Multiple sequence alignment - TraesCS1D01G223100

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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 TraesCS1D01G223100 chr1D 100.000 2288 0 0 1 2288 310776804 310774517 0.000000e+00 4226
1 TraesCS1D01G223100 chr1A 94.942 1641 62 11 660 2288 390641014 390639383 0.000000e+00 2551
2 TraesCS1D01G223100 chr1A 95.522 536 24 0 2 537 390641547 390641012 0.000000e+00 857
3 TraesCS1D01G223100 chr1B 93.101 1638 64 17 666 2288 420417524 420415921 0.000000e+00 2353
4 TraesCS1D01G223100 chr1B 92.095 253 16 3 208 458 420417810 420417560 1.010000e-93 353
5 TraesCS1D01G223100 chr1B 93.617 141 9 0 521 661 424541696 424541556 6.400000e-51 211
6 TraesCS1D01G223100 chr2D 78.059 474 88 13 1635 2100 618301901 618302366 3.720000e-73 285
7 TraesCS1D01G223100 chr2D 93.151 146 7 2 535 679 645613052 645613195 6.400000e-51 211
8 TraesCS1D01G223100 chr2B 77.925 453 89 8 1655 2100 754977203 754977651 2.900000e-69 272
9 TraesCS1D01G223100 chr2B 94.776 134 7 0 535 668 517437009 517436876 2.300000e-50 209
10 TraesCS1D01G223100 chr5A 77.826 460 82 15 1635 2087 697052061 697052507 1.350000e-67 267
11 TraesCS1D01G223100 chr3D 76.974 456 80 18 1635 2087 108287757 108288190 1.060000e-58 237
12 TraesCS1D01G223100 chr3D 93.571 140 6 1 534 673 11337924 11338060 2.980000e-49 206
13 TraesCS1D01G223100 chr4D 76.344 465 89 14 1635 2087 509095701 509096156 1.770000e-56 230
14 TraesCS1D01G223100 chr7A 95.588 136 5 1 535 669 462339312 462339177 1.380000e-52 217
15 TraesCS1D01G223100 chr7A 93.617 141 8 1 535 675 603025340 603025201 2.300000e-50 209
16 TraesCS1D01G223100 chr4A 96.241 133 4 1 534 665 177639011 177639143 1.380000e-52 217
17 TraesCS1D01G223100 chr5D 94.286 140 6 2 531 670 90314272 90314135 1.780000e-51 213
18 TraesCS1D01G223100 chr3A 94.891 137 6 1 530 666 469077563 469077428 1.780000e-51 213
19 TraesCS1D01G223100 chr4B 76.648 364 51 19 1624 1983 658180133 658179800 1.090000e-38 171


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 TraesCS1D01G223100 chr1D 310774517 310776804 2287 True 4226 4226 100.000 1 2288 1 chr1D.!!$R1 2287
1 TraesCS1D01G223100 chr1A 390639383 390641547 2164 True 1704 2551 95.232 2 2288 2 chr1A.!!$R1 2286
2 TraesCS1D01G223100 chr1B 420415921 420417810 1889 True 1353 2353 92.598 208 2288 2 chr1B.!!$R2 2080

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
545 547 0.043637 TCCCTTCATACCCCTTCCGT 59.956 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2021 0.909623 ATCAAGGTGGGGTTCTACGG 59.09 55.0 0.0 0.0 0.0 4.02 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
22 23 5.778459 CGATACATCAAATCACGCAATTG 57.222 39.130 0.00 0.00 0.00 2.32
87 88 7.755373 GTCTTTAGGAATTAAGAACCATTGTGC 59.245 37.037 0.00 0.00 32.59 4.57
200 201 4.318332 TCACCTGTTAGTGAAGCAATCAG 58.682 43.478 0.00 0.00 43.65 2.90
273 274 2.493675 TGTGCTTGTGCTTTGGTGTTTA 59.506 40.909 0.00 0.00 40.48 2.01
284 285 7.230510 TGTGCTTTGGTGTTTATGTCTTTAGAT 59.769 33.333 0.00 0.00 0.00 1.98
436 438 5.355350 CCTTCCTGAAACAACCTTATGCTAG 59.645 44.000 0.00 0.00 0.00 3.42
449 451 4.326255 GCTAGCACATGGTGGCTT 57.674 55.556 10.63 0.50 44.84 4.35
482 484 4.695455 AGCATACACACACACAATTAGTCC 59.305 41.667 0.00 0.00 0.00 3.85
