Multiple sequence alignment - TraesCS2D01G154000

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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 TraesCS2D01G154000 chr2D 100.000 4902 0 0 1 4902 97219137 97224038 0.000000e+00 9053
1 TraesCS2D01G154000 chr2D 100.000 187 0 0 5102 5288 97224238 97224424 3.920000e-91 346
2 TraesCS2D01G154000 chr2D 93.023 86 5 1 510 595 631407861 631407777 2.000000e-24 124
3 TraesCS2D01G154000 chr2A 97.728 4313 79 9 594 4902 95991405 95995702 0.000000e+00 7404
4 TraesCS2D01G154000 chr2A 93.897 426 17 1 3 428 95990960 95991376 7.470000e-178 634
5 TraesCS2D01G154000 chr2A 93.048 187 10 3 5102 5288 95995720 95995903 2.430000e-68 270
6 TraesCS2D01G154000 chr2B 97.450 4313 97 4 594 4902 148237114 148241417 0.000000e+00 7343
7 TraesCS2D01G154000 chr2B 91.553 438 26 3 3 438 148236644 148237072 1.270000e-165 593
8 TraesCS2D01G154000 chr2B 88.360 189 10 6 5102 5288 148241439 148241617 3.210000e-52 217
9 TraesCS2D01G154000 chr2B 89.796 98 9 1 511 608 90009406 90009502 2.000000e-24 124
10 TraesCS2D01G154000 chr3D 93.802 4082 188 36 594 4644 147817459 147821506 0.000000e+00 6076
11 TraesCS2D01G154000 chr3D 86.103 331 33 8 186 507 147817129 147817455 1.410000e-90 344
12 TraesCS2D01G154000 chr3D 93.023 86 6 0 511 596 26655328 26655413 5.560000e-25 126
13 TraesCS2D01G154000 chr3D 87.156 109 8 5 34 140 147817026 147817130 9.300000e-23 119
14 TraesCS2D01G154000 chr3A 93.534 4114 202 36 594 4674 165420504 165416422 0.000000e+00 6065
15 TraesCS2D01G154000 chr3A 85.714 525 45 15 1 507 165421020 165420508 1.300000e-145 527
16 TraesCS2D01G154000 chr3B 94.827 3789 159 20 594 4362 214564034 214560263 0.000000e+00 5877
17 TraesCS2D01G154000 chr3B 87.500 104 10 3 508 610 447254404 447254505 3.350000e-22 117
18 TraesCS2D01G154000 chr1D 86.993 3329 424 6 980 4301 309078545 309081871 0.000000e+00 3740
19 TraesCS2D01G154000 chr1D 81.169 462 60 11 69 507 108107476 108107019 3.920000e-91 346
20 TraesCS2D01G154000 chr1B 87.006 3317 425 5 980 4292 418810367 418813681 0.000000e+00 3733
21 TraesCS2D01G154000 chr1B 80.465 430 55 12 66 470 158537238 158537663 8.610000e-78 302
22 TraesCS2D01G154000 chr1A 86.685 3327 435 7 980 4301 388838810 388842133 0.000000e+00 3683
23 TraesCS2D01G154000 chr1A 81.425 463 58 11 69 507 111129733 111129275 2.340000e-93 353
24 TraesCS2D01G154000 chr1A 91.111 90 7 1 511 600 251695701 251695789 2.590000e-23 121
25 TraesCS2D01G154000 chr5B 82.269 3226 523 40 1082 4284 47579637 47576438 0.000000e+00 2743
26 TraesCS2D01G154000 chr5B 92.941 85 5 1 511 595 582158220 582158137 7.190000e-24 122
