Multiple sequence alignment - TraesCS2D01G029700

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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 TraesCS2D01G029700 chr2D 100.000 3629 0 0 1 3629 12289200 12292828 0.000000e+00 6702.0
1 TraesCS2D01G029700 chr2D 81.838 1806 267 42 884 2677 12525250 12523494 0.000000e+00 1461.0
2 TraesCS2D01G029700 chr2D 81.356 1652 270 27 1029 2667 12138762 12137136 0.000000e+00 1310.0
3 TraesCS2D01G029700 chr2D 82.064 1589 236 28 1097 2677 12304967 12303420 0.000000e+00 1310.0
4 TraesCS2D01G029700 chr2D 93.590 156 10 0 660 815 414960263 414960418 2.180000e-57 233.0
5 TraesCS2D01G029700 chrUn 94.670 2852 100 20 1 2808 12474631 12471788 0.000000e+00 4377.0
6 TraesCS2D01G029700 chrUn 82.478 1598 241 27 1097 2677 12461939 12463514 0.000000e+00 1363.0
7 TraesCS2D01G029700 chrUn 85.445 797 61 23 2869 3629 12471793 12471016 0.000000e+00 778.0
8 TraesCS2D01G029700 chrUn 88.649 185 17 4 656 837 65533281 65533098 4.720000e-54 222.0
9 TraesCS2D01G029700 chr5D 81.972 1775 263 35 880 2649 560883451 560885173 0.000000e+00 1452.0
10 TraesCS2D01G029700 chr5D 93.671 158 10 0 658 815 431780424 431780581 1.680000e-58 237.0
11 TraesCS2D01G029700 chr2A 80.124 1776 293 40 921 2667 12805612 12803868 0.000000e+00 1269.0
12 TraesCS2D01G029700 chr2A 81.359 971 157 15 928 1894 12611877 12610927 0.000000e+00 769.0
13 TraesCS2D01G029700 chr2A 82.635 835 130 9 1013 1845 34157584 34156763 0.000000e+00 725.0
14 TraesCS2D01G029700 chr2A 84.412 680 102 3 1997 2675 12610867 12610191 0.000000e+00 665.0
15 TraesCS2D01G029700 chr2A 84.867 641 97 0 2006 2646 34156660 34156020 0.000000e+00 647.0
16 TraesCS2D01G029700 chr2B 81.333 900 150 7 998 1894 52716967 52717851 0.000000e+00 715.0
17 TraesCS2D01G029700 chr2B 85.318 613 86 4 2006 2616 52718018 52718628 6.610000e-177 630.0
18 TraesCS2D01G029700 chr7A 91.860 172 14 0 658 829 138536623 138536794 1.300000e-59 241.0
19 TraesCS2D01G029700 chr3D 94.231 156 9 0 660 815 486424787 486424942 4.680000e-59 239.0
20 TraesCS2D01G029700 chr6B 92.121 165 13 0 660 824 144269660 144269496 2.180000e-57 233.0
21 TraesCS2D01G029700 chr6B 91.617 167 14 0 660 826 44844074 44844240 7.840000e-57 231.0
22 TraesCS2D01G029700 chr6B 89.474 57 2 2 566 622 151422373 151422425 6.500000e-08 69.4
23 TraesCS2D01G029700 chr6D 90.230 174 17 0 660 833 95373428 95373255 1.010000e-55 228.0
24 TraesCS2D01G029700 chr6D 100.000 28 0 0 595 622 448645772 448645799 7.000000e-03 52.8
25 TraesCS2D01G029700 chr5A 87.662 154 11 3 3484 3629 395061435 395061588 4.820000e-39 172.0
26 TraesCS2D01G029700 chr1D 86.869 99 5 4 3481 3571 462492749 462492651 1.780000e-18 104.0


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 TraesCS2D01G029700 chr2D 12289200 12292828 3628 False 6702.0 6702 100.0000 1 3629 1 chr2D.!!$F1 3628
