Multiple sequence alignment - TraesCS4A01G042800

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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 TraesCS4A01G042800 chr4A 100.000 3211 0 0 1 3211 36004373 36001163 0.000000e+00 5930
1 TraesCS4A01G042800 chr3B 96.906 3070 78 7 144 3211 452563152 452560098 0.000000e+00 5127
2 TraesCS4A01G042800 chr3B 96.579 3069 93 5 144 3211 73031281 73034338 0.000000e+00 5075
3 TraesCS4A01G042800 chr1A 96.808 3070 94 4 142 3209 444169077 444166010 0.000000e+00 5123
4 TraesCS4A01G042800 chr2B 96.158 3071 104 6 144 3211 553880197 553883256 0.000000e+00 5005
5 TraesCS4A01G042800 chr4B 96.025 3069 108 9 144 3211 629907329 629910384 0.000000e+00 4979
6 TraesCS4A01G042800 chr4B 95.801 3072 100 8 144 3211 665900183 665903229 0.000000e+00 4931
7 TraesCS4A01G042800 chr5A 95.295 2083 71 6 1129 3211 262471612 262469557 0.000000e+00 3278
8 TraesCS4A01G042800 chr5A 95.937 1969 56 4 144 2112 705867911 705869855 0.000000e+00 3171
9 TraesCS4A01G042800 chr5A 96.196 1104 42 0 2108 3211 705883335 705884438 0.000000e+00 1807
10 TraesCS4A01G042800 chr5A 91.840 723 33 3 144 840 310728835 310728113 0.000000e+00 985
11 TraesCS4A01G042800 chr2A 95.328 2076 70 6 1129 3204 694743563 694741515 0.000000e+00 3271
12 TraesCS4A01G042800 chr2A 97.895 285 6 0 847 1131 694743889 694743605 8.000000e-136 494
13 TraesCS4A01G042800 chr5D 96.454 987 34 1 2225 3211 309068222 309067237 0.000000e+00 1628
14 TraesCS4A01G042800 chr1D 96.353 987 36 0 2225 3211 97785404 97784418 0.000000e+00 1624
15 TraesCS4A01G042800 chr7A 94.460 704 35 4 140 840 699627694 699626992 0.000000e+00 1081
16 TraesCS4A01G042800 chr7A 97.880 283 6 0 849 1131 709138062 709137780 1.040000e-134 490


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 TraesCS4A01G042800 chr4A 36001163 36004373 3210 True 5930.0 5930 100.0000 1 3211 1 chr4A.!!$R1 3210
1 TraesCS4A01G042800 chr3B 452560098 452563152 3054 True 5127.0 5127 96.9060 144 3211 1 chr3B.!!$R1 3067
2 TraesCS4A01G042800 chr3B 73031281 73034338 3057 False 5075.0 5075 96.5790 144 3211 1 chr3B.!!$F1 3067
3 TraesCS4A01G042800 chr1A 444166010 444169077 3067 True 5123.0 5123 96.8080 142 3209 1 chr1A.!!$R1 3067
4 TraesCS4A01G042800 chr2B 553880197 553883256 3059 False 5005.0 5005 96.1580 144 3211 1 chr2B.!!$F1 3067
5 TraesCS4A01G042800 chr4B 629907329 629910384 3055 False 4979.0 4979 96.0250 144 3211 1 chr4B.!!$F1 3067
6 TraesCS4A01G042800 chr4B 665900183 665903229 3046 False 4931.0 4931 95.8010 144 3211 1 chr4B.!!$F2 3067
7 TraesCS4A01G042800 chr5A 262469557 262471612 2055 True 3278.0 3278 95.2950 1129 3211 1 chr5A.!!$R1 2082
