Multiple sequence alignment - TraesCS4A01G257300

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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 TraesCS4A01G257300 chr4A 100.000 3083 0 0 1 3083 570191999 570188917 0.000000e+00 5694
1 TraesCS4A01G257300 chr4D 90.682 2082 106 34 62 2115 32415151 32417172 0.000000e+00 2689
2 TraesCS4A01G257300 chr4D 86.750 1034 95 16 2075 3079 32432043 32433063 0.000000e+00 1112
3 TraesCS4A01G257300 chr4D 85.819 818 95 11 2208 3006 32417189 32418004 0.000000e+00 848
4 TraesCS4A01G257300 chr4B 89.916 2033 142 22 996 3006 47043628 47045619 0.000000e+00 2560
5 TraesCS4A01G257300 chr4B 84.571 175 16 4 399 570 47042944 47043110 2.460000e-36 163


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 TraesCS4A01G257300 chr4A 570188917 570191999 3082 True 5694.0 5694 100.0000 1 3083 1 chr4A.!!$R1 3082
1 TraesCS4A01G257300 chr4D 32415151 32418004 2853 False 1768.5 2689 88.2505 62 3006 2 chr4D.!!$F2 2944
2 TraesCS4A01G257300 chr4D 32432043 32433063 1020 False 1112.0 1112 86.7500 2075 3079 1 chr4D.!!$F1 1004
3 TraesCS4A01G257300 chr4B 47042944 47045619 2675 False 1361.5 2560 87.2435 399 3006 2 chr4B.!!$F1 2607

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
105 106 0.388520 GTCCCGCCAGACAAATTTGC 60.389 55.0 18.12 10.76 36.73 3.68 F
107 108 0.667184 CCCGCCAGACAAATTTGCAC 60.667 55.0 18.12 12.18 0.00 4.57 F
1630 1821 0.875908 CTGCATATCCCACGACCACG 60.876 60.0 0.00 0.00 45.75 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1871 0.394762 GCATGTTCCTGATCCAGCCA 60.395 55.0 0.00 0.00 0.00 4.75 R
1764 1955 0.882042 CGCAGAACAGCTGGTTGTCT 60.882 55.0 19.93 11.75 45.03 3.41 R
3013 3245 0.611714 ATGGACCGACGCCTTACTTT 59.388 50.0 0.00 0.00 0.00 2.66 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
50 51 4.717629 CCCGCTCGCTGTCGTTGA 62.718 66.667 0.00 0.00 36.96 3.18
51 52 3.175240 CCGCTCGCTGTCGTTGAG 61.175 66.667 0.00 0.00 36.96 3.02
54 55 3.150895 CTCGCTGTCGTTGAGCAC 58.849 61.111 0.00 0.00 36.12 4.40
55 56 2.355837 TCGCTGTCGTTGAGCACC 60.356 61.111 0.00 0.00 36.12 5.01
56 57 3.767230 CGCTGTCGTTGAGCACCG 61.767 66.667 0.00 0.00 36.12 4.94
57 58 2.661866 GCTGTCGTTGAGCACCGT 60.662 61.111 0.00 0.00 36.40 4.83
58 59 2.658707 GCTGTCGTTGAGCACCGTC 61.659 63.158 0.00 0.00 36.40 4.79
59 60 2.022129 CTGTCGTTGAGCACCGTCC 61.022 63.158 0.00 0.00 0.00 4.79
