Multiple sequence alignment - TraesCS1B01G013400

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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 TraesCS1B01G013400 chr1B 100.000 3457 0 0 1 3457 6396117 6399573 0.000000e+00 6384
1 TraesCS1B01G013400 chr1B 85.526 152 14 4 14 165 8219121 8219264 5.980000e-33 152
2 TraesCS1B01G013400 chr6B 98.482 3227 34 3 244 3457 712151898 712155122 0.000000e+00 5674
3 TraesCS1B01G013400 chr6B 95.425 3235 120 9 240 3457 366596287 366593064 0.000000e+00 5129
4 TraesCS1B01G013400 chr4A 97.308 3232 62 3 239 3457 58507666 58510885 0.000000e+00 5463
5 TraesCS1B01G013400 chr7A 97.118 3227 67 4 244 3457 11051444 11048231 0.000000e+00 5421
6 TraesCS1B01G013400 chr7A 93.770 626 26 6 2845 3457 12796603 12797228 0.000000e+00 928
7 TraesCS1B01G013400 chr2D 94.252 3236 149 18 244 3457 46693766 46690546 0.000000e+00 4911
8 TraesCS1B01G013400 chr7D 94.034 3235 155 20 244 3457 615778481 615781698 0.000000e+00 4870
9 TraesCS1B01G013400 chr3B 93.936 3232 149 15 245 3457 465857842 465861045 0.000000e+00 4839
10 TraesCS1B01G013400 chr5D 94.204 2933 144 18 244 3167 41776635 41779550 0.000000e+00 4451
11 TraesCS1B01G013400 chr5D 95.614 798 22 4 2673 3457 41783741 41784538 0.000000e+00 1267
12 TraesCS1B01G013400 chr6A 93.942 2443 128 6 915 3344 61567833 61565398 0.000000e+00 3674
13 TraesCS1B01G013400 chr6D 93.649 2409 130 16 240 2639 429473816 429476210 0.000000e+00 3579


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 TraesCS1B01G013400 chr1B 6396117 6399573 3456 False 6384 6384 100.000 1 3457 1 chr1B.!!$F1 3456
1 TraesCS1B01G013400 chr6B 712151898 712155122 3224 False 5674 5674 98.482 244 3457 1 chr6B.!!$F1 3213
2 TraesCS1B01G013400 chr6B 366593064 366596287 3223 True 5129 5129 95.425 240 3457 1 chr6B.!!$R1 3217
3 TraesCS1B01G013400 chr4A 58507666 58510885 3219 False 5463 5463 97.308 239 3457 1 chr4A.!!$F1 3218
4 TraesCS1B01G013400 chr7A 11048231 11051444 3213 True 5421 5421 97.118 244 3457 1 chr7A.!!$R1 3213
5 TraesCS1B01G013400 chr7A 12796603 12797228 625 False 928 928 93.770 2845 3457 1 chr7A.!!$F1 612
6 TraesCS1B01G013400 chr2D 46690546 46693766 3220 True 4911 4911 94.252 244 3457 1 chr2D.!!$R1 3213
7 TraesCS1B01G013400 chr7D 615778481 615781698 3217 False 4870 4870 94.034 244 3457 1 chr7D.!!$F1 3213
8 TraesCS1B01G013400 chr3B 465857842 465861045 3203 False 4839 4839 93.936 245 3457 1 chr3B.!!$F1 3212
9 TraesCS1B01G013400 chr5D 41776635 41779550 2915 False 4451 4451 94.204 244 3167 1 chr5D.!!$F1 2923
10 TraesCS1B01G013400 chr5D 41783741 41784538 797 False 1267 1267 95.614 2673 3457 1 chr5D.!!$F2 784
11 TraesCS1B01G013400 chr6A 61565398 61567833 2435 True 3674 3674 93.942 915 3344 1 chr6A.!!$R1 2429
12 TraesCS1B01G013400 chr6D 429473816 429476210 2394 False 3579 3579 93.649 240 2639 1 chr6D.!!$F1 2399

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
151 152 0.036164 TGGCTTGCGGTAGTTGATGT 59.964 50.0 0.00 0.00 0.00 3.06 F
232 233 0.454600 ATACGTAGTCACCGCTGTGG 59.545 55.0 8.50 5.54 43.93 4.17 F
389 392 0.914417 TCACACTCCCTCCAATCCCC 60.914 60.0 0.00 0.00 0.00 4.81 F
1845 1854 0.396974 ACTGCAAAAGGCCTGGACAA 60.397 50.0 5.69 0.00 43.89 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1086 1.462616 TGAGTTGTTGCTGTTGCTGT 58.537 45.000 0.00 0.00 40.48 4.40 R
1180 1189 2.101783 CAGAATTAACTGGGCATGCCA 58.898 47.619 36.56 21.67 37.98 4.92 R
1941 1950 3.447229 TCTTGGATGTAGTGAGATTCGCA 59.553 43.478 0.00 0.00 0.00 5.10 R
