Multiple sequence alignment - TraesCS3A01G252900

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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 TraesCS3A01G252900 chr3A 100.000 3380 0 0 1 3380 474211506 474208127 0.000000e+00 6242.0
1 TraesCS3A01G252900 chr3D 91.858 1916 58 20 640 2509 355320401 355318538 0.000000e+00 2584.0
2 TraesCS3A01G252900 chr3D 90.714 840 26 16 2529 3334 355318546 355317725 0.000000e+00 1072.0
3 TraesCS3A01G252900 chr3D 93.939 561 9 10 78 638 355320980 355320445 0.000000e+00 824.0
4 TraesCS3A01G252900 chr3D 90.909 66 1 1 14 79 355321066 355321006 2.160000e-12 84.2
5 TraesCS3A01G252900 chr3B 93.725 1737 54 23 757 2465 463202962 463204671 0.000000e+00 2553.0
6 TraesCS3A01G252900 chr3B 91.751 1782 71 31 795 2509 456324993 456323221 0.000000e+00 2407.0
7 TraesCS3A01G252900 chr3B 89.592 490 23 10 78 548 456325921 456325441 6.240000e-167 597.0
8 TraesCS3A01G252900 chr3B 87.891 512 21 8 2528 3030 456323230 456322751 6.330000e-157 564.0
9 TraesCS3A01G252900 chr3B 88.912 478 16 9 2873 3334 463211132 463211588 3.810000e-154 555.0
10 TraesCS3A01G252900 chr3B 94.245 278 13 1 2612 2886 463210830 463211107 4.030000e-114 422.0
11 TraesCS3A01G252900 chr3B 92.105 266 9 4 384 638 463201136 463201400 6.890000e-97 364.0
12 TraesCS3A01G252900 chr3B 96.815 157 1 1 78 230 463200675 463200831 3.350000e-65 259.0
13 TraesCS3A01G252900 chr3B 92.697 178 6 1 229 399 463200946 463201123 2.010000e-62 250.0
14 TraesCS3A01G252900 chr3B 83.465 254 13 11 3096 3334 456322732 456322493 3.420000e-50 209.0
15 TraesCS3A01G252900 chr3B 94.215 121 3 1 640 760 463201448 463201564 7.450000e-42 182.0
16 TraesCS3A01G252900 chr3B 90.756 119 4 4 640 757 456325108 456324996 5.840000e-33 152.0
17 TraesCS3A01G252900 chr3B 94.872 78 3 1 556 633 456325231 456325155 1.650000e-23 121.0
18 TraesCS3A01G252900 chr3B 90.909 66 1 1 14 79 456326007 456325947 2.160000e-12 84.2
19 TraesCS3A01G252900 chr1D 90.909 187 17 0 1887 2073 277094392 277094578 5.600000e-63 252.0
20 TraesCS3A01G252900 chr1B 90.909 187 17 0 1887 2073 376072626 376072812 5.600000e-63 252.0
21 TraesCS3A01G252900 chr1A 90.374 187 18 0 1887 2073 349360265 349360451 2.600000e-61 246.0
22 TraesCS3A01G252900 chr7D 86.697 218 19 8 1030 1238 234656763 234656979 2.030000e-57 233.0
23 TraesCS3A01G252900 chr7D 89.404 151 15 1 1317 1467 234656974 234657123 4.450000e-44 189.0
24 TraesCS3A01G252900 chr2D 100.000 29 0 0 1941 1969 477238249 477238277 2.000000e-03 54.7


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 TraesCS3A01G252900 chr3A 474208127 474211506 3379 True 6242.00 6242 100.000000 1 3380 1 chr3A.!!$R1 3379
