Multiple sequence alignment - TraesCS1D01G078200

Loading Multiple Alignment...

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 TraesCS1D01G078200 chr1D 100.000 2357 0 0 1 2357 60172442 60170086 0.000000e+00 4353
1 TraesCS1D01G078200 chr1D 97.386 1339 28 5 627 1964 205134697 205133365 0.000000e+00 2272
2 TraesCS1D01G078200 chr1D 96.963 1350 35 5 626 1972 247505759 247504413 0.000000e+00 2261
3 TraesCS1D01G078200 chr2D 98.068 1346 24 2 625 1969 73126874 73125530 0.000000e+00 2340
4 TraesCS1D01G078200 chr2D 97.253 1347 32 5 628 1972 621748803 621750146 0.000000e+00 2278
5 TraesCS1D01G078200 chr3D 97.543 1343 31 2 627 1968 584701392 584700051 0.000000e+00 2296
6 TraesCS1D01G078200 chr7D 97.398 1345 31 4 623 1965 497560901 497562243 0.000000e+00 2287
7 TraesCS1D01G078200 chr7D 96.738 1349 42 2 625 1972 50081833 50080486 0.000000e+00 2246
8 TraesCS1D01G078200 chr5D 96.943 1341 38 3 627 1966 275171748 275170410 0.000000e+00 2246
9 TraesCS1D01G078200 chr6D 96.808 1347 38 3 622 1966 142136699 142135356 0.000000e+00 2244
10 TraesCS1D01G078200 chr1A 97.120 625 15 2 1 622 58841939 58841315 0.000000e+00 1051
11 TraesCS1D01G078200 chr1A 95.342 365 12 3 1996 2356 58841311 58840948 2.030000e-160 575
12 TraesCS1D01G078200 chr2A 81.376 596 88 18 1 581 3760233 3760820 4.590000e-127 464


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 TraesCS1D01G078200 chr1D 60170086 60172442 2356 True 4353 4353 100.000 1 2357 1 chr1D.!!$R1 2356
1 TraesCS1D01G078200 chr1D 205133365 205134697 1332 True 2272 2272 97.386 627 1964 1 chr1D.!!$R2 1337
2 TraesCS1D01G078200 chr1D 247504413 247505759 1346 True 2261 2261 96.963 626 1972 1 chr1D.!!$R3 1346
3 TraesCS1D01G078200 chr2D 73125530 73126874 1344 True 2340 2340 98.068 625 1969 1 chr2D.!!$R1 1344
4 TraesCS1D01G078200 chr2D 621748803 621750146 1343 False 2278 2278 97.253 628 1972 1 chr2D.!!$F1 1344
5 TraesCS1D01G078200 chr3D 584700051 584701392 1341 True 2296 2296 97.543 627 1968 1 chr3D.!!$R1 1341
6 TraesCS1D01G078200 chr7D 497560901 497562243 1342 False 2287 2287 97.398 623 1965 1 chr7D.!!$F1 1342
7 TraesCS1D01G078200 chr7D 50080486 50081833 1347 True 2246 2246 96.738 625 1972 1 chr7D.!!$R1 1347
8 TraesCS1D01G078200 chr5D 275170410 275171748 1338 True 2246 2246 96.943 627 1966 1 chr5D.!!$R1 1339
