Multiple sequence alignment - TraesCS5A01G247500

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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 TraesCS5A01G247500 chr5A 100.000 2666 0 0 1 2666 461521459 461524124 0.000000e+00 4924.0
1 TraesCS5A01G247500 chr7D 92.242 1057 72 7 1 1052 631381689 631380638 0.000000e+00 1489.0
2 TraesCS5A01G247500 chr7D 89.266 354 36 2 2282 2635 623691723 623691372 2.440000e-120 442.0
3 TraesCS5A01G247500 chr7D 88.764 356 38 2 2282 2637 623704469 623704116 4.080000e-118 435.0
4 TraesCS5A01G247500 chr2D 91.887 1060 66 10 1 1052 520036825 520037872 0.000000e+00 1463.0
5 TraesCS5A01G247500 chr2D 93.220 59 4 0 3 61 602769692 602769634 1.310000e-13 87.9
6 TraesCS5A01G247500 chr5D 92.488 852 34 16 1053 1901 360750072 360750896 0.000000e+00 1192.0
7 TraesCS5A01G247500 chr5D 91.377 777 62 3 1890 2666 360751687 360752458 0.000000e+00 1059.0
8 TraesCS5A01G247500 chr5B 86.632 778 50 33 1053 1820 426086823 426087556 0.000000e+00 811.0
9 TraesCS5A01G247500 chr5B 90.164 61 6 0 1 61 452237044 452237104 2.200000e-11 80.5
10 TraesCS5A01G247500 chr6D 87.824 386 44 3 2282 2666 346071613 346071996 1.460000e-122 449.0
11 TraesCS5A01G247500 chr6D 88.858 359 38 2 2282 2639 287031186 287031543 8.760000e-120 440.0
12 TraesCS5A01G247500 chr6D 93.443 61 4 0 1 61 380033442 380033502 1.020000e-14 91.6
13 TraesCS5A01G247500 chr6D 93.443 61 4 0 1 61 441673054 441672994 1.020000e-14 91.6
14 TraesCS5A01G247500 chr2B 86.856 388 45 6 2282 2666 131902338 131901954 1.900000e-116 429.0
15 TraesCS5A01G247500 chr4D 87.500 368 45 1 2284 2651 8134336 8133970 8.820000e-115 424.0
16 TraesCS5A01G247500 chr4D 91.213 239 20 1 816 1053 456276195 456275957 9.210000e-85 324.0
17 TraesCS5A01G247500 chr4B 86.684 383 45 5 2284 2662 592078105 592077725 1.140000e-113 420.0
18 TraesCS5A01G247500 chr4B 86.614 381 48 3 2284 2662 592186553 592186174 4.100000e-113 418.0
19 TraesCS5A01G247500 chr3D 92.050 239 17 2 816 1052 561099354 561099592 4.250000e-88 335.0
20 TraesCS5A01G247500 chr3D 91.286 241 19 2 816 1054 368292333 368292573 7.120000e-86 327.0
21 TraesCS5A01G247500 chr3D 91.525 236 18 2 816 1050 561098693 561098459 9.210000e-85 324.0
22 TraesCS5A01G247500 chr2A 91.561 237 18 2 817 1052 18292630 18292865 2.560000e-85 326.0
23 TraesCS5A01G247500 chr1D 90.947 243 20 2 812 1052 38792116 38792358 2.560000e-85 326.0
24 TraesCS5A01G247500 chr1D 91.176 238 20 1 816 1052 38791404 38791167 3.310000e-84 322.0


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 TraesCS5A01G247500 chr5A 461521459 461524124 2665 False 4924.0 4924 100.0000 1 2666 1 chr5A.!!$F1 2665
1 TraesCS5A01G247500 chr7D 631380638 631381689 1051 True 1489.0 1489 92.2420 1 1052 1 chr7D.!!$R3 1051
