Multiple sequence alignment - TraesCS1D01G103600

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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 TraesCS1D01G103600 chr1D 100.000 2942 0 0 1 2942 93111353 93114294 0.000000e+00 5433
1 TraesCS1D01G103600 chr1B 92.178 2365 134 25 604 2942 148434251 148436590 0.000000e+00 3295
2 TraesCS1D01G103600 chr1B 97.746 488 8 2 1 487 148433766 148434251 0.000000e+00 837
3 TraesCS1D01G103600 chr1A 92.462 2189 94 20 811 2942 91060143 91057969 0.000000e+00 3062
4 TraesCS1D01G103600 chr1A 94.444 432 17 3 2 429 91060634 91060206 0.000000e+00 658
5 TraesCS1D01G103600 chr1A 82.129 263 41 6 525 782 558890113 558890374 1.370000e-53 220
6 TraesCS1D01G103600 chr1A 91.250 80 3 3 445 521 91060223 91060145 4.010000e-19 106
7 TraesCS1D01G103600 chr5A 83.271 269 39 6 525 788 703192975 703192708 2.930000e-60 243
8 TraesCS1D01G103600 chr5D 83.209 268 39 5 526 788 360026023 360025757 1.050000e-59 241
9 TraesCS1D01G103600 chr5B 83.146 267 41 4 523 785 400546035 400546301 1.050000e-59 241
10 TraesCS1D01G103600 chr4A 83.209 268 39 6 523 785 666201994 666202260 1.050000e-59 241
11 TraesCS1D01G103600 chr6A 82.955 264 37 8 524 782 127170890 127171150 6.340000e-57 231
12 TraesCS1D01G103600 chr2B 82.156 269 42 6 525 788 770696751 770696484 2.950000e-55 226
13 TraesCS1D01G103600 chr6B 81.481 270 44 6 524 788 51423850 51423582 1.780000e-52 217


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 TraesCS1D01G103600 chr1D 93111353 93114294 2941 False 5433.000000 5433 100.000000 1 2942 1 chr1D.!!$F1 2941
1 TraesCS1D01G103600 chr1B 148433766 148436590 2824 False 2066.000000 3295 94.962000 1 2942 2 chr1B.!!$F1 2941
2 TraesCS1D01G103600 chr1A 91057969 91060634 2665 True 1275.333333 3062 92.718667 2 2942 3 chr1A.!!$R1 2940

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
742 752 0.689745 TTCGGAGGTGGTCATAGGGG 60.69 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 2190 0.314935 GAACATGGTGTGTGGCCTTG 59.685 55.0 3.32 0.0 41.14 3.61 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
44 48 8.068110 TCCGATCCTGGGATATCTTCTAATATT 58.932 37.037 2.05 0.00 34.60 1.28
302 307 2.309755 AGAGAAATCTGATGGCCCAACA 59.690 45.455 0.00 0.00 0.00 3.33
428 434 7.286087 TGCATCTGATATATTGCAGGAGTTTTT 59.714 33.333 5.83 0.00 39.98 1.94
429 435 8.786898 GCATCTGATATATTGCAGGAGTTTTTA 58.213 33.333 2.83 0.00 35.22 1.52
500 509 9.683069 AGCACAAAAATATCACAAACTTTAGAG 57.317 29.630 0.00 0.00 0.00 2.43
531 540 4.123497 ACTATGTGTTAGCTGCGAATCA 57.877 40.909 0.00 2.63 0.00 2.57
