Multiple sequence alignment - TraesCS1A01G253500

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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 TraesCS1A01G253500 chr1A 100.000 3477 0 0 1 3477 445501535 445505011 0.000000e+00 6421.0
1 TraesCS1A01G253500 chr1A 92.208 77 5 1 3398 3474 52534532 52534607 1.320000e-19 108.0
2 TraesCS1A01G253500 chr1D 96.503 2574 71 9 81 2646 345374101 345376663 0.000000e+00 4237.0
3 TraesCS1A01G253500 chr1D 80.000 450 70 11 2948 3380 161036260 161035814 7.240000e-82 315.0
4 TraesCS1A01G253500 chr1D 84.571 175 17 5 3208 3382 407697174 407697338 7.720000e-37 165.0
5 TraesCS1A01G253500 chr1D 87.500 72 8 1 3398 3468 161035823 161035752 8.000000e-12 82.4
6 TraesCS1A01G253500 chr1B 92.732 2917 115 41 104 2947 465390286 465387394 0.000000e+00 4122.0
7 TraesCS1A01G253500 chr6A 87.829 797 86 8 1707 2495 15542478 15543271 0.000000e+00 924.0
8 TraesCS1A01G253500 chr6A 85.279 788 95 14 1722 2495 15457423 15456643 0.000000e+00 793.0
9 TraesCS1A01G253500 chr6A 83.061 797 124 7 1708 2495 15491582 15490788 0.000000e+00 713.0
10 TraesCS1A01G253500 chr6A 84.395 628 86 6 1006 1630 15540721 15541339 1.070000e-169 606.0
11 TraesCS1A01G253500 chr6A 84.286 630 85 8 1006 1634 15461668 15461052 1.380000e-168 603.0
12 TraesCS1A01G253500 chr6A 86.574 432 48 8 2948 3375 428726029 428725604 5.250000e-128 468.0
13 TraesCS1A01G253500 chr6A 90.000 80 7 1 3398 3477 428725608 428725530 6.140000e-18 102.0
14 TraesCS1A01G253500 chr6D 86.879 785 94 7 1707 2485 14241306 14242087 0.000000e+00 870.0
15 TraesCS1A01G253500 chr6D 85.554 803 95 13 1707 2495 14201992 14201197 0.000000e+00 821.0
16 TraesCS1A01G253500 chr6D 84.036 783 112 10 1723 2495 14231354 14230575 0.000000e+00 741.0
17 TraesCS1A01G253500 chr6D 84.945 631 82 7 1006 1634 14203504 14202885 8.190000e-176 627.0
18 TraesCS1A01G253500 chr6D 84.420 629 86 6 1006 1631 14239438 14240057 2.970000e-170 608.0
19 TraesCS1A01G253500 chr6D 82.306 633 92 7 1006 1634 14232267 14231651 6.610000e-147 531.0
20 TraesCS1A01G253500 chr6D 85.143 175 16 5 3208 3382 9827095 9827259 1.660000e-38 171.0
21 TraesCS1A01G253500 chr6D 93.827 81 4 1 3398 3477 9827248 9827328 1.700000e-23 121.0
22 TraesCS1A01G253500 chr6B 86.233 799 97 8 1707 2495 26004656 26005451 0.000000e+00 854.0
23 TraesCS1A01G253500 chr6B 85.480 792 98 9 1707 2491 26120974 26120193 0.000000e+00 809.0
24 TraesCS1A01G253500 chr6B 84.444 630 87 5 1006 1634 25976120 25975501 8.250000e-171 610.0
25 TraesCS1A01G253500 chr6B 82.989 629 92 6 1006 1631 26001816 26002432 3.920000e-154 555.0
26 TraesCS1A01G253500 chr6B 81.538 195 33 2 1006 1197 26123565 26123371 1.290000e-34 158.0
27 TraesCS1A01G253500 chr4A 92.906 437 28 3 2946 3382 141117840 141117407 1.760000e-177 632.0
28 TraesCS1A01G253500 chr4A 93.976 83 4 1 3396 3477 141117420 141117338 1.310000e-24 124.0
29 TraesCS1A01G253500 chr7A 92.575 431 30 2 2952 3382 150269993 150270421 4.930000e-173 617.0
