Multiple sequence alignment - TraesCS5D01G415800

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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 TraesCS5D01G415800 chr5D 100.000 3215 0 0 1 3215 478223934 478220720 0.000000e+00 5938.0
1 TraesCS5D01G415800 chr5B 96.545 2576 81 7 644 3215 585836322 585833751 0.000000e+00 4257.0
2 TraesCS5D01G415800 chr5B 92.193 538 22 10 1 534 585836847 585836326 0.000000e+00 743.0
3 TraesCS5D01G415800 chr5B 84.892 139 21 0 1001 1139 391144731 391144869 1.200000e-29 141.0
4 TraesCS5D01G415800 chr5A 96.065 1728 55 5 1498 3215 597329516 597327792 0.000000e+00 2802.0
5 TraesCS5D01G415800 chr5A 97.567 863 14 5 644 1499 597330539 597329677 0.000000e+00 1471.0
6 TraesCS5D01G415800 chr5A 91.466 539 15 8 3 539 597331047 597330538 0.000000e+00 712.0
7 TraesCS5D01G415800 chr5A 84.173 139 22 0 1001 1139 436089151 436089289 5.590000e-28 135.0
8 TraesCS5D01G415800 chr6A 90.780 141 13 0 999 1139 578887721 578887581 4.230000e-44 189.0
9 TraesCS5D01G415800 chr6A 90.164 122 3 3 532 645 543531423 543531543 2.000000e-32 150.0
10 TraesCS5D01G415800 chr6D 90.071 141 14 0 999 1139 432710582 432710442 1.970000e-42 183.0
11 TraesCS5D01G415800 chr4A 93.913 115 4 3 533 645 671947191 671947078 1.530000e-38 171.0
12 TraesCS5D01G415800 chr4A 92.174 115 6 1 537 648 583790388 583790274 3.320000e-35 159.0
13 TraesCS5D01G415800 chr4A 89.167 120 10 3 538 654 671947078 671947197 2.580000e-31 147.0
14 TraesCS5D01G415800 chr6B 92.373 118 3 2 534 645 39203612 39203495 2.570000e-36 163.0
15 TraesCS5D01G415800 chr1B 90.833 120 5 3 531 645 328825519 328825401 4.290000e-34 156.0
16 TraesCS5D01G415800 chr1B 88.618 123 7 5 532 648 328825395 328825516 3.340000e-30 143.0
17 TraesCS5D01G415800 chr1A 90.598 117 3 4 538 646 53467522 53467638 7.190000e-32 148.0
18 TraesCS5D01G415800 chr3A 89.167 120 7 4 534 648 162672372 162672254 9.300000e-31 145.0
19 TraesCS5D01G415800 chr3A 81.618 136 17 7 1000 1131 489311964 489311833 4.390000e-19 106.0
20 TraesCS5D01G415800 chr3B 81.618 136 17 7 1000 1131 478323394 478323263 4.390000e-19 106.0
21 TraesCS5D01G415800 chr3D 80.882 136 18 7 1000 1131 367236965 367236834 2.040000e-17 100.0
22 TraesCS5D01G415800 chr2B 83.871 93 15 0 1544 1636 45735367 45735275 4.420000e-14 89.8


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 TraesCS5D01G415800 chr5D 478220720 478223934 3214 True 5938.000000 5938 100.000000 1 3215 1 chr5D.!!$R1 3214
1 TraesCS5D01G415800 chr5B 585833751 585836847 3096 True 2500.000000 4257 94.369000 1 3215 2 chr5B.!!$R1 3214
