Multiple sequence alignment - TraesCS1D01G368400

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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 TraesCS1D01G368400 chr1D 100.000 2996 0 0 1 2996 447910192 447913187 0.000000e+00 5533.0
1 TraesCS1D01G368400 chr1D 98.852 784 9 0 1 784 464456028 464455245 0.000000e+00 1399.0
2 TraesCS1D01G368400 chr1D 89.552 67 7 0 2913 2979 447913167 447913101 5.320000e-13 86.1
3 TraesCS1D01G368400 chr1D 92.857 56 2 2 740 795 391683315 391683262 2.480000e-11 80.5
4 TraesCS1D01G368400 chr1A 89.908 1843 159 15 788 2630 543962472 543964287 0.000000e+00 2348.0
5 TraesCS1D01G368400 chr1A 94.643 56 3 0 2917 2972 47204574 47204519 1.480000e-13 87.9
6 TraesCS1D01G368400 chr1A 94.643 56 3 0 2917 2972 47204519 47204574 1.480000e-13 87.9
7 TraesCS1D01G368400 chr1A 96.078 51 2 0 740 790 68233072 68233022 1.910000e-12 84.2
8 TraesCS1D01G368400 chr1A 88.889 63 5 1 2917 2979 516690384 516690324 3.200000e-10 76.8
9 TraesCS1D01G368400 chr1B 92.424 1320 96 3 898 2215 613326319 613327636 0.000000e+00 1881.0
10 TraesCS1D01G368400 chr1B 93.007 429 27 3 2214 2641 613336873 613337299 9.120000e-175 623.0
11 TraesCS1D01G368400 chr1B 94.136 324 16 3 1881 2204 613338108 613338428 9.650000e-135 490.0
12 TraesCS1D01G368400 chr1B 92.059 340 23 3 2305 2641 613338464 613338802 2.700000e-130 475.0
13 TraesCS1D01G368400 chr1B 87.568 185 15 3 2667 2848 613339391 613339570 1.090000e-49 207.0
14 TraesCS1D01G368400 chr1B 94.828 58 1 1 2917 2972 668960688 668960745 4.110000e-14 89.8
15 TraesCS1D01G368400 chr1B 91.803 61 3 2 2917 2977 661577902 661577960 1.910000e-12 84.2
16 TraesCS1D01G368400 chr3D 99.070 753 7 0 1 753 547906884 547907636 0.000000e+00 1352.0
17 TraesCS1D01G368400 chr3D 98.938 753 8 0 1 753 612684541 612683789 0.000000e+00 1347.0
18 TraesCS1D01G368400 chr3D 76.459 977 200 17 1019 1971 484730352 484729382 1.240000e-138 503.0
19 TraesCS1D01G368400 chr7D 97.707 785 17 1 1 784 47941894 47941110 0.000000e+00 1349.0
20 TraesCS1D01G368400 chr6D 98.938 753 8 0 1 753 420901906 420901154 0.000000e+00 1347.0
21 TraesCS1D01G368400 chr5D 98.938 753 8 0 1 753 482739784 482740536 0.000000e+00 1347.0
22 TraesCS1D01G368400 chr4D 98.938 753 8 0 1 753 488790462 488791214 0.000000e+00 1347.0
23 TraesCS1D01G368400 chr4D 98.938 753 8 0 1 753 507020702 507021454 0.000000e+00 1347.0
24 TraesCS1D01G368400 chr4D 98.938 753 7 1 1 753 45629067 45629818 0.000000e+00 1345.0
25 TraesCS1D01G368400 chr4D 97.959 49 1 0 740 788 506482721 506482769 5.320000e-13 86.1
26 TraesCS1D01G368400 chr4D 97.959 49 0 1 740 788 500357829 500357782 1.910000e-12 84.2
27 TraesCS1D01G368400 chr2D 78.270 948 195 6 1034 1971 391396206 391395260 1.540000e-167 599.0
28 TraesCS1D01G368400 chr2D 96.154 52 1 1 2928 2979 637605952 637605902 1.910000e-12 84.2
29 TraesCS1D01G368400 chr2A 78.056 957 198 4 1020 1965 530675944 530676899 7.150000e-166 593.0
