Multiple sequence alignment - TraesCS1D01G318800

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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 TraesCS1D01G318800 chr1D 100.000 2631 0 0 569 3199 413212361 413214991 0.000000e+00 4859.0
1 TraesCS1D01G318800 chr1D 100.000 181 0 0 1 181 413211793 413211973 5.110000e-88 335.0
2 TraesCS1D01G318800 chr1D 84.000 75 9 3 1350 1423 143362372 143362444 5.730000e-08 69.4
3 TraesCS1D01G318800 chr1B 89.699 2728 139 58 569 3190 556988937 556991628 0.000000e+00 3350.0
4 TraesCS1D01G318800 chr1B 86.154 65 8 1 1359 1423 192534782 192534845 5.730000e-08 69.4
5 TraesCS1D01G318800 chr1A 90.072 2085 93 41 574 2578 510280563 510282613 0.000000e+00 2599.0
6 TraesCS1D01G318800 chr1A 92.616 474 20 6 2726 3199 510282836 510283294 0.000000e+00 667.0
7 TraesCS1D01G318800 chr1A 86.154 65 8 1 1359 1423 146631073 146631010 5.730000e-08 69.4
8 TraesCS1D01G318800 chr4B 73.853 218 36 16 1210 1412 139399326 139399537 2.060000e-07 67.6
9 TraesCS1D01G318800 chr4B 73.853 218 36 16 1210 1412 139472471 139472682 2.060000e-07 67.6
10 TraesCS1D01G318800 chr4B 73.853 218 36 16 1210 1412 139510919 139511130 2.060000e-07 67.6
11 TraesCS1D01G318800 chr4D 73.659 205 37 12 1210 1402 97508808 97509007 2.660000e-06 63.9
12 TraesCS1D01G318800 chr4D 73.272 217 39 16 1210 1412 97958114 97958325 9.580000e-06 62.1
13 TraesCS1D01G318800 chr4D 73.171 205 38 12 1210 1402 97605446 97605645 1.240000e-04 58.4
14 TraesCS1D01G318800 chr4D 94.444 36 2 0 1210 1245 97720821 97720856 4.460000e-04 56.5
15 TraesCS1D01G318800 chr7D 96.875 32 1 0 103 134 615680312 615680281 2.000000e-03 54.7


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 TraesCS1D01G318800 chr1D 413211793 413214991 3198 False 2597 4859 100.000 1 3199 2 chr1D.!!$F2 3198
1 TraesCS1D01G318800 chr1B 556988937 556991628 2691 False 3350 3350 89.699 569 3190 1 chr1B.!!$F2 2621
2 TraesCS1D01G318800 chr1A 510280563 510283294 2731 False 1633 2599 91.344 574 3199 2 chr1A.!!$F1 2625

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
963 1006 1.146263 ATTTCCACCCTCGATCGCC 59.854 57.895 11.09 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 2494 1.134877 CAGTGCAGGACTCGTCATGAT 60.135 52.381 15.03 0.0 43.36 2.45 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
47 48 9.831737 AAACTTCATCGAATATTGAAAACTGAG 57.168 29.630 0.00 0.00 31.85 3.35
