Multiple sequence alignment - TraesCS4B01G094300

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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 TraesCS4B01G094300 chr4B 100.000 2261 0 0 1 2261 96641393 96643653 0.000000e+00 4176.0
1 TraesCS4B01G094300 chr4D 96.313 1763 36 14 504 2260 65939669 65941408 0.000000e+00 2868.0
2 TraesCS4B01G094300 chr4D 96.237 372 14 0 1 372 65939243 65939614 5.340000e-171 610.0
3 TraesCS4B01G094300 chr4D 96.970 33 1 0 464 496 153023182 153023150 3.140000e-04 56.5
4 TraesCS4B01G094300 chr4A 96.203 1422 44 4 504 1923 529626527 529625114 0.000000e+00 2318.0
5 TraesCS4B01G094300 chr4A 95.946 370 15 0 1 370 529626953 529626584 3.210000e-168 601.0
6 TraesCS4B01G094300 chr4A 94.702 151 5 2 2112 2261 529624830 529624682 4.860000e-57 231.0
7 TraesCS4B01G094300 chr4A 92.073 164 7 2 1922 2080 529624990 529624828 2.260000e-55 226.0
8 TraesCS4B01G094300 chr4A 100.000 33 0 0 464 496 289740397 289740365 6.740000e-06 62.1
9 TraesCS4B01G094300 chr3D 89.796 49 1 3 449 496 548565568 548565523 2.430000e-05 60.2
10 TraesCS4B01G094300 chr5A 94.595 37 2 0 464 500 389234227 389234191 8.720000e-05 58.4
11 TraesCS4B01G094300 chr6D 96.970 33 1 0 464 496 152756477 152756509 3.140000e-04 56.5
12 TraesCS4B01G094300 chr6D 96.970 33 1 0 464 496 198952518 198952486 3.140000e-04 56.5
13 TraesCS4B01G094300 chr6D 96.970 33 1 0 464 496 199117257 199117225 3.140000e-04 56.5
14 TraesCS4B01G094300 chr1A 96.970 33 1 0 464 496 238332924 238332892 3.140000e-04 56.5
15 TraesCS4B01G094300 chr1A 96.970 33 1 0 464 496 378352633 378352665 3.140000e-04 56.5


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 TraesCS4B01G094300 chr4B 96641393 96643653 2260 False 4176 4176 100.000 1 2261 1 chr4B.!!$F1 2260
1 TraesCS4B01G094300 chr4D 65939243 65941408 2165 False 1739 2868 96.275 1 2260 2 chr4D.!!$F1 2259
2 TraesCS4B01G094300 chr4A 529624682 529626953 2271 True 844 2318 94.731 1 2261 4 chr4A.!!$R2 2260

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
370 371 0.106708 TGACCCAACAGTCAGTGAGC 59.893 55.0 0.0 0.0 41.78 4.26 F
371 372 0.106708 GACCCAACAGTCAGTGAGCA 59.893 55.0 0.0 0.0 36.73 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1212 0.033504 TCTTCGGTGCAAGTGAGGTC 59.966 55.0 0.0 0.0 0.0 3.85 R
1607 1622 1.698506 CCTACAAGATCCCTCTCGCT 58.301 55.0 0.0 0.0 0.0 4.93 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
32 33 1.000396 GCCCAGGTCATTGCTCCTT 60.000 57.895 0.00 0.00 30.91 3.36