3033 3051 0.880278 GTGAGCGTGCAACCTCAAGA 60.880 55.000 16.50 0.00 42.77 3.02 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
42 43 9.734620 TTCACAGAGATTACTGAAAACAAAATG 57.265 29.630 0.00 0.00 40.63 2.32
43 44 8.902806 TCACAGAGATTACTGAAAACAAAATGT 58.097 29.630 0.00 0.00 40.63 2.71
44 45 9.520204 CACAGAGATTACTGAAAACAAAATGTT 57.480 29.630 0.00 0.00 40.43 2.71
53 54 8.964420 ACTGAAAACAAAATGTTATATGTCGG 57.036 30.769 0.00 0.00 40.14 4.79
54 55 8.026607 ACTGAAAACAAAATGTTATATGTCGGG 58.973 33.333 0.00 0.00 40.14 5.14
55 56 6.809196 TGAAAACAAAATGTTATATGTCGGGC 59.191 34.615 0.00 0.00 40.14 6.13
56 57 4.911514 ACAAAATGTTATATGTCGGGCC 57.088 40.909 0.00 0.00 0.00 5.80
57 58 4.274147 ACAAAATGTTATATGTCGGGCCA 58.726 39.130 4.39 0.00 0.00 5.36
58 59 4.097286 ACAAAATGTTATATGTCGGGCCAC 59.903 41.667 4.39 1.32 0.00 5.01
59 60 2.561478 ATGTTATATGTCGGGCCACC 57.439 50.000 4.39 0.00 0.00 4.61
60 61 1.205055 TGTTATATGTCGGGCCACCA 58.795 50.000 4.39 0.00 36.13 4.17
61 62 1.771854 TGTTATATGTCGGGCCACCAT 59.228 47.619 4.39 7.27 36.13 3.55
62 63 2.224426 TGTTATATGTCGGGCCACCATC 60.224 50.000 4.39 0.00 36.13 3.51
63 64 2.024176 TATATGTCGGGCCACCATCT 57.976 50.000 4.39 0.00 36.13 2.90
64 65 0.397941 ATATGTCGGGCCACCATCTG 59.602 55.000 4.39 0.00 36.13 2.90
65 66 2.324014 TATGTCGGGCCACCATCTGC 62.324 60.000 4.39 0.00 36.13 4.26
66 67 4.101448 GTCGGGCCACCATCTGCT 62.101 66.667 4.39 0.00 36.13 4.24
67 68 2.364973 TCGGGCCACCATCTGCTA 60.365 61.111 4.39 0.00 36.13 3.49
68 69 2.203070 CGGGCCACCATCTGCTAC 60.203 66.667 4.39 0.00 36.13 3.58
69 70 2.998097 GGGCCACCATCTGCTACA 59.002 61.111 4.39 0.00 36.50 2.74
70 71 1.153086 GGGCCACCATCTGCTACAG 60.153 63.158 4.39 0.00 36.50 2.74
71 72 1.626356 GGGCCACCATCTGCTACAGA 61.626 60.000 4.39 0.00 44.99 3.41
72 73 0.462759 GGCCACCATCTGCTACAGAC 60.463 60.000 0.00 0.00 43.63 3.51
73 74 0.807667 GCCACCATCTGCTACAGACG 60.808 60.000 0.00 0.00 43.63 4.18
74 75 0.807667 CCACCATCTGCTACAGACGC 60.808 60.000 0.00 0.00 43.63 5.19
75 76 0.174389 CACCATCTGCTACAGACGCT 59.826 55.000 0.00 0.00 43.63 5.07
76 77 0.457851 ACCATCTGCTACAGACGCTC 59.542 55.000 0.00 0.00 43.63 5.03
77 78 0.743688 CCATCTGCTACAGACGCTCT 59.256 55.000 0.00 0.00 43.63 4.09
78 79 1.268999 CCATCTGCTACAGACGCTCTC 60.269 57.143 0.00 0.00 43.63 3.20
79 80 1.675483 CATCTGCTACAGACGCTCTCT 59.325 52.381 0.00 0.00 43.63 3.10
80 81 1.374560 TCTGCTACAGACGCTCTCTC 58.625 55.000 0.00 0.00 35.39 3.20
81 82 1.065782 TCTGCTACAGACGCTCTCTCT 60.066 52.381 0.00 0.00 35.39 3.10
82 83 1.330521 CTGCTACAGACGCTCTCTCTC 59.669 57.143 0.00 0.00 32.44 3.20
83 84 0.303493 GCTACAGACGCTCTCTCTCG 59.697 60.000 0.00 0.00 0.00 4.04
84 85 1.647346 CTACAGACGCTCTCTCTCGT 58.353 55.000 0.00 0.00 42.09 4.18
85 86 2.004017 CTACAGACGCTCTCTCTCGTT 58.996 52.381 0.00 0.00 39.22 3.85
86 87 0.800012 ACAGACGCTCTCTCTCGTTC 59.200 55.000 0.00 0.00 39.22 3.95
87 88 0.247497 CAGACGCTCTCTCTCGTTCG 60.247 60.000 0.00 0.00 39.22 3.95
88 89 1.581657 GACGCTCTCTCTCGTTCGC 60.582 63.158 0.00 0.00 39.22 4.70
89 90 1.973137 GACGCTCTCTCTCGTTCGCT 61.973 60.000 0.00 0.00 39.22 4.93
90 91 1.297304 CGCTCTCTCTCGTTCGCTC 60.297 63.158 0.00 0.00 0.00 5.03
91 92 1.063488 GCTCTCTCTCGTTCGCTCC 59.937 63.158 0.00 0.00 0.00 4.70
92 93 1.725066 CTCTCTCTCGTTCGCTCCC 59.275 63.158 0.00 0.00 0.00 4.30
93 94 1.002502 TCTCTCTCGTTCGCTCCCA 60.003 57.895 0.00 0.00 0.00 4.37
94 95 0.394488 TCTCTCTCGTTCGCTCCCAT 60.394 55.000 0.00 0.00 0.00 4.00
95 96 0.457851 CTCTCTCGTTCGCTCCCATT 59.542 55.000 0.00 0.00 0.00 3.16
96 97 0.456221 TCTCTCGTTCGCTCCCATTC 59.544 55.000 0.00 0.00 0.00 2.67
