Multiple sequence alignment - TraesCS1A01G208800

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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 TraesCS1A01G208800 chr1A 100.000 3197 0 0 1 3197 371075007 371078203 0.000000e+00 5904
1 TraesCS1A01G208800 chr1D 94.350 2124 72 10 435 2533 298000308 298002408 0.000000e+00 3214
2 TraesCS1A01G208800 chr1D 90.488 410 25 4 1 399 297999910 298000316 2.180000e-146 529
3 TraesCS1A01G208800 chr1D 89.028 319 30 3 2819 3133 298002751 298003068 1.080000e-104 390
4 TraesCS1A01G208800 chr1B 95.866 1016 25 7 675 1681 400572622 400573629 0.000000e+00 1628
5 TraesCS1A01G208800 chr1B 95.688 858 33 2 1675 2532 400579629 400580482 0.000000e+00 1376
6 TraesCS1A01G208800 chr1B 91.453 585 26 14 2621 3197 400580536 400581104 0.000000e+00 782
7 TraesCS1A01G208800 chr1B 84.084 333 40 4 1 321 400571927 400572258 3.100000e-80 309


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 TraesCS1A01G208800 chr1A 371075007 371078203 3196 False 5904.000000 5904 100.000000 1 3197 1 chr1A.!!$F1 3196
1 TraesCS1A01G208800 chr1D 297999910 298003068 3158 False 1377.666667 3214 91.288667 1 3133 3 chr1D.!!$F1 3132
2 TraesCS1A01G208800 chr1B 400579629 400581104 1475 False 1079.000000 1376 93.570500 1675 3197 2 chr1B.!!$F2 1522
3 TraesCS1A01G208800 chr1B 400571927 400573629 1702 False 968.500000 1628 89.975000 1 1681 2 chr1B.!!$F1 1680

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
60 61 0.588252 CAAGAGGTTCCTTGTGTGCG 59.412 55.0 0.0 0.0 38.87 5.34 F
954 1060 0.598562 CCGGAGACCAATCGATCGAT 59.401 55.0 24.6 24.6 36.23 3.59 F
1870 1982 0.322008 GCTGGACTGGGACAAGAAGG 60.322 60.0 0.0 0.0 38.70 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1555 0.321671 TCTTCTCCTTGAACGGCCAG 59.678 55.000 2.24 0.0 0.00 4.85 R
2064 2176 0.683973 CCAGCTTATCATCCGAGCCT 59.316 55.000 0.00 0.0 37.11 4.58 R
2935 3169 1.804151 TCGGAAATGAGAACAAAGCCG 59.196 47.619 0.00 0.0 37.77 5.52 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
52 53 6.542821 TCATGTTTAATCACAAGAGGTTCCT 58.457 36.000 0.00 0.00 0.00 3.36
60 61 0.588252 CAAGAGGTTCCTTGTGTGCG 59.412 55.000 0.00 0.00 38.87 5.34
80 81 1.293924 GACGCATGTGAGGATTCAGG 58.706 55.000 14.43 0.00 32.98 3.86
94 95 3.831911 GGATTCAGGGTGGTGATCAAAAA 59.168 43.478 0.00 0.00 0.00 1.94
175 179 5.819059 ACTCGAGGTAGCTAAATAAGAACG 58.181 41.667 18.41 0.00 0.00 3.95
201 205 3.122948 GTGATATTTATAGTGGTGGCGCG 59.877 47.826 0.00 0.00 0.00 6.86
207 211 2.757980 ATAGTGGTGGCGCGGGTTTT 62.758 55.000 8.83 0.00 0.00 2.43
