194 591 False 876 876 93.4230 2 592 1 chr2D.!!$F1 590
4 TraesCS3D01G146800 chr2D 217114191 217114789 598 True 837 837 91.9870 1 595 1 chr2D.!!$R2 594
5 TraesCS3D01G146800 chr5D 527929642 527930235 593 True 856 856 92.7610 2 592 1 chr5D.!!$R2 590
6 TraesCS3D01G146800 chr5D 273637000 273637593 593 False 846 846 92.4240 2 593 1 chr5D.!!$F1 591
7 TraesCS3D01G146800 chrUn 290617579 290618172 593 True 850 850 92.5930 2 592 1 chrUn.!!$R1 590
8 TraesCS3D01G146800 chr6D 300463771 300464358 587 True 846 846 92.6990 8 593 1 chr6D.!!$R1 585
9 TraesCS3D01G146800 chr6D 382335518 382336105 587 False 841 841 92.5170 7 592 1 chr6D.!!$F1 585
10 TraesCS3D01G146800 chr1D 363612972 363613559 587 False 846 846 92.6870 7 592 1 chr1D.!!$F2 585
11 TraesCS3D01G146800 chr1D 343482621 343483205 584 False 841 841 92.6500 8 590 1 chr1D.!!$F1 582

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
613 618 0.253894 AGCAGCCATCATACAGCACA 59.746 50.000 0.00 0.0 0.0 4.57 F
1519 1581 0.037590 TTCAAGGTTGCGGCCATACT 59.962 50.000 2.24 0.0 0.0 2.12 F
1522 1584 0.616371 AAGGTTGCGGCCATACTACA 59.384 50.000 2.24 0.0 0.0 2.74 F
2653 2807 1.945819 GCACCCGAGAGCAGAATTCAA 60.946 52.381 8.44 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1584 0.687354 AGCATTCGTGTTCCAGGACT 59.313 50.000 0.00 0.00 0.00 3.85 R
2351 2447 1.003928 TCAGGACATTGCTGCATCTGT 59.996 47.619 15.55 15.55 35.65 3.41 R
3183 3409 3.463944 ACACGACTTGGAAAAGGTGTAG 58.536 45.455 0.00 0.00 33.59 2.74 R
4159 4642 0.243907 AACATCGCGCACAGAGTACT 59.756 50.000 8.75 0.00 0.00 2.73 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
21 22 1.839747 TTGCCTCCTACGGTGGTGT 60.840 57.895 3.26 0.00 38.49 4.16
22 23 1.412453 TTGCCTCCTACGGTGGTGTT 61.412 55.000 3.26 0.00 38.49 3.32
55 56 3.986116 GAGGCCCCGGTCCTCTTCT 62.986 68.421 24.89 4.09 45.13 2.85
111 112 4.321974 CCAATTTGAAAGGGGACAACTAGC 60.322 45.833 0.00 0.00 0.00 3.42
268 269 2.754658 TCTCGGAACTCCTCGCCC 60.755 66.667 0.00 0.00 0.00 6.13
377 380 0.874175 CACGTCACGAGAACCTTGCA 60.874 55.000 2.91 0.00 0.00 4.08
595 600 0.882927 TCCCAGAACGCCGACAAAAG 60.883 55.000 0.00 0.00 0.00 2.27
596 601 1.082104 CCAGAACGCCGACAAAAGC 60.082 57.895 0.00 0.00 0.00 3.51
597 602 1.646540 CAGAACGCCGACAAAAGCA 59.353 52.632 0.00 0.00 0.00 3.91
