Multiple sequence alignment - TraesCS4A01G092000

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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 TraesCS4A01G092000 chr4A 100.000 3612 0 0 1 3612 98777205 98780816 0.000000e+00 6671
1 TraesCS4A01G092000 chr4D 94.768 2370 101 12 516 2873 366277698 366275340 0.000000e+00 3668
2 TraesCS4A01G092000 chr4D 90.891 505 17 14 1 489 366282924 366282433 0.000000e+00 651
3 TraesCS4A01G092000 chr4D 86.149 296 33 6 1962 2257 366274789 366274502 2.710000e-81 313
4 TraesCS4A01G092000 chr4B 95.409 2309 90 9 626 2927 450863585 450861286 0.000000e+00 3663
5 TraesCS4A01G092000 chr4B 95.067 446 17 3 1 445 450864123 450863682 0.000000e+00 697
6 TraesCS4A01G092000 chr4B 90.196 102 10 0 1962 2063 450860766 450860665 2.260000e-27 134
7 TraesCS4A01G092000 chr2B 90.634 694 56 5 2925 3612 224576760 224577450 0.000000e+00 913
8 TraesCS4A01G092000 chr7B 93.280 625 31 5 2994 3612 614887190 614886571 0.000000e+00 911
9 TraesCS4A01G092000 chr7D 84.993 693 96 5 2926 3612 64260395 64259705 0.000000e+00 697
10 TraesCS4A01G092000 chr5D 85.036 695 89 8 2924 3612 493128778 493129463 0.000000e+00 693
11 TraesCS4A01G092000 chr5B 84.582 694 94 5 2924 3612 608356446 608357131 0.000000e+00 676
12 TraesCS4A01G092000 chr5B 84.438 694 93 6 2924 3612 608211167 608211850 0.000000e+00 669
13 TraesCS4A01G092000 chr1A 84.672 685 96 6 2925 3602 566605821 566605139 0.000000e+00 675
14 TraesCS4A01G092000 chr1D 83.671 692 96 12 2935 3612 8239652 8238964 1.410000e-178 636
15 TraesCS4A01G092000 chr3D 83.633 611 90 5 2925 3528 575560307 575559700 1.880000e-157 566


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 TraesCS4A01G092000 chr4A 98777205 98780816 3611 False 6671.0 6671 100.000000 1 3612 1 chr4A.!!$F1 3611
1 TraesCS4A01G092000 chr4D 366274502 366277698 3196 True 1990.5 3668 90.458500 516 2873 2 chr4D.!!$R2 2357
2 TraesCS4A01G092000 chr4B 450860665 450864123 3458 True 1498.0 3663 93.557333 1 2927 3 chr4B.!!$R1 2926
3 TraesCS4A01G092000 chr2B 224576760 224577450 690 False 913.0 913 90.634000 2925 3612 1 chr2B.!!$F1 687
4 TraesCS4A01G092000 chr7B 614886571 614887190 619 True 911.0 911 93.280000 2994 3612 1 chr7B.!!$R1 618
5 TraesCS4A01G092000 chr7D 64259705 64260395 690 True 697.0 697 84.993000 2926 3612 1 chr7D.!!$R1 686
6 TraesCS4A01G092000 chr5D 493128778 493129463 685 False 693.0 693 85.036000 2924 3612 1 chr5D.!!$F1 688
7 TraesCS4A01G092000 chr5B 608356446 608357131 685 False 676.0 676 84.582000 2924 3612 1 chr5B.!!$F2 688
8 TraesCS4A01G092000 chr5B 608211167 608211850 683 False 669.0 669 84.438000 2924 3612 1 chr5B.!!$F1 688
9 TraesCS4A01G092000 chr1A 566605139 566605821 682 True 675.0 675 84.672000 2925 3602 1 chr1A.!!$R1 677
10 TraesCS4A01G092000 chr1D 8238964 8239652 688 True 636.0 636 83.671000 2935 3612 1 chr1D.!!$R1 677
11 TraesCS4A01G092000 chr3D 575559700 575560307 607 True 566.0 566 83.633000 2925 3528 1 chr3D.!!$R1 603

