Multiple sequence alignment - TraesCS5A01G346500

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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 TraesCS5A01G346500 chr5A 100.000 3080 0 0 1 3080 549221278 549218199 0.000000e+00 5688
1 TraesCS5A01G346500 chr5A 88.889 189 18 3 664 849 709520702 709520514 2.390000e-56 230
2 TraesCS5A01G346500 chr5D 95.466 2007 55 9 846 2826 435279432 435277436 0.000000e+00 3169
3 TraesCS5A01G346500 chr5D 92.837 363 21 3 19 381 435280388 435280031 3.520000e-144 521
4 TraesCS5A01G346500 chr5D 87.594 266 14 5 2828 3080 435277337 435277078 1.080000e-74 291
5 TraesCS5A01G346500 chr5D 82.486 177 14 3 463 638 435280028 435279868 4.140000e-29 139
6 TraesCS5A01G346500 chr5B 95.048 1858 57 8 849 2690 528591439 528589601 0.000000e+00 2889
7 TraesCS5A01G346500 chr5B 85.279 394 40 9 250 638 528592392 528592012 1.040000e-104 390
8 TraesCS5A01G346500 chr5B 92.917 240 15 1 11 250 528668974 528668737 6.320000e-92 348
9 TraesCS5A01G346500 chr6A 95.681 1343 39 4 1223 2550 573138745 573137407 0.000000e+00 2141
10 TraesCS5A01G346500 chr6A 94.557 937 42 2 1620 2550 615024985 615025918 0.000000e+00 1439
11 TraesCS5A01G346500 chr6A 93.048 374 17 2 1223 1587 615024613 615024986 3.490000e-149 538
12 TraesCS5A01G346500 chr2A 95.383 1343 43 4 1223 2550 561008636 561009974 0.000000e+00 2119
13 TraesCS5A01G346500 chr3A 94.862 1343 51 3 1223 2550 52208146 52206807 0.000000e+00 2082
14 TraesCS5A01G346500 chr2B 89.894 188 17 2 664 849 188465909 188465722 1.100000e-59 241
15 TraesCS5A01G346500 chr2B 88.947 190 17 4 664 849 682847411 682847600 6.640000e-57 231
16 TraesCS5A01G346500 chr4B 89.474 190 17 3 664 850 27784099 27783910 1.430000e-58 237
17 TraesCS5A01G346500 chr4B 88.482 191 18 4 664 850 1811867 1811677 8.590000e-56 228
18 TraesCS5A01G346500 chr3B 88.832 197 17 5 664 856 248246059 248245864 1.430000e-58 237
19 TraesCS5A01G346500 chr3B 90.164 183 15 3 664 843 618000425 618000243 5.130000e-58 235
20 TraesCS5A01G346500 chr1B 89.362 188 18 2 664 849 395230011 395230198 5.130000e-58 235
21 TraesCS5A01G346500 chr4A 87.562 201 19 6 664 859 665953946 665953747 8.590000e-56 228


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 TraesCS5A01G346500 chr5A 549218199 549221278 3079 True 5688.0 5688 100.00000 1 3080 1 chr5A.!!$R1 3079
1 TraesCS5A01G346500 chr5D 435277078 435280388 3310 True 1030.0 3169 89.59575 19 3080 4 chr5D.!!$R1 3061
2 TraesCS5A01G346500 chr5B 528589601 528592392 2791 True 1639.5 2889 90.16350 250 2690 2 chr5B.!!$R2 2440
3 TraesCS5A01G346500 chr6A 573137407 573138745 1338 True 2141.0 2141 95.68100 1223 2550 1 chr6A.!!$R1 1327
4 TraesCS5A01G346500 chr6A 615024613 615025918 1305 False 988.5 1439 93.80250 1223 2550 2 chr6A.!!$F1 1327
5 TraesCS5A01G346500 chr2A 561008636 561009974 1338 False 2119.0 2119 95.38300 1223 2550 1 chr2A.!!$F1 1327
