Multiple sequence alignment - TraesCS5B01G191700

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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 TraesCS5B01G191700 chr5B 100.000 2646 0 0 1 2646 345137376 345140021 0.000000e+00 4887.0
1 TraesCS5B01G191700 chr5D 93.420 1231 45 12 1 1210 302103825 302105040 0.000000e+00 1792.0
2 TraesCS5B01G191700 chr5D 93.294 850 39 11 1289 2126 302105087 302105930 0.000000e+00 1238.0
3 TraesCS5B01G191700 chr5D 90.395 354 30 4 2177 2528 302105917 302106268 1.860000e-126 462.0
4 TraesCS5B01G191700 chr5D 90.476 126 7 4 2279 2403 302161857 302161978 7.580000e-36 161.0
5 TraesCS5B01G191700 chr5A 90.760 855 41 15 1289 2126 395805482 395804649 0.000000e+00 1107.0
6 TraesCS5B01G191700 chr5A 87.416 890 53 17 363 1210 395806401 395805529 0.000000e+00 968.0
7 TraesCS5B01G191700 chr5A 91.525 118 9 1 2177 2294 395804661 395804545 7.580000e-36 161.0
8 TraesCS5B01G191700 chr5A 90.909 88 8 0 2559 2646 395804493 395804406 4.630000e-23 119.0
9 TraesCS5B01G191700 chr1D 97.674 43 1 0 1605 1647 191861276 191861318 1.020000e-09 75.0
10 TraesCS5B01G191700 chr1D 100.000 31 0 0 2311 2341 14966326 14966356 1.020000e-04 58.4
11 TraesCS5B01G191700 chr1B 97.674 43 1 0 1605 1647 265648393 265648435 1.020000e-09 75.0
12 TraesCS5B01G191700 chr1A 97.674 43 1 0 1605 1647 237746074 237746116 1.020000e-09 75.0
13 TraesCS5B01G191700 chr1A 90.909 55 3 2 1084 1136 361235807 361235861 3.650000e-09 73.1


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 TraesCS5B01G191700 chr5B 345137376 345140021 2645 False 4887.00 4887 100.000000 1 2646 1 chr5B.!!$F1 2645
1 TraesCS5B01G191700 chr5D 302103825 302106268 2443 False 1164.00 1792 92.369667 1 2528 3 chr5D.!!$F2 2527
2 TraesCS5B01G191700 chr5A 395804406 395806401 1995 True 588.75 1107 90.152500 363 2646 4 chr5A.!!$R1 2283

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
532 539 0.038166 CTCTGCCTTTACAAGCCCCA 59.962 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2234 0.173708 CAGACCCGGTAAGCAGTCTC 59.826 60.0 0.0 0.0 37.48 3.36 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
24 25 4.437587 GCAGCCCAGCCATCACCT 62.438 66.667 0.00 0.00 0.00 4.00
82 83 4.263462 TGACTATGTGGATCCCCATTATGC 60.263 45.833 15.35 3.99 45.68 3.14
109 110 3.736224 CCTCCCTGCTGGCACCAT 61.736 66.667 3.63 0.00 0.00 3.55
110 111 2.124403 CTCCCTGCTGGCACCATC 60.124 66.667 3.63 0.00 0.00 3.51
111 112 2.934932 TCCCTGCTGGCACCATCA 60.935 61.111 3.63 0.00 0.00 3.07
112 113 2.277737 CCCTGCTGGCACCATCAT 59.722 61.111 3.63 0.00 0.00 2.45
113 114 1.380785 CCCTGCTGGCACCATCATT 60.381 57.895 3.63 0.00 0.00 2.57
114 115 1.389609 CCCTGCTGGCACCATCATTC 61.390 60.000 3.63 0.00 0.00 2.67
115 116 0.681887 CCTGCTGGCACCATCATTCA 60.682 55.000 0.00 0.00 0.00 2.57
116 117 0.454600 CTGCTGGCACCATCATTCAC 59.545 55.000 0.00 0.00 0.00 3.18