1 TraesCS2D01G029700 chr2D 12523494 12525250 1756 True 1461.0 1461 81.8380 884 2677 1 chr2D.!!$R3 1793
2 TraesCS2D01G029700 chr2D 12137136 12138762 1626 True 1310.0 1310 81.3560 1029 2667 1 chr2D.!!$R1 1638
3 TraesCS2D01G029700 chr2D 12303420 12304967 1547 True 1310.0 1310 82.0640 1097 2677 1 chr2D.!!$R2 1580
4 TraesCS2D01G029700 chrUn 12471016 12474631 3615 True 2577.5 4377 90.0575 1 3629 2 chrUn.!!$R2 3628
5 TraesCS2D01G029700 chrUn 12461939 12463514 1575 False 1363.0 1363 82.4780 1097 2677 1 chrUn.!!$F1 1580
6 TraesCS2D01G029700 chr5D 560883451 560885173 1722 False 1452.0 1452 81.9720 880 2649 1 chr5D.!!$F2 1769
7 TraesCS2D01G029700 chr2A 12803868 12805612 1744 True 1269.0 1269 80.1240 921 2667 1 chr2A.!!$R1 1746
8 TraesCS2D01G029700 chr2A 12610191 12611877 1686 True 717.0 769 82.8855 928 2675 2 chr2A.!!$R2 1747
9 TraesCS2D01G029700 chr2A 34156020 34157584 1564 True 686.0 725 83.7510 1013 2646 2 chr2A.!!$R3 1633
10 TraesCS2D01G029700 chr2B 52716967 52718628 1661 False 672.5 715 83.3255 998 2616 2 chr2B.!!$F1 1618

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
856 876 0.597637 GCGTAGATGGTCCATGGACG 60.598 60.0 33.24 23.41 45.41 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2734 2987 0.098376 ATGACTAGCGACGAACGTCC 59.902 55.0 19.15 12.82 44.6 4.79 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
128 129 5.824624 ACACCTCATGCACCAAATTATCTAG 59.175 40.000 0.00 0.00 0.00 2.43
132 133 6.015688 CCTCATGCACCAAATTATCTAGCATT 60.016 38.462 0.00 0.00 39.00 3.56
179 184 8.679288 ATTTTCTCGTATCTGCTTTGAATTTG 57.321 30.769 0.00 0.00 0.00 2.32
190 195 4.681025 TGCTTTGAATTTGTTCTTCATCGC 59.319 37.500 0.00 0.00 32.94 4.58
192 197 3.469899 TGAATTTGTTCTTCATCGCGG 57.530 42.857 6.13 0.00 0.00 6.46
198 203 2.032634 TTCTTCATCGCGGGTGCAC 61.033 57.895 8.80 8.80 42.97 4.57
229 234 3.119352 GGGCATAGAAACTTTGCTCTTGG 60.119 47.826 12.18 0.00 36.31 3.61
230 235 3.505836 GCATAGAAACTTTGCTCTTGGC 58.494 45.455 0.00 0.00 35.97 4.52
262 267 9.932207 TGAGTAGTCGAAATTTCTATTGGTAAA 57.068 29.630 15.92 0.00 0.00 2.01
351 357 4.234530 AGTTTTTGATCTGCTGTTGAGC 57.765 40.909 0.00 0.00 46.44 4.26
422 442 2.283966 ACGGGGAGGAGTGGACAG 60.284 66.667 0.00 0.00 0.00 3.51
455 475 2.029623 GAGAGCACGGGAGGTATGTAA 58.970 52.381 0.00 0.00 0.00 2.41
485 505 6.944557 AATTTGCTGTCCGTAATTTTTAGC 57.055 33.333 0.00 0.00 0.00 3.09
491 511 6.071463 GCTGTCCGTAATTTTTAGCATATCG 58.929 40.000 0.00 0.00 0.00 2.92
502 522 1.364171 GCATATCGCGGGACAGACT 59.636 57.895 6.13 0.00 0.00 3.24
548 568 3.393800 AGTATTTGCTATGCGCTGTAGG 58.606 45.455 9.73 0.00 40.11 3.18
564 584 0.883153 TAGGTGCGCTTCGTAGAACA 59.117 50.000 9.73 0.00 45.90 3.18
643 663 4.521943 CAGCGTCTATAGATTTGCTTTGC 58.478 43.478 18.82 8.73 30.93 3.68
679 699 6.855763 TTGTACTCCCTCCGTTTCTAAATA 57.144 37.500 0.00 0.00 0.00 1.40
