Multiple sequence alignment - TraesCS3A01G363500

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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 TraesCS3A01G363500 chr3A 100.000 3713 0 0 1 3713 611949301 611953013 0.000000e+00 6857.0
1 TraesCS3A01G363500 chr3D 90.913 2256 130 37 1478 3713 469379164 469381364 0.000000e+00 2961.0
2 TraesCS3A01G363500 chr3D 88.205 585 31 19 862 1440 469378463 469379015 0.000000e+00 664.0
3 TraesCS3A01G363500 chr3B 88.452 1273 58 40 862 2104 623659576 623660789 0.000000e+00 1454.0
4 TraesCS3A01G363500 chr3B 93.392 802 51 1 1 800 472627005 472627806 0.000000e+00 1186.0
5 TraesCS3A01G363500 chr3B 92.131 826 47 10 2894 3711 623661912 623662727 0.000000e+00 1149.0
6 TraesCS3A01G363500 chr3B 93.029 416 28 1 2103 2517 623660874 623661289 1.140000e-169 606.0
7 TraesCS3A01G363500 chr3B 91.561 237 15 4 2517 2752 623661391 623661623 4.630000e-84 322.0
8 TraesCS3A01G363500 chr1A 98.500 800 12 0 1 800 491390229 491389430 0.000000e+00 1411.0
9 TraesCS3A01G363500 chr2B 93.052 806 53 3 1 806 748544242 748543440 0.000000e+00 1175.0
10 TraesCS3A01G363500 chr5D 85.540 574 67 3 3 561 529522499 529523071 1.490000e-163 586.0
11 TraesCS3A01G363500 chr5D 86.831 243 29 3 559 800 529524695 529524935 6.110000e-68 268.0
12 TraesCS3A01G363500 chr7D 78.626 786 128 30 1600 2378 204772046 204772798 5.580000e-133 484.0
13 TraesCS3A01G363500 chr7A 77.679 784 143 24 1600 2378 216786434 216787190 2.030000e-122 449.0
14 TraesCS3A01G363500 chr7B 77.411 788 147 22 1600 2378 169268596 169269361 1.220000e-119 440.0
15 TraesCS3A01G363500 chr7B 85.417 96 10 4 1181 1276 169268284 169268375 3.050000e-16 97.1


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 TraesCS3A01G363500 chr3A 611949301 611953013 3712 False 6857.00 6857 100.00000 1 3713 1 chr3A.!!$F1 3712
1 TraesCS3A01G363500 chr3D 469378463 469381364 2901 False 1812.50 2961 89.55900 862 3713 2 chr3D.!!$F1 2851
2 TraesCS3A01G363500 chr3B 472627005 472627806 801 False 1186.00 1186 93.39200 1 800 1 chr3B.!!$F1 799
3 TraesCS3A01G363500 chr3B 623659576 623662727 3151 False 882.75 1454 91.29325 862 3711 4 chr3B.!!$F2 2849
4 TraesCS3A01G363500 chr1A 491389430 491390229 799 True 1411.00 1411 98.50000 1 800 1 chr1A.!!$R1 799
5 TraesCS3A01G363500 chr2B 748543440 748544242 802 True 1175.00 1175 93.05200 1 806 1 chr2B.!!$R1 805
6 TraesCS3A01G363500 chr5D 529522499 529524935 2436 False 427.00 586 86.18550 3 800 2 chr5D.!!$F1 797
7 TraesCS3A01G363500 chr7D 204772046 204772798 752 False 484.00 484 78.62600 1600 2378 1 chr7D.!!$F1 778
8 TraesCS3A01G363500 chr7A 216786434 216787190 756 False 449.00 449 77.67900 1600 2378 1 chr7A.!!$F1 778
9 TraesCS3A01G363500 chr7B 169268284 169269361 1077 False 268.55 440 81.41400 1181 2378 2 chr7B.!!$F1 1197

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
851 2495 0.095417 GCTTCCATCACGTTCGCTTC 59.905 55.0 0.0 0.0 0.0 3.86 F
855 2499 0.108615 CCATCACGTTCGCTTCCTCT 60.109 55.0 0.0 0.0 0.0 3.69 F
858 2502 0.671796 TCACGTTCGCTTCCTCTTCA 59.328 50.0 0.0 0.0 0.0 3.02 F
1960 3748 0.107508 GCTAGGTGATCTGCTTGCCA 60.108 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 3531 1.070134 AGTCAGCCGTTAACAGCAGAA 59.930 47.619 15.88 0.00 0.00 3.02 R
