Multiple sequence alignment - TraesCS4D01G267200

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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 TraesCS4D01G267200 chr4D 100.000 2532 0 0 1 2532 437819960 437817429 0.000000e+00 4676.0
1 TraesCS4D01G267200 chr4B 93.953 2067 74 26 2 2063 540727514 540725494 0.000000e+00 3077.0
2 TraesCS4D01G267200 chr4B 86.667 345 12 9 2197 2532 540725374 540725055 4.010000e-93 351.0
3 TraesCS4D01G267200 chr4A 88.812 2011 100 58 232 2162 30286000 30287965 0.000000e+00 2351.0
4 TraesCS4D01G267200 chr4A 88.073 109 10 3 2309 2417 30288165 30288270 2.640000e-25 126.0
5 TraesCS4D01G267200 chr7D 78.628 379 26 27 1100 1470 489299592 489299923 1.540000e-47 200.0
6 TraesCS4D01G267200 chr7D 76.579 380 28 28 1100 1471 484068737 484069063 4.360000e-33 152.0
7 TraesCS4D01G267200 chr5A 83.036 224 29 6 1107 1324 496204803 496204583 7.150000e-46 195.0
8 TraesCS4D01G267200 chr7B 78.284 373 30 20 1105 1471 509732857 509733184 2.570000e-45 193.0
9 TraesCS4D01G267200 chr7B 76.364 275 35 16 1202 1470 517931000 517931250 1.230000e-23 121.0
10 TraesCS4D01G267200 chr7A 78.016 373 31 29 1105 1471 551540228 551540555 1.200000e-43 187.0
11 TraesCS4D01G267200 chrUn 82.143 224 22 11 1107 1324 332176341 332176130 2.590000e-40 176.0
12 TraesCS4D01G267200 chr5D 82.143 224 22 11 1107 1324 394548799 394548588 2.590000e-40 176.0
13 TraesCS4D01G267200 chr5D 82.143 224 22 11 1107 1324 394550812 394550601 2.590000e-40 176.0
14 TraesCS4D01G267200 chr5D 76.676 373 44 29 1107 1467 394163289 394162948 1.560000e-37 167.0
15 TraesCS4D01G267200 chr5D 83.505 194 15 8 1107 1296 394190508 394190328 5.600000e-37 165.0
16 TraesCS4D01G267200 chr5D 83.333 78 10 1 1481 1558 394190055 394189981 4.520000e-08 69.4
17 TraesCS4D01G267200 chr5B 80.932 236 27 10 1107 1324 474279005 474278770 1.200000e-38 171.0
18 TraesCS4D01G267200 chr5B 81.614 223 23 10 1108 1324 474453437 474453227 4.330000e-38 169.0
19 TraesCS4D01G267200 chr5B 75.393 382 47 29 1100 1467 474047939 474047591 9.440000e-30 141.0
20 TraesCS4D01G267200 chr5B 88.000 50 6 0 1481 1530 474055876 474055827 2.720000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G267200 chr4D 437817429 437819960 2531 True 4676.0 4676 100.0000 1 2532 1 chr4D.!!$R1 2531
1 TraesCS4D01G267200 chr4B 540725055 540727514 2459 True 1714.0 3077 90.3100 2 2532 2 chr4B.!!$R1 2530
2 TraesCS4D01G267200 chr4A 30286000 30288270 2270 False 1238.5 2351 88.4425 232 2417 2 chr4A.!!$F1 2185