6 TraesCS5A01G346500 chr3A 52206807 52208146 1339 True 2082.0 2082 94.86200 1223 2550 1 chr3A.!!$R1 1327

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
741 767 0.02877 CGACGCTGTTTTTGGCTCAA 59.971 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2708 3248 1.135915 CAACTGCCGAGAGACAGCTAT 59.864 52.381 0.0 0.0 37.42 2.97 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 24 4.900652 AGTCAATATGTGGATCAGAGAGCT 59.099 41.667 0.00 0.00 0.00 4.09
59 60 7.891183 TCATAATTTACAAAGGAAAGCCCACTA 59.109 33.333 0.00 0.00 37.41 2.74
60 61 8.695456 CATAATTTACAAAGGAAAGCCCACTAT 58.305 33.333 0.00 0.00 37.41 2.12
124 125 9.739276 AAACACTCCAGATTGTTTATCAATAGA 57.261 29.630 12.74 0.00 45.49 1.98
129 130 8.492673 TCCAGATTGTTTATCAATAGACACAC 57.507 34.615 0.00 0.00 45.49 3.82
131 132 7.277760 CCAGATTGTTTATCAATAGACACACGA 59.722 37.037 0.00 0.00 45.49 4.35
197 198 5.724370 TCCACCTATCATGAAAAGTAGTCCA 59.276 40.000 0.00 0.00 0.00 4.02
231 232 4.005650 TGATCTCCTCAGCACAAACATTC 58.994 43.478 0.00 0.00 0.00 2.67
269 271 3.323751 TTTCGTAAGTAGCCTGGAACC 57.676 47.619 0.00 0.00 39.48 3.62
281 283 2.555227 GCCTGGAACCAGAAATGAGGAA 60.555 50.000 20.79 0.00 46.30 3.36
296 298 8.502738 AGAAATGAGGAAACATATAGGGCTAAA 58.497 33.333 0.00 0.00 0.00 1.85
367 371 4.227527 ACCAGGTAGTTTTGGGATAAGAGG 59.772 45.833 0.00 0.00 38.82 3.69
420 425 9.323985 CATTAAGGTTTCCTTGACAAAAATCAA 57.676 29.630 10.82 0.00 44.44 2.57
423 428 6.706295 AGGTTTCCTTGACAAAAATCAAACA 58.294 32.000 0.00 0.00 38.12 2.83
424 429 7.337938 AGGTTTCCTTGACAAAAATCAAACAT 58.662 30.769 0.00 0.00 38.12 2.71
430 436 9.097257 TCCTTGACAAAAATCAAACATTTCTTC 57.903 29.630 0.00 0.00 38.12 2.87
451 457 6.368791 TCTTCAAAGGATGTTCAACTATGTCG 59.631 38.462 0.00 0.00 0.00 4.35
452 458 4.391830 TCAAAGGATGTTCAACTATGTCGC 59.608 41.667 0.00 0.00 0.00 5.19
453 459 2.906354 AGGATGTTCAACTATGTCGCC 58.094 47.619 0.00 0.00 0.00 5.54
458 464 4.217754 TGTTCAACTATGTCGCCAAAAC 57.782 40.909 0.00 0.00 0.00 2.43
460 466 2.485903 TCAACTATGTCGCCAAAACGT 58.514 42.857 0.00 0.00 0.00 3.99
472 478 3.720920 CGCCAAAACGTTGATAGAACTCG 60.721 47.826 0.00 0.00 36.83 4.18
490 496 1.202806 TCGATTGGAATCCATCAGGGC 60.203 52.381 1.39 0.00 36.21 5.19
492 498 2.236766 GATTGGAATCCATCAGGGCTG 58.763 52.381 1.39 0.00 36.21 4.85
493 499 0.259647 TTGGAATCCATCAGGGCTGG 59.740 55.000 1.39 0.00 36.21 4.85
494 500 1.152368 GGAATCCATCAGGGCTGGG 59.848 63.158 0.00 0.00 36.21 4.45
495 501 1.355718 GGAATCCATCAGGGCTGGGA 61.356 60.000 0.00 0.00 36.21 4.37
496 502 0.776176 GAATCCATCAGGGCTGGGAT 59.224 55.000 0.00 0.00 41.80 3.85
497 503 0.776176 AATCCATCAGGGCTGGGATC 59.224 55.000 0.00 0.00 39.17 3.36
498 504 1.138863 ATCCATCAGGGCTGGGATCC 61.139 60.000 1.92 1.92 35.22 3.36
499 505 2.080536 CCATCAGGGCTGGGATCCA 61.081 63.158 15.23 0.00 0.00 3.41