230 234 3.374988 TCATGCACCACTTCATTTCGATC 59.625 43.478 0.00 0.00 0.00 3.69
269 281 4.638421 CCAGCCTATCAATACGAACCAAAA 59.362 41.667 0.00 0.00 0.00 2.44
279 291 3.007473 ACGAACCAAAAGGTTCAAGGA 57.993 42.857 22.80 0.00 45.88 3.36
293 306 2.517959 TCAAGGACCAAAGAAGCCATG 58.482 47.619 0.00 0.00 0.00 3.66
339 352 6.209192 TCAACAAAAGCACATGTAATCTCCAT 59.791 34.615 0.00 0.00 0.00 3.41
354 367 9.383519 TGTAATCTCCATACTTCAGACATTTTC 57.616 33.333 0.00 0.00 0.00 2.29
358 371 6.655003 TCTCCATACTTCAGACATTTTCAACC 59.345 38.462 0.00 0.00 0.00 3.77
393 450 8.377799 ACAACCATAGATCATCTACATAATGCA 58.622 33.333 0.00 0.00 30.79 3.96
401 458 8.512956 AGATCATCTACATAATGCATGAAAAGC 58.487 33.333 0.00 0.00 38.10 3.51
410 467 3.861276 TGCATGAAAAGCATTCTCTGG 57.139 42.857 0.00 0.00 37.02 3.86
411 468 3.159472 TGCATGAAAAGCATTCTCTGGT 58.841 40.909 0.00 0.00 37.02 4.00
413 470 4.171754 GCATGAAAAGCATTCTCTGGTTC 58.828 43.478 0.00 0.00 44.60 3.62
414 471 4.741342 CATGAAAAGCATTCTCTGGTTCC 58.259 43.478 0.00 0.00 44.60 3.62
415 472 3.831323 TGAAAAGCATTCTCTGGTTCCA 58.169 40.909 4.23 0.00 44.60 3.53
416 473 4.214310 TGAAAAGCATTCTCTGGTTCCAA 58.786 39.130 4.23 0.00 44.60 3.53
417 474 4.648762 TGAAAAGCATTCTCTGGTTCCAAA 59.351 37.500 4.23 0.00 44.60 3.28
418 475 5.305128 TGAAAAGCATTCTCTGGTTCCAAAT 59.695 36.000 4.23 0.00 44.60 2.32
419 476 5.397142 AAAGCATTCTCTGGTTCCAAATC 57.603 39.130 0.00 0.00 44.60 2.17
420 477 4.038271 AGCATTCTCTGGTTCCAAATCA 57.962 40.909 0.00 0.00 29.07 2.57
421 478 4.607239 AGCATTCTCTGGTTCCAAATCAT 58.393 39.130 0.00 0.00 29.07 2.45
422 479 5.759059 AGCATTCTCTGGTTCCAAATCATA 58.241 37.500 0.00 0.00 29.07 2.15
423 480 6.189859 AGCATTCTCTGGTTCCAAATCATAA 58.810 36.000 0.00 0.00 29.07 1.90
424 481 6.664816 AGCATTCTCTGGTTCCAAATCATAAA 59.335 34.615 0.00 0.00 29.07 1.40
425 482 6.753744 GCATTCTCTGGTTCCAAATCATAAAC 59.246 38.462 0.00 0.00 0.00 2.01
426 483 7.363268 GCATTCTCTGGTTCCAAATCATAAACT 60.363 37.037 0.00 0.00 0.00 2.66
427 484 7.452880 TTCTCTGGTTCCAAATCATAAACTG 57.547 36.000 0.00 0.00 0.00 3.16
428 485 5.945784 TCTCTGGTTCCAAATCATAAACTGG 59.054 40.000 0.00 0.00 0.00 4.00
429 486 5.886609 TCTGGTTCCAAATCATAAACTGGA 58.113 37.500 0.00 0.00 36.16 3.86
430 487 5.710099 TCTGGTTCCAAATCATAAACTGGAC 59.290 40.000 0.00 0.00 37.69 4.02
431 488 5.389520 TGGTTCCAAATCATAAACTGGACA 58.610 37.500 0.00 0.00 37.69 4.02
432 489 6.015918 TGGTTCCAAATCATAAACTGGACAT 58.984 36.000 0.00 0.00 37.69 3.06
433 490 6.071447 TGGTTCCAAATCATAAACTGGACATG 60.071 38.462 0.00 0.00 37.69 3.21