30 TraesCS1D01G368400 chr3B 75.255 982 209 17 1019 1971 647477509 647476533 1.280000e-118 436.0
31 TraesCS1D01G368400 chr2B 77.201 693 138 8 1273 1965 464603832 464604504 1.300000e-103 387.0
32 TraesCS1D01G368400 chr5B 95.238 63 2 1 2913 2974 280982918 280982856 6.830000e-17 99.0
33 TraesCS1D01G368400 chr5B 94.643 56 3 0 2917 2972 280982858 280982913 1.480000e-13 87.9
34 TraesCS1D01G368400 chr6B 98.000 50 1 0 740 789 117324226 117324177 1.480000e-13 87.9
35 TraesCS1D01G368400 chr6A 96.078 51 2 0 740 790 18646775 18646825 1.910000e-12 84.2
36 TraesCS1D01G368400 chr3A 89.062 64 6 1 740 802 226430215 226430152 8.900000e-11 78.7


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 TraesCS1D01G368400 chr1D 447910192 447913187 2995 False 5533.00 5533 100.0000 1 2996 1 chr1D.!!$F1 2995
1 TraesCS1D01G368400 chr1D 464455245 464456028 783 True 1399.00 1399 98.8520 1 784 1 chr1D.!!$R3 783
2 TraesCS1D01G368400 chr1A 543962472 543964287 1815 False 2348.00 2348 89.9080 788 2630 1 chr1A.!!$F2 1842
3 TraesCS1D01G368400 chr1B 613326319 613327636 1317 False 1881.00 1881 92.4240 898 2215 1 chr1B.!!$F1 1317
4 TraesCS1D01G368400 chr1B 613336873 613339570 2697 False 448.75 623 91.6925 1881 2848 4 chr1B.!!$F4 967
5 TraesCS1D01G368400 chr3D 547906884 547907636 752 False 1352.00 1352 99.0700 1 753 1 chr3D.!!$F1 752
6 TraesCS1D01G368400 chr3D 612683789 612684541 752 True 1347.00 1347 98.9380 1 753 1 chr3D.!!$R2 752
7 TraesCS1D01G368400 chr3D 484729382 484730352 970 True 503.00 503 76.4590 1019 1971 1 chr3D.!!$R1 952
8 TraesCS1D01G368400 chr7D 47941110 47941894 784 True 1349.00 1349 97.7070 1 784 1 chr7D.!!$R1 783
9 TraesCS1D01G368400 chr6D 420901154 420901906 752 True 1347.00 1347 98.9380 1 753 1 chr6D.!!$R1 752
10 TraesCS1D01G368400 chr5D 482739784 482740536 752 False 1347.00 1347 98.9380 1 753 1 chr5D.!!$F1 752
11 TraesCS1D01G368400 chr4D 488790462 488791214 752 False 1347.00 1347 98.9380 1 753 1 chr4D.!!$F2 752
12 TraesCS1D01G368400 chr4D 507020702 507021454 752 False 1347.00 1347 98.9380 1 753 1 chr4D.!!$F4 752
13 TraesCS1D01G368400 chr4D 45629067 45629818 751 False 1345.00 1345 98.9380 1 753 1 chr4D.!!$F1 752
14 TraesCS1D01G368400 chr2D 391395260 391396206 946 True 599.00 599 78.2700 1034 1971 1 chr2D.!!$R1 937
15 TraesCS1D01G368400 chr2A 530675944 530676899 955 False 593.00 593 78.0560 1020 1965 1 chr2A.!!$F1 945
16 TraesCS1D01G368400 chr3B 647476533 647477509 976 True 436.00 436 75.2550 1019 1971 1 chr3B.!!$R1 952
17 TraesCS1D01G368400 chr2B 464603832 464604504 672 False 387.00 387 77.2010 1273 1965 1 chr2B.!!$F1 692

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
697 699 1.632948 GAACCGGTGCTAAAGGTCGC 61.633 60.0 8.52 0.0 37.26 5.19 F
1739 1764 0.888619 ATCGACTCCTCGTTCTGCAA 59.111 50.0 0.00 0.0 41.02 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1848 0.030504 CAACCAATGTCGCAGTGCAA 59.969 50.0 16.83 0.00 0.0 4.08 R