598 603 0.384725 CAGAACGCCGACAAAAGCAG 60.385 55.000 0.00 0.00 0.00 4.24
599 604 1.725973 GAACGCCGACAAAAGCAGC 60.726 57.895 0.00 0.00 0.00 5.25
600 605 3.194272 AACGCCGACAAAAGCAGCC 62.194 57.895 0.00 0.00 0.00 4.85
601 606 3.659092 CGCCGACAAAAGCAGCCA 61.659 61.111 0.00 0.00 0.00 4.75
602 607 2.964978 GCCGACAAAAGCAGCCAT 59.035 55.556 0.00 0.00 0.00 4.40
603 608 1.153958 GCCGACAAAAGCAGCCATC 60.154 57.895 0.00 0.00 0.00 3.51
604 609 1.865788 GCCGACAAAAGCAGCCATCA 61.866 55.000 0.00 0.00 0.00 3.07
605 610 0.813184 CCGACAAAAGCAGCCATCAT 59.187 50.000 0.00 0.00 0.00 2.45
606 611 2.016318 CCGACAAAAGCAGCCATCATA 58.984 47.619 0.00 0.00 0.00 2.15
607 612 2.223340 CCGACAAAAGCAGCCATCATAC 60.223 50.000 0.00 0.00 0.00 2.39
608 613 2.419673 CGACAAAAGCAGCCATCATACA 59.580 45.455 0.00 0.00 0.00 2.29
609 614 3.486375 CGACAAAAGCAGCCATCATACAG 60.486 47.826 0.00 0.00 0.00 2.74
610 615 2.165030 ACAAAAGCAGCCATCATACAGC 59.835 45.455 0.00 0.00 0.00 4.40
611 616 2.133281 AAAGCAGCCATCATACAGCA 57.867 45.000 0.00 0.00 0.00 4.41
612 617 1.386533 AAGCAGCCATCATACAGCAC 58.613 50.000 0.00 0.00 0.00 4.40
613 618 0.253894 AGCAGCCATCATACAGCACA 59.746 50.000 0.00 0.00 0.00 4.57
614 619 1.097232 GCAGCCATCATACAGCACAA 58.903 50.000 0.00 0.00 0.00 3.33
615 620 1.065102 GCAGCCATCATACAGCACAAG 59.935 52.381 0.00 0.00 0.00 3.16
616 621 1.674441 CAGCCATCATACAGCACAAGG 59.326 52.381 0.00 0.00 0.00 3.61
617 622 1.561076 AGCCATCATACAGCACAAGGA 59.439 47.619 0.00 0.00 0.00 3.36
618 623 1.945394 GCCATCATACAGCACAAGGAG 59.055 52.381 0.00 0.00 0.00 3.69
619 624 2.420547 GCCATCATACAGCACAAGGAGA 60.421 50.000 0.00 0.00 0.00 3.71
620 625 3.464907 CCATCATACAGCACAAGGAGAG 58.535 50.000 0.00 0.00 0.00 3.20
621 626 3.464907 CATCATACAGCACAAGGAGAGG 58.535 50.000 0.00 0.00 0.00 3.69
622 627 1.208052 TCATACAGCACAAGGAGAGGC 59.792 52.381 0.00 0.00 0.00 4.70
623 628 0.543749 ATACAGCACAAGGAGAGGCC 59.456 55.000 0.00 0.00 0.00 5.19
624 629 1.888436 TACAGCACAAGGAGAGGCCG 61.888 60.000 0.00 0.00 43.43 6.13
625 630 3.710722 AGCACAAGGAGAGGCCGG 61.711 66.667 0.00 0.00 43.43 6.13
626 631 3.706373 GCACAAGGAGAGGCCGGA 61.706 66.667 5.05 0.00 43.43 5.14
627 632 3.036429 GCACAAGGAGAGGCCGGAT 62.036 63.158 5.05 0.00 43.43 4.18
628 633 1.153289 CACAAGGAGAGGCCGGATG 60.153 63.158 5.05 0.00 43.43 3.51
