Multiple sequence alignment - TraesCS5B01G078600

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 TraesCS5B01G078600 chr5B 100.000 4045 0 0 1 4045 94679386 94675342 0.000000e+00 7470.0
1 TraesCS5B01G078600 chr5B 90.244 41 2 2 543 583 476903691 476903729 7.000000e-03 52.8
2 TraesCS5B01G078600 chr5D 91.495 4115 212 83 1 4045 89378979 89383025 0.000000e+00 5533.0
3 TraesCS5B01G078600 chr5A 90.982 4125 220 83 1 4044 83275453 83279506 0.000000e+00 5417.0
4 TraesCS5B01G078600 chr4B 84.797 592 82 4 2414 3001 74681907 74681320 4.500000e-164 588.0
5 TraesCS5B01G078600 chr4B 82.730 359 58 4 1943 2299 74682362 74682006 2.350000e-82 316.0
6 TraesCS5B01G078600 chr4A 84.122 592 86 4 2414 3001 546211420 546212007 2.110000e-157 566.0
7 TraesCS5B01G078600 chr4A 83.146 356 56 4 1943 2296 546210960 546211313 5.040000e-84 322.0
8 TraesCS5B01G078600 chr4D 83.784 592 88 4 2414 3001 50770648 50770061 4.570000e-154 555.0
9 TraesCS5B01G078600 chr4D 84.123 359 53 4 1943 2299 50771110 50770754 1.080000e-90 344.0


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 TraesCS5B01G078600 chr5B 94675342 94679386 4044 True 7470.0 7470 100.0000 1 4045 1 chr5B.!!$R1 4044
1 TraesCS5B01G078600 chr5D 89378979 89383025 4046 False 5533.0 5533 91.4950 1 4045 1 chr5D.!!$F1 4044
2 TraesCS5B01G078600 chr5A 83275453 83279506 4053 False 5417.0 5417 90.9820 1 4044 1 chr5A.!!$F1 4043
3 TraesCS5B01G078600 chr4B 74681320 74682362 1042 True 452.0 588 83.7635 1943 3001 2 chr4B.!!$R1 1058
4 TraesCS5B01G078600 chr4A 546210960 546212007 1047 False 444.0 566 83.6340 1943 3001 2 chr4A.!!$F1 1058
5 TraesCS5B01G078600 chr4D 50770061 50771110 1049 True 449.5 555 83.9535 1943 3001 2 chr4D.!!$R1 1058

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
731 858 0.713579 AGAGGAGGGTAAGCTCACCT 59.286 55.0 5.87 4.64 38.73 4.00 F
1445 1574 0.322975 TGTTGCTCCCTTCTCTGCTC 59.677 55.0 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2207 1.361271 GTTCCTCACGACACGACCA 59.639 57.895 0.0 0.0 0.0 4.02 R
3371 3512 0.798776 CTACCAAGGAAACAGCAGCG 59.201 55.000 0.0 0.0 0.0 5.18 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
23 26 2.058595 ACCGCCAGCTGGTAGTAGG 61.059 63.158 32.81 26.66 38.15 3.18
24 27 2.797278 CCGCCAGCTGGTAGTAGGG 61.797 68.421 32.81 19.60 37.57 3.53
26 29 3.108288 GCCAGCTGGTAGTAGGGGC 62.108 68.421 32.81 12.45 37.57 5.80
27 30 1.689233 CCAGCTGGTAGTAGGGGCA 60.689 63.158 25.53 0.00 0.00 5.36
41 45 2.613129 AGGGGCAAAGCATTTTTCTCT 58.387 42.857 0.00 0.00 35.03 3.10
45 49 3.329386 GGCAAAGCATTTTTCTCTTCCC 58.671 45.455 0.00 0.00 35.03 3.97
52 56 3.801983 GCATTTTTCTCTTCCCCGCAAAA 60.802 43.478 0.00 0.00 0.00 2.44
59 67 1.960689 TCTTCCCCGCAAAAGGAAAAG 59.039 47.619 0.00 0.00 41.54 2.27
65 73 3.130633 CCCGCAAAAGGAAAAGAAAAGG 58.869 45.455 0.00 0.00 0.00 3.11
70 78 5.580691 CGCAAAAGGAAAAGAAAAGGTTTCT 59.419 36.000 0.00 0.00 34.74 2.52
