Multiple sequence alignment - TraesCS5D01G338500

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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 TraesCS5D01G338500 chr5D 100.000 2775 0 0 1 2775 427518597 427521371 0.000000e+00 5125.0
1 TraesCS5D01G338500 chr5D 82.285 604 74 12 965 1562 427544918 427544342 2.480000e-135 492.0
2 TraesCS5D01G338500 chr5D 94.855 311 12 2 358 664 427514077 427514387 1.490000e-132 483.0
3 TraesCS5D01G338500 chr5A 92.131 1131 47 5 687 1792 541935398 541936511 0.000000e+00 1557.0
4 TraesCS5D01G338500 chr5A 90.896 692 46 9 2081 2765 541936735 541937416 0.000000e+00 913.0
5 TraesCS5D01G338500 chr5A 82.852 554 64 12 1064 1600 542002144 542001605 4.180000e-128 468.0
6 TraesCS5D01G338500 chr5B 93.441 1052 37 12 712 1753 517192213 517193242 0.000000e+00 1531.0
7 TraesCS5D01G338500 chr5B 90.166 783 63 7 2000 2775 517193600 517194375 0.000000e+00 1007.0
8 TraesCS5D01G338500 chr5B 77.594 665 76 20 965 1600 517208921 517208301 4.430000e-88 335.0
9 TraesCS5D01G338500 chr5B 83.165 297 49 1 46 342 475505246 475505541 1.270000e-68 270.0
10 TraesCS5D01G338500 chr5B 95.312 128 5 1 1835 1961 517193241 517193368 4.690000e-48 202.0
11 TraesCS5D01G338500 chr5B 95.000 40 2 0 687 726 517190668 517190707 2.310000e-06 63.9
12 TraesCS5D01G338500 chr6D 87.063 572 65 8 4 569 41889316 41888748 3.010000e-179 638.0
13 TraesCS5D01G338500 chr6D 80.818 318 48 11 357 664 41906399 41906085 1.280000e-58 237.0
14 TraesCS5D01G338500 chr3A 83.929 672 93 14 1 664 713954561 713955225 1.810000e-176 628.0
15 TraesCS5D01G338500 chr3A 84.795 342 51 1 34 375 393818439 393818779 2.650000e-90 342.0
16 TraesCS5D01G338500 chr6A 82.511 669 101 13 4 664 219621364 219620704 8.620000e-160 573.0
17 TraesCS5D01G338500 chr6A 84.043 282 37 6 102 375 53934645 53934364 5.890000e-67 265.0
18 TraesCS5D01G338500 chr2A 85.673 342 49 0 34 375 24896444 24896785 7.310000e-96 361.0
19 TraesCS5D01G338500 chr4D 86.939 245 32 0 90 334 450133770 450134014 2.720000e-70 276.0
20 TraesCS5D01G338500 chr2B 84.436 257 40 0 99 355 230259456 230259200 1.280000e-63 254.0


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 TraesCS5D01G338500 chr5D 427518597 427521371 2774 False 5125.000 5125 100.00000 1 2775 1 chr5D.!!$F2 2774
1 TraesCS5D01G338500 chr5D 427544342 427544918 576 True 492.000 492 82.28500 965 1562 1 chr5D.!!$R1 597
2 TraesCS5D01G338500 chr5A 541935398 541937416 2018 False 1235.000 1557 91.51350 687 2765 2 chr5A.!!$F1 2078
3 TraesCS5D01G338500 chr5A 542001605 542002144 539 True 468.000 468 82.85200 1064 1600 1 chr5A.!!$R1 536
4 TraesCS5D01G338500 chr5B 517190668 517194375 3707 False 700.975 1531 93.47975 687 2775 4 chr5B.!!$F2 2088
5 TraesCS5D01G338500 chr5B 517208301 517208921 620 True 335.000 335 77.59400 965 1600 1 chr5B.!!$R1 635
6 TraesCS5D01G338500 chr6D 41888748 41889316 568 True 638.000 638 87.06300 4 569 1 chr6D.!!$R1 565
7 TraesCS5D01G338500 chr3A 713954561 713955225 664 False 628.000 628 83.92900 1 664 1 chr3A.!!$F2 663
8 TraesCS5D01G338500 chr6A 219620704 219621364 660 True 573.000 573 82.51100 4 664 1 chr6A.!!$R2 660

