Multiple sequence alignment - TraesCS3D01G220000

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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 TraesCS3D01G220000 chr3D 100.000 3375 0 0 1 3375 299927810 299924436 0.000000e+00 6233.0
1 TraesCS3D01G220000 chr3D 79.727 439 67 11 2940 3358 553748052 553747616 7.080000e-77 298.0
2 TraesCS3D01G220000 chr3D 94.872 39 2 0 2960 2998 394114635 394114597 1.010000e-05 62.1
3 TraesCS3D01G220000 chr3B 91.314 3431 193 37 1 3375 421213068 421216449 0.000000e+00 4588.0
4 TraesCS3D01G220000 chr3B 94.872 39 2 0 2960 2998 91228810 91228772 1.010000e-05 62.1
5 TraesCS3D01G220000 chr3B 100.000 30 0 0 2834 2863 136811756 136811785 4.700000e-04 56.5
6 TraesCS3D01G220000 chr3A 93.261 1662 73 19 1 1649 435773323 435774958 0.000000e+00 2412.0
7 TraesCS3D01G220000 chr3A 94.405 983 35 7 1649 2628 435775029 435775994 0.000000e+00 1493.0
8 TraesCS3D01G220000 chr3A 82.749 342 50 6 3020 3353 111727009 111727349 2.550000e-76 296.0
9 TraesCS3D01G220000 chr3A 86.207 58 8 0 2941 2998 92992478 92992535 2.810000e-06 63.9
10 TraesCS3D01G220000 chr5D 84.412 340 45 3 3021 3353 462288929 462288591 9.030000e-86 327.0
11 TraesCS3D01G220000 chr6D 83.526 346 49 6 2960 3299 81177218 81176875 1.950000e-82 316.0
12 TraesCS3D01G220000 chr1D 86.007 293 35 4 3059 3350 299761906 299762193 3.270000e-80 309.0
13 TraesCS3D01G220000 chr5B 83.140 344 51 3 3018 3354 374368509 374368166 1.180000e-79 307.0
14 TraesCS3D01G220000 chr2D 81.234 389 64 6 2941 3321 7005380 7005767 4.230000e-79 305.0
15 TraesCS3D01G220000 chr2B 82.891 339 44 9 3020 3350 755060893 755061225 3.290000e-75 292.0
16 TraesCS3D01G220000 chr7B 88.136 59 5 2 2941 2998 100968715 100968772 6.040000e-08 69.4
17 TraesCS3D01G220000 chr1A 82.432 74 13 0 2883 2956 53464782 53464709 7.820000e-07 65.8


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 TraesCS3D01G220000 chr3D 299924436 299927810 3374 True 6233.0 6233 100.000 1 3375 1 chr3D.!!$R1 3374
1 TraesCS3D01G220000 chr3B 421213068 421216449 3381 False 4588.0 4588 91.314 1 3375 1 chr3B.!!$F2 3374
2 TraesCS3D01G220000 chr3A 435773323 435775994 2671 False 1952.5 2412 93.833 1 2628 2 chr3A.!!$F3 2627

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
478 481 0.390735 GCTTTTCTTAGGCGTCCCGA 60.391 55.0 0.0 0.0 35.76 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 2494 1.083015 CACAAGCAACACGTACGGC 60.083 57.895 21.06 13.06 0.0 5.68 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
266 267 0.960364 ATGGCTTACAAGGTGTGGCG 60.960 55.000 0.00 0.00 33.52 5.69
361 364 4.864334 GATGCCAGACGCCCAGGG 62.864 72.222 0.00 0.00 36.24 4.45
412 415 2.825982 CGTGGTGGTCCTTGGACA 59.174 61.111 19.90 5.23 34.23 4.02
421 424 2.210013 TCCTTGGACACAGCGAGCT 61.210 57.895 0.00 0.00 0.00 4.09