48 49 7.467623 ACTTCATCGAATATTGAAAACTGAGC 58.532 34.615 0.00 0.00 31.85 4.26
49 50 7.335422 ACTTCATCGAATATTGAAAACTGAGCT 59.665 33.333 0.00 0.00 31.85 4.09
50 51 8.716646 TTCATCGAATATTGAAAACTGAGCTA 57.283 30.769 0.00 0.00 0.00 3.32
51 52 8.893219 TCATCGAATATTGAAAACTGAGCTAT 57.107 30.769 0.00 0.00 0.00 2.97
52 53 8.982685 TCATCGAATATTGAAAACTGAGCTATC 58.017 33.333 0.00 0.00 0.00 2.08
53 54 8.986847 CATCGAATATTGAAAACTGAGCTATCT 58.013 33.333 0.00 0.00 0.00 1.98
54 55 8.948631 TCGAATATTGAAAACTGAGCTATCTT 57.051 30.769 0.00 0.00 0.00 2.40
55 56 9.383519 TCGAATATTGAAAACTGAGCTATCTTT 57.616 29.630 0.00 0.00 0.00 2.52
83 84 8.687824 AACAAAAGAAATGTTCAGTGTGTAAG 57.312 30.769 0.00 0.00 36.28 2.34
84 85 7.826690 ACAAAAGAAATGTTCAGTGTGTAAGT 58.173 30.769 0.00 0.00 0.00 2.24
85 86 8.952278 ACAAAAGAAATGTTCAGTGTGTAAGTA 58.048 29.630 0.00 0.00 0.00 2.24
86 87 9.781834 CAAAAGAAATGTTCAGTGTGTAAGTAA 57.218 29.630 0.00 0.00 0.00 2.24
91 92 9.783256 GAAATGTTCAGTGTGTAAGTAAAAAGT 57.217 29.630 0.00 0.00 0.00 2.66
92 93 9.567848 AAATGTTCAGTGTGTAAGTAAAAAGTG 57.432 29.630 0.00 0.00 0.00 3.16
93 94 7.675962 TGTTCAGTGTGTAAGTAAAAAGTGT 57.324 32.000 0.00 0.00 0.00 3.55
94 95 7.523219 TGTTCAGTGTGTAAGTAAAAAGTGTG 58.477 34.615 0.00 0.00 0.00 3.82
95 96 6.114221 TCAGTGTGTAAGTAAAAAGTGTGC 57.886 37.500 0.00 0.00 0.00 4.57
96 97 5.644206 TCAGTGTGTAAGTAAAAAGTGTGCA 59.356 36.000 0.00 0.00 0.00 4.57
97 98 6.317642 TCAGTGTGTAAGTAAAAAGTGTGCAT 59.682 34.615 0.00 0.00 0.00 3.96
98 99 6.632834 CAGTGTGTAAGTAAAAAGTGTGCATC 59.367 38.462 0.00 0.00 0.00 3.91
99 100 6.317642 AGTGTGTAAGTAAAAAGTGTGCATCA 59.682 34.615 0.00 0.00 0.00 3.07
100 101 6.413818 GTGTGTAAGTAAAAAGTGTGCATCAC 59.586 38.462 10.33 10.33 46.46 3.06
102 103 7.138736 GTGTAAGTAAAAAGTGTGCATCACAT 58.861 34.615 17.71 6.73 46.32 3.21
103 104 8.286800 GTGTAAGTAAAAAGTGTGCATCACATA 58.713 33.333 17.71 6.32 46.32 2.29
104 105 9.008965 TGTAAGTAAAAAGTGTGCATCACATAT 57.991 29.630 17.71 5.02 46.32 1.78
105 106 9.277565 GTAAGTAAAAAGTGTGCATCACATATG 57.722 33.333 17.71 0.00 46.32 1.78
106 107 7.686438 AGTAAAAAGTGTGCATCACATATGA 57.314 32.000 10.38 0.00 46.32 2.15
107 108 8.109705 AGTAAAAAGTGTGCATCACATATGAA 57.890 30.769 10.38 0.00 46.32 2.57
108 109 8.575589 AGTAAAAAGTGTGCATCACATATGAAA 58.424 29.630 10.38 0.00 46.32 2.69
109 110 9.190858 GTAAAAAGTGTGCATCACATATGAAAA 57.809 29.630 10.38 0.00 46.32 2.29
110 111 8.659925 AAAAAGTGTGCATCACATATGAAAAA 57.340 26.923 10.38 0.00 46.32 1.94