2966 3566 0.041135 CGCACGCTAGCTAGTACTCC 60.041 60.0 21.62 4.06 0.0 3.85 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
558 560 2.893398 GAGCTCGGGTGGACGAAT 59.107 61.111 0.00 0.00 42.98 3.34
697 699 1.632948 GAACCGGTGCTAAAGGTCGC 61.633 60.000 8.52 0.00 37.26 5.19
785 787 7.444487 ACATTTGACCCTTTTTCTACTAGTGAC 59.556 37.037 5.39 0.00 0.00 3.67
840 842 8.589629 CAAATCTCTTGTGTGTTTTTGAGAAAG 58.410 33.333 0.00 0.00 34.79 2.62
845 847 8.879342 TCTTGTGTGTTTTTGAGAAAGAAAAA 57.121 26.923 0.00 0.00 31.43 1.94
872 874 8.495949 ACACTCTCGTAATTAATCAACACAAAG 58.504 33.333 0.00 0.00 0.00 2.77
888 890 5.227152 ACACAAAGGAACAAAGTGTGAAAC 58.773 37.500 8.94 0.00 41.67 2.78
988 990 4.897357 TGCTCGGCATGGCGCTAG 62.897 66.667 34.34 27.34 41.91 3.42
990 992 2.963854 CTCGGCATGGCGCTAGTG 60.964 66.667 34.34 17.75 41.91 2.74
1561 1585 5.378332 GCCACTTACCAGAGAGTCTCTATA 58.622 45.833 22.24 14.47 38.99 1.31
1576 1601 5.744345 AGTCTCTATAACATTGTCGAAAGCG 59.256 40.000 0.00 0.00 39.35 4.68
1677 1702 1.329906 CATCACATCTTGCCGAAGCTC 59.670 52.381 0.00 0.00 40.80 4.09
1739 1764 0.888619 ATCGACTCCTCGTTCTGCAA 59.111 50.000 0.00 0.00 41.02 4.08
1823 1848 6.831976 AGCTATTCTTCGATAAATGGGAAGT 58.168 36.000 0.00 0.00 38.58 3.01
1827 1852 4.584874 TCTTCGATAAATGGGAAGTTGCA 58.415 39.130 0.00 0.00 38.58 4.08
1910 1941 0.179032 TGGAAAAGGCTCTTCACGCA 60.179 50.000 2.55 0.00 0.00 5.24
2167 2198 9.709495 CTCTCAAGGATATTGGAGATTAAGAAG 57.291 37.037 0.00 0.00 35.97 2.85
2187 2218 5.899547 AGAAGATGTTCCTTTTCTTTGGGTT 59.100 36.000 0.00 0.00 32.48 4.11
2303 2334 0.813184 AGAAGCATGTTGCCATTCCG 59.187 50.000 0.00 0.00 46.52 4.30
2326 2357 8.311836 TCCGTGGAAAATAAGATATATCAGACC 58.688 37.037 15.08 8.30 0.00 3.85
2355 2386 6.176975 TCACCATAATGCTAAAAACACTCG 57.823 37.500 0.00 0.00 0.00 4.18
2470 2502 0.317103 CTATCGACGAGGAAGTGGCG 60.317 60.000 3.01 0.00 0.00 5.69
2485 2517 5.163824 GGAAGTGGCGTACTGGTAAAATAAC 60.164 44.000 0.00 0.00 40.26 1.89
2652 3241 6.862209 TCCTCCATTTTAACATTTTCCATCG 58.138 36.000 0.00 0.00 0.00 3.84
2656 3245 7.846066 TCCATTTTAACATTTTCCATCGGAAT 58.154 30.769 0.00 0.00 41.71 3.01
2676 3273 2.872557 CGTGGTGCTGCATCTTGG 59.127 61.111 14.82 0.00 0.00 3.61
2754 3351 7.565323 TTTTGGTTTTGAAAATGAGGGATTG 57.435 32.000 0.00 0.00 0.00 2.67
2767 3364 2.721167 GGATTGCCCGGGCCTTTTC 61.721 63.158 41.75 29.24 41.09 2.29
2773 3370 1.754234 CCCGGGCCTTTTCCATCAG 60.754 63.158 8.08 0.00 0.00 2.90
2858 3458 3.848272 CACGCAATGTGTAGGGATTTT 57.152 42.857 0.00 0.00 43.88 1.82
2859 3459 3.758300 CACGCAATGTGTAGGGATTTTC 58.242 45.455 0.00 0.00 43.88 2.29
2860 3460 3.440173 CACGCAATGTGTAGGGATTTTCT 59.560 43.478 0.00 0.00 43.88 2.52
2861 3461 3.440173 ACGCAATGTGTAGGGATTTTCTG 59.560 43.478 0.00 0.00 0.00 3.02
2862 3462 3.731867 CGCAATGTGTAGGGATTTTCTGC 60.732 47.826 0.00 0.00 0.00 4.26
2863 3463 3.193267 GCAATGTGTAGGGATTTTCTGCA 59.807 43.478 0.00 0.00 0.00 4.41
2864 3464 4.321899 GCAATGTGTAGGGATTTTCTGCAA 60.322 41.667 0.00 0.00 0.00 4.08