629 634 2.203126 CAAGGAGAGGCCGGATGC 60.203 66.667 5.05 0.00 43.43 3.91
630 635 2.688666 AAGGAGAGGCCGGATGCA 60.689 61.111 5.05 0.00 43.89 3.96
631 636 3.036429 AAGGAGAGGCCGGATGCAC 62.036 63.158 5.05 0.00 43.89 4.57
632 637 4.554036 GGAGAGGCCGGATGCACC 62.554 72.222 5.05 0.00 43.89 5.01
633 638 3.785859 GAGAGGCCGGATGCACCA 61.786 66.667 5.05 0.00 43.89 4.17
634 639 4.101448 AGAGGCCGGATGCACCAC 62.101 66.667 5.05 0.00 43.89 4.16
635 640 4.101448 GAGGCCGGATGCACCACT 62.101 66.667 5.05 0.00 43.89 4.00
636 641 3.628646 GAGGCCGGATGCACCACTT 62.629 63.158 5.05 0.00 43.89 3.16
637 642 3.443045 GGCCGGATGCACCACTTG 61.443 66.667 5.05 0.00 43.89 3.16
638 643 2.359850 GCCGGATGCACCACTTGA 60.360 61.111 5.05 0.00 40.77 3.02
639 644 2.690778 GCCGGATGCACCACTTGAC 61.691 63.158 5.05 0.00 40.77 3.18
640 645 1.302431 CCGGATGCACCACTTGACA 60.302 57.895 0.00 0.00 38.90 3.58
641 646 1.577328 CCGGATGCACCACTTGACAC 61.577 60.000 0.00 0.00 38.90 3.67
642 647 1.868997 GGATGCACCACTTGACACG 59.131 57.895 0.00 0.00 38.79 4.49
643 648 1.207593 GATGCACCACTTGACACGC 59.792 57.895 0.00 0.00 0.00 5.34
644 649 1.227943 ATGCACCACTTGACACGCT 60.228 52.632 0.00 0.00 0.00 5.07
649 654 0.603569 ACCACTTGACACGCTCCTAG 59.396 55.000 0.00 0.00 0.00 3.02
667 672 3.557595 CCTAGATCACCAAAATGAGCGTC 59.442 47.826 0.00 0.00 40.01 5.19
698 703 0.824759 ATGGGTAACTGACTCTCGGC 59.175 55.000 0.00 0.00 0.00 5.54
953 997 4.077982 ACCTAATATTCCACCTCTCCCTGA 60.078 45.833 0.00 0.00 0.00 3.86
1060 1116 4.673375 CAGCAAGCCCAGCCCAGT 62.673 66.667 0.00 0.00 0.00 4.00
1270 1329 1.012234 GCGCGTGACATCGGATTTC 60.012 57.895 8.43 0.00 0.00 2.17
1343 1405 2.437359 GCGCTGAAGGTGCTGGAT 60.437 61.111 0.00 0.00 46.82 3.41
1519 1581 0.037590 TTCAAGGTTGCGGCCATACT 59.962 50.000 2.24 0.00 0.00 2.12
1520 1582 0.906066 TCAAGGTTGCGGCCATACTA 59.094 50.000 2.24 0.00 0.00 1.82
1521 1583 1.014352 CAAGGTTGCGGCCATACTAC 58.986 55.000 2.24 0.00 0.00 2.73
1522 1584 0.616371 AAGGTTGCGGCCATACTACA 59.384 50.000 2.24 0.00 0.00 2.74
1534 1596 3.679083 GCCATACTACAGTCCTGGAACAC 60.679 52.174 12.70 0.00 34.62 3.32
1584 1646 2.756760 GGGATGCTGATTGCTTCTTCAA 59.243 45.455 0.00 0.00 43.06 2.69
1831 1910 7.874252 TGGGTTTACTTTTGCTATATTCCCTA 58.126 34.615 0.00 0.00 0.00 3.53
1957 2053 3.898529 ACTTACTAAGTGTGTCGAGTGC 58.101 45.455 0.33 0.00 41.01 4.40