2 TraesCS5A01G247500 chr2D 520036825 520037872 1047 False 1463.0 1463 91.8870 1 1052 1 chr2D.!!$F1 1051
3 TraesCS5A01G247500 chr5D 360750072 360752458 2386 False 1125.5 1192 91.9325 1053 2666 2 chr5D.!!$F1 1613
4 TraesCS5A01G247500 chr5B 426086823 426087556 733 False 811.0 811 86.6320 1053 1820 1 chr5B.!!$F1 767

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
735 741 0.392998 ATAGCCAGGCAACAAGGACG 60.393 55.0 15.8 0.0 36.21 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2918 0.320247 CCTTAGCTGCTAGATGGCCG 60.32 60.0 9.62 0.0 0.0 6.13 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
25 26 7.430441 ACTTGGGAAACAAATGTTATACACAC 58.570 34.615 0.00 0.00 38.91 3.82
30 31 6.660094 GGAAACAAATGTTATACACACCCCTA 59.340 38.462 0.00 0.00 38.61 3.53
68 69 0.678950 AATCAACCCCTTTGCAACCG 59.321 50.000 0.00 0.00 34.88 4.44
143 144 4.899239 CCTCGATGACCGCAGCCC 62.899 72.222 0.00 0.00 38.37 5.19
280 281 0.758123 CTGCTCCTTCTCCATCCTCC 59.242 60.000 0.00 0.00 0.00 4.30
310 311 1.475169 CCTGTGCCCTCTCTGACACA 61.475 60.000 0.00 0.00 40.53 3.72
315 316 2.125753 CCTCTCTGACACAGCCGC 60.126 66.667 0.00 0.00 0.00 6.53
321 322 4.555709 TGACACAGCCGCCGGTTT 62.556 61.111 4.45 0.00 0.00 3.27
357 359 1.140816 GAGATCGCCCGATTTGCTAC 58.859 55.000 4.53 0.00 34.60 3.58
371 373 1.593196 TGCTACAAATCGCTATGGCC 58.407 50.000 0.00 0.00 34.44 5.36
409 411 2.189499 GTTGGATCCGAGCATGCCC 61.189 63.158 15.66 7.83 0.00 5.36
425 427 1.760086 CCCGATCTGGAGCACCTCT 60.760 63.158 0.71 0.00 42.00 3.69
469 471 2.631580 GCCTAGATCCGGAGCCTCG 61.632 68.421 17.84 8.53 0.00 4.63
509 511 4.431131 CCCCATTCCAGCCGCTGT 62.431 66.667 18.98 0.00 0.00 4.40
659 662 4.010414 GATCGCTGCAGCATCGGC 62.010 66.667 36.03 17.32 42.21 5.54
670 673 1.748879 GCATCGGCAAGCCAACCTA 60.749 57.895 12.19 0.00 40.72 3.08
732 735 2.496942 CCATAGCCAGGCAACAAGG 58.503 57.895 15.80 4.04 41.41 3.61
735 741 0.392998 ATAGCCAGGCAACAAGGACG 60.393 55.000 15.80 0.00 36.21 4.79
797 806 0.745845 CTTCGGCAGGAGGGATTGTG 60.746 60.000 0.00 0.00 0.00 3.33
815 824 3.935872 CACGGTGGTGTGCGTGTG 61.936 66.667 0.00 0.00 39.38 3.82
924 933 8.658499 ACTTGTAAGAAAGTGATTAAACGAGT 57.342 30.769 0.00 0.00 38.95 4.18
925 934 8.548721 ACTTGTAAGAAAGTGATTAAACGAGTG 58.451 33.333 0.00 0.00 38.95 3.51
932 941 9.003658 AGAAAGTGATTAAACGAGTGAAATCAT 57.996 29.630 13.18 2.83 39.70 2.45
933 942 9.612620 GAAAGTGATTAAACGAGTGAAATCATT 57.387 29.630 13.18 8.73 39.70 2.57
935 944 8.322906 AGTGATTAAACGAGTGAAATCATTCA 57.677 30.769 13.18 0.00 43.18 2.57
936 945 8.783093 AGTGATTAAACGAGTGAAATCATTCAA 58.217 29.630 13.18 0.00 46.66 2.69
969 978 4.555348 TGCAACGACTTAACCGATTTTT 57.445 36.364 0.00 0.00 0.00 1.94
970 979 4.283678 TGCAACGACTTAACCGATTTTTG 58.716 39.130 0.00 0.00 0.00 2.44