1 TraesCS3A01G252900 chr3D 355317725 355321066 3341 True 1141.05 2584 91.855000 14 3334 4 chr3D.!!$R1 3320
2 TraesCS3A01G252900 chr3B 463200675 463204671 3996 False 721.60 2553 93.911400 78 2465 5 chr3B.!!$F1 2387
3 TraesCS3A01G252900 chr3B 456322493 456326007 3514 True 590.60 2407 89.890857 14 3334 7 chr3B.!!$R1 3320
4 TraesCS3A01G252900 chr3B 463210830 463211588 758 False 488.50 555 91.578500 2612 3334 2 chr3B.!!$F2 722

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
954 2839 0.897863 TTGGCCGGGTCCATTTCTTG 60.898 55.0 2.18 0.0 35.77 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2487 4451 0.685097 TTACCTTTCTCCTGTGCGCT 59.315 50.0 9.73 0.0 0.0 5.92 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
35 36 2.853210 CGTGCGTGCTCGATTTGT 59.147 55.556 13.13 0.00 39.71 2.83
42 43 2.351726 GCGTGCTCGATTTGTTCCTATT 59.648 45.455 13.13 0.00 39.71 1.73
43 44 3.785505 GCGTGCTCGATTTGTTCCTATTG 60.786 47.826 13.13 0.00 39.71 1.90
44 45 3.242413 CGTGCTCGATTTGTTCCTATTGG 60.242 47.826 1.00 0.00 39.71 3.16
45 46 3.938963 GTGCTCGATTTGTTCCTATTGGA 59.061 43.478 0.00 0.00 41.36 3.53
46 47 4.034510 GTGCTCGATTTGTTCCTATTGGAG 59.965 45.833 0.00 0.00 44.24 3.86
186 223 4.092968 GCTAGTCATTAACCAACCGTCTTG 59.907 45.833 0.00 0.00 0.00 3.02
340 508 4.404654 GCGGTTTGCGCCCTCTTG 62.405 66.667 4.18 0.00 0.00 3.02
367 535 3.881688 CAGCTCTCCCCAAATCATTACTG 59.118 47.826 0.00 0.00 0.00 2.74
707 1166 1.665916 CACTCCACAGACCACAGCG 60.666 63.158 0.00 0.00 0.00 5.18
708 1167 1.832608 ACTCCACAGACCACAGCGA 60.833 57.895 0.00 0.00 0.00 4.93
709 1168 1.080230 CTCCACAGACCACAGCGAG 60.080 63.158 0.00 0.00 0.00 5.03
710 1169 2.740055 CCACAGACCACAGCGAGC 60.740 66.667 0.00 0.00 0.00 5.03
727 1186 4.863131 AGCGAGCACAGTTATTACTTGTAC 59.137 41.667 0.00 0.00 30.26 2.90
734 1193 8.189460 AGCACAGTTATTACTTGTACTAGTAGC 58.811 37.037 15.22 12.75 32.54 3.58
738 1197 7.648510 CAGTTATTACTTGTACTAGTAGCAGCC 59.351 40.741 15.22 6.32 32.54 4.85
765 2625 1.150536 AGTGACCAACGCAACCCAT 59.849 52.632 0.00 0.00 0.00 4.00
776 2636 4.434713 ACGCAACCCATAAAATCAACTC 57.565 40.909 0.00 0.00 0.00 3.01
777 2637 4.079253 ACGCAACCCATAAAATCAACTCT 58.921 39.130 0.00 0.00 0.00 3.24
874 2746 4.638304 GGCTCGGCTCTATATAAAACCAA 58.362 43.478 0.00 0.00 0.00 3.67
875 2747 4.451435 GGCTCGGCTCTATATAAAACCAAC 59.549 45.833 0.00 0.00 0.00 3.77
876 2748 4.451435 GCTCGGCTCTATATAAAACCAACC 59.549 45.833 0.00 0.00 0.00 3.77
877 2749 5.607477 CTCGGCTCTATATAAAACCAACCA 58.393 41.667 0.00 0.00 0.00 3.67