2865 3465 5.625197 GCAATGTGTAGGGATTTTCTGCAAT 60.625 40.000 0.00 0.00 0.00 3.56
2866 3466 5.841957 ATGTGTAGGGATTTTCTGCAATC 57.158 39.130 0.00 0.00 33.04 2.67
2867 3467 4.922206 TGTGTAGGGATTTTCTGCAATCT 58.078 39.130 0.00 0.00 34.12 2.40
2868 3468 5.324409 TGTGTAGGGATTTTCTGCAATCTT 58.676 37.500 0.00 0.00 34.12 2.40
2869 3469 5.774690 TGTGTAGGGATTTTCTGCAATCTTT 59.225 36.000 0.00 0.00 34.12 2.52
2870 3470 6.095377 GTGTAGGGATTTTCTGCAATCTTTG 58.905 40.000 0.00 0.00 34.12 2.77
2908 3508 3.358707 CAATCTTTGCTTGTCTGTGCA 57.641 42.857 0.00 0.00 37.42 4.57
2909 3509 3.909430 CAATCTTTGCTTGTCTGTGCAT 58.091 40.909 0.00 0.00 39.07 3.96
2910 3510 5.050644 CAATCTTTGCTTGTCTGTGCATA 57.949 39.130 0.00 0.00 39.07 3.14
2911 3511 5.463286 CAATCTTTGCTTGTCTGTGCATAA 58.537 37.500 0.00 0.00 39.07 1.90
2912 3512 4.488126 TCTTTGCTTGTCTGTGCATAAC 57.512 40.909 0.00 0.00 39.07 1.89
2913 3513 4.136796 TCTTTGCTTGTCTGTGCATAACT 58.863 39.130 0.00 0.00 39.07 2.24
2914 3514 5.304778 TCTTTGCTTGTCTGTGCATAACTA 58.695 37.500 0.00 0.00 39.07 2.24
2915 3515 5.179368 TCTTTGCTTGTCTGTGCATAACTAC 59.821 40.000 0.00 0.00 39.07 2.73
2916 3516 4.271696 TGCTTGTCTGTGCATAACTACT 57.728 40.909 0.00 0.00 33.94 2.57
2917 3517 5.400066 TGCTTGTCTGTGCATAACTACTA 57.600 39.130 0.00 0.00 33.94 1.82
2918 3518 5.168569 TGCTTGTCTGTGCATAACTACTAC 58.831 41.667 0.00 0.00 33.94 2.73
2919 3519 5.047306 TGCTTGTCTGTGCATAACTACTACT 60.047 40.000 0.00 0.00 33.94 2.57
2920 3520 5.517054 GCTTGTCTGTGCATAACTACTACTC 59.483 44.000 0.00 0.00 0.00 2.59
2921 3521 5.578005 TGTCTGTGCATAACTACTACTCC 57.422 43.478 0.00 0.00 0.00 3.85
2922 3522 4.401519 TGTCTGTGCATAACTACTACTCCC 59.598 45.833 0.00 0.00 0.00 4.30
2923 3523 4.401519 GTCTGTGCATAACTACTACTCCCA 59.598 45.833 0.00 0.00 0.00 4.37
2924 3524 4.401519 TCTGTGCATAACTACTACTCCCAC 59.598 45.833 0.00 0.00 0.00 4.61
2925 3525 4.350245 TGTGCATAACTACTACTCCCACT 58.650 43.478 0.00 0.00 0.00 4.00
2926 3526 4.159693 TGTGCATAACTACTACTCCCACTG 59.840 45.833 0.00 0.00 0.00 3.66
2927 3527 4.159879 GTGCATAACTACTACTCCCACTGT 59.840 45.833 0.00 0.00 0.00 3.55
2928 3528 5.359009 GTGCATAACTACTACTCCCACTGTA 59.641 44.000 0.00 0.00 0.00 2.74
2929 3529 5.953548 TGCATAACTACTACTCCCACTGTAA 59.046 40.000 0.00 0.00 0.00 2.41
2930 3530 6.438108 TGCATAACTACTACTCCCACTGTAAA 59.562 38.462 0.00 0.00 0.00 2.01
2931 3531 6.979238 GCATAACTACTACTCCCACTGTAAAG 59.021 42.308 0.00 0.00 0.00 1.85
2932 3532 7.147949 GCATAACTACTACTCCCACTGTAAAGA 60.148 40.741 0.00 0.00 0.00 2.52
2933 3533 8.746530 CATAACTACTACTCCCACTGTAAAGAA 58.253 37.037 0.00 0.00 0.00 2.52
2934 3534 7.607615 AACTACTACTCCCACTGTAAAGAAA 57.392 36.000 0.00 0.00 0.00 2.52
2935 3535 7.793948 ACTACTACTCCCACTGTAAAGAAAT 57.206 36.000 0.00 0.00 0.00 2.17
2936 3536 8.890410 ACTACTACTCCCACTGTAAAGAAATA 57.110 34.615 0.00 0.00 0.00 1.40
2937 3537 9.490083 ACTACTACTCCCACTGTAAAGAAATAT 57.510 33.333 0.00 0.00 0.00 1.28
2943 3543 7.988028 ACTCCCACTGTAAAGAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
