Multiple sequence alignment - TraesCS2B01G573800

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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 TraesCS2B01G573800 chr2B 100.000 3137 0 0 1 3137 763494390 763491254 0.000000e+00 5794.0
1 TraesCS2B01G573800 chr2B 79.817 1090 171 25 977 2034 762957879 762956807 0.000000e+00 749.0
2 TraesCS2B01G573800 chr2B 80.495 1010 156 26 1045 2034 763506318 763505330 0.000000e+00 736.0
3 TraesCS2B01G573800 chr2B 80.373 1019 157 24 1077 2069 763449630 763448629 0.000000e+00 734.0
4 TraesCS2B01G573800 chr2B 84.987 393 48 6 1006 1398 763334933 763334552 3.790000e-104 388.0
5 TraesCS2B01G573800 chr2B 85.000 240 33 1 1006 1245 762811767 762811531 1.120000e-59 241.0
6 TraesCS2B01G573800 chr2B 88.043 184 16 2 1270 1447 762806163 762805980 2.450000e-51 213.0
7 TraesCS2B01G573800 chr2B 100.000 28 0 0 2402 2429 763477155 763477128 6.000000e-03 52.8
8 TraesCS2B01G573800 chr2A 97.502 2042 36 7 187 2216 753435165 753433127 0.000000e+00 3474.0
9 TraesCS2B01G573800 chr2A 96.636 862 19 3 2215 3066 753433003 753432142 0.000000e+00 1423.0
10 TraesCS2B01G573800 chr2A 82.168 1116 157 23 975 2061 753405169 753404067 0.000000e+00 920.0
11 TraesCS2B01G573800 chr2A 78.556 900 153 19 1151 2026 753464740 753463857 9.830000e-155 556.0
12 TraesCS2B01G573800 chr2A 77.941 408 84 5 1588 1991 734798843 734799248 1.870000e-62 250.0
13 TraesCS2B01G573800 chr2A 98.165 109 2 0 1 109 753435270 753435162 1.150000e-44 191.0
14 TraesCS2B01G573800 chr2A 100.000 29 0 0 3068 3096 377068981 377068953 2.000000e-03 54.7
15 TraesCS2B01G573800 chr2A 100.000 28 0 0 2402 2429 753422815 753422788 6.000000e-03 52.8
16 TraesCS2B01G573800 chr2D 85.560 2133 199 49 978 3053 621671503 621669423 0.000000e+00 2132.0
17 TraesCS2B01G573800 chr2D 80.517 1083 170 19 996 2050 621590103 621589034 0.000000e+00 793.0
18 TraesCS2B01G573800 chr2D 79.763 1013 165 23 1077 2069 621610181 621609189 0.000000e+00 699.0
19 TraesCS2B01G573800 chr2D 76.923 429 94 4 1588 2012 601427419 601427846 4.040000e-59 239.0
20 TraesCS2B01G573800 chr5D 81.111 270 46 5 1741 2007 45874033 45874300 8.810000e-51 211.0
21 TraesCS2B01G573800 chr7B 76.309 401 86 6 1634 2027 692377152 692376754 4.100000e-49 206.0
22 TraesCS2B01G573800 chr7B 74.384 406 88 11 1634 2027 692339845 692339444 3.240000e-35 159.0
23 TraesCS2B01G573800 chr7B 74.169 391 87 11 1647 2029 690905063 690905447 1.950000e-32 150.0
24 TraesCS2B01G573800 chr7B 97.222 72 1 1 3067 3137 26654961 26655032 1.530000e-23 121.0
25 TraesCS2B01G573800 chr7B 94.366 71 3 1 3068 3137 384115287 384115217 1.190000e-19 108.0