741 761 7.023575 ACGAAGCAAAATGAATGAATCTACAC 58.976 34.615 0.00 0.00 0.00 2.90
811 831 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
815 835 7.166167 ACAAAGACTTACATTTAGGAACGGAT 58.834 34.615 0.00 0.00 0.00 4.18
856 876 0.597637 GCGTAGATGGTCCATGGACG 60.598 60.000 33.24 23.41 45.41 4.79
962 989 7.629222 GCTTATAAAAGGCTTCTCATTCTTGCA 60.629 37.037 0.00 0.00 32.98 4.08
996 1023 3.182590 AAGACTGCAAGCGCCCTCA 62.183 57.895 2.29 0.00 37.60 3.86
1006 1033 3.023949 GCGCCCTCAGTCATGGAGT 62.024 63.158 0.00 0.00 0.00 3.85
1011 1038 2.027192 GCCCTCAGTCATGGAGTTAACA 60.027 50.000 8.61 0.00 0.00 2.41
1020 1047 1.429930 TGGAGTTAACAGGAGCCACA 58.570 50.000 8.61 0.00 0.00 4.17
1372 1408 0.102300 CATCGCCATGACTCCGTACA 59.898 55.000 0.00 0.00 30.57 2.90
1842 1878 2.667470 CTTAGGATCAAGGACGAGGGA 58.333 52.381 0.00 0.00 0.00 4.20
1899 1938 4.304110 AGGCAATCATAATGGTACGTACG 58.696 43.478 18.98 15.01 0.00 3.67
2232 2460 3.088532 TCCAGTGGTGCCAATGTTAATC 58.911 45.455 16.05 0.00 39.98 1.75
2316 2544 2.507407 TGGTCAATACCTGGGCTTTC 57.493 50.000 0.00 0.00 46.91 2.62
2457 2685 0.252197 ACTGCCCCGGTGATAACTTC 59.748 55.000 0.00 0.00 0.00 3.01
2493 2721 2.821366 CTCATGGTGGCACGGCTC 60.821 66.667 12.17 0.00 0.00 4.70
2677 2911 7.074653 TGTGGGGAATAATAATAGTGGAGTC 57.925 40.000 0.00 0.00 0.00 3.36
2678 2912 6.043938 TGTGGGGAATAATAATAGTGGAGTCC 59.956 42.308 0.73 0.73 0.00 3.85
2690 2924 2.093106 GTGGAGTCCTACACACGATCT 58.907 52.381 11.33 0.00 43.81 2.75
2692 2926 3.884091 GTGGAGTCCTACACACGATCTAT 59.116 47.826 11.33 0.00 43.81 1.98
2693 2927 4.338682 GTGGAGTCCTACACACGATCTATT 59.661 45.833 11.33 0.00 43.81 1.73
2695 2929 4.023021 GGAGTCCTACACACGATCTATTCC 60.023 50.000 0.41 0.00 0.00 3.01
2696 2930 4.533815 AGTCCTACACACGATCTATTCCA 58.466 43.478 0.00 0.00 0.00 3.53
2697 2931 5.141182 AGTCCTACACACGATCTATTCCAT 58.859 41.667 0.00 0.00 0.00 3.41
2698 2932 5.598830 AGTCCTACACACGATCTATTCCATT 59.401 40.000 0.00 0.00 0.00 3.16
2706 2959 5.983720 ACACGATCTATTCCATTTAAGGTCG 59.016 40.000 2.55 2.55 45.66 4.79
2731 2984 2.356382 TGTAAGGTTTGTGCGGTTTCTG 59.644 45.455 0.00 0.00 0.00 3.02
2734 2987 0.310854 GGTTTGTGCGGTTTCTGGAG 59.689 55.000 0.00 0.00 0.00 3.86
2742 2995 1.007336 CGGTTTCTGGAGGACGTTCG 61.007 60.000 0.00 0.00 0.00 3.95
2758 3011 2.110226 GTTCGTCGCTAGTCATGCTAC 58.890 52.381 0.00 0.00 0.00 3.58
2957 3210 5.640732 CACAAAAATATCTCCCCGAGTTTG 58.359 41.667 0.00 0.00 0.00 2.93
2966 3219 1.314534 CCCCGAGTTTGCATGCATGA 61.315 55.000 30.64 10.85 0.00 3.07
2991 3244 0.737019 GCCACAATTGTCATTGCCGG 60.737 55.000 8.48 6.31 43.39 6.13
3021 3274 2.668457 CGTGTCACATCAAGCTAGGAAC 59.332 50.000 3.42 0.00 0.00 3.62
3032 3285 7.068716 ACATCAAGCTAGGAACTTTTGAGTTTT 59.931 33.333 0.00 0.00 41.75 2.43
3062 3315 1.667595 TCATGGGTTGATGAGGGACA 58.332 50.000 0.00 0.00 0.00 4.02