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
597 613 0.043334 ACCTAGCCCATCACTCCACT 59.957 55.0 0.0 0.0 0.00 4.00 F
634 650 0.105194 TTCCTCACAGTCCCCAGTGA 60.105 55.0 0.0 0.0 42.06 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 3254 1.440145 GCCGCTAACCATCTGCTTCC 61.440 60.0 0.0 0.0 0.00 3.46 R
2193 4070 1.951209 TCAGACCCATAGGCTGAACA 58.049 50.0 0.0 0.0 40.85 3.18 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
23 24 4.410400 CCGTCTTGAGCCCCACCC 62.410 72.222 0.00 0.00 0.00 4.61
34 35 4.547367 CCCACCCGATCGGCTTCC 62.547 72.222 29.12 0.00 33.26 3.46
202 203 2.899044 GAGGGAGGTCTCGATCGCG 61.899 68.421 11.09 3.99 39.35 5.87
249 250 1.939838 GCCTTCGTTGACGGACTTGAT 60.940 52.381 3.48 0.00 40.29 2.57
259 260 2.815211 GACTTGATGAGCGCGGCA 60.815 61.111 8.83 4.86 0.00 5.69
262 263 2.047370 TTGATGAGCGCGGCAAGA 60.047 55.556 8.83 0.00 0.00 3.02
274 275 1.164662 CGGCAAGATGCTCCTCCATG 61.165 60.000 2.00 0.00 44.28 3.66
288 289 2.745884 CATGGCCGCCGTCTTCAA 60.746 61.111 0.00 0.00 0.00 2.69
289 290 2.436646 ATGGCCGCCGTCTTCAAG 60.437 61.111 4.58 0.00 0.00 3.02
303 304 1.756538 CTTCAAGGCTTGTTTGGTGGT 59.243 47.619 25.39 0.00 0.00 4.16
310 311 0.591170 CTTGTTTGGTGGTGTAGCGG 59.409 55.000 0.00 0.00 0.00 5.52
313 314 3.198953 TTTGGTGGTGTAGCGGGGG 62.199 63.158 0.00 0.00 0.00 5.40
338 339 1.681538 GTAGGCAGTCTCCAGATCGA 58.318 55.000 0.00 0.00 0.00 3.59
340 341 1.040339 AGGCAGTCTCCAGATCGACC 61.040 60.000 0.00 0.00 0.00 4.79
412 413 3.181413 TGGATCAGATCTAGGAGGAAGGG 60.181 52.174 10.36 0.00 0.00 3.95
413 414 3.076785 GGATCAGATCTAGGAGGAAGGGA 59.923 52.174 10.36 0.00 0.00 4.20
415 416 3.135279 TCAGATCTAGGAGGAAGGGAGT 58.865 50.000 0.00 0.00 0.00 3.85
416 417 4.316872 TCAGATCTAGGAGGAAGGGAGTA 58.683 47.826 0.00 0.00 0.00 2.59
417 418 4.352595 TCAGATCTAGGAGGAAGGGAGTAG 59.647 50.000 0.00 0.00 0.00 2.57
418 419 4.105697 CAGATCTAGGAGGAAGGGAGTAGT 59.894 50.000 0.00 0.00 0.00 2.73
419 420 4.735020 AGATCTAGGAGGAAGGGAGTAGTT 59.265 45.833 0.00 0.00 0.00 2.24
420 421 4.252570 TCTAGGAGGAAGGGAGTAGTTG 57.747 50.000 0.00 0.00 0.00 3.16
421 422 2.255770 AGGAGGAAGGGAGTAGTTGG 57.744 55.000 0.00 0.00 0.00 3.77
422 423 0.542333 GGAGGAAGGGAGTAGTTGGC 59.458 60.000 0.00 0.00 0.00 4.52
423 424 0.175989 GAGGAAGGGAGTAGTTGGCG 59.824 60.000 0.00 0.00 0.00 5.69
425 426 1.551019 GGAAGGGAGTAGTTGGCGGT 61.551 60.000 0.00 0.00 0.00 5.68
426 427 0.108281 GAAGGGAGTAGTTGGCGGTC 60.108 60.000 0.00 0.00 0.00 4.79
427 428 0.834687 AAGGGAGTAGTTGGCGGTCA 60.835 55.000 0.00 0.00 0.00 4.02
432 433 1.218316 GTAGTTGGCGGTCAGGGAG 59.782 63.158 0.00 0.00 0.00 4.30
433 434 1.077805 TAGTTGGCGGTCAGGGAGA 59.922 57.895 0.00 0.00 0.00 3.71
434 435 0.970937 TAGTTGGCGGTCAGGGAGAG 60.971 60.000 0.00 0.00 0.00 3.20
436 437 3.539593 TTGGCGGTCAGGGAGAGGA 62.540 63.158 0.00 0.00 0.00 3.71
438 439 2.291043 GGCGGTCAGGGAGAGGAAA 61.291 63.158 0.00 0.00 0.00 3.13
454 462 5.108752 AGAGGAAAAGGAAGGGAAGGATAA 58.891 41.667 0.00 0.00 0.00 1.75
459 475 3.602205 AGGAAGGGAAGGATAATTGGC 57.398 47.619 0.00 0.00 0.00 4.52
466 482 2.158667 GGAAGGATAATTGGCGGAGGAA 60.159 50.000 0.00 0.00 0.00 3.36
483 499 1.135228 GGAACAGCCTCTCTCTCGTTC 60.135 57.143 0.00 0.00 33.62 3.95