26 TraesCS2B01G573800 chr7A 73.469 392 86 14 1647 2028 698730068 698730451 7.060000e-27 132.0
27 TraesCS2B01G573800 chr7A 97.183 71 1 1 3068 3137 699747417 699747487 5.500000e-23 119.0
28 TraesCS2B01G573800 chr7A 73.244 299 69 8 1736 2028 698822682 698822975 7.160000e-17 99.0
29 TraesCS2B01G573800 chr6B 94.366 71 3 1 3068 3137 117115287 117115357 1.190000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G573800 chr2B 763491254 763494390 3136 True 5794 5794 100.000000 1 3137 1 chr2B.!!$R7 3136
1 TraesCS2B01G573800 chr2B 762956807 762957879 1072 True 749 749 79.817000 977 2034 1 chr2B.!!$R3 1057
2 TraesCS2B01G573800 chr2B 763505330 763506318 988 True 736 736 80.495000 1045 2034 1 chr2B.!!$R8 989
3 TraesCS2B01G573800 chr2B 763448629 763449630 1001 True 734 734 80.373000 1077 2069 1 chr2B.!!$R5 992
4 TraesCS2B01G573800 chr2A 753432142 753435270 3128 True 1696 3474 97.434333 1 3066 3 chr2A.!!$R5 3065
5 TraesCS2B01G573800 chr2A 753404067 753405169 1102 True 920 920 82.168000 975 2061 1 chr2A.!!$R2 1086
6 TraesCS2B01G573800 chr2A 753463857 753464740 883 True 556 556 78.556000 1151 2026 1 chr2A.!!$R4 875
7 TraesCS2B01G573800 chr2D 621669423 621671503 2080 True 2132 2132 85.560000 978 3053 1 chr2D.!!$R3 2075
8 TraesCS2B01G573800 chr2D 621589034 621590103 1069 True 793 793 80.517000 996 2050 1 chr2D.!!$R1 1054
9 TraesCS2B01G573800 chr2D 621609189 621610181 992 True 699 699 79.763000 1077 2069 1 chr2D.!!$R2 992

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
566 567 0.254178 ATGCCCAAGGACTGTGCTAG 59.746 55.0 1.14 0.0 0.00 3.42 F
1035 1059 0.257616 CCCTAATTTCCCCTCCGCAA 59.742 55.0 0.00 0.0 0.00 4.85 F
1610 1688 1.747325 TTGCAAAACTGCTGGAGGGC 61.747 55.0 0.00 0.0 35.49 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1688 1.197721 GTCATGTCCGCTCCTTTGTTG 59.802 52.381 0.00 0.00 0.0 3.33 R
1991 2096 1.273327 TCAACGCATGCTTCTCTGAGA 59.727 47.619 17.13 2.58 0.0 3.27 R
2517 2760 2.299582 CACAATGGAGATGGTTTTGGCA 59.700 45.455 0.00 0.00 0.0 4.92 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
109 110 2.503061 CAGAGGCATAGCGCTGGT 59.497 61.111 22.90 5.61 41.91 4.00
110 111 1.886313 CAGAGGCATAGCGCTGGTG 60.886 63.158 22.90 19.50 41.91 4.17
111 112 2.590007 GAGGCATAGCGCTGGTGG 60.590 66.667 22.90 7.65 41.91 4.61
112 113 4.864334 AGGCATAGCGCTGGTGGC 62.864 66.667 30.64 30.64 41.91 5.01
121 122 2.514824 GCTGGTGGCGGGATCTTC 60.515 66.667 0.00 0.00 0.00 2.87
122 123 2.989639 CTGGTGGCGGGATCTTCA 59.010 61.111 0.00 0.00 0.00 3.02
123 124 1.450312 CTGGTGGCGGGATCTTCAC 60.450 63.158 0.00 0.00 0.00 3.18