34 35 0.394899 CCCAGGTCATTGCTCCTTCC 60.395 60.000 0.00 0.00 30.91 3.46
48 49 3.984186 CTTCCCCGCCTCCTCCTCA 62.984 68.421 0.00 0.00 0.00 3.86
92 93 1.880340 GCTCGCTTCGACTCCCATG 60.880 63.158 0.00 0.00 0.00 3.66
113 114 2.568612 CTCGCTCGCTGTCCAGAA 59.431 61.111 0.00 0.00 0.00 3.02
129 130 1.939934 CAGAACAACTTGCCGAGTTCA 59.060 47.619 0.00 0.00 45.40 3.18
285 286 2.729194 GCAGAGAGGGACAGACTAGAA 58.271 52.381 0.00 0.00 0.00 2.10
319 320 1.962144 GCCATGCATGTCATAGGCC 59.038 57.895 24.58 0.00 40.42 5.19
326 327 2.431454 ATGTCATAGGCCGCACGGA 61.431 57.895 14.43 0.00 37.50 4.69
370 371 0.106708 TGACCCAACAGTCAGTGAGC 59.893 55.000 0.00 0.00 41.78 4.26
371 372 0.106708 GACCCAACAGTCAGTGAGCA 59.893 55.000 0.00 0.00 36.73 4.26
372 373 0.179045 ACCCAACAGTCAGTGAGCAC 60.179 55.000 0.00 0.00 0.00 4.40
373 374 1.224069 CCCAACAGTCAGTGAGCACG 61.224 60.000 0.00 0.00 36.20 5.34
374 375 0.249447 CCAACAGTCAGTGAGCACGA 60.249 55.000 0.00 0.00 36.20 4.35
375 376 1.570813 CAACAGTCAGTGAGCACGAA 58.429 50.000 0.00 0.00 36.20 3.85
376 377 2.138320 CAACAGTCAGTGAGCACGAAT 58.862 47.619 0.00 0.00 36.20 3.34
377 378 2.071688 ACAGTCAGTGAGCACGAATC 57.928 50.000 0.00 0.00 36.20 2.52
378 379 1.615883 ACAGTCAGTGAGCACGAATCT 59.384 47.619 0.00 0.00 36.20 2.40
379 380 2.820197 ACAGTCAGTGAGCACGAATCTA 59.180 45.455 0.00 0.00 36.20 1.98
380 381 3.255888 ACAGTCAGTGAGCACGAATCTAA 59.744 43.478 0.00 0.00 36.20 2.10
381 382 4.237724 CAGTCAGTGAGCACGAATCTAAA 58.762 43.478 0.00 0.00 36.20 1.85
382 383 4.686091 CAGTCAGTGAGCACGAATCTAAAA 59.314 41.667 0.00 0.00 36.20 1.52
383 384 5.177511 CAGTCAGTGAGCACGAATCTAAAAA 59.822 40.000 0.00 0.00 36.20 1.94
408 409 5.528043 ACAGTCAGTGAGCATAATAGGAG 57.472 43.478 0.00 0.00 0.00 3.69
429 435 6.320672 AGGAGAAGGAATTAATTCAGCACATG 59.679 38.462 25.55 0.00 38.53 3.21
448 454 5.129815 CACATGGATGGGATTTCCTTCAAAT 59.870 40.000 0.00 0.00 40.41 2.32
449 455 6.324512 CACATGGATGGGATTTCCTTCAAATA 59.675 38.462 0.00 0.00 40.41 1.40
450 456 6.324770 ACATGGATGGGATTTCCTTCAAATAC 59.675 38.462 0.00 0.00 40.41 1.89
451 457 6.091076 TGGATGGGATTTCCTTCAAATACT 57.909 37.500 0.00 0.00 40.41 2.12
452 458 6.129179 TGGATGGGATTTCCTTCAAATACTC 58.871 40.000 0.00 0.00 40.41 2.59
453 459 5.536538 GGATGGGATTTCCTTCAAATACTCC 59.463 44.000 0.00 0.00 40.41 3.85
454 460 4.867086 TGGGATTTCCTTCAAATACTCCC 58.133 43.478 0.00 0.00 39.78 4.30
455 461 4.544152 TGGGATTTCCTTCAAATACTCCCT 59.456 41.667 5.92 0.00 39.94 4.20
456 462 5.133941 GGGATTTCCTTCAAATACTCCCTC 58.866 45.833 0.00 0.00 37.66 4.30