8 TraesCS4A01G042800 chr5A 705867911 705869855 1944 False 3171.0 3171 95.9370 144 2112 1 chr5A.!!$F1 1968
9 TraesCS4A01G042800 chr5A 705883335 705884438 1103 False 1807.0 1807 96.1960 2108 3211 1 chr5A.!!$F2 1103
10 TraesCS4A01G042800 chr5A 310728113 310728835 722 True 985.0 985 91.8400 144 840 1 chr5A.!!$R2 696
11 TraesCS4A01G042800 chr2A 694741515 694743889 2374 True 1882.5 3271 96.6115 847 3204 2 chr2A.!!$R1 2357
12 TraesCS4A01G042800 chr5D 309067237 309068222 985 True 1628.0 1628 96.4540 2225 3211 1 chr5D.!!$R1 986
13 TraesCS4A01G042800 chr1D 97784418 97785404 986 True 1624.0 1624 96.3530 2225 3211 1 chr1D.!!$R1 986
14 TraesCS4A01G042800 chr7A 699626992 699627694 702 True 1081.0 1081 94.4600 140 840 1 chr7A.!!$R1 700

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
760 791 0.178929 ACCTCTTCCTCCTCCGTTGT 60.179 55.000 0.0 0.0 0.0 3.32 F
1038 1069 1.388133 GGCCTTCACCCCCAAGAAT 59.612 57.895 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1760 0.179004 TGGCGACAAGAACACCCAAT 60.179 50.0 0.0 0.0 37.44 3.16 R
2362 2442 0.893727 ACCAAGGATCCGTTTGGCAC 60.894 55.0 25.6 0.0 46.16 5.01 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
58 59 3.932545 TTTTGGCAACGAATGTATGCT 57.067 38.095 0.00 0.00 40.49 3.79
59 60 3.485947 TTTGGCAACGAATGTATGCTC 57.514 42.857 0.00 0.00 39.94 4.26
60 61 2.401583 TGGCAACGAATGTATGCTCT 57.598 45.000 0.00 0.00 39.94 4.09
61 62 3.535280 TGGCAACGAATGTATGCTCTA 57.465 42.857 0.00 0.00 39.94 2.43
62 63 3.194861 TGGCAACGAATGTATGCTCTAC 58.805 45.455 0.00 0.00 39.94 2.59
63 64 3.118775 TGGCAACGAATGTATGCTCTACT 60.119 43.478 0.00 0.00 39.94 2.57
64 65 3.871594 GGCAACGAATGTATGCTCTACTT 59.128 43.478 0.00 0.00 39.94 2.24
65 66 4.332819 GGCAACGAATGTATGCTCTACTTT 59.667 41.667 0.00 0.00 39.94 2.66
66 67 5.493735 GCAACGAATGTATGCTCTACTTTC 58.506 41.667 0.00 11.94 37.12 2.62
67 68 5.502544 GCAACGAATGTATGCTCTACTTTCC 60.503 44.000 14.32 3.89 37.12 3.13
68 69 5.599999 ACGAATGTATGCTCTACTTTCCT 57.400 39.130 14.32 6.07 31.73 3.36
69 70 6.710597 ACGAATGTATGCTCTACTTTCCTA 57.289 37.500 14.32 0.00 31.73 2.94
70 71 7.108841 ACGAATGTATGCTCTACTTTCCTAA 57.891 36.000 14.32 0.00 31.73 2.69
71 72 7.553334 ACGAATGTATGCTCTACTTTCCTAAA 58.447 34.615 14.32 0.00 31.73 1.85
72 73 8.038944 ACGAATGTATGCTCTACTTTCCTAAAA 58.961 33.333 14.32 0.00 31.73 1.52
73 74 8.328864 CGAATGTATGCTCTACTTTCCTAAAAC 58.671 37.037 14.32 0.00 31.73 2.43
74 75 7.772332 ATGTATGCTCTACTTTCCTAAAACG 57.228 36.000 0.00 0.00 0.00 3.60
75 76 6.694447 TGTATGCTCTACTTTCCTAAAACGT 58.306 36.000 0.00 0.00 0.00 3.99
76 77 7.156673 TGTATGCTCTACTTTCCTAAAACGTT 58.843 34.615 0.00 0.00 0.00 3.99