2 TraesCS5D01G415800 chr5A 597327792 597331047 3255 True 1661.666667 2802 95.032667 3 3215 3 chr5A.!!$R1 3212

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
55 56 0.119155 ACCCACCATCCAGAAGAGGA 59.881 55.0 0.00 0.00 43.01 3.71 F
175 176 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.00 0.00 0.00 3.82 F
1315 1328 0.974010 ACCTCCGGCCGAACATAAGA 60.974 55.0 30.73 12.64 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1328 0.243907 CGTCTGAGAATCCACCGTGT 59.756 55.0 0.00 0.00 0.00 4.49 R
1920 2095 0.463833 GAGCTTCCCCGTACATTGGG 60.464 60.0 5.88 5.88 46.93 4.12 R
3184 3372 2.916702 TCTGTTGTGACATGCTGACT 57.083 45.0 0.00 0.00 34.72 3.41 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
55 56 0.119155 ACCCACCATCCAGAAGAGGA 59.881 55.000 0.00 0.00 43.01 3.71
92 93 6.146184 CAGTATCTATTGCGTCCACATTTAGG 59.854 42.308 0.00 0.00 0.00 2.69
174 175 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
175 176 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
176 177 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
241 243 7.402054 ACTAACTCCATTCCATAACACATGAA 58.598 34.615 0.00 0.00 0.00 2.57
286 288 9.667107 CTGGTCAACTGAAAATAATACCTCTAA 57.333 33.333 0.00 0.00 0.00 2.10
378 383 4.335400 AACAGTAAAATTTGCACCCAGG 57.665 40.909 0.00 0.00 0.00 4.45
414 419 5.648092 ACTTCATGTATACTTTTGGACAGGC 59.352 40.000 4.17 0.00 0.00 4.85
434 439 3.708544 CAAGGAACGGCGGGGGTA 61.709 66.667 13.24 0.00 0.00 3.69
435 440 3.709633 AAGGAACGGCGGGGGTAC 61.710 66.667 13.24 0.00 0.00 3.34
537 543 3.701040 GCATGAACCAATGGAACCATACT 59.299 43.478 6.16 0.00 35.31 2.12
538 544 4.887071 GCATGAACCAATGGAACCATACTA 59.113 41.667 6.16 0.00 35.31 1.82
539 545 5.221048 GCATGAACCAATGGAACCATACTAC 60.221 44.000 6.16 0.29 35.31 2.73
540 546 5.772393 TGAACCAATGGAACCATACTACT 57.228 39.130 6.16 0.00 35.31 2.57
541 547 5.741011 TGAACCAATGGAACCATACTACTC 58.259 41.667 6.16 2.36 35.31 2.59
542 548 4.772886 ACCAATGGAACCATACTACTCC 57.227 45.455 6.16 0.00 35.31 3.85
543 549 3.458487 ACCAATGGAACCATACTACTCCC 59.542 47.826 6.16 0.00 35.31 4.30
544 550 3.716872 CCAATGGAACCATACTACTCCCT 59.283 47.826 6.77 0.00 35.31 4.20
545 551 4.202367 CCAATGGAACCATACTACTCCCTC 60.202 50.000 6.77 0.00 35.31 4.30
546 552 3.042059 TGGAACCATACTACTCCCTCC 57.958 52.381 0.00 0.00 0.00 4.30
547 553 1.962100 GGAACCATACTACTCCCTCCG 59.038 57.143 0.00 0.00 0.00 4.63
548 554 2.664015 GAACCATACTACTCCCTCCGT 58.336 52.381 0.00 0.00 0.00 4.69
549 555 2.842645 ACCATACTACTCCCTCCGTT 57.157 50.000 0.00 0.00 0.00 4.44
550 556 2.664015 ACCATACTACTCCCTCCGTTC 58.336 52.381 0.00 0.00 0.00 3.95
