Multiple sequence alignment - TraesCS6B01G324600

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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 TraesCS6B01G324600 chr6B 100.000 3364 0 0 1 3364 574022648 574019285 0.000000e+00 6213.0
1 TraesCS6B01G324600 chr6A 89.815 3024 191 56 1 2959 525993791 525990820 0.000000e+00 3770.0
2 TraesCS6B01G324600 chr6A 88.434 415 33 12 2957 3363 525990619 525990212 1.400000e-133 486.0
3 TraesCS6B01G324600 chr6D 90.928 2469 131 45 1 2423 383746711 383744290 0.000000e+00 3232.0
4 TraesCS6B01G324600 chr6D 93.455 550 28 6 2414 2959 383744119 383743574 0.000000e+00 809.0
5 TraesCS6B01G324600 chr6D 94.118 238 9 4 2950 3187 383743397 383743165 1.150000e-94 357.0
6 TraesCS6B01G324600 chr7D 78.974 604 83 28 1163 1735 165634713 165635303 4.100000e-99 372.0
7 TraesCS6B01G324600 chr7D 85.333 150 19 3 3067 3213 231615398 231615249 5.810000e-33 152.0
8 TraesCS6B01G324600 chr7B 81.073 354 52 12 1392 1735 128822319 128822667 5.530000e-68 268.0
9 TraesCS6B01G324600 chr7B 91.034 145 12 1 1163 1306 128822081 128822225 9.520000e-46 195.0
10 TraesCS6B01G324600 chr7B 86.000 150 17 4 3067 3213 105210064 105209916 1.250000e-34 158.0
11 TraesCS6B01G324600 chr7A 80.170 353 61 7 1390 1735 167179925 167180275 4.310000e-64 255.0
12 TraesCS6B01G324600 chr7A 91.034 145 12 1 1163 1306 167179681 167179825 9.520000e-46 195.0
13 TraesCS6B01G324600 chr1D 87.333 150 16 3 3067 3213 254421334 254421185 5.770000e-38 169.0
14 TraesCS6B01G324600 chr5D 88.971 136 13 2 1165 1299 319254271 319254405 2.080000e-37 167.0
15 TraesCS6B01G324600 chr5D 85.333 150 18 4 3067 3213 432420856 432421004 5.810000e-33 152.0
16 TraesCS6B01G324600 chr5B 88.971 136 13 2 1165 1299 369485439 369485573 2.080000e-37 167.0
17 TraesCS6B01G324600 chr5B 85.333 150 19 3 3067 3213 413612018 413611869 5.810000e-33 152.0
18 TraesCS6B01G324600 chr5B 84.028 144 20 3 1602 1744 369485849 369485990 5.850000e-28 135.0
19 TraesCS6B01G324600 chr5A 88.971 136 13 2 1165 1299 414934854 414934720 2.080000e-37 167.0
20 TraesCS6B01G324600 chr5A 85.333 150 19 3 3067 3213 482024802 482024951 5.810000e-33 152.0
21 TraesCS6B01G324600 chr5A 85.385 130 18 1 1615 1744 414934422 414934294 2.110000e-27 134.0
22 TraesCS6B01G324600 chr4A 86.184 152 17 4 3066 3213 310767229 310767078 9.660000e-36 161.0
23 TraesCS6B01G324600 chr2D 74.085 355 74 14 1391 1737 424015293 424014949 2.720000e-26 130.0
24 TraesCS6B01G324600 chr2D 84.874 119 16 2 1405 1522 556365646 556365763 5.900000e-23 119.0
25 TraesCS6B01G324600 chr2A 85.586 111 14 2 1623 1732 696316052 696316161 7.630000e-22 115.0
26 TraesCS6B01G324600 chr3D 73.554 363 69 24 1393 1748 360048892 360048550 2.740000e-21 113.0
27 TraesCS6B01G324600 chr3B 73.278 363 70 24 1393 1748 466106707 466106365 1.280000e-19 108.0