77 78 7.658575 TGTATGCTCTACTTTCCTAAAACGTTT 59.341 33.333 7.96 7.96 0.00 3.60
78 79 6.535274 TGCTCTACTTTCCTAAAACGTTTC 57.465 37.500 15.01 0.00 0.00 2.78
79 80 6.285990 TGCTCTACTTTCCTAAAACGTTTCT 58.714 36.000 15.01 7.41 0.00 2.52
80 81 6.423001 TGCTCTACTTTCCTAAAACGTTTCTC 59.577 38.462 15.01 0.00 0.00 2.87
81 82 6.128607 GCTCTACTTTCCTAAAACGTTTCTCC 60.129 42.308 15.01 0.00 0.00 3.71
82 83 7.059202 TCTACTTTCCTAAAACGTTTCTCCT 57.941 36.000 15.01 0.62 0.00 3.69
83 84 7.150640 TCTACTTTCCTAAAACGTTTCTCCTC 58.849 38.462 15.01 0.00 0.00 3.71
84 85 5.926663 ACTTTCCTAAAACGTTTCTCCTCT 58.073 37.500 15.01 0.00 0.00 3.69
85 86 5.990386 ACTTTCCTAAAACGTTTCTCCTCTC 59.010 40.000 15.01 0.00 0.00 3.20
86 87 5.540400 TTCCTAAAACGTTTCTCCTCTCA 57.460 39.130 15.01 0.00 0.00 3.27
87 88 4.879598 TCCTAAAACGTTTCTCCTCTCAC 58.120 43.478 15.01 0.00 0.00 3.51
88 89 4.587684 TCCTAAAACGTTTCTCCTCTCACT 59.412 41.667 15.01 0.00 0.00 3.41
89 90 5.771666 TCCTAAAACGTTTCTCCTCTCACTA 59.228 40.000 15.01 0.00 0.00 2.74
90 91 6.436532 TCCTAAAACGTTTCTCCTCTCACTAT 59.563 38.462 15.01 0.00 0.00 2.12
91 92 7.613022 TCCTAAAACGTTTCTCCTCTCACTATA 59.387 37.037 15.01 0.00 0.00 1.31
92 93 7.916450 CCTAAAACGTTTCTCCTCTCACTATAG 59.084 40.741 15.01 7.21 0.00 1.31
93 94 6.837471 AAACGTTTCTCCTCTCACTATAGT 57.163 37.500 7.96 0.00 0.00 2.12
94 95 7.934855 AAACGTTTCTCCTCTCACTATAGTA 57.065 36.000 7.96 0.00 0.00 1.82
95 96 6.923928 ACGTTTCTCCTCTCACTATAGTAC 57.076 41.667 4.74 0.00 0.00 2.73
96 97 6.413052 ACGTTTCTCCTCTCACTATAGTACA 58.587 40.000 4.74 0.00 0.00 2.90
97 98 6.883217 ACGTTTCTCCTCTCACTATAGTACAA 59.117 38.462 4.74 0.00 0.00 2.41
98 99 7.392673 ACGTTTCTCCTCTCACTATAGTACAAA 59.607 37.037 4.74 0.00 0.00 2.83
99 100 7.911205 CGTTTCTCCTCTCACTATAGTACAAAG 59.089 40.741 4.74 1.69 0.00 2.77
100 101 8.958506 GTTTCTCCTCTCACTATAGTACAAAGA 58.041 37.037 4.74 5.81 0.00 2.52
101 102 8.508883 TTCTCCTCTCACTATAGTACAAAGAC 57.491 38.462 4.74 0.00 0.00 3.01
102 103 6.762187 TCTCCTCTCACTATAGTACAAAGACG 59.238 42.308 4.74 1.87 0.00 4.18
103 104 5.821470 TCCTCTCACTATAGTACAAAGACGG 59.179 44.000 4.74 9.34 0.00 4.79
104 105 5.008811 CCTCTCACTATAGTACAAAGACGGG 59.991 48.000 4.74 2.38 0.00 5.28
105 106 4.337555 TCTCACTATAGTACAAAGACGGGC 59.662 45.833 4.74 0.00 0.00 6.13
106 107 4.018490 TCACTATAGTACAAAGACGGGCA 58.982 43.478 4.74 0.00 0.00 5.36
107 108 4.647853 TCACTATAGTACAAAGACGGGCAT 59.352 41.667 4.74 0.00 0.00 4.40
108 109 4.745125 CACTATAGTACAAAGACGGGCATG 59.255 45.833 4.74 0.00 0.00 4.06
109 110 3.906720 ATAGTACAAAGACGGGCATGT 57.093 42.857 0.00 0.00 0.00 3.21
110 111 5.595542 ACTATAGTACAAAGACGGGCATGTA 59.404 40.000 2.75 0.00 0.00 2.29