88 96 8.310406 AGGTTTCTCTTTTTCTTTGTTTTGTG 57.690 30.769 0.00 0.00 0.00 3.33
91 99 9.929722 GTTTCTCTTTTTCTTTGTTTTGTGTTT 57.070 25.926 0.00 0.00 0.00 2.83
129 144 4.753610 GCATAGCATGAGAGTTGATTGCTA 59.246 41.667 0.00 5.51 46.47 3.49
133 148 5.191426 AGCATGAGAGTTGATTGCTATTGT 58.809 37.500 0.00 0.00 41.58 2.71
141 156 8.565896 AGAGTTGATTGCTATTGTTATGTGAA 57.434 30.769 0.00 0.00 0.00 3.18
160 175 6.437928 TGTGAAGAAAAGGAAATGTGAATCG 58.562 36.000 0.00 0.00 0.00 3.34
207 224 3.889520 AGGAAACGTGAGAGGTAATCC 57.110 47.619 0.00 0.00 0.00 3.01
213 231 2.298163 ACGTGAGAGGTAATCCGTGTTT 59.702 45.455 0.00 0.00 39.05 2.83
221 239 5.930569 AGAGGTAATCCGTGTTTCTTTGTAC 59.069 40.000 0.00 0.00 39.05 2.90
222 240 5.613329 AGGTAATCCGTGTTTCTTTGTACA 58.387 37.500 0.00 0.00 39.05 2.90
228 246 5.417811 TCCGTGTTTCTTTGTACAACACTA 58.582 37.500 20.03 9.59 45.40 2.74
229 247 5.873712 TCCGTGTTTCTTTGTACAACACTAA 59.126 36.000 20.03 9.32 45.40 2.24
254 289 7.148641 ACTCTTTGTACTACACACATTGAGAG 58.851 38.462 0.00 0.00 36.69 3.20
260 296 2.592102 ACACACATTGAGAGCCCAAT 57.408 45.000 0.00 0.00 37.24 3.16
270 306 2.092753 TGAGAGCCCAATCACATCTTCC 60.093 50.000 0.00 0.00 0.00 3.46
273 309 1.134280 AGCCCAATCACATCTTCCGAG 60.134 52.381 0.00 0.00 0.00 4.63
285 321 4.406003 ACATCTTCCGAGTTAGGTGCTTAT 59.594 41.667 0.00 0.00 0.00 1.73
287 323 5.511234 TCTTCCGAGTTAGGTGCTTATAC 57.489 43.478 0.00 0.00 0.00 1.47
289 325 6.359804 TCTTCCGAGTTAGGTGCTTATACTA 58.640 40.000 0.00 0.00 0.00 1.82
290 326 7.002879 TCTTCCGAGTTAGGTGCTTATACTAT 58.997 38.462 0.00 0.00 0.00 2.12
291 327 7.504911 TCTTCCGAGTTAGGTGCTTATACTATT 59.495 37.037 0.00 0.00 0.00 1.73
292 328 8.696043 TTCCGAGTTAGGTGCTTATACTATTA 57.304 34.615 0.00 0.00 0.00 0.98
293 329 8.696043 TCCGAGTTAGGTGCTTATACTATTAA 57.304 34.615 0.00 0.00 0.00 1.40
295 331 9.189723 CCGAGTTAGGTGCTTATACTATTAAAC 57.810 37.037 0.00 0.00 0.00 2.01
320 356 9.764363 ACATATCATTGTTCACATCGTATTAGT 57.236 29.630 0.00 0.00 0.00 2.24
370 408 3.851976 AGAGACGTGACTCATACAACC 57.148 47.619 0.00 0.00 39.14 3.77
371 409 3.154710 AGAGACGTGACTCATACAACCA 58.845 45.455 0.00 0.00 39.14 3.67
373 411 3.914312 AGACGTGACTCATACAACCAAG 58.086 45.455 0.00 0.00 0.00 3.61
374 412 3.572682 AGACGTGACTCATACAACCAAGA 59.427 43.478 0.00 0.00 0.00 3.02
375 413 4.038763 AGACGTGACTCATACAACCAAGAA 59.961 41.667 0.00 0.00 0.00 2.52
376 414 4.056050 ACGTGACTCATACAACCAAGAAC 58.944 43.478 0.00 0.00 0.00 3.01
377 415 3.121279 CGTGACTCATACAACCAAGAACG 59.879 47.826 0.00 0.00 0.00 3.95
381 419 4.056050 ACTCATACAACCAAGAACGTGTC 58.944 43.478 0.00 0.00 0.00 3.67
400 438 1.677576 TCGCGTGAGACCCGTTATTAT 59.322 47.619 5.77 0.00 0.00 1.28
415 453 4.961551 CGTTATTATGGCTTTACGTTGCTG 59.038 41.667 0.00 0.00 0.00 4.41
416 454 5.220510 CGTTATTATGGCTTTACGTTGCTGA 60.221 40.000 0.00 0.00 0.00 4.26
417 455 4.616181 ATTATGGCTTTACGTTGCTGAC 57.384 40.909 0.00 0.00 0.00 3.51