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
346 348 1.039068 CACACATGGGAAAAGGCACA 58.961 50.0 0.00 0.0 0.00 4.57 F
1251 1284 0.040067 CCAAGCTGAAACCTGCGAAC 60.040 55.0 0.00 0.0 34.27 3.95 F
2277 2312 0.598158 GGTAACACGGCGTCACTGAA 60.598 55.0 10.85 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2295 0.386476 AGTTCAGTGACGCCGTGTTA 59.614 50.000 0.00 0.0 0.00 2.41 R
2572 2607 1.077645 GCAGCAGCTCTCTGAACTCG 61.078 60.000 14.83 0.0 42.95 4.18 R
3204 3258 1.153549 GTGCAGATGGAGACCGACC 60.154 63.158 0.00 0.0 0.00 4.79 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
96 97 1.467342 GTGGTGGATACTTTTGCGGAC 59.533 52.381 0.00 0.00 37.61 4.79
165 166 2.285977 GAAAGTTATTCGGGGCGATGT 58.714 47.619 0.00 0.00 35.23 3.06
171 172 1.094785 ATTCGGGGCGATGTTTTCAG 58.905 50.000 0.00 0.00 35.23 3.02
199 201 2.103263 GTGAGCTTATCTGGATTCGGGT 59.897 50.000 0.00 0.00 0.00 5.28
217 219 1.394917 GGTGATGCAGCAAGTACTTCG 59.605 52.381 6.05 3.03 0.00 3.79
260 262 3.270027 TCAAGCGTCCATCCATTAACTG 58.730 45.455 0.00 0.00 0.00 3.16
275 277 5.385617 CATTAACTGGAGAAAAAGCTCACG 58.614 41.667 0.00 0.00 36.62 4.35
300 302 6.630413 GCGGAGGGATGATGATAATAAGCTAA 60.630 42.308 0.00 0.00 0.00 3.09
301 303 6.983307 CGGAGGGATGATGATAATAAGCTAAG 59.017 42.308 0.00 0.00 0.00 2.18
336 338 1.881973 CTGGTTCTGTTCACACATGGG 59.118 52.381 0.00 0.00 30.39 4.00
337 339 1.492599 TGGTTCTGTTCACACATGGGA 59.507 47.619 0.00 0.00 30.39 4.37
346 348 1.039068 CACACATGGGAAAAGGCACA 58.961 50.000 0.00 0.00 0.00 4.57
356 358 5.083122 TGGGAAAAGGCACAAAGAATGATA 58.917 37.500 0.00 0.00 0.00 2.15
451 453 9.865321 TCTTTTCTTGTAAACGCTATATACAGT 57.135 29.630 0.00 0.00 31.72 3.55
478 480 9.883142 AGAAAGTAGTAGAAATCATTTCCTCTG 57.117 33.333 6.50 0.00 40.54 3.35
479 481 8.499403 AAAGTAGTAGAAATCATTTCCTCTGC 57.501 34.615 6.50 8.80 40.54 4.26
480 482 6.587273 AGTAGTAGAAATCATTTCCTCTGCC 58.413 40.000 6.50 2.33 40.54 4.85
481 483 5.441718 AGTAGAAATCATTTCCTCTGCCA 57.558 39.130 6.50 0.00 40.54 4.92
482 484 5.819991 AGTAGAAATCATTTCCTCTGCCAA 58.180 37.500 6.50 0.00 40.54 4.52
483 485 6.248433 AGTAGAAATCATTTCCTCTGCCAAA 58.752 36.000 6.50 0.00 40.54 3.28
484 486 5.397142 AGAAATCATTTCCTCTGCCAAAC 57.603 39.130 6.50 0.00 40.54 2.93
485 487 4.221482 AGAAATCATTTCCTCTGCCAAACC 59.779 41.667 6.50 0.00 40.54 3.27
486 488 2.978156 TCATTTCCTCTGCCAAACCT 57.022 45.000 0.00 0.00 0.00 3.50
487 489 3.243359 TCATTTCCTCTGCCAAACCTT 57.757 42.857 0.00 0.00 0.00 3.50
488 490 3.575805 TCATTTCCTCTGCCAAACCTTT 58.424 40.909 0.00 0.00 0.00 3.11
489 491 3.573967 TCATTTCCTCTGCCAAACCTTTC 59.426 43.478 0.00 0.00 0.00 2.62
490 492 3.312736 TTTCCTCTGCCAAACCTTTCT 57.687 42.857 0.00 0.00 0.00 2.52
491 493 2.568623 TCCTCTGCCAAACCTTTCTC 57.431 50.000 0.00 0.00 0.00 2.87
492 494 1.774254 TCCTCTGCCAAACCTTTCTCA 59.226 47.619 0.00 0.00 0.00 3.27
493 495 1.882623 CCTCTGCCAAACCTTTCTCAC 59.117 52.381 0.00 0.00 0.00 3.51
494 496 2.487986 CCTCTGCCAAACCTTTCTCACT 60.488 50.000 0.00 0.00 0.00 3.41