2944 3544 6.984474 TCCCACTGTAAAGAAATATAAGAGCG 59.016 38.462 0.00 0.00 0.00 5.03
2945 3545 6.292919 CCCACTGTAAAGAAATATAAGAGCGC 60.293 42.308 0.00 0.00 0.00 5.92
2946 3546 6.480320 CCACTGTAAAGAAATATAAGAGCGCT 59.520 38.462 11.27 11.27 0.00 5.92
2947 3547 7.306866 CCACTGTAAAGAAATATAAGAGCGCTC 60.307 40.741 30.01 30.01 0.00 5.03
2948 3548 7.436673 CACTGTAAAGAAATATAAGAGCGCTCT 59.563 37.037 33.83 33.83 42.75 4.09
2962 3562 6.994868 AGAGCGCTCTTATATTTCTTTACG 57.005 37.500 33.83 0.00 36.31 3.18
2963 3563 5.921408 AGAGCGCTCTTATATTTCTTTACGG 59.079 40.000 33.83 0.00 36.31 4.02
2964 3564 5.839621 AGCGCTCTTATATTTCTTTACGGA 58.160 37.500 2.64 0.00 0.00 4.69
2965 3565 5.921408 AGCGCTCTTATATTTCTTTACGGAG 59.079 40.000 2.64 0.00 0.00 4.63
2966 3566 5.118817 GCGCTCTTATATTTCTTTACGGAGG 59.881 44.000 0.00 0.00 0.00 4.30
2967 3567 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2968 3568 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
2969 3569 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
2970 3570 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
2971 3571 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
2972 3572 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
2973 3573 8.773033 TTATATTTCTTTACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
2974 3574 9.866655 TTATATTTCTTTACGGAGGGAGTACTA 57.133 33.333 0.00 0.00 0.00 1.82
2975 3575 6.712179 ATTTCTTTACGGAGGGAGTACTAG 57.288 41.667 0.00 0.00 0.00 2.57
2976 3576 3.549794 TCTTTACGGAGGGAGTACTAGC 58.450 50.000 0.00 0.00 0.00 3.42
2977 3577 3.201708 TCTTTACGGAGGGAGTACTAGCT 59.798 47.826 0.00 0.00 0.00 3.32
2978 3578 4.410228 TCTTTACGGAGGGAGTACTAGCTA 59.590 45.833 0.00 0.00 0.00 3.32
2979 3579 2.934886 ACGGAGGGAGTACTAGCTAG 57.065 55.000 19.44 19.44 0.00 3.42
2980 3580 1.202794 ACGGAGGGAGTACTAGCTAGC 60.203 57.143 20.91 6.62 0.00 3.42
2981 3581 1.525941 GGAGGGAGTACTAGCTAGCG 58.474 60.000 20.91 0.00 0.00 4.26
2982 3582 1.202794 GGAGGGAGTACTAGCTAGCGT 60.203 57.143 20.91 5.75 0.00 5.07
2983 3583 1.874872 GAGGGAGTACTAGCTAGCGTG 59.125 57.143 20.91 8.74 0.00 5.34
2984 3584 0.311477 GGGAGTACTAGCTAGCGTGC 59.689 60.000 20.91 10.21 0.00 5.34
2985 3585 0.041135 GGAGTACTAGCTAGCGTGCG 60.041 60.000 20.91 1.60 38.13 5.34
2986 3586 0.657951 GAGTACTAGCTAGCGTGCGC 60.658 60.000 20.91 8.67 42.33 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 6.783892 ACATTACCAAATTGATGTTTGTGC 57.216 33.333 0.00 0.00 37.37 4.57
558 560 6.069905 TGCTAAAGGTCATCCTACATAAACCA 60.070 38.462 0.00 0.00 44.35 3.67
706 708 2.627945 CAGCCGCTTTCATTAGTACCA 58.372 47.619 0.00 0.00 0.00 3.25
853 855 8.789881 TTGTTCCTTTGTGTTGATTAATTACG 57.210 30.769 0.00 0.00 0.00 3.18
888 890 5.491982 ACAAGGCTTTAGGTTAGAGTGATG 58.508 41.667 0.00 0.00 0.00 3.07
892 894 4.838986 TGAGACAAGGCTTTAGGTTAGAGT 59.161 41.667 0.00 0.00 0.00 3.24
956 958 0.235926 GAGCAAGCAAACAGACGACC 59.764 55.000 0.00 0.00 0.00 4.79