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
120 122 0.809241 CAGAAGACGGAGCTGGCATC 60.809 60.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1826 0.603065 CACCATCGACTCACTGACCA 59.397 55.0 0.0 0.0 0.0 4.02 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
80 81 4.441792 TGCTCGCACTTATGAATGTACAT 58.558 39.130 1.41 1.41 0.00 2.29
94 96 5.599242 TGAATGTACATCCGTACCCTATGAA 59.401 40.000 9.23 0.00 46.33 2.57
96 98 4.279982 TGTACATCCGTACCCTATGAACA 58.720 43.478 0.00 0.00 46.33 3.18
97 99 4.710865 TGTACATCCGTACCCTATGAACAA 59.289 41.667 0.00 0.00 46.33 2.83
101 103 2.762327 TCCGTACCCTATGAACAACTCC 59.238 50.000 0.00 0.00 0.00 3.85
103 105 3.430374 CCGTACCCTATGAACAACTCCAG 60.430 52.174 0.00 0.00 0.00 3.86
120 122 0.809241 CAGAAGACGGAGCTGGCATC 60.809 60.000 0.00 0.00 0.00 3.91
128 130 1.226974 GAGCTGGCATCGCGTCTTA 60.227 57.895 5.77 0.00 0.00 2.10
157 159 3.172050 CGAAGTAATCACAGACACCTCG 58.828 50.000 0.00 0.00 0.00 4.63
160 162 4.966965 AGTAATCACAGACACCTCGTAG 57.033 45.455 0.00 0.00 0.00 3.51
163 165 1.154197 TCACAGACACCTCGTAGTCG 58.846 55.000 0.00 0.00 39.67 4.18
175 177 4.644103 CTCGTAGTCGGGGAATAAAGAA 57.356 45.455 0.00 0.00 37.69 2.52
176 178 5.197682 CTCGTAGTCGGGGAATAAAGAAT 57.802 43.478 0.00 0.00 37.69 2.40
212 214 6.322491 GCATGTGTAAACTCAATCCTTTACC 58.678 40.000 0.00 0.00 33.60 2.85
213 215 6.625081 GCATGTGTAAACTCAATCCTTTACCC 60.625 42.308 0.00 0.00 33.60 3.69
345 348 4.877823 CCATGCTGTCTTGTGCTATAGAAA 59.122 41.667 3.21 0.00 0.00 2.52
747 805 2.069775 CCCCATCTCTCCCTCTCTCTA 58.930 57.143 0.00 0.00 0.00 2.43
748 806 2.225017 CCCCATCTCTCCCTCTCTCTAC 60.225 59.091 0.00 0.00 0.00 2.59
751 809 1.525175 TCTCTCCCTCTCTCTACCCC 58.475 60.000 0.00 0.00 0.00 4.95
752 810 1.011545 TCTCTCCCTCTCTCTACCCCT 59.988 57.143 0.00 0.00 0.00 4.79
753 811 1.423921 CTCTCCCTCTCTCTACCCCTC 59.576 61.905 0.00 0.00 0.00 4.30
754 812 1.011545 TCTCCCTCTCTCTACCCCTCT 59.988 57.143 0.00 0.00 0.00 3.69
755 813 1.423921 CTCCCTCTCTCTACCCCTCTC 59.576 61.905 0.00 0.00 0.00 3.20
756 814 1.011545 TCCCTCTCTCTACCCCTCTCT 59.988 57.143 0.00 0.00 0.00 3.10
757 815 1.423921 CCCTCTCTCTACCCCTCTCTC 59.576 61.905 0.00 0.00 0.00 3.20
758 816 2.418669 CCTCTCTCTACCCCTCTCTCT 58.581 57.143 0.00 0.00 0.00 3.10
759 817 2.372172 CCTCTCTCTACCCCTCTCTCTC 59.628 59.091 0.00 0.00 0.00 3.20
760 818 3.318313 CTCTCTCTACCCCTCTCTCTCT 58.682 54.545 0.00 0.00 0.00 3.10