157 158 4.379813 GCATGACCAGTATTTCTGTTGTGG 60.380 45.833 0.00 0.00 42.19 4.17
211 212 2.724454 TGGAAACCGAAACTGAAACCA 58.276 42.857 0.00 0.00 0.00 3.67
258 259 5.601583 TGCAATGCAATCATAAGGAACAT 57.398 34.783 5.01 0.00 34.76 2.71
264 265 5.754782 TGCAATCATAAGGAACATACCACT 58.245 37.500 0.00 0.00 0.00 4.00
299 300 2.029369 TTCGCCGCCACGTAAAGT 59.971 55.556 0.00 0.00 0.00 2.66
306 307 0.796312 CGCCACGTAAAGTTGCTGAT 59.204 50.000 0.00 0.00 39.15 2.90
341 342 3.691609 AGAATTCCCAACGCTGATCTTTC 59.308 43.478 0.65 0.00 0.00 2.62
366 367 9.297037 TCATAAATCATCTCATGCATGAAGAAT 57.703 29.630 28.39 18.89 36.18 2.40
514 516 2.483889 GCTCACGGCTTAGCTTTATCCT 60.484 50.000 3.59 0.00 38.06 3.24
532 539 0.038166 CTCTGCCTTTACAAGCCCCA 59.962 55.000 0.00 0.00 0.00 4.96
768 808 2.341176 GCCTTGCCACAAAGCCAG 59.659 61.111 0.00 0.00 0.00 4.85
802 846 7.079451 GCCAAGGGCCTATATATATACACAT 57.921 40.000 6.41 0.00 44.06 3.21
824 873 1.130373 CAACCCATCGTTTGTCCATCG 59.870 52.381 0.00 0.00 29.93 3.84
826 875 1.006832 CCCATCGTTTGTCCATCGAC 58.993 55.000 0.00 0.00 39.66 4.20
859 908 4.942852 TCTCATCTCTAGCTAAGCTTTGC 58.057 43.478 22.97 22.97 40.44 3.68
860 909 3.711086 TCATCTCTAGCTAAGCTTTGCG 58.289 45.455 23.82 13.05 40.44 4.85
861 910 1.927895 TCTCTAGCTAAGCTTTGCGC 58.072 50.000 23.82 15.20 40.44 6.09
866 915 1.808411 AGCTAAGCTTTGCGCAAGTA 58.192 45.000 23.68 8.77 42.61 2.24
921 970 3.823873 TCAGGAAGAGAACAGAGTCTGAC 59.176 47.826 26.86 18.16 35.18 3.51
930 979 3.984352 GAGTCTGACTCGTCCGGT 58.016 61.111 20.91 0.00 35.28 5.28
931 980 1.795507 GAGTCTGACTCGTCCGGTC 59.204 63.158 20.91 0.00 35.28 4.79
932 981 1.646624 GAGTCTGACTCGTCCGGTCC 61.647 65.000 20.91 0.00 35.28 4.46
1011 1060 0.475632 TTGAGAGGATGGGTGTGGGT 60.476 55.000 0.00 0.00 0.00 4.51
1014 1063 2.941025 AGGATGGGTGTGGGTGGG 60.941 66.667 0.00 0.00 0.00 4.61
1192 1245 7.419203 AGGTATGCATACACATATCCTACCTA 58.581 38.462 32.19 0.00 33.97 3.08
1205 1258 8.424918 ACATATCCTACCTATCAACAACTCAAG 58.575 37.037 0.00 0.00 0.00 3.02
1210 1263 7.037586 TCCTACCTATCAACAACTCAAGGAATT 60.038 37.037 0.00 0.00 0.00 2.17
1212 1265 9.838339 CTACCTATCAACAACTCAAGGAATTAT 57.162 33.333 0.00 0.00 0.00 1.28
1215 1268 7.557719 CCTATCAACAACTCAAGGAATTATGGT 59.442 37.037 0.00 0.00 0.00 3.55
1216 1269 7.781324 ATCAACAACTCAAGGAATTATGGTT 57.219 32.000 0.00 0.00 0.00 3.67
1217 1270 8.877864 ATCAACAACTCAAGGAATTATGGTTA 57.122 30.769 0.00 0.00 0.00 2.85
1218 1271 8.335532 TCAACAACTCAAGGAATTATGGTTAG 57.664 34.615 0.00 0.00 0.00 2.34
1219 1272 8.160765 TCAACAACTCAAGGAATTATGGTTAGA 58.839 33.333 0.00 0.00 0.00 2.10
1220 1273 8.792633 CAACAACTCAAGGAATTATGGTTAGAA 58.207 33.333 0.00 0.00 0.00 2.10
1221 1274 8.934023 ACAACTCAAGGAATTATGGTTAGAAA 57.066 30.769 0.00 0.00 0.00 2.52
1222 1275 9.362151 ACAACTCAAGGAATTATGGTTAGAAAA 57.638 29.630 0.00 0.00 0.00 2.29