551 557 1.962100 CCATACTACTCCCTCCGTTCC 59.038 57.143 0.00 0.00 0.00 3.62
552 558 2.662866 CATACTACTCCCTCCGTTCCA 58.337 52.381 0.00 0.00 0.00 3.53
553 559 2.905415 TACTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
554 560 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
555 561 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
556 562 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
557 563 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
558 564 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
559 565 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
560 566 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
561 567 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
562 568 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
563 569 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
564 570 4.324267 CCTCCGTTCCAAATTACTTGTCT 58.676 43.478 0.00 0.00 32.65 3.41
565 571 4.760204 CCTCCGTTCCAAATTACTTGTCTT 59.240 41.667 0.00 0.00 32.65 3.01
566 572 5.334879 CCTCCGTTCCAAATTACTTGTCTTG 60.335 44.000 0.00 0.00 32.65 3.02
567 573 4.517453 TCCGTTCCAAATTACTTGTCTTGG 59.483 41.667 0.00 0.00 39.80 3.61
568 574 4.517453 CCGTTCCAAATTACTTGTCTTGGA 59.483 41.667 0.00 0.00 44.32 3.53
569 575 5.183140 CCGTTCCAAATTACTTGTCTTGGAT 59.817 40.000 3.38 0.00 45.10 3.41
570 576 6.294508 CCGTTCCAAATTACTTGTCTTGGATT 60.295 38.462 3.38 0.00 45.10 3.01
571 577 7.145323 CGTTCCAAATTACTTGTCTTGGATTT 58.855 34.615 3.38 0.00 45.10 2.17
572 578 7.114811 CGTTCCAAATTACTTGTCTTGGATTTG 59.885 37.037 3.38 0.00 45.10 2.32
573 579 7.595819 TCCAAATTACTTGTCTTGGATTTGT 57.404 32.000 0.00 0.00 41.83 2.83
574 580 7.657336 TCCAAATTACTTGTCTTGGATTTGTC 58.343 34.615 0.00 0.00 41.83 3.18
575 581 7.505585 TCCAAATTACTTGTCTTGGATTTGTCT 59.494 33.333 0.00 0.00 41.83 3.41
576 582 8.792633 CCAAATTACTTGTCTTGGATTTGTCTA 58.207 33.333 0.00 0.00 40.72 2.59
577 583 9.831737 CAAATTACTTGTCTTGGATTTGTCTAG 57.168 33.333 0.00 0.00 32.62 2.43
578 584 9.793259 AAATTACTTGTCTTGGATTTGTCTAGA 57.207 29.630 0.00 0.00 0.00 2.43
579 585 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
581 587 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
582 588 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
583 589 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
584 590 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
585 591 6.183360 TGTCTTGGATTTGTCTAGATACGGAG 60.183 42.308 0.00 0.00 0.00 4.63
587 593 5.515797 TGGATTTGTCTAGATACGGAGTG 57.484 43.478 0.00 0.00 45.73 3.51