474 477 1.366854 CGGGGCTTTTCTTAGGCGTC 61.367 60.000 0.00 0.00 41.33 5.19
478 481 0.390735 GCTTTTCTTAGGCGTCCCGA 60.391 55.000 0.00 0.00 35.76 5.14
515 518 4.332819 GCAATTAGTGAAGTAATGCGTCCT 59.667 41.667 0.00 0.00 0.00 3.85
516 519 5.163754 GCAATTAGTGAAGTAATGCGTCCTT 60.164 40.000 0.00 0.00 0.00 3.36
528 531 2.711922 CGTCCTTGCGAGTAGGCCT 61.712 63.158 11.78 11.78 32.59 5.19
530 533 1.609501 TCCTTGCGAGTAGGCCTGT 60.610 57.895 17.99 1.23 32.59 4.00
538 541 2.205074 CGAGTAGGCCTGTAGCAATTG 58.795 52.381 17.99 0.00 46.50 2.32
555 558 4.621034 GCAATTGGTGAAGTAATCAAACCG 59.379 41.667 7.72 0.00 40.50 4.44
565 568 7.640240 GTGAAGTAATCAAACCGATTAGCATTC 59.360 37.037 0.00 0.00 45.25 2.67
571 574 6.698008 TCAAACCGATTAGCATTCATCATT 57.302 33.333 0.00 0.00 0.00 2.57
580 587 7.043854 CGATTAGCATTCATCATTGGTGTTTTC 60.044 37.037 0.00 0.00 0.00 2.29
583 590 6.527423 AGCATTCATCATTGGTGTTTTCTTT 58.473 32.000 0.00 0.00 0.00 2.52
584 591 7.669427 AGCATTCATCATTGGTGTTTTCTTTA 58.331 30.769 0.00 0.00 0.00 1.85
585 592 8.316214 AGCATTCATCATTGGTGTTTTCTTTAT 58.684 29.630 0.00 0.00 0.00 1.40
588 595 9.643693 ATTCATCATTGGTGTTTTCTTTATCAC 57.356 29.630 0.00 0.00 0.00 3.06
590 597 6.007936 TCATTGGTGTTTTCTTTATCACGG 57.992 37.500 0.00 0.00 0.00 4.94
591 598 5.533154 TCATTGGTGTTTTCTTTATCACGGT 59.467 36.000 0.00 0.00 0.00 4.83
592 599 5.427036 TTGGTGTTTTCTTTATCACGGTC 57.573 39.130 0.00 0.00 0.00 4.79
594 601 4.882427 TGGTGTTTTCTTTATCACGGTCAA 59.118 37.500 0.00 0.00 0.00 3.18
595 602 5.533154 TGGTGTTTTCTTTATCACGGTCAAT 59.467 36.000 0.00 0.00 0.00 2.57
621 628 2.418628 CTGGTGCGGTGATTTTTACGAT 59.581 45.455 0.00 0.00 0.00 3.73
688 705 6.462073 TTTTTGCATACTCTCACTAACGAC 57.538 37.500 0.00 0.00 0.00 4.34
689 706 4.776795 TTGCATACTCTCACTAACGACA 57.223 40.909 0.00 0.00 0.00 4.35
704 721 1.739466 ACGACACATGCATCACATTCC 59.261 47.619 0.00 0.00 36.64 3.01
705 722 1.267682 CGACACATGCATCACATTCCG 60.268 52.381 0.00 0.00 36.64 4.30
706 723 2.009051 GACACATGCATCACATTCCGA 58.991 47.619 0.00 0.00 36.64 4.55
707 724 2.011947 ACACATGCATCACATTCCGAG 58.988 47.619 0.00 0.00 36.64 4.63
708 725 2.282407 CACATGCATCACATTCCGAGA 58.718 47.619 0.00 0.00 36.64 4.04
709 726 2.876550 CACATGCATCACATTCCGAGAT 59.123 45.455 0.00 0.00 36.64 2.75
758 775 1.671261 CCGGAGAGCAGAGAACACAAG 60.671 57.143 0.00 0.00 0.00 3.16
772 789 7.859875 CAGAGAACACAAGAGAATTCCTTTTTC 59.140 37.037 0.65 7.69 0.00 2.29
793 815 5.899120 TCTCGTGTAGAATAAAGTGAGCT 57.101 39.130 0.00 0.00 0.00 4.09
811 833 4.164030 TGAGCTGAGCCCTATAAAACATCA 59.836 41.667 0.00 0.00 0.00 3.07
845 867 4.217118 CCTGTCCACAAGAAAGAAATCCAG 59.783 45.833 0.00 0.00 30.30 3.86
857 879 3.878778 AGAAATCCAGAACCCGATGAAG 58.121 45.455 0.00 0.00 0.00 3.02
1039 1061 4.436998 GCGACCACCACTCCTCCG 62.437 72.222 0.00 0.00 0.00 4.63