1226 1279 9.305925 CTCAAGGAATTATGGTTAGAAAAATGC 57.694 33.333 0.00 0.00 0.00 3.56
1227 1280 9.034800 TCAAGGAATTATGGTTAGAAAAATGCT 57.965 29.630 0.00 0.00 0.00 3.79
1228 1281 9.090692 CAAGGAATTATGGTTAGAAAAATGCTG 57.909 33.333 0.00 0.00 0.00 4.41
1229 1282 8.366359 AGGAATTATGGTTAGAAAAATGCTGT 57.634 30.769 0.00 0.00 0.00 4.40
1230 1283 9.474313 AGGAATTATGGTTAGAAAAATGCTGTA 57.526 29.630 0.00 0.00 0.00 2.74
1243 1296 9.932207 AGAAAAATGCTGTAAAATTGATGATGA 57.068 25.926 0.00 0.00 0.00 2.92
1250 1303 9.932207 TGCTGTAAAATTGATGATGAAATTCTT 57.068 25.926 0.00 0.00 0.00 2.52
1261 1314 9.865321 TGATGATGAAATTCTTGATTCTTTTCC 57.135 29.630 0.00 0.00 0.00 3.13
1275 1328 8.891671 TGATTCTTTTCCTTTGAAAATCCTTG 57.108 30.769 1.37 0.00 46.44 3.61
1281 1334 7.693969 TTTCCTTTGAAAATCCTTGCAAAAA 57.306 28.000 0.00 0.00 39.20 1.94
1468 1540 1.192428 ACATCCCCTACAACCTCGTC 58.808 55.000 0.00 0.00 0.00 4.20
1501 1573 1.731613 CGCGCAGACCTACGACAAA 60.732 57.895 8.75 0.00 0.00 2.83
1674 1746 1.651138 GTGAAGCAAGAGACGTCGATG 59.349 52.381 10.46 11.48 0.00 3.84
1678 1750 0.452184 GCAAGAGACGTCGATGGAGA 59.548 55.000 10.46 0.00 0.00 3.71
1707 1785 1.152860 TTGGTGGCGGTGACATGTT 60.153 52.632 0.00 0.00 0.00 2.71
1750 1828 0.801872 TATGGCATGCGTGTGTTGTC 59.198 50.000 12.44 0.00 0.00 3.18
1879 1963 7.817478 TCGATCTTTTGCACTGTTAGATCTTTA 59.183 33.333 0.00 0.00 39.22 1.85
1897 1981 7.987458 AGATCTTTATTTTAGAGGATCGCACAA 59.013 33.333 0.00 0.00 42.67 3.33
1904 1988 7.482654 TTTTAGAGGATCGCACAATTAGATG 57.517 36.000 0.00 0.00 42.67 2.90
1917 2001 7.201376 CGCACAATTAGATGGTTGATTTTGAAG 60.201 37.037 0.00 0.00 0.00 3.02
1926 2010 4.273969 TGGTTGATTTTGAAGACGGTACAC 59.726 41.667 0.00 0.00 0.00 2.90
1930 2014 2.427232 TTTGAAGACGGTACACTCGG 57.573 50.000 0.00 0.00 0.00 4.63
1957 2041 4.518217 GCTCACATACACGCACAATTATC 58.482 43.478 0.00 0.00 0.00 1.75
1958 2042 4.751172 CTCACATACACGCACAATTATCG 58.249 43.478 0.00 0.00 0.00 2.92
1962 2046 5.404066 CACATACACGCACAATTATCGGATA 59.596 40.000 0.00 0.00 0.00 2.59
1992 2076 5.056894 ACTTACTGTAACCTAGCAGAACG 57.943 43.478 0.00 0.00 36.62 3.95
2012 2097 2.225963 CGTTAACCACCGGCAATTTACA 59.774 45.455 0.00 0.00 0.00 2.41
2013 2098 3.119779 CGTTAACCACCGGCAATTTACAT 60.120 43.478 0.00 0.00 0.00 2.29
2095 2181 6.801862 CCAGAAACAACTAAAACGATGGATTC 59.198 38.462 0.00 0.00 0.00 2.52
2115 2201 4.316375 TCGCGCAGAAACTAAACATAAC 57.684 40.909 8.75 0.00 0.00 1.89
2116 2202 3.123959 TCGCGCAGAAACTAAACATAACC 59.876 43.478 8.75 0.00 0.00 2.85
2117 2203 3.726782 CGCGCAGAAACTAAACATAACCC 60.727 47.826 8.75 0.00 0.00 4.11
2118 2204 3.726782 GCGCAGAAACTAAACATAACCCG 60.727 47.826 0.30 0.00 0.00 5.28
2119 2205 3.726782 CGCAGAAACTAAACATAACCCGC 60.727 47.826 0.00 0.00 0.00 6.13
2120 2206 3.189702 GCAGAAACTAAACATAACCCGCA 59.810 43.478 0.00 0.00 0.00 5.69
2121 2207 4.320641 GCAGAAACTAAACATAACCCGCAA 60.321 41.667 0.00 0.00 0.00 4.85