124 125 2.124695 GGTGGCGGGATCTTCACC 60.125 66.667 9.99 9.99 42.11 4.02
129 130 4.496670 CGGGATCTTCACCGTGTC 57.503 61.111 0.00 0.00 44.85 3.67
130 131 1.589630 CGGGATCTTCACCGTGTCA 59.410 57.895 0.00 0.00 44.85 3.58
131 132 0.458543 CGGGATCTTCACCGTGTCAG 60.459 60.000 0.00 0.00 44.85 3.51
132 133 0.895530 GGGATCTTCACCGTGTCAGA 59.104 55.000 0.00 2.34 0.00 3.27
133 134 1.275291 GGGATCTTCACCGTGTCAGAA 59.725 52.381 0.00 0.00 0.00 3.02
134 135 2.093447 GGGATCTTCACCGTGTCAGAAT 60.093 50.000 0.00 0.00 0.00 2.40
135 136 3.132289 GGGATCTTCACCGTGTCAGAATA 59.868 47.826 0.00 0.00 0.00 1.75
136 137 4.382685 GGGATCTTCACCGTGTCAGAATAA 60.383 45.833 0.00 0.00 0.00 1.40
137 138 5.360591 GGATCTTCACCGTGTCAGAATAAT 58.639 41.667 0.00 0.00 0.00 1.28
138 139 5.817816 GGATCTTCACCGTGTCAGAATAATT 59.182 40.000 0.00 0.00 0.00 1.40
139 140 6.316390 GGATCTTCACCGTGTCAGAATAATTT 59.684 38.462 0.00 0.00 0.00 1.82
140 141 6.480524 TCTTCACCGTGTCAGAATAATTTG 57.519 37.500 0.00 0.00 0.00 2.32
141 142 5.411361 TCTTCACCGTGTCAGAATAATTTGG 59.589 40.000 0.00 0.00 0.00 3.28
142 143 3.438781 TCACCGTGTCAGAATAATTTGGC 59.561 43.478 0.00 0.00 0.00 4.52
143 144 2.752903 ACCGTGTCAGAATAATTTGGCC 59.247 45.455 0.00 0.00 0.00 5.36
144 145 2.223249 CCGTGTCAGAATAATTTGGCCG 60.223 50.000 0.00 0.00 0.00 6.13
145 146 2.223249 CGTGTCAGAATAATTTGGCCGG 60.223 50.000 0.00 0.00 0.00 6.13
146 147 1.748493 TGTCAGAATAATTTGGCCGGC 59.252 47.619 21.18 21.18 0.00 6.13
147 148 1.067060 GTCAGAATAATTTGGCCGGCC 59.933 52.381 39.40 39.40 0.00 6.13
148 149 0.389025 CAGAATAATTTGGCCGGCCC 59.611 55.000 41.75 23.74 34.56 5.80
149 150 0.261696 AGAATAATTTGGCCGGCCCT 59.738 50.000 41.75 25.67 34.56 5.19
150 151 0.389025 GAATAATTTGGCCGGCCCTG 59.611 55.000 41.75 0.00 34.56 4.45
151 152 0.325203 AATAATTTGGCCGGCCCTGT 60.325 50.000 41.75 25.77 34.56 4.00
152 153 0.325203 ATAATTTGGCCGGCCCTGTT 60.325 50.000 41.75 31.45 34.56 3.16
153 154 0.543174 TAATTTGGCCGGCCCTGTTT 60.543 50.000 41.75 29.00 34.56 2.83
154 155 1.826340 AATTTGGCCGGCCCTGTTTC 61.826 55.000 41.75 16.63 34.56 2.78
155 156 2.730129 ATTTGGCCGGCCCTGTTTCT 62.730 55.000 41.75 16.84 34.56 2.52
156 157 2.937959 TTTGGCCGGCCCTGTTTCTT 62.938 55.000 41.75 0.00 34.56 2.52
157 158 3.373565 GGCCGGCCCTGTTTCTTG 61.374 66.667 36.64 0.00 0.00 3.02
158 159 4.056125 GCCGGCCCTGTTTCTTGC 62.056 66.667 18.11 0.00 0.00 4.01
159 160 3.373565 CCGGCCCTGTTTCTTGCC 61.374 66.667 0.00 0.00 40.54 4.52
160 161 3.373565 CGGCCCTGTTTCTTGCCC 61.374 66.667 0.00 0.00 40.87 5.36
161 162 2.203625 GGCCCTGTTTCTTGCCCA 60.204 61.111 0.00 0.00 37.94 5.36