434 491 6.071391 GGTTCCAAATCATAAACTGGACATGT 60.071 38.462 0.00 0.00 37.69 3.21
435 492 6.513806 TCCAAATCATAAACTGGACATGTG 57.486 37.500 1.15 0.00 32.97 3.21
436 493 5.104374 CCAAATCATAAACTGGACATGTGC 58.896 41.667 10.90 10.90 0.00 4.57
437 494 5.105635 CCAAATCATAAACTGGACATGTGCT 60.106 40.000 18.75 0.26 0.00 4.40
438 495 6.392354 CAAATCATAAACTGGACATGTGCTT 58.608 36.000 18.75 7.20 0.00 3.91
439 496 5.571784 ATCATAAACTGGACATGTGCTTG 57.428 39.130 18.75 13.12 0.00 4.01
440 497 4.650734 TCATAAACTGGACATGTGCTTGA 58.349 39.130 18.75 8.73 0.00 3.02
441 498 5.069318 TCATAAACTGGACATGTGCTTGAA 58.931 37.500 18.75 0.00 0.00 2.69
442 499 5.534278 TCATAAACTGGACATGTGCTTGAAA 59.466 36.000 18.75 2.10 0.00 2.69
443 500 3.715628 AACTGGACATGTGCTTGAAAC 57.284 42.857 18.75 0.00 0.00 2.78
444 501 1.956477 ACTGGACATGTGCTTGAAACC 59.044 47.619 18.75 3.98 0.00 3.27
445 502 2.233271 CTGGACATGTGCTTGAAACCT 58.767 47.619 18.75 0.00 0.00 3.50
446 503 2.227388 CTGGACATGTGCTTGAAACCTC 59.773 50.000 18.75 0.00 0.00 3.85
447 504 1.541588 GGACATGTGCTTGAAACCTCC 59.458 52.381 10.51 0.00 0.00 4.30
448 505 2.229792 GACATGTGCTTGAAACCTCCA 58.770 47.619 1.15 0.00 0.00 3.86
449 506 2.622942 GACATGTGCTTGAAACCTCCAA 59.377 45.455 1.15 0.00 0.00 3.53
488 545 7.436430 TGTTTTGCCATGTAGTTAACGAATA 57.564 32.000 0.00 0.00 0.00 1.75
511 568 5.772825 TGTAGCAACTCTTCAAGCAAAAT 57.227 34.783 0.00 0.00 0.00 1.82
519 576 7.911727 GCAACTCTTCAAGCAAAATTTTGAATT 59.088 29.630 30.40 21.04 41.10 2.17
596 654 6.307776 TGTAACATTACCCCTGTTTCAATGA 58.692 36.000 0.00 0.00 37.89 2.57
597 655 6.778069 TGTAACATTACCCCTGTTTCAATGAA 59.222 34.615 0.00 0.00 37.89 2.57
601 659 3.611025 ACCCCTGTTTCAATGAAAGGA 57.389 42.857 13.74 2.05 31.87 3.36
604 662 3.500289 CCCCTGTTTCAATGAAAGGAGGA 60.500 47.826 24.71 0.00 35.78 3.71
622 680 3.197790 CGCTCAGCCGTTGGATGG 61.198 66.667 0.72 0.00 39.86 3.51
633 691 1.202568 CGTTGGATGGCATCAGAGCTA 60.203 52.381 27.39 5.74 34.17 3.32
650 708 1.752501 CTAACGGGTCGCGAGCAATG 61.753 60.000 35.80 26.56 0.00 2.82
697 801 1.681264 CGCTCATAATTGGTTTCCCCC 59.319 52.381 0.00 0.00 0.00 5.40
704 808 6.507568 TCATAATTGGTTTCCCCCTATGTTT 58.492 36.000 0.00 0.00 0.00 2.83
706 810 5.497464 AATTGGTTTCCCCCTATGTTTTG 57.503 39.130 0.00 0.00 0.00 2.44
951 1057 0.750850 TTCCCGGAGACCAATCGATC 59.249 55.000 0.73 0.00 0.00 3.69
952 1058 1.007271 CCCGGAGACCAATCGATCG 60.007 63.158 9.36 9.36 0.00 3.69
953 1059 1.452953 CCCGGAGACCAATCGATCGA 61.453 60.000 21.86 21.86 0.00 3.59
954 1060 0.598562 CCGGAGACCAATCGATCGAT 59.401 55.000 24.60 24.60 36.23 3.59