27 TraesCS2D01G154000 chr4D 93.103 87 6 0 509 595 467755792 467755878 1.550000e-25 128
28 TraesCS2D01G154000 chr4D 91.954 87 7 0 509 595 67330912 67330998 7.190000e-24 122
29 TraesCS2D01G154000 chr7A 93.023 86 6 0 511 596 33885894 33885809 5.560000e-25 126


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 TraesCS2D01G154000 chr2D 97219137 97224424 5287 False 4699.500000 9053 100.000000 1 5288 2 chr2D.!!$F1 5287
1 TraesCS2D01G154000 chr2A 95990960 95995903 4943 False 2769.333333 7404 94.891000 3 5288 3 chr2A.!!$F1 5285
2 TraesCS2D01G154000 chr2B 148236644 148241617 4973 False 2717.666667 7343 92.454333 3 5288 3 chr2B.!!$F2 5285
3 TraesCS2D01G154000 chr3D 147817026 147821506 4480 False 2179.666667 6076 89.020333 34 4644 3 chr3D.!!$F2 4610
4 TraesCS2D01G154000 chr3A 165416422 165421020 4598 True 3296.000000 6065 89.624000 1 4674 2 chr3A.!!$R1 4673
5 TraesCS2D01G154000 chr3B 214560263 214564034 3771 True 5877.000000 5877 94.827000 594 4362 1 chr3B.!!$R1 3768
6 TraesCS2D01G154000 chr1D 309078545 309081871 3326 False 3740.000000 3740 86.993000 980 4301 1 chr1D.!!$F1 3321
7 TraesCS2D01G154000 chr1B 418810367 418813681 3314 False 3733.000000 3733 87.006000 980 4292 1 chr1B.!!$F2 3312
8 TraesCS2D01G154000 chr1A 388838810 388842133 3323 False 3683.000000 3683 86.685000 980 4301 1 chr1A.!!$F2 3321
9 TraesCS2D01G154000 chr5B 47576438 47579637 3199 True 2743.000000 2743 82.269000 1082 4284 1 chr5B.!!$R1 3202

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
507 525 0.394192 TCCAGCCATCTCCATTAGCG 59.606 55.000 0.00 0.0 0.0 4.26 F
592 610 0.474184 ATATTGTTGGGCGGAGGGAG 59.526 55.000 0.00 0.0 0.0 4.30 F
2768 2811 1.207329 CTCTTTTGGCCTAGGTACGCT 59.793 52.381 11.31 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2481 2524 1.202698 AGTGGCTTCGCTTCTTGAACT 60.203 47.619 0.00 0.0 0.0 3.01 R
3345 3388 2.799207 GCCTCTCAGAGAAGATTCAGCG 60.799 54.545 2.09 0.0 0.0 5.18 R
4762 4827 0.450184 GACAAACACAGCCACAACGT 59.550 50.000 0.00 0.0 0.0 3.99 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
153 154 4.039366 GCTATCTTTCTAGTACCACAGGGG 59.961 50.000 0.00 0.00 44.81 4.79
201 211 1.876156 CTGGTCAGGACTTTGCTCAAC 59.124 52.381 0.00 0.00 0.00 3.18
229 240 3.058639 GGCTTACATTCCTTCGATCATGC 60.059 47.826 0.00 0.00 0.00 4.06
308 319 4.092771 CAAGCATTGTCCAAGATGACAG 57.907 45.455 0.00 0.00 45.37 3.51
448 465 8.990163 ACTTAATAGAAAGGTCAAAGAACCAA 57.010 30.769 0.00 0.00 42.12 3.67
449 466 9.588096 ACTTAATAGAAAGGTCAAAGAACCAAT 57.412 29.630 0.00 0.00 42.12 3.16
456 473 4.145052 AGGTCAAAGAACCAATTCCACTC 58.855 43.478 0.00 0.00 42.12 3.51
457 474 3.058224 GGTCAAAGAACCAATTCCACTCG 60.058 47.826 0.00 0.00 39.27 4.18