2492 2588 4.281688 ACACTGCAAAGGCTGAATAATTGT 59.718 37.500 0.00 0.00 41.06 2.71
2653 2807 1.945819 GCACCCGAGAGCAGAATTCAA 60.946 52.381 8.44 0.00 0.00 2.69
2681 2835 6.391227 TTGGCTCTTGGCTATAATTTTAGC 57.609 37.500 16.86 16.86 43.16 3.09
3183 3409 7.867403 TGGCTTGAAACATCAGAAAAACTAATC 59.133 33.333 0.00 0.00 0.00 1.75
3307 3582 3.893200 CCCTGGTGTTCGGTATATAGTGA 59.107 47.826 0.00 0.00 0.00 3.41
3349 3624 2.291465 GCTGAAGCACATTCTGAACACA 59.709 45.455 0.00 0.00 38.72 3.72
3430 3912 0.746923 GGGCTACATTTCACCCCGTC 60.747 60.000 0.00 0.00 36.24 4.79
3804 4287 7.810759 TCTGGCATATTTTACGTTTTTCTTTCC 59.189 33.333 0.00 0.00 0.00 3.13
4210 4693 5.221621 TGACGCAATGTGGATCATATAGGAA 60.222 40.000 0.00 0.00 35.48 3.36
4330 4832 1.538629 TGAGATGGACCAGCCCACA 60.539 57.895 6.01 1.92 39.34 4.17
4372 4874 6.813649 AGCTCTTTTTCCTGTTTTTCTGTTTC 59.186 34.615 0.00 0.00 0.00 2.78
4377 4879 4.981806 TCCTGTTTTTCTGTTTCCTGTG 57.018 40.909 0.00 0.00 0.00 3.66
4447 4974 7.923414 ATCCCTAATAATAAAGCACGGATTC 57.077 36.000 0.00 0.00 0.00 2.52
4451 4978 8.237267 CCCTAATAATAAAGCACGGATTCATTC 58.763 37.037 0.00 0.00 0.00 2.67
4468 4995 4.289245 CCGTGGGTTCACCGTCGT 62.289 66.667 9.47 0.00 44.64 4.34
4481 5008 1.652930 CGTCGTGGTGTTTTTGCGG 60.653 57.895 0.00 0.00 0.00 5.69
4552 5079 1.504359 TTCGATCGTTTTTCACCGCT 58.496 45.000 15.94 0.00 0.00 5.52
4555 5082 1.153353 GATCGTTTTTCACCGCTGGA 58.847 50.000 1.50 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.482878 CGGGGCCTCTATAAATAGGACTAAA 59.517 44.000 0.00 0.00 41.09 1.85
22 23 5.021458 CGGGGCCTCTATAAATAGGACTAA 58.979 45.833 0.00 0.00 41.09 2.24
55 56 2.507886 TCCCTTCCCGCTCAATATTTGA 59.492 45.455 0.00 0.00 38.17 2.69
111 112 4.199432 ACTTCTGTCAGGATAAGCTGTG 57.801 45.455 0.00 0.00 0.00 3.66
158 159 2.738521 CCCAAGACGGCGTCACTG 60.739 66.667 37.71 31.20 34.60 3.66
159 160 4.681978 GCCCAAGACGGCGTCACT 62.682 66.667 37.71 23.53 39.64 3.41
268 269 3.810896 GTTAAGGGGGCAAGCGCG 61.811 66.667 0.00 0.00 39.92 6.86
435 439 1.209383 CGACGCAAGACCTTCTCGA 59.791 57.895 7.59 0.00 43.62 4.04
562 566 3.400054 GGGAACGGGGGTCTCAGG 61.400 72.222 0.00 0.00 0.00 3.86
566 570 2.206036 TTCTGGGAACGGGGGTCT 59.794 61.111 0.00 0.00 37.31 3.85
595 600 1.065102 CTTGTGCTGTATGATGGCTGC 59.935 52.381 0.00 0.00 0.00 5.25
