Multiple sequence alignment - TraesCS6D01G285600

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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 TraesCS6D01G285600 chr6D 100.000 2359 0 0 848 3206 393936546 393934188 0.000000e+00 4357
1 TraesCS6D01G285600 chr6D 100.000 638 0 0 1 638 393937393 393936756 0.000000e+00 1179
2 TraesCS6D01G285600 chr6A 95.036 2377 80 15 848 3206 540145998 540143642 0.000000e+00 3701
3 TraesCS6D01G285600 chr6A 86.282 554 23 29 3 508 540146911 540146363 1.300000e-153 553
4 TraesCS6D01G285600 chr6B 95.657 1957 63 9 848 2796 589129582 589127640 0.000000e+00 3123
5 TraesCS6D01G285600 chr6B 95.740 446 9 3 67 512 589130730 589130295 0.000000e+00 710
6 TraesCS6D01G285600 chr6B 95.181 83 4 0 1 83 589130823 589130741 7.220000e-27 132
7 TraesCS6D01G285600 chr6B 98.551 69 1 0 570 638 589129672 589129604 4.340000e-24 122
8 TraesCS6D01G285600 chr7D 77.730 1154 138 69 972 2076 140232496 140233579 5.920000e-167 597
9 TraesCS6D01G285600 chr7A 77.178 1148 150 61 973 2076 140536530 140537609 1.670000e-157 566
10 TraesCS6D01G285600 chr7B 77.038 1141 148 68 972 2076 105323152 105324214 4.670000e-153 551
11 TraesCS6D01G285600 chr5D 89.474 209 22 0 1197 1405 205995773 205995981 6.820000e-67 265
12 TraesCS6D01G285600 chr5A 89.474 209 22 0 1197 1405 264421493 264421701 6.820000e-67 265
13 TraesCS6D01G285600 chr5B 88.995 209 23 0 1197 1405 206102407 206102199 3.170000e-65 259
14 TraesCS6D01G285600 chr4D 84.937 239 31 4 1177 1414 65577854 65577620 1.490000e-58 237


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 TraesCS6D01G285600 chr6D 393934188 393937393 3205 True 2768.00 4357 100.00000 1 3206 2 chr6D.!!$R1 3205
1 TraesCS6D01G285600 chr6A 540143642 540146911 3269 True 2127.00 3701 90.65900 3 3206 2 chr6A.!!$R1 3203
2 TraesCS6D01G285600 chr6B 589127640 589130823 3183 True 1021.75 3123 96.28225 1 2796 4 chr6B.!!$R1 2795
3 TraesCS6D01G285600 chr7D 140232496 140233579 1083 False 597.00 597 77.73000 972 2076 1 chr7D.!!$F1 1104
4 TraesCS6D01G285600 chr7A 140536530 140537609 1079 False 566.00 566 77.17800 973 2076 1 chr7A.!!$F1 1103
5 TraesCS6D01G285600 chr7B 105323152 105324214 1062 False 551.00 551 77.03800 972 2076 1 chr7B.!!$F1 1104

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
538 616 0.032678 CACGCACACAACCTCTCTCT 59.967 55.0 0.0 0.0 0.0 3.1 F
539 617 0.315568 ACGCACACAACCTCTCTCTC 59.684 55.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2809 1.238625 GGCTAGACGATCCTCCTCCG 61.239 65.0 0.0 0.0 0.0 4.63 R
2519 3215 1.359848 TTCTCTTCCGCTCGCATTTC 58.640 50.0 0.0 0.0 0.0 2.17 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