28 TraesCS6B01G324600 chr3A 80.714 140 24 3 1393 1530 479481827 479481689 4.590000e-19 106.0
29 TraesCS6B01G324600 chr1B 88.462 78 9 0 1610 1687 487951129 487951052 9.940000e-16 95.3
30 TraesCS6B01G324600 chr1B 88.136 59 6 1 1385 1443 631967506 631967449 6.020000e-08 69.4
31 TraesCS6B01G324600 chr4B 83.133 83 14 0 1164 1246 413499438 413499520 3.600000e-10 76.8
32 TraesCS6B01G324600 chr1A 95.122 41 2 0 1403 1443 551592902 551592862 7.790000e-07 65.8


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 TraesCS6B01G324600 chr6B 574019285 574022648 3363 True 6213.0 6213 100.000000 1 3364 1 chr6B.!!$R1 3363
1 TraesCS6B01G324600 chr6A 525990212 525993791 3579 True 2128.0 3770 89.124500 1 3363 2 chr6A.!!$R1 3362
2 TraesCS6B01G324600 chr6D 383743165 383746711 3546 True 1466.0 3232 92.833667 1 3187 3 chr6D.!!$R1 3186
3 TraesCS6B01G324600 chr7D 165634713 165635303 590 False 372.0 372 78.974000 1163 1735 1 chr7D.!!$F1 572
4 TraesCS6B01G324600 chr7B 128822081 128822667 586 False 231.5 268 86.053500 1163 1735 2 chr7B.!!$F1 572
5 TraesCS6B01G324600 chr7A 167179681 167180275 594 False 225.0 255 85.602000 1163 1735 2 chr7A.!!$F1 572

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
302 309 0.108615 TGAGCCGAGCAAGTAAGAGC 60.109 55.0 0.0 0.0 0.0 4.09 F
2241 2354 0.179140 CTCACTCGCTTGCTCTCTCC 60.179 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2400 0.784178 CACGGACATGAACACTGACG 59.216 55.000 0.0 0.0 0.0 4.35 R
3293 3840 1.876156 CTGAGTTGTCCTTGCCTTGAC 59.124 52.381 0.0 0.0 0.0 3.18 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
69 73 8.958175 TTGCGACGTTTATCATCTAAAAATTT 57.042 26.923 0.00 0.00 0.00 1.82
189 193 3.165498 GCGGCAGTCGGTTGTAAG 58.835 61.111 0.00 0.00 39.69 2.34
190 194 1.666872 GCGGCAGTCGGTTGTAAGT 60.667 57.895 0.00 0.00 39.69 2.24
197 204 4.396166 GGCAGTCGGTTGTAAGTAGTACTA 59.604 45.833 2.50 0.00 33.46 1.82
296 303 1.140589 CGATCTGAGCCGAGCAAGT 59.859 57.895 0.00 0.00 0.00 3.16
302 309 0.108615 TGAGCCGAGCAAGTAAGAGC 60.109 55.000 0.00 0.00 0.00 4.09
338 345 1.070786 GGTTTGTCACGGAGCAGGA 59.929 57.895 0.00 0.00 0.00 3.86
390 400 1.433471 CATCAGACGCTCGCTGGTA 59.567 57.895 11.55 0.00 34.20 3.25
392 402 1.266989 CATCAGACGCTCGCTGGTATA 59.733 52.381 11.55 0.00 34.20 1.47
401 414 1.298863 CGCTGGTATACCCGTGTCG 60.299 63.158 19.42 10.86 35.15 4.35
405 418 1.065102 CTGGTATACCCGTGTCGTGAG 59.935 57.143 19.42 2.71 35.15 3.51
453 466 3.642755 CGTGCAAGACGGCTTCTT 58.357 55.556 0.00 0.00 46.29 2.52
476 489 1.229177 GTTGGGGTGGCCAGGAAAT 60.229 57.895 5.11 0.00 0.00 2.17
547 561 1.334992 CGTCGTTGTACTGCTGACCG 61.335 60.000 0.00 0.00 0.00 4.79
673 695 1.472990 GCACGGTACAAAGTTTGTGC 58.527 50.000 27.65 25.69 45.03 4.57
716 752 2.046285 CCCACGGTTCATTCAGCCC 61.046 63.158 0.00 0.00 0.00 5.19