532 541 4.503910 ACTATGTGTTAGCTGCGAATCAA 58.496 39.130 0.00 0.00 0.00 2.57
533 542 3.747099 ATGTGTTAGCTGCGAATCAAC 57.253 42.857 0.00 0.00 0.00 3.18
534 543 1.804151 TGTGTTAGCTGCGAATCAACC 59.196 47.619 0.00 0.00 0.00 3.77
535 544 2.076863 GTGTTAGCTGCGAATCAACCT 58.923 47.619 0.00 0.00 0.00 3.50
536 545 2.076100 TGTTAGCTGCGAATCAACCTG 58.924 47.619 0.00 0.00 0.00 4.00
537 546 2.076863 GTTAGCTGCGAATCAACCTGT 58.923 47.619 0.00 0.00 0.00 4.00
538 547 3.259064 GTTAGCTGCGAATCAACCTGTA 58.741 45.455 0.00 0.00 0.00 2.74
539 548 2.015736 AGCTGCGAATCAACCTGTAG 57.984 50.000 0.00 0.00 0.00 2.74
540 549 1.276421 AGCTGCGAATCAACCTGTAGT 59.724 47.619 0.00 0.00 0.00 2.73
541 550 2.076863 GCTGCGAATCAACCTGTAGTT 58.923 47.619 0.00 0.00 40.16 2.24
542 551 3.056107 AGCTGCGAATCAACCTGTAGTTA 60.056 43.478 0.00 0.00 36.18 2.24
543 552 3.307242 GCTGCGAATCAACCTGTAGTTAG 59.693 47.826 0.00 0.00 36.18 2.34
544 553 4.744570 CTGCGAATCAACCTGTAGTTAGA 58.255 43.478 0.00 0.00 36.18 2.10
545 554 5.339008 TGCGAATCAACCTGTAGTTAGAT 57.661 39.130 0.00 0.00 36.18 1.98
546 555 5.109210 TGCGAATCAACCTGTAGTTAGATG 58.891 41.667 0.00 0.00 36.18 2.90
547 556 4.508124 GCGAATCAACCTGTAGTTAGATGG 59.492 45.833 0.00 0.00 36.18 3.51
548 557 5.661458 CGAATCAACCTGTAGTTAGATGGT 58.339 41.667 0.00 0.00 36.18 3.55
549 558 6.106673 CGAATCAACCTGTAGTTAGATGGTT 58.893 40.000 0.00 0.00 41.12 3.67
550 559 7.262772 CGAATCAACCTGTAGTTAGATGGTTA 58.737 38.462 0.00 0.00 38.76 2.85
551 560 7.435488 CGAATCAACCTGTAGTTAGATGGTTAG 59.565 40.741 0.00 0.00 38.76 2.34
552 561 6.540438 TCAACCTGTAGTTAGATGGTTAGG 57.460 41.667 0.00 0.00 38.76 2.69
553 562 6.021030 TCAACCTGTAGTTAGATGGTTAGGT 58.979 40.000 0.00 0.00 38.76 3.08
554 563 7.184161 TCAACCTGTAGTTAGATGGTTAGGTA 58.816 38.462 0.00 0.00 38.76 3.08
555 564 7.341256 TCAACCTGTAGTTAGATGGTTAGGTAG 59.659 40.741 0.00 0.00 38.76 3.18
556 565 6.978261 ACCTGTAGTTAGATGGTTAGGTAGA 58.022 40.000 0.00 0.00 35.66 2.59
557 566 6.832900 ACCTGTAGTTAGATGGTTAGGTAGAC 59.167 42.308 0.00 0.00 35.66 2.59
558 567 6.832384 CCTGTAGTTAGATGGTTAGGTAGACA 59.168 42.308 0.00 0.00 0.00 3.41
559 568 7.013464 CCTGTAGTTAGATGGTTAGGTAGACAG 59.987 44.444 0.00 0.00 0.00 3.51
560 569 7.408543 TGTAGTTAGATGGTTAGGTAGACAGT 58.591 38.462 0.00 0.00 0.00 3.55
561 570 6.777213 AGTTAGATGGTTAGGTAGACAGTG 57.223 41.667 0.00 0.00 0.00 3.66
562 571 5.657302 AGTTAGATGGTTAGGTAGACAGTGG 59.343 44.000 0.00 0.00 0.00 4.00
563 572 4.062490 AGATGGTTAGGTAGACAGTGGT 57.938 45.455 0.00 0.00 0.00 4.16
564 573 5.202746 AGATGGTTAGGTAGACAGTGGTA 57.797 43.478 0.00 0.00 0.00 3.25