495 497 3.244561 CCTCTGCCAAACCTTTCTCACTA 60.245 47.826 0.00 0.00 0.00 2.74
496 498 4.389374 CTCTGCCAAACCTTTCTCACTAA 58.611 43.478 0.00 0.00 0.00 2.24
497 499 4.787551 TCTGCCAAACCTTTCTCACTAAA 58.212 39.130 0.00 0.00 0.00 1.85
498 500 5.197451 TCTGCCAAACCTTTCTCACTAAAA 58.803 37.500 0.00 0.00 0.00 1.52
499 501 5.833131 TCTGCCAAACCTTTCTCACTAAAAT 59.167 36.000 0.00 0.00 0.00 1.82
500 502 5.841810 TGCCAAACCTTTCTCACTAAAATG 58.158 37.500 0.00 0.00 0.00 2.32
501 503 5.596361 TGCCAAACCTTTCTCACTAAAATGA 59.404 36.000 0.00 0.00 0.00 2.57
502 504 6.097554 TGCCAAACCTTTCTCACTAAAATGAA 59.902 34.615 0.00 0.00 0.00 2.57
503 505 6.420903 GCCAAACCTTTCTCACTAAAATGAAC 59.579 38.462 0.00 0.00 0.00 3.18
504 506 6.923508 CCAAACCTTTCTCACTAAAATGAACC 59.076 38.462 0.00 0.00 0.00 3.62
505 507 7.201911 CCAAACCTTTCTCACTAAAATGAACCT 60.202 37.037 0.00 0.00 0.00 3.50
506 508 6.884280 ACCTTTCTCACTAAAATGAACCTG 57.116 37.500 0.00 0.00 0.00 4.00
603 636 7.532546 CGAACACTAGTCGAGATTATCTCATTC 59.467 40.741 20.49 10.51 43.55 2.67
604 637 8.458573 AACACTAGTCGAGATTATCTCATTCT 57.541 34.615 20.49 15.93 43.55 2.40
605 638 8.094798 ACACTAGTCGAGATTATCTCATTCTC 57.905 38.462 20.49 6.92 43.55 2.87
606 639 7.936847 ACACTAGTCGAGATTATCTCATTCTCT 59.063 37.037 20.49 12.55 43.55 3.10
607 640 8.783093 CACTAGTCGAGATTATCTCATTCTCTT 58.217 37.037 20.49 5.01 43.55 2.85
608 641 8.783093 ACTAGTCGAGATTATCTCATTCTCTTG 58.217 37.037 20.49 12.90 43.55 3.02
609 642 7.581213 AGTCGAGATTATCTCATTCTCTTGT 57.419 36.000 20.49 0.00 43.55 3.16
610 643 7.648142 AGTCGAGATTATCTCATTCTCTTGTC 58.352 38.462 20.49 1.93 43.55 3.18
611 644 7.502226 AGTCGAGATTATCTCATTCTCTTGTCT 59.498 37.037 20.49 3.92 43.55 3.41
612 645 8.134895 GTCGAGATTATCTCATTCTCTTGTCTT 58.865 37.037 20.49 0.00 43.55 3.01
613 646 8.134261 TCGAGATTATCTCATTCTCTTGTCTTG 58.866 37.037 20.49 1.27 43.55 3.02
614 647 8.134261 CGAGATTATCTCATTCTCTTGTCTTGA 58.866 37.037 20.49 0.00 43.55 3.02
615 648 9.985730 GAGATTATCTCATTCTCTTGTCTTGAT 57.014 33.333 16.53 0.00 42.90 2.57
616 649 9.767228 AGATTATCTCATTCTCTTGTCTTGATG 57.233 33.333 0.00 0.00 0.00 3.07
617 650 8.905660 ATTATCTCATTCTCTTGTCTTGATGG 57.094 34.615 0.00 0.00 0.00 3.51
618 651 6.556974 ATCTCATTCTCTTGTCTTGATGGA 57.443 37.500 0.00 0.00 0.00 3.41
619 652 6.556974 TCTCATTCTCTTGTCTTGATGGAT 57.443 37.500 0.00 0.00 0.00 3.41
620 653 6.580788 TCTCATTCTCTTGTCTTGATGGATC 58.419 40.000 0.00 0.00 0.00 3.36
621 654 6.155737 TCTCATTCTCTTGTCTTGATGGATCA 59.844 38.462 0.00 0.00 34.44 2.92
622 655 6.346896 TCATTCTCTTGTCTTGATGGATCAG 58.653 40.000 0.00 0.00 38.19 2.90
623 656 4.134379 TCTCTTGTCTTGATGGATCAGC 57.866 45.455 0.00 0.00 38.19 4.26
624 657 3.773667 TCTCTTGTCTTGATGGATCAGCT 59.226 43.478 0.00 0.00 38.19 4.24
625 658 4.224594 TCTCTTGTCTTGATGGATCAGCTT 59.775 41.667 0.00 0.00 38.19 3.74
626 659 4.914983 TCTTGTCTTGATGGATCAGCTTT 58.085 39.130 0.00 0.00 38.19 3.51
638 671 3.606065 CAGCTTTCTGCGCTGCACC 62.606 63.158 9.73 0.00 46.98 5.01