988 990 5.066505 GGTTTCCTGACATATCATGTTCCAC 59.933 44.000 0.00 0.00 45.03 4.02
990 992 5.440610 AGGTTTCCTGACATATCATGTTCC 58.559 41.667 0.00 0.00 45.03 3.62
1317 1335 4.451150 GCATCCGCCGTCTCCACA 62.451 66.667 0.00 0.00 0.00 4.17
1561 1585 4.201724 GCTTATCTCGCTTTCGACAATGTT 60.202 41.667 0.00 0.00 40.21 2.71
1576 1601 2.802816 CGTAGCCACCATTGCTTATCTC 59.197 50.000 0.00 0.00 40.23 2.75
1658 1683 1.661341 GAGCTTCGGCAAGATGTGAT 58.339 50.000 0.00 0.00 44.74 3.06
1677 1702 3.712655 TTCCGTGTGAACTGTGCG 58.287 55.556 0.00 0.00 0.00 5.34
1785 1810 6.568844 CGAAGAATAGCTCGGCTTCTAGTATT 60.569 42.308 15.83 0.00 40.44 1.89
1823 1848 0.030504 CAACCAATGTCGCAGTGCAA 59.969 50.000 16.83 0.00 0.00 4.08
1827 1852 1.951510 CTGCAACCAATGTCGCAGT 59.048 52.632 0.00 0.00 45.34 4.40
1910 1941 2.143925 GTTCGTTGGCAAGTAGCTCTT 58.856 47.619 0.00 0.00 44.79 2.85
1988 2019 1.641577 GGTCGATGCAGACTACCAAC 58.358 55.000 10.87 0.00 40.76 3.77
2131 2162 9.494271 TCCAATATCCTTGAGAGAATTTATTCG 57.506 33.333 0.00 0.00 41.56 3.34
2167 2198 5.276461 ACAACCCAAAGAAAAGGAACATC 57.724 39.130 0.00 0.00 0.00 3.06
2259 2290 9.973246 CTTGCTACAATACACTAAAATACACTG 57.027 33.333 0.00 0.00 0.00 3.66
2260 2291 9.938280 TCTTGCTACAATACACTAAAATACACT 57.062 29.630 0.00 0.00 0.00 3.55
2263 2294 9.704098 GCTTCTTGCTACAATACACTAAAATAC 57.296 33.333 0.00 0.00 38.95 1.89
2264 2295 9.443323 TGCTTCTTGCTACAATACACTAAAATA 57.557 29.630 0.00 0.00 43.37 1.40
2265 2296 8.335532 TGCTTCTTGCTACAATACACTAAAAT 57.664 30.769 0.00 0.00 43.37 1.82
2266 2297 7.737972 TGCTTCTTGCTACAATACACTAAAA 57.262 32.000 0.00 0.00 43.37 1.52
2267 2298 7.390440 ACATGCTTCTTGCTACAATACACTAAA 59.610 33.333 0.00 0.00 43.37 1.85
2268 2299 6.878923 ACATGCTTCTTGCTACAATACACTAA 59.121 34.615 0.00 0.00 43.37 2.24
2269 2300 6.406370 ACATGCTTCTTGCTACAATACACTA 58.594 36.000 0.00 0.00 43.37 2.74
2270 2301 5.248640 ACATGCTTCTTGCTACAATACACT 58.751 37.500 0.00 0.00 43.37 3.55
2271 2302 5.551760 ACATGCTTCTTGCTACAATACAC 57.448 39.130 0.00 0.00 43.37 2.90
2272 2303 5.619757 GCAACATGCTTCTTGCTACAATACA 60.620 40.000 10.59 0.00 40.96 2.29
2273 2304 4.795278 GCAACATGCTTCTTGCTACAATAC 59.205 41.667 10.59 0.00 40.96 1.89
2274 2305 4.142403 GGCAACATGCTTCTTGCTACAATA 60.142 41.667 15.76 0.00 44.28 1.90
2275 2306 3.367703 GGCAACATGCTTCTTGCTACAAT 60.368 43.478 15.76 0.00 44.28 2.71
2276 2307 2.030007 GGCAACATGCTTCTTGCTACAA 60.030 45.455 15.76 0.00 44.28 2.41
2277 2308 1.541147 GGCAACATGCTTCTTGCTACA 59.459 47.619 15.76 0.00 44.28 2.74
2278 2309 1.541147 TGGCAACATGCTTCTTGCTAC 59.459 47.619 15.76 4.16 46.17 3.58
2303 2334 8.926710 CGTGGTCTGATATATCTTATTTTCCAC 58.073 37.037 13.79 17.00 36.68 4.02
2326 2357 7.008266 GTGTTTTTAGCATTATGGTGATTCGTG 59.992 37.037 7.20 0.00 0.00 4.35
2382 2413 6.116806 TGTAACTGTTCATGTACAACTTGGT 58.883 36.000 6.62 0.00 0.00 3.67
2453 2485 1.028330 TACGCCACTTCCTCGTCGAT 61.028 55.000 0.00 0.00 37.61 3.59
2506 2538 1.336755 AGGTTTGGTTTGACGTCATGC 59.663 47.619 20.80 14.61 0.00 4.06