500 506 1.150081 CATCAGGGCTGGGATCCAC 59.850 63.158 15.23 3.53 0.00 4.02
501 507 1.308128 ATCAGGGCTGGGATCCACA 60.308 57.895 15.23 8.39 0.00 4.17
502 508 1.639635 ATCAGGGCTGGGATCCACAC 61.640 60.000 15.23 3.18 0.00 3.82
505 511 1.076549 GGGCTGGGATCCACACAAA 59.923 57.895 15.23 0.00 0.00 2.83
508 514 1.273327 GGCTGGGATCCACACAAAAAG 59.727 52.381 15.23 0.00 0.00 2.27
510 516 2.229784 GCTGGGATCCACACAAAAAGAG 59.770 50.000 15.23 0.00 0.00 2.85
547 553 5.478407 TCGAGAGAAAGTTCATGCACAATA 58.522 37.500 0.00 0.00 37.03 1.90
565 571 9.247126 TGCACAATAATGTTGTTTATATCATGC 57.753 29.630 0.00 0.00 37.82 4.06
566 572 8.702438 GCACAATAATGTTGTTTATATCATGCC 58.298 33.333 0.00 0.00 37.82 4.40
567 573 9.747293 CACAATAATGTTGTTTATATCATGCCA 57.253 29.630 0.00 0.00 37.82 4.92
624 641 7.974504 AGATACTTCTTTCTACAGGTCCAAAA 58.025 34.615 0.00 0.00 0.00 2.44
659 685 9.703892 ATAGATATGTTTCATAAGACACTGCTC 57.296 33.333 0.00 0.00 0.00 4.26
660 686 6.699204 AGATATGTTTCATAAGACACTGCTCG 59.301 38.462 0.00 0.00 0.00 5.03
662 688 4.377021 TGTTTCATAAGACACTGCTCGTT 58.623 39.130 0.00 0.00 0.00 3.85
663 689 5.534407 TGTTTCATAAGACACTGCTCGTTA 58.466 37.500 0.00 0.00 0.00 3.18
664 690 5.986741 TGTTTCATAAGACACTGCTCGTTAA 59.013 36.000 0.00 0.00 0.00 2.01
665 691 6.073980 TGTTTCATAAGACACTGCTCGTTAAC 60.074 38.462 0.00 0.00 0.00 2.01
666 692 5.128992 TCATAAGACACTGCTCGTTAACA 57.871 39.130 6.39 0.00 0.00 2.41
667 693 5.161358 TCATAAGACACTGCTCGTTAACAG 58.839 41.667 6.39 3.79 39.86 3.16
668 694 1.784525 AGACACTGCTCGTTAACAGC 58.215 50.000 17.75 17.75 37.42 4.40
669 695 1.341531 AGACACTGCTCGTTAACAGCT 59.658 47.619 22.16 9.18 37.42 4.24
670 696 1.721926 GACACTGCTCGTTAACAGCTC 59.278 52.381 22.16 12.75 37.42 4.09
671 697 0.710567 CACTGCTCGTTAACAGCTCG 59.289 55.000 22.16 17.26 37.42 5.03
672 698 1.009389 ACTGCTCGTTAACAGCTCGC 61.009 55.000 22.16 11.11 37.42 5.03
674 700 2.453638 GCTCGTTAACAGCTCGCCC 61.454 63.158 17.47 0.00 33.75 6.13
675 701 1.810030 CTCGTTAACAGCTCGCCCC 60.810 63.158 6.39 0.00 0.00 5.80
676 702 3.186047 CGTTAACAGCTCGCCCCG 61.186 66.667 6.39 0.00 0.00 5.73
677 703 2.818274 GTTAACAGCTCGCCCCGG 60.818 66.667 0.00 0.00 0.00 5.73
712 738 4.849329 AGCGCGTCGGATTCGGTC 62.849 66.667 8.43 0.00 36.95 4.79
713 739 4.849329 GCGCGTCGGATTCGGTCT 62.849 66.667 8.43 0.00 36.95 3.85
714 740 2.949678 CGCGTCGGATTCGGTCTG 60.950 66.667 0.00 0.00 36.95 3.51
715 741 2.582498 GCGTCGGATTCGGTCTGG 60.582 66.667 0.00 0.00 36.95 3.86
716 742 2.104331 CGTCGGATTCGGTCTGGG 59.896 66.667 0.00 0.00 36.95 4.45
717 743 2.707849 CGTCGGATTCGGTCTGGGT 61.708 63.158 0.00 0.00 36.95 4.51
718 744 1.141234 GTCGGATTCGGTCTGGGTC 59.859 63.158 0.00 0.00 36.95 4.46
719 745 2.056223 TCGGATTCGGTCTGGGTCC 61.056 63.158 0.00 0.00 36.95 4.46
721 747 2.202892 GATTCGGTCTGGGTCCGC 60.203 66.667 0.00 0.00 46.49 5.54