162 163 2.574018 GGCCCTGTTTCTTGCCCAC 61.574 63.158 0.00 0.00 37.94 4.61
163 164 1.531602 GCCCTGTTTCTTGCCCACT 60.532 57.895 0.00 0.00 0.00 4.00
164 165 1.527433 GCCCTGTTTCTTGCCCACTC 61.527 60.000 0.00 0.00 0.00 3.51
165 166 0.895559 CCCTGTTTCTTGCCCACTCC 60.896 60.000 0.00 0.00 0.00 3.85
166 167 1.237285 CCTGTTTCTTGCCCACTCCG 61.237 60.000 0.00 0.00 0.00 4.63
167 168 1.228124 TGTTTCTTGCCCACTCCGG 60.228 57.895 0.00 0.00 0.00 5.14
177 178 4.473520 CACTCCGGCGGCTCCAAT 62.474 66.667 23.83 0.00 34.01 3.16
178 179 4.473520 ACTCCGGCGGCTCCAATG 62.474 66.667 23.83 7.24 34.01 2.82
179 180 4.161295 CTCCGGCGGCTCCAATGA 62.161 66.667 23.83 0.00 34.01 2.57
180 181 3.680620 CTCCGGCGGCTCCAATGAA 62.681 63.158 23.83 0.00 34.01 2.57
181 182 3.508840 CCGGCGGCTCCAATGAAC 61.509 66.667 15.42 0.00 34.01 3.18
182 183 3.864686 CGGCGGCTCCAATGAACG 61.865 66.667 7.61 0.00 34.01 3.95
183 184 2.435938 GGCGGCTCCAATGAACGA 60.436 61.111 0.00 0.00 34.01 3.85
184 185 1.819632 GGCGGCTCCAATGAACGAT 60.820 57.895 0.00 0.00 34.01 3.73
185 186 0.531974 GGCGGCTCCAATGAACGATA 60.532 55.000 0.00 0.00 34.01 2.92
186 187 0.582005 GCGGCTCCAATGAACGATAC 59.418 55.000 0.00 0.00 0.00 2.24
187 188 1.806623 GCGGCTCCAATGAACGATACT 60.807 52.381 0.00 0.00 0.00 2.12
188 189 1.860950 CGGCTCCAATGAACGATACTG 59.139 52.381 0.00 0.00 0.00 2.74
189 190 2.213499 GGCTCCAATGAACGATACTGG 58.787 52.381 0.00 0.00 0.00 4.00
205 206 1.043022 CTGGAAAGCAAGTGGCCTTT 58.957 50.000 3.32 0.00 46.50 3.11
216 217 1.372499 TGGCCTTTTCGTCTCGTCG 60.372 57.895 3.32 0.00 0.00 5.12
248 249 1.292223 GCGGAGTTAGGCTGTGTCA 59.708 57.895 0.00 0.00 0.00 3.58
268 269 1.218316 CTCCCGTTCGGCTAGCTTT 59.782 57.895 15.72 0.00 0.00 3.51
269 270 1.079405 TCCCGTTCGGCTAGCTTTG 60.079 57.895 15.72 5.25 0.00 2.77
338 339 3.117175 GATGTGCGGATGCCAGTGC 62.117 63.158 0.00 0.00 41.78 4.40
359 360 1.462616 CGGCAACATCCATTTCTCCA 58.537 50.000 0.00 0.00 0.00 3.86
439 440 3.254060 CTGTCATACCACAAAGACTCGG 58.746 50.000 0.00 0.00 32.41 4.63
468 469 1.411394 CAGCTTTGTTTGCGATGGTG 58.589 50.000 0.00 0.00 35.28 4.17
473 474 3.361977 GTTTGCGATGGTGGCGGT 61.362 61.111 0.00 0.00 0.00 5.68
512 513 3.477224 GAAGCAACAACGGCGGCAA 62.477 57.895 13.24 0.00 36.08 4.52
566 567 0.254178 ATGCCCAAGGACTGTGCTAG 59.746 55.000 1.14 0.00 0.00 3.42
646 647 6.876257 TGTTTTGTGAGGTTGCTTTTACAATT 59.124 30.769 0.00 0.00 0.00 2.32
766 768 7.466746 AAAAAGCAGGAATTACAAGCTATGA 57.533 32.000 7.93 0.00 34.66 2.15
790 792 7.706179 TGATTGTTTTGGATCAAGAAACTGAAC 59.294 33.333 14.72 6.97 35.04 3.18
791 793 6.773976 TGTTTTGGATCAAGAAACTGAACT 57.226 33.333 14.72 0.00 35.04 3.01