1588 1610 3.387397 AGGTACACGTCCTTTTCTTTCG 58.613 45.455 0.00 0.00 30.18 3.46
1589 1611 2.477754 GGTACACGTCCTTTTCTTTCGG 59.522 50.000 0.00 0.00 0.00 4.30
1590 1612 2.320745 ACACGTCCTTTTCTTTCGGT 57.679 45.000 0.00 0.00 0.00 4.69
1665 1764 5.290885 CCTTGACGATGATGATACGTTTCAA 59.709 40.000 12.74 0.00 40.29 2.69
1906 2011 1.000496 GTCGACAGACCGGTCTTCTTT 60.000 52.381 34.54 18.50 41.41 2.52
1913 2018 2.813908 CGGTCTTCTTTCGGCCGG 60.814 66.667 27.83 9.82 38.86 6.13
2272 2377 4.035102 GAGTGGAGGTGGGTGCCC 62.035 72.222 0.00 0.00 0.00 5.36
2386 2491 4.052229 CGCTGAACCGGACCGTCT 62.052 66.667 9.46 0.00 0.00 4.18
2387 2492 2.126031 GCTGAACCGGACCGTCTC 60.126 66.667 9.46 9.22 0.00 3.36
2388 2493 2.178521 CTGAACCGGACCGTCTCG 59.821 66.667 9.46 0.00 0.00 4.04
2472 2580 1.303643 GGAGAGGTGTTTGGCCAGG 60.304 63.158 5.11 0.00 0.00 4.45
2513 2621 1.681793 CGATCATCCGAGTGGTACCTT 59.318 52.381 14.36 0.73 36.30 3.50
2573 2690 3.264193 TGATCCTGTGTGATAGCTTGGTT 59.736 43.478 0.00 0.00 0.00 3.67
2653 2773 6.328934 TCATAAATCTGGTATGTGCCTTCCTA 59.671 38.462 0.00 0.00 31.96 2.94
2712 2836 2.974935 TTTCGTGTTCACGTCCGGGG 62.975 60.000 21.61 0.00 0.00 5.73
2730 2863 1.004440 GGCCAAGAGAGAACGTGCT 60.004 57.895 0.00 0.00 0.00 4.40
2764 2897 4.258457 ACTGTCTACTAAGGGCATCTCT 57.742 45.455 0.00 0.00 0.00 3.10
2773 2906 3.460857 AAGGGCATCTCTAATGACGAC 57.539 47.619 0.00 0.00 0.00 4.34
2777 2910 2.037772 GGCATCTCTAATGACGACCCAT 59.962 50.000 0.00 0.00 0.00 4.00
2790 2923 4.817464 TGACGACCCATAAATTTTATCCCG 59.183 41.667 0.00 3.94 0.00 5.14
2807 2940 3.499737 GCATCCGGCCGTGAACAG 61.500 66.667 26.12 15.04 36.11 3.16
2808 2941 2.264480 CATCCGGCCGTGAACAGA 59.736 61.111 26.12 13.51 0.00 3.41
2809 2942 1.811266 CATCCGGCCGTGAACAGAG 60.811 63.158 26.12 5.84 0.00 3.35
2810 2943 2.283529 ATCCGGCCGTGAACAGAGT 61.284 57.895 26.12 1.89 0.00 3.24
2811 2944 2.227089 ATCCGGCCGTGAACAGAGTC 62.227 60.000 26.12 0.00 0.00 3.36
2812 2945 2.432628 CGGCCGTGAACAGAGTCC 60.433 66.667 19.50 0.00 0.00 3.85
2813 2946 2.047179 GGCCGTGAACAGAGTCCC 60.047 66.667 0.00 0.00 0.00 4.46
2814 2947 2.432628 GCCGTGAACAGAGTCCCG 60.433 66.667 0.00 0.00 0.00 5.14
2815 2948 2.432628 CCGTGAACAGAGTCCCGC 60.433 66.667 0.00 0.00 0.00 6.13
2816 2949 2.338620 CGTGAACAGAGTCCCGCA 59.661 61.111 0.00 0.00 0.00 5.69
2817 2950 1.079819 CGTGAACAGAGTCCCGCAT 60.080 57.895 0.00 0.00 0.00 4.73
2818 2951 1.078759 CGTGAACAGAGTCCCGCATC 61.079 60.000 0.00 0.00 0.00 3.91
2819 2952 0.741221 GTGAACAGAGTCCCGCATCC 60.741 60.000 0.00 0.00 0.00 3.51
2820 2953 1.519455 GAACAGAGTCCCGCATCCG 60.519 63.158 0.00 0.00 0.00 4.18
2836 2969 2.579201 CGGCCGTGAACAGAGGAT 59.421 61.111 19.50 0.00 0.00 3.24
2839 2972 0.036388 GGCCGTGAACAGAGGATCAA 60.036 55.000 0.00 0.00 37.82 2.57