457 463 5.133941 GGATTTCCTTCAAATACTCCCTCC 58.866 45.833 0.00 0.00 34.60 4.30
458 464 3.906720 TTCCTTCAAATACTCCCTCCG 57.093 47.619 0.00 0.00 0.00 4.63
459 465 2.829023 TCCTTCAAATACTCCCTCCGT 58.171 47.619 0.00 0.00 0.00 4.69
460 466 3.178865 TCCTTCAAATACTCCCTCCGTT 58.821 45.455 0.00 0.00 0.00 4.44
461 467 3.585732 TCCTTCAAATACTCCCTCCGTTT 59.414 43.478 0.00 0.00 0.00 3.60
462 468 3.939592 CCTTCAAATACTCCCTCCGTTTC 59.060 47.826 0.00 0.00 0.00 2.78
463 469 4.564821 CCTTCAAATACTCCCTCCGTTTCA 60.565 45.833 0.00 0.00 0.00 2.69
464 470 4.627284 TCAAATACTCCCTCCGTTTCAA 57.373 40.909 0.00 0.00 0.00 2.69
465 471 5.174037 TCAAATACTCCCTCCGTTTCAAT 57.826 39.130 0.00 0.00 0.00 2.57
466 472 6.302535 TCAAATACTCCCTCCGTTTCAATA 57.697 37.500 0.00 0.00 0.00 1.90
467 473 6.713276 TCAAATACTCCCTCCGTTTCAATAA 58.287 36.000 0.00 0.00 0.00 1.40
468 474 7.343357 TCAAATACTCCCTCCGTTTCAATAAT 58.657 34.615 0.00 0.00 0.00 1.28
469 475 7.282224 TCAAATACTCCCTCCGTTTCAATAATG 59.718 37.037 0.00 0.00 0.00 1.90
470 476 3.279434 ACTCCCTCCGTTTCAATAATGC 58.721 45.455 0.00 0.00 0.00 3.56
471 477 3.054361 ACTCCCTCCGTTTCAATAATGCT 60.054 43.478 0.00 0.00 0.00 3.79
472 478 4.163458 ACTCCCTCCGTTTCAATAATGCTA 59.837 41.667 0.00 0.00 0.00 3.49
473 479 4.703897 TCCCTCCGTTTCAATAATGCTAG 58.296 43.478 0.00 0.00 0.00 3.42
474 480 4.407621 TCCCTCCGTTTCAATAATGCTAGA 59.592 41.667 0.00 0.00 0.00 2.43
475 481 5.071788 TCCCTCCGTTTCAATAATGCTAGAT 59.928 40.000 0.00 0.00 0.00 1.98
476 482 6.269077 TCCCTCCGTTTCAATAATGCTAGATA 59.731 38.462 0.00 0.00 0.00 1.98
477 483 6.369065 CCCTCCGTTTCAATAATGCTAGATAC 59.631 42.308 0.00 0.00 0.00 2.24
478 484 6.929049 CCTCCGTTTCAATAATGCTAGATACA 59.071 38.462 0.00 0.00 0.00 2.29
479 485 7.604164 CCTCCGTTTCAATAATGCTAGATACAT 59.396 37.037 0.00 0.00 0.00 2.29
480 486 8.534333 TCCGTTTCAATAATGCTAGATACATC 57.466 34.615 0.00 0.00 0.00 3.06
481 487 7.602644 TCCGTTTCAATAATGCTAGATACATCC 59.397 37.037 0.00 0.00 0.00 3.51
482 488 7.387673 CCGTTTCAATAATGCTAGATACATCCA 59.612 37.037 0.00 0.00 0.00 3.41
483 489 8.939929 CGTTTCAATAATGCTAGATACATCCAT 58.060 33.333 0.00 0.00 0.00 3.41
489 495 6.814506 AATGCTAGATACATCCATTTGAGC 57.185 37.500 0.00 0.00 0.00 4.26
490 496 5.294734 TGCTAGATACATCCATTTGAGCA 57.705 39.130 0.00 0.00 35.18 4.26
491 497 5.683681 TGCTAGATACATCCATTTGAGCAA 58.316 37.500 0.00 0.00 34.66 3.91
492 498 5.528690 TGCTAGATACATCCATTTGAGCAAC 59.471 40.000 0.00 0.00 34.66 4.17
493 499 5.528690 GCTAGATACATCCATTTGAGCAACA 59.471 40.000 0.00 0.00 0.00 3.33
494 500 6.038603 GCTAGATACATCCATTTGAGCAACAA 59.961 38.462 0.00 0.00 36.65 2.83