224 256 3.325135 CCTAATAATTCTCCTCCGCCTGT 59.675 47.826 0.00 0.00 0.00 4.00
235 267 0.261991 TCCGCCTGTCTTATCCTCCT 59.738 55.000 0.00 0.00 0.00 3.69
236 268 0.676736 CCGCCTGTCTTATCCTCCTC 59.323 60.000 0.00 0.00 0.00 3.71
237 269 1.698506 CGCCTGTCTTATCCTCCTCT 58.301 55.000 0.00 0.00 0.00 3.69
238 270 2.035632 CGCCTGTCTTATCCTCCTCTT 58.964 52.381 0.00 0.00 0.00 2.85
305 347 0.884514 TCTCTGTCACTCAAGCTCCG 59.115 55.000 0.00 0.00 0.00 4.63
479 557 1.685517 TCTCCCAGATCGCAGATGAAG 59.314 52.381 0.00 0.00 45.12 3.02
512 590 5.509498 AGGCCATAAAATAGTGTGTGTGAT 58.491 37.500 5.01 0.00 0.00 3.06
513 591 5.590259 AGGCCATAAAATAGTGTGTGTGATC 59.410 40.000 5.01 0.00 0.00 2.92
514 592 5.590259 GGCCATAAAATAGTGTGTGTGATCT 59.410 40.000 0.00 0.00 0.00 2.75
515 593 6.238484 GGCCATAAAATAGTGTGTGTGATCTC 60.238 42.308 0.00 0.00 0.00 2.75
516 594 6.238484 GCCATAAAATAGTGTGTGTGATCTCC 60.238 42.308 0.00 0.00 0.00 3.71
517 595 6.260936 CCATAAAATAGTGTGTGTGATCTCCC 59.739 42.308 0.00 0.00 0.00 4.30
518 596 4.908601 AAATAGTGTGTGTGATCTCCCA 57.091 40.909 0.00 0.00 0.00 4.37
519 597 3.895232 ATAGTGTGTGTGATCTCCCAC 57.105 47.619 3.75 3.75 37.55 4.61
520 598 1.423584 AGTGTGTGTGATCTCCCACA 58.576 50.000 8.70 8.70 43.98 4.17
524 602 3.465701 TGTGATCTCCCACACGCA 58.534 55.556 0.00 0.00 41.63 5.24
525 603 1.005037 TGTGATCTCCCACACGCAC 60.005 57.895 0.00 0.00 41.63 5.34
526 604 1.005037 GTGATCTCCCACACGCACA 60.005 57.895 0.00 0.00 37.04 4.57
527 605 1.005037 TGATCTCCCACACGCACAC 60.005 57.895 0.00 0.00 0.00 3.82
528 606 1.005037 GATCTCCCACACGCACACA 60.005 57.895 0.00 0.00 0.00 3.72
529 607 0.602638 GATCTCCCACACGCACACAA 60.603 55.000 0.00 0.00 0.00 3.33
530 608 0.884704 ATCTCCCACACGCACACAAC 60.885 55.000 0.00 0.00 0.00 3.32
531 609 2.515057 TCCCACACGCACACAACC 60.515 61.111 0.00 0.00 0.00 3.77
532 610 2.515991 CCCACACGCACACAACCT 60.516 61.111 0.00 0.00 0.00 3.50
533 611 2.542907 CCCACACGCACACAACCTC 61.543 63.158 0.00 0.00 0.00 3.85
534 612 1.523711 CCACACGCACACAACCTCT 60.524 57.895 0.00 0.00 0.00 3.69
535 613 1.498865 CCACACGCACACAACCTCTC 61.499 60.000 0.00 0.00 0.00 3.20
536 614 0.530650 CACACGCACACAACCTCTCT 60.531 55.000 0.00 0.00 0.00 3.10
537 615 0.249489 ACACGCACACAACCTCTCTC 60.249 55.000 0.00 0.00 0.00 3.20
538 616 0.032678 CACGCACACAACCTCTCTCT 59.967 55.000 0.00 0.00 0.00 3.10
539 617 0.315568 ACGCACACAACCTCTCTCTC 59.684 55.000 0.00 0.00 0.00 3.20
540 618 0.600557 CGCACACAACCTCTCTCTCT 59.399 55.000 0.00 0.00 0.00 3.10
541 619 1.402194 CGCACACAACCTCTCTCTCTC 60.402 57.143 0.00 0.00 0.00 3.20
542 620 1.892474 GCACACAACCTCTCTCTCTCT 59.108 52.381 0.00 0.00 0.00 3.10