3074 3327 0.603569 GAGGGACAGAACTGAAGCGA 59.396 55.000 8.87 0.00 0.00 4.93
3134 3388 3.646715 AAGCCCTAGCACCGCCAA 61.647 61.111 0.00 0.00 43.56 4.52
3159 3413 0.036010 AACAAGGGCAGATCGACTGG 60.036 55.000 14.19 0.00 45.82 4.00
3160 3414 1.194781 ACAAGGGCAGATCGACTGGT 61.195 55.000 14.19 0.00 45.82 4.00
3161 3415 0.742281 CAAGGGCAGATCGACTGGTG 60.742 60.000 14.19 0.20 45.82 4.17
3162 3416 2.512515 GGGCAGATCGACTGGTGC 60.513 66.667 14.19 8.75 45.82 5.01
3164 3418 2.887568 GCAGATCGACTGGTGCCG 60.888 66.667 14.19 0.00 45.82 5.69
3165 3419 2.887568 CAGATCGACTGGTGCCGC 60.888 66.667 7.01 0.00 42.39 6.53
3166 3420 3.071206 AGATCGACTGGTGCCGCT 61.071 61.111 0.00 0.00 0.00 5.52
3167 3421 2.887568 GATCGACTGGTGCCGCTG 60.888 66.667 0.00 0.00 0.00 5.18
3189 3443 2.668212 CGACATTGGCCGTGGTGT 60.668 61.111 12.06 7.28 0.00 4.16
3191 3445 1.302511 GACATTGGCCGTGGTGTCT 60.303 57.895 17.33 0.00 38.29 3.41
3234 3488 3.838271 GGCAGGAGGATCGCGACA 61.838 66.667 12.93 0.00 34.37 4.35
3237 3491 2.043852 AGGAGGATCGCGACAGGT 60.044 61.111 12.93 0.00 34.37 4.00
3238 3492 2.122167 AGGAGGATCGCGACAGGTC 61.122 63.158 12.93 4.58 34.37 3.85
3240 3494 3.140225 GAGGATCGCGACAGGTCCC 62.140 68.421 20.09 11.02 0.00 4.46
3241 3495 4.222847 GGATCGCGACAGGTCCCC 62.223 72.222 12.93 0.15 0.00 4.81
3242 3496 3.148279 GATCGCGACAGGTCCCCT 61.148 66.667 12.93 0.00 0.00 4.79
3244 3498 2.907897 GATCGCGACAGGTCCCCTTG 62.908 65.000 12.93 0.00 0.00 3.61
3245 3499 3.691342 CGCGACAGGTCCCCTTGA 61.691 66.667 0.00 0.00 0.00 3.02
3246 3500 2.266055 GCGACAGGTCCCCTTGAG 59.734 66.667 0.00 0.00 0.00 3.02
3247 3501 2.283529 GCGACAGGTCCCCTTGAGA 61.284 63.158 0.00 0.00 0.00 3.27
3248 3502 1.592223 CGACAGGTCCCCTTGAGAC 59.408 63.158 0.00 0.00 0.00 3.36
3249 3503 1.592223 GACAGGTCCCCTTGAGACG 59.408 63.158 0.00 0.00 34.97 4.18
3250 3504 0.898789 GACAGGTCCCCTTGAGACGA 60.899 60.000 0.00 0.00 34.97 4.20
3251 3505 1.186267 ACAGGTCCCCTTGAGACGAC 61.186 60.000 0.00 0.00 34.97 4.34
3253 3507 0.702902 AGGTCCCCTTGAGACGACTA 59.297 55.000 0.00 0.00 34.97 2.59
3272 3554 3.989787 GGTGGCTTTTGTGGGCGG 61.990 66.667 0.00 0.00 0.00 6.13
3274 3556 2.443016 TGGCTTTTGTGGGCGGTT 60.443 55.556 0.00 0.00 0.00 4.44
3299 3581 3.755628 GTAGTCAGGGCGGCGACA 61.756 66.667 17.61 0.00 34.48 4.35
3339 3621 3.891366 CCCTATTGGCTTTTACATCCAGG 59.109 47.826 0.00 0.00 0.00 4.45
3376 3658 4.222588 CCAAAACTGATATTTCTTGCCCCA 59.777 41.667 0.00 0.00 0.00 4.96
3377 3659 5.413499 CAAAACTGATATTTCTTGCCCCAG 58.587 41.667 0.00 0.00 0.00 4.45
3378 3660 2.659428 ACTGATATTTCTTGCCCCAGC 58.341 47.619 0.00 0.00 40.48 4.85
3379 3661 2.243221 ACTGATATTTCTTGCCCCAGCT 59.757 45.455 0.00 0.00 40.80 4.24
3380 3662 3.459598 ACTGATATTTCTTGCCCCAGCTA 59.540 43.478 0.00 0.00 40.80 3.32
3381 3663 4.070716 CTGATATTTCTTGCCCCAGCTAG 58.929 47.826 0.00 0.00 42.43 3.42