919 2796 2.601666 ACCGAGAGCAGAGCCACA 60.602 61.111 0.00 0.00 0.00 4.17
920 2797 2.183811 CCGAGAGCAGAGCCACAG 59.816 66.667 0.00 0.00 0.00 3.66
921 2798 2.508887 CGAGAGCAGAGCCACAGC 60.509 66.667 0.00 0.00 40.32 4.40
922 2799 2.125188 GAGAGCAGAGCCACAGCC 60.125 66.667 0.00 0.00 41.25 4.85
923 2800 2.926779 AGAGCAGAGCCACAGCCA 60.927 61.111 0.00 0.00 41.25 4.75
924 2801 2.745492 GAGCAGAGCCACAGCCAC 60.745 66.667 0.00 0.00 41.25 5.01
927 2804 2.113774 CAGAGCCACAGCCACCAA 59.886 61.111 0.00 0.00 41.25 3.67
928 2805 1.529010 CAGAGCCACAGCCACCAAA 60.529 57.895 0.00 0.00 41.25 3.28
954 2839 0.897863 TTGGCCGGGTCCATTTCTTG 60.898 55.000 2.18 0.00 35.77 3.02
1845 3770 3.119708 CCAAGACCATAAGCTTCAGCAAC 60.120 47.826 0.00 0.00 45.16 4.17
1846 3771 2.350522 AGACCATAAGCTTCAGCAACG 58.649 47.619 0.00 0.00 45.16 4.10
1847 3772 0.804989 ACCATAAGCTTCAGCAACGC 59.195 50.000 0.00 0.00 45.16 4.84
1848 3773 0.099436 CCATAAGCTTCAGCAACGCC 59.901 55.000 0.00 0.00 45.16 5.68
1849 3774 0.247814 CATAAGCTTCAGCAACGCCG 60.248 55.000 0.00 0.00 45.16 6.46
1850 3775 0.673644 ATAAGCTTCAGCAACGCCGT 60.674 50.000 0.00 0.00 45.16 5.68
1851 3776 1.289109 TAAGCTTCAGCAACGCCGTC 61.289 55.000 0.00 0.00 45.16 4.79
1852 3777 4.430423 GCTTCAGCAACGCCGTCG 62.430 66.667 0.00 0.00 41.59 5.12
1853 3778 3.777925 CTTCAGCAACGCCGTCGG 61.778 66.667 6.99 6.99 40.69 4.79
2034 3968 1.361204 TCTCCAAGATGGACAAGGCA 58.639 50.000 0.00 0.00 42.67 4.75
2241 4187 2.591429 CAGCTGAACGTGGTGGCA 60.591 61.111 8.42 0.00 0.00 4.92
2405 4351 2.021380 CTGTAACAATCGCGCGGC 59.979 61.111 31.69 11.67 0.00 6.53
2406 4352 2.433491 TGTAACAATCGCGCGGCT 60.433 55.556 31.69 15.38 0.00 5.52
2407 4353 2.320044 GTAACAATCGCGCGGCTC 59.680 61.111 31.69 9.86 0.00 4.70
2408 4354 3.251763 TAACAATCGCGCGGCTCG 61.252 61.111 31.69 18.09 42.12 5.03
2409 4355 3.975083 TAACAATCGCGCGGCTCGT 62.975 57.895 31.69 18.78 41.07 4.18
2447 4411 2.286184 GCAACTGTCAACCGTTAGTGTG 60.286 50.000 0.00 0.00 0.00 3.82
2487 4451 1.736282 CGTGACTGCATGCCACGTA 60.736 57.895 28.62 7.08 45.79 3.57
2505 4469 1.203994 GTAGCGCACAGGAGAAAGGTA 59.796 52.381 11.47 0.00 0.00 3.08
2509 4473 2.488153 GCGCACAGGAGAAAGGTAAAAT 59.512 45.455 0.30 0.00 0.00 1.82
2510 4474 3.670627 GCGCACAGGAGAAAGGTAAAATG 60.671 47.826 0.30 0.00 0.00 2.32
2511 4475 3.119849 CGCACAGGAGAAAGGTAAAATGG 60.120 47.826 0.00 0.00 0.00 3.16
2512 4476 3.826729 GCACAGGAGAAAGGTAAAATGGT 59.173 43.478 0.00 0.00 0.00 3.55
2513 4477 4.082733 GCACAGGAGAAAGGTAAAATGGTC 60.083 45.833 0.00 0.00 0.00 4.02
2514 4478 5.070001 CACAGGAGAAAGGTAAAATGGTCA 58.930 41.667 0.00 0.00 0.00 4.02