9 TraesCS1D01G078200 chr6D 142135356 142136699 1343 True 2244 2244 96.808 622 1966 1 chr6D.!!$R1 1344
10 TraesCS1D01G078200 chr1A 58840948 58841939 991 True 813 1051 96.231 1 2356 2 chr1A.!!$R1 2355
11 TraesCS1D01G078200 chr2A 3760233 3760820 587 False 464 464 81.376 1 581 1 chr2A.!!$F1 580

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
536 550 0.179111 TCTTAAGGTCGGCGATGCAG 60.179 55.0 14.79 5.55 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2013 0.100146 GAGGGTAGTGTTACTCGCGG 59.9 60.0 6.13 0.0 35.32 6.46 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
136 138 4.412796 TGAATGTTTGTCCAATGCCAAA 57.587 36.364 0.00 0.00 0.00 3.28
246 256 1.335233 CGCAACTGCAAATTCAGAGCA 60.335 47.619 2.12 0.00 42.21 4.26
301 311 2.883253 GAGCGGAGAAGCGAGTGC 60.883 66.667 0.00 0.00 43.00 4.40
439 453 8.497745 ACAATTGTATTAGAAGATGAGGATGGT 58.502 33.333 9.97 0.00 0.00 3.55
495 509 2.829384 GCCTCAGTGGTGGGTGGAA 61.829 63.158 5.48 0.00 38.35 3.53
508 522 2.752354 TGGGTGGAATAGATTTGCAACG 59.248 45.455 0.00 0.00 0.00 4.10
517 531 1.739466 AGATTTGCAACGCGACATCAT 59.261 42.857 15.93 3.42 0.00 2.45
518 532 2.104144 GATTTGCAACGCGACATCATC 58.896 47.619 15.93 8.92 0.00 2.92
519 533 1.155889 TTTGCAACGCGACATCATCT 58.844 45.000 15.93 0.00 0.00 2.90
520 534 1.155889 TTGCAACGCGACATCATCTT 58.844 45.000 15.93 0.00 0.00 2.40
521 535 2.003196 TGCAACGCGACATCATCTTA 57.997 45.000 15.93 0.00 0.00 2.10
522 536 2.342179 TGCAACGCGACATCATCTTAA 58.658 42.857 15.93 0.00 0.00 1.85
523 537 2.348362 TGCAACGCGACATCATCTTAAG 59.652 45.455 15.93 0.00 0.00 1.85
524 538 2.285834 GCAACGCGACATCATCTTAAGG 60.286 50.000 15.93 0.00 0.00 2.69
525 539 2.930040 CAACGCGACATCATCTTAAGGT 59.070 45.455 15.93 0.00 0.00 3.50
526 540 2.810650 ACGCGACATCATCTTAAGGTC 58.189 47.619 15.93 0.89 0.00 3.85
529 543 2.128035 CGACATCATCTTAAGGTCGGC 58.872 52.381 18.03 0.00 45.36 5.54
530 544 2.128035 GACATCATCTTAAGGTCGGCG 58.872 52.381 0.00 0.00 0.00 6.46
531 545 1.754803 ACATCATCTTAAGGTCGGCGA 59.245 47.619 4.99 4.99 0.00 5.54
532 546 2.365617 ACATCATCTTAAGGTCGGCGAT 59.634 45.455 14.79 0.00 0.00 4.58
533 547 2.509052 TCATCTTAAGGTCGGCGATG 57.491 50.000 14.79 4.48 34.33 3.84
534 548 0.861837 CATCTTAAGGTCGGCGATGC 59.138 55.000 14.79 0.00 0.00 3.91