2122 2208 5.764131 CAGAAACTAAACATAACCCGCAAA 58.236 37.500 0.00 0.00 0.00 3.68
2123 2209 5.627780 CAGAAACTAAACATAACCCGCAAAC 59.372 40.000 0.00 0.00 0.00 2.93
2124 2210 5.533528 AGAAACTAAACATAACCCGCAAACT 59.466 36.000 0.00 0.00 0.00 2.66
2125 2211 5.777850 AACTAAACATAACCCGCAAACTT 57.222 34.783 0.00 0.00 0.00 2.66
2126 2212 5.777850 ACTAAACATAACCCGCAAACTTT 57.222 34.783 0.00 0.00 0.00 2.66
2127 2213 6.151663 ACTAAACATAACCCGCAAACTTTT 57.848 33.333 0.00 0.00 0.00 2.27
2128 2214 6.575267 ACTAAACATAACCCGCAAACTTTTT 58.425 32.000 0.00 0.00 0.00 1.94
2155 2241 8.662781 TTACATATATCAAGGTTTGAGACTGC 57.337 34.615 0.00 0.00 43.98 4.40
2156 2242 6.893583 ACATATATCAAGGTTTGAGACTGCT 58.106 36.000 0.00 0.00 43.98 4.24
2157 2243 7.341805 ACATATATCAAGGTTTGAGACTGCTT 58.658 34.615 0.00 0.00 43.98 3.91
2158 2244 8.486210 ACATATATCAAGGTTTGAGACTGCTTA 58.514 33.333 0.00 0.00 43.98 3.09
2159 2245 8.768955 CATATATCAAGGTTTGAGACTGCTTAC 58.231 37.037 0.00 0.00 43.98 2.34
2160 2246 3.740115 TCAAGGTTTGAGACTGCTTACC 58.260 45.455 0.00 0.00 34.08 2.85
2161 2247 2.457366 AGGTTTGAGACTGCTTACCG 57.543 50.000 0.00 0.00 0.00 4.02
2162 2248 1.002087 AGGTTTGAGACTGCTTACCGG 59.998 52.381 0.00 0.00 0.00 5.28
2163 2249 1.439679 GTTTGAGACTGCTTACCGGG 58.560 55.000 6.32 0.00 0.00 5.73
2164 2250 1.053424 TTTGAGACTGCTTACCGGGT 58.947 50.000 6.32 4.46 0.00 5.28
2165 2251 0.606604 TTGAGACTGCTTACCGGGTC 59.393 55.000 6.32 1.68 0.00 4.46
2166 2252 0.251653 TGAGACTGCTTACCGGGTCT 60.252 55.000 6.32 7.54 41.05 3.85
2167 2253 0.173708 GAGACTGCTTACCGGGTCTG 59.826 60.000 12.73 0.00 38.87 3.51
2168 2254 1.448013 GACTGCTTACCGGGTCTGC 60.448 63.158 6.32 10.21 0.00 4.26
2169 2255 2.125106 CTGCTTACCGGGTCTGCC 60.125 66.667 17.72 2.01 0.00 4.85
2170 2256 2.925706 TGCTTACCGGGTCTGCCA 60.926 61.111 17.72 4.29 36.17 4.92
2171 2257 2.436115 GCTTACCGGGTCTGCCAC 60.436 66.667 6.32 0.00 36.17 5.01
2172 2258 2.267961 CTTACCGGGTCTGCCACC 59.732 66.667 6.32 0.00 45.97 4.61
2179 2265 2.046604 GGTCTGCCACCCGGTAAC 60.047 66.667 0.00 0.00 39.69 2.50
2225 2312 4.698201 TTGGAGTTGTCTGAATGTACCA 57.302 40.909 0.00 0.00 0.00 3.25
2227 2314 6.367374 TTGGAGTTGTCTGAATGTACCATA 57.633 37.500 0.00 0.00 0.00 2.74
2234 2321 8.540388 AGTTGTCTGAATGTACCATATTAGTGT 58.460 33.333 0.00 0.00 0.00 3.55
2293 2380 8.939929 TGAACAGATGCTTTTCTTACTTCTATG 58.060 33.333 0.00 0.00 0.00 2.23
2319 2407 7.610580 TCCCTTTATTGAAAGAATTTGGTGT 57.389 32.000 0.00 0.00 44.23 4.16
2341 2429 6.595716 GTGTCTACAATAGCTTTTGATCCACT 59.404 38.462 21.69 2.80 0.00 4.00
2342 2430 6.595326 TGTCTACAATAGCTTTTGATCCACTG 59.405 38.462 21.69 5.45 0.00 3.66
2428 2516 3.256136 AGTGAAGAAGTGGTACTCCTTCG 59.744 47.826 14.94 0.00 40.26 3.79
2431 2519 0.108281 GAAGTGGTACTCCTTCGGGC 60.108 60.000 8.59 0.00 34.44 6.13
2442 2530 1.377333 CTTCGGGCCTTGAAGGGTC 60.377 63.158 22.90 0.00 39.30 4.46