543 621 2.094752 GCACACAACCTCTCTCTCTCTC 60.095 54.545 0.00 0.00 0.00 3.20
544 622 3.420893 CACACAACCTCTCTCTCTCTCT 58.579 50.000 0.00 0.00 0.00 3.10
545 623 3.440173 CACACAACCTCTCTCTCTCTCTC 59.560 52.174 0.00 0.00 0.00 3.20
546 624 3.330701 ACACAACCTCTCTCTCTCTCTCT 59.669 47.826 0.00 0.00 0.00 3.10
547 625 3.941483 CACAACCTCTCTCTCTCTCTCTC 59.059 52.174 0.00 0.00 0.00 3.20
548 626 3.846588 ACAACCTCTCTCTCTCTCTCTCT 59.153 47.826 0.00 0.00 0.00 3.10
549 627 4.080863 ACAACCTCTCTCTCTCTCTCTCTC 60.081 50.000 0.00 0.00 0.00 3.20
550 628 4.000928 ACCTCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
551 629 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
552 630 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
553 631 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
554 632 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
555 633 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
556 634 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
557 635 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
558 636 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
559 637 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
560 638 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
561 639 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
562 640 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
563 641 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
564 642 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
565 643 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
566 644 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
567 645 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
568 646 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
592 1235 5.654209 TCTCATCGTATCATATGAGGAAGGG 59.346 44.000 11.78 5.89 45.99 3.95
1175 1821 2.045926 GATGCAGGTGCGGAAGGT 60.046 61.111 0.00 0.00 45.83 3.50
1278 1927 2.656069 GGCGAGGGTGTTCCAGCTA 61.656 63.158 0.00 0.00 39.99 3.32
1704 2377 1.227031 GCAGCAGCAGCAACAACAA 60.227 52.632 4.63 0.00 45.49 2.83
1773 2446 2.282391 ACGCAGAGCCAAATGCCA 60.282 55.556 0.00 0.00 42.71 4.92
2332 3023 5.671463 TCCTCCACTCCTAGACATTAGAT 57.329 43.478 0.00 0.00 0.00 1.98
2457 3148 1.767681 CCATTGGAGAAGAGGAGGGAG 59.232 57.143 0.00 0.00 0.00 4.30
2519 3215 7.601856 TGTTCTTTTAGCATTAGGGTTTGATG 58.398 34.615 0.00 0.00 0.00 3.07
2537 3233 0.246360 TGAAATGCGAGCGGAAGAGA 59.754 50.000 0.00 0.00 0.00 3.10
2565 3261 1.002257 AGGCATGGCATTCGTCACA 60.002 52.632 22.64 0.00 0.00 3.58
2656 3353 0.683828 TTACACCATGCAGGGCCATG 60.684 55.000 19.26 14.45 43.89 3.66