535 549 0.464036 ATCTTAAGGTCGGCGATGCA 59.536 50.000 14.79 0.00 0.00 3.96
536 550 0.179111 TCTTAAGGTCGGCGATGCAG 60.179 55.000 14.79 5.55 0.00 4.41
537 551 0.460284 CTTAAGGTCGGCGATGCAGT 60.460 55.000 14.79 0.00 0.00 4.40
538 552 0.739462 TTAAGGTCGGCGATGCAGTG 60.739 55.000 14.79 0.00 0.00 3.66
539 553 2.572095 TAAGGTCGGCGATGCAGTGG 62.572 60.000 14.79 0.00 0.00 4.00
540 554 4.760047 GGTCGGCGATGCAGTGGT 62.760 66.667 14.79 0.00 0.00 4.16
541 555 3.188786 GTCGGCGATGCAGTGGTC 61.189 66.667 14.79 0.00 0.00 4.02
542 556 3.381983 TCGGCGATGCAGTGGTCT 61.382 61.111 4.99 0.00 0.00 3.85
543 557 2.434884 CGGCGATGCAGTGGTCTT 60.435 61.111 0.00 0.00 0.00 3.01
544 558 2.034879 CGGCGATGCAGTGGTCTTT 61.035 57.895 0.00 0.00 0.00 2.52
545 559 1.796796 GGCGATGCAGTGGTCTTTC 59.203 57.895 0.00 0.00 0.00 2.62
546 560 0.955428 GGCGATGCAGTGGTCTTTCA 60.955 55.000 0.00 0.00 0.00 2.69
547 561 0.874390 GCGATGCAGTGGTCTTTCAA 59.126 50.000 0.00 0.00 0.00 2.69
548 562 1.400242 GCGATGCAGTGGTCTTTCAAC 60.400 52.381 0.00 0.00 0.00 3.18
549 563 2.146342 CGATGCAGTGGTCTTTCAACT 58.854 47.619 0.00 0.00 0.00 3.16
550 564 2.158449 CGATGCAGTGGTCTTTCAACTC 59.842 50.000 0.00 0.00 0.00 3.01
551 565 1.581934 TGCAGTGGTCTTTCAACTCG 58.418 50.000 0.00 0.00 0.00 4.18
552 566 1.134521 TGCAGTGGTCTTTCAACTCGT 60.135 47.619 0.00 0.00 0.00 4.18
553 567 1.261619 GCAGTGGTCTTTCAACTCGTG 59.738 52.381 0.00 0.00 0.00 4.35
554 568 1.867233 CAGTGGTCTTTCAACTCGTGG 59.133 52.381 0.00 0.00 0.00 4.94
555 569 1.760613 AGTGGTCTTTCAACTCGTGGA 59.239 47.619 0.00 0.00 0.00 4.02
556 570 2.169769 AGTGGTCTTTCAACTCGTGGAA 59.830 45.455 0.00 0.00 0.00 3.53
557 571 2.287103 GTGGTCTTTCAACTCGTGGAAC 59.713 50.000 0.00 0.00 0.00 3.62
558 572 1.871676 GGTCTTTCAACTCGTGGAACC 59.128 52.381 0.00 0.00 0.00 3.62
559 573 2.557317 GTCTTTCAACTCGTGGAACCA 58.443 47.619 0.00 0.00 0.00 3.67
560 574 2.940410 GTCTTTCAACTCGTGGAACCAA 59.060 45.455 0.00 0.00 0.00 3.67
561 575 2.940410 TCTTTCAACTCGTGGAACCAAC 59.060 45.455 0.00 0.00 0.00 3.77
562 576 2.404923 TTCAACTCGTGGAACCAACA 57.595 45.000 0.00 0.00 0.00 3.33
563 577 2.404923 TCAACTCGTGGAACCAACAA 57.595 45.000 0.00 0.00 0.00 2.83
564 578 2.285083 TCAACTCGTGGAACCAACAAG 58.715 47.619 0.00 0.00 0.00 3.16