880 882 5.371344 AACAATAGCTAATCGTTCGTTCG 57.629 39.130 0.00 0.00 0.00 3.95
1035 1059 0.257616 CCCTAATTTCCCCTCCGCAA 59.742 55.000 0.00 0.00 0.00 4.85
1140 1167 2.019408 CACGTGTTCACGATCGCCA 61.019 57.895 27.77 4.08 36.85 5.69
1610 1688 1.747325 TTGCAAAACTGCTGGAGGGC 61.747 55.000 0.00 0.00 35.49 5.19
1714 1792 2.579241 TTCGACGCTCAGCTCTACGC 62.579 60.000 0.00 0.00 39.57 4.42
1908 2005 4.202090 GCCATGGAAAGGATGAAGTTGATC 60.202 45.833 18.40 0.00 0.00 2.92
2157 2263 3.586892 AGTTTCGCTAGGTTTAGAGTGC 58.413 45.455 0.00 0.00 0.00 4.40
2250 2483 3.740115 TGTTGCCTAGTCCTGAAGTTTC 58.260 45.455 0.00 0.00 0.00 2.78
2264 2497 3.128589 TGAAGTTTCCGCAGATAATTGGC 59.871 43.478 0.00 0.00 0.00 4.52
2286 2522 5.988561 GGCAGATGAGTAGGTTTATCAGAAG 59.011 44.000 0.00 0.00 0.00 2.85
2347 2583 8.857694 TTAGTCCTTTTAGAGGTATTTTGGTG 57.142 34.615 0.00 0.00 46.39 4.17
2431 2668 7.499232 AGCTCACTAGTTTTCTTGTAAATGTGT 59.501 33.333 0.00 0.00 34.45 3.72
2517 2760 7.870509 TTTCTAATTATCAATGAGCAGCACT 57.129 32.000 0.00 0.00 0.00 4.40
2635 2878 5.862924 TTCAGTCTATGCAAAGTGCTAAC 57.137 39.130 0.00 0.00 45.31 2.34
2735 2978 2.540769 GCTCGCAGCTTTGTTGTACAAA 60.541 45.455 10.51 5.04 44.91 2.83
2831 3084 4.750833 TCCTGGGTTAATTTTGGAGGAA 57.249 40.909 0.00 0.00 0.00 3.36
3021 3288 6.128688 GCAAATATCTATCGAAGCTGAGTTCC 60.129 42.308 0.00 0.00 0.00 3.62
3031 3298 1.964223 AGCTGAGTTCCGTTCTCTCAA 59.036 47.619 0.00 0.00 37.68 3.02
3041 3308 4.621991 TCCGTTCTCTCAAAGTTTCTCTG 58.378 43.478 0.00 0.00 0.00 3.35
3066 3333 5.380900 TCCAGTGTTAAATGACATTGACCA 58.619 37.500 0.34 0.00 38.95 4.02
3067 3334 5.473162 TCCAGTGTTAAATGACATTGACCAG 59.527 40.000 0.34 0.00 38.95 4.00
3068 3335 5.473162 CCAGTGTTAAATGACATTGACCAGA 59.527 40.000 0.34 0.00 38.95 3.86
3069 3336 6.151648 CCAGTGTTAAATGACATTGACCAGAT 59.848 38.462 0.34 0.00 38.95 2.90
3070 3337 7.025365 CAGTGTTAAATGACATTGACCAGATG 58.975 38.462 0.34 0.00 38.95 2.90
3071 3338 6.151648 AGTGTTAAATGACATTGACCAGATGG 59.848 38.462 0.34 0.00 42.17 3.51
3072 3339 6.150976 GTGTTAAATGACATTGACCAGATGGA 59.849 38.462 5.72 0.00 38.94 3.41
3073 3340 6.150976 TGTTAAATGACATTGACCAGATGGAC 59.849 38.462 5.72 0.00 38.94 4.02
3074 3341 2.385013 TGACATTGACCAGATGGACG 57.615 50.000 5.72 0.00 38.94 4.79
3075 3342 1.009829 GACATTGACCAGATGGACGC 58.990 55.000 5.72 0.00 38.94 5.19
3076 3343 0.615331 ACATTGACCAGATGGACGCT 59.385 50.000 5.72 0.00 38.94 5.07
3077 3344 1.293924 CATTGACCAGATGGACGCTC 58.706 55.000 5.72 0.00 38.94 5.03
3078 3345 1.134580 CATTGACCAGATGGACGCTCT 60.135 52.381 5.72 0.00 38.94 4.09