596 601 1.674441 CCTTGTGCTGTATGATGGCTG 59.326 52.381 0.00 0.00 0.00 4.85
597 602 1.561076 TCCTTGTGCTGTATGATGGCT 59.439 47.619 0.00 0.00 0.00 4.75
598 603 1.945394 CTCCTTGTGCTGTATGATGGC 59.055 52.381 0.00 0.00 0.00 4.40
599 604 3.464907 CTCTCCTTGTGCTGTATGATGG 58.535 50.000 0.00 0.00 0.00 3.51
600 605 3.464907 CCTCTCCTTGTGCTGTATGATG 58.535 50.000 0.00 0.00 0.00 3.07
601 606 2.158842 GCCTCTCCTTGTGCTGTATGAT 60.159 50.000 0.00 0.00 0.00 2.45
602 607 1.208052 GCCTCTCCTTGTGCTGTATGA 59.792 52.381 0.00 0.00 0.00 2.15
603 608 1.661341 GCCTCTCCTTGTGCTGTATG 58.339 55.000 0.00 0.00 0.00 2.39
604 609 0.543749 GGCCTCTCCTTGTGCTGTAT 59.456 55.000 0.00 0.00 0.00 2.29
605 610 1.888436 CGGCCTCTCCTTGTGCTGTA 61.888 60.000 0.00 0.00 0.00 2.74
606 611 2.753029 GGCCTCTCCTTGTGCTGT 59.247 61.111 0.00 0.00 0.00 4.40
607 612 2.435586 CGGCCTCTCCTTGTGCTG 60.436 66.667 0.00 0.00 0.00 4.41
608 613 3.710722 CCGGCCTCTCCTTGTGCT 61.711 66.667 0.00 0.00 0.00 4.40
609 614 3.036429 ATCCGGCCTCTCCTTGTGC 62.036 63.158 0.00 0.00 0.00 4.57
610 615 1.153289 CATCCGGCCTCTCCTTGTG 60.153 63.158 0.00 0.00 0.00 3.33
611 616 3.036429 GCATCCGGCCTCTCCTTGT 62.036 63.158 0.00 0.00 36.11 3.16
612 617 2.203126 GCATCCGGCCTCTCCTTG 60.203 66.667 0.00 0.00 36.11 3.61
613 618 2.688666 TGCATCCGGCCTCTCCTT 60.689 61.111 0.00 0.00 43.89 3.36
614 619 3.474570 GTGCATCCGGCCTCTCCT 61.475 66.667 0.00 0.00 43.89 3.69
615 620 4.554036 GGTGCATCCGGCCTCTCC 62.554 72.222 0.00 0.00 43.89 3.71
616 621 3.785859 TGGTGCATCCGGCCTCTC 61.786 66.667 0.00 0.00 43.89 3.20
617 622 4.101448 GTGGTGCATCCGGCCTCT 62.101 66.667 0.00 0.00 43.89 3.69
618 623 3.628646 AAGTGGTGCATCCGGCCTC 62.629 63.158 0.00 0.00 43.89 4.70
619 624 3.650950 AAGTGGTGCATCCGGCCT 61.651 61.111 0.00 0.00 43.89 5.19
620 625 3.443045 CAAGTGGTGCATCCGGCC 61.443 66.667 0.00 0.00 43.89 6.13
621 626 2.359850 TCAAGTGGTGCATCCGGC 60.360 61.111 0.00 0.00 45.13 6.13
622 627 1.302431 TGTCAAGTGGTGCATCCGG 60.302 57.895 0.00 0.00 39.52 5.14
623 628 1.868997 GTGTCAAGTGGTGCATCCG 59.131 57.895 0.00 0.00 39.52 4.18
624 629 1.868997 CGTGTCAAGTGGTGCATCC 59.131 57.895 0.00 0.00 0.00 3.51
625 630 1.207593 GCGTGTCAAGTGGTGCATC 59.792 57.895 0.00 0.00 0.00 3.91
626 631 1.227943 AGCGTGTCAAGTGGTGCAT 60.228 52.632 0.00 0.00 0.00 3.96