971 980 4.035324 TGCAACGACTTAACCGATTTTTGA 59.965 37.500 0.00 0.00 0.00 2.69
1008 1017 4.390603 CGGATTAACGAGTTGATGGTTTCA 59.609 41.667 0.00 0.00 35.47 2.69
1034 1043 0.676466 CCTAGCCGCAAATGTGGTGA 60.676 55.000 14.07 2.48 46.99 4.02
1038 1047 1.344114 AGCCGCAAATGTGGTGATTTT 59.656 42.857 14.07 0.00 46.99 1.82
1105 1114 4.873129 CCATCGCCGAGTCCACCG 62.873 72.222 0.00 0.00 0.00 4.94
1164 1173 4.648626 CCCATCATGCCGGCCGAT 62.649 66.667 30.73 22.69 0.00 4.18
1222 1231 1.007038 GCCGACGACAAGGTACACA 60.007 57.895 0.00 0.00 0.00 3.72
1228 1237 4.201940 CCGACGACAAGGTACACACATATA 60.202 45.833 0.00 0.00 0.00 0.86
1236 1245 6.127423 ACAAGGTACACACATATACTCTGTCC 60.127 42.308 0.00 0.00 0.00 4.02
1237 1246 5.516044 AGGTACACACATATACTCTGTCCA 58.484 41.667 0.00 0.00 0.00 4.02
1238 1247 5.594725 AGGTACACACATATACTCTGTCCAG 59.405 44.000 0.00 0.00 0.00 3.86
1254 1268 3.093057 GTCCAGAAAGCACTCCTAGAGA 58.907 50.000 0.00 0.00 33.32 3.10
1256 1270 4.890581 GTCCAGAAAGCACTCCTAGAGATA 59.109 45.833 0.00 0.00 33.32 1.98
1259 1273 5.229423 CAGAAAGCACTCCTAGAGATATGC 58.771 45.833 0.00 0.00 36.96 3.14
1263 1277 3.075882 AGCACTCCTAGAGATATGCTCCT 59.924 47.826 0.00 0.00 45.10 3.69
1264 1278 3.831911 GCACTCCTAGAGATATGCTCCTT 59.168 47.826 0.00 0.00 45.10 3.36
1265 1279 5.013547 GCACTCCTAGAGATATGCTCCTTA 58.986 45.833 0.00 0.00 45.10 2.69
1267 1281 5.652014 CACTCCTAGAGATATGCTCCTTAGG 59.348 48.000 0.00 0.00 45.10 2.69
1269 1283 6.506056 ACTCCTAGAGATATGCTCCTTAGGTA 59.494 42.308 0.00 0.00 45.10 3.08
1271 1285 6.274908 TCCTAGAGATATGCTCCTTAGGTACA 59.725 42.308 0.00 0.00 45.10 2.90
1273 1287 5.706447 AGAGATATGCTCCTTAGGTACACA 58.294 41.667 0.00 0.00 45.10 3.72
1274 1288 5.536916 AGAGATATGCTCCTTAGGTACACAC 59.463 44.000 0.00 0.00 45.10 3.82
1276 1290 3.895232 ATGCTCCTTAGGTACACACAG 57.105 47.619 0.00 0.00 0.00 3.66
1278 1292 1.275291 GCTCCTTAGGTACACACAGCA 59.725 52.381 0.00 0.00 0.00 4.41
1279 1293 2.675317 GCTCCTTAGGTACACACAGCAG 60.675 54.545 0.00 0.00 0.00 4.24
1280 1294 1.275291 TCCTTAGGTACACACAGCAGC 59.725 52.381 0.00 0.00 0.00 5.25
1281 1295 1.276421 CCTTAGGTACACACAGCAGCT 59.724 52.381 0.00 0.00 0.00 4.24
1282 1296 2.611518 CTTAGGTACACACAGCAGCTC 58.388 52.381 0.00 0.00 0.00 4.09
1283 1297 1.924731 TAGGTACACACAGCAGCTCT 58.075 50.000 0.00 0.00 0.00 4.09
1284 1298 1.924731 AGGTACACACAGCAGCTCTA 58.075 50.000 0.00 0.00 0.00 2.43
1285 1299 2.248248 AGGTACACACAGCAGCTCTAA 58.752 47.619 0.00 0.00 0.00 2.10
1286 1300 2.632996 AGGTACACACAGCAGCTCTAAA 59.367 45.455 0.00 0.00 0.00 1.85
1291 1305 4.136796 ACACACAGCAGCTCTAAAAATGA 58.863 39.130 0.00 0.00 0.00 2.57
1302 1316 4.706962 GCTCTAAAAATGACAGGATTGGGT 59.293 41.667 0.00 0.00 0.00 4.51
1303 1317 5.185828 GCTCTAAAAATGACAGGATTGGGTT 59.814 40.000 0.00 0.00 0.00 4.11