3079 3346 0.247460 TTGACCAGATGGACGCTCTG 59.753 55.000 5.72 0.00 39.88 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.824109 TCAGAGTAGCAATGTCGGGG 59.176 55.000 0.00 0.00 0.00 5.73
113 114 0.895530 TCTGACACGGTGAAGATCCC 59.104 55.000 16.29 0.00 0.00 3.85
114 115 2.743636 TTCTGACACGGTGAAGATCC 57.256 50.000 16.29 0.00 0.00 3.36
115 116 6.910536 AATTATTCTGACACGGTGAAGATC 57.089 37.500 16.29 2.17 0.00 2.75
116 117 6.094048 CCAAATTATTCTGACACGGTGAAGAT 59.906 38.462 16.29 9.45 0.00 2.40
117 118 5.411361 CCAAATTATTCTGACACGGTGAAGA 59.589 40.000 16.29 13.79 0.00 2.87
118 119 5.631026 CCAAATTATTCTGACACGGTGAAG 58.369 41.667 16.29 11.69 0.00 3.02
119 120 4.083003 GCCAAATTATTCTGACACGGTGAA 60.083 41.667 16.29 0.00 0.00 3.18
120 121 3.438781 GCCAAATTATTCTGACACGGTGA 59.561 43.478 16.29 0.00 0.00 4.02
121 122 3.427503 GGCCAAATTATTCTGACACGGTG 60.428 47.826 6.58 6.58 0.00 4.94
122 123 2.752903 GGCCAAATTATTCTGACACGGT 59.247 45.455 0.00 0.00 0.00 4.83
123 124 2.223249 CGGCCAAATTATTCTGACACGG 60.223 50.000 2.24 0.00 0.00 4.94
124 125 2.223249 CCGGCCAAATTATTCTGACACG 60.223 50.000 2.24 0.00 0.00 4.49
125 126 2.479560 GCCGGCCAAATTATTCTGACAC 60.480 50.000 18.11 0.00 0.00 3.67
126 127 1.748493 GCCGGCCAAATTATTCTGACA 59.252 47.619 18.11 0.00 0.00 3.58
127 128 1.067060 GGCCGGCCAAATTATTCTGAC 59.933 52.381 40.73 7.27 35.81 3.51
128 129 1.398692 GGCCGGCCAAATTATTCTGA 58.601 50.000 40.73 0.00 35.81 3.27
129 130 0.389025 GGGCCGGCCAAATTATTCTG 59.611 55.000 44.46 0.00 37.98 3.02
130 131 0.261696 AGGGCCGGCCAAATTATTCT 59.738 50.000 44.46 27.41 37.98 2.40
131 132 0.389025 CAGGGCCGGCCAAATTATTC 59.611 55.000 44.46 25.56 37.98 1.75
132 133 0.325203 ACAGGGCCGGCCAAATTATT 60.325 50.000 44.46 19.48 37.98 1.40
133 134 0.325203 AACAGGGCCGGCCAAATTAT 60.325 50.000 44.46 23.28 37.98 1.28
134 135 0.543174 AAACAGGGCCGGCCAAATTA 60.543 50.000 44.46 0.00 37.98 1.40
135 136 1.826340 GAAACAGGGCCGGCCAAATT 61.826 55.000 44.46 31.53 37.98 1.82
136 137 2.203773 AAACAGGGCCGGCCAAAT 60.204 55.556 44.46 28.05 37.98 2.32
137 138 2.915137 GAAACAGGGCCGGCCAAA 60.915 61.111 44.46 0.00 37.98 3.28
138 139 3.444818 AAGAAACAGGGCCGGCCAA 62.445 57.895 44.46 0.00 37.98 4.52
139 140 3.897122 AAGAAACAGGGCCGGCCA 61.897 61.111 44.46 0.00 37.98 5.36
140 141 3.373565 CAAGAAACAGGGCCGGCC 61.374 66.667 38.57 38.57 0.00 6.13
141 142 4.056125 GCAAGAAACAGGGCCGGC 62.056 66.667 21.18 21.18 0.00 6.13
142 143 3.373565 GGCAAGAAACAGGGCCGG 61.374 66.667 0.79 0.79 36.58 6.13
144 145 2.203625 TGGGCAAGAAACAGGGCC 60.204 61.111 0.00 0.00 46.62 5.80
145 146 1.527433 GAGTGGGCAAGAAACAGGGC 61.527 60.000 0.00 0.00 0.00 5.19