471 517 7.959175 ACTCCAACTTATAACACACACTCTAA 58.041 34.615 0.00 0.00 0.00 2.10
477 523 8.961294 ACTTATAACACACACTCTAACTTACG 57.039 34.615 0.00 0.00 0.00 3.18
487 533 4.684242 CACTCTAACTTACGTGACATGCAA 59.316 41.667 0.00 0.00 0.00 4.08
493 571 8.225107 TCTAACTTACGTGACATGCAATAAAAC 58.775 33.333 0.00 0.00 0.00 2.43
494 572 5.695818 ACTTACGTGACATGCAATAAAACC 58.304 37.500 0.00 0.00 0.00 3.27
508 586 4.935352 ATAAAACCAAAGCAACAGAGCA 57.065 36.364 0.00 0.00 36.85 4.26
509 587 3.608316 AAAACCAAAGCAACAGAGCAA 57.392 38.095 0.00 0.00 36.85 3.91
510 588 2.584492 AACCAAAGCAACAGAGCAAC 57.416 45.000 0.00 0.00 36.85 4.17
511 589 1.473258 ACCAAAGCAACAGAGCAACA 58.527 45.000 0.00 0.00 36.85 3.33
515 593 3.514645 CAAAGCAACAGAGCAACAACTT 58.485 40.909 0.00 0.00 36.85 2.66
518 596 4.192429 AGCAACAGAGCAACAACTTTTT 57.808 36.364 0.00 0.00 36.85 1.94
531 609 7.552330 AGCAACAACTTTTTCAAACACCATTAT 59.448 29.630 0.00 0.00 0.00 1.28
574 653 9.912634 AAATTAGATCAGAAATTTTCTCGCAAA 57.087 25.926 8.71 1.84 38.11 3.68
575 654 9.912634 AATTAGATCAGAAATTTTCTCGCAAAA 57.087 25.926 8.71 2.77 38.11 2.44
576 655 9.912634 ATTAGATCAGAAATTTTCTCGCAAAAA 57.087 25.926 8.71 1.40 38.11 1.94
608 687 9.775854 ACATCAAGAATAAATCAGATCTAGTGG 57.224 33.333 0.00 0.00 0.00 4.00
609 688 9.993454 CATCAAGAATAAATCAGATCTAGTGGA 57.007 33.333 0.00 0.00 0.00 4.02
611 690 8.646004 TCAAGAATAAATCAGATCTAGTGGAGG 58.354 37.037 0.00 0.00 0.00 4.30
612 691 8.646004 CAAGAATAAATCAGATCTAGTGGAGGA 58.354 37.037 0.00 0.00 0.00 3.71
613 692 8.789767 AGAATAAATCAGATCTAGTGGAGGAA 57.210 34.615 0.00 0.00 0.00 3.36
614 693 9.218525 AGAATAAATCAGATCTAGTGGAGGAAA 57.781 33.333 0.00 0.00 0.00 3.13
615 694 9.838339 GAATAAATCAGATCTAGTGGAGGAAAA 57.162 33.333 0.00 0.00 0.00 2.29
618 697 5.878406 TCAGATCTAGTGGAGGAAAATCC 57.122 43.478 0.00 0.00 40.03 3.01
632 711 5.665916 GGAAAATCCTGATGTTTGACCAT 57.334 39.130 0.00 0.00 32.53 3.55
633 712 5.654497 GGAAAATCCTGATGTTTGACCATC 58.346 41.667 0.00 0.00 41.32 3.51
634 713 5.394553 GGAAAATCCTGATGTTTGACCATCC 60.395 44.000 0.00 0.00 40.43 3.51
635 714 2.806945 TCCTGATGTTTGACCATCCC 57.193 50.000 0.00 0.00 40.43 3.85
636 715 1.991813 TCCTGATGTTTGACCATCCCA 59.008 47.619 0.00 0.00 40.43 4.37
637 716 2.582172 TCCTGATGTTTGACCATCCCAT 59.418 45.455 0.00 0.00 40.43 4.00
638 717 3.011595 TCCTGATGTTTGACCATCCCATT 59.988 43.478 0.00 0.00 40.43 3.16
639 718 4.229353 TCCTGATGTTTGACCATCCCATTA 59.771 41.667 0.00 0.00 40.43 1.90
640 719 4.581824 CCTGATGTTTGACCATCCCATTAG 59.418 45.833 0.00 0.00 40.43 1.73
641 720 3.953612 TGATGTTTGACCATCCCATTAGC 59.046 43.478 0.00 0.00 40.43 3.09
642 721 3.448093 TGTTTGACCATCCCATTAGCA 57.552 42.857 0.00 0.00 0.00 3.49
643 722 3.772387 TGTTTGACCATCCCATTAGCAA 58.228 40.909 0.00 0.00 0.00 3.91
644 723 4.155709 TGTTTGACCATCCCATTAGCAAA 58.844 39.130 0.00 0.00 0.00 3.68
645 724 4.590647 TGTTTGACCATCCCATTAGCAAAA 59.409 37.500 0.00 0.00 0.00 2.44
646 725 5.248020 TGTTTGACCATCCCATTAGCAAAAT 59.752 36.000 0.00 0.00 0.00 1.82