111 112 7.878477 AAAGTGTGCATCACATATGAAAAAG 57.122 32.000 10.38 0.00 46.32 2.27
112 113 6.579666 AGTGTGCATCACATATGAAAAAGT 57.420 33.333 10.38 0.00 46.32 2.66
113 114 6.985117 AGTGTGCATCACATATGAAAAAGTT 58.015 32.000 10.38 0.00 46.32 2.66
114 115 7.086376 AGTGTGCATCACATATGAAAAAGTTC 58.914 34.615 10.38 0.00 46.32 3.01
115 116 6.862608 GTGTGCATCACATATGAAAAAGTTCA 59.137 34.615 10.38 0.00 46.32 3.18
116 117 7.381948 GTGTGCATCACATATGAAAAAGTTCAA 59.618 33.333 10.38 0.00 45.24 2.69
117 118 8.089597 TGTGCATCACATATGAAAAAGTTCAAT 58.910 29.630 10.38 0.00 42.08 2.57
118 119 8.377681 GTGCATCACATATGAAAAAGTTCAATG 58.622 33.333 10.38 2.77 39.52 2.82
119 120 8.089597 TGCATCACATATGAAAAAGTTCAATGT 58.910 29.630 10.38 9.48 46.66 2.71
120 121 8.377681 GCATCACATATGAAAAAGTTCAATGTG 58.622 33.333 22.25 22.25 46.66 3.21
121 122 9.414295 CATCACATATGAAAAAGTTCAATGTGT 57.586 29.630 24.34 15.00 46.66 3.72
142 143 8.563289 TGTGTATTTGAAATAAAACGTTCACC 57.437 30.769 0.00 0.00 33.58 4.02
143 144 7.376336 TGTGTATTTGAAATAAAACGTTCACCG 59.624 33.333 0.00 0.00 44.03 4.94
157 158 4.092816 CGTTCACCGTATATTGCAAAACC 58.907 43.478 1.71 0.00 0.00 3.27
158 159 4.142773 CGTTCACCGTATATTGCAAAACCT 60.143 41.667 1.71 0.00 0.00 3.50
159 160 5.063691 CGTTCACCGTATATTGCAAAACCTA 59.936 40.000 1.71 0.00 0.00 3.08
160 161 6.402334 CGTTCACCGTATATTGCAAAACCTAA 60.402 38.462 1.71 0.00 0.00 2.69
161 162 7.306953 GTTCACCGTATATTGCAAAACCTAAA 58.693 34.615 1.71 0.00 0.00 1.85
162 163 7.633193 TCACCGTATATTGCAAAACCTAAAT 57.367 32.000 1.71 0.00 0.00 1.40
163 164 8.734218 TCACCGTATATTGCAAAACCTAAATA 57.266 30.769 1.71 0.00 0.00 1.40
164 165 8.832521 TCACCGTATATTGCAAAACCTAAATAG 58.167 33.333 1.71 0.00 0.00 1.73
165 166 8.832521 CACCGTATATTGCAAAACCTAAATAGA 58.167 33.333 1.71 0.00 0.00 1.98
166 167 9.398538 ACCGTATATTGCAAAACCTAAATAGAA 57.601 29.630 1.71 0.00 0.00 2.10
174 175 9.487790 TTGCAAAACCTAAATAGAAAGGAAATG 57.512 29.630 0.00 0.00 36.66 2.32
175 176 8.646900 TGCAAAACCTAAATAGAAAGGAAATGT 58.353 29.630 0.00 0.00 36.66 2.71
176 177 9.489084 GCAAAACCTAAATAGAAAGGAAATGTT 57.511 29.630 0.00 0.00 36.66 2.71
760 783 4.675303 CCCTCCCCTCACCCACCA 62.675 72.222 0.00 0.00 0.00 4.17
822 845 2.772691 GGCGGAGTCCGTCCTACTG 61.773 68.421 31.12 2.66 46.90 2.74
935 966 4.415150 CCCATCCACTGTGCCGCT 62.415 66.667 1.29 0.00 0.00 5.52
962 1005 1.160329 CCATTTCCACCCTCGATCGC 61.160 60.000 11.09 0.00 0.00 4.58
963 1006 1.146263 ATTTCCACCCTCGATCGCC 59.854 57.895 11.09 0.00 0.00 5.54