146 147 0.895559 GGAGTGGGCAAGAAACAGGG 60.896 60.000 0.00 0.00 0.00 4.45
147 148 1.237285 CGGAGTGGGCAAGAAACAGG 61.237 60.000 0.00 0.00 0.00 4.00
148 149 1.237285 CCGGAGTGGGCAAGAAACAG 61.237 60.000 0.00 0.00 0.00 3.16
149 150 1.228124 CCGGAGTGGGCAAGAAACA 60.228 57.895 0.00 0.00 0.00 2.83
150 151 3.668386 CCGGAGTGGGCAAGAAAC 58.332 61.111 0.00 0.00 0.00 2.78
160 161 4.473520 ATTGGAGCCGCCGGAGTG 62.474 66.667 7.68 0.00 40.66 3.51
161 162 4.473520 CATTGGAGCCGCCGGAGT 62.474 66.667 7.68 0.00 40.66 3.85
162 163 3.680620 TTCATTGGAGCCGCCGGAG 62.681 63.158 7.68 0.00 40.66 4.63
163 164 3.711814 TTCATTGGAGCCGCCGGA 61.712 61.111 7.68 0.00 40.66 5.14
164 165 3.508840 GTTCATTGGAGCCGCCGG 61.509 66.667 0.00 0.00 40.66 6.13
165 166 3.864686 CGTTCATTGGAGCCGCCG 61.865 66.667 0.00 0.00 40.66 6.46
166 167 0.531974 TATCGTTCATTGGAGCCGCC 60.532 55.000 0.00 0.00 37.10 6.13
167 168 0.582005 GTATCGTTCATTGGAGCCGC 59.418 55.000 0.00 0.00 0.00 6.53
168 169 1.860950 CAGTATCGTTCATTGGAGCCG 59.139 52.381 0.00 0.00 0.00 5.52
169 170 2.158957 TCCAGTATCGTTCATTGGAGCC 60.159 50.000 0.00 0.00 33.21 4.70
170 171 3.179443 TCCAGTATCGTTCATTGGAGC 57.821 47.619 0.00 0.00 33.21 4.70
171 172 4.034510 GCTTTCCAGTATCGTTCATTGGAG 59.965 45.833 0.00 0.00 38.99 3.86
172 173 3.938963 GCTTTCCAGTATCGTTCATTGGA 59.061 43.478 0.00 0.00 36.21 3.53
173 174 3.689161 TGCTTTCCAGTATCGTTCATTGG 59.311 43.478 0.00 0.00 0.00 3.16
174 175 4.944962 TGCTTTCCAGTATCGTTCATTG 57.055 40.909 0.00 0.00 0.00 2.82
175 176 5.003804 ACTTGCTTTCCAGTATCGTTCATT 58.996 37.500 0.00 0.00 0.00 2.57
176 177 4.393062 CACTTGCTTTCCAGTATCGTTCAT 59.607 41.667 0.00 0.00 0.00 2.57
177 178 3.745975 CACTTGCTTTCCAGTATCGTTCA 59.254 43.478 0.00 0.00 0.00 3.18
178 179 3.125316 CCACTTGCTTTCCAGTATCGTTC 59.875 47.826 0.00 0.00 0.00 3.95
179 180 3.074412 CCACTTGCTTTCCAGTATCGTT 58.926 45.455 0.00 0.00 0.00 3.85
180 181 2.699954 CCACTTGCTTTCCAGTATCGT 58.300 47.619 0.00 0.00 0.00 3.73
181 182 1.398390 GCCACTTGCTTTCCAGTATCG 59.602 52.381 0.00 0.00 36.87 2.92
182 183 1.745653 GGCCACTTGCTTTCCAGTATC 59.254 52.381 0.00 0.00 40.92 2.24
183 184 1.355720 AGGCCACTTGCTTTCCAGTAT 59.644 47.619 5.01 0.00 40.92 2.12
184 185 0.771127 AGGCCACTTGCTTTCCAGTA 59.229 50.000 5.01 0.00 40.92 2.74
185 186 0.106015 AAGGCCACTTGCTTTCCAGT 60.106 50.000 5.01 0.00 33.30 4.00
186 187 1.043022 AAAGGCCACTTGCTTTCCAG 58.957 50.000 5.01 0.00 38.50 3.86
187 188 1.412343 GAAAAGGCCACTTGCTTTCCA 59.588 47.619 5.01 0.00 38.50 3.53
188 189 1.602920 CGAAAAGGCCACTTGCTTTCC 60.603 52.381 5.01 0.00 38.50 3.13
189 190 1.067060 ACGAAAAGGCCACTTGCTTTC 59.933 47.619 5.01 3.15 38.50 2.62