2684 3381 0.598942 TTTGCATGCTGCTTGTGCTG 60.599 50.000 20.33 0.00 45.31 4.41
2773 3471 4.467438 CCTTTTGCTTTCTCCCATGGTATT 59.533 41.667 11.73 0.00 0.00 1.89
2801 3499 2.531672 ATCATGCCTGATCCACCGA 58.468 52.632 0.00 0.00 37.58 4.69
2816 3514 8.980143 TGATCCACCGAAAATAAAATTCTTTC 57.020 30.769 0.00 0.00 0.00 2.62
2827 3525 1.816074 AATTCTTTCGCGGGCACTTA 58.184 45.000 6.13 0.00 0.00 2.24
2845 3544 5.104374 CACTTACTCGTCCGGCTTTATTTA 58.896 41.667 0.00 0.00 0.00 1.40
2848 3547 4.395959 ACTCGTCCGGCTTTATTTATCA 57.604 40.909 0.00 0.00 0.00 2.15
2894 3593 9.447040 CAAACTTTGACCTTAGTTTTAACTAGC 57.553 33.333 0.00 0.00 41.34 3.42
2938 3637 9.206870 CACAAAATTAGTACCATTTGAATGCTT 57.793 29.630 13.77 0.00 36.52 3.91
2945 3644 7.701539 AGTACCATTTGAATGCTTGATAACA 57.298 32.000 0.00 0.00 35.08 2.41
2981 3680 5.164100 CGAATCCAAACAATGCGGTTTTTAG 60.164 40.000 0.00 0.00 38.86 1.85
2982 3681 4.657436 TCCAAACAATGCGGTTTTTAGT 57.343 36.364 0.00 0.00 38.86 2.24
2990 3689 7.068692 ACAATGCGGTTTTTAGTATGTACTC 57.931 36.000 0.00 0.00 37.73 2.59
2991 3690 6.877322 ACAATGCGGTTTTTAGTATGTACTCT 59.123 34.615 0.00 0.00 37.73 3.24
2997 3696 7.536855 CGGTTTTTAGTATGTACTCTCTCTGT 58.463 38.462 0.00 0.00 37.73 3.41
3046 3745 8.959734 TTACCATATAGTGATGTAAACGATCG 57.040 34.615 14.88 14.88 0.00 3.69
3070 3769 9.807649 TCGTATATTTCTTTACAAAGGGAGTAC 57.192 33.333 2.04 0.00 36.67 2.73
3071 3770 9.590451 CGTATATTTCTTTACAAAGGGAGTACA 57.410 33.333 0.00 0.00 36.67 2.90
3076 3775 9.856162 ATTTCTTTACAAAGGGAGTACAACTTA 57.144 29.630 0.00 0.00 36.67 2.24
3077 3776 9.856162 TTTCTTTACAAAGGGAGTACAACTTAT 57.144 29.630 0.00 0.00 36.67 1.73
3099 3798 6.755461 ATATTTTGCTAGTCGAGTCGAATG 57.245 37.500 24.49 15.10 37.72 2.67
3105 3804 4.515567 TGCTAGTCGAGTCGAATGTATGAT 59.484 41.667 24.49 3.43 37.72 2.45
3106 3805 5.699458 TGCTAGTCGAGTCGAATGTATGATA 59.301 40.000 24.49 2.55 37.72 2.15
3114 3813 9.129209 TCGAGTCGAATGTATGATATCAAAATC 57.871 33.333 13.98 3.78 31.06 2.17
3140 3839 2.888414 ACAAAATACGAGTTTGTGGGGG 59.112 45.455 12.65 0.00 45.19 5.40
3141 3840 2.888414 CAAAATACGAGTTTGTGGGGGT 59.112 45.455 0.00 0.00 32.43 4.95
3142 3841 2.194201 AATACGAGTTTGTGGGGGTG 57.806 50.000 0.00 0.00 0.00 4.61
3143 3842 0.322187 ATACGAGTTTGTGGGGGTGC 60.322 55.000 0.00 0.00 0.00 5.01
3144 3843 1.697082 TACGAGTTTGTGGGGGTGCA 61.697 55.000 0.00 0.00 0.00 4.57
3173 3872 3.056107 CGGATGGAGGAAGAACTACACAA 60.056 47.826 0.00 0.00 33.26 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 68 3.689649 GCGAATATCCCATTTAATCGGCT 59.310 43.478 0.00 0.00 0.00 5.52
224 256 3.538129 AGGGAGGAAAGAGGAGGATAAGA 59.462 47.826 0.00 0.00 0.00 2.10