565 574 5.778542 AGATGGTTAGGTAGACAGTGGTAT 58.221 41.667 0.00 0.00 0.00 2.73
566 575 5.834204 AGATGGTTAGGTAGACAGTGGTATC 59.166 44.000 0.00 0.00 0.00 2.24
567 576 4.284178 TGGTTAGGTAGACAGTGGTATCC 58.716 47.826 0.00 0.00 0.00 2.59
568 577 3.640498 GGTTAGGTAGACAGTGGTATCCC 59.360 52.174 0.00 0.00 0.00 3.85
569 578 4.544683 GTTAGGTAGACAGTGGTATCCCT 58.455 47.826 0.00 0.00 0.00 4.20
570 579 5.399497 GGTTAGGTAGACAGTGGTATCCCTA 60.399 48.000 0.00 0.00 0.00 3.53
571 580 4.894252 AGGTAGACAGTGGTATCCCTAA 57.106 45.455 0.00 0.00 0.00 2.69
572 581 4.544683 AGGTAGACAGTGGTATCCCTAAC 58.455 47.826 0.00 0.00 0.00 2.34
573 582 3.640498 GGTAGACAGTGGTATCCCTAACC 59.360 52.174 0.00 0.00 37.53 2.85
574 583 2.760581 AGACAGTGGTATCCCTAACCC 58.239 52.381 0.00 0.00 36.06 4.11
575 584 2.045326 AGACAGTGGTATCCCTAACCCA 59.955 50.000 0.00 0.00 36.06 4.51
576 585 3.046374 GACAGTGGTATCCCTAACCCAT 58.954 50.000 0.00 0.00 36.06 4.00
577 586 3.046374 ACAGTGGTATCCCTAACCCATC 58.954 50.000 0.00 0.00 36.06 3.51
578 587 3.045634 CAGTGGTATCCCTAACCCATCA 58.954 50.000 0.00 0.00 36.06 3.07
579 588 3.071602 CAGTGGTATCCCTAACCCATCAG 59.928 52.174 0.00 0.00 36.06 2.90
580 589 2.372172 GTGGTATCCCTAACCCATCAGG 59.628 54.545 0.00 0.00 43.78 3.86
596 605 5.594926 CCATCAGGGTTTAAATCTTGATGC 58.405 41.667 32.71 5.31 32.91 3.91
597 606 5.361857 CCATCAGGGTTTAAATCTTGATGCT 59.638 40.000 32.71 12.05 32.91 3.79
598 607 6.460676 CCATCAGGGTTTAAATCTTGATGCTC 60.461 42.308 32.71 4.40 32.91 4.26
599 608 4.635765 TCAGGGTTTAAATCTTGATGCTCG 59.364 41.667 9.07 0.00 0.00 5.03
600 609 3.378427 AGGGTTTAAATCTTGATGCTCGC 59.622 43.478 0.00 0.00 0.00 5.03
601 610 3.128589 GGGTTTAAATCTTGATGCTCGCA 59.871 43.478 0.00 0.00 0.00 5.10
602 611 4.202050 GGGTTTAAATCTTGATGCTCGCAT 60.202 41.667 3.70 3.70 39.69 4.73
603 612 5.343249 GGTTTAAATCTTGATGCTCGCATT 58.657 37.500 5.79 0.00 36.70 3.56
617 627 9.140286 TGATGCTCGCATTTATTAGTAGATTAC 57.860 33.333 5.79 0.00 36.70 1.89
699 709 4.201724 GCATTTGGTGACTACGTCAATCTC 60.202 45.833 0.00 0.00 44.49 2.75
714 724 6.145535 CGTCAATCTCAAGATGATATGTCGA 58.854 40.000 0.00 0.00 34.49 4.20
718 728 6.890979 ATCTCAAGATGATATGTCGACTCA 57.109 37.500 17.92 12.65 32.68 3.41
723 733 6.319911 TCAAGATGATATGTCGACTCAGTCTT 59.680 38.462 17.92 16.85 0.00 3.01
733 743 0.969894 ACTCAGTCTTTCGGAGGTGG 59.030 55.000 0.00 0.00 41.46 4.61
739 749 2.761208 AGTCTTTCGGAGGTGGTCATAG 59.239 50.000 0.00 0.00 0.00 2.23
742 752 0.689745 TTCGGAGGTGGTCATAGGGG 60.690 60.000 0.00 0.00 0.00 4.79
745 755 1.718280 GGAGGTGGTCATAGGGGTAG 58.282 60.000 0.00 0.00 0.00 3.18
746 756 1.219724 GGAGGTGGTCATAGGGGTAGA 59.780 57.143 0.00 0.00 0.00 2.59