2870 3004 0.322546 GGATGTGGAAGGGCGTCTTT 60.323 55.000 0.00 0.00 35.50 2.52
2871 3005 1.087501 GATGTGGAAGGGCGTCTTTC 58.912 55.000 2.81 2.81 35.50 2.62
2874 3008 0.804989 GTGGAAGGGCGTCTTTCATG 59.195 55.000 14.19 0.00 42.52 3.07
2875 3009 0.960364 TGGAAGGGCGTCTTTCATGC 60.960 55.000 14.19 0.00 36.11 4.06
2881 3015 0.179179 GGCGTCTTTCATGCTGCTTC 60.179 55.000 0.00 0.00 37.18 3.86
2889 3023 4.337274 TCTTTCATGCTGCTTCCATACATG 59.663 41.667 0.00 0.00 37.04 3.21
2891 3025 3.208594 TCATGCTGCTTCCATACATGTC 58.791 45.455 0.00 0.00 37.03 3.06
2894 3028 2.749076 TGCTGCTTCCATACATGTCAAC 59.251 45.455 0.00 0.00 0.00 3.18
2895 3029 2.749076 GCTGCTTCCATACATGTCAACA 59.251 45.455 0.00 0.00 0.00 3.33
2896 3030 3.191162 GCTGCTTCCATACATGTCAACAA 59.809 43.478 0.00 0.00 0.00 2.83
2897 3031 4.142315 GCTGCTTCCATACATGTCAACAAT 60.142 41.667 0.00 0.00 0.00 2.71
2898 3032 5.622914 GCTGCTTCCATACATGTCAACAATT 60.623 40.000 0.00 0.00 0.00 2.32
2911 3045 9.267084 ACATGTCAACAATTTTATAAACCAACC 57.733 29.630 0.00 0.00 0.00 3.77
2912 3046 7.932120 TGTCAACAATTTTATAAACCAACCG 57.068 32.000 0.00 0.00 0.00 4.44
2942 3076 0.596341 GTGCAAACACGGCGGATTTT 60.596 50.000 13.24 4.22 36.98 1.82
2958 3092 5.333568 GCGGATTTTATATAAACCGAACGCT 60.334 40.000 28.23 3.34 37.13 5.07
2974 3117 5.248087 CGAACGCTATTCATGTAAACACAG 58.752 41.667 0.00 0.00 0.00 3.66
2975 3118 5.163992 CGAACGCTATTCATGTAAACACAGT 60.164 40.000 0.00 0.00 0.00 3.55
3013 3166 7.336427 ACATTTCAAACAAAAGAAATTCCAGCA 59.664 29.630 0.00 0.00 41.20 4.41
3056 3209 0.110486 TGTTCCCTTCCTTGGACTGC 59.890 55.000 0.00 0.00 0.00 4.40
3063 3216 0.178891 TTCCTTGGACTGCCTCCTCT 60.179 55.000 0.00 0.00 40.26 3.69
3069 3222 0.178987 GGACTGCCTCCTCTATCCGA 60.179 60.000 0.00 0.00 35.89 4.55
3075 3229 1.515081 CCTCCTCTATCCGACGTCTC 58.485 60.000 14.70 0.00 0.00 3.36
3076 3230 1.071071 CCTCCTCTATCCGACGTCTCT 59.929 57.143 14.70 0.22 0.00 3.10
3109 3263 3.487574 GCGATAAGACCGATGAAGTGAAG 59.512 47.826 0.00 0.00 0.00 3.02
3110 3264 4.673441 CGATAAGACCGATGAAGTGAAGT 58.327 43.478 0.00 0.00 0.00 3.01
3115 3269 0.443869 CCGATGAAGTGAAGTTGCGG 59.556 55.000 0.00 0.00 0.00 5.69
3184 3338 0.250640 CACAAGGTCTTGCTGCCTCT 60.251 55.000 10.31 0.00 44.03 3.69
3199 3353 1.115467 CCTCTCGTGCCCTACTCATT 58.885 55.000 0.00 0.00 0.00 2.57
3212 3366 1.770294 ACTCATTCTCGGAGGAGTCC 58.230 55.000 0.00 0.00 41.26 3.85
3266 3420 1.656818 CGATGGAAATGGTGGCGCTT 61.657 55.000 7.64 0.00 0.00 4.68
3286 3440 3.986006 GCTGTCGTCGTCCCACCA 61.986 66.667 0.00 0.00 0.00 4.17
3306 3460 1.944676 GCCGCCTGATAGTTCGTCG 60.945 63.158 0.00 0.00 0.00 5.12
3309 3463 0.924363 CGCCTGATAGTTCGTCGACG 60.924 60.000 31.30 31.30 41.45 5.12
3311 3465 0.731417 CCTGATAGTTCGTCGACGGT 59.269 55.000 35.05 22.58 40.29 4.83