484 500 1.542030 GAACAGCCTCTCTCTCGTTCA 59.458 52.381 0.00 0.00 34.35 3.18
491 507 3.082548 CCTCTCTCTCGTTCACCAGTTA 58.917 50.000 0.00 0.00 0.00 2.24
500 516 7.122204 TCTCTCGTTCACCAGTTATCTCAATAA 59.878 37.037 0.00 0.00 0.00 1.40
522 538 1.257936 CGATACCGAAATTGTGGCTCG 59.742 52.381 7.13 7.13 38.22 5.03
539 555 0.899720 TCGCCCACCTACTTAACCAG 59.100 55.000 0.00 0.00 0.00 4.00
540 556 0.743345 CGCCCACCTACTTAACCAGC 60.743 60.000 0.00 0.00 0.00 4.85
574 590 2.355986 ATCGCTCGGCCCAACTACA 61.356 57.895 0.00 0.00 0.00 2.74
580 596 1.964373 CGGCCCAACTACACACACC 60.964 63.158 0.00 0.00 0.00 4.16
581 597 1.454539 GGCCCAACTACACACACCT 59.545 57.895 0.00 0.00 0.00 4.00
583 599 1.338769 GGCCCAACTACACACACCTAG 60.339 57.143 0.00 0.00 0.00 3.02
584 600 1.944430 GCCCAACTACACACACCTAGC 60.944 57.143 0.00 0.00 0.00 3.42
587 603 1.346395 CAACTACACACACCTAGCCCA 59.654 52.381 0.00 0.00 0.00 5.36
594 610 0.179000 CACACCTAGCCCATCACTCC 59.821 60.000 0.00 0.00 0.00 3.85
595 611 0.252696 ACACCTAGCCCATCACTCCA 60.253 55.000 0.00 0.00 0.00 3.86
597 613 0.043334 ACCTAGCCCATCACTCCACT 59.957 55.000 0.00 0.00 0.00 4.00
598 614 1.207791 CCTAGCCCATCACTCCACTT 58.792 55.000 0.00 0.00 0.00 3.16
603 619 1.687612 CCATCACTCCACTTGGCCT 59.312 57.895 3.32 0.00 34.44 5.19
604 620 0.393537 CCATCACTCCACTTGGCCTC 60.394 60.000 3.32 0.00 34.44 4.70
622 638 4.785453 CTGGCCCGGCTTCCTCAC 62.785 72.222 9.86 0.00 0.00 3.51
625 641 4.021925 GCCCGGCTTCCTCACAGT 62.022 66.667 0.71 0.00 0.00 3.55
628 644 2.266055 CGGCTTCCTCACAGTCCC 59.734 66.667 0.00 0.00 0.00 4.46
630 646 2.224159 GGCTTCCTCACAGTCCCCA 61.224 63.158 0.00 0.00 0.00 4.96
631 647 1.298014 GCTTCCTCACAGTCCCCAG 59.702 63.158 0.00 0.00 0.00 4.45
632 648 1.484444 GCTTCCTCACAGTCCCCAGT 61.484 60.000 0.00 0.00 0.00 4.00
634 650 0.105194 TTCCTCACAGTCCCCAGTGA 60.105 55.000 0.00 0.00 42.06 3.41
648 664 4.699522 GTGACTGGTGGGGTCGGC 62.700 72.222 0.00 0.00 36.58 5.54
665 681 4.701663 CCTGACAGGCGTGACAAT 57.298 55.556 14.38 0.00 0.00 2.71
666 682 3.832704 CCTGACAGGCGTGACAATA 57.167 52.632 14.38 0.00 0.00 1.90
667 683 2.315925 CCTGACAGGCGTGACAATAT 57.684 50.000 14.38 0.00 0.00 1.28
668 684 1.935873 CCTGACAGGCGTGACAATATG 59.064 52.381 14.38 1.35 0.00 1.78
669 685 1.328680 CTGACAGGCGTGACAATATGC 59.671 52.381 14.38 0.00 0.00 3.14
670 686 1.338579 TGACAGGCGTGACAATATGCA 60.339 47.619 14.38 0.00 34.26 3.96
671 687 1.062587 GACAGGCGTGACAATATGCAC 59.937 52.381 14.38 0.00 34.26 4.57
672 688 1.085893 CAGGCGTGACAATATGCACA 58.914 50.000 0.00 0.00 34.78 4.57
673 689 1.086696 AGGCGTGACAATATGCACAC 58.913 50.000 0.00 0.00 34.78 3.82
674 690 0.801872 GGCGTGACAATATGCACACA 59.198 50.000 0.00 0.00 34.78 3.72
675 691 1.465689 GGCGTGACAATATGCACACAC 60.466 52.381 0.00 0.00 34.78 3.82
676 692 2.143621 CGTGACAATATGCACACACG 57.856 50.000 0.00 0.00 43.10 4.49
678 694 3.804518 GTGACAATATGCACACACGAA 57.195 42.857 0.00 0.00 35.19 3.85
679 695 4.140518 GTGACAATATGCACACACGAAA 57.859 40.909 0.00 0.00 35.19 3.46
680 696 3.906008 GTGACAATATGCACACACGAAAC 59.094 43.478 0.00 0.00 35.19 2.78
681 697 3.561725 TGACAATATGCACACACGAAACA 59.438 39.130 0.00 0.00 0.00 2.83