60 61 2.338984 GTCGTTGAGCACCGTCCT 59.661 61.111 0.00 0.00 0.00 3.85
61 62 1.300697 GTCGTTGAGCACCGTCCTT 60.301 57.895 0.00 0.00 0.00 3.36
62 63 1.006571 TCGTTGAGCACCGTCCTTC 60.007 57.895 0.00 0.00 0.00 3.46
63 64 2.027625 CGTTGAGCACCGTCCTTCC 61.028 63.158 0.00 0.00 0.00 3.46
64 65 1.070786 GTTGAGCACCGTCCTTCCA 59.929 57.895 0.00 0.00 0.00 3.53
67 68 1.191489 TGAGCACCGTCCTTCCATGA 61.191 55.000 0.00 0.00 0.00 3.07
72 73 1.065491 CACCGTCCTTCCATGATTCCA 60.065 52.381 0.00 0.00 0.00 3.53
73 74 1.210478 ACCGTCCTTCCATGATTCCAG 59.790 52.381 0.00 0.00 0.00 3.86
89 90 4.115199 AGCATTCCGGGCCTGTCC 62.115 66.667 11.58 0.00 0.00 4.02
105 106 0.388520 GTCCCGCCAGACAAATTTGC 60.389 55.000 18.12 10.76 36.73 3.68
106 107 0.825425 TCCCGCCAGACAAATTTGCA 60.825 50.000 18.12 0.00 0.00 4.08
107 108 0.667184 CCCGCCAGACAAATTTGCAC 60.667 55.000 18.12 12.18 0.00 4.57
116 117 3.821033 AGACAAATTTGCACTACCAGGAC 59.179 43.478 18.12 0.00 0.00 3.85
125 126 2.422597 CACTACCAGGACGCAAATTCA 58.577 47.619 0.00 0.00 0.00 2.57
127 128 2.224426 ACTACCAGGACGCAAATTCACA 60.224 45.455 0.00 0.00 0.00 3.58
128 129 1.686355 ACCAGGACGCAAATTCACAA 58.314 45.000 0.00 0.00 0.00 3.33
129 130 2.028130 ACCAGGACGCAAATTCACAAA 58.972 42.857 0.00 0.00 0.00 2.83
155 156 4.792704 GCTTCGCTTGTCAGATTCCAAAAA 60.793 41.667 0.00 0.00 0.00 1.94
232 233 1.693627 TAGACTCGATCCAAGAGGGC 58.306 55.000 0.00 0.00 39.90 5.19
248 249 4.436998 GCGTGGAGTGTAGCGCCT 62.437 66.667 2.29 0.00 43.52 5.52
249 250 2.507102 CGTGGAGTGTAGCGCCTG 60.507 66.667 2.29 0.00 37.96 4.85
250 251 2.125512 GTGGAGTGTAGCGCCTGG 60.126 66.667 2.29 0.00 37.96 4.45
251 252 4.082523 TGGAGTGTAGCGCCTGGC 62.083 66.667 9.11 9.11 44.05 4.85
284 285 2.632136 TTTGTGGTCGCTTCGGTCGT 62.632 55.000 0.00 0.00 0.00 4.34
293 304 3.407046 CTTCGGTCGTACTCCCGGC 62.407 68.421 16.91 0.00 44.32 6.13
310 321 4.680237 CCGAAGCGCCCACAGTGA 62.680 66.667 2.29 0.00 0.00 3.41
311 322 3.414700 CGAAGCGCCCACAGTGAC 61.415 66.667 2.29 0.00 0.00 3.67
312 323 3.414700 GAAGCGCCCACAGTGACG 61.415 66.667 2.29 6.85 0.00 4.35
313 324 3.858868 GAAGCGCCCACAGTGACGA 62.859 63.158 17.21 0.00 0.00 4.20
314 325 3.240134 AAGCGCCCACAGTGACGAT 62.240 57.895 17.21 9.89 0.00 3.73
315 326 1.884075 AAGCGCCCACAGTGACGATA 61.884 55.000 17.21 0.00 0.00 2.92
316 327 1.227263 GCGCCCACAGTGACGATAT 60.227 57.895 17.21 0.00 0.00 1.63
317 328 1.215655 GCGCCCACAGTGACGATATC 61.216 60.000 17.21 0.00 0.00 1.63