30 TraesCS1A01G253500 chr7A 89.885 435 28 4 2948 3382 586324176 586324594 2.360000e-151 545.0
31 TraesCS1A01G253500 chr7A 89.165 443 27 6 2943 3382 644711434 644711858 1.840000e-147 532.0
32 TraesCS1A01G253500 chr7A 93.976 83 4 1 3396 3477 586324581 586324663 1.310000e-24 124.0
33 TraesCS1A01G253500 chr7A 94.444 36 2 0 1546 1581 93488862 93488897 4.850000e-04 56.5
34 TraesCS1A01G253500 chr5A 91.800 439 32 4 2944 3382 11242933 11243367 2.970000e-170 608.0
35 TraesCS1A01G253500 chr5A 92.771 83 5 1 3396 3477 11243354 11243436 6.100000e-23 119.0
36 TraesCS1A01G253500 chr4B 78.479 618 102 21 1006 1600 629852590 629853199 3.280000e-100 375.0
37 TraesCS1A01G253500 chr3D 81.153 451 61 13 2944 3377 374271095 374271538 1.200000e-89 340.0
38 TraesCS1A01G253500 chr3D 85.246 61 7 1 3408 3468 374271543 374271601 1.040000e-05 62.1
39 TraesCS1A01G253500 chr3A 81.152 382 56 10 2948 3317 746626354 746625977 3.390000e-75 292.0
40 TraesCS1A01G253500 chr3A 90.196 51 3 2 2875 2923 88212816 88212766 8.060000e-07 65.8
41 TraesCS1A01G253500 chr7D 84.571 175 17 5 3208 3382 536156490 536156654 7.720000e-37 165.0
42 TraesCS1A01G253500 chr7D 91.358 81 6 1 3398 3477 536156643 536156723 3.670000e-20 110.0
43 TraesCS1A01G253500 chr2A 92.683 41 3 0 2891 2931 14171894 14171934 3.750000e-05 60.2


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 TraesCS1A01G253500 chr1A 445501535 445505011 3476 False 6421.00 6421 100.0000 1 3477 1 chr1A.!!$F2 3476
1 TraesCS1A01G253500 chr1D 345374101 345376663 2562 False 4237.00 4237 96.5030 81 2646 1 chr1D.!!$F1 2565
2 TraesCS1A01G253500 chr1B 465387394 465390286 2892 True 4122.00 4122 92.7320 104 2947 1 chr1B.!!$R1 2843
3 TraesCS1A01G253500 chr6A 15540721 15543271 2550 False 765.00 924 86.1120 1006 2495 2 chr6A.!!$F1 1489
4 TraesCS1A01G253500 chr6A 15490788 15491582 794 True 713.00 713 83.0610 1708 2495 1 chr6A.!!$R1 787
5 TraesCS1A01G253500 chr6A 15456643 15461668 5025 True 698.00 793 84.7825 1006 2495 2 chr6A.!!$R2 1489
6 TraesCS1A01G253500 chr6D 14239438 14242087 2649 False 739.00 870 85.6495 1006 2485 2 chr6D.!!$F2 1479
7 TraesCS1A01G253500 chr6D 14201197 14203504 2307 True 724.00 821 85.2495 1006 2495 2 chr6D.!!$R1 1489
8 TraesCS1A01G253500 chr6D 14230575 14232267 1692 True 636.00 741 83.1710 1006 2495 2 chr6D.!!$R2 1489
9 TraesCS1A01G253500 chr6B 26001816 26005451 3635 False 704.50 854 84.6110 1006 2495 2 chr6B.!!$F1 1489
10 TraesCS1A01G253500 chr6B 25975501 25976120 619 True 610.00 610 84.4440 1006 1634 1 chr6B.!!$R1 628
11 TraesCS1A01G253500 chr6B 26120193 26123565 3372 True 483.50 809 83.5090 1006 2491 2 chr6B.!!$R2 1485
12 TraesCS1A01G253500 chr4A 141117338 141117840 502 True 378.00 632 93.4410 2946 3477 2 chr4A.!!$R1 531
13 TraesCS1A01G253500 chr5A 11242933 11243436 503 False 363.50 608 92.2855 2944 3477 2 chr5A.!!$F1 533