722 748 3.735037 GATTCGGTCTGGGTCCGCC 62.735 68.421 0.00 0.00 46.49 6.13
735 761 2.426752 CCGCCGACGCTGTTTTTG 60.427 61.111 0.00 0.00 38.22 2.44
736 762 2.426752 CGCCGACGCTGTTTTTGG 60.427 61.111 0.00 0.00 0.00 3.28
737 763 2.729491 GCCGACGCTGTTTTTGGC 60.729 61.111 0.00 0.00 35.04 4.52
741 767 0.028770 CGACGCTGTTTTTGGCTCAA 59.971 50.000 0.00 0.00 0.00 3.02
742 768 1.758783 GACGCTGTTTTTGGCTCAAG 58.241 50.000 0.00 0.00 0.00 3.02
755 781 1.072666 GCTCAAGCCGGCAAAAATCG 61.073 55.000 31.54 10.84 34.31 3.34
756 782 0.521291 CTCAAGCCGGCAAAAATCGA 59.479 50.000 31.54 12.29 0.00 3.59
757 783 0.955178 TCAAGCCGGCAAAAATCGAA 59.045 45.000 31.54 0.00 0.00 3.71
758 784 1.059942 CAAGCCGGCAAAAATCGAAC 58.940 50.000 31.54 0.00 0.00 3.95
761 787 0.456142 GCCGGCAAAAATCGAACTCC 60.456 55.000 24.80 0.00 0.00 3.85
762 788 1.165270 CCGGCAAAAATCGAACTCCT 58.835 50.000 0.00 0.00 0.00 3.69
763 789 1.135689 CCGGCAAAAATCGAACTCCTG 60.136 52.381 0.00 0.00 0.00 3.86
764 790 1.804151 CGGCAAAAATCGAACTCCTGA 59.196 47.619 0.00 0.00 0.00 3.86
766 792 3.074412 GGCAAAAATCGAACTCCTGAGA 58.926 45.455 0.22 0.00 0.00 3.27
767 793 3.120165 GGCAAAAATCGAACTCCTGAGAC 60.120 47.826 0.22 0.00 0.00 3.36
769 795 3.662247 AAAATCGAACTCCTGAGACGT 57.338 42.857 0.22 0.00 35.13 4.34
770 796 2.638556 AATCGAACTCCTGAGACGTG 57.361 50.000 0.00 0.00 35.13 4.49
771 797 1.822506 ATCGAACTCCTGAGACGTGA 58.177 50.000 0.00 0.00 35.13 4.35
772 798 0.873054 TCGAACTCCTGAGACGTGAC 59.127 55.000 0.00 0.00 35.13 3.67
773 799 0.875728 CGAACTCCTGAGACGTGACT 59.124 55.000 0.00 0.00 0.00 3.41
774 800 1.400371 CGAACTCCTGAGACGTGACTG 60.400 57.143 0.00 0.00 0.00 3.51
775 801 0.962489 AACTCCTGAGACGTGACTGG 59.038 55.000 0.00 0.00 0.00 4.00
776 802 0.896019 ACTCCTGAGACGTGACTGGG 60.896 60.000 0.00 0.00 0.00 4.45
777 803 2.219325 CTCCTGAGACGTGACTGGGC 62.219 65.000 0.00 0.00 0.00 5.36
778 804 2.262915 CTGAGACGTGACTGGGCC 59.737 66.667 0.00 0.00 0.00 5.80
798 1273 3.955101 TTTTTCGGCGCCGGTGTG 61.955 61.111 44.95 20.64 40.25 3.82
799 1274 4.912485 TTTTCGGCGCCGGTGTGA 62.912 61.111 44.95 26.01 40.25 3.58
800 1275 4.912485 TTTCGGCGCCGGTGTGAA 62.912 61.111 44.95 30.10 40.25 3.18
801 1276 4.912485 TTCGGCGCCGGTGTGAAA 62.912 61.111 44.95 29.35 40.25 2.69
803 1278 3.955101 CGGCGCCGGTGTGAAAAA 61.955 61.111 40.50 0.00 35.56 1.94
821 1296 4.505313 AAAAATCGTCTGGAAGGCTTTC 57.495 40.909 0.00 0.00 35.43 2.62
892 1367 1.002201 TCGGTCAAGTCTCGTCTCTCT 59.998 52.381 0.00 0.00 0.00 3.10
894 1369 1.741145 GGTCAAGTCTCGTCTCTCTCC 59.259 57.143 0.00 0.00 0.00 3.71
1374 1871 1.627297 GGATCTTGGACCGCCTCCTT 61.627 60.000 0.00 0.00 40.26 3.36
1587 2084 2.753043 TACCTCGACAGGACCGCC 60.753 66.667 0.00 0.00 43.65 6.13
1854 2385 1.620822 GGAGGTTTGTGCTGGATGTT 58.379 50.000 0.00 0.00 0.00 2.71
1857 2388 3.412386 GAGGTTTGTGCTGGATGTTACT 58.588 45.455 0.00 0.00 0.00 2.24