648 681 2.675056 CGCTGCACCAGACTTGCTC 61.675 63.158 0.00 0.00 40.86 4.26
667 700 6.363577 TGCTCGATTTTCCTTGATGTAATC 57.636 37.500 0.00 0.00 45.83 1.75
821 854 1.619827 CTGAAAGGGGCTTTGCAATCA 59.380 47.619 0.00 0.00 33.49 2.57
822 855 1.344114 TGAAAGGGGCTTTGCAATCAC 59.656 47.619 0.00 0.00 33.49 3.06
857 890 3.051210 GTTGCCCTCAACTTGCCC 58.949 61.111 1.31 0.00 46.81 5.36
866 899 2.874701 CCTCAACTTGCCCTATCGAATG 59.125 50.000 0.00 0.00 0.00 2.67
870 903 3.366052 ACTTGCCCTATCGAATGGTTT 57.634 42.857 0.00 0.00 0.00 3.27
886 919 8.889717 TCGAATGGTTTCTAATAATTTGACCTC 58.110 33.333 0.00 0.00 0.00 3.85
902 935 3.095332 GACCTCCTTAGTACTTTCCCGT 58.905 50.000 0.00 0.00 0.00 5.28
905 938 4.020751 ACCTCCTTAGTACTTTCCCGTTTC 60.021 45.833 0.00 0.00 0.00 2.78
927 960 2.045561 TTTCACCTCGTGGCTTGAAA 57.954 45.000 14.73 14.73 36.56 2.69
941 974 8.556194 TCGTGGCTTGAAATGTGTATATAATTC 58.444 33.333 0.00 0.00 0.00 2.17
1094 1127 2.299582 CCCACTCTCTCCAGATATGCAG 59.700 54.545 0.00 0.00 0.00 4.41
1186 1219 3.303881 TGTCTTTCTCCATCTGTGACG 57.696 47.619 0.00 0.00 0.00 4.35
1187 1220 2.029020 TGTCTTTCTCCATCTGTGACGG 60.029 50.000 0.00 0.00 0.00 4.79
1251 1284 0.040067 CCAAGCTGAAACCTGCGAAC 60.040 55.000 0.00 0.00 34.27 3.95
1305 1338 4.767255 GTCTGCGGGGTGCTCAGG 62.767 72.222 0.00 0.00 46.63 3.86
1431 1464 1.068250 GGTCTGCATCTACGAGGCC 59.932 63.158 0.00 0.00 38.67 5.19
1578 1611 2.109126 GCTGAATCTGGGCGTCACC 61.109 63.158 0.00 0.00 37.93 4.02
1588 1621 4.643387 GCGTCACCAACTGGGCCT 62.643 66.667 4.53 0.00 42.05 5.19
1695 1728 2.592993 GGTCCAGCTGTACTGCCCA 61.593 63.158 19.81 2.78 45.78 5.36
1739 1773 2.268920 CCGTCCCATCACCACCAG 59.731 66.667 0.00 0.00 0.00 4.00
1742 1776 1.377725 GTCCCATCACCACCAGCAG 60.378 63.158 0.00 0.00 0.00 4.24
1950 1984 8.798859 AACTGCACTAAATGATTTACTGATCT 57.201 30.769 8.22 0.00 0.00 2.75
1952 1986 7.019774 TGCACTAAATGATTTACTGATCTGC 57.980 36.000 8.22 1.94 0.00 4.26
2277 2312 0.598158 GGTAACACGGCGTCACTGAA 60.598 55.000 10.85 0.00 0.00 3.02
2465 2500 2.046892 GCGTGTGCTGGAGGATGT 60.047 61.111 0.00 0.00 38.39 3.06
2509 2544 1.274703 TGGAGTGGGAGATCAAGGGC 61.275 60.000 0.00 0.00 0.00 5.19
2572 2607 0.468400 ATACGGAGACCAGGAGGCTC 60.468 60.000 5.78 5.78 39.06 4.70
2613 2648 4.691175 CATCTCACCATTGGAGAGTAGTG 58.309 47.826 23.98 18.12 44.04 2.74
2747 2786 4.832590 ATAATACGCTAGCACTCGACTT 57.167 40.909 16.45 0.67 0.00 3.01
2760 2799 4.745620 GCACTCGACTTAGAAGTGAAAAGT 59.254 41.667 14.57 0.00 39.88 2.66
2761 2800 5.919141 GCACTCGACTTAGAAGTGAAAAGTA 59.081 40.000 14.57 0.00 39.88 2.24
2762 2801 6.586844 GCACTCGACTTAGAAGTGAAAAGTAT 59.413 38.462 14.57 0.00 39.88 2.12
2787 2826 5.499004 AAGCAGTAAAGGATTACACCAGA 57.501 39.130 2.01 0.00 43.20 3.86
2828 2867 5.425217 TGAAGATGAACCCATAGCTCACTTA 59.575 40.000 0.00 0.00 32.09 2.24
2842 2881 8.986847 CATAGCTCACTTATTCATTTCTACTGG 58.013 37.037 0.00 0.00 0.00 4.00
2873 2912 8.791327 TGAAAAACATGATATAGAGTCAGCAA 57.209 30.769 0.00 0.00 0.00 3.91