1102 1208 4.514577 ACCGCATCTTCGCCTCGG 62.515 66.667 0.00 0.00 45.04 4.63
1335 1447 4.900259 CCGGGGGAGGGCTACCAT 62.900 72.222 0.00 0.00 40.13 3.55
1381 1493 2.126031 GGCTCGTGTTCGTCTCCC 60.126 66.667 0.00 0.00 38.33 4.30
1416 1528 4.796231 CTCGTCCTCGCCAACCCG 62.796 72.222 0.00 0.00 36.96 5.28
1562 1674 4.129737 GCTCGTCGCCTACTGCCA 62.130 66.667 0.00 0.00 36.24 4.92
1870 1982 0.322008 GCTGGACTGGGACAAGAAGG 60.322 60.000 0.00 0.00 38.70 3.46
1877 1989 0.472471 TGGGACAAGAAGGTGTGGAC 59.528 55.000 0.00 0.00 31.92 4.02
2064 2176 0.107897 CGGAATCGTGGGTGGATGAA 60.108 55.000 0.00 0.00 0.00 2.57
2078 2190 2.972021 TGGATGAAGGCTCGGATGATAA 59.028 45.455 0.00 0.00 0.00 1.75
2179 2291 1.507140 TCCGGATGAAAGGGCTATGT 58.493 50.000 0.00 0.00 0.00 2.29
2213 2325 4.455606 GCCTAGCTAGTTGGAACATGAAT 58.544 43.478 19.31 0.00 39.30 2.57
2223 2335 6.585416 AGTTGGAACATGAATTTCTTGCTTT 58.415 32.000 0.00 1.33 39.30 3.51
2242 2354 2.738587 TTGGTAGGCTGGTTTGAACA 57.261 45.000 0.00 0.00 0.00 3.18
2330 2442 7.083875 TCTGTTCGTTTTGTCTGAAGAAAAT 57.916 32.000 0.00 0.00 31.20 1.82
2399 2511 6.884832 TCCTGTTCCTATATGATTCAAACGT 58.115 36.000 0.00 0.00 0.00 3.99
2434 2546 7.635423 CAACCAGCAATATATAAACGTAAGCA 58.365 34.615 0.00 0.00 45.62 3.91
2461 2573 7.311408 TCATTTATCGACAAATGTTGATTGCA 58.689 30.769 24.27 4.31 44.55 4.08
2505 2617 2.931325 GCCATATACACGAAACGGTGAA 59.069 45.455 0.00 0.00 40.38 3.18
2618 2759 9.997172 AGAGGATTATACCTTTTCCTTCAAAAT 57.003 29.630 0.00 0.00 40.73 1.82
2626 2767 9.997172 ATACCTTTTCCTTCAAAATAGAGGATT 57.003 29.630 0.00 0.00 33.34 3.01
2628 2769 9.997172 ACCTTTTCCTTCAAAATAGAGGATTAT 57.003 29.630 0.00 0.00 33.34 1.28
2805 2954 6.144175 CCCAAATCATGCAAAATTTCACAAC 58.856 36.000 6.67 0.00 0.00 3.32
2806 2955 6.238676 CCCAAATCATGCAAAATTTCACAACA 60.239 34.615 6.67 0.00 0.00 3.33
2807 2956 7.194278 CCAAATCATGCAAAATTTCACAACAA 58.806 30.769 6.67 0.00 0.00 2.83
2808 2957 7.166142 CCAAATCATGCAAAATTTCACAACAAC 59.834 33.333 6.67 0.00 0.00 3.32
2809 2958 6.922247 ATCATGCAAAATTTCACAACAACA 57.078 29.167 0.00 0.00 0.00 3.33
2810 2959 6.732531 TCATGCAAAATTTCACAACAACAA 57.267 29.167 0.00 0.00 0.00 2.83
2811 2960 6.541086 TCATGCAAAATTTCACAACAACAAC 58.459 32.000 0.00 0.00 0.00 3.32
2812 2961 5.929697 TGCAAAATTTCACAACAACAACA 57.070 30.435 0.00 0.00 0.00 3.33
2813 2962 6.304356 TGCAAAATTTCACAACAACAACAA 57.696 29.167 0.00 0.00 0.00 2.83
2815 2964 6.800408 TGCAAAATTTCACAACAACAACAATG 59.200 30.769 0.00 0.00 0.00 2.82