2232 2764 3.831323 TGGAAGCAGAAATCTGTTGGAA 58.169 40.909 11.77 0.00 45.45 3.53
2444 2982 6.372659 CACTCTGTGTGTGGATAAGCTATTTT 59.627 38.462 1.84 0.00 41.53 1.82
2567 3105 5.351465 TGGATATTTTGCGTTCTGACTTCTC 59.649 40.000 0.00 0.00 0.00 2.87
2740 3280 2.086869 CGGCAGTTGACCTTTGATCAT 58.913 47.619 0.00 0.00 0.00 2.45
2769 3309 2.749076 TGATGTTCCTTTTCGAGCCATG 59.251 45.455 0.00 0.00 0.00 3.66
2793 3335 4.097135 CGACTGAAGTCATATGTGTCCTCT 59.903 45.833 10.88 0.00 44.99 3.69
2846 3485 1.619332 GGGTTTCTCGACTCCTCACTT 59.381 52.381 0.00 0.00 0.00 3.16
2859 3498 6.573680 CGACTCCTCACTTTCCTTTACCATAA 60.574 42.308 0.00 0.00 0.00 1.90
2878 3517 6.057533 CCATAACATCCAGATTGCTACTGAA 58.942 40.000 0.00 0.00 37.54 3.02
2881 3520 4.521146 ACATCCAGATTGCTACTGAAAGG 58.479 43.478 0.00 0.00 39.30 3.11
2887 3526 6.207417 TCCAGATTGCTACTGAAAGGAAAAAG 59.793 38.462 0.00 0.00 39.30 2.27
2905 3546 5.411831 AAAAGAATCCAGATTCCAAAGCC 57.588 39.130 15.16 0.00 46.28 4.35
2906 3547 4.328118 AAGAATCCAGATTCCAAAGCCT 57.672 40.909 15.16 0.00 46.28 4.58
2907 3548 3.629087 AGAATCCAGATTCCAAAGCCTG 58.371 45.455 15.16 0.00 46.28 4.85
2909 3550 2.496899 TCCAGATTCCAAAGCCTGAC 57.503 50.000 0.00 0.00 0.00 3.51
2964 3616 8.713708 TGATCAATTTGGGTAAAAAGAAGGTA 57.286 30.769 0.00 0.00 0.00 3.08
2968 3620 9.320295 TCAATTTGGGTAAAAAGAAGGTATCAT 57.680 29.630 0.00 0.00 0.00 2.45
2979 3631 4.631234 AGAAGGTATCATTGGGGTGTCTA 58.369 43.478 0.00 0.00 0.00 2.59
2997 3649 9.555727 GGGTGTCTAATGCAATCTTAATTAGTA 57.444 33.333 0.00 0.00 36.00 1.82
3052 3704 3.439857 CCATGGGTGGTATAGGGAATG 57.560 52.381 2.85 0.00 40.83 2.67
3057 3709 1.202891 GGTGGTATAGGGAATGGGTGC 60.203 57.143 0.00 0.00 0.00 5.01
3059 3711 1.053424 GGTATAGGGAATGGGTGCGA 58.947 55.000 0.00 0.00 0.00 5.10
3068 3720 1.339929 GAATGGGTGCGAAACTGGTTT 59.660 47.619 0.00 0.00 35.14 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.900652 AGCTCTCTGATCCACATATTGACT 59.099 41.667 0.00 0.00 0.00 3.41
1 2 5.010922 AGAGCTCTCTGATCCACATATTGAC 59.989 44.000 11.45 0.00 38.75 3.18
2 3 5.146298 AGAGCTCTCTGATCCACATATTGA 58.854 41.667 11.45 0.00 38.75 2.57
3 4 5.471556 AGAGCTCTCTGATCCACATATTG 57.528 43.478 11.45 0.00 38.75 1.90
4 5 6.497624 AAAGAGCTCTCTGATCCACATATT 57.502 37.500 18.55 0.00 40.36 1.28
5 6 7.609097 TTAAAGAGCTCTCTGATCCACATAT 57.391 36.000 18.55 0.00 40.36 1.78
6 7 7.048629 CTTAAAGAGCTCTCTGATCCACATA 57.951 40.000 18.55 0.00 40.36 2.29
7 8 5.916318 CTTAAAGAGCTCTCTGATCCACAT 58.084 41.667 18.55 0.00 40.36 3.21
8 9 5.336150 CTTAAAGAGCTCTCTGATCCACA 57.664 43.478 18.55 0.00 40.36 4.17
48 49 8.970859 AGCATATGAATATATAGTGGGCTTTC 57.029 34.615 6.97 0.00 0.00 2.62
100 101 8.321353 TGTCTATTGATAAACAATCTGGAGTGT 58.679 33.333 0.00 0.00 44.77 3.55
104 105 7.277760 CGTGTGTCTATTGATAAACAATCTGGA 59.722 37.037 0.00 0.00 44.77 3.86