721 757 1.353022 ACGGTTCATTCAGCCCCTTTA 59.647 47.619 0.00 0.00 0.00 1.85
724 760 3.066760 CGGTTCATTCAGCCCCTTTATTC 59.933 47.826 0.00 0.00 0.00 1.75
849 890 1.450312 GTGCACCGCCTAGCAGAAT 60.450 57.895 5.22 0.00 42.14 2.40
884 925 0.552363 TATGCATGCATGGTCCACCT 59.448 50.000 37.43 15.82 37.82 4.00
915 962 2.892640 CGAGGCCGGTTGATGAGA 59.107 61.111 1.90 0.00 0.00 3.27
916 963 1.443407 CGAGGCCGGTTGATGAGAT 59.557 57.895 1.90 0.00 0.00 2.75
959 1006 2.283966 ACGTACTGGGGCTCTGCT 60.284 61.111 0.00 0.00 0.00 4.24
1081 1129 2.291282 ACTGACTGATTCCCTCGAGACT 60.291 50.000 15.71 0.00 0.00 3.24
1314 1366 2.092882 GGTCAGCGACGCTTACACC 61.093 63.158 29.31 24.94 36.40 4.16
1367 1431 2.261345 CCCTGCAAACGCATACATTTG 58.739 47.619 0.00 0.00 39.10 2.32
1372 1436 3.171277 GCAAACGCATACATTTGGTCTC 58.829 45.455 0.00 0.00 36.51 3.36
1376 1440 3.262420 ACGCATACATTTGGTCTCAGAC 58.738 45.455 0.00 0.00 0.00 3.51
1451 1525 3.081409 AACTACCTGCGCCCCGAT 61.081 61.111 4.18 0.00 0.00 4.18
1460 1534 4.514577 CGCCCCGATCTCAAGCGT 62.515 66.667 7.77 0.00 41.78 5.07
1808 1907 2.282180 GGCAAAGCCTCGTCCCAA 60.282 61.111 0.00 0.00 46.69 4.12
1822 1921 2.504032 CCAAGAATCGGCCGGCTA 59.496 61.111 28.56 15.89 0.00 3.93
1937 2042 4.465446 TCCCCCTGCTCCTCCTCG 62.465 72.222 0.00 0.00 0.00 4.63
2114 2219 2.126424 GACCAGTGCTCCGACGTC 60.126 66.667 5.18 5.18 0.00 4.34
2129 2234 0.242825 ACGTCGGCTTCGATCAAGAA 59.757 50.000 0.00 0.00 45.21 2.52
2144 2249 4.622260 TCAAGAAGTGTGGATGTGATCA 57.378 40.909 0.00 0.00 0.00 2.92
2145 2250 4.971939 TCAAGAAGTGTGGATGTGATCAA 58.028 39.130 0.00 0.00 0.00 2.57
2147 2252 3.341823 AGAAGTGTGGATGTGATCAAGC 58.658 45.455 0.00 0.00 0.00 4.01
2148 2253 1.730501 AGTGTGGATGTGATCAAGCG 58.269 50.000 0.00 0.00 0.00 4.68
2150 2255 1.026182 TGTGGATGTGATCAAGCGGC 61.026 55.000 0.00 0.00 0.00 6.53
2152 2257 0.745486 TGGATGTGATCAAGCGGCTG 60.745 55.000 1.81 0.00 0.00 4.85
2153 2258 0.745845 GGATGTGATCAAGCGGCTGT 60.746 55.000 1.81 0.00 0.00 4.40
2155 2260 2.279741 GATGTGATCAAGCGGCTGTTA 58.720 47.619 1.81 0.00 0.00 2.41
2156 2261 1.725641 TGTGATCAAGCGGCTGTTAG 58.274 50.000 1.81 0.00 0.00 2.34
2157 2262 1.001974 TGTGATCAAGCGGCTGTTAGT 59.998 47.619 1.81 0.00 0.00 2.24
2158 2263 2.232696 TGTGATCAAGCGGCTGTTAGTA 59.767 45.455 1.81 0.00 0.00 1.82
2159 2264 3.118775 TGTGATCAAGCGGCTGTTAGTAT 60.119 43.478 1.81 0.00 0.00 2.12
2160 2265 3.871594 GTGATCAAGCGGCTGTTAGTATT 59.128 43.478 1.81 0.00 0.00 1.89
2161 2266 4.025647 GTGATCAAGCGGCTGTTAGTATTC 60.026 45.833 1.81 0.00 0.00 1.75
2162 2267 2.536365 TCAAGCGGCTGTTAGTATTCG 58.464 47.619 1.81 0.00 0.00 3.34
2163 2268 2.164827 TCAAGCGGCTGTTAGTATTCGA 59.835 45.455 1.81 0.00 0.00 3.71
2164 2269 2.927477 CAAGCGGCTGTTAGTATTCGAA 59.073 45.455 1.81 0.00 0.00 3.71
2177 2282 7.067372 TGTTAGTATTCGAATCGAGGGTTAGAA 59.933 37.037 15.25 0.00 37.14 2.10