97 98 0.528684 CTCTCGTTCGCTCCCATTCC 60.529 60.000 0.00 0.00 0.00 3.01
98 99 0.970937 TCTCGTTCGCTCCCATTCCT 60.971 55.000 0.00 0.00 0.00 3.36
99 100 0.108138 CTCGTTCGCTCCCATTCCTT 60.108 55.000 0.00 0.00 0.00 3.36
100 101 0.391130 TCGTTCGCTCCCATTCCTTG 60.391 55.000 0.00 0.00 0.00 3.61
101 102 0.673644 CGTTCGCTCCCATTCCTTGT 60.674 55.000 0.00 0.00 0.00 3.16
102 103 1.404986 CGTTCGCTCCCATTCCTTGTA 60.405 52.381 0.00 0.00 0.00 2.41
103 104 2.007608 GTTCGCTCCCATTCCTTGTAC 58.992 52.381 0.00 0.00 0.00 2.90
104 105 1.271856 TCGCTCCCATTCCTTGTACA 58.728 50.000 0.00 0.00 0.00 2.90
105 106 1.626321 TCGCTCCCATTCCTTGTACAA 59.374 47.619 8.28 8.28 0.00 2.41
106 107 2.238646 TCGCTCCCATTCCTTGTACAAT 59.761 45.455 9.13 0.00 0.00 2.71
107 108 2.355756 CGCTCCCATTCCTTGTACAATG 59.644 50.000 9.13 6.65 0.00 2.82
108 109 3.620488 GCTCCCATTCCTTGTACAATGA 58.380 45.455 9.13 9.19 32.56 2.57
109 110 4.016444 GCTCCCATTCCTTGTACAATGAA 58.984 43.478 23.06 23.06 32.56 2.57
110 111 4.096984 GCTCCCATTCCTTGTACAATGAAG 59.903 45.833 24.34 17.66 32.56 3.02
111 112 4.599041 TCCCATTCCTTGTACAATGAAGG 58.401 43.478 24.34 23.74 40.26 3.46
112 113 4.290985 TCCCATTCCTTGTACAATGAAGGA 59.709 41.667 28.39 24.45 44.94 3.36
113 114 4.399303 CCCATTCCTTGTACAATGAAGGAC 59.601 45.833 28.39 0.00 46.01 3.85
114 115 5.009631 CCATTCCTTGTACAATGAAGGACA 58.990 41.667 28.39 14.97 46.01 4.02
115 116 5.476599 CCATTCCTTGTACAATGAAGGACAA 59.523 40.000 28.39 12.11 46.01 3.18
116 117 6.153340 CCATTCCTTGTACAATGAAGGACAAT 59.847 38.462 28.39 13.49 46.01 2.71
117 118 6.573664 TTCCTTGTACAATGAAGGACAATG 57.426 37.500 18.78 0.17 46.01 2.82
118 119 4.458989 TCCTTGTACAATGAAGGACAATGC 59.541 41.667 9.13 0.00 42.35 3.56
119 120 4.218200 CCTTGTACAATGAAGGACAATGCA 59.782 41.667 9.13 0.00 41.26 3.96
120 121 5.375417 TTGTACAATGAAGGACAATGCAG 57.625 39.130 3.59 0.00 33.13 4.41
121 122 3.758023 TGTACAATGAAGGACAATGCAGG 59.242 43.478 0.00 0.00 33.13 4.85
122 123 2.880443 ACAATGAAGGACAATGCAGGT 58.120 42.857 0.00 0.00 33.13 4.00
123 124 4.032960 ACAATGAAGGACAATGCAGGTA 57.967 40.909 0.00 0.00 33.13 3.08
124 125 4.012374 ACAATGAAGGACAATGCAGGTAG 58.988 43.478 0.00 0.00 33.13 3.18
125 126 2.113860 TGAAGGACAATGCAGGTAGC 57.886 50.000 0.00 0.00 45.96 3.58
135 136 1.227793 GCAGGTAGCAGAGGATGGC 60.228 63.158 0.00 0.00 44.79 4.40
136 137 1.694133 GCAGGTAGCAGAGGATGGCT 61.694 60.000 0.00 0.00 44.79 4.75
137 138 0.835941 CAGGTAGCAGAGGATGGCTT 59.164 55.000 0.00 0.00 41.41 4.35
138 139 0.835941 AGGTAGCAGAGGATGGCTTG 59.164 55.000 0.00 0.00 41.41 4.01
139 140 0.817229 GGTAGCAGAGGATGGCTTGC 60.817 60.000 0.00 0.00 41.41 4.01
140 141 1.144716 TAGCAGAGGATGGCTTGCG 59.855 57.895 0.00 0.00 41.41 4.85
141 142 2.315781 TAGCAGAGGATGGCTTGCGG 62.316 60.000 0.00 0.00 41.41 5.69
142 143 2.270205 CAGAGGATGGCTTGCGGT 59.730 61.111 0.00 0.00 0.00 5.68
143 144 1.522092 CAGAGGATGGCTTGCGGTA 59.478 57.895 0.00 0.00 0.00 4.02
144 145 0.531532 CAGAGGATGGCTTGCGGTAG 60.532 60.000 0.00 0.00 0.00 3.18
145 146 0.978146 AGAGGATGGCTTGCGGTAGT 60.978 55.000 0.00 0.00 0.00 2.73
146 147 0.107654 GAGGATGGCTTGCGGTAGTT 60.108 55.000 0.00 0.00 0.00 2.24
147 148 0.392998 AGGATGGCTTGCGGTAGTTG 60.393 55.000 0.00 0.00 0.00 3.16
148 149 0.392461 GGATGGCTTGCGGTAGTTGA 60.392 55.000 0.00 0.00 0.00 3.18
149 150 1.668419 GATGGCTTGCGGTAGTTGAT 58.332 50.000 0.00 0.00 0.00 2.57
150 151 1.331756 GATGGCTTGCGGTAGTTGATG 59.668 52.381 0.00 0.00 0.00 3.07
151 152 0.036164 TGGCTTGCGGTAGTTGATGT 59.964 50.000 0.00 0.00 0.00 3.06