108 109 8.604035 ACATCGTGTGTCTATTGATAAACAATC 58.396 33.333 0.00 0.00 41.64 2.67
112 113 8.402326 TGTACATCGTGTGTCTATTGATAAAC 57.598 34.615 0.00 0.00 42.29 2.01
118 119 6.364976 TGAAGTTGTACATCGTGTGTCTATTG 59.635 38.462 0.00 0.00 42.29 1.90
124 125 3.186409 GCATGAAGTTGTACATCGTGTGT 59.814 43.478 15.27 1.87 44.95 3.72
129 130 3.436704 ACCTTGCATGAAGTTGTACATCG 59.563 43.478 0.00 0.00 0.00 3.84
131 132 4.397420 TCACCTTGCATGAAGTTGTACAT 58.603 39.130 0.00 0.00 0.00 2.29
252 253 1.822990 TCTGGTTCCAGGCTACTTACG 59.177 52.381 17.37 0.00 35.01 3.18
269 271 6.302269 AGCCCTATATGTTTCCTCATTTCTG 58.698 40.000 0.00 0.00 0.00 3.02
410 414 9.447157 TCCTTTGAAGAAATGTTTGATTTTTGT 57.553 25.926 0.00 0.00 0.00 2.83
420 425 7.785033 AGTTGAACATCCTTTGAAGAAATGTT 58.215 30.769 17.01 17.01 41.06 2.71
423 428 9.082313 ACATAGTTGAACATCCTTTGAAGAAAT 57.918 29.630 0.00 0.00 0.00 2.17
424 429 8.463930 ACATAGTTGAACATCCTTTGAAGAAA 57.536 30.769 0.00 0.00 0.00 2.52
430 436 4.437390 GGCGACATAGTTGAACATCCTTTG 60.437 45.833 0.00 0.00 0.00 2.77
434 440 2.627945 TGGCGACATAGTTGAACATCC 58.372 47.619 0.00 0.00 33.40 3.51
451 457 3.430895 TCGAGTTCTATCAACGTTTTGGC 59.569 43.478 0.00 0.00 33.06 4.52
452 458 5.779806 ATCGAGTTCTATCAACGTTTTGG 57.220 39.130 0.00 0.00 33.06 3.28
453 459 6.015504 CCAATCGAGTTCTATCAACGTTTTG 58.984 40.000 0.00 0.00 0.00 2.44
458 464 5.175856 GGATTCCAATCGAGTTCTATCAACG 59.824 44.000 0.00 0.00 36.27 4.10
460 466 6.233905 TGGATTCCAATCGAGTTCTATCAA 57.766 37.500 1.94 0.00 36.27 2.57
472 478 2.236766 CAGCCCTGATGGATTCCAATC 58.763 52.381 9.98 8.55 36.95 2.67
490 496 2.821969 CCTCTTTTTGTGTGGATCCCAG 59.178 50.000 9.90 0.00 32.34 4.45
492 498 2.820197 GTCCTCTTTTTGTGTGGATCCC 59.180 50.000 9.90 0.85 0.00 3.85
493 499 3.756117 AGTCCTCTTTTTGTGTGGATCC 58.244 45.455 4.20 4.20 0.00 3.36
494 500 5.774498 AAAGTCCTCTTTTTGTGTGGATC 57.226 39.130 0.00 0.00 40.50 3.36
495 501 7.839680 ATTAAAGTCCTCTTTTTGTGTGGAT 57.160 32.000 0.00 0.00 42.84 3.41
496 502 7.654022 AATTAAAGTCCTCTTTTTGTGTGGA 57.346 32.000 0.00 0.00 42.84 4.02
497 503 8.197439 AGAAATTAAAGTCCTCTTTTTGTGTGG 58.803 33.333 0.00 0.00 42.84 4.17
498 504 9.586435 AAGAAATTAAAGTCCTCTTTTTGTGTG 57.414 29.630 0.00 0.00 42.84 3.82
499 505 9.803315 GAAGAAATTAAAGTCCTCTTTTTGTGT 57.197 29.630 0.00 0.00 42.84 3.72
500 506 8.958043 CGAAGAAATTAAAGTCCTCTTTTTGTG 58.042 33.333 0.00 0.00 42.84 3.33
501 507 8.899771 TCGAAGAAATTAAAGTCCTCTTTTTGT 58.100 29.630 0.00 0.00 42.84 2.83
502 508 9.387123 CTCGAAGAAATTAAAGTCCTCTTTTTG 57.613 33.333 0.00 0.00 39.50 2.44
505 511 8.368668 TCTCTCGAAGAAATTAAAGTCCTCTTT 58.631 33.333 0.00 0.00 40.95 2.52
508 514 8.535690 TTTCTCTCGAAGAAATTAAAGTCCTC 57.464 34.615 14.67 0.00 46.64 3.71
540 546 8.702438 GGCATGATATAAACAACATTATTGTGC 58.298 33.333 0.00 0.00 35.83 4.57
547 553 8.476447 TGTCATTGGCATGATATAAACAACATT 58.524 29.630 0.00 0.00 41.64 2.71