1304 1318 6.588719 TCTAAAAATGACAGGATTGGGTTG 57.411 37.500 0.00 0.00 0.00 3.77
1305 1319 4.622260 AAAAATGACAGGATTGGGTTGG 57.378 40.909 0.00 0.00 0.00 3.77
1313 1327 1.061735 AGGATTGGGTTGGGGTTTGTT 60.062 47.619 0.00 0.00 0.00 2.83
1314 1328 1.346395 GGATTGGGTTGGGGTTTGTTC 59.654 52.381 0.00 0.00 0.00 3.18
1420 1434 3.334054 GCTGGAGAAGGCCCTGGT 61.334 66.667 0.00 0.00 0.00 4.00
1468 1484 2.576317 GCTACCTCGACGTCGTGC 60.576 66.667 34.40 25.42 40.80 5.34
1605 1621 2.266055 GTGAAGGAGACCCTGCCG 59.734 66.667 0.00 0.00 43.48 5.69
1674 1693 3.438017 CTCGGCCTAGAGCAGCACC 62.438 68.421 0.00 0.00 46.50 5.01
1815 1835 0.834612 TCACACTCCCAGTTTCCGTT 59.165 50.000 0.00 0.00 0.00 4.44
1816 1836 2.040939 TCACACTCCCAGTTTCCGTTA 58.959 47.619 0.00 0.00 0.00 3.18
1911 2733 4.816786 ACAAAAATGACAAGGCAAATGC 57.183 36.364 0.00 0.00 41.14 3.56
1918 2740 2.029739 TGACAAGGCAAATGCACATCAG 60.030 45.455 7.80 0.00 44.36 2.90
1925 2747 3.922240 GGCAAATGCACATCAGTTACTTG 59.078 43.478 7.80 0.00 44.36 3.16
1935 2757 7.589587 TGCACATCAGTTACTTGTTATTTTTCG 59.410 33.333 0.00 0.00 0.00 3.46
1950 2772 5.649782 ATTTTTCGAATTGAGGAGCATGT 57.350 34.783 0.00 0.00 0.00 3.21
1966 2788 5.368256 AGCATGTCTCACAATTTCACTTC 57.632 39.130 0.00 0.00 0.00 3.01
1967 2789 4.823442 AGCATGTCTCACAATTTCACTTCA 59.177 37.500 0.00 0.00 0.00 3.02
1968 2790 5.475909 AGCATGTCTCACAATTTCACTTCAT 59.524 36.000 0.00 0.00 0.00 2.57
1995 2817 9.749490 CATGAAATTGATAAAACACAGCAAATC 57.251 29.630 0.00 0.00 0.00 2.17
2076 2898 3.006940 TGGCCTATAAAAAGTGACGCAG 58.993 45.455 3.32 0.00 0.00 5.18
2083 2905 0.381801 AAAAGTGACGCAGCACCAAG 59.618 50.000 2.61 0.00 39.59 3.61
2086 2908 0.952497 AGTGACGCAGCACCAAGATG 60.952 55.000 2.61 0.00 39.59 2.90
2096 2918 1.308998 CACCAAGATGATAACCCCGC 58.691 55.000 0.00 0.00 0.00 6.13
2099 2921 1.227853 AAGATGATAACCCCGCGGC 60.228 57.895 22.85 5.24 0.00 6.53
2105 2927 1.823169 GATAACCCCGCGGCCATCTA 61.823 60.000 22.85 6.37 0.00 1.98
2123 2945 2.665008 TAGCAGCTAAGGGCATGGCG 62.665 60.000 13.76 0.00 44.79 5.69
2151 2973 3.487563 AAAAATCTTCCGCATTCGTCC 57.512 42.857 0.00 0.00 0.00 4.79
2152 2974 2.107950 AAATCTTCCGCATTCGTCCA 57.892 45.000 0.00 0.00 0.00 4.02
2160 2982 0.526739 CGCATTCGTCCACGGACATA 60.527 55.000 16.23 3.62 44.77 2.29
2165 2987 1.758936 TCGTCCACGGACATAGATGT 58.241 50.000 16.23 0.00 44.77 3.06
2166 2988 2.921821 TCGTCCACGGACATAGATGTA 58.078 47.619 16.23 0.00 44.77 2.29
2196 3018 2.029244 CGCTACATCATCAACGACAACC 59.971 50.000 0.00 0.00 0.00 3.77
2205 3027 3.791973 TCAACGACAACCTGCAAAAAT 57.208 38.095 0.00 0.00 0.00 1.82
2209 3031 4.385358 ACGACAACCTGCAAAAATCTTT 57.615 36.364 0.00 0.00 0.00 2.52
2212 3034 4.359706 GACAACCTGCAAAAATCTTTCGT 58.640 39.130 0.00 0.00 0.00 3.85