647 726 6.438741 TGTTTGACCATCCCATTAGCAAAATA 59.561 34.615 0.00 0.00 0.00 1.40
648 727 7.125507 TGTTTGACCATCCCATTAGCAAAATAT 59.874 33.333 0.00 0.00 0.00 1.28
649 728 7.673641 TTGACCATCCCATTAGCAAAATATT 57.326 32.000 0.00 0.00 0.00 1.28
650 729 8.774546 TTGACCATCCCATTAGCAAAATATTA 57.225 30.769 0.00 0.00 0.00 0.98
651 730 8.177119 TGACCATCCCATTAGCAAAATATTAC 57.823 34.615 0.00 0.00 0.00 1.89
652 731 7.782168 TGACCATCCCATTAGCAAAATATTACA 59.218 33.333 0.00 0.00 0.00 2.41
653 732 8.546083 ACCATCCCATTAGCAAAATATTACAA 57.454 30.769 0.00 0.00 0.00 2.41
654 733 8.641541 ACCATCCCATTAGCAAAATATTACAAG 58.358 33.333 0.00 0.00 0.00 3.16
681 760 7.781324 AATCCTGGTGTATCACTCAAAAATT 57.219 32.000 0.00 0.00 34.40 1.82
682 761 8.877864 AATCCTGGTGTATCACTCAAAAATTA 57.122 30.769 0.00 0.00 34.40 1.40
683 762 8.877864 ATCCTGGTGTATCACTCAAAAATTAA 57.122 30.769 0.00 0.00 34.40 1.40
684 763 8.335532 TCCTGGTGTATCACTCAAAAATTAAG 57.664 34.615 0.00 0.00 34.40 1.85
687 805 8.877864 TGGTGTATCACTCAAAAATTAAGGAT 57.122 30.769 0.06 0.00 34.40 3.24
706 824 6.336842 AGGATTTTCTCAACATTCCAACAG 57.663 37.500 0.00 0.00 0.00 3.16
708 826 5.243730 GGATTTTCTCAACATTCCAACAGGA 59.756 40.000 0.00 0.00 0.00 3.86
710 828 2.766313 TCTCAACATTCCAACAGGACG 58.234 47.619 0.00 0.00 0.00 4.79
731 858 0.713579 AGAGGAGGGTAAGCTCACCT 59.286 55.000 5.87 4.64 38.73 4.00
895 1022 3.314331 CGCACCCCACTCCACTCT 61.314 66.667 0.00 0.00 0.00 3.24
1445 1574 0.322975 TGTTGCTCCCTTCTCTGCTC 59.677 55.000 0.00 0.00 0.00 4.26
1472 1601 6.596309 TCTTCTTGCTCTAGATTGAGTTCA 57.404 37.500 0.00 0.00 36.51 3.18
1487 1616 1.011451 GTTCACTCCAGTGCTCTCGC 61.011 60.000 1.49 0.00 45.25 5.03
1502 1631 3.368236 GCTCTCGCGAGTACAAATCTTTT 59.632 43.478 33.33 0.00 39.53 2.27
1546 1675 1.904287 TTGATTGCTACCGCCAACTT 58.096 45.000 0.00 0.00 34.43 2.66
1571 1700 7.103641 TCTTTTGGCTGGAATTAGTAGTACTG 58.896 38.462 13.29 0.00 0.00 2.74
1629 1758 6.403309 GGAGAAACTGTTCTTTGACGTTTTCT 60.403 38.462 4.67 4.67 44.42 2.52
1824 1955 7.711339 CAGTAGACCCCTTTAACAGATAATGTC 59.289 40.741 0.00 0.00 43.00 3.06
2076 2207 1.649390 CTACCGAGTGCGAGACAGCT 61.649 60.000 0.00 0.00 40.82 4.24
2079 2210 2.653702 GAGTGCGAGACAGCTGGT 59.346 61.111 19.93 4.31 38.13 4.00
2124 2255 4.383861 CGCTGTGCTGAGCCTGGA 62.384 66.667 0.23 0.00 35.36 3.86
2151 2282 2.513204 CTGTGGCAGATGGCTCCG 60.513 66.667 7.95 0.00 44.01 4.63
2340 2471 6.003950 CCATCTTTAGGTGGTCTTTTCTCAA 58.996 40.000 0.64 0.00 0.00 3.02
2354 2485 7.361286 GGTCTTTTCTCAATTCATCTACACACC 60.361 40.741 0.00 0.00 0.00 4.16
2356 2487 7.884877 TCTTTTCTCAATTCATCTACACACCAT 59.115 33.333 0.00 0.00 0.00 3.55
2630 2764 3.099905 TGTCCACCTCGAAGATTCTCAT 58.900 45.455 0.00 0.00 33.89 2.90
2735 2869 2.108952 GGTGGAGGGGATAATGATTGCT 59.891 50.000 0.00 0.00 0.00 3.91
2897 3031 2.774234 ACCCACTGATATCAAGTCTGGG 59.226 50.000 23.73 23.73 39.78 4.45