152 153 1.276705 TGGCTTGCGGTAGTTGATGTA 59.723 47.619 0.00 0.00 0.00 2.29
153 154 1.664151 GGCTTGCGGTAGTTGATGTAC 59.336 52.381 0.00 0.00 0.00 2.90
154 155 2.343101 GCTTGCGGTAGTTGATGTACA 58.657 47.619 0.00 0.00 0.00 2.90
155 156 2.936498 GCTTGCGGTAGTTGATGTACAT 59.064 45.455 8.43 8.43 0.00 2.29
156 157 3.242413 GCTTGCGGTAGTTGATGTACATG 60.242 47.826 14.43 0.00 0.00 3.21
157 158 2.899976 TGCGGTAGTTGATGTACATGG 58.100 47.619 14.43 0.00 0.00 3.66
158 159 2.498078 TGCGGTAGTTGATGTACATGGA 59.502 45.455 14.43 0.00 0.00 3.41
159 160 3.055747 TGCGGTAGTTGATGTACATGGAA 60.056 43.478 14.43 2.86 0.00 3.53
160 161 3.936453 GCGGTAGTTGATGTACATGGAAA 59.064 43.478 14.43 2.10 0.00 3.13
161 162 4.201783 GCGGTAGTTGATGTACATGGAAAC 60.202 45.833 14.43 14.06 0.00 2.78
177 178 5.097742 TGGAAACAGACTCTCTTTTGTCA 57.902 39.130 0.00 0.00 35.81 3.58
178 179 5.496556 TGGAAACAGACTCTCTTTTGTCAA 58.503 37.500 0.00 0.00 35.81 3.18
179 180 5.943416 TGGAAACAGACTCTCTTTTGTCAAA 59.057 36.000 0.00 0.00 35.81 2.69
180 181 6.432783 TGGAAACAGACTCTCTTTTGTCAAAA 59.567 34.615 10.27 10.27 35.81 2.44
181 182 7.040062 TGGAAACAGACTCTCTTTTGTCAAAAA 60.040 33.333 11.73 3.27 35.81 1.94
216 217 5.201713 TGGAAACAGAGGATCGATCATAC 57.798 43.478 25.93 15.70 42.67 2.39
217 218 4.230657 GGAAACAGAGGATCGATCATACG 58.769 47.826 25.93 15.67 42.67 3.06
218 219 4.261656 GGAAACAGAGGATCGATCATACGT 60.262 45.833 25.93 16.28 42.67 3.57
219 220 5.048921 GGAAACAGAGGATCGATCATACGTA 60.049 44.000 25.93 0.00 42.67 3.57
220 221 5.614923 AACAGAGGATCGATCATACGTAG 57.385 43.478 25.93 10.59 42.67 3.51
221 222 4.643463 ACAGAGGATCGATCATACGTAGT 58.357 43.478 25.93 11.16 43.95 2.73
222 223 4.691685 ACAGAGGATCGATCATACGTAGTC 59.308 45.833 25.93 6.18 40.50 2.59
223 224 4.691216 CAGAGGATCGATCATACGTAGTCA 59.309 45.833 25.93 0.00 40.50 3.41
224 225 4.691685 AGAGGATCGATCATACGTAGTCAC 59.308 45.833 25.93 4.76 40.50 3.67
225 226 3.752222 AGGATCGATCATACGTAGTCACC 59.248 47.826 25.93 5.34 43.93 4.02
226 227 3.424565 GGATCGATCATACGTAGTCACCG 60.425 52.174 25.93 1.42 43.93 4.94
227 228 1.262417 TCGATCATACGTAGTCACCGC 59.738 52.381 0.08 0.00 43.93 5.68
228 229 1.263484 CGATCATACGTAGTCACCGCT 59.737 52.381 0.08 0.00 43.93 5.52
229 230 2.651701 GATCATACGTAGTCACCGCTG 58.348 52.381 0.08 0.00 43.93 5.18
230 231 1.456296 TCATACGTAGTCACCGCTGT 58.544 50.000 0.08 0.00 43.93 4.40
231 232 1.131693 TCATACGTAGTCACCGCTGTG 59.868 52.381 1.20 1.20 43.93 3.66
232 233 0.454600 ATACGTAGTCACCGCTGTGG 59.545 55.000 8.50 5.54 43.93 4.17
389 392 0.914417 TCACACTCCCTCCAATCCCC 60.914 60.000 0.00 0.00 0.00 4.81
442 445 1.890979 CATGGCATCGGAGCAGGTC 60.891 63.158 0.00 0.00 35.83 3.85
596 599 3.869272 GAGTGCTGCGCCCAATCG 61.869 66.667 9.97 0.00 0.00 3.34
630 634 2.364973 TGCCTCCCGGTGCATCTA 60.365 61.111 0.00 0.00 31.31 1.98
648 652 2.695666 TCTATGCTTACTCCCTGTGCTC 59.304 50.000 0.00 0.00 0.00 4.26
844 851 5.331902 CCGGATTAAAATACTTGTGCAGTG 58.668 41.667 0.00 0.00 35.97 3.66
1180 1189 1.684983 GCAATTACATCAGCTGGGCAT 59.315 47.619 15.13 0.00 0.00 4.40
1293 1302 9.739276 AAACAGATCAATGATAGAGTTTTGGTA 57.261 29.630 11.72 0.00 0.00 3.25
1845 1854 0.396974 ACTGCAAAAGGCCTGGACAA 60.397 50.000 5.69 0.00 43.89 3.18
1941 1950 5.045286 AGGTCAAGGAGCTCATAAAAGACAT 60.045 40.000 17.19 9.87 35.30 3.06
2425 2440 3.517100 TGCTTTTCAGGAGCTAGAGACAT 59.483 43.478 0.00 0.00 40.75 3.06
2519 2537 3.632643 TGCATCATGCTTGTCTCCTAA 57.367 42.857 11.84 0.00 45.31 2.69
2895 2913 5.540337 TCAACATGGGGCAACTATTAAAACA 59.460 36.000 0.00 0.00 0.00 2.83