1762 3548 1.277557 AGATGTCCAGAACAGTCAGCC 59.722 52.381 0.00 0.00 42.37 4.85 R
2399 4275 1.604378 CTCGGAGGCCCAGACAAAT 59.396 57.895 0.00 0.00 0.00 2.32 R
3086 5255 1.117150 TTCGTACCATGGGAGCTACC 58.883 55.000 18.09 8.55 38.08 3.18 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
234 250 4.020543 ACTAGAGGAGTGGCAAAGAGTAG 58.979 47.826 0.00 0.00 36.87 2.57
816 2460 3.552132 AAAACAAAACAAATCCCGGCT 57.448 38.095 0.00 0.00 0.00 5.52
817 2461 2.812358 AACAAAACAAATCCCGGCTC 57.188 45.000 0.00 0.00 0.00 4.70
818 2462 0.596082 ACAAAACAAATCCCGGCTCG 59.404 50.000 0.00 0.00 0.00 5.03
819 2463 0.596082 CAAAACAAATCCCGGCTCGT 59.404 50.000 0.00 0.00 0.00 4.18
820 2464 1.000717 CAAAACAAATCCCGGCTCGTT 60.001 47.619 0.00 0.00 0.00 3.85
821 2465 1.324383 AAACAAATCCCGGCTCGTTT 58.676 45.000 0.00 0.00 0.00 3.60
822 2466 0.596082 AACAAATCCCGGCTCGTTTG 59.404 50.000 13.83 13.83 37.52 2.93
823 2467 1.241315 ACAAATCCCGGCTCGTTTGG 61.241 55.000 17.45 0.41 36.23 3.28
824 2468 1.677633 AAATCCCGGCTCGTTTGGG 60.678 57.895 0.00 0.00 44.75 4.12
825 2469 4.796495 ATCCCGGCTCGTTTGGGC 62.796 66.667 0.00 0.00 42.98 5.36
830 2474 4.456806 GGCTCGTTTGGGCGATAT 57.543 55.556 0.00 0.00 40.29 1.63
831 2475 2.702847 GGCTCGTTTGGGCGATATT 58.297 52.632 0.00 0.00 40.29 1.28
832 2476 0.307760 GGCTCGTTTGGGCGATATTG 59.692 55.000 0.00 0.00 40.29 1.90
833 2477 0.317020 GCTCGTTTGGGCGATATTGC 60.317 55.000 6.37 6.37 40.29 3.56
834 2478 1.299541 CTCGTTTGGGCGATATTGCT 58.700 50.000 14.65 0.00 40.29 3.91
835 2479 1.670811 CTCGTTTGGGCGATATTGCTT 59.329 47.619 14.65 0.00 40.29 3.91
836 2480 1.668751 TCGTTTGGGCGATATTGCTTC 59.331 47.619 14.65 8.12 35.83 3.86
837 2481 1.268539 CGTTTGGGCGATATTGCTTCC 60.269 52.381 14.65 8.85 34.52 3.46
838 2482 1.748493 GTTTGGGCGATATTGCTTCCA 59.252 47.619 14.65 11.30 34.52 3.53
839 2483 2.362077 GTTTGGGCGATATTGCTTCCAT 59.638 45.455 14.65 0.00 34.52 3.41
840 2484 1.896220 TGGGCGATATTGCTTCCATC 58.104 50.000 14.65 0.00 34.52 3.51
841 2485 1.142667 TGGGCGATATTGCTTCCATCA 59.857 47.619 14.65 2.20 34.52 3.07
842 2486 1.537202 GGGCGATATTGCTTCCATCAC 59.463 52.381 14.65 0.00 34.52 3.06
843 2487 1.195448 GGCGATATTGCTTCCATCACG 59.805 52.381 14.65 0.00 34.52 4.35
844 2488 1.867233 GCGATATTGCTTCCATCACGT 59.133 47.619 7.76 0.00 0.00 4.49
845 2489 2.287915 GCGATATTGCTTCCATCACGTT 59.712 45.455 7.76 0.00 0.00 3.99
846 2490 3.604772 GCGATATTGCTTCCATCACGTTC 60.605 47.826 7.76 0.00 0.00 3.95
847 2491 3.362014 CGATATTGCTTCCATCACGTTCG 60.362 47.826 0.00 0.00 0.00 3.95
848 2492 0.447801 ATTGCTTCCATCACGTTCGC 59.552 50.000 0.00 0.00 0.00 4.70
849 2493 0.602638 TTGCTTCCATCACGTTCGCT 60.603 50.000 0.00 0.00 0.00 4.93
850 2494 0.602638 TGCTTCCATCACGTTCGCTT 60.603 50.000 0.00 0.00 0.00 4.68
851 2495 0.095417 GCTTCCATCACGTTCGCTTC 59.905 55.000 0.00 0.00 0.00 3.86
852 2496 0.721718 CTTCCATCACGTTCGCTTCC 59.278 55.000 0.00 0.00 0.00 3.46
853 2497 0.320374 TTCCATCACGTTCGCTTCCT 59.680 50.000 0.00 0.00 0.00 3.36
854 2498 0.108804 TCCATCACGTTCGCTTCCTC 60.109 55.000 0.00 0.00 0.00 3.71
855 2499 0.108615 CCATCACGTTCGCTTCCTCT 60.109 55.000 0.00 0.00 0.00 3.69
856 2500 1.673033 CCATCACGTTCGCTTCCTCTT 60.673 52.381 0.00 0.00 0.00 2.85