111 112 2.968675 AGTACAAAGACGGGCATGTAC 58.031 47.619 17.38 17.38 45.26 2.90
112 113 2.968675 GTACAAAGACGGGCATGTACT 58.031 47.619 17.66 0.00 42.90 2.73
113 114 2.561478 ACAAAGACGGGCATGTACTT 57.439 45.000 0.00 0.00 0.00 2.24
114 115 2.858745 ACAAAGACGGGCATGTACTTT 58.141 42.857 0.00 0.00 0.00 2.66
115 116 4.010667 ACAAAGACGGGCATGTACTTTA 57.989 40.909 0.00 0.00 31.11 1.85
116 117 4.000988 ACAAAGACGGGCATGTACTTTAG 58.999 43.478 0.00 0.00 31.11 1.85
117 118 2.311124 AGACGGGCATGTACTTTAGC 57.689 50.000 0.00 0.00 0.00 3.09
118 119 1.553248 AGACGGGCATGTACTTTAGCA 59.447 47.619 0.00 0.00 0.00 3.49
119 120 1.664151 GACGGGCATGTACTTTAGCAC 59.336 52.381 0.00 0.00 0.00 4.40
120 121 1.014352 CGGGCATGTACTTTAGCACC 58.986 55.000 0.00 0.00 0.00 5.01
121 122 1.677518 CGGGCATGTACTTTAGCACCA 60.678 52.381 0.00 0.00 0.00 4.17
122 123 2.654863 GGGCATGTACTTTAGCACCAT 58.345 47.619 0.00 0.00 0.00 3.55
123 124 3.023832 GGGCATGTACTTTAGCACCATT 58.976 45.455 0.00 0.00 0.00 3.16
124 125 3.447229 GGGCATGTACTTTAGCACCATTT 59.553 43.478 0.00 0.00 0.00 2.32
125 126 4.081697 GGGCATGTACTTTAGCACCATTTT 60.082 41.667 0.00 0.00 0.00 1.82
126 127 5.102313 GGCATGTACTTTAGCACCATTTTC 58.898 41.667 0.00 0.00 0.00 2.29
127 128 5.336372 GGCATGTACTTTAGCACCATTTTCA 60.336 40.000 0.00 0.00 0.00 2.69
128 129 5.572896 GCATGTACTTTAGCACCATTTTCAC 59.427 40.000 0.00 0.00 0.00 3.18
129 130 6.570378 GCATGTACTTTAGCACCATTTTCACT 60.570 38.462 0.00 0.00 0.00 3.41
130 131 6.312399 TGTACTTTAGCACCATTTTCACTG 57.688 37.500 0.00 0.00 0.00 3.66
131 132 5.825679 TGTACTTTAGCACCATTTTCACTGT 59.174 36.000 0.00 0.00 0.00 3.55
132 133 5.852282 ACTTTAGCACCATTTTCACTGTT 57.148 34.783 0.00 0.00 0.00 3.16
133 134 6.220726 ACTTTAGCACCATTTTCACTGTTT 57.779 33.333 0.00 0.00 0.00 2.83
134 135 6.639563 ACTTTAGCACCATTTTCACTGTTTT 58.360 32.000 0.00 0.00 0.00 2.43
135 136 7.102993 ACTTTAGCACCATTTTCACTGTTTTT 58.897 30.769 0.00 0.00 0.00 1.94
136 137 8.254508 ACTTTAGCACCATTTTCACTGTTTTTA 58.745 29.630 0.00 0.00 0.00 1.52
137 138 9.260002 CTTTAGCACCATTTTCACTGTTTTTAT 57.740 29.630 0.00 0.00 0.00 1.40
138 139 9.606631 TTTAGCACCATTTTCACTGTTTTTATT 57.393 25.926 0.00 0.00 0.00 1.40
139 140 7.713764 AGCACCATTTTCACTGTTTTTATTC 57.286 32.000 0.00 0.00 0.00 1.75
140 141 7.271511 AGCACCATTTTCACTGTTTTTATTCA 58.728 30.769 0.00 0.00 0.00 2.57
173 174 5.091552 TCCTAATGTCTCAGTTGGTAGGTT 58.908 41.667 0.00 0.00 0.00 3.50
425 432 2.657102 AAAACCCCCGCACGTACGAA 62.657 55.000 24.41 0.00 34.06 3.85
508 515 2.584608 CCTTCATCCCTTCGCCGT 59.415 61.111 0.00 0.00 0.00 5.68
580 611 1.450669 ACTCGCACAACAAACCCGT 60.451 52.632 0.00 0.00 0.00 5.28