682 698 3.884169 ACAATATGCACACACGAAACAC 58.116 40.909 0.00 0.00 0.00 3.32
684 700 1.854227 TATGCACACACGAAACACGA 58.146 45.000 0.00 0.00 45.77 4.35
685 701 1.225855 ATGCACACACGAAACACGAT 58.774 45.000 0.00 0.00 45.77 3.73
812 2348 3.110178 CCCGCCTCAACGTTCGTC 61.110 66.667 0.00 0.00 0.00 4.20
828 2364 4.111016 TCACGCGCGACCGATTCT 62.111 61.111 39.36 8.45 36.29 2.40
853 2389 1.281925 ACCACCACCATCCAGATCCC 61.282 60.000 0.00 0.00 0.00 3.85
884 2420 4.720902 CCAGCATCACCGGCACCA 62.721 66.667 0.00 0.00 0.00 4.17
911 2447 0.761323 TTGGTCCAACGTCTCCTCCA 60.761 55.000 0.00 0.00 0.00 3.86
1139 2679 4.498520 CCCATGTCGTCGCTCGCT 62.499 66.667 0.00 0.00 39.67 4.93
1208 2748 4.129737 CTCTTCTCGGCGCCGGAA 62.130 66.667 44.95 38.78 40.25 4.30
1520 3096 2.764128 TCATGGGAGTCGGAGGCC 60.764 66.667 0.00 0.00 0.00 5.19
1546 3122 1.864082 GTACGGCGGAGACTACTAGAC 59.136 57.143 13.24 0.00 0.00 2.59
1547 3123 0.540923 ACGGCGGAGACTACTAGACT 59.459 55.000 13.24 0.00 0.00 3.24
1548 3124 1.759445 ACGGCGGAGACTACTAGACTA 59.241 52.381 13.24 0.00 0.00 2.59
1549 3125 2.134346 CGGCGGAGACTACTAGACTAC 58.866 57.143 0.00 0.00 0.00 2.73
1550 3126 2.224018 CGGCGGAGACTACTAGACTACT 60.224 54.545 0.00 0.00 0.00 2.57
1551 3127 3.005261 CGGCGGAGACTACTAGACTACTA 59.995 52.174 0.00 0.00 0.00 1.82
1552 3128 4.500545 CGGCGGAGACTACTAGACTACTAA 60.501 50.000 0.00 0.00 0.00 2.24
1553 3129 5.363939 GGCGGAGACTACTAGACTACTAAA 58.636 45.833 0.00 0.00 0.00 1.85
1647 3254 8.693542 AAAGACAAAATTGTGTTCAGAAAGAG 57.306 30.769 1.98 0.00 42.90 2.85
1665 3272 0.179000 AGGAAGCAGATGGTTAGCGG 59.821 55.000 0.00 0.00 35.69 5.52
1763 3371 1.571919 GCATGTAGCGTTACCTCCTG 58.428 55.000 6.98 1.33 0.00 3.86
1944 3628 2.095567 CAGTGCTCTTTCACGGGATTTG 60.096 50.000 0.00 0.00 41.61 2.32
1947 3631 1.463674 CTCTTTCACGGGATTTGGGG 58.536 55.000 0.00 0.00 0.00 4.96
1949 3633 0.611896 CTTTCACGGGATTTGGGGCT 60.612 55.000 0.00 0.00 0.00 5.19
1953 3637 1.286553 TCACGGGATTTGGGGCTAATT 59.713 47.619 0.00 0.00 0.00 1.40
1961 3645 4.019771 GGATTTGGGGCTAATTTTGTCCAA 60.020 41.667 3.94 4.37 33.11 3.53
1962 3646 5.513962 GGATTTGGGGCTAATTTTGTCCAAA 60.514 40.000 15.94 15.94 44.80 3.28
1963 3647 5.373812 TTTGGGGCTAATTTTGTCCAAAA 57.626 34.783 7.58 7.58 43.48 2.44
1964 3648 4.615588 TGGGGCTAATTTTGTCCAAAAG 57.384 40.909 10.58 0.00 42.72 2.27
1965 3649 3.970640 TGGGGCTAATTTTGTCCAAAAGT 59.029 39.130 10.58 10.25 42.72 2.66
1966 3650 5.148502 TGGGGCTAATTTTGTCCAAAAGTA 58.851 37.500 10.58 10.77 42.72 2.24
1977 3661 9.965824 ATTTTGTCCAAAAGTAGTATGTCAAAG 57.034 29.630 10.58 0.00 42.72 2.77
1978 3662 8.740123 TTTGTCCAAAAGTAGTATGTCAAAGA 57.260 30.769 0.00 0.00 0.00 2.52
1979 3663 8.918202 TTGTCCAAAAGTAGTATGTCAAAGAT 57.082 30.769 0.00 0.00 0.00 2.40
1980 3664 8.918202 TGTCCAAAAGTAGTATGTCAAAGATT 57.082 30.769 0.00 0.00 0.00 2.40
1981 3665 9.349713 TGTCCAAAAGTAGTATGTCAAAGATTT 57.650 29.630 0.00 0.00 0.00 2.17
2011 3888 4.202441 CCCCTTCAACATATCCTTGTCTG 58.798 47.826 0.00 0.00 0.00 3.51
2027 3904 4.186856 TGTCTGAATGTTCATCGCTACA 57.813 40.909 0.00 0.00 36.46 2.74
2033 3910 6.036408 TCTGAATGTTCATCGCTACATGAAAG 59.964 38.462 0.00 0.00 42.99 2.62