588 594 4.202121 TGGATTTGTCTAGATACGGAGTGC 60.202 45.833 0.00 0.00 45.73 4.40
589 595 4.038162 GGATTTGTCTAGATACGGAGTGCT 59.962 45.833 0.00 0.00 45.73 4.40
590 596 5.241064 GGATTTGTCTAGATACGGAGTGCTA 59.759 44.000 0.00 0.00 45.73 3.49
591 597 5.752892 TTTGTCTAGATACGGAGTGCTAG 57.247 43.478 0.00 0.00 45.73 3.42
592 598 4.684484 TGTCTAGATACGGAGTGCTAGA 57.316 45.455 0.00 0.00 46.07 2.43
596 602 6.356186 TCTAGATACGGAGTGCTAGATACA 57.644 41.667 0.00 0.00 44.65 2.29
597 603 6.948589 TCTAGATACGGAGTGCTAGATACAT 58.051 40.000 0.00 0.00 44.65 2.29
598 604 7.042950 TCTAGATACGGAGTGCTAGATACATC 58.957 42.308 0.00 0.00 44.65 3.06
599 605 4.944930 AGATACGGAGTGCTAGATACATCC 59.055 45.833 0.00 0.83 45.73 3.51
600 606 2.620779 CGGAGTGCTAGATACATCCG 57.379 55.000 16.15 16.15 43.09 4.18
601 607 1.880675 CGGAGTGCTAGATACATCCGT 59.119 52.381 18.81 0.00 43.53 4.69
602 608 3.072211 CGGAGTGCTAGATACATCCGTA 58.928 50.000 18.81 0.00 43.53 4.02
603 609 3.690139 CGGAGTGCTAGATACATCCGTAT 59.310 47.826 18.81 0.00 43.53 3.06
618 624 9.698309 ATACATCCGTATCTAGACAAATTCAAG 57.302 33.333 0.00 0.00 32.66 3.02
619 625 7.782049 ACATCCGTATCTAGACAAATTCAAGA 58.218 34.615 0.00 0.00 0.00 3.02
620 626 7.707035 ACATCCGTATCTAGACAAATTCAAGAC 59.293 37.037 0.00 0.00 0.00 3.01
621 627 7.165460 TCCGTATCTAGACAAATTCAAGACA 57.835 36.000 0.00 0.00 0.00 3.41
622 628 7.608153 TCCGTATCTAGACAAATTCAAGACAA 58.392 34.615 0.00 0.00 0.00 3.18
623 629 7.759886 TCCGTATCTAGACAAATTCAAGACAAG 59.240 37.037 0.00 0.00 0.00 3.16
624 630 7.545965 CCGTATCTAGACAAATTCAAGACAAGT 59.454 37.037 0.00 0.00 0.00 3.16
625 631 9.569167 CGTATCTAGACAAATTCAAGACAAGTA 57.431 33.333 0.00 0.00 0.00 2.24
630 636 9.746711 CTAGACAAATTCAAGACAAGTAATTCG 57.253 33.333 0.00 0.00 0.00 3.34
631 637 7.584987 AGACAAATTCAAGACAAGTAATTCGG 58.415 34.615 0.00 0.00 0.00 4.30
632 638 7.444183 AGACAAATTCAAGACAAGTAATTCGGA 59.556 33.333 0.00 0.00 0.00 4.55
633 639 7.936584 ACAAATTCAAGACAAGTAATTCGGAA 58.063 30.769 0.00 0.00 0.00 4.30
634 640 7.860872 ACAAATTCAAGACAAGTAATTCGGAAC 59.139 33.333 0.00 0.00 0.00 3.62
824 830 3.750639 ATTTTATTACCACCACACGCG 57.249 42.857 3.53 3.53 0.00 6.01
946 952 1.064389 GCCCTAACCAAAGCATCCTCT 60.064 52.381 0.00 0.00 0.00 3.69
997 1003 4.693058 GCTAGAAGAGGAGGAAGGATACCA 60.693 50.000 0.00 0.00 37.17 3.25
1315 1328 0.974010 ACCTCCGGCCGAACATAAGA 60.974 55.000 30.73 12.64 0.00 2.10
1920 2095 4.410400 CCACCGTGCCTTCCTCCC 62.410 72.222 0.00 0.00 0.00 4.30
1960 2135 3.583276 AACTTCGTGGCGCCATCGA 62.583 57.895 34.50 34.50 38.10 3.59
1968 2143 3.498834 GCGCCATCGATGCACACA 61.499 61.111 20.25 0.00 38.10 3.72