235 267 1.296715 GCAGCGAAGGGAGGAAAGA 59.703 57.895 0.00 0.00 0.00 2.52
236 268 1.746991 GGCAGCGAAGGGAGGAAAG 60.747 63.158 0.00 0.00 0.00 2.62
237 269 2.351276 GGCAGCGAAGGGAGGAAA 59.649 61.111 0.00 0.00 0.00 3.13
238 270 3.717294 GGGCAGCGAAGGGAGGAA 61.717 66.667 0.00 0.00 0.00 3.36
305 347 5.368145 TCTTGATGTAGAGAGAGAGAGAGC 58.632 45.833 0.00 0.00 0.00 4.09
479 557 5.828328 ACTATTTTATGGCCTTCTGGTAAGC 59.172 40.000 3.32 0.00 35.27 3.09
512 590 1.522806 GTTGTGTGCGTGTGGGAGA 60.523 57.895 0.00 0.00 0.00 3.71
513 591 2.542907 GGTTGTGTGCGTGTGGGAG 61.543 63.158 0.00 0.00 0.00 4.30
514 592 2.515057 GGTTGTGTGCGTGTGGGA 60.515 61.111 0.00 0.00 0.00 4.37
515 593 2.515991 AGGTTGTGTGCGTGTGGG 60.516 61.111 0.00 0.00 0.00 4.61
516 594 1.498865 GAGAGGTTGTGTGCGTGTGG 61.499 60.000 0.00 0.00 0.00 4.17
517 595 0.530650 AGAGAGGTTGTGTGCGTGTG 60.531 55.000 0.00 0.00 0.00 3.82
518 596 0.249489 GAGAGAGGTTGTGTGCGTGT 60.249 55.000 0.00 0.00 0.00 4.49
519 597 0.032678 AGAGAGAGGTTGTGTGCGTG 59.967 55.000 0.00 0.00 0.00 5.34
520 598 0.315568 GAGAGAGAGGTTGTGTGCGT 59.684 55.000 0.00 0.00 0.00 5.24
521 599 0.600557 AGAGAGAGAGGTTGTGTGCG 59.399 55.000 0.00 0.00 0.00 5.34
522 600 1.892474 AGAGAGAGAGAGGTTGTGTGC 59.108 52.381 0.00 0.00 0.00 4.57
523 601 3.420893 AGAGAGAGAGAGAGGTTGTGTG 58.579 50.000 0.00 0.00 0.00 3.82
524 602 3.330701 AGAGAGAGAGAGAGAGGTTGTGT 59.669 47.826 0.00 0.00 0.00 3.72
525 603 3.941483 GAGAGAGAGAGAGAGAGGTTGTG 59.059 52.174 0.00 0.00 0.00 3.33
526 604 3.846588 AGAGAGAGAGAGAGAGAGGTTGT 59.153 47.826 0.00 0.00 0.00 3.32
527 605 4.163078 AGAGAGAGAGAGAGAGAGAGGTTG 59.837 50.000 0.00 0.00 0.00 3.77
528 606 4.366267 AGAGAGAGAGAGAGAGAGAGGTT 58.634 47.826 0.00 0.00 0.00 3.50
529 607 3.964031 GAGAGAGAGAGAGAGAGAGAGGT 59.036 52.174 0.00 0.00 0.00 3.85
530 608 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
531 609 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
532 610 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
533 611 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
534 612 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
535 613 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
536 614 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
537 615 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
538 616 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
539 617 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
540 618 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
541 619 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
542 620 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