761 819 4.489737 CTCTCTCTACCCCTCTCTCTCTA 58.510 52.174 0.00 0.00 0.00 2.43
849 920 1.000884 TTCCCGCTATAAAACACGCG 58.999 50.000 3.53 3.53 44.69 6.01
850 921 1.011574 CCCGCTATAAAACACGCGC 60.012 57.895 5.73 0.00 43.84 6.86
851 922 1.366030 CCGCTATAAAACACGCGCG 60.366 57.895 30.96 30.96 43.84 6.86
852 923 1.342473 CGCTATAAAACACGCGCGT 59.658 52.632 32.73 32.73 39.11 6.01
1041 1113 3.353029 CAACCGTGCGTCCATGCA 61.353 61.111 0.00 0.00 43.95 3.96
1065 1137 4.636435 CGGCACTTCCCCGTGGTT 62.636 66.667 0.00 0.00 40.84 3.67
1087 1159 2.969950 TGTACTTTGTAGCTCACCTGGT 59.030 45.455 0.00 0.00 0.00 4.00
1106 1179 2.423185 GGTTTTGGCTTTGCTTTGCTTT 59.577 40.909 0.00 0.00 0.00 3.51
1559 1636 4.260355 CAATGGGATGCTGCGCGG 62.260 66.667 13.18 13.18 0.00 6.46
1701 1785 3.941483 CTCGAGCTGTTTATTCCACCATT 59.059 43.478 0.00 0.00 0.00 3.16
1709 1793 7.668052 AGCTGTTTATTCCACCATTAGTTTGTA 59.332 33.333 0.00 0.00 0.00 2.41
1726 1810 5.126545 AGTTTGTATACGCAGGTCTCATGTA 59.873 40.000 0.00 0.00 0.00 2.29
1727 1811 4.830826 TGTATACGCAGGTCTCATGTAG 57.169 45.455 0.00 0.00 0.00 2.74
1729 1813 3.992260 ATACGCAGGTCTCATGTAGTC 57.008 47.619 0.00 0.00 0.00 2.59
1730 1814 1.545841 ACGCAGGTCTCATGTAGTCA 58.454 50.000 0.00 0.00 0.00 3.41
1731 1815 2.103373 ACGCAGGTCTCATGTAGTCAT 58.897 47.619 0.00 0.00 34.21 3.06
1744 1828 5.872635 CATGTAGTCATGTGTTAAGCTTGG 58.127 41.667 9.86 0.00 44.37 3.61
1754 1842 3.495001 GTGTTAAGCTTGGTCAGTGAGTC 59.505 47.826 9.86 0.00 0.00 3.36
1802 1890 2.773487 TCGTGTCCAAAATGTACCCTG 58.227 47.619 0.00 0.00 0.00 4.45
1938 2027 1.611491 AGGGCATAAACCAAACACACG 59.389 47.619 0.00 0.00 0.00 4.49
1974 2067 2.488545 TCTCCCTTTCTTCTCTTCGTCG 59.511 50.000 0.00 0.00 0.00 5.12
1985 2078 0.242825 TCTTCGTCGCAATCTCGGTT 59.757 50.000 0.00 0.00 0.00 4.44
2039 2137 4.341235 AGGCAACCTGGAACTAAAGAAAAC 59.659 41.667 0.00 0.00 29.57 2.43
2043 2141 3.117776 ACCTGGAACTAAAGAAAACGGGT 60.118 43.478 0.00 0.00 0.00 5.28
2044 2142 3.887110 CCTGGAACTAAAGAAAACGGGTT 59.113 43.478 0.00 0.00 0.00 4.11
2055 2153 4.850680 AGAAAACGGGTTAGCAATCCATA 58.149 39.130 0.00 0.00 0.00 2.74
2056 2154 5.445964 AGAAAACGGGTTAGCAATCCATAT 58.554 37.500 0.00 0.00 0.00 1.78
2058 2156 5.514274 AAACGGGTTAGCAATCCATATTG 57.486 39.130 0.00 0.00 44.53 1.90
2059 2157 4.431416 ACGGGTTAGCAATCCATATTGA 57.569 40.909 2.38 0.00 44.50 2.57
2060 2158 4.389374 ACGGGTTAGCAATCCATATTGAG 58.611 43.478 2.38 0.00 44.50 3.02
2061 2159 4.102524 ACGGGTTAGCAATCCATATTGAGA 59.897 41.667 2.38 0.00 44.50 3.27