2186 2291 6.128795 CGAATCGAGGGTTAGAATTAGATTGC 60.129 42.308 0.00 0.00 0.00 3.56
2188 2293 4.098960 TCGAGGGTTAGAATTAGATTGCGT 59.901 41.667 0.00 0.00 0.00 5.24
2191 2296 5.116882 AGGGTTAGAATTAGATTGCGTCAC 58.883 41.667 0.00 0.00 0.00 3.67
2192 2297 5.104900 AGGGTTAGAATTAGATTGCGTCACT 60.105 40.000 0.00 0.00 0.00 3.41
2193 2298 5.234543 GGGTTAGAATTAGATTGCGTCACTC 59.765 44.000 0.00 0.00 0.00 3.51
2196 2301 5.078411 AGAATTAGATTGCGTCACTCACT 57.922 39.130 0.00 0.00 0.00 3.41
2198 2303 3.934457 TTAGATTGCGTCACTCACTCA 57.066 42.857 0.00 0.00 0.00 3.41
2199 2304 2.360553 AGATTGCGTCACTCACTCAG 57.639 50.000 0.00 0.00 0.00 3.35
2200 2305 1.889170 AGATTGCGTCACTCACTCAGA 59.111 47.619 0.00 0.00 0.00 3.27
2210 2315 2.214376 CTCACTCAGAGTCACCTCCT 57.786 55.000 0.00 0.00 39.62 3.69
2229 2342 3.005897 TCCTTCTGTTTTCCTCTCACTCG 59.994 47.826 0.00 0.00 0.00 4.18
2232 2345 2.365617 TCTGTTTTCCTCTCACTCGCTT 59.634 45.455 0.00 0.00 0.00 4.68
2241 2354 0.179140 CTCACTCGCTTGCTCTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
2261 2384 2.099098 CCGTGCTCTGTTTTCTTTGGTT 59.901 45.455 0.00 0.00 0.00 3.67
2277 2400 5.770162 TCTTTGGTTTCTTGGGAGAGAATTC 59.230 40.000 0.00 0.00 35.70 2.17
2281 2404 4.315803 GTTTCTTGGGAGAGAATTCGTCA 58.684 43.478 11.56 0.76 35.70 4.35
2282 2405 3.876274 TCTTGGGAGAGAATTCGTCAG 57.124 47.619 11.56 3.07 0.00 3.51
2289 2412 4.499183 GGAGAGAATTCGTCAGTGTTCAT 58.501 43.478 11.56 0.00 0.00 2.57
2290 2413 4.328440 GGAGAGAATTCGTCAGTGTTCATG 59.672 45.833 11.56 0.00 0.00 3.07
2291 2414 4.887748 AGAGAATTCGTCAGTGTTCATGT 58.112 39.130 0.00 0.00 0.00 3.21
2292 2415 4.926238 AGAGAATTCGTCAGTGTTCATGTC 59.074 41.667 0.00 0.00 0.00 3.06
2293 2416 3.997021 AGAATTCGTCAGTGTTCATGTCC 59.003 43.478 0.00 0.00 0.00 4.02
2294 2417 1.778334 TTCGTCAGTGTTCATGTCCG 58.222 50.000 0.00 0.00 0.00 4.79
2333 2458 6.677431 GCTTGCTTGTTGATAAGGAATGAGAG 60.677 42.308 0.00 0.00 37.37 3.20
2339 2464 8.868522 TTGTTGATAAGGAATGAGAGAAATGT 57.131 30.769 0.00 0.00 0.00 2.71
2340 2465 8.868522 TGTTGATAAGGAATGAGAGAAATGTT 57.131 30.769 0.00 0.00 0.00 2.71
2343 2468 8.498054 TGATAAGGAATGAGAGAAATGTTGAC 57.502 34.615 0.00 0.00 0.00 3.18
2348 2473 5.368256 AATGAGAGAAATGTTGACTGTGC 57.632 39.130 0.00 0.00 0.00 4.57
2351 2476 5.610398 TGAGAGAAATGTTGACTGTGCTTA 58.390 37.500 0.00 0.00 0.00 3.09
2352 2477 6.233434 TGAGAGAAATGTTGACTGTGCTTAT 58.767 36.000 0.00 0.00 0.00 1.73
2353 2478 6.148315 TGAGAGAAATGTTGACTGTGCTTATG 59.852 38.462 0.00 0.00 0.00 1.90
2354 2479 6.233434 AGAGAAATGTTGACTGTGCTTATGA 58.767 36.000 0.00 0.00 0.00 2.15
2358 2483 8.362639 AGAAATGTTGACTGTGCTTATGAAAAT 58.637 29.630 0.00 0.00 0.00 1.82
2360 2485 7.878477 ATGTTGACTGTGCTTATGAAAATTG 57.122 32.000 0.00 0.00 0.00 2.32