543 621 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
544 622 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
545 623 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
546 624 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
547 625 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
548 626 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
549 627 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
550 628 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
551 629 5.564455 CGATGAGAGAGAGAGAGAGAGAGAG 60.564 52.000 0.00 0.00 0.00 3.20
552 630 4.279420 CGATGAGAGAGAGAGAGAGAGAGA 59.721 50.000 0.00 0.00 0.00 3.10
553 631 4.038522 ACGATGAGAGAGAGAGAGAGAGAG 59.961 50.000 0.00 0.00 0.00 3.20
554 632 3.960755 ACGATGAGAGAGAGAGAGAGAGA 59.039 47.826 0.00 0.00 0.00 3.10
555 633 4.327982 ACGATGAGAGAGAGAGAGAGAG 57.672 50.000 0.00 0.00 0.00 3.20
556 634 5.538433 TGATACGATGAGAGAGAGAGAGAGA 59.462 44.000 0.00 0.00 0.00 3.10
557 635 5.783111 TGATACGATGAGAGAGAGAGAGAG 58.217 45.833 0.00 0.00 0.00 3.20
558 636 5.799827 TGATACGATGAGAGAGAGAGAGA 57.200 43.478 0.00 0.00 0.00 3.10
559 637 7.981225 TCATATGATACGATGAGAGAGAGAGAG 59.019 40.741 0.00 0.00 0.00 3.20
560 638 7.846066 TCATATGATACGATGAGAGAGAGAGA 58.154 38.462 0.00 0.00 0.00 3.10
592 1235 8.900781 GGTAAAGATTATAGGTTTGGAAGGAAC 58.099 37.037 0.00 0.00 0.00 3.62
1698 2362 2.008268 GCTGCTGCTGGTGTTGTTGT 62.008 55.000 8.53 0.00 36.03 3.32
1704 2377 2.124193 TGTTGCTGCTGCTGGTGT 60.124 55.556 17.00 0.00 40.48 4.16
1773 2446 2.607750 ACCATCCAGACGGTGCCT 60.608 61.111 0.00 0.00 33.05 4.75
2118 2809 1.238625 GGCTAGACGATCCTCCTCCG 61.239 65.000 0.00 0.00 0.00 4.63
2332 3023 3.428452 CCGAGTGTAATCCTTGCGAGTTA 60.428 47.826 0.00 0.00 0.00 2.24
2457 3148 1.794864 CTGCTGCTGCTGATGTGTC 59.205 57.895 17.00 0.00 40.01 3.67
2519 3215 1.359848 TTCTCTTCCGCTCGCATTTC 58.640 50.000 0.00 0.00 0.00 2.17
2537 3233 4.448210 GAATGCCATGCCTGATGAAAATT 58.552 39.130 0.00 0.00 33.31 1.82
2684 3381 9.988350 TCAAGAAAGAACAAATCGATTATAAGC 57.012 29.630 11.83 0.74 0.00 3.09
2736 3433 0.036306 AAAAGGACGTTGGCGGATCT 59.964 50.000 0.00 0.00 43.45 2.75
2801 3499 4.387559 GTGCCCGCGAAAGAATTTTATTTT 59.612 37.500 8.23 0.00 39.27 1.82
2816 3514 2.879462 GACGAGTAAGTGCCCGCG 60.879 66.667 0.00 0.00 0.00 6.46
2827 3525 4.142004 ACTGATAAATAAAGCCGGACGAGT 60.142 41.667 5.05 0.00 0.00 4.18
2869 3568 9.181061 TGCTAGTTAAAACTAAGGTCAAAGTTT 57.819 29.630 4.27 0.00 45.44 2.66
2871 3570 8.741603 TTGCTAGTTAAAACTAAGGTCAAAGT 57.258 30.769 4.27 0.00 40.70 2.66
2966 3665 6.877322 AGAGTACATACTAAAAACCGCATTGT 59.123 34.615 0.00 0.00 36.50 2.71