857 2501 1.656095 CATCACGTTCGCTTCCTCTTC 59.344 52.381 0.00 0.00 0.00 2.87
858 2502 0.671796 TCACGTTCGCTTCCTCTTCA 59.328 50.000 0.00 0.00 0.00 3.02
859 2503 1.067974 TCACGTTCGCTTCCTCTTCAA 59.932 47.619 0.00 0.00 0.00 2.69
860 2504 1.192534 CACGTTCGCTTCCTCTTCAAC 59.807 52.381 0.00 0.00 0.00 3.18
884 2528 1.005032 GCGTTCTTTTTGTTGCTTGGC 60.005 47.619 0.00 0.00 0.00 4.52
901 2545 2.121488 GCGAAACGAAACGGCTTTG 58.879 52.632 0.00 0.00 0.00 2.77
924 2568 2.930019 CTCCAGGTGTGCCCCTCA 60.930 66.667 0.00 0.00 34.57 3.86
927 2571 3.644606 CAGGTGTGCCCCTCAGCT 61.645 66.667 0.00 0.00 43.07 4.24
949 2593 2.450304 ATCGCATCCCCATCCCCA 60.450 61.111 0.00 0.00 0.00 4.96
952 2596 2.442413 GCATCCCCATCCCCATCC 59.558 66.667 0.00 0.00 0.00 3.51
953 2597 2.165656 GCATCCCCATCCCCATCCT 61.166 63.158 0.00 0.00 0.00 3.24
954 2598 2.081955 CATCCCCATCCCCATCCTC 58.918 63.158 0.00 0.00 0.00 3.71
955 2599 1.539869 ATCCCCATCCCCATCCTCG 60.540 63.158 0.00 0.00 0.00 4.63
956 2600 3.958860 CCCCATCCCCATCCTCGC 61.959 72.222 0.00 0.00 0.00 5.03
957 2601 3.958860 CCCATCCCCATCCTCGCC 61.959 72.222 0.00 0.00 0.00 5.54
1140 2789 1.319799 CCTCTCTCCCCATCCCCTT 59.680 63.158 0.00 0.00 0.00 3.95
1144 2793 3.123273 CTCTCTCCCCATCCCCTTTTTA 58.877 50.000 0.00 0.00 0.00 1.52
1145 2794 3.527665 CTCTCTCCCCATCCCCTTTTTAA 59.472 47.826 0.00 0.00 0.00 1.52
1151 2800 2.466846 CCATCCCCTTTTTAACCCCAG 58.533 52.381 0.00 0.00 0.00 4.45
1242 2896 1.954146 CGCGCCGCTGTACCATAAT 60.954 57.895 7.78 0.00 0.00 1.28
1259 2913 5.367060 ACCATAATGAGAAGGAGGTTAGTCC 59.633 44.000 0.00 0.00 36.79 3.85
1276 2934 2.824341 AGTCCGTCAGTTAACCCTGTAG 59.176 50.000 0.88 0.00 34.02 2.74
1281 2939 4.081862 CCGTCAGTTAACCCTGTAGATGAA 60.082 45.833 0.88 0.00 34.02 2.57
1320 2991 2.159653 GCACACGGCTTTGATCTACAAG 60.160 50.000 0.00 0.00 39.77 3.16
1336 3007 3.238108 ACAAGCAGATTACGAGGAGTG 57.762 47.619 0.00 0.00 0.00 3.51
1551 3333 6.403866 TTCTTCTGCATTTAAAGAAGCCAA 57.596 33.333 9.02 0.00 45.94 4.52
1562 3344 1.889545 AGAAGCCAAGAACTCTGCAC 58.110 50.000 0.00 0.00 0.00 4.57
1591 3373 5.806502 TCTGCATTTTGAAGAAAACTGTGTG 59.193 36.000 0.00 0.00 33.86 3.82
1594 3376 5.748152 GCATTTTGAAGAAAACTGTGTGCTA 59.252 36.000 0.00 0.00 33.86 3.49
1596 3378 6.509418 TTTTGAAGAAAACTGTGTGCTACT 57.491 33.333 0.00 0.00 0.00 2.57
1701 3483 7.589081 TGTGGATCTATACCTAGTAAGTTGGA 58.411 38.462 0.00 0.00 0.00 3.53
1704 3486 8.453681 TGGATCTATACCTAGTAAGTTGGATCA 58.546 37.037 0.00 0.00 0.00 2.92
1706 3488 8.653036 ATCTATACCTAGTAAGTTGGATCACC 57.347 38.462 0.00 0.00 0.00 4.02
1708 3490 8.287350 TCTATACCTAGTAAGTTGGATCACCTT 58.713 37.037 0.00 0.00 37.04 3.50
1710 3492 8.849543 ATACCTAGTAAGTTGGATCACCTTTA 57.150 34.615 0.00 0.00 37.04 1.85
1716 3498 4.927267 AGTTGGATCACCTTTACATGGA 57.073 40.909 0.00 0.00 37.04 3.41
1717 3499 5.456921 AGTTGGATCACCTTTACATGGAT 57.543 39.130 0.00 0.00 37.04 3.41
1718 3500 5.831103 AGTTGGATCACCTTTACATGGATT 58.169 37.500 0.00 0.00 37.04 3.01
1719 3501 5.888161 AGTTGGATCACCTTTACATGGATTC 59.112 40.000 0.00 0.00 37.04 2.52
1722 3504 4.444306 GGATCACCTTTACATGGATTCGGA 60.444 45.833 0.00 0.00 0.00 4.55
1724 3506 4.513442 TCACCTTTACATGGATTCGGAAG 58.487 43.478 0.00 0.00 0.00 3.46
1725 3507 4.019681 TCACCTTTACATGGATTCGGAAGT 60.020 41.667 0.00 0.00 0.00 3.01