507 525 0.394192 TCCAGCCATCTCCATTAGCG 59.606 55.000 0.00 0.00 0.00 4.26
509 527 1.224075 CAGCCATCTCCATTAGCGTG 58.776 55.000 0.00 0.00 0.00 5.34
510 528 0.833287 AGCCATCTCCATTAGCGTGT 59.167 50.000 0.00 0.00 0.00 4.49
511 529 2.039418 AGCCATCTCCATTAGCGTGTA 58.961 47.619 0.00 0.00 0.00 2.90
512 530 2.135933 GCCATCTCCATTAGCGTGTAC 58.864 52.381 0.00 0.00 0.00 2.90
513 531 2.224066 GCCATCTCCATTAGCGTGTACT 60.224 50.000 0.00 0.00 0.00 2.73
514 532 3.643763 CCATCTCCATTAGCGTGTACTC 58.356 50.000 0.00 0.00 0.00 2.59
515 533 3.553096 CCATCTCCATTAGCGTGTACTCC 60.553 52.174 0.00 0.00 0.00 3.85
516 534 2.029623 TCTCCATTAGCGTGTACTCCC 58.970 52.381 0.00 0.00 0.00 4.30
517 535 2.032620 CTCCATTAGCGTGTACTCCCT 58.967 52.381 0.00 0.00 0.00 4.20
518 536 2.029623 TCCATTAGCGTGTACTCCCTC 58.970 52.381 0.00 0.00 0.00 4.30
519 537 2.032620 CCATTAGCGTGTACTCCCTCT 58.967 52.381 0.00 0.00 0.00 3.69
520 538 2.223829 CCATTAGCGTGTACTCCCTCTG 60.224 54.545 0.00 0.00 0.00 3.35
521 539 2.211250 TTAGCGTGTACTCCCTCTGT 57.789 50.000 0.00 0.00 0.00 3.41
522 540 1.747709 TAGCGTGTACTCCCTCTGTC 58.252 55.000 0.00 0.00 0.00 3.51
523 541 0.966370 AGCGTGTACTCCCTCTGTCC 60.966 60.000 0.00 0.00 0.00 4.02
524 542 1.946475 GCGTGTACTCCCTCTGTCCC 61.946 65.000 0.00 0.00 0.00 4.46
525 543 0.611062 CGTGTACTCCCTCTGTCCCA 60.611 60.000 0.00 0.00 0.00 4.37
526 544 1.867363 GTGTACTCCCTCTGTCCCAT 58.133 55.000 0.00 0.00 0.00 4.00
527 545 2.685819 CGTGTACTCCCTCTGTCCCATA 60.686 54.545 0.00 0.00 0.00 2.74
528 546 3.371965 GTGTACTCCCTCTGTCCCATAA 58.628 50.000 0.00 0.00 0.00 1.90
529 547 3.967987 GTGTACTCCCTCTGTCCCATAAT 59.032 47.826 0.00 0.00 0.00 1.28
530 548 5.145564 GTGTACTCCCTCTGTCCCATAATA 58.854 45.833 0.00 0.00 0.00 0.98
531 549 5.780793 GTGTACTCCCTCTGTCCCATAATAT 59.219 44.000 0.00 0.00 0.00 1.28
532 550 6.952358 GTGTACTCCCTCTGTCCCATAATATA 59.048 42.308 0.00 0.00 0.00 0.86
533 551 7.453752 GTGTACTCCCTCTGTCCCATAATATAA 59.546 40.741 0.00 0.00 0.00 0.98
534 552 7.674348 TGTACTCCCTCTGTCCCATAATATAAG 59.326 40.741 0.00 0.00 0.00 1.73
535 553 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
536 554 7.491681 ACTCCCTCTGTCCCATAATATAAGAT 58.508 38.462 0.00 0.00 0.00 2.40
537 555 7.401493 ACTCCCTCTGTCCCATAATATAAGATG 59.599 40.741 0.00 0.00 0.00 2.90
538 556 7.256399 TCCCTCTGTCCCATAATATAAGATGT 58.744 38.462 0.00 0.00 0.00 3.06
539 557 7.739444 TCCCTCTGTCCCATAATATAAGATGTT 59.261 37.037 0.00 0.00 0.00 2.71
540 558 8.386264 CCCTCTGTCCCATAATATAAGATGTTT 58.614 37.037 0.00 0.00 0.00 2.83
541 559 9.799106 CCTCTGTCCCATAATATAAGATGTTTT 57.201 33.333 0.00 0.00 0.00 2.43