2088 2263 2.123428 ATGCTTCTTCGGCATGGGC 61.123 57.895 0.21 0.00 46.85 5.36
2643 2818 7.501225 TGGTCTAGAATACATGAGACATTCGTA 59.499 37.037 0.00 0.00 40.10 3.43
2649 2824 8.470805 AGAATACATGAGACATTCGTAGACTTT 58.529 33.333 0.00 0.00 34.32 2.66
2675 2850 3.693085 AGGCATGTCTGTAAAGCATCAAG 59.307 43.478 0.00 0.00 0.00 3.02
2679 2854 5.065602 GCATGTCTGTAAAGCATCAAGATCA 59.934 40.000 0.00 0.00 0.00 2.92
2775 2951 9.809096 TGACAGACATAGATAGAAAATGACTTC 57.191 33.333 0.00 0.00 0.00 3.01
2780 2956 9.396022 GACATAGATAGAAAATGACTTCCCAAA 57.604 33.333 0.00 0.00 0.00 3.28
2846 3024 6.013898 TCCAGTGATTTTGGCAAAAATGGATA 60.014 34.615 29.02 18.43 44.27 2.59
2926 3107 5.410746 AGTTGCTCACATTGTGTCAATCTAG 59.589 40.000 20.92 10.89 34.79 2.43
2979 3167 5.882557 AGTACTGTGGAATGATGAAATGGAC 59.117 40.000 0.00 0.00 0.00 4.02
2981 3169 5.266788 ACTGTGGAATGATGAAATGGACAT 58.733 37.500 0.00 0.00 0.00 3.06
3138 3326 4.035208 CACAACACTAAACTCCTTCCACAC 59.965 45.833 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 5.005779 CACGCTAATTGTACATCAGAAGTCC 59.994 44.000 0.00 0.00 0.00 3.85
131 132 6.262944 ACACACACACACACTGAATTGATATT 59.737 34.615 0.00 0.00 0.00 1.28
132 133 5.764686 ACACACACACACACTGAATTGATAT 59.235 36.000 0.00 0.00 0.00 1.63
133 134 5.007528 CACACACACACACACTGAATTGATA 59.992 40.000 0.00 0.00 0.00 2.15
241 243 8.463930 TGACCAGTCTCATTTGTTTTAAGAAT 57.536 30.769 0.00 0.00 0.00 2.40
260 262 9.667107 TTAGAGGTATTATTTTCAGTTGACCAG 57.333 33.333 0.00 0.00 0.00 4.00
378 383 8.833231 AGTATACATGAAGTTATACACATGGC 57.167 34.615 5.50 0.00 42.66 4.40
454 460 6.204688 TCTGTTGTTTGATCTTCGTGCTATTT 59.795 34.615 0.00 0.00 0.00 1.40
455 461 5.700832 TCTGTTGTTTGATCTTCGTGCTATT 59.299 36.000 0.00 0.00 0.00 1.73
456 462 5.237815 TCTGTTGTTTGATCTTCGTGCTAT 58.762 37.500 0.00 0.00 0.00 2.97
537 543 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
538 544 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
539 545 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
540 546 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
541 547 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
542 548 4.324267 AGACAAGTAATTTGGAACGGAGG 58.676 43.478 0.00 0.00 41.25 4.30
543 549 5.334879 CCAAGACAAGTAATTTGGAACGGAG 60.335 44.000 0.00 0.00 42.05 4.63
544 550 4.517453 CCAAGACAAGTAATTTGGAACGGA 59.483 41.667 0.00 0.00 42.05 4.69
545 551 4.517453 TCCAAGACAAGTAATTTGGAACGG 59.483 41.667 2.52 0.00 44.38 4.44
546 552 5.682943 TCCAAGACAAGTAATTTGGAACG 57.317 39.130 2.52 0.00 44.38 3.95
550 556 7.661040 AGACAAATCCAAGACAAGTAATTTGG 58.339 34.615 9.60 0.00 41.25 3.28