3382 3664 2.348411 TATTTCTTGCCCCAGCTAGC 57.652 50.000 6.62 6.62 41.06 3.42
3383 3665 0.749454 ATTTCTTGCCCCAGCTAGCG 60.749 55.000 9.55 4.28 41.06 4.26
3399 3682 3.066900 GCTAGCGAACAAGACTCCTATGA 59.933 47.826 0.00 0.00 0.00 2.15
3412 3695 4.152647 ACTCCTATGATCATAGCGTGGAA 58.847 43.478 29.90 13.51 39.48 3.53
3428 3711 2.046411 AATGGATCGTGTGGCGCA 60.046 55.556 10.83 0.00 41.07 6.09
3429 3712 2.309764 GAATGGATCGTGTGGCGCAC 62.310 60.000 20.87 20.87 44.36 5.34
3436 3719 3.052082 GTGTGGCGCACAGAGCAT 61.052 61.111 25.26 0.00 45.43 3.79
3454 3737 6.919662 CAGAGCATGCGGAATTGTAATAAAAT 59.080 34.615 13.01 0.00 0.00 1.82
3460 3743 9.044150 CATGCGGAATTGTAATAAAATGGAAAT 57.956 29.630 0.00 0.00 0.00 2.17
3469 3752 8.972458 TGTAATAAAATGGAAATGGATCGAGA 57.028 30.769 0.00 0.00 0.00 4.04
3473 3756 8.696043 ATAAAATGGAAATGGATCGAGATTGA 57.304 30.769 0.00 0.00 0.00 2.57
3477 3760 5.500234 TGGAAATGGATCGAGATTGACTTT 58.500 37.500 0.00 0.00 0.00 2.66
3478 3761 5.355071 TGGAAATGGATCGAGATTGACTTTG 59.645 40.000 0.00 0.00 0.00 2.77
3480 3763 6.238320 GGAAATGGATCGAGATTGACTTTGAG 60.238 42.308 0.00 0.00 0.00 3.02
3487 3772 7.095017 GGATCGAGATTGACTTTGAGTCTTTTT 60.095 37.037 9.27 0.00 45.27 1.94
3517 3802 3.884693 ACAATGAGAACTGCATGTGACAA 59.115 39.130 0.00 0.00 0.00 3.18
3520 3805 5.808042 ATGAGAACTGCATGTGACAATAC 57.192 39.130 0.00 0.00 0.00 1.89
3524 3809 5.308014 AGAACTGCATGTGACAATACAGAA 58.692 37.500 16.42 0.00 33.44 3.02
3546 3834 7.543868 CAGAAGAAAAGAGATACAATGTCGAGT 59.456 37.037 0.00 0.00 0.00 4.18
3571 3859 1.469308 TGACGACCCAACAACAACAAC 59.531 47.619 0.00 0.00 0.00 3.32
3574 3862 2.296471 ACGACCCAACAACAACAACAAA 59.704 40.909 0.00 0.00 0.00 2.83
3575 3863 3.243771 ACGACCCAACAACAACAACAAAA 60.244 39.130 0.00 0.00 0.00 2.44
3576 3864 3.741344 CGACCCAACAACAACAACAAAAA 59.259 39.130 0.00 0.00 0.00 1.94
3577 3865 4.143221 CGACCCAACAACAACAACAAAAAG 60.143 41.667 0.00 0.00 0.00 2.27
3579 3867 4.202367 ACCCAACAACAACAACAAAAAGGA 60.202 37.500 0.00 0.00 0.00 3.36
3580 3868 4.757149 CCCAACAACAACAACAAAAAGGAA 59.243 37.500 0.00 0.00 0.00 3.36
3581 3869 5.239525 CCCAACAACAACAACAAAAAGGAAA 59.760 36.000 0.00 0.00 0.00 3.13
3613 3901 3.327757 ACAGAAGCAATCCTAGGTGAACA 59.672 43.478 9.08 0.00 0.00 3.18
3623 3911 2.352814 CCTAGGTGAACAACGACCTCAG 60.353 54.545 0.00 0.00 41.90 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 8.972127 TCATTTAGCATCTGAGTAGTTCTTAGT 58.028 33.333 0.00 0.00 32.51 2.24
63 64 9.979578 ATCATTTAGCATCTGAGTAGTTCTTAG 57.020 33.333 0.00 0.00 0.00 2.18
64 65 9.973450 GATCATTTAGCATCTGAGTAGTTCTTA 57.027 33.333 0.00 0.00 0.00 2.10
65 66 8.703743 AGATCATTTAGCATCTGAGTAGTTCTT 58.296 33.333 0.00 0.00 0.00 2.52
69 70 7.594351 TCAGATCATTTAGCATCTGAGTAGT 57.406 36.000 7.81 0.00 46.61 2.73
79 80 7.543172 GTGCTCAAAATTTCAGATCATTTAGCA 59.457 33.333 8.52 8.52 0.00 3.49