495 501 6.446781 AGATACATCCATTTGAGCAACAAG 57.553 37.500 0.00 0.00 39.77 3.16
496 502 6.182627 AGATACATCCATTTGAGCAACAAGA 58.817 36.000 0.00 0.00 39.77 3.02
497 503 4.778534 ACATCCATTTGAGCAACAAGAG 57.221 40.909 0.00 0.00 39.77 2.85
498 504 3.508793 ACATCCATTTGAGCAACAAGAGG 59.491 43.478 0.00 0.00 39.77 3.69
499 505 2.517959 TCCATTTGAGCAACAAGAGGG 58.482 47.619 12.54 8.85 39.77 4.30
500 506 2.108075 TCCATTTGAGCAACAAGAGGGA 59.892 45.455 12.54 10.30 39.77 4.20
501 507 2.490903 CCATTTGAGCAACAAGAGGGAG 59.509 50.000 0.00 0.00 39.77 4.30
502 508 3.152341 CATTTGAGCAACAAGAGGGAGT 58.848 45.455 0.00 0.00 39.77 3.85
508 514 4.777896 TGAGCAACAAGAGGGAGTACTATT 59.222 41.667 0.00 0.00 0.00 1.73
535 541 6.648192 ACAAAAGATTCACAACAAATTGGGA 58.352 32.000 0.00 0.00 46.84 4.37
571 577 5.885230 TCTCATTCACACTAATGCTTTGG 57.115 39.130 0.00 0.00 36.89 3.28
590 596 6.704050 GCTTTGGGCTATGTTACAAAAAGAAA 59.296 34.615 0.00 0.00 38.06 2.52
605 611 8.340230 ACAAAAAGAAAGAAACATCATTCGTC 57.660 30.769 0.00 0.00 34.46 4.20
606 612 7.973388 ACAAAAAGAAAGAAACATCATTCGTCA 59.027 29.630 0.00 0.00 34.46 4.35
742 750 8.357402 GGAAAAGGCGGATACAAAATTATACAT 58.643 33.333 0.00 0.00 0.00 2.29
747 755 6.205853 GGCGGATACAAAATTATACATGTGGA 59.794 38.462 9.11 0.00 0.00 4.02
748 756 7.298122 GCGGATACAAAATTATACATGTGGAG 58.702 38.462 9.11 0.00 0.00 3.86
749 757 7.298122 CGGATACAAAATTATACATGTGGAGC 58.702 38.462 9.11 0.00 0.00 4.70
750 758 7.298122 GGATACAAAATTATACATGTGGAGCG 58.702 38.462 9.11 0.00 0.00 5.03
751 759 4.920376 ACAAAATTATACATGTGGAGCGC 58.080 39.130 9.11 0.00 0.00 5.92
752 760 4.397730 ACAAAATTATACATGTGGAGCGCA 59.602 37.500 11.47 0.00 0.00 6.09
753 761 5.105957 ACAAAATTATACATGTGGAGCGCAA 60.106 36.000 11.47 0.00 0.00 4.85
754 762 5.574891 AAATTATACATGTGGAGCGCAAA 57.425 34.783 11.47 0.00 0.00 3.68
755 763 4.552166 ATTATACATGTGGAGCGCAAAC 57.448 40.909 11.47 5.03 0.00 2.93
756 764 1.094785 ATACATGTGGAGCGCAAACC 58.905 50.000 11.47 10.90 0.00 3.27
1041 1056 0.321021 CAGCTGTGCTCTTCACCTCT 59.679 55.000 5.25 0.00 45.03 3.69
1197 1212 1.402968 CCCAGATCAACATTTCGGCTG 59.597 52.381 0.00 0.00 0.00 4.85
1254 1269 1.411977 CCACCAAACCATGTCTTTGCA 59.588 47.619 7.34 0.00 0.00 4.08
1289 1304 9.330063 CAACTGTGGAAGATACATGTGTTATAT 57.670 33.333 9.11 0.00 0.00 0.86
1350 1365 0.036388 ACCATGTCATGACACCGTCC 60.036 55.000 30.09 0.00 45.05 4.79
1607 1622 5.066893 GCATTCATATGGCAAGAGAAGTTCA 59.933 40.000 5.50 0.00 32.15 3.18
2028 2168 2.673114 TTACTTGAAAGCCGCCGCG 61.673 57.895 5.59 5.59 41.18 6.46