14 TraesCS1A01G253500 chr4B 629852590 629853199 609 False 375.00 375 78.4790 1006 1600 1 chr4B.!!$F1 594
15 TraesCS1A01G253500 chr3D 374271095 374271601 506 False 201.05 340 83.1995 2944 3468 2 chr3D.!!$F1 524


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
26 27 0.106469 ATACGCTCTCTCTCCTGGCA 60.106 55.0 0.00 0.0 0.00 4.92 F
1449 1520 0.034089 TGCTCGAGGTGATGAGGAGA 60.034 55.0 15.58 0.0 32.78 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1537 0.520404 GTAGTCGTCGACCTGCTTCA 59.48 55.0 21.40 0.0 32.18 3.02 R
2638 8366 0.320374 TCGTTGTCGGAGCTCCAAAT 59.68 50.0 31.67 0.0 37.69 2.32 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
22 23 4.425180 TGTCTTATACGCTCTCTCTCCT 57.575 45.455 0.00 0.00 0.00 3.69
23 24 4.130857 TGTCTTATACGCTCTCTCTCCTG 58.869 47.826 0.00 0.00 0.00 3.86
24 25 3.500680 GTCTTATACGCTCTCTCTCCTGG 59.499 52.174 0.00 0.00 0.00 4.45
25 26 1.898902 TATACGCTCTCTCTCCTGGC 58.101 55.000 0.00 0.00 0.00 4.85
26 27 0.106469 ATACGCTCTCTCTCCTGGCA 60.106 55.000 0.00 0.00 0.00 4.92
27 28 0.106469 TACGCTCTCTCTCCTGGCAT 60.106 55.000 0.00 0.00 0.00 4.40
28 29 0.106469 ACGCTCTCTCTCCTGGCATA 60.106 55.000 0.00 0.00 0.00 3.14
29 30 1.035923 CGCTCTCTCTCCTGGCATAA 58.964 55.000 0.00 0.00 0.00 1.90
30 31 1.410517 CGCTCTCTCTCCTGGCATAAA 59.589 52.381 0.00 0.00 0.00 1.40
31 32 2.545532 CGCTCTCTCTCCTGGCATAAAG 60.546 54.545 0.00 0.00 0.00 1.85
32 33 2.433970 GCTCTCTCTCCTGGCATAAAGT 59.566 50.000 0.00 0.00 0.00 2.66
33 34 3.118445 GCTCTCTCTCCTGGCATAAAGTT 60.118 47.826 0.00 0.00 0.00 2.66
34 35 4.100189 GCTCTCTCTCCTGGCATAAAGTTA 59.900 45.833 0.00 0.00 0.00 2.24
35 36 5.395768 GCTCTCTCTCCTGGCATAAAGTTAA 60.396 44.000 0.00 0.00 0.00 2.01
36 37 5.978814 TCTCTCTCCTGGCATAAAGTTAAC 58.021 41.667 0.00 0.00 0.00 2.01
37 38 5.483937 TCTCTCTCCTGGCATAAAGTTAACA 59.516 40.000 8.61 0.00 0.00 2.41
38 39 5.488341 TCTCTCCTGGCATAAAGTTAACAC 58.512 41.667 8.61 0.00 0.00 3.32
39 40 5.012664 TCTCTCCTGGCATAAAGTTAACACA 59.987 40.000 8.61 0.00 0.00 3.72
40 41 5.001232 TCTCCTGGCATAAAGTTAACACAC 58.999 41.667 8.61 0.00 0.00 3.82
41 42 3.749088 TCCTGGCATAAAGTTAACACACG 59.251 43.478 8.61 0.00 0.00 4.49
42 43 3.119990 CCTGGCATAAAGTTAACACACGG 60.120 47.826 8.61 0.00 0.00 4.94
43 44 3.478509 TGGCATAAAGTTAACACACGGT 58.521 40.909 8.61 0.00 0.00 4.83
44 45 3.251245 TGGCATAAAGTTAACACACGGTG 59.749 43.478 8.61 6.58 39.75 4.94
45 46 3.499157 GGCATAAAGTTAACACACGGTGA 59.501 43.478 16.29 0.00 36.96 4.02
46 47 4.460505 GCATAAAGTTAACACACGGTGAC 58.539 43.478 16.29 1.73 36.96 3.67
47 48 4.024725 GCATAAAGTTAACACACGGTGACA 60.025 41.667 16.29 0.00 36.96 3.58
48 49 5.504337 GCATAAAGTTAACACACGGTGACAA 60.504 40.000 16.29 0.09 36.96 3.18
49 50 6.664515 CATAAAGTTAACACACGGTGACAAT 58.335 36.000 16.29 0.70 36.96 2.71
50 51 7.571613 GCATAAAGTTAACACACGGTGACAATA 60.572 37.037 16.29 0.00 36.96 1.90
51 52 5.917541 AAGTTAACACACGGTGACAATAG 57.082 39.130 16.29 0.12 36.96 1.73