561 567 8.929827 TTTAGTTTAATCATGTCATTGGCATG 57.070 30.769 22.40 22.40 43.55 4.06
562 568 9.590451 CTTTTAGTTTAATCATGTCATTGGCAT 57.410 29.630 0.00 0.00 0.00 4.40
563 569 8.584157 ACTTTTAGTTTAATCATGTCATTGGCA 58.416 29.630 0.00 0.00 0.00 4.92
564 570 8.986477 ACTTTTAGTTTAATCATGTCATTGGC 57.014 30.769 0.00 0.00 0.00 4.52
652 678 0.710567 CGAGCTGTTAACGAGCAGTG 59.289 55.000 23.12 13.21 39.05 3.66
653 679 1.009389 GCGAGCTGTTAACGAGCAGT 61.009 55.000 23.12 10.39 39.05 4.40
654 680 1.687494 GGCGAGCTGTTAACGAGCAG 61.687 60.000 23.12 18.63 39.05 4.24
655 681 1.736645 GGCGAGCTGTTAACGAGCA 60.737 57.895 23.12 0.00 39.05 4.26
659 685 3.186047 CGGGGCGAGCTGTTAACG 61.186 66.667 0.00 0.00 0.00 3.18
660 686 2.818274 CCGGGGCGAGCTGTTAAC 60.818 66.667 0.00 0.00 0.00 2.01
696 722 4.849329 AGACCGAATCCGACGCGC 62.849 66.667 5.73 0.00 38.22 6.86
697 723 2.949678 CAGACCGAATCCGACGCG 60.950 66.667 3.53 3.53 38.22 6.01
698 724 2.582498 CCAGACCGAATCCGACGC 60.582 66.667 0.00 0.00 38.22 5.19
699 725 2.104331 CCCAGACCGAATCCGACG 59.896 66.667 0.00 0.00 38.22 5.12
700 726 1.141234 GACCCAGACCGAATCCGAC 59.859 63.158 0.00 0.00 38.22 4.79
701 727 2.056223 GGACCCAGACCGAATCCGA 61.056 63.158 0.00 0.00 38.22 4.55
702 728 2.499685 GGACCCAGACCGAATCCG 59.500 66.667 0.00 0.00 0.00 4.18
716 742 2.888998 AAAAACAGCGTCGGCGGAC 61.889 57.895 13.05 14.05 46.35 4.79
717 743 2.589442 AAAAACAGCGTCGGCGGA 60.589 55.556 13.05 0.00 46.35 5.54
718 744 2.426752 CAAAAACAGCGTCGGCGG 60.427 61.111 13.05 0.00 46.35 6.13
719 745 2.426752 CCAAAAACAGCGTCGGCG 60.427 61.111 4.29 4.29 46.35 6.46
721 747 1.082104 GAGCCAAAAACAGCGTCGG 60.082 57.895 0.00 0.00 0.00 4.79
722 748 0.028770 TTGAGCCAAAAACAGCGTCG 59.971 50.000 0.00 0.00 0.00 5.12
723 749 1.758783 CTTGAGCCAAAAACAGCGTC 58.241 50.000 0.00 0.00 0.00 5.19
736 762 1.072666 CGATTTTTGCCGGCTTGAGC 61.073 55.000 29.70 12.60 41.14 4.26
737 763 0.521291 TCGATTTTTGCCGGCTTGAG 59.479 50.000 29.70 12.32 0.00 3.02
741 767 0.521735 GAGTTCGATTTTTGCCGGCT 59.478 50.000 29.70 6.37 0.00 5.52
742 768 0.456142 GGAGTTCGATTTTTGCCGGC 60.456 55.000 22.73 22.73 0.00 6.13
745 771 3.074412 TCTCAGGAGTTCGATTTTTGCC 58.926 45.455 0.00 0.00 0.00 4.52
746 772 3.423645 CGTCTCAGGAGTTCGATTTTTGC 60.424 47.826 9.57 0.00 32.43 3.68
747 773 3.741344 ACGTCTCAGGAGTTCGATTTTTG 59.259 43.478 17.52 0.00 33.83 2.44
748 774 3.741344 CACGTCTCAGGAGTTCGATTTTT 59.259 43.478 17.52 0.22 33.83 1.94
749 775 3.005472 TCACGTCTCAGGAGTTCGATTTT 59.995 43.478 17.52 0.49 33.83 1.82
750 776 2.557056 TCACGTCTCAGGAGTTCGATTT 59.443 45.455 17.52 0.00 33.83 2.17
755 781 1.068194 CCAGTCACGTCTCAGGAGTTC 60.068 57.143 0.00 0.00 0.00 3.01
756 782 0.962489 CCAGTCACGTCTCAGGAGTT 59.038 55.000 0.00 0.00 0.00 3.01
757 783 0.896019 CCCAGTCACGTCTCAGGAGT 60.896 60.000 0.00 0.00 0.00 3.85
758 784 1.886585 CCCAGTCACGTCTCAGGAG 59.113 63.158 0.00 0.00 0.00 3.69