667 698 1.522355 AATCGCTGCCATCGTGGAG 60.522 57.895 8.04 4.43 40.96 3.86
726 757 1.728490 GCCTTCGTGGATCCATTGCC 61.728 60.000 19.62 3.60 38.35 4.52
760 791 0.178929 ACCTCTTCCTCCTCCGTTGT 60.179 55.000 0.00 0.00 0.00 3.32
1038 1069 1.388133 GGCCTTCACCCCCAAGAAT 59.612 57.895 0.00 0.00 0.00 2.40
1489 1567 3.563390 GGGAGCTCTCAATTCTGTATTGC 59.437 47.826 14.64 0.00 42.79 3.56
1490 1568 4.194640 GGAGCTCTCAATTCTGTATTGCA 58.805 43.478 14.64 0.00 42.79 4.08
1543 1621 3.752665 GATCTGATTGTGCCTCCATGAT 58.247 45.455 0.00 0.00 0.00 2.45
1682 1760 2.853542 TGCTGCAGGTCCTTGGGA 60.854 61.111 17.12 0.00 0.00 4.37
2151 2229 1.826054 CTTTTGTGGTGGGGCGTCA 60.826 57.895 0.00 0.00 0.00 4.35
2153 2231 2.559922 TTTTGTGGTGGGGCGTCACT 62.560 55.000 0.00 0.00 37.75 3.41
2192 2270 0.609957 TAGACCGTCTCGCTGGGAAA 60.610 55.000 3.74 0.00 0.00 3.13
2362 2442 3.534970 CTGATCGCGCTCTCCTCCG 62.535 68.421 11.66 0.00 0.00 4.63
2394 2474 4.243008 TTGGTTCGGAGGTGCGCA 62.243 61.111 5.66 5.66 0.00 6.09
2425 2505 3.928727 TGACAACCTTTCTATCGACGT 57.071 42.857 0.00 0.00 0.00 4.34
2549 2629 8.147058 TGTTTGGCATTTAGCTTTTTGATTCTA 58.853 29.630 0.00 0.00 44.79 2.10
2618 2698 5.304686 TCACTCCAGGTAATCTGTTTGTT 57.695 39.130 0.00 0.00 41.83 2.83
2687 2767 4.590850 AAAACTTCAATTGAGGGCACTC 57.409 40.909 20.35 9.72 44.23 3.51
2721 2801 7.112452 AGCTACATGTATCATGTAAGTGACA 57.888 36.000 18.74 0.00 43.97 3.58
2729 2809 7.851228 TGTATCATGTAAGTGACATCTTTCCT 58.149 34.615 0.00 0.00 46.33 3.36
2730 2810 7.981789 TGTATCATGTAAGTGACATCTTTCCTC 59.018 37.037 0.00 0.00 46.33 3.71
2779 2859 7.780745 CCTCTCAGACCCTTAGAAAAGTATCTA 59.219 40.741 0.00 0.00 0.00 1.98
2882 2962 2.737180 CGATCACCATCCCGAGGG 59.263 66.667 0.65 0.65 38.43 4.30
2967 3047 0.539051 CCTTCCTCTCTCCACGCAAT 59.461 55.000 0.00 0.00 0.00 3.56
3027 3107 5.337250 CCCATTATTGCGGCTACATAGTCTA 60.337 44.000 0.00 0.00 0.00 2.59
3205 3285 5.978919 TGCATTTTGTGTTGAGAAACATCTC 59.021 36.000 0.00 0.00 34.86 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.022416 AGAGCATACATTCGTTGCCAAAAA 60.022 37.500 0.00 0.00 37.07 1.94
38 39 3.505680 AGAGCATACATTCGTTGCCAAAA 59.494 39.130 0.00 0.00 37.07 2.44
39 40 3.081061 AGAGCATACATTCGTTGCCAAA 58.919 40.909 0.00 0.00 37.07 3.28
40 41 2.710377 AGAGCATACATTCGTTGCCAA 58.290 42.857 0.00 0.00 37.07 4.52
41 42 2.401583 AGAGCATACATTCGTTGCCA 57.598 45.000 0.00 0.00 37.07 4.92
42 43 3.458189 AGTAGAGCATACATTCGTTGCC 58.542 45.455 2.43 0.00 37.07 4.52
43 44 5.470845 AAAGTAGAGCATACATTCGTTGC 57.529 39.130 2.43 0.00 36.63 4.17
44 45 5.812642 AGGAAAGTAGAGCATACATTCGTTG 59.187 40.000 9.53 0.00 0.00 4.10
45 46 5.978814 AGGAAAGTAGAGCATACATTCGTT 58.021 37.500 9.53 1.53 0.00 3.85