2361 2486 7.036996 TGTTGACTGTGCTTATGAAAATTGA 57.963 32.000 0.00 0.00 0.00 2.57
2362 2487 7.660112 TGTTGACTGTGCTTATGAAAATTGAT 58.340 30.769 0.00 0.00 0.00 2.57
2364 2489 9.624697 GTTGACTGTGCTTATGAAAATTGATTA 57.375 29.630 0.00 0.00 0.00 1.75
2394 2519 4.517285 AGAAAGTGTCAAGAAGCAGTTCA 58.483 39.130 0.00 0.00 34.82 3.18
2429 2734 4.503910 TCACGGTATGATCTTTGGTTCAG 58.496 43.478 0.00 0.00 29.99 3.02
2660 2969 2.092429 TGGAAGTGTGAGGAGTGCTTTT 60.092 45.455 0.00 0.00 0.00 2.27
2712 3022 8.892723 CAAGATGTCTGTTGCTAATATAACCAA 58.107 33.333 0.00 0.00 0.00 3.67
2887 3201 0.741326 TCTCGAGAAGCATCCTTCCG 59.259 55.000 14.01 0.00 46.97 4.30
2929 3243 3.081804 CCTTGATTTGACCGTTAGGCTT 58.918 45.455 0.00 0.00 42.76 4.35
2934 3248 3.974871 TTTGACCGTTAGGCTTTGTTC 57.025 42.857 0.00 0.00 42.76 3.18
2945 3260 1.401539 GGCTTTGTTCGGATTGAGTGC 60.402 52.381 0.00 0.00 0.00 4.40
2994 3535 6.587273 CACAAGAAAAGACCCCCAATAAAAA 58.413 36.000 0.00 0.00 0.00 1.94
3002 3543 1.554617 CCCCCAATAAAAACAGGCCTG 59.445 52.381 31.60 31.60 0.00 4.85
3055 3596 9.914834 AAAATAACAGGCCTTTAGATATACACA 57.085 29.630 0.00 0.00 0.00 3.72
3072 3613 3.186119 ACACATTGTTTTGCTTGGTTCG 58.814 40.909 0.00 0.00 0.00 3.95
3158 3699 5.982890 ATGTTACATTTGAGAACCCCTTG 57.017 39.130 0.00 0.00 0.00 3.61
3161 3702 5.300792 TGTTACATTTGAGAACCCCTTGAAC 59.699 40.000 0.00 0.00 0.00 3.18
3189 3730 7.889873 TTCTCAAAGGGTTGTCAAAATTCTA 57.110 32.000 0.00 0.00 36.07 2.10
3191 3732 8.477419 TCTCAAAGGGTTGTCAAAATTCTAAT 57.523 30.769 0.00 0.00 36.07 1.73
3192 3733 8.923270 TCTCAAAGGGTTGTCAAAATTCTAATT 58.077 29.630 0.00 0.00 36.07 1.40
3197 3738 8.349568 AGGGTTGTCAAAATTCTAATTAGACC 57.650 34.615 14.85 9.00 34.93 3.85
3199 3740 8.803235 GGGTTGTCAAAATTCTAATTAGACCTT 58.197 33.333 14.85 8.83 34.93 3.50
3259 3806 6.274157 TGCTTTCCAGTTACACAAGAAAAA 57.726 33.333 0.00 0.00 0.00 1.94
3261 3808 6.071616 TGCTTTCCAGTTACACAAGAAAAAGT 60.072 34.615 0.00 0.00 0.00 2.66
3267 3814 6.250527 CCAGTTACACAAGAAAAAGTGTTTCG 59.749 38.462 3.39 0.00 46.04 3.46
3275 3822 6.864165 ACAAGAAAAAGTGTTTCGCAAACTAA 59.136 30.769 0.00 0.00 41.90 2.24
3315 3862 2.703536 TCAAGGCAAGGACAACTCAGTA 59.296 45.455 0.00 0.00 0.00 2.74
3319 3866 4.353777 AGGCAAGGACAACTCAGTAGATA 58.646 43.478 0.00 0.00 0.00 1.98
3363 3910 6.342111 TGTGCACAATTGAATCTACGGTATA 58.658 36.000 19.28 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.496873 GCTACATATATATGGGTTACAACACAA 57.503 33.333 23.44 0.00 46.84 3.33
183 187 7.018769 AGGAAAAGGGGTAGTACTACTTACAA 58.981 38.462 27.71 0.00 36.36 2.41
184 188 6.565036 AGGAAAAGGGGTAGTACTACTTACA 58.435 40.000 27.71 0.00 36.36 2.41
188 192 5.016031 TCAGAGGAAAAGGGGTAGTACTACT 59.984 44.000 27.71 10.87 36.36 2.57
189 193 5.267587 TCAGAGGAAAAGGGGTAGTACTAC 58.732 45.833 22.53 22.53 35.40 2.73
190 194 5.541258 TCAGAGGAAAAGGGGTAGTACTA 57.459 43.478 0.00 0.00 0.00 1.82