2652 3241 4.120331 GCAGCACCACGCCATTCC 62.120 66.667 0.00 0.00 44.04 3.01
2656 3245 3.848301 AAGATGCAGCACCACGCCA 62.848 57.895 4.07 0.00 44.04 5.69
2660 3249 0.890542 TGACCAAGATGCAGCACCAC 60.891 55.000 4.07 0.00 0.00 4.16
2661 3250 0.178995 TTGACCAAGATGCAGCACCA 60.179 50.000 4.07 0.00 0.00 4.17
2662 3251 0.242017 GTTGACCAAGATGCAGCACC 59.758 55.000 4.07 0.00 0.00 5.01
2731 3328 5.530543 GCAATCCCTCATTTTCAAAACCAAA 59.469 36.000 0.00 0.00 0.00 3.28
2734 3331 4.002982 GGCAATCCCTCATTTTCAAAACC 58.997 43.478 0.00 0.00 0.00 3.27
2754 3351 3.147595 GATGGAAAAGGCCCGGGC 61.148 66.667 38.57 38.57 41.06 6.13
2758 3355 3.099141 TCATTTCTGATGGAAAAGGCCC 58.901 45.455 0.00 0.00 45.56 5.80
2767 3364 6.713903 ACTAATATGGCAGTCATTTCTGATGG 59.286 38.462 0.00 0.00 37.61 3.51
2840 3440 3.731867 GCAGAAAATCCCTACACATTGCG 60.732 47.826 0.00 0.00 0.00 4.85
2888 3488 3.358707 TGCACAGACAAGCAAAGATTG 57.641 42.857 0.00 0.00 37.90 2.67
2889 3489 5.242393 AGTTATGCACAGACAAGCAAAGATT 59.758 36.000 0.00 0.00 44.88 2.40
2890 3490 4.763793 AGTTATGCACAGACAAGCAAAGAT 59.236 37.500 0.00 0.00 44.88 2.40
2891 3491 4.136796 AGTTATGCACAGACAAGCAAAGA 58.863 39.130 0.00 0.00 44.88 2.52
2892 3492 4.494350 AGTTATGCACAGACAAGCAAAG 57.506 40.909 0.00 0.00 44.88 2.77
2893 3493 5.063204 AGTAGTTATGCACAGACAAGCAAA 58.937 37.500 0.00 0.00 44.88 3.68
2894 3494 4.641396 AGTAGTTATGCACAGACAAGCAA 58.359 39.130 0.00 0.00 44.88 3.91
2895 3495 4.271696 AGTAGTTATGCACAGACAAGCA 57.728 40.909 0.00 0.00 45.92 3.91
2896 3496 5.411781 AGTAGTAGTTATGCACAGACAAGC 58.588 41.667 0.00 0.00 0.00 4.01
2897 3497 6.037098 GGAGTAGTAGTTATGCACAGACAAG 58.963 44.000 0.00 0.00 0.00 3.16
2898 3498 5.105473 GGGAGTAGTAGTTATGCACAGACAA 60.105 44.000 0.00 0.00 0.00 3.18
2899 3499 4.401519 GGGAGTAGTAGTTATGCACAGACA 59.598 45.833 0.00 0.00 0.00 3.41
2900 3500 4.401519 TGGGAGTAGTAGTTATGCACAGAC 59.598 45.833 0.00 0.00 0.00 3.51
2901 3501 4.401519 GTGGGAGTAGTAGTTATGCACAGA 59.598 45.833 0.00 0.00 0.00 3.41
2902 3502 4.402793 AGTGGGAGTAGTAGTTATGCACAG 59.597 45.833 0.00 0.00 0.00 3.66
2903 3503 4.159693 CAGTGGGAGTAGTAGTTATGCACA 59.840 45.833 0.00 0.00 0.00 4.57
2904 3504 4.159879 ACAGTGGGAGTAGTAGTTATGCAC 59.840 45.833 0.00 0.00 0.00 4.57
2905 3505 4.350245 ACAGTGGGAGTAGTAGTTATGCA 58.650 43.478 0.00 0.00 0.00 3.96
2906 3506 6.461110 TTACAGTGGGAGTAGTAGTTATGC 57.539 41.667 0.00 0.00 0.00 3.14
2907 3507 8.289939 TCTTTACAGTGGGAGTAGTAGTTATG 57.710 38.462 0.00 0.00 0.00 1.90
2908 3508 8.890410 TTCTTTACAGTGGGAGTAGTAGTTAT 57.110 34.615 0.00 0.00 0.00 1.89
2909 3509 8.710749 TTTCTTTACAGTGGGAGTAGTAGTTA 57.289 34.615 0.00 0.00 0.00 2.24
2910 3510 7.607615 TTTCTTTACAGTGGGAGTAGTAGTT 57.392 36.000 0.00 0.00 0.00 2.24
2911 3511 7.793948 ATTTCTTTACAGTGGGAGTAGTAGT 57.206 36.000 0.00 0.00 0.00 2.73
2917 3517 7.988028 GCTCTTATATTTCTTTACAGTGGGAGT 59.012 37.037 0.00 0.00 0.00 3.85
2918 3518 7.169982 CGCTCTTATATTTCTTTACAGTGGGAG 59.830 40.741 0.00 0.00 0.00 4.30