80 81 7.543172 TGTGCTCAAAATTTCAGATCATTTAGC 59.457 33.333 0.00 0.46 0.00 3.09
99 100 1.302752 GGTGCATGAGGTGTGCTCA 60.303 57.895 0.00 0.00 42.92 4.26
100 101 0.890542 TTGGTGCATGAGGTGTGCTC 60.891 55.000 0.00 0.00 42.92 4.26
179 184 2.032634 TGCACCCGCGATGAAGAAC 61.033 57.895 8.23 0.00 42.97 3.01
190 195 1.378882 CCCAGATTCATGTGCACCCG 61.379 60.000 15.69 5.22 0.00 5.28
192 197 0.966875 TGCCCAGATTCATGTGCACC 60.967 55.000 15.69 0.00 28.10 5.01
198 203 6.270815 CAAAGTTTCTATGCCCAGATTCATG 58.729 40.000 0.00 0.00 0.00 3.07
229 234 9.774742 ATAGAAATTTCGACTACTCAAAAATGC 57.225 29.630 12.42 0.00 0.00 3.56
351 357 4.537015 GTTTTCAGGACCAAAAGATGACG 58.463 43.478 0.00 0.00 0.00 4.35
422 442 4.686554 CCCGTGCTCTCTAAACTTATATGC 59.313 45.833 0.00 0.00 0.00 3.14
485 505 1.338337 AGAAGTCTGTCCCGCGATATG 59.662 52.381 8.23 0.00 0.00 1.78
491 511 3.528597 AATAAGAGAAGTCTGTCCCGC 57.471 47.619 0.00 0.00 31.37 6.13
548 568 2.875080 AAATGTTCTACGAAGCGCAC 57.125 45.000 11.47 1.68 0.00 5.34
551 571 4.811158 TCGTAAAATGTTCTACGAAGCG 57.189 40.909 0.00 0.00 44.97 4.68
629 649 3.313526 CGGCTACAGCAAAGCAAATCTAT 59.686 43.478 3.24 0.00 44.36 1.98
643 663 1.993370 GAGTACAAAGTGCGGCTACAG 59.007 52.381 0.00 0.00 0.00 2.74
763 783 9.273016 AGAGATTTCATTATAAACCACATACGG 57.727 33.333 0.00 0.00 0.00 4.02
838 858 0.032130 CCGTCCATGGACCATCTACG 59.968 60.000 34.05 22.74 41.76 3.51
856 876 0.391793 GCACCAGTACAAGCTCCTCC 60.392 60.000 0.00 0.00 0.00 4.30
962 989 4.137543 CAGTCTTGCTTGGTAAAGGAACT 58.862 43.478 0.00 0.00 38.65 3.01
991 1018 3.369892 CCTGTTAACTCCATGACTGAGGG 60.370 52.174 7.22 0.00 34.06 4.30
996 1023 2.237392 GGCTCCTGTTAACTCCATGACT 59.763 50.000 7.22 0.00 0.00 3.41
1006 1033 5.527214 CGATGAATAATGTGGCTCCTGTTAA 59.473 40.000 0.00 0.00 0.00 2.01
1011 1038 3.845781 ACGATGAATAATGTGGCTCCT 57.154 42.857 0.00 0.00 0.00 3.69
1020 1047 4.950050 AGGCGAGAGAAACGATGAATAAT 58.050 39.130 0.00 0.00 0.00 1.28
1842 1878 0.622665 CCATGGGGAAGTCAAGCTCT 59.377 55.000 2.85 0.00 35.59 4.09
1939 2105 5.741040 GCAATACTAGTCAACTACGTACCAC 59.259 44.000 0.00 0.00 0.00 4.16
1940 2106 5.415389 TGCAATACTAGTCAACTACGTACCA 59.585 40.000 0.00 0.00 0.00 3.25
1941 2107 5.883661 TGCAATACTAGTCAACTACGTACC 58.116 41.667 0.00 0.00 0.00 3.34
1942 2108 7.487189 ACAATGCAATACTAGTCAACTACGTAC 59.513 37.037 0.00 0.00 0.00 3.67
2232 2460 3.083349 TCTCGGCAGACATGGGGG 61.083 66.667 0.00 0.00 0.00 5.40
2493 2721 6.426646 AGGCTCCAGTCAAAATAGTATAGG 57.573 41.667 0.00 0.00 0.00 2.57
2677 2911 7.385205 CCTTAAATGGAATAGATCGTGTGTAGG 59.615 40.741 0.00 0.00 0.00 3.18
2678 2912 7.926555 ACCTTAAATGGAATAGATCGTGTGTAG 59.073 37.037 0.00 0.00 0.00 2.74
2690 2924 7.767198 CCTTACAACTCGACCTTAAATGGAATA 59.233 37.037 0.00 0.00 0.00 1.75
2692 2926 5.935789 CCTTACAACTCGACCTTAAATGGAA 59.064 40.000 0.00 0.00 0.00 3.53
2693 2927 5.012354 ACCTTACAACTCGACCTTAAATGGA 59.988 40.000 0.00 0.00 0.00 3.41