3033 3051 6.908825 TGCAGAGCGTAAAAATAGACATTTT 58.091 32.000 0.00 0.00 44.45 1.82
3070 3088 6.021596 CGCTCACTTATGTTTACAATGAACC 58.978 40.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.734620 CATTTTGTTTTCAGTAATCTCTGTGAA 57.265 29.630 0.00 0.00 36.85 3.18
17 18 8.902806 ACATTTTGTTTTCAGTAATCTCTGTGA 58.097 29.630 0.00 0.00 36.85 3.58
18 19 9.520204 AACATTTTGTTTTCAGTAATCTCTGTG 57.480 29.630 0.00 0.00 37.26 3.66
28 29 8.026607 CCCGACATATAACATTTTGTTTTCAGT 58.973 33.333 0.00 0.00 41.45 3.41
29 30 7.009174 GCCCGACATATAACATTTTGTTTTCAG 59.991 37.037 0.00 0.00 41.45 3.02
30 31 6.809196 GCCCGACATATAACATTTTGTTTTCA 59.191 34.615 0.00 0.00 41.45 2.69
31 32 6.254804 GGCCCGACATATAACATTTTGTTTTC 59.745 38.462 0.00 0.00 41.45 2.29
32 33 6.103330 GGCCCGACATATAACATTTTGTTTT 58.897 36.000 0.00 0.00 41.45 2.43
33 34 5.186021 TGGCCCGACATATAACATTTTGTTT 59.814 36.000 0.00 0.00 41.45 2.83
34 35 4.707448 TGGCCCGACATATAACATTTTGTT 59.293 37.500 0.00 0.00 43.88 2.83
35 36 4.097286 GTGGCCCGACATATAACATTTTGT 59.903 41.667 0.00 0.00 0.00 2.83
36 37 4.499019 GGTGGCCCGACATATAACATTTTG 60.499 45.833 0.00 0.00 0.00 2.44
37 38 3.634910 GGTGGCCCGACATATAACATTTT 59.365 43.478 0.00 0.00 0.00 1.82
38 39 3.219281 GGTGGCCCGACATATAACATTT 58.781 45.455 0.00 0.00 0.00 2.32
39 40 2.173782 TGGTGGCCCGACATATAACATT 59.826 45.455 0.00 0.00 0.00 2.71
40 41 1.771854 TGGTGGCCCGACATATAACAT 59.228 47.619 0.00 0.00 0.00 2.71
41 42 1.205055 TGGTGGCCCGACATATAACA 58.795 50.000 0.00 0.00 0.00 2.41
42 43 2.038557 AGATGGTGGCCCGACATATAAC 59.961 50.000 0.00 0.00 0.00 1.89
43 44 2.038426 CAGATGGTGGCCCGACATATAA 59.962 50.000 0.00 0.00 0.00 0.98
44 45 1.623311 CAGATGGTGGCCCGACATATA 59.377 52.381 0.00 0.00 0.00 0.86
45 46 0.397941 CAGATGGTGGCCCGACATAT 59.602 55.000 0.00 0.00 0.00 1.78
46 47 1.829456 CAGATGGTGGCCCGACATA 59.171 57.895 0.00 0.00 0.00 2.29
47 48 2.591753 CAGATGGTGGCCCGACAT 59.408 61.111 0.00 1.18 0.00 3.06
48 49 4.408821 GCAGATGGTGGCCCGACA 62.409 66.667 0.00 0.00 0.00 4.35
49 50 2.731571 TAGCAGATGGTGGCCCGAC 61.732 63.158 0.00 0.00 0.00 4.79
50 51 2.364973 TAGCAGATGGTGGCCCGA 60.365 61.111 0.00 0.00 0.00 5.14
51 52 2.203070 GTAGCAGATGGTGGCCCG 60.203 66.667 0.00 0.00 0.00 6.13
52 53 1.153086 CTGTAGCAGATGGTGGCCC 60.153 63.158 0.00 0.00 32.44 5.80
53 54 0.462759 GTCTGTAGCAGATGGTGGCC 60.463 60.000 0.00 0.00 42.73 5.36
54 55 0.807667 CGTCTGTAGCAGATGGTGGC 60.808 60.000 9.76 0.00 42.73 5.01
55 56 0.807667 GCGTCTGTAGCAGATGGTGG 60.808 60.000 16.96 1.85 44.83 4.61
56 57 2.670635 GCGTCTGTAGCAGATGGTG 58.329 57.895 16.96 4.22 44.83 4.17
58 59 0.743688 AGAGCGTCTGTAGCAGATGG 59.256 55.000 16.96 7.75 44.83 3.51
59 60 1.675483 AGAGAGCGTCTGTAGCAGATG 59.325 52.381 12.53 12.53 46.70 2.90
60 61 1.946768 GAGAGAGCGTCTGTAGCAGAT 59.053 52.381 1.99 0.00 42.73 2.90
61 62 1.065782 AGAGAGAGCGTCTGTAGCAGA 60.066 52.381 0.00 0.00 38.25 4.26
62 63 1.330521 GAGAGAGAGCGTCTGTAGCAG 59.669 57.143 0.00 0.00 34.71 4.24
63 64 1.374560 GAGAGAGAGCGTCTGTAGCA 58.625 55.000 0.00 0.00 34.71 3.49
64 65 0.303493 CGAGAGAGAGCGTCTGTAGC 59.697 60.000 0.00 0.00 34.71 3.58
65 66 1.647346 ACGAGAGAGAGCGTCTGTAG 58.353 55.000 0.00 0.00 35.59 2.74
66 67 2.001159 GAACGAGAGAGAGCGTCTGTA 58.999 52.381 0.00 0.00 40.23 2.74
67 68 0.800012 GAACGAGAGAGAGCGTCTGT 59.200 55.000 0.00 0.00 40.23 3.41
68 69 0.247497 CGAACGAGAGAGAGCGTCTG 60.247 60.000 0.00 0.00 40.23 3.51
69 70 1.973137 GCGAACGAGAGAGAGCGTCT 61.973 60.000 0.00 0.00 40.23 4.18
70 71 1.581657 GCGAACGAGAGAGAGCGTC 60.582 63.158 0.00 0.00 40.23 5.19
71 72 1.973137 GAGCGAACGAGAGAGAGCGT 61.973 60.000 0.00 0.00 43.39 5.07