46 47 5.599999 AGGAAAGTAGAGCATACATTCGT 57.400 39.130 9.53 8.03 0.00 3.85
47 48 8.328864 GTTTTAGGAAAGTAGAGCATACATTCG 58.671 37.037 9.53 0.00 0.00 3.34
48 49 8.328864 CGTTTTAGGAAAGTAGAGCATACATTC 58.671 37.037 7.97 7.97 0.00 2.67
49 50 7.822822 ACGTTTTAGGAAAGTAGAGCATACATT 59.177 33.333 2.43 0.00 0.00 2.71
50 51 7.328737 ACGTTTTAGGAAAGTAGAGCATACAT 58.671 34.615 2.43 0.00 0.00 2.29
51 52 6.694447 ACGTTTTAGGAAAGTAGAGCATACA 58.306 36.000 2.43 0.00 0.00 2.29
52 53 7.592439 AACGTTTTAGGAAAGTAGAGCATAC 57.408 36.000 0.00 0.00 0.00 2.39
53 54 8.092687 AGAAACGTTTTAGGAAAGTAGAGCATA 58.907 33.333 15.89 0.00 0.00 3.14
54 55 6.935208 AGAAACGTTTTAGGAAAGTAGAGCAT 59.065 34.615 15.89 0.00 0.00 3.79
55 56 6.285990 AGAAACGTTTTAGGAAAGTAGAGCA 58.714 36.000 15.89 0.00 0.00 4.26
56 57 6.128607 GGAGAAACGTTTTAGGAAAGTAGAGC 60.129 42.308 15.89 0.00 0.00 4.09
57 58 7.153315 AGGAGAAACGTTTTAGGAAAGTAGAG 58.847 38.462 15.89 0.00 0.00 2.43
58 59 7.015001 AGAGGAGAAACGTTTTAGGAAAGTAGA 59.985 37.037 15.89 0.00 0.00 2.59
59 60 7.153315 AGAGGAGAAACGTTTTAGGAAAGTAG 58.847 38.462 15.89 0.00 0.00 2.57
60 61 7.059202 AGAGGAGAAACGTTTTAGGAAAGTA 57.941 36.000 15.89 0.00 0.00 2.24
61 62 5.926663 AGAGGAGAAACGTTTTAGGAAAGT 58.073 37.500 15.89 0.00 0.00 2.66
62 63 5.989777 TGAGAGGAGAAACGTTTTAGGAAAG 59.010 40.000 15.89 0.00 0.00 2.62
63 64 5.756833 GTGAGAGGAGAAACGTTTTAGGAAA 59.243 40.000 15.89 0.00 0.00 3.13
64 65 5.070047 AGTGAGAGGAGAAACGTTTTAGGAA 59.930 40.000 15.89 0.00 0.00 3.36
65 66 4.587684 AGTGAGAGGAGAAACGTTTTAGGA 59.412 41.667 15.89 0.00 0.00 2.94
66 67 4.884247 AGTGAGAGGAGAAACGTTTTAGG 58.116 43.478 15.89 0.00 0.00 2.69
67 68 8.460428 ACTATAGTGAGAGGAGAAACGTTTTAG 58.540 37.037 15.89 9.97 0.00 1.85
68 69 8.345724 ACTATAGTGAGAGGAGAAACGTTTTA 57.654 34.615 15.89 0.00 0.00 1.52
69 70 7.229581 ACTATAGTGAGAGGAGAAACGTTTT 57.770 36.000 15.89 5.23 0.00 2.43
70 71 6.837471 ACTATAGTGAGAGGAGAAACGTTT 57.163 37.500 14.57 14.57 0.00 3.60
71 72 6.883217 TGTACTATAGTGAGAGGAGAAACGTT 59.117 38.462 15.90 0.00 0.00 3.99
72 73 6.413052 TGTACTATAGTGAGAGGAGAAACGT 58.587 40.000 15.90 0.00 0.00 3.99
73 74 6.922247 TGTACTATAGTGAGAGGAGAAACG 57.078 41.667 15.90 0.00 0.00 3.60
74 75 8.958506 TCTTTGTACTATAGTGAGAGGAGAAAC 58.041 37.037 15.90 2.17 0.00 2.78
75 76 8.958506 GTCTTTGTACTATAGTGAGAGGAGAAA 58.041 37.037 15.90 4.71 0.00 2.52
76 77 7.280428 CGTCTTTGTACTATAGTGAGAGGAGAA 59.720 40.741 15.90 0.00 0.00 2.87
77 78 6.762187 CGTCTTTGTACTATAGTGAGAGGAGA 59.238 42.308 15.90 8.18 0.00 3.71
78 79 6.017770 CCGTCTTTGTACTATAGTGAGAGGAG 60.018 46.154 15.90 6.15 0.00 3.69