2816 2965 6.250951 GCAAAATTTCACAACAACAACAATGG 59.749 34.615 0.00 0.00 0.00 3.16
2817 2966 5.482686 AATTTCACAACAACAACAATGGC 57.517 34.783 0.00 0.00 0.00 4.40
2820 3054 3.455327 TCACAACAACAACAATGGCATG 58.545 40.909 0.00 0.00 0.00 4.06
2892 3126 9.104965 GAGGTGCACTTACAATGTAATAACATA 57.895 33.333 17.98 0.00 45.79 2.29
2893 3127 9.109393 AGGTGCACTTACAATGTAATAACATAG 57.891 33.333 17.98 0.00 45.79 2.23
2935 3169 6.986250 AGTCTTTCCTGTTTTGATTGGAATC 58.014 36.000 0.00 0.00 38.24 2.52
2995 3231 8.824781 CCTATTTATATCATCGCAGAAGAATGG 58.175 37.037 0.00 0.00 43.58 3.16
3020 3256 6.715347 AGGCCATATCCATTAACTGTTTTC 57.285 37.500 5.01 0.00 0.00 2.29
3077 3313 8.568676 TGACGGAATTTTAGAATCATTGGTAA 57.431 30.769 0.00 0.00 0.00 2.85
3079 3315 9.849166 GACGGAATTTTAGAATCATTGGTAAAA 57.151 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.975147 TGATGATAGTCCCAAATGGTACCT 59.025 41.667 14.36 0.00 34.77 3.08
60 61 1.293924 CTGAATCCTCACATGCGTCC 58.706 55.000 0.00 0.00 0.00 4.79
175 179 6.427150 CGCCACCACTATAAATATCACAAAC 58.573 40.000 0.00 0.00 0.00 2.93
201 205 2.102252 TGAAGTGGTGCATGAAAAACCC 59.898 45.455 0.00 0.00 32.70 4.11
207 211 3.145286 TCGAAATGAAGTGGTGCATGAA 58.855 40.909 0.00 0.00 0.00 2.57
230 234 1.470098 GCTGGTGACTGTTTAGGCATG 59.530 52.381 0.00 0.00 45.54 4.06
269 281 2.587522 GCTTCTTTGGTCCTTGAACCT 58.412 47.619 0.00 0.00 40.20 3.50
279 291 3.084786 GTTAGAGCATGGCTTCTTTGGT 58.915 45.455 0.00 0.00 39.88 3.67
293 306 5.419542 TGATGTCCAACATACAGTTAGAGC 58.580 41.667 0.00 0.00 39.27 4.09
320 333 7.112122 TGAAGTATGGAGATTACATGTGCTTT 58.888 34.615 9.11 0.00 0.00 3.51
321 334 6.653020 TGAAGTATGGAGATTACATGTGCTT 58.347 36.000 9.11 0.00 0.00 3.91
339 352 7.338196 TCTTTGTGGTTGAAAATGTCTGAAGTA 59.662 33.333 0.00 0.00 0.00 2.24
354 367 3.799281 ATGGTTGTGTCTTTGTGGTTG 57.201 42.857 0.00 0.00 0.00 3.77
358 371 6.596888 AGATGATCTATGGTTGTGTCTTTGTG 59.403 38.462 0.00 0.00 0.00 3.33
393 450 4.410099 TGGAACCAGAGAATGCTTTTCAT 58.590 39.130 3.37 0.00 36.87 2.57
399 456 4.038271 TGATTTGGAACCAGAGAATGCT 57.962 40.909 0.00 0.00 0.00 3.79
400 457 4.996788 ATGATTTGGAACCAGAGAATGC 57.003 40.909 0.00 0.00 0.00 3.56
401 458 7.972277 CAGTTTATGATTTGGAACCAGAGAATG 59.028 37.037 0.00 0.00 0.00 2.67
402 459 7.123247 CCAGTTTATGATTTGGAACCAGAGAAT 59.877 37.037 0.00 0.00 32.34 2.40
403 460 6.434028 CCAGTTTATGATTTGGAACCAGAGAA 59.566 38.462 0.00 0.00 32.34 2.87
404 461 5.945784 CCAGTTTATGATTTGGAACCAGAGA 59.054 40.000 0.00 0.00 32.34 3.10
405 462 5.945784 TCCAGTTTATGATTTGGAACCAGAG 59.054 40.000 0.00 0.00 36.81 3.35