2874 2913 8.668353 TGAAAAACATGATATAGAGTCAGCAAC 58.332 33.333 0.00 0.00 0.00 4.17
2894 2935 5.065090 GCAACATTCAATTAAGGGATTTGGC 59.935 40.000 0.00 0.00 0.00 4.52
2904 2945 4.769345 AAGGGATTTGGCTGTTCAAAAA 57.231 36.364 0.00 0.00 39.64 1.94
2986 3029 4.846779 TTGGGTTACAATCAGAAGCAAC 57.153 40.909 0.00 0.00 33.18 4.17
2987 3030 3.826524 TGGGTTACAATCAGAAGCAACA 58.173 40.909 0.00 0.00 0.00 3.33
2990 3033 4.546570 GGTTACAATCAGAAGCAACAACC 58.453 43.478 0.00 0.00 0.00 3.77
3042 3096 7.911651 TGAAAGAAATCTCCATTCACTCTAGT 58.088 34.615 0.00 0.00 0.00 2.57
3202 3256 2.125832 GCGGCCACTACAGCGTTA 60.126 61.111 2.24 0.00 0.00 3.18
3204 3258 2.156446 CGGCCACTACAGCGTTACG 61.156 63.158 2.24 0.00 0.00 3.18
3229 3283 3.679917 CGGTCTCCATCTGCACTATGTTT 60.680 47.826 4.12 0.00 0.00 2.83
3275 3329 2.091665 AGACCAAAAGATAGGGCATGGG 60.092 50.000 0.00 0.00 34.45 4.00
3288 3342 0.969409 GCATGGGCTTCAGCTTCCTT 60.969 55.000 0.00 0.00 41.70 3.36
3349 3593 8.463930 AGAAGACAATTTCACCAAAACTATCA 57.536 30.769 0.00 0.00 0.00 2.15
3363 3607 1.148157 CTATCACTGCCAACCGCTCG 61.148 60.000 0.00 0.00 38.78 5.03
3443 3687 1.885163 CTCGGGCGGTTTAGTCCAGT 61.885 60.000 0.00 0.00 35.10 4.00
3498 3910 9.894783 AGTATACTGCGTATTAACTACATGAAG 57.105 33.333 4.10 0.00 30.79 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 7.011482 GCAAAAGTATCCACCACTAATCACTAG 59.989 40.741 0.00 0.00 0.00 2.57
67 68 6.821665 GCAAAAGTATCCACCACTAATCACTA 59.178 38.462 0.00 0.00 0.00 2.74
68 69 5.648092 GCAAAAGTATCCACCACTAATCACT 59.352 40.000 0.00 0.00 0.00 3.41
85 86 1.134175 CCAAGTGTTGTCCGCAAAAGT 59.866 47.619 0.00 0.00 36.22 2.66
96 97 2.624838 AGATTGCCTTCACCAAGTGTTG 59.375 45.455 0.00 0.00 34.79 3.33
165 166 6.650807 CAGATAAGCTCACCAACTACTGAAAA 59.349 38.462 0.00 0.00 0.00 2.29
171 172 4.737855 TCCAGATAAGCTCACCAACTAC 57.262 45.455 0.00 0.00 0.00 2.73
199 201 2.068519 CACGAAGTACTTGCTGCATCA 58.931 47.619 14.14 0.00 41.61 3.07
217 219 2.813754 TGCTTCAGGTAACATCAAGCAC 59.186 45.455 6.89 0.00 43.45 4.40
275 277 3.873952 GCTTATTATCATCATCCCTCCGC 59.126 47.826 0.00 0.00 0.00 5.54
300 302 3.446442 ACCAGATCCTTTTGTCATGCT 57.554 42.857 0.00 0.00 0.00 3.79
301 303 3.760684 AGAACCAGATCCTTTTGTCATGC 59.239 43.478 0.00 0.00 0.00 4.06
336 338 6.071952 TGAGGTATCATTCTTTGTGCCTTTTC 60.072 38.462 0.00 0.00 0.00 2.29
337 339 5.774690 TGAGGTATCATTCTTTGTGCCTTTT 59.225 36.000 0.00 0.00 0.00 2.27
356 358 1.826385 GCAGTTAGGTGCAATGAGGT 58.174 50.000 0.00 0.00 43.41 3.85
452 454 9.883142 CAGAGGAAATGATTTCTACTACTTTCT 57.117 33.333 16.58 3.07 39.59 2.52
453 455 8.608317 GCAGAGGAAATGATTTCTACTACTTTC 58.392 37.037 16.58 0.00 39.59 2.62
454 456 7.554476 GGCAGAGGAAATGATTTCTACTACTTT 59.446 37.037 16.58 0.00 39.59 2.66
455 457 7.051000 GGCAGAGGAAATGATTTCTACTACTT 58.949 38.462 16.58 0.00 39.59 2.24
456 458 6.156949 TGGCAGAGGAAATGATTTCTACTACT 59.843 38.462 16.58 5.72 39.59 2.57
457 459 6.349300 TGGCAGAGGAAATGATTTCTACTAC 58.651 40.000 16.58 10.71 39.59 2.73
458 460 6.560003 TGGCAGAGGAAATGATTTCTACTA 57.440 37.500 16.58 1.36 39.59 1.82