2971 3670 6.472808 CAGAGAGAGTACATACTAAAAACCGC 59.527 42.308 0.00 0.00 36.50 5.68
3020 3719 9.569167 CGATCGTTTACATCACTATATGGTAAT 57.431 33.333 7.03 0.00 0.00 1.89
3021 3720 8.570488 ACGATCGTTTACATCACTATATGGTAA 58.430 33.333 16.60 0.00 0.00 2.85
3022 3721 8.102800 ACGATCGTTTACATCACTATATGGTA 57.897 34.615 16.60 0.00 0.00 3.25
3023 3722 6.978338 ACGATCGTTTACATCACTATATGGT 58.022 36.000 16.60 0.00 0.00 3.55
3042 3741 9.543783 ACTCCCTTTGTAAAGAAATATACGATC 57.456 33.333 5.95 0.00 38.28 3.69
3058 3757 8.520351 GCAAAATATAAGTTGTACTCCCTTTGT 58.480 33.333 0.00 0.00 0.00 2.83
3064 3763 8.753175 CGACTAGCAAAATATAAGTTGTACTCC 58.247 37.037 0.00 0.00 0.00 3.85
3069 3768 7.220300 CGACTCGACTAGCAAAATATAAGTTGT 59.780 37.037 0.00 0.00 0.00 3.32
3070 3769 7.431376 TCGACTCGACTAGCAAAATATAAGTTG 59.569 37.037 0.00 0.00 0.00 3.16
3071 3770 7.478322 TCGACTCGACTAGCAAAATATAAGTT 58.522 34.615 0.00 0.00 0.00 2.66
3072 3771 7.024340 TCGACTCGACTAGCAAAATATAAGT 57.976 36.000 0.00 0.00 0.00 2.24
3073 3772 7.909777 TTCGACTCGACTAGCAAAATATAAG 57.090 36.000 0.00 0.00 34.89 1.73
3074 3773 7.919091 ACATTCGACTCGACTAGCAAAATATAA 59.081 33.333 0.00 0.00 34.89 0.98
3076 3775 6.273825 ACATTCGACTCGACTAGCAAAATAT 58.726 36.000 0.00 0.00 34.89 1.28
3077 3776 5.647589 ACATTCGACTCGACTAGCAAAATA 58.352 37.500 0.00 0.00 34.89 1.40
3078 3777 4.495422 ACATTCGACTCGACTAGCAAAAT 58.505 39.130 0.00 0.00 34.89 1.82
3079 3778 3.909430 ACATTCGACTCGACTAGCAAAA 58.091 40.909 0.00 0.00 34.89 2.44
3127 3826 1.178534 ATTGCACCCCCACAAACTCG 61.179 55.000 0.00 0.00 0.00 4.18
3131 3830 2.183679 GGATTATTGCACCCCCACAAA 58.816 47.619 0.00 0.00 0.00 2.83
3132 3831 1.859302 GGATTATTGCACCCCCACAA 58.141 50.000 0.00 0.00 0.00 3.33
3133 3832 0.395036 CGGATTATTGCACCCCCACA 60.395 55.000 0.00 0.00 0.00 4.17
3134 3833 1.106944 CCGGATTATTGCACCCCCAC 61.107 60.000 0.00 0.00 0.00 4.61
3135 3834 1.228793 CCGGATTATTGCACCCCCA 59.771 57.895 0.00 0.00 0.00 4.96
3139 3838 2.154462 CTCCATCCGGATTATTGCACC 58.846 52.381 16.19 0.00 41.79 5.01
3140 3839 2.154462 CCTCCATCCGGATTATTGCAC 58.846 52.381 16.19 0.00 41.79 4.57
3141 3840 2.054021 TCCTCCATCCGGATTATTGCA 58.946 47.619 16.19 0.00 41.79 4.08
3142 3841 2.859165 TCCTCCATCCGGATTATTGC 57.141 50.000 16.19 0.00 41.79 3.56
3143 3842 4.623932 TCTTCCTCCATCCGGATTATTG 57.376 45.455 16.19 4.77 41.79 1.90
3144 3843 4.660771 AGTTCTTCCTCCATCCGGATTATT 59.339 41.667 16.19 0.00 41.79 1.40
3165 3864 2.043992 TGTACTGCCCAGTTGTGTAGT 58.956 47.619 6.21 0.00 42.54 2.73
3173 3872 1.427368 TCCCAAAATGTACTGCCCAGT 59.573 47.619 6.17 6.17 45.02 4.00


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

AutoCloner maintained by Alex Coulton.