2062 2160 4.692625 CGGGTTAGCAATCCATATTGAGAG 59.307 45.833 2.38 0.00 44.50 3.20
2064 2162 5.221925 GGGTTAGCAATCCATATTGAGAGGA 60.222 44.000 2.38 0.00 44.50 3.71
2073 2171 9.135189 CAATCCATATTGAGAGGAAAATAACCA 57.865 33.333 0.00 0.00 44.50 3.67
2074 2172 8.930846 ATCCATATTGAGAGGAAAATAACCAG 57.069 34.615 0.00 0.00 34.62 4.00
2093 2194 4.165779 CCAGCCAATAATTTGAACGTCAC 58.834 43.478 0.00 0.00 34.60 3.67
2101 2202 7.332430 CCAATAATTTGAACGTCACACTACCTA 59.668 37.037 0.00 0.00 34.60 3.08
2102 2203 8.380644 CAATAATTTGAACGTCACACTACCTAG 58.619 37.037 0.00 0.00 34.60 3.02
2103 2204 4.924305 TTTGAACGTCACACTACCTAGT 57.076 40.909 0.00 0.00 36.90 2.57
2104 2205 6.579666 ATTTGAACGTCACACTACCTAGTA 57.420 37.500 0.00 0.00 34.13 1.82
2116 2217 7.503566 TCACACTACCTAGTACAAACAACTACT 59.496 37.037 0.00 0.00 34.13 2.57
2117 2218 8.786898 CACACTACCTAGTACAAACAACTACTA 58.213 37.037 0.00 0.00 34.13 1.82
2118 2219 9.354673 ACACTACCTAGTACAAACAACTACTAA 57.645 33.333 0.00 0.00 34.13 2.24
2150 2252 3.724914 GACGGCCTAGCACAGCTCC 62.725 68.421 0.00 0.00 40.44 4.70
2162 2264 2.097142 GCACAGCTCCATGAGATTTCAC 59.903 50.000 0.00 0.00 35.83 3.18
2164 2266 1.938577 CAGCTCCATGAGATTTCACCG 59.061 52.381 0.00 0.00 35.83 4.94
2168 2303 3.191371 GCTCCATGAGATTTCACCGTTTT 59.809 43.478 0.00 0.00 35.83 2.43
2169 2304 4.726416 CTCCATGAGATTTCACCGTTTTG 58.274 43.478 0.00 0.00 35.83 2.44
2172 2307 5.068460 TCCATGAGATTTCACCGTTTTGTTT 59.932 36.000 0.00 0.00 35.83 2.83
2192 2327 6.334202 TGTTTTCTTGTTGGATGTTGGTTAC 58.666 36.000 0.00 0.00 0.00 2.50
2200 2335 3.291584 TGGATGTTGGTTACTGCAACAA 58.708 40.909 10.27 0.00 41.34 2.83
2201 2336 3.067461 TGGATGTTGGTTACTGCAACAAC 59.933 43.478 10.27 8.19 41.34 3.32
2203 2338 4.537015 GATGTTGGTTACTGCAACAACTC 58.463 43.478 10.27 3.04 41.34 3.01
2205 2340 4.013728 TGTTGGTTACTGCAACAACTCTT 58.986 39.130 14.62 0.00 39.04 2.85
2206 2341 4.142491 TGTTGGTTACTGCAACAACTCTTG 60.142 41.667 14.62 0.00 39.04 3.02
2207 2342 3.879998 TGGTTACTGCAACAACTCTTGA 58.120 40.909 9.29 0.00 39.04 3.02
2234 2400 7.360269 CCCATTGATGTGTTGTTAATTCAAAGC 60.360 37.037 0.00 0.00 0.00 3.51
2237 2403 6.757237 TGATGTGTTGTTAATTCAAAGCCAT 58.243 32.000 0.00 0.00 0.00 4.40
2243 2409 5.798125 TGTTAATTCAAAGCCATGTTCCA 57.202 34.783 0.00 0.00 0.00 3.53
2259 2440 2.392933 TCCACGATCGTTGCAAAAAC 57.607 45.000 20.14 0.00 0.00 2.43
2298 2479 5.734855 AAGATGCACAATATTCACGGTAC 57.265 39.130 0.00 0.00 0.00 3.34