52 53 3.744426 AGTTAACACACGGTGACAATAGC 59.256 43.478 16.29 4.76 36.96 2.97
53 54 2.248280 AACACACGGTGACAATAGCA 57.752 45.000 16.29 0.00 36.96 3.49
54 55 2.472695 ACACACGGTGACAATAGCAT 57.527 45.000 16.29 0.00 36.96 3.79
55 56 2.778299 ACACACGGTGACAATAGCATT 58.222 42.857 16.29 0.00 36.96 3.56
56 57 3.146066 ACACACGGTGACAATAGCATTT 58.854 40.909 16.29 0.00 36.96 2.32
57 58 3.058293 ACACACGGTGACAATAGCATTTG 60.058 43.478 16.29 0.26 36.96 2.32
58 59 3.058293 CACACGGTGACAATAGCATTTGT 60.058 43.478 16.29 4.18 42.37 2.83
59 60 4.153296 CACACGGTGACAATAGCATTTGTA 59.847 41.667 16.29 0.00 39.85 2.41
60 61 4.941263 ACACGGTGACAATAGCATTTGTAT 59.059 37.500 16.29 0.00 39.85 2.29
61 62 5.414454 ACACGGTGACAATAGCATTTGTATT 59.586 36.000 16.29 0.00 39.85 1.89
62 63 5.965334 CACGGTGACAATAGCATTTGTATTC 59.035 40.000 0.74 0.15 39.85 1.75
63 64 5.065988 ACGGTGACAATAGCATTTGTATTCC 59.934 40.000 4.49 6.73 39.85 3.01
64 65 5.296780 CGGTGACAATAGCATTTGTATTCCT 59.703 40.000 4.49 0.00 39.85 3.36
65 66 6.511767 CGGTGACAATAGCATTTGTATTCCTC 60.512 42.308 4.49 0.00 39.85 3.71
66 67 6.543831 GGTGACAATAGCATTTGTATTCCTCT 59.456 38.462 4.49 0.00 39.85 3.69
67 68 7.715249 GGTGACAATAGCATTTGTATTCCTCTA 59.285 37.037 4.49 0.00 39.85 2.43
68 69 9.277783 GTGACAATAGCATTTGTATTCCTCTAT 57.722 33.333 4.49 0.00 39.85 1.98
69 70 9.851686 TGACAATAGCATTTGTATTCCTCTATT 57.148 29.630 4.49 0.00 39.85 1.73
71 72 9.851686 ACAATAGCATTTGTATTCCTCTATTCA 57.148 29.630 2.76 0.00 38.04 2.57
76 77 9.638176 AGCATTTGTATTCCTCTATTCAATCTT 57.362 29.630 0.00 0.00 0.00 2.40
77 78 9.890352 GCATTTGTATTCCTCTATTCAATCTTC 57.110 33.333 0.00 0.00 0.00 2.87
123 124 5.812642 ACAAATCTCGATGTGGTAATGAGTC 59.187 40.000 2.41 0.00 30.24 3.36
205 206 0.984230 TTCCTTGGAGGCTTCGACAT 59.016 50.000 0.00 0.00 34.61 3.06
248 249 1.154205 ATTAGGTGCATGCGACGCTC 61.154 55.000 22.08 10.56 0.00 5.03
249 250 2.225791 TTAGGTGCATGCGACGCTCT 62.226 55.000 22.08 5.48 0.00 4.09
578 582 4.023279 TCACAATTTGAACGACCCATTGAG 60.023 41.667 2.79 0.00 0.00 3.02
671 698 1.300233 CTAGCAGGGATCGAACCGC 60.300 63.158 5.55 10.89 0.00 5.68
727 754 4.917906 AACAAGGAGACAAGGATTAGCT 57.082 40.909 0.00 0.00 0.00 3.32
778 805 2.610374 TCTTTTTGTACGCTCCACACAC 59.390 45.455 0.00 0.00 0.00 3.82
779 806 1.301423 TTTTGTACGCTCCACACACC 58.699 50.000 0.00 0.00 0.00 4.16
780 807 0.466543 TTTGTACGCTCCACACACCT 59.533 50.000 0.00 0.00 0.00 4.00
782 809 1.366366 GTACGCTCCACACACCTGT 59.634 57.895 0.00 0.00 0.00 4.00
843 876 7.148188 GCAAGTAACCATATATGCATGCATAGT 60.148 37.037 36.05 27.50 41.51 2.12
872 905 2.414161 GCAACGTCATTTTCCCTAGCAC 60.414 50.000 0.00 0.00 0.00 4.40
877 910 2.952310 GTCATTTTCCCTAGCACCATCC 59.048 50.000 0.00 0.00 0.00 3.51
963 996 4.023878 CGTAGATCACCTTACTAGTGGAGC 60.024 50.000 5.39 0.00 35.87 4.70
970 1003 2.358267 CCTTACTAGTGGAGCACTACCG 59.642 54.545 5.39 0.00 43.46 4.02
1022 1075 1.226974 CATCGATCGAAGTGGCGGT 60.227 57.895 23.50 0.00 0.00 5.68