2045 3922 6.485648 TCGCTACATGAAAGACTAGCTATGTA 59.514 38.462 0.00 0.00 31.20 2.29
2059 3936 2.831333 CTATGTAGGCAGTTCCAGCTG 58.169 52.381 6.78 6.78 39.37 4.24
2107 3984 8.065473 TCTTATCTTGGCAAATTGAAGCAATA 57.935 30.769 0.00 0.00 32.43 1.90
2108 3985 8.698210 TCTTATCTTGGCAAATTGAAGCAATAT 58.302 29.630 0.00 0.00 32.43 1.28
2213 4090 2.237143 CTGTTCAGCCTATGGGTCTGAA 59.763 50.000 22.16 22.16 44.85 3.02
2246 4123 7.280876 GTCTTGATCACAATATTCAGTTAGCCA 59.719 37.037 0.00 0.00 35.37 4.75
2259 4136 4.019771 TCAGTTAGCCAACACACCATGATA 60.020 41.667 0.00 0.00 37.10 2.15
2292 4173 1.225376 GCGACCGTTGGATCAACACA 61.225 55.000 10.75 0.00 43.70 3.72
2293 4174 1.222300 CGACCGTTGGATCAACACAA 58.778 50.000 10.75 0.00 43.70 3.33
2299 4180 5.949735 ACCGTTGGATCAACACAAAATATC 58.050 37.500 10.75 0.00 43.70 1.63
2367 4248 1.352352 GACATCCTGATATGGGTGGGG 59.648 57.143 0.00 0.00 42.31 4.96
2393 4274 1.022451 CGGCCGGCAGCTAGTTTTTA 61.022 55.000 30.85 0.00 43.05 1.52
2432 4313 7.553881 TGTCTCTAAGTGGAAAGTTTTTCTG 57.446 36.000 2.03 0.00 0.00 3.02
2437 4318 4.376340 AGTGGAAAGTTTTTCTGCTGTG 57.624 40.909 2.03 0.00 0.00 3.66
2576 4457 1.328680 AGCGTCCACTATGTACGTACG 59.671 52.381 20.18 15.01 38.81 3.67
2608 4492 2.010145 TAGTTTGAGGCGTCTGATGC 57.990 50.000 13.40 13.40 0.00 3.91
2746 4630 0.519175 GCAATCTAACTGTGTGCGCG 60.519 55.000 0.00 0.00 0.00 6.86
2767 4651 5.276820 CGCGCACATATGAATCTAAAACTCA 60.277 40.000 10.38 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.664677 GTGGATCCGGGCCGATCG 62.665 72.222 30.79 11.48 39.72 3.69
72 73 3.060020 GAATCGACGGGTCCTGCGA 62.060 63.158 16.26 16.26 37.17 5.10
231 232 2.663602 CTCATCAAGTCCGTCAACGAAG 59.336 50.000 3.71 0.00 43.02 3.79
232 233 2.672714 CTCATCAAGTCCGTCAACGAA 58.327 47.619 3.71 0.00 43.02 3.85
237 238 1.446099 GCGCTCATCAAGTCCGTCA 60.446 57.895 0.00 0.00 0.00 4.35
249 250 4.765449 AGCATCTTGCCGCGCTCA 62.765 61.111 5.56 0.00 46.52 4.26
259 260 1.535685 GGCCATGGAGGAGCATCTT 59.464 57.895 18.40 0.00 41.22 2.40
262 263 4.575973 GCGGCCATGGAGGAGCAT 62.576 66.667 18.40 0.00 40.75 3.79
288 289 1.981256 CTACACCACCAAACAAGCCT 58.019 50.000 0.00 0.00 0.00 4.58
289 290 0.313987 GCTACACCACCAAACAAGCC 59.686 55.000 0.00 0.00 0.00 4.35
292 293 0.820074 CCCGCTACACCACCAAACAA 60.820 55.000 0.00 0.00 0.00 2.83
295 296 2.432563 CCCCGCTACACCACCAAA 59.567 61.111 0.00 0.00 0.00 3.28
313 314 3.851128 GAGACTGCCTACCCCCGC 61.851 72.222 0.00 0.00 0.00 6.13
325 326 0.748729 GGTCGGTCGATCTGGAGACT 60.749 60.000 0.00 0.00 37.52 3.24
412 413 1.218316 CCCTGACCGCCAACTACTC 59.782 63.158 0.00 0.00 0.00 2.59
413 414 1.229082 TCCCTGACCGCCAACTACT 60.229 57.895 0.00 0.00 0.00 2.57
415 416 0.970937 CTCTCCCTGACCGCCAACTA 60.971 60.000 0.00 0.00 0.00 2.24
416 417 2.203788 TCTCCCTGACCGCCAACT 60.204 61.111 0.00 0.00 0.00 3.16
417 418 2.266055 CTCTCCCTGACCGCCAAC 59.734 66.667 0.00 0.00 0.00 3.77
418 419 3.003173 CCTCTCCCTGACCGCCAA 61.003 66.667 0.00 0.00 0.00 4.52
419 420 3.539593 TTCCTCTCCCTGACCGCCA 62.540 63.158 0.00 0.00 0.00 5.69
420 421 1.838073 TTTTCCTCTCCCTGACCGCC 61.838 60.000 0.00 0.00 0.00 6.13
421 422 0.391793 CTTTTCCTCTCCCTGACCGC 60.392 60.000 0.00 0.00 0.00 5.68
422 423 0.250513 CCTTTTCCTCTCCCTGACCG 59.749 60.000 0.00 0.00 0.00 4.79