565 579 2.093394 TCAACTCGTGGAACCAACAAGA 60.093 45.455 0.00 0.00 0.00 3.02
566 580 2.878406 CAACTCGTGGAACCAACAAGAT 59.122 45.455 0.00 0.00 0.00 2.40
567 581 3.208747 ACTCGTGGAACCAACAAGATT 57.791 42.857 0.00 0.00 0.00 2.40
568 582 3.551846 ACTCGTGGAACCAACAAGATTT 58.448 40.909 0.00 0.00 0.00 2.17
569 583 4.710324 ACTCGTGGAACCAACAAGATTTA 58.290 39.130 0.00 0.00 0.00 1.40
570 584 5.127491 ACTCGTGGAACCAACAAGATTTAA 58.873 37.500 0.00 0.00 0.00 1.52
571 585 5.238650 ACTCGTGGAACCAACAAGATTTAAG 59.761 40.000 0.00 0.00 0.00 1.85
572 586 4.517453 TCGTGGAACCAACAAGATTTAAGG 59.483 41.667 0.00 0.00 0.00 2.69
573 587 4.556233 GTGGAACCAACAAGATTTAAGGC 58.444 43.478 0.00 0.00 0.00 4.35
574 588 3.254657 TGGAACCAACAAGATTTAAGGCG 59.745 43.478 0.00 0.00 0.00 5.52
575 589 3.504520 GGAACCAACAAGATTTAAGGCGA 59.495 43.478 0.00 0.00 0.00 5.54
576 590 4.379499 GGAACCAACAAGATTTAAGGCGAG 60.379 45.833 0.00 0.00 0.00 5.03
577 591 3.751518 ACCAACAAGATTTAAGGCGAGT 58.248 40.909 0.00 0.00 0.00 4.18
578 592 3.502211 ACCAACAAGATTTAAGGCGAGTG 59.498 43.478 0.00 0.00 0.00 3.51
579 593 3.492313 CAACAAGATTTAAGGCGAGTGC 58.508 45.455 0.00 0.00 41.71 4.40
580 594 3.059352 ACAAGATTTAAGGCGAGTGCT 57.941 42.857 0.00 0.00 42.25 4.40
581 595 3.412386 ACAAGATTTAAGGCGAGTGCTT 58.588 40.909 0.00 0.00 42.25 3.91
582 596 3.437049 ACAAGATTTAAGGCGAGTGCTTC 59.563 43.478 0.00 0.00 42.25 3.86
592 606 2.949714 CGAGTGCTTCGTCAATGTTT 57.050 45.000 3.48 0.00 44.27 2.83
593 607 3.253371 CGAGTGCTTCGTCAATGTTTT 57.747 42.857 3.48 0.00 44.27 2.43
594 608 4.383774 CGAGTGCTTCGTCAATGTTTTA 57.616 40.909 3.48 0.00 44.27 1.52
595 609 4.957971 CGAGTGCTTCGTCAATGTTTTAT 58.042 39.130 3.48 0.00 44.27 1.40
596 610 5.382303 CGAGTGCTTCGTCAATGTTTTATT 58.618 37.500 3.48 0.00 44.27 1.40
597 611 5.504755 CGAGTGCTTCGTCAATGTTTTATTC 59.495 40.000 3.48 0.00 44.27 1.75
598 612 5.699839 AGTGCTTCGTCAATGTTTTATTCC 58.300 37.500 0.00 0.00 0.00 3.01
599 613 5.240623 AGTGCTTCGTCAATGTTTTATTCCA 59.759 36.000 0.00 0.00 0.00 3.53
600 614 6.071952 AGTGCTTCGTCAATGTTTTATTCCAT 60.072 34.615 0.00 0.00 0.00 3.41
601 615 6.251376 GTGCTTCGTCAATGTTTTATTCCATC 59.749 38.462 0.00 0.00 0.00 3.51
602 616 6.072230 TGCTTCGTCAATGTTTTATTCCATCA 60.072 34.615 0.00 0.00 0.00 3.07
603 617 6.974622 GCTTCGTCAATGTTTTATTCCATCAT 59.025 34.615 0.00 0.00 0.00 2.45