1449 1520 0.034089 TGCTCGAGGTGATGAGGAGA 60.034 55.000 15.58 0.00 32.78 3.71
1603 1695 2.283173 TGCTCCAGAGGCTCGACA 60.283 61.111 9.22 1.48 0.00 4.35
1673 2965 9.796062 CAAATTTTACCATTTTCGTCAATCAAG 57.204 29.630 0.00 0.00 0.00 3.02
1789 7512 0.099968 CATTCTCACGGCCATTGCAG 59.900 55.000 2.24 0.00 40.13 4.41
1906 7629 1.135112 CAGGACAACGACATCATCCGA 60.135 52.381 0.00 0.00 34.46 4.55
2496 8224 1.136565 CCGGCCGCAACAACTTATG 59.863 57.895 22.85 0.00 0.00 1.90
2638 8366 9.965748 GTTCGTTTTGATTGAATTTCTTTTCAA 57.034 25.926 2.46 2.46 46.46 2.69
2655 8383 2.151202 TCAATTTGGAGCTCCGACAAC 58.849 47.619 27.43 3.23 39.43 3.32
2656 8384 1.135972 CAATTTGGAGCTCCGACAACG 60.136 52.381 27.43 10.58 39.43 4.10
2778 8506 3.003482 GCCGTTTGTGGTAATTGTACACA 59.997 43.478 0.00 7.36 31.21 3.72
2798 8526 4.357947 TGACGGTCACGCTCTGCC 62.358 66.667 6.76 0.00 46.04 4.85
2803 8531 4.357947 GTCACGCTCTGCCCGTCA 62.358 66.667 0.00 0.00 36.69 4.35
2804 8532 3.611674 TCACGCTCTGCCCGTCAA 61.612 61.111 0.00 0.00 36.69 3.18
2806 8534 2.125512 ACGCTCTGCCCGTCAATC 60.126 61.111 0.00 0.00 32.83 2.67
2858 8614 3.497942 GGCATCTCCAATACCCGGTATTT 60.498 47.826 18.63 3.21 36.70 1.40
2862 8618 3.135167 TCTCCAATACCCGGTATTTGTCC 59.865 47.826 18.63 0.00 36.70 4.02
2917 8676 1.380785 AGCCAGCCATCCAACCATG 60.381 57.895 0.00 0.00 0.00 3.66
2919 8678 1.669999 GCCAGCCATCCAACCATGTC 61.670 60.000 0.00 0.00 0.00 3.06
2921 8680 0.323633 CAGCCATCCAACCATGTCCA 60.324 55.000 0.00 0.00 0.00 4.02
2931 8690 5.942961 TCCAACCATGTCCACTAAAACTTA 58.057 37.500 0.00 0.00 0.00 2.24
2937 8696 5.347907 CCATGTCCACTAAAACTTACGTCTC 59.652 44.000 0.00 0.00 0.00 3.36
2939 8698 6.152932 TGTCCACTAAAACTTACGTCTCTT 57.847 37.500 0.00 0.00 0.00 2.85
2941 8700 6.698766 TGTCCACTAAAACTTACGTCTCTTTC 59.301 38.462 0.00 0.00 0.00 2.62
2950 8709 5.791666 ACTTACGTCTCTTTCTTTTAGGGG 58.208 41.667 0.00 0.00 0.00 4.79
3022 8781 7.747155 TTTCCAACCAATAATAGAACGACAA 57.253 32.000 0.00 0.00 0.00 3.18
3067 8826 3.535280 TTTGTGCATCTCCGCTGTATA 57.465 42.857 0.00 0.00 0.00 1.47
3188 8947 2.101582 AGCCTACTGATCCATCAACGTC 59.898 50.000 0.00 0.00 36.18 4.34
3198 8957 1.553248 CCATCAACGTCCCCTCTGTAA 59.447 52.381 0.00 0.00 0.00 2.41
3200 8959 1.263356 TCAACGTCCCCTCTGTAAGG 58.737 55.000 0.00 0.00 45.77 2.69
3201 8960 0.974383 CAACGTCCCCTCTGTAAGGT 59.026 55.000 0.00 0.00 44.56 3.50
3202 8961 1.067071 CAACGTCCCCTCTGTAAGGTC 60.067 57.143 0.00 0.00 44.56 3.85
3212 8979 3.529533 CTCTGTAAGGTCTGGCATCAAG 58.470 50.000 0.00 0.00 0.00 3.02
3376 9150 8.911918 TTAGCTTTGGAACTTCTACAATTACA 57.088 30.769 0.00 0.00 0.00 2.41
3377 9151 9.515226 TTAGCTTTGGAACTTCTACAATTACAT 57.485 29.630 0.00 0.00 0.00 2.29
3378 9152 8.409358 AGCTTTGGAACTTCTACAATTACATT 57.591 30.769 0.00 0.00 0.00 2.71
3379 9153 8.299570 AGCTTTGGAACTTCTACAATTACATTG 58.700 33.333 0.00 0.00 45.59 2.82
3438 9212 8.435430 CGCATAACTTACACTCATATTATGTGG 58.565 37.037 9.78 4.88 37.09 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.759693 CAGGAGAGAGAGCGTATAAGACAT 59.240 45.833 0.00 0.00 0.00 3.06