342 362 1.282930 GGACGAAACGAGGTGAGCAC 61.283 60.000 0.00 0.00 0.00 4.40
346 366 1.618640 GAAACGAGGTGAGCACGAGC 61.619 60.000 8.67 0.00 42.56 5.03
463 486 1.661197 GGCGTTGTGTTCGGTCGTA 60.661 57.895 0.00 0.00 0.00 3.43
464 487 1.010419 GGCGTTGTGTTCGGTCGTAT 61.010 55.000 0.00 0.00 0.00 3.06
465 488 1.616620 GCGTTGTGTTCGGTCGTATA 58.383 50.000 0.00 0.00 0.00 1.47
525 548 0.945265 TACGCTTGTACGGCACCAAC 60.945 55.000 10.46 0.00 37.37 3.77
641 699 4.144297 CTGGTGGTCAATGAGGAAAAAGA 58.856 43.478 0.00 0.00 0.00 2.52
642 700 4.739793 TGGTGGTCAATGAGGAAAAAGAT 58.260 39.130 0.00 0.00 0.00 2.40
643 701 4.523943 TGGTGGTCAATGAGGAAAAAGATG 59.476 41.667 0.00 0.00 0.00 2.90
646 704 5.710099 GTGGTCAATGAGGAAAAAGATGGTA 59.290 40.000 0.00 0.00 0.00 3.25
647 705 5.945784 TGGTCAATGAGGAAAAAGATGGTAG 59.054 40.000 0.00 0.00 0.00 3.18
648 706 5.163612 GGTCAATGAGGAAAAAGATGGTAGC 60.164 44.000 0.00 0.00 0.00 3.58
650 708 6.009589 TCAATGAGGAAAAAGATGGTAGCAA 58.990 36.000 0.00 0.00 0.00 3.91
682 772 3.494573 GGGTATCCCCGCAAAAACAAAAA 60.495 43.478 0.00 0.00 42.41 1.94
683 773 3.743911 GGTATCCCCGCAAAAACAAAAAG 59.256 43.478 0.00 0.00 0.00 2.27
685 775 1.134371 TCCCCGCAAAAACAAAAAGGG 60.134 47.619 0.00 0.00 37.20 3.95
849 989 2.419324 ACTGAACTCCTCGATACACGAC 59.581 50.000 0.00 0.00 46.45 4.34
861 1001 1.588824 TACACGACGCGAGGGAATGT 61.589 55.000 15.93 10.56 0.00 2.71
862 1002 1.138036 CACGACGCGAGGGAATGTA 59.862 57.895 15.93 0.00 0.00 2.29
863 1003 1.138047 CACGACGCGAGGGAATGTAC 61.138 60.000 15.93 0.00 0.00 2.90
953 1129 0.963962 TCGAAACCGGCTTCTACTGT 59.036 50.000 15.30 0.00 0.00 3.55
960 1136 1.139095 GGCTTCTACTGTCCGGACG 59.861 63.158 28.70 23.92 0.00 4.79
961 1137 1.516603 GCTTCTACTGTCCGGACGC 60.517 63.158 28.70 19.77 0.00 5.19
1103 1294 1.882623 CTTCCACCCAAAGAAGCAGAC 59.117 52.381 0.00 0.00 33.64 3.51
1116 1307 2.350895 CAGACCGGATGCCCAACA 59.649 61.111 9.46 0.00 0.00 3.33
1152 1343 4.704833 GCCGAGCTGCCTGAACCA 62.705 66.667 0.00 0.00 0.00 3.67
1304 1495 2.874780 GCTGTACGACGTCTGCGG 60.875 66.667 14.70 10.23 43.45 5.69
1401 1592 4.899239 CTCATCGAGGCGTGCCCC 62.899 72.222 7.39 0.00 36.58 5.80
1431 1622 2.111878 CCCGATCAGCCCCATCAC 59.888 66.667 0.00 0.00 0.00 3.06
1450 1641 3.130160 GCAGCTTCAAGGCCCTCG 61.130 66.667 0.00 0.00 0.00 4.63
1531 1722 3.449227 CGCCTCCCTACGTGCAGA 61.449 66.667 0.00 0.00 0.00 4.26
1552 1743 1.810030 CCCGGCTACGAACTCAAGC 60.810 63.158 0.00 0.00 44.60 4.01