544 562 9.683069 CTGTCCCATAATATAAGATGTTTTTGC 57.317 33.333 0.00 0.00 0.00 3.68
545 563 9.194972 TGTCCCATAATATAAGATGTTTTTGCA 57.805 29.630 0.00 0.00 0.00 4.08
548 566 8.981647 CCCATAATATAAGATGTTTTTGCAAGC 58.018 33.333 0.00 0.00 0.00 4.01
549 567 9.754382 CCATAATATAAGATGTTTTTGCAAGCT 57.246 29.630 0.00 0.00 0.00 3.74
553 571 9.492973 AATATAAGATGTTTTTGCAAGCTGTTT 57.507 25.926 0.00 0.00 0.00 2.83
554 572 7.790823 ATAAGATGTTTTTGCAAGCTGTTTT 57.209 28.000 0.00 0.00 0.00 2.43
555 573 8.885494 ATAAGATGTTTTTGCAAGCTGTTTTA 57.115 26.923 0.00 0.00 0.00 1.52
556 574 6.833342 AGATGTTTTTGCAAGCTGTTTTAG 57.167 33.333 0.00 0.00 0.00 1.85
574 592 8.885494 TGTTTTAGCTTGCAAAAACATCTTAT 57.115 26.923 18.58 0.00 45.66 1.73
575 593 9.973450 TGTTTTAGCTTGCAAAAACATCTTATA 57.027 25.926 18.58 0.51 45.66 0.98
581 599 8.928733 AGCTTGCAAAAACATCTTATATTGTTG 58.071 29.630 0.00 0.00 36.26 3.33
582 600 8.170553 GCTTGCAAAAACATCTTATATTGTTGG 58.829 33.333 0.00 0.00 36.26 3.77
583 601 8.545229 TTGCAAAAACATCTTATATTGTTGGG 57.455 30.769 0.00 0.00 36.26 4.12
584 602 6.593382 TGCAAAAACATCTTATATTGTTGGGC 59.407 34.615 0.00 0.00 36.26 5.36
585 603 6.237808 GCAAAAACATCTTATATTGTTGGGCG 60.238 38.462 0.00 0.00 36.26 6.13
586 604 5.514274 AAACATCTTATATTGTTGGGCGG 57.486 39.130 0.00 0.00 36.26 6.13
587 605 4.431416 ACATCTTATATTGTTGGGCGGA 57.569 40.909 0.00 0.00 0.00 5.54
588 606 4.389374 ACATCTTATATTGTTGGGCGGAG 58.611 43.478 0.00 0.00 0.00 4.63
589 607 3.485463 TCTTATATTGTTGGGCGGAGG 57.515 47.619 0.00 0.00 0.00 4.30
590 608 2.105821 TCTTATATTGTTGGGCGGAGGG 59.894 50.000 0.00 0.00 0.00 4.30
591 609 1.809133 TATATTGTTGGGCGGAGGGA 58.191 50.000 0.00 0.00 0.00 4.20
592 610 0.474184 ATATTGTTGGGCGGAGGGAG 59.526 55.000 0.00 0.00 0.00 4.30
617 635 9.120538 AGTATCTTCTTTTTCTTGTGCTGTTTA 57.879 29.630 0.00 0.00 0.00 2.01
706 732 3.481453 TGCAACATAACACCAGCTTACA 58.519 40.909 0.00 0.00 0.00 2.41
762 790 8.642020 GCTAATTTTGTTTGATGTCTTGATGAC 58.358 33.333 0.00 0.00 45.54 3.06
954 988 8.717717 TCCTGAATTGAGTTAGATTACATCCAT 58.282 33.333 0.00 0.00 0.00 3.41
977 1011 2.137523 GCTTGCCCTTTTGACACATTG 58.862 47.619 0.00 0.00 0.00 2.82
1048 1088 2.164624 AGTCATGCACGTAGAGACCTTC 59.835 50.000 0.00 0.00 0.00 3.46
2481 2524 5.014202 GCAGGGGAGTTTAATGGTAGAAAA 58.986 41.667 0.00 0.00 0.00 2.29
2766 2809 1.653151 GCTCTTTTGGCCTAGGTACG 58.347 55.000 11.31 0.00 0.00 3.67
2768 2811 1.207329 CTCTTTTGGCCTAGGTACGCT 59.793 52.381 11.31 0.00 0.00 5.07
2940 2983 6.349300 AGTATGGGAATATGTGTTCTGTGAC 58.651 40.000 0.00 0.00 0.00 3.67
3129 3172 1.462791 CTCGTGGTTTTCGTTGCAAC 58.537 50.000 19.89 19.89 0.00 4.17
3345 3388 4.517075 GCTTGGATGGAAGAAGTTATAGCC 59.483 45.833 0.00 0.00 0.00 3.93