459 461 5.441718 TGGCAGAGGAAATGATTTCTACT 57.558 39.130 16.58 12.81 39.59 2.57
460 462 6.325596 GTTTGGCAGAGGAAATGATTTCTAC 58.674 40.000 16.58 11.04 39.59 2.59
461 463 5.418840 GGTTTGGCAGAGGAAATGATTTCTA 59.581 40.000 16.58 0.00 39.59 2.10
462 464 4.221482 GGTTTGGCAGAGGAAATGATTTCT 59.779 41.667 16.58 4.08 39.59 2.52
463 465 4.221482 AGGTTTGGCAGAGGAAATGATTTC 59.779 41.667 9.36 9.36 38.94 2.17
464 466 4.162651 AGGTTTGGCAGAGGAAATGATTT 58.837 39.130 0.00 0.00 0.00 2.17
465 467 3.782992 AGGTTTGGCAGAGGAAATGATT 58.217 40.909 0.00 0.00 0.00 2.57
466 468 3.463048 AGGTTTGGCAGAGGAAATGAT 57.537 42.857 0.00 0.00 0.00 2.45
467 469 2.978156 AGGTTTGGCAGAGGAAATGA 57.022 45.000 0.00 0.00 0.00 2.57
468 470 3.575687 AGAAAGGTTTGGCAGAGGAAATG 59.424 43.478 0.00 0.00 0.00 2.32
469 471 3.829026 GAGAAAGGTTTGGCAGAGGAAAT 59.171 43.478 0.00 0.00 0.00 2.17
470 472 3.222603 GAGAAAGGTTTGGCAGAGGAAA 58.777 45.455 0.00 0.00 0.00 3.13
471 473 2.174639 TGAGAAAGGTTTGGCAGAGGAA 59.825 45.455 0.00 0.00 0.00 3.36
472 474 1.774254 TGAGAAAGGTTTGGCAGAGGA 59.226 47.619 0.00 0.00 0.00 3.71
473 475 1.882623 GTGAGAAAGGTTTGGCAGAGG 59.117 52.381 0.00 0.00 0.00 3.69
474 476 2.856222 AGTGAGAAAGGTTTGGCAGAG 58.144 47.619 0.00 0.00 0.00 3.35
475 477 4.431416 TTAGTGAGAAAGGTTTGGCAGA 57.569 40.909 0.00 0.00 0.00 4.26
476 478 5.514274 TTTTAGTGAGAAAGGTTTGGCAG 57.486 39.130 0.00 0.00 0.00 4.85
477 479 5.596361 TCATTTTAGTGAGAAAGGTTTGGCA 59.404 36.000 0.00 0.00 0.00 4.92
478 480 6.084326 TCATTTTAGTGAGAAAGGTTTGGC 57.916 37.500 0.00 0.00 0.00 4.52
479 481 6.923508 GGTTCATTTTAGTGAGAAAGGTTTGG 59.076 38.462 0.00 0.00 0.00 3.28
480 482 7.649306 CAGGTTCATTTTAGTGAGAAAGGTTTG 59.351 37.037 0.00 0.00 0.00 2.93
481 483 7.201911 CCAGGTTCATTTTAGTGAGAAAGGTTT 60.202 37.037 0.00 0.00 0.00 3.27
482 484 6.265422 CCAGGTTCATTTTAGTGAGAAAGGTT 59.735 38.462 0.00 0.00 0.00 3.50
483 485 5.770162 CCAGGTTCATTTTAGTGAGAAAGGT 59.230 40.000 0.00 0.00 0.00 3.50
484 486 6.003950 TCCAGGTTCATTTTAGTGAGAAAGG 58.996 40.000 0.00 0.00 0.00 3.11
485 487 7.510549 TTCCAGGTTCATTTTAGTGAGAAAG 57.489 36.000 0.00 0.00 0.00 2.62
486 488 7.777910 TCTTTCCAGGTTCATTTTAGTGAGAAA 59.222 33.333 0.00 0.00 0.00 2.52
487 489 7.287061 TCTTTCCAGGTTCATTTTAGTGAGAA 58.713 34.615 0.00 0.00 0.00 2.87
488 490 6.837312 TCTTTCCAGGTTCATTTTAGTGAGA 58.163 36.000 0.00 0.00 0.00 3.27
489 491 6.348868 GCTCTTTCCAGGTTCATTTTAGTGAG 60.349 42.308 0.00 0.00 0.00 3.51
490 492 5.473504 GCTCTTTCCAGGTTCATTTTAGTGA 59.526 40.000 0.00 0.00 0.00 3.41
491 493 5.241506 TGCTCTTTCCAGGTTCATTTTAGTG 59.758 40.000 0.00 0.00 0.00 2.74
492 494 5.385198 TGCTCTTTCCAGGTTCATTTTAGT 58.615 37.500 0.00 0.00 0.00 2.24
493 495 5.105997 CCTGCTCTTTCCAGGTTCATTTTAG 60.106 44.000 0.00 0.00 43.86 1.85
494 496 4.766891 CCTGCTCTTTCCAGGTTCATTTTA 59.233 41.667 0.00 0.00 43.86 1.52
495 497 3.575687 CCTGCTCTTTCCAGGTTCATTTT 59.424 43.478 0.00 0.00 43.86 1.82
496 498 3.160269 CCTGCTCTTTCCAGGTTCATTT 58.840 45.455 0.00 0.00 43.86 2.32