3312 3466 1.531264 CCTGATAGTTCGTCGACGGTG 60.531 57.143 35.05 16.35 40.29 4.94
3313 3467 0.179181 TGATAGTTCGTCGACGGTGC 60.179 55.000 35.05 24.20 40.29 5.01
3314 3468 1.192436 GATAGTTCGTCGACGGTGCG 61.192 60.000 35.05 12.18 40.29 5.34
3340 3494 2.861006 GGCGTTGTTCTCCTTCGC 59.139 61.111 0.00 0.00 44.95 4.70
3342 3496 3.011760 GCGTTGTTCTCCTTCGCGG 62.012 63.158 6.13 0.00 37.74 6.46
3345 3499 1.372499 TTGTTCTCCTTCGCGGTCG 60.372 57.895 6.13 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
266 267 1.152546 GCATGACCCCAATACCCCC 60.153 63.158 0.00 0.00 0.00 5.40
394 397 2.668550 GTCCAAGGACCACCACGC 60.669 66.667 8.06 0.00 39.08 5.34
412 415 2.670934 CAAGGCCAAGCTCGCTGT 60.671 61.111 5.01 0.00 0.00 4.40
478 481 2.257409 AATTGCTCTGGCCCGATCGT 62.257 55.000 15.09 0.00 37.74 3.73
489 492 5.178797 ACGCATTACTTCACTAATTGCTCT 58.821 37.500 0.00 0.00 0.00 4.09
515 518 1.254975 TGCTACAGGCCTACTCGCAA 61.255 55.000 3.98 0.00 40.92 4.85
516 519 1.254975 TTGCTACAGGCCTACTCGCA 61.255 55.000 3.98 9.66 40.92 5.10
528 531 7.367285 GTTTGATTACTTCACCAATTGCTACA 58.633 34.615 0.00 0.00 32.84 2.74
530 533 6.348950 CGGTTTGATTACTTCACCAATTGCTA 60.349 38.462 0.00 0.00 32.84 3.49
538 541 5.353123 TGCTAATCGGTTTGATTACTTCACC 59.647 40.000 0.00 0.00 45.51 4.02
555 558 7.977853 AGAAAACACCAATGATGAATGCTAATC 59.022 33.333 0.00 0.00 0.00 1.75
565 568 6.527722 CCGTGATAAAGAAAACACCAATGATG 59.472 38.462 0.00 0.00 0.00 3.07
571 574 4.452825 TGACCGTGATAAAGAAAACACCA 58.547 39.130 0.00 0.00 0.00 4.17
580 587 6.582295 CACCAGAAAAATTGACCGTGATAAAG 59.418 38.462 0.00 0.00 0.00 1.85
583 590 4.083003 GCACCAGAAAAATTGACCGTGATA 60.083 41.667 0.00 0.00 0.00 2.15
584 591 3.305335 GCACCAGAAAAATTGACCGTGAT 60.305 43.478 0.00 0.00 0.00 3.06
585 592 2.034053 GCACCAGAAAAATTGACCGTGA 59.966 45.455 0.00 0.00 0.00 4.35
588 595 1.665735 CCGCACCAGAAAAATTGACCG 60.666 52.381 0.00 0.00 0.00 4.79
590 597 2.034053 TCACCGCACCAGAAAAATTGAC 59.966 45.455 0.00 0.00 0.00 3.18
591 598 2.302260 TCACCGCACCAGAAAAATTGA 58.698 42.857 0.00 0.00 0.00 2.57
592 599 2.791383 TCACCGCACCAGAAAAATTG 57.209 45.000 0.00 0.00 0.00 2.32
594 601 4.335400 AAAATCACCGCACCAGAAAAAT 57.665 36.364 0.00 0.00 0.00 1.82
595 602 3.810310 AAAATCACCGCACCAGAAAAA 57.190 38.095 0.00 0.00 0.00 1.94
621 628 6.676950 CAGCAAACCACTACATTACATTTCA 58.323 36.000 0.00 0.00 0.00 2.69
634 641 2.862541 TGTCATTAGCAGCAAACCACT 58.137 42.857 0.00 0.00 0.00 4.00
635 642 3.855689 ATGTCATTAGCAGCAAACCAC 57.144 42.857 0.00 0.00 0.00 4.16
674 681 2.296190 TGCATGTGTCGTTAGTGAGAGT 59.704 45.455 0.00 0.00 0.00 3.24
675 682 2.946564 TGCATGTGTCGTTAGTGAGAG 58.053 47.619 0.00 0.00 0.00 3.20
676 683 3.056891 TGATGCATGTGTCGTTAGTGAGA 60.057 43.478 2.46 0.00 0.00 3.27
688 705 2.282407 TCTCGGAATGTGATGCATGTG 58.718 47.619 2.46 0.00 37.96 3.21