406 463 5.710099 GTCCAGTTTATGATTTGGAACCAGA 59.290 40.000 0.00 0.00 41.10 3.86
407 464 5.476599 TGTCCAGTTTATGATTTGGAACCAG 59.523 40.000 0.00 0.00 41.10 4.00
408 465 5.389520 TGTCCAGTTTATGATTTGGAACCA 58.610 37.500 0.00 0.00 41.10 3.67
409 466 5.975693 TGTCCAGTTTATGATTTGGAACC 57.024 39.130 0.00 0.00 41.10 3.62
410 467 6.808212 CACATGTCCAGTTTATGATTTGGAAC 59.192 38.462 0.00 0.00 41.10 3.62
411 468 6.572119 GCACATGTCCAGTTTATGATTTGGAA 60.572 38.462 0.00 0.00 41.10 3.53
412 469 5.105797 GCACATGTCCAGTTTATGATTTGGA 60.106 40.000 0.00 0.00 37.38 3.53
413 470 5.104374 GCACATGTCCAGTTTATGATTTGG 58.896 41.667 0.00 0.00 0.00 3.28
414 471 5.957798 AGCACATGTCCAGTTTATGATTTG 58.042 37.500 0.00 0.00 0.00 2.32
415 472 6.209192 TCAAGCACATGTCCAGTTTATGATTT 59.791 34.615 0.00 0.00 0.00 2.17
416 473 5.711506 TCAAGCACATGTCCAGTTTATGATT 59.288 36.000 0.00 0.00 0.00 2.57
417 474 5.255687 TCAAGCACATGTCCAGTTTATGAT 58.744 37.500 0.00 0.00 0.00 2.45
418 475 4.650734 TCAAGCACATGTCCAGTTTATGA 58.349 39.130 0.00 0.00 0.00 2.15
419 476 5.375417 TTCAAGCACATGTCCAGTTTATG 57.625 39.130 0.00 0.00 0.00 1.90
420 477 5.278957 GGTTTCAAGCACATGTCCAGTTTAT 60.279 40.000 0.00 0.00 0.00 1.40
421 478 4.037446 GGTTTCAAGCACATGTCCAGTTTA 59.963 41.667 0.00 0.00 0.00 2.01
422 479 3.181476 GGTTTCAAGCACATGTCCAGTTT 60.181 43.478 0.00 0.00 0.00 2.66
423 480 2.362077 GGTTTCAAGCACATGTCCAGTT 59.638 45.455 0.00 0.00 0.00 3.16
424 481 1.956477 GGTTTCAAGCACATGTCCAGT 59.044 47.619 0.00 0.00 0.00 4.00
425 482 2.227388 GAGGTTTCAAGCACATGTCCAG 59.773 50.000 0.00 0.00 0.00 3.86
426 483 2.229792 GAGGTTTCAAGCACATGTCCA 58.770 47.619 0.00 0.00 0.00 4.02
427 484 1.541588 GGAGGTTTCAAGCACATGTCC 59.458 52.381 0.00 0.00 0.00 4.02
428 485 2.229792 TGGAGGTTTCAAGCACATGTC 58.770 47.619 0.00 0.00 0.00 3.06
429 486 2.362077 GTTGGAGGTTTCAAGCACATGT 59.638 45.455 0.00 0.00 0.00 3.21
430 487 2.288395 GGTTGGAGGTTTCAAGCACATG 60.288 50.000 0.00 0.00 40.89 3.21
431 488 1.963515 GGTTGGAGGTTTCAAGCACAT 59.036 47.619 0.00 0.00 40.89 3.21
432 489 1.398692 GGTTGGAGGTTTCAAGCACA 58.601 50.000 0.00 0.00 40.89 4.57
433 490 0.673985 GGGTTGGAGGTTTCAAGCAC 59.326 55.000 8.02 0.00 42.39 4.40
434 491 0.555769 AGGGTTGGAGGTTTCAAGCA 59.444 50.000 8.02 0.00 42.39 3.91
435 492 1.202940 AGAGGGTTGGAGGTTTCAAGC 60.203 52.381 0.00 0.00 40.60 4.01
436 493 2.106511 TGAGAGGGTTGGAGGTTTCAAG 59.893 50.000 0.00 0.00 0.00 3.02
437 494 2.131854 TGAGAGGGTTGGAGGTTTCAA 58.868 47.619 0.00 0.00 0.00 2.69
438 495 1.814429 TGAGAGGGTTGGAGGTTTCA 58.186 50.000 0.00 0.00 0.00 2.69