1553 1744 2.158959 CCGGCTACGAACTCAAGCG 61.159 63.158 0.00 0.00 44.60 4.68
1614 1805 3.188786 GTCGGCGACACCATCTGC 61.189 66.667 33.07 3.71 39.03 4.26
1619 1810 1.151668 GGCGACACCATCTGCATATC 58.848 55.000 0.00 0.00 38.86 1.63
1630 1821 0.875908 CTGCATATCCCACGACCACG 60.876 60.000 0.00 0.00 45.75 4.94
1634 1825 2.201732 CATATCCCACGACCACGAAAG 58.798 52.381 0.00 0.00 42.66 2.62
1640 1831 1.594293 ACGACCACGAAAGCACCTG 60.594 57.895 0.00 0.00 42.66 4.00
1672 1863 4.577246 CTAGCCGCGAGTGGAGCC 62.577 72.222 8.23 0.00 0.00 4.70
1701 1892 1.141657 GGCTGGATCAGGAACATGCTA 59.858 52.381 0.00 0.00 31.21 3.49
1764 1955 0.181587 TCCGCTTTGTTTCCAGTGGA 59.818 50.000 8.12 8.12 45.59 4.02
1789 1980 3.684990 AGCTGTTCTGCGCCTCGA 61.685 61.111 4.18 0.00 38.13 4.04
1854 2045 2.508586 AAGAAGAAGCGCCCGAGGAC 62.509 60.000 2.29 0.00 0.00 3.85
1941 2132 4.351054 CTGGGCTCCGGCAGGTTT 62.351 66.667 1.81 0.00 40.87 3.27
1982 2173 4.016706 CGCGGGGGAGAGGTTTGT 62.017 66.667 0.00 0.00 0.00 2.83
2058 2249 0.319083 TGCGGTACAACTTGGACGAT 59.681 50.000 0.00 0.00 29.95 3.73
2091 2282 5.485708 CCAATGGGTATTTTAGGGGTTGAAA 59.514 40.000 0.00 0.00 0.00 2.69
2092 2283 6.013293 CCAATGGGTATTTTAGGGGTTGAAAA 60.013 38.462 0.00 0.00 0.00 2.29
2093 2284 7.454225 CAATGGGTATTTTAGGGGTTGAAAAA 58.546 34.615 0.00 0.00 0.00 1.94
2109 2300 3.854240 TGAAAAACAACGTACGTGTCGTA 59.146 39.130 23.57 1.73 41.54 3.43
2273 2479 5.300752 ACATCCATCTCAATTAAGTAGGCG 58.699 41.667 0.00 0.00 0.00 5.52
2281 2496 6.694447 TCTCAATTAAGTAGGCGTAAAGTGT 58.306 36.000 0.00 0.00 0.00 3.55
2324 2542 9.912634 TTTAGTTCTTAGGATTTTTCTTGCATG 57.087 29.630 0.00 0.00 0.00 4.06
2340 2558 1.539388 GCATGGGTCGTTTGATTCACA 59.461 47.619 0.00 0.00 0.00 3.58
2413 2631 7.281040 TCCATCCTAAAATGCAAGATCATTC 57.719 36.000 0.00 0.00 35.77 2.67
2454 2680 1.541588 GGAACAGATGGAGTGGCAAAC 59.458 52.381 0.00 0.00 0.00 2.93
2469 2696 8.872845 GGAGTGGCAAACATCATTTTTATTTAG 58.127 33.333 0.00 0.00 0.00 1.85
2502 2729 7.761651 ACTGCAATTTCTTTGTTCTTTCTTC 57.238 32.000 0.00 0.00 37.65 2.87
2533 2761 5.290885 GTCCAAAACAATTGCTTCGTTCTTT 59.709 36.000 5.05 0.00 0.00 2.52
2543 2771 6.621316 TTGCTTCGTTCTTTTTGTGGTATA 57.379 33.333 0.00 0.00 0.00 1.47
2649 2877 5.415366 CATTCGTTTCGTCGATATGTTCAG 58.585 41.667 0.00 0.00 39.57 3.02
2671 2899 3.857157 TTGTAGTCAAGGTCAAGGCTT 57.143 42.857 0.00 0.00 0.00 4.35