1420 1476 3.984200 GACGCCGTCTACCTGGTGC 62.984 68.421 10.56 2.52 39.39 5.01
1458 1514 6.204108 ACCACGACGAGAAGTTGATTTAATTT 59.796 34.615 0.00 0.00 37.67 1.82
1460 1516 7.287950 CACGACGAGAAGTTGATTTAATTTGA 58.712 34.615 0.00 0.00 37.67 2.69
1489 1545 1.080093 CACCGGCTCTCGTGCTTAA 60.080 57.895 0.00 0.00 37.11 1.85
1685 1741 3.764237 ACGCACTTTTCCTTTCCTCTA 57.236 42.857 0.00 0.00 0.00 2.43
1686 1742 4.287766 ACGCACTTTTCCTTTCCTCTAT 57.712 40.909 0.00 0.00 0.00 1.98
1761 1825 1.135199 GCACTGACAATGGCATCCTTG 60.135 52.381 0.00 0.00 0.00 3.61
1994 2058 1.226603 CTACTACCGCCACGTGCTC 60.227 63.158 10.91 2.79 38.05 4.26
2040 2104 4.459089 GCAGCCTCCTCCACGACC 62.459 72.222 0.00 0.00 0.00 4.79
2211 2275 4.157246 TGTTGACTAGCCTTAGGTTCAGA 58.843 43.478 0.00 0.00 0.00 3.27
2212 2276 4.021368 TGTTGACTAGCCTTAGGTTCAGAC 60.021 45.833 0.00 0.00 0.00 3.51
2213 2277 3.774734 TGACTAGCCTTAGGTTCAGACA 58.225 45.455 0.00 0.00 0.00 3.41
2239 2306 1.452110 TGCACATGACATACACTGGC 58.548 50.000 0.00 0.00 0.00 4.85
2245 2312 3.943381 ACATGACATACACTGGCTGATTG 59.057 43.478 0.00 0.00 32.21 2.67
2246 2313 3.701205 TGACATACACTGGCTGATTGT 57.299 42.857 0.00 0.00 32.21 2.71
2247 2314 4.817318 TGACATACACTGGCTGATTGTA 57.183 40.909 0.00 0.00 32.21 2.41
2248 2315 5.357742 TGACATACACTGGCTGATTGTAT 57.642 39.130 0.00 0.35 36.99 2.29
2253 2320 2.840038 ACACTGGCTGATTGTATGAGGA 59.160 45.455 0.00 0.00 0.00 3.71
2254 2321 3.457380 ACACTGGCTGATTGTATGAGGAT 59.543 43.478 0.00 0.00 0.00 3.24
2257 2324 6.057533 CACTGGCTGATTGTATGAGGATTTA 58.942 40.000 0.00 0.00 0.00 1.40
2258 2325 6.713903 CACTGGCTGATTGTATGAGGATTTAT 59.286 38.462 0.00 0.00 0.00 1.40
2259 2326 6.713903 ACTGGCTGATTGTATGAGGATTTATG 59.286 38.462 0.00 0.00 0.00 1.90
2260 2327 6.604171 TGGCTGATTGTATGAGGATTTATGT 58.396 36.000 0.00 0.00 0.00 2.29
2261 2328 6.712095 TGGCTGATTGTATGAGGATTTATGTC 59.288 38.462 0.00 0.00 0.00 3.06
2262 2329 6.939163 GGCTGATTGTATGAGGATTTATGTCT 59.061 38.462 0.00 0.00 0.00 3.41
2263 2330 7.118971 GGCTGATTGTATGAGGATTTATGTCTC 59.881 40.741 0.00 0.00 0.00 3.36
2282 2349 5.992829 TGTCTCTATACGGTTCTCTGATCTC 59.007 44.000 0.00 0.00 0.00 2.75
2283 2354 5.410439 GTCTCTATACGGTTCTCTGATCTCC 59.590 48.000 0.00 0.00 0.00 3.71
2285 2356 5.691896 TCTATACGGTTCTCTGATCTCCAA 58.308 41.667 0.00 0.00 0.00 3.53
2323 2408 5.048921 ACTGAAGATGCAAGACAGTTTCATG 60.049 40.000 11.46 0.00 38.41 3.07