761 787 2.262915 GGCCCAGTCACGTCTCAG 59.737 66.667 0.00 0.00 0.00 3.35
762 788 3.680786 CGGCCCAGTCACGTCTCA 61.681 66.667 0.00 0.00 0.00 3.27
763 789 2.710724 AAACGGCCCAGTCACGTCTC 62.711 60.000 0.00 0.00 40.31 3.36
764 790 2.319890 AAAACGGCCCAGTCACGTCT 62.320 55.000 0.00 0.00 40.31 4.18
766 792 1.452470 AAAAACGGCCCAGTCACGT 60.452 52.632 0.00 0.00 43.43 4.49
767 793 3.427670 AAAAACGGCCCAGTCACG 58.572 55.556 0.00 0.00 0.00 4.35
786 1261 3.955101 TTTTTCACACCGGCGCCG 61.955 61.111 41.00 41.00 39.44 6.46
800 1275 4.505313 GAAAGCCTTCCAGACGATTTTT 57.495 40.909 0.00 0.00 0.00 1.94
812 1287 2.751837 CGCCCCAGGAAAGCCTTC 60.752 66.667 0.00 0.00 43.90 3.46
832 1307 0.179034 CCACTAAGGGCATCTCCAGC 60.179 60.000 0.00 0.00 36.21 4.85
842 1317 2.436646 CGTGCTGGCCACTAAGGG 60.437 66.667 0.00 0.00 42.42 3.95
843 1318 1.741770 GTCGTGCTGGCCACTAAGG 60.742 63.158 0.00 0.00 42.42 2.69
844 1319 1.016130 CAGTCGTGCTGGCCACTAAG 61.016 60.000 0.00 0.00 42.42 2.18
995 1483 4.899239 CGAGAGCGTCCATGGGCC 62.899 72.222 11.65 3.51 0.00 5.80
1854 2385 3.702048 GCGGTGACCCTGCCAGTA 61.702 66.667 0.00 0.00 0.00 2.74
1942 2473 1.402787 GTGATTTCATCCCGGGCAAT 58.597 50.000 18.49 11.19 0.00 3.56
2232 2764 6.931840 ACAAACAACAAACCAACAACTACAAT 59.068 30.769 0.00 0.00 0.00 2.71
2444 2982 3.164268 AGTTTCATGCTATTGTTGCCCA 58.836 40.909 0.00 0.00 0.00 5.36
2686 3226 9.890629 GCTATAATAGACCAAATGTCCATATCA 57.109 33.333 0.00 0.00 45.68 2.15
2698 3238 5.473846 CCGAGAGACAGCTATAATAGACCAA 59.526 44.000 0.00 0.00 0.00 3.67
2708 3248 1.135915 CAACTGCCGAGAGACAGCTAT 59.864 52.381 0.00 0.00 37.42 2.97
2740 3280 6.349243 TCGAAAAGGAACATCACTACCTAA 57.651 37.500 0.00 0.00 32.06 2.69
2817 3359 2.820787 AGTCGAGAAACCCAGTCTACTG 59.179 50.000 3.02 3.02 43.40 2.74
2818 3360 3.083293 GAGTCGAGAAACCCAGTCTACT 58.917 50.000 0.00 0.00 0.00 2.57
2819 3361 2.164017 GGAGTCGAGAAACCCAGTCTAC 59.836 54.545 0.00 0.00 0.00 2.59
2826 3368 1.258676 AGTGAGGAGTCGAGAAACCC 58.741 55.000 0.00 0.00 0.00 4.11
2846 3485 6.321181 GCAATCTGGATGTTATGGTAAAGGAA 59.679 38.462 0.00 0.00 0.00 3.36
2859 3498 4.225942 TCCTTTCAGTAGCAATCTGGATGT 59.774 41.667 0.00 0.00 34.15 3.06
2878 3517 7.616528 TTTGGAATCTGGATTCTTTTTCCTT 57.383 32.000 18.80 0.00 44.90 3.36
2881 3520 5.871524 GGCTTTGGAATCTGGATTCTTTTTC 59.128 40.000 18.80 6.48 44.90 2.29
2887 3526 3.379688 GTCAGGCTTTGGAATCTGGATTC 59.620 47.826 13.20 13.20 44.82 2.52
2907 3548 4.442706 TGTTTCTCTTGTGACCAGAAGTC 58.557 43.478 6.77 0.00 46.51 3.01
2909 3550 4.214971 CCATGTTTCTCTTGTGACCAGAAG 59.785 45.833 0.96 0.96 33.46 2.85
2964 3616 3.668141 TGCATTAGACACCCCAATGAT 57.332 42.857 0.00 0.00 32.54 2.45
2968 3620 3.737559 AGATTGCATTAGACACCCCAA 57.262 42.857 0.00 0.00 0.00 4.12
3052 3704 1.310904 TACAAACCAGTTTCGCACCC 58.689 50.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.