551 557 9.831737 CTAGACAAATCCAAGACAAGTAATTTG 57.168 33.333 0.00 0.00 42.68 2.32
552 558 9.793259 TCTAGACAAATCCAAGACAAGTAATTT 57.207 29.630 0.00 0.00 0.00 1.82
553 559 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
555 561 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
556 562 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
557 563 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
558 564 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
559 565 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
560 566 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
561 567 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
562 568 5.892119 ACTCCGTATCTAGACAAATCCAAGA 59.108 40.000 0.00 0.00 0.00 3.02
563 569 5.980116 CACTCCGTATCTAGACAAATCCAAG 59.020 44.000 0.00 0.00 0.00 3.61
564 570 5.681437 GCACTCCGTATCTAGACAAATCCAA 60.681 44.000 0.00 0.00 0.00 3.53
565 571 4.202121 GCACTCCGTATCTAGACAAATCCA 60.202 45.833 0.00 0.00 0.00 3.41
566 572 4.038162 AGCACTCCGTATCTAGACAAATCC 59.962 45.833 0.00 0.00 0.00 3.01
567 573 5.189659 AGCACTCCGTATCTAGACAAATC 57.810 43.478 0.00 0.00 0.00 2.17
568 574 6.062749 TCTAGCACTCCGTATCTAGACAAAT 58.937 40.000 0.00 0.00 34.35 2.32
569 575 5.434408 TCTAGCACTCCGTATCTAGACAAA 58.566 41.667 0.00 0.00 34.35 2.83
570 576 5.032327 TCTAGCACTCCGTATCTAGACAA 57.968 43.478 0.00 0.00 34.35 3.18
571 577 4.684484 TCTAGCACTCCGTATCTAGACA 57.316 45.455 0.00 0.00 34.35 3.41
572 578 6.164876 TGTATCTAGCACTCCGTATCTAGAC 58.835 44.000 0.00 0.00 39.92 2.59
573 579 6.356186 TGTATCTAGCACTCCGTATCTAGA 57.644 41.667 0.00 0.00 40.94 2.43
574 580 6.259167 GGATGTATCTAGCACTCCGTATCTAG 59.741 46.154 0.00 0.00 0.00 2.43
575 581 6.114089 GGATGTATCTAGCACTCCGTATCTA 58.886 44.000 0.00 0.00 0.00 1.98
576 582 4.944930 GGATGTATCTAGCACTCCGTATCT 59.055 45.833 0.00 0.00 0.00 1.98
577 583 4.201832 CGGATGTATCTAGCACTCCGTATC 60.202 50.000 17.23 0.00 40.47 2.24
578 584 3.690139 CGGATGTATCTAGCACTCCGTAT 59.310 47.826 17.23 0.00 40.47 3.06
579 585 3.072211 CGGATGTATCTAGCACTCCGTA 58.928 50.000 17.23 0.00 40.47 4.02
580 586 1.880675 CGGATGTATCTAGCACTCCGT 59.119 52.381 17.23 0.00 40.47 4.69
581 587 2.620779 CGGATGTATCTAGCACTCCG 57.379 55.000 14.45 14.45 39.58 4.63
592 598 9.698309 CTTGAATTTGTCTAGATACGGATGTAT 57.302 33.333 0.00 0.00 43.97 2.29
593 599 8.909923 TCTTGAATTTGTCTAGATACGGATGTA 58.090 33.333 0.00 0.00 33.79 2.29
594 600 7.707035 GTCTTGAATTTGTCTAGATACGGATGT 59.293 37.037 0.00 0.00 39.77 3.06
595 601 7.706607 TGTCTTGAATTTGTCTAGATACGGATG 59.293 37.037 0.00 0.00 39.77 3.51