205 206 2.488355 GATGCCCGACGAGACGAA 59.512 61.111 0.00 0.00 35.09 3.85
216 217 3.595758 CCGCCAAATCCGATGCCC 61.596 66.667 0.00 0.00 0.00 5.36
248 249 3.839432 GCTAGCCGAACGGGAGCT 61.839 66.667 15.01 8.28 40.66 4.09
300 301 1.574428 CGCTTCGAAAACCCCACAG 59.426 57.895 0.00 0.00 0.00 3.66
332 333 4.465512 GATGTTGCCGCGCACTGG 62.466 66.667 8.75 0.78 38.71 4.00
338 339 0.248215 GAGAAATGGATGTTGCCGCG 60.248 55.000 0.00 0.00 0.00 6.46
359 360 2.159627 GTCGACTTCAACCAATGCGATT 59.840 45.455 8.70 0.00 0.00 3.34
419 420 2.611971 GCCGAGTCTTTGTGGTATGACA 60.612 50.000 0.00 0.00 32.41 3.58
439 440 2.229675 AACAAAGCTGCCTTTTCTGC 57.770 45.000 0.00 0.00 39.20 4.26
468 469 3.528597 AGAGAAATGAGAACTACCGCC 57.471 47.619 0.00 0.00 0.00 6.13
512 513 2.884639 CCCTCGTCACAAAATTGGACTT 59.115 45.455 10.76 0.00 0.00 3.01
566 567 9.882996 GGAATGATCCAAAAACAAGAAATTTTC 57.117 29.630 0.66 0.66 45.79 2.29
621 622 5.392767 TGTAAAAGCAACCTCACAAAACA 57.607 34.783 0.00 0.00 0.00 2.83
646 647 2.768253 ACAGATGCCGAGACATGAAA 57.232 45.000 0.00 0.00 0.00 2.69
766 768 7.785033 AGTTCAGTTTCTTGATCCAAAACAAT 58.215 30.769 13.76 0.00 35.77 2.71
867 869 1.342555 CTGCCACGAACGAACGATTA 58.657 50.000 11.97 0.00 37.03 1.75
1035 1059 0.746659 GCCGCCATTGCCTATTCTTT 59.253 50.000 0.00 0.00 0.00 2.52
1610 1688 1.197721 GTCATGTCCGCTCCTTTGTTG 59.802 52.381 0.00 0.00 0.00 3.33
1714 1792 2.124570 CTCGCTGTCCCCCATTGG 60.125 66.667 0.00 0.00 0.00 3.16
1908 2005 4.941657 TCTTGCATAGCATACTCTCACAG 58.058 43.478 0.00 0.00 38.76 3.66
1991 2096 1.273327 TCAACGCATGCTTCTCTGAGA 59.727 47.619 17.13 2.58 0.00 3.27
2157 2263 2.127345 CTAGTACGCGCGGATCCG 60.127 66.667 35.22 30.03 43.09 4.18
2198 2304 4.527816 AGGTGTTATGTTGCAAATGACCAT 59.472 37.500 0.00 2.41 0.00 3.55
2250 2483 2.483106 CTCATCTGCCAATTATCTGCGG 59.517 50.000 0.00 0.00 0.00 5.69
2264 2497 8.474025 ACTTCTTCTGATAAACCTACTCATCTG 58.526 37.037 0.00 0.00 0.00 2.90
2286 2522 2.028020 CCTGGTCTAAGGTGGTCACTTC 60.028 54.545 0.93 0.00 32.17 3.01
2517 2760 2.299582 CACAATGGAGATGGTTTTGGCA 59.700 45.455 0.00 0.00 0.00 4.92
2635 2878 7.624360 TTGCACTATTTTTGGTGAGGTATAG 57.376 36.000 0.00 0.00 35.69 1.31
2735 2978 8.102484 ACAACATTCAAACTAGATACCCCTAT 57.898 34.615 0.00 0.00 0.00 2.57
2831 3084 2.530460 TGGTTGCCCAAAGCTCATAT 57.470 45.000 0.00 0.00 44.23 1.78
3021 3288 5.050702 GGAACAGAGAAACTTTGAGAGAACG 60.051 44.000 0.00 0.00 0.00 3.95
3041 3308 6.149633 GGTCAATGTCATTTAACACTGGAAC 58.850 40.000 0.00 0.00 27.82 3.62


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

AutoCloner maintained by Alex Coulton.