2426 2612 1.139853 GAAGCATCTCTCCGGGTGAAT 59.860 52.381 0.00 0.00 0.00 2.57
2427 2613 0.755686 AGCATCTCTCCGGGTGAATC 59.244 55.000 0.00 0.00 0.00 2.52
2428 2614 0.755686 GCATCTCTCCGGGTGAATCT 59.244 55.000 0.00 0.00 0.00 2.40
2429 2615 1.139853 GCATCTCTCCGGGTGAATCTT 59.860 52.381 0.00 0.00 0.00 2.40
2430 2616 2.365617 GCATCTCTCCGGGTGAATCTTA 59.634 50.000 0.00 0.00 0.00 2.10
2493 2683 7.928706 AGTACTATTACACCGGTGTAGTACTAG 59.071 40.741 44.76 37.24 46.92 2.57
2494 2684 6.653989 ACTATTACACCGGTGTAGTACTAGT 58.346 40.000 38.06 33.69 45.57 2.57
2495 2685 7.792032 ACTATTACACCGGTGTAGTACTAGTA 58.208 38.462 38.06 25.57 45.57 1.82
2496 2686 6.927294 ATTACACCGGTGTAGTACTAGTAC 57.073 41.667 38.06 23.03 45.57 2.73
2497 2687 6.049955 TTACACCGGTGTAGTACTAGTACT 57.950 41.667 38.06 32.39 45.57 2.73
2498 2688 5.677319 ACACCGGTGTAGTACTAGTACTA 57.323 43.478 38.23 30.50 45.02 1.82
2511 2701 0.462581 AGTACTACCGGTCGATCGCA 60.463 55.000 12.40 1.01 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.900710 TGCTTTTATATGAGCGTTTAAGAAAAA 57.099 25.926 4.11 0.00 41.75 1.94
80 81 2.762327 GGAGTTGTTCATAGGGTACGGA 59.238 50.000 0.00 0.00 0.00 4.69
101 103 0.809241 GATGCCAGCTCCGTCTTCTG 60.809 60.000 0.00 0.00 0.00 3.02
103 105 1.880340 CGATGCCAGCTCCGTCTTC 60.880 63.158 0.00 0.00 0.00 2.87
128 130 6.366332 GTGTCTGTGATTACTTCGTCAATCTT 59.634 38.462 0.00 0.00 33.26 2.40
145 147 0.168348 CCGACTACGAGGTGTCTGTG 59.832 60.000 0.00 0.00 42.66 3.66
149 151 0.962356 TTCCCCGACTACGAGGTGTC 60.962 60.000 0.00 0.00 42.66 3.67
152 154 2.442236 TTATTCCCCGACTACGAGGT 57.558 50.000 0.00 0.00 42.66 3.85
157 159 6.110707 TGTTCATTCTTTATTCCCCGACTAC 58.889 40.000 0.00 0.00 0.00 2.73
160 162 5.890424 TTGTTCATTCTTTATTCCCCGAC 57.110 39.130 0.00 0.00 0.00 4.79
163 165 7.267857 CCATCTTTGTTCATTCTTTATTCCCC 58.732 38.462 0.00 0.00 0.00 4.81
166 168 8.814235 CATGCCATCTTTGTTCATTCTTTATTC 58.186 33.333 0.00 0.00 0.00 1.75
167 169 8.316214 ACATGCCATCTTTGTTCATTCTTTATT 58.684 29.630 0.00 0.00 0.00 1.40
168 170 7.762615 CACATGCCATCTTTGTTCATTCTTTAT 59.237 33.333 0.00 0.00 0.00 1.40
169 171 7.092079 CACATGCCATCTTTGTTCATTCTTTA 58.908 34.615 0.00 0.00 0.00 1.85
170 172 5.929992 CACATGCCATCTTTGTTCATTCTTT 59.070 36.000 0.00 0.00 0.00 2.52
171 173 5.011329 ACACATGCCATCTTTGTTCATTCTT 59.989 36.000 0.00 0.00 0.00 2.52
172 174 4.525487 ACACATGCCATCTTTGTTCATTCT 59.475 37.500 0.00 0.00 0.00 2.40
173 175 4.813027 ACACATGCCATCTTTGTTCATTC 58.187 39.130 0.00 0.00 0.00 2.67