596 602 7.782049 TGTCTTGAATTTGTCTAGATACGGAT 58.218 34.615 0.00 0.00 39.77 4.18
597 603 7.165460 TGTCTTGAATTTGTCTAGATACGGA 57.835 36.000 0.00 0.00 39.77 4.69
598 604 7.545965 ACTTGTCTTGAATTTGTCTAGATACGG 59.454 37.037 0.00 0.00 39.77 4.02
599 605 8.467402 ACTTGTCTTGAATTTGTCTAGATACG 57.533 34.615 0.00 0.00 39.77 3.06
604 610 9.746711 CGAATTACTTGTCTTGAATTTGTCTAG 57.253 33.333 0.00 0.00 0.00 2.43
605 611 8.717821 CCGAATTACTTGTCTTGAATTTGTCTA 58.282 33.333 0.00 0.00 0.00 2.59
606 612 7.444183 TCCGAATTACTTGTCTTGAATTTGTCT 59.556 33.333 0.00 0.00 0.00 3.41
607 613 7.581476 TCCGAATTACTTGTCTTGAATTTGTC 58.419 34.615 0.00 0.00 0.00 3.18
608 614 7.504924 TCCGAATTACTTGTCTTGAATTTGT 57.495 32.000 0.00 0.00 0.00 2.83
609 615 7.059488 CGTTCCGAATTACTTGTCTTGAATTTG 59.941 37.037 0.00 0.00 0.00 2.32
610 616 7.075741 CGTTCCGAATTACTTGTCTTGAATTT 58.924 34.615 0.00 0.00 0.00 1.82
611 617 6.348213 CCGTTCCGAATTACTTGTCTTGAATT 60.348 38.462 0.00 0.00 0.00 2.17
612 618 5.121768 CCGTTCCGAATTACTTGTCTTGAAT 59.878 40.000 0.00 0.00 0.00 2.57
613 619 4.449743 CCGTTCCGAATTACTTGTCTTGAA 59.550 41.667 0.00 0.00 0.00 2.69
614 620 3.991773 CCGTTCCGAATTACTTGTCTTGA 59.008 43.478 0.00 0.00 0.00 3.02
615 621 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
616 622 4.261578 TCCGTTCCGAATTACTTGTCTT 57.738 40.909 0.00 0.00 0.00 3.01
617 623 3.947910 TCCGTTCCGAATTACTTGTCT 57.052 42.857 0.00 0.00 0.00 3.41
618 624 3.308866 CCATCCGTTCCGAATTACTTGTC 59.691 47.826 0.00 0.00 0.00 3.18
619 625 3.055675 TCCATCCGTTCCGAATTACTTGT 60.056 43.478 0.00 0.00 0.00 3.16
620 626 3.527533 TCCATCCGTTCCGAATTACTTG 58.472 45.455 0.00 0.00 0.00 3.16
621 627 3.197116 ACTCCATCCGTTCCGAATTACTT 59.803 43.478 0.00 0.00 0.00 2.24
622 628 2.764572 ACTCCATCCGTTCCGAATTACT 59.235 45.455 0.00 0.00 0.00 2.24
623 629 3.175109 ACTCCATCCGTTCCGAATTAC 57.825 47.619 0.00 0.00 0.00 1.89
624 630 4.209538 TCTACTCCATCCGTTCCGAATTA 58.790 43.478 0.00 0.00 0.00 1.40
625 631 3.028850 TCTACTCCATCCGTTCCGAATT 58.971 45.455 0.00 0.00 0.00 2.17
626 632 2.662866 TCTACTCCATCCGTTCCGAAT 58.337 47.619 0.00 0.00 0.00 3.34
627 633 2.133281 TCTACTCCATCCGTTCCGAA 57.867 50.000 0.00 0.00 0.00 4.30
628 634 2.359981 ATCTACTCCATCCGTTCCGA 57.640 50.000 0.00 0.00 0.00 4.55
629 635 3.819337 TCTTATCTACTCCATCCGTTCCG 59.181 47.826 0.00 0.00 0.00 4.30
630 636 5.535406 TCTTCTTATCTACTCCATCCGTTCC 59.465 44.000 0.00 0.00 0.00 3.62
631 637 6.636562 TCTTCTTATCTACTCCATCCGTTC 57.363 41.667 0.00 0.00 0.00 3.95
632 638 7.007723 AGATCTTCTTATCTACTCCATCCGTT 58.992 38.462 0.00 0.00 34.40 4.44