3513 3556 5.512749 CCTGCAATTGGCTAGAGATGAGTAT 60.513 44.000 7.72 0.00 45.15 2.12
4143 4195 1.494721 AGAAGGCAGTTGGGTCTTGAA 59.505 47.619 0.00 0.00 31.73 2.69
4181 4233 2.742856 CGGTATTTGATGGAGCTGCTCA 60.743 50.000 28.95 16.39 31.08 4.26
4422 4475 3.141398 ACTGACACGTTTCATTCTGCAT 58.859 40.909 4.61 0.00 0.00 3.96
4455 4508 7.490962 TCTGTTGTAGTTTTTGTGTATGAGG 57.509 36.000 0.00 0.00 0.00 3.86
4456 4509 7.276658 TCTGTTGTAGTTTTTGTGTATGAGGA 58.723 34.615 0.00 0.00 0.00 3.71
4457 4510 7.936847 TCTGTTGTAGTTTTTGTGTATGAGGAT 59.063 33.333 0.00 0.00 0.00 3.24
4458 4511 8.458573 TGTTGTAGTTTTTGTGTATGAGGATT 57.541 30.769 0.00 0.00 0.00 3.01
4459 4512 8.349245 TGTTGTAGTTTTTGTGTATGAGGATTG 58.651 33.333 0.00 0.00 0.00 2.67
4460 4513 8.564574 GTTGTAGTTTTTGTGTATGAGGATTGA 58.435 33.333 0.00 0.00 0.00 2.57
4461 4514 8.684386 TGTAGTTTTTGTGTATGAGGATTGAA 57.316 30.769 0.00 0.00 0.00 2.69
4572 4632 0.964358 AGTGCAGCAGATTGGCCTTC 60.964 55.000 3.32 0.42 0.00 3.46
4573 4633 1.075305 TGCAGCAGATTGGCCTTCA 59.925 52.632 3.32 0.00 0.00 3.02
4658 4723 9.890629 TCTAAATCTGTGATAGTTGCTTATGTT 57.109 29.630 0.00 0.00 0.00 2.71
4735 4800 3.705604 CGTTCAGACAAATTTTGTGGCT 58.294 40.909 19.03 8.37 45.52 4.75
4736 4801 4.111916 CGTTCAGACAAATTTTGTGGCTT 58.888 39.130 19.03 0.28 45.52 4.35
4757 4822 1.750193 TGGATTTGGAGCGTGAATCC 58.250 50.000 13.72 13.72 45.77 3.01
4762 4827 2.123248 TTGGAGCGTGAATCCCAGCA 62.123 55.000 0.00 0.00 35.86 4.41
4858 4923 0.032615 TTTTGGGGGTTGTCTGCTGT 60.033 50.000 0.00 0.00 0.00 4.40
5234 5299 3.506398 CCCCTTTCCCTGTATGTGTTTT 58.494 45.455 0.00 0.00 0.00 2.43
5266 5331 3.716195 CTGCCGGTGGGGTCATCA 61.716 66.667 1.90 0.00 38.44 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 4.848562 ACCGAAAGTCCCTCAAAATTTC 57.151 40.909 0.00 0.00 0.00 2.17
201 211 4.755411 TCGAAGGAATGTAAGCCTACAAG 58.245 43.478 0.00 0.00 41.36 3.16
229 240 8.138074 TCTGGAGACAATATGTAAAGATCGAAG 58.862 37.037 0.00 0.00 42.06 3.79
308 319 1.145803 GTGCGTTTGGTACAGTCCTC 58.854 55.000 0.00 0.00 42.39 3.71
374 390 7.148573 CGTGGATGAAAGTTAGCATATGATACC 60.149 40.741 6.97 0.00 0.00 2.73
448 465 7.416664 CAATTAACATTGGATTCCGAGTGGAAT 60.417 37.037 9.21 9.21 46.97 3.01
449 466 6.127758 CAATTAACATTGGATTCCGAGTGGAA 60.128 38.462 0.00 0.00 45.50 3.53
456 473 4.654091 AGGCAATTAACATTGGATTCCG 57.346 40.909 0.00 0.00 40.36 4.30
457 474 4.571984 GCAAGGCAATTAACATTGGATTCC 59.428 41.667 0.00 0.00 40.36 3.01
460 477 4.223477 ACTGCAAGGCAATTAACATTGGAT 59.777 37.500 7.03 0.00 38.41 3.41
462 479 3.929094 ACTGCAAGGCAATTAACATTGG 58.071 40.909 7.03 0.00 38.41 3.16
507 525 3.376082 TGGGACAGAGGGAGTACAC 57.624 57.895 0.00 0.00 0.00 2.90