2 3 3.500680 CCAGGAGAGAGAGCGTATAAGAC 59.499 52.174 0.00 0.00 0.00 3.01
3 4 3.745799 CCAGGAGAGAGAGCGTATAAGA 58.254 50.000 0.00 0.00 0.00 2.10
4 5 2.227865 GCCAGGAGAGAGAGCGTATAAG 59.772 54.545 0.00 0.00 0.00 1.73
5 6 2.231529 GCCAGGAGAGAGAGCGTATAA 58.768 52.381 0.00 0.00 0.00 0.98
6 7 1.143073 TGCCAGGAGAGAGAGCGTATA 59.857 52.381 0.00 0.00 0.00 1.47
7 8 0.106469 TGCCAGGAGAGAGAGCGTAT 60.106 55.000 0.00 0.00 0.00 3.06
8 9 0.106469 ATGCCAGGAGAGAGAGCGTA 60.106 55.000 0.00 0.00 0.00 4.42
9 10 0.106469 TATGCCAGGAGAGAGAGCGT 60.106 55.000 0.00 0.00 0.00 5.07
10 11 1.035923 TTATGCCAGGAGAGAGAGCG 58.964 55.000 0.00 0.00 0.00 5.03
11 12 2.433970 ACTTTATGCCAGGAGAGAGAGC 59.566 50.000 0.00 0.00 0.00 4.09
12 13 4.751767 AACTTTATGCCAGGAGAGAGAG 57.248 45.455 0.00 0.00 0.00 3.20
13 14 5.483937 TGTTAACTTTATGCCAGGAGAGAGA 59.516 40.000 7.22 0.00 0.00 3.10
14 15 5.582665 GTGTTAACTTTATGCCAGGAGAGAG 59.417 44.000 7.22 0.00 0.00 3.20
15 16 5.012664 TGTGTTAACTTTATGCCAGGAGAGA 59.987 40.000 7.22 0.00 0.00 3.10
16 17 5.122396 GTGTGTTAACTTTATGCCAGGAGAG 59.878 44.000 7.22 0.00 0.00 3.20
17 18 5.001232 GTGTGTTAACTTTATGCCAGGAGA 58.999 41.667 7.22 0.00 0.00 3.71
18 19 4.142902 CGTGTGTTAACTTTATGCCAGGAG 60.143 45.833 7.22 0.00 0.00 3.69
19 20 3.749088 CGTGTGTTAACTTTATGCCAGGA 59.251 43.478 7.22 0.00 0.00 3.86
20 21 3.119990 CCGTGTGTTAACTTTATGCCAGG 60.120 47.826 7.22 0.00 0.00 4.45
21 22 3.500680 ACCGTGTGTTAACTTTATGCCAG 59.499 43.478 7.22 0.00 0.00 4.85
22 23 3.251245 CACCGTGTGTTAACTTTATGCCA 59.749 43.478 7.22 0.00 0.00 4.92
23 24 3.499157 TCACCGTGTGTTAACTTTATGCC 59.501 43.478 7.22 0.00 34.79 4.40
24 25 4.024725 TGTCACCGTGTGTTAACTTTATGC 60.025 41.667 7.22 0.00 34.79 3.14
25 26 5.660629 TGTCACCGTGTGTTAACTTTATG 57.339 39.130 7.22 0.00 34.79 1.90
26 27 6.870971 ATTGTCACCGTGTGTTAACTTTAT 57.129 33.333 7.22 0.00 34.79 1.40
27 28 6.073657 GCTATTGTCACCGTGTGTTAACTTTA 60.074 38.462 7.22 0.00 34.79 1.85
28 29 5.277634 GCTATTGTCACCGTGTGTTAACTTT 60.278 40.000 7.22 0.00 34.79 2.66
29 30 4.212636 GCTATTGTCACCGTGTGTTAACTT 59.787 41.667 7.22 0.00 34.79 2.66
30 31 3.744426 GCTATTGTCACCGTGTGTTAACT 59.256 43.478 7.22 0.00 34.79 2.24
31 32 3.495377 TGCTATTGTCACCGTGTGTTAAC 59.505 43.478 0.00 0.00 34.79 2.01
32 33 3.729966 TGCTATTGTCACCGTGTGTTAA 58.270 40.909 0.00 2.52 34.79 2.01
33 34 3.388345 TGCTATTGTCACCGTGTGTTA 57.612 42.857 0.00 0.00 34.79 2.41
34 35 2.248280 TGCTATTGTCACCGTGTGTT 57.752 45.000 0.00 0.00 34.79 3.32
35 36 2.472695 ATGCTATTGTCACCGTGTGT 57.527 45.000 0.00 0.00 34.79 3.72
36 37 3.058293 ACAAATGCTATTGTCACCGTGTG 60.058 43.478 0.00 0.00 39.23 3.82
37 38 3.146066 ACAAATGCTATTGTCACCGTGT 58.854 40.909 0.00 0.00 39.23 4.49
38 39 3.829886 ACAAATGCTATTGTCACCGTG 57.170 42.857 2.40 0.00 39.23 4.94
39 40 5.065988 GGAATACAAATGCTATTGTCACCGT 59.934 40.000 10.33 0.00 42.33 4.83