1727 3509 3.877508 CCTTTACATGGATTCGGAAGTCC 59.122 47.826 0.00 10.45 35.02 3.85
1749 3531 8.019925 AGTCCATAACTGAAAGATTGCCATCTT 61.020 37.037 7.20 7.20 43.13 2.40
1757 3543 3.083122 AGATTGCCATCTTTCTGCTGT 57.917 42.857 0.00 0.00 36.18 4.40
1762 3548 2.483877 TGCCATCTTTCTGCTGTTAACG 59.516 45.455 0.26 0.00 0.00 3.18
1763 3549 2.159517 GCCATCTTTCTGCTGTTAACGG 60.160 50.000 10.24 10.24 0.00 4.44
1791 3579 7.998964 TGACTGTTCTGGACATCTATGTAGATA 59.001 37.037 2.40 0.00 40.91 1.98
1875 3663 2.463589 TACCCAAGACCTGGCAAGCG 62.464 60.000 0.00 0.00 44.90 4.68
1908 3696 1.448540 CGATTCAGGCAAGGCTCGT 60.449 57.895 0.00 0.00 0.00 4.18
1960 3748 0.107508 GCTAGGTGATCTGCTTGCCA 60.108 55.000 0.00 0.00 0.00 4.92
2069 3857 5.529289 TGGGGTTCATCTATCAGTAAGTCT 58.471 41.667 0.00 0.00 0.00 3.24
2070 3858 5.363868 TGGGGTTCATCTATCAGTAAGTCTG 59.636 44.000 0.00 0.00 44.85 3.51
2071 3859 5.293560 GGGTTCATCTATCAGTAAGTCTGC 58.706 45.833 0.00 0.00 43.32 4.26
2072 3860 5.163405 GGGTTCATCTATCAGTAAGTCTGCA 60.163 44.000 0.00 0.00 43.32 4.41
2073 3861 6.463614 GGGTTCATCTATCAGTAAGTCTGCAT 60.464 42.308 0.00 0.00 43.32 3.96
2074 3862 6.644592 GGTTCATCTATCAGTAAGTCTGCATC 59.355 42.308 0.00 0.00 43.32 3.91
2094 3882 1.605232 CTGCATGTGTGTTTCTGAGCA 59.395 47.619 0.00 0.00 0.00 4.26
2095 3883 1.334556 TGCATGTGTGTTTCTGAGCAC 59.665 47.619 0.00 7.28 37.49 4.40
2111 3899 2.357637 GAGCACACTTGGCAAGTAACAA 59.642 45.455 30.72 0.00 40.46 2.83
2318 4194 2.160417 CGAGGTTGAAGGAGAACATTGC 59.840 50.000 0.00 0.00 0.00 3.56
2383 4259 6.479990 GCTTTCTGAAATAAAACAGGCAAGTT 59.520 34.615 2.88 0.00 35.20 2.66
2386 4262 7.106439 TCTGAAATAAAACAGGCAAGTTTCA 57.894 32.000 8.25 0.00 40.60 2.69
2399 4275 4.683781 GGCAAGTTTCAAACATCGCATTTA 59.316 37.500 2.41 0.00 0.00 1.40
2480 4356 3.004210 TGGCAAATGCGCATATACGAAAT 59.996 39.130 25.61 1.45 43.26 2.17
2481 4357 3.361644 GGCAAATGCGCATATACGAAATG 59.638 43.478 25.61 12.90 43.26 2.32
2533 4511 8.228035 ACTCATACTAGTAGTCTAAGCAAAGG 57.772 38.462 5.96 0.00 0.00 3.11
2534 4512 7.835181 ACTCATACTAGTAGTCTAAGCAAAGGT 59.165 37.037 5.96 0.00 0.00 3.50
2536 4514 8.467598 TCATACTAGTAGTCTAAGCAAAGGTTG 58.532 37.037 5.96 0.00 0.00 3.77
2537 4515 6.667558 ACTAGTAGTCTAAGCAAAGGTTGT 57.332 37.500 0.00 0.00 0.00 3.32
2553 4531 3.118884 AGGTTGTTGTAGTATACGCCTGG 60.119 47.826 0.00 0.00 46.99 4.45
2570 4548 5.706369 ACGCCTGGTTGTGTTTTGTTATATA 59.294 36.000 0.00 0.00 0.00 0.86
2601 4581 9.203421 TGTAGAATTGTTACTGATACAAGTGTG 57.797 33.333 0.00 0.00 38.74 3.82
2602 4582 9.204570 GTAGAATTGTTACTGATACAAGTGTGT 57.795 33.333 0.00 0.00 38.74 3.72
2725 4705 5.816777 GGAGAGATTTGAAAGGAGACATCAG 59.183 44.000 0.00 0.00 31.34 2.90
2944 5113 1.272147 CCCCCTTCACCTCCAAAAGAG 60.272 57.143 0.00 0.00 42.83 2.85
2946 5115 2.310052 CCCCTTCACCTCCAAAAGAGAT 59.690 50.000 0.00 0.00 46.50 2.75
2987 5156 2.153401 TGCCCTGGTGCACCTTACT 61.153 57.895 34.75 0.00 36.04 2.24
2988 5157 0.838554 TGCCCTGGTGCACCTTACTA 60.839 55.000 34.75 14.91 36.04 1.82
2989 5158 0.107654 GCCCTGGTGCACCTTACTAG 60.108 60.000 34.75 23.06 36.82 2.57
3016 5185 3.018856 TCCAAGCATAACTCTGCAATGG 58.981 45.455 12.14 12.14 45.45 3.16
3077 5246 5.755409 TTCAACTATACAGGAGCCAAGAA 57.245 39.130 0.00 0.00 0.00 2.52