2698 2926 5.947228 TCTTGGTCATTTTAGACTGCAAG 57.053 39.130 0.00 0.00 38.26 4.01
2788 3019 2.039879 GGGGAATAAGTGGTATGCGGAT 59.960 50.000 0.00 0.00 0.00 4.18
2799 3031 3.008594 TGGTATGCGGATATTACCAAGGG 59.991 47.826 7.50 0.00 37.81 3.95
2804 3036 2.925724 CGGATATTACCAAGGGTTGCA 58.074 47.619 0.00 0.00 37.09 4.08
2820 3052 3.780925 GCATGAAGCACCACTTGAC 57.219 52.632 0.00 0.00 44.79 3.18
2869 3101 3.210857 GCCTATAATGCGAAGGCGA 57.789 52.632 0.00 0.00 45.82 5.54
2888 3120 3.308323 GCGATTGAGCTCTTTAAGGACAG 59.692 47.826 16.19 0.00 0.00 3.51
2903 3135 3.908737 ACAGGGCGTGTCTTAACTC 57.091 52.632 7.07 0.00 31.90 3.01
3013 3245 0.105760 ATGCAACACTTCAACCCCCA 60.106 50.000 0.00 0.00 0.00 4.96
3024 3256 0.538746 CAACCCCCAAAGTAAGGCGT 60.539 55.000 0.00 0.00 0.00 5.68
3026 3258 1.743995 CCCCCAAAGTAAGGCGTCG 60.744 63.158 0.00 0.00 0.00 5.12
3041 3273 1.391933 CGTCGGTCCATGGATCCTCA 61.392 60.000 19.62 7.60 0.00 3.86
3042 3274 0.830648 GTCGGTCCATGGATCCTCAA 59.169 55.000 19.62 6.76 0.00 3.02
3046 3278 1.202580 GGTCCATGGATCCTCAAGTCG 60.203 57.143 19.62 0.00 0.00 4.18
3054 3286 2.480416 GGATCCTCAAGTCGTGTAGCTG 60.480 54.545 3.84 0.00 0.00 4.24
3059 3291 1.684450 TCAAGTCGTGTAGCTGGACAA 59.316 47.619 0.00 0.00 33.18 3.18
3066 3298 3.951680 TCGTGTAGCTGGACAAGATGATA 59.048 43.478 0.00 0.00 33.65 2.15
3079 3311 5.595885 ACAAGATGATACTCATGACCTTCG 58.404 41.667 0.00 0.00 37.20 3.79
3080 3312 5.360999 ACAAGATGATACTCATGACCTTCGA 59.639 40.000 0.00 0.00 37.20 3.71
3081 3313 6.127338 ACAAGATGATACTCATGACCTTCGAA 60.127 38.462 0.00 0.00 37.20 3.71
3082 3314 6.083098 AGATGATACTCATGACCTTCGAAG 57.917 41.667 18.51 18.51 37.20 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.717629 TCAACGACAGCGAGCGGG 62.718 66.667 0.00 0.00 41.64 6.13
34 35 3.175240 CTCAACGACAGCGAGCGG 61.175 66.667 0.00 0.00 41.64 5.52
35 36 3.832171 GCTCAACGACAGCGAGCG 61.832 66.667 0.00 0.00 42.42 5.03
37 38 2.375766 GGTGCTCAACGACAGCGAG 61.376 63.158 0.00 0.00 40.01 5.03
38 39 2.355837 GGTGCTCAACGACAGCGA 60.356 61.111 0.00 0.00 40.01 4.93
40 41 2.658707 GACGGTGCTCAACGACAGC 61.659 63.158 14.69 0.00 45.97 4.40
41 42 2.022129 GGACGGTGCTCAACGACAG 61.022 63.158 14.69 0.00 45.97 3.51
42 43 2.023414 AAGGACGGTGCTCAACGACA 62.023 55.000 14.69 0.00 45.97 4.35
43 44 1.282930 GAAGGACGGTGCTCAACGAC 61.283 60.000 14.69 7.78 45.97 4.34
44 45 1.006571 GAAGGACGGTGCTCAACGA 60.007 57.895 14.69 0.00 45.97 3.85