2695 2929 6.796705 AACCTTACAACTCGACCTTAAATG 57.203 37.500 0.00 0.00 0.00 2.32
2696 2930 6.769341 ACAAACCTTACAACTCGACCTTAAAT 59.231 34.615 0.00 0.00 0.00 1.40
2697 2931 6.037391 CACAAACCTTACAACTCGACCTTAAA 59.963 38.462 0.00 0.00 0.00 1.52
2698 2932 5.524646 CACAAACCTTACAACTCGACCTTAA 59.475 40.000 0.00 0.00 0.00 1.85
2706 2959 1.944709 ACCGCACAAACCTTACAACTC 59.055 47.619 0.00 0.00 0.00 3.01
2731 2984 1.062206 CTAGCGACGAACGTCCTCC 59.938 63.158 19.15 9.60 44.60 4.30
2734 2987 0.098376 ATGACTAGCGACGAACGTCC 59.902 55.000 19.15 12.82 44.60 4.79
2742 2995 2.190325 AACGTAGCATGACTAGCGAC 57.810 50.000 0.00 0.00 37.01 5.19
2758 3011 4.584029 ACAATAGACGAGCATGAAAACG 57.416 40.909 0.00 0.00 0.00 3.60
2866 3119 8.184848 CCGAACAACTCACGATCTGATATATAT 58.815 37.037 0.00 0.00 0.00 0.86
2867 3120 7.389607 TCCGAACAACTCACGATCTGATATATA 59.610 37.037 0.00 0.00 0.00 0.86
2907 3160 7.318141 CACTCAATCTTGGACAGCATTATTTT 58.682 34.615 0.00 0.00 0.00 1.82
2911 3164 4.264253 CCACTCAATCTTGGACAGCATTA 58.736 43.478 0.00 0.00 34.46 1.90
2912 3165 3.087031 CCACTCAATCTTGGACAGCATT 58.913 45.455 0.00 0.00 34.46 3.56
2916 3169 1.808945 GTGCCACTCAATCTTGGACAG 59.191 52.381 0.00 0.00 34.46 3.51
2957 3210 1.406180 TGTGGCTACATTCATGCATGC 59.594 47.619 22.25 11.82 0.00 4.06
2966 3219 4.497300 GCAATGACAATTGTGGCTACATT 58.503 39.130 17.58 15.18 44.34 2.71
2991 3244 4.379793 GCTTGATGTGACACGAATTGTTTC 59.620 41.667 0.22 0.00 39.17 2.78
3046 3299 1.351017 GTTCTGTCCCTCATCAACCCA 59.649 52.381 0.00 0.00 0.00 4.51
3062 3315 1.867363 AGGGGTATCGCTTCAGTTCT 58.133 50.000 0.00 0.00 31.69 3.01
3102 3355 2.901042 CTTGGGACCCCTAGCGTC 59.099 66.667 8.45 0.66 36.94 5.19
3134 3388 2.154462 CGATCTGCCCTTGTTTGAAGT 58.846 47.619 0.00 0.00 0.00 3.01
3174 3428 1.600636 CAGACACCACGGCCAATGT 60.601 57.895 2.24 0.00 0.00 2.71
3200 3454 1.283793 CCCAAGCAACTTCAGCACG 59.716 57.895 0.00 0.00 0.00 5.34
3201 3455 1.006922 GCCCAAGCAACTTCAGCAC 60.007 57.895 0.00 0.00 39.53 4.40
3237 3491 0.033405 CCCTAGTCGTCTCAAGGGGA 60.033 60.000 9.08 0.00 44.32 4.81
3238 3492 2.506065 CCCTAGTCGTCTCAAGGGG 58.494 63.158 9.08 3.45 44.32 4.79
3240 3494 0.818296 CCACCCTAGTCGTCTCAAGG 59.182 60.000 0.00 0.00 0.00 3.61
3241 3495 0.173708 GCCACCCTAGTCGTCTCAAG 59.826 60.000 0.00 0.00 0.00 3.02
3242 3496 0.251653 AGCCACCCTAGTCGTCTCAA 60.252 55.000 0.00 0.00 0.00 3.02
3244 3498 0.896226 AAAGCCACCCTAGTCGTCTC 59.104 55.000 0.00 0.00 0.00 3.36
3245 3499 1.002087 CAAAAGCCACCCTAGTCGTCT 59.998 52.381 0.00 0.00 0.00 4.18
3246 3500 1.270678 ACAAAAGCCACCCTAGTCGTC 60.271 52.381 0.00 0.00 0.00 4.20
3247 3501 0.763035 ACAAAAGCCACCCTAGTCGT 59.237 50.000 0.00 0.00 0.00 4.34
3248 3502 1.156736 CACAAAAGCCACCCTAGTCG 58.843 55.000 0.00 0.00 0.00 4.18
3249 3503 1.534729 CCACAAAAGCCACCCTAGTC 58.465 55.000 0.00 0.00 0.00 2.59