40 41 5.296780 AGGAATACAAATGCTATTGTCACCG 59.703 40.000 10.33 0.00 42.33 4.94
41 42 6.543831 AGAGGAATACAAATGCTATTGTCACC 59.456 38.462 10.33 11.60 42.33 4.02
42 43 7.559590 AGAGGAATACAAATGCTATTGTCAC 57.440 36.000 10.33 4.97 42.33 3.67
43 44 9.851686 AATAGAGGAATACAAATGCTATTGTCA 57.148 29.630 10.33 0.79 42.33 3.58
45 46 9.851686 TGAATAGAGGAATACAAATGCTATTGT 57.148 29.630 11.49 11.49 45.14 2.71
50 51 9.638176 AAGATTGAATAGAGGAATACAAATGCT 57.362 29.630 0.00 0.00 0.00 3.79
51 52 9.890352 GAAGATTGAATAGAGGAATACAAATGC 57.110 33.333 0.00 0.00 0.00 3.56
60 61 9.661954 AGGTATACAGAAGATTGAATAGAGGAA 57.338 33.333 5.01 0.00 0.00 3.36
98 99 6.873997 ACTCATTACCACATCGAGATTTGTA 58.126 36.000 0.00 0.00 0.00 2.41
101 102 5.812642 GTGACTCATTACCACATCGAGATTT 59.187 40.000 0.00 0.00 0.00 2.17
123 124 1.283736 GTACCGGTAAAGCATCCGTG 58.716 55.000 17.78 0.00 44.51 4.94
165 166 7.066781 AGGAAGGAACAAAACTCCTGAATTTA 58.933 34.615 0.00 0.00 42.77 1.40
205 206 1.295020 ATGGATGGAAGGGGTCGAAA 58.705 50.000 0.00 0.00 0.00 3.46
265 266 2.187599 GAAGGCATCGCACGCACTTT 62.188 55.000 0.00 0.00 0.00 2.66
578 582 1.133976 AGTACAGGGAAGGCATCATGC 60.134 52.381 0.00 0.00 44.08 4.06
658 685 1.043116 TGAGATGCGGTTCGATCCCT 61.043 55.000 6.94 0.00 0.00 4.20
671 698 5.529800 TCTCCATGTAACATGCATTGAGATG 59.470 40.000 6.61 0.00 39.00 2.90
754 781 2.158871 TGTGGAGCGTACAAAAAGAGGT 60.159 45.455 0.00 0.00 0.00 3.85
778 805 2.670934 GCTGGACAGGTGCACAGG 60.671 66.667 20.43 12.31 0.00 4.00
779 806 2.111669 TGCTGGACAGGTGCACAG 59.888 61.111 20.43 13.07 0.00 3.66
843 876 1.732941 AAATGACGTTGCCTATGCGA 58.267 45.000 0.00 0.00 41.78 5.10
872 905 6.611613 TGCTATATGTAGAGAAAGGGATGG 57.388 41.667 0.00 0.00 0.00 3.51
877 910 6.753180 TCAGCTTGCTATATGTAGAGAAAGG 58.247 40.000 0.00 0.00 0.00 3.11
952 985 2.238144 AGACGGTAGTGCTCCACTAGTA 59.762 50.000 5.40 0.00 45.88 1.82
963 996 4.010667 AGCTAGATCCTAGACGGTAGTG 57.989 50.000 5.27 0.00 0.00 2.74
1034 1087 1.542375 ACCCACCTCCTCTTGCCAT 60.542 57.895 0.00 0.00 0.00 4.40
1466 1537 0.520404 GTAGTCGTCGACCTGCTTCA 59.480 55.000 21.40 0.00 32.18 3.02
1603 1695 2.418983 GACTTTCCAGTCTCGACGTT 57.581 50.000 0.00 0.00 45.54 3.99
1684 2976 9.424319 CATGCGTTAGTATATTCAAATAGGAGT 57.576 33.333 0.00 0.00 0.00 3.85
1690 3775 7.040478 ACCATGCATGCGTTAGTATATTCAAAT 60.040 33.333 21.69 0.00 0.00 2.32
1696 3781 5.179368 GTCAACCATGCATGCGTTAGTATAT 59.821 40.000 24.10 6.82 0.00 0.86
1810 7533 1.733399 GAAGACGTCGAGTGGGTGC 60.733 63.158 10.46 0.00 0.00 5.01
1906 7629 2.758327 TACAGCTCCACCGCCGAT 60.758 61.111 0.00 0.00 0.00 4.18
2638 8366 0.320374 TCGTTGTCGGAGCTCCAAAT 59.680 50.000 31.67 0.00 37.69 2.32
2761 8489 5.006844 CGTCACTTGTGTACAATTACCACAA 59.993 40.000 0.00 13.09 35.02 3.33
2778 8506 1.007271 CAGAGCGTGACCGTCACTT 60.007 57.895 25.37 15.48 44.85 3.16
2796 8524 2.007608 GTGAAGTTAGGATTGACGGGC 58.992 52.381 0.00 0.00 0.00 6.13
2798 8526 3.000727 GTGGTGAAGTTAGGATTGACGG 58.999 50.000 0.00 0.00 0.00 4.79