757 767 2.304221 AGGGGTAGAGCATGCGTATA 57.696 50.000 13.01 3.69 0.00 1.47
758 768 2.821437 AGGGGTAGAGCATGCGTATAT 58.179 47.619 13.01 0.00 0.00 0.86
759 769 2.497675 AGGGGTAGAGCATGCGTATATG 59.502 50.000 13.01 0.00 0.00 1.78
762 772 4.315803 GGGTAGAGCATGCGTATATGTTT 58.684 43.478 13.01 0.00 0.00 2.83
768 778 7.170393 AGAGCATGCGTATATGTTTATAGGA 57.830 36.000 13.01 0.00 30.93 2.94
781 791 7.658179 ATGTTTATAGGAATGAGTGTATGCG 57.342 36.000 0.00 0.00 0.00 4.73
782 792 5.465390 TGTTTATAGGAATGAGTGTATGCGC 59.535 40.000 0.00 0.00 0.00 6.09
791 801 2.356695 TGAGTGTATGCGCGTATAGTGT 59.643 45.455 17.50 4.58 0.00 3.55
1161 1197 2.427245 CGAGATCCCAGAGGCCGTT 61.427 63.158 0.00 0.00 0.00 4.44
1411 1447 1.737029 CGCAAGGTGATCACTGATCGT 60.737 52.381 24.50 4.24 41.51 3.73
1412 1448 1.662629 GCAAGGTGATCACTGATCGTG 59.337 52.381 24.50 16.30 41.51 4.35
1486 1533 4.023279 ACACGCACTGATTAATTTGCTTCA 60.023 37.500 12.92 0.00 32.56 3.02
1666 1713 3.241530 TCCAACTGCACCGCCTCT 61.242 61.111 0.00 0.00 0.00 3.69
1700 1747 1.592223 GAGCCACAACTCTACCGCT 59.408 57.895 0.00 0.00 33.69 5.52
1736 1783 2.112190 GGGAGGAGTTTTCGAGGATCT 58.888 52.381 0.00 0.00 0.00 2.75
1743 1790 1.134907 GTTTTCGAGGATCTACCGGCA 60.135 52.381 0.00 0.00 44.74 5.69
1810 1857 2.610859 GGGGGTCCAGAGAAGGCA 60.611 66.667 0.00 0.00 0.00 4.75
1834 1881 2.743928 CTGGGCAAGGACGTGCTC 60.744 66.667 10.99 6.67 45.83 4.26
1897 1944 2.515854 GCCATGCTCATGATCTCCAAT 58.484 47.619 11.17 0.00 41.20 3.16
1914 1961 1.134640 CAATTCGTACCGATGACCCCA 60.135 52.381 0.00 0.00 35.23 4.96
1915 1962 1.196911 ATTCGTACCGATGACCCCAA 58.803 50.000 0.00 0.00 35.23 4.12
1919 1967 1.229561 TACCGATGACCCCAACCCA 60.230 57.895 0.00 0.00 0.00 4.51
1922 1970 2.602676 CGATGACCCCAACCCACCT 61.603 63.158 0.00 0.00 0.00 4.00
1928 1976 1.071314 ACCCCAACCCACCTGAATCA 61.071 55.000 0.00 0.00 0.00 2.57
1981 2029 5.326200 TCTTCTAGAACATTTCGGAGGTC 57.674 43.478 0.00 0.00 34.02 3.85
1984 2032 2.080286 AGAACATTTCGGAGGTCGTG 57.920 50.000 0.00 0.00 40.32 4.35
1992 2043 0.251033 TCGGAGGTCGTGGAAGAAGA 60.251 55.000 0.00 0.00 40.32 2.87
1993 2044 0.601558 CGGAGGTCGTGGAAGAAGAA 59.398 55.000 0.00 0.00 0.00 2.52
1994 2045 1.000506 CGGAGGTCGTGGAAGAAGAAA 59.999 52.381 0.00 0.00 0.00 2.52
2110 2162 4.137116 AGTGTTGCTGAAGTACTGAACA 57.863 40.909 0.00 0.00 0.00 3.18
2120 2172 4.772624 TGAAGTACTGAACAGGTCTGCTAT 59.227 41.667 0.00 0.00 0.00 2.97
2138 2190 5.065914 TGCTATTCTGCTACCATTTCATCC 58.934 41.667 0.00 0.00 0.00 3.51
2182 2234 7.515861 TCCCAATAGAGATACCAATAACATGGA 59.484 37.037 0.00 0.00 43.54 3.41