72 73 1.297304 GAGCGAACGAGAGAGAGCG 60.297 63.158 0.00 0.00 33.86 5.03
73 74 1.063488 GGAGCGAACGAGAGAGAGC 59.937 63.158 0.00 0.00 0.00 4.09
74 75 1.027255 TGGGAGCGAACGAGAGAGAG 61.027 60.000 0.00 0.00 0.00 3.20
75 76 0.394488 ATGGGAGCGAACGAGAGAGA 60.394 55.000 0.00 0.00 0.00 3.10
76 77 0.457851 AATGGGAGCGAACGAGAGAG 59.542 55.000 0.00 0.00 0.00 3.20
77 78 0.456221 GAATGGGAGCGAACGAGAGA 59.544 55.000 0.00 0.00 0.00 3.10
78 79 0.528684 GGAATGGGAGCGAACGAGAG 60.529 60.000 0.00 0.00 0.00 3.20
79 80 0.970937 AGGAATGGGAGCGAACGAGA 60.971 55.000 0.00 0.00 0.00 4.04
80 81 0.108138 AAGGAATGGGAGCGAACGAG 60.108 55.000 0.00 0.00 0.00 4.18
81 82 0.391130 CAAGGAATGGGAGCGAACGA 60.391 55.000 0.00 0.00 0.00 3.85
82 83 0.673644 ACAAGGAATGGGAGCGAACG 60.674 55.000 0.00 0.00 0.00 3.95
83 84 2.007608 GTACAAGGAATGGGAGCGAAC 58.992 52.381 0.00 0.00 0.00 3.95
84 85 1.626321 TGTACAAGGAATGGGAGCGAA 59.374 47.619 0.00 0.00 0.00 4.70
85 86 1.271856 TGTACAAGGAATGGGAGCGA 58.728 50.000 0.00 0.00 0.00 4.93
86 87 2.107950 TTGTACAAGGAATGGGAGCG 57.892 50.000 3.59 0.00 0.00 5.03
87 88 3.620488 TCATTGTACAAGGAATGGGAGC 58.380 45.455 19.87 0.00 31.59 4.70
88 89 4.641989 CCTTCATTGTACAAGGAATGGGAG 59.358 45.833 29.60 19.76 41.74 4.30
89 90 4.290985 TCCTTCATTGTACAAGGAATGGGA 59.709 41.667 29.60 28.19 44.35 4.37
90 91 4.599041 TCCTTCATTGTACAAGGAATGGG 58.401 43.478 29.60 26.79 44.35 4.00
95 96 4.458989 GCATTGTCCTTCATTGTACAAGGA 59.541 41.667 18.42 18.42 44.98 3.36
96 97 4.218200 TGCATTGTCCTTCATTGTACAAGG 59.782 41.667 13.96 13.96 40.69 3.61
97 98 5.375417 TGCATTGTCCTTCATTGTACAAG 57.625 39.130 14.65 6.58 35.48 3.16
98 99 4.218200 CCTGCATTGTCCTTCATTGTACAA 59.782 41.667 11.41 11.41 36.37 2.41
99 100 3.758023 CCTGCATTGTCCTTCATTGTACA 59.242 43.478 0.00 0.00 32.14 2.90
100 101 3.758554 ACCTGCATTGTCCTTCATTGTAC 59.241 43.478 0.00 0.00 32.14 2.90
101 102 4.032960 ACCTGCATTGTCCTTCATTGTA 57.967 40.909 0.00 0.00 32.14 2.41
102 103 2.880443 ACCTGCATTGTCCTTCATTGT 58.120 42.857 0.00 0.00 32.14 2.71
103 104 3.181493 GCTACCTGCATTGTCCTTCATTG 60.181 47.826 0.00 0.00 42.31 2.82
104 105 3.019564 GCTACCTGCATTGTCCTTCATT 58.980 45.455 0.00 0.00 42.31 2.57
105 106 2.648059 GCTACCTGCATTGTCCTTCAT 58.352 47.619 0.00 0.00 42.31 2.57
106 107 2.113860 GCTACCTGCATTGTCCTTCA 57.886 50.000 0.00 0.00 42.31 3.02
117 118 1.227793 GCCATCCTCTGCTACCTGC 60.228 63.158 0.00 0.00 43.25 4.85
118 119 0.835941 AAGCCATCCTCTGCTACCTG 59.164 55.000 0.00 0.00 36.66 4.00
119 120 0.835941 CAAGCCATCCTCTGCTACCT 59.164 55.000 0.00 0.00 36.66 3.08
120 121 0.817229 GCAAGCCATCCTCTGCTACC 60.817 60.000 0.00 0.00 36.66 3.18
121 122 1.156645 CGCAAGCCATCCTCTGCTAC 61.157 60.000 0.00 0.00 36.66 3.58
122 123 1.144716 CGCAAGCCATCCTCTGCTA 59.855 57.895 0.00 0.00 36.66 3.49
123 124 2.124819 CGCAAGCCATCCTCTGCT 60.125 61.111 0.00 0.00 40.17 4.24
124 125 2.593468 TACCGCAAGCCATCCTCTGC 62.593 60.000 0.00 0.00 0.00 4.26
125 126 0.531532 CTACCGCAAGCCATCCTCTG 60.532 60.000 0.00 0.00 0.00 3.35
126 127 0.978146 ACTACCGCAAGCCATCCTCT 60.978 55.000 0.00 0.00 0.00 3.69
127 128 0.107654 AACTACCGCAAGCCATCCTC 60.108 55.000 0.00 0.00 0.00 3.71
128 129 0.392998 CAACTACCGCAAGCCATCCT 60.393 55.000 0.00 0.00 0.00 3.24
129 130 0.392461 TCAACTACCGCAAGCCATCC 60.392 55.000 0.00 0.00 0.00 3.51
130 131 1.331756 CATCAACTACCGCAAGCCATC 59.668 52.381 0.00 0.00 0.00 3.51
131 132 1.340017 ACATCAACTACCGCAAGCCAT 60.340 47.619 0.00 0.00 0.00 4.40
132 133 0.036164 ACATCAACTACCGCAAGCCA 59.964 50.000 0.00 0.00 0.00 4.75