439 496 2.951229 TTGAGAGGGTTGGAGGTTTC 57.049 50.000 0.00 0.00 0.00 2.78
440 497 3.117131 ACATTTGAGAGGGTTGGAGGTTT 60.117 43.478 0.00 0.00 0.00 3.27
441 498 2.447047 ACATTTGAGAGGGTTGGAGGTT 59.553 45.455 0.00 0.00 0.00 3.50
442 499 2.065799 ACATTTGAGAGGGTTGGAGGT 58.934 47.619 0.00 0.00 0.00 3.85
443 500 2.887151 ACATTTGAGAGGGTTGGAGG 57.113 50.000 0.00 0.00 0.00 4.30
444 501 3.891366 ACAAACATTTGAGAGGGTTGGAG 59.109 43.478 11.24 0.00 40.55 3.86
445 502 3.909732 ACAAACATTTGAGAGGGTTGGA 58.090 40.909 11.24 0.00 40.55 3.53
446 503 4.670896 AACAAACATTTGAGAGGGTTGG 57.329 40.909 11.24 0.00 40.55 3.77
447 504 5.220643 GCAAAACAAACATTTGAGAGGGTTG 60.221 40.000 11.24 6.68 39.56 3.77
448 505 4.875536 GCAAAACAAACATTTGAGAGGGTT 59.124 37.500 11.24 0.00 39.56 4.11
449 506 4.441792 GCAAAACAAACATTTGAGAGGGT 58.558 39.130 11.24 0.00 39.56 4.34
488 545 5.772825 TTTTGCTTGAAGAGTTGCTACAT 57.227 34.783 0.00 0.00 0.00 2.29
511 568 1.839994 TGCCCCACCAACAATTCAAAA 59.160 42.857 0.00 0.00 0.00 2.44
519 576 1.302949 GAGCTATGCCCCACCAACA 59.697 57.895 0.00 0.00 0.00 3.33
560 618 6.532826 GGGTAATGTTACATAACCCCGATAA 58.467 40.000 0.00 0.00 43.42 1.75
561 619 6.112927 GGGTAATGTTACATAACCCCGATA 57.887 41.667 0.00 0.00 43.42 2.92
596 654 2.665603 GGCTGAGCGTCCTCCTTT 59.334 61.111 0.00 0.00 37.29 3.11
597 655 3.764466 CGGCTGAGCGTCCTCCTT 61.764 66.667 0.00 0.00 37.29 3.36
601 659 4.379243 CCAACGGCTGAGCGTCCT 62.379 66.667 0.00 0.00 0.00 3.85
604 662 2.434884 CATCCAACGGCTGAGCGT 60.435 61.111 0.00 0.00 0.00 5.07
615 673 2.742856 CGTTAGCTCTGATGCCATCCAA 60.743 50.000 1.49 0.00 0.00 3.53
622 680 0.872021 CGACCCGTTAGCTCTGATGC 60.872 60.000 0.00 0.00 0.00 3.91
633 691 3.118454 CATTGCTCGCGACCCGTT 61.118 61.111 3.71 0.00 38.35 4.44
650 708 3.049912 GGTTCTCATTTGCGTCCAAAAC 58.950 45.455 0.00 0.00 43.58 2.43
697 801 6.771076 TGCAATTCGTAGTAGCAAAACATAG 58.229 36.000 0.00 0.00 31.42 2.23
704 808 4.450082 TCTCTGCAATTCGTAGTAGCAA 57.550 40.909 0.00 0.00 34.45 3.91
706 810 5.975410 AAATCTCTGCAATTCGTAGTAGC 57.025 39.130 0.00 0.00 0.00 3.58
828 934 9.357161 TGGGCTTGTTTAAAGAAAATCTTACTA 57.643 29.630 0.00 0.00 35.27 1.82
829 935 8.245195 TGGGCTTGTTTAAAGAAAATCTTACT 57.755 30.769 0.00 0.00 35.27 2.24
830 936 8.880878 TTGGGCTTGTTTAAAGAAAATCTTAC 57.119 30.769 0.00 0.00 35.27 2.34
839 945 5.278266 CGTCAGATTTGGGCTTGTTTAAAGA 60.278 40.000 0.00 0.00 0.00 2.52
952 1058 0.931005 GTTGGTTGGCTCGATCGATC 59.069 55.000 19.78 14.83 0.00 3.69
953 1059 0.462047 GGTTGGTTGGCTCGATCGAT 60.462 55.000 19.78 0.00 0.00 3.59