197 204 1.005215 CAGCATCAGAGGAAAAGGGGT 59.995 52.381 0.00 0.00 0.00 4.95
231 238 0.389948 GACCATCGACCAAACGAGCT 60.390 55.000 0.00 0.00 45.22 4.09
338 345 3.692406 GTCCGTCCGTCCTTGGCT 61.692 66.667 0.00 0.00 0.00 4.75
390 400 2.890371 GGCTCACGACACGGGTAT 59.110 61.111 0.00 0.00 0.00 2.73
401 414 3.188786 GCGATGTCCACGGCTCAC 61.189 66.667 0.00 0.00 0.00 3.51
446 459 1.977009 CCCCAACCGGAAAGAAGCC 60.977 63.158 9.46 0.00 0.00 4.35
547 561 1.598130 ACTGGTGAACTTGCTCGCC 60.598 57.895 0.00 0.00 44.82 5.54
721 757 7.607223 GCGGTATATATCTACCTATCGGAGAAT 59.393 40.741 13.71 0.00 38.83 2.40
724 760 5.642919 GGCGGTATATATCTACCTATCGGAG 59.357 48.000 13.71 0.47 39.26 4.63
733 769 2.396160 CCGCGGCGGTATATATCTAC 57.604 55.000 32.14 0.00 42.73 2.59
849 890 3.274288 TGCATATACGCATGGTGTTTCA 58.726 40.909 0.00 0.00 36.86 2.69
884 925 3.625897 CTCGGCCTCACCCACACA 61.626 66.667 0.00 0.00 33.26 3.72
908 955 1.753073 TGCTCGCTCTGAATCTCATCA 59.247 47.619 0.00 0.00 0.00 3.07
911 958 1.404748 CTCTGCTCGCTCTGAATCTCA 59.595 52.381 0.00 0.00 0.00 3.27
912 959 1.269206 CCTCTGCTCGCTCTGAATCTC 60.269 57.143 0.00 0.00 0.00 2.75
913 960 0.746063 CCTCTGCTCGCTCTGAATCT 59.254 55.000 0.00 0.00 0.00 2.40
914 961 0.875474 GCCTCTGCTCGCTCTGAATC 60.875 60.000 0.00 0.00 33.53 2.52
915 962 1.143620 GCCTCTGCTCGCTCTGAAT 59.856 57.895 0.00 0.00 33.53 2.57
916 963 2.575993 GCCTCTGCTCGCTCTGAA 59.424 61.111 0.00 0.00 33.53 3.02
1155 1203 2.503061 CCTGCCCATCTCTGTCGG 59.497 66.667 0.00 0.00 0.00 4.79
1178 1230 2.270205 CCCACCTTCTCGCAGCAT 59.730 61.111 0.00 0.00 0.00 3.79
1314 1366 1.351430 CCGTCGCCATGCATATACGG 61.351 60.000 20.06 20.06 43.20 4.02
1367 1431 1.474478 TGCGATTGAGAGTCTGAGACC 59.526 52.381 9.33 0.86 32.18 3.85
1372 1436 1.593469 CTGCATGCGATTGAGAGTCTG 59.407 52.381 14.09 0.00 0.00 3.51
1376 1440 1.783031 GCCCTGCATGCGATTGAGAG 61.783 60.000 14.09 2.37 0.00 3.20
1451 1525 2.604686 AGGAGGCCACGCTTGAGA 60.605 61.111 5.01 0.00 0.00 3.27
1761 1860 4.767255 GTCCTGCTGCGGGTCCTG 62.767 72.222 25.92 1.27 0.00 3.86
1884 1983 3.325753 GGTGGAGGCAGAGCAGGT 61.326 66.667 0.00 0.00 0.00 4.00
2114 2219 1.391485 CACACTTCTTGATCGAAGCCG 59.609 52.381 9.51 5.10 43.22 5.52
2129 2234 1.676916 CCGCTTGATCACATCCACACT 60.677 52.381 0.00 0.00 0.00 3.55
2144 2249 2.953466 TCGAATACTAACAGCCGCTT 57.047 45.000 0.00 0.00 0.00 4.68
2145 2250 2.953466 TTCGAATACTAACAGCCGCT 57.047 45.000 0.00 0.00 0.00 5.52
2147 2252 3.624900 TCGATTCGAATACTAACAGCCG 58.375 45.455 11.38 7.17 31.06 5.52
2148 2253 3.982058 CCTCGATTCGAATACTAACAGCC 59.018 47.826 11.38 0.00 34.74 4.85
2150 2255 5.184340 ACCCTCGATTCGAATACTAACAG 57.816 43.478 11.38 1.15 34.74 3.16
2152 2257 6.963796 TCTAACCCTCGATTCGAATACTAAC 58.036 40.000 11.38 0.00 34.74 2.34
2153 2258 7.572523 TTCTAACCCTCGATTCGAATACTAA 57.427 36.000 11.38 0.00 34.74 2.24