133 134 1.664151 GTACATCAACTACCGCAAGCC 59.336 52.381 0.00 0.00 0.00 4.35
134 135 2.343101 TGTACATCAACTACCGCAAGC 58.657 47.619 0.00 0.00 0.00 4.01
135 136 3.309682 CCATGTACATCAACTACCGCAAG 59.690 47.826 5.07 0.00 0.00 4.01
136 137 3.055747 TCCATGTACATCAACTACCGCAA 60.056 43.478 5.07 0.00 0.00 4.85
137 138 2.498078 TCCATGTACATCAACTACCGCA 59.502 45.455 5.07 0.00 0.00 5.69
138 139 3.173668 TCCATGTACATCAACTACCGC 57.826 47.619 5.07 0.00 0.00 5.68
139 140 4.932799 TGTTTCCATGTACATCAACTACCG 59.067 41.667 5.07 0.00 0.00 4.02
140 141 6.092259 GTCTGTTTCCATGTACATCAACTACC 59.908 42.308 5.07 0.00 0.00 3.18
141 142 6.874134 AGTCTGTTTCCATGTACATCAACTAC 59.126 38.462 5.07 11.05 0.00 2.73
142 143 7.004555 AGTCTGTTTCCATGTACATCAACTA 57.995 36.000 5.07 0.70 0.00 2.24
143 144 5.869579 AGTCTGTTTCCATGTACATCAACT 58.130 37.500 5.07 4.87 0.00 3.16
144 145 5.934625 AGAGTCTGTTTCCATGTACATCAAC 59.065 40.000 5.07 9.81 0.00 3.18
145 146 6.014242 AGAGAGTCTGTTTCCATGTACATCAA 60.014 38.462 5.07 0.00 0.00 2.57
146 147 5.481824 AGAGAGTCTGTTTCCATGTACATCA 59.518 40.000 5.07 0.00 0.00 3.07
147 148 5.971763 AGAGAGTCTGTTTCCATGTACATC 58.028 41.667 5.07 0.00 0.00 3.06
148 149 6.365970 AAGAGAGTCTGTTTCCATGTACAT 57.634 37.500 1.41 1.41 0.00 2.29
149 150 5.808366 AAGAGAGTCTGTTTCCATGTACA 57.192 39.130 0.00 0.00 0.00 2.90
150 151 6.483640 ACAAAAGAGAGTCTGTTTCCATGTAC 59.516 38.462 15.04 0.00 0.00 2.90
151 152 6.591935 ACAAAAGAGAGTCTGTTTCCATGTA 58.408 36.000 15.04 0.00 0.00 2.29
152 153 5.440610 ACAAAAGAGAGTCTGTTTCCATGT 58.559 37.500 15.04 12.79 0.00 3.21
153 154 5.528690 TGACAAAAGAGAGTCTGTTTCCATG 59.471 40.000 15.04 12.22 35.81 3.66
154 155 5.684704 TGACAAAAGAGAGTCTGTTTCCAT 58.315 37.500 15.04 4.72 35.81 3.41
155 156 5.097742 TGACAAAAGAGAGTCTGTTTCCA 57.902 39.130 15.04 10.79 35.81 3.53
156 157 6.436843 TTTGACAAAAGAGAGTCTGTTTCC 57.563 37.500 15.04 8.68 35.81 3.13
181 182 7.062957 TCCTCTGTTTCCATCTTCTTCTTTTT 58.937 34.615 0.00 0.00 0.00 1.94
182 183 6.605119 TCCTCTGTTTCCATCTTCTTCTTTT 58.395 36.000 0.00 0.00 0.00 2.27
183 184 6.192970 TCCTCTGTTTCCATCTTCTTCTTT 57.807 37.500 0.00 0.00 0.00 2.52
184 185 5.832539 TCCTCTGTTTCCATCTTCTTCTT 57.167 39.130 0.00 0.00 0.00 2.52
185 186 5.395103 CGATCCTCTGTTTCCATCTTCTTCT 60.395 44.000 0.00 0.00 0.00 2.85
186 187 4.808364 CGATCCTCTGTTTCCATCTTCTTC 59.192 45.833 0.00 0.00 0.00 2.87
187 188 4.467795 TCGATCCTCTGTTTCCATCTTCTT 59.532 41.667 0.00 0.00 0.00 2.52
188 189 4.026744 TCGATCCTCTGTTTCCATCTTCT 58.973 43.478 0.00 0.00 0.00 2.85
189 190 4.392921 TCGATCCTCTGTTTCCATCTTC 57.607 45.455 0.00 0.00 0.00 2.87
190 191 4.406972 TGATCGATCCTCTGTTTCCATCTT 59.593 41.667 22.31 0.00 0.00 2.40
191 192 3.963374 TGATCGATCCTCTGTTTCCATCT 59.037 43.478 22.31 0.00 0.00 2.90
192 193 4.327982 TGATCGATCCTCTGTTTCCATC 57.672 45.455 22.31 0.00 0.00 3.51
193 194 4.970860 ATGATCGATCCTCTGTTTCCAT 57.029 40.909 22.31 3.17 0.00 3.41
194 195 4.261614 CGTATGATCGATCCTCTGTTTCCA 60.262 45.833 22.31 0.69 0.00 3.53
195 196 4.230657 CGTATGATCGATCCTCTGTTTCC 58.769 47.826 22.31 0.00 0.00 3.13
196 197 4.861210 ACGTATGATCGATCCTCTGTTTC 58.139 43.478 22.31 0.00 34.70 2.78
197 198 4.920640 ACGTATGATCGATCCTCTGTTT 57.079 40.909 22.31 0.00 34.70 2.83
198 199 5.064558 ACTACGTATGATCGATCCTCTGTT 58.935 41.667 22.31 5.49 34.70 3.16
199 200 4.643463 ACTACGTATGATCGATCCTCTGT 58.357 43.478 22.31 16.82 34.70 3.41
200 201 4.691216 TGACTACGTATGATCGATCCTCTG 59.309 45.833 22.31 12.19 34.70 3.35
201 202 4.691685 GTGACTACGTATGATCGATCCTCT 59.308 45.833 22.31 9.80 34.70 3.69