3086 5255 0.961753 GGAGCCAAGAAACCCACAAG 59.038 55.000 0.00 0.00 0.00 3.16
3122 5298 2.034558 ACGAACCGGAAGAGACGTTTAA 59.965 45.455 9.46 0.00 31.63 1.52
3180 5356 3.257393 CTTCCTGAATCTGTTGAGACGG 58.743 50.000 0.00 0.00 0.00 4.79
3322 5498 4.265073 ACCGAGTAGACCAACGTATAGTT 58.735 43.478 0.00 0.00 45.45 2.24
3423 5599 8.062065 TCTGGTTCTGTTGTAACTGAAATTTT 57.938 30.769 15.54 0.00 44.66 1.82
3430 5606 8.993121 TCTGTTGTAACTGAAATTTTGCAAAAA 58.007 25.926 27.10 10.91 34.54 1.94
3431 5607 8.941127 TGTTGTAACTGAAATTTTGCAAAAAC 57.059 26.923 27.10 20.14 30.50 2.43
3534 5720 6.268566 GCCACAAATATGAGTTGATCCTTTC 58.731 40.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 250 1.978617 CTGAACCATGGCCACCCAC 60.979 63.158 8.16 0.00 45.77 4.61
571 2213 8.868522 TGATTTCACTTCCTCTACAATTTGAT 57.131 30.769 2.79 0.00 0.00 2.57
800 2444 0.596082 ACGAGCCGGGATTTGTTTTG 59.404 50.000 2.18 0.00 0.00 2.44
804 2448 1.241315 CCAAACGAGCCGGGATTTGT 61.241 55.000 2.18 0.00 31.48 2.83
805 2449 1.506262 CCAAACGAGCCGGGATTTG 59.494 57.895 2.18 2.53 32.89 2.32
806 2450 1.677633 CCCAAACGAGCCGGGATTT 60.678 57.895 2.18 0.00 43.21 2.17
807 2451 2.045340 CCCAAACGAGCCGGGATT 60.045 61.111 2.18 0.00 43.21 3.01
808 2452 4.796495 GCCCAAACGAGCCGGGAT 62.796 66.667 2.18 0.00 43.21 3.85
811 2455 2.989055 ATATCGCCCAAACGAGCCGG 62.989 60.000 0.00 0.00 46.69 6.13
812 2456 1.157870 AATATCGCCCAAACGAGCCG 61.158 55.000 0.00 0.00 46.69 5.52
813 2457 0.307760 CAATATCGCCCAAACGAGCC 59.692 55.000 0.00 0.00 46.69 4.70
814 2458 0.317020 GCAATATCGCCCAAACGAGC 60.317 55.000 0.00 0.00 46.69 5.03
815 2459 1.299541 AGCAATATCGCCCAAACGAG 58.700 50.000 0.00 0.00 46.69 4.18
817 2461 1.268539 GGAAGCAATATCGCCCAAACG 60.269 52.381 0.00 0.00 0.00 3.60
818 2462 1.748493 TGGAAGCAATATCGCCCAAAC 59.252 47.619 0.00 0.00 0.00 2.93
819 2463 2.136298 TGGAAGCAATATCGCCCAAA 57.864 45.000 0.00 0.00 0.00 3.28
820 2464 2.229792 GATGGAAGCAATATCGCCCAA 58.770 47.619 0.00 0.00 0.00 4.12
821 2465 1.142667 TGATGGAAGCAATATCGCCCA 59.857 47.619 0.00 0.00 0.00 5.36
822 2466 1.537202 GTGATGGAAGCAATATCGCCC 59.463 52.381 0.00 0.00 28.10 6.13
823 2467 1.195448 CGTGATGGAAGCAATATCGCC 59.805 52.381 0.00 0.00 28.10 5.54
824 2468 1.867233 ACGTGATGGAAGCAATATCGC 59.133 47.619 0.00 0.00 28.10 4.58
825 2469 3.362014 CGAACGTGATGGAAGCAATATCG 60.362 47.826 0.00 0.00 28.10 2.92
826 2470 3.604772 GCGAACGTGATGGAAGCAATATC 60.605 47.826 0.00 0.00 28.10 1.63
827 2471 2.287915 GCGAACGTGATGGAAGCAATAT 59.712 45.455 0.00 0.00 28.10 1.28
828 2472 1.663643 GCGAACGTGATGGAAGCAATA 59.336 47.619 0.00 0.00 28.10 1.90
829 2473 0.447801 GCGAACGTGATGGAAGCAAT 59.552 50.000 0.00 0.00 28.10 3.56
830 2474 0.602638 AGCGAACGTGATGGAAGCAA 60.603 50.000 0.00 0.00 28.10 3.91
831 2475 0.602638 AAGCGAACGTGATGGAAGCA 60.603 50.000 0.00 0.00 0.00 3.91
832 2476 0.095417 GAAGCGAACGTGATGGAAGC 59.905 55.000 0.00 0.00 0.00 3.86
833 2477 0.721718 GGAAGCGAACGTGATGGAAG 59.278 55.000 0.00 0.00 0.00 3.46
834 2478 0.320374 AGGAAGCGAACGTGATGGAA 59.680 50.000 0.00 0.00 0.00 3.53
835 2479 0.108804 GAGGAAGCGAACGTGATGGA 60.109 55.000 0.00 0.00 0.00 3.41
836 2480 0.108615 AGAGGAAGCGAACGTGATGG 60.109 55.000 0.00 0.00 0.00 3.51
837 2481 1.656095 GAAGAGGAAGCGAACGTGATG 59.344 52.381 0.00 0.00 0.00 3.07