174 176 4.877378 ACACATGCCATCTTTGTTCATT 57.123 36.364 0.00 0.00 0.00 2.57
175 177 5.981088 TTACACATGCCATCTTTGTTCAT 57.019 34.783 0.00 0.00 0.00 2.57
176 178 5.301551 AGTTTACACATGCCATCTTTGTTCA 59.698 36.000 0.00 0.00 0.00 3.18
251 254 3.648339 TCTTTTGAGCAGTGCCAAATC 57.352 42.857 23.52 12.29 32.27 2.17
300 303 2.231235 GGTTGGATGGTAAAGTTGGCAG 59.769 50.000 0.00 0.00 0.00 4.85
747 805 1.228190 GAGGGTAGAGAGAGAGGGGT 58.772 60.000 0.00 0.00 0.00 4.95
748 806 1.423921 GAGAGGGTAGAGAGAGAGGGG 59.576 61.905 0.00 0.00 0.00 4.79
751 809 2.432874 TGTCGAGAGGGTAGAGAGAGAG 59.567 54.545 0.00 0.00 0.00 3.20
752 810 2.468915 TGTCGAGAGGGTAGAGAGAGA 58.531 52.381 0.00 0.00 0.00 3.10
753 811 2.992124 TGTCGAGAGGGTAGAGAGAG 57.008 55.000 0.00 0.00 0.00 3.20
754 812 3.546724 CAATGTCGAGAGGGTAGAGAGA 58.453 50.000 0.00 0.00 0.00 3.10
755 813 2.034053 GCAATGTCGAGAGGGTAGAGAG 59.966 54.545 0.00 0.00 0.00 3.20
756 814 2.025155 GCAATGTCGAGAGGGTAGAGA 58.975 52.381 0.00 0.00 0.00 3.10
757 815 1.067821 GGCAATGTCGAGAGGGTAGAG 59.932 57.143 0.00 0.00 0.00 2.43
758 816 1.112113 GGCAATGTCGAGAGGGTAGA 58.888 55.000 0.00 0.00 0.00 2.59
759 817 0.249073 CGGCAATGTCGAGAGGGTAG 60.249 60.000 0.00 0.00 29.41 3.18
760 818 1.672854 CCGGCAATGTCGAGAGGGTA 61.673 60.000 9.51 0.00 29.41 3.69
761 819 2.579201 CGGCAATGTCGAGAGGGT 59.421 61.111 0.00 0.00 29.41 4.34
850 921 3.803082 CAATGGCCTGGACGCACG 61.803 66.667 3.32 0.00 0.00 5.34
851 922 3.443045 CCAATGGCCTGGACGCAC 61.443 66.667 5.01 0.00 38.96 5.34
852 923 3.626996 CTCCAATGGCCTGGACGCA 62.627 63.158 9.65 0.00 40.71 5.24
934 1006 0.898320 TGGAGAAGAAGGAGAAGCGG 59.102 55.000 0.00 0.00 0.00 5.52
1021 1093 2.358247 ATGGACGCACGGTTGGTC 60.358 61.111 0.00 0.83 0.00 4.02
1034 1106 1.031571 GTGCCGATCCTTTGCATGGA 61.032 55.000 10.77 10.77 37.34 3.41
1041 1113 1.303282 GGGGAAGTGCCGATCCTTT 59.697 57.895 0.00 0.00 37.63 3.11
1065 1137 3.389983 ACCAGGTGAGCTACAAAGTACAA 59.610 43.478 0.00 0.00 0.00 2.41
1087 1159 3.672781 GCAAAAGCAAAGCAAAGCCAAAA 60.673 39.130 0.00 0.00 0.00 2.44
1273 1346 1.002624 CTTCTTGGGCGTGGGCTTA 60.003 57.895 0.00 0.00 39.81 3.09
1559 1636 7.227116 CACTACCACTACCACTCTAGAATAGAC 59.773 44.444 0.00 0.00 44.15 2.59
1701 1785 5.126545 ACATGAGACCTGCGTATACAAACTA 59.873 40.000 0.00 0.00 0.00 2.24
1709 1793 3.288092 TGACTACATGAGACCTGCGTAT 58.712 45.455 0.00 0.00 0.00 3.06
1726 1810 4.067896 CTGACCAAGCTTAACACATGACT 58.932 43.478 0.00 0.00 0.00 3.41