79 80 5.821470 CCGTCTTTGTACTATAGTGAGAGGA 59.179 44.000 15.90 5.76 0.00 3.71
80 81 5.008811 CCCGTCTTTGTACTATAGTGAGAGG 59.991 48.000 15.90 15.68 0.00 3.69
81 82 5.505985 GCCCGTCTTTGTACTATAGTGAGAG 60.506 48.000 15.90 6.77 0.00 3.20
82 83 4.337555 GCCCGTCTTTGTACTATAGTGAGA 59.662 45.833 15.90 10.07 0.00 3.27
83 84 4.097437 TGCCCGTCTTTGTACTATAGTGAG 59.903 45.833 15.90 8.07 0.00 3.51
84 85 4.018490 TGCCCGTCTTTGTACTATAGTGA 58.982 43.478 15.90 0.64 0.00 3.41
85 86 4.380841 TGCCCGTCTTTGTACTATAGTG 57.619 45.455 15.90 0.00 0.00 2.74
86 87 4.404715 ACATGCCCGTCTTTGTACTATAGT 59.595 41.667 10.87 10.87 0.00 2.12
87 88 4.945246 ACATGCCCGTCTTTGTACTATAG 58.055 43.478 0.00 0.00 0.00 1.31
88 89 5.835257 GTACATGCCCGTCTTTGTACTATA 58.165 41.667 0.00 0.00 40.64 1.31
89 90 3.906720 ACATGCCCGTCTTTGTACTAT 57.093 42.857 0.00 0.00 0.00 2.12
90 91 4.114058 GTACATGCCCGTCTTTGTACTA 57.886 45.455 0.00 0.00 40.64 1.82
91 92 2.565834 AGTACATGCCCGTCTTTGTACT 59.434 45.455 8.38 8.38 46.02 2.73
92 93 2.968675 AGTACATGCCCGTCTTTGTAC 58.031 47.619 0.00 4.35 42.91 2.90
93 94 3.688694 AAGTACATGCCCGTCTTTGTA 57.311 42.857 0.00 0.00 0.00 2.41
94 95 2.561478 AAGTACATGCCCGTCTTTGT 57.439 45.000 0.00 0.00 0.00 2.83
95 96 3.181510 GCTAAAGTACATGCCCGTCTTTG 60.182 47.826 0.00 0.00 32.01 2.77
96 97 3.007635 GCTAAAGTACATGCCCGTCTTT 58.992 45.455 0.00 0.02 33.76 2.52
97 98 2.027561 TGCTAAAGTACATGCCCGTCTT 60.028 45.455 0.00 0.00 0.00 3.01
98 99 1.553248 TGCTAAAGTACATGCCCGTCT 59.447 47.619 0.00 0.00 0.00 4.18
99 100 1.664151 GTGCTAAAGTACATGCCCGTC 59.336 52.381 0.00 0.00 0.00 4.79
100 101 1.677820 GGTGCTAAAGTACATGCCCGT 60.678 52.381 0.00 0.00 32.02 5.28
101 102 1.014352 GGTGCTAAAGTACATGCCCG 58.986 55.000 0.00 0.00 32.02 6.13
102 103 2.122783 TGGTGCTAAAGTACATGCCC 57.877 50.000 0.00 0.00 32.02 5.36
103 104 4.718940 AAATGGTGCTAAAGTACATGCC 57.281 40.909 0.00 0.00 32.02 4.40
104 105 5.572896 GTGAAAATGGTGCTAAAGTACATGC 59.427 40.000 0.00 0.00 32.02 4.06
105 106 6.803320 CAGTGAAAATGGTGCTAAAGTACATG 59.197 38.462 0.00 0.00 32.02 3.21
106 107 6.490040 ACAGTGAAAATGGTGCTAAAGTACAT 59.510 34.615 0.00 0.00 35.33 2.29
107 108 5.825679 ACAGTGAAAATGGTGCTAAAGTACA 59.174 36.000 0.00 0.00 35.33 2.90
108 109 6.313744 ACAGTGAAAATGGTGCTAAAGTAC 57.686 37.500 0.00 0.00 35.33 2.73
109 110 6.952773 AACAGTGAAAATGGTGCTAAAGTA 57.047 33.333 0.00 0.00 35.33 2.24
110 111 5.852282 AACAGTGAAAATGGTGCTAAAGT 57.148 34.783 0.00 0.00 35.33 2.66
111 112 7.538303 AAAAACAGTGAAAATGGTGCTAAAG 57.462 32.000 0.00 0.00 35.33 1.85
112 113 9.606631 AATAAAAACAGTGAAAATGGTGCTAAA 57.393 25.926 0.00 0.00 35.33 1.85
113 114 9.255304 GAATAAAAACAGTGAAAATGGTGCTAA 57.745 29.630 0.00 0.00 35.33 3.09