838 2482 1.272490 TGAAGAGGAAGCGAACGTGAT 59.728 47.619 0.00 0.00 0.00 3.06
839 2483 0.671796 TGAAGAGGAAGCGAACGTGA 59.328 50.000 0.00 0.00 0.00 4.35
840 2484 1.192534 GTTGAAGAGGAAGCGAACGTG 59.807 52.381 0.00 0.00 0.00 4.49
841 2485 1.499049 GTTGAAGAGGAAGCGAACGT 58.501 50.000 0.00 0.00 0.00 3.99
842 2486 0.790814 GGTTGAAGAGGAAGCGAACG 59.209 55.000 0.00 0.00 0.00 3.95
843 2487 2.070028 GAGGTTGAAGAGGAAGCGAAC 58.930 52.381 0.00 0.00 0.00 3.95
844 2488 1.336887 CGAGGTTGAAGAGGAAGCGAA 60.337 52.381 0.00 0.00 0.00 4.70
845 2489 0.243907 CGAGGTTGAAGAGGAAGCGA 59.756 55.000 0.00 0.00 0.00 4.93
846 2490 1.355066 GCGAGGTTGAAGAGGAAGCG 61.355 60.000 0.00 0.00 0.00 4.68
847 2491 1.355066 CGCGAGGTTGAAGAGGAAGC 61.355 60.000 0.00 0.00 0.00 3.86
848 2492 0.038159 ACGCGAGGTTGAAGAGGAAG 60.038 55.000 15.93 0.00 0.00 3.46
849 2493 0.391597 AACGCGAGGTTGAAGAGGAA 59.608 50.000 15.93 0.00 37.50 3.36
850 2494 0.038526 GAACGCGAGGTTGAAGAGGA 60.039 55.000 15.93 0.00 39.50 3.71
851 2495 0.038159 AGAACGCGAGGTTGAAGAGG 60.038 55.000 15.93 0.00 39.50 3.69
852 2496 1.784525 AAGAACGCGAGGTTGAAGAG 58.215 50.000 15.93 0.00 39.50 2.85
853 2497 2.234300 AAAGAACGCGAGGTTGAAGA 57.766 45.000 15.93 0.00 39.50 2.87
854 2498 3.035942 CAAAAAGAACGCGAGGTTGAAG 58.964 45.455 15.93 0.00 39.50 3.02
855 2499 2.420722 ACAAAAAGAACGCGAGGTTGAA 59.579 40.909 15.93 0.00 39.50 2.69
856 2500 2.011222 ACAAAAAGAACGCGAGGTTGA 58.989 42.857 15.93 0.00 39.50 3.18
857 2501 2.468532 ACAAAAAGAACGCGAGGTTG 57.531 45.000 15.93 10.37 39.50 3.77
858 2502 2.792749 CAACAAAAAGAACGCGAGGTT 58.207 42.857 15.93 0.00 42.96 3.50
859 2503 1.533129 GCAACAAAAAGAACGCGAGGT 60.533 47.619 15.93 0.00 0.00 3.85
860 2504 1.120437 GCAACAAAAAGAACGCGAGG 58.880 50.000 15.93 0.00 0.00 4.63
884 2528 0.305313 TCCAAAGCCGTTTCGTTTCG 59.695 50.000 0.00 0.00 0.00 3.46
911 2555 3.325753 GAGCTGAGGGGCACACCT 61.326 66.667 0.00 0.00 45.57 4.00
913 2557 4.008933 ACGAGCTGAGGGGCACAC 62.009 66.667 0.00 0.00 34.17 3.82
914 2558 4.007644 CACGAGCTGAGGGGCACA 62.008 66.667 0.00 0.00 34.17 4.57
915 2559 2.914777 GATCACGAGCTGAGGGGCAC 62.915 65.000 0.00 0.00 30.20 5.01
916 2560 2.685017 ATCACGAGCTGAGGGGCA 60.685 61.111 0.00 0.00 30.20 5.36
917 2561 2.107953 GATCACGAGCTGAGGGGC 59.892 66.667 0.00 0.00 30.20 5.80
924 2568 2.419198 GGGATGCGATCACGAGCT 59.581 61.111 0.00 0.00 42.66 4.09
927 2571 1.367471 GATGGGGATGCGATCACGA 59.633 57.895 0.00 0.00 42.66 4.35
981 2625 3.787001 CTCTTCTCCGGCCACCCC 61.787 72.222 2.24 0.00 0.00 4.95
982 2626 3.787001 CCTCTTCTCCGGCCACCC 61.787 72.222 2.24 0.00 0.00 4.61
983 2627 2.066999 ATCCTCTTCTCCGGCCACC 61.067 63.158 2.24 0.00 0.00 4.61
984 2628 1.144936 CATCCTCTTCTCCGGCCAC 59.855 63.158 2.24 0.00 0.00 5.01
985 2629 2.066393 CCATCCTCTTCTCCGGCCA 61.066 63.158 2.24 0.00 0.00 5.36
986 2630 2.825264 CCATCCTCTTCTCCGGCC 59.175 66.667 0.00 0.00 0.00 6.13
987 2631 2.110006 GCCATCCTCTTCTCCGGC 59.890 66.667 0.00 0.00 0.00 6.13
988 2632 2.825264 GGCCATCCTCTTCTCCGG 59.175 66.667 0.00 0.00 0.00 5.14
989 2633 2.419198 CGGCCATCCTCTTCTCCG 59.581 66.667 2.24 0.00 0.00 4.63
990 2634 2.110006 GCGGCCATCCTCTTCTCC 59.890 66.667 2.24 0.00 0.00 3.71
991 2635 2.110006 GGCGGCCATCCTCTTCTC 59.890 66.667 15.62 0.00 0.00 2.87