689 706 2.696989 TCTCGGAATGTGATGCATGT 57.303 45.000 2.46 0.00 37.96 3.21
704 721 4.513442 TCCCACTAAAATGGTTCATCTCG 58.487 43.478 0.00 0.00 38.16 4.04
705 722 6.038714 GTGATCCCACTAAAATGGTTCATCTC 59.961 42.308 0.00 0.00 40.10 2.75
706 723 5.888161 GTGATCCCACTAAAATGGTTCATCT 59.112 40.000 0.00 0.00 40.10 2.90
707 724 5.220854 CGTGATCCCACTAAAATGGTTCATC 60.221 44.000 0.00 0.00 41.06 2.92
708 725 4.640201 CGTGATCCCACTAAAATGGTTCAT 59.360 41.667 0.00 0.00 41.06 2.57
709 726 4.006989 CGTGATCCCACTAAAATGGTTCA 58.993 43.478 0.00 0.00 41.06 3.18
737 754 0.539669 TGTGTTCTCTGCTCTCCGGA 60.540 55.000 2.93 2.93 0.00 5.14
758 775 7.653767 TTCTACACGAGAAAAAGGAATTCTC 57.346 36.000 5.23 6.27 45.97 2.87
772 789 5.641709 TCAGCTCACTTTATTCTACACGAG 58.358 41.667 0.00 0.00 0.00 4.18
775 792 4.568760 GGCTCAGCTCACTTTATTCTACAC 59.431 45.833 0.00 0.00 0.00 2.90
793 815 5.957771 AGAGTGATGTTTTATAGGGCTCA 57.042 39.130 0.00 0.00 0.00 4.26
811 833 2.338809 TGTGGACAGGGATGAAAGAGT 58.661 47.619 0.00 0.00 0.00 3.24
845 867 5.692654 GCTAAATCTCTACTTCATCGGGTTC 59.307 44.000 0.00 0.00 0.00 3.62
857 879 2.159085 ACCTGGTGCGCTAAATCTCTAC 60.159 50.000 9.73 0.00 0.00 2.59
1588 1610 1.210722 GGATTTCCAGAGTCCTCCACC 59.789 57.143 0.00 0.00 35.64 4.61
1589 1611 2.192263 AGGATTTCCAGAGTCCTCCAC 58.808 52.381 0.00 0.00 37.88 4.02
1590 1612 2.649742 AGGATTTCCAGAGTCCTCCA 57.350 50.000 0.00 0.00 37.88 3.86
1677 1776 4.166144 AGAGAAACCTTGTTGGAGAGGAAA 59.834 41.667 0.00 0.00 39.71 3.13
1678 1777 3.716872 AGAGAAACCTTGTTGGAGAGGAA 59.283 43.478 0.00 0.00 39.71 3.36
1679 1778 3.318313 AGAGAAACCTTGTTGGAGAGGA 58.682 45.455 0.00 0.00 39.71 3.71
1680 1779 3.778954 AGAGAAACCTTGTTGGAGAGG 57.221 47.619 0.00 0.00 39.71 3.69
1685 1784 1.266989 GGCGAAGAGAAACCTTGTTGG 59.733 52.381 0.00 0.00 42.93 3.77
1888 1993 1.699343 GAAAGAAGACCGGTCTGTCG 58.301 55.000 36.87 0.00 40.36 4.35
1948 2053 1.509463 GTACACGTGGAGCCGATCA 59.491 57.895 21.57 0.00 0.00 2.92
2077 2182 3.958860 ACCAGCTGCCAGTCACCC 61.959 66.667 8.66 0.00 0.00 4.61
2080 2185 2.427320 GACACCAGCTGCCAGTCA 59.573 61.111 19.92 0.00 0.00 3.41
2116 2221 1.373570 GCTTCCTGAACCCTTCGATG 58.626 55.000 0.00 0.00 0.00 3.84
2224 2329 2.078914 GTCGTACGACAGCCACACG 61.079 63.158 36.60 1.32 44.02 4.49
2382 2487 3.599792 AACACGTACGGCCGAGACG 62.600 63.158 37.32 37.32 41.40 4.18
2383 2488 2.084681 CAACACGTACGGCCGAGAC 61.085 63.158 35.90 26.58 0.00 3.36
2384 2489 2.256158 CAACACGTACGGCCGAGA 59.744 61.111 35.90 17.13 0.00 4.04
2385 2490 3.475774 GCAACACGTACGGCCGAG 61.476 66.667 35.90 23.99 0.00 4.63
2386 2491 3.502990 AAGCAACACGTACGGCCGA 62.503 57.895 35.90 13.31 0.00 5.54
2387 2492 3.039588 AAGCAACACGTACGGCCG 61.040 61.111 26.86 26.86 0.00 6.13
2388 2493 2.248835 ACAAGCAACACGTACGGCC 61.249 57.895 21.06 0.00 0.00 6.13