2155 2260 6.651975 ATTCTAACCCTCGATTCGAATACT 57.348 37.500 11.38 0.00 34.74 2.12
2156 2261 8.295288 TCTAATTCTAACCCTCGATTCGAATAC 58.705 37.037 11.38 4.21 34.74 1.89
2157 2262 8.400184 TCTAATTCTAACCCTCGATTCGAATA 57.600 34.615 11.38 0.00 34.74 1.75
2158 2263 7.286215 TCTAATTCTAACCCTCGATTCGAAT 57.714 36.000 11.20 11.20 34.74 3.34
2159 2264 6.704289 TCTAATTCTAACCCTCGATTCGAA 57.296 37.500 10.38 0.00 34.74 3.71
2160 2265 6.896021 ATCTAATTCTAACCCTCGATTCGA 57.104 37.500 8.70 8.70 0.00 3.71
2161 2266 6.128795 GCAATCTAATTCTAACCCTCGATTCG 60.129 42.308 0.00 0.00 0.00 3.34
2162 2267 6.128795 CGCAATCTAATTCTAACCCTCGATTC 60.129 42.308 0.00 0.00 0.00 2.52
2163 2268 5.696724 CGCAATCTAATTCTAACCCTCGATT 59.303 40.000 0.00 0.00 0.00 3.34
2164 2269 5.221461 ACGCAATCTAATTCTAACCCTCGAT 60.221 40.000 0.00 0.00 0.00 3.59
2177 2282 4.158579 TCTGAGTGAGTGACGCAATCTAAT 59.841 41.667 16.79 0.00 33.53 1.73
2201 2306 3.071747 AGAGGAAAACAGAAGGAGGTGAC 59.928 47.826 0.00 0.00 0.00 3.67
2202 2307 3.318313 AGAGGAAAACAGAAGGAGGTGA 58.682 45.455 0.00 0.00 0.00 4.02
2203 2308 3.071602 TGAGAGGAAAACAGAAGGAGGTG 59.928 47.826 0.00 0.00 0.00 4.00
2204 2309 3.071747 GTGAGAGGAAAACAGAAGGAGGT 59.928 47.826 0.00 0.00 0.00 3.85
2206 2311 4.565022 GAGTGAGAGGAAAACAGAAGGAG 58.435 47.826 0.00 0.00 0.00 3.69
2208 2313 3.321497 CGAGTGAGAGGAAAACAGAAGG 58.679 50.000 0.00 0.00 0.00 3.46
2210 2315 2.365617 AGCGAGTGAGAGGAAAACAGAA 59.634 45.455 0.00 0.00 0.00 3.02
2229 2342 1.809209 GAGCACGGAGAGAGCAAGC 60.809 63.158 0.00 0.00 0.00 4.01
2232 2345 1.181741 AACAGAGCACGGAGAGAGCA 61.182 55.000 0.00 0.00 0.00 4.26
2241 2354 3.420839 AACCAAAGAAAACAGAGCACG 57.579 42.857 0.00 0.00 0.00 5.34
2261 2384 3.578716 ACTGACGAATTCTCTCCCAAGAA 59.421 43.478 3.52 0.00 39.49 2.52
2277 2400 0.784178 CACGGACATGAACACTGACG 59.216 55.000 0.00 0.00 0.00 4.35
2281 2404 3.631453 ATGCACGGACATGAACACT 57.369 47.368 0.00 0.00 0.00 3.55
2310 2435 6.475504 TCTCTCATTCCTTATCAACAAGCAA 58.524 36.000 0.00 0.00 0.00 3.91
2312 2437 6.992063 TTCTCTCATTCCTTATCAACAAGC 57.008 37.500 0.00 0.00 0.00 4.01
2324 2449 5.618640 GCACAGTCAACATTTCTCTCATTCC 60.619 44.000 0.00 0.00 0.00 3.01
2333 2458 7.928908 TTTTCATAAGCACAGTCAACATTTC 57.071 32.000 0.00 0.00 0.00 2.17
2358 2483 7.841915 TGACACTTTCTTCGCATATAATCAA 57.158 32.000 0.00 0.00 0.00 2.57
2360 2485 8.131455 TCTTGACACTTTCTTCGCATATAATC 57.869 34.615 0.00 0.00 0.00 1.75
2361 2486 8.492673 TTCTTGACACTTTCTTCGCATATAAT 57.507 30.769 0.00 0.00 0.00 1.28
2362 2487 7.413000 GCTTCTTGACACTTTCTTCGCATATAA 60.413 37.037 0.00 0.00 0.00 0.98
2364 2489 5.163814 GCTTCTTGACACTTTCTTCGCATAT 60.164 40.000 0.00 0.00 0.00 1.78
2365 2490 4.152402 GCTTCTTGACACTTTCTTCGCATA 59.848 41.667 0.00 0.00 0.00 3.14
2367 2492 2.287915 GCTTCTTGACACTTTCTTCGCA 59.712 45.455 0.00 0.00 0.00 5.10