2209 2262 0.591170 GGCAAGCAAGCAAAGACGTA 59.409 50.000 0.00 0.00 35.83 3.57
2307 2360 8.371699 AGCTAATTTACAGATCCTACAGATTCC 58.628 37.037 0.00 0.00 34.42 3.01
2313 2366 3.505680 CAGATCCTACAGATTCCTCCTCG 59.494 52.174 0.00 0.00 34.42 4.63
2314 2367 3.139397 AGATCCTACAGATTCCTCCTCGT 59.861 47.826 0.00 0.00 34.42 4.18
2327 2380 2.232452 CCTCCTCGTCTTCTTGTGTGAT 59.768 50.000 0.00 0.00 0.00 3.06
2341 2394 1.153784 GTGATGGGTTTGCGCCATG 60.154 57.895 4.18 0.00 0.00 3.66
2342 2395 1.606025 TGATGGGTTTGCGCCATGT 60.606 52.632 4.18 0.00 0.00 3.21
2343 2396 1.139520 GATGGGTTTGCGCCATGTC 59.860 57.895 4.18 0.00 0.00 3.06
2344 2397 2.597117 GATGGGTTTGCGCCATGTCG 62.597 60.000 4.18 0.00 0.00 4.35
2394 2448 3.044305 GAGAACAGCCGCTGCGTT 61.044 61.111 20.56 8.12 44.33 4.84
2453 2507 2.016961 CCTGCCCGAATTCATCACG 58.983 57.895 6.22 0.00 0.00 4.35
2515 2574 2.442236 ACAAGGGCAATGTCTATGGG 57.558 50.000 0.00 0.00 0.00 4.00
2646 2705 6.765036 CGACTACTCCTTAGGATAGTGTACAA 59.235 42.308 20.19 0.00 31.39 2.41
2687 2746 8.106462 TGTTGAACTCCTGAATATCACCAAATA 58.894 33.333 0.00 0.00 0.00 1.40
2688 2747 8.398665 GTTGAACTCCTGAATATCACCAAATAC 58.601 37.037 0.00 0.00 0.00 1.89
2689 2748 7.861629 TGAACTCCTGAATATCACCAAATACT 58.138 34.615 0.00 0.00 0.00 2.12
2690 2749 8.988060 TGAACTCCTGAATATCACCAAATACTA 58.012 33.333 0.00 0.00 0.00 1.82
2691 2750 9.482627 GAACTCCTGAATATCACCAAATACTAG 57.517 37.037 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 48 5.116180 GTGTGCAAATAGTCTATGGCTACA 58.884 41.667 14.49 13.44 0.00 2.74
54 58 4.084066 TGTGATTCACGTGTGCAAATAGTC 60.084 41.667 16.51 1.10 37.14 2.59
63 67 1.304254 TGGGTTGTGATTCACGTGTG 58.696 50.000 16.51 0.00 37.14 3.82
385 391 1.507713 CAACTCGTGTGATTGCGCG 60.508 57.895 0.00 0.00 42.91 6.86
510 519 4.123497 TGATTCGCAGCTAACACATAGT 57.877 40.909 0.00 0.00 33.87 2.12
511 520 4.260375 GGTTGATTCGCAGCTAACACATAG 60.260 45.833 0.00 0.00 34.52 2.23
512 521 3.621268 GGTTGATTCGCAGCTAACACATA 59.379 43.478 0.00 0.00 0.00 2.29
513 522 2.420022 GGTTGATTCGCAGCTAACACAT 59.580 45.455 0.00 0.00 0.00 3.21
514 523 1.804151 GGTTGATTCGCAGCTAACACA 59.196 47.619 0.00 0.00 0.00 3.72
515 524 2.076863 AGGTTGATTCGCAGCTAACAC 58.923 47.619 0.00 0.00 0.00 3.32
516 525 2.076100 CAGGTTGATTCGCAGCTAACA 58.924 47.619 0.00 0.00 0.00 2.41
517 526 2.076863 ACAGGTTGATTCGCAGCTAAC 58.923 47.619 0.00 0.00 0.00 2.34
519 528 2.496070 ACTACAGGTTGATTCGCAGCTA 59.504 45.455 0.00 0.00 0.00 3.32
520 529 1.276421 ACTACAGGTTGATTCGCAGCT 59.724 47.619 0.00 0.00 0.00 4.24
521 530 1.726853 ACTACAGGTTGATTCGCAGC 58.273 50.000 0.00 0.00 0.00 5.25