992 2636 3.854669 CGGCGGCCATCCTCTTCT 61.855 66.667 20.71 0.00 0.00 2.85
1011 2655 0.865111 CGGTGTTGAGCGTGAAATGA 59.135 50.000 0.00 0.00 38.30 2.57
1140 2789 3.203487 ACAGGTCTGAACTGGGGTTAAAA 59.797 43.478 25.29 0.00 40.23 1.52
1144 2793 0.474184 CACAGGTCTGAACTGGGGTT 59.526 55.000 25.29 2.68 40.23 4.11
1145 2794 2.056906 GCACAGGTCTGAACTGGGGT 62.057 60.000 25.25 2.71 39.73 4.95
1151 2800 1.595382 AGCACGCACAGGTCTGAAC 60.595 57.895 4.84 0.00 0.00 3.18
1193 2847 2.193248 GGTACCCTGCCTGCCATC 59.807 66.667 0.00 0.00 0.00 3.51
1242 2896 2.224942 TGACGGACTAACCTCCTTCTCA 60.225 50.000 0.00 0.00 36.31 3.27
1259 2913 4.713824 TCATCTACAGGGTTAACTGACG 57.286 45.455 5.42 0.00 40.97 4.35
1276 2934 5.514204 GCAAGCATGTGATTTACTGTTCATC 59.486 40.000 0.00 0.00 0.00 2.92
1281 2939 3.569277 TGTGCAAGCATGTGATTTACTGT 59.431 39.130 0.00 0.00 0.00 3.55
1320 2991 3.073144 GAGTCACTCCTCGTAATCTGC 57.927 52.381 0.00 0.00 0.00 4.26
1336 3007 1.534595 AGTACAGGAACACGACGAGTC 59.465 52.381 0.00 0.00 0.00 3.36
1342 3013 3.119245 GCCAATCTAGTACAGGAACACGA 60.119 47.826 0.00 0.00 0.00 4.35
1440 3111 4.082125 AGCCTTGTGGAAGAAAATGGTAG 58.918 43.478 0.00 0.00 34.57 3.18
1443 3217 3.119352 GCTAGCCTTGTGGAAGAAAATGG 60.119 47.826 2.29 0.00 34.57 3.16
1449 3223 3.084039 CAAATGCTAGCCTTGTGGAAGA 58.916 45.455 13.29 0.00 34.57 2.87
1551 3333 2.103771 TGCAGAAGAAGTGCAGAGTTCT 59.896 45.455 0.00 0.00 45.96 3.01
1587 3369 2.288825 TGCACCTACAGAAGTAGCACAC 60.289 50.000 0.00 0.00 45.15 3.82
1591 3373 1.646189 GCTGCACCTACAGAAGTAGC 58.354 55.000 0.00 0.00 45.15 3.58
1594 3376 0.898320 ATCGCTGCACCTACAGAAGT 59.102 50.000 0.00 0.00 40.25 3.01
1596 3378 1.135139 GAGATCGCTGCACCTACAGAA 59.865 52.381 0.00 0.00 40.25 3.02
1701 3483 4.771114 TCCGAATCCATGTAAAGGTGAT 57.229 40.909 0.00 0.00 0.00 3.06
1704 3486 4.514401 GACTTCCGAATCCATGTAAAGGT 58.486 43.478 0.00 0.00 0.00 3.50
1706 3488 4.513442 TGGACTTCCGAATCCATGTAAAG 58.487 43.478 7.72 0.00 40.17 1.85
1716 3498 6.049955 TCTTTCAGTTATGGACTTCCGAAT 57.950 37.500 0.00 0.00 36.10 3.34
1717 3499 5.477607 TCTTTCAGTTATGGACTTCCGAA 57.522 39.130 0.00 0.00 36.10 4.30
1718 3500 5.677319 ATCTTTCAGTTATGGACTTCCGA 57.323 39.130 0.00 0.00 36.10 4.55
1719 3501 5.447818 GCAATCTTTCAGTTATGGACTTCCG 60.448 44.000 0.00 0.00 36.10 4.30
1722 3504 5.324409 TGGCAATCTTTCAGTTATGGACTT 58.676 37.500 0.00 0.00 36.10 3.01
1724 3506 5.591877 AGATGGCAATCTTTCAGTTATGGAC 59.408 40.000 0.00 0.00 40.42 4.02
1725 3507 5.759059 AGATGGCAATCTTTCAGTTATGGA 58.241 37.500 0.00 0.00 40.42 3.41
1749 3531 1.070134 AGTCAGCCGTTAACAGCAGAA 59.930 47.619 15.88 0.00 0.00 3.02
1757 3543 1.689813 TCCAGAACAGTCAGCCGTTAA 59.310 47.619 0.00 0.00 0.00 2.01
1762 3548 1.277557 AGATGTCCAGAACAGTCAGCC 59.722 52.381 0.00 0.00 42.37 4.85
1763 3549 2.758736 AGATGTCCAGAACAGTCAGC 57.241 50.000 0.00 0.00 42.37 4.26
1875 3663 2.131183 GAATCGTACAGCTGCTCCATC 58.869 52.381 15.27 1.81 0.00 3.51
1960 3748 4.096003 CGGAGGGACACGGGCAAT 62.096 66.667 0.00 0.00 0.00 3.56
2070 3858 2.227149 TCAGAAACACACATGCAGATGC 59.773 45.455 0.00 0.00 42.50 3.91
2071 3859 3.669824 GCTCAGAAACACACATGCAGATG 60.670 47.826 0.00 0.00 35.49 2.90
2072 3860 2.486982 GCTCAGAAACACACATGCAGAT 59.513 45.455 0.00 0.00 0.00 2.90