954 1060 1.079405 GGTTGGTTGGCTCGATCGA 60.079 57.895 18.32 18.32 0.00 3.59
1102 1208 1.571773 AAGGTGATGTAGGGGGCCAC 61.572 60.000 4.39 0.00 0.00 5.01
1443 1555 0.321671 TCTTCTCCTTGAACGGCCAG 59.678 55.000 2.24 0.00 0.00 4.85
1528 1640 3.461773 CCTGTCCGTGGCGAGGAT 61.462 66.667 4.07 0.00 40.30 3.24
2024 2136 3.936203 AGAACCACGCGAGCCCAA 61.936 61.111 15.93 0.00 0.00 4.12
2064 2176 0.683973 CCAGCTTATCATCCGAGCCT 59.316 55.000 0.00 0.00 37.11 4.58
2179 2291 2.114670 GCTAGGCCTGCGATGCAAA 61.115 57.895 17.99 0.00 38.41 3.68
2213 2325 2.627699 CCAGCCTACCAAAAGCAAGAAA 59.372 45.455 0.00 0.00 0.00 2.52
2223 2335 2.738587 TGTTCAAACCAGCCTACCAA 57.261 45.000 0.00 0.00 0.00 3.67
2330 2442 9.422681 AGATATCTGCAACTTTTAGGACTACTA 57.577 33.333 3.89 0.00 0.00 1.82
2434 2546 8.810427 GCAATCAACATTTGTCGATAAATGATT 58.190 29.630 38.17 28.88 46.13 2.57
2461 2573 2.766651 ATCGCACCCCGGTATGGT 60.767 61.111 0.00 0.00 37.59 3.55
2592 2733 9.997172 ATTTTGAAGGAAAAGGTATAATCCTCT 57.003 29.630 0.00 0.00 41.39 3.69
2600 2741 9.997172 AATCCTCTATTTTGAAGGAAAAGGTAT 57.003 29.630 0.00 0.00 36.97 2.73
2602 2743 9.997172 ATAATCCTCTATTTTGAAGGAAAAGGT 57.003 29.630 0.00 0.00 36.97 3.50
2628 2769 9.667107 CTACACATGAAAACTTCCTAGGAAATA 57.333 33.333 24.31 3.45 33.34 1.40
2629 2770 7.121315 GCTACACATGAAAACTTCCTAGGAAAT 59.879 37.037 24.31 13.06 33.34 2.17
2630 2771 6.430000 GCTACACATGAAAACTTCCTAGGAAA 59.570 38.462 24.31 9.60 33.34 3.13
2631 2772 5.938125 GCTACACATGAAAACTTCCTAGGAA 59.062 40.000 22.94 22.94 0.00 3.36
2632 2773 5.248477 AGCTACACATGAAAACTTCCTAGGA 59.752 40.000 7.62 7.62 0.00 2.94
2633 2774 5.491982 AGCTACACATGAAAACTTCCTAGG 58.508 41.667 0.82 0.82 0.00 3.02
2634 2775 6.621596 GCAAGCTACACATGAAAACTTCCTAG 60.622 42.308 0.00 0.00 0.00 3.02
2738 2886 8.141268 TCCTTTAAAATTGCAAGTAAAGTGGAG 58.859 33.333 24.22 15.79 33.57 3.86
2816 2965 4.034742 GAAATTGGATTTCATGGCACATGC 59.965 41.667 9.54 0.00 46.05 4.06
2817 2966 5.728351 GAAATTGGATTTCATGGCACATG 57.272 39.130 8.18 8.41 46.05 3.21
2892 3126 5.284582 AGACTCCATCAAACTAAGGATCCT 58.715 41.667 9.02 9.02 0.00 3.24
2893 3127 5.622346 AGACTCCATCAAACTAAGGATCC 57.378 43.478 2.48 2.48 0.00 3.36
2935 3169 1.804151 TCGGAAATGAGAACAAAGCCG 59.196 47.619 0.00 0.00 37.77 5.52
2995 3231 7.502561 AGAAAACAGTTAATGGATATGGCCTAC 59.497 37.037 3.32 0.00 0.00 3.18
3098 3340 6.591935 TGTAGGGAGTATTTAGGCAGAAATG 58.408 40.000 7.44 0.00 31.51 2.32
3151 3393 3.584848 ACTCTACTTCAAACATCCCAGCT 59.415 43.478 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.