2324 2409 5.065235 TGAAGATGCAAGACAGTTTCATGA 58.935 37.500 0.00 0.00 32.61 3.07
2328 2413 2.810274 TGCAAGACAGTTTCATGAGCTC 59.190 45.455 6.82 6.82 0.00 4.09
2350 2435 5.207354 TCTTTAGCTCAGGAGATCATCACT 58.793 41.667 0.00 0.00 0.00 3.41
2410 2506 4.987832 ACTGTACAAGATCATGACGAGTC 58.012 43.478 4.68 0.00 0.00 3.36
2481 2605 0.467290 GGTCACCAAACTGGCCAGAA 60.467 55.000 39.19 11.69 42.67 3.02
2496 2620 9.435688 AACTGGCCAGAAATAACAAAATAATTC 57.564 29.630 39.19 0.00 0.00 2.17
2500 2624 7.011389 GGCCAGAAATAACAAAATAATTCAGCC 59.989 37.037 0.00 0.00 33.26 4.85
2517 2645 3.108289 CACAGAGTGCGTCAGCCG 61.108 66.667 0.00 0.00 44.33 5.52
2609 2818 1.803334 TGACCGGTGATGCACTAAAC 58.197 50.000 14.63 0.00 34.40 2.01
2610 2819 0.719465 GACCGGTGATGCACTAAACG 59.281 55.000 14.63 0.00 34.40 3.60
2614 2823 3.191669 CCGGTGATGCACTAAACGAATA 58.808 45.455 4.26 0.00 34.40 1.75
2615 2824 3.245284 CCGGTGATGCACTAAACGAATAG 59.755 47.826 4.26 0.00 34.40 1.73
2616 2825 3.302480 CGGTGATGCACTAAACGAATAGC 60.302 47.826 0.00 0.00 34.40 2.97
2617 2826 3.871594 GGTGATGCACTAAACGAATAGCT 59.128 43.478 0.00 0.00 34.40 3.32
2618 2827 4.332819 GGTGATGCACTAAACGAATAGCTT 59.667 41.667 0.00 0.00 34.40 3.74
2758 2989 3.885901 AGGAAAGCTTTGGAAAGAGACAC 59.114 43.478 18.30 0.00 38.28 3.67
2988 3220 2.025981 TGTGCTTACTGCTCCAATGGAT 60.026 45.455 0.87 0.00 43.37 3.41
3065 3297 3.561503 GTTGTACCTGCACGGAAATTTC 58.438 45.455 9.83 9.83 36.31 2.17
3070 3302 4.434713 ACCTGCACGGAAATTTCATAAC 57.565 40.909 19.49 6.98 36.31 1.89
3085 3317 9.846248 AAATTTCATAACTGAAGTGAGCATTAC 57.154 29.630 0.00 0.00 42.19 1.89
3087 3319 5.961272 TCATAACTGAAGTGAGCATTACGA 58.039 37.500 0.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.831737 CTCAGTTTTCAATATTCGATGAAGTTT 57.168 29.630 0.00 0.00 36.93 2.66
22 23 7.965107 GCTCAGTTTTCAATATTCGATGAAGTT 59.035 33.333 0.00 0.00 36.93 2.66
23 24 7.335422 AGCTCAGTTTTCAATATTCGATGAAGT 59.665 33.333 0.00 0.00 36.93 3.01
24 25 7.692088 AGCTCAGTTTTCAATATTCGATGAAG 58.308 34.615 0.00 0.00 36.93 3.02
25 26 7.615582 AGCTCAGTTTTCAATATTCGATGAA 57.384 32.000 0.00 0.00 33.93 2.57
26 27 8.893219 ATAGCTCAGTTTTCAATATTCGATGA 57.107 30.769 0.00 0.00 0.00 2.92
27 28 8.986847 AGATAGCTCAGTTTTCAATATTCGATG 58.013 33.333 0.00 0.00 0.00 3.84
28 29 9.553064 AAGATAGCTCAGTTTTCAATATTCGAT 57.447 29.630 0.00 0.00 0.00 3.59
29 30 8.948631 AAGATAGCTCAGTTTTCAATATTCGA 57.051 30.769 0.00 0.00 0.00 3.71
57 58 9.781834 CTTACACACTGAACATTTCTTTTGTTA 57.218 29.630 0.00 0.00 37.43 2.41