497 499 2.800250 CCTGCTCTTTCCAGGTTCATT 58.200 47.619 0.00 0.00 43.86 2.57
498 500 2.503895 CCTGCTCTTTCCAGGTTCAT 57.496 50.000 0.00 0.00 43.86 2.57
504 506 0.324285 AGTGCTCCTGCTCTTTCCAG 59.676 55.000 0.00 0.00 39.66 3.86
505 507 0.035881 CAGTGCTCCTGCTCTTTCCA 59.964 55.000 0.00 0.00 40.55 3.53
506 508 2.851798 CAGTGCTCCTGCTCTTTCC 58.148 57.895 0.00 0.00 40.55 3.13
550 555 5.407049 TGTTTTTCCTTGATAAATGGGGGA 58.593 37.500 0.00 0.00 0.00 4.81
551 556 5.338300 CCTGTTTTTCCTTGATAAATGGGGG 60.338 44.000 0.00 0.00 0.00 5.40
603 636 4.139859 AGCTGATCCATCAAGACAAGAG 57.860 45.455 0.00 0.00 36.18 2.85
604 637 4.564782 AAGCTGATCCATCAAGACAAGA 57.435 40.909 0.00 0.00 36.18 3.02
605 638 4.942483 AGAAAGCTGATCCATCAAGACAAG 59.058 41.667 0.00 0.00 36.18 3.16
606 639 4.698780 CAGAAAGCTGATCCATCAAGACAA 59.301 41.667 0.00 0.00 45.17 3.18
607 640 4.259356 CAGAAAGCTGATCCATCAAGACA 58.741 43.478 0.00 0.00 45.17 3.41
608 641 3.065095 GCAGAAAGCTGATCCATCAAGAC 59.935 47.826 0.00 0.00 45.17 3.01
609 642 3.276857 GCAGAAAGCTGATCCATCAAGA 58.723 45.455 0.00 0.00 45.17 3.02
610 643 2.031807 CGCAGAAAGCTGATCCATCAAG 59.968 50.000 0.00 0.00 45.17 3.02
611 644 2.011947 CGCAGAAAGCTGATCCATCAA 58.988 47.619 0.00 0.00 45.17 2.57
612 645 1.660167 CGCAGAAAGCTGATCCATCA 58.340 50.000 0.00 0.00 45.17 3.07
613 646 0.307146 GCGCAGAAAGCTGATCCATC 59.693 55.000 0.30 0.00 45.17 3.51
614 647 0.107312 AGCGCAGAAAGCTGATCCAT 60.107 50.000 11.47 0.00 45.17 3.41
615 648 1.297689 AGCGCAGAAAGCTGATCCA 59.702 52.632 11.47 0.00 45.17 3.41
616 649 4.215349 AGCGCAGAAAGCTGATCC 57.785 55.556 11.47 0.00 45.17 3.36
622 655 3.606065 CTGGTGCAGCGCAGAAAGC 62.606 63.158 11.47 5.98 40.08 3.51
623 656 1.962822 TCTGGTGCAGCGCAGAAAG 60.963 57.895 11.47 1.69 40.08 2.62
624 657 2.110835 TCTGGTGCAGCGCAGAAA 59.889 55.556 11.47 0.00 40.08 2.52
625 658 2.665008 AAGTCTGGTGCAGCGCAGAA 62.665 55.000 11.47 0.00 40.08 3.02
626 659 3.169155 AAGTCTGGTGCAGCGCAGA 62.169 57.895 11.47 6.63 40.08 4.26
638 671 3.748048 TCAAGGAAAATCGAGCAAGTCTG 59.252 43.478 0.00 0.00 0.00 3.51
648 681 7.545362 AGTGAGATTACATCAAGGAAAATCG 57.455 36.000 0.00 0.00 32.95 3.34
667 700 6.909895 CGTCAATCTACATCAAGTCTAGTGAG 59.090 42.308 0.00 0.00 0.00 3.51
708 741 1.124477 GTGCCCAGCCTAGAGCCTAT 61.124 60.000 0.00 0.00 45.47 2.57
821 854 4.816925 GCAACTGAAACTCTACTTTCCTGT 59.183 41.667 0.00 0.00 30.23 4.00
822 855 4.214332 GGCAACTGAAACTCTACTTTCCTG 59.786 45.833 0.00 0.00 30.23 3.86
866 899 9.682465 ACTAAGGAGGTCAAATTATTAGAAACC 57.318 33.333 0.00 0.00 0.00 3.27
884 917 5.143376 TGAAACGGGAAAGTACTAAGGAG 57.857 43.478 0.00 0.00 0.00 3.69
886 919 6.812879 AATTGAAACGGGAAAGTACTAAGG 57.187 37.500 0.00 0.00 0.00 2.69
893 926 3.958147 AGGTGAAATTGAAACGGGAAAGT 59.042 39.130 0.00 0.00 0.00 2.66
902 935 2.582052 AGCCACGAGGTGAAATTGAAA 58.418 42.857 0.00 0.00 35.23 2.69
905 938 1.879380 TCAAGCCACGAGGTGAAATTG 59.121 47.619 0.00 0.00 35.23 2.32
941 974 3.305676 GGACTCCATGATCACCTATGTCG 60.306 52.174 0.00 0.00 0.00 4.35