487 489 4.133820 CACACACACAATTAGTCCAGGAA 58.866 43.478 0.00 0.00 0.00 3.36
503 505 3.119602 CCAGGAAATCACATGTTGCTCTG 60.120 47.826 0.00 0.00 0.00 3.35
507 509 4.095483 GGAAATCACATGTTGCTCTGTAGG 59.905 45.833 0.00 0.00 0.00 3.18
534 536 0.706433 ATTGGTGCCTGTCCCTTCAT 59.294 50.000 0.00 0.00 0.00 2.57
535 537 1.367346 TTGGTGCCTGTCCCTTCATA 58.633 50.000 0.00 0.00 0.00 2.15
536 538 0.618458 TGGTGCCTGTCCCTTCATAC 59.382 55.000 0.00 0.00 0.00 2.39
537 539 0.107165 GGTGCCTGTCCCTTCATACC 60.107 60.000 0.00 0.00 0.00 2.73
538 540 0.107165 GTGCCTGTCCCTTCATACCC 60.107 60.000 0.00 0.00 0.00 3.69
539 541 1.279025 TGCCTGTCCCTTCATACCCC 61.279 60.000 0.00 0.00 0.00 4.95
540 542 0.988678 GCCTGTCCCTTCATACCCCT 60.989 60.000 0.00 0.00 0.00 4.79
541 543 1.596496 CCTGTCCCTTCATACCCCTT 58.404 55.000 0.00 0.00 0.00 3.95
542 544 1.490910 CCTGTCCCTTCATACCCCTTC 59.509 57.143 0.00 0.00 0.00 3.46
543 545 1.490910 CTGTCCCTTCATACCCCTTCC 59.509 57.143 0.00 0.00 0.00 3.46
544 546 0.468648 GTCCCTTCATACCCCTTCCG 59.531 60.000 0.00 0.00 0.00 4.30
545 547 0.043637 TCCCTTCATACCCCTTCCGT 59.956 55.000 0.00 0.00 0.00 4.69
546 548 0.468648 CCCTTCATACCCCTTCCGTC 59.531 60.000 0.00 0.00 0.00 4.79
547 549 0.468648 CCTTCATACCCCTTCCGTCC 59.531 60.000 0.00 0.00 0.00 4.79
548 550 0.104304 CTTCATACCCCTTCCGTCCG 59.896 60.000 0.00 0.00 0.00 4.79
549 551 1.332144 TTCATACCCCTTCCGTCCGG 61.332 60.000 0.00 0.00 0.00 5.14
550 552 1.759299 CATACCCCTTCCGTCCGGA 60.759 63.158 0.00 0.00 43.52 5.14
560 562 2.660189 TCCGTCCGGAAATACTTGTC 57.340 50.000 5.23 0.00 42.05 3.18
561 563 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
562 564 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
563 565 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
564 566 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
565 567 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
566 568 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
567 569 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
568 570 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
569 571 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
570 572 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
571 573 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
572 574 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
580 582 9.918630 ACTTGTCATCAAAATGAATAAAAGGAG 57.081 29.630 0.00 0.00 43.42 3.69
626 628 9.225682 AGTTCTAGATACATCCCTTTTTATCCA 57.774 33.333 0.00 0.00 0.00 3.41
632 634 9.713684 AGATACATCCCTTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
635 637 8.378115 ACATCCCTTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
636 638 8.260114 ACATCCCTTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
637 639 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
638 640 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
639 641 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
640 642 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
647 649 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
648 650 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
649 651 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