522 540 8.981647 GCTTGCAAAAACATCTTATATTATGGG 58.018 33.333 0.00 0.00 0.00 4.00
523 541 9.754382 AGCTTGCAAAAACATCTTATATTATGG 57.246 29.630 0.00 0.00 0.00 2.74
527 545 9.492973 AAACAGCTTGCAAAAACATCTTATATT 57.507 25.926 0.00 0.00 0.00 1.28
528 546 9.492973 AAAACAGCTTGCAAAAACATCTTATAT 57.507 25.926 0.00 0.00 0.00 0.86
529 547 8.885494 AAAACAGCTTGCAAAAACATCTTATA 57.115 26.923 0.00 0.00 0.00 0.98
530 548 7.790823 AAAACAGCTTGCAAAAACATCTTAT 57.209 28.000 0.00 0.00 0.00 1.73
531 549 8.351495 CTAAAACAGCTTGCAAAAACATCTTA 57.649 30.769 0.00 0.00 0.00 2.10
532 550 7.237920 CTAAAACAGCTTGCAAAAACATCTT 57.762 32.000 0.00 0.00 0.00 2.40
533 551 6.833342 CTAAAACAGCTTGCAAAAACATCT 57.167 33.333 0.00 0.00 0.00 2.90
555 573 8.928733 CAACAATATAAGATGTTTTTGCAAGCT 58.071 29.630 0.00 0.00 37.66 3.74
556 574 8.170553 CCAACAATATAAGATGTTTTTGCAAGC 58.829 33.333 0.00 0.00 37.66 4.01
557 575 8.658609 CCCAACAATATAAGATGTTTTTGCAAG 58.341 33.333 0.00 0.00 37.66 4.01
558 576 7.118971 GCCCAACAATATAAGATGTTTTTGCAA 59.881 33.333 0.00 0.00 37.66 4.08
559 577 6.593382 GCCCAACAATATAAGATGTTTTTGCA 59.407 34.615 0.00 0.00 37.66 4.08
560 578 6.237808 CGCCCAACAATATAAGATGTTTTTGC 60.238 38.462 0.00 0.00 37.66 3.68
561 579 6.255453 CCGCCCAACAATATAAGATGTTTTTG 59.745 38.462 0.00 0.00 37.66 2.44
562 580 6.153680 TCCGCCCAACAATATAAGATGTTTTT 59.846 34.615 0.00 0.00 37.66 1.94
563 581 5.654650 TCCGCCCAACAATATAAGATGTTTT 59.345 36.000 0.00 0.00 37.66 2.43
564 582 5.197451 TCCGCCCAACAATATAAGATGTTT 58.803 37.500 0.00 0.00 37.66 2.83
565 583 4.787551 TCCGCCCAACAATATAAGATGTT 58.212 39.130 0.00 0.00 40.24 2.71
566 584 4.389374 CTCCGCCCAACAATATAAGATGT 58.611 43.478 0.00 0.00 0.00 3.06
567 585 3.753272 CCTCCGCCCAACAATATAAGATG 59.247 47.826 0.00 0.00 0.00 2.90
568 586 3.244911 CCCTCCGCCCAACAATATAAGAT 60.245 47.826 0.00 0.00 0.00 2.40
569 587 2.105821 CCCTCCGCCCAACAATATAAGA 59.894 50.000 0.00 0.00 0.00 2.10
570 588 2.105821 TCCCTCCGCCCAACAATATAAG 59.894 50.000 0.00 0.00 0.00 1.73
571 589 2.105821 CTCCCTCCGCCCAACAATATAA 59.894 50.000 0.00 0.00 0.00 0.98
572 590 1.697432 CTCCCTCCGCCCAACAATATA 59.303 52.381 0.00 0.00 0.00 0.86
573 591 0.474184 CTCCCTCCGCCCAACAATAT 59.526 55.000 0.00 0.00 0.00 1.28
574 592 0.912487 ACTCCCTCCGCCCAACAATA 60.912 55.000 0.00 0.00 0.00 1.90
575 593 0.912487 TACTCCCTCCGCCCAACAAT 60.912 55.000 0.00 0.00 0.00 2.71
576 594 0.912487 ATACTCCCTCCGCCCAACAA 60.912 55.000 0.00 0.00 0.00 2.83
577 595 1.306654 ATACTCCCTCCGCCCAACA 60.307 57.895 0.00 0.00 0.00 3.33
578 596 1.049289 AGATACTCCCTCCGCCCAAC 61.049 60.000 0.00 0.00 0.00 3.77
579 597 0.326238 AAGATACTCCCTCCGCCCAA 60.326 55.000 0.00 0.00 0.00 4.12