2073 3861 1.875514 GCTCAGAAACACACATGCAGA 59.124 47.619 0.00 0.00 0.00 4.26
2074 3862 1.605232 TGCTCAGAAACACACATGCAG 59.395 47.619 0.00 0.00 0.00 4.41
2094 3882 4.644685 ACTCAATTGTTACTTGCCAAGTGT 59.355 37.500 20.12 3.12 42.84 3.55
2095 3883 4.977963 CACTCAATTGTTACTTGCCAAGTG 59.022 41.667 20.12 1.58 42.84 3.16
2111 3899 4.267536 AGCATATGAGCACAACACTCAAT 58.732 39.130 6.97 0.00 46.63 2.57
2318 4194 5.047021 TCAGGAATAGACCAGTCAAACAGAG 60.047 44.000 0.00 0.00 0.00 3.35
2383 4259 6.585702 CCAGACAAATAAATGCGATGTTTGAA 59.414 34.615 10.75 0.00 34.71 2.69
2386 4262 5.410067 CCCAGACAAATAAATGCGATGTTT 58.590 37.500 0.00 0.00 0.00 2.83
2399 4275 1.604378 CTCGGAGGCCCAGACAAAT 59.396 57.895 0.00 0.00 0.00 2.32
2480 4356 7.450074 ACCAGAACTAGTTTCATGTTATGACA 58.550 34.615 10.02 0.00 39.39 3.58
2481 4357 7.907214 ACCAGAACTAGTTTCATGTTATGAC 57.093 36.000 10.02 0.00 39.39 3.06
2503 4379 9.118300 TGCTTAGACTACTAGTATGAGTTAACC 57.882 37.037 2.33 0.00 27.44 2.85
2531 4509 3.118884 CCAGGCGTATACTACAACAACCT 60.119 47.826 0.56 0.00 0.00 3.50
2532 4510 3.192466 CCAGGCGTATACTACAACAACC 58.808 50.000 0.56 0.00 0.00 3.77
2533 4511 3.853475 ACCAGGCGTATACTACAACAAC 58.147 45.455 0.56 0.00 0.00 3.32
2534 4512 4.247258 CAACCAGGCGTATACTACAACAA 58.753 43.478 0.56 0.00 0.00 2.83
2536 4514 3.615496 CACAACCAGGCGTATACTACAAC 59.385 47.826 0.56 0.00 0.00 3.32
2537 4515 3.258872 ACACAACCAGGCGTATACTACAA 59.741 43.478 0.56 0.00 0.00 2.41
2601 4581 4.022935 TCCAACATGAGCATTGAACAAGAC 60.023 41.667 0.00 0.00 0.00 3.01
2602 4582 4.143543 TCCAACATGAGCATTGAACAAGA 58.856 39.130 0.00 0.00 0.00 3.02
2725 4705 7.740733 AACACTCTAGTGGTGCATCCAAATTC 61.741 42.308 14.30 0.00 45.59 2.17
2875 4878 1.189524 TAGTACCGTGCCAAGCCACT 61.190 55.000 0.00 0.00 33.60 4.00
2944 5113 4.081697 CACCCCCTGTTATGTTTTTCCATC 60.082 45.833 0.00 0.00 0.00 3.51
2946 5115 3.235200 CACCCCCTGTTATGTTTTTCCA 58.765 45.455 0.00 0.00 0.00 3.53
3042 5211 8.446273 CCTGTATAGTTGAAAGTTGAATCTGTG 58.554 37.037 0.00 0.00 0.00 3.66
3086 5255 1.117150 TTCGTACCATGGGAGCTACC 58.883 55.000 18.09 8.55 38.08 3.18
3088 5257 1.117150 GGTTCGTACCATGGGAGCTA 58.883 55.000 18.09 0.00 44.36 3.32
3180 5356 4.495422 TCAGAGAACGTAATCTGAAAGGC 58.505 43.478 23.22 0.00 46.74 4.35
3273 5449 7.810260 AGGCCATCTAATTAGAGTTTCAGAAT 58.190 34.615 19.51 0.00 35.50 2.40
3278 5454 6.424207 CGGTAAGGCCATCTAATTAGAGTTTC 59.576 42.308 19.51 9.99 35.50 2.78
3322 5498 2.241281 TTCCTGATAGTTCCGTGGGA 57.759 50.000 0.00 0.00 0.00 4.37
3423 5599 6.349300 TGCCATTTTTACCTTAGTTTTTGCA 58.651 32.000 0.00 0.00 0.00 4.08
3430 5606 8.632679 CACATATGATGCCATTTTTACCTTAGT 58.367 33.333 10.38 0.00 34.31 2.24
3431 5607 8.632679 ACACATATGATGCCATTTTTACCTTAG 58.367 33.333 10.38 0.00 34.31 2.18
3445 5623 5.126067 AGGTTGGTAGAACACATATGATGC 58.874 41.667 10.38 0.00 0.00 3.91
3584 5770 5.560953 CGGTTTCTTGGAGAGCTTTGTTTAG 60.561 44.000 0.00 0.00 0.00 1.85
3595 5781 3.899360 TCCTTTACTCGGTTTCTTGGAGA 59.101 43.478 0.00 0.00 0.00 3.71
3596 5782 4.267349 TCCTTTACTCGGTTTCTTGGAG 57.733 45.455 0.00 0.00 0.00 3.86
3657 5845 2.871795 TAGCGGCCCAGATGAGACCA 62.872 60.000 0.00 0.00 0.00 4.02
3668 5856 2.879813 TTCACCGGATTTAGCGGCCC 62.880 60.000 9.46 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.