2389 2494 1.083015 CACAAGCAACACGTACGGC 60.083 57.895 21.06 13.06 0.00 5.68
2513 2621 1.871418 CATGGAGGGGAGAACAGAGA 58.129 55.000 0.00 0.00 0.00 3.10
2573 2690 1.026182 GCCATCACTTGTCCGCATCA 61.026 55.000 0.00 0.00 0.00 3.07
2712 2836 0.246635 TAGCACGTTCTCTCTTGGCC 59.753 55.000 0.00 0.00 0.00 5.36
2720 2844 3.971150 ACTGATAGCATAGCACGTTCTC 58.029 45.455 0.00 0.00 31.32 2.87
2730 2863 9.286170 CCTTAGTAGACAGTAACTGATAGCATA 57.714 37.037 0.00 0.00 35.18 3.14
2764 2897 7.173562 CGGGATAAAATTTATGGGTCGTCATTA 59.826 37.037 2.58 0.00 0.00 1.90
2773 2906 4.380444 CGGATGCGGGATAAAATTTATGGG 60.380 45.833 2.58 0.00 0.00 4.00
2777 2910 2.554893 GCCGGATGCGGGATAAAATTTA 59.445 45.455 27.80 0.00 0.00 1.40
2790 2923 3.499737 CTGTTCACGGCCGGATGC 61.500 66.667 31.76 17.00 40.16 3.91
2805 2938 4.899239 GCCGGATGCGGGACTCTG 62.899 72.222 27.80 0.00 0.00 3.35
2814 2947 3.499737 CTGTTCACGGCCGGATGC 61.500 66.667 31.76 17.00 40.16 3.91
2815 2948 1.811266 CTCTGTTCACGGCCGGATG 60.811 63.158 31.76 20.13 0.00 3.51
2816 2949 2.579201 CTCTGTTCACGGCCGGAT 59.421 61.111 31.76 6.18 0.00 4.18
2817 2950 3.691342 CCTCTGTTCACGGCCGGA 61.691 66.667 31.76 20.83 0.00 5.14
2818 2951 2.907897 GATCCTCTGTTCACGGCCGG 62.908 65.000 31.76 18.67 0.00 6.13
2819 2952 1.519455 GATCCTCTGTTCACGGCCG 60.519 63.158 26.86 26.86 0.00 6.13
2820 2953 0.036388 TTGATCCTCTGTTCACGGCC 60.036 55.000 0.00 0.00 0.00 6.13
2821 2954 1.936547 GATTGATCCTCTGTTCACGGC 59.063 52.381 0.00 0.00 0.00 5.68
2822 2955 2.555199 GGATTGATCCTCTGTTCACGG 58.445 52.381 2.72 0.00 43.73 4.94
2823 2956 2.196749 CGGATTGATCCTCTGTTCACG 58.803 52.381 8.31 0.00 44.93 4.35
2824 2957 1.936547 GCGGATTGATCCTCTGTTCAC 59.063 52.381 8.31 0.00 44.93 3.18
2825 2958 1.471501 CGCGGATTGATCCTCTGTTCA 60.472 52.381 0.00 0.00 44.93 3.18
2826 2959 1.212616 CGCGGATTGATCCTCTGTTC 58.787 55.000 0.00 0.00 44.93 3.18
2827 2960 0.179073 CCGCGGATTGATCCTCTGTT 60.179 55.000 24.07 0.00 44.93 3.16
2828 2961 1.043116 TCCGCGGATTGATCCTCTGT 61.043 55.000 27.28 0.00 44.93 3.41
2829 2962 0.598680 GTCCGCGGATTGATCCTCTG 60.599 60.000 33.58 0.00 44.93 3.35
2842 2975 3.925362 TTCCACATCCGTGTCCGCG 62.925 63.158 0.00 0.00 41.93 6.46
2848 2981 2.819595 CGCCCTTCCACATCCGTG 60.820 66.667 0.00 0.00 43.21 4.94
2856 2989 0.960364 GCATGAAAGACGCCCTTCCA 60.960 55.000 0.00 0.00 33.02 3.53
2859 2992 1.589716 GCAGCATGAAAGACGCCCTT 61.590 55.000 0.00 0.00 39.69 3.95
2870 3004 3.208594 GACATGTATGGAAGCAGCATGA 58.791 45.455 0.00 0.00 39.69 3.07
2871 3005 2.946990 TGACATGTATGGAAGCAGCATG 59.053 45.455 0.00 0.00 41.67 4.06
2874 3008 2.749076 TGTTGACATGTATGGAAGCAGC 59.251 45.455 0.00 0.00 0.00 5.25
2875 3009 5.571784 ATTGTTGACATGTATGGAAGCAG 57.428 39.130 0.00 0.00 0.00 4.24
2889 3023 7.115236 GTCCGGTTGGTTTATAAAATTGTTGAC 59.885 37.037 0.00 0.00 36.30 3.18