2368 2493 2.287915 TGCTTCTTGACACTTTCTTCGC 59.712 45.455 0.00 0.00 0.00 4.70
2394 2519 1.403814 ACCGTGATCGATGATCCAGT 58.596 50.000 0.54 0.00 38.20 4.00
2675 2985 7.386299 AGCAACAGACATCTTGAACTTAAGTAG 59.614 37.037 8.92 2.92 0.00 2.57
2712 3022 8.456471 GCCTTTCTTATTTAACTAATCGGTGTT 58.544 33.333 0.00 0.00 0.00 3.32
2800 3114 9.559732 TTTGAATGATCTTTCTTTGAGTACTGA 57.440 29.630 18.92 0.00 0.00 3.41
2837 3151 0.521735 GAAGGTTTACAAGGCTGCGG 59.478 55.000 0.00 0.00 0.00 5.69
2887 3201 3.330267 GAGAATTATGCTCCCGGTGATC 58.670 50.000 0.00 0.00 0.00 2.92
2898 3212 5.066505 ACGGTCAAATCAAGGAGAATTATGC 59.933 40.000 0.00 0.00 0.00 3.14
2929 3243 1.588674 AACGCACTCAATCCGAACAA 58.411 45.000 0.00 0.00 0.00 2.83
2965 3506 1.248486 GGGTCTTTTCTTGTGCTCCC 58.752 55.000 0.00 0.00 0.00 4.30
3029 3570 9.914834 TGTGTATATCTAAAGGCCTGTTATTTT 57.085 29.630 5.69 0.00 0.00 1.82
3033 3574 8.491134 ACAATGTGTATATCTAAAGGCCTGTTA 58.509 33.333 5.69 6.62 0.00 2.41
3055 3596 3.063316 GCAAACGAACCAAGCAAAACAAT 59.937 39.130 0.00 0.00 0.00 2.71
3056 3597 2.413453 GCAAACGAACCAAGCAAAACAA 59.587 40.909 0.00 0.00 0.00 2.83
3072 3613 9.632807 TGTAATTATTTAGGTGTTGATGCAAAC 57.367 29.630 0.00 0.00 0.00 2.93
3216 3757 9.751542 GAAAGCATATATGTACCGCTCTATTAT 57.248 33.333 14.14 0.00 31.17 1.28
3217 3758 8.195436 GGAAAGCATATATGTACCGCTCTATTA 58.805 37.037 14.14 0.00 31.17 0.98
3218 3759 7.042335 GGAAAGCATATATGTACCGCTCTATT 58.958 38.462 14.14 0.00 31.17 1.73
3220 3761 5.479027 TGGAAAGCATATATGTACCGCTCTA 59.521 40.000 14.14 0.00 31.17 2.43
3221 3762 4.283467 TGGAAAGCATATATGTACCGCTCT 59.717 41.667 14.14 0.00 31.17 4.09
3222 3763 4.566004 TGGAAAGCATATATGTACCGCTC 58.434 43.478 14.14 3.50 31.17 5.03
3223 3764 4.040461 ACTGGAAAGCATATATGTACCGCT 59.960 41.667 14.14 1.79 33.45 5.52
3224 3765 4.315803 ACTGGAAAGCATATATGTACCGC 58.684 43.478 14.14 0.00 0.00 5.68
3225 3766 6.926826 TGTAACTGGAAAGCATATATGTACCG 59.073 38.462 14.14 10.34 0.00 4.02
3226 3767 7.713507 TGTGTAACTGGAAAGCATATATGTACC 59.286 37.037 14.14 11.91 38.04 3.34
3227 3768 8.657074 TGTGTAACTGGAAAGCATATATGTAC 57.343 34.615 14.14 6.10 38.04 2.90
3231 3772 9.461312 TTTCTTGTGTAACTGGAAAGCATATAT 57.539 29.630 0.00 0.00 38.04 0.86
3234 3775 7.575414 TTTTCTTGTGTAACTGGAAAGCATA 57.425 32.000 0.00 0.00 38.43 3.14
3259 3806 6.673154 AGTACTTTTAGTTTGCGAAACACT 57.327 33.333 12.28 5.18 43.79 3.55
3261 3808 6.844254 ACAAGTACTTTTAGTTTGCGAAACA 58.156 32.000 5.07 0.00 43.79 2.83
3293 3840 1.876156 CTGAGTTGTCCTTGCCTTGAC 59.124 52.381 0.00 0.00 0.00 3.18
3315 3862 6.552445 AGCATGGTCTAAAAGTGACTATCT 57.448 37.500 0.00 0.00 34.22 1.98
3319 3866 4.516698 CACAAGCATGGTCTAAAAGTGACT 59.483 41.667 0.00 0.00 35.04 3.41


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

AutoCloner maintained by Alex Coulton.