2915 3049 1.625818 GGGTCCATCAGTGAGACTGTT 59.374 52.381 11.17 0.00 46.03 3.16
3289 3424 5.015515 GGTGTAGTAGGTAGTCTTTCTGGT 58.984 45.833 0.00 0.00 0.00 4.00
3441 3582 0.391597 AAGGACTTCTTCGTCGGCAA 59.608 50.000 0.00 0.00 34.75 4.52
3770 3920 6.238484 CCCACTTTTACTATACATGCTGAAGC 60.238 42.308 0.00 0.00 42.50 3.86
3802 3952 3.853831 TTAGCTTTGTGATGTGCCATG 57.146 42.857 0.00 0.00 0.00 3.66
3832 3982 4.155063 ACCATAATGCAGCATCAGTGTA 57.845 40.909 8.77 0.00 0.00 2.90
3833 3983 4.722220 ACCATAATGCAGCATCAGTGTAT 58.278 39.130 8.77 0.00 0.00 2.29
3995 4146 4.701956 GCAATTAGCTTTGCCTCTTGTA 57.298 40.909 11.37 0.00 44.94 2.41
4010 4161 7.050377 TGCCTCTTGTATTATCTCTTCCTTTG 58.950 38.462 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 17 1.295020 ATGCTTTGCCCCTACTACCA 58.705 50.000 0.00 0.00 0.00 3.25
15 18 2.437085 AATGCTTTGCCCCTACTACC 57.563 50.000 0.00 0.00 0.00 3.18
23 26 3.329386 GGAAGAGAAAAATGCTTTGCCC 58.671 45.455 0.00 0.00 0.00 5.36
24 27 3.329386 GGGAAGAGAAAAATGCTTTGCC 58.671 45.455 0.00 0.00 0.00 4.52
26 29 3.578688 CGGGGAAGAGAAAAATGCTTTG 58.421 45.455 0.00 0.00 0.00 2.77
27 30 2.029020 GCGGGGAAGAGAAAAATGCTTT 60.029 45.455 0.00 0.00 0.00 3.51
41 45 2.074729 TCTTTTCCTTTTGCGGGGAA 57.925 45.000 0.00 0.00 39.52 3.97
45 49 3.792401 ACCTTTTCTTTTCCTTTTGCGG 58.208 40.909 0.00 0.00 0.00 5.69
52 56 8.816894 AGAAAAAGAGAAACCTTTTCTTTTCCT 58.183 29.630 14.44 7.68 45.43 3.36
65 73 9.929722 AAACACAAAACAAAGAAAAAGAGAAAC 57.070 25.926 0.00 0.00 0.00 2.78
81 89 8.457562 GCGCAACAATAAATAAAAACACAAAAC 58.542 29.630 0.30 0.00 0.00 2.43
82 90 8.175069 TGCGCAACAATAAATAAAAACACAAAA 58.825 25.926 8.16 0.00 0.00 2.44
85 93 6.828502 TGCGCAACAATAAATAAAAACACA 57.171 29.167 8.16 0.00 0.00 3.72
86 94 7.630606 GCTATGCGCAACAATAAATAAAAACAC 59.369 33.333 17.11 0.00 38.92 3.32
104 119 1.575244 TCAACTCTCATGCTATGCGC 58.425 50.000 0.00 0.00 39.77 6.09
115 130 8.201554 TCACATAACAATAGCAATCAACTCTC 57.798 34.615 0.00 0.00 0.00 3.20
119 134 9.624697 TTTCTTCACATAACAATAGCAATCAAC 57.375 29.630 0.00 0.00 0.00 3.18
123 138 9.023962 TCCTTTTCTTCACATAACAATAGCAAT 57.976 29.630 0.00 0.00 0.00 3.56
129 144 9.480053 CACATTTCCTTTTCTTCACATAACAAT 57.520 29.630 0.00 0.00 0.00 2.71
133 148 9.912634 GATTCACATTTCCTTTTCTTCACATAA 57.087 29.630 0.00 0.00 0.00 1.90
141 156 7.917505 GCAATATCGATTCACATTTCCTTTTCT 59.082 33.333 1.71 0.00 0.00 2.52
192 209 1.542492 ACACGGATTACCTCTCACGT 58.458 50.000 0.00 0.00 34.61 4.49
221 239 7.490079 TGTGTGTAGTACAAAGAGTTAGTGTTG 59.510 37.037 4.11 0.00 41.89 3.33
222 240 7.549839 TGTGTGTAGTACAAAGAGTTAGTGTT 58.450 34.615 4.11 0.00 41.89 3.32
228 246 7.497595 TCTCAATGTGTGTAGTACAAAGAGTT 58.502 34.615 4.11 0.00 41.89 3.01
229 247 7.050970 TCTCAATGTGTGTAGTACAAAGAGT 57.949 36.000 4.11 0.00 41.89 3.24
240 258 3.008923 TGATTGGGCTCTCAATGTGTGTA 59.991 43.478 0.00 0.00 37.47 2.90
241 259 2.224843 TGATTGGGCTCTCAATGTGTGT 60.225 45.455 0.00 0.00 37.47 3.72