2216 3038 6.983890 ACAACCTGCAAAAATCTTTCGTATTT 59.016 30.769 0.00 0.00 0.00 1.40
2217 3039 8.138712 ACAACCTGCAAAAATCTTTCGTATTTA 58.861 29.630 0.00 0.00 0.00 1.40
2230 3052 3.967401 TCGTATTTATTCGCGGACATGA 58.033 40.909 6.13 0.00 0.00 3.07
2252 3074 1.817099 CGAGAGGCAGCCATCCAAC 60.817 63.158 15.80 2.93 0.00 3.77
2258 3080 1.450312 GCAGCCATCCAACGCTAGT 60.450 57.895 0.00 0.00 32.92 2.57
2275 3097 4.142708 CGCTAGTGCATACATTTCAAACCA 60.143 41.667 0.00 0.00 39.64 3.67
2325 3147 3.161866 GGCAAATTCTACCCCTCAAACA 58.838 45.455 0.00 0.00 0.00 2.83
2327 3149 3.056821 GCAAATTCTACCCCTCAAACACC 60.057 47.826 0.00 0.00 0.00 4.16
2330 3152 1.196104 TCTACCCCTCAAACACCCGG 61.196 60.000 0.00 0.00 0.00 5.73
2364 3186 4.314440 GTCCGCTGGCACTGACCA 62.314 66.667 0.00 0.00 38.29 4.02
2381 3203 3.244770 TGACCAGACACCCCTCAAATAAC 60.245 47.826 0.00 0.00 0.00 1.89
2386 3208 4.390909 CAGACACCCCTCAAATAACGTAAC 59.609 45.833 0.00 0.00 0.00 2.50
2401 3223 0.611714 GTAACCCACATCCGGACACT 59.388 55.000 6.12 0.00 0.00 3.55
2406 3228 1.134788 CCCACATCCGGACACTTCTAC 60.135 57.143 6.12 0.00 0.00 2.59
2408 3230 2.417379 CCACATCCGGACACTTCTACTG 60.417 54.545 6.12 0.00 0.00 2.74
2415 3237 4.579340 TCCGGACACTTCTACTGTCATATC 59.421 45.833 0.00 0.00 39.97 1.63
2421 3243 7.489757 GGACACTTCTACTGTCATATCTCAAAC 59.510 40.741 1.29 0.00 39.97 2.93
2422 3244 7.324178 ACACTTCTACTGTCATATCTCAAACC 58.676 38.462 0.00 0.00 0.00 3.27
2445 3267 5.415701 CCCATACAAACTCATGCAACTAAGT 59.584 40.000 0.00 0.00 0.00 2.24
2472 3294 0.525668 CACACATCGTCCGGCTACTC 60.526 60.000 0.00 0.00 0.00 2.59
2500 3322 5.234329 CACTACTAACTAAACATGCCATCGG 59.766 44.000 0.00 0.00 0.00 4.18
2516 3338 4.610945 CCATCGGACTATCAAAATTTGGC 58.389 43.478 5.83 0.00 0.00 4.52
2586 3408 1.953231 GCCCTTGCCATCCTTCTTGC 61.953 60.000 0.00 0.00 0.00 4.01
2621 3443 3.900855 ACGCAGTACCGATCGAGT 58.099 55.556 18.66 15.06 41.94 4.18
2645 3467 1.029947 TCTGCTCGTCGCCATCACTA 61.030 55.000 0.00 0.00 38.05 2.74
2661 3483 3.135279 TCACTATCCTCCTTCTCCTCCT 58.865 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.584185 AGGGGTGTGTATAACATTTGTTTC 57.416 37.500 0.63 0.00 41.97 2.78
280 281 0.251634 GGGCACAGGGAGAAGAGAAG 59.748 60.000 0.00 0.00 0.00 2.85
321 322 3.083349 CCATGGAGGTCCTGCGGA 61.083 66.667 5.56 0.00 36.82 5.54
357 359 1.845809 GAGGCGGCCATAGCGATTTG 61.846 60.000 23.09 0.00 41.24 2.32
365 367 3.804329 GTTGGGGAGGCGGCCATA 61.804 66.667 23.09 0.00 0.00 2.74
371 373 2.742372 CGAGTTGTTGGGGAGGCG 60.742 66.667 0.00 0.00 0.00 5.52
425 427 3.219928 GCGCGAGGGAGATCAGGA 61.220 66.667 12.10 0.00 0.00 3.86
447 449 2.992114 CTCCGGATCTAGGCGGGG 60.992 72.222 3.57 1.22 0.00 5.73
581 584 0.933047 CAACGAAGTGCAGACGACGA 60.933 55.000 0.00 0.00 45.00 4.20
655 658 1.693627 TTTTTAGGTTGGCTTGCCGA 58.306 45.000 7.18 1.88 0.00 5.54