1727 1811 3.815401 ACTGACCAAGCTTAACACATGAC 59.185 43.478 0.00 0.00 0.00 3.06
1729 1813 3.814842 TCACTGACCAAGCTTAACACATG 59.185 43.478 0.00 0.00 0.00 3.21
1730 1814 4.067896 CTCACTGACCAAGCTTAACACAT 58.932 43.478 0.00 0.00 0.00 3.21
1731 1815 3.118408 ACTCACTGACCAAGCTTAACACA 60.118 43.478 0.00 0.00 0.00 3.72
1732 1816 3.467803 ACTCACTGACCAAGCTTAACAC 58.532 45.455 0.00 0.00 0.00 3.32
1735 1819 2.626266 TCGACTCACTGACCAAGCTTAA 59.374 45.455 0.00 0.00 0.00 1.85
1736 1820 2.235891 TCGACTCACTGACCAAGCTTA 58.764 47.619 0.00 0.00 0.00 3.09
1737 1821 1.040646 TCGACTCACTGACCAAGCTT 58.959 50.000 0.00 0.00 0.00 3.74
1738 1822 1.067283 CATCGACTCACTGACCAAGCT 60.067 52.381 0.00 0.00 0.00 3.74
1739 1823 1.354040 CATCGACTCACTGACCAAGC 58.646 55.000 0.00 0.00 0.00 4.01
1740 1824 1.273606 ACCATCGACTCACTGACCAAG 59.726 52.381 0.00 0.00 0.00 3.61
1741 1825 1.000843 CACCATCGACTCACTGACCAA 59.999 52.381 0.00 0.00 0.00 3.67
1742 1826 0.603065 CACCATCGACTCACTGACCA 59.397 55.000 0.00 0.00 0.00 4.02
1743 1827 0.603569 ACACCATCGACTCACTGACC 59.396 55.000 0.00 0.00 0.00 4.02
1744 1828 2.747989 TCTACACCATCGACTCACTGAC 59.252 50.000 0.00 0.00 0.00 3.51
1754 1842 3.256879 ACATGCCTAGATCTACACCATCG 59.743 47.826 0.00 1.15 0.00 3.84
1938 2027 1.943340 GGGAGAAGCATTGGATTCGAC 59.057 52.381 0.00 0.00 44.01 4.20
1974 2067 1.705256 TGTACGTCAACCGAGATTGC 58.295 50.000 0.00 0.00 40.70 3.56
1985 2078 1.193650 GCGCAAGAAACATGTACGTCA 59.806 47.619 0.30 0.00 43.02 4.35
2017 2115 4.617959 GTTTTCTTTAGTTCCAGGTTGCC 58.382 43.478 0.00 0.00 0.00 4.52
2039 2137 4.641396 TCTCAATATGGATTGCTAACCCG 58.359 43.478 0.00 0.00 42.01 5.28
2055 2153 4.934356 TGGCTGGTTATTTTCCTCTCAAT 58.066 39.130 0.00 0.00 0.00 2.57
2056 2154 4.380843 TGGCTGGTTATTTTCCTCTCAA 57.619 40.909 0.00 0.00 0.00 3.02
2058 2156 7.588497 ATTATTGGCTGGTTATTTTCCTCTC 57.412 36.000 0.00 0.00 0.00 3.20
2059 2157 7.978099 AATTATTGGCTGGTTATTTTCCTCT 57.022 32.000 0.00 0.00 0.00 3.69
2060 2158 8.257306 TCAAATTATTGGCTGGTTATTTTCCTC 58.743 33.333 0.00 0.00 37.15 3.71
2061 2159 8.144862 TCAAATTATTGGCTGGTTATTTTCCT 57.855 30.769 0.00 0.00 37.15 3.36
2062 2160 8.664798 GTTCAAATTATTGGCTGGTTATTTTCC 58.335 33.333 0.00 0.00 37.15 3.13
2064 2162 7.875554 ACGTTCAAATTATTGGCTGGTTATTTT 59.124 29.630 0.00 0.00 37.15 1.82
2073 2171 4.518970 AGTGTGACGTTCAAATTATTGGCT 59.481 37.500 0.00 0.00 37.15 4.75
2074 2172 4.794169 AGTGTGACGTTCAAATTATTGGC 58.206 39.130 0.00 0.00 37.15 4.52