650 652 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
651 653 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
652 654 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
653 655 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
654 656 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
655 657 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
656 658 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
657 659 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
658 660 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
689 691 5.612725 AAACTGGAATCATGTGGTGTTTT 57.387 34.783 0.00 0.00 0.00 2.43
690 692 6.723298 AAACTGGAATCATGTGGTGTTTTA 57.277 33.333 0.00 0.00 0.00 1.52
755 759 8.697507 AAGTATTCTAATGCTTAGGATTTGGG 57.302 34.615 3.97 0.00 39.15 4.12
821 827 9.683069 AGATGATTGATTTCTTTTGTTGTACAC 57.317 29.630 0.00 0.00 0.00 2.90
944 955 5.830991 TGCTCATCATGATGGATTGAATTGA 59.169 36.000 30.54 11.24 39.24 2.57
970 982 7.685532 GACTTTTGTCCATTTTTCTCACTTC 57.314 36.000 0.00 0.00 43.37 3.01
972 984 7.035612 ACTTTTGTCCATTTTTCTCACTTCAC 58.964 34.615 0.00 0.00 0.00 3.18
980 992 7.759433 TCCATTTTTCTCACTTCACTTTCAAAC 59.241 33.333 0.00 0.00 0.00 2.93
990 1002 7.443879 TCACTTCACTTTCAAACATATGCAGTA 59.556 33.333 1.58 0.00 0.00 2.74
1010 1022 0.392863 TCATCCACAATGTCTGGCGG 60.393 55.000 0.00 0.00 36.68 6.13
1012 1024 0.908910 ATCCACAATGTCTGGCGGTA 59.091 50.000 0.00 0.00 0.00 4.02
1015 1027 1.406751 CCACAATGTCTGGCGGTATCA 60.407 52.381 0.00 0.00 0.00 2.15
1017 1029 2.352651 CACAATGTCTGGCGGTATCAAG 59.647 50.000 0.00 0.00 0.00 3.02
1046 1058 0.110104 CCCCAGCCATCTTCATCTCC 59.890 60.000 0.00 0.00 0.00 3.71
1047 1059 1.138568 CCCAGCCATCTTCATCTCCT 58.861 55.000 0.00 0.00 0.00 3.69
1048 1060 1.072015 CCCAGCCATCTTCATCTCCTC 59.928 57.143 0.00 0.00 0.00 3.71
1060 1072 0.252881 ATCTCCTCCTGTGAAGCCCA 60.253 55.000 0.00 0.00 0.00 5.36
1151 1166 3.569491 AGTTTATTCATGCCTCCATGGG 58.431 45.455 13.02 2.26 47.00 4.00
1209 1224 1.317613 TGTTTGCGATGTCAAAGGCT 58.682 45.000 0.00 0.00 36.71 4.58
1336 1358 3.936453 TGTAGTGAAAGTTTGTCGCTGTT 59.064 39.130 0.00 0.00 36.54 3.16
1342 1364 6.482308 AGTGAAAGTTTGTCGCTGTTACTAAT 59.518 34.615 0.00 0.00 34.59 1.73
1368 1390 8.253810 TCATAATCCTCAAGTCAAACAGTAGAG 58.746 37.037 0.00 0.00 0.00 2.43
1369 1391 6.672266 AATCCTCAAGTCAAACAGTAGAGA 57.328 37.500 0.00 0.00 0.00 3.10
1585 1617 0.038166 ATGACCAGGACCGCACAAAT 59.962 50.000 0.00 0.00 0.00 2.32
1594 1626 3.008704 AGGACCGCACAAATAACTAACCT 59.991 43.478 0.00 0.00 0.00 3.50
1598 1630 3.936453 CCGCACAAATAACTAACCTAGCA 59.064 43.478 0.00 0.00 0.00 3.49
1668 1700 0.750182 GTCGTAGAGGGAGCTGAGCT 60.750 60.000 6.69 6.69 38.83 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.145243 GCAATTGCGTGATTTGATGTATCG 59.855 41.667 15.87 0.00 0.00 2.92
10 11 1.421382 GCAAGTGCAATTGCGTGATT 58.579 45.000 32.71 13.47 45.43 2.57
22 23 3.126686 ACCAAACAAAAACATGCAAGTGC 59.873 39.130 0.00 0.00 42.50 4.40
31 32 5.010012 ACAAAATTGCCACCAAACAAAAACA 59.990 32.000 0.00 0.00 34.05 2.83
87 88 6.742999 GCATCAAAGTGCAACACATATATG 57.257 37.500 11.29 11.29 44.43 1.78
128 129 0.179056 AGGTGACCGCCGATTATTGG 60.179 55.000 0.00 0.00 0.00 3.16
139 140 3.194968 ACAGGAGTACATTAAGGTGACCG 59.805 47.826 2.37 3.67 0.00 4.79