702 705 4.647615 CTATGGCCGCGACGAGGG 62.648 72.222 19.59 10.24 0.00 4.30
875 884 4.341235 GGGGCCAGATTGTAAGGAATTAAC 59.659 45.833 4.39 0.00 0.00 2.01
877 886 3.529734 TGGGGCCAGATTGTAAGGAATTA 59.470 43.478 4.39 0.00 0.00 1.40
882 891 0.625849 AGTGGGGCCAGATTGTAAGG 59.374 55.000 4.39 0.00 0.00 2.69
920 929 5.026462 GCACTGATTGAATGATTTCACTCG 58.974 41.667 0.00 0.00 41.82 4.18
922 931 6.585695 AAGCACTGATTGAATGATTTCACT 57.414 33.333 0.00 0.00 41.50 3.41
924 933 7.307514 GCAAAAAGCACTGATTGAATGATTTCA 60.308 33.333 0.00 0.00 44.79 2.69
925 934 7.013529 GCAAAAAGCACTGATTGAATGATTTC 58.986 34.615 0.00 0.00 44.79 2.17
953 962 5.338614 ACACTCAAAAATCGGTTAAGTCG 57.661 39.130 0.00 0.00 0.00 4.18
962 971 5.552472 CGTTGCAGAAAACACTCAAAAATCG 60.552 40.000 0.00 0.00 0.00 3.34
969 978 2.031258 TCCGTTGCAGAAAACACTCA 57.969 45.000 0.00 0.00 0.00 3.41
970 979 3.626028 AATCCGTTGCAGAAAACACTC 57.374 42.857 0.00 0.00 0.00 3.51
971 980 4.553938 CGTTAATCCGTTGCAGAAAACACT 60.554 41.667 0.00 0.00 0.00 3.55
1008 1017 1.135024 CATTTGCGGCTAGGTTTGCAT 60.135 47.619 0.00 0.00 37.17 3.96
1038 1047 5.534654 CACCTTCTTGGGAGTCAATTGTAAA 59.465 40.000 5.13 0.00 41.11 2.01
1041 1050 3.490348 CACCTTCTTGGGAGTCAATTGT 58.510 45.455 5.13 0.00 41.11 2.71
1089 1098 4.129737 ACGGTGGACTCGGCGATG 62.130 66.667 11.27 7.46 0.00 3.84
1185 1194 1.303643 GAACCTGGCCCAGAACCTG 60.304 63.158 13.74 0.00 32.44 4.00
1222 1231 5.423610 AGTGCTTTCTGGACAGAGTATATGT 59.576 40.000 1.92 0.00 39.64 2.29
1228 1237 1.346068 GGAGTGCTTTCTGGACAGAGT 59.654 52.381 1.92 0.00 39.64 3.24
1236 1245 5.010922 AGCATATCTCTAGGAGTGCTTTCTG 59.989 44.000 13.36 0.00 42.93 3.02
1237 1246 5.147032 AGCATATCTCTAGGAGTGCTTTCT 58.853 41.667 13.36 0.00 42.93 2.52
1238 1247 5.467035 AGCATATCTCTAGGAGTGCTTTC 57.533 43.478 13.36 0.00 42.93 2.62
1254 1268 4.202264 GCTGTGTGTACCTAAGGAGCATAT 60.202 45.833 0.00 0.00 0.00 1.78
1256 1270 2.093447 GCTGTGTGTACCTAAGGAGCAT 60.093 50.000 0.00 0.00 0.00 3.79
1259 1273 2.675317 GCTGCTGTGTGTACCTAAGGAG 60.675 54.545 0.00 0.00 0.00 3.69
1263 1277 2.248248 AGAGCTGCTGTGTGTACCTAA 58.752 47.619 7.01 0.00 0.00 2.69
1264 1278 1.924731 AGAGCTGCTGTGTGTACCTA 58.075 50.000 7.01 0.00 0.00 3.08
1265 1279 1.924731 TAGAGCTGCTGTGTGTACCT 58.075 50.000 7.01 0.00 0.00 3.08
1267 1281 5.179368 TCATTTTTAGAGCTGCTGTGTGTAC 59.821 40.000 7.01 0.00 0.00 2.90
1269 1283 4.023707 GTCATTTTTAGAGCTGCTGTGTGT 60.024 41.667 7.01 0.00 0.00 3.72
1271 1285 4.136796 TGTCATTTTTAGAGCTGCTGTGT 58.863 39.130 7.01 0.00 0.00 3.72
1273 1287 3.755378 CCTGTCATTTTTAGAGCTGCTGT 59.245 43.478 7.01 5.47 0.00 4.40
1274 1288 4.005650 TCCTGTCATTTTTAGAGCTGCTG 58.994 43.478 7.01 0.00 0.00 4.41
1276 1290 5.338365 CAATCCTGTCATTTTTAGAGCTGC 58.662 41.667 0.00 0.00 0.00 5.25