627 632 1.887242 GAGCGTGTCAAGTGGTGCA 60.887 57.895 0.00 0.00 0.00 4.57
628 633 2.607892 GGAGCGTGTCAAGTGGTGC 61.608 63.158 0.00 0.00 0.00 5.01
629 634 0.317160 TAGGAGCGTGTCAAGTGGTG 59.683 55.000 0.00 0.00 0.00 4.17
630 635 0.603569 CTAGGAGCGTGTCAAGTGGT 59.396 55.000 0.00 0.00 0.00 4.16
631 636 0.888619 TCTAGGAGCGTGTCAAGTGG 59.111 55.000 0.00 0.00 0.00 4.00
632 637 2.164422 TGATCTAGGAGCGTGTCAAGTG 59.836 50.000 0.00 0.00 0.00 3.16
633 638 2.164624 GTGATCTAGGAGCGTGTCAAGT 59.835 50.000 0.00 0.00 0.00 3.16
634 639 2.480416 GGTGATCTAGGAGCGTGTCAAG 60.480 54.545 0.00 0.00 0.00 3.02
635 640 1.476891 GGTGATCTAGGAGCGTGTCAA 59.523 52.381 0.00 0.00 0.00 3.18
636 641 1.103803 GGTGATCTAGGAGCGTGTCA 58.896 55.000 0.00 0.00 0.00 3.58
637 642 1.103803 TGGTGATCTAGGAGCGTGTC 58.896 55.000 0.00 0.00 0.00 3.67
638 643 1.557099 TTGGTGATCTAGGAGCGTGT 58.443 50.000 0.00 0.00 0.00 4.49
639 644 2.672961 TTTGGTGATCTAGGAGCGTG 57.327 50.000 0.00 0.00 0.00 5.34
640 645 3.197766 TCATTTTGGTGATCTAGGAGCGT 59.802 43.478 0.00 0.00 0.00 5.07
641 646 3.797039 TCATTTTGGTGATCTAGGAGCG 58.203 45.455 0.00 0.00 0.00 5.03
642 647 3.563390 GCTCATTTTGGTGATCTAGGAGC 59.437 47.826 0.00 0.00 38.49 4.70
643 648 3.806521 CGCTCATTTTGGTGATCTAGGAG 59.193 47.826 0.00 0.00 0.00 3.69
644 649 3.197766 ACGCTCATTTTGGTGATCTAGGA 59.802 43.478 0.00 0.00 0.00 2.94
649 654 1.999735 TCGACGCTCATTTTGGTGATC 59.000 47.619 0.00 0.00 0.00 2.92
667 672 2.764572 AGTTACCCATTCTGGTACCTCG 59.235 50.000 14.36 4.39 40.55 4.63
695 700 6.384178 TTTACAAATATATCATCGTCGCCG 57.616 37.500 0.00 0.00 0.00 6.46
826 831 0.101399 CGTCTGTTGATCTCTCCGGG 59.899 60.000 0.00 0.00 0.00 5.73
953 997 1.997256 TTAGGTTGTTGGGTGGCGGT 61.997 55.000 0.00 0.00 0.00 5.68
1060 1116 3.911698 CGGATCACGGATCGGCCA 61.912 66.667 2.24 0.00 39.72 5.36
1270 1329 1.224075 CACATCCGCCTAATCAGCAG 58.776 55.000 0.00 0.00 0.00 4.24
1343 1405 2.448542 GCCCCCTCCATGGCTCTA 60.449 66.667 6.96 0.00 44.46 2.43
1519 1581 2.611971 GCATTCGTGTTCCAGGACTGTA 60.612 50.000 0.00 0.00 33.57 2.74
1520 1582 1.878102 GCATTCGTGTTCCAGGACTGT 60.878 52.381 0.00 0.00 33.57 3.55
1521 1583 0.798776 GCATTCGTGTTCCAGGACTG 59.201 55.000 0.00 0.00 33.95 3.51
1522 1584 0.687354 AGCATTCGTGTTCCAGGACT 59.313 50.000 0.00 0.00 0.00 3.85