58 59 8.303876 ACTTACACACTGAACATTTCTTTTGTT 58.696 29.630 0.00 0.00 39.91 2.83
59 60 7.826690 ACTTACACACTGAACATTTCTTTTGT 58.173 30.769 0.00 0.00 0.00 2.83
60 61 9.781834 TTACTTACACACTGAACATTTCTTTTG 57.218 29.630 0.00 0.00 0.00 2.44
65 66 9.783256 ACTTTTTACTTACACACTGAACATTTC 57.217 29.630 0.00 0.00 0.00 2.17
66 67 9.567848 CACTTTTTACTTACACACTGAACATTT 57.432 29.630 0.00 0.00 0.00 2.32
67 68 8.736244 ACACTTTTTACTTACACACTGAACATT 58.264 29.630 0.00 0.00 0.00 2.71
68 69 8.181573 CACACTTTTTACTTACACACTGAACAT 58.818 33.333 0.00 0.00 0.00 2.71
69 70 7.523219 CACACTTTTTACTTACACACTGAACA 58.477 34.615 0.00 0.00 0.00 3.18
70 71 6.468000 GCACACTTTTTACTTACACACTGAAC 59.532 38.462 0.00 0.00 0.00 3.18
71 72 6.149640 TGCACACTTTTTACTTACACACTGAA 59.850 34.615 0.00 0.00 0.00 3.02
72 73 5.644206 TGCACACTTTTTACTTACACACTGA 59.356 36.000 0.00 0.00 0.00 3.41
73 74 5.874831 TGCACACTTTTTACTTACACACTG 58.125 37.500 0.00 0.00 0.00 3.66
74 75 6.317642 TGATGCACACTTTTTACTTACACACT 59.682 34.615 0.00 0.00 0.00 3.55
75 76 6.413818 GTGATGCACACTTTTTACTTACACAC 59.586 38.462 10.87 0.00 45.13 3.82
76 77 6.491394 GTGATGCACACTTTTTACTTACACA 58.509 36.000 10.87 0.00 45.13 3.72
77 78 6.969669 GTGATGCACACTTTTTACTTACAC 57.030 37.500 10.87 0.00 45.13 2.90
89 90 7.255555 TGAACTTTTTCATATGTGATGCACACT 60.256 33.333 16.70 8.06 40.85 3.55
90 91 6.862608 TGAACTTTTTCATATGTGATGCACAC 59.137 34.615 1.93 11.13 40.85 3.82
91 92 6.979465 TGAACTTTTTCATATGTGATGCACA 58.021 32.000 1.90 2.43 41.59 4.57
92 93 7.872163 TTGAACTTTTTCATATGTGATGCAC 57.128 32.000 1.90 0.00 41.50 4.57
93 94 8.089597 ACATTGAACTTTTTCATATGTGATGCA 58.910 29.630 1.90 0.00 41.50 3.96
94 95 8.470040 ACATTGAACTTTTTCATATGTGATGC 57.530 30.769 1.90 0.00 41.50 3.91
116 117 9.187455 GGTGAACGTTTTATTTCAAATACACAT 57.813 29.630 0.46 0.00 33.58 3.21
117 118 7.376336 CGGTGAACGTTTTATTTCAAATACACA 59.624 33.333 0.46 0.00 37.93 3.72
118 119 7.703840 CGGTGAACGTTTTATTTCAAATACAC 58.296 34.615 0.46 0.66 37.93 2.90
119 120 7.839438 CGGTGAACGTTTTATTTCAAATACA 57.161 32.000 0.46 0.00 37.93 2.29
136 137 5.305139 AGGTTTTGCAATATACGGTGAAC 57.695 39.130 0.00 0.00 0.00 3.18
137 138 7.450124 TTTAGGTTTTGCAATATACGGTGAA 57.550 32.000 0.00 0.00 0.00 3.18
138 139 7.633193 ATTTAGGTTTTGCAATATACGGTGA 57.367 32.000 0.00 0.00 0.00 4.02
139 140 8.832521 TCTATTTAGGTTTTGCAATATACGGTG 58.167 33.333 0.00 0.00 0.00 4.94