1278 1292 4.952335 CCCAATCCTGTCATTTTTAGAGCT 59.048 41.667 0.00 0.00 0.00 4.09
1279 1293 4.706962 ACCCAATCCTGTCATTTTTAGAGC 59.293 41.667 0.00 0.00 0.00 4.09
1280 1294 6.350445 CCAACCCAATCCTGTCATTTTTAGAG 60.350 42.308 0.00 0.00 0.00 2.43
1281 1295 5.480073 CCAACCCAATCCTGTCATTTTTAGA 59.520 40.000 0.00 0.00 0.00 2.10
1282 1296 5.337491 CCCAACCCAATCCTGTCATTTTTAG 60.337 44.000 0.00 0.00 0.00 1.85
1283 1297 4.530161 CCCAACCCAATCCTGTCATTTTTA 59.470 41.667 0.00 0.00 0.00 1.52
1284 1298 3.327464 CCCAACCCAATCCTGTCATTTTT 59.673 43.478 0.00 0.00 0.00 1.94
1285 1299 2.905736 CCCAACCCAATCCTGTCATTTT 59.094 45.455 0.00 0.00 0.00 1.82
1286 1300 2.539302 CCCAACCCAATCCTGTCATTT 58.461 47.619 0.00 0.00 0.00 2.32
1291 1305 0.565674 AAACCCCAACCCAATCCTGT 59.434 50.000 0.00 0.00 0.00 4.00
1302 1316 1.205893 GTTGCACTGAACAAACCCCAA 59.794 47.619 0.00 0.00 0.00 4.12
1303 1317 0.820871 GTTGCACTGAACAAACCCCA 59.179 50.000 0.00 0.00 0.00 4.96
1304 1318 0.248866 CGTTGCACTGAACAAACCCC 60.249 55.000 0.00 0.00 0.00 4.95
1305 1319 0.869880 GCGTTGCACTGAACAAACCC 60.870 55.000 0.00 0.00 0.00 4.11
1314 1328 4.465512 GATGGCGGCGTTGCACTG 62.466 66.667 9.37 0.00 36.28 3.66
1420 1434 1.140134 CCCCCAGAACTTCTTCCCCA 61.140 60.000 0.00 0.00 0.00 4.96
1468 1484 3.419759 GTGCGCGTACCACCCAAG 61.420 66.667 17.10 0.00 0.00 3.61
1483 1499 2.242572 CGATGATCGGCAGCCAGTG 61.243 63.158 13.30 0.00 36.00 3.66
1485 1501 1.664017 CTCGATGATCGGCAGCCAG 60.664 63.158 15.48 4.47 40.88 4.85
1662 1681 0.459237 CGGAACAGGTGCTGCTCTAG 60.459 60.000 0.00 0.00 34.37 2.43
1674 1693 1.743252 GCTGGAAGGCTCGGAACAG 60.743 63.158 0.00 0.00 0.00 3.16
1726 1745 3.202906 TGCTCACCGCTTATTTATCCAC 58.797 45.455 0.00 0.00 40.11 4.02
1911 2733 9.658475 TTCGAAAAATAACAAGTAACTGATGTG 57.342 29.630 0.00 0.00 0.00 3.21
1918 2740 9.887406 TCCTCAATTCGAAAAATAACAAGTAAC 57.113 29.630 0.00 0.00 0.00 2.50
1925 2747 7.029563 ACATGCTCCTCAATTCGAAAAATAAC 58.970 34.615 0.00 0.00 0.00 1.89
1935 2757 3.603532 TGTGAGACATGCTCCTCAATTC 58.396 45.455 12.70 4.44 43.26 2.17
1950 2772 7.748691 TTCATGATGAAGTGAAATTGTGAGA 57.251 32.000 3.29 0.00 31.83 3.27
1966 2788 8.468720 TGCTGTGTTTTATCAATTTCATGATG 57.531 30.769 0.00 0.00 40.21 3.07
1967 2789 9.491675 TTTGCTGTGTTTTATCAATTTCATGAT 57.508 25.926 0.00 0.00 42.52 2.45
1968 2790 8.883954 TTTGCTGTGTTTTATCAATTTCATGA 57.116 26.923 0.00 0.00 0.00 3.07
2028 2850 2.528743 CGGCCTTGTATGAGCGCTG 61.529 63.158 18.48 0.00 0.00 5.18
2029 2851 2.202932 CGGCCTTGTATGAGCGCT 60.203 61.111 11.27 11.27 0.00 5.92
2030 2852 3.272334 CCGGCCTTGTATGAGCGC 61.272 66.667 0.00 0.00 0.00 5.92
2076 2898 1.308998 CGGGGTTATCATCTTGGTGC 58.691 55.000 0.00 0.00 0.00 5.01
2083 2905 2.668550 GGCCGCGGGGTTATCATC 60.669 66.667 29.38 6.13 34.97 2.92