200 201 8.281893 GCTCAGAAGATACATTTCTTATCTTGC 58.718 37.037 8.91 3.78 43.38 4.01
284 285 6.127479 GGCAATCCACAATCAAATACTGGTAA 60.127 38.462 0.00 0.00 0.00 2.85
410 412 2.381752 AAGGTTGTTTCAGGAAGGGG 57.618 50.000 0.00 0.00 0.00 4.79
436 438 3.193267 TCAAAAGATAAGCCACCATGTGC 59.807 43.478 0.00 0.00 31.34 4.57
449 451 6.484977 TGTGTGTGTGTATGCTTCAAAAGATA 59.515 34.615 0.00 0.00 0.00 1.98
482 484 3.504906 ACAGAGCAACATGTGATTTCCTG 59.495 43.478 0.00 5.49 0.00 3.86
487 489 3.012518 GCCTACAGAGCAACATGTGATT 58.987 45.455 0.00 0.00 0.00 2.57
507 509 2.618709 GGACAGGCACCAATATTGTAGC 59.381 50.000 14.25 15.66 0.00 3.58
541 543 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
542 544 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
543 545 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
544 546 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
545 547 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
546 548 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
547 549 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
554 556 9.918630 CTCCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
600 602 9.225682 TGGATAAAAAGGGATGTATCTAGAACT 57.774 33.333 0.00 0.00 0.00 3.01
606 608 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
609 611 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
610 612 8.260114 GTCATCAAAATGGATAAAAAGGGATGT 58.740 33.333 0.00 0.00 33.42 3.06
611 613 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
612 614 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
613 615 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
614 616 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
622 624 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
623 625 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
624 626 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
625 627 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
626 628 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
627 629 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
628 630 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
629 631 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
630 632 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
631 633 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
632 634 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
633 635 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
634 636 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
635 637 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
636 638 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
637 639 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
638 640 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
639 641 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
640 642 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
641 643 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
642 644 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
643 645 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
644 646 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
645 647 0.750546 CATGTACTCCCTCCGTCCGA 60.751 60.000 0.00 0.00 0.00 4.55