242 260 2.163010 GTGATTGGGCTCTCAATGTGTG 59.837 50.000 0.00 0.00 37.47 3.82
243 261 2.224843 TGTGATTGGGCTCTCAATGTGT 60.225 45.455 0.00 0.00 37.47 3.72
254 289 1.303309 CTCGGAAGATGTGATTGGGC 58.697 55.000 0.00 0.00 40.84 5.36
260 296 2.094182 GCACCTAACTCGGAAGATGTGA 60.094 50.000 0.00 0.00 40.84 3.58
270 306 9.740239 TGTTTAATAGTATAAGCACCTAACTCG 57.260 33.333 0.00 0.00 0.00 4.18
336 372 9.088512 GAGTCACGTCTCTTTTCACATAATAAT 57.911 33.333 0.00 0.00 0.00 1.28
339 377 6.455647 TGAGTCACGTCTCTTTTCACATAAT 58.544 36.000 5.92 0.00 35.68 1.28
344 382 5.220381 TGTATGAGTCACGTCTCTTTTCAC 58.780 41.667 0.00 0.00 35.68 3.18
386 424 4.446719 CGTAAAGCCATAATAACGGGTCTC 59.553 45.833 0.00 0.00 31.11 3.36
392 430 4.961551 CAGCAACGTAAAGCCATAATAACG 59.038 41.667 0.00 0.00 36.48 3.18
400 438 1.332375 GTTGTCAGCAACGTAAAGCCA 59.668 47.619 0.00 0.00 44.40 4.75
415 453 3.870723 TGTTTATCTGCACACGTTGTC 57.129 42.857 0.00 0.00 0.00 3.18
416 454 3.609175 GCATGTTTATCTGCACACGTTGT 60.609 43.478 0.00 0.00 38.28 3.32
417 455 2.910482 GCATGTTTATCTGCACACGTTG 59.090 45.455 0.00 0.00 38.28 4.10
423 463 3.485947 TTTCCGCATGTTTATCTGCAC 57.514 42.857 0.00 0.00 38.30 4.57
477 523 4.749099 TGCTTTGGTTTTATTGCATGTCAC 59.251 37.500 0.00 0.00 0.00 3.67
487 533 4.935352 TGCTCTGTTGCTTTGGTTTTAT 57.065 36.364 0.00 0.00 0.00 1.40
493 571 2.159198 AGTTGTTGCTCTGTTGCTTTGG 60.159 45.455 0.00 0.00 0.00 3.28
494 572 3.155093 AGTTGTTGCTCTGTTGCTTTG 57.845 42.857 0.00 0.00 0.00 2.77
582 661 9.775854 CCACTAGATCTGATTTATTCTTGATGT 57.224 33.333 5.18 0.00 0.00 3.06
583 662 9.993454 TCCACTAGATCTGATTTATTCTTGATG 57.007 33.333 5.18 0.00 0.00 3.07
585 664 8.646004 CCTCCACTAGATCTGATTTATTCTTGA 58.354 37.037 5.18 0.00 0.00 3.02
586 665 8.646004 TCCTCCACTAGATCTGATTTATTCTTG 58.354 37.037 5.18 0.00 0.00 3.02
587 666 8.789767 TCCTCCACTAGATCTGATTTATTCTT 57.210 34.615 5.18 0.00 0.00 2.52
588 667 8.789767 TTCCTCCACTAGATCTGATTTATTCT 57.210 34.615 5.18 0.00 0.00 2.40
589 668 9.838339 TTTTCCTCCACTAGATCTGATTTATTC 57.162 33.333 5.18 0.00 0.00 1.75
592 671 8.432805 GGATTTTCCTCCACTAGATCTGATTTA 58.567 37.037 5.18 0.00 35.24 1.40
593 672 7.128573 AGGATTTTCCTCCACTAGATCTGATTT 59.871 37.037 5.18 0.00 45.66 2.17
594 673 6.619023 AGGATTTTCCTCCACTAGATCTGATT 59.381 38.462 5.18 0.00 45.66 2.57
595 674 6.043012 CAGGATTTTCCTCCACTAGATCTGAT 59.957 42.308 5.18 0.00 45.66 2.90
596 675 5.365025 CAGGATTTTCCTCCACTAGATCTGA 59.635 44.000 5.18 0.00 45.66 3.27
597 676 5.365025 TCAGGATTTTCCTCCACTAGATCTG 59.635 44.000 5.18 0.00 45.66 2.90
598 677 5.533112 TCAGGATTTTCCTCCACTAGATCT 58.467 41.667 0.00 0.00 45.66 2.75
599 678 5.878406 TCAGGATTTTCCTCCACTAGATC 57.122 43.478 0.00 0.00 45.66 2.75
600 679 5.669447 ACATCAGGATTTTCCTCCACTAGAT 59.331 40.000 0.00 0.00 45.66 1.98
601 680 5.032846 ACATCAGGATTTTCCTCCACTAGA 58.967 41.667 0.00 0.00 45.66 2.43
602 681 5.365021 ACATCAGGATTTTCCTCCACTAG 57.635 43.478 0.00 0.00 45.66 2.57