604 618 8.128582 GCTTCGTCAATGTTTTATTCCATCATA 58.871 33.333 0.00 0.00 0.00 2.15
778 794 4.541779 CAACATCTGTCGCTACTCCTATC 58.458 47.826 0.00 0.00 0.00 2.08
817 833 2.035449 CCGAATGTCCGAGCCTAATACA 59.965 50.000 0.00 0.00 0.00 2.29
897 913 3.936203 GGACTGGGTCACACGCCA 61.936 66.667 0.14 0.00 33.68 5.69
1241 1257 2.194212 ATGGAGGATACGACGCGCT 61.194 57.895 5.73 0.00 46.39 5.92
1977 2005 4.759205 GGGGCGAGGGGCAACATT 62.759 66.667 0.00 0.00 46.16 2.71
1978 2006 3.140814 GGGCGAGGGGCAACATTC 61.141 66.667 0.00 0.00 46.16 2.67
1979 2007 3.508840 GGCGAGGGGCAACATTCG 61.509 66.667 0.00 0.00 46.16 3.34
1980 2008 2.746277 GCGAGGGGCAACATTCGT 60.746 61.111 0.00 0.00 43.31 3.85
1981 2009 2.750888 GCGAGGGGCAACATTCGTC 61.751 63.158 0.00 0.00 43.31 4.20
1982 2010 2.452813 CGAGGGGCAACATTCGTCG 61.453 63.158 0.00 0.00 38.61 5.12
1983 2011 2.746277 AGGGGCAACATTCGTCGC 60.746 61.111 0.00 0.00 39.74 5.19
1984 2012 4.160635 GGGGCAACATTCGTCGCG 62.161 66.667 0.00 0.00 39.74 5.87
1985 2013 4.811761 GGGCAACATTCGTCGCGC 62.812 66.667 0.00 0.00 39.74 6.86
1986 2014 4.811761 GGCAACATTCGTCGCGCC 62.812 66.667 0.00 0.00 0.00 6.53
2081 2109 7.624360 ACATACTGAGAGAGAGTAAGTTCAG 57.376 40.000 0.00 0.00 38.34 3.02
2150 2178 0.398696 AACAACATGCCCGGTGAGTA 59.601 50.000 0.00 0.00 0.00 2.59
2154 2182 1.821216 ACATGCCCGGTGAGTAAAAG 58.179 50.000 0.00 0.00 0.00 2.27
2155 2183 1.073284 ACATGCCCGGTGAGTAAAAGT 59.927 47.619 0.00 0.00 0.00 2.66
2156 2184 2.303600 ACATGCCCGGTGAGTAAAAGTA 59.696 45.455 0.00 0.00 0.00 2.24
2157 2185 3.054655 ACATGCCCGGTGAGTAAAAGTAT 60.055 43.478 0.00 0.00 0.00 2.12
2159 2187 4.822685 TGCCCGGTGAGTAAAAGTATTA 57.177 40.909 0.00 0.00 0.00 0.98
2160 2188 5.362105 TGCCCGGTGAGTAAAAGTATTAT 57.638 39.130 0.00 0.00 0.00 1.28
2261 2292 2.943690 CTGATGAAGATGCCAAGTCCAG 59.056 50.000 0.00 0.00 0.00 3.86
2287 2318 2.526304 TCCAGAAGTCACCAAAGTCG 57.474 50.000 0.00 0.00 0.00 4.18
2310 2341 2.424601 CACCAACAAAGCATCCGATGAT 59.575 45.455 12.79 2.41 0.00 2.45
2324 2355 2.288457 CCGATGATGATAGCAACGACCT 60.288 50.000 0.00 0.00 0.00 3.85
2349 2380 2.256461 GAAGCAGCAGCAAACGGG 59.744 61.111 3.17 0.00 45.49 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 9.877178 ACAAACATTCAAACACCTAATAAACAA 57.123 25.926 0.00 0.00 0.00 2.83