2448 2536 1.704641 GGCCTTGAAGGGTCTGTTTT 58.295 50.000 13.99 0.00 35.37 2.43
2456 2544 5.633655 TGAAGGGTCTGTTTTGTTACCTA 57.366 39.130 0.00 0.00 32.38 3.08
2461 2549 5.072600 AGGGTCTGTTTTGTTACCTACATGA 59.927 40.000 0.00 0.00 36.44 3.07
2468 2556 9.528018 CTGTTTTGTTACCTACATGAATTTTGT 57.472 29.630 0.00 1.30 36.44 2.83
2476 2564 7.283625 ACCTACATGAATTTTGTGCACTTTA 57.716 32.000 19.41 0.64 0.00 1.85
2494 2582 0.671796 TACATATGTGGCCCGACTCG 59.328 55.000 18.81 0.00 0.00 4.18
2496 2584 1.760875 ATATGTGGCCCGACTCGGT 60.761 57.895 16.35 0.00 46.80 4.69
2497 2585 1.745320 ATATGTGGCCCGACTCGGTC 61.745 60.000 16.35 2.99 46.80 4.79
2514 2602 2.878406 CGGTCAGGTTGAGTGAAAACAT 59.122 45.455 0.00 0.00 0.00 2.71
2515 2603 3.303990 CGGTCAGGTTGAGTGAAAACATG 60.304 47.826 0.00 0.00 39.90 3.21
2516 2604 3.550842 GGTCAGGTTGAGTGAAAACATGC 60.551 47.826 0.00 0.00 38.76 4.06
2519 2607 3.798337 CAGGTTGAGTGAAAACATGCAAC 59.202 43.478 0.00 0.00 33.22 4.17
2540 2628 2.361757 CAAACCATGGTTGAGCAGAACA 59.638 45.455 30.44 0.00 38.47 3.18
2550 2638 1.417517 TGAGCAGAACACAGTCATGGT 59.582 47.619 0.00 0.00 0.00 3.55
2563 2651 2.499289 AGTCATGGTGTTTGGTTGCAAA 59.501 40.909 0.00 0.00 0.00 3.68
2564 2652 2.865551 GTCATGGTGTTTGGTTGCAAAG 59.134 45.455 0.00 0.00 0.00 2.77
2576 2664 4.114098 GGTTGCAAAGCGTTGTTATTTG 57.886 40.909 13.93 1.31 37.06 2.32
2635 2744 2.299013 TGGAGTGTGAGTTTACGAGCAT 59.701 45.455 0.00 0.00 0.00 3.79
2639 2748 5.073311 AGTGTGAGTTTACGAGCATACAT 57.927 39.130 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.573210 CCATGAGGTGATGGCTGG 57.427 61.111 0.00 0.00 36.69 4.85
19 20 2.672908 CCAGCTGCCATGAGGTGA 59.327 61.111 8.66 0.00 42.92 4.02
45 46 5.279708 CCACATAGTCATCCTAGGACCAATC 60.280 48.000 15.42 3.50 35.89 2.67
82 83 2.593978 CAGGGAGGGAGGTGCATG 59.406 66.667 0.00 0.00 0.00 4.06
109 110 0.884259 CTGTGTGCCGGTGTGAATGA 60.884 55.000 1.90 0.00 0.00 2.57
110 111 1.575922 CTGTGTGCCGGTGTGAATG 59.424 57.895 1.90 0.00 0.00 2.67
111 112 2.260869 GCTGTGTGCCGGTGTGAAT 61.261 57.895 1.90 0.00 35.15 2.57
112 113 2.899838 GCTGTGTGCCGGTGTGAA 60.900 61.111 1.90 0.00 35.15 3.18
113 114 3.689002 TTGCTGTGTGCCGGTGTGA 62.689 57.895 1.90 0.00 42.00 3.58
114 115 2.769539 TTTGCTGTGTGCCGGTGTG 61.770 57.895 1.90 0.00 42.00 3.82
115 116 2.439338 TTTGCTGTGTGCCGGTGT 60.439 55.556 1.90 0.00 42.00 4.16
116 117 2.026014 GTTTGCTGTGTGCCGGTG 59.974 61.111 1.90 0.00 42.00 4.94
157 158 1.228154 AGCCTGGACGTGGGTTTTC 60.228 57.895 0.00 0.00 30.18 2.29
258 259 2.749541 CGAGAATTGCGCAGTGGTA 58.250 52.632 11.31 0.00 0.00 3.25
306 307 8.238631 GCGTTGGGAATTCTACTTAAACATTTA 58.761 33.333 5.23 0.00 0.00 1.40
341 342 9.561270 GATTCTTCATGCATGAGATGATTTATG 57.439 33.333 27.25 7.48 38.19 1.90
366 367 2.108514 GCGTGCATGGCTAGCTTGA 61.109 57.895 15.72 0.00 0.00 3.02