633 639 6.548321 AGATCTTCTTATCTACTCCATCCGT 58.452 40.000 0.00 0.00 34.40 4.69
634 640 6.657117 TGAGATCTTCTTATCTACTCCATCCG 59.343 42.308 0.00 0.00 36.33 4.18
635 641 7.669722 AGTGAGATCTTCTTATCTACTCCATCC 59.330 40.741 0.00 0.00 36.33 3.51
636 642 8.635765 AGTGAGATCTTCTTATCTACTCCATC 57.364 38.462 0.00 0.00 36.33 3.51
638 644 9.567776 CTTAGTGAGATCTTCTTATCTACTCCA 57.432 37.037 0.00 0.00 36.33 3.86
639 645 9.010029 CCTTAGTGAGATCTTCTTATCTACTCC 57.990 40.741 0.00 0.00 36.33 3.85
640 646 9.569122 ACCTTAGTGAGATCTTCTTATCTACTC 57.431 37.037 0.00 0.00 36.33 2.59
641 647 9.569122 GACCTTAGTGAGATCTTCTTATCTACT 57.431 37.037 0.00 0.00 36.33 2.57
642 648 8.789762 GGACCTTAGTGAGATCTTCTTATCTAC 58.210 40.741 0.00 0.00 36.33 2.59
824 830 0.541764 TGACATGGGAAAAGGTGGCC 60.542 55.000 0.00 0.00 0.00 5.36
946 952 1.674651 CTCGTGTGAGAGGGGACGA 60.675 63.158 0.00 0.00 45.57 4.20
997 1003 2.765807 CGGAGCTCTCCCCATGGT 60.766 66.667 14.64 0.00 46.96 3.55
1160 1166 2.158914 TGGCAGCATCACTACATGGTAG 60.159 50.000 0.00 2.00 32.63 3.18
1315 1328 0.243907 CGTCTGAGAATCCACCGTGT 59.756 55.000 0.00 0.00 0.00 4.49
1800 1975 0.541764 TGCCTTCCACCATTGAACCC 60.542 55.000 0.00 0.00 0.00 4.11
1920 2095 0.463833 GAGCTTCCCCGTACATTGGG 60.464 60.000 5.88 5.88 46.93 4.12
1960 2135 2.762969 TTTAGCGGGGCTGTGTGCAT 62.763 55.000 0.00 0.00 45.15 3.96
1968 2143 2.267961 CCTTCGTTTAGCGGGGCT 59.732 61.111 0.00 0.00 43.41 5.19
2034 2209 3.069443 GCTTGACCTGGTTGAATTGGAAA 59.931 43.478 0.00 0.00 0.00 3.13
2088 2263 1.153489 CCACCTCATGCTCTGGTCG 60.153 63.158 0.00 0.00 30.72 4.79
2301 2476 9.140874 TCTTAATTCAGAGCTCTCATCATCTTA 57.859 33.333 14.96 2.68 0.00 2.10
2345 2520 5.076182 CAAGGCATCTCTCATCTAGGAGTA 58.924 45.833 0.00 0.00 36.30 2.59
2602 2777 5.551233 TCTAGACCATGTCTTTTTGACCAG 58.449 41.667 1.58 0.00 40.28 4.00
2624 2799 8.635877 AAAGTCTACGAATGTCTCATGTATTC 57.364 34.615 0.00 0.00 0.00 1.75
2643 2818 7.281100 GCTTTACAGACATGCCTTATAAAGTCT 59.719 37.037 17.11 0.00 36.84 3.24
2649 2824 6.591001 TGATGCTTTACAGACATGCCTTATA 58.409 36.000 0.00 0.00 0.00 0.98
2675 2850 6.141053 GCTTCTCTAACTTCGTAACGATGATC 59.859 42.308 0.00 0.00 35.23 2.92
2679 2854 5.564048 AGCTTCTCTAACTTCGTAACGAT 57.436 39.130 0.00 0.00 35.23 3.73
2722 2897 6.438259 TCCAAAAAGACGTGTAAAATCACA 57.562 33.333 0.00 0.00 38.12 3.58
2725 2901 5.516090 TGCTCCAAAAAGACGTGTAAAATC 58.484 37.500 0.00 0.00 0.00 2.17
3184 3372 2.916702 TCTGTTGTGACATGCTGACT 57.083 45.000 0.00 0.00 34.72 3.41


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

AutoCloner maintained by Alex Coulton.