2801 8529 4.588899 CCATGTGGTGAAGTTAGGATTGA 58.411 43.478 0.00 0.00 0.00 2.57
2869 8625 1.434188 TGTCCACAGACTGGTTGGAT 58.566 50.000 15.72 0.00 43.91 3.41
2870 8626 1.208706 TTGTCCACAGACTGGTTGGA 58.791 50.000 10.08 10.08 43.91 3.53
2871 8627 1.881973 CATTGTCCACAGACTGGTTGG 59.118 52.381 7.51 6.59 43.91 3.77
2872 8628 2.849942 TCATTGTCCACAGACTGGTTG 58.150 47.619 7.51 0.00 43.91 3.77
2873 8629 3.415212 CATCATTGTCCACAGACTGGTT 58.585 45.455 7.51 0.00 43.91 3.67
2874 8630 2.877300 GCATCATTGTCCACAGACTGGT 60.877 50.000 7.51 0.00 43.91 4.00
2875 8631 1.741706 GCATCATTGTCCACAGACTGG 59.258 52.381 7.51 0.00 43.91 4.00
2891 8650 4.575973 ATGGCTGGCTCCCGCATC 62.576 66.667 2.00 0.00 38.10 3.91
2901 8660 1.039233 GGACATGGTTGGATGGCTGG 61.039 60.000 0.00 0.00 31.31 4.85
2903 8662 0.323725 GTGGACATGGTTGGATGGCT 60.324 55.000 0.00 0.00 31.31 4.75
2931 8690 2.977580 ACCCCCTAAAAGAAAGAGACGT 59.022 45.455 0.00 0.00 0.00 4.34
2937 8696 6.946009 TCAAATAGACACCCCCTAAAAGAAAG 59.054 38.462 0.00 0.00 0.00 2.62
2939 8698 6.243148 GTCAAATAGACACCCCCTAAAAGAA 58.757 40.000 0.00 0.00 46.77 2.52
3067 8826 3.718434 TGGCCTTTCTCCTGATGACATAT 59.282 43.478 3.32 0.00 0.00 1.78
3105 8864 9.088987 ACATATGTTTGAAACTGGGTCTAATTT 57.911 29.630 9.69 0.00 0.00 1.82
3108 8867 7.227873 TCACATATGTTTGAAACTGGGTCTAA 58.772 34.615 5.37 0.00 0.00 2.10
3116 8875 7.445402 AGTTGTAGCTCACATATGTTTGAAACT 59.555 33.333 5.37 7.27 36.90 2.66
3198 8957 2.158842 GCTGTATCTTGATGCCAGACCT 60.159 50.000 12.93 0.00 0.00 3.85
3200 8959 2.158842 AGGCTGTATCTTGATGCCAGAC 60.159 50.000 11.37 10.08 45.42 3.51
3201 8960 2.121948 AGGCTGTATCTTGATGCCAGA 58.878 47.619 11.37 0.00 45.42 3.86
3202 8961 2.634815 AGGCTGTATCTTGATGCCAG 57.365 50.000 11.37 9.29 45.42 4.85
3212 8979 7.012421 CCCAAAAGATTGTAAGTAGGCTGTATC 59.988 40.741 0.00 0.00 34.60 2.24
3265 9032 5.105310 GCAAGTTACCATCAGACTCTAAGGA 60.105 44.000 0.00 0.00 0.00 3.36
3267 9034 5.724328 TGCAAGTTACCATCAGACTCTAAG 58.276 41.667 0.00 0.00 0.00 2.18
3391 9165 8.810652 ATGCGTAAATACACTGAATTGTTTTT 57.189 26.923 0.00 0.00 35.58 1.94
3392 9166 9.900710 TTATGCGTAAATACACTGAATTGTTTT 57.099 25.926 0.00 0.00 0.00 2.43
3393 9167 9.337091 GTTATGCGTAAATACACTGAATTGTTT 57.663 29.630 0.00 0.00 0.00 2.83
3394 9168 8.726988 AGTTATGCGTAAATACACTGAATTGTT 58.273 29.630 0.00 0.00 0.00 2.83
3395 9169 8.263940 AGTTATGCGTAAATACACTGAATTGT 57.736 30.769 0.00 0.00 0.00 2.71
3398 9172 9.373603 TGTAAGTTATGCGTAAATACACTGAAT 57.626 29.630 16.12 0.00 0.00 2.57
3399 9173 8.649841 GTGTAAGTTATGCGTAAATACACTGAA 58.350 33.333 28.29 9.99 39.42 3.02
3400 9174 8.030692 AGTGTAAGTTATGCGTAAATACACTGA 58.969 33.333 32.52 10.89 44.17 3.41
3433 9207 9.109393 GTCATAATGTCACTGTAATAACCACAT 57.891 33.333 0.00 0.00 0.00 3.21
3438 9212 6.982141 TCCGGTCATAATGTCACTGTAATAAC 59.018 38.462 0.00 0.00 0.00 1.89



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

AutoCloner maintained by Alex Coulton.