646 648 1.035932 ACATGTACTCCCTCCGTCCG 61.036 60.000 0.00 0.00 0.00 4.79
647 649 2.062971 TACATGTACTCCCTCCGTCC 57.937 55.000 0.08 0.00 0.00 4.79
648 650 4.081807 AGTTTTACATGTACTCCCTCCGTC 60.082 45.833 4.68 0.00 0.00 4.79
649 651 3.836562 AGTTTTACATGTACTCCCTCCGT 59.163 43.478 4.68 0.00 0.00 4.69
650 652 4.181578 CAGTTTTACATGTACTCCCTCCG 58.818 47.826 4.68 0.00 0.00 4.63
651 653 4.224370 TCCAGTTTTACATGTACTCCCTCC 59.776 45.833 4.68 0.00 0.00 4.30
652 654 5.416271 TCCAGTTTTACATGTACTCCCTC 57.584 43.478 4.68 0.00 0.00 4.30
653 655 5.836024 TTCCAGTTTTACATGTACTCCCT 57.164 39.130 4.68 0.00 0.00 4.20
654 656 6.177610 TGATTCCAGTTTTACATGTACTCCC 58.822 40.000 4.68 0.00 0.00 4.30
655 657 7.336931 ACATGATTCCAGTTTTACATGTACTCC 59.663 37.037 4.68 0.00 43.75 3.85
656 658 8.177663 CACATGATTCCAGTTTTACATGTACTC 58.822 37.037 4.68 0.00 43.74 2.59
657 659 7.121168 CCACATGATTCCAGTTTTACATGTACT 59.879 37.037 4.68 0.00 43.74 2.73
658 660 7.094377 ACCACATGATTCCAGTTTTACATGTAC 60.094 37.037 4.68 0.00 43.74 2.90
821 827 9.734620 TTTTACATTTGAGTTTCACAGAGAATG 57.265 29.630 0.00 0.00 35.83 2.67
901 912 7.596749 TGAGCACTAACAGAAAAATAGTAGC 57.403 36.000 0.00 0.00 0.00 3.58
904 915 8.671921 CATGATGAGCACTAACAGAAAAATAGT 58.328 33.333 0.00 0.00 0.00 2.12
914 925 4.758773 TCCATCATGATGAGCACTAACA 57.241 40.909 32.71 6.38 41.20 2.41
915 926 5.761726 TCAATCCATCATGATGAGCACTAAC 59.238 40.000 32.71 0.00 41.20 2.34
917 928 5.556006 TCAATCCATCATGATGAGCACTA 57.444 39.130 32.71 13.30 41.20 2.74
944 955 7.410120 AGTGAGAAAAATGGACAAAAGTCTT 57.590 32.000 0.00 0.00 0.00 3.01
970 982 7.859377 GGATGATACTGCATATGTTTGAAAGTG 59.141 37.037 4.29 0.00 0.00 3.16
972 984 7.859377 GTGGATGATACTGCATATGTTTGAAAG 59.141 37.037 4.29 0.00 0.00 2.62
980 992 6.653740 AGACATTGTGGATGATACTGCATATG 59.346 38.462 0.00 0.00 39.15 1.78
990 1002 1.671979 CGCCAGACATTGTGGATGAT 58.328 50.000 0.00 0.00 39.15 2.45
1010 1022 2.838202 TGGGGGACTTCAGACTTGATAC 59.162 50.000 0.00 0.00 32.27 2.24
1012 1024 1.912043 CTGGGGGACTTCAGACTTGAT 59.088 52.381 0.00 0.00 33.16 2.57
1015 1027 1.492993 GGCTGGGGGACTTCAGACTT 61.493 60.000 0.00 0.00 35.48 3.01
1017 1029 1.566298 ATGGCTGGGGGACTTCAGAC 61.566 60.000 0.00 0.00 37.89 3.51
1128 1143 4.209538 CCATGGAGGCATGAATAAACTCA 58.790 43.478 5.56 0.00 34.66 3.41
1151 1166 1.438651 TAAGCATGTCCTGTGTTCGC 58.561 50.000 0.00 0.00 0.00 4.70
1300 1322 7.952671 ACTTTCACTACAGAGAACTGACATTA 58.047 34.615 0.00 0.00 46.03 1.90
1342 1364 8.134202 TCTACTGTTTGACTTGAGGATTATGA 57.866 34.615 0.00 0.00 0.00 2.15
1469 1499 8.993424 AGTGTTGGGTAGTTTGATTCTATCTAT 58.007 33.333 0.00 0.00 0.00 1.98
1506 1536 9.651718 CGTTTTTATAGGCAAAAGATCAGATAC 57.348 33.333 0.00 0.00 0.00 2.24
1507 1537 9.607988 TCGTTTTTATAGGCAAAAGATCAGATA 57.392 29.630 0.00 0.00 0.00 1.98
1508 1538 8.506168 TCGTTTTTATAGGCAAAAGATCAGAT 57.494 30.769 0.00 0.00 0.00 2.90
1585 1617 4.350245 TGCTTCCTCTGCTAGGTTAGTTA 58.650 43.478 5.70 0.00 46.62 2.24
1594 1626 1.200760 TTGGGCTGCTTCCTCTGCTA 61.201 55.000 0.00 0.00 0.00 3.49
1598 1630 1.377994 CAGTTGGGCTGCTTCCTCT 59.622 57.895 0.00 0.00 38.52 3.69
1989 2021 0.909623 ATCAAGGTGGGGTTCTACGG 59.090 55.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.