532 539 5.221048 CCTCAACCGACTTCAGAAACAAATT 60.221 40.000 0.00 0.00 0.00 1.82
798 842 3.119990 GGACAAACGATGGGTTGTATGTG 60.120 47.826 11.42 0.00 39.30 3.21
799 843 3.078837 GGACAAACGATGGGTTGTATGT 58.921 45.455 11.42 0.00 39.30 2.29
802 846 2.932855 TGGACAAACGATGGGTTGTA 57.067 45.000 11.42 0.00 39.30 2.41
813 862 2.737252 GTTGGAGAGTCGATGGACAAAC 59.263 50.000 10.69 3.34 45.92 2.93
815 864 1.275291 GGTTGGAGAGTCGATGGACAA 59.725 52.381 10.69 0.00 45.92 3.18
824 873 3.960102 AGAGATGAGATGGTTGGAGAGTC 59.040 47.826 0.00 0.00 0.00 3.36
826 875 4.022068 GCTAGAGATGAGATGGTTGGAGAG 60.022 50.000 0.00 0.00 0.00 3.20
861 910 0.786581 CGCACTGACAGCACTACTTG 59.213 55.000 1.25 0.00 0.00 3.16
921 970 3.060615 AAGGACGGACCGGACGAG 61.061 66.667 25.24 12.33 44.74 4.18
929 978 0.949397 GAAAACACCCAAGGACGGAC 59.051 55.000 0.00 0.00 0.00 4.79
930 979 0.841289 AGAAAACACCCAAGGACGGA 59.159 50.000 0.00 0.00 0.00 4.69
931 980 1.336755 CAAGAAAACACCCAAGGACGG 59.663 52.381 0.00 0.00 0.00 4.79
932 981 2.032924 GTCAAGAAAACACCCAAGGACG 59.967 50.000 0.00 0.00 0.00 4.79
1011 1060 2.526432 GACAAGTAGTCCAGAGTCCCA 58.474 52.381 0.00 0.00 41.56 4.37
1192 1245 7.781324 AACCATAATTCCTTGAGTTGTTGAT 57.219 32.000 0.00 0.00 0.00 2.57
1212 1265 9.995003 ATCAATTTTACAGCATTTTTCTAACCA 57.005 25.926 0.00 0.00 0.00 3.67
1217 1270 9.932207 TCATCATCAATTTTACAGCATTTTTCT 57.068 25.926 0.00 0.00 0.00 2.52
1224 1277 9.932207 AAGAATTTCATCATCAATTTTACAGCA 57.068 25.926 0.00 0.00 0.00 4.41
1257 1310 7.693969 TTTTTGCAAGGATTTTCAAAGGAAA 57.306 28.000 0.00 0.00 41.13 3.13
1286 1339 7.665561 TGCCTTTAAATTTTCCAGCATTTAC 57.334 32.000 0.00 0.00 0.00 2.01
1301 1367 8.677300 TGCAAAATACAACAAAATGCCTTTAAA 58.323 25.926 0.00 0.00 0.00 1.52
1303 1369 7.041508 CCTGCAAAATACAACAAAATGCCTTTA 60.042 33.333 0.00 0.00 0.00 1.85
1305 1371 5.239087 CCTGCAAAATACAACAAAATGCCTT 59.761 36.000 0.00 0.00 0.00 4.35
1674 1746 3.012518 CCACCAAGAACACATGATCTCC 58.987 50.000 0.00 0.00 0.00 3.71
1678 1750 1.167851 CGCCACCAAGAACACATGAT 58.832 50.000 0.00 0.00 0.00 2.45
1707 1785 2.234661 CTCTGTCTGGAGCCACATACAA 59.765 50.000 0.00 0.00 28.84 2.41
1879 1963 7.173907 CCATCTAATTGTGCGATCCTCTAAAAT 59.826 37.037 0.00 0.00 0.00 1.82
1884 1968 3.389329 ACCATCTAATTGTGCGATCCTCT 59.611 43.478 0.00 0.00 0.00 3.69
1886 1970 3.845781 ACCATCTAATTGTGCGATCCT 57.154 42.857 0.00 0.00 0.00 3.24
1897 1981 6.659242 ACCGTCTTCAAAATCAACCATCTAAT 59.341 34.615 0.00 0.00 0.00 1.73
1904 1988 4.514066 AGTGTACCGTCTTCAAAATCAACC 59.486 41.667 0.00 0.00 0.00 3.77
1917 2001 1.423056 CGTCTCCGAGTGTACCGTC 59.577 63.158 0.00 0.00 35.63 4.79
1926 2010 0.733150 TGTATGTGAGCGTCTCCGAG 59.267 55.000 4.73 0.00 35.63 4.63
1930 2014 0.456142 TGCGTGTATGTGAGCGTCTC 60.456 55.000 0.58 0.58 0.00 3.36
1957 2041 8.411683 AGGTTACAGTAAGTAATCAACTATCCG 58.588 37.037 0.00 0.00 44.61 4.18