2515 4479 5.534654 CACAGGAGAAAGGTAAAATGGTCAA 59.465 40.000 0.00 0.00 0.00 3.18
2516 4480 6.209391 CACAGGAGAAAGGTAAAATGGTCAAT 59.791 38.462 0.00 0.00 0.00 2.57
2517 4481 6.209391 ACAGGAGAAAGGTAAAATGGTCAATG 59.791 38.462 0.00 0.00 0.00 2.82
2518 4482 5.716703 AGGAGAAAGGTAAAATGGTCAATGG 59.283 40.000 0.00 0.00 0.00 3.16
2519 4483 5.105351 GGAGAAAGGTAAAATGGTCAATGGG 60.105 44.000 0.00 0.00 0.00 4.00
2520 4484 4.777366 AGAAAGGTAAAATGGTCAATGGGG 59.223 41.667 0.00 0.00 0.00 4.96
2521 4485 4.412060 AAGGTAAAATGGTCAATGGGGA 57.588 40.909 0.00 0.00 0.00 4.81
2522 4486 3.981212 AGGTAAAATGGTCAATGGGGAG 58.019 45.455 0.00 0.00 0.00 4.30
2523 4487 3.031013 GGTAAAATGGTCAATGGGGAGG 58.969 50.000 0.00 0.00 0.00 4.30
2524 4488 1.571955 AAAATGGTCAATGGGGAGGC 58.428 50.000 0.00 0.00 0.00 4.70
2525 4489 0.712380 AAATGGTCAATGGGGAGGCT 59.288 50.000 0.00 0.00 0.00 4.58
2526 4490 1.607225 AATGGTCAATGGGGAGGCTA 58.393 50.000 0.00 0.00 0.00 3.93
2527 4491 1.607225 ATGGTCAATGGGGAGGCTAA 58.393 50.000 0.00 0.00 0.00 3.09
2528 4492 1.377690 TGGTCAATGGGGAGGCTAAA 58.622 50.000 0.00 0.00 0.00 1.85
2529 4493 1.713647 TGGTCAATGGGGAGGCTAAAA 59.286 47.619 0.00 0.00 0.00 1.52
2530 4494 2.291540 TGGTCAATGGGGAGGCTAAAAG 60.292 50.000 0.00 0.00 0.00 2.27
2531 4495 2.379005 GTCAATGGGGAGGCTAAAAGG 58.621 52.381 0.00 0.00 0.00 3.11
2532 4496 2.000048 TCAATGGGGAGGCTAAAAGGT 59.000 47.619 0.00 0.00 0.00 3.50
2533 4497 2.102578 CAATGGGGAGGCTAAAAGGTG 58.897 52.381 0.00 0.00 0.00 4.00
2534 4498 1.681229 ATGGGGAGGCTAAAAGGTGA 58.319 50.000 0.00 0.00 0.00 4.02
2535 4499 1.451449 TGGGGAGGCTAAAAGGTGAA 58.549 50.000 0.00 0.00 0.00 3.18
2536 4500 1.783979 TGGGGAGGCTAAAAGGTGAAA 59.216 47.619 0.00 0.00 0.00 2.69
2537 4501 2.168496 GGGGAGGCTAAAAGGTGAAAC 58.832 52.381 0.00 0.00 0.00 2.78
2577 4541 1.595311 ATCCCAGATTGCCAGTGGTA 58.405 50.000 11.74 2.55 0.00 3.25
2578 4542 0.911769 TCCCAGATTGCCAGTGGTAG 59.088 55.000 11.74 0.00 0.00 3.18
2579 4543 0.911769 CCCAGATTGCCAGTGGTAGA 59.088 55.000 11.74 0.00 0.00 2.59
2580 4544 1.492176 CCCAGATTGCCAGTGGTAGAT 59.508 52.381 11.74 2.94 0.00 1.98
2581 4545 2.092212 CCCAGATTGCCAGTGGTAGATT 60.092 50.000 11.74 0.00 0.00 2.40
2582 4546 3.209410 CCAGATTGCCAGTGGTAGATTC 58.791 50.000 11.74 5.04 0.00 2.52
2583 4547 3.118112 CCAGATTGCCAGTGGTAGATTCT 60.118 47.826 11.74 7.27 0.00 2.40
2584 4548 4.101585 CCAGATTGCCAGTGGTAGATTCTA 59.898 45.833 11.74 0.00 0.00 2.10
2620 4584 3.056607 GCACCTGGTTATCAATTTGCACT 60.057 43.478 0.00 0.00 0.00 4.40
2627 4591 7.083875 TGGTTATCAATTTGCACTTACTAGC 57.916 36.000 0.00 0.00 0.00 3.42
2794 4763 2.876645 CACGCGCTCTCTCCGTTC 60.877 66.667 5.73 0.00 32.18 3.95