202 203 4.142859 GGTGACTACGTATGATCGATCCTC 60.143 50.000 22.31 11.35 34.70 3.71
203 204 3.752222 GGTGACTACGTATGATCGATCCT 59.248 47.826 22.31 15.22 34.70 3.24
204 205 3.424565 CGGTGACTACGTATGATCGATCC 60.425 52.174 22.31 6.52 34.70 3.36
205 206 3.734031 CGGTGACTACGTATGATCGATC 58.266 50.000 18.72 18.72 34.70 3.69
206 207 2.095869 GCGGTGACTACGTATGATCGAT 60.096 50.000 0.00 0.00 34.70 3.59
207 208 1.262417 GCGGTGACTACGTATGATCGA 59.738 52.381 0.00 0.00 34.70 3.59
208 209 1.263484 AGCGGTGACTACGTATGATCG 59.737 52.381 0.00 0.00 0.00 3.69
209 210 2.033049 ACAGCGGTGACTACGTATGATC 59.967 50.000 23.44 0.00 0.00 2.92
210 211 2.022195 ACAGCGGTGACTACGTATGAT 58.978 47.619 23.44 0.00 0.00 2.45
211 212 1.456296 ACAGCGGTGACTACGTATGA 58.544 50.000 23.44 0.00 0.00 2.15
224 225 2.159043 ACAATCTCTCATACCACAGCGG 60.159 50.000 0.00 0.00 42.50 5.52
225 226 3.170791 ACAATCTCTCATACCACAGCG 57.829 47.619 0.00 0.00 0.00 5.18
226 227 3.624861 CCAACAATCTCTCATACCACAGC 59.375 47.826 0.00 0.00 0.00 4.40
227 228 4.633126 CACCAACAATCTCTCATACCACAG 59.367 45.833 0.00 0.00 0.00 3.66
228 229 4.041567 ACACCAACAATCTCTCATACCACA 59.958 41.667 0.00 0.00 0.00 4.17
229 230 4.393062 CACACCAACAATCTCTCATACCAC 59.607 45.833 0.00 0.00 0.00 4.16
230 231 4.041567 ACACACCAACAATCTCTCATACCA 59.958 41.667 0.00 0.00 0.00 3.25
231 232 4.579869 ACACACCAACAATCTCTCATACC 58.420 43.478 0.00 0.00 0.00 2.73
232 233 6.631016 TCTACACACCAACAATCTCTCATAC 58.369 40.000 0.00 0.00 0.00 2.39
233 234 6.850752 TCTACACACCAACAATCTCTCATA 57.149 37.500 0.00 0.00 0.00 2.15
234 235 5.745312 TCTACACACCAACAATCTCTCAT 57.255 39.130 0.00 0.00 0.00 2.90
235 236 5.745312 ATCTACACACCAACAATCTCTCA 57.255 39.130 0.00 0.00 0.00 3.27
236 237 7.766278 ACATTATCTACACACCAACAATCTCTC 59.234 37.037 0.00 0.00 0.00 3.20
237 238 7.624549 ACATTATCTACACACCAACAATCTCT 58.375 34.615 0.00 0.00 0.00 3.10
238 239 7.849804 ACATTATCTACACACCAACAATCTC 57.150 36.000 0.00 0.00 0.00 2.75
239 240 9.905713 ATTACATTATCTACACACCAACAATCT 57.094 29.630 0.00 0.00 0.00 2.40
389 392 4.267536 TGAGATTTGAGGGATTTGAGCTG 58.732 43.478 0.00 0.00 0.00 4.24
442 445 3.338249 AGGTCGAAATCACACAGGATTG 58.662 45.455 0.00 0.00 37.55 2.67
596 599 1.443802 GCAGTCAACAGGCTACCTTC 58.556 55.000 0.00 0.00 0.00 3.46
630 634 1.209019 CTGAGCACAGGGAGTAAGCAT 59.791 52.381 2.82 0.00 40.14 3.79
648 652 1.068748 GCAGCACAACATCCACTTCTG 60.069 52.381 0.00 0.00 0.00 3.02
844 851 2.780065 TTGCTCTCAAATGCACACAC 57.220 45.000 0.00 0.00 39.05 3.82
882 889 5.121811 CAAGCAGAGTTGATACTAGCCAAT 58.878 41.667 0.00 0.00 36.61 3.16
985 994 2.424601 CTGCCATGATTTACCACCACAG 59.575 50.000 0.00 0.00 0.00 3.66
1077 1086 1.462616 TGAGTTGTTGCTGTTGCTGT 58.537 45.000 0.00 0.00 40.48 4.40
1180 1189 2.101783 CAGAATTAACTGGGCATGCCA 58.898 47.619 36.56 21.67 37.98 4.92
1293 1302 5.140454 GGTTCCATGCTTCCTAATAACCAT 58.860 41.667 0.00 0.00 36.11 3.55
1845 1854 4.282703 AGCTCAAAGCATGAATCCTTTGTT 59.717 37.500 17.60 7.35 45.56 2.83
1941 1950 3.447229 TCTTGGATGTAGTGAGATTCGCA 59.553 43.478 0.00 0.00 0.00 5.10
2107 2116 4.406456 TGCATTGTAGAATTGTGGGTCTT 58.594 39.130 0.00 0.00 0.00 3.01
2425 2440 1.127567 CCAGTCCCCAACAGTCTCCA 61.128 60.000 0.00 0.00 0.00 3.86
2519 2537 6.459848 GCGATGGTGTAGTAGTAGTTCTTGAT 60.460 42.308 0.00 0.00 0.00 2.57
2895 2913 6.032956 TCTGTACCATTGTCTGAACGTAAT 57.967 37.500 0.00 0.00 0.00 1.89
3033 3051 0.880278 GTGAGCGTGCAACCTCAAGA 60.880 55.000 16.50 0.00 42.77 3.02
3070 3088 3.893326 CCCCCAAAGAAATTTAGGCAG 57.107 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.