1962 2046 8.130671 TGCTAGGTTACAGTAAGTAATCAACT 57.869 34.615 0.00 0.00 44.61 3.16
1992 2076 3.919223 TGTAAATTGCCGGTGGTTAAC 57.081 42.857 1.90 0.00 0.00 2.01
2095 2181 3.413558 GGTTATGTTTAGTTTCTGCGCG 58.586 45.455 0.00 0.00 0.00 6.86
2129 2215 9.109393 GCAGTCTCAAACCTTGATATATGTAAA 57.891 33.333 0.00 0.00 39.30 2.01
2130 2216 8.486210 AGCAGTCTCAAACCTTGATATATGTAA 58.514 33.333 0.00 0.00 39.30 2.41
2131 2217 8.023021 AGCAGTCTCAAACCTTGATATATGTA 57.977 34.615 0.00 0.00 39.30 2.29
2132 2218 6.893583 AGCAGTCTCAAACCTTGATATATGT 58.106 36.000 0.00 0.00 39.30 2.29
2133 2219 7.798596 AAGCAGTCTCAAACCTTGATATATG 57.201 36.000 0.00 0.00 39.30 1.78
2134 2220 7.934120 GGTAAGCAGTCTCAAACCTTGATATAT 59.066 37.037 0.00 0.00 39.30 0.86
2135 2221 7.272978 GGTAAGCAGTCTCAAACCTTGATATA 58.727 38.462 0.00 0.00 39.30 0.86
2136 2222 6.116126 GGTAAGCAGTCTCAAACCTTGATAT 58.884 40.000 0.00 0.00 39.30 1.63
2137 2223 5.488341 GGTAAGCAGTCTCAAACCTTGATA 58.512 41.667 0.00 0.00 39.30 2.15
2138 2224 4.327680 GGTAAGCAGTCTCAAACCTTGAT 58.672 43.478 0.00 0.00 39.30 2.57
2139 2225 3.740115 GGTAAGCAGTCTCAAACCTTGA 58.260 45.455 0.00 0.00 38.17 3.02
2140 2226 2.480419 CGGTAAGCAGTCTCAAACCTTG 59.520 50.000 0.00 0.00 0.00 3.61
2141 2227 2.550208 CCGGTAAGCAGTCTCAAACCTT 60.550 50.000 0.00 0.00 0.00 3.50
2142 2228 1.002087 CCGGTAAGCAGTCTCAAACCT 59.998 52.381 0.00 0.00 0.00 3.50
2143 2229 1.439679 CCGGTAAGCAGTCTCAAACC 58.560 55.000 0.00 0.00 0.00 3.27
2144 2230 1.270678 ACCCGGTAAGCAGTCTCAAAC 60.271 52.381 0.00 0.00 0.00 2.93
2145 2231 1.001633 GACCCGGTAAGCAGTCTCAAA 59.998 52.381 0.00 0.00 0.00 2.69
2146 2232 0.606604 GACCCGGTAAGCAGTCTCAA 59.393 55.000 0.00 0.00 0.00 3.02
2147 2233 0.251653 AGACCCGGTAAGCAGTCTCA 60.252 55.000 0.00 0.00 34.53 3.27
2148 2234 0.173708 CAGACCCGGTAAGCAGTCTC 59.826 60.000 0.00 0.00 37.48 3.36
2149 2235 1.889530 GCAGACCCGGTAAGCAGTCT 61.890 60.000 0.00 1.23 40.15 3.24
2150 2236 1.448013 GCAGACCCGGTAAGCAGTC 60.448 63.158 0.00 0.00 0.00 3.51
2151 2237 2.663196 GCAGACCCGGTAAGCAGT 59.337 61.111 0.00 0.00 0.00 4.40
2152 2238 2.125106 GGCAGACCCGGTAAGCAG 60.125 66.667 13.92 0.00 0.00 4.24
2153 2239 2.925706 TGGCAGACCCGGTAAGCA 60.926 61.111 13.92 0.67 35.87 3.91
2154 2240 2.436115 GTGGCAGACCCGGTAAGC 60.436 66.667 0.00 5.35 35.87 3.09
2155 2241 2.267961 GGTGGCAGACCCGGTAAG 59.732 66.667 0.00 0.00 39.10 2.34
2162 2248 2.046604 GTTACCGGGTGGCAGACC 60.047 66.667 10.66 0.00 45.28 3.85
2163 2249 2.046604 GGTTACCGGGTGGCAGAC 60.047 66.667 10.66 0.77 39.70 3.51
2164 2250 3.324108 GGGTTACCGGGTGGCAGA 61.324 66.667 10.66 0.00 39.70 4.26
2174 2260 0.251033 AGGGAAGTTTGCGGGTTACC 60.251 55.000 0.00 0.00 0.00 2.85
2175 2261 2.477845 TAGGGAAGTTTGCGGGTTAC 57.522 50.000 0.00 0.00 0.00 2.50
2176 2262 2.572556 TCATAGGGAAGTTTGCGGGTTA 59.427 45.455 0.00 0.00 0.00 2.85
2177 2263 1.353022 TCATAGGGAAGTTTGCGGGTT 59.647 47.619 0.00 0.00 0.00 4.11