2802 4771 1.754226 GCTCTCTCCGTTCCAGATCTT 59.246 52.381 0.00 0.00 0.00 2.40
2803 4772 2.167487 GCTCTCTCCGTTCCAGATCTTT 59.833 50.000 0.00 0.00 0.00 2.52
2819 4788 0.743345 CTTTACCTACACCCGCTGGC 60.743 60.000 0.00 0.00 33.59 4.85
2849 4818 4.157958 CTCGTCGGGTCGTCGTCC 62.158 72.222 0.00 0.00 39.12 4.79
3033 5052 3.532792 CGGTGTCGTCGCATCGTG 61.533 66.667 12.24 0.00 38.10 4.35
3091 5110 2.978565 CCTCCGATCGGCTCGCTA 60.979 66.667 29.62 10.12 46.25 4.26
3093 5112 2.203167 TCCGATCGGCTCGCTACT 60.203 61.111 29.62 0.00 46.25 2.57
3094 5113 2.177654 CTCCGATCGGCTCGCTACTC 62.178 65.000 29.62 0.00 46.25 2.59
3099 5118 4.615834 CGGCTCGCTACTCCTCGC 62.616 72.222 0.00 0.00 0.00 5.03
3163 5182 2.046892 GGCAGGCGATGTGTCAGT 60.047 61.111 0.00 0.00 0.00 3.41
3164 5183 2.103042 GGCAGGCGATGTGTCAGTC 61.103 63.158 0.00 0.00 0.00 3.51
3165 5184 1.374631 GCAGGCGATGTGTCAGTCA 60.375 57.895 0.00 0.00 0.00 3.41
3166 5185 1.357258 GCAGGCGATGTGTCAGTCAG 61.357 60.000 0.00 0.00 0.00 3.51
3214 5237 3.834373 CCGACGTTACGCGCCAAG 61.834 66.667 5.73 0.00 46.11 3.61
3227 5250 1.607148 GCGCCAAGAACCTTAAACAGT 59.393 47.619 0.00 0.00 0.00 3.55
3241 5264 6.320418 ACCTTAAACAGTAACCCTTTCAGTTG 59.680 38.462 0.00 0.00 0.00 3.16
3334 5382 7.803189 CACGCTTTAATCAAGTTACAATCAGTT 59.197 33.333 0.00 0.00 34.56 3.16
3335 5383 8.349983 ACGCTTTAATCAAGTTACAATCAGTTT 58.650 29.630 0.00 0.00 34.56 2.66
3336 5384 9.180678 CGCTTTAATCAAGTTACAATCAGTTTT 57.819 29.630 0.00 0.00 34.56 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 7.551617 GGAAAGAAAACGATACTCCAATAGGAA 59.448 37.037 0.00 0.00 45.19 3.36
42 43 3.592059 CCGGAAAGAAAACGATACTCCA 58.408 45.455 0.00 0.00 0.00 3.86
43 44 2.934553 CCCGGAAAGAAAACGATACTCC 59.065 50.000 0.73 0.00 0.00 3.85
44 45 2.350804 GCCCGGAAAGAAAACGATACTC 59.649 50.000 0.73 0.00 0.00 2.59
45 46 2.027469 AGCCCGGAAAGAAAACGATACT 60.027 45.455 0.73 0.00 0.00 2.12
46 47 2.095372 CAGCCCGGAAAGAAAACGATAC 59.905 50.000 0.73 0.00 0.00 2.24
186 223 1.340114 CCCAAGTTAACCCAGGAGCTC 60.340 57.143 4.71 4.71 0.00 4.09
340 508 2.505364 ATTTGGGGAGAGCTGGGCAC 62.505 60.000 0.00 0.00 0.00 5.01
478 680 3.123620 CGAGAACCTGCTGCCTGC 61.124 66.667 0.00 0.00 43.25 4.85
638 1051 1.403780 CGTACGACAAGGAAGGAAGGG 60.404 57.143 10.44 0.00 0.00 3.95
707 1166 9.719279 CTACTAGTACAAGTAATAACTGTGCTC 57.281 37.037 0.00 0.00 35.62 4.26
708 1167 8.189460 GCTACTAGTACAAGTAATAACTGTGCT 58.811 37.037 0.00 0.00 35.62 4.40
709 1168 7.972277 TGCTACTAGTACAAGTAATAACTGTGC 59.028 37.037 0.00 0.00 35.62 4.57
710 1169 9.504710 CTGCTACTAGTACAAGTAATAACTGTG 57.495 37.037 0.00 0.00 35.62 3.66