522 531 4.744570 TCTAACTACAGGTTGATTCGCAG 58.255 43.478 0.00 0.00 38.75 5.18
523 532 4.794278 TCTAACTACAGGTTGATTCGCA 57.206 40.909 0.00 0.00 38.75 5.10
524 533 4.508124 CCATCTAACTACAGGTTGATTCGC 59.492 45.833 0.00 0.00 38.75 4.70
525 534 5.661458 ACCATCTAACTACAGGTTGATTCG 58.339 41.667 0.00 0.00 38.75 3.34
526 535 7.711339 CCTAACCATCTAACTACAGGTTGATTC 59.289 40.741 0.00 0.00 42.19 2.52
527 536 7.182206 ACCTAACCATCTAACTACAGGTTGATT 59.818 37.037 0.00 0.00 42.19 2.57
528 537 6.672657 ACCTAACCATCTAACTACAGGTTGAT 59.327 38.462 0.00 0.00 42.19 2.57
529 538 6.021030 ACCTAACCATCTAACTACAGGTTGA 58.979 40.000 0.00 0.00 42.19 3.18
530 539 6.295719 ACCTAACCATCTAACTACAGGTTG 57.704 41.667 0.00 0.00 42.19 3.77
531 540 7.341512 GTCTACCTAACCATCTAACTACAGGTT 59.658 40.741 0.00 0.00 44.23 3.50
532 541 6.832900 GTCTACCTAACCATCTAACTACAGGT 59.167 42.308 0.00 0.00 38.63 4.00
533 542 6.832384 TGTCTACCTAACCATCTAACTACAGG 59.168 42.308 0.00 0.00 0.00 4.00
534 543 7.556996 ACTGTCTACCTAACCATCTAACTACAG 59.443 40.741 0.00 0.00 35.43 2.74
535 544 7.338703 CACTGTCTACCTAACCATCTAACTACA 59.661 40.741 0.00 0.00 0.00 2.74
536 545 7.201803 CCACTGTCTACCTAACCATCTAACTAC 60.202 44.444 0.00 0.00 0.00 2.73
537 546 6.832384 CCACTGTCTACCTAACCATCTAACTA 59.168 42.308 0.00 0.00 0.00 2.24
538 547 5.657302 CCACTGTCTACCTAACCATCTAACT 59.343 44.000 0.00 0.00 0.00 2.24
539 548 5.421374 ACCACTGTCTACCTAACCATCTAAC 59.579 44.000 0.00 0.00 0.00 2.34
540 549 5.586877 ACCACTGTCTACCTAACCATCTAA 58.413 41.667 0.00 0.00 0.00 2.10
541 550 5.202746 ACCACTGTCTACCTAACCATCTA 57.797 43.478 0.00 0.00 0.00 1.98
542 551 4.062490 ACCACTGTCTACCTAACCATCT 57.938 45.455 0.00 0.00 0.00 2.90
543 552 5.010820 GGATACCACTGTCTACCTAACCATC 59.989 48.000 0.00 0.00 0.00 3.51
544 553 4.900054 GGATACCACTGTCTACCTAACCAT 59.100 45.833 0.00 0.00 0.00 3.55
545 554 4.284178 GGATACCACTGTCTACCTAACCA 58.716 47.826 0.00 0.00 0.00 3.67
546 555 4.933505 GGATACCACTGTCTACCTAACC 57.066 50.000 0.00 0.00 0.00 2.85
573 582 5.361857 AGCATCAAGATTTAAACCCTGATGG 59.638 40.000 18.75 5.27 41.37 3.51
574 583 6.461110 AGCATCAAGATTTAAACCCTGATG 57.539 37.500 14.57 14.57 36.12 3.07
575 584 5.297776 CGAGCATCAAGATTTAAACCCTGAT 59.702 40.000 0.00 0.00 33.17 2.90
576 585 4.635765 CGAGCATCAAGATTTAAACCCTGA 59.364 41.667 0.00 0.00 33.17 3.86
577 586 4.731773 GCGAGCATCAAGATTTAAACCCTG 60.732 45.833 0.00 0.00 33.17 4.45
578 587 3.378427 GCGAGCATCAAGATTTAAACCCT 59.622 43.478 0.00 0.00 33.17 4.34
579 588 3.128589 TGCGAGCATCAAGATTTAAACCC 59.871 43.478 0.00 0.00 33.17 4.11
580 589 4.355543 TGCGAGCATCAAGATTTAAACC 57.644 40.909 0.00 0.00 33.17 3.27