423 424 1.657804 TCCTTTTCCTCTCCCTGACC 58.342 55.000 0.00 0.00 0.00 4.02
425 426 2.269940 CCTTCCTTTTCCTCTCCCTGA 58.730 52.381 0.00 0.00 0.00 3.86
426 427 1.283321 CCCTTCCTTTTCCTCTCCCTG 59.717 57.143 0.00 0.00 0.00 4.45
427 428 1.154434 TCCCTTCCTTTTCCTCTCCCT 59.846 52.381 0.00 0.00 0.00 4.20
432 433 5.452341 TTATCCTTCCCTTCCTTTTCCTC 57.548 43.478 0.00 0.00 0.00 3.71
433 434 6.197903 CAATTATCCTTCCCTTCCTTTTCCT 58.802 40.000 0.00 0.00 0.00 3.36
434 435 5.363868 CCAATTATCCTTCCCTTCCTTTTCC 59.636 44.000 0.00 0.00 0.00 3.13
436 437 4.716784 GCCAATTATCCTTCCCTTCCTTTT 59.283 41.667 0.00 0.00 0.00 2.27
438 439 3.688414 CGCCAATTATCCTTCCCTTCCTT 60.688 47.826 0.00 0.00 0.00 3.36
454 462 2.044946 GGCTGTTCCTCCGCCAAT 60.045 61.111 0.00 0.00 44.23 3.16
466 482 0.885196 GTGAACGAGAGAGAGGCTGT 59.115 55.000 0.00 0.00 0.00 4.40
483 499 7.273598 CGGTATCGATTATTGAGATAACTGGTG 59.726 40.741 1.71 0.00 39.00 4.17
484 500 7.176165 TCGGTATCGATTATTGAGATAACTGGT 59.824 37.037 1.71 0.00 40.88 4.00
491 507 8.712363 CACAATTTCGGTATCGATTATTGAGAT 58.288 33.333 27.08 12.06 45.51 2.75
500 516 3.131396 GAGCCACAATTTCGGTATCGAT 58.869 45.455 0.00 2.16 45.51 3.59
513 529 2.925706 TAGGTGGGCGAGCCACAA 60.926 61.111 16.65 0.00 39.66 3.33
514 530 3.702048 GTAGGTGGGCGAGCCACA 61.702 66.667 16.65 8.67 39.66 4.17
522 538 0.393944 GGCTGGTTAAGTAGGTGGGC 60.394 60.000 0.00 0.00 0.00 5.36
557 573 2.992689 TGTAGTTGGGCCGAGCGA 60.993 61.111 0.00 0.00 0.00 4.93
562 578 1.964373 GGTGTGTGTAGTTGGGCCG 60.964 63.158 0.00 0.00 0.00 6.13
574 590 0.905357 GAGTGATGGGCTAGGTGTGT 59.095 55.000 0.00 0.00 0.00 3.72
580 596 1.134280 CCAAGTGGAGTGATGGGCTAG 60.134 57.143 0.00 0.00 37.39 3.42
581 597 0.911769 CCAAGTGGAGTGATGGGCTA 59.088 55.000 0.00 0.00 37.39 3.93
583 599 2.048603 GCCAAGTGGAGTGATGGGC 61.049 63.158 0.18 0.00 37.39 5.36
584 600 1.379044 GGCCAAGTGGAGTGATGGG 60.379 63.158 0.00 0.00 37.39 4.00
587 603 0.548682 AGGAGGCCAAGTGGAGTGAT 60.549 55.000 5.01 0.00 37.39 3.06
612 628 2.190488 CTGGGGACTGTGAGGAAGCC 62.190 65.000 0.00 0.00 0.00 4.35
630 646 2.923035 CCGACCCCACCAGTCACT 60.923 66.667 0.00 0.00 33.70 3.41
631 647 4.699522 GCCGACCCCACCAGTCAC 62.700 72.222 0.00 0.00 33.70 3.67
648 664 1.935873 CATATTGTCACGCCTGTCAGG 59.064 52.381 15.15 15.15 38.80 3.86
649 665 1.328680 GCATATTGTCACGCCTGTCAG 59.671 52.381 0.00 0.00 0.00 3.51
652 668 1.086696 GTGCATATTGTCACGCCTGT 58.913 50.000 0.00 0.00 0.00 4.00
664 680 2.409012 TCGTGTTTCGTGTGTGCATAT 58.591 42.857 0.00 0.00 40.80 1.78
665 681 1.854227 TCGTGTTTCGTGTGTGCATA 58.146 45.000 0.00 0.00 40.80 3.14
666 682 1.225855 ATCGTGTTTCGTGTGTGCAT 58.774 45.000 0.00 0.00 40.80 3.96
667 683 1.010580 AATCGTGTTTCGTGTGTGCA 58.989 45.000 0.00 0.00 40.80 4.57
668 684 2.934107 TAATCGTGTTTCGTGTGTGC 57.066 45.000 0.00 0.00 40.80 4.57
669 685 3.204314 CGTTAATCGTGTTTCGTGTGTG 58.796 45.455 0.00 0.00 40.80 3.82
670 686 2.219216 CCGTTAATCGTGTTTCGTGTGT 59.781 45.455 0.00 0.00 40.80 3.72
671 687 2.410517 CCCGTTAATCGTGTTTCGTGTG 60.411 50.000 0.00 0.00 40.80 3.82
672 688 1.794116 CCCGTTAATCGTGTTTCGTGT 59.206 47.619 0.00 0.00 40.80 4.49