46 47 0.321653 ATGGAAGGACGGTGCTCAAC 60.322 55.000 1.62 0.00 0.00 3.18
47 48 0.321564 CATGGAAGGACGGTGCTCAA 60.322 55.000 1.62 0.00 0.00 3.02
48 49 1.191489 TCATGGAAGGACGGTGCTCA 61.191 55.000 1.62 0.00 0.00 4.26
49 50 0.179000 ATCATGGAAGGACGGTGCTC 59.821 55.000 1.62 0.00 0.00 4.26
50 51 0.620556 AATCATGGAAGGACGGTGCT 59.379 50.000 0.00 0.00 0.00 4.40
51 52 1.017387 GAATCATGGAAGGACGGTGC 58.983 55.000 0.00 0.00 0.00 5.01
52 53 1.065491 TGGAATCATGGAAGGACGGTG 60.065 52.381 0.00 0.00 0.00 4.94
53 54 1.210478 CTGGAATCATGGAAGGACGGT 59.790 52.381 0.00 0.00 0.00 4.83
54 55 1.959042 CTGGAATCATGGAAGGACGG 58.041 55.000 0.00 0.00 0.00 4.79
55 56 1.303309 GCTGGAATCATGGAAGGACG 58.697 55.000 0.00 0.00 0.00 4.79
56 57 2.425143 TGCTGGAATCATGGAAGGAC 57.575 50.000 0.00 0.00 0.00 3.85
57 58 3.559069 GAATGCTGGAATCATGGAAGGA 58.441 45.455 0.00 0.00 0.00 3.36
58 59 2.626743 GGAATGCTGGAATCATGGAAGG 59.373 50.000 0.00 0.00 0.00 3.46
59 60 2.292569 CGGAATGCTGGAATCATGGAAG 59.707 50.000 0.00 0.00 0.00 3.46
60 61 2.300433 CGGAATGCTGGAATCATGGAA 58.700 47.619 0.00 0.00 0.00 3.53
61 62 1.477377 CCGGAATGCTGGAATCATGGA 60.477 52.381 0.00 0.00 43.76 3.41
62 63 0.956633 CCGGAATGCTGGAATCATGG 59.043 55.000 0.00 0.00 43.76 3.66
63 64 0.956633 CCCGGAATGCTGGAATCATG 59.043 55.000 0.73 0.00 43.76 3.07
64 65 0.825010 GCCCGGAATGCTGGAATCAT 60.825 55.000 0.73 0.00 43.76 2.45
67 68 2.123726 GGCCCGGAATGCTGGAAT 60.124 61.111 0.73 0.00 43.76 3.01
72 73 4.115199 GGACAGGCCCGGAATGCT 62.115 66.667 0.73 0.00 0.00 3.79
89 90 0.314935 AGTGCAAATTTGTCTGGCGG 59.685 50.000 19.03 0.00 0.00 6.13
90 91 2.584791 GTAGTGCAAATTTGTCTGGCG 58.415 47.619 19.03 0.00 0.00 5.69
105 106 2.159627 GTGAATTTGCGTCCTGGTAGTG 59.840 50.000 0.00 0.00 0.00 2.74
106 107 2.224426 TGTGAATTTGCGTCCTGGTAGT 60.224 45.455 0.00 0.00 0.00 2.73
107 108 2.422597 TGTGAATTTGCGTCCTGGTAG 58.577 47.619 0.00 0.00 0.00 3.18
116 117 2.025571 CGAAGCGATTTGTGAATTTGCG 59.974 45.455 0.00 0.00 34.22 4.85
185 186 4.947147 ACAACGGGTGGCGCATGT 62.947 61.111 10.83 0.00 0.00 3.21
232 233 2.507102 CAGGCGCTACACTCCACG 60.507 66.667 7.64 0.00 0.00 4.94
253 254 4.368808 CACAAACAGCGACGCCCG 62.369 66.667 17.79 10.94 42.21 6.13
254 255 4.025401 CCACAAACAGCGACGCCC 62.025 66.667 17.79 0.00 0.00 6.13
255 256 3.236618 GACCACAAACAGCGACGCC 62.237 63.158 17.79 0.00 0.00 5.68
293 304 4.680237 TCACTGTGGGCGCTTCGG 62.680 66.667 7.64 5.83 0.00 4.30