1094 1127 3.193479 GGATTGGTTTGTGGATGGAGAAC 59.807 47.826 0.00 0.00 0.00 3.01
1146 1179 2.562738 CAAACTGAAGGGATGGGTTTCC 59.437 50.000 0.00 0.00 34.83 3.13
1197 1230 1.064946 GAGCGAGACTGGATCGTGG 59.935 63.158 5.82 0.00 42.13 4.94
1305 1338 1.337387 CTGCTAGAGTAAGGCCCGTAC 59.663 57.143 0.00 1.95 0.00 3.67
1560 1593 2.109126 GGTGACGCCCAGATTCAGC 61.109 63.158 0.00 0.00 0.00 4.26
1695 1728 1.078214 CATGGTCATGGCCACGACT 60.078 57.895 29.30 9.93 41.94 4.18
1716 1750 2.754375 GTGATGGGACGGGTGGTT 59.246 61.111 0.00 0.00 0.00 3.67
1952 1986 1.735198 CGCACCTGCATGCAAAAGG 60.735 57.895 22.88 21.19 46.47 3.11
2260 2295 0.386476 AGTTCAGTGACGCCGTGTTA 59.614 50.000 0.00 0.00 0.00 2.41
2509 2544 2.634940 CCAGTAGGTGACCCATATCCTG 59.365 54.545 0.00 0.00 0.00 3.86
2572 2607 1.077645 GCAGCAGCTCTCTGAACTCG 61.078 60.000 14.83 0.00 42.95 4.18
2639 2674 3.454375 ACGGCGACCATTTTATCAGTAG 58.546 45.455 16.62 0.00 0.00 2.57
2713 2751 7.117667 TGCTAGCGTATTATAACCATGATTGTG 59.882 37.037 10.77 0.00 0.00 3.33
2714 2752 7.117812 GTGCTAGCGTATTATAACCATGATTGT 59.882 37.037 10.77 0.00 0.00 2.71
2715 2753 7.331934 AGTGCTAGCGTATTATAACCATGATTG 59.668 37.037 10.77 0.00 0.00 2.67
2716 2754 7.386851 AGTGCTAGCGTATTATAACCATGATT 58.613 34.615 10.77 0.00 0.00 2.57
2725 2764 5.936686 AAGTCGAGTGCTAGCGTATTATA 57.063 39.130 10.77 0.00 0.00 0.98
2732 2771 2.096174 ACTTCTAAGTCGAGTGCTAGCG 59.904 50.000 10.77 0.00 32.86 4.26
2760 2799 9.391006 CTGGTGTAATCCTTTACTGCTTTAATA 57.609 33.333 0.00 0.00 38.81 0.98
2761 2800 8.107095 TCTGGTGTAATCCTTTACTGCTTTAAT 58.893 33.333 0.00 0.00 38.81 1.40
2762 2801 7.455058 TCTGGTGTAATCCTTTACTGCTTTAA 58.545 34.615 0.00 0.00 38.81 1.52
2787 2826 3.643320 TCTTCAGGTCACAATGTGAGTCT 59.357 43.478 17.28 13.96 43.57 3.24
2862 2901 6.599244 CCCTTAATTGAATGTTGCTGACTCTA 59.401 38.462 0.00 0.00 0.00 2.43
2863 2902 5.416952 CCCTTAATTGAATGTTGCTGACTCT 59.583 40.000 0.00 0.00 0.00 3.24
2870 2909 5.065090 GCCAAATCCCTTAATTGAATGTTGC 59.935 40.000 0.00 0.00 0.00 4.17
2873 2912 5.484998 ACAGCCAAATCCCTTAATTGAATGT 59.515 36.000 0.00 0.00 0.00 2.71
2874 2913 5.981174 ACAGCCAAATCCCTTAATTGAATG 58.019 37.500 0.00 0.00 0.00 2.67
2965 3006 4.211125 TGTTGCTTCTGATTGTAACCCAA 58.789 39.130 8.66 0.00 37.49 4.12
3042 3096 1.802365 CGCATGAGCTTGCTGCATATA 59.198 47.619 1.84 0.00 45.94 0.86
3046 3100 4.111016 GCGCATGAGCTTGCTGCA 62.111 61.111 14.75 0.00 45.94 4.41
3202 3256 2.711922 GCAGATGGAGACCGACCGT 61.712 63.158 0.00 0.00 0.00 4.83
3204 3258 1.153549 GTGCAGATGGAGACCGACC 60.154 63.158 0.00 0.00 0.00 4.79
3256 3310 1.689258 GCCCATGCCCTATCTTTTGGT 60.689 52.381 0.00 0.00 0.00 3.67
3288 3342 1.402787 TCGTGGATGCTCAGATGCTA 58.597 50.000 0.00 0.00 0.00 3.49
3363 3607 3.799755 CGGGTTTGGCTGCGCTAC 61.800 66.667 9.73 0.00 0.00 3.58
3498 3910 2.200373 TGTTAAGGGGAAGCAGAAGC 57.800 50.000 0.00 0.00 42.56 3.86


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

AutoCloner maintained by Alex Coulton.