1584 1646 7.968405 GCAAAACGAAACCATTAGATGAGTAAT 59.032 33.333 0.00 0.00 0.00 1.89
1734 1805 3.258372 TGACCTGACAACTCACTGATACC 59.742 47.826 0.00 0.00 0.00 2.73
1831 1910 4.643334 GGAATATAGCAAAAGGAAACCCGT 59.357 41.667 0.00 0.00 0.00 5.28
1957 2053 6.091577 TGCACATAGGTCAAATACTAAACACG 59.908 38.462 0.00 0.00 0.00 4.49
2351 2447 1.003928 TCAGGACATTGCTGCATCTGT 59.996 47.619 15.55 15.55 35.65 3.41
2492 2588 3.754850 CCTTTGCAGTGTGAATGATCTCA 59.245 43.478 0.00 0.00 0.00 3.27
2643 2797 4.563061 AGAGCCAAAATGTTGAATTCTGC 58.437 39.130 7.05 0.11 36.83 4.26
2653 2807 6.796785 AATTATAGCCAAGAGCCAAAATGT 57.203 33.333 0.00 0.00 45.47 2.71
3056 3217 9.651913 AAAATTGTGTGCTAAAAGAAGAAGAAA 57.348 25.926 0.00 0.00 0.00 2.52
3183 3409 3.463944 ACACGACTTGGAAAAGGTGTAG 58.536 45.455 0.00 0.00 33.59 2.74
3232 3507 3.633525 ACTAACGTACTGGCCAATCGATA 59.366 43.478 23.87 17.25 0.00 2.92
3349 3624 5.938125 GGTCAGGAAGTTACATTGTACACAT 59.062 40.000 0.00 0.00 0.00 3.21
3804 4287 5.001237 ACTGGTTAAAACAACGGGAAAAG 57.999 39.130 0.00 0.00 0.00 2.27
3894 4377 8.751302 ACATTGTTTTAAAGACTGAACGTTTT 57.249 26.923 0.46 0.00 0.00 2.43
4159 4642 0.243907 AACATCGCGCACAGAGTACT 59.756 50.000 8.75 0.00 0.00 2.73
4273 4760 1.025812 CGAAGGCGAGACATAGGAGT 58.974 55.000 0.00 0.00 40.82 3.85
4425 4928 7.687941 ATGAATCCGTGCTTTATTATTAGGG 57.312 36.000 0.00 0.00 0.00 3.53
4426 4929 8.237267 GGAATGAATCCGTGCTTTATTATTAGG 58.763 37.037 0.00 0.00 38.79 2.69
4442 4969 1.743394 GTGAACCCACGGAATGAATCC 59.257 52.381 0.00 0.00 45.57 3.01
4447 4974 1.296056 GACGGTGAACCCACGGAATG 61.296 60.000 9.54 0.00 43.69 2.67
4451 4978 4.289245 ACGACGGTGAACCCACGG 62.289 66.667 14.34 0.00 44.09 4.94
4481 5008 7.766738 TGTTTCCATAAAACTCAAGGGTTTTTC 59.233 33.333 15.21 1.30 46.19 2.29
4487 5014 5.989168 GGTTTGTTTCCATAAAACTCAAGGG 59.011 40.000 2.73 0.00 46.19 3.95
4530 5057 3.680937 AGCGGTGAAAAACGATCGAATTA 59.319 39.130 24.34 0.00 0.00 1.40
4531 5058 2.482721 AGCGGTGAAAAACGATCGAATT 59.517 40.909 24.34 13.39 0.00 2.17
4540 5067 1.001706 GAAGGTCCAGCGGTGAAAAAC 60.002 52.381 17.83 8.37 0.00 2.43
4552 5079 2.238847 ATAGCGCTTGCGAAGGTCCA 62.239 55.000 18.68 0.00 45.69 4.02
4555 5082 2.464459 GCATAGCGCTTGCGAAGGT 61.464 57.895 18.68 2.35 45.69 3.50


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

AutoCloner maintained by Alex Coulton.