673 689 1.794116 ACCCGTTAATCGTGTTTCGTG 59.206 47.619 0.00 0.00 40.80 4.35
674 690 2.153366 ACCCGTTAATCGTGTTTCGT 57.847 45.000 0.00 0.00 40.80 3.85
675 691 2.028404 GCTACCCGTTAATCGTGTTTCG 59.972 50.000 0.00 0.00 41.41 3.46
676 692 2.995258 TGCTACCCGTTAATCGTGTTTC 59.005 45.455 0.00 0.00 37.94 2.78
677 693 3.042871 TGCTACCCGTTAATCGTGTTT 57.957 42.857 0.00 0.00 37.94 2.83
678 694 2.747396 TGCTACCCGTTAATCGTGTT 57.253 45.000 0.00 0.00 37.94 3.32
679 695 2.747396 TTGCTACCCGTTAATCGTGT 57.253 45.000 0.00 0.00 37.94 4.49
680 696 4.093703 TGAAATTGCTACCCGTTAATCGTG 59.906 41.667 0.00 0.00 37.94 4.35
681 697 4.255301 TGAAATTGCTACCCGTTAATCGT 58.745 39.130 0.00 0.00 37.94 3.73
682 698 4.868450 TGAAATTGCTACCCGTTAATCG 57.132 40.909 0.00 0.00 39.52 3.34
683 699 5.945155 TGTTGAAATTGCTACCCGTTAATC 58.055 37.500 0.00 0.00 0.00 1.75
684 700 5.708230 TCTGTTGAAATTGCTACCCGTTAAT 59.292 36.000 0.00 0.00 0.00 1.40
685 701 5.064558 TCTGTTGAAATTGCTACCCGTTAA 58.935 37.500 0.00 0.00 0.00 2.01
812 2348 3.902063 CAGAATCGGTCGCGCGTG 61.902 66.667 30.98 20.31 0.00 5.34
878 2414 4.411136 CCAACGTTGTTTGGTGCC 57.589 55.556 25.63 0.00 41.18 5.01
1374 2944 4.214327 CCTCTTCCTCGCCCTCGC 62.214 72.222 0.00 0.00 35.26 5.03
1520 3096 3.129502 TCTCCGCCGTACCTCGTG 61.130 66.667 1.58 0.00 37.94 4.35
1547 3123 7.025520 ACCTGTGTACCTCTACTCTTTAGTA 57.974 40.000 0.00 0.00 37.15 1.82
1548 3124 5.890049 ACCTGTGTACCTCTACTCTTTAGT 58.110 41.667 0.00 0.00 39.91 2.24
1549 3125 7.337167 TCTACCTGTGTACCTCTACTCTTTAG 58.663 42.308 0.00 0.00 0.00 1.85
1550 3126 7.262990 TCTACCTGTGTACCTCTACTCTTTA 57.737 40.000 0.00 0.00 0.00 1.85
1551 3127 6.137104 TCTACCTGTGTACCTCTACTCTTT 57.863 41.667 0.00 0.00 0.00 2.52
1552 3128 5.775813 TCTACCTGTGTACCTCTACTCTT 57.224 43.478 0.00 0.00 0.00 2.85
1553 3129 5.488203 TCTTCTACCTGTGTACCTCTACTCT 59.512 44.000 0.00 0.00 0.00 3.24
1647 3254 1.440145 GCCGCTAACCATCTGCTTCC 61.440 60.000 0.00 0.00 0.00 3.46
1665 3272 6.866010 AATTTCAAATTCAAAAGGTGGAGC 57.134 33.333 0.00 0.00 0.00 4.70
1809 3485 6.403333 CTTGCAAGCAAACTATACGACTAA 57.597 37.500 14.65 0.00 35.33 2.24
1811 3487 4.928661 CTTGCAAGCAAACTATACGACT 57.071 40.909 14.65 0.00 35.33 4.18
1834 3510 3.499737 CCAAGATCGGTGGCGTGC 61.500 66.667 5.64 0.00 0.00 5.34
1944 3628 4.617253 ACTTTTGGACAAAATTAGCCCC 57.383 40.909 10.31 0.00 39.29 5.80
1947 3631 9.556030 GACATACTACTTTTGGACAAAATTAGC 57.444 33.333 23.43 11.24 42.42 3.09
1953 3637 8.740123 TCTTTGACATACTACTTTTGGACAAA 57.260 30.769 0.00 0.00 0.00 2.83
1983 3667 5.283876 AGGATATGTTGAAGGGGGAAAAA 57.716 39.130 0.00 0.00 0.00 1.94
1984 3668 4.965283 AGGATATGTTGAAGGGGGAAAA 57.035 40.909 0.00 0.00 0.00 2.29
1985 3669 4.045334 ACAAGGATATGTTGAAGGGGGAAA 59.955 41.667 2.13 0.00 0.00 3.13
1986 3670 3.596046 ACAAGGATATGTTGAAGGGGGAA 59.404 43.478 2.13 0.00 0.00 3.97
1987 3671 3.197983 ACAAGGATATGTTGAAGGGGGA 58.802 45.455 2.13 0.00 0.00 4.81
1988 3672 3.203040 AGACAAGGATATGTTGAAGGGGG 59.797 47.826 2.13 0.00 32.57 5.40
1989 3673 4.080356 TCAGACAAGGATATGTTGAAGGGG 60.080 45.833 2.13 0.00 32.57 4.79
1990 3674 5.102953 TCAGACAAGGATATGTTGAAGGG 57.897 43.478 2.13 0.00 32.57 3.95
1991 3675 6.600822 ACATTCAGACAAGGATATGTTGAAGG 59.399 38.462 11.56 11.56 37.68 3.46