2919 3519 6.984474 CGCTCTTATATTTCTTTACAGTGGGA 59.016 38.462 0.00 0.00 0.00 4.37
2920 3520 6.292919 GCGCTCTTATATTTCTTTACAGTGGG 60.293 42.308 0.00 0.00 0.00 4.61
2921 3521 6.480320 AGCGCTCTTATATTTCTTTACAGTGG 59.520 38.462 2.64 0.00 0.00 4.00
2922 3522 7.436673 AGAGCGCTCTTATATTTCTTTACAGTG 59.563 37.037 33.83 0.00 36.31 3.66
2923 3523 7.493367 AGAGCGCTCTTATATTTCTTTACAGT 58.507 34.615 33.83 5.67 36.31 3.55
2924 3524 7.938563 AGAGCGCTCTTATATTTCTTTACAG 57.061 36.000 33.83 0.00 36.31 2.74
2939 3539 5.921408 CCGTAAAGAAATATAAGAGCGCTCT 59.079 40.000 33.83 33.83 42.75 4.09
2940 3540 5.919141 TCCGTAAAGAAATATAAGAGCGCTC 59.081 40.000 30.01 30.01 0.00 5.03
2941 3541 5.839621 TCCGTAAAGAAATATAAGAGCGCT 58.160 37.500 11.27 11.27 0.00 5.92
2942 3542 5.118817 CCTCCGTAAAGAAATATAAGAGCGC 59.881 44.000 0.00 0.00 0.00 5.92
2943 3543 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2944 3544 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2945 3545 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2946 3546 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2947 3547 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2948 3548 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
2949 3549 9.512588 CTAGTACTCCCTCCGTAAAGAAATATA 57.487 37.037 0.00 0.00 0.00 0.86
2950 3550 7.039853 GCTAGTACTCCCTCCGTAAAGAAATAT 60.040 40.741 0.00 0.00 0.00 1.28
2951 3551 6.264067 GCTAGTACTCCCTCCGTAAAGAAATA 59.736 42.308 0.00 0.00 0.00 1.40
2952 3552 5.068855 GCTAGTACTCCCTCCGTAAAGAAAT 59.931 44.000 0.00 0.00 0.00 2.17
2953 3553 4.400567 GCTAGTACTCCCTCCGTAAAGAAA 59.599 45.833 0.00 0.00 0.00 2.52
2954 3554 3.950395 GCTAGTACTCCCTCCGTAAAGAA 59.050 47.826 0.00 0.00 0.00 2.52
2955 3555 3.201708 AGCTAGTACTCCCTCCGTAAAGA 59.798 47.826 0.00 0.00 0.00 2.52
2956 3556 3.553904 AGCTAGTACTCCCTCCGTAAAG 58.446 50.000 0.00 0.00 0.00 1.85
2957 3557 3.659183 AGCTAGTACTCCCTCCGTAAA 57.341 47.619 0.00 0.00 0.00 2.01
2958 3558 3.495806 GCTAGCTAGTACTCCCTCCGTAA 60.496 52.174 21.62 0.00 0.00 3.18
2959 3559 2.038295 GCTAGCTAGTACTCCCTCCGTA 59.962 54.545 21.62 0.00 0.00 4.02
2960 3560 1.202794 GCTAGCTAGTACTCCCTCCGT 60.203 57.143 21.62 0.00 0.00 4.69
2961 3561 1.525941 GCTAGCTAGTACTCCCTCCG 58.474 60.000 21.62 0.00 0.00 4.63
2962 3562 1.202794 ACGCTAGCTAGTACTCCCTCC 60.203 57.143 21.62 1.21 0.00 4.30
2963 3563 1.874872 CACGCTAGCTAGTACTCCCTC 59.125 57.143 21.62 1.92 0.00 4.30
2964 3564 1.970092 CACGCTAGCTAGTACTCCCT 58.030 55.000 21.62 0.00 0.00 4.20
2965 3565 0.311477 GCACGCTAGCTAGTACTCCC 59.689 60.000 21.62 3.35 0.00 4.30
2966 3566 0.041135 CGCACGCTAGCTAGTACTCC 60.041 60.000 21.62 4.06 0.00 3.85
2967 3567 0.657951 GCGCACGCTAGCTAGTACTC 60.658 60.000 21.62 8.51 38.26 2.59
2968 3568 1.355916 GCGCACGCTAGCTAGTACT 59.644 57.895 21.62 0.00 38.26 2.73
2969 3569 3.905060 GCGCACGCTAGCTAGTAC 58.095 61.111 21.62 5.51 38.26 2.73


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

AutoCloner maintained by Alex Coulton.