2154 2299 0.610687 GCTCAACTGGCTAGACAGGT 59.389 55.000 29.14 21.76 42.75 4.00
2155 2300 1.825474 GCTCAACTGGCTAGACAGGTA 59.175 52.381 29.14 12.92 42.75 3.08
2158 2303 4.500035 GCTCAACTGGCTAGACAGGTATAC 60.500 50.000 29.14 11.58 42.75 1.47
2174 2319 5.836898 CAGGTATACACTACATTGGGAGGTA 59.163 44.000 5.01 0.00 0.00 3.08
2215 2361 6.545298 GCCAGGAAATAGATTGAGAAGTTCAT 59.455 38.462 5.50 0.00 35.27 2.57
2220 2366 9.336171 GGAAATAGATTGAGAAGTTCATTAGCT 57.664 33.333 5.50 0.00 35.27 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.779733 GTGAGGAGGAGGCGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
48 49 1.445716 CCGGAAGATAGTCTCGCGGT 61.446 60.000 6.13 0.00 0.00 5.68
269 270 4.325030 CCTCTCTTTCTAGTCTGTCCCTCT 60.325 50.000 0.00 0.00 0.00 3.69
305 306 1.819208 GTGCGGCCTATGACATGCA 60.819 57.895 0.00 0.00 0.00 3.96
319 320 0.732880 CCTACTTGTCTGTCCGTGCG 60.733 60.000 0.00 0.00 0.00 5.34
326 327 4.315803 CGAAATGAACCCTACTTGTCTGT 58.684 43.478 0.00 0.00 0.00 3.41
382 383 7.168219 TCCTATTATGCTCACTGACTGTTTTT 58.832 34.615 0.00 0.00 0.00 1.94
383 384 6.711277 TCCTATTATGCTCACTGACTGTTTT 58.289 36.000 0.00 0.00 0.00 2.43
384 385 6.155221 TCTCCTATTATGCTCACTGACTGTTT 59.845 38.462 0.00 0.00 0.00 2.83
385 386 5.658634 TCTCCTATTATGCTCACTGACTGTT 59.341 40.000 0.00 0.00 0.00 3.16
386 387 5.204292 TCTCCTATTATGCTCACTGACTGT 58.796 41.667 0.00 0.00 0.00 3.55
387 388 5.781210 TCTCCTATTATGCTCACTGACTG 57.219 43.478 0.00 0.00 0.00 3.51
388 389 5.304101 CCTTCTCCTATTATGCTCACTGACT 59.696 44.000 0.00 0.00 0.00 3.41
389 390 5.303078 TCCTTCTCCTATTATGCTCACTGAC 59.697 44.000 0.00 0.00 0.00 3.51
390 391 5.458595 TCCTTCTCCTATTATGCTCACTGA 58.541 41.667 0.00 0.00 0.00 3.41
391 392 5.798125 TCCTTCTCCTATTATGCTCACTG 57.202 43.478 0.00 0.00 0.00 3.66
392 393 7.385894 AATTCCTTCTCCTATTATGCTCACT 57.614 36.000 0.00 0.00 0.00 3.41
393 394 9.732130 ATTAATTCCTTCTCCTATTATGCTCAC 57.268 33.333 0.00 0.00 0.00 3.51
408 409 6.455360 TCCATGTGCTGAATTAATTCCTTC 57.545 37.500 22.42 13.00 35.97 3.46
429 435 5.536538 GGAGTATTTGAAGGAAATCCCATCC 59.463 44.000 0.00 0.00 35.74 3.51
448 454 4.163458 AGCATTATTGAAACGGAGGGAGTA 59.837 41.667 0.00 0.00 0.00 2.59
449 455 3.054361 AGCATTATTGAAACGGAGGGAGT 60.054 43.478 0.00 0.00 0.00 3.85
450 456 3.545703 AGCATTATTGAAACGGAGGGAG 58.454 45.455 0.00 0.00 0.00 4.30
451 457 3.644966 AGCATTATTGAAACGGAGGGA 57.355 42.857 0.00 0.00 0.00 4.20
452 458 4.703897 TCTAGCATTATTGAAACGGAGGG 58.296 43.478 0.00 0.00 0.00 4.30