580 598 0.759436 GAAGATACTCCCTCCGCCCA 60.759 60.000 0.00 0.00 0.00 5.36
581 599 0.470268 AGAAGATACTCCCTCCGCCC 60.470 60.000 0.00 0.00 0.00 6.13
582 600 1.415200 AAGAAGATACTCCCTCCGCC 58.585 55.000 0.00 0.00 0.00 6.13
583 601 3.545366 AAAAGAAGATACTCCCTCCGC 57.455 47.619 0.00 0.00 0.00 5.54
584 602 5.346181 AGAAAAAGAAGATACTCCCTCCG 57.654 43.478 0.00 0.00 0.00 4.63
585 603 6.372937 CACAAGAAAAAGAAGATACTCCCTCC 59.627 42.308 0.00 0.00 0.00 4.30
586 604 6.128145 GCACAAGAAAAAGAAGATACTCCCTC 60.128 42.308 0.00 0.00 0.00 4.30
587 605 5.707764 GCACAAGAAAAAGAAGATACTCCCT 59.292 40.000 0.00 0.00 0.00 4.20
588 606 5.707764 AGCACAAGAAAAAGAAGATACTCCC 59.292 40.000 0.00 0.00 0.00 4.30
589 607 6.205658 ACAGCACAAGAAAAAGAAGATACTCC 59.794 38.462 0.00 0.00 0.00 3.85
590 608 7.195839 ACAGCACAAGAAAAAGAAGATACTC 57.804 36.000 0.00 0.00 0.00 2.59
591 609 7.573968 AACAGCACAAGAAAAAGAAGATACT 57.426 32.000 0.00 0.00 0.00 2.12
592 610 9.899226 ATAAACAGCACAAGAAAAAGAAGATAC 57.101 29.630 0.00 0.00 0.00 2.24
617 635 7.559533 TGTGTAGGTTGGTATATTTGATGCAAT 59.440 33.333 0.00 0.00 0.00 3.56
706 732 7.380423 ACTACAAGCTAATTATGGAGGTCAT 57.620 36.000 0.00 0.00 39.78 3.06
762 790 9.950680 AGAATCATAATAAACCATAAGCAAACG 57.049 29.630 0.00 0.00 0.00 3.60
948 982 3.385433 TCAAAAGGGCAAGCATATGGATG 59.615 43.478 4.56 0.00 36.02 3.51
954 988 2.591923 TGTGTCAAAAGGGCAAGCATA 58.408 42.857 0.00 0.00 0.00 3.14
1048 1088 3.312973 GCTTCTGATTGGATCTTGAGCAG 59.687 47.826 0.00 0.00 0.00 4.24
2481 2524 1.202698 AGTGGCTTCGCTTCTTGAACT 60.203 47.619 0.00 0.00 0.00 3.01
3345 3388 2.799207 GCCTCTCAGAGAAGATTCAGCG 60.799 54.545 2.09 0.00 0.00 5.18
3513 3556 1.464734 CCGCTCCACAAGAGAGTCTA 58.535 55.000 0.00 0.00 46.50 2.59
4143 4195 1.003355 CGGCAGGACCTCAACATGT 60.003 57.895 0.00 0.00 35.61 3.21
4572 4632 4.370917 AGGCAACAGCTGTAAACAAATTG 58.629 39.130 22.01 13.07 41.41 2.32
4573 4633 4.670896 AGGCAACAGCTGTAAACAAATT 57.329 36.364 22.01 0.00 41.41 1.82
4626 4691 7.547370 AGCAACTATCACAGATTTAGAACTGAC 59.453 37.037 0.00 0.00 37.54 3.51
4735 4800 3.056891 GGATTCACGCTCCAAATCCAAAA 60.057 43.478 8.17 0.00 45.13 2.44
4736 4801 2.491693 GGATTCACGCTCCAAATCCAAA 59.508 45.455 8.17 0.00 45.13 3.28
4757 4822 2.901840 ACAGCCACAACGTGCTGG 60.902 61.111 24.23 16.51 39.81 4.85
4762 4827 0.450184 GACAAACACAGCCACAACGT 59.550 50.000 0.00 0.00 0.00 3.99
4858 4923 2.636647 TGACAGACAACAATGGCTCA 57.363 45.000 0.00 0.00 43.21 4.26
5196 5261 1.610873 GGGGCGTGGAGGGATAAAA 59.389 57.895 0.00 0.00 0.00 1.52
5234 5299 1.809619 GCAGCGCCGTAGACAATGA 60.810 57.895 2.29 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.