3250 3504 0.112412 CCCACAAAAGCCACCCTAGT 59.888 55.000 0.00 0.00 0.00 2.57
3251 3505 1.250840 GCCCACAAAAGCCACCCTAG 61.251 60.000 0.00 0.00 0.00 3.02
3253 3507 2.524148 GCCCACAAAAGCCACCCT 60.524 61.111 0.00 0.00 0.00 4.34
3272 3554 2.813908 CTGACTACCGCGCCCAAC 60.814 66.667 0.00 0.00 0.00 3.77
3330 3612 3.838565 TGCTTTTGGTTTCCTGGATGTA 58.161 40.909 0.00 0.00 0.00 2.29
3339 3621 4.693095 TCAGTTTTGGTTGCTTTTGGTTTC 59.307 37.500 0.00 0.00 0.00 2.78
3376 3658 1.551452 AGGAGTCTTGTTCGCTAGCT 58.449 50.000 13.93 0.00 0.00 3.32
3377 3659 3.066900 TCATAGGAGTCTTGTTCGCTAGC 59.933 47.826 4.06 4.06 0.00 3.42
3378 3660 4.902443 TCATAGGAGTCTTGTTCGCTAG 57.098 45.455 0.00 0.00 0.00 3.42
3379 3661 4.887655 TGATCATAGGAGTCTTGTTCGCTA 59.112 41.667 0.00 0.00 0.00 4.26
3380 3662 3.701542 TGATCATAGGAGTCTTGTTCGCT 59.298 43.478 0.00 0.00 0.00 4.93
3381 3663 4.046938 TGATCATAGGAGTCTTGTTCGC 57.953 45.455 0.00 0.00 0.00 4.70
3382 3664 5.861251 GCTATGATCATAGGAGTCTTGTTCG 59.139 44.000 33.55 13.08 40.77 3.95
3383 3665 5.861251 CGCTATGATCATAGGAGTCTTGTTC 59.139 44.000 33.55 17.57 40.77 3.18
3399 3682 2.300152 ACGATCCATTCCACGCTATGAT 59.700 45.455 0.00 0.00 0.00 2.45
3428 3711 2.401583 TACAATTCCGCATGCTCTGT 57.598 45.000 17.13 13.01 0.00 3.41
3429 3712 3.976793 ATTACAATTCCGCATGCTCTG 57.023 42.857 17.13 7.84 0.00 3.35
3430 3713 6.449635 TTTTATTACAATTCCGCATGCTCT 57.550 33.333 17.13 0.00 0.00 4.09
3436 3719 7.493971 CCATTTCCATTTTATTACAATTCCGCA 59.506 33.333 0.00 0.00 0.00 5.69
3454 3737 4.760530 AGTCAATCTCGATCCATTTCCA 57.239 40.909 0.00 0.00 0.00 3.53
3460 3743 4.748892 GACTCAAAGTCAATCTCGATCCA 58.251 43.478 2.28 0.00 44.45 3.41
3487 3772 5.242069 TGCAGTTCTCATTGTTCGAAAAA 57.758 34.783 2.60 2.60 0.00 1.94
3497 3782 5.706833 TGTATTGTCACATGCAGTTCTCATT 59.293 36.000 0.00 0.00 0.00 2.57
3517 3802 9.307121 CGACATTGTATCTCTTTTCTTCTGTAT 57.693 33.333 0.00 0.00 0.00 2.29
3520 3805 7.543868 ACTCGACATTGTATCTCTTTTCTTCTG 59.456 37.037 0.00 0.00 0.00 3.02
3524 3809 7.827701 TGTACTCGACATTGTATCTCTTTTCT 58.172 34.615 0.00 0.00 31.20 2.52
3546 3834 3.195471 TGTTGTTGGGTCGTCATTGTA 57.805 42.857 0.00 0.00 0.00 2.41
3571 3859 9.508567 CTTCTGTCTTAGTTCTTTTCCTTTTTG 57.491 33.333 0.00 0.00 0.00 2.44
3574 3862 6.828785 TGCTTCTGTCTTAGTTCTTTTCCTTT 59.171 34.615 0.00 0.00 0.00 3.11
3575 3863 6.357367 TGCTTCTGTCTTAGTTCTTTTCCTT 58.643 36.000 0.00 0.00 0.00 3.36
3576 3864 5.930135 TGCTTCTGTCTTAGTTCTTTTCCT 58.070 37.500 0.00 0.00 0.00 3.36
3577 3865 6.619801 TTGCTTCTGTCTTAGTTCTTTTCC 57.380 37.500 0.00 0.00 0.00 3.13
3579 3867 7.001073 AGGATTGCTTCTGTCTTAGTTCTTTT 58.999 34.615 0.00 0.00 0.00 2.27
3580 3868 6.538263 AGGATTGCTTCTGTCTTAGTTCTTT 58.462 36.000 0.00 0.00 0.00 2.52
3581 3869 6.120507 AGGATTGCTTCTGTCTTAGTTCTT 57.879 37.500 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.