114 115 8.417106 TGAATAAAAACAGTGAAAATGGTGCTA 58.583 29.630 0.00 0.00 35.33 3.49
115 116 7.271511 TGAATAAAAACAGTGAAAATGGTGCT 58.728 30.769 0.00 0.00 35.33 4.40
116 117 7.475771 TGAATAAAAACAGTGAAAATGGTGC 57.524 32.000 0.00 0.00 35.33 5.01
136 137 9.206690 TGAGACATTAGGAGTAGAGAAATGAAT 57.793 33.333 0.00 0.00 32.99 2.57
137 138 8.595362 TGAGACATTAGGAGTAGAGAAATGAA 57.405 34.615 0.00 0.00 32.99 2.57
138 139 7.836685 ACTGAGACATTAGGAGTAGAGAAATGA 59.163 37.037 0.00 0.00 32.99 2.57
139 140 8.006298 ACTGAGACATTAGGAGTAGAGAAATG 57.994 38.462 0.00 0.00 34.48 2.32
140 141 8.474025 CAACTGAGACATTAGGAGTAGAGAAAT 58.526 37.037 0.00 0.00 0.00 2.17
425 432 2.261671 GAGGGCATGTGACGTCGT 59.738 61.111 11.62 0.00 0.00 4.34
462 469 1.076632 CGAGGGCAGGGAGTCTAGT 60.077 63.158 0.00 0.00 0.00 2.57
573 604 2.032071 CAGAAGGGCGACGGGTTT 59.968 61.111 0.00 0.00 0.00 3.27
636 667 2.636830 CAGCGATTGATCCAAGAAGGT 58.363 47.619 0.00 0.00 39.02 3.50
649 680 1.522355 CTCCACGATGGCAGCGATT 60.522 57.895 33.22 7.41 37.47 3.34
1405 1483 8.775527 TCACAATTAACGAAGTAAAGCACATAA 58.224 29.630 0.00 0.00 45.00 1.90
1489 1567 4.717877 TGTATCTACCTTGCCATCCATTG 58.282 43.478 0.00 0.00 0.00 2.82
1490 1568 5.589367 ATGTATCTACCTTGCCATCCATT 57.411 39.130 0.00 0.00 0.00 3.16
1550 1628 4.108299 TTCGGCGGTGGGCATCAT 62.108 61.111 7.21 0.00 46.16 2.45
1682 1760 0.179004 TGGCGACAAGAACACCCAAT 60.179 50.000 0.00 0.00 37.44 3.16
2042 2120 5.923684 GGAAAACGACCAATAAAGCATGAAA 59.076 36.000 0.00 0.00 0.00 2.69
2043 2121 5.465935 GGAAAACGACCAATAAAGCATGAA 58.534 37.500 0.00 0.00 0.00 2.57
2192 2270 2.493099 ATCAGGGGAGCATCTCTTCT 57.507 50.000 0.00 0.00 34.46 2.85
2246 2326 2.912956 TCTGCAACCACCTCCTTTCTAT 59.087 45.455 0.00 0.00 0.00 1.98
2362 2442 0.893727 ACCAAGGATCCGTTTGGCAC 60.894 55.000 25.60 0.00 46.16 5.01
2394 2474 1.738099 GGTTGTCATCGTCAGCGCT 60.738 57.895 2.64 2.64 38.14 5.92
2425 2505 2.042464 CATGAGCTCCTACTGCCCTTA 58.958 52.381 12.15 0.00 0.00 2.69
2549 2629 7.274447 TCTGAATCAAAAAGCTCACCAAAAAT 58.726 30.769 0.00 0.00 0.00 1.82
2555 2635 8.866956 CAAATTATCTGAATCAAAAAGCTCACC 58.133 33.333 0.00 0.00 0.00 4.02
2618 2698 7.676807 GCACTGAATCAAAAAGCAAAATGTCAA 60.677 33.333 0.00 0.00 0.00 3.18
2687 2767 8.522003 ACATGATACATGTAGCTAGAGAATCAG 58.478 37.037 20.91 9.05 37.82 2.90
2779 2859 8.378172 TCAACAGAAAGAAATCGAGTTAACAT 57.622 30.769 8.61 0.00 0.00 2.71
2882 2962 3.406361 CGCCAGTCTGTCGTGCAC 61.406 66.667 6.82 6.82 0.00 4.57
2967 3047 2.315176 ACTTAGCAACAATGGGCAACA 58.685 42.857 2.28 0.00 39.74 3.33
3027 3107 2.822707 AGAAGGCAGGCAAGATGAAT 57.177 45.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.