727 1186 2.621055 CTGGACTACAGGCTGCTACTAG 59.379 54.545 15.89 11.17 43.70 2.57
787 2647 7.361201 CGCCAAGAAGTTGATTTTCTATTCTCA 60.361 37.037 0.00 0.00 35.46 3.27
789 2649 6.623767 GCGCCAAGAAGTTGATTTTCTATTCT 60.624 38.462 0.00 0.00 35.46 2.40
791 2651 5.048083 TGCGCCAAGAAGTTGATTTTCTATT 60.048 36.000 4.18 0.00 35.46 1.73
793 2653 3.818210 TGCGCCAAGAAGTTGATTTTCTA 59.182 39.130 4.18 0.00 35.46 2.10
877 2749 0.107410 TGCTGGTTTTCACGGTCTGT 60.107 50.000 0.00 0.00 0.00 3.41
921 2798 2.919494 GCCAAGACGCCTTTGGTGG 61.919 63.158 12.86 0.00 37.55 4.61
922 2799 2.644992 GCCAAGACGCCTTTGGTG 59.355 61.111 12.86 0.00 39.41 4.17
923 2800 2.597510 GGCCAAGACGCCTTTGGT 60.598 61.111 0.00 0.00 46.10 3.67
954 2839 0.108756 GAGCGTTGGTAGGTCTGTCC 60.109 60.000 0.00 0.00 33.73 4.02
1123 3009 4.112341 GAGGTCGTACAGGCGCGT 62.112 66.667 8.43 0.00 0.00 6.01
1537 3441 0.522180 AGGAAGACGACTGTGCGTAG 59.478 55.000 0.00 0.00 45.72 3.51
1545 3449 0.832135 TGCAAGGGAGGAAGACGACT 60.832 55.000 0.00 0.00 0.00 4.18
1794 3719 2.522193 TGGGGTTTCGGTTTGGCC 60.522 61.111 0.00 0.00 0.00 5.36
1796 3721 1.805428 CTGCTGGGGTTTCGGTTTGG 61.805 60.000 0.00 0.00 0.00 3.28
1932 3866 3.050275 GCCTCCACGTGGTTCAGC 61.050 66.667 32.74 25.06 36.34 4.26
2118 4064 3.934391 CTTCACCTCCACGGACGGC 62.934 68.421 0.00 0.00 36.31 5.68
2231 4177 3.315142 ATGCTCGATGCCACCACGT 62.315 57.895 4.73 0.00 42.00 4.49
2411 4357 2.730090 CAGTTGCCTGTACGTACTACGG 60.730 54.545 25.12 21.40 38.77 4.02
2412 4358 2.512885 CAGTTGCCTGTACGTACTACG 58.487 52.381 25.12 13.62 39.64 3.51
2447 4411 2.093235 AGGAGCATGCTCACCTAAACTC 60.093 50.000 40.37 23.72 44.40 3.01
2487 4451 0.685097 TTACCTTTCTCCTGTGCGCT 59.315 50.000 9.73 0.00 0.00 5.92
2492 4456 5.319043 TGACCATTTTACCTTTCTCCTGT 57.681 39.130 0.00 0.00 0.00 4.00
2505 4469 1.079323 AGCCTCCCCATTGACCATTTT 59.921 47.619 0.00 0.00 0.00 1.82
2509 4473 1.377690 TTTAGCCTCCCCATTGACCA 58.622 50.000 0.00 0.00 0.00 4.02
2510 4474 2.379005 CTTTTAGCCTCCCCATTGACC 58.621 52.381 0.00 0.00 0.00 4.02
2511 4475 2.291605 ACCTTTTAGCCTCCCCATTGAC 60.292 50.000 0.00 0.00 0.00 3.18
2512 4476 2.000048 ACCTTTTAGCCTCCCCATTGA 59.000 47.619 0.00 0.00 0.00 2.57
2513 4477 2.102578 CACCTTTTAGCCTCCCCATTG 58.897 52.381 0.00 0.00 0.00 2.82
2514 4478 2.000048 TCACCTTTTAGCCTCCCCATT 59.000 47.619 0.00 0.00 0.00 3.16
2515 4479 1.681229 TCACCTTTTAGCCTCCCCAT 58.319 50.000 0.00 0.00 0.00 4.00
2516 4480 1.451449 TTCACCTTTTAGCCTCCCCA 58.549 50.000 0.00 0.00 0.00 4.96
2517 4481 2.168496 GTTTCACCTTTTAGCCTCCCC 58.832 52.381 0.00 0.00 0.00 4.81