203 210 6.400091 GCGTCTTCTGTAGATATTAATTGCCG 60.400 42.308 0.00 0.00 34.79 5.69
439 453 7.225931 GCTAGATAATTTGTATCAAACCGGTGA 59.774 37.037 8.52 1.36 0.00 4.02
495 509 2.935849 TGATGTCGCGTTGCAAATCTAT 59.064 40.909 5.77 0.00 0.00 1.98
508 522 2.128035 CCGACCTTAAGATGATGTCGC 58.872 52.381 19.54 0.00 45.37 5.19
517 531 0.179111 CTGCATCGCCGACCTTAAGA 60.179 55.000 3.36 0.00 0.00 2.10
518 532 0.460284 ACTGCATCGCCGACCTTAAG 60.460 55.000 0.00 0.00 0.00 1.85
519 533 0.739462 CACTGCATCGCCGACCTTAA 60.739 55.000 0.00 0.00 0.00 1.85
520 534 1.153647 CACTGCATCGCCGACCTTA 60.154 57.895 0.00 0.00 0.00 2.69
521 535 2.434884 CACTGCATCGCCGACCTT 60.435 61.111 0.00 0.00 0.00 3.50
522 536 4.457496 CCACTGCATCGCCGACCT 62.457 66.667 0.00 0.00 0.00 3.85
523 537 4.760047 ACCACTGCATCGCCGACC 62.760 66.667 0.00 0.00 0.00 4.79
524 538 3.188786 GACCACTGCATCGCCGAC 61.189 66.667 0.00 0.00 0.00 4.79
525 539 2.449031 AAAGACCACTGCATCGCCGA 62.449 55.000 0.00 0.00 0.00 5.54
526 540 1.970917 GAAAGACCACTGCATCGCCG 61.971 60.000 0.00 0.00 0.00 6.46
527 541 0.955428 TGAAAGACCACTGCATCGCC 60.955 55.000 0.00 0.00 0.00 5.54
528 542 0.874390 TTGAAAGACCACTGCATCGC 59.126 50.000 0.00 0.00 0.00 4.58
529 543 2.146342 AGTTGAAAGACCACTGCATCG 58.854 47.619 0.00 0.00 0.00 3.84
530 544 2.158449 CGAGTTGAAAGACCACTGCATC 59.842 50.000 0.00 0.00 0.00 3.91
531 545 2.146342 CGAGTTGAAAGACCACTGCAT 58.854 47.619 0.00 0.00 0.00 3.96
532 546 1.134521 ACGAGTTGAAAGACCACTGCA 60.135 47.619 0.00 0.00 0.00 4.41
533 547 1.261619 CACGAGTTGAAAGACCACTGC 59.738 52.381 0.00 0.00 0.00 4.40
534 548 1.867233 CCACGAGTTGAAAGACCACTG 59.133 52.381 0.00 0.00 0.00 3.66
535 549 1.760613 TCCACGAGTTGAAAGACCACT 59.239 47.619 0.00 0.00 0.00 4.00
536 550 2.234300 TCCACGAGTTGAAAGACCAC 57.766 50.000 0.00 0.00 0.00 4.16
537 551 2.557317 GTTCCACGAGTTGAAAGACCA 58.443 47.619 0.00 0.00 0.00 4.02
538 552 1.871676 GGTTCCACGAGTTGAAAGACC 59.128 52.381 0.00 0.00 0.00 3.85
539 553 2.557317 TGGTTCCACGAGTTGAAAGAC 58.443 47.619 0.00 0.00 0.00 3.01
540 554 2.940410 GTTGGTTCCACGAGTTGAAAGA 59.060 45.455 0.00 0.00 0.00 2.52
541 555 2.680841 TGTTGGTTCCACGAGTTGAAAG 59.319 45.455 0.00 0.00 0.00 2.62
542 556 2.712709 TGTTGGTTCCACGAGTTGAAA 58.287 42.857 0.00 0.00 0.00 2.69
543 557 2.404923 TGTTGGTTCCACGAGTTGAA 57.595 45.000 0.00 0.00 0.00 2.69