453 459 6.929049 TGTATCTAGCATTATTGAAACGGAGG 59.071 38.462 0.00 0.00 0.00 4.30
454 460 7.946655 TGTATCTAGCATTATTGAAACGGAG 57.053 36.000 0.00 0.00 0.00 4.63
455 461 7.602644 GGATGTATCTAGCATTATTGAAACGGA 59.397 37.037 0.00 0.00 0.00 4.69
456 462 7.387673 TGGATGTATCTAGCATTATTGAAACGG 59.612 37.037 0.00 0.00 0.00 4.44
457 463 8.310406 TGGATGTATCTAGCATTATTGAAACG 57.690 34.615 0.00 0.00 0.00 3.60
463 469 8.954350 GCTCAAATGGATGTATCTAGCATTATT 58.046 33.333 0.00 0.00 0.00 1.40
464 470 8.105197 TGCTCAAATGGATGTATCTAGCATTAT 58.895 33.333 0.00 0.00 32.88 1.28
465 471 7.452562 TGCTCAAATGGATGTATCTAGCATTA 58.547 34.615 0.00 0.00 32.88 1.90
466 472 6.301486 TGCTCAAATGGATGTATCTAGCATT 58.699 36.000 0.00 0.00 32.88 3.56
467 473 5.872963 TGCTCAAATGGATGTATCTAGCAT 58.127 37.500 0.00 0.00 32.88 3.79
468 474 5.294734 TGCTCAAATGGATGTATCTAGCA 57.705 39.130 0.00 0.00 35.26 3.49
469 475 5.528690 TGTTGCTCAAATGGATGTATCTAGC 59.471 40.000 0.00 0.00 0.00 3.42
470 476 7.496920 TCTTGTTGCTCAAATGGATGTATCTAG 59.503 37.037 0.00 0.00 35.48 2.43
471 477 7.337938 TCTTGTTGCTCAAATGGATGTATCTA 58.662 34.615 0.00 0.00 35.48 1.98
472 478 6.182627 TCTTGTTGCTCAAATGGATGTATCT 58.817 36.000 0.00 0.00 35.48 1.98
473 479 6.441093 TCTTGTTGCTCAAATGGATGTATC 57.559 37.500 0.00 0.00 35.48 2.24
474 480 5.359009 CCTCTTGTTGCTCAAATGGATGTAT 59.641 40.000 0.00 0.00 35.48 2.29
475 481 4.701651 CCTCTTGTTGCTCAAATGGATGTA 59.298 41.667 0.00 0.00 35.48 2.29
476 482 3.508793 CCTCTTGTTGCTCAAATGGATGT 59.491 43.478 0.00 0.00 35.48 3.06
477 483 3.119245 CCCTCTTGTTGCTCAAATGGATG 60.119 47.826 11.39 0.00 35.48 3.51
478 484 3.094572 CCCTCTTGTTGCTCAAATGGAT 58.905 45.455 11.39 0.00 35.48 3.41
479 485 2.108075 TCCCTCTTGTTGCTCAAATGGA 59.892 45.455 11.39 7.94 35.48 3.41
480 486 2.490903 CTCCCTCTTGTTGCTCAAATGG 59.509 50.000 0.00 0.00 35.48 3.16
481 487 3.152341 ACTCCCTCTTGTTGCTCAAATG 58.848 45.455 0.00 0.00 35.48 2.32
482 488 3.515602 ACTCCCTCTTGTTGCTCAAAT 57.484 42.857 0.00 0.00 35.48 2.32
483 489 3.391296 AGTACTCCCTCTTGTTGCTCAAA 59.609 43.478 0.00 0.00 35.48 2.69
484 490 2.972713 AGTACTCCCTCTTGTTGCTCAA 59.027 45.455 0.00 0.00 34.61 3.02
485 491 2.609747 AGTACTCCCTCTTGTTGCTCA 58.390 47.619 0.00 0.00 0.00 4.26
486 492 5.112686 CAATAGTACTCCCTCTTGTTGCTC 58.887 45.833 0.00 0.00 0.00 4.26
487 493 4.532521 ACAATAGTACTCCCTCTTGTTGCT 59.467 41.667 0.00 0.00 30.28 3.91
488 494 4.833390 ACAATAGTACTCCCTCTTGTTGC 58.167 43.478 0.00 0.00 30.28 4.17
508 514 7.493971 CCCAATTTGTTGTGAATCTTTTGTACA 59.506 33.333 0.00 0.00 0.00 2.90