140 141 8.967664 TCTATTTAGGTTTTGCAATATACGGT 57.032 30.769 0.00 0.00 0.00 4.83
148 149 9.487790 CATTTCCTTTCTATTTAGGTTTTGCAA 57.512 29.630 0.00 0.00 33.15 4.08
149 150 8.646900 ACATTTCCTTTCTATTTAGGTTTTGCA 58.353 29.630 0.00 0.00 33.15 4.08
150 151 9.489084 AACATTTCCTTTCTATTTAGGTTTTGC 57.511 29.630 0.00 0.00 33.15 3.68
583 584 0.960861 TCGTGGACTCGCAGTCAGAT 60.961 55.000 15.22 0.00 46.79 2.90
682 691 4.082523 CGGTGTCGGCTCCATGGT 62.083 66.667 12.58 0.00 0.00 3.55
746 769 2.856988 GGTTGGTGGGTGAGGGGA 60.857 66.667 0.00 0.00 0.00 4.81
750 773 0.396417 TTGGTTGGTTGGTGGGTGAG 60.396 55.000 0.00 0.00 0.00 3.51
751 774 0.684805 GTTGGTTGGTTGGTGGGTGA 60.685 55.000 0.00 0.00 0.00 4.02
752 775 1.681486 GGTTGGTTGGTTGGTGGGTG 61.681 60.000 0.00 0.00 0.00 4.61
753 776 1.382009 GGTTGGTTGGTTGGTGGGT 60.382 57.895 0.00 0.00 0.00 4.51
754 777 0.978146 TTGGTTGGTTGGTTGGTGGG 60.978 55.000 0.00 0.00 0.00 4.61
755 778 0.176910 GTTGGTTGGTTGGTTGGTGG 59.823 55.000 0.00 0.00 0.00 4.61
760 783 1.765904 GGATTGGTTGGTTGGTTGGTT 59.234 47.619 0.00 0.00 0.00 3.67
822 845 2.100031 TGTGTGACGCGATGGATGC 61.100 57.895 15.93 0.00 0.00 3.91
935 966 2.034999 GTGGAAATGGGGACGGCA 59.965 61.111 0.00 0.00 0.00 5.69
1426 1482 2.287668 ACTTCTCGTCGTGGTCTCTTTG 60.288 50.000 0.00 0.00 0.00 2.77
1427 1483 1.955080 ACTTCTCGTCGTGGTCTCTTT 59.045 47.619 0.00 0.00 0.00 2.52
1458 1514 0.881118 GCCGGTGAAAAAGATGCTCA 59.119 50.000 1.90 0.00 0.00 4.26
1460 1516 1.168714 GAGCCGGTGAAAAAGATGCT 58.831 50.000 1.90 0.00 0.00 3.79
1671 1727 6.761714 GTGAAGCGATATAGAGGAAAGGAAAA 59.238 38.462 0.00 0.00 0.00 2.29
2087 2151 2.021355 AGTCCTGGTAGTACTCGTCG 57.979 55.000 0.00 0.00 0.00 5.12
2245 2312 8.958506 ACCGTATAGAGACATAAATCCTCATAC 58.041 37.037 0.00 0.00 0.00 2.39
2246 2313 9.529823 AACCGTATAGAGACATAAATCCTCATA 57.470 33.333 0.00 0.00 0.00 2.15
2247 2314 8.423906 AACCGTATAGAGACATAAATCCTCAT 57.576 34.615 0.00 0.00 0.00 2.90
2248 2315 7.724506 AGAACCGTATAGAGACATAAATCCTCA 59.275 37.037 0.00 0.00 0.00 3.86
2249 2316 8.113173 AGAACCGTATAGAGACATAAATCCTC 57.887 38.462 0.00 0.00 0.00 3.71
2250 2317 7.945664 AGAGAACCGTATAGAGACATAAATCCT 59.054 37.037 0.00 0.00 0.00 3.24
2253 2320 8.693120 TCAGAGAACCGTATAGAGACATAAAT 57.307 34.615 0.00 0.00 0.00 1.40
2254 2321 8.693120 ATCAGAGAACCGTATAGAGACATAAA 57.307 34.615 0.00 0.00 0.00 1.40
2257 2324 6.539173 AGATCAGAGAACCGTATAGAGACAT 58.461 40.000 0.00 0.00 0.00 3.06
2258 2325 5.931294 AGATCAGAGAACCGTATAGAGACA 58.069 41.667 0.00 0.00 0.00 3.41