544 558 2.093394 TCTTGTTGGTTCCACGAGTTGA 60.093 45.455 0.00 0.00 0.00 3.18
545 559 2.285083 TCTTGTTGGTTCCACGAGTTG 58.715 47.619 0.00 0.00 0.00 3.16
546 560 2.702592 TCTTGTTGGTTCCACGAGTT 57.297 45.000 0.00 0.00 0.00 3.01
547 561 2.930826 ATCTTGTTGGTTCCACGAGT 57.069 45.000 0.00 0.00 0.00 4.18
548 562 5.334879 CCTTAAATCTTGTTGGTTCCACGAG 60.335 44.000 0.00 0.00 0.00 4.18
549 563 4.517453 CCTTAAATCTTGTTGGTTCCACGA 59.483 41.667 0.00 0.00 0.00 4.35
550 564 4.794169 CCTTAAATCTTGTTGGTTCCACG 58.206 43.478 0.00 0.00 0.00 4.94
551 565 4.556233 GCCTTAAATCTTGTTGGTTCCAC 58.444 43.478 0.00 0.00 0.00 4.02
552 566 3.254657 CGCCTTAAATCTTGTTGGTTCCA 59.745 43.478 0.00 0.00 0.00 3.53
553 567 3.504520 TCGCCTTAAATCTTGTTGGTTCC 59.495 43.478 0.00 0.00 0.00 3.62
554 568 4.215613 ACTCGCCTTAAATCTTGTTGGTTC 59.784 41.667 0.00 0.00 0.00 3.62
555 569 4.023193 CACTCGCCTTAAATCTTGTTGGTT 60.023 41.667 0.00 0.00 0.00 3.67
556 570 3.502211 CACTCGCCTTAAATCTTGTTGGT 59.498 43.478 0.00 0.00 0.00 3.67
557 571 3.670627 GCACTCGCCTTAAATCTTGTTGG 60.671 47.826 0.00 0.00 0.00 3.77
558 572 3.189287 AGCACTCGCCTTAAATCTTGTTG 59.811 43.478 0.00 0.00 39.83 3.33
559 573 3.412386 AGCACTCGCCTTAAATCTTGTT 58.588 40.909 0.00 0.00 39.83 2.83
560 574 3.059352 AGCACTCGCCTTAAATCTTGT 57.941 42.857 0.00 0.00 39.83 3.16
561 575 3.484229 CGAAGCACTCGCCTTAAATCTTG 60.484 47.826 0.00 0.00 41.49 3.02
562 576 2.673368 CGAAGCACTCGCCTTAAATCTT 59.327 45.455 0.00 0.00 41.49 2.40
563 577 2.271800 CGAAGCACTCGCCTTAAATCT 58.728 47.619 0.00 0.00 41.49 2.40
564 578 2.721129 CGAAGCACTCGCCTTAAATC 57.279 50.000 0.00 0.00 41.49 2.17
574 588 5.795441 GGAATAAAACATTGACGAAGCACTC 59.205 40.000 0.00 0.00 0.00 3.51
575 589 5.240623 TGGAATAAAACATTGACGAAGCACT 59.759 36.000 0.00 0.00 0.00 4.40
576 590 5.457140 TGGAATAAAACATTGACGAAGCAC 58.543 37.500 0.00 0.00 0.00 4.40
577 591 5.697473 TGGAATAAAACATTGACGAAGCA 57.303 34.783 0.00 0.00 0.00 3.91
578 592 6.321717 TGATGGAATAAAACATTGACGAAGC 58.678 36.000 0.00 0.00 0.00 3.86
625 639 9.705290 GTGCATCCTCCTTTTCTAAAATAAAAA 57.295 29.630 0.00 0.00 0.00 1.94
626 640 8.311109 GGTGCATCCTCCTTTTCTAAAATAAAA 58.689 33.333 0.00 0.00 0.00 1.52
627 641 7.093509 GGGTGCATCCTCCTTTTCTAAAATAAA 60.094 37.037 9.39 0.00 36.25 1.40