2086 2908 1.823169 TAGATGGCCGCGGGGTTATC 61.823 60.000 29.38 21.12 34.97 1.75
2096 2918 0.320247 CCTTAGCTGCTAGATGGCCG 60.320 60.000 9.62 0.00 0.00 6.13
2099 2921 0.761187 TGCCCTTAGCTGCTAGATGG 59.239 55.000 9.62 12.05 44.23 3.51
2105 2927 2.123982 GCCATGCCCTTAGCTGCT 60.124 61.111 7.57 7.57 44.23 4.24
2136 2958 1.445410 CGTGGACGAATGCGGAAGA 60.445 57.895 0.00 0.00 43.17 2.87
2151 2973 3.883489 TGTCTCCTACATCTATGTCCGTG 59.117 47.826 0.00 0.00 41.97 4.94
2152 2974 4.166246 TGTCTCCTACATCTATGTCCGT 57.834 45.455 0.00 0.00 41.97 4.69
2160 2982 3.353557 TGTAGCGTTGTCTCCTACATCT 58.646 45.455 0.00 0.00 37.21 2.90
2165 2987 3.951680 TGATGATGTAGCGTTGTCTCCTA 59.048 43.478 0.00 0.00 0.00 2.94
2166 2988 2.760650 TGATGATGTAGCGTTGTCTCCT 59.239 45.455 0.00 0.00 0.00 3.69
2196 3018 8.044409 GCGAATAAATACGAAAGATTTTTGCAG 58.956 33.333 0.00 0.00 0.00 4.41
2205 3027 4.422840 TGTCCGCGAATAAATACGAAAGA 58.577 39.130 8.23 0.00 0.00 2.52
2209 3031 3.967401 TCATGTCCGCGAATAAATACGA 58.033 40.909 8.23 0.00 0.00 3.43
2212 3034 5.029650 GCATTCATGTCCGCGAATAAATA 57.970 39.130 8.23 0.00 30.74 1.40
2252 3074 4.142708 TGGTTTGAAATGTATGCACTAGCG 60.143 41.667 0.00 0.00 46.23 4.26
2275 3097 5.934625 CCGGCTGTAGATGCTCTTAAAATAT 59.065 40.000 0.00 0.00 0.00 1.28
2297 3119 1.743394 GGGTAGAATTTGCCAAGTCCG 59.257 52.381 0.00 0.00 32.28 4.79
2311 3133 1.196104 CCGGGTGTTTGAGGGGTAGA 61.196 60.000 0.00 0.00 0.00 2.59
2364 3186 4.564199 GGTTACGTTATTTGAGGGGTGTCT 60.564 45.833 0.00 0.00 0.00 3.41
2366 3188 3.559811 GGGTTACGTTATTTGAGGGGTGT 60.560 47.826 0.00 0.00 0.00 4.16
2381 3203 0.738412 GTGTCCGGATGTGGGTTACG 60.738 60.000 7.81 0.00 0.00 3.18
2386 3208 1.134788 GTAGAAGTGTCCGGATGTGGG 60.135 57.143 7.81 0.00 0.00 4.61
2401 3223 6.867519 TGGGTTTGAGATATGACAGTAGAA 57.132 37.500 0.00 0.00 0.00 2.10
2406 3228 7.554118 AGTTTGTATGGGTTTGAGATATGACAG 59.446 37.037 0.00 0.00 0.00 3.51
2408 3230 7.552687 TGAGTTTGTATGGGTTTGAGATATGAC 59.447 37.037 0.00 0.00 0.00 3.06
2415 3237 4.218200 TGCATGAGTTTGTATGGGTTTGAG 59.782 41.667 0.00 0.00 0.00 3.02
2421 3243 5.415701 ACTTAGTTGCATGAGTTTGTATGGG 59.584 40.000 0.00 0.00 0.00 4.00
2422 3244 6.500684 ACTTAGTTGCATGAGTTTGTATGG 57.499 37.500 0.00 0.00 0.00 2.74
2472 3294 6.112734 TGGCATGTTTAGTTAGTAGTGATGG 58.887 40.000 0.00 0.00 0.00 3.51
2500 3322 6.402442 GCCAAACATGCCAAATTTTGATAGTC 60.402 38.462 10.72 0.00 31.79 2.59
2516 3338 2.726821 ACTCCACCATAGCCAAACATG 58.273 47.619 0.00 0.00 0.00 3.21
2547 3369 1.307517 TCGGGAAGGGTAAGGGCAT 60.308 57.895 0.00 0.00 0.00 4.40
2586 3408 1.594034 CGTCTTCGACCGATACTTCCG 60.594 57.143 0.00 0.00 39.71 4.30
2594 3416 1.499056 GTACTGCGTCTTCGACCGA 59.501 57.895 2.80 0.00 39.71 4.69
2645 3467 2.080654 CGAAGGAGGAGAAGGAGGAT 57.919 55.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.