513 519 6.767423 CCTTCCCAATTTGTTGTGAATCTTTT 59.233 34.615 0.00 0.00 0.00 2.27
571 577 8.865590 TGTTTCTTTCTTTTTGTAACATAGCC 57.134 30.769 0.00 0.00 0.00 3.93
590 596 7.433708 TTGTTGTATGACGAATGATGTTTCT 57.566 32.000 0.00 0.00 0.00 2.52
599 605 8.716646 TTCACAGATATTGTTGTATGACGAAT 57.283 30.769 0.00 0.00 38.16 3.34
602 608 9.030301 TGTATTCACAGATATTGTTGTATGACG 57.970 33.333 0.00 0.00 38.16 4.35
680 686 4.715523 TCCTTTTCAGCCGGCCGG 62.716 66.667 40.26 40.26 38.57 6.13
695 701 4.021192 TCCTCAAGCCACATTTTGATTTCC 60.021 41.667 0.00 0.00 33.25 3.13
742 750 3.286751 GCTGGTTTGCGCTCCACA 61.287 61.111 9.73 1.83 0.00 4.17
749 757 3.741476 GAGCCTGGCTGGTTTGCG 61.741 66.667 28.82 0.00 39.88 4.85
750 758 2.598394 TGAGCCTGGCTGGTTTGC 60.598 61.111 28.82 11.09 39.88 3.68
751 759 1.228367 AGTGAGCCTGGCTGGTTTG 60.228 57.895 28.82 0.00 39.88 2.93
752 760 1.228367 CAGTGAGCCTGGCTGGTTT 60.228 57.895 28.82 0.08 39.88 3.27
753 761 2.433446 CAGTGAGCCTGGCTGGTT 59.567 61.111 28.82 7.81 39.88 3.67
754 762 2.851102 ACAGTGAGCCTGGCTGGT 60.851 61.111 28.82 15.41 46.06 4.00
755 763 2.359602 CACAGTGAGCCTGGCTGG 60.360 66.667 28.82 14.73 46.06 4.85
756 764 3.054503 GCACAGTGAGCCTGGCTG 61.055 66.667 28.82 15.24 46.06 4.85
1041 1056 3.680490 TGTTGAATACATGCCCGAAGAA 58.320 40.909 0.00 0.00 0.00 2.52
1197 1212 0.033504 TCTTCGGTGCAAGTGAGGTC 59.966 55.000 0.00 0.00 0.00 3.85
1254 1269 2.159014 TCTTCCACAGTTGTGTTACGCT 60.159 45.455 11.02 0.00 44.21 5.07
1289 1304 8.904834 TGCAGAGTTAACATTTTTGTAAGGTTA 58.095 29.630 8.61 0.00 0.00 2.85
1290 1305 7.704899 GTGCAGAGTTAACATTTTTGTAAGGTT 59.295 33.333 8.61 0.00 0.00 3.50
1305 1320 6.544928 TGATTCTATCCTGTGCAGAGTTAA 57.455 37.500 10.34 0.00 0.00 2.01
1607 1622 1.698506 CCTACAAGATCCCTCTCGCT 58.301 55.000 0.00 0.00 0.00 4.93
2028 2168 5.824904 TTTTCAAAGAGCCATCTAGCATC 57.175 39.130 0.00 0.00 33.45 3.91
2073 2218 7.102346 GGAGACTATGAAATCCACTATCATGG 58.898 42.308 0.00 0.00 41.57 3.66
2082 2227 5.128827 GTGGTAGTGGAGACTATGAAATCCA 59.871 44.000 0.00 0.00 39.50 3.41
2154 2299 6.387127 ACCATACCTCCCAATGTAGTGTATA 58.613 40.000 0.00 0.00 0.00 1.47
2155 2300 5.224441 ACCATACCTCCCAATGTAGTGTAT 58.776 41.667 0.00 0.00 0.00 2.29
2158 2303 3.711704 AGACCATACCTCCCAATGTAGTG 59.288 47.826 0.00 0.00 0.00 2.74
2174 2319 6.432403 TTCCTGGCAAAATTTAAAGACCAT 57.568 33.333 0.00 0.00 0.00 3.55
2215 2361 9.003658 CAGTGAAAGATTTTCTTCCTTAGCTAA 57.996 33.333 5.94 5.94 35.27 3.09


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

AutoCloner maintained by Alex Coulton.