2891 3025 6.088350 CGTCCGGTTGGTTTATAAAATTGTTG 59.912 38.462 0.00 0.00 36.30 3.33
2894 3028 5.940595 TCGTCCGGTTGGTTTATAAAATTG 58.059 37.500 0.00 0.00 36.30 2.32
2895 3029 6.207221 ACTTCGTCCGGTTGGTTTATAAAATT 59.793 34.615 0.00 0.00 36.30 1.82
2896 3030 5.706833 ACTTCGTCCGGTTGGTTTATAAAAT 59.293 36.000 0.00 0.00 36.30 1.82
2897 3031 5.062528 ACTTCGTCCGGTTGGTTTATAAAA 58.937 37.500 0.00 0.00 36.30 1.52
2898 3032 4.640364 ACTTCGTCCGGTTGGTTTATAAA 58.360 39.130 0.00 0.00 36.30 1.40
2934 3068 4.842376 GCGTTCGGTTTATATAAAATCCGC 59.158 41.667 22.99 19.46 35.82 5.54
2935 3069 6.219302 AGCGTTCGGTTTATATAAAATCCG 57.781 37.500 22.28 22.28 36.64 4.18
2936 3070 9.750882 GAATAGCGTTCGGTTTATATAAAATCC 57.249 33.333 9.48 7.06 0.00 3.01
2942 3076 9.911138 TTACATGAATAGCGTTCGGTTTATATA 57.089 29.630 0.00 0.00 0.00 0.86
3000 3143 0.893447 GGCAGCTGCTGGAATTTCTT 59.107 50.000 35.82 0.00 41.70 2.52
3001 3144 1.310933 CGGCAGCTGCTGGAATTTCT 61.311 55.000 35.45 0.00 43.47 2.52
3002 3145 1.138247 CGGCAGCTGCTGGAATTTC 59.862 57.895 35.45 17.20 43.47 2.17
3003 3146 3.281240 CGGCAGCTGCTGGAATTT 58.719 55.556 35.45 0.00 43.47 1.82
3022 3175 0.310854 GAACAACAAGGGCTTGGACG 59.689 55.000 0.00 0.00 44.45 4.79
3026 3179 1.341209 GAAGGGAACAACAAGGGCTTG 59.659 52.381 0.00 0.00 45.58 4.01
3056 3209 1.071071 AGAGACGTCGGATAGAGGAGG 59.929 57.143 10.46 0.00 38.08 4.30
3063 3216 2.806818 GTGCTCATAGAGACGTCGGATA 59.193 50.000 10.46 4.93 0.00 2.59
3069 3222 2.005960 GCCGGTGCTCATAGAGACGT 62.006 60.000 1.90 0.00 33.53 4.34
3075 3229 1.269723 TCTTATCGCCGGTGCTCATAG 59.730 52.381 11.05 3.27 34.43 2.23
3076 3230 1.000607 GTCTTATCGCCGGTGCTCATA 60.001 52.381 11.05 0.00 34.43 2.15
3096 3250 0.443869 CCGCAACTTCACTTCATCGG 59.556 55.000 0.00 0.00 0.00 4.18
3101 3255 1.149148 GGAGACCGCAACTTCACTTC 58.851 55.000 0.00 0.00 0.00 3.01
3109 3263 3.423154 CTTGCCGGAGACCGCAAC 61.423 66.667 5.05 0.00 46.86 4.17
3110 3264 4.697756 CCTTGCCGGAGACCGCAA 62.698 66.667 5.05 14.87 46.86 4.85
3115 3269 2.032620 TCTATCTTCCTTGCCGGAGAC 58.967 52.381 5.05 0.00 44.28 3.36
3127 3281 2.223525 CCGTCTCCCGTGTTCTATCTTC 60.224 54.545 0.00 0.00 33.66 2.87
3156 3310 1.881973 CAAGACCTTGTGTCCCATGTG 59.118 52.381 1.75 0.00 45.68 3.21
3171 3325 2.386660 GCACGAGAGGCAGCAAGAC 61.387 63.158 0.00 0.00 0.00 3.01
3184 3338 0.738975 CGAGAATGAGTAGGGCACGA 59.261 55.000 0.00 0.00 0.00 4.35
3212 3366 4.003788 AGTGACGGACAAGGCGGG 62.004 66.667 0.00 0.00 0.00 6.13
3286 3440 2.017559 GACGAACTATCAGGCGGCCT 62.018 60.000 17.69 17.69 0.00 5.19
3306 3460 4.849329 CGCCTCCTACGCACCGTC 62.849 72.222 0.00 0.00 41.54 4.79
3313 3467 3.927163 AACAACGCCGCCTCCTACG 62.927 63.158 0.00 0.00 0.00 3.51
3314 3468 2.047560 AACAACGCCGCCTCCTAC 60.048 61.111 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.