319 330 0.886043 TCACCTCGTTTCGTCCTCGA 60.886 55.000 0.00 0.00 44.66 4.04
359 379 4.933064 GATCGTCCTCGCTGGCCG 62.933 72.222 0.00 0.00 38.75 6.13
360 380 4.933064 CGATCGTCCTCGCTGGCC 62.933 72.222 7.03 0.00 36.96 5.36
364 384 0.029567 GTTGATCGATCGTCCTCGCT 59.970 55.000 20.03 0.00 38.52 4.93
367 387 2.398498 CATGGTTGATCGATCGTCCTC 58.602 52.381 27.12 11.00 0.00 3.71
396 416 2.240667 ACTCCAAAGTAGAGCCATGCAT 59.759 45.455 0.00 0.00 34.56 3.96
397 417 1.630369 ACTCCAAAGTAGAGCCATGCA 59.370 47.619 0.00 0.00 34.56 3.96
445 468 1.010419 ATACGACCGAACACAACGCC 61.010 55.000 0.00 0.00 0.00 5.68
449 472 3.233684 TGCATATACGACCGAACACAA 57.766 42.857 0.00 0.00 0.00 3.33
453 476 2.542178 TGCATTGCATATACGACCGAAC 59.458 45.455 7.38 0.00 31.71 3.95
570 593 0.385473 CGTGATCACACAAAACCCGC 60.385 55.000 24.93 0.00 46.20 6.13
665 755 1.134371 CCCTTTTTGTTTTTGCGGGGA 60.134 47.619 0.00 0.00 34.94 4.81
666 756 1.304254 CCCTTTTTGTTTTTGCGGGG 58.696 50.000 0.00 0.00 0.00 5.73
703 793 8.211629 ACTACCATATTTTTCTACCTTAGCCTG 58.788 37.037 0.00 0.00 0.00 4.85
849 989 0.379669 ACGTAGTACATTCCCTCGCG 59.620 55.000 0.00 0.00 41.94 5.87
861 1001 1.246649 TCCTTGCGGTTCACGTAGTA 58.753 50.000 0.00 0.00 41.61 1.82
863 1003 1.722011 ATTCCTTGCGGTTCACGTAG 58.278 50.000 0.00 0.00 46.52 3.51
1298 1489 2.281484 GCACCTTGTTCCCGCAGA 60.281 61.111 0.00 0.00 0.00 4.26
1304 1495 1.600916 AAGGAGCGCACCTTGTTCC 60.601 57.895 34.05 18.90 46.85 3.62
1431 1622 2.035312 AGGGCCTTGAAGCTGCAG 59.965 61.111 10.11 10.11 0.00 4.41
1528 1719 1.447314 GTTCGTAGCCGGGGTTCTG 60.447 63.158 3.09 0.00 33.95 3.02
1531 1722 1.474332 TTGAGTTCGTAGCCGGGGTT 61.474 55.000 3.09 0.00 33.95 4.11
1607 1798 1.609061 GGTCGTGGGATATGCAGATGG 60.609 57.143 0.00 0.00 0.00 3.51
1614 1805 2.201732 CTTTCGTGGTCGTGGGATATG 58.798 52.381 0.00 0.00 38.33 1.78
1619 1810 2.280524 TGCTTTCGTGGTCGTGGG 60.281 61.111 0.00 0.00 38.33 4.61
1634 1825 2.029844 GTGTCGAAGGAGCAGGTGC 61.030 63.158 0.00 0.00 42.49 5.01
1640 1831 0.523757 GCTAGTCGTGTCGAAGGAGC 60.524 60.000 0.00 0.30 37.72 4.70
1680 1871 0.394762 GCATGTTCCTGATCCAGCCA 60.395 55.000 0.00 0.00 0.00 4.75
1684 1875 1.141657 GCCTAGCATGTTCCTGATCCA 59.858 52.381 0.00 0.00 0.00 3.41
1690 1881 2.190578 GCGGCCTAGCATGTTCCT 59.809 61.111 0.00 0.00 37.05 3.36
1764 1955 0.882042 CGCAGAACAGCTGGTTGTCT 60.882 55.000 19.93 11.75 45.03 3.41
1815 2006 2.256764 CAGACGCTGTCGCTGTCT 59.743 61.111 0.00 0.00 44.65 3.41