581 590 6.875926 AAATGCGAGCATCAAGATTTAAAC 57.124 33.333 11.26 0.00 35.31 2.01
583 592 9.882996 CTAATAAATGCGAGCATCAAGATTTAA 57.117 29.630 11.26 0.00 35.31 1.52
584 593 9.056005 ACTAATAAATGCGAGCATCAAGATTTA 57.944 29.630 11.26 6.42 35.31 1.40
585 594 7.934457 ACTAATAAATGCGAGCATCAAGATTT 58.066 30.769 11.26 4.40 35.31 2.17
586 595 7.502120 ACTAATAAATGCGAGCATCAAGATT 57.498 32.000 11.26 10.32 35.31 2.40
587 596 8.090831 TCTACTAATAAATGCGAGCATCAAGAT 58.909 33.333 11.26 0.39 35.31 2.40
588 597 7.433680 TCTACTAATAAATGCGAGCATCAAGA 58.566 34.615 11.26 3.57 35.31 3.02
589 598 7.643528 TCTACTAATAAATGCGAGCATCAAG 57.356 36.000 11.26 7.15 35.31 3.02
590 599 8.607441 AATCTACTAATAAATGCGAGCATCAA 57.393 30.769 11.26 3.11 35.31 2.57
591 600 9.140286 GTAATCTACTAATAAATGCGAGCATCA 57.860 33.333 11.26 3.11 35.31 3.07
592 601 9.360093 AGTAATCTACTAATAAATGCGAGCATC 57.640 33.333 11.26 0.00 37.23 3.91
593 602 9.712305 AAGTAATCTACTAATAAATGCGAGCAT 57.288 29.630 4.52 4.52 38.26 3.79
594 603 9.542462 AAAGTAATCTACTAATAAATGCGAGCA 57.458 29.630 0.00 0.00 38.26 4.26
617 627 1.267383 GCGTCGCCGAAAATCCTAAAG 60.267 52.381 5.75 0.00 35.63 1.85
641 651 0.539051 AGGCGTCTCTTCCCATTGAG 59.461 55.000 0.00 0.00 0.00 3.02
645 655 1.682684 ACGAGGCGTCTCTTCCCAT 60.683 57.895 16.21 0.00 33.69 4.00
670 680 0.323302 TAGTCACCAAATGCGCCTCA 59.677 50.000 4.18 0.00 0.00 3.86
689 699 5.917447 CGACATATCATCTTGAGATTGACGT 59.083 40.000 0.00 0.00 31.21 4.34
699 709 6.070897 AGACTGAGTCGACATATCATCTTG 57.929 41.667 19.50 3.80 37.67 3.02
714 724 0.969894 CCACCTCCGAAAGACTGAGT 59.030 55.000 0.00 0.00 0.00 3.41
718 728 1.645710 ATGACCACCTCCGAAAGACT 58.354 50.000 0.00 0.00 0.00 3.24
723 733 0.689745 CCCCTATGACCACCTCCGAA 60.690 60.000 0.00 0.00 0.00 4.30
733 743 1.337260 CGCATGCTCTACCCCTATGAC 60.337 57.143 17.13 0.00 0.00 3.06
739 749 2.233922 ACATATACGCATGCTCTACCCC 59.766 50.000 17.13 0.00 0.00 4.95
742 752 8.188799 TCCTATAAACATATACGCATGCTCTAC 58.811 37.037 17.13 0.00 0.00 2.59
745 755 7.827819 TTCCTATAAACATATACGCATGCTC 57.172 36.000 17.13 0.00 0.00 4.26
746 756 8.040727 TCATTCCTATAAACATATACGCATGCT 58.959 33.333 17.13 5.50 0.00 3.79
757 767 6.147821 GCGCATACACTCATTCCTATAAACAT 59.852 38.462 0.30 0.00 0.00 2.71
758 768 5.465390 GCGCATACACTCATTCCTATAAACA 59.535 40.000 0.30 0.00 0.00 2.83
759 769 5.388475 CGCGCATACACTCATTCCTATAAAC 60.388 44.000 8.75 0.00 0.00 2.01
762 772 3.254903 ACGCGCATACACTCATTCCTATA 59.745 43.478 5.73 0.00 0.00 1.31
768 778 3.981416 CACTATACGCGCATACACTCATT 59.019 43.478 5.73 0.00 0.00 2.57