628 642 6.379988 GGGTGCATCCTCCTTTTCTAAAATAA 59.620 38.462 9.39 0.00 36.25 1.40
629 643 5.891551 GGGTGCATCCTCCTTTTCTAAAATA 59.108 40.000 9.39 0.00 36.25 1.40
630 644 4.711846 GGGTGCATCCTCCTTTTCTAAAAT 59.288 41.667 9.39 0.00 36.25 1.82
631 645 4.086457 GGGTGCATCCTCCTTTTCTAAAA 58.914 43.478 9.39 0.00 36.25 1.52
632 646 3.563479 GGGGTGCATCCTCCTTTTCTAAA 60.563 47.826 17.44 0.00 36.25 1.85
817 833 4.895297 AGGATTTGGTGTGATGTCTGTTTT 59.105 37.500 0.00 0.00 0.00 2.43
1452 1473 1.447140 CTTCGCGGGTTTCGGATCA 60.447 57.895 6.13 0.00 39.69 2.92
1632 1653 2.994417 GGGTGCCGCCAAATCCAA 60.994 61.111 0.00 0.00 39.65 3.53
1811 1837 3.245650 GGCTTCTCCCCATCCTCC 58.754 66.667 0.00 0.00 0.00 4.30
1982 2010 2.202518 TAGTGTTACTCGCGGCGC 60.203 61.111 24.21 24.21 0.00 6.53
1983 2011 1.870901 GGTAGTGTTACTCGCGGCG 60.871 63.158 17.70 17.70 0.00 6.46
1984 2012 1.517913 GGGTAGTGTTACTCGCGGC 60.518 63.158 6.13 0.00 0.00 6.53
1985 2013 0.100146 GAGGGTAGTGTTACTCGCGG 59.900 60.000 6.13 0.00 35.32 6.46
1986 2014 1.093159 AGAGGGTAGTGTTACTCGCG 58.907 55.000 0.00 0.00 35.47 5.87
1987 2015 2.490903 TGAAGAGGGTAGTGTTACTCGC 59.509 50.000 0.00 0.00 35.32 5.03
1988 2016 4.398358 TCATGAAGAGGGTAGTGTTACTCG 59.602 45.833 0.00 0.00 35.32 4.18
1989 2017 5.916661 TCATGAAGAGGGTAGTGTTACTC 57.083 43.478 0.00 0.00 0.00 2.59
1990 2018 8.424918 CAATATCATGAAGAGGGTAGTGTTACT 58.575 37.037 0.00 0.00 0.00 2.24
1991 2019 8.421784 TCAATATCATGAAGAGGGTAGTGTTAC 58.578 37.037 0.00 0.00 0.00 2.50
1992 2020 8.547481 TCAATATCATGAAGAGGGTAGTGTTA 57.453 34.615 0.00 0.00 0.00 2.41
1993 2021 7.437713 TCAATATCATGAAGAGGGTAGTGTT 57.562 36.000 0.00 0.00 0.00 3.32
1994 2022 7.623999 ATCAATATCATGAAGAGGGTAGTGT 57.376 36.000 0.00 0.00 32.06 3.55
2058 2086 7.624360 ACTGAACTTACTCTCTCTCAGTATG 57.376 40.000 0.84 0.00 41.19 2.39
2081 2109 1.067142 TGAGTGCTCCATCGGTTGTAC 60.067 52.381 0.00 0.00 0.00 2.90
2261 2292 0.833949 GGTGACTTCTGGATCCTCCC 59.166 60.000 14.23 1.97 35.03 4.30
2287 2318 1.234821 TCGGATGCTTTGTTGGTGAC 58.765 50.000 0.00 0.00 0.00 3.67
2310 2341 5.543714 TCACTAAAAAGGTCGTTGCTATCA 58.456 37.500 0.00 0.00 0.00 2.15
2324 2355 4.111916 GTTTGCTGCTGCTTCACTAAAAA 58.888 39.130 17.00 3.50 40.48 1.94


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

AutoCloner maintained by Alex Coulton.