603 682 5.779241 AACATCAGGATTTTCCTCCACTA 57.221 39.130 0.00 0.00 45.66 2.74
604 683 4.664688 AACATCAGGATTTTCCTCCACT 57.335 40.909 0.00 0.00 45.66 4.00
605 684 4.766891 TCAAACATCAGGATTTTCCTCCAC 59.233 41.667 0.00 0.00 45.66 4.02
606 685 4.766891 GTCAAACATCAGGATTTTCCTCCA 59.233 41.667 0.00 0.00 45.66 3.86
607 686 4.158579 GGTCAAACATCAGGATTTTCCTCC 59.841 45.833 0.00 0.00 45.66 4.30
608 687 4.766891 TGGTCAAACATCAGGATTTTCCTC 59.233 41.667 0.00 0.00 45.66 3.71
610 689 5.654497 GATGGTCAAACATCAGGATTTTCC 58.346 41.667 3.15 0.00 45.11 3.13
620 699 3.953612 TGCTAATGGGATGGTCAAACATC 59.046 43.478 0.00 0.00 45.05 3.06
621 700 3.979911 TGCTAATGGGATGGTCAAACAT 58.020 40.909 0.00 0.00 0.00 2.71
622 701 3.448093 TGCTAATGGGATGGTCAAACA 57.552 42.857 0.00 0.00 0.00 2.83
623 702 4.799564 TTTGCTAATGGGATGGTCAAAC 57.200 40.909 0.00 0.00 0.00 2.93
624 703 7.673641 ATATTTTGCTAATGGGATGGTCAAA 57.326 32.000 0.00 0.00 0.00 2.69
625 704 7.673641 AATATTTTGCTAATGGGATGGTCAA 57.326 32.000 0.00 0.00 0.00 3.18
626 705 7.782168 TGTAATATTTTGCTAATGGGATGGTCA 59.218 33.333 0.00 0.00 0.00 4.02
627 706 8.177119 TGTAATATTTTGCTAATGGGATGGTC 57.823 34.615 0.00 0.00 0.00 4.02
628 707 8.546083 TTGTAATATTTTGCTAATGGGATGGT 57.454 30.769 0.00 0.00 0.00 3.55
629 708 8.859090 TCTTGTAATATTTTGCTAATGGGATGG 58.141 33.333 0.00 0.00 0.00 3.51
639 718 8.815912 ACCAGGATTTTCTTGTAATATTTTGCT 58.184 29.630 0.00 0.00 0.00 3.91
640 719 8.872845 CACCAGGATTTTCTTGTAATATTTTGC 58.127 33.333 0.00 0.00 0.00 3.68
641 720 9.927668 ACACCAGGATTTTCTTGTAATATTTTG 57.072 29.630 0.00 0.00 0.00 2.44
646 725 9.391006 GTGATACACCAGGATTTTCTTGTAATA 57.609 33.333 0.00 0.00 0.00 0.98
647 726 8.109634 AGTGATACACCAGGATTTTCTTGTAAT 58.890 33.333 0.00 0.00 34.49 1.89
648 727 7.458397 AGTGATACACCAGGATTTTCTTGTAA 58.542 34.615 0.00 0.00 34.49 2.41
649 728 7.016153 AGTGATACACCAGGATTTTCTTGTA 57.984 36.000 0.00 0.00 34.49 2.41
650 729 5.880901 AGTGATACACCAGGATTTTCTTGT 58.119 37.500 0.00 0.00 34.49 3.16
651 730 5.939883 TGAGTGATACACCAGGATTTTCTTG 59.060 40.000 0.00 0.00 34.49 3.02
652 731 6.126863 TGAGTGATACACCAGGATTTTCTT 57.873 37.500 0.00 0.00 34.49 2.52
653 732 5.762179 TGAGTGATACACCAGGATTTTCT 57.238 39.130 0.00 0.00 34.49 2.52
654 733 6.817765 TTTGAGTGATACACCAGGATTTTC 57.182 37.500 0.00 0.00 34.49 2.29
681 760 7.039784 CCTGTTGGAATGTTGAGAAAATCCTTA 60.040 37.037 0.00 0.00 34.57 2.69
682 761 6.239402 CCTGTTGGAATGTTGAGAAAATCCTT 60.239 38.462 0.00 0.00 34.57 3.36
683 762 5.244626 CCTGTTGGAATGTTGAGAAAATCCT 59.755 40.000 0.00 0.00 34.57 3.24
684 763 5.243730 TCCTGTTGGAATGTTGAGAAAATCC 59.756 40.000 0.00 0.00 39.87 3.01
687 805 4.036262 CGTCCTGTTGGAATGTTGAGAAAA 59.964 41.667 0.00 0.00 45.18 2.29
693 811 0.950836 TGCGTCCTGTTGGAATGTTG 59.049 50.000 0.00 0.00 45.18 3.33
706 824 1.817209 CTTACCCTCCTCTGCGTCC 59.183 63.158 0.00 0.00 0.00 4.79
708 826 1.305381 AGCTTACCCTCCTCTGCGT 60.305 57.895 0.00 0.00 0.00 5.24