2178 2264 0.988832 TCATAGGGAAGTTTGCGGGT 59.011 50.000 0.00 0.00 0.00 5.28
2179 2265 1.065418 AGTCATAGGGAAGTTTGCGGG 60.065 52.381 0.00 0.00 0.00 6.13
2249 2336 3.519908 TCAAAATCTTGCGACGTTGAG 57.480 42.857 7.08 0.00 32.14 3.02
2270 2357 7.108847 AGCATAGAAGTAAGAAAAGCATCTGT 58.891 34.615 0.00 0.00 0.00 3.41
2293 2380 6.591448 CACCAAATTCTTTCAATAAAGGGAGC 59.409 38.462 0.00 0.00 42.09 4.70
2319 2407 6.946340 TCAGTGGATCAAAAGCTATTGTAGA 58.054 36.000 0.00 0.00 0.00 2.59
2341 2429 7.148188 GGAAGTTTCTGATATGACATTTGCTCA 60.148 37.037 0.00 0.00 0.00 4.26
2342 2430 7.148188 TGGAAGTTTCTGATATGACATTTGCTC 60.148 37.037 0.00 0.00 0.00 4.26
2397 2485 7.746703 AGTACCACTTCTTCACTTAGGAAAAT 58.253 34.615 0.00 0.00 0.00 1.82
2403 2491 5.986501 AGGAGTACCACTTCTTCACTTAG 57.013 43.478 0.00 0.00 26.59 2.18
2428 2516 0.178961 AAACAGACCCTTCAAGGCCC 60.179 55.000 0.00 0.00 32.73 5.80
2431 2519 4.037565 GGTAACAAAACAGACCCTTCAAGG 59.962 45.833 0.00 0.00 34.30 3.61
2442 2530 9.528018 ACAAAATTCATGTAGGTAACAAAACAG 57.472 29.630 0.00 0.00 42.70 3.16
2448 2536 6.264292 AGTGCACAAAATTCATGTAGGTAACA 59.736 34.615 21.04 0.00 43.86 2.41
2456 2544 9.142515 CATATGTAAAGTGCACAAAATTCATGT 57.857 29.630 21.04 10.58 0.00 3.21
2461 2549 6.368516 GCCACATATGTAAAGTGCACAAAATT 59.631 34.615 21.04 10.66 32.09 1.82
2468 2556 2.374184 GGGCCACATATGTAAAGTGCA 58.626 47.619 8.32 0.00 32.09 4.57
2476 2564 1.441729 CGAGTCGGGCCACATATGT 59.558 57.895 4.39 1.41 0.00 2.29
2494 2582 3.550842 GCATGTTTTCACTCAACCTGACC 60.551 47.826 0.00 0.00 0.00 4.02
2496 2584 3.286353 TGCATGTTTTCACTCAACCTGA 58.714 40.909 0.00 0.00 0.00 3.86
2497 2585 3.713858 TGCATGTTTTCACTCAACCTG 57.286 42.857 0.00 0.00 0.00 4.00
2500 2588 5.445806 GGTTTGTTGCATGTTTTCACTCAAC 60.446 40.000 0.00 0.00 41.43 3.18
2501 2589 4.629200 GGTTTGTTGCATGTTTTCACTCAA 59.371 37.500 0.00 0.00 0.00 3.02
2514 2602 1.202510 GCTCAACCATGGTTTGTTGCA 60.203 47.619 27.82 6.67 41.21 4.08
2515 2603 1.202510 TGCTCAACCATGGTTTGTTGC 60.203 47.619 27.82 24.89 41.21 4.17
2516 2604 2.361757 TCTGCTCAACCATGGTTTGTTG 59.638 45.455 27.82 17.24 42.46 3.33
2519 2607 2.361757 TGTTCTGCTCAACCATGGTTTG 59.638 45.455 27.82 22.23 36.00 2.93
2540 2628 1.408702 GCAACCAAACACCATGACTGT 59.591 47.619 0.00 0.00 0.00 3.55
2550 2638 1.337260 ACAACGCTTTGCAACCAAACA 60.337 42.857 0.00 0.00 36.09 2.83
2563 2651 4.481463 GCATGTAACCAAATAACAACGCT 58.519 39.130 0.00 0.00 0.00 5.07
2564 2652 3.610677 GGCATGTAACCAAATAACAACGC 59.389 43.478 0.00 0.00 0.00 4.84
2566 2654 5.120053 GCAAGGCATGTAACCAAATAACAAC 59.880 40.000 0.00 0.00 0.00 3.32
2567 2655 5.221521 TGCAAGGCATGTAACCAAATAACAA 60.222 36.000 0.00 0.00 31.71 2.83
2569 2657 4.815269 TGCAAGGCATGTAACCAAATAAC 58.185 39.130 0.00 0.00 31.71 1.89
2616 2725 4.482386 TGTATGCTCGTAAACTCACACTC 58.518 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.