1941 2132 1.787057 CGTAAAACCTGGCGGTGCAA 61.787 55.000 0.00 0.00 44.73 4.08
2058 2249 1.344953 ATACCCATTGGAGCGGCTCA 61.345 55.000 29.33 12.23 34.81 4.26
2109 2300 5.936956 CAGCTCTCATGGTCTTAAGAAAAGT 59.063 40.000 6.78 0.00 0.00 2.66
2211 2417 8.682936 AATAATGAGATACACCATCTGTTTCC 57.317 34.615 0.00 0.00 44.41 3.13
2222 2428 8.480853 GTTGACGAGCTAAATAATGAGATACAC 58.519 37.037 0.00 0.00 0.00 2.90
2273 2479 9.797556 AAATCCTCAACAAAACTAACACTTTAC 57.202 29.630 0.00 0.00 0.00 2.01
2322 2540 1.812571 GCTGTGAATCAAACGACCCAT 59.187 47.619 0.00 0.00 0.00 4.00
2324 2542 1.523758 AGCTGTGAATCAAACGACCC 58.476 50.000 0.00 0.00 0.00 4.46
2413 2631 3.916172 CCAAAATGCAAGATCGTGTCAAG 59.084 43.478 10.41 2.41 0.00 3.02
2469 2696 7.617041 ACAAAGAAATTGCAGTATAGAGGTC 57.383 36.000 0.00 0.00 43.13 3.85
2487 2714 7.039363 TGGACAAAAAGGAAGAAAGAACAAAGA 60.039 33.333 0.00 0.00 0.00 2.52
2533 2761 9.562408 TGTCAAGTACTTTTGATATACCACAAA 57.438 29.630 5.07 0.00 39.13 2.83
2602 2830 3.491342 TGCAAACAAACATGTAGGGCTA 58.509 40.909 0.00 0.00 0.00 3.93
2649 2877 3.477530 AGCCTTGACCTTGACTACAAAC 58.522 45.455 0.00 0.00 35.49 2.93
2677 2905 5.695851 ACTTGCAGTCTAAAATGACCAAG 57.304 39.130 0.00 0.00 39.67 3.61
2707 2936 7.882791 TGTGATGATGACATTACCTAACAAGTT 59.117 33.333 0.00 0.00 40.68 2.66
2788 3019 3.699038 GCTTCATGCAACCCTTGGTAATA 59.301 43.478 0.00 0.00 42.31 0.98
2804 3036 1.568612 CGCGTCAAGTGGTGCTTCAT 61.569 55.000 0.00 0.00 34.69 2.57
2869 3101 3.623453 GCCCTGTCCTTAAAGAGCTCAAT 60.623 47.826 17.77 6.50 0.00 2.57
2903 3135 1.609501 TTGTCTCGGTCCTCAGGGG 60.610 63.158 0.00 0.00 0.00 4.79
2938 3170 1.412710 GCATATCCTCGTGTCCTTCCA 59.587 52.381 0.00 0.00 0.00 3.53
2939 3171 1.689273 AGCATATCCTCGTGTCCTTCC 59.311 52.381 0.00 0.00 0.00 3.46
2987 3219 3.316308 GGTTGAAGTGTTGCATCTTGACT 59.684 43.478 4.47 0.00 0.00 3.41
3013 3245 0.611714 ATGGACCGACGCCTTACTTT 59.388 50.000 0.00 0.00 0.00 2.66
3024 3256 1.123077 CTTGAGGATCCATGGACCGA 58.877 55.000 18.99 9.81 0.00 4.69
3026 3258 1.202580 CGACTTGAGGATCCATGGACC 60.203 57.143 18.99 19.61 0.00 4.46
3041 3273 1.961394 TCTTGTCCAGCTACACGACTT 59.039 47.619 0.00 0.00 0.00 3.01
3042 3274 1.617322 TCTTGTCCAGCTACACGACT 58.383 50.000 0.00 0.00 0.00 4.18
3046 3278 5.163509 TGAGTATCATCTTGTCCAGCTACAC 60.164 44.000 0.00 0.00 42.56 2.90


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

AutoCloner maintained by Alex Coulton.