710 828 0.176910 GTGAGCTTACCCTCCTCTGC 59.823 60.000 0.00 0.00 0.00 4.26
731 858 1.919308 TGGCTAGGGTTACCGCCAA 60.919 57.895 17.05 3.63 46.28 4.52
758 885 2.895372 GCGGGGCGGTTATCACAG 60.895 66.667 0.00 0.00 0.00 3.66
870 997 2.104111 TGGAGTGGGGTGCGAATATAAG 59.896 50.000 0.00 0.00 0.00 1.73
895 1022 2.447630 TGGCGACAAAGAGAGGGAA 58.552 52.632 0.00 0.00 37.44 3.97
1311 1438 1.903294 GAGCAGCATCCTCAGGTCA 59.097 57.895 0.00 0.00 0.00 4.02
1445 1574 4.428209 TCAATCTAGAGCAAGAAGAAGCG 58.572 43.478 0.00 0.00 35.48 4.68
1487 1616 6.727824 ATGGACAGAAAAGATTTGTACTCG 57.272 37.500 0.00 0.00 0.00 4.18
1546 1675 7.103641 CAGTACTACTAATTCCAGCCAAAAGA 58.896 38.462 0.00 0.00 0.00 2.52
1593 1722 8.533569 AAGAACAGTTTCTCCCATTTAAGAAA 57.466 30.769 0.00 0.00 41.56 2.52
1596 1725 7.862873 GTCAAAGAACAGTTTCTCCCATTTAAG 59.137 37.037 0.00 0.00 41.56 1.85
1603 1732 3.203716 ACGTCAAAGAACAGTTTCTCCC 58.796 45.455 0.00 0.00 41.56 4.30
1629 1758 5.652014 ACAAGTTTCTGGAACACATTTCAGA 59.348 36.000 0.98 0.00 46.96 3.27
1758 1888 6.530120 GGAAAGCCATTTTTCCCTTTTAGAA 58.470 36.000 6.30 0.00 46.78 2.10
2076 2207 1.361271 GTTCCTCACGACACGACCA 59.639 57.895 0.00 0.00 0.00 4.02
2079 2210 2.640989 CGGTTCCTCACGACACGA 59.359 61.111 0.00 0.00 0.00 4.35
2124 2255 4.539083 TGCCACAGCACGAACCGT 62.539 61.111 0.00 0.00 46.52 4.83
2151 2282 3.201290 CAGCTCAATGTACCACATCTCC 58.799 50.000 0.00 0.00 37.97 3.71
2374 2505 8.786826 ACAATAATCTTCATACTCCGTTTTCA 57.213 30.769 0.00 0.00 0.00 2.69
2386 2517 9.183368 GGAGAGAAAAGGAACAATAATCTTCAT 57.817 33.333 0.00 0.00 0.00 2.57
2599 2733 3.056328 GGTGGACAAGAAGCCCGC 61.056 66.667 0.00 0.00 0.00 6.13
2630 2764 2.890945 TGTGGACTGAATTCGAGTGAGA 59.109 45.455 13.14 0.01 0.00 3.27
2735 2869 4.838152 GCCGAGCGCCCAGAATGA 62.838 66.667 2.29 0.00 39.69 2.57
3077 3211 9.376075 CTACATTCATCAAAATGAGTCAGTAGT 57.624 33.333 0.00 0.00 42.72 2.73
3371 3512 0.798776 CTACCAAGGAAACAGCAGCG 59.201 55.000 0.00 0.00 0.00 5.18
3441 3582 3.512680 GAACGATGAAATCACTCTCGGT 58.487 45.455 9.05 3.15 45.97 4.69
3603 3752 4.080015 TGTGTGAAGGAGAAAGGGAGAAAA 60.080 41.667 0.00 0.00 0.00 2.29
3604 3753 3.458118 TGTGTGAAGGAGAAAGGGAGAAA 59.542 43.478 0.00 0.00 0.00 2.52
3605 3754 3.045634 TGTGTGAAGGAGAAAGGGAGAA 58.954 45.455 0.00 0.00 0.00 2.87
3770 3920 8.192774 ACATCACAAAGCTAAATATCACCAATG 58.807 33.333 0.00 0.00 0.00 2.82
3771 3921 8.192774 CACATCACAAAGCTAAATATCACCAAT 58.807 33.333 0.00 0.00 0.00 3.16
3802 3952 5.811399 TGCTGCATTATGGTACTAACAAC 57.189 39.130 0.00 0.00 0.00 3.32
3832 3982 0.615827 GCAGGAAGGGGGCAAAAGAT 60.616 55.000 0.00 0.00 0.00 2.40
3833 3983 1.228862 GCAGGAAGGGGGCAAAAGA 60.229 57.895 0.00 0.00 0.00 2.52
3995 4146 5.045286 AGTGGAGCACAAAGGAAGAGATAAT 60.045 40.000 0.00 0.00 36.74 1.28
4010 4161 1.950828 CATCTGATGGAGTGGAGCAC 58.049 55.000 9.82 0.00 34.10 4.40


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

AutoCloner maintained by Alex Coulton.