2259 2326 5.410439 GGAGATCAGAGAACCGTATAGAGAC 59.590 48.000 0.00 0.00 0.00 3.36
2260 2327 5.071923 TGGAGATCAGAGAACCGTATAGAGA 59.928 44.000 0.00 0.00 0.00 3.10
2261 2328 5.309638 TGGAGATCAGAGAACCGTATAGAG 58.690 45.833 0.00 0.00 0.00 2.43
2262 2329 5.306114 TGGAGATCAGAGAACCGTATAGA 57.694 43.478 0.00 0.00 0.00 1.98
2263 2330 5.563867 GCTTGGAGATCAGAGAACCGTATAG 60.564 48.000 0.00 0.00 0.00 1.31
2267 2334 1.205893 GCTTGGAGATCAGAGAACCGT 59.794 52.381 0.00 0.00 0.00 4.83
2268 2335 1.480137 AGCTTGGAGATCAGAGAACCG 59.520 52.381 0.00 0.00 0.00 4.44
2312 2386 5.215239 GCTAAAGAGCTCATGAAACTGTC 57.785 43.478 17.77 0.00 45.98 3.51
2328 2413 5.534207 AGTGATGATCTCCTGAGCTAAAG 57.466 43.478 0.00 0.00 0.00 1.85
2336 2421 6.169094 ACAAGTTACAAGTGATGATCTCCTG 58.831 40.000 0.00 0.00 0.00 3.86
2340 2425 8.902540 TTTGTACAAGTTACAAGTGATGATCT 57.097 30.769 8.56 0.00 38.47 2.75
2350 2435 8.380743 ACGTGGATTATTTGTACAAGTTACAA 57.619 30.769 9.05 0.00 35.84 2.41
2383 2472 8.683615 ACTCGTCATGATCTTGTACAGTATAAA 58.316 33.333 0.00 0.00 0.00 1.40
2396 2485 1.135915 GTGCAGGACTCGTCATGATCT 59.864 52.381 15.03 0.00 43.36 2.75
2398 2494 1.134877 CAGTGCAGGACTCGTCATGAT 60.135 52.381 15.03 0.00 43.36 2.45
2410 2506 2.350522 GACCAGATGTAACAGTGCAGG 58.649 52.381 0.00 0.00 0.00 4.85
2459 2582 1.303317 GGCCAGTTTGGTGACCGAT 60.303 57.895 0.00 0.00 40.46 4.18
2481 2605 8.806146 ACTCTGTGGCTGAATTATTTTGTTATT 58.194 29.630 0.00 0.00 0.00 1.40
2496 2620 2.025969 CTGACGCACTCTGTGGCTG 61.026 63.158 0.00 0.00 36.69 4.85
2500 2624 3.108289 CGGCTGACGCACTCTGTG 61.108 66.667 0.00 0.00 38.10 3.66
2572 2700 6.658391 ACCGGTCATTGGATAGTAGTAGTATC 59.342 42.308 14.40 14.40 31.31 2.24
2609 2818 5.469373 TTGTAGTGCATTGAAGCTATTCG 57.531 39.130 0.00 0.00 38.34 3.34
2610 2819 7.253883 GCAAATTGTAGTGCATTGAAGCTATTC 60.254 37.037 0.00 0.00 40.58 1.75
2614 2823 4.240096 GCAAATTGTAGTGCATTGAAGCT 58.760 39.130 0.00 0.00 40.58 3.74
2615 2824 3.989167 TGCAAATTGTAGTGCATTGAAGC 59.011 39.130 0.00 0.00 45.52 3.86
2758 2989 3.337358 TCACTGCAATGTACACTGGATG 58.663 45.455 6.43 4.51 0.00 3.51
2988 3220 4.269844 GCTTCGAAGTTGAAAATTTTGGCA 59.730 37.500 25.24 0.00 28.78 4.92
3065 3297 6.647212 TTCGTAATGCTCACTTCAGTTATG 57.353 37.500 0.00 0.00 0.00 1.90
3095 3327 7.676004 TGGTTAATTGACAGTCAGAACAGATA 58.324 34.615 19.15 0.09 0.00 1.98


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

AutoCloner maintained by Alex Coulton.