1992 3676 7.621428 ACATTCAGACAAGGATATGTTGAAG 57.379 36.000 2.13 0.00 35.67 3.02
1993 3677 7.665145 TGAACATTCAGACAAGGATATGTTGAA 59.335 33.333 0.00 0.00 36.62 2.69
1994 3678 7.167535 TGAACATTCAGACAAGGATATGTTGA 58.832 34.615 0.00 0.00 36.62 3.18
1995 3679 7.381766 TGAACATTCAGACAAGGATATGTTG 57.618 36.000 0.00 0.00 36.62 3.33
1996 3680 7.011763 CGATGAACATTCAGACAAGGATATGTT 59.988 37.037 0.00 0.00 41.08 2.71
1997 3681 6.481313 CGATGAACATTCAGACAAGGATATGT 59.519 38.462 0.23 0.00 41.08 2.29
1998 3682 6.565435 GCGATGAACATTCAGACAAGGATATG 60.565 42.308 0.23 0.00 41.08 1.78
2011 3888 6.036517 AGTCTTTCATGTAGCGATGAACATTC 59.963 38.462 7.97 0.00 41.11 2.67
2027 3904 5.600484 ACTGCCTACATAGCTAGTCTTTCAT 59.400 40.000 0.00 0.00 0.00 2.57
2033 3910 3.637229 TGGAACTGCCTACATAGCTAGTC 59.363 47.826 0.00 0.00 37.63 2.59
2108 3985 9.839817 GCTCTAGTCTCATGTACTCCATATATA 57.160 37.037 6.73 0.00 30.71 0.86
2115 3992 4.204012 ACAGCTCTAGTCTCATGTACTCC 58.796 47.826 6.73 0.00 0.00 3.85
2116 3993 5.124776 ACAACAGCTCTAGTCTCATGTACTC 59.875 44.000 6.73 0.00 0.00 2.59
2117 3994 5.013547 ACAACAGCTCTAGTCTCATGTACT 58.986 41.667 8.24 8.24 0.00 2.73
2118 3995 5.317733 ACAACAGCTCTAGTCTCATGTAC 57.682 43.478 0.00 0.00 0.00 2.90
2161 4038 8.458212 AGTGCGAGTAACATAAAACTTACTAC 57.542 34.615 0.00 0.00 34.08 2.73
2162 4039 9.480053 AAAGTGCGAGTAACATAAAACTTACTA 57.520 29.630 0.00 0.00 34.08 1.82
2163 4040 7.958053 AAGTGCGAGTAACATAAAACTTACT 57.042 32.000 0.00 0.00 36.17 2.24
2193 4070 1.951209 TCAGACCCATAGGCTGAACA 58.049 50.000 0.00 0.00 40.85 3.18
2198 4075 4.971924 ACTAAATCTTCAGACCCATAGGCT 59.028 41.667 0.00 0.00 36.11 4.58
2204 4081 6.213397 TGATCAAGACTAAATCTTCAGACCCA 59.787 38.462 0.00 0.00 44.99 4.51
2205 4082 6.536941 GTGATCAAGACTAAATCTTCAGACCC 59.463 42.308 0.00 0.00 44.99 4.46
2206 4083 7.099764 TGTGATCAAGACTAAATCTTCAGACC 58.900 38.462 0.00 0.00 44.99 3.85
2230 4107 5.182950 TGGTGTGTTGGCTAACTGAATATTG 59.817 40.000 14.47 0.00 37.68 1.90
2231 4108 5.321102 TGGTGTGTTGGCTAACTGAATATT 58.679 37.500 14.47 0.00 37.68 1.28
2246 4123 8.574251 TTAATTGCTAGTTATCATGGTGTGTT 57.426 30.769 0.00 0.00 0.00 3.32
2259 4136 2.277084 CGGTCGCCTTAATTGCTAGTT 58.723 47.619 0.00 0.00 0.00 2.24
2299 4180 9.045223 TCTATGAACTATCAATGTCCATTTTCG 57.955 33.333 0.00 0.00 39.49 3.46
2393 4274 8.295288 CACTTAGAGACAATCAGCAAAGAAAAT 58.705 33.333 0.00 0.00 0.00 1.82
2409 4290 6.261158 AGCAGAAAAACTTTCCACTTAGAGAC 59.739 38.462 0.00 0.00 0.00 3.36
2411 4292 6.038714 ACAGCAGAAAAACTTTCCACTTAGAG 59.961 38.462 0.00 0.00 0.00 2.43
2432 4313 2.576615 GTTCCCCTTATGATCCACAGC 58.423 52.381 0.00 0.00 0.00 4.40
2576 4457 4.023707 GCCTCAAACTATGCATCCACATAC 60.024 45.833 0.19 0.00 0.00 2.39
2608 4492 5.220854 CCAACTGCAGTTAATATTCCCTTCG 60.221 44.000 30.67 13.77 36.32 3.79
2660 4544 2.287547 TGTTGCTTGCTTCGGTTGAATC 60.288 45.455 0.00 0.00 32.61 2.52
2702 4586 7.435192 GCTTCCATTTCCGGATTTACTTAATTG 59.565 37.037 4.15 0.00 34.19 2.32
2746 4630 8.615211 TGTCATGAGTTTTAGATTCATATGTGC 58.385 33.333 0.00 0.00 30.77 4.57


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

AutoCloner maintained by Alex Coulton.