2125 2227 0.815734 GTGCTAGGCCGTCACTAAGA 59.184 55.000 14.93 0.00 0.00 2.10
2130 2232 2.815647 GCTGTGCTAGGCCGTCAC 60.816 66.667 15.22 15.22 0.00 3.67
2150 2252 6.697019 AGAAAACAAAACGGTGAAATCTCATG 59.303 34.615 0.00 0.00 33.05 3.07
2162 2264 4.867608 ACATCCAACAAGAAAACAAAACGG 59.132 37.500 0.00 0.00 0.00 4.44
2164 2266 6.148645 ACCAACATCCAACAAGAAAACAAAAC 59.851 34.615 0.00 0.00 0.00 2.43
2168 2303 5.413309 AACCAACATCCAACAAGAAAACA 57.587 34.783 0.00 0.00 0.00 2.83
2169 2304 6.475402 CAGTAACCAACATCCAACAAGAAAAC 59.525 38.462 0.00 0.00 0.00 2.43
2172 2307 4.037446 GCAGTAACCAACATCCAACAAGAA 59.963 41.667 0.00 0.00 0.00 2.52
2192 2327 1.679139 TGGGTCAAGAGTTGTTGCAG 58.321 50.000 0.00 0.00 0.00 4.41
2200 2335 3.795688 ACACATCAATGGGTCAAGAGT 57.204 42.857 0.00 0.00 41.40 3.24
2201 2336 3.822735 ACAACACATCAATGGGTCAAGAG 59.177 43.478 0.00 0.00 45.22 2.85
2203 2338 4.589216 AACAACACATCAATGGGTCAAG 57.411 40.909 0.00 0.00 45.22 3.02
2205 2340 6.266330 TGAATTAACAACACATCAATGGGTCA 59.734 34.615 0.00 0.00 45.22 4.02
2206 2341 6.686630 TGAATTAACAACACATCAATGGGTC 58.313 36.000 0.00 0.00 45.22 4.46
2237 2403 1.300481 TTTGCAACGATCGTGGAACA 58.700 45.000 26.70 16.34 35.74 3.18
2243 2409 2.031191 AGAACGTTTTTGCAACGATCGT 59.969 40.909 16.60 16.60 45.79 3.73
2304 2485 5.981315 CAGTTCAAATGAAGACAGTGCATTT 59.019 36.000 0.00 0.00 41.44 2.32
2306 2487 4.022589 CCAGTTCAAATGAAGACAGTGCAT 60.023 41.667 0.00 0.00 34.27 3.96
2307 2488 3.316029 CCAGTTCAAATGAAGACAGTGCA 59.684 43.478 0.00 0.00 34.27 4.57
2312 2498 2.942804 TGGCCAGTTCAAATGAAGACA 58.057 42.857 0.00 0.00 34.27 3.41
2313 2499 4.219288 AGATTGGCCAGTTCAAATGAAGAC 59.781 41.667 17.29 0.00 34.27 3.01
2320 2506 4.038271 AGATCAGATTGGCCAGTTCAAA 57.962 40.909 17.29 7.32 0.00 2.69
2426 2612 4.854173 TGCACAGCCCAGAATTAATAAGA 58.146 39.130 0.00 0.00 0.00 2.10
2427 2613 5.179045 CTGCACAGCCCAGAATTAATAAG 57.821 43.478 0.00 0.00 32.03 1.73
2493 2683 0.316524 GTGCGATCGACCGGTAGTAC 60.317 60.000 21.57 5.45 0.00 2.73
2494 2684 1.765161 CGTGCGATCGACCGGTAGTA 61.765 60.000 21.57 0.00 0.00 1.82
2495 2685 2.796651 GTGCGATCGACCGGTAGT 59.203 61.111 21.57 0.00 0.00 2.73
2496 2686 2.352001 CGTGCGATCGACCGGTAG 60.352 66.667 21.57 8.08 0.00 3.18
2497 2687 2.819154 TCGTGCGATCGACCGGTA 60.819 61.111 21.57 0.00 34.85 4.02
2511 2701 2.895062 GTTTAATTCGTTGCACGTCGT 58.105 42.857 0.00 0.00 43.14 4.34


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

AutoCloner maintained by Alex Coulton.