927 961 7.878477 TTGAGATCACTGATTGCAATTTTTC 57.122 32.000 14.33 1.72 0.00 2.29
933 967 9.932207 AATTATTTTTGAGATCACTGATTGCAA 57.068 25.926 0.00 0.00 0.00 4.08
1486 1533 1.812571 GAACGGGTTCAAGTCATGCAT 59.187 47.619 6.68 0.00 39.31 3.96
1495 1542 1.604755 CCAATTGTCGAACGGGTTCAA 59.395 47.619 11.69 0.32 39.46 2.69
1666 1713 4.306967 TCGTCCACGGCATGCACA 62.307 61.111 21.36 0.00 40.29 4.57
1725 1772 0.458669 GTGCCGGTAGATCCTCGAAA 59.541 55.000 1.90 0.00 0.00 3.46
1726 1773 0.681887 TGTGCCGGTAGATCCTCGAA 60.682 55.000 1.90 0.00 0.00 3.71
1736 1783 3.755628 GGTCGAGCTGTGCCGGTA 61.756 66.667 7.51 0.00 0.00 4.02
1914 1961 0.405585 CCTGGTGATTCAGGTGGGTT 59.594 55.000 2.93 0.00 46.89 4.11
1915 1962 2.078452 CCTGGTGATTCAGGTGGGT 58.922 57.895 2.93 0.00 46.89 4.51
1922 1970 1.974265 TTTGTTCGCCTGGTGATTCA 58.026 45.000 11.31 10.65 0.00 2.57
1959 2007 4.142447 CGACCTCCGAAATGTTCTAGAAGA 60.142 45.833 5.12 4.84 41.76 2.87
1984 2032 5.575995 GGTATACTGACGTGTTTCTTCTTCC 59.424 44.000 0.00 0.00 0.00 3.46
1992 2043 9.880157 ATTTACAATAGGTATACTGACGTGTTT 57.120 29.630 0.00 0.00 0.00 2.83
1993 2044 9.525409 GATTTACAATAGGTATACTGACGTGTT 57.475 33.333 0.00 0.00 0.00 3.32
1994 2045 8.139989 GGATTTACAATAGGTATACTGACGTGT 58.860 37.037 0.00 4.32 0.00 4.49
2110 2162 2.752030 TGGTAGCAGAATAGCAGACCT 58.248 47.619 10.17 0.00 41.07 3.85
2120 2172 4.272489 CCTTGGATGAAATGGTAGCAGAA 58.728 43.478 0.00 0.00 0.00 3.02
2138 2190 0.314935 GAACATGGTGTGTGGCCTTG 59.685 55.000 3.32 0.00 41.14 3.61
2182 2234 1.703411 TGCTTGCTTGCCTACCTTTT 58.297 45.000 0.00 0.00 0.00 2.27
2209 2262 2.928801 TGGCTAGTGTTGTGATGTGT 57.071 45.000 0.00 0.00 0.00 3.72
2307 2360 3.249091 CATCACACAAGAAGACGAGGAG 58.751 50.000 0.00 0.00 0.00 3.69
2313 2366 3.550842 GCAAACCCATCACACAAGAAGAC 60.551 47.826 0.00 0.00 0.00 3.01
2314 2367 2.622942 GCAAACCCATCACACAAGAAGA 59.377 45.455 0.00 0.00 0.00 2.87
2327 2380 3.361158 CGACATGGCGCAAACCCA 61.361 61.111 8.66 0.00 36.66 4.51
2341 2394 2.460918 ACAATGCTGCTACGTATCGAC 58.539 47.619 0.00 0.00 0.00 4.20
2342 2395 2.727777 GACAATGCTGCTACGTATCGA 58.272 47.619 0.00 0.00 0.00 3.59
2343 2396 1.448308 CGACAATGCTGCTACGTATCG 59.552 52.381 0.00 0.00 0.00 2.92
2344 2397 2.216488 CACGACAATGCTGCTACGTATC 59.784 50.000 0.00 0.00 32.04 2.24
2441 2495 1.490693 CGAGGGGCGTGATGAATTCG 61.491 60.000 0.04 0.00 34.64 3.34
2453 2507 1.019805 GTTAGACAACTGCGAGGGGC 61.020 60.000 0.00 0.00 43.96 5.80
2515 2574 6.165700 TCCAATTAGGGATCGGTTAACTAC 57.834 41.667 5.42 0.00 38.24 2.73


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

AutoCloner maintained by Alex Coulton.