2518 4482 2.168496 GGTTTCACCTTTTAGCCTCCC 58.832 52.381 0.00 0.00 34.73 4.30
2519 4483 2.168496 GGGTTTCACCTTTTAGCCTCC 58.832 52.381 0.00 0.00 38.64 4.30
2520 4484 2.168496 GGGGTTTCACCTTTTAGCCTC 58.832 52.381 0.00 0.00 38.64 4.70
2521 4485 1.787058 AGGGGTTTCACCTTTTAGCCT 59.213 47.619 0.00 0.00 38.64 4.58
2522 4486 2.304221 AGGGGTTTCACCTTTTAGCC 57.696 50.000 0.00 0.00 38.64 3.93
2530 4494 4.533318 GGGGAAAGGGGTTTCACC 57.467 61.111 3.45 3.45 46.07 4.02
2531 4495 1.338107 CTTGGGGAAAGGGGTTTCAC 58.662 55.000 0.66 0.00 33.71 3.18
2532 4496 0.938192 ACTTGGGGAAAGGGGTTTCA 59.062 50.000 0.66 0.00 40.51 2.69
2533 4497 1.338107 CACTTGGGGAAAGGGGTTTC 58.662 55.000 0.00 0.00 40.51 2.78
2534 4498 3.550692 CACTTGGGGAAAGGGGTTT 57.449 52.632 0.00 0.00 40.51 3.27
2538 4502 1.607467 CTGCCACTTGGGGAAAGGG 60.607 63.158 0.00 0.00 40.51 3.95
2546 4510 0.911769 TCTGGGATACTGCCACTTGG 59.088 55.000 0.00 0.00 30.85 3.61
2577 4541 6.989169 GGTGCACTACATGAATCTTAGAATCT 59.011 38.462 17.98 0.00 0.00 2.40
2578 4542 6.989169 AGGTGCACTACATGAATCTTAGAATC 59.011 38.462 17.98 0.00 0.00 2.52
2579 4543 6.765036 CAGGTGCACTACATGAATCTTAGAAT 59.235 38.462 17.98 0.00 43.52 2.40
2580 4544 6.108687 CAGGTGCACTACATGAATCTTAGAA 58.891 40.000 17.98 0.00 43.52 2.10
2581 4545 5.395657 CCAGGTGCACTACATGAATCTTAGA 60.396 44.000 17.98 0.00 43.52 2.10
2582 4546 4.813161 CCAGGTGCACTACATGAATCTTAG 59.187 45.833 17.98 0.00 43.52 2.18
2583 4547 4.225042 ACCAGGTGCACTACATGAATCTTA 59.775 41.667 17.98 0.00 43.52 2.10
2584 4548 3.009473 ACCAGGTGCACTACATGAATCTT 59.991 43.478 17.98 0.00 43.52 2.40
2620 4584 8.067751 AGATTTGATCTACTGTGTGCTAGTAA 57.932 34.615 0.00 0.00 38.00 2.24
2794 4763 2.483188 GCGGGTGTAGGTAAAGATCTGG 60.483 54.545 0.00 0.00 0.00 3.86
2802 4771 2.662070 GGCCAGCGGGTGTAGGTAA 61.662 63.158 4.36 0.00 36.17 2.85
2803 4772 3.078836 GGCCAGCGGGTGTAGGTA 61.079 66.667 4.36 0.00 36.17 3.08
2819 4788 1.798813 CCGACGAGGAAAACTTTCAGG 59.201 52.381 0.00 0.00 45.00 3.86
3033 5052 1.065109 GTTGTTGGGTTGCGGTCAC 59.935 57.895 0.00 0.00 0.00 3.67
3089 5108 2.277373 GCACGACGCGAGGAGTAG 60.277 66.667 15.93 0.00 0.00 2.57
3090 5109 3.051479 TGCACGACGCGAGGAGTA 61.051 61.111 15.93 0.00 46.97 2.59
3091 5110 4.702081 GTGCACGACGCGAGGAGT 62.702 66.667 15.93 3.64 46.97 3.85
3214 5237 6.544931 ACTGAAAGGGTTACTGTTTAAGGTTC 59.455 38.462 0.00 0.00 39.30 3.62
3227 5250 3.072476 CAGGTCCTCAACTGAAAGGGTTA 59.928 47.826 0.00 0.00 39.30 2.85
3241 5264 1.448540 CACGGCACATCAGGTCCTC 60.449 63.158 0.00 0.00 0.00 3.71
3275 5319 1.002430 GCATGGGTGAGTGAGTTCAGA 59.998 52.381 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.